srs/

/*********************************************************************************

  SRS and the copyright and other intellectual property rights in SRS are
  the property of Dr. Thure Etzold and the EMBL. 
  
  We are willing to licence SRS to you only on the following terms and
  your use of SRS indicates acceptance of these terms.  You have a
  non-exclusive, non-transferable, royalty free license to use SRS for
  your own research purposes only.  You may not sub-licence, copy or
  redistribute SRS to any other person and in particular your rights do
  not extend to any form of commercial use [other than use internally
  for research purposes by commercial organisations].  Your licence will
  terminate immediately if you do not comply with all of these terms.

*********************************************************************************/



SRS Version 5.0.4
=================


To install
----------
Change directory to the 'srs' directory and run

./srsinstall all


This will ask you a few questions regarding 'make' and 'cc' and then configure
the installation and compile the programs.

It is important that you do this the first time you run srsinstall. In this
way, the 'etc/prep_srs' and 'etc/prep_srs.sh' and the make procedure are
configured for your site.

To complete the installation
----------------------------
To install the SRSWWW change directory to the 'srs' directory again and invoke

./srsinstall www

You will be asked for the names of both the doc root and bin root of
SRSWWW. You must define aliases for these and restart the httpd.
You can access SRSWWW with the URL "http://your-httpd/srs/"

The top page of SRSWWW has a link to the documentation which you can install
on your site with

./srsinstall doc

Generating the documentation requires so much of the installation to be
working that once it has successfully completed, you can be certain that the
installation works, and is ready to be used.


To set the SRS environment
--------------------------
To set the SRS environment in the shell you are using, you should prepare the
shell for your installation of SRS by executing one of the following two
commands, based upon the type of shell you are using.

For C-shell and compatibles
source etc/prep_srs

For Bourne-shell and compatibles
. etc/prep_srs.sh


Icarus mode for emacs
---------------------
An Icarus mode for editing Icarus code inside emacs is located in the file
'srs/etc/icarus.el' . Installation instructions are provided in this file.


To customize
------------
The documentation contains a section "Adding Databanks - a Guided Tour" which
is well worth working through before customizing.

You will need to have the SRS environment set before performing customizations
(see above).

The Icarus files are in 'srs/icarus'. All databank defining files are
in the 'db' subdirectory. Right now there are definitions for
swissprot, prosite, enzyme ...you must edit srsdb.i and get the 
paths right - don't forget to run 'srssection' after that.

All databanks are defined by two files (eg, 'prosite.i' and 'prosite.is')
After a change in the .i file 'srssection' must be invoked. The .is 
file is interpreted - so you can just run the program again.

srscheck

This will report the status of the libraries and links. You should now update
these. Run

srsupdate


Please read the first chapters in the section "SRS Server Maintenance" to
get further information about setting up WWW servers and keeping indices
up to date.


19/3/1997
Thure Etzold    etzold@ebi.ac.uk
Giorgio Verde   verde@ebi.ac.uk

, 'prosite.i' andsrs/bin/


#include <stdio.h>
#include "srs.h"
#include "dict.h"

int main ()
{ 
  DICTv dict;
  
  

  struct X{
    int a;
    char b[100];
  }x[100], *tmp;
  Iter i;

  dict = DictCreate(DictCreateClassPtrKey ((KeyAccessor)KeyItself , 0, FALSE));

  x[0].a = 10;
  x[5].a = 5;
  x[1].a = 1;
  x[3].a = 3;
  DictSet (&dict, &x[0], struct X*) = &x[0];
  DictSet (&dict, &x[5], struct X*) = &x[5];
  DictSet (&dict, &x[1], struct X*) = &x[1];
  DictSet (&dict, &x[3], struct X*) = &x[3];

  DictDebug (dict);

  if ((i = DictWith (dict, &x[3]))) {
    tmp =  DictIn (i, struct X*);
    printf ("found %d\n", tmp->a);
  }
  else
    printf ("not found\n");
}
[100], *tmp;
  Iter i;

  dict = DictCreate(DictCreateClassPtrKey ((KeyAccessor)KeyItself , 0, FALSE));

  x[0].a = 10;
  x[5].a = 5;
  x[1].a = 1;
  x[3].a = 3;
  DictSet (&dict, &x[0], struct X*) = &x[0];
  DictSet (&dict, &x[5], struct X*) = &x[5];
  DictSet (&dict, &x[1], struct X*) = &x[1];
  Dicsrs/demo/first.i
$Print:"hello world\n"
  DictDebug (dict);

  if ((i = DictWith (dict, &x[3]))) {
    tmp =  DictIn (i, struct X*);
    printf ("found %d\n", tmp->a);
  }
  else
    printf ("not found\n");
}
[100], *tmp;
  Iter i;

  dict = DictCreate(DictCreateClassPtrKey ((KeyAccessor)KeyItself , 0, FALSE));

  x[0].a = 10;
  x[5].a = 5;
  x[1].a = 1;
  x[3].a = 3;
  DictSet (&dict, &x[0], struct X*) = &x[0];
  DictSet (&dict, &x[5], struct X*) = &x[5];
  DictSet (&dict, &x[1], struct X*¶ £¡Ü];
  Dicsrs/demo/genes.dat
DATE        07-JUN-1960
DEFINITION  Human amphiphysin mRNA, complete cds.
CITATION    DLOZTE95
SEQUENCE  
        1 ccaggtgcct actgactcct tcagaaatgt cagttcctgt cccatgccct taatatttcc
       61 cacatgcagg gctctgtgca caatgcgtga caatggcttt tagat

//
LOCUS       BTCHGE8
DATE        26-MAR-1970
DEFINITION  Bovine chymosin (cPC) gene, exon 8, clone lambda-CR72.
CITATION    ERAEW96
SEQUENCE  
        1 tgttctttag tttgacatcga ctgcgacaa cctgagctac atgcccactg tggtctttga
       61 gatcaatggc aaaatgtaccc actgacccc ctccgcctat accagccagg tatgcatct

//
LOCUS       PPTHGE1
DATE        17-JUN-1965
DEFINITION  Pongo pygmaeus tyrosine hydroxylase gene, exon 1.
CITATION    EDREV93
SEQUENCE  
        1 gcagaggcca tcatggtaaga gggcaggta ggtgcccggc ggccgcagtg gaccggagcc
       61 cagggctggt gccagctgcct ctgccactc cccaatctgg ctggcagcc
//









PC) gene, exon 8, clone lambda-CR72.
CITATION    ERAEW96
SEQUENCE  
        1 tgttctttag tttgacatcga ctgcgacaa cctgagctac atgcccactg tggtctttga
       61 gatcaatggc aaaatgtasrs/demo/genes.i
  format:@GENES_FORMAT maxNameLen:10 files:{
    $file:genes
  }
]

GENES_FORMAT:$libformat:[fileType:@MYSEQ_FILE syntax:@GENES_SYNTAX
  fields:{
    $field:[@DF_ID code:id index:id indexToken:id]    
    $field:[@DF_Description code:def index:str indexToken:def]
    $field:[@DF_Date code:date index:int indexToken:date]
    $field:[@DF_Citation code:cit]
  }
]

GENES_SYNTAX:$syntax:[file:'SRSDEMO:genes.is']
MYSEQ_FILE:$filetype:[typename:dat maxline:100]

$link:[@GENES_DB to:@?REFLIST_DB fromField:@DF_Citation toField:@DF_ID
  token:cit]

:10 files:{
    $file:genes
  }
]

GENES_FORMAT:$libformat:[fileType:@MYSEQ_FILE syntax:@GENES_SYNTAX
  fields:{
    $field:[@DF_ID code:id index:id indexToken:id]    
    $field:[@DF_Description code:def index:str indexToken:def]
    $field:[@DF_Date code:date index:int indexToken:date]
    $field:[@DF_Citation code:cit]
  }
]

GENES_SYNTAX:$syntax:[file:'SRSDEMO:genes.is']
MYSEQ_FILE:$filetype:[typename:dat maxline:100]

$linksrs/demo/genes.is

$rules={

  # the entry
  entry:     ~ {$In:[file:text] $Out pre{$Skip:0}} 
                ('LOCUS' {$entryFip=$Fip $Wrt} ln {$App}
                ('LOCUS' {$Not} ln {$App})*)?
             ~
  ln:        ~ /[^\n]*\n/ ~

  # the data-fields
  fields:    ~ {$In:entry $Out $Skip:1} id date def cit seq ~
  id:        ~ {$wrt:id}   'LOCUS'      ln ~
  date:      ~ {$wrt:date} 'DATE'       ln ~
  def:       ~ {$wrt:def}  'DEFINITION' ln ('  ' ln)* ~
  cit:       ~ {$wrt:cit}  'CITATION'   ln ~
  seq:       ~ {$wrt:seq}  'SEQUENCE'   ln ('  ' ln)* ~

  # indexing
  word:   ~ /[a-zA-Z0-9_]+/ ~
  i_id:   ~ {$In:[fields c:id] $out:id} word word {$Wrt} ~
  i_date: ~ {$In:[fields c:date] $out:date 
  	     init{$month={JAN:1 FEB:2 MAR:3 APR:4 MAY:5 JUN:6 JUL:7 AUG:8 
  			  SEP:9 OCT:10 NOV:11 DEC:12}
  		 }
  	    } word
  	    /([0-9]+)-([A-Z][A-Z][A-Z])-([0-9]+)/ 
  	    {$Wrt:[s:$3 * 10000 + $month.$2 * 100 + $1]}
  	  ~ 
  i_def:  ~ {$In:[fields c:def] $out:def} word
  	    ( '('? /[^)., \n]+/ {$Wrt} /[).,\n]+/? )* ~
  i_cit:  ~ {$In:[fields c:cit] $out:cit} word word {$Wrt} ~
}

if: $TestMode {
  $job = $JobNew:[prod:$rules skip:'\t ' fileName:"SRSDEMO:genes.dat"]
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields print:1]
    $JobNext:$job
  }
}
AUG:8 
  			  SEP:9 OCT:10 NOV:11 DEC:12}
  		 }
  	    } word
  	    /([0-9]+)-([A-Z][A-Z][A-Z])-([0-9]+)/ 
  	    {$Wrt:[s:$3 * 10000 + $month.$2 * 100 + $1]}
  	  ~ 
  i_def:  ~ {$In:[fields c:def] $out:def} word
  	    ( '('? /[^)., \n]+/ srs/demo/genes.it
  description:
    |A demonstration databank used to demonstrate SRS.
    |<P>
  literature:
    |<OL>
    |<LI>See the online documentation
    |
    |</OL>
#  address:
  contact:
    |<ADDRESS>
    |Thure Etzold<BR>
    |EMBL<BR>
    |</ADDRESS>
    |Giorgio Verde<BR>
    |EMBL<BR>
    |</ADDRESS><P>
    |<ADDRESS>
    |Johnathon Weare<BR>
    |EMBL<BR>
    |</ADDRESS><P>
    |<ADDRESS>
  www:
    |<A HREF="http://www.embl-heidelberg.de">\
    |http://www.embl-heidelberg.de</A>
  address:
    |EMBL<BR>
  telephone: '+49 (0)6221 387451'
  telefax:   '+49 (0)6221 387517'
  email: 'weare@embl-heidelberg.de'
  fields:{
    Date:
      | This is the DATE field
    Description:
      | This is the DEFINITION field
  }
}







 |EMBL<BR>
    |</ADDRESS>
    |Giorgio Verde<BR>
    |EMBL<BR>
    |</ADDRESS><P>
    |<ADDRESS>
    |Johnathon Weare<BR>
    |EMBL<BR>
    |</ADDRESS><P>
    |<ADDRESS>
  www:
    |<A HREF="http://www.embl-heidelberg.de">\
    |http://www.embl-heidelberg.de</A>
  address:
    |Esrs/demo/genes_debug.is

$rules={

  # the entry
  entry:     ~ {$In:[file:text] $Out pre{$Skip:0}} 
                ('LOCUS' {$entryFip=$Fip $Wrt} ln {$App}
                ('LOCUS' {$Not} ln {$App})*)?
             ~
  ln:        ~ /[^\n]*\n/ ~

  # the data-fields
  fields:    ~ {$In:entry $Out $Skip:1}
               id {pre{$Print:"...before: $It\n"} $Print:"...after: $It\n"}
               date def cit seq ~
  id:        ~ {$wrt:id}   'LOCUS'      ln ~
  date:      ~ {$wrt:date} 'DATE'       ln ~
  def:       ~ {$wrt:def}  'DEFINITION' ln ('  ' ln)* ~
  cit:       ~ {$wrt:cit}  'CITATION'   ln ~
  seq:       ~ {$wrt:seq}  'SEQUENCE'   ln ('  ' ln)* ~

  # indexing
  word:   ~ /[a-zA-Z0-9_]+/ ~
  i_id:   ~ {$In:[fields c:id] $out:id} word word {$Wrt} ~
  i_date: ~ {$In:[fields c:date] $out:date 
  	     init{$month={JAN:1 FEB:2 MAR:3 APR:4 MAY:5 JUN:6 JUL:7 AUG:8 
  			  SEP:9 OCT:10 NOV:11 DEC:12}
  		 }
  	    } word
  	    /([0-9]+)-([A-Z][A-Z][A-Z])-([0-9]+)/ 
  	    {$Wrt:[s:$3 * 10000 + $month.$2 * 100 + $1]}
  	  ~ 
  i_def:  ~ {$In:[fields c:def] $out:def} word
  	    ( '('? /[^)., \n]+/ {$Wrt} /[).,\n]+/? )* ~
  i_cit:  ~ {$In:[fields c:cit] $out:cit} word word {$Wrt} ~
}

if: $TestMode {
  $job = $JobNew:[prod:$rules skip:'\t ' fileName:"SRSDEMO:genes.dat"]
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields print:1]
    $JobNext:$job
  }
}
AUG:8 
  			  SEP:9 OCT:10 NOV:11 DEC:12}
  		 }
  	    } word
  	    /([0-9]+)-([A-Z][A-Z][A-Z])-([0-9]+)/ 
  	    {$Wrt:[s:$3 * 10000 + $month.$2 * 100 +srs/demo/libinfo.c
   and their data-fields */

#include <stdio.h>
#include "srs.h"

int main ()
{
  SLBo      *lib;
  SRSoGROUP *group;
  SLBoFIELD *field;
  int c1, c2, c3;
  
  SrsEnv ();
  LibOpen ("srswin");
  

  for (c1=0; (group = LibNextLibGroup (&c1));) {
    printf ("Group: %s\n", LibGetGroupName (group, "full"));
    
    for (c2=0; (lib = LibNextLib (group, &c2));) {
      printf ("    Library: %s\n", LibName (lib));
      
      for (c3=0; (field = LibNextField (lib, &c3));) {
	printf ("        Data-field: %s\n", 
		FieldGetName (field));
	
	/* see what can be done with the fields */
	
	if (FieldIs (field, "index"))
	  printf ("        ... is indexed\n");
	else if (FieldIs (field, "show") || FieldIs (field, "link"))
	  printf ("        ... can be displayed only\n");
      }
    }
  }
}
GroupName (group, "full"));
    
    for (c2=0; (lib = LibNextLib (group, &c2));) {
      printf ("    Library: %s\n", LibName (lib));
      
      for (c3=0; (field = Lsrs/demo/libinfo2.c

#include <stdio.h>
#include "srs.h"

int main ()
{
  SLBo      *lib;
  LIBoINDEX *libInx;
  char      *tmp;
  
  SrsEnv ();
  LibOpen ("srswin");
  
  lib = (SLBo *) LibObjByName ("library", "swissprot");
  libInx = LibIndexOpen (lib, LibGetIdField (lib), 0);

  printf ("Library \"%s\"\n", LibName (lib));
  if ((tmp = IdxGetReleaseName (libInx->idx)))
    printf ("  Release: \"%s\"\n", tmp);
  printf ("  Entries: %d\n", BtrGetRecordN (libInx->btree));
}
accesses information about an individual databank */

#include <stdio.h>
#include "srs.h"

int main ()
{
  SLBo      *lib;
  LIBoINDEX *libInx;
  char      *tmp;
  
  SrsEnv ();
  LibOpen ("srswin");
  
  lib = (SLBo *) LibObjByName ("library", "swissprot");
  libInx = LibIndexOpen (lib, LibGetIdField (lib), 0);

  printf ("Library \"%s\"\n", LibName (lib));
  if ((tmp = IdxGetReleaseName (libInx->idx)))
    printf ("  Release: \"%s\"\n", tmp);
  printf ("  Entries: %d\n", BtrGetRecordN (libsrs/demo/msguse.c

#include <stdio.h>
#include <stdarg.h>
#include "srs.h"

int MyPrintMessage (MSGo *msg)
{
  switch (msg->msg_code) {
  case e__objectunknown:
    fprintf (stderr, "ERROR: (%s) %s, %s\n",
	     msg->msg_nm, msg->primsg, msg->secmsg);
    break;
  default:
    if (msg->msg_t != MSGxINFO)
      fprintf (stderr, "ERROR: %s, %s\n", msg->primsg, msg->secmsg);
    else
      fprintf (stderr, "INFO: %s\n", msg->secmsg);
    break;
  }
  return 1;
}

int main ()
{
  SrsEnv ();
  LibOpen ("srswin");
  MsgSetFnct (MyPrintMessage);
  
  Query ("[swisprot-des:acetylchol*]", "Q");
  Query ("[swissprot-des:acetylchol*]", "Q");
  Query ("[swissprot-des:acetylchol*]", "Q");
  ParDefStr ("fieldList", "desription");
}


sg_nm, msg->primsg, msg->secmsg);
    break;
  default:
    if (msg->msg_t != MSGxINFO)
      fprintf (stderr, "ERROR: %s, %s\n", msg->primsg, msg->secmsg);
    else
      fprintf (stderr, "INFO: %s\n", msg->secmsg);
    break;
  }
  retsrs/demo/oddemo.c
#define _INITOBJS
#include "oddemo.h"

int main ()
{
  int k;

  for (k=0; k < topval->myObj2N; k++) {
    printf ("%d\n", topval->myObj2[k].a);
    printf ("  %d\n", topval->myObj2[k].cc->a);
  }
}
l*]", "Q");
  ParDefStr ("fieldList", "desription");
}


sg_nm, msg->primsg, msg->secmsg);
    break;
  default:
    if (msg->msg_t != MSGxINFO)
      fprintf (stderr, "ERROR: %s, %s\n", msg->primsg, msg->secmsg);
    else
      fprintf (stderr, "INFO: %s\n", msg->secmsg);
    ¶ £¡Ü }
  retsrs/demo/oddemo.i
X2:$myObj
X3:$myObj:[a:10]
$myObj2:[cc:@X1 a:1]
$myObj2:[cc:@X2 a:3]
$myObj2:[cc:@X3 a:3]

$top
   printf ("%d\n", topval->myObj2[k].a);
    printf ("  %d\n", topval->myObj2[k].cc->a);
  }
}
l*]", "Q");
  ParDefStr ("fieldList", "desription");
}


sg_nm, msg->primsg, msg->secmsg);
    break;
  default:
    if (msg->msg_t != MSGxINFO)
      fprintf (stderr, "ERROR: %s, %s\n", msg->primsg, msg->secmsg);
    else
      fprintf (stderr, "INFO: %s\n", msg->secmsg);
    ¶ £¡Ü }
  retsrs/demo/oddemo.ic

myClass2: $object:[myObj2 typname:myObj2 declname:myObj2val
  attrs: {
    $attribute:[a type:int]
    $attribute:[b type:string]
    $attribute:[cc type:object defaultval:@myClass]
  }
]

myClass: $object:[myObj typname:myObj declname:myObjval
  attrs: {
    $attribute:[a type:int]
    $attribute:[b type:string]
  }
]


Top:$object:[top typname:TOP declname:topval
  attrs: {
    $attribute:[myObj type:allobjects defaultval:@myClass]
    $attribute:[myObjN type:nr_of_objects defaultval:@myClass]
    $attribute:[myObj2 type:allobjects defaultval:@myClass2]
    $attribute:[myObj2N type:nr_of_objects defaultval:@myClass2]
  }
]

$def:[infile:"oddemo.i" outfile:"oddemo.h"]
ltval:@myClass]
  }
]

myClass: $object:[myObj typname:myObj declname:myObjval
  attrs: {
    $attribute:[a type:int]
    $attribute:[b type:string]
  }
]


Top:$object:[top typname:TOP declname:topval
  attrs: {
    $attribute:[myObj type:allobjects defaultval:@myClass]
    $attribute:[myObjN type:nr_of_objects defaultvsrs/demo/prfields.c

#include <stdio.h>
#include "srs.h"

int main ()
{
  SETo     *set;
  IDoENTRY id;
  ENTRYv   entry;
  int      n, entryN;
  
  SrsEnv ();
  LibOpen ();
  
  ParDefStr ("fieldList", "ID");
  ParDefStr ("fieldList", "Description");
  
  if (Query ("[swissprot-des:transferase]", "Q")) {
    set = SetGet ("Q"); 
    entryN = SetSize ("Q");
    
    for (n=1;  n <= entryN; n++) {
      SetGetID (set, n, &id); 
      entry = EntryOpen (&id);
      EntryPrintFields (entry, NULL);  
      EntryClose (&entry);
    }
  }
}
 <stdio.h>
#include "srs.h"

int main ()
{
  SETo     *set;
  IDoENTRY id;
  ENTRYv   entry;
  int      n, entryN;
  
  SrsEnv ();
  LibOpen ();
  
  ParDefStr ("fieldList", "ID");
  ParDefStr ("fieldList", "Description");
  
  if (Query ("[swissprot-des:transferase]", "Q")) {
    set = SetGet ("Q"); 
    entryN = SetSize ("Q");
    
    for (n=1;  n <= entryN; n++) {
      SetGetID (set, n, &id); 
      entry = EntryOpen (&id);
srs/demo/qasuse.c
   building an SRS query expression */

#include <stdio.h>
#include "srs.h"


int main ()
{ 
  QASvQUERY    qas;
  QASvRETRIEVE r;
  char s[1000];

  SrsEnv ();
  LibOpen ();
  
  /* search "swissprot" and "prosite" in the
     "description" and "seqlength" fields */
  qas = QasNew ();
  QasSetLibrary (qas, "swissprot");
  QasSetLibrary (qas, "prosite");
  r = QasNewRetrieve (qas, "description");
  QasSetRetrieveStr (qas, r, "kinase");
  r = QasNewRetrieve (qas, "seqlength");
  QasSetRangeBegin (qas, r, "400");
  QasSetRangeEnd (qas, r, "500");
  QasSetOp (qas, "and");
  strcpy (s, QasGetQueryString (qas));
  printf ("the query: \"%s\"\n", s);
  
  /* make a logical AND between current query and set Q1 */
  QasMakeOperand (qas);
  QasSetOp (qas, "and");
  QasAddOperand (qas, "Q1");
  strcpy (s, QasGetQueryString (qas));
  printf ("the query: \"%s\"\n", s);

  /* link the result to "prosite" and "pfam" */
  QasInitLink (qas);
  QasSetQueryToLink (qas, s);
  QasSetLinkWith (qas, "prosite");
  QasSetLinkWith (qas, "pfam");
  QasSetLinkType (qas, "notToSet");
  printf ("the query linked: \"%s\"\n", 
	  QasGetQueryString (qas));
}

ry: \"%s\"\n", s);
  
  /* make a logical AND between current query and set Q1 */
  QasMakeOperand (qas);
  QasSetOp (qas, "and");
  QasAddOperand (qas, "Q1");
  strcpy (s, QasGetQueryString (qas));
  printf ("the query: \"%s\"\n", s);

  /* link the result to "prosite" and "pfam" */
  QasInitLink (qas);
  QasSetQueryToLink (qasrs/demo/query.c

#include <stdio.h>
#include "srs.h"

int main ()
{
  SrsEnv ();
  LibOpen ();
  
  if (Query ("[embl-des:receptor]", "Q1")) {
    printf ("Q1 has %d entries\n", SetSize ("Q1"));
    
    Query ("[embl-des:acetylchol*] & Q1", "Q2");
    printf ("Q2 has %d entries\n", SetSize ("Q2"));
    
    Query ("Q2 > SWISSPROT", "Q3");
    printf ("%d SWISSPROT entries are linked to entries in Q2\n", 
	    SetSize ("Q3"));
    
    Query ("Q2 < SWISSPROT", "Q4");
    printf ("%d entries in Q2 are linked to SWISSPROT\n", 
	    SetSize ("Q4"));
  }
  else 
    printf ("no entries could be found\n");
}
 if (Query ("[embl-des:receptor]", "Q1")) {
    printf ("Q1 has %d entries\n", SetSize ("Q1"));
    
    Query ("[embl-des:acetylchol*] & Q1", "Q2");
    printf ("Q2 has %d entries\n", SetSize ("Q2"));
    
    Query ("Q2 > SWISSPROT", "Q3");
    printf ("%d SWISSPROT entries are linked to entries in Q2\n", 
	    SetSize ("Q3"));
    
    Query ("Q2 < SWISSPROT",srs/demo/reflist.dat
RA   Icarus J., Dedalus F.;
RT   Primary structure of human amphiphysin, the dominant autoantigen
RT   of paraneoplastic Stiff-Man syndrome, and mapping of its gene
RT   (AMPH) to chromosome 7.
RL   Hum. Mol. Genet. 4:265-268(1995).
//
ID   ERAEW96
RA   Tonic G.A., Mary B., Walker J.;
RT   Cloning and structural analysis of the calf prochymosin gene.
RL   Nature 13:197-203(1996).
//
ID   EDREV93
RA   Out A., Ceecee G., Macs E.;
RT   Increased heterogeneity of tyrosine hydroxylase in humans.
RL   Biochem. Biophys. Res. Commun. 195:158-165(1993).
//
tructure of human amphiphysin, the dominant autoantigen
RT   of paraneoplastic Stiff-Man syndrome, and mapping of its gene
RT   (AMPH) to chromosome 7.
RL   Hum. Mol. Genet. 4:265-268(1995).
//
ID   ERAEW96
RA   Tonic G.A., Mary B., Walker J.;
RT   Cloning and structural analysis of the calf prochymosin gene.
RL   Nature 13:197-203(1996).
//
ID   EDREV93
RA   Out A., Ceecee G., Macs E.;
RT   Increased heterogeneity of tyrosine hydroxylase in humans.
RLsrs/demo/reflist.i
REFLIST_DB:$library:[REFLIST group:@SEQUENCE_LIBS 
  format:@REFLIST_FORMAT cachesize:512 maxNameLen:10 files:{
    $file:reflist
  }
]

REFLIST_FORMAT:$libformat:[fileType:@DAT_FILE syntax:@REFLIST_SYNTAX
  fields:{
    $field:[@DF_ID code:id index:id indexToken:id]    
    $field:[@DF_Authors code:refaut index:str indexToken:authors]
    $field:[@DF_Title code:title index:str indexToken:title]
    $field:[@DF_MyReference code:ref index:str indexToken:ref]
  }
]

REFLIST_SYNTAX:$syntax:[file:'SRSDEMO:reflist.is' level3:1]
DF_MyReference:$srsfield:[SeqReference short:rff]
T_FORMAT cachesize:512 maxNameLen:10 files:{
    $file:reflist
  }
]

REFLIST_FORMAT:$libformat:[fileType:@DAT_FILE syntax:@REFLIST_SYNTAX
  fields:{
    $field:[@DF_ID code:id index:id indexToken:id]    
    $field:[@DF_Authors code:refaut index:str indexToken:authors]
    $field:[@DF_Title code:title index:str indexToken:title]
    $field:[@DF_MyReference code:ref index:str indexToken:ref]
  }
]

REFLIST_SYNTAX:$syntax:[file:'SRSDEMO:reflsrs/demo/reflist.is

$rules={

  # the entry
  entry:     ~ {$In:[file:text] $Out}
               ('ID' {$Not} ln)*
               ('ID   ' {$entryFip=$Fip $Wrt} ln {$App}
               ('ID' {$Not} ln {$App})*)?
             ~

  # the data-fields
  fields:    ~ {$In:entry $Out} id ra? rt? rl?
             ~
  id:        ~ {$Wrt:id}   'ID   ' ln   ~ 
  ra:        ~ {$Wrt:ra}  ('RA   ' ln)+ ~
  rt:        ~ {$Wrt:rt}  ('RT   ' ln)+ ~
  rl:        ~ {$Wrt:rl}  ('RL   ' ln)+ ~

  # indexing
  i_id:      ~ {$In:[fields c:id] $Out:id} 
               'ID' /[A-Z0-9_]+/ {$Wrt} ~
  authors:   ~ {$In:[fields c:ra] $Out} 
               ('RA' ( author {$Wrt} /[,;]/ )* )* ~
  title:     ~ {$In:[fields c:rt] $Out} 
               ('RT' /[";]/? /[^ .,";\n]+/* {$Wrt} ln )* ~
  ref:       ~ {$In:[fields c:rl] $Out} 
               unpubl | journal ~
  author:    ~ name /[^,;]+/ ~
  unpubl:    ~ 'RL   Unpublished' ln ~
  address:   ~ ( 'RL' ( /[^ .,\n]+/ {$Wrt:adr} /[.,]+/? )* ln )*
             ~
  journal:   ~ 'RL' /[^0-9]+/ {$Wrt:jrn}
               /([0-9]+):([0-9]+)-([0-9]+)\\(([0-9]+)\\)/
               {$Wrt:[vol s:$1] $Wrt:[pg1 s:$2] $Wrt:[pg2 s:$3] $Wrt:[year s:$4]}
             ~

  # useful
  name:      ~ /[a-zA-Z0-9_'-]+/ ~
  num:       ~ /[0-9]+/ ~
  ln:        ~ /[^\n]*\n/ ~
}

if: $TestMode {
  $job =  $JobNew:[prod:$rules skip:'\t ' fileName:"SRSDEMO:reflist.dat"]
  while:$JobHasInput:$job {
    $JobTokens:[$job name:entry print:1]
    $JobNext:$job
  }
}
]+/? )* ln )*
             ~
  journal:   ~ 'RL' /[^0-9]srs/demo/reflist.it
  description:
    |A demonstration databank used to demonstrate SRS.
    |<P>
  literature:
    |<OL>
    |<LI>See the online documentation
    |
    |</OL>
#  address:
  contact:
    |<ADDRESS>
    |Thure Etzold<BR>
    |EMBL<BR>
    |</ADDRESS>
    |Giorgio Verde<BR>
    |EMBL<BR>
    |</ADDRESS><P>
    |<ADDRESS>
    |Johnathon Weare<BR>
    |EMBL<BR>
    |</ADDRESS><P>
    |<ADDRESS>
  www:
    |<A HREF="http://www.embl-heidelberg.de">\
    |http://www.embl-heidelberg.de</A>
  address:
    |EMBL<BR>
  telephone: '+49 (0)6221 387451'
  telefax:   '+49 (0)6221 387517'
  email: 'weare@embl-heidelberg.de'
  fields:{
    Citation:
      | This is the RT field
    SeqReference:
      | This is the RL field
  }
  date:
    |6 Dec 1996
  signature:
    |Johnathon Weare
  }
}







BL<BR>
    |</ADDRESS><P>
    |<ADDRESS>
    |Johnathon Weare<BR>
    |EMBL<BR>
    |</ADDRESS><P>
    |<ADDRESS>
  www:
    |<A HREF="http://www.embl-heidelberg.de">\
    |http://www.embl-heidelberg.de</A>
  address:
    |Esrs/demo/useappl.c

#include <stdio.h>
#include "srs.h"

int main ()
{
  APPLo       *appl;
  APPLoOpt    *opt;
  APPLoOptVal *val;
  STRv        str;
  int         k, l;

  SrsEnv ();
  LibOpen ("srswin");
  
  appl = ApplNamed ("clustalw");
  printf ("application: %s\n", ApplGetName (appl));
  for (k=0; (opt=ApplNextOpt (appl, &k)); ) {
    printf ("  option: %s\n", ApplOptGetName (opt));
    if (ApplOptIs (opt, "list"))
      for (l=0; (val=ApplOptNextVal (opt, &l)); ) {
	printf ("    value: %s\n", ApplOptValGetName (val));
        if (ApplOptIs (opt, "real"))
	  printf ("%f", ApplOptValGetValue (opt, val));
      }
  }

  ParDefStr ("outFormat", "GDE");
  ParDefStr ("outOrder", "ALIGNED");

  ApplInit (appl);
  str = StrNew ();
  StrAppS (&str, "$opt.outFormat=$ParStr:outFormat\n");
  StrAppS (&str, "$opt.outOrder=$ParStr:outOrder\n");
  ApplEval (appl, _Str(str));
  printf ("\ncommand: %s\n", ApplGetCommand (appl));
  ApplLaunch (appl);

}


pplOptNextVal (opt, &l)); ) {
	printf ("    value: %s\n", ApplOptsrs/demo/views.c

#include <stdio.h>
#include "srs.h"

int main ()
{ 
  VIEWv      view;
  VIEWvLIB   vlib;
  VIEWvFIELD vfield;
  IDoENTRY   id;
  ENTRYv     entry;
  SETo       *set;
  int        n, entryN;

  SrsEnv ();
  LibOpen ();
  IcaInitSyntax (LibObjByName ("syntax", "icarus"));
  
  view = ViewNew (1, "swiss1");
  ViewSetFormat (view, "table");

  ViewAddRootLib (view, LibObjByName ("library", "swissprot"));
  ViewAddRootField (view, LibGetFieldType ("swissprot", "description"));
  ViewAddRootField (view, LibGetFieldType ("swissprot", "seqlength"));
  vfield = ViewAddRootField (view, LibGetFieldType ("swissprot", "sequence"));
  ViewSetFieldFormat (vfield, "gcg");
  
  vlib = ViewAddLeafLib (view, LibObjByName ("library", "prosite"));
  ViewAddField (vlib, LibGetFieldType ("prosite", "description"));
  ViewAddField (vlib, LibGetFieldType ("prosite", "patterns"));

  if (Query ("[swissprot-des:kinase]", "Q")) {
    set = SetGet ("Q"); 
    entryN = SetSize ("Q");
    printf ("query has %d entries\n", entryN);
    
    for (n=1;  n <= entryN; n++) {
      SetGetID (set, n, &id); 
      entry = EntryOpen (&id);
      EntryView (entry, view);
      EntryClose (&entry);
    }  
  }
}
iewAddLeafLib (view, LibObjByName ("library", "prosite"));
  ViewAddField (vlib, LibGetFieldType ("prosite", "description"));
  ViewAddField (vlib, LibGetFieldType ("prosite", "patterns"));

  if (Query ("[swissprot-des:kinase]", "Q")) {
    set = SetGet ("Q"); 
    entrsrs/etc/

#defines an 'alias' for the old srssection command
nodd $SRSICA/builtin.ic $SRSICA/builtin.i
) {
      SetGetID (set, n, &id); 
      entry = EntryOpe¶ £š°
      EntryView (entry, view);
¶ £rè¶ £tp (&entryxXÞÒÿÿ
(¶ £rÀeafLib (~ ¤{bObjByNa¶ £Ì
(¬ÞÒ
(

;; This file is NOT part of GNU Emacs.
;;
;; To install:
;; 1. Put the file icarus.el in your Emacs Lisp directory
;; 2. You can byte compile the file icarus.el if you want to
;; 3. Put the following code in your .emacs:
;;  (autoload 'icarus-mode "icarus")
;;  (setq auto-mode-alist
;;  	  (append '(("\\.i$"  . icarus-mode)
;;                  ("\\.is$" . icarus-mode)
;;                  ("\\.it$" . icarus-mode)
;;                  ("\\.ic$" . icarus-mode))
;;             auto-mode-alist))
;; 4. And if you don't have a global-font-lock on (emacs 19.32 or later), then
;; also add
;;  (add-hook 'icarus-mode-hook (function 'turn-on-font-lock)


(defvar icarus-font-lock-keywords
  (list
;  '("\\(/\\([^/\\n]\\|\\\\/\\)*/\\)" 1 my-id-create-face nil t)
   '("\\(~\\)[^~]*$" 1 font-lock-icarusprod-face t t)
   '("[a-zA-Z0-9_-]+ *: *\\(~\\)" 1 font-lock-icarusprod-face t t)
   '("\\([a-zA-Z0-9_-]+\\) *:" 1 font-lock-icarusargname-face t t)
;   '("\\([a-zA-Z0-9_-]+\\) *: *#" 1 font-lock-icarusprod-face t t)
;  '("[a-zA-Z0-9_'/\*-]+ *\\(<[^<>]*>\\)" 
;    1 font-lock-keyword-face t t )
;  '("[a-zA-Z0-9_'/\*-]+ *\\(<[^\n<>]*>\\)" 
;    1 font-lock-other-emphasized-face t t )
  '("\\(\$[a-zA-Z0-9_-]+\\)" 1 font-lock-keyword-face t t)
  '("[^a-zA-z]\\(pre\\|init\\|for\\|if\\|foreach\\|while\\|else\\|elif\\)[ \t\n]*[:{$]" 1 icarus-reserved-face t t)
  '("\\(/[^/\n]+/\\)" 1 my-id-create-face t t)
  '("\\('[^'\n]+'\\)" 1 my-reference-face t t)
  '("\\(@[?]*[a-zA-Z0-9_]+\\)" 1 my-oddreference-face t t)
;  '("\\(\"[^\"\n]+\"\\)" 1 font-lock-string-face t t)
;  '("<[^\n<>]*\\(\"[^>\"\n]+\"\\)[^\n<>]*>" 1 font-lock-other-string-face t t)
   '(")\\([0-9:]*\\(?\\|\*\\|\+\\)\\)" 1 font-lock-icarusprod-face t t)
  '("\\(#[^\n]*\\)" 1 font-lock-comment-face t t))
  "Additional expressions to highlight in Icarus mode.")

(defun icarus-mode ()
"Major Mode for editing Icarus code. Support for font locking, no support for indentation, although the indentation advice is: curly brackets 2, square brackets 2, parenthesis 1."
  (interactive)
  (kill-all-local-variables)
  (setq mode-name "Icarus")
  (setq major-mode 'icarus-mode)
  ;; Font lock.
  (make-local-variable 'font-lock-defaults)
  (make-local-variable	'comment-start)
  (make-local-variable	'comment-start-skip)
  (setq comment-start "#")
  (setq comment-end "")
  (setq font-lock-defaults '(icarus-font-lock-keywords))
  (run-hooks 'icarus-mode-hook)
)
;;~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
;; Define ICARUS face attributes
;;~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

(setq font-lock-face-attributes
;;;  font-name fgcolor bgcolor bold? slant? underl?
      '((font-lock-comment-face "springgreen4" "lemonchiffon2" nil t)
	(font-lock-doc-string-face "sienna4" nil nil t) 
	(font-lock-string-face "sienna4" nil nil t)
	(font-lock-keyword-face "firebrick2")
	(font-lock-function-name-face "blue4" nil t)
	(font-lock-icarusprod-face "maroon3" nil t)
	(font-lock-icarusargname-face "darkorange2")
	(font-lock-type-face "firebrick1" nil t)
	(font-lock-reference-face "sienna1")
	(font-lock-variable-name-face "sienna1")

	(my-face "sienna1")
        (my-reference-face "blue")
        (my-oddreference-face "blue4" nil t)
        (my-id-create-face "DarkSlateGray4" nil)
        (my-production-face "maroon" nil t)
        (icarus-reserved-face "maroon" nil t)
))

(provide 'icarus-mode)
ction-name-face "blue4" nil t)
	(font-lock-icarusprod-face "maroon3" nil t)
	(font-lock-icarusargname-facsrs/etc/killrunaway
#
# Identify srsbuild processes run by user www which have exceeded 15
# minutes of cpu time, and kill them.
#
# Run periodically from www's crontab on phenix (IRIX64).
# Not portable!
#
# David Starks-Browning
# starks@embl-heidelberg.de
# 20 Feb 97

# Username under which offending processes, and this script, run.
#
user=srswww

# Can be extended to work on multiple commands.
# Just make a space separated list here.
#
cmds='srsbuild wgetz'

# Threshold in minutes.  Commands running longer are killed.
#
mins='15'

# Notification by email.  Omit if none needed.
#
#maillist="$user etzold"

for cmd in $cmds ; do
    # First translate ':' to '.' so awk interprates min:sec field 
    # as decimal fraction. Then match on running jobs named $cmd taking more 
    # than $mins minutes, printing the pid. Note reliance of particular format of ps 
    # output.  THIS IS NOT PORTABLE!
    #
    pids=`ps -lu $user | tr ':' '.' | awk '$2 == "R" && $14 == cmd && $13 > mins { print $4 }' cmd=$cmd mins=$mins`
    if [ -n "$pids" ] ; then
        if [ -n "$maillist" ] ; then
            echo "Killing $cmd pids at `hostname` (TERM): $pids" | Mail -s "$0 output" $maillist
        fi
        kill -TERM $pids 1>/dev/null 2>&1
        sleep 5
        #
        # Still there?  Try harder this time.
        #
        pids=`ps -lu$user | tr ':' '.' | awk '$2 == "R" && $14 == cmd && $13 > mins { print $4 }' cmd=$cmd mins=$mins`
        if [ -n "$pids" ] ; then
            if [ -n "$maillist" ] ; then
                echo "Killing $cmd pids at `hostname` (KILL): $pids" | Mail -s "

$0 output" $maillist
            fi
            kill -KILL $pids 1>/dev/null 2>&1
        fi
    fi
done






i
        kill -TERM $pids 1>/dev/null 2>&1
        sleep 5
        #
        # Still there?  Try harder this time.
        #
        pids=`ps -lu$user | tr ':' '.' | awk '$2 == "R" && $14 == cmd && $13 > mins { print $4 }' cmd=$cmd mins=$mins`
        if [ -n "$pids" ] ; then
            if [ -n "$maillist" ] ; then
                echo "Kilsrs/etc/makedoc
cp $SRSDOC/srsman.html $SRSMAN/srsman.html
cp $SRSDOC/contents.html $SRSMAN/contents.html
echo "...making the Icarus class documentation"
$SRSEXE/icarus -class $SRSICA/srs.ic > $SRSMAN/class.html
echo "...making the Icarus function reference"
$SRSEXE/icarus -ci > $SRSMAN/icafunc.html
echo "...making the C API documentation"
$SRSEXE/icarus $SRSICA/man_capi.i
echo "...making the program usage"
$SRSEXE/icarus $SRSICA/man_usage.i
echo "...inserting additional HTML commands"
$SRSEXE/icarus $SRSICA/man_chap.i
echo "...making the index"
$SRSEXE/icarus $SRSICA/man_inx.i
echo "...making the table of contents"
$SRSEXE/icarus $SRSICA/man_toc.i
rm $SRSMAN/mff_*
icarus -class $SRSICA/srs.ic > $SRSMAN/class.html
echo "...making the Icarus function reference"
$SRSEXE/icarus -ci > $SRSMAN/icafunc.html
echo "...making the C API documentation"
$SRSEXE/icarus $SRSICA/man_capi.i
echo "...making the program usage"
$SRSEXE/icarus $SRSICA/man_usage.i
echo "...inserting additional HTML commands"
$SRSEXE/icarus $SRSICA/man_srs/etc/makefile.mms
LIB = srsexe:srs.olb
CFLAGS = $(XCFLAGS) /define="SRSINCLUDE=""srswin.h"""

.c.olb
	cc $(CFLAGS) $(mms$source)
	$(libr) $(librflags) $(mms$target) $(mms$target_name).obj
	delete $(mms$target_name).obj;

.c.obj
	cc $(CFLAGS)/obj=$(mms$target) $(mms$source)

LIBSRCS = futil.c message.c sm.c -
	script.c oddfncts.c oddtools.c parser.c -
	sdl.c sdlget.c -
	index.c btree.c ids.c hash.c -
	idx.c seq.c par.c -
	seqlib.c library.c entry.c -
	query.c set.c id.c -
	link.c stack.c expr.c -
	lst.c map.c regexp.c -
	arglist.c tm.c rtl.c 

EXES = srsexe:srsbuild.exe srsexe:getz.exe srsexe:odd.exe srsexe:srscheck.exe -
       srsexe:trembl.exe

all : $(LIB) $(EXES)
	continue

$(LIB) :	$(LIB)($(LIBSRCS))
	continue

srsexe:srsbuild.exe :	srsexe:srsbuild.obj srsexe:srs.lib
	link /execu=srsexe:srsbuild srsexe:srsbuild,$(LIB)/lib

srsexe:srscheck.exe :	srsexe:srscheck.obj
	link /execu=srsexe:srscheck srsexe:srscheck,$(LIB)/lib

srsexe:odd.exe : srsexe:bs_odd.obj srsexe:bs_parser.obj -
	srsexe:bs_sdl.obj srsexe:bs_sdlget.obj
	link /execute=srsexe:odd srsexe:bs_odd,srsexe:bs_parser,-
	srsexe:bs_sdl,srsexe:bs_sdlget,$(LIB)/lib

srsexe:getz.exe : srsexe:getz.obj srsexe:srs.lib
	link /execute=srsexe:getz srsexe:getz,$(LIB)/lib

srsexe:trembl.exe : srsexe:trembl.obj
	link /execute=srsexe:trembl srsexe:trembl,$(LIB)/lib

srsexe:bs_parser.obj : parser.c
	$(CC) $(CFLAGS) /object=srsexe:bs_parser /define=BOOTSTRAP parser

srsexe:bs_sdl.obj : srssou:sdl.c
	$(CC) $(CFLAGS) /object=srsexe:bs_sdl /define=BOOTSTRAP sdl

srsexe:bs_sdlget.obj : srssou:sdlget.c
	$(CC) $(CFLAGS) /object=srsexe:bs_sdlget /define=BOOTSTRAP sdlget

srsexe:bs_odd.obj : srssou:odd.c
	$(CC) $(CFLAGS) /object=srsexe:bs_odd /define=BOOTSTRAP odd

.c.obj:
	$(CC) $(CFLAGS) $<

#$(SRSSOU)/message.h : $(SRSETC)/message.dat
#	msgdef
#	mv -f message.h $(SRSSOU)/message.h


#depend
				   
$(LIB)(futil.c) : futil.c message.h msg.h futil.h sm.h 
$(LIB)(message.c) : message.c futil.h sm.h msg.h 
$(LIB)(sm.c) : sm.c message.h msg.h sm.h 
$(LIB)(oddfncts.c) : oddfncts.c message.h msg.h sm.h futil.h sdl.h sdl_def.h 
$(LIB)(oddtools.c) : oddtools.c message.h msg.h oddtools.h 
srsexe:bs_parser.obj $(LIB)(parser.c) : parser.c futil.h parser.h -
  message.h msg.h sm.h
srsexe:bs_sdl.obj $(LIB)(sdl.c) : sdl.c message.h msg.h futil.h sm.h parser.h -
sdlparser.h map.h sdl_def.h sdl.h  
srsexe:bs_sdlget.obj $(LIB)(sdlget.c) : sdlget.c futil.h message.h -
  msg.h sdl.h sdl_def.h
$(LIB)(index.c) : index.c sm.h message.h msg.h futil.h map.h binpack.h -
  btree.h  id.h ids.h idx.h index.h 
$(LIB)(btree.c) : btree.c message.h msg.h futil.h tm.h binpack.h -
  btree.h ids.h
$(LIB)(ids.c) : ids.c message.h msg.h binpack.h futil.h tm.h id.h -
  ids.h set.h idx.h library.h map.h 
$(LIB)(idx.c) : idx.c sm.h message.h msg.h futil.h binpack.h idx.h 
$(LIB)(seq.c) : seq.c sm.h message.h msg.h futil.h lst.h seq.h 
$(LIB)(par.c) : par.c message.h msg.h futil.h lst.h par.h 
$(LIB)(seqlib.c) : seqlib.c message.h msg.h lst.h futil.h par.h -
parser.h id.h library.h entry.h seq.h query.h seqlib.h stack.h expr.h srswin.h 
$(LIB)(library.c) : library.c message.h msg.h futil.h sm.h tm.h -
  btree.h ids.h par.h parser.h library.h srswin.h 
$(LIB)(entry.c) : entry.c message.h msg.h sm.h tm.h futil.h par.h -
  parser.h id.h library.h entry.h srswin.h 
$(LIB)(query.c) : query.c message.h msg.h futil.h parser.h par.h -
  regexp.h ids.h btree.h sm.h tm.h library.h id.h entry.h set.h link.h -
  query.h srswin.h  
$(LIB)(set.c) : set.c lst.h sm.h message.h msg.h futil.h parser.h -
id.h set.h library.h srswin.h
$(LIB)(id.c) : id.c message.h msg.h futil.h binpack.h id.h 
$(LIB)(link.c) : link.c message.h msg.h futil.h sm.h id.h set.h link.h -
  map.h btree.h ids.h library.h query.h srswin.h 
$(LIB)(stack.c) : stack.c stack.h message.h msg.h futil.h parser.h 
$(LIB)(expr.c) : expr.c message.h msg.h futil.h parser.h stack.h -
  expr.h srswin.h
$(LIB)(hash.c) : hash.c hash.h 
$(LIB)(lst.c) : lst.c lst.h 
$(LIB)(map.c) : map.c message.h msg.h futil.h map.h 
$(LIB)(script.c) : script.c script.h
$(LIB)(regexp.c) : regexp.c regexp.h regmagic.h 
$(LIB)(arglist.c) : arglist.c message.h msg.h futil.h parser.h par.h -
  srswin.h arglist.h
$(LIB)(tm.c) : tm.c message.h msg.h tm.h 
$(LIB)(rtl.c) : rtl.c rtl.h
srsexe:getz.obj : getz.c message.h msg.h futil.h parser.h seq.h par.h -
  arglist.h id.h set.h entry.h library.h seqlib.h query.h srswin.h -
  arglist.h entry.h id.h set.h ids.h library.h link.h index.h srswin.h 
srsexe:trembl.exe : trembl.c
srsexe:srsbuild.obj : srsbuild.c message.h msg.h futil.h sm.h -
  parser.h seq.h par.h btree.h
srsexe:srscheck.obj : srscheck.c message.h msg.h futil.h sm.h -
  seq.h par.h btree.h
srsexe:msgdef.obj : msgdef.c msg.h 
srsexe:bs_odd.obj : futil.h message.h msg.h sm.h parser.h sdl.h sdl_def.h
srsexe:bs_sdl.obj :  message.h msg.h futil.h sm.h parser.h sdlparser.h -
  map.h sdl_def.h sdl.h



 query.h srswin.h -
  arglist.h entry.h id.h set.h ids.h library.h link.h index.h srswin.h 
srsexe:trembl.exe : trembl.c
srsexe:srsbuild.obj : srsbuild.c message.h msg.h futil.h sm.h -
  parser.h seq.h par.h btree.h
srsexe:srschsrs/etc/message.dat
#    $RCSfile: message.dat,v $
#    $Revision: 1.16 $
#    $Date: 1997/03/07 11:32:43 $
#    $Author: srs $
#
e__msgfail, invalid message address - rebuild system
e__allocfail, insufficient memory - error during malloc
	"could not allocate \"%s\"\n\n"
e__freefail, allocated memory could not be freed
	"could not free \"%s\"\n\n"
e__settoobig, set size would exceed MAXIDS
e__readerr, error during fgets or fread
e__novalop, OR may not performed with sets of mixed type
e__novaltyp, set types may not be mixed in logical expression
	"types of set A: %d, set B: %d\n"
e__nosetfree, all sets occupied
e__userabort, name entered is empty 
e__filnotopen, file is not opened for specified access
e__filnotok, file could not be opened
	"\"%s\"\n\a\n "
e__filopenerr, file could not be opened
	"\"%s\"\n\a\n "
e__eof, end of file encountered
e__ltoolong, line read is too long for output array
e__invnodenum, invalid node number or step specification missing
e__missnode, step definition contains no number of target node
e__toomansym, symboltable already contains max number of symbols
e__eot, end of symbol table is reached, no more symbols can be loaded
e__parsefail, syntax error
	"Line nr. %d in file %s\n%s\n"        
e__bldparsefail, error during parsing
        "in %s, entry nr.: %d, name: \"%s\", field: %s \n%s\n\n"
e__strprsfail, syntax error
	"at \"%s\"   \n\n"                  
e__lnotsaved, line cannot be restored - was not saved
e__novalpnam, parameter name not known 
	"Line nr. %d in file %s\nname: \"%s\"\n\n"
e__novalsnam, structure name not known 
	"Line nr. %d in file %s\nname: \"%s\"\n\n"
e__invalnum, parameters value does not meet constraints
	"Line nr. %d in file %s\n%s\n\n"
e__procfail, program execution stopped due to reported errors
e__symnotuniq, symbol is already defined
        "symbol: \"%s\" value: %d\n\n"
o__parnotok, parameter does not meet constraints
        "Line nr. %d in file %s\n%s\n\n"
o__nossbeg, no begin of sub structure block was found 
        "Line nr. %d in file %s\n\n"
o__nossend, end of sub structure block ('}') missing 
        "Line nr. %d in file %s\n\n"
o__parismiss, required parameter is missing
	"before line nr. %d in file %s\nParameter name: \"%s\"\n\n"
e__toomanstrct, number of structures is greater than allocated for
        "structure nr.: %d - memory allocated for %d structures\n\n"
e__startismiss, no root node in parsing tree specified
e__isnotss, structure cannot be a substructure as declared
        "Line nr. %d in file %s \nstructure name: %s\n\n"
e__novalid, id of structure is not same as local count
        "Line nr. %d in file %s\nstructure: %s\n\n"
e__missingchar, expected character(s) not found
        "Line nr. %d in file %s %s\n\n"
e__unknownnterm, nonterminal symbol is not defined
        "\"%s\"\n\n"
e__charnotknown, character is not valid in this context
        "Line nr. %d in file %s\ncharacter: %c\n\n"
e__symnotknown, symbol is not defined
        "Line nr. %d in file %s\nsymbol: %s\n\n"
e__novalsyminfo, symbol information is not valid
        "Line nr. %d in file %s \n<%s>\n\n"
e__novalarg, invalid argument in command line
        "Argument nr. %d must be %s\n\n"
e__novalcommand, invalid command line
        "At least %d argument expected\n\n"
e__bnfbuildfail, could not process Backus-Naur expressions
        "before Line nr. %d\n\n"
e__wrongpartyp, parameter value has incorrect type
        "Line nr. %d in file %s\n %s\n\n"
e__novalptyp, parameter value is not allowed
        "Line nr. %d in file %s\nvalue: %d\n\n"
e__novalopt, option value unknown 
        "value %d for \"%s\""
e__misscolon, colon is missing 
        "in line: \"%s\""
e__nammismatch, names are not identical
	"\"%s\" and \"%s\"\n\n"
e__namnotuniq, name already exists in database
	"\"%s\"\n\n"
e__novalauthor, invalid author name
        "in \"%s\", entry nr.: %d, author: \"%s\"\n"
i__slbreportbeg, 4 parameters
        "\n________________________________________________________________________________\n\n"
	"Statistics of processing library \"%s\"\n\n"
	"  total nr. of entries: %d\n"
	"    nr. of new entries: %d\n"
	"nr. of updated entries: %d\n\n"
	"List of processed fields:\n"
i__slbreportend, 0 parameters
        "\n_______________________________________________________________________________\n\n"
i__inxreport,
        "%10s: %6d new keys, %6d key references, index-file size: %d blocks\n"
i__processing, 1 parameter
        "...processing %s"  
e__eom, attempt to write beyond map section
	"section name: %s, size of section (bytes): %d\n"
i__inxcmprss, 4 parameters
        "compressed file %s to %d blocks\n\n"                     
e__nofieldend, end-of-field-mark is missing
        "%s\n"
e__wrongfieldcnt, nr. of defined fields does not correspond with actual nr.
        "actual: %d, defined: %d \n"
e__strtoolong, string is too long
        "string: %s, max. len %d\n"
e__linenotexst, line is not pasted
        "row number: %d\n"
e__invalstr, invalid string
        "length must be between %d and %d "
e__invalnumber, invalid number
        "value must be between %d and %d  "
e__invalifn, invalid input file name   
        "file \"%s\" could not be opened"
e__invalofn, invalid output file name   
        "file \"%s\" could not be opened"
e__activesubmenu, can't delete menu with active submenu
        "menu-ID: %d, submenu-ID: %d;
e__allwinused, no free window available
e__exceedsize, attempt to write beyond end of block
        "name of block:%s, size: %d\n"
e__eob, end of buffer was reached
e__novalfield, inivalid field name
        "%s\n"
e__novalnam, invalid name                                                      
       "\"%s\"\n"                             
e__unexpectnum, number not as expected
        "%s, expected: %d found: %d\n"
e__noinit, item not initialized
        "%s\n"
e__strnotfou, string was not found
        "string %s in %s\n"
e__strnotfound, string was not found
        "\"%s\"\n"
e__novalstr, string is not valid
        "\"%s\"\n"
e__novalfadd, invalid fadd specified
        "%u, max fadd: %u\n"
e__novalnum, number to high or to small, not valid in this context
        "%d\n"
e__libnotinx, library has not index
        "Library: \"%s\", Index: \"%s\"\n"
i__wrotefile, wrote file
        "\"%s\"\n"
i__wrotefiles, ...done
        "wrote total of %d files\n"
e__novalpos, invalid begin/end positions
        "in \"%s\": %s\n"
e__novalseqlen, sequence length does not meet constraints
        "in \"%s\" - length: %d\n"
e__seqfrg, sequence fragmentary
        "in \"%s\": %s\n"
e__seekfail, fseek failure 
        "in file \"%s\"\n"
e__crmpscfail, map section too small 
        "requested: %d blocks, got: %d blocks\n"
e__maxlinksexceed, exceeded nr. of links per node
        "max. nr. of links: %d\n"
e__unknownnam, name is not known 
        "\"%s\"\n"
e__novallink, link cannot be performed
        "\"%s < %s\"\n"
e__toofew, array is too small
        "actual size:%d, minimum size:%d\n"
e__namreserved, name is reserved for internal use
        "\"%s\"\n"
i__sdlreport, 7 parameters
        "\n________________________________________________________________________________\n\n"
	" made section files:\n" 
        "      \"%s\" with %d blocks \n"
        "      \"%s\" with %d blocks \n\n" 
	" from input: \"%s\"\n\n"
	" defined %d objects of %d different classes\n"
        "\n_______________________________________________________________________________\n\n"
e__nopath, no linkage found
        "from \"%s\" to \"%s\"\n"
e__ambigouslink, linkage ambiguity
        "from \"%s\" to \"%s\"\n"
o__novalcol, invalid column number
        "\"%d\"\n"
o__novalrow, invalid row number
        "\"%d\"\n"
e__badarglist, wrong number of argument in function call
e__namnotdef, name is not defined
        "%s name: \"%s\"\n"
e__invaloutdir, invalid output directory name   
        "\"%s\"\n"
i__wroteseq, wrote sequence
        "\"%s\"\n"
i__wroteseqsfile, ...done
        "wrote %d entries to file \"%s\"\n"
e__complement, feature cannot be reverse complemented yet - have patience
        "\nin \"%s\": %s\n"
e__novalreference, link cannot be performed 
        "between libraries %s and %s using reference \"%s\"\n"
i__lnkreport, 
        "%10s: references to \"%s\": %d valid, %d invalid\n"
e__exceedquota, exceeded quota
        "%s\n"
e__rtlfail, RTL-function failed
        "function name: \"%s\"\n"
e__novalsettyp, no set operation with different set types
        "\"%s\", \"%s\"\n"
e__collidsfail, collected incorrect number of ID's
        "actual:%d, should be:%d"\n"
e__inheritfail, invalid inheritance
        "\"%s\" cannot inherit \"%s\"\n"
e__objnotfound, object is not defined
        "Line nr. %d in file %s\n Object-ID: %s\n\n"
e__objnotnhrt, object is not yet inherited - change order of attributes
        "Line nr. %d in file %s\n Object: %s\n"
e__missdefattr, attribute is missing in object class definition
        "Line nr. %d in file %s\n, Attribute: %s\n"
o__nolibslct, no libraries were selected - use the \"Library\" option! 
e__symappendfail, cannot append symbol - table is still empty
        "Symbol: %s"
e__exceedarr, too many elements
        "maximum number: %d\n"
e__novalterm, invalid terminal symbol 
        "Line nr. %d in file %s \"%s\"\n\n"
i__mappedset, libraries 
        "Mapped to \"%s\" -> %d entries"
i__loadlinkset,   
        "...loading link set \"%s\""
e__novalseqform, invalid format
        "\"%s\", expected \"%s\""
i__wroteseqlen, wrote sequence
        "\"%s\" with %d characters\n"
o__obsoletemsg, value is not defined
        "Line nr. %d in file %s\nvalue: %s\n\n"
e__novalpar, invalid parameter group value
        "%d, current number of groups: %d\n\n"
e__toomanpar, maximum number of parameter groups exceeded
        "%d, increase mm->maxpar\n\n"
i__procsubset, processing subset
        "first: %d, last: %d, from %d entries\n\n"
e__sicinvalgroups, groups add not to total sequence number
        "should be: %d, group sum: %d\n\n"
e__unknowncommand, unknown command
        "\"%c\"\b\n"
i__readingname, ...reading name
        "nr. %d in list: %s\n"
e__interrupt, aborted by Ctrl-C
i__wroteset, ...done
        "%d entries written to set \"%s\"\n"
e__sftop, location operator cannot be processed yet!
        "in \"%s\": %s\n"
e__libnotlinked, library has no links
        "\b\"%s\""
e__filnotfound, file was not found or could not be opened
        "\"%s\"\n\n"
e__filcloseerr, could not close file
	"\b\"%s\"\n\n "
e__filwriteerr, could not write to file
	"File: \"%s\", Number of bytes attempted to write: %d\n\n"
i__noentriesfound, no entries found
e__nonounix, internal SRS-unix error
	"The routine \"%s\" should not be called "
i__listtolib, read file of names
        "%d entries were successfully read from file \"%s\"\n"
e__eostack, end of stack
f__limitexceeded, limitexceeded
        "Maximum number of \"%s\" is %d\n"
e__nontermexpect, name of nonterminal expected
e__novalformat, line has incorrect format
        "<%s\n>"
e__parnottype, parameter has not requested type
        "parameter \"%s\" is not of type \"%s\"\n"
e__foundoneof, one-of operator encountered
        "in subentry \"%s\"\n"
e__unknownoption, option is not known in this context
        "\"%s\"\n"
e__parisdefined, parameter cannot be defined twice
        "\"%s\"\n"
e__parnotdefined, parameter is not defined
        "\"%s\"\n"
e__notwriteopen, file is not open for write access        
        "\"%s\"\n"
e__indexisbusy, index is busy or was never completed
        "\"%s\"\n"
e__doesnotexistfunction, function name does not exist
        "\"%s\"\n"
e__overflowstack, stack overflow
        "current stack size is \"%d\"\n"
f__failedtomovelist, FATAL: failed to move list
        "\"%s\"\n"
e__couldnotgetsequence, could not get sequence for accession number
        "\"%s\"\n"
e__nothingtoevaluate, nothing to evaluate
e__failureinslbgetx, could not get feature or sequence for entry
        "\"%s\"\n"
e__joinillegalpar, join has illegal parameter
        "\"%s\"\n"
e__entryparsefail, syntax error
        "in entry  \"%s\"\n"
e__illegalposition, illegal position (pos<=0) in range
        "in entry  \"%s\"\n"
e__illegalvalueonstack, illegal value (float) on stack
        "illegal value *%8.2f* on stack: position must be INT"
e__illegalvaluesonstack, illegal values (float) on stack
        "illegal values *%8.2f* *%8.2f* on stack: position must be INT"
e__illegaldirectioninrange, illegal direction in range
        "in entry  \"%s\"\n"
e__operatorbeforenotallowed, operator BEFORE not allowed
e__operatorafternotallowed, operator AFTER not allowed
e__postoohigh, position too high in range
        "in entry  \"%s\"\n"
i__entry, That was
        "entry  \"%s\"\n"
e__objectunknown, unknown object
        "%s \"%s\" does not exist\n"
e__noseqinlist, no sequence in range list
e__noresult, failed to evaluate result
e__illegalrangemod, illegal modification of position prohibited
e__illegalmodparam, illegal combination of modification parameters
e__illegalqueryparam, illegal combination of query parameters
e__noparamlist, parameter list for join missing
e__negativelength, negative length of subsequence in SlbEvalSequence
e__incorrectlength, incorrect length of subsequence in SlbEvalSequence
e__fnctnotdefined, function associated to ODD-object is not defined
       "you must define %s_M before including ODD generated header file
e__btreenotprep, btree is not prepared for building
       "could not start build phase %d\n"
i__writeindex, writing index
       "...writing index \"%s\" with %d records"  
e__invalidid, invalid entry ID
       "record with number %d cannot be accessed\n"
e__hasnotfixedrecord, index has not fixed length records
       "index: \"%s\"\n" 
e__fieldnotindex, data-field can not be indexed
       "\"%s\"\n"
e__iscompressed, index is already compressed
       "\"%s\"\n"
e__notcompressed, index needs to be compressed before use
       "\"%s\"\n"
i__processingentry,
       "...no. %d, %s"
i__wrotebtree, wrote btree file
       "\n...wrote index file \"%s\"\n" 
       "         size: %d kbytes, bucket size: %d, records: %d"
i__wroteidfile, wrote file with id-lists
       "...wrote IDs file \"%s\"\n" 
       "         size: %d kbytes, IDs: %d"
e__inxnotcompress, index cannot be compressed
       "\"%s\"\n"
e__listnotfilled, list is not completed
       "list \"%s\", expected: %d, received: %d\n"
e__buffexceeded, buffer size exceeded
       "buffer \"%s\", size %d\n"
i__openedidpatch, opened Id patch file
       "...opened ID patch file generated for \"%s\""
e__dupllibid, duplicate library ID
       "ID \"%d\" defined for \"%s\" is already occupied by \"%s\"\n"
e__novallibid, invalid library ID ...must range from 1 to 255
       "ID \"%d\" defined for \"%s\"\n
e__libidexst, library has already an ID
       "ID \"%d\" for \"%s\" with already defined ID \"%d\"\n"
e__libidnotknown, library ID does not exist
       "no library with ID \"%d\" is defined\n"
e__settoosmall, set has not enough space for IDs
       "attempt to copy %d IDs where only for %d is space\n"
i__builtlink, wrote link file
       "...wrote link from \"%s\" to \"%s\"\n"
       "         valid references: %d, invalid references: %d, \n"
       "         total number of links: %d\n"
i__checkinglib, 
       "...checking library \"%s\"\n"
e__novalentryidlen, length of ID hexnum string is not correct
       "length: %d, hexnum ID string: \"%s\""
e__indexnotuptodate, index not up to date 
       "ID-index for entry \"%s\" is from %s, library from %s\n
e__indexwrongversion, invalid index
       "can't open index \"%s\" with version %d ...should be %d"
e__regerror, regexp:
       "%s\n"
i__mustbuildinx,
       "======> must build indices for library \"%s\"\n"
i__mustbuildlink,
       "------> must build link between \"%s\" and \"%s\"\n"
i__diffentrynum,
       "library \"%s\" had previously %d, now %d entries\n"
e__labelnotfound, label not found in script file
       "label: \"%s\" in script file \"%s\"\n"
i__givinguplib, 
       "cannot do anything about library \"%s\" now\n
e__strnotinset, invalid string value
       "string \"%s\" is not in value set for parameter \"%s\"\n"
e__numnotinset, invalid number value
       "number \"%d\" is not in value set for parameter \"%s\"\n"
e__realnotinset, invalid real value
       "real \"%f\" is not in value set for parameter \"%s\"\n"
e__functionnotinset, invalid function value
       "function is not in value set for parameter \"%s\"\n"
e__charnotallowed, invalid character
       "character \"%c\" is not allowed within parameter \"%s\"\n"
e__realnotinrange, value is not in range
      "%f is outside the range of %f to %f for parameter \"%s\"\n"
e__checkerr, invalid value
      "for parameter \"%s\"\n"
e__setopneedsidtype, at least one of the two sets must have ID-type
      "set "\%s", set "\%s\"\n"
e__nolinklibselected, no library is selected for linking
      "use option \"%s\" first \n"
i__querynegative, no entries found
      "query: \"%s\"\n"
e__novalvar, invalid value of variable
      "%s is: %d, should be: %s"
e__novalvar2, invalid value of variable
      "%s is: %s, should be: %s"
e__novalvar3, invalid value of variable
      "%s is: %d, should be: %d"
e__formatnomatch, string and format do not match,
      "format \"%s\" does not match string \"%s\"\n"
e__relbegandend, invalid shift - cannot be relative to both begin and end
      "\"%s\""
e__invalidshift, invalid shift
      "\"%s\": begin: %d, end: %d, both relative to %s"
e__shiftseqisfrag, shifted sequence is fragmentary
      "\"%s\""
e__seqwithneglen, cannot extract subsequence
      "from \"%s\", beg: %d, end %d"
e__badfile, file cannot be accessed
      "%s\n"
i__indexnotexist,
       "++++++> must build index \"%s\" for %s, does not exist\n"
i__indexnotcompleted,
       "++++++> must rebuild index \"%s\" for %s, was never completed\n"
i__indexnotuptodate,
       "++++++> must rebuild index \"%s\" for %s, is not up to date\n"
i__indexnotcompressed,
       "++++++> must compress index \"%s\" for %s, is not compressed\n"
e__rangewithundefval, begin or end position is not defined
        "in entry \"%s\"\n"
e__argwrongnum, wrong number of arguments 
       "label: %s, arguments sent: %d, expected: %d\n"
e__argwrongtype, wrong argument type 
       "label: %s, argument no: %d,  type sent: %c, expected: %c\n"
e__argsendnull, sent NULL pointer
       "label: %s, argument no: %d\n"
e__fatal, fatal error
e__unknownarg, unknown argument name
      "\"%s\" for command \"%s\"\n"
e__nocurrentcommand, commands must be defined before their arguments
        "\"%s\""
e__onlyoneunnamed, only one unnamed argument allowed per command
        "\"%s\" for command \"%s\""
o__obsoletemess, wrong variable type
        "variable \"%s\" has type \"%s\", requested \"%s\" requires \"%s\"\n" 
e__varwrongclass, incompatible classes in assignment
        "variable \"%s\" has object of class \"%s\", not \"%s\"\n" 
e__varisreadonly, variable is readonly
        "variable \"%s\"\n"       
o__parsererror, parser error
	"production `%s' :\n%s ...\n%s\n  pattern ``%s'' did not fit.\n"
e__seqillegallength, sequence cannot be translated
        "begin position %d, sequence length\n"
e__novalchar, invalid character
        "%s \"%c\" is not valid\n"
e__missingarg, missing argument
        "insufficient number of arguments for %s\n"
e__nosetorlib, unknown set or databank
        "\"%s\"\n"
e__functionnotexist, function does not exist
        "\"%s\"\n"
e__emptyquerystring, empty query string
e__illegalbaseconv, illegal base conversion 
	"Maximum possible base for conversion is %d, continuing...\n"
e__dbnotlegal, databank name not legal in context
        "databank \"%s\" can not be an operator in logical operation\n"
e__noviewselect, no view selected for edit
	"No view selected for view edit .... \n"
e__querynotfound, query does not exist
        "query with number %d\n"
e__dbhasnotfield, non existing field
        "data bank \"%s\" does not have field \"%s\".\n"
e__icastackempty, stack is empty
        "stack number: %d\n"
e__icaunknownattr, unknown attribute
        "class \"%s\" has no attribute \"%s\"\n" 
o__icavartype, invalid type
        "variable: \"%s\", type: %s, %s operation requires %s\n" 
e__icaenumval, unknown value
        "\"%s\" for attribute \"%s\"\n"
e__icarequiredattr, attribute value is required
	"attribute \"%s\" of class \"%s\"\n"
e__icaattrval, invalid attribute value
        %s\n"
e__templNoCurrTemplate, no current template object selected
e__unknownformat, unknown format option
        "field \"%s\" has no format \"%s\"\n"
e__templEndOfHistory, invalid TemplEndWith
        "no more contexts on the stack\n"
i__invalidentry, invalid or empty entry name
      "entry: \"%s\"\n"
e__setnotuniqname, set with this name exists already
	set "\"%s\"\n"
e__icainvalidselect, attempt to access an element of a NON-list variable
        "\"%s\" cannot be an element of \"$%s\"\n"
e__icainvallistassign, attempt to assign a nonzero value to a list variable
        "only 0 can be assigned to \"$%s\" which deletes the list\n"
e__icaopTask, prodName not def for task
      "prdName: \"%s\" task: \"%s\"\n"
e__icaopEdit, Format has wrong numer of arguments
      "format: \"%s\" args: %d listSize: %d\n"
e__icaopAssign, assigment has a wrong type
      "Variable name: \"%s\"   Value name: \"%s\"\n"
e__icaopRestrictLen, cursor length restriction  has a wrong type
      "Value name: \"%s\"\n"
e__icaopMove, cursor move  has a wrong type
      "Value name: \"%s\"\n"
e__icabnfGetProd, production name is not uniq
      "Name: \"%s\" Syntax: \"%s\"\n"
e__icabnfExpression, Too many choice statments
      "Choice: \"%s\" Syntax: \"%s\"\n"
e__icabnfProgram, Wrong syntax
      "Syntax: \"%s\" Action: \"%s\"\n"
e__icabnfLinkBnfNet, production not defined
     "Production name: \"%s\"\n"
e__icabnfParser, wrt expected but found
     "Current token \"%s\"\n"
e__icarusFatal, (NULL) name for IcaGetTokenList call
e__toklistFind, Wrong token list name
     "Name: \"%s\"\n"
e__toklistReplace, toklist has ECHO style
     "Name: \"%s\"\n"
e__toklistIsUniq, toklist has FILE style
     "Name: \"%s\"\n"
e__parsererror1, syntax error
     "\n|%s|\n%s\n  -- end of input expected\n"
e__parsererror2, syntax error
     "production `%s' :\n  -- no more input\n"
e__parsererror3, syntax error
     "production `%s' :\n|%s|\n%s\n  no match with |%s|\n"
e__wwwnomatchingview, not all databanks represented by query are defined as root databanks in the view.
     "View \"%s\" is not suitable for displaying query \"%s\".
e__nolibslct, no libraries were selected.
e__wwwNoQueryOrEntriesSelected, no query or entries were selected
     "Try again!"
e__wwwNoQuerySpecified, no query was specified
     "Try again!"
e__toktablenotwritable, not possible to write to token table
     "\"%s\""
i__bldReadLink, processing read link
     "...reading links to \"%s\""
e__bldNoReadLinks, databank has no active read links
     "\"%s\""
f__noVarScope, variable scope does not exist
     "Please contact the program developer."
e__bldLibNotMerge, no indices to merge
     "Library \"%s\" is not partitioned and index merging not required."
e__genNoObjWithNo, object with specified number does not exist
     "No %s with no %d available.\n"
e__checkInvalidLibInfo, incorrect library information
     "Correct error in \"SRSDB:srsdb.i\" or \"%s\".\n"
e__icaMissingString, no string or NULL pointer to string was specified as argument
o__exception, fatal error
     "reason: \"%s\"\n"
e__duplicatekey, duplicate key during list insertion
     "\"%s\"\n"
f__exception, fatal error
     "reason: \"%s\", file: \"%s\", line: %d\n"
o__anyIsReadOnly, attempt to write to readonly ANY
e__icaUnknownClass, attempt to define object of unknown class
     "object named: \"%s\"\n"
e__icaErrorsQuit, exiting due to previous error(s) 
e__icavartype, invalid type
     "\n\"%s\" operation requires type "%s".\nVariable %s" 
e__anyIsReadOnly, attempt to write to readonly ANY
     "\nvariable %s"     











_duplicatekey, duplicate key during list insertion
     "\"%s\"\n"
f__excesrs/etc/prep_srs
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#    $RCSfile: prep_srs,v $
#    $Revision: 1.22 $
#    $Date: 1997/03/19 21:15:33 $
#    $Author: srs $
#
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# define the SRS root directory

setenv SRSROOT /u1/srs/srs5

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# find out operating system and define a symbolic name

setenv OS `uname`
if ($OS == "SunOS" && `uname -r` =~ [56]*) setenv OS 'Solaris'

switch($OS)
case Linux:
  set OS_SPECIFIC = linux
  breaksw
case AIX:
  set OS_SPECIFIC = aix
  breaksw
case HP-UX:
  set OS_SPECIFIC = hpux
  breaksw
case IRIX:
  set OS_SPECIFIC = irix
  breaksw
case IRIX64:
  set OS_SPECIFIC = irix64
  breaksw
case SunOS:
  set OS_SPECIFIC = sunos
  breaksw
case Solaris:
  set OS_SPECIFIC = solaris
  breaksw
case OSF1:
  set OS_SPECIFIC = osf
  breaksw
case ULTRIX:
  set OS_SPECIFIC = ultrix
  breaksw
default:
  echo "SRS does not support $OS"
  exit
endsw


#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# SRS internal directories

setenv SRSDAT ${SRSROOT}/etc
setenv SRSDB  ${SRSROOT}/icarus/db
setenv SRSICA ${SRSROOT}/icarus/util
setenv SRSSOU ${SRSROOT}/src
setenv SRSETC ${SRSROOT}/etc
setenv SRSWWW ${SRSROOT}/www
setenv SRSWWWTMP ${SRSROOT}/tmp
setenv SRSDOC ${SRSWWW}/doc
setenv SRSDEMO ${SRSROOT}/demo
setenv SRSMAN ${SRSWWW}/man
setenv SRSINX ${SRSROOT}/index
setenv SRSSEC ${SRSROOT}/etc/${OS_SPECIFIC}
setenv SRSEXE ${SRSROOT}/bin/${OS_SPECIFIC}

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# create OS specific directories

if (!(-e $SRSSEC)) then
  echo "directory SRSSEC does not exist ... $SRSSEC is created."
  mkdir -p $SRSSEC
endif
if (!(-e $SRSEXE)) then
  echo "directory SRSEXE does not exist ...$SRSEXE is created."
  mkdir -p $SRSEXE
endif
if (!(-e $SRSINX)) then
  echo "directory SRSINX does not exist ...$SRSINX is created."
  mkdir -p $SRSINX
endif


#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# SRS commands
#
# add to the path the srs/etc and the srs/bin directory ...remove any
# other srs..etc or srs..bin directory (from other versions) from the path first
#
set DIR = ($path)
set newpath = ()
while ($#DIR != 0)
  if (!($DIR[1] =~ */srs*etc  || $DIR[1] =~ */srs*bin*)) then
    set newpath=($newpath $DIR[1])
  endif
  shift DIR
end
set path = ($newpath)
set path = ($SRSEXE $SRSETC $path)


#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# type banner and exit

echo "---------- Welcome to SRS 5.0.4 -------------"
exit
 srs/bin directory ...remove any
# other srs..etc or srs..bin directory (from other versions) from the path first
#
set DIR = ($path)
set newpath = ()
while ($#DIR != 0)
  if (!($DIR[1] =~ */srs*etc  || $DIR[1] =~ */srs*bin*)) then
    set newpath=($newpath $DIR[1])
  endif
  shift DIR
end
set path = ($newpath)
set path = ($SRSEXE $SRSETC $path)


#~~~~~~~~~~~~~~~~~~~srs/etc/prep_srs.com
$ SAVE_VERIFY = f$VERIFY("NO") 
$ say := "write sys$output"
$ !
$ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$ !
$ !    $File: /home/etzold/srs/src/RCS/file.c,v $
$ !    $Revision: 1.1 $
$ !    $Date: 1996/05/06 16:24:30 $
$ !    $Author: srs $
$ !
$ ! DCL script defines environment for either the SRS user or the
$ ! SRS administrator (call script with parameter "admin").
$ !
$ !
$ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$ ! define the SRS root directory
$ !
$ assign /nolog /tran=CONCEALED $2:[ETZOLD.SRS4_0.] SRSROOT
$ !
$ !
$ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$ ! determine the mode: user or srs-administrator
$ !
$ if P1 .eqs. "SRSADMIN" 
$ then
$  ADMIN = 1
$ else
$  ADMIN = 0
$ endif
$ !
$ !
$ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$ ! find out operating system and define a symbolic name
$ !
$ if f$getsyi ("HW_MODEL") .gt. 1024
$ then
$  OS_SPECIFIC = "ALPHA"
$ else
$  OS_SPECIFIC = "VAX"
$ endif
$ !
$ !
$ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$ ! SRS internal directories
$ !
$ define /nolog	SRSCOM  SRSROOT:[ETC]
$ define /nolog SRSINX  SRSROOT:[INDEX]
$ define /nolog	SRSSOU  SRSROOT:[SRC]
$ define /nolog	SRSEXE  SRSROOT:[BIN.'OS_SPECIFIC']
$ define /nolog	SRSDAT  SRSROOT:[ETC]
$ define /nolog	SRSHELP SRSROOT:[ETC]
$ define /nolog	SRSSDL  SRSROOT:[ODD]
$ define /nolog	SRSSEC  SRSROOT:[ETC]
$ define /nolog	SRSETC  SRSROOT:[ETC]
$ !
$ !
$ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$ ! create OS specific directories
$ !
$ if ADMIN 
$ then 
$   if f$search ("SRSROOT:[BIN]''OS_SPECIFIC'.DIR") .eqs. "" 
$   then
$     say "directory SRSEXE does not exist ... will be created just now"
$     create /dir SRSEXE
$   endif
$ endif
$ !
$ !
$ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$ ! SRS commands
$ !
$ getz      :== $SRSEXE:GETZ
$ trembl    :== $SRSEXE:TREMBL
$ !
$ if ADMIN
$ then
$   odd         :== $SRSEXE:odd
$   etcdir = f$trnlnm ("SRSROOT") - "]" + "ETC]"
$   srscheck    :== $SRSEXE:srscheck 
$   srsu*pdate  :== @SRSETC:SRSUPDATE
$   srsb*uild   :== $SRSEXE:SRSBUILD
$   srsm*ake    :== @SRSCOM:SRSMAKE
$   msgdef      :== $SRSEXE:MSGDEF
$   srssec*tion :== "''odd' -ds srswin"
$ endif
$ !
$ !
$ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$ ! type banner and exit
$ !
$ say ""
$ say "                    *** Welcome to SRS, version 4.0 ***"
$ if ADMIN then -
 say "                         Administration environment
$ say ""
$ ! 	Restore verification to the status quo ante
$ if "''SAVE_VERIFY'" then set verify
$ exit

$ say ""
$ ! 	Restore verification to the status quo ante
$ if "''SAVE_VERIFY'" then set verify
$ exit

# define the SRS root directory

SRSROOT=/u1/srs/srs5

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# find out operating system and define a symbolic name

OS=`uname`
if [ "$OS" = "SunOS" ]; then
    case "`uname -r`" in
	[56]*)   OS='Solaris' ;;
    esac
fi
export OS

case "$OS" in
  "Linux")   OS_SPECIFIC="linux" ;;
  "AIX")     OS_SPECIFIC="aix" ;;
  "HP-UX")   OS_SPECIFIC="hpux" ;;
  "IRIX")    OS_SPECIFIC="irix" ;;
  "IRIX64")  OS_SPECIFIC="irix64" ;;
  "SunOS")   OS_SPECIFIC="sunos" ;;
  "Solaris") OS_SPECIFIC="solaris" ;;
  "OSF1")    OS_SPECIFIC="osf" ;;
  "ULTRIX")  OS_SPECIFIC="ultrix" ;;
  *)         echo "SRS does not support $OS" ; exit 1
esac
export OS_SPECIFIC

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# SRS internal directories

SRSDAT=$SRSROOT/etc
export SRSDAT
SRSDB=$SRSROOT/icarus/db
export SRSDB
SRSICA=$SRSROOT/icarus/util
export SRSICA
SRSSOU=$SRSROOT/src
export SRSSOU
SRSETC=$SRSROOT/etc
export SRSETC
SRSWWW=$SRSROOT/www
export SRSWWW
SRSWWWTMP=$SRSROOT/tmp
export SRSWWWTMP
SRSDOC=$SRSWWW/doc
export SRSDOC
SRSDEMO=$SRSROOT/demo
export SRSDEMO
SRSMAN=$SRSWWW/man
export SRSMAN
SRSINX=$SRSROOT/index
export SRSINX
SRSSEC=$SRSROOT/etc/$OS_SPECIFIC
export SRSSEC
SRSEXE=$SRSROOT/bin/$OS_SPECIFIC
export SRSEXE
pd=/data/prosite
export pd

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# create OS specific directories

if [ ! -d $SRSSEC ]; then
  echo "directory SRSSEC does not exist ... $SRSSEC is created."
  mkdir -p $SRSSEC
fi
if [ ! -d $SRSEXE ]; then
  echo "directory SRSEXE does not exist ...$SRSEXE is created."
  mkdir -p $SRSEXE
fi
if [ ! -d $SRSINX ]; then
  echo "directory SRSINX does not exist ...$SRSINX is created."
  mkdir -p $SRSINX
fi


#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# SRS commands
#
# add to the path the srs/etc and the srs/bin directory ...remove any
# other srs..etc or srs..bin directory (from other versions) from the path first
#
PATH=`echo "$PATH" | awk -F: '{ for ( i = 1; i <= NF; i++ ) if ( $i !~ /.*\/srs.*(etc|bin)/ ) printf ":"$i }'`
PATH="${SRSEXE}:${SRSETC}${PATH}"
export PATH

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# type banner and exit

#echo '---------- Welcome to SRS 5.0.3 -------------'
~~~~~~~~~~~~~~~~~~~~~~~~~
# SRS commands
#
# add to the path the srs/etc and the srs/bin directory ...remove any
# other srs..etc or srs..bin directory (from other versions) from the patsrs/etc/rcsalldiff
for i in $1 ; do
  rcsdiff $i >> /dev/null 2>&1
  if [ $? = 1 ]; then
    echo $i
    rcsdiff $i
  fi
done
}'`
PATH="${SRSEXE}:${SRSETC}${PATH}"
export PATH

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# type banner and exit

#echo '---------- Welcome to SRS 5.0.3 -------------'
~~~~~~~~~~~~~~~~~~~~~~~~~
# SRS commands
#
# add to the path the srs/etc and the srs/bin directory ...remove any
# other srs..etc or srs..bin directory (from other versio¶ £¡Ü the patsrs/etc/rmtmpdir

/bin/find $SRSTMP -mtime +7 -exec /bin/rm -rf {} \;
[ $? = 1 ]; then
    echo $i
    rcsdiff $i
  fi
done
}'`
PATH="${SRSEXE}:${SRSETC}${PATH}"
export PATH

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# type banner and exit

#echo '---------- Welcome to SRS 5.0.3 -------------'
~~~~~~~~~~~~~~~~~~~~~~~~~
# SRS commands
#
# add to the path the srs/etc and the srs/bin directory ...remove any
# other srs..etc or srs..bin directory (from other versio¶ £¡Ü the patsrs/etc/srscron
i
    rcsdiff $i
  fi
done
}'`
PATH="${SRSEXE}:${SRSETC}${PATH}"
export PATH

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# type banner and exit

#echo '---------- Welcome to SRS 5.0.3 -------------'
~~~~~~~~~~~~~~~~~~~~~~~~~
# SRS commands
#
# add to the path the srs/etc and the srs/bin directory ...remove any
# other srs..etc or srs..bin directory (from other versio¶ £¡Ü the patsrs/etc/srsinstall.com
$ say := "write sys$output"
$ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$ !
$ !    $File: /home/etzold/srs/src/RCS/file.c,v $
$ !    $Revision: 1.1 $
$ !    $Date: 1996/05/06 16:24:36 $
$ !    $Author: srs $
$ !
$ ! DCL script builds the srs system
$ !
$ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$ !
$ !
$ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$ ! change the file "prep_srs.com" to assign the correct SRSROOT
$ !
$ open/read RFILE [.etc]prep_srs.com
$ open/write WFILE [.etc]prep_srs.com
$ !
$ NEXT_LINE:
$ read /end_of_file=FILE_END RFILE LINE
$ if f$locate ("CONCEALED", LINE) .lt. f$length (LINE)
$ then
$   PDIR = f$directory ()
$   PWD = f$parse (PDIR,,,"DEVICE",) + PDIR
$   LINE = "$ assign /nolog /tran=CONCEALED " + PWD - "]" + ".]" + " SRSROOT"
$ endif
$ write WFILE LINE
$ goto NEXT_LINE
$ FILE_END:
$ close RFILE
$ close WFILE
$ !
$ !
$ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$ ! build the programs
$ !
$ @[.etc]prep_srs srsadmin
$ srsmake all
$ odd -ds srswin
$ exit
read /end_of_file=FILE_END RFILE LINE
$ if f$locate ("CONCEALED", LINE) .lt. f$length (LINE)
$ then
$   PDIR = f$directory ()
$   PWD = f$parse (PDIR,,,"DEVICE",) + PDIR
$   LINE = "$ assign /nolog /tran=CONCEALED " + PWD - "]" + ".]" + " SRSROOT"
$ endif
$ write WFILE LINE
$ goto NEXT_LINE
$ FILE_END:
$ close RFILE
$ close WFILE
$ !
$ !
$ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~srs/etc/srsmake
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#    $RCSfile: srsmake,v $
#    $Revision: 1.16 $
#    $Date: 1997/03/03 18:39:57 $
#    $Author: srs $
#
# Bourne-shell script that calls make on different UNIX operating systems; 
#
# script builds either all sources (call without parameters) or individual
# programs (program name as parameter);
# are parameters specified for calling this script will be handed over to
# make
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

ERR='srsmake: Stopping due to Error'

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# find out current operating system

OS=`uname`
if [ "$OS" = "SunOS" ]; then
    case "`uname -r`" in
	[56]*)   OS='Solaris' ;;
    esac
fi
export OS

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# define system dependend make command


# ranlib not defined on all systems ...search path

PLIST="`echo $PATH | sed -e 's/:/ /g'`"
RANLIB=touch
for DIR in ${PLIST}; do
  if [ -r ${DIR}/ranlib ]; then
    RANLIB=ranlib
  fi
done

# this part is edited by srsinstall
case "$OS" in
  Linux)
    MAKE='make SPEZ_FLAGS= CCOMP=cc RANLIB='$RANLIB
  ;;
  AIX)
    MAKE='make SPEZ_FLAGS=-Daix CCOMP=cc MALLOC= LIBS=-lPW'
  ;;
  HP-UX)
    MAKE='make SPEZ_FLAGS=-Dhpux'
  ;;
  IRIX)
    MAKE='make SPEZ_FLAGS= CCOMP=cc RANLIB='$RANLIB
  ;;
  IRIX64)
    MAKE='make SPEZ_FLAGS=-32 CCOMP=cc RANLIB='$RANLIB
    #MAKE='make SPEZ_FLAGS=-Dirix64 CCOMP=cc RANLIB='$RANLIB
  ;;
  OSF1)
    MAKE='make SPEZ_FLAGS=-Dosf CCOMP=cc MALLOC= RM= TO=\$@'
  ;;
  SunOS)
    MAKE='gmake SPEZ_FLAGS=-Dsun CCOMP=gcc MALLOC='
  ;;
  Solaris)
    MAKE='make SPEZ_FLAGS=-Xa LIBS=/usr/ccs/lib/libgen.a CCOMP=gcc MALLOC= RANLIB='$RANLIB
  ;;
  ULTRIX)
    MFLAGS=''
    export MFLAGS
    MAKE='make SPEZ_FLAGS=-Dultrix LFLAGS=-g CCOMP=gcc'
  ;;
  *)
    echo 'cannot make SRS on that operating system'
    echo 'srsmake: Stopping make procedure.'
    exit 1
esac

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# now make SRS, if no parameter is specified build all executables. 

if [ $# = 0 ]; then
  echo "$ERR - at least one argument required"
  exit 1
elif [ "$1" = 'depend' ]; then
  echo 'producing makefile dependencies for include files'
  cd ${SRSSOU} ; $MAKE -f ${SRSETC}/srsmakefile $*
  STATUS="$?"
elif [ "$1" = 'tags' ]; then
  echo 'making new tags file'
  cd ${SRSSOU} ; $MAKE -f ${SRSETC}/srsmakefile $*
  STATUS="$?"
elif [ "$1" = 'clean' ]; then
  echo 'making clean'
  $MAKE -f ${SRSETC}/srsmakefile $*
  STATUS="$?"
elif [ "$1" = 'cleanall' ]; then
  echo 'making cleanall'
  $MAKE -f ${SRSETC}/srsmakefile $*
  STATUS="$?"
else 
  echo "make for $OS with parameters: $*"
  cd ${SRSSOU} ; $MAKE -f ${SRSETC}/srsmakefile ${SRSEXE}/$*
  STATUS="$?"
fi

# pass any error status back up
if [ ! "$STATUS" = 0 ]; then
  echo "$ERR $STATUS"
  exit 1
fi
echo 'srsmake: end'
${SRSSOU} ; $MAKE -f ${SRSETC}/srsmakefile $*
  STATUS="$?"
elif [ "$1" = 'cleasrs/etc/srsmake.com
$ say := "write sys$output"
$ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$ !
$ !    $File: /home/etzold/srs/src/RCS/file.c,v $
$ !    $Revision: 1.1 $
$ !    $Date: 1996/05/06 16:24:39 $
$ !    $Author: srs $
$ !
$ ! DCL script calls mms on VMS or OpenVMS; 
$ ! SRS-administrator environment must be defined before calling;
$ !
$ ! script builds either all sources (call with parameter all) or individual
$ ! programs (program name as parameter);
$ ! all parameters specified for calling this script will be handed over to
$ ! make
$ !
$ !
$ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$ ! find out whether script is running on an alpha or not
$ !
$ if f$getsyi ("ARCH_NAME") .eqs. "Alpha"
$ then
$  XCFLAGS = """XCFLAGS = /nomember/standard=vaxc""" 
$  LINK_OPT = """LINK_OPT = /lib"""
$ else
$  XCFLAGS = """XCFLAGS ="""
$  LINK_OPT = """LINK_OPT = /opt"""
$ endif
$ !
$ !
$ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$ ! set default to both SRSSOU (sources) and SRSEXE (objects and images) using
$ ! a logical defined for that purpose
$ !
$ !
$ ! create a new library if not already there
$ if f$search ("srsexe:srs.olb") .eqs. "" then library /create srsexe:srs.olb
$ !
$ ! save current directory
$ PDIR = f$directory ()
$ PWD = f$parse (PDIR,,,"DEVICE",) + PDIR
$ !
$ define /nolog MAKELOC SRSSOU,SRSEXE        
$ set default MAKELOC
$ !
$ if P1 .eqs. "ALL"
$ then
$   mms /descript=SRSETC:makefile /ignore /macro=('XCFLAGS', 'LINK_OPT') -
        'P1' 'P2' 'P3' 'P4' 'P5' 'P6' 'P7' 'P8'
$ else
$   mms /descript=SRSETC:makefile /ignore /macro=('XCFLAGS', 'LINK_OPT') -
        SRSEXE:'P1'.exe 'P2' 'P3' 'P4' 'P5' 'P6' 'P7' 'P8'
$ endif
$ !     
$ set def 'PWD'
$ exit
srs.olb
$ !
$ ! save current directory
$ PDIR = f$directory ()
$ PWD = f$parse (PDIR,,,"DEVICE",) + PDIR
$ !
$ define /nolog MAKELOC SRSSOU,SRSEXE        
$ set default MAKELOC
$ !
$ if P1 .eqs. "ALL"
$ then
$   mms /descript=SRSETC:makefile /ignore /macro=('XCFLAGSsrs/etc/srsmakefile
#
#    $RCSfile: srsmakefile,v $
#    $Revision: 1.24 $
#    $Date: 1997/03/12 16:22:43 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# 
SHELL=/bin/sh

.SUFFIXES : .c .o .i .m .h .a

    #os specific flags (specified in 'srsmake')
SPEZ_FLAGS = 
    #for compiling ALL c-files
# This is edited by srsinstall - leave these comments in!
# CFLAGS Optimised
#CFLAGS     =  -O2 -D__ODD -DSRSINCLUDE=\"srs5.h\"
# CFLAGS Not Optimised
#CFLAGS     =  -D__ODD -DSRSINCLUDE=\"srs5.h\"
# CFLAGS Debug
CFLAGS     =  -g -D__ODD -DSRSINCLUDE=\"srs5.h\"
    #default compiler
SRSH       = srs5.h
CCOMP      = cc 
CC         = $(CCOMP) $(SPEZ_FLAGS) -I$(SRSEXE) 
MALLOC     = -lmalloc
BIN        = $(SRSEXE)/
LIB        = $(BIN)libsrs.a
    #variable for the target object name
TO         = $%
    #add. flags for compiling to normal objects
OCFLAGS    =  -c -o $@
    #add. flags for compiling lib members
LOCFLAGS   = -c -o $(TO)
#LIBENTER   = /usr/ccs/bin/ar rv $(LIB) $(TO) 
    #command puts object into archive
LIBENTER   = ar r $(LIB) $(TO)
#RANLIB     = ls
RANLIB     = ranlib
RMCMD      = /bin/rm -f
RM         = $(RMCMD) $% 


ODD_OBJS =     $(BIN)bs_odd.o \
               $(BIN)oddfncts.o \
               $(BIN)bs_parser.o \
	       $(BIN)bs_sdl.o \
               $(BIN)bs_sdlget.o


LOCAL_OBJS =   $(BIN)local.o


LIB_OBJS =     $(LIB)($(BIN)arglist.o) \
               $(LIB)($(BIN)lst.o) \
               $(LIB)($(BIN)oddfnctsnew.o) \
	       $(LIB)($(BIN)sdlnew.o) \
               $(LIB)($(BIN)error.o) \
               $(LIB)($(BIN)toklist.o) \
               $(LIB)($(BIN)cursor.o) \
               $(LIB)($(BIN)icarus.o) \
               $(LIB)($(BIN)icabnf.o) \
               $(LIB)($(BIN)icaop.o) \
               $(LIB)($(BIN)icaarg.o) \
               $(LIB)($(BIN)icatask.o) \
               $(LIB)($(BIN)icadebug.o) \
               $(LIB)($(BIN)ica2c.o) \
               $(LIB)($(BIN)bnf2c.o) \
               $(LIB)($(BIN)icainit.o) \
               $(LIB)($(BIN)dict.o) \
               $(LIB)($(BIN)strv.o) \
               $(LIB)($(BIN)listv.o) \
               $(LIB)($(BIN)def.o) \
               $(LIB)($(BIN)sm.o) \
               $(LIB)($(BIN)message.o) \
               $(LIB)($(BIN)futil.o) \
               $(LIB)($(BIN)set.o) \
               $(LIB)($(BIN)unix_map.o) \
               $(LIB)($(BIN)logicals.o) \
               $(LIB)($(BIN)sdlget.o) \
               $(LIB)($(BIN)btree.o) \
               $(LIB)($(BIN)ids.o) \
               $(LIB)($(BIN)idx.o)\
               $(LIB)($(BIN)index.o) \
               $(LIB)($(BIN)library.o) \
               $(LIB)($(BIN)field.o) \
               $(LIB)($(BIN)query.o) \
               $(LIB)($(BIN)queryass.o) \
               $(LIB)($(BIN)link.o) \
               $(LIB)($(BIN)seq.o) \
               $(LIB)($(BIN)par.o) \
               $(LIB)($(BIN)variable.o) \
               $(LIB)($(BIN)id.o) \
               $(LIB)($(BIN)entry.o) \
               $(LIB)($(BIN)regexp.o) \
               $(LIB)($(BIN)templ.o) \
               $(LIB)($(BIN)tm.o) \
               $(LIB)($(BIN)view.o) \
               $(LIB)($(BIN)merge.o) \
               $(LIB)($(BIN)hash.o) \
	       $(LIB)($(BIN)seqdb.o)\
	       $(LIB)($(BIN)appl.o)\
               $(LIB)($(BIN)termio.o) 


$(BIN)srs : 
	echo MAKE FOR COMPLETE SRS SYSTEM FINISHED

$(LIB) : $(LIB_OBJS)
	$(RANLIB) $(LIB)

$(BIN)odd : $(BIN)bs_odd.o $(LIB) $(ODD_OBJS)
	$(CC) -o $@  $(ODD_OBJS) $(LIB)

$(BIN)srsbuild : $(BIN)srsbuild.o $(LIB) $(LOCAL_OBJS) 
	$(CC) -o $@ $(BIN)srsbuild.o  $(LOCAL_OBJS) $(LIB) 

$(BIN)reflink :  $(BIN)reflink.o $(LIB)
	$(CC) -o $@  $(BIN)reflink.o $(LIB)

$(BIN)trembl :  $(BIN)trembl.o $(LIB)
	$(CC) -o $@  $(BIN)trembl.o $(LIB)

$(BIN)icarus : $(BIN)icarusi.o $(LIB)   $(LOCAL_OBJS)
	$(CC) -o $@ $(BIN)icarusi.o  $(LOCAL_OBJS) $(LIB)

$(BIN)x : $(BIN)x.o $(LIB)   $(LOCAL_OBJS)
	$(CC) -o $@ $(BIN)x.o  $(LOCAL_OBJS) $(LIB)

$(BIN)nodd : $(BIN)nodd.o $(LIB) $(LOCAL_OBJS) 
	$(CC) -o $@ $(BIN)nodd.o  $(LOCAL_OBJS) $(LIB)

$(BIN)getz : $(BIN)getz.o $(LIB)  $(LOCAL_OBJS)
	$(CC) -o $@ $(BIN)getz.o  $(LOCAL_OBJS) $(LIB)

$(BIN)srscheck :  $(BIN)srscheck.o $(LIB)
	$(CC) -o $@ $(BIN)srscheck.o $(LOCAL_OBJS) $(LIB)

$(BIN)msgdef : $(BIN)msgdef.o 
	$(CC) -o $@ $(BIN)msgdef.o 

$(BIN)wgetz :  $(BIN)wgetz.o $(BIN)srswww.o  $(LIB)  $(LOCAL_OBJS)
	$(CC) -o $@ $(BIN)srswww.o $(BIN)wgetz.o   $(LOCAL_OBJS) $(LIB)
	cp $(BIN)wgetz $(SRSWWW)/bin/wgetz

$(BIN)srspict :  $(BIN)srspict.o $(BIN)gd.o $(LIB) 
	$(CC) -o $@ $(BIN)gd.o $(BIN)srspict.o $(LIB)


# some modules of the ODD compiler must be compiled with BOOTSTRAP
#
$(BIN)bs_parser.o : parser.c futil.h  message.h msg.h sm.h 
	$(CC) $(CFLAGS) $(OCFLAGS) -DBOOTSTRAP parser.c
$(BIN)bs_sdl.o : sdl.c message.h msg.h futil.h sm.h  map.h odd.h 
	$(CC) $(CFLAGS) $(OCFLAGS) -DBOOTSTRAP sdl.c
$(BIN)bs_sdlget.o : sdlget.c futil.h message.h msg.h odd.h  
	$(CC) $(CFLAGS) $(OCFLAGS) -DBOOTSTRAP sdlget.c
$(BIN)bs_odd.o : odd.c futil.h message.h msg.h sm.h  odd.h  
	$(CC) $(CFLAGS) $(OCFLAGS) -DBOOTSTRAP odd.c
$(BIN)oddfncts.o : oddfncts.c message.h msg.h sm.h futil.h odd.h  
	$(CC) $(CFLAGS) $(OCFLAGS) -DBOOTSTRAP oddfncts.c
#$(BIN)oddfnctsnew.o : oddfnctsnew.c message.h msg.h sm.h futil.h odd.h  
#	$(CC) $(CFLAGS) $(OCFLAGS) -DBOOTSTRAP oddfnctsnew.c
$(BIN)oddtools.o : oddtools.c message.h msg.h oddtools.h 
	$(CC) $(CFLAGS) $(OCFLAGS) -DBOOTSTRAP oddtools.c

$(BIN)local.o : local.c message.h msg.h sm.h lst.h futil.h 
	$(CC) $(CFLAGS) $(OCFLAGS) local.c



#depend
$(LIB)($(BIN)bs_sdlnew.o): sdlnew.c message.h msg.h futil.h sm.h  map.h  odd.h 
	$(CC) $(CFLAGS) $(LOCFLAGS) sdlnew.c; $(LIBENTER); $(RM)) 

$(LIB)($(BIN)futil.o): futil.c message.h msg.h regexp.h futil.h sm.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  futil.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)message.o): message.c msg.h futil.h sm.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  message.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)sm.o): sm.c message.h msg.h sm.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  sm.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)parser.o): parser.c message.h msg.h futil.h  sm.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  parser.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)error.o): error.c error.h message.h msg.h futil.h sm.h toklist.h cursor.h 
	($(CC) $(CFLAGS) $(LOCFLAGS)  error.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)toklist.o): toklist.c toklist.h message.h msg.h futil.h sm.h 
	($(CC) $(CFLAGS) $(LOCFLAGS)  toklist.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)cursor.o): cursor.c cursor.h message.h msg.h futil.h sm.h 
	($(CC) $(CFLAGS) $(LOCFLAGS)  cursor.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)icarus.o): icarus.c icarus.h message.h msg.h regexp.h futil.h par.h sm.h 
	($(CC) $(CFLAGS) $(LOCFLAGS)  icarus.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)icabnf.o): icabnf.c icarus.h icabnf.h message.h msg.h regexp.h futil.h par.h sm.h 
	($(CC) $(CFLAGS) $(LOCFLAGS)  icabnf.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)icastack.o): icastack.c icastack.h message.h msg.h par.h 
	($(CC) $(CFLAGS) $(LOCFLAGS)  icastack.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)icatask.o): icatask.c icatask.h icarus.h message.h msg.h par.h 
	($(CC) $(CFLAGS) $(LOCFLAGS)  icatask.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)icadebug.o): icadebug.c icadebug.h icarus.h message.h msg.h par.h 
	($(CC) $(CFLAGS) $(LOCFLAGS)  icadebug.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)ica2c.o): ica2c.c ica2c.h message.h msg.h variable.h strv.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  ica2c.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)bnf2c.o): bnf2c.c message.h msg.h variable.h strv.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  bnf2c.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)icainit.o): icainit.c icarus.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  icainit.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)icaop.o): icaop.c message.h msg.h icarus.h sm.h  
	($(CC) $(CFLAGS) $(LOCFLAGS)  icaop.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)icaarg.o): icaarg.c message.h msg.h icarus.h sm.h  builtin.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  icaarg.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)sdl.o): sdl.c message.h msg.h futil.h sm.h tm.h   map.h par.h \
   odd.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  sdl.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)sdlnew.o): sdlnew.c message.h msg.h futil.h sm.h tm.h   map.h par.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  sdlnew.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)sdlget.o): sdlget.c message.h msg.h futil.h odd.h 
	($(CC) $(CFLAGS) $(LOCFLAGS)  sdlget.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)index.o): index.c message.h msg.h sm.h futil.h binpack.h btree.h id.h ids.h hash.h \
  index.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  index.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)btree.o): btree.c message.h msg.h futil.h sm.h tm.h binpack.h btree.h ids.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  btree.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)ids.o): ids.c message.h msg.h binpack.h futil.h tm.h id.h ids.h set.h library.h map.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  ids.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)idx.o): idx.c message.h msg.h sm.h tm.h futil.h binpack.h idx.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  idx.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)seq.o): seq.c message.h msg.h sm.h futil.h lst.h par.h seq.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  seq.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)par.o): par.c message.h msg.h sm.h futil.h sdlget.h lst.h par.h $(SRSH)
	($(CC) $(CFLAGS) $(LOCFLAGS)  par.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)variable.o): variable.c message.h msg.h sm.h futil.h lst.h variable.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  variable.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)seqlib.o): seqlib.c message.h msg.h sm.h lst.h futil.h par.h  id.h library.h \
  entry.h seq.h query.h seqlib.h  $(SRSH)
	($(CC) $(CFLAGS) $(LOCFLAGS)  seqlib.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)seqdb.o): seqdb.c message.h msg.h sm.h lst.h futil.h icaarg.h \
  icarus.h seq.h listv.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  seqdb.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)appl.o): appl.c message.h msg.h sm.h lst.h futil.h appl.h library.h srs5.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  appl.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)library.o): library.c message.h msg.h futil.h sm.h tm.h btree.h sdlget.h ids.h idx.h \
  par.h  library.h $(SRSH)
	($(CC) $(CFLAGS) $(LOCFLAGS)  library.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)field.o): field.c message.h msg.h futil.h sm.h tm.h btree.h sdlget.h ids.h idx.h \
  par.h  field.h $(SRSH)
	($(CC) $(CFLAGS) $(LOCFLAGS)  field.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)entry.o): entry.c message.h msg.h sm.h tm.h futil.h par.h icarus.h id.h set.h \
  library.h entry.h $(SRSH)
	($(CC) $(CFLAGS) $(LOCFLAGS)  entry.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)queryass.o): queryass.c queryass.h message.h msg.h futil.h par.h sm.h library.h 
	($(CC) $(CFLAGS) $(LOCFLAGS)  queryass.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)query.o): query.c message.h msg.h futil.h  par.h regexp.h ids.h btree.h \
    sm.h tm.h library.h id.h entry.h set.h link.h seqlib.h lst.h query.h \
  $(SRSH)
	($(CC) $(CFLAGS) $(LOCFLAGS)  query.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)set.o): set.c message.h msg.h lst.h sm.h futil.h  id.h set.h library.h \
  $(SRSH)
	($(CC) $(CFLAGS) $(LOCFLAGS)  set.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)id.o): id.c message.h msg.h futil.h binpack.h id.h library.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  id.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)link.o): link.c message.h msg.h futil.h sm.h id.h set.h par.h link.h map.h btree.h \
  ids.h library.h binpack.h query.h $(SRSH)
	($(CC) $(CFLAGS) $(LOCFLAGS)  link.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)stack.o): stack.c message.h msg.h futil.h 
	($(CC) $(CFLAGS) $(LOCFLAGS)  stack.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)expr.o): expr.c message.h msg.h futil.h   $(SRSH)
	($(CC) $(CFLAGS) $(LOCFLAGS)  expr.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)lst.o): lst.c lst.h sdlget.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  lst.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)unix_map.o): unix_map.c message.h msg.h futil.h map.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  unix_map.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)regexp.o): regexp.c regexp.h regmagic.h message.h msg.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  regexp.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)arglist.o): arglist.c message.h msg.h futil.h  par.h $(SRSH) arglist.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  arglist.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)logicals.o): logicals.c
	($(CC) $(CFLAGS) $(LOCFLAGS)  logicals.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)tm.o): tm.c message.h msg.h tm.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  tm.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)script.o): script.c message.h msg.h futil.h sm.h lst.h 
	($(CC) $(CFLAGS) $(LOCFLAGS)  script.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)templ.o): templ.c message.h icarus.h msg.h futil.h sm.h lst.h templ.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  templ.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)view.o): view.c message.h sm.h futil.h library.h set.h par.h view.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  view.c;$(LIBENTER); $(RM))
$(LIB)($(BIN)merge.o): merge.c message.h sm.h futil.h library.h set.h par.h view.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  merge.c;$(LIBENTER); $(RM))
$(LIB)($(BIN)hash.o): hash.c message.h msg.h hash.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  hash.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)termio.o): termio.c termio.h message.h msg.h strv.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  termio.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)oddfnctsnew.o): oddfnctsnew.c message.h msg.h sm.h futil.h odd.h  
	($(CC) $(CFLAGS) $(LOCFLAGS) -DBOOTSTRAP oddfnctsnew.c; $(LIBENTER); $(RM)) 


$(BIN)icarusi.o: icarusi.c message.h msg.h futil.h  sm.h seq.h par.h arglist.h id.h \
  idx.h set.h entry.h library.h seqlib.h query.h $(SRSH) $(SRSEXE)/srsenv.h
	$(CC) $(CFLAGS) $(OCFLAGS)  icarusi.c

$(BIN)x.o: x.c 
	$(CC) $(CFLAGS) $(OCFLAGS)  x.c

$(BIN)nodd.o: nodd.c  odd.h message.h msg.h futil.h  sm.h seq.h par.h arglist.h id.h \
  idx.h set.h entry.h library.h seqlib.h query.h $(SRSH) $(SRSEXE)/srsenv.h
	$(CC) $(CFLAGS) $(OCFLAGS)  nodd.c

$(BIN)tryz.o: tryz.c
	$(CC) $(CFLAGS) $(OCFLAGS)  tryz.c

$(BIN)ntry.o: ntry.c
	$(CC) $(CFLAGS) $(OCFLAGS)  ntry.c

$(BIN)getz.o: getz.c icarus.h message.h msg.h futil.h  sm.h seq.h par.h arglist.h id.h \
  idx.h set.h entry.h library.h seqlib.h query.h $(SRSH) $(SRSEXE)/srsenv.h
	$(CC) $(CFLAGS) $(OCFLAGS)  getz.c
$(BIN)srsbuild.o: srsbuild.c message.h msg.h futil.h sm.h  seq.h seqlib.h par.h \
  btree.h arglist.h entry.h id.h set.h ids.h idx.h library.h link.h index.h $(SRSH)
	$(CC) $(CFLAGS) $(OCFLAGS)  srsbuild.c
$(BIN)msgdef.o: msgdef.c msg.h futil.h
	$(CC) $(CFLAGS) $(OCFLAGS)  msgdef.c

$(LIB)($(BIN)dict.o): dict.c dict.h strv.h
	($(CC) $(CFLAGS) $(LOCFLAGS) dict.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)print.o): print.c print.h strv.h
	($(CC) $(CFLAGS) $(LOCFLAGS) print.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)oldlistbuf.o): oldlistbuf.c oldlistbuf.h strv.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  oldlistbuf.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)strv.o): strv.c strv.h 
	($(CC) $(CFLAGS) $(LOCFLAGS) strv.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)listv.o): listv.c listv.h 
	($(CC) $(CFLAGS) $(LOCFLAGS) listv.c; $(LIBENTER); $(RM)) 
$(LIB)($(BIN)def.o): def.c def.h
	($(CC) $(CFLAGS) $(LOCFLAGS)  def.c; $(LIBENTER); $(RM))
$(BIN)reflink.o: reflink.c message.h msg.h futil.h library.h par.h arglist.h  id.h \
  set.h entry.h seq.h seqlib.h query.h lst.h $(SRSH) $(SRSEXE)/srsenv.h
	$(CC) $(CFLAGS) $(OCFLAGS)  reflink.c

$(BIN)trembl.o: trembl.c message.h msg.h futil.h library.h par.h arglist.h  id.h \
  set.h entry.h seq.h seqlib.h query.h lst.h $(SRSH) $(SRSEXE)/srsenv.h
	$(CC) $(CFLAGS) $(OCFLAGS)  trembl.c

$(BIN)srscheck.o: srscheck.c message.h msg.h futil.h sm.h tm.h arglist.h par.h library.h \
  id.h ids.h set.h btree.h link.h  $(SRSH)
	$(CC) $(CFLAGS) $(OCFLAGS)  srscheck.c
$(BIN)odd.o: odd.c message.h msg.h futil.h sm.h  arglist.h par.h odd.h 
	$(CC) $(CFLAGS) $(OCFLAGS)  odd.c
$(BIN)wgetz.o: wgetz.c icarus.h message.h msg.h arglist.h sm.h tm.h futil.h  library.h \
  par.h id.h set.h entry.h query.h  srswww.h view.h $(SRSH) $(SRSEXE)/srsenv.h
	$(CC) $(CFLAGS) $(OCFLAGS)  wgetz.c
$(BIN)srswww.o: srswww.c message.h msg.h sm.h tm.h lst.h futil.h  par.h  \
  id.h set.h library.h btree.h idx.h entry.h link.h seq.h query.h seqlib.h  \
   srswww.h $(SRSH)
	$(CC) $(CFLAGS) $(OCFLAGS)  srswww.c
$(BIN)srspict.o: srspict.c srs.h gd.h
	$(CC) $(CFLAGS) $(OCFLAGS)  srspict.c
$(BIN)gd.o: gd.c gd.h 
	$(CC) $(CFLAGS) $(OCFLAGS)  gd.c

clean:
	-$(RMCMD) $(BIN)*.o
	-$(RMCMD) $(BIN)*.a

cleanall:
	-$(RMCMD) -r $(SRSEXE)
  srswww.h view.h $(SRSH) $(SRSEXE)/srsenv.h
	$(CC) $(CFLAGS) $(OCFLAGS)  wgetz.c
$(BIN)srswwwsrs/etc/srsnet.tcl
#
#    $RCSfile: srsnet.tcl,v $
#    $Revision: 1.1 $
#    $Date: 1996/05/06 16:24:42 $
#    $Author: srs $
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 


#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
# global variable initialisation
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 

set gvar(ch)        800
set gvar(cw)        600
set gvar(ZOOM)      100
set gvar(OLDSCALE)  1.0

#unix command for calling getz
set getz getz
set isQuery 0
#set color(0) chocolate1
#set color(1) turquoise
#set color(2) darkgoldenrod1
#set color(3) plum
#set color(4) palevioletred
#set color(5) grey
set color(0) turquoise
set color(1) turquoise
set color(2) turquoise
set color(3) turquoise
set color(4) turquoise
set color(5) turquoise



wm title . "SRS-Network"
wm maxsize . 1200 1200
wm minsize . 100 100
wm iconname . "SRS-Network"

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# widgets and layout
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

# buttons on right hand side

frame .f2  -relief ridge 
  scale .f2.zoom -label "Zoom" -orient horiz -relief raised  -length 150 -from 50 -to 250 \
	  -command "resize .f1.c"  
  .f2.zoom set 100
  button .f2.quit -text "QUIT" -relief raised  \
	  -command exit 
  button .f2.savedbs -text "SAVE" -relief raised  -command "SaveDBs"
  button .f2.loaddbs -text "LOAD" -relief raised -command "LoadDBs"
  pack .f2.zoom -side top -padx 5 -pady 2 -ipady 5
  pack .f2.loaddbs -side top -padx 5 -pady 2 -ipady 5 -fill x
  pack .f2.savedbs -side top -padx 5 -pady 2 -ipady 5 -fill x
  pack .f2.quit -side top -padx 5 -pady 2 -ipady 5 -fill x

#
# canvas with scroll bars
#

frame .f1 -relief ridge
  scrollbar .f1.scx -width 15 -orient horiz -relief flat \
	   -command ".f1.c xview" 
  frame .f1.f1 -relief flat
    frame .f1.f1.spacer -height 15.p -width 15.p
    scrollbar .f1.f1.scy -width 15  -orient verti -relief flat -command ".f1.c yview"
    pack .f1.f1.spacer -side bottom -expand n 
    pack .f1.f1.scy -side top -expand yes -fill both
  pack .f1.f1 -side right -expand n -fill both

  pack .f1.scx -side bottom  -expand n -fill x 
  canvas .f1.c  -w 200 -height 200 -bg bisque1 -yscrollc ".f1.f1.scy set" -xscrollc ".f1.scx set"     
  pack .f1.c -side left -fill both -expand yes
pack .f1 -side right -fill both -expand yes
pack .f2 -side left -fill y


#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# list of procedures
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


proc resize { c z } {
    global gvar isMustScaleCoord
    set sreg "0 0 [expr $z*$gvar(cw)/100.0] [expr $z*$gvar(ch)/100.0]"
    $c configure -scrollregion $sreg
    set sc [expr 1.0*$z/$gvar(ZOOM)]
    set gvar(ZOOM) $z
    set gvar(SCALE) [expr $z/100.0]
    $c scale all 0 0 $sc $sc

    set isMustScaleCoord 1

}

proc SaveDBs {} {
    global nodeX nodeY DBNodeName allDBs 


    if (![info exists allDBs]) {
	error "Nothing to save!"
	return
    }

    set stat "[catch {set file [open "srsnet.dat" w]} msg]"
    if {$stat} {
	puts "$msg"
	return
    }
    foreach node [.f1.c find withtag node] {
	puts $file "coord: $DBNodeName($node) $nodeX($node) $nodeY($node)"

    }
    close $file
}

proc ReadDBCoord {} {
    global nodeX nodeY DBname DBnodeX DBnodeY 

    set stat "[catch {set file [open "srsnet.dat" r]} msg]"
    if {$stat} {
	puts "$msg" 
	return
    }
    while {[gets $file line] >= 0} {
	if [regexp {coord: +([^ ]+) +([0-9]+) +([0-9]+)} \
		$line match libName x y ] {
	    set DBnodeX($libName) $x
	    set DBnodeY($libName) $y
	}
    }
    close $file
}


proc LoadDBs {} {
    global nodeX nodeY edgeFirst edgeSecond isActive DB DBname DBcolor getz \
           DBnodeX DBnodeY node curX curY color allDBs fields DBNodeName


    set yy 10
    set xx 40

    ReadDBCoord

    set f1 [open "|$getz -si" r]

    set groups {}

    while {[gets $f1 line] >= 0} {
	if [regexp {lib: ([^ ,]+), .*group: ([^ ,]+)} \
		$line match libName group ] {
	    
	    
	    set index [lsearch $groups $group]
	    if {$index == -1} {
		lappend groups $group
	    }
	    set index [lsearch $groups $group]


	    if {[info exists DBnodeX($libName)]} {
		set tmpx $DBnodeX($libName)
		set tmpy $DBnodeY($libName)
	    } else {
		set tmpx $xx 
		set tmpy $yy 
	    }

	    set tmp [string tolower $libName]
	    button .f1.c.$tmp -text "$libName" -relief raised -height 1\
		    -bg $color($index) \
                    -highlightcolor white -highlightbackground bisque1
	    set new [.f1.c create window $tmpx $tmpy -window .f1.c.$tmp \
		    -tags node ]
	    
#
# key bindings for each button in the graph ...don't know how to do one
# binding for all
#
            bind .f1.c.$tmp <Button-1> {
		global curX curY
		set curX %X
		set curY %Y
	    }

            bind .f1.c.$tmp <B1-Motion> {
		global node

		moveNode $node(%W) [expr (%X-$curX)] [expr (%Y-$curY)]
		set curX %X
		set curY %Y
	    }

	    set node(.f1.c.$tmp) $new
	    set DB($libName)  $new
	    set DBcolor(.f1.c.$tmp) $color($index)
	    set isActive($libName) 0
	    set nodeX($new) $tmpx
	    set nodeY($new) $tmpy
	    set edgeFirst($new) {}
	    set edgeSecond($new) {}
	    set DBname(.f1.c.$tmp) $libName
	    set DBNodeName($new) $libName
	    lappend allDBs $libName
	    if {$tmpy == $yy} {
		set yy [expr $yy + 20]
	    }

	} elseif  [regexp {field: +([^ ,]+), type: +(index|num|real|id)} \
		$line match fieldName ] {
	    lappend fields($libName) $fieldName

	} elseif  [regexp {link: +([^ ]+) +([^ ]+)} $line \
	match libName1 libName2] {
	    mkEdge $DB($libName1) $DB($libName2)
	}

    }

}



proc mkNode {x y} {
    global nodeX nodeY edgeFirst edgeSecond isActive
    
    set new [.f1.c create text  [expr $x] [expr $y] -text "hallo" \
	    -fill black -tags node ]
    
    set isActive($new) 0
    set nodeX($new) $x
    set nodeY($new) $y
    set edgeFirst($new) {}
    set edgeSecond($new) {}
}

proc mkEdge {first second} {
    global nodeX nodeY edgeFirst edgeSecond
    set edge [.f1.c create line  $nodeX($first) $nodeY($first) \
	    $nodeX($second) $nodeY($second) \
	    -width 1 -fill blue1]
    .f1.c lower $edge
    lappend edgeFirst($first) $edge
    lappend edgeSecond($second) $edge
}


focus .f1.c

proc moveNode {node xDist yDist} {
    global isMustScaleCoord nodeX nodeY edgeFirst edgeSecond gvar
    .f1.c move $node $xDist $yDist
    incr nodeX($node)  $xDist
    incr nodeY($node)  $yDist

    if {$isMustScaleCoord == 1} {
	set isMustScaleCoord 0
	foreach node [.f1.c find withtag node] {
	    set nodeX($node) [expr int ($nodeX($node) * \
		    $gvar(SCALE) / $gvar(OLDSCALE))]
	    set nodeY($node) [expr int ($nodeY($node) * \
		    $gvar(SCALE) / $gvar(OLDSCALE))] 
	}
	 set gvar(OLDSCALE) $gvar(SCALE)
    }
    
    foreach edge $edgeFirst($node) {
	.f1.c coords $edge \
            $nodeX($node) $nodeY($node) \
	    [lindex [.f1.c coords $edge] 2] \
	    [lindex [.f1.c coords $edge] 3] 

    }
    foreach edge $edgeSecond($node) {
	.f1.c coords $edge [lindex [.f1.c coords $edge] 0] \
		[lindex [.f1.c coords $edge] 1] \
		$nodeX($node) $nodeY($node) 
    }
}





var(OLDSCALE))]
	    set nodeY($node) [expr int ($nodeY($node) * \
		    $gvar(SCALE) / $gvar(OLDSCALE))] 
	}
	 set gvar(OLDSCALE) $gvar(SCALE)
    }
    
    foreach edge $edgeFirst($node) {
	.f1.c coords $edge \
            $nodeX($node) $nodeY($node) \
	    [lindex [.f1.c coords $edge] 2] \
	    [lindex [.f1.c coords $edge] 3] 

    }
    foreach edge $edgeSecond($node) {
	.f1.c coords $edge [lindex [.f1.srs/etc/srssection
# defines an 'alias' for the old srssection command
nodd -s $SRSICA/srs.ic $SRSICA/srs.i
exit
(OLDSCALE))]
	    set nodeY($node) [expr int ($nodeY($node) * \
		    $gvar(SCALE) / $gvar(OLDSCALE))] 
	}
	 set gvar(OLDSCALE) $gvar(SCALE)
    }
    
    foreach edge $edgeFirst($node) {
	.f1.c coords $edge \
            $nodeX($node) $nodeY($node) \
	    [lindex [.f1.c coords $edge] 2] \
	    [lindex [.f1.c coords $edge] 3] 

    }
    foreach edge $edgeSecond($node) {
	.f1.c coords $ed¶ £¡Üex [.f1.srs/etc/srsupd.pl
# modify by : Antoine de Daruvar
# date: March 17, 1995
#
# - move the logfile to /data/update/trace_job
# - move the update file to /data/update/temp
# - control the size of the log file (run file_restriction)
#
# =====================================================================


$tmp = `ps -edalf`;
@proc = split ("\n", $tmp);

foreach (@proc) {
    if (/srsbuild/ || /srscheck/ ) {
        exit; # some indexing job is running already
    }
}
$srsupd = "\$\SRSETC/srsupd.csh";
system ("date");
$com = 
       "srscheck -o $srsupd;" . 
       "$srsupd";
system ("$com");
system ("date");
exit;
date/trace_job
# - move the update file to /data/update/temp
# - control the size of the log file (run file_restriction)
#
# =====================================================================


$tmp = `ps -edalf`;
@proc = split ("\n", $tmp);

foreach (@proc) {
    if (/srsbuild/ || /srscheck/ ) {
        exit; # some indexing job is running alresrs/etc/srsupdate

echo '*** use srscheck to create the REAL srsupdate script ***'
srscheck -o $srsupd;" . 
       "$srsupd";
system ("$com");
system ("date");
exit;
date/trace_job
# - move the update file to /data/update/temp
# - control the size of the log file (run file_restriction)
#
# =====================================================================


$tmp = `ps -edalf`;
@proc = split ("\n", $tmp);

foreach (@proc) {
    if (/srsbuild/ || /srscheck/ ) {
        exit; # some indexing job¶ £¡Üing alresrs/etc/srsversion
if [ $# = 0 ]; then
  echo 'name of program (without path) required'
  exit 1
fi

if [ "$SRSEXE" = "" ]; then
  echo 'The SRS environment is not setup.'
  echo "Looking for $1 in your path instead"
  EXE="`which $1`"
else 
  EXE="$SRSEXE/$1"
fi
strings $EXE | grep '$Id' | sed 's/.*\(\$Id.* \$\)/\1/'
exit
========================================


$tmp = `ps -edalf`;
@proc = split ("\n", $tmp);

foreach (@proc) {
    if (/srsbuild/ || /srscheck/ ) {
        exit; # some indexing job¶ £¡Üing alresrs/icarus/

#
#    $RCSfile: appl.i,v $
#    $Revision: 1.3 $
#    $Date: 1997/03/18 13:16:24 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

GENERAL_OPTS:$optGroup:[General]
MULTALI_OPTS:$optGroup:['Multiple Alignment']
SLOWPAIRS_OPTS:$optGroup:['For Fast Pairwise Alignments']
FASTPAIRS_OPTS:$optGroup:['For Slow Pairwise Alignments']


CLUSTALW_APP:$application:[CLUSTALW type:multi
  title: 'Multiple Sequence Alignment'
  options:{

    $AppOpt:[output type:string prompt:'name of alignment' defStr:temp]

    # general options
    $appOpt:[outFormat type:string guiType:menu group:@GENERAL_OPTS
      prompt:|Output format
      values:{
        $optVal:[CLUSTAL on:y]
        $optVal:GDE
        $optVal:PHILIP
        $optVal:PIR
      }
    ]
    $appOpt:[outOrder guiType:menu group:@GENERAL_OPTS
      prompt:|Order of sequences in alignment
      values:{
        $optVal:[INPUT on:y]
        $optVal:ALIGNED
      }
    ]
    $appOpt:[guideTree type:string group:@GENERAL_OPTS guiType:radio
      prompt:|use for the alignment guide tree
      values:{
        $optVal:[valStr:FAST prompt:FAST on:y]
        $optVal:[valStr:SLOW prompt:'SLOW algorithm']
      }
    ]

    # multiple alignment options
    $appOpt:[matrix group:@MULTALI_OPTS guiType:menu 
      prompt:|use substitution matrix
      values:{
        $optVal:[blosum on:y]
        $optVal:pam
        $optVal:md
        $optVal:id
      }
    ]
    $appOpt:[gapOpen group:@MULTALI_OPTS type:real 
      prompt:'gap opening penalty'
      defReal:10.00
    ]
    $appOpt:[gapExt group:@MULTALI_OPTS type:real 
      prompt:'gap extension penalty'
      defReal:0.05
    ]
    $appOpt:[endGap group:@MULTALI_OPTS type:bool 
      prompt:'no end gap penalty' 
      defInt:0
    ]

    # fast pairwise alignment options
    $appOpt:[ktup group:@SLOWPAIRS_OPTS type:int defInt:1
      prompt:'word size (ktup)'
    ]
    $appOpt:[topDiagsN group:@SLOWPAIRS_OPTS type:int
      prompt:'number of best diagonals'
    ]
    $appOpt:[diagsWindow group:@SLOWPAIRS_OPTS type:int
      prompt:'window around best diagonals'
    ]
    $appOpt:[pairgap group:@SLOWPAIRS_OPTS type:real
      prompt:'gap penalty'
    ]
    $appOpt:[useScore group:@SLOWPAIRS_OPTS type:string guiType:menu
      prompt:'use score' 
      values:{
        $optVal:[percent on:y]
        $optVal:[absolute]
      }
    ]

    # slow pairwise alignment options
    $appOpt:[pairMatrix group:@FASTPAIRS_OPTS guiType:menu
      prompt:'use substitution matrix'
      values:{
        $optVal:[blosum on:y]
        $optVal:pam
        $optVal:md
        $optVal:id
      }
    ]
    $appOpt:[pairGapOpen group:@FASTPAIRS_OPTS type:real
      prompt:'gap opening penalty'
    ]
    $appOpt:[pairGapExt group:@FASTPAIRS_OPTS type:real
      prompt:'gap extension penalty'
    ]
  }
  command:@{
    $opt.command=    
      |/u/usr/local/bin/clustalw tmp.seq \
      |($Alt:[($opt.outFormat!=CLUSTAL) t:"/output=($opt.outFormat) "])\
      |/outorder=($opt.outOrder) \
      |($Alt:[$opt.guideTree==FAST  t:"/quicktree "])\
      |/matrix=($opt.matrix) \
      |/gapopen=($opt.gapOpen) \
      |/gapext=($opt.gapExt) \
      |($Alt:[$opt.endGap t:'/endgaps '])\
      |
  }@
  launch:@{
    $System:[scriptName:"($Env:SRSWWWTMP)/($userId)/clustalw.sh" 
      out:stdout error:stdout script:
      |#!/bin/csh 
      |#
      |# clustalw script
      |#
      |cd ($Env:SRSWWWTMP)/($userId); ($opt.command)\
      |echo '\\!Alignment: ($opt.output)' > ($opt.output).aln
      |grep '^\\!' tmp.seq >> ($opt.output).aln
      |cat tmp.aln >> ($opt.output).aln
      |rm tmp.aln
      |echo '</PRE>'
      |(source ($Env:SRSETC)/prep_srs;\
      |\$SRSEXE/srsbuild clustalw;\
      |\$SRSEXE/srsbuild -c clustalw;\
      |\$SRSEXE/srsbuild -l clustalw ) >& tmp.log
      |unsetenv REQUEST_METHOD # otherwise wgetz does not read command line
      |($Env:SRSEXE)/wgetz -id ($userId) -e -mime none \
      | '[clustalw-id:($opt.output)]'
      |exit
    ]
  }@
]





BLAST_APP:$application:[BLAST type:{single search} 
  title:'Sequence Similarity Search' 
  options:{
 
    $AppOpt:[search type:string guiType:menu
      prompt:'Search' values:{
        $OptVal:['SWISS-PROT' valStr:swiss]
        $OptVal:['PIR' valStr:pir]
      }
    ]
    $AppOpt:[output type:string prompt:'name of search']

    # output options
    $AppOpt:[inclGenInfo group:@OUTPUT_OPTS type:bool defInt:1
      prompt:'include general information'
    ]
    $AppOpt:[b group:@OUTPUT_OPTS type:int defInt:200
      prompt:'no. of high scoring alignments'
    ]
    $AppOpt:[hspMax group:@OUTPUT_OPTS type:int defInt:100
      prompt:'limit number of HSPS reported'
    ]
    $AppOpt:[v group:@OUTPUT_OPTS type:int defInt:500
      prompt:'no. of entries with one line descriptions'
    ]
    $AppOpt:[echoFilter group:@OUTPUT_OPTS type:bool defInt:1
      prompt:'filtered query sequence'
    ]
    $AppOpt:[prune group:@OUTPUT_OPTS type:bool defInt:1
      prompt:'include HSPs not statistically significant'
    ]
    $AppOpt:[filter group:@OUTPUT_OPTS type:string guiType:multi type:bool
      prompt:'filter' 
      values:{ 
        $OptVal:[xnu prompt:'short repeat']
        $OptVal:[seg prompt:'low complexity sequences']
      }
    ]
    $AppOpt:[sort group:@OUTPUT_OPTS type:bool guiType:multi type:bool
      prompt:'sort by'
      values:{
        $OptVal:[sortByValue prompt:pValue]
        $OptVal:[sortByCount prompt:count]
        $OptVal:[sortByHighScore prompt:'high score']
        $OptVal:[sortByTotalScore prompt:'total score']
      }
    ] 

    # search parameters 
    $AppOpt:[matrix group:@SEARCH_OPTS type:string guiType:menu
      prompt:'scoring matrix' 
      values:{
        $OptVal:[blosum62 on:y]
        $OptVal:[dayhoff]
        $OptVal:[gonnet]
        $OptVal:[identity]
        $OptVal:[pam30]
        $OptVal:[pam60]
        $OptVal:[pam90]
        $OptVal:[pam120]
        $OptVal:[pam150]
        $OptVal:[pam180]
        $OptVal:[pam210]
        $OptVal:[pam240]
      }
    ]
    $AppOpt:[e group:@SEARCH_OPTS type:real guiType:menu
      prompt: 'The E value'
      values:{
        $OptVal:[valReal:0.0001]
        $OptVal:[valReal:1]
        $OptVal:[valReal:10 on:y]
        $OptVal:[valReal:100]
        $OptVal:[valReal:1000]
      }
    ]
    $AppOpt:[e2 group:@SEARCH_OPTS type:int 
      prompt:'exp. number of HSPs (E2)'
    ]
    $AppOpt:[s2 group:@SEARCH_OPTS type:real
      prompt:'cutoff score (s2)'
    ]
    $AppOpt:[s group:@SEARCH_OPTS type:real
      prompt:'exp. score for MSP'
    ] 
    $AppOpt:[w group:@SEARCH_OPTS type:int guiType:menu
      prompt:'word length' 
      values:{
        $OptVal:[valInt:3 on:y]
        $OptVal:[valInt:4]
        $OptVal:[valInt:5]
        $OptVal:[valInt:6]
      }
    ]         
 
    # other options
    $AppOpt:[sump group:@OTHER_OPTS type:string guiType:radio
      prompt:'use' values:{
        $OptVal:[valStr:'sump' on:y prompt:'sum statistics']
        $OptVal:[valStr:'poissonp' prompt:'poisson statistics']
      }
    ]
    $AppOpt:[consistency group:@OTHER_OPTS type:bool guiType:multi
      prompt:'' values:{
  	$OptVal:[consistency valInt:1 prompt:consistency]
  	$OptVal:[span2 prompt:span2]
  	$OptVal:[span1 prompt:span1]
  	$OptVal:[span prompt:span]
      }
    ]
  }
  command: @{
    $opt.command=
      |/usr/local/bin/blastp ($opt.search) tmp.seq\
      | -matrix ($opt.matrix)\
      |($Alt:[$opt.e  t:" E=($opt.e)"])\
      |($Alt:[$opt.e2 t:" E2=($opt.e2)"])\
      |($Alt:[$opt.s2 t:" S2=($opt.s2)"])\
      |($Alt:[$opt.s  t:" S=($opt.s)"])\
      |($Alt:[$opt.h  t:" H=($opt.h)"])\
      |($Alt:[$opt.v  t:" V=($opt.v)"])\
      |($Alt:[$opt.w  t:" W=($opt.w)"])\
      |($Alt:[$opt.span1 t:' -span1'])\
      |($Alt:[$opt.span2 t:' -span2'])\
      |($Alt:[$opt.span t:' -span'])\
      |($Alt:[$opt.sump t:' -sump'])\
      |($Alt:[$opt.poissonp t:' -poissonp'])\
      |($Alt:[$opt.prune t:' -prune'])\
      |($Alt:[$opt.consistency t:' -consistency'])\
      |($Alt:[$opt.hspMax t:" -hspmax ($opt.hspMax)"])\
      |($Alt:[$opt.sortByPvalue t:' -sort_by_pvalue'])\
      |($Alt:[$opt.sortByPvalue t:' -sort_by_count'])\
      |($Alt:[$opt.sortByHighScore t:' -sort_by_highscore'])\
      |($Alt:[$opt.sortByTotalScore t:' -sort_by_totalscore'])\
      | > tmp.blast\
  }@
  launch:@{
    $System:[scriptName:"($Env:SRSWWWTMP)/($userId)/blast.csh" 
      out:stdout error:stdout script:
      |#!/bin/csh -f 
      |#
      |# blast command file
      |#
      |cd ($Env:SRSWWWTMP)/($userId)
      |cp /usr/local/bin/.ncbirc .
      |rsh columba '\
      |setenv BLASTDB /data/research/db; \
      |setenv BLASTMAT /u/usr/local/blast/matrix; \
      |cd ($Env:SRSWWWTMP)/($userId); ($opt.command)' 
      |#
      |#
      |sed -n '/^>/q;p' tmp.blast 
      |#    Create SRS indices for blast
      |#
      |(source ($Env:SRSETC)/prep_srs;\
      |cd \$SRSWWWTMP/($userId);\
      |\$SRSEXE/srsbuild blast;\
      |\$SRSEXE/srsbuild -c blast;\
      |\$SRSEXE/srsbuild -l blast)>& /dev/null
      |exit
    ]
  }@
]



FASTA_APP:$application:[FASTA type:{single search} 
  title:"Sequence Similarity Search"
  options:{

    $AppOpt:[search type:string guiType:menu
      prompt:'Search' values:{
        $OptVal:['SWISS-PROT' valStr:'/data/research/db/swiss']
        $OptVal:['PIR' valStr:pir]
      }
    ]
    $AppOpt:[output type:string prompt:'name of search']

    # search options
    $AppOpt:[matrix group:@SEARCH_OPTS type:string guiType:menu
      prompt:'scoring matrix'
      values:{
        $OptVal:[blosum50]
        $OptVal:[pam50]
      }
    ]
    $AppOpt:[ktup group:@SEARCH_OPTS type:int guiType:menu 
      prompt:'ktup (word size)'
      values:{
        $OptVal:[valInt:1 on:y]
        $OptVal:[valInt:2]
      }
    ]         
    $AppOpt:[gapInit group:@SEARCH_OPTS type:int defInt:-12
      prompt:'penalty for first resudue in gap'
    ]         
    $AppOpt:[gapExtend group:@SEARCH_OPTS type:int defInt:-2  
      prompt:'penalty for additional residues in gap'
    ]         

    # Output options
    $AppOpt:[ranking group:@OUTPUT_OPTS type:string guiType:radio  
      prompt:''
      values:{
        $OptVal:[valStr:z prompt:'rank with Z-score' on:y]
        $OptVal:[valStr:raw prompt:'raw score']
      }
    ]         
    $AppOpt:[nScores group:@OUTPUT_OPTS type:int defInt:200  
      prompt:'number of top scores in list'
    ]         
    $AppOpt:[nAlign group:@OUTPUT_OPTS type:int defInt:200  
      prompt:'number of alignments'
    ]         
  }

  command:@{
    $opt.command=
      |/usr/local/bin/fasta3_t -Q -t4\
      |($Alt:[$opt.matrix==PAM250 t:"-s 250 "]) \
      |-f ($opt.gapInit) \
      |-g ($opt.gapExtend) \
      |($Alt:[$opt.ranking==raw t:"-z "])\
      |-b ($opt.nAlign) \
      |-d ($opt.nScores) \
      |tmp.seq \
      |($opt.search) \
      |($opt.ktup) \
      |> tmp.fasta\
  }@
  launch:@{
    $System:[scriptName:"($Env:SRSWWWTMP)/($userId)/fasta.csh" 
      out:stdout error:stdout script:
  	|#!/bin/csh
  	|#
  	|# fasta script
  	|#
  	|cd ($Env:SRSWWWTMP)/($userId)
  	|rsh columba '\
  	|cd ($Env:SRSWWWTMP)/($userId); ($opt.command)'
  	|# print hit list to user
  	|sed -n '/>>/q;p' tmp.fasta
  	|#    Create SRS indices for fasta
  	|(source ($Env:SRSETC)/prep_srs;\
  	|cd \$SRSWWWTMP/($userId);\
  	|srsbuild fasta;\
  	|srsbuild -c fasta;\
  	|srsbuild -l fasta) >& /dev/null
  	|exit
    ]
  }@
]


SW_APP:$application:[SW type:{search single}
  title:'(Smith & Waterman) Search on the Bioccelerator'
  inSeqFormat:gcg
  options:{

    $AppOpt:[search type:string guiType:menu
      prompt:'Search' values:{
        $OptVal:['SWISS-PROT' valStr:'swiss:*']
        $OptVal:['PIR' valStr:'pir:*']
      }
    ]
    $AppOpt:[output type:string prompt:'name of search']

    # Search Parameters
    $AppOpt:[gapInit group:@SEARCH_OPTS type:real defReal:10.0
      prompt:'gap creation penalty'
    ]
    $AppOpt:[gapExt group:@SEARCH_OPTS type:real defReal:0.5
      prompt:'gap extension penalty'
    ]
    $AppOpt:[doNorm group:@SEARCH_OPTS type:string guiType:menu
      prompt:|adjust score for sequence length using method
      values:{
        $OptVal:[log]
        $OptVal:[gcg]
        $OptVal:[akc]
      } 
    ]
    $AppOpt:[minSeq group:@SEARCH_OPTS type:int defInt:50
      prompt:|minimum length sequence to examine in search
    ]
    $AppOpt:[doAverage group:@SEARCH_OPTS type:bool 
      prompt:|adjust quality scores for sequence composition
    ]

    # Output Options
    $AppOpt:[nAlign group:@OUTPUT_OPTS type:int defInt:100 
      prompt:|alignments done after search
    ]
    $AppOpt:[list group:@OUTPUT_OPTS type:int defInt:100
      prompt:|no. of sequences reported in the output list
    ]
    $AppOpt:[minList group:@OUTPUT_OPTS type:real defReal:2.5 
      prompt:|lowest Z-score to report in output list
    ]
    $AppOpt:[minQual group:@OUTPUT_OPTS type:real defReal:1
      prompt:|minimum quality score to report
    ]
    $AppOpt:[doPlot group:@OUTPUT_OPTS type:bool defInt:1
      prompt:|create histogram of score distribution
    ]
  }
  command:@{
    $opt.command=
      |/data/gcg8/Bic/exe/bic_sw \
      |-in1=tmp.seq \
      |-in2='($opt.search)' \
      |-gap=($opt.gapInit) \
#      |-pamfile=($opt.matrix) \
      |-len=($opt.gapExt) \
      |-align=($opt.nAlign) \
      |-list=($opt.list) \
      |-minlist=($opt.minList) \
      |-minseq=($opt.minSeq) \
      |-minqual=($opt.minQual) \
      |($Alt:[$opt.doNorm  t:" -norm=($opt.norm)"])\
      |($Alt:[$opt.doAverage  t:" -ave"]) \
      |($Alt:[$opt.doPlot  t:" -plot"]) \
      |-out=tmp.sw -mon -def\
  }@
  launch:@{
    $System:[scriptName:"($Env:SRSWWWTMP)/($userId)/sw.csh" 
      out:stdout error:stdout script:
    	|#!/bin/csh -f
    	|#
    	|# Smith/Waterman search with Bioaccelerator 
    	|#
    	|source /data/gcg8/gcgstartup
    	|source /homes/srswww/genetics
    	|cd ($Env:SRSWWWTMP)/($userId); ($opt.command)
    	|# print list of entries
    	|cd ($Env:SRSWWWTMP)/($userId);sed -n '/^ to:/q;p' tmp.sw
    	|#create SRS indices for SW
    	|(source ($Env:SRSETC)/prep_srs;\
    	|cd \$SRSWWWTMP/($userId);\
    	|srsbuild sw;\
    	|srsbuild -c sw;\
    	|srsbuild -l sw ) >& /dev/null
    	|exit
    ]
  }@
]

SEARCH_OPTS:$optGroup:['Search Parameters']
OUTPUT_OPTS:$optGroup:['Output Options']
OTHER_OPTS:$optGroup:['Others']





    	|source /homes/srswww/genetics
    	|cd ($Env:SRSWWWTMP)/($userId); ($opt.command)
    	|# print list of entries
    	|cd ($Env:SRSWWWTMP)/($userId);sed -n '/^ to:/q;p' tmp.sw
    	|#create SRS indices for SW
    	|(source ($Env:SRSETC)/prep_srs;\
    	|cd \$SRSWWWTMP/($userId);\
    	|srsbuild sw;\
    	|srsbuild -c sw;\
srs/icarus/db/blast.i
#    $RCSfile: blast.i,v $
#    $Revision: 1.4 $
#    $Date: 1997/03/03 18:33:46 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


BLAST_DB:$library:[BLAST group:@APPLICATION_LIBS 
  comment:"" 
  format:@BLAST_FORMAT maxNameLen:40 ifiles:{"blast.i" "blast.is"}
  type:user
  files:{
    $file:tmp
  }
]

BLAST_FORMAT:$libformat:[fileType:@BLAST_FILE syntax:@BLAST_SYNTAX 
  fields:{
    $field:[@DF_ID code:title index:id indexToken:id]
    $field:[@DF_TopMatch code:tmatch
      tableToken:t_tmatch tableFormat:left]
    $field:[@DF_TopScore code:tscore1 index:int indexToken:score
      tableToken:score tableFormat:right]
    $field:[@DF_PercIdent code:tscore2 index:int indexToken:percIdent
      tableToken:percIdent tableFormat:right]
    $field:[@DF_QueryBeg code:tmatch index:int indexToken:queryBeg
      tableToken:queryBeg tableFormat:right]
    $field:[@DF_QueryEnd code:tmatch index:int indexToken:queryEnd
      tableToken:queryEnd tableFormat:right]
    $field:[@DF_MatchLen code:tmatch index:int indexToken:matchLen
      tableToken:matchLen tableFormat:right]
    $field:[@DF_LINK index:link code:link indexToken:link]
  }
]

DF_TopMatch:$srsfield:[TopMatch short:tma]
DF_TopScore:$srsfield:[TopScore short:tsc]
DF_PercIdent:$srsfield:[PercentIdentity short:pid]
DF_QueryBeg:$srsfield:[QueryMatchBeginPos short:qbp]
DF_QueryEnd:$srsfield:[QueryMatchEndPos short:qep]
DF_MatchLen:$srsfield:[MatchLength short:mtl]


BLAST_SYNTAX:$syntax:[file:"SRSDB:blast.is" ignore:" "]
BLAST_FILE:$filetype:[typename:blast maxline:100]

$link:[@BLAST_DB to:@?SWISSPROT_DB token:'link|swiss' toField:@DF_Accession]
link code:link indexToken:link]
  }
]

DF_TopMatch:$srsfield:[TopMatch short:tma]
DF_TopScore:$srsfield:[TopScore short:tsc]
DF_PercIdent:$srsfield:[PercentIdentity short:pid]
DF_QueryBeg:$srsfield:[QueryMatchBeginPos short:qbp]
DF_QueryEnd:$srsfield:[QueryMatchEndPos short:qep]
DF_MatchLen:$srsrs/icarus/db/blast.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: blast.is,v $
#    $Revision: 1.9 $
#    $Date: 1997/03/03 18:33:47 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$rules={
  entry:    ~ {$In:[file:text] init{$count=0} $Out $count+=1 pre $skip:0}
              ('>' {$Not} ln)*
              '>' {$entryFip=$Fip $Wrt} appLn
              (/>/ {$Not} appLn)*
            ~

  # data fields
  fields:   ~ {$In:entry $Out $Skip:1} 
              title length tscores1 tscores2 
              tmatch (scores1 scores2 match)* ~
  title:    ~ {$Wrt:title}   '>'  ln (/ *Length/ {$Not} ln)* ~ 
  length:   ~ {$Wrt:length}  / *Length/ ln ln ~
  tscores1: ~ {$Wrt:tscore1} / *Score/ ln ~
  tscores2: ~ {$Wrt:tscore2} / *Identities/ ln ln ~
  tmatch:   ~ {$Wrt:tmatch}  ('Query' ln ln ln ln)* ~
  scores1:  ~ {$Wrt:score1}  / *Score / ln ~
  scores2:  ~ {$Wrt:score2}  / *Identities/ ln ln ~
  match:    ~ {$Wrt:match}   ('Query' ln ln ln ln)* ~

  # indexing
  id:       ~ {$In:[fields c:title] $Out} 
              />([a-zA-Z]+)\\|([a-zA-Z0-9]+)/ {$Wrt:[s:"$count\_$1\_$2"]} ~

  score:    ~ {$In:[fields c:tscore1] $Out} /.*Score = ([0-9]+)/{$Wrt:[s:$1]} ~
  percIdent:~ {$In:[fields c:tscore2] $Out} 
              /.*Identities[^a-z]*\\(([0-9]+)%/ {$Wrt:[s:$1]} ~
  queryBeg: ~ {$In:[fields c:tmatch] $Out}
              /Query: *([0-9]+)/ {$b=$1 $Wrt:[s:$1]} ~
  queryEnd: ~ {$In:[fields c:tmatch] $Out}
              /.*Query: *[0-9]+[^\n0-9]*([0-9]+)/ {$e=$1 $Wrt:[s:$1]} ~
  matchLen: ~ {$In:entry $Out pre{$Request:queryEnd $Request:queryBeg}} 
              x{$Wrt:[s:($e-$b+1)]} ~
  link:     ~ {$Out $In:[fields c:title]} '>' 
              (/(sp|swiss)\\|/ name {$Wrt:swiss})? ~ 

  # table display
  t_tmatch:  ~ {$Out $In:[fields c:tmatch]}
              /.+/ {$Wrt:[s:|<font size=2><textarea rows=6 cols=70>\
                            |$Ct</textarea>
                         ]
                   } ~

  # other  
  appLn:    ~ /[^\n]*\n/ {$App} ~
  ln:       ~ /[^\n]*\n/  ~
  name:     ~ /[a-zA-Z][a-zA-Z0-9]+/~
}


# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
           fileName:'/u1/srs/srs5/tmp/4kuFL163SPJ/tmp.blast']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields print:1] 
#    $JobTokens:[$job name:so print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}

0>\
                            |$Ct</textarea>
                         ]
                   } ~

  # other  
  apsrs/icarus/db/blocks.i
# Description: icarus/srs structure description for BLOCKS (9.0)
# Author:      Martin Hilbers
# Date:        3-9-1996 
# Note:        The accession and id fields are crossed - the ID in BLOCKS is
#              not unique, the accession number is. SRSWWW however uses the
#              The ID to retrieve sequences. So the accession number is used
#              as ID. The Shortaccession number (Accession number without
#              the [A-Z] at the end is used for links from prints.
#


BLOCKS_DB:$library:[BLOCKS group:@SEQRELATED_LIBS 
  format:@BLOCKS_FORMAT maxNameLen:30 ifiles:{"blocks.i" "blocks.is"}
  files:{
    $file:blocks
  }
]

BLOCKS_FORMAT:$libformat:[fileType:@DAT_FILE syntax:@BLOCKS_SYNTAX 
  fields:{
    $field:[@DF_ALL]
    $field:[@DF_ID code:acc index:id indexToken:acc]
    $field:[@DF_Accession code:id index:str indexToken:id]
    $field:[@DF_Shortaccession code:tacc index:str indexToken:tacc]
    $field:[@DF_Description code:def index:str indexToken:def]
    $field:[@DF_Motif code:mot index:str indexToken:mot]
    $field:[@DF_Width code:wid index:int indexToken:wid]
    $field:[@DF_Sequences code:seqs index:int indexToken:seqs]
    $field:[@DF_Rawscore code:raw index:int indexToken:raw]
    $field:[@DF_Medianscore code:med index:int indexToken:med]
    $field:[@DF_LINK code:link]
  }
]

BLOCKS_SYNTAX:$syntax:[file:"SRSDB:blocks.is" ignore:" "]

DF_Shortaccession:$srsfield:[Shortaccession short:sac]
DF_Motif:$srsfield:[Motif short:mot]
DF_Width:$srsfield:[Width short:wid]
DF_Sequences:$srsfield:[Sequences short:nsq]
DF_Rawscore:$srsfield:[Rawscore short:raw]
DF_Medianscore:$srsfield:[Medianscore short:med]

$link:[@BLOCKS_DB to:@?SWISSPROT_DB token:'link|swiss' toField:@DF_ID]
       
raw]
    $field:[@DF_Medianscore code:med index:int indexToken:med]
    $field:[@DF_LINK code:link]
  }
]

BLOCKS_SYNTAX:$syntax:[file:"SRSDB:blocks.is" ignore:" "]

DF_Shortaccession:$srsfield:[Shortaccession short:sac]
DF_Motif:$srsfield:[Motif short:mot]
DF_Width:$srsfield:[Width shosrs/icarus/db/blocks.is
#
# File:        blocks.is
# Description: icarus syntax file for BLOCKS
# Author:      Martin Hilbers
# Date:        3-9-1996
# Note:        
#



$rules={
#  entry:   ~ {$Out:entry pre{$Skip:0}}
  entry:   ~ { $In:[file:text] $Out:entry pre{$Skip:0}}
             ('ID' {$Not} ln)*
             ('ID   ' {$entryFip=$Fip $Wrt} ln {$App} )
             ('//' {$Not} ln {$App})*
             ('//' {$App} ln {$App})
           ~
  # fields
  fields:  ~ {$In:entry $Out} f_id f_acc f_def 
             f_bl  f_links*
           ~
  f_id:    ~ {$Wrt:id}   'ID   ' ln ~ 
  f_acc:   ~ {$Wrt:acc}  'AC   ' ln ~
  f_def:   ~ {$Wrt:def}  'DE   ' ln ~
  f_bl:    ~ {$Wrt:bl}   'BL   ' ln ~
  f_links: ~ {$Wrt:link}  ln     ~
  
  # indexing
  id:      ~ {$In:[fields c:id] $Out}  'ID   ' /[A-Z0-9_]+/ {$Wrt} ~
  acc:     ~ {$In:[fields c:acc] $Out} 'AC   '   /[A-Z0-9_]+/ {$Wrt} ~
  tacc:    ~ {$In:[fields c:acc] $Out} 'AC   '   /BL[0-9]+/ {$Wrt} ~
  def:     ~ {$In:[fields c:def] $Out} 'DE   ' ( /[A-Za-z0-9_]+/ {$Wrt} | 
             /[^A-Za-z0-9_]+/ )*  ~
  motif:   ~ {$In:[fields c:bl] pre{$Skip:1} $Out:motif} 
             'BL   ' /[A-Z]+/ {$Wrt:mot} 
             'motif; width=' /[0-9]+/ {$Wrt:wid}
             '; seqs=' /[0-9]+/ {$Wrt:seqs} 
             '; 99.5%=' /[0-9]+/ {$Wrt:raw}
             '; strength=' /[0-9]+/ {$Wrt:med}
            ~
  mot:      ~{$In:[motif c:mot] $Out} /.+/ {$Wrt} ~
  wid:      ~{$In:[motif c:wid] $Out} /.+/ {$Wrt} ~
  seqs:     ~{$In:[motif c:seqs] $Out} /.+/ {$Wrt}~
  raw:      ~{$In:[motif c:raw] $Out} /.+/ {$Wrt} ~
  med:      ~{$In:[motif c:med] $Out} /.+/ {$Wrt} ~


  link:     ~ {$In:[fields c:link] pre{$Skip:1} $Out}
             (/[A-Z0-9_]+/ {$Wrt:swiss}|ln)
            ~

  # html display
  hl_links:~ {$In:[fields c:link t:hl] pre{$Skip:1}}
             (name {$Rep:{$ParStr:swissIR $Ct $Ct}} ln | ln) *
           ~
  # other 
  name:    ~ /[a-zA-Z0-9_]+/ ~ 
  ln:      ~ /[^\n]*\n/ ~
}





Out} /.+/ {$Wrt} ~
  seqs:     ~{$In:[motif c:seqs] $Out} /.+/ {$Wrt}~
  raw:      srs/icarus/db/btkbase.i
#    $RCSfile: btkbase.i,v $
#    $Revision: 1.2 $
#    $Date: 1997/03/03 18:33:48 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


BTKBASE_DB:$library:[BTKBASE group:@MUTATION_LIBS
  format:@BTKBASE_FORMAT maxNameLen:30 ifiles:{"btkbase.i" "btkbase.is"}
  files:{
    $file:btkbase
  }
]

BTKBASE_FORMAT:$libformat:[fileType:@TXT_FILE syntax:@BTKBASE_SYNTAX 
  tableFormat:left
  fields:{
    $field:[@DF_ID code:id index:id indexToken:pin tableToken:pin]
    $field:[@DF_Code code:code index:str indexToken:code tableToken:code]
#    $field:[@DF_NuclPos code:nucl index:int indexToken:nucPos]
    $field:[@DF_NuclChange code:feature index:str indexToken:nuclChange
      tableToken:nuclChange]
    $field:[@DF_DnaChangePos code:feature index:int indexToken:dnaPos
      tableToken:dnaPos tableFormat:right]
    $field:[@DF_TranslEffect code:feature index:str indexToken:translEff
      tableToken:translEff]    
    $field:[@DF_AaChange code:feature index:str indexToken:aaChange
      tableToken:aaChange]
    $field:[@DF_ProtChangePos code:feature index:int indexToken:protPos
      tableToken:protPos tableFormat:right]
    $field:[@DF_ProteinDomain code:dom index:str indexToken:domain
      tableToken:domain]

  }
]

BTKBASE_SYNTAX:$syntax:[file:"SRSDB:btkbase.is" ignore:" "]

DF_Code:$srsfield:[Code short:cod]
DF_NuclPos:$srsfield:[NucleotidePosition short:nup]
DF_ProteinDomain:$srsfield:[ProteinDomain short:dom]


       
:[@DF_AaChange code:feature index:str indexToken:aaChange
      tableToken:aaChange]
    $field:[@DF_ProtChangePos code:feature index:int indexToken:protPos
      tableToken:protPos tableFormat:right]
    $field:[@DF_ProteinDomain code:dom index:str indexToken:domain
      tableToken:domain]

  }
]

BTKBASE_SYNTAX:$syntax:[file:"SRSDB:btkbase.is" ignore:" "]

DF_Code:$srsfield:[Code short:cod]
DF_NuclPos:$srsfield:[NucleotidePosition short:nup]
DF_ProteinDomain:$srsfieldsrs/icarus/db/btkbase.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: btkbase.is,v $
#    $Revision: 1.3 $
#    $Date: 1997/03/03 18:33:48 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  'ID':id                         'Symptoms':symptoms           
  'Original code':code		  'Sex':sex                     
  'Accession':acc		  'Age':age                     
  'Description':des		  'Relative':relative           
  'Date':date			  'Ethnic origin':ethnicOrig    
  'RefNumber':refNo		  'Family history':famHist      
  'RefCrossRef':refXRef		  'IgA':iga                     
  'RefAuthors':refAut		  'IgG':igg                     
  'Refauthors':refAut		  'IgG1':igg1                   
  'RefAuthros':refAut		  'IgG2':igg2                   
  'RefTitle':refTtl		  'IgG3':igg3                   
  'RefLoc':refLoc		  'IgG4':igg4                   
  'Feature':feature		  'IgM':igm                     
  'mRNA level':mrnaLevel	  'B cells':bcells              
  'Protein level':protLevel	  'CD19':cd19                   
  'Protein struct':protStruct	  'CD20':cd20                   
}

$rules={
  entry:      ~ {$In:[file:text] $Out pre $Skip:0}
              	('ID' {$Not} ln)*
              	('ID' {$Wrt $entryFip=$Fip} ln {$App} 
              	 ('ID' {$Not} ln {$App})+)?  
              ~
  # fields    
  fields:     ~ {$In:entry $Out $Skip:1} 
              	id f_code? acc des date 
              	(refNo refXRef? refAut? refTtl? refLoc?)* 
              	feature? mrnaLevel? protLevel? protStruct? 
              	symptoms? sex? age? relative? famhist? 
              	iga? igg? igg1? igg2? igg3? igg4? igm? 
              	bcells? cd19? cd20?
              ~
  id:         ~ {$Wrt:id} ('ID' ln)+ ~
  f_code:     ~ {$Wrt:code} ('Original code' ln)+ ~
  acc:        ~ {$Wrt:acc} ('Accession' ln)+ ~
  des:        ~ {$Wrt:des} ('Description' ln)+ ~
  date:       ~ {$Wrt:date} ('Date' ln)+ ~
  refNo:      ~ {$Wrt:refNo} ('RefNumber' ln)+ ~
  refXRef:    ~ {$Wrt:refXRef} ('RefCrossRef' ln)+ ~
  refAut:     ~ {$Wrt:refAut} (/RefAuthors|Refauthors|RefAuthros/ ln)+ ~
  refTtl:     ~ {$Wrt:refTtl} ('RefTitle' ln)+ ~
  refLoc:     ~ {$Wrt:refLoc} ('RefLoc' ln)+ ~
  feature:    ~ {$Wrt:feature} ('Feature' ln)+ ~
  mrnaLevel:  ~ {$Wrt:mrnaLevel} ('mRNA level' ln)+ ~
  protLevel:  ~ {$Wrt:protLevel} ('Protein level' ln)+ ~
  protStruct: ~ {$Wrt:protStruct} ('Protein struct' ln)+ ~
  symptoms:   ~ {$Wrt:symptoms} ('Symptoms' ln)+ ~
  sex:        ~ {$Wrt:sex} ('Sex' ln)+ ~
  age:        ~ {$Wrt:age} ('Age' ln)+ ~
  relative:   ~ {$Wrt:relative} ('Relative' ln)+ ~
  ethnicOrig: ~ {$Wrt:ethnicOrig} ('Ethnic origin' ln)+ ~
  famhist:    ~ {$Wrt:famhist} ('Family history' ln)+ ~
  iga:        ~ {$Wrt:iga} ('IgA' ln)+ ~
  igg:        ~ {$Wrt:igg} ('IgG' ln)+ ~
  igg1:       ~ {$Wrt:igg1} ('IgG1' ln)+ ~
  igg2:       ~ {$Wrt:igg2} ('IgG2' ln)+ ~
  igg3:       ~ {$Wrt:igg3} ('IgG3' ln)+ ~
  igg4:       ~ {$Wrt:igg4} ('IgG4' ln)+ ~
  igm:        ~ {$Wrt:igm} ('IgM' ln)+ ~
  bcells:     ~ {$Wrt:bcells} ('B cells' ln)+ ~
  cd19:       ~ {$Wrt:cd19} ('CD19' ln)+ ~
  cd20:       ~ {$Wrt:cd20} ('CD20' ln)+ ~

  # indexing 
  pin:        ~ {$In:[fields c:id] $Out} tag /[^;]+/ {$Wrt} ~
  code:       ~ {$In:[fields c:code] $Out} tag /[^\n ]+/ {$Wrt} ~
  nuclChange: ~ {$In:[fields c:feature] $Out}
                /.*\/change: *([a-z]) -> ([a-z])/ {$Wrt:[s:"$1>$2"]} ~
  aaChange:   ~ {$In:[fields c:feature] $Out}
                /.*aa_change: *([A-Z]) -> ([A-Z])/ {$Wrt:[s:"$1>$2"]} ~
  domain:     ~ {$In:[fields c:feature] $Out}
                /.*\/domain: *([A-Z0-9'_-]+)/ {$Wrt:[s:$1]} ~
  translEff:  ~ {$In:[fields c:feature] $Out}
                /.*translation_effect: *([a-zA-Z0-9'_-]+)/ {$Wrt:[s:$1]} ~
  dnaPos:     ~ {$In:[fields c:feature] $Out} 
                /.*EMBL[^\n]+ ([0-9]+)\n/ {$Wrt:[s:$1]} ~ 
  protPos:     ~ {$In:[fields c:feature] $Out}
                /.*SWISS-PROT[^\n]+ ([0-9]+)\n/ {$Wrt:[s:$1]} ~
  
  # html
  t_feature:  ~ {$In:[fields c:feature t:html]}
              	(/[^\/\n]+/ ('/' (emblRef | swissRef)?)? ln)+ ~  
  emblRef:    ~ 'EMBL:' name {$Rep:{$ParStr:emblR $Ct $Ct}} ~
  swissRef:   ~ 'SWISS-PROT;' name {$Rep:{$ParStr:swissR $Ct $Ct}} ~
	      
  # others    
  ln:         ~ /[^\n]*\n/ ~
  tag:        ~ /./ {$Len:15} ~
  name:       ~ /[A-Za-z][a-zA-Z0-9_]+/ ~

}


# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/opt/srs/data/mutdb/btkbase/btkbase.txt']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:pin print:1] 
    $JobTokens:[$job name:nuclChange print:1]
    $JobTokens:[$job name:aaChange print:1]
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}

T;' name {$Rep:{$ParStr:swissR $Ct $Ct}} ~
	      
  # others    
  ln:         ~ /[^\n]*\n/ ~
  tag:        ~ /./ {$Len:15} ~
  name:       ~ /[A-Za-z][a-zA-Z0-9_]+/ ~

}


# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/opt/srs/data/mutdb/btkbase/btkbase.txt']
  while:$JobHasInput:$job {
    $JobTokens:[$jobsrs/icarus/db/btkbase.it
  description:
    |X-linked agammaglobulinemia (XLA) is a hereditary immunodeficiency caused
    |by mutations in the gene coding for Bruton's agammaglobulinemia tyrosine
    |kinase (BTK). XLA patients have decreased number of mature B cells in
    |their peripheral blood and show a lack of all immunoglobulin isotypes
    |causing susceptibility to severe bacterial infections. The 37.5 kb gene
    |contains 19 exons, 18 of which code for a 77 kDa protein. BTK is expressed
    |in all hematopoietic lineages except for T lymphocytes and plasma cells.
    |<P>
    |To coordinate BTK mutation analysis, an international study group was
    |established in 1994. BTK mutation data, both published and directly
    |submitted information, are collected into the BTKbase. This database
    |contains information about the mutations and XLA patients including
    |immunoglobulin levels, B cell numbers, age of diagnosis, symptoms,
    |mRNA and protein data and structural consequences. The study group gives
    |for each patient an individual patient identity number (PIN) and a
    |running accession number.
    |<P>
    |The PIN consists of the type of mutation and a running number indicating
    |mutations affecting the same amino acid or the same non-coding region.
    |The PIN is given as soon as a mutation is available to the study group.
    |<P>
    |Scientists are encouraged to contact the study group before 
    |publishing their
    |mutation data to get the accession numbers and PINs. Data can be kept
    |confidential until published.
  literature:
    |<OL>
    |<LI>Vihinen, M., Cooper, M. D., de Saint Basile, G., Fischer, A., Good,
    |R. A., Hendriks, R. W., Kinnon, C., Kwan, S.-P., Litman, G. W.,
    |Notarangelo, L. D., Ochs, H. D., Rosen, F. S., Vetrie, D., Webster,
    |A. D. B., Zegers, B. J. M., and Smith, C. I. E., BTKbase: a database of
    |XLA causing mutations, Immunol. Today 16:460-465 (1995).
    |
    |<LI>Vihinen, M., Iwata, T., Kinnon, C., Kwan, S.-P., Ochs, H. D.,
    |Vorechovsky, I, and Smith, C. I. E., BTKbase, mutation database for
    |X-linked agammaglobulinemia, Nucleic Acids Res. 24:160-165 (1996).
    |</OL>
#  address:
  contact:
    |<ADDRESS>
    |Mauno Vihinen<BR>
    |Department of Biosciences<BR>
    |Division of Biochemistry<BR>
    |University of Helsinki<BR>
    |FIN-00014 Helsinki, FINLAND<BR>
    |</ADDRESS><P>
    |<ADDRESS>
    |Heikki Lehvaslaiho<BR>
    |CSC Scientific Computing<BR>
    |P.O.BOX 405<BR>
    |Tietotie 6<BR>
    |02101 Espoo, FINLAND<BR>
    |</ADDRESS><P>
    |<ADDRESS>
    |C. I. Edvard Smith<BR>
    |Center for BioTechnology<BR>
    |Department of Bioscience at NOVUM<BR>
    |Karolinska Institute<BR>
    |S-141 57 Huddinge<BR>
    |Sweden<BR>
    |</ADDRESS>
  www:
    |<A HREF="http://www.helsinki.fi/science/signal/btkbase.html">\
    |http://www.helsinki.fi/science/signal/btkbase.html</A>
  address:
    |Department of Biosciences<BR>
    |Division of Biochemistry<BR>
    |University of Helsinki<BR>
    |FIN-00014 Helsinki<BR>
    |Finland<BR>
  telephone: '+358-0-708 59081'
  telefax:   '+358-0-708 59068'
  email: 'Mauno.Vihinen@Helsinki.Fi'
  fields:{
    Identifier:
      |This name is the primary means of identifying the sequence within a
      |given release. The name indicates the type of mutation using the PIN
      |convention.
      |<P>
      |PINs are formed as follows. Point mutations in the coding region are
      |numbered according to the affected amino acids. The complete PIN
      |contains 1) the single letter amino acid code of the wild type
      |residue, 2) the number of the amino acid, 3) the single letter amino
      |acid code of the mutated residue, 4) running number for mutations at
      |this site, so that eg. R525Q(1) means the first listed mutation of
      |arginine 525 to glutamine. Members of the same family having the very
      |same mutation are indicated with alphabets following the PIN,
      |eg. R525Q(1a) and (1b). The relatives are also cross- referenced using
      |database "Relative" lines (see section 3.18) with the exact
      |description of the relation.
      |<P>

      |Insertions are marked with sign "@" and deletions with "#" in front of
      |the mutation site. If mutation causes a stop codon it is marked with X
      |and the number of the codon with the newly introduced stop
      |codon. Thus, @V377X404(1b) means insertion at codon 377 causing
      |frameshift mutation leading to appearance of the stop signal at codon
      |404. The last number in parentheses indicates the second patient in
      |this family.
      |<P>
      |
      |In the rare occasion of inframe insertions or deletions the number of
      |added of deleted residues is indicated by denoting the number of
      |residues preceded by "+" or "-", respectively. @V103+7(1) describes an
      |addition of seven residues inframe after valine 103.
      |<P>
      |
      |The nucleotide and amino acid numbering is according to Vetrie et
      |al. (1993). Due to possible variations in the size of non-coding
      |regions requiring future renumbering, the up- and downstream and
      |intron PINs have only running numbers without giving the actual
      |mutated nucleotide(s). Intron mutations are indicated by the intron
      |number followed by running number of mutations in the intron. Thus,
      |Intron 5(7) indicates the seventh described mutation affecting intron
      |5. Similar notation is used for up- and downstream sequences where
      |either "Upstream" of "Downstream" is written before number of the
      |mutation.
      |<P>
      |
      |Partially characterized gene rearrangements are listed separately, so
      |that eg. gross deletions have PINs starting from Deletion (1).
      |<P>
      |
      |In vitro mutations are indicated by using character "&" preceeding the
      |actual mutation site and natural polymorphisms have "%" character
      |before the affected location.
      |<P>
      |
      |If a PIN has to be changed and a mutation renamed eg. due to errors in
      |reported information, the original PIN will not be reused. The PIN
      |used previously will in that case be mentioned in the line
      |Original code. 
    MutationType:
      |Mutations come in four main types. 
      |<DL>
      |<DT> point_mutation<DD>change of a single nucleotide to another
      |<DT>deletion  <DD> absense of one or more nucleotides
      |<DT>insertion <DD> addition of one or more nucleotides
      |<DT>repeat    <DD> absense or addition of a short repeated region
      |e.g. dinu
      |</DT>
    TranslationEffect:
      |Verbal description of the effect of the nucleotide mutation
      |at amino acid level.
    aaChange:
      |Description of the change in the reference sequence.
      |Format: <UL><LI>character(s)>character(s), e.g., A>T
      |<LI>+character(s)
      |<LI> -character  
      |</Ul>
  }
}







r more nucleotides
      |<DT>insertion <DD> addition of one or more nucleotides
      |<DT>repeat    <DD> absense or addition of a short repeated region
      |e.g. dinu
      |</DT>
    TranslationEffecsrs/icarus/db/cabi.is
init = * <$hb := "<B>* "; 
          $he := " *</B> ";
          $fe := " <BR>";
          com:s2a f:IcaFunny2Ascii; arg:funny unnamed:y; return:ascii>;

entry <ct:entry;trigger:fields> = '<DT>' <wrt> ln <app> 
          { /<NR>/ <not> ln <app> };
#
# the fields
#
fields <rd:entry;ct> = dt cd sn jn aj cp yr vl no pp la it au 
                       aa cc ti [ab] ls de pb lp ;
dt = '<DT>' /(.+)<\/DT>/ <p:"$hb Source type$he$1 $fe\n"> ln;
cd = '<CD>' /(.+)<\/CD>/ <p:"$hb CODEN code$he$1 $fe\n"> ln;
sn = '<SN>' /(.+)<\/SN>/ <p:"$hb ISSN$he$1 $fe\n"> ln;
jn = '<JN>' /(.+)<\/JN>/ <p:"$hb Journal name$he$1 $fe\n"> ln;
aj = '<AJ>' /(.+)<\/AJ>/ <p:"$hb AJ$he$1 $fe\n"> ln;
cp = '<CP>' /(.+)<\/CP>/ <p:"$hb Country code publ.$he$1 $fe\n"> ln;
yr = '<YR>' /(.+)<\/YR>/ <p:"$hb Publication year$he$1 $fe\n"> ln;
vl = '<VL>' /(.+)<\/VL>/ <p:"$hb Volume$he$1 $fe\n"> ln;
no = '<NO>' /(.+)<\/NO>/ <p:"$hb Issue$he$1 $fe\n"> ln;
pp = '<PP>' /(.+)<\/PP>/ <p:"$hb Page numbers$he$1 $fe\n"> ln;
la = '<LA>' /(.+)<\/LA>/ <p:"$hb Article language code$he$1 $fe\n"> ln;
it = '<IT>' /(.+)<\/IT>/ <p:"$hb Item type$he$1 $fe\n"> ln;
au = '<AU>' *<p:"$hb Authors$he"> auLn '</AU>' *<p:"$fe \n"> ln;
aa = '<AA>' *<p:"$hb Author's address$he"> auAddr '</AA>' *<p:"$fe\n"> ln;
cc = '<CC>' /(.+)<\/CC>/ <p:"$hb CC$he$1 $fe\n"> ln;
ti = '<TI>' *<p:"$hb Title$he"> tiLn '</TI>' *<p:"$fe\n"> ln;
ab = '<AB>' *<p:"$hb Abstract$he"> abLn '</AB>' *<p:"$fe\n"> ln;
ls = '<LS>' /(.+)<\/LS>/ <p:"$hb Summary language code$he$1 $fe\n"> ln;
de = '<DE>' /(.+)<\/DE>/ <p:"$hb Author keywords$he$1 $fe\n"> ln;
pb = '<PB>' /(.+)<\/PB>/ <p:"$hb Publisher$he$1 $fe\n"> ln;
lp = '<LP>' /(.+)<\/LP>/ <p:"$hb Location of publisher$he$1 $fe\n"> ln;
nr = '<NR>' /(.+)<\/NR>/ <p:"$hb NR$he$1 $fe\n">;
#
# contents of fields
#
ln       = /[^$]*$?/;
auLn     = { '</AU>' <not;noskip> repLn } [/$/] ;
auAddr   = { '</AA>' <not;noskip> repLn } [/$/] ;
abLn     = { '</AB>' <not;noskip> repLn } [/$/] ;
tiLn     = { '</TI>' <not;noskip> repLn } [/$/] ;
repLn    = ( '<italic>' <noskip;p:"<I>"> | 
           '</italic>' <noskip;p:"</I>"> | 
           '<inf>' <noskip;p:""> | 
           '</inf>' <noskip;p:""> | 
           '<sup>' <noskip;p:""> | 
           '</sup>' <noskip;p:""> | 
           /&[a-zA-Z0-9]+;/ <p:(s2a:$to); noskip> |
           /[^$]/ <noskip;p:"$to">).
{ '</AU>' <not;noskip> repLn } [/$/] ;
auAddr   = { '</AA>' <not;noskip> repLn } [/$/] ;
abLn     = { '</AB>' <not;noskip> repLn } [/$/] ;
tiLn     = { '</TI>' <not;noskip> repLn } [/$/] ;
repLn    = ( '<italic>' <nsrs/icarus/db/cftr.i
#    $RCSfile: cftr.i,v $
#    $Revision: 1.2 $
#    $Date: 1997/03/03 18:33:49 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CFTR_DB:$library:[CFTR group:@MUTATION_LIBS
  format:@CFTR_FORMAT maxNameLen:30 ifiles:{'cftr.i' 'cftr.is' 'cftr.it'}
  files:{
    $file:'CFmutations96-1'
  }
]

CFTR_FORMAT:$libformat:[syntax:@CFTR_SYNTAX fileType:@TXT_FILE  
  printFormat:table tableFormat:left fields:{
    $field:[@DF_ID indexToken:id index:id
      tableToken:id tableFormat:right]
    $field:@DF_ALL
#    $field:[@DF_DnaSubst code:mut indexToken:'dnaMut|subst' index:str
#      tableToken:'dnaMut|subst' tableFormat:left]
    $field:[@DF_NuclChange code:mut indexToken:nuclChange index:str]
    $field:[@DF_DnaChangePos code:dnaSubst indexToken:dnaMutPos index:int
      tableFormat:right]
    $field:[@DF_AaChange code:aaSubst indexToken:aaChange index:str]
    $field:[@DF_ProtChangePos code:aaSubst indexToken:aaMutPos index:int
      tableFormat:right]
    $field:[@DF_Reference code:ref]
  }
]


CFTR_SYNTAX:$syntax:[file:"SRSDB:cftr.is" ignore:" "]
en:'dnaMut|subst' index:str
#      tableToken:'dnaMut|subst' tableFormat:left]
    $field:[@DF_NuclChange code:mut indexToken:nuclChange index:str]
    $field:[@DF_DnaChangePos code:dnaSubst indexToken:dnaMutPos index:int
      tableFormat:right]
    $field:[@DF_AaChange code:aaSubst indexToken:aaChange index:str]
    $field:[@DF_ProtChangesrs/icarus/db/cftr.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: cftr.is,v $
#    $Revision: 1.3 $
#    $Date: 1997/03/03 18:33:50 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$rules={
  entry:      ~ {$In:[file:text] $Out pre {$Skip:0 $entryN+=1} init $entryN=0}
                ('Summary' ln ln ln ln ln)*
                (/[^ ]+/ {$entryFip=$Fip $Wrt} ln {$App} 
                 (/([[A-Z0-9-][[A-Z0-9-]| *\n)/ {$Not} 
                 /[^\n]+/ {$App:[s:$StrPad:[$Ct c:' ' len:70]]} '\n' {$App})*)?
                
              ~
  # fields
  fields:     ~ { $In:entry $Out $Skip:1 
                  if:$Trim:[$id]!="" $Wrt:[s:$id c:id] 
                  if:$Trim:[$mut]!="" $Wrt:[s:$mut c:mut] 
                  if:$Trim:[$exon]!="" $Wrt:[s:$exon c:exon] 
                  if:$Trim:[$cons]!="" $Wrt:[s:$cons c:cons] 
                  if:$Trim:[$dom]!="" $Wrt:[s:$dom c:dom]
                  if:$Trim:[$ref]!="" $Wrt:[s:$ref c:ref]
                } 
                /.+/ {$id=$Ct $Len:13} sp
                /.+/ {$mut=$Ct $Len:14} sp
                /.+/ {$exon=$Ct $Len:9} sp
                /.+/ {$cons=$Ct $Len:18} sp
                /.+/ {$dom=$Ct $Len:6} 
                ln {$ref=$Ct} 
                (
                 /[^\n]+/ {$Print:[$Ct v:$id] $Len:13} sp? 
                 /[^\n]+/? {$Print:[$Ct v:$mut] $Len:14} sp? 
                 /[^\n]+/? {$Print:[$Ct v:$exon] $Len:9} sp?
                 /[^\n]+/? {$Print:[$Ct v:$cons] $Len:18} sp?
                 /[^\n]+/? {$Print:[$Ct v:$dom] $Len:6} sp?
                 ln? {$Print:[$Ct v:$ref]} 
                )*               
               ~
  sp:         ~ /[^\n][^\n]/ ~


  # indexing 
  id:         ~ {$In:[fields c:id] $Out} /[^ \n]+/ {$Wrt} ~ 
#  mut:        ~ {$In:entry $Out} /[^ \n]+/ {$Wrt} ~ 
#  exon:       ~ {$In:entry $Out} /[^ \n]+/ {$Wrt} ~ 
#  cons:       ~ {$In:entry $Out} /[^ \n]+/ {$Wrt} ~ 
#  dom:        ~ {$In:entry $Out} /[^ \n]+/ {$Wrt} ~ 
  dnaMutPos:  ~ {$In:[fields c:mut] $Out}
                (/(-?[0-9]+)((\\+|-)[0-9]+)?/ {$Wrt:[s:$1]} | /./)+ ~
  aaMutPos:   ~ {$In:[fields c:cons] $Out}
                (/[0-9]+/ {$Wrt} | /./)+ ~
  nuclChange: ~ {$In:[fields c:mut] $Out}
                (/.*([A-Za-z])->([a-zA-Z])/ {$Wrt:[s:"$1>$2"]} | /./)+ ~
  aaChange:   ~ {$In:[fields c:cons] $Out init $aa={Ile:I Leu:L Met:M 
                 Ala:A Val:V Ser:S Thr:T Phe:F Tyr:Y Gly:G Pro:P Trp:W Cys:C
                 Gln:Q Asn:N Arg:R Lys:K Asp:D Glu:E His:H Stop:Stop}}
                (/([A-Za-z]+)->([a-zA-Z]+)/ {$Wrt:[s:"($aa.$1)>($aa.$2)"]} 
                  | /./)+ . ~ 

  # table format
  t_class:    ~ {$In:[fields c:class]  $Out} tag /.*/ {$Wrt} ~
  t_patOri:   ~ {$In:[fields c:patOri] $Out} tag /.*/ {$Wrt} ~
  t_lab:      ~ {$In:[fields c:lab]    $Out} tag /.*/ {$Wrt} ~
  t_cmnt:     ~ {$In:[fields c:cmnt]   $Out} tag /.*/ {$Wrt} ~

#  table:      ~ {$In:[fields c:{cmnt patOri lab cmnt}] $Out} 
#                tag /.*/ {$Wrt:$Itc} ~

  # html
  h_fields:   ~ { $In:[fields t:html] 
                  init $f={id: Id mut:Mutation exon:Exon
                           cons: Consequence dom:Domain ref:Reference} 
                } /.*/ {if:$ParInt:[isTable]==0
                          $Rep:"<TR><TD><B>($f.$Itc)</B></TD><TD>$Ct</TD></TR>"
                       }
              ~ 

  # other stuff
  ln:         ~ /[^\n]*\n/ ~
  mut:        ~ /([A-Z])([0-9]+)([A-Z*])/ 
                {$Wrt:[s:"$2" c:pos] $Wrt:[s:"$1>$3" c:subst]} |  
                /[A-Za-z0-9]+/ {$Wrt:subst} ~
  num:        ~ /[0-9]+/ ~
  tag:        ~ /[^:]+:/ ~
  word:       ~ /[a-zA-Z0-9_$]+/ {$Uniq} ~
  sep:        ~ /[^a-zA-Z0-9_$]+/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/opt/srs/data/mutdb/cftr/CFmutations96-1.txt']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:id print:1] 
    $JobTokens:[$job name:aaSubst print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}



] $Wrt:[s:"$1>$3" c:subst]} |  
            srs/icarus/db/cftr.it
#    
#    $RCSfile: cftr.it,v $
#    $Revision: 1.1 $
#    $Date: 1996/11/05 19:54:17 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |Cystic Fibrosis Mutation Data Base
  www:
    |<A HREF="http://www.genet.sickkids.on.ca/cftr/">\
    |http://www.genet.sickkids.on.ca/cftr/</A>
  email:
    |lctsui@genet.sickkids.on.ca
  fax:
    |+1 416 813 4931
  contact:
    |Lap-Chee Tsui,<BR> 
    |Department of Genetics,<BR> 
    |The Hospital for Sick Children,<BR>
    |555 University Avenue, Toronto,<BR>
    |Ontario M5G 1X8, CANADA.
  fields:{
  }  
}
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |Cystic Fibrosis Mutation Data Base
  www:
    |<A HREF="http://www.genet.sickkids.on.ca/cftr/">\
    |http://www.genet.sickkids.on.ca/cftr/</A>
  email:
    |lctsui@genet.sickkids.on.ca
  fax:
    |+1 416 81srs/icarus/db/clustalw.i
#    $RCSfile: clustalw.i,v $
#    $Revision: 1.1 $
#    $Date: 1997/03/03 18:36:21 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


CLUSTALW_DB:$library:[CLUSTALW group:@APPLICATION_LIBS 
  comment:"" 
  format:@CLUSTALW_FORMAT maxNameLen:40 ifiles:{"clustalw.i" "clustalw.is"}
  type:user
]

CLUSTALW_FORMAT:$libformat:[fileType:@CLUSTALW_FILE syntax:@CLUSTALW_SYNTAX 
  tableFormat:left fields:{
    $field:[@DF_ID code:title index:id indexToken:id]
    $field:[@DF_NAlign code:seqList index:int indexToken:nali]
    $field:[@DF_SeqList code:seqList tableToken:t_seqList tableFormat:listing]
    $field:[@DF_Alignment code:ali tableToken:t_ali]
  }
]

DF_SeqList:$srsfield:[SeqList short:sql]

CLUSTALW_SYNTAX:$syntax:[file:"SRSDB:clustalw.is" ignore:" "]
CLUSTALW_FILE:$filetype:[typename:aln maxline:100 singleEntry:y]

$link:[@CLUSTALW_DB to:@?SWISSPROT_DB token:'link|swiss' toField:@DF_ID]

ft fields:{
    $field:[@DF_ID code:title index:id indexToken:id]
    $field:[@DF_NAlign code:seqList index:int indexToken:nali]
    $field:[@DF_SeqList code:seqList tableToken:t_seqList tableFormat:listing]
    $field:[@DF_Alignment code:ali tableToken:t_ali]
  }
]

DF_SeqList:$srsfield:[SeqList short:sql]

CLUSTALW_SYNTAX:$syntax:[file:"SRSDB:clustalw.is" ignore:" "]
CLUSTALW_FILE:$filetype:[typename:aln maxline:100 singleEntry:y]

$link:[@CLUSTALW_DB to:@?SWISSPROT_DB token:'link|swiss' toFiesrs/icarus/db/clustalw.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: clustalw.is,v $
#    $Revision: 1.1 $
#    $Date: 1997/03/03 18:36:23 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$rules={
  entry:    ~ {$In:[file:text] $Out pre $skip:0}
              ln {$Wrt $entryFip=0} (ln {$App})+ ~

  # data fields
  fields:   ~ {$In:entry $Out $Skip:1} 
              title seqList space alignment ~
  title:    ~ {$Wrt:title} ln ~
  seqList:  ~ {$Wrt:seqList}  (/!.*Length:/ ln)+ ~
  space:    ~ {$Wrt:space} (/[^ \n]+      *[A-Z-]+\n/ {$Not} ln)+ ~
  alignment:~ {$Wrt:ali} ln+ ~

  # indexing
  id:       ~ {$In:[fields c:title] $Out} /[^:]+:/ name {$Wrt} ~
  link:     ~ {$In:[fields c:seqList] $Out} 
              ('!' name {$lib=$Ct} ':' name {$Wrt:swiss} ln)+ ~
  nali:     ~ {$In:[fields c:seqList] $Out pre $n=0} 
              (ln {$n+=1})+ x {$Wrt:[s:$n]} ~

  # table display
  t_ali:    ~ {$Out $In:[fields c:ali]}
              /.+/ {$Wrt:[s:|<font size=2><textarea rows=10 cols=70>\
                            |$Ct</textarea>
                         ]
                   } ~
  t_seqList:~ {$Out $In:[fields c:seqList]} ('!' ln {$Wrt})+ ~

  # html display
  h_seqList:~ {$In:[fields c:seqList t:html]}
              ('!' name ':' name {$Rep:{$ParStr:swissidR $Ct $Ct}} ln)+ ~

  # other  
  appLn:    ~ /[^\n]*\n/ {$App} ~
  ln:       ~ /[^\n]*\n/  ~
  name:     ~ /[a-zA-Z0-9][a-zA-Z0-9_]+/~
}


# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
           fileName:'/scrap/etzold/otto.aln']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields print:1 task:html] 
    $JobTokens:[$job name:id print:1] 
    $JobTokens:[$job name:link print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}

('!' name ':' name {$Rep:{$ParStr:swissidR $Ct $Ct}} ln)+ ~

  # other  
  appLn:    ~ /[^\n]*\n/ {$App} ~
  ln:       ~ /[^\n]*\n/  ~
  name:     ~ /[a-zA-Z0-9][a-zA-Z0-9_]+/~
}


# debugging 
if:$Testsrs/icarus/db/dssp.i
#    $RCSfile: dssp.i,v $
#    $Revision: 1.5 $
#    $Date: 1997/03/19 21:06:52 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


DSSP_DB:$library:[DSSP group:@PROTSTRUCT_LIBS
  format:@DSSP_FORMAT maxNameLen:5 ifiles:{"dssp.i" "dssp.is"}
]

DSSP_FORMAT:$libformat:[fileType:@DSSP_FILE syntax:@DSSP_SYNTAX
  fields:{
    $field:[@DF_ID code:header index:id indexToken:id]
    $field:[@DF_Compound code:compnd index:str indexToken:comp]
    $field:[@DF_Source code:source index:str indexToken:src]
    $field:[@DF_Authors code:author index:str indexToken:authors]
    $field:[@DF_Histograms code:hist]
    $field:[@DF_Residues code:data]
    $field:[@DF_ResiduesN code:nums index:int indexToken:'n|resN']
    $field:[@DF_ChainN code:nums index:int indexToken:'n|chainN']
    $field:[@DF_SsBridgeTotN code:nums index:int indexToken:'n|ssbtot']
    $field:[@DF_SsBridgeIntraN code:nums index:int indexToken:'n|ssbintra']
    $field:[@DF_SsBridgeInterN code:nums index:int indexToken:'n|ssbinter']
    $field:[@DF_AccSurface code:surf index:real indexToken:surf]
    $field:[@DF_HydBondsJN code:hb index:int indexToken:'hb|hb']
    $field:[@DF_HydBondsParaP code:hb_pb index:int indexToken:'hb|hb_pb']
    $field:[@DF_HydBondsAntiP code:hb_ab index:int indexToken:'hb|hb_ab']
  }
]
DF_Histograms:    $srsfield:[Histograms short:his]
DF_Residues:      $srsfield:[Residues short:res]
DF_ResiduesN:     $srsfield:[NResiduesN short:rsn]
DF_ChainN:        $srsfield:[NChains short:chn]
DF_SsBridgeTotN:  $srsfield:[NSsBridgeTot short:ssn]
DF_SsBridgeIntraN:$srsfield:[NSsBridgeIntra short:ran]
DF_SsBridgeInterN:$srsfield:[NSsBridgeInter short:ern]
DF_AccSurface:    $srsfield:[AccSurface short:sur]
DF_HydBondsJN:    $srsfield:[NHydBondsJ short:hb]
DF_HydBondsParaP: $srsfield:[NHBondsParaBridge short:hpb]
DF_HydBondsAntiP: $srsfield:[NHBondsAntiParBridge short:hab]


DSSP_SYNTAX:$syntax:[file:"SRSDB:dssp.is" ignore:" "]
DSSP_FILE:$FileType:[typename:'dssp' singleEntry:y maxline:500
  saveName:file saveNameLength:20]

$link:[@DSSP_DB to:@?PDB_DB fromField:@DF_ID toField:@DF_ID]

dgeIntra short:ran]
DF_SsBridgeInterN:$srsfield:[NSsBridgeInter short:ern]
DF_AccSurface:    $srsfield:[AccSurface short:sur]
DF_HydBondsJN:    $srsfield:[NHydBondsJ short:hb]
DF_HydBondsParaP: $srsfield:[NHBondsParaBridge short:hpb]
DF_HydBondsAntiP: $srsfield:[NHBondsAntiParBridge short:hab]


DSSP_SYNTAX:$syntax:[file:"SRSDB:dssp.is" ignore:"srs/icarus/db/dssp.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: dssp.is,v $
#    $Revision: 1.1 $
#    $Date: 1996/12/06 22:26:34 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$rules={

  # the entry
  entry:     ~ {$In:[file:text] $Out pre $Skip:0}
               ln {$entryFip=$Fip $Wrt} appLn+
             ~

  # fields from text
  fields:    ~ {$In:entry $Out $Skip:1} 
               title header compnd source author nums hist data ~
  title:     ~ {$Wrt:title} ln ln ~
  header:    ~ {$Wrt:header} ('HEADER' ln)+ ~
  compnd:    ~ {$Wrt:compnd} ('COMPND' ln)+ ~
  source:    ~ {$Wrt:source} ('SOURCE' ln)+ ~
  author:    ~ {$Wrt:author} ('AUTHOR' ln)+ ~
  nums:      ~ ln {$Wrt:nums} ln {$Wrt:surf} 
               ln {$Wrt:hb} ln {$Wrt:hb_pb} ln {$Wrt:hb_ab} 
               ln {$Wrt:hb_im5} ln {$Wrt:hb_im4} ln {$Wrt:hb_im3} 
               ln {$Wrt:hb_im2} ln {$Wrt:hb_im1} ln {$Wrt:hb_ip0}  
               ln {$Wrt:hb_ip1} ln {$Wrt:hb_ip2} ln {$Wrt:hb_ip3} 
               ln {$Wrt:hb_ip4} ln {$Wrt:hb_ip5} ~
  hist:      ~ {$Wrt:hist} (/ +#/ {$Not} ln)+ ~  
  data:      ~ {$Wrt:data} ln+ ~

  # indexing production
  id:        ~ {$In:[fields c:header] $Out $Mov:62} /[A-Z0-9]+/ {$Wrt} ~
  comp:      ~ {$In:[fields c:compnd] $Out} (x{$Mov:10} words {$Len:60} ln)+ ~
  src:       ~ {$In:[fields c:source] $Out} (x{$Mov:10} words {$Len:60} ln)+ ~
  authors:   ~ {$In:[fields c:author] $Out} (x{$Mov:10} auts {$Len:60} ln)+ ~
  auts:      ~ aut (',' aut?)* ~
  aut:       ~ / *([^ ,]*\\.)([^ ,]*)/ {$Uniq:[s:"$2,$1"]} ~
  words:     ~ (/[A-Z0-9]+/ {$Uniq:$Itc} | /[^A-Z0-9]+/)+ ~
  n:         ~ {$In:[fields c:nums] $Out} num {$Wrt:resN} num {$Wrt:chainN} 
               num {$Wrt:ssbtot} num {$Wrt:ssbintra} num {$Wrt:ssbinter} ~
  surf:      ~ {$In:[fields c:surf] $Out} num {$Wrt} ~
  hb:        ~ {$In:[fields c:{hb hb_pb hb_ab hb_im5 hb_im4 hb_im3 hb_im2 
                   hb_im1 hb_ip0 hb_ip1 hp_ip2 hb_ip3 hb_ip4 hb_ip5}] $Out}
               num {$Wrt:$Itc} ~
  # html display
  h_com:     ~ {$In:[fields c:compnd t:html]}
               (/(E\\.C\\.|EC: *)([0-9]+\\.[0-9]+\\.[0-9]+\\.[0-9]+)/
	        {$Rep:{"$1($ParStr:enzymeR)" $2 $2}} |
                /./)+
             ~

  # other productions
  name:      ~  /[a-zA-Z0-9_]+/ ~
  num:       ~  /[0-9.]+/ ~
  word:      ~  /[^ ]+/ ~
  ln:        ~  /[^\n]*\n/ ~
  appLn:     ~  /[^\n]*\n/ {$App} ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/data/dssp/3apr.dssp']
  $JobTokens:[$job name:fields print:1]
  $JobNext:$job
}



:compnd t:html]}
               (/(E\\.C\\.|EC: *)([0-9]+\\.[0-9]+\\.[0-9]+\\.[0-9]+)/
	        {$Rep:{"$1($ParStr:enzymeR)" $2 $2}} |
                /./)+
             ~

  # other productions
  name:      ~  /[a-zA-Z0-9_]+/ ~
  num:       ~  /[0-9.]+/ ~
  word:      ~  /[^ ]+/ ~
  ln:        ~  /[^\n]*\n/ ~
  appLn:     ~  /[^\n]*\n/ {$App} ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fisrs/icarus/db/ecdc.is

$rules={
  entry:   ~ {init{$count=0} $out:entry $count=$count+1}
             ('ID' {$not} ln)*
             ('ID   ' {pre {$entryFip = $fip} $wrt} ln {$app} 
             ('//' {$not} ln {$app})*
              '//' {$app $fip:on})?
           ~
  # fields
  fields:  ~ {$in:entry $out} f_id f_xx f_acc f_xx f_def
             f_xx f_key? 
             f_xx f_org f_xx f_rl f_xx f_dr f_xx f_func f_map f_links
           ~
  f_id:    ~ {$wrt:id}   'ID   '  ln ~
  f_xx:    ~ ('XX' ln)* ~
  f_acc:   ~ {$wrt:acc}  ('AC   ' ln)* ~
  f_date:  ~ {$wrt:date} ('DT   ' ln)* ~
  f_def:   ~ {$wrt:def}  ('DE   ' ln)* ~
  f_key:   ~ {$wrt:key}  ('KW   ' ln)+ ~
  f_org:   ~ {$wrt:org}  ('OS   ' ln)* ~
  f_rl:    ~ {$wrt:rl}   ('RL   ' ln)* ~
  f_dr:    ~ {$wrt:dr}   ('DR   ' ln)* ~
  f_func:  ~ {$wrt:func} ('FT   FUNCTION' ln)* ~
  f_map:   ~ {$wrt:map}  ('FT   MAP' ln)* ~
  f_links: ~ {$wrt:link} ('FT   ' /(CDS|CONTIG)/ ln)* ~
  
  # indexing
  id:      ~ {$in:[fields c:id] $out:id} 'ID   '
             (/[A-Za-z0-9_][A-Za-z0-9_() -]+/ {$wrt} | ',' |
              /[^a-zA-Z0-9_ -]+/ )* ~
  acc:     ~ {$in:[fields c:acc] $out:acc} 'AC'   /[A-Z0-9_]+/? {$wrt} ~
  def:     ~ {$in:[fields c:def] $out} ( 'DE' ( /[A-Za-z0-9_]+/ {$wrt} | 
             /[^A-Za-z0-9_]+/ )* )* ~
  org:     ~ {$in:[fields c:org] $out:org} 'OS'   /[A-Za-z0-9_ ]+/ {$wrt} ~
  key:     ~ {$in:[fields c:key] $out:key} ('KW'   
              /[A-Za-z0-9_ -]+/? {$wrt} ln)* ~
  date:    ~ {$in:[fields c:date] $out} 'DT'
             datenum {$wrt:[s:$date c:cre]}     '(CREATED);'
             datenum {$wrt:[s:$date c:dupd]} '(DATA UPDATE);'
             datenum {$wrt:[s:$date c:iupd]} '(INFO UPDATE).' 
           ~ 
  allpos:  ~ {$in:[fields c:rule] $out}
             (/.*POSITIVE=([0-9]+)/ {$wrt:[s:$1]})? ~
  datenum: ~ {init {$month={JAN:1 FEB:2 MAR:3 APR:4 MAY:5 JUN:6 JUL:7 AUG:8 
                            SEP:9 OCT:10 NOV:11 DEC:12}}}
             /([A-Z][A-Z][A-Z])-([0-9]+)/ 
             {$date=$month.$1 * 100 + $2 * 10000} 
           ~ 
  links:   ~ {$in:[fields c:link] $out}
             (/DR/ (name {$wrt:swiss} ',' name ',' /[A-Z?]/ ';')* ln)*
             (/3D/ (name {$wrt:pdb} (';'|'.'))* ln)* 
             /DO/ name {$wrt:pd} 
           ~
  # table display 

  t_date:  ~ {$in:[fields c:date] $out} 
             /.* ([A-Z0-9-]+) *CREATED/ {$wrt:[s:$1]} ~

  # html display
  hl_links:~ {$in:[fields c:dr t:hl]}
             ('DR' 'EMBL;' name {$rep:{$parStr:emblR $ct $ct}} ln)* ~
  # other 
  name:    ~ /[a-zA-Z0-9_]+/ ~ 
  ln:      ~ /[^\n]*\n/ ~
} 

$fil =  $fileOpen:"/data/ecdc/div.dat"
$job = $jobNew:[prod:$rules skip:" "]

$jobNext:[$job file:$fil]
#for:{1 $jobTokens:[$job name:fields code:dr task:hl print:1] 1} {
$print:"-------->entry\n"
for:{1 $jobTokens:[$job name:fields code:id print:1] 1} {
#  $jobTokens:[$job name:acc print:1]
#  $jobTokens:[$job name:def print:1]
  $jobTokens:[$job name:fields print:1]
#  $jobTokens:[$job name:key print:1]
#  $jobTokens:[$job name:org print:1]
#  $jobTokens:[$job name:fields code:dr task:hl print:1]
  $jobEnd:$job
  $jobNext:[$job file:$fil]
  $print:"-------->entry\n"
}

 skip:" "]

$jobNext:[$job file:$fil]
#for:{1 $jobTokens:[$job name:fields code:dr task:hl print:1] 1} {
$print:"-------->entry\n"
for:{1 $jobTokens:[$job name:fields code:id print:1] 1} {
#  $jobTokens:[$job name:acc print:1]
#  $jobTokens:[$job name:def print:1]
  $jobTokens:[$job name:fields print:1]
#  $jobTokens:[$job name:key print:1]
#  $jobTokens:[$job name:org print:1]
#  $jobTokens:[$job name:fields code:dr task:hlsrs/icarus/db/embl.i
#
#    $RCSfile: embl.i,v $
#    $Revision: 1.15 $
#    $Date: 1997/03/12 19:06:40 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

EMBLNEW_DB:$library:[EMBLNEW group:@SEQUENCE_LIBS 
  format:@EMBL_FORMAT cachesize:6000 maxNameLen:12 
  subentries:@EmblnewFeatures_DB
  files:$file:em_new
]

EMBL_DB:$library:[EMBL group:@SEQUENCE_LIBS partSize:100000
  subentries:@EmblFeatures_DB
  format:@EMBL_FORMAT cachesize:6000 maxNameLen:12 files:{
    #orig format
#    $file:est1
#    $file:est2
#    $file:est3
#    $file:est4
#    $file:est5
#    $file:est6
#    $file:est7
#    $file:fun
#    $file:gss
#    $file:htg
#    $file:hum1
#    $file:hum2
#    $file:inv
#    $file:mam
#    $file:org
#    $file:patent
#    $file:phg
#    $file:pln
#    $file:pro
#    $file:rod
#    $file:sts
#    $file:syn
#    $file:unc
#    $file:vrl
#    $file:vrt 

    #gcg format
    $file:em_est1
    $file:em_est2
    $file:em_est3
    $file:em_est4
    $file:em_est5
    $file:em_est6
    $file:em_est7
    $file:em_est8
    $file:em_est9
    $file:em_ba
    $file:em_fun
    $file:em_gss
    $file:em_htg
    $file:em_hum1
    $file:em_hum2
    $file:em_in
    $file:em_om
    $file:em_or
    $file:em_ov
    $file:em_pat
    $file:em_ph
    $file:em_pl
    $file:em_ro
    $file:em_sts
    $file:em_sy
    $file:em_un
    $file:em_vi
  }
]

EMBL_FORMAT:$libformat:[syntax:@EMBL_SYNTAX contains:@DNASEQ_DATA
  tableFormat:left 
#fileType:{@DAT_FILE @SEQ_FILE} #orig format
  fileType:{@GCGREF_FILE @GCGSEQ_FILE} #GCG format
  fields:{
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:@DF_ALL
    $field:[@DF_Accession code:acc index:str indexToken:acc 
      tableToken:acc tableFormat:left]
    $field:[@DF_Division code:id index:str indexToken:div
      tableToken:div tableFormat:left]
    $field:[@DF_Molecule code:id index:str indexToken:mol
      tableToken:mol tableFormat:left]
#    $field:[@DF_DBOrigin code:acc index:str indexToken:dbOri
#      tableToken:dbOri tableFormat:left]
#    $field:[@DF_AccessionKey code:acc index:str indexToken:accKey
#      tableToken:accKey tableFormat:center]
    $field:[@DF_Description code:des index:str indexToken:des
      tableToken:'clFields|des']
    $field:[@DF_Keywords code:key index:str indexToken:key]
    $field:[@DF_Organism code:org index:str indexToken:org]
    $field:[@DF_Authors code:ra index:str indexToken:authors]
    $field:[@DF_Title code:rt index:str indexToken:ttl
      tableToken:'clFields|rt']
    $field:[@DF_Citation code:rl index:str indexToken:cit 
      tableToken:'clFields|rl']
    $field:[@DF_Date code:date index:int indexToken:date 
      tableToken:t_date]
    $field:[@DF_SeqLength code:sq  index:int indexToken:seqLen 
      tableToken:seqLen tableFormat:right]
    $field:[@DF_LINK code:dr]
    EMBLSeq:$field:[@DF_DNASequence token:gcgseq format:embl] #GCG format
#    EMBLSeq:$field:[@DF_DNASequence token:sequence format:embl] #orig format

    $field:[@DF_HeaderField name:'Feature Table Fields']
    $field:[@DF_FtKey code:ft index:str indexToken:ftKey 
      indexId:@SUBENTRY_ID tableToken:ftKey tableFormat:left]
    $field:[@DF_FtQualifier code:ft index:str indexToken:ftQual
      indexId:@SUBENTRY_ID]
    $field:[@DF_PID code:ft index:str indexToken:pid
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtDescription code:ft index:str indexToken:ftDes 
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtSource code:ft index:str indexToken:ftSrc
      indexId:@SUBENTRY_ID]
    $field:[@DF_ChrsNo code:ft index:str indexToken:chrsNo 
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtMap code:ft index:str indexToken:map
      indexId:@SUBENTRY_ID]
#    $field:[@DF_FtLength index:int indexToken:ftLen code:ft 
#      indexId:@SUBENTRY_ID]
  }
]


EMBL_SYNTAX:$syntax:[file:"SRSDB:embl.is" ignore:" \t"]
$syntax:[name:ftseq file:"SRSDB:ftseq.is" ignore:" \t\n"]

#$link:[@EMBL_DB to:@?GENBANK_DB   toField:@DF_ACCNO]
#$link:[@EMBL_DB to:@?PIR_DB       toField:@DF_ACCNO]
#$link:[@EMBL_DB to:@?REBASE_DB    toField:@DF_ID]
#$link:[@EMBL_DB to:@?OMIM_DB      toField:@DF_ID]
#$link:[@EMBL_DB to:@?MEDLINE_DB   toField:@DF_ID]


EmblFeatures_DB:$library:[EMBL_features format:@EmblFeature_Format]
EmblnewFeatures_DB:$library:[EMBLNEW_features format:@EmblFeature_Format]

EmblFeature_Format:$libformat:[syntax:@EMBL_SYNTAX  #idType:@SUBENTRY_ID
  tableFormat:left
  fields:{
    $field:[@DF_ID token:ftId]
#    $field:[@DF_Accession code:acc fromParent:y]
#    $field:[@DF_Description code:des fromParent:y]

    $field:[@DF_FtKey token:ft tableToken:'t_ft|key']
    $field:[@DF_FtQualifier token:ft tableToken:'t_ft|qual']
    $field:[@DF_PID token:ft tableToken:'t_ft|db_xref']
    $field:[@DF_FtDescription token:ft tableToken:'t_ft|note']
    $field:[@DF_FtGene token:ft tableToken:'t_ft|gene']
    $field:[@DF_FtProduct token:ft tableToken:'t_ft|product']
    $field:[@DF_FtPartial token:ft tableToken:'t_ft|partial']
    $field:[@DF_FtPseudo token:ft tableToken:'t_ft|pseudo']
    $field:[@DF_FtNumber token:ft tableToken:'t_ft|number']
    $field:[@DF_FtSource token:ft tableToken:ftSrc]
    $field:[@DF_ChrsNo token:ft tableToken:'t_ft|chromosome'] 
    $field:[@DF_FtMap token:ft tableToken:'t_ft|map']
    $field:[@DF_DNALocation token:ftLocat parent:@EMBLSeq
      tableFormat:listing]
  }
]

DF_FtGene:$srsfield:[Gene short:gen]
DF_FtProduct:$srsfield:[Product short:pro]
DF_FtPartial:$srsfield:[Partial short:par]
DF_FtPseudo:$srsfield:[Pseudo short:pse]
DF_FtNumber:$srsfield:[Number short:num]
F_FtNusrs/icarus/db/embl.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: embl.is,v $
#    $Revision: 1.16 $
#    $Date: 1997/03/17 23:21:01 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  ID:id      OG:org       KW:key   RN:rn  '//':sep
  AC:acc     OC:org       RP:rp    RT:rt  FH: fh
  DT:date    OS:org	  SQ:sq    RC:rc
  DE:des     CC:cmnt	  RL:rl    RA:ra
  NI:nid     DR:link	  RX:rx    XX:sep 
}

$rules={
  entry:     ~ {$In:[file:text] $Out  pre $Skip:0}
               ('ID  ' {$not} lnT?)*
               (/ID +([A-Z0-9]+)/ {$entryFip=$Fip $Wrt $entryName=$1} lnT {$App}
                (/(  |ID|>>)/ {$Not} lnT {$App})+ )? ~
  lnT:       ~ /[^\n]+\n?/ ~ # line terminator may be missing if truncated

  # extracting data fields
  fields:    ~ {$In:entry $Out $Skip:1} 
               (ftln |
               /../ { if:$Ct==$prev $App else $Wrt:$fn.$Ct
                       if:$fn.$Ct=="" $dp:"+++ unknown: $Ct in $entryName +++"
                       $prev=$Ct
                    } ln {$App})+ ~
  ftln:      ~ {$Wrt:ft} 'FT' ln ('FT     ' ln)* ~
  clFields:  ~ {$In:fields $Out $Skip:1}
               /.. */ ln {$Wrt:$Itc} (/.. */ ln {$App})* ~

  # parsing the sequence part from separate stream
  gcgseq:    ~ { $In:[file:seq] $Out}
               '>>>>' {$seqFip=$Fip} 
               (/[A-Z0-9]+_0/ {$Wrt:[s:$Ct] $s=$SeqNew:$Ct} seq 
               (/>>>>[A-Z0-9]+_[1-9]+/ {$SeqTrunc:[$s len:10000]} seq)+ |
               /[A-Z0-9]+/ {$Wrt:[s:$Ct] $s=$SeqNew:$Ct} seq) ~ 
  seq:       ~ /.*2BIT *Len:/ /[0-9]+/ {$len=$Ct} ln ln 
	       {$SeqGet2Bit:[$s file:$File len:$len]} 
               ('>>>>'{$Not} ln)* |
               /.*ASCII/ ln ln ('>>>>' {$Not} /.*/ {$SeqApp:[$s s:$Ct]})+
               x{$SeqMake:$s} ~

  sequence:  ~ {$In:[file:seq share:text] $Out 
                pre {$s=$SeqNew:$entryName $seqFip=$Fip} 
                $Wrt:[s:$entryName] $SeqMake:$s} 
               ('ID' {$Not} ln {$SeqApp:[$s s:$Ct]})* ~

  # for indexing
  i_id:      ~ {$In:[entry] $Out:id} /ID +/ name {$Wrt} ~
  i_div:     ~ {$In:[fields c:id] $Out:div}
                /ID +/ name  /[^;]+/ ';' /[^;]+/ ';' name {$Wrt} ~
  i_mol:     ~ {$In:[fields c:id] $Out:mol} 
               /ID +/ name  /[^;]+/ ';' /[^;]+/  {$Wrt} ~
  i_acc:     ~ {$In:[fields c:acc] $Out:acc} ('AC' (name {$Wrt} ';')+)+  ~
  i_nid:     ~ {$In:[fields c:nid] $Out:nid} 'NI' name {$Wrt}  ~
  i_dates:   ~ { $In:[fields c:date] $Out:date 
                 init $month={JAN:1 FEB:2 MAR:3 APR:4 MAY:5 JUN:6 JUL:7 AUG:8 
                              SEP:9 OCT:10 NOV:11 DEC:12}
               }
               /.* ([0-9]+)-([A-Z]+)-([0-9]+)[^\n]+Cre/ 
               {$Wrt:[credate s:($1 + $month.$2*100 + $3*10000)]} ~
  des:       ~ {$In:[fields c:des] $Out} 
               ('DE' (/\\(EC *([0-9]+\\.[0-9]+\\.[0-9]+\\.[0-9]+)/
               {$Wrt:[s:$1]}| word{$Wrt} | sp)+ ln)+ ~ 
  org:       ~ {$In:[fields c:org] $Out} 
               ('OC' (/[^;.\n]+/ {$Wrt} | /[^\n]/)*)+ |
                'OS' /[^(\n]+/ {$Wrt:[s:$Trim:$Ct]} 
                ('(' (/[^ \n)]+/ | /[^)]/)+)? |
                'OG'  /[^\n;.]+/ {$Wrt} ~
  key:       ~ {$In:[fields c:key] $Out} 
               ('KW' (/[^\n;.]+/ {$Wrt} | /[^\n]/)+)+ ~ 
  authors:   ~ {$In:[fields c:ra] $Out}
               (/RA/ (/([^.,\n]+) +([^,;\n]+)/ {$Uniq:[s:"$1,$2"]} /[,;]/)*
               ln)* ~
  ttl:       ~ {$In:[fields c:rt] $Out} (tag (word {$Wrt} | sp)* ln)+ ~ 
  cit:       ~ {$In:[fields c:rl] $Out} 
               tag / *([^\n]+) ([0-9]+):([0-9]+)-[0-9]+\\(([0-9]+)\\)/?


               {$Uniq:[jnl s:$Trim:$1] $Uniq:[vol s:$2] $Uniq:[page s:"$3-"] 
               $Uniq:[year s:$4]} ~
  accKey:    ~ {$In:[fields c:acc] $Out} 'AC' /[A-Z]+/ {$Wrt} ~
  dbOri:     ~ {$In:[fields c:acc] $Out
                 init { $dbOriN={
                         A:1 F:1 V:1 X:1 Y:1 Z:1
                         AA:2 AC:2 AD:2 B:2 G:2 H:2 I:2 J:2 K:2 
                         L:2 M:2 N:2 R:2 S:2 T:2 U:2 W:2 
                         AB:3 C:3 D:3 E:3}
                       $dbName={1:EMBL 2:GenBank 3:DDBJ}
                 }
               } 
               'AC' /[A-Z]+/ {$Wrt:[s:$dbName.$dbOriN.$Ct]} ~
  i_seqLen:  ~ {$In:[fields c:sq] $Out:seqLen}
               'SQ   Sequence' /[0-9]+/ {$Wrt} ~

  # indexing features
  ftWord:    ~ /[^" ,;:()\n.-]+/ ~ #"
  ftSep:     ~ /[ ,;.:()-]+/ ~
  ftKey:     ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               'FT' /[^ ]+/ {$Wrt:[n:$ftN]} ~
  ftQual:    ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               /[^\/]+/ 
               (/\/([a-zA-Z0-9_]+)/ {$Wrt:[s:$1 n:$ftN]} (/=[a-zA-Z0-9_]+/ |
               /="[^"]+"/)? /[^\/]+/)* ~ #"
  chrsNo:    ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               /.+\/chromosome="?/ 
               (/[^\n\" ]+/ {$Uniq:[n:$ftN]} | '\nFT' | ' ')+ ~ #"
  ftSrc:     ~ {$In:[fields c:ft count:ft var:$ftN] $Out} (/[^\/]+\// (
           /(tissue_type|cell_line|organism|strain|dev_stage|sex|clone_lib)="/ 
                ('\nFT' | ftWord {$Uniq:[n:$ftN]} | ftSep)+)?)* ~
  ftDes:     ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               (/[^\/]+\// (/[^\/]+\/(product|note|gene)="/ 
                ('\nFT' | /NCBI gi: *[0-9]+/ | 
                 ftWord {$Uniq:[n:$ftN]} | ftSep)+)?)* ~
  map:       ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               /.+\/map="/ (/[^a-zA-Z0-9"]+/|/[a-zA-Z0-9]+/{$Wrt:[n:$ftN]})+ #"
             ~
  pid:       ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               (/db_xref="?PID:([0-9a-zA-Z]+)/ {$Wrt:[n:$ftN s:$1]} |
                /[^\/]+\// )+ ~
  range:     ~ /([A-Z0-9]+:)?([0-9]+)\\. *\\.([0-9A-Z]+:)?([0-9]+)/ 
               {$l=$4-$2+1} ~
  ftLen:     ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               /[^ ]+/ (range {$Wrt:[n:$ftN s:$l]} | /.*join\\(/ {$ftl=0} 
                (range{$ftl+=$l} ','?)* ')'? {$Wrt:[n:$ftN s:$ftl]})? ~

  # displaying features
  ftClean:   ~ {$In:[fields c:ft count:ft var:$ftN select:$subEntryN] $Out } 
               'FT' ln {$Wrt} ('FT' ln {$App})* ~
  ftLoc:     ~ {$In:ftClean $Out} /[^ ]+/ /[^\/]+/ {$Wrt} ~
  ft:        ~ {$In:[fields c:ft count:ft var:$ftN select:$subEntryN] $Out}
               /.*/ {$Wrt} ~
  ftId:      ~ {$In:[fields c:id] $Out} 
               /.. *([A-Z0-9]+)/ {$Wrt:[s:"ID   $1\_$subEntryN;  parent: $1"]}~
  h_ftId:    ~ {$In:[ftId t:html]} /.*parent: */ 
               /[A-Z0-9]+/ {$Rep:{$ParStr:emblIdR $Ct $Ct}} ~
  t_ft:      ~ {$In:ftClean $Out} /(<A HREF)?[^ ]+/ {$Wrt:key} 
               /[^\/]+/ t_qual* ~
  t_qual:    ~ /[ \n]*\/([^ \n=]+)/ {$qn=$1 $Uniq:[qual s:$1]} 
               qualval? {$Wrt:[$qn s:$qv]} ~
  qualval:   ~ {pre $qv=""} /=([a-zA-Z0-9_]+)/ {$qv=$1} | 
               /="([^"]+)"/ {$qv=$1} | x{$qv='+'} ~

  # extracting feature sequences"

  ftCleanIter: ~ {$In:[fields c:ft] $Out } 
               'FT' ln {$Wrt} ('FT' ln {$App})* ~
  ftLocat:    ~ {$In:ftClean $Out init {$SdbFunctions}}
               /(<A HREF)?[^ ]+/ /[^\/]+/ {$Wrt} ~
               
  # table display
  t_date:    ~ {$In:[fields c:date] $Out} tag /[0-9A-Z-]+/ {$Wrt} ~

  # printing in HTML format
  h_ft:      ~ {$In:[fields c:ft t:html count:ft var:$ftN]} 
               'FT' /[^ ]+/ {$Rep:{$ParStr:emblFeatR $entryName $ftN $Ct}}  
#               /[^\/]+/ 
#               (/\/([a-zA-Z0-9_]+)/ {$Rep:{$ParStr:emblFtQualR $1 $Ct}}
#               (/=[a-zA-Z0-9_]+/ | /="[^"]+"/)? /[^\/]+/)* 
             ~
  h_id:      ~ {$In:[fields c:id t:html]} /../ name {$entryName=$Ct} ~
  h_rx:      ~ {$In:[fields c:rx t:html]}
               /../ 'MEDLINE;' /[0-9]+/ {$Rep:{$ParStr:medlineR $Ct $Ct}} ~
  htmlTag:   ~ /<[^<>]*>/ ~
  h_links:   ~ {$In:[fields c:link t:html] 
                init{$hl={
                       'SWISS-PROT':                    swissR
                       DICTYDB:   dictydbR   GCRDB:     gcrdbR
                       MAIZEDB:   maizedbR   WORMPEP:   wormpepR
                       LISTA:     listaR  
                       PIR:       pirR       YEPD:      yepdR        
                       SGD:       sgdR       STYGENE:   stygeneR     
                       HIV:       hivR         
                       ECOGENE:   ecogeneR   ECO2DBASE: eco2dbaseR   
                       MIM:       mimR       SUBTILIST: subtilistR   
                       FLYBASE:   flybaseR     
                       TRANSFAC:  transfacR  REBASE:    rebaseR
                     } 
                    } 
               }
               (/DR/ dbName {$db=$Ct} ';' 
                accno {$Rep:{$ParStr:$hl.$db $Ct $Ct}} ln)*
             ~
  # other stuff

  tag:       ~ /[A-Z][A-Z]/ ~
  word:      ~ /[^" ,;:()\/=\n.-]+/ ~
  sp:        ~ /[ ,;.:()\/=-]+/ ~
  lnCode:    ~ /\n[A-Z][A-Z]/ ~
  ln:        ~ /[^\n]*\n/ ~
  accno:     ~ /[A-Z0-9]+/ ~
  num:       ~ /(<|>)?[0-9?]+/ ~
  name:      ~ /[a-zA-Z0-9_-]+/ ~ 
  dbName:    ~ /[^;]+/ ~ 
}

if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/data/gcg/gcgembl/em_ba.ref']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:acc print:0] 
    $JobTokens:[$job name:t_ft print:1]
    $JobNext:$job
    #$print:"-------->entry\n"
  }
}


   ~ /[^" ,;:()\/=\n.-]+/ ~
  sp:        ~ /[ ,;.:()\/=-]+/ ~
  lnCode:    ~ /\n[A-Z][A-Z]/ ~
  ln:        ~ /[^\n]*\n/ ~
  accno:     ~ /[A-Z0-9]+/ ~
  num:       ~ /(<|>)?[0-9?]+/ ~
  name:      ~ /[a-zA-Z0-9_-]+/ ~ 
  dbName:    ~ /[^;]+/ ~ 
}

if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/data/gcg/gcgembl/em_ba.ref']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:acc print:0] 
    $JobTokens:[$job name:t_ft print:1]
    $JobNext:$job
    #$srs/icarus/db/embl.it
#    
#    $RCSfile: embl.it,v $
#    $Revision: 1.3 $
#    $Date: 1996/10/10 16:47:04 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |The European Bioinformatics Institute (EBI) maintains and distributes
    |the EMBL Nucleotide Sequence database, Europe's primary nucleotide
    |sequence data resource. The EBI also maintains and distributes the
    |SWISS-PROT Protein Sequence database, in collaboration with Amos
    |Bairoch of the University of Geneva. Over fifty additional specialist
    |molecular biology databases, as well as software and documentation
    |of interest to molecular biologists are available. The EBI network
    |services include database searching and sequence similarity searching
    |facilities.
  www:
    |<A HREF="http://www.ebi.ac.uk">\
    |http://www.ebi.ac.uk</A>
  citation:
    |Patricia Rodriguez-Tomé , Peter J. Stoehr , Graham N. Cameron and Tomas P.
    |Flores, "The European Bioinformatics Institute (EBI) databases",
    |Nucleic Acids Res.
    |24:(6-13), 1996
  ftpSite:''
  date:
    |25 Jul 1996
  signature:
    |Anatoly Ulyanov
}
interest to molecular biologists are available. The EBI network
    |services include database searching and sequence similarity searching
    |facilities.
  www:
    |<A HREF="http://www.ebi.ac.uk">\
    |http://www.ebi.ac.uk</A>
  citation:
    |Patricia Rodriguez-Tomé , Peter srs/icarus/db/emp.i
#    $RCSfile: emp.i,v $
#    $Revision: 1.9 $
#    $Date: 1997/03/17 23:21:02 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


EMP_DB:$library:[EMP group:@SEQRELATED_LIBS 
  comment:"Metabolic pathways - Selkov." 
  format:@EMP_FORMAT maxNameLen:30 ifiles:{"emp.i emp.is"}
  files:{
    $file:8612  $file:8912  $file:9211
    $file:8701  $file:9001  $file:9212
    $file:8702  $file:9002  $file:9301
    $file:8703  $file:9003  $file:9302
    $file:8704  $file:9004  $file:9303
    $file:8705  $file:9005  $file:9304
    $file:8706  $file:9006  $file:9305
    $file:8707  $file:9007  $file:9306
    $file:8708  $file:9008  $file:9307
    $file:8709  $file:9009  $file:9308
    $file:8710  $file:9010  $file:9309
    $file:8711  $file:9011  $file:9310
    $file:8712  $file:9012  $file:9311
    $file:8801  $file:9101  $file:9312
    $file:8802  $file:9102  $file:9401
    $file:8803  $file:9103  $file:9402
    $file:8804  $file:9104  $file:9403
    $file:8805  $file:9105  $file:9404
    $file:8806  $file:9106  $file:9405
    $file:8807  $file:9107  $file:9406
    $file:8808  $file:9108  $file:9407
    $file:8810  $file:9109  $file:9408
    $file:8811  $file:9110  $file:9409
    $file:8812  $file:9111  $file:9410
    $file:8901  $file:9112  $file:9411
    $file:8902  $file:9201  $file:9412
    $file:8903  $file:9202  $file:9501
    $file:8904  $file:9203  $file:9502
    $file:8905  $file:9204  $file:9503
    $file:8906  $file:9205  $file:9504
    $file:8907  $file:9206  $file:9509
    $file:8908  $file:9207  
    $file:8909  $file:9208  
    $file:8910  $file:9209
    $file:8911  $file:9210
  }
]

$link:[@EMP_DB to:@?MPW_DB toField:@DF_Name token:'links|mpw']
$link:[@EMP_DB to:@?ENZYME_DB toField:@DF_ID token:'links|enzyme']

EMP_FORMAT:$libformat:[fileType:@EMP_FILE syntax:@EMP_SYNTAX 
  tableFormat:left printFormat:topicList
  fields:{
    $field:@DF_ALL
    $field:[@DF_LINK index:link indexToken:links]
    $field:[@DF_HeaderField name:'Entry Identification']
    $field:[@DF_ID  code: AN index:id indexToken:id]
    $field:[@DF_StaffFootnote  code: '**']
    $field:[@DF_AnnotatorsFootnote  code: '***']
    $field:[@DF_ReferenceNumber  code: RN]

    $field:[@DF_HeaderField name:'Bibliographic Description']
    $field:[@DF_Author  code: AU]
    $field:[@DF_OrganizationalSource  code:OS
      index:str indexToken:'words|OS']
#    $field:[@DF_Title  code: TI
#      index:str indexToken:'words|TI']
    $field:[@DF_BibliographicSource  code: SO]
    $field:[@DF_PublicationYear  code: YR]
    $field:[@DF_SourceCode  code: SC]
    $field:[@DF_DocumentType  code: DT]
    $field:[@DF_Language  code: LA]
    $field:[@DF_CategoryCode  code: CC]
    $field:[@DF_IndexTerms  code: IT]
    $field:[@DF_SupplementaryTerms  code: ST]
    $field:[@DF_Abstract  code: AB]
    $field:[@DF_AnnotatorsAbstract  code: AAB]
    $field:[@DF_Reference  code: REF]

    $field:[@DF_HeaderField name:'Biological Source']
    $field:[@DF_CellLine  code: CLI]
    $field:[@DF_CellType  code: CTY]
    $field:[@DF_OrganismSystematicName  code: OR 
      index:str indexToken:'words|OR']
    $field:[@DF_OrganismSubspecies  code: SSP]
    $field:[@DF_OrganismCommonName  code: OCN]
    $field:[@DF_TaxonomicGroup  code: TG 
            index:str indexToken:'words|TG']
    $field:[@DF_CellSpeciesExtracellFluid  code: CS]
    $field:[@DF_Strain  code: STR]
    $field:[@DF_Genotype  code: GET]
    $field:[@DF_Phenotype  code: PHT]
    $field:[@DF_MetabolicType  code: MET]
    $field:[@DF_Age  code: AGE]
    $field:[@DF_Sex  code: SEX]
    $field:[@DF_OrganismWeight  code: WT]
    $field:[@DF_KeepingConditions  code: KCO]
    $field:[@DF_OrganismTreatment  code: OTR]
    $field:[@DF_PhysiologicalState  code: PHS]
    $field:[@DF_DevelopmentalStage  code: DEV]
    $field:[@DF_Pathology  code: PAT]
    $field:[@DF_LightConditions  code: LC]
    $field:[@DF_LightIntensity  code: LI]
    $field:[@DF_WaveLength  code: WL]
    $field:[@DF_TimeOftheDay  code: TOD]
    $field:[@DF_CellCultureCategory  code: CCC]

    $field:[@DF_HeaderField name:'Organism Phenotype']
    $field:[@DF_SubspeciesName  code: SSP]
    $field:[@DF_TypeSpecies  code: TSP]
    $field:[@DF_TypeStrainName  code: TSN]
    $field:[@DF_BactClassificationCode  code: BC]
#    $field:[@DF_OrganismCommonName  code: OCN]
#    $field:[@DF_TaxonomicGroup  code: TG]
    $field:[@DF_CellCultureCategoryCode  code: CCC]
#    $field:[@DF_CellType  code: CTY]
    $field:[@DF_molGCContentInDNA  code: GCC]
    $field:[@DF_GenomeSizeDaltons  code: GSZ]
    $field:[@DF_ColonyMorphology  code: CMO]
    $field:[@DF_CellMorphology  code: MOR]
    $field:[@DF_PeptidoglycanComposition  code: PGC]
    $field:[@DF_MembraneLipidComposition  code: LIP]
    $field:[@DF_CytochromePresent  code: CYT]
    $field:[@DF_MembrIsoprenoidQuinonesPresent  code: QUI]
    $field:[@DF_FlagellarArrangement  code: FLA]
    $field:[@DF_Physiology  code: PHY]
    $field:[@DF_CellOrSporeMotility  code: MOT]
    $field:[@DF_ConcentrationInCultivationMedium  code: CON]
    $field:[@DF_AbsoluteRequirementForGrowth  code: AR]
    $field:[@DF_GrowthInhibitor  code: GRI]
    $field:[@DF_GrowthActivator  code: GRA]
    $field:[@DF_CommonAntigeneName  code: CAN]
    $field:[@DF_AlternativePathwayNames  code: LAP]
    $field:[@DF_SystematicPathwayNames  code: LSP]
    $field:[@DF_EnzymeProduced  code: ENP]
    $field:[@DF_FermentationProduct  code: FPR]
    $field:[@DF_ProductionOf  code: PRD]
    $field:[@DF_AcidProducedFrom  code: ACD]
    $field:[@DF_GasProducedFrom  code: GAS]
    $field:[@DF_CarbonSourceUsed  code: CSO]
    $field:[@DF_NitrogenSourceUsed  code: NSO]
    $field:[@DF_Test  code: TST]
    $field:[@DF_NaturalHost  code: NHO]
    $field:[@DF_PathogenicityForHost  code: PGY]
    $field:[@DF_HostPathologyDescription  code: HPD]
    $field:[@DF_Habitat  code: HAB]
    $field:[@DF_GeographicalDistribution  code: GEO]
    $field:[@DF_CulturePreservationConditions  code: CPC]

    $field:[@DF_HeaderField name:'Host']
    $field:[@DF_LaboratoryHostSystematicName  code: HST]
    $field:[@DF_HostAge  code: HAG]
    $field:[@DF_HostCommonName  code: HCN]
    $field:[@DF_HostTaxonomicGroup  code: HTG]
    $field:[@DF_HostDevelopmentalStage  code: HDS]
    $field:[@DF_HostStrainName  code: HSN]
    $field:[@DF_HostSex  code: HSX]
    $field:[@DF_HostGenotype  code: HGT]
    $field:[@DF_HostPhenotype  code: HPT]
    $field:[@DF_HostSubcellularFraction  code: HSF]
    $field:[@DF_HostCellSpecies  code: HCS]
    $field:[@DF_HostCellularLocation  code: HSL]
    $field:[@DF_HostCellCultureCategory  code: HCC]
    $field:[@DF_HostCellLine  code: HCL]
    $field:[@DF_HostCellType  code: HCT]
    $field:[@DF_HostTreatment  code: HTR]
    $field:[@DF_NaturalHostSystematicName  code: NHO]
    $field:[@DF_ClonedVector  code: CLV]

    $field:[@DF_HeaderField name:'Biochemical Genetics']
    $field:[@DF_GeneAcronym  code: GN]
    $field:[@DF_AlternativeGeneAcronym  code: AGA]
    $field:[@DF_GeneMnemonics  code: GMN]
    $field:[@DF_GeneProduct  code: GNP]
    $field:[@DF_GeneticMapPosition  code: GMP]
    $field:[@DF_GeneLocation  code: GL]
    $field:[@DF_CoordinatelyExpressedGenes  code: CEG]
    $field:[@DF_NucleotideSequenceCrossref  code: NS]
    $field:[@DF_TypeofSynthesis  code: SYN]
    $field:[@DF_Inducer  code: IND]
    $field:[@DF_InductionDegree  code: IDE]
    $field:[@DF_Repressor  code: REP]
    $field:[@DF_RepressionDegree  code: RDE]
    $field:[@DF_DegradationActivator  code: DAC]
    $field:[@DF_DegradationInhibitor  code: DIN]
    $field:[@DF_EnzymeHalfLifeTime  code: T05]

    $field:[@DF_HeaderField name:'Cell Cultivation Conditions']
    $field:[@DF_CultivationConditions  code: CUC]
    $field:[@DF_CultivationTemperature  code: CUT]
    $field:[@DF_DilutionRate  code: DR]
    $field:[@DF_CultivationMedium  code: MED]
    $field:[@DF_NitrogenSource  code: NSO]
    $field:[@DF_CarbonSource  code: CSO]
    $field:[@DF_LimitingSubstrate  code: LS]
    $field:[@DF_GrowthSubstrate  code: GS]
    $field:[@DF_CultureDensity  code: CD]
    $field:[@DF_CellCyclePhase  code: CCP]
    $field:[@DF_GrowthPhase  code: GP]
    $field:[@DF_GenerationTime  code: GT]
    $field:[@DF_CellCyclePeriod  code: CPE]
    $field:[@DF_GrowthRate  code: GRR]
    $field:[@DF_SpecificGrowthRate  code: SGR]
    $field:[@DF_GrowthMode  code: GM]
    $field:[@DF_GrowthYield  code: GY]
    $field:[@DF_ColonySize  code: CSZ]

    $field:[@DF_HeaderField name:'Metabolism']
    $field:[@DF_MetabolicPathwayName  code: MPW]
    $field:[@DF_SystematicPathwayName  code: SPN]
    $field:[@DF_AlternativePathwayName  code: APN]
    $field:[@DF_OverallReaction  code: OVR]
    $field:[@DF_OverallReactionVelocity  code: VEL]
    $field:[@DF_MetabolicState  code: MES]

    $field:[@DF_HeaderField name:'Enzyme and Reaction']
    $field:[@DF_SubcellularLocation  code: SL]
    $field:[@DF_SubcellularFraction  code: SF]
    $field:[@DF_ActiveSiteLocation  code: ASL]
    $field:[@DF_MultifunctionalEnzymeName  code: MF]
    $field:[@DF_MultifunctionalEnzymeForm  code: MFF]
    $field:[@DF_AltMultifunctionalEnzymeName  code: AMF]
    $field:[@DF_MultifunctionalEnzymeCode  code: MFC]
    $field:[@DF_RecommendedEnzymeName  code: EN]
    $field:[@DF_SystematicEnzymeName  code: SEN]
    $field:[@DF_OtherEnzymeName  code: ON]
    $field:[@DF_EnzymeCode  code: EC index:str indexToken:enzCode]
    $field:[@DF_EnzymeForm  code: EF]
    $field:[@DF_ProteinName  code: PN]
    $field:[@DF_NonCatalyticFunction  code: NCF]
    $field:[@DF_ProteinForm  code: PRF]
#    $field:[@DF_ProteinConcentration  code: PCO]
    $field:[@DF_IsozymeNumber  code: IZN]
    $field:[@DF_ReactionEquation  code: RE
      index:str indexToken:'words|RE']
    $field:[@DF_ReactionIdentifier  code: RI]
    $field:[@DF_ReactionType  code: RET]
    $field:[@DF_ElementaryStepEquation  code: ESE]
#was never found
#    $field:[@DF_Substrate  code: SU
#      index:str indexToken:'words|SU']
    $field:[@DF_SiteofEnzymeAction  code: SEA]
    $field:[@DF_NonSubstrate  code: NSU
      index:str indexToken:'words|NSU']
    $field:[@DF_Coenzyme  code: CO]
    $field:[@DF_NonCoenzyme  code: NCO]
    $field:[@DF_Product  code: PR]
    $field:[@DF_NonProduct  code: NPR]
    $field:[@DF_AbsoluteRequirement  code: AR]
    $field:[@DF_ReactionPhase  code: RP]
    $field:[@DF_Reversibility  code: REV]
    $field:[@DF_ReactionDirection  code: RD]
    $field:[@DF_EnzymeApplication  code: APP]

    $field:[@DF_HeaderField name:'Assay and Purification']
    $field:[@DF_AssayConditions  code: ASS]
    $field:[@DF_TissueActivity  code: TA]
    $field:[@DF_PreparationSpecificActivity  code: PA]
    $field:[@DF_SpecificActivity  code: SA
      index:str indexToken:'words|SA']
    $field:[@DF_PurificationSteps  code: PS
      index:str indexToken:'words|PS']
    $field:[@DF_PurifFactorAndPurityDegree  code: PF]
    $field:[@DF_Yield  code: YD]
    $field:[@DF_EnzymeConcentration  code: ECO]
    $field:[@DF_ProteinConcentration  code: PCO]
    $field:[@DF_TotalProteinContent  code: TPC]
    $field:[@DF_PreparationSpecificBinding  code: PB]
    $field:[@DF_SpecificBinding  code: SB]
    $field:[@DF_StorageConditions  code: STO]
    $field:[@DF_Buffer  code: BUF]
    $field:[@DF_pHValue  code: PH]
    $field:[@DF_Temperature  code: TEM]
    $field:[@DF_IonicStrength  code: IS]
    $field:[@DF_OptimalConditions  code: OC]

    $field:[@DF_HeaderField name:'Enzyme Kinetics']
    $field:[@DF_TypeofKineticsOrFunctDependence  code: KT]
    $field:[@DF_MaxReactionVelocity  code: VM]
    $field:[@DF_PreparationMaxVelocity  code: PVM]
    $field:[@DF_RelativeMaxVelocity  code: RVM]
    $field:[@DF_RelativeActivity  code: RA]
    $field:[@DF_MolecularActivity  code: MA]
    $field:[@DF_CatalyticConst  code: KC]
    $field:[@DF_MichaelisConst  code: KM
      index:str indexToken:'words|KM']
    $field:[@DF_HalfSaturatingSubstrateConc  code: S05]
    $field:[@DF_Conditions  code: CND]
    $field:[@DF_CatalyticEfficiency  code: CEF]
    $field:[@DF_ApparentCatalyticConst  code: ACC]
    $field:[@DF_Ligand  code: LIG]
    $field:[@DF_FixedLigand  code: FL]
    $field:[@DF_VariableLigand  code: VL]
    $field:[@DF_MaxSpecificBinding  code: BM]
    $field:[@DF_HillsNumber  code: NH]
    $field:[@DF_ReactionMechanism  code: ME]
    $field:[@DF_RateLaw  code: RL]
    $field:[@DF_RateConstDesignation  code: RCD]
    $field:[@DF_RateConst  code: RC]
    $field:[@DF_TimeConst  code: TC]
    $field:[@DF_FunctionalDependence  code: FUN]

    $field:[@DF_HeaderField name:'Enzyme Regulation']
    $field:[@DF_Activator  code: AC]
    $field:[@DF_ActivationType  code: ACT]
    $field:[@DF_ActivationDegree  code: AD]
    $field:[@DF_MaxActivationDegree  code: MAD]
    $field:[@DF_ActivationConst  code: KA]
    $field:[@DF_HalfActivatingConcentration  code: A05]
    $field:[@DF_Inhibitor  code: IN
      index:str indexToken:'words|IN']
    $field:[@DF_InhibitionType  code: INT]
    $field:[@DF_InhibitionDegree  code: ID]
    $field:[@DF_MaxInhibitionDegree  code: MID]
    $field:[@DF_InhibitionConst  code: KI]
    $field:[@DF_HalfInhibitingConc  code: I05]
    $field:[@DF_InterceptInhibitionConst  code: KII]
    $field:[@DF_SlopeInhibitionConst  code: KIS]
    $field:[@DF_NonInfluencingCompound  code: NIC]

    $field:[@DF_HeaderField name:'Enzyme Modification']
    $field:[@DF_EnzymeModificationProcess  code: MP]
    $field:[@DF_EnzymeModifier  code: MOD]
    $field:[@DF_EnzymeBindingPartner  code: BPA]
    $field:[@DF_ModifyingEnzymeName  code: MEN]
    $field:[@DF_ModifyingEnzymeCode  code: MEC]
    $field:[@DF_ModifyingEnzymeForm  code: MEF]
    $field:[@DF_ModificationResidual  code: MRE]
    $field:[@DF_ModificationMechanism  code: MME]
    $field:[@DF_ModificationPromotor  code: MPR]
    $field:[@DF_ModificationAntagonist  code: MAN]
    $field:[@DF_ModificationEffect  code: MOE]
    $field:[@DF_EnzymeTreatment  code: TR]
    $field:[@DF_TreatmentEffect  code: EFF]

    $field:[@DF_HeaderField name:'Enzyme Structure']
    $field:[@DF_MolecularMass  code: MM
      index:str indexToken:'words|MM']
    $field:[@DF_SedimentationConst  code: ESC]
    $field:[@DF_SubunitMass  code: SM]
    $field:[@DF_SubunitSedimentationConst  code: SSC]
    $field:[@DF_SubunitName  code: SUN]
    $field:[@DF_SubunitDesignation  code: SUD]
    $field:[@DF_SubunitFunction  code: SUF]
    $field:[@DF_SubunitNumber  code: SN]
    $field:[@DF_SubunitComposition  code: SUC]
    $field:[@DF_SubunitStructure  code: SUS]
    $field:[@DF_SubunitBindingType  code: SBT]
    $field:[@DF_MolecularSymmetry  code: MS]
    $field:[@DF_PolypeptideChainNumber  code: PCN]
    $field:[@DF_ProstheticGroup  code: PRG]
    $field:[@DF_ProstheticGroupNumber  code: PGN]
    $field:[@DF_BindingType  code: BT]
    $field:[@DF_SHGroupNumber  code: SHN]
    $field:[@DF_DisulfideBondNumber  code: SSN]
    $field:[@DF_BindingSiteName  code: SNA]
    $field:[@DF_BindingSiteNumber  code: SNU]
    $field:[@DF_SiteAminoAcidSequence  code: SSQ]
    $field:[@DF_BindingSiteResidual  code: SRE]
    $field:[@DF_AminoAcids  code: AA]
    $field:[@DF_Content  code: CNT]
    $field:[@DF_AminoAcidSequenceOrCrossref  code: AAS]
    $field:[@DF_EnzymeComposition  code: ENC]
    $field:[@DF_TerminalAminoAcids  code: TAA]
    $field:[@DF_SignalPeptide  code: SP]
    $field:[@DF_SignalPeptideLength  code: SPL]
    $field:[@DF_IntramolecularLocation  code: LOC]
    $field:[@DF_PrimaryStructureHomology  code: HOM]

    $field:[@DF_HeaderField name:'Equilibrium and Thermodynamics']
    $field:[@DF_EquilibConst  code: KEQ]
    $field:[@DF_EquilibConstFormula  code: KEF]
    $field:[@DF_DissociationConstDesignation  code: KDD]
    $field:[@DF_DissociationConst  code: KD]
    $field:[@DF_AssociationConstDesignation  code: KAD]
    $field:[@DF_AssociationConst  code: KAS]
    $field:[@DF_EquilibConstDesignation  code: KED]
    $field:[@DF_ElementaryStepEquilibConst  code: KEE]
    $field:[@DF_MassActionRatio  code: MAR]
    $field:[@DF_StandardFreeEnergyChange  code: DG0]
    $field:[@DF_StandardEntropyChange  code: DS0]
    $field:[@DF_StandardEnthalpyChange  code: DH0]
    $field:[@DF_ActivationEnergy  code: EA]
    $field:[@DF_ActivationFreeEnergyChange  code: DGA]
    $field:[@DF_ActivationEnthalpyChange  code: DHA]
    $field:[@DF_ActivationEntropyChange  code: DSA]
    $field:[@DF_StandardRedoxPotential  code: E0]
    $field:[@DF_ElectronTransferNumber  code: ETN]
    $field:[@DF_HeatCapacityChange  code: DCP]

    $field:[@DF_HeaderField name:'Physical Chemistry and Spectral Properties']
    $field:[@DF_IsoelectricPoint  code: IP]
    $field:[@DF_OptimalPH  code: PHO]
    $field:[@DF_pHDependentParameter  code: PHD]
    $field:[@DF_pHRange  code: PHR]
    $field:[@DF_pKValues  code: PKV]
    $field:[@DF_InactivationConst  code: IC]
    $field:[@DF_OptimalTemperature  code: TO]
    $field:[@DF_TempDependentParameter  code: TD]
    $field:[@DF_TemperatureRange  code: TER]
    $field:[@DF_TemperatureCoefficient  code: Q10]
    $field:[@DF_NameofParameterorVariable  code: PAR]
    $field:[@DF_ValueofParameterorVariable  code: VAL]
    $field:[@DF_AbsorptionMaxWaveLength  code: AM]
    $field:[@DF_AbsorptionCoefficient  code: ABC]
    $field:[@DF_MolarAbsorptionCoefficient  code: MAC]
    $field:[@DF_AbsorptionShoulder  code: ASH]
    $field:[@DF_FluorescenceMax  code: FM]
    $field:[@DF_CDSpectrumMax  code: CMA]
    $field:[@DF_CDSpectrumMin  code: CMI]
    $field:[@DF_CDSpectrumShoulder  code: CSH]
    $field:[@DF_EPRSignals  code: EPR]

    $field:[@DF_HeaderField name:'Immunochemistry']
    $field:[@DF_Antigene  code: AGN]
    $field:[@DF_Antibody  code: ABD]
    $field:[@DF_CrossReactivity  code: CRR]

    $field:[@DF_HeaderField name:'Common fields']
    $field:[@DF_Abbreviation  code: ABB]
    $field:[@DF_Addition  code: ADD]
    $field:[@DF_BiologicalFunction  code: BFN]
    $field:[@DF_Comments  code: COM]
    $field:[@DF_Concentration  code: CON]
    $field:[@DF_Designation  code: DES]
    $field:[@DF_Formula  code: FOR]
    $field:[@DF_Method  code: MT]
    $field:[@DF_OscillationPeriod  code: OP]
    $field:[@DF_PhaseDifference  code: PDI]
    $field:[@DF_Process  code: PRS]
    $field:[@DF_Property  code: PRY]
    $field:[@DF_SubstanceComposition  code: SCN]
    $field:[@DF_StandardDeviation  code: SD]
    $field:[@DF_Substance  code: SUB]
    $field:[@DF_Synonyms  code: SYM]
    $field:[@DF_Time  code: TIM]
    $field:[@DF_Type  code: TYP]
    $field:[@DF_Unit  code: UN]
  }
]

DF_AccessionNumber: $srsfield:[AccessionNumber short: AN]
DF_StaffFootnote: $srsfield:[StaffFootnote short: SF]
DF_AnnotatorsFootnote: $srsfield:[AnnotatorsFootnote short: AF]
DF_ReferenceNumber: $srsfield:[ReferenceNumber short: RN]

DF_Author: $srsfield:[Author short: AU]
DF_OrganizationalSource: $srsfield:[OrganizationalSource short: OS]
DF_BibliographicSource: $srsfield:[BibliographicSource short: SO]
DF_PublicationYear: $srsfield:[PublicationYear short: YR]
DF_SourceCode: $srsfield:[SourceCode short: SC]
DF_DocumentType: $srsfield:[DocumentType short: DT]
DF_Language: $srsfield:[Language short: LA]
DF_CategoryCode: $srsfield:[CategoryCode short: CC]
DF_IndexTerms: $srsfield:[IndexTerms short: IT]
DF_SupplementaryTerms: $srsfield:[SupplementaryTerms short: ST]
DF_Abstract: $srsfield:[Abstract short: AB]
DF_AnnotatorsAbstract: $srsfield:[AnnotatorsAbstract short: AAB]

DF_CellLine: $srsfield:[CellLine short: CLI]
DF_CellType: $srsfield:[CellType short: CTY]
DF_OrganismSystematicName: $srsfield:[OrganismSystematicName short: OR]
DF_OrganismSubspecies: $srsfield:[OrganismSubspecies short: SSP]
DF_OrganismCommonName: $srsfield:[OrganismCommonName short: OCN]
DF_TaxonomicGroup: $srsfield:[TaxonomicGroup short:TG group:@DF_ALL]
DF_CellSpeciesExtracellFluid: $srsfield:[CellSpeciesExtracellFluid short: CS]
DF_Strain: $srsfield:[Strain short: STR]
DF_Genotype: $srsfield:[Genotype short: GET]
DF_Phenotype: $srsfield:[Phenotype short: PHT]
DF_MetabolicType: $srsfield:[MetabolicType short: MET]
DF_Age: $srsfield:[Age short: AGE]
DF_Sex: $srsfield:[Sex short: SEX]
DF_OrganismWeight: $srsfield:[OrganismWeight short: WT]
DF_KeepingConditions: $srsfield:[KeepingConditions short: KCO]
DF_OrganismTreatment: $srsfield:[OrganismTreatment short: OTR]
DF_PhysiologicalState: $srsfield:[PhysiologicalState short: PHS]
DF_DevelopmentalStage: $srsfield:[DevelopmentalStage short: DEV]
DF_Pathology: $srsfield:[Pathology short: PAT]
DF_LightConditions: $srsfield:[LightConditions short: LC]
DF_LightIntensity: $srsfield:[LightIntensity short: LI]
DF_WaveLength: $srsfield:[WaveLength short: WL]
DF_TimeOftheDay: $srsfield:[TimeOftheDay short: TOD]
DF_CellCultureCategory: $srsfield:[CellCultureCategory short: CCC]

DF_SubspeciesName: $srsfield:[SubspeciesName short: SSP]
DF_TypeSpecies: $srsfield:[TypeSpecies short: TSP]
DF_TypeStrainName: $srsfield:[TypeStrainName short: TSN]
DF_BactClassificationCode: $srsfield:[BactClassificationCode short: BC]
DF_CellCultureCategoryCode: $srsfield:[CellCultureCategoryCode short: CCC]
DF_molGCContentInDNA: $srsfield:[molGCContentInDNA short: GCC]
DF_GenomeSizeDaltons: $srsfield:[GenomeSizeDaltons short: GSZ]
DF_ColonyMorphology: $srsfield:[ColonyMorphology short: CMO]
DF_CellMorphology: $srsfield:[CellMorphology short: MOR]
DF_PeptidoglycanComposition: $srsfield:[PeptidoglycanComposition short: PGC]
DF_MembraneLipidComposition: $srsfield:[MembraneLipidComposition short: LIP]
DF_CytochromePresent: $srsfield:[CytochromePresent short: CYT]
DF_MembrIsoprenoidQuinonesPresent: $srsfield:[MembrIsoprenoidQuinonesPresent short: QUI]
DF_FlagellarArrangement: $srsfield:[FlagellarArrangement short: FLA]
DF_Physiology: $srsfield:[Physiology short: PHY]
DF_CellOrSporeMotility: $srsfield:[CellOrSporeMotility short: MOT]
DF_ConcentrationInCultivationMedium: $srsfield:[ConcentrationInCultivationMedium short: CON]
DF_AbsoluteRequirementForGrowth: $srsfield:[AbsoluteRequirementForGrowth short: AR]
DF_GrowthInhibitor: $srsfield:[GrowthInhibitor short: GRI]
DF_GrowthActivator: $srsfield:[GrowthActivator short: GRA]
DF_CommonAntigeneName: $srsfield:[CommonAntigeneName short: CAN]
DF_AlternativePathwayNames: $srsfield:[AlternativePathwayNames short: LAP]
DF_SystematicPathwayNames: $srsfield:[SystematicPathwayNames short: LSP]
DF_EnzymeProduced: $srsfield:[EnzymeProduced short: ENP]
DF_FermentationProduct: $srsfield:[FermentationProduct short: FPR]
DF_ProductionOf: $srsfield:[ProductionOf short: PRD]
DF_AcidProducedFrom: $srsfield:[AcidProducedFrom short: ACD]
DF_GasProducedFrom: $srsfield:[GasProducedFrom short: GAS]
DF_CarbonSourceUsed: $srsfield:[CarbonSourceUsed short: CSO]
DF_NitrogenSourceUsed: $srsfield:[NitrogenSourceUsed short: NSO]
DF_Test: $srsfield:[Test short: TST]
DF_NaturalHost: $srsfield:[NaturalHost short: NHO]
DF_PathogenicityForHost: $srsfield:[PathogenicityForHost short: PGY]
DF_HostPathologyDescription: $srsfield:[HostPathologyDescription short: HPD]
DF_Habitat: $srsfield:[Habitat short: HAB]
DF_GeographicalDistribution: $srsfield:[GeographicalDistribution short: GEO]
DF_CulturePreservationConditions: $srsfield:[CulturePreservationConditions short: CPC]

DF_LaboratoryHostSystematicName: $srsfield:[LaboratoryHostSystematicName short: HST]
DF_HostAge: $srsfield:[HostAge short: HAG]
DF_HostCommonName: $srsfield:[HostCommonName short: HCN]
DF_HostTaxonomicGroup: $srsfield:[HostTaxonomicGroup short: HTG]
DF_HostDevelopmentalStage: $srsfield:[HostDevelopmentalStage short: HDS]
DF_HostStrainName: $srsfield:[HostStrainName short: HSN]
DF_HostSex: $srsfield:[HostSex short: HSX]
DF_HostGenotype: $srsfield:[HostGenotype short: HGT]
DF_HostPhenotype: $srsfield:[HostPhenotype short: HPT]
DF_HostSubcellularFraction: $srsfield:[HostSubcellularFraction short: HSF]
DF_HostCellSpecies: $srsfield:[HostCellSpecies short: HCS]
DF_HostCellularLocation: $srsfield:[HostCellularLocation short: HSL]
DF_HostCellCultureCategory: $srsfield:[HostCellCultureCategory short: HCC]
DF_HostCellLine: $srsfield:[HostCellLine short: HCL]
DF_HostCellType: $srsfield:[HostCellType short: HCT]
DF_HostTreatment: $srsfield:[HostTreatment short: HTR]
DF_NaturalHostSystematicName: $srsfield:[NaturalHostSystematicName short: NHO]
DF_ClonedVector: $srsfield:[ClonedVector short: CLV]

DF_GeneAcronym: $srsfield:[GeneAcronym short: GN]
DF_AlternativeGeneAcronym: $srsfield:[AlternativeGeneAcronym short: AGA]
DF_GeneMnemonics: $srsfield:[GeneMnemonics short: GMN]
DF_GeneticMapPosition: $srsfield:[GeneticMapPosition short: GMP]
DF_GeneLocation: $srsfield:[GeneLocation short: GL]
DF_CoordinatelyExpressedGenes: $srsfield:[CoordinatelyExpressedGenes short: CEG]
DF_NucleotideSequenceCrossref: $srsfield:[NucleotideSequenceCrossref short: NS]
DF_TypeofSynthesis: $srsfield:[TypeofSynthesis short: SYN]
DF_Inducer: $srsfield:[Inducer short: IND]
DF_InductionDegree: $srsfield:[InductionDegree short: IDE]
DF_Repressor: $srsfield:[Repressor short: REP]
DF_RepressionDegree: $srsfield:[RepressionDegree short: RDE]
DF_DegradationActivator: $srsfield:[DegradationActivator short: DAC]
DF_DegradationInhibitor: $srsfield:[DegradationInhibitor short: DIN]
DF_EnzymeHalfLifeTime: $srsfield:[EnzymeHalfLifeTime short: T05]

DF_CultivationConditions: $srsfield:[CultivationConditions short: CUC]
DF_CultivationTemperature: $srsfield:[CultivationTemperature short: CUT]
DF_DilutionRate: $srsfield:[DilutionRate short: DR]
DF_CultivationMedium: $srsfield:[CultivationMedium short: MED]
DF_NitrogenSource: $srsfield:[NitrogenSource short: NSO]
DF_CarbonSource: $srsfield:[CarbonSource short: CSO]
DF_LimitingSubstrate: $srsfield:[LimitingSubstrate short: LS]
DF_GrowthSubstrate: $srsfield:[GrowthSubstrate short: GS]
DF_CultureDensity: $srsfield:[CultureDensity short: CD]
DF_CellCyclePhase: $srsfield:[CellCyclePhase short: CCP]
DF_GrowthPhase: $srsfield:[GrowthPhase short: GP]
DF_GenerationTime: $srsfield:[GenerationTime short: GT]
DF_CellCyclePeriod: $srsfield:[CellCyclePeriod short: CPE]
DF_GrowthRate: $srsfield:[GrowthRate short: GRR]
DF_SpecificGrowthRate: $srsfield:[SpecificGrowthRate short: SGR]
DF_GrowthMode: $srsfield:[GrowthMode short: GM]
DF_GrowthYield: $srsfield:[GrowthYield short: GY]
DF_ColonySize: $srsfield:[ColonySize short: CSZ]

DF_MetabolicPathwayName: $srsfield:[MetabolicPathwayName short: MPW group:@DF_ALL]
DF_SystematicPathwayName: $srsfield:[SystematicPathwayName short: SPN group:@DF_ALL]
DF_AlternativePathwayName: $srsfield:[AlternativePathwayName short: APN group:@DF_ALL]
DF_OverallReaction: $srsfield:[OverallReaction short: OVR group:@DF_ALL]
DF_OverallReactionVelocity: $srsfield:[OverallReactionVelocity short: VEL]
DF_MetabolicState: $srsfield:[MetabolicState short: MES]

DF_SubcellularLocation: $srsfield:[SubcellularLocation short: SL]
DF_SubcellularFraction: $srsfield:[SubcellularFraction short: SF]
DF_ActiveSiteLocation: $srsfield:[ActiveSiteLocation short: ASL]
DF_MultifunctionalEnzymeName: $srsfield:[MultifunctionalEnzymeName short: MF]
DF_MultifunctionalEnzymeForm: $srsfield:[MultifunctionalEnzymeForm short: MFF]
DF_AltMultifunctionalEnzymeName: $srsfield:[AltMultifunctionalEnzymeName short: AMF]
DF_MultifunctionalEnzymeCode: $srsfield:[MultifunctionalEnzymeCode short: MFC]
DF_RecommendedEnzymeName: $srsfield:[RecommendedEnzymeName short: EN]
DF_SystematicEnzymeName: $srsfield:[SystematicEnzymeName short: SEN]
DF_OtherEnzymeName: $srsfield:[OtherEnzymeName short: ON]
DF_EnzymeForm: $srsfield:[EnzymeForm short: EF]
DF_ProteinName: $srsfield:[ProteinName short: PN]
DF_NonCatalyticFunction: $srsfield:[NonCatalyticFunction short: NCF]
DF_ProteinForm: $srsfield:[ProteinForm short: PRF]
DF_ProteinConcentration: $srsfield:[ProteinConcentration short: PCO]
DF_IsozymeNumber: $srsfield:[IsozymeNumber short: IZN]
DF_ReactionEquation: $srsfield:[ReactionEquation short: RE]
DF_ReactionIdentifier: $srsfield:[ReactionIdentifier short: RI]
DF_ReactionType: $srsfield:[ReactionType short: RET]
DF_ElementaryStepEquation: $srsfield:[ElementaryStepEquation short: ESE]
DF_SiteofEnzymeAction: $srsfield:[SiteofEnzymeAction short: SEA]
DF_NonSubstrate: $srsfield:[NonSubstrate short: NSU]
DF_Coenzyme: $srsfield:[Coenzyme short: CO]
DF_NonCoenzyme: $srsfield:[NonCoenzyme short: NCO]
DF_Product: $srsfield:[Product short: PR]
DF_NonProduct: $srsfield:[NonProduct short: NPR]
DF_AbsoluteRequirement: $srsfield:[AbsoluteRequirement short: AR]
DF_ReactionPhase: $srsfield:[ReactionPhase short: RP]
DF_Reversibility: $srsfield:[Reversibility short: REV]
DF_ReactionDirection: $srsfield:[ReactionDirection short: RD]
DF_EnzymeApplication: $srsfield:[EnzymeApplication short: APP]

DF_AssayConditions: $srsfield:[AssayConditions short: ASS]
DF_TissueActivity: $srsfield:[TissueActivity short: TA]
DF_PreparationSpecificActivity: $srsfield:[PreparationSpecificActivity short: PA]
DF_SpecificActivity: $srsfield:[SpecificActivity short: SA]
DF_PurificationSteps: $srsfield:[PurificationSteps short: PS]
DF_PurifFactorAndPurityDegree: $srsfield:[PurifFactorAndPurityDegree short: PF]
DF_Yield: $srsfield:[Yield short: YD]
DF_EnzymeConcentration: $srsfield:[EnzymeConcentration short: ECO]
DF_TotalProteinContent: $srsfield:[TotalProteinContent short: TPC]
DF_PreparationSpecificBinding: $srsfield:[PreparationSpecificBinding short: PB]
DF_SpecificBinding: $srsfield:[SpecificBinding short: SB]
DF_StorageConditions: $srsfield:[StorageConditions short: STO]
DF_Buffer: $srsfield:[Buffer short: BUF]
DF_pHValue: $srsfield:[pHValue short: PH]
DF_Temperature: $srsfield:[Temperature short: TEM]
DF_IonicStrength: $srsfield:[IonicStrength short: IS]
DF_OptimalConditions: $srsfield:[OptimalConditions short: OC]

DF_TypeofKineticsOrFunctDependence: $srsfield:[TypeofKineticsOrFunctDependence short: KT]
DF_MaxReactionVelocity: $srsfield:[MaxReactionVelocity short: VM]
DF_PreparationMaxVelocity: $srsfield:[PreparationMaxVelocity short: PVM]
DF_RelativeMaxVelocity: $srsfield:[RelativeMaxVelocity short: RVM]
DF_RelativeActivity: $srsfield:[RelativeActivity short: RA]
DF_MolecularActivity: $srsfield:[MolecularActivity short: MA]
DF_CatalyticConst: $srsfield:[CatalyticConst short: KC]
DF_MichaelisConst: $srsfield:[MichaelisConst short: KM]
DF_HalfSaturatingSubstrateConc: $srsfield:[HalfSaturatingSubstrateConc short: S05]
DF_Conditions: $srsfield:[Conditions short: CND]
DF_CatalyticEfficiency: $srsfield:[CatalyticEfficiency short: CEF]
DF_ApparentCatalyticConst: $srsfield:[ApparentCatalyticConst short: ACC]
DF_Ligand: $srsfield:[Ligand short: LIG]
DF_FixedLigand: $srsfield:[FixedLigand short: FL]
DF_VariableLigand: $srsfield:[VariableLigand short: VL]
DF_MaxSpecificBinding: $srsfield:[MaxSpecificBinding short: BM]
DF_HillsNumber: $srsfield:[HillsNumber short: NH]
DF_ReactionMechanism: $srsfield:[ReactionMechanism short: ME]
DF_RateLaw: $srsfield:[RateLaw short: RL]
DF_RateConstDesignation: $srsfield:[RateConstDesignation short: RCD]
DF_RateConst: $srsfield:[RateConst short: RC]
DF_TimeConst: $srsfield:[TimeConst short: TC]
DF_FunctionalDependence: $srsfield:[FunctionalDependence short: FUN]

DF_Activator: $srsfield:[Activator short: AC]
DF_ActivationType: $srsfield:[ActivationType short: ACT]
DF_ActivationDegree: $srsfield:[ActivationDegree short: AD]
DF_MaxActivationDegree: $srsfield:[MaxActivationDegree short: MAD]
DF_ActivationConst: $srsfield:[ActivationConst short: KA]
DF_HalfActivatingConcentration: $srsfield:[HalfActivatingConcentration short: A05]
DF_Inhibitor: $srsfield:[Inhibitor short: IN]
DF_InhibitionType: $srsfield:[InhibitionType short: INT]
DF_InhibitionDegree: $srsfield:[InhibitionDegree short: IND]
DF_MaxInhibitionDegree: $srsfield:[MaxInhibitionDegree short: MID]
DF_InhibitionConst: $srsfield:[InhibitionConst short: KI]
DF_HalfInhibitingConc: $srsfield:[HalfInhibitingConc short: I05]
DF_InterceptInhibitionConst: $srsfield:[InterceptInhibitionConst short: KII]
DF_SlopeInhibitionConst: $srsfield:[SlopeInhibitionConst short: KIS]
DF_NonInfluencingCompound: $srsfield:[NonInfluencingCompound short: NIC]

DF_EnzymeModificationProcess: $srsfield:[EnzymeModificationProcess short: MP]
DF_EnzymeModifier: $srsfield:[EnzymeModifier short: MOD]
DF_EnzymeBindingPartner: $srsfield:[EnzymeBindingPartner short: BPA]
DF_ModifyingEnzymeName: $srsfield:[ModifyingEnzymeName short: MEN]
DF_ModifyingEnzymeCode: $srsfield:[ModifyingEnzymeCode short: MEC]
DF_ModifyingEnzymeForm: $srsfield:[ModifyingEnzymeForm short: MEF]
DF_ModificationResidual: $srsfield:[ModificationResidual short: MRE]
DF_ModificationMechanism: $srsfield:[ModificationMechanism short: MME]
DF_ModificationPromotor: $srsfield:[ModificationPromotor short: MPR]
DF_ModificationAntagonist: $srsfield:[ModificationAntagonist short: MAN]
DF_ModificationEffect: $srsfield:[ModificationEffect short: MOE]
DF_EnzymeTreatment: $srsfield:[EnzymeTreatment short: TR]
DF_TreatmentEffect: $srsfield:[TreatmentEffect short: EFF]

DF_MolecularMass: $srsfield:[MolecularMass short: MM]
DF_SedimentationConst: $srsfield:[SedimentationConst short: ESC]
DF_SubunitMass: $srsfield:[SubunitMass short: SM]
DF_SubunitSedimentationConst: $srsfield:[SubunitSedimentationConst short: SSC]
DF_SubunitName: $srsfield:[SubunitName short: SUN]
DF_SubunitDesignation: $srsfield:[SubunitDesignation short: SUD]
DF_SubunitFunction: $srsfield:[SubunitFunction short: SUF]
DF_SubunitNumber: $srsfield:[SubunitNumber short: SN]
DF_SubunitComposition: $srsfield:[SubunitComposition short: SUC]
DF_SubunitStructure: $srsfield:[SubunitStructure short: SUS]
DF_SubunitBindingType: $srsfield:[SubunitBindingType short: SBT]
DF_MolecularSymmetry: $srsfield:[MolecularSymmetry short: MS]
DF_PolypeptideChainNumber: $srsfield:[PolypeptideChainNumber short: PCN]
DF_ProstheticGroup: $srsfield:[ProstheticGroup short: PRG]
DF_ProstheticGroupNumber: $srsfield:[ProstheticGroupNumber short: PGN]
DF_BindingType: $srsfield:[BindingType short: BT]
DF_SHGroupNumber: $srsfield:[SHGroupNumber short: SHN]
DF_DisulfideBondNumber: $srsfield:[DisulfideBondNumber short: SSN]
DF_BindingSiteName: $srsfield:[BindingSiteName short: SNA]
DF_BindingSiteNumber: $srsfield:[BindingSiteNumber short: SNU]
DF_SiteAminoAcidSequence: $srsfield:[SiteAminoAcidSequence short: SSQ]
DF_BindingSiteResidual: $srsfield:[BindingSiteResidual short: SRE]
DF_AminoAcids: $srsfield:[AminoAcids short: AA]
DF_Content: $srsfield:[Content short: CNT]
DF_AminoAcidSequenceOrCrossref: $srsfield:[AminoAcidSequenceOrCrossref short: AAS]
DF_EnzymeComposition: $srsfield:[EnzymeComposition short: ENC]
DF_TerminalAminoAcids: $srsfield:[TerminalAminoAcids short: TAA]
DF_SignalPeptide: $srsfield:[SignalPeptide short: SP]
DF_SignalPeptideLength: $srsfield:[SignalPeptideLength short: SPL]
DF_IntramolecularLocation: $srsfield:[IntramolecularLocation short: LOC]
DF_PrimaryStructureHomology: $srsfield:[PrimaryStructureHomology short: HOM]

DF_EquilibConst: $srsfield:[EquilibConst short: KEQ]
DF_EquilibConstFormula: $srsfield:[EquilibConstFormula short: KEF]
DF_DissociationConstDesignation: $srsfield:[DissociationConstDesignation short: KDD]
DF_DissociationConst: $srsfield:[DissociationConst short: KD]
DF_AssociationConstDesignation: $srsfield:[AssociationConstDesignation short: KAD]
DF_AssociationConst: $srsfield:[AssociationConst short: KAS]
DF_EquilibConstDesignation: $srsfield:[EquilibConstDesignation short: KED]
DF_ElementaryStepEquilibConst: $srsfield:[ElementaryStepEquilibConst short: KEE]
DF_MassActionRatio: $srsfield:[MassActionRatio short: MAR]
DF_StandardFreeEnergyChange: $srsfield:[StandardFreeEnergyChange short: DG0]
DF_StandardEntropyChange: $srsfield:[StandardEntropyChange short: DS0]
DF_StandardEnthalpyChange: $srsfield:[StandardEnthalpyChange short: DH0]
DF_ActivationEnergy: $srsfield:[ActivationEnergy short: EA]
DF_ActivationFreeEnergyChange: $srsfield:[ActivationFreeEnergyChange short: DGA]
DF_ActivationEnthalpyChange: $srsfield:[ActivationEnthalpyChange short: DHA]
DF_ActivationEntropyChange: $srsfield:[ActivationEntropyChange short: DSA]
DF_StandardRedoxPotential: $srsfield:[StandardRedoxPotential short: E0]
DF_ElectronTransferNumber: $srsfield:[ElectronTransferNumber short: ETN]
DF_HeatCapacityChange: $srsfield:[HeatCapacityChange short: DCP]

DF_OptimalPH: $srsfield:[OptimalPH short: PHO]
DF_pHDependentParameter: $srsfield:[pHDependentParameter short: PHD]
DF_pHRange: $srsfield:[pHRange short: PHR]
DF_pKValues: $srsfield:[pKValues short: PKV]
DF_InactivationConst: $srsfield:[InactivationConst short: IC]
DF_OptimalTemperature: $srsfield:[OptimalTemperature short: TO]
DF_TempDependentParameter: $srsfield:[TempDependentParameter short: TD]
DF_TemperatureRange: $srsfield:[TemperatureRange short: TER]
DF_TemperatureCoefficient: $srsfield:[TemperatureCoefficient short: Q10]
DF_NameofParameterorVariable: $srsfield:[NameofParameterorVariable short: PAR]
DF_ValueofParameterorVariable: $srsfield:[ValueofParameterorVariable short: VAL]
DF_AbsorptionMaxWaveLength: $srsfield:[AbsorptionMaxWaveLength short: AM]
DF_AbsorptionCoefficient: $srsfield:[AbsorptionCoefficient short: ABC]
DF_MolarAbsorptionCoefficient: $srsfield:[MolarAbsorptionCoefficient short: MAC]
DF_AbsorptionShoulder: $srsfield:[AbsorptionShoulder short: ASH]
DF_FluorescenceMax: $srsfield:[FluorescenceMax short: FM]
DF_CDSpectrumMax: $srsfield:[CDSpectrumMax short: CMA]
DF_CDSpectrumMin: $srsfield:[CDSpectrumMin short: CMI]
DF_CDSpectrumShoulder: $srsfield:[CDSpectrumShoulder short: CSH]
DF_EPRSignals: $srsfield:[EPRSignals short: EPR]

DF_Antigene: $srsfield:[Antigene short: AGN]
DF_Antibody: $srsfield:[Antibody short: ABD]
DF_CrossReactivity: $srsfield:[CrossReactivity short: CRR]

DF_Abbreviation: $srsfield:[Abbreviation short: ABB]
DF_Addition: $srsfield:[Addition short: ADD]
DF_BiologicalFunction: $srsfield:[BiologicalFunction short: BFN]
DF_Comments: $srsfield:[Comments short: COM]
DF_Concentration: $srsfield:[Concentration short: CON]
DF_Designation: $srsfield:[Designation short: DES]
DF_Formula: $srsfield:[Formula short: FOR]
DF_OscillationPeriod: $srsfield:[OscillationPeriod short: OP]
DF_PhaseDifference: $srsfield:[PhaseDifference short: PDI]
DF_Process: $srsfield:[Process short: PRS]
DF_Property: $srsfield:[Property short: PRY]
DF_SubstanceComposition: $srsfield:[SubstanceComposition short: SCN]
DF_StandardDeviation: $srsfield:[StandardDeviation short: SD]
DF_Substance: $srsfield:[Substance short: SUB]
DF_Time: $srsfield:[Time short: TIM]
DF_Type: $srsfield:[Type short: TYP]
DF_Unit: $srsfield:[Unit short: UN]


EMP_SYNTAX:$syntax:[file:"SRSDB:emp.is" ignore:" "]
EMP_FILE:$filetype:[typename:bnk maxline:3000]


eld:[PhaseDifference short: PDI]
DF_Process: $srsfield:[Process short: PRS]
DF_Property: $srsfield:[Property short: PRY]
DF_SubstanceComposition: $srsfield:[SubstanceComposition short: SCN]
DF_StandardDeviation: $srsfield:[StandardDeviation short: SD]
DF_Substance: $srsfield:[Substance shorsrs/icarus/db/emp.is

$tags= {
  '**':  'Staff Footnote'
  '***': 'Annotators Footnote'
  A05: 'Half-Activating Concentration'
  AAB: 'Annotators Abstract'
  AA:  'Amino Acids'
  AAS: 'Amino Acid Sequence or Crossreference'
  AB:  'Abstract'
  ABB: 'Abbreviation'
  ABC: 'Absorption Coefficient'
  ABD: 'Antibody'
  AC:  'Activator'
  ACC: 'Apparent Catalytic Constant'
  ACT: 'Activation Type'
  AD:  'Activation Degree'
  ADD: 'Addition'
  AGD: 'Alternative Gene Designation'
  AGE: 'Age'
  AGN: 'Antigene'
  ALG: 'Alternative gene name'
  AM:  'Absorption Maximum Wave Length'
  AMF: 'Alternative Multifunctional Enzyme Name'
  AN:  'Accession Number'
  APN: 'Alternative Pathway Name'
  APP: 'Enzyme Application'
  AR:  'Absolute Requirement'
  ASH: 'Absorption Shoulder'
  ASL: 'Active Site Location'
  ASS: 'Assay Conditions'
  AU:  'Author'
  BFN: 'Biological Function'
  BM:  'Maximum Specific Binding'
  BPA: 'Enzyme Binding Partner'
  BT:  'Binding Type'
  BUF: 'Buffer'
  CC:  'Category Code'
  CCC: 'Cell Culture Category'
  CD:  'Culture Density'
  CEF: 'Catalytic Efficiency'
  CEG: 'Coordinately Expressed Genes'
  CLI: 'Cell Line'
  CLV: 'Cloned Vector'
  CMA: 'CD Spectrum Maximum'
  CMI: 'CD Spectrum Minimum'
  CND: 'Conditions'
  CNT: 'Content'
  CO:  'Coenzyme'
  COL: 'Solution color'
  COM: 'Comments'
  CON: 'Concentration'
  CPE: 'Cell Cycle Period'
  CCP: 'Cell Cycle Phase'
  CRR: 'Cross-Reactivity'
  CS:  'Cell Species or Extracellular Fluid'
  CSH: 'CD Spectrum Shoulder'
  CSO: 'Carbon Source'
  CSZ: 'Colony Size'
  CTY: 'Cell Type'
  CUC: 'Cultivation Conditions'
  CUT: 'Cultivation Temperature'
  DAC: 'Degradation Activator'
  DCP: 'Heat Capacity Change'
  DES: 'Designation'
  DEV: 'Developmental Stage'
  DG0: 'Standard Free Energy Change'
  DGA: 'Activation Free Energy Change'
  DH0: 'Standard Enthalpy Change'
  DHA: 'Activation Enthalpy Change'
  DIN: 'Degradation Inhibitor'
  DR:  'Dilution Rate'
  DS0: 'Standard Entropy Change'
  DSA: 'Activation Entropy Change'
  DT:  'Document Type'
  E0:  'Standard Redox Potential'
  EA:  'Activation Energy'
  EC:  'Enzyme Code'
  ECO: 'Enzyme Concentration'
  EF:  'Enzyme Form'
  EFF: 'Treatment Effect'
  EN:  'Recommended Enzyme Name'
  ENC: 'Enzyme Composition'
  EPR: 'EPR Signals'
  ESC: 'Sedimentation Constant'
  ESE: 'Elementary Step Equation'
  ESR: 'unknown field-ESR'
  ETN: 'Electron Transfer Number'
  FL:  'Fixed Ligand'
  FM:  'Fluorescence Maximum'
  FOR: 'Formula'
  FUN: 'Functional Dependence'
  GCC: 'unknown field GCC'
  GEN: 'Gene Name'
  GET: 'Genotype'
  GL:  'Gene Location'
  GM:  'Growth Mode'
  GMP: 'Genetic Map Position'
  GN:  'Gene Designation'
  GNP: 'Gene Product'
  GP:  'Growth Phase'
  GRR: 'Growth Rate'
  GS:  'Growth Substrate'
  GT:  'Generation Time'
  GY:  'Growth Yield'
  HAB: 'unknown field-HAB'
  HAG: 'Host Age'
  HCC: 'Host Cell Culture Category'
  HCL: 'Host Cell Line'
  HCN: 'Host Common Name'
  HCS: 'Host Cell Species'
  HCT: 'Host Cell Type'
  HDS: 'Host Developmental Stage'
  HGT: 'Host Genotype'
  HMT: 'Host metabolic type'
  HOM: 'Primary Structure Homology'
  HPT: 'Host Phenotype'
  HSF: 'Host Subcellular Fraction'
  HSL: 'Host Cellular Location'
  HSN: 'Host Strain Name'
  HST: 'Laboratory Host Systematic Name'
  HSX: 'Host Sex'
  HTG: 'Host Taxonomic Group'
  HTR: 'Host Treatment'
  I05: 'Half-Inhibiting Concentration'
  IC:  'Inactivation Constant'
  ID:  'Inhibition Degree'
  IDE: 'Induction Degree'
  IN:  'Inhibitor'
  IND: 'Inducer'
  INT: 'Inhibition Type'
  IP:  'Isoelectric Point (pI)'
  IS:  'Ionic Strength'
  IT:  'Index Terms'
  IZN: 'Isozyme Number'
  KA:  'Activation Constant'
  KAD: 'Association Constant Designation'
  KAS: 'Association Constant'
  KC:  'Catalytic Constant'
  KCO: 'Keeping Conditions'
  KD:  'Dissociation Constant'
  KDD: 'Dissociation Constant Designation'
  KED: 'Equilibrium Constant Designation'
  KEE: 'Elementary Step Equilibrium Constant'
  KEF: 'Equilibrium Constant Formula'
  KEQ: 'Equilibrium Constant'
  KI:  'Inhibition Constant'
  KII: 'Intercept Inhibition Constant'
  KIS: 'Slope Inhibition Constant'
  KM:  'Michaelis Constant'
  KT:  'Type of Kinetics or Functional Dependence'
  LA:  'Language'
  LC:  'Light Conditions'
  LI:  'Light Intensity'
  LIG: 'Ligand'
  LOC: 'Intramolecular Location'
  LS:  'Limiting Substrate'
  LSO: 'Light source'
  MA:  'Molecular Activity'
  MAC: 'Molar Absorption Coefficient'
  MAD: 'Maximum Activation Degree'
  MAN: 'Modification Antagonist'
  MAR: 'Mass Action Ratio'
  MCC: 'Membrane carrier code'
  MCF: 'Membrane carrier form'
  MCN: 'Membrane carrier name'
  ME:  'Reaction Mechanism'
  MEC: 'Modifying Enzyme Code'
  MED: 'Cultivation Medium'
  MEF: 'Modifying Enzyme Form'
  MEN: 'Modifying Enzyme Name'
  MES: 'Metabolic State'
  MET: 'Metabolic Type'
  MF:  'Multifunctional Enzyme Name'
  MFC: 'Multifunctional Enzyme Code'
  MFF: 'Multifunctional Enzyme Form'
  MID: 'Maximum Inhibition Degree'
  MM:  'Molecular Mass'
  MME: 'Modification Mechanism'
  MOD: 'Enzyme Modifier'
  MOE: 'Modification Effect'
  MOR: 'unknown field-MOR'
  MOT: 'unknown field-MOT'
  MP:  'Enzyme Modification Process'
  MPR: 'Modification Promotor'
  MPW: 'Metabolic Pathway Name'
  MRE: 'Modification Residual'
  MS:  'Molecular Symmetry'
  MT:  'Method'
  NCF: 'Non-Catalytic Function'
  NCO: 'Non-Coenzyme'
  NH:  'Hills Number'
  NHO: 'Natural Host Systematic Name'
  NIC: 'Non-Influencing Compound'
  NPR: 'Non-Product'
  NS:  'Nucleotide Sequence Crossreference'
  NSO: 'Nitrogen Source'
  NSU: 'Non-Substrate'
  OC:  'Optimal Conditions'
  OCN: 'Organism Common Name'
  ON:  'Other Enzyme Name'
  OP:  'Oscillation Period'
  OPN: 'unknown field OPN'
  OR:  'Organism Systematic Name'
  OS:  'Organizational Source'
  OTR: 'Organism Treatment'
  OVR: 'Overall Reaction'
  PA:  'Preparation Specific Activity'
  PAR: 'Name of Parameter or Variable'
  PAT: 'Pathology'
  PB:  'Preparation Specific Binding'
  PCN: 'Polypeptide Chain Number'
  PCO: 'Protein Concentration'
  PDI: 'Phase Difference'
  PF:  'Purification Factor and Purity Degree'
  PGN: 'Prosthetic Group Number'
  PH:  'pH Value'
  PHD: 'pH-Dependent Parameter'
  PHO: 'Optimal pH'
  PHR: 'pH Range'
  PHS: 'Physiological State'
  PHT: 'Phenotype'
  PHY: 'unknown Field'
  PKV: 'pK Values'
  PLO: 'Ploidy'
  PN:  'Protein Name'
  PR:  'Product'
  PRF: 'Protein Form'
  PRG: 'Prosthetic Group'
  PRI: 'Primer/Template'
  PRS: 'Process'
  PRY: 'Property'
  PS:  'Purification Steps'
  PSL: 'Polypeptide synthesis Location'
  PVM: 'Preparation Maximum Velocity'
  Q10: 'Temperature Coefficient'
  RA:  'Relative Activity'
  RC:  'Rate Constant'
  RCD: 'Rate Constant Designation'
  RD:  'Reaction Direction'
  RDE: 'Repression Degree'
  RE:  'Reaction Equation'
  REF: 'Reference'
  REP: 'Repressor'
  RET: 'Reaction_Type'
  REV: 'Reversibility'
  RI:  'Reaction Identifier'
  RL:  'Rate Law'
  RN:  'Reference Number'
  RP:  'Reaction Phase'
  RVM: 'Relative Maximum Velocity'
  S05: 'Half-Saturating Substrate Concentration'
  SA:  'Specific Activity'
  SAA: 'Site amino acid sequence'
  SB:  'Specific Binding'
  SBT: 'Subunit Binding Type'
  SC:  'Source Code'
  SCN: 'Substance Composition'
  SD:  'Standard Deviation'
  SEA: 'Site of Enzyme Action'
  SEN: 'Systematic Enzyme Name'
  SEX: 'Sex'
  SF:  'Subcellular Fraction'
  SGR: 'Specific Growth Rate'
  SHN: 'SH-Group Number'
  SL:  'Subcellular Location'
  SM:  'Subunit Mass'
  SN:  'Subunit Number'
  SNA: 'Binding Site Name'
  SNU: 'Binding Site Number'
  SO:  'Bibliographic Source'
  SP:  'Signal Peptide'
  SPL: 'Signal Peptide Length'
  SPN: 'Systematic Pathway Name'
  SRE: 'Binding Site Residual'
  SSC: 'Subunit Sedimentation constant'
  SSN: 'Disulfide Bond Number'
  SSP: 'Organism Subspecies'
  SSQ: 'Site Sequence'
  ST:  'Supplementary Terms'
  STA: 'Stabilizer'
  STO: 'Storage Conditions'
  STR: 'Strain'
  SU:  'Substrate'
  SUB: 'Substance'
  SUC: 'Subunit Composition'
  SUD: 'Subunit Designation'
  SUF: 'Subunit Function'
  SUN: 'Subunit Name'
  SUS: 'Subunit Structure'
  SYM: 'Synonyms'
  SYN: 'Type of Synthesis'
  T05: 'Half-Life Time'
  TA:  'Tissue Activity'
  TAA: 'Terminal Amino Acids'
  TC:  'Time Constant'
  TD:  'Temperature-Dependent Parameter'
  TEM: 'Temperature'
  TER: 'Temperature Range'
  TG:  'Taxonomic Group'
  TI:  'Title'
  TIM: 'Time'
  TO:  'Optimal Temperature'
  TOD: 'Time Of the Day'
  TPC: 'Total Protein Content'
  TR:  'Enzyme Treatment'
  TRT: 'Transition temperature'
  TYP: 'Type'
  UN:  'Unit'
  VAL: 'Value of Parameter or Variable'
  VEL: 'Overall Reaction Velocity'
  VL:  'Variable Ligand'
  VM:  'Maximum Reaction Velocity'
  WL:  'Wave Length'
  WT:  'Organism Weight'
  YD:  'Yield'
  YR:  'Publication Year'
}

$rules={
  entry:    ~ {$In:[file:text] $Out pre $Skip:0}
              (/[A-Z][A-Z]/ {$Not} ln)*
              (tag {pre {$Skip:0 $entryFip = $Fip} $Wrt} appLn 
              ('#'{$not} appLn)* '#' ln? )?
            ~
  # fields
  fields:   ~ {$In:entry $Out $Skip:1} 
              (tag {$c=$Ct $Wrt:$Ct } appLn (/[A-Z]/ {$Not} appLn)* | annot)+ 
            ~  
  annot:    ~ {$Wrt} '**' appLn ~

  # indexing  
  i_id:     ~ {$Out:id $In:[fields c:AN]} /../ name {$Wrt} ~
  i_str:    ~ /a-zA-Z_/ ~
  i_enzCode:~ {$Out:enzCode $In:[fields c:EC]} /... +/ str? {$Wrt} ~

  i_words:  ~ {$In:fields $Out:words pre{$Skip:0} $Skip:1} 
              tag? i_word* ~
  i_word:   ~ ( 
                /[0-9-]+\\.[0-9-]+\\.[0-9-]+\\.[0-9-]+/ {$Wrt:$Itc} | 
                /[a-zA-Z0-9]+/ {$Uniq:$Itc} | /./
              )+ ~  

  i_links:  ~ {$In:fields $Out:links pre{$Skip:1} $Skip:1}
              /[A-Z]+/ { if:($Ct==MFC || $Ct==EC)
                           {$Prod:ecLink}
                         elif:$Ct==MPW 
                           $Prod:mpwLink
                       }
            ~
  ecLink:   ~ /[A-Z ]+/ ec {$Wrt:enzyme} (/[:\/ ]+/ ec {$Wrt:enzyme})* ~
  ec:       ~ /[0-9-]+\\.[0-9-]+\\.[0-9-]+\\.[0-9-]+/ ~
  mpwLink:  ~ /MPW G +/ /[A-Z0-9]+\\.[A-Z0-9]+/ {$Wrt:mpw} ~
 
  # html display
  h_field:  ~ {$In:[fields t:hl]}
              tag {$t=$tags.$Ct if:$ParInt:isTable $Rep:"" 
                                 else $Rep:"<DT><B>$t</DT></B><DD>"
                                } 
              (h_Ttable | h_Mtable | (h_word '\n')+) ~

  h_Mtable: ~ 'M '{$Rep:"<TABLE BORDER><TR><TH>"} h_tabhdr 
              ('//'{$Rep:"<TR><TD>"} h_Mtabrow)* x{$Rep:[s:"</TABLE>"]}~
  h_Mtabrow:~ (/[^!\n]+/ ('!!' {$Rep:"</TD><TD ALIGN=RIGHT>"})?)* 
               '\n'{$Rep:"</TD></TR>\n"}~
  h_Ttabbeg:~ ('T ' | 'R ' | 'E ' | 'G ' | 'F ') ~
  h_Ttable: ~ h_Ttabbeg {$Rep:"<TABLE BORDER><TR><TH>"} h_tabhdr 
              ('//'{$Rep:"<TR><TD>"} h_Ttabrow)* x{$Rep:[s:"</TABLE>"]}~
  h_Ttabrow:~ (h_word ('!!' {$Rep:"</TD><TD>"})?)* '\n'{$Rep:"</TD></TR>\n"} ~
  h_tabhdr: ~ (h_word ('!!' {$Rep:"</TH><TH>"})?)* '\n'{$Rep:"</TH></TR>\n"} ~
  h_word:   ~ (
               (/(EC_)?[0-9-]+\\.[0-9-]+\\.[0-9-]+\\.[0-9-]+/ 
                {$Rep:{$ParStr:enzymeR $Ct $Ct}} 
                (/([^0-9])([0-9-]+\\.[0-9-]+\\.[0-9-]+\\.[0-9-]+)/ 
                 {$Rep:{$ParStr:enzymeR $Ct $Ct}})*) |
               /(SWISS-PROT)_([A-Z0-9]+)/{$Rep:{"$1\:($ParStr:swissR)" $2 $2}}|
               /(PIR)_([A-Z0-9]+)/ {$Rep:{"$1\:($ParStr:pirR)" $2 $2}} |
               /(EMBL)_([A-Z0-9]+)/ {$Rep:{"$1\:($ParStr:emblR)" $2 $2}} |
               /(GenBank)_([A-Z0-9]+)/ {$Rep:{"$1\:($ParStr:genbankR)" $2 $2}}|
               /[^[(`' !<>\n_]+/ | 
               /\\[(\\*[^]]*)\\]/ {$Rep:"<SUP>$1</SUP>"} |
               /`([a-zA-Z0-9]+)`/ {$Rep:"<I>$1</I>"} |
               /'([a-zA-Z0-9]+)'/ {$Rep:"<B>$1</B>"} |
               /\\(,([^)]+)\\)/ {$Rep:"<SUB>$1</SUB>"} |
               /\\('([^')]+)\\)/ {$Rep:"<SUP>$1</SUP>"} |
               '<' {$Rep:"&lt;"} |
               '>' {$Rep:"&gt;"} |
               '_' {$Rep:'&nbsp;'} |
               /[[(`']/ 
              )+ ~  
  h_head:   ~ {$In:[fields c:head t:hl]} /.*/ {$Rep:"<DL>\n"} ~
  h_tail:   ~ {$In:[fields c:tail t:hl]} /.*/ {$Rep:"\n</DL>\n"} ~
  h_pathway:~ {$In:[fields c:MPW t:hl]} 
              /.*<TABLE[^\/]+<TH> */ 
              /[0-9A-Z]+\\.[0-9A-Z]+/ {$Rep:{$ParStr:mpwR $Ct $Ct}}
            ~

  # other  
  tag:     ~ /[A-Z\*][0-9A-Z\*]+/ ~
  appLn:   ~ /[^\n]*\n/ {$App} ~
  more:    ~ (/    [^\n]*\n/)* ~
  name:    ~ /[A-Z0-9a-z-]+/ ~
  str:     ~ /[^\t \n]+/ ~
  ln:      ~ /[^\n]*\n/ ~
}


# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/opt/srs/data/emp/9311.bnk']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields print:0] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}



      /[0-9A-Z]+\\.[0-9A-Z]+/ {$Rep:{$ParStr:mpwR $Ct $Ct}}
            ~

  # other  
  tag:     ~ /[A-Z\*][0-9A-Z\*]+/ ~
  appLn:   ~srs/icarus/db/enzyme.i
#    $RCSfile: enzyme.i,v $
#    $Revision: 1.5 $
#    $Date: 1996/08/12 19:04:40 $
#
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


ENZYME_DB:$library:[ENZYME group:@SEQRELATED_LIBS 
  comment:" - A. Bairoch" 
  format:@ENZYME_FORMAT maxNameLen:10 ifiles:{"enzyme.i" "enzyme.is"}
  files:{
    $file:enzyme
  }
]

ENZYME_FORMAT:$libformat:[fileType:@DAT_FILE syntax:@ENZYME_SYNTAX 
  tableFormat:left
  fields:{
    $field:@DF_ALL
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:[@DF_AltName code:altnam index:str indexToken:i_altnam
      tableToken:t_altnam]
    $field:[@DF_Description code:des index:str indexToken:i_des
      tableToken:t_des]
    $field:[@DF_CatActivity code:i_catact
      tableToken:t_catact]
    $field:[@DF_COMMENT code:cc]
    $field:[@DF_LINK index:link code:link indexToken:links]
  }
]

ENZYME_SYNTAX:$syntax:[file:"SRSDB:enzyme.is" ignore:" "]

DF_CatActivity:$srsfield:[CatalyticActivity short:cat group:@DF_ALL]	
DF_AltName:$srsfield:[AltName short:alt group:@DF_ALL]	

#$link:[@ENZYME_DB to:@?SWISSPROT_DB token:'links|swiss' toField:@DF_ACCNO]
$link:[@ENZYME_DB to:@?PROSITEDOC_DB token:'links|pr' toField:@DF_ID]
       
s]
    $field:[@DF_CatActivity code:i_catact
      tableToken:t_catact]
    $field:[@DF_COMMENT code:cc]
    $field:[@DF_LINK index:link code:link indexToken:links]
  }
]

ENZYME_SYNTAX:$syntax:[file:"SRSDB:enzyme.is" ignore:" "]

DF_CatActivity:srs/icarus/db/enzyme.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: enzyme.is,v $
#    $Revision: 1.7 $
#    $Date: 1997/03/03 18:33:55 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  ID:id	     CA:catact	  DI:di      '//':sep
  DE:des     CF:cf        DR:link
  AN:altnam  CC:cc	  PR:link   
}


$rules={
  entry:   ~ {$In:[file:text] $Out pre $Skip:0}
             ('ID' {$Not} ln)*
             ('ID   ' {$entryFip=$fip $Wrt} ln {$App} 
              ('ID' {$Not} ln {$App})*)?
             
           ~
  # fields
  fields:   ~ {$In:entry $Out $Skip:1}
              (/../ { if:$Ct==$prev $App else $Wrt:$fn.$Ct
            	      if:$fn.$Ct=="" $dp:"+++ unknown: $Ct +++"
            	      $prev=$Ct
            	    } ln {$App})+ ~

  # indexing
  id:       ~ {$In:[fields c:id] $Out:id} 'ID' /[0-9.]+/ {$Wrt} ~
  i_des:    ~ {$In:[fields c:des] $Out} ('DE' ( /[A-Za-z0-9_]+/ {$Wrt} | 
              /[^A-Za-z0-9_]+/ )* )* ~
  i_altnam: ~ {$In:[fields c:altnam] $Out} ('AN' ( /[A-Za-z0-9_]+/ {$Wrt} | 
              /[^A-Za-z0-9_]+/ )* )* ~
  i_catact: ~ {$In:[fields c:catact] $Out} 'CA' /[A-Z0-9_]+/ {$Wrt} ~
  cf:       ~ {$In:[fields c:cf] $Out:cf} 'CF' /[A-Z0-9_]+/ {$Wrt} ~
  cc:       ~ {$In:[fields c:cc] $Out:cc} 'CC' /[A-Z0-9_]+/ {$Wrt} ~
  di:       ~ {$In:[fields c:di] $Out:di} 'DI' /[A-Z0-9_]+/ {$Wrt} ~

  links:    ~ {$In:[fields c:link] $Out}
              (/DR/ (name {$Wrt:swiss} ',' name ';')*)*
              (/PR/ 'PROSITE;' name {$Wrt:pr} ';'?)* ~

  # table display
  t_catact: ~ {$In:[fields c:catact] $Out} /../ ln {$Wrt} (/../ ln {$App})* ~ 
  t_des:    ~ {$In:[fields c:des] $Out} /../ ln {$Wrt} (/../ ln {$App})* ~ 
  t_altnam: ~ {$In:[fields c:altnam] $Out} /../ ln {$Wrt} (/../ ln {$App})* ~ 


  # html display
  hl_links: ~ {$In:[fields c:link t:hl]}
              ( 
               (/DR/  (name {$Rep:{$ParStr:swissR $Ct $Ct}}',' name ';')* ln) |
               (/PR/ name ';' name {$Rep:{$ParStr:prositedocR $Ct $Ct}} ln)
              )* 
            ~
  # other   
  name:     ~ /[a-zA-Z0-9_]+/ ~ 
  ln:       ~ /[^\n]*\n/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/data/ftp/pub/databases/enzyme/enzyme.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}






     (/DR/  (name {$Rep:{$ParStr:swissR $Ct $Ct}}',' name ';')* ln) |
               (/PR/ name ';' name {$Rep:{$ParStrsrs/icarus/db/enzyme.it
#    
#    $RCSfile: enzyme.it,v $
#    $Revision: 1.3 $
#    $Date: 1996/10/10 16:47:04 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |The ENZYME data bank contains the following data for each type of 
    |characterized enzyme for which an EC number has been provided: EC number, 
    |Recommended name,
    |Alternative names, Catalytic activity, Cofactors, Pointers to the SWISS-PROT 
    |entrie(s)
    |that correspond to the enzyme, Pointers to disease(s) associated with a 
    |deficiency of the enzyme.
    |
    |<p>
  www:
    |<A HREF="http://www.gdb.org/Dan/proteins/ec-enzyme.html">\
    |http://www.gdb.org/Dan/proteins/ec-enzyme.html</A>
  citation:
    |Bairoch A. (1993) The ENZYME data bank. Nucleic Acids Res, Jul
    |1;21(13):3155-6.
  fields:{
    ID:
      |The <EM>ID</EM>  (IDentification) line  is always the first line of an entry. The
      |format of the ID line is:
      |<p>
      |ID   EC NUMBER
    Description:
      | The <EM>DE</EM>  (DEscription) line(s) contain the NC-IUB recommended name for an
      | enzyme. The format of the DE line is:
      |<p>
      | DE   DESCRIPTION.
      |<p>
      | Important note:  enzymes are  sometimes deleted from the EC list, others
      | are renumbered;  however the  NC-IUBMB does not allocate the old numbers
      | to new  enzymes. Obsolete  EC numbers are indicated in this data bank by
      | the following DE line syntaxes. For deleted enzymes:
      |<p>
      | DE   DELETED ENTRY.
      |<p>
      | and for renumbered enzymes:
      |<p>
      | DE   TRANSFERRED ENTRY: x.x.x.x.
      |<p>
      | where x.x.x.x  is the  new, valid,  EC number; as shown in the following
      | example:
      |<p>
      | DE   TRANSFERRED ENTRY: 1.7.99.5.
    AltName:
      | The <EM>AN</EM>  (Alternate Name)  line(s) are  used to  indicate  the  different
      | name(s), other  than the NC-IUBMB recommended name, that are used in the
      | literature to describe an enzyme. The format of the AN line is:
      |<p>
      | AN   NAME.
      |<p>
    Reaction:
      | The CA (Catalytic Activity) line(s) are used to indicate the reaction(s)
      | catalyzed by an enzyme. The format of the CA line is:
      |<p>
      | CA   REACTION.
      |<p>
      | Where the reaction is indicated following the recommendations of the NC-
      | IUBMB. The  majority of  the reactions  are described  using a  standard
      | chemical reaction format:
      |<p>
      | CA   SUBSTRATE_11 + SUBSTRATE_12 [+ SUBSTRATE_1N...]  = SUBSTRATE_21 +
      | CA   SUBSTRATE_22 [+ SUBSTRATE_2N].
      |<p>
      | As shown in the following examples:
      |<p>
      | CA   L-MALATE + NAD(+) = OXALOACETATE + NADH.
      |<p>
      | CA   2 ATP + GLUTAMINE + CO(2) + H(2)O = 2 ADP + ORTHOPHOSPHATE +
      | CA   GLUTAMATE + CARBAMOYL PHOSPHATE.
      |<p>
      | In some  cases free text is used to describe a reaction. As shown in the
      | following examples:
      |<p>
      | CA   DEGRADES STARCH TO CYCLODEXTRINS BY FORMATION OF A 1,4-ALPHA-D-
      | CA   GLUCOSIDIC BOND.
      |<p>
      | CA   CLEAVES LEU-|-LEU BOND IN ANGIOTENSINOGEN TO GENERATE
      | CA   ANGIOTENSIN I.
      |<p>
      |      Notes
      |<p>
      | -  Subscript and superscript are indicated between brackets: for example
      |    NAD+ and NADP+ are indicated as NAD(+) and NADP(+), H2O as H(2)O, CO2
      |    as CO(2), etc.
      | -  Greek letters are spelled out.
      |<p>
    Cofactor:
      | The <EM>CO</EM>  (CoFactor) line(s)  are used  to indicate  which cofactor(s) are
      | required by an enzyme. The format of the CF line is:
      |<p>
      | CF   COFACTOR_1; COFACTOR_2 OR COFACTOR_3[; COFACTOR_N...].
      |<p>
    Comments:
      | The <EM>CC</EM>  lines are  free text  comments on  the entry, and may be used to
      | convey any useful information.
      |<p>
    Disease:
      | The <EM>DI</EM>  (DIsease) line(s)  are used  to indicate  the  known  disases(s)
      | associated with  a deficiency  of the enzyme. Currently this information
      | is only given for human diseases listed in the MIM book [2].
      |<p>
      | [2]  McKusick V.A.
      |      Mendelian Inheritance in Man
      |      Catalogs of autosomal dominant, autosomal recessive,  and  X-linked
      |      phenotypes
      |      Tenth edition
      |      Johns Hopkins University Press, Baltimore, (1991).
      |<p>
      | The format of the DI line is:
      |<p>
      | DI   DISEASE_NAME; MIM:NUMBER.
      |<p>
      | Where 'NUMBER' is the MIM catalog number of the disease (or phenotype).
      |<p>
    Ref:
      | The <EM>DR</EM>  (Data bank Reference) line(s) are used as pointers to the SWISS-
      | PROT entries  that corresponds to the enzyme being described. The format
      | of the DR line is:
      |<p>
      | DR   AC_NB, ENTRY_NAME;  AC_NB, ENTRY_NAME;  AC_NB, ENTRY_NAME;
      |<p>
      | where:
      |<p>
      | -  'AC_NB' is  the SWISS-PROT  primary accession  number of the entry to
      |    which reference is being made.
      | -  'ENTRY_NAME' is the SWISS-PROT entry name.
      |<p>
  }
  date:
    |25 Jul 1996
  signature:
    |Anatoly Ulyanov
}
used as pointers to the SWISS-
      | PROT entries  that corresponds to the enzyme being described. The format
      | of the DR line is:
      |<p>
      | DR   AC_NB, ENTRY_NAME;  AC_NB, ENTRY_NAME;  AC_NB, ENTRY_NAME;
      |<p>
      | where:
      |<p>
      | -  'AC_NB' is  the SWISS-PROT  prsrs/icarus/db/epd.i
#
#    $RCSfile: epd.i,v $
#    $Revision: 1.5 $
#    $Date: 1997/03/03 18:33:56 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

EPD_DB:$library:[EPD group:@SEQRELATED_LIBS
  comment:"Eukariotic Promoter Database - Philipp Bucher (1996)"
  format:@EPD_FORMAT cachesize:512 ifiles:{"epd.i" "epd.is"}
  files:{
    $file:epd
  }
]

EPD_FORMAT:$libformat:[fileType:@DAT_FILE syntax:@EPD_SYNTAX
  fields:{
    $field:[@DF_ID       code:id     index:id   indexToken:id]
    $field:[@DF_LINK     code:link   index:link indexToken:links]
    $field:[@DF_Organism  code:source index:str  indexToken:source   
      tableToken:t_source   tableFormat:left]
    $field:[@DF_GeneProduct  code:prod   index:str  indexToken:product  
      tableToken:t_product  tableFormat:left]
    $field:[@DF_Protocol code:prtcl  index:str  indexToken:protocol 
      tableToken:t_protocol tableFormat:center]
    $field:[@DF_Express  code:exprs  index:str  indexToken:express  
      tableToken:t_express  tableFormat:center]
  }
]

EPD_SYNTAX:$syntax:[file:"SRSDB:epd.is" ignore:" \t"]

$link:[@EPD_DB to:@?EMBL_DB token:link toField:@DF_ID]

DF_Protocol:$srsfield:[ExpProtocol short:ptc group:@DF_ALL]
DF_Express: $srsfield:[ExpresRegul short:ess group:@DF_ALL]
tableToken:t_product  tableFormat:left]
    $field:[@DF_Protocol code:prtcl  index:str  indexToken:protocol 
      tableToken:t_protocol tableFormat:center]
    srs/icarus/db/epd.is
$abbrev={
  specie: {
#    Code           Scientific name (English name)
#
     AAV2:          'Adeno-associated virus 2'
     Ac:            'Aplysia californica (gastropod mollusk)'
     AcNPV:         'Autographa californica nuclear polyhedrosis virus'
     Ad2:           'Human adenovirus type  2'
     Ad5:           'Human adenovirus type  5'
     Ad7:           'Human adenovirus type  7'
     Ad12:          'Human adenovirus type 12'
     Ag:            'Ateles geoffroyi (spider monkey)'
     ALV:           'Avian leukemia virus'
     Am:            'Antirrhinum majus (snapdragon)'
    'A-MLV':        'Abelson murine leukemia virus'
     Apo:           'Antheraea polyphemus (silkmoth)'
     Ap:            'Anas platyrhynchos (mallard, domestic duck)'
     As:            'Avena sativa'
     At:            'Agrobacterium tumefaciens'
     Ath:           'Arabidopsis thaliana (fam. cruciferae)'
     Atr:           'Aotus trivirgatus (owl or night monkey)'
     Ay:            'Antheraea yamamai (Japanese oak silkmoth)'
     B19:           'Human parvovirus B19'
     Be:            'Bertholletia excelsa (Brazil nut)'
     BKV:           '(Human) papovavirus BK'
     BLV:           'Bovine leukemia virus'
     Bm:            'Bombyx mori (silkmoth)'
     Bn:            'Brassica napus (rape)'
     BPV1:          'Bovine papilloma virus type 1'
     Bt:            'Bos taurus (cattle)'
     C4BP:          'Complement component C4b-binding protein'
     CaMV:          'Cauliflower mosaic virus'
     Cc:            'Cricetus cricetus (Chinese hamster)'
     Cco:           'Coturnix coturnix (Quail)'
     Ce:            'Caenorhabditis elegans (nematode)'
     Cg:            'Canavalia gladiata (Japanese jackbean)'
     Ch:            'Capra hircus (goat)'
     Cl:            'Canis lupus (dog)'
     Cm:            'Cairina moschata (muscovy duck)'
     Cp:            'Cavia porcellus (guinea pig)'
     Cpe:           'Cucurbita pepo (zucchini)'
     Ct:            'Chironomus thummi (midge)'
     Cte:           'Chironomus tentans (midge)'
     DAF:           'Decay-accelerating factor'
     Dc:            'Daucus carota (carrot)'
     Df:            'Drosophila funebris      (fruit fly)'
     Dh:            'Drosophila hydei         (fruit fly)'
     DHBV:          'Duck hepatitis virus'
     Dm:            'Drosophila melanogaster  (fruit fly)'
     Dma:           'Drosophila mauritiana    (fruit fly)'
     Dmo:           'Drosophila mojavensis    (fruit fly)'
     Dmu:           'Drosophila mulleri       (fruit fly)'
     Do:            'Drosophila orena         (fruit fly)'
     Dp:            'Drosophila pseudoobscura (fruit fly)'
     Ds:            'Drosophila simulans      (fruit fly)'
     Dse:           'Drosophila sechellia     (fruit fly)'
     Dv:            'Drosophila virilis       (fruit fly)'
     EBV:           '(Human) Epstein-Barr virus'
     Ec:            'Equus caballus (horse)'
    'FBJ-MSV':      'Finkel-Biskis-Jinkins murine osteosarcoma virus'
    'FBR-MSV':      'Finkel-Biskis-Reilly murine osteosarcoma virus'
    'F-MCF':        '(Murine) Friend mink cell focus-inducing virus'
     Fs:            'Felis silvestris (cat)'
    'F-SFFV':       '(Murine) Friend spleen focus forming virus'
     Ft:            'Flaveria trinervia (dicot plant)'
    'GA-FeLV':      'Gardner-Arnstein feline leukemia virus'
     GALV:          'Gibbon ape leukemia virus'
     Gg:            'Gallus gallus (chicken)'
     Ggo:           'Gorilla gorilla (gorilla)'
     Gm:            'Glycine max (soybean)'
     GSHV:          'Ground squirrel hepatitis virus'
    'H-1':          '(Murine) H-1 parvovirus'
     Ha:            'Helianthus annuus (sunflower)'
     Hb:            'Hevea brasiliensis (para rubber tree)'
     HBV:           'Human hepatitis B virus'
     HCMV:          'Human cytomegalovirus'
     Hg:            'Halichoerus grypus (grey seal)'
    'HIV-1':        'Human immunodeficiency virus type 1'
    'HIV-2':        'Human immunodeficiency virus type 2'
     HPV16:         'Human Pappilloma virus 16'
     HPV18:         'Human Pappilloma virus 18'
     Hs:            'Homo sapiens (man)'
    'HSV-1':        'Human herpes simplex virus type 1'
    'HSV-2':        'Human herpes simplex virus type 2'
    'HTLV-I':       'Human T-cell leukemia virus type I'
    'HTLV-II':      'Human T-cell leukemia virus type II'
     Hv:            'Hordeum vulgare (barley)'
     HVS:           'Herpesvirus saimiri'
     JCV:           '(Human) papovavirus JC'
     Le:            'Lycopersicon esculentum (tomato)'
     Leu:           'Lepus europeaeus (hare)'
     Lm:            'Locusta migratoria'
     Lp:            'Lytechinus pictus (sea urchin)'
     Lpe:           'Lycopersicon peruvianum (wild tomato)'
     Lv:            'Lytechinus variegatus (sea urchin)'
     Ma:            'Mesocricetus aureus (golden hamster)'
     Mc:            'Macaca cynomolgus (macaque)'
     MCF:           'Mink cell focus-inducing virus'
     MCMV:          'Murine cytomegalovirus'
     MLV:           'Murine leukemia virus'
     Mm:            'Mus musculus (mouse)'
    'M-MLV':        'Moloney murine leukemia virus'
    'M-MSV':        'Moloney murine sarcoma virus'
     MMTV:          'Mouse mammary tumor virus'
     Ms:            'Medicago sativa (alfalfa)'
     MSV:           'Maize streak virus'
     Np:            'Nicotiana plumbaginifolia (leadwort-leaved tobacco)'
     Ns:            'Nicotiana silvestris (wood tobacco)'
     Nt:            'Nicotiana tabacum (tobacco)'
     Nto:           'Nicotiana tomentosiformis'
     Oa:            'Ovis aries (sheep)'
     Oc:            'Oryctolagus cuniculus (rabbit)'
     Os:            'Oryza sativa (rice)'
     Ph:            'Petunia hybrida (e.g. Petunia strain Mitchell)'
     Pa:            'Papio anubis (olive baboon)'
     Pc:            'Petroselinum crispum (parsley)'
     Pl:            'Paracentrotus lividus (sea urchin)'
     Pm:            'Psammechinus miliaris (sea urchin)'
     Polyoma:       '(Murine) polyoma virus'
     Ppy:           'Photinus pyralis'
     Pp:            'Pongo pygmaeus (orangutan)'
     Ps:            'Pisum sativum (pea)'
     Pt:            'Pan troglodytes (chimpanzee)'
     Pth:           'Pinus thunbergii (Japanese black pine)'
     Pv:            'Phaseolus vulgaris (french bean, kidney bean)'
     RAV2:          '(Avian) Rous associated virus type 2'
     Rc:            'Ricinus communis'
    'R-MCF':        '(Murine) Rauscher mink cell focus-inducing virus'
     Rn:            'Rattus norvegicus (rat)'
     RSV:           '(Avian) Rous sarcoma virus'
     Sa:            'Sinapis alba (white mustard)'
     SA7P:          'Simian adenovirus 7P'
     Sd:            'Strongylocentrotus drobachiensis (sea urchin)'
     Se:            'Spalax ehrenbergi (blind mole rat)'
     Sg:            'Salmo gairdneri (rainbow trout)'
    'SIV-III':      'Simian immunodeficiency virus type III'
     SNV:           '(Avian) spleen necrosis virus'
     So:            'Spinacia oleracea (spinach)'
     Sp:            'Strongylocentrotus purpureatus (sea urchin)'
     Spe:           'Sarcophaga peregrina (flesh fly)'
     Sr:            'Sesbania rostrata'
     Ss:            'Sus scrofa (pig)'
     SSV:           'Simian sarcoma virus'
     St:            'Solanum tuberosum (potato)'
     Sv:            'Sorghum vulgare (sorghum)'
     SV40:          'Simian virus 40'
     Ta:            'Triticum aestivum (wheat)'
     Visna:         'Visna lentivirus'
     Xb:            'Xenopus borealis   (Kenyan clawed frog)'
     Xl:            'Xenopus laevis     (African clawed frog)'
     Xt:            'Xenopus tropicalis (western clawed frog)'
     Zm:            'Zea mays (maize)'
   }
#  iGene Product Abbreviations
#
   product: {
    '1-25OH2D3':    '1,25-(OH)_2 vitamin D_3'
    '20-OHE':       '20-Hydroxyecdysone'
     4CL:           '4-coumarate coenzyme A ligase'
     a1:            'Gene locus 1 involved in anthocyanin biosynthesis'
    'abd-g.':       'Abdominal ganglion'
     abl:           'Abelson murine leukemia virus oncogene'
     ACC:           '1-aminocyclopropane-1-carboxylic acid'
     AChR:          'Acetylcholin receptor'
     ACP:           'b^-ketoacyl-acyl carrier protein of fatty acid synthase'
     ACTH:          'Adrenocorticotropic hormone'
     ADA:           'Adenosine deaminase'
     ADH:           'Alcohol dehydrogenase'
    'ADPg-s':       'GT ADPglucose-starch glucosyltransferase'
    'adult-HA':     'Adult hermaphrodite'
     AFW1:          'Adult fast-white (myosin heavy chain) 1'
     Ag:            'Antigen'
    '(AGM)':        '"from african green monkey"'
     AGP:           'Acid glycoprotein'
     AGPP:          'ADP glucose pyrophosphorylase'
     AIRS:          'Aminoimidazole ribonucleotide synthase'
    'ALA-synt.':    '5-Aminolevulinate synthase'
     ALDH_2:        'Aldehyde dehydrogenase 2'
     AlkExo:        'Alkaline exonuclease'
     Amy:           'Amylase'
     antp:          '"antennapedia" locus'
     aP2:           'Adipocyte homologue of myelin P2'
    'apolipop.':    'Apolipoprotein'
     apoVLDLII:     'Very low densitiy apolipoprotein II'
     APRT:          'Adenine phosphoribosyltransferase'
     AR:            'Adrenergic receptor'
     ARF:           'ADP-ribosylation factor'
     arg:           'Arginine'
     AS:            'Argininosuccinate synthetase'
    'AS-C':         '"achaete-scute" complex locus'
     AspAT:         'Aspartate aminotransferase'
    'ass.':         'Associated'
     AT:            'Antitrypsin'
     ATIII:         'Antithrombin III'
     ATCase:        'Aspartate transcarbamylase'
     ATP:           'Adenosinetriphosphate'
     awd:           '"abnormal wing disk" locus'
     BB:            'Bowman-Birk (protease inhibitor)'
     BCKDHA:        'Branched-chain alpha-keto acid dehydrogenase complex'
    'Bcl-2':        'B-cell leukemia/lymphoma 2 proto-oncogene'
     BPTI:          'Bovine pancreatic trypsin inhibitor'
     BSF:           'B-cell stimulating factor'
     bsg25D:        'Blastoderm specific locus 25D'
    'c-':           'Cellular protooncogene '
     c1:            'Regulatory locus of anthocyanin synthesis (maize)'
     CA:            'Carbonic anhydrase'
     cab:           'Chlorophyll a/b-binding protein'
     cAMP:          'Cyclic AMP (Adenosinemonophosphate)'
    'card-m':       'Cardiac muscle'
    'cc-ind.':      'Cell cycle-independent'
     CD3:           'T-cell differentiation antigen CD3'
     CD4:           'T-cell differentiation antigen CD4'
     CD8:           'T-cell differentiation antigen CD8'
     CEA:           'Carcinoembryonic antigen'
     CG:            'Chorionic gonadotropin'
     CNS:           'Central nervous system'
     CNTF:          'Ciliary neurotrophic factor'
    'car.':         'Cartilage'
    'col.':         'Collagen'
    'conglyc.':     'Conglycinin'
    'cor.':         'Cornea'
    'cotyl.':       'Cotyledon'
     cp:            'Cytoplasm(ic)'
     CPS:           'Carbamyl-phosphate synthetase'
     CRF:           'Corticotropin-releasing factor'
     CRP:           'C-reactive protein'
     cs:            'Cytosol(ic)'
     CSF:           'Colony stimulating facter'
     cyt:           'Cytokinin gene (coding for isopentenyltransferase)'
     dbp:           'DNA binding protein'
     DDC:           'DOPA decarboxylase'
    'dep.':         'dependent'
    'dev.':         'Development(ally)'
     DHFR:          'Dihydrofolate reductase'
    'diff.':        'differentiation, differentiated'
    'DL/R':         'Left and right duplicated region'
     dUTPase:       'Deoxyuridinetriphosphatase'
     E:             '1. Early, 2. Erythroid cell-specific'
     E8:            'Ethylene inducible gene during fruit ripening 8'
     EAS:           '5-epi-aristolochene synthase (sesquiterpene cyclase)'
     EBNA:          'Epstein-Barr virus nuclear antigens'
    'ecd-ind.':     'Ecdysone-inducible'
     EDF:           'Eosinophil differentiation factor'
     EFW1:          'Embryonic fast-white (myosin heavy chain) 1'
     EGF:           'Epidermal growth factor'
     EIa:           'Adenovirus early Ia region (transactivating element)'
     Eip:           'Ecdysone-induced protein'
     ELH:           'Egg-laying hormone'
     em:            'Embryo, embryonic'
     EPSP:          '5-Enolpyruvylshikimate-3-phosphate'
     erbA:          '(Avian) erythroblastosis virus oncogene A'
     erbB:          '(Avian) erythroblastosis virus oncogene B'
    'E-resp.':      'Estrogen-responsive'
     ERV3:          'Endogenous retrovirus 3'
    'E.Tn':         'Early transposon'
    'et-hypocot.':  'Etiolated hypocotyl'
     ev1:           '(Avian) endogenous virus 1'
     eve:           '"even-skipped" locus'
    'exch.':        'Exchanger'
    'f.':           'Factor'
    'fibrob.':      'Fibroblasts'
     FMRFamide:     'Phe-Met-Arg-Phe-NH(2) neuropeptide'
     FNR:           'Ferredoxin-(NADP+)-oxidoreductase'
     fos:           'FBJ (Finkel-Biskis-Jinkins) osteosarcoma virus oncogene'
     FSH:           'Follicle stimulating hormone'
     ftz:           '"fushi tarazu" locus'
    'g.':           'Gene'
     G0S:           'G0/G1 switch regulatory gene '
     G6PD:          'Glucose-6-phosphate dehydrogenase'
     GA:            'Gibberellic acid'
     GADPH:         'Glyceraldehyde-3-phosphate dehydrogenase'
     GARS:          'Glycinamide ribonucleotide synthase'
     Gart:          '"Gart" locus (-> GARS, AIRS, GART)'
     GART:          'Glycinamide ribonucleotide transformylase'
     gC:            'Glycoprotein C'
    'G-CSF':        'Granulocyte colony stimulating factor'
     gD:            'Glycoprotein D'
     GdX:           'X-linked gene downstream of G6PD gene'
     gE:            'Glycoprotein E'
     GFAP:          'Glial fibrillary acidic protein'
     gln:           'Glutamine'
    'globul-12s':   '12s globulin (oat seed storage protein)'
     glucc:         'Glucocorticoid'
     GLUT1:         'Glucose transporter type 1'
    'GM-CSF':       'Granulocyte/Macrophage colony stimulating factor'
     GnRH:          'Gonadotropin-releasing hormone'
     gp:            'Glycoprotein'
     GPD:           'Glycerol-3-phosphate dehydrogenase'
     GRF:           'Growth hormone-releasing factor'
     GRP:           'Glycine-rich (cell wall) protein'
     GS17:          'Gastrula-specific transcript 17'
     GSHPx:         'Gluthathione peroxidase'
    'G-spec.':      'Gastrula-specific'
     GST:           'Gutathione S-transferase'
     H:             '1. Heavy chain, 2. Housekeeping-type promoter'
    'Ha-ras':       'Rat-derived Harvey murine sarcoma virus oncogene'
     hb:            '"hunchbank" locus'
     Hc:            'High-cysteine (chorion protein)'
     HGT:           'High-(glycine+tyrosine) keratin'
    'hist.':        'Histone'
    'HMG-':         'High mobility group chromosomal protein'
    'HMG-CoA':      '3-Hydroxy-3-methylglutaryl coenzyme A'
     HPRT:          'Hypoxanthine phosphoribosyltransferase'
     hs:            'Heatshock'
     hsc:           'Constitutive analogue of heatshock gene/protein'
     HSF:           'Hepatocyte-stimulating factor'
     hsp:           'Heatshock protein'
     HTF:           'Restriction endonuclease HpaII tiny fragments'
    'I-FABP':       'Intestinal fatty-acid binding protein'
     IAA:           'Indolacetic acid'
     IAP:           'Intracisternal A-particles'
     ICP:           'Infected cell protein'
     IE:            'Immediate early (gene, RNA)'
     IF:            'Intermediate filament'
     IFI:           'Interferon-induced gene/protein'
     IFN:           'Interferon'
     Ig:            'Immunoglobulin'
     IGF:           'Insulin-like growth factor'
     IL:            'Interleukin'
    'inf.':         'Infected'
    'inh.':         'Inhibitor'
     ISG:           'Interferon-stimulated gene'
    'k.':           'Kinase'
    'Ki-ras':       'Rat-derived Kirsten murine sarcoma virus oncogene'
     L:             '1. Light chain; 2. Late'
     larva:         'instar larva'
     LAT:           'Lycopersicon anther-specific gene '
     LCAT:          'Lecithin-cholesterol acyltransferase'
     LDH:           'Lactate dehydrogenase'
    'leghem.':      'Leghemoglobin'
     LeIF:          'Leukocyte interferon'
     LH:            'Luteinizing hormone'
     LHC:           'Light-harvesting complex'
     LHRH:          'Luteinizing hormone-releasing factor'
     LMW:           'Low molecular weight'
     LPH:           'Lipotropic hormone'
     LPS:           'Lipopolysaccharide'
     MBP:           'Myelin basic protein'
    '(MAC)':        'Macaque'
     MC:            'Methylcholanthrene'
     MCK:           'Muscle-specific creatine kinase'
     mGK:           'Submaxillary gland kallikrein'
    'MHCI/MHCII':   'Class I/II transplantation antigens of major histocompatibility complex'
     MIF:           'Macrophage migration inhibitory factor'
     mit:           'Mitochondrial'
    'mononuc-c.':   'Mononuclear cells'
     MOPC:          'Mineral oil-induced plasmacytoma'
     mos:           'Moloney murine sarcoma virus oncogene'
     MP:            'Macrophage'
     MPC:           'Mouse plasma cell tumor'
     MRP:           'MIF-related protein (see MIF)'
     MSF:           'Megakaryocyte stimulating factor'
     msp:           'Major sperm protein gene'
     MT:            'Metallothionein'
     mst:           'Male-specific transcript'
     MUP:           'Major urinary protein'
     myb:           '(Avian) myeoloblastosis virus oncogene'
     myc:           'Myelocytomatosis virus 29 oncogene'
     NCA:           'nonspecific cross-reacting (with -> CEA) antigen'
     neu:           'Ethyl-nitrosurea-induced rat neuroblastoma oncogene'
    'neuropep.':    'Neuropeptide'
     NGF:           'Nerve growth factor'
     ninaE:         '"neither inactivation nor afterpotential" locus E'
     NMDH:          'NADP-malate dehydrogenase'
     nos:           'Nopaline synthetase'
     NR:            'Nitrate reductase'
    'N-ras':        'Neuroblastoma ras-like (-> Ha-ras) oncogene'
     NS:            'Nervous system'
     OAT:           'Ornithine aminotransferase'
     ocs:           'Octopine synthetase'
     ODC:           'Ornithine decarboxylase'
     Ori:           'Origin of replication'
     OTC:           'Ornithine transcarbamylase'
    'ovalb.':       'Ovalbumin'
    'p.':           'Protein'
    'P-450':        'Cytochrome P-450'
     p53:           '53K phosphoprotein'
    'panc.':        'pancreas, pancreatic'
    'parath.':      'Parathyroid'
     PB:            'Phenobarbital'
     PBGD:          'Porphobilinogen deaminase'
     PCNA:          'Proliferating cell nuclear antigen'
     PDGF:          'Platelet-derived growth factor'
     PEPCase:       'Phosphoenolpyruvate carboxylase'
     PEPCK:         'Phosphoenolpyruvate carboxykinase'
     PG:            'Prostaglandin'
     PGK:           '3-Phosphoglycerate kinase'
     PHA:           'Phytohemagglutinin'
     PK:            'Protein kinase'
     P_L:           'Late promoter'
     PLP:           'Proteolipid protein'
     POL:           'Polymerase'
     POMC:          'Proopiomelanocortin'
     pp:            'Phosphoprotein '
     PR1a:          'Pathogenesis-related protein 1a'
     PRBP:          'Plasma retinol-binding protein'
     PRL:           'Prolactin'
    'prog.':        'Progesterone'
     prolyl:        '4-hydr. Prolyl 4-hydroxylase'
     PrP:           'Prion protein'
     PSG:           'Pregnancy-specific glycoproteins '
     PSBP:          'Prostatic steroid binding protein'
     PSP:           'Parotid secretory protein'
     PTH:           'Parathyroid hormone'
     pTiN:          'Nopaline type tumor inducing plasmid'
     pTiO:          'Octopine type tumor inducing plasmid'
     r:             '"rudimentary" locus'
     R:             '1. Regulatory subunit, 2. Erythroid cell-specific'
     RAB:           'Gene responsive to ABA'
     ras:           'Homologue of -> Ha-ras, Ki-ras, etc.'
    'rec.':         'Receptor'
    'red.':         'Reductase'
    'reg.':         'Regulated'
    'rep-dep.':     'Replication-dependent'
     rig:           'Rat insulinoma gene'
     RnBP:          'Renin-binding protein'
     RNR2:          'Ribonucleotide reductase large, small subunit'
     rp:            'Ribosomal protein'
     rTn:           'Retrotransposon'
     RuBPCss:       'Ribulose-1,5-biphosphate carboxylase small subunit'
     RuBPCA:        'Ribulose-1,5-biphosphate carboxylase/oxygenase activase'
    's.':           'Small'
    'saliv-g.':     'Salivary gland'
     SBP:           'Spermine-binding protein'
    'sem-v.':       'Seminal vesicle'
    'ser.':         'Serum'
     sgs:           'Salivary gland secretion protein'
     sis:           'Simian sarcoma virus oncogene'
    'sk-m.':        'Skeletal muscle'
    'skel-m.':      'Skeletal muscle'
    'smooth-m.':    'Smooth muscle'
     snRNA:         'Small nuclear RNA'
     snrp:          'Small nuclear ribonucleoprotein'
     SOD:           'Superoxide dismutase'
     som:           'Somatic'
    'spat-reg.':    'Spatially regulated'
     Spec:          'Strongylocentrotus purpureatus ectoderm enriched RNA'
     sry:           '"serendipity" locus'
     SV40T:         'Tumor antigen of simian virus 40 (SV40)'
     SVS:           'Seminal vesicle secretory protein'
     synt:          '^Synthase^'
     T3d:           'T-cell antigen receptor-associated T3-complex delta chain'
     TAT:           'Tyrosine aminotransferase'
     TCDD:          '2,3,7,8-Tetrachlorodibenzo-p-dioxin'
     TCGF:          'T-cell growth factor'
     TCR:           'T-cell receptor'
     TdT:           'Terminal deoxynucleotidyltransferase'
    'test.':        'testis'
     TF:            'Transcription factor'
     TGA1a:         'TGACG-specific DNA-binding protein 1a'
    'TGF-b':        'Transforming growth factor beta'
     TH:            'Tyrosin hydroxylase'
    'thyr.':        'Thyroxine'
    'Thy-1.2':      'Thy-1 (thymocyte) antigen/glycoprotein allotype 2'
     TIF:           'Trans-inducing factor'
     TIM:           'Triosephosphate isomerase'
    'tis.':         'Tissue'
     TM:            'Tropomyosin'
     tmr:           '"tumor morphology root" locus'
     TNF:           'Tumor necrosis factor'
     TnT:           'Troponin T (tropomyosin-binding subunit)'
     TO:            'Tryptophan oxygenase'
     TP1:           'Transition protein 1'
     TP2:           'Transition protein 2'
     TPA:           '12-O-tetradecaonyl-phorbol-13-acetate'
     TPI:           'Triosephosphate isomerase'
    'tr.':          'Transcript'
    'tr-':          'Transcript'
     TRF:           'T-cell replacing factor'
     TRH:           'Thyrotropin-releasing hormone'
     TS:            'Thymidylate sythetase'
     TSH:           'Thyroid stimulating hormone'
    'T/t':          'Large/small T(tumor) antigen'
     Ubx:           '"ultrabithorax" locus'
     uPA:           'Urine  plasminogen activator'
    'URO-D':        'Uroporphyrinogen decarboxylase'
     Vg1:           'Vegetal hemisphere-specific mRNA 1'
    'vir-inf.':     'Viral infection'
     VL30:          'Retrovirus-like 30s RNA'
     V_NP:          '(Immunoglobulin heavy chain) variable region specific for 4-hydroxyl-3-nitrophenacetyl'
     VP5:           'Virion protein 5 (HSV-1/2: =major capsid protein)'
     VSP:           'Virion stimulatory protein'
     vWf:           'von Willebrand factor'
     Zen:           '"zerknuellt" protein'
   }
 }
$rules={
  entry:      ~ {$In:[file:text] $Out:entry}
              	('FP' {$Not} ln)*
              	('FP   ' {pre {$entryFip = $Fip} $Wrt} ln {$App} 
              	('//' {$Not} ln {$App})*)?
              ~
  # fields    
  fields:     ~ {$In:entry $Out} f_id f_com? f_doc
              ~
  f_id:       ~ {$Wrt:id}   'FP   '  ln ~ 
  f_com:      ~ {$Wrt:com}  'XX'     ln ~ 
  f_doc:      ~ {$Wrt:doc} ('DO   '  ln)* ~

  # substitute abbreviations
  ab_spec:    ~ {$In:[fields c:id] $Out} 'FP' /[A-Za-z0-9-]+/
                {if:[$abbrev.specie.$Ct != ''] $Wrt:[s:$abbrev.specie.$Ct] 
    	         else $Wrt:[s:$Ct]}
              ~
  ab_prod:    ~ {$In:[fields c:id] $Out} 'FP' /[^ ]+/ 
                (/[^:][^ :]+/ { if:[$abbrev.product.$Ct != '']
	                          $Wrt:[s:$abbrev.product.$Ct]
	                        else
	                        $Wrt:[s:$Ct]} /'/? )* ~
  ab_proto:   ~ '(' {$exp="related"}
                | '<' {$exp="low-precision"}
	        | /[0-9]+/ {$exp=$Ct}
                | '*' {$exp="in_vitro"} 
	        | 'o' {$exp="oocyte"} 
	        | '#' {$exp="transfected"}
	        | '!' {$exp="transgenic"}
	      ~

  # indexing
  id:         ~ {$In:[fields c:id] $Out:id} x{$Mov:56} 
                ' '? /[A-Z0-9_]+/ {$Wrt} ~
  link:       ~ {$In:[fields c:id] $Out} x{$Mov:34} /[A-Z0-9_]+/ {$Wrt} ~
  source:     ~ {$In:ab_spec $Out:source} ('('? /[^ )(,]+/ {$Wrt} /[)(,]/?)* ~
  product:    ~ {$In:ab_prod $Out:product} ('('? /[^ )(,]+/ {$Wrt} /[)(,]/?)* ~
  protocol:   ~ {$In:[fields c:doc] $Out} (('DO        Experimental evidence:'
            	(ab_proto {$Wrt:[s:$exp]} /[)>,\/]/?)*) | ln)* ~
  express:    ~ {$In:[fields c:doc] $Out} (('DO        Expression/Regulation:'
	    	(/[\[(+-]+/? /[A-Za-z0-9_':-]+/ {$Wrt} /[\]);,.+-]+/?)* | ln)
            	| ln)* ~
  doc:        ~ {$In:[fields c:doc] $Out} ('DO' (
	    	 ('Experimental evidence:' (ab_proto {$Wrt:[prot s:$exp]}
	    	  /[)>,\/]/? )* ln ) | 
                 ('Expression/Regulation:' ( /[(+-]+/? 
	    	  /[A-Za-z0-9_':-]+/ {$Wrt:regul} /[);,.+-]+/? )* ln )))* ~
  sequence:   ~ {$In:[fields c:id] $Out:id} x{$Mov:34} 
            	/[A-Z0-9_]+/ {$accN=$Ct}
            	/[01]/ {$type=$Ct} /[+-]/ {$dir=$st} /[0-9]+/ ~

  # table display
  t_source:   ~ {$Out $In:[fields c:id]} 'FP' /[A-Za-z0-9-]+/ {$Wrt} ~
  t_product:  ~ {$Out $In:[fields c:id]} 'FP' /[^ ]+/ /[^:]+/? {$Wrt} ~
  t_protocol: ~ {$Out $In:[fields c:doc]} (('DO        Experimental evidence:'
                /[^\n]*/ {$Wrt} ) | ln )* ~
  t_express:  ~ {$Out $In:[fields c:doc]} (('DO        Expression/Regulation:'
                /[^\n]*/ {$Wrt} ) | ln )* ~

  # HTML display
  hl_links:   ~ {$In:[fields c:id t:hl]} x{$Mov:34}
                /[A-Z0-9_]+/ {$Rep:{$ParStr:epdR $Ct $Ct}}
              ~
  # other 
  ln:         ~ /[^\n]*\n/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/data/epd/epd.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:link print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}

 $In:[fields c:doc]} (('DO        Expression/Regulation:'
                /[^\n]*/ {$Wrt} ) | ln )* ~

  # HTML display
  hl_links:   ~ {$In:[fields c:id t:hl]} x{$Mov:34}
                /[A-Z0-9_]+/ {$Rep:{$ParStr:epdR $Ct $Ct}}
              ~
  # other 
  ln:         ~ /[^\n]*\n/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/data/epd/epd.dsrs/icarus/db/epd.it
#
#    $RCSfile: epd.it,v $
#    $Revision: 1.2 $
#    $Date: 1996/10/10 16:47:05 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$dbInfo={
   description: 
     |The Eukaryotic Promoter Database EPD was designed and developed at
     |the WeizmannInstitute of Science in Rehovot (Israel) and is currently
     |maintained at ISREC inEpalinges s/Lausanne (Switzerland). EPD is a
     |specialized annotation database ofthe EMBL Data Library. It provides
     |information about eukaryotic promoters avail-able in the EMBL Data
     |Library and is intended to assist experimental research-ers, as well as
     |computer analysts, in the investigation of eukaryotic transcrip-tion
     |signals. The present version originated from a previous compilation
     |pub-lished in an article (1) and is organized as a hierarchically
     |ordered and docu-mented "functional position set" (2) pointing to
     |transcription initiation sites. All information is directly abstracted
     |from scientific literature and is thusindependent of the EMBL sequence
     |entry descriptions. As a consequence, many ofthe initiation sites
     |referred to in EPD do not appear in corresponding EMBLfeature tables.
     |<p> A co-ordinated updating procedure has been set up by the two
     |laboratories thatwill ensure future compatibility between the position
     |references in EPD and thesequence data in the main data library.
     |Investigators who access EMBL via pub-licly available programs should
     |be aware of the fact that software producers oc-casionally modify the
     |sequence data in ways that render position referencesinaccurate. EPD is
     |generally not compatible with sequence data of anotherrelease because
     |EMBL sequence entries are not designed as stable data units. <p> The
     |completeness and accuracy of EPD greatly benefits from user-feedback.
     |Anyreport of mistakes or omissions would be very much appreciated.
     |Direct communi-cation of newly published transcript mapping or gene
     |expression data is alsowelcome. Please forward all correspondence
     |to the address given on top of thisdocument. Use electronic mail if
     |possible.

   more: ''
   citation: '' 
   ftpSite:''
   fields:{
     ID:
       |The entry code is a five-digit number which is the only part of a
       |promoter entry that is stable from release to release. The first two
       |digits designate the release of initial appearance.
     Organism:
       |Species codes consist of the       
       |initials of genus and species name. Occasionally, three characters    
       |are required to generate unique codes. Standard abbreviations identify 
       |viruses. The full names of the organisms can be used in a query. The   
       |names are given in appendix B.1. Subspecies or strains are specified   
       |in parentheses.                                                        
       |Chromosomal locations (genetic or cytogenetic loci, genomic map       
       |units, etc.) appear in square brackets immediately following species  
       |codes.                                                                
     GeneProduct:
       |Many gene products are listed in appendix B.3. Alternative initiation
       |sites are identified by right-justified P1,P2.., or E1,E2.., depending
       |on whether the corresponding 5'exons are 3'co-terminal or not. The
       |strongest initiation site is marked by trailing + if known.
     ExpProtocol:
       |Special characters appended to the number codes designate an
       |experimental geneexpression system where the RNA for the corresponding
       |experiments wassynthesized. A query may have next key words:
       |<UL>
       |	<LI> related
       |	<LI> low-precision
       |	<LI> in_vitro
       |	<LI> oocyte
       |	<LI> transfected
       |	<LI> transgenic
       |</UL>
       |or the transcript mapping experiments number that define the promoter,
       |that gives information about expression and regulation. The varies
       |experimental techniques are identified by number codes:
       |<TABLE>
       |<TR><TH>codes<TD><B>experiments</B>
       |<TR><TH>1<TD>direct RNA sequencing
       |<TR><TH>2<TD>length measurement of an RNA product
       |<TR><TH>3<TD>length measurement of a nuclease-protected complementary
       |RNA or DNA fragment by comparison with homologous sequence ladder
       |<TR><TH>4<TD>same as 3 but with heterologous size markers
       |<TR><TH>5<TD>RNA sequencing by dideoxy-terminated primer extension
       |<TR><TH>6<TD>DNA Sequencing of an in vitro generated strong-stop cDNA or
       |a full-length cDNA clone
       |<TR><TH>7<TD>length measurement of a primer-extension product by
       |comparison with homologous sequence ladder
       |<TR><TH>8<TD>same as 7 but with heterologous size markers
       |<TR><TH>9<TD>DNA sequencing of a full-length processed pseudogene
       |<TR><TH>10<TD>length measurement of a reverse direction primer-extension
       |product (blocked by RNA 5'end) by comparison with homologous sequence
       |ladder
       |</TABLE>
     ExpresRegul:
       |The information on expression/regulation may include indication of
       |developmentalstages, tissues, cell types, cell cycle stages, and
       |various regulatory features.
       |<DL>
       |<DT><B>;</B><DD>delimits different types of specifications
       |   (e.g. developmental stage and tissue).
       |
       |<DT><B>,</B><DD>delimits alternative keywords (e.g. liver,  kidney)
       |
       |<DT><B>+</B><DD>means "induced by" or "strongly expressed in".
       |
       |<DT><B>-</B><DD>means "repressed by" or "weakly expressed in".
       |
       |<DT><B>~</B><DD>means "modulated by".
       |
       |<DT><B>[...]</B><DD>delimits cell cycle stages.
       |</DL>
  }
  date:
    |25 Jul 1996
  signature:
    |Anatoly Ulyanov
}
of specifications
       |   (e.g. developmental stage and tissue).
       |
       |<DT><B>,</B><DD>delimsrs/icarus/db/esther.is


$rules={
  entry:    ~ { $Out pre $Skip:0}
              (/[0-9]+ / {$Not} ln)*
              (/[0-9]+ / {$Wrt $entryFip=$Fip} ln {$App} 
               (/[0-9]+ / {$Not} ln {$App})+)?  
            ~

  ln:       ~ /[^\n]*\n/ ~
}

if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:"/u/etzold/data/databases.data/Esther/shaff.txt"]
  while:$JobHasInput:$job {
    $JobTokens:[$job name:entry print:1] 
#    $JobTokens:[$job name:nucPos print:1]
#    $JobTokens:[$job name:nucChange print:1]
    $JobNext:$job
    $print:"-------->entry\n"
  }
}
      (/[0-9]+ / {$Not} ln)*
              (/[0-9]+ / {$Wrt $entryFip=$Fip} ln {$App} 
               (/[0-9]+ / {$Not} ln {$App})+)?  
            ~

  ln:       ~ /[^\n]*\n/ ~
}

if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:"/u/etzold/data/databases.data/Esther/shaff.txt"]
  while:$JobHasInput:$job {
    $JobTokens:[$job name:entry print:1] 
#    $JobTokens:[$job name:nucPos print:1]
#    $JobTokens:[$job name:nusrs/icarus/db/fasta.i
#    $RCSfile: fasta.i,v $
#    $Revision: 1.4 $
#    $Date: 1997/03/03 18:33:56 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


FASTA_DB:$library:[FASTA group:@APPLICATION_LIBS 
  comment:"" 
  format:@FASTA_FORMAT maxNameLen:40 ifiles:{"fasta.i" "fasta.is"}
  type:user
  files:{
    $file:tmp
  }
]

FASTA_FORMAT:$libformat:[fileType:@FASTA_FILE syntax:@FASTA_SYNTAX 
  fields:{
    $field:[@DF_ID code:title index:id indexToken:id]
    $field:[@DF_Init1 code:scores1 index:int indexToken:init1
      tableToken:init1 tableFormat:right]
    $field:[@DF_Initn code:scores1 index:int indexToken:initn
      tableToken:initn tableFormat:right]
    $field:[@DF_OptScore code:scores1 index:int indexToken:opt
      tableToken:opt tableFormat:right]
    $field:[@DF_PercentIdent code:scores2 index:int indexToken:percIdent
      tableToken:percIdent tableFormat:right]
    $field:[@DF_Alignment code:align
      tableToken:t_align tableFormat:left]
#    $field:[@DF_QueryBeg code:align index:int indexToken:queryBeg]
#    $field:[@DF_QueryEnd code:align index:int indexToken:queryEnd]
#    $field:[@DF_MatchLen code:align index:int indexToken:matchLen
#      tableToken:matchLen tableFormat:right]
    $field:[@DF_LINK code:title index:link indexToken:link]
  }
]


DF_Init1:$srsfield:[Init1 short:in1]
DF_Initn:$srsfield:[Initn short:inn ]
DF_OptScore:$srsfield:[OptScore short:opt]
DF_PercentIdent:$srsfield:[PercentIdentity short:pid]

FASTA_SYNTAX:$syntax:[file:"SRSDB:fasta.is" ignore:" "]
FASTA_FILE:$filetype:[typename:fasta maxline:500]

# links 
$link:[@FASTA_DB to:@?SWISSPROT_DB token:'link|swiss' toField:@DF_Accession]
$link:[@FASTA_DB to:@?SWISSNEW_DB token:'link|swissnew' toField:@DF_Accession]
$link:[@FASTA_DB to:@?PIR_DB token:'link|pir' toField:@DF_Accession]
$link:[@FASTA_DB to:@?TREMBL_DB token:'link|trembl' toField:@DF_Accession]
$link:[@FASTA_DB to:@?TREMBLNEW_DB token:'link|tremblnew' toField:@DF_Accession]
ty short:pid]

FASTA_SYNTAX:$syntax:[file:"SRSDB:fasta.is" ignore:" "]
FASTA_FILE:$filetype:[typename:fasta maxline:500]

# links 
$link:[@FASTA_DB to:@?SWISSPROT_DB token:'link|swiss' toField:@DF_Accession]
$link:[@FASTA_DB to:@?SWISSNEW_DB token:'link|swissnew' toField:@DF_Accession]
$link:[@FASTA_DB to:@?PIR_DB token:'link|pir' toField:@DF_Accession]
$link:[@FASTA_DB to:@?TREMBL_DB token:'link|trembl' toField:@DF_Accession]
$link:[@FASTA_DB to:@?TREMBLNEW_DB token:'link|tremblnew' srs/icarus/db/fasta.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: fasta.is,v $
#    $Revision: 1.7 $
#    $Date: 1997/03/03 18:33:57 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$rules={
  entry:    ~ {$In:[file:text] $Out pre{$Skip:0} init{$count=0}}
              ('>>' {$Not} ln)*
              ('>>' {$Wrt $entryFip=$Fip $count+=1} appLn
               ('>>' {$Not} appLn)+
              )? ~

  # data fields
  fields:   ~ {$In:entry $Out $Skip:1} 
              /(.*)(initn:[^\n]+\n)/ 
              {$Wrt:[title s:"$1\n"] $Wrt:[scores1 s:"$2"]}
              ln {$Wrt:scores2} 
              /.+/ {$Wrt:align} ~

  # indexing
  id:       ~ {$In:[fields c:title] $Out} 
              />>([^|]+)\\|[^|]+\\|([A-Z0-9a-z_]+)/ 
              {$Wrt:[s:"$count\_$1_$2"]} ~
  init1:    ~ {$In:[fields c:scores1] $Out} /.*init1: *([0-9]+)/{$Wrt:[s:$1]}~
  initn:    ~ {$In:[fields c:scores1] $Out} /.*initn: *([0-9]+)/{$Wrt:[s:$1]}~
  opt:      ~ {$In:[fields c:scores1] $Out} /.*opt: *([0-9]+)/{$Wrt:[s:$1]} ~
  percIdent:~ {$In:[fields c:scores2] $Out} 
              /.+ ([0-9.]+)%/ {$Wrt:[s:$1]} ~
  queryBeg: ~ {$In:[fields c:align] $Out}
              /[ \n]+([0-9]+)/ {$b=$1 $Wrt:[s:$1]} ~
  queryEnd: ~ {$In:[fields c:align] $Out}
              /.* ([0-9]+) *\n *[a-zA-Z0-9]/ {$e=$1 $Wrt:[s:$1]} ~
  matchLen: ~ {$Out pre{$Request:queryEnd $Request:queryBeg 
               $Wrt:[s:($e-$b+1)]}} / /~
  link:     ~ {$Out $In:[fields c:title]} 
              '>>'(/(sw|swiss|swissprot|sp)\\|/{$dp:$Ct} name {$Wrt:swiss})?~ 

  # table display

  t_align:  ~ {$Out $In:[fields c:align]}
              /.+/ {$Wrt:[s:"<font size=2><textarea rows=9 cols=70>$Ct</textarea>"]} ~

  # html display 

  h_title:  ~ {$In:[fields c:title t:html]} 
              '>>' ('sp|' name {$Rep:{$ParStr:swissR $Ct $Ct}})? ~

  # other  
  name:     ~ /[a-zA-Z0-9_]+/ ~
  appLn:    ~ /[^\n]*\n/ {$App} ~
  ln:       ~ /[^\n]*\n/  ~
}


if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'u/etzold/tmp.fasta']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields  print:1] 
    $JobTokens:[$job name:id print:1]
    $JobNext:$job
    $print:"----------------------------------------------\n"
  }
}
splay 

  h_title:  ~ {$In:[fields c:title t:html]} 
              '>>' ('sp|' name {$Rep:{$ParStr:swissR $Ct $Ct}})? ~

  # other  
  name:     ~ /[a-zA-Z0-9_]+/ ~
  appLn:    ~ /[^\n]*\n/ {$App} ~
  ln:       ~ /[^\n]*\n/  ~
}


if:$TestMode {
  $job srs/icarus/db/flygene.i
#    $RCSfile: flygene.i,v $
#    $Revision: 1.4 $
#    $Date: 1996/12/06 22:17:39 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

FLYGENE_DB:$library:[FLYGENE group:@GENOME_LIBS
   format:@FLYGENE_FORMAT maxNameLen:15 ifiles:{"flygene.i" "flygene.is"}
    files:{
       $file:genes
    }
]

FLYGENE_FORMAT:$libformat:[fileType:@TXT_FILE syntax:@FLYGENE_SYNTAX
  printFormat:table2 tableFormat:left fields:{
    $field:[@DF_ID code:id index:id indexToken:id tableToken:id]
#    $field:[@DF_FullName code:e index:str indexToken:e]
#    $field:[@DF_GenMapPos code:b index:str indexToken:b]
    $field:[@DF_MinCytologicLoc code:c index:str indexToken:'c|min']
    $field:[@DF_MaxCytologicLoc code:c index:str indexToken:'c|max']
  }
]
FLYGENE_SYNTAX:$syntax:[file:"SRSDB:flygene.is" ignore:" "]

DF_FullName:$srsfield:[FullName short:fnm group:@DF_ALL]
DF_GenMapPos:$srsfield:[GeneticMapPosition short:gmp]
DF_MinCytologicLoc:$srsfield:[MinCytologicLocation short:mcl]
DF_MaxCytologicLoc:$srsfield:[MaxCytologicLocation short:xcl]

#$link:[@FLYGENE_DB to:@?EMBL_DB toField:@DF_Accession token:'dr|embl']

  $field:[@DF_MinCytologicLoc code:c index:str indexToken:'c|min']
    $field:[@DF_MaxCytologicLoc code:c index:str indexToken:'c|max']
  }
]
FLYGENE_SYNTAX:$syntax:[file:"SRSDB:flygene.is" ignore:" "]

DF_FullName:$srsfield:[FullName short:fnm group:@DF_ALL]
DF_GenMapPos:$srsfield:[GeneticMasrs/icarus/db/flygene.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: flygene.is,v $
#    $Revision: 1.3 $
#    $Date: 1996/12/06 16:37:30 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  a: "Gene symbol"	     
  b: "Genetic map position"    
  c: "Cytological map position" 
  d: "Function(s) of product"  
  e: "Full name" 		     
  g: "D. mel. DNA/RNA AC no(s)" 
  h: "D. spp. DNA/RNA AC no(s)" 
  i: "Synonym(s)" 	     
  j: "Non-Drosophila homologue" 
  k: "Phenotypic information"  
  l: "Length (type\\ends\\total)" 
  m: "D. mel. protein AC no(s)" 
  n: "D. spp. protein AC no(s)" 
  o: "Origin/mutagen" 	     
  p: "Phenotypic information"  
  q: "Miscellaneous information on genes and alleles" 
  r: "Copy number" 	     
  s: "Molecular biology data"  
  t: "Target site duplication" 
  u: "Other information" 	     
  w: "Discoverer(s)" 	     
  x: "Genes References" 	     
  y: "Secondary FlyBase id(s)" 
  z: "FlyBase gene id number"  
  A: "Allele" 		     
  B: "Revised genetic map posn." 
  C: "Associated cytology"     
  D: "Revised cyto. map posn." 
  E: "References" 	     
  F: "Enzyme name/number(s)"   
  H: "Last update" 	     
  J: "Prosite protein domains" 
  K: "RNA space/time distrib." 
  N: "Cyto. location of clone" 
  O: "Progenitor allele/chromosome" 
  R: "Misc. allele information" 
  S: "Open reading frame size" 
  T: "cDNA clone length" 	     
  U: "RNA in situ distribution" 
  V: "Protein distribution"    
  Y: "Transcript size(s)"      
  Z: "Genomic length of clone" 
}

$dbRef={SWP:swiss PIR:pir}

$rules={
  entry:    ~ {$In:[file:text] $Out pre $Skip:0}  
              ('*a' {$Not} ln)*
              ('*a' {$entryFip=$Fip $Wrt} ln {$App} 
               ('*a' {$Not} ln {$App})+)?
            ~
  fields:   ~ {$In:entry $Out $Skip:1}
              (/\\*([a-zA-Z])/ {if:$1==$prev $App else $Wrt:$1 $prev=$1} 
               ln {$App})+
            ~
  
  # indexing
  id:       ~ {$In:[fields c:a] $Out}
              tag /[^ \n]+/ {$Wrt} ~
  c:        ~ {$In:[fields c:c] $Out}
              tag (/[A-Z0-9a-z]+/ {$Wrt:min} 
                   /-+([A-Z0-9a-z]+)/? {$Wrt:[max s:$1]})? ~
  # html
  h_x:      ~ {$In:[fields t:html c:x]}
              tag name {$Rep:{"<DL><DT>($ParStr:flyrefsR)" $Ct $Ct}} 
              '==' {$Rep:"<DD>"} ln
              (tag name {$Rep:{"<DT>($ParStr:flyrefsR)" $Ct $Ct}} 
              '==' {$Rep:"<DD>"} ln)* 
              x{$Rep:"</DL>"} ~
  h_E:      ~ {$In:[fields t:html c:E]}
              tag name {$Rep:{$ParStr:flyrefsR $Ct $Ct}} ~
  h_g:      ~ {$In:[fields t:html c:g]}
              (tag name {$Rep:{$ParStr:emblR $Ct $Ct}} ln)+ ~  
  h_m:      ~ {$In:[fields t:html c:m]}
              (tag name {$db=$Ct} '/'
               name {$Rep:{$ParStr:"($dbRef.$db)R" $Ct $Ct}} ln)+ ~  
  h_J:      ~ {$In:[fields t:html c:J]}
              tag x{$Rep:"<UL><LI>"} name {$Rep:{$ParStr:prositeR $Ct $Ct}} ln
              (tag x{$Rep:"<LI>"} name {$Rep:{$ParStr:prositeR $Ct $Ct}} ln)* 
              x{$Rep:"</UL>"} ~
  h_fields: ~ {$In:[fields t:html]}
              /\\*([a-zA-Z])/ 
              {$Rep:"<TR><TD VALIGN=TOP NOWRAP><B>($fn.$1)</B></TD><TD>"} ln
              (tag {$Rep:""} ln)* x{$Rep:"</TD></TR>"} ~              
  h_A:      ~ {$In:[fields t:html c:A]}
              /(.*)<B>(.*)<\/B>/ 
              {$Rep:"$1<FONT SIZE=+1 COLOR=#ff0000>$2</FONT>"} ~
              
  # others
  name:     ~ /[A-Z0-9a-z]+/ ~
  ln:       ~ /[^\n]*\n/ ~
  tag:      ~ /\\*[a-zA-Z]/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/opt/srs/data/flybase/genes.txt']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields code:c print:1] 
    $JobTokens:[$job name:c print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}







}
              /(.*)<B>(.*)<\/B>/ 
              {$Rep:"$1<FONT SIZE=+1 COLOR=#ff0000>$2</FONT>"} ~
              
  # others
  name:     ~ /[A-Z0-9a-z]+/ ~
  ln:       ~ /[^\n]*\n/ ~
  tag:      ~ /\\*[a-zA-Z]/srs/icarus/db/flygene.it
#    
#    $RCSfile: flygene.it,v $
#    $Revision: 1.1 $
#    $Date: 1996/11/25 19:45:49 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |
  www:
    |<A HREF="http://flybase.bio.indiana.edu:82/">\
    |http://flybase.bio.indiana.edu:82/</A><BR>
    |<A HREF="http://www.embl-ebi.ac.uk/flybase/">\
    |http://www.embl-ebi.ac.uk/flybase/</A><BR>
    |<A HREF="http://www.angis.su.oz.au:7081/">\ 
    |http://www.angis.su.oz.au:7081/</A><BR>
    |<A HREF="http://shigen.lab.nig.ac.jp:7081/">\
    |http://shigen.lab.nig.ac.jp:7081/</A><BR>
    |<A HREF="http://cbbridges.harvard.edu:7081/">\
    |http://cbbridges.harvard.edu:7081/</A><BR>
  ftp:
    |<A HREF="ftp://ftp.ebi.ac.uk/pub/databases/flybase/genes/">\
    |ftp://ftp.ebi.ac.uk/pub/databases/flybase/genes/</A>
  email:
    |Please send any communications about use of FlyBase services to: 
    |			   flybase-help@morgan.harvard.edu 
    |<P>
    |Please send any data corrections or updates to: 
    |			  flybase-updates@morgan.harvard.edu    |
  fax:
    |
  contact:
    |
  address:
    |FlyBase<BR>
    |Biological Laboratories<BR>
    |Harvard University<BR>
    |16 Divinity Ave<BR>
    |Cambridge, MA 02138 USA<BR>
  literature:
    |
  updates:
    |
  fields:{
  }  
}
bi.ac.uk/pub/databases/flybase/genes/</A>
  email:
    |Please send any communications about use of FlyBase services to: 
    srs/icarus/db/flyrefs.i
#    $RCSfile: flyrefs.i,v $
#    $Revision: 1.2 $
#    $Date: 1996/12/06 16:37:32 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

FLYREFS_DB:$library:[FLYREFS group:@GENOME_LIBS
   format:@FLYREFS_FORMAT maxNameLen:15 ifiles:{"flyrefs.i" "flyrefs.is"}
    files:{
       $file:genes
    }
]

FLYREFS_FORMAT:$libformat:[fileType:@TXT_FILE syntax:@FLYREFS_SYNTAX
  printFormat:table2 tableFormat:left fields:{
    $field:[@DF_ID code:id index:id indexToken:id tableToken:id]
  }
]
FLYREFS_SYNTAX:$syntax:[file:"SRSDB:flyrefs.is" ignore:" "]

 $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

FLYREFS_DB:$library:[FLYREFS group:@GENOME_LIBS
   format:@FLYREFS_FORMAT maxNameLen:15 ifiles:{"flyrefs.i" "flyrefs.is"}
    files:{
       $file:genes
    }
]

FLYREFS_FORMAT:$libformat:[fileType:@TXT_FILE syntax:@FLYREFS_SYNTAX
  printForsrs/icarus/db/flyrefs.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: flyrefs.is,v $
#    $Revision: 1.2 $
#    $Date: 1996/12/06 16:37:33 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  a: "Gene symbol"	     
  b: "Genetic map position"    
  c: "Cytological map position" 
  d: "Function(s) of product"  
  e: "Full name" 		     
  g: "D. mel. DNA/RNA AC no(s)" 
  h: "D. spp. DNA/RNA AC no(s)" 
  i: "Synonym(s)" 	     
  j: "Non-Drosophila homologue" 
  k: "Phenotypic information"  
  l: "Length (type\\ends\\total)" 
  m: "D. mel. protein AC no(s)" 
  n: "D. spp. protein AC no(s)" 
  o: "Origin/mutagen" 	     
  p: "Phenotypic information"  
  q: "Miscellaneous information on genes and alleles" 
  r: "Copy number" 	     
  s: "Molecular biology data"  
  t: "Target site duplication" 
  u: "Other information" 	     
  w: "Discoverer(s)" 	     
  x: "Genes References" 	     
  y: "Secondary FlyBase id(s)" 
  z: "FlyBase gene id number"  
  A: "Allele" 		     
  B: "Revised genetic map posn." 
  C: "Associated cytology"     
  D: "Revised cyto. map posn." 
  E: "References" 	     
  F: "Enzyme name/number(s)"   
  H: "Last update" 	     
  J: "Prosite protein domains" 
  K: "RNA space/time distrib." 
  N: "Cyto. location of clone" 
  O: "Progenitor allele/chromosome" 
  R: "Misc. allele information" 
  S: "Open reading frame size" 
  T: "cDNA clone length" 	     
  U: "RNA in situ distribution" 
  V: "Protein distribution"    
  Y: "Transcript size(s)"      
  Z: "Genomic length of clone" 
}

$dbRef={SWP:swiss PIR:pir}

$rules={
  entry:    ~ {$In:[file:text] $Out pre $Skip:0}  
              ('*a' {$Not} ln)*
              ('*a' {$entryFip=$Fip $Wrt} ln {$App} 
               ('*a' {$Not} ln {$App})+)?
            ~
  fields:   ~ {$In:entry $Out $Skip:1}
              (/\\*([a-zA-Z])/ {if:$1==$prev $App else $Wrt:$1 $prev=$1} 
               ln {$App})+
            ~
  
  # indexing
  id:       ~ {$In:[fields c:a] $Out}
              tag /[^ \n]+/ {$Wrt} ~
  c:        ~ {$In:[fields c:c] $Out}
              tag (/[A-Z0-9a-z]+/ {$Wrt:min} 
                   /-+([A-Z0-9a-z]+)/? {$Wrt:[max s:$1]})? ~
  # html
  h_x:      ~ {$In:[fields t:html c:x]}
              tag name {$Rep:{"<DL><DT>($ParStr:flyrefsR)" $Ct $Ct}} 
              '==' {$Rep:"<DD>"} ln
              (tag name {$Rep:{"<DT>($ParStr:flyrefsR)" $Ct $Ct}} 
              '==' {$Rep:"<DD>"} ln)* 
              x{$Rep:"</DL>"} ~
  h_E:      ~ {$In:[fields t:html c:E]}
              tag name {$Rep:{$ParStr:flyrefsR $Ct $Ct}} ~
  h_g:      ~ {$In:[fields t:html c:g]}
              (tag name {$Rep:{$ParStr:emblR $Ct $Ct}} ln)+ ~  
  h_m:      ~ {$In:[fields t:html c:m]}
              (tag name {$db=$Ct} '/'
               name {$Rep:{$ParStr:"($dbRef.$db)R" $Ct $Ct}} ln)+ ~  
  h_J:      ~ {$In:[fields t:html c:J]}
              tag x{$Rep:"<UL><LI>"} name {$Rep:{$ParStr:prositeR $Ct $Ct}} ln
              (tag x{$Rep:"<LI>"} name {$Rep:{$ParStr:prositeR $Ct $Ct}} ln)* 
              x{$Rep:"</UL>"} ~
  h_fields: ~ {$In:[fields t:html]}
              /\\*([a-zA-Z])/ 
              {$Rep:"<TR><TD VALIGN=TOP NOWRAP><B>($fn.$1)</B></TD><TD>"} ln
              (tag {$Rep:""} ln)* x{$Rep:"</TD></TR>"} ~              
  h_A:      ~ {$In:[fields t:html c:A]}
              /(.*)<B>(.*)<\/B>/ 
              {$Rep:"$1<FONT SIZE=+1 COLOR=#ff0000>$2</FONT>"} ~
              
  # others
  name:     ~ /[A-Z0-9a-z]+/ ~
  ln:       ~ /[^\n]*\n/ ~
  tag:      ~ /\\*[a-zA-Z]/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/opt/srs/data/flybase/genes.txt']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields code:c print:1] 
    $JobTokens:[$job name:c print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}







}
              /(.*)<B>(.*)<\/B>/ 
              {$Rep:"$1<FONT SIZE=+1 COLOR=#ff0000>$2</FONT>"} ~
              
  # others
  name:     ~ /[A-Z0-9a-z]+/ ~
  ln:       ~ /[^\n]*\n/ ~
  tag:      ~ /\\*[a-zA-Z]/srs/icarus/db/fssp.i
#    $RCSfile: fssp.i,v $
#    $Revision: 1.4 $
#    $Date: 1997/03/03 18:33:58 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


FSSP_DB:$library:[FSSP group:@PROTSTRUCT_LIBS 
  format:@FSSP_FORMAT maxNameLen:10 ifiles:{"fssp.i" "fssp.is"}
]

FSSP_FORMAT:$libformat:[fileType:@FSSP_FILE syntax:@FSSP_SYNTAX 
  fields:{
    $field:[@DF_ID code:pdbid keyConvert:none index:id indexToken:id]
    $field:[@DF_Header code:header index:str indexToken:hdr]
    $field:[@DF_Compound code:compnd index:str indexToken:comp]
    $field:[@DF_Source code:source index:str indexToken:src]
    $field:[@DF_Authors code:author index:str indexToken:authors]
    $field:[@DF_SeqLength code:seqlen index:int indexToken:seql]
    $field:[@DF_NAlign code:nalign index:int indexToken:nali]
    $field:[@DF_Summary code:summary]
    $field:[@DF_Alignment code:alignments]
    $field:[@DF_Equivalences code:equivalences]
    $field:[@DF_Matrices code:matrices]
  }
]

DF_NAlign:$srsfield:[NAlign short:nal]
DF_Summary:$srsfield:[Summary short:sum]
DF_Equivalences:$srsfield:[Equivalences short:eqv]
DF_Matrices:$srsfield:[Matrices short:mat]

FSSP_SYNTAX:$syntax:[file:"SRSDB:fssp.is" ignore:" "]
FSSP_FILE:$FileType:[typename:'fssp' singleEntry:y maxline:500]

$link:[@FSSP_DB to:@?PDB_DB token:pdbLink fromField:@DF_ID  toField:@DF_ID]
ry]
    $field:[@DF_Alignment code:alignments]
    $field:[@DF_Equivalences code:equisrs/icarus/db/fssp.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: fssp.is,v $
#    $Revision: 1.2 $
#    $Date: 1996/12/06 16:37:34 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$rules={

  # the entry
  entry:     ~ {$In:[file:text] $Out pre $Skip:0}
               ln {$entryFip=$Fip $Wrt} appLn+
             ~

  # fields from text
  fields:    ~ {$In:entry $Out $Skip:1} 
               title pdbid header source compnd author seqlen nalign
               summary alignments matrices footer ~
  title:     ~ {$Wrt:title}  ('PDBID'{$Not} ln)+ ~
  pdbid:     ~ {$Wrt:pdbid}  ('PDBID' ln)+ ~
  header:    ~ {$Wrt:header} ('HEADER' ln)+ ~
  compnd:    ~ {$Wrt:compnd} ('COMPND' ln)+ ~
  source:    ~ {$Wrt:source} ('SOURCE' ln)+ ~
  author:    ~ {$Wrt:author} ('AUTHOR' ln)+ ~
  seqlen:    ~ {$Wrt:seqlen} ('SEQLENGTH' ln)+ ~
  nalign:    ~ {$Wrt:nalign} ('NALIGN' ln)+ ~
  summary:   ~ {$Wrt:summary}    ln ln ('##' {$Not} ln)+ ~
  alignments:~ {$Wrt:alignments} ('## EQUIV' {$Not} ln)+ ~
  matrices:  ~ {$Wrt:matrices}   ln ('##' {$Not} ln)+ ~
  footer:    ~ {$Wrt:footer} ln+ ~

  # indexing production
  id:        ~ {$In:[fields c:pdbid] $Out pre $Skip:1} 
               tag /([a-z0-9]+)(-([A-Z0-9]))?/ {$Wrt:[s:"$1$2"]} ~
  hdr:       ~ {$In:[fields c:header] $Out} (x{$Mov:10} words {$Len:50} ln)+ ~
  comp:      ~ {$In:[fields c:compnd] $Out} (x{$Mov:10} words {$Len:60} ln)+ ~
  src:       ~ {$In:[fields c:source] $Out} (x{$Mov:10} words {$Len:60} ln)+ ~
  authors:   ~ {$In:[fields c:author] $Out} (x{$Mov:10} auts {$Len:60} ln)+ ~
  seql:      ~ {$In:[fields c:seqlen] $Out} tag num {$Wrt} ~
  nali:      ~ {$In:[fields c:nalign] $Out} tag num {$Wrt} ~
  auts:      ~ aut (',' aut?)* ~
  aut:       ~ / *([^ ,]*\\.)([^ ,]*)/ {$Uniq:[s:"$2,$1"]} ~
  words:     ~ (/[A-Z0-9]+/ {$Uniq:$Itc} | /./)+ ~
  pdbLink:   ~ {$In:[fields c:pdbid] $Out} 
               tag /([a-zA-Z0-9]+)/ {$Wrt} ~

  # html display
  h_com:     ~ {$In:[fields c:compnd t:html]}
               (/(E\\.C\\.|EC: *)([0-9]+\\.[0-9]+\\.[0-9]+\\.[0-9]+)/
	        {$Rep:{"$1($ParStr:enzymeR)" $2 $2}} |
                /./)+ ~
  h_pbd:     ~ {$In:[fields c:pdbid t:html]} 
               tag /[a-z0-9]+/ {$Rep:{$ParStr:pdbR $Ct $Ct}} ~
  h_sum:     ~ {$In:[fields c:summary t:html]}
               (/ *[0-9]+:/ /[^ ]+/ name {$Rep:{$ParStr:pdbR $Ct $Ct}} ln | 
                ln)+ ~

  # other productions
  tag:       ~  /[A-Z]+/ ~
  name:      ~  /[a-zA-Z0-9_]+/ ~
  num:       ~  /[0-9.]+/ ~
  word:      ~  /[^ ]+/ ~
  ln:        ~  /[^\n]*\n/ ~
  appLn:     ~  /[^\n]*\n/ {$App} ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/data/fssp/1psdB.fssp']
  $JobTokens:[$job name:fields print:1]
  $JobNext:$job
}


h_sum:     ~ {$In:[fields c:summary t:html]}
               (/ *[0-9]+:/ /[^ ]+/ name {$Rep:{$ParStr:pdbR $Ct $Ct}} ln | 
                ln)+ ~

  # other productions
  tag:       ~  /[A-Z]+/ ~
  name:      ~  /[a-zA-Z0-9_]+/ ~
  nusrs/icarus/db/ftseq.is
#
# the feature location
#

# $origin = { $BEG:0 $BOTH:1 $END:2 }

# a position is either known (a number) or a range

$c={ 
	unbounded:-1 
	sequenceLen:-2
	singleBase:-3
	optional:1 	  # chunk can be omitted
	left:2  	  # chunk varies left^right to right^right
	right:3 	  # chunk varies left^right to left^left
} 

$rules={
  #-- range to chunk converter -------------------------------------------
  position:     ~ /[0-9]+/ {$SdbChunk:[$seq to:$Ct+$offs]} |
  		  /\\(?([0-9]+) *\. *([0-9]+)\\)?/ {$SdbChunk:[$seq to:$1+$offs] 
                                                    $SdbChunk:[$seq to:$2+$offs uncertain:$dir]}|
 		  '>' /[0-9]+/ {$SdbChunk:[$seq to:$Ct+$offs] 
                                $SdbChunk:[$seq to:$c.unbounded uncertain:$dir]} |
 		  '<' /[0-9]+/ {$SdbChunk:[$seq to:$c.unbounded] 
                                $SdbChunk:[$seq to:$Ct+$offs uncertain:$dir]} |
		  'one-of' '(' /[0-9]+/ { $SdbChunk:[$seq to:$Ct+$offs]} 
                  (',' /[0-9]+/ { $SdbChunk:[$seq to:$Ct+$offs uncertain:$c.optional]}
		  )* ')' ~
 
  range: 	~   {pre {$db="" $seq=$SdbRetrieve:["" db:""] $SdbPush $offs=-1 $dir=$c.left}}  
		# get entry sequence # 
	 	    (/([A-Z]+[0-9]+)::/ {$db=$1} )? 
		    (/([A-Z]+[0-9]+)[ \n]*:/ {$seq=$SdbRetrieve:[$1 db:$db]} )? 
		# get chunk (chunks if range uncertain) from sequence # 
 		    position {$dir=$c.right} ( 
			/(\\.\\.|\\. \\.)/ {$offs=0}  position | 
			'^'  {$offs=-1}	position | 
			x{$SdbChunk:[$seq to:$c.singleBase]} 
		    ) ~ 
#----------------------------------------------------------------------
  
  sequence: 	~ literal|operator|range ~
  operator:     ~ join | complement | replace | order | group |one_of~
  
  literal:	~ '\"' /[a-zA-Z]*/ { $seq=$Ct } 
			( /[a-zA-Z]+/ { $StrApp:[$seq s:$Ct] })* 
		  '\"' { $SdbPush $SdbChunk:$seq } ~  
  
  replace: 	~ 'replace' '(' range ',' sequence { $SdbReplace } ')' ~

  join: 	~ 'join' '(' sequence  (',' sequence {$SdbJoin} )* ')' ~
  
  complement: 	~ 'complement' '(' sequence {$SdbComplement} ')' ~
  
  order: 	~ 'order' '(' sequence (',' sequence)* ')' ~
  group:	~ 'group' '(' sequence (',' sequence)* ')' ~
  one_of:	~ /one-of *\\([^\\)]*(\\.\\.|\\^)/ {$Probe} 
		  'one-of' '(' sequence (',' sequence )* ')'  ~

  # swissprot range
  swissrange:   ~ {pre {$db="" $seq=$SdbRetrieve:["" db:""] $SdbPush $offs=-1 $dir=$c.left}}  
 		  position {$dir=$c.right} position {$offs=0} ~
}















quence  (',' sequence {$SdbJoin} )* ')' ~
  
  complement: 	~ 'complement' '(' sequence {$SdbComplement} ')' ~srs/icarus/db/genbank.i
#
#    $RCSfile: genbank.i,v $
#    $Revision: 1.8 $
#    $Date: 1997/03/03 18:33:59 $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

GENBANK_DB:$library:[GENBANK group:@SEQUENCE_LIBS partSize:100000
  subentries:@GenbankFeatures_DB
  format:@GENBANK_FORMAT cachesize:512 maxNameLen:10 files:{
    $file:gbbct 
    $file:gbest1 
    $file:gbest2 
    $file:gbest3 
    $file:gbest4 
    $file:gbest5 
    $file:gbest6
    $file:gbest7 
    $file:gbest8
    $file:gbest9
    $file:gbest10
    $file:gbhtg 
    $file:gbgss 
    $file:gbinv 
    $file:gbmam 

    $file:gbpat 
    $file:gbphg 
    $file:gbpln 
    $file:gbpri 
    $file:gbrna 
    $file:gbrod 
    $file:gbsyn 
    $file:gbsts 
    $file:gbuna 
    $file:gbvrl
    $file:gbvrt 
  }
]


GENBANK_FORMAT:$libformat:[fileType:{@GBREF_FILE @GBSEQ_FILE} 
  syntax:@GENBANK_SYNTAX tableFormat:left fields:{
    $field:[@DF_ALL]
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:[@DF_Division code:str index:str indexToken:div]
    $field:[@DF_SeqLength code:id index:int indexToken:seqlen]
    $field:[@DF_Molecule code:id index:str indexToken:mol]
    $field:[@DF_Date code:id index:int indexToken:date
      tableToken:t_date]
    $field:[@DF_Description index:str code:def indexToken:des
      tableToken:'t_field|def']
    $field:[@DF_Accession code:acc index:str indexToken:acc]
    $field:[@DF_Nid code:nid index:str indexToken:nid]
    $field:[@DF_Keywords code:kwd index:str indexToken:keyw]
    $field:[@DF_Source code:src index:str indexToken:source]
    $field:[@DF_Organism code:srcorg index:str indexToken:org]
    $field:[@DF_Authors code:refaut index:str indexToken:authors]
    $field:[@DF_Title code:reftit index:str indexToken:title]
    $field:[@DF_Citation code:refjnl index:str indexToken:cit]

#    $field:[@DF_DNASequence token:gcgseq format:embl] #GCG format
    GenbankSeq:$field:[@DF_DNASequence token:sequence format:embl] #orig format

    $field:[@DF_HeaderField name:'Feature Table Fields']
    $field:[@DF_FtKey code:ft index:str indexToken:ftKey 
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtQualifier code:ft index:str indexToken:ftQual
      indexId:@SUBENTRY_ID]
    $field:[@DF_PID code:ft index:str indexToken:pid
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtDescription code:ft index:str indexToken:ftDes 
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtSource code:ft index:str indexToken:ftSrc
      indexId:@SUBENTRY_ID]
    $field:[@DF_ChrsNo code:ft index:str indexToken:chrsNo 
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtMap code:ft index:str indexToken:map
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtLength index:int indexToken:ftLen code:ft 
      indexId:@SUBENTRY_ID]

  }
]

DF_Nid:$srsfield:[Nid short:nid]
GENBANK_SYNTAX:$syntax:[file:"SRSDB:genbank.is"]

GBREF_FILE:$filetype:[text typename:seq maxline:200 fieldTokens:fields 
  fipVar:entryFip
]
GBSEQ_FILE:$filetype:[seq typename:seq maxline:200 shareWith:@GBREF_FILE 
  fieldTokens:sequence fipVar:seqFip
]

GenbankFeatures_DB:$library:[GENBANK_features format:@GenbankFeature_Format]
GenbankFeature_Format:$libformat:[syntax:@GENBANK_SYNTAX
  tableFormat:left
  fields:{
    $field:[@DF_ID token:ftId]
    $field:[@DF_FtKey token:ft tableToken:'t_ft|key']
    $field:[@DF_FtQualifier token:ft tableToken:'t_ft|qual']
    $field:[@DF_PID token:ft tableToken:'t_ft|db_xref']
    $field:[@DF_FtDescription token:ft tableToken:'t_ft|note']
    $field:[@DF_FtGene token:ft tableToken:'t_ft|gene']
    $field:[@DF_FtProduct token:ft tableToken:'t_ft|product']
    $field:[@DF_FtPartial token:ft tableToken:'t_ft|partial']
    $field:[@DF_FtPseudo token:ft tableToken:'t_ft|pseudo']
    $field:[@DF_FtNumber token:ft tableToken:'t_ft|number']
    $field:[@DF_FtSource token:ft tableToken:ftSrc]
    $field:[@DF_ChrsNo token:ft tableToken:'t_ft|chromosome'] 
    $field:[@DF_FtMap token:ft tableToken:'t_ft|map']
    $field:[@DF_DNALocation token:ftLocat parent:@GenbankSeq 
      tableFormat:listing]
  }
]


]
    $field:[@DF_FtProduct token:ft tableToken:'t_ft|product']
    $field:[@DF_FtPartial token:ft tableToken:'t_ft|partial']
    $field:[@DF_FtPseudo token:ft tableToken:'t_ft|pseudo']
    $field:[@DF_FtNumber token:ft tableToken:'t_ft|number']
    $field:[@DF_FtSource token:ft tableToken:ftSrc]
    $field:[@DF_ChrsNo token:ft tableToken:'t_ft|chromosome'] 
    $field:[@DF_FtMap token:ft tableToken:'t_ft|map']
    $field:[@DF_DNALocation token:ftLocat parent:@GenbankSeq 
      tableFormat:listing]
  }
srs/icarus/db/genbank.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: genbank.is,v $
#    $Revision: 1.10 $
#    $Date: 1997/03/17 23:21:03 $
#
#    Author: Antoine Daruvar
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  LOCUS:id       DEFINITION:def   ACCESSION:acc   NID:nid   
  SEGMENT:seg    SOURCE:src       ORGANISM:srcorg REFERENCE:reftit 
  AUTHORS:refaut TITLE:reftit     KEYWORDS:kwd    COMMENT:com 
  JOURNAL:refjnl MEDLINE:refmed   REMARK:refrem   BASE:bct 
}

$rules={
  # entry and fields
  entry:    ~ {$In:[file:text] pre{$Skip:0} $Out} 
              ('LOCUS' {$Not} lnT)*
              ('LOCUS' {$Wrt $entryFip=$Fip} lnT {$App} 
               ('ORIGIN' {$Not} lnT {$App})+)?
            ~ 
  lnT:      ~ /[^\n]+\n?/ ~ # line terminator may be missing if truncated
  fields:   ~ {$In:entry $Out $Skip:1} 
              (ftList | / *([A-Z]+)[^\n]*\n/ 
               {if:$fn.$1=="" $dp:"+++ unknown: $1 in $entryName +++" 
                $Wrt:$fn.$1} (/      [^\n]+\n/ {$App})*)+ ~
  ftList:   ~ /FEATURES[^\n]*\n/ {$Wrt:ftTitle} 
              (/     [^ ][^\n]+\n/ {$Wrt:ft} /      [^\n]+\n/* {$App})+ ~

  # parsing the sequence part from separate stream
  gcgseq:    ~ { $In:[file:seq] $Out pre $s=$SeqNew
                 $SeqMake:$s $Wrt:[s:$entryName]
               }
               '>>>>' {$seqFip=$Fip} (/[A-Z0-9]+/ seq |  
               /[A-Z0-9]+_0/ seq (/>>>>[A-Z0-9]+_[1-9]+/ 
               {$SeqTrunc:[$s len:10000]} seq)+) ~ 
  seq:       ~ (/.*2BIT *Len:/ /[0-9]+/ {$len=$Ct} ln ln 
	       {$SeqGet2Bit:[$s file:$File len:$len]} ('>>>>'{$Not} ln)*|
               /.*ASCII/ ln ln ('>>>>' {$Not} /.*/ {$SeqApp:[$s s:$Ct]})+) ~

  sequence:  ~ {$In:[file:seq share:text] $Out pre {$s=$SeqNew $seqFip=$Fip} 
               $Wrt:[s:$entryName] $SeqMake:$s} 
               ln ('LOCUS' {$Not} ln {$SeqApp:[$s s:$Ct]})* ~

  # indexing
  id:       ~ {$In:[fields c:id] $Out} /LOCUS */ iword {$Wrt} ~
  seqlen:   ~ {$In:[fields c:id]  $Out} /.+ ([0-9]+) *bp/ {$Wrt:[s:$1]} ~
  mol:      ~ {$In:[fields c:id] $Out} /.* bp +([a-zA-Z0-9-]+)/ {$Wrt:[s:$1]} ~
  div:      ~ {$In:[fields c:id]  $Out}  
              /.+([A-Z][A-Z][A-Z]) +[0-9]+-[A-Z][A-Z][A-Z]-[0-9]+/ 
              {$Wrt:[s:$1]} ~
  date:     ~ {$In:[fields c:id]  $Out} datenum {$Wrt:[s:$dateval]} ~
  datenum:  ~ {init {$month={JAN:1 FEB:2 MAR:3 APR:4 MAY:5 JUN:6 JUL:7 AUG:8 
                            SEP:9 OCT:10 NOV:11 DEC:12}}}
              /.+ ([0-9]+)-([A-Z][A-Z][A-Z])-([0-9]+)/ 
              {$dateval=$1 + $month.$2 * 100 + $3 * 10000} 
            ~ 
  des:      ~ {$In:[fields c:def] $Out} tag (iword {$Uniq} | /./)* ~
  acc:      ~ {$In:[fields c:acc] $Out} tag (iword {$Uniq} | /./)* ~
  nid:      ~ {$In:[fields c:nid] $Out} tag (iword {$Uniq} | /./)* ~
  keyw:     ~ {$In:[fields c:kwd] $Out} tag (/[^;.\n]+/ {$Wrt} | /./)* ~
  source:   ~ {$In:[fields c:src] $Out} tag (iword {$Uniq} | /./)* ~
  org:      ~ {$In:[fields c:srcorg] $Out} 
              tag ('Mitochondrion' | /[^;.\n]+/ {$Wrt} | /./)* ~
  authors:  ~ {$In:[fields c:refaut] $Out} 
              tag ((/([^,\n]+),([^ ,\n]+)/ {$Uniq:[s:"$1,$2"]}
              (/, */ | /and */)?)+ ln)+ ~
  title:    ~ {$In:[fields c:reftit] $Out} tag (iword {$Uniq} | /./)* ~
  cit:      ~ {$In:[fields c:refjnl] $Out} /./ ~
  medline:  ~ {$In:[fields c:refmed] $Out:medline} tag iword {$Wrt} ~ 
  i_ftsqua: ~ {$In:[fields c:fts count:fts var:$ftN] $Out:Features} 
              /[^\/]+/ ('/' (/translation[^\/]+/ | /[a-zA-Z_]+/
                (/[0-9a-zA-Z_]+/ {$Uniq:[n:$ftN]} | /[^0-9a-zA-Z\/]+/)+))* ~

  # indexing features
  ftWord:    ~ /[^" ,;:*()\n.-]+/ ~ #"
  ftSep:     ~ /[ ,;.:*()\n-]+/ ~
  ftKey:     ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               /[^ ]+/ {$Wrt:[n:$ftN]} ~
  ftQual:    ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               /[^\/]+/ (/\/([a-zA-Z0-9_]+)/ {$Wrt:[s:$1 n:$ftN]} 
               (/=[a-zA-Z0-9_]+/ | /="[^"]+"/)? /[^\/]+/)* ~ #"
  chrsNo:    ~ {$In:[fields c:ft count:ft var:$ftN] $Out} /.+\/chromosome="?/ 
               (/[^\n\" ]+/ {$Uniq:[n:$ftN]} | /[ \n]+/)+ ~ #"
  ftSrc:     ~ {$In:[fields c:ft count:ft var:$ftN] $Out} (/[^\/]+\// (
           /(tissue_type|cell_line|organism|strain|dev_stage|sex|clone_lib)="/
               (ftWord {$Uniq:[n:$ftN]} | ftSep)+)?)+ ~
  ftDes:     ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               (/[^\/]+\// (/(product|note|gene)="/
                (/NCBI gi: *[0-9]+/ | ftWord {$Uniq:[n:$ftN]} | ftSep)+)?)* ~
  map:       ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               /.+\/map="/ (/[^a-zA-Z0-9"]+/|/[a-zA-Z0-9]+/{$Wrt:[n:$ftN]})+ ~
  ftLen:     ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               /[^ ]+/ (range {$Wrt:[n:$ftN s:$l]} | /.*join\\(/ {$ftl=0} 
                (range{$ftl+=$l} ','?)* ')'? {$Wrt:[n:$ftN s:$ftl]})? ~
  range:     ~ /([A-Z0-9]+:)?([0-9]+)\\.\\.([0-9A-Z]+:)?([0-9]+)/ 
               {$l=$4-$2+1} ~
  pid:       ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               (/db_xref="?PID:([0-9a-zA-Z]+)/ {$Wrt:[n:$ftN s:$1]} |
                /[^\/]+\// )+ ~ #"

  # displaying features
  ft:        ~ {$In:[fields c:ft count:ft var:$ftN select:$subEntryN] $Out
                pre $Skip:0 $Skip:1}
               /.*/ {$Wrt} ~
  ftId:      ~ {$In:[fields c:id] $Out} 
               /LOCUS *([A-Z0-9]+)/ 
               {$Wrt:[s:"LOCUS      $1\_$subEntryN;  parent: $1"]}~
  h_ftId:    ~ {$In:[ftId t:html]} /.*parent: */ 
               /[A-Z0-9]+/ {$Rep:{$ParStr:genbankIdR $Ct $Ct}} ~
  t_ft:      ~ {$In:ft $Out} / *(<A HREF)?[^ ]+/ {$Wrt:key} 
               /[^\/]+/ t_qual* ~
  t_qual:    ~ /[ \n]*\/([^ \n=]+)/ {$qn=$1 $Uniq:[qual s:$1]} 
               qualval? {$Wrt:[$qn s:$qv]} ~
  qualval:   ~ {pre $qv=""} /=([a-zA-Z0-9_]+)/ {$qv=$1} | 
               /="([^"]+)"/ {$qv=$1} | x{$qv='+'} ~
  ftLocat:    ~ {$In:ft $Out init {$SdbFunctions}}
               / *(<A HREF)?[^ ]+/ /[^\/]+/ {$Wrt} ~

  # table display
  t_field:  ~ {$In:[fields c:{def}] $Out} tag /.*/ {$Wrt:$Itc} ~
  t_date:   ~ {$In:[fields c:id] $Out} 
              /.+ ([0-9]+-[A-Z]+-[0-9]+)/ {$Wrt:[s:$1]} ~

  # HTML display
  h_ftxref: ~ {$In:[fields c:fts t:html]}
              (/[^\/]+/ |
               /\/EC_number="?/ /[0-9.]+/ {$Rep:{$ParStr:enzymeR $Ct $Ct}} | 
               /\/db_xref="/ ('PID:' iword {$Rep:{$ParStr:pidR $Ct $Ct}} |
                'SWISS-PROT:' iword {$Rep:{$ParStr:swissR $Ct $Ct}} |
                'GDB:' /[A-Z0-9-]/+ {$Rep:{$ParStr:gdbR $Ct $Ct}} |
                'FLYBASE:' /[A-Za-z0-9-]/+ {$Rep:{$ParStr:flygeneR $Ct $Ct}}) |
               '/')+
            ~ 
  h_medline:~ {$In:[fields c:refmed t:html]}
              tag /[0-9]+/ {$Rep:{$ParStr:medlineR $Ct $Ct}} ~

  # utilities
  iword:    ~ /[a-zA-Z0-9_]+/ ~
  ln:       ~ /[^\n]*\n/ ~
  tag:      ~ / *[A-Z]+ */ ~
}

if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/data/genbank/gbmam.seq']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:id print:1] 
    $JobTokens:[$job name:fields print:1] 
    $JobNext:$job
    #$print:"-------->entry\n"
  }
}




             '/')+
            ~ 
  h_medline:~ {$In:[fields c:refmed t:html]}
              tag /[0-9]+/ {$Rep:{$ParStr:medlineR $Ct $Ct}} ~

  # utilities
  iword:    ~ /[a-zA-Z0-9_]+/ ~
  ln:       ~ /[^\n]*\n/ ~
  tag:      ~ / *[A-Z]+ */ ~
}

if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/data/genbank/gbmam.seq']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:id print:1] 
    $JobTokens:[$job name:fields print:1] 
    $JobNext:$job
    #$print:"-------->entry\nsrs/icarus/db/genbank.it
#
#    $RCSfile: genbank.it,v $
#    $Revision: 1.4 $
#    $Date: 1996/10/10 16:47:06 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |GenBank (1) is the NIH's database of all known nucleotide and protein
    |sequences including supporting bibliographic and biological
    |information.  Since 1992 it has been based at the National Center for
    |Biotechnology Information (NCBI), a division of the National Library of
    |Medicine, located on the NIH campus.  NCBI was created by Congress in
    |1988 and specifically charged with developing automated information
    |systems to support molecular biology and biotechnology.  Its other
    |mission is to conduct basic research and as part of the NIH Intramural
    |Program, NCBI scientists pursue research in genome analysis, molecular
    |structure modeling and prediction, and mathematical methods for
    |sequence analysis.
  www:
    |<A HREF="http://www.ncbi.nlm.nih.gov/Web/Genbank/index.html">\
    |http://www.ncbi.nlm.nih.gov/Web/Genbank/index.html</A>
  literature:
    |<OL>
    |<LI>Benson, D., Boguski, M., Lipman, D.J., and Ostell, J.  (1994)
    |Nucleic Acids Research, 22, 3441-3444.
    |<LI> Boguski, M.S. (1995) Trends in Biochemical Sciences, 20, 295-296.
    |<LI> Boguski, M.S., Tolstoshev, C. M. and Bassett, D. E. (1994) Science,
    |265, 1993-1994.
    |<LI> Boguski, M.S. and Schuler, G.D. (1995) Nature Genetics, 10, 369-371.
    |<LI> Levy-Lahad, E., Wasco, W., Poorkaj, P., Romano, D.M., Oshima, J.,
    |Pettingell, W.H., Yu, C.-E., Jondro, P.D., Schmidt, S.D., Wang, K.,
    |Crowley, A.C., Fu, Y.-H., Guenette, S.Y., Galas, D., Nemens, E.,
    |Wijsman, E.M., Bird, T.D., Schellenberg, G.D. and Tanzi, R.E.  (1995)
    |Science, 269, 973-977.
    |<LI> Bassett, D.E., Boguski, M.S., Spencer, F., Reeves, R. Goebl, M., and
    |Hieter, P.  (1995) Trends in Genetics, 11, 372-373.
    |<LI> Schuler, G.D., Epstein, J.A., Ohkawa, H., and Kans, J.A.  Methods in
    |Enzymology, in press.
    |<LI> Altschul, S.F., Boguski, M.S., Gish, W., and Wootton, J.C.  (1994)
    |Nature Genetics, 6, 119-129.
    |<LI> Madden, T.L., Tatusov, R.L. and Zhang, J.  Methods in Enzymology, in
    |press.
    |</OL>
  fields:{
    ID:
      |The pieces of information contained in the <EM>LOCUS</EM> (ID) 
      |record are always
      |found in fixed positions. The locus name (or entry name), which is
      |always ten characters or less, begins in position 13. The locus name
      |is designed to help group entries with similar sequences: the first
      |three characters usually designate the organism; the fourth and fifth
      |characters can be used to show other group designations, such as gene
      |product; for segmented entries the last character is one of a series
      |of sequential integers.
    AccNumber:
      |The <EM>ACCESSION</EM> number is assigned to a sequence and should 
      |remain 
      |linked with it for ever, whereas
      |entry names may change; also occasionally a few sequences may be 
      |merged to a 
      |single sequence
      |that will then inherit all accession numbers). 
      |<p>
      |Corresponding sequences in EMBL and GenBank should to have the same 
      |accession 
      |numbers. In
      |all current sequence libraries the accession number consists of an 
      |alphabetical character followed
      |by 5 digits, e.g "X12345". 
    Description:
      |The <EM>DEFINITION</EM> record gives a brief description of the 
      |sequence,
      |proceeding from general to specific. It starts with the common name of
      |the source organism, then gives the criteria by which this sequence is
      |distinguished from the remainder of the source genome, such as the
      |gene name and what it codes for, or the protein name and mRNA, or some
      |description of the sequence's function (if the sequence is
      |non-coding).
    Keywords:
      |Short phrases describing gene products and other
      |information about an entry. Mandatory keyword in all annotated
      |entries/one or more records.
    Organism:
      |Formal scientific name of the organism (first line)
      |and taxonomic classification levels (second and subsequent lines).
      |Mandatory subkeyword in all annotated entries/two or more records.
      |<p>
      |A taxon is either an organism name or the name of the family, 
      |group etc..
      |Usually  latin names are best (e.g. "EUKARYOTA", or "HOMO SAP*") 
      |but often
      |the english  common name is also given in this data field.
    Title:
      |Full title of citation. Optional subkeyword (present
      |in all but unpublished citations)/one or more records.
    Reference:
      |Four items of the literature reference are indexed: 
      |<UL>
      |<LI>  journal name (e.g., "EMBO JOURNAL"),
      |<LI>  volume number (e.g., "22"),
      |<LI>  first page (e.g., "1712-"),
      |<LI>  and publication year (e.g., "1987").
      |</UL>
      |<P>
      |<B>Note:</B>   The journal names are not yet converted to standard 
      |names; e.g.,
      |        the journal NAR  might be called  "Nucl. Acids Res." in one
      |        library and "Nucl. Acids Research" in  the other. 
      |<P>
      |<B>Note:</B>   When searching first page numbers a dash must be added 
      |to the
      |        number (e.g.,  122-) which is necessary to make the page number
      |        distinct from both volume  number and publication year.
    Features:
      |Table containing information on portions of the
      |sequence that code for proteins and RNA molecules and information on
      |experimentally determined sites of biological significance. Optional
      |keyword/one or more records.
  }
  date:
    |25 Jul 1996
  signature:
    |Anatoly Ulyanov
}
ers a dash must be added 
      |to the
      |        number (e.g.,  122-) which is necessary to make the page number
      |        distinct from both volume  number and publication year.
    Features:srs/icarus/db/gene.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: gene.is,v $
#    $Revision: 1.1 $
#    $Date: 1997/03/03 18:36:24 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  ID: id   DE:de   BS:bs
  AC: ac   OS:os   
  DT: dt   OC:oc   '//':xln
  SD: sd   BC:bc   XX:xln
}

$rules={
  entry:  ~ {$In:[file:text] $Out pre $Skip:0}
            ('AC' {$Not} ln)*
            ('AC  ' {$entryFip=$Fip $Wrt} ln {$App} 
             ('AC' {$Not} ln {$App})+)?
          ~
  # fields
  fields: ~ {$In:entry $Out $Skip:1}
            (/../ { if:$Ct==$prev $App else $Wrt:$fn.$Ct
                    if:$fn.$Ct=="" $dp:"+++ unknown: $Ct +++"
                    $prev=$Ct
                  } 
            ln {$App})+ ~

  # indexing
  id:     ~ {$In:[fields c:id] $Out $Break} tag /[0-9A-Za-z$_-]+/ {$Wrt} ~
  wrd:    ~ {$In:[fields c:{ac ty el se dt}] $Out} tag word {$Wrt:$Itc} ~
  dt:     ~ {$In:[fields c:dt] $Out} 'DT' 
            /([0-9]+).([0-9]+).([0-9]+)/ {$Wrt:[s:($1+$2*100+"19$3"*10000)]} ~
  words:  ~ {$In:[fields c:{bf so cc de os me}] $Out} 
            (tag (sep | /[a-zA-Z0-9+-]+/ {$Uniq:$Itc})* ln)+ ~
  el:     ~ {$In:[fields c:el] $Out} tag word {$Wrt} ~
  se:     ~ {$In:[fields c:se] $Out} tag word {$Wrt} ~
  sf:     ~ {$In:[fields c:sf] $Out} tag num {$Wrt} ~
  st:     ~ {$In:[fields c:st] $Out} tag num {$Wrt} ~
  #links:
  bfRef:  ~ {$In:[fields c:bf] $Out} (tag name {$Wrt} ln)+ ~
  soRef:  ~ {$In:[fields c:so] $Out} (tag name {$Wrt} ln)+ ~
  dr:     ~ {$In:[fields c:dr] $Out} (tag 
           ('EMBL;' word {$Wrt:embl} | 'Flybase;' name {$Wrt:flybase}) ln)+  ~

  # table display
  t_date: ~ {$In:[fields c:dt] $Out} tag /[0-9\.]+]/ {$Wrt} ~

  # HTML display
  h_bf:   ~ {$In:[fields c:bf t:html]} 
            (tag name {$Rep:{$ParStr:tffactorR $Ct $Ct}} ln)+ ~
  h_so:   ~ {$In:[fields c:so t:html]} 
            (tag /[0-9]+/ {$Rep:{$ParStr:tfcellR $Ct $Ct}} ln)+ ~
  h_dr:   ~ {$In:[fields c:dr t:html]} 
            (tag ('EMBL;' word {$Rep:{$ParStr:emblR $Ct $Ct}} |
                  'Flybase;' word {$Rep:{$ParStr:flybaseR $Ct $Ct}} ) ln)+ ~

  # others
  num:     ~ /-?[0-9]+/ ~
  tag:     ~ /[A-Z][A-Z0-9]/ ~
  ln:      ~ /[^\n]*\n/ ~
  name:    ~ /[a-zA-Z0-9$_-]+/ ~
  word:    ~ /[a-zA-Z0-9_]+/ ~
  sep:     ~ /[^a-zA-Z0-9_\n]+/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/opt/srs/data/transfac/gene.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields print:0] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}



            'Flybase;' word {$Rep:{$ParStr:flybaseR $Ct $Ct}} ) ln)+ ~

  # others
  num:     ~ /-?[0-9]+/ ~
  tag:     ~ /[A-Z][A-Z0-9]/ ~
  ln:      ~ /[^\n]*\n/ ~
  name:    ~ /[a-zA-Z0-9$_-]+/ ~
  word:    ~ /[a-zA-Z0-9_]+/ ~
  sep:     ~ /[^a-zA-Z0-9_\n]+/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/opt/srs/data/transfac/gene.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fisrs/icarus/db/general.it
#
#    $RCSfile: general.it,v $
#    $Revision: 1.5 $
#    $Date: 1997/03/03 18:34:00 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$main={
  AccNumber:
    |The accession number is assigned to a sequence and should remain linked
    |with it  for ever, whereas entry names may change; also occasionally a few
    |sequences may  be merged to a single sequence that will then inherit all
    |accession numbers). 
    |<P>
    |Corresponding sequences in <B>EMBL</B> and <B>GenBank</B> should to
    |have the same accession numbers. In all current sequence libraries the
    |accession number consists of an alphabetical character followed by 5
    |digits, e.g "X12345".
    |<P>
    |<A HREF="srsc?-ht||USING-WILDCARDS">Using Wildcards </A>
  Description:  
    |This is probably the best data field for searching an entry you don't know
    |very  much about; however, you can't expect to find all entries of a
    |class, since often  different conventions are used for naming enzymes,
    |organisms, genes, etc.. 
  Organism:
    |A taxon is either an organism name or the name of the family, group etc..
    |Usually  latin names are best (e.g. "EUKARYOTA", or "HOMO SAP*") but often
    |the english  common name is also given in this data field.
    |<P>
    |<A HREF="srsc?-ht||USING-WILDCARDS">Using Wildcards </A>
  Authors:
    |All author names of all libraries are converted to this format: surname
    |followed  by a comma, followed by the initials (no blanks before or after
    |the "," or between  initials!).
    |If you don't know the initials put a wildcard ("*") after the comma; e.g., 
    |"SCHULZ,*"; if you place it after the surname you might get "SCHULZKI,.."
    |as well. 
    |<P>
    |<A HREF="srsc?-ht||USING-WILDCARDS">Using Wildcards</A>
  SeqLength:
    |The sequence length is calculated by reading the sequence. Some libraries
    |(EMBL, SWISSPROT) have the length also in the first entry line so 
    |to display the sequence length in these libraries, select the ID field.
    |<P>
    |Note that ranges can be combined: "300-!500 | !600-700" or "300-700 !
    |500-600" retrieve the
    |same set of sequences, namely all sequences from 300 to 500,
    |excluding 500, plus sequences from 600 to
    |700 where the 600 is excluded.
  Date:
    |The date field contains in most cases the creation date of the entry and
    |is always stored in the index as an 8 digit number of the format 
    |<B>"yyyymmdd"</B> where y=year, m=month and d=day, e.g., "19940117". 
    |<P>
    |It is also possible to 
    |type the date to be searched in a different, more intuitive, format:
    |<B>"dd-mmm-yy"</B>
    |or </B>"dd-mmm-yyyy"</B>, e.g., "1-jan-97" or "01-jan-1997"
  Reference:
    |Four items of the literature reference are indexed: 
    |<UL>
    |<LI>  journal name (e.g., "EMBO JOURNAL"),
    |<LI>  volume number (e.g., "22"),
    |<LI>  first page (e.g., "1712-"),
    |<LI>  and publication year (e.g., "1987").
    |</UL>
    |<P>
    |<B>Note:</B>The journal names are not yet converted to standard
    | names; e.g.,
    |        the journal NAR  might be called  "Nucl. Acids Res." in one
    |        library and "Nucl. Acids Research" in  the other. 
    |<P>
    |<B>Note:</B>When searching first page numbers a dash must be added to the
    |        number (e.g.,  122-) which is necessary to make the page number
    |        distinct from both volume  number and publication year.
    |<P>
    |<A HREF="srsc?-ht||USING-WILDCARDS">Using Wildcards</A>
  Methods:
    |The <EM>ExpMethod</EM> field can contain one of the following:
    |<DL>
    |<DT> X
    |<DD> X-ray structure
    |<DT> NMR
    |<DD> NMR structure
    |<DT> FIBER
    |<DD> Fiber diffraction study
    |<DT> MODEL
    |<DD> A model without explicit experimental data
    |</DL>
    |The <EM>Exp-Method</EM> is derived from the <EM>EXPDTA</EM> field in
    |the <EM>PDB</EM> if present, otherwise it is derived from other sources.
  Resolution:
    |The <EM>Resolution</EM> is derived from <EM>REMARK 2</EM> in the <EM>PDB</EM>
    |file. For NMR structures and models no resolution is given.
  RFactor:
    |The <EM>R-Factor</EM> for X-ray structures is derived from <EM>REMARK
    |3</EM> and <EM>REMARK 4</EM> if possible. For X-ray structures lacking
    |a valid R-factor in the <EM>PDB</EM> file, the <EM>R-factor</EM> field
    |is based on the original literature. A number of corrections to values
    |found in the <EM>PDB</EM> have also been applied. In some cases no
    |R-factor could be found, or the original literature does contain an
    |R-factor but the published coordinates are C-alpha only. In those
    |cases no <EM>R-Factor</EM> field is present. Also no R-factor is given
    |for NMR structures, because the calculation methods are too diverse.
  NoHSSPAlign:
    |The <EM>HSSP-N-Align</EM> field gives the number of aligned sequences in 
    |the <EM>HSSP</EM> database, if a <EM>HSSP</EM> file for the structure 
    |exists (Normally: if the structure is a protein structure).
  TotFractHelix:
    |Gives the fraction of the assigned
    |secondary structure that is helical: it is the total of the
    |<EM>Helix</EM> fields for all chains divided by the total of all
    |<EM>Sec-Struc</EM> fields. This field is only present if there is a
    |secondary structure.
  TotFractBeta:
    |Gives the fraction of the assigned
    |secondary structure that is Beta: it is the total of the <EM>Beta</EM>
    |fields for all chains divided by the total of all <EM>Sec-Struc</EM>
    |fields. This field is only present if there is a secondary structure.
  TotNResProt:
    |Gives the total number of amino acid residues
    |in the structure, if any. Non-standard amino-acids are included.
  TotWaterMols:
    |Gives the total number of water molecules in
    |the structure, if any.
  NoHetGroups:
    |The <EM>HET-Groups</EM> field gives the number of <EM>HET</EM> cards
    |in the <EM>PDB</EM> file, if any. The following items are repeated for
    |every HET-group, and are all derived from the <EM>PDB HET</EM> cards.
}
sent if there is a secondary structure.
  TotNResProt:
    |Gives the total number of amino acid residues
    |in the structure, if any. Non-standard amino-acids are included.
  TotWaterMols:
    |Gives the total number of water molecules in
    |the structure, if any.
  NoHetGroups:
    |The <EM>HET-Groups</EM> field gives the number of <EM>HET</EM> cards
    |in the <EM>PDB</EM> file, if any. The following items are repeated for
 srs/icarus/db/haema.i
#    $RCSfile: haema.i,v $
#    $Revision: 1.1 $
#    $Date: 1996/11/05 19:54:21 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

HAEMA_DB:$library:[HAEMA group:@MUTATION_LIBS
  format:@HAEMA_FORMAT maxNameLen:30 ifiles:{'haema.i' 'haema.is' 'haema.it'}
  files:{
    $file:haema
  }
]

HAEMA_FORMAT:$libformat:[syntax:@HAEMA_SYNTAX fileType:@TXT_FILE  
  printFormat:table
  fields:{
    $field:@DF_ALL
    $field:[@DF_ID indexToken:id index:id
      tableToken:id tableFormat:right]
    $field:[@DF_NuclChange code:dnaChange indexToken:'inx|dnaChange' index:str
      tableToken:'inx|dnaChange' tableFormat:left]
    $field:[@DF_DnaChangePos code:loc indexToken:'inx|loc' index:int
      tableToken:'inx|loc' tableFormat:right]
    $field:[@DF_AaChange code:aaChange indexToken:'inx|aaChange' index:str
      tableToken:'inx|aaChange' tableFormat:right]
    $field:[@DF_Reference code:ref]
  }
]

HAEMA_SYNTAX:$syntax:[file:"SRSDB:haema.is" ignore:" "]
id
      tableToken:id tableFormat:right]
    $field:[@DF_NuclChange code:dnaChange indexToken:'inx|dnaChange' index:str
      tableToken:'inx|dnaChange' tableFormat:left]
    $field:[@DF_DnaChangePos code:loc indexToken:'inx|loc' index:int
      tableToken:'inx|loc' tableFormat:right]
    $field:[@DF_AaChange code:aaChange indexToken:'inx|aaChange' index:str
      tableToken:'inx|aaChange' tableFormat:right]
    $field:[@DF_Reference codsrs/icarus/db/haema.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: haema.is,v $
#    $Revision: 1.3 $
#    $Date: 1997/03/17 23:21:04 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


$field={
  inex:       {len:9  index:normal }
  loc:        {len:7  index:normal }
  dnaChange:  {len:14 index:dnaChange }
  aaChange:   {len:18 index:aaChange }
  patient:    {len:11 index:normal }
  fC:         {len:9  index:normal }
  fAg:        {len:11 index:normal }
  Severity:   {len:16 index:normal }
  inhib:      {len:15 index:normal }
  cmnt:       {len:33 index:cmnt }
  ref:        {len:50 index:ref }
}

$rules={
  entry:   ~ {$In:[file:text] $Out pre $Skip:0 init $count=0}
             (/ [0-9]/ {$Not} ln)*
             (/ [0-9]+/ {$entryFip=$Fip $Wrt $count+=1} ln {$App})?
           ~
  # fields
   fields:  ~ {$In:entry $Out}
             x{ for:{$k=1 $k<12 $k+=1} {
                  $l=$field[$k].len 
                  $c=$Key:$field[$k]
                  $Prod:cell
                }
              } ~
  cell:    ~ /.+/ {if:$Trim:$Ct!="" $Wrt:$c $Len:$l} ~

  # indexing
  id:        ~ {$In:entry $Out} x{$Wrt:[s:$count]} ~
  inx:       ~ {$In:fields $Out pre $Skip:1} x{$Prod:$field.($Itc).index} ~
  normal:    ~ /[^ ]+/ {$Wrt:$Itc} ~
  dnaChange: ~ /([A-Z]+) +([A-Z]+)/ {$Wrt:[$Itc s:"$1>$2"]} ~
  aaChange:  ~ {init $aa={Ile:I Leu:L Met:M Ala:A Val:V Ser:S Thr:T Phe:F 
                          Tyr:Y Gly:G Pro:P Trp:W Cys:C Gln:Q 
                          Asn:N Arg:R Lys:K Asp:D Glu:E His:H Stop:Stop}
               } /([A-Za-z]+) +([A-Za-z]+)/ 
               {$Wrt:[$Itc s:"($aa.$1)>($aa.$2)"]} ~
  cmnt:      ~ /./ ~
  ref:       ~ /./ ~

  # others
  ln:      ~ /[^\n]*\n/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/opt/srs/data/mutdb/haema/haema.txt']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:id print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}



srs/icarus/db/haema.it
#    
#    $RCSfile: haema.it,v $
#    $Revision: 1.1 $
#    $Date: 1996/11/05 19:54:29 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |Haemophilia A: Database of nucleotide substitutions, deletions, 
    |insertions and rearrangements of the factor VIII gene.
  www:
    |<A HREF="http://146.179.66.63/usr/WWW/WebPages/main.dir/main.htm">\
    |http://146.179.66.63/usr/WWW/WebPages/main.dir/main.htm</A>
  ftp:
    |<A HREF="ftp://www.ebi.ac.uk/pub/databases/haema">\
    |ftp://www.ebi.ac.uk/pub/databases/haema</A>
  email:
    |etuddenh@hgmp.mrc.ac.uk
  contact:
    |Professor E.G.D. Tuddenham,<BR>
    |Haemostasis  Research Group,<BR>
    |MRC Clinical Sciences Centre,<BR>
    |Royal Postgraduate Medical School,<BR>
    |Hammersmith Hospital,<BR>
    |Du Cane Road, London<BR>
    |W12 ONN<BR>
    |UK
  fax:
    |+44-0181-259-8319
  literature:
    |<OL>
    |<LI>Tuddenham,E.G.D. and Cooper,D.N.  (1994) The Molecular Genetics of 
    |Haemostasis 
    |and its Inherited Disorders.  Oxford University Press, Oxford.
    |<LI>Tuddenham,E.G.D., Cooper,D.N., Gitschier,J., Higuchi,M., Hoyer,L.W., 
    |Yoshioka,A., Peake,I.R., Schwaab,R., Olek,K., Kazazian,H.H., 
    |Lavergne,J-M., 
    |Giannelli,F. and 
    |Antonarakis,S.E.  Nucleic Acids Res. (1991)  19, 4821-4833.
    |</OL>
  fields:{
  }  
}
>
    |UK
  fax:
    |+44-0181-259-8319
  literaturesrs/icarus/db/haemb.i
#    $RCSfile: haemb.i,v $
#    $Revision: 1.1 $
#    $Date: 1996/11/05 19:54:20 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

HAEMB_DB:$library:[HAEMB group:@MUTATION_LIBS
  format:@HAEMB_FORMAT maxNameLen:30 ifiles:{'haemb.i' 'haemb.is' 'haemb.it'}
  files:{
    $file:'haemb'
  }
]

HAEMB_FORMAT:$libformat:[syntax:@HAEMB_SYNTAX fileType:@DAT_FILE  
  fields:{
    $field:@DF_ALL
    $field:[@DF_ID code:id indexToken:id index:id
      tableToken:id tableFormat:left]
    $field:[@DF_Date code:dt]
    $field:[@DF_Patient code:pt index:str indexToken:pt] 
    $field:[@DF_NuclChange code:mu indexToken:'mu|mut' index:str
      tableToken:'mu|mut' tableFormat:left]
    $field:[@DF_DnaChangePos code:mu indexToken:'mu|pos' index:int
      tableToken:'mu|pos' tableFormat:right]
    $field:[@DF_AaChange code:ac indexToken:'ac|mut' index:str
      tableToken:'ac|mut' tableformat:left]
    $field:[@DF_ProtChangePos code:ac indexToken:'ac|pos' index:int
      tableToken:'ac|pos' tableFormat:right]
    $field:[@DF_ClottingAct code:ct]
    $field:[@DF_FactorIXAntigen code:ag]
    $field:[@DF_Coordinator code:co]
    $field:[@DF_Comment code:co]
    $field:[@DF_Authors code:rl]
    $field:[@DF_Reference code:rl]
  }
]

DF_Patient:$srsfield:[Patient short:pat group:@DF_ALL]
DF_ClottingAct:$srsfield:[ClottingActivity short:cla]
DF_FactorIXAntigen:$srsfield:[FactorIXAntigen short:faa]
DF_Coordinator:$srsfield:[Coordinator short:coo]

HAEMB_SYNTAX:$syntax:[file:"SRSDB:haemb.is" ignore:" "]
bleFormat:right]
    $field:[@DF_ClottingAct code:ct]
    $field:[@DF_FactorIXAntigen code:ag]
    $field:[@DF_Coordinator code:co]
    $field:[@DF_Comment code:co]
    $field:[@DF_Authors code:rl]
    $field:[@DF_Reference code:rl]
  }
]

DF_Patient:$srsfield:[Patient short:pat group:@DF_ALL]
DF_ClottingAct:$srsfield:[ClottingActivity short:cla]
DF_FactorIXAntigen:$srsfield:[FactorIXAntigen short:faa]
DF_Cosrs/icarus/db/haemb.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: haemb.is,v $
#    $Revision: 1.2 $
#    $Date: 1996/12/06 16:37:36 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$rules={
  entry:   ~ {$In:[file:text] $Out}
             ('ID' {$Not} ln)*
             ('ID  ' {$entryFip=$Fip $Wrt} ln {$App} 
              ('ID' {$Not} ln {$App})+)?
           ~
  # fields
  fields:  ~ {$In:entry $Out $Break} 
             f_id f_pt? f_mu? f_ct? f_ag? f_ac? f_cc?
             (f_ra f_rl?)* f_co f_dt
           ~

   f_id: ~ {$Wrt:id}   'ID  ' ln ~
   f_pt: ~ {$Wrt:pt}   ('PT  ' ln)+ ~
   f_mu: ~ {$Wrt:mu}   ('MU  ' ln)+ ~
   f_ct: ~ {$Wrt:ct}   ('CT  ' ln)+ ~
   f_ag: ~ {$Wrt:ag}   ('AG  ' ln)+ ~
   f_ac: ~ {$Wrt:ac}   ('AC  ' ln)+ ~
   f_cc: ~ {$Wrt:cc}   ('CC  ' ln)+ ~
   f_ra: ~ {$Wrt:ra}   ('RA  ' ln)+ ~
   f_rl: ~ {$Wrt:rl}   ('RL  ' ln)+ ~
   f_co: ~ {$Wrt:co}   ('CO  ' ln)+ ~
   f_dt: ~ {$Wrt:dt}   ('DT  ' ln)+ ~

  # indexing
  id:   ~ {$In:[fields c:id] $Out} tag word {$Wrt} ~
  pt:   ~ {$In:[fields c:pt] $Out} tag (word {$Wrt} | sep)* ~
  mu:   ~ {$In:[fields c:mu] $Out} 
          tag (num {$Wrt:pos} ':'? 
          /([A-Z])->([A-Z])/? {$Wrt:[mut s:"$1>$2"]})? ~
  ac:   ~ {$In:[fields c:ac] $Out} 
          tag (num {$Wrt:pos} ':'? 
          /([A-Za-z]+)->([A-Za-z]+)/? {$Wrt:[mut s:"$1>$2"]})? ~

  # HTML display

  # others
  tag:     ~ /[A-Z][A-Z0-9]/ ~
  num:     ~ /-?[0-9]+/ ~
  ln:      ~ /[^\n]*\n/ ~
  word:    ~ /[a-zA-Z0-9_]+/ ~
  sep:     ~ /[^a-zA-Z0-9_\n]+/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/data/transfac/site.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:id print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}



 
          tag (num {$Wrt:pos} ':'? 
          /([A-Za-z]+)->([A-Za-z]+)/? {$Wrt:[mut s:"$1>$2"]})? ~

  # HTML display

  # others
  tag:     ~ /[A-Z][A-Z0-9]/ ~
  num:     ~ /-?[0-9]+/ ~
  ln:      ~ srs/icarus/db/haemb.it
#    
#    $RCSfile: haemb.it,v $
#    $Revision: 1.1 $
#    $Date: 1996/11/05 19:54:27 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |Haemophilia B - A data base of point mutations and short additions and
    |deletions.
    |
    |<H3>NOMENCLATURE</H3>
    |
    |<OL> Some points may need clarifying:
    |
    |<LI> The nucleotide numbering system is from Yoshitake et.al. (1985).
    |2965 must be added to the number specified in MU in this data base to
    |correspond to the numbering in the EMBL file, Accession number K02402,
    |of the Yoshitake et.al., complete factor IX gene sequence.
    |
    |<LI> The amino acid numbering is according to Anson et.al. (1984) and
    |Yoshitake et.al. (1985).  46 must be added to the number specified in
    |AC in this data base, to correspond to the number quoted for factor
    |IX, code KFHU, in the NBRF protein data base.
    |
    |<LI> A `Gla' mutant is one affecting a gammacarboxyglutamyl residue.
    |
    |<LI> A Bm mutant has an extended prothrombin clotting time (Hougie and
    |Twomey, 1967)
    |
    |<LI> The a-h nomenclature of Anson et.al. (1984) is used for exons.
    |Donor and acceptor splice sites are named according to the exon they
    |flank.
    |
    |<LI> Where the mutation is an insertion, as in ID 17 (Recklinghausen),
    |the numbers in the MU field correspond to the position of the first of
    |the inserted nucleotides.  Thus in this entry, `MU 114:insert AT', the
    |inserted dinucleotide, AT, occupies nucleotides 114 and 115,
    |displacing the residues there in the wild-type factor IX gene to 116
    |and 117.
    |
    |<LI> In frameshift mutations, for example ID 17, the amino acid
    |encoded by the frameshifted nucleotide is listed, i.e. AC -18, stating
    |there is a premature stop afterwards.  The extent of the short,
    |frameshifted, C-terminal sequence formed is not specified.
    |
    |<LI> Only deletions or additions shorter than 20 nucleotides are
    |included in this data base.  Thompson (1990) has reviewed studies on
    |about 30 patients with longer deletions or more complex
    |rearrangements.
    |
    |</OL>
  ftp:
    |<A HREF="ftp://www.ebi.ac.uk/pub/databases/haemb/">\
    |ftp://www.ebi.ac.uk/pub/databases/haemb/</A>
  email:
    |brownlee@molecular-biology.oxford.ac.uk
  contact:
    |by F. Giannelli (1), P.M. Green (1), K.A. High (2), S. Sommer (3), 
    |M.C. Poon
    |(4), M. Ludwig (5), R. Schwaab (5), P.H. Reitsma (6), M. Goossens
    |(7), A. Yoshioka (8), and G.G. Brownlee (9).
  address:
    |(1) Paediatric Research Unit, Guy's Tower, London Bridge,
    |London SE1 9RT,UK; (2) Hematology Laboratory, Children's Hospital of
    |Philadelphia, 34th Street & Civic Center Boulevard, Philadelphia, PA
    |19104, USA; (3) Mayo Clinic, 200 Southwest First Street, Rochester,
    |Minnesota 55905, USA; (4) University of Calgary, Foothills Hospital,
    |Calgary, AB T2N, Canada (5) Institute of Clinical Biochemistry and
    |Institute of Experimental Haematology and Blood Transfusion,
    |Sigmund-Freud-Strasse 25, 5300 Bonn 1, W. Germany, and Institute of
    |Clinical Biochemistry, University of Bonn; (6) Hemostasis and
    |Thrombosis Research Unit, University Hospital, PO Box 9600, 2300 RC
    |Leiden, The Netherlands; (7) National Institute of Health and Medical
    |Research, 51 Av.du Marechal de Lattre de Tassigny, 94010 Creteil,
    |France; (8) Department of Pediatrics, Nara Medical College, Kashihara
    |City, Nara, Japan; and (9) Sir William Dunn School of Pathology,
    |University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
  literature:
    |<OL>
    |<LI>Anson D.S., Choo K.H., Rees D.J.G. et.al., EMBO J. 3: 1054-1064
    |(1984)
    |<LI>Giannelli F., Green P.M., High K.A. et.al., Nucl. Acids Res. 21:
    |3075-3087 (1993)
    |<LI>Hougie C., Twomey J.J. Lancet i: 699 (1967)
    |<LI>Thompson A.R., Prog. Hemost. Thromb. 10: 175-214 (1990)
    |<LI>Yoshitake S., Schach B.G., Foster D.C., et.al., Biochemistry, 24:
    |3736-3750 (1985)
    |<LI>Giannelli F., Green P.M., Sommer S.S., et.al., Nucl. Acids Res. 22:
    |3534-3546 (1994)
    |</OL>
  fields:{
    Identifier:
      |Unique patient identity number, or accession number.
    Patient:
      |Original patient pseudonym, acronym, or location.
    ClottingActivity:
      |Clotting activity, if known, expressed as a percent of normal.
    FactorIXAntigen:
      |Factor IX antigen, if known, expressed as a percent of normal.
    Comment:
      |Comments, if any, with those of different types separated by a
      |semicolon.  All CG->CA or TG mutations, and some of the known de
      |novo mutations are listed here.
    Coordinator:
      |coordinator reference. 1, prepared by Giannelli and Green
      |representing the UK, Sweden and Iceland; 2, by High and Sommer,
      |USA; 3, by Poon, Canada; 4, by Ludwig and Schwaab, Germany; 5,
      |by Reitsma, The Netherlands; 6, by Goossens, France; 7, by
      |Yoshioka, Japan; 8, by Brownlee, rest of the world.

  }  
}
ith those of different types separated by a
      |semicolon.  All CG->CA or TG mutations, and some of the known de
      |novo mutations are listed here.
    Coordinator:
      |coordinator reference. 1, prepared by Giannelli and Green
      |representing the UK, Sweden and Iceland; 2, by High and Sommer,
      |USA; 3, by Poon, Canada; 4, by Ludwig and Schwaab, Germany; 5,
      |by Reitsma, The Netherlands; 6, by Goossensrs/icarus/db/hssp.i
#    $RCSfile: hssp.i,v $
#    $Revision: 1.2 $
#    $Date: 1997/03/03 18:34:02 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


HSSP_DB:$library:[HSSP group:@PROTSTRUCT_LIBS 
  format:@HSSP_FORMAT maxNameLen:30 ifiles:{"hssp.i" "hssp.is"}
]

HSSP_FORMAT:$libformat:[fileType:@HSSP_FILE syntax:@HSSP_SYNTAX 
  fields:{
    $field:[@DF_ID code:pdbid index:id indexToken:id]
    $field:[@DF_Date code:date index:int indexToken:creDate]
    $field:[@DF_Header code:header index:str indexToken:'wrds|header']
    $field:[@DF_Compound code:compnd index:str indexToken:'wrds|compnd'
      tableToken:'t_fields|com']
    $field:[@DF_Source code:com index:str indexToken:src]
    $field:[@DF_EntryAuthors code:entryAut index:str indexToken:entryAut]
    $field:[@DF_NAlign code:nalign index:int indexToken:'nums|nalign']
    $field:[@DF_NChain code:nchain index:int indexToken:'nums|nchain']
    $field:[@DF_KChain code:kchain index:int indexToken:'nums|kchain']
    $field:[@DF_SeqLength code:seqlen index:int indexToken:'nums|seqlen']
  }
]

DF_KChain:$srsfield:[KChain short:kch]
DF_NChain:$srsfield:[NChain short:nch]

HSSP_SYNTAX:$syntax:[file:"SRSDB:hssp.is" ignore:" "]
HSSP_FILE:$FileType:[typename:'hssp' singleEntry:y maxline:500]

$link:[@HSSP_DB to:@?SWISSPROT_DB token: 'link|swissprot' toField:@DF_ID]
$link:[@HSSP_DB to:@?PDB_DB token:'link|pdb' toField:@DF_ID]
 indexToken:'nums|nchain']
   srs/icarus/db/hssp.is
$rules={

  # the entry
  entry:     ~ {$In:[file:text] $Out pre $Skip:0}
               'HSSP' {pre {$entryFip=0} $Wrt} appLn
               appLn+
             ~

  # fields from text
  fields:    ~ {$In:entry $Out $Skip:1} 
               title pdbid f_date seqbase param info header compnd source 
               f_author seqlen nchain? kchain? nalign? notation? proteins? 
               alignments? profile? insList? ~

  title:     ~ {$Wrt:title} 'HSSP' ln ~
  pdbid:     ~ {$Wrt:pdbid} 'PDBID' ln ~
  f_date:    ~ {$Wrt:date} 'DATE' ln ~
  seqbase:   ~ {$Wrt:seqbase} ('SEQBASE' ln)+ ~
  param:     ~ {$Wrt:param} 'PARAMETER' ln ('REFERENCE' {$Not} ln)*~
  info:      ~ {$Wrt:info} ('HEADER' {$Not} ln)+ ~
  header:    ~ {$Wrt:header} ('HEADER' ln)+ ~
  compnd:    ~ {$Wrt:compnd} ('COMPND' ln)+ ~
  source:    ~ {$Wrt:source} ('SOURCE' ln)+ ~
  f_author:  ~ {$Wrt:author} ('AUTHOR' ln)+ ~
  seqlen:    ~ {$Wrt:seqlen} ('SEQLENGTH' ln)+ ~
  nchain:    ~ {$Wrt:nchain} ('NCHAIN' ln)+ ~
  kchain:    ~ {$Wrt:kchain} ('KCHAIN' ln)+ ~
  nalign:    ~ {$Wrt:nalign} ('NALIGN' ln)+ ~
  notation:  ~ {$Wrt:notation} ('##' {$Not} ln)+ ~
  proteins:  ~ {$Wrt:proteins} ('## ALIGNMENTS' {$Not} ln)+ ~
  alignments:~ {$Wrt:alignments} ('## SEQUENCE PROFILE' {$Not} ln)+ ~
  profile:   ~ {$Wrt:profile} ('## INSERTION LIST' {$Not} ln)+ ~
  insList:   ~ {$Wrt:insList} ln+ ~

  # indexing production
  id:        ~ {$In:[fields c:pdbid] $Out} tag /[a-zA-Z0-9]+/ {$Wrt} ~
  nums:      ~ {$In:[fields c:{nalign nchain kchain seqlen}] $Out}
               x{$Mov:10} /[0-9]+/ {$Wrt:$Itc} ~
  creDate:   ~ {$In:[fields c:date] $Out} 
               /.*generated on/ datenum {$Wrt:[s:$date]} ~
  wrds:      ~ {$In:[fields c:{compnd header}] $Out} 
               (x{$Mov:10 $Break} words {$Len:60} ln)+ ~
  src:       ~ {$In:[fields c:src] $Out} (x{$Mov:10} words {$Len:60} ln)+ ~
  entryAut:  ~ {$In:[fields c:entryAut] $Out} 
               (x{$Mov:10} authors {$Len:60} ln)+ ~
  aut:       ~ {$In:[fields c:aut] $Out} (x{$Mov:18} authors {$Len:52} ln)+ ~
  tit:       ~ {$In:[fields c:tit] $Out} (x{$Mov:18} words {$Len:52} ln)+ ~
  ref:       ~ {$In:[fields c:ref] $Out} (x{$Mov:18} words {$Len:52} ln)+ ~

  authors:   ~ author (',' author?)* ~
  author:    ~ / *([^ ,]*\\.)([^ ,]*)/ {$Uniq:[s:"$2,$1"]} ~
  words:     ~ (/[A-Z0-9_]+/ {$Uniq:$Itc} | /./)+ ~
  datenum:   ~ {init {$month={Jan:1 Feb:2 Mar:3 Apr:4 May:5 Jun:6 Jul:7 Aug:8 
                              Sep:9 Oct:10 Nov:11 Dec:12}}}
               / *([0-9]+)-([A-Z][a-z][a-z])-([0-9]+)/ 
               {$date=$1 + $month.$2 * 100 + $3 * 10000 + 19000000} ~

  link:      ~ {$In:[fields c:proteins] $Out}
               ln ln  (/[0-9]+ *:/ name {$Wrt:swissprot} 
               /[1-9][A-Z0-9]+/? {$Wrt:pdb} ln)+ ~

  # reformat multiple alignment
  mali:      ~ {$In:[fields c:alignments] $Out  
                pre {$Skip:0 $ali={} for:{$k=0 $k<501 $k+=1} $ali+=""}
                for:{$k=1 $k<501 $k+=1} $dp:$ali[$k]}
               (/.. ALIGNMENTS *([0-9]+)[ -]+([0-9]+)/ 
               {$from=$1 $to=$2+1 $dp:"$from - $to"} ln |
               (x{$Mov:51} x{for:{$k=$from $k<$to $k+=1} $Prod:aa}ln))+
             ~
  aa:        ~ /[A-Z.]/{$StrApp:[$ali[$k] s:$Ct]} | 
               / ?/{$StrApp:[$ali[$k] s:"~"]} ~
  # table display
  t_fields:  ~ {$In:fields $Out}
               (x{$Mov:9 $Getc:62 $Wrt:$Itc} ln)+
             ~
  # html display
  h_pdbid:   ~ {$In:[fields c:pdbid t:html]}
               tag name {$Rep:{$ParStr:pdbR $Ct $Ct}} ~
  h_proteins:~ {$In:[fields c:proteins t:html]}
               ln ln  (/[0-9]+ *:/ name {$Rep:{$ParStr:swissidR $Ct $Ct}} 
               /[1-9][A-Z0-9]+/? {$Rep:{$ParStr:pdbR $Ct $Ct}} ln)+ ~

  # other productions
  tag:       ~  /[A-Z0-9]+ */ ~
  name:      ~  /[a-zA-Z0-9_]+/ ~
  word:      ~  /[^ ]+/ ~
  ln:        ~  /[^\n]*\n/ ~
  appLn:     ~  /[^\n]*\n/ {$App} ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/data/hssp/1seb.hssp']
  $JobTokens:[$job name:creDate print:1] 
}



s:~ {$In:[fields c:proteins t:html]}
  srs/icarus/db/imgt.i
#
#    $RCSfile: imgt.i,v $
#    $Revision: 1.2 $
#    $Date: 1997/03/19 20:30:35 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

IMGT_DB:$library:[IMGT group:@SEQUENCE_LIBS partSize:100000
  comment:"Immunoglobulin Database from the EBI"
  subentries:@ImgtFeatures_DB
  format:@IMGT_FORMAT cachesize:2048 maxNameLen:30 files:{
    $file:imgt
    $file:imgt1
  }
]

IMGT_FORMAT:$libformat:[syntax:@IMGT_SYNTAX 
  fileType:{@DAT_FILE}
#  fileType:{@GCGREF_FILE @GCGSEQ_FILE}
  fields:{
    $field:@DF_ALL
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:[@DF_Accession code:acc index:str indexToken:acc 
      tableToken:acc tableFormat:left]
    $field:[@DF_Division code:id index:str indexToken:div
      tableToken:div tableFormat:left]
    $field:[@DF_Molecule code:id index:str indexToken:mol
      tableToken:mol tableFormat:left]
#    $field:[@DF_DBOrigin code:acc index:str indexToken:dbOri
#      tableToken:dbOri tableFormat:left]
#    $field:[@DF_AccessionKey code:acc index:str indexToken:accKey
#      tableToken:accKey tableFormat:center]
    $field:[@DF_Description code:des index:str indexToken:des
      tableToken:t_des tableFormat:left]
    $field:[@DF_Keywords code:key index:str indexToken:key
      tableToken:key tableFormat:left]
    $field:[@DF_Organism code:org index:str indexToken:org]
    $field:[@DF_Authors code:ra index:str indexToken:authors
      tableToken:authors tableFormat:left]
    $field:[@DF_Date code:date index:int indexToken:date 
      tableToken:date tableFormat:center]
    $field:[@DF_SeqLength code:sq  index:int indexToken:seqLen 
      tableToken:seqLen tableFormat:right]
    $field:[@DF_LINK code:dr]
    $field:[@DF_DNASequence code:seq format:imgt]

    $field:[@DF_HeaderField name:'Feature Table Fields']
    $field:[@DF_FtKey code:ft index:str indexToken:ftKey 
      indexId:@SUBENTRY_ID tableToken:ftKey tableFormat:left]
    $field:[@DF_FtQualifier code:ft index:str indexToken:ftQual
      indexId:@SUBENTRY_ID]
    $field:[@DF_PID code:ft index:str indexToken:pid
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtDescription code:ft index:str indexToken:ftDes 
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtSource code:ft index:str indexToken:ftSrc
      indexId:@SUBENTRY_ID]
    $field:[@DF_ChrsNo code:ft index:str indexToken:chrsNo 
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtMap code:ft index:str indexToken:map
      indexId:@SUBENTRY_ID]
  }
]


IMGT_SYNTAX:$syntax:[file:"SRSDB:imgt.is" ignore:" \t"]
$syntax:[name:ftseq file:"SRSDB:ftseq.is" ignore:" \t\n"]

#$link:[@IMGT_DB to:@?GENBANK_DB   toField:@DF_ACCNO]
#$link:[@IMGT_DB to:@?PIR_DB       toField:@DF_ACCNO]
#$link:[@IMGT_DB to:@?REBASE_DB    toField:@DF_ID]
#$link:[@IMGT_DB to:@?OMIM_DB      toField:@DF_ID]
#$link:[@IMGT_DB to:@?MEDLINE_DB   toField:@DF_ID]


ImgtFeatures_DB:$library:[IMGT_features format:@ImgtFeature_Format]

ImgtFeature_Format:$libformat:[syntax:@IMGT_SYNTAX  #idType:@SUBENTRY_ID
  tableFormat:left
  fields:{
    $field:[@DF_ID token:ftId]
#    $field:[@DF_Accession code:acc fromParent:y]
#    $field:[@DF_Description code:des fromParent:y]

    $field:[@DF_FtKey token:ft tableToken:'t_ft|key']
    $field:[@DF_FtQualifier token:ft tableToken:'t_ft|qual']
    $field:[@DF_PID token:ft tableToken:'t_ft|db_xref']
    $field:[@DF_FtDescription token:ft tableToken:'t_ft|note']
    $field:[@DF_FtGene token:ft tableToken:'t_ft|gene']
    $field:[@DF_FtProduct token:ft tableToken:'t_ft|product']
    $field:[@DF_FtPartial token:ft tableToken:'t_ft|partial']
    $field:[@DF_FtPseudo token:ft tableToken:'t_ft|pseudo']
    $field:[@DF_FtNumber token:ft tableToken:'t_ft|number']
    $field:[@DF_FtSource token:ft tableToken:ftSrc]
    $field:[@DF_ChrsNo token:ft tableToken:'t_ft|chromosome'] 
    $field:[@DF_FtMap token:ft tableToken:'t_ft|map']
    $field:[@DF_DNALocation token:ftLocat tableFormat:listing]
  }
]

n:ft tableToken:'t_ft|gene']
    $field:[@DF_FtProduct token:ft tableTokesrs/icarus/db/imgt.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: imgt.is,v $
#    $Revision: 1.2 $
#    $Date: 1997/03/19 20:30:35 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  ID: id      KW: key      RP: refp     RL: refln    SQ: seqln
  AC: acc     OS: org      RX: refx     DR: link     XX: space
  DT: date    OC: tax      RA: refaut   FH: fthead   '//': space
  DE: des     RN: refn     RT: refttl   CC: comment  NI:ni
  RC: refc
}

$rules={
  entry:     ~ {$In:[file:text] $Out  pre $Skip:0}
               ('ID  ' {$not} ln)*
               ('ID   '{$entryFip=$Fip $Wrt} ln {$App} 
                ('  ' {$Not} ln {$App})+ )? ~


  # data-fields
  fields:    ~ {$In:entry $Out $Skip:1}
               (ftln |
               /../ { if:$Ct==$prev $App else $Wrt:$fn.$Ct
                       if:$fn.$Ct=="" $dp:"+++ unknown: $Ct in $entryName +++"
                       $prev=$Ct
                    } ln {$App})+ ~
  ftln:        ~ {$Wrt:ft} 'FT' ln ('FT     ' ln)* ~
  clFields:  ~ {$In:fields $Out}
               (/.. */ ln {$Wrt:$Itc} (/.. */ ln {$App})*)? ~

  sequence:  ~ {pre {$seq=$SeqNew:$entryName $Wrt:[seq s:$entryName]} 
                $SeqMake:$seq} 
               (ln {$SeqApp:[$seq s:$Ct]})* ~

  # parsing the sequence in a GCG formatted file
  seqFields: ~ { $In:[file:data] 
                 $Out 
                 pre $s=$SeqNew
                 $SeqMake:$s 
                 $Wrt:[s:$entryName]
               }
               '>>>>' {$seqFip=$Fip} (/[A-Z0-9]+/ seq |  
               /[A-Z0-9]+_0/ seq (/>>>>[A-Z0-9]+_[1-9]+/ 
               {$SeqTrunc:[$s len:10000]} seq)+) ~ 
  seq:       ~ (/.*2BIT *Len:/ /[0-9]+/ {$len=$Ct} ln ln 
               {$s=$SeqGet2Bit:[$s file:$File len:$len]} ('>>>>'{$Not} ln)*|
               /.*ASCII/ ln ln ('>>>>' {$Not} /.*/ {$SeqApp:[$s s:$Ct]})+) ~


  # for indexing
  i_id:      ~ {$In:[entry] $Out:id} /ID +/ name {$Wrt} ~

  # indexing features
  ftWord:    ~ /[^" ,;:()\n.-]+/ ~ #"
  ftSep:     ~ /[ ,;.:()-]+/ ~
  ftKey:     ~ {$In:[clFields c:ft count:ft var:$ftN] $Out}
               ftK {$Wrt:[n:$ftN]} ~
  ftK:       ~ {pre $Skip:1} /[A-Za-z0-9_'-]+/ ~
  chrsNo:    ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               /.+\/chromosome="?/ 
               (/[^\n\" ]+/ {$Uniq:[n:$ftN]} | '\nFT' | ' ')+ ~ #"
  ftSrc:     ~ {$In:[fields c:ft count:ft var:$ftN] $Out} (/[^\/]+\// (
           /(tissue_type|cell_line|organism|strain|dev_stage|sex|clone_lib)="/ 
                ('\nFT' | ftWord {$Uniq:[n:$ftN]} | ftSep)+)?)* ~
  ftDes:     ~ {$In:[clFields c:ft count:ft var:$ftN] $Out}
               ftK num '..' num 
               (/[A-Za-z0-9_]+/ {$Uniq:[n:$ftN]} | /[^A-Za-z0-9_]+/)* ~
  ftQual:    ~ {$In:[clFields c:ft count:ft var:$ftN] $Out}
               /[^\/]+/ 
               (/\/([a-zA-Z0-9_]+)/ {$Wrt:[s:$1 n:$ftN]} (/=[a-zA-Z0-9_]+/ |
               /="[^"]+"/)? /[^\/]+/)* ~ #"
# borrowed from embl.is instead
#               ftK ftLoc (ftQualNm {$Wrt:[n:$ftN s:$name]} ftQualVal?)* ~
  ftQualNm:  ~ /\/([a-zA-Z0-9_-]+)/ {$Break $name=$1} ~
  ftQualVal: ~ '=' (/"([^"]+)"/ {$val=$1} | /[^ \n]+/ {$val=$Ct}) ~ #"
#  ftLoc:     ~ pos {$b=$Ct} '..' pos {$e=$Ct} ~
  pos:       ~ /[0-9]+/ ~
  ftLen:     ~ {$In:[clFields c:ft count:ft var:$ftN] $Out}
               ftK ftLoc {$Wrt:[n:$ftN s:($e-$b+1)]} ~



  i_div:     ~ {$In:[fields c:id] $Out:div}
               /.+ ([A-Z]+); +[0-9]+ +BP/ {$Wrt:[s:$1]} ~
  i_mol:     ~ {$In:[fields c:id] $Out:mol} 
               /[^;]+;[^;]+; +([A-Z]+)/  {$Wrt:[s:$1]} ~
  i_acc:     ~ {$In:[fields c:acc] $Out:acc} ('AC' (name {$Wrt} ';')+)+  ~
  i_nid:     ~ {$In:[fields c:nid] $Out:nid} 'NI' name {$Wrt}  ~
  i_dates:   ~ { $In:[fields c:date] $Out:date 
                 init $month={JAN:1 FEB:2 MAR:3 APR:4 MAY:5 JUN:6 JUL:7 AUG:8 
                              SEP:9 OCT:10 NOV:11 DEC:12}
               }
               /.* ([0-9]+)-([A-Z]+)-([0-9]+)[^\n]+Cre/ 
               {$Wrt:[credate s:($1 + $month.$2*100 + $3*10000)]} ~
  des:       ~ {$In:[fields c:des] $Out} 
               ('DE' (/\\(EC *([0-9]+\\.[0-9]+\\.[0-9]+\\.[0-9]+)/
               {$Wrt:[s:$1]}| word{$Wrt} | sp)+ ln)+ ~ 
  org:       ~ {$In:[fields c:org] $Out} 
               ('OC' (/[^;.\n]+/ {$Wrt} | /[^\n]/)*)+ |
                'OS' /[^(\n]+/ {$Wrt:[s:$Trim:$Ct]} 
                ('(' (/[^ \n)]+/ | /[^)]/)+)? |
                'OG'  /[^\n;.]+/ {$Wrt} ~
  key:       ~ {$In:[fields c:key] $Out} 
               ('KW' (/[^\n;.]+/ {$Wrt} | /[^\n]/)+)+ ~ 
  i_authors: ~ {$In:[fields c:ra] $Out:authors}
               (/RA/ (/([^.,\n]+) +([^,;\n]+)/ {$Uniq:[s:"$1,$2"]} /[,;]/)*
               ln)* ~
  i_seqLen:  ~ {$In:[fields c:sq] $Out:seqLen}
               'SQ   Sequence' /[0-9]+/ {$Wrt} ~

  # indexing features
  map:       ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               /.+\/map="/ (/[^a-zA-Z0-9"]+/|/[a-zA-Z0-9]+/{$Wrt:[n:$ftN]})+ #"
             ~
  pid:       ~ {$In:[fields c:ft count:ft var:$ftN select:$subEntryN] $Out}
               (/db_xref="?PID:([0-9a-zA-Z]+)/ {$Wrt:[n:$ftN s:$1]} |
                /[^\/]+\// )+ ~

  # displaying features
  ftClean:   ~ {$In:[fields c:ft count:ft var:$ftN select:$subEntryN] $Out } 
               'FT' ln {$Wrt} ('FT' ln {$App})* ~
  ftLoc:     ~ {$In:ftClean $Out} /[^ ]+/ /[^\/]+/ {$Wrt} ~
  ft:        ~ {$In:[fields c:ft count:ft var:$ftN select:$subEntryN] $Out}
               /.*/ {$Wrt} ~
  ftId:      ~ {$In:[fields c:id] $Out} 
               /.. *([A-Z0-9]+)/ {$Wrt:[s:"ID   $1\_$subEntryN;  parent: $1"]}~
  h_ftId:    ~ {$In:[ftId t:html]} /.*parent: */ 
               /[A-Z0-9]+/ {$Rep:{$ParStr:emblIdR $Ct $Ct}} ~
  t_ft:      ~ {$In:ftClean $Out} /(<A HREF)?[^ ]+/ {$Wrt:key} 
               /[^\/]+/ t_qual* ~
  t_qual:    ~ /[ \n]*\/([^ \n=]+)/ {$qn=$1 $Uniq:[qual s:$1]} 
               qualval? {$Wrt:[$qn s:$qv]} ~
  qualval:   ~ {pre $qv=""} /=([a-zA-Z0-9_]+)/ {$qv=$1} | 
               /="([^"]+)"/ {$qv=$1} | x{$qv='+'} ~

  # extracting feature sequences"

  ftCleanIter: ~ {$In:[fields c:ft] $Out } 
               'FT' ln {$Wrt} ('FT' ln {$App})* ~
  ftLocat:    ~ {$In:ftClean $Out init {$SdbFunctions}}
               /(<A HREF)?[^ ]+/ /[^\/]+/ {$Wrt} ~
               
  # printing tables
  t_authors: ~ {$In:[fields c:refaut] $Out} 'RA' ln {$Wrt} ('RA' ln {$App})* ~
  t_des:     ~ {$In:[fields c:des] $Out} 'DE' ln {$Wrt} ('DE' ln {$App})* ~ 

  # printing in HTML format
  h_ft:      ~ {$In:[fields c:ft t:html count:ft var:$ftN]} 
               'FT' /[^ ]+/ {$Rep:{$ParStr:emblFeatR $entryName $ftN $Ct}}  
#               /[^\/]+/ 
#               (/\/([a-zA-Z0-9_]+)/ {$Rep:{$ParStr:emblFtQualR $1 $Ct}}
#               (/=[a-zA-Z0-9_]+/ | /="[^"]+"/)? /[^\/]+/)* 
             ~
  h_id:      ~ {$In:[fields c:id t:html]} /../ name {$entryName=$Ct} ~
  h_rx:      ~ {$In:[fields c:rx t:html]}
               /../ 'MEDLINE;' /[0-9]+/ {$Rep:{$ParStr:medlineR $Ct $Ct}} ~
  htmlTag:   ~ /<[^<>]*>/ ~
  h_links:   ~ {$In:[fields c:link t:html] 
                init{$hl={
                       'SWISS-PROT':                    swissR
                       DICTYDB:   dictydbR   GCRDB:     gcrdbR
                       MAIZEDB:   maizedbR   WORMPEP:   wormpepR
                       LISTA:     listaR  
                       PIR:       pirR       YEPD:      yepdR        
                       SGD:        sgdR       
                       STYGENE:   stygeneR     
                       HIV:       hivR         
                       ECOGENE:   ecogeneR   ECO2DBASE: eco2dbaseR   
                       MIM:       mimR       SUBTILIST: subtilistR   
                       FLYBASE:   flybaseR     
                       TRANSFAC:  transfacR  REBASE:    rebaseR
                     } 
                    } 
               }
               (/DR/ dbName {$db=$Ct} ';' 
                accno {$Rep:{$ParStr:$hl.$db $Ct $Ct}} ln)*
             ~
  # other stuff

  word:      ~ /[^" ,;:()\/=\n.-]+/ ~
  sp:        ~ /[ ,;.:()\/=-]+/ ~
  lnCode:    ~ /\n[A-Z][A-Z]/ ~
  ln:        ~ /[^\n]*\n/ ~
  accno:     ~ /[A-Z0-9]+/ ~
  num:       ~ /(<|>)?[0-9?]+/ ~
  name:      ~ /[a-zA-Z0-9_-]+/ ~ 
  dbName:    ~ /[^;]+/ ~ 
}

if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" \n" fileName:'imgt.dat']
  while:$JobHasInput:$job {
#    $JobTokens:[$job name:fields print:1]
    $JobTokens:[$job name:acc print:1]
 
    $JobNext:$job
    $print:"-------->entry\n"
  }
}

er stuff

  word:      ~ /[^" ,;:()\/=\n.-]+/ ~
  sp:        ~ /[ ,;.:()\/=-]+/ ~
  lnCode:    ~ /\n[A-Z][A-Z]/ ~
  ln:        ~ /[^\n]*\n/ ~
  accno:     ~ /[A-Z0-9]+/ ~
 srs/icarus/db/ldlr.i
#    $RCSfile: ldlr.i,v $
#    $Revision: 1.1 $
#    $Date: 1997/03/19 16:15:08 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


LDLR_DB:$library:[LDLR group:@MUTATION_LIBS
  format:@LDLR_FORMAT maxNameLen:30 ifiles:{"ldlr.i" "ldlr.is"}
  files:{
    $file:csv
  }
]

LDLR_FORMAT:$libformat:[fileType:@TXT_FILE syntax:@LDLR_SYNTAX 
  printFormat:table tableFormat:left
  fields:{
    $field:[@DF_ID code:id index:id indexToken:id tableToken:id]
    $field:[@DF_Code code:code index:str indexToken:code tableToken:code]
#    $field:[@DF_NuclPos code:nucl index:int indexToken:nucPos]
    $field:[@DF_NuclChange code:nuclChange index:str indexToken:nuclChange
      tableToken:nuclChange]
    $field:[@DF_DnaChangePos code:dnaPos index:int indexToken:dnaPos
      tableToken:dnaPos tableFormat:right]
#    $field:[@DF_TranslEffect code:feature index:str indexToken:translEff
#      tableToken:translEff]    
    $field:[@DF_AaChange code:aaChange index:str indexToken:aaChange
      tableToken:aaChange]
    $field:[@DF_ProtChangePos code:aaPos index:int indexToken:aaPos
      tableToken:aaPos tableFormat:right]
    $field:[@DF_Population token:Pop index:str indexToken:Pop
      tableToken:Pop tableFormat:right]

  }
]

LDLR_SYNTAX:$syntax:[file:"SRSDB:ldlr.is"]
LDLR_FILE:$filetype:[typeName:dat maxline:300]

DF_Population:$srsfield:[Population short:pop]

#DF_Code:$srsfield:[Code short:cod]
#DF_NuclPos:$srsfield:[NucleotidePosition short:nup]



       
x:str indexToken:aaChange
      tableToken:aaChange]
    $field:[@DF_ProtChangePos code:aaPos index:int indexToken:aaPos
      tableToken:aaPos tableFormat:right]
    $field:[@DF_Population token:Pop index:str indexToken:Pop
      tableToken:Pop tableFormat:right]

  }
]

LDLR_SYNTAX:$syntax:[file:"SRSDB:ldlr.is"]
LDLR_FILE:$filetype:[typeName:dat maxline:300]

DF_Population:$srsfield:[Population short:pop]

#DF_Code:$srsfield:[Code short:cod]
#Dsrs/icarus/db/ldlr.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: ldlr.is,v $
#    $Revision: 1.1 $
#    $Date: 1997/03/19 16:14:42 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  id
  population
  mutation
  result
  name
  authors
  comment
  reference
}

$rules={
  entry:    ~ {$In:[file:text] $Out} 
              ln {$entryFip=$Fip $Wrt} ~
  ln:       ~ /[^\n]*\n/ ~

  # parsing fields 
  fields:   ~ {$In:entry $Out pre $n=1}
              (/("[^"]*"|[^,\n]+)/ 
                 { $s=$Trim:[$Ct skip:'"'] 
                   if: $s!=""  $Wrt:[c:$fn[$n] s:$s] 
                   $n+=1 
                 }
               /,|\n/)+ ~
  #indexing
  id:         ~ {$In:[fields c:id]  $Out}
                /.*/ {$Wrt} ~
  code:       ~ {$In:[fields c:name] $Out}
                /.*/ {$Wrt} ~
  nuclChange: ~ {$In:[fields c:mutation] $Out}
                /([A-Za-z]>[A-Za-z]).*/ {$Wrt:[s:"$1"]}|
                /.*/ {$Wrt}  ~
  dnaPos:     ~ {$In:[fields c:mutation] $Out}
                /[A-Za-z]>[A-Za-z] at ([0-9]+)/ {$Wrt:[s:"$1"]} ~
  aaChange:   ~ {$In:[fields c:result] $Out}
                /([A-Za-z])[0-9]+([A-Za-z])/ {$Wrt:[s:"$1>$2"]}|
                /.*/ {$Wrt}  ~
  aaPos:      ~ {$In:[fields c:result] $Out}
                /[A-Za-z]([0-9]+)[A-Za-z].*/ {$Wrt:[s:"$1"]} ~

  Pop:        ~ {$In:[fields c:population] $Out}
                /.*/ {$Wrt} ~

  authors:    ~ {$In:[fields c:authors] $Out}
                (/[^;]+/ {$Wrt} /;/)+ ~

  reference:  ~ {$In:[fields c:reference] $Out}
                (/[^;]+/ {$Wrt} /;/)+ ~

  comment:    ~ {$In:[fields c:comment] $Out}
                (/[^;]+/ {$Wrt} /;/)+ ~

  # for displaying HTML

  h_fields:   ~ {$In:[fields t:html]}
                x{if:$ParInt:[isTable] == 1 $Fail}
                /.*/ {$Rep:"<TR><TD><B>$Itc</B></TD><TD>$Ct</TD></TR>"} ~
                 


  #other
#  num:      ~ /[0-9]+/ ~
#  letter:   ~ /[A-Za-z]/ ~
#  word:     ~ /[A-Za-z]+/ ~
}


# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/u1/srs/data/mutdb/ldlr/csv.txt']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:aaPos  print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}
s:   ~ {$In:[fields t:html]}
                x{if:$ParInt:[isTable] == 1 $Fail}
                /.*/ {$Rep:"<TR><TD><B>$Itc</B></TD><TD>$Ct</TD></TR>"} ~
                 


  #other
#  num:      ~ /[0-9]+/ ~
#  letter:   ~ /[A-Za-z]/ ~
#  word:     ~ /[A-Za-z]+/ ~srs/icarus/db/ldlr.it

#  address:
  contact:
    |<ADDRESS>
    |Ian Day<BR>
    |Division of Cardiovascular Genetics<BR>
    |Department of Medicine<BR>
    |The Rayne Institute<BR>
    |University College London Medical School<BR>
    |London WC1E 6IJ, UK
    |</ADDRESS><P>
  www:
    |<A HREF="http://www.ucl.ac.uk/fh/">\
    |http://www.ucl.ac.uk/fh/</A>
#  telephone: '+358-0-708 59081'
#  telefax:   '+358-0-708 59068'
  email: 'iday@hgmp.mrc.ac.uk'

}







#  letter:   ~ /[A-Za-z]/ ~
#  word:    ¶ £¡Üb¨+/ ~srs/icarus/db/maketrembl.i
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: maketrembl.i,v $
#    $Revision: 1.3 $
#    $Date: 1996/12/14 18:18:59 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$rules={
  entry:     ~ {$In:[file:text] $Out pre {$Skip:0 $cdsN=0 $ft={} $ftN=0}}
               ('ID  ' {$not} ln)*
               ('ID   '{$entryFip=$Fip $Wrt} ln {$App} 
                ('SQ' {$Not} ln {$App})+ )? ~

  # fields
  fields:    ~ {$In:entry $Out $Skip:1} 
               id ('AC' {$Not} ln)* acc 
               ('DE' {$Not} ln)* des
               ('OS' {$Not} ln)* src sep tax sep org? 
               ('FT' {$Not} ln)* ft* x{$Break}~
  id:        ~ {$Wrt:id} 'ID' / *([A-Z0-9_]+)/ {$entryName=$1} ln ~
  acc:       ~ /AC +/ /[A-Z0-9]+/ {$accNo=$Ct} ('AC' ln)* ~
  des:       ~ {$des=$Ct} ('DE' ln)+ ~
  src:       ~ {$src=$Ct} ('OS' ln)+ ~  
  tax:       ~ {$tax=$Ct} ('OC' ln)+ ~  
  org:       ~ {$org=$Ct} ('OG' ln)+ ~  
  ft:        ~ {$Wrt:ft $ft+=$Ct}       'FT' ln ('FT     ' ln)* ~
  sep:       ~ ('XX' ln)* ~ 
 
  #feature
  ftClean:   ~ {$In:[fields c:ft] $Out}
               'FT' ln {$Wrt} ('FT' ln {$App})* ~
  cds:       ~ {$In:ftClean $Out pre $ftN+=1 
                $Break:[cond:$entryName=='A12061']}
               ('CDS'{$cdsN+=1 $product="" $gene="" $note="" $t="" $s=$SeqNew} 
                /[^\/]+/ 
                (gene | product | translate | note | other)+
                x{ if:$SeqLen:[$s]>0 {
 		     $Print:
 		       |ID   ($entryName)_$cdsN standard; PRT; ($SeqLen:$s) AA.
 		     $Print:|AC   $accNo;
 		     $Print:|DR   EMBL; $accNo; $entryName.
 		     if:($gene=="" && $product=="" && $note=="")
 		       $Print:|DE   unnamed ORF;
 		     else {
 		       if:$gene!="" $Print:["gene: \"$gene\"; " v:$t]
 		       if:$product!="" $Print:["product: \"$product\"; " v:$t]
 		       if:$t!=""
 		    	 $Print:"($StrFormat:[$StrTrans:[$t from:'\n' to:' '] 
 		    	   label:'DE   ' width:80])\n"
 		     }
 		     $Print:$des
 		     $Print:"$src$tax$org"
 		     $Print:$ft[$ftN]
 		     $SeqPrint:[format:embl]
                   }
                 }
               )? ~
  gene:      ~ '/gene=' value {$gene=$v} ~
  product:   ~ '/product=' value {$product=$v} ~
  translate: ~ '/translation=' '"'
               /[^"]+/ {$SeqApp:[$s s:$Ct] $SeqMake:$s} '"' ~ 
  note:      ~ '/note=' value {$note=$v} ~
  other:     ~ /\/[^= \n]+/ ('=' value)? ~
  value:     ~ '"' /[^"]+/ {$v="$Ct"} '"' | /[^ \n]+/ {$v="$Ct"} ~ 

  #other stuff
  ln:        ~ /[^\n]*\n/ ~
}

$files={
  mam
  est1 est2 est3 est4 est5 est6 est7
  fun gss hum1 hum2 inv org patent phg pln pro
  rod sts syn unc vrl vrt 
}



foreach:[$name in:$files] {
  $job = $JobNew:[prod:$rules skip:" \n" fileName:"/data/embl_dna/$name.dat"]
  while:$JobTokens:[$job name:cds] {
    $JobNext:$job
  }
}

:$s} '"' ~ 
  note:      ~ '/note=' value {$note=$v} ~
  other:     ~ /\/[^= \n]+/ ('=' value)? ~
  value:     ~ '"' /[^"]+/ {$v="$Ct"} '"' | /[^ \n]+/ {$v="$Ctsrs/icarus/db/medline.i
#    $RCSfile: medline.i,v $
#    $Revision: 1.1 $
#    $Date: 1997/03/03 18:36:27 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


MEDLINE_DB:$library:[MEDLINE group:@LITERATURE_LIBS partSize:200000
  format:@MEDLINE_FORMAT maxNameLen:10 ifiles:{"medline.i" "medline.is"}
  files:{
    $file:medlars001
    $file:medlars002
    $file:medlars003
    $file:medlars004
    $file:medlars005
    $file:medlars006
    $file:medlars007
    $file:medlars008
    $file:medlars009
    $file:medlars010
    $file:medlars011
    $file:medlars012
    $file:medlars013
    $file:medlars014
    $file:medlars015
  }
]

MEDLINE_FORMAT:$libformat:[fileType:@DAT_FILE syntax:@MEDLINE_SYNTAX 
  tableFormat:left fields:{
    $field:[@DF_UI code:ui index:id indexToken:ui]
    $field:[@DF_ALL]
    $field:[@DF_Authors code:au index:str indexToken:au]
    $field:[@DF_Title code:ti index:str indexToken:ti tableToken:'t_fd|ti']
    $field:[@DF_Abstract code:ab index:str indexToken:ab tableToken:'t_fd|ab']
    $field:[@DF_MeshTerm code:mh index:str indexToken:mh]
    $field:[@DF_Date code:dp index:int indexToken:dp]
    $field:[@DF_Journal code:ta index:str indexToken:ta]
    $field:[@DF_Citation code:so tableToken:'t_fd|so']
  }
]

MEDLINE_SYNTAX:$syntax:[file:"SRSDB:medline.is" ignore:" "]

DF_UI:$srsfield:[UI short:ui]
DF_MeshTerm:$srsfield:[MeshTerms short:mh]
DF_Journal:$srsfield:[JournalName short:jnl]

       
en:'t_fd|ti']
    $field:[@DF_Abstract code:ab index:str indexToken:ab tableToken:'t_fd|ab']
    $field:[@DF_MeshTerm code:mh index:str indexToken:mh]
    $field:[@DF_Date code:dp index:int indexToken:dp]
    $field:[@DF_Journal code:ta index:str indexToken:ta]
    $field:[@DF_Citation code:so tableToken:'t_fd|so']
  }
]

MEDLINE_SYNTAX:$syntax:[file:"SRSDB:medline.is" ignore:" "]

DF_UI:$srsfield:[UI short:ui]
DF_MeshTerm:$srsfield:[MeshTerms short:mh]
DF_Journal:$srsfield:[JournalName short:jnl]

 srs/icarus/db/medline.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: medline.is,v $
#    $Revision: 1.1 $
#    $Date: 1997/03/03 18:36:28 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  'UI  -': ui   'TA  -':ta   'SO  -':so  'GS  -':gs
  'AU  -': au   'DP  -':dp   'AB  -':ab  'AD  -':ad
  'MH  -': mh   'PG  -':pg   'IP  -':ip  'SI  -':si
  'TI  -': ti   'VI  -':vi   'RN  -':rn
}

$rules={
  entry:  ~ {$In:[file:text] $Out pre $Skip:0}
            ('UI' {$Not} ln)*
            ('UI' {$entryFip=$Fip $Wrt} ln {$App} 
             ('UI' {$Not} ln {$App})+)?
          ~
  # fields
  fields: ~ {$In:entry $Out $Skip:1}
            (tag { if:$Ct==$prev $App else $Wrt:$fn.$Ct
                    if:$fn.$Ct=="" $dp:"+++ unknown: $Ct +++"
                    $prev=$Ct
                 } 
            ln {$App} /  [^\n]+\n/* {$App})+ ~

  # indexing
  ui:     ~ {$In:[fields c:ui] $Out} tag name {$Wrt} ~
  au:     ~ {$In:[fields c:au] $Out} 
            (tag /([^\n]+) ([A-Z]+)( Jr| 2d| 3d)?\n/ {$Wrt:[s:"$1;$2"]})+ ~
  mh:     ~ {$In:[fields c:mh] $Out} 
            (tag '*'? /[^\/,\n]+/ {$Uniq} 
            (/[\/,]/ '*'?/[^\/,\n]+/ {$Uniq})* ln)+~
  ab:     ~ {$In:[fields c:ab] $Out} tag (word {$Uniq} | /./)+ ~
  ti:     ~ {$In:[fields c:ti] $Out} tag (word {$Uniq} | /./)+ ~
  ta:     ~ {$In:[fields c:ta] $Out} tag /[^\n]+/ {$Wrt} ~
  dp:     ~ {$In:[fields c:dp] $Out init $month={Jan:1 Feb:2 Mar:3 
                  Apr:4 May:5 Jun:6 Jul:7 Aug:8 Sep:9 Oct:10 Nov:11 Dec:12}
             pre {$m=1 $d=1} $Wrt:[s:($y*10000 + $m*100 + $d)]}
            tag num {$y=$Ct} (/[A-Z][a-z]+/ {$m=$month.$Ct} num? {$d=$Ct})? ~

  # table display
  t_fd:   ~ {$In:[fields c:{ab ti so}] $Out} tag /.*/ {$Wrt:$Itc} ~

  # HTML display

  # others
  num:     ~ /-?[0-9]+/ ~
  tag:     ~ /[A-Z][A-Z] +-/ ~
  ln:      ~ /[^\n]*\n/ ~
  name:    ~ /[a-zA-Z0-9$_-]+/ ~
  word:    ~ /[a-zA-Z0-9_]+/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
           fileName:'/data/medline1/medlars010.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:dp print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}



  # table display
  t_fd:   ~ {$In:[fields c:{ab ti so}] $Out} tag /.*/ {$Wrt:$Itc} ~

  # HTML display

  # others
  num:     ~ /-?[0-9]+/ ~
  tag:     ~ /[A-Z][A-Z] +-/ ~
  ln:      ~ /[^\n]*\n/ ~
  name:    ~ /[a-zA-Z0-9$_-]+/ ~
  word:    ~ /[a-zA-Z0-9_]+/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:srs/icarus/db/mpw.i
#    $RCSfile: mpw.i,v $
#    $Revision: 1.7 $
#    $Date: 1997/03/03 18:34:03 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


MPW_DB:$library:[MPW group:@SEQRELATED_LIBS 
  comment:"Metabolic pathways - Selkov." 
  format:@MPW_FORMAT maxNameLen:30 ifiles:{"prosite.i" "prosite.is"}
  files:{
    $file:pathway_graphics
#    $file:aac
#    $file:aro
#    $file:car
#    $file:coe
#    $file:enz
#    $file:hal
#    $file:hyd
#    $file:lip
#    $file:mtr
#    $file:nit
#    $file:nuc
#    $file:oxy
#    $file:pho
#    $file:pro
#    $file:pur
#    $file:pyr
#    $file:sig
#    $file:sul
  }
]

MPW_FORMAT:$libformat:[fileType:@MPW_FILE syntax:@MPW_SYNTAX 
  tableFormat:left printFormat:topicList
  fields:{
    $field:[@DF_ALL]
    $field:[@DF_ID index:id indexToken:id]
    $field:[@DF_Name code:MPW index:str indexToken:name]
    $field:[@DF_CellCultureCategoryCode 
      code:CCC indexToken:'words|CCC']
    $field:[@DF_AlternativePathwayNames code:APN index:str 
      indexToken:'words|APN' tableToken:'fields|APN']
    $field:[@DF_SystematicPathwayNames code:SPN index:str 
      indexToken:'words|SPN' tableToken:'fields|SPN']
#    $field:[@DF_SystematicPathwayNames code:SPW index:str 
#      indexToken:'words|SPW']
    $field:[@DF_MetabolicPathwayName code:MPW index:str 
      indexToken:'name' tableToken:'fields|MPW']
    $field:[@DF_TaxonomicGroup code:TG index:str 
      indexToken:'words|TG']
    $field:[@DF_Strain code:STR index:str 
      indexToken:'words|STR']
    $field:[@DF_OverallReaction code:OVR index:str 
      indexToken:'words|OVR']
    $field:[@DF_Diagram code:diag index:str indexToken:'words|diag' 
       tableToken:'fields|diag']
    $field:[@DF_EnzymeCode code:diag index:str indexToken:enzyme
      tableToken:enzyme]
    $field:[@DF_TransitionsN code:TRN index:int indexToken:'words|TRN']
  }
]

DF_Diagram:$srsfield:[Diagram short:dia group:@DF_ALL]
DF_TransitionsN:$srsField:[TransitionsN short:trn]

MPW_SYNTAX:$syntax:[file:"SRSDB:mpw.is" ignore:" "]
MPW_FILE:$filetype:[typename:txt maxline:1000]

$link:[@MPW_DB to:@?ENZYME_DB fromField:@DF_EnzymeCode toField:@DF_ID]       



exToken:'words|diag' 
       tableToken:'fields|diag']
    $field:[@DF_EnzymeCode code:diag index:str indexToken:enzyme
      tableToken:enzyme]
    $field:[@DF_TransitionsN code:TRN index:int indexToken:'words|TRN']
  }
]

DF_Diagram:$srsfield:[Diagram short:dia group:@DF_ALL]
DF_Transitionssrs/icarus/db/mpw.is
$tags= {
  UDP: 'UDP-Unknown data-field'
  COM: 'Comment'
  OVR: 'Overall Reaction'
  CCC: 'Cell Culture Category'
  STR: 'Strain'
  APN: 'Alternative Pathway Name'
  SPN: 'Systematic Pathway Name'
  SPW: 'Systematic Pathway Name'
  MPW: 'Metabolic Pathway Name'
  PN:  'Protein Name'
  GN:  'Gene Name'
  OR:  'Organism Name'
  TG:  'Taxonomic Group'
}

$rules={
  entry:   ~ {$In:[file:text] $Out init{$count=0} $count+=1 pre{$Skip:0}}
             ( /[A-Z][A-Z]/ {$Not} ln)*
               (tag {$entryFip=$Fip $Wrt} ln {$App}
               (/\12| *#/ {$Not} ln {$App})+ 
             )?
           ~

  # fields
  fields:  ~ {$In:entry $Out $Skip:1} 
             (trn | diag | id | date | field)+ ~
  field:   ~ {$Wrt:$code} /[A-Z]+/ {$code=$Ct} ln? more ~
  date:    ~ {$Wrt:date} '***' ln2 ~
  id:      ~ {$Wrt:name} 'MPW G' ln2 more ~
  diag:    ~ {$Wrt:diag} /\n+[^\n]+\n/ (/[A-Z][A-Z]/ {$Not} ln | '\n')+ ~
  trn:     ~ /\n*(TRN)/ {$Wrt:[TRN s:$1]} ln2 {$App} ~
  
  # indexing  
  i_id:    ~ {$In:[file:text] $Out:id} x{$Wrt:[s:$count]}~
  i_name:  ~ {$Out:name $In:[fields c:name]} /MPW G */ /[0-9A-Z.]+/ {$Wrt} ~
  i_enzyme:~ {$Out:enzyme $In:[fields c:diag]}
             (/[0-9-]+\\.[0-9]+\\.[0-9]+\\.[0-9]+/{$Wrt} | /[^0-9.]+/ | /./)* ~
  i_words: ~ {$In:fields $Out:words pre{$Skip:0}} 
             tag? i_word* ~
  i_word:  ~ (
               /[0-9-]+\\.[0-9-]+\\.[0-9-]+\\.[0-9-]+/ {$Uniq:$Itc $InWord=0} | 
               name {$Uniq:[$Itc s:$s]} |
               /./ {$inWord=0}
             )+ ~  
  name:    ~ {pre $s="" $Skip:1}
              (/'([a-zA-Z0-9]+)'/ {$StrApp:[$s s:$1] $Skip:0} |
              /`([a-zA-Z0-9]+)`/ {$StrApp:[$s s:$1] $Skip:0} |
              /\\([,']([0-9+-]+)\\)/ {$StrApp:[$s s:$1] $Skip:0} |
              /[a-zA-Z0-9]+/ {$StrApp:[$s s:$Ct] $Skip:0})+ 
           ~


  # html display
  h_field: ~ {$In:[fields t:hl]}
              tag {if:$tags.$Ct=="" $t=$Ct else $t=$tags.$Ct 
                   if:$parInt:isTable 
                     $Rep:""
                   else 
                     $Rep:"<DT><B>$t</DT></B><DD>"
                 } /[ \n]*G +([A-Z0-9.]+) +!!/? {$Rep:"<I>$1</I><DD>"} 
              (/[ \n|]+/ | h_word)* | x{if:$Itc==diag $Prod:h_diag}
           ~	         
  h_diag:  ~ {pre{$Skip:0} $Skip:1}
             ln x{$Rep:"<P><TABLE BORDER=3><TR><TD><PRE>"} 
             (/[ \n|]+/ | h_word 
             {if:$n $Rep:
          "($HtmlSpace:[($n/2) l:3 s:2])$Ct($HtmlSpace:[($n-$n/2) l:3 s:2])"})+
             x{$Rep:"</PRE></TD></TR></TABLE>"} 
           ~
  h_word:  ~ {pre{$n=0}}
             (
              /[0-9-]+\\.[0-9-]+\\.[0-9-]+\\.[0-9-]+/ 
               {$Rep:{$ParStr:enzymeR $Ct $Ct}} | 
              '_' {$Rep:'&nbsp;'} |
              /[^(`' \n]/ | 
              /`([a-zA-Z0-9,]+)`/ {$Rep:"<I>$1</I>" $n=$n+6} |
              /'([a-zA-Z0-9,]+)'/ {$Rep:"<B>$1</B>" $n=$n+6} |
              /\\(,'([^')]+)'\\)/{$Rep:"<SUB><b>$1</b></SUB>" $n=$n+9+$Strlen:[$1]+6}|
              /\\(,`([^`)]+)`\\)/{$Rep:"<SUB><i>$1</i></SUB>" $n=$n+9+$Strlen:[$1]+6}|
              /\\(,([^)]+)\\)/ {$Rep:"<SUB>$1</SUB>" $n=$n+9+$Strlen:$1} |
              /\\(''([^')]+)'\\)/ {$Rep:"<SUP><b>$1</B></SUP>" $n=$n+9+$Strlen:[$1]+6} |
              /\\('([^')]+)\\)/ {$Rep:"<SUP>$1</SUP>" $n=$n+9+$Strlen:$1} |
              /[(`']/ 
             )+ ~  

  # other  
  appLn:   ~ /[^\n]*\n/ {$App} ~
  more:    ~ (/    [^\n]*\n/)* ~
  ln:      ~ /[^\n]*\n/ ~
  ln2:     ~ /[^\n]+\n/ ~
  tag:     ~ /[A-Z][A-Z][A-Z]?/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" \n" 
    fileName:'/u1/srs/data/emp/pathway_graphics.txt']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}

#$fil =  $fileOpen:"/data/mpw/aac.asc"
#$job = $jobNew:[prod:$rules skip:" "]
#$jobNext:[$job file:$fil]
#while:$jobTokens:[$job name:fields print:1] {
#  $jobTokens:[$job name:words print:1] 
#  $jobEnd:$job
#  $jobNext:[$job file:$fil]
#}




-Z][A-Z]?/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skipsrs/icarus/db/nrl3d.i
#
#    $RCSfile: nrl3d.i,v $
#    $Revision: 1.3 $
#    $Date: 1996/12/06 22:17:40 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

NRL3D_DB:$library:[NRL3D group:@SEQUENCE_LIBS 
  subentries:@Nrl3dFeatures_DB
  format:@NRL3D_FORMAT maxNameLen:12 files:{
    $file:nrl_3d
  }
]

NRL3D_FORMAT:$libformat:[fileType:{@PIRREF_FILE @PIRSEQ_FILE} 
  syntax:@NRL3D_SYNTAX tableFormat:left fields:{
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:@DF_ALL
    $field:[@DF_Description code:des index:str indexToken:des
      tableToken:'clFields|des']
    $field:[@DF_Keywords code:key index:str indexToken:key]
    $field:[@DF_Comment code:cmnt index:str indexToken:cmnt]
    $field:[@DF_Organism code:spec index:str indexToken:spec]
    $field:[@DF_Authors code:aut index:str indexToken:aut]
    $field:[@DF_Title code:ttl index:str indexToken:ttl]
    $field:[@DF_Resolution code:res index:real indextoken:res]
    $field:[@DF_EXP_METHOD code:det index:str indexToken:det]
    $field:[@DF_R_FACTOR code:rFactor index:real indexToken:rval
      indexToken:rval tableToken:rval]
    $field:[@DF_FtKey index:str indexToken:ftKey code:ft indexId:@SUBENTRY_ID]
    $field:[@DF_FtDescription index:str indexToken:ftDes code:ft 
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtLength index:int indexToken:ftLen code:ft 
      indexId:@SUBENTRY_ID]
    $field:[@DF_ProtSequence token:sequence format:pir]
  }
]

NRL3D_SYNTAX:$syntax:[file:"SRSDB:nrl3d.is" ignore:" \t"]
DF_Determination:$srsfield:[Determination short:det]

$link:[@NRL3D_DB to:@?PDB_DB token:pdblink toField:@DF_ID]

Nrl3dFeatures_DB:$library:[Nrl3d_features 
  format:@PirFeature_Format
]
ndexId:@SUBENTRY_ID]
    $field:[@DF_FtDescription index:str indexToken:ftDes code:ft 
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtLength index:int indexToken:ftLen code:ft 
      indexId:@SUBENTRY_ID]
    $field:[@DF_ProtSequence token:sequence format:srs/icarus/db/nrl3d.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: nrl3d.is,v $
#    $Revision: 1.3 $
#    $Date: 1996/12/06 22:17:40 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  'C;Species:':             spec 
  'A;Note:':                note
  'A;Reference number:':    refn
  'A;Title:':               ttl
  'C;Resolution:':          res
  'C;Keywords:':            key
  'C;Determination:':       determ
  'C;R-value:':             rval
  'C;Comment:':             cmnt
  'N;Contains:':            cont
  'N;Alternate names:':     des
  'R;':                     aut
  'F;':                     ft
}

$rules={
  entry:     ~ {$In:[file:text] $Out pre $Skip:0}
               ('>' {$not} ln)*
               (/>[^;]+;([A-Z0-9]+)/ {$entryFip=$Fip $Wrt $entryName=$1} 
                ln{$App}
               ('>' {$Not} ln {$App})+ )? ~

  sequence:  ~ {$In:[file:seq] $Out pre $s=$SeqNew 
               $Wrt:[s:$entryName] $SeqMake:$s} 
               ('>' {$Not} ln)* ln {pre $seqFip=$Fip} ln 
               ('>' {$Not} ln {$SeqApp:[$s s:$Ct]})* ~

  # extracting data fields
  fields:    ~ {$In:entry $Out $Skip:1}
               ln {$Wrt:id} ln {$Wrt:des}
               (/[ACRFN];([a-zA-Z -]+:)?/ {$Wrt:$fn.$Ct
                 if:$fn.$Ct=="" $dp:"+++ unknown: $Ct in $entryName +++"}
                ln {$App} | ln {$App})+ ~

  # for indexing
  tag:       ~ /[ACRFN];([a-zA-Z -]+:)?/ ~ 
  id:        ~ {$In:entry $Out} />[^;]+;([A-Z0-9]+)/ {$Wrt:[s:$1]} ~
  aut:       ~ {$In:[fields c:aut] $Out} 
               'R;' (author {$Uniq:[s:$author]} ';'?)+ ~
  author:    ~ /([^,\n]+,) *([^;\n]+)/ {$author="$1$2"} ~
  key:       ~ {$In:[fields c:key] $Out} 
               tag (/[^\n;]+/ {$Wrt:[s:$Trim:$Ct]} ';'?)* ~
  ttl:       ~ {$In:[fields c:ttl] $Out} tag (/[a-zA-Z0-9]+/ {$Uniq} | /./)* ~
  des:       ~ {$In:[fields c:des] $Out} tag? (/[a-zA-Z0-9]+/ {$Uniq} | /./)* ~
  cmnt:      ~ {$In:[fields c:cmnt] $Out} tag? (/[a-zA-Z0-9]+/ {$Uniq} | /./)*~
  spec:      ~ {$In:[fields c:spec] $Out} 
               tag /[^(]+/ {$Wrt:[s:$Trim:$Ct]} ('('/[^)]+/ {$Wrt} ')')? ~
  res:       ~ {$In:[fields c:res] $Out} tag /[0-9.]+/? {$Wrt} ~
  rval:      ~ {$In:[fields c:rval] $Out} tag /[0-9.]+/? {$Wrt} ~
  det:       ~ {$In:[fields c:determ] $Out} tag /[^\n]+/ {$Wrt} ~
  pdblink:   ~ {$In:entry $Out} />[^;]+;(....)/ {$Wrt:[s:$1]} ~

  # indexing features
  ft:        ~ {$In:[fields c:ft] $Out}
               'F;'{$r={}} (/[^,\/]+/ {$r+=$Ct} ','?)+ 
               ln {foreach:[$e in:$r] $Wrt:[ft s:"F;$e$Ct"]} ~
  ftKey:     ~ {$In:[ft count:ft var:$ftN] $Out}
               /[^\/]+\/([^:]+):/ {$Wrt:[n:$ftN s:$1]} ~
  ftDes:     ~ {$In:[ft count:ft var:$ftN] $Out}
               /[^:]+:/ (/[A-Za-z0-9_]+/ {$Uniq:[n:$ftN]} | /./)* ~
  ftLen:     ~ {$In:[ft c:ft count:ft var:$ftN] $Out}
               'F;' /([0-9]+)(-([0-9]+))?/ 
               {if:$3=="" $Wrt:[n:$ftN s:1] else $Wrt:[n:$ftN s:($3-$1+1)]} ~

  # display features
  ftId:      ~ {$In:[fields c:id] $Out}
               /(>[^;]+;)([A-Z0-9]+)/
               {$Wrt:[s:"$1$2\_$subEntryN;  parent: $2"]} ~
  ftLine:    ~ {$In:[ft c:ft count:ft var:$ftN select:$subEntryN] $Out}
               /.*/ {$Wrt} ~
  t_ft:      ~ {$In:ftLine $Out $Skip:1}
               'F;' /([^\/]+)/ {$Wrt:[range s:$1]}
               /\/([^:]+):/ {$Wrt:[n:$ftN s:$1]} /.*/ {$Wrt:des} ~
  h_ftId:    ~ {$In:[ftId t:html]} /.*parent: */ 
               /[A-Z0-9_]+/ {$Rep:{$ParStr:pirR $Ct $Ct}} ~

  # printing in HTML format
  h_refn:    ~ {$In:[fields c:refn t:html]} 
               (/.*PDB:/ name {$Rep:{$ParStr:pdbR $Ct $Ct}})? ~

  # other stuff
  ln:        ~ /[^\n]*\n/ ~
  accno:     ~ /[A-Z0-9]+/ ~
  num:       ~ /(<|>)?[0-9?]+/ ~
  name:      ~ /[a-zA-Z0-9_-]+/ ~ 
  dbName:    ~ /[^;]+/ ~ 
}

# debugging 
$subEntryN=3
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/data/nrl3d/nrl_3d.ref']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:ft  print:1] 
#    $JobTokens:[$job name:aut print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}


           (/.*PDB:/ name {$Rep:{$ParStr:pdbR $Ct $Ct}})? ~

  # other stuff
  ln:        ~ /[^\n]*\n/ ~
  accno:     ~ /[A-Z0-9]+/ ~
  num:       ~ /(<|>)?[0-9?]+/ ~
  name:      ~ /[a-zA-Z0-9_-]+/ ~ 
  dbName:    ~ /[^;]+/ ~ 
}

# debugging 
$subEntryN=3
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/data/nrl3d/nrl_3d.ref']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:ft  print:1] 
#    $JobTokens:[$job name:aut psrs/icarus/db/omim.i
#    $RCSfile: omim.i,v $
#    $Revision: 1.1 $
#    $Date: 1996/10/01 18:30:44 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


OMIM_DB:$library:[OMIM group:@MUTATION_LIBS
  format:@OMIM_FORMAT maxNameLen:8 ifiles:{"omim.i" "omim.is"}
  files:{
    $file:omim
  }
]

OMIM_FORMAT:$libformat:[fileType:@TXT_FILE syntax:@OMIM_SYNTAX 
  printFormat:text fields:{
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:[@DF_Keywords code:title]
    $field:[@DF_MN code:mn]
    $field:[@DF_Text code:text index:str indexToken:text]
    $field:[@DF_AllelicVars code:allVar]
    $field:[@DF_SA code:date]
    $field:[@DF_Reference code:ref]
    $field:[@DF_ClinicalSymptoms code:clinSym]
    $field:[@DF_CN code:date]
    $field:[@DF_Date code:date]
    $field:[@DF_History code:history]
  }
]

OMIM_SYNTAX:$syntax:[file:"SRSDB:omim.is" ignore:" "]

DF_SA:$srsfield:[SA short:sa]
DF_MN:$srsfield:[MN short:mn]
DF_CN:$srsfield:[CN short:cn]
DF_Text:$srsfield:[Text short:txt]
DF_ClinicalSymptoms:$srsfield:[ClinicalSymptoms short:cls]
DF_History:$srsfield:[History short:his]
DF_AllelicVars:$srsfield:[AllelicVariants short:alv]


       
ence code:ref]
    $field:[@DF_ClinicalSymptoms code:clinSym]
    $field:[@DF_CN code:date]
    $field:[@DF_Date code:date]
    $field:[@DF_History code:history]
  }
]

OMIM_SYNTAX:$syntax:[file:"SRSDB:omim.is" ignore:" "]

DF_SA:$srsfield:[SA short:sa]
DF_Msrs/icarus/db/omim.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: omim.is,v $
#    $Revision: 1.3 $
#    $Date: 1996/12/18 19:44:45 $
#    $Author: weare $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$rules={
  entry:     ~ {$In:[file:text] $Out pre $Skip:0}
               ('*RECORD*' {$Not} ln)*
               ('*RECORD*'{$entryFip=$Fip $Wrt} ln {$App} 
                ('*RECORD*\n' {$Not} ln {$App})+ )? ~

  # data fields
  fields:    ~ {$In:entry $Out $Skip:1}
               ln id title mn? text? allVar? sa? ref? clinSyn? 
               cn? date? history ~
  id:        ~ {$Wrt:id} 
               '*FIELD* NO\n' ('*FIELD*' {$Not} ln)+ ~
  title:     ~ {$Wrt:title} 
               '*FIELD* TI\n' ('*FIELD*' {$Not} ln)+ ~
  mn:        ~ {$Wrt:mn} 
               '*FIELD* MN\n' ('*FIELD*' {$Not} ln)+ ~
  text:      ~ {$Wrt:text} 
               '*FIELD* TX\n' ('*FIELD*' {$Not} ln)+ ~
  allVar:    ~ {$Wrt:allVar}
               '*FIELD* AV\n' ('*FIELD*' {$Not} ln)+ ~
  sa:        ~ {$Wrt:sa} 
               '*FIELD* SA\n' ('*FIELD*' {$Not} ln)+ ~
  ref:       ~ {$Wrt:ref} 
               '*FIELD* RF\n' ('*FIELD*' {$Not} ln)+ ~
  clinSyn:   ~ {$Wrt:clinSyn} 
               '*FIELD* CS\n' ('*FIELD*' {$Not} ln)+ ~
  cn:        ~ {$Wrt:cn} 
               '*FIELD* CN\n' ('*FIELD*' {$Not} ln)+ ~
  date:      ~ {$Wrt:date} 
               '*FIELD* CD\n' ('*FIELD*' {$Not} ln)+ ~
  history:   ~ {$Wrt:history} 
               '*FIELD* ED\n' ('*FIELD*' {$Not} ln)+ ~

  # indexing

  i_id:      ~ {$In:[fields c:id] $Out:id}
               ln '^'? /[0-9]+/ {$Wrt} ~
  i_text:    ~ {$In:[fields c:text] $Out:text} 
               ln (word {$Uniq} | sep)+ ~

  # html display

  t_toc:     ~ {$In:[fields  t:html] 
                init $t={ text:    "TEXT" 
                          ref:     "REFERENCES"
                          sa:      "SEE ALSO" 
                          allVar:  "ALLELIC VARIANTS" 
                          clinSyn: "CLINICAL SYNOPSIS"
                          date:    "CREATION DATE"
                          history: "EDIT HISTORY"
                        }
               } 
               /./ { if:$t.$Itc!="" {
                       if:$toc=="" $toc="<H3>CONTENTS</H3><UL><H5>"
                       $print:["<LI><A HREF=\"#$Itc\">($t.$Itc)\n</A>" v:$toc]
                     }
                   } ~
  t_id:      ~ {$In:[fields c:id t:html]} 
               /.+/ {$Rep:""} ~
  t_title:   ~ {$In:[fields c:title t:html]}
               ln {$Rep:""} ln {$Rep:"<H3>$Ct</H3>"} ~  
  t_text:    ~ { $In:[fields c:text t:html]}
                 ln {$Rep:"$toc</H5></UL><H3><A NAME=\"$Itc\">TEXT</A></H3>" 
                 $toc=""
               } 
               (/\n/ {$Rep:"<P>"} | textln)+ ~  
  textln:    ~ (
                # make references in various formats hypertext links
              /([a-zA-Z-]+)[ \n]+et[ \n]+al.[ \n]+\\(([0-9][0-9][0-9][0-9])\\)/ 
                {$Rep:"<A HREF=#$1$2>$Ct</A>"} |
      /([a-zA-Z-]+)[ \n]+and[ \n]+[a-zA-Z-]+[ \n]+\\(([0-9][0-9][0-9][0-9])\\)/ 
                {$Rep:"<A HREF=#$1$2>$Ct</A>"} |
                /([a-zA-Z-]+)[ \n]+\\(([0-9][0-9][0-9][0-9])\\)/ 
                {$Rep:"<A HREF=#$1$2>$Ct</A>"} |
                /\\(([a-zA-Z-]+),[ \n]+([0-9][0-9][0-9][0-9])\\)/ 
                {$Rep:"<A HREF=#$1$2>$Ct</A>"} |


                /[^0-9 \n]+/ |
                /([1-6][0-9][0-9][0-9][0-9][0-9])(\\.[0-9]+)?/ 
                { if:$2!="" $Rep:{$ParStr:mimAllR $1 $2 $Ct}
                  else $Rep:{$ParStr:mimR $Ct $Ct}
                } | 
                /[0-9 ]+/)+ '\n'? ~
  t_ref1:     ~ {$In:[fields c:ref t:html]} 
                ln t_snglref+ ~
  t_snglref:  ~ 
        /[0-9]+\\. *([a-zA-Z-]+)([^\n]+\n)*[^\n]*([1-2][0-9][0-9][0-9])\\.\n\n/ 
                {$Rep:"<A NAME=$1$3></A>\n$Ct</DL>"} |
                /([^\n]+\n)+\n/ {$Rep:"<A NAME=unknown></A>\n$Ct</DL>"}  ~

  t_ref2:     ~ {$In:[fields c:ref t:html]} 
                ln {$Rep:"<H3><A NAME=\"$Itc\">REFERENCES</A></H3>"} 
                (ln /[0-9]+\\.[^:]+:/ {$Rep:"<DL><DT>$Ct<DD>"} 
                 /[^.]+./ {$Rep:"<B>$Ct</B>"} 
                 (/<\/DL>/{$Not} ln)*)+ ~
  t_allVar:  ~ {$In:[fields c:allVar t:html]} 
               ln {$Rep:"<H3><A NAME=\"$Itc\">ALLELIC VARIANTS</A></H3>"} 
               (/(\\.[0-9]+)[^\n]*\n/ {$Rep:"<H4><A NAME=\"$1\">$1</A> "} 
                mut {$Rep:"$Ct</H4>"} |
                /\n/ {$Rep:"<P>"} | ln)+ ~  
  mut:       ~ ln
               (/([^\n]* )([A-Z]+[0-9]+[A-Z]+)([\n]*\n)/ 
                {$Rep:"$1<A NAME=\"$2\">$2</A>$3"} | ln) ~
  t_clinSyn: ~ {$In:[fields c:clinSyn t:html]} 
               ln {$Rep:"<H3><A NAME=\"$Itc\">CLINICAL SYNOPSIS</A></H3>"} 
               (/\n/ {$Rep:"<P>"} | ln)+ ~  
  t_history: ~ {$In:[fields c:history t:html]} 
               ln {$Rep:"<H3><A NAME=\"$Itc\">EDIT HISTORY</A></H3>"} 
               ln+ {$Rep:"$Ct<BR>"} ~  
  t_date:    ~ {$In:[fields c:date t:html]} 
               ln {$Rep:"<H3><A NAME=\"$Itc\">CREATION DATE</A></H3>"} 
               (/\n/ {$Rep:"<P>"} | ln)+ ~  

  # other stuff

  ln:        ~ /[^\n]*\n/ ~
  word:      ~ /[a-zA-Z0-9_]+/ ~
  sep:       ~ /[^a-zA-Z0-9_]+/ ~ 
}



NICAL SYNOPSIS</A></H3>"} 
               (/\n/ {$Rep:"<P>"} | ln)+ ~  
  t_history: ~ {$In:[fields c:history t:html]} 
               ln {$Rep:"<H3><A NAME=\"$Itc\">EDIT HISTORY</A></H3>"} 
               ln+ {$Rep:"$Ct<BR>"} ~  
  t_date:    ~ {$In:[fields c:date t:html]} 
               ln {$Rep:"<H3><A NAME=\"$Itc\">CREATION DATE</A></H3>"} 
              srs/icarus/db/p53.i
#    File:		p53   .i               |
#    Version: 	1.0                    |
#    Date:		11-Sep-1996            |
#    Author:	Benny Shomer           |
# 				bshomer@ebi.ac.uk      |
#--------------------------------------    


P53_DB:$library:[P53 group:@MUTATION_LIBS
	format:@P53_FORMAT maxNameLen:10 files:{
		$file:p53
	}
]

P53_FORMAT:$libformat:[syntax:@P53_SYNTAX fileType:@P53_FILE  
  tableFormat:left fields:{
    $field:[@DF_ID code:id indexToken:id index:id]
    $field:[@DF_NuclChange code:bc indexToken:'dnaChange|mut' index:str]
    $field:[@DF_DnaChangePos code:bc indexToken:'dnaChange|pos' index:int
      tableFormat:right]
    $field:[@DF_TranslEffect code:cd index:str indexToken:'aaChange|eff']    
    $field:[@DF_AaChange code:cd indexToken:'aaChange|mut' index:str]
    $field:[@DF_ProtChangePos code:cd indexToken:'aaChange|pos' index:int
      tableFormat:right]
    $field:[@DF_CT code:ct indexToken:ct index:str]
    $field:[@DF_TS code:ts indexToken:ts index:str tableToken:t_ts]
    $field:[@DF_Comment code:cc indexToken:cc index:str]   
    $field:[@DF_RP code:rp indexToken:rp index:str]
  }
]


#data field types
DF_CD:$srsfield:[Codon_Change short:CD group:@DF_ALL]
DF_BC:$srsfield:[Base_Change short:BC group:@DF_ALL]
DF_CT:$srsfield:[CpG_Transition short:CT group:@DF_ALL]
DF_TS:$srsfield:[Tumor_Specific short:TS group:@DF_ALL]
DF_RP:$srsfield:[Reference short:RP group:@DF_ALL]



#links
$link:[@P53_DB to:@?P53REF_DB fromField:@DF_RP toField:@DF_ID  token:rp]


P53_SYNTAX:$syntax:[file:"SRSDB:p53.is" ignore:" \t"]
P53_FILE:$filetype:[typeName:dat maxline:200]


:rp indexToken:rp index:str]
  }
]


#data field types
DF_CD:$srsfield:[Codon_Change short:CD group:@DF_ALL]
DF_BC:$srsfield:[Base_Change short:BC group:@DF_ALL]
DF_CT:$srsfield:[CpG_Transition short:CT group:@DF_ALL]
DF_TS:$srsfield:[Tumor_Specific short:TS group:@DF_ALL]
DF_RP:$srsfield:[Reference short:RP group:@DF_ALL]



#links
$link:[@P53_DB to:@?P53REF_DB fromField:@DF_RP toField:@DF_ID  toksrs/icarus/db/p53.is
#--------------------------------------
#    File:		p53.is                 |
#    Version: 	1.0                    |
#    Date:		11-Sep-1996            |
#    Author:	Benny Shomer           |
# 				bshomer@ebi.ac.uk      |
#--------------------------------------    

$rules={

  #data record
  entry:  ~ {$In:[file:text] $Out}
  	    ('ID   ' {$entryFip=$Fip $Wrt} ln {$App}
  	    ('ID   ' {$Not} ln {$App})*)?
  	  ~
  		  
  ln:     ~  /[^\n]*\n/ ~
  
  
  # Data fields
  fields: ~ {$In:entry $Out} f_id 
            f_cd f_bc f_ct f_ts f_cc f_rp ~
  f_id:   ~ {$Wrt:id}  'ID'   ln ~
  f_cd:   ~ {$Wrt:cd}  ('CD' ln)* ~
  f_bc:   ~ {$Wrt:bc}  ('BC' ln)* ~
  f_ct:   ~ {$Wrt:ct}  ('CT' ln)* ~
  f_ts:   ~ {$Wrt:ts}  ('TS' ln)* ~
  f_cc:   ~ {$Wrt:cc}  ('CC' ln)* ~
  f_rp:   ~ {$Wrt:rp}  ('RP' ln)* ~
  
  # Indexing
  word:	     ~ /[A-Za-z0-9_-]+/ ~
  int:       ~ /[-]?[0-9]+/ ~
  real:      ~ /[-]?[0-9]+([\.]?[0-9]+)?/~
	     
  i_id:	     ~ {$In:[fields c:id]  $Out:id} 
               'ID' int  {$Wrt} ~
  aaChange:  ~ {$In:[fields c:cd] $Out init $aa={Ile:I Leu:L Met:M
                  Ala:A Val:V Ser:S Thr:T Phe:F Tyr:Y Gly:G Pro:P Trp:W Cys:C
                  Gln:Q Asn:N Arg:R Lys:K Asp:D Glu:E His:H Stop:'*'}
               }
               ('CD' (int {$Wrt:pos} ('-' int)? ';' | /[^;]+;/) /[^;]+;/
                (/([a-zA-Z?]+)-.?([a-zA-Z?]+)/ 
                 {$Wrt:[mut s:"($aa.$1)>($aa.$2)"] $Wrt:[eff s:substitution]}|
                 /[a-zA-Z?_-]+/ {$Wrt:eff}))*
             ~
  dnaChange: ~ {$In:[fields c:bc] $Out}
               ('BC' (int {$Wrt:pos} ';'| /[^;]+;/) 
               /([A-Z]+) *-> *([A-Z]+)/? {$Wrt:[mut s:"$1>$2"]})* ~
  ct:        ~ {$In:[fields c:ct]  $Out}
  	       ('CT' /[yesYES]+/ {$Wrt}|ln)+ ~
  ts:        ~ {$In:[fields c:ts]  $Out}
  	       ('TS' (/[^;>.? \'\/\n-]+/ {$Wrt}| /[;>.? \'\/\n-]+/)* )* ~
  cc:        ~ {$In:[fields c:cc]  $Out}
  	       ('CC' (/[^;>.? -]+/ {$Wrt}| /[;>.? -]*/)*)* ~
  rp:        ~ {$In:[fields c:rp]  $Out} 
  	       'RP' /[0-9]+/? {$Wrt} ~
  
  # table
  t_ts:      ~ {$In:[fields c:ts] $Out} (tag ln {$Wrt})* ~

  # printing in HTML format
  h_rp:      ~ {$In:[fields c:rp t:html]}
               ('RP' /[ ]*/ /[0-9]+/
               {$Rep:{$ParStr:p53refR $Ct $Ct}} ln)
             ~
  # other stuff
  tag:       ~ /../ ~
}
	


>.? \'\/\n-]+/ {$Wrt}| /[;>.? \'\/\n-]+/)* )* ~
  cc:        ~ {$In:[fields c:cc]  $Out}
  	       ('CC' (/[^;>.? -]+/ {$Wrt}| /[;>.? -]*/)*)* ~
  rp:        ~ {$In:[fields c:rp]  $Out} 
  	       'RP' /[0-9]+/? {$Wrtsrs/icarus/db/p53.it
#    
#    $RCSfile: p53.it,v $
#    $Revision: 1.1 $
#    $Date: 1996/11/05 19:54:19 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |This database is a compilation of p53 mutations in human tumor cells and cell
    |lines from a systematic search of reports published before 1 January 1994. These
    |mutations were identified by DNA sequencing of PCR-amplified material or cloned
    |PCR products. Preliminary screening for mutations by techniques such as those
    |employing SSCP or DGGE/CDGE (reviewed in Rossiter & Caskey, 1990; Grompe, 1993)
    |were often performed. Most analyses were confined to exons 5-8, since early
    |studies noted that mutations occurred primarily in this evolutionarily conserved
    |midregion. A bias against identification of DNA sequence alterations outside
    |this mutation cluster region can thus be expected. If the same mutations were
    |published in more than one article, only one report is referenced, either the
    |first or the most complete report, and the data are only entered once in the
    |database. If the identical mutation was found in two separate samples from the
    |same patient, for example in the primary tumor and in the metastatic tissue, the
    |mutation is considered to be a single event and is entered only once. Tandem
    |mutations, i.e. two adjacent base substitutions, are also considered as one
    |mutation event and are entered together; therefore there will be only one
    |identification number (see below) for this mutation pair. Discrepancies in
    |published reports that are clearly due to typographical errors or that can be
    |explained by other information in the publication have been corrected. In this
    |case, or if there are uncorrected errors or ambiguities regarding a mutation
    |record, the letter 'e' appears in column M (see below). Information that does
    |not permit us to identify the nature and location of the mutation has not been
    |entered. Mutations found by digestion of DNA with a restriction enzyme and
    |demonstration of an RFLP are not entered; however, publications reporting such
    |data will be cited in the electronic version as second appendix. Mutations
    |identified in tumors are presumed to be somatic unless 1) analysis of normal
    |tissue from the same patient demonstrated that the mutation was constitutional
    |in that individual, or 2) the mutation corresponded to one of the known
    |constitutional polymorphisms of the human p53 gene (at codons 21, 31, 47, 72,
    |and 213), as these are unlikely to be mutations that arose in the tumors.
    |Germline mutations, including those identified in families with the Li-Fraumeni
    |cancer syndrom are not in this database.
  literature:
    |<UL>
    |<LI>Caron de Fromentel, C. and Soussi, T. (1992) Genes Chromosomes Cancer 4, 1-15.
    |<LI>Donehower, L.A. and Bradley, A. (1993) Biochim. Biophys. Acta 1155, 181-207.
    |<LI>Greenblatt, M.S., Bennet, W.P., Hollstein, M.C. and Harris, C.C. (1994) Cancer
    |	 Res. (in press).
    |<LI>Grompe, M. (1993) Nature genetics 5, 111-117.
    |<LI>Harris, C.C. and Hollstein, M. (1993) New Engl. J. Med. 329, 1318-1327.
    |<LI>Hollstein, M.C, Sidranskym D., Vogelstein, B. and Harris, C.C. (1991) Science  
    |	 253, 49-53.
    |<LI>Jones, P.A., Buckley, J.D., Henderson, B.E., Ross, R.K. and Pike M.C. (1991)
    |	 Cancer Res. 51, 3617-3620.
    |<LI>Kunkel, T.A. (1990) Biochemistry 29, 8003-8011.
    |<LI>Kunkel, T.A. (1993) Nature 365, 207-208.
    |<LI>Levine, A.J. (1993) Annu. Rev. Biochem. 62, 623-651.
    |<LI>Lindahl, T. (1993) Nature 362, 709-715.
    |<LI>Mellon & Hanawalt (1989) Nature 342, 95-998.
    |<LI>Rice, C., Fuchs, R., Higgins, D.G., Stoehr, P.S. and Cameron, G.N. (1993) Nucl.
    |	 Acids Res. 21, 2967-2971.
    |<LI>Rossiter, B.J.F. and Caskey, C.T. (1990) J. Biol. Chem. 265, 12753-12756.
    |<LI>Selby & Sancar (1993) Science 260, 53-58.
    |<LI>Takeshima, S., Seyama, T., Bennett, W.P. et al. (1991) Lancet 342, 1520-2521.
    |</UL>
  ftp:
    |<A HREF="ftp://ftp.ebi.ac.uk/pub/databases/p53">ftp.ebi.ac.uk/pub/databases/p53</A>
  www:
    |Through the WWW server at:  http://www.ebi.ac.uk/
  email:
    |netserv@ebi.ac.uk and include the line "help p53"
  updates:
    |This compilation of p53 mutations is to provide the scientific community with a
    |database of rapidly accumulating data that can be useful to various disciplines
    |in cancer research, including epidemiology, medicine and basic science. Future
    |versions of the database may include separate sections on germline mutations,
    |mutations detected by RFLP, anamnestic data on patients, and standardization of
    |terminology with the International Classification of Diseases for Oncology
    |(ICD-O). Notifications of omissions and errors of the current version would be
    |gratefully received by the authors. When individual records in the present
    |version require correction they will be revised and the date of revision will be
    |noted in a new column, column N. Data published in th first six months of 1994
    |will be added at regular intervals during the second half of the year.
}
 standardization of
    |terminology with the International Classification of Diseases for Oncology
    |(ICD-O). Notifications of omissions and errors of the current version would be
    |gratefully received by the authors. When individual records in the present
    |version resrs/icarus/db/p53apc.i
#    $RCSfile: p53apc.i,v $
#    $Revision: 1.3 $
#    $Date: 1997/03/03 18:34:06 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#--------------------------------------
#    File:      p53.i                  |
#    Version:   1.0                    |
#    Date:      17-Sep-1996            |
#    Author:    Benny Shomer           |
#               bshomer@ebi.ac.uk      |
#--------------------------------------


P53APC_DB:$library:[P53APC group:@MUTATION_LIBS
  format:@P53APC_FORMAT maxNameLen:20 files:{
    $file:p53apc
  }
]


P53APC_FORMAT:$libformat:[syntax:@P53APC_SYNTAX fileType:@P53APC_FILE
  fields:{
    $field:[@DF_ID code:id indexToken:id index:id]
    $field:[@DF_GN code:gn indexToken:gn index:str]
    $field:[@DF_CG code:cg indexToken:cg index:str]
    $field:[@DF_DnaChangePos code:nn indexToken:nn index:int
      tableToken:nn tableFormat:right]
    $field:[@DF_NuclChange code:nc indexToken:nc index:str
      tableToken:nc tableFormat:left]
    $field:[@DF_ProtChangePos code:cn indexToken:cn index:int
      tableToken:cn tableFormat:right]
    $field:[@DF_CB code:cb indexToken:cb index:str]
    $field:[@DF_AaChange code:cc indexToken:cc index:str
      tableToken:cc tableFormat:left]
    $field:[@DF_LO code:lo indexToken:lo index:str]
    $field:[@DF_LE code:le indexToken:le index:str]
    $field:[@DF_EN code:en indexToken:en index:str]
    $field:[@DF_MT code:mt indexToken:mt index:str]
    $field:[@DF_MM code:mm indexToken:mm index:str]
    $field:[@DF_SP code:sp indexToken:sp index:str]
    $field:[@DF_GS code:gs indexToken:gs index:str]
    $field:[@DF_AS code:as indexToken:as index:str]
    $field:[@DF_TT code:tt indexToken:tt index:str]
    $field:[@DF_CI code:ci indexToken:ci index:str]
    $field:[@DF_CL code:cl indexToken:cl index:str]
    $field:[@DF_IM code:im indexToken:im index:str]
    $field:[@DF_DS code:ds indexToken:ds index:str]
    $field:[@DF_PT code:pt indexToken:pt index:str]
    $field:[@DF_RE code:re indexToken:re index:str]
    $field:[@DF_MR code:mr indexToken:mr index:str]
    $field:[@DF_UP code:up indexToken:up index:str]
    $field:[@DF_RM code:rm indexToken:rm index:str]
  }
]

#data field types
DF_GN:$srsfield:[Gene_Name        short:GN group:@DF_ALL]
DF_CG:$srsfield:[CpG_Site         short:CG group:@DF_ALL]
DF_NN:$srsfield:[Nucl_Number      short:NN group:@DF_ALL]
DF_NC:$srsfield:[Nucl_Change      short:NC group:@DF_ALL]
DF_CB:$srsfield:[Codon_Base       short:CB group:@DF_ALL]
DF_LO:$srsfield:[Location         short:LO group:@DF_ALL]
DF_LE:$srsfield:[Length           short:LE group:@DF_ALL]
DF_EN:$srsfield:[Exon_Number      short:EN group:@DF_ALL]
DF_MT:$srsfield:[Mutation_Type    short:MT group:@DF_ALL]
DF_MM:$srsfield:[Multiple_Mutant  short:MM group:@DF_ALL]
DF_SP:$srsfield:[Splicing         short:SP group:@DF_ALL]
DF_GS:$srsfield:[Germline_Somatic short:GS group:@DF_ALL]
DF_AS:$srsfield:[Allelic_Status   short:AS group:@DF_ALL]
DF_TT:$srsfield:[Tumor_Type       short:TT group:@DF_ALL]
DF_CI:$srsfield:[Clinical_Info    short:CI group:@DF_ALL]
DF_CL:$srsfield:[Cell_Line        short:CL group:@DF_ALL]
DF_IM:$srsfield:[Immuno_Stain     short:IM group:@DF_ALL]
DF_DS:$srsfield:[DNA_Source       short:DS group:@DF_ALL]
DF_PT:$srsfield:[Patient          short:PT group:@DF_ALL]
DF_RE:$srsfield:[Reference        short:RE group:@DF_ALL]
DF_MR:$srsfield:[Method_Reference short:MR group:@DF_ALL]
DF_UP:$srsfield:[Update_Reference short:UP group:@DF_ALL]
DF_RM:$srsfield:[Remarks          short:RM group:@DF_ALL]



#links
$link:[@P53APC_DB to:@?P53APCREF_DB fromField:@DF_RE toField:@DF_ID  token:re]
$link:[@P53APC_DB to:@?P53APCMET_DB fromField:@DF_MR toField:@DF_ID  token:mr]
$link:[@P53APC_DB to:@?P53APC_DB fromField:@DF_UP toField:@DF_ID  token:up]


P53APC_SYNTAX:$syntax:[file:"SRSDB:p53apc.is" ignore:" \t"]
P53APC_FILE:$filetype:[typeName:dat maxline:200]

ethod_Reference short:MR group:@DF_ALL]
DF_UP:$srsfield:[Update_Reference short:UP group:@DFsrs/icarus/db/p53apc.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: p53apc.is,v $
#    $Revision: 1.3 $
#    $Date: 1996/12/06 16:37:40 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#--------------------------------------
#    File:      p53apc.is              |
#    Version:   1.0                    |
#    Date:      17-Sep-1996            |
#    Author:    Benny Shomer           |
#               bshomer@ebi.ac.uk      |
#--------------------------------------



$rules={

  #data record
  entry:     ~ {$In:[file:text] $Out}
               ('Identifier      ' {$entryFip=$Fip $Wrt} ln {$App}
               ('Identifier      ' {$Not} ln {$App})*)?
             ~

  ln:        ~  /[^\n]*\n/ ~

  # Data fields
  fields:    ~ {$In:entry $Out} 
               id gn cg nn nc cn cb cc lo le en mt mm sp gs
                as tt ci cl im ds pt re mr up rm ~
  id:        ~ {$Wrt:id} 'Identifier      ' ln~
  gn:        ~ {$Wrt:gn} ('Gene_Name       ' ln)*   ~
  cg:        ~ {$Wrt:cg} ('CpG_Site        ' ln)*   ~
  nn:        ~ {$Wrt:nn} ('Nucl_Number     ' ln)*   ~
  nc:        ~ {$Wrt:nc} ('Nucl_Change     ' ln)*   ~
  cn:        ~ {$Wrt:cn} ('Codon_Number    ' ln)*   ~
  cb:        ~ {$Wrt:cb} ('Codon_Base      ' ln)*   ~
  cc:        ~ {$Wrt:cc} ('Codon_Change    ' ln)*   ~
  lo:        ~ {$Wrt:lo} ('Location        ' ln)*   ~
  le:        ~ {$Wrt:le} ('Length          ' ln)*   ~
  en:        ~ {$Wrt:en} ('Exon_Number     ' ln)*   ~
  mt:        ~ {$Wrt:mt} ('Mutation_Type   ' ln)*   ~
  mm:        ~ {$Wrt:mm} ('Multiple_Mutant ' ln)*   ~
  sp:        ~ {$Wrt:sp} ('Splicing        ' ln)*   ~
  gs:        ~ {$Wrt:gs} ('Germline_Somatic' ln)*   ~
  as:        ~ {$Wrt:as} ('Allelic_Status  ' ln)*   ~
  tt:        ~ {$Wrt:tt} ('Tumor_Type      ' ln)*   ~
  ci:        ~ {$Wrt:ci} ('Clinical_Info   ' ln)*   ~
  cl:        ~ {$Wrt:cl} ('Cell_Line       ' ln)*   ~
  im:        ~ {$Wrt:im} ('Immuno_Stain    ' ln)*   ~
  ds:        ~ {$Wrt:ds} ('DNA_Source      ' ln)*   ~
  pt:        ~ {$Wrt:pt} ('Patient         ' ln)*   ~
  re:        ~ {$Wrt:re} ('Reference       ' ln)*   ~
  mr:        ~ {$Wrt:mr} ('Method_Reference' ln)*   ~
  up:        ~ {$Wrt:up} ('Update_Reference' ln)*   ~
  rm:        ~ {$Wrt:rm} ('Remarks         ' ln)*   ~

  # Indexing
  word:      ~ /[A-Za-z0-9_-]+/ ~
  int:       ~ /[-]?[0-9]+/ ~
  real:      ~ /[-]?[0-9]+([\.]?[0-9]+)?/~
  
  i_id:      ~ {$In:[fields c:id]  $out:id}
               'Identifier' int {$Wrt} ~
  i_gn:      ~ {$In:[fields c:gn]  $out:gn}
               ('Gene_Name'  (  word  {$Wrt} )* )* ~
  i_cg:      ~ {$In:[fields c:cg]  $out:cg}
               ('CpG_Site'  (  word  {$Wrt} )* )* ~
  i_nn:      ~ {$In:[fields c:nn]  $out:nn}
               ('Nucl_Number'  (word  {$Wrt}/[;->.? ]*/ )* )* ~
  i_nc:      ~ {$In:[fields c:nc]  $out:nc}
               'Nucl_Change' /([A-Z]) *-> *([A-Z])/? {$Wrt:[s:"$1>$2"]} ~
  i_cn:      ~ {$In:[fields c:cn]  $out:cn}
               ('Codon_Number'  (int  {$Wrt} )* )* ~
  i_cb:      ~ {$In:[fields c:cb]  $out:cb}
               ('Codon_Base'  (/[^;->.? ]+/ {$Wrt} )* )* ~
  i_cc:      ~ {$In:[fields c:cc]  $out:cc}
               'Codon_Change ' /([A-Z]) *-> *([A-Z*])/? 
               {if:$2=='*' $to=Stop else $to=$2 $Wrt:[s:"$1>$to"]} ~
  i_lo:      ~ {$In:[fields c:lo]  $out:lo}
               ('Location'  (/[^;->? ]+/ {$Wrt} /[;->? ]*/ )* )* ~
  i_le:      ~ {$In:[fields c:le]  $out:le}
               ('Length'  (word {$Wrt} )* )* ~
  i_en:      ~ {$In:[fields c:en]  $out:en}
               ('Exon_Number'  (int {$Wrt} )* )* ~
  i_mt:      ~ {$In:[fields c:mt]  $out:mt}
               ('Mutation_Type' /[";]?/ ( /[^;->.? ]+/ {$Wrt} /[;->.? ]*/)* )* ~
  i_mm:      ~ {$In:[fields c:mm]  $out:mm}
               ('Multiple_Mutant'  (int {$Wrt} )* )* ~
  i_sp:      ~ {$In:[fields c:sp]  $out:sp}
               ('Splicing'  (word {$Wrt} )* )* ~
  i_gs:      ~ {$In:[fields c:gs]  $out:gs}
               ('Germline_Somatic'  (word {$Wrt} )* )* ~
  i_as:      ~ {$In:[fields c:as]  $out:as}
               ('Allelic_Status'  (int {$Wrt} )* )* ~
  i_tt:      ~ {$In:[fields c:tt]  $out:tt}
               ('Tumor_Type'  /[";]?/ ( /[^;->.? ]+/ {$Wrt} /[;->.? ]*/)* )* ~
  i_ci:      ~ {$In:[fields c:ci]  $out:ci}
               ('Clinical_Info'  (word {$Wrt} )* )* ~
  i_cl:      ~ {$In:[fields c:cl]  $out:cl}
               ('Cell_Line'  (/[^"; ]+/ {$Wrt} )* )* ~
  i_im:      ~ {$In:[fields c:im]  $out:im}
               ('Immuno_Stain'  (/[^"; ]+/ {$Wrt}/["; ]*/ )* )* ~
  i_ds:      ~ {$In:[fields c:ds]  $out:ds}
               ('DNA_Source'  ( /[^"; ]+/ {$Wrt}/["; ]*/ )* )* ~
  i_pt:      ~ {$In:[fields c:pt]  $out:pt}
               ('Patient' /[";]?/ ( /[^"; ]+/  {$Wrt}/["; ]*/ )* )* ~
  i_re:      ~ {$In:[fields c:re]  $out:re}
               ('Reference '  (int {$Wrt} /["; ]*/)* )* ~
  i_mr:      ~ {$In:[fields c:mr]  $out:mr}
               ('Method_Reference'  (int  {$Wrt}/["; ]*/ )* )* ~
  i_up:      ~ {$In:[fields c:up]  $out:up}
               ('Update_Reference'  ( int {$Wrt} /["; ]*/)* )* ~
  i_rm:      ~ {$In:[fields c:rm]  $out:rm}
               ('Remarks'  (/[^"; ]+/ {$Wrt} /["; ]*/)* )* ~

  #       # printing in HTML format

}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/opt/srs/data/mutdb/p53apc/p53apc.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:id print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}

]*/ )* )* ~
  i_up:      ~ {$In:[fields c:up]  $out:up}
               ('Update_Reference' srs/icarus/db/p53apc.it
  description:
    |This is a database of mutations in the p53
    |and APC tumor suppressor genes designed to facilitate molecular epidemiological
    |analyses. 
    |<H4>Sources</H4>
    |Mutations in this database are from journals published in the 
    |English language before September 1, 1993. The sources of 
    |references include the laboratory's collection of papers, Dr. 
    |Soussi's database, and searches of Medline, Cancerline, Chemical 
    |Abstracts, Biological Abstracts, Excerpta Medica, and Current 
    |Contents. While every effort has been made to be comprehensive, 
    |inadvertent omissions are unavoidable. Authors are encouraged to 
    |supply information updates in the future.
    |<H4>Design</H4>
    |The database is organized into three "relational" database 
    |tables that are interrelated through common key numbers. 
    |Explanations for each field of the relational database tables 
    |are described below.
#  literature:''
  address:
    |<PRE>
    |Guggenheim 1501B
    |Department of Biochemistry & Molecular Biology
    |Mayo Clinic/Foundation
    |Rochester, MN 55905
    |</PRE>
  ftp:
    |<A HREF="ftp://ftp.ebi.ac.uk/pub/databases/p53APC">\
    |ftp.ebi.ac.uk/pub/databases/p53APC</A>
#  www:''
  email:
    |liaod@Mayo.EDU
#  updates:''
}
l" database 
    |tables that are interrelated through common key numbers. 
    |Explanations for each field of the relational database tables 
    |are described below.
#  literature:''
  address:
    |<PRE>
    |Guggenheim 150srs/icarus/db/p53apcref.i
#    File:		p53apcref.i            |
#    Version: 	1.0                    |
#    Date:		11-Sep-1996            |
#    Author:	Benny Shomer           |
# 				bshomer@ebi.ac.uk      |
#--------------------------------------    


P53APCREF_DB:$library:[P53APCREF group:@MUTATION_LIBS
	format:@P53APCREF_FORMAT maxNameLen:10 files:{
		$file:p53apc
	}
]

P53APCREF_FORMAT:$libformat:[syntax:@P53APCREF_SYNTAX fileType:@P53APCREF_FILE  
fields:{
    $field:[@DF_ID code:id indexToken:id index:id]
    $field:[@DF_Authors code:ra indexToken:ra index:str]
    $field:[@DF_Title code:rt indexToken:rt index:str]
    $field:[@DF_Reference code:rl indexToken:rl index:str]
    $field:[@DF_JR2 code:jr indexToken:jr index:str]
  }
]


#data field types
DF_JR2:$srsfield:[Cross_Ref short:XR group:@DF_ALL]



#links
$link:[@P53APCREF_DB to:@?MEDLINE_DB fromField:@DF_JR toField:@DF_ID token:jr]


P53APCREF_SYNTAX:$syntax:[file:"SRSDB:p53apcref.is" ignore:" \t"]
P53APCREF_FILE:$filetype:[typeName:ref maxline:200]


   $field:[@DF_Authors code:ra indexToken:ra index:str]
    $field:[@DF_Title code:rt indexToken:rt index:str]
    $field:[@DF_Reference code:rl indexToken:rl index:str]
    $field:[@DF_JR2 code:jr indexToken:jr index:str]
  }
]


#data field types
DF_JR2:$srsfield:[Cross_Ref short:XR group:@DF_ALL]



#links
$link:[@P53APCREF_DB to:@?MEDLINE_DB fromField:@DF_JR toField:@DF_ID token:jr]


P53APCREF_SYNTAX:$syntax:[file:"SRSDB:p53apcref.is" ignore:" \t"]
P53APCREF_FILE:$filetype:[typeNasrs/icarus/db/p53apcref.is
#--------------------------------------
#    File:		p53apcref.is           |
#    Version: 	1.0                    |
#    Date:		11-Sep-1996            |
#    Author:	Benny Shomer           |
# 				bshomer@ebi.ac.uk      |
#--------------------------------------    

$rules={

	#data record
	entry:	~ {$In:[file:text] $Out}
	          ('ID  ' {$entryFip=$Fip $Wrt} ln {$App}
                  ('ID  ' {$Not} ln {$App})*)?
		~
			
	ln:		~  /[^\n]*\n/ ~
	
	
	# Data fields
	fields:	~ {$In:entry $Out} id  ra rt rl jr ~
	id:		~ {$Wrt:id}    'ID'  ln  ~
        ra:             ~ {$Wrt:ra}             ('RA' ln)*   ~
        rt:             ~ {$Wrt:rt}             ('RT' ln)*   ~
        rl:             ~ {$Wrt:rl}             ('RL' ln)*   ~
        jr:             ~ {$Wrt:jr}             ('XR' ln)*   ~

	# Indexing
	word:	~ /[A-Za-z0-9_-]+/ ~
	name:	~ /[A-Za-z0-9_'-\?^]+/ ~
	int:    ~ /[-]?[0-9]+/ ~
	real:    ~ /[-]?[0-9]+([\.]?[0-9]+)?/~
	author:  ~ name /[^,;]+/ ~
	
	i_id:	~ {$In:[fields c:id]  $out:id} 
                 'ID' /[0-9.]+/ {$Wrt} ~
    i_ra:   ~ {$In:[fields c:ra]  $out:ra}
                 ( 'RA' (/[^ .,;:"\n]+/ {$Wrt} (/[. ,;]*/|'et al'
                 /[.,;]?/))*)* ~
    i_rt:   ~ {$In:[fields c:rt]  $out:rt}
                 ( 'RT' (/[^ .,;:"\n]+/ {$Wrt}/[ .,;:"\n]*/)* ln)* ~
    i_rl:   ~ {$In:[fields c:rl]  $out:rl}
                 'RL' /[^0-9]+/ {$Wrt:jrn} 
                 /([0-9]+), ([0-9]+)-([0-9]+), ([0-9]+)[.]?/
                 {$Wrt:[vol s:$1] $Wrt:[pg1 s:$2] $Wrt:[pg2 s:$3] 
                 $Wrt:[year s:$4]} ~
    i_jr:   ~ {$In:[fields c:jr]  $out:jr}
                  'XR  MEDLINE:' int {$Wrt} ~


	# printing in HTML format
	h_jr:     ~ {$In:[fields c:jr t:html]}
				('XR  MEDLINE:' /[0-9]+/
				{$Rep:{$ParStr:medlineR $Ct $Ct}} ln)
			  ~


}
	


"\n]*/)* ln)* ~
    i_rl:   ~ {$In:[fields c:rl]  $out:rl}
                 'RL' /[^0-9]+/ {$Wrt:jrn} 
                 /([0-9]+), ([0-9]+)-([0-9]+), ([0-9]+)[.]?/
                 {$Wrt:[vol s:$1] $Wrt:[pg1 s:$2] $Wrt:[pg2 s:$3srs/icarus/db/p53ref.i
#    File:		p53ref.i               |
#    Version: 	1.0                    |
#    Date:		11-Sep-1996            |
#    Author:	Benny Shomer           |
# 				bshomer@ebi.ac.uk      |
#--------------------------------------    


P53REF_DB:$library:[P53REF group:@MUTATION_LIBS
	format:@P53REF_FORMAT maxNameLen:10 files:{
		$file:p53
	}
]

P53REF_FORMAT:$libformat:[syntax:@P53REF_SYNTAX fileType:@P53REF_FILE  
fields:{
    $field:[@DF_ID code:id indexToken:id index:id]
    $field:[@DF_RA code:ra indexToken:ra index:str]
    $field:[@DF_RT code:rt indexToken:rt index:str]
    $field:[@DF_RL code:rl indexToken:rl index:str]
    $field:[@DF_JR code:jr indexToken:jr index:str]
  }
]


#data field types
DF_RA:$srsfield:[Authors short:AU group:@DF_ALL]
DF_RT:$srsfield:[Title short:TI group:@DF_ALL]
DF_RL:$srsfield:[Source short:SO group:@DF_ALL]
DF_JR:$srsfield:[Cross_Ref short:XR group:@DF_ALL]



#links
$link:[@P53REF_DB to:@?MEDLINE_DB fromField:@DF_JR toField:@DF_ID token:jr]


P53REF_SYNTAX:$syntax:[file:"SRSDB:p53ref.is" ignore:" \t"]
P53REF_FILE:$filetype:[typeName:ref maxline:200]


@DF_RL code:rl indexToken:rl index:str]
    $field:[@DF_JR code:jr indexToken:jr index:str]
  }
]


#data field types
DF_RA:$srsfield:[Authors short:AU group:@DF_ALL]
DF_RT:$srsfield:[Title short:TI group:@DF_ALL]
DF_RL:$srsfield:[Source short:SO group:@DF_ALL]
DF_JR:$srsfield:[Cross_Ref short:XR group:@DF_ALL]



#links
$link:[@P53REF_DB to:@?MEDLINE_DB fromField:@DF_JR toField:@DF_ID token:jsrs/icarus/db/p53ref.is
#--------------------------------------
#    File:		p53ref.is              |
#    Version: 	1.0                    |
#    Date:		11-Sep-1996            |
#    Author:	Benny Shomer           |
# 				bshomer@ebi.ac.uk      |
#--------------------------------------    

$rules={

  #data record
  entry:    ~ {$In:[file:text] $Out}
              ('ID  ' {$entryFip=$Fip $Wrt} ln {$App}
              ('ID  ' {$Not} ln {$App})*)?
	     ~
  ln:        ~  /[^\n]*\n/ ~
	
  # Data fields
  fields:   ~ {$In:entry $Out} id  ra rt rl jr ~
  id:	    ~ {$Wrt:id}    'ID'  ln  ~
  ra:       ~ {$Wrt:ra}             ('RA' ln)*   ~
  rt:       ~ {$Wrt:rt}             ('RT' ln)*   ~
  rl:       ~ {$Wrt:rl}             ('RL' ln)*   ~
  jr:       ~ {$Wrt:jr}             ('XR' ln)*   ~

  # Indexing
  word:	    ~ /[A-Za-z0-9_-]+/ ~
  name:	    ~ /[A-Za-z0-9_'-\?^]+/ ~
  int:      ~ /[-]?[0-9]+/ ~
  real:     ~ /[-]?[0-9]+([\.]?[0-9]+)?/~
  author:   ~ name /[^,;]+/ ~
  
  i_id:	    ~ {$In:[fields c:id]  $out:id} 
              'ID' int  {$Wrt} ~
  i_ra:     ~ {$In:[fields c:ra]  $out:ra}
              ( 'RA' (/[^ .,;:"\n]+/ {$Wrt} (/[. ,;]*/|'et al'
              /[.,;]?/))*)* ~
  i_rt:     ~ {$In:[fields c:rt]  $out:rt}
               ( 'RT' (/[^ .,;:"\n]+/ {$Wrt}/[ .,;:"\n]*/)* ln)* ~
  i_rl:     ~ {$In:[fields c:rl]  $out:rl}
              'RL' /[^0-9]+/ {$Wrt:jrn} 
              /([0-9]+), ([0-9]+)-([0-9]+), ([0-9]+)[.]?/
              {$Wrt:[vol s:$1] $Wrt:[pg1 s:$2] $Wrt:[pg2 s:$3] 
              $Wrt:[year s:$4]} ~
  i_jr:     ~ {$In:[fields c:jr]  $out:jr}
                  'XR  MEDLINE:' int {$Wrt} ~

  # printing in HTML format
  h_jr:     ~ {$In:[fields c:jr t:html]}
              ('XR  MEDLINE:' /[0-9]+/
              {$Rep:{$ParStr:medlineR $Ct $Ct}} ln)
            ~
}
	


~
  i_rl:     ~ {$In:[fields c:rl]  $out:rl}
              'RL' /[^0-9]+/ {$Wrt:jrn} 
              /([0-9]+), ([0-9]+)-([0-9]+), ([0-9]+)[.]?/
              {$Wrt:[vol s:$1] $Wrt:[pg1 s:$2] $Wrt:[pg2 s:$3] 
              $Wrt:[year s:$4srs/icarus/db/pah.i
#    $RCSfile: pah.i,v $
#    $Revision: 1.2 $
#    $Date: 1997/03/03 18:34:08 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

PAH_DB:$library:[PAH group:@MUTATION_LIBS
  format:@PAH_FORMAT maxNameLen:30 ifiles:{'pah.i' 'pah.is' 'pah.it'}
  files:{
    $file:'CFmutations96-1'
  }
]

PAH_FORMAT:$libformat:[syntax:@PAH_SYNTAX fileType:@TXT_FILE  
  printFormat:table
  fields:{
    $field:[@DF_ID indexToken:id index:id
      tableToken:id tableFormat:right]
    $field:@DF_ALL
#    $field:[@DF_DnaSubst code:mut indexToken:'dnaMut|subst' index:str
#      tableToken:'dnaMut|subst' tableFormat:left]
    $field:[@DF_NuclChange code:mut indexToken:'nuclChange|mut' index:str
      tableToken:'nuclChange|mut' tableFormat:left]
 #   $field:[@DF_MutConseq code:aaSubst indexToken:mutConseq index:str
 #     tableToken:'aaSubst|subst' tableformat:left]
    $field:[@DF_DnaChangePos code:dnaSubst indexToken:dnaMutPos index:int
      tableToken:dnaMutPos tableFormat:right]
    $field:[@DF_ProtChangePos code:aaSubst indexToken:aaMutPos index:int
      tableToken:aaMutPos tableFormat:right]
    $field:[@DF_Reference code:ref]
  }
]


PAH_SYNTAX:$syntax:[file:"SRSDB:pah.is" ignore:" "]
tr
      tableToken:'nuclChange|mut' tableFormat:left]
 #   $field:[@DF_MutConseq code:aaSubst indexToken:mutConseq index:str
 #     tableToken:'aaSubst|subst' tableformat:left]
    $field:[@DF_DnaChangePos code:dnaSsrs/icarus/db/pah.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: pah.is,v $
#    $Revision: 1.2 $
#    $Date: 1996/12/06 16:37:42 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


$field={
  inex:       {len:9  index:normal }
  loc:        {len:7  index:normal }
  dnaChange:  {len:14 index:dnaChange }
  aaChange:   {len:18 index:aaChange }
  patient:    {len:11 index:normal }
  fC:         {len:9  index:normal }
  fAg:        {len:11 index:normal }
  Severity:   {len:16 index:normal }
  inhib:      {len:15 index:normal }
  cmnt:       {len:33 index:cmnt }
  ref:        {len:50 index:ref }
}

$rules={
  entry:   ~ {$In:[file:text] $Out pre $Skip:0 init $count=0}
             (/ [0-9]/ {$Not} ln)*
             (/ [0-9]+/ {$entryFip=$Fip $Wrt $count+=1} ln {$App})?
           ~
  # fields
   fields:  ~ {$In:entry $Out}
             x{ for:{$k=1 $k<12 $k+=1} {
                  $l=$field[$k].len 
                  $c=$Key:$field[$k]
                  $Prod:cell
                }
              } ~
  cell:    ~ /.+/ {if:$Trim:[$Ct]!="" $Wrt:$c $Len:$l} ~

  # indexing
  id:        ~ {$In:entry $Out} x{$Wrt:[s:$count]} ~
  inx:       ~ {$In:fields $Out pre $Skip:1} x{$Prod:$field.($Itc).index} ~
  normal:    ~ /[^ ]+/ {$Wrt:$Itc} ~
  dnaChange: ~ /([A-Z]+) +([A-Z]+)/ {$Wrt:[$Itc s:"$1>$2"]} ~
  aaChange:  ~ {init $aa={Ile:I Leu:L Met:M Ala:A Val:V Ser:S Thr:T Phe:F 
                          Tyr:Y Gly:G Pro:P Trp:W Cys:C Gln:Q 
                          Asn:N Arg:R Lys:K Asp:D Glu:E His:H Stop:Stop}
               } /([A-Za-z]+) +([A-Za-z]+)/ 
               {$Wrt:[$Itc s:"($aa.$1)>($aa.$2)"]} ~
  cmnt:      ~ /./ ~
  ref:       ~ /./ ~

  # others
  ln:      ~ /[^\n]*\n/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/opt/srs/data/mutdb/haema/haema.txt']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:id print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}



Cys:C Gln:Q 
                          Asn:N Arg:R Lys:K Asp:D Glu:E His:H Stop:Stop}
               } /([A-Za-z]+) +([A-Za-z]+)/ 
               {$Wrt:[$Itc s:"($aa.$1)>($aa.$2)"]} ~
  cmnt:      ~ /./ ~
  ref:       ~ /./ ~

  # others
  ln:      ~ /[^\n]*\n/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/opt/srs/data/mutdb/haema/haema.txt']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:id print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}
srs/icarus/db/pah.it
#    
#    $RCSfile: pah.it,v $
#    $Revision: 1.1 $
#    $Date: 1996/11/05 19:54:13 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |Mutations in the phenylalanine hydroxylase (PAH) gene, the majority of
    |which result in deficient enzyme activity and cause
    |hyperphenylalaninemia, occur in all 13 exons of the gene and flanking
    |sequence; Some in phenylketonuria, others cause non-PKU
    |hyperphenylalaninemia, while still others are silent polymorphisms
    |present on both normal and mutant chromosomes. Some PAH alleles are
    |present at elevated frequencies, 5 account for approximately 60%% of
    |European mutations and they tend to cluster in regions or are on only
    |one of a few haplotypes. Several hundred mutations and three-fold
    |greater mutation associations have been recorded. The majority of
    |changes are missense mutations, although splice ,nonsense and silent
    |mutations, as well as single base-pair frameshifts, and larger
    |deletions and insertions have been found.
    |
    |<H3>PAH Mutations Database</H3>
    |
    |Mutation data were collated from both published articles and personal
    |communications of 80 investigators from the PAH Mutation Analysis
    |Consortium in 26 countries. The curator has developed a database and
    |software package (WINPAHDB) which is stand-alone executable on an
    |IBM-compatible computer with Microsoft Windows. This enables us to
    |maintain and centralize mutation data on the PAH gene, while providing
    |fast and easy access for users. Searchable fields of the database
    |available to users are: mutation name, polymorphic haplotype,
    |population, geographic location, gene region, codon number, mutation
    |type, substitution, phenotype, and author's name.  The complete
    |information provided for each mutation is regularly updated from both
    |published data and personal communications. This database occupies a
    |WWW site on the internet and is a resource for the Human Genetic
    |Diversity Project (HUGO).
  www:
    |<A HREF="http://blizzard.cc.mcgill.ca/pahdb">\
    |http://blizzard.cc.mcgill.ca/pahdb</A>
  email:
    |mc77@musica.mcgill.ca
  phone:
    |+1 514 934 4417
  fax:
    |+1 514 934 4329
  contact:
    |Charles R. Scriver
  address:
    |McGill University-Montreal, 
    |Children's Hospital Research Institute, 
    |Debelle Laboratory for Biochemical Genetics, 
    |2300 Tupper St., Montreal, Quebec H3H 1P3, Canada.
  literature:
    |Nucleic Acids Research 24, 129-131, (1996)
  fields:{
  }  
}

  www:
    |<A HREF="http://blizzard.cc.mcgill.ca/pahdb">\
    |http://blizzard.cc.mcgill.ca/pahdb</A>
  email:
    |mc77@musica.mcgill.ca
  phone:
    |+1 514 934 4417
  fax:
    |+1 514 934 4329
  contact:
    |Charles R. Scriver
  address:
    |McGill University-Montreal, 
    |Children's Hospital Research Institute, 
    |Debelle Laboratory fsrs/icarus/db/pdb.i
#    $RCSfile: pdb.i,v $
#    $Revision: 1.6 $
#    $Date: 1997/03/19 20:30:37 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


PDB_DB:$library:[PDB group:@PROTSTRUCT_LIBS 
  format:@PDB_FORMAT maxNameLen:30 ifiles:{"pdb.i" "pdb.is"}
]

PDB_FORMAT:$libformat:[fileType:{@PDB_FILE} syntax:@PDB_SYNTAX 
  fields:{
    $field:[@DF_HeaderField name:'Title Section']
    $field:[@DF_ID code:header index:id indexToken:id]
    $field:[@DF_Date code:header index:int indexToken:date]
    $field:[@DF_Supersedes code:sprsde index:str indexToken:sprsde]
    $field:[@DF_Compound code:compnd index:str indexToken:'wordX|compnd'
      tableToken:'t_fields|compnd']
    $field:[@DF_Source code:source index:str indexToken:'wordX|source' 
      tableToken:'t_fields|source']
    $field:[@DF_EntryAuthors code:author index:str indexToken:author]
    $field:[@DF_Authors code:auth index:str indexToken:auth]
    $field:[@DF_Title code:titl index:str indexToken:'wordX|compnd']
    $field:[@DF_Remark code:remark index:str indexToken:'wordX|remark']
  
    $field:[@DF_HeaderField name:'Primary Structure Section']
    $field:[@DF_HeaderField name:'Annotation Section']
    $field:[@DF_HeaderField name:'Crystallographic Section']
    $field:[@DF_CRYST1 code:CRYST1 tableToken:'t_fields|CRYST1']
    $field:[@DF_ORIGXn code:ORIGX tableToken:'t_fields|ORIGX']
    $field:[@DF_SCALEn code:SCALE tableToken:'t_fields|SCALE']
    $field:[@DF_MTRIXn code:MTRIX tableToken:'t_fields|MTRIX']
    $field:[@DF_TVECT code:TVECT tableToken:'t_fields|TVECT']
    $field:[@DF_MODEL code:MODEL tableToken:'t_fields|MODEL']
#    $field:[@DF_Atoms token:'dfields|atom']
#    $field:[@DF_Master token:'dfields|master']

#    $field:[@DF_HeaderField name:'Coordinate Section']
#    $field:[@DF_SIGATM token:'fields2|SIGATM' tableToken:'t_fields2|SIGATM']
#    $field:[@DF_ANISOU token:'fields2|ANISOU' tableToken:'t_fields2|ANISOU']
#    $field:[@DF_SIGUJ token:'fields2|SIGUJ' tableToken:'t_fields2|SIGUJ']
#    $field:[@DF_TER token:'fields2|TER' tableToken:'t_fields2|TER']
#    $field:[@DF_HETATM token:'fields2|HETATM' tableToken:'t_fields2|HETATM']
  }
]
DF_EntryAuthors:$srsfield:[EntryAuthors short:eat]
DF_CRYST1:$srsfield:[CRYST1 short:cr1]
DF_ORIGXn:$srsfield:[ORIGXn short:ori]
DF_SCALEn:$srsfield:[SCALEn short:sca]
DF_MTRIXn:$srsfield:[MTRIXn short:mtr]
DF_TVECT:$srsfield:[TVECT short:tve]
DF_MODEL:$srsfield:[MODEL short:mod]
DF_Supersedes:$srsfield:[Supersedes short:spr]

DF_Atoms:$srsfield:[ATOM short:atm]
DF_SIGATM:$srsfield:[SIGATM short:sig]
DF_ANISOU:$srsfield:[ANISOU short:ani]
DF_SIGUJ:$srsfield:[SIGUJ short:sgu]
DF_TER:$srsfield:[TER short:ter]
DF_HETATM:$srsfield:[HETATM short:htm]
DF_ENDMDL:$srsfield:[ENDMDL short:end]
DF_Remark:$srsfield:[Remark short:rem]
DF_Master:$srsfield:[Master short:mas]

PDB_SYNTAX:$syntax:[file:"SRSDB:pdb.is" ignore:" "]

# compressed files named pdbXXX.ent.Z
#PDB_FILE:$FileType:[text  singleEntry:y maxline:100
#  saveName:file saveNameLength:20 pipe:"uncompress -c \%s" 
#  searchName:'pdb*.ent.Z'
#]

PDB_FILE:$FileType:[text  singleEntry:y maxline:100
  saveName:file saveNameLength:20 
  searchName:'3*.brk*'
]


#PDBDATA_FILE:$FileType:[data maxline:100 shareWith:@PDB_FILE 
#  fieldTokens:dfields fipVar:dataFip 
#]
emark short:rem]
DF_Master:$srsfield:[Master short:mas]

PDB_SYNTAX:$syntax:[file:"SRSDB:pdb.is" ignore:" "]

# compressed files named pdbXXX.ent.Z
#PDB_FILE:$FileType:[text  singleEntry:y maxlinsrs/icarus/db/pdb.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: pdb.is,v $
#    $Revision: 1.8 $
#    $Date: 1997/03/19 20:30:37 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  HEADER: header      HETNAM: hetnam       TVECT:  tvect
  TITLE:  title       HETSYN: hetsym       MODEL:  model
  SOURCE: source      HETSIT: hetsit               
  KEY:	  key	      FORMUL: formul       ATOM:   atom
  EXPDTA: expdta      HELIX:  helix        SIGATM: sigatm
  AUTHOR: author      SHEET:  sheet        ANISOU: anisou
  REVDAT: revdat      TURN:   turn         SIGUIJ: siguij
  SPRSDE: sprsde      SSBOND: ssbond       TER:    ter
  COMPND: compnd      SITE:   site         HETATM: hetatm
  MODRES: modres      CRYST1: cryst        ENDMDL: endmdl
  DBREF:  dbref	      ORIGX1: origx        CONECT: conect
  SEQADV: seqadv      ORIGX2: origx        MASTER: master
  SEQRES: seqres      ORIGX3: origx        END:    end
  FTNOTE: ftnote      SCALE1: scale        KEYWDS: keywds        
  HET:	  het	      SCALE2: scale        LINK:   link
  JRNL:   jrnl	      SCALE3: scale        CISPEP: cispep
  REMARK: remark      MTRIX2:  mtrix       MTRIX1: mtrix
  MTRIX3: mtrix
  'JRNL        AUTH': auth       'REMARK   1':           head 
  'JRNL        TITL': titl	 'REMARK   1 REFERENCE': head 
  'JRNL        REF':  ref	 'REMARK   1  AUTH':     auth  
  'JRNL        REFN': refn	 'REMARK   1  TITL':     titl 
  'JRNL        EDIT':  edit	 'REMARK   1  REF':      ref  
  'JRNL        PUBL':  publ	 'REMARK   1  REFN':     refn 
  				 'REMARK   1  EDIT':     edit
  				 'REMARK   1  PUBL':     publ
  				 'REMARK   1  RENF':     publ
}

$rules={
  # the entry
  entry:    ~ {$In:[file:text] $Out init{$Skip:0}}
              'HEADER    ' {pre {$entryFip=0} $Wrt} appLn 
              ('END   ' {$Not} appLn)*  ~
  data:     ~ {$In:[file:data share:text] $Out}
              ln {$Wrt $dataFip=$Fip} appLn+  ~

  # fields from text and data
  fields:   ~ {$In:entry $Out} 
              (tag { $t=$Ct 
                     if:$fn.$t!="" {if:$fn.$t!=$fPrev $Wrt:$fn.$t else $App
                     $fPrev = $fn.$t}
                   } ln {$App})+ ~
  dfields:  ~ {$In:data $Out} 
              (tag { $t=$Ct  
                     if:$fn.$t!="" {if:$fn.$t!=$fPrev $Wrt:$fn.$t else $App
                     $fPrev = $fn.$t}
                   } ln {$App})+ ~
  tag:      ~ /JRNL +[A-Z]+/ | /REMARK +1 +[A-Z]+/ | /[A-Z0-9]+/ ~ 

  #indexing productions
  id:       ~ {$In:[fields c:header] $Out $Mov:62} /[A-Z0-9]+/ {$Wrt} ~
  date:     ~ {$In:[fields c:header] $Out $Mov:50} datenum {$Wrt:[s:$date]} ~
  wordX:    ~ {$In:[fields c:{compnd source remark het}] $Out} 
              (x{$Mov:10} words {$Len:60} ln)+ ~
  author:   ~ {$In:[fields c:author] $Out} (x{$Mov:10} authors {$Len:60} ln)+ ~
  auth:     ~ {$In:[fields c:auth] $Out} (x{$Mov:18} authors {$Len:52} ln)+ ~
  titl:     ~ {$In:[fields c:titl] $Out} (x{$Mov:18} words {$Len:52} ln)+ ~
  ref:      ~ {$In:[fields c:ref] $Out} (x{$Mov:18} words {$Len:52} ln)+ ~
  master:   ~ {$In:[dfields c:master] $Out} 
              tag / */ word {$Wrt} ~
	   
  authors:  ~ sauthor (',' sauthor?)* ~
  sauthor:  ~ / *([^ ,]*\\.)([^ ,]*)/ {$Uniq:[s:"$2,$1"]} ~
  words:    ~ (/[A-Z0-9]+/ {$Uniq:$Itc} | /[^A-Z0-9]+/)+ ~
  datenum:  ~ {init {$month={JAN:1 FEB:2 MAR:3 APR:4 MAY:5 JUN:6 JUL:7 AUG:8 
                             SEP:9 OCT:10 NOV:11 DEC:12}}}
              / *([0-9]+)-([A-Z][A-Z][A-Z])-([0-9]+)/ 
              {$date=$1 + $month.$2 * 100 + $3 * 10000 + 19000000} ~
  sprsde:   ~ {$In:[fields c:sprsde] $Out $Mov:10}  
              / *[^ \n]+/ / *[^ \n]+ */ /[^ \n]+/ {$Wrt} ~

  # table display
  t_fields:  ~ {$In:[fields c:{source compnd}] $Out}
               (x{$Mov:9 $Getc:62 $Wrt:$Itc} ln)+ ~

  # html display
  h_com:     ~ {$In:[t_fields c:com t:html]}
               (/(E\\.C\\.|EC: *)([0-9]+\\.[0-9]+\\.[0-9]+\\.[0-9]+)/
	        {$Rep:{"$1($ParStr:enzymeR)" $2 $2}} |
                /./)+
             ~
  # other productions
  word:      ~  /[^ ]+/ ~
  ln:        ~  /[^\n]*\n/ ~
  appLn:     ~  /[^\n]*\n/ {$App} ~
}


# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
           fileName:'/data/research/pdb/2hya.brk']
  $JobTokens:[$job name:fields print:0] 
  $JobTokens:[$job name:id print:1] 
  $JobTokens:[$job name:date print:1] 
  $JobTokens:[$job name:wordX print:1] 
  $JobTokens:[$job name:author print:1] 
  $JobTokens:[$job name:auth print:1] 
}



             /./)+
             ~
  # othersrs/icarus/db/pdb.it
#    
#    $RCSfile: pdb.it,v $
#    $Revision: 1.4 $
#    $Date: 1996/10/30 10:20:21 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |The Protein Data Bank (PDB) is an archive of experimentally determined
    |three-dimensional structures of biological macromolecules, serving a
    |global community of researchers, educators, and students. The archives
    |contain atomic coordinates, bibliographic citations, primary and
    |secondary structure information, as well as crystallographic structure
    |factors and NMR experimental data. The PDB Newsletter and CD ROM are
    |published quarterly. <p> The PDB is supported by a combination of
    |Federal Government Agency funds and user fees. Support is provided
    |by the U.S. National Science Foundation, the U.S. Public Health
    |Service, National Institutes of Health, National Center for Research
    |Resources, National Institutes of General Medical Sciences, National
    |Library of Medicine, and the U.S. Department of Energy under contract
    |DE-AC02-76CH00016 and user fees.
  www:
    |<A HREF="http://www.pdb.bnl.gov/">http://www.pdb.bnl.gov/</A>
  literature:
    |<A HREF="http://www.pdb.bnl.gov/newslttr/txt/newslttr.txt">PDB
    |Quarterly Newsletter</A>
  date:
    |25 Jul 1996
  signature:
    |Anatoly Ulyanov
}
lth
    |Service, National Institutes of Health, National Center for Resrs/icarus/db/pdbfinder.i
#    $RCSfile: pdbfinder.i,v $
#    $Revision: 1.9 $
#    $Date: 1997/03/03 18:34:10 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


PDBFINDER_DB:$library:[PDBFINDER group:@PROTSTRUCT_LIBS
  comment:"Directory for the Brookhaven Protein Data Bank"
  format:@PDBFINDER_FORMAT ifiles:{'pdbfinder.i' 'pdbfinder.is'}
  subentries:@PdbfinderChains_DB 
  files:{
    $file:pdbfinder
  }
]

PDBFINDER_FORMAT:$libformat:[fileType:@PDBFINDER_FILE 
  syntax:@PDBFINDER_SYNTAX tableFormat:left fields:{
    $field:[@DF_ALL]
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:[@DF_Header code:header index:str indexToken:'wordX|header'
      tableToken:'fields|header']
    $field:[@DF_Compound code:compound index:str indexToken:'wordX|compound'
      tableToken:'fields|compound']
    $field:[@DF_EnzymeCode code:enzyme index:str indexToken:enzyme]
    $field:[@DF_Source code:source index:str indexToken:'wordX|source'
      tableToken:'fields|source']
    $field:[@DF_Authors code:author index:str indexToken:author]
    $field:[@DF_Date code:date index:int indexToken:date]
    $field:[@DF_Resolution code:resolution index:real 
      indexToken:'realX|resolution']
    $field:[@DF_R_FACTOR code:rFactor index:real
      indexToken:'numX|rFactor']
    $field:[@DF_N_HSSP_ALIGN code:hsspNAlign index:int 
      indexToken:'numX|hsspNAlign']
    $field:[@DF_N_HET_GROUPS code:nHetGroups index:int
       indexToken:'numX|nHetGroups']
    $field:[@DF_EXP_METHOD code:expMethod index:str 
      indexToken:'wordX|expMethod']
    $field:[@DF_tFracHelix code:tFracHelix index:int 
      indexToken:'realX|tFracHelix']
    $field:[@DF_T_NRES_PROT code:tNresProt index:int 
      indexToken:'numX|tNresProt']
    $field:[@DF_TWaterMols code:tWaterMols index:int 
      indexToken:'numX|tWaterMols']

    # chain subentry
    $field:[@DF_HeaderField name:'Chain Subentry Fields']
    $field:[@DF_ChainName code:chain index:str indexToken:chnName
       indexId:@SUBENTRY_ID]
    $field:[@DF_N_NUCLACIDS code:nuc index:int indexToken:nuc
      indexId:@SUBENTRY_ID]
    $field:[@DF_N_AMINOACIDS code:aa index:int indexToken:aa
      indexId:@SUBENTRY_ID]
    $field:[@DF_SecStruc code:secStruc]
    $field:[@DF_Helix code:helix index:int indexToken:helix]
    $field:[@DF_II3 code:ii3]
    $field:[@DF_II5 code:ii5]
    $field:[@DF_Beta code:beta]
    $field:[@DF_BBridge code:bBridge]
    $field:[@DF_ParaHb code:paraHn]
    $field:[@DF_AntiHb code:antiHB]
    $field:[@DF_MissBB code:missBB]
    $field:[@DF_MissSC code:missSC]
    $field:[@DF_Break code:break]
    $field:[@DF_Substrate code:substrate]
    $field:[@DF_WaterMols code:waterMols index:int indexToken:waterMols
      indexId:@SUBENTRY_ID tableToken:waterMols tableFormat:right]
    $field:[@DF_Sequence code:sequence tableToken:t_sequence]
  }
]

PdbfinderChains_DB:$library:[PDBFINDER_chains format:@PdbfinderChains_Format]

PdbfinderChains_Format:$libformat:[syntax:@PDBFINDER_SYNTAX
  tableFormat:left
  fields:{
    $field:[@DF_ID           token:chainId]
    $field:[@DF_ChainName    token:'chain|chain']
    $field:[@DF_N_NUCLACIDS  token:'chain|nuc' tableFormat:right]
    $field:[@DF_N_AMINOACIDS token:'chain|aa' tableFormat:right]
    $field:[@DF_SecStruc     token:'chain|secStruc']
    $field:[@DF_Helix        token:'chain|helix']
    $field:[@DF_II3          token:'chain|ii3']
    $field:[@DF_II5          token:'chain|ii5']
    $field:[@DF_Beta         token:'chain|beta']
    $field:[@DF_BBridge      token:'chain|bBridge']
    $field:[@DF_ParaHb       token:'chain|paraHb']
    $field:[@DF_MissBB       token:'chain|missBB']
    $field:[@DF_WaterMols    token:'chain|waterMols']
    $field:[@DF_ProtSequence token:chnSequence tableFormat:listing]
  }
]


DF_EXP_METHOD:$srsfield:[ExpMethod short:exp group:@DF_ALL]
DF_N_HET_GROUPS:$srsfield:[NoHetGroups short:het group:@DF_ALL]
DF_N_HSSP_ALIGN:$srsfield:[NoHSSPAlign short:nha] 
DF_tFracHelix:$srsfield:[TotFractHelix short:tfh group:@DF_ALL] 
DF_T_FRAC_BETA:$srsfield:[TotFractBeta short:tfb group:@DF_ALL] 
DF_T_NRES_PROT:$srsfield:[TotNResProt short:tnp group:@DF_ALL] 
DF_TWaterMols:$srsfield:[TotWaterMols short:twm group:@DF_ALL] 
DF_Resolution:$srsfield:[Resolution short:res group:@DF_ALL] 
DF_R_FACTOR:$srsfield:[RFactor short:rfa group:@DF_ALL] 
DF_ChainName:$srsfield:[ChainName short:chn group:@DF_ALL]
DF_N_NUCLACIDS:$srsfield:[NucleicAcids short:nuc]
DF_N_AMINOACIDS:$srsfield:[AminoAcids short:aa]
DF_SecStruc:$srsfield:[SecStruc short:ss]
DF_Helix:$srsfield:[Helix short:hel]
DF_II3:$srsfield:[II3 short:ii3]
DF_II5:$srsfield:[II5 short:ii5]
DF_Beta:$srsfield:[Beta short:bet]
DF_BBridge:$srsfield:[BetaBridge short:bbr]
DF_ParaHb:$srsfield:[ParaHb short:phb]
DF_AntiHb:$srsfield:[AntiHb short:ahb]
DF_MissBB:$srsfield:[MissBB short:mbb]
DF_MissSC:$srsfield:[MissSC short:msc]
DF_Break:$srsfield:[Break short:bre]
DF_NWaterMols:$srsfield:[NWaterMols short:nwm]


PDBFINDER_SYNTAX:$syntax:[file:"SRSDB:pdbfinder.is" ignore:" \t"]
PDBFINDER_FILE:$filetype:[typename:dat maxline:5000]

$link:[@PDBFINDER_DB to:@?PDB_DB fromField:@DF_ID toField:@DF_ID]
ii5]
DF_Beta:$srsfield:[Beta short:bet]
DF_BBridge:$srsfield:[BetaBridge short:bbr]
DF_ParaHb:$srsfield:[ParaHb short:phb]
DF_AntiHb:$srsfield:[AntiHb short:ahb]
DF_MissBB:$srsfield:[MissBB short:mbb]
DF_MissSC:$srsfield:[MissSC short:msc]
DF_Break:$srsfield:[Break short:bre]
DF_NWaterMols:$srsfield:[NWaterMols short:nwm]


PDBFINDER_SYNTAX:$syntax:[file:"SRSDB:pdbfinder.is" ignore:" \t"]
PDBFINDsrs/icarus/db/pdbfinder.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: pdbfinder.is,v $
#    $Revision: 1.7 $
#    $Date: 1996/12/18 19:44:50 $
#    $Author: weare $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


$fn={
  'ID':           id                 'Name':         hetName      
  'Header':       header 	     'Chain':        chain        
  'Date':         date 		     'Sec-Struc':    secStruc     
  'Compound':     compound	     'Helix':        helix        
  'Enzyme-Code':  enzyme	     'i,i+3':        ii3          
  'Source':       source	     'i,i+5':        ii5          
  'Author':       author	     'Beta':         beta         
  'Exp-Method':   expMethod	     'B-Bridge':     bBridge      
  'Resolution':   resolution	     'E-Beta':       missSC       
  'R-Factor':     rFactor	     'Para-Hb':      paraHb       
  'Free-R':       appLn		     'Anti-Hb':      antiHb       
  'Ref-Prog':     refProg	     'Amino-Acids':  aa           
  'N-Models':     nModels	     'non-Std':      missSC       
  'HSSP-N-Align': hsspNAlign	     'Miss-BB':      missBB       
  'T-Frac-Helix': tFracHelix	     'Miss-SC':      missSC       
  'T-Frac-Beta':  tFracBeta	     'only-Ca':      missSC       
  'T-Nres-Prot':  tNresProt	     'CYSS':         missSC       
  'T-non-Std':    appLn		     'Break':        break        
  'T-Nres-Nucl':  appLn		     'Nucl-Acids':   nuc          
  'T-Water-Mols': tWaterMols	     'Substrate':    substrate    
  'HET-Groups':   nHetGroups 	     'Water-Mols':   waterMols    
  'Het-Id':       hetId 	     'Sequence':     sequence     
  'Natom':        hetNAtom           'UNK':          unc
  'SF-Type':      unknown            'N-refl':       unknown
  'H-max':        unknown 	     'H-min':        unknown
  'K-max':        unknown 	     'K-min':        unknown
  'L-max':        unknown 	     'L-min':        unknown
}

$rules={
  entry:       ~ {$In:[file:text] $Out pre $Skip:0}
                 ('ID' {$Not} ln)*
                 'ID' {$entryFip = $Fip $Wrt} appLn 
                 ('ID' {$Not} appLn)+ ~             

  # data fields
  fields:      ~ {$In:entry $Out $Skip:1}
                 (/ *([^ ]+) *:/ { if:$1==$prev $App 
                                   else {
                                     if:$ParInt:isTable $Wrt:[s:"" c:$fn.$1]
                                     else $Wrt:$fn.$1
                                   }
                                   if:$fn.$1=="" $dp:"+++ unknown: $1 +++"
                                   $prev=$1
                                 } 
                 ln {$App})+ ~

  # indexing
  id:          ~ {$Out $In:[fields c:id]} 
                 tag /..../ {$Wrt} ~
  enzyme:      ~ {$Out $In:[fields c:enzyme]} tag /[0-9.-]+/ {$Wrt} ~
  author:      ~ {$Out $In:[fields c:author]} 
                 tag /([A-Za-z.-]+\\.)([a-zA-Z ]+)/ {$Wrt:[s:"$2,$1"]} ~
  date:        ~ {$Out $In:[fields c:date]} tag
                 /([0-9]+)-([0-9]+)-([0-9]+)/ {$Wrt:[s:"$1$2$3"]} ~
  wordX:       ~ {$In:[fields c:{header compound source expMethod}] $Out}
                 tag (word {$Uniq:$Itc} | sep)* ~
  realX:       ~ {$In:[fields c:{resolution rFactor tFracHelix}] $Out}
                 tag real {$Wrt:$Itc} ~ 
  numX:        ~ {$In:[fields c:{nHetGroups hsspNAlign tNresProt tWaterMods}]
                   $Out} tag int {$Wrt:$Itc} ~

  chnName:     ~ {$Out $In:[fields c:chain count:chain var:$chN]} 
                 tag str {$Wrt:[n:$chN]} ~
  nuc:         ~ {$Out $In:[fields c:nuc count:chain var:$chN]} 
                 tag int {$Wrt:[n:$chN]} ~
  aa:          ~ {$Out $In:[fields c:aa count:chain var:$chN]} 
                 tag int {$Wrt:[n:$chN]} ~
  helix:       ~ {$Out $In:[fields c:sequence]} ln {$Wrt:[s:'77777']} ~ 
  waterMols:   ~ {$Out $In:[fields c:waterMols count:chain var:$chN]} 
                 tag int {$Wrt:[n:$chN]} ~

  # display chain subentries
  chainId:     ~ {$In:[fields c:id] $Out pre $Skip:0} 
                 tag {$Wrt} / *([^ \n]+)/ 
                 {$entryName="$1\_$subEntryN" 
                  $App:[s:" $entryName ;  parent: $1"]} ~
  chain:       ~ {$In:[fields count:chain var:$chN select:$subEntryN
                    c:{chain nuc aa secStruc helix ii3 ii5 beta bBridge
                       paraHb missBB waterMols}] $Out pre $Skip:0}
                 tag {if:$ParInt:isTable $Wrt:[$Itc s:""] else $Wrt:$Itc} 
                 /.+/ {$App} ~
  chnSequence: ~ {$In:[fields count:chain var:$chN select:$subEntryN 
                  c:sequence] $Out}
                  tag /.+/ { pre $seq=$SeqNew:$entryName 
                             $SeqApp:[$seq s:$Ct]
                             $SeqMake:$seq $Wrt:[s:$entryName]
                           } ~

  # table display
  t_sequence:  ~ {$Out $In:[fields c:sequence]} tag 
                 ln {$Wrt:[s:"<textarea rows=1 cols=35>$Ct</textarea>"]} ~

  # HTML display
  th_enzyme:   ~ {$In:[enzyme t:hl]} /.*/ 
                 {$Rep:{$parStr:enzymeR $Ct $Ct}} ~
                
  # other
  wrtField:    ~ tag ln {$Wrt} ~
  appLn:       ~ /[^\n]*\n/ {$App} ~
  ln:          ~ /[^\n]*\n/ ~
  tag:         ~ /[^:]+:/? ~
  int:         ~ /[0-9]+/ ~
  real:        ~ /[0-9.]+/ ~
  str:         ~ /[0-9a-zA-Z_]+/ ~
  word:        ~ /[0-9a-zA-Z_]+/ ~
  sep:         ~ /[^0-9a-zA-Z_]+/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
	fileName:'/data/pdbfinder/pdbfinder.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:chainId print:1] 
    $JobTokens:[$job name:chain print:1] 
#    $JobTokens:[$job name:numInx print:1] 
#    $JobTokens:[$job name:wordInx print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}

/ ~
  real:        ~ /[0-9.]+/ ~
  str:         ~ /[0-9a-zA-Z_]+/ ~
  word:        ~ /[0-9a-zA-Z_]+/ ~
  sep:         ~ /[^0-9a-zA-Z_]+/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
	fileName:'/data/pdbfinder/pdbfinder.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:chainId print:1] 
    $JobTokens:[$job name:chain print:1] 
#    $JobTokens:[$job name:numInx psrs/icarus/db/pdbfinder.it
#    
#    $RCSfile: pdbfinder.it,v $
#    $Revision: 1.4 $
#    $Date: 1996/10/10 16:47:08 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |The PDBFINDER database is constructed using a PERL
    |script from the PDB, DSSP and HSSP databases. Many of the fields
    |contained in the PDBFINDER database are difficult to access from the
    |original databases. Some Information is retrieved from the original
    |literature.
  more:
    |<H4>
    |<A HREF="http://www.sander.embl-heidelberg.de/pdbfinder/overview.html">
    |More on PDBFINDER</A>
    |</H4>
  citation:''
  ftpSite:''
  fields:{
    ID:
      |The <EM>ID</EM> field contains the 4-letter <EM>PDB</EM> code of the
      |entry. It is always present.
    Header:
      |The <EM>Header</EM> field contains the information from the
      |<EM>HEADER</EM> records in the <EM>PDB</EM> file. It is always
      |present.
    Date:
      |from the <EM>HEADER</EM> records in the <EM>PDB</EM> file. 
      |It contains the
      |date in the form "YYYY-MM-DD". It is always present.
    Compound:
      |The <EM>Compound</EM> field contains the information from the
      |<EM>COMPND</EM> records in the <EM>PDB</EM> file.
    EnzymeCode:
      |The <EM>Enzyme-Code</EM> fields contain <EM>E.C.</EM> numbers
      |extracted from the <EM>COMPND</EM> records in the <EM>PDB</EM>
      |file. Wildcards for the last numbers may be present as "-" characters.
    Source:
      |The <EM>Source</EM> field contains the information from the
      |<EM>SOURCE</EM> records in the <EM>PDB</EM> file.
    ExprSys:
      |The <EM>Expr-Sys</EM> field contains the expression system
      |extracted from the <EM>SOURCE</EM> records in the <EM>PDB</EM>
      |file.
    Author:
      |Each of the <EM>Author</EM> fields contains an author name from the
      |<EM>PDB</EM> record <EM>AUTHOR</EM>.
    ExpMethod:
      |The <EM>Exp-Method</EM> field can contain one of the following:
      |<DL>
      |<DT> X
      |<DD> X-ray structure
      |<DT> NMR
      |<DD> NMR structure
      |<DT> FIBER
      |<DD> Fiber diffraction study
      |<DT> MODEL
      |<DD> A model without explicit experimental data
      |<DT> NEUTRON
      |<DD> Neutron diffraction study
      |<DT> OTHER
      |<DD> Currently Fluorescence Transfer and Electron Diffraction are
      |	    uncategorized.
      |</DL>
      |
      |The <EM>Exp-Method</EM> is derived from the <EM>EXPDTA</EM> field in
      |the <EM>PDB</EM> if present, otherwise it is derived from other sources.
      |
    Resolution:
      |The <EM>Resolution</EM> is derived from <EM>REMARK 2</EM> in the 
      |<EM>PDB</EM> file. For NMR structures and models no resolution is given.
      |
    RFactor:
      |The <EM>R-Factor</EM> for X-ray structures is derived from <EM>REMARK
      |3</EM> and <EM>REMARK 4</EM> if possible. For X-ray structures lacking
      |a valid R-factor in the <EM>PDB</EM> file, the <EM>R-factor</EM> field
      |is based on the original literature. A number of corrections to values
      |found in the <EM>PDB</EM> have also been applied. In some cases no
      |R-factor could be found, or the original literature does contain an
      |R-factor but the published coordinates are C-alpha only. In those
      |cases no <EM>R-Factor</EM> field is present. Also no R-factor is given
      |for NMR structures, because the calculation methods are too diverse.
      |
    FreeR:
      |The <EM>Free-R</EM> for X-ray structures is derived from <EM>REMARK
      |3</EM>. It is only given for some modern PDB files.
    NModels:
      |The <EM>N-Models</EM> field gives the number of models preceded by
      |<EM>MODEL</EM> cards in the <EM>PDB</EM> file, if any.
    RefProg:
      |The <EM>Ref-Prog</EM> field contains any recognized names of
      |refinement programs, separated by slashes.  Currently the following
      |program names are recognized:
      |
      |'AMBER',
      |'AMORE',
      |'ARP',
      |'ATOM',
      |'CALIBA',
      |'CEDAR',
      |'CHARMM',
      |'CORELS',
      |'CORMA',
      |'CRLS',
      |'CRYLSQ',
      |'DERIV',
      |'DGII',
      |'DIAMOND',
      |'DIANA',
      |'DINOSAUR',
      |'DISCOVER',
      |'DISGEO',
      |'DISMAN',
      |'DSPACE',
      |'ECEPP',
      |'EMBOSS',
      |'EREF',
      |'FANTOM',
      |'FREF',
      |'FRODO',
      |'GENERATE',
      |'GPRLSA',
      |'GRINCH',
      |'GROMOS',
      |'GROMOS-MDX',
      |'HABAS',
      |'HAFFIX',
      |'HKSCAT',
      |'INSIGHTII',
      |'IRMA',
      |'JACK-LEVITT',
      |'LOOP',
      |'MANOSK',
      |'MARDIGRAS',
      |'MIDGE',
      |'MM',
      |'MODELFIT',
      |'MUMOD',
      |'NCS',
      |'NOEMOL',
      |'NUCLIN',
      |'NUCLSQ',
      |'OMIT',
      |'OPAL',
      |'PIKSOL',
      |'PRESTO',
      |'PROFFT',
      |'PROLSQ',
      |'PROTEIN',
      |'PROTIN',
      |'PSFRODO',
      |'QUANTA',
      |'RESLSQ',
      |'RESTRAIN',
      |'ROTLSQ',
      |'RSREF',
      |'SCATT',
      |'SFALL',
      |'SFRK',
      |'SHELX',
      |'SHELXL',
      |'STEREOSEARCH',
      |'TNT',
      |'TOM',
      |'ULTIMA',
      |'VEMBED',
      |'X-PLOR',
      |'XEASY',
      |'YASAP'.
      |
    NoHSSPAlign:
      |The <EM>HSSP-N-Align</EM> field gives the number of
      |<STRONG>different</STRONG> aligned sequences in the <EM>HSSP</EM>
      |database, if a <EM>HSSP</EM> file for the structure exists (Normally:
      |if the structure is a protein structure).
    TotFracHelix:
      |The <EM>T-Frac-Helix</EM> field gives the fraction of the assigned
      |secondary structure that is helical: it is the total of the
      |<EM>Helix</EM> fields for all chains divided by the total of all
      |<EM>Sec-Struc</EM> fields. This field is only present if there is a
      |secondary structure.
    TotFracBeta:
      |The <EM>T-Frac-Beta</EM> field gives the fraction of the assigned
      |secondary structure that is Beta: it is the total of the <EM>Beta</EM>
      |fields for all chains divided by the total of all <EM>Sec-Struc</EM>
      |fields. This field is only present if there is a secondary structure.
    TotNresProt:
      |The <EM>T-Nres-Prot</EM> field gives the total number of amino acid 
      |residues in the structure, if any. Non-standard amino-acids are 
      |included.
    TotNonStd:
      |The <EM>T-non-Std</EM> field gives the total number of non-standard
      |amino acid residues in the structure, if any.
    TotNresNucl:
      |The <EM>T-Nres-Nucl</EM> field gives the total number of nucleic acid
      |residues in the structure, if any.
    TotWaterMols:
      |The <EM>T-Water-Mols</EM> field gives the total number of water 
      |molecules in the structure, if any.
    NoHetGroups:
      |The <EM>HET-Groups</EM> field gives the number of <EM>HET</EM> cards
      |in the <EM>PDB</EM> file, if any. The following items are repeated for
      |every HET-group, and are all derived from the <EM>PDB HET</EM> cards.
    HetId:
      |<EM>Het-Id</EM> gives the residue ID for each HET group.
    NAtom:
      |<EM>Natom</EM> gives the number of atoms in each HET group.
    Name:
      |<EM>Name</EM> gives the full name for each HET group.
    ChainName:
      |The <EM>Chain</EM> field and the subfields below are repeated once for 
      |each polymer chain (DNA, RNA, Protein) in the structure. 
      |The <EM>Chain</EM>
      |field contains the chain-identifier for the chain, if any. If there is 
      |no chain identifier, the <EM>Chain</EM> field contains "_".
    SecStruc:
      |The <EM>Sec-Struc</EM> field contains the number of residues in the
      |chain of which a secondary structure could be derived by the
      |<EM>DSSP</EM> program.
    Helix:
      |The <EM>Helix</EM> field contains the number of residues in the chain
      |for which the secondary structure is helical (either alpha helical,
      |pi-helical or 3/10 helical). 'i,i+3':
      |The <EM>i,i+3</EM> field contains the number of residues in the chain
      |for which the assigned secondary structure is "3/10 helix".
      |
      |<A NAME="i,i+5"><H4>Chain, Sec-Struc, Helix, i,i+5</H4></A>
      |
      |The <EM>i,i+5</EM> field contains the number of residues in the chain
      |for which the assigned secondary structure is "pi helix".
      |
      |<A NAME="Beta"><H3>Chain, Sec-Struc, Beta</H3></A>
      |
      |The <EM>Beta</EM> field contains the number of residues in the chain
      |for which the secondary structure is "beta".
      |
      |<A NAME="B-Bridge"><H4>Chain, Sec-Struc, Beta, B-Bridge</H4></A>
      |
      |The <EM>B-Bridge</EM> field contains the number of residues in the chain
      |for which the assigned secondary structure is "beta bridge"
      |
      |<A NAME="E-Beta"><H4>Chain, Sec-Struc, Beta, E-Beta</H4></A>
      |
      |The <EM>E-Beta</EM> field contains the number of residues in the chain
      |for which the assigned secondary structure is "extended beta"
      |
    ParaHb:
      |The <EM>Para-Hb</EM> field contains the number of "parallel strand"
      |hydrogen bonds found in the chain.
    AntiHb:
      |The <EM>Anti-Hb</EM> field contains the number of "antiparallel
      |strand" hydrogen bonds found in the chain.
    AminoAcids:
      |The <EM>Amino-Acids</EM> field contains the number of amino-acid
      |residues in the chain, including non-standard amino acids. Only 
      |present if non-zero.
    NonStd:
      |The <EM>non-Std</EM> field contains the number of non-standard amino
      |acids in the chain, if any.
      |
    MissBB:
      |The <EM>Miss-BB</EM> field contains the number of amino acids in the
      |chain for which part of the backbone coordinates are missing from the
      |<EM>PDB</EM> file.
    MissSC:
      |The <EM>Miss-SC</EM> field contains the number of amino acids in the
      |chain for which at least part of the side-chain coordinates are
      |missing from the <EM>PDB</EM> file.
    OnlyCa:
      |The <EM>only-Ca</EM> field contains the number of amino acids in the 
      |chain
      |for which only the alpha-carbon coordinates are given.
    Unk:
      |The <EM>UNK</EM> field contains the number of amino acids in the chain
      |for which the amino acid type is unknown.
    Cyss:
      |The <EM>CYSS</EM> field contains the number of Cysteine
      |residues in the chain that are involved in Cysteine bridges.
    Break:
      |The <EM>Break</EM> field contains the number of chain
      |breaks in the chain. A chain break is counted whenever two
      |successive C-alpha atoms have a distance larger than 4.5 Angstrom.
    NuclAcids:
      |The <EM>Nucl-Acids</EM> field contains the number of nucleic acid 
      |residues in the chain.
    Substrate:
      |The <EM>Substrate</EM> field contains the number of substrate atoms in 
      |the chain.
    NwaterMols:
      |The <EM>Water-Mols</EM> field contains the number of water molecules in 
      |the chain.
    Sequence:
      |The <EM>Sequence</EM> field contains the nucleic acid or protein 
      |sequence derived from the <EM>PDB</EM> file.
      |</BODY>
      |</HTML>
  }
}
Acids:
      |The <EM>Nsrs/icarus/db/pir.i
#
#    $RCSfile: pir.i,v $
#    $Revision: 1.4 $
#    $Date: 1997/03/17 23:21:06 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

PIR_DB:$library:[PIR group:@SEQUENCE_LIBS 
  subentries:@PirFeatures_DB
  format:@PIR_FORMAT maxNameLen:20 files:{
    $file:pir1
    $file:pir2
    $file:pir3
    $file:pir4
  }
]

PIR_FORMAT:$libformat:[fileType:{@PIRREF_FILE @PIRSEQ_FILE}
  contains:@PROTSEQ_DATA syntax:@PIR_SYNTAX tableFormat:left fields:{
    $field:@DF_ALL
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:[@DF_Accession code:acc index:str indexToken:acc]
    $field:[@DF_Description code:des index:str indexToken:des
      tableToken:'clFields|des']
    $field:[@DF_Keywords code:key index:str indexToken:key]
    $field:[@DF_SuperFamily code:sfam index:str indexToken:sfam]
    $field:[@DF_MoleculeType code:moltyp index:str indexToken:moltyp]
    $field:[@DF_Date code:date index:int indexToken:date
      tableToken:t_date]
    $field:[@DF_Organism code:spec index:str indexToken:spec]
    $field:[@DF_Authors code:aut index:str indexToken:aut]
    $field:[@DF_Title code:ttl index:str indexToken:ttl 
      tableToken:'clFields|ttl']
#    $field:[@DF_SeqLength token:sequence index:int indexToken:seqlen]
    $field:[@DF_FtKey index:str indexToken:ftKey code:ft indexId:@SUBENTRY_ID]
    $field:[@DF_FtDescription index:str indexToken:ftDes code:ft 
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtLength index:int indexToken:ftLen code:ft 
      indexId:@SUBENTRY_ID]
    $field:[@DF_ProtSequence token:sequence format:pir]
  }
]

PIR_SYNTAX:$syntax:[file:"SRSDB:pir.is" ignore:" \t"]
DF_SuperFamily:$srsfield:[SuperFamily short:sfa group:@DF_ALL]
DF_MoleculeType:$srsfield:[MoleculeType short:mot group:@DF_ALL]


PirFeatures_DB:$library:[PIR_features 
  format:@PirFeature_Format
]

PirFeature_Format:$libformat:[syntax:@PIR_SYNTAX
    contains:@PROTSEQ_DATA tableFormat:left fields:{
    $field:[@DF_ID token:ftId]
    $field:[@DF_FtKey token:ft tableToken:'t_ft|key']
    $field:[@DF_FtLength token:ft tableToken:'t_ft|len']
    $field:[@DF_FtDescription token:ft tableToken:'t_ft|des']
    $field:[@DF_FtLocation token:ft tableToken:'t_ft|loc' 
      tableFormat:listing]
  }
]
ld:[MoleculeType short:mot group:@DF_ALL]


PirFeatures_DB:$library:[PIR_features 
  format:@PirFeature_Format
]

PirFeature_Format:$libformat:[syntax:@PIR_SYNTAX
    contains:@PROTSEQ_DATA tableFormat:left fields:{
    srs/icarus/db/pir.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: pir.is,v $
#    $Revision: 1.4 $
#    $Date: 1997/03/17 23:21:06 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  'C;Species:':             spec 
  'C;Date:':                date
  'C;Accession:':           acc
  'A;Status:':              status
  'A;Description:':         des
  'A;Title:':               ttl
  'A;Reference number:':    refn
  'A;Contents:':            cont
  'A;Authors:':             aut
  'A;Variety:':             var
  'A;Accession:':           acc
  'A;Molecule type:':       moltyp
  'A;Residues:':            res
  'A;Mobile element:':      mobel
  'A;Cross-references:':    link
  'A;Introns:':             intron
  'A;Note:':                note
  'A;Gene:':                gene
  'A;Genome:':              genome
  'A;Pathway:':             pathway
  'A;Genetic code:':        genecode
  'A;Experimental source:': exp
  'A;Start codon:':         start
  'A;Map position:':        map
  'A;Genetics:':            genet
  'R;':                     aut
  'C;Genetics:':            genet
  'C;Superfamily:':         sfam
  'C;Keywords:':            key
  'C;Comment:':             comment
  'C;Complex:':             complex
  'C;Function:':            fun
  'F;':                     ft
  'N;Alternate names:':     alt
  'N;Contains:':            cont
}

$rules={
  entry:     ~ {$In:[file:text] $Out pre $Skip:0}
               ('>' {$not} ln)*
               (/>[^;]+;([A-Z0-9]+)/ {$entryFip=$Fip $Wrt $entryName=$1} 
                ln{$App}
               ('>' {$Not} ln {$App})+ )? ~

  sequence:  ~ {$In:[file:seq] $Out $SeqMake:$s} 
               ('>' {$Not} ln)* />[^;]+;([^ \n]+)/ 
               {$s=$SeqNew:$1 $Wrt:[s:$1]} ln {pre $seqFip=$Fip} ln 
               ('>' {$Not} ln {$SeqApp:[$s s:$Ct]})* ~

  # extracting data fields
  fields:    ~ {$In:entry $Out $Skip:1}
               ln {$Wrt:id} ln {$Wrt:des}
               (/[ACRFN];([a-zA-Z -]+:)?/ {$Wrt:$fn.$Ct
                 if:$fn.$Ct=="" $dp:"+++ unknown: $Ct in $entryName +++"}
                ln {$App} | ln {$App})+ ~

  # for indexing
  tag:       ~ /[ACRFN];([a-zA-Z -]+:)?/ ~ 
  id:        ~ {$In:entry $Out} />[^;]+;([A-Z0-9]+)/ {$Wrt:[s:$1]} ~
  aut:       ~ {$In:[fields c:aut] $Out} 
               'R;' (author {$Uniq:[s:$author]} ';'?)+ ~
  author:    ~ /([^,\n]+,) *([^;\n]+)/ {$author="$1$2"} ~
  acc:       ~ {$In:[fields c:acc] $Out} tag (/[A-Z0-9]+/ {$Uniq} ';'?)* ~
  sfam:      ~ {$In:[fields c:sfam] $Out} 
               tag (/[^\n;]+/ {$Wrt:[s:$Trim:$Ct]} ';'?)* ~
  moltyp:    ~ {$In:[fields c:moltyp] $Out} 
               tag (/[^\n;]+/ {$Uniq:[s:$Trim:$Ct]} ';'?)* ~
  key:       ~ {$In:[fields c:key] $Out} 
               tag (/[^\n;]+/ {$Wrt:[s:$Trim:$Ct]} ';'?)* ~
  ttl:       ~ {$In:[fields c:ttl] $Out} tag (/[a-zA-Z0-9]+/ {$Uniq} | /./)* ~
  des:       ~ {$In:[fields c:des] $Out} tag? (/[a-zA-Z0-9]+/ {$Uniq} | /./)* ~
  date:      ~ {$In:[fields c:date] $Out init $month={Jan:1 Feb:2 Mar:3 Apr:4
               May:5 Jun:6 Jul:7 Aug:8 Sep:9 Oct:10 Nov:11 Dec:12}} 
               tag /([0-9]+)-([a-zA-Z]+)-([0-9]+)/? 
               {$Wrt:[s:($month.$2*100 + $1 + $3*10000)]} ~
  spec:      ~ {$In:[fields c:spec] $Out} 
               tag /[^(]+/ {$Wrt:[s:$Trim:$Ct]} ('('/[^)]+/ {$Wrt} ')')? ~

  # indexing features
  ft:        ~ {$In:[fields c:ft] $Out}
               'F;'{$r={}} (/[^,\/]+/ {$r+=$Ct} ','?)+ 
               ln {foreach:[$e in:$r] {$Wrt:[ft s:"F;$e$Ct"]}} ~
  ftKey:     ~ {$In:[ft count:ft var:$ftN] $Out}
               /[^\/]+\/([^:]+):/ {$Wrt:[n:$ftN s:$1]} ~
  ftDes:     ~ {$In:[ft count:ft var:$ftN] $Out}
               /[^:]+:/ (/[A-Za-z0-9_]+/ {$Uniq:[n:$ftN]} | /./)* ~
  ftLen:     ~ {$In:[ft c:ft count:ft var:$ftN] $Out}
               'F;' /([0-9]+)(-([0-9]+))?/ 
               {if:$3=="" $Wrt:[n:$ftN s:1] else $Wrt:[n:$ftN s:($3-$1+1)]} ~

  # display features
  ftId:      ~ {$In:[fields c:id] $Out}
               /(>[^;]+;)([A-Z0-9]+)/
               {$Wrt:[s:"$1$2\_$subEntryN;  parent: $2"]} ~
  ftLine:    ~ {$In:[ft c:ft count:ft var:$ftN select:$subEntryN] $Out}
               /.*/ {$Wrt} ~
  t_ft:      ~ {$In:ftLine $Out $Skip:1}
               'F;' /([^\/]+)/ {$Wrt:[range s:$1]}
               /\/([^:]+):/ {$Wrt:[n:$ftN s:$1]} /.*/ {$Wrt:des} ~
  h_ftId:    ~ {$In:[ftId t:html]} /.*parent: */ 
               /[A-Z0-9_]+/ {$Rep:{$ParStr:pirR $Ct $Ct}} ~

  # table display
  clFields:  ~ {$In:[fields c:{ttl des}] $Out}
               tag? ln {$Wrt:$Itc} ~
  t_date:    ~ {$In:[fields c:date] $Out} tag /[0-9a-zA-Z-]+/? {$Wrt} ~

  # printing in HTML format
  h_ref:     ~ {$In:[fields c:refn t:html]} 
               /.*MUID:/ num {$Rep:{$ParStr:medlineR $Ct $Ct}} ~
  h_des:     ~ {$In:[fields c:des t:html]} 
               /.*\\(EC/ /[0-9.-]+/ {$Rep:{$ParStr:enzymeR $Ct $Ct}} ~
  h_link:    ~ {$In:[fields c:link t:html] init $l={GB:genbankR EMBL:emblR
               NCBIN:genbankR GDB:gdbR}} /.*nces:/ /[A-Za-z]+/ {$db=$Ct}':'
               /[^ \n]+/ {$Rep:{$ParStr:$l.$db $Ct $Ct}} ~

  # other stuff
  num:       ~ /[0-9]+/ ~
  ln:        ~ /[^\n]*\n/ ~
}

# debugging 
$subEntryN=3
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/data/pir/pir1.ref']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields  print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}

  ~ {$In:[fields c:link t:html] init $l={GB:genbankR EMBL:emblR
               NCBIN:genbankR GDB:gdbR}} /.*nces:/ /[A-Za-z]+/ {$db=$Ct}':'
               srs/icarus/db/pmd.is

#
# pmd.is
#
# Ramu C
#

$rules={
  entry:   ~ {init{$count=0} $out:entry $count=$count+1}
             ('ENTRY' {$not} ln)*
             ('ENTRY          ' {pre {$entryFip = $fip} $wrt} ln {$app} 
             ('///' {$not} ln {$app})*
              '///' {$app $fip:on})*              
           ~
  # fields
  fields:  ~ {$in:entry $out} f_entry f_authors f_journal f_title f_crosref
             f_protein f_source f_nterm f_expsys(f_change | f_function | 
             f_structure | f_stability | f_expr | f_trans | f_mut | f_var |
             f_cmnt)
           ~

  f_ac:    ~ {$wrt:ac}   'AC  ' ln ~
  f_dt:    ~ {$wrt:dt}  ('DT  ' ln)* ~
  f_so:    ~ {$wrt:so}  ('SO  ' ln)* ~
  f_os:    ~ {$wrt:os}  ('OS  ' ln)* ~
  f_cd:    ~ {$wrt:cd}  ('CD  ' ln)* ~
  f_xx:    ~ ('XX'  ln)? ~

  # indexing

  ac:   ~ {$in:[fields c:ac] $out:ac} 'AC' /[0-9A-Za-z]+/ {$wrt} ~
  dt:   ~ {$in:[fields c:dt] $out:dt} 'DT' 
          /([0-9]+).([0-9]+).([0-9]+)/ {$wrt:[s:($1+$2*100+"19$3"*10000)]} ~
  so:   ~ {$in:[fields c:so] $out:so} 'SO' (sep | word {$wrt})* ~
  os:   ~ {$in:[fields c:os] $out:os} 'OS' (sep | word {$wrt})* ~
  oc:   ~ {$in:[fields c:cd] $out:cd} 'CD' (sep | word {$wrt})* ~

# extra ...
  ln:      ~ /[^\n]*\n/ ~
  word:    ~ /[a-zA-Z0-9_]+/ ~
  sep:     ~ /[^a-zA-Z0-9_]+/ ~
}

#$fil =  $fileOpen:"/data/pmd/pmd.dat"
#$job = $jobNew:[prod:$rules skip:" "]
#$jobNext:[$job file:$fil]
#for:{1 $jobTokens:[$job name:dt print:1 ] 1} {
#  $jobEnd:$job
#  $jobNext:[$job file:$fil]
#}
#$jobEnd:$job




{$in:[fields c:so] $out:so} 'SO' (sep | word {$wrt})* ~
  os:   ~ {$in:[fields c:os] $out:os} 'OS' (sep | word {$wrt})* ~
  oc:   ~ {$in:[fields c:cd] $out:cd} 'CD' (sep | word {$wrt})* ~

# extra ...
  ln:      ~ /[^\n]*\n/ ~
  word:    ~ /[a-zA-Z0-9_]+/ ~
  sep:     ~ /[^a-zA-Z0-9_]+/ ~
}

#$fil =  $fileOpen:"/data/pmd/pmd.dat"
#$job = $jobNew:[prod:$rules skip:" "]
#$jobNext:[$job file:$fil]
#for:{1 $jobTokens:[$job name:dt print:1 ] 1} {
#  $jobEnd:$job
#  $jobNext:[$job file:$fil]
#}
#$jobEnd:$job



srs/icarus/db/primers.i
#    The PCR Primers Database - 19 Jan 1996.                             #
#    Last modified - 14 Feb 1996.                                        #
#    Author: Benny Shomer  (bshomer@ebi.ac.uk)                           #
#                                                                        #
#    Many thanks to Jack Leunissen from CAOS/CAMM Center in the          #
#    Netherlands for introducing independently a first working version   #
#    and for introducing many important corrections into this file.      #
#                                                                        #
#    Conversion to Icarus language by Thure Etzold                       #
#                                                                        #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#


PRIMERS_DB:$library:[PRIMERS group:@MISC_LIBS
  format:@PRIMERS_FORMAT ifiles:{"primers.i" "primers.is"}
  files:{
    $file:primers
  }
]

PRIMERS_FORMAT:$libformat:[syntax:@PRIMERS_SYNTAX fileType:@PRIMERS_FILE 
  fields:{  
    $field:[@DF_ID code:id indexToken:id index:str]
    $field:[@DF_Date code:date indexToken:date index:int]
    $field:[@DF_TARGET code:target index:str indexToken:target]
    $field:[@DF_NUMREF code:numref index:str indexToken:numref]
    $field:[@DF_Organism code:ospecs index:str indexToken:ospecs]
    $field:[@DF_SPAPLL code:spapll index:str indexToken:spapll]
    $field:[@DF_PNAME code:pname index:str indexToken:pname]    
    $field:[@DF_PSEQN code:pseqn index:str indexToken:pseqn]
    $field:[@DF_RESTR code:restr index:str indexToken:restr]
    $field:[@DF_MUTAT code:mutat index:str indexToken:mutat]
    $field:[@DF_POLYMR code:polymr index:str indexToken:polymr]
    $field:[@DF_ADITIV code:aditiv index:str indexToken:aditiv]
    $field:[@DF_SOURCE code:source index:str indexToken:source]
    $field:[@DF_LINK code:{dbxref refxrf}]
    $field:[@DF_CONTRIBUTOR code:contrib index:str indexToken:contrib]
    $field:[@DF_Authors code:refaut index:str indexToken:refaut]
    $field:[@DF_REFTTL code:refttl index:str indexToken:refttl]
    $field:[@DF_REF code:refsrc index:str indexToken:refsrc]
    $field:[@DF_COMMENT code:comment index:str indexToken:comment]
    $field:[@DF_LINK code:link index:str indexToken:links]
  }
]


#data field types
DF_ATARGET:$srsfield:[Target short:TRG group:@DF_ALL]
DF_NUMREF:$srsfield:[Number_ref short:NRF group:@DF_ALL]
DF_SPAPLL:$srsfield:[Application short:APP group:@DF_ALL]
DF_PNAME:$srsfield:[Primer_Name short:PNM group:@DF_ALL]
DF_PSEQN:$srsfield:[Primer_Sequence short:PSQ group:@DF_ALL]
DF_RESTR:$srsfield:[Restrict_Site short:RST group:@DF_ALL]
DF_MUTAT:$srsfield:[Mutation short:MUT group:@DF_ALL]
DF_POLYMR:$srsfield:[Polymerase short:POL group:@DF_ALL]
DF_ADITIV:$srsfield:[Additive short:ADD group:@DF_ALL]
DF_PSOURCE:$srsfield:[DNA_Source short:SRC group:@DF_ALL]
DF_CONTRIBUTOR:$srsfield:[Contributor short:CNT group:@DF_ALL]
DF_TARGET:$srsfield:[TargetSequence short:tsq group:@DF_ALL]
DF_REFTTL:$srsfield:[ReferenceTitle short:rtl group:@DF_ALL]
DF_SOURCE:$srsfield:[Source short:src group:@DF_ALL]


#links to other databanks
$link:[@PRIMERS_DB to:@?EMBL_DB token:'link:embl' toField:@DF_ID]
$link:[@PRIMERS_DB to:@?EMNEW_DB token:'link:emnew' toField:@DF_ID]
$link:[@PRIMERS_DB to:@?SWISSPROT_DB token:'link:swissprot' toField:@DF_ID]
$link:[@PRIMERS_DB to:@?SWISSNEW_DB token:'link:swissnew' toField:@DF_ID]
$link:[@PRIMERS_DB to:@?MEDLINE_DB token:'link:medline' toField:@DF_ID]
$link:[@PRIMERS_DB to:@?IMGT_DB token:'link:imgt' toField:@DF_ACCNO]
$link:[@PRIMERS_DB to:@?TFSITE_DB token:'link:tfsite' toField:@DF_ID]
$link:[@PRIMERS_DB to:@?PIR_DB token:'link:pir' toField:@DF_ID]


PRIMERS_SYNTAX:$syntax:[file:"SRSDB:primers.is" ignore:" "]
PRIMERS_FILE:$filetype:[typeName:dat maxline:200]

ISSPROT_DB token:'link:swissprot' toField:@DF_ID]
$link:[@PRIMERS_DB to:@?SWISSNEW_DB token:'link:swissnew' toField:@DF_ID]
$link:[@PRIMERS_DB to:@?MEDLINE_DB token:'link:medline' toField:@DF_ID]srs/icarus/db/primers.is
$rules={
  # the entry

  # the data fields
  fields:      ~ id s date s target s (numref)? ospecs s spapll 
                 lncdna s lngnda 
                 (pname s pseqn s (restr s)? (mutat s)? flank s restr)*
                 tcycle s probin s hotstr s idenat s denatr s anneal s tchdwn
                 extend s prgrss s finext s cycles s rxnvol s polymr s buffer
                 dntpcn s primcn s mgconc s aditiv s source s dbxref s cntnam
                 contrib s refaut s refttl refxrf s remark
               ~

  id:          ~ {$wrt:id}     'ACCESS' ln ~   
  s:           ~ {$wrt:s}      ('XXXXXX' ln)* ~ # line spacer
  date:        ~ {$wrt:}       'DATEIN' ln ~   
  target:      ~ {$wrt:target} 'TARGET' ln ~    
  numref:      ~ {$wrt:numref} 'NUMREF' ln ~    
  ospecs:      ~ {$wrt:ospecs} 'OSPECS' ln ~    
  spapll:      ~ {$wrt:spapll} 'SPAPPL' ln ~	      
  lncdna:      ~ {$wrt:lncdna} 'LNCDNA' ln ~
  lngdna:      ~ {$wrt:lngdna} 'LNGNDA' ln ~
  pname:       ~ {$wrt:pname}  /FPNAME|RPNAME/ ln ~   
  pseqn:       ~ {$wrt:pseqn}  /FPSEQN|RPSEQN/ ln ~   
  flank:       ~ {$wrt:flank}  /FFLANK|RFLANK/ ln ~
  restr:       ~ {$wrt:restr}  /FRESTR|RRESTR/ ln ~
  mutat:       ~ {$wrt:mutat}  /FMUTAT|RMUTAT/ ln ~
  tcycle:      ~ {$wrt:tcycle} 'TCYCLE' ln ~
  probin:      ~ {$wrt:probin} 'PROBIN' ln ~
  hotstr:      ~ {$wrt:hotstr} 'HOTSTR' ln ~
  idenat:      ~ {$wrt:idenat} 'IDENAT' ln ~
  denatr:      ~ {$wrt:denatr} 'DENATR' ln ~
  anneal:      ~ {$wrt:anneal} 'ANNEAL' ln ~
  tchdwn:      ~ {$wrt:tchdwn} 'TCHDWN' ln ~
  extend:      ~ {$wrt:extend} 'EXTEND' ln ~
  prgrss:      ~ {$wrt:prgrss} 'PRGRSS' ln ~
  finext:      ~ {$wrt:finext} 'FINEXT' ln ~
  cycles:      ~ {$wrt:cycles} 'CYCLES' ln ~
  rxnvol:      ~ {$wrt:rxnvol} 'RXNVOL' ln ~
  polymr:      ~ {$wrt:polymr} 'POLYMR' ln ~    
  aditiv:      ~ {$wrt:aditiv} 'ADITIV' ln ~    
  source:      ~ {$wrt:source} 'SOURCE' ln ~    
  contrib:     ~ {$wrt:contrib}/CNTNAM|CNTINS|CNTADR|CNTEML|CNTTEL|CNTFAX/ ln ~
  refaut:      ~ {$wrt:refaut} ('REFAUT' ln)+ ~    
  refttl:      ~ {$wrt:refttl} 'REFTTL' ln ~    
  refsrc:      ~ {$wrt:refsrc} 'REFSRC' ln ~    
  remark:      ~ {$wrt:remark}  ('REMARK' ln)+ ~	

  # indexing
  i_id:        ~ {$in:[fields c:id] $out:id} tag name {$wrt} ~
  i_target:    ~ {$in:[fields c:target] $out:id} (tag (word {$wrt} sep)* ln)* ~
  i_remark:    ~ {$in:[fields c:remark] $out:id} (tag (word {$wrt} sep)* ln)* ~
  i_link:      ~ (tag refdb ':' (name {$wrt:$c} ';')* ln)* ~

  # display HTML 
  h_link:      ~ {$in:[fields c:dbxref] $out:link}
                 (tag refdb ':' (name {$rep:$parStr:{"$db_hl" $ct $ct}} 
                 ';')* ln)* ~

  # other stuff
  refdb:       ~ 'EMBL/GENBANK/DDBJ' {$db=embl $c=$embl} | 
                 'MEDLINE' {$db=medline $c=$medline} |
                 'IMGT/LIGM' {$db=imgt $c=$imgt} |
                 'SWISS-PROT' {$db=swissprot $c=$swissprot} |
                 'TRANSFAC' {$db=transfac $c=$transfac} |
                 'PIR' {$db=pir $c=pir} 
               ~
  ln:          ~ /[^\n]\n/ ~
  word:        ~ /[a-zA-Z0-9_]+/ ~
  sep:         ~ /[^a-zA-Z0-9_]+/ ~
  name:        ~ /[a-zA-Z][a-zA-Z0-9_]*/ ~
  tag:         ~ /....../ ~
}
db:       ~ 'EMBL/GENBANK/DDBJ' {$db=embl $c=$embl} | 
                 'MEDLINE' {$db=medline $c=$medline} |
                 'IMGT/LIGM' {$db=imgt $c=$imgt} |
                 'SWISS-PROT' {$db=swissprot $c=$swissprot} |
                 'TRANSFAC' {$db=transfac $c=$transfac} |
                 'PIR' {$db=pir $c=pir} 
               ~
  ln:          ~srs/icarus/db/prints.i
# Description: icarus/srs structure description for PRINTS
# Author:      Martin Hilbers
# Date:        3-9-1996 
# Note:
#


PRINTS_DB:$library:[PRINTS group:@SEQRELATED_LIBS 
  comment:"PRINTS PROTEIN MOTIF FINGERPRINT DATABASE" 
  format:@PRINTS_FORMAT maxNameLen:30 ifiles:{"prints.i" "prints.is"}
  files:{
    $file:prints5_0
  }
]

PRINTS_FORMAT:$libformat:[fileType:@DAT_FILE syntax:@PRINTS_SYNTAX 
  fields:{
    $field:[@DF_ALL]
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:[@DF_Accession code:acc index:str indexToken:acc]
    $field:[@DF_Description code:def index:str indexToken:def]
    $field:[@DF_LINK code:link indexToken:link]
    $field:[@DF_Date code:date index:int indexToken:date]
    $field:[@DF_COMMENT code:cc index:str indexToken:cc]
    $field:[@DF_Authors code:refaut index:str indexToken:refaut]
    $field:[@DF_Title code:reftit index:str indexToken:reftit]
    $field:[@DF_Citation code:journal index:str indexToken:journal]
  }
]

PRINTS_SYNTAX:$syntax:[file:"SRSDB:prints.is" ignore:" "]


$link:[@PRINTS_DB to:@?OWL_DB token:'link|owl' toField:@DF_ID]
$link:[@PRINTS_DB to:@?PDB_DB token:'link|pdb' toField:@DF_ID]
$link:[@PRINTS_DB to:@?PROSITE_DB token:'link|prosite' toField:@DF_Accession]
$link:[@PRINTS_DB to:@?BLOCKS_DB token:'link|blocks' toField:@DF_Shortaccession]
#
# PRODOM links in PRINTS 12 are not correct for PRODOM 33
#$link:[@PRINTS_DB to:@?PRODOM_DB token:'link|prodom' toField:@DF_ID]
#
$link:[@PRINTS_DB to:@?SBASE_DB token:'link|sbase' toField:@DF_ID]
$link:[@PRINTS_DB to:@?GCRDB_DB token:'link|gcrdb' toField:@DF_ID]
$link:[@PRINTS_DB to:@?NRL_DB token:'link|nrl' toField:@DF_ID]
$link:[@PRINTS_DB to:@PRINTS_DB token:'link|prints' toName:PRINTS_IN 
toField:@DF_Accession]       


$href:[swissIR      link:"<A HREF=wgetz?-e+[swissprot-id:%s]>%s</A>"]
$href:[owlR         link:"<A HREF=http://www.seqnet.dl.ac.uk/srs/srsc?[owl-id:%s]>%s</A>"]
$href:[printsR      link:"<A HREF=wgetz?-e+[prints-acc:%s]>%s</A>"]
$href:[blocksR      link:"<A HREF=wgetz?-e+[blocks-acc:%s]>%s</A>"]
$href:[prodomR      link:"<A HREF=wgetz?-e+[prodom-id:%s]>%s</A>"]
$href:[sbaseR       link:"<A HREF=wgetz?-e+[sbase-acc:%s]>%s</A>"]
$href:[nrlR         link:"<A HREF=wgetz?-e+[nrl3d-acc:%s]>%s</A>"]
$href:[enzymeR      link:"<A HREF=wgetz?-e+[enzyme-id:%s]>%s</A>"]
$href:[scopR        link:"<A HREF=http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?key=%s>%s</A>"]
$href:[swiss3DR     link:"<A HREF=http://expasy.hcuge.ch/cgi-bin/sw3d-search-ac?%s>%s</A>"]
sR      link:"<A HREF=wgetzsrs/icarus/db/prints.is
#
# File:        prints.is
# Description: icarus syntax file for PRINTS
# Author:      Martin Hilbers
# Date:        3-9-1996
# Note:        (Un)comment things in html-display section to reflect local setup
#

$rules={
  entry:   ~ {$In:[file:text] $Out:entry}
#  entry:   ~ {$Out:entry}
             ('gc; ' {$entryFip=$Fip $Wrt} ln {$App} 
             ('gc; ' {$Not} ln {$App})*)?
           ~
  # fields
  fields:  ~ {$In:entry $Out} f_id f_acc f_gn f_date  f_def* 
             f_links* sp f_ref* sp f_cc* sp
             f_rest*
           ~
  f_id:    ~ {$Wrt:id}   'gc; ' ln ~ 
  f_acc:   ~ {$Wrt:acc}  'gx;' ln ~
  f_gn:    ~ {$Wrt:gn}   'gn;' ln ~
  f_date:  ~ {$Wrt:date} 'ga;' ln ~
  f_def:   ~ {$Wrt:def}  'gt;' ln ~
  f_links: ~ {$Wrt:link} 'gp;' ln ~
  f_ref:   ~ {$Wrt:ref}  'gr;' ln ~
  f_cc:    ~ {$Wrt:cc}   'gd;' ln ~
  f_rest:  ~ {$Wrt:link}  ln ~
  sp:      ~ {$Wrt:sp}   ('bb;' ln)* ~



  # indexing
  id:      ~ {$In:[fields c:id] $Out:id} 'gc;' (/[A-Z0-9]+/ {$Wrt}) ~
  acc:     ~ {$In:[fields c:acc] $Out:acc} 'gx;' /[A-Z0-9_]+/ {$Wrt} ~
  def:     ~ {$In:[fields c:def] $Out:def} 'gt;' ( /[A-Za-z0-9_]+/ {$Wrt}
              | /[^A-Za-z0-9_]+/ )*  ~
  date:    ~ {$In:[fields c:date] $Out:date} 'ga;'
             datenum {$Wrt:[s:$date c:cre]} 
             (';' 'UPDATE' datenum {$Wrt:[s:$date c:dupd]})?  
           ~  
  datenum: ~ {init {$month={JAN:1 FEB:2 MAR:3 APR:4 MAY:5 JUN:6 JUNE:6 JUL:7 
                            AUG:8 SEP:9 OCT:10 NOV:11 DEC:12}}}
             /([0-9]+)-([A-Z]+)-([0-9]+)/ 
             {$date=$1 +$month.$2 * 100 + $3 * 10000} 
           ~ 
  cc:      ~ {$In:[fields c:cc] $Out:cc} 'gd;' ( word {$Wrt}
              | noword )*  ~

  links:   ~ {$In:[fields c:link] $Out:link} 
             (/gp; PRINTS;/  (name {$Wrt:prints} ';'?  name ';'? )* ) |
             (/gp; PROSITE;/ (name {$Wrt:prosite} ';'? name ';'? )* )|
             (/gp; BLOCKS;/  (name {$Wrt:blocks} ';'?)* )|
             (/gp; PRODOM;/  (name {$Wrt:prodom} ';'?)* )|
             (/gp; SBASE;/   (name {$Wrt:sbase}  ';'?)* )|
             (/gp; GCRDB;/   (name {$Wrt:gcrdb}  ';'?)* )|
             (/gp; NRL;/     (name {$Wrt:nrl}    ';'?)* )|
             (/gp; PDB;/     (name {$Wrt:pdb}    ';'?)* )|
             (/gp;/ ln)|
             /tt;/ (name {$Wrt:owl})? ln | ln
           ~
   ref:    ~ {$In:[fields c:ref] $Out} 
             ('gr;' ( (/[ A-Zand0-9\.,\-]+\n/ {$Uniq:raut} ) |
                     (/[ A-Z0-9\.()\-]+\n/   {$Wrt:rjnl} ) | 
                      ln {$Wrt:rtit}))
           ~

   reftit: ~  {$In:[ref c:rtit] $Out}
              ( word {$Uniq:tit} | noword)*
           ~
   refaut: ~ {$In:[ref c:raut] $Out}
             ((/,|and|[0-9]+\./)? (author {$Uniq:aut}) (/,|and/)? )+
           ~
   journal:~ {$In:[ref c:rjnl] $Out}
             (/[^0-9]+/  {$Wrt:jrn}
             (/[0-9]+/ {$Wrt:vol}) ('('/[0-9]+/')')?
             (/[0-9]+/ {$Wrt:pg1}) '-' (/[0-9]+/ {$Wrt:pg2}) 
             '(' (/[0-9]+/ {$Wrt:year}))
           ~

  author:  ~ (/[A-Za-z\-]+/)+ ',' /[A-Z\.\-]+/ ~

  # html display
  hl_links:~ {$In:[fields c:link t:hl]}
     (/gp; PRINTS;/  (name {$Rep:{$ParStr:printsR $Ct $Ct}} ';'?  name ';'? )* ) |
     (/gp; PROSITE;/ (name {$Rep:{$ParStr:prositeR $Ct $Ct}} ';'? name ';'? )* )|
     (/gp; BLOCKS;/  (name {$Rep:{$ParStr:blocksR $Ct $Ct}} ';'?)* )|
#
#  links in PRINTS rel 12 do not point to the correct entries in PRODOM 33 
#     (/gp; PRODOM;/  (name {$Rep:{$ParStr:prodomR $Ct $Ct}} ';'?)* )|
#
#     (/gp; SBASE;/   (name {$Rep:{$ParStr:sbaseR $Ct $Ct}}  ';'?)* )|
#     (/gp; GCRDB;/   (name {$Rep:{$ParStr:gcrdbR $Ct $Ct}}  ';'?)* )|
#     (/gp; NRL;/     (name {$Rep:{$ParStr:nrlR $Ct $Ct}}    ';'?)* )|
#     (/gp; PDB;/     (name {$Rep:{$ParStr:pdbR $Ct $Ct}}    ';'?)* )|
     (/gp; SCOP;/    (name {$Rep:{$ParStr:scopR $Ct $Ct}}   ';'?)* )|
     (/gp; SWISS-3DIMAGE;/ (name {$Rep:{$ParStr:swiss3DR $Ct $Ct}} ';'?)* )|
     (/gp;/ ln) |
     (/tt;/ (name {$Rep:{$ParStr:owlR $Ct $Ct}})? ln) | ln
           ~

  # other 
  name:    ~ /[a-zA-Z0-9_]+/ ~ 
  word:    ~ /[^ ;:.,\(\)]+/ ~
  noword:  ~ /[;:.,\(\)]+/ ~
  ln:      ~ /[^\n]*\n/ ~
}





  (/gp; NRL;/     (name {$Rep:{$ParStr:nrlR $Ct $Ct}}    ';'?)* )|
#     (/gp; PDB;/     (name {$Rep:{$ParStr:pdbR $Ct $Ct}}    ';'?)* )|
     (/gp; SCOP;/    (name {$Rep:{$ParStr:scopR $Ct $Ct}}   ';'?)* )|
     (/gp; SWISS-3DIMAGE;/ (name {$Rep:{$ParStr:swiss3DR $Ct $Ct}} ';'?)* )|
     (/gp;/ ln) |
     (/tt;/ (name {$Rep:{$ParStr:owlR $Ct $Ct}})? ln) | ln
           ~

  # other 
  name:    ~ /[a-zA-Z0-9_]+/ ~ 
  word:    ~ /[^ ;:.,srs/icarus/db/prodom.i
# Description: icarus/srs structure description for PRINTS
# Author:      Martin Hilbers
# Date:        3-9-1996 
# Note:
#


PRODOM_DB:$library:[PRODOM group:@SEQRELATED_LIBS 
  comment:"a comprehensive collection of protein families " 
  format:@PRODOM_FORMAT maxNameLen:10 ifiles:{"prodom.i" "prodom.is"}
  files:{
    $file:prodom
  }
]

PRODOM_FORMAT:$libformat:[fileType:@PRODOM_FILE syntax:@PRODOM_SYNTAX 
  tableFormat:left
  fields:{
    $field:@DF_ALL
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:[@DF_Description code:des index:str indexToken:des]
    $field:[@DF_LINK index:link code:link indexToken:links]
    $field:[@DF_Sequences index:int code:seqs indexToken:seqs]
  }
]

PRODOM_SYNTAX:$syntax:[file:"SRSDB:prodom.is" ignore:" "]

$link:[@PRODOM_DB to:@?SWISSPROT_DB token:'links|swiss' toField:@DF_ID]
       
PRODOM_FILE:$filetype:[typename:mul maxline:10000]
_FILE syntax:@PRODOM_SYNTAX 
  tableFormat:left
  fields:{
    $field:@DF_ALL
    $field:[@DF_ID code:idsrs/icarus/db/prodom.is
#
# File:        prints.is
# Description: icarus syntax file for PRODOM
# Author:      Martin Hilbers
# Date:        3-9-1996
# Note:        
#

$rules={
   entry:   ~ {$In:[file:text] $Out}
#   entry:   ~ {$Out}
              ('>' {$Not} ln)*
              '>' {$entryFip=$fip $Wrt} ln {$App} 
              ('>' {$Not} ln {$App})*
            ~
  # fields
  fields:   ~ {$In:entry $Out} f_des f_ali*
            ~

  f_des:    ~ {$Wrt:idln} '>' ln ~
  f_ali:    ~ {$Wrt:link} ln ~
  
# indexing
  i_des:    ~ {$In:[fields c:idln] $Out} '>' 
              /[0-9]+/ {$Wrt:id} /[p0-9]+/ '('/[0-9]+/ {$Wrt:seqs} ')'
              ((/[A-Z0-9_]+/ {$Wrt:des}) (/[()0-9]+/)? )* '//' 
              ( /[A-Za-z0-9_]+/{$Wrt:des} | /[^A-Za-z0-9_]+/ )* ~

  id:       ~ {$In:[i_des c:id] $Out} /.+/ {$Wrt} ~
  des:      ~ {$In:[i_des c:des] $Out} /.+/ {$Wrt} ~
  seqs:     ~ {$In:[i_des c:seqs] $Out} /.+/ {$Wrt} ~
  links:    ~ {$In:[fields c:link] $Out} 
              name {$Wrt:swiss} ~

  # html display
  hl_links: ~ {$In:[fields c:link t:hl]}
               (name {$Rep:{$ParStr:swissIR $Ct $Ct}} ln)* 
            ~
  # other   
  name:     ~ /[a-zA-Z0-9_]+/ ~ 
  ln:       ~ /[^\n]*\n/ ~
}






          ( /[A-Za-z0-9_]+/{$Wrt:des} | /[^A-Za-z0-9_]+/ )* ~

  id:       ~ {$In:[i_des c:id] $Out} /.+/ {$Wrt} ~
  des:      ~ {$In:[i_des c:des] $Out} /.+/ {$Wrt} ~
  seqs:     ~ {$In:[i_des c:seqs] $Out} /.+/ {$Wrt} ~
  links:    ~ {$In:[fields c:link] $Out} 
              name {$Wrt:swiss} ~

  # html display
  hl_linsrs/icarus/db/prosite.i
#    $RCSfile: prosite.i,v $
#    $Revision: 1.9 $
#    $Date: 1997/03/03 18:34:13 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


PROSITE_DB:$library:[PROSITE group:@SEQRELATED_LIBS 
  comment:"A Dictionary of Protein Sites and Patterns - A. Bairoch" 
  format:@PROSITE_FORMAT maxNameLen:30 ifiles:{"prosite.i" "prosite.is"}
  files:{
    $file:prosite
  }
]

PROSITE_FORMAT:$libformat:[fileType:@DAT_FILE syntax:@PROSITE_SYNTAX 
  fields:{
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:[@DF_PATTERN code:patt tableToken:t_patt tableFormat:left]
    $field:[@DF_Accession code:acc index:str indexToken:acc
      tableToken:acc tableFormat:left]
    $field:[@DF_Description code:def index:str indexToken:def
      tableToken:t_descr tableFormat:left]
    $field:[@DF_LINK code:link]
    $field:[@DF_Date code:date index:int indexToken:date
      tableToken:t_date tableFormat:center]
#    $field:[@DF_TaxoRange index:str indexToken:taxrange]
#    $field:[@DF_MaxRepeat index:int indexToken:maxrep]
#    $field:[@DF_Site index:str indexToken:site]
#    $field:[@DF_SkipFlag index:str indexToken:skipflag]
    $field:[@DF_ALLPOS code:rule index:int indexToken:allpos
      tableToken:allpos tableFormat:right]
  }
]

PROSITE_SYNTAX:$syntax:[file:"SRSDB:prosite.is" ignore:" "]

DF_PATTERN:$srsfield:[Patterns short:pat]
DF_ALLPOS:$srsfield:[AllPositive short:alp]
DF_TaxoRange:$srsfield:[TaxoRange short:tax]
DF_MaxRepeat:$srsfield:[MaxRepeat short:max]
DF_SkipFlag:$srsfield:[SkipFlag short:skf]
DF_Site:$srsfield:[Site short:sit]

$link:[@PROSITE_DB to:@?SWISSPROT_DB token:'link|swiss' toField:@DF_Accession]
$link:[@PROSITE_DB to:@?PDB_DB token:'link|pdb' toField:@DF_ID]
$link:[@PROSITE_DB to:@?PROSITEDOC_DB token:'link|pd' toField:@DF_ID]
       
ile:"SRSDB:prosite.is" ignore:" "]

DF_PATTERN:$srsfield:[Patterns short:pat]
DF_ALLPOS:$srsfield:[AllPositive short:alp]
DF_TaxoRange:$srsfiesrs/icarus/db/prosite.is
$rules={
  entry:   ~ { $In:[file:text] $Out:entry}
             ('ID' {$Not} ln)*
             ('ID   ' {$entryFip=$Fip $Wrt} ln {$App} 
             ('ID' {$Not} ln {$App})*)?
           ~
  # fields
  fields:  ~ {$In:entry $Out} f_id f_acc f_date f_def 
             (f_mat)? f_patt f_rule f_cc f_links
           ~
  f_id:    ~ {$Wrt:id}   'ID   '  ln ~ 
  f_acc:   ~ {$Wrt:acc}  ('AC   ' ln)* ~
  f_date:  ~ {$Wrt:date} ('DT   ' ln)* ~
  f_def:   ~ {$Wrt:def}  ('DE   ' ln)* ~
  f_mat:   ~ {$Wrt:mat}  ('MA   ' ln)* ~
  f_patt:  ~ {$Wrt:patt} ('PA   ' ln)* ~
  f_rule:  ~ {$Wrt:rule} (/(NR|RU)   / ln)* ~
  f_cc:    ~ {$Wrt:cc}   ('CC   '  ln)* ~ 
  f_links: ~ {$Wrt:link} (/(DR|3D|DO)   / ln)* ~
  
  # indexing
  id:      ~ {$In:[fields c:id] $Out:id} 'ID' /[A-Z0-9_]+/ {$Wrt} ~
  acc:     ~ {$In:[fields c:acc] $Out:acc} 'AC'   /[A-Z0-9_]+/ {$Wrt} ~
  def:     ~ {$In:[fields c:def] $Out} ( 'DE' ( /[A-Za-z0-9_]+/ {$Wrt} | 
             /[^A-Za-z0-9_]+/ )* )* ~
  date:    ~ {$In:[fields c:date] $Out} 'DT'
             datenum {$Wrt:[s:$date c:cre]}     '(CREATED);'
             datenum {$Wrt:[s:$date c:dupd]} '(DATA UPDATE);'
             datenum {$Wrt:[s:$date c:iupd]} '(INFO UPDATE).' 
           ~ 
  allpos:  ~ {$In:[fields c:rule] $Out}
             (/.*POSITIVE=([0-9]+)/ {$Wrt:[s:$1]})? ~
  datenum: ~ {init {$month={JAN:1 FEB:2 MAR:3 APR:4 MAY:5 JUN:6 JUL:7 AUG:8 
                            SEP:9 OCT:10 NOV:11 DEC:12}}}
             /([A-Z][A-Z][A-Z])-([0-9]+)/ 
             {$date=$month.$1 * 100 + $2 * 10000} 
           ~ 
  link:    ~ {$In:[fields c:link] $Out}
             (/DR/ (name {$Wrt:swiss} ',' name ',' /[A-Z?]/ ';')* ln)*
             (/3D/ (name {$Wrt:pdb} (';'|'.'))* ln)* 
             /DO/ name {$Wrt:pd} 
           ~
  # table display 

  t_date:  ~ {$In:[fields c:date] $Out} 
             /.* ([A-Z0-9-]+) *\\(CREATED/ {$Wrt:[s:$1]} ~
  t_patt:  ~ {$In:[fields c:patt] $Out} /../ ln {$Wrt} (/../ ln {$App})* ~
  t_descr:  ~ {$In:[fields c:def] $Out} /../ ln {$Wrt} ~

  # html display
  hl_links:~ {$In:[fields c:link t:hl]}
             (/DR/(name {$Rep:{$ParStr:swissR $Ct $Ct}} ','name',' 
              /[A-Z?]/ ';')* ln)*
             (/3D/ (name {$Rep:{$ParStr:pdbR $Ct $Ct}} (';'|'.') )* ln)* 
             /DO/ name {$Rep:{$ParStr:prositedocR $Ct $Ct}} 
           ~
  # other 
  name:    ~ /[a-zA-Z0-9_]+/ ~ 
  ln:      ~ /[^\n]*\n/ ~
}


# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/data/prosite/prosite.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:id print:1] 
    $JobTokens:[$job name:date print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}




[A-Z?]/ ';')* ln)*
             (/3D/ (name {$Rep:{$ParStr:pdbR $Ct $Ct}} (';'|'.') )* ln)* 
             /DO/ name {$Rep:{$ParStr:prositedocR $Ct $Ct}} 
           ~
  # other 
  name:    ~ /[a-zA-Z0-9_]+/ ~ 
  ln:      ~ /[^\n]*\n/ ~
}


# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/data/prosite/prosite.dat']
  while:$JobHasInput:$job {
    $JobTokesrs/icarus/db/prosite.it
#    
#    $RCSfile: prosite.it,v $
#    $Revision: 1.3 $
#    $Date: 1996/10/10 16:47:08 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |The PROSITE  data bank  is composed  of two  ASCII (text) files. The first
    |file (PROSITE.DAT)  is a  computer readable  file that  contains  all  the
    |information necessary to programs that will scan sequence(s) with patterns
    |and/or  matrices.   The  second   file  (PROSITE.DOC)   contains   textual
    |information that  fully documents  each pattern and profile. We must point
    |out that we strongly urge software developers to build software tools that
    |make use  of both  files. A  list of  patterns or  profiles present  in  a
    |sequence  is   not  very   useful  to   biologists  without  the  relevant
    |documentation.
    |<p>
  www:
    |<A HREF="http://expasy.hcuge.ch/sprot/prosite.html">\
    |http://expasy.hcuge.ch/sprot/prosite.html</A>
  literature:
    |Bairoch A., Bucher P., PROSITE: recent developments. 
    |Nucleic Acids Res. 22:3583-3589(1994).
  fields:{
    ID:
      |The <EM>ID</EM> (IDentification) line is always the first line of an
      |entry. The general form of the ID line is:
      |<p>
      |ID   ENTRY_NAME; ENTRY_TYPE.
      |<p>
      |The first item on the ID line is the entry name. This name is a useful
      |means of identifying an entry. The entry name consists of from 2 to 21
      |uppercase alphanumeric characters. The characters that are allowed in an
      |entry name are: A-Z, 0-9, and the underscore character "_".
      |<p>
    AccNumber:
      |The <EM>AC</EM> (ACcession number) line lists the accession number
      |associated with an entry. It is always the second line of an entry.
      |Accession numbers provide a stable way of identifying entries
      |from release to release. It is sometimes necessary for reasons of
      |consistency to change the names of the entries between releases. <p>
      |An accession number, however, never change. Accession numbers allow
      |unambiguous citation of database entries. Researchers who wish to cite
      |a PROSITE entry in their publications should always cite the accession
      |number of that entry in order to ensure that readers can find the
      |relevant data in a subsequent release. <p> The format of the AC line
      |is: <p> AC PSnnnnn; <p> Where `PS' stands for PROSITE and `nnnnn' is a
      |five digit number. <p>
    Patterns:
      |The <EM>PA</EM> (PAttern) lines contains the definition of a PROSITE
      |pattern. The patterns are described using the following conventions:
      |<UL>
      |<LI>The standard IUPAC one-letter codes for the amino acids are used.
      |<LI>The symbol `x' is used for a position where any amino acid is
      |accepted.
      |<LI>Ambiguities are indicated by listing the acceptable amino acids for
      |a given position, between square parentheses `[ ]'. For example: [ALT]
      |stands for Ala or Leu or Thr.
      |</UL>
    Matrix:
      |The <EM>MA</EM> (MAtrix) lines contain the definition of a PROSITE
      |profile (or matrix) entry. The exact format content of this line is
      |fully described in a specific document (PROFILE.TXT) which is part of
      |the PROSITE distribution files. <p>
    Rule:
      |The <EM>RU</EM> (RUle) lines contain the definition of a PROSITE rule
      |entry. The format of the RU line is: <p>
      |<p>
      |DE   Rule_Description.
      |<p>
      |The rule is described in ordinary English and is free-format.
      |<p>
    Result:
      |The <EM>NR</EM> (Numerical Results) lines contain information relevant
      |to the results of the scan with a pattern on the complete SWISS-PROT
      |data bank.
    Comment:
      |The <EM>CC</EM> (Comments) lines contains various types of comments. The
      |format of the <EM>CC</EM> line is:
      |<p>
      |CC   /QUALIFIER=data; /QUALIFIER=data; .......
      |<p>
      |The qualifiers that are currently defined are:
      |<p>
      |/TAXO-RANGE Taxonomic range.
      |/MAX-REPEAT Maximum known  number of  repetitions of  the pattern  in a
      |            single protein.
      |/SITE       Indication of an `interesting' site in the pattern.
      |/SKIP-FLAG  Indication of  an entry that can be, in some cases, ignored
      |            by a program (because it is too unspecific).
      |<p>
    Ref:
      | The <EM>DR</EM> (Data bank Reference) line(s) are used as pointers to
      | the SWISS- PROT entries that corresponds to the enzyme being described.
      | The format
      | of the DR line is:
      |<p>
      | DR   AC_NB, ENTRY_NAME;  AC_NB, ENTRY_NAME;  AC_NB, ENTRY_NAME;
      |<p>
      | where:
      |<p>
      | -  'AC_NB' is  the SWISS-PROT  primary accession  number of the entry to
      |    which reference is being made.
      | -  'ENTRY_NAME' is the SWISS-PROT entry name.
      |<p>
    3D:
      |<p>
      |The <EM>3D</EM> (3D-structure) line is used to list the code(s) of X-ray
      |crystallography Protein Data Bank (PDB) entries that contain structural
      |data corresponding the sequence region described in a PROSITE entry. The
      |format of the 3D line is:
      |<p>
      |3D   name; [name2;...]
      |<p>
    Doc:
      |The <EM>DO</EM> (DOcumentation) line contains a pointer to the entry in
      |the PROSITE documentation file that describes the entry. The format of
      |the DO line is: <p> DO PDOCnnnnn; <p> Where `PDOC' stands for PROSITE
      |DOCumentation and `nnnnn' is a five digit number. <p> 
  }
  date:
    |25 Jul 1996
  signature:
    |Anatoly Ulyanov
}
ng the sequence region described in a PROSITE entry. The
      |format of the 3D line is:
      |<p>
      |3D   name; [name2;...]
      |<p>
    Doc:
      |The <EM>DO</EM> (DOcumentation) line contains a pointer to the entry in
      |the PROSITE documentation file that describes the entry. The format of
      |the DO line is: <p> DO PDOCnnnnn; <p> Where `PDOC' stands for PROSIsrs/icarus/db/prositedoc.i
#    $RCSfile: prositedoc.i,v $
#    $Revision: 1.4 $
#    $Date: 1996/08/11 22:51:53 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


PROSITEDOC_DB:$library:[PROSITEDOC group:@SEQRELATED_LIBS 
  comment:"A Dictionary of Protein Sites and Patterns - A. Bairoch" 
  format:@PROSITEDOC_FORMAT maxNameLen:10 
  ifiles:{"prositedoc.i" "prositedoc.is"}
  files:{
    $file:prosite
  }
]

PROSITEDOC_FORMAT:$libformat:[fileType:@PDOC_FILE syntax:@PROSITEDOC_SYNTAX 
  fields:{
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:[@DF_Description code:des]
    $field:[@DF_Authors index:str code:litref indexToken:authors]
    $field:[@DF_LINK index:link code:proslink indexToken:links]
  }
]

PROSITEDOC_SYNTAX:$syntax:[file:"SRSDB:prositedoc.is" ignore:" "]
PDOC_FILE:$filetype:[typename:doc maxline:200]

#$link:[@PROSITEDOC_DB to:@?PROSITE_DB token:'link' toField:@DF_Accession]
       


ROSITEDOC_FORMAT:$libformat:[fileType:@PDOC_FILE syntax:@PROSITEDOC_SYNTAX 
  fields:{
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:[@DF_Description code:des]
    $field:[@DF_Authors index:str code:litref indexToken:authors]
    $field:[@DF_LINK index:link code:proslink indexToken:links]
  }
]

PROSITEDOC_SYNTAX:$syntax:[file:"SRSDB:prositedoc.is" ignore:" "]
PDOC_FILE:$filetype:[typename:doc maxline:200]

#$link:[@PROSITEDOC_DB to:@?PROSITE_DB token:'link' toField:@DF_Accessionsrs/icarus/db/prositedoc.is

$rules={
  entry:   ~ {$In:[file:text] $Out pre{$Skip:0}}
             ('{PDOC' {$Not} ln)*
             ('{PDOC' {$entryFip=$Fip $Wrt} appLn 
             ('{END' {$Not} appLn)* appLn)? ~

  # fields
  fields:     ~ {$In:entry $Out $Skip:1} 
                f_id f_proslink f_title f_des (f_litref)* ~
  f_id:       ~ {$Wrt:id}       '{PDOC' ln ~ 
  f_proslink: ~ {$Wrt:proslink} ('{PS' ln)* ~ 
  f_title:    ~ {$Wrt:title}    '{BEGIN}' ln ln ln ln ~
  f_des:      ~ {$Wrt:des}      ('[' {$Not} ln)* ~
  f_litref:   ~ {$Wrt:litref}   /\\[[0-9 ][0-9 ]\\] / 
                ln (/(\\[|{END})/ {$Not} ln)* ~

  
  # indexing
  id:         ~ {$In:[fields c:id] $Out:id} '{' /[^}]+/ {$Wrt} ~
  authors:    ~ {$In:[fields c:litref] $Out} 
                /[^a-zA-Z]+/ author (',' author)*  ~
  link:       ~ {$In:[fields c:proslink] $Out}  '{' name {$Wrt} ~

  # html display
  hl_links:  ~ {$In:[fields c:proslink t:hl]}
               ('{' /[^;]+/ {$Rep:{$parStr:prositeR $ct $ct}} ln)+  ~
  h_des:     ~ {$In:[fields c:des t:hl]}  
               (/PDOC[0-9]+/ {$Rep:{$parStr:prositedocR $ct $ct}} |
                /(EC +)([0-9]\\.[0-9.]+)/{$Rep:{"$1($parStr:enzymeR)" $2 $2}} |
                /[a-zA-Z0-9]+/ | /[^a-zA-Z0-9]+/
               )* ~
  # other 
  name:       ~ /[a-zA-Z0-9_]+/ ~ 
  ln:         ~ /[^\n]*\n/ ~
  appLn:      ~ /[^\n]*\n/ {$App} ~
  author:     ~ /([^.,\n]+) +([^,;\n]+)/ {$Wrt:[s:"$1,$2"]} ~
}







               ('{' /[^;]+/ {$Rep:{$parStr:prositeR $ct $ct}} ln)+  ~
  h_des:     ~ {$Isrs/icarus/db/prositedoc.it
#    
#    $RCSfile: prositedoc.it,v $
#    $Revision: 1.3 $
#    $Date: 1996/10/10 16:47:09 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |The PROSITE  data bank  is composed  of two  ASCII (text) files. The first
    |file (PROSITE.DAT)  is a  computer readable  file that  contains  all  the
    |information necessary to programs that will scan sequence(s) with patterns
    |and/or  matrices.   The  second   file  (PROSITE.DOC)   contains   textual
    |information that  fully documents  each pattern and profile. We must point
    |out that we strongly urge software developers to build software tools that
    |make use  of both  files. A  list of  patterns or  profiles present  in  a
    |sequence  is   not  very   useful  to   biologists  without  the  relevant
    |documentation.
  www:
    |<A HREF="http://expasy.hcuge.ch/sprot/prosite.html">\
    |http://expasy.hcuge.ch/sprot/prosite.html">More on PROSITE</A>
  literature:
    |Bairoch A., Bucher P., PROSITE: recent developments. 
    |Nucleic Acids Res. 22:3583-3589(1994).
  date:
    |25 Jul 1996
  signature:
    |Anatoly Ulyanov
}
software tools that
    |make use  of both  files. A  list of  patterns or  profiles present  in  a
    |sequence  is   not  very   useful  to   biologists  without  the  relevant
    |documentation.
  www:
    |<A HREF="http://expasy.hcuge.ch/sprot/prosite.srs/icarus/db/reptax.i
#    $RCSfile: reptax.i,v $
#    $Revision: 1.1 $
#    $Date: 1997/03/03 18:36:29 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


REPTAX_DB:$library:[REPTAX group:@MISC_LIBS 
  format:@REPTAX_FORMAT maxNameLen:50 ifiles:{"reptax.i" "reptax.is"}
  files:{
    $file:taxonomy       
  }
]

REPTAX_FORMAT:$libformat:[fileType:@REPTAX_FILE syntax:@REPTAX_SYNTAX 
  printFormat:topicList tableFormat:left
  fields:{
    $field:[@DF_ID code:spec index:id indexToken:id]
    $field:[@DF_Taxon code:taxon index:str indexToken:taxon tableToken:'fields|taxon']
    $field:[@DF_Synonyms code:syn index:str indexToken:syn]
    $field:[@DF_Category code:cat index:str indexToken:'iword|cat']
    $field:[@DF_Up code:up]
    $field:[@DF_Status code:status index:str indexToken:'iword|status']
    $field:[@DF_Description code:des index:str indexToken:'iwords|cmnt']
    $field:[@DF_Distribution code:distrib index:str indexToken:'iwords|cmnt']
    $field:[@DF_Comment code:cmnt index:str indexToken:'iwords|cmnt']
    $field:[@DF_Reference code:reference index:str indexToken:ref]
  }
]

REPTAX_SYNTAX:$syntax:[file:"SRSDB:reptax.is"]
DF_Up:$srsfield:[Up short:up]
DF_Category:$srsfield:[Category short:cat]
DF_Status:$srsfield:[Status short:sta]
DF_Taxon:$srsfield:[Taxon short:tax]
REPTAX_FILE:$filetype:[typename:dat maxline:5000]

REPTAX_LINK:$link:[@REPTAX_DB to:@REPTAX_DB token:'up' toField:@DF_Taxon
  fromField:@DF_Up fromName:REPTAX_DOWN toName:REPTAX_UP]
$link:[@REPTAX_DB to:@REPTAX_DB toName:REPTAX_UP use:@REPTAX_LINK]
$link:[@REPTAX_DB to:@REPTAX_DB fromName:REPTAX_DOWN use:@REPTAX_LINK]
       
X:$syntax:[file:"SRSDB:reptax.is"]
DF_Up:$srsfield:[Up short:up]
DF_Category:$srsfield:[Category short:cat]
DF_Status:$srsfield:[Status short:sta]
DF_Taxon:$srsfield:[Taxon short:tax]
REPTAX_FILE:$filetype:[typename:dat maxline:5000]

REPTAX_LINK:$link:[@REPTAX_DB to:@REPTAX_DB token:'up' toField:@DF_Taxon
  frsrs/icarus/db/reptax.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: reptax.is,v $
#    $Revision: 1.1 $
#    $Date: 1997/03/03 18:36:30 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$rules={
  entry:     ~ {$In:[file:text] $Out pre $Skip:0 init $entryNo=0}
	       ('ID:'{$Not} ln)*
               (ln {pre{$entryFip=$Fip} $entryNo+=1 $Wrt}
               ('ID:'{$Not} ln {$App})+)?
             ~
  fields:    ~ {$In:entry $Out $Skip:1} 
               f_id f_taxon f_syn f_cat f_up f_status f_des f_distrib? 
               f_cmnt f_ref ~
  f_id:      ~ {$Wrt:id}       'ID:\n'  ~ 
  f_taxon:   ~ {$Wrt:taxon}       'Taxon:\n'      data ~ 
  f_syn:     ~ {$Wrt:syn}        'Synonyms:\n'     data* ~ 
  f_cat:     ~ {$Wrt:cat} 'Category:\n' data* ~ 
  f_distrib: ~ {$Wrt:distrib}    'Distribution:\n' data* ~ 
  f_up:      ~ {$Wrt:up}     'Up:\n' data* ~ 
  f_des:     ~ {$Wrt:des}    'Description:\n'      data* ~ 
  f_status:  ~ {$Wrt:status}    'Status:\n'      data* ~ 
  f_cmnt:    ~ {$Wrt:cmnt}  'Comment:\n'   data* ~ 
  f_ref:     ~ {$Wrt:ref}  'Reference:\n'   data* ~ 

  # indexing 
  id:        ~ {$In:entry $Out} x{$Wrt:[s:$entryNo]} ~
  taxon:     ~ {$In:[fields c:taxon] $Out} tag /[^ \n]+/ {$Wrt} ~
  iword:     ~ {$In:[fields c:{cat status}] $Out} tag /[^ \n]+/ {$Wrt:$Itc} ~
  up:        ~ {$In:[fields c:up] $Out} tag 'formerly'? /[^ \n]+/ {$Wrt} ~
  syn:       ~ {$In:[fields c:syn] $Out} tag (specName {$Uniq:[s:$name]}
               (/[ \t\n],[ \t\n]/ specName {$Uniq:[s:$name]})*)? ~
  iwords:    ~ {$In:[fields c:{distrib des cmnt}] $Out} 
               tag (word {$Uniq:$Itc} | sep) * ~
  ref:       ~ {$In:[fields c:ref] $Out} 
               tag (word {$Uniq} | sep) * ~

  # html
  h_taxon:   ~ {$In:[fields c:taxon t:html]}
               tag /[^ \n]+/ {$Rep:|<A HREF="wgetz?[reptax-taxon:$Ct]>reptax_down+-f+tax">$Ct</A>
                             } ~
  h_up:      ~ {$In:[fields c:up t:html]}
               tag /[^ \n]+/ {$Rep:{$ParStr:reptaxR $Ct $Ct}} ~
  h_field:   ~ {$In:[fields t:html]} 
               tag {if:$ParInt:isTable $Rep:"" 
                     else $Rep:"<DT><B>$Ct</B></DT><DD>"
                   } ~

  # others
  word:      ~ /[a-zA-Z0-9]+/ ~
  sep:       ~ /[^a-zA-Z0-9]+/ ~
  specName:  ~ / *([^ ]+ +[^ \n\t]+)/ {$name=$1} ~
  data:      ~ '  ' ln | / *\n/ ~
  ln:        ~ /[^\n]*\n/ ~
  tag:       ~ /[^:]+:\n/ ~
}

if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
           fileName:"/opt/srs/data/reptilia/taxonomy.dat"]
  while:$JobHasInput:$job {
    $JobTokens:[$job name:id print:1] 
    $JobTokens:[$job name:taxon print:1] 
    $JobTokens:[$job name:up print:1] 
    $JobNext:$job
  }
}
 } ~

  # others
  word:      ~ /[a-zA-Z0-9]+/ ~
  sep:       ~ /[^a-zA-Z0-9]+/ ~
  specName:  ~ / *([^ ]+ +[^ \n\t]+)/ {$name=$1} ~
  data:      ~ '  ' ln | / *\n/ ~
  ln:        ~ /[^\n]*\n/ ~
  tag:       ~ /[^:]+:\n/ ~
}

if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
           fileName:"srs/icarus/db/reptilia.i
#    $RCSfile: reptilia.i,v $
#    $Revision: 1.6 $
#    $Date: 1997/03/03 18:34:14 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


REPTILIA_DB:$library:[REPTILIA group:@MISC_LIBS 
  format:@REPTILIA_FORMAT maxNameLen:50 ifiles:{"reptilia.i" "reptilia.is"}
  files:{
    $file:agamidae        
    $file:amphisbaenia    
    $file:atractaspididae 
    $file:chamaeleonidae  
    $file:colubridae      
    $file:cordylidae      
    $file:crocodylidae    
    $file:dibamidae       
    $file:diploglossa     
    $file:elapidae        
    $file:gekkonidae      
    $file:henophidia      
    $file:hydrophiidae    
    $file:iguanidae       
    $file:lacertidae      
    $file:platynota       
    $file:pygopodidae     
    $file:scincidae       
    $file:sphenodontidae  
    $file:teiidae         
    $file:testudines      
    $file:typhlopoidea    
    $file:viperidae       
    $file:xantusiidae     
  }
]

REPTILIA_FORMAT:$libformat:[fileType:@REPTILIA_FILE syntax:@REPTILIA_SYNTAX 
  tableFormat:left printFormat:topicList
  fields:{
    $field:[@DF_Species code:spec index:id indexToken:id]
    $field:[@DF_Synonyms code:syn index:str indexToken:syn
      tableToken:'fields|syn']
    $field:[@DF_Family code:fam index:str indexToken:fam
      tabletoken:'fields|fam']
    $field:[@DF_Distribution code:distrib index:str indexToken:distrib
      tableToken:'fields|distrib']
    $field:[@DF_Comment code:distrib
      tableToken:'fields|comment']
    $field:[@DF_Reference code:reference index:str indexToken:ref
      tableToken:'fields|reference']
  }
]

REPTILIA_SYNTAX:$syntax:[file:"SRSDB:reptilia.is"]
DF_Species:$srsfield:[Species short:spc]
DF_Distribution:$srsfield:[Distribution short:dis]
DF_Family:$srsfield:[Family short:fam]


REPTILIA_FILE:$filetype:[typename:dat maxline:5000]

$link:[@REPTILIA_DB to:@GENBANK_DB fromField:@DF_ID toField:@DF_Organism]
$link:[@REPTILIA_DB to:@REPTAX_DB token:taxl fromField:@DF_ID toField:@DF_Taxon]
       
]
    $field:[@DF_Reference code:reference index:str indexToken:ref
      tableToken:'fields|reference']
  }
]

REPTILIA_SYNTAX:$syntax:[file:"SRSDB:reptilia.is"]
DF_Species:$srsfield:[Species short:spc]
DF_Distribution:$srsfield:[Distribution short:dis]
DF_Family:$srsfield:[Family short:fam]


REPTILIA_FILE:$filetype:[typename:dat maxline:5000]

$link:[@REPTILIA_DB to:@GENBANK_DB fromField:@DF_ID toField:@DF_Organism]
$link:[@REPTILIA_DB to:@srs/icarus/db/reptilia.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: reptilia.is,v $
#    $Revision: 1.6 $
#    $Date: 1997/03/03 18:34:15 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$rules={
  entry:     ~ {$In:[file:text] $Out pre $Skip:0}
	       ('Species:'{$Not} ln)*
               (ln {pre{$entryFip=$Fip} $Wrt}
               ('Species:'{$Not} ln {$App})+)?
             ~
  fields:    ~ {$In:entry $Out} 
               spec syn subSpec family distrib comment reference tail ~
  spec:      ~ {$Wrt:spec}       'Species:\n'      data ~ 
  syn:       ~ {$Wrt:syn}        'Synonyms:\n'     data* ~ 
  subSpec:   ~ {$Wrt:subspecies} 'Subspecies:\n' data* ~ 
  family:    ~ {$Wrt:fam}        'Family:\n' data* ~ 
  distrib:   ~ {$Wrt:distrib}    'Distribution:\n' data* ~ 
  comment:   ~ {$Wrt:comment}    'Comment:\n'      data* ~ 
  reference: ~ {$Wrt:reference}  'References:\n'   data* ~ 
  tail:      ~ {$Wrt:tail} '//\n' ~

  # indexing 
  i_species: ~ {$In:[entry] $Out:id} 
               tag specName {$Wrt:[s:$name]} ~
  i_syn:     ~ {$In:[fields c:syn] $Out:syn} 
               tag (specName {$Uniq:[s:$name]}
               (/[ \t\n],[ \t\n]/ specName {$Uniq:[s:$name]})*)? ~
  i_distrib: ~ {$In:[fields c:distrib] $Out:distrib} 
               tag (word {$Uniq} | sep) * ~
  fam:       ~ {$In:[fields c:fam] $Out} 
               tag (word {$Wrt} | /[: ]+/) * ~
  i_ref:     ~ {$In:[fields c:reference] $Out:ref} 
               tag (word {$Uniq} | sep) * ~
  taxl:      ~ {$In:[fields c:spec] $Out} tag / */ word {$Wrt} ~

  # html
  h_field:   ~ {$In:[fields t:html]} 
               tag {if:$ParInt:isTable $Rep:"" 
                     else $Rep:"<DT><B>$Ct</B></DT><DD>"
                   } ln* {$Rep:"$Ct<BR>"}~
  # others
  word:      ~ /[a-zA-Z0-9]+/ ~
  sep:       ~ /[^a-zA-Z0-9]+/ ~
  specName:  ~ / *([^ ]+ +[^ \n\t]+)/ {$name=$1} ~
  data:      ~ '  ' ln | / *\n/ ~
  ln:        ~ /[^\n]*\n/ ~
  tag:       ~ /[^:]+:\n/ | ln ~
}

if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
           fileName:"/opt/srs/data/reptilia/reptilia.dat"]
  while:$JobHasInput:$job {
    $JobTokens:[$job name:syn print:1] 
    $JobNext:$job
  }
}
  else $Rep:"<DT><B>$Ct</B></DT><DD>"
                   } ln* {$Rep:"$Ct<BR>"}~
  # others
  word:      ~ /[a-zA-Z0-9]+/ ~
  sep:       ~ /[^a-zA-Z0-9]+/ ~
  specName:  ~ / *([^ ]+ +[^ \n\t]+)/ {$name=$1} ~
  data:      ~ '  ' ln | / *\n/ ~
  ln:        ~ /[^\n]*\n/ ~
  tag:       ~ /[srs/icarus/db/sptrembl.i
#
#    $RCSfile: sptrembl.i,v $
#    $Revision: 1.2 $
#    $Date: 1996/12/06 16:38:08 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

SPTREMBL_DB:$library:[SPTREMBL group:@SEQUENCE_LIBS 
  subentries:@SptremblFeatures_DB
  format:@SPTREMBL_FORMAT maxNameLen:14 files:{
    $file:fun
    $file:hum
    $file:inv
    $file:mam
    $file:mhc
    $file:org
    $file:phg
    $file:pln
    $file:pro
    $file:rod
    $file:vrl
    $file:vrt
  }
]
REMTREMBL_DB:$library:[REMTREMBL group:@SEQUENCE_LIBS 
  format:@?SPTREMBL_FORMAT maxNameLen:14 files:{
    $file:immuno
    $file:patent
    $file:pseudo
    $file:smalls
  }
]

SPTREMBL_FORMAT:$libformat:[fileType:{@DAT_FILE @SEQ_FILE} 
  syntax:@SPTREMBL_SYNTAX tableFormat:left fields:{
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:@DF_ALL
    $field:[@DF_Accession code:acc index:str indexToken:acc]
    $field:[@DF_Description code:des index:str indexToken:des
      tableToken:'clFields|des']
    $field:[@DF_GeneName code:gene index:str indexToken:gene]
    $field:[@DF_Date code:date index:int indexToken:date]
    $field:[@DF_Organism code:{org tax} index:str indexToken:org]
    $field:[@DF_Organelle code:organ index:str indexToken:organ]
    $field:[@DF_Authors code:refaut index:str indexToken:authors]
    $field:[@DF_LINK index:link code:link indexToken:link]
    $field:[@DF_SeqLength index:int indexToken:seqlen code:seqln]
    $field:[@DF_MolWeight index:int indexToken:molweight code:seqln]
    $field:[@DF_CommentType index:str indexToken:'cc|ttl' code:cc]
    $field:[@DF_Comment index:str indexToken:'cc|word' code:cc 
      tableToken:'clFields|cc']
    $field:[@DF_FtKey index:str indexToken:ftKey code:ft indexId:@SUBENTRY_ID]
    $field:[@DF_FtDescription index:str indexToken:ftDes code:ft 
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtLength index:int indexToken:ftLen code:ft 
      indexId:@SUBENTRY_ID]
    $field:[@DF_ProtSequence token:'sequence' format:swiss]
  }
]


SPTREMBL_SYNTAX:$syntax:[file:"SRSDB:swissprot.is" ignore:" \t"]
REMTREMBL_SYNTAX:$syntax:[file:"SRSDB:swissprot.is" ignore:" \t"]

$link:[@SPTREMBL_DB to:@?GENBANK_DB token: 'link|EMBL' toField:@DF_Accession]
$link:[@SPTREMBL_DB to:@?EMBL_DB token:'link|EMBL' toField:@DF_Accession]
$link:[@SPTREMBL_DB to:@?PIR_DB token:'link|PIR' toField:@DF_Accession]
$link:[@SPTREMBL_DB to:@?PDB_DB token:'link|PDB'toField:@DF_ID]
$link:[@SPTREMBL_DB to:@?REBASE_DB toField:@DF_ID]
$link:[@SPTREMBL_DB to:@?OMIM_DB token:'link|MIM' toField:@DF_ID]
$link:[@SPTREMBL_DB to:@?MEDLINE_DB toField:@DF_ID]
$link:[@SPTREMBL_DB to:@?ENZYME_DB fromField:@DF_Description toField:@DF_ID]

SptremblFeatures_DB:$library:[SPTREMBL_features 
  format:@SptremblFeature_Format
]

SptremblFeature_Format:$libformat:[syntax:@SPTREMBL_SYNTAX
  tableFormat:left fields:{
    $field:[@DF_ID token:ftId]
    $field:[@DF_FtKey token:ft tableToken:'t_ft|key']
    $field:[@DF_FtLength token:ft tableToken:'t_ft|len']
    $field:[@DF_FtDescription token:ft tableToken:'t_ft|des']
    $field:[@DF_FtLocation token:ft tableToken:'t_ft|loc' 
      tableFormat:listing]
  }
]

fromField:@DF_Description toField:@DF_ID]

SptremblFeatures_DB:$library:[SPTREMBL_features 
  format:@SptremblFeature_Format
]

SptremblFeature_Format:$libformat:[syntax:@SPTREMBL_SYNTAX
  tableFormat:left fields:{
    $field:[@DF_ID token:ftId]
    $field:[@DF_FtKey token:ft tableToken:'t_ft|key']
    $field:[@DF_FtLength token:ft tableTokensrs/icarus/db/srsdb.i
#
#    $RCSfile: srsdb.i,v $
#    $Revision: 1.32 $
#    $Date: 1997/03/19 20:39:16 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

file:"SRSDB:swissprot.i"
file:"SRSDB:pir.i"
file:"SRSDB:nrl3d.i"
file:"SRSDB:embl.i"
file:"SRSDB:subtilist.i"
file:"SRSDB:sptrembl.i"
file:"SRSDB:trembl.i"
file:"SRSDB:imgt.i"
file:"SRSDB:prosite.i"
file:"SRSDB:prositedoc.i"
file:"SRSDB:blocks.i"
file:"SRSDB:prints.i"
file:"SRSDB:enzyme.i"
file:"SRSDB:pdbfinder.i"
file:"SRSDB:mpw.i"
file:"SRSDB:emp.i"
file:"SRSDB:clustalw.i"
file:"SRSDB:blast.i"
file:"SRSDB:fasta.i"
file:"SRSDB:sw.i"
file:"SRSDB:primers.i"
file:"SRSDB:tfcell.i"
file:"SRSDB:tffactor.i"
file:"SRSDB:tfsite.i"
file:"SRSDB:tfclass.i"
file:"SRSDB:tfmatrix.i"
file:"SRSDB:tfgene.i"
file:"SRSDB:genbank.i"
file:"SRSDB:epd.i"
file:"SRSDB:ypd.i"
file:"SRSDB:pdb.i"
file:"SRSDB:dssp.i"
file:"SRSDB:hssp.i"
file:"SRSDB:fssp.i"
file:"SRSDB:reptilia.i"
file:"SRSDB:reptax.i"
file:"SRSDB:medline.i"
file:"SRSDB:taxonomy.i"
file:"SRSDB:flygene.i"
file:"SRSDB:flyrefs.i"
file:"SRSDB:omim.i"
file:"SRSDB:p53.i"
file:"SRSDB:p53apc.i"
file:"SRSDB:p53ref.i"
file:"SRSDB:p53apcref.i"
file:"SRSDB:btkbase.i"
file:"SRSDB:vwf.i"
file:"SRSDB:cftr.i"
file:"SRSDB:pah.i"
file:"SRSDB:haema.i"
file:"SRSDB:haemb.i"
file:"SRSDB:ldlr.i"

file:"SRSDB:views.i"
file:"SRSDB:appl.i"

$dataRoot = '/data'
$dataRoot2 = '/u1/srs/data'
$dataRoot3 = '/data/research'
$dataRoot4 = '/data/ftp/pub/databases'
$dataRoot5 = '/ebi/services/data'

# for the demo in the "Guided Tour"
file:"SRSDEMO:genes.i"
file:"SRSDEMO:reflist.i"
$site:[name:demo
  libs:{
    $libloc:[@GENES_DB dir:"SRSDEMO:"]
    $libloc:[@REFLIST_DB dir:"SRSDEMO:"]
  }
]




$site:[name:unix 
  libs:{
    $libloc:[@SWISSPROT_DB dir:"$dataRoot/gcg/gcgswissprot/"]
#    $libloc:[@SWISSNEW_DB dir:"$dataRoot/gcg/gcgswissnew/"]
#    $libloc:[@PIR_DB dir:"$dataRoot/gcg/gcgpir/"]
#    $libloc:[@NRL3D_DB dir:"$dataRoot/gcg/gcgnrl_3d/"]
#    $libloc:[@TREMBL_DB dir:"$dataRoot/trembl/"]
#    $libloc:[@TREMBLNEW_DB dir:"$dataRoot/trembl/"]
#    $libloc:[@GENBANK_DB dir:"$dataRoot/genbank/"]
#    $libloc:[@EMBL_DB dir:"$dataRoot/gcg/gcgembl/"]
#    $libloc:[@EMBLNEW_DB dir:"$dataRoot/gcg/gcgembl/"]
#    $libloc:[@SPTREMBL_DB dir:"$dataRoot/sptrembl/"]
#    $libloc:[@REMTREMBL_DB dir:"$dataRoot/remtrembl/"]
#    $libloc:[@IMGT_DB dir:"$dataRoot/imgt"]
#    $libloc:[@EMBL_DB dir:"/data/gcg/gcgembl/"]
#    $libLoc:[@SUBTILIST_DB dir:"$dataRoot/subtilis/"]
#    $libloc:[@PROSITE_DB dir:"$dataRoot3/prosite/"]
#    $libloc:[@PROSITEDOC_DB dir:"$dataRoot3/prosite/"]
#    $libloc:[@BLOCKS_DB dir:"$dataRoot3/blocks/"]
#    $libloc:[@ENZYME_DB dir:"$dataRoot4/enzyme/"]
#    $libloc:[@PRINTS_DB dir:"$dataRoot/prints/"]
#    $libloc:[@PDBFINDER_DB dir:"$dataRoot3/pdbfinder/"]
#    $libloc:[@BLAST_DB dir:"" indexDir:""]
#    $libloc:[@FASTA_DB dir:"" indexDir:""]
#    $libloc:[@SW_DB dir:"" indexDir:""]
#    $libloc:[@CLUSTALW_DB dir:"" indexDir:""]
#    $libloc:[@PRIMERS_DB dir:"/data/primers/"]
#    $libloc:[@YPD_DB dir:"$dataRoot/ypd/"]

#    $libloc:[@TFCELL_DB dir:"$dataRoot2/transfac/"]
#    $libloc:[@TFFACTOR_DB dir:"$dataRoot2/transfac/"]
#    $libloc:[@TFSITE_DB dir:"$dataRoot2/transfac/"]
#    $libloc:[@TFCLASS_DB dir:"$dataRoot2/transfac/"]
#    $libloc:[@TFMATRIX_DB dir:"$dataRoot2/transfac/"]
#    $libloc:[@TFGENE_DB dir:"$dataRoot2/transfac/"]
    
#    $libloc:[@FLYGENE_DB dir:"$dataRoot2/flybase/"]
#    $libloc:[@FLYREFS_DB dir:"$dataRoot2/flybase/"]
 
#    $libloc:[@MEDLINE_DB dir:"$dataRoot/medline1"]

#    $libloc:[@EMP_DB dir:"$dataRoot2/emp/"]
#    $libloc:[@MPW_DB dir:"$dataRoot2/emp/"]
#    $libloc:[@OMIM_DB dir:"$dataRoot2/omim/"]
#    $libloc:[@EPD_DB dir:"$dataRoot/epd/"]
#    $libloc:[@PDB_DB 
#      dir:"/data/research/pdb/"]
#    $libloc:[@DSSP_DB dir:"$dataRoot3/dssp/"]
#    $libloc:[@HSSP_DB dir:"$dataRoot3/hssp/"]
#    $libloc:[@FSSP_DB dir:"$dataRoot3/fssp/"]
#    $libloc:[@REPTILIA_DB dir:"$dataRoot2/reptilia/"] 
#    $libloc:[@REPTAX_DB dir:"$dataRoot2/reptilia/"] 
#    $libloc:[@TAXONOMY_DB dir:"$dataRoot2/taxonomy/"] 

#    $libloc:[@P53APC_DB dir:"$dataRoot2/mutdb/p53apc/"]
#    $libloc:[@P53APCREF_DB dir:"$dataRoot2/mutdb/p53apc/"]
#    $libloc:[@P53_DB dir:"$dataRoot2/mutdb/p53/"]
#    $libloc:[@P53REF_DB dir:"$dataRoot2/mutdb/p53/"]
#    $libloc:[@BTKBASE_DB dir:"$dataRoot2/mutdb/btkbase/"]
#    $libloc:[@VWF_DB dir:"$dataRoot2/mutdb/vwf/"]
#    $libloc:[@CFTR_DB dir:"$dataRoot2/mutdb/cftr/"]
#    $libloc:[@PAH_DB dir:"$dataRoot2/mutdb/pah/"]
#    $libloc:[@HAEMA_DB dir:"$dataRoot2/mutdb/haema/"]
#    $libloc:[@HAEMB_DB dir:"$dataRoot2/mutdb/haemb/"]
#    $libloc:[@LDLR_DB dir:"$dataRoot2/mutdb/ldlr/"]
  }
]

# hypertext links to be inserted into entries before display

$href:[medlineR     link:
     |<A HREF="http://atlas.nlm.nih.gov:5700/htbin-post/Entrez/query?\
     |uid=%s&form=6&db=m&Dopt=b">%s</A>\
]
$href:[mpwR         link:"<A HREF=wgetz?-e+[mpw-name:%s]>%s</A>"]
$href:[swissR       link:"<A HREF=wgetz?-e+[swissprot-acc:%s]>%s</A>"]
$href:[swissidR     link:"<A HREF=wgetz?-e+[swissprot-id:%s]>%s</A>"]
$href:[swissprotFtR     
  link:"<A HREF=wgetz?-e+[swissprot_features-id:%s_%s]>%s</A>"]
$href:[sptremblFtR     
  link:"<A HREF=wgetz?-e+[sptrembl_features-id:%s_%s]>%s</A>"]
$href:[remtremblFtR     
  link:"<A HREF=wgetz?-e+[remtrembl_features-id:%s_%s]>%s</A>"]
$href:[pidR         link:"<A HREF=wgetz?-e+[UNKNOWN-id:%s]>%s</A>"]
$href:[pdbR         link:"<A HREF=wgetz?-e+[pdb-id:%s]>%s</A>"]
$href:[prositedocR  link:"<A HREF=wgetz?-e+[prositedoc-id:%s]>%s</A>"]
$href:[prositeR     link:"<A HREF=wgetz?-e+[prosite-acc:%s]>%s</A>"]
$href:[enzymeR      link:"<A HREF=wgetz?-e+[enzyme-id:%s]>%s</A>"]
$href:[pirR         link:"<A HREF=wgetz?-e+[pir-acc:%s]>%s</A>"]
$href:[emblR        link:"<A HREF=wgetz?-e+[embl-acc:%s]>%s</A>"]
$href:[emblIdR      link:"<A HREF=wgetz?-e+[embl-id:%s]>%s</A>"]
$href:[emblFeatR    link:"<A HREF=wgetz?-e+[embl_features-id:%s_%s]>%s</A>"]
$href:[subtilistFeatR    
  link:"<A HREF=wgetz?-e+[subtilist_features-id:%s_%s]>%s</A>"]
$href:[genbankR     link:"<A HREF=wgetz?-e+[genbank-acc:%s]>%s</A>"]
$href:[genbankIdR   link:"<A HREF=wgetz?-e+[genbank-id:%s]>%s</A>"]
$href:[hsspR        link:"<A HREF=wgetz?-e+[hssp-id:%s]>%s</A>"]
$href:[ecogeneR     link:"<A HREF=wgetz?-e+[ecogene-acc:%s]>%s</A>"]
$href:[mimR         link:"<A HREF=wgetz?-e+[omim-id:%s]>%s</A>"]
$href:[mimAllR      link:"<A HREF=wgetz?-e+[omim-id:%s]#%s>%s</A>"]
$href:[pdbR         link:"<A HREF=wgetz?-e+[pdb-id:%s]>%s</A>"]
$href:[epdR         link:"<A HREF=wgetz?-e+[epd-id:%s]>%s</A>"]
$href:[transfacR    link:"<A HREF=wgetz?-e+[tffactor-id:%s]>%s</A>"]
$href:[tffactorR    link:"<A HREF=wgetz?-e+[tffactor-id:%s]>%s</A>"]
$href:[tfsiteR      link:"<A HREF=wgetz?-e+[tfsite-acc:%s]>%s</A>"]
$href:[tfcellR      link:"<A HREF=wgetz?-e+[tfcell-id:%s]>%s</A>"]
$href:[tfmatrixR    link:"<A HREF=wgetz?-e+[tfmatrix-id:%s]>%s</A>"]
$href:[tfclassR     link:"<A HREF=wgetz?-e+[tfclass-id:%s]>%s</A>"]

$href:[listaR       link:"<A HREF=wgetz?-e+[UNKNOWN-id:%s]>%s</A>"]
$href:[yepdR        link:"<A HREF=wgetz?-e+[UNKNOWN-id:%s]>%s</A>"]
$href:[ypdrefR      link:"<A HREF=wgetz?-e+[ypdref-id:%s]>%s</A>"]
$href:[sgdR         link:"<A HREF=wgetz?-e+[UNKNOWN-id:%s]>%s</A>"]
$href:[stygeneR     link:"<A HREF=wgetz?-e+[UNKNOWN-id:%s]>%s</A>"]
$href:[hivR         link:"<A HREF=wgetz?-e+[UNKNOWN-id:%s]>%s</A>"]
$href:[eco2dbaseR   link:"<A HREF=wgetz?-e+[UNKNOWN-id:%s]>%s</A>"]
$href:[subtilistR   link:"<A HREF=wgetz?-e+[subtilist-id:%s]>%s</A>"]
$href:[flybaseR     link:"<A HREF=wgetz?-e+[UNKNOWN-id:%s]>%s</A>"]
$href:[flygeneR     link:"<A HREF=wgetz?-e+[flygene-id:%s]>%s</A>"]
$href:[flyrefsR     link:"<A HREF=wgetz?-e+[flyrefs-id:%s]>%s</A>"]
$href:[aarhusR      link:"<A HREF=wgetz?-e+[UNKNOWN-id:%s]>%s</A>"]
$href:[gcrdbR       link:"<A HREF=wgetz?-e+[UNKNOWN-id:%s]>%s</A>"]
$href:[wormpepR     link:"<A HREF=wgetz?-e+[UNKNOWN-id:%s]>%s</A>"]
$href:[swiss2dpageR link:"<A HREF=wgetz?-e+[UNKNOWN-id:%s]>%s</A>"]
$href:[swissFeatR   link:"<A HREF=wgetz?-e+[swissprot-id:%s]>%s</A>"]
$href:[gdbR         link:"<A HREF=wgetz?-e+[gdb-id:%s]>%s</A>"]
$href:[reptaxR      link:"<A HREF=wgetz?-e+[reptax-taxon:%s]>%s</A>"]

$href:[emblFtQualR link:
"<A HREF=http://www.ebi.ac.uk/ebi_docs/embl_db/ft/qual_summary.html#%s>%s</A>"]
$href:[emblFtKeyR link:
 "<A HREF=http://www.ebi.ac.uk/ebi_docs/embl_db/ft/key_defs.html#%s>%s</A>"]

# added ramu, useful for any database which has accno 
$href:[dbaseR       link:"<A HREF=wgetz?-e+[%s-acc:%s]>%s</A>"]
$href:[dbase_idR    link:"<A HREF=wgetz?-e+[%s-id:%s]>%s</A>"]
$href:[headR link:|<BODY BGCOLOR="#FFFFF0" LINK="#0000ff" 
        	  | VLINK="#ff0000" ALINK="#ff0000" TEXT="#000000">
]


$srsdb:[ 
  libIds:{
    $libid:[1 lib:@?SWISSPROT_DB] 
    $libid:[8 lib:@?SWISSNEW_DB]
    $libid:[2 lib:@?PIR_DB]
    $libid:[3 lib:@?EMBL_DB] 
    $libid:[4 lib:@?EMBLNEW_DB]
    $libid:[5 lib:@?GENBANK_DB] 
    $libid:[6 lib:@?NRL3D_DB]
    $libid:[7 lib:@?TREMBL_DB]
    $libid:[9 lib:@?TREMBLNEW_DB]
    $libid:[10 lib:@?REMTREMBL_DB]
    $libid:[11 lib:@?SPTREMBL_DB]
    $libid:[12 lib:@?IMGT_DB]
    $libid:[13 lib:@?SUBTILIST_DB]

    $libid:[21 lib:@?PDB_DB] 
    $libid:[22 lib:@?PDBNEW_DB] 
    $libid:[24 lib:@?DSSP_DB]  
    $libid:[23 lib:@?HSSP_DB] 
    $libid:[25 lib:@?ALI_DB] 
    $libid:[26 lib:@?FSSP_DB]
    $libid:[27 lib:@?PDBFINDER_DB]

    $libid:[41 lib:@?PROSITE_DB]
    $libid:[42 lib:@?PROSITEDOC_DB]
    $libid:[43 lib:@?BLOCKS_DB]
    $libid:[44 lib:@?EPD_DB]
    $libid:[46 lib:@?ECDC_DB] 
    $libid:[47 lib:@?MIM_DB]
    $libid:[48 lib:@?MIMMAP_DB]
    $libid:[49 lib:@?ENZYME_DB] 
    $libid:[50 lib:@?REBASE_DB]
    $libid:[51 lib:@?CPGISLE_DB]
    $libid:[52 lib:@?MOLPROBE_DB]
    $libid:[53 lib:@?PRODOM_DB]
    $libid:[54 lib:@?PMD_DB]
    $libid:[55 lib:@?FLYGENE_DB]
    $libid:[56 lib:@?FLYREFS_DB]
    $libid:[65 lib:@?PIRALN_DB]
    $libid:[66 lib:@?YPD_DB]
    $libid:[67 lib:@?MPW_DB]
    $libid:[68 lib:@?PRIMERS_DB]
    $libid:[69 lib:@?EMP_DB]
    $libid:[70 lib:@?TAXONOMY_DB]
    $libid:[71 lib:@?PRINTS_DB]
    $libid:[72 lib:@?OMIM_DB]

    $libid:[81 lib:@?SEQANALREF_DB]
    $libid:[82 lib:@?SEQANALRABS_DB]
    $libid:[83 lib:@?PROTSTRUCTLIT_DB] 
    $libid:[90 lib:@?MEDLINE_DB]
    $libid:[91 lib:@?YPDREF_DB]
    $libid:[101 lib:@?NAKAI_DB]
    $libid:[102 lib:@?LIMB_DB]
    $libid:[110 lib:@?TFSITE_DB]
    $libid:[111 lib:@?TFFACTOR_DB]
    $libid:[112 lib:@?TFCELL_DB]
    $libid:[113 lib:@?TFCLASS_DB]
    $libid:[114 lib:@?TFMATRIX_DB]
    $libid:[115 lib:@?TFGENE_DB]

# databanks for mutations and aberrations

    $libid:[130 lib:@?P53_DB]
    $libid:[131 lib:@?P53APC_DB]
    $libid:[132 lib:@?P53REF_DB]
    $libid:[133 lib:@?P53APCREF_DB]
    $libid:[134 lib:@?BTKBASE_DB]
    $libid:[135 lib:@?VWF_DB]
    $libid:[136 lib:@?CFTR_DB]
    $libid:[137 lib:@?PAH_DB]
    $libid:[138 lib:@?HAEMA_DB]
    $libid:[139 lib:@?HAEMB_DB]
    $libid:[140 lib:@?LDLR_DB]


    $libid:[201 lib:@?FASTA_DB] 
    $libid:[202 lib:@?BLAST_DB]
    $libid:[203 lib:@?PROFILE_DB]
    $libid:[204 lib:@?BLITZ_DB]
    $libid:[204 lib:@?SW_DB]
    $libid:[205 lib:@?CLUSTALW_DB]

    $libid:[230 lib:@?REPTILIA_DB]
    $libid:[231 lib:@?REPTAX_DB]
    $libid:[232 lib:@?MEDIA_DB]

    # the two demo databanks
    $libid:[254 lib:@?GENES_DB]
    $libid:[255 lib:@?REFLIST_DB]


  }
]
 lib:@?PAH_DB]
    $libid:[138 lib:@?HAEMA_DB]
    $libid:[139 lib:@?HAEMB_DB]
    $libid:[140 lib:@?LDLR_DB]


    $libid:[201 lib:@?FASTA_DB] 
    $libid:[202 lib:@?BLAST_DB]
    $libid:[203 lib:@?PROFILE_DB]
    $libid:[204 lib:@?BLITZ_DB]
    $libid:[204 lib:@?SW_DB]
    $libidsrs/icarus/db/srsgen.i
#    $RCSfile: srsgen.i,v $
#    $Revision: 1.7 $
#    $Date: 1997/03/18 18:48:25 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


# syntaxes
SRSQUERY_SYNTAX:$syntax:[file:"SRSICA:srsquery.i" name:srsquery 
  ignore:" \r\t\n"]
MakeWild_Syntax:$syntax:[file:"SRSICA:makewild.i" name:makeWild]
ICARUS_SYNTAX:$syntax:[file:"SRSICA:icarus.i"   level3:0
  comment:"^#[^\n]*\n" commandsyntax:@COMMAND_SYNTAX name:icarus 
  ignore:" \t\n"]
CABI_SYNTAX:$syntax:[file:"SRSICA:cabi.i" commandsyntax:@COMMAND_SYNTAX 
  name:cabi]
COMMAND_SYNTAX:$syntax:[file:"SRSICA:command.i" level3:0]
BOOTCOMMAND_SYNTAX:$syntax:[file:"SRSICA:bootcommand.i" level3:0]


# data bank groups
SEQUENCE_LIBS:$libgroup:[Sequence short:SQ search:all]
SEQRELATED_LIBS:$libgroup:[SeqRelated]
MISC_LIBS:$libgroup:[Others]
LITERATURE_LIBS:$libgroup:[Literature short:lit]
PROTSTRUCT_LIBS:$libgroup:[Protein3DStruct short:'3d']
GENOME_LIBS:$libgroup:[Genome short:gen]
TRANSFAC_LIBS:$libgroup:[TransFac short:'tf']
MUTATION_LIBS:$libgroup:['Human Mutations' short:'mut']

APPLICATION_LIBS:$libgroup:[Application short:app]

# data field types
DF_Class: $srsfield:[Class short:cla]
DF_Synonyms: $srsfield:[Synonyms short: SYM]
DF_HeaderField:$srsfield:[HeaderField type:header]
DF_ID:$srsfield:[ID short:id group:@DF_ALL]
DF_ALL:$srsfield:[AllText short:all isGroup:yes type:str] 
DF_ACCNO:$srsfield:[AccNumber short:acc group:@DF_ALL]
DF_Accession:$srsfield:[AccNumber short:acc group:@DF_ALL]
DF_SeqLength:$srsfield:[SeqLength short:sl]
DF_Date:$srsfield:[Date short:dat]
DF_Description:$srsfield:[Description short:des group:@DF_ALL]
DF_Keywords:$srsfield:[Keywords short:key group:@DF_ALL]
DF_Organism:$srsfield:[Organism short:org group:@DF_ALL]
DF_Organelle:$srsfield:[Organelle short:ogn group:@DF_ALL]
DF_GeneName:$srsfield:[GeneName short:gen group:@DF_ALL]
DF_Molecule:$srsfield:[Molecule short:mol group:@DF_ALL]
DF_Authors:$srsfield:[Authors short:aut group:@DF_ALL]
DF_Title:$srsfield:[Title short:tit group:@DF_ALL]
DF_Features:$srsfield:[Features short:fts group:@DF_ALL]
DF_Citation:$srsfield:[Citation short:cit]
DF_Division:$srsfield:[Division short:div]
DF_LINK:$srsfield:[Link short:lnk]
DF_COMMENT:$srsfield:[Comment short:cc group:@DF_ALL]
DF_Comment:$srsfield:[Comment short:cc group:@DF_ALL]
DF_CommentType:$srsfield:[CommentType short:cct group:@DF_ALL]
DF_REF:$srsfield:[Reference short:ref]
DF_Reference:$srsfield:[Reference short:ref]
DF_EnzymeCode:$srsfield:[EnzymeCode short:enz group:@DF_ALL]
DF_AccessionKey:$srsfield:[AccessionKey short:ack]
DF_DBOrigin:$srsfield:[DBOrigin short:dbo]

DF_Compound:$srsfield:[Compound short:com]
DF_Header:$srsfield:[Header short:hdr]
DF_Source:$srsfield:[Source short:src]
DF_Substrate:$srsfield:[Substrate short:sub]
DF_WaterMols:$srsfield:[WaterMols short:wat]
DF_Method:$srsfield:[Method short:met]

DF_GeneProduct: $srsfield:[GeneProduct short:pro group:@DF_ALL]
DF_IsoelectricPoint:$srsfield:[IsoelectricPoint short:iep]


# for sequence features
DF_FtKey:$srsfield:[FeatureKey short:ftk]
DF_FtQualifier:$srsfield:[FeatureQualifier short:ftq]
DF_FtSource:$srsfield:[FeatureSource short:fts]
DF_FtDescription:$srsfield:[FeatureDescription short:ftd]
DF_FtLength:$srsfield:[FeatureLength short:ftl]
DF_FtLocation:$srsfield:[FeatureLocation short:flo]
DF_PID:$srsfield:[PID short:pid]
DF_ChrsNo:$srsfield:[ChromosomeNo short:chn]
DF_FtMap:$srsfield:[MapLocation short:mpl]

DF_DNASequence:$srsfield:[Sequence short:seq
  format:{
    $fieldFormat:[fasta eval:'$SeqPrint:[name:$field format:fasta]'] 
    $fieldFormat:[gcg   eval:'$SeqPrint:[format:gcg width:60]'] 
    $fieldFormat:[pir   eval:'$SeqPrint:[format:pir width:60]'] 
    $fieldFormat:[embl  eval:'$SeqPrint:[format:embl width:60]'] 
    $fieldFormat:[plain eval:'$SeqPrint:[format:plain width:70]']
  }
]
DF_DNALocation:$srsfield:[Sequence short:seq
  format:{
    $fieldFormat:[gcg 
      eval:'$SeqPrint:[format:gcg s:$SeqGetFt:[$token db:embl]]'
    ]
    $fieldFormat:[location 
      eval:'$Print:$token'
    ]
    $fieldFormat:[fasta 
      eval:'$SeqPrint:[format:fasta s:$SeqGetFt:[$token db:embl]]'
    ]
    $fieldFormat:[plain
      eval:'$SeqPrint:[format:plain s:$SeqGetFt:[$token db:embl]]'
    ]
    $fieldFormat:[pir 
      eval:'$SeqPrint:[format:pir s:$SeqGetFt:[$token db:embl]]'
    ]
    $fieldFormat:[embl 
      eval:'$SeqPrint:[format:pir s:$SeqGetFt:[$token db:embl]]'
    ]
  }
]
DF_ProtLocation:$srsfield:[Sequence short:seq
  format:{
    $fieldFormat:[gcg 
      eval:'$SeqPrint:[format:gcg s:$SeqGetFt:[$token db:swissprot]]'
    ]
    $fieldFormat:[location 
      eval:'$Print:$token'
    ]
    $fieldFormat:[fasta 
      eval:'$SeqPrint:[format:fasta s:$SeqGetFt:[$token db:swissprot]]'
    ]
    $fieldFormat:[plain
      eval:'$SeqPrint:[format:plain s:$SeqGetFt:[$token db:swissprot]]'
    ]
    $fieldFormat:[pir 
      eval:'$SeqPrint:[format:pir s:$SeqGetFt:[$token db:swissprot]]'
    ]
    $fieldFormat:[swissprot 
      eval:'$SeqPrint:[format:swissprot s:$SeqGetFt:[$token db:swissprot]]'
    ]
  }
]
DF_Sequence:$srsfield:[Sequence short:seq]
DF_Name:$srsfield:[Name short:nam group:@DF_ALL]
DF_ProtSequence:$srsfield:[Sequence short:seq 
  format:{
    $fieldFormat:[fasta eval:'$SeqPrint:[name:$field format:fasta]'] 
    $fieldFormat:[gcg   eval:'$SeqPrint:[format:gcg width:60]'] 
    $fieldFormat:[pir   eval:'$SeqPrint:[format:pir width:60]'] 
    $fieldFormat:[swiss 
      eval:'$SeqPrint:[format:swiss width:60]'] 
    $fieldFormat:[plain 
      eval:'$SeqPrint:[format:plain width:70]']
    $fieldFormat:[ProteinChart
      eval:'$SeqPrint:[format:msf width:50]']
#      eval:'$AppletPrint:[proteinChart]'
  }
]
DF_ALIGNMENT:$srsfield:[Alignment short:ali
  format:{
    $fieldFormat:[msf eval:'$SeqPrint:[$SeqGet:$field format:msf width:50]'] 
    $fieldFormat:[fasta 
      eval:'$SeqPrint:[$SeqGet:$field format:fasta width:60]']
    $fieldFormat:[pir eval:'$SeqPrint:[$SeqGet:$field format:pir width:70]']
    $fieldFormat:[swiss 
      eval:'$SeqPrint:[$SeqGet:$field format:swiss width:60]']
    $fieldFormat:[clustal 
      eval:'$SeqPrint:[$SeqGet:$field format:clustal width:80]']
  }
]

DF_Alignment:$srsfield:[Alignment short:ali]

# for hum mut dbs

DF_ProtChangePos:$srsfield:[ProteinChangePos short:acp]
DF_DnaChangePos:$srsfield:[DnaChangePos short:dcp]
DF_AaChange:$srsfield:[AaChange short:aac]
DF_NuclChange:$srsfield:[NucleotideChange short:nuc]
DF_CodonChange:$srsfield:[CodonChange short:coc]
DF_CodonNo:$srsfield:[CodonNo short:cdn]
DF_TranslEffect:$srsfield:[TranslationEffect short:tre]
DF_LabName:$srsfield:[LabName short:lan group:@DF_ALL]
DF_FuncStudies:$srsfield:[FunctionalStudies short:fst]
DF_AlleleN:$srsfield:[NAlleles short:nal]
DF_FamilyN:$srsfield:[NFamilies short:nfa]
DF_PatientN:$srsfield:[NPatients short:npa]
DF_PatientOrig:$srsfield:[PatientOrigin short:por group:@DF_ALL]



# ID types
SRSxSEQID:$idtype:['Seq-ID' size:4 fipBeg:0 fipLen:3 libIdBeg:3 libIdLen:1]
ENTRY_ID:$idtype:['Entry-ID' size:4 fipBeg:0 fipLen:3 libIdBeg:3 libIdLen:1] 
STRUCTENT_ID:$idtype:['3D-ID' size:4 fipBeg:0 fipLen:3 libIdBeg:3 libIdLen:1] 
SUBENTRY_ID:$idtype:['SubEntry-ID' size:6 subNBeg:0 subNLen:2 fipBeg:2 fipLen:3 
  libIdBeg:5 libIdLen:1]
SRSxLINKID:$idtype:["Link-ID" size:8 fipBeg:0 fipLen:3 libIdBeg:3 libIdLen:1]


# file types

GCGREF_FILE:$filetype:[text typename:ref maxline:512 fieldTokens:fields
   fipVar:entryFip]
GCGSEQ_FILE:$filetype:[seq typename:seq maxline:10000 fieldTokens:gcgseq
   fipVar:seqFip]
REF_FILE:$filetype:[text typename:ref maxline:2000 fipVar:entryFip]
DAT_FILE:$filetype:[text typename:dat maxline:1000 fipVar:entryFip]
SEQ_FILE:$filetype:[seq shareWith:@DAT_FILE fieldTokens:sequence fipVar:seqFip]
TXT_FILE:$filetype:[text typename:txt maxline:500]
TXTSEQ_FILE:$filetype:[seq shareWith:@TXT_FILE fieldTokens:sequence 
  fipVar:seqFip]
PIRREF_FILE:$filetype:[text typename:ref maxline:10000 fipVar:entryFip]
PIRSEQ_FILE:$filetype:[seq typename:seq maxline:10000 fieldTokens:sequence 
  fipVar:seqFip]


# links
$link:[fromName:subentry toName:entry type:parent 
  idtype1:@ENTRY_ID idtype2:@SUBENTRY_ID]
    
$link:[fromName:subentry toName:parent type:parent
  idtype1:@ENTRY_ID idtype2:@SUBENTRY_ID]

# subentry types
#Feature_SubEntry:$subentry:[fields:{@DF_ID @DF_ACCNO @DF_FEATURE}]
#Chain_SubEntry:$subentry:[fields:{@DF_ID @DF_HEADER @DF_SEQUENCE}] 


# data types and applications

DNASEQ_DATA:$dataType:[DNASequence]
PROTSEQ_DATA:$dataType:[ProteinSequence 
  applications:{@BLAST_APP @SW_APP @FASTA_APP @CLUSTALW_APP}
]
fromName:subentry toName:ensrs/icarus/db/subtilist.i
#
#    $RCSfile: subtilist.i,v $
#    $Revision: 1.1 $
#    $Date: 1997/03/03 18:36:31 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

SUBTILIST_DB:$library:[SUBTILIST group:@SEQUENCE_LIBS 
  subentries:@SubtilistFeatures_DB
  format:@SUBTILIST_FORMAT cachesize:2000 maxNameLen:12 files:{
    $file:SLR12_embl
  }
]

SUBTILIST_FORMAT:$libformat:[syntax:@SUBTILIST_SYNTAX contains:@DNASEQ_DATA
  tableFormat:left fileType:{@TXT_FILE @TXTSEQ_FILE}
  fields:{
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:@DF_ALL
    $field:[@DF_Accession code:acc index:str indexToken:acc tableToken:acc]
    $field:[@DF_Division code:id index:str indexToken:div tableToken:div]
    $field:[@DF_Molecule code:id index:str indexToken:mol tableToken:mol]
    $field:[@DF_Description code:des index:str indexToken:des
      tableToken:'clFields|des' tableFormat:listing]
    $field:[@DF_Keywords code:key index:str indexToken:key]
    $field:[@DF_Organism code:org index:str indexToken:org]
    $field:[@DF_Authors code:ra index:str indexToken:authors]
    $field:[@DF_Title code:rt index:str indexToken:ttl
      tableToken:'clFields|rt']
    $field:[@DF_Citation code:rl index:str indexToken:cit 
      tableToken:'clFields|rl']
    $field:[@DF_Date code:date index:int indexToken:date 
      tableToken:t_date]
    $field:[@DF_SeqLength code:sq  index:int indexToken:seqLen 
      tableToken:seqLen tableFormat:right]
    $field:[@DF_LINK code:dr]
    SUBTILISTSeq:$field:[@DF_DNASequence token:sequence format:embl] 

    $field:[@DF_HeaderField name:'Feature Table Fields']
    $field:[@DF_FtKey code:ft index:str indexToken:ftKey 
      indexId:@SUBENTRY_ID tableToken:ftKey tableFormat:left]
    $field:[@DF_FtQualifier code:ft index:str indexToken:ftQual
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtAccession code:ft index:str indexToken:acnum
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtDescription code:ft index:str indexToken:ftDes 
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtGenetMapPos code:ft index:int indexToken:genetmap
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtPhysMapPos code:ft index:int indexToken:physmap
      indexId:@SUBENTRY_ID]
  }
]


DF_FtGenetMapPos:$srsfield:[GeneticMapPos short:gmp]
DF_FtPhysMapPos:$srsfield:[PhysicalMapPos short:pmp]
DF_FtAccession:$srsfield:[FtAccession short:fac]

SUBTILIST_SYNTAX:$syntax:[file:"SRSDB:subtilist.is" ignore:" \t"]
$syntax:[name:ftseq file:"SRSDB:ftseq.is" ignore:" \t\n"]


$link:[@SUBTILIST_DB to:@?EMBL_DB  toField:@DF_Accession token:embl]
$link:[@SUBTILIST_DB to:@?SWISSPROT_DB toField:@DF_Accession 
  token:'link|swiss']


SubtilistFeatures_DB:$library:[SUBTILIST_features 
  format:@SubtilistFeature_Format]
SubtilistFeature_Format:$libformat:[syntax:@SUBTILIST_SYNTAX
  tableFormat:left
  fields:{
    $field:[@DF_ID token:ftId]
    $field:[@DF_FtKey token:ft tableToken:'t_ft|key']
    $field:[@DF_FtQualifier token:ft tableToken:'t_ft|qual']
    $field:[@DF_PID token:ft tableToken:'t_ft|db_xref']
    $field:[@DF_FtDescription token:ft tableToken:'t_ft|note']
    $field:[@DF_FtGene token:ft tableToken:'t_ft|gene']
    $field:[@DF_FtProduct token:ft tableToken:'t_ft|product']
    $field:[@DF_FtPhysMapPos token:ft tableToken:'t_ft|physmap']
    $field:[@DF_FtGenetMapPos token:ft tableToken:'t_ft|genetmap']
    $field:[@DF_DNALocation token:ftLocat parent:@SUBTILISTSeq
      tableFormat:listing]
  }
]

_FtQualifier token:ft tableToken:'t_ft|qual']
    $fsrs/icarus/db/subtilist.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: subtilist.is,v $
#    $Revision: 1.1 $
#    $Date: 1997/03/03 18:36:32 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  ID:id	     OG:org	  KW:key   RN:rn  '//':sep
  AC:acc     OC:org       RP:rp    RT:rt  FH: fh
  DT:date    OS:org	  SQ:sq    RC:rc  PK: pk
  DE:des     CC:cmnt	  RL:rl    RA:ra  DB: db
             DR:link	  RX:rx    XX:sep PG: pg
}

$rules={
  entry:     ~ {$In:[file:text] $Out  pre $Skip:0}
               ('ID  ' {$not} ln?)*
               (/ID +([A-Z0-9_]+)/{$entryFip=$Fip $Wrt $entryName=$1} ln {$App}
                (/(  |ID|>>)/ {$Not} ln {$App})+ )? ~

  # extracting data fields
  fields:    ~ {$In:entry $Out $Skip:1} 
               (ftln |
               /../ { if:$Ct==$prev $App else $Wrt:$fn.$Ct
                       if:$fn.$Ct=="" $dp:"+++ unknown: $Ct in $entryName +++"
                       $prev=$Ct
                    } ln {$App})+ ~
  ftln:      ~ {$Wrt:ft} 'FT' ln ('FT     ' ln)* ~
  clFields:  ~ {$In:fields $Out $Skip:1}
               /.. */ ln {$Wrt:$Itc} (/.. */ ln {$App})* ~

  # parsing the sequence part from separate stream
  gcgseq:    ~ { $In:[file:seq] $Out $SeqMake:$s}
               '>>>>' {$seqFip=$Fip} 
               (/[A-Z0-9]+/ {$Wrt:[s:$Ct] $s=$SeqNew:$Ct} 
               seq | /[A-Z0-9]+_0/ seq (/>>>>[A-Z0-9]+_[1-9]+/ 
               {$SeqTrunc:[$s len:10000]} seq)+) ~ 
  seq:       ~ (/.*2BIT *Len:/ /[0-9]+/ {$len=$Ct} ln ln 
	       {$SeqGet2Bit:[$s file:$File len:$len]} ('>>>>'{$Not} ln)*|
               /.*ASCII/ ln ln ('>>>>' {$Not} /.*/ {$SeqApp:[$s s:$Ct]})+) ~

  sequence:  ~ {$In:[file:seq share:text] $Out 
                pre {$s=$SeqNew:$entryName $seqFip=$Fip} 
                $Wrt:[s:$entryName] $SeqMake:$s} 
               ('ID' {$Not} ln {$SeqApp:[$s s:$Ct]})* ~

  # for indexing
  i_id:      ~ {$In:[entry] $Out:id} /ID +/ name {$Wrt} ~
  i_div:     ~ {$In:[fields c:id] $Out:div}
                /ID +/ name  /[^;]+/ ';' /[^;]+/ ';' name {$Wrt} ~
  i_mol:     ~ {$In:[fields c:id] $Out:mol} 
               /ID +/ name  /[^;]+/ ';' /[^;]+/  {$Wrt} ~
  i_acc:     ~ {$In:[fields c:acc] $Out:acc} ('AC' (name {$Wrt} ';')+)+  ~
  i_dates:   ~ { $In:[fields c:date] $Out:date 
                 init $month={JAN:1 FEB:2 MAR:3 APR:4 MAY:5 JUN:6 JUL:7 AUG:8 
                              SEP:9 OCT:10 NOV:11 DEC:12}
               }
               /.* ([0-9]+)-([A-Z]+)-([0-9]+)[^\n]+Cre/ 
               {$Wrt:[credate s:($1 + $month.$2*100 + $3*10000)]} ~
  des:       ~ {$In:[fields c:des] $Out} 
               ('DE' (/\\(EC *([0-9]+\\.[0-9]+\\.[0-9]+\\.[0-9]+)/
               {$Wrt:[s:$1]}| word{$Wrt} | sp)+ ln)+ ~ 
  org:       ~ {$In:[fields c:org] $Out} 
               ('OC' (/[^;.\n]+/ {$Wrt} | /[^\n]/)*)+ |
                'OS' /[^(\n]+/ {$Wrt:[s:$Trim:$Ct]} 
                ('(' (/[^ \n)]+/ | /[^)]/)+)? |
                'OG'  /[^\n;.]+/ {$Wrt} ~
  key:       ~ {$In:[fields c:key] $Out} 
               ('KW' (/[^\n;.]+/ {$Wrt} | /[^\n]/)+)+ ~ 
  authors:   ~ {$In:[fields c:ra] $Out}
               (/RA/ (/([^.,\n]+) +([^,;\n]+)/ {$Uniq:[s:"$1,$2"]} /[,;]/)*
               ln)* ~
  ttl:       ~ {$In:[fields c:rt] $Out} (tag (word {$Wrt} | sp)* ln)+ ~ 
  cit:       ~ {$In:[fields c:rl] $Out} 
               tag / *([^\n]+) ([0-9]+):([0-9]+)-[0-9]+\\(([0-9]+)\\)/?


               {$Uniq:[jnl s:$Trim:$1] $Uniq:[vol s:$2] $Uniq:[page s:"$3-"] 
               $Uniq:[year s:$4]} ~
  accKey:    ~ {$In:[fields c:acc] $Out} 'AC' /[A-Z]+/ {$Wrt} ~
  dbOri:     ~ {$In:[fields c:acc] $Out
                 init { $dbOriN={
                         A:1 F:1 V:1 X:1 Y:1 Z:1
                         AA:2 AC:2 AD:2 B:2 G:2 H:2 I:2 J:2 K:2 
                         L:2 M:2 N:2 R:2 S:2 T:2 U:2 W:2 
                         AB:3 C:3 D:3 E:3}
                       $dbName={1:EMBL 2:GenBank 3:DDBJ}
                 }
               } 
               'AC' /[A-Z]+/ {$Wrt:[s:$dbName.$dbOriN.$Ct]} ~
  i_seqLen:  ~ {$In:[fields c:sq] $Out:seqLen}
               'SQ   Sequence' /[0-9]+/ {$Wrt} ~
  embl:      ~ {$In:[fields c:des] $Out}
               (/.. +[A-Z0-9]+ +\\(/ name {$Wrt} ln | ln)+ ~
  link:      ~ {$In:[fields c:link] $Out} 
               (/.. +SWISS-PROT;/ name {$Wrt:swiss} ln)+ ~

  # indexing features
  ftWord:    ~ /[^" ,;:()\n.-]+/ ~ #"
  ftSep:     ~ /[ ,;.:()-]+/ ~
  ftKey:     ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               'FT' /[^ ]+/ {$Wrt:[n:$ftN]} ~
  ftQual:    ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               /[^\/]+/ 
               (/\/([a-zA-Z0-9_]+)/ {$Wrt:[s:$1 n:$ftN]} (/=[a-zA-Z0-9_]+/ |
               /="[^"]+"/)? /[^\/]+/)* ~ #"
  ftDes:     ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
             (/[^\/]+\// (/[^\/]+\/(product|note|gene|alt_name|description)="/ 
                ('\nFT' | /NCBI gi: *[0-9]+/ | 
                 ftWord {$Uniq:[n:$ftN]} | ftSep)+)?)* ~
  acnum:     ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               /.+\/acnum="([0-9A-Z]+)"/ {$Wrt:[n:$ftN s:$1]} ~
  physmap:   ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               /.+\/physical_map=([0-9]+)/ {$Wrt:[n:$ftN s:$1]} ~
  genetmap:  ~ {$In:[fields c:ft count:ft var:$ftN] $Out}
               /.+\/genetic_map=([0-9]+)/ {$Wrt:[n:$ftN s:$1]} ~

  # displaying features
  ftClean:   ~ {$In:[fields c:ft count:ft var:$ftN select:$subEntryN] $Out } 
               'FT' ln {$Wrt} ('FT' ln {$App})* ~
  ftLoc:     ~ {$In:ftClean $Out} /[^ ]+/ /[^\/]+/ {$Wrt} ~
  ft:        ~ {$In:[fields c:ft count:ft var:$ftN select:$subEntryN] $Out}
               /.*/ {$Wrt} ~
  ftId:      ~ {$In:[fields c:id] $Out} 
               /.. *([A-Z0-9_]+)/{$Wrt:[s:"ID   $1\_$subEntryN;  parent: $1"]}~
  h_ftId:    ~ {$In:[ftId t:html]} /.*parent: */ 
               /[A-Z0-9_]+/ {$Rep:{$ParStr:subtilistR $Ct $Ct}} ~
  t_ft:      ~ {$In:ftClean $Out} /(<A HREF)?[^ ]+/ {$Wrt:key} 
               /[^\/]+/ t_qual* ~
  t_qual:    ~ /[ \n]*\/([^ \n=]+)/ {$qn=$1 $Uniq:[qual s:$1]} 
               qualval? {$Wrt:[$qn s:$qv]} ~
  qualval:   ~ {pre $qv=""} /=([a-zA-Z0-9_]+)/ {$qv=$1} | 
               /="([^"]+)"/ {$qv=$1} | x{$qv='+'} ~

  # extracting feature sequences"

  ftCleanIter: ~ {$In:[fields c:ft] $Out } 
               'FT' ln {$Wrt} ('FT' ln {$App})* ~
  ftLocat:    ~ {$In:ftClean $Out init {$SdbFunctions}}
               /(<A HREF)?[^ ]+/ /[^\/]+/ {$Wrt} ~
               
  # table display
  t_date:    ~ {$In:[fields c:date] $Out} tag /[0-9A-Z-]+/ {$Wrt} ~

  # printing in HTML format
  h_ft:      ~ {$In:[fields c:ft t:html count:ft var:$ftN]} 
               'FT' /[^ ]+/ {$Rep:{$ParStr:subtilistFeatR 
               $entryName $ftN $Ct}} ~
  h_ftswiss: ~ {$In:[fields c:ft t:html count:ft var:$ftN]} 
               /.+SWISS-PROT:/ name {$Rep:{$ParStr:swissR $Ct $Ct}} ~
  h_des:     ~ {$In:[fields c:des t:html]} 
               (/.. +[A-Z0-9]+ +\\(/ name {$Rep:{$ParStr:emblR $Ct $Ct}} ln |
               ln)+ ~
  h_id:      ~ {$In:[fields c:id t:html]} /../ name {$entryName=$Ct} ~
  h_rx:      ~ {$In:[fields c:rx t:html]}
               /../ 'MEDLINE;' /[0-9]+/ {$Rep:{$ParStr:medlineR $Ct $Ct}} ~
  htmlTag:   ~ /<[^<>]*>/ ~
  h_links:   ~ {$In:[fields c:link t:html] 
                init{$hl={
                       'SWISS-PROT':                    swissR
                       DICTYDB:   dictydbR   GCRDB:     gcrdbR
                       MAIZEDB:   maizedbR   WORMPEP:   wormpepR
                       LISTA:     listaR  
                       PIR:       pirR       YEPD:      yepdR        
                       SGD:       sgdR       STYGENE:   stygeneR     
                       HIV:       hivR         
                       ECOGENE:   ecogeneR   ECO2DBASE: eco2dbaseR   
                       MIM:       mimR       SUBTILIST: subtilistR   
                       FLYBASE:   flybaseR     
                       TRANSFAC:  transfacR  REBASE:    rebaseR
                     } 
                    } 
               }
               (/DR/ dbName {$db=$Ct} ';' 
                accno {$Rep:{$ParStr:$hl.$db $Ct $Ct}} ln)*
             ~
  # other stuff

  tag:       ~ /[A-Z][A-Z]/ ~
  word:      ~ /[^" ,;:()\/=\n.-]+/ ~
  sp:        ~ /[ ,;.:()\/=-]+/ ~
  lnCode:    ~ /\n[A-Z][A-Z]/ ~
  ln:        ~ /[^\n]*\n/ ~
  accno:     ~ /[A-Z0-9]+/ ~
  num:       ~ /(<|>)?[0-9?]+/ ~
  name:      ~ /[a-zA-Z0-9_-]+/ ~ 
  dbName:    ~ /[^;]+/ ~ 
}

if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/data/embl_dna/mam.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:acc print:0] 
    $JobTokens:[$job name:t_ft print:1]
    $JobNext:$job
    #$print:"-------->entry\n"
  }
}


  word:      ~ /[^" ,;:()\/=\n.-]+/ ~
  sp:        ~ /[ ,;.:()\/=-]+/ ~
  lnCode:    ~ /\n[A-Z][A-Z]/ ~
  ln:        ~ /[^\n]*\n/ ~
  accno:     ~ /[A-Z0-9]+/ ~
  num:       ~ /(<|>)?[0-9?]+/ ~
  name:      ~ /[a-zA-Z0-9_-]+/ ~ 
  dbName:    ~ /[^;]+/ ~ 
}

if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/data/embl_dna/mam.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:acc print:0] 
    $JobTokens:[$job namsrs/icarus/db/sw.i
#    $RCSfile: sw.i,v $
#    $Revision: 1.3 $
#    $Date: 1997/03/03 18:34:17 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


SW_DB:$library:[SW group:@APPLICATION_LIBS 
  comment:"" 
  format:@SW_FORMAT maxNameLen:40 ifiles:{"sw.i" "sw.is"}
  type:user
  files:{
    $file:tmp
  }
]

SW_FORMAT:$libformat:[fileType:@SW_FILE syntax:@SW_SYNTAX 
  fields:{
    $field:[@DF_ID code:title index:id indexToken:id]
    $field:[@DF_PercIdent code:scores index:real indexToken:percIdent
      tableToken:percIdent tableFormat:right]
    $field:[@DF_PercSim code:scores index:real indexToken:percSim
      tableToken:percIdent tableFormat:right]
#    $field:[@DF_QueryBeg code:tmatch 
#      tableToken:queryBeg tableFormat:right]
#    $field:[@DF_QueryEnd code:tmatch 
#      tableToken:queryEnd tableFormat:right]
    $field:[@DF_MatchLen code:tmatch index:int indexToken:length]
    $field:[@DF_Alignment code:tmatch tableToken:t_ali tableFormat:left]
    $field:[@DF_LINK index:link code:link indexToken:link]
  }
]

DF_PercSim:$srsfield:[PercentSimilarity short:psi]


SW_SYNTAX:$syntax:[file:"SRSDB:sw.is" ignore:" "]
SW_FILE:$filetype:[typename:sw maxline:500]

$link:[@SW_DB to:@?SWISSPROT_DB token:'link|swiss' toField:@DF_ID]




t]
#    $field:[@DF_QueryEnd code:tmatch 
#      tableToken:queryEnd tableFormat:right]
    $field:[@DF_MatchLen code:tmatch index:int indexToken:length]
    $field:[@srs/icarus/db/sw.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: sw.is,v $
#    $Revision: 1.4 $
#    $Date: 1997/03/03 18:34:18 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$rules={
  entry:    ~ {$In:[file:text] init{$count=0} $Out $count+=1 pre $Skip:0}
              (' to:' {$Not} ln)*
              ln {$entryFip=$Fip $Wrt} 
              (' to:' {$Not} appLn)+
            ~

  # data fields
  fields:   ~ {$In:entry $Out $Skip:0} 
              title comment scores ali ~
  title:    ~ {$Wrt:title} ln ~ 
  comment:  ~ {$Wrt:comment} (/ *Quality/ {$Not} ln)+ ~
  scores:   ~ {$Wrt:scores}  ln ln ln ~
  ali:      ~ {$Wrt:ali}     ln+ ~

  # indexing
  id:       ~ {$In:[fields c:title] $Out} 
              / *to: *([^ \n]+)/ {$Wrt:[s:"$count\_$1"]} ~
  quality:  ~ {$In:[fields c:scores] $Out} 
              /.*Quality: *([0-9.]+)/{$Wrt:[s:$1]} ~
  percSim:  ~ {$In:[fields c:scores] $Out} 
              /.*Similarity: *([0-9.]+)/{$Wrt:[s:$1]}~
  percIdent:~ {$In:[fields c:scores] $Out} 
              /.*Identity: *([0-9.]+)/{$Wrt:[s:$1]} ~
  length:   ~ {$In:[fields c:scores] $Out} /.*Length: *([0-9]+)/{$Wrt:[s:$1]} ~
  gaps:     ~ {$In:[fields c:scores] $Out} /.*Gaps: *([0-9]+)/{$Wrt:[s:$1]} ~
  link:     ~ {$Out $In:[fields c:title]} 
              / *to: *([^ \n]+)/ {$Wrt:[swiss s:$1]} ~ 

  # table display
  t_ali:    ~ {$Out $In:[fields c:ali]} /.+/ 
             {$Wrt:[s:"<font size=2><textarea rows=6 cols=70>$Ct</textarea>"]} 
            ~
  # html
  h_link:   ~ {$In:[fields c:title t:html]} / *to: */ 
              /[^ \n]+/ {$Rep:{$ParStr:swissidR $Ct $Ct}} ~ 

  # other  
  appLn:    ~ /[^\n]*\n/ {$App} ~
  ln:       ~ /[^\n]*\n/  ~
  name:     ~ /[a-zA-Z][a-zA-Z0-9]+/~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/opt/srs/srs5/tmp/1ujxx15V2BF/tmp.sw']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields code:ali print:0] 
    $JobTokens:[$job name:link print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}

:[fields c:title t:html]} / *to: */ 
              /[^ \n]+/ {$Rep:{$ParStr:swissidR $Ct $Ct}} ~ 

  # other  
  appLn:    ~ /[^\n]*\n/ {$App} ~
  ln:       ~ /[^\n]*\n/  ~
  name:     ~ /[a-zA-Z][a-zA-Z0-9]+/~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/opt/srs/srs5/tmp/1ujxx15V2BF/tmp.sw']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields code:ali print:0] 
    $JobTokens:[$job name:lisrs/icarus/db/swissprot.i
#
#    $RCSfile: swissprot.i,v $
#    $Revision: 1.16 $
#    $Date: 1997/03/12 19:06:41 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

SWISSPROT_DB:$library:[SWISSPROT group:@SEQUENCE_LIBS 
  subentries:@SwissprotFeatures_DB
  format:@SWISSPROT_FORMAT maxNameLen:20 files:{
    $file:swissprot #GCG format
#    $file:seq #orig format
  }
]
SWISSNEW_DB:$library:[SWISSNEW group:@SEQUENCE_LIBS 
  subentries:@?SwissnewFeatures_DB
  format:@SWISSPROT_FORMAT maxNameLen:20 files:{
    $file:swissnew
  }
]

SWISSPROT_FORMAT:$libformat:[contains:@PROTSEQ_DATA
  fileType:{@GCGREF_FILE @GCGSEQ_FILE} #GCG format
#  fileType:{@DAT_FILE @SEQ_FILE} #orig format
  syntax:@SWISSPROT_SYNTAX tableFormat:left fields:{
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:@DF_ALL
    $field:[@DF_Accession code:acc index:str indexToken:acc]
    $field:[@DF_Description code:des index:str indexToken:des
      tableToken:'clFields|des']
    $field:[@DF_GeneName code:gene index:str indexToken:gene]
    $field:[@DF_Date code:date index:int indexToken:date
      tableToken:t_date]
    $field:[@DF_Organism code:{org tax} index:str indexToken:org]
    $field:[@DF_Organelle code:organ index:str indexToken:organ]
    $field:[@DF_Authors code:refaut index:str indexToken:authors]
    $field:[@DF_Citation code:rl index:str indexToken:cit 
      tableToken:'clFields|rl']
    $field:[@DF_LINK index:link code:link indexToken:link]
    $field:[@DF_SeqLength index:int indexToken:seqlen code:seqln]
    $field:[@DF_MolWeight index:int indexToken:molweight code:seqln]
    $field:[@DF_CommentType index:str indexToken:'cc|ttl' code:cc]
    $field:[@DF_Comment index:str indexToken:'cc|word' code:cc 
      tableToken:'t_comment']
    $field:[@DF_FtKey index:str indexToken:ftKey code:ft 
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtDescription index:str indexToken:ftDes code:ft 
      indexId:@SUBENTRY_ID]
    $field:[@DF_FtLength index:int indexToken:ftLen code:ft 
      indexId:@SUBENTRY_ID]
#    SwissSeq:$field:[@DF_ProtSequence token:'sequence' format:swiss] #orig format
    SwissSeq:$field:[@DF_ProtSequence token:gcgseq format:swiss tableFormat:left] #GCG format
  }
]

SWISSPROT_SYNTAX:$syntax:[file:"SRSDB:swissprot.is" ignore:" \t"]

$link:[@SWISSPROT_DB to:@?GENBANK_DB token: 'link|EMBL' toField:@DF_Accession]
$link:[@SWISSPROT_DB to:@?EMBL_DB token:'link|EMBL' toField:@DF_Accession]
$link:[@SWISSPROT_DB to:@?PIR_DB token:'link|PIR' toField:@DF_Accession]
$link:[@SWISSPROT_DB to:@?PDB_DB token:'link|PDB'toField:@DF_ID]
$link:[@SWISSPROT_DB to:@?REBASE_DB toField:@DF_ID]
$link:[@SWISSPROT_DB to:@?OMIM_DB token:'link|MIM' toField:@DF_ID]
$link:[@SWISSPROT_DB to:@?MEDLINE_DB toField:@DF_ID]
$link:[@SWISSPROT_DB to:@?ENZYME_DB fromField:@DF_Description toField:@DF_ID]

SwissprotFeatures_DB:$library:[SWISSPROT_features 
  format:@SwissprotFeature_Format
]

SwissprotFeature_Format:$libformat:[syntax:@SWISSPROT_SYNTAX
  contains:@PROTSEQ_DATA tableFormat:left fields:{
    $field:[@DF_ID token:ftId]
    $field:[@DF_FtKey token:ft tableToken:'t_ft|key']
    $field:[@DF_FtLength token:ft tableToken:'t_ft|len']
    $field:[@DF_FtDescription token:ft tableToken:'t_ft|des']
    $field:[@DF_ProtLocation token:ftLoc parent:@SwissSeq]
  }
]


omField:@DF_Description toField:@DF_ID]

SwissprotFeatures_DB:$library:[SWISSPROT_features 
  format:@SwissprotFeature_Format
]

SwissprotFeature_Format:$libformat:[syntax:@SWISSPROT_SYNTAX
  csrs/icarus/db/swissprot.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: swissprot.is,v $
#    $Revision: 1.16 $
#    $Date: 1997/03/13 19:39:52 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  ID:id	     OG:organ	  KW:key      RN:refn
  AC:acc     OC:tax       RP:refp
  DT:date    OS:org	  SQ:seqln    RC:refc
  DE:des     CC:cc	  RL:rl       RA:refaut
  GN:gene    DR:link	  RM:refm     RX:refx
}

$rules={
  entry:     ~ {$In:[file:text] $Out pre $Skip:0}
               ('ID  ' {$not} lnT)*
               (/ID +([A-Z0-9_]+)/ {$entryFip=$Fip $Wrt $entryName=$1} 
                lnT {$App}
               (/(  |ID|>>)/ {$Not} lnT {$App})+ )? ~
  lnT:       ~ /[^\n]+\n?/ ~ # line terminator may be missing if truncated

  sequence:  ~ {$In:[file:seq share:text] $Out 
                pre {$s=$SeqNew:$entryName $seqFip=$Fip}
                $Wrt:[s:$entryName] $SeqMake:$s} 
               ('ID' {$Not} ln {$SeqApp:[$s s:$Ct]})* ~
  gcgseq:    ~ {$In:[file:seq] $Out pre {$seqFip=$Fip} $SeqMake:$s} 
               '>>>>' name {$Wrt:[s:$Ct] $s=$SeqNew:$Ct} ln
               ln ('>>>>' {$Not} ln {$SeqApp:[$s s:$Ct]})+ ~

  # extracting data fields
  fields:    ~ {$In:entry $Out $Skip:1} 
               (ftln | /../ 
                { $t=$Ct
                  if:$t==$prev $App else $Wrt:$fn.$t
                    if:$fn.$t=="" $dp:"+++ unknown: $t in $entryName +++"
                      $prev=$t
                } ln {$App})+ ~
  ftln:      ~ {$Wrt:ft} 'FT' ln ('FT     ' ln)* ~
  clFields:  ~ {$In:fields $Out $Skip:1}
               /.. */ ln {$Wrt:$Itc} (/.. */ ln {$App})* ~

  # for indexing
  date:      ~ {$In:[fields c:date] $Out init $month={JAN:1 FEB:2 MAR:3 
                  APR:4 MAY:5 JUN:6 JUL:7 AUG:8 SEP:9 OCT:10 NOV:11 DEC:12}}
               /.* ([0-9]+)-([A-Z]+)-([0-9]+).+CRE/ 
               {$Wrt:[credate s:($1 + $month.$2*100 + $3*10000)]} ~
  id:        ~ {$In:[entry] $Out} /ID +([a-zA-Z0-9_]+)/ {$Wrt:[s:$1]} ~
  acc:       ~ {$In:[clFields c:acc] $Out} (/[a-zA-Z0-9_]+/ {$Wrt} | ';')+ ~
  des:       ~ {$In:[clFields c:des] $Out} 
               (/[a-zA-Z0-9_]+/ {$Uniq} | 
                /\\(EC *([0-9]+\\.[0-9]+\\.[0-9]+\\.[0-9]+)/ {$Uniq:[s:$1]}|
                /[^a-aA-Z0-9(_\n]+/ | /[^\n]/)* ~
  gene:      ~ {$In:[clFields c:gene] $Out} 
               (/[^ .\n]+/ {$Wrt} ('AND' | 'OR')?)* ~
  authors:   ~ {$In:[clFields c:refaut] $Out}
               (/([^.,\n]+) +([^,;\n]+)/ {$Uniq:[s:"$1,$2"]} /[,;]/)* ~
  seqlen:    ~ {$In:[fields c:seqln] $Out} /.* ([0-9]+) * AA/ {$Wrt:[s:$1]}~
  molweight: ~ {$In:[fields c:seqln] $Out} /.* ([0-9]+) * MW/ {$Wrt:[s:$1]}~
  keywords:  ~ {$In:[clFields c:key] $Out} (/[^;.]+/ {$Wrt} | /[.;]+/)* ~
  org:       ~ {$In:[clFields c:{org tax}] $Out}
               (/(AND *)?([^;,.\n(]+[^ (;,.\n])/ {$Wrt:[s:$2]} | 
                /\\(([^)]+)\\)/ {$Wrt:[s:$1]} | /[,;.]/)* ~
  organ:     ~ {$In:[clFields c:organ] $Out} 
               (/(AND *)?([^,.\n]+)/ {$Wrt:[s:$2]} | /,./)* ~
  link:      ~ {$In:[clFields c:link] $Out} 
               (dbName {$db=$Ct} ';' accno {$Wrt:$db} ln )* ~
  cit:       ~ {$In:[fields c:rl] $Out} 
               /.. *([^\n]+) ([0-9]+):([0-9]+)-[0-9]+\\(([0-9]+)\\)/?
               {$Uniq:[jnl s:$Trim:$1] $Uniq:[vol s:$2] $Uniq:[page s:"$3-"] 
               $Uniq:[year s:$4]} ~
  cc:        ~ {$In:[clFields c:cc] $Out} 
               (/-!- *([^: \n]+( [^: \n]+)?):/ {$Wrt:[ttl s:$1]} |
                /[A-Z0-9_]+/{$Uniq:word} | /./)* ~

  # indexing features
  ftKey:     ~ {$In:[clFields c:ft count:ft var:$ftN] $Out}
               ftK {$Wrt:[n:$ftN]} ~
  ftK:       ~ /[A-Z0-9_]+/ ~
  ftDes:     ~ {$In:[clFields c:ft count:ft var:$ftN] $Out}
               ftK num num 
	       (/[A-Za-z0-9_]+/ {$Uniq:[n:$ftN]} | /[^A-Za-z0-9_]+/)* ~
  ftLen:     ~ {$In:[clFields c:ft count:ft var:$ftN] $Out}
               ftK ftl {if:$ftN>0 $Wrt:[n:$ftN s:$len]} ~
  ftl:       ~ /([0-9]+) +([0-9]+)/ {$len = $2-$1+1} | num {$len=0} num ~

  # display features
  ftId:      ~ {$In:[fields c:id] $Out}
               /.. *([A-Z0-9_]+)/{$Wrt:[s:"ID   $1\_$subEntryN;  parent: $1"]}~
  ft:        ~ {$In:[fields c:ft count:ft var:$ftN select:$subEntryN] $Out}
               /.*/ {$Wrt} ~
  ftLoc:     ~ {$In:ft $Out $Skip:1 init $SdbFunctions}
               'FT' /[^ \n]+/ ftl {$Wrt} ~
  t_ft:      ~ {$In:ft $Out $Skip:1}
               'FT' /[^ \n]+/ {$Wrt:key} 
               ftl {$Wrt:loc if:$len>0 $Wrt:[len s:$len]} 
               ln? {$Wrt:des} ('FT' ln {$App})* ~
  h_ftId:    ~ {$In:[ftId t:html]} /.*parent: */ 
               /[A-Z0-9_]+/ {$Rep:{$ParStr:swissidR $Ct $Ct}} ~

  # table view
  t_date:    ~ {$In:[fields c:date] $Out} 
               /.* ([0-9]+-[A-Z]+-[0-9]+).+CRE/ {$Wrt:[s:$1]} ~
  t_comment: ~ {$In:[clFields c:cc] $Out} /.+/ {$Wrt} ~

  # printing in HTML format
#  h_head:    ~ {$In:[fields c:_head t:html] pre $Print:$ParStr:headR} /./ ~
  h_id:      ~ {$In:[fields c:id t:html]} /../ name {$entryName=$Ct} ~
  h_refx:    ~ {$In:[fields c:refx t:html]}
               /../ 'MEDLINE;' /[0-9]+/ {$Rep:{$ParStr:medlineR $Ct $Ct}} ~
  h_des:     ~ {$In:[fields c:des t:html]}
               (/(\\(EC )([0-9.-]+)/ {$Rep:{"$1($ParStr:enzymeR)" $2 $2}} | 
                /[^ ]+/ )* ~ 
#  h_features:~ {$In:[fields c:ft t:html count:ft var:$ftN]} 
#               ('FT   ' /[A-Z0-9_]+/ 
#               {$Rep:{$ParStr:"($libName)FtR" $entryName $ftN $Ct}} )? ~
  htmlTag:   ~ /<[^<>]*>/ ~
  h_links:   ~ {$In:[fields c:link t:html] init $hl={
                  'AARHUS/GHENT-2DPAGE':           aarhusR
                  'SWISS-2DPAGE':                  swiss2dpageR
                  DICTYDB:   dictydbR   GCRDB:     gcrdbR
                  MAIZEDB:   maizedbR   WORMPEP:   ormpepR
                  ENZYME:    enzymeR    LISTA:     listaR  
                  PIR:       pirR       YEPD:      yepdR        
                  EMBL:      emblR      SGD:        sgdR       
                  HSSP:      hsspR      STYGENE:   stygeneR     
                  PROSITE:   prositeR   HIV:       hivR         
                  ECOGENE:   ecogeneR   ECO2DBASE: eco2dbaseR   
                  MIM:       mimR       SUBTILIST: subtilistR   
                  PDB:       pdbR       FLYBASE:   flybaseR     
                  TRANSFAC:  transfacR  REBASE:    rebaseR
                }} (/DR/ dbName {$db=$Ct} ';' 
                accno {$Rep:{$ParStr:$hl.$db $Ct $Ct}} ln)* ~
  h_comment: ~ {$In:[t_comment t:html]} 
               x{$Rep:'<DL>'}
               (/-!- *([^: \n]+( [^: \n]+)?):/ {$Rep:"<DT><B>$1</B><DD>"} |
                /[A-Z0-9_]+/ | /./)* 
               x{$Rep:'</DL>'} ~

  # other stuff
  ln:        ~ /[^\n]*\n/ ~
  accno:     ~ /[A-Z0-9]+/ ~
  num:       ~ /(<|>)?[0-9?]+/ ~
  name:      ~ /[a-zA-Z0-9_-]+/ ~ 
  dbName:    ~ /[^;]+/ ~ 
}

# debugging 
$subEntryN=3
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" \n" 
    fileName:'/data/gcg/gcgswissprot/swissprot.ref']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}


srs/icarus/db/swissprot.it
#    
#    $RCSfile: swissprot.it,v $
#    $Revision: 1.4 $
#    $Date: 1997/03/19 20:30:39 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |The SWISS-PROT Protein Sequence Database is a database of protein
    |sequences produced collaboratively by Amos Bairoch (University of
    |Geneva) and the EMBL Data Library. The data in Swiss-Prot are derived
    |from translations of DNA sequences from the EMBL Nucleotide Sequence
    |Database, adapted from the Protein Identification Resource (PIR)
    |collection, extracted from the literature and directly submitted by
    |researchers. It contains high-quality annotation,is non-redundant,
    |and cross-referenced to several other databases, notably the EMBL
    |nucleotide sequence database, PROSITE pattern database and PDB.
    |SWISS-PROT is a curated protein sequence database which strives to
    |provide a high level of annotation (such as the description of the
    |function of a protein, its domain structure, post-translational
    |modifications, variants, etc), a minimal level of redundancy and a
    |high level of integration with other databases. Recent developments
    |of the database include: an increase in the number and scope of model
    |organisms; cross-references to seven additional databases; a variety
    |of new documentation files; the creation of TREMBL, an unannotated
    |supplement to SWISS-PROT. This supplement consists of entries in
    |SWISS-PROT-like format derived from the translation of all coding
    |sequences (CDS) in the EMBL nucleotide sequence database, except CDS
    |already included in SWISS-PROT.
  www:
    |<A HREF="http://expasy.hcuge.ch/sprot/sprot-top.html">\
    |http://expasy.hcuge.ch/sprot/sprot-top.html</A>
  citation:
    |Amos Bairoch and Rolf Apweiler "The SWISS-PROT protein sequence
    |data bank and its new supplement TREMBL", Nucleic Acids Res.
    |24:(21-25), 1996
  ftp:'ftp.ebi.ac.uk'
  fields: {
     Features:
       |The FT (Feature Table) lines provide a precise but simple means for    
       |the annotation of the sequence data. The table describes regions       
       |or sites of interest in the sequence. In general the feature table     
       |lists post- translational modifications, binding sites, enzyme active  
       |sites, local secondary structure or other characteristics reported in  
       |the cited references. Sequence conflicts between references are also   
       |included in the feature table. The feature table is updated when more  
       |becomes known about a given sequence.                                  
     FeatureLength:
       |Length of an amino acid sequence corresponed to some feature. The
       |length are defined by `FROM' and `TO' endpoint specifications. in
       |the Feature Table. entry. <p> <b>Note:</b> Ranges can be combined:
       |"300-!500 | !600-700" or "300-700 ! 500-600" retrieve the same set
       |of entries, namely all entries with feature lengths from 300 to 500,
       |excluding 500, plus lengths from 600 to 700 where the 600 is excluded.
     MolWeight:
       |Molecular  Weight (MW) is rounded to the nearest gram.
    }
  date:
    |25 Jul 1996
  signature:
    |Anatoly Ulyanov
}
 are defined by `FROM' and `TO' endpoint specifications. in
       |the Feature Table. entry. <p> <b>Note:</b> Ranges can be combined:
       |"300-!500 | !600-700" or "300-700 ! 500-600" retrieve the same srs/icarus/db/taxonomy.i
#    $RCSfile: taxonomy.i,v $
#    $Revision: 1.2 $
#    $Date: 1997/03/03 18:34:21 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


TAXONOMY_DB:$library:[TAXONOMY group:@SEQRELATED_LIBS 
  format:@TAXONOMY_FORMAT maxNameLen:10
  files:{
    $file:tax
  }
]

TAXONOMY_FORMAT:$libformat:[fileType:@DAT_FILE syntax:@TAXONOMY_SYNTAX 
  fields:{
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:[@DF_ParentId code:parentId index:link indexToken:'parentId|ga']
    $field:[@DF_Name code:name index:str indexToken:name]
  }
]

TAXONOMY_SYNTAX:$syntax:[file:"SRSDB:taxonomy.is"]

DF_ParentId:$srsfield:[ParentId short:pid]

TAX_LINK:$link:[@TAXONOMY_DB to:@TAXONOMY_DB token:'parentId|ga' toField:@DF_ID
  fromField:@DF_ParentId fromName:TAX_DOWN toName:TAX_UP]
$link:[@TAXONOMY_DB to:@TAXONOMY_DB toName:TAX_UP use:@TAX_LINK]
$link:[@TAXONOMY_DB to:@TAXONOMY_DB fromName:TAX_DOWN use:@TAX_LINK]
       
field:[@DF_ParentId code:parentId index:link indexToken:'parentId|ga']
    $field:[@DF_Name code:name index:str indexToken:name]
  }
]

TAXONOMY_SYNTAX:$syntax:[file:"SRSDB:taxonomy.is"]

DF_ParentId:$srsfield:[ParentId short:pid]

TAX_LINK:$link:[@TAXONOMY_DB to:@TAXONOMY_DB token:'parentId|ga' toField:@DF_ID
  fromField:@DF_ParentId fromName:TAX_DOWN toName:TAX_UP]
$link:[@TAXONOMY_DB to:@TAXONOMY_DB toName:TAX_UP use:@TAX_LINK]
$link:[@TAXONOMY_DB to:@TAXONOMY_DB fromName:TAX_DOWN srs/icarus/db/taxonomy.is


$rules={
  entry:      ~ {$In:[file:text] $Out} 
                ('ID' {$Not} ln)*
                ('ID   ' {$entryFip=$Fip $Wrt} ln {$App} 
                ('ID' {$Not} ln {$App})*)?
              ~
  fields:     ~ {$In:entry $Out} 
                f_id f_parentId f_taxLevel f_tlInd f_name ~
  f_id:       ~ {$Wrt:id} /ID.[^:]+:/ ln ~
  f_parentId: ~ {$Wrt:parentId} /Parent ID[^:]+:/ ln ~ 
  f_taxLevel: ~ {$Wrt:taxLevel} /Taxonom.[^:]+:/ ln ~
  f_tlInd:    ~ {$Wrt:tlInd} /TlInd[^:]+:/ ln ~
  f_name:     ~ {$Wrt:name} /Name[^:]+:/ ln ~

  # indexing
  id:         ~ {$In:[fields c:id] $Out} tag num {$Wrt} ~
  parentId:   ~ {$In:[fields c:parentId] $Out} tag num {$Wrt:ga} ~
  name:       ~ {$In:[fields c:name] $Out} tag str {$Wrt} ~


  tag:        ~ /[^:]+: */ ~
  ln:         ~ /[^\n]*\n/ ~
  num:        ~ /[-0-9]*/ ~
  str:        ~ /[^\n]+/ ~
}


Id: ~ {$Wrt:parentId} /Parent ID[^:]+:/ ln ~ 
  f_taxLevel: ~ {$Wrt:taxLevel} /Taxonom.[^:]+:/ ln ~
  f_tlInd:    ~ {$Wrt:tlInd} /TlInd[^:]+:/ lnsrs/icarus/db/template.it
#    
#    $RCSfile: template.it,v $
#    $Revision: 1.2 $
#    $Date: 1996/10/30 10:20:22 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |
  www:
    |
  ftp:
    |
  email:
    |
  fax:
    |
  contact:
    |
  address:
    |
  literature:
    |
  updates:
    |
  fields:{
  }  
}
[^:]+:/ ln ~
  f_tlInd:    ~ {$Wrt:tlInd} ¶ £¡ÜŽ¸/ lnsrs/icarus/db/tfcell.i
#    $RCSfile: tfcell.i,v $
#    $Revision: 1.4 $
#    $Date 1996/02/28
#
#    Author: Chenna Ramu
#

TFCELL_DB:$library:[TFCELL group:@TRANSFAC_LIBS
  comment:"The TRANSFAC Database by Edgar Wingender and Rainer Knueppel"
   format:@TFCELL_FORMAT maxNameLen:10 ifiles:{"tfcell.i" "tfcell.is"}
    files:{
       $file:cell
    }
]

TFCELL_FORMAT:$libformat:[fileType:@DAT_FILE syntax:@TFCELL_SYNTAX
  tableFormat:left fields:{
    $field:[@DF_ID code:ac index:id indexToken:ac]
    $field:[@DF_Date code:dt index:int indexToken:dt]
    $field:[@DF_Source code:so index:str indexToken:so]
    $field:[@DF_Organism code:os index:str indexToken:os]
    $field:[@DF_Description code:cd index:str indexToken:cd
      tableToken:'t_field|cd']
  }
]
TFCELL_SYNTAX:$syntax:[file:"SRSDB:tfcell.is" ignore:" "]

"}
    files:{
       $file:cell
    }
]

TFCELL_FORMAT:$libformat:[fileType:@DAT_FILE syntax:@TFCELL_SYNTAX
  tableFormat:left fields:{
    $field:[@DF_ID code:ac index:id indexToken:ac]
    $field:[@DF_Date code:dt insrs/icarus/db/tfcell.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: tfcell.is,v $
#    $Revision: 1.4 $
#    $Date: 1997/03/03 18:34:22 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$rules={
  entry:   ~ {$In:[file:text] $Out}
             ('AC' {$Not} ln)*
              ('AC  ' {pre {$entryFip=$Fip} $Wrt} ln {$App} 
              ('AC' {$Not} ln {$App})*)?
           ~
  # fields
  fields:  ~ {$In:entry $Out} f_ac f_xx f_dt f_xx  f_so f_xx 
                              f_os f_xx f_cd f_xx f_xx
           ~

  f_ac:    ~ {$Wrt:ac}   'AC  ' ln ~
  f_dt:    ~ {$Wrt:dt}  ('DT  ' ln)* ~
  f_so:    ~ {$Wrt:so}  ('SO  ' ln)* ~
  f_os:    ~ {$Wrt:os}  ('OS  ' ln)* ~
  f_cd:    ~ {$Wrt:cd}  ('CD  ' ln)* ~
  f_xx:    ~ {$Wrt:xx}  ('XX'  ln | '//' ln)? ~

  # indexing
  ac:   ~ {$In:[fields c:ac] $Out:ac} 'AC' /[0-9A-Za-z]+/ {$Wrt} ~
  dt:   ~ {$In:[fields c:dt] $Out:dt} 'DT' 
          /([0-9]+).([0-9]+).([0-9]+)/ {$Wrt:[s:($1+$2*100+"19$3"*10000)]} ~
  so:   ~ {$In:[fields c:so] $Out:so} 'SO' (sep | word {$Wrt})* ~
  os:   ~ {$In:[fields c:os] $Out:os} 'OS' (sep | word {$Wrt})* ~
  oc:   ~ {$In:[fields c:cd] $Out:cd} 'CD' (sep | word {$Wrt})* ~

  # table display
  t_field:~ {$In:[fields c:{cd}] $Out}
            tag ln {$Wrt:$Itc} (tag ln {$App})* ~


  # other stuff
  tag:     ~ /[^ \n][^ \n]/ ~
  ln:      ~ /[^\n]*\n/ ~
  word:    ~ /[a-zA-Z0-9_]+/ ~
  sep:     ~ /[^a-zA-Z0-9_]+/ ~
}

if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/data/transfac/cell.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:entry print:1] 
    $JobNext:$job
    $print:"===============> entry <==============\n"
  }
}




sep | word {$Wrt})* ~

  # table display
  t_field:~ {$In:[fields c:{cd}] $Out}
            tag ln {$Wrt:$Itc} (tag ln {$App})* ~


  # other stuff
  tag:     ~ /[^ \n][^ \n]/ ~
  ln:      ~ /[^\n]*\n/ ~
  word:    ~ /[a-zA-Z0-9_]+/ ~
  sep:     ~ /[^a-zA-Z0-9_]+/ ~
}

if:$TestMode {
  $job = $JobNew:[psrs/icarus/db/tfcell.it
#    
#    $RCSfile: tfcell.it,v $
#    $Revision: 1.3 $
#    $Date: 1996/10/10 16:47:13 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |This table gives short explanations of the cellular sources of proteins
    |that interact with the sites listed in the SITES table. Among them
    |may be defined cell lines, tissues / organs, even whole organisms, or
    |recombinant expression systems.
    |<p>
  www:
    |<A HREF="http://transfac.gbf-braunschweig.de/TRANSFAC/">\
    |http://transfac.gbf-braunschweig.de/TRANSFAC/</A>
  citation:
    |E. Wingender , P. Dietze , H. Karas and R. Knüppel,
    |"TRANSFAC: a database on transcription factors and their DNA binding sites"
    |Nucleic Acids Res.
    |24:(21-25), 1996
  fields:{
    Source:
      |The terminology of the factor sources (SO) corresponds to that used
      |in the SITES table (See TFSITE Source Field). Cell lines are given
      |with their most common name (e. g. , HeLa, 3T3), the most frequently
      |used tissues may be abbreviated (e.g., rl for rat liver), others are
      |explicitly mentioned. 
    Organism:
      |Recombinant materials are explained by the denotation rec([source
      |organism] - [expressing cell]). Occasionally, a viral expression system
      |is also indicated: rec(chick-baculovirus-Sf9).
    Description:
      |The field contains line cell description. Sometimes some characteristics
      |of cell matirial are inclided.
    }
  date:
    |25 Jul 1996
}
e most frequently
      |used tissues may be abbreviated (e.g., rl for rat liver), others are
      |explicitly mentioned. 
    Organism:
      |Recombinant materials are explained by the denotation rec([source
      |organism] - [expressing cell]). Occasionally, a viral expression system
      |is also indicated: rec(chick-baculovirus-Sf9).
    Description:
      |The field contains line cell description. Somsrs/icarus/db/tfclass.i
#    $RCSfile: tfclass.i,v $
#    $Revision: 1.5 $
#    $Date 1996/02/28
#
#    Author: Chenna Ramu
#

TFCLASS_DB:$library:[TFCLASS group:@TRANSFAC_LIBS
  comment:"The TRANSFAC Database by Edgar Wingender and Rainer Knueppel"
   format:@TFCLASS_FORMAT maxNameLen:10 ifiles:{"tfclass.i" "tfclass.is"}
    files:{
       $file:class
    }
]

TFCLASS_FORMAT:$libformat:[fileType:@DAT_FILE syntax:@TFCLASS_SYNTAX
  tableFormat:left fields:{
    $field:[@DF_Accession code:ac index:id indexToken:ac]
    $field:[@DF_ID code:sd index:str indexToken:id]
    $field:[@DF_Date code:dt index:int indexToken:date]
    $field:[@DF_CLASS code:cl index:str indexToken:class
      tableToken:'t_field|cl']
    $field:[@DF_Comment   code:cc index:str indexToken:cc
      tableToken:'t_field|cc']
  }
]

DF_CLASS:$srsfield:[Class short:cl]
DF_STRDES:$srsfield:[StrDescrip short:sd]
DF_COMM:$srsfield:[Comment short:cc]

TFCLASS_SYNTAX:$syntax:[file:"SRSDB:tfclass.is" ignore:" "]

$link:[@TFCLASS_DB to:@?PROSITE_DB token:'links|pr' toField:@DF_Accession]
$link:[@TFCLASS_DB to:@?TFFACTOR_DB token:'bflink' toField:@DF_Accession]


    $field:[@DF_CLASS code:cl index:str indexToken:class
      tableToken:'t_field|cl']
    $field:[@DF_Comment   code:cc index:str indexToken:cc
      tableToken:'t_field|cc']
  }
]

DF_CLASS:$srsfield:[Class short:cl]
DF_STRDES:$srsfield:[StrDescrip short:sd]
DF_COMM:$srsfield:[Comment short:cc]

TFCLASS_SYNTAX:$syntax:[file:"SRSDB:tfclass.is" ignore:" "]

$link:[@TFCLASS_DB to:@?PROSITE_DB token:'links|pr' toFielsrs/icarus/db/tfclass.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: tfclass.is,v $
#    $Revision: 1.4 $
#    $Date: 1997/03/03 18:34:23 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


$fn={
  ID: id   SD:sd   RN:rn
  AC: ac   CC:cc   RA:ra   XX:sp 
  DT: dt   BF:bf   RT:rt   '//':sp
  CL: cl   DR:dr   RL:rl     
}  
$rules={
  entry:    ~ {$In:[file:text] $Out pre $Skip:0}
              ('AC' {$Not} ln)*
               ('AC  ' {$entryFip=$Fip $Wrt} ln {$App} 
               ('AC' {$Not} ln {$App})+)?
            ~
  # fields
  fields:      ~ {$In:entry $Out $Skip:1}
                 (/../ { if:$Ct==$prev $App else $Wrt:$fn.$Ct
                         if:$fn.$Ct=="" $dp:"+++ unknown: $Ct +++"
                         $prev=$Ct
                       } 
                 ln {$App})+ ~

  # indexing
  id:       ~ {$In:[fields c:id] $Out} 'ID' /[0-9A-Za-z]+/ {$Wrt} ~
  ac:       ~ {$In:[fields c:ac] $Out} 'AC' /[0-9A-Za-z]+/ {$Wrt} ~
  sd:       ~ {$In:[fields c:sd] $Out} 'SD' /[0-9A-Za-z+_]+/ {$Wrt} ~
  date:     ~ {$In:[fields c:dt] $Out} 'DT' /([0-9]+).([0-9]+).([0-9]+)/ 
              {$Wrt:[s:($1+$2*100+"19$3"*10000)]} ~
  class:    ~ {$In:[fields c:cl] $Out} 'CL' (sep | word {$Uniq})* ~
  strDes:   ~ {$In:[fields c:sd] $Out} 'SD' (sep | word {$Uniq})* ~
  cc:       ~ {$In:[fields c:cc] $Out} 'CC' (sep | word {$Uniq})* ~

  links:    ~ {$In:[fields c:dr] $Out}
              (tag 'Prosite:' word {$Wrt:pr} ln)+ ~
  bflink:   ~ {$In:[fields c:bf] $Out} (tag word {$Wrt} ln)+ ~

  # table display
  t_field:  ~ {$In:[fields c:{cc cl}] $Out}
              tag ln {$Wrt:$Itc} (tag ln {$App})* ~
  

  # html display
  h_links:  ~ {$In:[fields c:dr t:html]}
              (tag word ':' word {$Rep:{$ParStr:prositeR $Ct $Ct}} ln)+ ~
  h_bf:     ~ {$In:[fields c:bf t:html]} 
              (tag word {$Rep:{$ParStr:tffactorR $Ct $Ct}} ln)+ ~

  # other things
  ln:      ~ /[^\n]*\n/ ~
  word:    ~ /[a-zA-Z0-9_]+/ ~
  tag:     ~ /[A-Z][A-Z]/ ~
  sep:     ~ /[^a-zA-Z0-9_]+/ ~
}

if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
           fileName:'/opt/srs/data/transfac/class.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:links print:1]
    $JobNext:$job
    $print:"===============> entry <==============\n"
  }
}




+ ~
  h_bf:     ~ {$In:[fields c:bf t:html]} 
              (tag word {$Rep:{$ParStr:tffactorR $Ct $Ct}} ln)+ ~

  # other things
  ln:      ~ /[^\n]*\n/ ~
  word:    ~ /[a-zA-Z0-9_]+/ ~
  tag:     srs/icarus/db/tfclass.it
#    
#    $RCSfile: tfclass.it,v $
#    $Revision: 1.3 $
#    $Date: 1996/10/10 16:47:13 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |This record briefly explains some of the main features of the
    |DNA- binding domains of 26 transcription factor classes. In those
    |cases where an amino acid consensus motif has been identified, the
    |corresponding accession number of the PROCLASS database (A. Bairoch) is
    |included.
  www:
    |<A HREF="http://transfac.gbf-braunschweig.de/TRANSFAC/">\
    |http://transfac.gbf-braunschweig.de/TRANSFAC/</A>
  citation:
    |E. Wingender , P. Dietze , H. Karas and R. Knüppel,
    |"TRANSFAC: a database on transcription factors and their DNA binding sites"
    |Nucleic Acids Res.
    |24:(21-25), 1996
  fields:{
    Class:
      |<b>List of avaliable classes:</b>
      |<UL>
      |<LI>Factor family with homology to the ets-protooncogenes
      |<LI>LIM domain
      |<LI>MCM1-agamous-deficiens-SRF
      |<LI>POU domain
      |<LI>Rel-related factor
      |<LI>TEA domain
      |<LI>basic region + helix-loop-helix motif
      |<LI>basic region + helix-loop-helix motif + leucine zipper
      |<LI>basic region + leucine zipper
      |<LI>fork head domain
      |<LI>helix-loop-helix motif
      |<LI>helix-loop-helix motif + leucine zipper
      |<LI>helix-turn-helix
      |<LI>high-mobility group protein-like factors
      |<LI>homeodomain plus leucine zipper
      |<LI>homeodomain; homeobox protein
      |<LI>leucine zipper
      |<LI>myb-like DNA-binding domains
      |<LI>paired domain, paired box
      |<LI>paired domain, paired box + homeo domain
      |<LI>protamine-like domain
      |<LI>zinc cluster; zinc-cysteine cluster; C6 zinc finger
      |<LI>zinc finger
      |<LI>zinc finger + homeo domain
      |<LI>zinc finger; zinc twist
      |</UL>
    Comment:
      |This field contains description of the class entry. It is a plain text
      |describing main characterisitics of DNA-binding protein class.
    StrDescrip:
      |<b>List of avaliable structure descriptors:</b>
      |<UL>
      |<LI>C6
      |<LI>CC
      |<LI>CC (g)
      |<LI>CC (rec)
      |<LI>CH
      |<LI>CH+homeo
      |<LI>ETS
      |<LI>HLH
      |<LI>HLH-ZIP
      |<LI>HMG
      |<LI>HTH
      |<LI>LIM-homeo
      |<LI>MADS
      |<LI>POU
      |<LI>Rel
      |<LI>TEA
      |<LI>ZIP
      |<LI>bHLH
      |<LI>bHLH-ZIP
      |<LI>bZIP
      |<LI>fork head
      |<LI>homeo
      |<LI>homeo-Zip
      |<LI>myb
      |<LI>paired
      |<LI>paired-homeo
      |<LI>protamine-like
      |</UL>
    }
}
ors:</b>
      |<UL>
      |<LI>C6
      |<LI>CC
      |<LI>CC (g)
      |<LI>CC (rec)
      |<LI>CH
      |<LI>CH+homeo
      |<LI>ETS
      |<LI>HLH
      |<LI>HLH-ZIP
      |<LI>HMG
      |<LI>HTH
      |<LI>LIM-homeo
      |<LI>MADS
      |<LI>POU
      |<LI>Rel
      |<LI>TEA
      |<LI>ZIP
      |<LI>bHLH
      |<LI>bHLH-ZIP
      |<LI>srs/icarus/db/tffactor.i
#    $RCSfile: tffactor.i,v $
#    $Revision: 1.8 $
#    $Date 1996/02/28
#
#    Author: Chenna Ramu
#

TFFACTOR_DB:$library:[TFFACTOR group:@TRANSFAC_LIBS
  comment:"The TRANSFAC Database by Edgar Wingender and Rainer Knueppel"
   format:@TFFACTOR_FORMAT maxNameLen:15 ifiles:{"tffactor.i" "tffactor.is"}
    files:{
       $file:factor
    }
]

TFFACTOR_FORMAT:$libformat:[fileType:@DAT_FILE syntax:@TFFACTOR_SYNTAX
  fields:{
    $field:[@DF_Accession code:id index:id indexToken:id]
    $field:[@DF_ID code:id index:str indexToken:id]
    $field:[@DF_Date code:dt index:int indexToken:dt]
    $field:[@DF_Organism code:os index:str indexToken:os]
    $field:[@DF_FF code:ff index:str indexToken:ff]
    $field:[@DF_Authors code:author index:str indexToken:author]
    $field:[@DF_Title code:rt index:str indexToken:title]
    $field:[@DF_REF code:reference index:str indexToken:reference]
    $field:[@DF_Interaction code:interact index:link indexToken:interact]
  }
]
DF_FF:$srsfield:[FuncFeature short:ff]
DF_Interaction:$srsfield:[Interaction short:ia]

TFFACTOR_SYNTAX:$syntax:[file:"SRSDB:tffactor.is" ignore:" "]
$link:[@TFFACTOR_DB to:@TFFACTOR_DB token:'interact' 
  toName:TFFACTOR_IN fromField:@DF_Interaction toField:@DF_ID]
$link:[@TFFACTOR_DB to:@?SWISSPROT_DB token:'links|swiss' 
  toField:@DF_Accession]
$link:[@TFFACTOR_DB to:@?EMBL_DB token:'links|embl' 
  toField:@DF_Accession]
$link:[@TFFACTOR_DB to:@?PIR_DB token:'links|pir' 
  toField:@DF_Accession]

  }
]
DF_FF:$srsfield:[FuncFeature short:ff]
DF_Interacsrs/icarus/db/tffactor.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: tffactor.is,v $
#    $Revision: 1.10 $
#    $Date: 1997/03/17 23:21:09 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$refDb={EMBL: embl SwissProt:swiss PIR:pir Flybase:flybase}

$fn={
  ID: id   SY:sy   CS:cs   IN:interact  RN:rn   DR:xref  CP:cp   
  AC: ac   HO:ho   SZ:sz   FF:ff        RA:ra   XX:sp    CN:cn
  DT: dt   OS:os   CL:cl   BS:bs        RT:rt   '//':sp
  FA: fa   OC:oc   SF:sf   MX:mx        RL:rl   FT:ft  
}  


$rules={
  entry:   ~ {$In:[file:text] $Out pre $Skip:0}
             ('AC' {$Not} ln)*
             ('AC  ' {$entryFip=$Fip $Wrt} ln {$App} 
              ('AC' {$Not} ln {$App})+)?
           ~
  # fields
  fields:      ~ {$In:entry $Out $Skip:1}
                 (/../ { if:$Ct==$prev $App else $Wrt:$fn.$Ct
                         if:$fn.$Ct=="" $dp:"+++ unknown: $Ct +++"
                         $prev=$Ct
                       } 
                 ln {$App})+ ~

  # indexing
  id:        ~ {$In:[fields c:id] $Out} 'ID' /[0-9A-Za-z]+/ {$Wrt} ~
  dt:        ~ {$In:[fields c:dt] $Out:dt} 'DT' 
               /([0-9]+).([0-9]+).([0-9]+)/ 
               {$Wrt:[s:($1+$2*100+"19$3"*10000)]} ~
  os:        ~ {$In:[fields c:os] $Out:os} 'OS' (sep | word {$Uniq})* ~
  ff:        ~ {$In:[fields c:ff] $Out:ff} 'FF' (sep | word {$Uniq})* ~
  author:    ~ {$In:[fields c:author] $Out:author} 
               'RA' (sep | word {$Uniq})* ~
  title:     ~ {$In:[fields c:rt] $Out:title} 
               'RT' (sep | word {$Uniq})* ~
  reference: ~ {$In:[fields c:reference] $Out:reference} 
               'RL' (sep | word {$Uniq})* ~
  interact:  ~ {$In:[fields c:interact] $Out}
               (/../ word {$Wrt} ln)* ~ 
  links:     ~ {$In:[fields c:xref] $Out}
               ('DR' name {$db=$Ct} ':' word {$Wrt:$refDb.$db} ln)+ ~

  # HTML display
  h_links:   ~ {$In:[fields c:xref t:html]}
               (/DR/ word {$db=$Ct} ':' word 
               {$Rep:{$parStr:"($refDb.$db)R" $Ct $Ct}} ln)* ~
  h_bs:      ~ {$In:[fields c:bs t:html]}
               (tag name ';' name {$Rep:{$ParStr:tfsiteR $Ct $Ct}} ln)+ ~
  h_mx:      ~ {$In:[fields c:mx t:html]}
               (tag name {$Rep:{$ParStr:tfmatrixR $Ct $Ct}} ln)+ ~
  h_cl:      ~ {$In:[fields c:cl t:html]}
               (tag /[a-zA-Z0-9+_-]+/ {$Rep:{$ParStr:tfclassR $Ct $Ct}} ln)+
             ~

  # other stuff
  ln:      ~ /[^\n]*\n/ ~
  tag:     ~ /[A-Z][A-Z]/ ~
  name:    ~ /[A-Za-z][A-Za-z0-9$_]+/ ~
  word:    ~ /[a-zA-Z0-9_]+/ ~
  sep:     ~ /[^a-zA-Z0-9_]+/ ~
}

if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/data/transfac/factor.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields print:1] 
    $JobNext:$job
    $print:"===============> entry <==============\n"
  }
}




             (tag /[a-zA-Z0-9+_-]+/ {$Rep:{$ParStr:tfclassR $Ct $Ct}} ln)+
             ~

  # other stuff
  ln:      ~ /[^\n]*\n/ ~
  tag:     ~ /[A-Z][A-Z]/ ~
  name:    ~ /[A-Za-z][Asrs/icarus/db/tffactor.it
#    
#    $RCSfile: tffactor.it,v $
#    $Revision: 1.4 $
#    $Date: 1996/10/30 10:20:24 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |The FACTORS table contains 1236 entries, but this figure doesn't
    |reflect the number of independent transcription factors. First of all,
    |homologous factors from different species such as human and mouse SRF
    |are given in different entries since they may differ in some molecular
    |aspects. Moreover, factors which have originally been described by
    |different research groups to bind to different genes may turn out to
    |be identical as soon as they have been cloned. On the other hand,
    |more and more factors are recognized to be representatives of whole
    |transcription factor families comprising products of distinct but very
    |similar genes or alternative splice products. In many cases, a more
    |general term originally defining just a specific DNA-binding activity
    |such as AP-1 appears as one entry. In most cases, this activity has not
    |been analyzed for its subunit composition by members of the Jun and
    |Fos families. Nevertheless, all known fos- and jun-related proteins
    |are included as separate entries. <p> All factors that are mentioned
    |in the SITES table appear in the FACTORS table as well. However, it
    |includes also polypeptides which do not bind to DNA by themselves. One
    |well-known example is c-Fos which is forced to contact DNA not until
    |being complexed with, e. g., c-Jun. Information about non-DNA binding
    |subunits of transcription factor complexes such as the TAFs is given by
    |FACTORS as well. There are also proteins that act as inhibitors for a 
    |particular DNA-binding activity and which are of regulatory importance.
    |Therefore, proteins such as Id, IkappaB or hsp90 have been included in
    |TRANSFAC FACTORS. <p> On the other hand, we have in general not yet
    |entered proteins just because of the presence of a putative DNA-binding
    |motif. Thus, there are much more zinc finger or homeo domain proteins
    |known than are included in FACTORS, but for many of them, no data about
    |DNA- binding specificity or about other gene important regulatory
    |features are available.
    |<p>
    |<B>List of Line Codes</B>
    |<LISTING>
    |ID    Identifier
    |XX
    |AC    Accession no.
    |XX
    |DT    Date; author
    |XX
    |FA    Factor name
    |XX
    |SY    Synonyms
    |XX
    |HO    Homologs (suggested)
    |XX
    |OS    Species
    |OC    Classification
    |XX
    |CS    Cell specificity
    |XX
    |SZ    Size
    |XX
    |CL    Class
    |XX
    |SF    Structural features
    |XX
    |IN    Interacting factors
    |XX
    |FF    Functional features
    |XX
    |BS    Bound sites
    |XX
    |MX    Matrix (0/1)
    |XX
    |RN    Reference no.
    |RA    Reference authors
    |RT    Reference title
    |RL    Reference data
    |XX
    |DR    External databases (EMBL/GenBank accession no.; EMBL identifier
    |	   DR    (_g_ene/_r_na); SwissProt accession no.; identifier; PIR
    |		 number;
    |DR    code)
    |</LISTING>
  www:
    |<A HREF="http://transfac.gbf-braunschweig.de/TRANSFAC/">\
    |http://transfac.gbf-braunschweig.de/TRANSFAC/</A>
  literature:
    |E. Wingender , P. Dietze , H. Karas and R. Knüppel,
    |"TRANSFAC: a database on transcription factors and their DNA binding sites"
    |Nucleic Acids Res.
    |24:(21-25), 1996
  ftpSite:''
  date:
    |25 Jul 1996
  signature:
    |Anatoly Ulyanov
  fields:{
    Synonyms:
      |<H3>TFFACTOR Synonyms Field</H3>
      |<BR>The field <EM>Synonyms</EM> covers different spelling (AP-1/AP1)
      |as well as real alternative names (HNF-1: HNF-1alpha, APF, LF-B1). In
      |contrast, the field Suggested Homologs indicates the names of other
      |proteins, frequently from evolutionarily more distant species, which
      |may be functionally and/or structurally related to the factor under
      |consideration. <p>
    CellSpecif:
      |<H3>TFFACTOR CellSpecif Field</H3>
      |<BR><EM>Cell Specificity</EM> gives predominant occurrence of a factor
      |in certain cell types or tissues. Gradual differences between groups of
      |cells/tissues are indicated by a semicolon. Occasionally, cells from
      |which the factor has been isolated are indicated in brackets; this
      |information does not necessarily point to a true cell specificity.
      |<p> <BR>The Size field shows the number of amino acid residues of a
      |polypeptide and its molecular weight. The method by which this figure
      |has been obtained is indicated in brackets; (cDNA) or (gene) means that
      |it has been calculated after cloning, (SDS) or (sedim.) hints on the
      |corresponding experimental approaches. <p>
    Features:
      |<H3>TFFACTOR Features Field</H3>
      |The field <EM>Structural Features</EM> may contain information on:
      |<DIR> <LI> regions that are enriched in some amino acid residues and
      |may therefore represent trans-activating domains; S/T stands for
      |serine/threonine-rich, ac for acidic, Pro for proline-rich, Q for
      |glutamine-rich, A for alanine-rich regions, W for peculiar tryptophan
      |patterns. <LI> the nature of a leucine zipper: L4 means that it
      |consists of four leucine residues spaced by 6-AA-intervals, L2EL2
      |indicates a motif such as <STRONG>L-X6-L-X6-E-X6-L-X6-L</STRONG>.
      |<LI> posttranslational modifications: P or Ph indicates a site of
      |phosphorylation, glyc of glycosylation. </DIR> <p>
    Interaction:
      |<H3>TFFACTOR Interaction Field</H3>
      |The field <EM>Interactions</EM>: <DIR> <LI> Since most transcription
      |factors bind to DNA as dimers, the dimerization partners are
      |indicated in this field. Repeating the factors name in this
      |field means that it forms homodimers. Also given are inhibitory
      |protein-protein-interactions such as NF-kappaB - IkappaB.</DD></DL>
      |</DIR> <LI> <p>
    Matrix:
      |<H3>TFFACTOR Matrix Field</H3>
      |The field <EM>Matrix</EM> indicates a crossreference if there exists a
      |nucleotide distribution matrix for this factor in the MATRIX table. <p>
    }
}
factors bind to DNA as dimers, the dimerization partners are
      |indicated in this field. Repeating the factors name in this
      |field means that it forms homodimers. Also given are inhibitory
      |protein-protein-interactions such as NF-kappaB - IkappaB.</DD></srs/icarus/db/tfgene.i
#    $RCSfile: tfgene.i,v $
#    $Revision: 1.1 $
#    $Date: 1997/03/03 18:34:25 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

TFGENE_DB:$library:[TFGENE group:@TRANSFAC_LIBS
   format:@TFGENE_FORMAT maxNameLen:15 ifiles:{"tfgene.i" "tfgene.is"}
    files:{
       $file:gene
    }
]

TFGENE_FORMAT:$libformat:[fileType:@DAT_FILE syntax:@TFGENE_SYNTAX
  tableFormat:left fields:{
    $field:[@DF_ID code:id index:id indexToken:id tableToken:id]
    $field:[@DF_Accession code:ac index:str indexToken:'wrd|ac']
    $field:[@DF_Description code:de index:str indexToken:'words|de'
      tableToken:'t_field|de']
    $field:[@DF_Date code:dt index:int indexToken:dt tableToken:t_date]
    $field:[@DF_Organism code:os index:str indexToken:'words|os']
  }
]
TFGENE_SYNTAX:$syntax:[file:"SRSDB:tfgene.is" ignore:" "]


$link:[@TFGENE_DB to:@?TFSITE_DB toField:@DF_Accession token:bsRef] 



elds:{
    $field:[@DF_ID code:id index:id indexToken:id tableToken:id]
    $field:[@DF_Accession code:ac index:str indexToken:'wrd|ac']
    $field:[@DF_Description code:de index:str indexToken:'words|de'
      tableToken:'t_field|de']
    $field:[@DF_Date code:dt index:int indexToken:dt tableToken:t_date]
    $field:[@DF_Organism code:os index:str indexToken:'words|os']
  }
]
TFGENE_SYNTAX:$syntax:[file:"SRSDB:tfgene.is" ignore:" "]


$link:[@TFGENE_DB to:@?TFSITE_DB toField:@DF_Accession token:bsRef] 


srs/icarus/db/tfgene.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: tfgene.is,v $
#    $Revision: 1.1 $
#    $Date: 1997/03/03 18:34:26 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  ID: id   DE:de   BS:bs   TR:tr
  AC: ac   OS:os   CO:co 
  DT: dt   OC:oc   '//':xln
  SD: sd   BC:bc   XX:xln
}

$rules={
  entry:  ~ {$In:[file:text] $Out pre $Skip:0}
            ('AC' {$Not} ln)*
            ('AC  ' {$entryFip=$Fip $Wrt} ln {$App} 
             ('AC' {$Not} ln {$App})+)?
          ~
  # fields
  fields: ~ {$In:entry $Out $Skip:1}
            (/../ { if:$Ct==$prev $App else $Wrt:$fn.$Ct
                    if:$fn.$Ct=="" $dp:"+++ unknown: $Ct +++"
                    $prev=$Ct
                  } 
            ln {$App})+ ~

  # indexing
  id:     ~ {$In:[fields c:id] $Out $Break} tag /[0-9A-Za-z$_-]+/ {$Wrt} ~
  wrd:    ~ {$In:[fields c:{ac ty el se dt}] $Out} tag word {$Wrt:$Itc} ~
  dt:     ~ {$In:[fields c:dt] $Out} 'DT' 
            /([0-9]+).([0-9]+).([0-9]+)/{$Wrt:[s:($1+$2*100+"19$3"*10000)]}~
  words:  ~ {$In:[fields c:{os de oc}] $Out} 
            (tag (sep | /[a-zA-Z0-9+-]+/ {$Uniq:$Itc})* ln)+ ~
  bsRef:  ~ {$In:[fields c:bs] $Out}
            (tag (name {$Wrt} ';'?)+ ln)+ ~
    
  # table display
  t_date: ~ {$In:[fields c:dt] $Out} tag /[0-9\.]+]/ {$Wrt} ~
  t_field:~ {$In:[fields c:{de}] $Out}
            tag ln {$Wrt:$Itc} (tag ln {$App})* ~

  # HTML display
  h_bs:   ~ {$In:[fields c:bs t:html] $Out}
            (tag (name {$Rep:{$ParStr:tfsiteR $Ct $Ct}} ';'?)+ ln)+ ~

  # others
  num:     ~ /-?[0-9]+/ ~
  tag:     ~ /[A-Z][A-Z0-9]/ ~
  ln:      ~ /[^\n]*\n/ ~
  name:    ~ /[a-zA-Z0-9$_-]+/ ~
  word:    ~ /[a-zA-Z0-9_]+/ ~
  sep:     ~ /[^a-zA-Z0-9_\n]+/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/opt/srs/data/transfac/gene.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields print:0] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}




            (tag (name {$Rep:{$ParStr:tfsiteR $Ct $Ct}} ';'?)+ ln)+ ~

  # others
  num:     ~ /-?[0-9]+/ ~
  tag:     ~ /[A-Z][A-Z0-9]/ ~
  ln:      ~ /[^\n]*\n/ ~
  name:    ~ /[a-zA-Z0-9$_-]+/ ~
  word:    ~ /[a-zA-Z0-9_]+/ ~
  sep:     ~ /[^a-zA-Z0-9_\n]+/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/opt/srs/data/transfac/gene.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields print:0] 
    $JobNext:$job
    $print:"-------->entrsrs/icarus/db/tfmatrix.i
#    $RCSfile: tfmatrix.i,v $
#    $Revision: 1.7 $
#    $Date 1996/02/28
#
#    Author: Chenna Ramu
#

TFMATRIX_DB:$library:[TFMATRIX group:@TRANSFAC_LIBS
  comment:"The TRANSFAC Database by Edgar Wingender and Rainer Knueppel"
   format:@TFMATRIX_FORMAT maxNameLen:15 ifiles:{"tfmatrix.i" "tfmatrix.is"}
    files:{
       $file:matrix
    }
]

TFMATRIX_FORMAT:$libformat:[fileType:@DAT_FILE syntax:@TFMATRIX_SYNTAX
  fields:{
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:[@DF_Accession code:acc index:str indexToken:acc]
    $field:[@DF_Date code:date index:int indexToken:date]
    $field:[@DF_BINDFAC code:bf index:str indexToken:bf]
    $field:[@DF_STATBAS code:statBas index:str indexToken:statBas]
    $field:[@DF_COMMENT code:comm index:str indexToken:comm]
    $field:[@DF_Authors code:ra index:str indexToken:ra]
    $field:[@DF_REFTITLE code:refTit index:str indexToken:refTit]
    $field:[@DF_REF code:refData index:str indexToken:refData]

  }
]

DF_BINDFAC:$srsfield:[BindingFactor short:bf]
DF_STATBAS:$srsfield:[StatisticBasis short:stb]
DF_REFTITLE:$srsfield:[Title short:tit]

TFMATRIX_SYNTAX:$syntax:[file:"SRSDB:tfmatrix.is" ignore:" "]
eld:[@DF_STATBAS code:statBas index:str indexToken:statBas]
    $field:[@DF_COMMENT code:comm index:str indexToken:comm]
    $field:[@DF_Authors code:ra index:str indexToken:ra]
    $field:[@DF_REFTITLE code:refTit index:str indexToken:refTit]
    $field:[@DF_REF code:refData index:str indexToken:refData]

  }
]

DF_BINDFAC:$srsfield:[BindingFactor short:bfsrs/icarus/db/tfmatrix.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: tfmatrix.is,v $
#    $Revision: 1.8 $
#    $Date: 1997/03/03 18:34:26 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  ID:id	     BF:bf	  RN:refNum    XX:sep
  AC:acc     BA:statBas   RP:refp      '//':sep
  DT:date    CC:comm	  SQ:seqln     RT:refTit     
  NA:na      DE:de        RL:refData   RA:ra
}

$rules={
  entry:    ~ {$In:[file:text] $Out:entry pre $Skip:0}
              ('AC' {$Not} ln)*
              ('AC' {$entryFip=$Fip $Wrt} ln {$App} 
               ('AC' {$Not} ln {$App})+)?
            ~
  # fields 
  fields:   ~ {$In:entry $Out $Skip:1}
              (po |
               /../ { if:$Ct==$prev $App else $Wrt:$fn.$Ct
                       if:$fn.$Ct=="" $dp:"+++ unknown: $Ct in $entryName +++"
                       $prev=$Ct
                    } ln {$App})+ ~
  po:       ~ {$Wrt:po}       'P0' ln (/[0-9][0-9]/ ln)+ ~
	   
  # indexing
  id:       ~ {$In:[fields c:id] $Out} tag /[0-9A-Za-z$_]+/ {$Wrt} ~
  ac:       ~ {$In:[fields c:acc] $Out:acc} tag /[0-9A-Za-z]+/ {$Wrt} ~
  dt:       ~ {$In:[fields c:date] $Out:date} tag skipChar
              /([0-9]+).([0-9]+).([0-9]+)/ {$Wrt:[s:($1+$2*100+"19$3"*10000)]}~
  bf:       ~ {$In:[fields c:bf] $Out} (tag (sp | word {$Uniq})* '\n')+ ~
  ra:       ~ {$In:[fields c:ra] $Out:ra $Break} 
              (tag (/([^.,\n]+) +([^,;\n]+)/ {$Uniq:[s:"$1,$2"]} /[,;]/)*)+ ~
  statBas:  ~ {$In:[fields c:statBas] $Out:statBas} tag (sp | word {$Uniq})* ~
  refTit:   ~ {$In:[fields c:refTit] $Out:refTit} tag (sp | word {$Uniq})* ~
  refData:  ~ {$In:[fields c:refData] $Out:refData} tag (sp | word {$Uniq})* ~
  comm:     ~ {$In:[fields c:comm] $Out:comm} tag (sp | word {$Uniq})* ~

  # common things 
  tag:      ~ /[A-Z][A-Z]/ ~
  ln:       ~ /[^\n]*\n/ ~
  word:     ~ /[a-zA-Z0-9_]+/ ~
  sp:       ~ /[^a-zA-Z0-9_]+/ ~  
  skipChar: ~ /[^0-9.]+/ ~
}

if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/data/transfac/matrix.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields print:1] 
    $JobNext:$job
    $print:"===============> entry <==============\n"
  }
}

 (sp | word {$Uniq})* ~
  comm:     ~ {$In:[fields c:comm] $Out:comm} tag (sp | word {$Uniq})* ~

  # common things 
  tag:      ~ /[A-Z][A-Z]/ ~
  ln:       ~ /[^\n]*\n/ ~
  word:     ~ /[a-zA-Z0-9_]+/ ~
  sp:       ~ /[^a-zA-Z0-9_]+/ ~  
  skipChar: ~ /[^0-9.]+/ ~
}

if:$TestMode {
  $job = $JobNew:[prod:$rulesrs/icarus/db/tfmatrix.it
#    
#    $RCSfile: tfmatrix.it,v $
#    $Revision: 1.4 $
#    $Date: 1996/10/30 10:20:25 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |The MATRIX table contains 26 nucleotide distribution matrices of
    |aligned binding sequences. These sequences may have been obtained by in
    |vitro selection studies or may be compiled sites of genes. The source
    |is appropriately indicated.
    |<p>
    |<B>List of Line Codes</B>
    |<LISTING>
    |AC    Accession no.
    |DT    Date; author
    |BF    Binding factor
    |PO          A     C     G     T           Position within the aligned
    |					       sequences,
    |					       frequency of A, C, G, T
    |					       residues, resp.
    |BA    Statistical basis
    |CC    Comments
    |RN    Reference no.
    |RA    Reference authors
    |RT    Reference title
    |RL    Reference data
    |</BLOCKQUOTE>
  www:
    |<H4>
    |<A HREF="http://transfac.gbf-braunschweig.de/TRANSFAC/">\
    |http://transfac.gbf-braunschweig.de/TRANSFAC/</A>
    |</H4>
  citation:
    |E. Wingender , P. Dietze , H. Karas and R. Knüppel,
    |"TRANSFAC: a database on transcription factors and their DNA binding sites"
    |Nucleic Acids Res.
    |24:(21-25), 1996
  date:
    |25 Jul 1996
  signature:
    |Anatoly Ulyanov
}
nce no.
    |RA    Reference authors
    |RT    Reference title
    |RL    Reference data
  srs/icarus/db/tfsite.i
#    $RCSfile: tfsite.i,v $
#    $Revision: 1.10 $
#    $Date: 1997/03/03 18:34:27 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

TFSITE_DB:$library:[TFSITE group:@TRANSFAC_LIBS
  comment:"The TRANSFAC Database by Edgar Wingender and Rainer Knueppel"
   format:@TFSITE_FORMAT maxNameLen:15 ifiles:{"tfsite.i" "tfsite.is"}
    files:{
       $file:site
    }
]

TFSITE_FORMAT:$libformat:[fileType:@DAT_FILE syntax:@TFSITE_SYNTAX
  tableFormat:left fields:{
    $field:[@DF_ID code:id index:id indexToken:id tableToken:id]
    $field:[@DF_Accession code:ac index:str indexToken:'wrd|ac']
    $field:[@DF_Date code:dt index:int indexToken:dt tableToken:t_date]
    $field:[@DF_SequenceType code:ty index:str indexToken:'wrd|ty']
    $field:[@DF_ElemDenom code:el index:str indexToken:'wrd|el']
    $field:[@DF_SiteFirstPos code:sf index:int indexToken:sf]
    $field:[@DF_SiteLastPos code:st index:int indexToken:st]
    $field:[@DF_DefineFirstPos code:s1]
    $field:[@DF_Organism code:os index:str indexToken:'words|os']
    $field:[@DF_Method code:me index:str indexToken:'words|me']
    $field:[@DF_Description code:de index:str indexToken:'words|de'
      tableToken:'t_field|de']
    $field:[@DF_BindingFactor code:bf index:str indexToken:'words|bf']
    $field:[@DF_FactorSource code:so index:str indexToken:'words|so']
    $field:[@DF_Comment code:cc index:str indexToken:'words|cc'
      tableToken:'t_field|cc']
    $field:[@DF_Sequence code:se index:str indexToken:'wrd|se']
  }
]
TFSITE_SYNTAX:$syntax:[file:"SRSDB:tfsite.is" ignore:" "]

DF_BindingFactor:$srsfield:[BindingFactor short:bf]
DF_SequenceType:$srsfield:[SequenceType short:st]
DF_FactorSource:$srsfield:[FactorSource short:so]
DF_SiteFirstPos:$srsfield:[SiteFirstPos short:sfp]
DF_SiteLastPos:$srsfield:[SiteLastPos short:slp]
DF_DefineFirstPos:$srsfield:[DefineFirstPos short:dfp]
DF_ElemDenom:$srsfield:[ElementDenomination short:eld]

$link:[@TFSITE_DB to:@?TFFACTOR_DB toField:@DF_ID token:bfRef] 
$link:[@TFSITE_DB to:@?TFCELL_DB toField:@DF_ID token:soRef] 
$link:[@TFSITE_DB to:@?EMBL_DB weight:9 toField:@DF_Accession token:'dr|embl']
$link:[@TFSITE_DB to:@?FLYGENE_DB toField:@DF_ID token:'dr|flybase']



[FactorSource short:so]
DF_SiteFirstPos:$srsfield:[SiteFirstPos short:sfp]
DF_SiteLastPos:$srsfield:[SiteLastPos short:slp]
DF_DefineFirstPos:$srsfield:[DefineFirstPos short:dfp]
DF_ElemDenom:$srsfield:[ElementDenomination short:eld]
srs/icarus/db/tfsite.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: tfsite.is,v $
#    $Revision: 1.8 $
#    $Date: 1997/03/03 18:34:27 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  ID: id   DE:de   ST:st   OS:os  RN:rn   DR:xref   MM:mm
  AC: ac   SE:se   S1:s1   OC:oc  RA:ra   XX:xln    SQ:sq
  DT: dt   EL:el   CL:cl   SO:so  RT:rt   '//':xln  RE:re
  TY: ty   SF:sf   BF:bf   ME:me  RL:rl   CC:cc
}

$rules={
  entry:  ~ {$In:[file:text] $Out pre $Skip:0}
            ('AC' {$Not} ln)*
            ('AC  ' {$entryFip=$Fip $Wrt} ln {$App} 
             ('AC' {$Not} ln {$App})+)?
          ~
  # fields
  fields: ~ {$In:entry $Out $Skip:1}
            (/../ { if:$Ct==$prev $App else $Wrt:$fn.$Ct
                    if:$fn.$Ct=="" $dp:"+++ unknown: $Ct +++"
                    $prev=$Ct
                  } 
            ln {$App})+ ~

  # indexing
  id:     ~ {$In:[fields c:id] $Out $Break} tag /[0-9A-Za-z$_-]+/ {$Wrt} ~
  wrd:    ~ {$In:[fields c:{ac ty el se dt}] $Out} tag word {$Wrt:$Itc} ~
  dt:     ~ {$In:[fields c:dt] $Out} 'DT' 
            /([0-9]+).([0-9]+).([0-9]+)/ {$Wrt:[s:($1+$2*100+"19$3"*10000)]} ~
  words:  ~ {$In:[fields c:{bf so cc de os me}] $Out} 
            (tag (sep | /[a-zA-Z0-9+-]+/ {$Uniq:$Itc})* ln)+ ~
  el:     ~ {$In:[fields c:el] $Out} tag word {$Wrt} ~
  se:     ~ {$In:[fields c:se] $Out} tag word {$Wrt} ~
  sf:     ~ {$In:[fields c:sf] $Out} tag num {$Wrt} ~
  st:     ~ {$In:[fields c:st] $Out} tag num {$Wrt} ~
  #links:
  bfRef:  ~ {$In:[fields c:bf] $Out} (tag name {$Wrt} ln)+ ~
  soRef:  ~ {$In:[fields c:so] $Out} (tag name {$Wrt} ln)+ ~
  dr:     ~ {$In:[fields c:dr] $Out} (tag 
           ('EMBL;' word {$Wrt:embl} | 'Flybase;' name {$Wrt:flybase}) ln)+  ~

  # table display
  t_date: ~ {$In:[fields c:dt] $Out} tag /[0-9\.]+]/ {$Wrt} ~
  t_field:~ {$In:[fields c:{de cc}] $Out}
            tag ln {$Wrt:$Itc} (tag ln {$App})* ~

  # HTML display
  h_bf:   ~ {$In:[fields c:bf t:html]} 
            (tag name {$Rep:{$ParStr:tffactorR $Ct $Ct}} ln)+ ~
  h_so:   ~ {$In:[fields c:so t:html]} 
            (tag /[0-9]+/ {$Rep:{$ParStr:tfcellR $Ct $Ct}} ln)+ ~
  h_dr:   ~ {$In:[fields c:dr t:html]} 
            (tag ('EMBL;' word {$Rep:{$ParStr:emblR $Ct $Ct}} |
                  'Flybase;' word {$Rep:{$ParStr:flybaseR $Ct $Ct}} ) ln)+ ~

  # others
  num:     ~ /-?[0-9]+/ ~
  tag:     ~ /[A-Z][A-Z0-9]/ ~
  ln:      ~ /[^\n]*\n/ ~
  name:    ~ /[a-zA-Z0-9$_-]+/ ~
  word:    ~ /[a-zA-Z0-9_]+/ ~
  sep:     ~ /[^a-zA-Z0-9_\n]+/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " fileName:'/data/transfac/site.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields print:0] 
    $JobTokens:[$job name:so print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}



d {$Rep:{$ParStr:flybaseR $Ct $Ct}} ) ln)+ ~

  # others
  num:     ~ /-?[0-9]+/ ~
  tag:     ~ /[A-Z][A-Z0-9]/ ~
  ln:      ~ /[^\n]*\n/ ~
  name:    ~ /[a-zA-Z0-9$_-]+/ ~
  word:    ~ /[a-zA-Z0-srs/icarus/db/tfsite.it
#    
#    $RCSfile: tfsite.it,v $
#    $Revision: 1.5 $
#    $Date: 1997/03/03 18:34:28 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |As outlined above, SITES gives information on individual (putatively)
    |regulatory protein binding sites. It contains 4303 entries, 4038
    |of them referring to sites within more than 841 eukaryotic genes,
    |the species of which ranging from yeast to human. Additionally,
    |this table comprises 315 artificial sequences which resulted from
    |mutagenesis studies, in vitro selection procedures starting from random
    |oligonucleotide mixtures or from specific theoretical considerations.
    |And finally, there are 224 consensus binding sequences given in the
    |IUPAC code, many of them being taken from the compilation of Faisst and
    |Meyer <CITE>(Nucleic Acids Res. 20:3-26, 1992)</CITE>. The symbols used
    |in addition to A, C, G, or T for these consensi are: </P>
    |<PRE>
    |W: A or T                           S: C or G
    |R: A or G                           Y: C or T
    |K: G or T                           M: A or C
    |B: C, G, or T                       D: A, G, or T
    |H: A, C, or T                       V: A, C, or G
    |N: A, C, G, or T
    |</PRE>
    |<p>

    |<B>List of Line Codes</B>
    |<LISTING>
    |ID    Identifier
    |XX
    |AC    Accession no.
    |XX
    |DT    Date; author
    |XX
    |TY    Sequence type
    |XX
    |DE    Description (gene or gene product)
    |XX
    |SE    Sequence of the regulatory element
    |XX
    |EL    Denomination of the element
    |XX
    |SF    First position of factor binding site
    |ST    Last position of factor binding site
    |S1    Definition of first position (if not transcription start site)
    |XX
    |BF    Binding factor (TRANSFAC FACTORS accession no.; name)
    |XX
    |OS    Species
    |OC    Classification
    |XX
    |SO    Factor source (TRANSFAC CELLS accession no.; name)
    |XX
    |ME    Method
    |XX
    |RN    Reference no.
    |RA    Reference authors
    |RT    Reference title
    |RL    Reference data        
    |XX
    |CC    Comments
    |XX
    |DR    External databases (EMBL/GenBank accession no.; 
    |DR    EMBL identifier (1st:last position of the TRANSFAC sequence
    |DR    element)
    |</LISTING>
  ftp:
    |<A HREF="ftp://transfac.gbf-braunschweig.de/pub/transfac/ascii/">\
    |ftp.gbf-braunschweig.de/pub/transfac/<BR>
    |<A HREF="ftp://ftp.ebi.ac.uk/pub/databases/transfac/">\
    |ftp.ebi.ac.uk/pub/databases/transfac/</A><BR>
    |file: site.dat
  address:
    |Gesellschaft fuer Biotechnologische Forschung mbH
    |Mascheroder Weg 1, D-38124  Braunschweig, Germany
  contact:
    |Edgar Wingender<BR>
    |Rainer Knueppel
  email:
    |ewi@venus.gbf-braunschweig.d400.de	
  www:
    |<A HREF="http://transfac.gbf-braunschweig.de/TRANSFAC/">
    |http://transfac.gbf-braunschweig.de/TRANSFAC/</A>
  literature:
    |<Ol>
    |<LI>E. Wingender, Recognition of regulatory regions in genomic sequences.
    |J. Biotechnol. 35:273-280, 1994    
    |<LI>E. Wingender , P. Dietze , H. Karas and R. Knüppel,
    |"TRANSFAC: a database on transcription factors and their DNA binding sites"
    |Nucleic Acids Res.
    |24:(21-25), 1996
    |</OL>
  example:
    |HS\$EGFR_12
  date:
    |6-OCT-1996
}

 |<A HREF="http://transfac.gbf-braunschweig.de/TRANSFAC/">
    |http://transfac.gbf-braunschweig.de/TRANSFAC/</A>srs/icarus/db/trembl.i
#
#    $RCSfile: trembl.i,v $
#    $Revision: 1.2 $
#    $Date: 1997/03/03 18:34:28 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

TREMBL_DB:$library:[TREMBL group:@SEQUENCE_LIBS 
  format:@TREMBL_FORMAT maxNameLen:12 files:{
    $file:trembl
  }
]
TREMBLNEW_DB:$library:[TREMBLNEW group:@SEQUENCE_LIBS 
  format:@TREMBL_FORMAT maxNameLen:12 files:{
    $file:tremblnew
  }
]

TREMBL_FORMAT:$libformat:[contains:@PROTSEQ_DATA 
  fileType:{@DAT_FILE @SEQ_FILE}
  syntax:@TREMBL_SYNTAX tableFormat:left fields:{
    $field:[@DF_ID code:id index:id indexToken:id]
    $field:@DF_ALL
    $field:[@DF_Description index:str indexToken:des code:des]
    $field:[@DF_ProtSequence token:sequence]
  }
]

TREMBL_SYNTAX:$syntax:[file:"SRSDB:trembl.is" ignore:" \t"]




]
TREMBLNEW_DB:$library:[TREMBLNEW group:@SEQUENCE_LIBS 
  format:@TREMBL_FORMAT maxNameLen:12 files:{
    $file:tremblnew
  }
srs/icarus/db/trembl.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: trembl.is,v $
#    $Revision: 1.1 $
#    $Date: 1997/03/03 18:36:33 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$fn={
  ID:id	     OG:organ	OS:org OC:tax DR:link 
  AC:acc     FT:ft      SQ:sq
  DE:des     CC:cc	
}

$rules={
  entry:     ~ {$In:[file:text] $Out pre $Skip:0}
               ('ID  ' {$not} lnT)*
               (/ID +([A-Z0-9_]+)/ {$entryFip=$Fip $Wrt $entryName=$1} 
                lnT {$App}
               (/(  |ID|>>)/ {$Not} lnT {$App})+ )? ~
  lnT:       ~ /[^\n]+\n?/ ~ # line terminator may be missing if truncated

  sequence:  ~ {$In:[file:seq share:text] $Out 
                pre {$s=$SeqNew:$entryName $seqFip=$Fip}
                $Wrt:[s:$entryName] $SeqMake:$s} 
               ('ID' {$Not} ln {$SeqApp:[$s s:$Ct]})* ~
  gcgseq:    ~ {$In:[file:seq] $Out pre {$seqFip=$Fip} $SeqMake:$s} 
               '>>>>' name {$Wrt:[s:$Ct] $s=$SeqNew:$Ct} ln
               ln ('>>>>' {$Not} ln {$SeqApp:[$s s:$Ct]})+ ~

  # extracting data fields
  fields:    ~ {$In:entry $Out $Skip:1} 
               (ftln | /../ 
                { $t=$Ct
                  if:$t==$prev $App else $Wrt:$fn.$t
                    if:$fn.$t=="" $dp:"+++ unknown: $t in $entryName +++"
                      $prev=$t
                } ln {$App})+ ~
  ftln:      ~ {$Wrt:ft} 'FT' ln ('FT     ' ln)* ~
  clFields:  ~ {$In:fields $Out $Skip:1}
               /.. */ ln {$Wrt:$Itc} (/.. */ ln {$App})* ~

  # for indexing
  id:        ~ {$In:[entry] $Out} /ID +([a-zA-Z0-9_]+)/ {$Wrt:[s:$1]} ~
  acc:       ~ {$In:[clFields c:acc] $Out} (/[a-zA-Z0-9_]+/ {$Wrt} | ';')+ ~
  des:       ~ {$In:[clFields c:des] $Out} 
               (/[a-zA-Z0-9_]+/ {$Uniq} | 
                /\\(EC *([0-9]+\\.[0-9]+\\.[0-9]+\\.[0-9]+)/ {$Uniq:[s:$1]}|
                /[^a-aA-Z0-9(_\n]+/ | /[^\n]/)* ~
  seqlen:    ~ {$In:[fields c:seqln] $Out} /.* ([0-9]+) * AA/ {$Wrt:[s:$1]}~
  molweight: ~ {$In:[fields c:seqln] $Out} /.* ([0-9]+) * MW/ {$Wrt:[s:$1]}~
  org:       ~ {$In:[clFields c:{org tax}] $Out}
               (/(AND *)?([^;,.\n(]+[^ (;,.\n])/ {$Wrt:[s:$2]} | 
                /\\(([^)]+)\\)/ {$Wrt:[s:$1]} | /[,;.]/)* ~
  organ:     ~ {$In:[clFields c:organ] $Out} 
               (/(AND *)?([^,.\n]+)/ {$Wrt:[s:$2]} | /,./)* ~


  # printing in HTML format
  h_id:      ~ {$In:[fields c:id t:html]} /../ name {$entryName=$Ct} ~
  hl_links:  ~ {$In:[fields c:link t:html]}
               (/DR/ 'EMBL;' name {$Rep:{$ParStr:emblR $Ct $Ct}} ln)+ ~
  h_des:     ~ {$In:[fields c:des t:html]}
               (/(\\(EC )([0-9.-]+)/ {$Rep:{"$1($ParStr:enzymeR)" $2 $2}} | 
                /[^ ]+/ )* ~ 
  h_ft:      ~ {$In:[fields c:ft t:html]} 
               /.*EC_number="/ /[^"]+/ {$Rep:{$ParStr:enzymeR $Ct $Ct}} ~

  # other stuff
  ln:        ~ /[^\n]*\n/ ~
  accno:     ~ /[A-Z0-9]+/ ~
  num:       ~ /(<|>)?[0-9?]+/ ~
  name:      ~ /[a-zA-Z0-9_-]+/ ~ 
  dbName:    ~ /[^;]+/ ~ 
}

# debugging 
$subEntryN=3
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" \n" fileName:'/data/trembl/trembl.dat']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:id print:1] 
    $JobTokens:[$job name:des print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}


/.*EC_number="/ /[^"]+/ {$Rep:{$ParStr:enzymeR $Ct $Ct}} ~

  # other stuff
  ln:        ~ /[^\n]*\n/ ~
  accno:     ~ /[A-Z0-9]+/ ~
  num:       ~ /(<|>)?[0-9?]+/ ~
  name:      ~ /[a-zA-Z0-9_-]+/ ~ 
  dbName:    ~ /[^;]+/ ~ 
}

# debugging 
$subEntsrs/icarus/db/views.i
#
#    $RCSfile: views.i,v $
#    $Revision: 1.5 $
#    $Date: 1997/03/12 19:05:51 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$View:["* Names only *"]   

$View:[sequence_simple useShortFieldNames:1
  root:{$Vlib:@?SWISSPROT_DB $Vlib:@?SWISSNEW_DB $Vlib:@?PIR_DB 
        $Vlib:@?EMBL_DB $Vlib:@?EMBLNEW_DB $Vlib:@?GENBANK_DB}
  rootFields:{
    $Vfield:@?DF_Description 
    $Vfield:@?DF_Date
    $Vfield:@?DF_SeqLength
  }
]   

$View:[proteinChart 
  root:{$Vlib:@?SWISSPROT_DB $Vlib:@?PIR_DB}
  rootFields:{
    $Vfield:@?DF_Description 
    $Vfield:[@?DF_ProtSequence format:proteinChart]
  }
]   


$View:[Blast_Ali_Swissprot
  root:$Vlib:@?BLAST_DB 
  rootFields:{
    $Vfield:@?DF_TopScore
    $Vfield:@?DF_TopMatch 
  }
  leaves:$Vlib:[@?SWISSPROT_DB 
    fields:{
      $Vfield:@?DF_Description
      $Vfield:@?DF_SeqLength
    }
  ]
]   

$View:[Blast_Swissprot useShortFieldNames:1
  root:$Vlib:@?BLAST_DB 
  rootFields:{
    $Vfield:@?DF_TopScore
  }
  leaves:{
    $Vlib:[@?SWISSPROT_DB 
      fields:{
        $Vfield:@?DF_Description
        $Vfield:@?DF_SeqLength
      }
    ]
    $Vlib:[@?PROSITE_DB 
      fields:{
        $Vfield:@?DF_Description
        $Vfield:@?DF_ALLPOS
      }
    ]
    $Vlib:[@?ENZYME_DB 
      fields:{
        $Vfield:@?DF_CatActivity
      }
    ]
  }
]   

$View:[Blast_families useShortFieldNames:1
  root:$Vlib:@?BLAST_DB 
  rootFields:{
    $Vfield:@?DF_TopScore
  }
  leaves:{
    $Vlib:[@?SWISSPROT_DB 
      fields:{
        $Vfield:@?DF_Description
        $Vfield:@?DF_SeqLength
      }
    ]
    $Vlib:[@?PROSITE_DB]
    $Vlib:[@?BLAST_DB query:'entry>prosite>blast' printOnlyEntryN:1
      viewName:Blast_Ali_Swissprot
    ]
  }
]   

$View:[Fasta_families useShortFieldNames:1
  root:$Vlib:@?FASTA_DB 
  rootFields:{
    $Vfield:@?DF_OptScore
  }
  leaves:{
    $Vlib:[@?SWISSPROT_DB 
      fields:{
        $Vfield:@?DF_Description
        $Vfield:@?DF_SeqLength
      }
    ]
    $Vlib:[@?PROSITE_DB]
    $Vlib:[@?FASTA_DB query:'entry>prosite>fasta' printOnlyEntryN:1
      viewName:Fasta_Ali_Swissprot
    ]
  }
]   


$View:[Fasta_Ali_Swissprot
  root:$Vlib:@?FASTA_DB 
  rootFields:{
    $Vfield:@?DF_OptScore
    $Vfield:@?DF_Alignment 
  }
  leaves:$Vlib:[@?SWISSPROT_DB 
    fields:{
      $Vfield:@?DF_Description
      $Vfield:@?DF_SeqLength
    }
  ]
]   


$View:[Sw_Ali_Swissprot
  root:$Vlib:@?SW_DB 
  rootFields:{
    $Vfield:@?DF_PercIdent
    $Vfield:@?DF_Alignment
  }
  leaves:$Vlib:[@?SWISSPROT_DB 
    fields:{
      $Vfield:@?DF_Description
      $Vfield:@?DF_SeqLength
    }
  ]
]   

$View:[Sw_Swissprot useShortFieldNames:1
  root:$Vlib:@?SW_DB 
  rootFields:{
    $Vfield:@?DF_PercIdent
    $Vfield:@?DF_MatchLen
  }
  leaves:{
    $Vlib:[@?SWISSPROT_DB 
      fields:{
        $Vfield:@?DF_Description
        $Vfield:@?DF_SeqLength
      }
    ]
    $Vlib:[@?PROSITE_DB 
      fields:{
        $Vfield:@?DF_Description
        $Vfield:@?DF_ALLPOS
      }
    ]
    $Vlib:[@?ENZYME_DB 
      fields:{
        $Vfield:@?DF_CatActivity
      }
    ]
  }
]   


$View:[prosite_simple
  root:$Vlib:@?PROSITE_DB
  rootFields:{
    $Vfield:@?DF_Description 
  }
]

$View:[clustalw_ali
  root:$Vlib:@?CLUSTALW_DB
  rootFields:{
    $Vfield:@?DF_NAlign
    $Vfield:@?DF_SeqList
    $Vfield:@?DF_Alignment
  }
]

#$View:[familystat 
#  root:[$Vlib:@ReptiliaTax_DB]
#  rootFields:{$Vfield:@DF_Name}
#  leaves:
#    $Vlib:[@GENBANK printOnlyEntryN:y 
#	      query:"entry >^ Reptiliatax_down > genbank"
#	      query:"entry >^ Reptiliatax_down > reptilia"
#    ]
#]

$View:[reptilia root:$Vlib:@?REPTILIA_DB
  rootFields:{
    $Vfield:@?DF_Synonyms
    $Vfield:@?DF_Distribution
  }
]
ew:[clustalw_ali
  root:$Vlib:@?CLUSTALW_DB
  rootFields:{
    $Vfield:@?DF_NAlign
    $Vfield:@?DF_SeqList
    $Vfield:@?DF_Alignment
  }
]

#$View:[familystat 
#  root:[$Vlib:@ReptiliaTax_DB]
#  rootFields:{$Vfield:@DF_Name}
#  leaves:
#    $Vlib:[@GENBANK printOnlyEntryN:y 
#	      querysrs/icarus/db/vwf.i
#    $RCSfile: vwf.i,v $
#    $Revision: 1.3 $
#    $Date: 1997/03/17 23:22:07 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

VWF_DB:$library:[VWF group:@MUTATION_LIBS
  format:@VWF_FORMAT maxNameLen:30 ifiles:{'vwf.i' 'vwf.is' 'vwf.it'}
  files:{
    $file:'mut-LONG-list'
  }
]

VWF_FORMAT:$libformat:[syntax:@VWF_SYNTAX fileType:@TXT_FILE  
  printFormat:table tableFormat:left
  fields:{
    $field:@DF_ALL
    $field:[@DF_ID indexToken:id index:id
      tableToken:id tableFormat:right]
    $field:[@DF_Class indexToken:class index:str tableToken:t_class]
    $field:[@DF_NuclChange code:dnaSubst indexToken:'dnaSubst|subst' index:str
      tableToken:'dnaSubst|subst' tableFormat:left]
    $field:[@DF_DnaChangePos code:dnaSubst indexToken:'dnaSubst|pos' 
      index:int tableToken:'dnaSubst|pos' tableFormat:right]
    $field:[@DF_AaChange code:aaSubst indexToken:'aaSubst|subst' index:str
      tableToken:'aaSubst|subst' tableformat:left]
    $field:[@DF_ProtChangePos code:aaSubst indexToken:'aaSubst|pos' index:int
      tableToken:'dnaSubst|pos' tableFormat:right]
    $field:[@DF_FamilyN code:families indexToken:families index:int
      tableToken:families tableFormat:right]
    $field:[@DF_PatientN code:patent indexToken:patient index:int
      tableToken:patient tableFormat:right]
    $field:[@DF_PatientOrig code:patOri indexToken:patOri index:str
      tableToken:t_patOri tableFormat:left]
    $field:[@DF_AlleleN code:nAllele indexToken:nAllele index:int
      tableToken:nAllele tableFormat:right]
    $field:[@DF_FuncStudies code:funcStud indexToken:funcStud index:str
      tableToken:funcStud]
    $field:[@DF_LabName code:lab indextoken:lab index:str
      tableToken:t_lab]
    $field:[@DF_Comment code:cmnt indexToken:cmnt index:str
      tableToken:t_cmnt tableFormat:left]
  }
]


VWF_SYNTAX:$syntax:[file:"SRSDB:vwf.is" ignore:" "]
tOri index:str
      tableToken:t_patOri tabsrs/icarus/db/vwf.is
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: vwf.is,v $
#    $Revision: 1.4 $
#    $Date: 1997/03/18 13:43:24 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$rules={
  entry:    ~ {$In:[file:text] $Out pre {$Skip:0 $entryN+=1} init $entryN=0}
              ('Class:' {$Not} ln)*
              ('Class: ' {$entryFip=$Fip $Wrt} ln {$App} 
               ('---' {$Not} ln {$App})+)?
            ~
  # fields
  fields:     ~ {$In:entry $Out $Skip:1} 
                f_class f_subst f_families f_patient f_patOri f_nAllele 
                f_funcStud f_lab f_cmnt (f_refTit f_ref+)?
              ~

  f_class:    ~ {$Wrt:class}    ('Class:' ln)+ ~
  f_subst:    ~ {$Wrt:[s:$aa c:aaSubst] $Wrt:[s:$dna c:dnaSubst]}    
                /[^\n]+/ {$aa=$Ct $Len:40} ln {$dna=$Ct} 
                ('   ' /[^\n]+/ {$Print:[$Ct v:$aa] $Len:37}
                ln {$Print:[$Ct v:$dna]})* ~
  f_families: ~ {$Wrt:families} /[^:]+:[^A-Z]+/  ~
  f_patient:  ~ {$Wrt:patient}  'Affected patients' ln ~
  f_patOri:   ~ {$Wrt:patOri}   'Patient country' ln ~
  f_nAllele:  ~ {$Wrt:nAllele}  /[^:]+:[^A-Z]+/ ~
  f_funcStud: ~ {$Wrt:funcStud} /Function[^:]+:[^L]+/ ~
  f_lab:      ~ {$Wrt:lab}      'Lab:' ln ~
  f_cmnt:     ~ {$Wrt:cmnt}     'Comments:' ln (/ *\n/{$Not} ln)* ln ~
  f_refTit:   ~ {$Wrt:refTit}   'References' ln ln ~
  f_ref:      ~ {$Wrt:ref}      (/ *\n/{$Not} ln)* ln ~ 

  # indexing 
  id:         ~ {$In:entry $Out} /./ 
                {$Break:[cond:$entryN=='20'] $print:$ga $Wrt:[s:$entryN]} ~ 
  class:      ~ {$In:[fields c:class] $Out} 
                tag (word | sep)+ ~  
  families:   ~ {$In:[fields c:families] $Out} tag num {$Wrt} ~  
  patient:    ~ {$In:[fields c:patient] $Out} tag num {$Wrt} ~  
  patOri:     ~ {$In:[fields c:patOri] $Out} tag (word | sep)+ ~
  nAllele:    ~ {$In:[fields c:nAllele] $Out} tag num {$Wrt} ~  
  funcStud:   ~ {$In:[fields c:funcStud] $Out} tag /[yn?]/? {$Wrt} ~  
  lab:        ~ {$In:[fields c:lab] $Out} tag (word  | sep)+ ~  
  cmnt:       ~ {$In:[fields c:cmnt] $Out} tag (word | sep)+ ~  
  aaSubst:    ~ {$In:[fields c:aaSubst] $Out} tag (mut ('and' mut)*)? ~  
  dnaSubst:   ~ {$In:[fields c:dnaSubst] $Out} tag (mut ('and' mut)*)? ~  

  # table format
  t_class:    ~ {$In:[fields c:class]  $Out} tag /.*/ {$Wrt} ~
  t_patOri:   ~ {$In:[fields c:patOri] $Out} tag /.*/ {$Wrt} ~
  t_lab:      ~ {$In:[fields c:lab]    $Out} tag /.*/ {$Wrt} ~
  t_cmnt:     ~ {$In:[fields c:cmnt]   $Out} tag /.*/ {$Wrt} ~

#  table:      ~ {$In:[fields c:{cmnt patOri lab cmnt}] $Out} 
#                tag /.*/ {$Wrt:$Itc} ~

  # html
  h_fields:   ~ {$In:[fields t:html]} 
                (x{if:$ParInt:[isTable] == 1 $Fail}
                 (/Refere.+/ {$Rep:"<TR><TD COLSPAN=2><B>$Ct</B></TD></TR>"} |
                  /[0-9]\..+/ {$Rep:"<TR><TD COLSPAN=2>$Ct</TD></TR>"} |
                  /[^:]+:/ {$Rep:"<TR><TD NOWRAP VALIGN=TOP><B>$Ct</B></TD>"} 
                  /.*/? {$Rep:"<TD>$Ct</TD></TR>"})?)?
              ~ 

  # other stuff
  ln:         ~ /[^\n]*\n/ ~
  mut:        ~ /([A-Z])([0-9]+)([A-Z*])/ 
                {$Wrt:[s:"$2" c:pos] $Wrt:[s:"$1>$3" c:subst]} |  
                /[A-Za-z0-9]+/ {$Wrt:subst} ~
  num:        ~ /[0-9]+/ ~
  tag:        ~ /[^:]+:/ ~
  word:       ~ /[a-zA-Z0-9_$]+/ {$Uniq} ~
  sep:        ~ /[^a-zA-Z0-9_$]+/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/u1/srs/data/mutdb/vwf/mut-LONG-list.txt']
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields print:1] 
    $JobTokens:[$job name:id print:1] 
    $JobNext:$job
    $print:"-------->entry\n" 
  }
}



c:pos] $Wrt:[s:"$1>$3" c:subst]} |  
                /[A-Za-z0-9]+/ {$Wrt:subst} ~
  num:        ~ /[0-9]+/ ~
  tag:        ~ /[^:]+:/ ~
  word:       ~ /[a-zA-Z0-9_$]+/ {$Uniq} ~
  sep:        ~ /[^a-zA-Z0-9_$]+/ ~
}

# debugging 
if:$TestMode {
  $job = $JobNew:[prod:$rules skip:" " 
    fileName:'/u1/srs/data/mutdb/vwf/mut-LONG-list.txt']
  while:$JobHasInputsrs/icarus/db/vwf.it
#    
#    $RCSfile: vwf.it,v $
#    $Revision: 1.1 $
#    $Date: 1996/11/05 19:54:25 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |The database
    |of point mutations, insertions, deletions, and polymorphisms found in von
    |Willebrand Factor is maintained by David Ginsburg and J. Evan Sadler.
  www:
    |<A HREF="http://mmg2.im.med.umich.edu/vWF/">\
    |http://mmg2.im.med.umich.edu/vWF/</A>
#  ftp:
#    |
  email:
    |vwfdb@umich.edu
#  contact:
#    |
#  address:
#    |
#  literature:
#    |
#  updates:
#    |
#  fields:{
#  }  
}
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$dbInfo={
  description:
    |The database
    |of point mutations, insertions, deletions, and polymorphisms found in von
    |Willebrand Factor is maintained by David Ginsburg and J. Evan Sadler.
  www:
    |<A HREF="http://mmg2.im.med.usrs/icarus/db/ypd.i
#    $RCSfile: ypd.i,v $
#    $Revision: 1.7 $
#    $Date: 1997/03/03 18:34:30 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


YPD_DB:$library:[YPD group:@SEQRELATED_LIBS 
  comment:"Yeast Protein Databank" 
  format:@YPD_FORMAT maxNameLen:12 ifiles:{"ypd.i" "ypd.is"}
  files:{
    $file:YPD_ASCII
  }
]

YPD_FORMAT:$libformat:[fileType:@YPD_FILE syntax:@YPD_SYNTAX 
  tableFormat:left printFormat:table
  fields:{
    $field:@DF_ALL
    $field:[@DF_ID code:ygn index:id indexToken:id
      tableToken:'id']
    $field:[@DF_SwissProtName code:sgn index:link indexToken:'words|sgn'
      tableToken:'words|sgn']
    $field:[@DF_SaccGenomeDbName code:sgdn index:link indextoken:'words|sgdn'
      tableToken:'words|sgdn']
    $field:[@DF_Synonyms code:syn index:str indextoken:'words|syn' 
      tableToken:'words|syn']

    $field:[@DF_HeaderField name:'Technical Flags']
    $field:[@DF_IdentSeqFlag code:idf index:int indextoken:'number|idf'
      tableToken:'words|idf']
    $field:[@DF_RelatedSeqFlag code:csf index:int indextoken:'number|csf' 
      tableToken:'words|csf']
    $field:[@DF_DatabaseSource code:dbs index:int indextoken:'number|dbs'
      tableToken:'words|dbs']
    $field:[@DF_SystSeqFlag code:ssf index:int indextoken:'number|ssf'
      tableToken:'words|ssf']

    $field:[@DF_HeaderField name:'Calculated Data']
    $field:[@DF_IsoelectricPoint code:isop index:real indextoken:'number|isop'
      tableToken:'number|isop' tableFormat:right]
    $field:[@DF_IsoelectricPointPlusPos code:isopp index:real 
      indextoken:'number|isopp' tableToken:'number|isopp' tableFormat:right]
    $field:[@DF_IsoelectricPointPlusNeg code:isopn index:real 
      indextoken:'number|isopn' tableToken:'number|isopn' tableFormat:right]
    $field:[@DF_MolWeight code:molw index:int indextoken:'number|molw'
      tableToken:'number|molw' tableFormat:right]
    $field:[@DF_CodonBias code:codb index:real indextoken:'number|codb'
      tableToken:'number|codb' tableFormat:right]
    $field:[@DF_CodonAdaptIndex code:coda index:real indextoken:'number|coda'
      tableToken:'number|coda' tableFormat:right]

    $field:[@DF_HeaderField name:'Genetic data']
    $field:[@DF_ChromosomeNumber code:chrn index:str indextoken:'words|chrn'
      tableToken:'words|chrn']
    $field:[@DF_IsIntronInGene code:intg index:str indextoken:'words|intg'
      tableToken:'words|intg']
    $field:[@DF_KnockoutMut code:knm index:str indextoken:'words|knm'
      tableToken:'words|knm']

    $field:[@DF_HeaderField name:'Accession numbers']
    $field:[@DF_GenbankLink code:gb index:link indextoken:'words|gb'
      tableToken:'t_gb']
    $field:[@DF_PIRLink code:pir index:link indextoken:'words|pir'
      tableToken:'t_pir']
    $field:[@DF_SwissProtLink code:sw index:link indextoken:'words|sw'
      tableToken:'t_sw']
    $field:[@DF_YEPDLink code:yepd index:link indextoken:'words|yepd'
      tableToken:'words|yepd']

    $field:[@DF_HeaderField 
      name:'Subcellular localization and functional classification']
    $field:[@DF_MajorLocCategory code:malc index:str indextoken:'words|malc'
      tableToken:'words|malc']
    $field:[@DF_MinorLocCategory code:milc index:str indextoken:'words|milc'
      tableToken:'words|milc']
    $field:[@DF_MolecEnv code:mole index:str indextoken:'words|mole'
      tableToken:'words|mole']
    $field:[@DF_FunctClassific code:func index:str indextoken:'words|func'
      tableToken:'words|func']

    $field:[@DF_HeaderField name:'Post-translational modifications and length']
    $field:[@DF_NTermModif code:ntm index:str indextoken:'words|ntm'
      tableToken:'words|ntm']
    $field:[@DF_CTermModif code:ctm index:str indextoken:'words|ctm'
      tableToken:'words|ctm']
    $field:[@DF_Phosphorylation code:phos index:str indextoken:'words|phos'
      tableToken:'words|phos']
    $field:[@DF_Glycosylation code:glyc index:str indextoken:'words|glyc'
      tableToken:'words|glyc']
    $field:[@DF_NTermPrecursorLen code:ntpl index:int indextoken:'number|ntpl'
      tableToken:'number|ntpl' tableFormat:right]
    $field:[@DF_MatureProteinLen code:mpl index:int indextoken:'number|mpl'
      tableToken:'number|mpl' tableFormat:right]

    $field:[@DF_MetAdjustField code:maf  indextoken:'words|maf']

    $field:[@DF_HeaderField name:'Motifs']
    $field:[@DF_PotPhosphorylCdc28 code:pcdc index:int 
      indextoken:'number|pcdc' tableToken:'number|pcdc' tableFormat:right]
    $field:[@DF_PotPhosphorylCKII code:pckii index:int 
      indextoken:'number|pckii' tableToken:'number|pckii' tableFormat:right]
    $field:[@DF_PotPhosphorylPKA code:ppka index:int indextoken:'number|ppka'
      tableToken:'number|ppka' tableFormat:right]
    $field:[@DF_PotNLinkedGlycosyl code:nglyc index:int 
      indextoken:'number|nglyc' tableToken:'number|nglyc' tableFormat:right]
    $field:[@DF_PotTransmem code:ptm index:int indextoken:'number|ptm'
      tableToken:'number|ptm' tableFormat:right]

    $field:[@DF_HeaderField name:'N- and C-terminal sequence fragments']
    $field:[@DF_NtermPrecursorProt code:nspp]
    $field:[@DF_NtermMatureProt code:nsmp]
    $field:[@DF_CtermMatureProt code:csmp]

    $field:[@DF_HeaderField name:'Protein name/description and references']
    $field:[@DF_Description code:pn index:str indextoken:'words|pn'
      tableToken:'words|pn']
    $field:[@DF_RefList code:refs]     
  }
]

YPD_SYNTAX:$syntax:[file:"SRSDB:ypd.is" ignore:" \t\n"]
YPD_FILE:$filetype:[typename:'' maxline:10000]


DF_SwissProtName:$srsfield:[SwissProtName short:swn]
DF_SaccGenomeDbName:$srsfield:[SaccGenomeDbName  short:sgn]
DF_IdentSeqFlag:$srsfield:[IdentSeqFlag  short:isf]
DF_RelatedSeqFlag:$srsfield:[RelatedSeqFlag short:rsf]
DF_DatabaseSource:$srsfield:[DatabaseSource short:dbs]
DF_SystSeqFlag:$srsfield:[SystSeqFlag short:ssf]
DF_IsoelectricPointPlusPos:$srsfield:[IsoelectricPointPlusPos short:ipp]
DF_IsoelectricPointPlusNeg:$srsfield:[IsoelectricPointPlusNeg short:ipn]
DF_MolWeight:$srsfield:[MolWeight short:mow]
DF_CodonBias:$srsfield:[CodonBias short:cob]
DF_CodonAdaptIndex:$srsfield:[CodonAdaptIndex short:cai]
                          
DF_ChromosomeNumber:$srsfield:[ChromosomeNumber short:chn]
DF_IsIntronInGene:$srsfield:[IsIntronInGene short:iig group:@DF_ALL]
DF_KnockoutMut:$srsfield:[KnockoutMut short:knm group:@DF_ALL]
                          
DF_GenbankLink:$srsfield:[GenbankLink short:gbl]
DF_PIRLink:$srsfield:[PIRLink short:pil]
DF_SwissProtLink:$srsfield:[SwissProtLink short:swl]
DF_YEPDLink:$srsfield:[YEPDLink short:yel]
                          
DF_MajorLocCategory:$srsfield:[MajorLocCategory short:mal group:@DF_ALL]
DF_MinorLocCategory:$srsfield:[MinorLocCategory short:mil group:@DF_ALL]
DF_MolecEnv:$srsfield:[MolecEnv short:moe group:@DF_ALL]
DF_FunctClassific:$srsfield:[FunctClassific short:fcl group:@DF_ALL]
DF_NTermModif:$srsfield:[NTermModif short:ntm]
DF_CTermModif:$srsfield:[CTermModif short:ctm]
DF_Phosphorylation:$srsfield:[Phosphorylation short:pho]
DF_Glycosylation:$srsfield:[Glycosylation short:glc]
DF_NTermPrecursorLen:$srsfield:[NTermPrecursorLen short:npl]
DF_MatureProteinLen:$srsfield:[MatureProteinLen short:mpl]
                          
DF_MetAdjustField:$srsfield:[MetAdjustField short:maf]
DF_PotPhosphorylCdc28:$srsfield:[PotPhosphorylCdc28 short:ppc]
DF_PotPhosphorylCKII:$srsfield:[PotPhosphorylCKII short:ppk]
DF_PotPhosphorylPKA:$srsfield:[PotPhosphorylPKA short:ppp]
DF_PotNLinkedGlycosyl:$srsfield:[PotNLinkedGlycosyl short:png]
DF_PotTransmem:$srsfield:[PotTransmem short:ptm]
                          
DF_NtermPrecursorProt:$srsfield:[NtermPrecursorProt short:ntp]
DF_NtermMatureProt:$srsfield:[NtermMatureProt short:ntm]
DF_CtermMatureProt:$srsfield:[CtermMatureProt short:ctm]
DF_RefList:$srsfield:[RefList short:rel]
eld:[PotPhosphorylCdc28 short:ppc]
DF_PotPhosphorylCKII:$srsfield:[PotPhosphorylCKII short:ppk]
DF_PotPhosphorylPKA:$srsfield:[PotPhosphorylPKA short:ppp]
DF_PotNLinkedGlycosyl:$srsfield:[PotNLinkedGlycosyl short:png]
DF_PotTransmem:$srsfield:[PotTransmem short:ptm]
                    srs/icarus/db/ypd.is

$abbrev={          
  malc: {                                                        
    csk: "cytoskeletal"                                          
    cyt: "cytoplasmic"                                           
    nuc: "nuclear"                                               
    mit: "mitochondrial"                                         
    ves: "vesicles of secretory system"                          
    end: "endoplasmic reticulum"                                 
    gol: "Golgi"                                                 
    vac: "vacuolar"                                              
    lip: "lipid particles"                                       
    pla: "plasma membrane"                                       
    pox: "peroxisomal"                                           
    exc: "extracellular, including cell wall"                    
    mem: "unspecified membrane"                                  
  }                                                              
  milc: {                                                        
    mim: "mitochondrial inner membrane"                          
    mom: "mitochondrial outer membrane"                          
    spb: "spindle pole body"                                     
    ncl: "nucleolus"                                             
    num: "nuclear matrix"                                        
    nup: "nuclear pore"                                          
    wal: "cell wall"                                             
  }                                                              
  mole: {                                                        
    sol: "soluble"                                               
    int: "integral membrane"                                     
    per: "peripheral membrane"                                   
    act: "actin cytoskeleton-associated"                         
    tub: "tubulin cytoskeleton-associated"                       
    dna: "dna-associated (direct or indirect)"                   
    psf: "protein synthesis factor"                              
    rna: "rna-associated"                                        
    rib: "ribosome-associated"                                   
  }                                                              
  func: {                                                        
    aaa: "conserved ATPase domain (CDC48/PAS1/SEC18 family)"     
    aam: "amino acid metabolism"                                 
    abc: "ATP-binding cassette"                                  
    cyc: "cyclin"                                                
    gap: "GTPase activating protein"                             
    glm: "glucose metabolism (glycolysis)"                       
    gtp: "GTP-binding protein"                                   
    gef: "guanine nucleotide exchange factor"                    
    hsp: "Heat shock protein"                                    
    pep: "protease (other than proteasomal)"                     
    pki: "protein kinase"                                        
    ppa: "protein phosphatase"                                   
    pre: "proteasomal protein"                                   
    srp: "serine-rich protein (Tip1p/Tir1p) family"              
    trf: "transcription factor"                                  
    trs: "tRNA synthetase"                                       
    ubc: "ubiquitin-conjugating enzyme"                          
  }                                                              
  ntm: {                                                         
    A: acetylation                                               
    M: myristoylation                                            
    0: none                                                      
  }                                                              
  ctm: {                                                         
    F: farnesylation                                             
    G: geranylgeranylation                                       
    I: "gpi anchor"                                              
  }                                                              
  phos: {                                                        
    P: phosphorylation                                           
  }                                                              
  glyc: {                                                        
    N: "N-linked glycosylation"                                  
    O: "O-linked glycosylation"                                  
  }                                                              
}                                                                



$names={
  ygn:   {norm str "YPD gene name"}
  sgn:   {norm str "SWISS-PROT/LISTA gene name"}
  sgdn:  {norm str "Saccharomyces Genome Database name"}
  syn:   {norm str "Synonym list"}

         {titl nil "Technical flags"}
  idf:   {norm num "Identical sequence flags"}
  csf:   {norm num "Closely-related sequence flags"}
  dbs:   {norm num "Database source"}
  ssf:   {norm num "Systematic sequence flag"}

         {titl nil "Calculated data"}
  isop:  {norm num "Isoelectric point"}
  isopp: {norm num "Isoelectric point after adding 1 positive charge"}
  isopn: {norm num "Isoelectric point after adding 1 negative charge"}
  molw:  {norm num "Molecular weight"}
  codb:  {norm num "Codon bias"}
  coda:  {norm num "Codon adaptation index"}

         {titl nil "Genetic data"}
  chrn:  {norm str "Chromosome number"}
  intg:  {norm str "Presence or absence of intron in gene"}
  knm:   {norm str "Knockout mutation"}

         {titl nil "Accession numbers"}
  gb:    {norm str "GenBank"}
  pir:   {norm str "PIR-International"}
  sw:    {norm str "SWISS-PROT"}
  yepd:  {norm str "YEPD"}

         {titl nil "Subcellular localization and functional classification"}
  malc:  {abbr str "Major localization category"}
  milc:  {abbr str "Minor localization category"}
  mole:  {abbr str "Molecular environment"}
  func:  {abbr str "Functional classification"}

         {titl nil "Post-translational modifications and length"}
  ntm:   {abbr str "N-terminal modification"}
  ctm:   {abbr str "C-terminal modification"}
  phos:  {abbr str "Phosphorylation"}
  glyc:  {abbr str "N- or O-linked glycosylation"}
  ntpl:  {norm num "N-terminal precursor length"}
  mpl:   {norm num "Mature protein length"}

         {aa   nil "Amino acid composition"}
  maf:   {norm str "Met-adjust field"}

         {titl nil "Motifs"}
  pcdc:  {norm num 
                 "Potential sites for phosphorylation by Cdc28 protein kinase"}
  pckii: {norm num 
                  "Potential sites for phosphorylation by CKII protein kinase"}
  ppka:  {norm num "Potential sites for phosphorylation by PKA protein kinase"}
  nglyc: {norm num "Potential sites for N-linked glycosylation"}
  ptm:   {norm num "Potential transmembrane domains"}

         {titl nil "N- and C-terminal sequence fragments"}
  nspp:  {norm str "N-terminal sequence of precursor protein"}
  nsmp:  {norm str "N-terminal sequence of mature protein"}
  csmp:  {norm str "C-terminal sequence of mature protein"}

         {titl nil "Protein name/description and references"}
  pn:    {norm str "Protein name and descriptive phrases"}
  refs:  {norm str "List of references"}
}


$rules={
  tablehdr: ~ {$Out $exit} 
              (/[^\t\n]+/ {$print:"$Ct\n"} '\t'*)+ ~
  entry:    ~ {$In:[file:text] $Out} 
              (('YPD name' ln)? ln {$entryFip=$Fip $Wrt} ln?)?  ~

  # parsing fields
  fields:   ~ {$In:entry $Out pre{$n=1 $Skip:0} $Skip:1}
              (/[^\t\n]*/ {$tag=$names[$n][3] $code=$Key:$names[$n] 
                           $Prod:$names[$n][1] $n=$n+1}
              /\t|\n/)+ ~ 

  titl:     ~ x{$Wrt:[$code s:"\n** $tag **\n\n"]} ~
  norm:     ~ x{if:$Ct!="" $Wrt:[$code s:{"%s\n    %s\n" $tag $Ct}]} ~
  abbr:     ~ x{if:$Ct!="" 
                   $Wrt:[$code s:{"$tag\n    %s\n" $abbrev."$code".$Ct}]} ~
  aa:       ~ {init{$res={'    A' C D E F G H I K L M N P Q R S T V W Y}}}
              /\t|\n/ /[^\t\n]*/
              { $Wrt:[$code s:"$tag\n"]
                foreach:[$aa in:$res] {$Prod:residue $App:[s:"$aa:$num "]}
                $App:[s:"\n"]
              } ~
  residue:  ~ /[^\t\n]*/ {$num=$Ct} /\t|\n/ ~

  # indexing
  id:       ~ {$In:[fields c:ygn] $Out:id $Wrt:[s:$1]} 
              ln / *"?([,a-zA-Z0-9_-]+)"?/ ~ 
  number:   ~ {$In:[fields] $Out pre{$Skip:1}}
              x{if:$Itc == "" || $names.($Itc)[2]!=num $Fail} 
              tag num ~
  words:      ~ {$In:[fields] $Out pre{$Skip:1}}
              x{if:$Itc == "" || $names.($Itc)[2]!=str $Fail} 
              tag word+ ~

  # table display
  t_gb:     ~ {$In:[fields c:gb] $Out} t_dr ~ 
  t_pir:    ~ {$In:[fields c:pir] $Out} t_dr ~
  t_sw:     ~ {$In:[fields c:sw] $Out} t_dr ~ 
  t_dr:     ~ tag (/(<TD>)?(.+)(<\/TD>)/ {$Wrt:[s:$2]} | /[^\n]+/ {$Wrt}) ~ 
 

  # html display
  h_gb:     ~ {$In:[fields t:html c:gb] $Out} 
              tag acc {$Rep:{$ParStr:genbankR $Ct $Ct}}~
  h_pir:    ~ {$In:[fields t:html c:pir] $Out} 
              tag acc {$Rep:{$ParStr:pirR $Ct $Ct}}~
  h_sw:     ~ {$In:[fields t:html c:sw] $Out} 
              tag acc {$Rep:{$ParStr:swissR $Ct $Ct}} ~
  h_refs:   ~ {$In:[fields t:html c:refs] $Out} 
              tag (acc {$Rep:{$ParStr:ypdrefR $Ct $Ct}})* ~

  h_fields: ~ {$In:[fields t:html] $Out}
              ( /.*\\*\\*([^\\*]+)\\*\\*/
                {$Rep:"</TABLE><H3>$1</H3><TABLE BORDER=0>"} |
                /[^ ][^\n]+/ {$Rep:"<TR><TD VALIGN=TOP><I>$Ct:</I></TD>"} 
                /.+/ {$Rep:"<TD>$Ct</TD></TR>"}
              )? ~
  # other 
  acc:      ~ /[A-Z0-9]+/ ~
  ln:       ~ /[^\n]*\n/ ~
  num:      ~ /<[^>]+>/* /-?[0-9.]+/ {$Wrt:$Itc}~
  word:     ~ /[a-z0-9A-Z_-]+/ {$Uniq:$Itc} | /<[^>]+>/ | /[^a-z0-9A-Z_-]/ ~
  tag:      ~ /[^\n]*/ ~
}             

#$fil =  $fileOpen:"/data/ypd/YPD_ASCII"
#$job = $jobNew:[prod:$rules skip:" \n\t"]
#
#$jobNext:[$job file:$fil]
#while:$jobTokens:[$job name:words print:1 withCode:1] {
##  $jobTokens:[$job name:molw print:1]
##  $jobTokens:[$job name:fields withCode:0 print:1]
#  $jobEnd:$job
#  $jobNext:[$job file:$fil]
#  $print:"//\n"
#}
 ~ /[^\n]*\n/ ~
  num:      ~ /<[^>]+>/* /-?[0-9.]+/ {$Wrt:$Itc}~
  word:     ~ /[a-z0-9A-Z_-]+/ {$Uniq:$Itc} | /<[^>]+>/ | /[^a-z0-9A-Z_-]/ ~
  tag:      ~ /[^\n]*/ ~
}             

#$fil =  $fileOpen:"/data/ypd/YPD_ASCII"
#$job = $jobNew:[prod:$rules skip:" \n\t"]
#
#$jobNext:[$job file:$fil]
#while:$jobTokens:[$job name:words print:1 withCode:1] {
##  $jobTokens:[$job name:molw print:1]
##  $jobTokens:[$job name:fields withCode:0 print:1srs/icarus/util/

#
#    $RCSfile: arglist.i,v $
#    $Revision: 1.20 $
#    $Date: 1997/03/17 23:18:59 $
#    $Author: srs $
#
#
# definition of command line options for SRS programs
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$command:[name:srsbuild usage:"libName [libName]" 
  vars:{
    $arg:[name:"-help" type:help comment:"this message"]
    $arg:[name:"-w" parameter:showWarnings]
    $arg:[name:"-c" parameter:compress]
    $arg:[name:"-m" parameter:mergeIndex]
    $arg:[name:"-t" parameter:touchIndex]
    $arg:[name:"-f" parameter:fieldList]
    $arg:[name:"-b" parameter:buildIndex]
    $arg:[name:"-d" parameter:parseTest]
    $arg:[name:"-l" parameter:readLink]
    $arg:[name:"-r" parameter:relocateLib]
    $arg:[name:"-i" parameter:indexLink]
    $arg:[name:"-pn" parameter:buildPartIndex]
    $arg:[name:"-xdir" parameter:indexDirName]
    $arg:[name:"-odir" parameter:outDirName]
    $arg:[name:"-info" parameter:printLibInfo]
    $arg:[name:"-libs" parameter:printLibs]
    $arg:[name:"-rel" parameter:releaseName]
    $arg:[name:"-s" parameter:environment]
    $arg:["-debug" parameter:icaIsDebug]
  }
]
$command:[name:wgetz usage:"'queryExpression'" 
  vars:{
    $arg:[name:"-help"  comment:"this message" type:help]
    $arg:[name:"-e"     parameter:printEntireEntry]
    $arg:[name:"-fun"   parameter:wwwFunctionName]
    $arg:[name:"-id"    parameter:"userId"]
    $arg:[name:"-l"     parameter:"libList"] 
    $arg:[name:"-lib"   parameter:libName] 
    $arg:[name:"-entry" parameter:entryName] 
    $arg:[name:"-h3"    parameter:"isHtml3"]
    $arg:[name:"-style" parameter:"style"]
    $arg:[name:"-dbg"   parameter:"isDebug"]
    $arg:[name:"-lo"    parameter:"linkToLibs"]
    $arg:[name:"-qm"    parameter:"wwwFunctionName" 
      defaultstr:"PageQueryManager"]
    $arg:[name:"-qf"    parameter:"wwwFunctionName" 
      defaultstr:"PageQueryForm"]
    $arg:[name:"-top"   parameter:"wwwFunctionName" 
      defaultstr:PageStart]
    $arg:[name:"-start" parameter:"wwwFunctionName" 
      defaultstr:"PageSelectLibrary"]
    $arg:[name:"-libs"  parameter:"wwwFunctionName" 
      defaultstr:"WwwPrintLibList"]
    $arg:[name:"-rep"   parameter:"doRepeat"]
    $arg:[name:"-info"  parameter:"libInfo"]
    $arg:[name:"-linfo" parameter:"wwwFunctionName"
      defaultstr:"PageLinkInfo"]
    $arg:[name:"-from"    parameter:fromLibName]
    $arg:[name:"-to"      parameter:toLibName]
    $arg:[name:"-blast"   parameter:"prepBlastSearch"]
    $arg:[name:"-ht"      parameter:"printHelpTopic"]
    $arg:[name:"-viv"     parameter:"visitIndexValue"]
    $arg:[name:"-f"       parameter:fieldList]
    $arg:[name:"-bl"      parameter:listEntriesStartN]
    $arg:[name:"-ll"      parameter:listEntriesChunkSize]
    $arg:[name:"-bv"      parameter:viewEntriesStartN]
    $arg:[name:"-lv"      parameter:viewEntriesChunkSize]
    $arg:[name:"-lset"    parameter:listSetNumber]
    $arg:[name:"-vset"    parameter:viewSetNumber]
    $arg:[name:"-lquery"  parameter:listQuery]
    $arg:[name:"-msg"     parameter:getMessage] 
    $arg:[name:"-sf"      parameter:"seqFormat"]
    $arg:[name:"-sn"      parameter:subEntryN]
    $arg:[name:"-tr"      parameter:translateSequence]
    $arg:[name:"-network" parameter:printNetwork]
    $arg:[name:"-ls"      parameter:linkLibSelect]
    $arg:[name:"-link"    parameter:printLinkTable] 
    $arg:[name:"-odd"     parameter:getOddFile]
    $arg:[name:"-s"     parameter:environment]
    $arg:[name:"-q"       parameter:queryString]
    $arg:[name:"-use"     parameter:"readUserFile"]   
    $arg:[name:"-w"       parameter:"makeWild"]
    $arg:[name:"-mime"    parameter:"mimeType"]
    $arg:[name:"-qnum"    parameter:"queryNumber"]
    $arg:[name:"-dp" parameter:"deleteParam"]
    $arg:[name:"-bm" parameter:"mimeEntriesStartN"]
    $arg:[name:"-lm" parameter:"mimeEntriesChunkSize"]

    $arg:[name:"-m" parameter:"method"]

    $arg:[name:"-vroot" parameter:viewLibListRoot]
    $arg:[name:"-vleaf" parameter:viewLibListLeaf]


    $arg:[name:"-cv" parameter:currentView]
    $arg:[name:"-vt" parameter:isTable]
    $arg:[name:"-vn" parameter:viewNumber]

    $arg:[name:"-fbegs"     parameter:shiftbeginpos]
    $arg:[name:"-fends"     parameter:shiftendpos]
    $arg:[name:"-fbegsrend" parameter:isshiftbeginrelend]
    $arg:[name:"-fendsrbeg" parameter:isshiftendrelbegin]
    $arg:[name:"-takeuncf"  parameter:takeuncompletefeature]
    $arg:[name:"-takeuncsf" parameter:takeuncompleteshiftfeature]
    $arg:[name:"-bf" parameter:browseIndex]
    $arg:[name:"-blib" parameter:browseLibs]
    $arg:[name:"-color" parameter:wwwColorScheme]
    $arg:[name:"-sl" parameter:wwwSessionEntryList]
    $arg:[name:"-ifile" parameter:icarusFileType]
    $arg:[name:"-newId" parameter:makeNewUserId]
  }
]

$command:[name:getz usage:"'queryExpression'" 
  vars:{
    $arg:[name:"-help" comment:"this message" type:help]
    $arg:[name:"-e" parameter:printEntireEntry]
    $arg:[name:"-f" parameter:fieldList]
    $arg:[name:"-vf" parameter:viewFieldList]
    $arg:[name:"-l" parameter:libList]
    $arg:[name:"-w" parameter:makeWild]
    $arg:[name:"-r" parameter:doQueryReport]
    $arg:[name:"-lv" parameter:queryListValues]
    $arg:[name:"-lvf" parameter:queryListFromMatch]
    $arg:[name:"-lmin" parameter:minIndexValN]
    $arg:[name:"-xdir" parameter:indexDirName]
    $arg:[name:"-info" parameter:printLibInfo]
    $arg:[name:"-libs" parameter:printLibs]
    $arg:[name:"-view" parameter:viewName]
    $arg:[name:"-rs" parameter:viewRecordSep]
    $arg:[name:"-cs" parameter:viewColumnSep]
#    $arg:[name:"-fosn" parameter:listFOSN]
#    $arg:[name:"-fil" parameter:printToFile]
    $arg:[name:"-sf" parameter:seqFormat]
#    $arg:[name:"-pos" parameter:fosnWithPos]
#    $arg:[name:"-link" parameter:linkTable]
    $arg:[name:"-si" parameter:getStartupInfo]
    $arg:[name:"-html" parameter:isHTMLFormat]
#    $arg:[name:"options for retrieval of sequence features" type:title]
#    $arg:[name:"-fbegs" parameter:shiftbeginpos]
#    $arg:[name:"-fends" parameter:shiftendpos]
#    $arg:[name:"-fbegsrend" parameter:isshiftbeginrelend]
#    $arg:[name:"-fendsrbeg" parameter:isshiftendrelbegin]
#    $arg:[name:"-takeuncf" parameter:takeuncompletefeature]
#    $arg:[name:"-takeuncsf" parameter:takeuncompleteshiftfeature]
    $arg:[name:"-s" parameter:environment]
    $arg:[name:"-ifile" parameter:icarusFileType]
    $arg:["-debug" parameter:icaIsDebug]
  }
]
$command:[name:try usage:"'dataFile'" 
  vars:{
    $arg:["-help" comment:"this message" type:help]
    $arg:["-t" parameter:printTrace]
    $arg:["-debug" parameter:icaIsDebug]
    $arg:["-tt" parameter:printSyntaxTree]
    $arg:["-task" parameter:productionName]
    $arg:["-synx" parameter:syntaxName]
    $arg:["-pall" parameter:printAllTokLists]
    $arg:["-des" parameter:icaDbgExecStack defaultnum:2]
    $arg:["-dbs" parameter:icaDbgBuildStack defaultnum:4]
    $arg:["-2c" parameter:ica2cName]
    $arg:["-use" parameter:useIni]
    $arg:["-rb" parameter:readBuiltin]
    $arg:["-class" parameter:doClassInfo]
    $arg:["-ci" parameter:doCommandInfo]
  }
]
$command:[name:srscheck usage:""
  vars:{
    $arg:[name:"-help" type:help comment:"this message"]
    $arg:[name:"-xdir" parameter:indexDirName]
    $arg:[name:"-odir" parameter:outDirName]
    $arg:[name:"-info" parameter:printLibInfo]
    $arg:[name:"-e" parameter:etcDir]
    $arg:[name:"-l" parameter:checkLibList]
    $arg:[name:"-L" parameter:notCheckLibList]
    $arg:[name:"-header" parameter:srsEnvHeader]
    $arg:[name:"-o" parameter:updateScriptName]
    $arg:[name:"-s" parameter:environment]
  }
]
$command:[name:srspict usage:"" vars:{
    $arg:[name:"-help" type:help comment:"this message"]
    $arg:[name:"-n" parameter:doNetworkPict]
    $arg:[name:"-t" parameter:doGraphTablePict]
  }
]
arg:[name:"-info" parameter:printLibInfo]
    $arg:[name:"-e" parameter:etcDir]
    $arg:[name:"-l" parameter:checkLibList]
    $arg:[name:"-L" parameter:notCheckLibList]
    $arg:[name:"-header" parameter:srsEnvHeader]
    $arg:[name:"-o" parameter:updateScriptName]
    $arg:[nsrs/icarus/util/arglist.ic
#    $RCSfile: arglist.ic,v $
#    $Revision: 1.2 $
#    $Date: 1996/07/24 22:07:11 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

O_GETARG:$object:[name:arg typname:"arg_t" declname:args status:system 
  attrs:{
    $attribute:[name:name type:string declname:name valtype:{name text}
      required:y unnamed:y]
    $attribute:[name:type declname:type type:int valtype:name defaultval:0 
      enum:{
        $value:[name:bool val:2]
        $value:[name:string val:6]
        $value:[name:number val:3]
        $value:[name:real val:4]
        $value:[name:parameter val:0]
        $value:[name:help val:1]
        $value:[name:title val:2]
      }
    ]
    $attribute:[name:parameter declname:parameter type:string 
      valtype:{name text}
    ]
    $attribute:[name:comment declname:comment type:string valtype:{name text}]
    $attribute:[name:check type:function declname:check defaultstr:"(void *)" 
      valtype:constant]
    $attribute:[name:defaultnum type:int valtype:num declname:defaultNum]
    $attribute:[name:defaultstr type:string valtype:{name text}
      declname:defaultStr]
    $attribute:[name:defaultreal type:float valtype:num declname:defaultReal]
  }
]

O_COMMAND:$object:[name:command typname:"ARGoLIST" declname:"argList" 
  nchilds:1 child:@O_GETARG status:system 
  attrs:{
    $attribute:[name:name declname:name type:string valtype:name unnamed:y]
    $attribute:[name:usage declname:usage type:string valtype:{name text}]
    $attribute:[name:vars declname:"arg" type:child defaultval:@O_GETARG]
    $attribute:[declname:"argN" type:nr_of_childs defaultval:@O_GETARG]
  }
]
    $attribute:[name:defaultreal type:float valtype:num declname:defaultReal]
  }
]

O_COMMAND:$object:[name:command typname:"ARGoLIST" declname:"argList" 
  nchilds:1 child:@O_GETARG status:system 
  attrs:{
    $attribute:[name:name declname:name type:string valtype:name unnamed:y]
    $attribsrs/icarus/util/ascii.it
#    $RCSfile: ascii.it,v $
#    $Revision: 1.4 $
#    $Date: 1997/03/17 23:19:21 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$queryReport={
  head:
    |
    |////////////////////////////////////////////////////////////////////////////
  library:
    |
    |Values in "%s"
  value: 
    |    %-65s %d
  tail:
    |
    |////////////////////////////////////////////////////////////////////////////
    |
    |report of query "%s"
    |
}


$libInfo={
  head:
    |Databank: "%s" from group "%s", Release: %s
    |    
    |Data Fields (B=busy, C=compressed):
    |
    |Name                 Short  Type    Inx     Ids   No       No     Creation  B C
    |                     Name           (kb)    (kb)  Words    IDs    Date        
    |-------------------------------------------------------------------------------
  field:{
    head:
      |%-20s %-5s %-5s
    index:
      |%6d %7d %8d %9s  %d %d
    tail:
      |%s
  }
  links:{
    head:
      |
      |Links:
      |
    link:
      |%s "%s" to "%s"
  }
  Source:{
    dir:{
      head:
        |Directory: 
      name: 
        | "%s"
      tail:
        |    
    }
    files:{
      head:
        |Filename(s):
    }
  }
}

$linkInfo={
}

$classInfo={
}



$entry={
  inList:{
    envelope:{
      head: {
  	preformatted: ''
  	topicList:    ''
  	table:        ''
      }
      tail: {
  	preformatted: ''
  	topicList:    ''
  	table:        ''
      }
    }
    entry:{
      name:'' #?
      inListNoId: |%s
      rootName:   |%s
      leafName:   |%s
      head:''
      tail:''
    }
  }
  inTable:{
    # before first entry in a set
    head: ''
    # table header
    title:{
      library: ''
      field:   ''
      tail:    ''
    }
    entry:{
      head: ''
      tail: "($ParStr:viewRecordSep)"
      rootName: "%s($ParStr:viewColumnSep)"
      leafName: "%s($ParStr:viewColumnSep)"
      value:{
  	leftAlign:  ''
  	rightAlign: ''
  	center:     ''
  	listing:    ''
  	value:      '%s'
        empty:      ' '
        next:       '|'
  	tail:       "($ParStr:viewColumnSep)"
      }
      emptyValue:   " ($ParStr:viewColumnSep)"
      onlyEntryN:   "%d ($ParStr:viewColumnSep)"
    }
    tail: ''
  }
}


ld:   ''
      tail:    ''
    }
    entry:{
      head: ''
      tail: "($ParStr:viewRecordSep)"
      rootName: "%s($ParStr:viewColumnSep)"
      leafName: "%s($ParStr:viewColumnSep)"
      value:{
  	leftAlign:  ''
  	rightAlign:srs/icarus/util/builtin.i

#
# commands for processing icarus 4 with icarus 4
#
$com:[_prog f:IopProg_]
$com:[_opnd f:IopOpnd_ return:var
  args:{
    $var:[opnd t:strv unnamed:y]
    $var:[t t:strv]
  }
]
$com:[_list f:IopList_ return:var]
$com:[_assoc f:IopAssoc_ return:var
  args:{
    $var:[val t:var unnamed:y]
    $var:[key t:var]
  }
]
$com:[_binop f:IopBinop_ return:var
  args:{
    $var:[op t:strv unnamed:y] 
    $var:[a t:var] 
    $var:[b t:var]
  }
]
$com:[_strmake f:IopStrMake_ return:var]
$com:[_makearg f:IopMakeArg_ return:var
  args:{
    $var:[val t:var unnamed:y]
    $var:[name t:var]
  }
]
$com:[_select f:IopSelect_ return:var
  args:{
    $var:[key t:var]
    $var:[index t:var]
    $var:[var t:var]
  }
]
$com:[_setwrt f:IopSetWrite_ return:var
  args:{
    $var:[var t:var unnamed:y]
  }
]
$com:[_func f:IopFunc_ return:var]
$com:[_body f:IopBody_ return:var]
$com:[_ref f:IopRef_ return:var
  args:{
    $var:[name t:var unnamed:y]
    $var:[opt t:int]
  }
]

#flow control
$com:[_file f:IopFile_ return:var args:{$var:[file t:var unnamed:y]}]
$com:[_pre f:IopPre_ return:var args:{$var:[body unnamed:y t:var]}]
$com:[_init f:IopInit_ return:var args:{$var:[body unnamed:y t:var]}]
$com:[_for f:IopFor_ return:var
  args:{
    $var:[i t:var] 
    $var:[c t:var] 
    $var:[u t:var] 
    $var:[b t:var] 
  }
]
$com:[_foreach f:IopForeach_ return:var
  args:{
    $var:[body t:var] 
    $var:[list t:var] 
    $var:[var t:var] 
  }
]
$com:[_while f:IopWhile_ return:var
  args:{
    $var:[c t:var] 
    $var:[b t:var] 
  }
]
$com:[_if f:IopIf_ return:var]

#parsinge BNF rules
$com:[_prod f:IopProd_ return:object returnClass:node]
$com:[_endProd f:IopEndProd_ return:var
  args:{
    $var:[node t:object class:node]
    $var:[prod t:object class:node]
  }
]
$com:[_expr f:IopExpr_ return:object returnClass:node]
$com:[_term f:IopTerm_ return:object returnClass:node]
$com:[_regexp f:IopRegexp_ return:object returnClass:node 
  args:{$var:[reStr t:strv unnamed:y]}
]
$com:[_literal f:IopLiteral_ return:object returnClass:node 
  args:{$var:[name t:strv unnamed:y]}
]
$com:[_makeOpt f:IopMakeOpt_ return:object returnClass:node 
  args:{
    $var:[node t:object unnamed:y]
    $var:[t t:strv]
  }
]
$com:[_nodeProg f:IopNodeProg_ return:object returnClass:node 
  args:{
    $var:[node t:object unnamed:y]
    $var:[prog t:var unnamed:y ]
  }
]
$com:[_prodName f:IopProdName_ return:object returnClass:node 
  args:{
    $var:[name t:strv unnamed:y]
    $var:[lookahead t:int]
  }
]
$com:[_doCom f:IopCommand_ return:object returnClass:node]
$com:[_doInputEnd f:IopInputEnd_ return:object returnClass:node]
$com:[_nullNode f:IopNullNode_ return:object returnClass:node]

######



$com:[_push f:IopPush_
  args:{$var:[value t:var unnamed:y] $var:[stack t:int defInt:0]}]
$com:[_push1 f:IopPush_
  args:{$var:[value t:var unnamed:y] $var:[stack t:int defInt:1]}]
$com:[_push2 f:IopPush_ 
  args:{$var:[value t:var unnamed:y] $var:[stack t:int defInt:2]}]
$com:[_push3 f:IopPush_ 
  args:{$var:[value t:var unnamed:y] $var:[stack t:int defInt:3]}]
$com:[_push4 f:IopPush_ 
  args:{$var:[value t:var unnamed:y] $var:[stack t:int defInt:4]}]
$com:[_push5 f:IopPush_ 
  args:{$var:[value t:var unnamed:y] $var:[stack t:int defInt:5]}]

$com:[_pop f:IopPop_ return:var args:{$var:[stack t:int defInt:0]}]
$com:[_pop1 f:IopPop_ return:var args:{$var:[stack t:int defInt:1]}]
$com:[_pop2 f:IopPop_ return:var args:{$var:[stack t:int defInt:2]}]
$com:[_pop3 f:IopPop_ return:var args:{$var:[stack t:int defInt:3]}]
$com:[_pop4 f:IopPop_ return:var args:{$var:[stack t:int defInt:4]}]
$com:[_pop5 f:IopPop_ return:var args:{$var:[stack t:int defInt:5]}]

#
# end of icarus 4 build commands


##############################################################################
#
# commands for debugging icarus productions
#

$com:[Break show:y f:IopBreak time:initpre
  args:{
    $var:[prod unnamed:y t:strv]
    $var:[cond t:int rem:"Breaks only if condition is met." defInt:1]
    $var:[time t:int    
      enum:{
        $val:[pre n:1]
        $val:[post n:2]
      } 
    ]
  }
]
$com:[break f:IopBreak time:init
  args:{
    $var:[prod unnamed:y t:strv]
    $var:[time t:int    
      enum:{
        $val:[pre n:1]
        $val:[post n:2]
      } 
    ]
  }
]
$com:[next show:y f:IopNext]
$com:[cont show:y f:IopContinue]
$com:[tree show:y f:IopTree]
$com:[TestMode show:y f:IopTestMode return:int]

###### end debugging ###############################  



$com:[prod f:IopProd 
  args:{
    $var:[name unnamed:y]
  }
]
$com:[Prod f:IopProd show:y
  args:{
    $var:[name unnamed:y]
  }
]

$com:[CDefine f:IopCDefine
  args:{
    $var:[n t:int unnamed:y]
    $var:[name]
  }
]

# 'normal' icarus commands (level 3)
$com:[test f:IopTest rem:"Test command." return:int 
  args:{
    $var:[x t:int]
    $var:[y t:int]
    $var:[color]
  }
]

$com:[printProd f:IopPrintProduction rem:"Prints a production." return:int 
  args:{
    $var:[prod t:object class:production unnamed:y]
  }
]

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# commands for parsing
#
$com:[Parse show:y f:IopParse rem:"Parses a string."
  args:{
    $var:[prod t:list]
    $var:[string t:strv unnamed:y]
    $var:[start t:strv
      rem:"The name of the start symbol (production)."]
    $var:[file t:object class:file 
      rem:"Selects opened file to be read for input."]
    $var:[fileName t:strv
      rem:"Selects opened file to be read for input."]
    $var:[show t:int 
      rem:"Sets display of the syntax before parsing."]
    $var:[skip t:strv
      rem:"The set of characters to be skipped as white space"]
    $var:[comment t:strv
      rem:"Regular expression for skipping comments"]
    $var:[tree t:int 
      rem:"Flag if set requests printing the syntax tree."]
  }
]
$com:[JobNew show:y f:IopJobNew rem:"" return:object returnClass:job
  rem:
    |Creates a new parsing job and associates it with a syntax and
    |the input. Use \$JobTokens to start the parsing (lazy parsing) and
    |\$JobNext to move to the next job in the input stream.
  args:{
    $var:[prod t:list unnamed:y]
    $var:[skip t:strv
      rem:"The set of characters to be skipped as white space"]
    $var:[comment t:strv
      rem:"Regular expression for skipping comments"]
    $var:[file t:object class:file 
      rem:"Sets opened file as input."]
    $var:[str t:strv 
      rem:"Sets string as input."]
    $var:[show t:int 
      rem:"Sets display of the syntax before parsing."]
    $var:[tree t:int 
      rem:"Flag if set requests printing the syntax tree."]
    $var:[fileName t:strv
      rem:"Name of the file to be opened as input."]
  }
]
$com:[Fail show:y f:IopFail 
  rem:
    |Can be used only in an action symbol (like x{...}). If called the action node reports
    |a parsing error which is treated in the same way as a 'normal' parsing
    |error from, eg, a literal. 
]
$com:[JobHasInput show:y f:IopJobHasInput return:int
  rem:|Returns TRUE if the input file of the job is not 
      | finished
  args: {
    $var:[job t:object class:job unnamed:y]
  }

]

$com:[JobNext show:y f:IopJobNext rem:""
  args:{
    $var:[job t:object class:job unnamed:y]
    $var:[string t:string]
    $var:[start 
      rem:"The name of the start symbol (production)."]
    $var:[file t:object class:file 
      rem:"Selects opened file to be read for input."]
    $var:[fileName 
      rem:"Selects opened file to be read for input."]
  }
]
$com:[JobHasInput show:y f:IopJobHasInput return:int
  rem:|Returns TRUE if the input file of the job is not 
      | finished
  args: {
    $var:[job t:object class:job unnamed:y]
  }

]

$com:[JobKill show:y f:IopJobEnd rem:"" 
  args: {
    $var:[job t:object class:job unnamed:y]
  }
]
$com:[JobTokens show:y f:IopJobTokens return: int
  args:{
    $var:[job t:object class:job unnamed:y]
    $var:[name rem:"Name of the token list."]
    $var:[code]
    $var:[n t:int]
    $var:[print t:int]
    $var:[task]
    $var:[withCode t:int defInt:1]
    $var:[outFile t:object class:file rem:"Output file object."]
  }
]

$com:[In f:IopIn show:y time:initpre return:int
  rem:
    |Sets the input token table for parsing. 
    |Controls the lazy parsing execution by defining the connections
    |between productions 
  args:{ 
    $var:[in unnamed:y required:y t:strv rem:"Name of the input token table."]
    $var:[ic t:strv rem:"Token code."]
    $var:[n t:int defInt:-1 rem:"Numerical token code."]
    $var:[p t:strv rem:"Name of production to be linked."] 
    $var:[t t:strv rem:"Name of task that if results in forced parsing."]
    $var:[count t:strv rem:""]
    $var:[var t:var rem:""]
    $var:[file t:strv rem:"Symbolic name of the input file."]
    $var:[share t:strv rem:"Symbolic name file that shares physical file."]
    $var:[select t:int rem:|Selects token with specified count number. 
                           |The value 0 selects all tokens 
                           |(only in combination with "count").
    ]
    $var:[c t:var rem:""]
  } 
] 
$com:[Out f:IopOut show:y time:initpre   
  rem:
    |Sets the output table for all writing of tokens for the 
    |current production and its dependants.
  args:{
    $var:[name unnamed:y t:strv rem:"Name of ouput token table."]
  } 
] 
$com:[out f:IopOut time:initpre   
  rem:
    |Sets the output table for all writing of tokens for the 
    |current production and its dependants.
  args:{
    $var:[name unnamed:y t:strv rem:"Name of ouput token table."]
  } 
] 

$com:[Getc f:IopGetc  call:direct 
  args:{$var:[len]}
  rem:
    |Defines \$Ct to be a token starting at the current position
    |and with the given length. Moves the current position, as if
    | the given number of characters would have been really parsed
]
$com:[Len f:IopRestrictLength  time:prepost call:direct 
  args:{$var:[len]}
  rem:
    |Limits the parsing to stop after 'len' characters
    |Must be the last command in a production. See also \$Mov
]
$com:[Mov f:IopMove show:y call:direct time:pre 
  args:{$var:[len]}
  rem:
    |Skips the next 'len' characters while parsing 
]
$com:[Wrt f:IopWrt show:y call:direct 
  rem:
    |This function can be called inside an action attached to the symbol of
    |a production. It writes the match of the current symbol or a specified
    |string into the output table specified by the most recent call of \$out.
  args:{ 
    $var:[c unnamed:y rem:"token code as a name"]
    $var:[n t:int rem:"token code as a number"]
    $var:[s rem:
      |string to be written to the token table.
      |If left unspecified the current match, or current token (\$Ct)
      |is written.
    ]
  } 
] 
$com:[wrt f:IopWrt call:direct 
  rem:
    |This function can be called inside an action attached to the symbol of
    |a production. It writes the match of the current symbol or a specified
    |string into the output table specified by the most recent call of \$out.
  args:{ 
    $var:[c unnamed:y rem:"token code as a name"]
    $var:[n t:int rem:"token code as a number"]
    $var:[s rem:
      |string to be written to the token table.
      |If left unspecified the current match, or current token (\$Ct)
      |is written.
    ]
  } 
] 
$com:[Uniq f:IopUniq show:y call:direct 
  rem:
    |Exactly as \$Wrt but writes the token only into the table if it does
    |not already exist. Unique here means that both the token string as the
    |token code are used for comparison.
  args:{ 
    $var:[c unnamed:y rem:"token code as a name"]
    $var:[n t:int rem:"token code as a number"]
    $var:[s rem:
      |string to be written to the token table.
      |If left unspecified the current match, or current token (\$Ct)
      |is written.
    ]
  } 
] 
$com:[App show:y f:IopApp call:direct 
  args:{ 
    $var:[s unnamed:y rem:"String to be written to the token table."] 
  } 
  rem:|Appends the string token to the output token table
] 
$com:[app f:IopApp call:direct 
  args:{ 
    $var:[s unnamed:y rem:"String to be written to the token table."] 
  } 
  rem:|Old syntax, see \$App
] 
$com:[Rep show:y f:IopRep 
  rem:
    |Replaces the current token (\$Ct) in case of a symbol match. The
    |input cursor is moved after the replaced string. 
  args:{ 
    $var:[s t:var unnamed:y 
      rem:"String with which current match is to be replaced"]
  } 
] 
$com:[rep f:IopRep 
  rem:|Old syntax, see \$Rep 
  args:{ 
    $var:[s t:var unnamed:y 
      rem:"String with which current match is to be replaced"]
  } 
] 
$com:[Not show:y f:IopNot time:init
  rem:|The rest of the production matches only if the preceding 
      |terminal doesn't match. (see \$Probe) The parsing position  
      |(cursor) is not moved when matching the preceding terminal  
] 
$com:[not f:IopNot time:init] 
$com:[Probe show:y f:IopProbe time:init
  rem:|The rest of the production matches only if the preceding 
      |terminal matches. (see \$Not) The parsing position  
      |(cursor) is not moved when matching the preceding terminal  
] 
$com:[Noskip show:y f:IopNoskip time:init
  rem:|Inactivates skipping of white space
] 
$com:[noskip f:IopNoskip time:init] 

$com:[Request show:y f:IopRequest 
  args:{ 
    $var:[name unnamed:y rem:"Name of requested token table."]
  } 
  rem:|Activates the lazy parsing chain producing the 
      |requested token table, but doesn't connect the input 
      |to it. (see \$In)
] 

$com:[Nocase show:y f:IcaOpSetFlag 
  args:{$var:[flag defStr:nocase]}
] 

$com:[push f:IopPush 
  args:{ 
    $var:[value t:var unnamed:y]  
    $var:[stack t:int defInt:0] 
  }
]
$com:[push1 f:IopPush 
  args:{
    $var:[value t:var unnamed:y] 
    $var:[stack t:int defInt:1]
  }
]
$com:[push2 f:IopPush 
  args:{
    $var:[value t:var unnamed:y] 
    $var:[stack t:int defInt:2]
  }
]
$com:[push3 f:IopPush 
  args:{
    $var:[value t:var unnamed:y] 
    $var:[stack t:int defInt:3]
  }
]
$com:[push4 f:IopPush 
  args:{
    $var:[value t:var unnamed:y] 
    $var:[stack t:int defInt:4]
  }
]
$com:[push5 f:IopPush 
  args:{
    $var:[value t:var unnamed:y] 
    $var:[stack t:int defInt:5]
  }
]

$com:[pop f:IopPop return:var 
  args:{$var:[stack t:int defInt:0]}]
$com:[pop1 f:IopPop return:var  
  args:{$var:[stack t:int defInt:1]}]
$com:[pop2 f:IopPop return:var  
  args:{$var:[stack t:int defInt:2]}]
$com:[pop3 f:IopPop return:var  
  args:{$var:[stack t:int defInt:3]}]
$com:[pop4 f:IopPop return:var 
  args:{$var:[stack t:int defInt:4]}]
$com:[pop5 f:IopPop return:var  
  args:{$var:[stack t:int defInt:5]}]

$com:[Exit show:y f:IopExit
  args:{$var:[val unnamed:y defInt:0]}]
$com:[exit f:IopExit
  args:{$var:[val unnamed:y defInt:0]}]


# global parameter list
$com:[parStr f:IopParStr return:strv rem:
    |Returns the value of a 'string' parameter or sets its value if ".set" is 
    |defined.
  args:{
    $var:[name t:strv unnamed:y rem:"Parameter name."]
    $var:[set t:strv]
  }
]
$com:[parInt f:IopParInt return:int rem:
    |Returns the value of an 'int' parameter or sets its value if ".set" is 
    |defined.
  args:{
    $var:[name t:strv unnamed:y rem:"Parameter name."]
    $var:[set t:int defInt:2]
  }
]
$com:[ParStr show:y f:IopParStr return:strv rem:
    |Returns the value of a 'string' parameter or sets its value if ".set" is 
    |defined.
  args:{
    $var:[name t:strv unnamed:y rem:"Parameter name."]
    $var:[set t:strv]
  }
]
$com:[ParInt show:y f:IopParInt return:int rem:
    |Returns the value of an 'int' parameter or sets its value if ".set" is 
    |defined.
  args:{
    $var:[name t:strv unnamed:y rem:"Parameter name."]
    $var:[set t:int defInt:2]
  }
]
$com:[ParDel show:y f:IopParDel rem:
    |Deletes the parameter with specified name.
  args:{
    $var:[name t:strv unnamed:y rem:"Parameter name."]
  }
]

$com:[Env show:y f:IopEnv return:strv 
  rem:
    |Optionally sets and returns the value an environment variable.
  args:{
    $var:[name t:strv unnamed:y rem:"Name of environment variable."]
    $var:[set t:strv rem:"New string value of the environment variable."]
  }
]
$com:[AltStr  f:IopAltStr return:strv
  rem:|Returns one of two strings depending whether condition is 
      |true or false.
  args:{
    $var:[cond t:int required:y unnamed:y rem:"The condition."]
    $var:[t t:strv rem:"String to be returned if condition is true."]
    $var:[f t:strv rem:"String to be returned if condition is false"]
  }
]
$com:[Alt  f:IopAltStr show:y return:strv
  rem:|Returns one of two strings depending whether condition is 
      |true or false.
  args:{
    $var:[cond t:int required:y unnamed:y rem:"The condition."]
    $var:[t t:strv rem:"String to be returned if condition is true."]
    $var:[f t:strv rem:"String to be returned if condition is false"]
  }
]
$com:[Foreach f:IopPrintForeach show:y return:strv
  rem:|prints each element in the list with specified separators.
  args:{
    $var:[var t:var unnamed:y rem:'Name of variable used for iteration']
    $var:[in t:list rem:'The list.']
    $var:[s t:var rem:'String to print for each list element']
    $var:[sep t:var rem:'Separator strings to be printed between elements']
  }
]

$com:[subStr f:IcaOpSubStr return:strv
  args:{
    $var:[str t:strv  unnamed:y rem:"Classical substr function"]
    $var:[s t:int required:y rem:"Start posilion inside of string"]
    $var:[l t:int required:n defInt:0 rem:"subStr length if ommited - suffix"]
  }
]

$com:[System f:IopSystem return:strv
  args:{
    $var:[com required:y t:strv unnamed:y rem:"Unix command"]
    $var:[script t:strv rem:"String (text) that is written to a script and then executed"]
    $var:[scriptName t:strv rem:"Name of the script that is to be generated."]
    $var:[out t:strv rem:"Name of output file  (Use 'stdout' for standard output)."]
    $var:[error t:strv rem:"Name of error output file  (Use 'stdout' for standard output)."]
  }
]

$com:[FileOpen show:y f:IopFileOpen return:object returnClass:file 
  args:{
    $var:[name t:strv unnamed:y 
      rem:|The name of the file; if omitted stdin (for read access mode) 
          |or stdout (write access mode) are assumed.
    ]
    $var:[mode t:int defInt:1 rem:'Access mode for opened file'
      enum:{
        $val:[read n:1]
        $val:[write n:2]
      }
    ]
  }    
]
$com:[FileClose show:y f:IopFileClose
  args:{
    $var:[file t:object class:file unnamed:y]
  }    
]
$com:[FileName show:y f:IopFileName return:strv
  args:{
    $var:[type t:int unnamed:y defInt:1
      enum:{
        $val:[path n:1]
        $val:[dir  n:2]
        $val:[name n:3]
        $val:[file n:4]
        $val:[ext  n:5]
      }
    ]
  }
] 


$com:[Print show:y f:IopPrint rem:"Prints a string."
  args:{
    $var:[s t:var unnamed:y]
    $var:[f t:object class:file]
    $var:[mode t:int
      enum:{
	 $val:[normal n:0]
	 $val:[raw    n:1]
      }
    ]
    $var:[v t:var rem:"Appends the string to specified string variable."]
  }
]

$com:[dp show:y f:IopDebugPrint rem:"Printing within the debugger"
  args:{
    $var:[s t:var unnamed:y]
  }
]

$com:[print f:IopPrint rem:"Prints a string."
  args:{
    $var:[s t:var unnamed:y]
    $var:[f t:object class:file]
    $var:[mode t:int
      enum:{
	 $val:[normal n:0]
	 $val:[raw    n:1]
      }
    ]
    $var:[v t:var rem:"Appends the string to specified string variable."]
  }
]



$com:[StrFormat f:IopPrintFormat return:strv
  rem:|Prints a string with the specified format.
  args:{
    $var:[s t:strv unnamed:y]
    $var:[label t:strv rem:"Label to be printed at begin of each line."]
    $var:[width t:int rem:"Maximum width of output lines."]
    $var:[indent t:int rem:"Indentation for all lines."]
    $var:[firstIndent t:int rem:"Indentation of first line."]
  }
]

$com:[It show:y f:IopInToken return:strv
  args:{
    $var:[n t:int unnamed:y]
  }
  rem:
  |Returns the input token (token which serves as input for 
  |the current production through the \$In command)
]
$com:[itc f:IopInTokenCode return:strv]
$com:[Itc show:y f:IopInTokenCode return:strv rem:
  |Returns the token code of the input token (see \$It)
]


$com:[ct  f:IopCurrToken return:strv]
$com:[Ct  show:y f:IopCurrToken return:strv rem:
  |Returns the current token (string parsed in the preceding
  |parsing block)
]
$com:[Key  show:y f:IopKey return:strv
  args:{
    $var:[val t:var unnamed:y]
  }
  rem:|Returns the symbolic tag associated with the given list element
]

$com:[IsLast  show:y f:IopIsLast return:int
  rem:|Returns TRUE if the element is the last in the list.
]
$com:[IsFirst  show:y f:IopIsFirst return:int
  rem:|Returns TRUE if the element is the first in the list.
]
$com:[ListLen show:y f:IopListLen return:int
  rem:|Returns the number of elements in the list
  args: {
    $var:[list t:var unnamed:y]
  }
]

$com:[Fip show:y f:IopFip return:int 
  args:{
    $var:[switch t:int unnamed:y]
  }
  rem:
    |Returs the file pointer to the current 
    |position in the input file
]
$com:[fip f:IopFip return:int 
  args:{
    $var:[switch t:int unnamed:y]
  }
]
$com:[File show:y f:IopFile return:object returnClass:file
  rem:|Returns the file object of the currrent job.
]

$com:[skip  f:IopSetSkip 
  rem:
    |Controls skipping of white space during parsing which is
    |active by default.
  args:{
    $var:[state t:int  unnamed:y rem:
      |0: turns skipping white space off<BR>
      |1: turns it on again
    ]
    $var:[s t:strv]
  }
]
$com:[Skip show:y f:IopSetSkip 
  rem:
    |Controls skipping of white space during parsing which is
    |active by default.
  args:{
    $var:[state t:int  unnamed:y rem:
      |0: turns skipping white space off<BR>
      |1: turns it on again
    ]
    $var:[s t:strv]
  }
]

$com:[Eval show:y f:IopEval
  args:{
    $var:[prog t:strv unnamed:y]
  }
]

$com:[Trim show:y f:IopStrTrim return:strv 
  rem:"Cuts leading or trailing white space from the string."
  args:{
    $var:[s t:strv unnamed:y]
    $var:[skip t:strv 
      rem:|String containing characters to be removed from ends.
    ]

  }
]

$com:[1 show:y f:IopSubMatch return:strv args:{$var:[n defInt:1 t:int]}
  rem:
    |Returns the first submatch of the most recent regular expression
    |matching. The submatch is indicated by parentheses within the
    |regular expression and the opening parenthesis is used for counting.
    |\$2, \$3 until \$9 will return the submatches with the respective
    |number. \$0 returns the entire match.
  ]
$com:[2 f:IopSubMatch return:strv args:{$var:[n defInt:2 t:int]}]
$com:[3 f:IopSubMatch return:strv args:{$var:[n defInt:3 t:int]}]
$com:[4 f:IopSubMatch return:strv args:{$var:[n defInt:4 t:int]}]
$com:[5 f:IopSubMatch return:strv args:{$var:[n defInt:5 t:int]}]
$com:[6 f:IopSubMatch return:strv args:{$var:[n defInt:6 t:int]}]
$com:[7 f:IopSubMatch return:strv args:{$var:[n defInt:7 t:int]}]
$com:[8 f:IopSubMatch return:strv args:{$var:[n defInt:8 t:int]}]
$com:[9 f:IopSubMatch return:strv args:{$var:[n defInt:9 t:int]}]

$com:[SetFunctions f:IopSetFunctions 
  args:{
    $var:[name unnamed:y]
  }
]

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#                                                                              
# implementation of the srs query language
#                                                                              
$com:[SetResult f:QuerySaveResult 
  args:{
    $var:[set t:object class:set unnamed:y]
    $var:[q t:strv]
  }
]
$com:[DbGroup f:QueryDBGroup return:object returnClass:dbGroup 
  args:{ 
    $var:[init]
    $var:[db t:string]
    $var:[group t:object class:dbGroup unnamed:y]
  }
]

$com:[SetRetrRange f:QueryRangeSearch return:object returnClass:set 
  args:{
    $var:[index required:y]
    $var:[group t:object class:dbGroup unnamed:y]
    $var:[l t:string]
    $var:[h t:string]
    $var:[le t:int]
    $var:[re t:int]
  }
]

$com:[SetRetrStr f:QueryStrSearch return:object returnClass:set 
  args:{
    $var:[s t:strv]  
    $var:[index required:y]
    $var:[group t:object class:dbGroup unnamed:y]
  }
]
$com:[SetLogOp f:QueryLogOp return:object returnClass:set 
  args:{
    $var:[op unnamed:y]
    $var:[s1 t:object class:set]
    $var:[s2 t:object class:set]
  }
]
$com:[SetLinkOp f:QueryLinkOp return:object returnClass:set 
  args:{
    $var:[op unnamed:y]
    $var:[s1 t:object class:set]
    $var:[s2 t:object class:set]
  }
]
$com:[SetAssign f:QuerySetAssign return:object returnClass:set
  args:{
    $var:[name unnamed:y t:strv]
    $var:[s t:object class:set]
  }
]
$com:[SetGet f:QuerySetGet return:object returnClass:set 
  args:{
    $var:[name unnamed:y]
    $var:[fileName]
  }
]
$com:[MakeWild f:QueryOpMakeWild return:strv 
  args:{
    $var:[s t:strv unnamed:y]
  }
]
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



$com:[GCGwordsearch f:GCGWordsearch 
  args:{
    $var:[infile1 rem:"Name of input file with the search probe."]
    $var:[infile2 rem:"Name of input file with the data bank."]
  }
]


$com:[setFormat f:EntryIopSetFieldFormat
  args:{
    $var:[field t:strv unnamed:y ]
    $var:[set t:strv]
  }
]

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# sequence manipulation
#


$com:[SeqGet2Bit show:y f:SeqIopGet2Bit
  rem:
    |Reads a sequence in GCG's 2BIT format into supplied sequence object 
    |which can be created by \$SeqNew. If the sequence object contains 
    |a sequence already the sequence read is appended. This is useful
    |to collect split sequences as found in the GCG formatted sequence
    |databanks.
  args:{
    $var:[s unnamed:y t:object class:sequence
      rem:"Sequence in which to store the sequence."]
    $var:[file t:object class:file unnamed:y
      rem:"File object with the sequence."]
    $var:[len t:int rem:"Length of the sequence to be read."]
#    $var:[overlap t:int rem:"Overlap of split sequence parts."]
  }
]

$com:[SeqCut show:y f:SeqIopCut
  rem:
    |Cuts away specified part of the sequence
  args:{
    $var:[s unnamed:y t:object class:sequence]
    $var:[from t:int]
    $var:[len t:int]
  }
]

$com:[SeqNew show:y f:SeqIopNew return:object returnClass:sequence 
  rem:
    |Creates a new sequence object.
  args:{
    $var:[name t:strv unnamed:y ]
    $var:[list t:object class:sequence]
  }
]
$com:[SeqApp show:y f:SeqIopApp return:object returnClass:sequence 
  args:{
    $var:[seq unnamed:y t:object class:sequence]
    $var:[s t:strv]
  }
]
$com:[SeqMake show:y f:SeqIopMake return:object returnClass:sequence 
  args:{
    $var:[seq unnamed:y t:object class:sequence]
  }
]
$com:[SeqTrunc show:y f:SeqIopTrunc return:object returnClass:sequence 
  args:{
    $var:[seq unnamed:y t:object class:sequence]
    $var:[len t:int]
  }
]

$com:[SeqLen show:y f:SeqIopLen return:int
  args:{$var:[seq unnamed:y t:object class:sequence]}
  rem:"Returns the length of the sequence."
]
$com:[SeqPrint show:y f:SeqIopPrint 
  rem:"Prints a sequence in various formats."
  args:{
    $var:[seq unnamed:y t:object class:sequence]
    $var:[s t:strv rem:'The sequence as a string value.']
    $var:[name]
    $var:[format t:int
      enum:{
        $val:[gcg     n:1] 
        $val:[msf     n:2]
        $val:[pir     n:3]
        $val:[plain   n:4]
        $val:[fasta   n:5]
        $val:[embl    n:6]
        $val:[swiss   n:7]
        $val:[clustal n:8]
      } 
    ]
    $var:[width t:int defInt:60]
  }
]

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$com:[calc f:IopCalc return:int
  args:{
    $var:[op unnamed:y]
    $var:[l t:int]
    $var:[r t:int]
  }
]

$com:[strlen  f:IopStrlen return:int
  args:{
    $var:[s unnamed:y]
  }
]
$com:[Strlen f:IopStrlen return:int
  args:{
    $var:[s unnamed:y]
  }
]

$com:[StrLen show:y f:IopStrLen return:int
  args:{
    $var:[s unnamed:y t:strv]
  }
]
$com:[StrApp show:y f:IopStrApp 
  args: {
    $var:[v unnamed:y t:var]
    $var:[s t:strv]
  }
]
$com:[StrTrans f:IopStrTrans show:y return:strv
  rem:|Translates all characters in the 'from' set to the character
      |at the equivalent position in the 'to' set.
  args:{
    $var:[s t:strv unnamed:y]
    $var:[from t:strv]
    $var:[to t:strv]
  }
]

$com:[StrReplace f:IopStrReplace show:y return:strv
  rem:|Translates all occurences of 'from' 
      |to strings specified by 'to'.
  args:{
    $var:[s t:strv unnamed:y]
    $var:[from t:strv]
    $var:[to t:strv]
  }
]

$com:[StrLower f:IopStrLower show:y return:strv
  rem:|Converts all characters of the input string into lower case.
  args:{
    $var:[s t:strv unnamed:y]
  }
]
$com:[StrUpper f:IopStrUpper show:y return:strv
  rem:|Converts all characters of the input string into upper case.
  args:{
    $var:[s t:strv unnamed:y]
  }
]


$com:[StrPad show:y f:IopStrPad return:strv
  rem:|Pads a string with specified character if input string is 
      |shorter than requested length. 
  args:{
    $var:[s t:strv unnamed:y rem:"Input string."]
    $var:[len t:int rem:"Length of the result string."]
    $var:[c t:strv rem:"Character used for padding."]
  }
]
$com:[HtmlSpace f:IopHtmlSpace return:string 
  args:{
    $var:[thirds t:int unnamed:y]
    $var:[s t:int]
    $var:[l t:int]
  }
]

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# binary operators
#
#$com:['+' f:IopAdd return:int args:{$var:[t:int] $var:[t:int]}]
#$com:['+' f:IopPlusReal return:real args:{$var:[t:real] $var:[t:real]}]
#$com:['+' f:IopPlusStr return:string args:{$var:l $var:r}]
#$com:['+' f:IopPlusVar return:string args:{$var:l $var:r}]

$com:['='  f:IopAss    return:var args:{$var:[l t:var] $var:[r t:var]}]
$com:['+'  f:IopAdd    return:int args:{$var:[l t:var] $var:[r t:var]}]
$com:['<'  f:IopLT     return:int args:{$var:[l t:var] $var:[r t:var]}]
$com:['>'  f:IopGT     return:int args:{$var:[l t:var] $var:[r t:var]}]
$com:['==' f:IopEq     return:int args:{$var:[l t:var] $var:[r t:var]}]
$com:['*'  f:IopMul    return:int args:{$var:[l t:var] $var:[r t:var]}]
$com:['/'  f:IopDivide return:int args:{$var:[l t:var] $var:[r t:var]}]
$com:['!=' f:IopNEq    return:int args:{$var:[l t:var] $var:[r t:var]}]
$com:['-'  f:IopSubt   return:int args:{$var:[l t:var] $var:[r t:var]}]
$com:['+=' f:IopAddAss return:int args:{$var:[l t:var] $var:[r t:var]}]
$com:['&&' f:IopLogAnd return:int args:{$var:[l t:var] $var:[r t:var]}]
$com:['||' f:IopLogOr return:int args:{$var:[l t:var] $var:[r t:var]}]

#$convert:[int to:string cost:]
#$convert:[int to:strv cost:]
#$convert:[int to:strv]


$com:[debug  f:IopSetDebug
  args:{
    $var:[state t:int unnamed:y defInt:0]
  }
]
# for the 'templ' module
$com:[labelAdd f:TemplIcaAddLabel 
  args:{
    $var:[name t:strv unnamed:y]
    $var:[fip t:int]
  }
]


#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# commands for feature parsing
#

#calculator stack

$com:[SdbRetrieve f:SdbRetrieve return:strv
  args:	{
    $var:[acc t:strv unnamed:y defstr:""]
    $var:[db  t:strv defstr:""]
  }
]

$com:[SdbPop f:SdbPop ]
$com:[SdbPush f:SdbPush]
$com:[SdbEval f:SdbEval return:strv]

$com:[SdbChunk f:SdbChunk 
  args:{
    $var:[seq t:strv unnamed:y]
    $var:[to t:int defint:-2]
    $var:[uncertain t:int defint:0]
  }	
]

$com:[SdbFeature f:SdbFeature 
  args:{
    $var:[feature t:int unnamed:y]
  }
]
$com:[SdbComplement f:SdbComplement]
$com:[SdbReplace f:SdbReplace]
$com:[SdbJoin f:SdbJoin]

$com: [SeqGetFt f:SdbGetFeatureSequence return:strv
  args: {
    $var:[expr t:strv unnamed:y]
    $var:[db t:strv]
    $var:[shift t:int defint:0]
    $var:[left t:int defint:0]
    $var:[right t:int defint:0]
  }
]
$com: [SdbFunctions f:SdbFunctions]


# NULL terminator - must be the last definition in the file
$com:["" ]








]

$com:[SdbFeature f:SdbFeature 
  args:{
    $var:[feature t:int unnamed:y]
  }
]
$com:[SdbComplement f:SdbComplement]
$com:[SdbReplace f:SdbReplace]
$srs/icarus/util/builtin.ic
$object:[function  declname:"X" status:system 
  attrs:{ 
    $attribute:[name type:protofunction declname:"fnctnam" 
      max:30 valtype:text] 
    $attribute:[args type:string declname:"args" 
      max:132 valtype:text required:y] 
    $attribute:[module type:string declname:"module" max:30] 
  }
] 

file:"SRSICA:icacom.ic"

$def:[infile:"SRSICA:srswin.sdl" outfile:"SRSSOU:builtin.h" 
  section_name:"builtin" section_size:2000 
]
}
]
$com:[SdbComplement f:SdbComplement]
$com:[SdbReplace¶ £¡Üplace]
$srs/icarus/util/classes.i
#
#    $RCSfile: classes.i,v $
#    $Revision: 1.4 $
#    $Date: 1996/10/01 18:32:20 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#

O_VALUE:$object:[name:value typname:ODDoVAL ppname:SDL declname:defval 
  attrs:{
    $attribute:[name:name declname:nam type:string valtype:name unnamed:y]
    $attribute:[name:val declname:val type:uint valtype:{num constant}]
  }
]

O_ATTRTYPE:$object:[name:attrtype typname:ODDoATYP ppname:SDL declname:defatyp
  attrs:{
    $attribute:[name:make type:function declname:make valtype:constant 
      defaultstr:"(struct SDLoOBJ *, struct SDLoATTR *, unsigned int *)"]
    $attribute:[name:insert type:function declname:insert 
      defaultstr:"(void *, void *, void *, void ***, char *, unsigned int,int)"
      valtype:constant]
    $attribute:[name:calcsize type:function declname:size valtype:constant
      defaultstr:"(struct SDLoOBJ *, struct SDLoATTR *)"]
    $attribute:[name:write type:function declname:write defaultstr:"(void)"
      valtype:constant]
    $attribute:[name:declare type:function declname:declare 
      defaultstr:"(FILE *, struct SDLoATTR *, char *, char *)" 
      valtype:constant]
    $attribute:[name:check type:function declname:check 
      defaultstr:"(struct SDLoATTR *, int, char *)" valtype:constant]
    $attribute:[name:gentype type:function declname:gentype 
      defaultstr:"(struct SDLoOBJ *, struct SDLoATTR *)" valtype:constant]
    $attribute:[name:save_address type:uchar declname:save_f defaultval:0
      enum:{
        $value:[name:yes val:1]
        $Value:[name:no val:0]
      }
    ] 
    $attribute:[name:typname type:string declname:tnam max:20]
  }
]

O_ATTR:$object:[name:attribute typname:SDLoATTR ppname:SDL 
  declname:defpar CHILD:{@O_VALUE @O_ATTR} NCHILDS:2 
  attrs:{
    $attribute:[name:rem declname:rem type:string valtype:{name text}
      min:0 max:512]
    $attribute:[declname:class type:object defaultval:@O_OBJECT]
    # pointer to list of possible values
    $attribute:[name:enum declname:val type:child defaultval:@O_VALUE]
    # number of values in list
    $attribute:[declname:val_n type:nr_of_childs defaultval:@O_VALUE]
    $attribute:[name:name declname:nam type:string min:0 max:$SDLxXNAM 
      valtype:{name text} unnamed:y] 
    $attribute:[name:typname declname:tnam type:string min:0 max:$SDLxXNAM 
      valtype:{name text}] 
    # switch used for alternative SDLxUSER type name
    $attribute:[name:switchname declname:sw_nm type:string valtype:{name text}
      min:0 max:$SDLxXNAM]
    # alternative SDLxUSER type name 
    $attribute:[name:alttypname declname:alt_nm type:string valtype:{name text}
      min:0 max:$SDLxXNAM]
    # declaration name in C interface
    $attribute:[name:declname declname:dnam type:string min:0 max:$SDLxXNAM 
      valtype:{name text}] 
    $attribute:[name:unnamed declname:unnamed type:int min:0 defaultval:0 
      enum:{
        $value:[name:y val:1]
        $value:[name:n val:0]
      }
    ]
    $attribute:[name:type declname:typ type:uchar required:y valtype:name 
      enum:{
        $value:[name:int val:@AT_INT]
        $value:[name:uint val:@AT_UINT]
        $value:[name:uchar val:@AT_UCHAR]
        $value:[name:string val:@AT_STRING]
        $value:[name:protofunction val:@AT_PROTOFNCT]
        $value:[name:function val:@AT_FNCT]
        $value:[name:child val:@AT_CHILD]
        $value:[name:nr_of_childs val:@AT_CHILD_N]
        $value:[name:object val:@AT_OBJECT]
        $value:[name:clone val:@AT_CLONE]
        $value:[name:defer val:@AT_DEFER]
        $value:[name:inherit val:@AT_INHERIT]
        $value:[name:user val:@AT_USER]
        $value:[name:float val:@AT_FLOAT]
        $value:[name:allobjects val:@AT_ALLOBJ]
        $value:[name:nr_of_objects val:@AT_ALLOBJ_N]
        $value:[name:generic val:@AT_GENERIC]
        $value:[name:generic_typ val:@AT_GENERIC_TYP]
        $value:[name:generic_obj val:@AT_GENERIC_OBJ]
        $value:[name:overload val:@AT_OVERLOAD]
        $value:[name:store val:@AT_STORE]
        $value:[name:bnf val:@AT_EBNF]
      }
    ]
    # type of value attribute may receive
    $attribute:[name:valtype declname:ptyp type:uchar defaultval:0 repeat:4 
      valtype:name enum:{
        $value:[name:num val:$SDLxPNUM]
        $value:[name:name val:$SDLxPNAM]
        $value:[name:text val:$SDLxPTXT]
        $value:[name:constant val:$SDLxPCNST]
      }
    ]
    # array size if multivalued attribute
    $attribute:[name:repeat declname:arrsz type:int min:1 max:10000 
      defaultval:1 valtype:{num constant}] 
    $attribute:[name:min declname:min type:int min:-1000000000 max:1000000000
      defaultval:-1000000000 valtype:{num constant}] 
    $attribute:[name:max declname:max type:int min:0 max:1000000000 
      valtype:{num constant} defaultval:1000000000]
    $attribute:[declname:off type:int]
    $attribute:[name:required declname:req type:uchar valtype:name defaultval:0
      enum:{
        $value:[name:y val:$TRUE]
        $value:[name:n val:$FALSE]
      }
    ]
    $attribute:[name:status declname:status type:uchar valtype:name 
      defaultval:0 repeat:2 enum:{
        $value:[name:obsolete val:1]
        $value:[name:system val:2]
        $value:[name:api val:3]
      }
    ]
    $attribute:[declname:isrd type:uchar min:0 max:0 required:n]
    $attribute:[name:defaultval declname:dfltv type:int valtype:{num constant}
       min:-1000000000 max:1000000000 defaultval:0]
    $attribute:[name:defaultstr declname:dflts type:string 
      valtype:{name constant text} min:0 max:$SDLxXLN defaultstr:""]
    $attribute:[name:defaultvalf declname:dfltvf type:float valtype:num 
      min:-1000000000 max:1000000000 defaultvalf:0]
    $attribute:[declname:scnt type:int]
    # some attribute types need object-class ID's
    $attribute:[name:objectclass declname:obj type:object defaultval:@O_OBJECT
      valtype:constant]
    $attribute:[declname:hasObjsN type:int defaultval:-1]
    $attribute:[declname:"*hasFirstObj" type:user typname:void]
  }
]

O_OBJECT:$object:[name:object typname:SDLoOBJ ppname:SDL declname:defstrct 
  child:@O_ATTR nchilds:1 attrs:{
    #used in SDL
    $attribute:[name:name declname:nam type:string valtype:{name text}
      min:0 max:$SDLxXNAM unnamed:y]
    $attribute:[name:rem declname:rem type:string valtype:{name text}
      min:0 max:512]
    # `typedef' name to get access through C interface
    $attribute:[name:typname declname:tnam type:string valtype:{name text}
      min:0 max:$SDLxXNAM]
    #used for #define's - preprocessor name
    $attribute:[name:ppname declname:pp_nm type:string valtype:{name text}
      min:0 max:$SDLxXNAM]
    $attribute:[name:declname declname:dnam type:string min:0 max:$SDLxXNAM 
      valtype:{name text}] 
    $attribute:[name:type declname:typ type:uchar valtype:{num constant}
      min:0 max:12 defaultval:0]
    $attribute:[name:status declname:status type:uchar valtype:name 
      defaultval:0 repeat:2 
      enum:{
        $value:[name:obsolete val:1]
        $value:[name:system val:2]
        $value:[name:api val:3]
      }
    ]
    $attribute:[declname:siz type:int]
    $attribute:[declname:s type:string]
    $attribute:[declname:ns type:int min:0 max:10000]
    $attribute:[declname:uobj_coff type:string]
    $attribute:[declname:gbl_n type:int]
    $attribute:[declname:loc_n type:int]
    $attribute:[name:nchilds declname:nss type:uchar valtype:num max:$SDLxXSS]
    $attribute:[name:child declname:ss type:uchar repeat:$SDLxXSS 
      valtype:constant min:0 max:255 defaultval:0]
    $attribute:[declname:np type:nr_of_childs min:1 max:256 defaultval:@O_ATTR]
    $attribute:[name:attrs declname:p typname:SDLoATTR type:child 
      defaultval:@O_ATTR]
    #Inheritance 
    #Pointer(s) to object class descriptor(s)
    $attribute:[declname:gtyp_n type:int defaultval:0]
    #generic typedef name that object typedef using generic type receives
    $attribute:[declname:gtypdef_nm type:string repeat:$SDLxXSS 
      repeat:$SDLxXSS]
    #generic type
    $attribute:[declname:gtyp_nm type:string repeat:$SDLxXSS repeat:$SDLxXSS]
    #typdef name for the object with functions and data-header
    $attribute:[name:orgtypname declname:orgtyp_nm type:string 
      valtype:{text name} max:40]
  }
]

O_SDL:$object:[name:def typname:SDLo declname:def ppname:SDL child:@O_OBJECT
  nchilds:1 attrs:{
    $attribute:[name:infile declname:ifnam type:string min:1 max:$FILxXNAM
      required:y valtype:{constant text}]
    $attribute:[name:outfile declname:ofnam type:string min:1 max:$FILxXNAM 
    valtype:{constant text}]
    #name of map-section
    $attribute:[name:section_name declname:sec_nm type:string min:0 max:50 
      valtype:{name text}]
    #section size in blocks
    $attribute:[name:section_size declname:sec_z type:int min:1 max:100000 
      valtype:num defaultval:1000]
    # objects
    $attribute:[declname:oc_n type:nr_of_objects defaultval:@O_OBJECT]
    $attribute:[declname:oc type:allobjects defaultval:@O_OBJECT]
    # attribute types
    $attribute:[declname:at_n type:nr_of_objects defaultval:@O_ATTRTYPE]
    $attribute:[declname:at type:allobjects defaultval:@O_ATTRTYPE]
    $attribute:[declname:error type:uchar defaultval:0]
    $attribute:[declname:action type:uchar defaultval:0]
    $attribute:[declname:pass_n type:uchar defaultval:0]
    $attribute:[declname:keepst_f type:uchar defaultval:0]
    $attribute:[declname:section_f type:uchar defaultval:0]
  }
]
te:[declname:oc type:allobjects defaultval:@O_OBJECT]
    # attribute types
    $attribute:[declname:at_n type:nr_of_objects defaultval:@O_srs/icarus/util/colicarus.i
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: colicarus.i,v $
#    $Revision: 1.1 $
#    $Date: 1997/03/03 18:33:15 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$nameBeg = "<FONT COLOR=#EEAA00> "
$nameEnd = "</FONT>"
$resBeg  = "<B><FONT FACE=BOLD COLOR=#a000a0>"
$resEnd  = "</FONT></B>"
$varBeg  = "<B><FONT COLOR=#FF0000>"
$varEnd  = "</FONT></B>"
$funcBeg  = "<B><A HREF=\"http://www/srs5/man/mi_icafunc.html#Ica_%s\">"
$funcEnd  = "</A></B>"
$refBeg  = "<B><FONT COLOR=#000099>"
$refEnd  = "</FONT></B>"
$sqBeg   = "<FONT COLOR=#0000FF>"
$sqEnd   = "</FONT>"
$dqBeg   = "<I><FONT COLOR=#808000>"
$dqEnd   = "</FONT></I>"
$reBeg   = "<FONT COLOR=#A080A0>"
$reEnd   = "</FONT>"
$cmntBeg = "<I><FONT COLOR=#00AA70>"
$cmntEnd = "</FONT></I>"

$rules={
  readProg:   ~ {$In:[file:text] $Out pre $Skip:0 $Skip:1}
                ln {$Wrt:[s:$StrReplace:[$Ct from:'<' to:'&lt;']]} 
                ln* {$App:[s:$StrReplace:[$Ct from:'<' to:'&lt;']]} ~
  ln:         ~ /[^\n]*\n/ ~

  prog:       ~ {$In:[readProg t:color]} x{$Rep:
                  |<body bgcolor=#fffff0 LINK=FF0000 VLINK=#BB0000 
                  | ALINK=#FF0000><BASE TARGET="help"> <PRE> 
                } 
                stmnt+ ~
  body:       ~ ('{' stmnt* '}' | stmnt) ~
  stmnt:      ~ (if | foreach | for | while | init | pre | file | 
                 stassoc | expr | comment) ~
  stassoc:    ~ key ident ~
  comment:    ~ {$Rep:"$cmntBeg$Ct$cmntEnd"} ('#' ln)+ ~

  # expression
  expr:       ~ term (op term)* ~
  term:       ~ '(' expr ')' | value ~
  op:         ~ /[+|&=*\/%!>-]+/ | '&lt;' ~

  list:       ~ '{' comment? (assoc comment? | value comment?)* '}' ~
  assoc:      ~ key (value | '~' {$Rep:"$resBeg$Ct$resEnd"} 
                production '~' {$Rep:"$resBeg$Ct$resEnd"})  ~
  key:        ~ /([a-zA-Z0-9_]+)(:)/ {$Rep:"$nameBeg$1$nameEnd$2"} |
                /('(([^']+|\\\\.)*)')(:)/ {$Rep:"$nameBeg$1$nameEnd$4"} ~
  value:      ~ int | name | string | ident | list | reference ~
  int:        ~ /-?[0-9]+/ ~

  # variable names, paths and function calls
  path:       ~ name {$Rep:{"$funcBeg$Ct$funcEnd$varEnd" $Ct}} 
                ('.' (name {$Rep:"$varBeg$Ct$varEnd"} | '(' ident ')' |
                 string | ident) | '[' expr ']')* args? ~
  ident:      ~ '$' {$Rep:"$varBeg$Ct"}  path ~ 
  args:       ~ ':' ('[' (named | unnamed)? named* ']' | unnamed) ~
  unnamed:    ~ argvalue comment? ~
  named:      ~ /([a-zA-Z_0-9]+) *:/ {$Rep:"$nameBeg$Ct$nameEnd"} argvalue 
                comment? ~
  argvalue:   ~ int | expr | reference ~
  name:       ~ /[a-zA-Z0-9_]+/ ~
  strname:    ~ /[a-zA-Z_][a-zA-Z0-9_]*/ ~
  reference:  ~ {$Rep:"$refBeg$Ct$refEnd"} /@\\??/ name ~

  # strings
  string:     ~ /[^"'|]/ {$Not} (sqString | bqString | 
                '"'{$Rep:"$dqBeg$Ct"} dqString '"' {$Rep:"$Ct$dqEnd"})~
  sqString:   ~ {$Rep:"$sqBeg$Ct$sqEnd"} /'/ /[^']*/  /'/ ~ #'"
  bqString:   ~ ('|' {$Rep:"$resBeg$Ct$resEnd" $Skip:0} bqLine {$Skip:1})+ ~
  bqLine:     ~ (/[^\n\\$(]+/  | /\\\\[^\n]/ | var | var2 | /[^\n]/)* '\n' ~ 
  dqString:   ~ (/[^"\\$(]+/ | /\\\\./ | var | var2 | '(')* ~ #"
  var2:       ~ /(\\()($)/  path ')' ~
  var:        ~ /\\$([a-zA-Z0-9_]+)/ ~

  # flow control
  file:       ~ 'file'{$Rep:"$resBeg$Ct$resEnd"} ':' string ~
  pre:        ~ 'pre' {$Rep:"$resBeg$Ct$resEnd"} body ~
  init:       ~ 'init' {$Rep:"$resBeg$Ct$resEnd"} body ~
  foreach:    ~ 'foreach'{$Rep:"$resBeg$Ct$resEnd"} 
                 ':''[' ident  'in' ':' expr ']' body ~
  for:        ~ 'for' {$Rep:"$resBeg$Ct$resEnd"} ':''{' expr+ '}' body ~
  while:      ~ 'while' {$Rep:"$resBeg$Ct$resEnd"} ':' cond body ~
  if:         ~ 'if' {$Rep:"$resBeg$Ct$resEnd"} ':' 
                cond body ('elif' {$Rep:"$resBeg$Ct$resEnd"} ':' cond body)*
                ('else' {$Rep:"$resBeg$Ct$resEnd"} body)? ~
  cond:       ~ '(' expr ')' | '{' expr '}' | '[' expr ']' | expr ~
 
  production: ~ nodeProg? bnfExpr ~
  bnfExpr:    ~ bnfTerm ('|' bnfTerm)* ~
  bnfTerm:    ~ factor comment? (factor comment?)* ~
  factor:     ~ (/x[ {\n\t]/ {$Probe} command | 
                 ((regexp | literal | eoi | prodName | laProdName) occur?))
                nodeProg | '(' bnfExpr ')' occur? ~
  regexp:     ~ {$skip:1 $Rep:"$reBeg$Ct$reEnd"} '/' {$skip:0} reStr '/' ~
  reStr:      ~ (/[^\/\\]+/ | /\\\\./)+ ~
  literal:    ~ {$skip:1 $Rep:"$sqBeg$Ct$sqEnd"} /'/ {$skip:0} litStr /'/ ~
  litStr:     ~ (/[^'\\]+/ | /\\\\./)+ ~
  command:    ~ {$Rep:"$resBeg$Ct$resEnd"} /x:?/  ~
  eoi:        ~ '.'  ~
  occur:      ~ {$Rep:"$resBeg$Ct$resEnd"} '?'  | '*'  | '+'  ~
  nodeProg:   ~ ('{' stmnt+ '}')? ~
  prodName:   ~ /[a-zA-Z0-9_]+/ ~
  laProdName: ~ '_' /[a-zA-Z0-9_]+/ ~
}


$job = $JobNew:[prod:$rules skip:" \n\t" 
         fileName:'SRSDB/embl.is']
$JobTokens:[$job name:readProg print:1 task:color withCode:0] 


~
  literal:    ~ {$skip:1 $Rep:"$sqBeg$Ct$sqEnd"} /'/ {$skip:0} litStr /'/ ~
  litStr:     ~ (/[^'\\]+/ | /\\\\./)+ ~
  command:    ~ {$Rep:"$resBeg$Ct$resEnd"} /x:?/  ~
  eosrs/icarus/util/command.i
programm =     [ '$' ] command  { ';' <wrt c:0>  [ '$' ] [command] }
;              
command =        ica_instruct
               | user_instruct 
               | check 
               | equation
               | usercom
;              
ica_instruct =   'rd'  <wrt s:IcaOpReadToken c:36>
                    ':' ( name | variable )
		  [ 'c' <wrt c:110> ':' value ]
		  [ 't' <wrt c:110> ':' name 
		  [ 'l' <wrt c:110> ':' name  ] ]
               | 'ct'  <wrt s:IcaOpSetCopyOut   c:32> [':' ( name |variable )] 
               | 'et'  <wrt s:IcaOpSetEchoOut   c:32> [':' ( name |variable )] 
               | 'wrt' <wrt s:IcaOpWriteToken   c:42> { argument }
               | 'app' <wrt s:IcaOpAppendToken  c:42> { argument }
               | 'rep' <wrt s:IcaOpReplaceToken c:42> { argument }
               | 'len' <wrt s:IcaOpRestrictLen  c:47> ':' integer 
               | 'mov' <wrt s:IcaOpMove         c:47> ':' integer 
               | 'not'    <wrt c:103; wrt s:IcaOpSetFlag c:13>
               | 'noskip' <wrt c:103; wrt s:IcaOpSetFlag c:13>
               | 'nocase' <wrt c:103; wrt s:IcaOpSetFlag c:13>
               | 'uniq'   <wrt c:103; wrt s:IcaOpSetFlag c:13>
;
argument =       'c'  <wrt c:110> ':' value
               | 's'  <wrt c:110> ':' ( format | string | value )
;
check =          'if' '(' variable '==' <wrt s:IcaOpCheckEq c:42> 
                 (integer | variable | name) ')'
;
equation =       variable ('=' <wrt s:IcaOpAssign c:42> |
                           ':=' <wrt s:IcaOpAssign c:12> ) expression ;
expression =     operand { op operand }
;
operand =        variable
               | float
	       | integer
	       | l_bracket expression r_bracket
               | command 
               | string 
;
op =             '+' <wrt s:IcaOpAdd c:48> 
               | '-' <wrt s:IcaOpSub c:48> 
               | '*' <wrt s:IcaOpMul c:49>
               | '/' <wrt s:IcaOpDev c:49>
;
identifier =     float | integer | variable | name
;
value =          integer | variable | name
;
format =         l_brace (string|variable) { variable } r_brace
;
arglist =        name { ',' identifier }
;
string =         '"' /[^"]*/ <wrt c:103> '"'
;              
integer =        /[0-9]+/                    <wrt c:101>
;              
float =          /[0-9]+\.[0-9]/             <wrt c:102>
;              
name =           /[A-Za-z][0-9A-Za-z_-]*/    <wrt c:103>
;              
oneword =        /[^ \t]+/                   <wrt c:103>
;              
variable =       '$$' /[0-9A-Za-z]*/         <wrt c:104>
;              
l_bracket =      '('                         <wrt c:1>
; 
r_bracket =      ')'                         <wrt c:1>
;
l_brace =        '{'                         <wrt c:112> 
;
r_brace =        '}'                         <wrt c:113>
;

user_instruct=   'push1'   <wrt s:IcaOpPushUserStack1 c:43> ':' userval
               | 'push2'   <wrt s:IcaOpPushUserStack2 c:43> ':' userval
               | 'push3'   <wrt s:IcaOpPushUserStack3 c:43> ':' userval
               | 'push4'   <wrt s:IcaOpPushUserStack4 c:43> ':' userval
               | 'push5'   <wrt s:IcaOpPushUserStack5 c:43> ':' userval
               | 'push'    <wrt s:IcaOpPushUserStack0 c:43> ':' userval
               | 'pop1'    <wrt s:IcaOpPopUserStack1 c:43> 
               | 'pop2'    <wrt s:IcaOpPopUserStack2 c:43> 
               | 'pop3'    <wrt s:IcaOpPopUserStack3 c:43> 
               | 'pop4'    <wrt s:IcaOpPopUserStack4 c:43> 
               | 'pop5'    <wrt s:IcaOpPopUserStack5 c:43> 
               | 'pop'     <wrt s:IcaOpPopUserStack0 c:43> 
               | 'test'    <wrt s:IcaOpTest          c:43> 
               | 'com'     <wrt s:IcaOpNewCommand c:13> 
                 ':' value 'f' <wrt c:110> ':' value 
               | 'arg'     <wrt s:IcaOpAddArg c:13> 
	         ':' name { /(t|unnamed|required)/ <wrt c:110> ':' name }
               | 'return'  <wrt s:IcaOpAddRetVal c:13> 
	         ':' name { /(t|unnamed|required)/ <wrt c:110> ':' name }
                  {/(a|b|c|d)/ <wrt c:110> ':'  /[0-9]+/ <wrt c:103>}
               | 'p'       <wrt s:IcaOpPrint   c:43> ':' ( string | oneword )
               | 'trigger' <wrt s:IcaOpTrigger c:43> ':' name
               | 'setTask' <wrt s:IcaOpSetTask c:43> ':' name
;
userval      = l_bracket command r_bracket | /[0-9a-zA-Z-_]+/ <wrt c:103>
               | variable | string;
usercom      = /[a-zA-Z]+[a-zA-Z0-9_-]+/ 
	       <wrt c:103; wrt s:"114" c:114; wrt s:IcaOpExecCommand c:43> 
               [ ':' userval] 
               { /[a-zA-Z0-9_-]+/ <wrt c:110> ':' userval} 
..

# 0: separator (';')
# 1-59: operators, first digit: 1: build time, 2:preparse, 4:postparse
#       second is priority
# 100-109,112,113 operands
# 110: argName
# 111: end of the argument list
# 114: end of user argument list

nd r_bracket | /[0-9a-zA-Z-_]+/ <wrt c:103>
               | variable | string;
usercom      = /[a-zA-Z]+[a-zA-Z0-9_-]+/ 
	       <wrt c:103; wrt s:"114" c:114; wrt s:IcaOpExecCommand c:43> 
               [ ':' userval] 
               { /[a-zA-Z0-9_-]+/ <wrt c:110> ':' userval} 
..

# 0: separator (';')
srs/icarus/util/ica2c.it
#
#    $RCSfile: ica2c.it,v $
#    $Revision: 1.15 $
#    $Date: 1997/03/12 16:18:50 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


###############################################################################
#
# for conversion of the icarus commands to C functions
#
$prog={
  head:
    |#include <stdio.h>
    |#include "srs.h"
    | 
    |#include "odd.h"
    |#define _INITOBJS
    |#define _CONSTANTS
    |#define _SDL
    |#define _FUNCTION 
    |#include "oddclass.h"
    | 
    |static VARoSCOPE *scope = NULL;
    | 
    |main ()
    |{
    |  SrsEnv ();
    |  LibOpen ("srs5");
    | 
    |  IcarusFunc1 ();
    |}
    | 
    |INT4 %s ()
    |{
  func:{
    end:
      |}
  }
  body:{
    head:
      |
      |void %s ()
      |{
    tail:
      |}
  }
  stmnt:{
    head:  |  \
    tail: |;
  }
  binop:{
    '=': | = \
  }
  call:{
    name:   |%s (0\
    argint: |%d\
    argstr: |"%s"\
    argstrv:|StrCpyS ("%s")\
    argval: |%s\
    argvar: |%s\
#    argvar: |VarGet (&scope, "%s")\
    argsep: |, \
    tail:  |)\
  }
  var:
    |%s
#    |VarGet (&scope, "%s")\
  convert:{
    int:{
#      var:     |VarSetInt (VarTemp (), \
      string:  |VarSetInt (VarTemp (), \
    }
    string:{
      var:  |VarSetStr (VarTemp (), \
      strv: |StrCpyS (\
    }
    strv:{
      string: |_Str (\"
      var:    |VarSetStrv (VarTemp (), \
    }
    object:{
      var:  |VarSetObject (NULL, VarTemp (), (void*)\
    }
    var:{
      object:  |VarGetObject (NULL, (void*)\
      strv:    |VarGetStrv (\
    }
    alias:{
       object: |VarGetObject (NULL, (void*)\
#      int:   |VarGetInt (\
    }
    tail:       |)\
  }
  staticStrv:
    |static struct { int u; int l; int d; char arr[8]} str1={1,7,8,"\$ct := "};
}

###############################################################################
#
# for conversion of the syntax tree to C structures
#

$bnf2c = {
  str: "%s"
  prologue:
    |#include <stdio.h>
    |#include <strings.h>
    |#include <string.h>
    |#include <ctype.h>
    |#include <stdlib.h>
    |#include <stdio.h>
    |
    |#define DECLARE_ONLY
    |#define DEFIGNORE " \\n\\t"
    |#define DEFCOMMENT "^#[^\\n]*\\n"
    |
    |#include "srs.h"
    |#include "regexp.h"
    |
    |static VARoSCOPE *scope = NULL;
    |
    |extern ICAoJOB *Job;
    |extern ICAoSYNTAX *Syntax;
    |
    |INT4  BnfParseProduction(BNFoPRODUCTION *);
    |INT4  BnfParseProdLoop(BNFoPRODUCTION *);
    |INT4  BnfParseRegExp(BNFoREGEXP *); 
    |INT4  BnfParseLiteral(BNFoLITERAL *);
    |INT4  BnfParseCommand(BNFoNODE *);
    |INT4  BnfParseLineStart(BNFoNODE *);
    |INT4  BnfParseInputEnd(BNFoNODE *);
    |INT4  BnfParseTerm(BNFoTERM *);
    |INT4  BnfParseChoice(BNFoCHOICE *);
    |INT4  BnfParseProdName(BNFoPRODNAME *); 
    |void  BnfPruneTree (BNFoNODE **, Int4 passN);
    |
    |VARo *IopPop_(INT4, INT4);
    |VARo *IopBody_ (Int4 runTime);
    |
    |STRv  IopInterpStr_(VARo *var, STRv str, ...);
    |STRv  IopInterpStr2(VARo *var, STRv str, ...);
    |STRv  IopSubMatch(INT4, INT4);
    |STRv  IopCurrToken();
    |
    |/* Declaration of C variables used by some translated functions */
    |VARo  *a, *b, *c, *d, *e, *u, *i, *str;
    |Int4  opt;
    |
  epilogue:
    |ICAoSYNTAX *IcaInitSyntax(ICAoSYNTAX *syntax)
    |{
    |  static ICAoSYNTAX  syntaxStatic;
    |  static ICAoJOB     job;
    |  BNFoNODE *tmp;
    |  VARo     *prodList=VarNew ();
    |  INT4     i,j;
    |
    |  if (syntax && syntax->prod) /* already initialized */
    |    return syntax;
    |
    |  if (!syntax)
    |    syntax = &syntaxStatic;
    |
    |
    |  Job = &job;
    |  Job->time = BNFxBUILDTIME;
    |
    |  j = 0;
    |  for(i=0; i<TERMNUM; i++) {
    |    _term[i].factorList = &_report[j];
    |    while(_report[j++].node);
    |  }
    |  
    |  j = 0;
    |  for(i=0; i<CHOINUM; i++) {
    |    _choi[i].termList = &_choiceSet[j];
    |    while(_choiceSet[j++]);
    |  }
    |
    |  AnySetList (prodList, AnyNewList ());
    |  for(i=0; i<PRODNUM; i++) {
    |    VarSetObject ("prod", AnyGetListAssoc(prodList, _prod[i].name), &_prod[i]);
    |    Job->currNode = (BNFoNODE *) &_prod[i];
    |    _BnfExecInit (&_prod[i]);
    |  }
    |
    |  for(i=0; i<PRODNNUM; i++) {
    |    Job->currNode = (BNFoNODE *) &_prodN[i];
    |    _BnfExecInit (&_prodN[i]);
    |  }  
    |
    |#ifdef LITLNUM 
    |
    |  for(i=0; i<LITLNUM; i++) {
    |    Job->currNode = (BNFoNODE *) &_lit[i];
    |    _BnfExecInit (&_lit[i]);
    |  }  
    |
    |#endif
    |#ifdef REGNUM 
    |
    |  for(i=0; i<REGNUM; i++) {
    |    _reg[i].expression = RegComp(_reg[i].name);
    |    Job->currNode = (BNFoNODE *) &_reg[i];
    |    _BnfExecInit (&_reg[i]);
    |  }  
    |
    |#endif
    |#ifdef COMMNUM 
    |
    |  for(i=0; i<COMMNUM; i++) {
    |    Job->currNode = (BNFoNODE *) &_comm[i];
    |    _BnfExecInit (&_comm[i]);
    |  }  
    |
    |#endif
    |#ifdef STRTNUM 
    |
    |  for(i=0; i<STRTNUM; i++) {
    |    Job->currNode = (BNFoNODE *) &_strt[i];
    |    _BnfExecInit (&_strt[i]);
    |  }  
    |
    |#endif
    |#ifdef EOINNUM 
    |
    |  for(i=0; i<EOINNUM; i++) {
    |    Job->currNode = (BNFoNODE *) &_eoin[i];
    |    _BnfExecInit (&_eoin[i]);
    |  }  
    |
    |#endif
    |
    |  VarGet (&job.scope, "");
    | 
    |  syntax->prod = prodList;
    |  syntax->ign = DEFIGNORE;
    |  if (syntax == &syntaxStatic) {
    |    syntax->cmnt = DEFCOMMENT;
    |    syntax->ignAlt = "";
    |  }
    |  if ((syntax->cmntRe = RegComp (syntax->cmnt)) == NULL)
    |    _ErrExit2 (e__regerror, syntax->cmntRe);
    |
    |  Syntax = syntax;
    |  for (i=0; i<PRODNUM; i++) {
    |	 tmp = (BNFoNODE*) &_prod[i];
    |	 BnfPruneTree (&tmp, 1);
    |  }
    |  for (i=0; i<PRODNUM; i++) {
    |	 tmp = (BNFoNODE*) &_prod[i];
    |	 BnfPruneTree (&((BNFoPRODUCTION*)tmp)->node, 2);
    |  }
    |  return syntax;
    |}
  node: {
    prod: {
      arrName:  |_prod\
      defNumber:|#define PRODNUM %d
      typeDef:  |BNFoPRODUCTION %%s[] = {
      format:   | {\"%%s\",Production,0,One, \
                |BnfParseProduction, 0,0,0,0%%s, \
                |(BNFoNODE*)&%%s[%%d], NULL, 0, 0},
    }
    prodN: {  
      arrName:  |_prodN\
      defNumber:|#define PRODNNUM %d
      typeDef:  |BNFoPRODNAME %%s[] = {
      format:   | {\"%%s\",ProdName, 0, One, \
                |BnfParseProdName, 0,0,0,0%%s, &%%s[%%d]},
    }
    lit: {
      arrName:  |_lit\
      defNumber:|#define LITLNUM %d
      typeDef:  |BNFoLITERAL %%s[] = {
      format:   | {\"%%s\",Literal,0,One, BnfParseLiteral, 0,0,0,0%%s },
    }
    reg: {
      arrName:  |_reg\
      defNumber:|#define REGNUM %d
      typeDef:  |BNFoREGEXP %%s[] = {
      format:   | {\"%%s\",Regexp,0,One, BnfParseRegExp, 0,0,0,0%%s },
    }
    term: {
      arrName:  |_term\
      defNumber:|#define TERMNUM %d
      typeDef:  |BNFoTERM %%s[] = {
      format:   | {"TERM",Term,0, One, BnfParseTerm },
    }
    choi: {
      arrName:  |_choi\
      defNumber:|#define CHOINUM %d
      typeDef:  |BNFoCHOICE %%s[] = {
      format:   | {"CHOI",Choice,0, One, BnfParseChoice },
    }
    comm: {
      arrName:  |_comm\
      defNumber:|#define COMMNUM %d
      typeDef:  |BNFoNODE %%s[] = {
      format:   | {"COMM",Command,0, One, BnfParseCommand, 0,0,0,0%%s },
    }
    strt: {
      arrName:  |_strt\
      defNumber:|#define STRTNUM %d
      typeDef:  |BNFoNODE %%s[] = {
      format:   | {"STRT",LineStart,0,One, BnfParseLineStart, 0,0,0,0%%s },
    }
    eoin: {
      arrName:  |_eoin\
      defNumber:|#define EOINNUM %d
      typeDef:  |BNFoNODE %%s[] = {
      format:   | {"EOIN",EndOfInput,0,One, BnfParseInputEnd, 0,0,0,0%%s },
    }
    reprt: {
      arrName:  | { 0, NULL },
      defNumber:|#define RAPORTNUM %d
      typeDef:  |BNFoREPORT _report[] = {
      format:   | { %%d, (BNFoNODE *)&%%s[%%d] },
    }
    set: {
      arrName:  | NULL,
      defNumber:|#define SETNUM %d
      typeDef:  |BNFoNODE *_choiceSet[] = {
      format:   | (BNFoNODE *)&%%s[%%d],
    }
    var: {
      arrName:  |_var\
      defNumber:|#define VARNUM %d
      typeDef:  |VARo %%s[] = {
      format:   | { NULL,1,0,1,1,0,0,0, {(Func) %%s}, NULL, NULL },
    }
    scope: {
      arrName:  |_scopeName\
      defNumber:|#define NAMENUM %d
      typeDef:  |char *%%s[] = {
      format:   | \"%%s\",
    }
  }
}

ODE *)&%%s[%%d] },
    }
    set: {
      arrName:  | NULL,
      defNumber:|#define SETNUM %d
      typeDef:  |BNFoNODE *_choiceSet[] = {
      format:   | (BNFoNODE *)&%%s[%%d],
    }
    var: {
      arrName:  |_var\
      srs/icarus/util/icacom.ic
#
#    $RCSfile: icacom.ic,v $
#    $Revision: 1.4 $
#    $Date: 1997/03/06 20:15:32 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



Class_Value:$object:[val 
  typname:"ODDoVALUE" declname:"ODDValue" 
  rem:"Value in an enumeration" 
  attrs:{ 
    $attribute:[name declname:name unnamed:y required:y type:string 
      rem:"Name of value."]
    $attribute:[n declname:n required:y type:int rem:"Number value."] 
    $attribute:[rem declname:"rem" type:string rem:"Comment field."] 
  }
]

Class_Var:$object:[var 
  typname:"IARGoVALUE" declname:"IARGVALUE" nchilds:1 child:@Class_Value
  rem:"Argument of Icarus command." 
  attrs:{ 
    $attribute:[name declname:"name" type:string unnamed:y   
      rem:"Name of the argument in an Icarus program."] 
    $attribute:[rem declname:"rem" type:string rem:"Comment field."] 
    $attribute:[unnamed declname:isUnnamed type:uchar defaultval:0 
      rem:"Defines if parameter may be unnamed." 
      enum:{ 
        $value:[y val:1] 
        $value:[n val:0]  
      } 
    ] 
    $attribute:[required 
      declname:isRequired type:uchar defaultval:0 
      rem:"Defines if parameter is required." 
      enum:{ 
        $value:[y val:1] 
        $value:[n val:0]  
      } 
    ] 
    $attribute:[t 
      declname:type type:uchar defaultval:2 
      rem:"Type of the argument" 
      enum:{ 
        $value:[int    val:1]  
        $value:[string val:2] 
        $value:[strv   val:9] 
        $value:[object val:3] 
        $value:[real   val:4] 
        $value:[var    val:6] 
        $value:[list   val:16] 
      } 
    ] 
    $attribute:[class declname:className type:string]
    $attribute:[defInt 
      declname:defInt type:int 
      rem:"Default value of type 'int' arguments."] 
    $attribute:[defStr  
      declname:defaultStr type:string 
      rem:"Default value of type 'string' arguments."] 
    $attribute:[enum declname:vals type:child defaultval:@Class_Value] 
    $attribute:[declname:valsN type:nr_of_childs defaultval:@Class_Value] 
    $attribute:[declname:isSet type:uchar defaultval:0] 
    $attribute:[declname:"*val" typname:"struct VARo" type:user] 
  } 
] 
 

Class_Com: $object:[com 
  typname:IARGoCOM declname:IARGCOM nchilds:1 child:@Class_Var
  attrs:{  
    $attribute:[name unnamed:y declname:"name" type:string required:y 
      rem:"Name of command in Icarus programs."] 
    $attribute:[f declname:"functionName" type:string 
      rem:"C function that implements the command."] 
    $attribute:[show declname:isShow type:int
      rem:
        |Determines whether the command should appear in the 
        |Icarus functions reference list.
      enum:{
        $value:[n val:0]
        $value:[y val:1]
      }
    ]
    $attribute:[rem declname:"rem" type:string rem:"Comment field."] 
    $attribute:[return 
      declname:returnType defaultval:2 type:uchar 
      rem:"Type of value to be returned (if any)." 
      enum:{ 
        $value:[int    val:1]  
        $value:[string val:2] 
        $value:[strv   val:9] 
        $value:[object val:3] 
        $value:[real   val:4] 
        $value:[var    val:6] 
        $value:[list   val:16] 
      } 
    ] 
    $attribute:[time 
      declname:time defaultval:8 type:int  
      rem:"Execution time of command." 
      enum:{ 
        $value:[init     val:2]  
        $value:[pre      val:4] 
        $value:[initpre  val:6] 
        $value:[post     val:8] 
        $value:[prepost  val:12] 
      } 
    ] 
    $attribute:[returnClass declname:returnClass type:string]
    $attribute:[call 
      declname:isDirectCall defaultval:0 type:uchar 
      rem:"Call function directly or via C-interface." 
      enum:{ 
        $value:[direct    val:1] 
        $value:[interface val:0]  
      } 
    ] 
    $attribute:[methodOf declname:methodOf type:string 
       rem:|The class of which this function is a method otherwise treated as
           |normal function.
    ]
    $attribute:[args declname:args type:child defaultval:@Class_Var] 
    $attribute:[declname:argsN type:nr_of_childs defaultval:@Class_Var] 
    $attribute:[declname:"(*function)()" typname:INT4 type:user 
      rem:"Function to be executed for command."]
    $attribute:[declname:"orderN" type:int 
      rem:"Number of arguments ordered from C function (via 'IargGetArgs')."]
    $attribute:[declname:"orderAllocN" type:int 
      rem:"Number of orders currently allocated."]
    $attribute:[declname:"**order" typname:"struct IARGoVALUE" type:user 
      rem:"Array with a list of argument orders."]
  } 
] 
type:nr_of_childs defaultval:@Class_Var] 
    $attribute:[declname:"(*function)()" typname:INT4 type:user 
      rem:"Function to be executed for command."]
    $attribute:[declname:"orderN" type:int 
      rem:"Number of arguments ordered from C function (via 'IargGetArgs')."]
    $attribute:[declname:"orderAllocN" type:int 
      rem:"Number of orders currently allocated."]
    $attribute:[declname:"**order" typname:"struct IARGoVALUE" typesrs/icarus/util/icarus.i
# functions for building the executable structure
#
#
# high level productions
#
entry     <ct; trigger:prog;> = 
            ln <wrt> { ln <app>} ;   
ln        = /[^$]+/ ;

prog <ct> = * <push:(opnd t:mark)> stmnt { stmnt } 
            * <Prog:IopProg> ;
body      = * <push:(opnd t:mark)> ('{' { stmnt  } '}' | stmnt ) 
            * <push:(body:"IopBody")>;
stmnt     <ct:stmnt> = (if | for | while | init | pre | file | stassoc | expr);

stassoc   = key <push5:(opnd:"$1" t:string)> 
            ident <push:(assoc val:(pop) key:(pop5))>;
#
# expression
#
expr      = term1 {logop term1 makeop};
term1     = term2 {(compop|assop) term2 <push:(op2:(pop1) b:(pop) a:(pop))>};
term2     = term3 {op1  term3 <push:(op2:(pop1) b:(pop) a:(pop))>};
term3     = term4 {op2 term4 makeop};
term4     = '(' expr ')' | [unopleft] value [unopright];
makeop    = * <push:(op2:(pop1) b:(pop) a:(pop))>;
nullopnd  = * <push:(opnd t:null)>;
#
# operators
#
logop     = '&&' <push1:IcaOpAnd   > | '||' <push1:IcaOpOr    > ;
assop     = '=+' <push1:IopAddAss  > | '='  <push1:IopAss     > | 
            '-=' <push1:IcaOpAssSub> | '*=' <push1:IcaOpAssMul> |
            '/=' <push1:IcaOpAssDiv> ;	     
compop    = '<=' <push1:IcaOpLE    > | '=<' <push1:IcaOpLE    > | 
            '>=' <push1:IcaOpGE    > | '=>' <push1:IcaOpGE    > | 
            '<'  <push1:IopLT      > | '>'  <push1:IcaOpGT    > | 
            '==' <push1:IopEq      > | '!=' <push1:IopNEq     > ;	     
op1       = '+'  <push1:IopAdd   >   | '-'  <push1:IopSubt    > |
            '%'  <push1:IcaOpMod   > ;	        
op2       = '*'  <push1:IopMul   >   | '/'  <push1:IopDivide  > ;
unopleft  = '++' <push1:IcaOpIncr  > | '--' <push1:IcaOpDecr  > | 
            '-'  <push1:IcaOpNeg   > | '+'  <push1:IcaOpPos   > ;
unopright = '++' <push1:IcaOpIncr  > | '--' <push1:IcaOpDecr  > ;
#
# variables values and lists
#
list      = '{' <push:(opnd t:mark)>
             {assoc|value} '}' <push:(list)>;
assoc     = key <push5:(opnd:"$1" t:string)> 
            (value |'~' production '~') * <push:(assoc val:(pop) key:(pop5))>;
key       = /([a-zA-Z0-9_]+):/;
value     = int <push:(opnd:"$ct" t:int)> |
            string | ident | list | namestr | reference;

#
# flow control
#
file      = 'file' ':' string * <push:(file:(pop))>;
pre       = 'pre' body <push:(Pre:(pop))>;
init      = 'init' body <push:(init:(pop))>;
for       = 'for'':''{' (expr|nullopnd) (expr|nullopnd) (expr|nullopnd)
            '}' body <push:(for:IopFor b:(pop) u:(pop) c:(pop) i:(pop))>;
while     = 'while'':' cond body <push:(while b:(pop) c:(pop))>;
if        = 'if'':'<push:(opnd t:mark)> cond body {'elif'':' cond body}
            ['else' <push:(opnd:1 t:int)>  body] *<push:(IF)>;
cond      = '(' expr ')' | '{' expr '}' | '[' expr ']' |  expr;
case      = 'case'ident <p:"\ncase $ct\n">
            '{' { '?' value <p:"| ?$ct:\n"> ':' body } '}'
            <p:"\n...end case\n">; 

#/(else|for|while|if|case|\?)[^a-zA-Z0-9]/ <not> 
ic         = 'installClasses'<push:(opnd:IopInstallClasses t:function);push:(func)>;
print      = 'print' <push:(opnd:IopPrint t:function)> args * <push:(func)>;
#
# variable name or function call
#
ident     = '$$' path;
path      = name  <push:(opnd:"$ct" t:ident)>
            { '.'(name <push:(select:(pop) key:"$ct")> | 
              '(' ident ')' <push:(select keyvar:(pop) var:(pop))> |
              string <push:(select keyvar:(pop) var:(pop))> |
              ident <push:(select keyvar:(pop) var:(pop))>)|
            /\\[([0-9]+)\\]/ <push:(select:(pop) n:"$1")> |
            '[' expr ']' <push:(select inxvar:(pop) var:(pop))> } 
            [ args <push:(func)>];
args      = ':'<push:(opnd t:mark)> 
            ('[' [named | unnamed] {named} ']' | unnamed );
unnamed   = argvalue <push:(Makearg:(pop) name:(opnd:":::::" t:str))> | ':::::' ;
named     = /([a-zA-Z_0-9]+) *:/ <push:(opnd:"$1" t:str)>
            argvalue <push:(Makearg:(pop) name:(pop))>;
argvalue  = int <push:(opnd:"$ct" t:int)> |
            ident | string | strname | list | '(' expr ')' | reference;


reference = '@' ('?'<$opt=1> | *<$opt=0>) 
            name <push:(oddRef:"$ct" opt:$opt)>;
name      = /[a-zA-Z0-9_]+/;
real      = /[0-9]*\\.[0-9]*/;
int       = /-?[0-9]+/;
namestr   = /[a-zA-Z0-9_]+/ <push:(opnd:"$ct" t:str)>;
string    = '"' mystring <noskip; push:(opnd:"$ct" t:istr)> '"'  
            | /'/ /[^']*/ <noskip; push:(opnd:"$ct" t:str)> /'/;



mystring <noskip>= *<push:(opnd t:mark);noskip> 
            {/((\\\\.)+|[^"\\$$]+)/<noskip> | '$$$$' | strident };
strident   = '$$(' path | '$$' path;
            
strname   = /[a-zA-Z_][a-zA-Z0-9_]*/ <push:(opnd:"$ct" t:str)>;
#"
#
# commands for creating the syntax tree
#
#
# the 'Backus-Naur format' derived syntax description'
#
production = * <push3:(Prod)> [nodeProg] 
             bnfExpr <push:(endProd node:(pop3) prod:(pop3))>; 
bnfExpr    = * <push3:(nullNode)> term  { '|' term } * <push3:(expr)>;
term       = * <push3:(nullNode)> factor { factor } * <push3:(term)>;
factor     = (regexp | literal | command | prodName | laProdName) [occur]
             [nodeProg] | '(' bnfExpr ')' [occur];
regexp     =  '/'  sqString <noskip; push3:(regexp:"$ct")> '/';
sqString   =  {/((\\\\.)+|[^\/\\]+)/};
literal    =  /'/ /[^']*/ <noskip; push3:(literal:"$ct")> /'/ ;
command    = 'x:' <push3:(doCom)>;
occur      = '?' <push3:(makeOpt:(pop3) t:once)> | 
             '*' <push3:(makeOpt:(pop3) t:multi)> | 
             '+' <push3:(makeOpt:(pop3) t:onemore)>;
nodeProg   = '{' *<push:(opnd t:mark)> stmnt{stmnt} *<push:(body:IopBody)> '}'
             <push3:(nodeProg:(pop3) prog:(pop))>;
prodName   =  /[0-9a-zA-Z_]+/ <push3:(ProdName:"$ct" lookahead:0)>;
laProdName = '_' /[a-zA-Z_]+/ <push3:(ProdName:"$ct" lookahead:1)>;

end = 'end'.




skip; push3:(literal:"$ct")> /'/ ;
command    = 'x:' <push3:(doCom)>;
occur      = '?' <push3:(makeOpt:(pop3) t:once)> | 
             '*' <push3:(makeOpt:(pop3) t:multi)> | 
             '+' <push3:(makeOpt:(pop3) t:onemore)>;
nodeProg   = '{' *<push:(opnd t:mark)> stmnt{stmnt} *<push:(body:IopBody)> '}'
             <push3:(nodeProg:(pop3) prog:(pop))>;
srs/icarus/util/icarus.is
  prog:       ~ {$out pre{$push:$opnd:[ga t:mark]} $prog} stmnt (stmnt)* ~
  stmnt:      ~ {$out} for | init | pre | doFile | assoc | expr ~
  body:       ~ {pre{$push:$opnd:[t:mark]} $push:$body:"IopBody"} 
                ('{' (stmnt)* '}' | stmnt) ~ 

  # expression
  expr:       ~ term1 (logop term1 makeop)* ~  
  term1:      ~ term2 ((compop | assop) term2 makeop)* ~
  term2:      ~ term3 (op1  term3 makeop)* ~
  term3:      ~ term4 (op2 term4 makeop)* ~
  term4:      ~ '(' expr ')' | (unopleft)? value (unopright)? ~
  makeop:     ~ x:{$push:$op2:[$pop1 b:$pop a:$pop]} ~
  nullopnd:   ~ x:{$push:$opnd:[t:null]} ~
  
  # operators
  logop:      ~ '&&' {$push1:IcaOpAnd}    | '||' {$push1:IcaOpOr} ~
  assop:      ~ '=+' {$push1:IopAddAss}   | '='  {$push1:IopAss} | 
                '-=' {$push1:IcaOpAssSub} | '*=' {$push1:IcaOpAssMul} |
                '/=' {$push1:IcaOpAssDiv} ~
  compop:     ~ '<=' {$push1:IcaOpLE}     | '=<' {$push1:IcaOpLE} | 
                '>=' {$push1:IcaOpGE}     | '=>' {$push1:IcaOpGE} | 
                '<'  {$push1:IopLT}       | '>'  {$push1:IcaOpGT} | 
                '==' {$push1:IcaOpGE} ~ 
  op1:        ~ '+'  {$push1:IopAdd}      | '-'  {$push1:IopSubt} |
                '%'  {$push1:IcaOpMod} ~ 
  op2:        ~ '*'  {$push1:IopMul}      | '/'  {$push1:IcaOpDev} ~
  unopleft:   ~ '++' {$push1:IcaOpIncr}   | '--' {$push1:IcaOpDecr} | 
                '-'  {$push1:IcaOpNeg}    | '+'  {$push1:IcaOpPos} ~
  unopright:  ~ '++' {$push1:IcaOpIncr}   | '--' {$push1:IcaOpDecr} ~

  # variables values and lists
  list:       ~ '{' {$push:$opnd:[t:mark]} (assoc | value) '}' {$push:$list} ~
  assoc:      ~ {$push:$assoc:[val:$pop key:$pop5]}
                key {$push5:$opnd:["$1" t:string]} (value|'~' production '~') ~
  key:        ~ /([a-zA-Z0-9_]+):/ ~
  value:      ~ int {$push:$opnd:["$ct" t:int]} |
                string | ident | list | namestr | reference ~
  # flow control
  doFile:     ~ {$push:$file:$pop} 'file' ':' string ~
  pre:        ~ {$push:$Pre:$pop} 'pre' body ~
  init:       ~ {$push:$init:$pop} 'init' body ~
  for:        ~ 'for'':''{' (expr | nullopnd) (expr | nullopnd) (expr|nullopnd)
                '}' body {$push:$for:[IopFor b:$pop u:$pop c:$pop i:$pop]} ~

  # variable name or function call
  objId:      ~ /_[a-zA-Z0-9_]+/ {$newId:"$ct"} ~
  ident:      ~ '$' path ~ #'
  path:       ~ name {$push:$opnd:["$ct" t:ident]} 
                ('.'(name {$push:$select:[$pop key:"$ct"]} | 
                '(' ident ')' {$push:$select:[keyvar:$pop var:$pop]} |
                string {$push:$select:[keyvar:$pop var:$pop]} |
                ident {$push:$select:[keyvar:$pop var:$pop]}) |
                /\\[([0-9]+)\\]/ {$push:$select:[$pop n:"$1"]})* 
                (args {$push:$func})? ~
  args:       ~ ':' {$push:$opnd:[t:mark]} 
                ('[' ((named | unnamed) (named)*)* ']' | unnamed) ~
  unnamed:    ~ argvalue {$push:$Makearg:[$pop name:$opnd:[":::::" t:str]]} ~
  named:      ~ /([a-zA-Z_0-9]+) *:/ {$push:$opnd:["$1" t:str]}
                argvalue {$push:$Makearg:[$pop name:$pop]} ~
  argvalue:   ~ int {$push:$opnd:["$ct" t:int]} |
                ident | string | strname | list | '(' expr ')' | reference ~
  reference:  ~ '@' ('?'{$opt=1} | x:{$opt=0}) 
                name {$push:$oddRef:["$ct"]} ~
  name:       ~ /[a-zA-Z0-9_]+/ ~
  real:       ~ /[0-9]*\\.[0-9]*/ ~
  int:        ~ /-?[0-9]+/ ~
  namestr:    ~ /[a-zA-Z0-9_]+/ {$push:$opnd:["$ct" t:str]} ~
  string:     ~ '"' mystring {$noskip $push:$opnd:["$ct" t:istr]} '"'  
                | /'/ /[^']*/ {$noskip $push:$opnd:["$ct" t:str]} /'/ ~ #'
  mystring:   ~ {$noskip pre{$push:$opnd:[t:mark]}} 
                (/((\\\\.)+|[^"\\$$]+)/ {$noskip} | '$$' | strident)* ~ #"
  strident:   ~ '$(' path | '$' path ~ #'
  strname:    ~ /[a-zA-Z_][a-zA-Z0-9_]*/ {$push:$opnd:["$ct" t:str]} ~


  # the 'Backus-Naur format' derived syntax description
  production: ~ {pre{$push3:$prod}} (nodeProg)?
                bnfExpr {$push:$endProd:[node:$pop3 prod:$pop3]} ~
  bnfExpr:    ~ {pre{$push3:$nullNode} $push3:$expr} term ('|' term)* ~
  term:       ~ {pre{$push3:$nullNode} $push3:$term} factor (factor)* ~
  factor:     ~ (regexp | literal | command | prodName | laProdName)
                (nodeProg)? | '(' bnfExpr ')' (optional | repeat)? ~
  regexp:     ~ '/' /[^\|]*/ {$noskip $push3:$regexp:"$ct"} '/' ~
  literal:    ~ /'/ /[^']*/ {$noskip $push3:$literal:"$ct"} /'/ ~ #'
  command:    ~ 'x:' {$push3:$doCom} ~
  optional:   ~ '?' {$push3:$makeOpt:[$pop3 t:once]} ~
  repeat:     ~ x:{$push3:$makeOpt:[$pop3 t:multi]} ~
  nodeProg:   ~ {$push3:$nodeProg:[$pop3 prog:$pop]} 
                '{' {$push:$opnd:[t:mark]} stmnt (stmnt)*
                x:{$push:$body:IopBody} '}' ~
  prodName:   ~ /[a-zA-Z_]+/ {$push3:$ProdName:"$ct"} ~
  laProdName: ~ '_' /[a-zA-Z_]+/ {$push3:$ProdName:["$ct" lookahead:1]} ~
}
/' ~
  literal:    ~ /'/ /[^']*/ {$noskip $push3:$literal:"$ct"} /'/ ~ #'
  command:    ~ 'x:' {$push3:$doCom} ~
  optional:   ~ '?' {$push3:$makeOpt:[$pop3 t:once]} ~
  repeat:     ~ x:{$push3:$makeOpt:[$pop3 t:msrs/icarus/util/makewild.i
#    $RCSfile: makewild.i,v $
#    $Revision: 1.3 $
#    $Date: 1997/03/03 18:32:49 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$rules={
  query:    ~ {init{$SetFunctions:QuerySetFunctions}}
              factor (op factor)* ~
  op:       ~ /[|&<>!=]/ ~
  factor:   ~ set | retrieve | '(' query ')' ~
  set:      ~ /[a-zA-Z0-9_]+/ ~
  retrieve: ~ '[' libs '-' name (':' wordExpr | /#[^]]+/) ']' ~
  wordExpr: ~ wordTerm (logop wordTerm)* ~
  wordTerm: ~ '(' wordExpr ')' | word ~  
  logop:    ~ /[!|&]/ ~
  name:     ~ /[a-zA-Z0-9_]+/ ~
  word:     ~ '"' /([^"\\]+|\\\\.)*/ 
               {if:$parInt:makeWild $rep:$MakeWild:$ct} '"' | #"
               '\'' /([^'\\]+|\\\\.)*/ 
               {if:$parInt:makeWild $rep:$MakeWild:$ct} '\'' |
               /\/([^\/\\]+|\\\\.)*\//  | # regexp - do nothing!
               /[^]|&!)]*[^]|&!) ]/ {if:$parInt:makeWild $rep:$MakeWild:$ct}
            ~
  libs:     ~ /([a-zA-Z0-9_]+) *=/? ('{' (name)* '}' | name) ~
}

#$parInt:[makeWild set:1]
#$parse:['(a&[a={pir embl}-def:1&"arg"])' prod:$rules start:expr skip:" "]
 /([^"\\]+|\\\\.)*/ 
               {if:$parInt:makeWild $rep:$MakeWild:$ct} '"' | #"
               '\'' /([^'\\]+|\\\\.)*/ 
               {if:$parInt:makeWild $rep:$MakeWild:$ct} '\'' |
               /\/([^\/\\]+|\\\\.)*\//  | # regexp - do nothing!
               /[^]|&!)]*[^]|&!) ]/ {if:$parInt:makeWild $rep:$MakeWild:$csrs/icarus/util/man_capi.i
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: man_capi.i,v $
#    $Revision: 1.12 $
#    $Date: 1997/03/19 21:13:47 $
#    $Author: srs $
#
# Generates the HTML with the documentation of the functions in C language
# modules
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#

$entry = { 
           name:"" api:0 comment:"" 
           input:{
             {write:"" type:"" name:"" rem:""}
             {write:"" type:"" name:"" rem:""}
             {write:"" type:"" name:"" rem:""}
             {write:"" type:"" name:"" rem:""}
             {write:"" type:"" name:"" rem:""}
             {write:"" type:"" name:"" rem:""}
             {write:"" type:"" name:"" rem:""}
             {write:"" type:"" name:"" rem:""}
             {write:"" type:"" name:"" rem:""}
             {write:"" type:"" name:"" rem:""}
             {write:"" type:"" name:"" rem:""}
             {write:"" type:"" name:"" rem:""}
             {write:"" type:"" name:"" rem:""}
             {write:"" type:"" name:"" rem:""}
             {write:"" type:"" name:"" rem:""}
           }
           retCom:{"" "" "" "" "" "" "" "" "" ""}
         }

$Xfiles={
  templ	    
}

$files={
  arglist
  bnf2c     
  btree        
  cursor
  dict         
  entry        
  field
  futil        
  hash         
  ica2c     
  icaarg    
  icabnf      
  icaop     
  icarus    
  icatask   
  id           
  ids          
  idx       
  index          
  library      
  link         
  logicals     
  lst
  message      
  oldlistbuf   
  par         
  print        
  query        
  queryass     
  regexp       
  sdlget       
  seq          
  seqlib       
  set          
  sm           
  srswww
  strv         
  templ	    
  tm           
  toklist
  unix_map     
  variable     
  view
  wgetz	    
}

$testfiles={
  variable     
}


$rules={

  # the entire function header
  header:    ~ { $Out 
                 pre{
                   $Skip:0 
                   $inputN=1
                   $argN=1
                   $returnN=1
                   $implicitN=1
                   $entry.name=''
                   $entry.fname=''
                   $entry.api=0
                 }
               }
               (/.\\*\\*+(API|api).+[a-zA-Z0-9]+ +\\*+/ {$Not} ln)* 
               (/[*\/]+(API|api)/ {$Wrt} 
                 ln {$App}(/[*\/]+/ appLn)* x{$App:[s:'@@\n']} 
                 (/.*{ *\n/ {$Not} appLn)+ /[^{]*/ {$App} 
               )? ~

  # fields inside the function header
  fields:    ~ {$Out $In:header}
               title comment input? implicit? return? proto ~
  title:     ~ /\/\\*\\*/ ('api' {$entry.api=1} | 'API' {$entry.api=2})? 
               /\\** */ name {$entry.fname=$Ct} ln ~
  comment:   ~ {$entry.comment=$Ct} (/([ \t]+[A-Z]+ *:|@@)/{$Not} ln)+ ~ 
  input:     ~ /[ \t]+INPUT *:/ ln {$Wrt:input}
               (/([ \t]+[A-Z]+ *:|@@)/{$Not} appLn)* ~ 
  implicit:  ~ /[ \t]+IMPLICIT:/ ln {$Wrt:implicit}
               (/([ \t]+[A-Z]+ *:|@@)/{$Not} appLn)* ~ 
  return:    ~ /[ \t]+RETURNS? *:/ ln {$Wrt:return}
               ('@@'{$Not} appLn)* ~ 
  proto:     ~ ln /.*/ {$Wrt:proto}  ~

  # break lists
  l_input:   ~ {$In:[fields c:input] $Out:input} l_item* ~
  l_implicit:~ {$In:[fields c:implicit t:dod] $Out:implicit}
               l_item* ~
  l_return:  ~ { $In:[fields c:return] $Out:return} 
               l_item* {$entry.retCom[$returnN] = $Ct $returnN=$returnN+1} ~
  l_item:    ~ /[ \t]+o[ \t]/ ln {$Wrt $s=$Ct} (/[ \t]+o[ \t]/ {$Not} appLn)* |
               /[ \t\n]+([^\n \t][^\n]+)\n/ {$Wrt:[s:$1] $s=$1} ~  
  i_inputRW: ~ { $In:[input] $Out:gaga 
                 pre{$arg=$entry.input[$inputN] $arg.write='<I>read</I>'}
                 $arg.rem=$Ct 
                 $inputN=$inputN+1
                 
               } (/[^[]*/ ('[W]'{$arg.write='<I>write</I>' $Rep:''}|
                 '[R]'{$arg.write='<I>read</I>' $Rep:''} | '[')? )+ ~

  # break prototype into single arguments
  l_proto:   ~ { $In:[fields c:proto] 
                 $Out:proto 
                 pre{$Skip:1}
                 $Skip:0
               } 
               typeName {$entry.return = $Ct}
               name {$entry.name=$Ct} '(' (l_arg (',' l_arg)*)? ')' 
             ~
  l_arg:     ~ { pre{$arg=$entry.input[$argN]}
                 $argN=$argN+1
               }
               typeName {$arg.type=$Ct} 
                argName {$arg.name=$Ct} | 
                '...' {$arg.type=$Ct $arg.name='&nbsp;'} ~

  # for replacing function names by hypertext links
  function:  ~ {$Out pre{$Skip:1}}
               ('<H3>' {$Not} ln {$Print:[$Ct f:$outf]})*
               ('<H3>' {$Wrt} appLn 
               ('<H3>' {$Not} appLn)*)?
             ~               
  h_function:~ {$In:function $Out}
               /[^\n]+A>([a-zA-Z0-9]+)[^\n]+\n/ 
               { $Print:[$Ct f:$outf]
                 if:$example.($1).isOk {
#                   $Print:"... linking function $1 to examples\n"
                   $Print:['<I>Used in:</I>' f:$outf]
                   foreach:[$ex in:$example.($1).link]
                     $Print:[$ex f:$outf]
                   $Print:['<BR>' f:$outf]
                 }
               }
               h_line+ {$Print:[$Ct f:$outf]}
             ~
  h_line:    ~ ( /[A-Za-z0-9_]+/  
                 { if:$funct.$Ct !="" 
                     $Rep: |<A HREF="mf_($funct.$Ct).html#$Ct">$Ct</A>\
                 } | /[^A-Za-z0-9_\n]+/ 
               )* '\n'
             ~

  # others
  typeName:  ~ /(static|struct|enum|unsigned|long)/? 
               /[a-zA-Z0-9_]+/ /[ *]*/{$Noskip} ~
  argName:   ~ (/[][a-zA-Z0-9_*]+/ /[ *]*/{$Noskip} |
                 '(*' /[^)]+\\)/ /\\([^)]*\\)/)  ~
  name:      ~ /[a-zA-Z0-9_*]+/ ~
  ln:        ~ /[^\n]*\n/ ~
  appLn:     ~ /[^\n]*\n/ {$App} ~
}



#
# build the functions index and the function documentation page
#

$outf = $FileOpen:["SRSMAN:mtoc2_func.html" mode:write]
$outt = $FileOpen:["SRSMAN:mtoc_func.html" mode:write]
$Print:[f:$outf s:
  |<HTML>
  |<HEAD>
  |<TITLE>Module $SRS functions list</TITLE>
  |</HEAD>
  |<BODY BGCOLOR="#FFFFF0" LINK="#0000ff" VLINK="#ff0000" 
  | ALINK="#ff0000" TEXT="#000000">
  |<BASE TARGET="text">
]  
$Print:[f:$outt s:
  |<HTML>
  |<HEAD>
  |<TITLE>Module $SRS module list</TITLE>
  |</HEAD>
  |<BODY BGCOLOR="#FFFFF0" LINK="#0000ff" VLINK="#ff0000" 
  | ALINK="#ff0000" TEXT="#000000">
  |<BASE TARGET="index">
  |<H4>Modules in SRS</H4>
  |<UL>
]  


$Print:|...parsing C files
foreach:[$module in:$files] {
  $fil = $FileOpen:"SRSSOU:$module.c"
  $outm = $FileOpen:["SRSMAN:mff_$module.html" mode:write]

  $Print:[f:$outt s:
    |<LI><A HREF="mtoc2_func.html#$module">$module</A>
  ]
  $Print:[f:$outf s:
    |<H4><A NAME="$module"></A>Module "$module"</H4>
    |<UL>
  ]

  $Print:[f:$outm s:
    |<HTML>
    |<HEAD>
    |<TITLE>Descriptions of module "$module" functions</TITLE>
    |</HEAD>
    |<BODY BGCOLOR="#FFFFF0" LINK="#0000ff" VLINK="#ff0000" 
    | ALINK="#ff0000" TEXT="#000000">
  ] 

  $job = $JobNew:[prod:$rules skip:" \n\t" file:$fil]
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields] 
    $JobTokens:[$job name:gaga] 
    $JobTokens:[$job name:return] 
    $JobTokens:[$job name:proto] 

    if:($entry.name!='' && $entry.api) {
      $nam = $entry.name
      $funct.$nam  = $module # save for inserting hypertext links
      $Print:[f:$outf s:
      	|<LI><A HREF="mf_$module.html#($entry.name)">($entry.name)</A>
      ]
      # print the function information
      $Print:[f:$outm s: 
      	|<H3><A NAME="$nam"></A>$nam</H3>
      	|($entry.comment)<P>
      ]
      # print the function arguments
      $Print:[f:$outm s: 
        |<CENTER>
        |<TABLE BORDER>
        |<TR><TH><FONT SIZE=-1>Type</TH><TH><FONT SIZE=-1>Name</TH>
        |<TH><FONT SIZE=-1>R/W</TH>
        |<TH><FONT SIZE=-1>Comment</TH></TR>
        |<TR><TH COLSPAN=4 BGCOLOR="#d3b5b5">
        |<FONT SIZE=-1>Arguments</TH></TR>
      ]
      for:{$l=1 $l<$inputN $l=$l+1} {
  	$Print:[f:$outm s: 
      	  |<TR><TD VALIGN=top>($entry.input[$l].type)</TD>
      	  |<TD VALIGN=top>($entry.input[$l].name)</TD>
      	  |<TD ALIGN=center VALIGN=top>($entry.input[$l].write)</TD>
      	  |<TD VALIGN=top>($entry.input[$l].rem)</TD>
      	  |</TR>
      	]
      }
      if:$l==1
        $Print:[f:$outm s:
          |<TR><TD>&nbsp</TD><TD>&nbsp</TD><TD>&nbsp</TD>
          |<TD ALIGN=CENTER><I>none<I></TD></TR>      
        ]      

      # type of return value
      if:$entry.return=="void "
        $rem="<CENTER><I>nothing<I></CENTER>"
      else
        $rem=$entry.retCom[1]
      
      $Print:[f:$outm s: 
        |<TR><TH COLSPAN=4 BGCOLOR="#d3b5b5">
        |<FONT SIZE=2>Returns</TH></TR>
        |<TR><TD VALIGN=top>($entry.return)</TD>
        |<TD VALIGN=top>&nbsp;</TD>
        |<TD VALIGN=top ALIGN=center>&nbsp;</TD>
        |<TD VALIGN=top>($rem)</TD>
        |</TR>
        |</TABLE>
        |</CENTER>
      ]
    }
    $JobNext:$job
  }
  $FileClose:$fil
  $FileClose:$outm
  $Print:['</UL>'f:$outf]
}
$FileClose:$outt

#
# read the programming manual insert hypertext links and examples
#

$progRules={
  file:    ~ {pre{$Skip:0}} 
             (title {$Print:[$Ct f:$mprog]} | 
             include | line { $Print:[$Ct f:$mprog]})+
           ~
  title:   ~ /.*(name|NAME)="([a-zA-Z0-9_-]+)".*\n/ 
             {$chapter=$2} ~
  line:    ~ ( /[^\na-zA-Z0-9_]+/ | /[a-zA-Z0-9_]+/ 
               {if:$funct.$Ct !="" 
                  $Rep:|<A HREF="mf_($funct.$Ct).html#$Ct">$Ct</A>\
               }
             )* '\n' ~
  include: ~ /.*INCLUDE EXAMPLE:/ /[a-zA-Z0-9.]+/ {
              $Print:[|
                       |<TABLE><TR><td BGCOLOR=\"#D0D0D0\"><PRE>\
                 f:$mprog] 
               $exName = $Ct
               $Parse:[prod:$exRules start:file 
                 fileName:"SRSDEMO:$Ct"]
               $Print:['</TD></TR></TABLE></PRE>' f:$mprog]
             } ~
}

$exRules={
  file:    ~ {pre{$Skip:0}} line+ {$Print:[$Ct f:$mprog]} ~
  line:    ~ ( /[^\na-zA-Z0-9_]+/ | /[a-zA-Z0-9_]+/ 
               { $name = $Ct if:$funct.$Ct !="" {
                   $Rep:|<A HREF="mf_($funct.$Ct).html#$Ct">$Ct</A>\
#                   $Print:|found $name <-> $exName
                   $example.($name).isOk = 1
                   $example.($name).link.$exName = 
                     | <A HREF="mi_prog.html#$chapter">$exName</A>\
                 } 
               }
             )* '\n' 
           ~
}

$mprog = $FileOpen:["SRSMAN:m_prog.html" mode:write]
$Print:|...parsing the C API manual
$Parse:[prod:$progRules start:file fileName:"SRSDOC:prog.html"]
 
#
# go over the function documentation page again and search for 
# known function names that will be promoted to  hypertext links
#

$Print:|...parsing the module descriptions in HTML 
foreach:[$module in:$files] {
  $inf = $FileOpen:["SRSMAN:mff_$module.html"]
  $outf = $FileOpen:["SRSMAN:mf_$module.html" mode:write]
  $job = $JobNew:[prod:$rules skip:" \t" file:$inf]
  $Print:'.'
  while:$JobHasInput:$job{
    $JobTokens:[$job name:h_function print:0] 
    $JobNext:$job
  }
  $FileClose:$inf
  $FileClose:$outf
}
  $Print:'\n'






mentation page again and searsrs/icarus/util/man_chap.i

$chapter={
  {path:"SRSDOC:srswww.html"     part:srswww}
  {path:"SRSDOC:tour.html"       part:tour}
  {path:"SRSDOC:srsmaint.html"   part:srsmaint}
  {path:"SRSDOC:icarus.html"     part:icarus}
  {path:"SRSDOC:install.html"    part:install}
  {path:"SRSDOC:query.html"      part:query}
  {path:"SRSDOC:debugger.html"   part:debugger}
  {path:"SRSMAN:class.html"      part:class}
  {path:"SRSMAN:icafunc.html"    part:icafunc}
  {path:"SRSMAN:usage.html"      part:usage}
  {path:"SRSDOC:internal.html"   part:internal}
}


# get the list of all documented icarus functions
$icaFunRules={
  title: ~ (/.*<[Hh][1-4]>/ /<(A NAME|a name)="?([^>"]+)"?>/ {$name=$2} #"
            /.*(\\$[a-zA-Z0-9_]+)<\/[hH]/? 
	    {$fun.($1).flag=1 $fun.($1).file=$fileName $fun.($1).name=$name}
            | ln
           )+ ~
  ln:    ~ /[^\n]*\n/  ~
}


$rules={

  # extract titles and bodies
  field:  ~ {$Out pre $skip:0}
            x{$Wrt:dummy} (
              (/[ \t\n]*<[Hh][1-6]>/ {$Not} ln {$App})+ 
              (/[ \t\n]*<[Hh][1-6]>/ {$Wrt:title} 
              (/.*<\/[Hh][1-6]>/ {$Not} ln {$App})*
              /.*<\/[Hh][1-6]>/ {$App} ln {$Wrt:text})?
            )+
          ~

  # inserting of links to index words
  text:   ~ {$In:[field t:rep] $Out} word* ~            
  word:   ~ /<(BODY|body)>/ {$Rep:|<BODY BGCOLOR="#FFFFF0" LINK="#0000ff" 
                           | VLINK="#ff0000" ALINK="#ff0000" TEXT="#000000">
            } | 
            /<[hH][1-4]>.*<\/[hH][1-4]>/ |
            /<(PRE|pre)>/
            {$Rep:"<P><TABLE><TR><td BGCOLOR=\"#D0D0D0\"><PRE>"}|
            /<\/(PRE|pre)>/{$Rep: "</td></TR></TABLE><P>"} |
            /\\$[a-zA-Z0-9_]+/ 
            {if:$fun.($Ct).flag==1 
               $Rep:
                 |<A HREF="mi_($fun.($Ct).file).html#\
                 |($fun.($Ct).name)">$Ct</A>\
            } | /[^$<]+/ | /./           
          ~
  # other stuff
  ln:     ~ /[^\n]*\n?/~

}

# make a list of all icarus functions and classes
foreach:[$fileName in:{'icafunc' 'class'}] {
  $Parse:[fileName:"SRSMAN:$fileName.html" 
    prod:$icaFunRules start:title
  ]
}

# process the chapters 
$job = $JobNew:[prod:$rules skip:" "]
foreach:[$chap in:$chapter] {
  $ifil = $FileOpen:"($chap.path)"
  $ofil = $FileOpen:["SRSMAN:m_($chap.part).html" mode:write]
  $print:|...processing ($chap.path)
  $JobNext:[$job file:$ifil]
  while:$JobHasInput:$job {
    $JobTokens:[$job name:field task:rep print:1 withCode:0 outFile:$ofil] 
    $JobNext:$job
  }
  $FileClose:$ofil
  $FileClose:$ifil
}




{
  srs/icarus/util/man_inx.i

$chapter={
  {path:"SRSMAN:m_install.html" part:install n:1}
  {path:"SRSMAN:m_srswww.html" part:srswww n:1}
  {path:"SRSMAN:m_query.html" part:query n:2}
  {path:"SRSMAN:m_usage.html" part:usage n:3}
  {path:"SRSMAN:m_icarus.html" part:icarus n:4}
  {path:"SRSMAN:m_icafunc.html" part:icafunc n:5}
  {path:"SRSMAN:m_debugger.html" part:debugger n:6}
  {path:"SRSMAN:m_tour.html" part:tour n:7}
  {path:"SRSMAN:m_srsmaint.html" part:srsmaint n:8}
  {path:"SRSMAN:m_prog.html" part:prog n:9}
  {path:"SRSMAN:m_class.html" part:class n:11}
#  {path:"SRSMAN:m_internal.html" part:internal n:11}
}

$indexWords={
  'action'        
  'argument'       
  'associative list'    
  'class'         
  'data-field'    
  'databank'    
  'element'       
  'expression'    
  'flatfile'
  'for statement'
  'forced parsing'
  'foreach statement'
  'grammar'       
  'icarus'        
  'if statement'
  'input'         
  'instance'      
  'interpretation' 
  'interpreter'   
  'language'      
  'lazy parsing'
  'nonterminal'   
  'object class'        
  'output'        
  'perl'          
  'position'      
  'production'    
  'recursive'     
  'regular expression'       
  'scanner'       
  'strings'       
  'substitution'  
  'symbol'        
  'syntax'        
  'task'          
  'tcl'           
  'terminal'      
  'token table'         
  'token code'         
  'variable'      
  'while statement'
}


$rules={

  # extract sections
  section: ~ {$Out pre{$Skip:0}}
             x{$Wrt}
             (/[ \t\n]*<[Hh][1-2]>/ {$Not} ln {$App})*
             (/[ \t\n]*<[Hh][1-2]>/ {$Wrt} 
              (/[ \t\n]*<[Hh][1-2]>/ {$Not} ln {$App})*)+
           ~

  # inserting of links to index words
  inxSect: ~ {$In:[section t:inx] pre{foreach:[$i in:$inx] $i.n=0}} index ~
  index:   ~ (/[a-zA-Z_][a-zA-Z0-9_-]+/ 
              {if:$inx.($Ct).ok {
                  $key=$inx.($Ct)
                  if:$inx.($Ct).n < 1 {
                    $inx.($Ct).n += 1 
                    $locN += 1
                    $key.list += 
                      |<A HREF="mi_$fileName#inx_$locN">$chapN</A>\
                    $Rep:"<A NAME=inx_$locN></A>$Ct"
                  }
                }
                if:$concat && $inx."$prev $Ct".ok {
                  $s = "$prev $Ct"
                  $key=$inx."$prev $Ct" 
                  if:$inx.($s).n < 1 {
                    $inx.($s).n += 1 
                    $locN += 1
                    $key.list += 
                      |<A HREF="mi_$fileName#inx_$locN">$chapN</A>\
                    $Rep:"<A NAME=inx_$locN></A>$Ct"
                  }
                }
                $concat=0
                $prev=$Ct
              } |
              /[ \n\t]+/ {$concat=1} | /[^a-zA-Z]+/ | /./)* ~

  # other stuff
  ln:     ~ /[^\n]*\n/ ~
}

# initialize index word list
foreach:[$iw in:$indexWords] {
  $inx.($iw).name = $iw
  $inx.($iw).ok = 1
  $inx.($iw).list = {}
}

$job = $JobNew:[prod:$rules]
foreach:[$chap in:$chapter] {
  $print:|...processing "($chap.path)"
  $fil = $FileOpen:"($chap.path)"
  $ofil = $FileOpen:["SRSMAN:mi_($chap.part).html" mode:write]
  $fileName="($chap.part).html"
  $chapN = $chap.n
  $locN = 0
  $JobNext:[$job file:$fil]
  while:$JobHasInput:$job {
    $JobTokens:[$job name:section withCode:0 print:1 outFile:$ofil task:inx]
    $JobNext:$job
  }
  $FileClose:$ofil
}


# print the index file
$inxFile=$FileOpen:["SRSMAN:m_inx.html" mode:write]
$print:[
  |<HTML>
  |<HEAD>
  |<TITLE>SRS Manual - Index</TITLE>
  |</HEAD>
  |<BODY BGCOLOR="#FFFFF0" LINK="#0000ff" VLINK="#ff0000" 
  |	ALINK="#ff0000" TEXT="#000000">
  |<BASE TARGET="text">
  |<H2>Index</H2>
  f:$inxFile]

foreach:[$i in:$inx]
  if:$i.ok {
    $print:["($i.name) <B>" f:$inxFile]
    foreach:[$p in:$i.list]
      $print:[" $p" f:$inxFile]
    $print:["</B><BR>\n" f:$inxFile]
  }

$print:[
  |</BODY>
  |</HTML>
  f:$inxFile]


ex file
$inxFile=$FileOpen:["SRSMAN:m_inx.html" mode:write]
$print:[
  |<HTML>
  |<HEAD>
  |<TITLE>SRS Manual - Index</TITLE>
  |</HEAD>
  |<BODY BGCOLOR="#FFFFF0" LINK="#0000ffsrs/icarus/util/man_toc.i
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: man_toc.i,v $
#    $Revision: 1.11 $
#    $Date: 1997/03/03 18:32:53 $
#    $Author: srs $
#
# Generates a table of contents for a list of  HTML files
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#

$chapter={
  {path:"SRSMAN:m_srswww.html" part:srswww}
  {path:"SRSMAN:m_query.html" part:query}
  {path:"SRSMAN:m_icarus.html" part:icarus}
  {path:"SRSMAN:m_prog.html" part:prog}
  {path:"SRSMAN:m_class.html" part:class}
  {path:"SRSMAN:m_debugger.html" part:debugger}
  {path:"SRSMAN:m_icafunc.html" part:icafunc}
  {path:"SRSMAN:m_tour.html" part:tour}
  {path:"SRSMAN:m_srsmaint.html" part:srsmaint}
  {path:"SRSMAN:m_install.html" part:install}
  {path:"SRSMAN:m_usage.html" part:usage}
  {path:"SRSMAN:m_internal.html" part:internal}
}

$rules={

  # extract titles and bodies
  field:  ~ {$Out pre{$Skip:0}}
            x{$Wrt:dummy} (
              (/[ \t\n]*<[Hh][1-6]>/ {$Not} ln {$App})+ 
              (/[ \t\n]*<[Hh][1-6]>/ {$Wrt:title} 
              (/.*<\/[Hh][1-6]>/ {$Not} ln {$App})*
              /.*<\/[Hh][1-6]>/ {$App} ln {$Wrt:text})?
            )+
          ~

  # table of contents
  index:  ~ {init{$prev=0} $In:[field c:title] $Out} 
            /<.1>/ label+ /(.*)<\/.1>/ 
            {$print:["<FONT SIZE=+1><B>$1</B></FONT></A>\n" f:$toc] $prev=0} |
            /<.([2-4])>/ {$n=$1-1} label+ /(.*)<\/.[2-4]>/ 
            { if:$prev==0 {
                $prev=$n-1
              }
              if:$n>$prev
                for:{$k=$n-$prev $k $k=$k-1}
                  $print:[ "<UL>" f:$toc]
              elif:$prev>$n
                for:{$k=$prev-$n $k $k=$k-1}
                  $print:["</UL>" f:$toc]

              $print:["<LI><A HREF=\"$fileName#$label\">\n" f:$toc]
              if:$n==1 
                $print:["<B>$1</B></A>\n" f:$toc]
              elif:$n==2
                $print:["$1</A>\n" f:$toc]
              else 
                $print:["$1</A>\n" f:$toc]
              $prev = $n
            } 
          ~
  # other stuff
  ln:     ~ /[^\n]*\n?/ ~
  label:  ~ / *<(A +NAME|a +name)="?([^">]+)"?>(<\/[Aa]>)?/ {$label="$2"}~ #"
}

foreach:[$chap in:$chapter] {
  $fil = $FileOpen:"($chap.path)"
  $toc = $FileOpen:["SRSMAN:mtoc_($chap.part).html" mode:write]
  $fileName="mi_($chap.part).html"

  $print:[f:$toc s:
    |<HTML>
    |<HEAD>
    |<TITLE>Table of Contents for Chapter "$part"</TITLE>
    |</HEAD>
    |<BODY BGCOLOR="#FFFFF0" LINK="#0000ff" VLINK="#ff0000" 
    |	ALINK="#ff0000" TEXT="#000000">
    |<BASE TARGET="text">
  ]

  $job = $JobNew:[prod:$rules skip:" " file:$fil]
  while:$JobHasInput:$job {
    $JobTokens:[$job name:index withCode:0] 
    $JobNext:$job
  }
  $print:['</HTML></HEAD></BODY>' f:$toc]
  $FileClose:$toc
}





.html" mode:write]
  $fileName="mi_($chap.part).html"

  $print:[f:$toc s:
    |<HTML>
    |<HEAD>
    |<TITLE>Table of Contents for Chapter "$part"</TITLE>
    |</HEAD>
    |<BODY BGCOLOR="#FFFFF0" LINK="#000srs/icarus/util/man_usage.i
$optRules={
  arg:   ~ {pre{$skip:0}} 
           (/ +-/ {$not} ln)+ 
           (name type value? text? | ln)+ ~
  name:  ~ / +-([a-zA-Z0-9]+)/ {$n=$1 $arg.($n).name=$1} ~
  text:  ~ {$arg.($n).text=$ct} ln (/     [^\n]+\n/)* ~
  type:  ~ / *<n>/ {$arg.($n).type=int} | 
           / *<string>/ {$arg.($n).type=string} |
           x{$arg.($n).type=bool} ~ 
  value: ~ / *\\[([^]]+)\\]/ {$arg.($n).value=$1} ~
  ln:    ~ /[^\n]*\n/ ~
}

$rules={
  file:  ~ (/INCLUDE OPTIONS ([a-zA-Z0-9]+)/ 
           { $arg={}
             $Parse:[$System:"$1 -help" prod:$optRules start:arg]
             $Print:[f:$oFile s:
              	|<TABLE BORDER CELLPADDING=3>
              	|<TH BGCOLOR="#d3b5b5"><FONT SIZE=2>Name</TH>
              	|<TH BGCOLOR="#d3b5b5"><FONT SIZE=2>Type</TH> 
              	|<TH BGCOLOR="#d3b5b5"><FONT SIZE=2>Default</TH>
              	|<TH BGCOLOR="#d3b5b5"><FONT SIZE=2>Comment</TH>
             	|</TR>
             ]
             foreach:[$a in:$arg]
             	if:$a.name!="" && $Trim:[$a.text skip:" \n"] != ""
             	  $Print:[f:$oFile s:
                    |<TR>
                    |<TD VALIGN=TOP><B>($a.name)</B></TD>
                    |<TD VALIGN=TOP><I>($a.type)</I></TD>
             	    |<TD VALIGN=TOP ALIGN=CENTER>($a.value)</TD>
             	    |<TD VALIGN=TOP>($a.text)</TD>
             	    |</TR>
                  ]
             $Print:['</TABLE>\n' f:$oFile]
           } | ln {$Print:[f:$oFile s:$ct]})+
         ~
  ln:    ~ /[^\n]*\n/ ~
}

$arg={}
$oFile = $FileOpen:["SRSMAN:usage.html" mode:write]
$Parse:[fileName:"SRSDOC:usage.html" prod:$rules start:file]
$FileClose:$oFile


N=TOP><B>($a.name)</B></TD>
                    |<TD VALIGN=TOP><I>($a.type)</I></TD>
             	    |<TD VALIGN=TOP ALIGN=CENTER>($a.value)</TD>
             	    |<TD VALIGN=TOP>($a.text)</TD>
             	    |</TR>
                  ]
             $Print:['</TABLE>\n' f:$oFile]
           } | ln {$Print:[f:$oFile s:$ct]})+
         ~
  ln:    ~ /[^\n]*\n/ ~
}

$arg={}
$oFile = $FileOpen:[srs/icarus/util/odd.i
#
#    $RCSfile: odd.i,v $
#    $Revision: 1.2 $
#    $Date: 1996/05/24 14:11:51 $
#    $Author: ulyanov $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

file:"SRSICA:oddgen.i"
file:"SRSICA:oddfncts.i"
file:"SRSICA:icacom.ic"
file:"SRSICA:classes.i"


$partable:[ 
  vars:{
    $parameter:[name:"doInitHeader" type:bool num:0 
      comment:"h-file with struct declaration and initialization"]
    $parameter:[name:"doHeader" type:bool num:0 
      comment:"h-file with struct declaration"]
    $parameter:[name:"doSection" type:bool num:0 
      comment:"binary section file (can be combined with '-h')"]
    $parameter:[name:"doMetaData" type:bool num:0 
      comment:"h-file with meta data initialization"]
    $parameter:[name:"doClassInfo" type:bool num:0 
      comment:"file with class information"]
    $parameter:[name:"printProgress" type:bool num:0 
      comment:"print a line for each ODD-file read"]
    $parameter:[name:"printProgress" type:bool num:0 
      comment:"print a line for each ODD-file read"]
    $parameter:[name:"printDots" type:bool num:0 
      comment:"print a dot for each ODD-file read"]
    PART_BOOLEAN:$partype:[name:"boolean" max:3 min:0 charset:"yYnN01oOfFjJ"]
  }
]

$command:[name:odd usage:"sectionName" 
  vars:{
    $arg:[name:"-help" type:help comment:"this message"]
    $arg:[name:"-i" parameter:doInitHeader]
    $arg:[name:"-h" parameter:doHeader]
    $arg:[name:"-s" parameter:doSection]
    $arg:[name:"-m" parameter:doMetaData]
    $arg:[name:"-c" parameter:doClassInfo]
    $arg:[name:"-r" parameter:printProgress]
    $arg:[name:"-d" parameter:printDots]
  }
]

$def:[infile:"SRSICA:sdl.sdl" outfile:"SRSSOU:odd5.h" section_name:"sdl" 
  section_size:50]
"]
  }
]

$command:[name:odd usage:"sectionName" 
  vars:{
    $arg:[name:"-help" type:help comment:"this message"]
    $arg:[name:"-i" parameter:doInitHeader]
    $arg:[name:"-h" parameter:doHeader]
    $arg:[name:"-s" psrs/icarus/util/odd.ic
#
#    $RCSfile: odd.ic,v $
#    $Revision: 1.2 $
#    $Date: 1996/05/24 14:11:52 $
#    $Author: ulyanov $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

file:"SRSICA:oddgen.i"
file:"SRSICA:oddfncts.i"
file:"SRSICA:classes.i"
file:"SRSICA:parameter.ic"
file:"SRSICA:arglist.ic"

$def:[infile:"SRSICA:odd.i" outfile:"SRSSOU:oddclass.h" section_name:"sdl" 
  section_size:500]
   $¶ £¡Üe:"-s" psrs/icarus/util/oddfncts.i
#
#    $RCSfile: oddfncts.i,v $
#    $Revision: 1.1 $
#    $Date: 1996/05/06 16:14:03 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

# functions return attribute size
F_SIZINHERIT:$function:[name:OFInheritSize args:"(SDLoOBJ *, SDLoATTR *)"]
F_SIZ4BARR:$function:[name:OF4BArrSize args:"(SDLoOBJ *, SDLoATTR *)"]
F_SIZ4B:$function:[name:OF4BSize args:"(SDLoOBJ *, SDLoATTR *)"]
F_SIZPTRARR:$function:[name:OFPtrArrSize args:"(SDLoOBJ *, SDLoATTR *)"]
F_SIZPTR:$function:[name:OFPtrSize args:"(SDLoOBJ *, SDLoATTR *)"]
F_SIZBNF:$function:[name:OFBNFSize args:"(SDLoOBJ *, SDLoATTR *)"]
F_SIZBARR:$function:[name:OFBArrSize args:"(SDLoOBJ *, SDLoATTR *)"]

# function to postprocess attributes
F_MAKEDFLT:$function:[name:OFMakeDefault
  args:"(SDLoOBJ *, SDLoATTR *, unsigned int *)"]
F_MAKENODFLT:$function:[name:OFMakeNoDefault 
  args:"(SDLoOBJ *, SDLoATTR *, unsigned int *)"]
F_MAKECHILD:$function:[name:OFMakeChild 
  args:"(SDLoOBJ *, SDLoATTR *, unsigned int *)"]
F_MAKECHILDN:$function:[name:OFMakeChildN 
  args:"(SDLoOBJ *, SDLoATTR *, unsigned int *)"]
F_MAKEALLOBJ:$function:[name:OFMakeAllObj 
  args:"(SDLoOBJ *, SDLoATTR *, unsigned int *)"]
F_MAKEALLOBJN:$function:[name:OFMakeAllObjN 
  args:"(SDLoOBJ *, SDLoATTR *, unsigned int *)"]

# functions to write member declarations
F_DEFSIMPLE:$function:[name:OFDefSimple
   args:"(FILE *, SDLoATTR *, char *, char *)"]
F_DEFSTR:$function:[name:OFDefStr 
  args:"(FILE *, SDLoATTR *, char *, char *)"]
F_DEFFNCT:$function:[name:OFDefFnct 
  args:"(FILE *, SDLoATTR *, char *, char *)"]
F_DEFHEADER:$function:[name:OFDefHeader 
  args:"(FILE *, SDLoATTR *, char *, char *)"]
F_DEFSTRUCTPTR:$function:[name:OFDefStructPtr 
  args:"(FILE *, SDLoATTR *, char *, char *)"]
F_DEFGENERICTYP:$function:[name:OFDefGenericTyp 
  args:"(FILE *, SDLoATTR *, char *, char *)"]
F_DEFUSER:$function:[name:OFDefUser 
  args:"(FILE *, SDLoATTR *, char *, char *)"]
F_DEFEBNF:$function:[name:OFDefEbnf 
  args:"(FILE *, SDLoATTR *, char *, char *)"]

# functions for inserting attributes in target structures
F_INSERTFLOAT:$function:[name:OFInsertFloat 
  args:"(void *, void *, void *, void ***, char *, unsigned int, int)"]
F_INSERTINT:$function:[name:OFInsertInt 
  args:"(void *, void *, void *, void ***, char *, unsigned int, int)"]
F_INSERTUINT:$function:[name:OFInsertUInt 
  args:"(void *, void *, void *, void ***, char *, unsigned int, int)"]
F_INSERTUCHAR:$function:[name:OFInsertUChar
  args:"(void *, void *, void *, void ***, char *, unsigned int, int)"]
F_INSERTUSER:$function:[name:OFInsertUser 
  args:"(void *, void *, void *, void ***, char *, unsigned int, int)"]
F_INSERTSTR:$function:[name:OFInsertStr 
  args:"(void *, void *, void *, void ***, char *, unsigned int, int)"]
F_INSERTFUNCTION:$function:[name:OFInsertFunction 
  args:"(void *, void *, void *, void ***, char *, unsigned int, int)"]
F_INSERTOBJECT:$function:[name:OFInsertObject 
  args:"(void *, void *, void *, void ***, char *, unsigned int, int)"]
F_INSERTHEADER:$function:[name:OFInsertHeader 
  args:"(void *, void *, void *, void ***, char *, unsigned int, int)"]
F_INHERIT:$function:[name:OFInherit 
  args:"(void *, void *, void *, void ***, char *, unsigned int, int)"]
F_GENERIC:$function:[name:OFGeneric 
  args:"(void *, void *, void *, void ***, char *, unsigned int, int)"]

# functions for writing attribute values to the header file
F_WRTINT:$function:[name:OFWrtInt args:"(SDLoATTR *, char *, void **)"]
F_WRTUCHAR:$function:[name:OFWrtUChar args:"(SDLoATTR *, char *, void **)"]
F_WRTUINT:$function:[name:OFWrtUInt args:"(SDLoATTR *, char *, void **)"]
F_WRTFLOAT:$function:[name:OFWrtFloat args:"(SDLoATTR *, char *, void **)"]
F_WRTSTR:$function:[name:OFWrtStr args:"(SDLoATTR *, char *, void **)"]
F_WRTNAME:$function:[name:OFWrtName args:"(SDLoATTR *, char *, void **)"]
F_WRTNULL:$function:[name:OFWrtNULL args:"(SDLoATTR *, char *, void **)"]
F_WRTADDR:$function:[name:OFWrtAddr args:"(SDLoATTR *, char *, void **)"]
F_WRTEBNF:$function:[name:OFWrtEBNF args:"(SDLoATTR *, char *, void **)"]

# functions for checking attribute values
F_CHECKNUM:$function:[name:OFCheckNum args:"(SDLoATTR *, int, char *)"]
F_CHECKSTR:$function:[name:OFCheckStr args:"(SDLoATTR *, int, char *)"]

# functions for generic attribute types
F_GENSIMPLE:$function:[name:OFGenSimple args:"(SDLoOBJ *, SDLoATTR *)"]
F_GENOBJECT:$function:[name:OFGenObject args:"(SDLoOBJ *, SDLoATTR *)"]


# attribute type definitions
AT_FLOAT:$attrtype:[calcsize:@F_SIZ4BARR make:@F_MAKEDFLT declare:@F_DEFSIMPLE
  insert:@F_INSERTFLOAT write:@F_WRTFLOAT check:@F_CHECKNUM 
  typname:float gentype:@F_GENSIMPLE]
AT_UCHAR:$attrtype:[calcsize:@F_SIZBARR make:@F_MAKEDFLT declare:@F_DEFSIMPLE 
  insert:@F_INSERTUCHAR write:@F_WRTUCHAR check:@F_CHECKNUM 
  typname:"unsigned char"]
AT_INT:$attrtype:[calcsize:@F_SIZ4BARR make:@F_MAKEDFLT declare:@F_DEFSIMPLE 
  insert:@F_INSERTINT write:@F_WRTINT check:@F_CHECKNUM typname:INT4 
  gentype:@F_GENSIMPLE]
AT_UINT:$attrtype:[calcsize:@F_SIZ4BARR make:@F_MAKEDFLT declare:@F_DEFSIMPLE
  insert:@F_INSERTUINT write:@F_WRTUINT check:@F_CHECKNUM typname:UINT4]
AT_STRING:$attrtype:[calcsize:@F_SIZPTRARR make:@F_MAKEDFLT declare:@F_DEFSTR
  insert:@F_INSERTSTR write:@F_WRTSTR save_address:yes check:@F_CHECKSTR 
  gentype:@F_GENSIMPLE typname:char]
AT_ALLOBJ:$attrtype:[calcsize:@F_SIZPTR make:@F_MAKEALLOBJ 
  declare:@F_DEFSTRUCTPTR write:@F_WRTADDR save_address:yes]
AT_CHILD:$attrtype:[calcsize:@F_SIZPTR make:@F_MAKECHILD 
  declare:@F_DEFSTRUCTPTR write:@F_WRTADDR save_address:yes]
AT_CHILD_N:$attrtype:[calcsize:@F_SIZ4B make:@F_MAKECHILDN
  declare:@F_DEFSIMPLE write:@F_WRTINT typname:INT4]
AT_ALLOBJ_N:$attrtype:[calcsize:@F_SIZ4B make:@F_MAKEALLOBJN 
  declare:@F_DEFSIMPLE write:@F_WRTINT typname:INT4]
AT_OBJECT:$attrtype:[calcsize:@F_SIZPTRARR make:@F_MAKEDFLT 
  declare:@F_DEFSTRUCTPTR insert:@F_INSERTOBJECT write:@F_WRTADDR 
  save_address:yes gentype:@F_GENOBJECT]
AT_PROTOFNCT:$attrtype:[calcsize:@F_SIZPTR make:@F_MAKENODFLT 
  insert:@F_INSERTSTR write:@F_WRTNAME check:@F_CHECKSTR]
AT_FNCT:$attrtype:[calcsize:@F_SIZPTR make:@F_MAKEDFLT declare:@F_DEFFNCT 
  insert:@F_INSERTFUNCTION write:@F_WRTNAME save_address:yes]
AT_USER:$attrtype:[calcsize:@F_SIZPTRARR make:@F_MAKEDFLT declare:@F_DEFUSER
  insert:@F_INSERTUSER write:@F_WRTNULL save_address:yes]
AT_GENERIC_TYP:$attrtype:[insert:@F_GENERIC]
AT_GENERIC_OBJ:$attrtype:[insert:@F_GENERIC]
AT_GENERIC:$attrtype:[calcsize:@F_SIZPTRARR declare:@F_DEFGENERICTYP 
  save_address:yes]
AT_DEFER:$attrtype:[]
AT_INHERIT:$attrtype:[calcsize:@F_SIZINHERIT make:@F_MAKENODFLT 
  insert:@F_INHERIT]
AT_OVERLOAD:$attrtype:[]
AT_STORE:$attrtype:[calcsize:@F_SIZPTRARR make:@F_MAKEDFLT 
  declare:@F_DEFHEADER insert:@F_INSERTHEADER write:@F_WRTNULL 
  save_address:yes]
AT_CLONE:$attrtype:[calcsize:@F_SIZPTRARR make:@F_MAKEDFLT 
  declare:@F_DEFSTRUCTPTR insert:@F_INSERTOBJECT save_address:yes]
AT_EBNF:$attrtype:[calcsize:@F_SIZBNF declare:@F_DEFEBNF write:@F_WRTEBNF]

$CDefine:[@AT_CHILD name:AT_CHILD]
$CDefine:[@AT_PROTOFNCT name:AT_PROTOFNCT]
$CDefine:[@AT_FNCT name:AT_FNCT]
$CDefine:[@AT_CLONE name:AT_CLONE]



AD:$attrtype:[]
AT_STORE:$attrtype:[calcsize:@F_SIZPTRARR make:@F_MAKEDFLT 
  declare:@F_DEFHEADER insert:@F_INSERTHEADER write:@F_WRTNULL 
  save_address:yes]
AT_CLONE:$attrtype:[calcsize:@F_SIZPTRARR make:@F_MAKEDFLT 
  declare:@F_DEFSTRUCTPTR insert:@F_INSERTOBJECT save_address:yes]
AT_EBNF:$attrtype:[calcsize:@F_SIZBNF declare:@F_DEFEBNF write:@F_WRTEBNF]

$CDefine:[@AT_CHILD name:AT_CHILD]srs/icarus/util/oddgen.i
#
#    $RCSfile: oddgen.i,v $
#    $Revision: 1.2 $
#    $Date: 1997/03/12 16:18:51 $
#    $Author: srs $
#
#  Some general definitions needed for the ODD compiler
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$FALSE=0
$TRUE=1
$SDLxXOBJCLASS=255
$SDLxFLOAT=0
$SDLxUCH=1
$SDLxINT=2
$SDLxUINT=3
$SDLxSTR=4
$SDLxGBLSS=5
$SDLxOWN=6
$SDLxOWN_N=7
$SDLxGBLNSS=8
$SDLxCHILD=9
$SDLxPFNCT=10
$SDLxFNCT=11
$SDLxUSER=12
$SDLxGTYP=13
$SDLxGTYPDEF=14
$SDLxGTYP_P=15
$SDLxDEFER=16
$SDLxINHERIT=17
$SDLxOVERLAY=18
$SDLxORG=19
$SDLxCLONE=20
$SDLxBNF=21
#
$SDLxVIRTUAL=1
#
$SDLxPNUM=9
$SDLxPNAM=10
$SDLxPTXT=11
$SDLxPCNST=12
#
$SDLxREQ=1
$SDLxNOREQ=0
$SDLxXSS=7
$SDLxXNAM=25
$SDLxXLN=132
$FILxXNAM=132
$SDLxHDR=1
$SDLxHDR2=2
$SDLxNOHDR=0

O_FUNCTION:$object:[name:function type:$SDLxFNCT declname:"X" status:system 
  attrs:{
    $attribute:[name type:protofunction declname:"fnctnam" max:30 
      valtype:text]
    $attribute:[args type:string declname:"args" max:132 valtype:text 
      required:y]
    $attribute:[module type:string declname:"module" max:30 
      valtype:{text name}]
  }
]

$SDLxPNAM=10
$SDLxPTXT=11
$SDLxPCNST=12
#
$SDLxREQ=1
$SDLxNOREQ=0
$SDLxXSS=7
$SDLxXNAM=25
$SDLxXLN=132
$FILxXNAM=132
$SDLxHDR=1
$SDLxHDR2=2
$SDLxNOHDR=0

O_FUNCTION:$object:[name:function type:$SDLxFNCT declname:"X" status:system 
  attrs:{
    $attribute:[name type:protofunction declname:"fnctnam" max:30 
      valtype:text]
    $attribusrs/icarus/util/parameter.i
#
#    $RCSfile: parameter.i,v $
#    $Revision: 1.18 $
#    $Date: 1997/03/17 23:18:58 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# functions for checking
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

F_CHECKFIELDLIST:$function:[name:LibParSetFields args:"(char *)"]
F_CHECKLIBLIST:$function:[name:LibParSetLibs args:"(char *)"]
F_CHECKLINKLIBLIST:$function:[name:LibParSetLinkLibs args:"(char *)"]
F_SETENVIRONMENT:$function:[name:LibSetEnvironment args:"(char *)"]


F_CHECKLIBLISTVIEWR:$function:[name:"LibParSetLibsViewRoot" args:"(char *)"]
F_CHECKLIBLISTVIEWL:$function:[name:"LibParSetLibsViewLeaf" args:"(char *)"]


$partable:[ 
  vars:{
    $parameter:[seqFormat type:string 
      set:'$setFormat:[Sequence set:"%s"]' get:'$setFormat:Sequence'
      comment:"format of sequence output file"]
    $parameter:[printText type:bool num:0 isVolatile:1
      comment:"copy complete text (annotation) part of entry"]
    $parameter:[printData type:bool num:0 isVolatile:1
      comment:"copy data (eg, sequence) part of entry"]
    $parameter:[printEntireEntry type:bool num:0 isVolatile:1 
      comment:"Print entire entry."]
    $parameter:[viewFieldList type:string
      comment:"List of fields that will be placed into a table view."]
    $parameter:[fieldList type:string parType:@PART_FIELDLIST 
      comment:"include fields in entry list <string>"]
    $parameter:[doQueryReport type:bool num:0 
      comment:"write a report about the query"]
    $parameter:[queryListValues type:bool num:0 isVolatile:1 
      comment:"List all values that match the query."]
    $parameter:[queryListValues type:bool num:0 isVolatile:1 
      comment:"List all values that match the query."]
    $parameter:[queryListFromMatch type:bool num:0 isVolatile:1 
      comment:"List all values after the first match of."]
    $parameter:[minIndexValN type:number num:0 
      comment:
        |List only values that occur at least specified number of times. \
        |Use together with "lv".
    ]
    $parameter:[listFOSN type:bool num:0 
      comment:"produces a FOSN (File Of Sequence Names)"]
    $parameter:[printToFile type:bool num:0 
      comment:"print resultant entries to file(s)"]
    $parameter:[fosnWithPos type:bool num:0 
      comment:"output FOSN includes sequence feature locations"]
    $parameter:[isHTMLFormat type:bool num:0 isVolatile:1 
      comment:"Select HTML format for output."]
    #
    #file and directory names
    #
    $parameter:[indexDirName type:string str:"SRSINX:" 
      comment:"directory with the indices"]
    $parameter:[outDirName type:string str:"SRSINX:" 
      comment:"name of output directory"]
    $parameter:[etcDir type:string str:"SRSETC:" 
      comment:"path of script that prepares SRS environment"]
    $parameter:[updateScriptName type:string str:"" 
      comment:"File name of output script file."]
    $parameter:[environment type:string partype:@PART_ENVIRONMENT 
      comment:"Name of the library environment" str:unix]
#
#query options
#
    $parameter:[setName type:string partype:@PART_SETNAME]
    $parameter:[makeWild type:bool partype:@PART_BOOLEAN num:0 
      comment:"appends a wildcard to each search word"]
    $parameter:[linkToLibs type:bool partype:@PART_BOOLEAN num:0 
      comment:"links a single entry to selected libraries"]
    $parameter:[linkToSet type:bool partype:@PART_BOOLEAN num:0 
      comment:"links result of query to selected libraries"]
    $parameter:[libList type:string parType:@PART_LIBLIST 
      comment:"select libraries of group"]
    $parameter:[linkLibList type:string parType:@PART_LINKLIBLIST 
      comment:"list of libraries to be linked to"]
    $parameter:[queryFileName type:string 
      comment:"name of file containing a list of queries"]
#
#others
#
    $parameter:[printLibInfo type:bool num:0 
      comment:"prints info about specified library"]
    $parameter:[printLibs type:bool num:0 
      comment:"prints a list of all active libraries"]
    $parameter:[linkTable type:string 
      comment:"print link table of entries found by query to selected libs"]
    $parameter:[getStartupInfo type:bool partype:@PART_BOOLEAN 
      comment:"Startup info for client programs."]
#
#options for retrieval of sequence features
#
    $parameter:[shiftbeginpos type:number 
      comment:"shift feature begin position"]
    $parameter:[shiftendpos type:number 
      comment:"shift feature end position"]
    $parameter:[isshiftbeginrelend type:bool num:0 
      comment:"shift of feature begin is relative to end pos"]
    $parameter:[isshiftendrelbegin type:bool 
      comment:"shift of feature end is relative to begin pos"]
    $parameter:[takeuncompletefeature type:bool 
      comment:"accecpt incomplete features" num:1]
    $parameter:[takeuncompleteshiftfeature type:bool 
      comment:"accecpt incomplete shifted features"]
#
#building indices
#
    $parameter:[showWarnings num:0 type:bool 
      comment:"display warnings caused by errors in the databank"]
    $parameter:[buildPartIndex num:0 type:number
      comment:
        |specifies the number of the library part or flat file for which  
        |indices shall be built separately.
    ]
    $parameter:[compress type:bool 
      comment:"compresses indices built previously"]
    $parameter:[touchIndex type:bool 
      comment:"touch index"]
    $parameter:[mergeIndex type:bool 
      comment:"Merge index partitions to a single index."]
    $parameter:[relocateLib type:bool 
      comment:"relocate library, ie, build a new IDX file"]
    $parameter:[buildIndex num:1 type:bool 
      comment:"build all or selected search indices for library"]
    $parameter:[parseTest type:bool 
      comment:"display only extracted values"]
    $parameter:[readLink type:bool 
      comment:"read library and process link information"]
    $parameter:[indexLink type:bool 
      comment:"build a link using two indices"]
    $parameter:[releaseName type:string 
      comment:"assign a release name to a set of indices"]
#
#checking and maintaining indices
#
    $parameter:[procIndexSize type:number num:15000 
      comment:"total index size (kb) to be processed in one go"]
    $parameter:[checkLibList type:string 
      comment:"list of libraries to be checked - else all libraries"]
    $parameter:[notCheckLibList type:string 
      comment:"list of libraries to be exclued from checking"]
    $parameter:[srsEnvHeader type:bool 
      comment:"produces 'srsenv.h' defining all SRS env variables"]
#
#options for WWW programs
#
    $parameter:[getOddFile type:string 
      comment:"The name of the file with the databank description."]
    $parameter:[dontShowOrig type:bool 
      comment:"don't list the query..only links to it"]
    $parameter:[userId type:string 
      comment:"user ID, or file, name associated with a WWW session"]
    $parameter:[visitIndexValue type:string 
      comment:"visit the set of entries belonging to an index value"]
    $parameter:[queryManager type:bool 
      comment:"activates query manager"]
    $parameter:[setListPar type:bool 
      comment:"allows to set parameters for viewing a set"]
    $parameter:[printHelpTopic type:string 
      comment:"prints specified help topic"]
    $parameter:[queryCombine type:bool 
      comment:"executes query that was specified in the query manager"]
    $parameter:[topPage type:bool 
      comment:"revisists top page"]
    $parameter:[doRepeat type:bool 
      comment:"revisits query form with same input as before"]
    $parameter:[doHyperTextLinks type:bool 
      comment:"revisits query form with same input as before"]
    $parameter:[doQueryForm type:bool 
      comment:"present the query form"]
    $parameter:[doQuery type:bool 
      comment:"do the query"]
    $parameter:[libInfo type:string 
      comment:"print some info about library"]
    $parameter:[linkInfo type:bool 
      comment:"print some info about link between 2 libraries"]
    $parameter:[listSetNumber type:number isVolatile:1
      comment:"number (in history) of set to be listed"]
    $parameter:[viewSetNumber type:number 
      comment:"number (in history) of set to be viewed"]
    $parameter:[listQuery type:string 
      comment:"query of set to be listed"]
    $parameter:[doBlastSearch type:bool 
      comment:"perform a search with Blast and index results"]
    $parameter:[prepBlastSearch type:bool 
      comment:"collect user input for a search with Blast"]
    $parameter:[listEntriesChunkSize type:number num:50 
      comment:"number of entries to be listed in one go"]
    $parameter:[listEntriesStartN type:number isVolatile:1
      comment:"number of first entry in set to be listed"]
    $parameter:[viewEntriesChunkSize type:number num:30 
      comment:"number of entries to be viewed in one go"]
    $parameter:[viewEntriesStartN type:number isVolatile:1
      comment:"number of first entry in set to be viewed"]
    $parameter:[maxValN type:number num:0 
      comment:"print only words that occur <n> number of times"]
    $parameter:[getMessage type:bool 
      comment:"get a message from user"]
    $parameter:[sendMessage type:bool 
      comment:"send a user message to the messages file"]
    $parameter:[subEntryN type:number 
      comment:"number of subentry to be accessed"]
    $parameter:[translateSequence type:bool
      comment:"print the translation product instead of DNA sequence"]
    $parameter:[linkLibSelect type:bool 
      comment:"display a table with all possible links"]
    $parameter:[linkToLibs type:bool 
      comment:"link set/entry to other libraries"]
    $parameter:[printLinkTable type:bool 
      comment:"print a link table"]
    $parameter:[printNetwork type:bool 
      comment:"print a network in tabular form."]
    $parameter:[linksPicture type:bool 
      comment:"Print page with picture describing network in tabular form."]
    $parameter:[networkPicture type:bool 
      comment:"Print page with network picture."]
#
# new wgetz
#
    $parameter:[printEntireEntry type:bool isVolatile:1]
    $parameter:[downloadEntireEntry type:bool isVolatile:1]
    $parameter:[libName type:string isVolatile:1 
      comment:
        |Name of the input library.
    ]
    $parameter:[entryName type:string isVolatile:1 
      comment:
        |Name of the input entry without library name.
    ]
    $parameter:[makeNewUserId type:bool isVolatile:1
      comment:|Forces wgetz to create a new user-ID if none exists yet.
    ]
    $parameter:[fromLibName type:string]
    $parameter:[toLibName type:string]
    $parameter:[useMime type:bool
      comment:
        |Mime type for saving the results on clients disk.
        |Argument "none" prevents output of a Content-type header.
    ]
    $parameter:[mimeType type:string
      comment:"MIME type to printed on top of the output page."]
    $parameter:[readUserFile type:bool
      comment:"readUserFile switch associated with a WWW session"]
    $parameter:["wwwFunctionName" type:string isVolatile:1
      comment:"Name of function to be called in wgetz."]
    $parameter:["isHtml3" type:bool num:1
      comment:"Client supports new HTML3 standard"]
    $parameter:["style" type:string
      comment:"Mode can be 'fancy' or nothing."]
    $parameter:["isDebug" type:bool
      comment:"Determines whether or not to print debug information."]
    $parameter:["queryString" type:string
      comment:"A string with an SRS query language expression."]
    $parameter:["delete" type:string set:'$ParDel:"%s"' isVolatile:1 
      comment:
        |A command to delete all the parameters matching the regular 
        |expression assigned to it.
    ]
    $parameter:["nextFunction" type:string
      comment:"A Function to be called by WWW Link Page."]
    $parameter:["viewNumber" type:number
      comment:"For internal use of wgetz."]
    $parameter:[queryNumber type:number
      comment:"refer query by number"]
    $parameter:[deleteParam type:string
      comment:"delete parameters in history from command line"]
    $parameter:[mimeEntriesChunkSize type:number num:100
      comment:"number of entries exported to client at a time"]
    $parameter:[mimeEntriesStartN type:number 
      comment:"nth Entry to start with for mime export "]


    $parameter:[viewName type:string
      comment:"Name of view to be used when displaying entries."]
    $parameter:[viewRecordSep type:string str:'\n'
      comment:"String of one or more characters to separate records in view."]
    $parameter:[viewColumnSep type:string str:'\t'
      comment:"String of one or more characters to separate columns in view."]

    $parameter:[currentView type:number
      comment:"to print fields set for this view number"]
    $parameter:[isTable type:bool
      comment:"prints view result in table format"]
    $parameter:[method type:string
      comment:"method function to apply on a querystring"]
    $parameter:["viewLibListRoot" type:string isVolatile:1
      parType:@PART_LIBLISTVIEWROOT
      comment:"select libraries of group as root for view"]
    $parameter:["viewLibListLeaf" type:string isVolatile:1
      parType:@PART_LIBLISTVIEWLEAF
      comment:"select libraries of group as leaf for view"]
    $parameter:[wwwColorScheme type:string str:plain]
    $parameter:[wwwSessionEntryList type:bool isVolatile:1]
    $parameter:[icarusFileType type:string
      comment:
        |Selects the type of the Icarus file: 'i' (structure), 'is' (syntax), 
        |'it' (info)."
    ]
    $parameter:["viewNumber" type:number isVolatile:1]
    $parameter:["browseIndex" type:string isVolatile:1
      comment:
        |Selects a data-field or index to be displayed for browsing on
        |the next page.
    ]
    $parameter:["browseLibs" type:string isVolatile:1]
#
#trembl options
#
    $parameter:[tremblInFile type:string 
      comment:
        |Optional input file name. The file extension and format must be 
        |the same as of the specified library.
    ]
    $parameter:[findAccNoCommand type:string 
      comment:
        |The command with which to obtain a sequence file from an accession 
        |number. Put a '%%s' where the accession number should be placed 
        |within the command (eg, 'findacc %%s').
    ]
    $parameter:[inputSeqFile type:string 
      comment:
        |Name of the file obtained by the above command; again a '%%s' 
        |must be placed in lieu of the accession number (eg, '%%s.seq').
    ]
#
#reflink
#
    $parameter:[readLib type:string 
      comment:"name of library to be read for references"]
    $parameter:[searchLib type:string str:medline 
      comment:"name of library to be searched for references"]
    $parameter:[journalListFile type:string 
      comment:"name of journal list to be read/written"]
    $parameter:[doJournalList type:bool comment:"make a new journal list"]
    $parameter:[doMergeJournalLists type:bool 
      comment:"merge two journal lists to one"]
    $parameter:[doRefLink type:bool 
      comment:"link the two libraries using their references"]
    $parameter:[doRefLinkFile type:bool 
      comment:"write a text file with all links found"]
    $parameter:[printSeparateFiles type:bool 
      comment:"If set then each entry will be written into a separate file."]
    $parameter:[outputFileName type:string
      comment:
        |Name of the output file name. Prints to terminal if no name 
        |is specified.
    ]
#
#srspict
#
    $parameter:[doNetworkPict type:bool
      comment:"Create a file with the network picture."]
    $parameter:[doGraphTablePict type:bool
      comment:"Create a file with the graph table picture."]
#
#try
#
    $parameter:[icaIsDebug type:bool 
      comment:"Puts the Icarus interpreter into debugging mode."]
    $parameter:[doClassInfo type:bool
      comment:
        |Prints information about all object classes that were defined in
        |the Icarus file.
    ]
    $parameter:[doCommandInfo type:bool
      comment:
        |Prints information about the builtin functions of Icarus.
    ]
    $parameter:[printTrace type:bool
      comment:"Prints the trace information."]
    $parameter:[printSyntaxTree type:bool
      comment:"Prints the syntax tree."]
    $parameter:[syntaxName type:string
      comment:"Name of the file with test syntax."]
    $parameter:[productionName type:string
      comment:"Name of the target production name."]
    $parameter:[printAllTokLists type:bool
      comment:"Prints the contents of all token lists."]
    $parameter:[icaDbgExecStack type:number
      comment:"Prints all program stack before execution."]
    $parameter:[icaDbgBuildStack type:number
      comment:"Prints Icarus commands and the generated program stacks."]
    $parameter:[ica2cName type:string
      comment:
        |Program is not executed but written to a C language file with the
        |specified file name.
    ]
    $parameter:[useIni type:bool
      comment:"Use interpreter written to a C language file."]
    $parameter:[readBuiltin type:bool
      comment:"Read the file 'builtin.i' before starting."]
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# parameter type objects
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

    PART_SETNAME:$partype:[name:setName max:20 min:0 charset:"a-zA-Z0-9_"]
    PART_BOOLEAN:$partype:[name:boolean max:3 min:0 charset:"yYnN01oOfFjJ"]
    $partype:[name:fieldQuery max:200 min:0 
      charset:"a-zA-Z0-9\-_\$[]().;*?&|!'"]
    $partype:[name:inFileName max:200 min:0 
      charset:"a-zA-Z0-9\-_\$[]().;*?&|!'"]
    $partype:[name:outFileName max:200 min:0
      charset:"a-zA-Z0-9\-_\$[]().;*?&|!'"]
    $partype:[name:query max:200 min:0 
      charset:"a-zA-Z0-9\-_\$[]().;*?&|!'"]
    PART_FIELDLIST:$partype:[name:fieldList check:@F_CHECKFIELDLIST 
      charset:"a-zA-Z0-9 "]
    PART_LIBLIST:$partype:[name:libList check:@F_CHECKLIBLIST
       charset:"a-zA-Z0-9_\- "]
    PART_LINKLIBLIST:$partype:[name:libList check:@F_CHECKLINKLIBLIST 
      charset:"a-zA-Z0-9_\- "]
    PART_ENVIRONMENT:$partype:[name:env check:@F_SETENVIRONMENT 
      charset:"a-zA-Z0-9_\- "]

# --
# added by ramu  
# --
    PART_LIBLISTVIEWROOT:$partype:[name:viewLibListRoot
      check:@F_CHECKLIBLISTVIEWR charset:"a-zA-Z0-9_\-~ "]
    PART_LIBLISTVIEWLEAF:$partype:[name:"viewLibLisLeaf"
      check:@F_CHECKLIBLISTVIEWL charset:"a-zA-Z0-9_\-~ "]
    PART_ENVIRONMENT2:$partype:[name:"env"
      check:@F_SETENVIRONMENT charset:"a-zA-Z0-9_\- "]
  }
]
@F_CHECKLINKLIBLIST 
      charset:"a-zA-Z0-9_\- "]
    PART_ENVIRONMENT:$partype:[name:env check:@F_SETENVIRONMENT 
      charset:"a-zA-Z0-9_\- "]

# --
# added by ramu  
# --
    PART_LIBLISTVIEWROOT:$partype:[nasrs/icarus/util/parameter.ic
#    $RCSfile: parameter.ic,v $
#    $Revision: 1.1 $
#    $Date: 1996/05/06 16:14:05 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

O_PAR:$object:[name:parameter typname:PARo declname:ODD_par 
  attrs:{
    $attribute:[declname:"*intern" type:user typname:"char" 
      rem:"for internal use for the list manager"]
    $attribute:[declname:classId type:int defaultval:0 
      rem:"for internal use for the list manager"]
    $attribute:[name:name declname:"name" type:string valtype:{text name}
      unnamed:y rem:"name of associated global parameter"]
    $attribute:[name:str declname:str type:string valtype:{text name}
      rem:"Value of 'string' parameter."]
    $attribute:[name:num declname:num type:int valtype:num
      rem:"Value of 'number' parameter."]
    $attribute:[name:real declname:real type:float 
      rem:"Value of 'real' parameter."]
    $attribute:[name:function declname:function type:function valtype:constant 
      rem:"Value of 'function' parameter."]
    $attribute:[name:object typname:"void" declname:"*object" type:user 
      rem:"Value of 'object' parameter."]
    $attribute:[name:isVolatile type:uchar declname:isVolatile]
    $attribute:[name:type type:uchar declname:type valtype:name 
      rem:"Parameter type." enum:{
        $value:[name:string val:1]
        $value:[name:number val:2]
        $value:[name:real val:4]
        $value:[name:function val:8]
        $value:[name:bool val:16]
        $value:[name:object val:32]
      }
    ]
    $attribute:[name:comment declname:comment type:string valtype:text 
      rem:"Short description of parameter."]
    $attribute:[name:helpTopic declname:helpTopic type:string 
      valtype:{name text} status:obsolete 
      rem:"help topic associated to parameter"]
    $attribute:[name:key type:string declname:key max:1 valtype:{text name}
      rem:"keystroke associated to parameter or value" status:obsolete]
    $attribute:[name:partype declname:parType type:object 
      defaultval:@O_PARTYPE valtype:constant 
      rem:"Object 'partype' for validating the parameter value."]
    $attribute:[name:check declname:check type:object defaultval:@O_PARTYPE
      valtype:constant status:obsolete 
      rem:"Object 'partype' for validating the parameter value."]
    $attribute:[declname:isLocked type:int defaultval:0 rem:"internal use..."]
    $attribute:[set declname:set type:string 
      rem:"Icarus command to set the current value."]
    $attribute:[get declname:get type:string 
      rem:"Icarus command to get the current value."]
  }
]

O_PARTYPE:$object:[name:partype typname:PARoTYPE declname:Odd_parType 
  rem:"Describes further a parameter type by specifying constraints or a function for checking the parameter value." 
  attrs:{
    $attribute:[declname:"*intern" type:user typname:"char" 
      rem:"for internal use for the list manager"]
    $attribute:[declname:classId type:int defaultval:0 
      rem:"for internal use for the list manager"]
    $attribute:[name:name declname:"name" type:string valtype:{text name}
      rem:"Name of associated global parameter."]
    $attribute:[name:check declname:check type:function valtype:constant 
      defaultstr:"(void *)" rem:"Function that checks parameter value."]
    $attribute:[name:max declname:max type:int defaultval:0 valtype:num 
      rem:"Max value, or max length."]
    $attribute:[name:min declname:min type:int defaultval:0 valtype:num 
      rem:"Mmin value, or min length."]
    $attribute:[name:maxReal declname:maxReal type:float defaultval:0 
      valtype:num rem:"Max real value."]
    $attribute:[name:minReal declname:minReal type:float defaultval:0 
      valtype:num rem:"Min real value."]
    $attribute:[name:charSet declname:"charSet" type:string valtype:{text name}
      rem:"Permissible set of chars for parameter value string."]
  }]

O_PARTABLE:$object:[name:partable typname:PARoLIST status:system nchilds:2 
  child:{@O_PAR @O_PARTYPE} declname:ODD_parTable 
  attrs:{
    $attribute:[name:vars declname:"par" type:child defaultval:@O_PAR 
      rem:"List of all predefined parameters."]
    $attribute:[declname:"parN" type:nr_of_childs defaultval:@O_PAR 
      rem:"Number of predefined parameters."]
    $attribute:[declname:"parType" type:child defaultval:@O_PARTYPE 
      rem:"List of all predefined parameter types."]
    $attribute:[declname:"parTypeN" type:nr_of_childs defaultval:@O_PARTYPE 
      rem:"Number of predefined parameter types."]
  }]
DD_parTasrs/icarus/util/script.i
$parStr:[agazik set:'asfd \n\n\n\n\nsafdkljalksdfjlkasjf']
$viewManager={
  head: "this ($parStr:outDirName) is \n $$%d %s |%10d| \the\" heaT\n"      
  aa: |aarararar
      | end
  gu:{
    ra: 
      | holo
      | holo \
      | hala \
    ru: 
      | ..     .....    ruhhhhh($parStr:outDirName)HHHHHHHHH holo
      | ru holo \
      | ru hala 
  }
  bb: 'bbrararar\n'
  cc: 'ccrararar'
  dd: 'ddrararar'
  ee: 'eerararar'
  ff: "ffra(\$arrr.asfd) rarar"
}


$viewManagerl={
  head:
    |<HTML>
    |<TITLE>:SRS: NEWSRS VIEW Manager Page </TITLE>
    |<FORM METHOD=POST ACTION="wgetz">
    |($buttons:viewManager)
    |<HR>
    |<TABLE>
    |
    |<TR>
    |<TD>
    |<IMG SRC=%(docdir)/redball.gif>
    |</TD>
    |<TD>
    |<INPUT TYPE=SUBMIT NAME=WwwViewCreateNew VALUE="CREATE">
    |<INPUT TYPE=HIDDEN NAME=wwwFunctionName4 VALUE=WwwViewCreateNew>
    |</TD><TD>a new view</TD></TR>
    |
    |<TR><TD>
    |<IMG SRC=%(docdir)/redball.gif>
    |</TD><TD>
    |<INPUT TYPE=SUBMIT NAME=WwwViewEditLibs VALUE=EDIT></TD>
    |<INPUT TYPE=HIDDEN NAME=wwwFunctionName5 VALUE=WwwViewEditLibs>
    |<TD>selected view</TD></TR>
    |
    |<TR><TD><IMG SRC=%(docdir)/redball.gif></TD>
    |<TD><INPUT TYPE=SUBMIT NAME=WwwViewDelete VALUE=DELETE></TD> 
    |<INPUT TYPE=HIDDEN NAME=wwwFunctionName6 VALUE=WwwViewDelete>
    |<TD>selected view</TD>
    |</TR></TABLE>
    |<P>
    |<TABLE BORDER>
    |<TR>
    |  <TH COLSPAN=5> View Listing </TH>
    |</TR>
    |<TR> 
    |	<TH> View Name </TH>
    |	<TH> Root Libs </TH>
    |	<TH> Root Fields </TH>
    |	<TH> Leaf Libs </TH>
    |	<TH> Leaf Fields </TH>
    |</TR>
  root:  |%s <BR>
  leaf:  |%s <BR>
  field:{
    head: |</TD> <TD>
    tail: | </TD>
    root: |%s <BR>
    leaf: |%s <BR>
  }
  listing:
    |<TR> <TD>
    |<input type=checkbox name=viewNo_%d value="%s">  %s
    |</TD>
    |<TD>
  footer: |</TR>
  tail:   |</TABLE> </FORM> </HTML>
}
 


$viewtable={
  header: 
    |%(mimehtml)                                                
    |									
    |<HTML>                                                     
    |<TITLE> View Print Fields: </TITLE>                        
    |<BODY> 
    |<FORM>                                                     
    |<BASE TARGET=otherclient>                                  
    |<INPUT TYPE=HIDDEN NAME=userId VALUE=%s>                   
    |<TABLE BORDER CELLPADDING CELLSPACING>                     
    |<CAPTION ALIGN=TOP> <H3><i>View:</I> %s </H3></CAPTION>  
    |<TR>                                                        
  title: {
    libname:
      |<TH>%s</TH>
    field:        
      |<TD ALIGN=CENTER><I>%s</I></TD>
    trail:
      |</TR>
  }
  rowbeg:
    |<TR>
  rowend:
    |</TR>
  entry: {
    name:
      |<TD VALIGN=TOP>
      |  <a href=($cgidir)/wgetz?%s-fun+RWwwEntryPrint+[%s-id:%s]>%s</a>
      |</TD>
    field: {    
      empty:
        |<TD></TD>
      listing:
        |<TD VALIGN=top><LISTING>
      left:
        |<TD valign=top ALIGN=left>
      right:
        |<TD valign=top ALIGN=right>
      center:
        |@@<VIEWTABLE-ENTRY-FIELD-VALUE>
      value:
        |%s<BR>
      end:
        |</TD>
    }
  }
}



$queryform={
  header:
    |@@<QUERYFORM>
    |%(mimehtml)
    | 
    |<HTML> ($gaga)
    |<HEAD>
    |<TITLE>SRS:Query Form Page </TITLE>
    |</HEAD>
    | 
    |<form method=POST action=%(cgidir)/wgetz>
    |<INPUT TYPE=hidden NAME=userId VALUE=%s>
    | 
    |<INPUT TYPE=hidden NAME=fieldList VALUE=reset>
    |<input type=hidden name=delete value=subEntry_.+>
    |@@print2 %(FANCY)HEADER-BUTTONS srsbar_qf2.gif fafa
    |<P>
    |<I>Search</I>
  lib:
    |<A HREF=%(cgidir)/wgetz?-fun+rwwwlibinfo+-info+%s><B>%s</B></A>
  title:
    |<P>
    |<IMG SRC=%(docdir)/arrow_icon.gif ALIGN=MIDDLE>
    |<input type=submit NAME=RWwwConstructQuery value=DO-QUERY>  
    |<input type=hidden name=wwwFunctionName9 VALUE=RWwwConstructQuery>
    |<input type=reset value=RESET> 
    |<HR>
    |<I>Compose query and select fields to be included in entry list. 
    | Not all fields may be searchable or to be displayed</I>
  table:{
    header:
      |<P>
      |<TABLE  NOBORDER CELLPADDING CELLSPACING>
      |<TR><TH> 
      |<A HREF=bla>Field Name</A></TH>
      |<TH colspan=4 align=middle><A HREF=bla>Query</A></TH>
      |<TH><A HREF=%(cgidir)/wgetz?-ht+select-fields>Include in List</A></TH>
      |<TH><A HREF=sub>Retrieve <BR>Subentries</A></TH>
      |</TR>
    field:
      |<TR> 
      |<TD>
      |<A HREF=%(cgidir)/wgetz?-fun+RWwwPrintHelpTopic+-ht+FIELDTYPE-%s>%s
      |</A>%s</TD>
      |	
      |<TD colspan=4 align=middle>
      |<INPUT SIZE=50 NAME=query_%s VALUE=> 
      |</TD>
      |	
      |<TD align=middle>
      |<INPUT TYPE=CHECKBOX NAME=fieldList VALUE=%s><BR>
      |</TD>
    rangefield:
      |<TR> 
      |<TD>
      |<A HREF=%(cgidir)/wgetz?-fun+RWwwPrintHelpTopic+-ht+FIELDTYPE-%s>%s
      |</A>%s</TD>
      |	
      |<TD ALIGN=MIDDLE>
      |<SELECT NAME=query_%s_beginmod>
      |<OPTION %s> &gt;=
      |<OPTION %s> &gt;
      |</SELECT> 
      |</TD> 
      |	
      |<TD ALIGN=MIDDLE>
      |<input name=query_%s_begin size=10 value=> 
      |</TD>
      |	
      |<TD ALIGN=MIDDLE>
      |<SELECT NAME=query_%s_endmod>
      |<OPTION %s> &lt;=
      |<OPTION %s> &lt; 
      |</SELECT>
      |</TD>
      |	
      |<TD ALIGN=MIDDLE>
      |<input name=query_%s_end size=10 value=>
      |</TD>
      |	
      |<TD align=middle>
      |<INPUT TYPE=CHECKBOX NAME=fieldList  VALUE=%s>
      |</TD>
    subentry:
      |<TD align=middle>
      |<input type=checkbox name=subEntry_%s value=1 %s>
      |<a href=%(cgidir)/wgetz?-fun+RWwwPrintHelpTopic+-ht+FIELDTYPE-SubEntry>
      |Subentry only </A>
      |</TD>
    noquery:
      |<TR>
      |<TD>
      |<A HREF=%(cgidir)/wgetz?-fun+RWwwPrintHelpTopic+-ht+FIELDTYPE-%s>%s
      | </A>%s
      |</TD>
      |	
      |<TD colspan=4 align=middle>
      |</TD>
      |	
      |<TD align=middle>
      |<INPUT TYPE=CHECKBOX NAME=fieldList VALUE=%s><BR>
      |</TD>
    rowend:
      |</TR>
    trailer:
      |</TABLE>
    }
  getbool:
    |<HR>
    |Combine searches with
    |<SELECT NAME=operator>
    |<OPTION SELECTED> AND
    |<OPTION > OR
    |</SELECT> 
    |	Append wildcard '*' to search words <input type=checkbox 
    |NAME=makeWild value=1 %s> 
    |<a href=wgetz?-fun+rwwwprinthelptopic+-ht+makewild>?!</a><P>
  chunkset:
    |Entry list in chunks of  
    |<SELECT NAME=viewEntriesChunkSize>
  chunksize:
    |<OPTION %s> %d
  chunksizeend:
    |</SELECT>
  view:{
    header:
      |Select a view 
      |<SELECT NAME=viewNumber>
    name:
      |<OPTION VALUE=%d %s> %s
    trail:
      |</SELECT>
    }
  trailer:      
    |</FORM>
    |</BODY>
    |</HTML>
  
}



$result={
  header:
    |@@<QUERY-RESULT>
    |%(mimehtml)
    |	 
    |<TITLE> QueryResult </TITLE>
    |	 
    |<form method=POST action=%(cgidir)/wgetz>
    |<INPUT TYPE=hidden NAME=userId VALUE=%s>
    |	 
    |<INPUT TYPE=HIDDEN NAME=printText VALUE=0>
    |<INPUT TYPE=HIDDEN NAME=printData VALUE=0>
    |	 
    |<i> <a name=top> Query </a></i><b>"%s"</b> found  %d entries</a>
    |<input type=hidden name=numberOfEntries value=%d>
    |	 
    |<BLOCKQUOTE>
    |<IMG SRC=%(docdir)/redball.gif>
    |<input type=submit name=RWwwLinkPage value="Link Set">
    |<input type=hidden name=wwwFunctionName6 value=RWwwLinkPage>
    |	 
    |<IMG SRC=%(docdir)/redball.gif>
    |<input type=submit name=RWwwRefineOutput value="Receive all entries">
    |<input type=hidden name=wwwFunctionName7 value=RWwwRefineOutput>
    |	 
    |<INPUT TYPE=HIDDEN NAME=viewSetNumber VALUE=%d>
    |<INPUT TYPE=HIDDEN NAME=viewEntriesStartN VALUE=%d>
    |<INPUT TYPE=HIDDEN NAME=viewEntriesChunkSize VALUE=%d>
    |<INPUT TYPE=HIDDEN NAME=queryNumber VALUE=%d>
    | with  chunk size
    |<SELECT NAME=viewEntriesChunkSize>
  entriesBeg:  
    |</BLOCKQUOTE>
  goChunk:{
    header:
      |<P>
      |<i> go to entries in chunk  </i> [ .. 
    other:
      |<A HREF=wgetz?%s-lset+%d+-bv+%d+-lv+%d+-fun+WwwListMoreEntries><B>%d
      |</B></A> ..
    current:
      |<A HREF=wgetz?%s-lset+%d+-bv+%d+-lv+%d+-fun+WwwListMoreEntries><B>(%d)
      |</B></A>..
    end:
      |]
  }
}

$result={
  header:
    |@@<QUERY-RESULT>
    |%(mimehtml)
    |	 
    |<TITLE> QueryResult </TITLE>
    |	 
    |<form method=POST action=%(cgidir)/wgetz>
    |<INPUT TYPE=hidden NAME=userId VALUE=%s>
    |	 
    |<INPUT TYPE=HIDDEN NAME=printText VALUE=0>
    |<INPUT TYPE=HIDDEN NAME=printData VALUE=0>
    |	 
    |<i> <a name=top> Query </a></i><b>"%s"</b> found  %d entries</a>
    |<input type=hidden name=numberOfEntries value=%d>
    |	 
    |<BLOCKQUOTE>
    |<IMG SRC=%(docdir)/redball.gif>
    |<input type=submit name=RWwwLinkPage value="Link Set">
    |<input type=hidden name=wwwFunctionName6 value=RWwwLinkPage>
    |	 
    |<IMG SRC=%(docdir)/redball.gif>
    |<input type=submit name=RWwwRefineOutput value="Receive all entries">
    |<input type=hidden name=wwwFunctionName7 value=RWwwRefineOutput>
    |	 
    |<INPUT TYPE=HIDDEN NAME=viewSetNumber VALUE=%d>
    |<INPUT TYPE=HIDDEN NAME=viewEntriesStartN VALUE=%d>
    |<INPUT TYPE=HIDDEN NAME=viewEntriesChunkSize VALUE=%d>
    |<INPUT TYPE=HIDDEN NAME=queryNumber VALUE=%d>
    | with  chunk size
    |<SELECT NAME=viewEntriesChunkSize>
  entriesBeg:  
    |</BLOCKQUOTE>
  goChunk:{
    header:
      |<P>
      |<i> go to entries in chunk  </i> [ .. 
    other:
      |<A HREF=wgetz?%s-lset+%d+-bv+%d+-lv+%d+-fun+WwwListMoreEntries><B>%d
      |</B></A> ..
    current:
      |<A HREF=wgetz?%s-lset+%d+-bv+%d+-lv+%d+-fun+WwwListMoreEntries><B>(%d)
      |</B></A>..
    end:
      |]
  }
}




$viewManager={
  head: "this ($parStr:outDirName) is \n $$%d %s |%10d| \the\" heaT\n"      
  aa: |aarararar ($parStr:agazik)
      | end
  gu:{
    ra: 
      | holo
      | holo \
      | hala \
    ru: 
      | ..     .....    ruhhhhh($parStr:outDirName)HHHHHHHHH holo
      | ru holo \
      | ru hala 
  }
  bb: 'bbrararar\n'
  cc: 'ccrararar'
  dd: 'ddrararar'
  ee: 'eerararar'
  ff: "ffra(\$arrr.asfd) rarar"
}
+-bv+%d+-lv+%d+-fun+WwwListMoreEntries><B>(%d)
      |</B></A>..
    end:
      |]
  }
}




$viewManager={
  head: "thisrs/icarus/util/script.is

$rules={

  # quick scanning
  scan:       ~ {$out pre{$Fip:1 $_push:$_opnd:[t:mark]} $_prog} 
                (arr | ident | ln)* ~
  arr:        ~ /\\$([a-zA-Z0-9]+) *= *{/ {$labelAdd:[$1 fip:$Fip]} ln  
                (/ *[a-zA-Z0-9]+:| *\\|| *}/ /[^\n]*/{$noskip})* ~
  ln:         ~ /[^\n]*\n/ ~
  real:       ~ /[0-9]+\\.[0-9]+/ ~
  str:        ~ /[a-zA-Z0-9_]+/ ~
  
  # get a template
  template:   ~ {$_prog} var '=' {$_push1:$_opnd:[$ct t:string]}
                list {$b=$_pop $_push:$_binop:[$_pop1 b:$b a:$_pop]} ~

  prog:       ~ {$out pre{$_push:$_opnd:[t:mark]}} stmnt+ x{$_prog}~
  body:       ~ x{$_push:$_opnd:[t:mark]} ('{' stmnt* '}' | stmnt ) 
                x{$_push:$_body} ~
  stmnt:      ~ (if | foreach | for | while | init | pre | file | 
                 stassoc | expr) ~
  stassoc:    ~ key {$_push5:$_opnd:[$1 t:string]}
                ident {$_push:$_assoc:[val:$_pop key:$_pop5]} ~
  

  # expression
  expr:       ~ term1 (logop term1 makeop)* ~
  term1:      ~ term2 ((compop|assop {$_push:$_setwrt:$_pop}) term2 
                {$b=$_pop $_push:$_binop:[$_pop1 b:$b a:$_pop]})* ~
  term2:      ~ term3 (/[+%-][^=]/ {$not} | 
                  (op1  term3 {$b=$_pop $_push:$_binop:[$_pop1 b:$b a:$_pop]})*
                )? ~
  term3:      ~ term4 (op2 term4 makeop)* ~
  term4:      ~ '(' expr ')' | unopleft? value unopright? ~
  makeop:     ~ x{$b=$_pop $_push:$_binop:[$_pop1 b:$b a:$_pop]} ~
  nullopnd:   ~ x{$_push:$_opnd:[t:null]} ~

  # operators
  logop:      ~ /(&&|\\|\\|)/ {$_push1:$_opnd:[$ct t:str]} ~
  assop:      ~ /(\\+=|=|-=|\\*=|\/=)/ {$_push1:$_opnd:[$ct t:str]} ~
  compop:     ~ /(<=|=<|>=|=>|<|>|==|!=)/ {$_push1:$_opnd:[$ct t:str]} ~
  op1:        ~ /[%+-]/ {$_push1:$_opnd:[$ct t:str]}~        
  op2:        ~ /(\\*|\/)/ {$_push1:$_opnd:[$ct t:str]}~
  unopleft:   ~ /(\\+\\+|--|\\+)/ {$_push1:$_opnd:[$ct t:str]}~
  unopright:  ~ /(\\+\\+|--)/ {$_push1:$_opnd:[$ct t:str]}~

  # lists     
  list:       ~ '{' {$_push:$_opnd:[t:mark]} (assoc | value)* '}' 
                 {$_push:$_list} ~
  assoc:      ~ {$_push:$_assoc:[val:$_pop key:$_pop5]} 
                key {$_push5:$_opnd:[$1 t:string]}(value |'~' production '~') ~
  key:        ~ /([a-zA-Z0-9_]+):/ | /'(([^']+|\\\\.)*)':/ ~
  value:      ~ real {$_push:$_opnd:[$Ct t:real]} | 
                int {$_push:$_opnd:[$Ct t:int]} | 
                name {$_push:$_opnd:[$Ct t:str]} |
                string | ident | list | lambda | reference ~
  int:        ~ /-?[0-9]+/ ~
  lambda:     ~ '@{' {$Skip:0 $str=""} 
                (/[^\n]*}@/ {$Not} ln {$StrApp:[$str s:$ct]})* 
                /([^\n]*)}@/{$StrApp:[$str s:$1] $_push:$_opnd:[$str t:lambda]
                             $Skip:1}
              ~

  # variable names, paths and function calls
  path:       ~ name {$_push:$_opnd:[$ct t:ident]}
                ('.' 
                 (
                  name {$_push:$_select:[var:$_pop  key:$_opnd:[$ct t:str]]} | 
                  '(' ident ')' {$a=$_pop $_push:$_select:[key:$a var:$_pop]} |
                  string {$a=$_pop $_push:$_select:[key:$a var:$_pop]} |
                  ident {$a=$_pop $_push:$_select:[key:$a var:$_pop]} 
                 ) | '[' expr ']' 
                 {$i=$_pop $_push:$_select:[var:$_pop index:$i]} 
                )* 
                (args {$_push:$_func})? 
              ~
  ident:      ~ '$' path ~ 
  args:       ~ ':' {$_push:$_opnd:[t:mark]} 
                ('[' (named | unnamedin)? named* ']' | unnamedout) ~
  unnamedin:  ~ argvalue 
                {$_push:$_makearg:[$_pop name:$_opnd:[":::::" t:str]]} ~
  unnamedout: ~ (value | '(' expr ')') 
                x{$_push:$_makearg:[$_pop name:$_opnd:[":::::" t:str]]} ~
  named:      ~ /([a-zA-Z_0-9]+) *:/ {$_push:$_opnd:[$1 t:str]}
                argvalue {$a=$_pop $_push:$_makearg:[$a name:$_pop]} ~
  argvalue:   ~ expr  ~
  name:       ~ /[a-zA-Z0-9_]+/ ~
  strname:    ~ /[a-zA-Z_][a-zA-Z0-9_]*/ {$_push:$_opnd:[$ct t:str]} ~
  reference:  ~ '@' ('?'{$opt=1} | x{$opt=0}) 
                name {$_push:$_ref:[$ct opt:$opt]} ~

  # strings
  string:     ~ {$_push:$_strmake} /[^"'|]/ #'"
                {$not $_push:$_opnd:[t:mark]} 
                (sqString | bqString | 
                '"'{$skip:0} dqString {$_push:$_opnd:[$ct t:str]} '"' 
                {$Skip:1})~
  sqString:   ~ /'/ /[^'\n]*/ {$noskip $_push:$_opnd:[$ct t:str]} /'/ ~ #'
  bqString:   ~ ('|' {$skip:0} bqLine {$skip:1})+ ~
  bqLine:     ~ (/[^\n\\$(]+/ {$_push:$_opnd:[$ct t:str]} | 
                 /\\\\[^\n]/ {$_push:$_opnd:[$ct t:str]} | 
                 var {$_push:$_opnd:['\2' t:str]} |
                 var2 {$_push:$_opnd:['\2' t:str]} |
                 /[($]/ {$_push:$_opnd:[$ct t:str]})* 
                (/\\\\\n/ |'\n' {$_push:$_opnd:['\n' t:str]}) ~

  dqString:   ~ (/[^\n"\\$(]+/ | /\\\\./ | 
                 var {$Rep:'\2'} | 
                 var2 {$Rep:'\2'} | 
                 '(')* ~ #"
  var2:       ~ '($' path {pre{$skip:1} $skip:0} ')' ~
  var:        ~ /\\$([a-zA-Z0-9_]+)/ {$_push:$_opnd:[$1 t:ident]}~

  # flow control
  file:       ~ 'file' ':' string {$_push:$_file:$_pop} ~
  pre:        ~ 'pre' body {$_push:$_pre:$_pop} ~
  init:       ~ 'init' body {$_push:$_init:$_pop} ~
  foreach:    ~ 'foreach'':''[' ident  'in' ':' expr ']' body 
                { $a=$_pop $b=$_pop 
                  $_push:$_foreach:[body:$a list:$b var:$_pop]}~
  for:        ~ 'for'':''{' (expr|nullopnd) (expr|nullopnd) (expr|nullopnd)
                '}' body 
                {$b=$_pop $u=$_pop $c=$_pop 
                 $_push:$_for:[b:$b u:$u c:$c i:$_pop]} ~
  while:      ~ 'while'':' cond body {$b=$_pop $_push:$_while:[b:$b c:$_pop]} ~
  if:         ~ 'if'':'{$_push:$_opnd:[t:mark]} cond body 
               ('elif'':' cond body)*
                ('else' {$_push:$_opnd:['1' t:int]} body)? 
                x{$_push:$_if} ~
  cond:       ~ '(' expr ')' | '{' expr '}' | '[' expr ']' |  expr ~

  # the 'Backus-Naur format' derived syntax description
  production: ~ {pre{$_push3:$_prod}} nodeProg?
                bnfExpr {$a=$_pop3 $_push:$_endProd:[node:$a prod:$_pop3]} ~
  bnfExpr:    ~ {pre{$_push3:$_nullNode} $_push3:$_expr} term ('|' term)* ~
  term:       ~ {pre{$_push3:$_nullNode} $_push3:$_term} factor (factor)* ~
  factor:     ~ (/x[ {\n\t]/ {$Probe} command | 
                 ((regexp | literal | eoi | prodName | laProdName) occur?))
                nodeProg | '(' bnfExpr ')' occur? ~
  regexp:     ~ {$skip:1} '/' {$skip:0} reStr {$_push3:$_regexp:$ct} '/' ~
  reStr:      ~ (/[^\/\\\n]+/ | /\\\\./)+ ~
  literal:    ~ {$skip:1} /'/ {$skip:0} litStr {$_push3:$_literal:$ct} /'/ ~
  litStr:      ~ (/[^'\\\n]+/ | /\\\\./)+ ~
  command:    ~ /x:?/ {$_push3:$_doCom} ~
  eoi:        ~ '.' {$_push3:$_doInputEnd} ~
  occur:      ~ '?' {$_push3:$_makeOpt:[$_pop3 t:once]} | 
                '*' {$_push3:$_makeOpt:[$_pop3 t:multi]} | 
                '+' {$_push3:$_makeOpt:[$_pop3 t:onemore]} ~
  nodeProg:   ~ {pre{$a=0} $_push3:$_nodeProg:[$_pop3 prog:$a]} 
                ('{' {$_push:$_opnd:[t:mark]} stmnt+ 
                '}' {$a=$_body})? ~
  prodName:   ~ /[a-zA-Z0-9_]+/ {$_push3:$_prodName:$ct} ~
  laProdName: ~ '_' /[a-zA-Z0-9_]+/ {$_push3:$_prodName:[$ct lookahead:1]} ~
}

#$print:"starting\n"
#$parse:[fileName:"/home/srs/srs5/odd/srswww.i" 
#  prod:$rules start:scan skip:" \t\n"]
#$print:"finished\n"

Opt:[$_pop3 t:multi]} | 
                '+' {$_push3:$_makeOpt:[$_pop3 t:onemore]} ~
  nodeProg:   ~ {pre{$a=0} $_push3:$_nodeProg:[$_pop3 prog:$a]} 
                ('{' {$_push:$_opnd:[t:mark]} stmnt+ 
                '}' {$a=$_body})? ~
  prodsrs/icarus/util/srs.i
#
#    $RCSfile: srs.i,v $
#    $Revision: 1.3 $
#    $Date: 1996/11/20 16:43:06 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$FALSE=0
$TRUE=1

file:"SRSICA:parameter.i"
file:"SRSICA:arglist.i"
file:"SRSDB:srsgen.i"
file:"SRSDB:srsdb.i"
push3:$_nodeProg:[$_pop3 prog:$a]} 
                ('{' {$_push:$_opnd:[t:mark]} stmnt+ 
                '}' {$a=$_¶ £¡Ü~
  prodsrs/icarus/util/srs.ic
#
#    $RCSfile: srs.ic,v $
#    $Revision: 1.2 $
#    $Date: 1996/05/06 19:22:07 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

file:"SRSICA:oddgen.i"
file:"SRSICA:syntax.ic"
file:"SRSICA:parameter.ic"
file:"SRSICA:arglist.ic"
file:"SRSICA:srsgen.ic"
file:"SRSICA:icacom.ic"

$def:[infile:"SRSICA:srs.i" outfile:"SRSSOU:srs5.h" 
  section_name:"srs5" section_size:2000]

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#    $RCSfile: srs.ic,v $
#    $Revision: 1.2 $
#    $Date: 1996/05/06 19:22:07 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

file:"SRSICA:oddgen.i"
file:"SRSICA:syntax.ic"
file:"SRSICA:parameter.ic"
file:"SRSICA:arglist.ic"
file:"SRSICA:srsgen.ic"
file:"SRSICA:icacom.ic"

$def:[infile:"SRSICA:srs.i" outfile:"SRSSOU:srs5.h" 
  section_name:"srs5" section_size:2000]
srs/icarus/util/srscheck.i
#
#   $RCSfile: srscheck.i,v $
#   $Revision: 1.7 $
#   $Date: 1997/03/17 23:19:32 $
#   $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$srscheck={
  head:{
    unix:
      |#!/bin/sh 
      |#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |# This file is generated by srscheck.i
      |# Do not edit this file directly.
      |#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |
      |. %s/prep_srs.sh
      |set -x
  }
  build:{
    head:
      |#
      |# build indices of library "%s"
      |#
    indexList:
      |srsbuild %s -f '%s' -xdir '%s' -odir '%s' -s '%s'
  }
  compress:{
    all:
      |srsbuild %s -c -xdir '%s' -odir '%s' -s '%s'
    index:
      |srsbuild %s -c -f ' %s' -xdir '%s' -odir '%s' -s '%s'
  }
  merge:{
    all:
      |srsbuild %s -m -xdir '%s' -odir '%s' -s '%s'
    index:
      |srsbuild %s -m -f ' %s' -xdir '%s' -odir '%s' -s '%s'
    deleteIndex:
      |\\rm %s_*.i*
  }
  link:{
    indexLink:{
      head:
        |#
        |# build all "index" links
        |#
      do:
        |srsbuild -i %s %s -xdir '%s' -odir '%s' -s '%s'
    }
    readLink:{
      head:
        |#
        |# build all "read" links
        |#
      do:
        |srsbuild %s -l -xdir '%s' -odir '%s'  -s '%s'
    }
  }
  tail:
    |exit
}
:
      |srsbuild %s -m -xdir '%s' -odir '%s' -s '%s'
    index:
      |srsbuild %s -m -f 'srs/icarus/util/srsenv.i
  unix:{
    head:
      |/*******************************************************************\
      |***********
      |**
      |**    generated automatically from srsenv.i
      |**
      |*/
      |
      |extern int putenv ();
      |
      |void SrsEnv ()
      |{
      |#ifndef VMS
    name:
      |  if (!getenv ("%s"))
      |    putenv ("%s=%s");
    tail:
      |#endif
      |}
  }
}

    |exit
}
:
      |srsbuild %s -m -xdir '%s' -odir '%s' -s '%s'
    index:
      |srs¶ £¡Ü -m -f 'srs/icarus/util/srsgen.ic
#    $RCSfile: srsgen.ic,v $
#    $Revision: 1.25 $
#    $Date: 1997/03/13 19:39:57 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


$SRSxXDATAFILS=4

O_FILE:$object:[file typname:SLBoFIL declname:slbfil ppname:SRS 
  attrs:{
    $attribute:[name declname:nam type:string valtype:name required:y 
      unnamed:y rem:"File name without extension and directory name."] 
    $attribute:[logicname declname:lnam type:string valtype:name 
      rem:"Logical name (meaningful only for GCG programs)/"]
    $attribute:[declname:isBad defaultval:0 type:int 
      rem:"This flag will be set upon failure to open this file"]
  }
]

O_SEQLIB:$object:[library typname:SLBo declname:seqlib nchilds:1 
  child:@O_FILE ppname:SRS 
  rem:"Top level object of the databank (library) description." 
  attrs:{
    $attribute:[name declname:nam type:string valtype:{name text}
      required:y rem:"Name of library." status:api unnamed:y]
    $attribute:[shortName declname:shortName type:string 
      valtype:{name text} required:n 
      rem:"Short name for library - needed for DOS file names." status:api]
    $attribute:[logicname declname:lnam type:string valtype:{name text}
      repeat:3 required:n rem:"Logical name(s) for the library (GCG)."]
    $attribute:[group declname:group type:object defaultval:@O_SRSGROUP 
      rem:"Library group this library belongs to."]
    $attribute:[parent type:object defaultval:@O_SEQLIB
      rem:|Library can be a virtual library of subentries. In that case this
          |attribute must point to the library of parent entries.
    ]
    $attribute:[format declname:form type:object defaultval:@O_SLBFORM 
      rem:"Pointer to the format description."]
    $attribute:[declname:"*dirName" type:user typname:char repeat:3 
      rem:"Address of Name of directory with all flat files."]
    $attribute:[comment declname:cmnt type:string valtype:text max:80 
      rem: "One line comment on library."]
    $attribute:[ifiles declname:ifiles type:string 
      rem: "Name of the Icarus file(s) with the databank description."]
      repeat:2
    $attribute:[declname:idNum type:int defaultval:0]
    # pointer to same flag which will be at diff. loc. at run time
    $attribute:[maxNameLen declname:maxNameLen type:int valtype:num 
      required:n defaultval:20 
      rem:"max length of unique entry name - important for ID-index"]
    # size of largest INX-file in kilobytes
    $attribute:[maxIndexSizeKb declname:maxIndexSizeKb type:int 
      valtype:num required:n]
    # size of cache in blocks used for building file of pointers
    $attribute:[cachesize declname:csiz type:int valtype:num 
      defaultval:1000]
    $attribute:[files declname:fil type:child defaultval:@O_FILE 
      rem:"list of pointers to file descriptions"]
    $attribute:[declname:nfil type:nr_of_childs defaultval:@O_FILE 
      rem:"number of file descriptions"]
    # attribute name of secondary key
    $attribute:[declname:skey name:SKEY type:uchar defaultval:255 
      valtype:constant]
    # key to be assoxiated with library in menus
    $attribute:[type declname:isFromUser type:uchar defaultval:0 
      valtype:name enum:{
        $value:[system val:0]
        $value:[user val:1]
      }
    ]
    $attribute:[dataType declname:dataType type:uchar defaultval:0 
      valtype:name enum:{
        $value:[noseq val:0]
        $value:[protein val:1]
        $value:[dna val:2]
      }
    ]
    $attribute:[declname:"*indexDirName" type:user typname:char 
      rem:"Address of the name of the directory with the SRS indices."]
    #for menu system
    $attribute:[declname:pargroup type:int defaultval:100000]
    #for updating
    $attribute:[declname:upd_f type:uchar defaultval:0]
    $attribute:[declname:updlink_f type:uchar defaultval:0]
    # for internal use only

    $attribute:[declname:isActive type:uchar defaultval:0 
      rem:"Flag if library is active."]
    $attribute:[declname:isInit type:uchar defaultval:0 
      rem:"Flag if library is initiated."]
    # pointer to file descriptors of data file(s)
    $attribute:[declname:"*file" type:user typname:"struct FILo" 
      repeat:$SRSxXDATAFILS]
    $attribute:[declname:allEntryCnt type:int defaultval:0]
    $attribute:[declname:newEntryCnt type:int defaultval:0]
    $attribute:[declname:updEntryCnt type:int defaultval:0]
    # current entry name
    $attribute:[declname:"*entryNam" type:user typname:char]
    # current entry-ID
    $attribute:[declname:"*idCurr" typname:"struct IDoENTRY" type:user]
    # for parsing   
    $attribute:[declname:"*tokList" typname:"struct TOKoLIST" type:user]
    $attribute:[declname:"*job" typname:"struct ICAoJOB" type:user]
    $attribute:[partFiles type:uchar defaultval:0
      enum:{
        $value:[no val:0]
        $value:[yes val:1]
      }
      rem:
        |Single flat files are to be indexed as separate parts for later 
        |merging.
    ]
    $attribute:[subEntries repeat:10 type:object
      defaultval:@O_SEQLIB
      rem:
        |List of all \$library objects that represent subentry types.
    ]
    $attribute:[partSize type:int
      rem:
        |Size of the databank part in number of entries to be indexed 
        |separately for later merging.
    ]
  }
]

O_LIBID:$object:[libid typname:LIBoID declname:libid ppname:SRS 
  rem:
    |Associates a number between 1 and 255 (library-ID) and a library 
    |(databank).
  attrs:{
    # pointer to the library object 
    $attribute:[lib declname:library type:object 
      defaultval:@O_SEQLIB rem:"Library object. "]
    $attribute:[n declname:n type:int valtype:num required:y min:1 
      max:255 unnamed:y rem:"Library-ID to be associated to the library"]
  }
]

O_ENVIRONMENT:$object:[site typname:LIBoENV declname:ODD_env 
  ppname:SRS nchilds:1 child:@O_LIBENV 
  rem:
    |List of active libraries together with their directory names. 
    |A particular environment can be selected by defining the 
    |parameter 'environment'
  attrs:{
    $attribute:[name declname:name type:string valtype:name required:y 
      rem:"Name of the environment."]
    $attribute:[libs declname:libenv type:child defaultval:@O_LIBENV 
      rem:"List of active libraries."]
    $attribute:[declname:libenvN type:nr_of_childs defaultval:@O_LIBENV 
      rem:"Number of libraries in that list."]
  }
]

O_LIBENV:$object:[libloc typname:LIBoLIBENV declname:ODD_libenv 
  ppname:SRS attrs:{
    $attribute:[lib declname:lib type:object defaultval:@O_SEQLIB
      unnamed:y rem:"Library object."]
    $attribute:[dir declname:dirName type:string repeat:3 
    rem:
      |List of directory names with the library's flat files. 
      |The files will be searched in the directories in the same order as of 
      |the list.
    ]
    $attribute:[indexDir declname:indexDirName type:string 
      defaultstr:"SRSINX:" rem:"Name of the directory with the SRS indices."]
  }
]

$CDefine:[@O_SRSDB name:O_SRSDB]
O_SRSDB:$object:[srsdb typname:SRSoDB declname:srsdb ppname:SRS 
  nchilds:1 child:@O_LIBID attrs:{
    $attribute:[libIds declname:libId type:child defaultval:@O_LIBID]
    $attribute:[declname:libIdN type:nr_of_childs defaultval:@O_LIBID]
    $attribute:[declname:environment type:allobjects 
      defaultval:@O_ENVIRONMENT rem:"List of defined library environments."]
    $attribute:[declname:environmentN type:nr_of_objects 
      defaultval:@O_ENVIRONMENT rem:"Number of defined library environments."]
    $attribute:[declname:slb type:allobjects defaultval:@O_SEQLIB]
    $attribute:[declname:nslb type:nr_of_objects defaultval:@O_SEQLIB]
    $attribute:[declname:group type:allobjects defaultval:@O_SRSGROUP]
    $attribute:[declname:ngroup type:nr_of_objects defaultval:@O_SRSGROUP]
    $attribute:[declname:fld type:allobjects defaultval:@O_SRSFLD]
    $attribute:[declname:nfld type:nr_of_objects defaultval:@O_SRSFLD]
    $attribute:[declname:iddsc type:allobjects defaultval:@O_IDDSC]
    $attribute:[declname:niddsc type:nr_of_objects defaultval:@O_IDDSC]
    $attribute:[declname:filtyp type:allobjects defaultval:@O_FILTYP]
    $attribute:[declname:nfiltyp type:nr_of_objects defaultval:@O_FILTYP]
    $attribute:[declname:lnk type:allobjects defaultval:@O_LINK]
    $attribute:[declname:nlnk type:nr_of_objects defaultval:@O_LINK]
    $attribute:[declname:syntax type:allobjects defaultval:@O_SYNTAX]
    $attribute:[declname:syntaxN type:nr_of_objects defaultval:@O_SYNTAX]
    $attribute:[declname:command type:allobjects defaultval:@O_COMMAND]
    $attribute:[declname:commandN type:nr_of_objects defaultval:@O_COMMAND]
    $attribute:[declname:application type:allobjects defaultval:@O_APPLICATION]
    $attribute:[declname:applicationN type:nr_of_objects 
      defaultval:@O_APPLICATION]
    $attribute:[declname:parTable type:allobjects defaultval:@O_PARTABLE
      rem:"table of predefined global parameters"]
    $attribute:[declname:view type:allobjects defaultval:@O_VIEW]
    $attribute:[declname:viewN type:nr_of_objects defaultval:@O_VIEW]

    $attribute:[declname:href type:allobjects defaultval:@O_HREF]
    $attribute:[declname:hrefN type:nr_of_objects defaultval:@O_HREF]
    $attribute:[copy_max_entries declname:xcopy_n type:int 
      defaultval:100000]
    $attribute:[list_max_entries declname:xlist_n type:int 
      defaultval:100000]
    $attribute:[declname:copy_fst type:int defaultval:1]
    $attribute:[declname:list_fst type:int defaultval:1]
    $attribute:[declname:"**libTable" type:user typname:"struct SLBo"]
  }
]

O_SRSGROUP:$object:[libgroup typname:SRSoGROUP declname:libgroup 
  ppname:SRS rem:"Description of a library (databank) group."
  attrs:{
    # key to be assoxiated with library in menus
    $attribute:[key declname:key type:string max:1 valtype:name 
      required:n status:obsolete]
    $attribute:[name declname:com type:string max:60 
      valtype:{name text} required:y unnamed:y 
      rem:"Name of library group." status:api]
    $attribute:[short declname:short_nm type:string max:4 
      valtype:{name text}
      rem:"Short name (abbreviation) of library group." status:api]
    # short comment
    $attribute:[comment declname:cmnt type:string valtype:text max:80 
      rem:"A single line of text describing the group."]
    $attribute:[help declname:help type:string valtype:text max:60 
      status:obsolete]
    $attribute:[search type:uchar declname:single_f defaultval:1
      rem:
        |This flag determines if all libraries in the group can be searched
        |simultaneously or one at a time (this is advisable if the libraries 
        |differ greatly in their data-fields.
      enum:{
        $value:[single val:1]
        $value:[all val:0]
      }
    ]
    # table of libraries in the group...filled at runtime
    $attribute:[declname:library type:object repeat:50 defaultval:@O_SEQLIB
      rem:"Pointers to the libraries in the group"]
    $attribute:[declname:libraryN type:int defaultval:0]

    $attribute:[declname:field type:object repeat:500 defaultval:@O_DFIELD]
    $attribute:[declname:fieldN type:int]
    $attribute:[declname:'*fieldCount' typname:char type:user]
    $attribute:[declname:upd_f type:uchar]
  }
]

$SRSxID=1
$SRSxKEY=2
$SRSxLINK=3
$SRSxSHOW=4
$SRSxHEADER=5
$SRSxNUM=6
$SRSxREAL=7
$SRSxGROUP=8
$SLBxNULL=255


O_DFIELD:$object:[field typname:SLBoFIELD declname:field
  rem:"Description of a data-field within a library." 
  attrs:{
    $attribute:[index declname:index type:uchar required:n valtype:name
      defaultval:$SRSxSHOW
      rem:
        |Index type - 'show' means that the field can be displayed only; 
        |'group' points to a group of indices.
      enum:{
        $value:[id val:$SRSxID]
        $value:[str val:$SRSxKEY]
        $value:[link val:$SRSxLINK]
        $value:[show val:$SRSxSHOW]
        $value:[int val:$SRSxNUM]
        $value:[real val:$SRSxREAL]
        $value:[group val:$SRSxGROUP]
      }
    ]
    $attribute:[name declname:name type:string]
    $attribute:[code declname:code type:string max:30 defaultstr:"" 
      valtype:{text name}
      rem:
        |Code of the token in the 'fields' token list that contains the 
        |data-field.
    ]
    $attribute:[declname:fieldTokCode type:int]
    $attribute:[token declname:token type:string max:50 
      rem:
        |If the data-field is not contained in the 'fields' token list the 
        |full name 'tokenList|code' must be specified here.
    ]
    $attribute:[indexId declname:indexId type:object
      defaultval:@O_IDDSC 
      rem: 
        |The ID-type description for the IDs that will be put into the index.
    ]
    $attribute:[indexToken declname:indexToken type:string max:30
      defaultstr:"" valtype:{text name} repeat:5 
      rem:
        |The name of the token list that supplies the values for indexing. 
        |The list name may be followed by a token code separated by ':'.
    ]
    $attribute:[indexTokCode declname:indexTokCode type:int repeat:5]
    $attribute:[isSystem declname:isSystem type:uchar valtype:num 
      defaultval:0 
      rem:
        |A 'system' data field is only for internal use and should be 
        |ignored by a user interface.
    ]
    $attribute:[keyConvert type:uchar required:n valtype:name
      defaultval:0
      rem:
        |Directs conversion of index strings.
      enum:{
        $value:[none val:0]
        $value:[toupper val:1]
        $value:[tolower val:2]
      }
    ]
    $attribute:[type declname:type type:object required:y 
      defaultval:@O_SRSFLD valtype:constant status:api unnamed:y
      rem:"Object that describes the data-field type."]
    $attribute:[replace type:object required:n
      defaultval:@O_SRSFLD valtype:constant status:api
      rem:|Field type of corresponding field object from parent entry in case
          |it is not the same.
    ]
    $attribute:[parent type:object defaultval:@O_DFIELD
      rem:
        |Indicates if the field definition of the parent entry library should
        |be taken instead.
    ]
    # pointer to index processing info
    $attribute:[declname:"*idx" typname:"struct IDXo" type:user]
    $attribute:[declname:"*inx" typname:"struct INXo" type:user]
    $attribute:[declname:"*btree" typname:"struct BTRo" type:user]
    $attribute:[declname:"*idFile" typname:"struct IDSoFILE" type:user]
    # flag to indicate if field is to be processed at all
    $attribute:[declname:do_f type:uchar defaultval:0]
    # pointer to flag indicating if field is to displayed
    $attribute:[declname:"*on_fp" typname:INT4 type:user defaultval:0]
    # flag to indicate if field is to be a secondary index
    $attribute:[declname:pargroup type:int defaultval:100000]
    # flag to indicate if field was encountered during entry's processing
    $attribute:[declname:done_f type:uchar defaultval:0]
    # flag to indicate if identifier for ID-field has to be created
    $attribute:[suppress_error declname:noerrmsg_f type:uchar 
      defaultval:0 valtype:name 
      rem:"Supresses printing of parsing error messages."
      enum:{
        $value:[yes val:1]
        $value:[no val:0]
      }]
    $attribute:[format type:string
      rem:|Name of default format of the contents of a 
          |field (see \$srsfield).
    ]
    #
    # retrieving the data-field for printing it inside a table
    $attribute:[tableToken declname:tableToken type:string
      rem:"Name of the table and the token code."]
    $attribute:[declname:tableTokCode type:int]
    $attribute:[tableFormat declname:tableFormat type:uchar 
      defaultval:0
      enum:{
        $value:[listing val:1]
        $value:[left val:2]
        $value:[right val:3]
        $value:[center val:4]
        $value:[preformat val:5]
      }
      rem:
        |The format of the default as displayed inside a 'table view'.
        |If left unspecified then the same attribute of the 'format'
        |object is read.
    ]
  }
]

O_SLBFORM:$object:[libformat typname:SLBoFORM declname:slb
  ppname:SLB child:{@O_DFIELD} nchilds:2 
  rem:
    |Specifies the parser to be used for parsing all data-fields of a library, 
    |its flat file format and has a list of all data-field descriptions.
  attrs:{
    $attribute:[fields declname:f type:child defaultval:@O_DFIELD]
    $attribute:[declname:nf type:nr_of_childs defaultval:@O_DFIELD]
    $attribute:[declname:access_f type:uchar defaultval:0]
    $attribute:[syntax declname:syntax type:object defaultval:@O_SYNTAX
      required:y valtype:constant rem:"The syntax of the flat file entry."]
    $attribute:[fileType declname:fil_t type:object 
      repeat:$SRSxXDATAFILS defaultval:@O_FILTYP 
      rem:
        |List of flat file types. There can be more than (eg, the sequence 
        |and annotation are stored in two different files).
    ]
    $attribute:[tableFormat declname:tableFormat type:uchar 
      defaultval:0
      enum:{
        $value:[listing val:1]
        $value:[left val:2]
        $value:[right val:3]
        $value:[center val:4]
        $value:[preformat val:5]
      }
    ]
    $attribute:[printFormat declname:printFormat type:uchar 
      defaultval:0
      enum:{
        $value:[listing val:1]
        $value:[left val:2]
        $value:[right val:3]
        $value:[center val:4]
        $value:[preformat val:5]
        $value:[topiclist val:6]
        $value:[numberList val:7]
        $value:[bulletList val:8]
        $value:[table val:9]
        $value:[table2 val:10]
        $value:[text val:11]
      }
    ]
    # attributes for use from C only
    $attribute:[declname:"*tokenDict" typname:"struct DICTo" type:user]
    $attribute:[declname:isInit type:int]
    $attribute:[contains type:object defaultval:@O_DATATYPE repeat:5
      rem:|List of types of data contained in the databank described.
    ]
  }
]

O_FIELDFORMAT:$object:[fieldFormat typname:LIBoFieldFormat
  attrs:{  
    $attribute:[name type:string declname:name required:y unnamed:y]
    $attribute:[eval type:string declname:eval]
    $attribute:[type:int declname:isSelected]
  }
]

O_SRSFLD:$object:[ppname:SRS name:srsfield typname:SRSoFLD 
  rem:
    |The abstract description of a data-field. The definition is independent
    |from a certain data bank and must be referenced from each field
    |definition of a library format.
    |The purpose of this object is to allow specification of equivalent
    |data-fields among different databanks (eg, 'author name' or 
    |'creation date').
  child:@O_FIELDFORMAT nchilds:1
  declname:SDL_srsfields 
  rem:"Description of a data-field Type (eg, 'Authors')."
  attrs:{
    $attribute:[short declname:shortn type:string max:3 valtype:text 
      rem:"Short name (abbreviation) of data-field type" status:api]
    $attribute:[name declname:nam type:string min:2 max:100 required:y 
      valtype:{text name} unnamed:y
      rem:"Short name of data-field type" status:api]
    $attribute:[comment declname:cmnt type:string max:80 valtype:text]
    $attribute:[declname:pargroup type:int defaultval:100000]
    $attribute:[type declname:ityp type:uchar required:n valtype:name 
      enum:{
        $value:[show val:$SRSxSHOW]
        $value:[header val:$SRSxHEADER]
        $value:[id val:$SRSxID]
        $value:[str val:$SRSxKEY]
        $value:[link val:$SRSxLINK]
        $value:[num val:$SRSxNUM]
        $value:[real val:$SRSxREAL]
        $value:[group val:$SRSxGROUP]
      }
      rem:
        |The type of the field type. At the moment only 'header' is used.
        |The other types should be used to enforce a certain type on all
        |the library fields referencing them.

    ]
    $attribute:[isGroup declname:isGroup type:uchar required:n valtype:name 
      defaultval:0 rem:"field type: single or group (of other field types)" 
      enum:{
        $value:[no val:0]
        $value:[yes val:1]
      }
    ]
    $attribute:[group declname:group type:object defaultval:@O_SRSFLD 
      rem:"pointer to the field type group"]
    $attribute:[format declname:format type:child defaultval:@O_FIELDFORMAT]
    $attribute:[declname:formatN type:nr_of_childs defaultval:@O_FIELDFORMAT]
  }
]

O_IDDSC:$object:[ppname:SRS name:idtype typname:IDoTYPE declname:ID_type 
  rem:
    |Every entry of every databank indexed in SRS is represented by an 
    |entry-ID which uniquely identifies it. Several ID types are defined 
    |(eg, entry-ID, seq-ID, 3D-ID). Only the subentry-ID is structurally 
    |different from the others.
  attrs:{
    $attribute:[name declname:nam type:string min:2 max:20 required:y 
      valtype:{text name} unnamed:y
      rem:"Name of Id-type."]
    $attribute:[size declname:siz type:int valtype:num required:y 
      rem:"Size of ID in number of bytes."]
    $attribute:[fipBeg declname:fddbeg type:int valtype:num required:y
      min:0 max:7 
      rem:"Offset of fadd (file address within IDX file) within ID."]
    $attribute:[fipLen declname:fddlen type:int valtype:num required:y
      min:2 max:4 rem:"Size of fadd in bytes."]
    $attribute:[libIdBeg declname:lbxbeg type:int valtype:num min:0
      max:7 rem:"Offset of databank-ID within ID."]
    $attribute:[libIdLen declname:lbxlen type:int valtype:num min:0
      max:2 defaultval:0 rem:"Size of databank-ID in bytes."]
    $attribute:[subNBeg declname:lxbeg type:int valtype:num min:0
      max:7 rem:"Offset of subentry number within ID."]
    $attribute:[subNLen declname:lxlen type:int valtype:num min:0
      max:2 defaultval:0 rem:"Size of subentry number in bytes."]
    $attribute:[copyfunction type:function declname:cpy valtype:constant
      rem:"Function for printing an individual entry represented by  ID."]
  }
]
$CDefine:[1 name:LIBxFILE]
$CDefine:[2 name:LIBxNAME]
$CDefine:[3 name:LIBxPATH]

O_FILTYP:$object:[ppname:SRS name:filetype typname:SRSoFILTYP 
  declname:SDL_filtyp 
  rem:
    |Describes a flat file type. Databanks may have more than one flat file
    |type, eg, databanks in PIR or GCG with 'ref'-files containing the 
    |sequence annotation and 'seq'-files with the sequence.
  attrs:{
    $attribute:[name type:string max:20 defaultstr:text unnamed:y
      rem:"Symbolic name of the file."]
    $attribute:[typename declname:typ_nm type:string max:20 valtype:{text name}
      rem:"File extension name."]
    $attribute:[searchname declname:searchName type:string max:40 
      required:n valtype:{text name}
      rem:
        |A search string used for finding all files in the specified 
        |directory (only for file per entry databanks). Any number of 
        |wildcards ('*' - matches all, '?' matches all single character) may 
        |be used.
    ]
    $attribute:[maxline declname:ln_z type:int valtype:num min:80 
      max:20000 defaultval:132]
    $attribute:[declname:context type:uint]
    $attribute:[name:fipVar declname:fipVar type:string defaultStr:entryFip
      rem:
        |Name of the Icarus variable containing the file address of the
        |entry begin.
    ]
    $attribute:[shareWith type:object defaultval:@O_FILTYP rem:
        |The file type can be only logical and the actual file object
        |shared with another file type. It is to pretend that input comes
        |from two different files where in fact it doesn't.
    ]        
    $attribute:[name:fieldTokens declname:fieldTokens type:string 
      defaultStr:fields rem:
        |Name of the token table that has one token for each data-field of
        |the entry.
    ]
    $attribute:[saveName type:int
      defaultval:0
      enum:{
        $value:[none val:0]
        $value:[file val:1]
        $value:[name val:2]
        $value:[path val:3]
      }
      rem:|For databanks where each entry resides in a separate file where the
          |file name cannot be inferred from the entry name. Option
          |to request the whole or part of the file name to be saved in the
          |IDX index.
    ]
    $attribute:[saveNameLength type:int
      rem:|Max. length of the name saved according to 'saveName'.
    ]
    $attribute:[singleEntry declname:sngl_f type:uchar valtype:name
      defaultval:0
      rem:"Selects a file has only one single entry."
      enum:{
        $value:[y val:1]
        $value:[n val:0]
      }
    ]
    $attribute:[pipe declname:pipe type:string max:132 repeat:1 
      defaultstr:"" valtype:text 
      rem:
        |Format string (printf style) to create a command for processing the 
        |entry file before reading (eg, 'uncompress %%s'). 
    ]
  }
]

O_SUBENTRY:$object:[subentry declname:SDL_subentry typname:LIBoSUBENTRY
  nchilds:1 child:@O_DFIELD 
  attrs:{
    $attribute:[name type:string unnamed:y required:y]
    $attribute:[idType declname:idType type:object defaultval:@O_IDDSC]
    $attribute:[first declname:first type:object defaultval:@O_SRSFLD]
    $attribute:[fields declname:fields type:child defaultval:@O_DFIELD
      rem:
        |The Definition of the fields of the subentry. Each field must 
        |correspond to a field in the parent entry. Part of the definition
        |(such as 'token' can 'shadow' the definition of the parent).
    ]
    $attribute:[declname:fieldsN type:nr_of_childs defaultval:@O_DFIELD]
  }
]

O_HREF:$object:[href declname:SDL_href typname:LIBoHREF
  attrs:{
    $attribute:[name declname:name type:string unnamed:y]
    $attribute:[link declname:link type:string]
  }
]


O_LINK:$object:[ppname:SRS name:link declname:SDL_link typname:LINKo 
  rem:
    |Specifies a link between two libraries. A link can be built by using two
    |indices built from one data-field of each library ('type=index') or by
    |reading one library and processing cross-reference data ('type=read').
  attrs:{
    $attribute:[weight declname:val type:int valtype:num defaultval:10 
      rem:
        |The weight attached to a link can be used to eliminate ambiguities
        |during path resolution, or to force a certain path.
    ]
    $attribute:[token declname:token type:string]
    $attribute:[declname:tokCode type:int]
    $attribute:[declname:codeNum type:int]
    $attribute:[fromName declname:nam1 type:string max:15 
      valtype:{name text}
      rem:"Name of the first library - in case not the library name itself."]
    $attribute:[toName declname:nam2 type:string max:15 
      valtype:{name text}
      rem:"Name of the first library - in case not the library name itself."]
    $attribute:[idtype1 declname:id1_d type:object defaultval:@O_IDDSC
      valtype:constant
      rem:"Object describing the first library's ID's to be linked."]
    $attribute:[idtype2 declname:id2_d type:object defaultval:@O_IDDSC
      valtype:constant 
      rem:"Object describing the second library's ID's to be linked."]
    $attribute:[from declname:lib1 type:object defaultval:@O_SEQLIB
       unnamed:y valtype:constant rem:"Object desribing the first library."]
    $attribute:[to declname:lib2 type:object defaultval:@O_SEQLIB
       valtype:constant rem:"Object desribing the second library."]
    $attribute:[fromField declname:fromField type:object defaultval:@O_SRSFLD
       valtype:constant 
       rem:
         |Object describing the data-field of first library providing link
         |information (only for index links).
    ]
    $attribute:[toField declname:toField type:object defaultval:@O_SRSFLD
      valtype:constant 
      rem:
        |Object describing the data-field of second library providing link 
        |information (for both index- and read-links).
     ]
    $attribute:[declname:rev_f type:uchar defaultval:0]
    $attribute:[declname:init_f type:uchar defaultval:0]
    # TRUE if link is between active libraries
    $attribute:[declname:isActive type:uchar defaultval:0]
    # for srsbuild whether to perform linkage
    $attribute:[declname:do_f type:uchar defaultval:0]
    # count of successful links
    $attribute:[declname:goodRefN type:int defaultval:0]
    $attribute:[declname:badRefN type:int defaultval:0 
      rem:"count of unsuccessful links"]
    $attribute:[declname:lib1EntryN type:int defaultval:0 
      rem:"number of entries from library 1 linked"]
    $attribute:[declname:lib2EntryN type:int defaultval:0 
      rem:"number of entries from library 2 linked"]
    # total number of link Ids
    $attribute:[declname:linkIdN type:int defaultval:0]
    # pointer to block of link ID's
    $attribute:[declname:id_p type:user typname:IDPTR]
    $attribute:[declname:"*idWrtOff" type:user typname:char]
    $attribute:[declname:"*toFile" type:user typname:"struct FILEo"]
    $attribute:[declname:"*fromFile" type:user typname:"struct FILEo"]
    $attribute:[declname:"*btree1" type:user typname:"struct BTRo"]
    $attribute:[declname:"*btree2" type:user typname:"struct BTRo"]
    $attribute:[declname:"*ids1" type:user typname:"struct IDSoFILE"]
    $attribute:[declname:"*ids2" type:user typname:"struct IDSoFILE"]
    # index of descriptors of libraries to be linked
    $attribute:[use type:object defaultval:@O_LINK rem:
      |Reference to the link object to be used to resolve the link.
    ]
    $attribute:[declname:isOpen type:int defaultval:0]
    $attribute:[type declname:typ type:uchar defaultval:1 valtype:name 
      rem:
        |Type of the link. 'read': first library must be read to find 
        |cross-references to second library; 'index': two indices, one from
        |each library will be used to build the link; 'parent': link between 
        |entry and subentry.
      enum:{
        $value:[read val:1]
        #LINKxREAD
        $value:[index val:2]
        #LINKxINDEX
        $value:[parent val:3]
        #LINKxMAPRNT
      }
    ]
  }
]

O_VIEWFIELD:$Object:[Vfield typname:VIEWoFIELD
  rem:|Description of individual data-fields of both root and leaf databanks
      |of a view.
  attrs:{
    $attribute:[type type:object required:y defaultval:@O_SRSFLD unnamed:y
      rem:|Reference the object describing the field type.
    ]
    $attribute:[format type:string 
      rem:|If the field type has additional format options a format can be
          |specified for the field, otherwise the default will be taken.
    ]
  }
]

O_VIEWLIB:$Object:[Vlib typname:VIEWoLIB  nchilds:1 child:@O_VIEWFIELD
  attrs:{
    $attribute:[lib type:object required:y defaultval:@O_SEQLIB unnamed:y]
    $attribute:[fields type:child defaultval:@O_VIEWFIELD]
    $attribute:[fieldsN type:nr_of_childs defaultval:@O_VIEWFIELD]
    $attribute:[declname:fieldsAllocN type:int]
    $attribute:[query type:string]
    $attribute:[viewName type:string]
    $attribute:[printOnlyEntryN type:uchar]
  }   
]
O_VIEW:$object:[View typname:VIEWo nchilds:1 child:@O_VIEWLIB
  attrs:{
    $Attribute:[name type:string required:y unnamed:y]
    $attribute:[format type:int defaultval:1
      enum:{
        $value:[table val:1]
        $value:[list val:2]
      }
    ]
    $attribute:[isEntryNamePrinting type:uchar]
    $attribute:[useShortFieldNames type:uchar]

    $attribute:[root  type:child defaultval:@O_VIEWLIB required:y]
    $attribute:[rootN type:nr_of_childs defaultval:@O_VIEWLIB]
    $attribute:[declname:rootAllocN type:int]

    $attribute:[rootFields  type:child defaultval:@O_VIEWFIELD]
    $attribute:[rootFieldsN type:nr_of_childs defaultval:@O_VIEWFIELD]
    $attribute:[declname:rootFieldsAllocN type:int]

    $attribute:[leaves type:child defaultval:@O_VIEWLIB]
    $attribute:[leavesN type:nr_of_childs defaultval:@O_VIEWLIB]
    $attribute:[declname:leavesAllocN type:int]

    $Attribute:[declname:n type:int]
    $Attribute:[declname:isNascent type:int]
    $Attribute:[declname:isDeleted type:int]

    $attribute:[templateFile type:string]
    $attribute:[declname:"*templ" type:user typname:"struct TEMPLo"]
    $attribute:[declname:"(*entryNamePrint)()" type:user typname:"void"]
    $attribute:[declname:"(*entryNPrint)()" type:user typname:"void"]
  }
]

O_DATATYPE:$Object:[DataType typname:LIBoDataType
  rem:|Description of a data type which can be linked to applications.
  attrs:{
    $attribute:[name unnamed:y type:string 
      rem:|Symbolic name of the data-type, eg, "DNASequence"
    ]
    $attribute:[applications type:object defaultval:@O_APPLICATION repeat:20
      rem:|List of applications that can be called with data of this type.
    ]
  }
]

O_APPLICATION:$Object:[application typname:APPLo
  nchilds:1 child:@O_APPLOPT
  rem:|Description of an application to be called on data of a certain type.
  attrs:{
    $attribute:[name unnamed:y type:string 
      rem:|Symbolic name of the application.
    ]
    $attribute:[title type:string 
      rem:|Short description of the program that can be used in a title line.
    ]
    $attribute:[type type:int required:y repeat:5
      rem:|Type of the application.
      enum:{
        $value:[search val:1]
        $value:[single val:2]
        $value:[multi val:3]
      }
    ]
    $attribute:[inSeqFormat type:int 
      rem:|Format of the input sequence(s)
      defaultval:2 enum:{
        $value:[gcg val:1]
        $value:[fasta val:2]
        $value:[pir val:3]
      }
    ]
    $attribute:[options type:child defaultval:@O_APPLOPT
      rem:|List of command line options.
    ]
    $attribute:[optionsN type:nr_of_childs defaultval:@O_APPLOPT]
    $attribute:[command type:string rem:
      |Icarus script used to defined the command line to call the 
      |application program.
    ]
    $attribute:[launch type:string rem:
      |Icarus script used to launch the program. The script relies on
      |\$opt.command being defined
    ]
 
    # Internal attributes
    $attribute:[interp declName:'*interp' type:user typName:'struct ICAoJOB']
    $attribute:[com declName:'*com' type:user typName:'struct STRo']
  }
]

O_APPLOPT:$Object:[AppOpt typname:APPLoOpt nchilds:1 child:@O_APPLOPTVAL
  attrs:{
    $attribute:[name type:string unnamed:y]
    $attribute:[group type:object defaultval:@O_APPLOPTGROUP]
    $attribute:[prompt type:string]
    $attribute:[type defaultval:4 type:int 
      enum:{
        $value:[int val:1]
        $value:[real val:2]
        $value:[bool val:3]
        $value:[string val:4]
      }
    ]
    $attribute:[guiType type:int defaultval:0
      enum:{
        $value:[checkbox val:1]
        $value:[multi val:2]
        $value:[radio val:3]
        $value:[menu val:4]
      }
    ]
    $attribute:[values type:child defaultval:@O_APPLOPTVAL
      rem:|List of option values.
    ]
    $attribute:[valuesN type:nr_of_childs defaultval:@O_APPLOPTVAL]
    $attribute:[defStr type:string]
    $attribute:[defInt type:int]
    $attribute:[defReal type:float]
  }
]

O_APPLOPTVAL:$Object:[OptVal typName:APPLoOptVal
  attrs:{
    $attribute:[name type:string unnamed:y]
    $attribute:[prompt type:string]
    $attribute:[valStr type:string]
    $attribute:[valInt type:int]
    $attribute:[valReal type:float]
    $attribute:[on type:int defaultval:0 enum:{
        $value:[y val:1]
        $value:[n val:0]
      }
    ] 
  }
]

O_APPLOPTGROUP:$Object:[OptGroup typName:APPLoOptGroup
  attrs:{
    $attribute:[name type:string unnamed:y]
  }
]


te:[defReal type:float]
  }
]

O_APPLOPTVAL:$Object:[OptVal typName:APPLoOptVal
  attrs:{
    $attribute:[name type:string unnamed:y]
    $attribute:[prompt type:string]
    $attribute:[valStr type:string]
    $attribute:[valInt type:int]
    $attribute:[valReal srs/icarus/util/srsquery.i
#    $RCSfile: srsquery.i,v $
#    $Revision: 1.7 $
#    $Date: 1997/03/03 18:32:55 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$rules={
  query:      ~ { init{$SetFunctions:QuerySetFunctions
                       $var:[t t:int]
                       $var:[l t:var]
                       $var:[v t:strv]
                       $var:[month t:int]
                       $var:[ga t:string]
                  }
                  $SetResult:[$_pop q:$ct]
                } 
                assign ~
  assign:     ~ /([a-zA-Z0-9_]+)[ \t\n]*=/ {$_push2:$_opnd:[$1 t:str]} expr 
                {$_push:$SetAssign:[$_pop2 s:$_pop]} | expr ~
  expr:       ~ term (logOp term doLogOp)* ~
  term:       ~ factor (linkOp factor 
                {$_push:$SetLinkOp:[$_pop1 s2:$_pop s1:$_pop]})*
              ~
  factor:     ~ set | retrieval | '(' assign ')' ~
  retrieval:  ~ '[' searchLibs '-' indexName
                (':' strRetr | '#' numRetr) ']' ~
  numRetr:    ~ range (logOp range doLogOp)* ~
  strRetr:    ~ searchStr (logOp searchStr doLogOp)* ~ 
  doLogOp:    ~ x{$_push:$SetLogOp:[$_pop1 s2:$_pop s1:$_pop]} ~
  searchStr:  ~ ( '"' /([^"\\]+|\\\\.)*/ {$s=$Ct} '"' | #"
                  '\'' /([^'\\]+|\\\\.)*/ {$s=$Ct} '\'' |
                  /\/([^\/\\]+|\\\\.)*\// {$s=$Ct}  |
                  /[^]|&!]+/ {$s=$Ct}
                ) x{$_push:$SetRetrStr:[$g s:$s index:$inx]}
              ~
  range:      ~ {pre{$l='min' $h='max' $el=0 $er=0}}
                ('!' {$el=1})? (val {$l=$num})?
                (':' ('!' {$er=1})? (val {$h=$num})? | x{$h='null'})
                x{$_push:$SetRetrRange: [$g index:$inx l:$l 
                     h:$h le:$el re:$er]}
              ~
  date:       ~ {init{$month={JAN:1 FEB:2 MAR:3 APR:4 MAY:5 JUN:6 JUL:7 AUG:8
                              SEP:9 OCT:10 NOV:11 DEC:12}}}
                /([0-9]+)-([A-Za-z][A-Za-z][A-Za-z])-([0-9][0-9]+)/
                {if:$StrLen:[$3]==2 $y="19$3" else $y=$3
                 $num = $1 + $month.($StrUpper:$2) * 100 + 10000 * $y} 
              ~
  val:        ~ date | /[0-9.+-]+/ {$num=$ct} ~
  set:        ~ name {$_push:$SetGet:$ct} | 
                '@' fileName {$print:"set"} ~
  logOp:      ~ /[|&!]/ {$_push1:$_opnd:[$ct t:str]} ~
  linkOp:     ~ /[<>]/ {$_push1:$_opnd:[$ct t:str]} ~
  name:       ~ /[a-zA-Z0-9_]+/ ~
  fileName:   ~ /[a-zA-Z0-9_]+/ ~
  indexName:  ~ /[a-zA-Z0-9_-]+/ {$inx=$ct} ~
  searchLibs: ~ ( /([a-zA-Z0-9_]+) *=/ {$g=$DbGroup:[init:$1]} |
                x{$g=$DbGroup:[init:default]})
                ('{' (name {$DbGroup:[$g db:$ct]})* '}' | 
                name {$g=$DbGroup:[$g db:$ct]} )
              ~
}







              '@' fileName {$print:"set"} ~
  logOp:      ~ /[|&!]/ {$_push1:$_opnd:[$ct t:str]} ~
  linkOp:     ~ /[<>]/ {$_push1:$_opnd:[$ct t:str]} ~
  name:       ~ /[a-zA-Z0-9_]+/ ~
  fileName:   ~ /[a-zA-Z0-9_]+/ ~
  indexName:  ~ /[a-zA-Z0-9_-]+/ {$inx=$ct} ~
  searchLibs: ~srs/icarus/util/srswww.i
#
# The template file for the SRSWWW server
#
# some definitions to customize the server
#
#

$parStr:[docdir set:'/srs5']
$parStr:[imgdir set:"($parStr:docdir)/images"]
$parStr:[mandir set:"($parStr:docdir)/man"]
$parStr:[cgidir set:'/srs5bin/cgi-bin']
$parStr:[siteName set:'EMBL-EBI, Hinxton, UK']
$parStr:[srsAdmin set:'etzold@ebi.ac.uk']
$parStr:[srsVersion set:"5.0.4"]

###############################################################################
#
#  the SRS start page
#

$startPage={
  head:
    |<HTML>
    |<TITLE>SRSWWW at ($parStr:siteName)</TITLE>
    |<BODY ($parStr:pageColor)>
    |<CENTER>
    |<TABLE><TR><TD>
    |<TABLE>
    |<TR>
    |<TD ALIGN=CENTER><FONT SIZE=+3>
    |<FONT SIZE=+5>S</FONT>equence 
    |<FONT SIZE=+5>R</FONT>etrieval 
    |<FONT SIZE=+5>S</FONT>ystem
    |</FONT></H1>
    |<P>
    |<I>
    |<FONT SIZE=+1> Network Browser for 
    |<A HREF="($parStr:cgidir)/wgetz?\
    |-fun+pageliblist+-color+($parStr:wwwColorScheme)">Databanks</A> 
    |in Molecular Biology
    |</I>
    |</TD>
    |<TD>
    |<IMG SRC="($parStr:imgdir)/smallsrsnet.gif">
    |</TD>
    |</TR>
    |</TABLE><P></TD></TR>
    |
    |<TR><TD ALIGN=center>
    |<FORM method=POST action="($parStr:cgidir)/wgetz">
    |<TABLE  cellpadding=1>
    |<FONT SIZE=+2>
    |
    |<TR><TD align=center>
    |<TABLE CELLSPACING=15><TR><TD>
    |<INPUT TYPE="submit" VALUE="Start">
    |</TD></TR></TABLE>
    |<INPUT TYPE=hidden NAME=wwwFunctionName VALUE=PageSelectLibrary>
    |<INPUT TYPE=hidden NAME=isHtml3 VALUE=1>
    |
    |</TD><TD ><FONT SIZE=+2>
    |Start a new SRS session
    |</FONT>
    |</TD>
    |</TR>

    |<TR><TD align=center>
    |<A HREF="($parStr:docdir)/man/srsman.html">
    |<IMG SRC="($parStr:imgdir)/manual_icon.gif"
    | ALT="The SRS Manual"></A> 
    |</TD>
    |<TD COLSPAN=3><FONT SIZE=+2>
    |The SRS Manual
    |</TD></TR>

    |<TR><TD align=center>
    |<A HREF="http://www.embl-heidelberg.de/srsdoc/status.html">
    |<IMG SRC="($parStr:imgdir)/status_icon.gif"
    | ALT="Status of all databanks served by all SRSWWW sites"></A>
    |</TD><TD  COLSPAN=3 ><FONT SIZE=+2>
    |Status of all databanks served by all SRSWWW sites
    |</TD></TR>

    |<TR><TD align=center>
    |<A HREF="news:bionet.software.srs">
    |<IMG SRC="($parStr:imgdir)/news_icon.gif" ALT="The SRS Newsgroup"></A> 
    |</TD><TD COLSPAN=3><FONT SIZE=+2>The SRS newsgroup
    |</TD></TR>

    # developers
    |<TR><TD align=center>
    |<A HREF="http://srs.ebi.ac.uk:5000/about.html">\
    |<IMG SRC="($ParStr:imgdir)/brain_icon.gif" ALT="SRS Brains"></A> 
    |</TD>
    |<TD COLSPAN=3><FONT SIZE=+2>SRS Developers
    |</TD></TR>

    # the link to the home page
    |<TR><TD align=center>
    |<A HREF="http://www.embl-heidelberg.de/">\
    |<IMG SRC="($parStr:imgdir)/home_icon.gif" ALT="Home Page"></A> 
    |</TD>
    |<TD COLSPAN=3><FONT SIZE=+2>Back to the EMBL home page
    |</TD></TR>
    |
    |</TABLE></TD></TR>
    |</FORM>
    |</FONT>
    |<TR><TD ALIGN=CENTER>
    |&nbsp;<p><I>This is the SRSWWW server at ($parStr:siteName), 
    |version ($parStr:srsVersion)</I>
    |</TD></TR>
    |</TABLE>
    |</BODY>
}


###############################################################################
#
#  displays help for one or all Icarus command
#

$icarusCommand={
  title:
    |<HTML>
    |<HEAD>
    |<TITLE>Descriptions of built in Icarus functions</TITLE>
    |</HEAD>
    |<BODY BGCOLOR="#fffff0" LINK="#0000ff" VLINK="#ff0000" 
    | ALINK="#ff0000" TEXT="#000000">
    |<H1><A NAME="Ica_top"></A>The Icarus Commands</H1>
    |The names are still not alphabetically ordered.
  head:
    |<H2><A NAME="Ica_%s"></A>$%s</H2>
    |%s
    |<P>
    |<CENTER>
    |<TABLE BORDER>
    |<TR><TH><FONT SIZE=2>Name</TH> <TH><FONT SIZE=2>Type</TH>
    |<TH><FONT SIZE=2>Unn</TH> <TH><FONT SIZE=2>Req</TH>
    |<TH><FONT SIZE=2>Default</TH> <TH><FONT SIZE=2>Comment</TH>
    |</TR>
    |<TR><TH ALIGN=CENTER COLSPAN=6 BGCOLOR="#d3b5b5">
    |<FONT SIZE=2>Arguments</TH></TR>
  noArgs:
    |<TR><TD ALIGN=CENTER COLSPAN=6><I>none</I></TD></TR>
  arglist:{
    name:
      |<TR><TD VALIGN=TOP><B>%s</B></TD>
    type:{
      int:    |<TD VALIGN=TOP>int</TD>
      string: |<TD VALIGN=TOP>string</TD>
      object: |<TD VALIGN=TOP><I>%s</I> object</TD>
      real:   |<TD VALIGN=TOP>real</TD>
      alias:  |<TD VALIGN=TOP>alias</TD>
      var:    |<TD VALIGN=TOP>var</TD>
      d1:     |<TD VALIGN=TOP>unknown</TD>
      d2:     |<TD VALIGN=TOP>unknown</TD>
      strv:   |<TD VALIGN=TOP>strv</TD>
      d3:     |<TD VALIGN=TOP>unknown</TD>
      d4:     |<TD VALIGN=TOP>unknown</TD>
      d5:     |<TD VALIGN=TOP>unknown</TD>
      d6:     |<TD VALIGN=TOP>unknown</TD>
      d7:     |<TD VALIGN=TOP>unknown</TD>
      d8:     |<TD VALIGN=TOP>unknown</TD>
      list:   |<TD VALIGN=TOP>list</TD>
      enum:{
        head:  |<TD VALIGN=TOP><I>enum:</I><BR>
        value: |%s 
        tail:  |</TD>
      }
    }
    unnamed:
      |<TH VALIGN=TOP>+</TH>
    named:
      |<TH VALIGN=TOP>&nbsp;</TH>
    required:
      |<TH VALIGN=TOP>+</TH>
    optional:  
      |<TH VALIGN=TOP>-</TH>
    comment:
      |<TD>%s</TD>
    defaultNum:
      |<TH VALIGN=TOP>%d</TH>
    defaultStr:
      |<TH VALIGN=TOP>%s</TH>
    empty:
      |<TD>&nbsp;</TD>
    tail:
      |</TR>
  }
  return:{
    head:
      |<TR><TH ALIGN=center COLSPAN=6 BGCOLOR="#d3b5b5">
      |<FONT SIZE=2>Returns</TH></TR>
    preType:
      |<TR><TD>&nbsp;</TD>
    postType:
      |<TD>&nbsp;</TD> <TD>&nbsp;</TD> <TD>&nbsp;</TD> <TD>&nbsp;</TD></TR>
    nothing:
      |<TR><TD COLSPAN=6 ALIGN=center><I>Nothing</I></TD></TR>
  }
  tail:
    |</TABLE>
    |</CENTER>
    |<PR>
}


###############################################################################
#
#  displays help for one or all SRS object classes.
#
#

$classInfo={
  head:
    |<HTML>
    |<BODY BGCOLOR="#FFFFF0" LINK="#0000ff" VLINK="#ff0000" 
    | ALINK="#ff0000" TEXT="#000000">
    |<H1><A NAME="SRSObjClass"></A>List of SRS Object Classes</H1>
    |<BLOCKQUOTE>
    |<H5>Date: %s</H5>                
    |</BLOCKQUOTE>
    |The following lists among others the object classes that are used to
    |describe the integrated databanks.
  dir:{
    head:
      |<H1>List Object Classes in SRS</H1> 
      |<H5>Date: %s</H5>                
      |<UL>                             
    class:
      |<LI><B>\$%s</B>
    tail:
      |</UL><P>
  }
  class:{
    head:
      |<H2><A NAME="class%d"></A>\$%s</H2>
    remark:
      |%s<P>
      |<CENTER>
      |<TABLE BORDER CELLPADDING=3>
      |<TR><TH COLSPAN=6><FONT SIZE=2>Arguments</TH><TR> 
      |<TR><TH BGCOLOR="#d3b5b5"><FONT SIZE=2>Name</TH> 
      |<TH BGCOLOR="#d3b5b5"><FONT SIZE=2>Comment</TH>
      |<TH BGCOLOR="#d3b5b5"><FONT SIZE=2>Unn</TH> 
      |<TH BGCOLOR="#d3b5b5"><FONT SIZE=2>Req</TH>
      |<TH BGCOLOR="#d3b5b5"><FONT SIZE=2>Type</TH>
      |<TH BGCOLOR="#d3b5b5"><FONT SIZE=2>Default</TH> 
      |</TR>
    attrib:{
      head:
        |<TR><TD VALIGN=TOP><B>%s</B></TD>
      empty:
        |<TD VALIGN=TOP>&nbsp;</TD>
      remark:
        |<TD VALIGN=TOP>%s</TD>
      unnamed:
        |<TD VALIGN=TOP ALIGN=CENTER><B>+</B></TD> 
      named:
        |<TD>&nbsp;</TD> 
      typeHead:
        |<TD VALIGN=TOP>
      typeTail:
        |</TD>
      type:
        |<I>%s</I>
      listType:
        |<I>list of</I> $%s
      ptrType:
        |<I>%s</I> $%s
      arrSize:
        |<BR><B>list size:</B> %d
        |
      default:{
        option:
          |<TD VALIGN=TOP ALIGN=CENTER>%s
        string:
          |<TD VALIGN=TOP ALIGN=CENTER>"%s"</TD>
        num:
          |<TD VALIGN=TOP ALIGN=CENTER>%d</TD>
        real:
          |<TD VALIGN=TOP ALIGN=CENTER>%f</TD>
      }      
      minmaxNum:
        |<BR><B>min:</B> %d<BR><B>max:</B> %d
      minmaxStr:
        |<BR><B>min length:</B> %d<BR><B>max length:</B> %d
      required:
        |<TD VALIGN=TOP ALIGN=CENTER><B>+</B></TD> 
      optionList:{
        head:
          |\
        option:
          |<LI>%s
        tail:
          |\       
      }
      infoEnd:
        |</TR>
      tail:''
    }
    tail:
      |</TABLE></CENTER><P>
  }
}

###############################################################################
#
#  Very importantly, sets a few color schemas
#
#

$colorScheme={
  plain:{
    page: ''
    cell: |BGCOLOR="#d3b5b5"\
  }
  white:{
    page: |text="#000000" bgcolor="#FFFFF0" link="#0000FF" \
          | vlink="#FF0000" alink="#FF0000"\
    cell: |BGCOLOR="#d3b5b5"\
  }
  yellow:{
    page: |text="#400040" bgcolor="#FFFF80" link="#0000FF" 
          |vlink="#008000" alink="#FF0080"                 
    cell: |BGCOLOR="#"\
  }
  blue:{
    page: |text="#FFFFFF" bgcolor="#000080" link="#FFFF00" 
          |vlink="#8080FF" alink="#FF00FF"  
    cell: |BGCOLOR="#0000A0"\
  }
  black:{
    page: |text="#FFFFFF" bgcolor="#000000" link="#FFFF00" 
          |vlink="#C0C0C0" alink="#COFFCO"                 
    cell: |BGCOLOR="#0000A0"\
  }
  grayRock:{
    page: |background=($parStr:imgdir)/gray_rock.gif
    cell: |BGCOLOR="#C0C0C0"\
  }
  yellowWeave:{
    page: |background=($parStr:imgdir)/yellow_weave.gif
    cell: |BGCOLOR="#d3b5b5"\
  }    
  greenPaper:{
    page: |background=($parStr:imgdir)/greenwhite_paper.gif
    cell: |BGCOLOR=\"#edeafb\"\
  }    
  bluePaper:{
    page: |background=($parStr:imgdir)/blue_paper.gif
    cell: |BGCOLOR=\"#edeafb\"\
  }    
  grayAluminium:{
    page: |background=($parStr:imgdir)/gray_aluminum.gif
    cell: |BGCOLOR=\"#edeafb\"\
  }    
  tanPaper:{
    page: |background=($parStr:imgdir)/tan_paper.gif
    cell: |BGCOLOR=\"#edeafb\"\
  }    
  yellowStucco:{
    page: |background=($parStr:imgdir)/yellow_stucco.gif
    cell: |BGCOLOR="#d3b5b5"\
  }    
  purpleWeave:{
    page: |background=($parStr:imgdir)/lipurple_weave.gif
    cell: |BGCOLOR=\"#edeafb\"\
  }    
  orangePaper:{
    page: |background=($parStr:imgdir)/orange_paper.gif
    cell: |BGCOLOR=\"#edeafb\"\
  }    
  tealPaper:{
    page: |background=($parStr:imgdir)/teal_paper.gif
    cell: |BGCOLOR=\"#edeafb\"\
  }    
  summerPaper:{
    page: |background=($parStr:imgdir)/summer_paper.gif
    cell: |BGCOLOR=\"#edeafb\"\
  }    
  peachPaper:{
    page: |background=($parStr:imgdir)/peach_paper.gif
    cell: |BGCOLOR=\"#edeafb\"\
  }    
  greenMarble:{
    page: |background=($parStr:imgdir)/greenred_marble.gif
    cell: |BGCOLOR="#d3b5b5"\
  }    
}

###############################################################################
#
#  the list of libraries
#
#

$libList={
  head:
    |<HEAD>
    |<TITLE>SRSWWW at ($parStr:siteName): list of available data banks</TITLE>
    |</HEAD>
    |<BODY ($parStr:pageColor)>
    |<FORM method=POST action="($parStr:cgidir)/wgetz">
    |<INPUT TYPE=hidden NAME=userId VALUE=($parStr:userId)>
  title:
    |<H2>Data Banks Available at ($parStr:siteName)</H2>
    |<I>%s</I><P>
    |<BLOCKQUOTE>
    |<input type=hidden name=wwwColorScheme VALUE=($parStr:wwwColorScheme)>
    |<input type=submit NAME=PageLibNetwork value="Show Library Network">
    |<input type=hidden name=wwwFunctionName9 VALUE=PageLibNetwork>
    |</BLOCKQUOTE>
    |</FORM>
    |<P>
    |<TABLE BORDER CELLPADDING=2>
    |<TR>
    |<TH><FONT SIZE=-1>Data Bank</TH>
    |<TH><FONT SIZE=-1>Release</TH>
    |<TH><FONT SIZE=-1>No Entries</TH>
    |<TH><FONT SIZE=-1>Indexing Date</TH>
    |<TH><FONT SIZE=-1>Group</TH>
    |<TH><FONT SIZE=-1>Availability</TH>
    |</TR>
  libraryGood:
    |<TR>
    |<TD ALIGN=LEFT><A HREF="($parStr:cgidir)/wgetz?\
    |%s-fun+pagelibinfo+-info+%s">
    |<B>%s</B></A></TD>
    |<TD>%s</TD>
    |<TD ALIGN=RIGHT>%d</TD>
    |<TD ALIGN=CENTER>%s</TD>
    |<TD ALIGN=CENTER>%s</TD>
    |<TD ALIGN=CENTER><I>ok</I></TD>
    |</TR>
  libraryBad:
    |<TR>
    |<TD ALIGN=LEFT><A HREF="($parStr:cgidir)/wgetz?\
    |%s-fun+pagelibinfo+-info+%s">
    |<B>%s</B></A></TD>
    |<TD>&nbsp;</TD>
    |<TD ALIGN=RIGHT>&nbsp;</TD>
    |<TD>&nbsp;</TD>
    |<TD ALIGN=CENTER>%s</TD>
    |<TD><I>&nbsp;</I></TD>
    |</TR>
  tail:
    |</TABLE>
    |</BODY>
}


###############################################################################
#
#  the "Select databanks" or "top" page
#
#
$selectLibrary={
  head:
    |<HEAD>
    |<TITLE>NEW SRS:Select Libraries Page </TITLE>
    |</HEAD>
    |<BODY ($parStr:pageColor)>
    |<form method=POST action=($parStr:cgidir)/wgetz>
    |<INPUT TYPE=hidden NAME=userId VALUE=($parStr:userId)>
    |<INPUT TYPE=hidden NAME=libList VALUE=reset>
  submit:
    |<input type=CHECKBOX NAME=isOnlyCommonFields~ VALUE=1 CHECKED> \ 
    |Show only fields that selected databanks have in common
    |<P> 
    |<IMG SRC=($parStr:imgdir)/arrow_icon.gif ALIGN=MIDDLE>
    |<INPUT TYPE=submit NAME=PageQueryForm VALUE="  Continue  ">
    |<INPUT TYPE=hidden NAME=wwwFunctionName3 VALUE=PageQueryForm>
    |<INPUT TYPE=reset VALUE="  Reset  ">
  libs:{
    html3:{
      libGroupName:
        |<HR>
        |<b>%s</b><br>
        |<TABLE noborder cellspacing=2>
        |<TR>
      libGroupNameSearch:
        |<HR>
        |<b>%s</b>
        | <INPUT TYPE=SUBMIT NAME=PageSearchOpt 
        |VALUE="Launch">
        |<INPUT TYPE=hidden NAME=wwwFunctionName8~ VALUE=PageSearchOpt>
        |<P>
        |<TABLE noborder cellspacing=2>
        |<TR>
      newRow:
        |</TR>
        |<TR>
      library:
        |<TD><input type=checkbox name=libList value=%s %s></TD>
        |<TD><A HREF=($parStr:cgidir)/wgetz?\
        |($parStr:userIdOpt)-fun+Pagelibinfo+-info+%s>
        |%s</a>%s</TD>
      tail:
        |</TR>
        |</TABLE>
    }
    html2:{
      libGroupsName:
        |<PRE>
        |<HR><b>%s</b><P>
      newRow: '\n'
      library:
        |<input type=checkbox name=libList value=%s %s> \
        |<A HREF=($parStr:cgidir)/wgetz?\
        |-id+($parStr:userId)+-fun+Pagelibinfo+-info+%s>%s</a>\
        |%-($parStr:l)s\
      tools:{
        blast:
          |<A HREF=($parStr:cgidir)/wgetz?-fun+WwwPrepBlast+-id+%s%s>\
          |Do BLAST Search</a>
      }
      tail:
        |</PRE>
    }
  }
  tail:
    |<HR>
    |<TABLE><TR><TD NOWRAP>
    |<FONT SIZE=-1>
    |<I>... tired of looking at all this data? Change their color!</I> 
    | <INPUT TYPE=submit NAME=PageSelectLibrary VALUE=Try>\
    |<INPUT TYPE=hidden NAME=wwwFunctionName20 VALUE=PageSelectLibrary>
  colorScheme:{
    head:
      |<SELECT NAME=wwwColorScheme>
    color:
      |<OPTION %s>%s
    tail:
      |</SELECT> 
      |</TD><TD>
      |
    |<FONT SIZE=-1>
    |<I>If you find problems or have suggestions please mail the</I>
    |<A HREF=mailto:($ParStr:srsAdmin)>SRS&nbsp;administrator</A>
      |</TD></TR></TABLE>
      |</FORM>
      |</BODY>
      |</HTML>
  }
}


###############################################################################
#
#  the  Page with the library network
#
#

$libNetwork={
  head:
    |<HTML>
    |<HEAD>
    |<TITLE>SRSWWW at ($parStr:siteName): Library Network Distance Table
    |</TITLE>
    |</HEAD>
    |<BODY ($parStr:pageColor)>
    |<form method=POST action=($parStr:cgidir)/wgetz>
    |<INPUT TYPE=hidden NAME=userId VALUE=($parStr:userId)>
  title:
    |<H2>The Library Network shown as a Distance Table</H2>
    |<BLOCKQUOTE>
    |<input type=hidden name=wwwColorScheme VALUE=($parStr:wwwColorScheme)>
    |<input type=submit NAME=PageLibList value="Show Library List">
    |<input type=hidden name=wwwFunctionName9 VALUE=PageLibList>
    |</BLOCKQUOTE>
    |<P>
    |<TABLE NOBORDER>
  fromLib:
    |<TR> 
    |<TH ALIGN=RIGHT><font size=1>\
    |<A HREF="($parStr:cgidir)/wgetz?-info+%s">%s</A></TH>
  link:{
    direct:
      |<TH><font size=1><A HREF="($parStr:cgidir)/wgetz?\
      |-linfo+-from+%s+-to+%s+-id+($parStr:userId)">1</A></TH>
    indirect:
      |<TD ALIGN=CENTER><font size=1><A HREF="($parStr:cgidir)/wgetz?\
      |-linfo+-from+%s+-to+%s+-id+($parStr:userId)">%d</A></TD>
    none:
      |<TH><font size=1>.</TH>
  }
  rowEnd:
    |</TR>
  toLibs:
    |<TR><TD></TD>
  toLib:{
    head:   |<TH VALIGN=TOP><FONT SIZE=1>
    letter: |%c<BR>
    last:   |%c\
    tail:   |</TH>
  }
  tail:
    |</TR>
    |</TABLE>
    |</FORM>
    |<BODY>
    |</HTML>
}


###############################################################################
#
#   the information about a pairwise  link
#

$linkInfo={
  head:
    |<HTML>
    |<HEAD>
    |<TITLE>SRSWWW at ($parStr:siteName): Link Information
    |</TITLE>
    |</HEAD>
    |<BODY ($parStr:pageColor)>
    |<form method=POST action=($parStr:cgidir)/wgetz>
    |<INPUT TYPE=hidden NAME=userId VALUE=($parStr:userId)>
  title:
    |</FORM>
    |<H2>Link Information</H2>
  noLink:
    |A link from <B>%s</B> to <B>%s</B> does not exist.
  direct:
    |The link from <B>%s</B> to <B>%s</B> is direct.
    |<P>
  indirect:{
    head:
      |%d entries in <B>%s</B> are linked to %d entries in <B>%s</B>.<BR>
      |The link is indirect and has been resolved to the path "<TT>%s&gt\
    pathLib:
      |%s&gt;\
    lastLib:
      |%s</TT>".
      |<P>
  }
  table:{
    head:
      |<TABLE BORDER CELLPADDING=4><TR>
      |<TH><FONT SIZE=-1>From</TH>
      |<TH><FONT SIZE=-1>Linked<BR>Entries</TH>
      |<TH><FONT SIZE=-1>To</TH>
      |<TH><FONT SIZE=-1>Linked<BR>Entries</TH>
      |<TH><FONT SIZE=-1>Total No<BR>of Links</TH>
      |<TH><FONT SIZE=-1>Information Used</TH>
      |<TH><FONT SIZE=-1>Creation<BR>Time</TH>
      |</TR>
    names:
      |<TR>
      |<TD VALIGN=TOP><A HREF="($parStr:cgidir)/wgetz?\
      |-fun+pagelibinfo+-info+%s">\
      |%s</A></TD>
      |<TD ALIGN=RIGHT VALIGN=TOP>%d</TD>
      |<TD VALIGN=TOP><A HREF="($parStr:cgidir)/wgetz?-fun+pagelibinfo+-info+%s">\
      |%s</A></TD>
      |<TD ALIGN=RIGHT VALIGN=TOP>%d</TD>
    total:
      |<TD ALIGN=RIGHT VALIGN=TOP>%d</TD>
    read:
      |<TD>Cross-references in %s referring to contents of the
      |%s field in %s</TD>     
    index:
      |<TD>Matching strings in the %s field of %s and the %s field in %s.</TD>
    creTime:
      |<TD ALIGN=CENTER VALIGN=TOP>%s</TD>
    notCreated:
      |<TD ALIGN=CENTER VALIGN=TOP><I>not available</I></TD>
    rowEnd:
      |</TR>
  }
  tail:
    |</TABLE>
    |</BODY>
    |</HTML>
}



###############################################################################
#
#  the  Query form page
#
#
$queryForm={
   head:
     |<HTML>
     |<HEAD>
     |<TITLE>SRS:Query Form Page </TITLE>
     |</HEAD>
     |<BODY ($parStr:pageColor)>
     |<form method=POST action=($parStr:cgidir)/wgetz>
     |<INPUT TYPE=hidden NAME=fieldList VALUE=reset>
     |<INPUT TYPE=hidden NAME=userId VALUE=($parStr:userId)>
     |<input type=hidden name=delete value=subEntry_.+>
     |<P>  
   searchInfo:
     |<I>Search</I>
   listLibs:
     |<A HREF=($parStr:cgidir)/wgetz?\
     |-id+($parStr:userId)+-fun+Pagelibinfo+-info+%s><B>%s</B></A>
   submit:
     |<P>
     |<TABLE>
     |<TR><TD ROWSPAN>
     |<IMG SRC=($parStr:imgdir)/arrow_icon.gif ALIGN=MIDDLE>\
     |<input type=submit NAME=PageConstructQuery value="Do Query">  
     |<input type=hidden name=wwwFunctionName9 VALUE=PageConstructQuery>
     |</TD>
   chunkSize:{
     head:
       |<TD NOWRAP>
       |Entry List in chunks of\
       |<SELECT NAME=viewEntriesChunkSize>
     size:
       |<OPTION %s> %d
     tail:
       |</SELECT>
       |</TD>
   }      
   selectView:{
     head:
       |<TD NOWRAP>
       |Use view
       |<SELECT NAME=viewNumber>
     name:
       |<OPTION VALUE=%d %s> %s
     tail:
       |</SELECT>
       |<TD></TR>
   }
   searchOptions:
     |<TR><TD ALIGN=RIGHT>
     |&nbsp;
     |</TD>
     |<TD>
     |Combine&nbsp;searches&nbsp;with&nbsp;\
     |<SELECT NAME=query_operator>
     |<OPTION SELECTED>AND
     |<OPTION >OR
     |<OPTION >NOT
     |</SELECT> 
     |</TD>
     |<TD>
     |<INPUT type=hidden name=delete value=makeWild>
     |<input type=checkbox NAME="makeWild" value=1 %s>
     | Append wildcard '*' to words.
     |</TD></TR></TABLE>
   queryInput: {
      html3: {
        head:
          |<TABLE  NOBORDER CELLPADDING CELLSPACING>
          |<TR><TH ALIGN=left> 
          |<A HREF="($parStr:docdir)/man/mi_srswww.html#fieldname">\
          |Field Name</A></TH>
          |<TH colspan=4 align=middle>
          |<A HREF="($parStr:docdir)/man/mi_srswww.html#fieldname">\
          |Query</A></TH>
          |<TH><A HREF="($parStr:docdir)/man/mi_srswww.html#fieldname">\
          |Include<BR>in List</A>
          |</TH><TH><A HREF="($parStr:docdir)/man/mi_srswww.html#fieldname">\
          |Retrieve <BR>SubEntries (SE)</A></TH>
          |</TR>
        fieldHeader:
  	  |<TR>
          |<TD COLSPAN=7><HR>
          |<B><font size=+1>%s</B></TD>
        fieldNum:
  	  |<TR> 
  	  |<TD>
  	  |<A HREF=($parStr:cgidir)/wgetz?\
          |($parStr:userIdOpt)-fun+PageIndexBrowseOpt+-bf+%s>%s</A>%s
  	  |</TD>
  	  |<TD ALIGN=LEFT>\
  	  |<SELECT NAME=query_%s_beginmod>
  	  |<OPTION %s> &gt;=
  	  |<OPTION %s> &gt;
  	  |</SELECT> 
  	  |</TD> 
  	  |<TD ALIGN=LEFT>
  	  |<input name=query_%s_begin size=8 value=> 
  	  |</TD>
  	  |<TD ALIGN=RIGHT>
  	  |<SELECT NAME=query_%s_endmod>
  	  |<OPTION %s> &lt;=
  	  |<OPTION %s> &lt; 
  	  |</SELECT>
  	  |</TD>
  	  |<TD ALIGN=RIGHT>
  	  |<input name=query_%s_end size=8></TD>
  	  |<TD valign=center align=center>\
  	  |<INPUT TYPE=CHECKBOX NAME=fieldList  VALUE=%s>\
  	  |</TD>
        fieldText:
          |<TR> 
          |<TD>
          |<A HREF=($parStr:cgidir)/wgetz?\
          |-id+($parStr:userId)+-fun+PageIndexBrowseOpt+-bf+%s>%s</A>%s
          |</TD>
          |<TD colspan=4>
          |<INPUT SIZE=44 NAME=query_%s VALUE=> 
          |</TD>
          |
          |<TD valign=middle align=center>\
          |<INPUT TYPE=CHECKBOX NAME=fieldList VALUE=%s></TD>
       subEntry:
          |<TD valign=middle align=center nowrap>\
          |<input type=checkbox name="subEntry_%s~" value=1 checked> 
          |<I>feature SE</i>
#          |<a href=($parStr:cgidir)/wgetz?-fun+WwwPrintHelpAbout+-ht\
#          |+SubEntry>Subentry only</A>
          |</TD>
      rowEnd:
          |</TR>
      tail:
          |</TABLE>
      }
   }
   tail:
     |<HR>
     |<input type=reset value=Reset> &nbsp;&nbsp;
     |<i>Separate multiple values by <B>&</B> (and), <B>|</B> (or), 
     |<B>!</B> (and not)
     |</FORM>
     |</BODY>
     |</HTML>
}


###############################################################################
#
# the "Library Information" page
#
$parStr:[cellCols set:"bgcolor=\"#000080\"><FONT color=\"#FFFFFF\""]
#$parStr:[cellCols set:""]
$libInfo={
  head:
    |<HTML>
    |<HEAD>
    |<TITLE> View Select Page</TITLE>
    |<BODY ($parStr:pageColor)>
    |<form method=POST action=($parStr:cgidir)/wgetz>
    |<INPUT TYPE=hidden NAME=userId VALUE=($parStr:userId)>
  title:
    |</FORM>
    |<P><TABLE CELLPADDING=6>
    |<TR><TD VALIGN=TOP ($ParStr:cellCols)><B>Name</B></TD><TD>
    |<H1>%s</H1>
    |</TD><TD ALIGN=center><FORM method=POST action=($parStr:cgidir)/wgetz>
    |<INPUT TYPE=hidden NAME=userId VALUE=($parStr:userId)>
    |<input type=hidden name=wwwFunctionName VALUE=PageQueryForm>
    |<INPUT type=hidden name=libList VALUE=reset>
    |<INPUT type=hidden name=libList VALUE=%s>
    |<INPUT type=submit VALUE="Search %s"></FORM></TD></TR>
    |<TR><TD VALIGN=TOP ($ParStr:cellCols)><B>Status</B></TD><TD COLSPAN=2>
  noRelease:
    |The current release has %d entries and was indexed %s.
  release:
    |The current release %s has %d entries and was indexed %s.
  notIndexed:
    |The databank is currently not available.
  t:{
    head: 
      |</TD></TR>
    description:{
      head:
        |<TR><TD VALIGN=TOP ($ParStr:cellCols)><B>Description</B></TD>
        |<TD COLSPAN=2>
      tail:
        |</TD></TR>
    }
    literature:{
      head:
        |<TR><TD VALIGN=TOP ($ParStr:cellCols)><B>Literature</B></TD>
        |<TD COLSPAN=2>
      tail:
        |</TD></TR>
    }
    address:{
      head:
        |<TR><TD VALIGN=TOP ($ParStr:cellCols)><B>Address</B></TD>
        |<TD COLSPAN=2>
      tail:
        |</TD></TR>
    }
    contact:{
      head:
        |<TR><TD VALIGN=TOP ($ParStr:cellCols)><B>Contact</B></TD>
        |<TD COLSPAN=2>
      tail:
        |</TD></TR>
    }
    email:{ 
      head:
        |<TR><TD VALIGN=TOP ($ParStr:cellCols)><B>E-mail</B></TD><TD COLSPAN=2>
      tail:
        |</TD></TR>
    }
    www:{
      head:
        |<TR><TD VALIGN=TOP ($ParStr:cellCols)><B>WWW</B></TD><TD COLSPAN=2>
      tail:
        |</TD></TR>
    }
    ftp:{
      head:
        |<TR><TD VALIGN=TOP ($ParStr:cellCols)><B>FTP</B></TD><TD COLSPAN=2>
      tail:
        |</TD></TR>
    }
    updates:{
      head:
        |<TR><TD VALIGN=TOP ($ParStr:cellCols)><B>Updates</B></TD>
        |<TD COLSPAN=2>
      tail:
        |</TD></TR>
    }
    tail:''
  }  

  example:
    |<TR><TD VALIGN=TOP ($ParStr:cellCols)><B>Example&nbsp;Entry</B></TD>
    |<TD COLSPAN=2>
    |<a href=/srsbin/wgetz?-e+[%s-id:"%s"]>%s</a>
    |</TD></TR>
  fields:{
    head:
      |<TR><TD VALIGN=TOP ($ParStr:cellCols)>
      |<B>Data-fields<BR>in SRS</B></TD><TD  COLSPAN=2>
      |<TABLE BORDER CELLPADDING=4><TR>
      |<TH><FONT SIZE=-1>Name</TH>
      |<TH><FONT SIZE=-1>Short<BR>Name</TH>
      |<TH><FONT SIZE=-1>Type</TH>
      |<TH><FONT SIZE=-1>No of<BR>Keys</TH>
      |<TH NOWRAP><FONT SIZE=-1>No of Entry<BR>References</TH>
      |<TH><FONT SIZE=-1>Indexing Date</TH>
      |<TH><FONT SIZE=-1>Status</TH>
      |</TR>
    name:
      |<A HREF=($parStr:cgidir)/wgetz?\
      |($parStr:userIdOpt)-fun+PageIndexBrowseOpt+-bf+%s+-lib+%s>%s</A><BR>
    short:  |%s<BR>
    type:   |%s<BR>
    valN:   |%d<BR>
    refN:   |%d<BR>
    date:   |%s<BR>
    status: |%s<BR>
    empty:  |<BR>
    tail:
      |<TR>
      |<TD>%s</TD>
      |<TD>%s</TD>
      |<TD>%s</TD>
      |<TD ALIGN=RIGHT>%s</TD>
      |<TD ALIGN=RIGHT>%s</TD>
      |<TD ALIGN=CENTER NOWRAP>%s</TD>
      |<TD ALIGN=CENTER NOWRAP>%s</TD>
      |</TR></TABLE></TD></TR>
  }
  links:{
    to:
      |<TR><TD VALIGN=TOP ($ParStr:cellCols)>
      |<B>Links To</B></TD><TD COLSPAN=2><UL>
    toLib:
      |<LI><A HREF="($parStr:cgidir)/wgetz?\
      |-id+($parStr:userId)+-fun+Pagelinkinfo+-from+%s+-to+%s">%s</A> 
    from:
      |</Ul>
      |</TD></TR>
      |<TR><TD VALIGN=TOP ($ParStr:cellCols)>
      |<B>Links From</B></TD><TD COLSPAN=2><UL>
    fromLib:
      |<LI><A HREF="($parStr:cgidir)/wgetz?\
      |-id+($parStr:userId)+-fun+Pagelinkinfo+-to+%s+-from+%s">%s</A> 
    none:
      |<I>none</I>
    tail:
      |</UL>
  }
  icarusFiles:{
    head:
      |<TR><TD VALIGN=TOP ($ParStr:cellCols)><B>SRS&nbsp;Description</B></TD>
      |<TD COLSPAN=2><UL>
    structure:
      |<LI><A HREF="($parStr:cgidir)/wgetz?\
      |-fun+PageIcarusFile+-l+%s+-ifile+i">\
      |Structure</A>
    syntax:
      |<LI><A HREF="($parStr:cgidir)/wgetz?\
      |-fun+PageIcarusFile+-l+%s+-ifile+is">\
      |Syntax</A>
    information:
      |<LI><A HREF="($parStr:cgidir)/wgetz?\
      |-fun+PageIcarusFile+-l+%s+-ifile+it">\
      |Information</A>
    tail:
      |</UL></TD></TR>
  }
  tail:
    |</TD></TR></TABLE>
    |</BODY>
    |</HTML>
}

###############################################################################
#
# page with an icarus file
#

$icarusFile={
  head: 
    |<HTML>
    |<BODY text="#000000" bgcolor="#FFFFF0" link="#0000FF" \
    |vlink="#FF0000" alink="#FF0000">
    |<PRE>
  tail:
    |</PRE>
    |</BODY>
    |</HTML>
}

###############################################################################
#
# the "View Create" page - part I of creating views
#
$viewCreate={
  head:
    |<HTML>
    |<HEAD>
    |<TITLE> View Select Page</TITLE>
    |<BODY ($parStr:pageColor)>
    |<FORM method=POST action=($parStr:cgidir)/wgetz>
    |<INPUT TYPE=hidden NAME=userId VALUE=($parStr:userId)>
    |

    # help
    |<TD ALIGN=CENTER><TABLE BORDER=3><TR><TD bgcolor="#ffff00">
    |<font color="#ffffff"><A HREF=
    |"($parStr:docdir)/man/mi_srswww.html#CreateView"
    |>Help</A></TD></TR></TABLE>
    |<HR>
    |</FORM>
  edit:{
    head:
      |<FORM method=POST action=($parStr:cgidir)/wgetz>
      |<INPUT TYPE=hidden NAME=userId VALUE=($parStr:userId)>
      |<INPUT TYPE=HIDDEN NAME=viewNumber VALUE=%d>
      |<INPUT type=hidden name=delete value=view%d_Nam.+>
      |<h3> <IMG SRC=($parStr:imgdir)/redball.gif> 
      |Edit an existing view</h3>
      |<BLOCKQUOTE>
      |<INPUT TYPE=submit NAME=PageViewEdit VALUE="Edit">
      |<INPUT TYPE=hidden NAME=wwwFunctionName2 VALUE=PageViewEdit>
      |
      |<SELECT NAME="viewName~">
    viewName:
      |<OPTION %s> %s
    tail:
      |</SELECT>
      |or use the 
      |<INPUT TYPE=SUBMIT NAME=PageViewManager VALUE="View Manager">
      |<INPUT TYPE=HIDDEN NAME=wwwFunctionName3 VALUE=PageViewManager>
      |
      |</BLOCKQUOTE>
      |</FORM>
  }
  create:{
    logo:
      |<h2>Create new view</h2>   
    head:
      |<FORM method=POST action=($parStr:cgidir)/wgetz>
      |<INPUT TYPE=hidden NAME=userId VALUE=($parStr:userId)>
      |<INPUT TYPE=HIDDEN NAME=viewNumber VALUE=%d>
      |<INPUT TYPE=HIDDEN NAME=delete value=v%d_R_.+>
      |<INPUT TYPE=HIDDEN NAME=delete value=v%d_L_.+>
      |<INPUT type=hidden name=delete value=view%d_Name>
  }
  rootHeader:
    |<TABLE CELLSPACING=5>
    #view name
    |<TR><TD VALIGN=TOP ROWSPAN=3><TABLE>
    |<TR>
    |<TD  VALIGN=TOP>
    |Name of view (<i>optional</I>)<BR> 
    |<input name=view%d_Name SIZE=20 value=%s> 
    |</TD>
    |</TR>
    #display as table
    |<TR>
    |<TD VALIGN=BOTTOM>
    |<input type=hidden name=delete value=view%d_isTable>
    |<input type=checkbox VALUE=1 %s name=view%d_isTable> 
    |Display view as table
    |</TD>
    |</TR>
    # print short or long field names in header
    |<TR>
    |<TD VALIGN=BOTTOM>
    |<input type=hidden name=delete value=view%d_isShortNames>
    |<input type=checkbox VALUE=1 %s name=view%d_isShortNames> 
    |Print short field names in header
    |</TD>
    |</TR>
    # common fields only
    |<TR>
    |<TD  VALIGN=TOP>
    |<INPUT TYPE=CHECKBOX NAME=isOnlyCommonFields VALUE=1 CHECKED> 
    |Show only fields common<BR>to selected root databanks
    |<P>
    |<CENTER>
    |<IMG SRC=($parStr:imgdir)/arrow_icon.gif ALIGN=MIDDLE>
    |<INPUT TYPE=submit NAME=PageViewSelectFields VALUE="Continue">
    |<INPUT TYPE=HIDDEN NAME=wwwFunctionName4 VALUE=PageViewSelectFields>
    |<P>
    |<INPUT TYPE=RESET VALUE=Reset>
    |</TD>
    |</TR>
    |</TABLE></TD>

    |<TD VALIGN=TOP NOWRAP> 
    |Select databanks for whose<BR> entries you want to define<BR> the view
    |</TD>
    |<TD NOWRAP>
    |Select databanks to be linked<BR> to displayed entries (optional)<BR>
    |</TD>
    |</TR>

    |<TR>
    |<TD ALIGN=CENTER>
    |<SELECT NAME="viewLibListRoot" MULTIPLE size=20 align=middle>
  nascentName:
    |<INPUT TYPE=hidden NAME=view%d_Name VALUE=nascent> 
  separator:
    |<OPTION> ~~~~~~~~~~~~~~~~
  rootLibsSelect:
    |<OPTION value=v%d_R_%s %s> %s
  rootLibSubentrySelect:
    |<OPTION value=v%d_R_%s_%s %s> %s_%s
  rootTrailer:
    |</SELECT>
    |</TD>
  leafHeader:
    |<TD ALIGN=CENTER>
    |<SELECT NAME="viewLibListLeaf" MULTIPLE SIZE=20>
  leafLibsSelect:
    |<OPTION value=v%d_L_%s %s> %s
  leafTrailer:
    |</SELECT>
    |</TD> 
    |</TR> 
    |</TABLE>
    |</FORM>
    |</BODY>
    |</HTML>
}

###############################################################################
#
# the "select fields" page - part II of creating views
#

$viewSelectFields={
  head:
    |<HTML>
    |<TITLE> NEWSRS View Field Select Page </TITLE>
    |<BODY ($parStr:pageColor)>
    |<P>
    |<form method=POST action="($parStr:cgidir)/wgetz">
    |<INPUT TYPE=hidden NAME=userId VALUE=($parStr:userId)>
    |<INPUT type=hidden name=delete~ value=v%d_RF_.+>
    |<INPUT type=hidden name=delete~ value=v%d_LF_.+>
    |<INPUT type=hidden name=delete~ value=v%d_Lextra_.+>
    |<INPUT type=hidden name=delete~ value=v%d_isNascent>
    |

    # help
    |<TD ALIGN=CENTER><TABLE BORDER=3><TR><TD bgcolor="#ffff00">
    |<font color="#ffffff"><A HREF=
    |"($parStr:docdir)/man/mi_srswww.html#ViewField"
    |>Help</A></TD></TR></TABLE>
    |<INPUT TYPE=HIDDEN NAME=wwwFunctionName6 VALUE=WwwPrintHelp>
    |<HR>
    |
    |<H2>Select Fields for View "%s"</H2>
    |Select fields to be appended to entries displayed and continue with
    |one of the options below
    |<P>
    |<IMG SRC=($parStr:imgdir)/arrow_icon.gif ALIGN=MIDDLE>
    |<INPUT TYPE=SUBMIT NAME=PageSelectLibrary VALUE="Top Page">
    |<INPUT TYPE=HIDDEN NAME=wwwFunctionName1 VALUE=PageSelectLibrary>
    |
    |<INPUT TYPE=SUBMIT NAME=PageQueryForm VALUE="Query Form">
    |<INPUT TYPE=HIDDEN NAME=wwwFunctionName2 VALUE=PageQueryForm>
    |
    |<INPUT TYPE=SUBMIT NAME=PageQueryManager VALUE="Query Manager">
    |<INPUT TYPE=HIDDEN NAME=wwwFunctionName3 VALUE=PageQueryManager>
    |
    |<INPUT TYPE=SUBMIT NAME=PageViewManager VALUE="View Manager">
    |<INPUT TYPE=HIDDEN NAME=wwwFunctionName4 VALUE=PageViewManager>
    |<HR>
    |<P>
    |<TABLE><TR><TD ALIGN=CENTER>
    |<TABLE BORDER=3> 
  root:{   
    lib:{
      head:
        |<TR><TH>
        |<font size=5>
      name:
        |<A HREF="($parStr:cgidir)/wgetz?\
        |-id+($parStr:userId)+-fun+Pagelibinfo+-info+%s">
        |<B>%s</B></A>
      tail:
        |</TH></TR><TR><TD><TABLE noborder>
    }
    rowBeg: |<TR>
    rowEnd: |</TR>
    newRow: |</TR> <TR>
    fieldHeader:
      |<TD COLSPAN=%d><HR><B>%s</B></TD></TR><TR>
    field:
      |<TD><input type=checkbox name="v%d_RF_%s" value=1 %s>&nbsp;\
      |<A HREF=
      |"($parStr:cgidir)/wgetz?-fun+PageIndexBrowseOpt+-bf+%s+-lib+%s">\
      |%s</A>\
    format:{
      head: |<SELECT NAME=v%d_RF_%s_format>
      name: |<OPTION %s>%s
      tail: |</SELECT>\
    }
    fieldTail:|</TD>
    tail:
      |</TABLE></TD></TR>
      |</TABLE>
      |<P>
  }
  leaf:{
    head:
      |<TABLE border=3>
      |<TR><TH>
      |%30.*s 
      |<font size=5><A HREF="($parStr:cgidir)/wgetz?\
      |-id+($parStr:userId)+-fun+Pagelibinfo+-info+%s">
      |<B>%s</B></a> </font>
      |</TH></TR>
      |
      |
      |<TR><TD>
      |<TABLE NOBORDER  CELLSPACING=1>
      |<TR>
    newRow: |</TR> <TR>
    fieldHeader:
      |<TD COLSPAN=%d><HR><B>%s</B></TD></TR><TR>
    field:
      |<TD nowrap><input type=checkbox name="v%d_LF_%s_%s" value=1 %s>\
      |<A HREF=
      |"($parStr:cgidir)/wgetz?-fun+PageIndexBrowseOpt+-bf+%s+-lib+%s">
      |%s</A>%s
    format:{
      head: |<SELECT NAME=v%d_LF_%s_%s_format>
      name: |<OPTION %s> %s
      tail: |</SELECT>
    }
    fieldTail:|</TD>
    extraOptions:
      |</TR>
      |</TABLE></TD></TR>
      |
      |<TR><TD><table noborder cellpadding=0 cellspacing=0>
      |<TR>
      |<TD>
      |&nbsp;<img src="($parStr:imgdir)/redball.gif">
      |</TD>
      |<TD>
      |Use query 
      |instead link 
      |<input size=30 NAME=v%d_Lextra_%s_query VALUE=%s>
      |</TD></TR>
      |<TR>
      |<TD>
      |&nbsp;<img src="($parStr:imgdir)/redball.gif">
      |</TD>
      |<TD>
    selectView:{
       head:
         |use view to display entries 
         |<SELECT NAME=v%d_Lextra_%s_view>
         |<OPTION VALUE="" %s>none
       name:
         |<OPTION %s>%s
       tail:
         |</SELECT>
    }
    tail:
      |</TD>
      |</tr>
#      |<TR>
#      |<TD>
#      |&nbsp;<img src="($parStr:imgdir)/redball.gif">
#      |</TD>
#      |<TD>
#      |Input form for
#      |<SELECT>
#      |<OPTION> none 
#      |<OPTION> Sequence analysis
#      |<OPTION> Statistics
#      |</SELECT>
#      |</TD>
#      |</TR>
      |<TR>
      |<tD>
      |&nbsp;<img src="($parStr:imgdir)/redball.gif">
      |</TD>
      |<TD>
      |Display only number of linked entries
      |<input NAME=v%d_Lextra_%s_onlyEntryN VALUE=1 type=checkbox %s></TD>
      |
      |</TR>
      |</TABLE>
      |</TD>
      |</TR>
      |</TABLE>
      |
      |<p>
  }
  tail:
    |</TD></TR></TABLE>
    |<font>
    |<INPUT TYPE=reset value="Reset"> 
    |</FORM>
    |</BODY>
    |</HTML>
}


###############################################################################
#
# the queryResult page
#
$queryResult={
  head:
    |<TITLE> QueryResult </TITLE>
    |<BODY ($parStr:pageColor)>
    |<form method=POST action=($parStr:cgidir)/wgetz>
    |<INPUT TYPE=hidden NAME=userId VALUE=($parStr:userId)>
  title:
    |<i> <a name=top> Query </a></i><b>"%s"</b> found  %d entries</a>
    |<input type=hidden name=numberOfEntries value=%d><p>
  options:{
    head:
#      |<TABLE border><TR><TD>
      |<INPUT TYPE=HIDDEN NAME=linkSetNumber~ VALUE=%d>
      |<INPUT TYPE=HIDDEN NAME=viewEntriesChunkSize VALUE=%d>
      |<INPUT TYPE=HIDDEN NAME=queryNumber VALUE=%d>
      |<TABLE><TR><TD nowrap>
      |<I>Perform operation<BR>on selected entries</I><BR>
      |</TD>
      |<TD>
      |<IMG SRC=($parStr:imgdir)/redball.gif >
      |<input type=submit name=PageLinkOpt value="link">
      |<input type=hidden name=wwwFunctionName8 value=PageLinkOpt>
      |</TD><TD>
    launch:{
      head:
  	|<IMG SRC=($parStr:imgdir)/redball.gif >
  	|<input type=submit name=PageLaunchAppl~ value="launch">
  	|<input type=hidden name=wwwFunctionName11~ 
  	|value=PageLaunchAppl>
  	|<SELECT NAME=applicationName~>
      appl:
  	|<OPTION>%s
      tail:
  	|</SELECT>
    }
    download:
      |</TD>
      |</TR><TR>

      |<TD>
      |<input type=reset value="Reset">
      |</TD>

      |<TD nowrap>
      |<IMG SRC=($parStr:imgdir)/redball.gif >
      |<input type=submit name=PageDownloadSetOpt~ value="save">
      |<input type=hidden name=wwwFunctionName9~ value=PageDownloadSetOpt>
      |</TD>
      |<TD nowrap>
      |<IMG SRC=($parStr:imgdir)/redball.gif >
      |<input type=submit name=PageViewSelectedEntries value="view">
      |<input type=hidden name=wwwFunctionName10~ 
      |value=PageViewSelectedEntries>
    selectView:{
       head:
  	 | with 
  	 |<SELECT NAME=viewNumber>
       name:
  	 |<OPTION VALUE=%d %s> %s
       tail:
  	 |</SELECT></TD><TD nowrap>
    }
    tail:
      |</TD></TR></TABLE>
      |<P>
  }
  entriesStart:
    |
  tail:
    |</FORM>
    |</BODY>
    |</HTML>
} 

# to be placed at the bottom of the query result page
$chunkSet={
  head:
    |<P>
    |<i> go to entries in chunk</i>
    |<A HREF=wgetz?%s-lset+%d+-bv+1+-lv+%d+-fun+PageMoreEntries+-vn+%d> \
    |[</A> .. 
  current:
    |<A HREF=wgetz?%s-lset+%d+-bv+%d+-lv+%d+-fun+PageMoreEntries+-vn+%d>
    |<B>(%d)</B></A>..
  other:
    |<A HREF=wgetz?%s-lset+%d+-bv+%d+-lv+%d+-fun+PageMoreEntries+-vn+%d>
    |<B>%d</B></A> .. 
  tail:
    |<A HREF=wgetz?%s-lset+%d+-bv+%d+-lv+%d+-fun+PageMoreEntries+-vn+%d> ]</A>
}

#   |</BLOCKQUOTE>


###############################################################################
#
#
#  the querymanager page
#
#
#
$queryManager={
   head:
    |<HTML>
    |<TITLE> NEWSRS Query Manager Page </TITLE>
    |<BODY ($parStr:pageColor)>

    |<FORM METHOD=POST  ACTION="wgetz">
    |<INPUT TYPE=hidden NAME=userId VALUE=($parStr:userId)>
    |<INPUT TYPE=HIDDEN NAME=delete VALUE=QueryCom.+>
  queryOptions:{
    html3:{
      head:
      |<P>
      |<TABLE>

      |<TR>
      |<TD COLSPAN=3 VALIGN=BOTTOM>
      |Use one of the six options <BR>on one or more selected queries.
      |</TD>
      |<TD VALIGN=BOTTOM ROWSPAN=2>
      |<textarea name=expr rows=3 cols=25></textarea>
      |</TD>
      |</TR>

      |<TR>
      |<TD VALIGN=bottom>
      |<IMG SRC="($parStr:imgdir)/redball.gif">&nbsp;\
      |<input type=submit name=PageDownloadSetOpt value="SAVE">
      |<input type=hidden name=wwwFunctionName9 value=PageDownloadSetOpt>
      |</TD>

      |<TD VALIGN=bottom>
      |<IMG SRC="($parStr:imgdir)/redball.gif">&nbsp;\
      |<INPUT TYPE=SUBMIT NAME=PageQueryManager VALUE="DELETE"> 
      |<INPUT TYPE=HIDDEN NAME=wwwFunctionName10~ VALUE=PageQueryManager>
      |</TD>

      |<TD VALIGN=BOTTOM>
      |<IMG SRC="($parStr:imgdir)/redball.gif">&nbsp;\
      |<INPUT TYPE=SUBMIT NAME=PageQueryExpression VALUE=EXPRESSION> 
      |<INPUT TYPE=HIDDEN NAME=wwwFunctionName11~ VALUE=PageQueryExpression>
      |</TD>
      |</TR>

      |<TR>
      |<TD VALIGN=TOP>
      |<IMG SRC="($parStr:imgdir)/redball.gif">&nbsp;\
      |<INPUT TYPE=SUBMIT NAME=PageReinspectQuery VALUE="VIEW"> 
      |<INPUT TYPE=HIDDEN NAME=wwwFunctionName12~ VALUE=PageReinspectQuery>
      |</TD>

      |<TD VALIGN=TOP>
      |<IMG SRC="($parStr:imgdir)/redball.gif">&nbsp;\
      |<input type=submit name=PageLinkOpt value="LINK">
      |<input type=hidden name=wwwFunctionName13 value=PageLinkOpt>
      |</TD>

      |<TD VALIGN=TOP>
      |<IMG SRC="($parStr:imgdir)/redball.gif">&nbsp;\
      |<INPUT TYPE=SUBMIT NAME=PageCombineQueries VALUE="COMBINE"> 
      |<INPUT TYPE=HIDDEN NAME=wwwFunctionName14 VALUE=PageCombineQueries>
      |</TD>
      |<TD VALIGN=BOTTOM>
      |select queries with
      |<SELECT NAME=operator>
      |<OPTION SELECTED> AND
      |<OPTION SELECTED> OR
      |<OPTION SELECTED> BUTNOT 
      |</SELECT>
      |</TD>
      |</TR>

      |</TABLE>
      |<P>
    queryInfo:{
        head:
          |<P>
   	  |<TABLE border>
   	  |<TR><TH COLSPAN=7>Successful Queries</TH></TR>
   	  |<TR>
   	  |<TH><FONT SIZE=-1>Name</TH>
   	  |<TH><FONT SIZE=-1>Type</TH>
   	  |<TH><FONT SIZE=-1>N<BR>total 
   	  |</TH>
   	  |<TH>
   	  |<FONT SIZE=-1>From Library
   	  |</TH>
   	  |<TH>
   	  |N
   	  |</TH>
   	  |<TH>
   	  |<FONT SIZE=-1>Query Expression
   	  |</TH>
   	  |<TH>
   	  |<FONT SIZE=-1>Comment
   	  |</TH>
   	  |</TR>
   	  |<TR>
        title:
          |<TD valign=top>
          |<INPUT TYPE="checkbox" NAME="qmstr%d~" VALUE=%s>&nbsp;\
          |<font size=4><B>%s</B></font>
          |</TD>
          |<TD valign=top>
          |<I>%s</I>
          |</TD>
          |<TD align=right valign=top>
          |%d
          |</TD>
        numAlign:
          |</TD>
          |<TD align=right valign=top>
        libAlign:
          |<TD valign=top>
        queryStr:
          |</TD>
          |<TD align=left>
          |<FONT SIZE=-1><textarea  rows=1 cols=30>%s</textarea></TD>
          |<TD VALIGN=TOP><FONT SIZE=-1>\
          |<input size=25 name=QueryComm%d value="%s"><BR>
        library:
          |%s<BR>\
        entryN:
          |%d<BR>\
        subEntry:
          | <CENTER><I>set of subentries</I> </CENTER>
        rowEnd:
          |</TD>
          |</TR>
   	}
   }
   html2:{
    head:
      |<IMG SRC=($parStr:imgdir)/redball.gif ALIGN=MIDDLE>
      |<INPUT TYPE=SUBMIT NAME=PageCombineQueries VALUE="   COMBINE   "> 
      |<INPUT TYPE=HIDDEN NAME=wwwFunctionName7 VALUE=PageCombineQueries>
      |&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      |<I>selected queries with</I>
      |&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      |<SELECT NAME=operator>
      |<OPTION SELECTED> AND
      |<OPTION> OR
      |<OPTION> BUTNOT
      |</SELECT>
      |<BR>
      |<IMG SRC=($parStr:imgdir)/redball.gif ALIGN=MIDDLE>
      |<INPUT TYPE=SUBMIT NAME=PageQueryManager VALUE="      ERASE     "> 
      |<INPUT TYPE=HIDDEN NAME=wwwFunctionName8~ VALUE=PageQueryManager>
      |&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      |<I>selected queries</I>
      |<BR>
      |<IMG SRC=($parStr:imgdir)/redball.gif ALIGN=MIDDLE>
      |<INPUT TYPE=SUBMIT NAME=PageReinspectQuery VALUE="  VIEW "> 
      |<INPUT TYPE=HIDDEN NAME=wwwFunctionName9~ VALUE=PageReinspectQuery>
      |&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      |<I>selected query </I>
      |<BR>
      |<IMG SRC=($parStr:imgdir)/redball.gif ALIGN=MIDDLE>
      |<INPUT TYPE=SUBMIT NAME=PageQueryExpression VALUE=EXPRESSION> 
      |<INPUT TYPE=HIDDEN NAME=wwwFunctionName10~ VALUE=PageQueryExpression>
      |&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
      |<textarea name=expr rows=3 cols=35></textarea>
      |<BR>
   queryInfo: {
       head:
         |<h3> Successful Queries</h3>
         |<HR>
         |<DL>
       title:
         |<DT>
         |<INPUT TYPE="checkbox" NAME="qmstr%d~" VALUE=%s> 
         |<font size=4><B>%s</B></font> 
         |(<B><I>%s</I></B>) 
         |:= <strong>" %s "</strong>
         |Total %d entries found
      numAlign: 
         |
      libAlign: |
      queryStr: |
      entryN:
         | <DD> %6d entries  from %s 
      subEntry:
         |<BR>
         |<IMG SRC=http://kappa:8000/newsrsdoc/redball.gif> set of <B>\
         |Sequence Features</B> 
     }
   }
  }
  chunkSize:{
    head:
       |Entry list in chunks of \
       |<SELECT NAME=viewEntriesChunkSize>
     size:
       |<OPTION %s> %d
     tail:
       |</SELECT>
  }      
  selectView:{
     head:
       |using&nbsp;the&nbsp;view&nbsp;\
       |<SELECT NAME=viewNumber>
     name:
       |<OPTION VALUE=%d %s> %s
     tail:
       |</SELECT>
#       |</BLOCKQUOTE>
  }
   tail:
     |</table>
     |<p>
     |<I>Save in history queries of type </I> 
     |<INPUT TYPE=checkbox CHECKED>query
     |<INPUT TYPE=checkbox CHECKED>expression
     |<INPUT TYPE=checkbox>link
     |<INPUT TYPE=checkbox>selection
     |</form>
     |</BODY>
     |</html>
}

###############################################################################
#
# the data-field browse and help page
#

$parStr:[fCellCols set:"bgcolor=\"#AA0000\"><FONT color=\"#FFFFFF\""]
$dataField={
  head:
    |<HTML>
    |<HEAD>
    |<TITLE>SRSWWW at ($parStr:siteName): Data-field information
    |</TITLE>
    |</HEAD>
    |<BODY ($parStr:pageColor)>
    |<FORM method=POST action=($parStr:cgidir)/wgetz>
  title:
    |<INPUT TYPE=hidden NAME=userId VALUE=($parStr:userId)>
    |<P><TABLE CELLPADDING=6>
    |<TR><TD VALIGN=TOP ($ParStr:fCellCols)><B>Field&nbsp;Name</B></TD><TD>
    |<H1>%s</H1>
    |</TD></TR>
  inEntry:
    |
  description:{
    headFrom:
      |<TR><TD VALIGN=TOP ($ParStr:fCellCols)><B>Description</B><BR>
      |(<I>%s</I>)</TD><TD COLSPAN=2>
    head:
      |<TR><TD VALIGN=TOP ($ParStr:fCellCols)><B>Description</B></TD>
      |<TD COLSPAN=2>
    tail:
      |</TD></TR>
  }
  fields:{
    group:{
      head:
  	|<TR><TD VALIGN=TOP ($ParStr:fCellCols)>
  	|<B>Field&nbspGroup<BR>Members</B></TD><TD  COLSPAN=2>
  	|<TABLE BORDER CELLPADDING=4><TR>
  	|<TH><FONT SIZE=-1>Databank</TH>
  	|<TH><FONT SIZE=-1>Fields in Group</TH>
  	|</TR>
      lib:
  	|<TR><TD>%s</TD><TD>
      member:
  	|<A HREF="($parStr:cgidir)/wgetz?\
  	|-fun+PageIndexBrowseOpt+-bf+%s+-lib+%s"><B>%s</B></A>
      tail:
        |</TD></TR>
    }
    head:
      |<TR><TD VALIGN=TOP ($ParStr:fCellCols)>
      |<B>Data-fields<BR>in SRS</B></TD><TD  COLSPAN=2>
      |<TABLE BORDER CELLPADDING=4><TR>
      |<TH><FONT SIZE=-1>Databank</TH>
      |<TH><FONT SIZE=-1>Name</TH>
      |<TH><FONT SIZE=-1>Short<BR>Name</TH>
      |<TH><FONT SIZE=-1>Type</TH>
      |<TH><FONT SIZE=-1>No of<BR>Keys</TH>
      |<TH NOWRAP><FONT SIZE=-1>No of Entry<BR>References</TH>
      |<TH><FONT SIZE=-1>Indexing Date</TH>
      |<TH><FONT SIZE=-1>Status</TH>
      |</TR>
    name:   |%s<BR>
    short:  |%s<BR>
    type:   |%s<BR>
    valN:   |%d<BR>
    refN:   |%d<BR>
    date:   |%s<BR>
    status: |%s<BR>
    empty:  |<BR>
    data:
      |<TR>
      |<TD>%s</TD>
      |<TD>%s</TD>
      |<TD>%s</TD>
      |<TD>%s</TD>
      |<TD ALIGN=RIGHT>%s</TD>
      |<TD ALIGN=RIGHT>%s</TD>
      |<TD ALIGN=CENTER NOWRAP>%s</TD>
      |<TD ALIGN=CENTER NOWRAP>%s</TD>
    tail:
      |</TR></TABLE></TD></TR>
  }
  browse:
    |<TR><TD VALIGN=TOP ($ParStr:fCellCols)><B>Browse&nbsp;Index</B></TD><TD>
    |<INPUT TYPE=hidden NAME="browseIndex~" VALUE=%s>
    |<INPUT TYPE=hidden NAME="browseLibs~" VALUE="%s">
    |<INPUT TYPE=hidden NAME=wwwFunctionName10~ value=PageIndexBrowse>
    |<input type=hidden name=printIndexValN value=100>
    |<TABLE><TR><TD ROWSPAN=2 VALIGN=top>
    |<input type=submit name=PageIndexBrowse VALUE="List values">
    |</TD><TD>
    |that 
    |<a href="($parStr:cgidir)/srsc?-ht+display-match">match</a>
    |<INPUT NAME="browseMatch~" SIZE=20 VALUE="*"></TD><TR>
    |<TD><TD>and occur in at least
    |<input name="minIndexValN" size=8 value="1"> entries
    |</TD></TR></TABLE>
    |</FORM>
    |</TD></TR>
  tail:
    |</TABLE>
    |</BODY>
    |</HTML>
}


###############################################################################
#
# the index Value list page
#

$browseList={
  head:
    |<HTML>
    |<BODY ($parStr:pageColor)>
    |<FORM method=POST action=($parStr:cgidir)/wgetz>
  title:
    |<H2>Values in the index of the <I>%s</I> field</H2>
    |<INPUT TYPE=hidden NAME=userId VALUE="($parStr:userId)">
    |<INPUT type=hidden NAME="minIndexValN~" VALUE="($parStr:minIndexValN)"> 
    |<INPUT type=hidden NAME="browseMatch~" VALUE="($parStr:browseMatch)"> 
    |<INPUT TYPE=hidden NAME="browseIndex~" VALUE=%s>
    |<INPUT TYPE=hidden NAME="browseLibs~" VALUE="%s">
    |<INPUT TYPE=hidden NAME="printIndexValN~" VALUE=($parStr:printIndexValN)>
    |<INPUT TYPE=hidden NAME="printIndexFirstValN~" VALUE=%d>
      |<IMG SRC=($parStr:imgdir)/redball.gif>
    |<INPUT TYPE=submit NAME=PageIndexBrowse VALUE="More Values">
    |<INPUT TYPE=hidden NAME=wwwFunctionName11 VALUE=PageIndexBrowse>
      |<IMG SRC=($parStr:imgdir)/redball.gif>
    |<INPUT TYPE=submit NAME=PageValues2Query VALUE="Make Query">
    |<INPUT TYPE=hidden NAME=wwwFunctionName12 VALUE=PageValues2Query>
    |<INPUT TYPE=reset>
    |<BLOCKQUOTE>
    |<P>
  values:{
    head:
      |<TABLE BORDER>
      |<TR><TH>Value</TH><TH>No. Entries</TH></TR>
    library:
      |<TR><TD COLSPAN=2><I>Values in %s</I></TD></TR>
    value:
      |<TR><TD>
      |<input type=checkbox name="value_%d~" value="[%s-%s:'%s']">
      |<A HREF="($parStr:cgidir)/wgetz?-f+%s+[%s-%s:'%s']">%s</A></TD> 
      |<TD ALIGN=RIGHT>%d</TD>
      |</TR>
    tail:
      |</TABLE>
      |</BLOCKQUOTE>
      |</FORM>
      |</BODY>
      |</HTML>
  }
}


###############################################################################
#
# an entry with various formats - to be included into other pages
#

$entry={
  inList:{
    envelope:{
      head: {
        head: 
          |<HTML>
          |<BODY ($parStr:pageColor)>
          |<FORM method=POST action=($parStr:cgidir)/wgetz>
          |<INPUT TYPE=HIDDEN NAME=userId VALUE=($ParStr:userId)>
#          |<TABLE BORDER=3><TR><TD>
          |<IMG SRC=($parStr:imgdir)/redball.gif >
          |<INPUT TYPE=SUBMIT NAME=PageLinkEntryOpt VALUE="link">
          |<INPUT TYPE=hidden NAME=wwwFunctionName7 VALUE=PageLinkEntryOpt>
          |<INPUT TYPE=hidden NAME=libName VALUE=%s>
          |<INPUT TYPE=hidden NAME=entryName VALUE="%s">
          |<IMG SRC=($parStr:imgdir)/redball.gif >
          |<input type=submit name=PageDownloadSetOpt~ value="save">
          |<input type=hidden name=wwwFunctionName9~ \
          |value=PageDownloadSetOpt>
          |<INPUT TYPE=HIDDEN NAME=numberOfEntries~ VALUE=1>
          |<INPUT TYPE=HIDDEN NAME=EntryNum_1~ VALUE="%s">
    	launch:{
    	  head:
    	    |<IMG SRC=($parStr:imgdir)/redball.gif >
    	    |<input type=submit name=PageLaunchAppl~ value="launch">
    	    |<input type=hidden name=wwwFunctionName8~ 
    	    |value=PageLaunchAppl>
    	    |<SELECT NAME=applicationName~>
    	  appl:
    	    |<OPTION>%s
    	  tail:
    	    |</SELECT>
        }
        selectView:{
          head:
    	    |<IMG SRC=($parStr:imgdir)/redball.gif>
            |<INPUT TYPE=SUBMIT NAME=PageViewSelectedEntries VALUE="view">
            |<INPUT TYPE=HIDDEN NAME=wwwFunctionName10~ \
            |VALUE=PageViewSelectedEntries>
            |<SELECT NAME=viewNumber>
          name:
            |<OPTION VALUE=%d %s> %s
          tail:
            |</SELECT>
        }
        tail:
#          |</TD></TR></TABLE>
          |<HR>
          |</FORM>
        preformatted: |<PRE>\
        topicList:    |<DL>
        table:        |<TABLE BORDER=0>
        table2:       |<TABLE BORDER=1>
        text:         |\
      }
      tail: {
        preformatted: |</PRE>
        topicList:    |</DL>\
        table:        |</TABLE>
        table2:       |</TABLE>
        text:         |\
      }
    }
    entry:{
      name:
  	|<BR>
  	|<input type=checkbox name=EntryNum_%d~ value="%s:%s">
  	|<a href=($parStr:cgidir)/wgetz?\
  	|($parStr:userIdOpt)-e+[%s-id:"%s"]>
  	|%s:%s</a>
      inListNoId:
  	|<BR>
  	|<a href=($parStr:cgidir)/wgetz?($parStr:userIdOpt)-e+%s>
  	|%s:%s</a>
      rootName:
  	|<BR><input type=checkbox name=EntryNum_%d~ value="%s">
  	|<a href="($parStr:cgidir)/wgetz?\
  	|($parStr:userIdOpt)-e+%s">\
  	|%s</a>
      leafName:
  	|<BR>
  	|<IMG SRC=($parStr:imgdir)/linked_icon.gif>
  	| <a href="($parStr:cgidir)/wgetz?\
  	|($parStr:userIdOpt)-e+%s">\
  	|%s</a>
      head:''
      tail:''
    }
  }  
  inTable:{
    head:
      |<TABLE BORDER CELLPADDING=2 CELLSPACING>
      |<TR>                                                       
    title:{
      library: |<TH ($parStr:cellColor)>%s</TH>
      field:   |<TD ALIGN=CENTER ($parStr:cellColor)>
               |<A HREF="($parStr:cgidir)/wgetz?\
               |($parStr:userIdOpt)-fun+pageindexbrowseopt+-lib+%s+-bf+%s">
               |<I>%s</I></A></TD>
      tail:    |</TR>
    }
    entry:{
      head: '<TR>'
      tail: '</TR>'
      rootNameManyLibs: 
  	|<TD VALIGN=top ($parStr:cellColor) ROWSPAN=%d nowrap>
        |<input type=checkbox name=EntryNum_%d~ value="%s">&nbsp;\
  	|<a href="($parStr:cgidir)/wgetz?\
        |($parStr:userIdOpt)-e+%s">%s:%s</a>\
  	|</TD>
      leafName: 
  	|<TD VALIGN=top ($parStr:cellColor) ROWSPAN=%d>
  	|<a href=($parStr:cgidir)/wgetz?\
        |($parStr:userIdOpt)-e+%s>%s</a>\
  	|</TD>
      value:{
  	leftAlign:  |<TD valign=top ALIGN=left ROWSPAN=%d>
  	rightAlign: |<TD valign=top ALIGN=right ROWSPAN=%d>
  	center:     |<TD valign=top ALIGN=middle ROWSPAN=%d>
  	listing:    |<TD VALIGN=top ROWSPAN=%d><LISTING>
  	preformat:    |<TD VALIGN=top ROWSPAN=%d><PRE>
  	value:      |%s\
        empty:      |&nbsp;
        next:       |<BR>\
  	tail:       |</TD>
      }
      emptyValue:   |<TD ROWSPAN=%d></TD>
      onlyEntryN:
        |<TD ALIGN=RIGHT VALIGN=TOP ROWSPAN=%d>
        |<A HREF="($parStr:cgidir)/wgetz?\
        |($parStr:userIdOpt)-sl+-vn+%d+%s"><B>%d</B></A> </TD>
    }
    tail:
      |</TABLE>
  }
}

###############################################################################
#
#
#    the view manager page
#
#

$viewManager={
    head:
      |<HTML>
      |<HEAD>
      |<SCRIPT LANGUAGE='JavaScript'>
      |
      |<!--
      |
      |function opensearch() {
      |  window.name="mainsrs"
      |  str="($parStr:cgidir)/wgetz?\
      |-id+($parStr:userId)+-fun+pageviewmanager";
      |  searchWin = window.open(str,'searchWin','resizable=yes,width=50,\
      |  height=50,status=no,location=no,toolbar=no');
      |}
      |
      |//-->
      |</SCRIPT>
      |
      |<TITLE>Welcome to bla</TITLE>
      |</HEAD>
      |<TITLE>:SRS: NEWSRS VIEW Manager Page </TITLE>
      |<BODY ($parStr:pageColor)>
      |<FORM METHOD=POST ACTION="wgetz">
      |<input type=hidden name=userId value=($parStr:userId)>
      |
    actions:
      |<!better end the form - view manager button deletes selected views!>
      |</FORM>
      |<FORM METHOD=POST ACTION="wgetz">
      |<input type=hidden name=userId value=($parStr:userId)>
      |Click here with middle mouse button 
      |<INPUT TYPE=Button onClick="opensearch()" 
      |VALUE="Independent View Manager">
      |<P>
      |<TABLE>
      |<TR>
      |<TD>
      |<IMG SRC=($parStr:imgdir)/redball.gif>
      |</TD>
      |<TD>
      |<INPUT TYPE=SUBMIT NAME=PageViewMgrCreate VALUE="CREATE">
      |<INPUT TYPE=hidden NAME=wwwFunctionName7 VALUE=PageViewMgrCreate>
      |</TD><TD>a new view</TD></TR>
      |
      |<TR><TD>
      |<IMG SRC=($parStr:imgdir)/redball.gif>
      |</TD><TD>
      |<INPUT TYPE=SUBMIT NAME=PageViewEdit VALUE="   EDIT   "></TD>
      |<INPUT TYPE=hidden NAME=wwwFunctionName8 VALUE=PageViewEdit>
      |<TD>selected view</TD></TR>
      |
      |<TR><TD><IMG SRC=($parStr:imgdir)/redball.gif></TD>
      |<TD><INPUT TYPE=SUBMIT NAME=PageViewManager VALUE=DELETE></TD> 
      |<INPUT TYPE=hidden NAME=wwwFunctionName9 VALUE=PageViewManager>
      |<TD>selected view</TD>
      |</TR></TABLE>
      |<P>
      |<TABLE BORDER>
      |<TR>
      |<TH COLSPAN=9>List of Views</TH>
      |</TR>
      |<TR> 
      |<TH ROWSPAN=2>View Name</TH>
      |<TH ROWSPAN=2>Format</TH>
      |<TH COLSPAN=2>Root</TH>
      |<TH COLSPAN=5>Leaves</TH></TR>
      |<TR>
      |<TH><FONT SIZE=-1>Libraries</TH>
      |<TH><FONT SIZE=-1>Fields</TH>
      |<TH><FONT SIZE=-1>Libraries</TH>
      |<TH><FONT SIZE=-1>Fields</TH>
      |<TH><FONT SIZE=-1>Query</TH>
      |<TH><FONT SIZE=-1>View</TH>
      |<TH><FONT SIZE=-1>Comment</TH>
      |</TR>
  viewList:{
    head:
      |<TR>
      |<TD  VALIGN=top rowspan=%d>
      |<input type=checkbox name=selectedViewNo_%d~ value="%s">&nbsp;%s
      |</TD>
      |<TD  VALIGN=top ALIGN=MIDDLE ROWSPAN=%d>
      |%s
    shortNames:
      |<BR><I>(short field names)</i>
      |</TD>
      |<TD  VALIGN=top ROWSPAN=%d>
    longNames:
      |</TD>
      |<TD  VALIGN=top ROWSPAN=%d>
    root:
      |%s<BR>
    rootField:
      |%s<BR>\
    tableData:
      |</TD>
      |<TD  VALIGN=top, ROWSPAN=%d>
    tableDataEnd:
      |</TD>
    format:
      |(<I>%s</I>)
    leaf:{
      lib:
        |<TD VALIGN=top>%s</TD><TD VALIGN=TOP> 
      field:
        |%s<BR>
      format:
        |(<I>%s</I>)
      query:
        |</TD><TD VALIGN=TOP>%s</TD>
      view:
        |</TD><TD VALIGN=TOP>%s</TD>
      onlyEntryN:
        |<TD VALIGN=TOP><I>display No of linked&nbsp;entries</I></TD>
      noComment:
        |<TD>&nbsp;</TD>
    }
    emptyCell:
      |</TD><TD>&nbsp;</TD>
    separator: 
      |<HR>
    rowEnd: 
      |</TR><TR>
    tail:
      | </TD>
      |</TR>
  }
  tail:
    |</TABLE>
    |</FORM>
    |</BODY>
    |</HTML>
}

###############################################################################
#
#    the link page
#

$linkPage={
  head:
    |<HTML>
    |<HEAD>
    |<TITLE>LINK  Page </TITLE> 
    |</HEAD>
    |<BODY  ($parStr:pageColor)>
    |<form method=POST action="($parStr:cgidir)/wgetz">
    |<input type="hidden" name = "fieldList" value = "reset">
    |<INPUT TYPE=hidden NAME=userId VALUE=($parStr:userId)>
    |<INPUT TYPE="hidden" NAME="queryString" VALUE="%s">
    |<INPUT TYPE=HIDDEN NAME=listEntriesStartN value=1>
  linkEntry:
    |<H3>Link entry "%s:%s" to other databanks</H3>
    |<IMG SRC=($parStr:imgdir)/arrow_icon.gif ALIGN=MIDDLE>
    |<INPUT TYPE="hidden" NAME="libName" VALUE="%s">
    |<INPUT TYPE="hidden" NAME="entryName" VALUE="%s">
    |<INPUT TYPE=SUBMIT NAME=PageLinkToLibs VALUE="Continue">
    |<INPUT TYPE=hidden NAME=wwwFunctionName8 VALUE=PageLinkToLibs>
    |<INPUT TYPE=RESET VALUE="Reset"><P>
  linkType:
    |<INPUT TYPE=HIDDEN NAME="linkSetNumber~" VALUE=%d>
    |<TABLE NOBORDER>
    |<TR><TD ROWSPAN=3>
    |<i> Find<BR>all<BR> entries </i>
    |</TD>
    |<TD>
    |<input type=radio name=linkSetType~ value="toLib"  CHECKED>
    |</TD>
    |<TD>
    |in the selected <B>databanks</B> which are linked to the current set 
    |</TD>
    |<TD valign=top ROWSPAN=3><IMG SRC=($parStr:imgdir)/linkopts.gif></TD>
    |</TR>
    |<TR><TD>
    |<input type=radio name=linkSetType~ value="toSet">
    |</TD>
    |<TD>
    |in the current <B>set</B> which are linked to <B>all</B> 
    |selected databanks 
    |</TD></TR>
    |<TR><TD>
    |<input type=radio name=linkSetType~ value="notToSet"> 
    |</TD>
    |<TD>
    |in the current <B>set</B> which are <B>not</B> linked to <B>any</B> of 
    |the selected 
    |databanks
    |</TD>
    |</TR></TABLE>
#    |<input type=radio name=linkSetType~ value="linkStat"> 
#    |Display a table with linking statistics <BR>
    |<P>
    |<IMG SRC=($parStr:imgdir)/arrow_icon.gif ALIGN=MIDDLE>
    |<INPUT TYPE=SUBMIT NAME=PageLinkToLibs VALUE="Continue">
    |<INPUT TYPE=hidden NAME=wwwFunctionName8 VALUE=PageLinkToLibs>
    |<INPUT TYPE=RESET VALUE="Reset"><P>
    |
  html3:{
    dbGroup:
      |<HR>
      |<b>%s</b>
      |<TABLE noborder cellspacing=1>
      |<TR>
    newRow:
      |</TR> 
      |<TR>
    library:
      |<TD><input type = "checkbox" name= "%sLink~" value="1" %s></TD>
      |<TD><A HREF="($parStr:cgidir)/wgetz?\
      |-id+($parStr:userId)+-fun+Pagelibinfo+-info+%s">%s</a>
      |%s</TD>
    tail:
      |</TR>
      |</TABLE>
  }
  html2:{
    dbGroup:
      |<PRE>
      |%s</b>
    newRow:
      |<BR>
    library:
      |<input type = "checkbox" name= "%sLink~" value="1" %s> \
      |<A HREF="%(cgidir)/wgetz?\
      |-id+($parStr:userId)+-fun+Pagelibinfo+-info+%s">%s</a>%-%(l)s \
    tail: ''
  }
  tail:
    |</FORM>
    |</BODY>
    |</HTML>
}



###############################################################################
#
# the "buttons" part that most pages have at the top
#
$buttons={
  head:
    |<TABLE><TR>
  busy:
    |<TD><TABLE><TR><TD bgcolor="#ffff00">
    |<FONT size=-1 COLOR="#FF0000"><i>job<BR>pending</i></TD></TR></TABLE></TD>
  completed:
    |<TD><A HREF=asf>job<BR>completed</A></TD>
  help: {
    head:
      |<TD ALIGN=CENTER><TABLE BORDER=3><TR><TD bgcolor="#ffff00">
      |<font color="#ffffff"><A HREF=
    queryManager:
      |"($parStr:docdir)/man/mi_srswww.html#QueryManager"
    viewManager:
      |"($parStr:docdir)/man/mi_srswww.html#ViewManager"
    browseIndex:
      |"($parStr:docdir)/man/mi_srswww.html#browseIndex"
    createView:
      |"($parStr:docdir)/man/mi_srswww.html#CreateView"
    editView:
      |"($parStr:docdir)/man/mi_srswww.html#editView"
    viewField:
      |"($parStr:docdir)/man/mi_srswww.html#ViewField"
    query: 
      |"($parStr:docdir)/man/mi_srswww.html#QueryForm"
    databanks:
      |"($parStr:docdir)/man/mi_srswww.html#databanks"
    links:
      |"($parStr:docdir)/man/mi_srswww.html#Link"
    default: 
      |"($parStr:docdir)/man/mi_srswww.html"
    top: 
      |"($parStr:docdir)/man/mi_srswww.html#Top"
    tail:
      |>Help</A></TD></TR></TABLE></TD>
  }
  databank:
    |<TD ALIGN=CENTER>
    |<INPUT TYPE=SUBMIT NAME=PageLibList~ VALUE="Databanks">
    |<INPUT TYPE=HIDDEN NAME=wwwFunctionName2~ VALUE=PageLibList>
    | </TD>
  selectDatabanks:
    |<TD ALIGN=CENTER>
    |<INPUT TYPE=SUBMIT NAME=PageSelectLibrary~ VALUE="Top Page">
    |<INPUT TYPE=HIDDEN NAME=wwwFunctionName3~ VALUE=PageSelectLibrary>
    | </TD>
  queryForm:
    |<TD ALIGN=CENTER>
    |<INPUT TYPE=SUBMIT NAME=PageQueryForm~ VALUE="Query Form">
    |<INPUT TYPE=HIDDEN NAME=wwwFunctionName4~ VALUE=PageQueryForm>
    | </TD>
  queryManager:
    |<TD ALIGN=CENTER>
    |<INPUT TYPE=SUBMIT NAME=PageQueryManager~ VALUE="Query Manager">
    |<INPUT TYPE=HIDDEN NAME=wwwFunctionName5~ VALUE=PageQueryManager>
    | </TD>
  oops:
    |<TD ALIGN=CENTER>
    |<INPUT TYPE=SUBMIT NAME=WwwGetMessage~ VALUE="Oops!">
    |<INPUT TYPE=HIDDEN NAME=wwwFunctionName6~ VALUE=WwwGetMessage>
    | </TD>
  views:
    |<TD ALIGN=CENTER>
    |<INPUT TYPE=SUBMIT NAME=PageViewManager~ VALUE="View Manager">
    |<INPUT TYPE=HIDDEN NAME=wwwFunctionName7~ VALUE=PageViewManager>
    |</TD>
  tail:
    |</TR></TABLE>
    |<HR>
}



###############################################################################
#
# messages printed during execution
#

$messages={
  head:
    |<HTML>
    |<BODY  ($parStr:pageColor)>
  parseError:
    |<TABLE>
    |<TR><TD ALIGN=LEFT>
    |<IMG SRC=($parStr:imgdir)/achtung.gif ALIGN=middle></TD></TR>
    |<TR><TD><font size=+2>%s</TD></TR>
    |<TR><TD><PRE>%s</PRE></TD></TR>
    |</TABLE>
  error:
    |<TABLE>
    |<TR><TD ALIGN=LEFT>
    |<IMG SRC=($parStr:imgdir)/achtung.gif ALIGN=middle></TD></TR>
    |<TR><TD><font size=+2>%s</TD></TR>
    |<TR><TD>%s</TD></TR>
    |</TABLE>
  info:
    |<H2>Information:</H2><P>
    |%s, %s<P>
}

#################################################################
#
#   arglist
#  

$argListOption={
    header:
      | </PRE><DL>
    option:
      |<DT><B>%s</B>
      |<DD> %s 
      |<P>
}


###############################################################################
#
#  link set result 
#


$linkSet={
   head: 
     |<HTML>
     |<TITLE> SRS link result page </TITLE>
     |<BODY  ($parStr:pageColor)>
     |<FORM METHOD=POST ACTION="wgetz">
     |<INPUT TYPE=hidden NAME=userId VALUE=($parStr:userId)>
   tableHead:
     |<TABLE BORDER>
     |<TR><TH COLSPAN=4> Link result for the set <i> %s </i> </TH> </TR>
     |<TR>
     |  <TH align=center><b> Selected Databanks </TH> 
     |  <TH align=center> Entries in set<BR> Linked with Databanks</TH>
     |  <TH align=center> Databank entries<BR> Linked with set</TH>
     |  <TH align=center> Entries in set<BR> <b>NOT</B> 
     |                    <BR> linked with Databank</TH>
     |</TR>
  libName:
     |<TD>
     |&nbsp;&nbsp;<input type=checkbox name=linkLibs_%d~ value=%s>
     |<T> %s </T> </TD>
  libEntriesH:
     |<TD align=right> <a href=wgetz?\
     |-id+%s+-lset+%d+-fun+PageMoreEntries>%d</A></TD>
  libEntries:
     |<TD align=right> %d </TD>
  endRow:
     |</TR>
  newRow:
     |<TR>
  tail:
     |</TABLE>
     |<P>
     |</FORM>
     |</BODY>
     |</HTML>
}


###############################################################################
#
#
#  the refine output page
#
#

$downloadSet={
    head:
      |<HTML>
      |<HEAD>
      |<TITLE> SRS:Download query </TITLE>
      |</HEAD>
      |<BODY  ($parStr:pageColor)>
      |<FORM METHOD=POST ACTION=($parStr:cgidir)/wgetz>
      |<INPUT TYPE=HIDDEN NAME=wwwFunctionName10~ VALUE=PageDownloadSet>
      |<INPUT TYPE=HIDDEN NAME=userId VALUE=($parStr:userId)>
#      |<IMG SRC=($parStr:imgdir)/constrct.gif ALIGN=middle><p><font size=+2>
#      |<I>Sorry, this page is still under construction,<BR> none of the 
#      |options work yet.</font></I><p>
   inputInfo:{
      html3:{
        shift:
          |<P>
          |Additional options for saving sequence features:
          |<BLOCKQUOTE>
          |<TABLE BORDER=3><TR><TD>
          |<TABLE noborder>
          |<TR>
          |<TD>shift begin
          |<input name=shiftbeginpos size=5 value=%s>
          |</TD>
          |<TD>shift end
          |<input name=shiftendpos size=5 value=%s>
          |</TD>
          |</TR>
          |<TD>
          |<SELECT NAME=checkbegin>
          |<OPTION SELECTED> relative to begin position
          |<OPTION SELECTED> relative to end position
          |</SELECT>
          |</TD>
          |<TD>
          |<SELECT NAME=checkend>
          |<OPTION SELECTED> relative to begin position
          |<OPTION SELECTED> relative to end position
          |</SELECT>
          |</TD>
          |</TR>
          |</TABLE>
      }
      html2:{
        shift:
           |<BLOCKQUOTE>
           |<PRE>
           |shift begin \
           |<input name=shiftbeginpos size=5 value=%s> \
           |		       shift end \
           |<input name=shiftendpos size=5 value=%s>
           |<SELECT NAME=checkbegin>
           |<OPTION SELECTED> relative to begin position
           |<OPTION SELECTED> relative to end position
           |</SELECT> \
           |<SELECT NAME=checkend>
           |<OPTION SELECTED> relative to begin position
           |<OPTION SELECTED> relative to end position
           |</SELECT>
           |</BLOCKQUOTE>
           |<P>
           |</PRE>
     }
   }
   unComplete:   
       |<INPUT TYPE=CHECKBOX NAME=takeuncompletefeature value=on checked> \
       |reject incomplete features 
       |<BR>
       |<INPUT TYPE=CHECKBOX NAME=takeuncompleteshiftfeature value=on checked>\
       |reject incomplete shifted features 
       |</TD>
       |</TR>
       |</TABLE>
       |</BLOCKQUOTE>
   seqFormat:
       |<BLOCKQUOTE>
       |List sequences with 
       |<SELECT NAME="seqFormat">
       |<OPTION %s> PIR
       |<OPTION %s> GCG
       |<OPTION %s> FASTA
       |<OPTION %s> EMBL
       |<OPTION %s> SWISSPROT
       |</SELECT> 
       |format.
       |</BLOCKQUOTE>
   mime:{
     head:
       |<TABLE><TR><TD>
       |Download chunk with entries
       |<SELECT NAME=viewEntriesBlock>
     size:
       |<option %s>%d - %d
     tail:
       |</SELECT></TD><TD>&nbsp;</TD></TR>
   }
   useMime:''
#     |<HR>
#     |<input type=checkbox name=useMime value=1 %s> Use MIME type 
#     |(for downloading the result to your local directory!)
#     |<BLOCKQUOTE>
#     |Local Directory Name <input name=localDirName size=30 value=%s><BR>
#     |<I>If you do not have client support srsmime, fetch a copy of 
#     |<a href=/newsrs/wgetz?-fun+WwwPrintHelpAbout+-ht+MIME-FETCH-SOURCE>\
#     |srsmime.c</A></I>
#     |</BLOCKQUOTE>
    selectView:{
       head:
         |<TR><TD VALIGN=TOP>
  	 |Use view 
  	 |<SELECT NAME=viewNumber>
  	 |<OPTION VALUE= SELECTED> * Complete Entries *
       name:
  	 |<OPTION VALUE=%d %s> %s
       tail:
  	 |</SELECT></TD>
    }
   tail:
     |<TD>
     |<INPUT TYPE=CHECKBOX NAME=saveTableAsAscii VALUE=1> Save table as
     |ASCII table with <BR>
     |column separator
     |<SELECT><OPTION>tab character</SELECT>
     |<BR>
     |record separator
     |<SELECT><OPTION>line feed character</SELECT><P>
     |</TD>
     |</TR></TABLE>
     |<INPUT TYPE=hidden NAME=listSetNumber VALUE=%d>
     |<HR>
     |<IMG SRC=($parStr:imgdir)/arrow_icon.gif ALIGN=MIDDLE>
     |<input type=submit  NAME=PageDownloadSet~ value="SAVE"> 
     |<input type=Reset value=Reset>  
     |</FORM>
     |</BODY>
     |</HTML>
}


###############################################################################
#
#   the list refined page
#


$listRefined={
   head:
     |Content-type: application/srsresult
     |
     |
     |
   start:
     |>>>>>>>%s;%s;%s;%s;%s<<<<<<<
}




###############################################################################
#
# the form to launch an application
#

$applOpt={
  head:
    |<HTML>
    |<BODY ($parStr:pageColor)>
    |<TITLE> SRS: application "%s" options page </TITLE>
    |<form method=POST action="($parStr:cgidir)/wgetz">
    |<INPUT TYPE=hidden name=userId VALUE=($parStr:userId)> 
    |<INPUT TYPE=hidden name=applName~ VALUE=%s> 
  title:
    |<H2><A HREF=\
    |  "($parStr:cgidir)/wgetz?\
    |($parStr:userIdOpt)-fun+pagelibinfo+-info+%s">%s</A>
    |%s</H2>
    |<P>
  sequence:{
    head:
      |<TABLE>
    multi:
      |  <TR>
      |    <TD COLSPAN=2>&nbsp;<BR>
      |      <A HREF="($parStr:cgidir)/wgetz?($parStr:userIdOpt)-e+%s">
      |      %s</A>
      |    </TD>
      |  </TR>
      |  <TR>
      |    <TD NOWRAP VALIGN=BOTTOM ALIGN=RIGHT>
      |      begin <INPUT SIZE=6 VALUE=1>
      |    </TD>
      |    <TD ROWSPAN=2>
      |      <TEXTAREA name=inputSequence%d~ rows=4 cols=50>%s\
      |      </TEXTAREA>
      |    </TD>
      |  </TR>
      |  <TR>
      |    <TD VALIGN=TOP ALIGN=RIGHT>
      |      end <INPUT SIZE=6 VALUE=%d>
      |    </TD>
      |  </TR>
      |<INPUT TYPE=HIDDEN name=inputSequenceName%d~ VALUE="%s"> 
      |<INPUT TYPE=HIDDEN name=inputSequenceComment%d~ 
      | VALUE="!%s Length: %d\n"> 
    single:
      |<P>query protein sequence<BR>
      |<TEXTAREA name="inputSequence~" rows=10 cols=60>%s</TEXTAREA>
      |<P>
  }
  submit:
    |</TABLE>
    |<P>
    |
    |<IMG SRC=($parStr:imgdir)/arrow_icon.gif ALIGN=MIDDLE>
    |<INPUT TYPE=SUBMIT NAME=PageDoAppl~ VALUE="Continue">
    |<INPUT TYPE=HIDDEN NAME=wwwFunctionName8~ VALUE=PageDoAppl>
    |<INPUT TYPE=RESET VALUE=Reset> &nbsp;
  options:{
    head:
      |<P>
      |<TABLE BORDER=3><CAPTION><B>Options</B></CAPTION>
    group:{
      head:
        |<TR>
        |<TH VALIGN=TOP ALIGN=LEFT ROWSPAN=%d>%s</TH>
      option:{
        head:
          |<TD VALIGN=TOP NOWRAP> 
        prompt:
          |%s
        menu:{
          head:
            |<SELECT NAME="%s_%s~">
          val:
            |<OPTION %s>%s
          valNamed:
            |<OPTION VALUE=%s %s>%s
          tail:
            |</SELECT>
        }
        radio:{
          head:
            |\
          val:
            |<INPUT TYPE=RADIO NAME="%s_%s~" VALUE="%s" %s> %s
          tail:
            |\
        }
        multi:{
          head:
            |\
          val:
            |<INPUT TYPE=CHECKBOX NAME="%s_%s~" VALUE=1 %s> %s
          tail:
            |\
        }
        real:
          |<INPUT SIZE=8 VALUE=%s NAME="%s_%s~">
        int:
          |<INPUT SIZE=6 VALUE=%s NAME="%s_%s~">
        bool:
          |<INPUT TYPE=CHECKBOX %s VALUE=1 NAME="%s_%s~">
        string:
          |<INPUT TYPE SIZE=20 VALUE="%s" NAME="%s_%s~">
        checkList:{
          head:
            |\
          val:
            |\
          tail:
            |\
        }
        tail:
      	  |</TD>
      	  |</TR>
      } 
      next:
        |<TR>
    }
    tail:
      |</TABLE>
  }
  tail:
    |</FORM>
    |</BODY>
    |</HTML>
}

###############################################################################
#
# the result page of an application
#

$applResult={
  head:
    |<HTML>
    |<TITLE>SRSWWW:%s Result</TITLE>
    |<BODY  ($ParStr:pageColor)>
    |<form method=POST action="($ParStr:cgidir)/wgetz">
    |<INPUT TYPE=hidden name=userId VALUE=($ParStr:userId)> 
    |<INPUT type=hidden name=libList VALUE=reset>
    |<INPUT type=hidden name=libList VALUE=%s>
  title:
    |<H2>%s Result Page</H2>
  search:{
    head:
      |<font size=+1>Wait until page is completed</FONT>
      | and continue with one of the options 
      |below.
      |<FORM method=POST action="($parStr:cgidir)/wgetz">
      |<input type=hidden name=userId value=($parStr:userId)>
      |<input type=hidden name=wwwSessionEntryList~ value=1>
      |<input type=hidden name=wwwFunctionName7~ value=PageQueryForm>
      |<input type=hidden name=isPendingJob value=1>
      |<BLOCKQUOTE>
      |<IMG SRC=($parStr:imgdir)/redball.gif>
      |<input type=submit name=PageQueryForm~ value="Search %s Results"><P>
      |<input type=hidden name=pageQuery value="[%s-id:*]">
      |<IMG SRC=($parStr:imgdir)/redball.gif>
      |<input type=hidden name=wwwFunctionName8~ value=PageEntry>
      |<input type=submit NAME=PageEntry~ value="List Entries">
    chunkSize:{
      head:
  	|<TD NOWRAP>
  	| in chunks of 
  	|<SELECT NAME=viewEntriesChunkSize>
      size:
  	|<OPTION %s> %d
      tail:
  	|</SELECT>
  	|</TD>
    }      
    selectView:{
      head:
  	|<TD NOWRAP>
  	| with view
  	|<SELECT NAME=viewNumber>
      name:
  	|<OPTION VALUE=%d %s> %s
      tail:
  	|</SELECT>
  	|<TD></TR>
    }
    tail:
      |</BLOCKQUOTE>
  }
  tail:
    |<TEXTAREA ROWS=1 COLS=65>running command: %s</TEXTAREA>
    |</FORM>
    |<PRE>
}











List Entries">
    chunkSize:{
      head:
  	|<TD NOWRAP>
  	| in chunks of 
  	|<SELECT NAME=viewEntriesChunkSize>
      size:
  	|<OPTION %s> %d
      tail:
  	|</SELECT>
  	|</TD>
    }      
    selectView:{
      head:
  	|<TDsrs/icarus/util/syntax.ic
#    $RCSfile: syntax.ic,v $
#    $Revision: 1.2 $
#    $Date: 1996/07/24 22:07:19 $
#    $Author: etzold $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

$SMxMIXCASE=0
$SMxLOWCASE=4
$SMxUPCASE=2

O_SYNTAX:$object:[name:Syntax typname:ICAoSYNTAX declname:syntax
  ppname:SRS attrs:{
    $attribute:[name:name declname:name type:string valtype:{name text}
      required:n rem:"Name of the syntax."]
    $attribute:[name:file declname:fileName type:string 
      rem:"Name of the Icarus file with the production list."]
    $attribute:[name:rules declname:rules type:string 
      rem:"Pointer to the production list."]
    $attribute:[typname:"struct SMoBUFF_" declname:"*buff" type:user 
      rem:"Name of the file with ICA rules"]
    $attribute:[name:commandSyntax declname:commandSyntax type:object 
      defaultval:@O_SYNTAX required:n valtype:constant status:obsolete
      rem:"The syntax of for the commands"]
    $attribute:[typname:"struct ICAoNAMELIST" declname:"*prodList" type:user
      rem:"List of productions"]
    $attribute:[typname:"struct ICAoCOMMAND" declname:"*userCommand" type:user]
    $attribute:[typname:"struct taskList" type:user declname:"*taskList"]
    $attribute:[name:ignore declname:ign type:string defaultstr:" " max:20
      valtype:text
      rem:|
        |String containing characters to be ignored or skipped during 
        |parsing (white space).
    ]
    $attribute:[name:comment declname:lf type:string defaultstr:"" max:50 
      valtype:text 
      rem:"A regular expression to skip comments."]
    $attribute:[name:level3 declname:linkFlag type:uchar 
      status:obsolete defaultval:1]
    $attribute:[declname:"*prod" typname:"struct VARo" type:user]
    $attribute:[declname:"*scope" typname:"struct VARoSCOPE" type:user]
    $attribute:[declname:"*cmntRe" typname:"struct regexp" type:user]
    $attribute:[declname:"ignAlt" type:string]
  }
]
e).
    ]
    $attribute:[name:srs/icarus/util/translation.i
$geneticCode:["Standard" code:SGC0 id:1 
  ncbieaa: "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
  sncbieaa:"-----------------------------------M----------------------------" 
]
$geneticCode:["Vertebrate Mitochondrial" code:SGC1 id: 2
  ncbieaa: "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG" 
  sncbieaa:"--------------------------------MMMM---------------M------------" 
]
$geneticCode:["Yeast Mitochondrial" code:SGC2 id:3
  ncbieaa: "FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG" 
  sncbieaa:"-----------------------------------M----------------------------" 
]
$geneticCode:["Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma"
  code:SGC3 id: 4
  ncbieaa: "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG" 
  sncbieaa:"--MM---------------M------------MMMM---------------M------------" 
]
$geneticCode:["Invertebrate Mitochondrial"  code:SGC4 id:5
  ncbieaa: "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG"
  sncbieaa:"---M----------------------------M-MM---------------M------------"
]
$geneticCode:["Ciliate Macronuclear; Dasycladacean Nuclear" code:SGC5 id:6
  ncbieaa: "FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
  sncbieaa:"-----------------------------------M----------------------------"
]
$GeneticCode:["Echinoderm Mitochondrial" code:SGC8 id:9
  ncbieaa: "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG"
  sncbieaa:"-----------------------------------M----------------------------"
]
$geneticCode:["Euplotid Macronuclear" code:SGC9 id: 10
  ncbieaa: "FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
  sncbieaa:"-----------------------------------M----------------------------"
]
$geneticCode:["Bacterial" id:11 
  ncbieaa: "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
  sncbieaa:"---M---------------M------------M--M---------------M------------"
]
$geneticCode:["Alternative Yeast Nuclear" id:12
  ncbieaa: "FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
  sncbieaa:"-------------------M---------------M----------------------------"
]
$geneticCode:["Ascidian Mitochondrial" id:13
  ncbieaa: "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG"
  sncbieaa:"-----------------------------------M----------------------------"
]
$geneticCode:["Flatworm Mitochondrial" id:14
  ncbieaa: "FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG"
  sncbieaa:"-----------------------------------M----------------------------"
]
$geneticCode:["Blepharisma Macronuclear" id:15
  ncbieaa: "FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
  sncbieaa:"-----------------------------------M----------------------------"
]

KSSGGVVVVAAAADDEEGGGG"
  sncbieaa:"-----------------------------------M----------------------------"
]
$geneticCode:["Flatworm Mitochondrial" id:14
  ncbieaa: "FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG"
  sncbieaa:"----------------------------srs/icarus/util/translation.ic
$object:[name:function declname:"X" 
  status:system 
  attrs:{ 
    $attribute:[name:name type:protofunction declname:"fnctnam" 
      max:30 valtype:text] 
    $attribute:[name:args type:string declname:"args" 
      max:132 valtype:text required:y] 
    $attribute:[name:module type:string declname:"module" max:30] 
  }
] 

$object:[name:geneticCode  typname:"SEQoTranslTable" declname:translTable 
  attrs:{ 
    $attribute:[name:name type:string declname:name unnamed:y 
      rem:"Name of translation table." required:y] 
    $attribute:[name:code type:string declname:code unnamed:y 
      rem:"Short name of translation table."] 
    $attribute:[name:id type:int declname:id 
      rem:"Numeric id."] 
    $attribute:[name:ncbieaa type:string declname:"aa" required:y 
      rem:"Amino acid encoded by triplett."] 
    $attribute:[type:string declname:"aaAlt" 
      rem:"Alternative (edited) Amino acid encoded by triplett."] 
    $attribute:[name:sncbieaa type:string declname:"saa" required:y 
      rem:"Amino acid encoded by triplett at translation start."] 
  }
] 



$def:[infile:"SRSICA:srswin.sdl" outfile:"SRSSOU:transl.h" 
  section_name:"builtin" section_size:2000 
]

me:id 
      rem:"Numeric id."] 
    $attribute:[name:ncbieaa type:string declname:"aa" required:y 
      rem:"Amino acid encoded by triplett."] 
    $attribute:[type:string declname:"aaAlt" 
      rem:"Alternative (edited) Amino acid encoded by triplett."] 
    $attribute:[name:sncbieaa type:string declname:"saa" required:y 
      rem:"Amino srs/index/


#include <stdio.h>
#include <stdlib.h>

#include "message.h"
#include "futil.h"
#include "sm.h"
#include "strv.h"
#include "dict.h"
#include "variable.h"
#include "icarus.h"
#include "library.h"
#include "appl.h"

#define _SRS
#define _SLB
#include SRSINCLUDE






APPLo *ApplNamed (char *name)
{
  APPLo *appl;
  appl = (APPLo*) LibObjByName ("application", name);
  return appl;
}



/**api* function **************************************************************
**
** 	Returns next application object for Data type object.
** 
** 	INPUT:	 o  address o data type object object [R]
**               o  address of context [W]
** 	        IMPLICIT:
** 
** 	RETURNS:  application object 
**                NULL: the list is exhausted (next call will start at begin)
*/ 

APPLo *ApplNextInDataType (LIBoDataType *dataType, INT4 *c)
{
  if (*c >= 20/*te!!!*/ || !dataType->applications[*c]) {
    *c=0;
    return NULL;
  }
  else
    return dataType->applications[(*c)++];
}

char *ApplGetName (APPLo *appl)
{
  return appl->name;
}

char *ApplGetTitle (APPLo *appl)
{
  return appl->title;
}


/**api* function **************************************************************
**
** 	Returns whether specified characteristic is true or false.
** 
** 	INPUT:	 o  application object [R]
**               o  characteristic: "search", "multi", "single" [R]
** 
** 	RETURNS:  1: characteristic is true
**                0: not true
*/ 

Int4 ApplIs (APPLo *appl, char *option)
{
  Int4 flag=0, type, k;

  for (k=0; k < 5; k++) {
    type = appl->type[k];
    switch (_Index (tolower(option[0]), tolower (option[1]))) {
    case _Index('s','e'):  /* search */
      if (type == 1)
	flag = 1;
      break;
    case _Index('m','u'):  /* multi */
      if (type == 3)
	flag = 1;
      break;
    case _Index('s','i'):  /* single */
      if (type == 2)
	flag = 1;
      break;
    default:
      _ErrExit2 (e__unknownoption, option);
    }
  }
  return flag;
}

Int4 ApplIsInSeq (APPLo *appl, char *option)
{
  Int4 flag=0, type, k;

  switch (_Index (tolower(option[0]), tolower (option[1]))) {
  case _Index('g','c'):  /* gcg */
    if (appl->inSeqFormat == 1)
      flag = 1;
    break;
  case _Index('p','i'):  /* pir */
    if (appl->inSeqFormat == 3)
      flag = 1;
    break;
  case _Index('f','a'):  /* fasta */
    if (appl->inSeqFormat == 2)
      flag = 1;
    break;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
  return flag;
}

void ApplInit (APPLo *appl)
{
  if (appl->com)
    StrClear (&appl->com);
}

void ApplEval (APPLo *appl, char *s)
{
  IcaEval (&appl->interp, s);
}


char *ApplGetCommand (APPLo *appl)
{
  ANYv list, any;

  if (!appl->com || !StrLen (appl->com)) {
    IcaEval (&appl->interp, appl->command);
    list = VarGet (&appl->interp->scope, "opt");
    any = AnyGetListAssoc (list, "command");
    appl->com = VarGetStrv (any);
  }
  return _Str (appl->com);
}

void ApplLaunch (APPLo *appl)
{
  ApplGetCommand (appl);
  IcaEval (&appl->interp, appl->launch);
}



APPLoOpt *ApplNextOpt (APPLo *appl, Int4 *c)
{
  if (*c >= appl->optionsN) {
    *c=0;
    return NULL;
  }
  else
    return &appl->options[(*c)++];
}

APPLoOpt *ApplOptNamed (APPLo *appl, char *name)
{
  APPLoOpt *opt;
  Int4     k;

  for (k=0; (opt=ApplNextOpt (appl, &k));) {
    if (SmEqs (ApplOptGetName (opt), name))
      return opt;
  }
  return NULL;
}

char *ApplOptGetName (APPLoOpt *opt)
{
  return opt->name;
}

char *ApplOptGetDefValue (APPLoOpt *opt)
{
  static char tmp[100];
  Int4 k;

  if (ApplOptIs (opt, "real")) {
    sprintf (tmp, "%f", opt->defReal);
    for (k=strlen (tmp)-1; k>0 && tmp[k]=='0'; k--)
      ;
    tmp[tmp[k]=='.' ? k+2 : k+1] = '\0';
    return tmp;
  }
  else if (ApplOptIs (opt, "int")) {
    sprintf (tmp, "%d", opt->defInt);
    return tmp;
  }
  else 
    return *opt->defStr ? opt->defStr : "";
}

Int4 ApplOptGetDefInt (APPLoOpt *opt)
{
  return opt->defInt;
}

/**api* function **************************************************************
**
** 	Returns whether specified characteristic is true or false.
** 
** 	INPUT:	 o  application object [R]
**               o  characteristic: "list", "int", "real" [R]
** 
** 	RETURNS:  1: characteristic is true
**                0: not true
*/ 

Int4 ApplOptIs (APPLoOpt *opt, char *option)
{
  Int4 flag=0;

  switch (_Index (tolower(option[0]), tolower (option[1]))) {
  case _Index('l','i'):  /* list */
    if (opt->valuesN)
      flag = 1;
    break;
  case _Index('m','e'):  /* menu */
    if (opt->guiType==4)
      flag = 1;
    break;
  case _Index('r','a'):  /* radio */
    if (opt->guiType==3)
      flag = 1;
    break;
  case _Index('m','u'):  /* multi */
    if (opt->guiType==2)
      flag = 1;
    break;
  case _Index('r','e'):  /* real */
    if (opt->type==2)
      flag = 1;
    break;
  case _Index('i','n'):  /* int */
    if (opt->type==1)
      flag = 1;
    break;
  case _Index('b','o'):  /* bool */
    if (opt->type==3)
      flag = 1;
    break;
  case _Index('s','t'):  /* string */
    if (opt->type==4)
      flag = 1;
    break;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
  return flag;
}

APPLoOptGroup *ApplOptGetGroup (APPLoOpt *opt)
{
  return opt->group;
}

char *ApplOptGetPrompt (APPLoOpt *opt)
{
  return *opt->prompt ? opt->prompt : "";
}

APPLoOptVal *ApplOptNextVal (APPLoOpt *opt, Int4 *c)
{
  if (*c >= opt->valuesN) {
    *c=0;
    return NULL;
  }
  else
    return &opt->values[(*c)++];
}

char *ApplOptValGetName (APPLoOptVal *val)
{
  return val->name;
}
char *ApplOptValGetPrompt (APPLoOptVal *val)
{
  return val->prompt;
}
char *ApplOptValGetValue (APPLoOpt *opt, APPLoOptVal *val)
{
  static char tmp[100];
  Int4 k;

  if (ApplOptIs (opt, "real")) {
    sprintf (tmp, "%f", val->valReal);
    for (k=strlen (tmp)-1; k>0 && tmp[k]=='0'; k--)
      ;
    tmp[tmp[k]=='.' ? k+2 : k+1] = '\0';
    return tmp;
  }
  else if (ApplOptIs (opt, "int")) {
    sprintf (tmp, "%d", val->valInt);
    return tmp;
  }
  else 
    return *val->valStr ? val->valStr : ApplOptValGetName (val);
}
Int4 ApplOptValGetInt (APPLoOpt *opt, APPLoOptVal *val)
{
  return val->valInt;
}

Int4 ApplOptValIs (APPLoOptVal *val, char *option)
{
  Int4 flag=0;

  switch (_Index (tolower(option[0]), tolower (option[1]))) {
  case _Index('n','a'):  /* named */
    if (*val->name)
      flag = 1;
    break;
  case _Index('o','n'):  /* menu */
    if (val->on)
      flag = 1;
    break;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
  return flag;
}


char *ApplOptGroupGetName (APPLoOptGroup *group)
{
  return group->name;
}

Int4 ApplOptGroupGetSize (APPLo *appl, APPLoOptGroup *group)
{
  APPLoOpt *opt;
  Int4     i, n;

  for (i=0, n=0; (opt=ApplNextOpt (appl, &i));)
    if (group == ApplOptGetGroup (opt))
      n++;
  return n;
}
n','a'):  /* named */
    if (*val->name)
      flag = 1;
    break;
  case _Index('o','n'):  /* menu */
    if (val->on)
      flag = 1;
    break;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
  return flag;
}


char *ApplOptGroupGetName (APPLoOptGroup *group)
{
  return group->name;
}

Int4 ApplOptGroupGetSize (APPLo *appl, APPLoOptGroup *group)
{
  APPLoOpt *srs/src/appl.h
struct APPLo *ApplNamed (char *name);
char *ApplGetTitle (struct APPLo *appl);
struct APPLo *ApplNextInDataType (struct LIBoDataType *dataType, INT4 *c);


    /* accessing an application object */

char *ApplGetName (struct APPLo *appl);
char *ApplGetCommand (struct APPLo *appl);
void ApplLaunch (struct APPLo *appl);
Int4 ApplIsInSeq (struct APPLo *appl, char *option);
struct APPLoOpt *ApplNextOpt (struct APPLo *appl, Int4 *c);
struct APPLoOpt *ApplOptNamed (struct APPLo *appl, char *name);

    /* accessing an application's option object */

char *ApplOptGetName (struct APPLoOpt *opt);
char *ApplOptGetDefValue (struct APPLoOpt *opt);
struct APPLoOptVal *ApplOptNextVal (struct APPLoOpt *opt, Int4 *c);
struct APPLoOptGroup *ApplOptGetGroup (struct APPLoOpt *opt);
char *ApplOptGetPrompt (struct APPLoOpt *opt);


    /* accessing an application's option's value object */

char *ApplOptValGetName (struct APPLoOptVal *val);
char *ApplOptValGetValue (struct APPLoOpt *opt, struct APPLoOptVal *val);
Int4 ApplOptValGetInt (struct APPLoOpt *opt, struct APPLoOptVal *val);
char *ApplOptValGetPrompt (struct APPLoOptVal *val);

    /* accessing an application's option's group object */

char *ApplOptGroupGetName (struct APPLoOptGroup *group);
Int4 ApplOptGroupGetSize (struct APPLo *appl, struct APPLoOptGroup *group);
*opt);


    /* accessing an application's option's value object */

char *ApplOptValGetName (struct APPLoOptVal *val);
char *ApplOptValGetValue (struct APPLoOpt *opt, struct APPLoOptVal *val);
Int4 ApplOptValsrs/src/arglist.c
char arglist_ID[] = "$Id: arglist.c,v 1.4 1997/03/04 21:56:27 srs Exp $";
/*
**
**    $RCSfile: arglist.c,v $
**    $Revision: 1.4 $
**    $Date: 1997/03/04 21:56:27 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
*/
/*      arglist - command line argument processor for C programs
 * 
 * See getargs.doc and header file for full explanation
 * (C)  Copyright 1985, Allen I. Holub.  All rights reserved.
 * This program may be copied for personal, non-profit use only
 * 
 * history...
 * 
 * May 1985     published in Dr. Dobb's Journal #103.
 * 19 May 85    Transcribed by James R. Van Zandt
 * Oct 1993     Extended/modified by Philip lijnzaad@embl-heidelberg.de
 *
 * ------------------------------------------------------------------ *
 *								      *
 * Permission to copy all or part of this work is granted, provided   *
 *  that this NO WARRANTY and this copyright notice are retained      *
 *  verbatim and are displayed conspicuously.  If anyone needs other  *
 *  permissions that aren't covered by the above, please contact the  *
 *  author.							      *
 *								      *
 * NO WARRANTY: THIS WORK IS PROVIDED ON AN "AS IS" BASIS.  THE       *
 *  AUTHOR PROVIDES NO WARRANTY WHATSOEVER, EITHER EXPRESS OR         *
 *  IMPLIED, REGARDING THE WORK, INCLUDING WARRANTIES WITH THE WORK,  *
 *  INCLUDING WARRANTIES WITH RESPECT TO ITS MERCHANTABILITY OR       *
 *  FITNESS FOR ANY PARTICULAR PURPOSE.				      *
 *								      *
 *								      *
 * ------------------------------------------------------------------ */

#include <stdio.h>
#include <stdlib.h> 
#include <stdarg.h>
#include <string.h>


#include "message.h"
#include "futil.h"
#include "par.h"
#include "strv.h"

#define _SRS
#define _SLB
#include SRSINCLUDE
#include "arglist.h"

typedef void (*PFV)(void);
typedef void (*PFS)(char*);

#define USAGE_MESSAGE "Usage:"

#define OPT_FIRSTCHAR "-+"		/* first chars that imply an option */

#define ERR_EXIT_STATUS 1		/* exit status upon user error */
#define INT_ERR_EXIT_STATUS 2		/* exit status upon internal error */


enum arg_type {ARGxPARAMETER, ARGxHELP, ARGxTITLE};


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  external, global and module wide variables
*/

static INT4 (*print)(char *,...)=NULL; /* function for printing errors */
static INT4 boolval;			/* used in setarg */
static INT4 help=0;
char * usage_message;			/* printed by ArgUsage; user-setable */

/* BCB */
/* static INT4 (*myexit)(INT4); */      /* function for handling errors */
/*
#define exit myexit
*/
/* end BCB */

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of static functions
*/

static INT4 ArgSet (arg_t *argp, char **argv);
static arg_t *ArgFind (char * name, ARGoLIST *arglist);



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  default function for printing lines
*/

static INT4 ArgPrintMessage (char *formatStr, ...)
{
    va_list ap;

    va_start (ap, formatStr);
    vfprintf (stdout, formatStr, ap);
    va_end (ap);
    return 1;
}


/****** ArgSet ****************************************************************
**
**      set an argument.  argp points at the argument table entry corresponding
**      to argv[0]. Returns number of items that now can be taken out of
**      argument list, ie. 1 for BOOLEAN and PROC, 2 for rest, and 0 for
**      error 
** 
** 	INPUT:	    name [R]
** 		    arglist object [R]
** 	        IMPLICIT:
**                  help (int) [W]
**                  boolval (int) [R]
** 
** 	RETURNS:    returns pointer to argument object
*/ 

static INT4 ArgSet (arg_t *arg, char **argv) 
{
  PARo  *par;
  INT4  parType, rv;
  char *cp;

  if (arg->type == ARGxHELP) {
    help=1;
    return (0);
  }

  if (!(par = ParGetWrite (arg->parameter, NULL)))
    _ErrExit2 (e__parnotdefined, arg->parameter);
  
  if ((parType = ParOGetType (par)) & PARxBOOL) {
    ParODefNum (par, boolval);  
    return 1;
  }

  /* was added for the new SRSWWW ...transmitting function names */

  if ((parType = ParOGetType (par)) == PARxSTR && *arg->defaultStr) { 
    ParODefStr (par, arg->defaultStr);  
    return 1;
  }
  /* was added for the new SRSWWW ...transmitting function names */

  else if (parType == PARxNUM && arg->defaultNum) { 
    ParODefNum (par, arg->defaultNum);  
    return 1;
  }


  /* following functions all need a value, so see if it's there: */

  if ( (! argv[1]) || (!argv[1][0] ) ) {
    print ("option %s needs additional argument", argv[0]);
    return(0);
  }

  switch (parType) {

  case PARxNUM:
    rv = ParODefNum (par, strtol (argv[1], &cp, 0));
    if (_ErrIs (rv))
      exit (INT_ERR_EXIT_STATUS);
    if (*cp) {
      print ("malformed integer: %s\n", argv[1]); 
      return 0; 
    }
    return 2;

  case PARxSTR:
    rv = ParODefStr (par, argv[1]);
    if (_ErrIs (rv))
      exit (INT_ERR_EXIT_STATUS);
    return 2;

  case PARxREAL:
    rv = ParODefReal (par, strtod (argv[1], &cp));
    if (_ErrIs (rv))
      exit (INT_ERR_EXIT_STATUS);
    if (*cp) {
      print ("malformed double: %s\n", argv[1]); 
      return 0; 
    }
    return 2;

  default:
    break;
  }

  print ("getargs internal error: bad argument type %d for %s in %s %s\n", 
	 parType, par->name, argv[0], argv[1]);
  exit (INT_ERR_EXIT_STATUS);
  return 1; /* compilers ..please shut up!*/
} 



/****** ArgFind ***************************************************************
**
** 	searches an argument in the table by name
** 
** 	INPUT:	    name [R]
** 		    arglist object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    returns pointer to argument object
*/ 

static arg_t *ArgFind (char * name, ARGoLIST *arglist) 
{
  arg_t *arg;
  INT4   k;

  for (k=0 ; k < arglist->argN; k++) {
    arg = &arglist->arg[k];
    if (arg->type != ARGxTITLE && ! strcmp (arg->name, name) )
      return (arg);
  } 
  return (NULL);
} 


/**api* ArgUsageBuild *********************************************************
**
** 	prints a list with all commmand line options
** 
** 	INPUT:	    address of symboltable [R]
** 		    address of file descr. [W]
** 	        IMPLICIT:
**                  help (int) [R]
** 
** 	RETURNS:    1
*/ 

char *ArgUsageBuild (ARGoLIST *arglist) 
{
  static STRv str=NULL;
  STRv  tmp=StrNew ();
  PARo  *par;
  arg_t *arg;
  INT4  k, isBoolOpts=0;
  
  if (!str) str = StrNew (str);
  StrPrintf (&str, "Usage: %s", arglist->name);
  StrAppS (&tmp, "[-");

  /*
  ** collect all boolean options ...should be all optional and one letter names
  */

  for (k=0; k < arglist->argN; k++) {
    arg = &arglist->arg[k];
    if (arg->type == ARGxPARAMETER) {
      par = ParGetRead (arg->parameter, NULL);
      if (ParOGetType (par) & PARxBOOL && strlen (arg->name) == 2) {  
	isBoolOpts = 1;
	StrAppS (&tmp, &arg->name[1]);
      }
    }
  }
  if (isBoolOpts)
    StrPrintf (&str, " %s]", _Str (tmp));

  /*
  ** now the others
  */

  for (k=0; k < arglist->argN; k++) {
    arg = &arglist->arg[k];
    if (arg->type == ARGxPARAMETER) {
      par = ParGetRead (arg->parameter, NULL);
      if (ParOGetType (par) & PARxBOOL || strlen (arg->name) > 2) {
	if (ParOGetType (par) == PARxBOOL)
	  StrPrintf (&str, " [%s]", arg->name);
	else
	  StrPrintf (&str, " [%s %s]", arg->name, par->name);
      }
    }
  }
  StrPrintf (&str, " %s", arglist->usage);
  StrSet (&str, StrFormat (str, 80, 0, 10, NULL));
  StrDel (tmp);
  return _Str (str);
}

/**api* ArgUsage **************************************************************
**
** 	prints a list with all commmand line options
** 
** 	INPUT:	    address of symboltable [R]
** 		    address of file descr. [W]
** 	        IMPLICIT:
**                  help (int) [R]
** 
** 	RETURNS:    1
*/ 

void ArgUsage (ARGoLIST *arglist) 
{
  PARo    *par;
  arg_t   *arg;
  STRv    s;
  char    assign[40], tmp[132], *str;
  INT4    k;

  print ("%s\n\n", ArgUsageBuild (arglist));

  /* this is an error, not a HELP type */

  if (!help) { 
    print ("Info: %s -help\n", arglist->name);
    return;
  }

  s = StrNew ();
  for (k=0; k < arglist->argN; k++) {
    StrClear (&s);
    arg = &arglist->arg[k];
    if (arg->type == ARGxPARAMETER) {
      par = ParGetRead (arg->parameter, NULL);
      switch (ParOGetType (par))  {
      case PARxBOOL:
	StrPrintf (&s, "  %-20s[%s] %s", arg->name, 
		 ParOGetNum (par) ? "TRUE" : "FALSE", par->comment);
	break;
      case PARxNUM:
	sprintf (assign, "%s <n>", arg->name);
	StrPrintf (&s, "  %-20s[%d] %s", assign, ParOGetNum (par),
		    par->comment);
	break;
      case PARxSTR:		
	sprintf (assign, "%s <string>", arg->name);
	if ((str = ParOGetStr (par)))
	  sprintf (tmp, "[\"%s\"]" , str);
	StrPrintf (&s, "  %-20s%s %s", assign, str ? tmp : "",
		    par->comment);
	break;
      case PARxREAL:		
	sprintf (assign, "%s <real>", arg->name);
	StrPrintf (&s, "  %-20s[%f] %s", assign, 
		    ParOGetReal (par), par->comment);
	break;
      }
      StrTrim (&s, "\n");
      StrTranslate (&s, "\n", " ");
      print ("%s\n", _Str (StrFormat (s, 80, 0, 22, NULL)));
    }

    else if (arg->type == ARGxTITLE)
      print ("\n%s\n\n", arg->name);
    else if (arg->type == ARGxHELP)
      print ("  %-20s%s\n", arg->name, arg->comment);
  }
} 


/**api* ArgGet ***************************************************************
**
**       Process command line arguments, stripping all command line switches 
**       out of argv.  Return a new argc. If an error is found, 
**       exit(ERR_EXIT_STATUS) is called (getargs won't return) and a usage 
**       message is printed, showing all arguments in the table 
** 	 module must be initialized before first query is done
** 
** 	INPUT:	 o  name of command, for which command line is to be 
**                  processed [R]
**               o  number of args on command line [R]
**               o  pointer to address of argument array [W]
**
** 	        IMPLICIT:
**                  print (INT4 (*print)(char *,...)) [W]
** 
** 	RETURNS:    new value for "argc" 
*/ 

INT4 ArgGet (ARGoLIST *arglist, INT4 argc, char **argv) 
{
  INT4     nargc, i;
  char    **nargv, *cp, oneletter[3], *savarg;
  arg_t   *argp;
  
  if (!print)
    print = ArgPrintMessage;

/*
** BCB /MS : major !
*/


  if (ParGetFunction ("ArgPrintf") != NULL) 
    print = (INT4 (*)(char *, ...)) ParGetFunction ("ArgPrintf");

#define USAGE_EXIT ArgUsage (arglist),exit(ERR_EXIT_STATUS)

/* would be nice to have _this_ in a further release */ 
/*
  if ( ParGetFunction ("UserExit") != NULL ) {
    myexit = (INT4 (*)(INT4)) ParGetFunction ("UserExit");
  }
  else {
    myexit = exit;
  }
#define USAGE_EXIT ArgUsage (arglist),myexit(ERR_EXIT_STATUS)
*/

  nargc = 1;			        /* argv[0] is program name  */
  memset (oneletter, 0, sizeof (oneletter)); /* make zero */
  
  for (nargv = ++argv; --argc > 0; argv++) { /* walk all arguments */
    /* for now no provision for '\-'; do it with '--' */
    if ( strchr( OPT_FIRSTCHAR, (INT4)*argv[0]) ) { /* an option (or more) */
      if (! strcmp("--", *argv)) {	/* signals end of options */
	argv++;				/* skip this one */
	nargc += (argc-1);		/* all the rest but '--' */
	for ( ; --argc > 0 ; argv++)	/* shift the rest */
	  *nargv++ = *argv;
	return (nargc); 
      }
      if (! argv[0][1] ) {		/* "-" or "+": never an option, */
	*nargv++ = *argv;		/* always an argument: shift it  */
	nargc++;
	continue;
      }
      boolval = (*argv[0] == '-');	/* 1 if -option, 0 if +option */
      if ((argp = ArgFind (*argv, arglist))) { /* first try to find this arg 
						  as a complete word in the 
						  table */ 
	if ((i=ArgSet (argp, argv))) {
	  i--;
	  argv += i;
	  argc -= i;
	  continue;
	} else
	  USAGE_EXIT;			/* wrong or no argument */
      } else {				/* try finding it as a letter arg */
	oneletter[0]= argv[0][0];	/* any of OPT_FIRSTCHAR (typically -)*/
	for ( cp = &argv[0][1]; *cp; cp++ ) {
	  oneletter[1] = *cp;
	  if ((argp = ArgFind (oneletter, arglist))){ /* find  arg in table */

	    /*
	    ** we seem to have found a matching one-letter option. 
	    ** Temporarily change this *argv, so as not to confuse 
	    ** the error messages: 
	    */

	    savarg = *argv;		/* save current arg */
	    *argv = &oneletter[0];	/* argv[1] still 'normal' */
	    if ((i = ArgSet (argp, argv))) { /* not-nil: succes !  */
	      *argv = savarg;		/* restore original */
	      if (i==2) {		/* option that takes a value: */
		argv++;			/* must have been eaten */
		argc--;
		break;			/* continues at upper for-loop */
	      }	/* else: continues at cp++ */
	    } else			/* 0: failure */
	      USAGE_EXIT;		/* wrong or no argument */
	  } else {
	    print ("Unrecognized option \'%s\'\n", *argv);
	    USAGE_EXIT;			/* option not found */
	  }
	}
      }
    } else {				/* not an option: shift arguments */
      *nargv++ = *argv;
      nargc++;
    }
  } 
  return(nargc);
} /* getargs */



/**api* ArgSetPrint ************************************************************
** 
**	allows other modules to set their own function for outputting
**	messages;
**
**	INPUT:	    address of function [R]
**	        IMPLICIT:
**		    print (int (*)) [W]
**
*/ 
   
void ArgSetPrint (INT4 (*fnct)(char *,...))
{
  if (fnct)
    print = fnct;
}

 not found */
	  }
	}
      }
srs/src/arglist.h
 * 
 * See arglist.doc and header file for full explanation
 * (C)  Copyright 1985, Allen I. Holub.  All rights reserved.
 * This program may be copied for personal, non-profit use only
 * 
 * history...
 * 
 * May 1985     published in Dr. Dobb's Journal #103.
 * 19 May 85    Transcribed by James R. Van Zandt
 * Oct 1993     Extended/modified by Philip lijnzaad@embl-heidelberg.de
 *
 * ------------------------------------------------------------------ *
 *								      *
 * Permission to copy all or part of this work is granted, provided   *
 *  that this NO WARRANTY and this copyright notice are retained      *
 *  verbatim and are displayed conspicuously.  If anyone needs other  *
 *  permissions that aren't covered by the above, please contact the  *
 *  author.							      *
 *								      *
 * NO WARRANTY: THIS WORK IS PROVIDED ON AN "AS IS" BASIS.  THE       *
 *  AUTHOR PROVIDES NO WARRANTY WHATSOEVER, EITHER EXPRESS OR         *
 *  IMPLIED, REGARDING THE WORK, INCLUDING WARRANTIES WITH THE WORK,  *
 *  INCLUDING WARRANTIES WITH RESPECT TO ITS MERCHANTABILITY OR       *
 *  FITNESS FOR ANY PARTICULAR PURPOSE.				      *
 *								      *
 *								      *
 * ------------------------------------------------------------------ */

/*	arglist.h - typedefs and defines needed for getargs	*/


#include <stdio.h> 			/* for prototypes */
#include <stdlib.h>  
#include <string.h>

#ifndef _ARGoLIST
#define _ARGoLIST
typedef struct ARGoLIST {
  char                    *name;
  char                    *usage;
  struct arg_t            *arg;
  INT4                    argN;
} ARGoLIST;
#endif

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of exported functions
*/

INT4 ArgGet (ARGoLIST *arglist, INT4 argc, char **argv);
void ArgUsage (ARGoLIST *arglist);
void ArgSetPrint (INT4 (*fnct)(char *,...));

otypes */
#include <stdlib.h>  
#include <string.h>

#ifndef _ARGoLIST
#define _ARGoLIST
typedef struct ARGoLIST {
  chasrs/src/auxinfo.c
#include <stdarg.h>
#include "srs.h"

INT4 PrintMessage (MSGo *msg) 
{ 
  if (msg->msg_code == i__readingname)
    putc ('.', stderr); 

  switch (msg->msg_code) {
  case i__wroteset:
    return 0;
    
  default:
    if (msg->msg_t != MSGxINFO) 
      fprintf (stderr, "ERROR: %s, %s\n", msg->primsg, msg->secmsg);
    else
      fprintf (stderr, "%s\n", msg->secmsg);
    return 1;
  }
}

#ifdef BUILD
int main (int argc, char **argv)
{
  SMoBUFF      *buff=NULL, *auxBuff=NULL;
  struct IDXo *idx;
  SLBoFIELD    *field;
  SLBo         *lib;
  ENTRYv       entry;
  char         *name, *ln, indexName[133], *format;
  int          errCode, n=0, len;

  SrsEnv ();
  LibOpen ("srswin");
  MsgSetFnct (PrintMessage);
  argc = ArgGet ((ARGoLIST *) LibObjByName ("arglist", "srsbuild"), 
		 argc, argv);

  if (!(lib = (SLBo *) LibObjByName ("library", argv[1])))
    _ErrExit3 (e__objectunknown, "library", argv[1]);

  if (SmEqs(LibGetName (lib, "full"), "swissprot"))
    format =  "ID %*s %*[^;]; %*[^;]; %d";
  else if (SmEqs(LibGetName (lib, "full"), "embl"))
    format =  "ID %*s %*[^;]; %*[^;]; %*[^;]; %d";
  
  entry = EntryOpenStream (lib);
  LibGetIndexName (lib, NULL, indexName, "write");
  idx = IdxOpen (indexName, "write", 0, &errCode);
  _ErrExit2 (errCode, indexName);
  
  while (EntryNext (entry)) {
    while (field = EntryToNextField (entry)) {
      name = LibGetFieldName (field);
      if (SmEqs (name, "ID")) {
	while (ln = EntryFieldNextLine (entry)) {
	  sscanf (ln, format, &len);
	}
      }
      else if (SmEqs (name, "Definition")) {
	buff = BuffInit (buff, 100);
	auxBuff = BuffInit (auxBuff, 100);
	while (ln = EntryFieldNextLine (entry))
	  BuffCopyString (buff, ln);
	;
	while (BuffMatch (buff, "((DE   )|(GN   ))"))
	  BuffSubstMatch (buff, 1, "");
	while (BuffMatch (buff, "(\n)"))
	  BuffSubstMatch (buff, 1, " ");
	
	BuffPack (auxBuff, "ia60", len, BuffGetPtr (buff));
	IdxPutBuff (idx, auxBuff);
      } 
      else	
	EntrySkipField (entry);
    }
    if (!(++n % 300))
      _ErrMsg3 (i__processingentry, n, EntryGetFullName (entry));
  }
  IdxClose (idx);
}



#else
int main ()
{
  SMoBUFF  *buff;
  SETo     *set;
  IDoENTRY id;
  ENTRYv   entry;
  int      n, entryN, len;
  char     ln[100];
  
  SrsEnv ();
  LibOpen ("srswin");
  
  if (QryDo ("[swissprot-definition:protein]", "Q")) {
    set = SetGet ("Q"); 
    entryN = SetSize ("Q");
    
    for (n=1;  n <= entryN; n++) {
      SetGetID (set, n, &id); 
      entry = EntryOpen (&id);
      buff = EntryGetAuxInfo (entry);
      BuffUnpack (buff, "ia60", &len, ln);
      printf ("entry: %s, len: %d | %s\n",
	      EntryGetFullName (entry), len, ln);
      EntryClose (&entry);
    }
  }
}
#endif

  int      n, entryN, len;
  char     ln[100];
  
  SrsEnv ();
  LibOpen ("srswin");
  
  if (QryDo ("[swissprot-definition:protein]", "Q")) {
    set = SetGet ("Q"); 
    entryN = SetSize ("Q");
    
    for (n=1;  n <= entryN; n++) {
      SetGetID (set, n, &id); 
      entry = EntryOpen (&id);
      buff = EntryGetAuxInfo (entry);
      BuffUnsrs/src/binpack.h
**
**    $RCSfile: binpack.h,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:16:18 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**    Macros for packing and unpacking data into/from platform independent
**    binary format.
**
*/

#define BYTE1   0xFFUL
#define BYTE2   0xFF00UL
#define BYTE3   0xFF0000UL
#define BYTE4   0xFF000000UL


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  macros for packing and unpacking filepointers and numbers
*/

#define _BinUnpackFip(buff, fip) \
     do { \
     fip = ((UINT4) ((unsigned char) buff[0])) + \
           ((UINT4) ((unsigned char) buff[1]) << 8) + \
	   ((UINT4) ((unsigned char) buff[2]) << 16) + \
           ((UINT4) ((unsigned char) buff[3]) << 24); \
     buff += 4; \
     } while (0)

#define _BinUnpackNum(buff, num) \
     do { \
     (num) = ((UINT4) ((unsigned char) buff[0])) + \
             ((UINT4) ((unsigned char) buff[1]) << 8) + \
	     ((UINT4) ((unsigned char) buff[2]) << 16) + \
             ((UINT4) ((unsigned char) buff[3]) << 24); \
     buff += 4; \
     } while (0)

#define _BinUnpack3Byte(buff, num) \
     do { \
     (num) = ((UINT4) ((unsigned char) buff[0])) + \
             ((UINT4) ((unsigned char) buff[1]) << 8) + \
	     ((UINT4) ((unsigned char) buff[2]) << 16); \
     buff += 3; \
     } while (0)

#define _BinUnpack2Byte(buff, num) \
     do { \
     (num) = ((UINT4) ((unsigned char) buff[0])) + \
             ((UINT4) ((unsigned char) buff[1]) << 8); \
     buff += 2; \
     } while (0)

#define _BinUnpackByte(buff, byte) \
     byte = buff[0]; \
     buff += 1

#define _BinUnpackStr(buff, s) \
     s = buff; \
     buff += strlen (buff) + 1

#define _BinUnpackFixStr(buff, s, len) \
     strcpy (s, buff); \
     buff += len + 1

#define _BinFileUnpackNum(file, num) \
     do { char buff[4]; \
     fread (buff, 4, 1, file); \
     num = ((UINT4) ((unsigned char) buff[0])) + \
           ((UINT4) ((unsigned char) buff[1]) << 8) + \
	   ((UINT4) ((unsigned char) buff[2]) << 16) + \
           ((UINT4) ((unsigned char) buff[3]) << 24); \
     } while (0)

#define _BinPackFip(buff, fip) \
  do { \
  buff[0] = fip & BYTE1; \
  buff[1] = (fip & BYTE2) >> 8; \
  buff[2] = (fip & BYTE3) >> 16; \
  buff[3] = (fip & BYTE4) >> 24; \
  buff += 4; \
  } while (0)
  
#define _BinPackNum(buff, num) \
  do { \
  buff[0] = num & BYTE1; \
  buff[1] = (num & BYTE2) >> 8; \
  buff[2] = (num & BYTE3) >> 16; \
  buff[3] = (num & BYTE4) >> 24; \
  buff += 4; \
  } while (0)

#define _BinPack3Byte(buff, num) \
  do { \
  buff[0] = num & BYTE1; \
  buff[1] = (num & BYTE2) >> 8; \
  buff[2] = (num & BYTE3) >> 16; \
  buff += 3; \
  } while (0)

#define _BinPack2Byte(buff, num) \
  do { \
  buff[0] = num & BYTE1; \
  buff[1] = (num & BYTE2) >> 8; \
  buff += 2; \
  } while (0)

#define _BinPackByte(buff, byte) \
  buff[0] = byte; \
  buff += 1

#define _BinPackFixStr(buff, s, len) \
     strcpy(buff, s); \
     buff += len + 1

#define _BinPackStr(buff, s) \
     strcpy(buff, s); \
     buff += strlen (s) + 1;

#define _BinFilePackNum(file, num) \
     do { char buff[4]; \
     buff[0] = num & BYTE1; \
     buff[1] = (num & BYTE2) >> 8; \
     buff[2] = (num & BYTE3) >> 16; \
     buff[3] = (num & BYTE4) >> 24; \
     fwrite (buff, 4, 1, file); \
     } while (0)







hile (0)

#define _BinPackByte(buff, byte) \
  buff[0] = byte; \
  buff += 1

#define _BinPackFixStr(buff, s, len) \
     strcpy(buff, s); \
     buff += len + 1

#define _Bisrs/src/blub.c
#include <stdlib.h>
#include "def.h"
#include "blub.h"
#include "parse.h"
#include "listv.h"

/****************************************************
** ALLOCATION
*/

#define MAX_OFFS 0xFFFFFFFFL

#define _getVal(obj) (obj)

STRoStatic_20 attrDescr_strs[] = {
    {{}, "int"},
    {{}, "PTR"},  
    {{}, "STRv"}, 
    {{}, "OBJv"},
    {{}, "ListAttr"}, 
    {{}, "CLASSBODYv"}, 
    {{}, "ATTRv"},
};
     
ATTRoDescr attrDescr[] = {
    {(STRv)(attrDescr_strs+ATTR_int), sizeof(int)}, 
    {(STRv)(attrDescr_strs+ATTR_PTR), sizeof(PTR)}, 
    {(STRv)(attrDescr_strs+ATTR_STRv), sizeof(STRv)}, 
    {(STRv)(attrDescr_strs+ATTR_OBJv), sizeof(OBJv)}, 
    {(STRv)(attrDescr_strs+ATTR_ListAttr), sizeof(ListAttr)},
    {(STRv)(attrDescr_strs+ATTR_CLASSBODYv), sizeof(CLASSBODYv)},
    {(STRv)(attrDescr_strs+ATTR_ATTRv), sizeof(ATTRv)}
};    


/* the descriptor for all list attribute headers */ 

STRoStatic_20 attrListName= {{}, "list"};

ATTRv attrListAttr= {
    (STRv)&attrListName,
    ATTR_ListAttr,
    NULL,
    0
};

void AttrNamesInit() {
    _StrInitStatic(attrDescr_strs,7); 
    _StrInitStatic(&attrListName,1);
}
    

/****************************************************
** POLYMORPHIC OPERATIONS ON ATTRIBUTES
****************************************************/

void ObjDoAttrRecursive(void* obj, CLASSv descr, AttrAction act, void* info) {
    CLASSv inherits=descr->inherits;
    ATTRv* attr;
    ATTRv* list=descr->attrs;
    if (inherits) ObjDoAttrRecursive(obj, inherits, act, info);
    for (attr=list; attr<descr->fixed; attr++) {
	call(act)(offset(obj, attr->offs, void*), attr, info);
    }
}

void ObjDoAttr(void* obj, AttrAction act, void* info) {
    CLASSv descr=ObjClass(obj);
    ObjDoAttrRecursive(obj, descr, act, info);
}

void ObjDoInList(void* obj, AttrAction act, ATTRv* elem, void* info, void* from, void* to) {
    int elemSize=attrDescr[elem->type].size;
    while (from<to) {
	call (act)(from, elem, info);
	from=cast(from,BYTE*)+elemSize;
    }
}

void ObjDoInListReverse(void* obj, AttrAction act, ATTRv* elem, void* info, void* from, void* to) {
    int elemSize=attrDescr[elem->type].size;
    to=cast(to,BYTE*)-elemSize;
    while (to>=from) {
	call (act)(to, elem, info);
	to=cast(to,BYTE*)-elemSize;
    }
}

void ObjDoList(void* obj, AttrAction act, void* info) {
    ListAttr* list; ATTRv* elem;
    ASSERT (ObjListInfo(obj, &elem, &list),"NotAList"); 
    ObjDoInList(obj, act, elem, info, list+1, list->tail); 
}

void ObjDoAll(void* obj, AttrAction act, void* info) {
    ListAttr* list; ATTRv* elem;
    ObjDoAttr(obj, act, info);
    if (ObjListInfo(obj, &elem, &list)) {
	call (act)(list, &attrListAttr, info);
	ObjDoInList(obj, act, elem, info, list+1, list->tail); 
    }
}

BOOL ObjDoCondRecursive(void* obj, CLASSv descr, AttrCondition act, void* info) {
    CLASSv inherits=descr->inherits;
    ATTRv* attr;
    ATTRv* list=descr->attrs;
    if (inherits) 
	if (!ObjDoCondRecursive(obj, inherits, act, info)) return FALSE;
    for (attr=list; attr<descr->fixed; attr++) {
	if (!call(act)(offset(obj, attr->offs, void*), attr, info)) return FALSE;
    }
    return TRUE;
}

/* operates on attributes, performing an AND operation on cond.
 * Stops as soon as the result is FALSE
 */

BOOL ObjDoCond(void* obj, AttrCondition act, void* info) {
    ListAttr* list; ATTRv* elem;
    if (!ObjDoCondRecursive(obj, _getObj(obj)->descr, act, info)) return FALSE;
    if (ObjListInfo(obj, &elem, &list)) {
	int elemSize; void *from,*to;
	if (!call (act)(list, &attrListAttr, info)) return FALSE;
	elemSize=attrDescr[elem->type].size;
	from=list+1;
	to=list->tail;
	while (from<to) {
	    if (!call (act)(from, elem, info)) return FALSE;
	    from=cast(from,BYTE*)+elemSize;
	}
    }    
    return TRUE;
}


/******************************************************************
** BASIC ACTION DEFINITIONS
******************************************************************/

void PolyNotImpl() { THROW("NotImplemented"); }
void PolyNothing() {}

/****************************************************
** COPYING
*/

typedef void (*ValCopier)  (void* dest, void* src);

void PolyIntCpy(int* dest,  int* src) { *dest=*src; }
void PolyPtrCpy(void** dest, void** src) { *dest=*src; } 
void PolyStrCpy(STRv* dest, STRv* src) { *dest=StrCpy(*src);}
void PolyObjCpy(void** dest, void** src) { *dest=ObjCpy(*src);}
void PolyListCpy(ListAttr* d, ListAttr* s) { 
    d->tail=offset(d,displ(s->tail, s),BYTE*);
    d->end=d->tail; /* ??? what if grow is reserved? */
}

void PolyClassCpy(CLASSBODYv* d, CLASSBODYv* s) {
    d->inherits=ObjCpy(s->inherits);
    d->fixed=offset(d, displ(s->fixed, s), ATTRv*);
    d->byName=s->byName;
    d->values=NULL; 
}

void PolyAttrCpy(ATTRv* d, ATTRv* s) {
    if (s->name) d->name=StrCpy(s->name);
    else d->name=NULL;
    d->offs=s->offs;
    d->type=s->type;
    d->more=s->more; /*...???? how do I copy this? */    
}

void AttrCopyAction(void* attr, ATTRv* a, void* copyOffs) {
    static ValCopier copyOp[] = {
	(ValCopier) PolyIntCpy, 
	(ValCopier) PolyPtrCpy, 
	(ValCopier) PolyStrCpy, 
	(ValCopier) PolyObjCpy, 
	(ValCopier) PolyListCpy, 
	(ValCopier) PolyClassCpy, 
	(ValCopier) PolyAttrCpy
    };
    call (copyOp[a->type])(offset(attr, (int)copyOffs, void*), attr); 
};

/****************************************************
** MOVING
*/

typedef void (*ValMover)  (void* dest, void* src);

void PolyClassMove(CLASSBODYv* d, CLASSBODYv* s) {
    DICTv byName=s->byName;
    if (byName && (s->inherits && byName!=s->inherits->byName)) {
	/* had a local dictionary, offset attributes */
        ListAttr* slist=cast(s+1,ListAttr*);
	ListAttr* dlist=cast(d+1,ListAttr*);
	DictOffsetWithin(byName, slist, displ(slist->tail,slist), dlist);
    }
    d->inherits=s->inherits;
    d->fixed=offset(d, displ(s->fixed, s), ATTRv*);
    d->byName=s->byName;
    d->values=s->values; 
}

void PolyAttrMove(ATTRv* d, ATTRv* s) {
    d->name=s->name;
    d->offs=s->offs;
    d->type=s->type;
    d->more=s->more;
}

void AttrMoveAction(void* attr, ATTRv* a, void* moveOffs) {
    static ValMover moveOp[] = {
	(ValMover) PolyIntCpy, 
	(ValMover) PolyPtrCpy, 
	(ValMover) PolyPtrCpy, 
	(ValMover) PolyPtrCpy, 
	(ValMover) PolyListCpy, 
	(ValMover) PolyClassMove, 
	(ValMover) PolyAttrMove 
    };
    call (moveOp[a->type])(offset(attr,(int)moveOffs,void*),attr);
}

/****************************************************
** DELETING
*/

typedef void (*ValDeleter) (void* val);

void PolyStrDel(STRv* v, void* nothing) { StrDel(*v); }
void PolyObjDel(void** v, void* nothing) { ObjDel(*v); }
void PolyClassDel(CLASSBODYv* c) {
    DICTv* byName=&c->byName;
    if (*byName && (c->inherits && *byName!=c->inherits->byName)) {
	/* had a local dictionary, delete */
	DictDestroy(*byName);
    }
    if (c->values) DictDestroy(c->values);
    ObjDel(c->inherits);    
}

void PolyAttrDel(ATTRv* a, void* nothing) {
    if (a->name) StrDel(a->name);
}

void AttrDelAction(void* attr, ATTRv* a, void* nothing) {
    static ValDeleter delOp[] = {
	(ValDeleter) PolyNothing, 
	(ValDeleter) PolyNothing, 
	(ValDeleter) PolyStrDel, 
	(ValDeleter) PolyObjDel,  
	(ValDeleter) PolyNothing, 
	(ValDeleter) PolyClassDel, 
	(ValDeleter) PolyAttrDel	
    };
    call (delOp[a->type])(attr);
}

/****************************************************
** HASHING
*/

/* rotates right sum by 5 bits (*index) and xores with num */
#define _hash(sum, num) sum=(sum>>5)^(sum<<27)^num;
#define _hashGo(sum,index) {int disp=(index<<2+index)&31;sum=(sum>>disp)^(sum<<(32-disp));}

UINT4 StrHash1(STRv s) {
    UINT4 sum=0;
    if (s) {
	int len=StrLen(s);
	char* p=Str(s);
	char* stop=p+len;
	_hash(sum,len);
	while (p!=stop) _hash(sum,*p++);
    }
    return sum;
}

typedef UINT4  (*ValHasher1)  (void* val);

UINT4 PolyIntHash1(int* i)  { return i; }
UINT4 PolyPtrHash1(PTR* p)  { return (WORD) *p; }
UINT4 PolyStrHash1(STRv* sp) { return StrHash1(*sp); }
UINT4 PolyObjHash1(void** obj) { return ObjHash1(*obj); }
UINT4 PolyListHash(ListAttr* l) { return displ(l->tail,l); }

UINT4 PolyClassHash(CLASSBODYv* c) {
    return ObjHash1(c->inherits);
}

UINT4 PolyAttrHash(ATTRv* a) {
    UINT4 sum=0;
    _hash(sum, StrHash1(a->name));
    _hash(sum, a->type);
    return sum;
}

void AttrHashAction(void* attr, ATTRv* a, void* hashVal) {
    static ValHasher1 hashOp[]= {
	(ValHasher1) PolyIntHash1,
	(ValHasher1) PolyPtrHash1, 
	(ValHasher1) PolyStrHash1, 
	(ValHasher1) PolyObjHash1, 
	(ValHasher1) PolyListHash, 
	(ValHasher1) PolyClassHash, 
	(ValHasher1) PolyAttrHash 
    };
    UINT4 hash=*(WORD*)hashVal;
    _hash(hash, call (hashOp[a->type])(attr));
    *(WORD*)hashVal=hash;
}

/****************************************************
** COMPARING
*/

typedef BOOL (*ValComparer1) (void* val1, void* val2);

BOOL PolyObjEqual(void** obj1,void** obj2) { return ObjEqual(*obj1,*obj2); }

BOOL PolyListEqual(ListAttr* l1, ListAttr* l2) { return displ(l1->tail,l1)==displ(l2->tail,l2);}

BOOL PolyClassEqual(CLASSBODYv* c1, CLASSBODYv* c2) {
    return c1->inherits==c2->inherits;
}

BOOL PolyAttrEqual(ATTRv* a1,ATTRv* a2) {
    return 
	StrEqual(a1->name,a2->name) &&
	a1->type==a2->type &&
	ObjEqual(a1->more,a2->more);
}

BOOL AttrEqualCond(void* attr, ATTRv* a, void* compOffs) {
    static ValComparer equalCond[]= {
	(ValComparer1) PolyIntEqual, 
	(ValComparer1) PolyPtrEqual, 	
	(ValComparer1) PolyStrEqual, 
	(ValComparer1) PolyObjEqual,
	(ValComparer1) PolyListEqual,
	(ValComparer1) PolyClassEqual,
	(ValComparer1) PolyAttrEqual
    };
    return call(equalCond[a->type])(attr, offset(attr,(int)compOffs, void*));
}

/*************************************************
** PREDEFINED CLASSES
*************************************************/

#define SIZE_HEAD sizeof(OBJo)
#define SIZE_CLASSHEAD (sizeof(CLASSo)-sizeof(ListAttr)-sizeof(ATTRv)*10)
#define SIZE_ATTR sizeof(ATTRv)

CLASSo bootClassClass= {
    { 2, &bootClassClass }, 
    NULL, /* should inherit BootObjClass */
    &bootClassClass.attrs[1],
    NULL, NULL,
    {(BYTE*)&bootClassClass.attrs[2], (BYTE*)&bootClassClass.attrs[2]}, {
	{ NULL, ATTR_CLASSBODYv, NULL, SIZE_HEAD }, 
	{ NULL, ATTR_ATTRv, NULL, SIZE_CLASSHEAD } 
    }
};

CLASSo bootObjClass = {
    { 2, &bootClassClass},
    NULL,
    &bootObjClass.attrs[0], 
    NULL, NULL, 
    { (BYTE*)&bootObjClass.attrs[1], (BYTE*)&bootObjClass.attrs[1] }, {
	{ NULL, -1, NULL, SIZE_HEAD }
    }
};

OBJo objBuf = {
    1, &bootObjClass
};

void* Object=&objBuf;
void* Class=&bootObjClass;

/*************************************************************************
** NAMED VALUES MNGM.
*************************************************************************/

/* a val can have several names associated with it, but the first one counts */

struct {
    DICTv vals;
    DICTv names;
    DICTv ids;
    int   lastId;
} sysVals;


void SysInclude(SYSoName* list) {
    static CLASSoDICT* valsIndex=NULL;
    static CLASSoDICT* namesIndex=NULL;
    static CLASSoDICT* idsIndex=NULL;
    if (!valsIndex) {
	valsIndex=DictCreateClassPtrKey(NULL, mPtr(SYSoName, val), TRUE);
	namesIndex=DictCreateClassStrKey(NULL, mPtr(SYSoName, name), FALSE);
	idsIndex=DictCreateClassIntKey(NULL, mPtr(SYSoName, id), FALSE);
	sysVals.vals=DictCreate(valsIndex);
	sysVals.names=DictCreate(namesIndex);
	sysVals.ids=DictCreate(idsIndex);
    }
    while (list->name) {
       list->id=sysVals.lastId++;
       DictAddPtr(&sysVals.names,list);
       DictAddPtr(&sysVals.vals,list);
       DictAddPtr(&sysVals.ids,list);
       list++; 
    }
}

int SysIdNum() {
    return sysVals.lastId;
}

void SysName(STRv name,void* val) {
    struct SYSoName* v = 
	_palloc(SYSoName);
    v->name=StrCpy(name);
    v->val=ObjCpy(val);
    v->id=-1;
    DictAddPtr(&sysVals.vals, v);
    DictAddPtr(&sysVals.names, v);
}

void SysForgetName(STRv name) {
    Iter i=DictWith(sysVals.names,&name);
    SYSoName* v=DictIn(i,SYSoName*);
    if (v->id==-1) {
	/* only forget if run-time defined */
	DictRemovePtr(&sysVals.vals,v);
	DictRemove(&sysVals.names,i);
	StrDel(v->name);
	ObjDel(v->val);
	_pfree(v);
    }
}

void** SysFromName(STRv name) {
    Iter n=DictWith(sysVals.names,&name);
    if (n) return &DictIn(n,SYSoName*)->val;
    else return NULL;
}

void** SysFromId(int id) {
    Iter n=DictWith(sysVals.ids,&id);
    if (n) return &DictIn(n,SYSoName*)->val;
    else return NULL;
}    


STRv SysToName(void* val) {
    Iter n=DictWith(sysVals.vals,&val);
    if (n) return DictIn(n,SYSoName*)->name;
    else return NULL;
}

int SysToId(void* val) {
    Iter n=DictWith(sysVals.vals,&val);
    if (n) return DictIn(n,SYSoName*)->id;
    else return -1;
}
    


/**********************************************************
** INITIALIZATION
**********************************************************/

STRoStatic_20 blubNames[]= {
    {{},"NULL"},
    {{},"Class"}, 
    {{},"Object"}    
}; 

SYSoName blubValues[]= {
    {(STRv)&blubNames[0], NULL },     
    {(STRv)&blubNames[1], &bootClassClass}, 
    {(STRv)&blubNames[2], &bootObjClass}, 
    {NULL, NULL}
};

CLASSoDICT byNameProp = {
    PolyStrEqual, 
    PolyStrHash, 
    (KeyAccessor)KeyOffset, 
    0, /* to be initialized */
    FALSE
};    

void ObjInit() {
    AttrNamesInit();
    _StrInitStatic(blubNames,3);
    SysInclude(blubValues);
    byNameProp.toKeyInfo=mPtr(ATTRv,name); 
}

/************************************************************
** INTERNAL IMPLEMENTATION hiding functions
*/


int ObjSize(OBJv obj) {
    ATTRv* fixed=ObjClass(obj)->fixed;
    int size=fixed->offs;
    if (fixed->type!=-1) {
	/* it's a list */
	ListAttr* list=offset(obj, size, ListAttr*);
	size+=displ(list->tail, list);
    }
    return size;
}


OBJv ObjRealloc(OBJv obj, int grow) {
    OBJv o=(OBJv)malloc(ObjSize(obj)+grow);
    o->usage=1;
    o->descr=ObjCpy(obj->descr);
    return o;
}

void ObjFree(OBJv obj) {
    CLASSv descr=obj->descr;
    if (descr->values) {
	Iter i=DictWith(descr->values,obj);
	/* is the object is under value-management, remove it */
	if (DictIn(i,OBJv)==obj) DictRemove(&descr->values, i);
    }
    ObjDel(obj->descr);
    free(obj);
}

CLASSv ObjClass(void* obj) {
    return _getObj(obj)->descr;
}


/*****************************************************************
** Object buffer operations 
*/

void* ObjChangeImpl(void** obj) {
    OBJv o=_getObj(*obj);
    if (o->usage>1) {
	OBJv old=o;
	*obj=o=ObjRealloc(old, 0);
	ObjDoAll(old, AttrCopyAction, (void*)displ(o, old));
	old->usage--;
    }
    else {
	DICTv vals=o->descr->values;
	if (vals) {
	    /* if value managed, uncommit value */
	    DictRemoveWith(&vals,o);
	    o->descr->values=vals;
	}
    }   
    return _getVal(o);
}

void ObjDel(void* obj) {
    if (obj) {
      OBJv o=_getObj(obj);
      if (!--o->usage) {
	ObjDoAll(obj, AttrDelAction, NULL);
	ObjFree(o);
      }
    }
}

CLASSoDICT dictValueClass = {
    (ValComparer) ObjEqual,
    (ValHasher) ObjHash,
    (KeyAccessor) KeyItself,
    NULL,
    FALSE
};
    
void ObjCommit(void** obj) {
    OBJv o=*obj; OBJv *vp, v;
    CLASSv descr=_getObj(o)->descr;
    if (!descr->values) {
	/* create class value dictionary in class */
	descr->values=DictCreate(&dictValueClass);
    } 
    vp=&DictSet(&descr->values, o, OBJv);
    v=*vp;
    if (v) ObjSet(obj, v);  /* equal value already there */
    else *vp=o;		    /* new value */
}

/*****************************************************************
** REFERENCE COUNTING operations 
*/

void* ObjCpy(void* obj) { 
    if (obj) _getObj(obj)->usage++; 
    return obj; 
}

void ObjSet(void** dest, void* src) { 
    ObjDel(*dest); *dest=ObjCpy(src); 
}

int ObjShared(void* obj) { 
    return _getObj(obj)->usage-1; 
}

UINT4 ObjHash1(void* obj) {
    UINT4 hash=0;
    if (obj) ObjDoAll(obj, AttrHashAction, &hash);
    return hash;
}

int ObjHash(void* obj, int max) {
    int n= ObjHash1(obj)%max;
    return n;
}

BOOL ObjEqual(void* obj1, void* obj2) {
    if (obj1==obj2) return TRUE;
    /* if value managed, I can only check the pointers here */
    if (_getObj(obj1)->descr!=_getObj(obj2)->descr) return FALSE;
    if (ObjSize(obj1)!=ObjSize(obj2)) return FALSE;
    return ObjDoCond(obj1, AttrEqualCond, displ(obj2, obj1));
}

/****************************************************************************
** CLASS MANAGEMENT
****************************************************************************/


void ObjMakeClass(void* obj, STRv name) {
    PATHv p; CLASSv descr=_getObj(obj)->descr;
    SysName(name,descr);
}

AttrIter ClassAttrNew(CLASSv* cl, STRv name, AttrTypeId type, void* more) {
    CLASSv descr=*cl;
    ATTRv* attr;
    int offs;
    offs=descr->fixed->offs;
    offs+=align(offs,attrDescr[type].size);
    ASSERT(descr->fixed->type==-1, "CannotInheritFromList");
    if (ObjShared(descr)) {
	CLASSv old=descr;
        descr=ObjCpy(Class);
	attr=&ObjListApp(&descr, ATTRv);
	descr->inherits=old;
    }
    else {
        attr=&ObjListApp(&descr, ATTRv);
    }
    /* last ATTRv is fake, only for size: set it */
    descr->fixed=attr;
    attr->offs=offs+attrDescr[type].size;
    attr->type=-1;
    attr->name=NULL;

    /* now set attribute descriptor */
    attr--;
    attr->type=type;
    attr->more=more;
    attr->offs=offs;

    /* manage now name */
    if (name) {
	DICTv* byName=&descr->byName;
	if (!*byName) *byName=DictCreate(&byNameProp);
	else if (descr->inherits && *byName==descr->inherits->byName) {
	    /* copy old dictionary if it was shared */
	    *byName=DictCopy(descr->inherits->byName);
	}
	DictAdd(byName, &name, ATTRv*)=attr;
	attr->name=StrCpy(name); 
    }
    else attr->name=NULL;
    /* now value manage */
    ObjCommit(&descr);
    *cl=descr; return offs;
}

AttrIter ClassListNew(CLASSv* cl, AttrTypeId type, void* more) {
    CLASSv descr=*cl;
    ATTRv* attr;int offs;
    ASSERT(descr->fixed->type==-1, "CannotInheritFromList");
    offs=descr->fixed->offs;
    offs+=align(offs,attrDescr[type].size);
    if (ObjShared(descr)) {
	CLASSv old=descr;
        descr=ObjCpy(Class);
	attr=ObjChange(&descr, CLASSv)->fixed;
	descr->inherits=old;
    }
    else {
        attr=ObjChange(&descr, CLASSv)->fixed;
    }
    attr->type=type;
    attr->more=more;
    attr->name=NULL;
    attr->offs=offs;
    ObjCommit(&descr);
    *cl=descr; return offs;
}

AttrIter ClassAttrWith(CLASSv descr, STRv name, ATTRv** attr) {
    AttrIter i;
    ATTRv* ia=NULL;
    if (isalpha(Str(name)[0])) {
        /* a normal attribute name */
        Iter a=DictWith(descr->byName, &name);
	if (a) {
	    ia=DictIn(a, ATTRv*);
	    i=ia->offs;
	}
	else i=NULL;
    }
    else {
        /* a list element */
        int pos=atoi(Str(name));
	ia=descr->fixed;
	ASSERT(ia->type!=-1,"NotAList");
	i=ia->offs+sizeof(ListAttr)+attrDescr[ia->type].size*pos;
    }
    *attr=ia;
    return i;
}

AttrIter ClassAttrFirst(CLASSv descr) {
    if (descr->inherits && descr!=Class) return ClassAttrFirst(descr->inherits);
    else {
	ATTRv* first=&descr->attrs[0];
	if (first->type!=-1) return first->offs;
	else return NULL;
    }
}

void ClassAttrNext(CLASSv descr, AttrIter* i) {
    
}

void* ClassAlloc(CLASSv cl, int nElem) {
    ATTRv* fixed=cl->fixed;
    int size=fixed->offs; int lSize;
    OBJv o; BOOL isList=fixed->type!=-1;
    if (isList) {
	lSize=nElem*attrDescr[fixed->type].size;
	size+=sizeof(ListAttr)+lSize;
    }
    o=(OBJv)malloc(size);
    o->descr=ObjCpy(cl);
    o->usage=1;
    if (isList) {
	/* init list attribute, empty list of given size */
	ListAttr* l=offset(o, fixed->offs, ListAttr*);
	l->tail=(BYTE*)(l+1);
	l->end=l->tail+lSize;
	l->tail=l->end;
    }
    return o;
}

/**************************************************************
** ATTRIBUTE OPERATIONS
***************************************************************/

void* ObjAttrNewImpl(void** obj, STRv name, int type, void* more) {
    OBJv old=_getObj(*obj);
    OBJv   o; int offs;
    o=ObjRealloc(old, attrDescr[type].size); 
    ObjDoAttr(old, AttrCopyAction, (void*)displ(o,old));
    ObjDel(old);
    offs=ClassAttrNew(&o->descr, name, type, more);
    *obj=o; return offset(o, offs, void*);
}

/* attribute access */
void* ObjAttrInImpl(void* obj, AttrIter i) {
    return offset(obj, i, void*);
}

ATTRp lastAttr=NULL;

void* ObjAttrImpl(void* obj, STRv name, int type) {
    AttrIter offs=ObjAttrWith(obj,name);
    ASSERT(type!=-1 || lastAttr->type==type, "TypeMismatch");
    return offset(obj, offs, void*);
}

/* attribute iteration */

AttrIter  ObjAttrWith(void* obj, STRv name) {
    CLASSv descr=_getObj(obj)->descr;
    AttrIter i;
    if (isalpha(Str(name)[0])) {
        /* a normal attribute name */
        lastAttr=DictAt(descr->byName, &name, ATTRv*);
	i=lastAttr->offs;
    }
    else {
        /* a list element */
        int pos=atoi(Str(name));
	void* a=ObjListWith(obj,pos);
	ASSERT(a,"NoSuchElem");
	i=displ(a,obj);
    }
    return i;
}

AttrIter  ObjAttrFirst(void* obj) {
    return sizeof(OBJo);
}

void ObjAttrNext(void* obj, AttrIter* i) {
    AttrIter p=*i;
    ATTRv* attr=ObjAttrInfo(obj, p); 
    p=p+attrDescr[attr->type].size;
    if (p>=ObjSize(obj)) p=NULL;
    *i=p;
}

/* attribute information */

ATTRv* ObjAttrInfoFixed(CLASSv descr, int offs) {
    ATTRv* minAttr=&descr->attrs[0];
    if (offs<minAttr->offs) {
	CLASSv inherits=descr->inherits;
	ASSERT(inherits, "InvalidAttribute"); 
	return ObjAttrInfoFixed(inherits,offs);
	
    }
    else {
	/* perform a binary search on offsets, 
	   they are sorted */
	ATTRv* maxAttr=descr->fixed;
	int diff=maxAttr-minAttr;
	while (diff>1) {
	    ATTRv* attr=minAttr+(diff>>1);
	    if (offs<attr->offs) maxAttr=attr;
	    else minAttr=attr;
	    diff=maxAttr-minAttr;
	}
	return minAttr;
    }
}

ATTRv* ObjAttrInfo(void* obj, AttrIter offs) {
    void* a=offset(obj, offs, void*);
    ATTRv* elem; ListAttr* l;
    if (ObjListInfo(obj, &elem, &l) && a>=(void*)l && a<(void*)l->tail) {
	/* it's a list element */
        if (a==l) return &attrListAttr;
	return elem;
    }
    else {
	CLASSv descr=_getObj(obj)->descr;
	ASSERT(offs<descr->fixed->offs, "InvalidAttribute");
	return ObjAttrInfoFixed(descr, offs);
    }
}

STRv ObjAttrName(void* obj, AttrIter offs) {
    void* a=offset(obj, offs, void*);
    ATTRv* elem; ListAttr* l;
    if (ObjListInfo(obj, &elem, &l) && a>=(void*)l && a<(void*)l->tail) {
	/* it's a list element */
        if (a==l) return StrCpy(attrListAttr.name);
	else {
	    int pos=ObjListPos(obj,a);
	    return StrFromInt(pos);
	}
    }
    else {
	CLASSv descr=_getObj(obj)->descr;
	ASSERT(offs<descr->fixed->offs, "InvalidAttribute");
	return StrCpy(ObjAttrInfoFixed(descr, offs)->name);
    }
}


/**************************************************************************
** LIST OPERATIONS 
**************************************************************************/


void* ObjListNewImpl(void** obj, int dim, int type, void* more) {
    OBJv old=_getObj(*obj);
    OBJv   o; int offs; ListAttr* list;
    int dimSize=attrDescr[type].size*dim;
    o=ObjRealloc(old, sizeof(ListAttr)+dimSize); 
    ObjDoAttr(old, AttrCopyAction, (void*)displ(o,old));
    ObjDel(old); 
    offs=ClassListNew(&o->descr, type, more);
    /* initialize the ListAttr */
    list = offset(o,offs,ListAttr*);
    list->tail=offset(list+1,dimSize,BYTE*);
    list->end=list->tail;
    *obj=o;
    return offset(o, offs+sizeof(ListAttr), void*);
}

void* ObjListAddImpl(void** obj, Iter pos, int numAdd) {
    OBJv o=_getObj(*obj);
    ListAttr* list; ATTRv* elem; 
    int addSize; BYTE* head; BYTE* tail;
    ASSERT(ObjListInfo(o, &elem, &list), "NotAList");
    head=(BYTE*)(list+1); tail=list->tail;
    addSize=numAdd*attrDescr[elem->type].size;
    if (!pos) pos=tail; /* append */
    if (o->usage>1) {
	/* make a real copy with space for new elements */
	OBJv old=o; int offs;
	o=ObjRealloc(old, addSize);
	offs=displ(o, old);
	ObjDoAttr(old, AttrCopyAction, (void*)offs);
	ObjDoInList(old, AttrCopyAction, elem, (void*)offs, head, pos);
	ObjDoInList(old, AttrCopyAction, elem, cast(offs+addSize,void*), pos, tail);
	list=offset(list, offs, ListAttr*);
	list->tail=tail+offs+addSize;
	list->end=list->tail; 
	old->usage--; pos=cast(pos,BYTE*)+offs;
    }
    else {
	if (tail+addSize<=list->end) {
	    /* can grow, only move tail */
	    ObjDoInListReverse(obj, AttrMoveAction, elem, (void*)addSize, pos, tail);
	    list->tail+=addSize;
	}
	else {
	    /* allocate a buffer, move old obj in new */
	    OBJv old=o; int offs;
	    o=ObjRealloc(old, addSize);
	    offs=displ(o, old);
	    ObjDoAttr(old, AttrMoveAction, (void*)offs);
	    ObjDoInList(old, AttrMoveAction, elem, (void*)offs, head, pos);
	    ObjDoInList(old, AttrMoveAction, elem, cast(offs+addSize,void*), pos, list->tail);
	    list=offset(list, offs, ListAttr*);
	    list->tail=tail+offs+addSize;
	    list->end=list->tail; 
	    ObjFree(old); pos=cast(pos,BYTE*)+offs;
	}
    }
    *obj=_getVal(o);
    return pos;
}

void* ObjListAppImpl(void** obj, int num) {
    return ObjListAddImpl(obj, NULL, num);
}

void* ObjListInsImpl(void** obj, int num) {
    return ObjListAddImpl(obj, ObjListFirst(*obj), num);
}

void ObjListCut(void** obj, Iter pos, int numRem) {
    OBJv o=_getObj(*obj);
    ListAttr* list; ATTRv* elem; 
    int remSize; BYTE* head; BYTE* tail; void* cutPos;
    ASSERT(ObjListInfo(o, &elem, &list),"NotAList");
    head=(BYTE*)(list+1); tail=list->tail;
    remSize=attrDescr[elem->type].size*numRem;
    if (!pos) pos=offset(tail, -remSize, Iter); /* remove at the end */
    cutPos=offset(pos, remSize, void*);
    if (o->usage>1) {
	/* make a real copy skipping the removed elements */
	OBJv old=o; int offs;
	o=ObjRealloc(old, -remSize);
	offs=displ(o, old);
	ObjDoAttr(old, AttrCopyAction, (void*)offs);	     
	ObjDoInList(old, AttrCopyAction, elem, (void*)offs, head, pos);
	ObjDoInList(old, AttrCopyAction, elem, cast(offs-remSize,void*), cutPos, tail);
	list=offset(list, offs, ListAttr*);
	list->tail=tail+offs-remSize;
	list->end=list->tail; 	
	old->usage--;
    }
    else {
	/* only move tail,leave space for grow */
        ObjDoInList(o, AttrDelAction, elem, NULL, pos, cutPos);
	ObjDoInList(o, AttrMoveAction, elem, (void*)(-remSize), cutPos, tail);
	list->tail-=remSize;
    }
    *obj=_getVal(o);
}

void ObjListGrow(void** obj, int num) {
    OBJv o=_getObj(*obj);
    ListAttr* list; ATTRv* elem; 
    int size; BYTE* head; BYTE* tail; void* cutPos;
    ASSERT(ObjListInfo(o, &elem, &list),"NotAList");
    head=(BYTE*)(list+1); tail=list->tail;
    size=attrDescr[elem->type].size*num;
    if (o->usage>1 || offset(tail, size, BYTE*)>list->end) {
	/* copy the list into a new buffer, making space for n elements */
	OBJv old=o; int offs;
	o=ObjRealloc(old, size-displ(tail, head));
	offs=displ(o, old);
	ObjDoAll(old, AttrCopyAction, (void*)offs);	     
	list=offset(list, offs, ListAttr*);
	list->end=offset(list->tail, size, BYTE*); 	
	ObjDel(old);
    }
    *obj=o;
}

/* list access */

void* ObjListInImpl(Iter i) {
    ASSERT(i, "NoSuchElem");
    return i;
}

/* list iteration */

Iter ObjListFirst(void* obj) {
    Iter i;
    ATTRv* elem; ListAttr* list;
    ASSERT(ObjListInfo(obj, &elem, &list), "NotAList");
    i=list+1;
    if (i>=(void*)list->tail) i=NULL;
    return i;
}

void ObjListNext(void* obj, Iter* i) {
    Iter p=*i;
    ATTRv* elem; ListAttr* list;
    ASSERT(ObjListInfo(obj, &elem, &list), "NotAList");
    p=offset(p, attrDescr[elem->type].size, Iter);
    if (p>=(void*)list->tail) p=NULL;
    *i=p;
}

Iter ObjListLast(void* obj) {
    Iter i;
    ATTRv* elem; ListAttr* list;
    ASSERT(ObjListInfo(obj, &elem, &list), "NotAList");
    i=offset(list->tail, -attrDescr[elem->type].size, Iter);
    if (i<cast(list+1,void*)) i=NULL;
    return i;    
}

void ObjListPrev(void* obj, Iter* i) {
    Iter p=*i;
    ATTRv* elem; ListAttr* list;
    ASSERT(ObjListInfo(obj, &elem, &list), "NotAList");
    p=offset(p, -attrDescr[elem->type].size, Iter);
    if (p<cast(list+1,void*)) p=NULL;
    *i=p;
}  

Iter ObjListWith(void* obj, int pos) {
    Iter i;
    ATTRv* elem; ListAttr* list;
    ASSERT(ObjListInfo(obj, &elem, &list), "NotAList");
    i=offset(list+1,pos*attrDescr[elem->type].size,Iter);
    if (i>=(void*)list->tail) i=NULL;
    return i;
}

/* conversions */

int ObjListPos(void* obj, Iter i) {
    ATTRv* elem; ListAttr* list;
    ASSERT(ObjListInfo(obj, &elem, &list), "NotAList");
    ASSERT(i,"NoSuchElem");
    return displ(i, list+1)/attrDescr[elem->type].size;
}    

/* information */

int ObjListCard(void* obj) {
    ATTRv* elem; ListAttr* list;
    if (ObjListInfo(obj, &elem, &list))
	return displ(list->tail, list+1)/attrDescr[elem->type].size;    
    else return 0;
}

BOOL ObjListInfo(void* obj, ATTRp* elem, struct ListAttr** list) {
    ATTRv* fixed=ObjClass(obj)->fixed;
    if (fixed->type==-1) return FALSE;
    *list=offset(obj, fixed->offs, ListAttr*);
    lastAttr=*elem=fixed;
    return TRUE;
}



typedef struct IntList {
    int num;
    int size;
    int arr[1];
} IntList;

typedef struct STRvList {
    int num;
    int size;
    STRv arr[1];
} STRvList;

typedef struct OBJvList {
    int   num;
    void* end;
    OBJv  arr[1];
} OBJvList;

    else return 0;
}

BOOL ObjListInfo(void* srs/src/blub.h
#define _OBJ_H

#include "strv.h"
#include "dict.h"

/****************************************************
** BASIC ATTRIBUTE TYPE DEFINITIONS
****************************************************/

typedef enum AttrTypeId { 
    ATTR_int, 
    ATTR_PTR, 
    ATTR_STRv, 
    ATTR_OBJv, 
    ATTR_ListAttr, 
    ATTR_CLASSBODYv, 
    ATTR_ATTRv, 
    ATTR_UNDEF 
} AttrTypeId;

typedef struct ATTRoDescr {
    STRv        name;
    int		size;
} ATTRoDescr;

extern ATTRoDescr attrDescr[];

/* pre-defined  attribute types */

typedef void*              PTR;
typedef struct CLASSo*     CLASSv;
typedef struct PATHo*	   PATHv;
typedef void*		   REF;
typedef int		   AttrIter;

typedef struct ListAttr {
    BYTE* tail;
    BYTE* end;
} ListAttr;

typedef struct ATTRv {
    STRv	name;
    AttrTypeId	type;
    /* int		num; *//* 0=list obj, 1=single attr, >=2 array */
    void*	more;
    int		offs;
} ATTRv, *ATTRp;

typedef struct CLASSBODYv {
    CLASSv      inherits;
    ATTRv*	fixed;
    DICTv	byName;
    DICTv	values;
} CLASSBODYv;

/* pre-defined  object types */


typedef struct OBJo {
    int	       usage;
    CLASSv     descr;
} OBJo, *OBJv;

typedef struct CLASSo {
    OBJo	head;
    CLASSv 	inherits;
    ATTRv*	fixed;
    DICTv	byName;
    DICTv	values;
    /* ATTRv list, open */
    ListAttr	list;
    ATTRv	attrs[10];
} CLASSo;


typedef void (*AttrAction) (void* attr, ATTRp a, void* more);
typedef BOOL (*AttrCondition) (void* attr, ATTRp a, void* more);

/* pre-defined objects */
extern void* Object;
extern void* Class;

/* system definition mngm */

typedef struct SYSoName {
    STRv name;
    void* val;
    int  id;
} SYSoName;

void SysInclude(SYSoName* list);
int  SysIdNum();
void SysName(STRv name,void* val);
void SysForgetName(STRv name);
void** SysFromName(STRv name);
void** SysFromId(int id);
STRv SysToName(void* val);
int  SysToId(void* val);

void ObjInit();

/* object operations */
#define _getObj(val) ((OBJv)(val))

void*	ObjCpy(void* obj);
void	ObjDel(void* obj);
void	ObjSet(void** dest, void* src);
void*	ObjChangeImpl(void** obj);
#define ObjChange(valPtr,type) ((type)ObjChangeImpl((void**)valPtr))
void    ObjMakeClass(void* obj, STRv name);

/* object information */
int	ObjShared(void* obj);
int	ObjSize(OBJv obj);

/* attribute operations */
void*	ObjAttrNewImpl  (void** obj, STRv name, int type, void* more);
#define ObjAttrNew(valPtr,name,type) (*(type*)ObjAttrNewImpl((void**)valPtr,name,ATTR_##type,NULL))
#define ObjAttrNewRef(valPtr,name,refType) (*(refType*)ObjAttrNewImpl((void**)valPtr,name,ATTR_OBJv,NULL))
ATTRp	ObjAttrInfo(void* obj, AttrIter i);

/* attribute access */
void*	ObjAttrInImpl(void* obj, AttrIter i);
void*	ObjAttrImpl(void* obj, STRv name, int type);
#define ObjAttrIn(obj, iter, type) (*(type*)ObjAttrInImpl(obj, iter))
#define ObjAttr(obj, name, type) (*(type*)ObjAttrImpl(obj, name, ATTR_##type))

/* attribute iteration */
AttrIter  ObjAttrWith(void* obj, STRv name);
AttrIter  ObjAttrFirst(void* obj);
void	  ObjAttrNext(void* obj, AttrIter* i);
STRv	  ObjAttrName(void* obj, AttrIter offs);

/* member pointer support */
CLASSv    ObjClass(void* obj);
AttrIter  ClassAttrWith(CLASSv descr, STRv name, ATTRp* attr);
AttrIter  ClassAttrFirst(CLASSv descr);
void	  ClassAttrNext(CLASSv descr, AttrIter* i);

/* list operations */
void*	ObjListNewImpl(void** obj, int dim, int type, void* more);
void*   ObjListAddImpl(void** obj, Iter pos, int numAdd);
void*   ObjListAppImpl(void** obj, int num);
void*   ObjListInsImpl(void** obj, int num);
void    ObjListCut    (void** obj, Iter pos, int numRem);
void	ObjListGrow   (void** obj, int num);

#define ObjListNew(valPtr,dim,type) (*(type*)ObjListNewImpl((void**)valPtr,dim,ATTR_##type,NULL))
#define ObjListApp(valPtr,type) (*(type*)ObjListAppImpl((void**)valPtr,1))
#define ObjListIns(valPtr,type) (*(type*)ObjListInsImpl((void**)valPtr,1))
#define ObjListAdd(valPtr,pos,type) (*(type*)ObjListAddImpl((void**)valPtr,pos,1))
#define ObjListAppMany(valPtr,num, type) (*(type*)ObjListAppImpl((void**)valPtr,num))
#define ObjListInsMany(valPtr,num, type) (*(type*)ObjListInsImpl((void**)valPtr,num))
#define ObjListAddMany(valPtr,pos, num, type) (*(type*)ObjListAddImpl((void**)valPtr,pos,num))

/* list access */
void*	 ObjListInImpl(Iter i);
#define  ObjListAt(obj, pos, type) ObjListIn(ObjListWith(obj, pos), type)
#define  ObjListIn(iter, type) (*(type*)ObjListInImpl(iter))

/* list iteration */
Iter	 ObjListFirst(void* obj);
void	 ObjListNext(void* obj, Iter* i);
Iter	 ObjListLast(void* obj);
void	 ObjListPrev(void* obj, Iter* i);

/* id conversions */
Iter	 ObjListWith(void* obj, int pos);
int	 ObjListPos(void* obj, Iter pos);
AttrIter ObjListAttr(void* obj, Iter pos);
Iter     ObjListWithAttr(void* obj, AttrIter a);

/* information */
int	ObjListCard(void* obj);
BOOL	ObjListInfo(void* obj, ATTRp* elem, struct ListAttr** list);

/* services */
void	ObjPrint(void* obj);
void	ObjScan(void* obj);
BOOL	ObjEqual(void* obj1, void* obj2);
UINT4   ObjHash1(void* obj);
int     ObjHash(void* obj,int max);
void    ObjDebug(void* obj);

/* dictionary services */


/* action dispatchers */
void	ObjDoAttr(void* obj, AttrAction act, void* info);
void	ObjDoInList(void* obj, AttrAction act, ATTRp elem, 
	    void* info, void* from, void* to);
void	ObjDoInListReverse(void* obj, AttrAction act, ATTRp elem, 
	    void* info, void* from, void* to);
void	ObjDoList(void* obj, AttrAction act, void* info);
void	ObjDoAll(void* obj, AttrAction act, void* info);

/* predefined actions */
void	AttrCopyAction(void* attr, ATTRp a, void* copyOffs);
void	AttrMoveAction(void* attr, ATTRp a, void* moveOffs);
void	AttrDelAction(void* attr, ATTRp a, void* nothing);
void    AttrHashAction(void* attr, ATTRp a, void* hashVal);
BOOL    AttrEqualCond(void* attr, ATTRp a, void* compOffs);

/* exported polymorphic functions */

void PolyNotImpl();
void PolyNothing();


#endif



bjDoList(void* obj, AttrAction act, void* info);
void	ObjDoAll(void* obj, AttrAction act, void* info);

/* predefined actions */
void	AttrCopyAction(void* attr, ATTRp a, void* copyOffs);
void	AttrMoveAction(void* attr, ATTRp a, srs/src/bnf2c.c
**
**    $RCSfile: bnf2c.c,v $
**    $Revision: 1.9 $
**    $Date: 1997/03/19 11:17:25 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
*/

#include <string.h>
#include <ctype.h>
#include <stdlib.h>
#include <stdio.h>

#include "message.h"
#include "regexp.h"
#include "futil.h"
#include "templ.h"
#include "sm.h"
#include "lst.h"
#include "par.h"
#include "strv.h"
#include "dict.h"
#include "variable.h"
#include "toklist.h"
#include "cursor.h"
#include "icatask.h"
#include "icarus.h"
#include "icaarg.h"
#include "icabnf.h"                                           

#define i2cNodeClassNum 9

#define _PrintClose(x) {	   \
  char *p;			   \
  p = strrchr(BuffGetPtr(x), ','); \
  if(p) {			   \
    *p = ' ';			   \
    p = BuffGetPtr(x);		   \
    BuffPrintF(x, "};\n\n");	   \
    TemplPrint("str", p);	   \
  }				   \
} (void *)NULL

typedef struct I2CoNode {
  void	*ptr;
  INT4	 index;
  INT4	 exeIndex[3];
} I2CoNode, *I2CpNode;

CLASSoDICT nodeDictClass = {
  PolyPtrEqual,
  PolyPtrHash,
  (KeyAccessor)KeyOffset,
  NULL,
  FALSE
};

static char     s1[999];
static char     s2[999];
static char     s3[999];
static DICTv    i2cNodeDict;
static I2CpNode i2cNode;
static INT4     i2cNodeCount[i2cNodeClassNum];
static SMpBUFF  i2cNodeBuff[i2cNodeClassNum],
		i2cVarBuff,
		i2cScopeNameBuff,
		i2cTermReportBuff,
		i2cChoiceSetBuff;

extern ICAoJOB *Job;


/****** I2cPrintVar *****************************************************
**
*/

static INT4 I2cPrintVar(VARo *var)
{
  static INT4 i2cVarCount=-1;
  
  if(var) {
    BuffPrintF(i2cVarBuff, TemplSPrint(s3, TemplN(12, "format")), I2cBody(var));
    return(++i2cVarCount);
  }
  else
   return(-1);
}

/****** I2cRegisterNode *****************************************************
**
*/

static void I2cRegisterNode(BNFoNODE *bnfNode, INT4 level)
{
  I2CpNode *p;

  INT4 i;

/*   printf("Name:%s, level=%d\n", bnfNode->name, level); */
  p=&DictSet(&i2cNodeDict, &bnfNode, I2CpNode);
  if(!*p) {
    if(bnfNode->name) {
      SmSwapS(bnfNode->name, "\\", "\\\\");/* do this first!*/
      SmSwapS(bnfNode->name, "\"", "\\\"");
      SmSwapS(bnfNode->name, "\n", "\\n");
      SmSwapS(bnfNode->name, "\t", "\\t");
    }
    i2cNode = typeAlloc(I2CoNode);
    i2cNode->ptr  = (void *)bnfNode;
    i2cNode->index  = i2cNodeCount[bnfNode->type]++;
    if(bnfNode->type != Term && bnfNode->type != Choice)
      for(i=0; i<3; i++)
        i2cNode->exeIndex[i] = I2cPrintVar(bnfNode->exec[i]);
    *p=i2cNode;
  }
  return;
}

/****** I2cPrintVarPtr *****************************************************
**
*/

static char *I2cPrintVarPtr(INT4 *counter)
{
  static char buff[999];
  static char ref[999];
  INT4 i;
  
  buff[0]='\0';
  
  for(i=0; i<3; i++) {
    if(*counter == -1)
      strcat(buff, ", 0");
    else {
      sprintf(ref, ", &%s[%d]",
        TemplSPrint(s3, TemplN(12, "arrName")), *counter);
      strcat(buff, ref);
    }
    counter++;
  }
  return(buff);
}

/****** I2cPrintNode *****************************************************
**
*/

static void I2cPrintNode(BNFoPRODUCTION *node, INT4 level)
{
  I2CoNode *dependNode;

  INT4 i;

  i = node->type;
  i2cNode = DictAt(i2cNodeDict, &node, I2CpNode);

  switch (i) {
  case Production:
    dependNode = DictAt(i2cNodeDict, &(node->node), I2CpNode);
    BuffPrintF(i2cNodeBuff[i], TemplSPrint(s1, TemplN(i+1, "format")),
      node->name, I2cPrintVarPtr(i2cNode->exeIndex),
               TemplSPrint(s2, TemplN(node->node->type+1, "arrName")),
	       dependNode->index); 
    break;
  case ProdName:
    dependNode=DictAt(i2cNodeDict,&((BNFoPRODNAME *)node)->production,
		      I2CpNode);
    BuffPrintF(i2cNodeBuff[i], TemplSPrint(s1, TemplN(i+1, "format")),
               node->name, I2cPrintVarPtr(i2cNode->exeIndex),
               TemplSPrint(s2, TemplN(Production+1, "arrName")),
	       dependNode->index); 
    break;
  case Literal:
    BuffPrintF(i2cNodeBuff[i], TemplSPrint(s1, TemplN(i+1, "format")),
               node->name, I2cPrintVarPtr(i2cNode->exeIndex));
    break;
  case Regexp:
    BuffPrintF(i2cNodeBuff[i], TemplSPrint(s1, TemplN(i+1, "format")),
               node->name, I2cPrintVarPtr(i2cNode->exeIndex));
    break;
  case Command:
  case LineStart:
    BuffPrintF(i2cNodeBuff[i], TemplSPrint(s1, TemplN(i+1, "format")),
               I2cPrintVarPtr(i2cNode->exeIndex));
    break;
  case Choice:
  case Term:
    BuffPrintF(i2cNodeBuff[i], TemplSPrint(s1, TemplN(i+1, "format")));
    break;
  default:
    break;
  }
}

/****** I2cPrintTermReport *************************************************
**
*/

static void I2cPrintTermReport(BNFoNODE *node, INT4 level)
{
  BNFoREPORT *report;
  BNFoNODE   *nextNode;

  switch (node->type) {
  case Term:
    report = ((BNFoTERM *)node)->factorList;                                
    while( report->node ) {                            
      nextNode = report->node;
      i2cNode = DictAt(i2cNodeDict, &nextNode, I2CpNode);
      BuffPrintF(i2cTermReportBuff, TemplSPrint(s1, TemplN(10, "format")),
        report->counter, TemplSPrint(s2, TemplN(nextNode->type+1, "arrName")),
        i2cNode->index);  
      report++;
    }
    BuffPrintF(i2cTermReportBuff, TemplSPrint(s1, TemplN(10, "arrName")));
    break;
  default:
    break;
  }
}

/****** I2cPrintChoiceSet *************************************************
**
*/

static void I2cPrintChoiceSet(BNFoNODE *node, INT4 level)
{
  BNFoNODE    **termList;
  BNFoNODE     *nextNode;

  switch (node->type) {
  case Choice:
    termList = ((BNFoCHOICE *)node)->termList;
    while( *termList ) {                            
      nextNode = *termList;
      i2cNode = DictAt(i2cNodeDict, &nextNode, I2CpNode);
      BuffPrintF(i2cChoiceSetBuff, TemplSPrint(s1, TemplN(11, "format")),
                 TemplSPrint(s2, TemplN(nextNode->type+1, "arrName")),
		 i2cNode->index);  
      termList++;
    }
    BuffPrintF(i2cChoiceSetBuff, TemplSPrint(s1, TemplN(11, "arrName")));
    break;
  default:
    break;
  }
}

/*api** I2cBnfGenerator *************************************************
**
**   Take the BNF production list and generate initialization arrays and
**   C code to reproduce this list in the computer memory
**
**      INPUT:      address of production list object [R]
** 
**      RETURNS:
*/

void I2cBnfGenerator(VARo *prodList)
{

  VARo  *var;
  TEMPLv template;
  INT4 i;

  nodeDictClass.toKeyInfo = mPtr(I2CoNode, ptr);
  i2cNodeDict = DictCreate(&nodeDictClass);

  template=TemplOpen("SRSICA:ica2c.it", ParGetStr("ica2cName"));
  I2cSetTemplate(template);
  TemplWith(template, "$bnf2c");
  TemplPrint("prologue");
  TemplWith(template, "node");
  for(i=0; i<i2cNodeClassNum; i++) {
    i2cNodeBuff[i] = BuffInit(NULL, 99);
    BuffPrintF(i2cNodeBuff[i], TemplSPrint(s1, TemplN(i+1, "typeDef")),
                               TemplSPrint(s2, TemplN(i+1, "arrName")));
  }
  i2cVarBuff = BuffInit(NULL, 99);
  i2cScopeNameBuff = BuffInit(NULL, 99);
  i2cTermReportBuff = BuffInit(NULL, 99);
  i2cChoiceSetBuff = BuffInit(NULL, 99);
  BuffPrintF (i2cTermReportBuff, TemplSPrint(s1, TemplN(10, "typeDef")));
  BuffPrintF (i2cChoiceSetBuff, TemplSPrint(s2, TemplN(11, "typeDef")));
  BuffPrintF (i2cVarBuff, TemplSPrint(s1, TemplN(12, "typeDef")),
                         TemplSPrint(s2, TemplN(12, "arrName")));
  BuffPrintF (i2cScopeNameBuff, TemplSPrint(s1, TemplN(13, "typeDef")),
                               TemplSPrint(s2, TemplN(13, "arrName")));

  
  /* collect all the nodes from BNF tree */
  for (i=0; (var = AnyNextInList(prodList, &i)); )
    BnfTreeTraverse((BNFoNODE *)VarGetObject (NULL, var), I2cRegisterNode, 0);

  /* print to buffer the Node initialization arrays */
  for (i=0; (var = AnyNextInList(prodList, &i)); )
    BnfTreeTraverse((BNFoNODE *)VarGetObject (NULL, var), I2cPrintNode, 0);

  /* print to buffer the Term reports */
  for (i=0; (var = AnyNextInList(prodList, &i)); )
    BnfTreeTraverse((BNFoNODE *)VarGetObject (NULL, var), 
		    I2cPrintTermReport, 0);

  /* print to buffer the Choice sets */
  for (i=0; (var = AnyNextInList(prodList, &i)); )
    BnfTreeTraverse((BNFoNODE *)VarGetObject (NULL, var),I2cPrintChoiceSet, 0);

  for(i=0; i<Job->scope->varN; i++) {
    BuffPrintF(i2cScopeNameBuff, TemplSPrint(s1, TemplN(13, "format")),
               VarGetName(&Job->scope->var[i]));
  }

  for(i=0; i<i2cNodeClassNum; i++)
    if( i2cNodeCount[i] )
      TemplPrint(TemplN(i+1, "defNumber"), i2cNodeCount[i]);
  TemplPrint( TemplN(13, "defNumber"), Job->scope->varN);
  TemplEndWith();
  TemplPrint("str", "\n");
  
  
  _PrintClose(i2cScopeNameBuff);
  _PrintClose(i2cVarBuff);
  for(i=2; i<i2cNodeClassNum; i++)
    _PrintClose(i2cNodeBuff[i]);
  _PrintClose(i2cNodeBuff[0]);
  _PrintClose(i2cNodeBuff[1]);
  _PrintClose(i2cTermReportBuff);
  _PrintClose(i2cChoiceSetBuff);

  TemplPrint("epilogue");
  TemplEndWith();

  DictDestroy(i2cNodeDict); 
}
nt[i] )
      TemplPrint(TemplN(i+1, "defNumber"), i2cNodeCount[i]);
  TemplPrint( TemplN(13, "defNumber"), Job->scope->varN);
  TemplEndWith();
  TemplPrint("str", "\n");
  
  
  _PrintClose(i2cScopeNameBuff);
  _Psrs/src/btree.c
char btree_ID[] = "$Id: btree.c,v 1.9 1997/03/18 17:20:17 srs Exp $";
/*
**
**    $RCSfile: btree.c,v $
**    $Revision: 1.9 $
**    $Date: 1997/03/18 17:20:17 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.x Copyright by Thure Etzold
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**     
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>


#include "message.h"
#include "futil.h"
#include "sm.h"
#include "tm.h"
#include "binpack.h"
#include "btree.h"
#include "ids.h"

#ifdef __ALPHA
# define MBCW  , "mbc=16"
# define MBCR  , "mbf=10" , "mbc=16" 
#else
# ifdef VAX
#  define MBCW  , "mbc=16"
#  define MBCR  , "mbf=10" , "mbc=16"  
# else
#  define MBCW
#  define MBCR
# endif
#endif




/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  for encapsulating bucket types as 'objects'
*/

#ifdef xxx
RecordHasher

    switch (indexCurr->valueType) { 
        case BTRxSTR: 
        case BTRxIDENTRY: 
            p = ((HASHSTROBJ*) obj)->value;
            len = strlen(p);
            break; 
        case BTRxNUM: 
            p = (char*) &((HASHNUMOBJ*) obj)->value;
            len = sizeof(((HASHNUMOBJ*) obj)->value);
            break; 
        case BTRxREAL: 
            p = (char*) &((HASHREALOBJ*) obj)->value;
            len = sizeof(((HASHREALOBJ*) obj)->value);
            break; 
    }

    for (i=0; i<len; i++) {
        h= (h << 4) + *(p+i);
        if ((g= (h & 0xf0000000)))
            h= (h ^ (g >> 24)) ^ g;
    }

    return (INT4) h % table->max_hash_elem;


RecordPacker

    case BTRxIDENTRY:
      _BinPackFip (bucketBuff, record->r.id.textFip);
      _BinPackFip (bucketBuff, record->r.id.dataFip);
      _BinPackByte (bucketBuff, record->r.id.fileX);
      break;
    case BTRxVALUE:
      _BinPackFip (bucketBuff, record->r.value.firstIdFip);
      _BinPackFip (bucketBuff, record->r.value.lastIdFip);
      _BinPackNum (bucketBuff, record->r.value.idN);
     break;
    case BTRxPOINTER:
      _BinPackFip (bucketBuff, record->r.pointer.downFip);
      _BinPackNum (bucketBuff, record->r.pointer.downSize);
      break;

RecordCopier

  switch (record->type) {
  case BTRxIDENTRY:
    recordSize = 9;
    break;
  case BTRxVALUE:
    recordSize = 12;
    break;
  case BTRxPOINTER:
    recordSize = 8;
    break;
  }

RecordUnpacker

    case BTRxIDENTRY:
      _BinUnpackFip (bucketBuff, record->r.id.textFip);
      _BinUnpackFip (bucketBuff, record->r.id.dataFip);
      _BinUnpackByte (bucketBuff, record->r.id.fileX);
      break;
    case BTRxVALUE:
      _BinUnpackFip (bucketBuff, record->r.value.firstIdFip);
      _BinUnpackFip (bucketBuff, record->r.value.lastIdFip);
      _BinUnpackNum (bucketBuff, record->r.value.idN);
      break;
    case BTRxPOINTER:
      _BinUnpackFip (bucketBuff, record->r.pointer.downFip);
      _BinUnpackNum (bucketBuff, record->r.pointer.downSize);
      break;

RecordComparer


    switch (indexCurr->valueType) { 
        case BTRxSTR: 
        case BTRxIDENTRY: 
            return  strcmp( ((HASHSTROBJ*)obj1)->value,
                            ((HASHSTROBJ*)obj2)->value );
        case BTRxNUM: 
            return  ((HASHNUMOBJ*)obj1)->value - ((HASHNUMOBJ*)obj2)->value;
        case BTRxREAL: 
            if ( ((HASHREALOBJ*)obj1)->value < ((HASHREALOBJ*)obj2)->value )
                return -1;
            if ( ((HASHREALOBJ*)obj1)->value > ((HASHREALOBJ*)obj2)->value )
                return 1;
            return 0;
    }


#endif

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  function BTRoComparer
*/

static Int4 BtrCompareInt (BTRoREC *rec1, BTRoREC *rec2)
{
  return (atoi (rec1->str) - atoi (rec2->str));
}
static Int4 BtrCompareStr (BTRoREC *rec1, BTRoREC *rec2)
{
  return SmStrCmp (rec1->str, rec2->str);
}
static Int4 BtrCompareReal (BTRoREC *rec1, BTRoREC *rec2)
{
  return (atof (rec1->str) - atof (rec2->str));
}

  
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  some contants
*/

#define BTRxMAXLEVEL 2
#define BTRxPTRRECADDSIZ 8
#define BTRxBUCKETADDSIZ 16

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of static functions
*/

static void BtrWriteInfo (BTRo *btree);
static INT4 BtrReadInfo (BTRo *btree);
static void BtrFlush (BTRo *btree);
static FIP BtrWrite (BTRo *btree, char *buff, INT4 size, INT4 levelN);
static BTRoBUCKET *BtrBucketGet (BTRo *btree, enum BtrStep option);
static BTRoBUCKET *BtrReadBucket (BTRo *btree, FIP bucketFip, INT4 bucketSize);
static FIP BtrGetRecordNumber (BTRo *btree, BTRoBUCKET *bucket, 
			       INT4 bucketRecX);
static INT4 BtrFixedBucketSize (BTRo *btree, FIP fip);
static void BtrSetMethods (BTRo *btree);
static void BtrBucketKill (BTRoBUCKET **bucket);

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  external or module wide variables
*/

static BTRo *btreeCurr;


/**api* BtrOpen *************************************************************
** 
**      Opens a B-tree for various access types. To close it again use
**      BtrClose.
**
** 	INPUT:	 o  address of file name [R]
**               o  string specifying access type: 
**                  "read", "update", "write", "merge" [R]
**               o  address of error code [W] or NULL if not wanted<BR>
**                  returned values can be<BR>
**                  e__filopenerr <BR>
**                  e__indexbusy <BR>
**                  e__iscompressed 
**        
** 	        IMPLICIT:
** 
** 	RETURNS:    new btree object
** 		    NULL if there is a problem 
*/ 

BTRo *BtrOpen (char *indexName, char *option, INT4 *errCode)
{
  BTRo *btree;
  INT4  rv;

  *errCode = 0;

  if ((btree = (BTRo *) calloc (1, sizeof (BTRo))) == NULL)
    _ErrExit2 (e__allocfail, "btree-object");
  btree->file = FileNew (indexName);
  FileSetName (btree->file, "ext", "inx");
  FileSetUnixIo (btree->file);

  switch (tolower (option[0])) {
  case 'r': /* read */
    if (!FileOpen (btree->file)) {
      _ErrSet (errCode, e__filopenerr);
      break;
    } 
    rv = BtrReadInfo (btree);
    _ErrIf (rv)
      break;
    if (btree->isBusy) {
      _ErrSet (errCode, e__indexisbusy);
      break;
    }
    btree->isFixedRecordSiz = btree->fixedRecordSiz ? 1 : 0;
    btree->firstBucketFip = btree->levelFip[2];
    btree->lastBucketFip = btree->fileSize - btree->lastBucketSize;
    btree->bucketCurr = NULL;
    BtrSetMethods (btree);
    return btree;

  case 'c': /* compress */
  case 'u': /* update */
    if (!FileOpen (FileSetUpdate (btree->file))) {
      _ErrSet (errCode, e__filopenerr);
      break;
    }
    if (_ErrIs (BtrReadInfo (btree)))
      return NULL;
    
    if (btree->isBusy) {
      _ErrSet (errCode, e__indexisbusy);
      return NULL;
    }
    if (btree->isCompressed && option[0] == 'c') { 
      _ErrExit2 (e__iscompressed, FileGetName (btree->file, "path"));
    }

    btree->isFixedRecordSiz = btree->fixedRecordSiz ? 1 : 0;
    btree->firstBucketFip = btree->levelFip[2];
    btree->lastBucketFip = btree->fileSize - btree->lastBucketSize;
    btree->bucketCurr = NULL;
    btree->isBusy = 1;
    btree->levelWriteFip[2] = btree->firstBucketFip;
    BtrWriteInfo (btree);
    BtrSetMethods (btree);
    return btree;
    
  case 'm': /* merge */
    btree->isCompressed = 1;
  case 'w': /* write */  
    if (!FileOpen (FileSetWrite (btree->file))) {
      _ErrSet (errCode, e__filopenerr);
      break;
    }
    btree->bucketRecordN = 0;  
    btree->isWriteOpen = 1;
    btree->isBusy = 1;
    return btree;
    
  default:
    _ErrExit2 (e__unknownoption, option);
  }
  
  return btree;
}


/**api* BtrClose *************************************************************
** 
**      Closes a btree which was opened by BtrOpen.
**
** 	INPUT:	    address of B-tree object [R]
** 
*/ 

void BtrClose (BTRo *btree)
{
  if (btree->isBusy) {
    if (btree->isWriteOpen) {
      BtrFlush (btree);
      btree->fileSize = btree->levelWriteFip[2];
      _ErrMsg5 (i__wrotebtree, FileGetName (btree->file, "path"),
		((btree->fileSize + 999) / 1000), 
		btree->bucketRecordN, btree->recordN);
    }
    btree->isBusy = 0;
    btree->timeCreated = TimeGet ();
    BtrWriteInfo (btree);
  }
  FileDelete (btree->file);
  if (btree->bucketCurr)
    BtrBucketKill (&btree->bucketCurr);
  free (btree);
}


/****** BtrBucketNew **********************************************************
** 
**      creates a new bucket;
**
** 	INPUT:	    address of Btree object [R]
**                  level number [R]
**
** 	        IMPLICIT:
** 
** 	RETURNS:    
**                  address of new bucket
*/ 

static BTRoBUCKET *BtrBucketNew (BTRo *btree, INT4 levelN)
{
  BTRoBUCKET *bucket;
  INT4 size;
  
  if ((bucket = (BTRoBUCKET *) calloc (1, sizeof (BTRoBUCKET))) == NULL)
    _ErrExit2 (e__allocfail, "bucket");
  if ((bucket->record = 
       (BTRoREC *) malloc (btree->bucketRecordN * sizeof (BTRoREC))) == NULL)
    _ErrExit2 (e__allocfail, "bucket buffer");
  size = btree->bucketRecordN * BTRxTMPRECORDSIZ;
  if ((bucket->bucketBuff = 
       (char *) malloc (size)) == NULL)
    _ErrExit2 (e__allocfail, "bucket buffer");
  
  bucket->recordN = 0;
  bucket->up = 0;
  bucket->writePtr = 0;

  if (levelN == 2) {
    bucket->type = btree->leafType;
    bucket->fixedRecordSize = btree->fixedRecordSiz;
  }
  else {
    bucket->type = BTRxPOINTER;
    bucket->fixedRecordSize = 0;
  }
  return bucket;
}


/****** BtrBucketKill ***********************************************************
**      deletes a bucket
**
** 	INPUT:	    address of Btree object [R]
**                  type of record to be put into bucket [R]
**
** 	        IMPLICIT:
** 
** 	RETURNS:    
**                  address of new bucket
*/ 

static void BtrBucketKill (BTRoBUCKET **bucket)
{
  if (*bucket) {
    if ((*bucket)->record)
      free ((*bucket)->record);
    if ((*bucket)->bucketBuff)
      free ((*bucket)->bucketBuff);
    free (*bucket);
    *bucket = NULL;
  }
}


/**api* BtrSetType ************************************************************
** 
**      Sets the type of a Btree. See also BtrSetNumType.
**
** 	INPUT:	 o  address of btree object [R]
**               o  string specifying btree type: 
**                  "ID", "str", "num", "real" [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    
*/ 

void BtrSetType (BTRo *btree, char *option)
{
  if (btree->type)
    _ErrExit2 (e__parisdefined, "B-tree type");

  switch (tolower (option[0])) {
  case 'i': 
    BtrSetNumType (btree, BTRxIDENTRY);
    break;
  case 's':
    BtrSetNumType (btree, BTRxSTR);
    break;
  case 'n':
    BtrSetNumType (btree, BTRxNUM);
    break;
  case 'r':
    BtrSetNumType (btree, BTRxREAL);
    break;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
}

/**api* BtrSetNumType *********************************************************
** 
**      Sets the type of a Btree. Same as BtrSetType but takes type number
**      instead of the name
**
** 	INPUT:	 btree object [W]
**               type number [R]
*/ 

void BtrSetNumType (BTRo *btree, Int4 type)
{
  if (btree->type)
    _ErrExit2 (e__parisdefined, "B-tree type");

  switch (type) {
  case BTRxIDENTRY: 
    btree->leafType = BTRxID;
    btree->isFixedRecordSiz = 1;
    btree->recordSiz = 9;
    break;
  case BTRxSTR:
    btree->leafType = BTRxVALUE;
    btree->recordSiz = 12;
    btree->compare = BtrCompareStr;
    break;
  case BTRxNUM:
    btree->leafType = BTRxVALUE;
    btree->recordSiz = 12;
    btree->compare = BtrCompareInt;
    break;
  case BTRxREAL:
    btree->leafType = BTRxVALUE;
    btree->recordSiz = 12;
    btree->compare = BtrCompareReal;
    break;
  default:
    _ErrExit2 (e__unknownoption, type);
  }
  btree->type = type;
  BtrSetMethods (btree);
}

static void BtrSetMethods (BTRo *btree)
{
  switch (btree->type) {
  case BTRxIDENTRY: 
    break;
  case BTRxSTR:
    btree->compare = BtrCompareStr;
    break;
  case BTRxNUM:
    btree->compare = BtrCompareInt;
    break;
  case BTRxREAL:
    btree->compare = BtrCompareReal;
    break;
  default:
    _ErrExit2 (e__unknownoption, btree->type);
  }
}


/****** BtrWrite **************************************************************
** 
**      writes a buffer to a file and returns its file offset;
**
** 	INPUT:	 o  address of Btree object [R]
**               o  buffer [R] or NULL 
**               o  size of bucket buffer [R]
**               o  level number (0,1,2 and -1 for info block) [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    file pointer to data written out
*/ 

static FIP BtrWrite (BTRo *btree, char *buff, INT4 size, INT4 levelN)
{
#define BTRxTMPBUFSIZ 20000
  char tmp[BTRxTMPBUFSIZ];
  long  writeFip;
  INT4  sizeWritten;

  /* 
  ** go to appropriate file offset
  */

  if (levelN == -1)
    FileSeek (btree->file, 0);
  else { 
    FileSeek (btree->file, btree->levelWriteFip[levelN]);
  }

  /*
  ** if buffer address is NULL write junk of specified size to file
  */

  if (!buff) {  
    for (sizeWritten=0; sizeWritten + BTRxTMPBUFSIZ <= size; 
	 sizeWritten += BTRxTMPBUFSIZ)
      FileWrite (btree->file, tmp, BTRxTMPBUFSIZ); 
    FileWrite (btree->file, tmp, size - sizeWritten); 
  }
  else 
    FileWrite (btree->file, buff, size); 

  /* 
  ** and go back to previous location - assumed to be the end of file
  */ 

  if (levelN < BTRxMAXLEVEL)
    FileSeekEnd (btree->file, 0);

  if (levelN == -1)
    return 0;
  else {
    writeFip = btree->levelWriteFip[levelN];
    btree->levelWriteFip[levelN] += size;
    return writeFip;
  }
}


/****** BtrCopyRecord *********************************************************
** 
**      copies a record into the appropriate position in the bucket
**
** 	INPUT:	    address of bucket object [W]
**                  address of record [R]
** 	        IMPLICIT:
**                  btreeCurr (BTRo *) [R]
** 
** 	RETURNS:    
**                  the number of new record within bucket
*/ 

static INT4 BtrCopyRecord (BTRoBUCKET *bucket, BTRoREC *record)
{
  BTRoREC *outrecord;
  INT4     recordSize;

  switch (record->type) {
  case BTRxIDENTRY:
    recordSize = 9;
    break;
  case BTRxVALUE:
    recordSize = 12;
    break;
  case BTRxPOINTER:
    recordSize = 8;
    break;
  }

  if (!bucket->writePtr) {
    bucket->writePtr = bucket->bucketBuff + 
                       (bucket->fixedRecordSize ? 0 : BTRxBUCKETADDSIZ);
  }
  bucket->writePtr += recordSize;

  outrecord = &bucket->record[bucket->recordN++];
  memcpy (outrecord, record, sizeof (BTRoREC));
  outrecord->str = bucket->writePtr;
  strcpy (outrecord->str, record->str);

  bucket->writePtr += bucket->fixedRecordSize ? btreeCurr->maxStrSiz :
                  strlen (record->str) + 1;

  return bucket->recordN;
}


/****** BtrWriteInfo **********************************************************
** 
**      writes an info block to the beginning of the file;
**
** 	INPUT:	    address of B-tree object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    
*/ 

static void BtrWriteInfo (BTRo *btree)
{
  char *buff = btree->infoBuff;
  char *buffSave = buff;
  INT4  buffSize;

  _BinPackNum (buff, BTRxINFOSIZE);
  _BinPackNum (buff, BTRxCURRENT_VERSION);  /* version number */
  _BinPackFip (buff, btree->writeFip);
  _BinPackFip (buff, btree->levelFip[0]);
  _BinPackFip (buff, btree->levelFip[1]);
  _BinPackFip (buff, btree->levelFip[2]);
  _BinPackFip (buff, btree->rootSize);
  _BinPackFip (buff, btree->firstBucketSize);
  _BinPackFip (buff, btree->lastBucketSize);
  _BinPackNum (buff, btree->leafType);
  _BinPackNum (buff, btree->type);
  _BinPackNum (buff, btree->bucketRecordN);
  _BinPackNum (buff, btree->recordN);
  _BinPackNum (buff, btree->fileSize);
  _BinPackNum (buff, btree->fixedRecordSiz);
  _BinPackNum (buff, btree->maxStrSiz);
  _BinPackNum (buff, btree->timeCreated);
  _BinPackByte (buff, btree->isCompressed);
  _BinPackByte (buff, btree->isBusy);
  _BinPackNum (buff, 0);        /* dummies for later use */
  _BinPackNum (buff, 0);
  _BinPackNum (buff, 0);
  _BinPackNum (buff, 0);
  _BinPackNum (buff, 0);

  FileSeek (btree->file, 0);
  buffSize = buff - buffSave;

  /* 
  ** info block is written twice to the file ...once just after opening
  ** the index for writing (busy flag set to 1) and again just befor the
  ** index is closed;
  */

  if (!btree->writeFip)  
    BtrWrite (btree, buffSave, buffSize, -1);
  else
    FileWrite (btree->file, buffSave, buffSize);
}


/****** BtrReadInfo ***********************************************************
** 
**      Reads and unpacks info block of btree;
**
** 	INPUT:	    address of B-tree object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:  1 if OK  
**                e__indexwrongversion <fileName, wrongVersionN, VersionN> +
*/ 

static INT4 BtrReadInfo (BTRo *btree)
{
  char *buff = btree->infoBuff;
  INT4  tmp;

  FileSeek (btree->file, 0);
  FileRead (btree->file, buff, BTRxINFOSIZE);

  if (FileIsEof (btree->file))
    return e__filnotok;

  _BinUnpackNum (buff, btree->infoSize);
  _BinUnpackNum (buff, btree->versionN);
  if (btree->versionN != BTRxCURRENT_VERSION)
    _ErrRet4 (e__indexwrongversion, FileGetName (btree->file, "path"), 
	      btree->versionN, BTRxCURRENT_VERSION);
  _BinUnpackFip (buff, btree->writeFip);
  _BinUnpackFip (buff, btree->levelFip[0]);
  _BinUnpackFip (buff, btree->levelFip[1]);
  _BinUnpackFip (buff, btree->levelFip[2]);
  _BinUnpackFip (buff, btree->rootSize);
  _BinUnpackFip (buff, btree->firstBucketSize);
  _BinUnpackFip (buff, btree->lastBucketSize);
  _BinUnpackNum (buff, tmp);
  btree->leafType = (enum recType) tmp;
  _BinUnpackNum (buff, tmp);
  btree->type = (enum btrType) tmp;
  _BinUnpackNum (buff, btree->bucketRecordN);
  _BinUnpackNum (buff, btree->recordN);
  _BinUnpackNum (buff, btree->fileSize);
  _BinUnpackNum (buff, btree->fixedRecordSiz);
  _BinUnpackNum (buff, btree->maxStrSiz);
  _BinUnpackNum (buff, btree->timeCreated);
  _BinUnpackByte (buff, btree->isCompressed);
  _BinUnpackByte (buff, btree->isBusy);

  btree->rootFip = btree->levelFip[0];
  return 1;
}



/****** BtrBucketPack ***********************************************************
** 
**      packs a bucket into platform independent format;
**
** 	INPUT:	    btree object [R]
**                  address of bucket object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    
**                  size of bucket in bytes
*/ 

static INT4 BtrBucketPack (BTRo *btree, BTRoBUCKET *bucket)
{
  BTRoREC *record;
  char    *bucketBuff = bucket->bucketBuff; 
  char    *bucketBuffSave = bucketBuff; 
  INT4     k;

  if (!bucket->fixedRecordSize) {
    _BinPackNum (bucketBuff, bucket->bucketSize);
    _BinPackNum (bucketBuff, bucket->prevBucketSize);
    _BinPackNum (bucketBuff, bucket->type);
    _BinPackNum (bucketBuff, bucket->recordN);
  }
  for (k=0; k < bucket->recordN; k++) {
    record = &bucket->record[k];
    switch (bucket->type) {
    case BTRxIDENTRY:
      _BinPackFip (bucketBuff, record->r.id.textFip);
      _BinPackFip (bucketBuff, record->r.id.dataFip);
      _BinPackByte (bucketBuff, record->r.id.fileX);
      break;
    case BTRxVALUE:
      _BinPackFip (bucketBuff, record->r.value.firstIdFip);
      _BinPackFip (bucketBuff, record->r.value.lastIdFip);
      _BinPackNum (bucketBuff, record->r.value.idN);
     break;
    case BTRxPOINTER:
      _BinPackFip (bucketBuff, record->r.pointer.downFip);
      _BinPackNum (bucketBuff, record->r.pointer.downSize);
      break;
    }
    bucketBuff += bucket->fixedRecordSize ? btree->maxStrSiz :
                  strlen (bucketBuff) + 1;
  }
  bucket->bucketSize = bucketBuff - bucketBuffSave;
  if (!bucket->fixedRecordSize)
    _BinPackNum (bucketBuffSave, bucket->bucketSize);  /* to page begin */
  return bucket->bucketSize;
}


/****** BtrBucketUnpack *********************************************************
** 
**      unpacks a bucket from platform independent format; if readSize
**      is by 4 bytes greater the actual bucket size then it reads the
**      first four bytes of the next bucket with its size;
**
** 	INPUT:	    btree object [R]
**                  address of bucket object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    
**                  size of bucket in bytes
*/ 

static void BtrBucketUnpack (BTRo *btree, BTRoBUCKET *bucket, INT4 readSize)
{
  BTRoREC *record;
  char    *bucketBuff = bucket->bucketBuff; 
  INT4     k, tmp;

  if (!bucket->fixedRecordSize) {
    _BinUnpackNum (bucketBuff, bucket->bucketSize);
    _BinUnpackNum (bucketBuff, bucket->prevBucketSize);
    _BinUnpackNum (bucketBuff, tmp);
    bucket->type = (enum recType) tmp;
    _BinUnpackNum (bucketBuff, bucket->recordN);
  }
  else {
    bucket->type = btree->leafType;
    bucket->bucketSize = BtrFixedBucketSize (btree, bucket->fip);
    bucket->recordN = bucket->bucketSize / bucket->fixedRecordSize;
    bucket->prevBucketSize = btree->firstBucketFip == bucket->fip ? 0 :
                             BtrFixedBucketSize (btree, btree->firstBucketFip);
  }
  for (k=0; k < bucket->recordN; k++) {
    record = &bucket->record[k];
    switch (bucket->type) {
    case BTRxIDENTRY:
      _BinUnpackFip (bucketBuff, record->r.id.textFip);
      _BinUnpackFip (bucketBuff, record->r.id.dataFip);
      _BinUnpackByte (bucketBuff, record->r.id.fileX);
      break;
    case BTRxVALUE:
      _BinUnpackFip (bucketBuff, record->r.value.firstIdFip);
      _BinUnpackFip (bucketBuff, record->r.value.lastIdFip);
      _BinUnpackNum (bucketBuff, record->r.value.idN);
      break;
    case BTRxPOINTER:
      _BinUnpackFip (bucketBuff, record->r.pointer.downFip);
      _BinUnpackNum (bucketBuff, record->r.pointer.downSize);
      break;
    }
    record->str = bucketBuff;
    bucketBuff += bucket->fixedRecordSize ? btree->maxStrSiz :
                  strlen (bucketBuff) + 1;
  }

  if (bucket->fip == btree->lastBucketFip)
    bucket->nextBucketSize = 0;
  else if (bucket->fixedRecordSize)
    bucket->nextBucketSize = BtrFixedBucketSize (btree, bucket->fip + 
						 bucket->bucketSize);
  else
    _BinUnpackNum (bucketBuff, bucket->nextBucketSize);
}



/****** BtrBucketInsertRecord ***************************************************
** 
**      inserts a record into bucket - recursive!
**
** 	INPUT:	    address of btree object [R]
**                  pointer to address of bucket object [W]
**                  address of record to be inserted [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    
*/ 

static void BtrBucketInsertRecord (BTRo *btree, BTRoBUCKET **bucketPtr, 
				 BTRoREC *record, INT4 levelN)
{
  BTRoBUCKET    *newbucket, *bucket = *bucketPtr;
  BTRoREC     ptrrec;
  char        stringBuff[133];

  if (levelN < 0)
    return;

  /*
  ** if bucket == NULL it is assumed that the bucket is the new root bucket
  ** the first bucket of each
  ** level becomes the root ..since the tree grows from leafs to root ...the
  ** first bucket of the highest level will finally be the root 
  */

  if (!bucket) {
    bucket = BtrBucketNew (btree, levelN);
    btree->root = bucket;
    *bucketPtr = bucket;
  }

  /*
  ** if the bucket is full now, it can be written out 
  ** ....a pointer to the bucket must be created and inserted in the upper 
  ** level (recursive procedure) 
  ** ... then a new empty bucket must be created
  */

  if (BtrCopyRecord (bucket, record) == btree->bucketRecordN) {
    ptrrec.type = BTRxPOINTER;
    bucket->bucketSize = ptrrec.r.pointer.downSize = 
      BtrBucketPack (btree, bucket);

    if (levelN == 2) {  /* record bucket size of first and last */
      if (bucket == btree->root)  /* first in level 2 */
	btree->firstBucketSize = bucket->bucketSize;
      else
	btree->lastBucketSize = bucket->bucketSize;
    }

    ptrrec.r.pointer.downFip = BtrWrite (btree,bucket->bucketBuff, 
					 bucket->bucketSize, levelN);
    ptrrec.str = stringBuff;
    strcpy (ptrrec.str, record->str); 

    newbucket = BtrBucketNew (btree, levelN);
    newbucket->prevBucketSize = bucket->bucketSize;
    newbucket->up = bucket->up;
    newbucket->type = record->type;
    BtrBucketKill (&bucket);  /* old bucket can now be deleted */
    BtrBucketInsertRecord (btree, &newbucket->up, &ptrrec, levelN-1);
    *bucketPtr = newbucket;
  }
}



/****** BtrFlush **************************************************************
** 
**      writes all buckets that exist in memory to file proceeds from leaves to
**      root;
**
** 	INPUT:	    address of Btree object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    
*/ 

static void BtrFlush (BTRo *btree)
{
  BTRoBUCKET *bucket, *nextbucket;
  BTRoREC    ptrrec, *record;
  char       stringBuff[133];
  INT4        level;

  if (!(bucket = btree->bucket))
    return;
  for (level=2; level >= 0; level--) {

    /*
    ** if bucket contains any records then the last record must be inserted
    ** one level above as a pointer to the bucket; 
    */

    if (bucket->recordN || bucket->bucketSize == 1) {
      ptrrec.type = BTRxPOINTER;
      bucket->bucketSize = ptrrec.r.pointer.downSize = 
	BtrBucketPack (btree, bucket);

      if (level == 2) 
	btree->lastBucketSize = bucket->bucketSize;

      ptrrec.r.pointer.downFip = BtrWrite (btree, bucket->bucketBuff, 
					   bucket->bucketSize, level);

      record = &bucket->record[bucket->recordN-1];  /** last record in bucket*/
      ptrrec.str = stringBuff;
      strcpy (ptrrec.str, record->str); 
      if (level == 0)  /** root level is reached */
	break;
      BtrBucketInsertRecord (btree, &bucket->up, &ptrrec, level-1);
    }
    nextbucket = bucket->up;
    BtrBucketKill (&bucket);  
    bucket = nextbucket;
  }

  btree->rootSize = btree->root->bucketSize;
  if (bucket == btree->root)
    BtrBucketKill (&bucket);  
}



/****** BtrReadBucket *********************************************************
** 
**      reads a bucket from Btree;
**
** 	INPUT:	    address of Btree object [W]
**                  file pointer to bucket [R]
**                  size of bucket in bytes [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    
*/ 

static BTRoBUCKET *BtrReadBucket (BTRo *btree, FIP bucketFip, INT4 bucketSize)
{
  BTRoBUCKET *bucket;
  INT4        size;

  /*
  ** get a bucket object
  */

  bucket = BtrBucketNew (btree, 
			 bucketFip >= btree->firstBucketFip ? 2 : 0);
  bucket->fip = bucketFip;  

  /*
  ** read from file and unpack bucket
  */

  FileSeek (btree->file, bucketFip);

  /* 
  ** try to read the bucket + the first 4 bytes of the next bucket that
  ** specifies its size ...this can be used for traversing a level
  */

  size = bucketSize + (btree->isFixedRecordSiz ? 0 : 4);
  FileRead (btree->file, bucket->bucketBuff, size);
  BtrBucketUnpack (btree, bucket, size);
  return bucket;
}


/**api* BtrSearch *************************************************************
** 
**      searches a value in btree; string comparison is case insensitive
**
** 	INPUT:	    btree object [R]
**                  string value [R]
**                  address of record ID [W] or NULL
**                  comparison length [R] or 0
**
** 	        IMPLICIT:
** 
** 	RETURNS:    pointer to found record or NULL
*/ 

BTRoREC *BtrSearch (BTRo *btree, char *str, FIP *recNPtr, INT4 cmpLen)
{
  BTRoBUCKET *bucket=btree->bucketCurr;
  BTRoREC    *recordCurr;
  FIP        bucketFip = btree->rootFip;
  INT4       bucketSize = btree->rootSize, k, l;
  double     cmp;
  double     searchval = 0;


  if (recNPtr)
    *recNPtr = 0;  /*PURIFY*/

  if (bucket) {
    BtrBucketKill (&bucket);
    btree->bucketCurr = NULL;
  }

  if (btree->type == BTRxNUM)   searchval = atoi(str);
  if (btree->type == BTRxREAL)  searchval = atof(str);

  for (k=0; k < 3; k++) {
    bucket = BtrReadBucket (btree, bucketFip, bucketSize);

    for (l=0; l < bucket->recordN; l++) {
      recordCurr = &bucket->record[l];

      /*
      ** goto lower level bucket if current record's value is equal or lesser
      */
      
      switch (btree->type) {
      case BTRxNUM: 
	cmp = searchval - atoi(recordCurr->str);
	break;
      case BTRxREAL:
	cmp = searchval - atof(recordCurr->str);
	break;
      default:  cmp = (cmpLen) ? SmStrCmpLen (str, recordCurr->str, cmpLen) : 
                	SmStrCmp (str, recordCurr->str);
      }
      
      if (cmp <= 0) {
	if (bucket->type != BTRxPOINTER) {
	  
	  /* 
	  ** if found then save the record number and the context
          ** and return ...don't delete the bucket
          */
	  
	  if (bucket->type == BTRxID && recNPtr)
	    *recNPtr = BtrGetRecordNumber (btree, bucket, l);
	  btree->bucketCurr = bucket; 
	  bucket->recordXCurr = l;
	  recordCurr->type = btree->leafType;
	  return (cmp == 0) ? recordCurr : NULL; 
	  
	}
	else {
	  bucketFip = recordCurr->r.pointer.downFip;
	  bucketSize = recordCurr->r.pointer.downSize;
	  break;
	}
      }
    }
    BtrBucketKill (&bucket);
    btree->bucketCurr = NULL;
    if (cmp > 0) {  /* value is even greater than last string ...no hope! */  
      return NULL;
    }    
  }
  return recordCurr;
}

/**api* BtrIsSearchGreaterMaxVal **********************************************
** 
**      Returns 1 if value from previous search exceeded the max value in 
**      index;
**
** 	INPUT:	 o  btree object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    pointer to found record or NULL
*/ 

INT4 BtrIsSearchGreaterMaxVal (BTRo *btree) 
{
  return btree->bucketCurr ? 0 : 1;
}


/**api* BtrIsSearchLessMinVal ***********************************************
** 
**      Returns 1 if value from previous search is below the min value in 
**      index; Use only after unsuccessful search.
**
** 	INPUT:	 o  btree object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    pointer to found record or NULL
*/ 

INT4 BtrIsSearchLessMinVal (BTRo *btree) 
{
  return  (btree->bucketCurr->fip == btree->firstBucketFip) &&
	   (btree->bucketCurr->recordXCurr == 0) ? 1 : 0;
}


/**api* BtrSearchId ***********************************************************
** 
**      searches a string value in btree;
**
** 	INPUT:	 o  btree object [R]
**               o  string value [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    pointer to found record or NULL
*/ 

BTRoID *BtrSearchId (BTRo *btree, char *str, FIP *fip)
{
  BTRoREC *record;

  if (!(record = BtrSearch (btree, str, fip, 0)))
    return NULL;

  return &(record->r.id);
}


/**api* BtrSearchStr **********************************************************
** 
**      searches a string value in btree;
**
** 	INPUT:	 o  btree object [R]
**               o  string value [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    pointer to found record or NULL
*/ 

BTRoVALUE *BtrSearchStr (BTRo *btree, char *str)
{
  BTRoREC  *record;

  if (!(record = BtrSearch (btree, str, NULL, 0)))
    return NULL;

  return &(record->r.value);
}

/**api* BtrSearchNum **********************************************************
** 
**      searches a num (integer) value in btree;
**
** 	INPUT:	 o  btree object [R]
**               o  num value [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    pointer to found record or NULL
*/ 

BTRoVALUE *BtrSearchNum (BTRo *btree, INT4 num)
{
  BTRoREC  *record;
  char str[20];

  sprintf(str, "%d", num);

  if (!(record = BtrSearch (btree, str, NULL, 0)))
    return NULL;

  return &(record->r.value);
}

/**api* BtrSearchReal *******************************************************
** 
**      searches a real (double) value in btree;
**
** 	INPUT:	 o  btree object [R]
**               o  real value [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    pointer to found record or NULL
*/ 

BTRoVALUE *BtrSearchReal (BTRo *btree, double real)
{
  BTRoREC  *record;
  char str[20];

  sprintf(str, "%18.6f", real);

  if (!(record = BtrSearch (btree, str, NULL, 0)))
    return NULL;

  return &(record->r.value);
}


/****** BtrGetRecordNumber ****************************************************
** 
**      searches a string value in btree;
**
** 	INPUT:	    btree object [R]
**                  bucket object [R]
**                  index of record in bucket [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    number of record within the whole btree
*/ 

static FIP BtrGetRecordNumber (BTRo *btree, BTRoBUCKET *bucket, INT4 bucketRecX)
{
  return (bucket->fip + (bucketRecX+1) * btree->fixedRecordSiz -
	 btree->firstBucketFip) / btree->fixedRecordSiz;
}


/**api* BtrBuildStartPhase1 ***************************************************
** 
**      Initializes building phase 1.<BR>
**
** 	INPUT:	    address of Btree object [W]
**                  number of records to be inserted [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    
*/ 

void BtrBuildStartPhase1 (BTRo *btree, INT4 recordN)
{
  INT4  k, bucketRecordN;

  if (!btree->isWriteOpen)
    _ErrExit2 (e__notwriteopen, FileGetName (btree->file, "path"));
  if (!btree->type)
    _ErrExit2 (e__parnotdefined, "B-tree type");

  /*
  ** calculate the bucket size ... the btree must have three
  ** levels so the calculation is: bucketsize^3 > no of values
  */

  if (recordN == 1)
    bucketRecordN = 1; /* k*k*k >= recordN should also work now ...*/
  else
    for (k=0; k < 1000; k += k<10 ? 1 : 10)
      if (k*k*k > recordN) {
	bucketRecordN = k;
	break;
      }

  btree->bucketRecordN = bucketRecordN;
  btree->buildPhase = 1;
  btree->isBuildPhaseInit = 0;
  btreeCurr = btree;
}


/**api* BtrBuildStartPhase2 **********************************************
** 
**      initializes building phase 2;
**
** 	INPUT:	    address of Btree object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    
*/ 

void BtrBuildStartPhase2 ()
{
  if (btreeCurr->buildPhase != 1)
    _ErrExit2 (e__btreenotprep, 2);
  btreeCurr->buildPhase = 2;
  btreeCurr->isBuildPhaseInit = 0;
}


/**api* BtrInsertValue ***************************************************
** 
**
** 	INPUT:	    address of Btree object [W]
**                  file pointer to bucket [R]
**                  size of bucket in bytes [R]
** 	        IMPLICIT:
**                  btreeCurr [W]
** 
** 	RETURNS:    
*/ 

void BtrInsertRecord (BTRoREC *record)
{
  static INT4 bucketRecordN, levelFip[3], recordCnt[3], strSiz;

  switch (btreeCurr->buildPhase) {

    /*
    ** phase I calculates the size of all records of all three levels
    */

  case 1:
    if (!btreeCurr->isBuildPhaseInit) {  /* init counters at begin */
      btreeCurr->isBuildPhaseInit = 1;

      bucketRecordN = btreeCurr->bucketRecordN;
      levelFip[0] = levelFip[1] = levelFip[2] = 0;
      recordCnt[0] = recordCnt[1] = recordCnt[2] = 0;
      btreeCurr->maxStrSiz = 0;
    }

    /* 
    ** add record string length and level specific record size to overall 
    ** level size ....if record is last in bucket then do the same in uppper
    ** level 
    */

    strSiz = strlen (record->str) + 1;
    if (strSiz > btreeCurr->maxStrSiz)
      btreeCurr->maxStrSiz = strSiz;
    recordCnt[2]++;                          /* level 2 */
    if (!(recordCnt[2] % bucketRecordN)) {  
      recordCnt[1]++;                        /* level 1 */
      levelFip[2] += strSiz + BTRxPTRRECADDSIZ; 
      if (!(recordCnt[1] % bucketRecordN)) {
	recordCnt[0]++;                      /* level 0 - root bucket */
        levelFip[1] += strSiz + BTRxPTRRECADDSIZ;  
      }
    }
    break;

  case 2:
    if (!btreeCurr->isBuildPhaseInit) {
      btreeCurr->isBuildPhaseInit = 1;
      if (btreeCurr->isFixedRecordSiz)
	btreeCurr->fixedRecordSiz = btreeCurr->recordSiz + 
	                            btreeCurr->maxStrSiz;
      else
	btreeCurr->fixedRecordSiz = 0;
      /*
      ** if the last record counted in phase one is not at the end(level II)
      ** of bucket then it must be entered in levels I and 0
      */

      btreeCurr->recordN = recordCnt[2];

      {
	int isAddedToLevel2 = 0;
	if (recordCnt[2] % bucketRecordN) {
	  recordCnt[1]++;
	  levelFip[2] += strSiz + BTRxPTRRECADDSIZ; 
	  isAddedToLevel2 = 1;
	}
	if (recordCnt[1] % bucketRecordN || isAddedToLevel2) {
	  recordCnt[0]++;
	  levelFip[1] += strSiz + BTRxPTRRECADDSIZ; 
	}
      }

      /*
      ** now, to get the sizes of the levels right the size of the
      ** extra information per bucket must be added
      */

      levelFip[1] += BTRxBUCKETADDSIZ;  /* only 1 bucket in level 0 */
      levelFip[2] += ((recordCnt[1] + bucketRecordN-1) / bucketRecordN) *
                      BTRxBUCKETADDSIZ;

      /*
      ** finally we can give for each level the offset within the output
      ** file (..offset for level 0 is directly after the btree-info-block)
      */

      levelFip[0] = BTRxINFOSIZE;
      btreeCurr->levelFip[0] = btreeCurr->levelWriteFip[0] = levelFip[0];
      btreeCurr->levelFip[1] = btreeCurr->levelWriteFip[1] = 
	levelFip[0] + levelFip[1];
      btreeCurr->levelFip[2] = btreeCurr->levelWriteFip[2] = 
	levelFip[0] + levelFip[1] + levelFip[2];
      
      /*
      ** reserve some space for all internal nodes in levels 0 and 1
      ** this is done by writing some junk to the file
      */

      BtrWrite (btreeCurr, NULL, btreeCurr->levelFip[2], -1);
      BtrWriteInfo (btreeCurr);
      btreeCurr->bucket = NULL;
    }
    BtrBucketInsertRecord (btreeCurr, &btreeCurr->bucket, record, 2); 
    break;
  default:
    _ErrExit2 (e__btreenotprep, 1);
  }
}



/**api* BtrCompress ***********************************************************
** 
**      compress an btree, that is it's associated ID-list file;
**
** 	INPUT:	    address of Btree object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    
*/ 

void BtrCompress (char *fileName)
{
  IDSoFILE   *idsFile;
  BTRoBUCKET *bucket;
  BTRo       *btree;
  BTRoREC    *record;
  INT4        opt, idN, errCode, k=0;

  btree = BtrOpen (fileName, "compress", &errCode);
  _ErrExit2 (errCode, FileGetName (btree->file, "path"));
  if (!(idsFile = IdsOpen (fileName, "compress", 512, NULL, &errCode)))
    _ErrExit2 (errCode, fileName);
  
  if (btree->recordN) {
    btree->levelWriteFip[2] = btree->firstBucketFip;
    
    for (opt=BTRxFIRST; (record = BtrRecordGet (btree, opt)); opt=BTRxNEXT) {
      k++;
      idN = IdsCompress (idsFile, &record->r.value.firstIdFip);
      record->r.value.lastIdFip = record->r.value.firstIdFip;
      
      if (idN != record->r.value.idN)
	printf ("old: %d, new: %d\n", record->r.value.idN, idN);
      
      bucket = btree->bucketCurr;
      if (bucket->recordXCurr == bucket->recordN - 1) {
	BtrBucketPack (btree, bucket);
	BtrWrite (btree, bucket->bucketBuff, bucket->bucketSize, 2);
      }
    }
  }
  IdsClose (idsFile);
  btree->isCompressed = 1;
  BtrClose (btree);
}


/**api* BtrTouch **************************************************************
** 
**      sets the internal index time to current time;
**
** 	INPUT:	    address of Btree object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    
*/ 

void BtrTouch (char *fileName)
{
  BTRo       *btree;
  INT4       errCode;

  btree = BtrOpen (fileName, "update", &errCode);
  _ErrExit2 (errCode, FileGetName (btree->file, "path"));
  btree->timeCreated = TimeGet ();
  BtrClose (btree);
}

/****** BtrFixedBucketSize ****************************************************
** 
**      calculates the size of a bucket in a btree with fixed record size
**
** 	INPUT:	    address of Btree object [W]
**                  file address of bucket
** 	        IMPLICIT:
** 
** 	RETURNS:    bucket size in Bytes
*/ 

static INT4 BtrFixedBucketSize (BTRo *btree, FIP fip)
{
  INT4 size;

  if (!(fip == btree->lastBucketFip))
    return (btree->fixedRecordSiz * btree->bucketRecordN);

  size = ((size = btree->recordN % btree->bucketRecordN) ? size :
         btree->bucketRecordN) * btree->fixedRecordSiz;
  return size;
}


/**api* BtrRecordById *********************************************************
** 
**      gets record with specified number; recordId ranges from 0 to
**      total no of records - 1;
**
** 	INPUT:	    address of Btree object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    pointer to record
**                  NULL if not found
*/ 

BTRoREC *BtrRecordById (BTRo *btree, FIP recordId)
{
  BTRoBUCKET *bucket=btree->bucketCurr;
  FIP fip;
  INT4 recordX, bucketSize=btree->fixedRecordSiz * btree->bucketRecordN; 

  recordId--;  /* convert number into index */

  fip = recordId * btree->fixedRecordSiz; 
  fip = btree->firstBucketFip + (fip / bucketSize) * bucketSize; 

  if (!bucket || bucket->fip != fip) {  /* get new bucket */
    bucket = BtrReadBucket (btree, fip, BtrFixedBucketSize (btree, fip));
    BtrBucketKill (&btree->bucketCurr);
    btree->bucketCurr = bucket;
  }
  recordX = recordId % btree->bucketRecordN; 
  btree->bucketCurr->recordXCurr = recordX;

  return &btree->bucketCurr->record[recordX];
}



/**api* BtrRecordGet **********************************************************
** 
**      gets record by specified option;
**
** 	INPUT:	    address of Btree object [W]
**                  location: BTRxFIRST, BTRxLAST, BTRxPREV, BTRxCURR, 
**                            BTRxNEXT [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    pointer to record
**                  NULL if no more records
*/ 

BTRoREC *BtrRecordGet (BTRo *btree, enum BtrStep option)
{
  BTRoBUCKET *bucket=btree->bucketCurr;
  BTRoREC    *record;
  INT4        recordX;

  if (!btree->recordN)
    return NULL;

  switch (option) {
  case BTRxFIRST:
    bucket = BtrBucketGet (btree, BTRxFIRST);
    recordX = 0;
    break;
  case BTRxLAST:
    bucket = BtrBucketGet (btree, BTRxLAST);
    recordX = bucket->recordN - 1;
    break;
  case BTRxPREV:
    if (bucket->recordXCurr == 0) {
      if (!(bucket = BtrBucketGet (btree, BTRxPREV)))
	return NULL;
      recordX = bucket->recordN - 1;
    }
    else recordX = bucket->recordXCurr - 1;
    break;
  case BTRxCURR:
    if (!bucket)
      return NULL;
    recordX = bucket->recordXCurr;
    break;
  case BTRxNEXT:
    if (bucket->recordXCurr == bucket->recordN-1) {
      if (!(bucket = BtrBucketGet (btree, BTRxNEXT))) {
	BtrBucketKill (&btree->bucketCurr);
	btree->bucketCurr = NULL;
	return NULL;
      }
      recordX = 0;
    }
    else recordX = bucket->recordXCurr + 1;
    break;
  default:
    return NULL;
  }

  record = &bucket->record[recordX];
  bucket->recordXCurr = recordX;
  record->type = btree->leafType;
  return record;
}


/****** BtrBucketGet **********************************************************
** 
**      gets specified bucket
**
** 	INPUT:	    address of Btree object [W]
**                  location: BTRxFIRST, BTRxLAST, BTRxPREV, BTRxNEXT [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    pointer to bucket
**                  NULL if no more buckets
*/ 

static BTRoBUCKET *BtrBucketGet (BTRo *btree, enum BtrStep option)
{
  BTRoBUCKET *bucket, *bucketCurr=btree->bucketCurr;

  switch (option) {
  case BTRxFIRST:
    bucket = BtrReadBucket (btree, btree->firstBucketFip, 
			    btree->firstBucketSize);
    break;
  case BTRxLAST:
    bucket = BtrReadBucket (btree, btree->lastBucketFip, 
			    btree->lastBucketSize);
    break;
  case BTRxPREV:
    if (bucketCurr && bucketCurr->fip == btree->firstBucketFip)
      return NULL;  /* end of file */
    bucket = BtrReadBucket (btree, 
			    bucketCurr->fip - bucketCurr->prevBucketSize,
			    bucketCurr->prevBucketSize);
    break;
  case BTRxNEXT:
    if (bucketCurr && (bucketCurr->fip >= btree->lastBucketFip ||
	btree->bucketRecordN == btree->recordN)) /*btree has only one bucket */
      return NULL;  /* end of file */
    bucket = BtrReadBucket (btree, bucketCurr->fip + bucketCurr->bucketSize,
			    bucketCurr->nextBucketSize);
    break;
  default:
    return NULL;
  }
  if (bucket) {
    BtrBucketKill (&btree->bucketCurr);
    btree->bucketCurr = bucket;
  }
  return bucket;
}


/**api* BtrGetFileSize ********************************************************
** 
**      gets file size in bytes;
**
** 	INPUT:	    address of Btree object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    file size in bytes
*/ 

INT4 BtrGetFileSize (BTRo *btree)
{
  return btree->fileSize;
}

/**api* BtrGetRecordN *********************************************************
** 
**      gets number of records in btree;
**
** 	INPUT:	    address of Btree object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    number of records
*/ 

INT4 BtrGetRecordN (BTRo *btree)
{
  return btree->recordN;
}

/**api* BtrGetType ************************************************************
** 
**      Returns the type of the btree.
**
** 	INPUT:	    address of Btree object [R]
**
** 	RETURNS:    type of btree (enumeration) 
*/ 

INT4 BtrGetType (BTRo *btree)
{
  return btree->type;
}

/**api* BtrGetTimeCreated *****************************************************
** 
**      gets creation time
**
** 	INPUT:	    address of Btree object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    number of records
*/ 

UINT4 BtrGetTimeCreated (BTRo *btree)
{
  return btree->timeCreated;
}

/**api* BtrIsBusy *************************************************************
** 
**      returns TRUE if the btree is still busy
**
** 	INPUT:	    address of Btree object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 or 0;
*/ 

INT4 BtrIsBusy (BTRo *btree)
{
  return btree->isBusy;
}

/**api* BtrCompare ************************************************************
** 
**      Compares two records.
**
** 	INPUT:	    address of Btree object [R]
**                  first record [R]
**                  second record [R]
** 
** 	RETURNS:    1: first record greater than second
**                  0: first and second records are equal
**                  -1: first record is lesser than second
*/ 

Int4 BtrCompare (BTRo *btree, BTRoREC *rec1, BTRoREC *rec2)
{
  return (*btree->compare)(rec1, rec2);
}
i* BtrCompare srs/src/btree.h
**
**    $RCSfile: btree.h,v $
**    $Revision: 1.3 $
**    $Date: 1996/09/09 20:17:12 $
**    $Author: etzold $
**
**    $Locker:  $
**    $State: Exp $
**
**                  SRS Copyright by Thure Etzold
**
*/


#define BTRxCURRENT_VERSION 1000000
#define BTRxTMPRECORDSIZ 132
#define BTRxINFOSIZE    96
  

enum btrType {BTRxIDENTRY=1, BTRxSTR, BTRxNUM, BTRxREAL};
enum recType {BTRxID=1, BTRxVALUE, BTRxPOINTER};
enum BtrStep {BTRxFIRST=1, BTRxLAST, BTRxCURR, BTRxNEXT, BTRxPREV};


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  record of various types to be inserted into a bucket of a btree
*/

typedef struct BTRoPOINTER {
  FIP  downFip;   /* fip of lower level bucket */
  INT4  downSize;  /* size of lower level bucket */
} BTRoPOINTER;

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  record of various types to be inserted into a bucket of a btree
*/

typedef struct BTRoVALUE {
  INT4  idN;         /* number of IDs associated to value */
  FIP  firstIdFip;  /* file address of first ID */
  FIP  lastIdFip;   /* file address of last ID */
} BTRoVALUE;

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  record of various types to be inserted into a bucket of a btree
*/

typedef struct BTRoID {
  FIP  textFip;  /* file address of text part of entry */
  FIP  dataFip;  /* file address of data part of entry */
  char fileX;    /* file index to point to source file in array of flatfiles */
} BTRoID;



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  record of various types to be inserted into a bucket of a btree
*/

typedef struct BTRoREC {
  union {
    BTRoPOINTER pointer;
    BTRoID      id;
    BTRoVALUE   value;
  } r;
  char *str;   /* string value */
  enum recType  type;
} BTRoREC;



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  bucket object;
*/

typedef struct BTRoBUCKET {
  char             *bucketBuff;    /* pointer to the buffer containing the
				      packed bucket */
  FIP              fip;            /* buckets address in the file */ 
  enum recType     type;
  char             *writePtr;
  BTRoREC          *record;        /* array of records */
  INT4              recordN;        /* number of records in bucket */
  struct BTRoBUCKET *up;          /* address to upper level bucket */
  INT4              bucketSize;     /* size of bucket in bytes */
  INT4              fixedRecordSize;    
  INT4              nextBucketSize; /* size of bucket in bytes */
  INT4              prevBucketSize; /* size of bucket in bytes */
  INT4              recordXCurr;    /* index of current record - 
				      for iteration */
} BTRoBUCKET;




/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  top level object describing a Btree
*/

/* types of the method functions */
typedef Int4 (*BTRoComparer) (BTRoREC*, BTRoREC*);

typedef struct BTRo {
  struct FILEo*      file;         /* file handle to INX file */
  BTRoBUCKET*        root;            /* pointer to root bucket */
  struct BTRoBUCKET* bucketCurr; 
  FIP                rootFip;          /* file pointer to root node */
  INT4               rootSize;         /* size of root node */
  char               infoBuff[BTRxINFOSIZE]; /* buffer for info block */
  char               infoSize;
  FIP                writeFip;         /* write file pointer */
  FIP                levelWriteFip[3]; /* write file pointer */
  FIP                levelFip[3];      /* write file pointer */
  INT4               buildPhase;
  INT4               isBuildPhaseInit;
  INT4               isWriteOpen;      /* file open for write access */
  INT4               isBusy;
  INT4               isCompressed;
  INT4               isFixedRecordSiz;
  INT4               maxStrSiz;
  INT4               recordSiz;      /* size of record without string */
  INT4               fixedRecordSiz;
  enum btrType       type;            /* type of Btree */
  enum recType       leafType;        /* type of records in leaf */
  INT4               bucketRecordN;
  INT4               fileSize;
  INT4               recordN;
  INT4               firstBucketSize;
  INT4               lastBucketSize;
  FIP                firstBucketFip;
  FIP                lastBucketFip;
  UINT4              timeCreated;
  INT4               versionN;
  BTRoBUCKET*        bucket;  /* pointer to leaf bucket currently written */
  /* methods */
  BTRoComparer        compare;
} BTRo;



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of exported functions
*/

BTRo *BtrOpen (char *file_nm, char *opt, INT4 *errCode); 
void BtrClose (BTRo *btree); 
void BtrCompress (char *fileName);
void BtrTouch (char *fileName);

    /* manipulating or writing to Btree */

void BtrSetBucketSize (BTRo *btree, INT4 size);
void BtrSetType (BTRo *btree, char *option);
void BtrSetNumType (BTRo *btree, Int4 type);

void BtrBuildStartPhase1 (BTRo *btree, INT4 recordN);
void BtrBuildStartPhase2 ();
void BtrInsertRecord (BTRoREC *record);

    /* reading from Btree */

BTRoREC *BtrSearch (BTRo *btree, char *str, FIP *fip, INT4 compLen);
BTRoVALUE *BtrSearchStr (BTRo *btree, char *value);
BTRoVALUE *BtrSearchNum (BTRo *btree, INT4 num);
BTRoVALUE *BtrSearchReal (BTRo *btree, double real);
BTRoID *BtrSearchId (BTRo *btree, char *str, FIP *idFip);
INT4 BtrIsSearchGreaterMaxVal (BTRo *btree);
INT4 BtrIsSearchLessMinVal (BTRo *btree);

BTRoREC *BtrRecordGet (BTRo *btree, enum BtrStep option);
BTRoREC *BtrRecordById (BTRo *btree, FIP recordId);

Int4 BtrCompare (BTRo *btree, BTRoREC *rec1, BTRoREC *rec2);

    /* info about btree */

INT4 BtrGetFileSize (BTRo *btree);
INT4 BtrGetRecordN (BTRo *btree);
INT4 BtrIsBusy (BTRo *btree);
UINT4 BtrGetTimeCreated (BTRo *btree);
Int4 BtrGetType (BTRo *btree);
ID *BtrSearchId (BTRo *btree, char *str, FIP *idFip);
INT4 BtrIsSearchGreaterMaxVal (BTRo *btree);
INT4 BtrIsSearchLessMinVal (BTRo *btree);

BTRoREC *BtrRecordGet (BTRo *btree, enum BtrStep option);
BTRoREC *BtrRecordById (BTRo *btree, FIP recordsrs/src/builtin.h
**
**    $RCSfile: builtin.h,v $
**    $Revision: 1.26 $
**    $Date: 1997/03/13 17:04:49 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**             from ODD file: "srsica:srswin.sdl"
**   date of ODD compilation: 13-MAR-1997 12:06
**
*/




/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Value in an enumeration
*/

#ifndef _ODDoVALUE
#define _ODDoVALUE
typedef struct ODDoVALUE {
  char                    *name;         /* Name of value. */
  INT4                    n;             /* Number value. */
  char                    *rem;          /* Comment field. */
} ODDoVALUE;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Argument of Icarus command.
*/

#ifndef _IARGoVALUE
#define _IARGoVALUE
typedef struct IARGoVALUE {
  char                    *name;         /* Name of the argument in an Icarus
                                            program. */
  char                    *rem;          /* Comment field. */
  unsigned char           isUnnamed;     /* Defines if parameter may be
                                            unnamed. */
  unsigned char           isRequired;    /* Defines if parameter is required. */
  unsigned char           type;          /* Type of the argument */
  char                    *className;
  INT4                    defInt;        /* Default value of type 'int'
                                            arguments. */
  char                    *defaultStr;   /* Default value of type 'string'
                                            arguments. */
  struct ODDoVALUE        *vals;
  INT4                    valsN;
  unsigned char           isSet;
  struct VARo             *val;
} IARGoVALUE;
#endif

#ifndef _IARGoCOM
#define _IARGoCOM
typedef struct IARGoCOM {
  char                    *name;         /* Name of command in Icarus programs.
                                            */
  char                    *functionName; /* C function that implements the
                                            command. */
  INT4                    isShow;        /* Determines whether the command
                                            should appear in the 
Icarus functions
                                            reference list.
 */
  char                    *rem;          /* Comment field. */
  unsigned char           returnType;    /* Type of value to be returned (if
                                            any). */
  INT4                    time;          /* Execution time of command. */
  char                    *returnClass;
  unsigned char           isDirectCall;  /* Call function directly or via
                                            C-interface. */
  char                    *methodOf;     /* The class of which this function is
                                            a method otherwise treated
                                            as
normal function.
 */
  struct IARGoVALUE       *args;
  INT4                    argsN;
  INT4                    (*function)(); /* Function to be executed for
                                            command. */
  INT4                    orderN;        /* Number of arguments ordered from C
                                            function (via 'IargGetArgs'). */
  INT4                    orderAllocN;   /* Number of orders currently
                                            allocated. */
  struct IARGoVALUE       **order;       /* Array with a list of argument
                                            orders. */
} IARGoCOM;
#endif

extern ODDoVALUE    ODDValue[];
extern IARGoVALUE    IARGVALUE[];
extern IARGoCOM    IARGCOM[];

#ifdef _INITOBJS

ODDoVALUE    ODDValue[] = {
    {"pre", 1, ""},
    {"post", 2, ""},
    {"pre", 1, ""},
    {"post", 2, ""},
    {"read", 1, ""},
    {"write", 2, ""},
    {"path", 1, ""},
    {"dir", 2, ""},
    {"name", 3, ""},
    {"file", 4, ""},
    {"ext", 5, ""},
    {"normal", 0, ""},
    {"raw", 1, ""},
    {"normal", 0, ""},
    {"raw", 1, ""},
    {"gcg", 1, ""},
    {"msf", 2, ""},
    {"pir", 3, ""},
    {"plain", 4, ""},
    {"fasta", 5, ""},
    {"embl", 6, ""},
    {"swiss", 7, ""},
    {"clustal", 8, ""}
};

IARGoVALUE    IARGVALUE[] = {
    {"opnd", "", 1, 0, 9, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"t", "", 0, 0, 9, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"val", "", 1, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"key", "", 0, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"op", "", 1, 0, 9, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"a", "", 0, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"b", "", 0, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"val", "", 1, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"name", "", 0, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"key", "", 0, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"index", "", 0, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"var", "", 0, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"var", "", 1, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"name", "", 1, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"opt", "", 0, 0, 1, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"file", "", 1, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"body", "", 1, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"body", "", 1, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"i", "", 0, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"c", "", 0, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"u", "", 0, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"b", "", 0, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"body", "", 0, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"list", "", 0, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"var", "", 0, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"c", "", 0, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"b", "", 0, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"node", "", 0, 0, 3, "node", 0, "", &ODDValue[0], 0, 0, NULL},
    {"prod", "", 0, 0, 3, "node", 0, "", &ODDValue[0], 0, 0, NULL},
    {"reStr", "", 1, 0, 9, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"name", "", 1, 0, 9, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"node", "", 1, 0, 3, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"t", "", 0, 0, 9, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"node", "", 1, 0, 3, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"prog", "", 1, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"name", "", 1, 0, 9, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"lookahead", "", 0, 0, 1, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"value", "", 1, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"value", "", 1, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 1, "", &ODDValue[0], 0, 0, NULL},
    {"value", "", 1, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 2, "", &ODDValue[0], 0, 0, NULL},
    {"value", "", 1, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 3, "", &ODDValue[0], 0, 0, NULL},
    {"value", "", 1, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 4, "", &ODDValue[0], 0, 0, NULL},
    {"value", "", 1, 0, 6, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 5, "", &ODDValue[0], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 1, "", &ODDValue[0], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 2, "", &ODDValue[0], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 3, "", &ODDValue[0], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 4, "", &ODDValue[0], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 5, "", &ODDValue[0], 0, 0, NULL},
    {"prod", "", 1, 0, 9, "", 0, "", &ODDValue[0], 0, 0, NULL},
    {"cond", "Breaks only if condition is met.", 0, 0, 1, "", 1, "",
    &ODDValue[0], 0, 0, NULL},
    {"time", "", 0, 0, 1, "", 0, "", &ODDValue[0], 2, 0, NULL},
    {"prod", "", 1, 0, 9, "", 0, "", &ODDValue[2], 0, 0, NULL},
    {"time", "", 0, 0, 1, "", 0, "", &ODDValue[2], 2, 0, NULL},
    {"name", "", 1, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"name", "", 1, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"n", "", 1, 0, 1, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"name", "", 0, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"x", "", 0, 0, 1, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"y", "", 0, 0, 1, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"color", "", 0, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"prod", "", 1, 0, 3, "production", 0, "", &ODDValue[4], 0, 0, NULL},
    {"prod", "", 0, 0, 16, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"string", "", 1, 0, 9, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"start", "The name of the start symbol (production).", 0, 0, 9, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"file", "Selects opened file to be read for input.", 0, 0, 3, "file", 0,
    "", &ODDValue[4], 0, 0, NULL},
    {"fileName", "Selects opened file to be read for input.", 0, 0, 9, "", 0,
    "", &ODDValue[4], 0, 0, NULL},
    {"show", "Sets display of the syntax before parsing.", 0, 0, 1, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"skip", "The set of characters to be skipped as white space", 0, 0, 9, "",
    0, "", &ODDValue[4], 0, 0, NULL},
    {"comment", "Regular expression for skipping comments", 0, 0, 9, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"tree", "Flag if set requests printing the syntax tree.", 0, 0, 1, "", 0,
    "", &ODDValue[4], 0, 0, NULL},
    {"prod", "", 1, 0, 16, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"skip", "The set of characters to be skipped as white space", 0, 0, 9, "",
    0, "", &ODDValue[4], 0, 0, NULL},
    {"comment", "Regular expression for skipping comments", 0, 0, 9, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"file", "Sets opened file as input.", 0, 0, 3, "file", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"str", "Sets string as input.", 0, 0, 9, "", 0, "", &ODDValue[4], 0, 0,
    NULL},
    {"show", "Sets display of the syntax before parsing.", 0, 0, 1, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"tree", "Flag if set requests printing the syntax tree.", 0, 0, 1, "", 0,
    "", &ODDValue[4], 0, 0, NULL},
    {"fileName", "Name of the file to be opened as input.", 0, 0, 9, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"job", "", 1, 0, 3, "job", 0, "", &ODDValue[4], 0, 0, NULL},
    {"job", "", 1, 0, 3, "job", 0, "", &ODDValue[4], 0, 0, NULL},
    {"string", "", 0, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"start", "The name of the start symbol (production).", 0, 0, 2, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"file", "Selects opened file to be read for input.", 0, 0, 3, "file", 0,
    "", &ODDValue[4], 0, 0, NULL},
    {"fileName", "Selects opened file to be read for input.", 0, 0, 2, "", 0,
    "", &ODDValue[4], 0, 0, NULL},
    {"job", "", 1, 0, 3, "job", 0, "", &ODDValue[4], 0, 0, NULL},
    {"job", "", 1, 0, 3, "job", 0, "", &ODDValue[4], 0, 0, NULL},
    {"job", "", 1, 0, 3, "job", 0, "", &ODDValue[4], 0, 0, NULL},
    {"name", "Name of the token list.", 0, 0, 2, "", 0, "", &ODDValue[4], 0, 0,
    NULL},
    {"code", "", 0, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"n", "", 0, 0, 1, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"print", "", 0, 0, 1, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"task", "", 0, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"withCode", "", 0, 0, 1, "", 1, "", &ODDValue[4], 0, 0, NULL},
    {"outFile", "Output file object.", 0, 0, 3, "file", 0, "", &ODDValue[4], 0,
    0, NULL},
    {"in", "Name of the input token table.", 1, 1, 9, "", 0, "", &ODDValue[4],
    0, 0, NULL},
    {"ic", "Token code.", 0, 0, 9, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"n", "Numerical token code.", 0, 0, 1, "", -1, "", &ODDValue[4], 0, 0,
    NULL},
    {"p", "Name of production to be linked.", 0, 0, 9, "", 0, "", &ODDValue[4],
    0, 0, NULL},
    {"t", "Name of task that if results in forced parsing.", 0, 0, 9, "", 0,
    "", &ODDValue[4], 0, 0, NULL},
    {"count", "", 0, 0, 9, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"var", "", 0, 0, 6, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"file", "Symbolic name of the input file.", 0, 0, 9, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"share", "Symbolic name file that shares physical file.", 0, 0, 9, "", 0,
    "", &ODDValue[4], 0, 0, NULL},
    {"select",
    "Selects token with specified count number. \nThe value 0 selects all tokens \n(only in combination with \"count\").\n",
    0, 0, 1, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"c", "", 0, 0, 6, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"name", "Name of ouput token table.", 1, 0, 9, "", 0, "", &ODDValue[4], 0,
    0, NULL},
    {"name", "Name of ouput token table.", 1, 0, 9, "", 0, "", &ODDValue[4], 0,
    0, NULL},
    {"len", "", 0, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"len", "", 0, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"len", "", 0, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"c", "token code as a name", 1, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"n", "token code as a number", 0, 0, 1, "", 0, "", &ODDValue[4], 0, 0,
    NULL},
    {"s",
    "string to be written to the token table.\nIf left unspecified the current match, or current token ($Ct)\nis written.\n",
    0, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"c", "token code as a name", 1, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"n", "token code as a number", 0, 0, 1, "", 0, "", &ODDValue[4], 0, 0,
    NULL},
    {"s",
    "string to be written to the token table.\nIf left unspecified the current match, or current token ($Ct)\nis written.\n",
    0, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"c", "token code as a name", 1, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"n", "token code as a number", 0, 0, 1, "", 0, "", &ODDValue[4], 0, 0,
    NULL},
    {"s",
    "string to be written to the token table.\nIf left unspecified the current match, or current token ($Ct)\nis written.\n",
    0, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"s", "String to be written to the token table.", 1, 0, 2, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"s", "String to be written to the token table.", 1, 0, 2, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"s", "String with which current match is to be replaced", 1, 0, 6, "", 0,
    "", &ODDValue[4], 0, 0, NULL},
    {"s", "String with which current match is to be replaced", 1, 0, 6, "", 0,
    "", &ODDValue[4], 0, 0, NULL},
    {"name", "Name of requested token table.", 1, 0, 2, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"flag", "", 0, 0, 2, "", 0, "nocase", &ODDValue[4], 0, 0, NULL},
    {"value", "", 1, 0, 6, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"value", "", 1, 0, 6, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 1, "", &ODDValue[4], 0, 0, NULL},
    {"value", "", 1, 0, 6, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 2, "", &ODDValue[4], 0, 0, NULL},
    {"value", "", 1, 0, 6, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 3, "", &ODDValue[4], 0, 0, NULL},
    {"value", "", 1, 0, 6, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 4, "", &ODDValue[4], 0, 0, NULL},
    {"value", "", 1, 0, 6, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 5, "", &ODDValue[4], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 1, "", &ODDValue[4], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 2, "", &ODDValue[4], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 3, "", &ODDValue[4], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 4, "", &ODDValue[4], 0, 0, NULL},
    {"stack", "", 0, 0, 1, "", 5, "", &ODDValue[4], 0, 0, NULL},
    {"val", "", 1, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"val", "", 1, 0, 2, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"name", "Parameter name.", 1, 0, 9, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"set", "", 0, 0, 9, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"name", "Parameter name.", 1, 0, 9, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"set", "", 0, 0, 1, "", 2, "", &ODDValue[4], 0, 0, NULL},
    {"name", "Parameter name.", 1, 0, 9, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"set", "", 0, 0, 9, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"name", "Parameter name.", 1, 0, 9, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"set", "", 0, 0, 1, "", 2, "", &ODDValue[4], 0, 0, NULL},
    {"name", "Parameter name.", 1, 0, 9, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"name", "Name of environment variable.", 1, 0, 9, "", 0, "", &ODDValue[4],
    0, 0, NULL},
    {"set", "New string value of the environment variable.", 0, 0, 9, "", 0,
    "", &ODDValue[4], 0, 0, NULL},
    {"cond", "The condition.", 1, 1, 1, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"t", "String to be returned if condition is true.", 0, 0, 9, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"f", "String to be returned if condition is false", 0, 0, 9, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"cond", "The condition.", 1, 1, 1, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"t", "String to be returned if condition is true.", 0, 0, 9, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"f", "String to be returned if condition is false", 0, 0, 9, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"var", "Name of variable used for iteration", 1, 0, 6, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"in", "The list.", 0, 0, 16, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"s", "String to print for each list element", 0, 0, 6, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"sep", "Separator strings to be printed between elements", 0, 0, 6, "", 0,
    "", &ODDValue[4], 0, 0, NULL},
    {"str", "Classical substr function", 1, 0, 9, "", 0, "", &ODDValue[4], 0,
    0, NULL},
    {"s", "Start posilion inside of string", 0, 1, 1, "", 0, "", &ODDValue[4],
    0, 0, NULL},
    {"l", "subStr length if ommited - suffix", 0, 0, 1, "", 0, "",
    &ODDValue[4], 0, 0, NULL},
    {"com", "Unix command", 1, 1, 9, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"script", "String (text) that is written to a script and then executed",
    0, 0, 9, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"scriptName", "Name of the script that is to be generated.", 0, 0, 9, "",
    0, "", &ODDValue[4], 0, 0, NULL},
    {"out", "Name of output file  (Use 'stdout' for standard output).", 0, 0,
    9, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"error", "Name of error output file  (Use 'stdout' for standard output).",
    0, 0, 9, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"name",
    "The name of the file; if omitted stdin (for read access mode) \nor stdout (write access mode) are assumed.\n",
    1, 0, 9, "", 0, "", &ODDValue[4], 0, 0, NULL},
    {"mode", "Access mode for opened file", 0, 0, 1, "", 1, "", &ODDValue[4],
    2, 0, NULL},
    {"file", "", 1, 0, 3, "file", 0, "", &ODDValue[6], 0, 0, NULL},
    {"type", "", 1, 0, 1, "", 1, "", &ODDValue[6], 5, 0, NULL},
    {"s", "", 1, 0, 6, "", 0, "", &ODDValue[11], 0, 0, NULL},
    {"f", "", 0, 0, 3, "file", 0, "", &ODDValue[11], 0, 0, NULL},
    {"mode", "", 0, 0, 1, "", 0, "", &ODDValue[11], 2, 0, NULL},
    {"v", "Appends the string to specified string variable.", 0, 0, 6, "", 0,
    "", &ODDValue[13], 0, 0, NULL},
    {"s", "", 1, 0, 6, "", 0, "", &ODDValue[13], 0, 0, NULL},
    {"s", "", 1, 0, 6, "", 0, "", &ODDValue[13], 0, 0, NULL},
    {"f", "", 0, 0, 3, "file", 0, "", &ODDValue[13], 0, 0, NULL},
    {"mode", "", 0, 0, 1, "", 0, "", &ODDValue[13], 2, 0, NULL},
    {"v", "Appends the string to specified string variable.", 0, 0, 6, "", 0,
    "", &ODDValue[15], 0, 0, NULL},
    {"s", "", 1, 0, 9, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"label", "Label to be printed at begin of each line.", 0, 0, 9, "", 0, "",
    &ODDValue[15], 0, 0, NULL},
    {"width", "Maximum width of output lines.", 0, 0, 1, "", 0, "",
    &ODDValue[15], 0, 0, NULL},
    {"indent", "Indentation for all lines.", 0, 0, 1, "", 0, "", &ODDValue[15],
    0, 0, NULL},
    {"firstIndent", "Indentation of first line.", 0, 0, 1, "", 0, "",
    &ODDValue[15], 0, 0, NULL},
    {"n", "", 1, 0, 1, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"val", "", 1, 0, 6, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"list", "", 1, 0, 6, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"switch", "", 1, 0, 1, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"switch", "", 1, 0, 1, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"state", "0: turns skipping white space off<BR>\n1: turns it on again\n",
    1, 0, 1, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"s", "", 0, 0, 9, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"state", "0: turns skipping white space off<BR>\n1: turns it on again\n",
    1, 0, 1, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"s", "", 0, 0, 9, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"prog", "", 1, 0, 9, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"s", "", 1, 0, 9, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"skip", "String containing characters to be removed from ends.\n", 0, 0,
    9, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"n", "", 0, 0, 1, "", 1, "", &ODDValue[15], 0, 0, NULL},
    {"n", "", 0, 0, 1, "", 2, "", &ODDValue[15], 0, 0, NULL},
    {"n", "", 0, 0, 1, "", 3, "", &ODDValue[15], 0, 0, NULL},
    {"n", "", 0, 0, 1, "", 4, "", &ODDValue[15], 0, 0, NULL},
    {"n", "", 0, 0, 1, "", 5, "", &ODDValue[15], 0, 0, NULL},
    {"n", "", 0, 0, 1, "", 6, "", &ODDValue[15], 0, 0, NULL},
    {"n", "", 0, 0, 1, "", 7, "", &ODDValue[15], 0, 0, NULL},
    {"n", "", 0, 0, 1, "", 8, "", &ODDValue[15], 0, 0, NULL},
    {"n", "", 0, 0, 1, "", 9, "", &ODDValue[15], 0, 0, NULL},
    {"name", "", 1, 0, 2, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"set", "", 1, 0, 3, "set", 0, "", &ODDValue[15], 0, 0, NULL},
    {"q", "", 0, 0, 9, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"init", "", 0, 0, 2, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"db", "", 0, 0, 2, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"group", "", 1, 0, 3, "dbGroup", 0, "", &ODDValue[15], 0, 0, NULL},
    {"index", "", 0, 1, 2, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"group", "", 1, 0, 3, "dbGroup", 0, "", &ODDValue[15], 0, 0, NULL},
    {"l", "", 0, 0, 2, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"h", "", 0, 0, 2, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"le", "", 0, 0, 1, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"re", "", 0, 0, 1, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"s", "", 0, 0, 9, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"index", "", 0, 1, 2, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"group", "", 1, 0, 3, "dbGroup", 0, "", &ODDValue[15], 0, 0, NULL},
    {"op", "", 1, 0, 2, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"s1", "", 0, 0, 3, "set", 0, "", &ODDValue[15], 0, 0, NULL},
    {"s2", "", 0, 0, 3, "set", 0, "", &ODDValue[15], 0, 0, NULL},
    {"op", "", 1, 0, 2, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"s1", "", 0, 0, 3, "set", 0, "", &ODDValue[15], 0, 0, NULL},
    {"s2", "", 0, 0, 3, "set", 0, "", &ODDValue[15], 0, 0, NULL},
    {"name", "", 1, 0, 9, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"s", "", 0, 0, 3, "set", 0, "", &ODDValue[15], 0, 0, NULL},
    {"name", "", 1, 0, 2, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"fileName", "", 0, 0, 2, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"s", "", 1, 0, 9, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"infile1", "Name of input file with the search probe.", 0, 0, 2, "", 0,
    "", &ODDValue[15], 0, 0, NULL},
    {"infile2", "Name of input file with the data bank.", 0, 0, 2, "", 0, "",
    &ODDValue[15], 0, 0, NULL},
    {"field", "", 1, 0, 9, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"set", "", 0, 0, 9, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"s", "Sequence in which to store the sequence.", 1, 0, 3, "sequence", 0,
    "", &ODDValue[15], 0, 0, NULL},
    {"file", "File object with the sequence.", 1, 0, 3, "file", 0, "",
    &ODDValue[15], 0, 0, NULL},
    {"len", "Length of the sequence to be read.", 0, 0, 1, "", 0, "",
    &ODDValue[15], 0, 0, NULL},
    {"s", "", 1, 0, 3, "sequence", 0, "", &ODDValue[15], 0, 0, NULL},
    {"from", "", 0, 0, 1, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"len", "", 0, 0, 1, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"name", "", 1, 0, 9, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"list", "", 0, 0, 3, "sequence", 0, "", &ODDValue[15], 0, 0, NULL},
    {"seq", "", 1, 0, 3, "sequence", 0, "", &ODDValue[15], 0, 0, NULL},
    {"s", "", 0, 0, 9, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"seq", "", 1, 0, 3, "sequence", 0, "", &ODDValue[15], 0, 0, NULL},
    {"seq", "", 1, 0, 3, "sequence", 0, "", &ODDValue[15], 0, 0, NULL},
    {"len", "", 0, 0, 1, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"seq", "", 1, 0, 3, "sequence", 0, "", &ODDValue[15], 0, 0, NULL},
    {"seq", "", 1, 0, 3, "sequence", 0, "", &ODDValue[15], 0, 0, NULL},
    {"s", "The sequence as a string value.", 0, 0, 9, "", 0, "", &ODDValue[15],
    0, 0, NULL},
    {"name", "", 0, 0, 2, "", 0, "", &ODDValue[15], 0, 0, NULL},
    {"format", "", 0, 0, 1, "", 0, "", &ODDValue[15], 8, 0, NULL},
    {"width", "", 0, 0, 1, "", 60, "", &ODDValue[23], 0, 0, NULL},
    {"op", "", 1, 0, 2, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"l", "", 0, 0, 1, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"r", "", 0, 0, 1, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"s", "", 1, 0, 2, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"s", "", 1, 0, 2, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"s", "", 1, 0, 9, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"v", "", 1, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"s", "", 0, 0, 9, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"s", "", 1, 0, 9, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"from", "", 0, 0, 9, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"to", "", 0, 0, 9, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"s", "", 1, 0, 9, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"from", "", 0, 0, 9, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"to", "", 0, 0, 9, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"s", "", 1, 0, 9, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"s", "", 1, 0, 9, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"s", "Input string.", 1, 0, 9, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"len", "Length of the result string.", 0, 0, 1, "", 0, "", &ODDValue[23],
    0, 0, NULL},
    {"c", "Character used for padding.", 0, 0, 9, "", 0, "", &ODDValue[23], 0,
    0, NULL},
    {"thirds", "", 1, 0, 1, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"s", "", 0, 0, 1, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"l", "", 0, 0, 1, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"l", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"r", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"l", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"r", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"l", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"r", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"l", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"r", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"l", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"r", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"l", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"r", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"l", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"r", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"l", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"r", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"l", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"r", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"l", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"r", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"l", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"r", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"l", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"r", "", 0, 0, 6, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"state", "", 1, 0, 1, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"name", "", 1, 0, 9, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"fip", "", 0, 0, 1, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"acc", "", 1, 0, 9, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"db", "", 0, 0, 9, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"seq", "", 1, 0, 9, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"to", "", 0, 0, 1, "", -2, "", &ODDValue[23], 0, 0, NULL},
    {"uncertain", "", 0, 0, 1, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"feature", "", 1, 0, 1, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"expr", "", 1, 0, 9, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"db", "", 0, 0, 9, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"shift", "", 0, 0, 1, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"left", "", 0, 0, 1, "", 0, "", &ODDValue[23], 0, 0, NULL},
    {"right", "", 0, 0, 1, "", 0, "", &ODDValue[23], 0, 0, NULL}
};

IARGoCOM    IARGCOM[] = {
    {"_prog", "IopProg_", 0, "", 2, 8, "", 0, "", &IARGVALUE[0], 0, NULL, 0, 0,
    NULL},
    {"_opnd", "IopOpnd_", 0, "", 6, 8, "", 0, "", &IARGVALUE[0], 2, NULL, 0, 0,
    NULL},
    {"_list", "IopList_", 0, "", 6, 8, "", 0, "", &IARGVALUE[2], 0, NULL, 0, 0,
    NULL},
    {"_assoc", "IopAssoc_", 0, "", 6, 8, "", 0, "", &IARGVALUE[2], 2, NULL, 0,
    0, NULL},
    {"_binop", "IopBinop_", 0, "", 6, 8, "", 0, "", &IARGVALUE[4], 3, NULL, 0,
    0, NULL},
    {"_strmake", "IopStrMake_", 0, "", 6, 8, "", 0, "", &IARGVALUE[7], 0, NULL,
    0, 0, NULL},
    {"_makearg", "IopMakeArg_", 0, "", 6, 8, "", 0, "", &IARGVALUE[7], 2, NULL,
    0, 0, NULL},
    {"_select", "IopSelect_", 0, "", 6, 8, "", 0, "", &IARGVALUE[9], 3, NULL,
    0, 0, NULL},
    {"_setwrt", "IopSetWrite_", 0, "", 6, 8, "", 0, "", &IARGVALUE[12], 1,
    NULL, 0, 0, NULL},
    {"_func", "IopFunc_", 0, "", 6, 8, "", 0, "", &IARGVALUE[13], 0, NULL, 0,
    0, NULL},
    {"_body", "IopBody_", 0, "", 6, 8, "", 0, "", &IARGVALUE[13], 0, NULL, 0,
    0, NULL},
    {"_ref", "IopRef_", 0, "", 6, 8, "", 0, "", &IARGVALUE[13], 2, NULL, 0, 0,
    NULL},
    {"_file", "IopFile_", 0, "", 6, 8, "", 0, "", &IARGVALUE[15], 1, NULL, 0,
    0, NULL},
    {"_pre", "IopPre_", 0, "", 6, 8, "", 0, "", &IARGVALUE[16], 1, NULL, 0, 0,
    NULL},
    {"_init", "IopInit_", 0, "", 6, 8, "", 0, "", &IARGVALUE[17], 1, NULL, 0,
    0, NULL},
    {"_for", "IopFor_", 0, "", 6, 8, "", 0, "", &IARGVALUE[18], 4, NULL, 0, 0,
    NULL},
    {"_foreach", "IopForeach_", 0, "", 6, 8, "", 0, "", &IARGVALUE[22], 3,
    NULL, 0, 0, NULL},
    {"_while", "IopWhile_", 0, "", 6, 8, "", 0, "", &IARGVALUE[25], 2, NULL, 0,
    0, NULL},
    {"_if", "IopIf_", 0, "", 6, 8, "", 0, "", &IARGVALUE[27], 0, NULL, 0, 0,
    NULL},
    {"_prod", "IopProd_", 0, "", 3, 8, "node", 0, "", &IARGVALUE[27], 0, NULL,
    0, 0, NULL},
    {"_endProd", "IopEndProd_", 0, "", 6, 8, "", 0, "", &IARGVALUE[27], 2,
    NULL, 0, 0, NULL},
    {"_expr", "IopExpr_", 0, "", 3, 8, "node", 0, "", &IARGVALUE[29], 0, NULL,
    0, 0, NULL},
    {"_term", "IopTerm_", 0, "", 3, 8, "node", 0, "", &IARGVALUE[29], 0, NULL,
    0, 0, NULL},
    {"_regexp", "IopRegexp_", 0, "", 3, 8, "node", 0, "", &IARGVALUE[29], 1,
    NULL, 0, 0, NULL},
    {"_literal", "IopLiteral_", 0, "", 3, 8, "node", 0, "", &IARGVALUE[30], 1,
    NULL, 0, 0, NULL},
    {"_makeOpt", "IopMakeOpt_", 0, "", 3, 8, "node", 0, "", &IARGVALUE[31], 2,
    NULL, 0, 0, NULL},
    {"_nodeProg", "IopNodeProg_", 0, "", 3, 8, "node", 0, "", &IARGVALUE[33],
    2, NULL, 0, 0, NULL},
    {"_prodName", "IopProdName_", 0, "", 3, 8, "node", 0, "", &IARGVALUE[35],
    2, NULL, 0, 0, NULL},
    {"_doCom", "IopCommand_", 0, "", 3, 8, "node", 0, "", &IARGVALUE[37], 0,
    NULL, 0, 0, NULL},
    {"_doInputEnd", "IopInputEnd_", 0, "", 3, 8, "node", 0, "", &IARGVALUE[37],
    0, NULL, 0, 0, NULL},
    {"_nullNode", "IopNullNode_", 0, "", 3, 8, "node", 0, "", &IARGVALUE[37],
    0, NULL, 0, 0, NULL},
    {"_push", "IopPush_", 0, "", 2, 8, "", 0, "", &IARGVALUE[37], 2, NULL, 0,
    0, NULL},
    {"_push1", "IopPush_", 0, "", 2, 8, "", 0, "", &IARGVALUE[39], 2, NULL, 0,
    0, NULL},
    {"_push2", "IopPush_", 0, "", 2, 8, "", 0, "", &IARGVALUE[41], 2, NULL, 0,
    0, NULL},
    {"_push3", "IopPush_", 0, "", 2, 8, "", 0, "", &IARGVALUE[43], 2, NULL, 0,
    0, NULL},
    {"_push4", "IopPush_", 0, "", 2, 8, "", 0, "", &IARGVALUE[45], 2, NULL, 0,
    0, NULL},
    {"_push5", "IopPush_", 0, "", 2, 8, "", 0, "", &IARGVALUE[47], 2, NULL, 0,
    0, NULL},
    {"_pop", "IopPop_", 0, "", 6, 8, "", 0, "", &IARGVALUE[49], 1, NULL, 0, 0,
    NULL},
    {"_pop1", "IopPop_", 0, "", 6, 8, "", 0, "", &IARGVALUE[50], 1, NULL, 0, 0,
    NULL},
    {"_pop2", "IopPop_", 0, "", 6, 8, "", 0, "", &IARGVALUE[51], 1, NULL, 0, 0,
    NULL},
    {"_pop3", "IopPop_", 0, "", 6, 8, "", 0, "", &IARGVALUE[52], 1, NULL, 0, 0,
    NULL},
    {"_pop4", "IopPop_", 0, "", 6, 8, "", 0, "", &IARGVALUE[53], 1, NULL, 0, 0,
    NULL},
    {"_pop5", "IopPop_", 0, "", 6, 8, "", 0, "", &IARGVALUE[54], 1, NULL, 0, 0,
    NULL},
    {"Break", "IopBreak", 1, "", 2, 6, "", 0, "", &IARGVALUE[55], 3, NULL, 0,
    0, NULL},
    {"break", "IopBreak", 0, "", 2, 2, "", 0, "", &IARGVALUE[58], 2, NULL, 0,
    0, NULL},
    {"next", "IopNext", 1, "", 2, 8, "", 0, "", &IARGVALUE[60], 0, NULL, 0, 0,
    NULL},
    {"cont", "IopContinue", 1, "", 2, 8, "", 0, "", &IARGVALUE[60], 0, NULL, 0,
    0, NULL},
    {"tree", "IopTree", 1, "", 2, 8, "", 0, "", &IARGVALUE[60], 0, NULL, 0, 0,
    NULL},
    {"TestMode", "IopTestMode", 1, "", 1, 8, "", 0, "", &IARGVALUE[60], 0,
    NULL, 0, 0, NULL},
    {"prod", "IopProd", 0, "", 2, 8, "", 0, "", &IARGVALUE[60], 1, NULL, 0, 0,
    NULL},
    {"Prod", "IopProd", 1, "", 2, 8, "", 0, "", &IARGVALUE[61], 1, NULL, 0, 0,
    NULL},
    {"CDefine", "IopCDefine", 0, "", 2, 8, "", 0, "", &IARGVALUE[62], 2, NULL,
    0, 0, NULL},
    {"test", "IopTest", 0, "Test command.", 1, 8, "", 0, "", &IARGVALUE[64], 3,
    NULL, 0, 0, NULL},
    {"printProd", "IopPrintProduction", 0, "Prints a production.", 1, 8, "", 0,
    "", &IARGVALUE[67], 1, NULL, 0, 0, NULL},
    {"Parse", "IopParse", 1, "Parses a string.", 2, 8, "", 0, "",
    &IARGVALUE[68], 9, NULL, 0, 0, NULL},
    {"JobNew", "IopJobNew", 1,
    "Creates a new parsing job and associates it with a syntax and\nthe input. Use $JobTokens to start the parsing (lazy parsing) and\n$JobNext to move to the next job in the input stream.\n",
    3, 8, "job", 0, "", &IARGVALUE[77], 8, NULL, 0, 0, NULL},
    {"Fail", "IopFail", 1,
    "Can be used only in an action symbol (like x{...}). If called the action node reports\na parsing error which is treated in the same way as a 'normal' parsing\nerror from, eg, a literal. \n",
    2, 8, "", 0, "", &IARGVALUE[85], 0, NULL, 0, 0, NULL},
    {"JobHasInput", "IopJobHasInput", 1,
    "Returns TRUE if the input file of the job is not \n finished\n", 1, 8, "",
    0, "", &IARGVALUE[85], 1, NULL, 0, 0, NULL},
    {"JobNext", "IopJobNext", 1, "", 2, 8, "", 0, "", &IARGVALUE[86], 5, NULL,
    0, 0, NULL},
    {"JobHasInput", "IopJobHasInput", 1,
    "Returns TRUE if the input file of the job is not \n finished\n", 1, 8, "",
    0, "", &IARGVALUE[91], 1, NULL, 0, 0, NULL},
    {"JobKill", "IopJobEnd", 1, "", 2, 8, "", 0, "", &IARGVALUE[92], 1, NULL,
    0, 0, NULL},
    {"JobTokens", "IopJobTokens", 1, "", 1, 8, "", 0, "", &IARGVALUE[93], 8,
    NULL, 0, 0, NULL},
    {"In", "IopIn", 1,
    "Sets the input token table for parsing. \nControls the lazy parsing execution by defining the connections\nbetween productions \n",
    1, 6, "", 0, "", &IARGVALUE[101], 11, NULL, 0, 0, NULL},
    {"Out", "IopOut", 1,
    "Sets the output table for all writing of tokens for the \ncurrent production and its dependants.\n",
    2, 6, "", 0, "", &IARGVALUE[112], 1, NULL, 0, 0, NULL},
    {"out", "IopOut", 0,
    "Sets the output table for all writing of tokens for the \ncurrent production and its dependants.\n",
    2, 6, "", 0, "", &IARGVALUE[113], 1, NULL, 0, 0, NULL},
    {"Getc", "IopGetc", 0,
    "Defines $Ct to be a token starting at the current position\nand with the given length. Moves the current position, as if\n the given number of characters would have been really parsed\n",
    2, 8, "", 1, "", &IARGVALUE[114], 1, NULL, 0, 0, NULL},
    {"Len", "IopRestrictLength", 0,
    "Limits the parsing to stop after 'len' characters\nMust be the last command in a production. See also $Mov\n",
    2, 12, "", 1, "", &IARGVALUE[115], 1, NULL, 0, 0, NULL},
    {"Mov", "IopMove", 1, "Skips the next 'len' characters while parsing \n",
    2, 4, "", 1, "", &IARGVALUE[116], 1, NULL, 0, 0, NULL},
    {"Wrt", "IopWrt", 1,
    "This function can be called inside an action attached to the symbol of\na production. It writes the match of the current symbol or a specified\nstring into the output table specified by the most recent call of $out.\n",
    2, 8, "", 1, "", &IARGVALUE[117], 3, NULL, 0, 0, NULL},
    {"wrt", "IopWrt", 0,
    "This function can be called inside an action attached to the symbol of\na production. It writes the match of the current symbol or a specified\nstring into the output table specified by the most recent call of $out.\n",
    2, 8, "", 1, "", &IARGVALUE[120], 3, NULL, 0, 0, NULL},
    {"Uniq", "IopUniq", 1,
    "Exactly as $Wrt but writes the token only into the table if it does\nnot already exist. Unique here means that both the token string as the\ntoken code are used for comparison.\n",
    2, 8, "", 1, "", &IARGVALUE[123], 3, NULL, 0, 0, NULL},
    {"App", "IopApp", 1,
    "Appends the string token to the output token table\n", 2, 8, "", 1, "",
    &IARGVALUE[126], 1, NULL, 0, 0, NULL},
    {"app", "IopApp", 0, "Old syntax, see $App\n", 2, 8, "", 1, "",
    &IARGVALUE[127], 1, NULL, 0, 0, NULL},
    {"Rep", "IopRep", 1,
    "Replaces the current token ($Ct) in case of a symbol match. The\ninput cursor is moved after the replaced string. \n",
    2, 8, "", 0, "", &IARGVALUE[128], 1, NULL, 0, 0, NULL},
    {"rep", "IopRep", 0, "Old syntax, see $Rep \n", 2, 8, "", 0, "",
    &IARGVALUE[129], 1, NULL, 0, 0, NULL},
    {"Not", "IopNot", 1,
    "The rest of the production matches only if the preceding \nterminal doesn't match. (see $Probe) The parsing position  \n(cursor) is not moved when matching the preceding terminal  \n",
    2, 2, "", 0, "", &IARGVALUE[130], 0, NULL, 0, 0, NULL},
    {"not", "IopNot", 0, "", 2, 2, "", 0, "", &IARGVALUE[130], 0, NULL, 0, 0,
    NULL},
    {"Probe", "IopProbe", 1,
    "The rest of the production matches only if the preceding \nterminal matches. (see $Not) The parsing position  \n(cursor) is not moved when matching the preceding terminal  \n",
    2, 2, "", 0, "", &IARGVALUE[130], 0, NULL, 0, 0, NULL},
    {"Noskip", "IopNoskip", 1, "Inactivates skipping of white space\n", 2, 2,
    "", 0, "", &IARGVALUE[130], 0, NULL, 0, 0, NULL},
    {"noskip", "IopNoskip", 0, "", 2, 2, "", 0, "", &IARGVALUE[130], 0, NULL,
    0, 0, NULL},
    {"Request", "IopRequest", 1,
    "Activates the lazy parsing chain producing the \nrequested token table, but doesn't connect the input \nto it. (see $In)\n",
    2, 8, "", 0, "", &IARGVALUE[130], 1, NULL, 0, 0, NULL},
    {"Nocase", "IcaOpSetFlag", 1, "", 2, 8, "", 0, "", &IARGVALUE[131], 1,
    NULL, 0, 0, NULL},
    {"push", "IopPush", 0, "", 2, 8, "", 0, "", &IARGVALUE[132], 2, NULL, 0, 0,
    NULL},
    {"push1", "IopPush", 0, "", 2, 8, "", 0, "", &IARGVALUE[134], 2, NULL, 0,
    0, NULL},
    {"push2", "IopPush", 0, "", 2, 8, "", 0, "", &IARGVALUE[136], 2, NULL, 0,
    0, NULL},
    {"push3", "IopPush", 0, "", 2, 8, "", 0, "", &IARGVALUE[138], 2, NULL, 0,
    0, NULL},
    {"push4", "IopPush", 0, "", 2, 8, "", 0, "", &IARGVALUE[140], 2, NULL, 0,
    0, NULL},
    {"push5", "IopPush", 0, "", 2, 8, "", 0, "", &IARGVALUE[142], 2, NULL, 0,
    0, NULL},
    {"pop", "IopPop", 0, "", 6, 8, "", 0, "", &IARGVALUE[144], 1, NULL, 0, 0,
    NULL},
    {"pop1", "IopPop", 0, "", 6, 8, "", 0, "", &IARGVALUE[145], 1, NULL, 0, 0,
    NULL},
    {"pop2", "IopPop", 0, "", 6, 8, "", 0, "", &IARGVALUE[146], 1, NULL, 0, 0,
    NULL},
    {"pop3", "IopPop", 0, "", 6, 8, "", 0, "", &IARGVALUE[147], 1, NULL, 0, 0,
    NULL},
    {"pop4", "IopPop", 0, "", 6, 8, "", 0, "", &IARGVALUE[148], 1, NULL, 0, 0,
    NULL},
    {"pop5", "IopPop", 0, "", 6, 8, "", 0, "", &IARGVALUE[149], 1, NULL, 0, 0,
    NULL},
    {"Exit", "IopExit", 1, "", 2, 8, "", 0, "", &IARGVALUE[150], 1, NULL, 0, 0,
    NULL},
    {"exit", "IopExit", 0, "", 2, 8, "", 0, "", &IARGVALUE[151], 1, NULL, 0, 0,
    NULL},
    {"parStr", "IopParStr", 0,
    "Returns the value of a 'string' parameter or sets its value if \".set\" is \ndefined.\n",
    9, 8, "", 0, "", &IARGVALUE[152], 2, NULL, 0, 0, NULL},
    {"parInt", "IopParInt", 0,
    "Returns the value of an 'int' parameter or sets its value if \".set\" is \ndefined.\n",
    1, 8, "", 0, "", &IARGVALUE[154], 2, NULL, 0, 0, NULL},
    {"ParStr", "IopParStr", 1,
    "Returns the value of a 'string' parameter or sets its value if \".set\" is \ndefined.\n",
    9, 8, "", 0, "", &IARGVALUE[156], 2, NULL, 0, 0, NULL},
    {"ParInt", "IopParInt", 1,
    "Returns the value of an 'int' parameter or sets its value if \".set\" is \ndefined.\n",
    1, 8, "", 0, "", &IARGVALUE[158], 2, NULL, 0, 0, NULL},
    {"ParDel", "IopParDel", 1, "Deletes the parameter with specified name.\n",
    2, 8, "", 0, "", &IARGVALUE[160], 1, NULL, 0, 0, NULL},
    {"Env", "IopEnv", 1,
    "Optionally sets and returns the value an environment variable.\n", 9, 8,
    "", 0, "", &IARGVALUE[161], 2, NULL, 0, 0, NULL},
    {"AltStr", "IopAltStr", 0,
    "Returns one of two strings depending whether condition is \ntrue or false.\n",
    9, 8, "", 0, "", &IARGVALUE[163], 3, NULL, 0, 0, NULL},
    {"Alt", "IopAltStr", 1,
    "Returns one of two strings depending whether condition is \ntrue or false.\n",
    9, 8, "", 0, "", &IARGVALUE[166], 3, NULL, 0, 0, NULL},
    {"Foreach", "IopPrintForeach", 1,
    "prints each element in the list with specified separators.\n", 9, 8, "",
    0, "", &IARGVALUE[169], 4, NULL, 0, 0, NULL},
    {"subStr", "IcaOpSubStr", 0, "", 9, 8, "", 0, "", &IARGVALUE[173], 3, NULL,
    0, 0, NULL},
    {"System", "IopSystem", 0, "", 9, 8, "", 0, "", &IARGVALUE[176], 5, NULL,
    0, 0, NULL},
    {"FileOpen", "IopFileOpen", 1, "", 3, 8, "file", 0, "", &IARGVALUE[181], 2,
    NULL, 0, 0, NULL},
    {"FileClose", "IopFileClose", 1, "", 2, 8, "", 0, "", &IARGVALUE[183], 1,
    NULL, 0, 0, NULL},
    {"FileName", "IopFileName", 1, "", 9, 8, "", 0, "", &IARGVALUE[184], 1,
    NULL, 0, 0, NULL},
    {"Print", "IopPrint", 1, "Prints a string.", 2, 8, "", 0, "",
    &IARGVALUE[185], 4, NULL, 0, 0, NULL},
    {"dp", "IopDebugPrint", 1, "Printing within the debugger", 2, 8, "", 0, "",
    &IARGVALUE[189], 1, NULL, 0, 0, NULL},
    {"print", "IopPrint", 0, "Prints a string.", 2, 8, "", 0, "",
    &IARGVALUE[190], 4, NULL, 0, 0, NULL},
    {"StrFormat", "IopPrintFormat", 0,
    "Prints a string with the specified format.\n", 9, 8, "", 0, "",
    &IARGVALUE[194], 5, NULL, 0, 0, NULL},
    {"It", "IopInToken", 1,
    "Returns the input token (token which serves as input for \nthe current production through the $In command)\n",
    9, 8, "", 0, "", &IARGVALUE[199], 1, NULL, 0, 0, NULL},
    {"itc", "IopInTokenCode", 0, "", 9, 8, "", 0, "", &IARGVALUE[200], 0, NULL,
    0, 0, NULL},
    {"Itc", "IopInTokenCode", 1,
    "Returns the token code of the input token (see $It)\n", 9, 8, "", 0, "",
    &IARGVALUE[200], 0, NULL, 0, 0, NULL},
    {"ct", "IopCurrToken", 0, "", 9, 8, "", 0, "", &IARGVALUE[200], 0, NULL, 0,
    0, NULL},
    {"Ct", "IopCurrToken", 1,
    "Returns the current token (string parsed in the preceding\nparsing block)\n",
    9, 8, "", 0, "", &IARGVALUE[200], 0, NULL, 0, 0, NULL},
    {"Key", "IopKey", 1,
    "Returns the symbolic tag associated with the given list element\n", 9, 8,
    "", 0, "", &IARGVALUE[200], 1, NULL, 0, 0, NULL},
    {"IsLast", "IopIsLast", 1,
    "Returns TRUE if the element is the last in the list.\n", 1, 8, "", 0, "",
    &IARGVALUE[201], 0, NULL, 0, 0, NULL},
    {"IsFirst", "IopIsFirst", 1,
    "Returns TRUE if the element is the first in the list.\n", 1, 8, "", 0, "",
    &IARGVALUE[201], 0, NULL, 0, 0, NULL},
    {"ListLen", "IopListLen", 1,
    "Returns the number of elements in the list\n", 1, 8, "", 0, "",
    &IARGVALUE[201], 1, NULL, 0, 0, NULL},
    {"Fip", "IopFip", 1,
    "Returs the file pointer to the current \nposition in the input file\n", 1,
    8, "", 0, "", &IARGVALUE[202], 1, NULL, 0, 0, NULL},
    {"fip", "IopFip", 0, "", 1, 8, "", 0, "", &IARGVALUE[203], 1, NULL, 0, 0,
    NULL},
    {"File", "IopFile", 1, "Returns the file object of the currrent job.\n", 3,
    8, "file", 0, "", &IARGVALUE[204], 0, NULL, 0, 0, NULL},
    {"skip", "IopSetSkip", 0,
    "Controls skipping of white space during parsing which is\nactive by default.\n",
    2, 8, "", 0, "", &IARGVALUE[204], 2, NULL, 0, 0, NULL},
    {"Skip", "IopSetSkip", 1,
    "Controls skipping of white space during parsing which is\nactive by default.\n",
    2, 8, "", 0, "", &IARGVALUE[206], 2, NULL, 0, 0, NULL},
    {"Eval", "IopEval", 1, "", 2, 8, "", 0, "", &IARGVALUE[208], 1, NULL, 0, 0,
    NULL},
    {"Trim", "IopStrTrim", 1,
    "Cuts leading or trailing white space from the string.", 9, 8, "", 0, "",
    &IARGVALUE[209], 2, NULL, 0, 0, NULL},
    {"1", "IopSubMatch", 1,
    "Returns the first submatch of the most recent regular expression\nmatching. The submatch is indicated by parentheses within the\nregular expression and the opening parenthesis is used for counting.\n$2, $3 until $9 will return the submatches with the respective\nnumber. $0 returns the entire match.\n",
    9, 8, "", 0, "", &IARGVALUE[211], 1, NULL, 0, 0, NULL},
    {"2", "IopSubMatch", 0, "", 9, 8, "", 0, "", &IARGVALUE[212], 1, NULL, 0,
    0, NULL},
    {"3", "IopSubMatch", 0, "", 9, 8, "", 0, "", &IARGVALUE[213], 1, NULL, 0,
    0, NULL},
    {"4", "IopSubMatch", 0, "", 9, 8, "", 0, "", &IARGVALUE[214], 1, NULL, 0,
    0, NULL},
    {"5", "IopSubMatch", 0, "", 9, 8, "", 0, "", &IARGVALUE[215], 1, NULL, 0,
    0, NULL},
    {"6", "IopSubMatch", 0, "", 9, 8, "", 0, "", &IARGVALUE[216], 1, NULL, 0,
    0, NULL},
    {"7", "IopSubMatch", 0, "", 9, 8, "", 0, "", &IARGVALUE[217], 1, NULL, 0,
    0, NULL},
    {"8", "IopSubMatch", 0, "", 9, 8, "", 0, "", &IARGVALUE[218], 1, NULL, 0,
    0, NULL},
    {"9", "IopSubMatch", 0, "", 9, 8, "", 0, "", &IARGVALUE[219], 1, NULL, 0,
    0, NULL},
    {"SetFunctions", "IopSetFunctions", 0, "", 2, 8, "", 0, "",
    &IARGVALUE[220], 1, NULL, 0, 0, NULL},
    {"SetResult", "QuerySaveResult", 0, "", 2, 8, "", 0, "", &IARGVALUE[221],
    2, NULL, 0, 0, NULL},
    {"DbGroup", "QueryDBGroup", 0, "", 3, 8, "dbGroup", 0, "", &IARGVALUE[223],
    3, NULL, 0, 0, NULL},
    {"SetRetrRange", "QueryRangeSearch", 0, "", 3, 8, "set", 0, "",
    &IARGVALUE[226], 6, NULL, 0, 0, NULL},
    {"SetRetrStr", "QueryStrSearch", 0, "", 3, 8, "set", 0, "",
    &IARGVALUE[232], 3, NULL, 0, 0, NULL},
    {"SetLogOp", "QueryLogOp", 0, "", 3, 8, "set", 0, "", &IARGVALUE[235], 3,
    NULL, 0, 0, NULL},
    {"SetLinkOp", "QueryLinkOp", 0, "", 3, 8, "set", 0, "", &IARGVALUE[238], 3,
    NULL, 0, 0, NULL},
    {"SetAssign", "QuerySetAssign", 0, "", 3, 8, "set", 0, "", &IARGVALUE[241],
    2, NULL, 0, 0, NULL},
    {"SetGet", "QuerySetGet", 0, "", 3, 8, "set", 0, "", &IARGVALUE[243], 2,
    NULL, 0, 0, NULL},
    {"MakeWild", "QueryOpMakeWild", 0, "", 9, 8, "", 0, "", &IARGVALUE[245], 1,
    NULL, 0, 0, NULL},
    {"GCGwordsearch", "GCGWordsearch", 0, "", 2, 8, "", 0, "", &IARGVALUE[246],
    2, NULL, 0, 0, NULL},
    {"setFormat", "EntryIopSetFieldFormat", 0, "", 2, 8, "", 0, "",
    &IARGVALUE[248], 2, NULL, 0, 0, NULL},
    {"SeqGet2Bit", "SeqIopGet2Bit", 1,
    "Reads a sequence in GCG's 2BIT format into supplied sequence object \nwhich can be created by $SeqNew. If the sequence object contains \na sequence already the sequence read is appended. This is useful\nto collect split sequences as found in the GCG formatted sequence\ndatabanks.\n",
    2, 8, "", 0, "", &IARGVALUE[250], 3, NULL, 0, 0, NULL},
    {"SeqCut", "SeqIopCut", 1, "Cuts away specified part of the sequence\n", 2,
    8, "", 0, "", &IARGVALUE[253], 3, NULL, 0, 0, NULL},
    {"SeqNew", "SeqIopNew", 1, "Creates a new sequence object.\n", 3, 8,
    "sequence", 0, "", &IARGVALUE[256], 2, NULL, 0, 0, NULL},
    {"SeqApp", "SeqIopApp", 1, "", 3, 8, "sequence", 0, "", &IARGVALUE[258], 2,
    NULL, 0, 0, NULL},
    {"SeqMake", "SeqIopMake", 1, "", 3, 8, "sequence", 0, "", &IARGVALUE[260],
    1, NULL, 0, 0, NULL},
    {"SeqTrunc", "SeqIopTrunc", 1, "", 3, 8, "sequence", 0, "",
    &IARGVALUE[261], 2, NULL, 0, 0, NULL},
    {"SeqLen", "SeqIopLen", 1, "Returns the length of the sequence.", 1, 8, "",
    0, "", &IARGVALUE[263], 1, NULL, 0, 0, NULL},
    {"SeqPrint", "SeqIopPrint", 1, "Prints a sequence in various formats.", 2,
    8, "", 0, "", &IARGVALUE[264], 5, NULL, 0, 0, NULL},
    {"calc", "IopCalc", 0, "", 1, 8, "", 0, "", &IARGVALUE[269], 3, NULL, 0, 0,
    NULL},
    {"strlen", "IopStrlen", 0, "", 1, 8, "", 0, "", &IARGVALUE[272], 1, NULL,
    0, 0, NULL},
    {"Strlen", "IopStrlen", 0, "", 1, 8, "", 0, "", &IARGVALUE[273], 1, NULL,
    0, 0, NULL},
    {"StrLen", "IopStrLen", 1, "", 1, 8, "", 0, "", &IARGVALUE[274], 1, NULL,
    0, 0, NULL},
    {"StrApp", "IopStrApp", 1, "", 2, 8, "", 0, "", &IARGVALUE[275], 2, NULL,
    0, 0, NULL},
    {"StrTrans", "IopStrTrans", 1,
    "Translates all characters in the 'from' set to the character\nat the equivalent position in the 'to' set.\n",
    9, 8, "", 0, "", &IARGVALUE[277], 3, NULL, 0, 0, NULL},
    {"StrReplace", "IopStrReplace", 1,
    "Translates all occurences of 'from' \nto strings specified by 'to'.\n", 9,
    8, "", 0, "", &IARGVALUE[280], 3, NULL, 0, 0, NULL},
    {"StrLower", "IopStrLower", 1,
    "Converts all characters of the input string into lower case.\n", 9, 8, "",
    0, "", &IARGVALUE[283], 1, NULL, 0, 0, NULL},
    {"StrUpper", "IopStrUpper", 1,
    "Converts all characters of the input string into upper case.\n", 9, 8, "",
    0, "", &IARGVALUE[284], 1, NULL, 0, 0, NULL},
    {"StrPad", "IopStrPad", 1,
    "Pads a string with specified character if input string is \nshorter than requested length. \n",
    9, 8, "", 0, "", &IARGVALUE[285], 3, NULL, 0, 0, NULL},
    {"HtmlSpace", "IopHtmlSpace", 0, "", 2, 8, "", 0, "", &IARGVALUE[288], 3,
    NULL, 0, 0, NULL},
    {"=", "IopAss", 0, "", 6, 8, "", 0, "", &IARGVALUE[291], 2, NULL, 0, 0,
    NULL},
    {"+", "IopAdd", 0, "", 1, 8, "", 0, "", &IARGVALUE[293], 2, NULL, 0, 0,
    NULL},
    {"<", "IopLT", 0, "", 1, 8, "", 0, "", &IARGVALUE[295], 2, NULL, 0, 0,
    NULL},
    {">", "IopGT", 0, "", 1, 8, "", 0, "", &IARGVALUE[297], 2, NULL, 0, 0,
    NULL},
    {"==", "IopEq", 0, "", 1, 8, "", 0, "", &IARGVALUE[299], 2, NULL, 0, 0,
    NULL},
    {"*", "IopMul", 0, "", 1, 8, "", 0, "", &IARGVALUE[301], 2, NULL, 0, 0,
    NULL},
    {"/", "IopDivide", 0, "", 1, 8, "", 0, "", &IARGVALUE[303], 2, NULL, 0, 0,
    NULL},
    {"!=", "IopNEq", 0, "", 1, 8, "", 0, "", &IARGVALUE[305], 2, NULL, 0, 0,
    NULL},
    {"-", "IopSubt", 0, "", 1, 8, "", 0, "", &IARGVALUE[307], 2, NULL, 0, 0,
    NULL},
    {"+=", "IopAddAss", 0, "", 1, 8, "", 0, "", &IARGVALUE[309], 2, NULL, 0, 0,
    NULL},
    {"&&", "IopLogAnd", 0, "", 1, 8, "", 0, "", &IARGVALUE[311], 2, NULL, 0, 0,
    NULL},
    {"||", "IopLogOr", 0, "", 1, 8, "", 0, "", &IARGVALUE[313], 2, NULL, 0, 0,
    NULL},
    {"debug", "IopSetDebug", 0, "", 2, 8, "", 0, "", &IARGVALUE[315], 1, NULL,
    0, 0, NULL},
    {"labelAdd", "TemplIcaAddLabel", 0, "", 2, 8, "", 0, "", &IARGVALUE[316],
    2, NULL, 0, 0, NULL},
    {"SdbRetrieve", "SdbRetrieve", 0, "", 9, 8, "", 0, "", &IARGVALUE[318], 2,
    NULL, 0, 0, NULL},
    {"SdbPop", "SdbPop", 0, "", 2, 8, "", 0, "", &IARGVALUE[320], 0, NULL, 0,
    0, NULL},
    {"SdbPush", "SdbPush", 0, "", 2, 8, "", 0, "", &IARGVALUE[320], 0, NULL, 0,
    0, NULL},
    {"SdbEval", "SdbEval", 0, "", 9, 8, "", 0, "", &IARGVALUE[320], 0, NULL, 0,
    0, NULL},
    {"SdbChunk", "SdbChunk", 0, "", 2, 8, "", 0, "", &IARGVALUE[320], 3, NULL,
    0, 0, NULL},
    {"SdbFeature", "SdbFeature", 0, "", 2, 8, "", 0, "", &IARGVALUE[323], 1,
    NULL, 0, 0, NULL},
    {"SdbComplement", "SdbComplement", 0, "", 2, 8, "", 0, "", &IARGVALUE[324],
    0, NULL, 0, 0, NULL},
    {"SdbReplace", "SdbReplace", 0, "", 2, 8, "", 0, "", &IARGVALUE[324], 0,
    NULL, 0, 0, NULL},
    {"SdbJoin", "SdbJoin", 0, "", 2, 8, "", 0, "", &IARGVALUE[324], 0, NULL, 0,
    0, NULL},
    {"SeqGetFt", "SdbGetFeatureSequence", 0, "", 9, 8, "", 0, "",
    &IARGVALUE[324], 5, NULL, 0, 0, NULL},
    {"SdbFunctions", "SdbFunctions", 0, "", 2, 8, "", 0, "", &IARGVALUE[329],
    0, NULL, 0, 0, NULL},
    {"", "", 0, "", 2, 8, "", 0, "", &IARGVALUE[329], 0, NULL, 0, 0, NULL}
};

#endif
NULL, 0, 0, NULL},
    {"SdbReplace"srs/src/cursor.c
char cursor_ID[] = "$Id: cursor.c,v 1.12 1996/12/04 19:49:28 etzold Exp $"; 
/*               
**  
**    $RCSfile: cursor.c,v $ 
**    $Revision: 1.12 $
**    $Date: 1996/12/04 19:49:28 $
**    $Author: etzold $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  Copyright by Thure Etzold
**
**             Author: Anatoly Ulyanov
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387451
**                     Email: ulyanov@embl-heidelberg.de
**
*/  

#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include "message.h"
#include "futil.h"
#include "regexp.h"
#include "sm.h"
#include "toklist.h"
#include "cursor.h"



/**api* CursorNew ***************************************************
**
**      Create a new cursor object.
** 
**      INPUT:
** 
**      RETURNS:    cursor object
*/

CURSORo *CursorNew()
{
  CURSORo *cursor;
  
  if( (cursor = (CURSORo *) calloc (sizeof(CURSORo), 1)) == NULL )
    _ErrExit2 (e__allocfail, "Cursor object");
  
  return(cursor);
}

/**api* CursorDelete ***************************************************
**
**      Delete the cursor object.
** 
**      INPUT:      address of cursor object [W]
** 
**              IMPLICIT:
** 
**      RETURNS:
*/

void CursorDelete(CURSORo **cursor)
{
  if (*cursor)
    free (*cursor);
  *cursor = NULL;
}

/**api* CursorSave ***************************************************
**
**      Copy the content of cursor object.
** 
**      INPUT:      target cursor object [W]
**                  cursor object to be saved [R]
**
**      RETURNS:
*/

void CursorSave(CURSORo *cursorSave, CURSORo *cursor)
{
  memcpy(cursorSave, cursor, sizeof(CURSORo));
}

/**api* CursorRestore ***************************************************
**
**
**      Restore the content of cursor object.
** 
**      INPUT:      target cursor object [W]
**                  cursor object to be restored [R]
**
**      RETURNS:
*/

void CursorRestore(CURSORo *cursor, CURSORo *cursorRestore)
{
  memcpy(cursor, cursorRestore, sizeof(CURSORo));
}

/**api* CursorAdvance ***************************************************
**
**   Move cursor to the next non space position in input stream.
**
**      INPUT:  o   pointer to the  cursor object [R]
**              o   string of the white space characters [R]
**              o   white space character represented as a regular
**                  expression. NULL if it is represented as string
**              o   flag to suppress skipping [R]
**              o   flag is set to FALSE when skipping is already done
**
**   RETURN:	o   TRUE if cursor can be proceed
**		o   FALSE if input is exhausted
*/

INT4 CursorAdvance(CURSORo *cursor, char *skipChars, regexp *re, 
		   INT4 isNoSkip, INT4 *doAdvance)
{
  char *string;
  INT4  len;


  /* skip white space AND comments using regular expression */
  if (!isNoSkip && *skipChars) {
    while (cursor->len) {
      *doAdvance = 0;
      len = MIN(cursor->len, strspn(cursor->current, skipChars));
      cursor->len -= len;
      cursor->current += len;
      if (re) { /* test regular expr for comments */
	if (RegExec (re, cursor->current) == 1) {
	  len = MIN(cursor->len, (INT4)(re->endp[0] - re->startp[0])); 
	  cursor->current += len;
	  cursor->len -= len;
	  continue;
	}
      }
      break;
    }
  }

  if (cursor->len)
    return(TRUE);
  else
    if (!cursor->tokList || !TokGetMore(cursor->tokList, &string, &len)) {
      return(FALSE);
    }
    else {
      cursor->current = string;
      cursor->len = len;
      return(CursorAdvance(cursor, skipChars, re, isNoSkip, doAdvance));
    }  
}

/**api* CursorIterate ***************************************************
**
**   Move cursor to the next token skipping the rest of the token
**
**      INPUT:  o   pointer to the  cursor object [R]
**              o   string of the white space characters [R]
**              o   white space character represented as a regular
**                  expression. NULL if it is represented as string
**              o   flag to suppress skipping [R]
**              o   flag is set to FALSE when skipping is already done
**
**   RETURN:	o   TRUE if cursor can be proceed
**		o   FALSE if input is exhausted
*/

INT4 CursorIterate(CURSORo *cursor, char *skipChars, regexp *re, 
		   INT4 isNoSkip, INT4 *doAdvance)
{
  char *string;
  INT4  len;

    if (!TokGetMore(cursor->tokList, &string, &len) )
      return(FALSE);
    else {
      cursor->current = string;
      cursor->len = len;
      return(CursorAdvance(cursor, skipChars, re, isNoSkip, doAdvance));
    }  
}

/**api* CursorResetMatch ***************************************************
**
**     This function sets match length to zero
**
**      INPUT:      pointer to the  cursor object [R]
**
**   RETURN:
*/

void CursorResetMatch (CURSORo *cursor)
{
  cursor->matchLen = 0;
}

/**api* CursorIncrement ***************************************************
**
**     This function must be called after (not) matches.
**
**      INPUT:      pointer to the  cursor object [R]
**
**   RETURN:
*/

void CursorIncrement(CURSORo *cursor)
{
  if (cursor) {
    cursor->current += cursor->matchLen;
    cursor->len -= cursor->matchLen;
    cursor->matchLen = 0;
  }
}

/**api* CursorMove ***************************************************
**
**     This function must be called after move statement
**
**      INPUT:      pointer to the  cursor object [R]
**
**   RETURN:
*/

void CursorMove(CURSORo *cursor)
{
  cursor->current += cursor->matchLen;
  cursor->len -= cursor->matchLen;
  if( cursor->len < 0 )
    cursor->len = 0;
  cursor->matchLen = 0;
}

/**api* CursorRestrictLength ***********************************************
**
**     Restrict the cursor length to some particular size by temporarily
**     string terminator. It is required to find correct biggest regular
**     expression. See CursorRestoreChar
**
**      INPUT:      pointer to the  cursor object [R]
**
**   RETURN:
*/

void CursorRestrictLength(CURSORo *cursor)
{
  INT4 length;

  length = cursor->len;
  cursor->saveChar = cursor->current[length];
  cursor->saveCharPtr = &cursor->current[length];
  *cursor->saveCharPtr = '\0'; 
} 

/**api* CursorRestrictLength ***********************************************
**
**     Restrict the cursor length to some particular size by temporarily
**     string terminator. It is required to find correct biggest regular
**     expression. See CursorRestoreChar
**
**      INPUT:      pointer to the  cursor object [R]
**
**   RETURN:
*/

Int4 CursorSetTmpLength (CURSORo *cursor, Int4 len)
{
  return (cursor->len = MIN(len, cursor->len));
} 

Int4 CursorResetLength (CURSORo *cursor, Int4 length)
{
  cursor->len = length;
} 

void CursorReset (CURSORo *cursor)
{
  cursor->len = 0;
}


Int4 CursorGetLength (CURSORo *cursor)
{
  return cursor->len;
}

Int4 CursorSetFile (CURSORo *cursor, FILEo *file)
{
  Int4  l;
  char *s;
  if (file && (s = FileGetLn (file))) {
    l = strlen (s);
    CursorSetString (cursor, s, l);
  }
}

Int4 CursorSetString (CURSORo *cursor, char *s, Int4 len)
{
  cursor->current = s;
  cursor->len = len;
}


/**api* CursorRestoreChar ***********************************************
**
**     Restore the temporal string terminator in the input token
**     See CursorRestrictLength
**
**      INPUT:      pointer to the  cursor object [R]
**
**   RETURN:
*/

void CursorRestoreChar(CURSORo *cursor)
{                                                           

  *cursor->saveCharPtr = cursor->saveChar;
} 


/**api* CursorDefineAnchor ***********************************************
**
**     Set a cursor anchor. The anchor is used for determination of
**     global cursor movement.
**
**      INPUT:      pointer to the  cursor object [R]
**
**   RETURN:

*/

void CursorDefineAnchor(CURSORo *cursor, CURSORoANCHOR *anchor)
{
  anchor->begin = cursor->current;
  anchor->tokListBuff = TokGetBuff (cursor->tokList);
}

/**api* CursorGetBegin ***********************************************
**                                                          
**     Get the beginning of the current input token
**
**      INPUT:      pointer to the  cursor object [R]
**
**   RETURN:        pointer to the beginning of input token
*/

char *CursorGetBegin(CURSORo *cursor)
{
    return(cursor->begin);
}

/**api* CursorGetPtr ***********************************************
**                                                          
**     Get the pointer to the current position the the input token
**
**      INPUT:      pointer to the  cursor object [R]
**
**   RETURN:        current position the the input token
*/

char *CursorGetPtr(CURSORo *cursor)
{
  static char *emptyStr = "";

  if(cursor->len == 0)
    return(emptyStr);
  else
    return(cursor->current);
}

/**api* CursorGetMatch ***********************************************
**
**     Get the last match and its length
**
**      INPUT:      pointer to the  cursor object [R]
**		    pointer to the last match [W]
**		    length of the last match [W]
**
**   RETURN:
*/

void CursorGetMatch(CURSORo *cursor, char **ptr, INT4 *length)
{
  *length = cursor->matchLen;
  *ptr = cursor->current;
}  

/**api* CursorGetMatchCopy ***********************************************
**                                                          
**     Get the copy of the current match. It would be store in a static
**     buffer until the next call of the function.
**
**      INPUT:      pointer to the  cursor object [R]
**
**   RETURN:        pointer to copy of the match
*/

char *CursorGetMatchCopy(CURSORo *cursor)
{
  static SMoBUFF *matchBuff = NULL;

  matchBuff = BuffInit(matchBuff, TOKxMAXTOKBUFFSIZE);
  if(cursor->len == 0)
    return("");
  else {
    BuffCopyNChar(matchBuff, cursor->current, cursor->matchLen);
    BuffCopyNChar(matchBuff, "\0", 1);
    return(BuffGetPtr(matchBuff));
  }
}

/**api* CursorSetMatch ***********************************************
**                                                          
**     Set the match length
**
**      INPUT:      pointer to the  cursor object [W]
**                  length of the match [R]
**
**   RETURN:
*/

void CursorSetMatch(CURSORo *cursor, INT4 len)
{
    cursor->matchLen = len;
}

/**api* CursorSetLength ***********************************************
**                                                          
**     Set the match length
**
**      INPUT:      pointer to the  cursor object [W]
**                  length of the match [R]
**
**   RETURN:
*/

void CursorSetLength(CURSORo *cursor, INT4 len)
{
    cursor->matchLen = MIN(len, cursor->len);
}

/**api* CursorReplaceMatch ***********************************************
**                                                          
**     Replace the match by defined string
**
**      INPUT:      pointer to the  cursor object [W]
**                  string to replace [R]
**                  length of the string [R]
**
**   RETURN:
**
*/

void CursorReplaceMatch(CURSORo *cursor, char *newMatch, INT4 newLen)
{
  cursor->current += TokReplaceIn(cursor->tokList, cursor->current,
                                  cursor->matchLen, newMatch, newLen);
  cursor->len += (newLen - cursor->matchLen);
  cursor->matchLen = newLen;
}

/**api* CursorSetGlobalMatch ***********************************************
**                                                          
**     Set the global match 
**
**      INPUT:      pointer to the  cursor object [W]
**                  anchor of the cursor object [R]
**
**   RETURN:
*/

void CursorSetGlobalMatch(CURSORo *cursor, CURSORoANCHOR *anchor)
{
  INT4 len;
  char *tokListBuff;

  tokListBuff = TokGetBuff (cursor->tokList);
  if (tokListBuff && tokListBuff != anchor->tokListBuff)
    anchor->begin += tokListBuff - anchor->tokListBuff;

  len  = (INT4)(cursor->current - anchor->begin);
  cursor->matchLen = len;
  cursor->len += len;
  cursor->current = anchor->begin;
}

/**api* CursorLength ***********************************************
**                                                          
**     Get the the size of the string from current position in the 
**     token until the end.
**
**      INPUT:      pointer to the  cursor object [W]
**
**   RETURN:        rest length of input token 
*/

INT4 CursorLength(CURSORo *cursor)
{
  return(cursor->len);
}

/**api* CursorIsBegin ***********************************************
**                                                          
**   Check if the cursor is at the beginning of the input token
**
**      INPUT:      pointer to the  cursor object [R]
**
**   RETURN:	    TRUE if cursor points to the token beginning
**		    FALSE otherwise
*/

INT4 CursorIsBegin(CURSORo *cursor)
{
  return(cursor->current == cursor->begin);
}

/**api* CursorIsLineStart ***********************************************
**                                                          
**   Check if the cursor is at the beginning of the input token
**   and if the previous character is the "new line"
**
**      INPUT:      pointer to the  cursor object [R]
**
**   RETURN:	    TRUE if cursor points to the token beginning
**		    FALSE otherwise
*/

INT4 CursorIsLineStart(CURSORo *cursor)
{
  return(cursor->begin == cursor->current || cursor->begin[-1] == '\n');
}

/**api* CursorIsEnd ***********************************************
**                                                          
**   Check if the cursor is at the end of the input token
**
**      INPUT:      pointer to the  cursor object [R]
**
**   RETURN:	    TRUE if cursor points to the token end
**		    FALSE otherwise
*/

INT4 CursorIsEnd(CURSORo *cursor)
{
  return (cursor->len == 0);
}

/**api* CursorIsMoved ***********************************************
**                                                          
**   Check if the cursor is not at the beginning of the input token
**   It is opposite to CursorIsBegin function.
**
**      INPUT:      pointer to the  cursor object [R]
**
**   RETURN:	    TRUE if cursor does not point to the token beginning
**		    FALSE otherwise
*/

INT4 CursorIsMoved(CURSORo *cursor, CURSORoANCHOR *anchor)
{
  return(cursor->current != anchor->begin);
}

/**api* CursorIsInstall ***********************************************
**                                                          
**   Check if the cursor is installed at the beginning of the input token
**
**      INPUT:      pointer to the  cursor object [R]
**
**   RETURN:	    TRUE if cursor installs to the token beginning
**		    FALSE otherwise
*/

INT4 CursorIsInstall(CURSORo *cursor)
{
    return(cursor->isInstall);
}

/**api* CursorInstall ***************************************************
**
**   Install the cursor is at the beginning of the input token
**
**      INPUT:      pointer to the  cursor object [W]
**                  input token [R]
**                  input token list [R]
**
**   RETURN:
*/      

void CursorInstall(CURSORo *cursor, TOKoTOKEN *token, TOKoLIST *tokList)
{
  if(token) {
    cursor->len = TokGetLength(token);
    cursor->begin = TokGetString(tokList, token);
    cursor->isInstall = TRUE;
  }
  else {
    cursor->len = 0;
    cursor->begin = "";
    cursor->isInstall = FALSE;
  }
  cursor->current = cursor->begin;
  cursor->tokList = tokList;
} 
:      pointer to the  cursor object [W]
**                  input token [R]
**                  input token list [R]
**
**   RETURN:
*/      

void CursorInstall(CURSORo *cursor, TOKoTOKEN *token, TOKoLIST *tokList)
{
  if(token) {
    cursor->len = TokGetLength(token);
    cursor->begin = TokGetString(tokList, token);
    cursor->isInstall = TRUE;
  }
  else {
    cursor->len = 0;
    cursor->begin = ""srs/src/cursor.h
  char             *current;
  INT4              len;
  INT4              matchLen;
  char              saveChar;
  char             *saveCharPtr;
  char             *begin;
  TOKoLIST         *tokList;
  INT4              isInstall;   
} CURSORo;

typedef struct CURSORoANCHOR {
  char             *begin;
  char             *tokListBuff;
} CURSORoANCHOR;


typedef struct regexp *dummytointroducestructtagregexp;

CURSORo *CursorNew();
INT4     CursorAdvance(CURSORo *cursor, char *skipChars, struct regexp *re, 
		       INT4 isNoSkip, INT4 *doAdvance);
INT4     CursorIsBegin(CURSORo *cursor);
INT4     CursorIsEnd(CURSORo *cursor);
INT4     CursorIsLineStart(CURSORo *cursor);
INT4     CursorIsMoved(CURSORo *cursor, CURSORoANCHOR *anchor);
INT4     CursorIterate(CURSORo *cursor, char *skipChars, struct regexp *re, 
		   INT4 isNoSkip, INT4 *doAdvance);
INT4     CursorIsInstall(CURSORo *cursor);
INT4     CursorLength(CURSORo *cursor);
char    *CursorGetPtr(CURSORo *cursor);
char    *CursorGetBegin(CURSORo *cursor);
void     CursorDefineAnchor(CURSORo *cursor, CURSORoANCHOR *anchor);
void     CursorDelete(CURSORo **cursor);
void     CursorGetMatch(CURSORo *cursor, char **ptr, INT4 *length);
void     CursorMove(CURSORo *cursor);
void     CursorIncrement(CURSORo *cursor);
void     CursorInstall(CURSORo *cursor, TOKoTOKEN *token, TOKoLIST *tokList);
void     CursorResetMatch(CURSORo *cursor);
void     CursorRestore(CURSORo *cursor, CURSORo *cursorRestore);
void     CursorRestoreChar(CURSORo *cursor);
void     CursorRestrictLength(CURSORo *cursor);
void     CursorSave(CURSORo *cursorSave, CURSORo *cursor);
void     CursorSetGlobalMatch(CURSORo *cursor, CURSORoANCHOR *anchor);
void     CursorSetLength(CURSORo *cursor, INT4 len);
void     CursorSetMatch(CURSORo *cursor, INT4 len);
void     CursorReplaceMatch(CURSORo *cursor, char *newMatch, INT4 newLen);
char*    CursorGetMatchCopy (CURSORo *cursor);









sorRestore(CURSORo *cursor, CURSORo *cursorRestore);
void     CursorRestoreChar(CURSORo *cursrs/src/def.c
char def_ID[] = "$Id: def.c,v 1.8 1997/03/19 20:41:40 srs Exp $";
/*
**
**    $RCSfile: def.c,v $
**    $Revision: 1.8 $
**    $Date: 1997/03/19 20:41:40 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    module with general purpose functions.
**    file has sections for individual programmers
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include "def.h"


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Thure's functions
*/

/* function is called via _addObj macro */
void *addObj (char **ptr, Int4 *n, Int4 *allocN, Int4 size)
{
  char *tmp;

  if (*n >= *allocN) {
    if (!*n) {
      *allocN = 10;
      *ptr = malloc (size * *allocN);
    }
    else {
      *allocN *= 2;
      *ptr = realloc (*ptr, size * *allocN);
    }
  }
  tmp = *ptr + size * (*n)++;
  memset (tmp, 0, size);
  return tmp;
}


void MemMove (char *to, char *from, int len)  
{
#ifdef sun
  char *tmp;

  tmp = (char *) malloc (len);
  memcpy (tmp, from, len);
  memcpy (to, tmp, len);
  free (tmp);
#else
  memmove (to, from, len);
#endif
}



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Anatoly's functions
*/


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Giorgio's functions
*/

/**api* align  ************************************************************
**
**      Calculates a Word-aligned offset for a data item 
**
**      INPUT:          the current offset
**                      the size of the item to be aligned
**      RETURNS:        the aligned offset for the item
*/

int align(int pos, int sz) {
    int off;
    if (sz>=sizeof(Word)) sz=sizeof(Word);
    off=pos%sz;
    return off?(sz-off):0;
}

/**api* HashGo ***********************************************************
**
**	Incremental rehashing macro for hash values calculated with _hash
**      This function "rewinds" or "fast forwards" the hash value
**      If the n-th last value from which 'sum' was calculated was 
**      modified, sum can be updated with the formula:
**      hashGo(sum,-n); sum^=old_val; ...; sum^=new_val; hashGo(sum, n);
**     
**      INPUT:          [W] the hash value to be modified (32 bit)
**			the index of the modified item
*/

void hashGo(UINT4* s, INT4 index) {
    UINT4 sum=*s;
    UINT4 disp=(UINT4)index & 31;
    disp=(disp<<2+disp)&31;
    *s=(sum>>disp)^(sum<<(32-disp));
}

UINT4 CharHash(char* p) {
  UINT4 sum=0;
  char* stop=p+strlen(p);
  while (p!=stop) _hash(sum,*p++);
  return sum;
}

UINT4 CharHashLen(char* p, int len) {
  UINT4 sum=0;
  char* stop=p+len;
  while (p!=stop) _hash(sum,tolower(*p++));
  return sum;
}

char MPtrBuffer[100];

void stopProg(char *msg) {
   printf(msg); printf("\n");
   exit(1);
}

void checkProg(char *msg) {
   printf(msg); printf("\n");
}



   srs/src/def.h
**
**    $RCSfile: def.h,v $
**    $Revision: 1.8 $
**    $Date: 1997/03/17 23:23:58 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**    this file is included by all SRS modules.
**    sections exist for each programmer to insert definitions they
**    think should be visible to all modules
**
*/

#ifndef DEF
#define DEF

typedef char *ID;
typedef char *IDo;
typedef unsigned char *IDPTR;
typedef unsigned long ULONG;

#ifdef dos
typedef long INT4;
typedef long Int4;
typedef unsigned long UINT4;
typedef unsigned long Uint4;
#else
typedef int INT4;
typedef int Int4;
typedef unsigned int UINT4;
typedef unsigned int Uint4;
#endif
typedef UINT4 FIP;
typedef UINT4 Fip;

#ifndef TRUE
# define TRUE 1
# define FALSE 0
#endif

#ifndef NULL
# define NULL 0L
#endif

typedef INT4 (*FUNC)();
typedef INT4 (*Func)();
typedef void (*VFUNC)();
typedef struct SMoBUFF *(*BFUNC)();


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Thure's definitions
*/

void *addObj (char **ptr, Int4 *n, Int4 *allocN, Int4 size);
#define _addObj(x, n, allocN, type)\
(type *) addObj ((char **) &x, &n, &allocN, sizeof (type))

#define _Index(x,y) ( ((x)-'a'+1) << 5) +((y)-'a'+1)

void MemMove (char *to, char *from, int len);
#ifndef sun
# define _MemMove(x,y,l) memmove ((x),(y),(l))
/* _tolower returns uppercase letter if initially lowercase - on irix64!*/
# define _ToLower(x) tolower (x); 
# define _ToUpper(x) toupper (x)
#else
# define _MemMove(x,y,l) MemMove ((x),(y),(l))
# define _ToLower(x) tolower (x)
# define _ToUpper(x) toupper (x)
#endif



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Anatoly's definitions
*/

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Giorgio's definitions
*/


/*********************************************
** MACHINE-DESCRIBING DEFINITIONS
*/

/* UNIX */

/* description of the register width of the machine
** WORD=	int type exactly fitting in one register
** WORD_BITS=	number of bits of the register 
** also used for alignement purposes
*/
 
#ifndef WORD
#define WORD	    unsigned long  
#define Word	    unsigned long  
#define WORD_BITS   32
#endif

/* definition of the type which can contain both a pointer
** and an integer value */

typedef WORD IntOrPtr; 

/*********************************************
** BASIC TYPE DEFINITIONS
*/

/* the type containing a logical variable
** in bit-fields, the use of unsigned is mandatory
*/

#ifndef BOOL 
#define BOOL unsigned int
#endif

/* good when casting/shifting bits */

#ifndef BYTE
#define BYTE unsigned char
#endif

/* the iterator type, hiding implementation in the
** various data structures... as much as it is efficient
*/

/* typedef IntOrPtr Iter */
typedef void* Iter;

/*********************************************
** LOW-LEVEL UTILITIES
*/

/* useful for making type-casts in complex pointer expressions 
** a bit more readable
*/

#define cast(ptr,type) ((type)(ptr))

/* makes calls to function pointers more readable */

#define call(funcPtr) (*(funcPtr))

/* makes allocation of structs easier and more readable */

/**api* macro ************************************************************
**
**	Incremental hashing macro
**      Rotates right sum by 5 bits (*index) and xores with num
**
**      INPUT:          [W] the hash value to be modified (32 bit)
**			an unsigned integer (32 bit) to be added to 
**                      the hash value
*/

#define _hash(sum, num) sum=(sum>>5)^(sum<<27)^num
void hashGo(UINT4* sum, INT4 index);

#define _talloc(type) ((type*)malloc(sizeof(type)))

/* returns the pointer moved of the specified number of bytes
** and casts it to the required type. 
*/

#define _ptrMove(ptr,nbyte,type) cast(cast(ptr,char*)+nbyte,type)

/* returns the difference in bytes between 2 pointers */

#define _ptrDiff(ptr1, ptr2) (cast(ptr1, char*)-cast(ptr2, char*))

/* returns the offset of a certain attribute within a struct,
** cl=struct name,  attr=name of the attribute
** can only be used in function bodies (cc complains)
*/

extern char MPtrBuffer[];
#define _attrOffs(cl, attr) displ(&cast(MPtrBuffer,cl*)->attr, MPtrBuffer)

/* function to allocate aligned byte offset of attributes in a struct 
** given: 
**    offset of the end of the struct
**    the number of bytes to allocate to the new attribute
** returns:
**    the offset where the new attribute starts
*/   

int align(int currOffs, int allocSize);
UINT4 CharHash (char* p);
UINT4 CharHashLen (char *p, int len);

/******************************
** OLD macros
******************************/

#define typeAlloc(type)         _talloc(type)
#define offset(ptr,nbyte,type)  _ptrMove(ptr,nbyte,type)
#define displ(ptr1, ptr2)       _ptrDiff(ptr1, ptr2)
#define mPtr(cl, attr)          _attrOffs(cl,attr)

/***********************************************************************
** DEBUGGING SUPPORT
** 
** <not yet implemented> this macro generate debugging code if DEBUG
** is defined, else they do nothing
***********************************************************************/

/* the function used to stop the program when an exception is thrown.
** Set a breakpoint here if you want to see where the exception comes from
*/
 
void stopProg(char *msg);

/* throws an exception */

#ifndef THROW
#define THROW(except) \
(void)Message (6, f__exception, MSGxEXIT, (except), __FILE__, __LINE__)
#endif

/* if the condition specified is false, throws an exception */

#ifndef ASSERT
#define ASSERT(cond,except) ((cond)? (void)0:THROW(except))
#endif

/* <not implemented> prints a debug message */

#ifndef TRACE
#define TRACE(cmd) ((void)0)
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

#endif



comes from
*/
 
void stopProg(char *msg);

/* throws an exception */

#ifndef THROW
#define THROW(except) \
(void)Message (6, f__exception, MSGxEXIT, (except), __FILE__, __LINE__)
#endif

/* if the condition specified is false, throws an exception */

#ifndef ASSERT
#define ASSERT(cond,except) ((cond)? (void)0:THROW(except))
#endif

/* <not implementesrs/src/dict.c
**
**  MODULE for management of indexes (dictionaries) of pointers 
**	to structures organized as hash tables 
**  
**            Authors: Giorgio Verde
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387451
**                     Email: verde@embl-heidelberg.de
**
*************************************************************************/

#include "def.h"
#include "message.h"
#include "dict.h"
#include "strv.h"
#include <stdlib.h>
#include <string.h>

/***********************************************************************
** DICTIONARY size management 
*/

UINT4 primes[]= {
   1U,3U,7U,17U,31U,61U,127U,257U,509U,
   1021U,2053U,4093U,8191U,16381U,32771U,65537U,131071U,
   262147U,524287U,1048573U,2097143U,4194301U,8388617U,16777213U,33554467U,
   67108859U,134217689U,268435459U,536870909U,1073741827U,2147483647U,4294967291U
};

int numPrimes=32;

UINT4 FindNextPrime(UINT4 num) {
  /* performs a range search on the prime number array */
  int bott,top,curr;
  bott=0; top=numPrimes;
  while (top-bott>1) {
    curr=bott+((top-bott)>>1);
    if (num==primes[curr]) return primes[curr+1];
    if (num<primes[curr]) top=curr;
    else bott=curr;
  }
  return primes[curr];
}

UINT4 FindPrevPrime(UINT4 num) {
  /* performs a range search on the prime number array */
  int bott,top,curr;
  bott=0; top=numPrimes;
  while (top-bott>1) {
    curr=bott+((top-bott)>>1);
    if (num==primes[curr]) return primes[curr-1];
    if (num<primes[curr]) top=curr;
    else bott=curr;
  }
  return primes[curr-1];
}

void DictClearImpl (DICTv dict) {
    DictElem* curr;
    for (curr=dict->tab; curr<dict->tab+dict->dim; curr++) *curr=NULL;
    dict->num=0;
}

DICTv DictCopyImpl(DICTv dict) {
    int size=sizeof(DICTo)+sizeof(DictElem)*(dict->dim-1);
    DICTv d=(DICTv)malloc(size);
    memcpy(d, dict, size);
    d->usage=1;
    return d;
}
DictElem* DictAddImpl (DICTv dict, void* key) {
    int dim=dict->dim;
    DictElem* curr=dict->tab+call(dict->myClass->hash)(key,dim);
    DictElem* last=dict->tab+dim;
    while (*curr) if (++curr==last) curr=dict->tab; 
    return curr;
}

/* get element with same key if present, else add */
DictElem* DictSetImpl(DICTv dict, void* key) {
    CLASSoDICT* cl=dict->myClass;
    ValComparer equal=cl->equal;
    KeyAccessor toKey=cl->toKey;
    IntOrPtr toKeyInfo=cl->toKeyInfo;
    int dim=dict->dim;
    DictElem* curr=dict->tab+call(cl->hash)(key,dim);
    DictElem* last=dict->tab+dim;
    while (*curr && !call(equal)(key, toKey(curr, toKeyInfo))) {
	if (++curr==last) curr=dict->tab;
    }
    return curr;
}


/*********************************************************************/

int DictCreateDim=7;

/**API* DictCreate *********************************************************
**
**	Creates a new empty DICTv
**
**      INPUT:          a dictionary class (CLASSoDICT structure) 
**	IMPLICIT:	o the variable DictCreateDim (default=7) storing the
**			  initial size of the dictionary
**      RETURNS:        a dictionary
*/


DICTv DictCreate(CLASSoDICT* c) {
    DICTv d=(DICTv)malloc(sizeof(DICTo)+sizeof(DictElem)*(DictCreateDim-1));
    d->myClass=c;
    d->dim=DictCreateDim;
    d->usage=1;
    DictClearImpl(d);
    return d;
}

/**API* DictDestroy *********************************************************
**
**	Destroys a dictionary. It does'nt destroy the dictionary class 
**
**      INPUT:          [W] a DICTv
*/


void  DictDestroy(DICTv dict) {
    if (dict && !--dict->usage) {
      DictClearImpl(dict); 
      free(dict); 
    }
   
}

/**API* DictCopy *********************************************************
**
**	Creates a dictionary copying another one.
**
**      INPUT:          a DICTv
**      RETURNS:        a new dictionary
*/

DICTv DictCopy(DICTv dict) {
    if (dict) dict->usage++;
    return dict;
}



/**API* DictOffset *********************************************************
**
**	Offsets all valid pointers inside a dictionary by a specified amount.
**	Useful when the dictionary is used to index positions in a memory 
**	buffer which is being reallocated. The user can use this function
**	to switch indexing to the new buffer. If not all entries in the DICTv
**	are pointing to the buffer, DictOffsetWithin should be used.
**
**      INPUT:          [W] a DICTv
**			a memory offset
*/

void DictOffset (DICTv dict, int offs) {
    DictElem* curr;
    for (curr=dict->tab; curr<dict->tab+dict->dim; curr++) 
       if (*curr) *(BYTE**)curr+=offs;    
}

/**API* DictOffsetWithin *********************************************************
**
**	Offsets all pointers in a given address range inside a dictionary 
**	by a specified amount
**	Useful when some entries in  dictionary index positions in a memory 
**	buffer which is being reallocated. The user can use this function
**	to switch indexing to the new buffer. If all valid entries in the DICTv
**	are pointing to the buffer, DictOffset should be used.
**
**      INPUT:          [W] a DICTv
**			the starting address of the memory range
**			the length in bytes of the memory range
**			the destination address
**			
*/

void  DictOffsetWithin(DICTv dict, DictElem buf, int len, DictElem newBuf) {
    DictElem* curr;
    DictElem  elem;
    int offs=displ(newBuf,buf);
    for (curr=dict->tab; curr<dict->tab+dict->dim; curr++) {
	elem=*curr;
	if (elem && elem>=buf && elem<offset(buf, len, void*))
	    *(BYTE**)curr+=offs;        
    }
}

/**API* DictResize *********************************************************
**
**	Grows or shrinks a dictionary, re-hashing entries.
**
**      INPUT:          [W] a pointer to DICTv
**			the new size
*/


void DictResize(DICTv* dict, int newDim) {
    DICTv old=*dict;
    DictElem* curr;
    DICTv d=(DICTv)malloc(sizeof(DICTo)+sizeof(DictElem)*(newDim-1));
    CLASSoDICT* cl=old->myClass;
    KeyAccessor toKey=cl->toKey;
    IntOrPtr toKeyInfo=cl->toKeyInfo;
    d->myClass=cl;
    d->num=old->num;
    d->dim=newDim;
    d->usage=1;
    ASSERT(d->num<newDim,"TooMany");
    for (curr=d->tab; curr<d->tab+newDim; curr++) *curr=NULL;
    for (curr=old->tab; curr<old->tab+old->dim; curr++) {
	/* move value to new place */
	if (*curr) *DictAddImpl(d, toKey(curr, toKeyInfo))=*curr;
    }
    DictDestroy(old); 
    *dict=d;
}

/* insertion/removal */



/**API* DictAddGrow *********************************************************
**
**	Allocates a new entry, given the key where to insert. If 
**	the dictionary class allows repetitions, then more than one
**	entry can have the same key. See also DictWith, DictNextWith
**
**      INPUT:          [W] a pointer to DICTv
**			the pointer to the key value
**      RETURNS:        o the pointer to the entry (a void*) to be assigned
**			  to the structure to be inserted
*/

DictElem* DictAddGrow(DICTv* dict,void* key) {
    DICTv d=*dict;
    if (d->usage>1) {
        DictResize(dict,FindNextPrime(d->dim));
        d=*dict;
    }
    if (d->myClass->repetitions) {
	if (++d->num>(d->dim*3>>2)) DictResize(dict,FindNextPrime(d->dim));
	return DictAddImpl(*dict,key);
    }
    else {
	DictElem* el=DictSetGrow(dict, key);
	ASSERT(!*el, "DuplicateKey");
	return el;
    }
}

/**API* DictSetGrow *********************************************************
**
**	Given a key, allocates a new entry if the key is not found, 
**	else returns the first entry which has the same key. Useful when
**	adding a new element with the same key must replace the old element.
**	See also DictAdd
**
**      INPUT:          [W] a pointer to DICTv
**			the pointer to the key value
**      RETURNS:        o the pointer to the new entry (a void*) to be assigned
**			  if the key is not found, else a pointer to the already
**			  present entry
*/

DictElem* DictSetGrow(DICTv* dict, void* key) {
    DictElem* elem;
    if ((*dict)->usage>1) *dict=DictCopyImpl(*dict);
    elem=DictSetImpl(*dict,key);
    if (!*elem) {
        int num=++((*dict)->num);
	int dim=(*dict)->dim;
	if (num>(dim*3>>2)) {
	    DictResize(dict,FindNextPrime(dim));
	    return DictAddImpl(*dict,key);
	}
    }
    return elem;
}

/**API* DictAddPtr *********************************************************
**
**	Adds a new element to the dictionary. The element must contain
**	a valid key. While inserted into the dictionary, the key cannot be
**      modified nor the structure reallocated.
**      If the user to perform such an operation, it must remove the structure
**	with DictRemovePtr,  do the operation and insert it again with DictAddPtr.
**	To reallocate an array of indexed structure, see DictOffsetWithin.
**
**      INPUT:          [W] a pointer to DICTv
**			the pointer to the element
**      RETURNS:        o an iterator with the position of the inserted element
**			  the iterator is only valid until the next dictionary-modifying
**			  operation is performed 
*/


Iter DictAddPtr(DICTv* dict, DictElem elem) {
    CLASSoDICT* cl=(*dict)->myClass;
    void* key=call(cl->toKey)(&elem, cl->toKeyInfo);
    DictElem* e=DictAddGrow(dict,key);
    *e=cast(elem, DictElem);
    return e; 
}

/**API* DictSetPtr *********************************************************
**
**	Adds a new element to the dictionary or substitutes an already present
**	element with the same key (see DictSetGrow)
**	The element must contain a valid key. While inserted into the 
**	dictionary, the key cannot be modified nor the structure reallocated.
**      If the user to perform such an operation, it must remove the structure
**	with DictRemovePtr,  do the operation and insert it again with DictAddPtr.
**	To reallocate an array of indexed structure, see DictOffsetWithin.
**
**      INPUT:          [W] a pointer to DICTv
**			the pointer to the element
**      RETURNS:        o an iterator with the position of the inserted/replaced element
**			  the iterator is only valid until the next dictionary-modifying
**			  operation is performed 
*/

Iter DictSetPtr(DICTv* dict, DictElem elem) {
    CLASSoDICT* cl=(*dict)->myClass;
    void* key=call(cl->toKey)(&elem, cl->toKeyInfo);
    DictElem* e=DictSetGrow(dict,key);
    *e=cast(elem, DictElem);
    return e;     
}

/**API* DictRemove *********************************************************
**
**	Removes the element at a given position 
**	The iterator can be obtained by using DictAddPtr, DictSetPtr,
**	DictWith, DictWithPtr, DictFirst, DictNext, DictNextWith. 
**
**      INPUT:          [W] a pointer to DICTv
**			the iterator of the element
*/


void  DictRemove  (DICTv* dict, Iter i) {
    DICTv d=*dict; BOOL shared=d->usage>1;
    int dim=d->dim;
    DictElem* hole=(DictElem*)i; DictElem sharedVal;
    ASSERT(hole && *hole, "NoSuchElem");
    if ((--d->num)<(dim>>2) || shared) {
        sharedVal=*hole; *hole=NULL;
        DictResize(dict, dim=FindPrevPrime(dim));
        if (shared) *hole=sharedVal; /* revert value for shared*/
    }
    else {
	CLASSoDICT* dc=d->myClass;
	ValHasher hash=dc->hash;
	KeyAccessor toKey=dc->toKey;
	IntOrPtr toKeyInfo=dc->toKeyInfo;
	DictElem* curr=hole+1;
	DictElem* last=d->tab+dim;
	if (curr==last) curr=d->tab;
	while (*curr) {
	    DictElem* wanted=d->tab+call(hash)(toKey(curr,toKeyInfo),dim);
	    if ((hole<curr)?
		(wanted<=hole || wanted>curr):
		(wanted<=hole && wanted>curr)) { 
		*hole=*curr;
		hole=curr;
	    }    
	    if (++curr==last) curr=d->tab;
	}
	*hole=NULL;
    }
}

/**API* DictRemoveWith *********************************************************
**
**	Removes the elements having a given key value
**
**      INPUT:          [W] a pointer to DICTv
**			the pointer to the key value
*/

void   DictRemoveWith (DICTv* dict, void* key) {
    Iter i;
    while (i=DictWith(*dict,key)) DictRemove(dict,i);
}

/**API* DictRemovePtr *********************************************************
**
**	Removes a certain element (identified by it's memory pointer)
**
**      INPUT:          [W] a pointer to DICTv
**			the pointer to the element
*/

void   DictRemovePtr     (DICTv* dict, DictElem elem) {
    DictRemove(dict,DictWithPtr(*dict, elem));
}

/**API* DictClear *********************************************************
**
**	Removes all the elements of the dictionary without reallocating it
**
**      INPUT:          [W] a pointer to DICTv
*/


void DictClear(DICTv* dict) {
  DICTv d=*dict;
  if (d->usage==1) DictClearImpl(d);
  else {
    d->usage--;
    *dict=DictCreate(d->myClass);
  }
}

/* access */

/**API* DictAtImpl *********************************************************
**
**	Accesses the element at a given key. If repetitions are allowed, 
**	a run-time check for unicity of the key value is performed.
**      A NotSuchElement exception is thrown if the key is not found. 
**
**      INPUT:          a DICTv
**			a pointer to the key value
**	RETURNS:	a pointer to the element
*/


DictElem* DictAtImpl (DICTv dict, void* key) {
    Iter i=DictWith(dict, key);
    ASSERT(i, "NoSuchElement");
    if (dict->myClass->repetitions) {
	Iter next=i;
	DictNextWith(dict, key, &next);
	ASSERT(!next, "AmbigousAssociation");
    }
    return (DictElem*)i;
}

/**API* DictKey *********************************************************
**
**	Accesses the key at a given position. The iterator must be valid
**
**      INPUT:          a DICTv
**			an iterator
**	RETURNS:	a pointer to the key value
*/

void* DictKey(DICTv dict, Iter i) {
    CLASSoDICT* cl=dict->myClass;
    return call(cl->toKey)(*cast(i, DictElem*),cl->toKeyInfo);
}

/* iterator support */

/**API* DictWith *********************************************************
**
**	Retrieves the iterator position of the first element 
**	with a given key value. If the key value does'nt
**	exist, returns NULL. Useful also for testing the
**	presence of a key in the dictionary. The successive elements
**	with the same key value can be obtained using DictNextWith.
**	
**
**      INPUT:          a DICTv
**			a pointer to the key value
**	RETURNS:	the iterator
*/

Iter  DictWith (DICTv dict, void* key) {
    CLASSoDICT* cl=dict->myClass;
    ValComparer equal=cl->equal;
    KeyAccessor toKey=cl->toKey;
    IntOrPtr toKeyInfo=cl->toKeyInfo;
    int dim=dict->dim;
    DictElem* curr=dict->tab+call(cl->hash)(key,dim);
    DictElem* last=dict->tab+dim;
    while (*curr) {
	if (call(equal)(key, toKey(curr, toKeyInfo))) return curr;
	if (++curr==last) curr=dict->tab;
    }        
    return NULL;
}

/**API* DictWithPtr *********************************************************
**
**	Retrieves the iterator position given the memory
**	pointer to the element. The element must have been 
**	inserted in the dictionary. 	
**
**      INPUT:          a DICTv
**			a pointer to the element
**	RETURNS:	the iterator
*/


Iter  DictWithPtr(DICTv dict, DictElem elem) {
    CLASSoDICT* cl=dict->myClass;
    void* key=call(cl->toKey)(&elem,cl->toKeyInfo);
    DictElem* i=(DictElem*)DictWith(dict, key);
    if (!i) return NULL;
    while (*i!=elem) { 
	i++; if (!*i) return NULL;
    }  
    return i;
}

/**API* DictFirst *********************************************************
**
**	Retrieves an iterator for scanning the dictionary sequentially.
**	No specific ordering is given for the iteration, and the dictionary
**	should not be modified while iterating.
**
**      INPUT:          a DICTv
**	RETURNS:	the iterator
*/

Iter  DictFirst(DICTv dict) {
    Iter i=NULL; DictNext(dict,&i); return i;    
}

/**API* DictNext *********************************************************
**
**	Retrieves an iterator for scanning the dictionary sequentially.
**	No specific ordering is given for the iteration, and the dictionary
**	should not be modified while iterating. The iterator is set to NULL
**	when there are no more elements.
**
**      INPUT:          a DICTv
**			[W] a pointer to an iterator
*/

void  DictNext (DICTv dict, Iter* i) {
    if (*i) (*cast(i, DictElem**))++; else *i=dict->tab; 
    while (*i!=dict->tab+dict->dim) {
	if (*cast(*i, DictElem*)) return;
	(*cast(i, DictElem**))++;
    }
    *i=NULL;
}

Iter  DictLast (DICTv dict) {
    Iter i=NULL; DictPrev(dict, &i); return i;
}

void  DictPrev (DICTv dict, Iter* i) {
    if (*i) (*cast(i, DictElem**))--; else *i=dict->tab+dict->dim; 
    while (*i!=dict->tab-1) {
	if (*cast(*i, DictElem*)) return;
	(*cast(i, DictElem**))--;
    }
    *i=NULL;
}

/**API* DictNextWith *********************************************************
**
**	Retrieves an iterator for scanning all insterted elements having
**	a given key value. The order of the elements is the insertion order.
**	The first element can be obtained using the DictWith function.
**	The iterator is set to NULL when there are no more elements.
**
**      INPUT:          a DICTv
**			a pointer to the key value
**			[W] a pointer to an iterator
*/

void  DictNextWith (DICTv dict, void* key, Iter* i) {
    int dim=dict->dim;
    DictElem* curr=*i;
    CLASSoDICT* cl=dict->myClass;
    ValComparer equal=cl->equal;
    KeyAccessor toKey=cl->toKey;
    IntOrPtr toKeyInfo=cl->toKeyInfo;
    if (curr) { 
        curr++; if (curr==dict->tab+dict->dim) curr=dict->tab;
    }
    else curr=dict->tab+call(cl->hash)(key,dim); 
    while (*curr) {
	if (call(equal)(key, toKey(curr, toKeyInfo))) {
	    *i=curr; return;
	}
	curr++; if (curr==dict->tab+dict->dim) curr=dict->tab;
    }
    *i=NULL;
}

/* information */

/**API* DictCard *********************************************************
**
**	Returns the number of elements in the dictionary
**
**      INPUT:          a DICTv
**	RETURNS:	the number of elements
*/

int   DictCard (DICTv dict) {
    return dict->num;
}

/**API* DictCardWith *********************************************************
**
**	Returns the number of elements in the dictionary with a given key value
**
**      INPUT:          a DICTv
**			a pointer to the key value
**	RETURNS:	the number of elements
*/

int   DictCardWith(DICTv dict, void* key) {
    Iter i; int num=0;
    for (i=DictWith(dict, key);i;DictNextWith(dict, key, &i)) num++;
    return num;
}

/**API* DictEmpty *********************************************************
**
**	Tells whether a dictionary is empty. 
**
**      INPUT:          a DICTv
**	RETURNS:	TRUE if the dictionary is empty
*/

BOOL  DictEmpty(DICTv dict) {
    return dict->num!=0;
}

/**API* DictHas *********************************************************
**
**	Tells weather a dictionary contains an element with the given key.
**	See also DictWith
**
**      INPUT:          a DICTv
**			a pointer to a key value
**	RETURNS:	TRUE if the dictionary contains the key
*/


BOOL  DictHas  (DICTv dict, void* key) {
    return DictWith(dict, key)!=NULL;
}

/*************************************************************************/

/**API* PolyStrEqual *********************************************************
**
**	Compares 2 pointers to STRv for equality
**
**      INPUT:          a pointer to STRv
**			a pointer to STRv
**	RETURNS:	TRUE if the STRv's are equal
*/

BOOL PolyStrEqual(void* s1, void* s2) { 
    return StrEqual(*cast(s1, STRv*), *cast(s2, STRv*)); 
}

/**API* PolyStrHash *********************************************************
**
**	Hashes the STRv identified by a pointer to STRv
**
**      INPUT:          a pointer to STRv
**	RETURNS:	an hash value
*/

int  PolyStrHash(void* s, int max) { 
    return StrHash(*cast(s, STRv*), max);
}

/**API* PolyIntEqual *********************************************************
**
**	Compares 2 pointers to int for equality
**
**      INPUT:          a pointer to int
**			a pointer to int
**	RETURNS:	TRUE if the int's are equal
*/

BOOL PolyIntEqual(void* i1, void* i2) { 
    return *cast(i1, int*)==*cast(i2, int*);
}

/**API* PolyIntHash *********************************************************
**
**	Hashes the int identified by a pointer to int
**
**      INPUT:          a pointer to int
**	RETURNS:	an hash value
*/

int  PolyIntHash(void* i, int max) { 
    return *cast(i, int*)%max;
}

/**API* PolyPtrEqual *********************************************************
**
**	Compares 2 pointers to pointer for equality
**
**      INPUT:          a pointer to pointer
**			a pointer to pointer
**	RETURNS:	TRUE if the pointed pointers are equal
*/


BOOL PolyPtrEqual(void* p1, void* p2) {
    return *cast(p1, void**)==*cast(p2, void**);
}

/**API* PolyPtrHash *********************************************************
**
**	Hashes the pointer identified by a pointer to pointer
**
**      INPUT:          a pointer to pointer
**	RETURNS:	an hash value
*/

int PolyPtrHash(void* p, int max) {
    return *cast(p, IntOrPtr*)%max;
}

#include <stdio.h>

/**API* strhash *********************************************************
**
**	Hashes a C string
**
**      INPUT:          a char*
**	RETURNS:	an hash value
*/


int strhash(char* s, int max) {
    WORD h=0, g;
    while (*s) {
      h=(h << 4 | (h&0xf0000000L)>>28) ^ *s++;
    }
    return h%max;
}

/**API* strequal *********************************************************
**
**	compares 2 C strings
**
**      INPUT:          a char*
**			a char*
**	RETURNS:	TRUE if equal
*/

BOOL strequal(char* s1,char* s2) {
    return strcmp(s1,s2)==0;
}

/**API* PtrEqual *********************************************************
**
**	compares 2 pointers
**
**      INPUT:          a pointer
**			a pointer
**	RETURNS:	TRUE if equal
*/


BOOL PtrEqual(void* p1, void* p2) {
    return p1==p2;
}

/**API* PtrHash *********************************************************
**
**	Hashes a pointer
**
**      INPUT:          a pointer
**	RETURNS:	an hash value
*/

int  PtrHash(void* p, int max) {
    return cast(p, WORD)%max;
}

/**API* KeyItself *********************************************************
**
**	Used in definitions of dictionary classes, used with DictCreate.
**	Defines the dictionary to be a set, so that the entire value of 
**	elements that are inserted is the key of the dictionary.
**
**      INPUT:          a pointer to the element (a pointer inside the dictionary)
**	RETURNS:	a pointer to the key 
*/

void* KeyItself(DictElem* entry) 
{ 
  return *entry; 
}

/**API* KeyOffset *********************************************************
**
**	Used in definitions of dictionary classes, used with DictCreate.
**	Defines the dictionary to be a dictionary of structures in which
**	one attribute is the key.
**
**      INPUT:          a pointer to the element (a pointer inside the dictionary)
**	RETURNS:	a pointer to the key 
*/

void* KeyOffset(DictElem* entry, int offs) 
{ 
  return offset(*entry, offs, void*);
}

void* KeyOffsetDeref(DictElem* entry, int offs) {
  return *offset(*entry,offs,void**);
}

/**API* DictDebug *********************************************************
**
**	Prints the status of the dictionary. Especially useful if the 
**	dictionary class has been defined using the functions provided
**	by this module.
**
**      INPUT:          a DICTv
*/

void DictDebug(DICTv d) {
    printf("DICTv:%p", d);
    if (d) { 
	DictElem* curr;
	CLASSoDICT* info=d->myClass; 
	printf("[num:%d dim:%d", d->num, d->dim);
        if (d->usage!=1) printf(" shared:%d",d->usage-1);
        printf("\n");
	for (curr=d->tab; curr<d->tab+d->dim; curr++) if (*curr) {
	    void* key=call(info->toKey)(curr, info->toKeyInfo);
	    ValComparer equal=info->equal;
	    printf("\t[ix:%d elem:%p ", curr-d->tab, *curr);
	    if (equal==(ValComparer)strequal) printf("key:%s", (char*)key);
	    else if (equal==PtrEqual) printf("key:%p", key);
	    else if (equal==PolyStrEqual) printf("key:%s", Str(*(STRv*)key));
	    else if (equal==PolyIntEqual) printf("key:%d", *(int*)key);
	    else if (equal==PolyPtrEqual) printf("key:%p", *(void**)key);
	    else printf("key: DontKnow");
	    printf(" hash:%d ]\n", call(info->hash)(key, d->dim));
	}
	printf("]");
    }
    printf("\n");
}

/*******************************************************************
** PROPERTY MANAGEMENT
*/

DICTv AccessMethods=NULL;
DICTv Properties=NULL;

typedef struct AccessMethod {
    KeyAccessor toKey;
    DICTv accessInfo;
} AccessMethod;


KeyAccessor* AccessMethodToKey(AccessMethod** entry) {
    return &(*entry)->toKey;
}

BOOL PropertyCompare(Prop prop1, Prop prop2) {
    if (prop1==prop2) return TRUE;
    else if (prop1->toKey==prop2->toKey && 
	prop1->toKeyInfo==prop2->toKeyInfo &&
	prop1->equal==prop2->equal && 
	prop1->hash==prop2->hash &&
	prop1->repetitions==prop2->repetitions) return TRUE;
    return FALSE;
}

int PropertyHash(Prop p, int max) {
    int val=(cast(p->toKey, WORD)+cast(p->equal, WORD)+cast(p->hash, WORD)+
	p->toKeyInfo+p->repetitions)%max;
    return val;
}

void InitProperties() {
    Prop cl=typeAlloc(CLASSoDICT);
    cl->toKey=(KeyAccessor)AccessMethodToKey;
    cl->toKeyInfo=NULL;
    cl->equal=(ValComparer)PolyPtrEqual;
    cl->hash=(ValHasher)PolyPtrHash;
    cl->repetitions=FALSE;
    AccessMethods=DictCreate(cl);
    cl=typeAlloc(CLASSoDICT);
    cl->toKey=(KeyAccessor)KeyItself;
    cl->toKeyInfo=NULL;
    cl->equal=(ValComparer)PropertyCompare;
    cl->hash=(ValHasher)PropertyHash;
    cl->repetitions=FALSE;
    Properties=DictCreate(cl);
}


AccessId RegisterAccessMethod(KeyAccessor toKey, ValComparer toKeyInfoEqual, ValHasher toKeyInfoHash) {
    AccessMethod** am;
    AccessMethod* m;
    ASSERT (AccessMethods, "NotInitialized");
    am =&DictSet(&AccessMethods, toKey, AccessMethod*);
    m =*am;
    if (!m) {
	Prop p=typeAlloc(CLASSoDICT);
	p->toKey=(KeyAccessor)KeyItself;
	p->toKeyInfo=NULL;
	p->equal=(ValComparer)toKeyInfoEqual;
	p->hash=(ValHasher)toKeyInfoHash;
	m=typeAlloc(AccessMethod);
	m->toKey=toKey;
	m->accessInfo=DictCreate(p);
	*am=m;
    }
    else {
	Prop p=m->accessInfo->myClass;
	ASSERT(p->equal==toKeyInfoEqual && p->hash==toKeyInfoHash, 
	       "InconsistentIdMethods");
    }
    return m;
}

void RegisterAccessInfo(AccessId how, void** info) {
    void** i=&DictSet(&how->accessInfo, info, void*);
    if (*i) { free (*info); *info=*i; }
    else *i=*info;
}

void RegisterProperty(Prop* property) {
    Prop* p;
    ASSERT (Properties, "NotInitialized");
    p=&DictSet(&Properties, *property, Prop);
    if (!*p) *p=*property;
    else { free(*property); *property=*p; }
}

BOOL RegisteredProp(Prop property) {
    return DictWith(Properties, property)!=NULL;
}

void* GetProp(Prop p, DictElem* elem) {
    return call(p->toKey)(elem, p->toKeyInfo);
}

/***********************************************************************************/

DICTv DictCreateKeyStr(int offs, BOOL repetitions) {
    CLASSoDICT* cl=typeAlloc(CLASSoDICT);
    cl->equal=(ValComparer)PolyStrEqual;
    cl->hash=(ValHasher)PolyStrHash;
    cl->toKey=(KeyAccessor)KeyOffset;
    cl->toKeyInfo=offs;
    cl->repetitions=repetitions;
    return DictCreate(cl);
}

DICTv DictCreateKeyInt(int offs, BOOL repetitions) {
    CLASSoDICT* cl=typeAlloc(CLASSoDICT);
    cl->equal=(ValComparer)PolyIntEqual;
    cl->hash=(ValHasher)PolyIntHash;
    cl->toKey=(KeyAccessor)KeyOffset;
    cl->toKeyInfo=offs;
    cl->repetitions=repetitions;
    return DictCreate(cl);            
}

void DictDestroyWithClass(DICTv d) {
    free(d->myClass);
    DictDestroy(d);
}

CLASSoDICT* DictCreateClassStrKey(KeyAccessor toKey, IntOrPtr toKeyInfo, BOOL repetitions) {
    CLASSoDICT* cl=typeAlloc(CLASSoDICT);
    cl->equal=(ValComparer)PolyStrEqual;
    cl->hash=(ValHasher)PolyStrHash;
    if (toKey) cl->toKey=toKey;
    else cl->toKey=(KeyAccessor)KeyOffset;
    cl->toKeyInfo=toKeyInfo;
    cl->repetitions=repetitions;
    return cl;
}

/**API* function *************************************************************
**
**	Creates a new dictionary for 0 terminated strings within structs.
**      For accessing the key either the second or the third argument must
**      be defined. 
**
**      INPUT:        function to access the key within the item [R]
**		      offset of the key within the item [R] (use mPtr) or NULL
**                    flag if repetitions of values are allowed [R] or NULL
**		
**	RETURNS:      the new dictionary class
*/

CLASSoDICT* DictCreateClassStrZKey (KeyAccessor toKey, IntOrPtr toKeyInfo, 
				    BOOL repetitions) {
    CLASSoDICT* cl=typeAlloc(CLASSoDICT);
    cl->equal=(ValComparer)strequal;
    cl->hash=(ValHasher)strhash;
    if (toKey) cl->toKey=toKey;
    else cl->toKey=(KeyAccessor)KeyOffsetDeref;
    cl->toKeyInfo=toKeyInfo;
    cl->repetitions=repetitions;
    return cl;
}

CLASSoDICT* DictCreateClassIntKey(KeyAccessor toKey, IntOrPtr toKeyInfo, BOOL repetitions) {
    CLASSoDICT* cl=typeAlloc(CLASSoDICT);
    cl->equal=(ValComparer)PolyIntEqual;
    cl->hash=(ValHasher)PolyIntHash;
    if (toKey) cl->toKey=toKey;
    else cl->toKey=(KeyAccessor)KeyOffset;
    cl->toKeyInfo=toKeyInfo;
    cl->repetitions=repetitions;
    return cl;
}

/**API* function *************************************************************
**
**	Creates a new dictionary for pointers within structs.
**      For accessing the key either the second or the third argument must
**      be defined. 
**
**      INPUT:        function to access the key within the item [R]
**		      offset of the key within the item [R] (use mPtr) or NULL
**                    flag if repetitions of values are allowed [R] or NULL
**		
**	RETURNS:      the new dictionary class
*/

CLASSoDICT* DictCreateClassPtrKey(KeyAccessor toKey, IntOrPtr toKeyInfo, BOOL repetitions) {
    CLASSoDICT* cl=typeAlloc(CLASSoDICT);
    cl->equal=(ValComparer)PolyPtrEqual;
    cl->hash=(ValHasher)PolyPtrHash;
    if (toKey) cl->toKey=toKey;
    else cl->toKey=(KeyAccessor)KeyOffset;
    cl->toKeyInfo=toKeyInfo;
    cl->repetitions=repetitions;
    return cl;
}


/**API* function *************************************************************
**
**	Creates a new dictionary where they key is the address of the item
**      itself
**
**      INPUT:        flag if repetitions of values are allowed [R] or NULL
**		
**	RETURNS:      the new dictionary class
*/

CLASSoDICT* DictCreateClassSelfPtrKey (BOOL repetitions) {
    CLASSoDICT* cl=typeAlloc(CLASSoDICT);
    cl->equal=(ValComparer)PtrEqual;
    cl->hash=(ValHasher)PtrHash;
    cl->toKey=(KeyAccessor)KeyItself;
    cl->repetitions=repetitions;
    return cl;
}







***************************
**
**	Creates a new dictionary where they key is the address of the item
**      itself
**
**      INPUT:        flag if repetitions of values are allowed [R] or NULL
**		
**	RETURNS:      the new dictionary class
*/

CLASSoDICT* DictCreateClassSelfPtrKey (BOOL repetitions) {
    CLASSoDICT* cl=typeAlloc(CLASSoDICT);
    cl->equal=(ValComparer)PtrEqual;
    cl->hash=(ValHasher)PtrHsrs/src/dict.h
#define _DICT_H


/*******************************************************************************
** DICTIONARY data structure
** associates values with other values
*******************************************************************************/

/* Dictionary is an index built on some other (owning) data structure
   It is composed by aliases to the indexed values (hmmm. bad, should always
   be notified on changes on the index in the indexed value)
*/


typedef void* DictElem;
typedef void* (*KeyAccessor)(DictElem* entry, IntOrPtr info);
typedef BOOL  (*ValComparer)(void* val1, void* val2);
typedef int   (*ValHasher)  (void* val, int N);

typedef struct CLASSoDICT {
    ValComparer equal; /* key compare */
    ValHasher   hash;  /* key hash */
    KeyAccessor toKey;
    IntOrPtr    toKeyInfo;
    BOOL	repetitions;
} CLASSoDICT;


typedef struct DICTo {
    CLASSoDICT* myClass;
    int   dim;                              
    int   num;  
    int   usage;                          /* num of hashed elements */
    DictElem tab[1];
} DICTo;

typedef DICTo* DICTv;                     /* dictionary value is polymorphic */

/* creation/deletion */
DICTv DictCreate(CLASSoDICT* cl);
void  DictDestroy(DICTv dict);
DICTv DictCopy(DICTv dict);
void  DictOffset(DICTv dict, int offs);
void  DictOffsetWithin(DICTv dict, DictElem buf, int len, DictElem newBuf); 

/* insertion/removal */
DictElem* DictAddGrow(DICTv* dict, void* key);
DictElem* DictSetGrow(DICTv* dict, void* key);

#define DictAdd(dict, key, type) (*cast(DictAddGrow(dict,key), type*)) 
#define DictSet(dict, key, type) (*cast(DictSetGrow(dict,key), type*))
Iter   DictAddPtr(DICTv* dict, DictElem elem);
Iter   DictSetPtr(DICTv* dict, DictElem elem);
void   DictRemove        (DICTv* dict, Iter i);
void   DictRemoveWith    (DICTv* dict, void* key);
void   DictRemovePtr     (DICTv* dict, DictElem elem);
void   DictClear         (DICTv* dict);


/* access */
DictElem* DictAtImpl (DICTv dict, void* key);
DictElem* DictInImpl (DICTv dict, Iter i); 
#define DictAt(dict, key, type) (*(type*)DictAtImpl(dict, key))
#define DictIn(iter, type) (*(ASSERT(iter, "Undefined"), cast(iter,type*))) 

/* iterator support */
Iter  DictWith (DICTv dict, void* key);
Iter  DictWithPtr(DICTv dict, DictElem elem);
void  DictNextWith (DICTv dict, void* key, Iter* i);

Iter  DictFirst(DICTv dict);
void  DictNext (DICTv dict, Iter* i);
Iter  DictLast (DICTv dict);
void  DictPrev (DICTv dict, Iter* i);

/* information */

int   DictCard (DICTv dict);
int   DictCardWith(DICTv dict, void* key);
BOOL  DictEmpty(DICTv dict);
BOOL  DictHas  (DICTv dict, void* key);
void* DictKey(DICTv dict, Iter i);

/*********************************************************
** Useful support functions
*/
BOOL PolyStrEqual(void* s1, void* s2);
int  PolyStrHash(void* s, int max);
BOOL PolyIntEqual(void* i1, void* i2);
int  PolyIntHash(void* i, int max);
BOOL PolyPtrEqual(void* p1, void* p2);
int  PolyPtrHash(void* p, int max);
int  strhash(char* s, int max);
BOOL strequal(char* s1,char* s2);
BOOL PtrEqual(void* p1, void* p2);
int  PtrHash(void* p, int max);

void* KeyItself(DictElem* entry);
void* KeyOffset(DictElem* entry, int offs); 
 
/**********************************************************
** Dictionary class management 
*/

typedef CLASSoDICT* Prop;
typedef struct AccessMethod* AccessId;

void InitProperties();
AccessId RegisterAccessMethod(KeyAccessor toKey, ValComparer toKeyInfoEqual, ValHasher toKeyInfoHash);
void RegisterAccessInfo(AccessId how, void** info);
void RegisterProperty(Prop* property);
BOOL RegisteredProp(Prop property);

void* GetProp(Prop p, DictElem* elem);

/*********************************************************
** Useful dictionary constructors/destructors 
*/

DICTv DictCreateKeyStr(int offs, BOOL repetitions);
DICTv DictCreateKeyInt(int offs, BOOL repetitions);
void DictDestroyWithClass(DICTv d);

/********************************************************
** CLASSoDICT creators
** if toKey is null, then it is assumed that:
**   - the dictionary contains pointers to struct
**   - toKeyInfo is the offset to the key attribute
*******************************************************/

CLASSoDICT* DictCreateClassStrKey(KeyAccessor toKey, IntOrPtr toKeyInfo, BOOL repetitions);
CLASSoDICT* DictCreateClassStrZKey(KeyAccessor toKey, IntOrPtr toKeyInfo, BOOL repetitions);
CLASSoDICT* DictCreateClassIntKey(KeyAccessor toKey, IntOrPtr toKeyInfo, BOOL repetitions);
CLASSoDICT* DictCreateClassPtrKey(KeyAccessor toKey, IntOrPtr toKeyInfo, BOOL repetitions);
CLASSoDICT* DictCreateClassSelfPtrKey (BOOL repetitions);

#endif
 the key attribute
*******************************************************/

CLASSoDICT* DictCreateClassStrKey(KeyAccessor toKey, IntOrPtr toKeyInfo, BOOL repetitions);
CLASSoDICT* DictCreateClassStrZKey(KeyAccessor toKey, IntOrPtr toKeyInfo, BOOL repetitions);
CLASSoDICT* DictCreateClassIntKey(KeyAccessor toKey, IntOrPtr toKeyInfo, BOOL repetitions);
CLASSoDICT* DictCreateClassPtrKey(KeyAccessor toKey, IntOrPtr toKeyInfo, BOOL repetitions);
CLASSoDICT* DictCreateClassSelfPtrsrs/src/entry.c
char entry_ID[] = "$Id: entry.c,v 1.26 1997/03/03 18:20:29 srs Exp $";
/*
**
**    $RCSfile: entry.c,v $
**    $Revision: 1.26 $
**    $Date: 1997/03/03 18:20:29 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**             Unix port by Lukas Rosenthaler and Reinhard
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     D-69012 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    functions open flat files and indices for read access only - compare 
**    time stamps and retrieve entry information from ID-indices
**
**    Global Parameters:
**        "printf"
**        "parseTest"
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdarg.h>

#include "message.h"
#include "sm.h"
#include "strv.h"
#include "dict.h"
#include "tm.h"
#include "futil.h"
#include "par.h"
#include "id.h"
#include "idx.h"
#include "set.h"
#include "library.h"
#include "field.h"
#include "entry.h"
#include "toklist.h"
#include "variable.h"
#include "icarus.h"
#include "templ.h"
#include "view.h"
#include "query.h"
#include "regexp.h"
#include "binpack.h"

#define _SRS
#define _SLB
#include SRSINCLUDE

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Describes an entry in a flat file opened for read access. All
**  different sections (eg, text, data) can be opened simultaneously.
*/

typedef struct ENTRYo {
  struct IDoENTRY   *id;            /* pointer to ID-object */
  struct SLBo       *lib;           /* (API) address of library object */
  char              entry_nm[132];  /* unique entry name */
  char              file_nm[132];   /* complete or partial file name */
  char              full_nm[132];   /* unique entry name */
  FIP               fip[2];         /* file ptr to the section in flat file */
  Int4              fileX[2];       /* file index for each file type */
  struct FILEo      *file[2];       /* file descriptor for a section */
  struct SLBoFIELD  *field;
  struct TOKoLIST   **tokList;       /* token list with the "field" tokens */
  Int4              tokListN;
  Int4              tokListAllocN;
  DICTv             tokListDict;
  UINT4             indexTime;
  UINT4             fileCreTime[2];
  Int4              partNo;         /* current library part number */
} ENTRYo;



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  private functions
*/

static FILEo *EntryJobNextFile (char *symName, void* data);
static FILEo *EntryJobFile (char *symName, void* data);
static void EntryEmptyViewInTable (VIEWoLIB *vlib, Int4 rowN);
static void EntryPrintTableField (ENTRYo *entry, SLBoFIELD *field, 
			   LIBoFieldFormat *format, Int4 rowN);
static INT4 EntryViewInTable (ENTRYo *entry, VIEWo *view, VIEWoLIB *vlib,
			      Int4 entryNo, Int4 isRoot, Int4 rowN);
static void EntryViewInList (ENTRYo *entry, VIEWo *view, VIEWoLIB *vlib,
			     Int4 entryNum, Int4 isRoot);
static void EntrySetJob (ENTRYo *entry, ICAoJOB *job);
static void EntrySetInputNames (ENTRYo *entry);
void EntryIdRecordUnpack (ENTRYv entry, char *buff);
static char *EntryGetFileName (ENTRYo *entry);


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  extern or module wide variables
*/

static FILE   *outFile=NULL;

#ifdef sun
extern INT4 printf ();
#endif

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  default function for printing lines
*/

static INT4 EntryPrintF (char *formatStr, ...)
{
    va_list ap;

    va_start (ap, formatStr);
    vfprintf (outFile, formatStr, ap);
    va_end (ap);

    if (formatStr[strlen (formatStr) -1] != '\n')
    fprintf (outFile, "\n");

    return 1;
}


static void EntrySetInputNames (ENTRYo *entry)
{
  SRSoFILTYP *ft;
  Int4       k, c;

  for (k=0, c=0; (ft=LibNextFileType (EntryGetLib (entry), &c)); k++) {
    IcaSetLogicStream (EntryGetJob (entry), LibGetFileTypeName (ft));
  }
}


/**API* EntryOpen *************************************************************
** 
**      Creates and returns an entry object which 
**      is a 'handle' to the 'real' entry 
**      contained in the flat file 
**      which can be accessed using functions such as
**      EntryPrint, EntryPritntFields. To destroy the entry object again use
**      EntryClose.
**
** 	INPUT:	    address of ID-object (see SetGetID) [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    new entry-object
** 		    NULL if there is a problem with the ID or the ID index
*/ 

ENTRYo *EntryOpen (IDoENTRY *id)
{
  LIBoINDEX *libInx;
  SLBo      *lib;
  ICAoJOB   *job;
  ENTRYo    *entry;

  entry = (ENTRYo *) calloc (1, sizeof (ENTRYo));
  if (!(lib = (SLBo *) LibObjById ("library", id->lib_x))) {
    _ErrMsg2 (e__libidnotknown, id->lib_x);
    EntryClose(&entry); /*PURIFY*/
    return NULL;
  }
  entry->lib = lib;
  entry->id = id;

  /* get information how to access entry within the library flat file */
  if (!(libInx = LibIndexOpen (lib, LibGetIdField (lib), 0)))
    _ErrExit (e__error);
  EntryIdRecordUnpack (entry, IdxRecordGet (libInx->idx, id->fip));

  if (IdIsSub (id)) {
    entry->lib = LibGetSubEntryLib (entry->lib, IdGetSubN (id));
    sprintf (entry->entry_nm, "%s_%d", entry->entry_nm, IdGetSubN (id));
  }

  entry->fileX[1] = entry->fileX[0];

  if (!EntryGetJob (entry)) {
    ParDefNum ("fromSrs", 1); /* turn off debugging in .is file */
    job = IcaCreateJob (entry->lib->form->syntax);
    IcaSetInputStreamer (job, EntryJobFile);
    EntrySetJob (entry, job);
    EntrySetInputNames (entry);
  }
  else 
    job = EntryGetJob (entry);
  IcaSetInputStreamerData (job, (void*)entry);
  IcaJobNext (job);
  return entry;
}


/**api* function **************************************************************
** 
**      Writes an entry record into a buffer which can then be appended to 
**      the IDX file.
**
** 	INPUT:	    address entry-object [R]
**                  address of write buffer (must be allocated) [W]
*/ 

void EntryIdRecordPack (ENTRYv entry, char *buff)
{
  SLBo *lib=EntryGetLib (entry);
  Int4 len;

  _BinPackFip (buff, EntryGetFip (entry, 0));
  _BinPackFip (buff, EntryGetFip (entry, 1));
  _BinPackNum (buff, EntryGetFileX (entry));
  _BinPackFixStr (buff, EntryGetName (entry), LibGetMaxNameLength (lib));
  if ((len=LibGetSaveNameLength (lib))) {
    switch (LibGetSaveNameType (lib)) {
    case LIBxFILE:
      _BinPackFixStr (buff, 
        FileGetName (IcaJobGetFile (EntryGetJob (entry)), "file"), len);
      break;
    case LIBxNAME:
      _BinPackFixStr (buff, 
        FileGetName (IcaJobGetFile (EntryGetJob (entry)), "name"), len);
      break;
    case LIBxPATH:
      _BinPackFixStr (buff, 
        FileGetName (IcaJobGetFile (EntryGetJob (entry)), "path"), len);
      break;
    }
  }  
}

/**api* function **************************************************************
** 
**      Reads an entry record which must be obtained from an IDX file and 
**      translates and stores its contents as attribtutes in the entry 
**      object.
**
** 	INPUT:	    address entry-object [W]
**                  address of write buffer [R]
*/ 

void EntryIdRecordUnpack (ENTRYv entry, char *buff)
{
  SLBo *lib=EntryGetLib (entry);
  Int4 len;

  _BinUnpackFip (buff, entry->fip[0]);
  _BinUnpackFip (buff, entry->fip[1]);
  _BinUnpackNum (buff, entry->fileX[0]);
  _BinUnpackFixStr (buff, entry->entry_nm, LibGetMaxNameLength (lib));
  if (len=LibGetSaveNameLength (lib))
    _BinUnpackFixStr (buff, entry->file_nm, len);
}


/**API* EntryClose ************************************************************
** 
**      Closes an entry object by deleting it. Sets entry pointer
**      to NULL to prevent freeing it a second time.
**
** 	INPUT:	    address of pointer to entry-object [W]
*/ 

void EntryClose (ENTRYo **entry)
{
  if ((*entry)->tokList)
    free ((*entry)->tokList);
  if ((*entry)->tokListDict)
    DictDestroy ((*entry)->tokListDict);
  if (*entry) {
    free(*entry);
    *entry = NULL;
  }
}

void EntryClosePtr (ENTRYo *entry)
{
  free(entry);
}


Fip EntryGetFip (ENTRYo *entry, Int4 index)
{
  return entry->fip[index];
}

Int4 EntryGetFileX (ENTRYo *entry)
{
  return entry->fileX[0];
}



SLBoFIELD *EntryTokenToField (ENTRYo *entry, TOKoLIST *tokList, 
			      TOKoTOKEN *token)
{
  TOKoTOKEN *tok;
  SLBoFIELD *field;
  SLBo      *lib;
  char      tokName[200];
  Int4      c;

  sprintf (tokName, "%s|%s", TokListGetName (tokList), 
	   TokCodeToStr (TokGetCode (tok)));
  lib = EntryGetLib (entry);
  for (c=0; (field=LibNextField (lib, &c));)
    if (SmEqs (tokName, ""))
      return field;
  return NULL;
}

TOKoLIST *EntryNextTokList (ENTRYo *entry, Int4 *c) 
{
  if (*c >= entry->tokListN) {
    *c = 0;
    return NULL;
  }
  else 
    return entry->tokList[(*c)++];
}

/**API* function *************************************************************
** 
** 	Returns the token table with the specified name. This function may
**      initiate the parsing of the entry.
** 
** 	INPUT:	    entry object [W]
**                  name of the token table [R]
** 
** 	RETURNS:    token table object
*/ 

TOKoLIST *EntryGetTokList (ENTRYo *entry, char *name) 
{
  TOKoLIST *tokList, **tokListPtr;
  Iter     i;

  if (!entry->tokListDict) {
    entry->tokListDict = 
      DictCreate (DictCreateClassStrZKey ((KeyAccessor) TokListPtrGetName, 
					  NULL, FALSE));
  }
  tokListPtr = &DictSet (&entry->tokListDict, name, TOKoLIST*);
  tokList = *tokListPtr;
  if (!tokList) {
    tokList = IcaGetTokenList (EntryGetJob (entry), name);
    *tokListPtr = tokList;
    *(_addObj (entry->tokList, entry->tokListN, 
	       entry->tokListAllocN, TOKoLIST*)) = tokList;
  }  
  return tokList;
}


STRv EntryNextFieldToken (ENTRYo *entry, SLBoFIELD **fieldPtr, 
			   Int4 isOnlyActive, Int4 *c)
{
  static TOKoLIST *tokList;
  static Int4     tokC, tokListC;
  TOKoTOKEN *tok;
  SLBoFIELD *field, *tmp;
  SLBo      *lib=EntryGetLib (entry);
  STRv      s=NULL;
  char      *name;
  Int4      k, c2, doPrint=0;

  if (!(*c)++) {
    VarSetInt (EntryGetIcarusVar (entry, "subEntryN"), 
	       IdIsSub (entry->id) ? IdGetSubN (entry->id) : 0);

    /* request all token tables */
    for (k=0; (field = LibNextField (lib, &k));) {
      if (!FieldIs (field, "show") || 
	  (isOnlyActive && !FieldIs (field, "active")))
	continue;
      if (*(name = FieldGetTokListName (field, "field")))
	EntryGetTokList (entry, name);
      if ((tmp = FieldInherits (field)))
	if (*(name = FieldGetTokListName (tmp, "field")))
          /* contents will not be printed */
	  tokList = IcaGetTokenList (EntryGetJob (entry), name);
    }
    tokList = NULL;
    tokListC = 0;
  }
  
  *fieldPtr = NULL;
  while (1) {
    if (tokList && (tok = TokNext (tokList, &tokC))) {
      for (c2=0, doPrint=0; 
	   (field=FieldNextFromToken (lib, tokList, tok, &c2));) {
	if (isOnlyActive && !FieldIs (field, "active"))
	  continue;
	else if (!isOnlyActive || FieldIs (field, "active")) {
	  *fieldPtr = field;
	  doPrint=1;
	  break;
	}
      }      
      if (!isOnlyActive || doPrint) {
	s = TokGetStrv (tokList, tok);
	break;
      }
    }    
    else {
      if ((tokList = EntryNextTokList (entry, &tokListC))) {
	tokC = 0;
      }
      else {
	*c = 0;
	break;
      }
    }
  }
  return s;
}



/**API* EntryPrint ******************************************************
** 
** 	Prints entire entry using the "printField" function (see also
**      EntryPrintFields).
** 
** 	INPUT:	 o  address of entry object [W]
**               o  pointer to user data to be given to print function [R]
**                  (or NULL).
** 
** 	RETURNS:    1 if success
**                  e__filnotok <file name>+
**                  e__badfile <file name>
*/ 

void EntryPrint (ENTRYo *entry, void *data)
{
  SLBoFIELD *field;
  char      *com;
  STRv      s;
  INT4      c, (*print)(char *,...) =
		 (INT4(*)(char *,...)) ParGetFunction ("printField");

  IcaSetTask (EntryGetJob (entry), "hl", ParGetBool ("isHTMLFormat"));
  IcaSetTask (EntryGetJob (entry), "html", ParGetBool ("isHTMLFormat"));
  ParDefBool ("printEntireEntry", 1);

  VarSetStr (EntryGetIcarusVar (entry, "libName"), 
	      SmEdit (LibName (EntryGetLib (entry)), SMxLOWCASE)); 
  for (c=0; (s = EntryNextFieldToken (entry, &field, 0, &c));) {
    if (field && FieldIs (field, "formatted")) {
      if ((com = FieldGetFormatEval (field))) {
	VarSetStrv (EntryGetIcarusVar (entry, "token"), s); 
	IcaEvalInJob (com, EntryGetJob (entry));
      }
    }
    else if (StrLen (s)) {
      print (_Str (s), field, data);
      StrDel (s);
    }
  }
}


/**API* EntryPrintFields ******************************************************
** 
** 	Prints one ore more of the entry's fields using the "printField" 
**      parameter function (prints to STDOUT if not defined).
** 
** 	INPUT:	  o address of entry object [W]
**                o pointer to user data to be given to print function [R]
**                  (or NULL).
** 
** 	RETURNS:    1 if success
**                  e__filnotok <file name>+
**                  e__badfile <file name>
*/ 

INT4 EntryPrintFields (ENTRYo *entry, void *data)
{
  SLBoFIELD *field;
  VARo      *var;
  char      *com;
  STRv      s;
  INT4      c, (*print)(char *,...) =
		 (INT4(*)(char *,...)) ParGetFunction ("printField");

  IcaSetTask (EntryGetJob (entry), "hl", ParGetBool ("isHTMLFormat"));
  IcaSetTask (EntryGetJob (entry), "html", ParGetBool ("isHTMLFormat"));

  LibSetActiveFields (entry->lib);  /** activate fields to be printed */

  VarSetStr (EntryGetIcarusVar (entry, "libName"), 
	      SmEdit (LibName (EntryGetLib (entry)), SMxLOWCASE)); 
  for (c=0; (s = EntryNextFieldToken (entry, &field, TRUE, &c));) {
    if (field && FieldIs (field, "formatted")) {
      if ((com = FieldGetFormatEval (field))) {
	if ((var = EntryGetIcarusVar (entry, "token")))
	  VarSetStrv (var, s);
	IcaEvalInJob (com, EntryGetJob (entry));
      }
    }
    else if (StrLen (s)) {
      print (_Str (s), field, data);
      StrDel (s);
    }
  }
}



/**API* EntryGetField ********************************************************
** 
** 	Retrieves the specfied field from the entries record using the 
**      table token.
**      If the table token for the field is not specified then it selects
**      a table and a printing format itself.
** 
** 	INPUT:	    entry object [W]
**                  field object [R]
**                  address of iteration variable [W] or NULL
** 	        IMPLICIT:
** 
** 	RETURNS:    pointer to the string containing the field
*/ 

STRv EntryGetField (ENTRYo *entry, SLBoFIELD *field, INT4 *c)
{
  static TOKoLIST *tokList;
  SLBoFIELD *tmp;
  TOKoTOKEN *tok;
  STRv      s=NULL;
  char      *tokListName, *name;
  INT4      rv, code, cDummy;

  if (!c)
    c = &cDummy;

  if (!entry->tokList) {
    IcaSetTask (EntryGetJob (entry), "hl", ParGetBool ("isHTMLFormat"));
    IcaSetTask (EntryGetJob (entry), "html", ParGetBool ("isHTMLFormat"));
  } 

  VarSetInt (EntryGetIcarusVar (entry, "subEntryN"), 
	     IdIsSub (entry->id) ? IdGetSubN (entry->id) : 0);

  if (*(tokListName = FieldGetTokListName (field, "table")))
    code = FieldGetTokCode (field, "table");
  else if (*(tokListName = FieldGetTokListName (field, "index"))) {
    code = FieldGetTokCode (field, "index");
    if ((FieldIs (field, "num") || FieldIs (field, "real")) &&
	!FieldGetTableFormat (NULL, field))
      FieldSetTableFormat (field, LIBxRIGHT);
  }
  else { 
    tokListName = FieldGetTokListName (field, "fields");
    code = FieldGetTokCode (field, "fields");
  }  

  /* activate token of inherited field */
  if ((tmp = FieldInherits (field)))
    if (*(name = FieldGetTokListName (tmp, "field")))
      /* contents will not be printed */
      tokList = IcaGetTokenList (EntryGetJob (entry), name);
  tokList = IcaGetTokenList (EntryGetJob (entry), tokListName);
  if ((tok = TokNextWithCode (tokList, code, c)))
    s = TokGetStrv (tokList, tok);
  return s;
}



void EntryViewEntryNamePrint (VIEWo *view, ENTRYo *entry, 
			    Int4 entryNo, Int4 rowN, Int4 isRoot)
{
  TemplPrint (isRoot ? "rootName" : "leafName", EntryGetFullName (entry));
}



/**API* EntryView ************************************************************
**
**      Print a single entry with selected root library
**      fields, links with leaf libraries and prints leaf
**      library entries with selected fields in a tabular format.
**      Needs the "view" from Www?.
**     
**      INPUT:      entry object [W] 
**                  view object [R]
*/

void EntryView (ENTRYo *entry, struct VIEWo *view)
{
  static Int4 entryNum=0;
  SETo         *set;
  IDoENTRY     id;
  ENTRYo       *leafEntry;
  VIEWoLIB     *vlib;
  VIEWoLEAFSET *leaves[50], *leaf;
  INT4         n, i, maxEntryN=1, leafLibsN=0, isTable=ViewIsTable (view);

  if (!view->entryNamePrint) /* improve !!!te*/
    ViewSetEntryNamePrint (view, EntryViewEntryNamePrint);
  ViewTemplateBegin (view);

  /* do the link to the leaf libs and collect the resulting sets */
  for (n=0; (vlib = ViewGetNextLeafLib (view, &n)); ) {
    set = Query (ViewGetLeafQuery (vlib, entry), NULL);
    leaf = (VIEWoLEAFSET *) malloc (sizeof (VIEWoLEAFSET));
    leaf->vlib = vlib;
    leaf->set = set;
    leaf->entryN = set ? SetGetSize (set) : 0;
    if (leaf->entryN > maxEntryN && !ViewLeafIsOnlyEntryN (leaf->vlib)) 
      maxEntryN = leaf->entryN;
    leaves[leafLibsN++] = leaf;
  }
  leaves[leafLibsN] = NULL;

  /* print the root entry */
  for (i=0, vlib=NULL; (vlib = ViewGetNextRootLib (view, &i));) 
    if (EntryGetLib (entry) == vlib->lib)
      break;
  if (isTable)
    EntryViewInTable (entry, view, vlib, ++entryNum, 1, maxEntryN);
  else
    EntryViewInList (entry, view, vlib, ++entryNum, 1);


  /* print the leaf entries */
  if (!maxEntryN)
    TemplPrint ("tail");
  else {
    for (n=1; n <= maxEntryN; n++) { 
      for (i=0; (leaf = leaves[i]); i++) { 
	if (n > leaf->entryN) {
	  if (isTable && n==1) /* no linked entries */
	    EntryEmptyViewInTable (leaf->vlib, maxEntryN);
	  continue;
	}
	if (ViewLeafIsOnlyEntryN (leaf->vlib)) {
	  ViewLeafEntryNPrint (view, leaf, entry, maxEntryN);
	  leaf->entryN = 0; /* prevent printing of more entries from set */
	}
	else {
	  SetGetID (leaf->set, n, &id);
	  leafEntry = EntryOpen (&id);
	  if (isTable)
	    EntryViewInTable (leafEntry, view, leaf->vlib, entryNum, 0, 
			      n==leaf->entryN ? maxEntryN-n+1 : 1);
	  else
	    EntryViewInList (leafEntry, view, leaf->vlib, entryNum, 0);
	  EntryClose (&leafEntry);
	}
      }

      TemplPrint ("tail");
    }
  }
  SetClean (); /* remove temp. sets */
  ViewTemplateEnd (view);
}


/****** WwwViewEntryInTable ***************************************************
**
**      Prints an entry view inside a table.
**     
** 	INPUT:	  entry object [R]
**                view object [R]
**
**      RETURNS:  number of fields printed for the entry
*/

static INT4 EntryViewInTable (ENTRYo *entry, VIEWo *view, VIEWoLIB *vlib,
			      Int4 entryNo, Int4 isRoot, Int4 rowN)
{
  SLBoFIELD *field;
  INT4      k, fieldsN;

  ViewEntryNamePrint (view, entry, entryNo, rowN, isRoot);

  for(k=0, fieldsN=1; (field = ViewGetNextField (vlib, &k)); fieldsN++) {
    TemplWith (ViewGetTemplate (view), "value");
    EntryPrintTableField (entry, field,  
			FieldIs (field, "formatted") ?
			ViewGetFieldFormat (vlib, field) : NULL, rowN);
    TemplEndWith ();
  }
  return fieldsN;
}

/****** EntryEmptyViewInTable ************************************************
**
**      Prints an empty entry inside a table.
**     
** 	INPUT:	  view library object [R]
**                number of rows entry should span [R]
*/

static void EntryEmptyViewInTable (VIEWoLIB *vlib, Int4 rowN)
{
  SLBoFIELD *field;
  INT4      k;

  TemplPrint ("emptyValue", rowN);
  for(k=0; (field = ViewGetNextField (vlib, &k));) 
    TemplPrint ("emptyValue", rowN);

}


void EntryViewPrintEnvelope (ENTRYo *entry, char *option)
{
  if (option[0] == 'h') {/* head */
    switch (entry->lib->form->printFormat) {
    case LIBxTOPICLIST:
      TemplPrint ("$entry.inList.envelope.head.topicList");
      break;
    case LIBxTABLE:
      TemplPrint ("$entry.inList.envelope.head.table");
      break;
    case LIBxTABLE2:
      TemplPrint ("$entry.inList.envelope.head.table2");
      break;
    case LIBxTEXT:
      TemplPrint ("$entry.inList.envelope.head.text");
      break;
    default:
      TemplPrint ("$entry.inList.envelope.head.preformatted");
    }
  }
  else /* tail */
    switch (entry->lib->form->printFormat) {
    case LIBxTOPICLIST:
      TemplPrint ("$entry.inList.envelope.tail.topicList");
      break;
    case LIBxTABLE:
      TemplPrint ("$entry.inList.envelope.tail.table");
      break;
    case LIBxTABLE2:
      TemplPrint ("$entry.inList.envelope.tail.table2");
      break;
    case LIBxTEXT:
      TemplPrint ("$entry.inList.envelope.tail.text");
      break;
    default:
      TemplPrint ("$entry.inList.envelope.tail.preformatted");
    }
}


/****** EntryViewInList ******************************************************
**
**      Prints an entry view inside a list.
**     
** 	INPUT:	  template object [W]
**                entry object [R]
**
*/

static void EntryViewInList (ENTRYo *entry, VIEWo *view, VIEWoLIB *vlib,
			     Int4 entryNo, Int4 isRoot)
{
  LIBoFieldFormat *format;
  SLBoFIELD       *field;
  INT4            k;

  if (ViewIsEntryNamePrinting (view))
    ViewEntryNamePrint (view, entry, entryNo, 1, isRoot);

  ParDefStr ("fieldList", "reset"); 
  for(k=0; (field = ViewGetNextField (vlib, &k));) {
    ParDefStr ("fieldList", LibGetFieldName (field));
    if (FieldIs (field, "formatted")) {
      format = ViewGetFieldFormat (vlib, field);
      LibSelectFieldFormat (field->type, format->name);
    }
  }
  EntryViewPrintEnvelope (entry, "head");
  EntryPrintFields (entry, NULL);
  EntryViewPrintEnvelope (entry, "tail");
  ParDefStr ("fieldList", "reset"); 
}


/****** WwwPrintTableField ****************************************************
**
**      Prints a data field inside a table.
**     
** 	INPUT:	  entry object [R]
**                field object [R]
**                the field format object [R] or NULL 
**                number of rows the cell should span [R}
*/

static void EntryPrintTableField (ENTRYo *entry, SLBoFIELD *field, 
			   LIBoFieldFormat *format, Int4 rowN)
{
  STRv s;
  INT4 c, type, l, k;
  
  if (!(type = FieldGetTableFormat (entry->lib, field)))
    type = LIBxLISTING;

  for (c=0, k=0; (s=EntryGetField (entry, field, &c)) || !k; k++) {
    if (!k) /* must print format here: EntryGetField decides the format! */
      switch (type) {
      case LIBxLEFT:
	TemplPrint ("leftAlign", rowN);
	break;
      case LIBxRIGHT:    
	TemplPrint ("rightAlign", rowN);
	break;
      case LIBxCENTER:
	TemplPrint ("center", rowN);
	break;
      case LIBxLISTING:
	TemplPrint ("listing", rowN);
	break;
      case LIBxPREFORMAT:
	TemplPrint ("preformat", rowN);
	break;
      }
    else 
      TemplPrint ("next");

    if (s) { /* if a token was found */
      if (format) {
	char *com;
	if ((com = format->eval)) {
	  VarSetStrv (EntryGetIcarusVar (entry, "token"), s); 
	  IcaEvalInJob (com, EntryGetJob (entry));
	}
      }
      else {
	StrCutLF (&s);
	TemplPrint ("value", _Str (s));
      }

    }
    else /* print empty token */
      TemplPrint ("empty");
    StrDel (s);
  }  
  TemplPrint ("tail");
}


/**api* EntrySourceName *******************************************************
**  
**  	returns the name of the entry source...is resolved in the following
**      order: the logical name of the flatfile (GCG), the logical name of
**      the whole library, just the library name
**  
**  	INPUT:	    address of entry objcect [R]
**  		    address of output string receiving the source name [W]
**  	        IMPLICIT:
**  
**  	RETURNS: 
*/ 
   
void EntrySourceName (ENTRYo *entry, char *source_nm)
{
  char *name;

  if (*(name = (entry->lib->fil[ entry->fileX[0] ].lnam)) ||
      *(name = entry->lib->lnam[0]) ||
      (name = entry->lib->nam))
    strcpy (source_nm, name);
}

FILEo *EntryGetNextJobFile (ENTRYo *entry, char *name)
{
  
}

/**api* EntryJobFile **********************************************************
**  
**      Opens the file to access access the current entry.
**  
**  	INPUT:	    entry object [R]
**                  symbolic file name [R]
**  
**  	RETURNS:    file object 
**                  NULL: end of input stream
*/ 

static FILEo *EntryJobFile (char *symName, void* data)
{
  ENTRYo      *entry=(ENTRYo*)data;
  SRSoFILTYP  *ft, *ftShares;
  FILEo       **file;
  Int4        ftX, rv, ftXShares;

  if (!(ft=LibGetFileType (EntryGetLib (entry), symName, &ftX)))
    _ErrExit3 (e__objectunknown, "input file type", symName);
 
  file = &entry->file[ftX];
  if (ftShares = LibGetFileTypeSharesFile (entry->lib, ft, &ftXShares)) {
    ft = ftShares;
  }

  /* single file per entry */
  if (LibIsFilePerEntry (entry->lib)) { 
    if (ftShares)
      return entry->file[ftXShares];
    else if (LibOpenEntryFile (EntryGetLib (entry), file, ft, 
			  EntryGetFileName (entry))) 
      return *file;
    else
      return NULL;
  }
  /* entry is in flat file */
  else {
    if (!(*file = LibOpenFlatFile (entry->lib, entry->fileX[ftX], ft, &rv)))
      _ErrExit2 (rv, FileGetName (*file, "full"));
    FileSeek (*file, entry->fip[ftX]);
    return *file;
  }
}




/**api* EntryJobNextFile *****************************************************
**  
**      Opens the next entry file mathing some criterion. To be used only
**      as argument for IcaSetInputStreamer and for databanks where entries 
**      reside in separate files. See also EntryJobFile.
**  
**  	INPUT:	    entry object [R]
**                  symbolic file name [R]
**  
**  	RETURNS:    file object 
**                  NULL: end of input stream
*/ 

FILEo *EntryJobNextFile (char *symName, void* data)
{
  ENTRYo     *entry=(ENTRYo*)data;
  SLBo       *lib=EntryGetLib (entry);
  FILEo      **file;
  SRSoFILTYP *ft, *ftShares;
  Int4       ftX, rv, ftXShares;

  if (!(ft=LibGetFileType (lib, symName, &ftX)))
    _ErrExit3 (e__objectunknown, "input file type", symName);
  file = &entry->file[ftX];

  if (ftShares = LibGetFileTypeSharesFile (lib, ft, &ftXShares))
    ft = ftShares;

  /* single file per entry */
  if (LibIsFilePerEntry (lib)) { 
    if (ftShares) 
      return entry->file[ftXShares];
    else if (LibOpenNextEntryFile (lib, file, ft)) {
      strcpy (entry->entry_nm, FileGetName (*file, "name"));
      return *file;
    }
  }
  /* entry is in flat file */
  else { 
    if (!(rv = LibOpenNextFlatFile (lib, file, ft, &entry->fileX[ftX])))
      return NULL;
    else if (rv == -1)
      _ErrExit2 (e__filnotok, FileGetName (*file, "full"));
    else if (rv == 1)
      return *file;
    else if (rv == 2) {
      _ErrMsg2 (i__processing, FileGetName (*file, "full"));
      FileSetGetFip (*file, 1);
      return *file;
    }
  }
  return NULL;
}



/**API* EntryOpenStream *******************************************************
**  
**      Opens an entry stream. Entries can be read in sequential order with
**      "EntryNext"
**  
**  	INPUT:	    address of library object [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    entry object 
*/ 

ENTRYo *EntryOpenStream (SLBo *lib)
{
  ENTRYo *entry;

  if ((entry = (ENTRYo *) calloc (1, sizeof (ENTRYo))) == NULL)
    _ErrExit2 (e__allocfail, "entry-object");
  if ((entry->id = (IDoENTRY *) calloc (1, sizeof (IDoENTRY))) == NULL)
    _ErrExit2 (e__allocfail, "id-object");

  entry->id->idType = (IDoTYPE*) LibObjByName ("idtype", "Entry-ID");
  entry->lib = lib;
  ParDefNum ("fromSrs", 1); /* turn off debugging in .is file */
  EntrySetJob (entry, IcaCreateJob (lib->form->syntax));
  entry->lib->allEntryCnt=0;
  IcaSetInputStreamer (EntryGetJob (entry), EntryJobNextFile);
  IcaSetInputStreamerData (EntryGetJob (entry), (void*)entry);
  EntrySetInputNames (entry);
  entry->fileX[0] = -1; 
  entry->fileX[1] = -1; 
  return entry;
}


/**API* EntryIsPartBegin ******************************************************
**  
**      Checks if the entry stream opend with EntryOpenStream and processed
**      with EntryNext is currently at a part begin. A part is a subsection of
**      the databank which is independently indexed for a later merge.
**      <BR>
**      In case the databank is not partioned the function returns TRUE only
**      for the first entry.
**  
**  	INPUT:	    address of entry object object [R]
**
**  	RETURNS:    TRUE or FALSE
*/ 

Int4 EntryIsPartBegin (ENTRYo *entry)
{
  SLBo *lib;
  Int4 partSize, rv;
  
  lib = EntryGetLib (entry);
  if (LibIs (lib, "partitioned")) {
    if (partSize = LibGetPartSize (lib))
      rv = !((lib->allEntryCnt-1) % partSize) ? 1 : 0;
  }
  else
    rv = entry->lib->allEntryCnt == 1 ? 1 : 0;

  if (rv)
    entry->partNo++;
  return rv;
}

Int4 EntryGetPartNo (ENTRYo *entry)
{
  return entry->partNo;
}


/**API* EntryNext *************************************************************
** 
** 	Opens next entry in the entry stream (opened by "EntryOpenStream").
** 
** 	INPUT:	    address of entry object [W]
** 		IMPLICIT:
** 
** 	RETURNS:    1 if success
**                  0 if all entries have been accessed
*/ 

INT4 EntryNext (ENTRYo *entry)
{
  ICAoJOB *job=EntryGetJob (entry);

  if (IcaIsInputEnd (job)) {
    IcaEndJob (job);
    return 0;
  }
  IcaJobNext (job);
  if (entry->tokListDict)
    DictClear (&entry->tokListDict);
  entry->tokListN = 0;
  /*
  if (!job->file)
    IcaSetInputFile (job, NULL, NULL);
    */
  entry->lib->allEntryCnt++;
  return 1;
}


/**API* EntryGetName *******************************************************
** 
** 	Returns the plain entry name without the library name prefixed.
** 
** 	INPUT:	    address of entry object [R]
** 
** 	RETURNS:    entry name
*/ 
   
char *EntryGetName (ENTRYo *entry)
{
  return entry->entry_nm;
}

/**API* EntryGetFullName *****************************************************
** 
** 	Returns the full entry name: databank name ':' entry name.
** 
** 	INPUT:	    address of entry object [R]
** 
** 	RETURNS:    address of entry name
*/ 
   
char *EntryGetFullName (ENTRYo *entry)
{
  if (!*entry->full_nm) 
    sprintf (entry->full_nm, "%s:%s", LibName (entry->lib), entry->entry_nm);
  return entry->full_nm;
}

/**api* function **************************************************************
** 
** 	Returns the entry's file name or entry name if it has not been
**      defined.
** 
** 	INPUT:	    address of entry object [R]
** 
** 	RETURNS:    address of entry file name
*/ 
   
static char *EntryGetFileName (ENTRYo *entry)
{
  return *entry->file_nm ? entry->file_nm : entry->entry_nm;
}

/**API* EntryGetGCGName *******************************************************
** 
** 	Returns the full entry name in GCG style.
** 
** 	INPUT:	    address of entry object [R]
** 
** 	RETURNS:    address of entry name
*/ 
   
char *EntryGetGCGName (ENTRYo *entry)
{
  static char name[200];
  char   libName[40];

  EntrySourceName (entry, libName);
  sprintf (name, "%s:%s", libName, EntryGetName (entry));
  return name;
}

/**API* EntryGetLib ***********************************************************
** 
** 	Returns the library object of entry's source databank;
** 
** 	INPUT:	    address of entry object [R]
** 
** 	RETURNS:    library object
*/ 
   
SLBo *EntryGetLib (ENTRYo *entry)
{
  return entry->lib;
}

/**api* function **************************************************************
** 
** 	Returns job object for entry;
** 
** 	INPUT:	    address of entry object [R]
** 
** 	RETURNS:    job object
*/ 
   
ICAoJOB *EntryGetJob (ENTRYo *entry)
{
  SLBo *lib;

  lib = (LibIs (entry->lib, "subentries")) ? 
    LibGetParentLib (entry->lib) : entry->lib;
  return lib->job;
}

/**api* function **************************************************************
** 
** 	Sets a job object for entry.
** 
** 	INPUT:	    entry object [W]
**                  job object [R]
** 
** 	RETURNS:    library object
*/ 
   
static void EntrySetJob (ENTRYo *entry, ICAoJOB *job)
{
  SLBo *lib;

  lib = (LibIs (entry->lib, "subentries")) ? 
    LibGetParentLib (entry->lib) : entry->lib;
  lib->job = job;
}


/**API* function **************************************************************
** 
** 	Returns the subentry number of an entry and 0 if it is not a subentry.
** 
** 	INPUT:	    address of entry object [R]
** 
** 	RETURNS:    0: entry is not a subentry
**                  number greater 0: subentry number
*/ 
   
Int4 EntryGetSubEntryNo (ENTRYo *entry)
{
  return IdIsSub (entry->id) ? IdGetSubN (entry->id) : 0;
}

/**API* EntryGetIcarusVar *****************************************************
** 
** 	Returns an Icarus variable with the specified name that is created
**      during parsing of the entry. Access the value of the variable
**      with VarGetInt, VarGetStrV, VarGetObject etc.
** 
** 	INPUT:	    address of entry object [R]
**                  name of the variable [R]
** 
** 	RETURNS:    a variable object 
*/ 
   
VARo *EntryGetIcarusVar (ENTRYo *entry, char *name)
{
  ICAoJOB *job=EntryGetJob (entry);
  return VarGet (&job->scope, name);
}


/**api* EntryParse ***********************************************************
** 
** 	Forces parsing of the field productions for all file sources of the
**      entry.
** 
** 	INPUT:	    address of entry object [R]
** 
** 	RETURNS:    1: success
**                  0: parsing unsuccessful
*/ 
   
Int4 EntryParse (ENTRYo *entry)
{
  SRSoFILTYP *ft;
  Int4       c, k;

  for (c=0, k=0; (ft=LibNextFileType (EntryGetLib (entry), &c)); k++) {
    IcaGetTokenList (EntryGetJob (entry), LibGetFileTypeTokenTableName (ft));
    entry->fip[k] = 
      VarGetInt (EntryGetIcarusVar (entry, LibGetFileTypeFipName (ft)));
  }

}




/**API* EntryGetId ***********************************************************
** 
** 	Returns the entry's ID object.
** 
** 	INPUT:	    address of entry object [R]
** 
** 	RETURNS:    ID object
*/ 
   
IDoENTRY *EntryGetId (ENTRYo *entry)
{
  return entry->id;
}


/**API* EntryGetAuxInfo *******************************************************
** 
** 	Returns auxilliary information about an entry.
** 
** 	INPUT:	    address of entry object [R]
** 
** 	RETURNS:    buffer object
*/ 
   
SMoBUFF *EntryGetAuxInfo (ENTRYo *entry)
{
  static SMoBUFF *buff=NULL;

  buff = BuffInit (buff, 100);
  LibGetEntryAuxInfo (entry->id->fip, entry->lib, buff);
  return buff;
}


void EntryIopSetFieldFormat (Int4 runTime, STRv fieldName, STRv formatName) 
{
  LIBoFieldFormat *format;
  SRSoFLD         *fieldType;
  Int4            c, k, isFound;

  if (runTime)
    IargGetArgs ("field|set", &fieldName, &formatName);
  if (!StrLen(fieldName) || !StrLen(formatName)) 
    return; /* return if empty strings */

  for (k=0, isFound=0; (fieldType = LibNextFieldType (_Str(fieldName),  &k));){
    for (c=0; (format = LibNextFieldFormat (fieldType, &c));) {
      if (SmEqs (format->name, _Str(formatName))) {
	isFound=1;
	format->isSelected = 1;
      }
      else
	format->isSelected = 0;
    }	
  }
  if (!isFound)
    _ErrExit3 (e__unknownformat, _Str(fieldName), _Str(formatName));
  
  StrDel (fieldName);
  StrDel (formatName);
}

(!StrLen(fieldName) || !StrLen(formatName)) 
    return; /* return if empty strings */

  for (k=0, isFound=0; (fieldType = LibNextFieldType (_Str(fieldName), srs/src/entry.h
**
**    $RCSfile: entry.h,v $
**    $Revision: 1.8 $
**    $Date: 1996/11/20 16:35:57 $
**    $Author: etzold $
**
**    $Locker:  $
**    $State: Exp $
**
**                  SRS V3.0 Copyright by Thure Etzold
**
*/


typedef struct ENTRYo *ENTRYv;

typedef struct VIEWo *dummytointroducestructtagVIEWo;
typedef struct IDoENTRY *dummytointroducestructtagIDoENTRY;
#ifndef _SLBo
typedef struct SLBo *dummytointroducestructtagSLBo;
#endif

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of exported functions
*/

    /* accessing an entry */

ENTRYv EntryOpen (struct IDoENTRY *id);
INT4   EntryOpenText (ENTRYv entry);
INT4   EntryOpenData (ENTRYv entry);
void   EntryClose (ENTRYv *entry);
INT4   EntryBeginSub (ENTRYv entry);
INT4   EntryNextSub (ENTRYv entry);

ENTRYv EntryOpenStream (struct SLBo *lib);
INT4   EntryNext (ENTRYv entry);
struct SLBoFIELD *EntryNextField (ENTRYv entry, 
				   INT4 doLabelRemove, INT4 doNotReadLine);
struct STRo *EntryGetField (ENTRYv entry, struct SLBoFIELD *field, INT4 *c);

    /* printing and parsing entries */

Int4             EntryParse (ENTRYv entry);
struct TOKoLIST *EntryGetTokList (ENTRYv entry, char *name);
void             EntryPrint (ENTRYv entry, void *data);
INT4             EntryPrintFields (ENTRYv entry, void *data);
void             EntryView (ENTRYv entry, struct VIEWo *view);

    /* get entry information */

INT4             EntryIsSub ();
INT4             EntryIsEndLine (ENTRYv entry);
void             EntrySourceName (ENTRYv entry, char *source_nm);
char*            EntryGetFullName (ENTRYv entry);
char*            EntryGetName (ENTRYv entry);
char*            EntryGetGCGName (ENTRYv entry);
struct SLBo*     EntryGetLib (ENTRYv entry);
struct SMoBUFF*  EntryGetAuxInfo (ENTRYv entry);
struct TOKoLIST* EntryGetTokList (ENTRYv entry, char *name);
struct VARo*     EntryGetIcarusVar (ENTRYv entry, char *name);
struct ICAoJOB*  EntryGetJob (ENTRYv entry);
struct IDoENTRY* EntryGetId (ENTRYv entry);
Fip              EntryGetFip (ENTRYv entry, Int4 index);
Int4             EntryGetFileX (ENTRYv entry);
Int4             EntryGetSubEntryNo (ENTRYv entry);

har*            EntryGetGCGName (ENTRYv entry);
struct SLBo*     EntryGetLib (ENTRYv entry);
struct SMoBUFF*  EntryGetAuxInfo (ENTRYv entry);
struct TOKoLIST* EntryGetTokList (ENTRYv entry, char *name);
struct VARo*     EntryGetIcarusVar (ENTRYv entry, char *name);
struct ICAoJOB*  EntryGetJob (ENTRYv entry);
stsrs/src/error.c
#include <stdlib.h>
#include <string.h>

#include "message.h"
#include "futil.h"
#include "sm.h"
#include "toklist.h"
#include "cursor.h"
#include "error.h"

/******* ErrPop ***************************************************
**
*/

static ERRo *ErrPop(ERRoSTACK *errStack)
{
  if(errStack->current > errStack->top)
    return(--errStack->current);
  else
    return(NULL);
}

/******* ErrPush ***************************************************
**
*/

static ERRo *ErrPush(ERRoSTACK *errStack)
{
  if(errStack->current <= errStack->bottom)
    return(errStack->current++);
  else
    return(NULL);
}

/******* ErrNewStack ***************************************************
**
*/
ERRoSTACK  *ErrNewStack()
{
  ERRoSTACK  *errStack;

  if( (errStack = (ERRoSTACK *)malloc(sizeof(ERRoSTACK))) == NULL )
    _ErrExit2 (e__allocfail, "Error object");
  memset(errStack, NULL, sizeof(ERRoSTACK));
  errStack->top = errStack->error;
  errStack->bottom = errStack->error+1-1; /* maxstacksize not needed any more?*/
  errStack->current = errStack->top;

  return(errStack);
}  

/******* ErrErase ***************************************************
**
*/

void *ErrErase(ERRoSTACK *errStack)
{
  errStack->current = errStack->top;
/*   printf("*********** ERASE **********************\n"); */
  return;
}

/******* ErrIsFound ***************************************************
**
*/

INT4 ErrIsFound(ERRoSTACK *errStack, INT4 code)
{
  ERRo *error;

  error = errStack->top;
  while(error <= errStack->current && error->code != code)
    error++;
  error--;
  return(errStack->current != error);
}

/******* ErrThrow ***************************************************
**
*/
void *ErrThrow(ERRoSTACK *errStack, char *pattern, INT4 code)
{
  ERRo *error;
  
  if( (error = ErrPush(errStack)) ) {
    error->pattern = pattern;
    error->code = code;
/*     printf("Throw error now\t\t%s\n", pattern); */
  }
/*   else */
/*     _ErrMsg2 (e__overflowstack, MAXSTACKSIZE); */

  return;
}

/******* ErrCatch ***************************************************
**
*/
ERRo *ErrCatch(ERRoSTACK *errStack, INT4 code)
{
  ERRo *error;

  while( (error = ErrPop(errStack)) && code != error->code)
    ;
  return(error);
}

/******* ErrPrint ***************************************************
**
*/

void *ErrPrint(ERRoSTACK *errStack, char *name, INT4 code)
{
  static char line[ERRxMAXPRINTSIZE+1],
	      dots[ERRxMAXPRINTSIZE+1];

  char *begin,
       *position,
       *ptr;

  INT4  len;
  ERRo *error;

  memset(line, NULL, ERRxMAXPRINTSIZE);
  memset(dots, NULL, ERRxMAXPRINTSIZE);
  begin = CursorGetBegin(Cursor);
  position = CursorGetPtr(Cursor);

  ptr = position;
  len = 0;
  while(ptr > begin && len < ERRxMAXPRINTSIZE/2 && *ptr != '\n') {
    len++;
    ptr--;
  }
  if(*ptr == '\n' && len) {
    ptr++;
    len--;
  }
  if(len) {
    strncpy(line, ptr, len);
    memset(dots, '.', len);
  }  
  strcat(dots, "^");
  ptr = position;
  len = 1;
  while(ptr<position+strlen(position) && len < ERRxMAXPRINTSIZE/2 && *ptr != '\n') {
    len++;
    ptr++;
  }
  if(*ptr == '\n' && len)
    len--;
  if(len)
    strncat(line, position, len);

  if( (error = ErrCatch(errStack, code)) ) {
    printf("Error (%d) to parse production `%s' :\n%s ...\n%s\n",
         error->code, name, line, dots);
    do {
      printf("	|%s|\n", error->pattern);
    } while( error = ErrCatch(errStack, code) );
    printf("	did not succeed to fit.\n");
  }
  return;
}

#ifdef MAIN
/*
 USAGE: cc -g -L /home/srs/srs5/bin/irix -I/home/srs/srs5/src 
        -DSRSINCLUDE=\"srswin.h\" -DMAIN error.c 
*/

static char *Test1 = "1234567890 Test String #1";
static char *Test2 = "1234567890 Test Long Long Long Long Long Long Long Long Long Long Long Long Long Long Long Long  String #2";
static char *Test3 = "\n1234567890 Empty Test String #3";
static char *Test4 = "1234567890\nTest String with NewLine \n Continue #4";

char *ErrStrBegin,
     *ErrStrPtr;

CURSORo *Cursor = NULL;
 
                    /******make SRS happy*****/

char *CursorGetBegin(CURSORo *cursor){ return(ErrStrBegin); }
char *CursorGetPtr(CURSORo *cursor){ return(ErrStrPtr); }
INT4 Message (INT4 i, INT4 j, INT4 k, ...){ printf("Mess: %d %d %d\n",i,j,k); }
FUNC SDL_fnct[1];

main() {

  ERRoSTACK *errStack;

  errStack = ErrNewStack();

  printf("******* Test1 *******\n");
  ErrStrBegin = Test1;
  ErrStrPtr = Test1 + 5;
  ErrErase(errStack);
  ErrThrow(errStack, "err1.1", 1);
  ErrThrow(errStack, "err1.2", 1);
  ErrThrow(errStack, "err1.3", 1);
  ErrThrow(errStack, "err1.4", 1);
  if(ErrIsFound(errStack, 1))
    ErrPrint(errStack, "Dummy", 1);

  printf("******* Test2 *******\n");
  ErrStrBegin = Test2;
  ErrStrPtr = Test2 + 80;
  ErrErase(errStack);
  ErrThrow(errStack, "err2.1", 1);
  ErrThrow(errStack, "err2.2", 2);
  ErrThrow(errStack, "err2.3", 1);
  ErrThrow(errStack, "err2.4", 2);
  ErrPrint(errStack, "Dummy", 2);

  printf("******* Test3 *******\n");
  ErrStrBegin = Test3;
  ErrStrPtr = Test3;
  ErrErase(errStack);
  ErrThrow(errStack, "err3.1", 3);
  ErrThrow(errStack, "err3.2", 1);
  ErrThrow(errStack, "err3.3", 1);
  ErrThrow(errStack, "err3.4", 1);
  ErrPrint(errStack, "Dummy", 3);

  printf("******* Test4 *******\n");
  ErrStrBegin = Test4;
  ErrStrPtr = Test4 + 9;
  ErrErase(errStack);
  ErrThrow(errStack, "err4.1", 1);
  ErrThrow(errStack, "err4.2", 1);
  ErrThrow(errStack, "err4.3", 1);
  ErrThrow(errStack, "err4.4", 4);
  ErrPrint(errStack, "Dummy", 4);

  printf("******* Test5 *******\n");
  ErrStrBegin = Test1;
  ErrStrPtr = Test1+4;
  ErrErase(errStack);
  ErrThrow(errStack, "err4.1", 1);
  ErrThrow(errStack, "err4.2", 1);
  ErrThrow(errStack, "err4.3", 1);
  ErrThrow(errStack, "err4.4", 1);
  if( ErrIsFound(errStack, 5) )
    ErrPrint(errStack, "Dummy", 5);
  else
    printf("No error level 5 was detected\n");
}
#endif
rThrow(errStack, "err4.2", 1);
  ErrThrow(errStack, "err4.3", 1);
  ErrThrow(errStack, "err4.4", 4);
  ErrPrint(errStack, "Dummy", 4);

  printf("******* Test5 *******\n");
  ErrStrBegin = Test1;
  ErrStrPtr = Test1+4;
  ErrErase(errStack);
  ErrThrow(errStack, "err4.1", 1);
  ErrThrow(errStack, "ersrs/src/error.h
**    
**    $RCSfile: error.h,v $
**    $Revision: 1.2 $
**    $Date: 1996/05/06 19:20:33 $
**    $Author: etzold $
**    
**    $Locker:  $ 
**    $State: Exp $
**                  
**                  
**                  Copyright by Thure Etzold
**             
**             Author: Anatoly Ulyanov
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387451
**                     Email: ulyanov@embl-heidelberg.de
**
*/

#define ERRxMAXPRINTSIZE 72

typedef struct ERRo {
  char	*pattern;		/* patternt that does not fit */
  INT4	 code;			/* error code */
} ERRo;

typedef struct ERRoSTACK {

  ERRo  error[1]; /* not needed any more ?  */
  ERRo *top;
  ERRo *bottom;
  ERRo *current;
} ERRoSTACK;

/* prototypes and external */

extern CURSORo *Cursor;

ERRoSTACK  *ErrNewStack();
void       *ErrErase(ERRoSTACK *errStack);
void	   *ErrThrow(ERRoSTACK *errStack, char *pattern, INT4 code);
ERRo       *ErrCatch(ERRoSTACK *errStack, INT4 code);
void       *ErrPrint(ERRoSTACK *errStack, char *name, INT4 code);
INT4        ErrIsFound(ERRoSTACK *errStack, INT4 code);

 ERRo;

typedef struct ERRoSTACK {

  ERRo  error[1]; /* not needed any more ?  */
  ERRo *top;
  ERRo *bottom;
  ERRo *current;
} ERRoSTACK;

/* prototypes and external */

extern CURSORo *Cursor;

ERRoSTACK  *ErrNewStack();
void       *ErrErase(ERRoSTACK *errStack);
void	   *ErrThrow(ERRoSTACK *errStack, char *pattern, INT4 code);
ERRo       *ErrCatch(ERRoSTACK *errStasrs/src/field.c
char field_ID[] = "$Id: field.c,v 1.4 1997/03/03 18:20:30 srs Exp $";
/*
**
**    $RCSfile: field.c,v $
**    $Revision: 1.4 $
**    $Date: 1997/03/03 18:20:30 $
**    $Author: srs $
**
**                  SRS Copyright by Thure Etzold
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: message, file, sm
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include <stdarg.h>
#include <ctype.h>
#include <string.h>

#include "message.h"
#include "futil.h"
#include "sm.h"
#include "strv.h"
#include "toklist.h"
#include "dict.h"
#include "library.h"
#include "field.h"

#define _SRS
#define _SLB
#include SRSINCLUDE


/**API* function **************************************************************
**
**      supersedes: LibIsField<BR>
** 	Returns 1 if the specified characteristic is true for the specified 
**      data-field.
** 
** 	INPUT:	  o address of field object [R]
**                o type: "index", "ID", "link", "show", "num", "real" 
**                        "doquery", "group", "active", "system"  "subentry" 
**                        "formatted", "header" [R]
** 
** 	RETURNS:    1: specified characteristic is true 
** 		    0: not
*/ 
   
Int4 FieldIs (FIELDv field, char *option)
{
  if (!field)
    return 0;

  switch (_Index (tolower(option[0]), tolower (option[1]))) {
  case _Index('i','n'):  /* index */
    return (field->index == SRSxID || field->index == SRSxKEY ||
            field->index == SRSxNUM || field->index == SRSxREAL) ? 1 : 0;
  case _Index('i','d'):  /* ID */
    return (field->index == SRSxID) ? 1 : 0;
  case _Index('l','i'):  /* link */
    return (field->index == SRSxLINK) ? 1 : 0;
  case _Index('h','e'):  /* header */
    return (field->type->ityp == SRSxHEADER) ? 1 : 0;
  case _Index('s','h'):  /* show */
    return (field->type->isGroup ? 0 : 1);
  case _Index('d','o'):  /* doquery */
    return (field->index == SRSxID || field->index == SRSxKEY ||
            field->index == SRSxNUM || field->index == SRSxREAL ||
            field->type->isGroup) ? 1 : 0;
  case _Index('n', 'u'):  /* num */
    return (field->index == SRSxNUM) ? 1 : 0;
  case _Index('r','e'):  /* real */
    return (field->index == SRSxREAL) ? 1 : 0;
  case _Index('g','r'):  /* group */
    return (field->type->isGroup) ? 1 : 0;
  case _Index('a','c'):  /* active */
    return (ParGetBool (field->type->nam) || field->do_f);
  case _Index('s','y'):  /* system */
    return field->isSystem;
  case _Index('s','u'):  /* subentry */
    return !field->indexId ? 0 : ((field->indexId->siz == 6) ? 1 : 0);
  case _Index('f','o'):  /* formatted */
    return field->type->formatN ? 1 : 0;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
  return 0;
}
 

/**api* function *************************************************************
** 
** 	Returns the name of a the token table that contains the specified 
**      tokens. Use FieldGetTokCode to get their token code.
** 
** 	INPUT:	    field object [R]
**                  option: "fields", "index", "table"
** 	        IMPLICIT:
** 
** 	RETURNS:    name of token table
*/ 

char *FieldGetTokListName (FIELDv field, char *option)
{
  switch (tolower (option[0])) {
  case 'f': /* field */
    if (field->code && *field->code)
      return "fields";
    else
      return field->token;
  case 'i': /* index */
      return field->indexToken[0];
  case 't': /* table */
      return field->tableToken;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
}

/**api* function *************************************************************
** 
**      Use FieldGetTokListName to get the token table name.
** 
** 	INPUT:	    field object [R]
**                  option: "fields", "index", "table"
** 	        IMPLICIT:
** 
** 	RETURNS:    token code
*/ 

Int4 FieldGetTokCode (FIELDv field, char *option)
{
  Int4 k=0;

  switch (tolower (option[0])) {
  case 'f': /* field */
    if (field->fieldTokCode == 0 && *field->code)
      field->fieldTokCode = TokStrToCode (field->code);
    return field->fieldTokCode;
  case 'i': /* index */
      return field->indexTokCode[0];
  case 't': /* table */
      return field->tableTokCode;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
}



/**api* function **************************************************************
**
** 	Returns the format for printing the field inside a table.
** 
** 	INPUT:	  library object [R] or NULL
**                field object [R]
** 
** 	RETURNS:  table print format
*/ 

INT4 FieldGetTableFormat (SLBo *lib, SLBoFIELD *field)
{
  Int4 format;

  if ((format = field->tableFormat)) 
    return format;
  else if (lib && (format = lib->form->tableFormat))
    return format;
  return 0;
}

/**api* function **************************************************************
**
** 	Sets the table printing format for a field.
** 
** 	INPUT:	  field object [W]
**                format code
** 
*/ 

void FieldSetTableFormat (SLBoFIELD *field, Int4 format)
{
  field->tableFormat = format;
}


/**api* function *************************************************************
** 
** 	Returns the name of a data-field. Returns "unknown" if the field
**      name could not be found. See also LibGetFieldTypeName.
** 
** 	INPUT:	    address of field object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    field name
*/ 

char *FieldGetName (FIELDv field)
{
  static char unknown[30] = "unknown field";

  if (field && field->type) {
    if (field->type->ityp == SRSxHEADER)
      return (field->name);
    else 
      return field->type->nam;
  }
  else
    return unknown;
}


/**API* function **************************************************************
** 
** 	Returns the short name of a data-field. 
** 
** 	INPUT:	    address of field object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    short field name
*/ 

char *FieldGetShortName (FIELDv field)
{
  if (field->type->ityp == SRSxHEADER)
    return (field->name);
  else 
    return field->type->shortn;
}

/**API* function **************************************************************
** 
** 	Returns the index type of a field as string.
** 
** 	INPUT:	    address of field object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    field name
**                  NULL
*/ 

char *FieldGetIndexType (FIELDv field)
{
  static char *fieldIType[10]={"", "id", "index", "link", "show",
                                      "tree", "num", "real", "group"};
  return fieldIType[field->index];
}



/**api* function **************************************************************
**
** 	Returns for a field object the object describing its type. See also
**      LibGetFieldType.
**  
** 	INPUT:	    field object [R]
**  
** 	RETURNS:    field type object
*/   

SRSoFLD *FieldGetType (FIELDv field)
{
  return field->type;
}


static int FieldTokenHash (FIELDv field, int max)
{
  UINT4 sum;

  sum = CharHash (FieldGetTokListName (field, "field"));
  _hash (sum, (UINT4) FieldGetTokCode (field, "field"));
  return sum%max;
}

static Int4 FieldTokenEqual (FIELDv a, FIELDv b)
{
  if (SmEqs (FieldGetTokListName (a, "field"),
	     FieldGetTokListName (b, "field")) &&
      FieldGetTokCode (a, "field") == FieldGetTokCode (b, "field"))
    return 1;
  else
    return 0;
}

/**api* function **************************************************************
**
**      Exchanges a "field" token for one or more field objects that match
**      both token table name and code.
**  
** 	INPUT:	    library object [W]
**                  token table from which the token is [R]
**                  token [R]
**  
** 	RETURNS:    field object
*/   

FIELDv FieldNextFromToken (struct SLBo *lib, struct TOKoLIST *tokList, 
			   struct TOKoTOKEN *tok, Int4 *c)
{
  static CLASSoDICT cl={(ValComparer)FieldTokenEqual, 
			(ValHasher)FieldTokenHash, 
			(KeyAccessor)KeyItself, 0, TRUE};
  static Iter   i=NULL;
  SLBoFIELD fieldKey;
  FIELDv *fieldPtr, field;
  Int4   k;

  if (!lib->form->tokenDict) {
    lib->form->tokenDict = DictCreate (&cl);
    for (k=0; (field=LibNextField (lib, &k));) {
      fieldPtr = &DictAdd (&lib->form->tokenDict, field, FIELDv);
      *fieldPtr = field;
    }
  }
  field = NULL;
  fieldKey.fieldTokCode = TokGetCode (tok);
  fieldKey.token = TokListGetName (tokList);
  fieldKey.code = "";

  if (!i || !(*c)++) {
    if (i=DictWith (lib->form->tokenDict, &fieldKey))
      field = DictIn (i, FIELDv);
  }  
  else {
    DictNextWith (lib->form->tokenDict, &fieldKey, &i);
    if (i)
      field = DictIn (i, FIELDv);
    else {
      field = NULL;
      *c = 0;
    }
  }
  return field;
}


/**api* function **************************************************************
**
**      Gets an Icarus eval statement for a field.
**  
** 	INPUT:	    the field object [R]
**  
** 	RETURNS:    string with Icarus statement
*/   

char *FieldGetFormatEval (FIELDv field)
{
  SRSoFLD *fieldType = field->type;
  Int4 k;

  if (!fieldType->formatN)
    return NULL;
  for (k=0; k<fieldType->formatN; k++)
    if (fieldType->format[k].isSelected)
      return fieldType->format[k].eval;
  if (*field->format)
    return (FieldGetFormat (field, field->format))->eval;
  else
    return field->type->format[0].eval; /* first in list is default */
}


/**api* FieldGetFormat ********************************************************
**
** 	Returns the field format object if there is the field has a format with
**      the specified name. if an empty name is specified then the first
**      format in the list is returned (default format).
** 
** 	INPUT:	  address of field object [R]
**                format name (or NULL or empty string) [R]
** 
** 	RETURNS:  data-field format object
*/ 

LIBoFieldFormat *FieldGetFormat (FIELDv field, char *name)
{
  LIBoFieldFormat *format;
  Int4            c;

  for (c=0; (format = LibNextFieldFormat (field->type, &c));)
    if (!name || !*name || SmEqs (format->name, name))
      return format;
  _ErrExit3 (e__objectunknown, "field format", name);
  return NULL;
}

Int4 FieldIsKeyConvert (FIELDv field)
{
  return field->keyConvert;
}

/**api* function **************************************************************
**
** 	Only for fields of subentries. Returns the "parent" field of a field
**      which may be optionally specified.
** 
** 	INPUT:	  address of field object [R]
** 
** 	RETURNS:  parent field object 
**                NULL: not specified
*/ 

FIELDv FieldInherits (FIELDv field)
{
  return field->parent;
}


nknown, "field format", name);
  return NULL;
}

Int4 FieldIsKeyConvert (FIELDv field)
{
  return field->keyConvert;
}

/**api* function **************************************************************
**
** 	Only for fields of subentries. Returns the "parent" field of a field
**      which may be optionally specified.
** 
** 	INPUT:	  address of field object [R]
** 
** 	srs/src/field.h
**
**    $RCSfile: field.h,v $
**    $Revision: 1.5 $
**    $Date: 1997/03/03 18:20:30 $
**    $Author: srs $
**
**
**                  SRS Copyright by Thure Etzold
**
*/

typedef struct SLBoFIELD *FIELDv;

typedef struct TOKoTOKEN *dummytointroducestructtagTOKoTOKENfield;
typedef struct TOKoLIST *dummytointroducestructtagTOKoLISTfield;
typedef struct SLBoFIELD *dummytointroducestructtagSLBoFIELDfield;
typedef struct SLBo *dummytointroducestructtagSLBofield;



  /* get attributes */
Int4      	        FieldIs (FIELDv field, char *option);
char*     	        FieldGetTokListName (FIELDv field, char *option);
char*     	        FieldGetName (FIELDv field);
char*     	        FieldGetShortName (FIELDv field);
char*     	        FieldGetIndexType (FIELDv field);
struct SRSoFLD*         FieldGetType (FIELDv field);
char*                   FieldGetFormatEval (FIELDv field);
struct LIBoFieldFormat* FieldGetFormat (FIELDv field, char *name);
Int4                    FieldIsKeyConvert (FIELDv field);
FIELDv                  FieldInherits (FIELDv field);

  /* iteration */
FIELDv          FieldNextFromToken (struct SLBo *lib, 
				    struct TOKoLIST *tokList, 
				    struct TOKoTOKEN *tok, Int4 *c);


(FIELDv field);
char*     	        FieldGetIndexType (FIELDv field);
struct SRSoFLD*         FieldGetType (FIELDv field);
char*                   FieldGetFormatEval (FIELDv field);
struct LIBoFieldFormat* FieldGetFormat (FIELDv field, char *nasrs/src/futil.c
char file_srs_ID[] = "$Id: futil.c,v 1.19 1997/03/03 18:20:31 srs Exp $";
/*
**
**    $RCSfile: futil.c,v $
**    $Revision: 1.19 $
**    $Date: 1997/03/03 18:20:31 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**        Unix port: This module has been modified in major parts
**                   by Lukas Rosenthaler and Reinhard
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: sm, message 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    contains routines for opening files, testing filenames;
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/


#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <ctype.h>

#include "message.h"
#include "regexp.h"

#ifdef dos
#else
# ifdef VMS
#  include <descrip.h>
#  include <fscndef.h>
#  include <rmsdef.h>
#  include "rtl.h"
# else
#  include <sys/types.h>
#  include <dirent.h>
#  include <unistd.h>
#  include <sys/stat.h>
#  include <fcntl.h>
#  define TMPSTR_LEN 256  
# endif
#endif

#include "futil.h"
#include "sm.h"
#include "strv.h"


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  defining file with variable record length under VMS
*/

#ifdef VMS
#  define VARFILE  , "rat=cr", "rfm=var"
#  define READ  "r"
#else
#  define VARFILE
#  define READ  "rb"
#endif


#ifndef TRUE
#define TRUE 1
#endif

#ifndef FALSE
#define FALSE 0
#endif

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  objectwide variables
*/

#ifndef VMS
static char *FilTranslate (char *, INT4);
char *(*filTranslate)(char *, INT4) = FilTranslate;
static FILEo *FilePipeOpen (FILEo *file);

# define PATH_BUF_LEN 132	/* maximal length of pathname */

/**api* FilTranslate **********************************************************
**
**      called using the macro _FilLN;
**	converts a name containing logicals into the expanded name, works
**      with both VMS and UNIX syntax; overwrites input name!!! and
**      assumes that input character array is large enough to handle output;
**
**	INPUT:	  o address of file name string [W]
**                o TRUE if output should not overwrite input - instead
**                  functions own static array is used - be sure you
**                  don't need output name after next call! [R] 
**
**	RETURNS:    address of translated string - same address as input
*/

static char *FilTranslate (char *fileName, int isTemp)
{
  static int count=0;
  static char tmpNames[5][PATH_BUF_LEN+1], *tmp;
  extern int LogNameTranslate (char *name, char *trans_name, int len);

  tmp = tmpNames[count++%5];

  LogNameTranslate (fileName, tmp, PATH_BUF_LEN);
  if (!isTemp) {
    strcpy (fileName, tmp);
    return fileName;
  }
  else
    return tmp;
}
#endif




/**api* FilOpenR **************************************************************
** 
** 	open file for read access; has the "b" option for opening binary files
** 	under DOS;
** 
** 	INPUT:	    address of file name [R]
** 	      	    address of error code [W] or NULL
**                  e__filnotok <fileName> 
** 	        IMPLICIT:
** 
** 	RETURNS:    file pointer
**              ...NULL if not successfull
*/ 

FILE *FilOpenR (char *fnam, int *errCode)
{
  FILE *fptr;

  if ((fptr = fopen (_FilTempLN (fnam), "rb")) == NULL) {
	_ErrSet (errCode, e__filnotok);
	return NULL;
  }
  rewind (fptr);
  _ErrSet (errCode, 1);
  return fptr;
}

/**api* FilOpenRF *************************************************************
** 
** 	open file for read access; has the "b" option for opening binary files
** 	under DOS + varible record format under VMS;
** 
** 	INPUT:	    address of file name [R]
** 	      	    address of error code [W] or NULL
**                  e__filnotok <fileName> 
** 	        IMPLICIT:
** 
** 	RETURNS:    file pointer
**              ...NULL if not successfull
*/ 

FILE *FilOpenRF (char *fnam, int *errCode)
{
  FILE *fptr;

  if ((fptr = fopen (_FilTempLN (fnam), READ)) == NULL) {
	_ErrSet (errCode, e__filnotok);
	return NULL;
  }
  rewind (fptr);
  _ErrSet (errCode, 1);
  return fptr;
}



/**api* FilOpenWV *************************************************************
**
**	open file in variable record format for write access
**
** 	INPUT:	    address of file name [R]
** 	      	    address of error code [W] or NULL
**                  e__filnotok <fileName> 
** 	        IMPLICIT:
** 
** 	RETURNS:    file pointer
**              ...NULL if not successfull
*/

FILE *FilOpenWV (char *fileName, int *errCode)
{
  FILE *file_d;

  if ((file_d = fopen (_FilTempLN (fileName), "w" VARFILE)) == NULL) {
	_ErrSet (errCode, e__filnotok);
    return NULL;
  }
  rewind (file_d);
  _ErrSet (errCode, 1);
  return file_d;
}



/**api* FilOpenW *************************************************************
**
**	open file for write access
**
** 	INPUT:	    address of file name [R]
** 	      	    address of error code [W] or NULL
**                  e__filnotok <fileName> 
** 	        IMPLICIT:
** 
** 	RETURNS:    file pointer
**              ...NULL if not successfull
*/

FILE *FilOpenW (char *fileName, int *errCode)
{
  FILE *file_d;

  if ((file_d = fopen (_FilTempLN (fileName), "wb+")) == NULL) {
	_ErrSet (errCode, e__filnotok);
    return NULL;
  }
  rewind (file_d);
  _ErrSet (errCode, 1);
  return file_d;
}


/**api* FilOpenU *************************************************************
**
**	open file for write access
**
** 	INPUT:	    address of file name [R]
** 	      	    address of error code [W] or NULL
**                  e__filnotok <fileName> 
** 	        IMPLICIT:
** 
** 	RETURNS:    file pointer
**              ...NULL if not successfull
*/

FILE *FilOpenU (char *fileName, int *errCode)
{
  FILE *file_d;

  if ((file_d = fopen (_FilTempLN (fileName), "r+")) == NULL) {
	_ErrSet (errCode, e__filnotok);
    return NULL;
  }
  fseek (file_d, 0, 2);
  _ErrSet (errCode, 1);
  return file_d;
}


/**api* FilTestW **************************************************************
**
**	tests whether a file can be opened (created) for write access;
**	tests also a directory specification;
**
**	INPUT:	    address of file name [R]
**
**	RETURNS:    	1 if ok
**				e__invalofn <name>
*/

INT4 FilTestW (char *fileName)
{
  FILE *fil;
  char tmpName[FILxXNAM+1], testName[FILxXNAM+1];
  char tmp2Name[256];
    
  strcpy (testName, _FilTempLN (fileName));


  if ((fil = fopen (testName, "w")) == NULL)
    return e__invalofn;
#ifdef VMS
  fgetname (fil, tmpName, 1);			 /* delete correct file */
  fclose( fil);
  if (delete (tmpName) != 0)
    return e__invalofn;
#else
  fclose (fil);
  unlink (testName);
#endif
  if (!FilParse (tmpName, tmp2Name, FILxNAME)) return e__invalofn;
  return 1;
}


/**api* FilTestDirW ***********************************************************
**
**	tests whether a directory can be opened for write access;
**
**	INPUT:	    address of file name [R]
**                 name option: FILxNAME, FILxDEST [R]
**
**	RETURNS:	1 if ok
**				e__invalofn <name>
*/

INT4 FilTestDirW (char *fileName)
{
  FILE *fil;
  char tmpName[FILxXNAM+1], testName[FILxXNAM+1];
  char tmp2Name[256];
    
  if (!FilParse (_FilTempLN (fileName), testName, FILxDEST)) 
    return e__invalofn;
  strcat(testName, "x.x");  /** conv. to ordinary filspec */
  FilParse (testName, tmp2Name, FILxNAME);

  if ((fil = fopen (testName, "w")) == NULL)
    return e__invalofn;
#ifdef VMS
  fgetname (fil, tmpName, 1);			 /* delete correct file */
  fclose( fil);
  if (delete (tmpName) != 0)
    return e__invalofn;
#else
  fclose (fil);
  unlink (testName);
#endif
  if (!FilParse (tmpName, tmp2Name, FILxNAME)) return e__invalofn;
  return 1;
}



/**api* FilTestR **************************************************************
**
**	tests whether a file can be accessed for reading;
**
**	INPUT:	    name of file
**
**	RETURNS:	1 if ok
**				e__invalifn <name>
*/

INT4 FilTestR(char *fileName)
{
  if (access (_FilTempLN (fileName), 4) == EOF)
    return e__invalifn;
  return 1;
}


/**api* FilParse **************************************************************
** 
** 	parses a file name and returns:
** 	FILxNODE, FILxDEV, FILxROOT, FILxDIR, FILxNAME, FILxTYPE, FILxVERS
** 
** 	INPUT:	    address of file name [R]
** 		    address where to put part of file name [W]
** 		    type (see above) [R]
** 
** 	RETURNS:    1 if successful
** 		    0 if specified part was not found	
*/

INT4 FilParse(char *innam, char *outnam, INT4 typ)
{
#ifdef VMS
  struct itemdesc {
    unsigned short len;
    unsigned short code;
    char *item;
  } itemd[8];
  INT4 k, ret, len;

  itemd[FILxNODE].code = FSCN$_NODE; 
  itemd[FILxDEV].code  = FSCN$_DEVICE; 
  itemd[FILxROOT].code = FSCN$_ROOT; 
  itemd[FILxDIR].code  = FSCN$_DIRECTORY; 
  itemd[FILxNAME].code = FSCN$_NAME; 
  itemd[FILxTYPE].code = FSCN$_TYPE; 
  itemd[FILxVERS].code = FSCN$_VERSION; 
  itemd[7].len	= 0; /* longword at end of list = 0 */
  itemd[7].code	= 0; 

  ret = sys$filescan (
	      _Psi(innam), 
	      itemd, 0); 
  _StopIfEven(ret);

  if (typ == FILxDEST) {
    for (k = FILxDEV;  k <= FILxNAME && itemd[k].item == NULL; k++)
      ;
    if (k == FILxNAME) return 0;	    
    len = itemd[FILxDEV].len + itemd[FILxROOT].len + itemd[FILxDIR].len;    
    strncpy(outnam, itemd[k].item, len);
  }
  else if (typ == FILxSPEC) {
    for (k = FILxNAME;  k <= FILxVERS && itemd[k].item == NULL; k++)
      ;
    if (k == FILxVERS) return 0;	    
    len = itemd[FILxNAME].len + itemd[FILxTYPE].len;    
    strncpy(outnam, itemd[k].item, len);
    
  }
  else {
    if (itemd[typ].item == NULL) return 0;
    len = itemd[typ].len;    
    strncpy(outnam, itemd[typ].item, len);    
  }
  outnam[len] = '\0';
#else

#define DIR_LEN 256

  char cwd[DIR_LEN], t_innam[DIR_LEN];
  INT4 i;
    
  strcpy (t_innam, innam);
  (void) getcwd (cwd, DIR_LEN);
  
  switch (typ) {

    /*
    ** return node name only (void on UNIX)
    */

  case FILxNODE : {
    (void) strcpy (outnam, "");
    break;
  }

    /*
    ** return device (void on UNIX)
    */

  case FILxDEV : {
    (void) strcpy (outnam, "");
    break;
  }

    /*
     * return root directory (current working directory on UNIX)
     */
  case FILxROOT : {
    (void) strcpy (outnam, cwd);
    break;
  }

    /*
     * get directory path of file
     */
  case FILxDIR : {
    for (i = strlen (_FilLN (t_innam)) - 1; 
	 (i >= 0) && (t_innam[i] != '/'); i--);
    if (t_innam[0] != '/') {
      /*
       * relative path, add absolute path of current working directory
       */
      strcpy (outnam, cwd);
      strcat (outnam, "/");
      if (i > 0) 
	strncat (outnam, t_innam, i);
    }
    else {
      /*
       * absolute path
       */
      (void) strncpy (outnam, t_innam, i);
      outnam[i] = '\0';
    }
    break;
  }
    
    /*
     * return filename only without extension
     */
  case FILxNAME : {
    for (i = strlen (t_innam) - 1; (i >= 0) && !strchr ("/:", t_innam[i]); i--)
      ;
    strcpy (outnam, &(t_innam[i+1]));
    for (i = strlen (outnam) - 1; (i >= 0) && (outnam[i] != '.'); i--);
    outnam[i] = '\0';
    break;
  }
    
    /*
     * return file type (extension of the form file.ext)
     *                                              ^^^
     */
  case FILxTYPE : {
    /*
     * scan file name from tail. If a '.' or a '/' is encountered, stop!
     */
    for (i = strlen (t_innam) - 1;
	 (i >= 0) && (t_innam[i] != '.') && (t_innam[i] != '/'); i--)
      ;
    if ((i <= 0) || (t_innam[i] == '/')) { /* no "file type"... */
      (void) strcpy (outnam, "");
    }
    else {
      (void) strcpy (outnam, &(t_innam[i+1])); /* o.k, "file type" found */
    }
    break;
  }
    
    /*
     * file version (void on UNIX)
     */
  case FILxVERS : {
    (void) strcpy (outnam, "");
    break;
  }
    
    /*
     * full directory path
     */
  case FILxDEST : {
    for (i = strlen (t_innam) - 1; (i >= 0) && (t_innam[i] != '/'); i--)
      ;
    if (t_innam[0] != '/') { /* relative path */
      strcpy (outnam, cwd);
      strcat (outnam, "/");
      if (i > 0) 
	strncat (outnam, t_innam, i - 1);
    }
    else {
      if (i > 1) {
	(void) strncpy (outnam, t_innam, i);
	outnam[i] = '\0';
      }
      else {
	(void) strncpy (outnam, t_innam, 1);
	outnam[1] = '\0';
      }
    }
    break;
  }
    
    /*
     * full file name with extension (but without preceeding directory)
     */
  case FILxSPEC : {
    for (i = strlen (t_innam) - 1; (i >= 0) && (t_innam[i] != '/'); i--);
    if (i >= 0) {
      (void) strcpy (outnam, &(t_innam[i+1]));
    }
    else {
      (void) strcpy (outnam, "");
    }
    break;
  }
  }
#endif
  return 1;
}



/**api* FilReadLn *************************************************************
**
**	reads a line and discards new line character;
**
**	INPUT:	    address of file pointer
**		    address of output string
**		    max number of characters to be read
**
**	RETURNS:	1 if success
**				e__filnotok if not
*/

INT4 FilReadLn(FILE *fil, char *ln, INT4 nchar)
{
    INT4	len;

    if (fgets(ln, nchar, fil) == NULL)               
	return e__filnotok;

    len = strlen(ln);
    if (ln[len-1] == '\n')
	ln[len-1] = '\0';
    return 1;
}


/**api* FilUOpen **************************************************************
** 
** 	opens file for read access and allocates an array that is to hold
** 	the lines read and reads first line
** 
** 	INPUT:	    address of FILo
** 		    address of file name
** 		    max line length
** 		    file type: FILxSTREAM or FILxVAR 
** 
** 	RETURNS	    1 if success
** 		    e__filopenerr <file name>
** 		    e__allocfail 
** 		    e__eof 
** 		    e__filnotok 
** 		    e__ltoolong if line len > max len
** 
*/

INT4 FilUOpen (FILo *file, char *fileName, INT4 len, INT4 ft)
{
  INT4 rv;

  if (ft == FILxVAR) {
    if ((file->fil = fopen (_FilTempLN (fileName), READ)) == NULL)
      return e__filnotok;    
  }
  else
    if ((file->fil = fopen (_FilTempLN (fileName), READ)) == NULL) 
      return e__filopenerr;

  rewind (file->fil); 
  if ((file->ln = malloc(len)) == 0)
    return e__allocfail;
  (void) strcpy (file->nam, _FilTempLN (fileName));
  file->n = 0;
  file->len = len;
  file->eof = FALSE;
  file->c_s = 0;
  file->isPipe = 0;

  /*
  ** read first line of file...if that fails free the buffer for the
  ** current line and return error
  */

  rv = FilURead (file);  /* read first line */
  _ErrIf (rv)
    free (file->ln);
  return rv;
}


/**api* FilUOpenPipe **********************************************************
** 
** 	opens a pipe for read access and allocates an array that is to hold
** 	the lines read and reads first line
** 
** 	INPUT:	    address of FILo
** 		    address of file name
** 		    max line length
** 		    file type: FILxSTREAM or FILxVAR 
** 
** 	RETURNS	    1 if success
** 		    e__filopenerr <file name>
** 		    e__allocfail 
** 		    e__eof 
** 		    e__filnotok 
** 		    e__ltoolong if line len > max len
** 
*/

INT4 FilUOpenPipe (FILo *file, char *fileName, char *comFormat, INT4 maxLen)
{
  INT4 rv;
  char com[500];

  sprintf (com, comFormat, _FilTempLN (fileName));

#ifndef VMS
  if (!(file->fil = popen (com , "r")))
    return e__filopenerr;
#endif
  if ((file->ln = malloc (maxLen)) == 0)
    return e__allocfail;
  (void) strcpy (file->nam, _FilTempLN (fileName));

  file->n = 0;
  file->len = maxLen;
  file->eof = FALSE;
  file->c_s = 0;
  file->isPipe = 1;

  /*
  ** read first line of file...if that fails free the buffer for the
  ** current line and return error
  */

  rv = FilURead (file);  /* read first line */
  _ErrIf (rv)
    free (file->ln);
  return rv;
}


/**api* FilUOpen2 *************************************************************
** 
**      should become obsolete!
**      Allocates file-descriptor,
** 	opens file for read access and allocates an array that is to hold
** 	the lines read and reads first line
** 
** 
** 	INPUT:	    address of pointer to FILo [W]
** 		    address of file name [R]
** 		    max line length [R]
** 		    file type: FILxSTREAM or FILxVAR  [R]
** 
** 	RETURNS	    1 if success
** 		    e__filopenerr <file name>
** 		    e__allocfail 
** 		    e__eof 
** 		    e__filnotok 
** 		    e__ltoolong if line len > max len
** 
*/

INT4 FilUOpen2 (FILo **file_p, char *fileName, INT4 len, INT4 ft)
{
  FILo *file;
  INT4  rv;

  if ((file = malloc (sizeof (FILo))) == 0) {
    return e__allocfail;
  }

  if (ft == FILxVAR) {
    if ((file->fil = fopen (_FilTempLN (fileName), READ)) == NULL)
      return e__filnotok;    
  }
  else
    if ((file->fil = fopen (_FilTempLN (fileName), READ)) == NULL) {
      free (file);
      return e__filopenerr;
    }
  rewind (file->fil);
  if ((file->ln = malloc(len)) == 0)
    return e__allocfail;
  (void) strcpy (file->nam, fileName);

  file->n = 0;
  file->len = len;
  file->eof = FALSE;
  file->svn = 0;
  file->c_s = '\0';
  file->isPipe = 0;
  *file_p = file;  

  /*
  ** read first line of file...if that fails free the buffer for the
  ** current line and return error
  */

  rv = FilURead (file);  /* read first line */
  _ErrIf (rv)
    free (file->ln);
  return rv;
}


/**api* FilUClose *************************************************************
** 
** 	closes file opened with FilUOpen and frees again the line buffer;
** 
** 	INPUT:	    address of file descr. (FILo)
** 
** 	RETURNS:    1 if ok
** 		    e__freefail <item> +
*/ 
   
INT4 FilUClose (FILo *file)
{
  if (file == NULL) 
    return 1;
  if (file->fil != NULL) {
#ifndef VMS
    if (file->isPipe)
      pclose (file->fil);

    else
#endif
      fclose (file->fil);
    file->fil = NULL;
  }
  
  if (file->ln)
    free (file->ln);
  
  return 1;
}


/**api* FilUClose2 ************************************************************
** 
**      should become obsolete!
**      closes file opened with FilUOpen and frees again the line buffer;
**      frees storage used by FILo;
** 
** 	INPUT:	    address of file descr. (FILo)
** 
** 	RETURNS:    1 if ok
** 		    e__freefail <item> +
*/ 
   
INT4 FilUClose2 (FILo *file)
{
  if (file == NULL) return 1;
    if (file->fil != NULL)
	fclose (file->fil);
    free (file->ln);
    free (file);
    file = NULL;
    return 1;
}


/**api* FilURead **************************************************************
** 
** 	reads a line in file; input and output ATTRIBUTEs are contained in 
** 	FILo; checks whether read line ends with a '\n' if not
** 	error is reported and f->n is not incremented;
** 
** 	INPUT:	    address of FILo
** 
** 	RETURNS:    e__eof <>
** 		    e__filnotok <>
** 		    e__ltoolong <>
** 		    1 if successful
*/

INT4 FilURead (FILo *f)
{
  INT4 rv = 1;

  f->crfdd = ftell(f->fil);			 /* save file address	    */
  if (fgets(f->ln, f->len, f->fil) == NULL) {
    if (feof(f->fil) != 0) {
      f->eof = TRUE;
      *f->ln = '\n';
      *(f->ln+1) = '\0';
      f->l = f->ln;
      return e__eof;
    }
    return e__filnotok;                    
  }
  /*    if (f->ln[strlen(f->ln) - 1] != '\n') 
	rv =  e__ltoolong; */
  
  f->l = f->ln;
  if (rv == 1) 
    (f->n)++;
  return rv;
}


/**api* FilUSave **************************************************************
** 
** 	saves info about current line + offset so that it can be restored 
** 	again with FilUBack
** 
** 	INPUT:	    address of FILo
** 		    address of FILoL_S
** 
** 	RETURNS:    1
*/

INT4 FilUSave (FILo *f, FILoL_S *svl)
{
    svl->svfdd = f->crfdd;
    svl->svoff = f->l - &(f->ln)[0];
    svl->svn = f->n;
    return 1;
}

/**api* FilUSave2 *************************************************************
** 
**      should be removed again!
** 	saves info about current line + offset so that it can be restored 
** 	again with FilUBack
** 
** 	INPUT:	    address of FILo [W]
** 
** 	RETURNS:    1
*/

INT4 FilUSave2 (FILo *f)
{
    f->svfdd = f->crfdd;
    f->svoff = f->l - &(f->ln)[0];
    f->svn = f->n;
    return 1;
}


/**api* FilUBack **************************************************************
** 
** 	restores line saved by FilUSave - i.e. goes back in the file
** 
** 	INPUT:	    address of FILo
** 		    address of FILoL_S
** 
** 	RETURNS:    1
** 		    e__lnotsaved if info is missing
*/                           

INT4 FilUBack (FILo *f, FILoL_S *svl)
{
  INT4 rv;

  if (svl->svn == 0)
    return e__lnotsaved;
  
  if (svl->svn != f->n) {
    fseek(f->fil, svl->svfdd, 0);
    rv = FilURead(f);
    _ErrRet(rv);
    f->n = svl->svn;    
  }
  
  f->l = f->ln + svl->svoff;
  return 1;
}



/**api* FilUBack2 *************************************************************
** 
**      should be removed again!
** 	restores line saved by FilUSave - i.e. goes back in the file
** 
** 	INPUT:	    address of FILo
** 
** 	RETURNS:    1
** 		    e__lnotsaved if info is missing
*/                           

INT4 FilUBack2 (FILo *f)
{
  INT4 rv;

  if (f->svn == 0)
    return e__lnotsaved;
  
  if (f->svn != f->n) {
    fseek(f->fil, f->svfdd, 0);
    rv = FilURead(f);
    _ErrRet(rv);
    f->n = f->svn;    
  }
  
  f->l = f->ln + f->svoff;
  return 1;
}


/**api* FilEof ****************************************************************
** 
** 	checks whether end of file has been reached and sets f->eof flag to 
**     FALSE;
** 
** 	INPUT:	    address of FILo
** 
** 	RETURNS:    TRUE (EOF)
** 		    FALSE
*/

INT4 FilEof(FILo *f)
{
    if (f->eof)
    {
	f->eof = FALSE;
	return TRUE;
    }
    return FALSE;
}

#ifndef dos

/**api* FilSearch *************************************************************
** 
** 	returns full specification for a file - if name has a wildcard
** 	then the first is found and context is returned for further calls;
** 
** 	INPUT:	    address of input name [R]
** 		    address of output name [W] or NULL
** 		    address of search context [W]  (0 if first call) or NULL
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if name contains no wildcard
** 		    2 if yes
** 		    0 if no more file found
*/ 
   
INT4 FilSearch (char *wildfileName, char *efileName, UINT4 *c)
#ifdef VMS
{
  char  fileName[FILxXNAM+1];
  UINT4 c2=0;
  INT4  k, rv;

  if (efileName == NULL)
    efileName = fileName;
  if (c == NULL)
    c = &c2;
  
  rv = lib$find_file (
	    _Psi (wildfileName), 
	    _Pso (efileName), 
            c);

  if (rv == RMS$_NMF) {
    lib$find_file_end (
	    c);	
    return 0;
  }
  else if (rv%2 == 0)  /** file not found */
    return 0;    

  for (k=0; efileName[k] != ' '; k++)
    ;	    
  efileName[k] = '\0';
  if (strpbrk (wildfileName, "%*") == NULL)
    return 1;
  else 
    return 2;
}
#else

/*
** UNIX implementation
*/

{
  regexp        *regExp;
  char          dirName[DIR_LEN], fil_str[DIR_LEN], regexp_str[DIR_LEN];
  char          twildfileName[DIR_LEN], tmp_nm[DIR_LEN];
  static char   fileName[FILxXNAM+1];
  static DIR    *dirStream = NULL;
  struct dirent *dirEntry;
  INT4           i;
  
  if (efileName == NULL)
    efileName = fileName;


  strcpy (twildfileName, wildfileName);

  /*
  **  first get the directory part of "twildfileName";
  **  if it is a relative path (does not start with '/') then add the
  **  absolute path of the current working directory
  */
  
  for (i=strlen (_FilLN (twildfileName)) - 1;
       (i >= 0) && (twildfileName[i] != '/'); i--);
  if (twildfileName[0] != '/') {
    (void) getcwd (dirName, DIR_LEN);
    if (i > 0) {
      if ((i - 1) > 0) {
	(void) strcat (dirName, "/");
	(void) strncat (dirName, twildfileName, i);
      }
    }
  }
  else { /** absolute path */
    if (i > 0) {
      (void) strncpy (dirName, twildfileName, i);
      dirName[i] = '\0';
    }
    else {
      (void) strcpy (dirName, "/");
    }
  }
  
  /*
  ** now get file part (including wildcarts a la regexp)
  */
  
  for (i=strlen (twildfileName) - 1; (i >= 0) && (twildfileName[i] != '/'); i--);
  if ((i > 0) || (strpbrk (twildfileName, "?*") != NULL)) {
    (void) strcpy (fil_str, &(twildfileName[i+1]));
  }
  else {
    (void) strcpy (fil_str, twildfileName);  /** used to be "./" ??? */
  }
  
  
  RegWildToRegexp (fil_str, regexp_str, 1);
  regExp = RegComp (regexp_str);
  if (regExp == NULL)
    _ErrRet2 (e__regerror, "regcomp failure");
  
  /* 
  ** open directory, read all file names and compare each name to the
  ** regular expression - if match then construct the complete file name
  ** and return;
  ** 
  */
  
  if (!c || *c == 0) {
    if ((dirStream = opendir (dirName)) == NULL) {
      return (0);
    }
    if (c)
      *c = 1;
  }
  
  while ((dirEntry = readdir (dirStream)) != NULL) {
    strcpy(tmp_nm, dirEntry->d_name);
    if (!RegExec (regExp, tmp_nm)) 
      continue;  /** get next entry */
    
    strcpy (efileName, dirName);  /** construct complete file name */
    if (dirName[strlen (dirName) - 1] != '/') 
      strcat (efileName, "/");
    strcat (efileName, tmp_nm);
    
    if (!c)
      closedir (dirStream);

    return (strpbrk (twildfileName, "?*") == NULL) ? 1 : 2;
  }

  /* no more matching files can be found */

  if (c) 
    *c = 0;
  closedir (dirStream);
  free (regExp);
  return (0); 
}

#endif   
#endif

/**api* FilCutLn **************************************************************
** 
** 	makes a line look shorter as is - line can be restored to full
** 	length by FilRestoreLn - line can be cut at both ends;
** 
** 	INPUT:	    address of file-dsc [W]
** 		    begin of cut line [R] first col=1
** 		    length of cut line [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
**                  0 if beg + length is greater than actual line
**                  e__novalnum <number> +
*/ 
   
INT4 FilCutLn (FILo *file, INT4 beg, INT4 len)
{
  INT4 ln_z;
  
  ln_z = strlen (file->ln);
  if (ln_z < beg)
    _ErrRet2 (e__novalnum, beg);
  
  file->l = &(file->ln[--beg]);
  if (strlen (file->ln) < beg + len)
    return 0;
  
  file->c_sp = &(file->ln[beg+len]);
  file->c_s = *file->c_sp;
  *(file->c_sp) = '\0';
  file->n_s = file->n;
  return 1;
}


/**api* FilUSeek **************************************************************
** 
** 	goes to file address and reads first line; current line number (FILo.n)
**     is set to 0 (-> of no use any more)
** 
** 	INPUT:	    address of file descriptor [W]
**                 file address [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
*/ 
   
INT4 FilUSeek (FILo *file, UINT4 fadd)
{
  if (!file->isPipe) {
    fseek (file->fil, fadd, 0);
    file->n = 0;
    return FilURead (file);
  }
  return 0;
}


/**api* FilRestoreLn **********************************************************
** 
** 	restores cut line to full length line - does not if context (line nr.) 
** 	different.
** 
** 	INPUT:	    address of file->dsc [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if restored
** 		    0 if not
*/ 
   
INT4 FilRestoreLn (FILo *file)
{
    if (file->n != file->n_s)
	return 0;
    *(file->c_sp) = file->c_s;
    file->c_s = 0;
    return 0;
}


/****** FilMsg ****************************************************************
**
**	forms string for error message containg erroneous line + position wher;
**
**	INPUT:	    address of FILo
**
**	RETURNS:    pointer to message string
*/ 
   
char *FilMsg (FILo *file)
{
    static char msgLine[2*MSGxXLN+2];
    char        spacer[MSGxXLN+1];
    INT4 len;

    len = strlen (file->ln) - strlen (file->l);
    SmFill(spacer, len<MSGxXLN?len:MSGxXLN, '.');
    if (len > MSGxXLN)
       file->ln[MSGxXLN]='\0';
    sprintf (msgLine, "%s%s^\n", file->ln, spacer);
    SmEdit (msgLine, SMxDETAB);
    return &msgLine[0];

}


/****** FilChMod **************************************************************
**
**	changes file mod to executable...function ignores second argument...
**  expandable;
**
**	INPUT:	    file name [R]
**              mode specifier [R] ...ignored
**
**	RETURNS:    
*/ 

void FilChMod (char *fileName, char *mode)
{
#ifndef VMS
  chmod (_FilTempLN(fileName), 00744);  /* no need to do that under VMS */
#endif
}


/**API* FilSetTranslate *******************************************************
**
**	Sets a new function for the translation of filenames of the 
**      form "someName:fileName" where "someName" is an environment 
**      variable or a logical name defining a directory location. File
**      names in this format render SRS independent of the different naming 
**      conventions of the operating systems supported.
**      
**
**	INPUT:	  o address of the function to supersede the default 
**                  function [W]
**
**	RETURNS:    
*/ 

void FilSetTranslate (char *(*translate)(char *, INT4))
{
#ifndef vms
  if (translate)
    filTranslate = translate;
#endif
}



/*****************************************************************************/
/*******the better futil starts from here! ***********************************/
/*****************************************************************************/

#define _Index(x,y) ( ((x)-'a'+1) << 5) +((y)-'a'+1)

static void FileInitNames (FILEo *file);


/**api* FileNew ***************************************************************
** 
**      Creates a new file object. Use FileOpen to open the file, FileClose
**      to close it again and FileDelete to delete the object.
**      <BR>The file name is optional and can be also set with FileSetName.
** 
** 	INPUT:	  o the file name (or NULL, stdin/stdout (see FileOpen) will 
**                  be assumed) [R]
** 
** 	RETURNS:    the new file object
** 
*/

FILEo *FileNew (char *fileName)
{
  FILEo *file;

  if (!(file = (FILEo *) calloc (1, sizeof (FILEo))))
    _ErrExit2 (e__allocfail, "file object");
  file->isRead = 1;

  file->fullName = BuffNew (0);
  file->dirName = BuffNew (0);
  file->fileName = BuffNew (0);
  file->extName = BuffNew (0);
  file->name = BuffNew (0);

  file->ln = NULL;
  file->lnMaxLength = 2000;
  file->fd = -1;

  if (fileName)
    BuffCopyString (file->fullName, fileName);

  return file;
}

/**api* FileSetMaxLine ********************************************************
** 
**      Sets the size of the longest line in the file for read operations.
** 
** 	INPUT:	    the file object [W]
**                  the maximum line length [R]
** 
** 	RETURNS:    the file object
** 
*/

FILEo *FileSetMaxLine (FILEo *file, INT4 length)
{
  file->lnMaxLength = length;
  return file;
}

/**api* FileSetName ***********************************************************
** 
**      Sets the entire ("full") or specified part of the name for the file.
**      See also FileGetName.
**
** 	INPUT:	    file object [W]
**                  option: "full", "dir", "file", "name", "ext"
**                  the name [R]
** 
*/

void FileSetName (FILEo *file, char *opt, char *name)
{
  ASSERT (name, "no name specified");

  switch (_Index (tolower(opt[0]), tolower (opt[1]))) {
  case _Index('f','u'):  /* full */
    BuffReset (file->fullName);
    BuffCopyString (file->fullName, name);
    break;
  case _Index('d','i'):  /* dir */
    BuffReset (file->dirName);
    BuffCopyString (file->dirName, name);
    if (BuffMatch (file->dirName, "[^/]$"))
      BuffCopyString (file->dirName, "/");
    break;
  case _Index('f','i'):  /* file */
    BuffReset (file->fileName);
    BuffCopyString (file->fileName, name);
    break;
  case _Index('e','x'):  /* ext */
    BuffReset (file->extName);
    BuffCopyString (file->extName, name);
    break;
  case _Index('n','a'):  /* name */
    BuffReset (file->fileName);
    BuffReset (file->name);
    BuffCopyString (file->name, name);
    break;
  default:
    _ErrExit2 (e__unknownoption, opt);
  }
  file->isNameInit = 0;
}

/**api* FileSetMode ***********************************************************
** 
**      Sets the access mode for the file. The mode is specified as a
**      string with 9 letters for owner, group and world access.
**      The first in a triple must be 'r' (read) followed by 'w' (write) and
**      'x' (execute). Missing characteristics must be indicated by '-'.
**      Eg, "rw-r--r--" or "rwxr-x--x"
**
** 	INPUT:	    the file object [W]
**                  the mode string [R]
** 
*/

void FileSetMode (FILEo *file, char *mode)
{
  strcpy (file->mode, mode);
}


/**api* FileOpen **************************************************************
** 
**      Opens a file described by the file object created by FileNew.
**      The file object can be further described or modified before opening
**      with FileSetName, FileSetUpdate, FileSetWrite, FileSetMaxLine, 
**      FileSetGetFip, FileSetUnixIo, FileSetWrite.
**      If the input file name is not defined, stdin/stdout is assumed depending on the access mode.
** 
** 	INPUT:	    the file object [W]
** 
** 	RETURNS:    the file object 
**                  NULL: if not successful
** 
*/

FILEo *FileOpen (FILEo *file)
{
  char *fileName, *optStr;
  Int4 option;

  if (!file->isNameInit)
    FileInitNames (file);

  FileClose (file); /* in case object is reused */

  if (!file->ln)
    if (!(file->ln = (char *) malloc (file->lnMaxLength+1)))
      _ErrExit2 (e__allocfail, "file line");
  *file->ln = '\0';

  fileName = FileGetName (file, "path");
  if (file->isUnixIo) {
    if (file->isRead && file->isWrite)
      option = O_RDWR;
    else if (file->isWrite) 
      option = O_WRONLY | O_CREAT | O_TRUNC;
    else
      option = O_RDONLY;

    if ((file->fd = open (fileName, option, 0666)) == -1)
      return NULL;
  }
  else if (file->pipeCom) { /* open pipe for reading */
    FilePipeOpen (file);
  }
  else {
    if (!*fileName)
      file->file = file->isWrite ? stdout : stdin;
    else {
      if (file->isRead && file->isWrite)
	optStr = "r+";
      else if (file->isWrite)
	optStr = "w";
      else
	optStr = "r";
      if (!(file->file = fopen (fileName, optStr)))
	return NULL;
    }
  }
  return file;
}


static FILEo *FilePipeOpen (FILEo *file)
{
  STRv com=StrNew ();

  StrPrintf (&com, _Str(file->pipeCom), FileGetName (file, "path"));
  if (!(file->file = popen (_Str (com) , "r"))) {
    StrDel (com);
    return NULL;
  }
  StrDel (com);
  return file;
}


/**api* FileReadLn ************************************************************
** 
** 
** 	INPUT:	    the file object [W]
** 
** 	RETURNS:    the address of the line just read.
** 
*/

char *FileReadLn (FILEo *file)
{
  if (file->doGetFip)
    file->fip = ftell (file->file); 

  if (fgets (file->ln, file->lnMaxLength, file->file) == NULL) {
    if (feof (file->file) != 0) 
      file->isEof = 1;
    *file->ln = '\0';
    return NULL;
  }
  file->lnN++;
  return file->ln;
}

/**api* FileWrite *************************************************************
** 
**      Writes specified number of bytes to the stream.
** 
** 	INPUT:	    the file object [W]
**                  the input buffer [R]
**                  the number of bytes to write [R]
** 
*/

void FileWrite (FILEo *file, char *buff, Int4 nBytes)
{
  Int4 nWriteBytes;

  if (file->isUnixIo)
    write (file->fd, buff, nBytes);
  else 
    nWriteBytes = fwrite (buff, 1, nBytes, file->file);
}


/**api* FileRead **************************************************************
** 
**      Reads specified number of bytes from the stream.
** 
** 	INPUT:	    the file object [W]
**                  the output buffer [W]
**                  the number of bytes to read [R]
** 
** 	RETURNS:    1 if the read operation was successful
**                  0 if at the end of the file
** 
*/

char *FileRead (FILEo *file, char *buff, Int4 nBytes)
{
  Int4 nReadBytes;

  if (file->isUnixIo)
    nReadBytes = read (file->fd, buff, nBytes);
  else 
    nReadBytes = fread (buff, 1, nBytes, file->file);

  if (!nReadBytes)
    file->isEof = 1;
  return file->isEof ? NULL : buff;
}


/**api* FileIsEof *************************************************************
** 
** 
** 	INPUT:	    a
** 
** 	RETURNS:    1 or 0
** 
*/

INT4 FileIsEof (FILEo *file)
{
  return file->isEof;
}

/**api* FileDelete ************************************************************
** 
**      Deletes a file object created with FileNew and closes it if
**      the file object describes a still opened file.
** 
** 	INPUT:	    the file object [W]
** 
** 	RETURNS:    NULL
** 
*/

FILEo *FileDelete (FILEo *file)
{
  if (file->ln)
    free (file->ln);
  BuffDelete (&file->fullName);
  BuffDelete (&file->dirName);
  BuffDelete (&file->fileName);
  FileClose (file);
  free (file);
  return NULL;
}

/**api* FileClose *************************************************************
** 
**      Closes the file but checks first if there is a file to be closed
**      at all.
** 
** 	INPUT:	    file object [W]
*/

void FileClose (FILEo *file)
{
  if (file->isUnixIo) {
    if (!(file->fd == -1)){
      close (file->fd);   
      file->fd = -1;
    }	
  }
  else if (file->file && file->pipeCom) {
    /* consume file - otherwise 'broken pipe' */
    if (!FileIsEof (file))
      while (fgets (file->ln, file->lnMaxLength, file->file)) 
	;
    pclose (file->file);
    file->file = NULL;
  }
  else if (file->file) {
    fclose (file->file);
    file->file = NULL;
  }
  file->lnN = 0;
  file->fip = 0;
  file->fd = -1;
  file->isEof = FALSE;

  if (*file->mode) /* improve !!!te*/
    chmod (FileGetName (file, "path"), 00755);

}

/**api* FileGetLn *************************************************************
** 
**      Returns the most recently read line.
**
** 	INPUT:	    file object [R]
** 
** 	RETURNS:    the current line
*/

char *FileGetLn (FILEo *file)
{
  return file->ln;
}

/**api* FileGetName ***********************************************************
** 
**      Returns the full file name or optionally parses it and returns parts 
**      of it. Use "path" to get the real name where all logical names are
**      translated.
**
** 	INPUT:	    file object [R]
**                  option: "full", "dir", "file", "name", "ext", "path"
** 
** 	RETURNS:    the requested name
*/

char *FileGetName (FILEo *file, char *opt)
{
  if (!file->isNameInit)
    FileInitNames (file);

  switch (_Index (tolower(opt[0]), tolower (opt[1]))) {
  case _Index('f','u'):  /* full */
    return BuffGetPtr (file->fullName);
  case _Index('p','a'):  /* path */
    return _FilTempLN (BuffGetPtr (file->fullName));
  case _Index('d','i'):  /* dir */
    BuffMatch (file->fullName, "^(.+/)[^/]+$");
    return BuffGetMatch (1);
  case _Index('f','i'):  /* file */
    BuffMatch (file->fullName, "^(.+/)?([^/]+)$");
    return BuffGetMatch (2);
  case _Index('e','x'):  /* ext */
    BuffMatch (file->fullName, "^.+/[^\\.]+\\.([^/]+)$");
    return BuffGetMatch (1);
  case _Index('n','a'):  /* name */
    BuffMatch (file->fullName, "^.+/([^\\.]+)\\.[^/]+$");
    return BuffGetMatch (1);
  default:
    _ErrExit2 (e__unknownoption, opt);
    return NULL;
  }
}


/**api* FileGetTime **********************************************************
** 
**      Returns various times (in seconds after 1.jan 1970) for a file 
**      which must have been opened with FileOpen.
**      the "create" time corresponds to the "status change" time returned
**      by fstat.
** 
** 	INPUT:	    the file object [R]
**                  option: "create", "mod", "access".
** 
** 	RETURNS:    the time of specified type
** 
*/

Int4 FileGetTime (FILEo *file, char *option)
{
  struct stat buff;
  Int4        fileNo;
  
  fileNo = fileno (file->file);
  fstat (fileNo, &buff);
  switch (option[0]) {
  case 'c': /* create */
    return buff.st_ctime;
  case 'm': /* mod */
    return buff.st_mtime;
  case 'a': /* access - last access */
    return buff.st_atime;
  default:
    _ErrExit3 (e__novalopt, option, "FileGetTime");
  }
  return 0;
}

/**api* FileGetFile ***********************************************************
** 
**      Returns the 'real' file descriptor as returned by fopen.
**
** 	INPUT:	    the file object [R]
** 
** 	RETURNS:    the stdio ('FILE') file descriptor
** 
*/

FILE *FileGetFile (FILEo *file)
{
  return file->file;
}


/**api* FileGetFileN **********************************************************
** 
**      Returns the number of a file during an iteration with FileNext.
**
** 	INPUT:	    the file object [R]
** 
** 	RETURNS:    the iteration number
** 
*/

INT4 FileGetFileN (FILEo *file)
{
  return file->fileN;
}

/**api* FileGetFileN **********************************************************
** 
**      Returns the number of the last line read from the file.
**
** 	INPUT:	    file object [W]
** 
** 	RETURNS:    the line number
** 
*/

INT4 FileGetLineN (FILEo *file)
{
  return file->lnN;
}


/**api* FileGetFip ************************************************************
** 
**      Returns the file pointer to the position in the file BEFORE the
**      last line read. 
** 
** 	INPUT:	    file object
** 
** 	RETURNS:    the current file pointer
** 
*/

FIP FileGetFip (FILEo *file)
{
  return file->fip;
}


/**api* FileSetPipe ***********************************************************
** 
**      Sets a command to be opened as a pipe. The command must have up
**      to three "%s" wherever the file name should be inserted.
** 
** 	INPUT:	    file object [W]
**                  the pipe command [R]
** 
*/

void FileSetPipe (FILEo *file, char *command)
{
  if (!file->pipeCom)
    file->pipeCom = StrNew ();
  StrSetS (&file->pipeCom, command);
}


/**api* FileSetGetFip *********************************************************
** 
**      Selects whether the file pointer should be memorized after each
**      reading a line from the file.
** 
** 	INPUT:	    file object [W]
**                  true or false [R]
** 
*/

void FileSetGetFip (FILEo *file, INT4 flag)
{
  if (file && !file->pipeCom)
    file->doGetFip = flag;
}

/**api* FileSetWrite **********************************************************
** 
**      Selects write access for the file.
** 
** 	INPUT:	    file object [W]
** 
**      RETURNS:    the file object
*/

FILEo *FileSetWrite (FILEo *file)
{
  file->isRead = 0;
  file->isWrite = 1;
  return file;
}

/**api* FileSetUpdate *********************************************************
** 
**      Selects "update" access for the file.
** 
** 	INPUT:	    file object [W]
** 
**      RETURNS:    the file object
*/

FILEo *FileSetUpdate (FILEo *file)
{
  file->isRead = 1;
  file->isWrite = 1;
  return file;
}

/**api* FileSetUnixIo *********************************************************
** 
**      Selects the file to be opened with UNIX/IO functions.
** 
** 	INPUT:	    file object [W]
** 
**      RETURNS:    the file object
*/

FILEo *FileSetUnixIo (FILEo *file)
{
  file->isUnixIo = 1;
  return file;
}


/**api* FileNext **************************************************************
** 
**      Opens the next file that matches a file name that may
**      contain '*' and '?' as wildcards.
** 
** 	INPUT:	    the file object [W}
** 
** 	RETURNS:    the number of the file found 
**                  0: no more files found
*/

INT4 FileNext (FILEo *file)
{
  struct dirent *dirEntry;
  char          reStr[512], *tmp;

  if (file->fileN && !file->isWildFile)
    return 0;

  if (!file->isNameInit) {
    FileInitNames (file);
    if (file->regExp) {
      free (file->regExp); file->regExp = NULL;
    }
    BuffReset (file->dirName);
    BuffCopyString (file->dirName, FileGetName (file, "dir"));
    BuffReset (file->fileName);
    BuffCopyString (file->fileName, FileGetName (file, "file"));
    if (RegWildToRegexp (BuffGetPtr (file->fileName), reStr, 1)) {
      file->isWildFile = 1;
    }    
  }

  if (!file->regExp && file->isWildFile) {
    file->fileN = 0;
    RegWildToRegexp (BuffGetPtr (file->fileName), reStr, 1);
    if (!(file->regExp = RegComp (reStr))) {
      _ErrMsg2 (e__regerror, "regcomp failure");
      return 0;
    }
    tmp = BuffGetPtr (file->dirName);
    if (!(file->dirStream = opendir (*tmp ? tmp : "./"))) {
      _ErrMsg2 (e__filopenerr, BuffGetPtr (file->dirName));
      return 0;
    }
  }

  if (file->isWildFile) {
    while ((dirEntry = readdir ((DIR *) file->dirStream))) {
      if (!RegExec (file->regExp, dirEntry->d_name))
	continue;
      
      BuffReset (file->fullName);
      BuffPrintF (file->fullName, "%s%s", 
		  BuffGetPtr (file->dirName), dirEntry->d_name);
      
      FileOpen (file);
      return ++file->fileN;
    }
    closedir (file->dirStream);
  }
  else {
    file->fileN = 1;
    if (!FileOpen (file))
      _ErrExit2 (e__filnotok, FileGetName (file, "path"));
    return 1;
  }
  return 0;
}


/****** FileInitNames *********************************************************
** 
** 
** 	INPUT:	    a
** 
** 	RETURNS:    1
** 
*/

static void FileInitNames (FILEo *file)
{
  if (BuffLength (file->dirName)) {
    BuffReset (file->fullName);
    BuffCat (file->fullName, file->dirName);
  }
  if (BuffLength (file->fileName))
    BuffCat (file->fullName, file->fileName);
  else {
    if (BuffLength (file->name))
      BuffCat (file->fullName, file->name);
    if (BuffLength (file->extName)) {
      BuffCopyString (file->fullName, ".");
      BuffCat (file->fullName, file->extName);
    }
  }

  file->isNameInit = 1;
}

/**api* FileSeek **************************************************************
** 
**      Sets the file pointer to file address. 
**      The current line number is set to 0.
** 
** 	INPUT:	    file object [W]
**                  file address relative from file start [R]
** 
** 	RETURNS:    1
** 
*/

void FileSeek (FILEo *file, FIP fip)
{
  if (file->isUnixIo)
    lseek (file->fd, fip, 0);
  else if (!file->pipeCom)
    fseek (file->file, fip, 0);
  file->fip = fip;
  file->ln[0] = '\0';
  file->lnN=0;
  file->isEof = 0;
}

/**api* FileSeekEnd ***********************************************************
** 
** 
** 	INPUT:	    file object [W]
**                  file address relative from file start [R]
** 
** 	RETURNS:    1
** 
*/

void FileSeekEnd (FILEo *file, FIP fip)
{
  if (file->isUnixIo)
    lseek (file->fd, fip, 2);
  else if (!file->pipeCom)
    fseek (file->file, fip, 2);
  file->fip = fip;
  file->ln[0] = '\0';
}

eek (file->file, fip, 0);
  file->fip = fip;
  file->ln[0] = '\0';
  file->lnN=0;
  file->isEof = 0;
}

/**api* FileSeekEnd ***********************************************************
** 
** 
** 	INPUT:	    file object [W]
**                  file address relative from file start [R]
** 
** srs/src/futil.h
**
**    $RCSfile: futil.h,v $
**    $Revision: 1.7 $
**    $Date: 1997/03/03 18:20:32 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
*/



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  different parts of the file name; 
**      DEST = NODE+DEV+ROOT+DIR, SPEC = NAME+TYPE+VERS
*/

enum fil_nametag {FILxNODE=0, FILxDEV, FILxROOT, FILxDIR, FILxNAME,
                  FILxTYPE, FILxVERS, FILxDEST, FILxSPEC};


#define FILxXNAM	132   /* max size of a file name */

#define FILxVAR		1     /* variable record format */
#define FILxSTREAM	2     /* c-stream file */

#define FILxWRITE	1
#define FILxREAD	2



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  macro that calls FilLogicName on UNIX but not on VMS
*/

#ifndef VMS
extern char * (*filTranslate)(char *, INT4);
#  define _FilLN(x) (char *) (*filTranslate) (x, 0)
#  define _FilTempLN(x) (char *) (*filTranslate) (x, 1)
#else
#  define _FilLN(x) x
#  define _FilTempLN(x) x
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  descriptor of a file opened with FilUOpen
*/

typedef struct FILo {
  FILE  *fil;             /* C-lib file descriptor */
  char  nam[FILxXNAM+1];  /* file name */
  char  *ln;              /* current line = line buffer */
  char  *l;               /* read pointer within current line */
  INT4  n;                /* no of lines */
  INT4  len;              /* length of line buffer */
  UINT4 crfdd;            /* current file address */
  char  eof;	          /* flag if eof has been reached */
  char  c_s;              /* saved character at CUT position */
  char  *c_sp;            /* pointer to CUT position */
  INT4  n_s;              /* line no of CUT line */
  UINT4 svfdd;            /* saved file offset of line */
  INT4  svoff;            /* saved offset within saved line */
  INT4  svn;              /* saved line no */
  INT4  isPipe;           /* flag if file was opened as pipe */
} FILo;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  structure to save a read position within a file opened by FilUSave
*/

typedef struct {
  UINT4 svfdd;  /* saved file offset of line */
  INT4  svoff;  /* saved offset within saved line */
  INT4	svn;    /* saved line no */
} FILoL_S;



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of exported functions
*/

FILE *FilOpenW (char *, int *errCode);
FILE *FilOpenU (char *, int *errCode);
FILE *FilOpenR (char *, int *errCode);
FILE *FilOpenRF (char *, int *errCode);
FILE *FilOpenWV (char *, int *errCode);

INT4 FilUOpen (FILo *f, char *fil_nm, INT4 len, INT4 ft);
INT4 FilUOpen2 (FILo **f, char *fil_nm, INT4 len, INT4 ft);
INT4 FilURead (FILo *f);
INT4 FilUSeek (FILo *file, UINT4 fip);
INT4 FilUClose (FILo *f);
INT4 FilUClose2 (FILo *f);
INT4 FilEof(FILo *f);
void FilChMod (char *fileName, char *mode);

INT4 FilSearch (char *wildfil_nm, char *efil_nm, UINT4 *cntxt);
INT4 FilParse (char *innam, char *outnam, INT4 typ);

INT4 FilUSave (FILo *f, FILoL_S *svl);
INT4 FilUSave2 (FILo *f);
INT4 FilUBack (FILo *f, FILoL_S *svl);
INT4 FilUBack2 (FILo *f);

char *FilMsg (FILo *file);
INT4 FilCutLn (FILo *file, INT4 beg, INT4 len);
INT4 FilRestoreLn (FILo *file);

void FilSetTranslate (char *(*translate)(char *, INT4));


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  descriptor of a file opened with FilNew/FilOpen
*/

typedef struct FILEo {
  FILE            *file;            /* C-lib file descriptor */
  Int4            fd;
  struct SMoBUFF  *fullName;
  struct SMoBUFF  *dirName;
  struct SMoBUFF  *fileName;
  struct SMoBUFF  *extName;
  struct SMoBUFF  *name;
  struct STRo     *pipeCom;
  struct regexp   *regExp;
  void            *dirStream;
  char            *ln;              /* line buffer */
  INT4            lnMaxLength;      /* max length of line read from file */
  INT4            lnN;              /* no of lines currently read */
  INT4            fileN;            /* number of file in 'search' context */
  FIP             fip;              /* file address of current line */
  char            isEof;	          /* flag if eof has been reached */
  char            isPipe;           /* flag if file was opened as pipe */
  char            isWildFile;
  char            isNameInit;
  char            isWrite;
  char            isRead;
  char            isUnixIo;
  char            doGetFip;
  char            mode[20];
} FILEo;


    /* create, set and delete files */

FILEo* FileNew (char *fileName);
FILEo* FileOpen (FILEo *file);
void   FileClose (FILEo *file);
FILEo* FileDelete (FILEo *file);
INT4   FileNext (FILEo *file);
 
    /* set characteristics */

FILEo* FileSetWrite (FILEo *file);
FILEo* FileSetUpdate (FILEo *file);
FILEo* FileSetMaxLine (FILEo *file, INT4 length);
void   FileSetPipe (FILEo *file, char *pipeCommand);
void   FileSetName (FILEo *file, char *opt, char *name);
FILEo* FileSetUnixIo (FILEo *file);


    /* read and write and set position */

char*  FileReadLn (FILEo *file);
char*  FileRead (FILEo *file, char *buff, Int4 nBytes);
void   FileWrite (FILEo *file, char *buff, Int4 nBytes);
void   FileSeek (FILEo *file, FIP fip);

    /* get info */

INT4   FileIsEof (FILEo *file);
INT4   FileGetFileN (FILEo *file);
char*  FileGetName (FILEo *file, char *opt);
void   FileSetGetFip (FILEo *file, INT4 flag);
FIP    FileGetFip (FILEo *file);
INT4   FileGetLineN (FILEo *file);
Int4   FileGetTime (FILEo *file, char *option);
FILE*  FileGetFile (FILEo *file);
char*  FileGetLn (FILEo *file);

#ifdef ready
void FileSetTranslate ();
void FileChangeMod ();
#endif
(FILEo *file, char *buff, Int4 nBytes);
void   FileSeek (FILEo *file, FIP fip);

    /* get info */

INT4   FileIsEof (FILEo *file);
INT4   FileGetFileN (FILEo *file);
char*  FileGetName (FILEo *file, char *opt);
void   FileSetGetFip (FILEo *file, INT4 flag);
FIP    FileGetFip (FILEo *file);
INT4   FileGetLsrs/src/gd.c
char gd_ID[] = "$Id: gd.c,v 1.1 1996/05/06 15:16:31 srs Exp $";
/*
**
**    $RCSfile: gd.c,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:16:31 $
**
**    $Locker:  $
**    $State: Exp $
**
**
**    Written by Tom Boutell, 5/94.
**    Copyright 1994, Cold Spring Harbor Labs.
**    Permission granted to use this code in any fashion provided
**    that this notice is retained and any alterations are
**    labeled as such. It is requested, but not required, that
**    you share extensions to this module with us so that we
**    can incorporate them into new versions. 
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**     
**    The original file "gd.c" was modified ...it now contains also gdfontl.c 
**    gdfonts.c and mtables.c by thure etzold, March 10, 1995
*/

#include <malloc.h>
#include <stdio.h>
#include <math.h>
#include <string.h>
#include <stdlib.h>

#include "gd.h"

/* begin of gdfontl.c */

char gdFontLargeData[] = {
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  0,0,1,1,1,0,0,0,
  0,0,1,1,1,0,0,0,
  0,0,1,1,1,0,0,0,
  0,0,1,1,1,0,0,0,
  0,0,1,1,1,0,0,0,
  0,0,1,1,1,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,1,1,1,0,0,0,
  0,0,0,1,0,0,0,0,

  0,1,1,0,1,1,0,0,
  0,1,1,0,1,1,0,0,
  0,0,1,0,0,1,0,0,
  0,0,1,0,0,1,0,0,
  0,1,0,0,1,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  0,0,0,1,0,0,1,0,
  0,0,0,1,0,0,1,0,
  0,0,0,1,0,0,1,0,
  0,1,1,1,1,1,1,1,
  0,0,1,0,0,1,0,0,
  0,0,1,0,0,1,0,0,
  0,0,1,0,0,1,0,0,
  0,0,1,0,0,1,0,0,
  0,0,1,0,0,1,0,0,
  1,1,1,1,1,1,1,0,
  0,1,0,0,1,0,0,0,
  0,1,0,0,1,0,0,0,
  0,1,0,0,1,0,0,0,
  0,1,0,0,1,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,1,0,0,0,0,
  0,0,1,1,1,0,0,0,
  0,1,0,1,0,1,0,0,
  1,0,0,1,0,0,1,0,
  1,0,0,1,0,1,1,0,
  1,0,0,1,0,0,0,0,
  0,1,0,1,0,0,0,0,
  0,0,1,1,1,0,0,0,
  0,0,0,1,0,1,0,0,
  0,0,0,1,0,0,1,0,
  1,1,0,1,0,0,1,0,
  1,0,0,1,0,0,1,0,
  1,0,0,1,0,1,0,0,
  0,1,1,1,1,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,

  0,0,0,0,0,0,1,0,
  0,1,1,0,0,0,1,0,
  1,0,0,1,0,1,0,0,
  1,0,0,1,0,1,0,0,
  1,0,0,1,0,1,0,0,
  1,0,0,1,1,0,0,0,
  0,1,1,0,1,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,1,0,1,1,0,0,
  0,0,1,1,0,0,1,0,
  0,1,0,1,0,0,1,0,
  0,1,0,1,0,0,1,0,
  0,1,0,1,0,0,1,0,
  1,0,0,0,1,1,0,0,
  1,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  0,0,1,1,0,0,0,0,
  0,1,0,0,1,0,0,0,
  0,1,0,0,1,0,0,0,
  0,1,0,0,1,0,0,0,
  0,1,0,1,0,0,0,0,
  0,0,1,0,0,0,0,0,
  0,0,1,0,1,1,1,0,
  0,1,0,1,0,1,0,0,
  0,1,0,1,0,1,0,0,
  1,0,0,1,0,1,0,0,
  1,0,0,0,1,0,0,0,
  1,0,0,0,1,1,0,0,
  0,1,1,1,0,0,1,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  1,1,1,0,0,0,0,0,
  1,1,1,0,0,0,0,0,
  0,0,1,0,0,0,0,0,
  0,0,1,0,0,0,0,0,
  1,1,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,1,0,
  0,0,0,0,0,1,0,0,
  0,0,0,0,1,0,0,0,
  0,0,0,0,1,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,0,1,0,0,0,
  0,0,0,0,1,0,0,0,
  0,0,0,0,0,1,0,0,
  0,0,0,0,0,0,1,0,

  1,0,0,0,0,0,0,0,
  0,1,0,0,0,0,0,0,
  0,0,1,0,0,0,0,0,
  0,0,1,0,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,1,0,0,0,0,0,
  0,0,1,0,0,0,0,0,
  0,1,0,0,0,0,0,0,
  1,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,1,1,1,0,0,0,
  1,0,0,1,0,0,1,0,
  1,1,0,1,0,1,1,0,
  0,0,1,1,1,0,0,0,
  1,1,0,1,0,1,1,0,
  1,0,0,1,0,0,1,0,
  0,0,1,1,1,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  1,1,1,1,1,1,1,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  1,1,1,0,0,0,0,0,
  1,1,1,0,0,0,0,0,
  0,0,1,0,0,0,0,0,
  0,0,1,0,0,0,0,0,
  1,1,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  1,1,1,1,1,1,1,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
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  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  1,1,1,1,1,1,1,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  0,0,0,1,1,1,1,1,
  0,0,0,0,0,0,1,0,
  0,0,0,0,0,0,1,0,
  0,0,0,0,0,0,1,0,
  0,0,0,0,0,0,1,0,
  0,0,0,0,0,0,1,0,
  0,0,0,0,0,0,1,0,
  0,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  0,1,0,0,0,1,0,0,
  0,0,1,1,1,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  1,1,1,0,0,1,1,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,1,0,0,0,
  0,1,0,0,1,0,0,0,
  0,1,1,1,0,0,0,0,
  0,1,0,1,0,0,0,0,
  0,1,0,0,1,0,0,0,
  0,1,0,0,1,0,0,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,0,1,0,
  1,1,1,0,0,0,1,1,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  1,1,1,1,0,0,0,0,
  0,1,0,0,0,0,0,0,
  0,1,0,0,0,0,0,0,
  0,1,0,0,0,0,0,0,
  0,1,0,0,0,0,0,0,
  0,1,0,0,0,0,0,0,
  0,1,0,0,0,0,0,0,
  0,1,0,0,0,0,0,0,
  0,1,0,0,0,0,0,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  1,1,1,1,1,1,1,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  1,0,0,0,0,0,1,0,
  1,1,0,0,0,1,1,0,
  1,0,1,0,1,0,1,0,
  1,0,1,0,1,0,1,0,
  1,0,1,0,1,0,1,0,
  1,0,0,1,0,0,1,0,
  1,0,0,1,0,0,1,0,
  1,0,0,1,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,1,0,0,0,1,1,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  1,0,0,0,0,1,1,1,
  1,1,0,0,0,0,1,0,
  1,0,1,0,0,0,1,0,
  1,0,1,0,0,0,1,0,
  1,0,1,0,0,0,1,0,
  1,0,0,1,0,0,1,0,
  1,0,0,1,0,0,1,0,
  1,0,0,1,0,0,1,0,
  1,0,0,0,1,0,1,0,
  1,0,0,0,1,0,1,0,
  1,0,0,0,1,0,1,0,
  1,0,0,0,0,1,1,0,
  1,1,0,0,0,0,1,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  0,0,1,1,1,0,0,0,
  0,1,0,0,0,1,0,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  0,1,0,0,0,1,0,0,
  0,0,1,1,1,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  1,1,1,1,1,0,0,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,1,0,0,
  0,1,1,1,1,0,0,0,
  0,1,0,0,0,0,0,0,
  0,1,0,0,0,0,0,0,
  0,1,0,0,0,0,0,0,
  0,1,0,0,0,0,0,0,
  1,1,1,1,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  0,0,1,1,1,0,0,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,1,0,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,1,1,1,0,1,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,1,0,0,
  0,0,1,1,1,0,0,0,
  0,0,0,0,1,0,0,0,
  0,0,0,0,0,1,1,0,

  0,0,0,0,0,0,0,0,
  1,1,1,1,1,0,0,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,1,0,0,
  0,1,1,1,1,0,0,0,
  0,1,0,0,1,0,0,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,0,1,0,
  1,1,1,0,0,0,1,1,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  0,0,1,1,0,1,0,0,
  0,1,0,0,1,1,0,0,
  1,0,0,0,0,1,0,0,
  1,0,0,0,0,0,0,0,
  1,0,0,0,0,0,0,0,
  0,1,1,0,0,0,0,0,
  0,0,0,1,1,0,0,0,
  0,0,0,0,0,1,0,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,1,0,0,0,1,0,0,
  1,0,1,1,1,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  1,1,1,1,1,1,1,0,
  1,0,0,1,0,0,1,0,
  1,0,0,1,0,0,1,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,1,1,1,1,1,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  1,1,1,0,0,1,1,1,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,0,1,1,1,1,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  1,1,0,0,0,1,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,1,0,0,
  0,0,1,0,1,0,0,0,
  0,0,1,0,1,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  1,1,0,0,0,1,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,1,0,0,1,0,
  1,0,0,1,0,0,1,0,
  1,0,0,1,0,0,1,0,
  1,0,1,0,1,0,1,0,
  1,0,1,0,1,0,1,0,
  1,0,1,0,1,0,1,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,1,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  1,1,1,0,1,1,1,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,1,0,0,
  0,0,1,0,1,0,0,0,
  0,0,1,0,1,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,1,0,1,0,0,0,
  0,0,1,0,1,0,0,0,
  0,0,1,0,1,0,0,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,1,0,0,
  1,0,0,0,0,0,1,0,
  1,1,0,0,0,1,1,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  1,1,0,0,0,1,1,0,
  1,0,0,0,0,0,1,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,1,0,0,
  0,0,1,0,1,0,0,0,
  0,0,1,0,1,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,1,1,1,1,1,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  1,1,1,1,1,1,1,0,
  1,0,0,0,0,1,0,0,
  1,0,0,0,1,0,0,0,
  0,0,0,0,1,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,1,0,0,0,0,0,
  0,0,1,0,0,0,0,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,1,1,1,1,1,1,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,1,1,1,1,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,1,1,1,0,

  0,0,0,0,0,0,0,0,
  1,0,0,0,0,0,0,0,
  1,0,0,0,0,0,0,0,
  0,1,0,0,0,0,0,0,
  0,1,0,0,0,0,0,0,
  0,0,1,0,0,0,0,0,
  0,0,1,0,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,0,1,0,0,0,
  0,0,0,0,1,0,0,0,
  0,0,0,0,0,1,0,0,
  0,0,0,0,0,1,0,0,
  0,0,0,0,0,0,1,0,
  0,0,0,0,0,0,1,0,
  0,0,0,0,0,0,0,0,

  1,1,1,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,1,0,0,0,0,
  1,1,1,1,0,0,0,0,

  0,0,0,1,0,0,0,0,
  0,0,1,0,1,0,0,0,
  0,1,0,0,0,1,0,0,
  1,0,0,0,0,0,1,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  1,1,1,1,1,1,1,0,

  0,0,1,1,0,0,0,0,
  0,0,1,1,0,0,0,0,
  0,0,1,0,0,0,0,0,
  0,0,1,0,0,0,0,0,
  0,0,0,1,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,1,1,1,1,0,0,
  0,1,0,0,0,0,1,0,
  0,0,0,0,0,0,1,0,
  0,0,1,1,1,1,1,0,
  0,1,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,1,1,0,
  0,1,1,1,1,0,1,1,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  1,1,0,0,0,0,0,0,
  0,1,0,0,0,0,0,0,
  0,1,0,0,0,0,0,0,
  0,1,0,0,0,0,0,0,
  0,1,1,1,1,0,0,0,
  0,1,0,0,0,1,0,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,1,0,0,0,1,0,0,
  0,1,1,1,1,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,
  0,0,1,1,1,0,1,0,
  0,1,0,0,0,1,1,0,
  1,0,0,0,0,0,1,0,
  1,0,0,0,0,0,0,0,
  1,0,0,0,0,0,0,0,
  1,0,0,0,0,0,0,0,
  1,0,0,0,0,0,1,0,
  0,1,0,0,0,0,1,0,
  0,0,1,1,1,1,0,0,
  0,0,0,0,0,0,0,0,
  0,0,0,0,0,0,0,0,

  0,0,0,0,0,0,0,0,
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};

gdFont gdFontLargeRep = {
	96,
	32,
	8,
	16,
	gdFontLargeData
};

gdFontPtr gdFontLarge = &gdFontLargeRep;


/* end of gdfontl.c */

/* begin of gdfonts.c */

char gdFontSmallData[] = {
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  0,0,0,0,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,
  1,0,0,0,1,0,
  0,1,0,1,0,0,
  0,0,1,0,0,0,
  0,1,0,1,0,0,
  1,0,0,0,1,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,

  0,0,0,0,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,
  1,0,0,0,1,0,
  1,0,0,0,1,0,
  1,0,0,0,1,0,
  0,1,0,1,0,0,
  0,0,1,0,0,0,
  0,1,0,0,0,0,
  1,0,0,0,0,0,
  0,0,0,0,0,0,

  0,0,0,0,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,
  1,1,1,1,1,0,
  0,0,0,1,0,0,
  0,1,1,1,0,0,
  0,1,0,0,0,0,
  1,1,1,1,1,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,

  0,0,0,0,0,0,
  0,0,0,0,1,0,
  0,0,0,1,0,0,
  0,0,0,1,0,0,
  0,0,0,1,0,0,
  0,0,1,0,0,0,
  0,0,0,1,0,0,
  0,0,0,1,0,0,
  0,0,0,1,0,0,
  0,0,0,0,1,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,

  0,0,0,0,0,0,
  0,0,1,0,0,0,
  0,0,1,0,0,0,
  0,0,1,0,0,0,
  0,0,1,0,0,0,
  0,0,1,0,0,0,
  0,0,1,0,0,0,
  0,0,1,0,0,0,
  0,0,1,0,0,0,
  0,0,1,0,0,0,
  0,0,1,0,0,0,
  0,0,0,0,0,0,

  0,0,0,0,0,0,
  1,0,0,0,0,0,
  0,1,0,0,0,0,
  0,1,0,0,0,0,
  0,1,0,0,0,0,
  0,0,1,0,0,0,
  0,1,0,0,0,0,
  0,1,0,0,0,0,
  0,1,0,0,0,0,
  1,0,0,0,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,

  0,0,0,0,0,0,
  0,1,1,0,1,0,
  1,0,1,1,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,

  0,0,0,0,0,0,
  0,0,0,0,0,0,
  1,0,0,0,0,0,
  1,0,0,0,0,0,
  1,1,1,1,0,0,
  1,0,0,0,1,0,
  1,0,0,0,1,0,
  1,0,0,0,1,0,
  1,1,1,1,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0,
  0,0,0,0,0,0
};

gdFont gdFontSmallRep = {
	96,
	32,
	6,
	12,
	gdFontSmallData
};

gdFontPtr gdFontSmall = &gdFontSmallRep;

/* end of gdfonts.c */

/* begin of mtables.c */

#define costScale 1024
int cost[] = {
  1024,
  1023,
  1023,
  1022,
  1021,
  1020,
  1018,
  1016,
  1014,
  1011,
  1008,
  1005,
  1001,
  997,
  993,
  989,
  984,
  979,
  973,
  968,
  962,
  955,
  949,
  942,
  935,
  928,
  920,
  912,
  904,
  895,
  886,
  877,
  868,
  858,
  848,
  838,
  828,
  817,
  806,
  795,
  784,
  772,
  760,
  748,
  736,
  724,
  711,
  698,
  685,
  671,
  658,
  644,
  630,
  616,
  601,
  587,
  572,
  557,
  542,
  527,
  512,
  496,
  480,
  464,
  448,
  432,
  416,
  400,
  383,
  366,
  350,
  333,
  316,
  299,
  282,
  265,
  247,
  230,
  212,
  195,
  177,
  160,
  142,
  124,
  107,
  89,
  71,
  53,
  35,
  17,
  0,
  -17,
  -35,
  -53,
  -71,
  -89,
  -107,
  -124,
  -142,
  -160,
  -177,
  -195,
  -212,
  -230,
  -247,
  -265,
  -282,
  -299,
  -316,
  -333,
  -350,
  -366,
  -383,
  -400,
  -416,
  -432,
  -448,
  -464,
  -480,
  -496,
  -512,
  -527,
  -542,
  -557,
  -572,
  -587,
  -601,
  -616,
  -630,
  -644,
  -658,
  -671,
  -685,
  -698,
  -711,
  -724,
  -736,
  -748,
  -760,
  -772,
  -784,
  -795,
  -806,
  -817,
  -828,
  -838,
  -848,
  -858,
  -868,
  -877,
  -886,
  -895,
  -904,
  -912,
  -920,
  -928,
  -935,
  -942,
  -949,
  -955,
  -962,
  -968,
  -973,
  -979,
  -984,
  -989,
  -993,
  -997,
  -1001,
  -1005,
  -1008,
  -1011,
  -1014,
  -1016,
  -1018,
  -1020,
  -1021,
  -1022,
  -1023,
  -1023,
  -1024,
  -1023,
  -1023,
  -1022,
  -1021,
  -1020,
  -1018,
  -1016,
  -1014,
  -1011,
  -1008,
  -1005,
  -1001,
  -997,
  -993,
  -989,
  -984,
  -979,
  -973,
  -968,
  -962,
  -955,
  -949,
  -942,
  -935,
  -928,
  -920,
  -912,
  -904,
  -895,
  -886,
  -877,
  -868,
  -858,
  -848,
  -838,
  -828,
  -817,
  -806,
  -795,
  -784,
  -772,
  -760,
  -748,
  -736,
  -724,
  -711,
  -698,
  -685,
  -671,
  -658,
  -644,
  -630,
  -616,
  -601,
  -587,
  -572,
  -557,
  -542,
  -527,
  -512,
  -496,
  -480,
  -464,
  -448,
  -432,
  -416,
  -400,
  -383,
  -366,
  -350,
  -333,
  -316,
  -299,
  -282,
  -265,
  -247,
  -230,
  -212,
  -195,
  -177,
  -160,
  -142,
  -124,
  -107,
  -89,
  -71,
  -53,
  -35,
  -17,
  0,
  17,
  35,
  53,
  71,
  89,
  107,
  124,
  142,
  160,
  177,
  195,
  212,
  230,
  247,
  265,
  282,
  299,
  316,
  333,
  350,
  366,
  383,
  400,
  416,
  432,
  448,
  464,
  480,
  496,
  512,
  527,
  542,
  557,
  572,
  587,
  601,
  616,
  630,
  644,
  658,
  671,
  685,
  698,
  711,
  724,
  736,
  748,
  760,
  772,
  784,
  795,
  806,
  817,
  828,
  838,
  848,
  858,
  868,
  877,
  886,
  895,
  904,
  912,
  920,
  928,
  935,
  942,
  949,
  955,
  962,
  968,
  973,
  979,
  984,
  989,
  993,
  997,
  1001,
  1005,
  1008,
  1011,
  1014,
  1016,
  1018,
  1020,
  1021,
  1022,
  1023,
  1023
};
#define sintScale 1024
int sint[] = {
  0,
  17,
  35,
  53,
  71,
  89,
  107,
  124,
  142,
  160,
  177,
  195,
  212,
  230,
  247,
  265,
  282,
  299,
  316,
  333,
  350,
  366,
  383,
  400,
  416,
  432,
  448,
  464,
  480,
  496,
  512,
  527,
  542,
  557,
  572,
  587,
  601,
  616,
  630,
  644,
  658,
  671,
  685,
  698,
  711,
  724,
  736,
  748,
  760,
  772,
  784,
  795,
  806,
  817,
  828,
  838,
  848,
  858,
  868,
  877,
  886,
  895,
  904,
  912,
  920,
  928,
  935,
  942,
  949,
  955,
  962,
  968,
  973,
  979,
  984,
  989,
  993,
  997,
  1001,
  1005,
  1008,
  1011,
  1014,
  1016,
  1018,
  1020,
  1021,
  1022,
  1023,
  1023,
  1024,
  1023,
  1023,
  1022,
  1021,
  1020,
  1018,
  1016,
  1014,
  1011,
  1008,
  1005,
  1001,
  997,
  993,
  989,
  984,
  979,
  973,
  968,
  962,
  955,
  949,
  942,
  935,
  928,
  920,
  912,
  904,
  895,
  886,
  877,
  868,
  858,
  848,
  838,
  828,
  817,
  806,
  795,
  784,
  772,
  760,
  748,
  736,
  724,
  711,
  698,
  685,
  671,
  658,
  644,
  630,
  616,
  601,
  587,
  572,
  557,
  542,
  527,
  512,
  496,
  480,
  464,
  448,
  432,
  416,
  400,
  383,
  366,
  350,
  333,
  316,
  299,
  282,
  265,
  247,
  230,
  212,
  195,
  177,
  160,
  142,
  124,
  107,
  89,
  71,
  53,
  35,
  17,
  0,
  -17,
  -35,
  -53,
  -71,
  -89,
  -107,
  -124,
  -142,
  -160,
  -177,
  -195,
  -212,
  -230,
  -247,
  -265,
  -282,
  -299,
  -316,
  -333,
  -350,
  -366,
  -383,
  -400,
  -416,
  -432,
  -448,
  -464,
  -480,
  -496,
  -512,
  -527,
  -542,
  -557,
  -572,
  -587,
  -601,
  -616,
  -630,
  -644,
  -658,
  -671,
  -685,
  -698,
  -711,
  -724,
  -736,
  -748,
  -760,
  -772,
  -784,
  -795,
  -806,
  -817,
  -828,
  -838,
  -848,
  -858,
  -868,
  -877,
  -886,
  -895,
  -904,
  -912,
  -920,
  -928,
  -935,
  -942,
  -949,
  -955,
  -962,
  -968,
  -973,
  -979,
  -984,
  -989,
  -993,
  -997,
  -1001,
  -1005,
  -1008,
  -1011,
  -1014,
  -1016,
  -1018,
  -1020,
  -1021,
  -1022,
  -1023,
  -1023,
  -1024,
  -1023,
  -1023,
  -1022,
  -1021,
  -1020,
  -1018,
  -1016,
  -1014,
  -1011,
  -1008,
  -1005,
  -1001,
  -997,
  -993,
  -989,
  -984,
  -979,
  -973,
  -968,
  -962,
  -955,
  -949,
  -942,
  -935,
  -928,
  -920,
  -912,
  -904,
  -895,
  -886,
  -877,
  -868,
  -858,
  -848,
  -838,
  -828,
  -817,
  -806,
  -795,
  -784,
  -772,
  -760,
  -748,
  -736,
  -724,
  -711,
  -698,
  -685,
  -671,
  -658,
  -644,
  -630,
  -616,
  -601,
  -587,
  -572,
  -557,
  -542,
  -527,
  -512,
  -496,
  -480,
  -464,
  -448,
  -432,
  -416,
  -400,
  -383,
  -366,
  -350,
  -333,
  -316,
  -299,
  -282,
  -265,
  -247,
  -230,
  -212,
  -195,
  -177,
  -160,
  -142,
  -124,
  -107,
  -89,
  -71,
  -53,
  -35,
  -17
};

/* end of mtables.c */

static void gdImageBrushApply(/* gdImagePtr im, int x, int y */);
static void gdImageTileApply(/* gdImagePtr im, int x, int y */);

gdImagePtr gdImageCreate(sx, sy)
	int sx;
	int sy;
{
	int i;
	gdImagePtr im;
	im = (gdImage *) malloc(sizeof(gdImage));
	im->pixels = (unsigned char **) malloc(sizeof(unsigned char *) * sx);
	im->polyInts = 0;
	im->polyAllocated = 0;
	im->brush = 0;
	im->tile = 0;
	im->style = 0;
	for (i=0; (i<sx); i++) {
		im->pixels[i] = (unsigned char *) calloc(
			sy, sizeof(unsigned char));
	}	
	im->sx = sx;
	im->sy = sy;
	im->colorsTotal = 0;
	im->transparent = (-1);
	im->interlace = 0;
	return im;
}

void gdImageDestroy(im)
	gdImagePtr im;
{
	int i;
	for (i=0; (i<im->sx); i++) {
		free(im->pixels[i]);
	}	
	free(im->pixels);
	if (im->polyInts) {
			free(im->polyInts);
	}
	if (im->style) {
		free(im->style);
	}
	free(im);
}

int gdImageColorClosest(im, r, g, b)
	gdImagePtr im;
	int r;
	int g;
	int b; 
{
	int i;
	long rd, gd, bd;
	int ct = (-1);
	long mindist;
	for (i=0; (i<(im->colorsTotal)); i++) {
		long dist;
		if (im->open[i]) {
			continue;
		}
		rd = (im->red[i] - r);	
		gd = (im->green[i] - g);
		bd = (im->blue[i] - b);
		dist = rd * rd + gd * gd + bd * bd;
		if ((i == 0) || (dist < mindist)) {
			mindist = dist;	
			ct = i;
		}
	}
	return ct;
}

int gdImageColorExact(im, r, g, b)
	gdImagePtr im;
	int r;
	int g;
	int b; 
{
	int i;
	for (i=0; (i<(im->colorsTotal)); i++) {
		if (im->open[i]) {
			continue;
		}
		if ((im->red[i] == r) && 
			(im->green[i] == g) &&
			(im->blue[i] == b)) {
			return i;
		}
	}
	return -1;
}

int gdImageColorAllocate(im, r, g, b)
	gdImagePtr im;
	int r;
	int g;
	int b; 
{
	int i;
	int ct = (-1);
	for (i=0; (i<(im->colorsTotal)); i++) {
		if (im->open[i]) {
			ct = i;
			break;
		}
	}	
	if (ct == (-1)) {
		ct = im->colorsTotal;
		if (ct == gdMaxColors) {
			return -1;
		}
		im->colorsTotal++;
	}
	im->red[ct] = r;
	im->green[ct] = g;
	im->blue[ct] = b;
	im->open[ct] = 0;
	return ct;
}

void gdImageColorDeallocate(im, color)
	gdImagePtr im;
	int color;
{
	/* Mark it open. */
	im->open[color] = 1;
}

void gdImageColorTransparent(im, color)
	gdImagePtr im;
	int color;
{
	im->transparent = color;
}

void gdImageSetPixel(im, x, y, color)
	gdImagePtr im;
	int x; 
	int y;
	int color;
{
	int p;
	switch(color) {
		case gdStyled:
		if (!im->style) {
			/* Refuse to draw if no style is set. */
			return;
		} else {
			p = im->style[im->stylePos++];
		}
		if (p != (gdTransparent)) {
			gdImageSetPixel(im, x, y, p);
		}
		im->stylePos = im->stylePos %  im->styleLength;
		break;
		case gdStyledBrushed:
		if (!im->style) {
			/* Refuse to draw if no style is set. */
			return;
		}
		p = im->style[im->stylePos++];
		if ((p != gdTransparent) && (p != 0)) {
			gdImageSetPixel(im, x, y, gdBrushed);
		}
		im->stylePos = im->stylePos %  im->styleLength;
		break;
		case gdBrushed:
		gdImageBrushApply(im, x, y);
		break;
		case gdTiled:
		gdImageTileApply(im, x, y);
		break;
		default:
		if (gdImageBoundsSafe(im, x, y)) {
			 im->pixels[x][y] = color;
		}
		break;
	}
}

static void gdImageBrushApply(im, x, y)
	gdImagePtr im;
	int x;
	int y;
{
	int lx, ly;
	int hy;
	int hx;
	int x1, y1, x2, y2;
	int srcx, srcy;
	if (!im->brush) {
		return;
	}
	hy = gdImageSY(im->brush)/2;
	y1 = y - hy;
	y2 = y1 + gdImageSY(im->brush);	
	hx = gdImageSX(im->brush)/2;
	x1 = x - hx;
	x2 = x1 + gdImageSX(im->brush);
	srcy = 0;
	for (ly = y1; (ly < y2); ly++) {
		srcx = 0;
		for (lx = x1; (lx < x2); lx++) {
			int p;
			p = gdImageGetPixel(im->brush, srcx, srcy);
			/* Allow for non-square brushes! */
			if (p != gdImageGetTransparent(im->brush)) {
				gdImageSetPixel(im, lx, ly,
					im->brushColorMap[p]);
			}
			srcx++;
		}
		srcy++;
	}	
}		

static void gdImageTileApply(im, x, y)
	gdImagePtr im;
	int x;
	int y;
{
	int srcx, srcy;
	int p;
	if (!im->tile) {
		return;
	}
	srcx = x % gdImageSX(im->tile);
	srcy = y % gdImageSY(im->tile);
	p = gdImageGetPixel(im->tile, srcx, srcy);
	/* Allow for transparency */
	if (p != gdImageGetTransparent(im->tile)) {
		gdImageSetPixel(im, x, y,
			im->tileColorMap[p]);
	}
}		

int gdImageGetPixel(im, x, y)
	gdImagePtr im; 
	int x; 
	int y; 
{
	if (gdImageBoundsSafe(im, x, y)) {
		return im->pixels[x][y];
	} else {
		return 0;
	}
}

/* Bresenham as presented in Foley & Van Dam */

void gdImageLine(im, x1, y1, x2, y2, color)
	gdImagePtr im;
	int x1;
	int y1;
	int x2;
	int y2;
	int color; 
{
	int dx, dy, incr1, incr2, d, x, y, xend, yend, xdirflag, ydirflag;
	dx = abs(x2-x1);
	dy = abs(y2-y1);
	if (dy <= dx) {
		d = 2*dy - dx;
		incr1 = 2*dy;
		incr2 = 2 * (dy - dx);
		if (x1 > x2) {
			x = x2;
			y = y2;
			ydirflag = (-1);
			xend = x1;
		} else {
			x = x1;
			y = y1;
			ydirflag = 1;
			xend = x2;
		}
		gdImageSetPixel(im, x, y, color);
		if (((y2 - y1) * ydirflag) > 0) {
			while (x < xend) {
				x++;
				if (d <0) {
					d+=incr1;
				} else {
					y++;
					d+=incr2;
				}
				gdImageSetPixel(im, x, y, color);
			}
		} else {
			while (x < xend) {
				x++;
				if (d <0) {
					d+=incr1;
				} else {
					y--;
					d+=incr2;
				}
				gdImageSetPixel(im, x, y, color);
			}
		}		
	} else {
		d = 2*dx - dy;
		incr1 = 2*dx;
		incr2 = 2 * (dx - dy);
		if (y1 > y2) {
			y = y2;
			x = x2;
			yend = y1;
			xdirflag = (-1);
		} else {
			y = y1;
			x = x1;
			yend = y2;
			xdirflag = 1;
		}
		gdImageSetPixel(im, x, y, color);
		if (((x2 - x1) * xdirflag) > 0) {
			while (y < yend) {
				y++;
				if (d <0) {
					d+=incr1;
				} else {
					x++;
					d+=incr2;
				}
				gdImageSetPixel(im, x, y, color);
			}
		} else {
			while (y < yend) {
				y++;
				if (d <0) {
					d+=incr1;
				} else {
					x--;
					d+=incr2;
				}
				gdImageSetPixel(im, x, y, color);
			}
		}
	}
}

/* As above, plus dashing */

#define dashedSet \
	{ \
		dashStep++; \
		if (dashStep == gdDashSize) { \
			dashStep = 0; \
			on = !on; \
		} \
		if (on) { \
			gdImageSetPixel(im, x, y, color); \
		} \
	}

void gdImageDashedLine(im, x1, y1, x2, y2, color)
	gdImagePtr im;
	int x1;
	int y1;
	int x2;
	int y2;
	int color; 
{
	int dx, dy, incr1, incr2, d, x, y, xend, yend, xdirflag, ydirflag;
	int dashStep = 0;
	int on = 1;
	dx = abs(x2-x1);
	dy = abs(y2-y1);
	if (dy <= dx) {
		d = 2*dy - dx;
		incr1 = 2*dy;
		incr2 = 2 * (dy - dx);
		if (x1 > x2) {
			x = x2;
			y = y2;
			ydirflag = (-1);
			xend = x1;
		} else {
			x = x1;
			y = y1;
			ydirflag = 1;
			xend = x2;
		}
		dashedSet;
		if (((y2 - y1) * ydirflag) > 0) {
			while (x < xend) {
				x++;
				if (d <0) {
					d+=incr1;
				} else {
					y++;
					d+=incr2;
				}
				dashedSet;
			}
		} else {
			while (x < xend) {
				x++;
				if (d <0) {
					d+=incr1;
				} else {
					y--;
					d+=incr2;
				}
				dashedSet;
			}
		}		
	} else {
		d = 2*dx - dy;
		incr1 = 2*dx;
		incr2 = 2 * (dx - dy);
		if (y1 > y2) {
			y = y2;
			x = x2;
			yend = y1;
			xdirflag = (-1);
		} else {
			y = y1;
			x = x1;
			yend = y2;
			xdirflag = 1;
		}
		dashedSet;
		if (((x2 - x1) * xdirflag) > 0) {
			while (y < yend) {
				y++;
				if (d <0) {
					d+=incr1;
				} else {
					x++;
					d+=incr2;
				}
				dashedSet;
			}
		} else {
			while (y < yend) {
				y++;
				if (d <0) {
					d+=incr1;
				} else {
					x--;
					d+=incr2;
				}
				dashedSet;
			}
		}
	}
}

int gdImageBoundsSafe(im, x, y)
	gdImagePtr im;
	int x;
	int y; 
{
	return (!(((y < 0) || (y >= im->sy)) ||
		((x < 0) || (x >= im->sx))));
}

void gdImageChar(im, f, x, y, c, color)
	gdImagePtr im; 
	gdFontPtr f;
	int x;
	int y;
	int c;
	int color;
{
	int cx, cy;
	int px, py;
	int fline;
	cx = 0;
	cy = 0;
	if ((c < f->offset) || (c >= (f->offset + f->nchars))) {
		return;
	}
	fline = (c - f->offset) * f->h * f->w;
	for (py = y; (py < (y + f->h)); py++) {
		for (px = x; (px < (x + f->w)); px++) {
			if (f->data[fline + cy * f->w + cx]) {
				gdImageSetPixel(im, px, py, color);	
			}
			cx++;
		}
		cx = 0;
		cy++;
	}
}

void gdImageCharUp(im, f, x, y, c, color)
	gdImagePtr im; 
	gdFontPtr f;
	int x;
	int y;
	char c;
	int color;
{
	int cx, cy;
	int px, py;
	int fline;
	cx = 0;
	cy = 0;
	if ((c < f->offset) || (c >= (f->offset + f->nchars))) {
		return;
	}
	fline = (c - f->offset) * f->h * f->w;
	for (py = y; (py > (y - f->w)); py--) {
		for (px = x; (px < (x + f->h)); px++) {
			if (f->data[fline + cy * f->w + cx]) {
				gdImageSetPixel(im, px, py, color);	
			}
			cy++;
		}
		cy = 0;
		cx++;
	}
}

void gdImageString(im, f, x, y, s, color)
	gdImagePtr im;
	gdFontPtr f;
	int x;
	int y;
	char *s;
	int color;
{
	int i;
	int l;
	l = strlen(s);
	for (i=0; (i<l); i++) {
		gdImageChar(im, f, x, y, s[i], color);
		x += f->w;
	}
}

void gdImageStringUp(im, f, x, y, s, color)
	gdImagePtr im;
	gdFontPtr f;
	int x;
	int y;
	char *s;
	int color;
{
	int i;
	int l;
	l = strlen(s);
	for (i=0; (i<l); i++) {
		gdImageCharUp(im, f, x, y, s[i], color);
		y -= f->w;
	}
}

/* s and e are integers modulo 360 (degrees), with 0 degrees
  being the rightmost extreme and degrees changing clockwise.
  cx and cy are the center in pixels; w and h are the horizontal 
  and vertical diameter in pixels. Nice interface, but slow, since
  I don't yet use Bresenham (I'm using an inefficient but
  simple solution with too much work going on in it; generalizing
  Bresenham to ellipses and partial arcs of ellipses is non-trivial,
  at least for me) and there are other inefficiencies (small circles
  do far too much work). */

void gdImageArc(im, cx, cy, w, h, s, e, color)
	gdImagePtr im;
	int cx;
	int cy;
	int w;
	int h;
	int s;
	int e;
	int color;
{
	int i;
	int smod, emod;
	int lx, ly;
	int w2, h2;
	w2 = w/2;
	h2 = h/2;
	while (e < s) {
		e += 360;
	}
	for (i=s; (i <= e); i++) {
		int x, y;
		x = ((long)cost[i % 360] * (long)w2 / costScale) + cx; 
		y = ((long)sint[i % 360] * (long)h2 / sintScale) + cy;
		if (i != s) {
			gdImageLine(im, lx, ly, x, y, color);	
		}
		lx = x;
		ly = y;
	}
}


#if 0
	/* Bresenham octant code, which I should use eventually */
	int x, y, d;
	x = 0;
	y = w;
	d = 3-2*w;
	while (x < y) {
		gdImageSetPixel(im, cx+x, cy+y, color);
		if (d < 0) {
			d += 4 * x + 6;
		} else {
			d += 4 * (x - y) + 10;
			y--;
		}
		x++;
	}
	if (x == y) {
		gdImageSetPixel(im, cx+x, cy+y, color);
	}
#endif

void gdImageFillToBorder(im, x, y, border, color)
	gdImagePtr im;
	int x;
	int y;
	int border;
	int color;
{
	int lastBorder;
	/* Seek left */
	int leftLimit, rightLimit;
	int i;
	leftLimit = (-1);
	if (border < 0) {
		/* Refuse to fill to a non-solid border */
		return;
	}
	for (i = x; (i >= 0); i--) {
		if (gdImageGetPixel(im, i, y) == border) {
			break;
		}
		gdImageSetPixel(im, i, y, color);
		leftLimit = i;
	}
	if (leftLimit == (-1)) {
		return;
	}
	/* Seek right */
	rightLimit = x;
	for (i = (x+1); (i < im->sx); i++) {	
		if (gdImageGetPixel(im, i, y) == border) {
			break;
		}
		gdImageSetPixel(im, i, y, color);
		rightLimit = i;
	}
	/* Look at lines above and below and start paints */
	/* Above */
	if (y > 0) {
		lastBorder = 1;
		for (i = leftLimit; (i <= rightLimit); i++) {
			int c;
			c = gdImageGetPixel(im, i, y-1);
			if (lastBorder) {
				if ((c != border) && (c != color)) {	
					gdImageFillToBorder(im, i, y-1, 
						border, color);		
					lastBorder = 0;
				}
			} else if ((c == border) || (c == color)) {
				lastBorder = 1;
			}
		}
	}
	/* Below */
	if (y < ((im->sy) - 1)) {
		lastBorder = 1;
		for (i = leftLimit; (i <= rightLimit); i++) {
			int c;
			c = gdImageGetPixel(im, i, y+1);
			if (lastBorder) {
				if ((c != border) && (c != color)) {	
					gdImageFillToBorder(im, i, y+1, 
						border, color);		
					lastBorder = 0;
				}
			} else if ((c == border) || (c == color)) {
				lastBorder = 1;
			}
		}
	}
}

void gdImageFill(im, x, y, color)
	gdImagePtr im;
	int x;
	int y;
	int color;		
{
	int lastBorder;
	int old;
	int leftLimit, rightLimit;
	int i;
	old = gdImageGetPixel(im, x, y);
	if (color == gdTiled) {
		/* Tile fill -- got to watch out! */
		int p, tileColor;	
		int srcx, srcy;
		if (!im->tile) {
			return;
		}
		/* Refuse to flood-fill with a transparent pattern --
			I can't do it without allocating another image */
		if (gdImageGetTransparent(im->tile) != (-1)) {
			return;
		}	
		srcx = x % gdImageSX(im->tile);
		srcy = y % gdImageSY(im->tile);
		p = gdImageGetPixel(im->tile, srcx, srcy);
		tileColor = im->tileColorMap[p];
		if (old == tileColor) {
			/* Nothing to be done */
			return;
		}
	} else {
		if (old == color) {
			/* Nothing to be done */
			return;
		}
	}
	/* Seek left */
	leftLimit = (-1);
	for (i = x; (i >= 0); i--) {
		if (gdImageGetPixel(im, i, y) != old) {
			break;
		}
		gdImageSetPixel(im, i, y, color);
		leftLimit = i;
	}
	if (leftLimit == (-1)) {
		return;
	}
	/* Seek right */
	rightLimit = x;
	for (i = (x+1); (i < im->sx); i++) {	
		if (gdImageGetPixel(im, i, y) != old) {
			break;
		}
		gdImageSetPixel(im, i, y, color);
		rightLimit = i;
	}
	/* Look at lines above and below and start paints */
	/* Above */
	if (y > 0) {
		lastBorder = 1;
		for (i = leftLimit; (i <= rightLimit); i++) {
			int c;
			c = gdImageGetPixel(im, i, y-1);
			if (lastBorder) {
				if (c == old) {	
					gdImageFill(im, i, y-1, color);		
					lastBorder = 0;
				}
			} else if (c != old) {
				lastBorder = 1;
			}
		}
	}
	/* Below */
	if (y < ((im->sy) - 1)) {
		lastBorder = 1;
		for (i = leftLimit; (i <= rightLimit); i++) {
			int c;
			c = gdImageGetPixel(im, i, y+1);
			if (lastBorder) {
				if (c == old) {
					gdImageFill(im, i, y+1, color);		
					lastBorder = 0;
				}
			} else if (c != old) {
				lastBorder = 1;
			}
		}
	}
}
	
#ifdef TEST_CODE
void gdImageDump(im)
	gdImagePtr im; 
{
	int i, j;
	for (i=0; (i < im->sy); i++) {
		for (j=0; (j < im->sx); j++) {
			printf("%d", im->pixels[j][i]);
		}
		printf("\n");
	}
}
#endif

/* Code drawn from ppmtogif.c, from the pbmplus package
**
** Based on GIFENCOD by David Rowley <mgardi@watdscu.waterloo.edu>. A
** Lempel-Zim compression based on "compress".
**
** Modified by Marcel Wijkstra <wijkstra@fwi.uva.nl>
**
** Copyright (C) 1989 by Jef Poskanzer.
**
** Permission to use, copy, modify, and distribute this software and its
** documentation for any purpose and without fee is hereby granted, provided
** that the above copyright notice appear in all copies and that both that
** copyright notice and this permission notice appear in supporting
** documentation.  This software is provided "as is" without express or
** implied warranty.
**
** The Graphics Interchange Format(c) is the Copyright property of
** CompuServe Incorporated.  GIF(sm) is a Service Mark property of
** CompuServe Incorporated.
*/

/*
 * a code_int must be able to hold 2**GIFBITS values of type int, and also -1
 */
typedef int             code_int;

#ifdef SIGNED_COMPARE_SLOW
typedef unsigned long int count_int;
typedef unsigned short int count_short;
#else /*SIGNED_COMPARE_SLOW*/
typedef long int          count_int;
#endif /*SIGNED_COMPARE_SLOW*/

static int colorstobpp(/* int colors */);
static void BumpPixel (/* void */);
static int GIFNextPixel (/* gdImagePtr im */);
static void GIFEncode (/* FILE* fp, int GWidth, int GHeight, int GInterlace, int Background, int Transparent, int BitsPerPixel, int* Red, int* Green, int* Blue, gdImagePtr im */);
static void Putword (/* int w, FILE* fp */);
static void compress (/* int init_bits, FILE* outfile, gdImagePtr im */);
static void output (/* code_int code */);
static void cl_block (/* void */);
static void cl_hash (/* count_int hsize */);
static void char_init (/* void */);
static void char_out (/* int c */);
static void flush_char (/* void */);
/* Allows for reuse */
static void init_statics(/* void */);

void gdImageGif(im, out)
	gdImagePtr im; 
	FILE *out;
{
	int interlace, transparent, BitsPerPixel;
	interlace = im->interlace;
	transparent = im->transparent;

	BitsPerPixel = colorstobpp(im->colorsTotal);
	/* Clear any old values in statics strewn through the GIF code */
	init_statics();
	/* All set, let's do it. */
	GIFEncode(
		out, im->sx, im->sy, interlace, 0, transparent, BitsPerPixel,
		im->red, im->green, im->blue, im);
}

static int
colorstobpp( colors )
int colors;
    {
    int bpp;

    if ( colors <= 2 )
        bpp = 1;
    else if ( colors <= 4 )
        bpp = 2;
    else if ( colors <= 8 )
        bpp = 3;
    else if ( colors <= 16 )
        bpp = 4;
    else if ( colors <= 32 )
        bpp = 5;
    else if ( colors <= 64 )
        bpp = 6;
    else if ( colors <= 128 )
        bpp = 7;
    else if ( colors <= 256 )
        bpp = 8;
    return bpp;
    }

/*****************************************************************************
 *
 * GIFENCODE.C    - GIF Image compression interface
 *
 * GIFEncode( FName, GHeight, GWidth, GInterlace, Background, Transparent,
 *            BitsPerPixel, Red, Green, Blue, gdImagePtr )
 *
 *****************************************************************************/

#define TRUE 1
#define FALSE 0

static int Width, Height;
static int curx, cury;
static long CountDown;
static int Pass = 0;
static int Interlace;

/*
 * Bump the 'curx' and 'cury' to point to the next pixel
 */
static void
BumpPixel()
{
        /*
         * Bump the current X position
         */
        ++curx;

        /*
         * If we are at the end of a scan line, set curx back to the beginning
         * If we are interlaced, bump the cury to the appropriate spot,
         * otherwise, just increment it.
         */
        if( curx == Width ) {
                curx = 0;

                if( !Interlace )
                        ++cury;
                else {
                     switch( Pass ) {

                       case 0:
                          cury += 8;
                          if( cury >= Height ) {
                                ++Pass;
                                cury = 4;
                          }
                          break;

                       case 1:
                          cury += 8;
                          if( cury >= Height ) {
                                ++Pass;
                                cury = 2;
                          }
                          break;

                       case 2:
                          cury += 4;
                          if( cury >= Height ) {
                             ++Pass;
                             cury = 1;
                          }
                          break;

                       case 3:
                          cury += 2;
                          break;
                        }
                }
        }
}

/*
 * Return the next pixel from the image
 */
static int
GIFNextPixel( im )
gdImagePtr im;
{
        int r;

        if( CountDown == 0 )
                return EOF;

        --CountDown;

        r = gdImageGetPixel(im, curx, cury);

        BumpPixel();

        return r;
}

/* public */

static void
GIFEncode( fp, GWidth, GHeight, GInterlace, Background, Transparent,
           BitsPerPixel, Red, Green, Blue, im )

FILE* fp;
int GWidth, GHeight;
int GInterlace;
int Background;
int Transparent;
int BitsPerPixel;
int Red[], Green[], Blue[];
gdImagePtr im;
{
        int B;
        int RWidth, RHeight;
        int LeftOfs, TopOfs;
        int Resolution;
        int ColorMapSize;
        int InitCodeSize;
        int i;

        Interlace = GInterlace;

        ColorMapSize = 1 << BitsPerPixel;

        RWidth = Width = GWidth;
        RHeight = Height = GHeight;
        LeftOfs = TopOfs = 0;

        Resolution = BitsPerPixel;

        /*
         * Calculate number of bits we are expecting
         */
        CountDown = (long)Width * (long)Height;

        /*
         * Indicate which pass we are on (if interlace)
         */
        Pass = 0;

        /*
         * The initial code size
         */
        if( BitsPerPixel <= 1 )
                InitCodeSize = 2;
        else
                InitCodeSize = BitsPerPixel;

        /*
         * Set up the current x and y position
         */
        curx = cury = 0;

        /*
         * Write the Magic header
         */
        fwrite( Transparent < 0 ? "GIF87a" : "GIF89a", 1, 6, fp );

        /*
         * Write out the screen width and height
         */
        Putword( RWidth, fp );
        Putword( RHeight, fp );

        /*
         * Indicate that there is a global colour map
         */
        B = 0x80;       /* Yes, there is a color map */

        /*
         * OR in the resolution
         */
        B |= (Resolution - 1) << 5;

        /*
         * OR in the Bits per Pixel
         */
        B |= (BitsPerPixel - 1);

        /*
         * Write it out
         */
        fputc( B, fp );

        /*
         * Write out the Background colour
         */
        fputc( Background, fp );

        /*
         * Byte of 0's (future expansion)
         */
        fputc( 0, fp );

        /*
         * Write out the Global Colour Map
         */
        for( i=0; i<ColorMapSize; ++i ) {
                fputc( Red[i], fp );
                fputc( Green[i], fp );
                fputc( Blue[i], fp );
        }

	/*
	 * Write out extension for transparent colour index, if necessary.
	 */
	if ( Transparent >= 0 ) {
	    fputc( '!', fp );
	    fputc( 0xf9, fp );
	    fputc( 4, fp );
	    fputc( 1, fp );
	    fputc( 0, fp );
	    fputc( 0, fp );
	    fputc( Transparent, fp );
	    fputc( 0, fp );
	}

        /*
         * Write an Image separator
         */
        fputc( ',', fp );

        /*
         * Write the Image header
         */

        Putword( LeftOfs, fp );
        Putword( TopOfs, fp );
        Putword( Width, fp );
        Putword( Height, fp );

        /*
         * Write out whether or not the image is interlaced
         */
        if( Interlace )
                fputc( 0x40, fp );
        else
                fputc( 0x00, fp );

        /*
         * Write out the initial code size
         */
        fputc( InitCodeSize, fp );

        /*
         * Go and actually compress the data
         */
        compress( InitCodeSize+1, fp, im );

        /*
         * Write out a Zero-length packet (to end the series)
         */
        fputc( 0, fp );

        /*
         * Write the GIF file terminator
         */
        fputc( ';', fp );
}

/*
 * Write out a word to the GIF file
 */
static void
Putword( w, fp )
int w;
FILE* fp;
{
        fputc( w & 0xff, fp );
        fputc( (w / 256) & 0xff, fp );
}


/***************************************************************************
 *
 *  GIFCOMPR.C       - GIF Image compression routines
 *
 *  Lempel-Ziv compression based on 'compress'.  GIF modifications by
 *  David Rowley (mgardi@watdcsu.waterloo.edu)
 *
 ***************************************************************************/

/*
 * General DEFINEs
 */

#define GIFBITS    12

#define HSIZE  5003            /* 80% occupancy */

#ifdef NO_UCHAR
 typedef char   char_type;
#else /*NO_UCHAR*/
 typedef        unsigned char   char_type;
#endif /*NO_UCHAR*/

/*
 *
 * GIF Image compression - modified 'compress'
 *
 * Based on: compress.c - File compression ala IEEE Computer, June 1984.
 *
 * By Authors:  Spencer W. Thomas       (decvax!harpo!utah-cs!utah-gr!thomas)
 *              Jim McKie               (decvax!mcvax!jim)
 *              Steve Davies            (decvax!vax135!petsd!peora!srd)
 *              Ken Turkowski           (decvax!decwrl!turtlevax!ken)
 *              James A. Woods          (decvax!ihnp4!ames!jaw)
 *              Joe Orost               (decvax!vax135!petsd!joe)
 *
 */
#include <ctype.h>

#define ARGVAL() (*++(*argv) || (--argc && *++argv))

static int n_bits;                        /* number of bits/code */
static int maxbits = GIFBITS;                /* user settable max # bits/code */
static code_int maxcode;                  /* maximum code, given n_bits */
static code_int maxmaxcode = (code_int)1 << GIFBITS; /* should NEVER generate this code */
#ifdef COMPATIBLE               /* But wrong! */
# define MAXCODE(n_bits)        ((code_int) 1 << (n_bits) - 1)
#else /*COMPATIBLE*/
# define MAXCODE(n_bits)        (((code_int) 1 << (n_bits)) - 1)
#endif /*COMPATIBLE*/

static count_int htab [HSIZE];
static unsigned short codetab [HSIZE];
#define HashTabOf(i)       htab[i]
#define CodeTabOf(i)    codetab[i]

static code_int hsize = HSIZE;                 /* for dynamic table sizing */

/*
 * To save much memory, we overlay the table used by compress() with those
 * used by decompress().  The tab_prefix table is the same size and type
 * as the codetab.  The tab_suffix table needs 2**GIFBITS characters.  We
 * get this from the beginning of htab.  The output stack uses the rest
 * of htab, and contains characters.  There is plenty of room for any
 * possible stack (stack used to be 8000 characters).
 */

#define tab_prefixof(i) CodeTabOf(i)
#define tab_suffixof(i)        ((char_type*)(htab))[i]
#define de_stack               ((char_type*)&tab_suffixof((code_int)1<<GIFBITS))

static code_int free_ent = 0;                  /* first unused entry */

/*
 * block compression parameters -- after all codes are used up,
 * and compression rate changes, start over.
 */
static int clear_flg = 0;

static int offset;
static long int in_count = 1;            /* length of input */
static long int out_count = 0;           /* # of codes output (for debugging) */

/*
 * compress stdin to stdout
 *
 * Algorithm:  use open addressing double hashing (no chaining) on the
 * prefix code / next character combination.  We do a variant of Knuth's
 * algorithm D (vol. 3, sec. 6.4) along with G. Knott's relatively-prime
 * secondary probe.  Here, the modular division first probe is gives way
 * to a faster exclusive-or manipulation.  Also do block compression with
 * an adaptive reset, whereby the code table is cleared when the compression
 * ratio decreases, but after the table fills.  The variable-length output
 * codes are re-sized at this point, and a special CLEAR code is generated
 * for the decompressor.  Late addition:  construct the table according to
 * file size for noticeable speed improvement on small files.  Please direct
 * questions about this implementation to ames!jaw.
 */

static int g_init_bits;
static FILE* g_outfile;

static int ClearCode;
static int EOFCode;

static void
compress( init_bits, outfile, im )
int init_bits;
FILE* outfile;
gdImagePtr im;
{
    register long fcode;
    register code_int i /* = 0 */;
    register int c;
    register code_int ent;
    register code_int disp;
    register code_int hsize_reg;
    register int hshift;

    /*
     * Set up the globals:  g_init_bits - initial number of bits
     *                      g_outfile   - pointer to output file
     */
    g_init_bits = init_bits;
    g_outfile = outfile;

    /*
     * Set up the necessary values
     */
    offset = 0;
    out_count = 0;
    clear_flg = 0;
    in_count = 1;
    maxcode = MAXCODE(n_bits = g_init_bits);

    ClearCode = (1 << (init_bits - 1));
    EOFCode = ClearCode + 1;
    free_ent = ClearCode + 2;

    char_init();

    ent = GIFNextPixel( im );

    hshift = 0;
    for ( fcode = (long) hsize;  fcode < 65536L; fcode *= 2L )
        ++hshift;
    hshift = 8 - hshift;                /* set hash code range bound */

    hsize_reg = hsize;
    cl_hash( (count_int) hsize_reg);            /* clear hash table */

    output( (code_int)ClearCode );

#ifdef SIGNED_COMPARE_SLOW
    while ( (c = GIFNextPixel( im )) != (unsigned) EOF ) {
#else /*SIGNED_COMPARE_SLOW*/
    while ( (c = GIFNextPixel( im )) != EOF ) {  /* } */
#endif /*SIGNED_COMPARE_SLOW*/

        ++in_count;

        fcode = (long) (((long) c << maxbits) + ent);
        i = (((code_int)c << hshift) ^ ent);    /* xor hashing */

        if ( HashTabOf (i) == fcode ) {
            ent = CodeTabOf (i);
            continue;
        } else if ( (long)HashTabOf (i) < 0 )      /* empty slot */
            goto nomatch;
        disp = hsize_reg - i;           /* secondary hash (after G. Knott) */
        if ( i == 0 )
            disp = 1;
probe:
        if ( (i -= disp) < 0 )
            i += hsize_reg;

        if ( HashTabOf (i) == fcode ) {
            ent = CodeTabOf (i);
            continue;
        }
        if ( (long)HashTabOf (i) > 0 )
            goto probe;
nomatch:
        output ( (code_int) ent );
        ++out_count;
        ent = c;
#ifdef SIGNED_COMPARE_SLOW
        if ( (unsigned) free_ent < (unsigned) maxmaxcode) {
#else /*SIGNED_COMPARE_SLOW*/
        if ( free_ent < maxmaxcode ) {  /* } */
#endif /*SIGNED_COMPARE_SLOW*/
            CodeTabOf (i) = free_ent++; /* code -> hashtable */
            HashTabOf (i) = fcode;
        } else
                cl_block();
    }
    /*
     * Put out the final code.
     */
    output( (code_int)ent );
    ++out_count;
    output( (code_int) EOFCode );
}

/*****************************************************************
 * TAG( output )
 *
 * Output the given code.
 * Inputs:
 *      code:   A n_bits-bit integer.  If == -1, then EOF.  This assumes
 *              that n_bits =< (long)wordsize - 1.
 * Outputs:
 *      Outputs code to the file.
 * Assumptions:
 *      Chars are 8 bits long.
 * Algorithm:
 *      Maintain a GIFBITS character long buffer (so that 8 codes will
 * fit in it exactly).  Use the VAX insv instruction to insert each
 * code in turn.  When the buffer fills up empty it and start over.
 */

static unsigned long cur_accum = 0;
static int cur_bits = 0;

static unsigned long masks[] = { 0x0000, 0x0001, 0x0003, 0x0007, 0x000F,
                                  0x001F, 0x003F, 0x007F, 0x00FF,
                                  0x01FF, 0x03FF, 0x07FF, 0x0FFF,
                                  0x1FFF, 0x3FFF, 0x7FFF, 0xFFFF };

static void
output( code )
code_int  code;
{
    cur_accum &= masks[ cur_bits ];

    if( cur_bits > 0 )
        cur_accum |= ((long)code << cur_bits);
    else
        cur_accum = code;

    cur_bits += n_bits;

    while( cur_bits >= 8 ) {
        char_out( (unsigned int)(cur_accum & 0xff) );
        cur_accum >>= 8;
        cur_bits -= 8;
    }

    /*
     * If the next entry is going to be too big for the code size,
     * then increase it, if possible.
     */
   if ( free_ent > maxcode || clear_flg ) {

            if( clear_flg ) {

                maxcode = MAXCODE (n_bits = g_init_bits);
                clear_flg = 0;

            } else {

                ++n_bits;
                if ( n_bits == maxbits )
                    maxcode = maxmaxcode;
                else
                    maxcode = MAXCODE(n_bits);
            }
        }

    if( code == EOFCode ) {
        /*
         * At EOF, write the rest of the buffer.
         */
        while( cur_bits > 0 ) {
                char_out( (unsigned int)(cur_accum & 0xff) );
                cur_accum >>= 8;
                cur_bits -= 8;
        }

        flush_char();

        fflush( g_outfile );

        if( ferror( g_outfile ) )
		exit(1);
    }
}

/*
 * Clear out the hash table
 */
static void
cl_block ()             /* table clear for block compress */
{

        cl_hash ( (count_int) hsize );
        free_ent = ClearCode + 2;
        clear_flg = 1;

        output( (code_int)ClearCode );
}

static void
cl_hash(hsize)          /* reset code table */
register count_int hsize;
{

        register count_int *htab_p = htab+hsize;

        register long i;
        register long m1 = -1;

        i = hsize - 16;
        do {                            /* might use Sys V memset(3) here */
                *(htab_p-16) = m1;
                *(htab_p-15) = m1;
                *(htab_p-14) = m1;
                *(htab_p-13) = m1;
                *(htab_p-12) = m1;
                *(htab_p-11) = m1;
                *(htab_p-10) = m1;
                *(htab_p-9) = m1;
                *(htab_p-8) = m1;
                *(htab_p-7) = m1;
                *(htab_p-6) = m1;
                *(htab_p-5) = m1;
                *(htab_p-4) = m1;
                *(htab_p-3) = m1;
                *(htab_p-2) = m1;
                *(htab_p-1) = m1;
                htab_p -= 16;
        } while ((i -= 16) >= 0);

        for ( i += 16; i > 0; --i )
                *--htab_p = m1;
}

/******************************************************************************
 *
 * GIF Specific routines
 *
 ******************************************************************************/

/*
 * Number of characters so far in this 'packet'
 */
static int a_count;

/*
 * Set up the 'byte output' routine
 */
static void
char_init()
{
        a_count = 0;
}

/*
 * Define the storage for the packet accumulator
 */
static char accum[ 256 ];

/*
 * Add a character to the end of the current packet, and if it is 254
 * characters, flush the packet to disk.
 */
static void
char_out( c )
int c;
{
        accum[ a_count++ ] = c;
        if( a_count >= 254 )
                flush_char();
}

/*
 * Flush the packet to disk, and reset the accumulator
 */
static void
flush_char()
{
        if( a_count > 0 ) {
                fputc( a_count, g_outfile );
                fwrite( accum, 1, a_count, g_outfile );
                a_count = 0;
        }
}

static void init_statics() {
	/* Some of these are properly initialized later. What I'm doing
		here is making sure code that depends on C's initialization
		of statics doesn't break when the code gets called more
		than once. */
	Width = 0;
	Height = 0;
	curx = 0;
	cury = 0;
	CountDown = 0;
	Pass = 0;
	Interlace = 0;
	a_count = 0;
	cur_accum = 0;
	cur_bits = 0;
	g_init_bits = 0;
	g_outfile = 0;
	ClearCode = 0;
	EOFCode = 0;
	free_ent = 0;
	clear_flg = 0;
	offset = 0;
	in_count = 1;
	out_count = 0;	
	hsize = HSIZE;
	n_bits = 0;
	maxbits = GIFBITS;
	maxcode = 0;
	maxmaxcode = (code_int)1 << GIFBITS;
}


/* +-------------------------------------------------------------------+ */
/* | Copyright 1990, 1991, 1993, David Koblas.  (koblas@netcom.com)    | */
/* |   Permission to use, copy, modify, and distribute this software   | */
/* |   and its documentation for any purpose and without fee is hereby | */
/* |   granted, provided that the above copyright notice appear in all | */
/* |   copies and that both that copyright notice and this permission  | */
/* |   notice appear in supporting documentation.  This software is    | */
/* |   provided "as is" without express or implied warranty.           | */
/* +-------------------------------------------------------------------+ */


#define        MAXCOLORMAPSIZE         256

#define        TRUE    1
#define        FALSE   0

#define CM_RED         0
#define CM_GREEN       1
#define CM_BLUE                2

#define        MAX_LWZ_BITS            12

#define INTERLACE              0x40
#define LOCALCOLORMAP  0x80
#define BitSet(byte, bit)      (((byte) & (bit)) == (bit))

#define        ReadOK(file,buffer,len) (fread(buffer, len, 1, file) != 0)

#define LM_to_uint(a,b)                        (((b)<<8)|(a))

static struct {
       unsigned int    Width;
       unsigned int    Height;
       unsigned char   ColorMap[3][MAXCOLORMAPSIZE];
       unsigned int    BitPixel;
       unsigned int    ColorResolution;
       unsigned int    Background;
       unsigned int    AspectRatio;
} GifScreen;

static struct {
       int     transparent;
       int     delayTime;
       int     inputFlag;
       int     disposal;
} Gif89 = { -1, -1, -1, 0 };

static int ReadColorMap ( /* FILE *fd, int number, gdImagePtr im, int *flag */);
static int DoExtension (/* FILE *fd, int label */);
static int GetDataBlock (/* FILE *fd, unsigned char  *buf */);
static int GetCode (/* FILE *fd, int code_size, int flag */);
static int LWZReadByte (/* FILE *fd, int flag, int input_code_size */);
static void ReadImage (/* gdImagePtr im, FILE *fd, int len, int height, int interlace, int ignore */);

int ZeroDataBlock;

gdImagePtr
gdImageCreateFromGif(fd)
FILE   *fd;
{
       int imageNumber;
       int BitPixel;
       int ColorResolution;
       int Background;
       int AspectRatio;
       int Transparent = (-1);
       unsigned char   buf[16];
       unsigned char   c;
       unsigned char   ColorMap[3][MAXCOLORMAPSIZE];
       unsigned char   localColorMap[3][MAXCOLORMAPSIZE];
       int             imw, imh;
       int             useGlobalColormap;
       int             bitPixel;
       int             imageCount = 0;
       char            version[4];
       gdImagePtr im;
       ZeroDataBlock = FALSE;

       imageNumber = 1;
       if (! ReadOK(fd,buf,6)) {
		return 0;
	}
       if (strncmp((char *)buf,"GIF",3) != 0) {
		return 0;
	}
       strncpy(version, (char *)buf + 3, 3);
       version[3] = '\0';

       if ((strcmp(version, "87a") != 0) && (strcmp(version, "89a") != 0)) {
		return 0;
	}
       if (! ReadOK(fd,buf,7)) {
		return 0;
	}
       BitPixel        = 2<<(buf[4]&0x07);
       ColorResolution = (((buf[4]&0x70)>>3)+1);
       Background      = buf[5];
       AspectRatio     = buf[6];

       if (BitSet(buf[4], LOCALCOLORMAP)) {    /* Global Colormap */
               if (ReadColorMap(fd, BitPixel, ColorMap)) {
			return 0;
		}
       }
       for (;;) {
               if (! ReadOK(fd,&c,1)) {
                       return 0;
               }
               if (c == ';') {         /* GIF terminator */
                       int i;
                       if (imageCount < imageNumber) {
                               return 0;
                       }
		       /* Check for open colors at the end, so
                          we can reduce colorsTotal and ultimately
                          BitsPerPixel */
                       for (i=((im->colorsTotal-1)); (i>=0); i--) {
                               if (im->open[i]) {
                                       im->colorsTotal--;
                               } else {
                                       break;
                               }
                       } 
                       return im;
               }

               if (c == '!') {         /* Extension */
                       if (! ReadOK(fd,&c,1)) {
                               return 0;
                       }
                       DoExtension(fd, c, &Transparent);
                       continue;
               }

               if (c != ',') {         /* Not a valid start character */
                       continue;
               }

               ++imageCount;

               if (! ReadOK(fd,buf,9)) {
	               return 0;
               }

               useGlobalColormap = ! BitSet(buf[8], LOCALCOLORMAP);

               bitPixel = 1<<((buf[8]&0x07)+1);

               imw = LM_to_uint(buf[4],buf[5]);
               imh = LM_to_uint(buf[6],buf[7]);
	       if (!(im = gdImageCreate(imw, imh))) {
			 return 0;
	       }
               im->interlace = BitSet(buf[8], INTERLACE);
               if (! useGlobalColormap) {
                       if (ReadColorMap(fd, bitPixel, localColorMap)) { 
                                 return 0;
                       }
                       ReadImage(im, fd, imw, imh, localColorMap, 
                                 BitSet(buf[8], INTERLACE), 
                                 imageCount != imageNumber);
               } else {
                       ReadImage(im, fd, imw, imh,
                                 ColorMap, 
                                 BitSet(buf[8], INTERLACE), 
                                 imageCount != imageNumber);
               }
               if (Transparent != (-1)) {
                       gdImageColorTransparent(im, Transparent);
               }	   
       }
}

static int
ReadColorMap(fd,number,buffer)
FILE           *fd;
int            number;
unsigned char  buffer[3][MAXCOLORMAPSIZE];
{
       int             i;
       unsigned char   rgb[3];


       for (i = 0; i < number; ++i) {
               if (! ReadOK(fd, rgb, sizeof(rgb))) {
                       return TRUE;
               }
               buffer[CM_RED][i] = rgb[0] ;
               buffer[CM_GREEN][i] = rgb[1] ;
               buffer[CM_BLUE][i] = rgb[2] ;
       }


       return FALSE;
}

static int
DoExtension(fd, label, Transparent)
FILE   *fd;
int    label;
int    *Transparent;
{
       static char     buf[256];

       switch (label) {
       case 0xf9:              /* Graphic Control Extension */
               (void) GetDataBlock(fd, (unsigned char*) buf);
               Gif89.disposal    = (buf[0] >> 2) & 0x7;
               Gif89.inputFlag   = (buf[0] >> 1) & 0x1;
               Gif89.delayTime   = LM_to_uint(buf[1],buf[2]);
               if ((buf[0] & 0x1) != 0)
                       *Transparent = buf[3];

               while (GetDataBlock(fd, (unsigned char*) buf) != 0)
                       ;
               return FALSE;
       default:
               break;
       }
       while (GetDataBlock(fd, (unsigned char*) buf) != 0)
               ;

       return FALSE;
}

static int
GetDataBlock(fd, buf)
FILE           *fd;
unsigned char  *buf;
{
       unsigned char   count;

       if (! ReadOK(fd,&count,1)) {
               return -1;
       }

       ZeroDataBlock = count == 0;

       if ((count != 0) && (! ReadOK(fd, buf, count))) {
               return -1;
       }

       return count;
}

static int
GetCode(fd, code_size, flag)
FILE   *fd;
int    code_size;
int    flag;
{
       static unsigned char    buf[280];
       static int              curbit, lastbit, done, last_byte;
       int                     i, j, ret;
       unsigned char           count;

       if (flag) {
               curbit = 0;
               lastbit = 0;
               done = FALSE;
               return 0;
       }

       if ( (curbit+code_size) >= lastbit) {
               if (done) {
                       if (curbit >= lastbit) {
                                /* Oh well */
                       }                        
                       return -1;
               }
               buf[0] = buf[last_byte-2];
               buf[1] = buf[last_byte-1];

               if ((count = GetDataBlock(fd, &buf[2])) == 0)
                       done = TRUE;

               last_byte = 2 + count;
               curbit = (curbit - lastbit) + 16;
               lastbit = (2+count)*8 ;
       }

       ret = 0;
       for (i = curbit, j = 0; j < code_size; ++i, ++j)
               ret |= ((buf[ i / 8 ] & (1 << (i % 8))) != 0) << j;

       curbit += code_size;

       return ret;
}

static int
LWZReadByte(fd, flag, input_code_size)
FILE   *fd;
int    flag;
int    input_code_size;
{
       static int      fresh = FALSE;
       int             code, incode;
       static int      code_size, set_code_size;
       static int      max_code, max_code_size;
       static int      firstcode, oldcode;
       static int      clear_code, end_code;
       static int      table[2][(1<< MAX_LWZ_BITS)];
       static int      stack[(1<<(MAX_LWZ_BITS))*2], *sp;
       register int    i;

       if (flag) {
               set_code_size = input_code_size;
               code_size = set_code_size+1;
               clear_code = 1 << set_code_size ;
               end_code = clear_code + 1;
               max_code_size = 2*clear_code;
               max_code = clear_code+2;

               GetCode(fd, 0, TRUE);
               
               fresh = TRUE;

               for (i = 0; i < clear_code; ++i) {
                       table[0][i] = 0;
                       table[1][i] = i;
               }
               for (; i < (1<<MAX_LWZ_BITS); ++i)
                       table[0][i] = table[1][0] = 0;

               sp = stack;

               return 0;
       } else if (fresh) {
               fresh = FALSE;
               do {
                       firstcode = oldcode =
                               GetCode(fd, code_size, FALSE);
               } while (firstcode == clear_code);
               return firstcode;
       }

       if (sp > stack)
               return *--sp;

       while ((code = GetCode(fd, code_size, FALSE)) >= 0) {
               if (code == clear_code) {
                       for (i = 0; i < clear_code; ++i) {
                               table[0][i] = 0;
                               table[1][i] = i;
                       }
                       for (; i < (1<<MAX_LWZ_BITS); ++i)
                               table[0][i] = table[1][i] = 0;
                       code_size = set_code_size+1;
                       max_code_size = 2*clear_code;
                       max_code = clear_code+2;
                       sp = stack;
                       firstcode = oldcode =
                                       GetCode(fd, code_size, FALSE);
                       return firstcode;
               } else if (code == end_code) {
                       int             count;
                       unsigned char   buf[260];

                       if (ZeroDataBlock)
                               return -2;

                       while ((count = GetDataBlock(fd, buf)) > 0)
                               ;

                       if (count != 0)
                       return -2;
               }

               incode = code;

               if (code >= max_code) {
                       *sp++ = firstcode;
                       code = oldcode;
               }

               while (code >= clear_code) {
                       *sp++ = table[1][code];
                       if (code == table[0][code]) {
                               /* Oh well */
                       }
                       code = table[0][code];
               }

               *sp++ = firstcode = table[1][code];

               if ((code = max_code) <(1<<MAX_LWZ_BITS)) {
                       table[0][code] = oldcode;
                       table[1][code] = firstcode;
                       ++max_code;
                       if ((max_code >= max_code_size) &&
                               (max_code_size < (1<<MAX_LWZ_BITS))) {
                               max_code_size *= 2;
                               ++code_size;
                       }
               }

               oldcode = incode;

               if (sp > stack)
                       return *--sp;
       }
       return code;
}

static void
ReadImage(im, fd, len, height, cmap, interlace, ignore)
gdImagePtr im;
FILE   *fd;
int    len, height;
unsigned char  cmap[3][MAXCOLORMAPSIZE];
int    interlace, ignore;
{
       unsigned char   c;      
       int             v;
       int             xpos = 0, ypos = 0, pass = 0;
       int i;
       /* Stash the color map into the image */
       for (i=0; (i<gdMaxColors); i++) {
               im->red[i] = cmap[CM_RED][i];	
               im->green[i] = cmap[CM_GREEN][i];	
               im->blue[i] = cmap[CM_BLUE][i];	
               im->open[i] = 1;
       }
       /* Many (perhaps most) of these colors will remain marked open. */
       im->colorsTotal = gdMaxColors;
       /*
       **  Initialize the Compression routines
       */
       if (! ReadOK(fd,&c,1)) {
               return; 
       }
       if (LWZReadByte(fd, TRUE, c) < 0) {
               return;
       }

       /*
       **  If this is an "uninteresting picture" ignore it.
       */
       if (ignore) {
               while (LWZReadByte(fd, FALSE, c) >= 0)
                       ;
               return;
       }

       while ((v = LWZReadByte(fd,FALSE,c)) >= 0 ) {
               /* This how we recognize which colors are actually used. */
               if (im->open[v]) {
                       im->open[v] = 0;
               }
               gdImageSetPixel(im, xpos, ypos, v);
               ++xpos;
               if (xpos == len) {
                       xpos = 0;
                       if (interlace) {
                               switch (pass) {
                               case 0:
                               case 1:
                                       ypos += 8; break;
                               case 2:
                                       ypos += 4; break;
                               case 3:
                                       ypos += 2; break;
                               }

                               if (ypos >= height) {
                                       ++pass;
                                       switch (pass) {
                                       case 1:
                                               ypos = 4; break;
                                       case 2:
                                               ypos = 2; break;
                                       case 3:
                                               ypos = 1; break;
                                       default:
                                               goto fini;
                                       }
                               }
                       } else {
                               ++ypos;
                       }
               }
               if (ypos >= height)
                       break;
       }

fini:
       if (LWZReadByte(fd,FALSE,c)>=0) {
               /* Ignore extra */
       }
}

void gdImageRectangle(im, x1, y1, x2, y2, color)
	gdImagePtr im;
	int x1; 
	int y1; 
	int x2; 
	int y2; 
{
	gdImageLine(im, x1, y1, x2, y1, color);		
	gdImageLine(im, x1, y2, x2, y2, color);		
	gdImageLine(im, x1, y1, x1, y2, color);
	gdImageLine(im, x2, y1, x2, y2, color);
}

void gdImageFilledRectangle(im, x1, y1, x2, y2, color)
	gdImagePtr im;
	int x1; 
	int y1; 
	int x2; 
	int y2; 
	int color;
{
	int x, y;
	for (y=y1; (y<=y2); y++) {
		for (x=x1; (x<=x2); x++) {
			gdImageSetPixel(im, x, y, color);
		}
	}
}

void gdImageCopy(dst, src, dstX, dstY, srcX, srcY, w, h)
	gdImagePtr dst;
	gdImagePtr src;
        int dstX; 
	int dstY; 
	int srcX; 
	int srcY; 
	int w; 
	int h;
{
	int c;
	int x, y;
	int tox, toy;
	int i;
	int colorMap[gdMaxColors];
	for (i=0; (i<gdMaxColors); i++) {
		colorMap[i] = (-1);
	}
	toy = dstY;
	for (y=srcY; (y < (srcY + h)); y++) {
		tox = dstX;
		for (x=srcX; (x < (srcX + w)); x++) {
			int nc;
			c = gdImageGetPixel(src, x, y);
			/* Have we established a mapping for this color? */
			if (colorMap[c] == (-1)) {
				/* If it's the same image, mapping is trivial */
				if (dst == src) {
					nc = c;
				} else { 
					/* First look for an exact match */
					nc = gdImageColorExact(dst,
						src->red[c], src->green[c],
						src->blue[c]);
				}	
				if (nc == (-1)) {
					/* No, so try to allocate it */
					nc = gdImageColorAllocate(dst,
						src->red[c], src->green[c],
						src->blue[c]);
					/* If we're out of colors, go for the
						closest color */
					if (nc == (-1)) {
						nc = gdImageColorClosest(dst,
							src->red[c], src->green[c],
							src->blue[c]);
					}
				}
				colorMap[c] = nc;
			}
			gdImageSetPixel(dst, tox, toy, colorMap[c]);
			tox++;
		}
		toy++;
	}
}			

#ifdef xxx /* missing function 'floor' */
void gdImageCopyResized(dst, src, dstX, dstY, srcX, srcY,
	dstW, dstH, srcW, srcH)
	gdImagePtr dst;
	gdImagePtr src;
        int dstX; 
	int dstY; 
	int srcX; 
	int srcY; 
        int dstW; 
	int dstH; 
	int srcW; 
	int srcH; 
{
	int c;
	int x, y;
	int tox, toy;
	int ydest;
	int i;
	int colorMap[gdMaxColors];
	/* Stretch vectors */
	int *stx;
	int *sty;
	/* We only need to use floating point to determine the correct
		stretch vector for one line's worth. */
	double accum;
	stx = (int *) malloc(sizeof(int) * srcW);
	sty = (int *) malloc(sizeof(int) * srcH);
	accum = 0;
	for (i=0; (i < srcW); i++) {
		int got;
		accum += (double)dstW/(double)srcW;
		got = floor(accum);
		stx[i] = got;
		accum -= got;
	}
	accum = 0;
	for (i=0; (i < srcH); i++) {
		int got;
		accum += (double)dstH/(double)srcH;
		got = floor(accum);
		sty[i] = got;
		accum -= got;
	}
	for (i=0; (i<gdMaxColors); i++) {
		colorMap[i] = (-1);
	}
	toy = dstY;
	for (y=srcY; (y < (srcY + srcH)); y++) {
		for (ydest=0; (ydest < sty[y-srcY]); ydest++) {
			tox = dstX;
			for (x=srcX; (x < (srcX + srcW)); x++) {
				int nc;
				if (!stx[x - srcX]) {
					continue;
				}
				c = gdImageGetPixel(src, x, y);
				/* Have we established a mapping for this color? */
				if (colorMap[c] == (-1)) {
					/* If it's the same image, mapping is trivial */
					if (dst == src) {
						nc = c;
					} else { 
						/* First look for an exact match */
						nc = gdImageColorExact(dst,
							src->red[c], src->green[c],
							src->blue[c]);
					}	
					if (nc == (-1)) {
						/* No, so try to allocate it */
						nc = gdImageColorAllocate(dst,
							src->red[c], src->green[c],
							src->blue[c]);
						/* If we're out of colors, go for the
							closest color */
						if (nc == (-1)) {
							nc = gdImageColorClosest(dst,
								src->red[c], src->green[c],
								src->blue[c]);
						}
					}
					colorMap[c] = nc;
				}
				for (i=0; (i < stx[x - srcX]); i++) {
					gdImageSetPixel(dst, tox, toy, colorMap[c]);
					tox++;
				}
			}
			toy++;
		}
	}
	free(stx);
	free(sty);
}
#endif

int gdGetWord(result, in)
	int *result;
	FILE *in;
{
	int r;
	r = getc(in);
	if (r == EOF) {
		return 0;
	}
	*result = r << 8;
	r = getc(in);	
	if (r == EOF) {
		return 0;
	}
	*result += r;
	return 1;
}

void gdPutWord(w, out)
	int w;
	FILE *out;
{
	putc((unsigned char)(w >> 8), out);
	putc((unsigned char)(w & 0xFF), out);
}

int gdGetByte(result, in)
	int *result;
	FILE *in;
{
	int r;
	r = getc(in);
	if (r == EOF) {
		return 0;
	}
	*result = r;
	return 1;
}

gdImagePtr gdImageCreateFromGd(in) 
	FILE *in; 
{
	int sx, sy;
	int x, y;
	int i;
	gdImagePtr im;
	if (!gdGetWord(&sx, in)) {
		goto fail1;
	}
	if (!gdGetWord(&sy, in)) {
		goto fail1;
	}
	im = gdImageCreate(sx, sy);
	if (!gdGetByte(&im->colorsTotal, in)) {
		goto fail2;
	}
	if (!gdGetWord(&im->transparent, in)) {
		goto fail2;
	}
	if (im->transparent == 257) {
		im->transparent = (-1);
	}
	for (i=0; (i<gdMaxColors); i++) {
		if (!gdGetByte(&im->red[i], in)) {
			goto fail2;
		}
		if (!gdGetByte(&im->green[i], in)) {
			goto fail2;
		}
		if (!gdGetByte(&im->blue[i], in)) {
			goto fail2;
		}
	}	
	for (y=0; (y<sy); y++) {
		for (x=0; (x<sx); x++) {	
			int ch;
			ch = getc(in);
			if (ch == EOF) {
				gdImageDestroy(im);
				return 0;
			}
			im->pixels[x][y] = ch;
		}
	}
	return im;
fail2:
	gdImageDestroy(im);
fail1:
	return 0;
}
	
void gdImageGd(im, out)
	gdImagePtr im; 
	FILE *out; 
{
	int x, y;
	int i;
	int trans;
	gdPutWord(im->sx, out);
	gdPutWord(im->sy, out);
	putc((unsigned char)im->colorsTotal, out);
	trans = im->transparent;
	if (trans == (-1)) {
		trans = 257;
	}	
	gdPutWord(trans, out);
	for (i=0; (i<gdMaxColors); i++) {
		putc((unsigned char)im->red[i], out);
		putc((unsigned char)im->green[i], out);	
		putc((unsigned char)im->blue[i], out);	
	}
	for (y=0; (y < im->sy); y++) {	
		for (x=0; (x < im->sx); x++) {	
			putc((unsigned char)im->pixels[x][y], out);
		}
	}
}

gdImagePtr
gdImageCreateFromXbm(fd)
FILE   *fd;
{
	gdImagePtr im;	
	int bit;
	int w, h;
	int bytes;
	int ch;
	int spaceat;
	int i, x, y;
	int bits;
	char *sp;
	char s[161];
	if (!fgets(s, 160, fd)) {
		return 0;
	}
	sp = &s[0];
	/* Skip #define */
	sp = strchr(sp, ' ');
	if (!sp) {
		return 0;
	}
	/* Skip width label */
	sp++;
	sp = strchr(sp, ' ');
	if (!sp) {
		return 0;
	}
	/* Get width */
	w = atoi(sp + 1);
	if (!w) {
		return 0;
	}
	if (!fgets(s, 160, fd)) {
		return 0;
	}
	sp = s;
	/* Skip #define */
	sp = strchr(sp, ' ');
	if (!sp) {
		return 0;
	}
	/* Skip height label */
	sp++;
	sp = strchr(sp, ' ');
	if (!sp) {
		return 0;
	}
	/* Get height */
	h = atoi(sp + 1);
	if (!h) {
		return 0;
	}
	/* Skip declaration line */
	if (!fgets(s, 160, fd)) {
		return 0;
	}
	bytes = (w * h / 8) + 1;
	im = gdImageCreate(w, h);
	gdImageColorAllocate(im, 255, 255, 255);
	gdImageColorAllocate(im, 0, 0, 0);
	x = 0;
	y = 0;
	for (i=0; (i < bytes); i++) {
		char h[3];
		int b;
		/* Skip spaces, commas, CRs, 0x */
		while(1) {
			ch = getc(fd);
			if (ch == EOF) {
				goto fail;
			}
			if (ch == 'x') {
				break;
			}	
		}
		/* Get hex value */
		ch = getc(fd);
		if (ch == EOF) {
			goto fail;
		}
		h[0] = ch;
		ch = getc(fd);
		if (ch == EOF) {
			goto fail;
		}
		h[1] = ch;
		h[2] = '\0';
		sscanf(h, "%x", &b);		
		for (bit = 1; (bit <= 128); (bit = bit << 1)) {
			gdImageSetPixel(im, x++, y, b & bit);	
			if (x == im->sx) {
				x = 0;
				y++;
				if (y == im->sy) {
					return im;
				}
			}
		}
	}
	/* Shouldn't happen */
	fprintf(stderr, "Error: bug in gdImageCreateFromXbm!\n");
	return 0;
fail:
	gdImageDestroy(im);
	return 0;
}

void gdImagePolygon(im, p, n, c)
	gdImagePtr im;
	gdPointPtr p;
	int n;
	int c;
{
	int i;
	int lx, ly;
	if (!n) {
		return;
	}
	lx = p->x;
	ly = p->y;
	gdImageLine(im, lx, ly, p[n-1].x, p[n-1].y, c);
	for (i=1; (i < n); i++) {
		p++;
		gdImageLine(im, lx, ly, p->x, p->y, c);
		lx = p->x;
		ly = p->y;
	}
}	
	
int gdCompareInt(/* int *a, int *b */);
	
void gdImageFilledPolygon(im, p, n, c)
	gdImagePtr im;
	gdPointPtr p;
	int n;
	int c;
{
	int i;
	int y;
	int y1, y2;
	int ints;
	if (!n) {
		return;
	}
	if (!im->polyAllocated) {
		im->polyInts = (int *) malloc(sizeof(int) * n);
		im->polyAllocated = n;
	}		
	if (im->polyAllocated < n) {
		while (im->polyAllocated < n) {
			im->polyAllocated *= 2;
		}	
		im->polyInts = (int *) realloc(im->polyInts,
			sizeof(int) * im->polyAllocated);
	}
	y1 = p[0].y;
	y2 = p[0].y;
	for (i=1; (i < n); i++) {
		if (p[i].y < y1) {
			y1 = p[i].y;
		}
		if (p[i].y > y2) {
			y2 = p[i].y;
		}
	}
	for (y=y1; (y <= y2); y++) {
		int interLast;
		int dirLast;
		int interFirst = 1;
		ints = 0;
		for (i=0; (i <= n); i++) {
			int x1, x2;
			int y1, y2;
			int dir;
			int ind1, ind2;
			if ((i == n) || (!i)) {
				ind1 = n-1;
				ind2 = 0;
			} else {
				ind1 = i-1;
				ind2 = i;
			}
			y1 = p[ind1].y;
			y2 = p[ind2].y;
			if (y1 < y2) {
				y1 = p[ind1].y;
				y2 = p[ind2].y;
				x1 = p[ind1].x;
				x2 = p[ind2].x;
				dir = -1;
			} else if (y1 > y2) {
				y2 = p[ind1].y;
				y1 = p[ind2].y;
				x2 = p[ind1].x;
				x1 = p[ind2].x;
				dir = 1;
			} else {
				/* Horizontal; just draw it */
				gdImageLine(im, p[ind1].x, y1, p[ind2].x, y1);
				continue;
			}
			if ((y >= y1) && (y <= y2)) {
				int inter = 
					(y-y1) * (x2-x1) / (y2-y1) + x1;
				/* Only count intersections once
					except at maxima and minima */
				if (!interFirst) {
					if (inter == interLast) {
						if (dir == dirLast) {
							continue;
						}
					}
				} 
				if (i > 0) {
					im->polyInts[ints++] = inter;
				}
				dirLast = dir;
				interLast = inter;
				interFirst = 0;
			}
		}
		qsort(im->polyInts, ints, sizeof(int), gdCompareInt);
		for (i=0; (i < (ints-1)); i+=2) {
			gdImageLine(im, im->polyInts[i], y,
				im->polyInts[i+1], y, c);
		}
	}
}
	
int gdCompareInt(a, b)
	int *a;
	int *b;
{
	return *a - *b;
}

void gdImageSetStyle(im, style, noOfPixels)
	gdImagePtr im;
	int *style; 
	int noOfPixels;
{
	if (im->style) {
		free(im->style);
	}
	im->style = (int *)  /* used to be unsigned int ...fixed by Thure Etzold */ 
		malloc(sizeof(int) * noOfPixels);
	memcpy(im->style, style, sizeof(unsigned int) * noOfPixels);
	im->styleLength = noOfPixels;
	im->stylePos = 0;
}

void gdImageSetBrush(im, brush)
	gdImagePtr im;
	gdImagePtr brush;
{
	int i;
	im->brush = brush;
	for (i=0; (i < gdImageColorsTotal(brush)); i++) {
		int index;
		index = gdImageColorExact(im, 
			gdImageRed(brush, i),
			gdImageGreen(brush, i),
			gdImageBlue(brush, i));
		if (index == (-1)) {
			index = gdImageColorAllocate(im,
				gdImageRed(brush, i),
				gdImageGreen(brush, i),
				gdImageBlue(brush, i));
			if (index == (-1)) {
				index = gdImageColorClosest(im,
					gdImageRed(brush, i),
					gdImageGreen(brush, i),
					gdImageBlue(brush, i));
			}
		}
		im->brushColorMap[i] = index;
	}
}
	
void gdImageSetTile(im, tile)
	gdImagePtr im;
	gdImagePtr tile;
{
	int i;
	im->tile = tile;
	for (i=0; (i < gdImageColorsTotal(tile)); i++) {
		int index;
		index = gdImageColorExact(im, 
			gdImageRed(tile, i),
			gdImageGreen(tile, i),
			gdImageBlue(tile, i));
		if (index == (-1)) {
			index = gdImageColorAllocate(im,
				gdImageRed(tile, i),
				gdImageGreen(tile, i),
				gdImageBlue(tile, i));
			if (index == (-1)) {
				index = gdImageColorClosest(im,
					gdImageRed(tile, i),
					gdImageGreen(tile, i),
					gdImageBlue(tile, i));
			}
		}
		im->tileColorMap[i] = index;
	}
}

void gdImageInterlace(im, interlaceArg) 
	gdImagePtr im;
	int interlaceArg;
{
	im->interlace = interlaceArg;
}

	gdImageRed(tile, i),
			gdImageGreen(tile, i),
			gdImageBlue(tile, i));
		if (index == (-1)) {
			index = gdImageColorAllocate(im,
				gdImageRed(tile, i),
				gdImageGreen(tile, i),
				gdImageBlue(tile, i));
			if (index == (-1)) {
				index = gdImageColorClosest(im,
					gdImageRed(tile, i),srs/src/gd.h
**
**    $RCSfile: gd.h,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:16:32 $
**
**    $Locker:  $
**    $State: Exp $
**
**
**
**    gd.h: declarations file for the gifdraw module.
**
**    Written by Tom Boutell, 5/94.
**    Copyright 1994, Cold Spring Harbor Labs.
**    Permission granted to use this code in any fashion provided
**    that this notice is retained and any alterations are
**    labeled as such. It is requested, but not required, that
**    you share extensions to this module with us so that we
**    can incorporate them into new versions. 
**
**
**    this file was modified so that it now contains also the include files
**    gdfonts.h and gdfontl.h by thure etzold, March 10, 1995
*/


/* This can't be changed, it's part of the GIF specification. */

#define gdMaxColors 256

/* Image type. See functions below; you will not need to change
	the elements directly. Use the provided macros to
	access sx, sy, the color table, and colorsTotal for 
	read-only purposes. */

typedef struct gdImageStruct {
	unsigned char ** pixels;
	int sx;
	int sy;
	int colorsTotal;
	int red[gdMaxColors];
	int green[gdMaxColors];
	int blue[gdMaxColors]; 
	int open[gdMaxColors];
	int transparent;
	int *polyInts;
	int polyAllocated;
	struct gdImageStruct *brush;
	struct gdImageStruct *tile;	
	int brushColorMap[gdMaxColors];
	int tileColorMap[gdMaxColors];
	int styleLength;
	int stylePos;
	int *style;
	int interlace;
} gdImage;

typedef gdImage * gdImagePtr;

typedef struct {
	/* # of characters in font */
	int nchars;
	/* First character is numbered... (usually 32 = space) */
	int offset;
	/* Character width and height */
	int w;
	int h;
	/* Font data; array of characters, one row after another.
		Easily included in code, also easily loaded from
		data files. */
	char *data;
} gdFont;

/* Text functions take these. */
typedef gdFont *gdFontPtr;

/* For backwards compatibility only. Use gdImageSetStyle()
	for MUCH more flexible line drawing. Also see
	gdImageSetBrush(). */
#define gdDashSize 4

/* Special colors. */

#define gdStyled (-2)
#define gdBrushed (-3)
#define gdStyledBrushed (-4)
#define gdTiled (-5)

/* NOT the same as the transparent color index.
	This is used in line styles only. */
#define gdTransparent (-6)

/* Functions to manipulate images. */

gdImagePtr gdImageCreate(/* int sx, int sy */);
gdImagePtr gdImageCreateFromGif(/* FILE *fd */);
gdImagePtr gdImageCreateFromGd(/* FILE *fd */);
gdImagePtr gdImageCreateFromXbm(/* FILE *fd */);
void gdImageDestroy(/* gdImagePtr im */);
void gdImageSetPixel(/* gdImagePtr im, int x, int y, int color */);
int gdImageGetPixel(/* gdImagePtr im, int x, int y */);
void gdImageLine(/* gdImagePtr im, int x1, int y1, 
	int x2, int y2, int color */);
/* For backwards compatibility only. Use gdImageSetStyle()
	for much more flexible line drawing. */
void gdImageDashedLine(/* gdImagePtr im, int x1, int y1, 
	int x2, int y2, int color */);
/* Corners specified (not width and height). Upper left first, lower right
 	second. */
void gdImageRectangle(/* gdImagePtr im, int x1, int y1, 
	int x2, int y2, int color */);
/* Solid bar. Upper left corner first, lower right corner second. */
void gdImageFilledRectangle(/* gdImagePtr im, int x1, int y1, 
	int x2, int y2, int color */);
int gdImageBoundsSafe(/* gdImagePtr im, int x, int y */);
void gdImageChar(/* gdImagePtr im, gdFontPtr font, int x, int y, 
	int c, int color */);
void gdImageCharUp(/* gdImagePtr im, gdFontPtr font, int x, int y, 
	int c, int color */);
void gdImageString(/* gdImagePtr im, gdFontPtr font, int x, int y, 
	char *s, int color */);
void gdImageStringUp(/* gdImagePtr im, gdFontPtr font, int x, int y, 
	char *s, int color */);

/* Point type for use in polygon drawing. */

typedef struct {
	int x, y;
} gdPoint, *gdPointPtr;

void gdImagePolygon(/* gdImagePtr im, gdPointPtr p, 
	int pointsTotal, int color */);
void gdImageFilledPolygon(/* gdImagePtr im, gdPointPtr p, int pointsTotal,
	int color */);

int gdImageColorAllocate(/* gdImagePtr im, int r, int g, int b */);
int gdImageColorClosest(/* gdImagePtr im, int r, int g, int b */);
int gdImageColorExact(/* gdImagePtr im, int r, int g, int b */);
void gdImageColorDeallocate(/* gdImagePtr im, int color */);
void gdImageColorTransparent(/* gdImagePtr im, int color */);
void gdImageGif(/* gdImagePtr im, FILE *out */);
void gdImageGd(/* gdImagePtr im, FILE *out */);
void gdImageArc(/* gdImagePtr im, int cx, int cy, int w, int h, 
	int s, int e, int color */);
void gdImageFillToBorder(/* gdImagePtr im, int x, int y, 
	int border, int color */);
void gdImageFill(/* gdImagePtr im, int x, int y, int color */);
void gdImageCopy(/* gdImagePtr dst, gdImagePtr src,
	int dstX, int dstY, int srcX, int srcY, int w, int h */);
/* Stretches or shrinks to fit, as needed */
void gdImageCopyResized(/* gdImagePtr dst, gdImagePtr src,
	int dstX, int dstY, int srcX, int srcY, int destw, int desth,
	int srcw, int srch */);
void gdImageSetBrush(/* gdImagePtr im, gdImagePtr brush */);
void gdImageSetTile(/* gdImagePtr im, gdImagePtr tile */);
void gdImageSetStyle(/* gdImagePtr im, int *style,
	int noOfPixels */);
/* On or off (1 or 0) */
void gdImageInterlace(/* gdImagePtr im, int interlace */);

/* Macros to access information about images. READ ONLY. Changing
	these values will NOT have the desired result. */
#define gdImageSX(im) ((im)->sx)
#define gdImageSY(im) ((im)->sy)
#define gdImageColorsTotal(im) ((im)->colorsTotal)
#define gdImageRed(im, c) ((im)->red[(c)])
#define gdImageGreen(im, c) ((im)->green[(c)])
#define gdImageBlue(im, c) ((im)->blue[(c)])
#define gdImageGetTransparent(im) ((im)->transparent)
#define gdImageGetInterlaced(im) ((im)->interlace)



/* formerly gdfontl.h */

/* 8x16 font derived from a public domain font in the X
        distribution. Only contains the 96 standard ascii characters,
        sorry. Feel free to improve on this. */

extern gdFontPtr gdFontLarge;

/* formerly gdfonts.h */

/* 6x12 font derived from a public domain font in the X
        distribution. Only contains the 96 standard ascii characters,
        sorry. Feel free to improve on this. */

extern gdFontPtr gdFontSmall;

e gdImageGetInterlaced(im) ((im)->interlace)



/* formerly gdfontl.h */

/* 8x16 font derived from a public domain font in the X
        distribution. Only contains the 96 standard ascii characters,
        sorry. Feel free to improve on this. */

extern gdFontPtr gdFontLarge;

/* formerly gdfonts.h */

/* 6x12 font derived from a public domain font in the X
        distribution. Only contains the 96 standardsrs/src/getz.c
char getz_ID[] = "$Id: getz.c,v 1.10 1997/03/18 17:20:18 srs Exp $";
/*
**    $RCSfile: getz.c,v $
**    $Revision: 1.10 $
**    $Date: 1997/03/18 17:20:18 $
**    $Author: srs $
**
**                  Copyright by Thure Etzold
**
**            Author: Thure Etzold
**                    EMBL, Meyerhofstrasse 1
**                    Heidelberg, Germany
**                    Tel: 06221 387529  
**                    Email: etzold@embl-heidelberg.de
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
** 
**  
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include "srs.h"

static VIEWo *BuildView (SETo *set);

int main(int argc, char **argv)
{
  ARGoLIST  *argList;
  TEMPLv    templ;
  SETo      *set;
  VIEWo     *view=NULL;
  ENTRYv    entry;
  IDoENTRY  id;
  char      *tmp;
  INT4      i;
  
  SrsEnv ();
  LibOpen ();
  LibInitHyperLinks ();

  MsgSetFnct ((FUNC)IcaPrintMessage);
  templ = TemplOpen ("SRSICA:ascii.it", NULL);

  /* process command line */
  argList = (ARGoLIST*) LibObjByName ("arglist", "getz");
  argc = ArgGet (argList, argc, argv);
  if (ParGetNum ("printLibInfo") && argc == 2) {  /* print only info ? */
    LibPrintInfo (argv[1]);
    exit (0);
  }
  else if (ParGetNum ("printLibs")) {
    LibPrintLibs ();
    exit (0);
  }
  else if (ParGetNum ("getStartupInfo")) {
    LibPrintStartupInfo ();
    exit (0);
  }
  else if (argc != 2) {
    ArgUsage (argList);
    exit (0);
  }

  /* do the query */
  TemplWith (templ, "$queryReport");
  if ((set = Query (argv[1], "Q1"))) {

    if (*ParGetStr ("viewFieldList"))
      view = BuildView (set);
    else if (*(tmp=ParGetStr ("viewName")))
      if (!(view = ViewGetNamed (tmp)))
	_ErrExit3 (e__objectunknown, "view", tmp);

    /* iterate over elements in the retrieved set */
    for (i=1; i <= set->n; i++) {
      SetGetID (set, i, &id);
      entry = EntryOpen (&id);
      if (view)
	EntryView (entry, view);
      else if (ParGetBool ("printEntireEntry"))
	EntryPrint (entry, NULL);
      else if (*ParGetStr ("fieldList"))
	EntryPrintFields (entry, NULL); 
      else
	printf ("%s\n", EntryGetFullName (entry));
      EntryClose (&entry);
    }
  }
  TemplEndWith ();
  exit (0);
}


static VIEWo *BuildView (SETo *set)
{
  VIEWo   *view;
  SRSoFLD *ft;
  char    *libName, *name, *tmp;
  Int4    k;
  
  if (*(tmp = ParGetStr ("viewFieldList"))) {
    view = ViewNew (1, "getz");
    ViewSetFormat (view, "table");
    
    for (k=0; SetGetNextLibStat (SetGetName (set), &libName, &k);)
      ViewAddRootLib (view, LibObjByName ("library", libName));
    
    while ((name = strtok (tmp, " "))) {
      tmp = NULL;
      if (!(ft = LibGetFieldType (libName, name)))
	_ErrExit3 (e__objectunknown, "data-field", name);
      ViewAddRootField (view, ft);
    }
  }    
  else
    view=NULL;
  return view;
} 
  k;
  
  if (*(tmp = ParGetStr ("viesrs/src/hash.c
char hash_srs_ID[] = "$Id: hash.c,v 1.1 1996/05/06 15:16:33 srs Exp $";
/*
**
**    $RCSfile: hash.c,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:16:33 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.1 Copyright by Thure Etzold
**             Unix port by Lukas Rosenthaler and Reinhard
**
**             Author: Gerald Schaefer
**                     EMBL, Meyerhofstrasse 1
**                     D-69012 Heidelberg, Germany
**                     Tel: 06221 387372
**                     Email: schaefer@embl-heidelberg.de
**
**
**    Requires:
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**
**    Description
**    ===========
**
**    implementation of a hash table used for generating indices   
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*/

#include <stdio.h>
#include <string.h>
#include <stdlib.h>

/* #include SRSINCLUDE  */

#include "message.h"
#include "hash.h"

#define  HSHxDEFHASHSIZE  111
#define  HSHxDEFMAXFILL    80

/*
**   HSHxHFREE means that this hash table element was never used before
**   HSHxHDEL  means that the element was used before but deleted now
*/
#define  HSHxHFREE  (void*)1L
#define  HSHxHDEL   (void*)0L

INT4 (*compare)(void *, void *) = NULL;

/****************************************************************
*  heap_sort:     original by  J.F.Korsh, L.J.Garrett           *
*     Data Structures, Algorithms, and Program Style using C    *
*  modification: ascendant order, list contains object pointers *                             *
****************************************************************/

/* function prototypes */
void heapsort(void **list, INT4 n);
void shift(void **list, INT4 root, INT4 last);

/* sorts the n elements of list in ascendant order */
void heapsort(void **list, INT4 n)
{
    INT4 root, last;
    void *temp;
    
    list--;  /* because the algorithm works from 1 to n */
    root = n/2;
    last = n;
    while (root > 0) {
        shift(list, root, last);
        root--;
    }
    
    root = 1;
    while (last > 1) {
        /* interchange(list,1,last) */
        temp = list[1];
        list[1] = list[last];
        list[last] = temp;
       
        last--;
        shift(list, root, last);
    }
}


/******************************************************************
*  Makes the subtree of the root into a heap (min heap).
*  The left and right subtrees of root must be heaps.
*  All subtrees are stored in array list in sequential representation.
*  Only the nodes between root and last are considered to be
*  in the subtrees.
******************************************************************/
void shift(void **list, INT4 root, INT4 last)
{
    INT4 ptr, succ;
    void *rootptr;

    ptr = root;
    
    succ = 2 * ptr;
    
    if (succ < last)
        if (compare(list[succ+1],list[succ]) > 0)   /* ascendant order */
            succ++;
    
    rootptr = list[root];
    
    while ((succ <= last) && (compare(list[succ],rootptr) > 0))  { /* asc. */
        list[ptr] = list[succ];   /*copy*/
        ptr = succ;
        succ = 2 * ptr;
        if (succ < last)
            if (compare(list[succ+1],list[succ]) > 0)  /* ascendant */
                succ++;
    }
    
    list[ptr] = rootptr;   /*copy*/
}


INT4 dummy_func(void *obj)
{
#if defined (TRACE1)
    printf("*** dummy function called ***\n");
#endif
    return 1;
}

INT4 dummy_func2(void *obj1, void *obj2)
{
#if defined (TRACE1)
    printf("*** dummy2 function called ***\n");
#endif
    return 1;
}


/****** HshFunc ***********************************************************
**
**      computes a hash index for a given string object. 
**      Needs the hash table manager object
**      to get the maximum size of the hash table.
**
**      INPUT:      address of an existing hash table object [R]
**                  address of a string object  to hash [R]
**              IMPLICIT:
**
**      RETURNS:     the computed hash index
*/

static INT4 HshFunc (HSHo *table, void *s)
{
  register unsigned long h=0, g;
  register char *p = (char *) s;

  while (*p) {
    h= (h << 4) + *p++;
    if ((g= (h & 0xf0000000)))
      h= (h ^ (g >> 24)) ^ g;
  }

#ifdef xxxx
    while (*s)
      h = (h<<5) + *s++;   /* horner's function ...segdewick */
      /*  h = (h << 1) ^ *s++; */
#endif

    return (INT4) h % table->max_hash_elem;
}



/**api* HshNewTable ********************************************************
**
**      creates and initializes a hash table manager object for a new  
**      hash table and allocates memory for an array, later used to 
**      store addresses of objects.
**
**      INPUT:      maximum size of hash table  [R]
**                  maximum fill in percentage  [R]
**                  address of a hash function  [R]
**                  address of a compare function  [R]
**                  address of a print function  [R]
**                  address of a delete function  [R]
**              IMPLICIT:
**
**      RETURNS:    address of the hash table manager object on success,
**                  NULL otherwise
*/

HSHo *HshNewTable(INT4 size, INT4 fill,
                         INT4 (*hash_func)(HSHo *, void *),
                         INT4 (*compare_func)(void *, void *),
                         INT4 (*print_func) (void *), 
                         INT4 (*delete_func) (void *) ) 
{
    INT4 i;

    HSHo *table = (HSHo*) malloc(sizeof(HSHo));
    if (!table) return NULL;  /* error handling ... */

    /*
    **  initialize hash table
    */
    if (size > 0)
        table->max_hash_elem = size;
    else
        table->max_hash_elem = HSHxDEFHASHSIZE;
        
    if (fill>=50 && fill<=100)
        table->max_fill = fill;
    else
        table->max_fill = HSHxDEFMAXFILL;
        
    table->hash_list = 
           (void**)malloc(table->max_hash_elem*sizeof(void*));
           
    if (!table->hash_list) {
        free(table);
        return NULL;  /* error handling ... */
    }
    
    table->cur_hash_elem = 0;
    for (i=0; i < table->max_hash_elem; i++)
        table->hash_list[i] = HSHxHFREE;
        
    table->hash_f = hash_func ? hash_func : HshFunc;
    table->compare_f = compare_func ? compare_func : dummy_func2;
    table->print_f = print_func ? print_func : dummy_func;
    table->delete_f = delete_func ? delete_func : dummy_func;
    
    /*
    ** allow insert and search operations (after compressing
    ** and sorting disabled !)
    */
    table->insert_search_allowed = 1;
    
    return table;
}


/****** HshHashObject *********************************************************
**
**      puts an existing object into the hash table.
**      If there exists a collision with the hash index the next free
**      position will be occupied (round robin).
**
**      INPUT:      address of an existing hash table object [R]
**                  address of an existing object [R]
**              IMPLICIT:
**                  modifies hash table
**
**      RETURNS:    1
*/

static INT4 HshHashObject(HSHo *table, void *obj)
{
    INT4 i;
    INT4 hash_index;

    /* get hash index */
    hash_index = (*table->hash_f)(table, obj);
#if defined(TRACE1)
    printf("hash_index is %d\n", hash_index);
#endif

    /* search for next free place */
    for (i=hash_index; i<table->max_hash_elem; i++) 
        if (table->hash_list[i] <= HSHxHFREE) {
            table->hash_list[i] = obj; /* no entry yet */
            table->cur_hash_elem++;
            return 1;
        }

    /* if no free slot until end ...try from begin of table */
    for (i=0; i<hash_index; i++) 
        if (table->hash_list[i] <= HSHxHFREE) {
            table->hash_list[i] = obj; /* no entry yet */
            table->cur_hash_elem++;
            return 1;
        }
    
    return 1;
}

/**api* HshInsertObject ****************************************************
**
**      inserts the new object into the hash table.
**      If the hash table is not big enough, it will be doubled before
**      hashing objects.
**
**      INPUT:      address of an existing hash table manager object [R]
**                  address of the new object [R]
**              IMPLICIT:
**                  modifies hash table  
**
**      RETURNS:    1 if the object has been successfully inserted,
**                  0 otherwise
*/

INT4 HshInsertObject(HSHo *table, void *obj)
{
    INT4 i, rv=1;
    void **old_hash_list = table->hash_list;
    INT4 old_max_hash_elem = table->max_hash_elem;

    if (!table || !obj) {
        printf("ERROR:  hash table or object is NULL\n");
        return 0;
    }

    /* be sure that hash table is big enough */
    if (table->cur_hash_elem > table->max_hash_elem * table->max_fill / 100) {
        void **tmp;

        /* extend hash table and rehash all elements in list */
        table->max_hash_elem = table->max_hash_elem * 2  + 7;
#if defined(TRACE2)
        printf("*** INFO: Expanding hash table from %d to %d elements ***\n",
                          old_max_hash_elem, table->max_hash_elem);
#endif 
        tmp =  (void**) malloc(table->max_hash_elem * sizeof(void*));
        if (!tmp) return 0;  /* no errror message to keep list module 
                                independent from other modules */

        table->hash_list = tmp;  /* use new array  */

        /* mark all elements as unused */
        for (i=0; i < table->max_hash_elem; i++)
            table->hash_list[i] = HSHxHFREE;
        table->cur_hash_elem = 0;

        /* hash all already used old elements */
        for (i = 0; i < old_max_hash_elem; i++)
            if (old_hash_list[i] > HSHxHFREE)  /* NULL check would fail */
                rv &= HshHashObject(table, old_hash_list[i]);
                
        free(old_hash_list);  /* free old array */
    }
    
    /* hash new object */
    rv &= HshHashObject(table, obj);

    return rv;
}


/**api* HshSearchObject ***************************************************
**
**      checks if an object with the same key value as the specified object
**      is already in the hash table.
**      Passes the address of the found object back to the calling function.
**
**      INPUT:      address of an existing hash table manager object [R]
**                  address of an object to search for duplicate [R]
**              IMPLICIT:
**
**      RETURNS:    address of an existing object, if found
**                  0 otherwise
*/

void *HshSearchObject(HSHo *table, void *obj)
{
    void* tmp;
    INT4 i;
    INT4 stop_search = 0;
    INT4 hash_index;

    if (!table || !obj) {
        printf("ERROR:  hash table or object is NULL\n");
        return 0;
    }

    /* get hash index for the specified object */
    hash_index = (*table->hash_f)(table, obj);
#if defined(TRACE1)
    printf("hash_index is %d\n", hash_index);
#endif

    /* search for object in hash table beginning with hash index */
    for (i=hash_index; i<table->max_hash_elem; i++) {
        tmp = table->hash_list[i];
        if (tmp == HSHxHFREE) {stop_search = 1;  break;}
        if (tmp == HSHxHDEL)  continue;
        if (!(*table->compare_f)(tmp, obj)) {
            /* object found */
            return tmp;
        }
    }

    if (!stop_search)
        for (i=0; i<hash_index; i++) {
            tmp = table->hash_list[i];
            if (tmp == HSHxHFREE) {stop_search = 1;  break;}
            if (tmp == HSHxHDEL)  continue;
            if (!(*table->compare_f)(tmp, obj)) {
                /* object found */
                return tmp;
            }
        }

    return 0;  /* duplicate object not found */
}


/**api* HshRehash ******************************************************
**
**      rehashes a (e.g. sorted) hash table. Inserting of and searching
**      for objects is possible again, afterwards.
**
**      INPUT:      address of an existing hash table manager object [R]
**              IMPLICIT:
**                  modifies hash table  
**
**      RETURNS:    1 on success,
**                  0 otherwise
*/

INT4 HshRehash(HSHo *table)
{
    INT4 i, rv=1;
    void **old_hash_list = table->hash_list;
    INT4 old_max_hash_elem = table->max_hash_elem;
    void **tmp;

    if (!table) {
        printf("*** ERROR: hash table does not exist !!! \n");
        return 0;
    }

    tmp =  (void**) malloc(table->max_hash_elem * sizeof(void*));
    if (!tmp) return 0;  /* no errror message to keep list module 
                            independent from other modules */

    table->hash_list = tmp;  /* use new array  */

    /* mark all elements as unused */
    for (i=0; i < table->max_hash_elem; i++)
        table->hash_list[i] = HSHxHFREE;
    table->cur_hash_elem = 0;

    /* hash all old elements */
    for (i = 0; i < old_max_hash_elem; i++)
        if (old_hash_list[i]) 
            rv &= HshHashObject(table, old_hash_list[i]);
                
    /*
    ** enable insert and search operations after successful rehashing
    */
    if (rv) {
        table->insert_search_allowed = 1;
        free(old_hash_list);  /* free old array */
    }
    else {
        table->hash_list = old_hash_list;
        free(tmp); 
    }
    
    return rv;
}


/**api* HshCompress *****************************************************
**
**      compresses the specified hash table. Inserting of and searching 
**      for objects is not possible before rehashing.
**
**      INPUT:      address of an existing hash table manager object [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success
**                  0 otherwise
*/
 
INT4 HshCompress(HSHo *table)
{
    INT4 i,j;
    void **list;
    
    if (!table) {
        printf("*** ERROR: hash table does not exist !!! \n");
        return 0;
    }
    
    /*
    ** compress hash table
    */
    list = table->hash_list;
    for (i=0,j=table->max_hash_elem-1; i<j; i++,j--) {
        while (list[i] >  HSHxHFREE) i++;
        while (list[j] <= HSHxHFREE) j--;
        if (i>j) break;
        list[i] = list[j];
        list[j] = NULL;
    }
    
    /*
    ** disable insert and search operations after compressing
    */
    table->insert_search_allowed = 0;
    return 1;    
}

/**api* HshSort *********************************************************
**
**      compresses and sorts the specified hash table.
**      Inserting of and searching for objects is no more possible.
**
**      INPUT:      address of an existing hash table manager object [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success
**                  0 otherwise
*/
 
INT4 HshSort(HSHo *table)
{
    int rv = 1;
    
    if (!table) {
        printf("*** ERROR: hash table does not exist !!! \n");
        return 0;
    }
    
    rv = HshCompress(table);
    
    /*
    ** sort compressed hash table using heap sort
    */
    compare = table->compare_f;  /* set global function pointer */
    heapsort(table->hash_list, table->cur_hash_elem);
    
    /*
    ** disable insert and search operations after compressing
    ** and sorting 
    */
    table->insert_search_allowed = 0;
    return rv;
}


/**api* HshDeleteAll *******************************************************
**
**      HshDeleteAll may be called externally to delete all hashed objects
**      inclusive the hash table manager object. A NULL pointer is given back
**      to the calling function, so that the old pointer to the hash table
**      can not be used anymore.
**
**      INPUT:      address of an address of an existing hash table object [R,W]
**              IMPLICIT:
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 HshDeleteAll(HSHo **table_pt)
{
    HSHo *table;
    INT4 i;

    if ( !table_pt || !(table = *table_pt) ) {
        printf("*** ERROR: hash table does not exist !!! \n");
        return 0;
    }

    /*
    ** delete all objects in the hash table
    */
    for (i=0; i < table->max_hash_elem; i++) {
        if (table->hash_list[i] <= HSHxHFREE) continue;
        (*table->delete_f)(table->hash_list[i]);
    }
     
    /*
    ** delete the hash table array and the manager object
    */
    free(table->hash_list);  /* delete hash table   */
    free(table);             /* delete hash table manager object */

    /*
    ** modify the hash table pointer to signal that the hash table
    ** has been destroyed
    */
    *table_pt = NULL;
    return 1;
}


/**api* HshPrintAll ***********************************************************
**
**      Prints the attribute values of the hash table manager object and the
**      attribute values of all objects in the hash table.
**
**      INPUT:      address of an existing hash table manager object [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 HshPrintAll(HSHo *table)
{
    INT4 i;
 
    if (!table) {
        printf("*** ERROR: hash table does not exist !!! \n");
        return 0;
    }

    printf("********** HASH TABLE DUMP *********************\n");
    printf("* Table has %d entries:\n", table->cur_hash_elem);
    printf("* Table could have %d entries:\n", table->max_hash_elem);
    printf("* Table will be extended, if more than %d %% of the elements used\n",
              table->max_fill);
              
    /*
    ** print the attribute values of all objects in the hash table
    */
    for (i=0; i < table->max_hash_elem; i++) {
        if (table->hash_list[i] <= HSHxHFREE) continue;
        printf("%8d", i);
        (*table->print_f)(table->hash_list[i]);
    }
 
    return 1;
}

 
/**api* HshLength ********************************************************
**
**      returns the current number of elements if the hash table exists.
**
**      INPUT:      address of an existing hash table object [R]
**              IMPLICIT:
**
**      RETURNS:    current number of elements on success, 0 otherwise
*/

INT4 HshLength(HSHo *table)
{
    if (!table) {
        printf("*** ERROR: hash table does not exist !!! \n");
        return 0;
    }

#if defined(TRACE1)
    printf("*** List has %d entries (max. is %d)***\n",
                table->cur_hash_elem, table->max_hash_elem);
#endif
    return table->cur_hash_elem;
}


the hash table exists.
**
**      INPUT:      address of an existing hash table object [R]
**              IMPLICIT:
**
**      RETURNS:    current number of elements on success, 0 otherwise
*/

INT4 srs/src/hash.h
*  File: hash_ind.h 
*  implementation of a hash table used for generating indices      *
*  structures and prototypes                                       *
*******************************************************************/

/*
** structure definition of the hash table manager object
*/
typedef struct HSHo {
    INT4 max_hash_elem;  /* max. number of objects in the hash table */
    INT4 cur_hash_elem;  /* current number of objects in the hash table */
    void **hash_list;  /* address of an array of void pointers  */
                        /* pointing to the objects. The array is */
                        /* automatically doubled, if overflow    */
    INT4 max_fill;       /* determines when hash table should be extended */
    INT4 insert_search_allowed; /* insert and search allowed (before sort) */
    INT4 (*hash_f)(struct HSHo *, void *); /* pointer to hash function */
    INT4 (*compare_f)(void *, void *);  /* pointer to compare function */
    INT4 (*print_f)(void *);    /* pointer to print function for objects */
    INT4 (*delete_f)(void *);   /* pointer to delete function for objects */   
    /* INT4 isUnused;   e.g. HSHxHFREE
       INT4 isFreed;    e.g. HSHxHDEL
    */
} HSHo;


void *HshSearchObject(HSHo *table, void *obj);
INT4 HshInsertObject(HSHo *table, void *obj);
HSHo *HshNewTable(INT4 size, INT4 fill,
                         INT4 (*hash_func)(HSHo *, void *),
                         INT4 (*compare_func)(void *, void *),
                         INT4 (*print_func) (void *), 
                         INT4 (*delete_func) (void *) ) ;

INT4 HshRehash(HSHo *table);
INT4 HshLength(HSHo *table);
INT4 HshPrintAll(HSHo *table);
INT4 HshCompress(HSHo *table);
INT4 HshSort(HSHo *table);
INT4 HshDeleteAll(HSHo **table_pt);

bj);
INT4 HshInsertObject(HSHo *table, void *obj);
HSHo *HshNewTable(INT4 size, INT4 fill,
                         INT4 (*hash_func)(HSHo *, void *),
                         INT4 (*compare_func)(void *, voisrs/src/ica.c
char ica__ID[] = "$Id: ica.c,v 1.2 1996/07/18 09:10:23 ulyanov Exp $";
/*
**
**    $RCSfile: ica.c,v $
**    $Revision: 1.2 $
**    $Date: 1996/07/18 09:10:23 $
**    $Author: ulyanov $
**
**    $Locker:  $
**    $State: Exp $
**             Author: Anatoly Ulyanov
**                     EMBL, Meyerhofstrasse 1
**                     D-69012 Heidelberg, Germany
**                     Tel: 06221 387451
**                     Email: ulyanov@embl-heidelberg.de
**
*/


#include <stdio.h>
#include <stdlib.h>
#include <stdarg.h>
#include "def.h"
#include "srs.h"


#include "odd.h"
#define _INITOBJS
#define _CONSTANTS
#define _SDL
#define _ODD
#define _FUNCTION 
#include "oddclass.h"

ICAoSYNTAX *IcaInitSyntax(ICAoSYNTAX *);

main(int argc, char **argv)
{
  ARGoLIST     *arglist;
  FILEo        *dataFile;
  ICAoJOB      *job; 
  ICAoSYNTAX   *syntax;
  char         line[MAXLINESIZE], *tokStr, *name;
  INT4         printAll, tokCode, c, rv;
  
  SrsEnv ();
  LibOpen ("srs5");
  
  arglist = LibObjByName ("arglist", "try");
  argc = ArgGet (arglist, argc, argv);
  if (argc != 2) {
    ArgUsage (arglist);
    _ErrorExit ();
  }

  OddInit (def, 1); 

  name = ParGetStr ("syntaxName");

  dataFile = FileNew(argv[1]);
  if( !FileOpen (dataFile) )
    _ErrExit2(e__filopenerr,  argv[1]);

  if( !ParGetBool("useIni") ) {
    syntax = IcaInitSyntax(LibObjByName("syntax", "icarus"));
    syntax->ign = " \t\n";
    job = IcaCreateJob (syntax);
    IcaNewJob (job, dataFile, NULL);
    if ( strcmp(name,"") != 0 )
      IcaDoJob(job, name);
    else
      IcaDoJob(job, "prog");
    IcaEndJob (job);
    VarExec (job->prog);
    exit(0);
  }

  if ( strcmp(name,"") != 0 )
    syntax = (ICAoSYNTAX *)LibObjByName ("syntax", name);
  else
    syntax  = (ICAoSYNTAX*)LibObjByName ("syntax", "icarus");

  job = IcaCreateJob (syntax);
  IcaNewJob (job, dataFile, NULL);
  IcaGetTokenList ("prog");
  IcaEndJob (job);

  if( job->prog )
    VarExec(job->prog);
}  
Icsrs/src/ica2c.c
char ica2c_ID[] = "$Id: ica2c.c,v 1.9 1997/03/12 16:17:33 srs Exp $";
/*
**    $RCSfile: ica2c.c,v $
**    $Revision: 1.9 $
**    $Date: 1997/03/12 16:17:33 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  Copyright by Thure Etzold
**
**            Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Module Code: i2c
**
**    Description
**    =========== 
**
**    Writes out an icarus program into a C program.

**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>

#include "message.h"
#include "sm.h"
#include "futil.h"
#include "templ.h"
#include "strv.h"
#include "variable.h"
#include "icarus.h"
#include "icaarg.h"


static char* I2cFunctionName (VARo *var);
static void  I2cStmnt (VARo *var);
static void  I2cExpr (VARo *var, INT4 type);
static void  I2cFor (VARo *var);
static void  I2cCall (VARo *var, INT4 type, Int4 isConvertOK);
static void  I2cFunc (VARo *var);
static INT4  I2cTypeConvert (INT4 type, INT4 newType);
static void  I2cProtoTypes ();


static struct TEMPLo *i2cTempl=NULL;



void I2cSetTemplate (struct TEMPLo *templ)
{
  i2cTempl = templ;
}

void I2cDeclareVariables ()
{
  IARGoVALUE* var = (IARGoVALUE*) OddGetObjectPtr (OddGetClass("var"), 0);
  Int4        varN = OddGetObjectN (OddGetClass("var"));
}



char *I2cProg (VARo *var)
{
  static INT4 funcN=0;
  static char funcName[100];
  VARo **arg;

  sprintf (funcName, "IcarusProg%d", ++funcN);

  TemplPrint ("function.head", funcName);

  /* the first argument has the program name */
  for (arg=VarGetArgs (var) + 1; *arg; arg++)
    I2cStmnt (*arg);

  TemplPrint ("function.tail");
  return funcName;
}

char *I2cBody (VARo *var)
{
  static INT4 funcN=0;
  static char funcName[100];
  VARo **arg, **arg2;

  sprintf (funcName, "IcarusBody%d", ++funcN);

  TemplWith (i2cTempl, "$prog");
  TemplPrint ("body.head", funcName);

  /* the first argument has the program name */
  for (arg=VarGetArgs (var); *arg; arg++) {
    if ((*arg)->isReadFunction && 
	SmEqs (IcaFunctionName ((*arg)->v.intGet), "IopBody")) {
      for (arg2=VarGetArgs (*arg); *arg2; arg2++)
	I2cStmnt (*arg2); /* nested body */
    }
    else 
      I2cStmnt (*arg);
  }
  TemplPrint ("body.tail");
  TemplEndWith ();
  return funcName;
}


static void I2cStmnt (VARo *var)
{
  char *funcName;

  TemplPrint ("stmnt.head");
  funcName = I2cFunctionName (var);
  if (funcName && SmEqs (funcName, "IopFor"))
    I2cFor (var);
  else {
    I2cExpr (var, 0);
    TemplPrint ("stmnt.tail");
  }
}

static void I2cExpr (VARo *var, INT4 type)
{
  STRv str;
  INT4 isConvert=0;

  if (var->type)
    isConvert = I2cTypeConvert (var->type, type);

  if (VarGetCode (var) & IARGxCALL)
    I2cCall (var, type, isConvert);
  else if (var->isDelayedType || var->isReadFunction)
    I2cFunc (var);
  else switch (var->type) {
  case VARxINT: 
    TemplPrint ("call.argint", VarGetInt (var)); 
    break;
  case VARxSTRING: 
    TemplPrint ("call.argstr", VarGetStr (var)); 
    break;
  case VARxSTRV: 
    str = VarGetStrv (var); 
    TemplPrint ("call.argstrv", _Str (StrEncode (&str)));
    break;
  case VARxLIST: 
  case VARxOBJECT: 
    TemplPrint ("call.argstr", "NULL"); 
    break;
  case VARxALIAS: 
    TemplPrint ("call.argvar", VarGetName (var));
    break;
  default:
    _ErrExit2 (e__unknownoption, "type in I2cCall");
  }
  if (isConvert)
    TemplPrint ("convert.tail");
}

static void I2cCall (VARo *var, INT4 type, Int4 isConvertOK)
{
  VARo       **args=VarGetArgs (var);
  IARGoCOM   *com;
  IARGoVALUE *arg;
  char       *funcName;
  INT4       k, isConvert=0;

  if (!(funcName = I2cFunctionName (var)))
    return;
  if (SmEqs (funcName, "IopExecCom"))
    com = (IARGoCOM *) VarGetObject (NULL, args[0]);
  else 
    com = (IARGoCOM *) IargFunc2Com (funcName);


  if (com->returnType && !isConvertOK)
    isConvert = I2cTypeConvert (com->returnType, type);

  TemplPrint ("call.name", com->functionName);
  if (args[0])
    IargBuildArgs (com, &args[1], TRUE);
  for (k=0; k < com->argsN; k++) {
    if (!(k == com->argsN))
      TemplPrint ("call.argsep");

    arg = &com->args[k];
    if (arg->isSet) 
      I2cExpr (arg->val, arg->type);
    else /* argument not defined, default value */
      switch (arg->type) {
	case VARxINT: 
	  TemplPrint ("call.argint", arg->defInt); 
	  break;
	case VARxSTRING: 
	case VARxSTRV: 
	case VARxLIST: 
	case VARxOBJECT: 
	case VARxVAR: 
	  TemplPrint ("call.argval", "NULL"); 
	  break;
      default:
	_ErrExit2 (e__unknownoption, "type in I2cCall");
      }
  }
  TemplPrint ("call.tail");
  if (isConvert)
    TemplPrint ("convert.tail");
}

static void I2cFunc (VARo *var) 
{
  VARo     **arg;
  IARGoCOM *com;
  char     *funcName;
  INT4     k;

  funcName = I2cFunctionName (var);
  com = (IARGoCOM *) IargFunc2Com (funcName);

  if (com && SmEqs (com->name, "=")) {
    arg=VarGetArgs (var);
    I2cExpr (arg[0], com->args[0].type);
    TemplPrint ("binop.=");
    I2cExpr (arg[1], com->args[1].type);
  }      
  else {
    TemplPrint ("call.name", funcName);
    for (k=0, arg=VarGetArgs (var); *arg; arg++) {
      TemplPrint ("call.argsep");
      if (com)
	I2cExpr (*arg, com->args[k++].type);
      else
	I2cExpr (*arg, 0);
    }
    TemplPrint ("call.tail");
  }  
}

static void I2cFor (VARo *var)
{
  ;
}

#define _cvt(x,y) ((x) << 4) +(y)

static INT4 I2cTypeConvert (INT4 type, INT4 newType)
{
  if (!newType || type == newType)
    return 0;

  switch (_cvt(type, newType)) {
  case _cvt (VARxALIAS, VARxVAR):
    return 0;
  case _cvt (VARxINT, VARxVAR):
    return 0;
    /*
    TemplPrint ("convert.int.var");
    break;
    */
  case _cvt (VARxINT, VARxSTRING):
    TemplPrint ("convert.int.string");
    break;
  case _cvt (VARxSTRING, VARxVAR):
    TemplPrint ("convert.int.var");
    break;
  case _cvt (VARxSTRING, VARxSTRV):
    TemplPrint ("convert.string.strv");
    break;
  case _cvt (VARxSTRV, VARxSTRING):
    TemplPrint ("convert.strv.string");
    break;
  case _cvt (VARxSTRV, VARxVAR):
    TemplPrint ("convert.strv.var");
    break;
  case _cvt (VARxOBJECT, VARxVAR):
    TemplPrint ("convert.object.var");
    break;
  case _cvt (VARxVAR, VARxOBJECT):
    TemplPrint ("convert.var.object");
    break;
  case _cvt (VARxVAR, VARxSTRV):
    TemplPrint ("convert.var.strv");
    break;
  case _cvt (VARxVAR, VARxSTRING): /*te!!!!!*/
    TemplPrint ("convert.var.strv");
    break;
  case _cvt (VARxALIAS, VARxOBJECT):
    TemplPrint ("convert.alias.object");
    break;
  case _cvt (VARxALIAS, VARxINT):
    return 0;
  case _cvt (VARxALIAS, VARxSTRING): /*te!!!!!*/
    return 0;
  case _cvt (VARxALIAS, VARxSTRV): /*te!!!!!*/
    TemplPrint ("convert.var.strv");
    break;
  case _cvt (VARxLIST, VARxALIAS): /*te!!!!!*/
    return 0;
  case _cvt (VARxLIST, VARxVAR): /*te!!!!!*/
    return 0;
    /*
    TemplPrint ("convert.alias.int");
    break;
    */
  default:
   printf ("conversion is not possible\n");
    exit (0);
  }
  return 1;
}


static char *I2cFunctionName (VARo *var)
{
  if (var->isDelayedType)
    return IcaFunctionName ((FUNC) var->typeGet);
  else if (var->isReadFunction)
    return IcaFunctionName (var->v.intGet);
  return NULL;
}


void I2cProtoTypes ()
{
}

#ifdef ready



typedef struct I2CoSyntax {
  char            *name;
  nodeN           nodeN[BNFxNodeTypeN];
} I2CoSyntax;

typedef struct I2CoNodeInfo {
  void	*ptr;
  INT4	index;
  INT4	progIndex[3];
} I2CoNodeInfo, *I2CvNodeInfo;


typedef struct I2CoSyntaxInfo {
  TEMPLv     templ;
  DICTv      niDict;
  STRv       initNodes[9];
  I2CoSyntax *syntax;
  Int4       syntaxN;
  Int4       syntaxAllocN;
} I2CoSyntaxInfo;


char *I2cProg (VARo *var, char *name)
{

  

  I2cSyntaxPrint (si);
  

  TemplPrint ("tail");
  TemplEndWith ();
}


void  I2cSyntaxPrint (I2CoSyntaxInfo *si)
{
  I2cInitPrint (si->progInit);
  for (i=2; i < BNFxNodeTypesN; i++)
    I2cInitPrint (si->progInit[i]);
  for (i=0; i < 2; i++)
    I2cInitPrint (si->progInit[i]);
  I2cInitPrint (si->termReportInit[i]);
  I2cInitPrint (si->choiceSetInit[i]);
}





void  I2cProdList (VARo *prodList) 
{
  VARo *var;
  Int4 i;
  
  /* collect all nodes from BNF tree */
  for (i=0; (var = AnyNextInList (prodList, &i)); )
    BnfTreeTraverse ((BNFoNODE *)VarGetObject (NULL, var), 
		     I2cNodeRegister, 0, syntaxInfo);

  /* print to buffer the Node initialization arrays */
  for (i=0; (var = AnyNextInList (prodList, &i)); )
    BnfTreeTraverse ((BNFoNODE *)VarGetObject (NULL, var), 
		     I2cNodePrint, 0, syntaxInfo);
  
  /* print to buffer the Term reports */
  for (i=0; (var = AnyNextInList (prodList, &i)); )
    BnfTreeTraverse ((BNFoNODE *)VarGetObject (NULL, var), 
		     I2cTermReportPrint, 0, syntaxInfo);
  
  /* print to buffer the Choice sets */
  for (i=0; (var = AnyNextInList (prodList, &i)); )
    BnfTreeTraverse ((BNFoNODE *)VarGetObject (NULL, var),
		     I2cChoiceSetPrint, 0, syntaxInfo);
}


static void I2cNodeRegister (BNFoNODE *node, Int4 level, void *data)
{
  I2CoSyntaxInfo* si=(I2CoSyntaxInfo*)data;
  I2CvNode        ni, niPtr;
  STRv            s;
  INT4            i;

  niPtr = &DictSet(&i2cniDict, &bnfNode, I2CpNode);
  if (!*ni) {
    if (node->name) {
      s = StrCpyS (node->name);
      StrEncode (&s);
      bnfNode->name = _Str (s); 
    }
    ni = typeAlloc (I2CvNode);
    ni->node  = (void *) nodeNode;
    ni->index  = si->nodeN[node->type]++;
    if (node->type != Term && node->type != Choice)
      for (i=0; i<3; i++)
        ni->progIndex[i] = I2cNodeProgs (node->exec[i]);
    *niPtr = ni;
  }
  return;
}



static void I2cNodePrint (BNFoPRODUCTION *node, INT4 level, void *data)
{
  I2CoSyntaxInfo* si=(I2CoSyntaxInfo*)data;
  I2CvNodeInfo    niImpl, ni;
  char            tmp[1000];
  INT4            type;

  type = node->type;
  si->syntaxCurr->nodeN[type]++;
  ni = DictAt (si->niDict, &node, I2CvNode);

  /* print array header */
  if (!StrLen (si->nodeInit[type]))
    StrCpyS (TemplSPrint (tmp, TemplN (type+1, "head")));

  switch (i) {
  case Production:
    niImpl = DictAt (si->niDict, &(node->node), I2CvNode);
    TemplStrPrint (&si->nodeInit[type], "prod.init", node->name, 
		   I2cNodeProgs (si, ni->progs),
		   TemplSPrint (tmp, TemplN (node->node->type+1, "arrName")),
		   niImpl->index);
    break;
  case ProdName:
    niImpl=DictAt(si->niDict, &((BNFoPRODNAME *)node)->production, I2CvNode);
    TemplStrPrint (&si->nodeInit[type], "prodname.init", node->name, 
		    I2cNodeProgs (si, ni->progs),
		    TemplSPrint (tmp, TemplN (Production+1, "arrName")),
		    niImpl->index); 
    break;
  case Literal:
  case Command:
  case LineStart:
  case Regexp:
    TemplStrPrint (&si->nodeInit[type], TemplN (type+1, "init"), node->name,
		   I2cNodeProgs (si, ni->progs));
    break;
  case Choice:
  case Term:
    TemplStrPrint (&si->nodeInit[type], TemplN (type+1, "init"), node->name);
    break;
  default:
    break;
  }
}


/****** I2cPrintVarPtr *****************************************************
**
*/

static char *I2cPrintVarPtr(INT4 *counter)
{
  static char buff[999];
  static char ref[999];
  INT4 i;
  
  buff[0]='\0';
  
  for(i=0; i<3; i++) {
    if(*counter == -1)
      strcat(buff, ", 0");
    else {
      sprintf(ref, ", &%s[%d]",
        TemplSPrint(s3, TemplN(12, "arrName")), *counter);
      strcat(buff, ref);
    }
    counter++;
  }
  return(buff);
}


static Int4 I2cNodeProgs (I2CoSyntaxInfo *si, VARo *var)
{
  static Int4 varN=-1;
  
  if (var) {
    StrApps (si->varInit, TemplSPrint (tmp, "var.init", I2cBody (var)));
    return (++varN);
  }
  else
   return -1;
}


static void I2cPrintTermReport(BNFoNODE *node, INT4 level, void *data)
{
  BNFoREPORT *report;
  BNFoNODE   *tmp;

  if (node->type == BNFxTerm) {
    for (report=((BNFoTERM *)node)->factorList; (tmp=report->node); report++){
      ni = DictAt (niDict, &nextNode, I2CvNode);
      TemplStrPrint (&si->reportInit, "report.init", report->counter,
                TemplSPrint (s, TemplN (tmp->type+1, "arrName")), ni->index);  
    }
    TemplStrPrint (&si->reportInit, TemplN(10, "arrName")));
  }
}

static void I2cChoiceSetPrint (BNFoNODE *node, INT4 level, void *data)
{
  BNFoNODE **term, *tmp;

  if (node->type = BNFxChoice) {
    for (term=((BNFoCHOICE *)node)->termList; (tmp = *term); term++)
      ni = DictAt (si->niDict, &tmp, I2CvNode);
      StrAppS (si->nodeInit[BNFxChoice], TemplSPrint(s1, TemplN(11, "format")),
                 TemplSPrint(s2, TemplN(nextNode->type+1, "arrName")),
		 i2cNode->index);  
    }
    BuffPrintF(i2cChoiceSetBuff, TemplSPrint(s1, TemplN(11, "arrName")));
  }
}



#endif
 void I2cChoiceSetPrint (BNFoNODE *node, INT4 level, void *data)
{
  BNFoNODE **term, *tmp;

  if (node->type = BNFxChoice) {
    for (term=((BNFoCHOICE *)node)->termList; (tmp = *term); term++)
      ni = DictAt (si->niDict, &tmp, I2CvNode);
      StrAppS (si->nodeInit[BNFxChoice], TemplSPrint(s1, TemplN(11, "format")),
                 TemplSPsrs/src/ica2c.h
**
**    $RCSfile: ica2c.h,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:16:35 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**                  Copyright by Thure Etzold
**
*/

void I2cOpen (char *fileName);
char *I2cProg (VARo *var);
char *I2cBody (VARo *var);
ictAt (si->niDict, &tmp, I2CvNode);
      StrAppS (si->nodeI¶ £¡@Choice], TemplSPrint(s1, TemplN(11, "format")),
        ¶ £¡Ü}plSPsrs/src/icaarg.c
char icarg_ID[] = "$Id: icaarg.c,v 1.8 1997/03/19 11:17:26 srs Exp $";
/*
**
**    $RCSfile: icaarg.c,v $
**    $Revision: 1.8 $
**    $Date: 1997/03/19 11:17:26 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS Copyright by Thure Etzold
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     69012 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    The functions in this module let the user define his own commands in 
**    icarus command lists.
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <stdarg.h>
#include <ctype.h>

#include "message.h"
#include "sm.h"
#include "lst.h"
#include "dict.h"
#include "templ.h"
#include "futil.h"
#include "toklist.h"
#include "strv.h"
#include "variable.h"
#include "regexp.h"
#include "icarus.h"
#define _INITOBJS
#include "icaarg.h"
#undef _INITOBJS

#define _SRS
#include SRSINCLUDE




/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  static functions and modulewide variables
*/

static void IargAddOrder (IARGoCOM *command, IARGoVALUE *arg);
static void* IargToKey (DictElem* e)
{
  return (*(IARGoCOM **)e)->name;
}

extern ICAoJOB   *Job;
static IARGoCOM   *comCurr=NULL;
static VARoSTACK  *stack;
static DICTv      comDict=0;
static CLASSoDICT IargDictClass = {

  (ValComparer)strequal, (ValHasher)strhash, (KeyAccessor)IargToKey, NULL, 0
};




IargComStack (IARGoCOM *com, char *option)
{
  static INT4 count=-1;
  static IARGoCOM *stack[100];

  if (option[1] == 'u') {/* push */
    if (count >= 100 - 1)
      _ErrExit3 (f__limitexceeded, "command objects", 100);
    stack[++count] = comCurr;
    comCurr = com;
  }
  else 
    comCurr = stack[--count];
}


void IargInit ()
{
  static INT4 isInit=0;
  IARGoCOM *com;
  INT4     k, l;
  
  if (isInit)
    return;

  comDict = DictCreate (&IargDictClass);
  for (k=0; (*(com = &IARGCOM[k])->name); k++) {
    DictSet (&comDict, com->name, IARGoCOM*) = com;
    com->function = IcaGetFunction (com->functionName);
  }
  isInit=1;

}

/**API* IargSetCom ************************************************************
**
**      Declares a new command or overwrites existing command.
**  
**  	INPUT:	    command object [R]
**                  command name [R]
**  	        IMPLICIT:
**                  comDict (DICTv) 
**  
**  	RETURNS:   
*/ 

void IargSetCom (IARGoCOM *com, char *name)
{
  IargInit ();
  DictSet (&comDict, name, IARGoCOM*) = com;
}


/**API* IargGetCom ************************************************************
**
**      Gets the command object for specified command name.
**  
**  	INPUT:	    command name [R]
**  	        IMPLICIT:
**                  comDict (DICTv) 
**  
**  	RETURNS:    command object
*/ 

IARGoCOM *IargGetCom (char *name)
{
  IARGoCOM **com;

  IargInit ();
  com = (IARGoCOM**) DictWith (comDict, name);
  return com ? *com : NULL;
}

char *IargGetComName (IARGoCOM *com)
{
  return com->name;
}


/**API* IargFunc2Com *************************************************************
**
**      Gets the command object for specified C function name.
**  
**  	INPUT:	    C-function name [R]
**  	        IMPLICIT:
**                  comDict (DICTv) 
**  
**  	RETURNS:    command object
**                  NULL if not found
*/ 

IARGoCOM *IargFunc2Com (char *name)
{
  Iter     i;
  IARGoCOM *com;

  for (i=DictFirst (comDict); i; DictNext (comDict, &i)) {
    com = DictIn (i, IARGoCOM*);
    if (SmEqs (com->functionName, name))
      return com; 
  }
  return NULL;
}




/**API* IargGetArgs ***********************************************************
**
**      This function must be called from the C-function associated to 
**      an Iargrus command in order to obtain the input parameters.
**      The first argument specifies the names and order of the arguments,
**      the following arguments are pointers that will be set to the
**      respective values.
**  
**  	INPUT:	    name of command within icarus [R]
**                  name of C function [R]
**  	        IMPLICIT:
**                  comCurr (IARGoVALUE)
**  
**  	RETURNS:    1 if success
**                  0 if not
*/ 

INT4 IargGetArgs (char *orderList, ...)
{
  va_list     ap;
  VARo        **var, **list, *varSave;
  IARGoVALUE   *arg;  
  STRv        *str, opt;
  char        *argName, *s, tmp[132];
  void        **p;
  INT4        k, *i, l;

  if (!comCurr)
    _ErrExit (e__fatal);
  else
    arg = comCurr->args;

  /*
  ** initialize order list
  */
  if (!comCurr->orderN) {
    strcpy (tmp, orderList); /* SmStrTok modifies string */
    while ((argName = SmStrTok (tmp, "|"))) {
      for (k=0; k < comCurr->argsN; k++) {
	arg = &comCurr->args[k];
	if (SmEqs (argName, arg->name))
	  break;
      }
      if (k == comCurr->argsN) {
	_ErrMsg3 (e__unknownarg, argName, comCurr->name);
	return 0;
      }
      IargAddOrder (comCurr, arg);
    }
  }

  va_start (ap, orderList);  			      
  for (k=0; k < comCurr->orderN; k++) {
    arg = comCurr->order[k];
    varSave = arg->val; /* save in case it gets changed by underlying function */
    /* execute in case it is 'type executed' */
    if (arg->isSet) 
      VarGetType (arg->val); 
    if (arg->isSet) 
      arg->val =  VarGetVar (varSave, 1);
    switch (arg->type) {
    case VARxSTRING: 
      s = va_arg (ap, char *);
      if (arg->isSet)
	strcpy (s, VarGetStr (arg->val));
      else 
	*s = '\0';
      break;
    case VARxSTRV: 
      str = va_arg (ap, STRv *);
      *str = arg->isSet ? VarGetStrv (arg->val) : NULL;
      break;
    case VARxINT: 
      i = va_arg (ap, INT4 *);
      if (arg->valsN && arg->isSet) {
	for (opt = VarGetStrv (arg->val), l=0; l < arg->valsN; l++) {
	  if (SmEqs (_Str (opt), arg->vals[l].name))
	    *i = arg->vals[l].n;
	  StrDel (opt);
	}
      }	      
      else
	*i = arg->isSet ? VarGetInt (arg->val) : arg->defInt;
      break;
    case VARxOBJECT: 
      p = va_arg (ap, void **);
      *p =  arg->isSet ? VarGetObject (NULL, VarFreeze(arg->val)) : NULL;
      break;
    case VARxLIST: 
      list = va_arg (ap, VARo **);
      *list =  arg->isSet ? AnyListCpy (arg->val): NULL;
      break;
    case VARxVAR: 
      var = va_arg (ap, VARo **);
      *var =  arg->isSet ? arg->val : NULL;
      break;
      
    default:
      break;
    }
  }
  va_end (ap);
  return 0;
}


/**API* IargReturn *************************************************************
**
**      This function must be called from the C-function associated to 
**      an Icarus command in order to obtain the input parameters.
**      The first argument specifies the names and order of the arguments,
**      the following arguments are pointers that will be set to the
**      respective values.
**  
**  	INPUT:	    name of command within icarus [R]
**                  name of C function [R]
**  	        IMPLICIT:
**                  comCurr (IARGoCOM *) [R]
**                  stack   (IARGoSTACK
**  
**  	RETURNS:    1 if success
**                  0 if not
*/ 

INT4 IargReturn (char *orderList, ...)
{
  static VARo  value;
  va_list ap;

  VarReset (&value);

  va_start (ap, orderList);  			      
  switch (comCurr->returnType) {
  case IARGxSTRING: 
    VarSetStr (&value, va_arg (ap, char *));
    break;
  case IARGxINT: 
    VarSetInt (&value, va_arg (ap, INT4));
    break;
  case IARGxOBJECT: 
    VarSetObject (NULL, &value, va_arg (ap, void *));
    break;
  default:
    break;
  }
  va_end (ap);
  
  VarPushCopy (stack, &value);
  return 0;
}

VARo     *iargRetVal;

/**api* function *************************************************************
**
**      Can be used from a C function implementing an Icarus command 
**      to return a value to Icarus. Note that when returning a string value
**      it will NOT be copied.
**
**	INPUT:	    type name of the returned value [W]
**                  the value [R]
**
*/ 

INT4 IcaReturn (char *typeName, ...)
{
  static VARo value;
  STRv str;
  va_list ap;

  VarReset (&value);
  iargRetVal = &value;

  va_start (ap, typeName);
  switch (comCurr->returnType) {
  case VARxSTRING: 
    VarSetStr (&value, va_arg (ap, char *));
    break;
  case VARxSTRV: 
    str = va_arg(ap, STRv);
    VarSetStrv (&value, str);
    break;
  case VARxINT: 
    VarSetInt (&value, va_arg (ap, INT4));
    break;
  case VARxOBJECT: 
    VarSetObject (NULL, &value, va_arg (ap, void *));
    break;
  case VARxVAR:
    VarSetVar (&value, va_arg (ap, VARo *));
    break;
  default:
    _ErrExit2 (e__unknownoption, "type in IcaReturn");
    break;
  }
  va_end (ap);
  
  return 0;
}




/**api* IargNewCommand *********************************************************
**
**  
**  	INPUT:	    name of command within icarus [R]
**                  name of C function [R]
**  	        IMPLICIT:
**                  comCurr (IARGoCOM *) [W]
**  
**  	RETURNS:   
*/ 

IARGoCOM *IargNewCommand (char *name, char *funName, IARGoCOM **c)
{
#ifdef xxx
  static INT4 classId=0;

  if(!classId)
    LstManageClass (&classId, sizeof (IARGoCOM), NULL, NULL, NULL);
  LstNewNamed ((void **) c, classId, name);
  command = *c;
  command->function = IargGetFunction (funName);
  command->arg = NULL;  
  command->retVal = NULL;  
  command->unNamedArg = NULL;

  command->orderN = 0;
  command->orderAllocN = 0;
  command->order = NULL;
#endif
  return comCurr;
}

/**api* IargMakeValue **********************************************************
**
**  
**  	INPUT:	    type of value: "arg" or "value" [R]
**                  name of value [R]
**                  type of value content: "string", "int", "object" [R]
**                  flag if value can occur unnamed [R]
**                  flag if value is required [R]
**                  name of the class (for value type "object") [R]
**  	        IMPLICIT:
**                  command (IARGoCOM *) [R]
**  
**  	RETURNS:   
*/ 

void IargAddValue (char *valType, char *name, char *type, INT4 isUnNamed, 
		  INT4 isRequired, char *className)
{
#ifdef xxx
  static INT4 classId=0;
  IARGoVALUE   *value;  

  if (!command)
    _ErrExit2 (e__nocurrentcommand, name);

  if(!classId)
    LstManageClass (&classId, sizeof (IARGoVALUE), NULL, NULL, NULL);

  /*
  ** create a new value and insert in 'arg' or 'return' list 
  */

  switch (tolower (valType[0])) {
  case 'a':  /* argument */
    LstNewNamed ((void **) &(command->arg), classId, name);
    value = command->arg;
    break;
  case 'r':  /* retVal */
    LstNewNamed ((void **) &(command->retVal), classId, name);
    value = command->retVal;
    break;
  default:
    _ErrExit2 (e__unknownoption, type);
  }

  /*
  ** build the value descriptor
  */

  if (isUnNamed) {
    if (command->unNamedArg)
      _ErrExit3 (e__onlyoneunnamed, value->name, command->name); 
    command->unNamedArg = value;
  }
  value->isRequired = isRequired;
  switch (tolower (type[0])) {
  case 's':  /* string */
    value->type = IARGxSTRING;
    break;
  case 'i':  /* int */
    value->type = IARGxINT;
    break;
  case 'o':  /* object */
    value->type = IARGxOBJECT;
    strcpy (value->className, className);
    break;
  default:
    _ErrExit2 (e__unknownoption, type);
  }
#endif
}


/**api* IargBuildArgs *********************************************************
**
**  
**  	INPUT:	    command object [W]
**                  array of pointers to values (last is NULL pointer) [R]
**  	        IMPLICIT:
**                  comCurr (IARGoCOM *) [W] 
**  
**  	RETURNS:   
*/ 

void IargBuildArgs (IARGoCOM *com, VARo **val, Int4 isInfo)
{
  IARGoVALUE *arg;
  VARo       *tmp;
  INT4       k;

  comCurr = com;

  if (!com->function && !isInfo)
    if (!(com->function = IcaGetFunction (com->functionName)))
      _ErrExit3 (e__objectunknown, "Icarus user function", com->functionName);

  
  /* initialize all argument values */
  for (k=0; k < comCurr->argsN; k++)
    comCurr->args[k].isSet = 0;
  
  /* process arguments on the stack */
  while ((tmp = *val++)) {
    for (k=0; k < comCurr->argsN; k++) {
      arg = &comCurr->args[k];
      if (SmEqs (arg->name, tmp->name)||(*tmp->name == ':' && arg->isUnnamed))
	break;
    }
    if (k == comCurr->argsN) {
      _ErrMsg3 (e__unknownarg, tmp->name, comCurr->name);
      return;
    }
    arg->isSet = 1;
    arg->val = tmp;
  }
}


/**api* IargExecCommand ********************************************************
**
**  
**  	INPUT:	    name of command within icarus [R]
**                  name of C function [R]
**  	        IMPLICIT:
**                  comCurr (IARGoCOM *) [R] 
**                  stack (VARoSTACK *) [W]
**  
**  	RETURNS:   
*/ 

void IargExecCommand (char *comName, VARoSTACK *s)
{
  IARGoVALUE *arg;
  VARo       *value;
  INT4       listSize, k;
  STRv       argName;

  IargInit ();
  comCurr = DictAt (comDict, comName, IARGoCOM*);
  stack = s;
  
  /* initialize all argument values */
  for (k=0; k < comCurr->argsN; k++)
    comCurr->args[k].isSet = 0;
  
  /* process arguments on the stack */
  while ((value = VarNextArg (stack, &argName, &listSize))) {
    for (k=0; k < comCurr->argsN; k++) {
      arg = &comCurr->args[k];
      if (SmEqs (arg->name, _Str(argName)) || 
	  (*_Str(argName) == ':' && arg->isUnnamed)) 
	break;
      
    }
    if (k == comCurr->argsN) {
      _ErrMsg3 (e__unknownarg, _Str(argName), comCurr->name);
      return;
    }
    arg->isSet = 1;
    arg->val = value;
  }
  
  (*comCurr->function)();
}





/**api* IargAddOrder **********************************************************
**
**      Adds a new element to the dynamically growing order list.
**  
**  	INPUT:	    name of command within icarus [R]
**                  name of C function [R]
**  	        IMPLICIT:
**  
**  	RETURNS:   
*/ 

static void IargAddOrder (IARGoCOM *command, IARGoVALUE *arg)
{
  if (!command->orderAllocN) {
    if ((command->order = (void *) malloc (2 * sizeof (void *))) == NULL)
      _ErrExit2 (e__allocfail, "command order list");
    command->orderN = 0;
    command->orderAllocN = 2;
  }
  else if (command->orderN >= command->orderAllocN) {
    command->orderAllocN *= 2;
    if ((command->order= (void *) realloc
	 (command->order, command->orderAllocN * sizeof (void *))) == NULL)
      _ErrExit2 (e__allocfail, "command order list");
  }
  command->order[command->orderN++] = arg;
}

/**api* IargPrintInfo *********************************************************
**
**      Prints out information for all Icarus commands.
**  
*/ 

void IargPrintInfo ()
{
  TEMPLv     templ;
  IARGoCOM   *com;
  IARGoVALUE *arg;
  INT4       k, l, i;
  
  templ = TemplOpen ("SRSICA:srswww.i", NULL);
  TemplWith (templ, "$icarusCommand");
  TemplPrint ("title");

  for (k=0; (*(com = &IARGCOM[k])->name); k++) {
    if (!com->isShow)
      continue;
    TemplPrint("head", com->name, com->name, com->rem);
    if (!com->argsN) 
      TemplPrint ("noArgs");
    else {
      TemplWith (templ, "arglist");
      for (l=0; l<com->argsN; l++) {
	arg = &com->args[l];
	TemplPrint ("name", arg->name);
	
        /* argument type */
        TemplWith (templ, "type");
	if (arg->valsN) {
	  TemplPrint ("enum.head");
	  for (i=0; i < arg->valsN; i++)
	    TemplPrint ("enum.value", arg->vals[i].name);
	  TemplPrint ("enum.tail");
        }
	else if (arg->type == VARxOBJECT)
	  TemplPrint (TemplN (arg->type, NULL), arg->className);
	else
	  TemplPrint (TemplN (arg->type, NULL));
        TemplEndWith ();
	
	TemplPrint (arg->isUnnamed ? "unnamed" : "named");
	TemplPrint (arg->isRequired ? "required" : "optional");
	
	/* default value */
	if (arg->defInt)
	  TemplPrint ("defaultNum", arg->defInt);
	else if (*arg->defaultStr)
	  TemplPrint ("defaultStr", arg->defaultStr);
	else 
	  TemplPrint ("empty");
	
	if (*arg->rem)
	  TemplPrint ("comment", arg->rem); 
	else
	  TemplPrint ("empty");
	TemplPrint ("tail"); 
      }
      TemplEndWith ();
    }
    TemplWith (templ, "return");
    TemplPrint ("head");
    if (com->returnType) {
      TemplPrint ("preType");

      /* return value type */
      if (com->returnType) {
	TemplWith (templ, "$icarusCommand.arglist.type");
	if (com->returnType == VARxOBJECT)
	  TemplPrint (TemplN (com->returnType, NULL), com->returnClass);
	else
	  TemplPrint (TemplN (com->returnType, NULL));
	TemplEndWith ();

	TemplPrint ("postType");
      }
      else
	TemplPrint ("nothing");
      TemplEndWith ();
      TemplPrint ("tail"); 
    }
  }  
  TemplEndWith ();
}


nt ("head");
    if (com->returnType) {
      TemplPrint ("preType");

      /* return vasrs/src/icaarg.h
**
**    $RCSfile: icaarg.h,v $
**    $Revision: 1.2 $
**    $Date: 1996/07/09 20:38:13 $
**    $Author: etzold $
**
**    $Locker:  $
**    $State: Exp $
**
**                  Copyright by Thure Etzold
**
*/


#include "builtin.h"


#define IARGxCALL         16
#define IARGxINDIRECTCALL 32
#define IARGxODD          1
#define IARGxINIT         2
#define IARGxPRE          4
#define IARGxPOST         8

/* this is now exactly the same as the VARxINT...enum - should be replaced */
typedef enum {IARGxINT=1, IARGxSTRING, IARGxOBJECT, IARGxREAL, IARGxALIAS,
	      IARGxVAR, IARGxANY, IARGxSTRV, IARGxLIST=16} IARGeType;


typedef struct IARGoCOM *IARGvCOM;

    /* API */

INT4 IcaGetArgs (char *orderList, ...);
struct IARGoCOM *IargFunc2Com (char *name);

    /* build time */

IARGvCOM IargGetCom (char *name);
char *IargGetComName (struct IARGoCOM *com);
void IargSetCom (struct IARGoCOM *com, char *name);
struct ICAoCOMMAND *IcaNewCommand (char *name, char *funName, 
				   struct ICAoCOMMAND **c);

void IcaAddValue (char *valType, char *name, char *type, INT4 isUnNamed, 
		  INT4 isRequired, char *className);
  
    /* ececution time */

typedef struct VARoSTACK *dummytointroducestructtagVARoSTACK;
void IcaExecCommand (struct ICAoCOMMAND *command, struct VARoSTACK *stack);
void IargBuildArgs (struct IARGoCOM *com, struct VARo **val, Int4 isInfo);

/* the extra arguments are in case variables are defined as parameters */
#define _IargCall(com)  (*(com)->function)(1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0)




void IcaAddValue (char *valType, char *name, char *type, INT4 isUnNamed, 
		  INT4 isRequired, char *className);
  
    /* ececution time */

typedef struct VARoSTACK *dummytointroducestructtagVARoSTACK;
void IcaExecCommand (struct ICAoCOMMAND *command, struct VARoSTACK *stack);
void IargBuildArgs (struct IARGoCOM *com, struct VARo **val, Int4 isInfo);

/* the extra arguments are in case variables are defined as parameters */
#define _IargCallsrs/src/icabnf.c
char icabnf_ID[] = "$Id: icabnf.c,v 1.25 1997/03/18 22:52:30 srs Exp $"; 
/*               
**  
**    $RCSfile: icabnf.c,v $ 
**    $Revision: 1.25 $
**    $Date: 1997/03/18 22:52:30 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  Copyright by Thure Etzold
**
**             Authors: Anatoly Ulyanov
**                      Thure Etzold
**                      EMBL, Meyerhofstrasse 1
**                      W-6900 Heidelberg, Germany
**                      Tel: 06221 387451
**                      Email: ulyanov@embl-heidelberg.de
**
**
**
**
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**
**    Description
**    =========== 
**  
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*/  

#include <string.h>
#include <ctype.h>
#include <stdlib.h>
#include <stdio.h>

#include "message.h"
#include "regexp.h"
#include "futil.h"
#include "library.h"
#include "sm.h"
#include "strv.h"
#include "lst.h"
#include "variable.h"
#include "toklist.h"
#include "cursor.h"
#include "icatask.h"
#include "icarus.h"
#include "icaarg.h"
#include "icabnf.h"
#include "icadebug.h"


#define _ErrCheckJump() if(Job->parseError) return(FALSE)
#define _ErrThrow(x) Job->parseError = (x)
#define _ErrCatch() Job->parseError = 0

#define _SRS
#include SRSINCLUDE

extern ICAoJOB   *Job;
extern VARoStack icaStack2[6];
extern INT4      NameListId;
extern ICAoSYNTAX  *newSyntax;

static INT4         TokCode;		/* build time curr token code */
static char        *BuffPtr;		/* build time Ptr to syntax buff */
static char        *BuffBegin;		/* save the beginnig of syntax buff */
static char         TokStr[10000];      /* build time curr token */
ICAoSYNTAX  *Syntax; 

static INT4      BnfCompareLiteral(CURSORo *, INT4, char *);
static INT4      BnfCompareRegExp(CURSORo *, regexp *);
static void      BnfLinkBnfNet();
static void      BnfNextToken();
static void      BnfPrintTree(BNFoCHOICE *);
static void      BnfTrace(INT4, char *, char *);
void             BnfInitRules (ICAoSYNTAX *, INT4);


/**api* BnfBuild **************************************************************
**
**      function calls recursively BnfMakeTree function until all the
**      parser syntaxes will be obtained.
**
**      INPUT:          syntax to build up BNF tree
*/ 
   
void BnfBuild(ICAoSYNTAX *syntax)

{
  FILEo      *file;
  ICAoJOB    *job;

  if (*syntax->cmnt && ! syntax->cmntRe)
    if ((syntax->cmntRe = RegComp (syntax->cmnt)) == NULL)
      _ErrExit2 (e__regerror, syntax->cmntRe);
  
  if (!FileOpen ((file = FileNew (syntax->fileName))))
    _ErrExit2 (e__filnotok, syntax->fileName);

  job = IcaCreateJob ((ICAoSYNTAX *)LibObjByName ("syntax", "icarus"));
  IcaNewJob (job, file, NULL);
  IcaGetTokenList (job, "prog");
  syntax->prod = VarGet (&job->scope, "rules");
  IcaEndJob (job);
  IcaExecProg (job);
  syntax->scope = (VARoSCOPE *)VarCopyScope (job->scope);

  return;
}

/****** BnfGetProduction *****************************************************
**       
**       if a new name
**         allocate memory for production and put into
**         production list
**       else
**         return pointer
**      INPUT:          production name
**              IMPLICIT:
**
**      RETURNS:
*/ 
   
BNFoPRODUCTION *BnfGetProduction (ICAoSYNTAX *syntax, 
				  char *name, enum classtype type )

{
  BNFoPRODUCTION *production;

  if (!syntax) syntax = Syntax;

  if (syntax->prod) { /* level 3 */
    VARo *var;

    if (!(var = AnyGetListAssoc (syntax->prod, name)))
      production = NULL;
    else 
      production = VarGetObject (NULL, var);
      
  }
  else if( LstHashSearch((void **) &syntax->prodList, name) ) {
    if( syntax->prodList->isInit && type == Production)
      _ErrExit3(e__icabnfGetProd, name, BuffPtr);
    production = syntax->prodList->pointer;
  }
  return(production);
}


/****** BnfExecTask ************************************************************
**
**      prepare and make local parser task. The parser should parse line
**      with instruction and create token list. This list is an input of
**      BnfStackProgram
**
**      INPUT:		string cointains BNF action commands
**			corresponding production node pointer 
**              IMPLICIT:
**
**      RETURNS:
*/ 

static void BnfExecTask(BNFoPRODUCTION *taskNode)

{
  BNFoPRODUCTION *node;
  TOKoLIST       *inTokList;
  CURSORo         cursorSave;

  INT4 c;

/*
     output token list of taskNode is input for dependent tasks
*/
  inTokList = taskNode->wrtTokList;
  for (c=0; (node = TaskNextActiveNode(taskNode->taskLinks, &c));) {
    CursorSave(&cursorSave, Job->cursor);
    Job->cursor = CursorNew();
    CursorInstall(Job->cursor, TokGetFirst(inTokList), inTokList);
    BnfParseProdLoop(node);
    CursorRestore(Job->cursor, &cursorSave);
  }
}


/****** BnfParseProduction ****************************************************
**
**      parse production: do pre-parsing actions, shift cursor to fist
**      non space character, save it position, parse and if the parser
**      succeed restore cursor and do post-parsing actions, move cursor
**      in new position.
**
**      INPUT:		production pointer
**              IMPLICIT:
**
**      RETURNS:	TRUE if parser succeed
**			FALSE otherwise
*/

INT4 BnfParseProduction(BNFoPRODUCTION *production)

{
  BNFoNODE      *node;
  CURSORoANCHOR  anchor;

  INT4        rv;

  Job->currNode = (BNFoNODE *)production;
  _BnfExecPre (production)

  if (Job->doAdvance)
    CursorAdvance(Job->cursor, Job->syntax->ign, Job->syntax->cmntRe,
		  production->action&BNFxNOSKIP, &Job->doAdvance);

    /*  if (!Job->doAdvance || CursorAdvance(Job->cursor, Job->syntax->ign, 
			 Job->syntax->cmntRe,
                         production->action&BNFxNOSKIP, &Job->doAdvance) ){
			 */
    CursorDefineAnchor(Job->cursor, &anchor);
    node = production->node;
    rv = (*node->parse) (node);
    if (Job->parseError)
      switch(Job->parseError) {
      case(ICAxNEWPARSEERROR):
	_ErrCatch();
        IcaErrPrint(production->name, Job->failPattern,
	            CursorGetBegin(Job->cursor), CursorGetPtr(Job->cursor));
	        _ErrThrow(ICAxPARSEERROR); /*te!!! why???*/
        return(FALSE);
        break;
      case(ICAxPARSEERROR):
        return(FALSE);
        break;
      }
    if( rv == TRUE ) {
      Job->failPattern = NULL;
      CursorSetGlobalMatch(Job->cursor, &anchor);
      _BnfExecPost (production)
      CursorIncrement(Job->cursor);
    }
    if(production->taskLinks) /* should task be executed even if
                                 production failed? te!!! */
      BnfExecTask(production);
    return(rv);
    /*
  }
  return(FALSE);
  */
}

/****** BnfParseProdLoop ****************************************************
**
**      parse production in loop. It takes corresponded token list
**      and parse all the token with corresponded token-coder in it, do
**      pre-parsing actions, shift cursor to fist non space character,
**      save it position, parse and if the parser succeed restore cursor
**      and do post-parsing actions, move cursor in new position.
**
**      INPUT:		production pointer
**              IMPLICIT:
**
**      RETURNS:	TRUE if all tokens was parsed
**			FALSE otherwise
*/

INT4 BnfParseProdLoop(BNFoPRODUCTION *production)

{
  BNFoNODE      *node;
  CURSORoANCHOR anchor;
  INT4          rv, isExcept;

  TokRewindList(production->rdTokList);
  while (TRUE) {
    Job->currNode = (BNFoNODE *)production;
    _BnfExecPre (production)
    if (Job->parseError) {
      _ErrCatch();
      isExcept = 1;
    }
    else 
      isExcept =0;

    if (isExcept || !Job->cursor->len)
      return 0; 

    if (Job->doAdvance)
      CursorAdvance(Job->cursor, Job->syntax->ign, Job->syntax->cmntRe,
		    production->action&BNFxNOSKIP, &Job->doAdvance);
    
    CursorDefineAnchor(Job->cursor, &anchor);
    node = production->node;
    rv = (*node->parse) (node);
    if(Job->parseError)
      switch(Job->parseError) {
      case(ICAxNEWPARSEERROR):
	_ErrCatch();
	IcaErrPrint(production->name, Job->failPattern,
		    CursorGetBegin(Job->cursor), CursorGetPtr(Job->cursor));
	continue;
	break;
      default:
	continue;
	break;
      }
    if( rv == TRUE ) {
      Job->failPattern = NULL;
      CursorSetGlobalMatch(Job->cursor, &anchor);
      Job->currNode = (BNFoNODE *)production;
      _BnfExecPost (production)
        CursorIncrement(Job->cursor);
      if(production->taskLinks)
	BnfExecTask(production);
    }
  }
}

/****** BnfParseProdName ******************************************************
**
**      parse production name: do pre-parsing actions, shift cursor
**      to fist non space character, save it position, call the
**      production parser and if the parser succeed restore cursor
**      and do post-parsing actions, move cursor in new position. if
**      production name is optiinal restore the cursor.
**
**      INPUT:          production name pointer
**              IMPLICIT:
**
**      RETURNS:        TRUE if parser succeed
**                      FALSE otherwise
*/

INT4 BnfParseProdName(BNFoPRODNAME *prodName)

{
  BNFoPRODUCTION *production;
  CURSORo         cursorSave;
  CURSORoANCHOR   anchor;
  
  INT4            rv;

  Job->currNode = (BNFoNODE *)prodName;
  _BnfExecPre (prodName)

  if(Job->doAdvance)
    CursorAdvance(Job->cursor, Job->syntax->ign, Job->syntax->cmntRe,
		  prodName->action&BNFxNOSKIP, &Job->doAdvance);

    production = prodName->production;
    if(prodName->optional) { 
      CursorSave(&cursorSave, Job->cursor);
      Job->isOptional = TRUE;
    }
    CursorDefineAnchor(Job->cursor, &anchor);
    rv = (*production->parse) (production);
    _ErrCheckJump();
    if( rv == TRUE ) {
      Job->currNode = (BNFoNODE *)prodName;
      CursorSetGlobalMatch(Job->cursor, &anchor);
      _BnfExecPost (prodName)
      CursorIncrement(Job->cursor);
    }
    else if(prodName->optional) {
      Job->isOptional = FALSE;
      CursorRestore(Job->cursor, &cursorSave);
    }
    return(rv);
}

/****** BnfParseRegExp ********************************************************
**
**      parse regular expression: do pre-parsing actions, shift cursor
**      to fist non space character, compare input parsing string with
**      the regular expression, and if it fits do post-parsing actions,
**      move cursor in new position. The "NOT" action has special treatment.
**
**      INPUT:          regular expression name pointer
**              IMPLICIT:
**
**      RETURNS:        TRUE if regular expression succeed
**                      FALSE otherwise
**			attention! NOT action reverse RETURN value
*/

INT4 BnfParseRegExp(BNFoREGEXP *pattern)

{
  INT4            rv;

  Job->currNode = (BNFoNODE *)pattern;
  _BnfExecPre (pattern)

  if(!Job->doAdvance || CursorAdvance(Job->cursor, Job->syntax->ign, 
		        Job->syntax->cmntRe,
                        pattern->action&BNFxNOSKIP, &Job->doAdvance) ){
    rv = BnfCompareRegExp(Job->cursor, pattern->expression);

    /* only a probe */
    if(pattern->action&(BNFxNOT|BNFxPROBE)) {
      if (pattern->action & BNFxNOT)
	rv = !rv;
      if (rv) { /* braces, macro! te!!! */
	_BnfExecPost (pattern)
      }
      CursorResetMatch (Job->cursor);
      return(rv);
    }

    if(rv) {
      Job->regExp = pattern->expression;
      _BnfExecPost (pattern)
      if( Job->isTrace & 1 )
         BnfTrace(1, "RegExp", pattern->name);
      CursorIncrement(Job->cursor);
      Job->doAdvance = 1;
    }
    else {
      Job->doAdvance = Job->cursor->len ? 1 : 1;
      Job->failPattern = pattern->name;
    }
    return(rv);
  }
  return(FALSE);
}

/****** BnfParseLiteral *******************************************************
**
**      parse literal expression: do pre-parsing actions, shift cursor
**      to fist non space character, compare input parsing string with
**      the literal expression, and if it fits do post-parsing actions,
**      move cursor in new position. The "NOT" action has special treatment.
**
**      INPUT:          literal expression pointer
**              IMPLICIT:
**
**      RETURNS:        TRUE if literal expression succeed
**                      FALSE otherwise
**			attention! NOT action reverse RETURN value
*/

INT4 BnfParseLiteral(BNFoLITERAL *literal)

{
  INT4            rv;

  Job->currNode = literal;
  _BnfExecPre (literal)

  if (!Job->doAdvance || CursorAdvance(Job->cursor, Job->syntax->ign, 
		         Job->syntax->cmntRe,
                         literal->action&BNFxNOSKIP, &Job->doAdvance) ){
    rv = BnfCompareLiteral(Job->cursor, literal->action, literal->name);

    /* only a probe */
    if(literal->action&(BNFxNOT|BNFxPROBE)) {
      if (literal->action & BNFxNOT)
	rv = !rv;
      if (rv) { /* braces, macro! te!!! */
	_BnfExecPost (literal)
      }
      CursorResetMatch (Job->cursor);
      return rv;
    }

    if(rv) {
      _BnfExecPost (literal)
      if( Job->isTrace & 1 )
         BnfTrace(1, "Literal", literal->name);
      CursorIncrement(Job->cursor);
      Job->doAdvance = 1;
    }
    else {
      Job->doAdvance = Job->cursor->len ? 1 : 1;
      Job->failPattern = literal->name;
    }
    return(rv);
  }
  return(FALSE);
}

/****** BnfParseCommand *******************************************************
**
**      parse asterisk expression: do pre-parsing actions do
**      post-parsing actions, move cursor in new position.
**
**      INPUT:          command node pointer
**              IMPLICIT:
**
**      RETURNS:        TRUE if input is expire
*/

INT4 BnfParseCommand(BNFoNODE *node)
{
  INT4 flag;

  flag = CursorIsEnd(Job->cursor);
  Job->currNode = node;
  _BnfExecPre (node)
  _BnfExecPost (node)
  if (Job->parseError) {
    _ErrCatch();
    return 0;
  }
  CursorIncrement(Job->cursor);		/* program may set a match */
  if(flag)
    return(TRUE);
  else
    return( !CursorIsEnd(Job->cursor) );
}

/****** BnfParseInputEnd *****************************************************
**
**      check end of the input stream condition.
**      It check end of file/token_list 
**
**      INPUT:          end of input node pointer
**              IMPLICIT:
**
**      RETURNS:        TRUE if ther is nothing to read
**                      FALSE otherwise
*/

INT4 BnfParseInputEnd(BNFoNODE *node)

{
  Job->currNode = node;
  if (CursorAdvance(Job->cursor, Job->syntax->ign, Job->syntax->cmntRe,
                     node->action&BNFxNOSKIP, &Job->doAdvance) ){
    _ErrThrow(ICAxPARSEERROR);
    IcaErrPrint(node->name, ENDOFINPUT, CursorGetBegin(Job->cursor),
                CursorGetPtr(Job->cursor));
    return(FALSE);
  }
  else {
    _BnfExecPre (node)
    _BnfExecPost (node)
    return(TRUE);
  }
}

/****** BnfParseLineStart *****************************************************
**
**      check the cursor position, if it at the beginning of the line do
**      pre/post-parsing action.
**
**      INPUT:          line start node pointer
**              IMPLICIT:
**
**      RETURNS:        TRUE if literal expression succeed
**                      FALSE otherwise
*/

INT4 BnfParseLineStart(BNFoNODE *node)

{
  INT4 rv;

  Job->currNode = node;
  rv = CursorIsLineStart(Job->cursor);
  if( rv == TRUE ) {
    _BnfExecPre (node)
    _BnfExecPost (node)
    CursorIncrement(Job->cursor);		/* program may set a match */
  }
  return(rv);
}

/****** BnfParseTerm **********************************************************
**
**      a term node has a list of nodes that should be parsed
**      one by one. In the loop it calls all the nodes and checks the
**      return value. The return value can be changed depending on the
**      type of node.
**
**      INPUT:          term node pointer
**              IMPLICIT:
**
**      RETURNS:        TRUE if term succeed
**                      FALSE otherwise
*/

INT4 BnfParseTerm(BNFoTERM *term)

{
  INT4         rv, 
               trueCount;
  BNFoREPORT  *factor;
  BNFoNODE    *node;
  enum repeat  counter;

  rv = TRUE;
  trueCount = 0;

  factor = term->factorList;
  while( factor->node != NULL && rv == TRUE) {
    node = factor->node;
    counter = factor->counter;
    rv = (*node->parse) (node);
    _ErrCheckJump();
    if(rv)
      trueCount++;
    switch(counter) {
      case One:
	if(trueCount >= 1 && !rv) {
	  _ErrThrow(ICAxNEWPARSEERROR);
	  return(FALSE);
	}
	break;

      case ZeroOrOne:
        rv = TRUE;
        break;
      
      case ZeroOrMore:
	if( rv == TRUE )
          while( (*node->parse)(node) );
        _ErrCheckJump();
        rv = TRUE;
	break;
      
      case OneOrMore:
	if(trueCount >= 1 && !rv) {
	  _ErrThrow(ICAxNEWPARSEERROR);
	  return(FALSE);
	}
	if( rv == TRUE )
          while( (*node->parse)(node) );
        _ErrCheckJump();
	break;
    }
  factor++;
  }
  return(rv);
}

/****** BnfParseChoice ********************************************************
** 
**      a choice node has a list of nodes that should be parsed one by
**      one until some of them does not succeed. It calls all the nodes
**      and checks the return value. If the return value is TRUE - stop
**      and return TRUE. If no one node in choise list did not succeed -
**      restore the cursor position and return FALSE
**
**      INPUT:          choice node pointer
**              IMPLICIT:
**
**      RETURNS:        TRUE if choice succeed
**                      FALSE otherwise
*/

INT4 BnfParseChoice(BNFoCHOICE *choice)

{
  INT4          rv;
  CURSORoANCHOR anchor;
  BNFoNODE     *node,
              **termList;

  termList = choice->termList;
  rv = FALSE;
  CursorDefineAnchor(Job->cursor, &anchor);
  while(*termList != NULL && rv == FALSE) {
    node = *termList;
    rv = (*node->parse) (node);
    _ErrCheckJump();
    termList++;
  }
  return(rv);
}

/****** BnfCompareLiteral *****************************************************
**
**      compare to strings. One defined by cursor the other is given
**      as the argument. If "NOCASE" flag sets on case unsensitive
**      comparison will be done.
**
**      INPUT:          pointer to cursor function
**			action flag
**			string to compare
**              IMPLICIT:
**
**      RETURNS:        TRUE if strings are equal
**                      FALSE otherwise
*/

static INT4 BnfCompareLiteral(CURSORo *cursor, INT4 action, char *literal) 

{
  char	*string1,
	*string2;       
 
  INT4	len,
	l;

  len = strlen(literal);
  if( len > CursorLength(cursor) )
    return(FALSE);
    
  string1 = literal;
  string2 = CursorGetPtr(cursor);
  if (BNFxNOCASE&action) {
    l = 0;
    while ((toupper(*string1++) == toupper(*string2++)) && l++ <= len)
      ;
    if (l != len)
      return 0;
  }
  else if (memcmp(string1, string2, len) != 0)
    return 0;
  CursorSetMatch(cursor, len);
  return 1;
}

/****** BnfCompareRegExp ******************************************************
**
**      function trys to fit given regular expression to the string
**      defined by cursor every time starting from the fist character.
**      Every regExp should have ^ at the beginning. To be certain the
**      next to last character in the line temporary substitute to NULL.
**
**      INPUT:          pointer to cursor function
**			string to compare
**              IMPLICIT:
**
**      RETURNS:        TRUE if strings are equal
**      
**      function trys to fit given regular expresiion fo the string defined by cursor. To be certain the next to last character in the line temporary substitude to NULL.
**                      FALSE otherwise
*/

static INT4 BnfCompareRegExp(CURSORo *cursor, regexp *regExp)

{ 
 INT4 rv;
  
  CursorRestrictLength(cursor);
  rv = RegExec(regExp, CursorGetPtr(cursor));
  CursorRestoreChar(cursor);
  if( rv == 1 ) {
    CursorSetMatch(cursor,(INT4)(regExp->endp[0] - regExp->startp[0]));
    return(TRUE);
  }
  return(FALSE);
}



/****** BnfTrace **************************************************************
**      
**      produce debug output
*/ 

static void BnfTrace(INT4 mode, char *tag, char *name)

{

#define MAXLEN 1000

  char *token,
       *listInName,
       *listOutName,
        str[MAXLEN]; 
  
  INT4  i;
  
  token = CursorGetMatchCopy(Job->cursor);
  i = MIN(MAXLEN-1, strlen(token));
  memset(str, 0,MAXLEN);
  listInName = VarGetStr(VarGet(&Job->scope, VARTOKLISTIN));
  listOutName = VarGetStr(VarGet(&Job->scope, VARTOKLISTOUT));
  switch(mode) {
    case 0:
      printf("Input: %s\n",listInName);
      break;
    case 1:
      printf("Input: %s Output: %s\n", listInName, listOutName);
      break;
  }
  printf("%s shift: %s |%s|\n", tag, name, strncpy(str, token ,i));
}

/****** BnfIsNodeActive *******************************************************
**
*/

static INT4 BnfIsNodeActive(BNFoNODE *node)
{
  if (node->exec[0] || node->exec[1] || node->exec[2])
    return 1;
  return 0;
}

/****** BnfPruneTree **********************************************************
**
*/

void BnfPruneTree (BNFoNODE **nodePtr, Int4 passN)
{
  BNFoREPORT *report;
  BNFoNODE   **term, *node=*nodePtr;
  Int4       k;

  return;
  switch (node->type) {
  case Choice:
    for (term=((BNFoCHOICE *)node)->termList; *term; term++)
      BnfPruneTree (term, passN);
    break;
  case Term:
    for (k=0, report=((BNFoTERM *)node)->factorList; report->node; 
	 report++,k++)
      BnfPruneTree (&report->node, passN);
    if (k==1 && passN==1) { /* term list with only one term and no counter */
      report--;
      if (!report->counter)
	node = report->node;
    }
    break;
  case Production:
    if (passN == 2) {
      if (!BnfIsNodeActive (node)) {
	node = ((BNFoPRODUCTION *) node)->node;
      }
    }
    else {
      BnfPruneTree (&((BNFoPRODUCTION*) node)->node, passN);
      LstSetObjCurrent((void **) &Syntax->prodList, node);
    }
    break;
  case ProdName:
    if (!BnfIsNodeActive (node)) {
      node = (BNFoNODE*) BnfGetProduction (Syntax, node->name, ProdName);
    }
    break;
  }
  *nodePtr = node;
}

/****** BnfLinkBnfNet *********************************************************
**
*/

static void BnfLinkBnfNet()

{
  LstFirst((void **) &Syntax->prodList);
  do {
    if( !Syntax->prodList->isInit )
      _ErrExit2(e__icabnfLinkBnfNet, Syntax->prodList->name);
/*     BnfPruneTree(Syntax->prodList->pointer); */
  } while( LstNext((void **) &Syntax->prodList) );
}


/****** BnfPrintTree **********************************************************
**
*/

static char *tabs = " 							";
static INT4   Level = 1;

static void BnfPrintTree(BNFoCHOICE *choiceNode)

{
  BNFoREPORT     *report;
  BNFoCHOICE     *choice;
  BNFoTERM       *term;
  BNFoNODE       *node,
                **termList;
  BNFoPRODUCTION *production,
                 *extendNode;
  enum repeat     counter;
  char            marg[MAXPRINTSIZE],
                  edit[MAXPRINTSIZE];

  strcpy(marg, tabs);
  marg[Level] = '\0';
  if(choiceNode->name != NULL) {
    strcpy(edit,choiceNode->name);
    SmSwapS(edit,"\n","$");
  }
  printf("%sLevel: %d\n%s%s ", marg, Level, marg, edit);
  extendNode = (BNFoPRODUCTION *)choiceNode;
  switch(choiceNode->type) {
    case ProdName:
      printf("ProdName\n");
      break;
    case Production:
      printf("Production\n");
      break;
    case Literal:
      printf("Literal\n");
      break;
    case Regexp:
      printf("RegExp\n");
      break;
    case Term:
      printf("Term\n");
      break;
    case Choice:
      printf("Choice\n");
      break;
    case Command:
      printf("Command\n");
      break;
    case LineStart:
      printf("LineStart\n");
      break;
    default:
      printf("%s unknown\n" ,marg);
      break;
  }
  Level++;
  if(choiceNode->type == Production) {
    production = (BNFoPRODUCTION *)choiceNode;
    choice = (BNFoCHOICE *)production->node;
    BnfPrintTree(choice);
  }
  else if(choiceNode->type == Choice ) {
    termList = choiceNode->termList;
    while( *termList != NULL) {
      printf("%s======= Choice =======\n", marg);
      node = *termList;
      choice = (BNFoCHOICE *)node;
      BnfPrintTree(choice);
      termList++;
    }
  }
  else if(choiceNode->type == Term) {
    term = (BNFoTERM *)choiceNode;
    report = term->factorList;
    while( report->node != NULL) {
      node = report->node;
      counter = report->counter;
      switch(counter) {
        case ZeroOrOne:
        printf("%s======= ZeroOrOne =======\n", marg);
        break;
      case One:
        printf("%s======= One =======\n", marg);
	break;
      case ZeroOrMore:
        printf("%s======= ZeroOrMore =======\n", marg);
	break;
      }
      choice = (BNFoCHOICE *)node;
      BnfPrintTree(choice);
      report++;
    }
  }
  Level--;  
}


/*****************************************************************************/
/* for 2nd bootstrapping of icarus */
/*****************************************************************************/


/******************* making syntax tree **********************************/

static  BNFoPRODUCTION *currProduction;

INT4 IopBody (VARo *var);

BNFoNODE *IopNodeProg_ (Int4 runTime, BNFoNODE *node, VARo *nodeProg)
{
  VARo     *prog[3], **stmnt[3], **tmp;
  INT4     count[3], k, time;

  if (runTime)
    IargGetArgs ("node|prog", &node, &nodeProg);

  /*
  ** find out how many statements for each execution time 
  ** commands can have multiple execution times!
  */


  count[0]=count[1]=count[2]=0;
  if (nodeProg)
    for (tmp = VarGetArgs (nodeProg); *tmp; tmp++){
      time = VarGetCode (*tmp); 
      if (time & IARGxINIT)
	count[0]++;
      if (time & IARGxPRE)
	count[1]++;
      if (time & IARGxPOST || !time) 
	count[2]++;
    }

  if (ParGetBool ("icaIsDebug")) {
    count[1]++; count[2]++;
  }

  /* allocate program vars and argument lists */
  for (k=0; k < 3; k++)
    if (count[k]) {
      prog[k] = VarNew ();
      stmnt[k] = (VARo **) malloc ((count[k] + 1) * sizeof (void *));
      VarSetArgs (prog[k], stmnt[k]);
      VarSetReadInt (prog[k], (FUNC)IopBody);
    }
    else
      prog[k] = NULL;


  count[0]=count[1]=count[2]=0;
  if (ParGetBool ("icaIsDebug")) {
    stmnt[1][count[1]++] = DbgGetStatement (IARGxPRE);
    stmnt[2][count[2]++] = DbgGetStatement (IARGxPOST);
  }

  /* distribute statements into time specific programs */
  if (nodeProg)
    for (tmp = VarGetArgs (nodeProg); *tmp; tmp++){
      time = VarGetCode (*tmp); 
      if (time & IARGxINIT)
	stmnt[0][count[0]++] = *tmp;
      if (time & IARGxPRE)
	stmnt[1][count[1]++] = *tmp;
      if (time & IARGxPOST || !time)
	stmnt[2][count[2]++] = *tmp;
    }

  for (k=0; k < 3; k++)
    if (count[k])
      stmnt[k][count[k]] = NULL;

  for (k=0; k < 3; k++)
    node->exec[k] = prog[k];

  if (runTime)
    IcaReturn ("node", node);
  else
    return node;
}



BNFoNODE *IopProd_ (Int4 runTime)
{
  BNFoPRODUCTION *prod;
  BNFoNODE       *node;

  prod = (BNFoPRODUCTION *) calloc (sizeof(BNFoPRODUCTION), 1);
  prod->type = Production;
  prod->parse = BnfParseProduction;

  if (runTime)
    IcaReturn ("node", prod);
  else 
    return (BNFoNODE*)prod;
}




VARo *IopEndProd_ (Int4 runTime, BNFoNODE *node, BNFoPRODUCTION *prod)
{
  VARo           *var;

  if (runTime)
    IargGetArgs ("node|prod", &node, &prod); 

  prod->node = node; 
  var = VarNew ();
    VarSetObject ("production", var, prod);

  if (runTime)
    IcaReturn ("var", var);
  else 
    return var;
}


BNFoNODE *IopExpr_ (Int4 runTime)
{
  static VARoStack *stack=NULL;
  VARo       *tmp;
  BNFoCHOICE *node;
  INT4       k, l;

  /* init tmp stack and copy from userstack until NULLNODE is found */
  stack = VarStackInit (stack);
  for (k=0; (tmp = VarPop2 (&icaStack2[3])); k++){
    if (((BNFoNODE *) VarGetObject (NULL, VarFreeze(tmp)))->type 
	== NullNode)
      break;
    VarPush2 (stack, tmp); 
  }

  if (k == 1) /* no use creating choice with one node only */
    node = (BNFoCHOICE *) VarGetObject (NULL, VarFreeze(VarPop2 (stack))); 
  else {
    /* create a 'term' node */
    node = (BNFoCHOICE *) calloc (sizeof(BNFoCHOICE), 1);
    node->type = Choice;
    node->parse = BnfParseChoice;
    node->termList = malloc ((k+1) * sizeof (BNFoNODE *));
    
    /* pop nodes and assign them to the factor list */
    for (l=0; k && (tmp = VarPop2 (stack)); k-- , l++){
      node->termList[l] = (BNFoNODE *) VarGetObject (NULL, VarFreeze(tmp));
    }
    node->termList[l] = NULL;
  }
  if (runTime)
    IcaReturn ("node", node);
  else 
    return (BNFoNODE*)node;
}



BNFoNODE *IopTerm_ (Int4 runTime)
{
  static VARoStack *stack=NULL;
  VARo     *tmp;
  BNFoTERM *node;
  INT4     k, l;
   
  /* init tmp stack and copy from userstack until NULLNODE is found */ 
  stack = VarStackInit (stack);
  for (k=0; (tmp = VarPop2 (&icaStack2[3])); k++){
    if (((BNFoNODE *) VarGetObject (NULL, VarFreeze (tmp)))->type 
	== NullNode)
      break;
    node = VarGetObject (NULL, VarFreeze(tmp));
    VarPush2 (stack, tmp); 
  }

  if (k == 100000 && !node->counter) /* no use creating term with one node only */
    node = (BNFoTERM *) VarGetObject (NULL, VarFreeze(VarPop2 (stack))); 
  else {
    /* create a 'term' node */
    node = (BNFoTERM *) calloc (sizeof(BNFoTERM), 1);
    node->type = Term;
    node->parse = BnfParseTerm;
    node->factorList = malloc ((k+1) * sizeof (BNFoREPORT));
    
    /* pop nodes and assign them to the factor list */
    for (l=0; k && (tmp = VarPop2 (stack)); k-- , l++){
      tmp->isTypeEval = 1;
      node->factorList[l].node = 
	(BNFoNODE *) VarGetObject (NULL, VarFreeze(tmp));
      node->factorList[l].counter = node->factorList[l].node->counter;
    }
    node->factorList[l].node = NULL;
  }  
  if (runTime)
    IcaReturn ("node", node);
  else 
    return (BNFoNODE*)node;
}

BNFoNODE *IopNullNode_ (Int4 runTime)
{
  static BNFoNODE node;

  node.type = NullNode;
  if (runTime)
    IcaReturn ("node", &node);
  else 
    return &node;
}


BNFoNODE *IopProdName_ (Int4 runTime, STRv name, Int4 isLookAhead)
{
  BNFoPRODNAME *node;

  if (runTime)
    IargGetArgs ("name|lookahead", &name, &isLookAhead);

  node = (BNFoPRODNAME *) calloc (sizeof (BNFoPRODNAME), 1);
  node->name = (char *) malloc (strlen (_Str(name)) + 1);
  strcpy (node->name, _Str(name));
  node->type = ProdName;
  node->parse= BnfParseProdName;
  node->optional = isLookAhead;

  if (runTime)
    IcaReturn ("node", node);
  else
    return (BNFoNODE*)node;
}

BNFoNODE *IopRegexp_ (Int4 runTime, STRv reStr)
{
  BNFoREGEXP *node;
  
  if (runTime)
    IargGetArgs ("reStr", &reStr);
  StrDecode (&reStr);

  node = (BNFoREGEXP *) calloc (sizeof(BNFoREGEXP), 1);
  node->name = (char *) malloc (strlen (_Str(reStr))+2);
  node->name[0] = '^';
  strcpy (node->name + 1, _Str(reStr));
  node->type = Regexp;
  node->parse = BnfParseRegExp;
  if ((node->expression = RegComp (node->name)) == NULL)
    _ErrExit2 (e__regerror, node->name);

  if (runTime)
    IcaReturn ("node", node);
  else 
    return (BNFoNODE*)node;
}
BNFoNODE *IopLiteral_ (Int4 runTime, STRv litStr)
{
  BNFoLITERAL *node;

  if (runTime)
    IargGetArgs ("name", &litStr);
  StrDecode (&litStr);

  node = (BNFoLITERAL *) calloc (sizeof (BNFoLITERAL), 1);
  node->name = (char *) malloc (strlen (_Str(litStr))+1);
  strcpy (node->name, _Str(litStr));
  node->type = Literal;
  node->parse = BnfParseLiteral;

  if (runTime)
    IcaReturn ("node", node);
  else
    return (BNFoNODE*)node;
}

BNFoNODE *IopCommand_ (Int4 runTime)
{
  BNFoNODE *node;

  node = (BNFoNODE *) calloc (sizeof (BNFoNODE), 1);
  node->type = Command;
  node->parse = BnfParseCommand;

  if (runTime)
    IcaReturn ("node", node);
  else
    return node;
}

BNFoNODE *IopInputEnd_ (Int4 runTime)
{
  BNFoNODE *node;

  node = (BNFoNODE *) calloc (sizeof (BNFoNODE), 1);
  node->type = EndOfInput;
  node->parse = BnfParseInputEnd;

  if (runTime)
    IcaReturn ("node", node);
  else
    return node;
}


BNFoNODE *IopMakeOpt_ (Int4 runTime, BNFoNODE *node, STRv type)
{
  if (runTime)
    IargGetArgs ("node|t", &node, &type);

  switch (_Str(type)[2]) {
  case 'c': /* once */
    node->counter = ZeroOrOne;
    break;
  case 'l': /* multi */
    node->counter = ZeroOrMore;
    break;
  case 'e': /* onemore */
    node->counter = OneOrMore;
    break;
  default:
    _ErrExit2 (e__unknownoption, _Str(type));
  }
  if (runTime)
    IcaReturn ("node", node);
  else
    return node;
}

void BnfPrintNode (BNFoNODE *node, INT4 level);

void BnfTreeTraverse (BNFoNODE *node, INT4 (*func)(BNFoNODE*, INT4 level), 
		      INT4 level)
{
  BNFoPRODUCTION *production;
  BNFoNODE       *nextNode, **term;
  INT4           k;
  
  (*func)((BNFoNODE *) node, level);

  if (node->type == Choice ) 
    for (term=((BNFoCHOICE *)node)->termList; (nextNode = *term); term++) 
      BnfTreeTraverse (nextNode, func, level+1);

  else if (node->type == Term) 
    for (k=0; (nextNode = ((BNFoTERM *)node)->factorList[k].node); k++)
      BnfTreeTraverse (nextNode, func, level+1);

  else if(node->type == Production) 
    BnfTreeTraverse (((BNFoPRODUCTION *)node)->node, func, level+1);
}


void BnfLinkProdName (BNFoNODE *node, INT4 level)
{
  BNFoPRODNAME *prodName;

  Job->currNode = node; /* sets the context for the node programs */
  switch (node->type) {
  case ProdName:
    prodName = (BNFoPRODNAME *) node;
    if (!(prodName->production = BnfGetProduction (Syntax, prodName->name, 0)))
      _ErrMsg3 (e__objectunknown, "production", prodName->name);
    _BnfExecInit (node)
    break;

  case Production:
  case Literal:
  case Regexp:
  case Command:
    _BnfExecInit (node)
    break;
  }
}

void BnfInitRules (ICAoSYNTAX *syntax, INT4 doPrintTree)
{
  VARo           *var;
  BNFoPRODUCTION *prod;
  Int4           c;

  Syntax = syntax;
  for (c=0; (var = AnyNextInList (syntax->prod, &c)); ) {
    prod = VarGetObject (NULL, var);
    prod->name = VarGetName (var);
    if (doPrintTree)
      BnfTreeTraverse ((BNFoNODE *) prod, (FUNC)BnfPrintNode, 1);
    BnfTreeTraverse ((BNFoNODE *) prod, (FUNC)BnfLinkProdName, 1);
    BnfPruneTree (((BNFoNODE **) &prod), 1);
  }  
  for (c=0; (var = AnyNextInList (syntax->prod, &c)); ) {
    prod = VarGetObject (NULL, var);
    BnfPruneTree (&prod->node, 2);
  }
  

}


INT4 IopParse (Int4 runTime, VARo *prod, STRv str, 
	       STRv startName, STRv fileName, Int4 doPrintTree,
               STRv skip, STRv cmnt)
{
  static ICAoSYNTAX syntax;
  ICAoSYNTAX     *tmp;
  FILEo          *file;
  BNFoPRODUCTION *start;
  ICAoJOB        *job=NULL;

  if (runTime)
    IargGetArgs ("prod|string|start|fileName|tree|skip|comment", 
		 &prod, &str, &startName, &fileName, &doPrintTree, 
		 &skip, &cmnt);

  if (fileName) {
    file = FileNew (_Str(fileName));
    if (!FileOpen (file))
      _ErrExit2 (e__filnotok, _Str (fileName));
  }
  else
    file = NULL;

  if (prod) {
    memset (&syntax, 0, sizeof (ICAoSYNTAX));
    syntax.ign = skip ? _Str (skip) : "";
    syntax.ignAlt = "";
    syntax.cmnt = cmnt ? _Str (cmnt) : "";
    syntax.commandSyntax = (ICAoSYNTAX *) LibObjByName ("syntax", "icarus");
    syntax.prod = prod;

    BnfInitRules (&syntax, doPrintTree);
    tmp = &syntax;
  }
  else
    tmp = Job->syntax;

  job = IcaCreateJob (tmp); /* retain variable scope of calling context */
  job->scope = Job->scope;
  job->fileName = IcaGetCurrFileName ("progFlag");
  if (str)
    IcaJobSetString (job, _Str(str));
  else if (file)
    IcaJobSetFile (job, file);
  else 
    _ErrExit2 (e__error, "IopParse");

  if (startName)
    IcaDoJob (job, _Str(startName));
  else
    _ErrExit2 (e__error, "IopParse");

  job->scope = NULL; /* scope was 'borrowed' from parent job */
  IcaJobDestroy (&job); 

  StrDel (str);
  StrDel (startName);
  StrDel (fileName);
  StrDel (skip);
  StrDel (cmnt);
}


char *BnfNodeString (BNFoNODE *node)
{
  static STRv s=NULL;
  if (!s)
    s = StrNew ();
  else
    StrClear (&s);

  switch(node->type) {
    case ProdName:
      StrPrintf (&s, "%-10s %s", "ProdName", node->name);
      break;
    case Production:
      StrPrintf (&s, "%-10s %s", "Prod", node->name);
      break;
    case Literal:
      StrPrintf (&s, "%-10s '%s'", "Lit", node->name);
      break;
    case Regexp:
      StrPrintf (&s, "%-10s /%s/", "Regexp", node->name);
      break;
    case Term:
      StrPrintf (&s, "%-10s", "Term");
      break;
    case Choice:
      StrPrintf (&s, "%-10s", "Choice");
      break;
    case Command:
      StrPrintf (&s, "%-10s", "Action");
      break;
    default:
      StrPrintf (&s, "%-10s", "Unknown");
      break;
  }  
  return _Str (StrEncode (&s));
}


void IopTree ()
{
  printf ("====================================\n");
  BnfTreeTraverse ((BNFoNODE *) Job->currNode, (FUNC)BnfPrintNode, 1);
  printf ("====================================\n");
}



/******************* making syntax tree - END ********************************/



INT4 BnfSetOpFunctions ()
{
  IcaSetFunction("IopProd_",       (Func)IopProd_);
  IcaSetFunction("IopEndProd_",    (Func)IopEndProd_);
  IcaSetFunction("IopExpr_",       (Func)IopExpr_);   
  IcaSetFunction("IopTerm_",       (Func)IopTerm_);   
  IcaSetFunction("IopNullNode_",   (Func)IopNullNode_);
  IcaSetFunction("IopRegexp_",     (Func)IopRegexp_); 
  IcaSetFunction("IopProdName_",   (Func)IopProdName_);
  IcaSetFunction("IopLiteral_",    (Func)IopLiteral_);
  IcaSetFunction("IopCommand_",    (Func)IopCommand_);
  IcaSetFunction("IopInputEnd_",    (Func)IopInputEnd_);
  IcaSetFunction("IopMakeOpt_",    (Func)IopMakeOpt_);
  IcaSetFunction("IopNodeProg_",   (Func)IopNodeProg_);

  IcaSetFunction("IopParse",        (Func)IopParse);
  IcaSetFunction("IopTree",        (Func)IopTree);
}

IopNullNode_);
  IcaSetFunction("IopRegexp_",     (Func)IopRegexp_); 
  IcaSetFunction("IopProdName_",   (Func)IopProdName_);
  IcaSetFunction("IopLiteral_",    (Func)IopLiteral_);
  IcaSetFunction("IopCommand_srs/src/icabnf.h
**    
**    $RCSfile: icabnf.h,v $
**    $Revision: 1.7 $
**    $Date: 1996/11/20 16:36:04 $
**    $Author: etzold $
**    
**    $Locker:  $ 
**    $State: Exp $
**                  
**                  
**                  Copyright by Thure Etzold
**             
**             Author: Anatoly Ulyanov
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387451
**                     Email: ulyanov@embl-heidelberg.de
**
*/

enum repeat     {One, ZeroOrMore, ZeroOrOne, OneOrMore};
enum tokCode    {BNFxNAM=1, BNFxCOM, BNFxLSTART, BNFxACT, BNFxLIT, BNFxREG,
                 BNFxEQUAL='=', BNFxEOT='.', BNFxEOS=';'};
enum classtype  {Production, ProdName, Literal, Regexp, Term, Choice,
                 Command, LineStart, EndOfInput, ProdLoop, NullNode};
enum BNFeClass  {BNFxProduction, BNFxProdName, BNFxLiteral, BNFxRegexp, 
		 BNFxTerm, BNFxChoice, BNFxCommand, BNFxLineStart, 
		 BNFxEndOfInput, BNFxProdLoop, BNFxNodeTypesN};

enum BNFeTime {BNFxBUILDTIME=1, BNFxPREPARSE=2, BNFxPOSTPARSE=4};


#define BNFxNOACTION	  0  /*	all action is turned off */
#define BNFxACTION	  8  /*	an action is associated with token */
#define BNFxNOT		 16  /*	match inversion */
#define BNFxNOSKIP	 32  /*	do not skip whitespaces till next token */
#define BNFxNOCASE       64  /* disregard case */
#define BNFxUNIQ   	128  /*	token must be uniq */
#define BNFxPROBE       256  /* like NOT but assertive */

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  MACROs for common elements of structures
*/

#define BASECLASS  \
char              *name;     	/* name, literal, regexp ... */ \
enum classtype    type;     	/* Production Regexp Term Choice ... */ \
char              dbgBreak;      /* for the debugger */ \
enum repeat	  counter;      /* loop counter(), {}, [] or {}  */ \
INT4	          (*parse)()  	/* method to parse */ \
 
#define BASEACTION \
INT4	           action;	/* action mask */ \
struct TOKoLIST   *rdTokList;	/* toklist to be read */ \
struct TOKoLIST   *wrtTokList;	/* toklist where to write */ \
struct PROGo      *prog;        /* program attached to node */ \
struct VARo       *exec[3]

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
** definition of main classes
*/

typedef struct BNFoNODE {
  BASECLASS;
  BASEACTION;
} BNFoNODE, BNFoLITERAL;

typedef struct BNFoPRODUCTION {
  BASECLASS;        
  BASEACTION;	    
  struct BNFoNODE   *node; 
  struct TASKoLINKS *taskLinks;
  Int4              *inCode;
  Int4              inCodeN;
  Int4              inCodeAllocN;
} BNFoPRODUCTION;

typedef struct BNFoPRODNAME {
  BASECLASS;
  BASEACTION;
  struct BNFoPRODUCTION *production; /* pointer to coresponded production */
  INT4                   optional;   /* optinal `?' operation TRUE/FALSE*/
} BNFoPRODNAME;

typedef struct BNFoREGEXP {
  BASECLASS;
  BASEACTION;
  struct regexp        *expression;
} BNFoREGEXP;

typedef struct BNFoTERM {
  BASECLASS;
  struct BNFoREPORT    *factorList;
} BNFoTERM;

typedef struct BNFoCHOICE {
  BASECLASS;
  struct BNFoNODE **termList;
} BNFoCHOICE;

typedef struct BNFoREPORT {
  enum repeat	    counter;    /* loop counter(), {}, [] or {}  */
  struct BNFoNODE  *node;    
} BNFoREPORT;

/* module prototypes ***************************************/

void BnfBuild(ICAoSYNTAX *);
INT4 BnfParseProduction(BNFoPRODUCTION *);
BNFoPRODUCTION *BnfGetProduction (ICAoSYNTAX *syntax, char *, enum classtype);
char *BnfNodeString (struct BNFoNODE *node);


#define _BnfExecInit(node) \
      if ((node)->exec[0]) {\
        Job->time=BNFxBUILDTIME; VarExec ((node)->exec[0]);}

#define _BnfExecPre(node) \
      if (Job->isDebug) IopDebug (BNFxPREPARSE);\
      if ((node)->exec[1]) \
        {Job->time=BNFxPREPARSE; VarExec ((node)->exec[1]);}

#define _BnfExecPost(node) \
      if (Job->isDebug) IopDebug (BNFxPOSTPARSE);\
      if ((node)->exec[2]) \
        {Job->time=BNFxPOSTPARSE; VarExec ((node)->exec[2]);}


;
char *BnfNodeString (struct BNFoNODE *node);


#define _BnfExecInit(node) \
      if (srs/src/icadebug.c
#include <stdlib.h>
#include <string.h>

#include "message.h"
#include "sm.h"
#include "dict.h"
#include "strv.h"
#include "termio.h"
#include "variable.h"
#include "icarus.h"
#include "icabnf.h"
#include "icaarg.h"

#define _SRS
#include SRSINCLUDE

typedef struct IDBGoStatus {
  ICAoJOB *job;
  struct  DBGoBreak *breaks;
  Int4    breaksN;
  Int4    breaksAllocN;
  Int4    isNext;
  Int4    isBreak;
  Int4    isContinue;
  Int4    time;
} DBGoStatus;


extern ICAoJOB     *Job;
static DBGoStatus dbgStatusBuff;
static DBGoStatus *dbgStatus=&dbgStatusBuff;


void DbgSetNext ()
{
  dbgStatus->isBreak = 1;
  dbgStatus->isContinue = 1;
}

void DbgSetContinue ()
{
  dbgStatus->isBreak = 0;
  dbgStatus->isContinue = 1;
}

Int4 DbgIsBreak (DBGoStatus *dbgStatus)
{
  if (dbgStatus->isBreak) {
    dbgStatus->isBreak = 0;
    return 1;
  }
  else if (dbgStatus->time & dbgStatus->job->currNode->dbgBreak)
    return 1;
  else
    return 0;
}

Int4 DbgIsContinue (DBGoStatus *dbgStatus)
{
  if (dbgStatus->isContinue) {
    dbgStatus->isContinue = 0;
    return 1;
  }
  else
    return 0;
}

static Int4 DbgIopStatement (VARo *var)
{
  static TERMvLine led=NULL;
  VARo **arg=VarGetArgs (var);
  STRv ln;
  char prompt[500];
  Int4 time;

  if (!led)
    led = TermNewLineEditor ();

  time = VarGetInt (arg[0]);
  dbgStatus->job = Job;
  dbgStatus->time = time;

  if (DbgIsBreak (dbgStatus)) {
    while (!DbgIsContinue (dbgStatus)) {
      sprintf (prompt, "[%s %s]> ", 
	       time == IARGxPRE ? "-" : "+", BnfNodeString (Job->currNode));
      ln = TermLineEdit (led, prompt);
      IcaEvalInJob (_Str (ln), Job);
    }
  }
}


VARo *DbgGetStatement (Int4 time)
{
  VARo **args, *stmnt = VarNew (), *val;

  /* one argument with execution time */
  args = (VARo **) malloc (2*sizeof (void *));
  val = VarNew ();
  VarSetInt (val, time);
  args[0] = val; args[1] = NULL;

  
  VarSetArgs (stmnt, args);
  VarSetCode (stmnt,  IARGxCALL | IARGxPOST);
  VarSetReadInt (stmnt, (Func)DbgIopStatement);
  return stmnt;
}


 Bnfsrs/src/icadebug.h
rmLineEdit (led, prompt);
      IcaEvalInJob (_Str (ln), Job);
    }
  }
}


VARo *DbgGetStatement (Int4 time)
{
  VARo **args, *stmnt = VarNew (), *val;

  /* one argument with execution time */
  args = (VARo **) malloc (2*sizeof (void *));
  val = VarNew ();
  VarSetInt (val, time);
  args[0] = val; args[1] = NULL;

  
  VarSetArgs (stmnt, args);
  VarSetCode (stmnt,  IARGxCALL | IARG¶ £¡@  VarSetReadInt (stmnt, (Func)DbgIopStatement);
  return¶ £¡ÜŽX Bnfsrs/src/icainit.c
#include <strings.h>
#include <string.h>
#include <ctype.h>
#include <stdlib.h>
#include <stdio.h>

#define DECLARE_ONLY
#define DEFIGNORE " \n\t"
#define DEFCOMMENT "^#[^\n]*\n"

#include "srs.h"
#include "regexp.h"

static VARoSCOPE *scope = NULL;

extern ICAoJOB *Job;
extern ICAoSYNTAX *Syntax;

INT4  BnfParseProduction(BNFoPRODUCTION *);
INT4  BnfParseProdLoop(BNFoPRODUCTION *);
INT4  BnfParseRegExp(BNFoREGEXP *); 
INT4  BnfParseLiteral(BNFoLITERAL *);
INT4  BnfParseCommand(BNFoNODE *);
INT4  BnfParseLineStart(BNFoNODE *);
INT4  BnfParseInputEnd(BNFoNODE *);
INT4  BnfParseTerm(BNFoTERM *);
INT4  BnfParseChoice(BNFoCHOICE *);
INT4  BnfParseProdName(BNFoPRODNAME *); 
void  BnfPruneTree (BNFoNODE **, Int4 passN);

VARo *IopPop_(INT4, INT4);
VARo *IopBody_ (Int4 runTime);

STRv  IopInterpStr_(VARo *var, STRv str, ...);
STRv  IopInterpStr2(VARo *var, STRv str, ...);
STRv  IopSubMatch(INT4, INT4);
STRv  IopCurrToken();

/* Declaration of C variables used by some translated functions */
VARo  *a, *b, *c, *d, *e, *u, *i, *str;
Int4  opt;


void IcarusBody1 ()
{
  
IopOut (0
, 
NULL
)
;
}

void IcarusBody2 ()
{
  
IopOut (0
, 
NULL
)
;
  
IopFip (0
, 
1
)
;
  
IopPush_ (0
, 
IopOpnd_ (0
, 
NULL
, 
StrCpyS (
"mark"
)
)
, 
0
)
;
}

void IcarusBody3 ()
{
  
IopProg_ (0
)
;
}

void IcarusBody4 ()
{
  
TemplIcaAddLabel (0
, 
IopSubMatch (0
, 
1
)
, 
IopFip (0
, 
0
)
)
;
}

void IcarusBody5 ()
{
  
IopNoskip (0
)
;
}

void IcarusBody6 ()
{
  
IopProg_ (0
)
;
}

void IcarusBody7 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"string"
)
)
, 
1
)
;
}

void IcarusBody8 ()
{
  
b
 = 
IopPop_ (0
, 
0
)
;
  
IopPush_ (0
, 
IopBinop_ (0
, 
VarGetStrv (
IopPop_ (0
, 
1
)
)
, 
IopPop_ (0
, 
0
)
, 
b
)
, 
0
)
;
}

void IcarusBody9 ()
{
  
IopOut (0
, 
NULL
)
;
}

void IcarusBody10 ()
{
  
IopOut (0
, 
NULL
)
;
  
IopPush_ (0
, 
IopOpnd_ (0
, 
NULL
, 
StrCpyS (
"mark"
)
)
, 
0
)
;
}

void IcarusBody11 ()
{
  
IopProg_ (0
)
;
}

void IcarusBody12 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
NULL
, 
StrCpyS (
"mark"
)
)
, 
0
)
;
}

void IcarusBody13 ()
{
  
IopPush_ (0
, 
IopBody_ (0
)
, 
0
)
;
}

void IcarusBody14 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopSubMatch (0
, 
1
)
, 
StrCpyS (
"string"
)
)
, 
5
)
;
}

void IcarusBody15 ()
{
  
IopPush_ (0
, 
IopAssoc_ (0
, 
IopPop_ (0
, 
0
)
, 
IopPop_ (0
, 
5
)
)
, 
0
)
;
}

void IcarusBody16 ()
{
  
IopPush_ (0
, 
IopSetWrite_ (0
, 
IopPop_ (0
, 
0
)
)
, 
0
)
;
}

void IcarusBody17 ()
{
  
b
 = 
IopPop_ (0
, 
0
)
;
  
IopPush_ (0
, 
IopBinop_ (0
, 
VarGetStrv (
IopPop_ (0
, 
1
)
)
, 
IopPop_ (0
, 
0
)
, 
b
)
, 
0
)
;
}

void IcarusBody18 ()
{
  
IopNot (0
)
;
}

void IcarusBody19 ()
{
  
b
 = 
IopPop_ (0
, 
0
)
;
  
IopPush_ (0
, 
IopBinop_ (0
, 
VarGetStrv (
IopPop_ (0
, 
1
)
)
, 
IopPop_ (0
, 
0
)
, 
b
)
, 
0
)
;
}

void IcarusBody20 ()
{
  
b
 = 
IopPop_ (0
, 
0
)
;
  
IopPush_ (0
, 
IopBinop_ (0
, 
VarGetStrv (
IopPop_ (0
, 
1
)
)
, 
IopPop_ (0
, 
0
)
, 
b
)
, 
0
)
;
}

void IcarusBody21 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
NULL
, 
StrCpyS (
"null"
)
)
, 
0
)
;
}

void IcarusBody22 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"str"
)
)
, 
1
)
;
}

void IcarusBody23 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"str"
)
)
, 
1
)
;
}

void IcarusBody24 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"str"
)
)
, 
1
)
;
}

void IcarusBody25 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"str"
)
)
, 
1
)
;
}

void IcarusBody26 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"str"
)
)
, 
1
)
;
}

void IcarusBody27 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"str"
)
)
, 
1
)
;
}

void IcarusBody28 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"str"
)
)
, 
1
)
;
}

void IcarusBody29 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
NULL
, 
StrCpyS (
"mark"
)
)
, 
0
)
;
}

void IcarusBody30 ()
{
  
IopPush_ (0
, 
IopList_ (0
)
, 
0
)
;
}

void IcarusBody31 ()
{
  
IopPush_ (0
, 
IopAssoc_ (0
, 
IopPop_ (0
, 
0
)
, 
IopPop_ (0
, 
5
)
)
, 
0
)
;
}

void IcarusBody32 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopSubMatch (0
, 
1
)
, 
StrCpyS (
"string"
)
)
, 
5
)
;
}

void IcarusBody33 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"real"
)
)
, 
0
)
;
}

void IcarusBody34 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"int"
)
)
, 
0
)
;
}

void IcarusBody35 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"str"
)
)
, 
0
)
;
}

void IcarusBody36 ()
{
  
IopSetSkip (0
, 
0
, 
NULL
)
;
  
str
 = 
VarSetStrv (VarTemp (), 
StrCpyS ("")
)
;
}

void IcarusBody37 ()
{
  
IopNot (0
)
;
}

void IcarusBody38 ()
{
  
IopStrApp (0
, 
str
, 
IopCurrToken (0
)
)
;
}

void IcarusBody39 ()
{
  
IopStrApp (0
, 
str
, 
IopSubMatch (0
, 
1
)
)
;
  
IopPush_ (0
, 
IopOpnd_ (0
, 
VarGetStrv (
str
)
, 
StrCpyS (
"lambda"
)
)
, 
0
)
;
  
IopSetSkip (0
, 
1
, 
NULL
)
;
}

void IcarusBody40 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"ident"
)
)
, 
0
)
;
}

void IcarusBody41 ()
{
  
IopPush_ (0
, 
IopSelect_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"str"
)
)
, 
NULL
, 
IopPop_ (0
, 
0
)
)
, 
0
)
;
}

void IcarusBody42 ()
{
  
a
 = 
IopPop_ (0
, 
0
)
;
  
IopPush_ (0
, 
IopSelect_ (0
, 
a
, 
NULL
, 
IopPop_ (0
, 
0
)
)
, 
0
)
;
}

void IcarusBody43 ()
{
  
a
 = 
IopPop_ (0
, 
0
)
;
  
IopPush_ (0
, 
IopSelect_ (0
, 
a
, 
NULL
, 
IopPop_ (0
, 
0
)
)
, 
0
)
;
}

void IcarusBody44 ()
{
  
a
 = 
IopPop_ (0
, 
0
)
;
  
IopPush_ (0
, 
IopSelect_ (0
, 
a
, 
NULL
, 
IopPop_ (0
, 
0
)
)
, 
0
)
;
}

void IcarusBody45 ()
{
  
i
 = 
IopPop_ (0
, 
0
)
;
  
IopPush_ (0
, 
IopSelect_ (0
, 
NULL
, 
i
, 
IopPop_ (0
, 
0
)
)
, 
0
)
;
}

void IcarusBody46 ()
{
  
IopPush_ (0
, 
IopFunc_ (0
)
, 
0
)
;
}

void IcarusBody47 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
NULL
, 
StrCpyS (
"mark"
)
)
, 
0
)
;
}

void IcarusBody48 ()
{
  
IopPush_ (0
, 
IopMakeArg_ (0
, 
IopPop_ (0
, 
0
)
, 
IopOpnd_ (0
, 
StrCpyS (":::::")
, 
StrCpyS (
"str"
)
)
)
, 
0
)
;
}

void IcarusBody49 ()
{
  
IopPush_ (0
, 
IopMakeArg_ (0
, 
IopPop_ (0
, 
0
)
, 
IopOpnd_ (0
, 
StrCpyS (":::::")
, 
StrCpyS (
"str"
)
)
)
, 
0
)
;
}

void IcarusBody50 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopSubMatch (0
, 
1
)
, 
StrCpyS (
"str"
)
)
, 
0
)
;
}

void IcarusBody51 ()
{
  
a
 = 
IopPop_ (0
, 
0
)
;
  
IopPush_ (0
, 
IopMakeArg_ (0
, 
a
, 
IopPop_ (0
, 
0
)
)
, 
0
)
;
}

void IcarusBody52 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"str"
)
)
, 
0
)
;
}

void IcarusBody53 ()
{
  
opt
 = 
1
;
}

void IcarusBody54 ()
{
  
opt
 = 
0
;
}

void IcarusBody55 ()
{
  
IopPush_ (0
, 
IopRef_ (0
, 
VarSetStrv (VarTemp (), 
IopCurrToken (0
)
)
, 
opt
)
, 
0
)
;
}

void IcarusBody56 ()
{
  
IopPush_ (0
, 
IopStrMake_ (0
)
, 
0
)
;
}

void IcarusBody57 ()
{
  
IopNot (0
)
;
}

void IcarusBody58 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
NULL
, 
StrCpyS (
"mark"
)
)
, 
0
)
;
}

void IcarusBody59 ()
{
  
IopSetSkip (0
, 
0
, 
NULL
)
;
}

void IcarusBody60 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"str"
)
)
, 
0
)
;
}

void IcarusBody61 ()
{
  
IopSetSkip (0
, 
1
, 
NULL
)
;
}

void IcarusBody62 ()
{
  
IopNoskip (0
)
;
}

void IcarusBody63 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"str"
)
)
, 
0
)
;
}

void IcarusBody64 ()
{
  
IopSetSkip (0
, 
0
, 
NULL
)
;
}

void IcarusBody65 ()
{
  
IopSetSkip (0
, 
1
, 
NULL
)
;
}

void IcarusBody66 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"str"
)
)
, 
0
)
;
}

void IcarusBody67 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"str"
)
)
, 
0
)
;
}

void IcarusBody68 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
StrCpyS ("\2")
, 
StrCpyS (
"str"
)
)
, 
0
)
;
}

void IcarusBody69 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
StrCpyS ("\2")
, 
StrCpyS (
"str"
)
)
, 
0
)
;
}

void IcarusBody70 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopCurrToken (0
)
, 
StrCpyS (
"str"
)
)
, 
0
)
;
}

void IcarusBody71 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
StrCpyS ("\n")
, 
StrCpyS (
"str"
)
)
, 
0
)
;
}

void IcarusBody72 ()
{
  
IopRep (0
, 
VarSetStrv (VarTemp (), 
StrCpyS ("\2")
)
)
;
}

void IcarusBody73 ()
{
  
IopRep (0
, 
VarSetStrv (VarTemp (), 
StrCpyS ("\2")
)
)
;
}

void IcarusBody74 ()
{
  
IopSetSkip (0
, 
1
, 
NULL
)
;
}

void IcarusBody75 ()
{
  
IopSetSkip (0
, 
0
, 
NULL
)
;
}

void IcarusBody76 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
IopSubMatch (0
, 
1
)
, 
StrCpyS (
"ident"
)
)
, 
0
)
;
}

void IcarusBody77 ()
{
  
IopPush_ (0
, 
IopFile_ (0
, 
IopPop_ (0
, 
0
)
)
, 
0
)
;
}

void IcarusBody78 ()
{
  
IopPush_ (0
, 
IopPre_ (0
, 
IopPop_ (0
, 
0
)
)
, 
0
)
;
}

void IcarusBody79 ()
{
  
IopPush_ (0
, 
IopInit_ (0
, 
IopPop_ (0
, 
0
)
)
, 
0
)
;
}

void IcarusBody80 ()
{
  
a
 = 
IopPop_ (0
, 
0
)
;
  
b
 = 
IopPop_ (0
, 
0
)
;
  
IopPush_ (0
, 
IopForeach_ (0
, 
a
, 
b
, 
IopPop_ (0
, 
0
)
)
, 
0
)
;
}

void IcarusBody81 ()
{
  
b
 = 
IopPop_ (0
, 
0
)
;
  
u
 = 
IopPop_ (0
, 
0
)
;
  
c
 = 
IopPop_ (0
, 
0
)
;
  
IopPush_ (0
, 
IopFor_ (0
, 
IopPop_ (0
, 
0
)
, 
c
, 
u
, 
b
)
, 
0
)
;
}

void IcarusBody82 ()
{
  
b
 = 
IopPop_ (0
, 
0
)
;
  
IopPush_ (0
, 
IopWhile_ (0
, 
IopPop_ (0
, 
0
)
, 
b
)
, 
0
)
;
}

void IcarusBody83 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
NULL
, 
StrCpyS (
"mark"
)
)
, 
0
)
;
}

void IcarusBody84 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
StrCpyS ("1")
, 
StrCpyS (
"int"
)
)
, 
0
)
;
}

void IcarusBody85 ()
{
  
IopPush_ (0
, 
IopIf_ (0
)
, 
0
)
;
}

void IcarusBody86 ()
{
  
IopPush_ (0
, 
VarSetObject (NULL, VarTemp (), (void*)
IopProd_ (0
)
)
, 
3
)
;
}

void IcarusBody87 ()
{
  
a
 = 
IopPop_ (0
, 
3
)
;
  
IopPush_ (0
, 
IopEndProd_ (0
, 
VarGetObject (NULL, (void*)
a
)
, 
VarGetObject (NULL, (void*)
IopPop_ (0
, 
3
)
)
)
, 
0
)
;
}

void IcarusBody88 ()
{
  
IopPush_ (0
, 
VarSetObject (NULL, VarTemp (), (void*)
IopNullNode_ (0
)
)
, 
3
)
;
}

void IcarusBody89 ()
{
  
IopPush_ (0
, 
VarSetObject (NULL, VarTemp (), (void*)
IopExpr_ (0
)
)
, 
3
)
;
}

void IcarusBody90 ()
{
  
IopPush_ (0
, 
VarSetObject (NULL, VarTemp (), (void*)
IopNullNode_ (0
)
)
, 
3
)
;
}

void IcarusBody91 ()
{
  
IopPush_ (0
, 
VarSetObject (NULL, VarTemp (), (void*)
IopTerm_ (0
)
)
, 
3
)
;
}

void IcarusBody92 ()
{
  
IopProbe (0
)
;
}

void IcarusBody93 ()
{
  
IopSetSkip (0
, 
1
, 
NULL
)
;
}

void IcarusBody94 ()
{
  
IopSetSkip (0
, 
0
, 
NULL
)
;
}

void IcarusBody95 ()
{
  
IopPush_ (0
, 
VarSetObject (NULL, VarTemp (), (void*)
IopRegexp_ (0
, 
IopCurrToken (0
)
)
)
, 
3
)
;
}

void IcarusBody96 ()
{
  
IopSetSkip (0
, 
1
, 
NULL
)
;
}

void IcarusBody97 ()
{
  
IopSetSkip (0
, 
0
, 
NULL
)
;
}

void IcarusBody98 ()
{
  
IopPush_ (0
, 
VarSetObject (NULL, VarTemp (), (void*)
IopLiteral_ (0
, 
IopCurrToken (0
)
)
)
, 
3
)
;
}

void IcarusBody99 ()
{
  
IopPush_ (0
, 
VarSetObject (NULL, VarTemp (), (void*)
IopCommand_ (0
)
)
, 
3
)
;
}

void IcarusBody100 ()
{
  
IopPush_ (0
, 
VarSetObject (NULL, VarTemp (), (void*)
IopInputEnd_ (0
)
)
, 
3
)
;
}

void IcarusBody101 ()
{
  
IopPush_ (0
, 
VarSetObject (NULL, VarTemp (), (void*)
IopMakeOpt_ (0
, 
VarGetObject (NULL, (void*)
IopPop_ (0
, 
3
)
)
, 
StrCpyS (
"once"
)
)
)
, 
3
)
;
}

void IcarusBody102 ()
{
  
IopPush_ (0
, 
VarSetObject (NULL, VarTemp (), (void*)
IopMakeOpt_ (0
, 
VarGetObject (NULL, (void*)
IopPop_ (0
, 
3
)
)
, 
StrCpyS (
"multi"
)
)
)
, 
3
)
;
}

void IcarusBody103 ()
{
  
IopPush_ (0
, 
VarSetObject (NULL, VarTemp (), (void*)
IopMakeOpt_ (0
, 
VarGetObject (NULL, (void*)
IopPop_ (0
, 
3
)
)
, 
StrCpyS (
"onemore"
)
)
)
, 
3
)
;
}

void IcarusBody104 ()
{
  
a
 = 
0
;
}

void IcarusBody105 ()
{
  
IopPush_ (0
, 
VarSetObject (NULL, VarTemp (), (void*)
IopNodeProg_ (0
, 
VarGetObject (NULL, (void*)
IopPop_ (0
, 
3
)
)
, 
a
)
)
, 
3
)
;
}

void IcarusBody106 ()
{
  
IopPush_ (0
, 
IopOpnd_ (0
, 
NULL
, 
StrCpyS (
"mark"
)
)
, 
0
)
;
}

void IcarusBody107 ()
{
  
a
 = 
IopBody_ (0
)
;
}

void IcarusBody108 ()
{
  
IopPush_ (0
, 
VarSetObject (NULL, VarTemp (), (void*)
IopProdName_ (0
, 
IopCurrToken (0
)
, 
0
)
)
, 
3
)
;
}

void IcarusBody109 ()
{
  
IopPush_ (0
, 
VarSetObject (NULL, VarTemp (), (void*)
IopProdName_ (0
, 
IopCurrToken (0
)
, 
1
)
)
, 
3
)
;
}
#define PRODNUM 69
#define PRODNNUM 123
#define LITLNUM 69
#define REGNUM 43
#define TERMNUM 166
#define CHOINUM 30
#define COMMNUM 8
#define NAMENUM 8

char *_scopeName
[] = {
 "rules",
 "b",
 "str",
 "a",
 "i",
 "opt",
 "u",
 "c" 
};

VARo _var
[] = {
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody1}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody2}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody3}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody4}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody5}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody6}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody7}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody8}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody9}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody10}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody11}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody12}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody13}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody14}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody15}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody16}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody17}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody18}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody19}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody20}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody21}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody22}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody23}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody24}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody25}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody26}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody27}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody28}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody29}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody30}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody31}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody32}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody33}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody34}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody35}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody36}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody37}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody38}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody39}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody40}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody41}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody42}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody43}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody44}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody45}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody46}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody47}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody48}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody49}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody50}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody51}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody52}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody53}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody54}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody55}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody56}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody57}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody58}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody59}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody60}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody61}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody62}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody63}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody64}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody65}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody66}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody67}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody68}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody69}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody70}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody71}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody72}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody73}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody74}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody75}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody76}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody77}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody78}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody79}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody80}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody81}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody82}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody83}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody84}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody85}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody86}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody87}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody88}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody89}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody90}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody91}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody92}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody93}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody94}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody95}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody96}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody97}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody98}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody99}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody100}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody101}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody102}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody103}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody104}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody105}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody106}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody107}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody108}, NULL, NULL },
 { NULL,1,0,1,1,0,0,0, {(Func) IcarusBody109}, NULL, NULL } 
};

BNFoLITERAL _lit
[] = {
 {"=",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[6] },
 {"{",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"}",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"(",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {")",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"{",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[28] },
 {"}",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[29] },
 {"~",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"~",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"@{",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[35] },
 {".",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"(",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {")",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[41] },
 {"[",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"]",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[44] },
 {"$",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {":",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[46] },
 {"[",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"]",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"(",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {")",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"@",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"?",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[52] },
 {"\"",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[58] },
 {"\"",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[60] },
 {"|",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[63] },
 {"\n",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[70] },
 {"(",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"($",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {")",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"file",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {":",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"pre",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"init",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"foreach",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {":",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"[",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"in",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {":",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"]",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"for",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {":",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"{",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"}",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"while",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {":",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"if",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {":",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[82] },
 {"elif",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {":",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"else",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[83] },
 {"(",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {")",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"{",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"}",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"[",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"]",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"|",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"(",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {")",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {"/",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[93] },
 {"/",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 },
 {".",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[99] },
 {"?",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[100] },
 {"*",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[101] },
 {"+",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[102] },
 {"{",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[105] },
 {"}",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, &_var
[106] },
 {"_",Literal,0,One, BnfParseLiteral, 0,0,0,0, 0, 0, 0 } 
};

BNFoREGEXP _reg
[] = {
 {"^\\$([a-zA-Z0-9]+) *= *{",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[3] },
 {"^ *[a-zA-Z0-9]+:| *\\|| *}",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^[^\n]*",Regexp,0,One, BnfParseRegExp, 0,0,0,0, &_var
[4], 0, 0 },
 {"^[^\n]*\n",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^[0-9]+\\.[0-9]+",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^[a-zA-Z0-9_]+",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^[+%-][^=]",Regexp,0,One, BnfParseRegExp, 0,0,0,0, &_var
[17], 0, 0 },
 {"^(&&|\\|\\|)",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[21] },
 {"^(\\+=|=|-=|\\*=|/=)",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[22] },
 {"^(<=|=<|>=|=>|<|>|==|!=)",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[23] },
 {"^[%+-]",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[24] },
 {"^(\\*|/)",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[25] },
 {"^(\\+\\+|--|\\+)",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[26] },
 {"^(\\+\\+|--)",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[27] },
 {"^([a-zA-Z0-9_]+):",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^'(([^']+|\\\\.)*)':",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^-?[0-9]+",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^[^\n]*}@",Regexp,0,One, BnfParseRegExp, 0,0,0,0, &_var
[36], 0, 0 },
 {"^([^\n]*)}@",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[38] },
 {"^([a-zA-Z_0-9]+) *:",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[49] },
 {"^[a-zA-Z0-9_]+",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^[a-zA-Z_][a-zA-Z0-9_]*",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[51] },
 {"^[^\"'|]",Regexp,0,One, BnfParseRegExp, 0,0,0,0, &_var
[56], 0, &_var
[57] },
 {"^'",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^[^'\n]*",Regexp,0,One, BnfParseRegExp, 0,0,0,0, &_var
[61], 0, &_var
[62] },
 {"^'",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^[^\n\\$(]+",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[65] },
 {"^\\\\[^\n]",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[66] },
 {"^[($]",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[69] },
 {"^\\\\\n",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^[^\n\"\\$(]+",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^\\\\.",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^\\$([a-zA-Z0-9_]+)",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[75] },
 {"^x[ {\n\t]",Regexp,0,One, BnfParseRegExp, 0,0,0,0, &_var
[91], 0, 0 },
 {"^[^/\\\n]+",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^\\\\.",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^'",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[96] },
 {"^'",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^[^'\\\n]+",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^\\\\.",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, 0 },
 {"^x:?",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[98] },
 {"^[a-zA-Z0-9_]+",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[107] },
 {"^[a-zA-Z0-9_]+",Regexp,0,One, BnfParseRegExp, 0,0,0,0, 0, 0, &_var
[108] } 
};

BNFoTERM _term
[] = {
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm },
 {"TERM",Term,0, One, BnfParseTerm } 
};

BNFoCHOICE _choi
[] = {
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice },
 {"CHOI",Choice,0, One, BnfParseChoice } 
};

BNFoNODE _comm
[] = {
 {"COMM",Command,0, One, BnfParseCommand, 0,0,0,0, 0, 0, &_var
[10] },
 {"COMM",Command,0, One, BnfParseCommand, 0,0,0,0, 0, 0, &_var
[11] },
 {"COMM",Command,0, One, BnfParseCommand, 0,0,0,0, 0, 0, &_var
[12] },
 {"COMM",Command,0, One, BnfParseCommand, 0,0,0,0, 0, 0, &_var
[19] },
 {"COMM",Command,0, One, BnfParseCommand, 0,0,0,0, 0, 0, &_var
[20] },
 {"COMM",Command,0, One, BnfParseCommand, 0,0,0,0, 0, 0, &_var
[48] },
 {"COMM",Command,0, One, BnfParseCommand, 0,0,0,0, 0, 0, &_var
[53] },
 {"COMM",Command,0, One, BnfParseCommand, 0,0,0,0, 0, 0, &_var
[84] } 
};

BNFoPRODUCTION _prod
[] = {
 {"scan",Production,0,One, 
BnfParseProduction, 0,0,0,0, &_var
[0], &_var
[1], &_var
[2], 
(BNFoNODE*)&_term
[0], NULL, 0, 0},
 {"arr",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[4], NULL, 0, 0},
 {"ln",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[6], NULL, 0, 0},
 {"real",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[7], NULL, 0, 0},
 {"str",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[8], NULL, 0, 0},
 {"template",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, &_var
[5], 
(BNFoNODE*)&_term
[9], NULL, 0, 0},
 {"prog",Production,0,One, 
BnfParseProduction, 0,0,0,0, &_var
[8], &_var
[9], 0, 
(BNFoNODE*)&_term
[10], NULL, 0, 0},
 {"body",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[11], NULL, 0, 0},
 {"stmnt",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[14], NULL, 0, 0},
 {"stassoc",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[24], NULL, 0, 0},
 {"expr",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[25], NULL, 0, 0},
 {"term1",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[27], NULL, 0, 0},
 {"term2",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[31], NULL, 0, 0},
 {"term3",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[35], NULL, 0, 0},
 {"term4",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_choi
[5], NULL, 0, 0},
 {"makeop",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[39], NULL, 0, 0},
 {"nullopnd",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[40], NULL, 0, 0},
 {"logop",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[41], NULL, 0, 0},
 {"assop",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[42], NULL, 0, 0},
 {"compop",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[43], NULL, 0, 0},
 {"op1",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[44], NULL, 0, 0},
 {"op2",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[45], NULL, 0, 0},
 {"unopleft",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[46], NULL, 0, 0},
 {"unopright",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[47], NULL, 0, 0},
 {"list",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[48], NULL, 0, 0},
 {"assoc",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, &_var
[30], 
(BNFoNODE*)&_term
[51], NULL, 0, 0},
 {"key",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_choi
[8], NULL, 0, 0},
 {"value",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_choi
[9], NULL, 0, 0},
 {"int",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[64], NULL, 0, 0},
 {"lambda",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[65], NULL, 0, 0},
 {"path",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[67], NULL, 0, 0},
 {"ident",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[75], NULL, 0, 0},
 {"args",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[76], NULL, 0, 0},
 {"unnamedin",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[81], NULL, 0, 0},
 {"unnamedout",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[82], NULL, 0, 0},
 {"named",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[85], NULL, 0, 0},
 {"argvalue",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[86], NULL, 0, 0},
 {"name",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[87], NULL, 0, 0},
 {"strname",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[88], NULL, 0, 0},
 {"reference",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[89], NULL, 0, 0},
 {"string",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, &_var
[55], 
(BNFoNODE*)&_term
[92], NULL, 0, 0},
 {"sqString",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[96], NULL, 0, 0},
 {"bqString",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[97], NULL, 0, 0},
 {"bqLine",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[99], NULL, 0, 0},
 {"dqString",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[107], NULL, 0, 0},
 {"var2",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[113], NULL, 0, 0},
 {"var",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[114], NULL, 0, 0},
 {"file",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[115], NULL, 0, 0},
 {"pre",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[116], NULL, 0, 0},
 {"init",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[117], NULL, 0, 0},
 {"foreach",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[118], NULL, 0, 0},
 {"for",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[119], NULL, 0, 0},
 {"while",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[126], NULL, 0, 0},
 {"if",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[127], NULL, 0, 0},
 {"cond",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_choi
[23], NULL, 0, 0},
 {"production",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, &_var
[85], 0, 
(BNFoNODE*)&_term
[134], NULL, 0, 0},
 {"bnfExpr",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, &_var
[87], &_var
[88], 
(BNFoNODE*)&_term
[135], NULL, 0, 0},
 {"term",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, &_var
[89], &_var
[90], 
(BNFoNODE*)&_term
[137], NULL, 0, 0},
 {"factor",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_choi
[24], NULL, 0, 0},
 {"regexp",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, &_var
[92], 
(BNFoNODE*)&_term
[149], NULL, 0, 0},
 {"reStr",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[150], NULL, 0, 0},
 {"literal",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, &_var
[95], 
(BNFoNODE*)&_term
[153], NULL, 0, 0},
 {"litStr",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[154], NULL, 0, 0},
 {"command",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[157], NULL, 0, 0},
 {"eoi",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[158], NULL, 0, 0},
 {"occur",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_choi
[29], NULL, 0, 0},
 {"nodeProg",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, &_var
[103], &_var
[104], 
(BNFoNODE*)&_term
[162], NULL, 0, 0},
 {"prodName",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[164], NULL, 0, 0},
 {"laProdName",Production,0,One, 
BnfParseProduction, 0,0,0,0, 0, 0, 0, 
(BNFoNODE*)&_term
[165], NULL, 0, 0} 
};

BNFoPRODNAME _prodN
[] = {
 {"arr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[1]},
 {"ident",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[31]},
 {"ln",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[2]},
 {"ln",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[2]},
 {"var",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[46]},
 {"list",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[7], &_prod
[24]},
 {"stmnt",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[8]},
 {"stmnt",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[8]},
 {"stmnt",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[8]},
 {"if",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[53]},
 {"foreach",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[50]},
 {"for",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[51]},
 {"while",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[52]},
 {"init",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[49]},
 {"pre",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[48]},
 {"file",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[47]},
 {"stassoc",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[9]},
 {"expr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[10]},
 {"key",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[13], &_prod
[26]},
 {"ident",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[14], &_prod
[31]},
 {"term1",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[11]},
 {"logop",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[17]},
 {"term1",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[11]},
 {"makeop",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[15]},
 {"term2",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[12]},
 {"compop",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[19]},
 {"assop",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[15], &_prod
[18]},
 {"term2",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[16], &_prod
[12]},
 {"term3",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[13]},
 {"op1",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[20]},
 {"term3",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[18], &_prod
[13]},
 {"term4",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[14]},
 {"op2",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[21]},
 {"term4",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[14]},
 {"makeop",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[15]},
 {"expr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[10]},
 {"unopleft",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[22]},
 {"value",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[27]},
 {"unopright",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[23]},
 {"assoc",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[25]},
 {"value",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[27]},
 {"key",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[31], &_prod
[26]},
 {"value",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[27]},
 {"production",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[55]},
 {"real",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[32], &_prod
[3]},
 {"int",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[33], &_prod
[28]},
 {"name",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[34], &_prod
[37]},
 {"string",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[40]},
 {"ident",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[31]},
 {"list",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[24]},
 {"lambda",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[29]},
 {"reference",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[39]},
 {"ln",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[37], &_prod
[2]},
 {"name",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[39], &_prod
[37]},
 {"name",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[40], &_prod
[37]},
 {"ident",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[31]},
 {"string",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[42], &_prod
[40]},
 {"ident",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[43], &_prod
[31]},
 {"expr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[10]},
 {"args",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[45], &_prod
[32]},
 {"path",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[30]},
 {"named",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[35]},
 {"unnamedin",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[33]},
 {"named",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[35]},
 {"unnamedout",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[34]},
 {"argvalue",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[47], &_prod
[36]},
 {"value",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[27]},
 {"expr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[10]},
 {"argvalue",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[50], &_prod
[36]},
 {"expr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[10]},
 {"name",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[54], &_prod
[37]},
 {"sqString",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[41]},
 {"bqString",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[42]},
 {"dqString",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[59], &_prod
[44]},
 {"bqLine",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[64], &_prod
[43]},
 {"var",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[67], &_prod
[46]},
 {"var2",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[68], &_prod
[45]},
 {"var",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[71], &_prod
[46]},
 {"var2",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[72], &_prod
[45]},
 {"path",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, &_var
[73], &_var
[74], &_prod
[30]},
 {"string",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[76], &_prod
[40]},
 {"body",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[77], &_prod
[7]},
 {"body",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[78], &_prod
[7]},
 {"ident",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[31]},
 {"expr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[10]},
 {"body",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[79], &_prod
[7]},
 {"expr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[10]},
 {"nullopnd",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[16]},
 {"expr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[10]},
 {"nullopnd",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[16]},
 {"expr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[10]},
 {"nullopnd",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[16]},
 {"body",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[80], &_prod
[7]},
 {"cond",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[54]},
 {"body",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[81], &_prod
[7]},
 {"cond",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[54]},
 {"body",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[7]},
 {"cond",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[54]},
 {"body",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[7]},
 {"body",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[7]},
 {"expr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[10]},
 {"expr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[10]},
 {"expr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[10]},
 {"expr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[10]},
 {"nodeProg",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[66]},
 {"bnfExpr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[86], &_prod
[56]},
 {"term",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[57]},
 {"term",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[57]},
 {"factor",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[58]},
 {"factor",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[58]},
 {"command",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[63]},
 {"regexp",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[59]},
 {"literal",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[61]},
 {"eoi",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[64]},
 {"prodName",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[67]},
 {"laProdName",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[68]},
 {"occur",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[65]},
 {"nodeProg",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[66]},
 {"bnfExpr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[56]},
 {"occur",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[65]},
 {"reStr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[94], &_prod
[60]},
 {"litStr",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, &_var
[97], &_prod
[62]},
 {"stmnt",ProdName, 0, One, 
BnfParseProdName, 0,0,0,0, 0, 0, 0, &_prod
[8]} 
};

BNFoREPORT _report[] = {
 { 1, (BNFoNODE *)&_choi
[0] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[0] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[1] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[2] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[0] },
 { 0, (BNFoNODE *)&_prodN
[3] },
 { 1, (BNFoNODE *)&_term
[5] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[1] },
 { 0, (BNFoNODE *)&_reg
[2] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[3] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[4] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[5] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[4] },
 { 0, (BNFoNODE *)&_lit
[0] },
 { 0, (BNFoNODE *)&_prodN
[5] },
 { 0, NULL },
 { 3, (BNFoNODE *)&_prodN
[6] },
 { 0, (BNFoNODE *)&_comm
[0] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_comm
[1] },
 { 0, (BNFoNODE *)&_choi
[1] },
 { 0, (BNFoNODE *)&_comm
[2] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[1] },
 { 1, (BNFoNODE *)&_prodN
[7] },
 { 0, (BNFoNODE *)&_lit
[2] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[8] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_choi
[2] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[9] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[10] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[11] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[12] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[13] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[14] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[15] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[16] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[17] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[18] },
 { 0, (BNFoNODE *)&_prodN
[19] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[20] },
 { 1, (BNFoNODE *)&_term
[26] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[21] },
 { 0, (BNFoNODE *)&_prodN
[22] },
 { 0, (BNFoNODE *)&_prodN
[23] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[24] },
 { 1, (BNFoNODE *)&_term
[28] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_choi
[3] },
 { 0, (BNFoNODE *)&_prodN
[27] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[25] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[26] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[28] },
 { 2, (BNFoNODE *)&_choi
[4] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[6] },
 { 0, NULL },
 { 1, (BNFoNODE *)&_term
[34] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[29] },
 { 0, (BNFoNODE *)&_prodN
[30] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[31] },
 { 1, (BNFoNODE *)&_term
[36] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[32] },
 { 0, (BNFoNODE *)&_prodN
[33] },
 { 0, (BNFoNODE *)&_prodN
[34] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[3] },
 { 0, (BNFoNODE *)&_prodN
[35] },
 { 0, (BNFoNODE *)&_lit
[4] },
 { 0, NULL },
 { 2, (BNFoNODE *)&_prodN
[36] },
 { 0, (BNFoNODE *)&_prodN
[37] },
 { 2, (BNFoNODE *)&_prodN
[38] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_comm
[3] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_comm
[4] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[7] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[8] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[9] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[10] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[11] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[12] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[13] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[5] },
 { 1, (BNFoNODE *)&_choi
[6] },
 { 0, (BNFoNODE *)&_lit
[6] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[39] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[40] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[41] },
 { 0, (BNFoNODE *)&_choi
[7] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[42] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[7] },
 { 0, (BNFoNODE *)&_prodN
[43] },
 { 0, (BNFoNODE *)&_lit
[8] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[14] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[15] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[44] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[45] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[46] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[47] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[48] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[49] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[50] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[51] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[16] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[9] },
 { 1, (BNFoNODE *)&_term
[66] },
 { 0, (BNFoNODE *)&_reg
[18] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[17] },
 { 0, (BNFoNODE *)&_prodN
[52] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[53] },
 { 1, (BNFoNODE *)&_choi
[10] },
 { 2, (BNFoNODE *)&_term
[74] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[10] },
 { 0, (BNFoNODE *)&_choi
[11] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[54] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[11] },
 { 0, (BNFoNODE *)&_prodN
[55] },
 { 0, (BNFoNODE *)&_lit
[12] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[56] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[57] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[13] },
 { 0, (BNFoNODE *)&_prodN
[58] },
 { 0, (BNFoNODE *)&_lit
[14] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[59] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[15] },
 { 0, (BNFoNODE *)&_prodN
[60] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[16] },
 { 0, (BNFoNODE *)&_choi
[12] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[17] },
 { 2, (BNFoNODE *)&_choi
[13] },
 { 1, (BNFoNODE *)&_prodN
[63] },
 { 0, (BNFoNODE *)&_lit
[18] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[61] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[62] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[64] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[65] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_choi
[14] },
 { 0, (BNFoNODE *)&_comm
[5] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[66] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[19] },
 { 0, (BNFoNODE *)&_prodN
[67] },
 { 0, (BNFoNODE *)&_lit
[20] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[19] },
 { 0, (BNFoNODE *)&_prodN
[68] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[69] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[20] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[21] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[21] },
 { 0, (BNFoNODE *)&_choi
[15] },
 { 0, (BNFoNODE *)&_prodN
[70] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[22] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_comm
[6] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[22] },
 { 0, (BNFoNODE *)&_choi
[16] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[71] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[72] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[23] },
 { 0, (BNFoNODE *)&_prodN
[73] },
 { 0, (BNFoNODE *)&_lit
[24] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[23] },
 { 0, (BNFoNODE *)&_reg
[24] },
 { 0, (BNFoNODE *)&_reg
[25] },
 { 0, NULL },
 { 3, (BNFoNODE *)&_term
[98] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[25] },
 { 0, (BNFoNODE *)&_prodN
[74] },
 { 0, NULL },
 { 1, (BNFoNODE *)&_choi
[17] },
 { 0, (BNFoNODE *)&_choi
[18] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[26] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[27] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[75] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[76] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[28] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[29] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[26] },
 { 0, NULL },
 { 1, (BNFoNODE *)&_choi
[19] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[30] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[31] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[77] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[78] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[27] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[28] },
 { 0, (BNFoNODE *)&_prodN
[79] },
 { 0, (BNFoNODE *)&_lit
[29] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[32] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[30] },
 { 0, (BNFoNODE *)&_lit
[31] },
 { 0, (BNFoNODE *)&_prodN
[80] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[32] },
 { 0, (BNFoNODE *)&_prodN
[81] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[33] },
 { 0, (BNFoNODE *)&_prodN
[82] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[34] },
 { 0, (BNFoNODE *)&_lit
[35] },
 { 0, (BNFoNODE *)&_lit
[36] },
 { 0, (BNFoNODE *)&_prodN
[83] },
 { 0, (BNFoNODE *)&_lit
[37] },
 { 0, (BNFoNODE *)&_lit
[38] },
 { 0, (BNFoNODE *)&_prodN
[84] },
 { 0, (BNFoNODE *)&_lit
[39] },
 { 0, (BNFoNODE *)&_prodN
[85] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[40] },
 { 0, (BNFoNODE *)&_lit
[41] },
 { 0, (BNFoNODE *)&_lit
[42] },
 { 0, (BNFoNODE *)&_choi
[20] },
 { 0, (BNFoNODE *)&_choi
[21] },
 { 0, (BNFoNODE *)&_choi
[22] },
 { 0, (BNFoNODE *)&_lit
[43] },
 { 0, (BNFoNODE *)&_prodN
[92] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[86] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[87] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[88] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[89] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[90] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[91] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[44] },
 { 0, (BNFoNODE *)&_lit
[45] },
 { 0, (BNFoNODE *)&_prodN
[93] },
 { 0, (BNFoNODE *)&_prodN
[94] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[46] },
 { 0, (BNFoNODE *)&_lit
[47] },
 { 0, (BNFoNODE *)&_prodN
[95] },
 { 0, (BNFoNODE *)&_prodN
[96] },
 { 1, (BNFoNODE *)&_term
[128] },
 { 2, (BNFoNODE *)&_term
[129] },
 { 0, (BNFoNODE *)&_comm
[7] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[48] },
 { 0, (BNFoNODE *)&_lit
[49] },
 { 0, (BNFoNODE *)&_prodN
[97] },
 { 0, (BNFoNODE *)&_prodN
[98] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[50] },
 { 0, (BNFoNODE *)&_prodN
[99] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[51] },
 { 0, (BNFoNODE *)&_prodN
[100] },
 { 0, (BNFoNODE *)&_lit
[52] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[53] },
 { 0, (BNFoNODE *)&_prodN
[101] },
 { 0, (BNFoNODE *)&_lit
[54] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[55] },
 { 0, (BNFoNODE *)&_prodN
[102] },
 { 0, (BNFoNODE *)&_lit
[56] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[103] },
 { 0, NULL },
 { 2, (BNFoNODE *)&_prodN
[104] },
 { 0, (BNFoNODE *)&_prodN
[105] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[106] },
 { 1, (BNFoNODE *)&_term
[136] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[57] },
 { 0, (BNFoNODE *)&_prodN
[107] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[108] },
 { 1, (BNFoNODE *)&_term
[138] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[109] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_choi
[25] },
 { 0, (BNFoNODE *)&_prodN
[117] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[33] },
 { 0, (BNFoNODE *)&_prodN
[110] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_term
[142] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_choi
[26] },
 { 2, (BNFoNODE *)&_prodN
[116] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[111] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[112] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[113] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[114] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_prodN
[115] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[58] },
 { 0, (BNFoNODE *)&_prodN
[118] },
 { 0, (BNFoNODE *)&_lit
[59] },
 { 2, (BNFoNODE *)&_prodN
[119] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[60] },
 { 0, (BNFoNODE *)&_prodN
[120] },
 { 0, (BNFoNODE *)&_lit
[61] },
 { 0, NULL },
 { 3, (BNFoNODE *)&_choi
[27] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[34] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[35] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[36] },
 { 0, (BNFoNODE *)&_prodN
[121] },
 { 0, (BNFoNODE *)&_reg
[37] },
 { 0, NULL },
 { 3, (BNFoNODE *)&_choi
[28] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[38] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[39] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[40] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[62] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[63] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[64] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[65] },
 { 0, NULL },
 { 2, (BNFoNODE *)&_term
[163] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[66] },
 { 3, (BNFoNODE *)&_prodN
[122] },
 { 0, (BNFoNODE *)&_lit
[67] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_reg
[41] },
 { 0, NULL },
 { 0, (BNFoNODE *)&_lit
[68] },
 { 0, (BNFoNODE *)&_reg
[42] },
 { 0, NULL } 
};

BNFoNODE *_choiceSet[] = {
 (BNFoNODE *)&_term
[1],
 (BNFoNODE *)&_term
[2],
 (BNFoNODE *)&_term
[3],
 NULL,
 (BNFoNODE *)&_term
[12],
 (BNFoNODE *)&_term
[13],
 NULL,
 (BNFoNODE *)&_term
[15],
 (BNFoNODE *)&_term
[16],
 (BNFoNODE *)&_term
[17],
 (BNFoNODE *)&_term
[18],
 (BNFoNODE *)&_term
[19],
 (BNFoNODE *)&_term
[20],
 (BNFoNODE *)&_term
[21],
 (BNFoNODE *)&_term
[22],
 (BNFoNODE *)&_term
[23],
 NULL,
 (BNFoNODE *)&_term
[29],
 (BNFoNODE *)&_term
[30],
 NULL,
 (BNFoNODE *)&_term
[32],
 (BNFoNODE *)&_term
[33],
 NULL,
 (BNFoNODE *)&_term
[37],
 (BNFoNODE *)&_term
[38],
 NULL,
 (BNFoNODE *)&_term
[49],
 (BNFoNODE *)&_term
[50],
 NULL,
 (BNFoNODE *)&_term
[52],
 (BNFoNODE *)&_term
[53],
 NULL,
 (BNFoNODE *)&_term
[54],
 (BNFoNODE *)&_term
[55],
 NULL,
 (BNFoNODE *)&_term
[56],
 (BNFoNODE *)&_term
[57],
 (BNFoNODE *)&_term
[58],
 (BNFoNODE *)&_term
[59],
 (BNFoNODE *)&_term
[60],
 (BNFoNODE *)&_term
[61],
 (BNFoNODE *)&_term
[62],
 (BNFoNODE *)&_term
[63],
 NULL,
 (BNFoNODE *)&_term
[68],
 (BNFoNODE *)&_term
[73],
 NULL,
 (BNFoNODE *)&_term
[69],
 (BNFoNODE *)&_term
[70],
 (BNFoNODE *)&_term
[71],
 (BNFoNODE *)&_term
[72],
 NULL,
 (BNFoNODE *)&_term
[77],
 (BNFoNODE *)&_term
[80],
 NULL,
 (BNFoNODE *)&_term
[78],
 (BNFoNODE *)&_term
[79],
 NULL,
 (BNFoNODE *)&_term
[83],
 (BNFoNODE *)&_term
[84],
 NULL,
 (BNFoNODE *)&_term
[90],
 (BNFoNODE *)&_term
[91],
 NULL,
 (BNFoNODE *)&_term
[93],
 (BNFoNODE *)&_term
[94],
 (BNFoNODE *)&_term
[95],
 NULL,
 (BNFoNODE *)&_term
[100],
 (BNFoNODE *)&_term
[101],
 (BNFoNODE *)&_term
[102],
 (BNFoNODE *)&_term
[103],
 (BNFoNODE *)&_term
[104],
 NULL,
 (BNFoNODE *)&_term
[105],
 (BNFoNODE *)&_term
[106],
 NULL,
 (BNFoNODE *)&_term
[108],
 (BNFoNODE *)&_term
[109],
 (BNFoNODE *)&_term
[110],
 (BNFoNODE *)&_term
[111],
 (BNFoNODE *)&_term
[112],
 NULL,
 (BNFoNODE *)&_term
[120],
 (BNFoNODE *)&_term
[121],
 NULL,
 (BNFoNODE *)&_term
[122],
 (BNFoNODE *)&_term
[123],
 NULL,
 (BNFoNODE *)&_term
[124],
 (BNFoNODE *)&_term
[125],
 NULL,
 (BNFoNODE *)&_term
[130],
 (BNFoNODE *)&_term
[131],
 (BNFoNODE *)&_term
[132],
 (BNFoNODE *)&_term
[133],
 NULL,
 (BNFoNODE *)&_term
[139],
 (BNFoNODE *)&_term
[148],
 NULL,
 (BNFoNODE *)&_term
[140],
 (BNFoNODE *)&_term
[141],
 NULL,
 (BNFoNODE *)&_term
[143],
 (BNFoNODE *)&_term
[144],
 (BNFoNODE *)&_term
[145],
 (BNFoNODE *)&_term
[146],
 (BNFoNODE *)&_term
[147],
 NULL,
 (BNFoNODE *)&_term
[151],
 (BNFoNODE *)&_term
[152],
 NULL,
 (BNFoNODE *)&_term
[155],
 (BNFoNODE *)&_term
[156],
 NULL,
 (BNFoNODE *)&_term
[159],
 (BNFoNODE *)&_term
[160],
 (BNFoNODE *)&_term
[161],
 NULL 
};

ICAoSYNTAX *IcaInitSyntax(ICAoSYNTAX *syntax)
{
  static ICAoSYNTAX  syntaxStatic;
  static ICAoJOB     job;
  BNFoNODE *tmp;
  VARo     *prodList=VarNew ();
  INT4     i,j;

  if (syntax && syntax->prod) /* already initialized */
    return syntax;

  if (!syntax)
    syntax = &syntaxStatic;


  Job = &job;
  Job->time = BNFxBUILDTIME;

  j = 0;
  for(i=0; i<TERMNUM; i++) {
    _term[i].factorList = &_report[j];
    while(_report[j++].node);
  }
  
  j = 0;
  for(i=0; i<CHOINUM; i++) {
    _choi[i].termList = &_choiceSet[j];
    while(_choiceSet[j++]);
  }

  AnySetList (prodList, AnyNewList ());
  for(i=0; i<PRODNUM; i++) {
    VarSetObject ("prod", AnyGetListAssoc(prodList, _prod[i].name), &_prod[i]);
    Job->currNode = (BNFoNODE *) &_prod[i];
    _BnfExecInit (&_prod[i]);
  }

  for(i=0; i<PRODNNUM; i++) {
    Job->currNode = (BNFoNODE *) &_prodN[i];
    _BnfExecInit (&_prodN[i]);
  }  

#ifdef LITLNUM 

  for(i=0; i<LITLNUM; i++) {
    Job->currNode = (BNFoNODE *) &_lit[i];
    _BnfExecInit (&_lit[i]);
  }  

#endif
#ifdef REGNUM 

  for(i=0; i<REGNUM; i++) {
    _reg[i].expression = RegComp(_reg[i].name);
    Job->currNode = (BNFoNODE *) &_reg[i];
    _BnfExecInit (&_reg[i]);
  }  

#endif
#ifdef COMMNUM 

  for(i=0; i<COMMNUM; i++) {
    Job->currNode = (BNFoNODE *) &_comm[i];
    _BnfExecInit (&_comm[i]);
  }  

#endif
#ifdef STRTNUM 

  for(i=0; i<STRTNUM; i++) {
    Job->currNode = (BNFoNODE *) &_strt[i];
    _BnfExecInit (&_strt[i]);
  }  

#endif
#ifdef EOINNUM 

  for(i=0; i<EOINNUM; i++) {
    Job->currNode = (BNFoNODE *) &_eoin[i];
    _BnfExecInit (&_eoin[i]);
  }  

#endif

  VarGet (&job.scope, "");
 
  syntax->prod = prodList;
  syntax->ign = DEFIGNORE;
  if (syntax == &syntaxStatic) {
    syntax->cmnt = DEFCOMMENT;
    syntax->ignAlt = "";
  }
  if ((syntax->cmntRe = RegComp (syntax->cmnt)) == NULL)
    _ErrExit2 (e__regerror, syntax->cmntRe);

  Syntax = syntax;
  for (i=0; i<PRODNUM; i++) {
	 tmp = (BNFoNODE*) &_prod[i];
	 BnfPruneTree (&tmp, 1);
  }
  for (i=0; i<PRODNUM; i++) {
	 tmp = (BNFoNODE*) &_prod[i];
	 BnfPruneTree (&((BNFoPRODUCTION*)tmp)->node, 2);
  }
  return syntax;
}
ob.scope, "");
 
  syntax->prod srs/src/icaop.c
char icaop_ID[] = "$Id: icaop.c,v 1.43 1997/03/18 23:28:03 srs Exp $";
/*
**    $RCSfile: icaop.c,v $
**    $Revision: 1.43 $
**    $Date: 1997/03/18 23:28:03 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  Copyright by Thure Etzold
**
**            Authors: Anatoly Ulyanov
**		       Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387451
**                     Email: ulyanov@embl-heidelberg.de
**
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**
**    Description
**    =========== 
**  
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*/  

#include <string.h>
#include <stdlib.h>
#include <stdio.h>
#include <ctype.h>
/*
#include <sys/types.h>
#include <sys/stat.h>
*/
#include <fcntl.h>

#include "message.h"
#include "regexp.h"
#include "futil.h"
#include "sm.h"
#include "lst.h"
#include "par.h"
#include "strv.h"
#include "listv.h"
#include "variable.h"
#include "toklist.h"
#include "cursor.h"
#include "icarus.h"
#include "icabnf.h"
#include "icaarg.h"
#include "print.h"
#include "icatask.h"
#include "odd.h"

#define _SRS
#include SRSINCLUDE

#define IOPxMARK 111


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  external and modulewide variables
*/

extern ICAoJOB     *Job;
extern VARoSCOPE   *globalScope;
extern ICAoSYNTAX  *Syntax; 

static char    *currObjId=NULL; 
VARoSTACK *icaStack[6]={NULL, NULL, NULL, NULL, NULL, NULL};
VARoSTACK *icaStack1[6]={NULL, NULL, NULL, NULL, NULL, NULL};
VARoStack icaStack2[6];


/***************** stack for variable.c **************/


VARoStack *VarStackInit (VARoStack *stack)
{
  if (!stack)
    stack = calloc (1, sizeof (VARoStack));
  stack->n = 0;
  return stack;
}
void VarPush2 (VARoStack *stack, VARo *var)
{
  *(_addObj (stack->ptr, stack->n, stack->allocN, VARo*)) = var;
}
VARo *VarPop2 (VARoStack *stack)
{
  return (!stack->n) ? NULL : stack->ptr[--stack->n];
}

/*********** end of stack ****************/




/****** IopSystem *************************************************************
**
**      Take the string as a unix command, execute it and return result
**      as a string
**  
**  	INPUT:
**  
**  	RETURNS:   output of unix command
*/ 


INT4 IopSystem (Int4 runTime, STRv com, STRv script, STRv scriptName, STRv out, STRv error)
{
  FILEo *file;
  STRv str;
  char *tmp, s[1000];
  Int4 flag,
       fd;
  FILE *fp;

  str = StrNew();

  if (runTime)
    IargGetArgs("com|script|scriptName|out|error", 
		&com, &script, &scriptName, &out, &error);
  if (script) {
    tmp = scriptName ? _Str (scriptName) : "tmpscript";
    file = FileNew (tmp);
    FileSetMode (file, "rwxr-xr-x");
    FileOpen (FileSetWrite (file));
    FileWrite (file, _Str (script), StrLen (script));
    FileClose (file);
    if (!com)
      com = StrPrintf (NULL, "%s", tmp);
  }
  if (out && SmEqs (_Str (out), "stdout")) {
    if (error) {
      if (SmEqs (_Str (error), "stdout")) 
	StrPrintf (&com, " 2>&1");
      else 
	StrPrintf (&com, " 2>%s", _Str (error));
    }
    system (_Str (com));
  }
  else if((fp = popen (_Str(com), "r")) != NULL)
    while (fgets(s, BUFSIZ, fp) != NULL)
      StrAppS (&str, s);

  IcaReturn("strv", str);
  return 1;
}


/****** IcaFunGetFip **********************************************************
**
**      Gets the current file pointer.
**
**      INPUT:
**
**      RETURNS:
*/

INT4 IcaFunGetFip ()
{
  return (INT4) FileGetFip (Job->file);
}


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Strings Library
*/


INT4 IcaOpSubStr()
{
  STRv str;
  Int4 start,
       len;

  IargGetArgs("str|s|l", &str, &start, &len);
  
  if(len)  
    IcaReturn("strv", StrSub(str, start-1, len));
  else
    IcaReturn("strv", StrRight(str, start-1));
  
  return(TRUE);

}

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  functions for building the icarus interpreted stacks
*/

#ifdef __ODD
INT4 IopObject (VARo *var);
INT4 IopReference (VARo *var);
#endif

#define _Index(x,y) ( ((x)-'a'+1) << 5) +((y)-'a'+1)


VARo *IopFile_ (Int4 runTime, VARo *var)
{
  FILEo   *file;
  ICAoJOB *job;
  VARo    *prog;
  STRv    fileName;

  if (runTime)
    IargGetArgs ("file", &var);

  fileName = VarGetStrv (var);
  file = FileNew (_Str(fileName));
  if (!FileOpen (file) )
    _ErrExit2 (e__filnotok, _Str(fileName));

  /* create new job with current job's syntax */
  job = IcaCreateJob (Job->syntax);
  job->scope = Job->scope;
  IcaJobSetFile (job, file);
  IcaGetTokenList (job, "prog");
  /*  IcaJobDestroy (job);*/
  Job->scope = job->scope;
  job->file = FileDelete (job->file);
  
  if (IcaJobIsError (job))
    _ErrExit (e__icaErrorsQuit);

  StrDel (fileName);
  if (runTime)
    IargReturn ("var", job->prog);
  else
    return job->prog;
}  

void IopEval (Int4 runTime, STRv prog)
{
  if (runTime)
    IargGetArgs("prog", &prog);
  
  IcaEvalInJob (_Str(prog), Job);
  StrDel (prog);
}


VARo *IopRef_ (Int4 runTime, VARo *name, Int4 index)
{
  VARo *var, *val, **args;

  if (runTime)
    IargGetArgs("name|opt", &name, &index);

  var = VarNew ();
  VarSetReadInt (var, (FUNC)IopReference);
  args = (VARo **) malloc (2*sizeof (void *));
  VarSetArgs (var, args);

  val = VarNew ();
  VarSetInt (val, index);
  args[0] = val;

  val = VarNew ();
  VarSetStrv (val, VarGetStrv (name));
  args[1] = val;

  if (runTime)
    IcaReturn ("var", var);
  else
    return var;
}



VARo *IopOpnd_ (Int4 runTime, STRv opnd, STRv type)
{
  IARGvCOM com;
  FUNC     function;
  VARo     *var, *istr, **args, *func, *val;
  char     *t;
  void     *tmp;

  if (runTime)
    IargGetArgs("opnd|t", &opnd, &type);

  var = VarNew ();
  t = _Str (type);
  switch (_Index(t[0], t[1])) {
  case _Index('i','n'): /* int */
    VarSetType (var, VARxINT);
    VarSetStrv (var, StrCpy(opnd));
    break;
  case _Index('r','e'): /* real */
    VarSetType (var, VARxREAL);
    VarSetStrv (var, StrCpy(opnd));
    break;
  case _Index('s','t'): /* string */
    VarSetType (var, VARxSTRING);
    VarSetStrv (var, StrCpy(opnd));
    break;
  case _Index('l','a'): /* lambda */
    VarSetType (var, VARxSTRING);
    /* StrEncode (&opnd);*/
    VarSetStrv (var, StrCpy(opnd));
    break;
  case _Index('n','u'): /* null */
    VarSetInt (var, 0);
    break;
  case _Index('m','a'): /* mark */
    VarSetInt (var, 0);
    VarSetCode (var, IOPxMARK);
    break;
  case _Index('i','d'): /* ident */
    
    /* check if the name is a class name */
    if (OddIsActive () && (tmp = (void *) OddGetClass (_Str(opnd)))) {  
      OddRegisterObj ((struct SDLoOBJ *) tmp);
      function = IopObject;
      VarSetClassName (var, OddGetClassName ((struct SDLoOBJ *) tmp));
      VarSetReadType (var, function);
      VarSetCode (var, IARGxCALL | IARGxODD);
    }
    /* or a function name */
    else if ((com = IargGetCom (_Str(opnd)))) {

      if (com->isDirectCall) {
	VarSetCode (var, IARGxCALL | com->time);	
	switch (com->returnType) {
	case 1:
	  VarSetReadInt (var, com->function); 
	  break;
	case 2:
	  VarSetReadStr (var, (BFUNC)com->function); 
	  break;
	}
	args = (VARo **) malloc (1*sizeof (void *));
	args[0] = NULL;
	VarSetArgs (var, args);

      }
      else {
	/* generate new function if call is indirect */
	VarSetObject (NULL, var, (void *) com);
	func = VarNew ();
	VarSetCode (func,  IARGxINDIRECTCALL | IARGxCALL | com->time);
	VarSetReadType (func, IcaGetFunction ("IopExecCom"));
	args = (VARo **) malloc (2*sizeof (void *));
	args[0] = var; args[1] = NULL;
	VarSetArgs (func, args);
	var = func;
      }
    }
    /* else it is a variable */
    else {
      VARo *tmp;

      var = VarNew ();
      tmp = VarGet (&Job->scope, _Str(opnd));
      VarSetAlias (var, tmp, Job->scope);
    }
  break;

  default:
    _ErrExit2 (e__unknownoption, type);
  }
  VarSetLineN (var, IcaGetCurrLineN ("input"));

  StrDel (opnd);
  if (runTime)
    IcaReturn ("val", var);
  return var;
}


Int4 IopGetBinOperator (char *op, VARo *a, VARo *b, Func *func)
{
  IARGoCOM *com;
  char funcName[80]="IopAss";
  
  if (!(com = IargGetCom (op)))
    _ErrExit3 (e__objectunknown, "Icarus function", op);
  if (!(*func = IcaGetFunction (com->functionName)))
    _ErrExit3 (e__objectunknown, "icarus function", com->functionName);

  return com->returnType;
}


VARo *IopBinop_ (Int4 runTime, STRv opName, VARo *a, VARo *b)
{
  Func func;
  VARo *var, **args;
  Int4 type;

  if (runTime)
    IargGetArgs("op|a|b", &opName, &a, &b);

  var = VarNew ();
  VarSetLineN (var, IcaGetCurrLineN ("input"));
  args = (VARo **) malloc (3*sizeof (void *));
  args[0] = a; args[1] = b; args[2] = NULL;
  VarSetArgs (var, args);

  switch ((type = IopGetBinOperator (_Str(opName), a, b, &func))) {
  case VARxINT:
    VarSetReadInt (var, func);
    break;
  case VARxVAR:
    VarSetReadType (var, func);
    break;
  default:
    _ErrExit2 (e__unknownoption, "type in IopBinop");
  }
 
  if (runTime)
    IcaReturn ("var", var);
  else 
    return var;
}


VARo *IopInit_ (Int4 runTime, VARo *body)
{
  if (runTime)
    IargGetArgs("body", &body);
  VarSetCode (body, VarGetCode (body) | IARGxINIT);
  if (runTime)
    IcaReturn ("var", body);
  else
    return body;
}

VARo *IopPre_ (Int4 runTime, VARo *body)
{
  if (runTime)
    IargGetArgs("body", &body);
  VarSetCode (body, VarGetCode (body) | IARGxPRE);
  if (runTime)
    IcaReturn ("var", body);
  else
    return body;
}

VARo *IopFor_ (Int4 runTime, VARo *i, VARo *c, VARo *u, VARo *b)
{
  FUNC function;
  VARo *var, **args;

  var = VarNew ();
  if (runTime)
    IargGetArgs("i|c|u|b", &i, &c, &u, &b);
  if (!(function = IcaGetFunction ("IopFor")))
    _ErrExit3 (e__objectunknown, "function", "IopFor");
  VarSetReadInt (var, function);
  args = (VARo **) malloc (4*sizeof (void *));
  args[0] = i; args[1] = c; args[2] = u; args[3] = b;
  VarSetArgs (var, args);
  VarSetLineN (var, IcaGetCurrLineN ("input"));
  if (runTime)
    IcaReturn ("var", var);
  else
  return var;
}

VARo *IopForeach_ (Int4 runTime, VARo *body, VARo *list, VARo *val)
{
  FUNC function;
  VARo *var, **args;

  var = VarNew ();
  if (runTime)
    IargGetArgs("body|list|var", &body, &list, &val);
  if (!(function = IcaGetFunction ("IopForeach")))
    _ErrExit3 (e__objectunknown, "function", "IopForeach");
  VarSetReadInt (var, function);
  args = (VARo **) malloc (3*sizeof (void *));
  args[0] = val; args[1] = list; args[2] = body; 
  VarSetArgs (var, args);
  VarSetLineN (var, IcaGetCurrLineN ("input"));
  if (runTime)
    IcaReturn ("var", var);
  else
  return var;
}

VARo *IopWhile_ (Int4 runTime, VARo *b, VARo *c)
{
  FUNC function;
  VARo *var, **args;

  var = VarNew ();
  if (runTime)
    IargGetArgs("c|b", &c, &b);

  if (!(function = IcaGetFunction ("IopWhile")))
    _ErrExit3 (e__objectunknown, "function", "IopWhile");
  VarSetReadInt (var, function);
  args = (VARo **) malloc (2*sizeof (void *));
  args[0] = c; args[1] = b; 
  VarSetArgs (var, args);
  VarSetLineN (var, IcaGetCurrLineN ("input"));

  if (runTime)
    IcaReturn ("var", var);
  else
    return var;
}

VARo *IopIf_ (Int4 runTime)
{
  static VARoStack *stack=NULL;
  FUNC function;
  VARo *var, *tmp, **args;
  INT4 k, l;
  
  var = VarNew ();
  if (!(function = IcaGetFunction ("IopIf")))
    _ErrExit3 (e__objectunknown, "function", "IopIf");
  VarSetReadInt (var, function);


  /* init tmp stack and copy from userstack until NULLNODE is found */
  stack = VarStackInit (stack);
  for (k=0; (tmp = VarPop2 (&icaStack2[0])); k++){
    tmp = VarGetVar (tmp, 0);
    if (VarGetCode (tmp) == IOPxMARK)
      break;
    VarPush2 (stack, tmp); 
  }

  /* allocate a list of pointers to the statements whose number is known now */
  args = (VARo **) malloc ((k+1)*sizeof (void *));
  VarSetArgs (var, args);

  /* pop nodes and assign them to the factor list */
  for (l=0; k && (tmp = VarPop2 (stack)); k-- , l++){
    args[l] = tmp;
  }
  args[l] = NULL;
  VarSetLineN (var, IcaGetCurrLineN ("input"));
 
  if (runTime)
    IcaReturn ("var", var);
  else
    return var;
}

VARo *IopAssoc_ (Int4 runTime, VARo *val, VARo *key)
{
  FUNC function;
  char *tmp;
  STRv str;
  Int4 code;

  if (runTime)
    IargGetArgs("key|val", &key, &val);
  str = VarGetStrv (key);
  StrDecode (&str);
  VarSetName (val, _Str(str));
  code = VarGetCode (val);
  if (code & (IARGxODD|IARGxCALL)) { /* name is object-id */
    char *className;
    VarGetClassName (val);
    if ((className = VarGetClassName (val)))
      OddIdRegister (OddGetClass (VarGetClassName (val)), _Str(str));
    else
      _ErrExit2 (e__icaUnknownClass, tmp = VarGetName (val) ? tmp : "unknown");
  }

  if (runTime)
    IcaReturn ("var", val);
  else
    return val;
}

/* builds a list creator */
VARo *IopList_ (Int4 runTime)
{
  static VARoStack *stack=NULL;
  VARo *(*function)();
  VARo *var, *tmp, **args;
  INT4 k, l;
  
  /* init tmp stack and copy from user stack until NULLNODE is found */
  stack = VarStackInit (stack);
  for (k=0; (tmp = VarPop2 (&icaStack2[0])); k++){
    tmp = VarGetVar (tmp, 0);
    if (VarGetCode (tmp) == IOPxMARK)
      break;
    VarPush2 (stack, tmp); 
  }

  /* make the variable that creates the list */
  var = VarNew ();
  if (!(function = (VARo *(*)()) IcaGetFunction ("IopList")))
    _ErrExit3 (e__objectunknown, "function", "IopList");
  VarSetReadList (var, function);
  args = (VARo **) malloc ((k+1)*sizeof (void *));
  VarSetArgs (var, args);

  /* pop list elements and assign them to the list */
  for (l=0; k && (tmp = VarPop2 (stack)); k--, l++)
    args[l] = tmp;
  args[l] = NULL;
 
  if (runTime)
    IcaReturn ("var", var);
  else
    return var;
}



VARo *IopSelect_ (Int4 runTime, VARo *key, VARo *index, VARo *var)
{
  VARo *val, **args;

  val = VarNew ();
  if (runTime)
    IargGetArgs("key|index|var", &key, &index,  &var);

  args = (VARo **) malloc (2*sizeof (void *));
  args[0] = var; 
  if (key) { 
    VarSetReadVar (val, IcaGetFunction ("IopSelectAssoc"));
    args[1] = key;
  }  
  else if (index) {
    VarSetReadVar (val, IcaGetFunction ("IopSelect"));
    args[1] = index;
  }
  VarSetArgs (val, args);

  if (runTime)
    IcaReturn ("var", val);
  else
    return val;
}

ANYv IopSetWrite_ (Int4 runTime, VARo *var)
{
  ANYv *arg=VarGetArgs  (var);

  AnySetWrite (var);
  if (arg) /* set recursively write access to nested assoc selects !!!te*/
    AnySetWrite (arg[0]);

  if (runTime)
    IcaReturn ("var", var);
  else
    return var;
}


VARo *IopMakeArg_ (Int4 runTime, VARo *val, VARo *name)
{
  STRv str;

  if (runTime)
    IargGetArgs("val|name", &val, &name);

  name = VarGetVar (name, 1);
  str = VarGetStrv (name);

  VarDefName (val, _Str (str));
  StrDel (str);
  if (runTime)
    IcaReturn ("opnd", val);
  else
    return val;
}

VARo *IopFunc_ (Int4 runTime)
{
  static VARoStack *stack=NULL;
  VARo *func, *tmp, **args;
  INT4 k, l, code, lineN;
  
  /* init stack and copy from user stack until mark is found */
  stack = VarStackInit (stack);
  for (k=0; (tmp = VarPop2 (&icaStack2[0])); k++){
    tmp = VarGetVar (tmp, 0);
    if (VarGetCode (tmp) == IOPxMARK) {
      func = VarPop2 (&icaStack2[0]);
      break;
    }
    VarPush2 (stack, tmp);
  }

  if (VarIsAlias (func)) {
    tmp = VarNew ();
    lineN = VarGetLineN (func);

    VarSetStrvS (tmp, VarGetName (VarGetAlias (func, Job->scope)));

    func = VarNew ();
    VarSetLineN (func, lineN);
    args = (VARo **) malloc (2*sizeof (void *));
    args[0] = tmp; args[1] = NULL;
    VarSetArgs (func, args);
    VarSetCode (func,  IARGxINDIRECTCALL | IARGxCALL | IARGxPOST);
    VarSetReadType (func, IcaGetFunction ("IopExecCom"));
  }
  if ((VarGetCode (func)) & IARGxINDIRECTCALL) {
    args = VarGetArgs (func); /* has already a list with the 'com' object */
    args = (VARo **) realloc (args, (k+2)*sizeof (void *));
    VarSetArgs (func, args);
    args++; /* set it past the 'com' object */
  }
  else {
    args = (VARo **) malloc ((k+1)*sizeof (void *));
    VarSetArgs (func, args);
  }

  /* pop nodes and assign them to the argument list */
  for (l=0; k && (tmp = VarPop2 (stack)); k-- , l++){
    args[l] = tmp;
  }
  args[l] = NULL;
 
  if (runTime)
    IcaReturn ("var", func);
  else
    return func;
}

INT4 IopProg_ ()
{
  static VARoStack *stack=NULL;
  FUNC function;
  VARo *prog, *tmp, **args;
  INT4 k, l;
  
  /* init tmp stack and copy from user stack until end mark is found */
  stack = VarStackInit (stack);
  for (k=0; (tmp = VarPop2 (&icaStack2[0])); k++){
    tmp = VarGetVar (tmp, 0);
    if (VarGetCode (tmp) == IOPxMARK)
      break;
    VarPush2 (stack, tmp); 
  }

  /* allocate a list of pointers to the statements whose number is known now */
  if (!(function = IcaGetFunction ("IopProg")))
    _ErrExit3 (e__objectunknown, "function", "IopProg");
  prog = VarNew ();
  VarSetReadInt (prog, function);
  args = (VARo **) malloc ((k+2) * sizeof (VARo *));
  VarSetArgs (prog, args);

  /* add file name of program to program variable */
  args[0] = VarNew(); 
  if (Job->file)
    VarSetStrvS (args[0], FileGetName (Job->file, "full"));

  /* pop nodes and add them to the statement list */
  for (l=1; k && (tmp = VarPop2 (stack)); k--, l++)
    args[l] = tmp;
  args[l] = NULL;
 
  Job->prog = prog;
  return 1;
}

VARo *IopStrMake_ (Int4 runTime)
{
  static VARoStack *stack=NULL;
  static VARoStack *varStack=NULL;
  STRv str, s;
  VARo *tmp, *var, *val, **args;
  char *t;
  INT4 strN, varN, len, l;

  
  /* init tmp stack and copy from user stack until end mark is found */
  stack = VarStackInit (stack);
  varStack = VarStackInit (varStack);
  for (strN=varN=0; (tmp = VarPop2 (&icaStack2[0]));){
    tmp = VarGetVar (tmp, 0);
    if (VarGetCode (tmp) == IOPxMARK)
      break;
    if (VarIsAlias (tmp) || VarGetCode (tmp) & IARGxCALL) {
      VarPush2 (varStack, tmp);
      varN++;
    }
    else {
      VarPush2 (stack, tmp); 
      strN++;
    }
  }

  /* concatenate the string: '\' at end of line removes the line feed */
  str = StrNew ();
  for (; strN && (tmp = VarPop2 (stack)); strN--) {
    s = VarGetStrv (tmp);
    len = StrLen (s);
    t = _Str (s);
    if (len >= 2 && t[len-2] == '\\' && t[len-1] == '\n')
	t[len-2] = '\0';
    StrApp (&str, s);
    StrDel (s);
  }
  StrDecode (&str);
  var = VarNew ();
  VarSetStrv (var, str);

  /* get all variables inside string for interpretation and create new var */
  if (varN) {
    val = var;
    var = VarNew ();
    VarSetReadStrv (var, (STRv (*)(char *)) IcaGetFunction ("IopInterpStr_"));
	
    args = (VARo **) malloc ((varN+2)*sizeof (void *));
    VarSetArgs (var, args);
	
    args[0] = val;
    for (l=1; varN && (tmp = VarPop2 (varStack)); varN-- , l++){
      args[l] = tmp;
    }
    args[l] = NULL;
  }

  if (runTime)
    IcaReturn ("var", var);
  else return var;
}


VARo *IopBody_ (Int4 runTime)
{
  static VARoStack *stack=NULL;
  FUNC function;
  VARo *var, *tmp, **args;
  INT4 k, l;
  
  var = VarNew ();
  if (!(function = IcaGetFunction ("IopBody")))
    _ErrExit3 (e__objectunknown, "function", "IopBody");
  VarSetReadInt (var, function);

  /* init tmp stack and copy from userstack until NULLNODE is found */
  stack = VarStackInit (stack);
  for (k=0; (tmp = VarPop2 (&icaStack2[0])); k++){
    tmp = VarGetVar (tmp, 0);
    if (VarGetCode (tmp) == IOPxMARK)
      break;
    VarPush2 (stack, tmp); 
  }

  /* allocate a list of pointers to the statements whose number is known now */
  args = (VARo **) malloc ((k+1)*sizeof (void *));
  VarSetArgs (var, args);

  /* pop nodes and assign them to the factor list */
  for (l=0; k && (tmp = VarPop2 (stack)); k-- , l++){
    args[l] = tmp;
  }
  args[l] = NULL;
 
  if (runTime)
    IcaReturn ("var", var);
  else
    return var;
}

/* functions for level 3 icarus commands */


STRv IopInterpStr_ (VARo *var, STRv str, ...)
{
  va_list ap;
  VARo    **arg;
  STRv    tmp;
  char    *s;
  INT4    k, i, begin;

  if (var) {
    arg=VarGetArgs (var);
    str = VarGetStrv (arg[0]);
  }
  else 
    va_start (ap, str);  			      
  StrBufChange (&str, 0, 0);
  
  for (s = _Str(str), i=0, k=1; s[i];) {
    i += strcspn (&s[i], "\2");
    if (s[i] == '\0')
      break;
    else {
      /* replace the mark with variables content */
      tmp = VarGetStrv (var ? arg[k++] : va_arg (ap, VARo*));
      if (!tmp)
	_ErrExit (e__icaMissingString);
      StrSubst (&str, i, 1, tmp);
      i += StrLen (tmp);
      StrDel (tmp);
      s = _Str(str);
    }
  }
  if (!var)
    va_end (ap);
  return str;
}




Int4 IopExecCom (VARo *var)
{
  extern VARo *iargRetVal;
  VARo **args=VarGetArgs (var);
  IARGvCOM com;
  STRv     str;
  Int4     type;

  type = VarType (args[0]);
  if (type == VARxSTRING || type == VARxSTRV) {
    str = VarGetStrv (args[0]);
    if (!(com = IargGetCom (_Str (str))))
      _ErrExit3 (e__objectunknown, "Icarus function", _Str (str));
    StrDel (str);
  }
  else
    com = (IARGvCOM) VarGetObject (NULL, args[0]);

  IargBuildArgs (com, &args[1], 0);

  iargRetVal = NULL;
  IargComStack (com, "push");
  _IargCall (com);
  IargComStack (com, "pop");

  if (iargRetVal) {
    switch (VarType (iargRetVal)) {
    case 0: /* function returns nothing */
      break;
    case VARxINT:
      VarSetInt (var, (VarGetInt (iargRetVal)));
      break;
    case VARxSTRING:
      VarSetStr (var, (VarGetStr (iargRetVal)));
      break;
    case VARxSTRV:
      str = VarGetStrv (iargRetVal);
      VarSetStrv (var, str);
      break;
    case VARxOBJECT:
      VarSetObject (NULL, var, (VarGetObject (NULL, iargRetVal)));
      break;
    case VARxREAL:
      break;
    case VARxLIST:
      AnySetList (var, iargRetVal);
      break;
    case VARxVAR:
      var = VarSetVar (var, VarGetVar (iargRetVal, 1));
      break;
    default:
      _ErrExit2 (e__unknownoption, "type in IopExecCom");
    }
  }
  return 1;
}



INT4 IopProg (VARo *var)
{
  static ICAoSYNTAX syntax;
  static INT4       i2cFlag = TRUE;

  INT4 k;
  VARo **arg=VarGetArgs (var);
  STRv str;
  char *fileNameSave = Job->fileName;

  globalScope = Job->scope;

  str = VarGetStrv (arg[0]);
  Job->fileName = _Str (str);
  for (k=1; arg[k] != NULL; k++) {
    Job->lineN = VarGetLineN (arg[k]);
    VarExec (arg[k]);
    if( *ParGetStr("ica2cName") && i2cFlag) {
      i2cFlag = FALSE;
      syntax.prod =  VarGet(&globalScope, "rules");
      BnfInitRules (&syntax, FALSE);
      I2cBnfGenerator(syntax.prod);
      exit(0);
    }
  }
  StrDel (str);
  Job->fileName = fileNameSave; /* nested progs with "file" command */
  return 1;
}

INT4 IopTest ()
{
  INT4 x, y;
  char color[44];

  IargGetArgs ("x|y|color", &x, &y, color);

  printf ("x:%d y:%d color:%s\n", x, y, color);
  return 1;
}

INT4 IopBody (VARo *var)
{
  INT4 k;
  VARo **arg=VarGetArgs (var);

  for (k=0; arg[k] != NULL; k++) {
    Job->lineN = VarGetLineN (arg[k]);
    VarExec (arg[k]);
  }
  return 1;
}



INT4 IopAss (VARo *var, VARo *store, VARo *val)
{
  VARo **arg;
  INT4 type, tmpInt;
  STRv str;

  if (var) {
    arg = VarGetArgs (var);
    store = arg[0];
    val = arg[1];
  }
 
  if (VarGetCode (store) & IARGxCALL || !VarIsAlias (store))
    _ErrExit2 (e__anyIsReadOnly, AnyDebugStr (store));

  _VarGetType (val, type); 
  switch (type) {
  case VARxINT:
    tmpInt = VarGetInt (val);
    VarSetInt (store, tmpInt);
    break;
  case VARxSTRING:
    VarSetStr (store, VarGetStr (val));
    break;
  case VARxSTRV:
    str = VarGetStrv (val);
    VarSetStrv (store, str); 
    break;
  case VARxLIST:
    AnySetList (store, val);
    break;
  case VARxOBJECT:
    VarSetObject (NULL, store, VarGetObject (NULL, val));
    break;
  case VARxUNKNOWN:
    _ErrExit3 (e__objectunknown, "variable", VarGetName (val));
  default:
    _ErrExit2 (e__unknownoption, "type in IopAss");
  }
  return 1;
}

INT4 IopMul (VARo *var)
{
  VARo **args=VarGetArgs (var);

  return VarGetInt (args[0]) * VarGetInt (args[1]);
}

INT4 IopAdd (VARo *var , VARo *val1, VARo *val2)
{
  VARo **arg;

  if (var) {
    arg = VarGetArgs (var);
    val1 = arg[0];
    val2 = arg[1];
  }
  return VarGetInt (val1) + VarGetInt (val2);
}
INT4 IopDivide (VARo *var)
{
  VARo **args=VarGetArgs (var);

  return VarGetInt (args[0]) / VarGetInt (args[1]);
}
INT4 IopSubt (VARo *var)
{
  VARo **args=VarGetArgs (var);

  return VarGetInt (args[0]) - VarGetInt (args[1]);
}

INT4 IopAddAss (VARo *var)
{
  VARo **arg=VarGetArgs (var);

  if (VarType (arg[0]) == VARxLIST) {
    AnyListApp (arg[0], VarCopy (arg[1], NULL));
    return 0;
  }  
  else {
    VarSetInt (arg[0], VarGetInt (arg[0]) + VarGetInt (arg[1]));
    return VarGetInt (arg[0]); 
  }
}

INT4 IopEq (VARo *var)
{
  VARo **arg=VarGetArgs (var);
  Int4 typ1, typ2, rv;
  STRv s1, s2;
  
  typ1 = VarGetType (arg[0]);
  typ2 = VarGetType (arg[1]);
  if ((typ1 == VARxSTRING || typ1 == VARxSTRV) || 
      (typ2 == VARxSTRING || typ2 == VARxSTRV)) {
    s1=VarGetStrv (arg[0]); s2=VarGetStrv (arg[1]);
    rv = SmEqs (_Str(s1), _Str(s2));
    StrDel (s1); StrDel (s2);
    return rv;
  }
  else
    return (VarGetInt (arg[0]) == VarGetInt (arg[1]));
}
INT4 IopNEq (VARo *var)
{
  VARo **arg=VarGetArgs (var);
  INT4 typ1, typ2, rv;
  STRv s1, s2;
  
  typ1 = VarGetType (arg[0]);
  typ2 = VarGetType (arg[1]);
  if ((typ1 == VARxSTRING || typ1 == VARxSTRV) || 
      (typ2 == VARxSTRING || typ2 == VARxSTRV)) {
    s1=VarGetStrv (arg[0]); s2=VarGetStrv (arg[1]);
    rv = SmEqs (_Str(s1), _Str(s2));
    StrDel (s1); StrDel (s2);
    return !rv;
  }
  else
    return !(VarGetInt (arg[0]) == VarGetInt (arg[1]));
}

INT4 IopLogAnd (VARo *var)
{
  VARo **arg=VarGetArgs (var);
  INT4 typ1, typ2;
  
  if (!VarGetInt (arg[0]))
    return 0;
  if (!VarGetInt (arg[1]))
    return 0;
  return 1;
}

INT4 IopLogOr (VARo *var)
{
  VARo **arg=VarGetArgs (var);
  INT4 typ1, typ2;
  
  if (VarGetInt (arg[0]))
    return 1;
  if (VarGetInt (arg[1]))
    return 1;
  return 0;
}

INT4 IopLT (VARo *var)
{
  VARo **args=VarGetArgs (var);

  return (VarGetInt (args[0]) < VarGetInt (args[1]));
}
INT4 IopGT (VARo *var)
{
  VARo **args=VarGetArgs (var);

  return (VarGetInt (args[0]) > VarGetInt (args[1]));
}

INT4 IopFor (VARo *var)
{
  VARo **args=VarGetArgs (var);

  VarExec (args[0]);
  while (VarGetInt (args[1])) {
    VarExec (args[3]);
    VarExec (args[2]);
  }
  return 1;
}

enum IOPeInList {IOPxFIRST, IOPxMIDDLE, IOPxLAST};
enum IOPeInList inListPos;

INT4 IopForeach (ANYv any)
{
  STRv str;
  ANYv list, var, tmp, *arg=VarGetArgs (any);
  char *name;
  Int4 type, i;

  var = arg[0];
  list = AnyListCpy (arg[1]);

  for (i=0; (tmp = AnyNextInList (list, &i));){
    if (i==1)
      inListPos = IOPxFIRST;
    else if (i==AnyListLen (list))
      inListPos = IOPxLAST;
    else
      inListPos = IOPxMIDDLE;
	
    switch (VarGetType (tmp)) {
    case VARxSTRING: 
      VarSetStr (var, VarGetStr (tmp));
      break;
    case VARxSTRV: 
      str = VarGetStrv (tmp);
      VarSetStrv (var, str);
      break;
    case VARxINT: 
      VarSetInt (var, VarGetInt (tmp));
      break;
    case VARxOBJECT: 
      VarSetObject (NULL, var, VarGetObject (NULL, tmp));
      break;
    case VARxVAR:
      VarSetVar (var, VarGetVar (tmp, 0));
      break;
    case VARxLIST:
      AnySetList (var, tmp);
      break;
    case VARxUNKNOWN:
      break;
    default:
      _ErrExit2 (e__unknownoption, "type in IopForeach");
      break;
    }
    VarExec (arg[2]);
    if (tmp == list)
      break;
  }
  VarDestroy2 (list);


  return 1;
}


STRv IopIsFirst (Int4 runTime, ANYv elem, ANYv list)
{
  IcaReturn ("strv", inListPos == IOPxFIRST);
}

STRv IopIsLast (Int4 runTime, ANYv elem, ANYv list)
{
  IcaReturn ("strv", inListPos == IOPxLAST);
}


INT4 IopWhile (VARo *var)
{
  VARo **args=VarGetArgs (var);

  while (VarGetInt (args[1])) {
    VarGetInt (args[0]);
  }
  return 1;
}


INT4 IopExit ()
{
  INT4 val;

  IargGetArgs ("val", &val);
  exit (val);
}

/* builds a list */
VARo *IopList (VARo *var)
{
  INT4 k;
  ANYv *arg=VarGetArgs (var), any, varList;

  varList = VarNew ();
  for (k=0; arg[k] != NULL; k++) {
    any = arg[k];
    VarGetType (any);
    if (any->type == VARxLIST)
      any = AnyListCpy (any);
    AnyListApp (varList, any); 
  }
  if (!k)
    AnySetList (varList, AnyNewList ());

  return varList;
}


INT4 IopIf (VARo *var)
{
  VARo **arg;
  
  for (arg=VarGetArgs (var); *arg; arg++)
    if (VarGetInt (*arg++)) {
      VarGetInt (*arg);
      break;
    }

  return 1;
}

VARo *IopSelect (VARo *var)
{
  VARo **arg=VarGetArgs (var), *val;

  return (val = AnyGetListIndex (arg[0], VarGetInt (arg[1])-1)); 
}

VARo *IopSelectAssoc (VARo *var)
{
  static ANYv empty;
  STRv str;
  ANYv *arg=VarGetArgs (var), val, tmp;
  
  if (!empty)
    empty = VarNew ();

  str = VarGetStrv (arg[1]);
  if (AnyIsWrite (var)) /* read/write */
    tmp = AnyGetListAssoc (arg[0], _Str(str));
  else {
    if (!(tmp = AnyFindListAssoc (arg[0], _Str(str)))) {
      VarReset (empty);
      tmp = empty;
    }
  }
  StrDel (str);
  return tmp;
}



/* only for ODD compiler */

#ifdef __ODD

extern ODDoCDEFINE cDefine[100];
extern INT4         cDefineN;
INT4 IopCDefine ()
{
  char name[80];
  INT4 k, n;

  IargGetArgs("n|name", &n, name);

  for (k=0; k < cDefineN; k++)
    if (SmEqs (name, cDefine[k].name))
      return;

  strcpy (cDefine[cDefineN].name, name);
  cDefine[cDefineN].n = n;
  cDefineN++;
}

INT4 IopReference (VARo *var)
{
  VARo **arg=VarGetArgs (var);
  STRv str=VarGetStrv (arg[1]);
  Int4 id=OddIdRetrieve (_Str(str), VarGetInt (arg[0]));
  StrDel (str);
  return id;
}

INT4 IopObject (VARo *var)
{
  struct SDLoOBJ *class;
  ANYv           tmp, attr, list, *arg=VarGetArgs (var);
  char           *className;
  void           *obj;
  INT4           k, c;

  OddInitDepot ();
  Job->lineN = VarGetLineN (var);

  className = VarGetClassName (var);
  if (!(class = (struct SDLoOBJ *)OddGetClass (className)))
    _ErrExit3 (e__objectunknown, "class", className);

  OddRegisterObj (class);
  while (arg && (attr = *arg++)) {
    list = AnyListCpy (attr);
    if (OddIsPartOfList (class, VarGetRealName (attr))) {
      for (k=0,c=0; (tmp = AnyNextInList (list, &c)); k++)
	VarGetType (tmp);
      OddSetObjListSize (class, VarGetRealName (list), k);
    }
    else
      OddObjAttribute (class, VarGetRealName (attr), list);
    VarDestroy2 (list);
  }
  VarSetObject (NULL, var, (obj = OddFinishObj (class)));

  if (SmEqs (className, "com"))
    IargSetCom ((struct IARGoCOM *)obj, 
		IargGetComName ((struct IARGoCOM *)obj));

  return 1;
}

#endif

typedef struct {
  INT4 count;
} BNFoLEVEL;

INT4 BnfPrintProgs (BNFoNODE *node, SMoBUFF *buff)
{
  VARo **stmnt;
  INT4 n[3], k;

  for (k=0, n[0]=n[1]=n[2]=0; k<3; k++) {
    if (node->exec[k]) {
      stmnt = VarGetArgs (node->exec[k]);
      for (n[k]=0; stmnt && *stmnt; stmnt++, n[k]++)
	;
    }
  }      

  /* substract from 'pre' and 'post' the debug statement */
  if (n[1])
    n[1]--;
  if (n[2])
    n[2]--; 

  if (n[0]+n[1]+n[2]) {
    BuffPrintF (buff, " {");
    if (n[0])
      BuffPrintF (buff, " *%d", n[0]);
    if (n[1])
      BuffPrintF (buff, " -%d", n[1]);
    if (n[2])
      BuffPrintF (buff, " +%d", n[2]);
    BuffPrintF (buff, " }");
  }      
  return (n[0]+n[1]+n[2]);
}

void BnfPrintNode (BNFoNODE *node, INT4 level)
{
  static SMoBUFF *buff=NULL;
  static STRv str=NULL;
  char   c;

  buff = BuffInit (buff, 40);
  if (!str)
    str = StrNew ();

  switch (node->counter) {
  case 0:
      c = ' ';
      break;
  case ZeroOrOne:
      c = '?';
      break;
  case ZeroOrMore:
      c = '*';
      break;
  case OneOrMore:
      c = '+';
      break;
  }

  if (node->name) {
    StrSetS (&str, node->name);
    StrEncode (&str);
  }
  switch(node->type) {
  case ProdName:
    BuffPrintF (buff, "ProdName: %s%c", _Str(str), c);
    BnfPrintProgs (node, buff);
    break;
  case Production:
    BuffPrintF (buff, "Production: %s%c", 
		node->name ? node->name : "?", c);
    BnfPrintProgs (node, buff);
    break;
  case Literal:
    BuffPrintF (buff, "Literal: '%s'%c", _Str(str), c);
    BnfPrintProgs (node, buff);
    break;
  case Regexp:
    BuffPrintF (buff, "RegExp: /%s/%c", _Str(str), c);
    BnfPrintProgs (node, buff);
    break;
  case Term:
    BuffPrintF (buff, "Term%c", c);
    break;
  case Choice:
    BuffPrintF (buff, "Choice%c", c);
    break;
  case Command:
    BuffPrintF (buff, "Command%c", c);
    BnfPrintProgs (node, buff);
    break;
  case LineStart:
    BuffPrintF (buff, "LineStart%c", c);
    break;
  default:
    BuffPrintF (buff, "unknown%c", c);
    break;
  }
  printf ("%s\n", BuffFormat (buff, 80, level*4, level*4, NULL));
}


INT4 IopPrintProduction (VARo *var)
{
  BNFoPRODUCTION *prod;

  IargGetArgs("prod", &prod);
  BnfTreeTraverse ((BNFoNODE *) prod, BnfPrintNode, 1);
}


STRv IopPrintFormat (Int4 runTime, STRv s, STRv label, Int4 width,
		     Int4 firstIndent, Int4 indent)
{
  STRv tmp;
  char *p, *pSave;
  Int4 k, lineLen;

  if (runTime)
    IargGetArgs ("s|label|width|indent|firstIndent", 
		 &s, &label, &width, &indent, &firstIndent);

  tmp=StrNew ();
  if (label)
    indent = StrLen (label);

  /* text or ident to the left of first line */
  if (label)
    StrApp (&tmp, label);
  else if (firstIndent)
    StrFill (&tmp, firstIndent, ' ');
  
  lineLen = StrLen (tmp);
  for (k=lineLen + StrLen (s), p=_Str (s); k >= width; ) {
    pSave = p;
    p += width - lineLen;
    while (*p != ' ' && p > pSave) /* find the next ' ' backwards */
      p--;

    if (p == pSave) /* no space was found break at line end */
      p += width - lineLen;
    *(p++) = '\0';
    StrAppS (&tmp, pSave);
    StrAppS (&tmp, "\n");

    /* text or ident to the left of following lines */
    if (label)
      StrApp (&tmp, label);
    else
      StrFill (&tmp, firstIndent, ' ');

    lineLen = indent;
    k = k - strlen (pSave) + lineLen; 
  }
  StrAppS (&tmp, p);
  StrDel (s); StrDel (label);

}



INT4 IopPrint (INT4 runTime, VARo *val, FILEo *file, Int4 mode, VARo *var)
{
  STRv str;

  if (runTime)
    IargGetArgs("s|f|mode|v", &val, &file, &mode, &var);

  if (!val) {
    _ErrMsg (e__icaMissingString);
    return 0;
  }
  str = VarPrintf (val);
  if (var)
    VarAppStrv (var, str);
  else if (file)
    fwrite (_Str (str), StrLen (str), 1, file->file);
  else
    printf ("%s", _Str (str));
  StrDel (str);
  return 1;
}

STRv IopAltStr (Int4 runTime, Int4 cond, STRv t, STRv f)
{
  STRv s;

  if (runTime)
    IargGetArgs("cond|t|f", &cond, &t, &f);

  if (!t) t = StrNew ();
  if (!f) f = StrNew ();

  if (cond) {
    StrDel (f);
    s = t;
  }
  else {
    StrDel (t);
    s = f;
  }

  if (runTime)
    IcaReturn ("strv", s);
  else 
    return s;
}

STRv IopPrintForeach (Int4 runTime, ANYv var, ANYv in, ANYv s, ANYv sep)
{
  ANYv tmp;
  STRv str=StrNew();
  Int4 i;

  if (runTime)
    IargGetArgs("var|in|s|sep", &var, &in, &s, &sep);

  for (i=0; (tmp = AnyNextInList (in, &i));){
    VarCopy (tmp, var);
    StrApp (&str, VarPrintf (s));
    if (i != AnyListLen (in))
      StrApp (&str, VarPrintf (sep));
  }

  if (runTime)
    IcaReturn ("strv", str);
  else 
    return str;
}


INT4 IopDebugPrint (INT4 runTime, VARo *val)
{
  STRv str;

  if (runTime)
    IargGetArgs("s", &val);

  str = VarPrintf (val);

  printf ("|%s|\n", _Str (StrEncode (&str)));
  StrDel (str);
  return 1;
}



INT4 IopOut (INT4 runTime, STRv name)
{
  char *tableName;

  if (Job->time == BNFxBUILDTIME) {
    if (runTime)
      IargGetArgs("name", &name);
    tableName = name ? _Str(name) : Job->currNode->name;

    Job->tokList = TokGetList (tableName, &Job->tokList);
    Job->currNode->wrtTokList = Job->outTokList = Job->tokList;
    TokSetStyle(Job->currNode->wrtTokList, COPYSTYLE);
    if (name) 
      StrDel (name);
  }
  else 
    /*Job->tokList =*/ Job->outTokList = Job->currNode->wrtTokList;
  return 1;
}

INT4 IopNot ()
{
  Job->currNode->action |= BNFxNOT;
  return 1;
}

INT4 IopProbe ()
{
  Job->currNode->action |= BNFxPROBE;
  return 1;
}

INT4 IopNoskip ()
{
  Job->currNode->action |= BNFxNOSKIP;
  return 1;
}

INT4 IopProd ()
{
  BNFoPRODUCTION *prod;

  char name[80];
  IargGetArgs("name", name);

  if (!(prod = BnfGetProduction (Job->syntax, name, 0)))
      _ErrMsg3 (e__objectunknown, "production", name);
  BnfParseProduction (prod);
}




INT4 IopIn (Int4 runTime, STRv in, STRv codeName, Int4 code, STRv prodName, 
	    STRv inFileName, STRv sharesFile, STRv task, STRv countCodeName, 
            VARo *countVar, Int4 selectN, VARo *inCode)
{
  static INT4 c = 0, tokCount; 
  BNFoPRODUCTION *prod, *prodCurr=(BNFoPRODUCTION *) Job->currNode;
  TOKoLIST       *tokList;
  TOKoTOKEN      *tok;
  INT4           countCode=-1, codeCurr, k;

  if (runTime)
    IargGetArgs("in|ic|n|p|file|share|t|count|var|select|c", 
		&in, &codeName, &code, &prodName, &inFileName, &sharesFile,
		&task, &countCodeName, &countVar, &selectN, &inCode); 

  /* INIT and PRE time */
  if (in) {
    if (countCodeName)
      countCode = TokStrToCode (_Str(countCodeName));
    tokList = TokGetList (_Str(in), &Job->tokList);
    Job->tokList = Job->currNode->rdTokList = tokList;
  }    

  /* convert list of code names to numeric codes and attach to current node */
  if (Job->time == BNFxBUILDTIME && inCode) {
    ANYv tmp, list;
    Int4 i;
    STRv s;

    list = AnyListCpy (inCode);
    for (i=0; (tmp=AnyNextInList (list, &i));) {
      s = VarGetStrv (tmp);
      *_addObj (prodCurr->inCode, prodCurr->inCodeN,
		prodCurr->inCodeAllocN, Int4)
	= TokStrToCode (_Str (s));
      StrDel (s);
    }
    VarDestroy2 (list);
  }    

  if (Job->time == BNFxBUILDTIME) {
    if (inFileName)
      ;
    else if (task) {
      if (prodName)
	prod = BnfGetProduction (NULL, _Str(prodName), 0);
      else
	prod = IcaGetSupplyNode (Job->currNode->rdTokList->name);
      
      prod->taskLinks = 
	TaskRequestLink (&Job->syntax->taskList, _Str(task), 
			 (BNFoPRODUCTION *) Job->currNode, 
			 prod->taskLinks);
    }
  }
  /* PRE time only */
  else {
    if (inFileName) {
      FILEo *file;
      if (!(file = (*Job->inputStreamer) (_Str (inFileName), 
					 Job->inputStreamerData)))
	IcaSetInputEnd (Job);
      IcaSetInputFile (Job, file, sharesFile ? sharesFile : inFileName);
    }
    else if (TokIsListActive (tokList)) {
      if (countCodeName) { /* client asked for a counter */
	if (TokIsListStart (tokList))
	  tokCount = 0;

	while ((tok = TokNext (tokList, &c))) {
	  if ((code = TokGetCode (tok)) == countCode)
	    tokCount++;

	  for (k=0; k < prodCurr->inCodeN; k++)
	    if (prodCurr->inCode[k] == code) 
	      break;
	  if ((k < prodCurr->inCodeN || !prodCurr->inCodeN) 
	      && (!selectN || selectN == tokCount)) {
	    if (countVar)
	      VarSetInt (countVar, tokCount);
	    break;
	  }
	}
	Job->inToken = tok;
	CursorInstall (Job->cursor, tok, tokList);
      }
      else {
	Job->inToken = NULL;
	while ((tok = TokNext (tokList, &c))) {
	  for (k=0, code=TokGetCode (tok); k < prodCurr->inCodeN; k++)
	    if (prodCurr->inCode[k] == code)
	      break;
	  if (k < prodCurr->inCodeN || !prodCurr->inCodeN) 
	    break;
	}
	Job->inToken =  tok;
	CursorInstall (Job->cursor, Job->inToken, tokList);
      }
    }
  }

  StrDel (in);
  StrDel (codeName);
  StrDel (prodName);
  StrDel (inFileName);
  StrDel (sharesFile);
  StrDel (task);
  StrDel (countCodeName);
}


void IopSetDebug (Int4 runTime, Int4 isOn)
{
  if (runTime)
    IargGetArgs ("state", &isOn);
    
  Job->isDebug = isOn;
}

void IopDebug (Int4 time)
{
  static STRv str=NULL;
  BNFoNODE *node;
  char input[100];

  if (!str)
    str = StrNew ();

  if (time == PROGxPREPARSE)
    printf ("  * before *\n");
  else if (time == PROGxPOSTPARSE)
    printf ("  * after *\n");

  if (Job->isDebug) {
    node = Job->currNode;
    BnfPrintNode (node, 1);
    strncpy (input, Job->cursor->current, 50); 
    input[50] = '\0';
    StrSetS (&str, input);
    StrEncode (&str);
    printf ("      Input: |%s|\n", _Str(str));
  }
}


INT4 IopWrt (VARo *var)
{
  TOKoLIST *tokList;
  char     *match;
  INT4     code=-1, k, length;
  VARo     **arg=VarGetArgs (var);
  STRv     str=NULL, c;

  if (arg)
    for (k=0; arg[k] != NULL; k++)
      switch (VarGetRealName (arg[k])[0]) {
      case 's':
        str = VarPrintf (arg[k]);
	break;
      case 'c':
      case ':':
	c = VarGetStrv (arg[k]);
	code = TokStrToCode (_Str(c));
	StrDel (c);
	break;
      case 'n':
	code = VarGetInt (arg[k]);
	break;
      default:
	_ErrExit2 (e__unknownoption, "IopWrt");
      }


  tokList = Job->outTokList;
  if (str)
    TokAdd (tokList, _Str(str), StrLen (str), code);
  else {
    CursorGetMatch (Job->cursor, &match, &length);
    TokAdd (tokList, match, length, code);
  }
  if (str)
    StrDel (str);
  return 1;
}


void IopUniq (VARo *var)
{
  TOKoLIST *tokList;
  char     *match, *s=NULL;
  INT4     code=0, k, length;
  VARo     **arg=VarGetArgs (var);
  STRv     str=NULL, c;

  if (arg)
    for (k=0; arg[k] != NULL; k++)
      switch (VarGetRealName (arg[k])[0]) {
      case 's':
        str = VarPrintf (arg[k]);
	break;
      case 'c':
      case ':':
	c = VarGetStrv (arg[k]);
	code = TokStrToCode (_Str(c));
	StrDel (c);
	break;
      case 'n':
	code = VarGetInt (arg[k]);
	break;
      default:
	_ErrExit2 (e__unknownoption, "IopWrt");
      }

  tokList = Job->outTokList;
  if (str) {
      TokAddUniq (tokList, _Str(str), StrLen (str), code);

    /*    if (TokIsUniq (tokList, s, (length=strlen(s)), code))
      TokAdd (tokList, s, length, code);*/
  }
  else {
    CursorGetMatch (Job->cursor, &match, &length);
      TokAddUniq (tokList, match, length, code);
    /*    if (TokIsUniq (tokList, match, length, code))
      TokAdd (tokList, match, length, code);*/
  }
  if (str)
    StrDel (str);
}


INT4 IopApp (VARo *var)
{
  VARo **arg=VarGetArgs (var);
  char *match, *s=NULL;
  INT4 length, k;
  STRv str=NULL;

  if (arg)
    for (k=0; arg[k] != NULL; k++)
      switch (VarGetRealName (arg[k])[0]) {
      case 's':
        str = VarPrintf (arg[k]);
	s = _Str (str);
	break;
      }

  if (s)
    TokAppend (Job->outTokList, s, strlen (s));
  else {
    CursorGetMatch (Job->cursor, &match, &length);
    TokAppend (Job->outTokList, match, length);
  }
  if (str)
    StrDel (str);
}


INT4 IopRep (Int4 runTime, VARo *list)
{
  VARo *value;
  STRv str;

  if (runTime)
    IargGetArgs("s", &list);
  str = VarPrintf (list);

  CursorReplaceMatch (Job->cursor, _Str (str), StrLen (str));
  StrDel (str);
}

STRv IopStrTrim (Int4 runTime, STRv str, STRv skip)
{
  if (runTime)
    IargGetArgs("s|skip", &str, &skip);

  StrTrim (&str, skip ? _Str (skip) : NULL);
  StrDel (skip);
  StrDel (str); /* StrTrim makes a new copy */
  if (runTime)
    IcaReturn ("strv", str);
  return str;
}

void IopStrApp(Int4 runTime, VARo* v, STRv s) {
    if (runTime) IargGetArgs("v|s",&v,&s);
    if (v) VarAppStrv (v, s);
}

INT4 IopGetc (VARo *var)
{
  VARo **arg=VarGetArgs (var);

  CursorSetLength (Job->cursor, VarGetInt (arg[0]));
  return 1;
}

void IopRestrictLength (VARo *var)
{
  static Int4     cursorLenSave, tmpLenSave;
  VARo **arg=VarGetArgs (var);
  Int4 len;

  len = arg[0] ? VarGetInt (arg[0]) : 0;
  if (len && Job->currNode) { 
    if (Job->time == BNFxPREPARSE) {
      cursorLenSave = CursorGetLength (Job->cursor);
      tmpLenSave = CursorSetTmpLength (Job->cursor, len);
    }  
    else if (Job->time == BNFxPOSTPARSE) {
      CursorSetMatch (Job->cursor, CursorGetLength (Job->cursor));
      CursorIncrement (Job->cursor);
      CursorResetLength (Job->cursor, cursorLenSave - tmpLenSave);
    }
  }
}


void IopMove (VARo *var)
{
  VARo **arg=VarGetArgs (var);
  Int4 len= arg[0] ? VarGetInt(arg[0]) : 0;
  
  if (len > CursorGetLength (Job->cursor))
    Job->parseError = 1;
  else {
    CursorSetLength (Job->cursor, VarGetInt (arg[0]));
    CursorMove (Job->cursor);
    Job->doAdvance = 1; /* make sure next symbol advances input */
  }
}





INT4 IopRequest ()
{
  TOKoLIST *tokList, *tokListCurr;
  char name[80];

  IargGetArgs("name", name);
  
  tokListCurr = Job->outTokList;
  tokList = IcaGetTokenList (Job, name);
  Job->outTokList = tokListCurr;
  return 1;
}



INT4 IopJobTokens ()
{
  FILEo     *outFile;
  ICAoJOB   *job;
  TOKoLIST  *tokList;
  TOKoTOKEN *tok;
  char      name[80], codeName[80], taskName[80], *s;
  INT4      c, code, doPrint, withCode;

  IargGetArgs("job|name|n|code|print|task|withCode|outFile", 
	      &job, name, &code, codeName, &doPrint, taskName, &withCode, 
	      &outFile);

  if (*codeName)
    code = TokStrToCode (codeName);
  else
    code = -1;

  if (*taskName)
    IcaSetTask (job, taskName, 1);
  if ((tokList = IcaGetTokenList (job, name))) {
    if (doPrint) {
      if (withCode)
	printf ("\n----- list: %s ------\n", TokListGetName (tokList));
      for (c=0; (tok = TokNextWithCode (tokList, code, &c));) {
	if (withCode) {
	  char* code=TokCodeToStr (TokGetCode (tok));
	  s=TokGetStringCopy (tokList, tok);
	  printf ("code: %s string: |%s|\n",code,s);
	}
	else {
	  s = TokGetStringCopy (tokList, tok);
	  fwrite (s, strlen (s), 1, outFile ? FileGetFile (outFile) : stdout);
	}
      }
    }
  }
  IcaReturn ("int", 1);
}

Int4 IopJobHasInput ()
{
    ICAoJOB *job;
    IargGetArgs ("job", &job);

  if (IcaIsJobEnd (job))
      IcaReturn ("int", 0);
  else
      IcaReturn ("int", 1);
}

void IopFail (Int4 runTime)
{
  Job->parseError = 1;
  Job->doAdvance = 1;
}


INT4 IopSetSkip (Int4 runTime, Int4 state, STRv ws)
{
  char *tmp;

  if (runTime)
    IargGetArgs("state|s", &state, &ws);
  if (ws) {
    Job->syntax->ign = malloc (StrLen(ws) + 1);
    strcpy (Job->syntax->ign, _Str(ws));
    StrDel (ws);
  }
  if ((!state && *Job->syntax->ign) || (state && !*Job->syntax->ign)) {
    tmp = Job->syntax->ign;
    Job->syntax->ign = Job->syntax->ignAlt;
    Job->syntax->ignAlt = tmp;
  }
}

Int4 IopFip (INT4 runTime, Int4 flag)
{
  Int4 fip;

  if (runTime)
    IargGetArgs ("switch", &flag);
  if (flag)
    FileSetGetFip (Job->file, (flag == 1) ? 1 : 0);
  else if (Job->file) {
    fip = (Int4) FileGetFip (Job->file);
    if (runTime)
      IcaReturn ("int", fip);
    else 
      return fip;
  }
  else
    return 0;
}

FILEo *IopFile (Int4 runTime)
{
  if (runTime)
    IcaReturn ("file", Job->file);
  else 
    return Job->file;
}

STRv IopSubMatch (INT4 runTime, INT4 n)
{
  STRv str;
  
  if (runTime)
    IargGetArgs("n", &n);
  
  str = StrNCpyS (Job->regExp->startp[n],
	   (Int4)(Job->regExp->endp[n] - Job->regExp->startp[n]));

  if (runTime)
    IcaReturn ("strv", str);
  else 
    return str;
}


/* should be called directly */
STRv IopCurrToken (INT4 runTime)
{
  STRv str;
  char *p;
  Int4 len;

  CursorGetMatch (Job->cursor, &p, &len);
  str = StrNCpyS (p, len);
  if (runTime)
    IcaReturn ("strv", str);
  else
    return str;
}

STRv IopInTokenCode (INT4 runTime)
{
  static STRv str=NULL;

  if (!str)
    str = StrNew ();
  if (Job->inToken)
    StrSetS (&str, TokCodeToStr (TokGetCode (Job->inToken)));
  else
    StrClear (&str);
  if (runTime)
    IcaReturn ("strv", StrCpy (str));
  else
    return StrCpy(str);
}

STRv IopInToken (INT4 runTime, Int4 n)
{
  STRv str=StrNew ();

  if (runTime)
    IargGetArgs ("n", &n);

  if (n && n<Job->cursor->len)
    StrAppN (&str, Job->cursor->current, n);
  else
    StrAppN (&str, Job->cursor->current, Job->cursor->len);

  if (runTime)
    IcaReturn ("strv", str);
  else
    return str;
}


char *IopKey ()
{
  static STRv str=NULL;
  VARo *val;
  char *tmp;

  if (!str)
    str = StrNew ();

  IargGetArgs ("val", &val);
  if ((tmp = VarGetName (val)))
    StrSetS (&str, tmp);
  else 
    StrClear (&str);

  IcaReturn ("strv", StrCpy (str));
}


void IopPush_ (INT4 runTime, VARo *var, INT4 stackN)
{
  VARoStack *stack;

  if (runTime)
    IargGetArgs ("value|stack", &var, &stackN);

  VarPush2 (&icaStack2[stackN], VarDuplicate(var));
}

VARo *IopPop_ (INT4 runTime, INT4 stackN)
{
  VARo *var;

  if (runTime)
    IargGetArgs ("stack", &stackN);
  
  if (!(var = VarPop2 (&icaStack2[stackN])))
    _ErrExit2 (e__icastackempty, stackN);
  if (runTime)
    IcaReturn ("var", var);
  else 
    return var;
}


INT4 IopPush (INT4 runTime, VARo *var, INT4 stackN)
{
  VARoSTACK *stack;
  VARo *tmp;

  if (runTime)
    IargGetArgs ("value|stack", &var, &stackN);
  
  stack = icaStack[stackN];
  if (!stack) {
    stack = VarStackNew (10);
    icaStack[stackN] = stack;
  }

  tmp = VarPushNew (stack);
  switch (VarGetType (var)) {
  case VARxSTRING: 
    VarSetStr (tmp, VarGetStr (var));
    break;
  case VARxINT: 
    VarSetInt (tmp, VarGetInt (var));
    break;
  case VARxOBJECT: 
    VarSetObject (NULL, tmp, VarGetObject (NULL, var));
    break;
  case VARxSTRV:
    VarSetStrv (tmp, VarGetStrv (var));
    break;
  default:
    _ErrExit2 (e__unknownoption, "type in IopPush");
  }
}

VARo *IopPop (INT4 runTime, INT4 stackN)
{
  VARo *var;

  if (runTime)
    IargGetArgs ("stack", &stackN);

  if (!icaStack[stackN] || !(var = VarPop (icaStack[stackN])))
    _ErrExit2 (e__icastackempty, stackN);
  if (runTime)
    IcaReturn ("var", var);
  else
    return var;
}

INT4 IopSetFunctions ()
{
  FUNC function;
  char name[132];

  IargGetArgs ("name", name);
  if (!(function = IcaGetFunction (name)))
    _ErrExit3 (e__objectunknown, "function", name);

  (*function)();
  return 1;
}

/* gcg programs */

INT4 GCGWordsearch ()
{
  static SMoBUFF *buff=NULL;
  FUNC function;
  char inFile1Name[132], inFile2Name[132];

  buff = BuffInit (buff, 100);
  IargGetArgs ("inFile1|inFile2", inFile1Name, inFile2Name);


  BuffPrintF (buff, "wordsearch ");
  BuffPrintF (buff, "-infile1=%s ", inFile1Name);
  BuffPrintF (buff, "-infile2=%s ", inFile2Name);
  BuffPrintF (buff, "-def ");
  printf ("%s\n", BuffGetPtr (buff));
  system (BuffGetPtr (buff)); 
  return 1;
}

INT4 IopParDel (Int4 runTime, STRv name)
{
  if (runTime)
    IargGetArgs ("name", &name);
  if (name) {
    ParDeleteMatch (_Str (name));
    StrDel (name);
  }
}


INT4 IopParStr (Int4 runTime, STRv name, STRv set)
{
  if (runTime)
    IargGetArgs ("name|set", &name, &set);
  if (set) {
    ParDefStr (_Str(name), _Str(set));
    StrDel (set);
  }
  else
    IcaReturn ("strv", StrCpyS (ParGetStr (_Str(name))));
  StrDel (name);
}

INT4 IopParInt (Int4 runTime, STRv name, Int4 set)
{
  if (runTime)
    IargGetArgs ("name|set", &name, &set);
  if (set != 2)
    ParDefNum (_Str(name), set);
  else
    IcaReturn ("int", ParGetNum (_Str(name)));
  StrDel (name);
}

INT4 IopEnv (Int4 runTime, STRv name, STRv set)
{
  STRv com, s;
  char *tmp;

  if (runTime)
    IargGetArgs ("name|set", &name, &set);
  if (set) {
    com=StrNew ();
    StrPrintf (&com, "%s=%s", _Str(name), _Str(set));
    putenv (_Str (com));
    StrDel (com);
    StrDel (set);
  }
  s = StrNew ();
  if ((tmp = getenv (_Str(name))))
    StrAppS (&s , tmp);

  IcaReturn ("strv", s);
  StrDel (name);
}



INT4 IopHtmlSpace ()
{
  static SMoBUFF *buff=NULL;
  INT4 bigN, sn=0, n, ln=0, s, l;

  buff=BuffInit (buff, 20);

  /* question: represent a number n of 1/4 or 1/3 characters
     by a combination of 3/4 and 4/4 or 2/3 and 3/3 resp. 


     solution: 
       s is the smaller of 3,4 or 2,3 -> 3 or 2
       l is the larger of the pair -> 3 or 4
       sn, ln refers to the numbers in the combination
       
       ln = n % s; sn = n - (ln*l) / s
   */
  
  /*  s=3;
  l=4;*/
  IargGetArgs ("thirds|s|l", &n, &s, &l);

  if (n == s)
    sn = 1;
  else if (n == l && n < 2*s) /* an approximation here */
    ln = 1;
  else if (n >= 2*s) 
    if (n) {
      ln = n%s;
      sn = (n - ln*l) / s;
    }      

  if (ln)
    BuffFill (buff, ln, ' ');
  if (sn) {
    BuffCopyString (buff, "<SUB>");
    BuffFill (buff, sn, ' ');
    BuffCopyString (buff, "</SUB>");
  }
  IcaReturn ("string", BuffGetPtr (buff));
}

INT4 IopStrlen ()
{
  char s[500];

  IargGetArgs ("s", s);
  IcaReturn ("int", strlen(s));
}

INT4 IopStrLen (Int4 runTime, STRv s)
{
  Int4 len;
  if (runTime)
      IargGetArgs ("s", &s);
  len = StrLen (s);
  if (runTime)
      IcaReturn ("int", len);
  StrDel (s);
  return len;

}

STRv IopStrPad (Int4 runTime, STRv s, Int4 len, STRv c)
{
  STRv t;
  char padS[1000];
  Int4 padLen, k;

  if (runTime)
    IargGetArgs ("s|len|c", &s, &len, &c);
  
  t = StrCpy (s);
  if (StrLen (t) < len) {
    padLen = len - StrLen (t);
    for (k=0; k < padLen; k++)
      padS[k] = *(_Str (c));
    padS[k] = '\0';
    StrAppS (&t, padS);
  }    
  StrDel (c);
  StrDel (s);
  IcaReturn ("strv", t);
}

STRv IopStrTrans (Int4 runTime, STRv s, STRv from, STRv to)
{
  STRv t;
  if (runTime)
    IargGetArgs ("s|from|to", &s, &from, &to);

  t = StrCpy (s);
  StrTranslate (&t, _Str(from), _Str(to));
  StrDel (from);
  StrDel (to);
  StrDel (s);
  IcaReturn ("strv", t);
}

STRv IopStrUpper (Int4 runTime, STRv s)
{
  STRv t;
  if (runTime)
    IargGetArgs ("s", &s);
  
  t = StrCpy (s);
  StrDel (s);
  StrUpper (&t);
  IcaReturn ("strv", t);
}

STRv IopStrLower (Int4 runTime, STRv s)
{
  STRv t;
  if (runTime)
    IargGetArgs ("s", &s);
  
  t = StrCpy (s);
  StrDel (s);
  StrLower (&t);
  IcaReturn ("strv", t);
}

STRv IopStrReplace (Int4 runTime, STRv s, STRv from, STRv to)
{
  STRv t;
  if (runTime)
    IargGetArgs ("s|from|to", &s, &from, &to);
  
  t = StrCpy (s);
  StrDel (s);
  StrReplace (&t, _Str(from), _Str (to));
  StrDel (from);
  StrDel (to);
  IcaReturn ("strv", t);
}



INT4 IopFileOpen (Int4 runTime, STRv name, Int4 mode)
{
  FILEo *file;

  IargGetArgs ("name|mode", &name, &mode);
  file = FileNew (name ? _Str(name) : NULL);
  if (mode==2) /* write access */
    FileSetWrite (file);
  
  if (!FileOpen (file) )
    _ErrExit2 (e__filnotok, _Str(name));
  StrDel (name);
  IcaReturn ("file", file);
}

void IopFileClose ()
{
  FILEo *file;

  IargGetArgs ("file", &file);

  if (file) {
    FileDelete (file);
  }
}

STRv IopFileName (Int4 runTime, Int4 option)
{
  STRv  s;
  FILEo *file;

  if (runTime)
    IargGetArgs ("type", &option);
  
  if ((file = IcaJobGetFile (Job))) {
    switch (option) {
    case 1:
      s = StrCpyS (FileGetName (file, "path"));
      break;		
    case 2:
      s = StrCpyS (FileGetName (file, "dir"));
      break;		
    case 3:
      s = StrCpyS (FileGetName (file, "name"));
      break;		
    case 4:
      s = StrCpyS (FileGetName (file, "file"));
      break;		
    case 5:
      s = StrCpyS (FileGetName (file, "ext"));
      break;		
    }
  }
  else 
    s = StrNew ();
  IcaReturn ("strv", s);
}



/* used by IopJobNew as optional input streamer */
FILEo *IopInputStreamer (char *name, void *data)
{
  FILEo   *file;

  if (Job->file) 
    return FileIsEof (Job->file) ? NULL : Job->file;
  else {
    file = FileNew (_Str ((STRv) data));
    if (!FileOpen (file) )
      _ErrExit2 (e__filnotok, _Str ((STRv) data));
    return file;
  }
}

ICAoJOB *IopJobNew (Int4 runTime, VARo *prod, STRv skip, STRv comment, 
		    FILEo *file, STRv str, Int4 doShow, Int4 doTree, 
		    STRv fileName)
{
  ICAoSYNTAX *syntax;
  ICAoJOB    *job;

  if (runTime)
    IargGetArgs ("prod|skip|comment|file|str|show|tree|fileName", 
		 &prod, &skip, &comment, &file, &str, &doShow, &doTree,
		 &fileName);

  /* new syntax object */
  if ((syntax = (ICAoSYNTAX *) calloc (sizeof(ICAoSYNTAX), 1)) == NULL)
    _ErrExit2 (e__allocfail, "syntax object");;
  syntax->ign = skip ? _Str (skip) : "";
  syntax->ignAlt = "";
  syntax->cmnt = comment ? _Str (comment) : "";
  syntax->prod = prod;

  /* new job object */
  if ((job = (ICAoJOB *) calloc (sizeof(ICAoJOB), 1)) == NULL)
    _ErrExit2 (e__allocfail, "job object");
  job->fileName = Job->fileName; /* for error messages */
  IcaContext ("push", &job);
  job->syntax = syntax;
  job->time = BNFxBUILDTIME;
  BnfInitRules (syntax, doTree);
  job->time = 0;
  IcaContext ("pop", NULL);
  IcaCursorSet (&job->inCursor, CursorNew (), NULL);

  /* which input to parse? */
  if (fileName) {
    IcaSetInputStreamer (job, IopInputStreamer);
    IcaSetInputStreamerData (job, (void*) fileName);
    IcaJobNext (job);
    /*    TokGetList (INTOKLIST, &job->tokList); */
  }
  else if (file)
    IcaJobSetFile (job, file);
  else if (str)
    IcaJobSetString (job, _Str (str));

  if (runTime)
    IcaReturn ("job", job);
  else 
    return job;
}

INT4 IopJobNext (Int4 runTime, ICAoJOB *job, FILEo *file)
{
  if (runTime)
    IargGetArgs ("job|file", &job, &file);
  if (file)
    IcaJobSetFile (job, file);
  IcaJobNext (job);
}

INT4 IopJobEnd ()
{
  ICAoJOB *job;

  IargGetArgs ("job", &job);
  IcaEndJob (job); 
}


void IopBreak (Int4 runTime, Int4 cond, Int4 time)
{
  if (runTime)
    IargGetArgs ("cond|time", &cond, &time);

  Job->currNode->dbgBreak = IARGxPRE | IARGxPOST;

  if (Job->time != BNFxBUILDTIME && cond) 
    Job->currNode->dbgBreak = IARGxPRE | IARGxPOST;
  else 
    Job->currNode->dbgBreak = 0;
}

void IopContinue ()
{
  DbgSetContinue ();
}

void IopNext ()
{
  DbgSetNext ();
}


Int4 IopTestMode ()
{
  IcaReturn ("int", ParGetNum ("fromSrs") ? 0 : 1);
}

Int4 IopListLen(Int4 runTime, ANYv list) {
  Int4 len;
  if (runTime) IargGetArgs("list",&list);
  len=AnyListLen(list);
  if (runTime) IcaReturn("int",len);
  return len;
}

void EntryIopSetFieldFormat (); 
INT4 QuerySetFunctions ();
INT4 SeqIopNew ();
INT4 SeqIopLen ();
INT4 SeqIopApp ();
INT4 SeqIopPrint ();
INT4 SeqIopMake ();
INT4 SeqIopTrunc ();
void SdbFunctions ();
void SeqIopGet2Bit ();


/****** IcaOpLibrary ******************************************************
*/

INT4 IcaOpLibrary()
{
  
  /* for icarus interpreter */


  IcaSetFunction("IcaOpSubStr", (FUNC)IcaOpSubStr);

  /* for icarus interpreter but level 4 */
  IcaSetFunction("IopList_",    (Func)IopList_);
  IcaSetFunction("IopProg_",    (Func)IopProg_);
  IcaSetFunction("IopBinop_",   (Func)IopBinop_);
  IcaSetFunction("IopStrMake_", (Func)IopStrMake_);
  IcaSetFunction("IopPush_",    (Func)IopPush_);
  IcaSetFunction("IopPop_",     (Func)IopPop_);
  IcaSetFunction("IopOpnd_",    (Func)IopOpnd_);
  IcaSetFunction("IopAssoc_",   (Func)IopAssoc_);
  
  IcaSetFunction("IopBody_",    (Func)IopBody_);
  IcaSetFunction("IopSelect_",  (Func)IopSelect_);
  IcaSetFunction("IopFunc_",    (Func)IopFunc_);
  IcaSetFunction("IopSetWrite_", (Func)IopSetWrite_);
  IcaSetFunction("IopMakeArg_", (Func)IopMakeArg_);
  IcaSetFunction("IopRef_",     (Func)IopRef_);
  IcaSetFunction("IopPre_",     (Func)IopPre_);
  IcaSetFunction("IopInit_",    (Func)IopInit_);
  IcaSetFunction("IopFor_",     (Func)IopFor_);
  IcaSetFunction("IopForeach_", (Func)IopForeach_);
  IcaSetFunction("IopWhile_",   (Func)IopWhile_);
  IcaSetFunction("IopIf_",      (Func)IopIf_);
  IcaSetFunction("IopFile_",      (Func)IopFile_);

  /* new level 3 icarus commands */

  IcaSetFunction("IopSystem",          (FUNC)IopSystem);
  IcaSetFunction("IopInterpStr_",      (FUNC)IopInterpStr_);
  IcaSetFunction("IopTest",            (FUNC)IopTest);
  IcaSetFunction("IopExecCom",         (FUNC)IopExecCom);
  IcaSetFunction("IopProg",            (FUNC)IopProg);
  IcaSetFunction("IopBody",            (FUNC)IopBody);
  IcaSetFunction("IopFor",             (FUNC)IopFor);
  IcaSetFunction("IopForeach",         (FUNC)IopForeach);
  IcaSetFunction("IopIf",              (FUNC)IopIf);
  IcaSetFunction("IopWhile",           (FUNC)IopWhile);
  IcaSetFunction("IopList",            (FUNC)IopList);
  IcaSetFunction("IopExit",            (FUNC)IopExit);
  IcaSetFunction("IopMul",             (FUNC)IopMul);
  IcaSetFunction("IopAdd",             (FUNC)IopAdd);
  IcaSetFunction("IopDivide",          (FUNC)IopDivide);
  IcaSetFunction("IopSubt",            (FUNC)IopSubt);
  IcaSetFunction("IopAss",             (FUNC)IopAss);
  IcaSetFunction("IopAddAss",          (FUNC)IopAddAss);
  IcaSetFunction("IopEq",              (FUNC)IopEq);
  IcaSetFunction("IopNEq",             (FUNC)IopNEq);
  IcaSetFunction("IopLogAnd",          (FUNC)IopLogAnd);
  IcaSetFunction("IopLogOr",           (FUNC)IopLogOr);
  IcaSetFunction("IopLT",              (FUNC)IopLT);
  IcaSetFunction("IopGT",              (FUNC)IopGT);
  IcaSetFunction("IopSetSkip",         (FUNC)IopSetSkip);
  IcaSetFunction("IopSelect",          (FUNC)IopSelect);
  IcaSetFunction("IopSelectAssoc",     (FUNC)IopSelectAssoc);
  IcaSetFunction("IopPrintProduction", (FUNC)IopPrintProduction);
  IcaSetFunction("IopPrintFormat",     (FUNC)IopPrintFormat);
  IcaSetFunction("IopPrint",           (FUNC)IopPrint);
  IcaSetFunction("IopDebugPrint",      (FUNC)IopDebugPrint);
  IcaSetFunction("IopAltStr",          (FUNC)IopAltStr);
  IcaSetFunction("IopPrintForeach",    (FUNC)IopPrintForeach);
  IcaSetFunction("IopOut",             (FUNC)IopOut);
  IcaSetFunction("IopIn",              (FUNC)IopIn);
  IcaSetFunction("IopGetc",            (FUNC)IopGetc);
  IcaSetFunction("IopRestrictLength",  (FUNC)IopRestrictLength);
  IcaSetFunction("IopMove",            (FUNC)IopMove);
  IcaSetFunction("IopWrt",             (FUNC)IopWrt);
  IcaSetFunction("IopUniq",            (FUNC)IopUniq);
  IcaSetFunction("IopApp",             (FUNC)IopApp);
  IcaSetFunction("IopRep",             (FUNC)IopRep);
  IcaSetFunction("IopNot",             (FUNC)IopNot);
  IcaSetFunction("IopProbe",           (FUNC)IopProbe);
  IcaSetFunction("IopProd",            (FUNC)IopProd);
  IcaSetFunction("IopNoskip",          (FUNC)IopNoskip);
  IcaSetFunction("IopRequest",         (FUNC)IopRequest);
  IcaSetFunction("IopJobTokens",       (FUNC)IopJobTokens);
  IcaSetFunction("IopJobHasInput",     (FUNC)IopJobHasInput);
  IcaSetFunction("IopFileOpen",        (FUNC)IopFileOpen);
  IcaSetFunction("IopFileClose",       (FUNC)IopFileClose);
  IcaSetFunction("IopFileName",        (FUNC)IopFileName);
  IcaSetFunction("IopCurrToken",       (FUNC)IopCurrToken);
  IcaSetFunction("IopInTokenCode",     (FUNC)IopInTokenCode);
  IcaSetFunction("IopInToken",         (FUNC)IopInToken);
  IcaSetFunction("IopFail",            (FUNC)IopFail);
  IcaSetFunction("IopFip",             (FUNC)IopFip);
  IcaSetFunction("IopFile",            (FUNC)IopFile);
  IcaSetFunction("IopKey",             (FUNC)IopKey);
  IcaSetFunction("IopIsFirst",         (FUNC)IopIsFirst);
  IcaSetFunction("IopIsLast",          (FUNC)IopIsLast);
  IcaSetFunction("IopListLen",         (FUNC)IopListLen);
  IcaSetFunction("IopPush",            (FUNC)IopPush);
  IcaSetFunction("IopPop",             (FUNC)IopPop);
  IcaSetFunction("IopSubMatch",        (FUNC)IopSubMatch);
  IcaSetFunction("IopSetFunctions",    (FUNC)IopSetFunctions);
  IcaSetFunction("IopCDefine",         (FUNC)IopCDefine);
  IcaSetFunction("IopHtmlSpace",       (FUNC)IopHtmlSpace);
  IcaSetFunction("IopStrlen",          (FUNC)IopStrlen);
  IcaSetFunction("IopStrLen",          (FUNC)IopStrLen);
  IcaSetFunction("IopStrPad",          (FUNC)IopStrPad);
  IcaSetFunction("IopStrTrans",        (FUNC)IopStrTrans);
  IcaSetFunction("IopStrLower",        (FUNC)IopStrLower);
  IcaSetFunction("IopStrUpper",        (FUNC)IopStrUpper);
  IcaSetFunction("IopStrReplace",      (FUNC)IopStrReplace);
  IcaSetFunction("IopStrTrim",         (FUNC)IopStrTrim);
  IcaSetFunction("IopStrApp",          (FUNC)IopStrApp);
  IcaSetFunction("IopJobNew",          (FUNC)IopJobNew);
  IcaSetFunction("IopJobNext",         (FUNC)IopJobNext);
  IcaSetFunction("IopJobEnd",          (FUNC)IopJobEnd);
  IcaSetFunction("IopParStr",          (FUNC)IopParStr);
  IcaSetFunction("IopParInt",          (FUNC)IopParInt);
  IcaSetFunction("IopParDel",          (FUNC)IopParDel);
  IcaSetFunction("IopEnv",             (FUNC)IopEnv);
  IcaSetFunction("IopEval",             (FUNC)IopEval);
  IcaSetFunction("IopSetDebug",        (FUNC)IopSetDebug);
  IcaSetFunction("IopBreak",           (FUNC)IopBreak);
  IcaSetFunction("IopContinue",        (FUNC)IopContinue);
  IcaSetFunction("IopNext",            (FUNC)IopNext);
  IcaSetFunction("IopTestMode",        (FUNC)IopTestMode);
  IcaSetFunction("QuerySetFunctions",  (FUNC)QuerySetFunctions);
  IcaSetFunction("GCGWordsearch",      (FUNC)GCGWordsearch);
  IcaSetFunction("SeqIopGet2Bit",      (FUNC)SeqIopGet2Bit);
  IcaSetFunction("SeqIopNew",          (FUNC)SeqIopNew);
  IcaSetFunction("SeqIopLen",          (FUNC)SeqIopLen);
  IcaSetFunction("SeqIopApp",          (FUNC)SeqIopApp);
  IcaSetFunction("SeqIopPrint",        (FUNC)SeqIopPrint);
  IcaSetFunction("SeqIopMake",         (FUNC)SeqIopMake);
  IcaSetFunction("SeqIopTrunc",        (FUNC)SeqIopTrunc);
  IcaSetFunction("SdbFunctions",       (FUNC)SdbFunctions);
  IcaSetFunction("EntryIopSetFieldFormat", (FUNC)EntryIopSetFieldFormat);
  return(TRUE);
}
IopGet2Bit);
  IcaSetFunction("SeqIopNew",          (FUNC)SeqIopNew);
  IcaSetFunction("SeqIopLen",          (FUNC)SeqIopLen);
  IcaSetFunction("SeqIopApp",          (FUNC)SeqIopApp);
  IcaSetFunction("SeqIopPrint",        (FUNC)SeqIopPrint);
  IcaSetFunction("SeqIopMake",         (FUNC)SeqIopMake);
  IcaSetFunction("SeqIopTrunc",        (FUNC)SeqIopTrunc);
  srs/src/icarus.c
char icarus_ID[] = "$Id: icarus.c,v 1.29 1997/03/12 16:17:37 srs Exp $"; 
/*               
**  
**    $RCSfile: icarus.c,v $ 
**    $Revision: 1.29 $
**    $Date: 1997/03/12 16:17:37 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  Copyright by Thure Etzold
**
**             Author: Anatoly Ulyanov
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387451
**                     Email: ulyanov@embl-heidelberg.de
**
**
**
**
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**
**    Description
**    =========== 
**  
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*/  

#include <string.h>
#include <stdlib.h>
#include <stdio.h>

#include "message.h"
#include "regexp.h"
#include "futil.h"
#include "lst.h"
#include "sm.h"
#include "library.h"
#include "strv.h"
#include "variable.h"
#include "toklist.h"
#include "cursor.h"
#include "icatask.h"
#include "icarus.h"
#include "icabnf.h"

#define _SRS
#include SRSINCLUDE

INT4       NameListId = 0;
ICAoJOB    *Job;
VARoSCOPE  *globalScope;
ICAoSYNTAX *newSyntax;

INT4    IcaFunGetFip();
static void IcaJobActivate (ICAoJOB *job);

void LocalSetFunctions ();

static void NameDump(FILE *f, void *o)
{
  ICAoNAMELIST *t = (ICAoNAMELIST *)o;
  printf("Namelist: %s\n", t->name);
}
static void NameKill(void *o){}



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  defines a list of input cursors which are needed for multiple 
**  stream input
*/

typedef struct ICAoCursor {
  CURSORo *cursorCurr;
  CURSORo *cursor[5];
  STRv    name[5];
  Int4    cursorN;
} ICAoCursor;
  

static CURSORo *IcaCursorGet (ICAoCursor *c, STRv name)
{
  Int4 k;
  
  if (!c)
    return NULL;
  
  for (k=0; k < c->cursorN; k++)
    if (!name || !c->name[k] || StrEqual (name, c->name[k]))
      return c->cursor[k];
  return NULL;
}

static Int4 IcaCursorIsInput (ICAoCursor *c, CURSORo *cursor)
{
  Int4 k;
  
  if (!c)
    return 0;
  
  for (k=0; k < c->cursorN; k++)
    if (c->cursor[k] == cursor)
      return 1;
  return 0;
}


CURSORo *IcaCursorSet (ICAoCursor **c, CURSORo *cursor, STRv name)
{
  Int4 k;
  
  if (!*c) 
    if ((*c = (ICAoCursor *) calloc (sizeof(ICAoCursor), 1)) == NULL)
      _ErrExit2 (e__allocfail, "icarus cursor list");

  for (k=0; k < (*c)->cursorN; k++)
    if (!name || !(*c)->name || StrEqual (name, (*c)->name[k])) {
      (*c)->cursorN--;
      break;
    }

   (*c)->cursorN++;

  (*c)->cursor[k] = cursor;
  (*c)->name[k] = name ? StrCpy (name) : NULL;
  (*c)->cursorCurr = cursor;
  return cursor;
}

static CURSORo *IcaCursorGetCurr (ICAoCursor *c)
{
  return c->cursorCurr;
} 

static void IcaCursorDelete (ICAoCursor **c)
{
  Int4 k;

  if (!*c)
    return;

  for (k=0; k < (*c)->cursorN; k++) {
    CursorDelete (&(*c)->cursor[k]);
    if ((*c)->name[k])
      StrDel ((*c)->name[k]);
  }
  free (*c);
  *c=NULL;
  return;
}


void IcaSetLogicStream (ICAoJOB *job, char *name)
{
  STRv s=StrTemp (name);

  if (!IcaCursorGet (job->inCursor, s)) 
    IcaCursorSet (&job->inCursor, CursorNew (), s);
}



/**API* IcaCreateJob *********************************************************
**
**	This function creates and initializes a new job object which is 
**      needed for iterating through, eg, a flat file databank. A job object
**      is generally needed when the parser should step through a file and
**      halt at some position, eg, the entry end. 
**      <P>
**      To associate the 'job' to the input (file or string) use IcaNewJob.
**
**      INPUT:          the syntax object [W]
**		IMPLICIT:
**			Job (ICAoJOB *)
**
**      RETURNS:        address of new job object
*/

ICAoJOB *IcaCreateJob(ICAoSYNTAX *syntax)
{
  ICAoJOB  *job;
  
  if ((job = (ICAoJOB *) calloc (sizeof(ICAoJOB), 1)) == NULL)
    _ErrExit2 (e__allocfail, "job object");
  
  if (!NameListId)
    LstManageClass(&NameListId, sizeof(ICAoNAMELIST), NULL, NameKill,NameDump);

  job->syntax = syntax;
  job->parseError = 0;
  job->syntax->taskList = NULL;

  /* define icarus commands */
  LocalSetFunctions (); 
  BnfSetOpFunctions (); 
  IcaOpLibrary();

  /* initialize syntax */
  if (!syntax->prod) {
    job->time = BNFxBUILDTIME;
    BnfBuild (syntax);
    job->scope = (VARoSCOPE *) VarCopyScope (syntax->scope);
    IcaContext ("push", &job);
    BnfInitRules (syntax, 0); /* run "init" programs */
    IcaContext ("pop", NULL);
    job->time = 0;
  }
  else 
    job->scope = (VARoSCOPE *) VarCopyScope (syntax->scope);

  return job;
}

/**API* IcaJobDestroy *********************************************************
**
**      Deletes a job object.
**
**      INPUT:          address of the pointer to the job object [W]
**
*/

void IcaJobDestroy (ICAoJOB **job)
{
  ICAoJOB *tmp;

  if (job && *job) {
    tmp = *job;
    if (tmp->inCursor)
      IcaCursorDelete (&tmp->inCursor);
    if (tmp->tokList)
      TokDeleteAllLists (tmp->tokList);
    if (tmp->scope)
      VarScopeDestroy (&tmp->scope);
    free (tmp);
    *job = NULL;
  }
}


/**API* IcaDoJob *************************************************************
**
**      Activates the parser with the specified start production. Function
**      requires a job object created with JobCreateJob which is already
**      associated with the input (file, string) using IcaJobSetFile or
**      IcaJobSetString.
**
**      INPUT:          the job object [W]
**                      the name of the start production (start symbol) [R]
**		IMPLICIT:
**			Job (ICAoJOB *)
**
**      RETURNS:        TRUE if parsing was successful
**                      FALSE otherwise
*/

INT4 IcaDoJob (ICAoJOB *job, char *startName)
{
  BNFoPRODUCTION *start;
  Int4 rv;

  if (!(start = BnfGetProduction (job->syntax, startName, 0)))
    _ErrRet3 (e__objectunknown, "start production", startName);

  IcaContext ("push", &job);
  rv = BnfParseProduction (start); 
  IcaContext ("pop", NULL);
  return rv;
}


void IcaExecProg (ICAoJOB *job)
{
  if (job->prog) {
    IcaContext ("push", &job);
    VarExec (job->prog); 
    IcaContext ("pop", NULL);
  }
}

void IcaContext (char *option, ICAoJOB **job)
{
  static INT4 count=-1;
  static struct {
    ICAoJOB   *job;
    CURSORo   *cursor;
    VARoSCOPE *globalScope;
  } context[100];

  switch (option[1]) {
  case 'u': /* push */

    if (count >= 100 - 1)
      _ErrExit3 (f__limitexceeded, "Parsing contexts", 100);
    count++;
    context[count].job = Job;
    context[count].globalScope = globalScope;
    Job = *job;
    if (Job->scope)
      globalScope = Job->scope;
    break;
  case 'o': /* pop */
    if (count) {
      Job = context[count].job;
      globalScope = context[count].globalScope;
      count--;
      if (job)
	*job = Job;
    }
    break;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
}


static void IcaJobActivate (ICAoJOB *job)
{
  job->parseError = 0;
  job->doAdvance = 1;
  job->isActive = 1;
  job->cursor = IcaCursorGetCurr (job->inCursor);
}

/**API* IcaNewJob ************************************************************
**
**	Takes a job object created by IcaCreateJob and associates it 
**      with the input to be parsed. The input can
**      be either a file or a string. The parsing itself can be initiated
**      by IcaDoJob (forced parsing) or by IcaGetTokenList (lazy parsing).
**      Both functions may parse through only part of the input. To continue
**      call first IcaEndJob and then IcaNewJob again.
**      <P>
**      The parsing can process can be influenzed for both lazy and forced
**      parsing by activating a 'task' with IcaSetTask.
**
**      INPUT:       o  job object [W]
**		     o  file object (file must be opened for read access) 
**                      [R] or NULL
**		     o  string to be parsed [R] or NULL
**		IMPLICIT:
**			Job (ICAoJOB *)
**
**      RETURNS:        TRUE - new job prepared
**		        FALSE - if the input (file) is exhausted
*/

INT4 IcaNewJob(ICAoJOB *job, FILEo *file, char *string)
{
  CURSORo *cursor;

  job->file   = file;
  TokGetList(INTOKLIST, &job->tokList);

  if (!TokIsListActive (job->tokList) || file || string) {
    if (TokIsListActive (job->tokList))
      TokResetList (job->tokList);

    if (string && strlen(string) ) {
      TokSetStyle (job->tokList, "copy");
      TokAdd (job->tokList, string, strlen (string), ICAxUNDEFCODE);
    }
    else if (file) {
      if (FileIsEof (file))
	return(FALSE);
      TokSetFile(job->tokList, file);
    }
    else
      return(FALSE);
    
    cursor = IcaCursorSet (&job->inCursor, CursorNew (), NULL);
    CursorInstall (cursor, TokGetFirst (job->tokList), job->tokList);
  }
  IcaJobActivate (job);
  return(TRUE);
} 


/**API* IcaJobNext ************************************************************
**
**	Takes a job object created by IcaCreateJob.
**
**      INPUT:          job object 
**		IMPLICIT:
**			Job (ICAoJOB *)
**
**      RETURNS:        TRUE - new job prepared
**		        FALSE - if the input (file) is exhausted
*/

void IcaJobNext(ICAoJOB *job)
{
  CURSORo  *cursor;
  TOKoLIST *tokList;
  Int4     k;

  if (IcaIsActive (job))
    IcaEndJob (job);

  job->tokList = tokList = TokGetList (INTOKLIST, &job->tokList);
  if (!TokIsListActive(tokList)) {
    for (k=0; k < job->inCursor->cursorN; k++) {
      cursor = job->inCursor->cursor[k];
      CursorInstall (cursor, TokGetFirst (tokList), tokList);
    }
  }
  IcaJobActivate (job);
} 


/**API* IcaJobSetString *******************************************************
**
**	Sets a new input string with which to continue next job.
**
**      INPUT:          job object [W]
**                      string [R]
*/

void IcaJobSetString (ICAoJOB *job, char *str)
{
  CURSORo   *cursor;
  TOKoLIST *tokList;

  tokList = TokGetList (INTOKLIST, &job->tokList);
  if (TokIsListActive (tokList)) 
    TokResetList (tokList);

  TokSetStyle (tokList, "copy");
  TokAdd (tokList, str, strlen (str), ICAxUNDEFCODE);
  cursor = IcaCursorSet (&job->inCursor, CursorNew (), NULL);
  CursorInstall (cursor, TokGetFirst (tokList), tokList);
  IcaJobActivate (job);
}

/**API* IcaJobSetFile ********************************************************
**
**	Sets a new input file with which to continue next job.
**
**      INPUT:          job object [W]
**                      string [R]
*/

void IcaJobSetFile (ICAoJOB *job, FILEo *file)
{
  CURSORo   *cursor;
  TOKoLIST *tokList;

  tokList = TokGetList (INTOKLIST, &job->tokList);
  if (TokIsListActive (tokList)) 
    TokResetList (tokList);

  job->file = file;
  TokSetFile (tokList, file);
  cursor = IcaCursorSet (&job->inCursor, CursorNew (), NULL);
  CursorInstall (cursor, TokGetFirst (tokList), tokList);
  IcaJobActivate (job);
}


/**api* IcaIsActive ***********************************************************
**
**	Returns TRUE if the job object is active ie initiated by IcaNewJob,
**      IcaNextJob. The job can be terminated by IcaEndJob. 
**      See also IcaNextJob.
**
**      INPUT:          job object [W]
**
**      RETURNS:        1: active
**                      0: not active
*/

Int4 IcaIsActive (ICAoJOB *job)
{
  return job->isActive;
}


/**api* IcaIsActive ***********************************************************
**
**      Returns TRUE if the input for the next job is exhausted. Applicable
***     for both input from a file or from a string.
**
**      INPUT:          job object [R]
**
**      RETURNS:        1: no more input
**                      0: input still left
*/

Int4 IcaIsJobEnd (ICAoJOB *job)
{
  if (!job->file && job->inputStreamer)
    return 0;
  else 
    return job->file ? FileIsEof (job->file) : 
    CursorIsEnd (IcaCursorGetCurr (job->inCursor));
}

Int4 IcaIsInputEnd (ICAoJOB *job)
{
  return job->isInputEnd;
}

Int4 IcaSetInputEnd (ICAoJOB *job)
{
  job->isInputEnd = 1;
}


/**API* IcaEndJob *************************************************************
**
**	Resets a job object and prepares it for the next call to IcaNewJob.
**      It does NOT delete the job object.
**      Use of this function should be replaced by the combination of
**      IcaJobNext and IcaJobSetString.
**
**      INPUT:          job object [W]
**		IMPLICIT:
**			Job (ICAoJOB *)
**
*/

void IcaEndJob(ICAoJOB *job)
{
  TOKoLIST *tokList = job->tokList;

  if (job->isActive) {
    if (tokList) {
      LstFirst((void **) &tokList);
      do {
	if (!SmEqs (tokList->name, INTOKLIST))
	  TokResetList(tokList);
      }while(LstNext((void **) &tokList));
    }
    
    TaskDisableAll(Job->syntax->taskList);  
    job->isActive = 0;
    job->isInputEnd = 0;
  }
}

/**API* IcaGetInputString *****************************************************
**
**	Returns the input string of the specified job. This is used when
**      the parsing job modifies the string which must be reallocated to
**      (most probably) a new address if the string grows in size.
**      Must be called before IcaEndJob.
**
**      INPUT:          job object [W]
**
**      RETURNS:        the input string 
**                  
*/

char *IcaGetInputString (ICAoJOB *job)
{
  /* pointer is not enough since token is not 0 terminated - would be
     nice to return a STRv */
  return TokGetStringCopy (job->tokList, TokGetFirst (job->tokList));
}


void IcaPrintMessage (MSGo *msg) 
{ 
  char *fileName, fileLoc[200]="";
  INT4 lnN;

  switch(msg->msg_code) {
  case e__duplicatekey:
  case e__icaUnknownClass:
  case e__parsererror3: /* report position in current input file */
  case e__parsererror2: /* report position in current input file */
    if ((fileName = IcaGetCurrFileName ("input"))) {
      lnN = IcaGetCurrLineN ("input");
      sprintf (fileLoc, "%s:%d: ", fileName, lnN);
    }
    break; 
  default: /* report position in program */
    if (!MsgIs (msg, "info")) {
      if ((fileName = IcaGetCurrFileName ("prog"))) {
	lnN = IcaGetCurrLineN ("prog");
	sprintf (fileLoc, "%s:%d: ", fileName, lnN);
      }
    }
    break;
  }

  if (msg->msg_t == MSGxINFO)
    fprintf (stderr, "%s\n", msg->secmsg);
  else {
    IcaJobSetErrorFlag (Job, 1);
    if (*fileLoc) 
      fprintf (stderr, fileLoc);
    if (msg->secmsg && *msg->secmsg)
      fprintf (stderr, "error: %s, %s\n", msg->primsg, msg->secmsg);
    else 
      fprintf (stderr, "error: %s\n", msg->primsg);
  }
}

/**api* IcaJobSharesScope *****************************************************
**
**      Lets a job share its variable scope with another job.
**      The sharing works only if the other job does not have a scope
**      already.
**
**      INPUT:	        job with the scope to be shared [W]
**                      job with which to share the scope [W]
**
**      RETURNS:        1: if the two jobs can share
**			0: if the second job has a scope already
*/

Int4 IcaJobSharesScope (ICAoJOB *job1, ICAoJOB *job2)
{
  return 0;
  if (job2->scope)
    return 0;
  else 
    /*    job2->scope = job1->scope;*/
  return 1;
}


/**API* IcaGetTokenList *******************************************************
**
**      Retrieves a token list from the current job. If the token table
**      does not yet exist it will result in the initiation of the parsing
**      process. This behaviour is called "lazy parsing". The function
**      requires an active 'job' which is provided by IcaNewJob.
**
**      INPUT:	        the job object [W]
**                      name of the desired output token list [W]
**
**      RETURNS:        address of the token list 
**			NULL: parsing failed to produce the token list
*/

TOKoLIST *IcaGetTokenList (ICAoJOB *job, char *name)
{
  TOKoLIST       *tokList, *tokListRead;
  BNFoPRODUCTION *production;                                 
  INT4            rv;
 
  IcaJobSharesScope (Job, job);
  IcaContext("push", &job); 
  tokList = TokGetList(name, &job->tokList);

  /* if tokList is empty, activate producer production */
  if( !TokIsListActive(tokList) ) {
    production = IcaGetSupplyNode(name);

    /* "parent" tokList found, it is possible to read it and to parse  */
    if(production->rdTokList) {
      tokListRead = IcaGetTokenList (job, production->rdTokList->name);
      if(TokIsListActive (tokListRead)) {
        job->cursor = CursorNew();
        rv = BnfParseProdLoop (production);
      }
    }
    else { /* chose job input token list  */
      tokListRead = TokFindList(INTOKLIST, &job->tokList);
      job->cursor = IcaCursorGetCurr (job->inCursor);
      rv = BnfParseProduction(production);
    }
    if (!IcaCursorIsInput (job->inCursor, job->cursor)) {
      CursorDelete (&job->cursor);
      job->cursor = NULL;
    }
  }

  IcaContext("pop", NULL); 
  tokList->isActive=1; /* te!!!*/
  return(tokList);                                          
}                                                           


/**API* IcaSetInputStreamer ***************************************************
**
**      Sets a function to be called by the $In command.
**
**      INPUT:       o  job object [W}
**                   o  function that returns a file object and takes the
**                      symbolic stream name (see LibGetFileType), and
**                      the streamer data (see IcaSetInputStreamerData).
*/

void IcaSetInputStreamer (ICAoJOB *job, FILEo *(*func)(char*, void*))
{
  job->inputStreamer = func;
}

/**API* IcaSetInputStreamerData ***********************************************
**
**      Sets optionally 
**      the data for the input streamer defined by IcaSetInputStreamer.
**
**      INPUT:         job object [W}
**                     pointer to the data object [R]
*/

void IcaSetInputStreamerData (ICAoJOB *job, void* data)
{
  job->inputStreamerData = data;
}

/**API* IcaSetInputFile *******************************************************
**
**      Sets an input file for a job activated with IcaJobNext.
**
**      INPUT:         job object [W}
**                     file object [R] or NULL (end of file input)
**                     logical name of the file [R] or NULL
*/

void IcaSetInputFile (ICAoJOB *job, FILEo *file, STRv name)
{
  TokSetFile (job->tokList, file);
  job->cursor = IcaCursorGet (job->inCursor, name);
  if (file && !file->lnN) /* if file just opened */
    CursorSetFile (job->cursor, file);
  job->file = file;
}
                                                            
/**API* IcaSetTask ************************************************************
**
**      Enable or disable a 'task' for the current 'job' set by 
**      IcaNewJob. This function must be called BEFORE initiating the
**      parsing process.
**
**      INPUT:          the job object [W]
**                      task name [R]
**                      flag: TRUE activates, FALSE deactivates 
**		IMPLICIT:
**
**      RETURNS:
*/

void IcaSetTask (ICAoJOB *job, char *taskName, INT4 flag)
{
  if (flag)
    TaskEnable (job->syntax->taskList, taskName);
  else
    TaskDisable (job->syntax->taskList, taskName);
}



static struct ICAoNAMELIST *funcList=NULL; /* list of function pointers */


/**API* IcaSetFunction *******************************************************
**
**      Put the function pointer in the special named list
**
**      INPUT:          name of a function
**                      pointer to the function
**		IMPLICIT:
**                      list reference Job->funcList  
**
**      RETURNS:
*/
 

void IcaSetFunction(char *functionName, FUNC function)

{

  if( !LstHashSearch((void **) &funcList, functionName) ) {
    LstNew((void **) &funcList, NameListId);
    strcpy(funcList->name, functionName);
    funcList->pointer = (void *)function;
  }
}
 
/**API* IcaGetFunction *******************************************************
**
**      Get the pointer to function by it name in the list of 
**      function pointers.
**
**      INPUT:          name of a function
**		IMPLICIT:
**                      list reference Job->funcList  
**
**      RETURNS:
**                      pointer to the function
*/
 
FUNC IcaGetFunction(char *functionName)

{
  if (LstFirstNamed ((void **) &funcList, functionName))
    return (FUNC)funcList->pointer;
  else
    return NULL;
}

/**API* IcaFunctionName ******************************************************
**
**      Find function name by it pointer in the function list.
**
**      INPUT:          function pointer
**		IMPLICIT:
**                      list reference Job->funcList  
**
**      RETURNS:
**                      function name
*/
 
char *IcaFunctionName (Func function)

{
  if( LstFirst((void **) &funcList) )
    do {
      if(function == (Func) funcList->pointer)
        return(funcList->name);
    }while( LstNext((void **) &funcList) );
  return(NULL);
}

/**API* IcaGetSupplyNode *****************************************************
**
**      Find a node that can supply input token list for given toklist
**
**      INPUT:          token list name
**		IMPLICIT:
**                      list of production names: Job->prodList  
**
**      RETURNS:
**                      node pointer
**                      exit otherwise
*/

BNFoPRODUCTION *IcaGetSupplyNode(char *tokListName)

{
  VARo           *var;
  TOKoLIST       *tokList;
  BNFoPRODUCTION *prod;
  Int4           i;
  
  if (Job->syntax->prod) {
    for (i=0; (var = AnyNextInList (Job->syntax->prod, &i)); ) {
      prod = VarGetObject (NULL, var);
      if( (tokList = prod->wrtTokList) != NULL)
	if( !strcmp(tokListName, tokList->name) )
	  return(prod);
    }
  }
  _ErrExit3 (e__objectunknown, "Output token list", tokListName);
}
 
/**API* IcaErrPrint **********************************************************
**
**      Pretty-print function to print parsing error
**
**      INPUT:          production name
**			fail pattern
**			beginning of input token
**			point where pattern fail
**		IMPLICIT:
**
**      RETURNS:
*/
 
void IcaErrPrint(char *nodeName, char *pattern, char *begin, char *point) 

{ 
  static char line[MAXPRINTSIZE+1],
              dots[MAXPRINTSIZE+1];
  static STRv pat=NULL;
  char *ptr;           
  INT4  len, isEOL;
                       
  if (pattern) {
    if (!pat)
      pat=StrNew ();
    StrSetS (&pat, pattern);
    StrEncode (&pat);
  }
  memset(line, 0, MAXPRINTSIZE);
  memset(dots, 0, MAXPRINTSIZE);
  isEOL = FALSE;
  ptr = point;
  len = 0;

  if(*ptr == '\n') {
    ptr--;
    len++;
    isEOL = TRUE;
  }
  
  while(ptr > begin && len < MAXPRINTSIZE/2 && *ptr != '\n') {
    len++;                                                    
    ptr--;                                                    
  }                                                           
  if(*ptr == '\n' && len) {                                   
    ptr++;                                                    
    len--;                                                    
  }                                                           
  if(len) {                                                   
    strncpy(line, ptr, len);                                  
    memset(dots, '.', len+1);
    if(isEOL) 
      line[len] = ' ';
  }                                                           
  strcat(dots, "^");                                          
  ptr = point;                                                
  len = 1;                                                    
  while(ptr<point+strlen(point) && len < MAXPRINTSIZE/2 && *ptr != '\n') {
    len++;                                                    
    ptr++;                                                    
  }                                                           
  if(*ptr == '\n' && len)                                     
    len--;                                                    
  if(len)                                                     
    strncat(line, point, len);                                
  
  if (!pattern && !strlen (line) )
    _ErrMsg2(e__parsererror2, nodeName);
  else if (pattern && !strcmp(pattern, ENDOFINPUT) ) {
    _ErrMsg3 (e__parsererror1, line, dots);
    return;
  }
  else 
    _ErrMsg5(e__parsererror3, nodeName, line, dots, 
	     pat ? _Str (pat) : "unknown" );  
  
  return;                                                     
}                                                             
/**API* IcaGetCurrFileName ****************************************************
**
**      Returns the name of the file that is currently being parsed.
**
**      INPUT:      option "input" or "prog" [R]
**		IMPLICIT:
**                  Job (ICAoJOB *job) [R]
**
**      RETURNS: a file name
**               NULL: no job file defined
*/

char *IcaGetCurrFileName (char *option)
{
  char *name=NULL;

  switch (option[0]) {
  case 'i': /* input */
    name = Job->file ? FileGetName (Job->file, "file") : NULL;
    break;
  case 'p':
    if (Job->fileName)
      name = Job->fileName;
    else if (Job->syntax)
      name = Job->syntax->fileName;
    break;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
  return name;
}



/**api* function **************************************************************
**
**      Returns the name of the file that is currently being parsed.
**
**      INPUT:      option "input" or "prog" [R]
**		IMPLICIT:
**                  Job (ICAoJOB *job) [R]
**
**      RETURNS: a file name
*/

INT4 IcaGetCurrLineN (char *option)
{
  switch (option[0]) {
  case 'i': /* input */
    return Job->file ? FileGetLineN (Job->file) : 0;
  case 'p':
    return Job->lineN;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
}

/**api* function **************************************************************
**
**      Evaluates an string with a list of icarus statements.
**
**      INPUT:      the address of job object [W] or NULL.
**                  string with one or more Icarus statements [R]
**
**      RETURNS:    1
*/

INT4 IcaEval (ICAoJOB **jobPtr, char *prog)
{
  static ICAoJOB *jobStatic=NULL; 
  ICAoJOB **job;
  ICAoSYNTAX *syntax;

  job = jobPtr ? jobPtr : &jobStatic;
  if (!*job) {
    syntax  = (ICAoSYNTAX*)LibObjByName ("syntax", "icarus");
    *job = IcaCreateJob (syntax);
  }
  else
    IcaJobNext (*job);

  IcaJobSetString (*job, prog);
  IcaGetTokenList (*job, "prog");
  IcaExecProg (*job); 
}

/**api* function **************************************************************
**
**      Like IcaEval but takes the specified job with all its variables as
**      environment.
**
**      INPUT:      string with one or more Icarus statements [R]
**                  job object to be used as environment [W]
**
**      RETURNS:    1
*/

INT4 IcaEvalInJob (char *prog, ICAoJOB *job)
{
  static ICAoJOB *iJob=NULL, tmpJob; 
  ICAoSYNTAX *syntax;

  if (!iJob) {
    syntax  = (ICAoSYNTAX*)LibObjByName ("syntax", "icarus");
    iJob = IcaCreateJob (syntax);
    iJob->scope = job->scope;
  }
  else
    IcaJobNext (iJob);
  IcaJobSetString (iJob, prog);
  IcaGetTokenList (iJob, "prog");
  memcpy (&tmpJob, job, sizeof (ICAoJOB));
  tmpJob.prog = iJob->prog;
  IcaExecProg (&tmpJob); 
}

FILEo *IcaJobGetFile (ICAoJOB *job)
{
  return job->file;
}


IcaJobSetErrorFlag (ICAoJOB *job, int flag)
{
  job->isError=flag;
}

IcaJobIsError (ICAoJOB *job)
{
  return job->isError;
}
  syntax  = (ICAoSYNTAX*)LibObjByName ("syntax", "icarus");
    iJob = IcaCreateJob (syntax);
    iJob->scope = job->scope;
  }
  else
    IcaJobNext (iJob);
  IcaJobSetString (iJob, prog);
  IcaGetTokenList (iJob, "prog");
  memcpy (&tmpJob, job, sizeof (ICAoJOB));
  tmpJob.prog = iJob->prog;
  IcaExecProg (&tmpJob); 
}

FILEo *IcaJosrs/src/icarus.h
**               
**    $RCSfile: icarus.h,v $
**    $Revision: 1.14 $
**    $Date: 1997/03/19 11:17:27 $
**    $Author: srs $ 
**    
**    $Locker:  $
**    $State: Exp $
**    
**    
**                  Copyright by Thure Etzold
**                  
**             Author: Anatoly Ulyanov
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387451
**                     Email: ulyanov@embl-heidelberg.de
**                     
*/                     


#define ICAxMAXNAMESIZE 32

#define MAXKEYWORDS         8
#define MAXARGSNUM         32 
#define MAXNAMESIZE        32
#define MAXPRINTSIZE       72     
#define MAXBRANCHES       128
#define MAXLINESIZE       512
 
#define NODE		"NODE"
#define COPYSTYLE	"copy"
#define ECHOSTYLE	"echo"
#define ENDOFINPUT      "\001\003\005\007\009\013"
#define TMPIN		"@TmpStackIn"
#define TMPOUT		"@TmpStackOut"
#define INTOKLIST	"@DefStackIn"
#define OUTTOKLIST	"@DefStackOut"

#define VARTOKLISTIN	"tli"
#define VARTOKLISTOUT	"tlo"
#define VARCODEIN	"ci"
#define VARCODEOUT	"co"
#define VARCURRTOKEN	"ct"

#define ICAxUNDEFCODE    -1
#define ICAxNEWPARSEERROR 1
#define ICAxPARSEERROR    2

/* rename or delete */
#define PROGxBUILDTIME       1
#define PROGxPREPARSE        2
#define PROGxPOSTPARSE       4


typedef struct ICAoJOB {
  char                    *string;	  /* !obsolete! */
  struct FILEo            *file;          /* file to parse */
  struct TOKoLIST         *tokList;       /* list of tokLists */
  struct ICAoSYNTAX       *syntax;        /* ICARUS syntax */ 
  struct TOKoLIST         *outTokList;	  /* current output tokList */
  struct TOKoTOKEN        *inToken;	  /* current input token */
  struct regexp		  *regExp;    	  /* current regExp */
  struct BNFoNODE         *currNode;  	  /* current node */
  struct VARoSCOPE        *scope;         /* the scope containing variables */
  struct CURSORo          *cursor;        /* currently active cursor */
  struct ICAoCursor       *inCursor;      /* state of 1 or more input streams*/
  char                    *failPattern;   /* pattern that fail to parse */ 
  INT4                    parseError;     /* error code */
  INT4			  isNew;          /* flag */
  INT4			  isOptional;	  /* flag */
  INT4			  time;	          /* time of Icarus statement execution */
  INT4			  isTrace;	  /* flag */
  INT4			  isTraceTree;	  /* flag */
  INT4                    isDebug;
  INT4                    isActive;
  INT4                    isInputEnd;    
  Int4                    isError;
  INT4                    doAdvance;    
  INT4                    lineN;         /* curr line no of curr program */
  char                    *fileName;      /* name of current program file */
  struct VARo             *prog;        /* Icarus program compiled by "job" */
  struct FILEo            *(*inputStreamer)(char*,void*);
  void                    *inputStreamerData;
} ICAoJOB;

typedef struct ICAoSYNTAX {
  char                    *name;          /* Name of the syntax. */
  char                    *fileName;      /* Name of the file with ICA rules */ 
  char                    *rules;	  /* Pointer to rules */
  struct SMoBUFF          *buff;          /* Buffer with ICA productions */
  struct ICAoSYNTAX       *commandSyntax; /* The syntax of for the commands. */
  struct ICAoNAMELIST     *prodList;
  struct ICAoCOMMAND      *userCommand;
  struct TASKo            *taskList; 	  /* pool of task links */
  char                    *ign;           /* Chars to be ignored  */
  char                    *cmnt;          /* reg exp for comments */
  INT4                    initflag;
  struct VARo             *prod;        /* list of productions as var objects*/
  struct VARoSCOPE        *scope;
  struct regexp           *cmntRe;      
  char                    *ignAlt;       /* alternative set of skip chars */
} ICAoSYNTAX;
#define _ICAoSYNTAX

typedef struct ICAoNAMELIST {
  char                   *list;
  int                     listId;
  char                    name[ICAxMAXNAMESIZE];
  void                   *pointer;
  INT4			  isInit;
} ICAoNAMELIST;

/* module prototypes ***************************************/
typedef struct FILEo  *dummytointroducestructtagFILEo;

typedef struct ICAoJOB *ICAvJOB;

struct BNFoPRODUCTION *IcaGetSupplyNode(char *tokListName);

FUNC  IcaGetFunction(char *);
char *IcaFunctionName(FUNC);
char *IcaGetCodeName(INT4);
void  IcaErrPrint(char *nodeName, char *pattern, char *begin, char *point);
void  IcaSetFunction(char *, FUNC);
char *IcaGetCurrFileName ();
INT4 IcaInterprete (char *prog);
void IcaPrintMessage (MSGo *msg);

    /* working with parsing jobs */

void             IcaContext (char *option, ICAoJOB **job);

ICAvJOB          IcaCreateJob (struct ICAoSYNTAX *);
void             IcaEndJob (ICAvJOB);
Int4             IcaNewJob (ICAvJOB, struct FILEo *, char *);
void             IcaJobNext(ICAoJOB *job);
void             IcaJobSetString (ICAoJOB *job, char *str);
void             IcaJobDestroy (ICAoJOB **job);
struct FILEo*    IcaJobGetFile (ICAoJOB *job);

void             IcaSetTask (ICAvJOB, char *taskName, INT4 flag);
void             IcaSetInputStreamer (ICAvJOB, 
				      struct FILEo *(*func)(char*, void*));
void             IcaSetInputStreamerData (ICAvJOB, void* data);
void             IcaSetInputFile (ICAvJOB, struct FILEo *file, 
				  struct STRo *name);

struct TOKoLIST* IcaGetTokenList (ICAvJOB, char *);
char*            IcaGetInputString (ICAvJOB);
Int4             IcaIsActive (ICAvJOB);

INT4 IcaEvalInJob (char *prog, ICAvJOB job);
INT4 IcaEval (ICAvJOB *job, char *prog);


vJOB, char *taskName, INT4 flag);
void             IcaSetInputStreamer (ICAvJOB, 
				      struct FILEo *(*func)(char*, void*));
void             IcaSetInputStreamerData (ICAvJOB, void* data);
void             IcaSetInputFile (ICAvJOB, struct FILEo *file, 
				  struct STRo *name);

struct TOKoLIST* IcaGetTokenList (ICAvJOB, char *);
char*            IcaGetInputString (ICAvJOB);
Int4             IcaIsActive (ICAvJOB);

INT4 IcaEvalInJob (char *prog, ICAvJOB josrs/src/icarusi.c

#include <stdio.h>
#include <stdlib.h>
#include <stdarg.h>
#include "srs.h"

ICAoSYNTAX *IcaInitSyntax (ICAoSYNTAX *);

static INT4 PrintMessage (MSGo *msg);

void ReadBuiltin (ICAoSYNTAX *syntax)
{
  FILEo   *file;
  ICAoJOB *job;
  SDLo    *odd;
  Int4    opt;

  /* never write C-conversion */
  opt = ParGetBool("ica2C");
  ParDefBool("ica2C", 0);
  ParDefBool ("doSection", 1); /* pointers instead of numbers */

  job = IcaCreateJob (syntax);

  /* process class information */
  odd = OddInit (oddObjs, 1);
  file = FileNew ("SRSSDL:builtin.ic");
  if (!FileOpen (file))
    _ErrExit2 (e__filnotok, "SRSSDL:builtin.ic");
  IcaJobSetFile (job, file);
  IcaGetTokenList (job, "prog");
  IcaExecProg (job);

  /* process objects */
  odd = OddInit (odd, 2); 
  file = FileNew ("SRSSDL:builtin.i");
  if (!FileOpen (file))
    _ErrExit2 (e__filnotok, "SRSSDL:builtin.i");
  IcaJobSetFile (job, file, NULL);
  IcaGetTokenList (job, "prog");
  FileClose (job->file);
  job->file = NULL;
  IcaExecProg (job);

  ParDefBool ("ica2C", opt);
}


main(int argc, char **argv)
{
  SDLo         *odd;
  ARGoLIST     *arglist;
  FILEo        *file;
  ICAoJOB      *job; 
  ICAoSYNTAX   *syntax;
  char         line[MAXLINESIZE], *tokStr, *name;
  INT4	       printAll, tokCode, c, rv;
  
  SrsEnv ();
  LibOpen ("srs5");
  MsgSetFnct ((FUNC)IcaPrintMessage);
  
  arglist = LibObjByName ("arglist", "try");
  argc = ArgGet (arglist, argc, argv);

  if (!ParGetBool ("useIni"))
    syntax = IcaInitSyntax ((ICAoSYNTAX*)LibObjByName ("syntax", "icarus"));
  else
    syntax  = (ICAoSYNTAX*)LibObjByName ("syntax", "icarus");
  odd = OddInit (def, 1); 

  if (ParGetBool ("doCommandInfo")) {
    IargPrintInfo ();
    exit (0);
  }

  if (argc != 2) {
    ArgUsage (arglist);
    _ErrorExit ();
  }

  job = IcaCreateJob (syntax);


  file = FileNew(argv[1]);
  if (!FileOpen (file))
    _ErrExit2 (e__filnotok, argv[1]);

  IcaJobSetFile (job, file);
  IcaGetTokenList (job, "prog");
  FileClose (job->file);
  job->file = NULL;

  if (IcaJobIsError (job))
    _ErrExit (e__icaErrorsQuit);
  if (job->prog) {
    if (ParGetBool ("readBuiltin"))
      ReadBuiltin (syntax);
    IcaExecProg (job); 
  }  

  if (ParGetBool ("doClassInfo")) {
    odd = OddInit (odd, 2);
    OddWriteClassInfo (odd);
  }
}  



}

  job = IcaCreateJob (syntax);


  file = FileNew(argv[1]);
  if (!FileOpen (file))
    _ErrExit2 (e__filnotok, argv[1]);

  IcaJobSetFile (job, file);
  IcaGetTokenList (job, "psrs/src/icatask.c
char icatask_srs_ID[] = "$Id: icatask.c,v 1.1 1996/05/06 15:16:43 srs Exp $";
/*
**    $RCSfile: icatask.c,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:16:43 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  Copyright by Thure Etzold
**
**             Authors: Thure Etzold
**                      Anatoly Ulyanov
**
**                      EMBL, Meyerhofstrasse 1
**                      W-6900 Heidelberg, Germany
**                      Tel: 06221 387529  
**                      Email: etzold@embl-heidelberg.de
**
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**    Description
**    =========== 
**
** 
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>

#include "message.h"
#include "lst.h"
#include "icatask.h"

#define _SRS
#include SRSINCLUDE





/****** TaskLinkNew ***********************************************************
**
**      Returns a new link object in the list of links.
**  
**    INPUT:      link object list [W]
**            IMPLICIT:
**                  
**    RETURNS:    new link object 
*/ 

static TASKoLINK *TaskLinkNew (TASKoLINKS *links)
{
  if (!links->linkAllocN) {
    if ((links->link = (void *) malloc (sizeof (TASKoLINK))) == NULL)
      _ErrExit2 (e__allocfail, "task link list");
    links->linkN = 0;
    links->linkAllocN = 1;
  }
  else if (links->linkN >= links->linkAllocN) {
    links->linkAllocN *= 2;
    if ((links->link = (void *) realloc
       (links->link, links->linkAllocN * sizeof (TASKoLINK))) == NULL)
      _ErrExit2 (e__allocfail, "task link list");
  }
  return &links->link[links->linkN++];
}

/****** TaskIsRegister ********************************************************
**
**      Checks if the task is not already registered.
**
**	INPUT:	    the name of the task [R]
**                  the syntax with which to register [W]
**	        IMPLICIT:
**
**    RETURNS:    TRUE if task registered
**		  FALSE otherwise
**                  
*/ 
   
INT4 TaskIsRegister (TASKo *task, char *name)
{
  return(LstHashSearch((void **) &task, name));
}

/****** TaskRegister **********************************************************
**
**      Registers a new task for the specified syntax and disables it.
**      Checks first if the task is not already registered.
**
**	INPUT:	    the name of the task [R]
**                  the syntax with which to register [W]
**	        IMPLICIT:
**
**    RETURNS:    the address of the flag whether the task is enabled or not
**                  
*/ 
   
static INT4 *TaskRegister (TASKo **task, char *name)
{
  static int classId=0;
  
  if(!classId)
    LstManageClass (&classId, sizeof (TASKo), NULL, NULL, NULL);
  
  if (!LstHashSearch ((void **) task, name)) {
    LstNewNamed ((void **) task, classId, name);
    (*task)->isEnabled = 0;
  }
  return &((*task)->isEnabled);
}

/****** TaskEnable ************************************************************
**
**      Disables or deactivates a task for specified syntax.
**
**	INPUT:	    task name [R]
**                  task object (list) [W]
**	        IMPLICIT:
**
**	RETURNS:    
**                  
*/ 
   
void TaskEnable (TASKo *task, char *name)
{
  if (LstHashSearch ((void **) &task, name)) 
    task->isEnabled = 1;
}


/****** TaskDisable ***********************************************************
**
**      Disable or inactivates  a task for specified syntax.
**
**	INPUT:	    task name [R]
**                  task object (list) [W]
**	        IMPLICIT:
**
**	RETURNS:    
**                  
*/ 
   
void TaskDisable (TASKo *task, char *name)
{
  if (LstHashSearch ((void **) &task, name)) 
    task->isEnabled = 0;
}

/****** TaskDisablAll ***********************************************************
**      Disable or inactivates all tasks.
**
**      INPUT:      task name [R]
**                  task object (list) [W]
**              IMPLICIT:
**
**      RETURNS:
**
*/

void TaskDisableAll(TASKo *task)
{
  if( LstFirst((void **) &task) )
  do {
    task->isEnabled = 0;
  } while( LstNext((void **) &task) );
}

/**api* TaskAllocLinks ********************************************************
**
**      This function must be called during parser build time whenever
**      a new link object requered for a node
**
**    INPUT:
**    RETURNS: 
*/ 
   
static TASKoLINKS *TaskAllocLinks()
{
  TASKoLINKS *links;

  if( (links = (TASKoLINKS *)malloc(sizeof(TASKoLINKS))) == NULL)
    _ErrExit2 (e__allocfail, "task links ");
  memset(links, NULL, sizeof(TASKoLINKS));
  return(links);
}

/**api* TaskRequestLink *******************************************************
**
**      This function must be called during parser build time whenever
**      a node (production) getting input from another production 
**      is associated with a task. 
**      This function will also register the task.
**
**    INPUT:   o  task object (list) [W]
**             o  name of the task [R]
**             o  name of the input token list [R]
**             o  the token code if only tokens with that code should 
**                trigger the task [R]
**    RETURNS:    
*/ 
   
TASKoLINKS *TaskRequestLink (TASKo **task, char *taskName,
                      struct BNFoPRODUCTION *currNode, TASKoLINKS *taskLinks)

{
  TASKoLINK       *link;
 
  if( !taskLinks )
    taskLinks = TaskAllocLinks();
  link = TaskLinkNew(taskLinks);
  link->node = currNode;
  link->isEnabledPtr = TaskRegister (task, taskName);
  return(taskLinks);
}

/**api* TaskNextActiveNode ****************************************************
**
**      Returns the next (if any) active node associated with a currently
**      active task and matching token code.
**  
**    INPUT:      link object list [W]
**                  token code [R]
**                  pointer to iteration context - set to 0 to begin iter. [W]
**            IMPLICIT:
**                  
**    RETURNS:    new link object 
*/ 

struct BNFoPRODUCTION *TaskNextActiveNode (TASKoLINKS *linkList, INT4 *context)

{
  TASKoLINK *link;

  while (1) {
    if (*context >= linkList->linkN) {
      *context = 0;
      return NULL;
    }
    link = &linkList->link[(*context)++];
    if (*link->isEnabledPtr)
      break;
  }
  return link->node;
}

**                  token code [R]
**                  pointer to iteration context - set to 0 to begin iter. [W]
**            IMPLICIT:
**                  
**    RETURNS:    new link object 
*/ 

struct BNFoPRODUCTION *TaskNextActiveNode (TASKoLINKS *linkList, INTsrs/src/icatask.h
**
**    $RCSfile: icatask.h,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:16:44 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**                  Copyright by Thure Etzold
**
*/

typedef struct TASKo {
  char *list;     /* for usage of module "list" only! */
  INT4 class_id;  /* for "list" module */  
  char name[30];
  INT4 isEnabled;
} TASKo;

typedef struct TASKoLINK {
  struct BNFoPRODUCTION *node;
  INT4                  *isEnabledPtr;
} TASKoLINK;

typedef struct TASKoLINKS {
  TASKoLINK *link;
  INT4      linkAllocN;
  INT4      linkN;
} TASKoLINKS;


/* module prototypes ***************************************/

void  TaskEnable (TASKo *task, char *name);
void  TaskDisable (TASKo *task, char *name);
void  TaskDisableAll (TASKo *task);
INT4  TaskIsRegister (TASKo *task, char *name);

struct BNFoPRODUCTION *TaskNextActiveNode (TASKoLINKS *, INT4 *);
TASKoLINKS *TaskRequestLink (TASKo  **, char *,
                                        struct BNFoPRODUCTION *, TASKoLINKS *);
 {
  TASKoLINK *link;
  INT4      linkAllocN;
  INT4      linkN;
} TASKoLINKS;


/* module prototypes ***************************************/

void  TaskEnable (TASKo *task, char *name);
void  TaskDisable (TASKo *task, char *name);
void  TaskDisableAll (TASKo *task);
INT4  TaskIsRegister (TASKo *task, char *name);

struct BNFoPRODUCTION *TaskNextActiveNode (TASKoLINKS *, INT4 *);
TASKoLINKS *TaskRequestLink (TASKo  **, char *srs/src/id.c
char id_ID[] = "$Id: id.c,v 1.4 1997/03/03 18:20:38 srs Exp $";
/*
**
**    $RCSfile: id.c,v $
**    $Revision: 1.4 $
**    $Date: 1997/03/03 18:20:38 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: file, sm, message 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    functions for manupulating IDs
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/


#include <stdio.h>
#include <string.h>

#include "message.h"
#include "sm.h"
#include "futil.h"
#include "binpack.h"
#include "id.h"
#include "library.h"



/**api* IdSplit ***************************************************************
**
** 	Splits an ID into its components and
**      populates all fields of the id object. ID object can be obtained 
**      by IdBuild.
** 
** 	INPUT:	    id object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    
*/ 
   
void IdSplit (IDoENTRY *id)
{
  IDPTR tmp;

  tmp = id->id + id->idType->fddbeg;  
  _BinUnpack3Byte (tmp, id->fip);

  id->siz = id->idType->siz;
  id->lib_x = (unsigned char) id->id[id->idType->lbxbeg];  /* library index */
  
  tmp = id->id + id->idType->lxbeg; 
  if (id->idType->lxlen > 0) 
    _BinUnpack2Byte (tmp, id->subentry_n);  /* subentry number */
  else
    id->subentry_n = 0;
}

/**api* IdMakeFromBuff ********************************************************
**
** 	Takes a buffer to an ID buffer and creates a temporary ID object which
**      will be overwritten in the next call to IdMakeFromBuff.
**      Populates all fields of the id object. 
** 
** 	INPUT:	    id buffer [R]
**                  id type object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    temporary ID object
*/ 
   
IDoENTRY *IdMakeFromBuff (IDPTR tmp, IDoTYPE *idType)
{
  static IDoENTRY id;

  memset (&id, 0, sizeof (IDoENTRY));
  id.idType = idType;
  memcpy (id.id, tmp, idType->siz);
  IdSplit (&id);
  return &id;
}

/**api* IdBuild ** ************************************************************
**
** 	builds an ID from fadd and library-index; function assumes fixed l
**      lengths for all parts of the ID ...which is because of the byte anding
**      and shifting - macros should be done for packing and unpacking 
**      numbers with a flexible byte length (as argument...switch..)
**      <p>
**      Function assigns the id an ID-type object if still missing.
** 
** 	INPUT:	    address of ID [W]
**                  library ID [R]
** 		    file pointer to record in ID index [R] 
**                  list index [R] or 0
**                  
** 	        IMPLICIT:
** 
** 	RETURNS:    1
*/ 
   
INT4 IdBuild (IDoENTRY *id, INT4 libId, UINT4 fip, INT4 list_x)
{ 
  IDoTYPE *idType=id->idType;
  IDPTR   tmp;

  /* get the ID-type if missing */
  if (!idType) {
    idType = LibGetIdType (NULL, libId, list_x ? 6 : 4);
    id->idType = idType;
  }

  id->lib_x = libId;
  id->fip = fip;

  tmp = id->id + idType->fddbeg;  /* fip */
  _BinPack3Byte (tmp, fip);

  id->siz = id->idType->siz;
  id->id[idType->lbxbeg] = libId;  /* library ID */

  if (idType->lxlen == 2) {  /* subentry ID */
    tmp = id->id + idType->lxbeg;
    _BinPack2Byte (tmp, list_x);
  }

  return 1;
}


/**API* IdCopy ***************************************************************
**
** 	Copies an ID. 
** 
** 	INPUT:	    address of output ID [W]
**                  address of input ID [R]
** 	        IMPLICIT:
** 
** 	RETURNS:
*/ 

void IdCopy (IDoENTRY *a, IDoENTRY *b)
{
  memcpy (a->id, b->id, b->siz);
  a->siz = b->siz;
  a->lib_x = b->lib_x;
  a->idType = b->idType;
  a->fip = b->fip;
  a->subentry_n = b->subentry_n;
}




/**API* IdToStr ***************************************************************
**
**      Converts an ID into a string with a hexadecimal number.
**      An ID of four byte is converted to a string 8 byte long.
** 
** 	INPUT:	    address of ID-object [R]
**                  address of output hex number string [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    
*/ 

INT4 IdToStr (IDoENTRY *id, char *numstr)
{
  char  *tmp;
  INT4   k;

  /*
  ** go through each byte of ID (from first to last) convert it into 
  ** two digit hex num - one digit numbers gets a '0' in front and copy
  ** it into a growing number string;
  */

  for (k=0; k < id->idType->siz; k++) {
    tmp = &numstr[k*2];
    sprintf (tmp, "%2x", id->id[k]);
    if (*tmp == ' ')
      *tmp = '0';  /** prefix a "0" if it is a one digit hexnum */
  }
  return 1;
}


/**API* IdFromStr ************************************************************
**
**      Converts a string with a hexadecimal number into an ID object.
** 
** 	INPUT:	    address of ID object [W]
**                  string with hex number [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if success
**                  e__novalentryidlen <id-numstr-len, numstr> +
*/ 

INT4 IdFromStr (IDoENTRY *id, char *numstr)
{
  INT4  len, k, num;
  char *tmp;

  len = strlen (numstr);
  id->siz = len / 2;

  /* 
  ** find an appropriate id type description...this is only preliminary
  ** to give IdSplit the ID description with correct offsets...should
  ** be replaced later by correct ID type
  */

  if (!(id->idType = LibGetIdType (NULL, 0, id->siz)))
    _ErrRet3 (e__novalentryidlen, id->siz, numstr);

  /*
  ** exactly reverse SrsIDToStr ...go through number string from the
  ** end to the beginning in steps of two characters;
  */

  for (k= id->siz - 1; k >= 0; k--) {
    tmp = &numstr[k*2];
    sscanf (tmp, "%x", &num);
    id->id[k] = num;
    *tmp = '\0';
  }

  IdSplit (id);

  /*
  ** now we can access the library-ID and assign the correct 
  ** idType 
  */

  id->idType = LibGetIdType (NULL, id->lib_x, id->siz);
  return 1;
}


/**api* IdIsSub ************************************************************
**
**      returns TRUE if the ID is pointing to a subentry;
** 
** 	INPUT:	    address of number string [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    ID-object
*/ 

INT4 IdIsSub (IDoENTRY *id)
{
  if (id->idType && id->idType->siz < 6)
    return 0;
  if (id->siz < 6)
    return 0;
  return 1;
}


/**api* IdGetSubN *************************************************************
**
**      Returns the subentry number;
** 
** 	INPUT:	    ID object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    subentry number
*/ 

INT4 IdGetSubN (IDoENTRY *id)
{
  return id->subentry_n;
}

/**api* IdSize ***************************************************************
**
**      Returns the size of the ID in bytes 
** 	INPUT:	    address of ID-type object [R]
** 
** 	RETURNS:    size of ID in bytes
*/ 

Int4 IdSize (IDoTYPE *idType)
{
  return idType->siz;
}

/**api* IdGetName *************************************************************
**
**      Returns the name of the ID type in bytes 
** 	INPUT:	    address of ID-type object [R]
** 
** 	RETURNS:    id name
*/ 

char *IdGetName (IDoTYPE *idType)
{
  return idType->nam;
}


/**api* IdPatch ***************************************************************
**
** 
** 	INPUT:	    address of ID-object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    hexnumber string
*/ 

INT4 IdPatch (IDoENTRY *id, char *patchList)
{
  return 1;
}

/**api* IdBuildSub ************************************************************
**
**      combines an entry-ID and a subentry number to a subentry-ID
** 
** 	INPUT:	    address of output subentry-ID object [W]
**                  input entry-ID object [R]
**                  subentry number [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    0: if subEntryN is not valid
**                  1: success
*/ 

INT4 IdBuildSub (IDoENTRY *idSub, IDoENTRY *id, INT4 subEntryN)
{
  static IDoTYPE  *idType=NULL;
  IDPTR tmp;

  if (!idType) 
    idType = (IDoTYPE*) LibObjByName ("idType", "SubEntry-ID");

  if (subEntryN < 0 || subEntryN > 65536)
    return 0;

  memcpy ((idSub->id + idType->fddbeg), id->id, id->siz); 
  tmp = idSub->id + idType->lxbeg;
    _BinPack2Byte (tmp, subEntryN);

  idSub->idType = idType;
  idSub->siz = idType->siz;
  return 1;
}

if subEntryN is not valid
**                  1: success
*/ 

INT4 IdBuildSub (IDoENTRY *idSub, IDoENTRY *id, INT4 subEntryN)
{
  static IDoTYPE  *idType=NULL;
  IDPTR tmp;

  if (!idType) 
    idsrs/src/id.h
**
**    $RCSfile: id.h,v $
**    $Revision: 1.3 $
**    $Date: 1996/11/20 16:36:16 $
**    $Author: etzold $
**
**    $Locker:  $
**    $State: Exp $
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
*/


#define IDxXID		12	       /* same as SRSxXID, max size of ID */


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  definition of an ID type - this object class is also defined in ODD
*/

#ifndef _IDoTYPE
#define _IDoTYPE
typedef struct IDoTYPE {
  char                    *nam;
  INT4                     siz;
  INT4                     fddbeg;
  INT4                     fddlen;
  INT4                     lbxbeg;
  INT4                     lbxlen;
  INT4                     lxbeg;
  INT4                     lxlen;
  INT4                     (*cpy) ();
} IDoTYPE;
#endif

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Descriptor of an entry- or subentry-ID. This ID can be obtained 
**  from a "set" and used to open the corresponding "entry".
*/

typedef struct IDoENTRY {
  INT4           siz;        /* length of the ID */
  INT4           lib_x;      /* (API) part of entry-ID that identifies the 
			       library where the entry resides */
  UINT4          fip;        /* part of entry-ID: pointer to node in ID-inx */
  INT4           subentry_n; /* (API) part of subentry-ID: number of subentry 
			       within entry*/
  unsigned char  id[IDxXID]; /* entry-ID itself */
  struct IDoTYPE *idType;      /* descriptor of entry-ID type */
} IDoENTRY;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  ...
*/

#define _IdPatch(id, idPatch, idType)


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  function prototypes
*/


INT4 IdBuild (IDoENTRY *id, INT4 libId, UINT4 fip, INT4 list_x);
INT4 IdToStr (IDoENTRY *id, char *numstr);
INT4 IdFromStr (IDoENTRY *id, char *numstr);
INT4 IdIsSub (IDoENTRY *id);
INT4 IdBuildSub (IDoENTRY *idSub, IDoENTRY *id, INT4 subEntryN);
INT4 IdPatch (IDoENTRY *id, char *patchList);
void IdSplit (IDoENTRY *id);
IDoENTRY *IdMakeFromBuff (IDPTR tmp, IDoTYPE *idType);
void IdCopy (IDoENTRY *a, IDoENTRY *b);
Int4 IdSize (struct IDoTYPE *idType);
char *IdGetName (struct IDoTYPE *idType);



otypes
*/


INT4 IdBuild (IDoENTRY *id, INT4 libId, UINT4 fip, INT4 list_x);
INT4 IdToStr (IDoENTRY *id, char *numstr);
INT4 IdFromStr (IDoENTRY *id, char *numstr);
INT4 IdIsSubsrs/src/ids.c
char ids_ID[] = "$Id: ids.c,v 1.5 1997/03/18 17:20:21 srs Exp $";
/*
**
**    $RCSfile: ids.c,v $
**    $Revision: 1.5 $
**    $Date: 1997/03/18 17:20:21 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.x Copyright by Thure Etzold
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**     
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include <string.h>

#include "message.h"
#include "sm.h"
#include "binpack.h"
#include "futil.h"
#include "tm.h"
#include "id.h"
#include "ids.h"
#include "set.h"
#include "library.h"
#include "map.h"

#define IDSxCURRENT_VERSION 1000000
#define IDSxMAXINFOBUFF 300

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of static functions
*/

static void IdsInfoWrite (IDSoFILE *idsFile);
static INT4 IdsInfoRead (IDSoFILE *idsFile);


/**api* IdsOpen ***************************************************************
** 
**      opens an IDS file (ID or entry pointer list);
**
** 	INPUT:	 o  address of file name [R]
**               o  string specifying access type: 
**                  "read", "write", "compress", "merge" [R]
**               o  size of cache (in blocks of 512 bytes) 
**                  used for writing the IDS, or NULL [R]
**               o  name of id-type [R] or NULL 
**               o  address of error code [W] or NULL
**                  e__iscompressed <fileName>
**                  e__indexisbusy <fileName>
**                  e__notcompressed <fileName>
**                  e__filopenerr <fileName>
**
** 	        IMPLICIT:
** 
** 	RETURNS:    new btree object
** 		    NULL if there is a problem 
*/ 

IDSoFILE *IdsOpen (char *name, char *option, INT4 cacheSize, char *idTypeName, INT4 *errCode)
{
  IDSoFILE *idsFile;
  char     fileName[FILxXNAM+1];
  INT4      rv;

  /* main object */
  if ((idsFile = (IDSoFILE *) calloc (1, sizeof (IDSoFILE))) == NULL)
    _ErrExit2 (e__allocfail, "idsFile-object");

  sprintf (fileName, "%s.ids", name);
  strcpy (idsFile->fileName, _FilTempLN (fileName));

  if (idTypeName) {
    if (!(idsFile->idType = (IDoTYPE *) LibObjByName ("idtype", idTypeName)))
      _ErrExit3 (e__objectunknown, "idType", idTypeName);
    strcpy (idsFile->idTypeName, idTypeName);
  }

  switch (tolower (option[0])) {


  case 'r': /* read */
    if (!(idsFile->file = fopen (idsFile->fileName, "rb"))) {
      _ErrSet (errCode, e__filopenerr);
      return NULL;
    }
    rv = IdsInfoRead (idsFile);
    _ErrIf (rv)
      return NULL;

    if (!(idsFile->idType = (IDoTYPE *) LibObjByName ("idtype", 
						      idsFile->idTypeName)))
      _ErrExit3 (e__objectunknown, "idType", idTypeName);

    if (idsFile->isBusy) 
      _ErrSet (errCode, e__indexisbusy);
    else if (!idsFile->isCompressed) {
      _ErrSet (errCode, e__notcompressed);
      return idsFile;
    }
    else
      return idsFile;

    fclose (idsFile->file);
    free (idsFile);
    return NULL;

  case 'c': /* compress */
    /* virtual memory object */
    if ((idsFile->vm = (MAPo *) calloc (1, sizeof (MAPo))) == NULL)
      _ErrExit2 (e__allocfail, "virtual memory object");
    
    rv = MapMem ((MAPo *) idsFile->vm, idsFile->fileName, NULL, 0);
    _ErrIf (rv) {
      free (idsFile);
      return NULL;
    }
    IdsInfoRead (idsFile);
    rv = IdsInfoRead (idsFile);
    _ErrIf (rv) {
      free (idsFile);
      return NULL;
    }

    idsFile->idType = (IDoTYPE *) LibObjByName ("idtype", idsFile->idTypeName);
    if (idsFile->isBusy) {
      _ErrSet (errCode, e__indexisbusy);
      return NULL;
    }
    else if (idsFile->isCompressed) {
      _ErrSet (errCode, e__iscompressed);
      return NULL;
    }

#ifndef VMS
    /* 
    ** delete the IDS previously opened for read access - only one
    ** version of the file can exist at a time (the output file) the 
    ** input file has been just read into memory
    */ 
    remove (idsFile->fileName);
#endif
    
    /* cache */
    if ((idsFile->cache = (MAPoCCH *) calloc (1, sizeof (MAPoCCH))) == NULL)
      _ErrExit2 (e__allocfail, "ids-cache-object");
    idsFile->cache->nbloc = cacheSize;
    MapInitCache (idsFile->cache, idsFile->fileName, 
		  &idsFile->fileSize, 1);

    idsFile->isBusy = 1;
    idsFile->isCompressed = 1;
    idsFile->idsInsertedN = 0;
    IdsInfoWrite (idsFile);
    break;


  case 'm': /* merge */
    idsFile->isCompressed = 1;
  case 'w': /* write */
    if (!idsFile->idType)
      _ErrExit2 (e__parnotdefined, "Id-type");

    /* cache */
    if ((idsFile->cache = (MAPoCCH *) calloc (1, sizeof (MAPoCCH))) == NULL)
      _ErrExit2 (e__allocfail, "ids-cache-object");
    idsFile->cache->nbloc = cacheSize;
    rv = MapInitCache (idsFile->cache, idsFile->fileName, 
		       &idsFile->fileSize, 1);

    _ErrIf (rv) {
      free (idsFile);
      return NULL;
    }
    idsFile->isBusy = 1;
    IdsInfoWrite (idsFile);
    idsFile->idsInsertedN = 0;
    break;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
  return idsFile;
}


/**api* IdsClose **************************************************************
** 
**      closes an ids file;
**
** 	INPUT:	    address of IDS-file object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    
*/ 

void IdsClose (IDSoFILE *idsFile)
{
  idsFile->isBusy = 0;

  if (idsFile->cache) {
    _ErrMsg4 (i__wroteidfile, idsFile->fileName, (idsFile->fileSize+999)/1000, 
	      idsFile->idsInsertedN);
    MapCloseCache (idsFile->cache);
    idsFile->cache = NULL;
    idsFile->file = fopen (idsFile->fileName, "r+"); 
    idsFile->timeCreated = TimeGet ();
    IdsInfoWrite (idsFile);
  }
  if (idsFile->set)
    SetDelete (idsFile->set->nam);
  if (idsFile->file)
    fclose (idsFile->file);
  if (idsFile->vm) {
    MapFree (idsFile->vm);
    free (idsFile->vm);
  }    
  if (idsFile->infoBuff)
    free (idsFile->infoBuff);
  free (idsFile);
}


/****** IdsInfoWrite **********************************************************
** 
**      writes information about the file to the begin of file;
**      writes an integer with the size of the info buffer in the front;
**
** 	INPUT:	    address of IDS-file object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:  
*/ 

static void IdsInfoWrite (IDSoFILE *idsFile)
{
  INT4  infoBuffSize=0;
  char *buff, *buffOff;

  if ((idsFile->infoBuff = (char *) malloc (IDSxMAXINFOBUFF)) == NULL)
    _ErrExit2 (e__allocfail, "info-buffer");
  
  buff = idsFile->infoBuff;
  _BinPackNum (buff, infoBuffSize);  /* size of following buffer */
  buffOff = buff;  /* real start of info buffer */

  _BinPackNum (buff, IDSxCURRENT_VERSION);  /* version number */
  _BinPackNum (buff, idsFile->fileSize);
  _BinPackNum (buff, idsFile->isBusy);
  _BinPackNum (buff, idsFile->isCompressed);
  _BinPackNum (buff, idsFile->idsInsertedN);
  _BinPackNum (buff, idsFile->timeCreated);
  _BinPackFixStr (buff, idsFile->idTypeName, 20);

  infoBuffSize = buff - buffOff;
  buff = idsFile->infoBuff;
  _BinPackNum (buff, infoBuffSize);  /* size of following buffer */
  
  if (idsFile->cache)
    MapCWrite (idsFile->cache, idsFile->infoBuff, infoBuffSize + 4);
  else if (idsFile->file) {
    fseek (idsFile->file, 0, 0);
    fwrite (idsFile->infoBuff, infoBuffSize + 4, 1, idsFile->file);
  }
}


/****** IdsInfoRead ***********************************************************
** 
**      compresses a linked list of IDs into a block
**
** 	INPUT:	 o  address of IDS-file object [R]
**               o  address of ID object [R]
**               o  file address of previous ID in list 
**                  or 0 if first in list [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    address of inserted ID
*/ 

static INT4 IdsInfoRead (IDSoFILE *idsFile)
{
  INT4 infoBuffSize;
  char *buff;

  if (idsFile->vm) { /* file is already in memory */
    buff = idsFile->vm->data;
    _BinUnpackNum (buff, infoBuffSize);  
  }
  else {
    _BinFileUnpackNum (idsFile->file, infoBuffSize);
    if ((idsFile->infoBuff = (char *) malloc (infoBuffSize)) == NULL)
      _ErrExit2 (e__allocfail, "info-buffer");
    fread (idsFile->infoBuff, infoBuffSize, 1, idsFile->file);
    buff = idsFile->infoBuff;
  }

  _BinUnpackNum (buff, idsFile->versionN);  /* check version number */
  if (idsFile->versionN != IDSxCURRENT_VERSION)
    _ErrRet4 (e__indexwrongversion, idsFile->fileName, 
	      idsFile->versionN, IDSxCURRENT_VERSION);
  _BinUnpackNum (buff, idsFile->fileSize);
  _BinUnpackNum (buff, idsFile->isBusy);
  _BinUnpackNum (buff, idsFile->isCompressed);
  _BinUnpackNum (buff, idsFile->idsInsertedN);
  _BinUnpackNum (buff, idsFile->timeCreated);
  _BinUnpackFixStr (buff, idsFile->idTypeName, 20);
  return 1;
}


/**api* IdsInsert *************************************************************
** 
**      inserts an ID into the IDS-file
**
** 	INPUT:	 o  address of IDS-file object [R]
**               o  address of ID object [R]
**               o  file address of previous ID in list 
**                  or 0 if first in list [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    address of inserted ID
*/ 

FIP IdsInsert (IDSoFILE *idsFile, IDoENTRY *id, FIP idPrevFip)
{
  static char nullFipBuff[4] = {0,0,0,0};
  MAPoCCH *idsCache = idsFile->cache;
  char    idFipBuff[4];
  char    *idPrev, *idFipBuffPtr = idFipBuff;
  FIP     idFip;

  /*
  ** get file address of write offset, write then the address to the next
  ** ID (initially 0) and then the ID which is already in packed format
  */

  MapCNew (idsCache, &idFip);
  MapCWrite (idsCache, nullFipBuff, 4);
  MapCWrite (idsCache, (char *) id->id, id->siz);

  /*
  ** if this is not the first ID in the list then the "pointer-to-next" of 
  ** previous ID in list must be updated -> the previous ID is either still
  ** in cache or has been already written to the file
  */

  if (idPrevFip) {
    if (!MapInCache (idsCache, idPrevFip, (void **) &idPrev)) {
      _BinPackFip (idFipBuffPtr, idFip);
      MapCUpdate (idsCache, idPrevFip, idFipBuff); 
      MapDuplicateOverlap (idsCache, idPrevFip, idFipBuff, 4);
    } 
    else 
      _BinPackFip (idPrev, idFip); 

  }
  idsFile->idsInsertedN++;
  return idFip;
}

#define IDSxTMPSETSIZE 200000

/**api* IdsCompress ***********************************************************
** 
**      compresses a linked list of IDs into a block
**
** 	INPUT:	    address of IDS-file object [R]
**                  file pointer to first ID in the list [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    number of IDs found in linked list
*/ 

INT4 IdsCompress (IDSoFILE *idsFile, FIP *idsFirstFip)
{
  SETo    *set = idsFile->set;
  MAPoCCH *idsCache=idsFile->cache;
  IDoTYPE *idType=idsFile->idType;
  FIP     idNextFip, idFipSave;
  INT4    idN=0, k;
  char    *tmpPtr, *idPtrSave;
  
  if (!set) {
    idsFile->set = SetNew (NULL, "temp");
    set = idsFile->set;
    SetAlloc (set, IDSxTMPSETSIZE, idType);
  }
  else
    set->n = 0;

  /* 
  ** get pointer to the begin of the ID list, save it... for the calculation
  ** of the next ID's address  and unpack the address of the next ID in list
  */

  tmpPtr = idsFile->vm->data + *idsFirstFip;  /* ptr to begin of IID */
  idFipSave = *idsFirstFip;
  idPtrSave = tmpPtr;
  _BinUnpackFip (tmpPtr, idNextFip);  /* get fip to next ID ... pointer now at
					 begin of ID */ 

  do {
    if (!idN++)
      MapCNew (idsCache, idsFirstFip);  /* address of first ID */
    else {
      tmpPtr = idPtrSave + (idNextFip - idFipSave);  /* address of next ID */
      _BinUnpackFip (tmpPtr, idNextFip); 
    }
    if (set->n >= set->allocN)
      SetRealloc (set, set->n + IDSxTMPSETSIZE, idType);

      /*_ErrExit3 (f__limitexceeded, "IDSxTMPSETSIZE", IDSxTMPSETSIZE);*/
      
    memcpy (set->id_p + set->n++ * idType->siz, tmpPtr, idType->siz);
  } while (idNextFip);

  for (k=0; k < set->n; k++) {
    MapCWrite (idsCache, (char *) (set->id_p + k*idType->siz), idType->siz);
    idsFile->idsInsertedN++;
  }
  return idN;
}

/**api* IdsPut ****************************************************************
** 
**      Writes a block of entry-IDs into the IDS file and returns the
**      file address of the first ID written.
**
** 	INPUT:	    address of IDS-file object [W]
**                  buffer with IDs [R]
**                  number of IDs to write [R]
**
**      RETURNS:    file address of first ID in IDS file
*/ 

FIP IdsPut (IDSoFILE *ids, char *buff, Int4 n)
{
  FIP fip;
  Int4 k, size=IdSize(ids->idType);

  MapCNew (ids->cache, &fip);
  for (k=0; k < n; k++)
    MapCWrite (ids->cache, buff+(k*size), size);
  ids->idsInsertedN += n;
  return fip;
}


/**api* IdsGet ****************************************************************
** 
**      compresses a linked list of IDs into a block
**
** 	INPUT:	    address of IDS-file object [R]
**                  file pointer to first ID in the list [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    number of IDs
*/ 

INT4 IdsGet (IDSoFILE *idsFile, IDPTR idBuff, FIP idsFip, INT4 idN)
{
  fseek (idsFile->file, idsFip, 0);
  fread (idBuff, idsFile->idType->siz, idN, idsFile->file);
  return idN; /* or correct number, if less ? */
}


void IdsEntryIncrement (IDSoFILE *idsFile, IDPTR buff, Int4 idN, Int4 add)
{
  fprintf (stderr, "IdsEntryIncrement is not implemented\n");
}

/**api* IdsGetRange ***********************************************************
** 
**      compresses a linked list of IDs into a block
**
** 	INPUT:	    address of IDS-file object [R]
**                  id-buffer or NULL (no read!) [R]
**                  file pointer to first group of ID's [R]
**                  number of ID's in first group of ID's [R]
**                  file pointer to last group of ID's [R]
**                  number of ID's in last group of ID's [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    number of IDs found in linked list
*/ 

INT4 IdsGetRange (IDSoFILE *idsFile, IDPTR idBuff, 
		  FIP idsFip1, FIP idsFip2, INT4 idN1, INT4 idN2)
{
  INT4 idBlockSize;
  FIP tmpFip;

  if (idsFip1 > idsFip2)     /* obsolete */
    tmpFip = idsFip1, idsFip1 = idsFip2, idsFip2 = tmpFip, idN2 = idN1;

  idBlockSize = idsFip2 - idsFip1 + idN2 * idsFile->idType->siz;
  
  if (idBuff) {   /* read id's */
    fseek (idsFile->file, idsFip1, 0);
    fread (idBuff, idBlockSize, 1, idsFile->file);
  }

  return idBlockSize / idsFile->idType->siz;
}


/**api* IdsGetFileSize ********************************************************
** 
**      gets the file size in bytes;
**
** 	INPUT:	    address of IDS-file object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    file size in bytes
*/ 

INT4 IdsGetFileSize (IDSoFILE *idsFile)
{
  return idsFile->fileSize;
}

/**api* IdsGetTimeCreated *****************************************************
** 
**      gets creation time;
**
** 	INPUT:	    address of IDS-file object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    creation time
*/ 

INT4 IdsGetTimeCreated (IDSoFILE *idsFile)
{
  return idsFile->timeCreated;
}

/**api* IdsGetIdN *************************************************************
** 
**      gets the number of IDs;
**
** 	INPUT:	    address of IDS-file object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    number of IDs
*/ 

INT4 IdsGetIdN (IDSoFILE *idsFile)
{
  return idsFile->idsInsertedN;
}

/**api* IdsIsCompressed *******************************************************
** 
**      returns TRUE if the ids file is compressed
**
** 	INPUT:	    address of ids file object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 or 0
*/ 

INT4 IdsIsCompressed (IDSoFILE *idsFile)
{
  return idsFile->isCompressed;
}

/**api* IdsGetIdType *********************************************************
** 
**      Returns the object describing the IDs stored in the file.
**
** 	INPUT:	    Ids file object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    ID type object
*/ 

IDoTYPE *IdsGetIdType (IDSoFILE *idsFile)
{
  return idsFile->idType;
}


pressed
**
** 	INPUT:	    address of ids file object [R]
** 	    srs/src/ids.h
**
**    $RCSfile: ids.h,v $
**    $Revision: 1.3 $
**    $Date: 1996/09/09 20:17:17 $
**    $Author: etzold $
**
**    $Locker:  $
**    $State: Exp $
**
*/


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  ids-file object
*/

typedef struct IDSoFILE {
  FILE            *file;         /* file handle to IDS file */
  char            *infoBuff;
  char            idTypeName[20];
  struct IDoTYPE  *idType;
  struct MAPo     *vm;
  struct MAPoCCH  *cache;
  char            fileName[FILxXNAM+1]; /* file name of index file */
  INT4            idsInsertedN;
  INT4            isBusy;
  INT4            isCompressed;
  FIP             fileSize;   /* write offset which defines also the size 
				    of the file -> pointer after last byte */
  UINT4           timeCreated;
  INT4            versionN;
  struct SETo     *set;        /* needed for compression */
} IDSoFILE;

#ifndef _IDoENTRY
typedef struct IDoENTRY *IDSdummytointroducestructtagIDoENTRY;
#endif

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of exported functions
*/

IDSoFILE *IdsOpen (char *name, char *option, INT4 cacheSize,
                   char *idTypeName, INT4 *errCode);
void IdsClose (IDSoFILE *idsFile);

FIP  IdsInsert (IDSoFILE *idsFile, struct IDoENTRY *id, FIP previous);
INT4 IdsCompress (IDSoFILE *idsFile, FIP *idsFirstFip);
FIP IdsPut (IDSoFILE *ids, char *buff, Int4 n);
INT4 IdsGet (IDSoFILE *idsFile, IDPTR idBuff, FIP idsFip, INT4 idN);
INT4 IdsGetRange (IDSoFILE *idsFile, IDPTR idBuff, 
		  FIP idsFip1, FIP idsFip2, INT4 idN1, INT4 idN2);
void IdsEntryIncrement (IDSoFILE *idsFile, IDPTR buff, Int4 idN, Int4 add);

    /* info about ids-file */

INT4 IdsGetFileSize (IDSoFILE *idsFile);
INT4 IdsGetTimeCreated (IDSoFILE *idsFile);
INT4 IdsGetIdN (IDSoFILE *idsFile);
INT4 IdsIsCompressed (IDSoFILE *idsFile);
struct IDoTYPE *IdsGetIdType (IDSoFILE *idsFile);





f, Int4 n);
INT4 IdsGet (IDSoFILE *idsFile, IDPTR srs/src/idx.c
char idx_ID[] = "$Id: idx.c,v 1.7 1997/03/18 17:20:22 srs Exp $";
/*
**
**    $RCSfile: idx.c,v $
**    $Revision: 1.7 $
**    $Date: 1997/03/18 17:20:22 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.x Copyright by Thure Etzold
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: file, sm, message
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**     
**    Creates a list of fixed length records for each entry in the databank
**    the record format is originally:
**
**    fip1 (fip) | fip2 (fip)| fileX (num) | entryName (fixed length ascii) |
**
**    The propoese extension is to optionally add to this:
**    o more file pointers 
**    o numbers of subentries in the entry (there can be more than one
**      subentry type in the databank)
**    o parts of the file name (for databanks with one file per entry)
**    
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include <string.h>

#include "message.h"
#include "sm.h"
#include "tm.h"
#include "futil.h"
#include "binpack.h"



#define IDXxMAXRELNAMELEN   50
#define IDXxWRITEBUFFSIZ    500
#define IDXxREADBUFFSIZ     1
#define IDXxCURRENT_VERSION 1002

#define _IDXo
typedef struct IDXo {
  FILE    *file;                  /* file handle to ID file */
  char    fileName[FILxXNAM+1];   /* file name of ID file */
  SMoBUFF *infoBuff;              /* buffer for info block */
  SMoBUFF *flatFileNames;         /* buffer for info block */
  FIP     firstRecordFip;         /* fip of first record in file */
  INT4    isWriteOpen;            /* file open for write access */
  INT4    isUpdateOpen;           /* file open for update access */
  INT4    isBusy;
  INT4    recordSize;             /* total (fixed) record size */  
  INT4    recordN;                /* number of ID-records in the file */
  INT4    fileSize;               /* file size in Bytes */
  UINT4   timeCreated;      
  INT4    versionN;
  char    *buff;                  /* temporary buffer for reading/writing */
  char    *buffPtr;               /* current offset in buffer */
  INT4    buffSize;               /* allocated size (n * recordSize); */
  INT4    flatFileNameN;          /* number of those file names */
  char    relName[IDXxMAXRELNAMELEN+1];  /* release name (eg, "23.0") */
} IDXo;

#include "idx.h"


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of static functions
*/

static INT4 IdxInfoRead (IDXo *idx);
static void IdxInfoWrite (IDXo *idx);
static void IdxWriteBlock (IDXo *idx);



/**api* IdxOpen ***************************************************************
** 
**      opens an ID-index file;
**
** 	INPUT:	 o  address of file name (without extension) [R]
**               o  string specifying access type: 
**                  "read", "write", "update" [R]
**               o  maximum string length (reserved space) for the ID-names [R]
**                  or 0
**               o  address of error code [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    new ID-index object
** 		    NULL if there is a problem 
*/ 

IDXo *IdxOpen (char *name, char *option, int recordSize, INT4 *errCode)
{
  IDXo *idx;

  if ((idx = (IDXo *) calloc (1, sizeof (IDXo))) == NULL)
    _ErrExit2 (e__allocfail, "id-index-object");
  sprintf (idx->fileName, "%s.idx", name);
  idx->infoBuff = BuffNew (50);
  idx->flatFileNames = BuffNew (20);

  _ErrSet (errCode, 0);
  switch (tolower (option[0])) {

  case 'r':  /* read */ 
    if (!(idx->file = fopen (_FilTempLN (idx->fileName), "rb"))) {
      _ErrSet (errCode, e__filopenerr); 
      return NULL;
    }
    if (idx->isBusy) {
      _ErrSet (errCode, e__indexisbusy);
      return NULL;
    }
    IdxInfoRead (idx);
    idx->isWriteOpen = 0;
    idx->isUpdateOpen = 0;
    idx->buffSize = idx->recordSize * IDXxREADBUFFSIZ; 
    if (!(idx->buff = (char *) malloc (idx->buffSize)))
      _ErrExit2 (e__allocfail, "id-index-object");
    break;
    
  case 'u':
    if (!(idx->file = fopen (_FilTempLN (idx->fileName), "r+b"))) 
      _ErrSet (errCode, e__filopenerr);
    if (idx->isBusy) {
      _ErrSet (errCode, e__indexisbusy);
      break;
    }
    IdxInfoRead (idx);
    idx->buffSize = idx->recordSize * IDXxREADBUFFSIZ; 
    if (!(idx->buff = (char *) malloc (idx->buffSize)))
      _ErrExit2 (e__allocfail, "id-index-object");
    idx->isBusy = 1; 
    idx->isWriteOpen = 0;
    idx->isUpdateOpen = 1;
    break;


  case 'w':  /* write */  
    if (!(idx->file = fopen (_FilTempLN (idx->fileName), "wb"))) {
      _ErrSet (errCode, e__filopenerr);
      return NULL;
    }

    idx->recordSize = recordSize;
    idx->buffSize = idx->recordSize * IDXxWRITEBUFFSIZ; 
    if (!(idx->buff = (char *) malloc (idx->buffSize)))
      _ErrExit2 (e__allocfail, "id-index-object");

    idx->buffPtr = idx->buff;
    idx->recordN = 0;
    idx->isBusy = 1; 
    idx->isWriteOpen = 1;
    idx->isUpdateOpen = 0;
    idx->flatFileNameN = 0;
    idx->relName[0] = '\0';
    IdxInfoWrite (idx);
    break;
    
  default:
    _ErrExit2 (e__unknownoption, option);
  }
  return idx;
}


/**api* IdxClose **************************************************************
** 
**      closes an ID-index opened for read or write access;
**
** 	INPUT:	    patch file object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    
*/ 

void IdxClose (IDXo *idx)
{
  if (idx->isWriteOpen || idx->isUpdateOpen) {
    if (idx->isWriteOpen)
      IdxWriteBlock (idx);  /* flush buffer */
    idx->isBusy = 0;
    if (!idx->isUpdateOpen)
      idx->timeCreated = TimeGet ();
    IdxInfoWrite (idx);
    if (idx->isWriteOpen)
      _ErrMsg4 (i__wroteidfile, idx->fileName, (idx->fileSize+999)/1000, 
		idx->recordN);
  }
  fclose (idx->file);
  if (idx->buff)
    free (idx->buff);
  free (idx);
}



/****** IdxInfoWrite **********************************************************
** 
**      writes information about the file to the begin of file;
**      writes an integer with the size of the info buffer in the front;
**
** 	INPUT:	    address of IDS-file object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:  
*/ 

static void IdxInfoWrite (IDXo *idx)
{
  SMoBUFF *buff;
  INT4    size;

  buff = idx->infoBuff;
  BuffReset (buff);
  BuffPack (buff, "i7a50i", 
	    0,
	    IDXxCURRENT_VERSION, 
	    idx->fileSize, 
	    idx->isBusy, 
	    idx->recordN, 
	    idx->timeCreated, 
	    idx->recordSize, 
	    idx->relName, 
	    idx->flatFileNameN);
  
  BuffResetRead (idx->flatFileNames);
  BuffCat (buff, idx->flatFileNames);
  size = BuffLength (buff);
  idx->firstRecordFip = size;
  BuffReset (buff);
  BuffPack (buff, "i", size);
  fseek (idx->file, 0, 0);
  fwrite (BuffGetPtr (idx->infoBuff), size, 1, idx->file);
}


/****** IdsInfoRead ***********************************************************
** 
**      compresses a linked list of IDs into a block
**
** 	INPUT:	 o  address of IDS-file object [R]
**               o  address of ID object [R]
**               o  file address of previous ID in list 
**                  or 0 if first in list [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    address of inserted ID
*/ 

static INT4 IdxInfoRead (IDXo *idx)
{
  INT4    size, k;
   SMoBUFF *buff=idx->infoBuff;

  fseek (idx->file, 0, 0);
  BuffReset (buff);
  BuffReadFile (buff, idx->file, 20);
  if (feof (idx->file))
    return e__filnotok;
  BuffUnpack (buff, "i2", &size, &idx->versionN);

  if (idx->versionN != IDXxCURRENT_VERSION && idx->versionN != 1001)
    _ErrRet4 (e__indexwrongversion, idx->fileName, 
	      idx->versionN, IDXxCURRENT_VERSION);

  BuffReadFile (buff, idx->file, size - 20);
  BuffUnpack (buff, "i5a50i", 
	      &idx->fileSize,
	      &idx->isBusy,
	      &idx->recordN,
	      &idx->timeCreated,
	      &idx->recordSize,
	      idx->relName,
	      &idx->flatFileNameN);
  BuffCat (idx->flatFileNames, buff);
  idx->firstRecordFip = BuffLength (buff);

  /* compatibility with old version */
  if (idx->versionN == 1001)
    idx->firstRecordFip += 4;

  fseek (idx->file, idx->firstRecordFip, 0);
  return 1;
}

/**api* IdxWriteBlock *********************************************************
** 
**      writes a block with ID-records to file
**
** 	INPUT:	    address of IDX-file object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    
*/ 

static void IdxWriteBlock (IDXo *idx)
{
  int size;

  size = (unsigned long) idx->buffPtr - (unsigned long) idx->buff;
  fwrite (idx->buff, size, 1, idx->file);
  idx->buffPtr = idx->buff;
  idx->fileSize += size;
}


/**API* IdxPutBuff ************************************************************
** 
**      Puts the contents of a "buff" object into the index file as a 
**      record.
**
** 	INPUT:	    address of IDX-file object [R]
**                  address of "buff" object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    file pointer to inserted record
*/ 

FIP IdxPutBuff (IDXo *idx, SMoBUFF *buff)
{
  static INT4 isInit=0;
  INT4 size = BuffLength (buff);

  if (!isInit) {
    idx->recordSize = size;
    idx->buffSize = idx->recordSize * IDXxWRITEBUFFSIZ; 
    if (!(idx->buff = (char *) malloc (idx->buffSize)))
      _ErrExit2 (e__allocfail, "id-index-object");
    idx->buffPtr = idx->buff;
    isInit = 1;
  }
  else if (idx->recordSize != size) {
    _ErrExit4 (e__novalvar3, "IDX record size", size, idx->recordSize);
  }    

  if ((unsigned long) idx->buffPtr - (unsigned long)idx->buff >= idx->buffSize)
    IdxWriteBlock (idx);
  
  memcpy (idx->buffPtr, BuffGetPtr (buff), size);
  idx->buffPtr += size;
  return ++(idx->recordN);
}


/**API* IdxGetBuff ************************************************************
** 
**      Retrieves a record from the index.
**
** 	INPUT:	    address of IDX-file object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    file pointer to inserted record
*/ 

void IdxGetBuff (IDXo *idx, FIP fip, SMoBUFF *buff)
{
  fip = idx->firstRecordFip + (fip-1) * idx->recordSize;
  fseek (idx->file, fip, 0);
  BuffReadFile (buff, idx->file, idx->recordSize);
}

/**API* IdxNextBuff ***********************************************************
** 
**      Retrieves a record from the index.
**
** 	INPUT:	    address of IDX-file object [R]
**                  address of iteration variable [W]
** 
** 	RETURNS:    buff object with next record
**                  NULL: if at end of file
*/ 

SMoBUFF *IdxNextBuff (IDXo *idx, Int4 *c)
{
  static SMoBUFF *buff=NULL;
  FIP fip;

  if (!buff)
    buff = BuffNew (idx->recordSize);
  else
    BuffReset (buff);
  if (*c >= IdxGetRecordN (idx)) {
    *c = 0;
    return NULL;
  }
  fip = idx->firstRecordFip + *c * idx->recordSize;
  fseek (idx->file, fip, 0);
  BuffReadFile (buff, idx->file, idx->recordSize);
  (*c)++;
  return buff;
}


/**api* function **************************************************************
** 
**      Returns the address of a new record in the IDX file. The record can
**      be filled from externally and will not be written to the file until
**      the next call to IdxRecordNew.
**
** 	INPUT:	    address of IDX-file object [R]
** 
** 	RETURNS:    pointer to new record
*/ 

char *IdxRecordNew (IDXo *idx)
{
  char *buff;

  ASSERT ((idx!=NULL), "idx not opened");
  if ((unsigned long) idx->buffPtr - (unsigned long)idx->buff >= idx->buffSize)
    IdxWriteBlock (idx);
  buff = idx->buffPtr;
  idx->buffPtr += idx->recordSize;
  idx->recordN++;
  return buff;
}


/**api* function ***********************************************************
** 
**      Returns a record with specified fip (file pointer) from the opened
**      IDX file for read access.
**
** 	INPUT:	    address of IDX-file object [R]
**                  file pointer [R]
** 
** 	RETURNS:    record buffer
*/ 

char *IdxRecordGet (IDXo *idx, FIP fip)
{

  fip = idx->firstRecordFip + (fip-1) * idx->recordSize;
  fseek (idx->file, fip, 0);
  fread (idx->buff, 1, idx->recordSize, idx->file);
  idx->buffPtr = idx->buff;
  return idx->buff;
}


/**API* IdxGetRecordN *********************************************************
** 
**      Returns number of records in the IDX-file.
**
** 	INPUT:	    address of IDX object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    number of records
*/ 

INT4 IdxGetRecordN (IDXo *idx)
{
  return idx->recordN;
}

/**API* IdxGetTimeCreated *****************************************************
** 
**      Returns creation time of IDX file.
**
** 	INPUT:	    address of IDX object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    number of records
*/ 

UINT4 IdxGetTimeCreated (IDXo *idx)
{
  return idx->timeCreated;
}


/**api* IdxTouch **************************************************************
** 
**      sets the internal index time to current time;
**
** 	INPUT:	    address of Idx object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    
*/ 

void IdxTouch (char *fileName)
{
  IDXo *idx;
  INT4 errCode;

  if (!(idx = IdxOpen (fileName, "update", 0, &errCode)))
    _ErrExit2 (errCode, fileName);
  idx->timeCreated = TimeGet ();
  IdxClose (idx);
}



/**api* IdxSetReleaseName *****************************************************
** 
**      sets a release name (typically a number, eg, "23.0";
**
** 	INPUT:	    address of idx object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:   
*/ 

void IdxSetReleaseName (IDXo *idx, char *relName)
{
  if (strlen (relName) > IDXxMAXRELNAMELEN)
    _ErrExit3 (e__strtoolong, relName, IDXxMAXRELNAMELEN);
  strcpy (idx->relName, relName);
}

/**API* IdxGetReleaseName *****************************************************
** 
**      Return release name (release number) of IDX file.
**
** 	INPUT:	    address of IDX object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    release name
*/ 

char *IdxGetReleaseName (IDXo *idx)
{
  return idx->relName;
}

/**api* IdxGetFlatFileNameN ***************************************************
** 
**      gets release name;
**
** 	INPUT:	    address of Btree object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    release name
*/ 

INT4 IdxGetFlatFileNameN (IDXo *idx)
{
  return idx->flatFileNameN;
}

/**api* IdxGetFlatFileName ****************************************************
** 
**      get the next file name.
**
** 	INPUT:	    address of Btree object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    file name
**                  or NULL if no more names
*/ 

char *IdxGetFlatFileName (IDXo *idx, INT4 *c)
{
  char *s=NULL;
  INT4 k;

  if (idx->flatFileNameN) {
    if (*c == 0) {
      BuffResetRead (idx->flatFileNames);
      *c = 1;
    }
    if (!BuffUnpack (idx->flatFileNames, "z", &s)) {
      *c = 0;
      s = NULL;
    }
  }
  return s;
}


/**api* IdxSetFlatFileName ****************************************************
** 
**      gets release name;
**
** 	INPUT:	    address of Btree object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    index that new file name receives in the list (first=0)
*/ 

INT4 IdxSetFlatFileName (IDXo *idx, char *flatFileName)
{
  BuffPack (idx->flatFileNames, "a", flatFileName);  
  return ++idx->flatFileNameN;
}



/**api* IdxWriteFlatFileNames *************************************************
** 
**      Commits accumulated file names to index file;
**
** 	INPUT:	    address of Btree object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    index that new file name receives in the list (first=0)
*/ 

INT4 IdxWriteFlatFileNames (IDXo *idx)
{
  IdxInfoWrite (idx);
  return idx->flatFileNameN;
}

eName (IDXo *idx, char *flatFileName)
{
  BuffPack (idx->flatFileNames, "a", flatFileName);  
  return ++idsrs/src/idx.h
**
**    $RCSfile: idx.h,v $
**    $Revision: 1.3 $
**    $Date: 1997/03/03 18:20:39 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
*/


typedef struct IDXo *IDXv;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of exported functions
*/

struct IDXo *IdxOpen (char *name, char *option, int maxStrLen, INT4 *errCode);
void IdxClose (struct IDXo *idx);
void IdxTouch (char *fileName);

FIP IdxPutBuff (struct IDXo *idx, struct SMoBUFF *buff);
void IdxGetBuff (struct IDXo *idx, FIP fip, struct SMoBUFF *buff);
struct SMoBUFF *IdxNextBuff (struct IDXo *idx, Int4 *c);
FIP IdxPut (struct IDXo *idx, char *name, FIP textFip, FIP dataFip, 
	    int fileX);
void IdxGet (struct IDXo *idx, FIP fip, char *name, FIP *textFip, 
	     FIP *dataFip, int *fileX);
char *IdxRecordNew (struct IDXo *idx);
char *IdxRecordGet (struct IDXo *idx, FIP fip);

    /* get and set of some individual attributes */

char *IdxGetReleaseName (struct IDXo *idx);
void IdxSetReleaseName (struct IDXo *idx, char *relName);
UINT4 IdxGetTimeCreated (struct IDXo *idx);
INT4 IdxGetRecordN (struct IDXo *idx);
INT4 IdxSetFlatFileName (struct IDXo *idx, char *fileName);
char *IdxGetFlatFileName (struct IDXo *idx, INT4 *context);
INT4 IdxWriteFlatFileNames (struct IDXo *idx);
INT4 IdxGetFlatFileNameN (struct IDXo *idx);


DXo *idx);
char *IdxRecordGet (struct IDXo *idx, FIP fip);

    /* get and set of some individual attributes srs/src/index.c
char index_srs_ID[] = "$Id: index.c,v 1.7 1996/11/20 16:36:17 etzold Exp $";
/*
**
**    $RCSfile: index.c,v $
**    $Revision: 1.7 $
**    $Date: 1996/11/20 16:36:17 $
**    $Author: etzold $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.x Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     D-69012 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: file, sm, message, parser, map
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**     
**    module for building index-files
** 
**    index of type KEY or TREE consists of two files: 
**    seqlibname_indexname.inx and *.ids                                 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>

#include "message.h"
#include "sm.h"
#include "futil.h"
#include "binpack.h"
#include "btree.h"
#include "id.h"
#include "ids.h"
#include "hash.h"
#include "index.h"



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  declaration of global or module wide variables
*/

static INXo *indexCurr;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of static functions
*/

static INT4 InxHashSearch (void *value, void *record, HSHo *table);
static void InxIdListUpdate (BTRoVALUE  *idList, void *record);
static void InxBtreeInsert (HSHo *table);
static void InxDelete (INXo *inx);


/************************************************************
**  definitions and functions for use of hash table
*/
typedef struct {
    BTRoVALUE  idList;
    INT4  value;
} HASHNUMOBJ;

typedef struct {
    BTRoVALUE  idList;
    double  value;
} HASHREALOBJ;

typedef struct {
    BTRoVALUE  idList;
    char value[1];
} HASHSTROBJ;

typedef struct {
    BTRoVALUE  idList;
} HASHANYOBJ;


INT4 myhash_func (HSHo *table, void *obj)
{
    register unsigned long h=0, g, i;
    register char *p;
    INT4 len;

    switch (indexCurr->valueType) { 
        case BTRxSTR: 
        case BTRxIDENTRY: 
            p = ((HASHSTROBJ*) obj)->value;
            len = strlen(p);
            break; 
        case BTRxNUM: 
            p = (char*) &((HASHNUMOBJ*) obj)->value;
            len = sizeof(((HASHNUMOBJ*) obj)->value);
            break; 
        case BTRxREAL: 
            p = (char*) &((HASHREALOBJ*) obj)->value;
            len = sizeof(((HASHREALOBJ*) obj)->value);
            break; 
    }

    for (i=0; i<len; i++) {
        h= (h << 4) + *(p+i);
        if ((g= (h & 0xf0000000)))
            h= (h ^ (g >> 24)) ^ g;
    }

    return (INT4) h % table->max_hash_elem;
}


INT4 mycompare_func(void *obj1, void *obj2)
{
    switch (indexCurr->valueType) { 
        case BTRxSTR: 
        case BTRxIDENTRY: 
            return  strcmp( ((HASHSTROBJ*)obj1)->value,
                            ((HASHSTROBJ*)obj2)->value );
        case BTRxNUM: 
            return  ((HASHNUMOBJ*)obj1)->value - ((HASHNUMOBJ*)obj2)->value;
        case BTRxREAL: 
            if ( ((HASHREALOBJ*)obj1)->value < ((HASHREALOBJ*)obj2)->value )
                return -1;
            if ( ((HASHREALOBJ*)obj1)->value > ((HASHREALOBJ*)obj2)->value )
                return 1;
            return 0;
    }

    return -9999;  /* no legal valueType */
}

INT4 myprint_func(void *obj)
{
    if (!obj) {
        printf("no object\n");
	return 0;
    }
    else
      switch (indexCurr->valueType) { 
        case BTRxSTR: 
        case BTRxIDENTRY: 
            printf("%s\n", ((HASHSTROBJ*) obj)->value);
            break; 
        case BTRxNUM: 
            printf("%20d\n", ((HASHNUMOBJ*) obj)->value);
            break; 
        case BTRxREAL: 
            printf("%20.2f\n", ((HASHREALOBJ*) obj)->value);
            break; 
      }

    return 1;
}

INT4 mydelete_func(void *obj)
{
  if (obj)
    free (obj);
  return 1;
}



/****** InxHashSearch **************************************************
** 
** 	searches an element in hash table and inserts the element,
** 	if not found. The hash table must be initialized before 
**      in InxOpen. 
** 
** 	INPUT:	    address of keyword [R]
** 		    address of pointer to hash table [R] 
** 		IMPLICIT:
** 
** 	OUTPUT:	    
** 		    returns:	1 if keyword was found
** 				0 if new element was added
*/

static INT4 InxHashSearch (void *value, void *record, HSHo *table)
{
  HASHANYOBJ  *insertObj, *foundObj=NULL;
  BTRoVALUE   *idList;
  INT4        errCode, size;
  FIP         fip;

  /*
  ** construct object to search for depending on index value type.
  ** search for the object in the existing hash table
  */

  switch (indexCurr->valueType) { 
			     
  case BTRxSTR: 
  case BTRxIDENTRY: 
    size = sizeof (HASHSTROBJ) + strlen((char*)value);
    insertObj = (HASHANYOBJ*) malloc (size);
    strcpy (((HASHSTROBJ*) insertObj)->value, (char*)value);
    break; 

  case BTRxNUM: 
    insertObj = (HASHANYOBJ*) malloc (sizeof(HASHNUMOBJ));
    ((HASHNUMOBJ*) insertObj)->value = atol((char*)value);
    break; 

  case BTRxREAL: 
    insertObj = (HASHANYOBJ*) malloc (sizeof(HASHREALOBJ));
    ((HASHREALOBJ*) insertObj)->value = atof((char*)value);
    break; 
  }

  if ((foundObj = HshSearchObject(table, (void*)insertObj))) {
      free((void*)insertObj); 
      InxIdListUpdate(&((HASHANYOBJ*)foundObj)->idList, record); 
  }
  else {
    if (!indexCurr->idsFile)
      indexCurr->idsFile = IdsOpen (indexCurr->fileName, "write", 
				    indexCurr->idsCacheSize,
				    ((IDoENTRY *) record)->idType->nam, &errCode);


    HshInsertObject(table, (void*)insertObj);
    idList = &insertObj->idList;
    fip = IdsInsert (indexCurr->idsFile, (IDoENTRY *) record, 0);
    idList->firstIdFip = idList->lastIdFip = fip;
    idList->idN = 1;
  }
  
/* ERROR HANDLING ????????????? */

  return foundObj ? 1 : 0;
}



/**api* InxInsertStr **********************************************************
** 
**       searches a key in an index and inserts a new node if not found;
** 
** 	INPUT:	    address of index object (INXo) [W]
**                  address of value string [R]
**                  address of ID object [R]
** 		IMPLICIT:
**                  indexCurr (INXo *) current index object [W]
** 
** 	RETURNS:    1 if value was found in tree 
**                  0 if it was newly inserted
*/ 
   
INT4 InxInsertStr (INXo *inx, char *value, IDoENTRY *id)
{
  INT4 rv, errCode;

  /*
  ** ...check index
  */

  if (!inx->isWriteOpen)
    _ErrExit2 (e__notwriteopen, inx->fileName);
  if (!inx->type)
    _ErrExit2 (e__parnotdefined, "index type");
  
  indexCurr = inx;  /** make index object wide */
  
  if (!indexCurr->idsFile)
    indexCurr->idsFile = IdsOpen (indexCurr->fileName, "write", 
				  indexCurr->idsCacheSize,
				  id->idType->nam, &errCode);
  if ((rv = InxHashSearch (value, id, inx->table)))
    inx->valueFoundN++;
  else 
    inx->valueInsertedN++;
  return rv;
}



/****** InxIdListUpdate ******************************************************
** 
** 	updates idList
** 
** 	INPUT:	    pointer to BTRoVALUE
** 		    address of new id-record
** 		IMPLICIT:
**                  indexCurr (INXo *) [W]
** 
** 	RETURNS:
*/ 

static void InxIdListUpdate(BTRoVALUE *idList, void *record)
{
  FIP   fip;

  if (indexCurr->valueType == BTRxIDENTRY)
      return;

  fip = IdsInsert(indexCurr->idsFile, (IDoENTRY*) record, idList->lastIdFip);
  idList->lastIdFip = fip;
  idList->idN++;
}


/****** InxBtreeInsert ******************************************************
** 
**
** 	INPUT:	    pointer to hash table [R]
** 		IMPLICIT:
**                  indexCurr (INXo *) [R]
** 
** 	RETURNS:
*/ 

static void InxBtreeInsert (HSHo *table)
{
  HASHANYOBJ *obj;
  BTRoREC record;
  char       valStr[80];
  INT4 i;

  for (i=0; i < table->cur_hash_elem; i++) {
    obj = (HASHANYOBJ*) table->hash_list[i];
    switch (indexCurr->valueType) {
    case BTRxNUM:
      sprintf (valStr, "%d", ((HASHNUMOBJ*) obj)->value);
      record.str = valStr;
      break;
      
    case BTRxREAL:
      sprintf (valStr, "%f", ((HASHREALOBJ*) obj)->value);
      record.str = valStr;
      break;
      
    case BTRxIDENTRY:
    case BTRxSTR:
      record.str = ((HASHSTROBJ*) obj)->value;
      break;
    }
    record.type = BTRxVALUE;
    memcpy (&record.r.value, &obj->idList, sizeof (BTRoVALUE));
    BtrInsertRecord (&record);
  }
}



/**api* InxSetType ************************************************************
** 
**       searches a key in an index and inserts a new node if not found;
** 
** 	INPUT:	    address of index object (INXo)
**                  index type: "id", "string", "number", "real" [R]
** 		IMPLICIT:
** 
** 	RETURN:	
*/ 

void InxSetType (INXo *inx, char *option)
{
  if (inx->type)
    _ErrExit2 (e__parisdefined, "index type");

  switch (tolower (option[0])) {
  case 'i':
  case 's':
    inx->type = BTRxVALUE;
    inx->valueType = BTRxSTR;
    break;
  case 'n':
    inx->type = BTRxVALUE;
    inx->valueType = BTRxNUM;
    break;
  case 'r':
    inx->type = BTRxVALUE;
    inx->valueType = BTRxREAL;
    break;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
}


/**api* InxSetCache ***********************************************************
** 
**       sets the cache with specified size for the ID-list
** 
** 	INPUT:	    address of index object (INXo)
**                  cache size in ? [R]
** 		IMPLICIT:
** 
** 	RETURN:	
*/ 

void InxSetCache (INXo *inx, INT4 cacheSize)
{
  inx->idsCacheSize = cacheSize;
}




/**api* InxClose **************************************************************
** 
** 	close index  and ids-file (if not INXxID);
** 
** 	INPUT:	    address of index description (INXo) [W]
**              IMPLICIT:
**                  indexCurr (INXo *inx) [W] 
**
**      RETURNS:    1 if success
*/ 
   
INT4 InxClose (INXo *inx)
{
  BTRo *btree;
  INT4  errCode;
  
  if (!inx || /*!inx->valueInsertedN ||*/ !inx->table)
    return 0;

  btree = BtrOpen (inx->fileName, "write", &errCode);
  _ErrExit2 (errCode, FileGetName (btree->file, "path"));

  switch (inx->valueType) {
  case BTRxIDENTRY: 
  case BTRxSTR: 
    BtrSetType (btree, "str");
    break;
  case BTRxNUM: 
    BtrSetType (btree, "num");
    break;
  case BTRxREAL: 
    BtrSetType (btree, "real");
    break;
  }
  
  indexCurr = inx;

  HshSort(inx->table);

  BtrBuildStartPhase1 (btree, inx->valueInsertedN);
  InxBtreeInsert (inx->table);

  BtrBuildStartPhase2 ();
  InxBtreeInsert (inx->table);
  BtrClose (btree);
  if (!inx->idsFile) 
    inx->idsFile = IdsOpen (inx->fileName, "write", 
			    inx->idsCacheSize, "Entry-ID", &errCode);
  IdsClose (inx->idsFile);

  InxDelete (inx);
  return 1;
}


static void InxDelete (INXo *inx)
{
  HshDeleteAll (&inx->table);
  free (inx);
}

/**api* InxOpen ***************************************************************
** 
**      opens an index and return an index object
** 
** 	INPUT:	    name of index file name [R]
**                  option: "new" [R]
** 		IMPLICIT:
** 
** 	RETURNS:	1
*/ 
   
INXo *InxOpen (char *nam, char *option)
{
  INXo     *inx;

  switch (tolower (option[0])) {

  /*
  ** write new index 
  */

  case 'n': 
    if ((inx = (INXo *) calloc (1, sizeof (INXo))) == NULL)
      _ErrExit2 (e__allocfail, "index-object");
    inx->valueType = 0;
    inx->type = 0;
    inx->isWriteOpen = 1;
    strcpy (inx->fileName, nam);
    inx->table = HshNewTable(5013, 70,
		             myhash_func, mycompare_func,
	                     myprint_func, mydelete_func);
    
    break;

  default:
    _ErrExit2 (e__unknownoption, option);
  }

  return inx;
}




 (tolower (option[0])) {

  /*
  ** write new index 
  */

  case 'n': 
    if ((inx = (INXo *) calloc (1, sizeof (INXo))) == NULL)
      _ErrExit2 (e__allocfail, "index-object");
    inx->valueType = 0;
    inx->type = 0;
    inx->isWriteOpen = 1;
    strcpy (inx->fileName, nam);
    inx->table = HshNewTable(5013, 70,
		       srs/src/index.h
**
**    $RCSfile: index.h,v $
**    $Revision: 1.2 $
**    $Date: 1996/11/25 19:42:46 $
**    $Author: etzold $
**
**    $Locker:  $
**    $State: Exp $
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**           Implementing HashTable instead of AVL Tree: Gerald Schaefer
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**     
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/


#define INXxXKEY 80


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  describes an index of all types
*/

typedef struct INXo {

  struct HSHo     *table;          /* hash table */
  char             fileName[133];   /* name of index output file */
  char             patchName[133];   
  INT4              type;           /* index type */
  INT4              valueType;      /* value type */
  INT4              valueInsertedN; /* no of inserted values */
  INT4              valueFoundN;    /* no of times value was found in index */
  INT4              isWriteOpen;    /* flag if index is open for "write" */
  struct IDSoFILE *idsFile;
  struct IDPoFILE *idpFile;
  FIP              idFip;
/*  INT4              avlOff;  obsolete */
/*  INT4              nodeCnt; obsolete */
  INT4              idsCacheSize;
} INXo;


typedef struct IDoENTRY *dummytagIDoENTRYindex;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of exported functions
*/

    /* manipulating indices */

INXo *InxOpen (char *nam, char *option);
INT4 InxClose (INXo *inx);
void InxSetType (INXo *inx, char *option);
void InxSetCache (INXo *inx, INT4 cacheSize);
void InxSetPatch (INXo *inx, char *patchName);

    /* inserting */

INT4 InxInsertStr (INXo *inx, char *value, struct IDoENTRY *id);
FIP InxInsertId (INXo *inx, char *str, struct BTRoID *idRec);

    /* searching */

struct BTRoID *InxSearchId (INXo *inx, char *str, FIP *idFip);

**  prototypes of exported functions
*/

    /* manipulating indices */

INXo *InxOpen (char *nam, char *option);
INT4 InxClose (INXo *inx);
void InxSetType (INXo *inx, char *option);
void InxSetCache (INXo *inx, INT4 cacheSize);
void InxSetPatch (INXo *inx, char *patchName);

    /* inserting */

INT4 InxInsertStr (INXo *inx, char *value, struct IDoENTRY *id);
FIP InxInsertId (INXo *inx, char *str, struct BTRoID *idRec);

    /* searchinsrs/src/library.c
char library_ID[] = "$Id: library.c,v 1.23 1997/03/12 19:07:35 srs Exp $";
/*
**
**    $RCSfile: library.c,v $
**    $Revision: 1.23 $
**    $Date: 1997/03/12 19:07:35 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**             Unix port by Lukas Rosenthaler and Reinhard
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: message, file, sm
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    functions open flat files and indices for read access only - compare 
**    time stamps and retrieve entry information from ID-indices
**
**    Global Parameters:
**        "printf"
**        "parSetFields" - fields are turned on/off by parameters
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include <stdarg.h>
#include <ctype.h>
#include <string.h>

#include "message.h"
#include "futil.h"
#include "sm.h"
#include "strv.h"
#include "lst.h"
#include "tm.h"
#include "btree.h"
#include "sdlget.h"
#include "ids.h"
#include "idx.h"
#include "par.h"
#include "dict.h"
#include "field.h"
#include "appl.h"
#include "library.h"

#define _SRS
#define _SLB
#include SRSINCLUDE


#ifndef TRUE
# define TRUE 1
# define FALSE 0
#endif

#ifdef sun
extern INT4 printf ();
#endif

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  constants and enums
*/

#define	LIBxMAXINXOPEN    10  /* max no of indices opened */
#define	LIBxMAXFILESOPEN  20     /* max no of indices opened */



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  description of a library flat file opened for read access
*/

typedef struct {
  FILEo             *file;     /* file object...opened with FilURead */
  struct SLBo       *lib;      /* address of library object */
  INT4              fileX;     /* index to file within library */
  struct SRSoFILTYP *fileType; /* address of file type object */
} LIBoFLATFILE;



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  static functions
*/

static LibActivate (SLBo *lib);


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  external, global and module wide variables
*/

#ifdef O_WIN
  struct WINo *winBase;
#endif

extern struct SDLo    *oddObjs; /* defined in oddclass.h */
SRSoDB *srsdb;
INT4 SdlGetObjects (long int **obj_n, void ***obj_p, char *sec_nm);
static INT4 LibGetTokenCode (char *tokName);


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  for the 'group' dictionarya
*/

static void* GroupToKey (void* e)
{
  return (*(SRSoGROUP **)e)->com;
}
static CLASSoDICT groupDictClass = {
  (ValComparer)strequal, (ValHasher)strhash, (KeyAccessor)GroupToKey, NULL, 0
};
static DICTv groupDict=NULL;



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  default function for printing lines
*/

static INT4 LibPrint (char *s)
{
  Int4 len;
  
  len = strlen (s);
  if (len) {
    if (s[len-1] != '\n')
      puts (s);
    else
      fwrite (s, len, 1, stdout);
  }
  return 1;
}

static INT4 LibPrintField (char *s, SLBoFIELD *field, void *data)
{
  Int4 len;
  
  len = strlen (s);
  if (len) {
    if (s[len-1] != '\n')
      puts (s);
    else
      fwrite (s, len, 1, stdout);
  }
  return 1;
}

static INT4 LibPrintf (char *formatStr, ...)
{
  va_list ap;

  va_start (ap, formatStr);
  vprintf (formatStr, ap);
  va_end (ap);

  if (formatStr[strlen (formatStr) -1] != '\n')
    putc ('\n', stdout);
  return 1;
}


/**api* LibIndexOpen **********************************************************
**
** 	opens the btree and the ids file (if not ID field) but first checks
**      if these are in a list of up to MAXINXOPEN open files;
** 
** 	INPUT:	    library object [R]
** 		    field object [R] or NULL to open auxilliary index
**                  flag if opening for info only [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    lib index object
**                  or NULL
*/ 

LIBoINDEX *LibIndexOpen ( SLBo *lib, SLBoFIELD *field, INT4 isForInfo)
{
  static LIBoINDEX libInx[LIBxMAXINXOPEN], *libInxPtr; 
  static INT4      libInxCnt = 0;
  BTRo             *btree=NULL;
  IDSoFILE         *idsFile = NULL;
  struct IDXo      *idx = NULL;
  char             indexName[132];
  INT4             errCode, k, isIdIndex;

  if (LibIs (lib, "subentries"))
    lib = LibGetParentLib (lib);

  /*
  ** check if requested index is among those that are already open...index
  ** is defined by library and field objects
  */

  for (k=0;  k < LIBxMAXINXOPEN && k < libInxCnt;  k++) 
    if (lib == libInx[k].lib && field == libInx[k].field) 
      return &libInx[k];

  /*
  ** open both btree and ids file (if ID field also the IDX file
  */

  /* open auxilliary index if field not specified */
  if (!field) {
    LibGetIndexName (lib, NULL, indexName, "read");
    if (!(idx = IdxOpen (indexName, "read", 0, &errCode))) {
      if (!isForInfo)
	_ErrMsg2 (errCode, indexName);
      return NULL;
    }  
  }    
  else {

    LibGetIndexName (lib, field, indexName, "read");
    btree = BtrOpen (indexName, "read", &errCode);
    if (_ErrIs (errCode)) {
      if (!isForInfo)
	_ErrMsg2 (errCode, FileGetName (btree->file, "path"));
      return NULL;
    }
    isIdIndex = 0;
    if (!(idsFile = IdsOpen (indexName, "read", 0, NULL, &errCode))) {
      if (!isForInfo)
	_ErrMsg2 (errCode, indexName);
      return NULL;
    }
    if (_ErrIs (errCode) && !isForInfo) {  /* index is not compressed */
      _ErrMsg2 (errCode, indexName);
      return NULL;
    }
    
    if (FieldIs (field, "id")) {
      isIdIndex = 1;
      if (!(idx = IdxOpen (indexName, "read", lib->maxNameLen, &errCode))) {
	if (!isForInfo)
	  _ErrMsg2 (errCode, indexName);
	return NULL;
      }
      if (LibHasNoFiles (lib))
	LibSetLibFlatFiles (lib, idx);
    }
  }


  /*
  ** get new lib index object ...if all are in use then close btree and
  ** ids file (if opened)
  */

  libInxPtr = &libInx[libInxCnt % LIBxMAXINXOPEN];
  if (libInxCnt++ >= LIBxMAXINXOPEN) {
    if (libInxPtr->btree)
      BtrClose (libInxPtr->btree);
    if (libInxPtr->idsFile) {
      IdsClose (libInxPtr->idsFile);
      libInxPtr->idsFile = NULL;
    }
    if (libInxPtr->idx) {
      IdxClose (libInxPtr->idx);
      libInxPtr->idx = NULL;
    }
  }

  libInxPtr->isIdIndex = isIdIndex;
  libInxPtr->idsFile = idsFile;
  libInxPtr->idx = idx;
  libInxPtr->btree = btree;
  libInxPtr->lib = lib;
  libInxPtr->field = field;

  return libInxPtr;
}

/**API* LibName ***************************************************************
** 
** 	Returns the library name.
** 
** 	INPUT:	    library object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    library name if found
**                  NULL if the library name is unknown
*/ 

char *LibName (SLBo *lib)
{
  return lib->nam;
}

/**API* LibName ***************************************************************
** 
** 	Returns the name of the subentry type.
** 
** 	INPUT:	    subentry type object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    subentry type name
*/ 

char *LibGetSubEntryName (LIBoSUBENTRY *se)
{
  return se->name;
}


/**API* LibGetLinkFromName ****************************************************
** 
** 	Returns the "from" name of a link. This name is usually a databank
**      name but can also be a symbolic one, such as "parent" or "tax_parent".
** 
** 	INPUT:	    link object [R]
**
** 	RETURNS:    the name or empty string if there is none
*/ 

char *LibGetLinkFromName (LINKo *link)
{
  return (link->nam1 ? link->nam1 : "");
}
/**API* LibGetLinkToName *****************************************************
** 
** 	Returns the "to" name of a link. See also LibGetLinkFromName.
** 
** 	INPUT:	    link object [R]
**
** 	RETURNS:    the name or empty string if there is none
*/ 

char *LibGetLinkToName (LINKo *link)
{
  return (link->nam2 ? link->nam2 : "");
}


/**API* LibGetName ************************************************************
** 
** 	Returns the library name in various formats.
** 
** 	INPUT:	    address of library object [R]
** 		    option: "full", "short", "logical" [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    library name if found
**                  NULL if the library name is unknown
*/ 

char *LibGetName (SLBo *lib, char *option)
{
  switch (tolower (option[0])) {
  case 'f':  /* full */
    return lib->nam;
  case 's':  /* short */
    return NULL;
  case 'l':  /* logical */
    return NULL;
  default:
    _ErrExit2 (e__unknownoption, option);
    return NULL;
  }
}

/**API* LibGetPartSize ********************************************************
** 
** 	Returns the part size in number of entries used for 
**      partioning the indexes. Use LibIs with option "partitioned" to find
**      out if library indices should be partitioned.
** 
** 	INPUT:	    library object [R]
** 
** 	RETURNS:    the part size
*/ 

Int4 LibGetPartSize (SLBo *lib)
{
  return lib->partSize;
}

/**API* LibGetIcarusFileName **************************************************
** 
** 	Returns the name of the icarus file which has the specified 
**      information for a library. The function uses information in
**      the section if specified otherwise it makes an 'educated guess' so
**      the file with the returned name is not guaranteed to exist.
** 
** 	INPUT:	    address of library object [R]
** 		    option: "info", "syntax", "structure" [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    the full file name (path)
*/ 

char *LibGetIcarusFileName (SLBo *lib, char *option)
{
  static STRv name=NULL;
  char tmp[100];

  if (!name)
    name = StrNew ();
  else
    StrClear (&name);

  strcpy (tmp, LibName (lib));
  SmEdit (tmp, SMxLOWCASE);
  StrSetS (&name, "SRSDB:");
  StrAppS (&name, tmp);
  switch (tolower (option[1])) {
  case 'n':  /* info */
    StrAppS (&name, ".it");
    break;
  case 'y':  /* syntax */
    StrAppS (&name, ".is");
    break;
  case 't':  /* structure */
    StrAppS (&name, ".i");
    break;
  default:
    _ErrExit2 (e__unknownoption, option);
    return NULL;
  }
  return _Str(name);
}




/**API* LibGetGroupName *******************************************************
** 
** 	Returns the library group name in various formats.
** 
** 	INPUT:	    address of library object [R]
** 		    option: "full", "short" [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    library name if found
**                  NULL if the library name is unknown
*/ 

char *LibGetGroupName (SRSoGROUP *group, char *option)
{
  switch (tolower (option[0])) {
  case 'f':  /* full */
    return group->com;
  case 's':  /* short */
    return group->short_nm;
  default:
    _ErrExit2 (e__unknownoption, option);
    return NULL;
  }
}

/**API* LibGetFieldName *******************************************************
** 
**      obsolete: see FieldGetName<BR>
** 	Returns the name of a data-field. Returns "unknown" if the field
**      name could not be found. See also LibGetFieldTypeName.
** 
** 	INPUT:	    address of field object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    field name
*/ 

char *LibGetFieldName (SLBoFIELD *field)
{
  static char unknown[30] = "unknown field";

  if (field && field->type && field != (SLBoFIELD *) 1L) {
    if (field->type->ityp == SRSxHEADER)
      return (field->name);
    else 
      return field->type->nam;
  }
  else
    return unknown;
}

/**API* LibGetFieldTypeName ***************************************************
** 
** 	Returns the name of a data-field type. 
** 
** 	INPUT:	    address of field type object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    field name
*/ 

char *LibGetFieldTypeName (SRSoFLD *type)
{
  return type->nam;
}

/**API* LibGetFieldShortName **************************************************
** 
**      obsolete: see FieldGetShortName<BR>
** 	Returns the short name of a data-field. 
** 
** 	INPUT:	    address of field object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    short field name
*/ 

char *LibGetFieldShortName (SLBoFIELD *field)
{
  if (field->type->ityp == SRSxHEADER)
    return (field->name);
  else 
    return field->type->shortn;
}

/**api* function **************************************************************
** 
**      Returns the max name length of the entry used for the ID index.
** 
** 	INPUT:	    address of library object [R]
** 
** 	RETURNS:    max name length
*/ 

Int4 LibGetMaxNameLength (SLBo *lib)
{
  return lib->maxNameLen;
}
/**api* function **************************************************************
** 
**      Returns the type describing which part of the file name is to be
**      stored in the ID record of an entry. Only one of possibly several
**      file types of a library can specify a name to be saved.
** 
** 	INPUT:	    address of library object [R]
** 
** 	RETURNS:    max name length
*/ 

Int4 LibGetSaveNameType (SLBo *lib)
{
  SRSoFILTYP *ft;
  Int4       c;
  
  for (c=0; (ft=LibNextFileType (lib, &c));)
    if ((ft->saveNameLength))
      return ft->saveName;
  return 0;
}

/**api* function **************************************************************
** 
**      Returns the max length of part of the file name that is to be
**      stored in the ID record of an entry. Only one of possibly several
**      file types of a library can specify a name to be saved.
** 
** 	INPUT:	    address of library object [R]
** 
** 	RETURNS:    max name length
*/ 

Int4 LibGetSaveNameLength (SLBo *lib)
{
  SRSoFILTYP *ft;
  Int4       c, len;
  
  for (c=0; (ft=LibNextFileType (lib, &c));)
    if ((len=ft->saveNameLength))
      return len;
  return 0;
}



/**API* LibGetFieldIType ******************************************************
** 
**      obsolete: see FieldGetIndexType<BR>
** 	Returns the index type of a field as string.
** 
** 	INPUT:	    address of field object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    field name
**                  NULL
*/ 

char *LibGetFieldIType (SLBoFIELD *field)
{
  static char *fieldIType[10]={"", "id", "index", "link", "show",
                                      "tree", "num", "real", "group"};
  return fieldIType[field->index];
}


/**api* LibOpenFlatFile *******************************************************
** 
** 	Opens a flat file.
** 	More than one file may be open at a time - 
**      so if limit is exceeded some files
** 	have to be closed again;
**      selects global "library"
**      If a file could not be opened it will be marked bad - so no attempt
**      will be done to open it again.
** 
** 	INPUT:	    address of library object [W]
** 		    file index [R]
** 		    file type object [R]
**                  pointer to address of file object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if file was opened
**                  2 if already open
**                  file could not be opened: e__filnotok <name> +
**                  file is known to be 'unopenable': e__badfile <name> 
*/ 

FILEo *LibOpenFlatFile (SLBo *lib, INT4 fileX, SRSoFILTYP *ft, INT4 *errCode)
{
  static LIBoFLATFILE openFiles[LIBxMAXFILESOPEN]; 
  static INT4  count = 0;
  FILEo        *file;
  LIBoFLATFILE *openFile;
  char         fileName[FILxXNAM+1], *dirName;
  INT4         k, c;

  if (LibIs (lib, "subentries"))
    lib = LibGetParentLib (lib);

  /*
  ** check first if the file is already opened ...find out by comparing
  ** the library and the file index;
  */

  for (k=0;  k < LIBxMAXFILESOPEN;  k++) {	
    if (lib == openFiles[k].lib && fileX == openFiles[k].fileX 
	&& ft ==  openFiles[k].fileType) 
      return openFiles[k].file;
  }

  /*
  ** return error if there were previous unsuccessful attempts to open
  */

  if (lib->fil[fileX].isBad) {
    if (errCode)
      *errCode = e__badfile;
    return NULL;
  }

  /*
  ** get the next 'openfile' object in the ring
  */

  openFile = &(openFiles[count++ % LIBxMAXFILESOPEN]);
  if (!openFile->file)
    openFile->file = FileNew(NULL);
  file = openFile->file;

  /* iterate over directory names - first can be empty! */
  for (c=0, k=0; (dirName = LibGetNextFlatFileDirName (lib, &c)) || !k; k++) {
    if (!dirName)
      dirName ="";
    FileSetName (file, "dir", dirName);
    FileSetName (file, "name", lib->fil[fileX].nam);
    FileSetName (file, "ext", ft->typ_nm);
    FileSetMaxLine (file, ft->ln_z);
    if (!FileOpen (file)) {
      lib->fil[fileX].isBad = 1; /* don't try again to open it */
      _ErrMsg2 (e__filnotok, FileGetName (file, "path"));
      return NULL;
    }
    else
      break;
  }

  openFile->lib   = lib;    
  openFile->fileX = fileX;    
  openFile->fileType = ft;
  return file;
}


/**api* LibGetFileType ********************************************************
** 
**      Returns the file type object with the specified name or the first
**      in the list if no name was specified. See also LibNextFileType.
**      If the file type name is not specified then the first file type
**      is returned.
** 
** 	INPUT:	    the library object [R]
**                  symbolic name of the file stream (or NULL) [R]
**                  pointer to the index of the file type object (or NULL) [W]
** 
** 	RETURNS:    the file type object
**                  NULL: not found
*/ 
   
SRSoFILTYP *LibGetFileType (SLBo *lib, char *name, Int4 *index)
{
  SRSoFILTYP *ft;
  Int4       c=0, k;

  if (LibIs (lib, "subentries"))
    lib = LibGetParentLib (lib);

  for (c=0, k=0; (ft=LibNextFileType (lib, &c)); k++) {
    if (!name)
      return ft;
    if (SmEqs (LibGetFileTypeName (ft), name)) {
      if (index)
	*index = k;
      return ft;
    }
  }
  return NULL;
}

/**api* LibNextFileType ****************************************************** 
**
**      Can be used to iterate over all file types specified for a databank.
**      Eg, GCG formatted EMBL has two file types: one for the file with
**      the annotation and one for the sequence file. See also LibGetFileType.
** 
** 	INPUT:	    the library object [R]
**                  pointer to iterator which must be set to 0 to start [W]
** 
** 	RETURNS:    the file type object
**                  NULL: end of iteration
*/ 
   
SRSoFILTYP *LibNextFileType (SLBo *lib, Int4 *c)
{
  if (LibIs (lib, "subentries"))
    lib = LibGetParentLib (lib);

  if (*c >= 2 || *c < 0 || !lib->form->fil_t[*c]) {
    *c = 0;
    return NULL;
  }
  return lib->form->fil_t[(*c)++];
}

/**api* LibGetFileTypeName ****************************************************
**
**      Returns the name of the file type object.
** 
** 	INPUT:	    the file type object [R]
**
** 	RETURNS:    the file type name
*/ 
   
char *LibGetFileTypeName (SRSoFILTYP *ft)
{
  return ft->name;
}

/**api* LibGetFileTypeFipName *************************************************
**
**      Returns the name variable which stores the file pointer obtained
**      by parsing the entry.
** 
** 	INPUT:	    the file type object [R]
**
** 	RETURNS:    a variable name
*/ 
   
char *LibGetFileTypeFipName (SRSoFILTYP *ft)
{
  return ft->fipVar;
}

/**api* LibGetFileTypeTokenTableName ******************************************
**
**      Returns the name of the token table with the field tokens parsed 
**      from the file with specified file type.
** 
** 	INPUT:	    the file type object [R]
**
** 	RETURNS:    a token table name
*/ 
   
char *LibGetFileTypeTokenTableName (SRSoFILTYP *ft)
{
  return ft->fieldTokens;
}

SRSoFILTYP *LibGetFileTypeSharesFile (SLBo *lib, SRSoFILTYP *ft, Int4 *index)
{
  SRSoFILTYP *tmp;
  Int4       c=0, k;

  if (LibIs (lib, "subentries"))
    lib = LibGetParentLib (lib);

  if (ft->shareWith) {
    for (c=0, k=0; (tmp=LibNextFileType (lib, &c)); k++) {
      if (tmp == ft->shareWith) {
	*index = k;
	return tmp;
      }
    }
  }
  return NULL;
}


/**api* LibOpenNextFlatFile ***************************************************
** 
**      Opens the next flat file.
** 
** 	INPUT:	    the library object [R]
**                  address of file object (set to NULL the first time) [W]
**                  the file type object [R]
** 
** 	RETURNS:    1: next entry is in current file
**                  2: new flat file was opened
**                  0: end of the input stream (no more flat files)
**                 -1: failure during open
*/ 
   
Int4 LibOpenNextFlatFile (SLBo *lib, FILEo **file, SRSoFILTYP *ft, Int4 *fileX)
{
  Int4 rv;

  if (!*file || FileIsEof (*file)) {
    if (++(*fileX) >= lib->nfil)
      return 0;
    if ((*file = LibOpenFlatFile (lib, *fileX, ft, &rv))) 
      return 2;
    else {
      _ErrExit (e__eof);
      return -1;
    }
  }    
  return 1;
}

/**api* LibOpenNextEntryFile **************************************************
** 
**      Opens the next file that matches a search expression specified
**      by the library object. To begin start with file set to NULL.
**      The file object holds the iteration context itself.
** 
** 	INPUT:	    the library object [R]
**                  address of file object (set to NULL the first time) [W]
**                  the file type object [R]
** 
** 	RETURNS:    number of files in the iteration
*/ 
   
Int4 LibOpenNextEntryFile (SLBo *lib, FILEo **file, SRSoFILTYP *ft)
{
  char *tmp;
  Int4 c;

  if (!*file) {
    *file = FileNew (NULL);
    FileSetMaxLine (*file, ft->ln_z);
    if (*ft->pipe)
      FileSetPipe (*file, ft->pipe);
    
    c=0; tmp = LibGetNextFlatFileDirName (lib, &c); 
    FileSetName (*file, "dir", tmp ? tmp : "");
    FileSetName (*file, "name", *ft->searchName ? ft->searchName : "*");
    if (!*ft->searchName)
      FileSetName (*file, "ext", ft->typ_nm);
  }

  /* construct file name */

  return FileNext (*file);
}

   
/**api* LibOpenEntryFile ******************************************************
** 
**      Opens the file that matches a search expression specified
**      by the library object. To begin start with file set to NULL.
**      The file object holds the iteration context itself.
** 
** 	INPUT:	    the library object [R]
**                  address of file object (set to NULL the first time) [W]
**                  the file type object [R]
** 
** 	RETURNS:    number of files in the iteration
*/ 
   
Int4 LibOpenEntryFile (SLBo *lib, FILEo **file, SRSoFILTYP *ft, char *name)
{
  Int4 c;
  char tmp[100]="", *t;

  /*SmEdit (name, SMxLOWCASE);*/
  if (!*file) {
    *file = FileNew (NULL);
    FileSetMaxLine (*file, ft->ln_z);
    if (*ft->pipe)
      FileSetPipe (*file, ft->pipe);
    
    c=0; t = LibGetNextFlatFileDirName (lib, &c); 
    FileSetName (*file, "dir", t ? t : "");
    FileSetName (*file, "name", name);
    FileSetName (*file, "ext", ft->typ_nm);

    /* complete or partial file name has been saved */
    if ((LibGetSaveNameLength (lib))) {
      switch (LibGetSaveNameType (lib)) {
      case LIBxFILE:
	FileSetName (*file, "file", name);
	break;
      case LIBxNAME:
	FileSetName (*file, "name", name);
	break;
      case LIBxPATH:
	FileSetName (*file, "path", name);
	break;
      }
    }  
    return FileNext (*file); 
  }
  return 1;
}

/**api* function **************************************************************
** 
**      Writes an entry record into a buffer which can then be appended to 
**      the IDX file.
**
** 	INPUT:	    address entry-object [R]
**                  address of write buffer (must be allocated) [W]
*/ 

Int4 LibGetIdRecordSize (SLBo *lib)
{
  Int4 size;

  size = LibGetMaxNameLength (lib) + 1;
  size += 8; /* size for two file pointers is default */
  size += 4; /* index into the $file list */
  size += LibGetSaveNameLength (lib) + 1;
  return size;
}



/**api* LibGetEntryAuxInfo ****************************************************
** 
** 	Retrieves a record with auxilliary information.
** 
** 	INPUT:	    file pointer in to node in ID-index [R]
**                  library object [R]
**                  initialized buffer object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
*/ 
   
INT4 LibGetEntryAuxInfo (UINT4 fip, SLBo *lib, SMoBUFF *buff)
{
  LIBoINDEX *libInx;

  if (!(libInx = LibIndexOpen (lib, NULL, 0)))
    _ErrRet (e__error);

  IdxGetBuff (libInx->idx, fip, buff);
  return 1;    
}


/**api* LibSetField ***********************************************************
**
**      selects a field-type for processing; field type can be specified
**      directly or through a library - field type is only switched on if a 
**      library (if specified) points to it; 
**
**	INPUT:	 o  name of library [R] 
**		 o  name of field type [R] or NULL 
**               o  option: "init"     - all fields are turned off<BR>
**                          "set"      - field is turned on [R]<BR>
**                          "unset"    - specified field is turned off<BR>
**                          "xinit"    - same as "init" but ID-field is 
**                                       turned on...init for indexing<BR>
**                          "readlink" - turns on ID field + link fields<BR>
**                          "allindex" - all index fields are turned on<BR>
**                          "compress" - all compressable index fields are 
**                                       turned on<BR>
**                          "entry"    - all fields of entry are turned on
**	        IMPLICIT:
**
**	RETURNS:    1 if field was set (ie, was not set before);
**		    0 if not
*/ 

INT4 LibSetField (char *libName, char *fieldName, char *option)
{
  SLBo      *lib;
  SLBoFORM  *form;
  SLBoFIELD *field;
  SRSoFLD   *fieldTypeCurr, *fieldType=NULL;
  INT4       k, setF = 0;

  /*
  ** get objects for library [and fieldtype]
  */

  if (!(lib = (SLBo *) LibObjByName ("library", libName)))
    _ErrExit3 (e__objectunknown, "library", libName);

  if (fieldName) {
    if ((field = LibHasFieldNamed (lib, fieldName)))
      fieldType = field->type;
    else 
      _ErrExit3 (e__objectunknown, "data-field", fieldName);
  }
  /*
  ** loop over all data-fields of selected library
  ** and set or unset the "do" flag
  */

  form = lib->form;
  for (k=0;  k < form->nf;  k++) {
    field = &(form->f[k]);
    fieldTypeCurr = field->type; 
      
    switch (tolower (option[0])) {
    case 'u':  /* unset */ 
      if (fieldType != fieldTypeCurr)  /* otherwise fall through case */  
	break;
    case 'i':  /* init */
      field->do_f = 0;
      break;
    case 's':  /* set */
      if (fieldType == fieldTypeCurr && !field->do_f) {
	field->do_f = 1;
	setF = 1;
      }
      break;
    case 'r':  /* readlink */
      field->do_f = (field->index==SRSxID || field->index == SRSxLINK) ? 1 : 0;
      break;
    case 'x':  /* xinit */
      field->do_f = (field->index == SRSxID) ? 1 : 0;
      break;
    case 'a':  /* allindex */
    case 'c':  /*compress */
      if (FieldIs (field, "index")) {
	field->do_f = 1;
	setF = 1;
      }  
      break;
    case 'e':  /* entry */
      field->do_f = 1;
      setF = 1;
      break;
    default:
    _ErrExit2 (e__unknownoption, option);
    }
  }
  return setF;
}


/****** LibSetActiveFields ****************************************************
**
** 	sets fields to be listed within entry list by what is specified in
**      the global parameter list;
** 
** 	INPUT:	    address of library descr. [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
*/ 
   
void LibSetActiveFields (SLBo *lib)
{
  SLBoFORM	*form;
  SLBoFIELD	*df;
  INT4		k;

  if (!(ParGetBool ("parSetFields")))
    return;
      

  form = lib->form;
  form->access_f = FALSE;
  for (k=0;  k < form->nf; k++) { 
    df = &form->f[k];
    df->do_f = ParGetBool (df->type->nam) ? TRUE : FALSE;
    if (df->do_f)
      form->access_f = TRUE;
    }
}




/****** LibFieldIsActive ******************************************************
** 
** 	checks if certain field is to be processed;
** 
** 	INPUT:	    library object [R]
**                  field index [R]
**                  pointer to flag if field is first in entry [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    FALSE if not
** 		    TRUE if yes
*/ 
   
INT4 LibFieldIsActive (SLBo *lib, INT4 fieldInx, INT4 *isFirst)
{
  SLBoFIELD *field;

  field = &(lib->form->f)[fieldInx];
  
  if (FieldIs (field, "id")) { /* or the ID field is first field */
    *isFirst = TRUE;
    return 1;	
  }
  
  *isFirst = FALSE;
  if (field->do_f) 
    return 1;
  
  return 0;
}



/**api* LibHasField ***********************************************************
**
** 	Checks if library has field with specified type and returns it.
**      See also LibHasFieldNamed to get a field by name and LibGetFieldType.
** 
** 	INPUT:	    library object [R]
** 		    field type object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    the field object
** 		    NULL: not found
*/ 
   
SLBoFIELD *LibHasField (SLBo *lib, SRSoFLD *fieldType)
{
  SLBoFIELD *field;
  Int4 k;
  
  for (k=0;  k < lib->form->nf;  k++) {
    field = &lib->form->f[k];
    if (field->type == fieldType)
      return field;
  }
  return NULL;
}

/**api* LibHasFieldNamed ******************************************************
**
** 	Checks if library has field with specified name returns it.
**      Function assumes that the library has only ONE field with that
**      name.
**      See also LibHasField, LibGetFieldType, LibGetIdField, LibSetField, 
**      LibNextFieldInGroup, LibNextField, LibNextGroupField,
**      LibGetFieldWithCode.
** 
** 	INPUT:	    library object [R]
** 		    long or short field name [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    the field object
** 		    NULL: not found
*/ 
   
SLBoFIELD *LibHasFieldNamed (SLBo *lib, char *name)
{
  SLBoFIELD *field;
  SRSoFLD   *fieldType;
  Int4      c;
  
  for (c=0; (fieldType = LibNextFieldType (name, &c));) {
    if ((field = LibHasField (lib, fieldType)))
      return field;
  }
  return NULL;
}



/**api* LibGetFieldType *******************************************************
**
** 	checks if data-field for specified library or library group exists 
**      and return pointer to 
**      the data-field type object; field name can be the short name or the 
**      full name. See also LibFieldType.
**  
** 	INPUT:	    library name [R]
**                  field name [R]
**  
** 	RETURNS:    field type object
** 		    NULL: not found
*/   

SRSoFLD *LibGetFieldType (char *lib_nm, char *field_nm)
{
  SRSoFLD    *df_t;
  SRSoGROUP  *libgroup;
  SLBo       *lib;
  INT4        k;

  if (!LibGetLibGroup (lib_nm, &libgroup, &lib))
    return NULL;

  /*
  ** name of a library was specified 
  */

  if (lib != NULL)
    for (k=0;  k < lib->form->nf;  k++) {
      df_t = lib->form->f[k].type;
      if (SmEqs (field_nm, df_t->shortn) || SmEqs (field_nm, df_t->nam))
	return df_t;
    }

  /*
  ** else fields of the library group must be checked
  */

  else
    exit (0);

  return NULL;
}

/**api* LibFieldType **********************************************************
**
**      obsolete: see FielGetType<BR>
** 	Returns for a field object the object describing its type. See also
**      LibGetFieldType.
**  
** 	INPUT:	    field object [R]
**  
** 	RETURNS:    field type object
*/   

SRSoFLD *LibFieldType (SLBoFIELD *field)
{
  return field->type;
}


/**api* LibGetIdField *********************************************************
**
**      returns the ID field object of specified library;
**  
** 	INPUT:	    library object [R]
** 		IMPLICIT: 
**  
** 	RETURNS:    data-field object 
** 		    NULL
*/   

SLBoFIELD *LibGetIdField (SLBo *lib)
{
  INT4 context;
  SLBoFIELD *field;

  if (LibIs (lib, "subentries"))
    lib = LibGetParentLib (lib);
  
for (context=0; (field = LibNextField (lib, &context)); )
    if (FieldIs (field, "id"))
      return field;
  return NULL;
}


/****** LibAlias **************************************************************
**
**	checks if an alias name (library name or logical name for either the 
**      library itself or for a single of its flatfiles) corresponds to a 
**      libary;
**
**	INPUT:	    alias name [R]
**	        IMPLICIT: 
**
**	RETURNS:    pointer to the library 
**		    NULL if not found
*/ 

SLBo *LibAlias (char *lib_nm)
{
  SRSoGROUP *group;
  SLBo      *lib;
  INT4      l, c1, c2; 

  for (c1=0; (group = LibNextLibGroup (&c1)); )
    for (c2=0; (lib = LibNextLib (group, &c2)); ) {
      if (!lib->isActive)
	continue;  /* library is not active */

      if (SmEqs (lib->nam, lib_nm))
	return lib;
      
      for (l=0;  l < lib->nfil;  l++)
	if (SmEqs (lib->fil[l].lnam, lib_nm))
	  return lib;
      
      for (l=0;  *(lib->lnam[l]) != '\0';  l++) /* search all lib names */
	if (SmEqs (lib->lnam[l], lib_nm))
	  return lib;
    }
  return NULL;
}

/**api* LibNextFieldInGroup ***************************************************
**
**	Iterates for specified library over all fields that belong to
**      specified field group.
**
**	INPUT:	    library object [R]
**                  group field object [R]
**                  address of iterator [W} must be set to 0 to start
**
**	RETURNS:    address of field object 
**		    NULL: the list has been exhausted
*/ 

SLBoFIELD *LibNextFieldInGroup (SLBo *lib, SLBoFIELD *fieldGroup, Int4 *c)
{
  SLBoFIELD *field;

  while ((field = LibNextField (lib, c)))
    if (fieldGroup->type == field->type->group)
      return field;

  *c = 0;
  return NULL;
}





/**api* LibGetLibGroup ********************************************************
** 
**  	takes either library group name and library name and returns address
**  	of library and libgroup (library name) or only libgroup;
**      comparison is case insensitive; sets "library" to NULL if name of
**      library group.<P>
**      function is also useful for testing if library or group names are 
**      valid!
**  
**  	INPUT:	    address of name [R]
**                  address of pointer to libgroup descr. [W] or NULL
**                  address of pointer to library descr. [W] or NULL
**  	        IMPLICIT:
**  		    srsdb (SRSoDB *) [R]
**  
**  	RETURNS:    1 if name found 
**  		    0 if not
*/ 
   
INT4 LibGetLibGroup (char *nam, SRSoGROUP **libgroup, SLBo **library)
{
  SRSoGROUP *group;
  SLBo      *lib;
  INT4	    c1, c2; 

  /*
  ** if name is from a library group set "library" to NULL and return
  */

  for (c1=0; (group = LibNextLibGroup (&c1)); )
    if (SmEqs (nam, group->short_nm) ||
	SmEqs (nam, group->com)) { 
      if (libgroup) 
	*libgroup = group;
      if (library)
	*library = NULL;
      return 1; 
    } 
  
  for (c1=0; (group = LibNextLibGroup (&c1)); )
    for (c2=0; (lib = LibNextLib (group, &c2)); ) {
      if (!lib->isActive)
	continue;  /* library is not active */
      if (SmEqs (nam, lib->nam)) {
	if (!library)
	  return 1;
	*library = lib;
	break;
      }
    }
  
  if (!library || *library == NULL)
    return 0;			 /* name not known	    */
  
  /*
  ** find library's group
  */

  for (c1=0; (group = LibNextLibGroup (&c1)); ) {
    *libgroup = group;
    for (c2=0; (lib = LibNextLib (group, &c2)); ) {
      if (lib == *library)
	return 1;
    }
  }
  return 1;
}



/**api* LibRegisterObj ********************************************************
** 
**  	Registers an object so that it can be retrieved again by "LibObjByName"
**  
**  	INPUT:	 o  name of class: "library", "fieldtype", "group" 
**                  "parser", "idtype", "arglist", "expression", 
**                  "environment", "syntax" [R]
**  		 o  pointer to object [R] or NULL to initialize dictionary
**  	        IMPLICIT:
**  
**  	RETURNS:    pointer to object
**  		    NULL if not found
*/ 
   
void LibRegisterObj (char *className, void *obj)
{
  INT4 c;
  SRSoGROUP *group;

  switch (tolower (className[2])) {
      case 'o':  /* group */
    if (!groupDict) {
      groupDict = DictCreate (&groupDictClass);
      for (c=0; (group = LibNextLibGroup (&c)); )
	DictSet (&groupDict, group->com, SRSoGROUP*) = group;
    }
    if (obj)
      DictSet (&groupDict, ((SRSoGROUP*) obj)->com, SRSoGROUP*) = 
      (SRSoGROUP*) obj;
    break;
  default:
    _ErrExit2 (e__unknownnam, className);
  } 
}


/**api* LibObjByName **********************************************************
** 
**  	returns pointer to object with specified name from specified
**  	object class; case insensitive!
**  
**  	INPUT:	 o  name of class: "library", "fieldtype", "group" 
**                  "parser", "idtype", "arglist" 
**                  "environment", "syntax", "application" [R]
**  		 o  name of object [R]
**  	        IMPLICIT:
**  		    srsdb (SRSoDB *) [R]
**  
**  	RETURNS:    pointer to object
**  		    NULL if not found
*/ 
   
void *LibObjByName (char *class_nm, char *objName)
{
  Iter i;
  INT4 k;
  
  switch (tolower (class_nm[2])) {
    
  case 'o':  /* group */
    if (!groupDict)
      LibRegisterObj ("group", NULL);
    i = DictWith (groupDict, objName);
    return i ? DictIn (i, SRSoGROUP*) : NULL;
    break;
  case 'b':  /* library */
    for (k=0; k < srsdb->nslb; k++) {
      if (!srsdb->slb[k].isActive)
	continue;  /* library is not active */
      if (SmEqs (objName, srsdb->slb[k].nam)) 
	return (void *) &srsdb->slb[k];
    }
    break;
  case 'e':  /* fieldtype */
    for (k=0; k < srsdb->nfld; k++)  /* long name */
      if (SmEqs (objName, srsdb->fld[k].nam))
	return (void *) &srsdb->fld[k];
    for (k=0; k < srsdb->nfld; k++)   /* short name */
      if (SmEqs (objName, srsdb->fld[k].shortn))
	return (void *) &srsdb->fld[k];
    break;
  case 't':  /* idtype */
    for (k=0; k < srsdb->niddsc; k++) 
      if (SmEqs (objName, srsdb->iddsc[k].nam)) 
	return (void *) &srsdb->iddsc[k];
    break;
  case 'g':  /* arglist */
    for (k=0; k < srsdb->commandN; k++)
      if (!strcmp (objName, srsdb->command[k].name))
	return (void *) &srsdb->command[k];
    break;
  case 'v':  /* environment */
    for (k=0; k < srsdb->environmentN; k++) 
      if (SmEqs (objName, srsdb->environment[k].name)) 
	return (void *) &srsdb->environment[k];
  case 'n':  /* syntax */
    for (k=0; k < srsdb->syntaxN; k++) 
      if (SmEqs (objName, srsdb->syntax[k].name)) 
	return (void *) &srsdb->syntax[k];
  case 'p':  /* application */
    for (k=0; k < srsdb->applicationN; k++) 
      if (SmEqs (objName, ApplGetName (&srsdb->application[k]))) 
	return (void *) &srsdb->application[k];
  default:
    _ErrExit2 (e__unknownnam, class_nm);
  } 
 return NULL;
}

/**api* LibNextFieldType ******************************************************
** 
**  	Returns the next field type with the specified long or short name.
**  
**  	INPUT:	 o  name of class: "library", "link" "fetch" [R]
**  		 o  object-ID [R]
**  	        IMPLICIT:
**  		    srsdb (SRSoDB *) [R]
**  
**  	RETURNS:    pointer to object
**  		    NULL if not found
*/ 

SRSoFLD *LibNextFieldType (char *name, Int4 *c)
{
  for (; *c < srsdb->nfld; (*c)++) 
    if (SmEqs (name, srsdb->fld[*c].nam) ||
	SmEqs (name, srsdb->fld[*c].shortn))
      return &srsdb->fld[(*c)++];

  /* not found */
  *c = 0;
  return NULL;
}


/**api* LibObjById **********************************************************
** 
**  	returns pointer of object with specified object-ID from specified
**  	object class; case insensitive!
**  
**  	INPUT:	 o  name of class: "library", "link" "fetch" [R]
**  		 o  object-ID [R]
**  	        IMPLICIT:
**  		    srsdb (SRSoDB *) [R]
**  
**  	RETURNS:    pointer to object
**  		    NULL if not found
*/ 
   
void *LibObjById (char *class_nm, INT4 objId)
{
  switch (tolower (class_nm[2])) {
  case 'b':  /* library */
    if (objId < 256 && objId > 0)
      return (void *) srsdb->libTable[objId];
    break;
  case 'n':  /* link */
    if (objId < srsdb->nlnk)
      return (void *) &(srsdb->lnk)[objId];
    break;
  default:
    _ErrExit2 (e__unknownnam, class_nm);
  } 
 return NULL;
}

static INT4 LibGetTokenCode (char *tokName)
{
  /* separate 'tokentable|code' into two fields */
  for (; *tokName && *tokName != '|'; tokName++)
    ;
  if (*tokName == '|') {
    *tokName = '\0';
    return TokStrToCode (tokName+1);
  }
  return -1;
}


/**api* LibActiveLinks ********************************************************
** 
**  	marks links between active libraries; sets link names to library names;
**  
**  	INPUT:
**  	        IMPLICIT:
**  		    srsdb (SRSoDB *) [R]
**  
**  	RETURNS:    1
*/ 
   
INT4 LibActiveLinks ()
{
  SRSoGROUP  *group;
  SLBo	     *lib;
  LINKo      *link;
  IDoTYPE    *idType = (IDoTYPE*) LibObjByName ("idtype", "Entry-ID");
  INT4	     c1, c2, k; 

  for (k=0;  k < srsdb->nslb;  srsdb->slb[k++].upd_f=FALSE)
    ;

  for (c1=0; (group = LibNextLibGroup (&c1)); )
    for (c2=0; (lib = LibNextLib (group, &c2)); ) 
      lib->upd_f = 1;	    

  for (k=0; k < srsdb->nlnk; k++) { /* can't use the function LibNextLink! */
    link = &srsdb->lnk[k];
    if (LinkIsMapsToParent (link))
      link->isActive = TRUE;
    else if (!link->lib2)
      link->isActive = FALSE;
    else if (!link->lib1) /* parent links */ 
      link->isActive = TRUE;
    else {
      if (!link->lib1->upd_f || !link->lib2->upd_f) 
	link->isActive = FALSE;
      else {
	if (!link->id1_d)
	  link->id1_d = idType;
	if (!link->id2_d)
	  link->id2_d = idType;
	if (!*link->nam1)
	  link->nam1 = link->lib1->nam;
	if (!*link->nam2)
	  link->nam2 = link->lib2->nam;
	link->isActive = TRUE;
	link->tokCode = LibGetTokenCode (link->token);
      }
    }
  }    
  return 1;
}


/**api* LibIsIdField **********************************************************
**
** 	returns TRUE if the specified field is an ID field;
** 
** 	INPUT:	    library name [R]
**                  data-field type name [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
** 		    0
*/ 
   
INT4 LibIsIdField (char *libName, char *fieldName)
{
  SLBo      *lib;
  SLBoFIELD *field;
  INT4      c;
  
  if (!(lib = (SLBo *) LibObjByName ("library", libName)))
    _ErrExit3 (e__objectunknown, "data bank", fieldName);

  for (c=0; field = LibNextField (lib, &c);)
    if(SmEqs(field->type->nam,fieldName)||SmEqs(field->type->shortn,fieldName))
      return (field->index == SRSxID) ? 1 : 0;
  return 0; 
}


/**api* LibIsFieldType ********************************************************
**
** 	returns TRUE if the specified field is of specified type;
** 
** 	INPUT:	    field object [R]
**                  type: "index", "ID", "link", "show", "num", "real" 
**                        "group", "active" [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
** 		    0
*/ 
   
INT4 LibIsFieldType (SRSoFLD *fType, char *option)
{
  switch (tolower (option[1])) {
  case 'n':  /* index */
    return (fType->ityp == SRSxID || fType->ityp == SRSxKEY ||
            fType->ityp == SRSxNUM || fType->ityp == SRSxREAL) ? 1 : 0;
  case 'd':  /* ID */
    return (fType->ityp == SRSxID) ? 1 : 0;
  case 'i':  /* link */
    return (fType->ityp == SRSxLINK) ? 1 : 0;
  case 'h':  /* show */
    return (fType->ityp != SRSxGROUP) ? 1 : 0;
  case 'o':  /* doquery */
    return (fType->ityp == SRSxID || fType->ityp == SRSxKEY ||
            fType->ityp == SRSxNUM || fType->ityp == SRSxREAL ||
	    fType->ityp == SRSxGROUP) ? 1 : 0;
  case 'u':  /* num */
    return (fType->ityp == SRSxNUM) ? 1 : 0;
  case 'e':  /* real */
    return (fType->ityp == SRSxREAL) ? 1 : 0;
  case 'r':  /* group */
    return (fType->ityp == SRSxGROUP) ? 1 : 0;
  case 'c':  /* active */
    return (ParGetBool (fType->nam));
  default:
    _ErrExit2 (e__unknownoption, option);
  }
  return 0;
}



/**API* LibGetSubEntryField ***************************************************
**
** 	Exchanges a field object for the parent entry for the one the 
**      corresponds with it in the subentry objects. If none found it is
**      simply returned.
** 
** 	INPUT:	  o library object [R]
**                o subentry object [R]
**                o field object to be exchanged for subentry field [R]
** 
** 	RETURNS:  subentry field object
*/ 
   
SLBoFIELD *LibGetSubEntryField (SLBo *lib, LIBoSUBENTRY *subEntry, 
				SLBoFIELD *entryField)
{
  SLBoFIELD *field, *tmp;
  Int4       k;
  
  field = entryField;
  for (k=0; (tmp = LibNextSubEntryField (subEntry, &k));)
    if (tmp->type == entryField->type || tmp->replace == entryField->type)
      field = tmp;
  return field;
}



/**API* LibFieldHeaderHasWith *************************************************
**
** 	Returns the number of field with the specified characteristic that 
**      is associated with the specified header field. Associated here means
**      simply the fields following the header field in the $libformat
**      definition until the next header field.
** 
** 	INPUT:	  o address of library object [R]
**                o header field object [R]
**                o one of options suitable for FieldIs [R] or NULL
** 
** 	RETURNS:    number of fields in the group defined by the header field
*/ 
   
INT4 LibFieldHeaderHasWith (SLBo *lib, SLBoFIELD *header, char *option)
{
  SLBoFIELD *field;
  Int4      c, k;

  for (c=0, k=0; (field = LibNextField (lib, &c));) {
    if (field == header)
      k++;
    else if (k) {
      if (FieldIs (field, "header"))
	break;
      else if (!option || FieldIs (field, option))
	k++;
    }
  }
  return k ? k-1 : 0;
}




/**API* LibIsSubField *********************************************************
**
** 	Returns TRUE if the specified characteristic is true for the specified 
**      data-field of a subentry.
** 
** 	INPUT:	  o field object [R]
**                o subentry object [R]
**                o option: "inSubEntry", "first", "fromParent" [R]
** 
** 	RETURNS:    TRUE or FALSE
*/ 
   
INT4 LibIsSubField (SLBoFIELD *field, LIBoSUBENTRY *subEntry, char *option)
{
  Int4      i;

  if (!field)
    return 0;
  switch (tolower (option[1])) {
  case 'n':  /* insubEntry */
    for (i=0; i < subEntry->fieldsN; i++)
      if (subEntry->fields[i].type == field->type)
	return 1;
    return 0;
  case 'i':  /* first */
    return (subEntry->first == field->type) ? 1 : 0;
  case 'r': /* fromParent */
    return field->indexId == subEntry->idType ? 0 : 1;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
  return 0;
}


/**api* LibGetFieldWithCode **************************************************
**
** 	Returns for the field object with specified "fields" token code.
** 
** 	INPUT:	    library object [R]
**                  (numeric) token code [R]
**
** 	RETURNS:    the field object 
**                  NULL: if not found
*/ 

SLBoFIELD *LibGetFieldWithCode (SLBo *lib, Int4 code)
{
  SLBoFIELD *field;
  Int4 i;

  for (i=0; (field=LibNextField (lib, &i));) {
    if (field->fieldTokCode == 0)
      field->fieldTokCode = TokStrToCode (field->code);
    if (field->fieldTokCode == code)
      return field;
  }
  return NULL;
}


/**api* LibGetIndexTokenType **************************************************
**
** 	Returns for specified data-field the name of the token table containing
**      the words to be indexed and their token code if specified.
** 
** 	INPUT:	    address of field object [R]
**                  address of code [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    the name of the token table
*/ 

char *LibGetIndexTokenType (SLBoFIELD *field, INT4 *code)
{
  return field->indexToken[0];
}



/**api* LibIsGenericId ********************************************************
**
** 	returns TRUE if the ID name for each entry is to be generated during 
**      indexing, ie, no suitable data-field with unique identifiers exist;
** 
** 	INPUT:	    address of library object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
** 		    0
*/ 
   
INT4 LibIsGenericId (SLBo *lib)
{
#ifdef xxx
  return lib->form->f[0].gnrc_f;  /* field with index 0 is ID-field */
#endif
return 1;
}

/**api* LibIsFilePerEntry *****************************************************
**
** 	returns TRUE if the library is organized as a directory of files, each
**      containing a single entry;
** 
** 	INPUT:	    address of library object [R]
** 
** 	RETURNS:    1
** 		    0
*/ 
   
INT4 LibIsFilePerEntry (SLBo *lib)
{
  if (LibIs (lib, "subentries"))
    lib = LibGetParentLib (lib);
  return lib->form->fil_t[0]->sngl_f;
}


int (*funct)(char *, int);



/**API* LibOpen ***************************************************************
**
** 	Opens specified depot file with all the run-time-data defined in the 
**      ODD files.
** 
** 	INPUT:	    name of depot file [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    
** 		    
*/ 

void LibOpen ()
{
  LIBoID    *libId;
  SLBo      *seLib;
  SRSoGROUP *group;
  char      **object_p;
  long      *object_n;
  INT4       idNum, k, c, i;

  SdlGetObjects (&object_n, (void ***) &object_p, "srs5");
  srsdb = (SRSoDB *) object_p[O_SRSDB];

  /* initialize the icarus syntax */
  IcaInitSyntax (LibObjByName ("syntax", "icarus"));

  ParSetTable ("global", NULL, "PRIVATE");
  ParInit (srsdb->parTable);
  ViewInitDefined (srsdb->view, srsdb->viewN);

  if ((srsdb->libTable = (SLBo **) calloc (256, sizeof (SLBo *))) == NULL)
    _ErrExit2 (e__allocfail, "library-ID list");

  /*
  ** go through defined library-Ids, check and create a table of 
  ** library objects where the Id serves as index
  */

  for (k=0; k < srsdb->libIdN; k++) {
    libId = &srsdb->libId[k];
    if (!libId->library) /* pointer is still a forward */
      continue;
    idNum = libId->n;

    if (idNum <= 0 || idNum > 255)  /* check range */
      _ErrExit3 (e__novallibid, idNum, libId->library->nam);

    if (srsdb->libTable[idNum])  /* is ID already in use? */
      _ErrExit4 (e__dupllibid, idNum,
		 libId->library->nam, srsdb->libTable[idNum]->nam);
    srsdb->libTable[idNum] = libId->library;

    if (libId->library->idNum)  /* has library an ID already? */
      _ErrExit4 (e__libidexst, idNum, libId->library->nam, 
		 libId->library->idNum);
    libId->library->idNum = idNum;

    /* assign library plus potential sub libraries to a group */
    if ((group = libId->library->group)) {  
      group->library[group->libraryN++] = libId->library;
      for (c=0; (seLib = LibNextSubEntryLib (libId->library, &c));) {
	seLib->parent = libId->library;
	for (i=0; i<group->libraryN; i++) /* check if already in */
	  if (group->library[i] == seLib) break;
	if (i==group->libraryN)
	  group->library[group->libraryN++] = seLib;
      }
    }
  }

  /*
  ** set an initial default environment ...can be changed later
  */

#ifdef VMS
    LibSetEnvironment ("vms");
#else
    LibSetEnvironment ("unix");
#endif

  OddInit (oddObjs, 1); /* for odd compiler */
}


/**api* function **************************************************************
**
** 	Initializes the templates for hypertext links. If a link is to
**      the local SRSWWW server then the "-id" option is added to the 
**      command line which means that the function should be called after
**      the global parameter "userIdOpt" is defined.
** 
*/ 

void LibInitHyperLinks ()
{
  STRv hl=NULL;
  char *userId=ParGetStr ("userIdOpt"), *tmp, *p;
  Int4 k;

  hl = StrNew ();
  for (k=0; k < srsdb->hrefN; k++) {
    tmp = srsdb->href[k].link;
    if (*userId && (p=strstr (tmp, "=wgetz?"))) {
      p += 7; /* point after "=wgetz?" */
      StrNSetS (&hl, tmp, p-tmp);
      StrAppS (&hl, userId);
      StrAppS (&hl, p);
      ParDefStr (srsdb->href[k].name, _Str(hl));
    }
    else
      ParDefStr (srsdb->href[k].name, tmp);
    ParSetVolatile (srsdb->href[k].name);
  }
  StrDel (hl);
}


/**API* LibSetEnvironment *****************************************************
**
** 	Sets library environment with specified name.
** 
** 	INPUT:	    name of environment object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    
** 		    
*/ 

INT4 LibSetEnvironment (char *envName)
{
  SLBo       *lib, *seLib;
  LIBoENV    *env;
  LIBoLIBENV *libenv;
  INT4       k, l, c;
  

  ParDefStr ("env", envName);

  if (!(env = (LIBoENV *) LibObjByName ("environment", envName)))
    _ErrExit3 (e__objectunknown, "environment", envName);

  for (k=0; k < srsdb->nslb; k++) /* turn all libs OFF */
    srsdb->slb[k].isActive = 0;
  
  /* iterate over databanks in "site" and init libraries */
  for (k=0; k < env->libenvN; k++) {
    libenv = &env->libenv[k];
    for (l=0; *(libenv->lib->dirName[l] = libenv->dirName[l]) && l < 3; l++)
      ;
    lib = libenv->lib;
    lib->indexDirName = libenv->indexDirName;
    lib->isActive = 1;
    LibActivate (lib);
    /* activate also subentry libraries */
    for (c=0; (seLib = LibNextSubEntryLib (lib, &c));) 
      LibActivate (seLib);
  }

  /*
  ** initialize links...links between existing libs are activated
  */

  LibActiveLinks ();
  ParDefFunction ("printf", (Func) LibPrintf);
  ParDefFunction ("print", (Func) LibPrint);
  ParDefFunction ("printField", (Func) LibPrintField);
  return 1;
}


static LibActivate (SLBo *lib)
{
  IDoTYPE   *idType = (IDoTYPE *) LibObjByName ("idtype", "Entry-ID");
  SLBoFIELD *field;
  Int4      i, c;

  lib->isActive = 1;
  if (!lib->isInit && !lib->form->isInit) {
    lib->isInit = 1;
    lib->form->isInit = 1;
    for (c=0; (field = LibNextField (lib, &c));) {
      for (i=0; i<5; i++)
	if (*field->indexToken[i])
	  field->indexTokCode[i] = LibGetTokenCode (field->indexToken[i]);
      
      if (*field->tableToken)
	field->tableTokCode = LibGetTokenCode (field->tableToken);

      if (*field->token)
	field->fieldTokCode = LibGetTokenCode (field->token);
      
      if (!field->indexId)
	field->indexId = idType;
    }
  }
} 


/**API* LibNextLink ***********************************************************
**
** 	Returns next link object if available. The context must be initially 
**      set to 0. The function returns only 'active' links, ie, links between
**      existing databanks. See also LinkNext.
** 
** 	INPUT:	    address of context [W]
** 	        IMPLICIT:
** 
** 	RETURNS:  address of link object
**                NULL if the list is exhausted (next call will start at begin)
*/ 

LINKo *LibNextLink (INT4 *context)
{
  LINKo *link;

  if (*context >= srsdb->nlnk) {
    *context = 0;
    return NULL;
  }
  while (*context < srsdb->nlnk) {
    link = &srsdb->lnk[(*context)++];
    if (link->isActive)
      return link;
  }
  *context = 0;
  return NULL;
}



/**API* LibNextLibGroup *******************************************************
**
** 	Returns next library group object if available. The context must be 
**      initially set to 0.
** 
** 	INPUT:	    address of context [W]
** 	        IMPLICIT:
** 
** 	RETURNS:  address of library group object
**                NULL if the list is exhausted (next call will start at begin)
*/ 

SRSoGROUP *LibNextLibGroup (INT4 *context)
{
  if (*context >= srsdb->ngroup) {
    *context = 0;
    return NULL;
  }
  return &srsdb->group[(*context)++]; 
}


/**API* LibNextLib ************************************************************
**
** 	Returns next library object of specified library group if available.
**      The context must be initially set to 0.
** 
** 	INPUT:	 o  address of library group object [W]
**               o  address of context [W]
** 	        IMPLICIT:
** 
** 	RETURNS:  address of library object
**                NULL if the list is exhausted (next call will start at begin)
*/ 

SLBo *LibNextLib (SRSoGROUP *group, INT4 *context)
{
  SLBo *lib;

  while ((lib = group->library[(*context)++]) && !lib->isActive)
    ;
  if (!lib)
    *context = 0;
  
  return lib;
}

/**API* LibNextSubEntryLib ******************************************************
**
** 	Returns next subentry object for specified library if available.
**      The context must be initially set to 0.
** 
** 	INPUT:	 o  address of library object [R]
**               o  address of context [W]
** 	        IMPLICIT:
** 
** 	RETURNS:  subentry object
**                NULL if the list is exhausted (next call will start at begin)
*/ 

SLBo *LibNextSubEntryLib (SLBo *lib, Int4 *context)
{
  SLBo *seLib;

  if (!(seLib = lib->subEntries[(*context)++])) {
    *context = 0;
    return NULL;
  }
  else
    return seLib;
}

/**API* LibNextField **********************************************************
**
** 	Returns next field object of specified library if available; 
**      The context must be initially set to 0.
** 
** 	INPUT:	 o  address of library object [R]
**               o  address of context [W]
** 	        IMPLICIT:
** 
** 	RETURNS:  address of field object
**                NULL if the list is exhausted (next call will start at begin)
*/ 

SLBoFIELD *LibNextField (SLBo *lib, INT4 *context)
{
  static SLBo *libCurr;

  if (*context == 0)
    libCurr = lib;
  if (*context >= libCurr->form->nf) {
    *context = 0;
    return NULL;
  }
  return &libCurr->form->f[(*context)++]; 
}

/**api* LibNextDataType *******************************************************
**
** 	Returns next data type object.
** 
** 	INPUT:	 o  address of library object [R]
**               o  address of context [W]
** 	        IMPLICIT:
** 
** 	RETURNS:  data type object 
**                NULL: the list is exhausted (next call will start at begin)
*/ 

LIBoDataType *LibNextDataType (SLBo *lib, INT4 *c)
{
  if (*c >= 5/*te!!!*/ || !lib->form->contains[*c]) {
    *c=0;
    return NULL;
  }
  else
    return lib->form->contains[(*c)++];
}

/**API* LibNextSubEntryField **************************************************
**
** 	Returns next field object of specified library's subentry type if 
**      available; 
**      The context must be initially set to 0.
** 
** 	INPUT:	 o  address of subentry object [R]
**               o  address of context [W]
** 	        IMPLICIT:
** 
** 	RETURNS:  address of field object
**                NULL if the list is exhausted (next call will start at begin)
*/ 

SLBoFIELD *LibNextSubEntryField (LIBoSUBENTRY *subEntry, INT4 *context)
{
  if (*context >= subEntry->fieldsN) {
    *context = 0;
    return NULL;
  }
  return &subEntry->fields[(*context)++]; 
}

/**API* LibNextFieldFormat ****************************************************
**
** 	Returns next field object of specified library if available; 
**      The context must be initially set to 0.
** 
** 	INPUT:	 o  address of library object [R]
**               o  address of context [W]
** 	        IMPLICIT:
** 
** 	RETURNS:  address of field object
**                NULL if the list is exhausted (next call will start at begin)
*/ 

LIBoFieldFormat *LibNextFieldFormat (SRSoFLD *fieldType, INT4 *context)
{
  static SLBo *libCurr;

  if (fieldType->formatN <= *context) {
    *context = 0;
    return NULL;
  }
  else 
    return &fieldType->format[(*context)++];
}

/**api* LibFieldFormat ********************************************************
**
**      obsolete! see FieldGetFormat
**
** 	Returns the field format object if there is the field has a format with
**      the specified name. if an empty name is specified then the first
**      format in the list is returned (default format).
** 
** 	INPUT:	  address of field object [R]
**                format name (or NULL or empty string) [R]
** 
** 	RETURNS:  data-field format object
*/ 

LIBoFieldFormat *LibFieldFormat (SLBoFIELD *field, char *name)
{
  LIBoFieldFormat *format;
  Int4            c;

  for (c=0; (format = LibNextFieldFormat (field->type, &c));)
    if (!name || !*name || SmEqs (format->name, name))
      return format;
  return NULL;
}

void LibSelectFieldFormat (SRSoFLD *fieldType, char *name)
{
  LIBoFieldFormat *format;
  Int4            c;

  if (name && *name)
    for (c=0; (format=LibNextFieldFormat (fieldType, &c));) {
      if (SmEqs (format->name, name))
	format->isSelected = 1;
      else
	format->isSelected =0;
    }
}

char *LibGetFieldFormatEval (SLBoFIELD *field)
{
  SRSoFLD *fieldType = field->type;
  Int4 k;

  if (!fieldType->formatN)
    return NULL;
  for (k=0; k<fieldType->formatN; k++)
    if (fieldType->format[k].isSelected)
      return fieldType->format[k].eval;
  return field->type->format[0].eval; /* first in list is default */
}



/**api* LibGroupNew ***********************************************************
**
** 	Creates a new (empty) databank group with specified name (if any).
** 
** 	INPUT:	    name of the group [R] or NULL
** 
** 	RETURNS:    the group object
*/ 

SRSoGROUP *LibGroupNew (char *name)
{
  SRSoGROUP *group;

  if (!(group = (SRSoGROUP *) calloc (sizeof (SRSoGROUP), 1)))
    _ErrExit2 (e__allocfail, "db group");
  if (name) {
    group->com = malloc (strlen (name) + 1);
    strcpy (group->com, name);
    LibRegisterObj ("group", group);
  }
  return group;
}

/**api* LibGroupAddDb *********************************************************
**
** 	Adds one more data bank to the group.
** 
** 	INPUT:	    group object [W]
**                  databank object [R]
** 
*/

void LibGroupAddDb (SRSoGROUP *group, SLBo *lib)
{
  group->library[group->libraryN++] = lib;
}


#define LIBxMaxFieldsInGroup 800
/**api* LibNextGroupField *****************************************************
**
** 	Iterates over all field objects in an entire databank group.
**      See also LibGroupNew and LibGroupAddDb for creating and extending
**      library groups.
** 
** 	INPUT:	 o group object [W]
**               o flag if to show all fields or only those that all
**                 databanks in the group have in common [R]
**               o iterator [W]
** 
*/

SLBoFIELD *LibNextGroupField (SRSoGROUP *group, INT4 isOnlyCommon, INT4 *c)
{
  SLBo      *lib;
  SLBoFIELD *field;
  INT4      c1, c2, k;

  /* init first */
  if (!group->fieldN) {
    group->fieldCount = (char *) calloc (LIBxMaxFieldsInGroup, sizeof(char));
    for (c1=0; (lib = LibNextLib (group, &c1));) 
      for (c2=0; (field = LibNextField (lib, &c2));) {
	for (k=0; k < group->fieldN; k++) 
	  if (group->field[k]->type == field->type && 
	      !FieldIs (field, "header")) {
	    group->fieldCount[k]++; 
	    break;
	  }
	if (k == group->fieldN) {
	  if (k == LIBxMaxFieldsInGroup)
	    _ErrExit3 (f__limitexceeded, "fields in group", 
		       LIBxMaxFieldsInGroup);
	  else {
	    group->fieldCount[group->fieldN] = 1;
	    group->field[group->fieldN++] = field;
	  }
	}
      }	      
  }

  /* return next field */
  if (!*c)
    *c = 0;
  else if (*c == group->fieldN) {
    *c = 0;
    return NULL;
  }
  if (isOnlyCommon) {
    for (; *c < group->fieldN; (*c)++)
      if (group->fieldCount[*c] == group->libraryN)
	return (group->field[(*c)++]);
  }		
  else
    return group->field[(*c)++];
  return NULL;
}



/**api* LibToId ***************************************************************
**
** 	finds a library-ID for a library object;
** 
** 	INPUT:	    address of library object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    library ID or -1 if not found
*/ 

INT4 LibToId (SLBo *lib)
{
  return lib->isActive ? lib->idNum : -1;
}

/**api* LibLinkToId ***********************************************************
**
** 	finds a link-ID for a link object;
** 
** 	INPUT:	    address of link object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    link ID or -1 if not found
*/ 

INT4 LibLinkToId (LINKo *link)
{
  INT4 k;

  for (k=0; k < srsdb->nlnk; k++)
    if (link == &srsdb->lnk[k])
      return k;
  return -1;
}


/**API* LibGetNextFlatFileDirName *********************************************
**
**      Returns the next flat file directory name in the list. To get the
**      first the context must be set to 0.
** 
** 	INPUT:	    address of library object [R]
**                  context (must be set to 0 for first in list) [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    o pointer to directory name
**                  o NULL if the list is exhausted (next call will start 
**                    at begin)
*/ 

char *LibGetNextFlatFileDirName (SLBo *lib, INT4 *context)
{
  char *dirName, parName[80];

  if (!lib->dirName[*context] || !*lib->dirName[*context] || *context > 3) {
    *context = 0;
    return NULL;
  }

  if (LibIs (lib, "user")) {
    sprintf (parName, "%sDirName", lib->nam);
    if (!(dirName = ParGetStr (parName)) || !*dirName) 
      dirName = lib->dirName[(*context)++];
  }
  else
    dirName = lib->dirName[(*context)++];
  return dirName;
}


/**API* LibGetNextFlatFileName **********************************************
**
**      Returns the next flat file directory name in the list. To get the
**      first the context must be set to 0.
** 
** 	INPUT:	    address of library object [R]
**                  context (must be set to 0 for first in list) [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    o pointer to directory name
**                  o NULL if the list is exhausted (next call will start 
**                    at begin)
*/ 

char *LibGetNextFlatFileName (SLBo *lib, UINT4 *context)
{
  static char *dirName;
  static char fileName[300];
  static INT4 c;
  SRSoFILTYP  *fileType=lib->form->fil_t[0];

  if (LibIs (lib, "subentries"))
    lib = LibGetParentLib (lib);

  if (!*context) {
    c = 0;
    dirName =  LibGetNextFlatFileDirName (lib, &c);
  }

  do {
    if (*fileType->searchName)
      sprintf (fileName, "%s%s", dirName, fileType->searchName);
    else
      sprintf (fileName, "%s*.%s", dirName, fileType->typ_nm);
    
    if (FilSearch (fileName, fileName, context)) 
      return fileName;

    *context = 0;
  } while ((dirName = LibGetNextFlatFileDirName (lib, &c)));  

  /* no more file names */

  return NULL;
}




/**api* LibGetIndexName *******************************************************
**
** 	finds a library-ID for a library object; composes a name that contains
**      the directory + lib name and short field name...the extensions 
**      have to be added by the index modules;
**
**      If the field object is omitted (NULL instead) then the name for
**      the auxilliary index is returned.
** 
** 	INPUT:	    address of library object [R]
**                  field object [R] or NULL
**                  address of output string [W] or NULL (uses static string)
**                  mode: "read" or "write" [R]
** 	        IMPLICIT:
**                  global parameter "indexDirName" [R]
** 
** 	RETURNS:    pointer to index name 
**                  NULL: not successful
*/ 

char *LibGetIndexName (SLBo *lib, SLBoFIELD *field, char *indexName, 
		       char *mode)
{
  static char statIndexName[200];
  char *indexDirName=NULL, tmp1[80], tmp2[80], *libName, *name;

  if (LibIs (lib, "subentries"))
    lib = LibGetParentLib (lib);

  libName = *lib->shortName ? lib->shortName : LibName (lib);

  if (LibIs (lib, "user")) {
    sprintf (tmp1, "%sDirName", libName);
    if (!(indexDirName = ParGetStr (tmp1)) || !*indexDirName) 
      indexDirName = lib->indexDirName;
  }

  else {
    switch (tolower (mode[0])) {
    case 'r':
      if (!(indexDirName = ParGetStr ("indexDirName")) || !*indexDirName) 
	indexDirName = lib->indexDirName;
      break;
    case 'w':
      
      /*
      ** check if either output dir or (with lesser priority) index dir
      ** are defined (command line)
      */
      
      if (!(indexDirName = ParGetStr ("outDirName")) || !*indexDirName) 
	if (!(indexDirName = ParGetStr ("indexDirName")) || !*indexDirName) 
	  indexDirName = lib->indexDirName;
      break;
    default:
      _ErrExit2 (e__unknownoption, mode);
    }
  }  

  name = indexName ? indexName : statIndexName;
  if (field)
    sprintf (name, "%s%s_%s", indexDirName,
	     SmEdit (strcpy (tmp1, libName), SMxLOWCASE), 
	     SmEdit (strcpy (tmp2, field->type->shortn), SMxLOWCASE));
  else
    sprintf (name, "%s%s", indexDirName,
	     SmEdit (strcpy (tmp1, libName), SMxLOWCASE));
    
  return name;
}

/**API* function **************************************************************
**
** 	Returns subentry library identified by specified subentry number.
**      See also LibGetParentLib.
** 
** 	INPUT:	    parent library object [R]
**                  subentry number [R]
** 
** 	RETURNS:    subentry library object
*/ 

SLBo *LibGetSubEntryLib (SLBo *lib, Int4 subEntryN)
{
  return lib->subEntries[0];
}

/**API* function **************************************************************
**
** 	Returns parent library of subentry library. See also LibGetSubEntryLib.
** 
** 	INPUT:	    subentry library object [R]
** 
** 	RETURNS:    parent library object
*/ 

SLBo *LibGetParentLib (SLBo *lib)
{
  return lib->parent;
}


/**API* LibGetLink ************************************************************
**
** 	Returns link between the libraries specified.
** 
** 	INPUT:	    first library's name [R]
**                  second library's name [R]
** 	        IMPLICIT:
** 
** 	RETURNS:  o address of link object
**                o NULL if the library names could not be resolved or if
**                  there is no link specified between the two.
*/ 

LINKo *LibGetLink (char *lib1Name, char *lib2Name)
{
  LINKo *link;
  SLBo  *lib1,*lib2;
  INT4  context;
  
  if (!(lib1 = (SLBo *) LibObjByName ("library", lib1Name))) {
    _ErrMsg3 (e__objectunknown, "library", lib1Name);
    return NULL;
  }
  if (!(lib2 = (SLBo *) LibObjByName ("library", lib2Name))) {
    _ErrMsg3 (e__objectunknown, "library", lib2Name);
    return NULL;
  }
  
  for (context=0; (link = LibNextLink (&context)); ) 
    if ( (link->lib1 == lib1 && link->lib2 == lib2) ||
	 (link->lib1 == lib2 && link->lib2 == lib1)) 
      return link;
  return NULL;
}


/**api* LibGetLinkName *******************************************************
**
** 	composes the file name for a link file
** 
** 	INPUT:	    address of link object [R]
**                  flag if file with link in reverse dir [R]
**                  address of output string [W]
**                  mode: "read" or "write" [R]
** 	        IMPLICIT:
**                  global parameter "indexDirName" [R]
** 
** 	RETURNS:    1 if ok
*/ 

void LibGetLinkName (LINKo *link, INT4 isReverse, char *fileName, char *mode)
{
  char *indexDirName=NULL, tmp1[80], tmp2[80];

  if (LibIs (link->lib1, "user") || LibIs (link->lib2, "user")) {
    sprintf (tmp1, "%sDirName", link->lib1->nam);
    if (!(indexDirName = ParGetStr (tmp1)) || !*indexDirName) 
      indexDirName = link->lib1->indexDirName;
  }
  else {
    switch (tolower (mode[0])) {
    case 'r':
      if (!(indexDirName = ParGetStr ("indexDirName")) || !*indexDirName) 
	indexDirName = link->lib1->indexDirName;
      break;
    case 'w':
      
      /*
      ** check if either output dir or (with lesser priority) index dir
      ** are defined (command line)
      */

      if (!(indexDirName = ParGetStr ("outDirName")) || !*indexDirName) 
	if (!(indexDirName = ParGetStr ("indexDirName")) || !*indexDirName) 
	  indexDirName = link->lib1->indexDirName;
      break;
    default:
      _ErrExit2 (e__unknownoption, mode);
    }
  }

  if (!isReverse)
    sprintf (fileName, "%s%s_%s.link", indexDirName,
	     SmEdit (strcpy (tmp1, link->nam1), SMxLOWCASE), 
	     SmEdit (strcpy (tmp2, link->nam2), SMxLOWCASE));
  else
    sprintf (fileName, "%s%s_%s.link", indexDirName,
	     SmEdit (strcpy (tmp1, link->nam2), SMxLOWCASE), 
	     SmEdit (strcpy (tmp2, link->nam1), SMxLOWCASE));
}


/**API* LibPrintLibs **********************************************************
**
** 	Lists all active libraries + some information
** 
** 	INPUT:
** 	        IMPLICIT:
** 		    srsdb (SRSoDB *) [R]
** 
** 	RETURNS:    
*/ 
   
void LibPrintLibs ()
{
  SRSoGROUP *group;
  SLBo      *lib;
  LIBoINDEX *libInx;
  INT4       context1, context2, (*print)(char *,...);

  if (!(print = (INT4 (*)(char *, ...)) ParGetFunction ("printf")))
    print = (INT4 (*)(char *, ...)) printf;

  print ("                 Library   Group              Entries    Index Date\n");
  print ("-------------------------------------------------------------------\n");
  
  for (context1=0; (group = LibNextLibGroup (&context1)); )
    for (context2=0; (lib = LibNextLib (group, &context2)); ) {
      if (LibIs (lib, "subentries"))
	continue;
      if ((libInx = LibIndexOpen (lib, LibGetIdField (lib), 1))) {
		print ("%24s   %-18s %7d  %12s\n", 
			   lib->nam, group->com,
			   BtrGetRecordN (libInx->btree),  
			   TimeToString (BtrGetTimeCreated (libInx->btree), "short"));
      }
    }
}




/****** LibPrintInfo **********************************************************
**
** 	displays info about library
** 
** 	INPUT:	    address of library name [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
*/ 
   
void LibPrintInfo (char *libName)
{
  static char ln[132], *fieldType[10]={"", "id", "index", "link", "show",
                                      "tree", "num", "real", "group"},
              *linkType[3]={"", " read-link", "index-link"};
  SRSoGROUP  *group;
  SLBo	     *lib;
  LINKo      *link;
  SRSoFILTYP *fileType;
  SLBoFIELD  *field;
  LIBoINDEX  *libInx;
  char       *dirName, relName[100], *tmp;
  INT4       c, k, l, isIdField, (*print)(char *, ...);

  if (!(lib = (SLBo *) LibObjByName ("library", libName)))
    _ErrExit3 (e__objectunknown, "library", libName);

  if (!(print = (INT4 (*)(char *, ...))ParGetFunction ("printf")))
    print = (INT4 (*)(char *, ...)) printf;

  LibGetLibGroup (libName, &group, &lib);

  field = LibGetIdField (lib);

  /*
  ** find the release name if available
  */

  relName[0] = '\0';
  if ((libInx = LibIndexOpen (lib, field, 1))) 
    if ((tmp = IdxGetReleaseName (libInx->idx)) && *tmp) 
      sprintf (relName, ", release: %s, ", tmp);
  print ("\nLibrary: \"%s\"%s from group: \"%s\"\n\n", 
	 lib->nam, relName, group->com);

  /*
  ** list all indices
  */
  print ("Data Fields (B=busy, C=compressed):\n\n");

  print ("Name                 Short  Type    Inx     Ids   No       No     Creation  B C\n");
  print ("                     Name           (kb)    (kb)  Words    IDs    Date         \n");
  print ("-------------------------------------------------------------------------------\n");

  for (c=0, *ln='\0'; (field = LibNextField (lib, &c)); ) {
    sprintf (ln, "%-20s", LibGetFieldName (field));
    sprintf (ln, "%s %-5s", ln, field->type->shortn);
    sprintf (ln, "%s  %-5s", ln, fieldType[field->index]);

    if (FieldIs (field, "index") && (libInx = LibIndexOpen (lib, field, 1))) {
      isIdField = FieldIs (field, "id");
      sprintf (ln, "%s %6d", ln, BtrGetFileSize (libInx->btree) / 1000); 
      sprintf (ln, "%s %6d", ln, !isIdField 
	                     ? IdsGetFileSize (libInx->idsFile) /1000 : 0);

      sprintf (ln, "%s %7d", ln, BtrGetRecordN (libInx->btree)); 
      sprintf (ln, "%s %8d", ln, !isIdField ? IdsGetIdN (libInx->idsFile) : 0);

      sprintf (ln, "%s %9s", ln, 
                       TimeToString (BtrGetTimeCreated (libInx->btree), "short"));
      sprintf (ln, "%s  %d", ln, BtrIsBusy (libInx->btree)); 
      sprintf (ln, "%s %d", ln, IdsIsCompressed (libInx->idsFile));
    }
    print ("%s\n", ln);
  }	

  /*
  ** print link info
  */

  print ("\n\nLinks:\n\n");

  for (c=0; (link = LibNextLink (&c)); ) 
    if (lib == link->lib1)
      print ("%s \"%s\" to \"%s\"\n", linkType[link->typ], lib->nam, 
	     link->lib2->nam);
  print (" \n");
  for (c=0; (link = LibNextLink (&c)); ) 
    if (lib == link->lib2)
      print ("%s \"%s\" to \"%s\"\n", linkType[link->typ], link->lib1->nam, 
	     lib->nam);
  print (" \n");

  /* 
  ** list names of flatfiles
  */
  
  print ("Directory: ");   
  for (c=0; (dirName = LibGetNextFlatFileDirName (lib, &c));) 
    print ("    \"%s\" ", dirName);
  print ("\n\n");   

  print ("Filename(s):\n");
  if (LibIsFilePerEntry (lib))
    print ("   \"*\"\n");
  else
    for (k=0;  k < lib->nfil;  k++) {
      *ln = '\0';
      for (l=0; (fileType = lib->form->fil_t[l]); l++)
	sprintf (ln, "%s %15s.%s", ln, lib->fil[k].nam, fileType->typ_nm);
      print ("%s\n", ln);
    }
  print (" \n");
}



/**api* LibParSetLibs ********************************************************
**
** 	sets a list of libraries by taking a string with lib names separated 
**      by space; the "libList" "reset" will turn all libraries OFF;
** 
** 	INPUT:	    string with a list of field names [R]
**                  
** 	        IMPLICIT:
** 
** 	RETURNS:    1
**                  0 if something is wrong
*/ 
   
INT4 LibParSetLibs (char *libList)
{
  SRSoGROUP *group;
  SLBo      *lib;
  char      *tok, *tokList, tmp[132];
  int       context1, context2;

  strcpy (tmp, libList);
  tokList = tmp;

  if (SmEqs (libList, "reset")) {
    for (context1=0; (group = LibNextLibGroup (&context1));) 
      for (context2=0; (lib = LibNextLib (group, &context2));) 
	ParDefNum (lib->nam, 0);
    return 1;
  }
  
  while ((tok = strtok (tokList, " "))) { 
    tokList = NULL;
    if ((lib = LibAlias (tok)))
      ParDefNum (lib->nam, 1);
    else {
      _ErrMsg3 (e__objectunknown, "library", tok);
      return 0;
    }
  }
  return 1;
}



/**api* LibParSetLinkLibs *****************************************************
**
** 	sets a list of libraries by taking a string with lib names separated 
**      by space; the "libList" "reset" will turn all libraries OFF;
** 
** 	INPUT:	    string with a list of field names [R]
**                  
** 	        IMPLICIT:
** 
** 	RETURNS:    1
**                  0 if something is wrong
*/ 
   
INT4 LibParSetLinkLibs (char *libList)
{
  SRSoGROUP *group;
  SLBo      *lib;
  char      *tok, *tokList, tmp[132], parName[80];
  int       context1, context2;

  if (SmEqs (libList, "reset")) {
    for (context1=0; (group = LibNextLibGroup (&context1));) 
      for (context2=0; (lib = LibNextLib (group, &context2));) {
	sprintf (parName, "%sLink", lib->nam);
	ParDefNum (parName, 0);
      }
    return 1;
  }

  strcpy (tmp, libList);
  tokList = tmp;
  
  while ((tok = strtok (tokList, " "))) { 
    tokList = NULL;
    if ((lib = LibAlias (tok))) {
      sprintf (parName, "%sLink", lib->nam);
      ParDefNum (parName, 1);
      ParDefNum ("linkToLibs", 1);
    }
    else {
      _ErrMsg3 (e__objectunknown, "library", tok);
      return 0;
    }
  }
  return 1;
}


/**api* LibParSetFields *******************************************************
**
** 	sets a list of fields by taking a string with fields separated by 
**      space; the "fieldList" "reset" will turn all fields OFF
** 
** 	INPUT:	    string with a list of field names [R]
**                  
** 	        IMPLICIT:
** 		    srsdb (SRSoDB *) [R]
** 
** 	RETURNS:    1
**                  0 if something is wrong
*/ 

   
INT4 LibParSetFields (char *fieldList)
{
  SRSoFLD *fieldType;
  char    *tok, *tokList, tmp[132];
  int     k, c, isFound;

  if (SmEqs (fieldList, "reset")) {
    for (k=0; k < srsdb->nfld; k++) {
      ParDefNum (srsdb->fld[k].nam, 0);
      ParSetVolatile (srsdb->fld[k].nam);
    }
    return 1;
  }

  strcpy (tmp, fieldList);
  tokList = tmp;
  
  ParDefNum ("parSetFields", 1);
  while ((tok = strtok (tokList, " "))) { 
    tokList = NULL;
    for (isFound=0, c=0; (fieldType=LibNextFieldType (tok, &c));) {
      ParDefNum (fieldType->nam, 1);
      isFound=1; 
    }
    if (!isFound) {
      _ErrMsg3 (e__objectunknown, "data-field", tok);
      return 0;
    }
  }
  return 1;
}


/**api* LibIs *****************************************************************
**
** 	returns some boolean information about the library;
**
** 	INPUT:	  o  library object [R]
**                o  option: "marked", "user", "selected", "linkTarget",
**                   "subEntries", "partitioned" [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 
**                  0 
*/ 

INT4 LibIs (SLBo *lib, char *option)
{
  char parName[80];

  switch (_Index(tolower (option[0]), tolower (option[1]))) {
  case _Index('s','e'):  /* selected */
    return (ParGetBool (lib->nam));
  case _Index('m','a'):  /* marked */
    return lib->upd_f;
  case _Index('u','s'):  /* user */
    return lib->isFromUser;
  case _Index('l','i'):  /* linkTarget */
    sprintf (parName, "%sLink",  lib->nam);
    return (ParGetBool (parName));
  case _Index('p','a'):  /* partitioned */
    return lib->partFiles || lib->partSize ? 1 : 0;
  case _Index('s','u'):  /* subentries */
    return lib->parent ? 1 : 0;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
  return 0;
}


/**api* LibMarkLinkedLibs *****************************************************
**
** 	marks all libraries that are either directly or indirectly linked - all
**      others are unmarked; the mark can be questioned by the function
**      "LibIs"; marking includes library specified as argument;
** 
** 	INPUT:	    library name [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if library is linked to at least one other
**                  0 otherwise
*/ 

INT4 LibMarkLinkedLibs (char *libName)
{
  SRSoGROUP *group;
  SLBo      *lib;
  LINKo     *link;
  INT4      isLinked=0, context1, context2, k, l;

  /* unmark all libraries */

  for (context1=0; (group = LibNextLibGroup (&context1)); )
    for (context2=0; (lib = LibNextLib (group, &context2)); ) 
      lib->upd_f = 0;

  /* test if library is linked at all */

  for (k=0, context1=0; (link = LibNextLink (&context1)); k++) 
    if (link->typ != 3 && (SmEqs (libName, link->lib1->nam) || 
	SmEqs (libName, link->lib2->nam))) {
      link->lib1->upd_f = link->lib2->upd_f = 1;    
      isLinked = 1;
    }

  /* propagate all links by marking all libs that have a marked partner
     in a link - repeat number of link times */

  for (l=0; l < k; l++)
    for (context1=0; (link = LibNextLink (&context1));) 
      if (link->typ != 3 && (link->lib1->upd_f || link->lib2->upd_f)) 
	link->lib1->upd_f = link->lib2->upd_f = 1;    

  return isLinked;
}



/**api* LibIsAnyFieldActive ***************************************************
**
** 	tests is any field of library has been activated;
** 
** 	INPUT:	    library name [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if at least one field is active
**                  0 otherwise
*/ 

INT4 LibIsAnyFieldActive (char *libName)
{
  SLBo      *lib;
  SLBoFIELD *field;
  INT4      context;

  if (!(lib = (SLBo *) LibObjByName ("library", libName)))
    _ErrExit3 (e__objectunknown, "library", libName);

  for (context=0; (field = LibNextField (lib, &context)); )
    if (FieldIs (field, "active"))
      return 1;
  return 0;
}


/**api* LibIsFieldInGroup *****************************************************
**
** 	returns 1 if field type belongs logically to the field type group;
** 
** 	INPUT:	    field type object [R]
** 		    field type (group) object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 
**                  0 
*/ 

INT4 LibIsFieldInGroup (struct SRSoFLD *fieldType,
			struct SRSoFLD *fieldTypeGroup)
{
  return fieldType->group == fieldTypeGroup ? 1 : 0;
}


/**API* LibIsDataType *********************************************************
**
** 	Returns 1 if databank contains protein sequences.
** 
** 	INPUT:	    library object [R]
**                  one of: "protein", "dna"
** 	        IMPLICIT:
** 
** 	RETURNS:    1 
**                  0 
*/ 

INT4 LibIsDataType (struct SLBo *lib, char *option)
{
  switch (tolower (option[0])) {
  case 'p':  /* protein */
    return lib->dataType == 1 ? 1 : 0;
  case 'd':  /* dna */
    return lib->dataType == 2 ? 1 : 0;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
}


/**API* LibSetStatus **********************************************************
**
**      Activates/Deactivates the specified library.
** 
**      INPUT:      library name [R]
**                  1=activate, 0=deactivate [R]
**              IMPLICIT:
** 
**      RETURNS:    
**                  library object 
**                  NULL if library name not valid
*/ 

SLBo *LibSetStatus (char *libName, int doActivate)
{
  SLBo *lib;
  INT4 k, isActive;

  /* iterate over all libraries - not just the active ones */
  for (k=0; k < srsdb->nslb; k++) {
    lib = &srsdb->slb[k];
    if (SmEqs (libName, lib->nam)) {
      isActive = lib->isActive;
      lib->isActive = doActivate;
      if (isActive != doActivate)
	LibActiveLinks ();
      return lib;
    }
  }
  return NULL;
}


/**API* LibSetIndexDir *****************************************************
**
**      Sets a new index directory for the specified library.
** 
**      INPUT:      library object [W]
**                  directory name [R]
**              IMPLICIT:
** 
**      RETURNS:    
*/ 

void LibSetIndexDir (SLBo *lib, char *dirName)
{
  char *tmp;

  if (!(tmp = (char *) malloc (strlen (dirName)+1)))
    _ErrExit2 (e__allocfail, "directory name");
  strcpy (tmp, dirName);

  if (!OddIsInDepot (lib->indexDirName))
    free (lib->indexDirName);

  lib->indexDirName = tmp;
}

/**API* LibSetFlatFileName *****************************************************
**
**      Sets a new flat file name without the extension (!) that is specified
**      by the file type object.
** 
**      INPUT:      library object [W]
**                  file name [R]
** 
**      RETURNS:    
*/ 

void LibSetFlatFileName (SLBo *lib, char *fileName)
{
  SLBoFIL *file;
  char    *tmp;

  if (!(file = (SLBoFIL *) malloc (sizeof (SLBoFIL))))
    _ErrExit2 (e__allocfail, "file object");

  /* file name */
  if (!(tmp = (char *) malloc (strlen (fileName)+1)))
    _ErrExit2 (e__allocfail, "file name");
  strcpy (tmp, fileName);
  file->nam = tmp;

  /* (empty) logical file name */
  if (!(tmp = (char *) malloc (4)))
    _ErrExit2 (e__allocfail, "logical file name");
  *tmp = '\0';
  file->lnam = tmp;

  lib->fil = file;
  lib->nfil = 1;

}


/**API* LibSetFlatFileDir *****************************************************
**
**      Sets a new flat file directory for specified library.
** 
**      INPUT:      library object [W]
**                  directory name [R]
** 
**      RETURNS:    
*/ 

void LibSetFlatFileDir (SLBo *lib, char *dirName)
{
  char *tmp;

  if (!(tmp = (char *) malloc (strlen (dirName)+1)))
    _ErrExit2 (e__allocfail, "directory name");
  strcpy (tmp, dirName);

  lib->dirName[0] = tmp;
}

/**API* LibGetIdType *********************************************************
**
**      Returns an IDtype object.
**      If either library name or library ID are specified the ID type 
**      specific for that library is returned otherwise a default ID type that
**      corresponds with the specified ID size.
** 
**      INPUT:      library name [R] or NULL
**                  library-ID [R] or 0
**                  length of ID [R]
** 
**      RETURNS:    
**                  address of ID-type object 
*/ 

IDoTYPE *LibGetIdType (char *libName, INT4 libId, INT4 idSize)
{
  SLBo    *lib=NULL;

  if (idSize == 4) {
    if (libName) {
      if (!(lib = (SLBo *) LibObjByName ("library", libName))) 
	_ErrMsg3 (e__objectunknown, "library", libName);
    }
    else if (libId) { 
      if (!(lib = (SLBo *) LibObjById ("library", libId))) 
	_ErrMsg2 (e__libidnotknown, libId);
    }
    else {
      return (IDoTYPE *) LibObjByName ("idtype", "entry-id");
    }
    if (lib)
      return (LibGetIdField (lib))->indexId;

  }    
  else if (idSize == 6) {
    /* there is no other at the moment */
    return (IDoTYPE *) LibObjByName ("idtype", "seq-ft-id");
  }
  else {
    _ErrMsg4 (e__novalvar, "IDlength", idSize, "4 or 6");
  }
  return NULL;
}

/**api* LibGetIdTypeName ******************************************************
**
**      Returns the name of the ID type object.
** 
**      INPUT:      ID-type object [R]
**
**      RETURNS:    the name of the ID-type
*/ 

char *LibGetIdTypeName (IDoTYPE *idType)
{
  return idType->nam;
}


/**API* LibHasNoFiles ****************************************************
**
**      Returns TRUE if no flat file name records are associated with
**      library object, ie, no source flat files were specified in
**      the ODD specificiation.
**      Returns TRUE only if entries of library are not in separate files -
**      here flat file names are never directly specified.
** 
**      INPUT:      library object [W]
** 
**      RETURNS:    
**                  1
**                  0 
*/ 

INT4 LibHasNoFiles (SLBo *lib)
{
  if (lib->nfil || LibIsFilePerEntry (lib))
    return 0;
  else
    return 1;
}


/**API* LibSetLibFlatFiles ****************************************************
**
**      Searches directory for files that match the search string or the
**      name '*.externsion' and puts these names into the array of flat file
**      source names. These names are also stored in the IDX file.
** 
**      INPUT:      library object [W]
**                  IDX file object [R]
** 
**      RETURNS:    
**                  number of files found
**                  0 files
*/ 

INT4 LibSetLibFlatFiles (SLBo *lib, struct IDXo *idx)
{
  static char emptyLNam[1]="";
  SLBoFIL *libFile;
  char *fileName, name[80];
  INT4  c1=0, k;
  UINT4 c2;
  
  if (!IdxGetFlatFileNameN (idx)) {
    for (c2=0; (fileName = LibGetNextFlatFileName (lib, &c2));) {
      FilParse(fileName, name, FILxNAME);
      IdxSetFlatFileName (idx, name);
    }
    IdxWriteFlatFileNames (idx); /* flush file names into IDX file */
  }

  k = IdxGetFlatFileNameN (idx);
  if (!(libFile = (SLBoFIL *) calloc (k, sizeof (SLBoFIL))))
    _ErrExit2 (e__allocfail, "library file objects");
  
  for (c1=0, k=0; (fileName = IdxGetFlatFileName (idx, &c1)); k++) {
    libFile[k].nam = fileName;
    libFile[k].lnam = emptyLNam;
  }
  lib->fil = libFile;
  lib->nfil = k;
  return k;
}




/**API* LibPrintStartupInfo ***************************************************
**
**      Prints selected information about the library groups, databanks, fields
**      and links that are needed by interfaces talking to some remote 
**      server.Prints to stdout.
** 
**      INPUT:      
** 
**      RETURNS:    
*/ 

void LibPrintStartupInfo () 
{
  static classId = 0;
  static struct LibCoords {
    char *intern;   
    INT4 type_id;   
    char name[100]; 
    INT4 x, y;
  } *coords=NULL;
  FILo      file;
  SRSoGROUP *group;
  SLBo      *lib;
  LINKo     *link;
  SLBoFIELD *field;
  LIBoINDEX *libInx;
  INT4      c1, c2, c3, x, y; 
  char      *tmp;

  /*
  ** init list for storing the libraries coordinates in the network 
  ** picture
  ** Try to read the file (if exists) and save the coordinates
  */

  if (!classId)
    LstManageClass (&classId, sizeof (struct LibCoords), NULL, NULL, NULL); 
  if (!_ErrIs (FilUOpen (&file, "SRSWWW:srsnet.dat", 100, 0))) { 
    while (!FilEof (&file)) {
      LstNew ((void **) &coords, classId);
      if (sscanf (file.ln, "coord: %s %d %d", 
		  coords->name, &coords->x, &coords->y) == 3)
      FilURead (&file);
    }
  }

  for (c1=0; (group = LibNextLibGroup (&c1)); ) {
    printf ("group: %s, searchall: %d\n",
	    group->com, !group->single_f);
  }
  for (c1=0; (group = LibNextLibGroup (&c1)); )
    for (c2=0; (lib = LibNextLib (group, &c2)); ) 
      if ((libInx = LibIndexOpen (lib, LibGetIdField (lib), 1))) {

	if (LstHashSearch ((void **) &coords, lib->nam))
	  x = coords->x, y = coords->y;
	else
	  x = y = 0;

	/* print library */
	printf 
        ("lib: %s, rel: %s, entries: %d, date: %s, group: %s, x: %d, y: %d\n", 
		lib->nam, 
		(tmp = IdxGetReleaseName (libInx->idx)) ? tmp : "",
		BtrGetRecordN (libInx->btree),  
		TimeToString (BtrGetTimeCreated (libInx->btree), "date"),
		group->com, x, y);

	/* print fields */
	for (c3=0; (field = LibNextField (lib, &c3)); ) 
	  if (!FieldIs (field, "system"))
	    printf ("field: %s, type: %s\n", LibGetFieldName (field), 
		    LibGetFieldIType (field));
      }

  /* print links */
  for (c1=0; (link = LibNextLink (&c1)); ) 
    if (link->lib1 && link->lib2)
      printf ("link: %s %s\n",  link->lib1->nam, link->lib2->nam);

}

/**api* LibGetMaxNameSize *****************************************************
** 
** 	Returns the maximum size for a library name or field name.
**      The max field length can include the max format name length 
**      ("formattedField"). The function can return the max length
**      within the specified library, group, or if neither are specified
**      in all groups.
** 
** 	INPUT:	    group object (or NULL) [R]
**                  library object (or NULL) [R]
**                  option: "library", "field", "formattedField"
** 	        IMPLICIT:
** 
** 	RETURNS:    the maximum string length
*/ 
   
Int4 LibGetMaxNameSize (SRSoGROUP *group, SLBo *lib, char *option)
{	
  LIBoFieldFormat *format;
  SLBoFIELD       *field;
  INT4            c1, c2, c3, c4, len, fLen=0,
                  isSingleGroup=0, isSingleLib=0,
                  maxLen=0, maxFLen=0;

  if (group)
    isSingleGroup = 1;
  if (lib) {
    isSingleGroup = 1;
    isSingleLib = 1;
  }
  
  if (option[2] == 'b') { /* library */
    for (c1=0; isSingleGroup || (group = LibNextLibGroup (&c1)); ) {
      for (c2=0; isSingleLib || (lib = LibNextLib (group, &c2)); ) {
	if (LibIs (lib, "subentries")) /* don't count subentry libs */
	  continue;
	if ((len = strlen (LibName (lib))) > maxLen)
	  maxLen = len;
      }
      if (isSingleGroup)
	break;
    }
  }

  else { /* field or formattedField */
    for (c1=0; isSingleGroup || (group = LibNextLibGroup (&c1)); ) {
      for (c2=0; isSingleLib || (lib = LibNextLib (group, &c2)); ) {
	for (c3=0; (field = LibNextField(lib, &c3));) {
	  if (!FieldIs (field, "header")) {
	    len = strlen (LibGetFieldName (field));
	    if (option[2] == 'r') /* formattedField */ {
	      for (c4=0; (format=LibNextFieldFormat (field->type, &c4));)
		if ((fLen = strlen (format->name)) > maxFLen)
		  maxFLen = fLen;
	      len += fLen;
	    }
	    if (len > maxLen) 
	      maxLen = len;
	  }
	}
	if (isSingleLib)
	  break;
      }
      if (isSingleGroup)
	break;
    }
  }
  return maxLen;
}


/**api* LibParViewSetLibsRoot *************************************************
**
** 	sets a list of libraries by taking a string with lib names separated 
**      by space; the "viewLibListRoot" "reset" will turn all libraries OFF;
** 
** 	INPUT:	    string with a list of field names [R]
**                  
** 	        IMPLICIT:
** 
** 	RETURNS:    1
**                  0 if something is wrong
*/ 
   
INT4 LibParSetLibsViewRoot (char *libList)
{
  SRSoGROUP *group;
  SLBo      *lib;
  char      *tok, *tokList, tmp[132];
  int       context1, context2;
  char parName[80];
  char libName[80];
  int viewNumber;

  strcpy (tmp, libList);
  tokList = tmp;

  if (SmEqs (libList, "reset")) {
    for (context1=0; (group = LibNextLibGroup (&context1));) 
      for (context2=0; (lib = LibNextLib (group, &context2));) {
	sprintf(parName,"v%d_R_%s",ParGetNum("viewNumber"),libName);
	ParDefNum (parName, 0);
      }
    return 1;
  }
  
  while ((tok = strtok (tokList, " "))) { 
    tokList = NULL;
    if(SmEqs(tok,"~~~~~~~~~~~~~~")) continue;
    sscanf(tok,"v%d_R_%s",&viewNumber,libName);
    if ((lib = LibAlias (libName))) {
      sprintf(parName,"v%d_R_%s",viewNumber,libName);
      ParDefNum (parName, 1);
    }
    else {
      _ErrMsg3 (e__objectunknown, "library", tok);
      return 0;
    }
  }
  return 1;
}


/**api* LibParViewSetLibsLeaf *************************************************
**
** 	sets a list of libraries by taking a string with lib names separated 
**      by space; the "viewLibListLeaf" "reset" will turn all libraries OFF;
** 
** 	INPUT:	    string with a list of field names [R]
**                  
** 	        IMPLICIT:
** 
** 	RETURNS:    1
**                  0 if something is wrong
*/ 
   
INT4 LibParSetLibsViewLeaf (char *libList)
{
  SRSoGROUP *group;
  SLBo      *lib;
  char      *tok, *tokList, tmp[132];
  int       context1, context2;
  char parName[80];
  char libName[80];
  int viewNumber;

  strcpy (tmp, libList);
  tokList = tmp;

  if (SmEqs (libList, "reset")) {
    for (context1=0; (group = LibNextLibGroup (&context1));) 
      for (context2=0; (lib = LibNextLib (group, &context2));) {
	sprintf(parName,"v%d_L_%s",ParGetNum("viewNumber"),libName);
	ParDefNum (parName, 0);
      }
    return 1;
  }
  
  while ((tok = strtok (tokList, " "))) { 
    tokList = NULL;
    if(SmEqs(tok,"~~~~~~~~~~~~~~")) continue;
    sscanf(tok,"v%d_L_%s",&viewNumber,libName);
    if ((lib = LibAlias (libName))) {
      sprintf(parName,"v%d_L_%s",viewNumber,libName);
      ParDefNum (parName, 1);
    }
    else {
      _ErrMsg3 (e__objectunknown, "library", tok);
      return 0;
    }
  }
  return 1;
}


));) {
	sprintf(parName,"v%d_L_%s",ParGetNum("viewNumber"),libName);
	ParDefNum (parName, 0);
      }
    return 1;
  }
  
  while ((tok = strtok (tokList, " "))) { 
    tokList = NULL;
    if(SmEqs(tok,"~~~~~~~~~~~~~~")) continue;
    sscanf(tok,"v%d_L_%s",&viewNumber,libName);
    if ((lib = LibAlias (libName))) {
      sprintf(parName,"v%d_L_%s",viewNumber,libName);
      ParDefNum (parName, 1);
    }
    else {
      _ErrMsg3 (e__objectunknown, "library", tok);
     srs/src/library.h
**
**    $RCSfile: library.h,v $
**    $Revision: 1.16 $
**    $Date: 1997/03/12 16:17:41 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
*/


#define LIBxNULL        255   /* formerly SLBxNULL */

/* definition of data field types */

enum srs_dft {SRSxID=1, SRSxKEY, SRSxLINK, SRSxSHOW, SRSxHEADER, SRSxNUM, 
	      SRSxREAL, SRSxGROUP}; 

enum LIBeFORMAT {LIBxLISTING=1, LIBxLEFT, LIBxRIGHT, LIBxCENTER, LIBxPREFORMAT,
                 LIBxTOPICLIST, LIBxNUMBERLIST, LIBxBULLETLIST, LIBxTABLE, 
                 LIBxTABLE2, LIBxTEXT};


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  contains neccessary info for accessing indexes to search a key and for 
**  retrieval of IDs
*/

typedef struct LIBoINDEX {
  struct SLBo      *lib;                /* library descriptor */
  struct SLBoFIELD *field;              /* data-field descriptor */
  struct BTRo      *btree;              /* b-tree object */
  struct IDSoFILE  *idsFile;            /* file with ID-lists */
  struct IDXo      *idx;                /* id-index */
  INT4              isIdIndex;
} LIBoINDEX;




/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  list of functions exported by module "seqlib"
*/

#ifndef _SRSoGROUP
typedef struct SRSoGROUP *dummytointroducestructtagSRSoGROUP;
#endif
#ifndef _SRSoFLD
typedef struct SRSoFLD *dummytointroducestructtagSRSoFLD;
#endif
#ifndef _LINKo
typedef struct LINKo *dummytointroducestructtagLINKo;
#endif
#ifndef _LIBoSUBENTRY
typedef struct LIBoSUBENTRY *dummytointroducestructtagLIBoSUBENTRY;
#endif


    /* get info */ 

char *LibName (struct SLBo *lib);
char *LibGetName (struct SLBo *lib, char *option);
char *LibGetSubEntryName (struct LIBoSUBENTRY *se);
char *LibGetGroupName (struct SRSoGROUP *group, char *option);
char *LibGetIcarusFileName (struct SLBo *lib, char *option);
void LibPrintInfo (char *libName);
void LibPrintStartupInfo ();
void LibPrintLibs ();
INT4 LibGetEntryAuxInfo (UINT4 fip, struct SLBo *lib, struct SMoBUFF *buff);
INT4 LibGetLibGroup (char *nam, struct SRSoGROUP **libgroup, 
		    struct SLBo **library);
Int4 libGetMaxNameSize (struct SRSoGROUP *group, 
			struct SLBo *lib, char *option);
struct LIBoFieldFormat *LibFieldFormat (struct SLBoFIELD *field, char *name);

struct SLBo *LibAlias (char *lib_nm);
void *LibObjByName (char *class_nm, char *obj_nm);
void *LibObjById (char *class_nm, INT4 ObjId);
struct SRSoFLD *LibGetFieldType (char *lib_nm, char *field_nm);
struct SRSoFLD *LibFieldType (struct SLBoFIELD *field);
INT4 LibToId (struct SLBo *lib);
INT4 LibLinkToId (struct LINKo *link);
INT4 LibMarkLinkedLibs (char *libName);
struct LINKo *LibGetLink (char *lib1Name, char *lib2Name);
struct IDoTYPE *LibGetIdType (char *libName, INT4 libId, INT4 idSize);
struct SLBoFIELD *LibGetFieldWithCode (struct SLBo *lib, Int4 code);
struct SLBoFIELD *LibGetSubEntryField (struct SLBo *lib, 
				       struct LIBoSUBENTRY *subEntry, 
				       struct SLBoFIELD *entryField);
struct SLBo *LibGetSubEntryLib (struct SLBo *lib, Int4 subEntryN);
struct SLBo *LibGetParentLib (struct SLBo *lib);

   /* functions returning booleans */

INT4 LibIs (struct SLBo *lib, char *option);
INT4 LibFieldIsActive (struct SLBo *lib, INT4 fd_x, INT4 *first_f);
INT4 LibIsIdField (char *libName, char *fieldName);
INT4 LibIsFilePerEntry (struct SLBo *lib);
INT4 LibIsGenericId (struct SLBo *lib);
INT4 LibIsFieldType (struct SRSoFLD *fieldType, char *option);
struct SLBoFIELD *LibHasFieldNamed (struct SLBo *lib, char *name);
struct SLBoFIELD *LibHasField (struct SLBo *lib, struct SRSoFLD *fieldType);
INT4 LibIsAnyFieldActive (char *libName);
INT4 LibIsFieldInGroup (struct SRSoFLD *fieldType,
			struct SRSoFLD *fieldTypeGroup);
INT4 LibIsDataType (struct SLBo *lib, char *option);
INT4 LibHasNoFiles (struct SLBo *lib);

    /* working on databank groups */

struct SLBoFIELD *LibNextGroupField (struct SRSoGROUP *group, 
				     INT4 isOnlyCommon, INT4 *c);
void LibGroupAddDb (struct SRSoGROUP *group, struct SLBo *lib);
struct SRSoGROUP *LibGroupNew (char *name);

    /* for iteration */


struct SRSoFLD *LibNextFieldType (char *name, Int4 *c);
struct SLBoFIELD *LibNextFieldInGroup (struct SLBo *lib, 
				     struct SLBoFIELD *fieldGroup, Int4 *c);
struct SRSoGROUP *LibNextLibGroup (INT4 *context);
struct SLBo *LibNextLib (struct SRSoGROUP *group, INT4 *context);
struct SLBoFIELD *LibNextField (struct SLBo *lib, INT4 *context);
struct SLBo *LibNextSubEntryLib (struct SLBo *lib, Int4 *context);
struct SLBoFIELD *LibNextSubEntryField (struct LIBoSUBENTRY *subEntry, 
					 INT4 *context);
struct LINKo *LibNextLink (INT4 *context);
struct LIBoFieldFormat *LibNextFieldFormat (struct SRSoFLD *field,
					    INT4 *context);
struct LIBoDataType *LibNextDataType (struct SLBo*, INT4*);
struct LIBoApplication *LibNextAppl (struct LIBoDataType*, INT4*);

    /* working with file types */

struct SRSoFILTYP *LibGetFileType (struct SLBo *lib, char *name, Int4 *index);
struct SRSoFILTYP *LibNextFileType (struct SLBo *lib, Int4 *c);
char *LibGetFileTypeName (struct SRSoFILTYP *ft);
char *LibGetFileTypeFipName (struct SRSoFILTYP *ft);
char *LibGetFileTypeTokenTableName (struct SRSoFILTYP *ft);
struct SRSoFILTYP *LibGetFileTypeSharesFile (struct SLBo *lib, 
					     struct SRSoFILTYP *ft, 
					     Int4 *index);



    /* others */

char *LibGetFieldFormatEval (struct SLBoFIELD *field);
INT4 LibSetField (char *lib_nm, char *field_nm, char *optiona);
void LibSetActiveFields (struct SLBo *lib);
char *LibGetIndexName (struct SLBo *lib, struct SLBoFIELD *field, 
		     char *indexName, char *mode);
void LibGetLinkName (struct LINKo *link, INT4 isReverse, char *fileName, 
					 char *mode);
struct SLBoFIELD *LibGetIdField (struct SLBo *lib);
INT4 LibActiveLinks ();
void LibSetIndexDir (struct SLBo *lib, char *dirName);
struct SLBo *LibSetStatus (char *libName, int doActivate);
void LibSetFlatFileDir (struct SLBo *lib, char *dirName);
void LibSetFlatFileName (struct SLBo *lib, char *fileName);
INT4 LibSetLibFlatFiles (struct SLBo *lib, struct IDXo *idx);
char *LibGetNextFlatFileDirName (struct SLBo *lib, INT4 *context);
char *LibGetFieldName (struct SLBoFIELD *field);
char *LibGetFieldTypeName (struct SRSoFLD *type);
char *LibGetFieldShortName (struct SLBoFIELD *field);
char *LibGetFieldIType (struct SLBoFIELD *field);
char *LibGetIdTypeName (struct IDoTYPE *idType);
INT4 LibSetEnvironment (char *envName);
char *LibGetLinkToName (struct LINKo *link);
char *LibGetLinkFromName (struct LINKo *link);

    /* for checking parameters */

INT4 LibParSetLib (char *libName);


    /* open files */

void LibOpen ();
LIBoINDEX *LibIndexOpen (struct SLBo*, struct SLBoFIELD*, INT4);
struct FILEo *LibOpenFlatFile (struct SLBo*, INT4, struct SRSoFILTYP*, INT4*);
Int4 LibOpenNextEntryFile (struct SLBo*, struct FILEo**, struct SRSoFILTYP *);
Int4 LibOpenEntryFile(struct SLBo*, struct FILEo**, struct SRSoFILTYP*, char*);
Int4 LibOpenNextFlatFile (struct SLBo*, struct FILEo**, struct SRSoFILTYP*, 
			  Int4*);









   /* for checking parameters */

INT4 LibParSetLib (char *libName);


    /* open files */

void LibOpen ();
LIBoINDEX *LibIndexOpen (struct SLBo*, struct SLBoFIELD*, INT4);
struct FILEo *LibOpenFlatFile (struct SLBo*, INT4, struct SRSoFILTYP*, INT4*);
Int4 LibOpenNextEntryFile (struct SLBo*, struct FILEo**, struct SRSoFILTYP *);
Int4 LibOpenEntryFile(struct SLBo*, struct FILEo**, struct SRSoFILTYP*, char*);
Int4 LibOpenNextFlasrs/src/link.c
char link_srs_ID[] = "$Id: link.c,v 1.16 1997/03/03 18:20:42 srs Exp $";
/*
**
**    $RCSfile: link.c,v $
**    $Revision: 1.16 $
**    $Date: 1997/03/03 18:20:42 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: query, sm, setop, srs, message 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    module has functions for linkage of sets of different
**    types and/or origin (library).
**
**    Global Parameters:
**    "isPrintNoPath"  - if "1" print error message if a path between to
**                       libs was not found

** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/


#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>

#include "message.h"
#include "futil.h"
#include "sm.h"
#include "id.h"
#include "lst.h"
#include "set.h"
#include "par.h"
#include "link.h"
#include "map.h"
#include "btree.h"
#include "ids.h"
#include "library.h"
#include "binpack.h"
#include "query.h"

#define _CONSTANTS
#define _SRS
#define _SLB
#include SRSINCLUDE


#define LINKxMAXIDN 600000
#define LINKxMAXCOST 1000000

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  points to other link-node and to the link descrition;
*/

typedef struct LINKoEDGE {
  char              *list;     /* for usage of module "list" only! */
  INT4              class_id;  /* for "list" module */  
  struct LINKoNODE *fromNode;
  struct LINKoNODE *toNode;
  struct LINKo     *link;
  INT4		    cost;
  INT4              isReverse; /* TRUE if link specified in node is 
                                  reverse to link in link-descripton */
} LINKoEDGE;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  describes a node in linkage map;
*/

typedef struct LINKoNODE {
  char              *list;     /* for usage of module "list" only! */
  INT4              class_id;  /* for "list" module */  
  char		    name[100];
  struct LINKoEDGE *fromEdge;
  struct LINKoEDGE *edge;
  INT4              minCost;
} LINKoNODE;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  extern, global or modulewide variables
*/

static char     linkbuff[LNKxBUFFSIZ];	    
static LINKoNODE *node=NULL;

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of static functions
*/

static void LinkConnectNodes (LINKo *link, INT4 isReverse);
static void LinkExplore (LINKoEDGE *fromEdge, LINKoNODE *startNode, 
			 INT4 minCost);
static INT4 LinkAnalNames (char *a_nm, char *b_nm, char **liba_nm, 
			char **libb_nm, INT4 *a_n, INT4 *b_n);
static INT4 LinkGoPath (char *fromName, char *toName, 
			INT4 fromLibN, INT4 toLibN, 
			LINKoNODE *node, SETo *outSet);
static INT4 LinkCheckIdTyp (LINKo *Link, IDoTYPE *id1_d, IDoTYPE *id2_d);
static INT4 LinkMapSingle (LINKo *lnk, char *a_nm, INT4 a_n, SETo *c, 
			   INT4 rev_f);
static INT4 LinkGetLSet (LINKo *lnk, unsigned char **id_p, INT4 *n, 
			 INT4 rev_f);
static INT4 LinkGetSet (SETo *s, unsigned char **id_p, INT4 *n, INT4 lib_x);
static void LinkAddLink (LINKo *link, IDoENTRY *fromId, IDoENTRY *toId);



/**api* LinkInit **************************************************************
**
**      selects links to active libraries;
** 	Copies library-names to link-descriptors where neccessary, initializes 
** 	linkage map;
** 
** 	INPUT:	    address of array of link-descriptors [R]
** 		    number of link-descriptors [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
*/ 
   
INT4 LinkInit ()
{
  static INT4 isInit=0;
  LINKo *link;
  INT4	c;

  if (isInit)
    return 0;

  LibActiveLinks ();

  for (c=0; (link = LibNextLink (&c)); ) {
    if (!link->isActive || !link->lib1 || !link->lib2)
      continue;

    LinkConnectNodes (link, 1);
    LinkConnectNodes (link, 0);
  }    
  isInit=1;
  return 1;
}


static void LinkNewNode (LINKoNODE *node)
{
  node->edge = NULL;
}

Int4 LinkIsMapsToParent (LINKo *link)
{
  return link->typ == LINKxToParent ? 1 : 0;
}


/****** LinkConnectNode *******************************************************
**
**      Connects to nodes. Creates both nodes if they don't exist and
**      creates an edge object for first node.
**      The connection is unidirectional and must be repeated in reverse order
**      to achieve bidirectionality of the link.
** 
** 	INPUT:	 o  link object [R]
**               o  TRUE if direction is reverse to direction 
**                  specified in ODD [R]
** 	        IMPLICIT:
**                  node (LINKoNODE *) [W]
** 
** 	RETURNS:    
*/ 
   
static void LinkConnectNodes (LINKo *link, INT4 isReverse)
{
  static INT4 nodeClassId=0, edgeClassId=0;
  LINKoEDGE *edge;
  char      fromName[100], toName[100];

  if (!nodeClassId) {
    LstManageClass (&nodeClassId, sizeof (LINKoNODE), 
		    (void *) LinkNewNode, NULL, NULL);
    LstManageClass (&edgeClassId, sizeof (LINKoEDGE), NULL, NULL, NULL);
    node = NULL;
  }

  if (isReverse) { 
    strcpy (fromName, LibGetLinkToName (link));
    strcpy (toName, LibGetLinkFromName (link));
  }
  else {
    strcpy (fromName, LibGetLinkFromName (link));
    strcpy (toName, LibGetLinkToName (link));
  }

  if (!LstHashSearch ((void **) &node, SmEdit (fromName, SMxLOWCASE)))
    LstNewNamed ((void **) &node, nodeClassId, fromName);

  LstNew ((void **) &node->edge, edgeClassId);
  edge = node->edge;
  edge->fromNode = node;
  edge->cost = link->val;

  /*
  ** has to be reverse the other way round since
  ** the path is searched always in reverse direction 
  ** ...to 'go' the path one has then to backtrack
  */
  edge->isReverse = !isReverse; 
  edge->link = link;

  if (!LstHashSearch ((void **) &node, SmEdit (toName, SMxLOWCASE)))
    LstNewNamed ((void **) &node, nodeClassId, toName);
  edge->toNode = node;
}


/**API* LinkSearchPath ********************************************************
**
** 	Searches shortest path from one (library) node to another.
**      Searches way from target to start - optimal way to target is recorded
**      and placed in list of "LINKoSTEP" which can be "walked" in reverse 
**      direction.
** 
** 	INPUT:	    first node's name [R]
** 		    second node's name [R]
** 	        IMPLICIT:
**                  node (LINKoNODE *)
** 
** 	RETURNS:    address of first node in path
** 		    NULL if no path found
*/ 
   
LINKoNODE *LinkSearchPath (char *from, char *to)
{
  SLBo *lib;
  char fromName[100], toName[100];
  
  LinkInit ();
  strcpy (fromName, from);
  strcpy (toName, to);

  /* init all nodes */
  LstFirst ((void **) &node);
  do 
    node->minCost = LINKxMAXCOST;
  while (LstNext ((void **) &node));

  if (!LstHashSearch ((void **) &node, SmEdit (fromName, SMxLOWCASE)))
    return NULL;
  LinkExplore (NULL, node, 0); 

  if (LstHashSearch ((void **) &node, SmEdit (toName, SMxLOWCASE)))
    return (node->minCost == LINKxMAXCOST || node->minCost == 0) ? NULL : node;
  else
    return NULL;
}

/****** LinkExplore ***********************************************************
**
** 
** 	INPUT:	    node (current) location at function call [R] or NULL
** 		    node where exploration should be commenced [W]
**                  minCost so far [R]
** 	        IMPLICIT:
**                  node (LINKoNODE *)
** 
** 	RETURNS:    address of first node in path
** 		    NULL if no path found
*/ 
   
static void LinkExplore (LINKoEDGE *fromEdge, LINKoNODE *startNode, 
			 INT4 minCost)
{
  LINKoEDGE *edge=startNode->edge;
  INT4      newMinCost;

  startNode->minCost = minCost;
  startNode->fromEdge = fromEdge;
  LstFirst ((void **) &edge);
  
  do {
    newMinCost = minCost + edge->cost;
    if (edge->toNode->minCost > newMinCost)
      LinkExplore (edge, edge->toNode, newMinCost);
  } while (LstNext ((void **) &edge));
}


/**API* LinkBackTrack ********************************************************
**
** 
** 	INPUT:	    node from which to backtrack [R]
** 		    pointer to address of link object [W] or NULL
**                  pointer to flag whether link is reverse or not [W] or NULL
** 	        IMPLICIT:
** 
** 	RETURNS:    NULL if already at end of path
** 		    node one step back in path
*/ 
   
LINKoNODE *LinkBackTrack (LINKoNODE *toNode, LINKo **link, 
				 INT4 *isReverse)
{
  LINKoEDGE *edge=toNode->fromEdge;

  if (!edge)
    return NULL;

  if (link)
    *link = edge->link;
  if (isReverse)
    *isReverse = edge->isReverse;

  return edge->fromNode;
}


/**API* LinkGetPathLength *****************************************************
**
** 	Returns the number of steps in a path
** 
** 	INPUT:	    address of target node [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    nr. of steps in path
*/ 

INT4 LinkGetPathLength (LINKoNODE *toNode)
{
  INT4 k;

  for (k=0; (toNode = LinkBackTrack (toNode, NULL, NULL)); k++)
    ;
  return k;
}


/**API* LinkGetNextInPath *****************************************************
**
** 	Walks back one step and returns node object.
** 
** 	INPUT:	    address of target node [R]
**                  address of flag for link direction [W] or NULL
**
** 	RETURNS:    node object one step back in the path
**                  NULL if at end of path
*/ 

LINKoNODE *LinkGetNextInPath (LINKoNODE *toNode, INT4 *isReverse)
{
  return LinkBackTrack (toNode, NULL, isReverse);
}



/****** LinkMap ***************************************************************
**
** 	top level function of this module;
** 	processes all possible linkages, set "b" will be mapped unto set "a"
** 	resulting in set c that is a subset of set "a";
**      set with second identifier will be mapped (i.e. has type of) onto 
**      set with first identifier;
** 
** 	INPUT:	    address of first identifier [R]
** 		    address of second identifier [R]
** 		    address of resultant set [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
** 		    e__unknownnam <name> +
** 		    e__ambigouslink <nam1, nam2> +
**                  e__unknownnam <nam> +
**                  e__filopenerr <file name> +
*/ 
   
INT4 LinkMap (char *toName, char *fromName, SETo *c)
{
  LINKoNODE *node;   
  char	    *toLibName, *fromLibName;
  INT4       fromLibN, toLibN, rv;

  LinkInit ();    	

  if ((rv = LinkToParent (toName, fromName, c)) != 0) {
    _ErrIf (rv) {
      SetDelete (c->nam);
      return rv;
    }
    else
      return 1;	
  }

  for (fromLibN=toLibN=0; (rv = LinkAnalNames (toName, fromName, 
                                             &toLibName, &fromLibName, 
					     &toLibN, &fromLibN)) != 0;) {
    _ErrRet (rv);

    /* search path in reverse direction ...then backtrack */

    if (!(node = LinkSearchPath (toLibName, fromLibName))) {
      if (ParGetNum ("isPrintNoPath"))
	_ErrMsg3 (e__nopath, fromLibName, toLibName);
      continue;
    }
    rv = LinkGoPath (fromName, toName, fromLibN, toLibN, node, c); 
    _ErrRet (rv);
  }
  return 1;
}


/**api* LinkToParent **********************************************************
**
** 	processes two kinds of linkages which involve both a conversion
** 	from CHILD-type to PARENT-type IDs;
** 	1) conversion of set of CHILD-type IDs directly to PARENT-type ID's
** 	   here second identifier must be name of conversion-link descriptor;
** 	2) mapping of set of CHILD-type IDs to set of PARENT-type ids;
** 
** 	INPUT:	    name of first set or "parent" [R]
** 		    name of second set [R]
** 		    address of resul set [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    1: success
** 		    0: no path known to connect sets
** 		    e__unknownnam: one of the two names is known
** 		    e__novallink: link is known but not valid
*/ 
     
INT4 LinkToParent (char *a_nm, char *b_nm, SETo *c)
{
  SETo	*a, *b;
  LINKo	*lnka=NULL, *lnkb, *lnk;
  INT4   a_t, b_t;

  if ((a_t = LinkIdentify (a_nm, &a, &lnka)) == 0)
    _ErrRet2 (e__unknownnam, a_nm);
  
  if ((b_t = LinkIdentify (b_nm, &b, &lnkb)) == 0)
    _ErrRet2 (e__unknownnam, b_nm);
  
  LinkIdentify ("PARENT", NULL, &lnk);
  
  if (a_t == LNKxSET && b_t == LNKxSET) {
    if (LinkCheckIdTyp (lnk, a->idType, b->idType)) {
      c->id_p = SetMapIds (a->id_p, b->id_p, a->n, b->n, &c->n,
			   a->idType->siz, b->idType->siz, 
			   a->idType->fddbeg, b->idType->fddbeg, 
			   a->idType->fddlen + a->idType->lbxlen);
      SetMakeOwn (c, a->idType);
      return 1;
    }
  }
  else if (b_t == LNKxSET && (lnka && lnka->typ == LNKxMAPRNT)) {
    if (lnka->id2_d == b->idType) {
      c->id_p = SetMapToParent (b->id_p, b->n, &c->n, b->idType->siz, 
				b->idType->fddbeg,
				b->idType->fddlen + b->idType->lbxlen);
      SetMakeOwn (c, lnk->id1_d);
      return 1;
    }
    else if (b->idType)
      _ErrRet3 (e__novallink, a_nm, b_nm);
  }
  return 0;
}


/****** LinkCheckIdTyp ********************************************************
**
** 	checks if both ID-types are listed in link-descriptor;
** 
** 	INPUT:	    address of link-descr. [R]
** 		    address of first id-descr. [R]
** 		    address of second id-descr. [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if ok
** 		    0 if not
*/ 
   
static INT4 LinkCheckIdTyp (LINKo *lnk, IDoTYPE *id1_d, IDoTYPE *id2_d)
{
  if (id1_d == lnk->id1_d) {
    if (id2_d == lnk->id2_d)
      return 1;	
  }
  else if (id1_d == lnk->id2_d) {
    if (id2_d == lnk->id1_d)
      return 1;	
  }
  return 0;
}


/****** LinkAnalNames *********************************************************
**
** 	input names may be set or library names; function gets for a
** 	set-name the associated library name with specified number (there may
**      be many libraries associated with a set!).
** 	numbers must be 0 initially and will be incremented by one if there is
** 	a library name left.
** 
** 	INPUT:	    address of first identifier [R]
** 		    address of second identifier [R]
** 		    output address of first library name [W]
** 		    output address of second library name [W]
** 		    output address of library number of first set [W]
** 		    output address of library number of second set [W]
** 	        IMPLICIT:
** 
** 
** 	RETURNS:    0 if no library name left
**                  1 if success
** 		    e__unknownnam <name> +
** 		    e__ambigouslink <nam1, nam2> +
*/ 
   
static INT4 LinkAnalNames (char *a_nm, char *b_nm, 
			   char **liba_nm, char **libb_nm, 
			   INT4 *a_n, INT4 *b_n)
{
  LINKo *lnka, *lnkb;
  SETo     *a, *b;
  INT4      a_t, b_t, libb_f = FALSE, liba_f = FALSE;
	
  if ((a_t = LinkIdentify (a_nm, &a, &lnka)) == 0)
    _ErrRet2 (e__unknownnam, a_nm);
  if ((b_t = LinkIdentify (b_nm, &b, &lnkb)) == 0)
    _ErrRet2 (e__unknownnam, b_nm);

  if (a_t == LNKxSET) {
    if (a->n == 0)
      return 0;
    if (!a->anal_f)
      SetLibStat (a);
  }
  if (b_t == LNKxSET) {
    if (b->n == 0)
      return 0;
    if (!b->anal_f)
      SetLibStat (b);
  }

  if (a_t == LNKxSET && b_t == LNKxSET) {
    if (a->lib_n > 1 && b->lib_n > 1)
      _ErrRet3 (e__ambigouslink, a_nm, b_nm);
  }
  if (a_t == LNKxSET && *a_n < a->lib_n) {
    *liba_nm = a->lib_nm[(*a_n)++];	
    liba_f = TRUE;
  }
  else if (*a_n < 1) {
    *liba_nm = a_nm;
    liba_f = TRUE;
  }
  if (b_t == LNKxSET && *b_n < b->lib_n) {
    *libb_nm = b->lib_nm[(*b_n)++];	
    libb_f = TRUE;
  }
  else if (*b_n < 1) {
    *libb_nm = b_nm;
    libb_f = TRUE;
  }
  if (a_t == LNKxLINK && b_t == LNKxLINK) {
    (*b_n)++;
    (*a_n)++;
  }
  return liba_f && libb_f ? 1 : 0;
}



/****** LinkGoPath ************************************************************
**
** 	processes each step of a path in sequential order; and adds set of
**      found entries to resultant set;
** 
** 	INPUT:	    address of first identifier [R]
** 		    address of second identifier [R]
** 		    number of library in first set [R]
** 		    number of library in second set [R]
** 		    address of path's first step [R]
**                  address of resultant set [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
**                  e__unknownnam <nam> +
**                  e__filopenerr <file name> +
*/ 
   
static INT4 LinkGoPath (char *fromName, char *toName, 
			INT4 fromLibN, INT4 toLibN, 
			LINKoNODE *node, SETo *outSet)
{
  SETo	    *tmp, *toSet;
  LINKo	    *link;
  INT4      rv, nStep, isReverse;
  char	    tmp1Name[SETxXNAM+1], tmp2Name[SETxXNAM+1];
  char	    *nextFromName;

  tmp1Name[0] = tmp2Name[0] = '\0';

  for (nStep=0; (node = LinkBackTrack (node, &link, &isReverse)); nStep++){
    if (!nStep) /* first step */
      nextFromName = fromName;
    else {
      strcpy (tmp2Name, tmp1Name);
      nextFromName = tmp2Name;
    }
    
    /*
    ** perform next link and put result into newly created temporary set
    ** delete input temporary sets
    */

    tmp = SetNew (tmp1Name, "temp"); /* output set */
    rv = LinkMapSingle (link, nextFromName, nStep ? 1 : fromLibN, 
			tmp, isReverse); 
    _ErrRet (rv);
    SetMakeOwn (tmp, isReverse ? link->id1_d : link->id2_d);
    if (*tmp2Name)
      SetDelete (tmp2Name);
  }

  if (LinkIdentify (toName, &toSet, NULL) == LNKxSET)
    SetOp (tmp, toSet, NULL, SETxAND);
  SetOp (outSet, tmp, NULL, SETxOR);
  SetDelete (tmp1Name);
  return 1;
}



/**api* LinkIdentify **********************************************************
**
** 	takes and identifier and finds out if its either a set name or a 
** 	library name or nothing
** 
** 	INPUT:	    address of name string [R]
** 		    address of pointer to link-dscr. [W] or NULL
** 		    address of pointer to set-dscr [W] or NULL
** 	        IMPLICIT:
** 
** 	RETURNS:    0 if unknown identifier
** 		    LNKxLINK if a link 
** 		    LNKxSET if a set
*/ 
   
INT4 LinkIdentify (char *name, SETo **setPtr, LINKo **linkPtr)
{
  SETo*  set;
  LINKo* link;
  INT4   c;
    
  LinkInit ();

  if (SmEqs ("parent", name))
    for (c=0; (link = LibNextLink (&c)); ) 
      if (SmEqs (name, link->nam1) || SmEqs(name, link->nam2)) {
	if (linkPtr) 
	  *linkPtr = link;
	return LNKxLINK;
      }

  if ((set = (SETo *) SetGet (name)) != NULL) {
    if (setPtr != NULL) *setPtr = set;
    if (SetIsDB (set))
      return LNKxLINK;
    else
      return LNKxSET;
  }
  else
    return 0;
}



/****** LinkDoLink ************************************************************
**
** 	performs a single step in an linkage path; set's identifier
**      must be either a setname or a library name; map is performed to the
**      other library specified in the link-dsc.
** 
** 	INPUT:	    address of linkage descriptor [R]
**                  set identifier [R]
**                  number of subset [R]
** 		    address of resultant set's descr. [W]
**                  reverse flag [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
**                  e__unknownnam <nam> +
**                  e__filopenerr <file name> +
*/ 
   
static INT4 LinkMapSingle (LINKo *lnk, char *a_nm, INT4 a_n, SETo *c, 
			   INT4 rev_f)
{
  LINKo	        *lnka;
  SETo 	        *a;
  unsigned char *aid_p, *bid_p;
  INT4		a_t, a_z, b_z, rv;
	
  if ((a_t = LinkIdentify (a_nm, &a, &lnka)) == 0)
    _ErrRet2 (e__unknownnam, a_nm);
  
  rv = LinkGetLSet (lnk, &bid_p, &b_z, a_t == LNKxSET ? rev_f : !rev_f);
  _ErrRet (rv);
  if (a_t == LNKxSET) {
    LinkGetSet (a, &aid_p, &a_z, a_n);
    c->id_p = SetLink (aid_p, a_z, bid_p, b_z, &c->n, rev_f);
  }
  else
    c->id_p = SetCutLink (bid_p, b_z, &c->n, rev_f);	
  
  SetRemoveDouble (c->id_p, c->n, 4, &c->n);
  
  if (ParGetNum ("doQueryReport"))
    Message (5, i__mappedset, 0, rev_f ? lnk->nam1 : lnk->nam2, c->n);
  return 1;
}



/****** LinkGetSet ************************************************************
**
** 	returns pointer to ids and number of ids - the returned set is a subset
**      of the input set containing ids of only one library - specified by
**      number;
**      if s->anal_f = FALSE it is assumed that the set contains ID's of
**      only one primary library;
** 
** 	INPUT:	    address of set-descr. [R]
** 		    address of pointer to id's [W]
** 		    address of set size [W]
** 		    library index within set [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
*/ 
   
static INT4 LinkGetSet (SETo *s, unsigned char **id_p, INT4 *n, INT4 lib_x)
{
  INT4	k, fst_x;
  
  if (!s->anal_f) {
    *id_p = s->id_p;
    *n = s->n;
  }
  else {
    for (k=0, fst_x=0;  k < lib_x-1;  fst_x += (INT4) s->lib_z[k++]) /*$$$$*/
      ;
    *n = s->lib_z[k];
    *id_p = s->id_p + s->idType->siz * fst_x;
    }
  return 1;
}



/****** LinkGetLSet ***********************************************************
**
** 	gets a set of link Id's: set is either already in memory or has
** 	to be read; set must be sorted depending on linkage (reverse or not)
**      after first of second id.
** 
** 	INPUT:	    address of link descr. [W]
** 		    address of pointer to ID-block [W]
** 		    address of set size [R]
**                  flag if link is in reverse direction [R]
** 	        IMPLICIT:
**                  linkbuff (char []) [W]
** 
** 	RETURNS:    1
**                  e__filopenerr <file name> +
*/ 
   
static INT4 LinkGetLSet (LINKo *link, unsigned char  **id_p, INT4 *n, 
			 INT4 rev_f)
{
  static MAPo map;
  static char nam_s[FILxXNAM+1];
  INT4	      rv;
  char        nam[FILxXNAM+1], *tmp;

  if (link->use)
    link = link->use;

  LibGetLinkName (link, rev_f, nam, "read");
  
  if (strcmp (nam, nam_s) != 0) {
    if (nam_s[0] != '\0')
      MapFree (&map);



#ifdef VMS
    rv = MapMem (&map, nam, linkbuff, LNKxBUFFSIZ);
#else
    rv = MapMem (&map, nam, linkbuff, LNKxBUFFSIZ - 512);
#endif
    _ErrRet (rv);
      strcpy (nam_s, nam);
  }

  /*
  ** first INT4 in mapsection contains the number of IDs - copy that
  ** number ...the set of link IDs start right after that number
  */

  tmp = map.data;
  _BinUnpackNum (tmp, link->linkIdN);
  if (rev_f)
    _BinUnpackNum (tmp, link->lib2EntryN);
  else
    _BinUnpackNum (tmp, link->lib1EntryN);

  if (LNKxBUFFSIZ/8 < link->linkIdN)
    _ErrExit3 (f__limitexceeded, "links in buffer", LNKxBUFFSIZ/8);

  *n = link->linkIdN;
  *id_p = (unsigned char *) tmp;
  
  return 1;
}    



/****** LinkReadLSet **********************************************************
**
** 	reads a set of link ID's from file;
** 
** 	INPUT:	    set name [R]
** 		    address of set pointer [W]
**                  address of link-desc. [R]
**                  reverse flag [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
** 		    e__filnotok <file_nm> +
*/ 
   
INT4 LinkReadLSet (char *nam, SETo **set_p, LINKo *lnk, INT4 rev_f)
{
    SETo *set;
    FILE *fil;
    char fil_nm[FILxXNAM+1];
    int  errCode;

    sprintf (fil_nm, "%s%s.lnk", lnk->lib1->indexDirName, nam);
    fil = (FILE *) FilOpenR (fil_nm, &errCode);
    _ErrRet2 (errCode, fil_nm);
    set = SetNew (nam, "temp");
    fread ((void *) &set->n, sizeof (INT4), 1, fil);
    fread (set->id_p, 8, set->n, fil);
    fclose (fil);
    SetMakeOwn (set, (IDoTYPE *) LibObjByName ("idtype", "link-id"));
    
    *set_p = set;
    return 1;
}


/**api* LinkOpen **************************************************************
**
** 
** 	INPUT:	    link object obtained by, eg, LibGetLink [W]
**                  option: "read", "writeread" or "writeindex" [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    the link object 
**                  NULL: if the index does not exist ("read")
*/ 

LINKo *LinkOpen (LINKo *link, char *opt)
{
  FILEo *file;
  SLBoFIELD *field;
  char  fileName[FILxXNAM+1];
  INT4  buffSize, errCode;

  /* 
  ** read access
  */
  
  if (SmEqs ("read", opt)) { 
    LibGetLinkName (link, 0, fileName, "read");
    file = FileNew (fileName);
    link->toFile = file;
    if (!(file = FileOpen (file)))
      return NULL;
    _BinFileUnpackNum (FileGetFile (file), link->linkIdN);
    _BinFileUnpackNum (FileGetFile (file), link->lib1EntryN);
    link->toFile = file;
    
    LibGetLinkName (link, 1, fileName, "read");
    file = FileNew (fileName);
    link->fromFile = file;
    if (!(file = FileOpen (file)))
      return NULL;
    _BinFileUnpackNum (FileGetFile (file), link->linkIdN);
    _BinFileUnpackNum (FileGetFile (file), link->lib2EntryN);
    return link;
  }
  
  /* 
  ** write access
  */
  
  else { 
    buffSize = LINKxMAXIDN * (link->id1_d->siz + link->id2_d->siz);
    if ((link->id_p = (unsigned char *) malloc (buffSize)) == NULL) {
      _ErrMsg2 (e__allocfail, "link ID buffer");
      return NULL;
    }
    link->idWrtOff = (char *) link->id_p;
    link->goodRefN = link->badRefN = link->linkIdN = 0;
    
    /*
    ** open associated indices
    */
    
    if (SmEqs ("writeindex", opt)) {  /* if this is an index link */
      if ((field = LibHasField (link->lib1, link->fromField))) {
	LibGetIndexName (link->lib1, field, fileName, "read");
	link->btree1 = BtrOpen (fileName, "read", &errCode);
	_ErrMsg2 (errCode, FileGetName (link->btree1->file, "path"));
	link->ids1 = IdsOpen (fileName, "read", 0, NULL, &errCode);
	_ErrMsg2 (errCode, fileName);
      }
      else 
	_ErrExit3 (e__dbhasnotfield, LibName(link->lib1),link->fromField->nam);

    }
    
    if ((field = LibHasField (link->lib2, link->toField))) {
      LibGetIndexName (link->lib2, field, fileName, "read");
      link->btree2 = BtrOpen (fileName, "read", &errCode);
      _ErrMsg2 (errCode, FileGetName (link->btree2->file, "path"));
      link->ids2 = IdsOpen (fileName, "read", 0, NULL, &errCode);
      _ErrMsg2 (errCode, fileName);
      link->isOpen = 1;
    }
    else 
      _ErrExit3 (e__dbhasnotfield, LibName (link->lib2), 
		 link->toField ? link->toField->nam : "unspecified");

    return link;
  }
}


/**api* LinkGetCreTime *****************************************************
**
**      Returns the creation time of the link indices. Link must be 
**      already opened for read access with LinkOpen.
** 
** 	INPUT:	    link object (must be opened for read access) [R]
** 
** 	RETURNS:    creation time
*/ 

Int4 LinkGetCreTime (LINKo *link)
{
  return FileGetTime (link->toFile, "create");
}


/**api* LinkGetLinkN **********************************************************
**
**      returns the number of links found in link index
** 
** 	INPUT:	    link object (must be opened for read access) [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    number of links
*/ 

INT4 LinkGetLinkN (LINKo *link)
{
  return link->linkIdN;
}

/**api* LinkGetEntryN *********************************************************
**
**      returns the number of entries of library used as sorting criterion
**      found in the link (always the first library name in the link name);
** 
** 	INPUT:	    link object (must be opened for read access) [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    number of entries
*/ 

INT4 LinkGetEntryN (LINKo *link, INT4 isReverse)
{
  return isReverse ? link->lib2EntryN : link->lib1EntryN;
}


/**api* LinkSets **************************************************************
**
** 
** 	INPUT:	    link object [W]
**                  first set [R]
**                  second set [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
*/ 

void LinkSets (LINKo *link, SETo *fromSet, SETo *toSet)
{
  IDoENTRY  fromId, toId;
  INT4      i, j;

  for (i=0; SetNextId (fromSet, &fromId, &i);)
    for (j=0; SetNextId (toSet, &toId, &j);) 
      LinkAddLink (link, &fromId, &toId); 
}


/**api* LinkClose *************************************************************
** 
** 	writes two files with link ID's - first with with link-IDs sorted
** 	afters first entry-ID, second with link-IDs sorted after second
** 	entry ID;
** 
** 	INPUT:	    link object [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
*/
   
void LinkClose (LINKo *link)
{
  FILE  *file;
  char  fileName[FILxXNAM+1];
  int   errCode;

  /*
  ** close indices
  */

  if (link->btree1)
    BtrClose (link->btree1);
  if (link->btree2)
    BtrClose (link->btree2);

  if (link->ids1)
    IdsClose (link->ids1);
  if (link->ids2)
    IdsClose (link->ids2);


  /*
  ** sort after first entry and write to file
  */

  LibGetLinkName (link, 0, fileName, "write");
  file = FilOpenW (fileName, &errCode);
  _ErrExit2 (errCode, fileName);

  SetHeapSort (link->id_p, link->linkIdN, 8, 0, 4);
  SetRemoveDouble (link->id_p, link->linkIdN, 8, &link->linkIdN);	
  link->lib1EntryN = SetCountKey (link->id_p, link->linkIdN, 8, 0, 4);

  /* 
  ** convert number of IDs to platform independent format
  */ 

  _BinFilePackNum (file, link->linkIdN);
  _BinFilePackNum (file, link->lib1EntryN);
  fwrite (link->id_p, 8, link->linkIdN, file);
  fclose (file);

  /*
  ** sort after second entry and write out
  */

  LibGetLinkName (link, 1, fileName, "write");
  file = FilOpenW (fileName, &errCode);
  _ErrExit2 (errCode, fileName);


  
  SetHeapSort (link->id_p, link->linkIdN, 8, 4, 4);
  link->lib2EntryN = SetCountKey (link->id_p, link->linkIdN, 8, 4, 4);

  _BinFilePackNum (file, link->linkIdN);
  _BinFilePackNum (file, link->lib2EntryN);
  fwrite (link->id_p, 8, link->linkIdN, file);
  fclose (file);
  
  _ErrMsg6 (i__builtlink, link->lib1->nam, link->lib2->nam, 
	    link->goodRefN, link->badRefN, link->linkIdN);
  link->isOpen = 0;
}


/**api* LinkNext ************************************************************
** 
** 	Returns the next link where the specified library participates and 
**      which has the specified characteristic.
**      See also LibNextLink.
** 
** 	INPUT:	    the library object [R]
** 		    address of iterator which must be set to 0 to start [R] 
**                  option: "read" [R]
** 
** 	RETURNS:    the link object
**                  NULL: list is exhausted
*/ 

LINKo *LinkNext (SLBo *lib, char *option, Int4 *i)
{
  LINKo *link;

  switch (option[0]) {
  case 'r': /* read */
    while (link = LibNextLink (i)) {
      if (link->lib1 == lib && *link->token)
	return link;
    }  
    break;
  default:
    _ErrExit2 (e__unknownoption, option);
  }

  *i = 0;
  return NULL;
}   


/**api* LinkIs ***************************************************************
** 
** 	Returns whether or not the specified characteristic is true for
**      the link.
** 
** 	INPUT:	    the link object [R]
** 		    option: "read", "index", "user", "libs", "using" [R]
** 
** 	RETURNS:    TRUE or FALSE
*/ 

Int4 LinkIs (LINKo *link, char *option)
{
  switch (tolower (option[2])) {
  case 'a':  /* read */
    return *link->token ? 1 : 0;
  case 'd':  /* index */
    return *link->token ? 0 : 1;
  case 'e':  /* user */
    return (LibIs (link->lib1, "user") || LibIs (link->lib2, "user")) ? 1: 0;
  case 'b':  /* libs */
    return link->lib1 && link->lib2 ? 1 : 0;
  case 'i':  /* using */
    return link->use ? 1 : 0;
  default:
    _ErrExit2 (e__unknownoption, option);
    return NULL;
  }

}

/**api* LinkNextToken *********************************************************
** 
** 	Iterates over the tokens used for building 'read' links. 
**      The token is characterized by token table name and token code. 
**      Returns the name of the token table. The token code is written 
**      into specified address.
** 
** 	INPUT:	    the link object [R]
** 		    address of token code [W]
**                  address of iterator. Must be set to 0 to start [W]
** 
** 	RETURNS:    name of token table
**                  NULL: list is exhausted
*/ 

char *LinkNextToken (LINKo *link, Int4 *code, Int4 *i)
{
  if (!*i) {
    (*i)++;
    *code = link->tokCode;
    return link->token;
  }
  else {
    *i = 0;
    return NULL;
  }
    
}   


/**api* LinkIdWithString ************************************************************
** 
** 	Links an entry-ID with a all entries that 'have' the string in 
**      the index specified by the link.
** 
** 	INPUT:	    link object [W]
** 		    ID object [R]
**                  string [R]
** 
** 	RETURNS:    TRUE if entries to be linked where identified by string
*/ 
   
Int4 LinkIdWithString (LINKo *link, IDoENTRY *fromId, char *s)
{
  static SETo set;
  IDoENTRY toId;
  BTRoREC  *record;
  FIP      idFip;
  Int4     i;

  SmEdit (s, SMxLOWCASE);
  if ((record = BtrSearch (link->btree2, s, &idFip, 0))) {
    LinkCollectSet (&set, record, link->ids2);
    for (i=0; SetNextId (&set, &toId, &i);)
      LinkAddLink (link, fromId, &toId); 
    link->goodRefN++;
    return 1;
  }
  else {
    link->badRefN++;
    return 0;
  }
}


/**api* LinkAddLink ************************************************************
** 
** 	Adds a new link to the link-ID buffer.
** 
** 	INPUT:	    link object [W]
** 		    from-ID object [R]
**                  to-ID object [R]
*/ 
   
static void LinkAddLink (LINKo *link, IDoENTRY *fromId, IDoENTRY *toId)
{
  if (link->linkIdN + 1 > LINKxMAXIDN)
    _ErrExit3 (e__settoosmall, link->linkIdN + 1, LINKxMAXIDN);
  
  memcpy (link->idWrtOff, fromId->id, fromId->siz);
  link->idWrtOff += fromId->siz;
  memcpy (link->idWrtOff, toId->id, toId->siz);
  link->idWrtOff += toId->siz;

  link->linkIdN++;
}

/**api* LinkCollectSet *********************************************************
** 
** 	Collects all the Ids linked to btree records into specified set.
** 
** 	INPUT:	    set object [W]
** 		    record from btree object [R]
**                  Ids file object [R]
*/ 

void LinkCollectSet (SETo *set, BTRoREC *record, IDSoFILE *idsFile) 
{
  IDoTYPE *idType;
  IDPTR   tmp;

  idType = IdsGetIdType (idsFile);
  tmp = SetGetIdBuff (set, record->r.value.idN * IdSize (idType));
  IdsGet (idsFile, tmp, record->r.value.firstIdFip, record->r.value.idN);
  SetSetEntryN (set, record->r.value.idN);
  SetSetIdType (set, idType);
}

to btree records into specified set.
** 
** 	INPUT:	    set object [W]
** 		    record from btree object [R]
**                  Ids file object [R]
*/ 

void LinkCollectSet (SETo *set, BTRoREC *record, IDSoFILE *idsFile) 
{
  IDoTYPE *idType;
  IDPTR   tmp;

  idType = IdsGetIdType (idsFile);
  tmp = SetGetIdBuff (set, record->r.value.idN * IdSize (idType));
  IdsGet (idsFile, tmp, record->r.value.firstIdFip, record->r.value.idN);
  SetSetEntryN (set, record->r.value.idN);
  SetSesrs/src/link.h
**
**    $RCSfile: link.h,v $
**    $Revision: 1.6 $
**    $Date: 1997/03/17 23:24:50 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**                  Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
*/



#define LNKxSET		1
#define LNKxLINK	2

#define LNKxBUFFSIZ	8*600000

#define LNKxREAD	1
#define LNKxINDEX	2
#define LNKxMAPRNT      3
#define LINKxToParent   3

typedef struct LINKo *LINKv;
typedef struct LINKoNODE *LINKvNode;

#ifndef _SLBo
typedef struct SLBo *dummytointroducestructtagSLBolink;
#endif
typedef struct BTRoREC *dummytointroducestructtagBTRoREClink;
typedef struct IDSoFILE *dummytointroducestructtagIDSoFILElink;

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of exported functions
*/

INT4 LinkInit ();
INT4 LinkMap (char *a_nm, char *b_nm, SETo *c);
INT4 LinkIdentify (char *nam, SETo **s_p, LINKv *linkPtr);


LINKv LinkOpen (LINKv link, char *opt);
void  LinkSets (LINKv link, struct SETo *set1, struct SETo *set2);
void  LinkIds (LINKv link, struct IDoENTRY *id1, IDoENTRY *id2);
void  LinkClose (LINKv link);
Int4  LinkGetCreTimeLinkN (LINKv link);
INT4  LinkGetLinkN (LINKv link);
INT4  LinkGetEntryN (LINKv link, INT4 isReverse);
INT4  LinkToParent (char *a_nm, char *b_nm, SETo *c);
Int4  LinkIsMapsToParent (LINKv link);
LINKv LinkNext (struct SLBo *lib, char *option, Int4 *i);
char *LinkNextToken (LINKv link, Int4 *code, Int4 *i);

void LinkCollectSet (struct SETo *set, struct BTRoREC *record, 
		     struct IDSoFILE *idsFile);

    /* for playing with paths */

struct LINKoNODE *LinkSearchPath (char *fromName, char *toName);
INT4 LinkGetPathLength (struct LINKoNODE *toNode);
struct LINKoNODE *LinkBackTrack (struct LINKoNODE *fromNode, 
				  LINKv *link, INT4 *isReverse);
struct LINKoNODE *LinkGetNextInPath (struct LINKoNODE *toNode, 
				      INT4 *isReverse);







nt4 *i);
char *LinkNextToken (LINKv link, Int4 *code,srs/src/listv.c
#include <stdio.h>

#include "def.h"
#include "message.h"
#include "listv.h"

/********************************************************************
** SIMPLE LIST: 
** only for elements that can be created, destroyed, copied and moved 
** without the need of calling management functions. 
********************************************************************/

int listPos;
int listAddPos;

LISTo* ListAllocImpl(int sz) {
    LISTo* l=(LISTo*)malloc(sizeof(LISTo)+sz);
    ASSERT(l,"CouldNotAllocList");
    l->h.usage=1;
    l->h.end=sz;
    return l;
}

void* ListNewImpl(int sz) {
    LISTo* l=(LISTo*)malloc(sizeof(LISTo)+sz);
    ASSERT(l,"CouldNotAllocList");
    l->h.usage=1;
    l->h.end=sz;
    l->h.len=0;
    return l+1;
}

void ListChangeImpl(void** list, int beg, int end) {
    LISTo* l=(LISTo*)cast(*list, LISTo*)-1;
    int len=l->h.len;
    int dlen=end-beg;
    if (l->h.end<len+dlen || l->h.usage>1) {
	LISTo* old=l+1;
	l=ListAllocImpl(len+dlen);
	l->h.len=len+dlen;l++;
	memcpy(offset(l, end, void*), offset(old,beg,void*), len-beg);
	if (dlen>0) memcpy(l, old, beg);
	else memcpy(l, old, end);
	ListDel(old);
    }
    else {
    	l->h.len+=dlen; l++;
	_MemMove(offset(l,end, void*), offset(l,beg,void*), len-beg);
    }
    *list=l;    
}

void ListDel(void* list) {
    LISTo* l=cast(list, LISTo*)-1;
    if (!--l->h.usage) free(l);
}

void ListDebug(void* list, int sz) {
    LISTo* l=(LISTo*)list-1;
    printf("LISTo:%p len:%d",list,l->h.len/sz);
    if (l->h.end!=l->h.len) printf(" grow:%d",(l->h.end-l->h.len)/sz);
    if (l->h.usage>1) printf(" shared:%d",l->h.usage-1);
    printf("\n");
}

void ListIntDebug(int* list) {
    int i;
    ListDebug(list,sizeof(int));
    printf("{ ");
    for (i=0; i<_ListLen(list); i++) {
        printf("%d ",list[i]);
    }
    printf("}\n");
}    

void ListPtrDebug(void** list) {
    int i;
    ListDebug(list,sizeof(void*));
    printf("{ ");
    for (i=0; i<_ListLen(list); i++) {
        printf("%p ",list[i]);
    }
    printf("}\n");
}    

/**************************************************************************
** ALLOCATION POOL
**************************************************************************/

/*#define POOL_DEBUG*/

#define POOL_MAX_ELEM_SIZE 256
#define POOL_CHUNK_SIZE 4096
#define ALIGN_SIZE_LOG 3

/* const WORD SMALL_OBJ_MASK=(POOL_MAX_ELEM_SIZE-1);
const WORD TOO_BIG_MASK=~(POOL_CHUNK_SIZE-1);
const WORD NOT_FITTING_OBJ_MASK=~((POOL_CHUNK_SIZE-1)&~SMALL_OBJ_MASK);
*/

void** pools[POOL_MAX_ELEM_SIZE>>ALIGN_SIZE_LOG];
long   poolAllocated[POOL_MAX_ELEM_SIZE>>ALIGN_SIZE_LOG];
long   poolAvailable[POOL_MAX_ELEM_SIZE>>ALIGN_SIZE_LOG]; 

void* palloc(int size) {
    if (size<=POOL_MAX_ELEM_SIZE) {
	void** pool; 
	size=(size-1)>>ALIGN_SIZE_LOG;
	pool=pools[size];
	if (pool) {
	    /* return the first free element, and remove from list */
	    pools[size]=(void**)*pool;
	}
	else {
	    /* create a new pool */
	    void **curr,**prev; 
	    int elemSize=(size+1)<<ALIGN_SIZE_LOG; /* aligned */
	    int poolNum=POOL_CHUNK_SIZE/elemSize;
	    pool=malloc(POOL_CHUNK_SIZE);
	    ASSERT(pool,"CouldNotGrowPool");
	    /* initialize linked list of free blocks */
	    curr=offset(pool,elemSize*(poolNum-1), void**);
	    prev=NULL; /* all allocated marker */
	    while (curr>pool) {
		*curr=prev;
		prev=curr; curr=offset(curr,-elemSize, void**);
	    }
	    pools[size]=prev; /* first free elem */
#ifdef POOL_DEBUG
	    poolAvailable[size]+=poolNum;
#endif
	}
#ifdef POOL_DEBUG
	poolAllocated[size]++;
	poolAvailable[size]--;
#endif
	return pool;
    }
    else return malloc(size);
}

void pfree(void* obj, int size) {
    ASSERT(obj, "FreeingNull");
    if (size<=POOL_MAX_ELEM_SIZE) {
	void** elem=(void**)obj;
	/* add elem to free list */
	size=(size-1)>>ALIGN_SIZE_LOG;
	*elem=pools[size];
	pools[size]=elem;
#ifdef POOL_DEBUG
	poolAllocated[size]--;
	poolAvailable[size]++;
#endif
    }
    else free(obj);
}

void PoolDebug(int size) {
#ifdef POOL_DEBUG
    int sz=(size-1)>>ALIGN_SIZE_LOG;
    printf("POOL size:%d allocated:%ld available:%ld\n", 
	size, poolAllocated[sz], poolAvailable[sz]);
#endif
}

void PoolDebugAll() {
#ifdef POOL_DEBUG
    int sz;
    for (sz=0; sz<POOL_MAX_ELEM_SIZE>>ALIGN_SIZE_LOG; sz++) {
	if (pools[sz]) PoolDebug((sz+1)<<ALIGN_SIZE_LOG);
    }
#endif
}

=pools[size];
	pools[size]=elem;
#ifdef POOL_DEBUG
	poolAllocated[size]--;
	poolAvailable[size]++;
#endif
    }
    else free(obj);
}

void PoolDebug(int size) {
#ifdef POOL_DEBUG
    int sz=(size-1)>>ALIGN_SIZE_LOG;
    printf("POOL size:%d allocated:%ld available:%ld\n", 
	size, poolAllsrs/src/listv.h
#define _SLIST_H

/********************************************************************
** SIMPLE LIST: 
** only for elements that can be created, destroyed, copied and moved 
** without the need of calling management functions. 
********************************************************************/

/* internals */

    typedef union LISTo {
	struct {
	    int usage;
	    int len;
	    int end;
	} h;
	void* tail_aligned;
    } LISTo;

    void* ListNewImpl  (int sz);
    void  ListChangeImpl(void** list, int beg, int end);

    extern int listAddPos;
    extern int listPos;

#define _ListAddImpl(plist,pos) listAddPos=(pos)*sizeof(**(plist)),ListChangeImpl((void**)(plist),listAddPos,\
listAddPos+sizeof(**(plist))),*(plist)+(pos)
/* end internals */


/*******************************************************************
**  API: the List type
*******************************************************************/

#define _List(type) type*

/* creation/deletion */
void    ListDel(void* list);

/**api* macro ************************************************************
**
**	Creates a new empty LISTv with space allocated for 'num' elements
**
**      INPUT:          the type name of the list element
**			the number of elements to be allocated
**	RETURNS:	the emtpy LISTv
*/

#define _ListNew(type,num)     ((type*)ListNewImpl(num*sizeof(type)))

/**api* macro ************************************************************
**
**	Sets the given LISTv to a new empty LISTv with space allocated 
**      for 'num' elements. The LISTv must NOT contain a valid list
**      value, must be unassigned (can contain a random pointer)
**
**      INPUT:          [W] the LISTv to be assigned
**			the number of elements to be allocated
*/

#define _ListNewIn(plist,num) (ListDel(*(plist)),*(void**)(plist)=ListNewImpl(num*sizeof(**(plist))))  

/**api* macro ************************************************************
**
**	Just an alias to the ListDel function
**
**      INPUT:          the LISTv
*/

#define _ListDel(list) ListDel(list)

/* debugging */
void    ListDebug	(void* list, int sz);
void	ListIntDebug	(int* list); 
void	ListPtrDebug	(void** list);

/* virtual copy management */

/**api* macro ************************************************************
**
**	If the list buffer is shared between multiple copies, creates 
**      a private copy ready to be modified. Returns the modified copy
**
**      INPUT:          [W] the pointer to the LISTv
**      RETURNS:        the LISTv ready to be modified
*/

#define _ListChange(plist)	(ListChangeImpl((void**)(plist),0,0),*plist)

/**api* macro ************************************************************
**
**	Returns a (virtual) copy of the list
**
**      INPUT:          the LISTv to be copied
**      RETURNS:        the copied LISTv
*/

#define _ListCpy(list)		(!(list)||((LISTo*)(list)-1)->h.usage++,(list))

/**api* macro ************************************************************
**
**	Assignes to a LISTv a (virtual) copy of a list value
**
**      INPUT:          [W] the pointer to the LISTv to be assigned
**                      the new LISTv value
*/

#define _ListSet(plist,list)	(ListDel(*(plist)),*(plist)=_ListCpy(list))

/* element operations */

/**api* macro ************************************************************
**
**	Inserts a new element at the beginning of a LISTv
**
**      INPUT:          [W] the pointer to the LISTv to be modified
**      RETURNS:        the new element
*/

#define _ListIns(plist)		*(ListChangeImpl((void**)(plist),0,sizeof(**(plist))),*(plist))

/**api* macro ************************************************************
**
**	Adds a new element at the given poisition 'pos' in the LISTv. 
**
**      INPUT:          [W] the pointer to the LISTv to be modified
**                      pos=the insertion position 
**      RETURNS:        the new element
*/

#define _ListAdd(plist,pos)	*(_ListAddImpl(plist,pos))

/**api* macro ************************************************************
**
**	Appends a new element at the end of a LISTv
**
**      INPUT:          [W] the pointer to the LISTv to be modified
**      RETURNS:        the new element
*/

#define _ListApp(plist)		*(listPos=_ListLen(*(plist)),_ListAddImpl(plist,listPos))

/**api* macro ************************************************************
**
**	Deletes an element at the given position 'pos' of a LISTv
**
**      INPUT:          [W] the pointer to the LISTv to be modified
**                      pos=the deletion position 
*/

#define _ListCut(plist,pos)	(listPos=(pos)*sizeof(**(plist)),ListChangeImpl((void**)(plist),listPos+sizeof(**(plist)),listPos))


/* multiple elem operations */

/**api* macro ************************************************************
**
**	Deletes a given number 'num' of elements at the given 
**      position 'pos' of a LISTv
**
**      INPUT:          [W] the pointer to the LISTv to be modified
**                      pos=the deletion position
**                      num=the number of elements 
*/

#define _ListCutMany(plist,pos,num) (listPos=(pos)*sizeof(**(plist)),ListChangeImpl((void**)(plist),listPos+sizeof(**(plist))*(num),listPos))

/**api* macro ************************************************************
**
**	Inserts a given number 'num' of new elements at the  
**      beginning of a LISTv
**
**      INPUT:          [W] the pointer to the LISTv to be modified
**                      num=the number of elements
**      RETURNS:        a pointer to the first of the new elements 
*/

#define _ListInsMany(plist,num)	    (ListChangeImpl((void**)plist,0,sizeof(**plist)*(num)),(*plist)[pos])

/**api* macro ************************************************************
**
**	Adds a given number 'num' of new elements at the given 
**      position 'pos' of a LISTv
**
**      INPUT:          [W] the pointer to the LISTv to be modified
**                      pos=the insertion position
**                      num=the number of elements
**      RETURNS:        a pointer to the first of the new elements 
*/

#define _ListAddMany(plist,pos,num) (listAddPos=(pos)*sizeof(**(plist)),\
ListChangeImpl((void**)(plist),listAddPos,listAddPos+sizeof(**(plist))*(num)),*(plist)+(pos))

/**api* macro ************************************************************
**
**	Appends a given number 'num' of new elements at the  
**      end of a LISTv
**
**      INPUT:          [W] the pointer to the LISTv to be modified
**                      num=the number of elements
**      RETURNS:        a pointer to the first of the new elements 
*/

#define _ListAppMany(plist,num)	    (listPos=_ListLen(*(plist)),_ListAddMany(plist,listPos,num))

/**api* macro ************************************************************
**
**	Adds a  number 'num' of elements from a C array 'arr' at the given 
**      position 'pos' of a LISTv
**
**      INPUT:          [W] the pointer to the LISTv to be modified
**                      pos=the insertion position
**                      arr=the array of elements
**                      num=the number of elements
*/

#define _ListAddArr(plist,pos,arr,num) memcpy(_ListAddMany(plist,pos,num),arr,sizeof(*plist)*(num))

/**api* macro ************************************************************
**
**	Inserts a number 'num' of elements from a C array 'arr' at  
**      the beginning of a LISTv
**
**      INPUT:          [W] the pointer to the LISTv to be modified
**                      arr=the array of elements
**                      num=the number of elements
*/

#define _ListInsArr(plist,arr,num)     memcpy(_ListInsMany(plist,num),arr,sizeof(*plist)*(num))

/**api* macro ************************************************************
**
**	Appends a number 'num' of elements from a C array 'arr' at  
**      the end of a LISTv
**
**      INPUT:          [W] the pointer to the LISTv to be modified
**                      arr=the array of elements
**                      num=the number of elements
*/

#define _ListAppArr(plist,arr,num)     memcpy(_ListAppMany(plist,num),arr,sizeof(*plist)*(num))

/**api* macro ************************************************************
**
**	Adds the elements of a LISTv at the position 'pos' of a LISTv
**
**      INPUT:          [W] the pointer to the LISTv to be modified
**                      pos=the insertion position
**                      the LISTv to be added
*/

#define _ListAddList(plist,pos,list) _ListAddArr(plist,pos,list,_ListLen(list))

/**api* macro ************************************************************
**
**	Inserts the elements of a LISTv at the beginning of a LISTv
**
**      INPUT:          [W] the pointer to the LISTv to be modified
**                      the LISTv to be inserted
*/

#define _ListInsList(plist,list)     _ListInsArr(plist,list,_ListLen(list))

/**api* macro ************************************************************
**
**	Appends the elements of a LISTv at the end of a LISTv
**
**      INPUT:          [W] the pointer to the LISTv to be modified
**                      the LISTv to be appended
*/

#define _ListAppList(plist,list)     _ListAppArr(plist,list,_ListLen(list))

/* access */

/**api* macro ************************************************************
**
**      INPUT:          the LISTv
**      RETURNS:        the lenght of the LISTv
*/

#define _ListLen(list)		(((LISTo*)(list)-1)->h.len/sizeof(*(list)))

/**api* macro ************************************************************
**
**      INPUT:          the LISTv
**      RETURNS:        the number of other LISTvs sharing this buffer
*/

#define _ListShared(list) (((LISTo*)(list)-1)->h.usage-1)


/**api* macro ************************************************************
**
**      INPUT:          the LISTv
**                      access position
**      RETURNS:        the element in the position. 
**                      fails with OutOfBounds if element cannot be retrieved
*/

#define _ListAt(list,pos)	*(ASSERT((pos)<_ListLen(list), "OutOfBounds"),(list)+(pos))

/**api* macro ************************************************************
**
**      INPUT:          the LISTv
**      RETURNS:        the first element of the LISTv
*/

#define _ListFirst(list)        _ListAt(list,0)

/**api* macro ************************************************************
**
**      INPUT:          the LISTv
**      RETURNS:        the last element of the LISTv
*/

#define _ListLast(list) 	*(listPos=_ListLen(list),ASSERT(listPos>0, "OutOfBounds"),(list)+(listPos-1))

/* STACK operations */

/**api* macro ************************************************************
**
**	Alias for ListApp 
**      See also: _ListPop, _ListTop
**
**      INPUT:          [W] the pointer to the LISTv to be modified
**      RETURNS:        the new element
*/

#define _ListPush(plist)	_ListApp(plist)

/**api* macro ************************************************************
**
**	Removes the last element of the LISTv
**      See also: _ListPush, _ListTop
**
**      INPUT:          [W] the pointer to the LISTv to be modified
*/

#define _ListPop(plist)		(listPos=_ListLen(*(plist))-1,_ListCut(plist, listPos))

/**api* macro ************************************************************
**
**	Returns the last element of the LISTv. Alias to _ListLast
**      See also: _ListPush, _ListTop
**
**      INPUT:          [W] the pointer to the LISTv to be modified
*/

#define _ListTop(list)          _ListLast(list)

/**************************************************************************
** ALLOCATION POOL
**************************************************************************/

void* palloc(int size);
void  pfree(void* obj, int size);

#define _palloc(type) ((type*)palloc(sizeof(type))) 
#define _pfree(ptr)   (pfree(ptr, sizeof(*(ptr))))

void PoolDebug(int size);
void PoolDebugAll();

#endif











UT:          [W] the pointer to the LISTv to be modified
*/

#define _ListTop(list)          _ListLast(list)

/**************************************************************************
** ALLOCATION POOL
**************************************************************************/

void* palloc(int size);
void  pfree(void* obj, int size);

#define _palloc(type) ((type*)palloc(sizeof(type))) 
#define _pfree(ptr)   srs/src/local.c
#include <stdio.h>
#include <stdlib.h>
#include <stdarg.h>
#include <ctype.h>

#define DECLARE_ONLY
#include "srs.h"


INT4 IopCalc ()
{
  INT4 l, r, result;
  char op[10];
  
  IargGetArgs ("op|r|l", op, &r, &l);
  switch (*op) {
  case '+':
    result = l + r;
    break;
  case '-':
    result = l - r;
    break;
  case '/':
    result = l / r;
    break;
  case '*':
    result = l * r;
    break;
  }
  IcaReturn ("int", result);
}

void LocalSetFunctions ()
{
  IcaSetFunction("IopCalc", (FUNC)IopCalc);
}
include <stdio.h>
#include <stdlib.h>
#include <stdarg.h>
#include <ctype.h>

#define DECLARE_ONLY
#include "srs.h"


INT4 IopCalc ()
{
  INT4 l, r, result;
  char op[10];
  
  IargGetArgs ("op|r|l", op, &r, &l);
  switch (*op) {
  case '+':
    result = l + r;
    break;
  case '-':
    result = l - r;
    break;
  case '/':
    result = l / r;
    break;
  case '*':
    result = l * r;
    break;
  }
  IcaReturn ("int", result);
}

void LocalSetFunctions ()
{
  IcaSetFunction("IopCalcsrs/src/logicals.c
char logicals_ID[] = "$Id: logicals.c,v 1.2 1996/11/25 20:14:55 etzold Exp $";
/*
**
**    $RCSfile: logicals.c,v $
**    $Revision: 1.2 $
**    $Date: 1996/11/25 20:14:55 $
**    $Author: etzold $
**
**    $Locker:  $
**    $State: Exp $
**
**    Author of this module: Lukas Rosenthaler and Reinhard Doelz
**    Heavy Modifications by Thure Etzold and John Smith
** Copyright granted to Thure Etzold for distribution withing the SRS package
**
******************************************************************************
**
 *    ***********************************************************
 *    *                                                         *
 *    *         BIOFTP.UNIBAS.CH SOFTWARE DISTRIBUTION          * 
 *    *                                                         *
 *    *---------------------------------------------------------*
 *    *                    Copyright notice                     *
 *    *                                                         *
 *    * This program package has been written starting from '92 *
 *    * at the Biocomputing Laboratory, University of Basel, by *
 *    * Lukas Rosenthaler. Though it has been a major effort to *
 *    * make it work, no responsibility can be taken for errors *
 *    * occuring while running the programs  or  resulting from *
 *    * processing  the program's output.  The writing of these *
 *    * was supported by Basel  University.                     *
 *    *                                                         *
 *    * This  program is public domain and can by used,  copied *
 *    * and  modified  without  restriction  as  long  as  this *
 *    * copyright notice is included.                           *
 *    *                                                         *
 *    * This program version can be obtained  from  the  bioftp *
 *    * anonymous ftp server,  together with the  README  file. *
 *    * Software may be used without charge following the rules *
 *    * stated therein. Users should   acknowledge  the program *
 *    * properly  if  results  to  be  published  are obtained. *
 *    ***********************************************************
 *
 *
 * +----------------------------+--------------------------------------+
 * |   Dr. Lukas Rosenthaler    | RF *   rosenth@urz.unibas.ch         |
 * |      Biocomputing          | DECNET 20579::48130::rosenth         |
 * |Biozentrum der Universitaet |                                      |
 * |   Klingelbergstrasse 70    | FAX    +41 61 261- 6760 or 267- 2078 |
 * |     CH-4056 Basel          | TEL    +41 61 267- 2076 or 2247      |   
 * +----------- bioftp.unibas.ch is the SWISS EMBnet node -------------+
 *             -----------------------------------------
 *
 ******************************************************************************
 */


/******************************************************************************
 *
 * Description, Purpose
 * ^^^^^^^^^^^^^^^^^^^^
 *
 * This modules implements a consistent handling of VMS logicals and
 * Unix environment variables (furtheron the term "logicals" is applied
 * both to VMS logical names and Unix environment variables).
 * The logicals may be nested, as long as the first component of a pathname
 * is a logical. A logical itself may reference another logical up to a
 * nesting depth of 32.
 *
 * Examples:
 *    VMS:
 *       $ define GCGDIR D$DISK:[SOFTWARE.GCG.]
 *       $ define DATADIR GCGDIR:[PROTDATA.]
 *       $ define WORKDB DATADIR:[WORK]WORKING_DATABASE.DAT
 *
 *          WORKDB will translate to:
 *             "D$DISK:[SOFTWARE.GCG][.PROTDATA.][WORK]WORKING_DATABASE.DAT"
 *       
 *    Unix: (assuming /bin/csh)
 *       % setenv GCGDIR /usr/software/gcg
 *       % setenv DATADIR GCGDIR/protdata
 *       % setenv WORKDB DATADIR/work/working_database.dat
 *
 *          WORKDB will translate to:
 *             "/usr/software/gcg/protdata/work/working_database.dat"
 *
 ******************************************************************************
 *
 * include files:
 *
 */

#include <string.h>
#include <ctype.h>

#ifdef VMS
#  include unixio
#  include stdio
#  include stdlib
#else
#  include <stdio.h>
#  include <stdlib.h>
#endif


#if defined dos
# define SLASH '\\'
# else
# define SLASH '/'
#endif

#define PATH_BUF_LEN 132	/* maximal length of pathname */


/***api* LogNameTranslate *****************************************************
**
**   Translation of (possibly recursive) definition of VMS logical names of
**   Unix environment variables. The routine uses the "getenv()" call which,
**   in Unix, just returns the value of an environment variable. On VMS,
**   "getenv()" first tries to use it's argument as a logical name that is to
**   be translated, then searches the symbol name space.
**
**   translate_logical() can resolve recursive definition of logiacls/environ-
**   ment variables as long as the logical is always the first component of
**   the path. The nesting depth may *NOT* be greater than 32 in order to
**   prevent infinite loops which may occur (logical ONE points to TWO, which
**   itself is a logical pointing to ONE...)
**
**   If there is no translation, the routine returns the original path.
**   The routine does *NOT* allocate memory for the translated path, so the
**   caller has to provide the buffer and indicate it's length!
**
 * Parameters          :
 *    char *name       : path to translate
 *    char *trans_name : translated path
 *    int  len         : length of string supplied as trans_name
 *
**	RETURNS:       success or failure
*/

int LogNameTranslate (char *name, char *trans_name, int len)
{
  char strbuf1[PATH_BUF_LEN], strbuf2[PATH_BUF_LEN], log[PATH_BUF_LEN];
  char *strptr;
  int depth, i, l;
  int no_more_trans;

  no_more_trans = 0;
  depth = 0;
  (void) strncpy (strbuf1, name, PATH_BUF_LEN);
	
  do {
   /*
    * search first delimiter in string.
    */
#   ifdef VMS
    strptr = strchr (strbuf1, ':');
#   else
    if ((strptr = strchr (strbuf1, ':')) == NULL) {
      strptr = strchr (strbuf1, SLASH);
    }
    else {
      strptr[0] = SLASH;
    }
#   endif
    if (strptr != NULL) { /* we do have a delimiter, we try to translate
                               only up to the delimiter */
      l = strptr - strbuf1;
      for (i = 0; i < l; i++) log[i] = strbuf1[i];
      log[i] = '\0';
    }
    else { /* no delimiter, we try to translate the whole string */
      l = 0;
      (void) strcpy (log, strbuf1);
    }

#   ifdef VMS
    for (i = 0; i _LT_ strlen (log); i++) log[i] = (char) toupper ((int) log[i]);
#   endif
    if ((strptr = getenv (log)) != NULL) {
     /*
      * ok, we found translation
      */
      (void) strcpy (strbuf2, strptr);
      if (l > 0) {
#ifdef VMS
       /*
        * delimiter ":" included
        */
	(void) strcat (strbuf2, &(strbuf1[l + 1])); 
#else
       /*
        * delimiter "/" or "\" for dos, *NOT* included
        */
	(void) strcat (strbuf2, &(strbuf1[l]));
#endif
      }
      (void) strcpy (strbuf1, strbuf2);
    }
    else { /* sorry, no translation */
      no_more_trans = 1;
    }
    depth++;
  } while ((! no_more_trans) && (depth < 32));

 /*
  * check, if logicals are too deeply nested, as e.g.
  *
  * VMS: define TEST MIST:
  *      define MIST TEST:
  * unix: setenv TEST MIST
  *       setenv MIST TEST
  *
  * These declarations will produce infinte loops
  * in resolving the "logicals".
  * Therefore we allow only a depth of 32 !
  */
  if (depth == 32) { /* infinite loop ? */
    return (999);
  }

 /*
  * result string supplied was too short
  */
  if (strlen (strbuf1) > len) {
    return (999);
  }
  else {
#if defined dos
	{
	char * ds;
	if((ds=strstr(strbuf1,"\\\\"))==NULL); /* no double bslashes found */
	else{
		/* conv \\ to :\ */
		*ds=':';
		}
	}
#endif
    (void) strcpy (trans_name, strbuf1);
  }

  return (0);
}


ons will produce infinte loops
  * in resolving the "logicals".
  * Therefore we allow only a depth of 32 !
  */
  if (depth == 32) { /* infinite loop ? */
    return (999);
  }

 /*
  * result string supplied was too short
  */
srs/src/logicals.h
**
**    $RCSfile: logicals.h,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:16:54 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**    Author of this module: Lukas Rosenthaler and Reinhard Doelz
** Copyright granted to Thure Etzold for distribution withing the SRS package
**
**
**    ********************************************************************
**    *                                                                  *
**    *          BIOFTP.UNIBAS.CH SOFTWARE DISTRIBUTION                  *
**    *                                                                  *
**    *                     Copyright Notice                             *
**    *                     ================                             *
**    *                                                                  *
**    * This include file contains the declarations for "logcials.c"     *
**    * Biocomputing Laboratory,  University of Basel,  by  Lukas Rosen- *
**    * thaler.  For a detailed copyright notice  see the README file or *
**    * or the C source files!                                           *
**    ********************************************************************
**
*******************************************************************************
*/

#ifdef _NO_PROTO

extern INT4 translate_logical ();

#else

extern INT4 translate_logical (char *name, char *trans_name, INT4 len);

#endif
uting Laboratory,  Unisrs/src/lst.c
char lst_ID[] = "$Id: lst.c,v 1.3 1997/03/17 23:24:01 srs Exp $";
/*
**
**    $RCSfile: lst.c,v $
**    $Revision: 1.3 $
**    $Date: 1997/03/17 23:24:01 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**             Author: Gerald Schaefer
**                     EMBL, Meyerhofstrasse 1
**                     69012 Heidelberg, Germany
**                     Tel: 06221 387372
**                     Email: schaefer@embl-heidelberg.de
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**
**    Description
**    ===========
**
**    management of a list of generic objects
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*/

#include <stdio.h>
#include <string.h>
#include <stdlib.h>

typedef int INT4;
/*#include "message.h"*/
#include "lst.h"
#include "sdlget.h"

#if !defined(TRUE)
#define TRUE   1
#define FALSE  0
#endif

#define  LSTxOBJNAMELEN   20
#define  LSTxDEFLISTSIZE  2
#define  LSTxDEFHASHSIZE  2

/*
**   LSTxHFREE means that this hash table element was never used before
**   LSTxHDEL  means that the element was used before but deleted now
*/
#define  LSTxHFREE  (void*)1L
#define  LSTxHDEL   (void*)0L

/*
** structure definition of the manager object, each list
** has one manager
*/
typedef struct {
    void **first_list_elem;  /* address of an array of void pointers  */
                        /* pointing to the objects. The array is */
                        /* automatically doubled, if overflow    */
    INT4 max_list_elem;  /* max. number of objects to be handled by the list */
    INT4 last;      /* index of last inserted element in the list */
    INT4 current;   /* index of currently active object           */
    
    INT4 flex;      /* flexible names */
    INT4 not_hashed;     /* counter for not-hashed objects (see delete) */

    void **first_hash_elem;  /* address of an array of void pointers  */
                        /* pointing to the objects. The array is */
                        /* automatically doubled, if overflow    */
    INT4 max_hash_elem;  /* max. number of objects in the hash table */
    INT4 cur_hash_elem;  /* current number of objects in the hash table */
} LSTo;

/*
** type definition of the smallest object that can be stored
** in any list. All user defined objects must have these three
** attributes before its problem specific attributes.
** The first two attributes are initialized and maintained by
** the list module. The third attribute must be initialized
** by the application modules. If the application module never
** uses a search by name this attribute may be skipped.
*/
typedef struct {
    LSTo *manager;  /* the first three attributes are necessary  */
    INT4 type_id;   /* for all objects to be managed by the list */
    char name[LSTxOBJNAMELEN];
} LSToOBJ;

typedef struct {
    LSTo *manager;  /* the first three attributes are necessary  */
    INT4 type_id;   /* for all objects to be managed by the list */
    char *name;     /* flexible name length */
} LSToOBJFLEXNAME;


/*
** by means of the following object type, any object may be fully
** described, that should be handled by the list module. The list
** module needs for each type of object the size (for allocation)
** and the functions to initialize, delete, or dump the objects.
*/
typedef struct {
    LSTo *manager;  /* manager of list of manager_objects        */
    INT4 type_id;    /* manager_object has type_id = 0            */
    char name[LSTxOBJNAMELEN];  /* unused here */
    INT4 obj_id;     /* object_id (i.e. type_id of object to be managed) */
                    /* not really necessary at the moment == manager->last  */
    INT4 size;       /* size of object */
    INT4 flex;       /* flexible names (pointer instead of array) */
    void (*init_f)(void *);    /* pointer to initialization function */
    void (*delete_f)(void *);  /* pointer to destructor function */
    void (*print_f)(FILE *, void *);   /* pointer to dump function */
} LSToMANAGER;


/*
** static function prototypes of list module
*/
static LSTo *LstNewList(INT4 type_id);
static INT4 LstIsList(LSTo *man);
static LSTo *LstGetManager(void *obj);
static unsigned LstHashFunc (LSTo *man, char *s);
static INT4 LstHashObject(LSTo *man, void *obj);
static INT4 LstHashUpdate(LSTo *man);
static INT4 LstInsert(LSTo *man, void *obj);
static INT4 LstGetObjSize(INT4 type_id);
static void LstDeleteOne(void *obj);
static INT4 LstRemoveFromList(void **obj);


/*
** info_list is the internal list of the list module, by which the
** types of that objects are managed that will be able to be inserted
** into any other list. The pointer value NULL means that the list
** has not been initialized yet.
*/
static LSToMANAGER *info_list = NULL;

/*
** normally there are object type dependent functions used to initialize
** new objects, to delete an object or to print the attribute values of
** an object. But there could be situations were you do not need one of
** these functions (e.g., you do not need a delete function if there are
** no pointers to subobjects, which should be deleted recursively).
** To supply the application programmer with a comfortable solution when
** he does not want to provide a special function, it has been implemented
** that the application programmer may supply NULL, if he does not need
** to program a special function. To prevent a segmentation fault the 
** following dummy function is used in that case.
** For better testing there are now three different dummy functions
**   init_dummy, delete_dummy, print_dummy
**  calling the functions supplying a NULL-Pointer as parameter should print
**  the function name (for use in LstInfo)
*/
static void init_dummy(void *x)
{
    if (!x) printf(" *init_dummy* ");  /* see LstInfo */
#if defined(TRACE)
    printf("*** function init_dummy called ***\n");
#endif
    /*
    **  may be called, if nothing to initialize
    */
}
static void delete_dummy(void *x)
{
    if (!x) printf(" *delete_dummy* ");  /* see LstInfo */
#if defined(TRACE)
    printf("*** function delete_dummy called ***\n");
#endif
    /*
    **  may be called, if nothing to delete
    */
}
static void print_dummy(FILE *file,  void *x)
{
    if (!x) printf(" *print_dummy* ");  /* see LstInfo */
#if defined(TRACE)
    printf("*** function print_dummy called ***\n");
#endif
    /*
    **  may be called, if nothing to print
    */
}


/**api* LstInfo ***********************************************************
**
**      gets the manager object of the info_list and checks it.
**      Prints the information on all classes that can be managed.
**
**      INPUT:
**              IMPLICIT:
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstInfo()
{
    LSTo *man;
    INT4 i;

    man = LstGetManager(info_list);
    if (!man) {
        return 0;
    }

    printf("*******  List Info  ***************\n");
    printf("* List Module can manage %d different classes:\n", man->last + 1);

    /*
    ** print the attribute values of all objects in the ordered object list
    */
    for (i=0; i <= man->last; i++) {
        printf("...Class%d: ", i);
        printf("  ..ObjID: %d ", ((LSToMANAGER*)man->first_list_elem[i])->obj_id);
	printf("  ..Size:  %d ", ((LSToMANAGER*)man->first_list_elem[i])->size);
        ((LSToMANAGER*)man->first_list_elem[i])->init_f(NULL);
	((LSToMANAGER*)man->first_list_elem[i])->delete_f(NULL);
	((LSToMANAGER*)man->first_list_elem[i])->print_f(NULL, NULL);
    }
    
    return 1;
}
   

/**api* LstManageClass ********************************************************
**
**      registers a new class to be managed by the list module. The type_id is 
**      passed back to the calling function. The class description (object 
**      size, functions to be used to initialize, delete or print an object
**      of that class) is put into the info_list as a special manager object.
**      If the info list does not already exist, it will be created 
**      automatically.
**      If size is negative, flexible names (char*) are used !
**
**      INPUT:      type id of a new class to be managed by the list module [W]
**                  size of an object of the new class [R]
**                  address of a function to be called to init an object [R]
**                  address of a function to be called to delete an object [R]
**                  address of a function to be called to dump an object [R]
**              IMPLICIT:
**                  info_list (LSToMANAGER *) [W]
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstManageClass(INT4 *newtype_id, INT4 size, void (*init_func)(void *), 
		    void (*delete_func)(void *), 
		    void (*print_func)(FILE *,void *))
{
    /*
    **  only register classes that are not already registered
    **  it is convenient to pass 0 as newtype_id
    */
    if (*newtype_id > 0)  return 0;  /* maybe already registered */

    /*
    **  if info list does not already exist, create info list automatically
    */
    if (!info_list) {
        if (!LstNew((void**)&info_list, 0)) return 0;
        /* the next initializations would not be necessary     */
        /* the values can not be asked for during runtime, as  */
        /* there would result some strange side effects !!     */
        info_list->type_id = 0;
        info_list->obj_id = 0;
	info_list->flex = FALSE;  /* default */
        info_list->size = sizeof(LSToMANAGER);
        info_list->init_f = init_dummy;
        info_list->delete_f = delete_dummy;
        info_list->print_f = print_dummy;
    }

    /*
    **  create a special manager object for the new class and 
    **  put it into info list
    */
    if (!LstNew((void**)&info_list, 0)) return 0;
    info_list->type_id = 0;
    info_list->obj_id = info_list->manager->last;
    if (size>0) {
      info_list->size = size;
      info_list->flex = FALSE;
    }
    else {
      info_list->size = -size;
      info_list->flex = TRUE;
    }
    info_list->init_f = init_func ? init_func : init_dummy;
    info_list->delete_f = delete_func ? delete_func : delete_dummy;
    info_list->print_f = print_func ? print_func : print_dummy;
    *newtype_id = info_list->manager->last;

    return 1;
}


/**api* LstManageClassFlex ************************************************
**
**      registers a new class to be managed by the list module. The type_id is 
**      passed back to the calling function.
**      The object names will have dynamic (flexible) names.
**      More details: see LstManageClass()
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstManageClassFlex(INT4 *newtype_id, INT4 size, void (*init_func)(void *),
			void (*delete_func)(void *), 
			void (*print_func)(FILE *, void *))
{
  return LstManageClass(newtype_id, -size, init_func, delete_func, print_func);
}

/****** LstNewList ************************************************************
**
**      creates and initializes a manager object for a new list and 
**      allocates memory for an array, later used to store addresses 
**      of objects.
**      To increase the speed when searching for named but unordered
**      objects a hash table has been implemented, too.
**
**      INPUT:      type_id of object to create the list for [R]
**              IMPLICIT:
**
**      RETURNS:    address of the manager object on success, NULL otherwise
*/

static LSTo *LstNewList(INT4 type_id)
{
    INT4 i;

    LSTo *list = (LSTo*) malloc(sizeof(LSTo));
    if (!list) return NULL;  /* error handling ... */

    /*
    **  initialize list
    */
    list->max_list_elem = LSTxDEFLISTSIZE;
    list->first_list_elem = (void**)malloc(list->max_list_elem*sizeof(void*));
    if (!list->first_list_elem) {
        free(list);
        return NULL;  /* error handling ... */
    }
    list->last = -1;
    list->current = -1;

    list->flex = FALSE; /* default */
    if (type_id > 0)
      list->flex = ((LSToMANAGER*)info_list->manager->
		    first_list_elem[type_id]) -> flex;

    list->not_hashed = 0;

    /*
    **  initialize hash table
    */
    list->max_hash_elem = LSTxDEFHASHSIZE;
    list->first_hash_elem = (void**)malloc(list->max_hash_elem*sizeof(void*));
    if (!list->first_hash_elem) {
        free(list->first_list_elem);  /* the above allocated array */
        free(list);
        return NULL;  /* error handling ... */
    }
    list->cur_hash_elem = 0;
    for (i=0; i < list->max_hash_elem; i++)
        list->first_hash_elem[i] = LSTxHFREE;

    return list;
}

/****** LstIsList *************************************************************
**
**      checks if the manager object exists an has convenient attribute values.
**
**      INPUT:      address of an existing manager object [R]
**              IMPLICIT:
**
**      RETURNS:    1 if manager object seems ok, 0 otherwise
*/

static INT4 LstIsList(LSTo *man)
{
    /* how to look for correct initialized lists ... ??? */
    if (!man)  return 0;
    if (man->max_list_elem < LSTxDEFLISTSIZE)  return 0;
    if (man->last < 0)  return 0;
    if (man->current < 0)  return 0;

    /* how to look for correct initialized hash table ... ??? */

    return 1;
}

/****** LstGetManager *********************************************************
**
**      checks, if the object exists and if the manager attribute of the object
**      points to a correct manager object.
**
**      INPUT:      address of an existing object [R]
**              IMPLICIT:
**
**      RETURNS:    address of manager object on success, 0 otherwise
*/

static LSTo *LstGetManager(void *obj)
{
    LSTo *man;

    if (!obj) return 0;
    man = ((LSToOBJ*)obj)->manager;
    if (!LstIsList(man)) return 0;
    return man;
}


/****** LstHashFunc ***********************************************************
**
**      computes a hash index for a given string. Needs the manager object
**      to get the current size of the hash table.
**
**      INPUT:      address of an existing manager object [R]
**                  address of an object name to hash [R]
**              IMPLICIT:
**
**      RETURNS:     the computed hash index
*/

static unsigned LstHashFunc (LSTo *man, char *s)
{
  register unsigned long h=0, g;
  register char *p = s;

  while (*p) {
    h= (h << 4) + *p++;
    if ((g= (h & 0xf0000000)))
      h= (h ^ (g >> 24)) ^ g;
  }

#ifdef xxxx
    while (*s)
      h = (h<<5) + *s++;   /* horner's function ...segdewick */


/*        h = (h << 1) ^ *s++; */

#endif
    return h % man->max_hash_elem;
}


/****** LstHashObject *********************************************************
**
**      puts an existing object into the hash table of the specified manager,
**      but only if the object has a name (i.e. name length > 0). 
**      If there exists a collision with the hash index the next free
**      position will be occupied (round robin).
**
**      INPUT:      address of an existing manager object [R]
**                  address of an existing object [R]
**              IMPLICIT:
**                  modifies hash table and manager
**
**      RETURNS:    1
*/

static INT4 LstHashObject(LSTo *man, void *obj)
{
    INT4 i;
    char *key;
    INT4 hash_index;

    /*
    **  insert object in hash table if name is longer than 0
    */

    if (man->flex)
      key =  ((LSToOBJFLEXNAME*)obj)->name;
    else
      key =  ((LSToOBJ*)obj)->name;

    if (key && strlen(key)>0) {
        /* hash object */
        hash_index = (INT4) LstHashFunc(man, key);
#if defined(TRACE)
        printf("hash_index for key *%s* is %d\n", key, hash_index);
#endif

        /* search for next free place */
        for (i=hash_index; i<man->max_hash_elem; i++) 
            if (man->first_hash_elem[i] <= LSTxHFREE) {
                man->first_hash_elem[i] = obj; /* no entry yet */
                man->cur_hash_elem++;
                return 1;
            }

        for (i=0; i<hash_index; i++) 
            if (man->first_hash_elem[i] <= LSTxHFREE) {
                man->first_hash_elem[i] = obj; /* no entry yet */
                man->cur_hash_elem++;
                return 1;
            }
    }
    else 
      return 1;
    return 1;
}

/****** LstHashUpdate *********************************************************
**
**      updates the hash table of the specified manager. All at the moment
**      not-hashed objects will be hashed, if their name length is > 0.
**      If the hash table is not big enough, it will be doubled before
**      hashing objects. For the sake of simplicity the table will be also
**      doubled, if there would be not-hashed unnamed objects.
**
**      INPUT:      address of an existing manager object [R]
**              IMPLICIT:
**                  modifies hash table and manager
**
**      RETURNS:    1 if all named objects have been successfully inserted,
**                  0 otherwise
*/

static INT4 LstHashUpdate(LSTo *man)
{
    INT4 i, rv=1;

    /* be sure that hash table is big enough */
    if (man->cur_hash_elem + man->not_hashed > (man->max_hash_elem * 0.8)) {
       void **tmp;
#if defined(TRACE)
       printf("*** INFO: Expanding hash table from %d to ",
                          man->max_hash_elem);
#endif
        /* extend hash table and rehash all elements in list */
        while (man->cur_hash_elem + man->not_hashed > man->max_hash_elem)
            man->max_hash_elem = man->max_hash_elem * 2  + 7;
#if defined(TRACE)
       printf("%d elements ***\n", man->max_hash_elem);
#endif
        tmp =  (void**) malloc(man->max_hash_elem * sizeof(void*));
        if (!tmp) return 0;  /* no errror message to keep list module 
                                independent from other modules */
        free(man->first_hash_elem);  /* free old array */
        man->first_hash_elem = tmp;  /* use new array  */

        /* mark all elements as not-hashed */
        man->not_hashed = man->last +1;
        for (i=0; i < man->max_hash_elem; i++)
            man->first_hash_elem[i] = LSTxHFREE;
    }

    /* hash all elements not currently hashed */
    for (i = man->last - man->not_hashed + 1; i<=man->last; i++)
        rv &= LstHashObject(man, man->first_list_elem[i]);

    man->not_hashed = 0;
    return rv;
}


/**api* LstHashSearch *********************************************************
**
**      gets the manager object of an existing object list and checks it.
**      Then an object with name obj_name is searched for using the
**      hash table. If there are not-hashed objects the hash table needs
**      to be updated first.
**      Passes the address of the found object back to the calling function.
**
**      INPUT:      address of an address of an existing object [R,W]
**                  address of an object name to search for [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstHashSearch(void **obj, char *obj_name)
{
    LSTo *man;
    LSToOBJ *tmp1;
    LSToOBJFLEXNAME *tmp2;
    INT4 i, rv = 1;
    INT4 stop_search = 0;
    INT4 hash_index;

    if (!strlen(obj_name)) return 0;
    man = LstGetManager(*obj);
    if (!man) return 0;

    /*
    ** if there are not-hashed objects (objects that are only
    ** inserted in the ordered list) update the hash table first
    */
    if (man->not_hashed > 0) 
      rv = LstHashUpdate(man);
    if (rv == 0) 
      return 0;  /* if malloc failed */

    /* get hash index for object name */
    hash_index = (INT4) LstHashFunc(man, obj_name);
#if defined(TRACE)
    printf("hash_index for obj_name *%s* is %d\n", obj_name, hash_index);
#endif

    /* search for object in hash table beginning with hash index */

    if (man->flex) {
      for (i=hash_index; i<man->max_hash_elem; i++) {
        tmp2 = (LSToOBJFLEXNAME*)man->first_hash_elem[i];
        if ((void*)tmp2 == LSTxHFREE) {stop_search = 1;  break;}
        if ((void*)tmp2 == LSTxHDEL)  continue;
        if (!strcmp(tmp2->name, obj_name)) {
	  /* named object found */
	  *obj = (void*)tmp2;
	  return 1;
        }
      }
      
      if (!stop_search)
        for (i=0; i<hash_index; i++) {
	  tmp2 = (LSToOBJFLEXNAME*)man->first_hash_elem[i];
	  if ((void*)tmp2 == LSTxHFREE) {stop_search = 1;  break;}
	  if ((void*)tmp2 == LSTxHDEL)  continue;
	  if (!strcmp(tmp2->name, obj_name)) {
	    /* named object found */
	    *obj = (void*)tmp2;
	    return 1;
	  }
        }
    }
    else {
      for (i=hash_index; i<man->max_hash_elem; i++) {
        tmp1 = (LSToOBJ*)man->first_hash_elem[i];
        if ((void*)tmp1 == LSTxHFREE) {stop_search = 1;  break;}
        if ((void*)tmp1 == LSTxHDEL)  continue;
        if (!strcmp(tmp1->name, obj_name)) {
	  /* named object found */
	  *obj = (void*)tmp1;
	  return 1;
        }
      }
      
      if (!stop_search)
        for (i=0; i<hash_index; i++) {
	  tmp1 = (LSToOBJ*)man->first_hash_elem[i];
	  if ((void*)tmp1 == LSTxHFREE) {stop_search = 1;  break;}
	  if ((void*)tmp1 == LSTxHDEL)  continue;
	  if (!strcmp(tmp1->name, obj_name)) {
	    /* named object found */
	    *obj = (void*)tmp1;
	    return 1;
	  }
        }
    }

    return 0;  /* named object not found */
}


/****** LstInsert *************************************************************
**
**      inserts the address of the object into the list managed 
**      by the manager object.
**      If the list will overflow, the array is automatically doubled in size.
**      If the name of the object is not an empty string, then the object
**      will be inserted into a hash table, too (see LstHashUpdate).
**
**      INPUT:      address of an existing manager object [R]
**                  address of an existing object [R]
**              IMPLICIT:
**                  man (LSTo*) [W]
**
**      RETURNS:    1 on success, 0 otherwise
*/

static INT4 LstInsert(LSTo *man, void *obj)
{
    /*
    ** if list overflows, double object list and restore addresses
    */
    if (man->last >= man->max_list_elem - 1) {
	INT4 i;
        void **tmp =  (void**) malloc(2 * man->max_list_elem * sizeof(void*));
        if (!tmp) return 0;
#if defined(TRACE)
       printf("*** INFO: Expanding object list from %d to ",
                          man->max_list_elem);
#endif

        /*
        ** copy addresses of existing objects
        */
        for (i=0; i < man->max_list_elem; i++)
            tmp[i] = man->first_list_elem[i];
        free(man->first_list_elem);  /* free old array */
        man->first_list_elem = tmp;  /* use new array  */
        man->max_list_elem *= 2;
#if defined(TRACE)
       printf("%d elements ***\n", man->max_list_elem);
#endif
    }
    man->last++;
    man->first_list_elem[man->last] = obj;
    man->current = man->last;
    ((LSToOBJ*)obj)->manager = man;

    /*
    **   update the counter of not-hashed objects
    */
    man->not_hashed++;

    return 1;
}

/****** LstGetObjSize *********************************************************
**
**      The size of the object with type type_id is read from the info_list
**      and returned.
**
**      INPUT:      type id of object [R]
**              IMPLICIT:
**                  info_list (LSToMANAGER *) [R]
**
**      RETURNS:    size of object with type type_id; 0 if type_id incorrect
*/

static INT4 LstGetObjSize(INT4 type_id)
{
    /*
    ** in the initialization phase info_list does not already
    ** exist when the size of the manager object (type_id == 0)
    ** has to be queried. The order of the following if-statements
    ** is very important to prevent a segmentation fault !
    */
    if (type_id == 0)  return sizeof(LSToMANAGER);
    if (type_id < 0)   return 0;
    if (!info_list)  return 0;
    if (type_id > info_list->manager->last)  return 0;

    return ((LSToMANAGER*)info_list->manager->first_list_elem[type_id])->size;
}

/**api* LstInsertObject *******************************************************
**
**      inserts an already existing object into an object list.
**      If the object list does not already exist, it will be created
**      automatically.
**      Remember that the user of this function has to set the name and
**      the type_id of the object correctly before inserting: there will
**      be no initialization here.
**      If this function fails, 0 will be returned, but the object will
**      not be destroyed.
**      If the complete list will be destroyed later, the object inserted
**      by this function will be destroyed, too. 
**      If the name of the object is not an empty string, the object will 
**      be inserted into a hash table, if LstHashSearch will be used.
**
**      INPUT:      address of an address of an existing object [W]
**                  address of an existing object [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstInsertObject(void **obj, void *new_obj)
{
    LSTo *man;

    /*
    ** if the object list does already exist, get the manager,
    ** if not, create a new list automatically and get the manager.
    */
    if (*obj) {
        man = ((LSToOBJ*)*obj)->manager;
        if (!LstIsList(man)) return 0;
    }
    else 
      man = LstNewList(((LSToOBJ*)new_obj)->type_id);

    /*
    ** insert the new object into the object list. On success modify the first
    ** function parameter to point to the new object, and return 1
    */
    if (LstInsert(man, new_obj)) {
        *obj = new_obj;
        return 1;
    }
    else return 0;  /* object will not be destroyed automatically */
}


/**api* LstNewNamed ***********************************************************
**
**      creates a new object of type type_id and inserts this object into
**      a list. The size of the object (obj_size) is read from the info_list.
**      If the object list does not already exist, it will be created
**      automatically.
**      If name is not NULL, the name will be set after initialization.
**      If the name is not an empty string, the object will be inserted
**      into a hash table, too.
**
**      INPUT:      address of an address of an existing object [W]
**                  type id of object to be created [R]
**                  address of name of object [R]
**              IMPLICIT:
**                  info_list (LSToMANAGER *) [R]
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstNewNamed(void **obj, INT4 type_id, char *name)
{
    LSTo *man;
    void  *tmp;
    INT4  obj_size;

    /*
    ** read object size from info_list and fail if zero
    */
    obj_size = LstGetObjSize(type_id);
    if (obj_size == 0) return 0;

    /*
    ** if the object list does already exist, get the manager,
    ** if not, create a new list automatically and get the manager.
    */
    if (*obj) {
        man = ((LSToOBJ*)*obj)->manager;
        if (!LstIsList(man)) return 0;
    }
    else man = LstNewList(type_id);

    /*
    ** allocate memory for the new object, fail if not enough memory available.
    */
    tmp = (void*) calloc(1, obj_size);
    if (!tmp) return 0;

    /*
    ** save the type_id within the new object, which is important
    ** for initializing, deleting, and printing of the object 
    ** (object type dependent functions)
    */
    ((LSToOBJ*)tmp)->type_id = type_id;
    if (man->flex)  /* name is pointer */
      ((LSToOBJFLEXNAME*)tmp)->name = NULL;

    /* initializing of objects depends on object type !!! */
    if (type_id > 0)
    ((LSToMANAGER*)info_list->manager->
          first_list_elem[((LSToOBJ*)tmp)->type_id]) -> init_f(tmp);

    /* if name is not NULL, set name */
    if (name) {
      if (man->flex) {
	((LSToOBJFLEXNAME*)tmp)->name = (char*)malloc(strlen(name)+1);
	strcpy(((LSToOBJFLEXNAME*)tmp)->name, name);
      }
      else
	strcpy(((LSToOBJ*)tmp)->name, name);
    }
    else {
      if (man->flex)
	((LSToOBJFLEXNAME*)tmp)->name = NULL;
      else
	strcpy(((LSToOBJ*)tmp)->name, "");
    }

    /*
    ** insert the new object into the object list. On success modify the first
    ** function parameter to point to the new object, and return 1
    */
    if (LstInsert(man, tmp)) {
        *obj = tmp;
        return 1;
    }
    else {
        free(tmp);  /* release memory of object that could not be inserted */
        return 0;
    }
}

/**api* LstNew ****************************************************************
**
**      creates a new object of type type_id and inserts this object into 
**      a list. The size of the object (obj_size) is read from the info_list.
**      If the object list does not already exist, it will be created 
**      automatically.
**
**      INPUT:      address of an address of an existing object [W]
**                  type id of object to be created [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstNew(void **obj, INT4 type_id)
{
    return LstNewNamed(obj, type_id, NULL);
}


/**api* LstNewNamedUnique *************************************************
**
**      creates a new object of type type_id and inserts this object into 
**      a list, if there exists no object with the specified name. 
**      The size of the object (obj_size) is read from the info_list.
**      If the object list does not already exist, it will be created 
**      automatically.
**
**      INPUT:      address of an address of an existing object [W]
**                  type id of object to be created [R]
**                  address of the unique object name [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstNewNamedUnique(void **obj, INT4 type_id, char *name)
{
  void **tmp = obj; /* don't modify the object handle if no object inserted */
  
  if (LstHashSearch(tmp, name))
    return 0;
  
  return LstNewNamed(obj, type_id, name);
}


/**api* LstFirst **************************************************************
**
**      gets the manager object of an existing object list and checks it.
**      Sets the attribute 'current' of the manager to 0 (first object).
**      Passes the address of the current object back to the calling function.
**
**      INPUT:      address of an address of an existing object [R,W]
**              IMPLICIT:
**                  man->current (INT4) [W]
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstFirst(void **obj)
{
    LSTo *man;

    man = LstGetManager(*obj);
    if (!man) return 0;

    man->current = 0;  /* it's sure that last >= 0 */

    /*
    ** modify the object list handle to point to the new current object
    */
    *obj = man->first_list_elem[man->current];

    return 1;
}

/**api* LstLast ***************************************************************
**
**      gets the manager object of an existing object list and checks it.
**      Sets the attribute 'current' of the manager to 'last' (last object).
**      Passes the address of the current object back to the calling function.
**
**      INPUT:      address of an address of an existing object [R,W]
**              IMPLICIT:
**                  man->current (INT4) [W]
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstLast(void **obj)
{
    LSTo *man;

    man = LstGetManager(*obj);
    if (!man) return 0;

    man->current =  man->last;  /* it's sure that last >= 0 */

    /*
    ** modify the object list handle to point to the new current object
    */
    *obj = man->first_list_elem[man->current];

    return 1;
}

INT4 LstIsLast(void *obj)
{
    LSTo *man;

    man = LstGetManager(obj);
    if (!man) return 0;

    return  (man->current ==  man->last) ? 1 : 0;
}



/**api* LstNext  ****************************************************************
**
**      gets the manager object of an existing object list and checks it.
**      Increments the attribute 'current' of the manager (next object).
**      Passes the address of the current object back to the calling function.
**
**      INPUT:      address of an address of an existing object [R,W]
**              IMPLICIT:
**                  man->current (INT4) [W]
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstNext(void **obj)
{
    LSTo *man;

    man = LstGetManager(*obj);
    if (!man) return 0;

    if (man->current ==  man->last)  return 0;
    man->current++;

    /*
    ** modify the object list handle to point to the new current object
    */
    *obj = man->first_list_elem[man->current];

    return 1;
}

/**api* LstPrev ****************************************************************
**
**      gets the manager object of an existing object list and checks it.
**      Decrements the attribute 'current' of the manager (previous object).
**      Sets the attribute 'current' of the manager to 0 (first object).
**      Passes the address of the current object back to the calling function.
**
**      INPUT:      address of an address of an existing object [R,W]
**              IMPLICIT:
**                  man->current (INT4) [W]
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstPrev(void **obj)
{
    LSTo *man;

    man = LstGetManager(*obj);
    if (!man) return 0;

    if (man->current ==  0)  return 0;
    man->current--;

    /*
    ** modify the object list handle to point to the new current object
    */
    *obj = man->first_list_elem[man->current];

    return 1;
}

/**api* LstGetPosition ********************************************************
**
**      gets the manager object of an existing object and checks it.
**      Gets the attribute 'current' of the manager and returns it via 'n'.
**
**      INPUT:      address of an existing object contained in a list [R]
**                  address of an integer to return the current index [W]
**              IMPLICIT:
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstGetPosition(void *obj, INT4 *n)
{
    LSTo *man;

    man = LstGetManager(obj);
    if (!man) return 0;

    *n = man->current;

    return 1;
}

/**api* LstSetPosition *****************************************************
**
**      gets the manager object of an existing object list and checks it.
**      Sets the attribute 'current' of the manager to 'n', if correct.
**      Passes the address of the current object back to the calling function.
**
**      INPUT:      address of an address of an existing object [R,W]
**                  position of an existing object in manager array [R]
**              IMPLICIT:
**                  man->current (INT4) [W]
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstSetPosition(void **obj, INT4 n)
{
    LSTo *man;

    man = LstGetManager(*obj);
    if (!man) return 0;

    if (n < 0 || n > man->last)  return 0;
    man->current = n;

    /*
    ** modify the object list handle to point to the new current object
    */
    *obj = man->first_list_elem[man->current];

    return 1;
}

/**api* LstSetObjCurrent ***************************************************
**
**      gets the manager object of an existing object list and checks it.
**      Then the object 'newcurr' is searched for in the object list.
**      The search begins with the first object.
**      Sets the attribute 'current' of the manager to the index of the
**      object 'newcurr'.
**      Passes the address of the current object back to the calling function.
**
**      INPUT:      address of an address of an existing object [R,W]
**                  address of an object to search for [R]
**              IMPLICIT:
**                  man->current (INT4) [W]
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstSetObjCurrent(void **obj, void *newcurr)
{
    LSTo *man;
    INT4 i;

    man = LstGetManager(*obj);
    if (!man) return 0;

    for (i=0; i <= man->last; i++)
        if (man->first_list_elem[i] == newcurr) {
            man->current = i;
            *obj = man->first_list_elem[man->current];
            return 1;
        }

    return 0;
}


/**api* LstFirstNamed *********************************************************
**
**      gets the manager object of an existing object list and checks it.
**      Then an object with name obj_name is searched for in the object list.
**      The search begins with the first object.
**      Sets the attribute 'current' of the manager to the index of the
**      object found first.
**      Passes the address of the current object back to the calling function.
**
**      INPUT:      address of an address of an existing object [R,W]
**                  address of an object name to search for [R]
**              IMPLICIT:
**                  man->current (INT4) [W]
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstFirstNamed(void **obj, char *obj_name)
{
  LSTo *man;
  INT4 i, startpos=0;
  char *name;

  man = LstGetManager(*obj);
  if (!man) return 0;
  
  for (i=startpos; i <= man->last; i++) {
    if (man->flex)
      name = ((LSToOBJFLEXNAME*)man->first_list_elem[i])->name;
    else
      name = ((LSToOBJ*)man->first_list_elem[i])->name;

    if (!strcmp(name, obj_name)) {
      man->current = i;
      *obj = man->first_list_elem[man->current];
      return 1;
    }
  }
  
  return 0;
}

/**api* LstNextNamed **********************************************************
**
**      gets the manager object of an existing object list and checks it.
**      Then an object with name obj_name is searched for in the object list.
**      The search begins with the object after current.
**      So you can't find the first object using this function !
**      Sets the attribute 'current' of the manager to the index of the
**      object found first.
**      Passes the address of the current object back to the calling function.
**
**      INPUT:      address of an address of an existing object [R,W]
**                  address of an object name to search for [R]
**              IMPLICIT:
**                  man->current (INT4) [W]
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstNextNamed(void **obj, char *obj_name)
{
  LSTo *man;
  INT4 i;
  char *name;
  
  man = LstGetManager(*obj);
  if (!man) return 0;
  
  for (i=man->current+1; i <= man->last; i++) {
    if (man->flex)
      name = ((LSToOBJFLEXNAME*)man->first_list_elem[i])->name;
    else
      name = ((LSToOBJ*)man->first_list_elem[i])->name;

    if (!strcmp(name, obj_name)) {
      man->current = i;
      *obj = man->first_list_elem[man->current];
      return 1;
    }
  }
  
  return 0;
}

/****** LstDeleteOne **********************************************************
**
**      deletes the specified object using a special function depending on
**      the object type.  LstDeleteOne can be used only internally in the
**      context of LstDeleteAll or LstDelete because there are no changes
**      to the pointer array of the manager.
**
**      INPUT:      address of an existing object [R]
**              IMPLICIT:
**                  info_list (LSToMANAGER *) [R]
**
**      RETURNS:    nothing
*/

static void LstDeleteOne(void *obj)
{
    /* deletion of objects depends on object type !!! */
    if (((LSToMANAGER*)info_list->manager->
        first_list_elem[((LSToOBJ*)obj)->type_id]) -> flex)
      free( ((LSToOBJFLEXNAME*)obj)->name );

    ((LSToMANAGER*)info_list->manager->
        first_list_elem[((LSToOBJ*)obj)->type_id]) -> delete_f(obj);
    if (!OddIsInDepot ((char *) obj))
      free(obj);
}

/****** LstRemoveFromList *****************************************************
**
**      gets the manager object of an existing object list and checks it.
**      If the current object is not equal to the object passed as argument,
**      the current index is modified first.
**      The pointer array of the manager is rearranged. Also the current
**      object changes. It will be the next object, that has been moved to
**      the position of the deleted object. If there is a reference to the 
**      object in the hash table this reference is removed, too. 
**      IMPORTANT: if the last object is removed from the list, the ordered
**      list, the hash table and the manager is removed also.
**
**      INPUT:      address of an address of an existing object [R,W]
**              IMPLICIT:
**                  man->current (INT4) [W]
**
**      RETURNS:    1 on success, 0 otherwise
*/

static INT4 LstRemoveFromList(void **obj)
{
    LSTo *man;
    INT4 i;
    INT4 rv = 1;

    man = LstGetManager(*obj);
    if (!man) return 0;

    /*
    ** deleting an object is only possible if the object
    ** equals the current object in the ordered list !
    ** if this is not true compute the correct current index
    */
    if (man->first_list_elem[man->current] != *obj)  {
        for (i=0; i <= man->last; i++) {
            if (man->first_list_elem[i] == *obj) {
                man->current = i;
                break;
            }
        }
        if (i > man->last) return 0;  /* object not in ordered list */
        /* -> if it should be possible to delete a hash table object, that */
        /*    is not in the ordered list a boolean variable is needed here */
        /* -> in the current implementation this case will never arise     */
    }

    /*
    ** if the last object is removed from the list, free the
    ** administration objects, too
    */
    if (man->last == 0) {
        free(man->first_list_elem);
        free(man->first_hash_elem);
        free(man);
        /*
        ** modify the object list handle to signal that list deleted;
        ** remember to delete the object in the calling function !!!!
        */
        *obj = NULL;
        return 1;
    }

    /*
    ** if a hash table exists already and there are not-hashed objects
    ** in the ordered list, the hash table needs to be updated before
    ** the pointer to the object is removed
    */
    if (man->cur_hash_elem > 0 && man->not_hashed > 0)  {
        rv = LstHashUpdate(man);
        if (rv == 0) return 0;  /* hash table update failed */
    }

    if (man->cur_hash_elem > 0)  {   /* hash table exists */
        for (i=0; i < man->max_hash_elem; i++)
            if (man->first_hash_elem[i] == *obj) {
                man->first_hash_elem[i] = LSTxHDEL;
                break;
            }
    }
    else man->not_hashed--;  /* up to now hash table does not exist */

    /*
    ** rearrange the pointer array of the manager. Be sure to do this
    ** after!! updating hashtable
    */
    for (i=man->current; i < man->last; i++)
        man->first_list_elem[i] =  man->first_list_elem[i+1];

    man->first_list_elem[man->last] = 0;
    man->last--;
    if (man->current>man->last) man->current = man->last; /* if last deleted */

    /*
    ** modify the object list handle to point to the new current object
    */
    *obj = man->first_list_elem[man->current];
    return 1;
}


/**api* LstDelete *************************************************************
**
**      LstDelete may be called externally. The object is removed from the list
**      i.e. the pointer array of the manager is rearranged. Also the current
**      object changes. It will be the next object, that has been moved to
**      the position of the deleted object. If there is a reference to the 
**      object in the hash table this reference is removed, too. This is all 
**      done by LstRemoveFromList. After all the object is deleted.
**      Caution: the programmer is responsible that the object has the 
**               correct type_id set !
**
**      INPUT:      address of an address of an existing object [R,W]
**              IMPLICIT:
**                  man->current (INT4) [W]
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstDelete(void **obj)
{
    void *tmp;

    /*
    ** remember the object to delete
    */
    tmp = *obj;
    if (!tmp) return 0;

    /*
    ** removes all references to the object
    */
    if (!LstRemoveFromList(obj)) {
      fprintf(stderr, "FATAL_ERROR in LstDelete\n");
      return 0;
    }

    /*
    ** delete the data structure of the object
    ** be sure that the object has the correct type_id set !
    */
    LstDeleteOne(tmp);

    return 1;
}

/**api* LstDeleteNamed ********************************************************
**
**      searchs for the object with the given name and deletes it, if found.
**      LstDeleteNamed may be called externally to delete one named object.
**
**      INPUT:      address of an address of an existing object [R,W]
**                  address of name of object [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstDeleteNamed(void **obj, char *name)
{
    if (!LstFirstNamed(obj, name)) return 0;
    return LstDelete(obj);
}

/**api* LstDeleteToEndOfList **************************************************
**
**      LstDeleteToEndOfList may be called externally to delete all objects 
**      (including the current object) up to the end of the list.
**      Warning: If the first object is the current object, the effect
**               is identical to LstDeleteAll.
**
**      INPUT:      address of an address of an existing object [R,W]
**              IMPLICIT:
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstDeleteToEndOfList(void **obj)
{
    LSTo *man;
    INT4 save;
    INT4 rv=1;

    man = LstGetManager(*obj);
    if (!man) return 0;

    /*
    **  if current object equals first object, delete the complete list
    */
    if (man->current == 0)  return LstDeleteAll(obj);

    /*
    **  Remember index of object, that should be the last afterwards,
    **  and remove all objects behind
    */
    save = man->current - 1;
    while (save < man->last)  rv = LstDelete(obj);

    return rv;
}

/**api* LstDeleteAll **********************************************************
**
**      gets the manager object of an existing object list and checks it.
**      Then deletes all data structures belonging to the list.
**      LstDeleteAll may be called externally to delete all objects
**      inclusive the manager. A NULL pointer is given back to the
**      calling function, so that the next insertion of a new object
**      will automatically generate a new list.
**
**      INPUT:      address of an address of an existing object [R,W]
**              IMPLICIT:
**                  info_list (LSToMANAGER *) [R]
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstDeleteAll(void **obj)
{
    LSTo *man;
    INT4 i;

    man = LstGetManager(*obj);
    if (!man) return 0;

    /*
    ** delete the data structures of all objects
    */
    for (i=0; i <= man->last; i++)
        LstDeleteOne(man->first_list_elem[i]);

    /*
    ** delete the arrays of the manager and the manager itself
    */
    free(man->first_list_elem);  /* delete ordered list */
    free(man->first_hash_elem);  /* delete hash table   */
    free(man);

    /*
    ** modify the object list handle to signal that the list is empty
    */
    *obj = NULL;
    return 1;
}

/**api* LstPrint **************************************************************
**
**      prints the attribute values of the specified object using a
**      special function depending on the object type.
**
**      INPUT:      file descriptor [W]
**                  address of an existing object [R]
**              IMPLICIT:
**                  info_list (LSToMANAGER *) [R]
**
**      RETURNS:    nothing
*/

void LstPrint(FILE *file, void *obj)
{
    /* printing of objects depends on object type !!! */
    ((LSToMANAGER*)info_list->manager->
          first_list_elem[((LSToOBJ*)obj)->type_id]) -> print_f(file, obj);
}

/**api* LstPrintAll ***********************************************************
**
**      gets the manager object of an existing object list and checks it.
**      Prints the attribute values of all objects in the object list.
**
**      INPUT:      address of an existing object [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstPrintAll(void *obj)
{
    LSTo *man;
    INT4 i;

    man = LstGetManager(obj);
    if (!man) {
#if defined(TRACE)
        printf("*** ERROR: no object list found !!! \n");
#endif
        return 0;
    }

#if defined(TRACE)
    printf("* List has %d entries:\n", man->last + 1);
    /* test: generate hash table */  LstHashUpdate(man);
#endif

    /*
    ** print the attribute values of all objects in the ordered object list
    */
    for (i=0; i <= man->last; i++) {
#if defined(TRACE)
        printf("...Object%d: ", i);
#endif
        LstPrint(NULL, man->first_list_elem[i]);
    }

#if defined(TRACE)
    /*
    ** print the attribute values of all objects in the hash table
    */
    if (man->first_hash_elem)  /* hash table exists ? */
    for (i=0; i < man->max_hash_elem; i++) {
        if (man->first_hash_elem[i] <= LSTxHFREE) continue;
        printf("...HashObject%d: ", i);
        LstPrint(NULL, man->first_hash_elem[i]);
    }
#endif

    return 1;
}

/**api* LstPrintAllNames *****************************************************
**
**      gets the manager object of an existing object list and checks it.
**      Prints the names of all objects in the ordered object list.
**
**      INPUT:      address of an existing object [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstPrintAllNames(void *obj)
{
    LSTo *man;
    INT4 i;
    char *name;

    man = LstGetManager(obj);
    if (!man)
        return 0;

    printf("* List has %d entries:\n", man->last + 1);

    /*
    ** print the names of all objects in the ordered object list
    */
    for (i=0; i <= man->last; i++) {
      if (man->flex)
	name = ((LSToOBJFLEXNAME*)man->first_list_elem[i])->name;
      else
	name = ((LSToOBJ*)man->first_list_elem[i])->name;

      printf("...Object%2d: *%s*\n", i, name);
    }
    return 1;
}


/**api* LstLength *************************************************************
**
**      gets the manager object of an existing object list and checks it.
**      If there is a correct list, computes the number of objects in
**      the list and returns it.
**
**      INPUT:      address of an existing object [R]
**              IMPLICIT:
**
**      RETURNS:    length of list  on success, 0 otherwise
*/

INT4 LstLength(void *obj)
{
    LSTo *man;

    man = LstGetManager(obj);
    if (!man) {
#if defined(TRACE)
        printf("*** ERROR: no object list found !!! \n");
#endif
        return 0;
    }

#if defined(TRACE)
    printf("* List has %d entries:\n", man->last + 1);
#endif
    return man->last + 1;
}


/**api* LstRelease ************************************************************
**
**      LstRelease may be called externally. The object is removed from list,
**      i.e. the pointer array of the manager is rearranged. Also the current
**      object changes. It will be the next object, that has been moved to
**      the position of the deleted object. If there is a reference to the
**      object in the hash table this reference is removed, too. This is all
**      done by LstRemoveFromList. The data structures of the
**      object will still survive and the address will be returned.
**
**      INPUT:      address of an address of an existing object [R,W]
**              IMPLICIT:
**                  man->current (INT4) [W]
**
**      RETURNS:    address of released object on success, 0 otherwise
*/

void *LstRelease(void** obj)
{
    void *tmp;

    /*
    ** remember the object to release
    */
    tmp = *obj;
    if (!tmp) return 0;

    /*
    ** removes all references to the object
    */
    if (!LstRemoveFromList(obj)) return 0;

    /*
    ** remove the pointer to the manager and return the address of
    ** the released object
    */
    ((LSToOBJ*)tmp)->manager = NULL;

    return tmp;
}

/**api* LstMove ***************************************************************
**
**      the current object of the source object list is released (see above).
**      Then gets the manager object of the destination list and checks it.
**      If the destination list does not already exist, it is created
**      automatically. Last the released object is inserted into
**      the destination object list.
**
**      As a side effect the current objects of both lists change.
**      In case of the destination list, it will be the inserted object.
**      In case of the source list, it will be the next object that has 
**      been moved to the position of the released object.
**
**      INPUT:    address of an address of the destination object [R,W]
**                address of an address of an existing source object [R,W]
**             IMPLICIT:
**                man->current (INT4) [W]
**
**      RETURNS:   1 on success, 0 otherwise
*/

INT4 LstMove(void** dest, void **source)
{
    LSTo *man;
    void *tmp;

    /*
    ** release the current object in the source list and save
    ** it in tmp. Fail, if there is no object to release.
    */
    tmp = LstRelease(source);
    if (!tmp) {
      fprintf(stderr, "FATAL_ERROR in LstMove (1)\n");
      return 0;
    }

    /*
    ** get the manager of the destination list; if the list does
    ** not already exist, create it automatically.
    */
    if (*dest) {
        man = ((LSToOBJ*)*dest)->manager;
        if (!LstIsList(man)) {
	  fprintf(stderr, "FATAL_ERROR in LstMove (2)\n");
	  return 0;
	}
    }
    else man = LstNewList(((LSToOBJ*)tmp)->type_id);

    /*
    ** insert released object (tmp) into destination list
    */
    if (LstInsert(man, tmp)) {
        *dest = tmp;
        return 1;
    }
    else {
        LstDeleteOne(tmp);   /* delete released object !!??? */
        /*
        ** if failed to insert first object into destination list,
        ** delete the arrays of the manager and the manager itself
        */
        if (man->last < 0) {  /* empty list */
            free(man->first_list_elem);  /* delete ordered list */
            free(man->first_hash_elem);  /* delete hash table   */
            free(man);
        }
	fprintf(stderr, "FATAL_ERROR in LstMove (3)\n");
        return 0;
    }

}


/**api* LstAssign *************************************************************
**
**      assigns an existing parameter list to a sublist of another object.
**      If the destination sublist does already exist, the parameter 
**      list cannot be inserted. The case that the parameter list does
**      not exist is not checked, because LstAssign changes no values
**      in that case. After assignment the parameter list is reset and
**      may therefore be used to initialize any other parameter list.
**
**      INPUT:    address of an empty destination sublist [W]
**                address of an (existing) parameter list [R,W]
**             IMPLICIT:
**
**      RETURNS:   1 on success, 0 otherwise
*/

INT4 LstAssign(void** sublist, void **paramlist)
{
    /*
    ** you can only assign a complete list
    ** no insertion is possible
    */
    if (*sublist) return 0;
    *sublist = *paramlist;

    /*
    ** reset paramlist, so that it can be used for a new list later 
    */
    *paramlist = NULL;
    return 1;
}


/**api* LstChangeObjectName ********************************************
**
**      gets the manager object of an existing object list and checks it.
**      Then changes the name of the specified object.
**      Works for character pointer and character array!
**
**      INPUT:      address of an existing object [R]
**                  address of the new object name [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 LstChangeObjectName(void *tmp, char *name)
{
  LSTo *man;
  char *old_name=NULL;

  man = LstGetManager(tmp);
  if (!man) return 0;

  /* check, if there is an old name that must be freed */
  if (man->flex) {
    old_name = ((LSToOBJFLEXNAME*)tmp)->name;
    if (old_name)
      free(old_name);
  }

  /* set name */
  if (name) {
    if (man->flex) {
      ((LSToOBJFLEXNAME*)tmp)->name = (char*)malloc(strlen(name)+1);
      strcpy(((LSToOBJFLEXNAME*)tmp)->name, name);
    }
    else
      strcpy(((LSToOBJ*)tmp)->name, name);
  }
  else {
    if (man->flex)
      ((LSToOBJFLEXNAME*)tmp)->name = NULL;
    else
      strcpy(((LSToOBJ*)tmp)->name, "");
  }
  
  return 1;
}
me that must be freed */
  if (man->flex) {
    old_name = ((LSToOBJFLEXNAME*)tmp)->name;
    if (old_name)
      free(old_name);
  }

  /* set name */
  if (name) {
    if (man->flex) {
      ((LSToOBJFLEXNAME*)tmp)->name = (chsrs/src/lst.h
**
**    $RCSfile: lst.h,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:16:55 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**             Author: Gerald Schaefer
**                     EMBL, Meyerhofstrasse 1
**                     69012 Heidelberg, Germany
**                     Tel: 06221 387451
**                     Email: schaefer@embl-heidelberg.de
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**
**    Description
**    ===========
**
**    management of a list of generic objects
**    contains prototypes of non-static functions of the list module
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*/

INT4 LstInfo();
INT4 LstManageClass(INT4 *newtype_id, INT4 size, void (*init_func)(void *),
                   void (*delete_func)(void *), 
		   void (*print_func)(FILE *, void *));
INT4 LstManageClassFlex(INT4 *newtype_id, INT4 size, void (*init_func)(void *),
			void (*delete_func)(void *), 
			void (*print_func)(FILE *,void *));
INT4 LstHashSearch(void **obj, char *obj_name);
INT4 LstInsertObject(void **obj, void *new_obj);
INT4 LstNewNamed(void **obj, INT4 obj_id, char *name);
INT4 LstNewNamedUnique(void **obj, INT4 obj_id, char *name);
INT4 LstNew(void **obj, INT4 obj_id);
INT4 LstFirst(void **obj);
INT4 LstLast(void **obj);
INT4 LstNext(void **obj);
INT4 LstPrev(void **obj);
INT4 LstGetPosition(void *obj, INT4 *n);
INT4 LstSetPosition(void **obj, INT4 n);
INT4 LstSetObjCurrent(void **obj, void *newcurr);
INT4 LstFirstNamed(void **obj, char *obj_name);
INT4 LstNextNamed(void **obj, char *obj_name);
INT4 LstDelete(void **obj);
INT4 LstDeleteNamed(void **obj, char *name);
INT4 LstDeleteToEndOfList(void **obj);
INT4 LstDeleteAll(void **obj);
void LstPrint(FILE *file, void *obj);
INT4 LstPrintAll(void *obj);
INT4 LstPrintAllNames(void *obj);
INT4 LstLength(void *obj);
void *LstRelease(void** obj);
INT4 LstMove(void** dest, void **source);
INT4 LstAssign(void** sublist, void **paramlist);
INT4 LstChangeObjectName(void *obj, char *name);

   /* info */
INT4 LstIsLast(void *obj);

/* following functions would be nice .....
       INT4 LstChangeName(char *old_name, char *new_name);
************************************************************/
obj);
void LstPrint(FILE *file, void *obj);
INT4 LstPrintAll(void *obj);
INT4 LstPrintAllNames(void *obj);
INT4 LstLength(void *obj);
void *LstRelease(void** obj);
INT4 LstMove(void** dest, void srs/src/map.c
char map_srs_ID[] = "$Id: map.c,v 1.1 1996/05/06 15:16:56 srs Exp $";
/*
**
**    $RCSfile: map.c,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:16:56 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: rtl, file, sm, message 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    maps a file to memory and provides functions for writing to
**    the file, saving and delteing the mapped memory; Either a
**    file can be created with specified nr. of blocks or existing
**    file can be extended by nr. of blocks.
**    before deleting the mapsection the memory is saved to the file
**    and the unused space of it is deleted; the output file is a
**    Two functions for writing are provided for assuring that
**    the map section is written to in a sequential manner.
**
**    map-section-file:
**	 1) LF-stream file (C-stream-file)
**	 2) first longword contains number of bytes written to file  
**  
**  
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/


#include <stdio.h>
#include <string.h>

#include <ssdef.h>	 /* services definitions */
#include <secdef.h>
#include <rms.h>         /* RMS data structures system */
#include <syidef.h>      /* defines codes for sys$getsyiw */

#include "rtl.h"
#include "message.h"
#include "futil.h"
#include "map.h"


#ifdef __ALPHA

/****** MapPageSize ***********************************************************
** 
** 	determines system's page size at run time - for compatibility 
**      of vms and openvms!
** 
** 	INPUT:	    address of MAPo [W]
**                  address of buffer [W] or NULL
** 		    size of section in bytes [R]
** 
** 	RETURNS:    1
** 		    e__allocfail <item> +
*/ 

int MapPageSize (long *cpupage_z)
{
  /*
  **  structure with item list returned from sys$getsyiw (returns
  **  the size of the page size at run time
  */

  static struct itm {    
    short int buflen;    /* length of buffer in byte */
    short int item_code; /* symbolic item code */
    long      bufadr;    /* address of return value buffer */
    long      retlenadr; /* address of return value buffer length */
  } itemlist[2];
  long cpupage_zlen;
  int  rv;

  itemlist[0].buflen = 4;
  itemlist[0].item_code = SYI$_PAGE_SIZE;
  itemlist[0].bufadr = cpupage_z;
  itemlist[0].retlenadr = &cpupage_zlen;
  itemlist[1].buflen = 0;
  itemlist[1].item_code = 0;

  rv = sys$getsyiw (0, 0, 0, &itemlist, 0, 0, 0);
  _StopIfEven(rv);
  return 1;
}
#endif


/****** MapCreSec *************************************************************
** 
** 	creates a map section - alignes the begin of the buffer to next page 
**      boundary which means the buffer shrinks! make sure it is big enough!
**      buffer size will be tailored so that the end of the
**      buffer falls onto a page boundary as well...
** 
** 	INPUT:	    address of MAPo [W]
**                  address of buffer [W] or NULL
** 		    size of section in bytes [R]
** 
** 	RETURNS:    1
** 		    e__allocfail <item> +
*/ 
   
int MapCreSec (MAPo *m, char *buff, int buff_z)
{
    unsigned int    mapaddr[2], secmask, pagelet_n ;
    int		    rv;						 
    long            pagesize;
    char            *buff_s;

    /*
    ** get cpu specific page size first ...mapped memorymust be aligned 
    ** on that;
    */

#ifdef __ALPHA
    MapPageSize (&pagesize);
#else
    pagesize = 512;
#endif

    /*
    ** calculate new begin of buffer -> to next block boundary ...since
    ** these may result in a decrease of the buffer size the amount of 
    ** bytes shifted must be subtracted from the buffer size;
    */

    if (buff) {
      buff_s = buff;
      buff = (char *) ((((unsigned long) buff - 1) / pagesize) * pagesize +
	      pagesize);  
      buff_z -= buff - buff_s;
      buff_z = (buff_z / pagesize) * pagesize;
      pagelet_n = buff_z / 512;
    }

    /*
    ** define start and end addresses of map section - if buff and buff_z != 0
    */

    mapaddr[0] = buff; 
    mapaddr[1] = mapaddr[0] + buff_z - 1; /* MUST point to last byte in buff */
    secmask = (buff ? 0 : SEC$M_EXPREG) | (m->wrt_f == TRUE ? SEC$M_WRT : 0);
    
    rv = sys$crmpsc (				 
	      &mapaddr, 
	      &(m->raddr), 
	      0, 
	      secmask, 
	      0, 
	      0, 
	      0, 
	      m->chan, 
              pagelet_n, 0, 0, 0);
    _StopIfEven(rv);

    m->data = m->raddr[0];
    m->xbyt = m->raddr[1] - (unsigned int) m->data;  
    if (m->xbyt < buff_z -1 && buff_z != 0 && m->wrt_f)
	_ErrExit3 (e__crmpscfail, pagelet_n, (m->xbyt/512));
    m->trnc_f = TRUE;
    return 1;
}



/**api* MapMem ****************************************************************
**
**  	opens file and maps it to memory for read access only;
**  
**  	INPUT:	    address of map-descriptor [W]
**  		    address of filename [R]
**                  address of buffer [W] or NULL
**                  size of buffer in bytes [R] or 0
**  	        IMPLICIT:
**  
**  	RETURNS:    1 if success
**                  e__filopenerr <file name> +
*/ 

int MapMem (MAPo *m, char *fil_n, void *buff, int buff_z)
{
    struct  FAB	fab;
    struct  RAB	rab;
    int	    k, n, rv, size = 0;

    fab = cc$rms_fab;				 /* init fab		    */
    fab.fab$l_dna = fil_n;
    fab.fab$b_dns = strlen(fil_n);
    fab.fab$l_fop = FAB$M_UFO;			 /* user file open	    */
    /* fab.fab$b_shr = FAB$M_NIL;*/               /* no sharing */
    fab.fab$b_rfm = FAB$C_STMLF;		 /* C stream file	    */
    rv = sys$open (&fab);			 /* open file + get channel */
    if (!(rv % 2))
	_ErrRet2 (e__filopenerr, fil_n);

    m->chan = fab.fab$l_stv;

    m->wrt_f = FALSE;
    rv = MapCreSec(m, buff, buff_z);
    m->foff = m->data;
    m->off = (unsigned int) m->data +  *(m->foff);
    strcpy(m->filn, fil_n);
    return 1;
}




/**api* MapAlloc **************************************************************
**
**  	allocates nr. of blocks, opens file of same size and creates map
**  	section;
**  
**  	INPUT:	    address of MAPo
**  		    address of file name
**  		    nr. of blocks to be allocated
**  
**  	OUTPUT:
**  		    returns:	1 if success 
**  				e__allocfail <item> +
**                               e__filopenerr <fil_nm> +
*/

int MapAlloc (MAPo *m, char *filn, int nbloc)
{
    struct FAB	    fab;
    register	    rv;

    fab = cc$rms_fab;				 /* create file access	    */
    fab.fab$l_dna = filn;			 /* block descr. of file    */
						 /* name		    */
    fab.fab$b_dns = strlen(filn);
    fab.fab$l_alq = nbloc;			 /* nr. of blocks to	    */
    fab.fab$l_fop = FAB$M_UFO;			 /* allocate user file open */
    fab.fab$b_rfm = FAB$C_STMLF;		 /* C stream file no	    */
    fab.fab$b_shr = FAB$M_NIL;			 /* sharing		    */

    rv = sys$create (&fab);			 /* open file + get channel */
    if (rv % 2 == 0)
	_ErrRet2 (e__filopenerr, filn);

    m->chan = fab.fab$l_stv;

    m->wrt_f = TRUE;
    rv = MapCreSec(m, NULL, nbloc*512);

    strcpy(m->filn, filn);
    m->off = m->data + 4;			 /* room for offset	    */
    m->foff = m->data;
    *(m->foff) = 4;
    return 1;
}


/**api* MapExtend *************************************************************
**
**  	opens existing file and adds specified nr. of blocks to it - resultant
**  	file is mapped to memory;
**      If nbloc ==0 file has to be opened in order to get the section's size;
**  
**  	INPUT:	    address of MAPo
**  		    address of filename
**  		    nr. of blocks to add
**  
**  	OUTPUT:
**  		    returns:	1
**                              e__filopenerr <fil_nm> +
*/ 
   
int MapExtend (MAPo *m, char *filn, int nbloc)
{
    struct  FAB	fab;
    struct  RAB	rab;
    char    blocks[32767];			 /* 64 blocks		    */
    int	    k, n, rv, size;

    fab = cc$rms_fab;				 /* init fab		    */
    fab.fab$l_dna = filn;
    fab.fab$b_dns = strlen(filn);

    fab.fab$b_fac = FAB$M_UPD | FAB$M_BIO | FAB$M_PUT;
    fab.fab$w_mrs = sizeof(blocks);		 /* max. record size	    */

    rab = cc$rms_rab;				 /* init rab		    */
    rab.rab$l_fab = &fab;
    rab.rab$l_rbf = &blocks;
    rab.rab$b_rac = RAB$C_RFA;			 /* acc. by record file	    */
    rab.rab$l_rop = RAB$M_EOF;			 /* addr.  pos. at EOF	    */
						 /* after open		    */
    rab.rab$w_rsz = fab.fab$w_mrs;

    rv = sys$open (&fab);			 /* open file + get channel */
    if (rv % 2 == 0)
    {
	_ErrMsg2 (e__filopenerr, filn);
	_StopIfEven(rv); 
    
    }
    rv = sys$connect (&rab);
    if (rv % 2 == 0)
	_ErrRet2 (e__filopenerr, filn);

    rv = sys$write (&rab);			 /* get file siz after	    */
						 /* $write		    */
    _StopIfEven(rv); 
    size = 64 + (int) rab.rab$w_rfa[0] - 1;

    if ((nbloc = nbloc - 64) > 0)		 /* write more if necess.   */
    {
	n = MapMOD(nbloc, 64);
	for (k = 0;  k < n;  k++)
	{
	    size += 64; 
	    rv = sys$write (&rab);
	    _StopIfEven(rv); 
	}
    }
    rv = sys$close (&fab);
    _StopIfEven(rv); 
    
    fab.fab$l_fop = FAB$M_UFO;			 /* user file open no	    */
						 /* sharing C stream file   */
    if (!m->wrt_f) fab.fab$b_fac = FAB$M_GET;
    fab.fab$b_shr = m->wrt_f ? FAB$M_NIL : FAB$M_SHRGET;
    fab.fab$b_rfm = FAB$C_STMLF;		 /* open file + get channel */
    rv = sys$open (&fab);
    _StopIfEven(rv); 
    m->chan = fab.fab$l_stv;

    rv = MapCreSec(m, NULL, size*512);
    m->foff = m->data;
    m->off = m->data +  *(m->foff);
    strcpy(m->filn, filn);
    return 1;
}



/**api* MapFree ***************************************************************
**
**  	frees map section + updates i.e. writes mapped file;
**       writes two extra '\n' - the first is supposed to be the last record's 
**       end and the second is for rfa-access in MapTruncate - otherwise
**  	unpredictable positioning
**  
**  	INPUT:	    address of MAPo
**  
**  	OUTPUT:
**    		    returns:	1
*/

int MapFree(MAPo *m)
{
    int	    rv;
    
    if (m->wrt_f)
    {
	*(m->off) = '\n';			 /* for rfa access for rfa  */
	*(m->off+1) = '\n';			 /* access		    */
    }	
    rv = sys$deltva (				 /* del map sect + update   */
						 /* fil			    */
	      &(m->raddr), 0, 0); 
    _StopIfEven(rv);
/*    free(m->alloc);*/

    rv = sys$dassgn (m->chan);			 /* close file		    */
    _StopIfEven(rv);

    if (m->trnc_f && m->wrt_f)
	MapTruncate(m);				 /* cut off unused space    */
    return 1;
}




/****** MapTruncate ***********************************************************
** 
** 	truncates a file to the size that is really used (MAPo->off);
** 
** 	INPUT:	    address of MAPo
** 
** 	OUTPUT:
** 		    returns:	1
*/ 
   
int MapTruncate (MAPo *m)
{
    struct  FAB	fab;
    struct  RAB	rab;
    int	    rv, nbyte, blocn, off;

    fab = cc$rms_fab;				 /* init fab		    */
    fab.fab$l_dna = m->filn;
    fab.fab$b_dns = strlen(m->filn);
    fab.fab$b_fac = FAB$M_TRN | FAB$M_UPD;	 /* truncate access trunc   */
    fab.fab$l_fop = FAB$M_TEF;			 /* alloc at EOF C stream   */
    fab.fab$b_rfm = FAB$C_STMLF;		 /* file no sharing	    */
    fab.fab$b_shr = FAB$M_NIL;

    rab = cc$rms_rab;				 /* init rab		    */
    rab.rab$l_fab = &fab;
    rab.rab$b_rac = RAB$C_RFA;			 /* acc. by record file	    */
						 /* addr.		    */

    rv = sys$open (&fab);			 /* access file		    */
    _StopIfEven(rv); 
    rv = sys$connect (&rab);
    _StopIfEven(rv); 
						 /* goto end of file	    */
    nbyte = (unsigned int) m->off - (unsigned int) m->data;
    blocn = nbyte / 512;
    off = nbyte - blocn * 512+1;
    blocn = off == 0 ? blocn: blocn + 1;
    rab.rab$w_rfa[0] = blocn;
    rab.rab$w_rfa[2] = off;
    rv = sys$find (&rab);
    _StopIfEven(rv); 

    rv = sys$truncate (&rab);			 /* truncate		    */
    _StopIfEven(rv); 

    rv = sys$close (&fab);
    _StopIfEven(rv); 
    return 1;
}




/****** MapNew ****************************************************************
** 
** 	returns relative section file's address of begin of unused space;
** 	only MapPutS and MapWrite may be used for writing to the map-section;
** 
** 	INPUT:	    address of MAPo
** 		    address of address where to put file address
** 
** 	OUTPUT:	    places file address into transm. address
** 		    returns:	1 if success
*/ 
   
int MapNew (MAPo *m, unsigned int *fadd)
{
    *fadd = *(m->foff);
    return 1;
}


/**api* MapCNew ***************************************************************
** 
** 	returns relative file address of begin of unused space in cache;
** 	only MapCWrite may be used for writing to the cache;
** 
** 	INPUT:	    address of MAPoCCH
** 		    address of address where to put file address
** 
** 	OUTPUT:	    places file address into transm. address
** 		    returns:	1 if success
*/ 
   
int MapCNew (MAPoCCH *c, unsigned int *fadd)
{
    *fadd = *(c->foff);
    return 1;
}


/****** MapPutS ***************************************************************
** 
** 	puts a 0-terminated string at the end of used space in map-section
** 	map->off and map->foff are updated according to string length;
** 
** 	INPUT:	    address of MAPo
** 		    address of string
** 
** 	OUTPUT:
** 		    returns:	1 if success
** 				e__eom < file-name, max nr. of bytes>
*/ 
   
int MapPutS (MAPo *m, char *s)
{
    int	len;
    
    len = strlen(s);
    if (*m->foff + len + 1 > m->xbyt)
	return e__eom;
    strcpy(m->off, s);
    m->off = (unsigned int) m->off + len + 1;
    *(m->foff) = *(m->foff) + len + 1;
    return 1;
}



/****** MapWrite **************************************************************
** 
** 	appends specified nr. of bytes to end of used map-section;
** 
** 	INPUT:	    address of MAPo
** 		    address of source
**                  nr. of bytes to be transferred
** 
** 	OUTPUT:
** 		    returns:	1 if ok
** 				e__eom < file-name, max nr. of bytes>
*/ 
   
int MapWrite (MAPo *m, char *s, int n)
{
    if (*m->foff + n > m->xbyt)
	return e__eom;
    memcpy(m->off, s, n);
    m->off = (unsigned int) m->off + n;
    *(m->foff) +=  n;
    return 1;
}

/****** MapMalloc *************************************************************
** 
** 	same as malloc but allocates in map-section;
** 
** 	INPUT:	    address of MAPo
**                  nr. of bytes to be allocated
** 
** 	OUTPUT:
** 		    returns:	address of allocated area if ok
** 				NULL if e__eom 
*/ 
char *MapMalloc (MAPo *m, int n)
{
    char    *off_s;
    
    if (*m->foff + n > m->xbyt)
	return NULL;
    off_s = m->off;
    m->off = (unsigned int) m->off + n;
    *(m->foff) +=  n;
    return off_s;
}


/**api* MapCWrite *************************************************************
** 
** 	appends specified nr. of bytes to end of used cache;
** 
** 	INPUT:	    address of MAPoCCH
** 		    address of source
**                  nr. of bytes to be transferred
** 
** 	OUTPUT:
** 		    returns:	1 if ok
** 				e__eoc
*/ 
   
int MapCWrite (MAPoCCH *c, char *s, int n)
{
    memcpy(c->off, s, n);
    c->off = (unsigned int) c->off + n;
    *(c->foff) = *(c->foff) + n;

    if (c->off > c->buff + (c->nbloc - 1) * 512)
	MapFlush(c);
    return 1;
}



/**api* MapInitCache **********************************************************
** 
** 	initializes a cache, i.e. allocates memory, opens files etc.;
**      MAPoCCH->foff must be set before calling (0 = no existing file)
** 
** 	INPUT:	    cache descriptor MAPoCCH [W]
**                  file name [R]
**                  address of cache's file offset [W]
** 		    flag if new file should be opened [R]
** 
** 	RETURNS:    1 if success
** 		    e__allocfail <item> +
** 				e__filopen <name> +
*/ 
   
int MapInitCache (MAPoCCH *c, char *fil_nm, unsigned *foff, int new_f)
{
    int	    nbloc;

    c->filn = fil_nm;
    c->foff = foff;
    if (new_f)
	*foff = 0;

    c->hbloc = MapMOD(c->nbloc, 2);
    c->nbloc = c->hbloc * 2;			 /* even number		    */

    if ((c->buff = malloc(c->nbloc * 512)) == 0)
	_ErrRet2(e__allocfail, "cache buffer");
    c->fab = 0;
    c->rab = 0;

    if (*(c->foff) == 0)
    {
	c->new_f = TRUE;
	c->off = c->buff;
	c->fstbloc = 1;
	c->coff = 0;
    }
    else
    {
	c->new_f = FALSE;
	nbloc = MapMOD(*(c->foff), 512);  
	if ((c->fstbloc = nbloc - c->hbloc + 1) <= 1)
	{
	    c->fstbloc = 1;
	    c->coff = 0;
	}
	else
	{
	    nbloc = c->hbloc;
	    c->coff = (c->fstbloc-1) * 512;
	}
	c->off = c->buff + *c->foff - c->coff;
	MapReadBlk (c, nbloc, c->fstbloc);
    }
    return 1;
}




/****** MapFlush **************************************************************
** 
** 	closes file theat was opend for read/update access (for fseek)
** 	writes 1st half of cache to file, shifts 2nd half of cache to begin
** 	and opens file again for read/upd access (no sharing possible);
** 
** 	INPUT:	    address of MAPoCCH
** 
** 	OUTPUT:
** 		    returns:	1 if OK
*/ 
   
int MapFlush (MAPoCCH *c)
{
    int	    shift = c->hbloc * 512;

    
    MapWriteBlk(c, c->hbloc+1, c->fstbloc);
    memcpy(c->buff, c->buff + shift, shift);

    c->fstbloc += c->hbloc;
    c->off  -= shift;
    c->coff = c->coff + shift;
    return 1;
}


/****** MapCloseCache *********************************************************
** 
** 	flushes cache to file and deletes memory;
** 
** 	INPUT:	    address of MAPoCCH
** 
** 	OUTPUT:
** 		    returns:	1 if success
*/ 
   
int MapCloseCache (MAPoCCH *c)
{
    int	nbloc, rv;

    nbloc = MapMOD(*(c->foff) - c->coff, 512);
    MapWriteBlk(c, nbloc, c->fstbloc);

    rv = sys$close (c->fab);
    _StopIfEven(rv); 	
    return 1;
}



/****** MapWriteBlk ***********************************************************
** 
** 	opens file for block-IO and writes specified number of blocks to 
** 	block offset and closes file;
**      writes in portions of 64 blocks which is the max size of block-IO;
** 
** 	INPUT:	    address of MAPoCCH
** 		    nr of blocks to write
** 		    block offset in file
** 
** 	OUTPUT:
** 		    returns:	1 if OK
*/ 
   
int MapWriteBlk (MAPoCCH *c, int nbloc, int off)
{
    struct FAB	*fab;
    struct RAB	*rab;
    char	*data = c->buff;
    int		n, rv;

    if (c->rab == 0)
	rv = MapFOpen(c, MAPxWRITE);
    fab = c->fab;
    rab = c->rab;

    fab->fab$w_deq = nbloc;			 /* extend quantity	    */
    rab->rab$l_bkt = off;

    while (nbloc > 0)
    {
	n = nbloc - 64;
	n = n < 0 ? nbloc : 64;
	rab->rab$w_rsz = n * 512;
	rab->rab$l_rbf = data;
	data = (unsigned int) data + n * 512;
	nbloc -= n;

	rv = sys$write (rab);
	_StopIfEven(rv); 	
	rab->rab$l_bkt += n;
    }

    return 1;
}


/****** MapFOpen **************************************************************
** 
** 	opens file for block-IO, read and write access - creates a new file
** 	if c->fstblock = 1;
** 
** 	INPUT:	    address of MAPoCCH
**                  access mode: MAPxWRITE, MAPxREAD
** 
** 	OUTPUT:
** 		    returns:	1 if success
** 				e__allocfail <item> +
*/ 
   
int MapFOpen (MAPoCCH *c, int acc_o)
{
    struct FAB	*fab;
    struct RAB	*rab;
    int		rv;

    if ((fab = malloc(sizeof(struct FAB))) == 0)
	_ErrRet2(e__allocfail, "FAB");
    if ((rab = malloc(sizeof(struct RAB))) == 0)
	_ErrRet2(e__allocfail, "RAB");

    *fab = cc$rms_fab;
    fab->fab$l_dna = c->filn;
    fab->fab$b_dns = strlen(c->filn);
    fab->fab$b_fac = acc_o == MAPxWRITE 
        ? FAB$M_BIO | FAB$M_GET | FAB$M_PUT : FAB$M_BIO | FAB$M_GET;
    fab->fab$b_rfm = FAB$C_STMLF;		 /* C stream file	    */
    if (!c->new_f) 
	fab->fab$l_fop = FAB$M_CIF;		 /* open existing file 	    */

    *rab = cc$rms_rab;
    rab->rab$l_fab = fab;

    rv = sys$create (fab);			 /* open file		    */
    _StopIfEven(rv); 
    rv = sys$connect (rab);
    _StopIfEven(rv); 

    c->fab = fab;
    c->rab = rab;
    return 1;
}




/****** MapReadBlk ************************************************************
** 
** 	opens file for block-IO and reads specified number of blocks from 
** 	block offset and closes file;
**      reads in portions of 64 blocks which is the max size of block-IO;
** 
** 	INPUT:	    address of MAPoCCH
** 		    nr of blocks to read
** 		    block offset in file (first block = 1)
** 
** 	OUTPUT:     
** 		    returns:	1 if OK
*/ 
   
int MapReadBlk (MAPoCCH *c, int nbloc, int off)
{               
    struct FAB  *fab;
    struct RAB  *rab;
    char	*data = c->buff;
    int		n, rv;

    if (c->fab == 0)
	rv = MapFOpen(c, MAPxWRITE);

    fab = c->fab;
    rab = c->rab;

    rab->rab$l_bkt = off;

    while (nbloc > 0)
    {
	n = nbloc - 64;
	n = n < 0 ? nbloc : 64;
	rab->rab$w_usz = n * 512;
	rab->rab$l_ubf = data;
	data = (unsigned int) data + n * 512;
	nbloc -= n;

	rv = sys$read (rab);
	_StopIfEven(rv); 	
    }

    return 1;
}

/****** MapRdMem **************************************************************
** 
** 	reads sectin file into private memory;
**      reads in portions of 64 blocks which is the max size of block-IO;
** 
** 	INPUT:	    section file name
** 		    pointer to memory block
** 
** 	OUTPUT:     
** 		    returns:	1 if OK
**                              e__allocfail <item> +
*/ 
   
int MapRdMem (char *fil_nm, void **p)
{               
    struct FAB  *fab;
    struct RAB  *rab;
    MAPoCCH	*c;
    char	*data;
    int		n, rv, size;

    c = calloc (1, sizeof (MAPoCCH));
    strcpy (c->filn, fil_nm);
    rv = MapFOpen(c, MAPxREAD);
    _ErrRet (rv);

    size = c->fab->fab$l_alq; 
    c->rab->rab$l_bkt = 1;			 /* start reading with	    */
						 /* first block		    */
    if ((data = malloc (size * 512)) == 0)
	_ErrExit2(e__allocfail, "memory by MapRdMem");

    *p = data;

    while (size > 0)
    {
	n = size - 64;
	n = n < 0 ? size : 64;
	c->rab->rab$w_usz = n * 512;
	c->rab->rab$l_ubf = data;
	data = (unsigned int) data + n * 512;
	size -= n;

	rv = sys$read (c->rab);
	_StopIfEven(rv); 	
    }
    rv = sys$close (c->fab);
    _StopIfEven(rv); 	
    return 1;
}



/**api* MapCUpdate ************************************************************
** 
** 	overwrites an integer at desired file offset; this corresponds
** 	to fseek + putw, here however block-IO is used to get block, modify it
** 	and write it back;
** 
** 	INPUT:	    address of MAPoCCH
** 		    relative file position
** 		    value
** 
** 	OUTPUT:
** 		    returns:	1 if success
*/ 
   
int MapCUpdate (MAPoCCH *c, unsigned int fadd, char *fip)
{
    struct RAB	    *rab = c->rab;
    static char	    buffer[1024];
    static char	    *buff = &(buffer[0]);
    char            *updloc;
    int		    rv, blocn, nbyte, blocoff;

    blocn = MapMOD(fadd, 512);			 /* number of block	    */
    blocoff = fadd - (fadd/512)*512; 
    if (blocoff == 0)
	blocn++;

    nbyte = blocoff > 508 ? 1024 : 512;

    rab->rab$w_usz = nbyte;
    rab->rab$l_ubf = buff;
    rab->rab$w_rsz = nbyte;
    rab->rab$l_rbf = buff;

    rab->rab$l_bkt = blocn;
    rv = sys$read (rab);
    _StopIfEven(rv); 	

    updloc = buff + blocoff;
    memcpy (updloc, fip, 4);

    rab->rab$l_bkt = blocn;
    rv = sys$write (rab);
    _StopIfEven(rv); 	
    return 1;
}



/**api* MapInCache ************************************************************
** 
** 	translates relative byte offset in file into cache address if referring
** 	to location in cache;
** 
** 	INPUT:	    address of MAPoCCH
**                  relative file address
** 		    address that receives translation
** 
** 	OUTPUT:	    places address into address
** 		    returns:	1 if translation was done
** 				0 if location is not in cache
*/ 
   
int MapInCache (MAPoCCH *c, unsigned int fadd, void **ptr)
{
    if (fadd < c->coff)
	return 0;
    else
	*ptr = fadd - c->coff + (unsigned int) c->buff;
    return 1;
}



/****** MapMOD ****************************************************************
**  
** 
** 	INPUT:	    divident
** 		    divisor
** 
** 	OUTPUT:
**		    returns:	divident MOD divisor
*/ 
   
int MapMOD (int a, int b)
{
    int quot;

    quot = a/b;
    return a == quot*b ? quot : ++quot;
}

/**api* MapDuplicateOverlap ***************************************************
** 
**      Addresses that need updating may be exactly on the boundary between
**      file and memory cache ...in that case both locations need updating.
**      This function updates in the cache only those bytes that overlaps.
**
** 	INPUT:	    address of IDS-file object [R]
**                  file pointer to first ID in the list [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    length of overlap
**                  0 if no overlap exists
*/ 

INT4 MapDuplicateOverlap  (MAPoCCH *cache, UINT4 fip, void *buff, INT4 size)
{
  INT4 overlapLen;

  overlapLen = size - (cache->coff - fip);
  if ((cache->coff > fip) && overlapLen > 0) {
    memcpy (cache->buff, (char *) buff + size - overlapLen, overlapLen);
    return overlapLen;
  }
  else
    return 0;
}








of IDS-file object [R]
**                  file pointer to first ID in the list [srs/src/map.h
**
**    $RCSfile: map.h,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:16:57 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
*/

#define MAPxWRITE   1
#define MAPxREAD    2


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  virtual memory (map) section
*/

typedef struct MAPo {
  char		 filn[FILxXNAM+1]; /* file name */
  unsigned short chan;             /* channel number returned by sys$create */
  UINT4	         xbyt;             /* size of section in bytes */
  UINT4	         *foff;            /* pointer to relative file address in 
				      section file */
  char		 *off;             /* pointer to relative file address in 
				      section file */
  char		 *alloc;           /* start address of allocated memory */
  char		 *data;            /* buffers start address */
  UINT4	         raddr[2];         /* array of start and end address returned 
				      by sys$crmpsc used by sys$deltva */
  unsigned char	 trnc_f;           /* TRUE: resultant file is truncated to 
				      size actually used */
  unsigned char  wrt_f;            /* TRUE: mapsection has write access - 
				      changes are saved on disk  */
  unsigned char  isAllocBuff;      /* buffer has been allocated for section */ 
} MAPo;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  cache object
*/

typedef struct MAPoCCH {
  char		*filn;     /* file name */ 
#ifdef VMS
  struct FAB	*fab;           
  struct RAB	*rab;          
#else
  INT4           fid;           
#endif
  char		*buff;     /* address of buffer */
  INT4		nbloc;     /* size of cache in blocks */
  INT4           hbloc;     /* half of ->nbloc */
  INT4           fstbloc;   /* first block of file to receive flushing */
  char 	        *off;      /* current address (after last byte added)
			      in cache */
  UINT4  coff;      /*  rel. file address of first byte in cache */
  UINT4  *foff;     /* pointer to current address (after last 
			      byte added) rel. file address  */
  INT4		new_f;     /* flag set if a new cache file is opened during 
			      program execution */
} MAPoCCH;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of exported functions
*/

INT4 MapMem (MAPo *m, char *fil_n, void *buff, INT4 buff_z);
INT4 MapFree (MAPo *m);
INT4 MapAlloc (MAPo *m, char *filn, INT4 nbloc);
char *MapMalloc (MAPo *m, INT4 n);

INT4 MapInitCache (MAPoCCH *c, char *fil_nm, unsigned *foff, INT4 new_f);
INT4 MapCNew (MAPoCCH *c, UINT4 *fadd);
INT4 MapCWrite (MAPoCCH *c, char *s, INT4 n);
INT4 MapInCache (MAPoCCH *c, UINT4 fadd, void **ptr);
INT4 MapCUpdate (MAPoCCH *c, UINT4 fadd, char *fip);
INT4 MapCloseCache (MAPoCCH *c);
INT4 MapDuplicateOverlap  (MAPoCCH *cache, UINT4 fip, void *buff, INT4 size);


d *buff, INT4 buff_z);
INT4 MapFree (MAPo *m);
INT4 MapAlloc (MAPo *m, char *filn, INT4srs/src/merge.c
char merge_ID[] = "$Id: merge.c,v 1.4 1996/11/20 16:36:28 etzold Exp $";
/*
**
**    $RCSfile: merge.c,v $
**    $Revision: 1.4 $
**    $Date: 1996/11/20 16:36:28 $
**    $Author: etzold $
**
**
**                  Copyright by Thure Etzold
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     D-69012 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**     
**    Functions for merging indices built from parts of a databank.
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>

#include "def.h"
#include "message.h"
#include "sm.h"
#include "futil.h"
#include "library.h"
#include "ids.h"
#include "idx.h"
#include "btree.h"
#include "merge.h"

#define	_SRS      
#define _SLB      
#include "srs5.h"

typedef struct MERGEoPart {
  Int4     partNo;
  SLBoFIL  *file;
  Int4     entryN;
  Int4     firstEntryN;
  IDSoFILE *ids;
  IDXv     idx;
  BTRo     *btree;
} MERGEoPart;

typedef struct MERGEoSet {
  SLBo       *lib;
  char       *idTypeName;
  MERGEoPart *part;
  Int4       partN;
  Int4       partAllocN;
  BTRoREC    *minRecord;
  MERGEoPart **minPart;
  Int4       minPartN;
  Int4       minPartAllocN;
} MERGEoSet;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  declaration of global or module wide variables
*/


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of static functions
*/

static void MergeValue ();
static BTRoREC *MergeNextRecord (MERGEoSet *merge, Int4 *recordNo);
static void MergePartIndexOpen (MERGEoSet *merge, SLBoFIELD *field);
static void MergePartIndexClose (MERGEoPart *part);
static void MergeIds (MERGEoSet *merge, IDSoFILE *ids, BTRoREC *rec);
static void MergeIdx (MERGEoSet *merge, SLBoFIELD *field);



/**api* MergeGetIndexPartName *************************************************
** 
**      Returns the name of the index part with the specified number.
** 
** 	INPUT:	    library object [R]
**                  field object [R]
**                  the part number [R]
**                  option "read" or "write" [R]
**                  address of index name [W] or NULL (returns static string)
**
** 	RETURNS:    address of the name
*/ 

char *MergeGetIndexPartName (SLBo *lib, SLBoFIELD *field, Int4 partN, 
			     char *mode, char *indexName)
{
  static char statIndexName[500];
  char *name, tmp[200];

  LibGetIndexName (lib, field, tmp, mode);
  name = indexName ? indexName : statIndexName;
  sprintf (name, "%s_%d", tmp, partN);
  return name;
}

/**api* MergeNextPartNo *******************************************************
** 
**      Returns whether the next part exists and the new part number.
**      In case the databank is not partitioned returns the first time TRUE
**      but sets the part number to -1.
** 
** 	INPUT:	 o  library object [R]
**               o  address of part number which must be set to 0 for
**                  first call [R]
**
** 	RETURNS:    TRUE if a next part exist
*/ 

Int4 MergeNextPartNo (SLBo *lib, Int4 *partNo)
{
  static Int4 entryN;
  IDXv idx;
  char *name;
  Int4 errCode;
  
  if (*partNo == 0)
    entryN = 0;
  else if (*partNo == -1)
    return 0;

  if (!LibIs (lib, "partitioned")) {
    *partNo = -1;
    return 1;
  }
  else {
    /* last part if less entries in part than part size */
    /*if (*partNo && entryN < LibGetPartSize (lib))  
      return 0;*/
    (*partNo)++;
    name = MergeGetIndexPartName (lib, LibGetIdField (lib), 
				  *partNo, "read", NULL);
    if ((idx = IdxOpen (name, "read", 0, &errCode))) {
      entryN = IdxGetRecordN (idx);
      return 1;
    }
    else {
      return 0;
    }
  }
}


/**api* MergeInit *************************************************************
** 
**      Creates a 'merge' object for specified library.
** 
** 	INPUT:	    the library object [R]
**
**      RETURNS:    the merge object
*/ 

MERGEoSet *MergeInit (SLBo *lib)
{
  IDXv       idx;
  MERGEoSet  *merge;
  MERGEoPart *part;
  Int4       partNo;

  if ((merge = (MERGEoSet *) calloc (1, sizeof (MERGEoSet))) == NULL)
    _ErrExit2 (e__allocfail, "merge set");
  merge->lib = lib;
  
  for (partNo=0; MergeNextPartNo (lib, &partNo); ) {
    part = _addObj (merge->part,merge->partN, merge->partAllocN, MERGEoPart);
    memset (part, 0, sizeof (MERGEoPart));
    part->partNo = partNo;
  }
  return merge;
}


/**api* MergeIndex ************************************************************
** 
** 	This merges all indices for the specified field.
**      it creates a new index, opens all the indices of the parts
**      and iterates over the sorted value list three times.
**      First for counting the number of values and second and third to
**      'feed' the B+ tree.
** 
** 	INPUT:	    the merge object [W]
**                  the field object [R]
*/ 

void MergeIndex (MERGEoSet *merge, SLBoFIELD *field)
{
  BTRoREC  *record;
  IDXv     idx;
  BTRo     *btree;
  IDSoFILE *ids;
  Int4     k, errCode, recordN;
  char     *indexName;

  /* open files */
  indexName = LibGetIndexName (merge->lib, field, NULL, "write");
  MergePartIndexOpen (merge, field);
  btree = BtrOpen (indexName, "merge", &errCode);
  BtrSetNumType (btree, BtrGetType (merge->part[0].btree));
  ids = IdsOpen (indexName, "merge", 1048, merge->idTypeName, &errCode);

  /* merge IDX file if ID-field */
  if (FieldIs (field, "id"))
    MergeIdx (merge, field);
  
  /* count number of different records */
  for (recordN=0; MergeNextRecord (merge, &recordN);)
    ;
  BtrBuildStartPhase1 (btree, recordN);
  for (recordN=0; (record = MergeNextRecord (merge, &recordN));)
    BtrInsertRecord (record);
  BtrBuildStartPhase2 ();
  for (recordN=0; (record = MergeNextRecord (merge, &recordN));) {
    MergeIds (merge, ids, record);
    BtrInsertRecord (record);
  }

  /* close files */
  BtrClose (btree);
  IdsClose (ids);
  for (k=0; k < merge->partN; k++) {
    MergePartIndexClose (&merge->part[k]);
  }
}


/**api* MergeNextRecord *******************************************************
** 
** 	Gives the next value from a list of opened indices.
** 
** 	INPUT:	    the merge object [W]
*/
 
static BTRoREC *MergeNextRecord (MERGEoSet *merge, Int4 *recordNo)
{
  MERGEoPart *part, **tmp;
  BTRoREC    *record;
  Int4       k, cmp;

  merge->minRecord = NULL;
  if (!*recordNo) /* call for first element */
    for (k=0; k < merge->partN; k++)
      BtrRecordGet (merge->part[k].btree, BTRxFIRST);
  else
    for (k=0; k < merge->minPartN; k++)
      BtrRecordGet (merge->minPart[k]->btree, BTRxNEXT);


  for (k=0; k < merge->partN; k++) {
    part = &merge->part[k];
    if ((record = BtrRecordGet (part->btree, BTRxCURR))) {
      cmp = merge->minRecord ? 
	BtrCompare (part->btree, record, merge->minRecord) : -1;

      /* lesser */
      if (cmp < 0) {
	merge->minRecord = record;
	merge->minPartN = 0;
	tmp = _addObj (merge->minPart, merge->minPartN, merge->minPartAllocN,
		 MERGEoPart*);
	*tmp = part;
      }
      /* equal */
      else if (cmp == 0) {
	tmp = _addObj (merge->minPart, merge->minPartN, merge->minPartAllocN,
		 MERGEoPart*);
	*tmp = part;
      }
    }
  }
  if (!merge->minRecord) /* all lists are exhausted */
    return NULL;

  (*recordNo)++;
  return merge->minRecord;
}


/**api* MergeIds **************************************************************
** 
** 	Merges the Id blocks from the part indices.
**      For all parts the entry IDs are recalculated since the entry-IDs for
**      all parts start from entry count 1.
** 
** 	INPUT:	  o the merge object [W]
**                o address of the start address of the block in the 
**                  IDS file [W]
**
**      RETURNS:    the number of IDs in the merged block
*/

static void MergeIds (MERGEoSet *merge, IDSoFILE *ids, BTRoREC *rec)
{
  MERGEoPart *part;
  char       buff[2000000];
  BTRoREC    *tmpRec;
  BTRoVALUE  *tmp;
  FIP        fip;
  Int4       k, idN;

  for (k=0, idN=0; k < merge->minPartN; k++) {
    part = merge->minPart[k];
    tmpRec = BtrRecordGet (part->btree, BTRxCURR);
    tmp = &tmpRec->r.value;
    IdsGet (part->ids, (IDPTR)buff, tmp->firstIdFip, tmp->idN);

    /*    IdsEntryIncrement (part->ids, buff, partIdN, part->firstEntryN);*/
    fip = IdsPut (ids, buff, tmp->idN); 
    if (!idN) {
      rec->r.value.firstIdFip = fip;
      rec->r.value.lastIdFip = fip;
    }
    idN += tmp->idN;
  }
  rec->r.value.idN = idN;
}


/**api* MergeIdx **************************************************************
** 
** 	INPUT:	   the merge object [W]
**                 field object
**
*/

static void MergeIdx (MERGEoSet *merge, SLBoFIELD *field)
{
  IDXv    idx;
  SMoBUFF *buff;
  Int4    errCode, k, c;

  idx = IdxOpen (LibGetIndexName (merge->lib, field, NULL, "write"),
		 "write", merge->lib->maxNameLen, &errCode);
  for (k=0; k < merge->partN; k++)
    for (c=0; (buff = IdxNextBuff (merge->part[k].idx, &c));)
      IdxPutBuff (idx, buff);
  IdxClose (idx);
}



static void MergePartIndexOpen (MERGEoSet *merge, SLBoFIELD *field)
{
  MERGEoPart *part;
  char       *indexName;
  Int4       k, rv;

  for (k=0; k<merge->partN; k++) {
    indexName=MergeGetIndexPartName (merge->lib, field, k+1, "read", NULL);
    part = &merge->part[k];

    if (FieldIs (field, "id"))
      if (!(part->idx = IdxOpen (indexName, "read", 0, &rv))) 
	_ErrExit2 (rv, indexName);

    part->btree = BtrOpen (indexName, "read", &rv);
    _ErrExit2 (rv, FileGetName (field->btree->file, "path"));
    if (!(part->ids = IdsOpen (indexName, "read", 0, NULL, &rv)))
      _ErrExit (rv);
    if (!k)
      merge->idTypeName = LibGetIdTypeName (IdsGetIdType (part->ids));

  }    
}

static void MergePartIndexClose (MERGEoPart *part)
{
  if (part->btree)
    BtrClose (part->btree);
  if (part->ids)
    IdsClose (part->ids);
  if (part->idx)
    IdxClose (part->idx);
  part->ids = NULL;
  part->idx = NULL;
  part->btree = NULL;
}

e, "read", &rv);
    _ErrExit2 (rv, FileGetName (field->btree->file, "path"));
    if (!(part->ids = IdsOpen (indexName, "read", 0, NULL, &rv)))
      _ErrExit (rv);
    if (!k)
      merge->idTypeName = LibGetIdTypeName (IdsGetIdType (part->ids));

  }    
}

static void MergePartIndexClose (MERGEoPart *part)
{
  if (part->btree)
    BtrClose (part->btree);
  if (part->ids)
    IdsClose (part->ids);
  if (part->idx)
    IdxClose (part->idx);
  part->ids = NULL;
  part->idx = NULL;
srs/src/merge.h
typedef struct MERGEoSet *MERGEvSet;

Int4 MergeNextPartNo (struct SLBo *lib, Int4 *partNo);
MERGEvSet MergeInit (struct SLBo *lib);
void MergeIndex (MERGEvSet merge, struct SLBoFIELD *field);
 if (!k)
      merge->idTypeName = LibGetIdTypeName (IdsGetIdType (part->ids));

  }    
}

static void MergePartIndexClose (MERGEoPart *part)
{
  if (part->btree)
    BtrClose (part->btree);
  if (part->ids)
    IdsClose (part->ids);
  i¶ £¡@>idx)
    IdxClose (part->idx);
  part->ids = NULL;
  pa¶ £¡Ü{¸LL;
srs/src/message.c
char message_srs_ID[] = "$Id: message.c,v 1.4 1997/03/12 16:17:42 srs Exp $";
/*
**
**    $RCSfile: message.c,v $
**    $Revision: 1.4 $
**    $Date: 1997/03/12 16:17:42 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: file, sm 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    default opens "SYS$ERROR" as output file which ** receives the
**    error or informational messages; output can be directed to a
**    file with "MsgSetOut" at the begin of the program;
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <ctype.h>
#include <stdarg.h>
#include <string.h>

#ifndef VMS
#  include <unistd.h>
#endif

#include "msg.h"
#include "futil.h"
#include "sm.h"



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  global or module wide variables
*/

static int    (*PrintMessage)(MSGo *) = NULL; /* pointer to print function */
static MSGo   msg;    /* message object - input to user specified function */
static FILEo* msgFile=NULL;



/***** MsgPrintMessage ********************************************************
**
**	default function for message printing;
**
**	INPUT:	    message object [R]
**		IMPLICIT:
**
**	RETURNS:    1
*/ 

INT4 MsgPrintMessage (MSGo *msg)
{
  if (msg->msg_t != MSGxINFO)
    fprintf (stderr, "%s, %s\n", msg->msg_nm, msg->primsg);
  if (*(msg->secmsg))
    fprintf (stderr, "%s", msg->secmsg);
  return 1;
}


/**api* function **************************************************************
**
**	Returns whether specified characteristic of the message is true or
**      not.
**	
**	INPUT:	   message object [R]
**                 characteristic: "fatal", "error", "info"
**
**	RETURNS:   1: message has the characteristic
**                 0: negative
*/

Int4 MsgIs (MSGo *msg, char *option)
{
  switch (_Index (option[0], option[1])) {
  case _Index('f','a'):  /* fatal */
    return msg->msg_t == MSGxFATAL ? 1 : 0;
  case _Index('e','r'):  /* error */
    return msg->msg_t == MSGxERROR ? 1 : 0;
  case _Index('i','n'):  /* info */
    return msg->msg_t == MSGxINFO ? 1 : 0;
  }
}


/****** MsgInit ***************************************************************
**
**	opens the message file and the output file;
**	
**	INPUT:	   
**          IMPLICIT:
**                 msgFile (FILEo *) [W]
**
**	RETURNS:   1 if success
*/

INT4 MsgInit ()
{
  int rv;

  /*
  ** open message file
  */

  msgFile = FileNew (MSGxFILE);
  FileSetMaxLine (msgFile, 200);
  /*  FileSetUnixIo (msgFile);*/
  if (!FileOpen (msgFile)) {
    fprintf (stderr, "\"%s\" could not be opened\n", 
	     FileGetName (msgFile, "path"));
    exit(-1);
  }
  
  if (PrintMessage == NULL)
    PrintMessage = MsgPrintMessage;
  return 1;
}



/**api* MsgAnalCode **********************************************************
** 
** 	analyzes a message code: calculates the file pointer and finds out
**      the message type
** 
** 	INPUT:	    message object [W]
**                  message code [R]
**                  address of file pointer [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if a real message code
** 		    0 if not
*/ 

INT4 MsgAnalCode (MSGo *msg, int msg_code, unsigned int *fip)
{
  int  msg_t;

  if (msg_code > MSGxMAX || msg_code < MSGxMIN || msg_code == e__error)
    return 0;
  
  /*
  ** msg_code = fip + msg_t * -MSGxMAX
  */

  msg_t = msg_code / MSGxMAX;
  *fip = -msg_code + MSGxMAX * msg_t;

  msg->msg_code = msg_code;
  msg->msg_t = (enum msg_typ) msg_t;
  return 1;
}




/**api* Message ***************************************************************
**
**	checks if the number is really error code;	
**	opens file with error messages, goes to address specified in error code
**	forms message object and prints it;
**	if more arguments are transmitted and the next line(s) in file begins
**	with a non alpha character then the line + arguments are transmitted 
**	to "printf".
**	aborts program if MSGxEXIT	
**	if MSGxMSG then the line containing the message name is not printed
**	note that after that line several output lines may occur - they will
**	simply be concatenated to one;
**	
**	INPUT:	  o  number of arguments following
**                o  error code	
**		  o  MSGxEXIT or MSGxNOEX or MSGxMSG
**		  o  (optional)
**		  o  up to 10 arguments for "printf"
**           IMPLICIT:
**                msg (MSGo) [W]
**                msgFile (FILEo *) [W]
**
**      RETURNS:     1 if success
**                   0 if number is not a message code
*/

INT4 Message (INT4 arg_n, INT4 msg_code, INT4 opt, ...)
{
  static int   first_f=TRUE;
  va_list      ap;				 
  unsigned int fip;
  int	       rv;
  char	       secmsg[MSGxXLN * MSGxXNLN+1], *tmp;

  /*
  ** open message file + output file
  */

  if (first_f) {
    MsgInit ();
    first_f = FALSE;
  }

  /*
  ** convert message number into a file pointer and set file pointer in message
  ** file to this address;
  */ 

  if (!MsgAnalCode (&msg, msg_code, &fip))
    return 0;
  FileSeek (msgFile, fip);

  /*
  ** first line contains message name and primary message - extract those;
  ** all following lines that do not start with either of "fewi" are copied 
  ** into one string - the secondary message;
  */ 

  sscanf (FileReadLn (msgFile), "%[^,] , %[^\n]", msg.msg_nm, msg.primsg);
  SmEdit (msg.primsg, SMxTRIM); /* cut of trailing white space */

  if (arg_n > 3) {
    secmsg[0] = '\0';
    while (tmp = FileReadLn (msgFile)) {
      if (strchr ("fewio", tmp[0]) != NULL) 
	break;
      SmEdit (tmp, SMxTRIM2 | SMxDECODE);
      strcat (secmsg, tmp);
    }

    /*
    ** secondary message is a format specification for printf - make final
    ** message line - argument list is the one given to "Message"
    */

    va_start (ap, opt);
    vsprintf (msg.secmsg, secmsg, ap);
    va_end (ap);
  }
  else
    msg.secmsg[0] = '\0';

  /*
  ** print message and exit program if requested;
  */

  (*PrintMessage) (&msg);

  if (opt == MSGxEXIT)
    exit (256);
  
  return 1;	
}





/**API* MsgSetFnct ************************************************************
** 
**	Replaces the default function for printing error and information
**      messages. 
**
**	INPUT:	    address of function [R]
**	        IMPLICIT:
**		    fnct_f (int)
**		    outfnct (int) [W]
**
**	RETURNS:
*/ 
   
void MsgSetFnct (INT4 (*fnct)())
{
    PrintMessage = fnct;
}
*
  ** print message and exit program if requested;
  */

  (*PrintMessage) (&msg);

  if (opt == MSGxEXIT)
    exit (256);
  
  return 1;	
}





/**API* MsgSetFnct ************************************************************
** 
**	Replaces the default funcsrs/src/message.h
#define e__msgfail   -3000112
#define e__allocfail   -3000165
#define e__freefail   -3000254
#define e__settoobig   -3000332
#define e__readerr   -3000375
#define e__novalop   -3000415
#define e__novaltyp   -3000472
#define e__nosetfree   -3000569
#define e__userabort   -3000601
#define e__filnotopen   -3000638
#define e__filnotok   -3000693
#define e__filopenerr   -3000748
#define e__eof   -3000805
#define e__ltoolong   -3000837
#define e__invnodenum   -3000889
#define e__missnode   -3000954
#define e__toomansym   -3001017
#define e__eot   -3001082
#define e__parsefail   -3001152
#define e__bldparsefail   -3001219
#define e__strprsfail   -3001322
#define e__lnotsaved   -3001388
#define e__novalpnam   -3001442
#define e__novalsnam   -3001526
#define e__invalnum   -3001610
#define e__procfail   -3001700
#define e__symnotuniq   -3001762
#define e__toomanstrct   -3002220
#define e__startismiss   -3002356
#define e__isnotss   -3002411
#define e__novalid   -3002528
#define e__missingchar   -3002635
#define e__unknownnterm   -3002723
#define e__charnotknown   -3002795
#define e__symnotknown   -3002903
#define e__novalsyminfo   -3002990
#define e__novalarg   -3003083
#define e__novalcommand   -3003170
#define e__bnfbuildfail   -3003252
#define e__wrongpartyp   -3003344
#define e__novalptyp   -3003437
#define e__novalopt   -3003530
#define e__misscolon   -3003595
#define e__nammismatch   -3003653
#define e__namnotuniq   -3003718
#define e__novalauthor   -3003779
#define i__slbreportbeg   -1003868
#define i__slbreportend   -1004171
#define i__inxreport   -1004297
#define i__processing   -1004390
#define e__eom   -3004446
#define i__inxcmprss   -1004541
#define e__nofieldend   -3004635
#define e__wrongfieldcnt   -3004694
#define e__strtoolong   -3004807
#define e__linenotexst   -3004877
#define e__invalstr   -3004939
#define e__invalnumber   -3005011
#define e__invalifn   -3005086
#define e__invalofn   -3005168
#define e__activesubmenu   -3005251
#define e__allwinused   -3005345
#define e__exceedsize   -3005385
#define e__eob   -3005476
#define e__novalfield   -3005510
#define e__novalnam   -3005560
#define e__unexpectnum   -3005687
#define e__noinit   -3005765
#define e__strnotfou   -3005812
#define e__strnotfound   -3005875
#define e__novalstr   -3005931
#define e__novalfadd   -3005983
#define e__novalnum   -3006049
#define e__libnotinx   -3006131
#define i__wrotefile   -1006210
#define i__wrotefiles   -1006254
#define e__novalpos   -3006313
#define e__novalseqlen   -3006380
#define e__seqfrg   -3006473
#define e__seekfail   -3006531
#define e__crmpscfail   -3006586
#define e__maxlinksexceed   -3006673
#define e__unknownnam   -3006757
#define e__novallink   -3006810
#define e__toofew   -3006873
#define e__namreserved   -3006947
#define i__sdlreport   -1007016
#define e__nopath   -3007424
#define e__ambigouslink   -3007486
#define e__badarglist   -3007660
#define e__namnotdef   -3007717
#define e__invaloutdir   -3007779
#define i__wroteseq   -1007847
#define i__wroteseqsfile   -1007894
#define e__complement   -3007964
#define e__novalreference   -3008066
#define i__lnkreport   -1008174
#define e__exceedquota   -3008250
#define e__rtlfail   -3008296
#define e__novalsettyp   -3008362
#define e__collidsfail   -3008447
#define e__inheritfail   -3008535
#define e__objnotfound   -3008612
#define e__objnotnhrt   -3008703
#define e__missdefattr   -3008823
#define e__symappendfail   -3009011
#define e__exceedarr   -3009094
#define e__novalterm   -3009157
#define i__mappedset   -1009240
#define i__loadlinkset   -1009306
#define e__novalseqform   -3009362
#define i__wroteseqlen   -1009428
#define e__novalpar   -3009582
#define e__toomanpar   -3009672
#define i__procsubset   -1009768
#define e__sicinvalgroups   -3009852
#define e__unknowncommand   -3009954
#define i__readingname   -1010010
#define e__interrupt   -3010073
#define i__wroteset   -1010105
#define e__sftop   -3010171
#define e__libnotlinked   -3010250
#define e__filnotfound   -3010307
#define e__filcloseerr   -3010386
#define e__filwriteerr   -3010440
#define i__noentriesfound   -1010540
#define e__nonounix   -3010576
#define i__listtolib   -1010657
#define e__eostack   -3010753
#define f__limitexceeded   -4010778
#define e__nontermexpect   -3010853
#define e__novalformat   -3010900
#define e__parnottype   -3010959
#define e__foundoneof   -3011058
#define e__unknownoption   -3011132
#define e__parisdefined   -3011205
#define e__parnotdefined   -3011275
#define e__notwriteopen   -3011337
#define e__indexisbusy   -3011415
#define e__doesnotexistfunction   -3011487
#define e__overflowstack   -3011560
#define f__failedtomovelist   -4011634
#define e__couldnotgetsequence   -3011701
#define e__nothingtoevaluate   -3011788
#define e__failureinslbgetx   -3011830
#define e__joinillegalpar   -3011914
#define e__entryparsefail   -3011979
#define e__illegalposition   -3012040
#define e__illegalvalueonstack   -3012124
#define e__illegalvaluesonstack   -3012242
#define e__illegaldirectioninrange   -3012371
#define e__operatorbeforenotallowed   -3012455
#define e__operatorafternotallowed   -3012512
#define e__postoohigh   -3012567
#define i__entry   -1012638
#define e__objectunknown   -3012683
#define e__noseqinlist   -3012753
#define e__noresult   -3012795
#define e__illegalrangemod   -3012834
#define e__illegalmodparam   -3012898
#define e__illegalqueryparam   -3012965
#define e__noparamlist   -3013027
#define e__negativelength   -3013075
#define e__incorrectlength   -3013144
#define e__fnctnotdefined   -3013215
#define e__btreenotprep   -3013355
#define i__writeindex   -1013449
#define e__invalidid   -3013529
#define e__hasnotfixedrecord   -3013612
#define e__fieldnotindex   -3013695
#define e__iscompressed   -3013761
#define e__notcompressed   -3013824
#define i__processingentry   -1013900
#define i__wrotebtree   -1013943
#define i__wroteidfile   -1014080
#define e__inxnotcompress   -3014201
#define e__listnotfilled   -3014265
#define e__buffexceeded   -3014356
#define i__openedidpatch   -1014428
#define e__dupllibid   -3014521
#define e__novallibid   -3014626
#define e__libidexst   -3014727
#define e__libidnotknown   -3014830
#define e__settoosmall   -3014922
#define i__builtlink   -1015032
#define i__checkinglib   -1015222
#define e__novalentryidlen   -3015277
#define e__indexnotuptodate   -3015385
#define e__indexwrongversion   -3015492
#define e__regerror   -3015593
#define i__mustbuildinx   -1015628
#define i__mustbuildlink   -1015702
#define i__diffentrynum   -1015781
#define e__labelnotfound   -3015858
#define i__givinguplib   -1015954
#define e__strnotinset   -3016025
#define e__numnotinset   -3016128
#define e__realnotinset   -3016231
#define e__functionnotinset   -3016331
#define e__charnotallowed   -3016436
#define e__realnotinrange   -3016540
#define e__checkerr   -3016648
#define e__setopneedsidtype   -3016706
#define e__nolinklibselected   -3016806
#define i__querynegative   -1016898
#define e__novalvar   -3016957
#define e__novalvar2   -3017029
#define e__novalvar3   -3017102
#define e__formatnomatch   -3017175
#define e__relbegandend   -3017278
#define e__invalidshift   -3017367
#define e__shiftseqisfrag   -3017454
#define e__seqwithneglen   -3017520
#define e__badfile   -3017602
#define i__indexnotexist   -1017651
#define i__indexnotcompleted   -1017735
#define i__indexnotuptodate   -1017830
#define i__indexnotcompressed   -1017922
#define e__rangewithundefval   -3018017
#define e__argwrongnum   -3018104
#define e__argwrongtype   -3018202
#define e__argsendnull   -3018308
#define e__fatal   -3018380
#define e__unknownarg   -3018402
#define e__nocurrentcommand   -3018475
#define e__onlyoneunnamed   -3018561
#define e__varwrongclass   -3018778
#define e__varisreadonly   -3018899
#define e__seqillegallength   -3019068
#define e__novalchar   -3019166
#define e__missingarg   -3019233
#define e__nosetorlib   -3019317
#define e__functionnotexist   -3019375
#define e__emptyquerystring   -3019439
#define e__illegalbaseconv   -3019479
#define e__dbnotlegal   -3019587
#define e__noviewselect   -3019709
#define e__querynotfound   -3019794
#define e__dbhasnotfield   -3019866
#define e__icastackempty   -3019960
#define e__icaunknownattr   -3020022
#define e__icaenumval   -3020203
#define e__icarequiredattr   -3020272
#define e__icaattrval   -3020358
#define e__templNoCurrTemplate   -3020411
#define e__unknownformat   -3020471
#define e__templEndOfHistory   -3020557
#define i__invalidentry   -1020642
#define e__setnotuniqname   -3020711
#define e__icainvalidselect   -3020780
#define e__icainvallistassign   -3020904
#define e__icaopTask   -3021049
#define e__icaopEdit   -3021128
#define e__icaopAssign   -3021225
#define e__icaopRestrictLen   -3021321
#define e__icaopMove   -3021415
#define e__icabnfGetProd   -3021488
#define e__icabnfExpression   -3021572
#define e__icabnfProgram   -3021659
#define e__icabnfLinkBnfNet   -3021730
#define e__icabnfParser   -3021807
#define e__icarusFatal   -3021877
#define e__toklistFind   -3021930
#define e__toklistReplace   -3021990
#define e__toklistIsUniq   -3022054
#define e__parsererror1   -3022117
#define e__parsererror2   -3022195
#define e__parsererror3   -3022272
#define e__wwwnomatchingview   -3022361
#define e__nolibslct   -3022528
#define e__wwwNoQueryOrEntriesSelected   -3022570
#define e__wwwNoQuerySpecified   -3022654
#define e__toktablenotwritable   -3022719
#define i__bldReadLink   -1022794
#define e__bldNoReadLinks   -3022865
#define f__noVarScope   -4022932
#define e__bldLibNotMerge   -3023022
#define e__genNoObjWithNo   -3023134
#define e__checkInvalidLibInfo   -3023234
#define e__icaMissingString   -3023343
#define e__duplicatekey   -3023476
#define f__exception   -4023545
#define e__icaUnknownClass   -3023670
#define e__icaErrorsQuit   -3023762
#define e__icavartype   -3023814
#define e__anyIsReadOnly   -3023902

#define e__toktablenotwritable   -3022719
#define i__bldReadLink   -1022794
#define e__bldNoReadLinks   -3022865
#define f__noVarScope   -4022932
#define e__bldLibNotMerge   -3023022
#define e__genNoObjWithNo   -3023134
#define e__checkInvalidLibInfo   -3023234
#define e__icaMissingString   -3023343
#define e__duplicatekey   -3023476srs/src/mi.c

int headTable[]={0,1,2,2,3,3,3,3};
int tailTable[]={0,0,1,0,3,2,1,0};

char* MIFromULong(ULONG x, int* len) {
    static char buf[16];
    int l=1; char* pos=buf;
    ULONG r;
    /* get the first byte */
    *pos++=x&0x3F;
    x>>=6; /* unsigned! */
    while (x) {
	*pos++=(char)x;
	x>>=8; l++;
    }
    ASSERT(l<8,"IntTooLong");
    /* get log2 lenght */
    buf[0] |= headTable[l-1]<<6; 
    r=tailTable[l-1];
    /* add filling bytes */
    while (r--) {
	*pos++=(char)x; l++;
    }
    *len=l; return buf;
}

ULONG MIToULong(char* buf) {
    ULONG n; int shift=6;
    /* get lenght */
    int l=1<<((*buf>>6)&0x3);
    n=(*buf++)&0x3F;
    while (--l) {
        n|=(*buf++)<<shift;
	shift+=8;
    }
    return n;
}

int MIToLongSize(char head) {
    return 1<<((head>>6)&0x3);
}

char* MIFromLong(long x, int* len) {
    /* make an unsigned out of the signed, rotating right 1 */
    ULONG encoded;
    if (x>=0) encoded=(ULONG)x<<1;
    else encoded=(((ULONG)-x)<<1)+1;
    return MIFromULong(encoded, len);
}

long MIToLong(char* buf) {
    ULONG encoded=MIToULong(buf);
    if (encoded&0x1) return -(encoded>>1);
    else return encoded>>1;
}


/**************************************************************************
** FLOATING-POINT CODEC
*/


#include <math.h>

typedef struct {
    int lMant;
    int lExp;
} FloatFormat;


FloatFormat floatFormats[]= {
    {1,0}, /* small int */
    {1,1},
    {2,1},
    {3,1},
    {3,2},
    {7,2},
    {15,2},
    {7,3},
    {15,3}
};

#define WORD_BITS 32

void MIFromMantissa(double m, char** buf) {
    char* p=*buf; double mInt;
    WORD chunk; int bit=0;
    /* convert first, encoded with sign(msb:0=-,1=+) */
    if (m>0) {
        m=modf(ldexp(m,WORD_BITS),&mInt);
	chunk=(WORD)mInt;
    }
    else {
        m=modf(ldexp(-m,WORD_BITS),&mInt);
	chunk=((WORD)mInt)^(1<<WORD_BITS-1); 
    } 
    /* convert chunk */
    for (bit=WORD_BITS-8; bit>=0; bit-=8) {
	*p++=(chunk>>bit)&0xFF;
    }
    while (m!=0) {
	m=modf(ldexp(m,WORD_BITS),&mInt);
	chunk=(WORD)mInt; 
	/* convert chunk */
	for (bit=WORD_BITS-8; bit>=0; bit-=8) {
	    *p++=(chunk>>bit)&0xFF;
	}
    };
    /* go back to last non-zero byte to find real lenght */
    p--;
    while (!*p) p--;
    p++; *buf=p;
}    

double MIToMantissa(char* p, int len) {
    double m=0; int exp;
    WORD chunk=0; int bit,sign;
    /* first chunk encodes sign */
    for (bit=0; bit<WORD_BITS; bit+=8) {
	chunk<<=8; 
	if (len) { len--; chunk|=*p++; }
    }
    if (chunk&(1<<WORD_BITS-1)) sign=1;
    else { sign=-1; chunk|=(1<<WORD_BITS-1); }
    exp=-WORD_BITS; m+=ldexp(chunk, exp);
    while (len) { 
	chunk=0;
	for (bit=0; bit<WORD_BITS; bit+=8) {
	    chunk<<=8; 
	    if (len) { len--; chunk|=*p++; }
	} 
	exp-=WORD_BITS; m+=ldexp(chunk, exp);
    };
    return m*sign;
}

char* MIFromDouble(double d, int* len) {
    static char buf[20]; int exp; double mInt;
    int lMant, lExp; FloatFormat* f;
    char *p=buf;
    if (modf(d, &mInt)==0 && (mInt>=-16 && mInt<16)) {
	/* small int, encode in 1 byte */
	char c=((int)mInt)&0x1F;
	*p++=c;
    }
    else {
	char mant[20], *m=mant; int l; 
	ULONG coded;

	d=frexp(d,&exp);

	/* code exponent */
	if (exp>=0) coded=exp<<1;
	else coded=(-exp<<1)|0x1;
	*p++=coded&0x1F; coded>>=5;
	if (coded) {*p++=coded; coded>>=8;}
	if (coded) {*p++=coded; }
	ASSERT(!(coded>>8), "ExpOutOfRange");

	/* code mantissa */
	MIFromMantissa(d, &m);

	/* find and set format */
	lMant=m-mant; lExp=p-buf; f=floatFormats+1;
	while (lMant>f->lMant || lExp>f->lExp) {
	    f++; ASSERT(f<floatFormats+8, "FloatOverFlow");
	}
	buf[0]|=(f-floatFormats)<<5;

	/* adjust exp lenght */
	lExp=f->lExp-lExp;
	while (lExp--) *p++=0;

	/* copy mantissa */
	m=mant; l=lMant;
	while (l--) *p++=*m++;

	/* adjust mant. lenght */
	lMant=f->lMant-lMant;
	while (lMant--) *p++=0;
    }
    *len=(p-buf); return buf;
}

double MIToDouble(char* buf) {
    char* p=buf; int format;
    format=(*p>>5)&0x7;
    if (format==0) {
	/* small int */
	int coded=*p&0x1F; 
	/* extend sign */
	if (coded&0x10) coded |= ~0x1F;
	return coded;
    }
    else {
	int exp; FloatFormat* f; ULONG coded; 
	int lExp; double d; 
	f=floatFormats+(*p>>5);
	
	/* get exponent */
	coded=(*p++)&0x1F;lExp=f->lExp-1;
	if (lExp--) {
	   coded|=(*p++)<<5;
	   if (lExp--) coded|=(*p++)<<13;
	}
	if (coded&0x1) exp=-(coded>>1);
	else exp=coded>>1;
	
	/* get mantissa */
	d=MIToMantissa(p, f->lMant);
	return ldexp(d, exp);
    }
}

int MIToDoubleSize(char head) {
    FloatFormat* format=floatFormats+((head>>5)&0x7);
    return format->lMant+format->lExp;
}

  
    
        
    






	int esrs/src/mi.h
#define _MI_H

/******************************************************
** MACHINE-INDEPENDENT CODING/DECODING of numbers
******************************************************/

/* int codec */
char* 		MIFromULong(unsigned long x, int* len);
char* 		MIFromLong(long x, int* len);
unsigned long 	MIToULong(char* buf);
long 		MIToLong(char* buf);
int             MIToLongSize(char head);

/* floating-point codec */
char* 		MIFromDouble(double d, int* len);
double 		MIToDouble(char* buf);
int             MIToDoubleSize(char head);

#endif
*******************************************
** MACHINE-INDEPENDENT CODING/DECODING of numbers
******************************************************/

/* int codec */
char* 		MIFromULong(unsigned long x, int* len);
char* 		MIFromLong(long x, int* len);
unsigned long 	MIToULong(char* buf);
long 		MIToLong(char* buf);
int             MIToLongSize(char head);

/* floating-point codec */
char* 		MIFromDouble(double d, int* len);
double 		MIToDouble(char* buf);
int       srs/src/msg.h
**
**    $RCSfile: msg.h,v $
**    $Revision: 1.3 $
**    $Date: 1996/11/20 16:36:29 $
**    $Author: etzold $
**
**    $Locker:  $
**    $State: Exp $
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
*/

#define MSGxFILE	"SRSDAT:message.dat"

#define MSGxHHDR	"msg.h"
#define MSGxHDR		"message.h"
#define MSGxSCM		"MESSAGE BUFFER"

#define MSGxXNLN        5
#define MSGxXLN		132
#define MSGxXARG	10

enum msg_typ {MSGxINFO=1, MSGxWARNING, MSGxERROR, MSGxFATAL};

#define MSGxMAX		-1000000 * (INT4) MSGxINFO
#define MSGxMIN		-1000000 * (INT4) MSGxFATAL - 100000

#define MSGxMSG		0
#define MSGxEXIT	1
#define MSGxNOEX	2

#define e__error        -3000001 

#include "def.h"


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Description of a message.
*/

typedef struct MSGo {
  INT4  msg_code;                  /* message code number */
  char msg_nm[30];                 /* (API) message code name */
  char primsg[MSGxXLN+1];          /* (API) primary message  */
  char secmsg[MSGxXLN*MSGxXNLN+1]; /* (API) secondary message - additional 
				      lines that may contain arguments */
  enum msg_typ msg_t;              /* (API) message type: one of MSGxINFO, 
				      MSGxWARNING, MSGxERROR, MSGxFATAL */
} MSGo;


#ifdef LONG_ERROR_MSG
#  define __ERRMSG fprintf (stderr, "File: %s, Line: %d\n", __FILE__,__LINE__);
#else
#  define __ERRMSG
#endif

#define _ErrorExit() exit(-1)

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  macro checks if number of arguments is correct
*/

#define _CheckArgN(arg_n, min, max, errmsg) \
	if (((arg_n) > (max)) || ((arg_n) < (min))) return (errmsg)
    

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  checks some return value if it is message code, prints message 
**  and aborts program brutally;...does it no longer! behaves like 
**  _ErrExit now;
*/

#define _ErrStop(rv)\
do {if ((((INT4) rv) < MSGxMAX) && (((INT4) rv > MSGxMIN))) { __ERRMSG \
   Message (3, ((INT4) rv), MSGxEXIT); }} while (0)

#define _ErrStop2(rv, p2)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
   Message (4, ((INT4) rv), MSGxEXIT, p2);}} while (0)

#define _ErrStop3(rv, p2, p3)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
   Message (5, ((INT4) rv), MSGxEXIT, p2, p3);}} while (0)

#define _ErrStop4(rv, p2, p3, p4)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
   Message (6, ((INT4) rv), MSGxEXIT, p2, p3, p4);}} while (0)


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  checks some return value if it is message code and only prints 
**  message 
*/

#define _ErrMsg(rv)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
   Message (3, ((INT4) rv), MSGxNOEX);}} while (0)

#define _ErrMsg2(rv, p2)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
   Message (4, ((INT4) rv), MSGxNOEX, p2);}} while (0)

#define _ErrMsg3(rv, p2, p3)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
   Message (5, ((INT4) rv), MSGxNOEX, p2, p3);}} while (0)

#define _ErrMsg4(rv, p2, p3, p4)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
   Message (6, ((INT4) rv), MSGxNOEX, p2, p3, p4);}} while (0)

#define _ErrMsg5(rv, p2, p3, p4, p5)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
   Message (7, ((INT4) rv), MSGxNOEX, (p2), (p3), (p4), (p5));}} while (0)

#define _ErrMsg6(rv, p2, p3, p4, p5, p6)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
   Message (8, ((INT4) rv), MSGxNOEX, p2, p3, p4, p5, p6);}} while (0)


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  checks some return value if it is message code, prints message 
**  and returns message code to calling function
*/

#define _ErrRet(rv) \
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { \
   return (INT4) rv;}} while (0)

#define _ErrRet1(rv)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
   if (Message (3, ((INT4) rv), MSGxNOEX)) return (INT4) rv;}} while (0)

#define _ErrRet2(rv, p2)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
   if (Message (4, ((INT4) rv), MSGxNOEX, p2)) return (INT4) rv;}} while (0)

#define _ErrRet3(rv, p2, p3)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
   if (Message (5, ((INT4) rv), MSGxNOEX, p2, p3)) return (INT4) rv;}} while (0)

#define _ErrRet4(rv, p2, p3, p4)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
if (Message (6, ((INT4) rv), MSGxNOEX, p2, p3, p4)) return (INT4) rv;}} while (0)

#define _ErrRet5(rv, p2, p3, p4, p5)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
if (Message (6, ((INT4) rv), MSGxNOEX, p2, p3, p4, p5)) return (INT4) rv;}} while (0)


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  checks some return value if it is message code, prints message 
**  and exits program
*/

#define _ErrExit(rv)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
   if (Message (3, ((INT4) rv), MSGxNOEX)) exit(-1);}} while (0)

#define _ErrExit2(rv, p2)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
   if (Message (4, ((INT4) rv), MSGxNOEX, p2)) exit(-1);}} while (0)

#define _ErrExit3(rv, p2, p3)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
   {if (Message (5, ((INT4) rv), MSGxNOEX, p2, p3)) exit(-1);}}} while (0)

#define _ErrExit4(rv, p2, p3, p4)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
   if (Message (6, ((INT4) rv), MSGxNOEX, p2, p3, p4)) exit(-1);}} while (0)

#define _ErrExit5(rv, p2, p3, p4, p5)\
do {if (((INT4) rv) < MSGxMAX && ((INT4) rv > MSGxMIN)) { __ERRMSG \
   if (Message (7, ((INT4) rv), MSGxNOEX, p2, p3, p4, p5)) exit(-1);}} while (0)


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  checks some return value if it is message code
*/

#define _ErrIf(rv)\
 if ( (INT4) rv < MSGxMAX && (INT4) rv > MSGxMIN) 

#define _ErrIs(rv)\
 ( (INT4) rv < MSGxMAX && (INT4) rv > MSGxMIN) 

#define _ErrSet(errCodePtr, errCode)\
 do { \
   if (errCodePtr) \
     *errCodePtr = (INT4) errCode; \
 } while (0)

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of exported functions 
*/

INT4 Message (INT4 arg_n, INT4 msg_code, INT4 opt, ...);
void MsgSetFnct (INT4 (*fnct)());
Int4 MsgIs (struct MSGo *msg, char *option);
ode
srs/src/msgdef.c
char msgdef_srs_ID[] = "$Id: msgdef.c,v 1.2 1996/07/09 23:38:09 etzold Exp $";
/*
**
**    $RCSfile: msgdef.c,v $
**    $Revision: 1.2 $
**    $Date: 1996/07/09 23:38:09 $
**    $Author: etzold $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**             Unix port by Lukas Rosenthaler and Reinhard
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: none
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    this program generates the file message.h which defines
**    unique values for all error messages in message.dat;   
**    this value is calculated as the file address (by ftell)
**    multipied by -1 minus 1 000 000; (i. e. the error      
**    value is always smaller than -1 000 000 = MAXERR);               
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/


#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include "msg.h"

int main()
{
  FILE *inf, *outf;
  int  fip, errcode;
  int  k;
  char line[MSGxXLN];
  char errnam[MSGxXLN];
  char dummy;

  inf = fopen ("../etc/message.dat", "r");
  if (inf == NULL) {
    printf("\"%s\" could not be opened\n",MSGxFILE);
    exit(1);
  }
  outf = fopen("message.h", "w");
  if (outf == NULL) {
    printf("\"%s\" could not be opened\n",MSGxHDR);
    exit(1);
  }
  fprintf(outf, "#include \"%s\"\n", MSGxHHDR);	

  /*
  ** read file with messages until line starts with either of "iwef"
  ** (info, warning, error, fatal), get the fip (file pointer) multiply by
  ** -1 and add MSGxMAX * message type (enum msg_typ);
  */

  while (1) {
    do {
      fip = ftell(inf);
      fgets(line, MSGxXLN, inf);
    }
    while (strchr ("iwef", line[0]) == NULL && !feof(inf));
    if (feof(inf)) break;

    switch (line[0]) {
    case 'i':
      errcode = -1 * fip + (MSGxMAX * MSGxINFO);      
      break;
    case 'w':
      errcode = -1 * fip + (MSGxMAX * MSGxWARNING);      
      break;
    case 'e':
      errcode = -1 * fip + (MSGxMAX * MSGxERROR);      
      break;
    case 'f':
      errcode = -1 * fip + (MSGxMAX * MSGxFATAL);      
      break;
    case 'o': /* obsolete */
      errcode = 0;      
      break;
    default:
      printf ("messages starting with \"%d__\" have unknown type\n=> %s\n",
	      line[0], line);
      exit(1);
      break;
    }

    
    dummy = fgetc(inf);		/* for RMS to see that record end is */
    ungetc(dummy, inf);		/* reached otherwise ftell = bullshit */
    
    for (k = 0;  (line[k] != ',') && (k < 80) ;  k++)
      errnam[k] = line[k];
    errnam[k] = '\0';
    if (k == 80) {
      printf("error message is in wrong format:\n %s\n", errnam);
      exit(1);
    }
    if (errcode != 0)
      fprintf(outf, "#define %s   %d\n", errnam, errcode);
  }
  printf("message.h is created in the current folder\n");
  exit (0);
}





    
    dummy = fgetc(inf);		/* for RMS to see that record end is */
    ungetc(dummy, inf);		/* reached otherwise ftell = bullshit */
    
    for (k = 0;  (line[k] != ',') && (k < 80) ;  k++)
      errnam[k] = line[k];
    errnam[k] = '\0';
    if (k == 80) {
      printf("error message is in wrong format:\n %s\n", errnam);
      exit(1);
    }
    if (errcode != 0)
 srs/src/nodd.c
#include <stdio.h>
#include <stdlib.h>
#include <stdarg.h>

#include "message.h"
#include "futil.h"
#include "sm.h"
#include "arglist.h"
#include "toklist.h"
#include "icarus.h"

#include "odd.h"
#define _INITOBJS
#define _CONSTANTS
#define _SDL
#define _ODD
#define _FUNCTION 
#include "oddclass.h"


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  object wide and global variables
*/

typedef INT4 (*SDLoFNCTx)();
SDLoFNCTx    SDL_fnctx[] = {NULL};
static INT4 PrintMessage (MSGo *msg);
struct ICAoSYNTAX *IcaInitSyntax(struct ICAoSYNTAX *syntax);


main(int argc, char **argv)
{
  SDLo         *odd;
  ARGoLIST     *arglist;
  FILEo        *file;
  ICAoJOB      *job; 
  ICAoSYNTAX   *syntax;
  
  ParSetTable ("global", NULL, "PRIVATE");
  ParInit (ODD_parTable);
  MsgSetFnct ((FUNC)IcaPrintMessage);
  argc = ArgGet (&argList[0], argc, argv); 
  
  if (argc != 3) { /* process command line options */
    ArgUsage (argList);
    exit (1);
  }

  syntax = IcaInitSyntax (NULL);

  /* process class information */

  job = IcaCreateJob (syntax);
  odd = OddInit (def, 1);
  file = FileNew (argv[1]);
  if (!FileOpen (file))
    _ErrExit2 (e__filnotok, argv[2]);
  IcaJobSetFile (job, file);
  IcaGetTokenList (job, "prog");

  if (IcaJobIsError (job))
    _ErrExit (e__icaErrorsQuit);
  IcaExecProg (job);

  /* process objects */

  if (IcaJobIsError (job))
    _ErrExit (e__icaErrorsQuit);
  job = IcaCreateJob (syntax);
  odd = OddInit (odd, 2); 
  file = FileNew (argv[2]);
  if (!FileOpen (file))
    _ErrExit2 (e__filnotok, argv[2]);
  IcaJobSetFile (job, file);
  IcaGetTokenList (job, "prog");
  job->file = FileDelete (job->file);

  if (IcaJobIsError (job))
    _ErrExit (e__icaErrorsQuit);
  IcaExecProg (job);

  if (IcaJobIsError (job))
    _ErrExit (e__icaErrorsQuit);
  OddOut (odd);
  exit (0);
}

b);

  /* process objects */

  if (IcaJobIsError (job))
    _ErrExit (e__icaErrorsQuit);
  job = IcaCreateJob (syntax);
  odd = OddInit (odd, 2); 
  file = FileNew (argv[2]);
  if (!FileOpen (file))
    _Esrs/src/ntry.c
#include <stdio.h>
#include <stdlib.h>
#include "srs.h"

#include "odd.h"
#define _INITOBJS
#define _CONSTANTS
#define _SDL
#define _ODD
#define _FUNCTION 
#include "oddclass.h"

int main(int argc, char **argv)
{
  SETo      *set;
  ENTRYo    *entry;
  IDoENTRY  id;
  INT4      i;
  
  SrsEnv ();
  LibOpen ("srs5");
  OddInit (def, 1); 
  IcaInitSyntax (LibObjByName ("syntax", "icarus"));

  MsgSetFnct ((FUNC)IcaPrintMessage);

  argc = ArgGet (LibObjByName ("arglist", "getz"), argc, argv);
  if (ParGetNum ("printLibInfo") && argc == 2) {  /* print only info ? */
    LibPrintInfo (argv[1]);
    exit (0);
  }
  else if (ParGetNum ("printLibs")) {
    LibPrintLibs ();
    exit (0);
  }

  if ((set = Query (argv[1], "Q1")))
    for (i=1; i <= set->n; i++) {
      SetGetID (set, i, &id);
      entry = EntryOpen (&id);
      if (ParGetBool ("printEntireEntry"))
	EntryPrint (entry);
      else
	EntryPrintFields (entry); 
      EntryClose (&entry);
    }
  exit (0);
}


glist", "getz"), argc, argv);
  if (ParGetNumsrs/src/objstream.c
#include "listv.h"
#include "strv.h"
#include "dict.h"
#include "blub.h"
#include "objstream.h"
#include <stdio.h>


/******************************************************
** ATTRIBUTE PRINTING ACTION
******************************************************/

typedef void (*ValPrinter) (void* val);

void PolyIntPrint(int* v) { printf("%d", *v); }

void PolyPtrPrint(PTR* v) { printf("%p", *v); }

void PolyStrPrint(STRv* v, void* nothing) {
    if (*v) printf("%s", Str(*v));
    else printf("NULL");
}

void PolyObjPrint(void** obj) { ObjPrint(*obj); }

void PolyListPrint(ListAttr* l) {
    printf("[n:%d", displ(l->tail,l+1));
    if (l->end!=l->tail) printf(" g:%d", displ(l->end,l->tail));
    printf("]");
}

void PolyAttrPrint(ATTRv* a) {
    if (a->type!=-1) {
	if (a->name) printf("%s:", Str(a->name));
	printf("%s", Str(attrDescr[a->type].name));
	printf("[o:%d]",a->offs);
    }
}

void PolyClassPrint(CLASSBODYv* c) {
    /*if (c->name) printf(" name:%s", Str(c->name));*/
    if (c->inherits) {
	printf("inherits: ");
	ObjPrint(c->inherits);
    }
    if (c->fixed->type!=-1) {
	printf("list: %s",Str(attrDescr[c->fixed->type].name));
    }
}
   
void AttrPrintAction(void* val, ATTRp attr, void* nothing) {
    static ValPrinter printOp[]={
	(ValPrinter) PolyIntPrint, 
	(ValPrinter) PolyPtrPrint, 
	(ValPrinter) PolyStrPrint, 
	(ValPrinter) PolyObjPrint, 
	(ValPrinter) PolyListPrint, 
	(ValPrinter) PolyClassPrint, 
	(ValPrinter) PolyAttrPrint
    };
    printf(" ");
    if (attr->type!=-1) {
	if (attr->name) printf("%s:", Str(attr->name));
	call (printOp[attr->type])(val);
    }
}



/* services */

void ObjPrintDescr(CLASSv descr) {
    STRv name=SysToName(descr);
    if (name) {
	printf("%s",_Str(name));
    } 
    else {
        ObjPrintDescr(descr->inherits);
	printf(" with:{");
	ObjDoList(descr, AttrPrintAction, NULL);
	printf("}");
    }
}
    
void ObjPrint(void* obj) {
    if (obj) {
	ObjPrintDescr(_getObj(obj)->descr);
	printf("[");
	ObjDoAll(obj, AttrPrintAction, NULL);
	printf("]");
    }
    else printf("NULL");
}

void ObjDebug(void* obj) {
    printf("%p: ", obj);
    if (obj) {
	OBJv o=_getObj(obj);
	ObjPrint(obj);
	printf(" ");
	/*ObjPrint(o->descr);*/
    }
    printf("\n");
}

	
/*********************************************************
** OBJECT STREAM DEFINITION
*********************************************************/

typedef struct MapEntry {
    void* val;
    int	  usage;
    int   id;
} MapEntry;

void* MapEntryToKey(MapEntry** m, IntOrPtr nothing) {
    return (*m)->val;
}

typedef struct OBJoStream {
    FILE*      file;
    DICTv      objs;   /* object value management */
    DICTv      strs;   /* string value management */
    DICTv      ptrs;
    int	       idLast;
    void**     ids;
} OBJoStream;

/***************************
***************** writing */

void* ObjStreamMapDef(DICTv* map, void* val) {
    MapEntry **mp,*m;
    if (SysToId(val)!=-1) return NULL;
    mp=&DictSet(map, val, MapEntry*);
    m=*mp;
    if (m) { 
	m->usage++; 
	if (val!=m->val) return m->val;
	else return NULL;
    }
    else {
	m=*mp=_palloc(MapEntry);
	m->val=val;
	m->usage=1;
	m->id=0;
	return NULL;
    } 
}   

#define OBJSTREAM_ID       1
#define OBJSTREAM_DEFVALID 2
int objStreamDefineVal=0;

BOOL ObjStreamVal(OBJpStream stream, DICTv* map, void* val) {
    int id=SysToId(val);
    if (id==-1) {
	/* not in the system culture */
	MapEntry* m;
	Iter mi=DictWith(*map, val);
	objStreamDefineVal=0;
	if (!mi) return TRUE;
	m=DictIn(mi, MapEntry*); m->usage--;
	id=m->id;
	if (id==0) {
	    if (m->usage>0) {
		/* define new id if first time and reused */
		objStreamDefineVal=OBJSTREAM_DEFVALID;
		id=m->id=stream->idLast++;
	    }
	    else {
		_pfree(m); DictRemove(map, mi);
	    }
	    return TRUE;
	}
	if (m->usage==0) {
	    /* remove entry */
	    _pfree(m); DictRemove(map, mi);
	}
    }
    /* now stream id */
    IntStore((id<<1) | OBJSTREAM_ID, stream);
    return FALSE;
}

void ObjStreamHead(OBJpStream stream, int head) {
    IntStore((head<<2)|objStreamDefineVal, stream);
}

/*******************************
********************* reading */

UINT4 streamFirstVal; 

BOOL ObjStreamGetVal(OBJpStream stream, void** val) {
    UINT4 n=IntLoad(stream);
    if (n & OBJSTREAM_ID) {
	int sysMax=SysIdNum(); 
	n>>=1;
	if (n<sysMax) *val=*SysFromId(n);
	else *val=stream->ids[n-sysMax];
	return FALSE;
    }
    /* must read value */
    streamFirstVal=n>>2; 
    if (n & OBJSTREAM_DEFVALID) {
	void** e=&_ListApp(&stream->ids);
	*e=NULL; *val=e; 
    }
    else *val=NULL; 
    return TRUE;
}    

CLASSoDICT objMapIndex = {
    (ValComparer) ObjEqual, 
    (ValHasher) ObjHash, 
    (KeyAccessor) MapEntryToKey, 
    NULL, 
    FALSE
};

CLASSoDICT strMapIndex = {
    (ValComparer) StrEqual, 
    (ValHasher) StrHash, 
    (KeyAccessor) MapEntryToKey, 
    NULL, 
    FALSE
};

CLASSoDICT ptrMapIndex = {
    (ValComparer) PtrEqual, 
    (ValHasher) PtrHash, 
    (KeyAccessor) MapEntryToKey, 
    NULL, 
    FALSE    
};

OBJpStream ObjStreamOpen(char* fileName,char* mode) {
    OBJpStream os;
    os=typeAlloc(OBJoStream);
    os->ptrs=DictCreate(&ptrMapIndex);
    os->strs=DictCreate(&strMapIndex);
    os->objs=DictCreate(&objMapIndex);
    os->file=fopen(fileName, mode);
    os->idLast=SysIdNum();
    os->ids=_ListNew(10,void*);
    return os;
}

void ObjStreamClose(OBJpStream os) {
    /* frees elements of ptr map, removing from pos map */
    DICTv map; Iter i; MapEntry* e;
    map=os->ptrs;
    for (i=DictFirst(map); i; DictNext(map,&i)) {
	e=DictIn(i, MapEntry*); _pfree(e);
    }
    DictDestroy(map);
    map=os->strs;
    for (i=DictFirst(map); i; DictNext(map,&i)) {
	e=DictIn(i, MapEntry*); _pfree(e);
    }
    DictDestroy(map);
    map=os->objs;
    for (i=DictFirst(map); i; DictNext(map,&i)) {
	e=DictIn(i, MapEntry*); _pfree(e);
    }
    DictDestroy(map);
    ListDel(os->ids);
    fclose(os->file);
    free (os);
}


/******************************************************
** ATTRIBUTE MAPPING ACTION
******************************************************/

typedef void (*ValMapper)(void* val, OBJpStream s);
void AttrMapAction(void* val, ATTRv* attr, void* stream);

void PtrMap(PTR* val, OBJpStream s) { 
    ObjStreamMapDef(&s->ptrs, *val); 
}

void StrMap(STRv* val, OBJpStream stream) {
    if (*val && StrShared(*val)) {
	STRv s=(STRv)ObjStreamMapDef(&stream->strs, *val);
	if (s) StrSet(val, s);
    }
}

void ObjMap(void** val, OBJpStream stream) {
    if (*val && SysToId(*val)==-1) {
	void* o;
	CLASSv descr=ObjClass(*val);
	ObjMap(&descr,stream);
	ObjDoAll(*val, AttrMapAction, stream);
	o=ObjStreamMapDef(&stream->objs, *val);
	if (o) ObjSet(val, o);    
    }
}

void ClassMap(CLASSBODYv* val, OBJpStream stream) {
    ObjMap(&val->inherits, stream);
}

void AttrMap(ATTRv* val, OBJpStream stream) {
    StrMap(&val->name, stream);
    ObjMap(&val->more, stream);
}


void AttrMapAction(void* val, ATTRv* attr, void* stream) {
    static ValMapper mapOp[]={
	(ValMapper) PolyNothing, 
	(ValMapper) PtrMap, 
	(ValMapper) StrMap, 
	(ValMapper) ObjMap, 
	(ValMapper) PolyNothing, 
	(ValMapper) ClassMap, 
	(ValMapper) AttrMap
    };
    call (mapOp[attr->type])(val, (OBJpStream)stream);
}

/***************************************************
** ATTRIBUTE STORING ACTION
***************************************************/

typedef (*ValStorer) (void* val, OBJpStream s);

void PolyIntStore(int* v, OBJpStream stream) { IntStore(*v, stream); }

void PolyPtrStore(PTR* v, OBJpStream stream) { 
    ASSERT (!ObjStreamVal(stream, &stream->ptrs,*v), "StoringUnmappedPtr");
}

void PolyStrStore(STRv* v, OBJpStream stream) { StrStore(*v, stream); }
void PolyObjStore(void** obj, OBJpStream stream) { ObjStore(*obj, stream); }

void PolyAttrStore(ATTRv* attr, OBJpStream stream) { 
    StrStore(attr->name, stream);
    IntStore(attr->type, stream);
    ObjStore(attr->more, stream);
}

void AttrStoreAction(void* val, ATTRp attr, void* stream) {
    static ValStorer storeOp[]={
	(ValStorer) PolyIntStore, 
	(ValStorer) PolyPtrStore, 
	(ValStorer) PolyStrStore, 
	(ValStorer) PolyObjStore, 
	(ValStorer) PolyNothing, 
	(ValStorer) PolyNothing, 
	(ValStorer) PolyAttrStore
    };
    call (storeOp[attr->type])(val, (OBJpStream) stream);
}

/****************************************************
** STORING FUNCTIONS
*/

void IntStore(int i, OBJpStream stream) {
    int n; char* b=MIFromLong(i, &n);
    fwrite(b, 1, n, stream->file);
}

void StrStore(STRv s, OBJpStream stream) {
    if (ObjStreamVal(stream, &stream->strs, s)) {
	int len=StrLen(s);
	ObjStreamHead(stream, len);
	fwrite(Str(s), 1, len, stream->file); 
    }
}
    
void ClassStore(CLASSv c, OBJpStream stream) {
    if (ObjStreamVal(stream, &stream->objs, c)) {
	ATTRv *a,*fixed; int nAttr;
        fixed=c->fixed; a=c->attrs; nAttr=fixed-a;
	ObjStreamHead(stream, nAttr);	
	/* save class value */
	ClassStore(c->inherits, stream);
	while (a!=fixed) {
	    /* save attribute name and type name */
	    StrStore(a->name, stream);
	    IntStore(a->type, stream);
	    a++;
	}
	/* save type of fixed, not null if list */
	IntStore(fixed->type, stream);
    }
}

void ObjStore(void* obj, OBJpStream stream) {
    if (ObjStreamVal(stream, &stream->objs, obj)) {
	int nElem; 
	ObjMap(&obj,stream);
	nElem=ObjListCard(obj);
	ObjStreamHead(stream, nElem);
	ClassStore(_getObj(obj)->descr, stream);
	ObjDoAll(obj, AttrStoreAction, stream);
    }
}

/***************************************************************
** ATTRIBUTE LOADING ACTION
***************************************************************/

typedef (*ValLoader) (void* val, OBJpStream s);

void PolyIntLoad(int* v, OBJpStream stream) { *v=IntLoad(stream); }

void PolyPtrLoad(PTR* v, OBJpStream stream) {
    ASSERT(!ObjStreamGetVal(stream,v), "StreamUnmappedPtr");
}

void PolyStrLoad(STRv* v, OBJpStream stream) { *v=StrLoad(stream); }
void PolyObjLoad(void** obj, OBJpStream stream) { *obj=ObjLoad(stream); }

void PolyAttrLoad(ATTRv* attr, OBJpStream stream) { 
    attr->name=StrLoad(stream);
    attr->type=IntLoad(stream);
    attr->more=ObjLoad(stream);
}

void AttrLoadAction(void* val, ATTRp attr, void* stream) {
    static ValLoader loadOp[]={
	(ValLoader) PolyIntLoad, 
	(ValLoader) PolyPtrLoad, 
	(ValLoader) PolyStrLoad, 
	(ValLoader) PolyObjLoad, 
	(ValLoader) PolyNothing, 
	(ValLoader) PolyNothing, 
	(ValLoader) PolyAttrLoad
    };
    call (loadOp[attr->type])(val, (OBJpStream) stream);
}

int IntLoad(OBJpStream stream) {
    int n; char buf[8];
    buf[0]=getc(stream->file);
    n=MIToLongSize(buf[0]); 
    fread(buf+1, 1, n-1, stream->file);
    return MIToLong(buf);    
}

STRv StrLoad(OBJpStream stream) {
    void* val;
    if (ObjStreamGetVal(stream, &val)) {
	UINT4 len=streamFirstVal;
	STRv s=StrBufNew(len); s->len=len;  
	fread(Str(s), 1, len, stream->file);
	Str(s)[len]='\0';
	if (val) *((STRv**)val)=s;
	return s;
    }
    else return StrCpy((STRv)val);
}

CLASSv ClassLoad(OBJpStream stream) {
    void* val;
    if (ObjStreamGetVal(stream, &val)) {
	int nAttr=streamFirstVal; 
        int type; 
	CLASSv c=ClassLoad(stream); /* loads base class */
	while (nAttr--) {
	    STRv attrName=StrLoad(stream);
	    type=IntLoad(stream);
	    ClassAttrNew(&c, attrName, type, NULL);
	}
	type=IntLoad(stream);
	if (type!=-1) ClassListNew(&c, type, NULL);
	if (val) *((CLASSv**)val)=c;
	return c;
    }
    else return ObjCpy((CLASSv)val);
}

void* ObjLoad(OBJpStream stream) {
    void* val;
    if (ObjStreamGetVal(stream, &val)) {
	void* o;
	int numElem=streamFirstVal;
	CLASSv c=ClassLoad(stream);
	o=ClassAlloc(c, numElem);
	ObjDoAll(o, AttrLoadAction, stream);
	if (val) *((void**)val)=o;
	return o;
    }
    else return ObjCpy(val);
}
stream);
	    ClassAttrNew(&c, attrName, tsrs/src/objstream.h

/* storing/loading */
OBJpStream  ObjStreamOpen(char* fileName, char* mode);
void	    ObjStreamClose(OBJpStream stream);
void	    ObjStore(void* obj, OBJpStream stream);
void*	    ObjLoad(OBJpStream stream);
void	    StrStore(STRv s, OBJpStream stream);
STRv	    StrLoad(OBJpStream stream);
void	    IntStore(int i, OBJpStream stream);
int	    IntLoad(OBJpStream stream);
*)val)=o;
	return o;¶ £¡@   else return ObjCpy(val);
}
stream);
	    ClassAttrNew¶ £¡Ü\°e, tsrs/src/odd.c
char readsdl_srs_ID[] = "$Id: odd.c,v 1.1 1996/05/06 15:17:00 srs Exp $";
/*
**
**    $RCSfile: odd.c,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:17:00 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.x Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>

#include "message.h"
#include "futil.h"
#include "sm.h"
#include "parser.h"
#include "arglist.h"
#include "par.h"


#include "sdl.h"
#define _INITOBJS
#define _CONSTANTS
#define	_SDL
#define	_ODD
#define _FUNCTION 
#include "sdl_def.h"

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  object wide variables
*/

PRSoST	    *gblst_s;


main(int argc, char **argv)
{
  SDLo *odd;
  char infil[FILxXNAM+1], outfil[FILxXNAM+1];
  int  opt1, opt2;

#ifndef BOOTSTRAP
  void **o_p;
  int  *o_n;
#endif

  /* 
  ** process command line options
  */

  ParSetTable ("global", NULL, "PRIVATE");
  ParInit (ODD_parTable);
  argc = ArgGet (&argList[0], argc, argv); 
  
  if (argc != 2) { /* process command line options */
    ArgUsage (argList);
    exit (1);
  }

  if (ParGetBool ("doInitHeader"))
    opt1 = SDLxNOHDR, opt2 = SDLxHDR;
  else if (ParGetBool ("doMetaData"))
    opt1 = SDLxHDR;
  else if (ParGetBool ("doSection") && ParGetBool ("doHeader"))
    opt1 = SDLxPRESEC, opt2 = SDLxHDRSEC;
  else if (ParGetBool ("doSection"))
    opt1 = SDLxNOHDR, opt2 = SDLxSECTION;
  else if (ParGetBool ("doHeader"))
    opt1 = SDLxNOHDR, opt2 = SDLxHDR2;
  else if (ParGetBool ("doClassInfo"))
    opt1 = SDLxNOHDR, opt2 = SDLxHDR2;
  else
    exit (0);


#ifndef BOOTSTRAP 
# ifdef VMS
  SdlGetObjects (&o_n, &o_p, "SDL");
# else
  SdlGetObjects (&o_n, &o_p, "sdl");
# endif
  odd = (SDLo *) o_p[O_SDL];
#else
  odd = (&def[0]); 
#endif


  sprintf(infil,  "SRSSDL:%s_def.sdl", argv[1]);    
  sprintf(outfil, "SRSSOU:%s_def.h", argv[1]);
  odd->ifnam = &infil[0];
  odd->ofnam = &outfil[0];
  
  SdlProc(odd, opt1);
  if (opt1 == SDLxHDR) 
    exit(0);
  


  odd = (SDLo *) odd->oc[odd->oc_n-1].s;
  SdlProc(odd, opt2);
  exit (0);
}


HDR2;
  else
    exit (0);


#ifndef BOOTSTRAP 
# ifdef VMS
  SdlGetObjects (&o_n, &o_p, "SDL");
# else
  SdlGetObjects (&o_n, &o_p, "sdl");
# endif
  odd = (SDLo *) o_p[O_SDL];
#else
  odd = (&def[0]); 
#endif


  sprintf(infil,  "SRSSDL:%s_def.sdl", argv[1]);    
  sprintf(outfil, "SRSSOU:%s_def.h", argv[1]);
  odd->ifnam = &infil[0];
  odd->ofnam = &outfil[0];
  
  SdlProc(odd, opt1);
  if (optsrs/src/odd.h
**
**    $RCSfile: odd.h,v $
**    $Revision: 1.6 $
**    $Date: 1997/03/12 19:07:38 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**                  SRS V3.x Copyright by Thure Etzold
**
*/


#define SDLxXSS		7	       /* max nr of substrt a strct may have */
#define SDLxXNAM	15	       /* maxlen of names in definition file */
#define SDLxXLN		512	       /* max line len in definition file */
#define SDLxXHLN	79	       /* max line len in header file */
#define SDLxXLOG        2000	       /* max nr. of logicals */
#define SDLxXSYM        5000	       /* max nr. of symbols per table */
#define SDLxXLSYM       132	       /* max size of symbol */
#define SDLxXSYMTBL     100000	       /* max size of symbol table */
#define SDLxXLOGTBL     30000	       /* max size of table for logicals */
#define SDLxXASSGSTR    132            /* max length of string assignement */
#define SDLxXADDR	40000          /* max length of string assignement */
#define SDLxXOBJCLASS   255
#define SDLxXOBJ	2048            /* max nr. of objects per class */
#define SDLxXFNCT	200            /* max nr. of transm. functions */
#define SDLxNULLFNCT	10000
#define ODDxNULL	4294967295U

enum ODDeAct {SDLxNOHDR, SDLxHDR, SDLxHDR2, SDLxSECTION,SDLxPRESEC,SDLxHDRSEC};


#define SDLxRD		1	       /* ATTRIBUTE read  */
#define SDLxNORD        2              /* ATTRIBUTE not yet read  */
#define SDLxREQ         1              /* ATTRIBUTE is required */
#define SDLxNOREQ       0              /* ATTRIBUTE is not required */
        
#define SDLxDFLT	1
#define SDLxNODFLT	2
        
#define	SDLxPNUM	9
#define SDLxFNCT	11	       /* object type			    */

#define SDLxPFNCT	10
#define SDLxCLONE	20
#define SDLxOVERLAY     18
#define SDLxDEFER       16        
#define SDLxBNF         21        

#define SDLxVIRTUAL     1

#define SDLxGTYPDEFNAM  "GenTypeDef"
#define SDLxGTYPNAM	"GenType"

				       /* lm bit on: turns bit off + TRUE */
#define _SdlIsStr(x)  (x != (x & SDLxLBOFF)) ? (x = x & SDLxLBOFF) : 0 
#define _SdlMarkStr(x)  x |= SDLxLBON  /* turn leftmost bit on */
#define __SdlAddr(addr)	{ if (odd->section_f) SdlListAddr (addr); }
#define _SdlMalloc(n)	\
  ((odd->section_f) ? SdlMalloc (n) : (void *) malloc (n))



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  macros for alignment
*/

#if defined  (VMS) || defined (dos)
# define ALI4 1
# define ALI8 1
#else
#if defined (osf) /* columba!!!! || defined (irix64) */
# define ALI4 4
# define ALI8 8
#else
# define ALI4 4
# define ALI8 4
#endif
#endif

#define _SdlAlignFour(off) (off) = (((off) + (ALI4-1))/ALI4)*ALI4 
#define _SdlAlignEight(off) (off) = (((off) + (ALI8-1))/ALI8)*ALI8 


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  pointer into the data structure built by ODD
*/

typedef char *SDLoPTR;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  holds pointers to addresses of both function name and argument list
*/

typedef struct {
  char **nam;
  char **args;
  char **module;
  char isDone;
} ODDoFNCT_P;

typedef struct ODDoCDEFINE {
  char name[80];
  INT4 n;
} ODDoCDEFINE;

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of exported functions
*/

#ifndef _SDL
typedef struct SDLo *dummytointroducestructtagSDLo;
#endif

#ifndef _ODDoHEAD
typedef struct ODDoHEAD *dummytointroducestructtagODDoHEAD;
#endif

#ifndef _SDLoOBJ
typedef struct SDLoOBJ *dummytointroducestructtagSDLoOBJ;
#endif

#ifndef _SDLoATTR
typedef struct SDLoATTR *dummytointroducestructtagSDLoATTR;
#endif

void *SdlMalloc (int n);
int SdlListAddr (SDLoPTR a);
int SdlSaveAddr (struct SDLoOBJ *obj, SDLoPTR uobj);
int SdlGenericNames (struct SDLoOBJ *obj, int typ, char *typ_nm);
int SdlCheckPar (struct SDLoATTR *attr, char *s, int v);
struct SDLo *OddInit (struct SDLo *oddBase, INT4 level);
struct SDLoOBJ *OddGetClass (char *className);
void *OddFinishObj (struct SDLoOBJ *class);
void OddWriteClassInfo (struct SDLo *odd);

char *OddGetClassName (struct SDLoOBJ *class);
void *OddGetObjectPtr (struct SDLoOBJ *class, Int4 n);
Int4 OddGetObjectN (struct SDLoOBJ *class);
void OddSetObjListSize (struct SDLoOBJ *class, char *attrName, Int4 n);
char *OddGetAttrDeclName (struct SDLoATTR *attr);
char *OddGetClassDeclName (struct SDLoOBJ *class);
struct SDLoATTR *OddGetAttribute (struct SDLoOBJ *class, char *name);
struct SDLoOBJ *OddGetPartofClass (struct SDLoATTR *attr);


 SDLoOBJ *class);
void OddWriteClassInfo (struct SDLo *odd);

char *OddGetClassName (struct SDsrs/src/oddclass.h
**
**    $RCSfile: oddclass.h,v $
**    $Revision: 1.4 $
**    $Date: 1997/03/03 18:20:43 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**             from ODD file: "srsica:odd.i"
**   date of ODD compilation: 16-SEP-1996 10:14
**
*/


#define  AT_CHILD           6
#define  AT_PROTOFNCT       10
#define  AT_FNCT            11
#define  AT_CLONE           20

#if defined(_SDL) && !defined(_ODDoVAL)
#define _ODDoVAL
typedef struct ODDoVAL {
  char                    *nam;
  UINT4                   val;
} ODDoVAL;
#endif

#if defined(_SDL) && !defined(_ODDoATYP)
#define _ODDoATYP
typedef struct ODDoATYP {
  INT4                    (*make) ();
  INT4                    (*insert) ();
  INT4                    (*size) ();
  INT4                    (*write) ();
  INT4                    (*declare) ();
  INT4                    (*check) ();
  INT4                    (*gentype) ();
  unsigned char           save_f;
  char                    *tnam;
} ODDoATYP;
#endif

#if defined(_SDL) && !defined(_SDLoATTR)
#define _SDLoATTR
typedef struct SDLoATTR {
  char                    *rem;
  struct SDLoOBJ          *class;
  struct ODDoVAL          *val;
  INT4                    val_n;
  char                    *nam;
  char                    *tnam;
  char                    *sw_nm;
  char                    *alt_nm;
  char                    *dnam;
  INT4                    unnamed;
  unsigned char           typ;
  unsigned char           ptyp[4];
  INT4                    arrsz;
  INT4                    min;
  INT4                    max;
  INT4                    off;
  unsigned char           req;
  unsigned char           status[2];
  unsigned char           isrd;
  INT4                    dfltv;
  char                    *dflts;
  float                   dfltvf;
  INT4                    scnt;
  struct SDLoOBJ          *obj;
  INT4                    hasObjsN;
  void                    *hasFirstObj;
} SDLoATTR;
#endif

#if defined(_SDL) && !defined(_SDLoOBJ)
#define _SDLoOBJ
typedef struct SDLoOBJ {
  char                    *nam;
  char                    *rem;
  char                    *tnam;
  char                    *pp_nm;
  char                    *dnam;
  unsigned char           typ;
  unsigned char           status[2];
  INT4                    siz;
  char                    *s;
  INT4                    ns;
  char                    *uobj_coff;
  INT4                    gbl_n;
  INT4                    loc_n;
  unsigned char           nss;
  unsigned char           ss[7];
  INT4                    np;
  struct SDLoATTR         *p;
  INT4                    gtyp_n;
  char                    *gtypdef_nm[7];
  char                    *gtyp_nm[7];
  char                    *orgtyp_nm;
} SDLoOBJ;
#endif

#if defined(_SDL) && !defined(_SDLo)
#define _SDLo
typedef struct SDLo {
  char                    *ifnam;
  char                    *ofnam;
  char                    *sec_nm;
  INT4                    sec_z;
  INT4                    oc_n;
  struct SDLoOBJ          *oc;
  INT4                    at_n;
  struct ODDoATYP         *at;
  unsigned char           error;
  unsigned char           action;
  unsigned char           pass_n;
  unsigned char           keepst_f;
  unsigned char           section_f;
} SDLo;
#endif

#ifndef _PARo
#define _PARo
typedef struct PARo {
  char                    *intern;       /* for internal use for the list
                                            manager */
  INT4                    classId;       /* for internal use for the list
                                            manager */
  char                    *name;         /* name of associated global parameter
                                            */
  char                    *str;          /* Value of 'string' parameter. */
  INT4                    num;           /* Value of 'number' parameter. */
  float                   real;          /* Value of 'real' parameter. */
  INT4                    (*function) (); /* Value of 'function' parameter. */
  void                    *object;       /* Value of 'object' parameter. */
  unsigned char           isVolatile;
  unsigned char           type;          /* Parameter type. */
  char                    *comment;      /* Short description of parameter. */
  char                    *helpTopic;    /* help topic associated to parameter
                                            */
  char                    *key;          /* keystroke associated to parameter
                                            or value */
  struct PARoTYPE         *parType;      /* Object 'partype' for validating the
                                            parameter value. */
  struct PARoTYPE         *check;        /* Object 'partype' for validating the
                                            parameter value. */
  INT4                    isLocked;      /* internal use... */
  char                    *set;          /* Icarus command to set the current
                                            value. */
  char                    *get;          /* Icarus command to get the current
                                            value. */
} PARo;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Describes further a parameter type by specifying constraints or a function for checking the parameter value.
*/

#ifndef _PARoTYPE
#define _PARoTYPE
typedef struct PARoTYPE {
  char                    *intern;       /* for internal use for the list
                                            manager */
  INT4                    classId;       /* for internal use for the list
                                            manager */
  char                    *name;         /* Name of associated global
                                            parameter. */
  INT4                    (*check) ();   /* Function that checks parameter
                                            value. */
  INT4                    max;           /* Max value, or max length. */
  INT4                    min;           /* Mmin value, or min length. */
  float                   maxReal;       /* Max real value. */
  float                   minReal;       /* Min real value. */
  char                    *charSet;      /* Permissible set of chars for
                                            parameter value string. */
} PARoTYPE;
#endif

#ifndef _PARoLIST
#define _PARoLIST
typedef struct PARoLIST {
  struct PARo             *par;          /* List of all predefined parameters.
                                            */
  INT4                    parN;          /* Number of predefined parameters. */
  struct PARoTYPE         *parType;      /* List of all predefined parameter
                                            types. */
  INT4                    parTypeN;      /* Number of predefined parameter
                                            types. */
} PARoLIST;
#endif

#ifndef _arg_t
#define _arg_t
typedef struct arg_t {
  char                    *name;
  INT4                    type;
  char                    *parameter;
  char                    *comment;
  INT4                    (*check) ();
  INT4                    defaultNum;
  char                    *defaultStr;
  float                   defaultReal;
} arg_t;
#endif

#ifndef _ARGoLIST
#define _ARGoLIST
typedef struct ARGoLIST {
  char                    *name;
  char                    *usage;
  struct arg_t            *arg;
  INT4                    argN;
} ARGoLIST;
#endif

#ifdef _FUNCTION
#undef _FUNCTION

INT4 OFInheritSize (SDLoOBJ *, SDLoATTR *);
#define OFInheritSize_F (INT4(*)()) OFInheritSize
INT4 OF4BArrSize (SDLoOBJ *, SDLoATTR *);
#define OF4BArrSize_F (INT4(*)()) OF4BArrSize
INT4 OF4BSize (SDLoOBJ *, SDLoATTR *);
#define OF4BSize_F (INT4(*)()) OF4BSize
INT4 OFPtrArrSize (SDLoOBJ *, SDLoATTR *);
#define OFPtrArrSize_F (INT4(*)()) OFPtrArrSize
INT4 OFPtrSize (SDLoOBJ *, SDLoATTR *);
#define OFPtrSize_F (INT4(*)()) OFPtrSize
INT4 OFBNFSize (SDLoOBJ *, SDLoATTR *);
#define OFBNFSize_F (INT4(*)()) OFBNFSize
INT4 OFBArrSize (SDLoOBJ *, SDLoATTR *);
#define OFBArrSize_F (INT4(*)()) OFBArrSize
INT4 OFMakeDefault (SDLoOBJ *, SDLoATTR *, unsigned int *);
#define OFMakeDefault_F (INT4(*)()) OFMakeDefault
INT4 OFMakeNoDefault (SDLoOBJ *, SDLoATTR *, unsigned int *);
#define OFMakeNoDefault_F (INT4(*)()) OFMakeNoDefault
INT4 OFMakeChild (SDLoOBJ *, SDLoATTR *, unsigned int *);
#define OFMakeChild_F (INT4(*)()) OFMakeChild
INT4 OFMakeChildN (SDLoOBJ *, SDLoATTR *, unsigned int *);
#define OFMakeChildN_F (INT4(*)()) OFMakeChildN
INT4 OFMakeAllObj (SDLoOBJ *, SDLoATTR *, unsigned int *);
#define OFMakeAllObj_F (INT4(*)()) OFMakeAllObj
INT4 OFMakeAllObjN (SDLoOBJ *, SDLoATTR *, unsigned int *);
#define OFMakeAllObjN_F (INT4(*)()) OFMakeAllObjN
INT4 OFDefSimple (FILE *, SDLoATTR *, char *, char *);
#define OFDefSimple_F (INT4(*)()) OFDefSimple
INT4 OFDefStr (FILE *, SDLoATTR *, char *, char *);
#define OFDefStr_F (INT4(*)()) OFDefStr
INT4 OFDefFnct (FILE *, SDLoATTR *, char *, char *);
#define OFDefFnct_F (INT4(*)()) OFDefFnct
INT4 OFDefHeader (FILE *, SDLoATTR *, char *, char *);
#define OFDefHeader_F (INT4(*)()) OFDefHeader
INT4 OFDefStructPtr (FILE *, SDLoATTR *, char *, char *);
#define OFDefStructPtr_F (INT4(*)()) OFDefStructPtr
INT4 OFDefGenericTyp (FILE *, SDLoATTR *, char *, char *);
#define OFDefGenericTyp_F (INT4(*)()) OFDefGenericTyp
INT4 OFDefUser (FILE *, SDLoATTR *, char *, char *);
#define OFDefUser_F (INT4(*)()) OFDefUser
INT4 OFDefEbnf (FILE *, SDLoATTR *, char *, char *);
#define OFDefEbnf_F (INT4(*)()) OFDefEbnf
INT4 OFInsertFloat (void *, void *, void *, void ***, char *, unsigned int, int);
#define OFInsertFloat_F (INT4(*)()) OFInsertFloat
INT4 OFInsertInt (void *, void *, void *, void ***, char *, unsigned int, int);
#define OFInsertInt_F (INT4(*)()) OFInsertInt
INT4 OFInsertUInt (void *, void *, void *, void ***, char *, unsigned int, int);
#define OFInsertUInt_F (INT4(*)()) OFInsertUInt
INT4 OFInsertUChar (void *, void *, void *, void ***, char *, unsigned int, int);
#define OFInsertUChar_F (INT4(*)()) OFInsertUChar
INT4 OFInsertUser (void *, void *, void *, void ***, char *, unsigned int, int);
#define OFInsertUser_F (INT4(*)()) OFInsertUser
INT4 OFInsertStr (void *, void *, void *, void ***, char *, unsigned int, int);
#define OFInsertStr_F (INT4(*)()) OFInsertStr
INT4 OFInsertFunction (void *, void *, void *, void ***, char *, unsigned int, int);
#define OFInsertFunction_F (INT4(*)()) OFInsertFunction
INT4 OFInsertObject (void *, void *, void *, void ***, char *, unsigned int, int);
#define OFInsertObject_F (INT4(*)()) OFInsertObject
INT4 OFInsertHeader (void *, void *, void *, void ***, char *, unsigned int, int);
#define OFInsertHeader_F (INT4(*)()) OFInsertHeader
INT4 OFInherit (void *, void *, void *, void ***, char *, unsigned int, int);
#define OFInherit_F (INT4(*)()) OFInherit
INT4 OFGeneric (void *, void *, void *, void ***, char *, unsigned int, int);
#define OFGeneric_F (INT4(*)()) OFGeneric
INT4 OFWrtInt (SDLoATTR *, char *, void **);
#define OFWrtInt_F (INT4(*)()) OFWrtInt
INT4 OFWrtUChar (SDLoATTR *, char *, void **);
#define OFWrtUChar_F (INT4(*)()) OFWrtUChar
INT4 OFWrtUInt (SDLoATTR *, char *, void **);
#define OFWrtUInt_F (INT4(*)()) OFWrtUInt
INT4 OFWrtFloat (SDLoATTR *, char *, void **);
#define OFWrtFloat_F (INT4(*)()) OFWrtFloat
INT4 OFWrtStr (SDLoATTR *, char *, void **);
#define OFWrtStr_F (INT4(*)()) OFWrtStr
INT4 OFWrtName (SDLoATTR *, char *, void **);
#define OFWrtName_F (INT4(*)()) OFWrtName
INT4 OFWrtNULL (SDLoATTR *, char *, void **);
#define OFWrtNULL_F (INT4(*)()) OFWrtNULL
INT4 OFWrtAddr (SDLoATTR *, char *, void **);
#define OFWrtAddr_F (INT4(*)()) OFWrtAddr
INT4 OFWrtEBNF (SDLoATTR *, char *, void **);
#define OFWrtEBNF_F (INT4(*)()) OFWrtEBNF
INT4 OFCheckNum (SDLoATTR *, int, char *);
#define OFCheckNum_F (INT4(*)()) OFCheckNum
INT4 OFCheckStr (SDLoATTR *, int, char *);
#define OFCheckStr_F (INT4(*)()) OFCheckStr
INT4 OFGenSimple (SDLoOBJ *, SDLoATTR *);
#define OFGenSimple_F (INT4(*)()) OFGenSimple
INT4 OFGenObject (SDLoOBJ *, SDLoATTR *);
#define OFGenObject_F (INT4(*)()) OFGenObject
typedef INT4 (*SDLoFNCT)();


SDLoFNCT    SDL_fnct[] = {
    OFInheritSize_F, OF4BArrSize_F, OF4BSize_F, OFPtrArrSize_F, OFPtrSize_F,
    OFBNFSize_F, OFBArrSize_F, OFMakeDefault_F, OFMakeNoDefault_F,
    OFMakeChild_F, OFMakeChildN_F, OFMakeAllObj_F, OFMakeAllObjN_F,
    OFDefSimple_F, OFDefStr_F, OFDefFnct_F, OFDefHeader_F, OFDefStructPtr_F,
    OFDefGenericTyp_F, OFDefUser_F, OFDefEbnf_F, OFInsertFloat_F,
    OFInsertInt_F, OFInsertUInt_F, OFInsertUChar_F, OFInsertUser_F,
    OFInsertStr_F, OFInsertFunction_F, OFInsertObject_F, OFInsertHeader_F,
    OFInherit_F, OFGeneric_F, OFWrtInt_F, OFWrtUChar_F, OFWrtUInt_F,
    OFWrtFloat_F, OFWrtStr_F, OFWrtName_F, OFWrtNULL_F, OFWrtAddr_F,
    OFWrtEBNF_F, OFCheckNum_F, OFCheckStr_F, OFGenSimple_F, OFGenObject_F
};
#endif

#ifdef _INITOBJS

ODDoVAL    defval[] = {
    {"y", 1},
    {"n", 0},
    {"y", 1},
    {"n", 0},
    {"int", 1},
    {"string", 2},
    {"strv", 9},
    {"object", 3},
    {"real", 4},
    {"var", 6},
    {"list", 16},
    {"n", 0},
    {"y", 1},
    {"int", 1},
    {"string", 2},
    {"strv", 9},
    {"object", 3},
    {"real", 4},
    {"var", 6},
    {"list", 16},
    {"init", 2},
    {"pre", 4},
    {"initpre", 6},
    {"post", 8},
    {"prepost", 12},
    {"direct", 1},
    {"interface", 0},
    {"yes", 1},
    {"no", 0},
    {"y", 1},
    {"n", 0},
    {"int", 2},
    {"uint", 3},
    {"uchar", 1},
    {"string", 4},
    {"protofunction", 10},
    {"function", 11},
    {"child", 6},
    {"nr_of_childs", 7},
    {"object", 9},
    {"clone", 20},
    {"defer", 16},
    {"inherit", 17},
    {"user", 12},
    {"float", 0},
    {"allobjects", 5},
    {"nr_of_objects", 8},
    {"generic", 15},
    {"generic_typ", 13},
    {"generic_obj", 14},
    {"overload", 18},
    {"store", 19},
    {"bnf", 21},
    {"num", 9},
    {"name", 10},
    {"text", 11},
    {"constant", 12},
    {"y", 1},
    {"n", 0},
    {"obsolete", 1},
    {"system", 2},
    {"api", 3},
    {"obsolete", 1},
    {"system", 2},
    {"api", 3}
};

ODDoATYP    defatyp[] = {
    {OFMakeDefault, OFInsertFloat, OF4BArrSize, OFWrtFloat, OFDefSimple,
    OFCheckNum, OFGenSimple, 0, "float"},
    {OFMakeDefault, OFInsertUChar, OFBArrSize, OFWrtUChar, OFDefSimple,
    OFCheckNum, NULL, 0, "unsigned char"},
    {OFMakeDefault, OFInsertInt, OF4BArrSize, OFWrtInt, OFDefSimple,
    OFCheckNum, OFGenSimple, 0, "INT4"},
    {OFMakeDefault, OFInsertUInt, OF4BArrSize, OFWrtUInt, OFDefSimple,
    OFCheckNum, NULL, 0, "UINT4"},
    {OFMakeDefault, OFInsertStr, OFPtrArrSize, OFWrtStr, OFDefStr, OFCheckStr,
    OFGenSimple, 1, "char"},
    {OFMakeAllObj, NULL, OFPtrSize, OFWrtAddr, OFDefStructPtr, NULL, NULL, 1,
    ""},
    {OFMakeChild, NULL, OFPtrSize, OFWrtAddr, OFDefStructPtr, NULL, NULL, 1,
    ""},
    {OFMakeChildN, NULL, OF4BSize, OFWrtInt, OFDefSimple, NULL, NULL, 0,
    "INT4"},
    {OFMakeAllObjN, NULL, OF4BSize, OFWrtInt, OFDefSimple, NULL, NULL, 0,
    "INT4"},
    {OFMakeDefault, OFInsertObject, OFPtrArrSize, OFWrtAddr, OFDefStructPtr,
    NULL, OFGenObject, 1, ""},
    {OFMakeNoDefault, OFInsertStr, OFPtrSize, OFWrtName, NULL, OFCheckStr,
    NULL, 0, ""},
    {OFMakeDefault, OFInsertFunction, OFPtrSize, OFWrtName, OFDefFnct, NULL,
    NULL, 1, ""},
    {OFMakeDefault, OFInsertUser, OFPtrArrSize, OFWrtNULL, OFDefUser, NULL,
    NULL, 1, ""},
    {NULL, OFGeneric, NULL, NULL, NULL, NULL, NULL, 0, ""},
    {NULL, OFGeneric, NULL, NULL, NULL, NULL, NULL, 0, ""},
    {NULL, NULL, OFPtrArrSize, NULL, OFDefGenericTyp, NULL, NULL, 1, ""},
    {NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, ""},
    {OFMakeNoDefault, OFInherit, OFInheritSize, NULL, NULL, NULL, NULL, 0, ""},
    {NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, ""},
    {OFMakeDefault, OFInsertHeader, OFPtrArrSize, OFWrtNULL, OFDefHeader, NULL,
    NULL, 1, ""},
    {OFMakeDefault, OFInsertObject, OFPtrArrSize, NULL, OFDefStructPtr, NULL,
    NULL, 1, ""},
    {NULL, NULL, OFBNFSize, OFWrtEBNF, OFDefEbnf, NULL, NULL, 0, ""}
};

SDLoATTR    defpar[] = {
    {"", NULL, &defval[0], 0, "name", "", "", "", "fnctnam", 0, 10, 11, 11, 11,
    11, 1, -1000000000, 30, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[0], 0, "args", "", "", "", "args", 0, 4, 11, 11, 11, 11,
    1, -1000000000, 132, 0, 1, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[0], 0, "module", "", "", "", "module", 0, 4, 11, 10, 10,
    10, 1, -1000000000, 30, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"Name of value.", NULL, &defval[0], 0, "name", "", "", "", "name", 1, 4,
    0, 0, 0, 0, 1, -1000000000, 1000000000, 0, 1, 0, 0, 0, 0, "", 0.000000, 0,
    NULL, -1, NULL},
    {"Number value.", NULL, &defval[0], 0, "n", "", "", "", "n", 0, 2, 0, 0, 0,
    0, 1, -1000000000, 1000000000, 0, 1, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1,
    NULL},
    {"Comment field.", NULL, &defval[0], 0, "rem", "", "", "", "rem", 0, 4, 0,
    0, 0, 0, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0,
    NULL, -1, NULL},
    {"Name of the argument in an Icarus program.", NULL, &defval[0], 0, "name",
    "", "", "", "name", 1, 4, 0, 0, 0, 0, 1, -1000000000, 1000000000, 0, 0, 0,
    0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"Comment field.", NULL, &defval[0], 0, "rem", "", "", "", "rem", 0, 4, 0,
    0, 0, 0, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0,
    NULL, -1, NULL},
    {"Defines if parameter may be unnamed.", NULL, &defval[0], 2, "unnamed",
    "", "", "", "isUnnamed", 0, 1, 0, 0, 0, 0, 1, -1000000000, 1000000000, 0,
    0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"Defines if parameter is required.", NULL, &defval[2], 2, "required", "",
    "", "", "isRequired", 0, 1, 0, 0, 0, 0, 1, -1000000000, 1000000000, 0, 0,
    0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"Type of the argument", NULL, &defval[4], 7, "t", "", "", "", "type", 0,
    1, 0, 0, 0, 0, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 2, "", 0.000000,
    0, NULL, -1, NULL},
    {"", NULL, &defval[11], 0, "class", "", "", "", "className", 0, 4, 0, 0, 0,
    0, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1,
    NULL},
    {"Default value of type 'int' arguments.", NULL, &defval[11], 0, "defInt",
    "", "", "", "defInt", 0, 2, 0, 0, 0, 0, 1, -1000000000, 1000000000, 0, 0,
    0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"Default value of type 'string' arguments.", NULL, &defval[11], 0,
    "defStr", "", "", "", "defaultStr", 0, 4, 0, 0, 0, 0, 1, -1000000000,
    1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[11], 0, "enum", "", "", "", "vals", 0, 6, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 1, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[11], 0, "", "", "", "", "valsN", 0, 7, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 1, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[11], 0, "", "", "", "", "isSet", 0, 1, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[11], 0, "", "struct VARo", "", "", "*val", 0, 12, 0, 0,
    0, 0, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL,
    -1, NULL},
    {"Name of command in Icarus programs.", NULL, &defval[11], 0, "name", "",
    "", "", "name", 1, 4, 0, 0, 0, 0, 1, -1000000000, 1000000000, 0, 1, 0, 0,
    0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"C function that implements the command.", NULL, &defval[11], 0, "f", "",
    "", "", "functionName", 0, 4, 0, 0, 0, 0, 1, -1000000000, 1000000000, 0, 0,
    0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"Determines whether the command should appear in the \nIcarus functions reference list.\n",
    NULL, &defval[11], 2, "show", "", "", "", "isShow", 0, 2, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"Comment field.", NULL, &defval[13], 0, "rem", "", "", "", "rem", 0, 4, 0,
    0, 0, 0, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0,
    NULL, -1, NULL},
    {"Type of value to be returned (if any).", NULL, &defval[13], 7, "return",
    "", "", "", "returnType", 0, 1, 0, 0, 0, 0, 1, -1000000000, 1000000000, 0,
    0, 0, 0, 0, 2, "", 0.000000, 0, NULL, -1, NULL},
    {"Execution time of command.", NULL, &defval[20], 5, "time", "", "", "",
    "time", 0, 2, 0, 0, 0, 0, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 8, "",
    0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[25], 0, "returnClass", "", "", "", "returnClass", 0, 4,
    0, 0, 0, 0, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0,
    NULL, -1, NULL},
    {"Call function directly or via C-interface.", NULL, &defval[25], 2,
    "call", "", "", "", "isDirectCall", 0, 1, 0, 0, 0, 0, 1, -1000000000,
    1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"normal function.", NULL, &defval[27], 0, "methodOf", "", "", "",
    "methodOf", 0, 4, 0, 0, 0, 0, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0,
    "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[27], 0, "args", "", "", "", "args", 0, 6, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 2, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[27], 0, "", "", "", "", "argsN", 0, 7, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 2, "", 0.000000, 0, NULL, -1, NULL},
    {"Function to be executed for command.", NULL, &defval[27], 0, "", "INT4",
    "", "", "(*function)()", 0, 12, 0, 0, 0, 0, 1, -1000000000, 1000000000, 0,
    0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"Number of arguments ordered from C function (via 'IargGetArgs').", NULL,
    &defval[27], 0, "", "", "", "", "orderN", 0, 2, 0, 0, 0, 0, 1, -1000000000,
    1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"Number of orders currently allocated.", NULL, &defval[27], 0, "", "", "",
    "", "orderAllocN", 0, 2, 0, 0, 0, 0, 1, -1000000000, 1000000000, 0, 0, 0,
    0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"Array with a list of argument orders.", NULL, &defval[27], 0, "",
    "struct IARGoVALUE", "", "", "**order", 0, 12, 0, 0, 0, 0, 1, -1000000000,
    1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[27], 0, "name", "", "", "", "nam", 1, 4, 10, 10, 10, 10,
    1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1,
    NULL},
    {"", NULL, &defval[27], 0, "val", "", "", "", "val", 0, 3, 9, 12, 12, 12,
    1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1,
    NULL},
    {"", NULL, &defval[27], 0, "make", "", "", "", "make", 0, 11, 12, 12, 12,
    12, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0,
    "(struct SDLoOBJ *, struct SDLoATTR *, unsigned int *)", 0.000000, 0, NULL,
    -1, NULL},
    {"", NULL, &defval[27], 0, "insert", "", "", "", "insert", 0, 11, 12, 12,
    12, 12, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0,
    "(void *, void *, void *, void ***, char *, unsigned int,int)", 0.000000,
    0, NULL, -1, NULL},
    {"", NULL, &defval[27], 0, "calcsize", "", "", "", "size", 0, 11, 12, 12,
    12, 12, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0,
    "(struct SDLoOBJ *, struct SDLoATTR *)", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[27], 0, "write", "", "", "", "write", 0, 11, 12, 12, 12,
    12, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "(void)", 0.000000, 0,
    NULL, -1, NULL},
    {"", NULL, &defval[27], 0, "declare", "", "", "", "declare", 0, 11, 12, 12,
    12, 12, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0,
    "(FILE *, struct SDLoATTR *, char *, char *)", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[27], 0, "check", "", "", "", "check", 0, 11, 12, 12, 12,
    12, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0,
    "(struct SDLoATTR *, int, char *)", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[27], 0, "gentype", "", "", "", "gentype", 0, 11, 12, 12,
    12, 12, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0,
    "(struct SDLoOBJ *, struct SDLoATTR *)", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[27], 2, "save_address", "", "", "", "save_f", 0, 1, 0,
    0, 0, 0, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0,
    NULL, -1, NULL},
    {"", NULL, &defval[29], 0, "typname", "", "", "", "tnam", 0, 4, 0, 0, 0, 0,
    1, -1000000000, 20, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[29], 0, "rem", "", "", "", "rem", 0, 4, 10, 11, 11, 11,
    1, 0, 512, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[29], 0, "", "", "", "", "class", 0, 9, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 7, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[29], 0, "enum", "", "", "", "val", 0, 6, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 4, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[29], 0, "", "", "", "", "val_n", 0, 7, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 4, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[29], 0, "name", "", "", "", "nam", 1, 4, 10, 11, 11, 11,
    1, 0, 25, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[29], 0, "typname", "", "", "", "tnam", 0, 4, 10, 11, 11,
    11, 1, 0, 25, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[29], 0, "switchname", "", "", "", "sw_nm", 0, 4, 10, 11,
    11, 11, 1, 0, 25, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[29], 0, "alttypname", "", "", "", "alt_nm", 0, 4, 10,
    11, 11, 11, 1, 0, 25, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[29], 0, "declname", "", "", "", "dnam", 0, 4, 10, 11,
    11, 11, 1, 0, 25, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[29], 2, "unnamed", "", "", "", "unnamed", 0, 2, 0, 0, 0,
    0, 1, 0, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[31], 22, "type", "", "", "", "typ", 0, 1, 10, 10, 10,
    10, 1, -1000000000, 1000000000, 0, 1, 0, 0, 0, 0, "", 0.000000, 0, NULL,
    -1, NULL},
    {"", NULL, &defval[53], 4, "valtype", "", "", "", "ptyp", 0, 1, 10, 10, 10,
    10, 4, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL,
    -1, NULL},
    {"", NULL, &defval[57], 0, "repeat", "", "", "", "arrsz", 0, 2, 9, 12, 12,
    12, 1, 1, 10000, 0, 0, 0, 0, 0, 1, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[57], 0, "min", "", "", "", "min", 0, 2, 9, 12, 12, 12,
    1, -1000000000, 1000000000, 0, 0, 0, 0, 0, -1000000000, "", 0.000000, 0,
    NULL, -1, NULL},
    {"", NULL, &defval[57], 0, "max", "", "", "", "max", 0, 2, 9, 12, 12, 12,
    1, 0, 1000000000, 0, 0, 0, 0, 0, 1000000000, "", 0.000000, 0, NULL, -1,
    NULL},
    {"", NULL, &defval[57], 0, "", "", "", "", "off", 0, 2, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[57], 2, "required", "", "", "", "req", 0, 1, 10, 10, 10,
    10, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL,
    -1, NULL},
    {"", NULL, &defval[59], 3, "status", "", "", "", "status", 0, 1, 10, 10,
    10, 10, 2, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0,
    NULL, -1, NULL},
    {"", NULL, &defval[62], 0, "", "", "", "", "isrd", 0, 1, 0, 0, 0, 0, 1, 0,
    0, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[62], 0, "defaultval", "", "", "", "dfltv", 0, 2, 9, 12,
    12, 12, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0,
    NULL, -1, NULL},
    {"", NULL, &defval[62], 0, "defaultstr", "", "", "", "dflts", 0, 4, 10, 12,
    11, 11, 1, 0, 132, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[62], 0, "defaultvalf", "", "", "", "dfltvf", 0, 0, 9, 9,
    9, 9, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL,
    -1, NULL},
    {"", NULL, &defval[62], 0, "", "", "", "", "scnt", 0, 2, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[62], 0, "objectclass", "", "", "", "obj", 0, 9, 12, 12,
    12, 12, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 7, "", 0.000000, 0,
    NULL, -1, NULL},
    {"", NULL, &defval[62], 0, "", "", "", "", "hasObjsN", 0, 2, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, -1, "", 0.000000, 0, NULL, -1,
    NULL},
    {"", NULL, &defval[62], 0, "", "void", "", "", "*hasFirstObj", 0, 12, 0, 0,
    0, 0, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL,
    -1, NULL},
    {"", NULL, &defval[62], 0, "name", "", "", "", "nam", 1, 4, 10, 11, 11, 11,
    1, 0, 25, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[62], 0, "rem", "", "", "", "rem", 0, 4, 10, 11, 11, 11,
    1, 0, 512, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[62], 0, "typname", "", "", "", "tnam", 0, 4, 10, 11, 11,
    11, 1, 0, 25, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[62], 0, "ppname", "", "", "", "pp_nm", 0, 4, 10, 11, 11,
    11, 1, 0, 25, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[62], 0, "declname", "", "", "", "dnam", 0, 4, 10, 11,
    11, 11, 1, 0, 25, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[62], 0, "type", "", "", "", "typ", 0, 1, 9, 12, 12, 12,
    1, 0, 12, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[62], 3, "status", "", "", "", "status", 0, 1, 10, 10,
    10, 10, 2, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0,
    NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "siz", 0, 2, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "s", 0, 4, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "ns", 0, 2, 0, 0, 0, 0, 1, 0,
    10000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "uobj_coff", 0, 4, 0, 0, 0, 0,
    1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1,
    NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "gbl_n", 0, 2, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "loc_n", 0, 2, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "nchilds", "", "", "", "nss", 0, 1, 9, 9, 9, 9,
    1, -1000000000, 7, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "child", "", "", "", "ss", 0, 1, 12, 12, 12, 12,
    7, 0, 255, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "np", 0, 7, 0, 0, 0, 0, 1, 1,
    256, 0, 0, 0, 0, 0, 6, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "attrs", "SDLoATTR", "", "", "p", 0, 6, 0, 0, 0,
    0, 1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 6, "", 0.000000, 0, NULL, -1,
    NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "gtyp_n", 0, 2, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "gtypdef_nm", 0, 4, 0, 0, 0, 0,
    7, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1,
    NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "gtyp_nm", 0, 4, 0, 0, 0, 0, 7,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "orgtypname", "", "", "", "orgtyp_nm", 0, 4, 11,
    10, 10, 10, 1, -1000000000, 40, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL,
    -1, NULL},
    {"", NULL, &defval[65], 0, "infile", "", "", "", "ifnam", 0, 4, 12, 11, 11,
    11, 1, 1, 132, 0, 1, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "outfile", "", "", "", "ofnam", 0, 4, 12, 11,
    11, 11, 1, 1, 132, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "section_name", "", "", "", "sec_nm", 0, 4, 10,
    11, 11, 11, 1, 0, 50, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "section_size", "", "", "", "sec_z", 0, 2, 9, 9,
    9, 9, 1, 1, 100000, 0, 0, 0, 0, 0, 1000, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "oc_n", 0, 8, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 7, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "oc", 0, 5, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 7, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "at_n", 0, 8, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 5, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "at", 0, 5, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 5, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "error", 0, 1, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "action", 0, 1, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "pass_n", 0, 1, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "keepst_f", 0, 1, 0, 0, 0, 0, 1,
    -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1, NULL},
    {"", NULL, &defval[65], 0, "", "", "", "", "section_f", 0, 1, 0, 0, 0, 0,
    1, -1000000000, 1000000000, 0, 0, 0, 0, 0, 0, "", 0.000000, 0, NULL, -1,
    NULL}
};

SDLoOBJ    defstrct[] = {
    {"function", "", "", "", "X", 11, 2, 2, 0, "", 0, "", 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 3, &defpar[0], 0, "", "", "", "", "", "", "", "", "", "", "", "",
    "", "", ""},
    {"val", "Value in an enumeration", "ODDoVALUE", "", "ODDValue", 0, 0, 0, 0,
    "", 0, "", 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, &defpar[3], 0, "", "", "", "",
    "", "", "", "", "", "", "", "", "", "", ""},
    {"var", "Argument of Icarus command.", "IARGoVALUE", "", "IARGVALUE", 0, 0,
    0, 0, "", 0, "", 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 12, &defpar[6], 0, "", "",
    "", "", "", "", "", "", "", "", "", "", "", "", ""},
    {"com", "", "IARGoCOM", "", "IARGCOM", 0, 0, 0, 0, "", 0, "", 0, 0, 1, 2,
    0, 0, 0, 0, 0, 0, 15, &defpar[18], 0, "", "", "", "", "", "", "", "", "",
    "", "", "", "", "", ""},
    {"value", "", "ODDoVAL", "SDL", "defval", 0, 0, 0, 0, "", 0, "", 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 2, &defpar[33], 0, "", "", "", "", "", "", "", "", "",
    "", "", "", "", "", ""},
    {"attrtype", "", "ODDoATYP", "SDL", "defatyp", 0, 0, 0, 0, "", 0, "", 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 9, &defpar[35], 0, "", "", "", "", "", "", "", "",
    "", "", "", "", "", "", ""},
    {"attribute", "", "SDLoATTR", "SDL", "defpar", 0, 0, 0, 0, "", 0, "", 0, 0,
    2, 4, 6, 0, 0, 0, 0, 0, 26, &defpar[44], 0, "", "", "", "", "", "", "", "",
    "", "", "", "", "", "", ""},
    {"object", "", "SDLoOBJ", "SDL", "defstrct", 0, 0, 0, 0, "", 0, "", 0, 0,
    1, 6, 0, 0, 0, 0, 0, 0, 21, &defpar[70], 0, "", "", "", "", "", "", "", "",
    "", "", "", "", "", "", ""},
    {"def", "", "SDLo", "SDL", "def", 0, 0, 0, 0, "", 0, "", 0, 0, 1, 7, 0, 0,
    0, 0, 0, 0, 13, &defpar[91], 0, "", "", "", "", "", "", "", "", "", "", "",
    "", "", "", ""}
};

SDLo    def[] = {
    {"SRSICA:sdl.sdl", "SRSSOU:odd5.h", "sdl", 50, 9, &defstrct[0], 22,
    &defatyp[0], 0, 0, 0, 0, 0}
};
SDLo *oddObjs = &def[0];

PARo    ODD_par[] = {
    {NULL, 0, "doInitHeader", "", 0, 0.000000, NULL, NULL, 0, 16,
    "h-file with struct declaration and initialization", "", "", NULL, NULL, 0,
    "", ""},
    {NULL, 0, "doHeader", "", 0, 0.000000, NULL, NULL, 0, 16,
    "h-file with struct declaration", "", "", NULL, NULL, 0, "", ""},
    {NULL, 0, "doSection", "", 0, 0.000000, NULL, NULL, 0, 16,
    "binary section file (can be combined with '-h')", "", "", NULL, NULL, 0,
    "", ""},
    {NULL, 0, "doMetaData", "", 0, 0.000000, NULL, NULL, 0, 16,
    "h-file with meta data initialization", "", "", NULL, NULL, 0, "", ""},
    {NULL, 0, "doClassInfo", "", 0, 0.000000, NULL, NULL, 0, 16,
    "file with class information", "", "", NULL, NULL, 0, "", ""},
    {NULL, 0, "printProgress", "", 0, 0.000000, NULL, NULL, 0, 16,
    "print a line for each ODD-file read", "", "", NULL, NULL, 0, "", ""},
    {NULL, 0, "printProgress", "", 0, 0.000000, NULL, NULL, 0, 16,
    "print a line for each ODD-file read", "", "", NULL, NULL, 0, "", ""},
    {NULL, 0, "printDots", "", 0, 0.000000, NULL, NULL, 0, 16,
    "print a dot for each ODD-file read", "", "", NULL, NULL, 0, "", ""}
};

PARoTYPE    Odd_parType[] = {
    {NULL, 0, "boolean", NULL, 3, 0, 0.000000, 0.000000, "yYnN01oOfFjJ"}
};

PARoLIST    ODD_parTable[] = {
    {&ODD_par[0], 8, &Odd_parType[0], 1}
};

arg_t    args[] = {
    {"-help", 1, "", "this message", NULL, 0, "", 0.000000},
    {"-i", 0, "doInitHeader", "", NULL, 0, "", 0.000000},
    {"-h", 0, "doHeader", "", NULL, 0, "", 0.000000},
    {"-s", 0, "doSection", "", NULL, 0, "", 0.000000},
    {"-m", 0, "doMetaData", "", NULL, 0, "", 0.000000},
    {"-c", 0, "doClassInfo", "", NULL, 0, "", 0.000000},
    {"-r", 0, "printProgress", "", NULL, 0, "", 0.000000},
    {"-d", 0, "printDots", "", NULL, 0, "", 0.000000}
};

ARGoLIST    argList[] = {
    {"odd", "sectionName", &args[0], 8}
};

#endif
his message", NULL, 0, "", 0.000000},
    {"-i", 0, "doInitHeader", "", NULL, 0, "", 0.000000},
    {"-h", 0, "doHeader", "", NULL, 0, "", 0.000000},
    {"-s", 0, "doSection", "", NULL, 0, "", 0.000000},
    {"-m", 0, "doMetaData", "", NULL, 0, "", 0.000000},
    {"-c", 0, "doClassInfo", "", NULL, 0, "", 0.000000},
    {"-r", 0, "printProgress", "", NULL, 0, "", 0.000000},
    {"-d", 0, "printDots", "", NULL, 0, "", 0.000000}
};

ARGoLIST    argList[] = {
    {"odd", "sesrs/src/oddfncts.c
char oddfncts_srs_ID[] = "$Id: oddfncts.c,v 1.3 1997/03/12 16:17:42 srs Exp $";
/*
**
**    $RCSfile: oddfncts.c,v $
**    $Revision: 1.3 $
**    $Date: 1997/03/12 16:17:42 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**                  Copyright by Thure Etzold
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/


#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include "message.h"
#include "sm.h"
#include "futil.h"
#include "sdl.h"
#include "strv.h"
#define _CONSTANTS
#define _SDL
#define _ODD
#include "sdl_def.h"

typedef int (*SDLoFNCT)();
INT4 OddIsAttr (SDLoATTR *attr, char *option);
INT4 OddIsClass (SDLoOBJ *class, char *option);


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  object wide variables
*/

extern SDLo	    *odd;
extern SDLoFNCT	    SDL_fnct[];  
extern ODDoFNCT_P   function[SDLxXFNCT];
extern FILo	    *f; 






/******************************************************************************
****** Group of functions calculating object size *****************************
*******************************************************************************
**
**	INPUT:	    address of parent object [R]
**		    address of attribute [R]
**                  address of offset within structure [W]
**	        IMPLICIT:
**		    odd (SDLo *)
*/   

int OFInheritSize (SDLoOBJ *obj, SDLoATTR *attr, int *off)
{
#ifdef nhrt  
  (obj->nhrt)[obj->nhrt_n] = &((odd->oc)[attr->dfltv]);
  (obj->nhrt_offp)[obj->nhrt_n] = &(attr->off);
  obj->nhrt_n++;
#endif
  return 0;
} 

int OF4BArrSize (SDLoOBJ *obj, SDLoATTR *attr, int *off)
{
  _SdlAlignFour (*off);
  return 4 * attr->arrsz;
}

int OF4BSize (SDLoOBJ *obj, SDLoATTR *attr, int *off)
{
  _SdlAlignFour (*off);
  return 4;
}

int OFPtrArrSize (SDLoOBJ *obj, SDLoATTR *attr, int *off)
{
  _SdlAlignEight (*off);
  return (sizeof (char *) * attr->arrsz);
}

int OFPtrSize (SDLoOBJ *obj, SDLoATTR *attr, int *off)
{
  _SdlAlignEight (*off);
  return sizeof (char *);
}

int OFBNFSize (SDLoOBJ *obj, SDLoATTR *attr, int *off)
{
  _SdlAlignEight (*off);
  return (sizeof (char *) + sizeof (int));
}

int OFBArrSize (SDLoOBJ *obj, SDLoATTR *attr, int *off)
{
  return 1 * attr->arrsz;
}



/******************************************************************************
****** group of functions for posprocesssing attributes ***********************
*******************************************************************************
**
**
**	INPUT:	    address of parent object [R]
**		    address of attribute [R]
**		    address of header [W]
**		    address of current offset in target structure [W]
**	        IMPLICIT:
**		    odd (SDLo *) [R]
**
**	RETURNS:    e__parismiss <ln_nr, file_name, attr_name> +
**		    1
*/ 
   
int OFMakeDefault (SDLoOBJ *obj, SDLoATTR *attr, SDLoPTR *off)
{
  int (*insert)();
  int l, rv;

  if (!(attr->isrd)) {
    if (attr->req)                                                 
      _ErrRet (e__parismiss);
    else                                                           
      if ((insert = odd->at[attr->typ].insert) != NULL)
	for (l = 0;  l < attr->arrsz;  l++) {
	  rv = (*insert) (obj, attr, attr, off, 0, ODDxNULL, TRUE);
	  _ErrRet (rv);
	}
  }
  return 1;                                                             
}

int OFMakeNoDefault (SDLoOBJ *obj, SDLoATTR *attr, SDLoPTR *off)
{
  if (!(attr->isrd))                                                 
    _ErrRet (e__parismiss);
  return 1;
}

int OFMakeChildN (SDLoOBJ *obj, SDLoATTR *attr, SDLoPTR *off)
{
  memcpy (*off, &((odd->oc)[attr->dfltv].loc_n), sizeof (int));
  return 1;
}

int OFMakeAllObjN (SDLoOBJ *obj, SDLoATTR *attr, SDLoPTR *off)
{
  memcpy (*(int **) off, &((odd->oc)[attr->dfltv].gbl_n), sizeof (int)); 
  return 1;
}

int OFMakeChild (SDLoOBJ *obj, SDLoATTR *attr, SDLoPTR *off)
{
  SDLoOBJ  *referredClass;
  SDLoPTR  tmp;
  int      rv, fst_x, l, i;
  
  referredClass = &(odd->oc[attr->dfltv]);	
  fst_x = referredClass->gbl_n - referredClass->loc_n; /* inx of first obj */
  
  attr->dflts = &(referredClass->dnam[0]);
  attr->tnam = &(referredClass->tnam[0]);
  
  if (odd->action != SDLxNOHDR)	    
    memcpy (*(int **) off, &fst_x, sizeof (int));	
  else { 
    SDLoPTR tmp;

    tmp = referredClass->s + (referredClass->siz * fst_x);
    memcpy (*off, &tmp, sizeof (SDLoPTR));
  }
  return 1;
}

int OFMakeAllObj (SDLoOBJ *obj, SDLoATTR *attr, SDLoPTR *off)
{
  SDLoOBJ *referredClass;

  referredClass = & (odd->oc[attr->dfltv]); 

  if (odd->action != SDLxNOHDR)	    
    memset (*off, 0, sizeof (SDLoPTR)); 
  else
    memcpy (*off, &(referredClass->s), sizeof (SDLoPTR));	
  attr->dflts = &(referredClass->dnam[0]);
  attr->tnam = &(referredClass->tnam[0]);
  return 1;
}




/****** OfArraySiz ***********************************************************/
/**
 **	returns string with array size for declaration of arrays
 **     if not array string is empty;
 **
 **	INPUT:	    attribute object [R]
 **	        IMPLICIT:
 **
 **	RETURNS:    address of string
**/ 
   
char *OFArraySiz (SDLoATTR *attr)
{
    static char    as[10];

    if (attr->arrsz > 1)	
	sprintf(as, "[%d]", attr->arrsz);
    else
	as[0] = '\0';
    return &as[0];
}


/******************************************************************************
***** group of functions for writing attribute definition to header file ******
*******************************************************************************
**
**
**	INPUT:	    attribute object [R]
**		    generic type [R]
**		    generic object type [R]
**	        IMPLICIT:
**                 odd (SDLo *) [R]
**
**	RETURNS:  
**		  
*/




char *OddRemark (SDLoATTR *attr)
{
  static char remark[550];

  if (!*attr->rem)
    remark[0] = '\0';
  else
    sprintf (remark, "  /*%s %s */", OddIsAttr (attr, "api") ? "API" : "",
	     attr->rem);
  return remark;
}

char *OddAddRemark (char *ln, SDLoATTR *attr)
{
  static char newLn[600];
  char remark[550];
  char *lastBlankPtr;
  int  l, k, lSave;

  if (!*attr->rem)
    return ln;
  else {
    sprintf (newLn, "%-40s ", ln);
    sprintf (remark, "/*%s %s */", OddIsAttr (attr, "api") ? "API" : "",
	     attr->rem);
    l = 0;
    while (1) {
      for (k=strlen (newLn); (k % 80) && remark[l]; k++, l++) {
	newLn[k] = remark[l];
	if (newLn[k] == ' ') {
	  lastBlankPtr = &newLn[k];
	  lSave = l;
	}
      }
      if (remark[l]) {  /* comment string is not yet finished */
	*lastBlankPtr = '\0'; 
	sprintf (newLn, "%s\n%43s", newLn, " ");
	l = lSave;
      }
      else {
	newLn[k] = '\0';
	break;
      }
    }
  }
  return newLn;
}



int OFDefSimple (FILE *fil, SDLoATTR *attr, char *gtyp_nm, char *typdef_nm)
{
  char l[133];

  sprintf(l, "  %-24s%s%s;", odd->at[attr->typ].tnam, attr->dnam, 
	                           OFArraySiz (attr));
  fprintf (fil, "%s\n", OddAddRemark (l, attr));
  return 1;
}

int OFDefStr (FILE *fil, SDLoATTR *attr, char *gtyp_nm, char *typdef_nm)
{
  char l[133];

  sprintf (l, "  %-24s*%s%s;", "char", attr->dnam, OFArraySiz (attr));
  fprintf (fil, "%s\n", OddAddRemark (l, attr));
  return 1;
}

int OFDefFnct (FILE *fil, SDLoATTR *attr, char *gtyp_nm, char *typdef_nm)
{
  char l[133];
  char tnam[80], args[80], tmp[80];
  
  strcpy (args, attr->dflts); 
  
  if (gtyp_nm != NULL) {			 /* generic argument type   */
    if (typdef_nm != NULL) {
      sprintf (tmp, "struct %s", typdef_nm);
      SmSwapS (args, SDLxGTYPDEFNAM, tmp);
    }
    SmSwapS (args, SDLxGTYPNAM, gtyp_nm);
  }
  else	
    SmSwapS (args, SDLxGTYPDEFNAM, "void");
  
                                               /* generic return val type */
  if (strcmp (SDLxGTYPNAM, attr->tnam) == 0 && gtyp_nm != NULL)
    sprintf (tnam, "%-24s*", gtyp_nm);
  else
    strcpy (tnam, "INT4");
  
  sprintf (l, "  %-24s(*%s)%s;", tnam, attr->dnam, " ()" /*args*/ );
  fprintf (fil, "%s\n", OddAddRemark (l, attr));
  return 1;
}

int OFDefHeader (FILE *fil, SDLoATTR *attr, char *gtyp_nm, char *typdef_nm)
{
  char l[133];

  sprintf (l, "  %-24s*%s;", attr->tnam, attr->dnam);
  fprintf (fil, "%s\n", OddAddRemark (l, attr));
  return 1;
}

int OFDefStructPtr (FILE *fil, SDLoATTR *attr, char *gtyp_nm, char *typdef_nm)
{
  char l[133];
  char tnam[80];

  sprintf (tnam, "struct %s", attr->tnam);
  sprintf (l, "  %-24s*%s%s;", tnam, attr->dnam, OFArraySiz (attr));
  fprintf (fil, "%s\n", OddAddRemark (l, attr));

  return 1;
}

int OFDefGenericTyp (FILE *fil, SDLoATTR *attr, char *gtyp_nm, char *typdef_nm)
{
  char l[133];

  if (gtyp_nm == NULL)
    sprintf (l, "  %-24s*%s;", "void", attr->dnam);
  else
    sprintf(l, "  %-24s*%s;", gtyp_nm, attr->dnam);

  fprintf (fil, "%s\n", OddAddRemark (l, attr));
  return 1;
}

int OFDefUser (FILE *fil, SDLoATTR *attr, char *gtyp_nm, char *typdef_nm)
{
  char l[133];
  int	    pp_f;
  
  pp_f = *(attr->sw_nm) != '\0' ? TRUE : FALSE;
  
  if (pp_f)					 /* if preprocessor switch  */
    fprintf(fil, "#ifdef %s\n", attr->sw_nm);
  
  sprintf (l, "  %-24s%s%s;", attr->tnam, attr->dnam, OFArraySiz (attr));
  fprintf (fil, "%s\n", OddAddRemark (l, attr));
  
  if (pp_f) {
    fprintf(fil, "#else\n");
    fprintf(fil, "  %-24s%s%s;%s\n", 
	    (*attr->alt_nm == '\0') ? "unsigned int" : attr->alt_nm, 
	    attr->dnam, OFArraySiz (attr), OddRemark (attr));
    fprintf(fil, "#endif\n");
  }			    
  return 1;
}

int OFDefEbnf (FILE *fil, SDLoATTR *attr, char *gtyp_nm, char *typdef_nm)
{
  fprintf(fil, "  %-24s%s;\n", "char", "**ebnfln");
  fprintf(fil, "  %-24s%s;\n", "INT4", "nebnfln");
  return 1;
} 



/******************************************************************************
****** group of functions for inserting attribute values **********************
*******************************************************************************
**
**
**	INPUT:	    address of parent object [R]
**		    address of attribute [R]
**		    address of header [W]
**		    address of current offset in target structure [W]
**	        IMPLICIT:
**		    odd (SDLo *) [R]
**                  f (FILo *) [R]
** 
**	RETURNS:    e__parismiss <ln_nr, file_name, attr_name> +
**		    e__parnotok <ln nr., str> +
**		    e__allocfail <name of item to be alloc> +
**		    e__objnotfound <filnam, linenr., obj-ID> +
**		    1
*/ 

   
int OFInsertFloat (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
		   float **dest, char *tokstr, unsigned int tokval, int dflt_f)
{
  float value;
  
  if (dflt_f) 
    value =  dfltattr->dfltvf;
  else
    sscanf (tokstr, "%f", &value);
  
  _ErrRet (SdlCheckPar (attr, 0, value));
  
  memcpy (*dest, &value, sizeof (float)); 
  *dest += 1;
  return 1;
}


int OFInsertInt (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, int **dest, 
                char *tokstr, unsigned int tokval, int dflt_f)
{
  int value;
  
  if (tokval == ODDxNULL)
    value = dflt_f ? dfltattr->dfltv : atoi(tokstr);
  else
    value = tokval;
  
  _ErrRet (SdlCheckPar (attr, 0, value));
  
  memcpy (*dest, &value, sizeof (int)); 
  *dest += 1;
  return 1;
}


int OFInsertUInt (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
               unsigned int **dest, char *tokstr, unsigned int tokval, 
               int dflt_f)
{
  unsigned int value;

  if (tokval == ODDxNULL)
    value = dflt_f ? dfltattr->dfltv : atoi(tokstr);
  else
    value = tokval;
  
  _ErrRet (SdlCheckPar (attr, 0, value));
  
  memcpy (*dest, &value, sizeof (unsigned int)); 
  *dest += 1;
  return 1;
}

int OFInsertUChar (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
                unsigned char **dest, 
                char *tokstr, unsigned int tokval, int dflt_f)
{
  unsigned char value;

  if (tokval == ODDxNULL)
    value = dflt_f ? dfltattr->dfltv : atoi(tokstr);
  else
    value = tokval;
  
  _ErrRet (SdlCheckPar (attr, 0, value));
  
  memcpy (*dest, &value, sizeof (char)); 
  *dest += 1;
  return 1;
}

int OFInsertUser (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
		  void ***dest, char *tokstr, unsigned int tokval, int dflt_f)
{
  memset (*dest, 0, sizeof (char *));
  *dest += 1; 
  return 1;
}

int OFInsertStr (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
		 char ***dest, char *tokstr, unsigned int tokval, int dflt_f)
{
  char	   *newvalue, *value = NULL;
  int	   rv;
  
  /*  if (tokval == ODDxNULL) ...does this ever happen? */
    value = dflt_f ? &((dfltattr->dflts)[0]) : tokstr;	    
    /*  else
    value += _SdlIsStr (tokval); */
  
  rv = SdlCheckPar (attr, value, 0);
  _ErrRet (rv);
  
  /* insert into user-object */
  if ((newvalue = (char *) _SdlMalloc (strlen (value) + 1)) == 0) 
    _ErrRet2(e__allocfail, "symbol string");
  memcpy (*dest, &newvalue, sizeof (char *));
  
  if (attr->typ == AT_PROTOFNCT)		 /* copy function to array  */
    OddAddFunction (*dest);
  
  *dest = *dest + 1;	

  strcpy (newvalue, value);
  /*  
  if (odd->action == SDLxNOHDR)
    SmEdit (newvalue, SMxDECODE);
    */  
  return 1;
}

int OFInsertFunction (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
		      unsigned int **dest, char *tokstr, unsigned int tokval, 
		      int dflt_f)
{
  unsigned int value;
  SDLoPTR  tmp=NULL;
  
  value = dflt_f ? SDLxNULLFNCT : tokval;
  
  if (odd->action == SDLxNOHDR) {
    if (odd->section_f)	{  /* function index */
      tmp += dflt_f ? SDLxXFNCT : value;
      memcpy (*dest, &tmp, sizeof (SDLoPTR));
    }
    else {  /* function address */
      tmp = dflt_f ? NULL : (SDLoPTR) SDL_fnct[value]; 
      memcpy (*dest, &tmp, sizeof (SDLoPTR));
    }
  }
  else {  /* function name	    */
    tmp = dflt_f ? "NULL" : *(function[value].nam);
     memcpy (*(char ***) dest, &tmp, sizeof (SDLoPTR));} 

  if (!dflt_f) 
    attr->dflts = *(function[value].args);
  *dest += 1; 
  return 1;
}



int OFInsertObject (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
       	    void ***dest, char *tokstr, unsigned int tokval, int dflt_f)
{
  SDLoOBJ  *refClass;
  SDLoPTR  obj_p;
  int	   rv;
  
  refClass = &(odd->oc[attr->dfltv]);	
  /*tokval = atoi (tokstr);*/
  if (!dflt_f) {
    if (attr->typ == AT_CLONE) {
      if ((obj_p = (SDLoPTR) _SdlMalloc (refClass->siz)) == 0) 
	_ErrRet2(e__allocfail, "object clone");
      memcpy (obj_p, (void *) (refClass->s + refClass->siz * tokval), 
	      refClass->siz);
    }
    else 		
      obj_p = (void *) (refClass->s + refClass->siz * tokval);
  }
  else
    obj_p = NULL;
  
  /*
  ** copy object address into output object
  */

  if (odd->action == SDLxNOHDR)  
    memcpy (*dest, &obj_p, sizeof (SDLoPTR));	
  else
    memcpy (*dest, &tokval, sizeof (SDLoPTR));
  (*dest)++; 
  attr->dflts = &(refClass->dnam[0]);  /* declaration name */
  
  
  /* 
  ** give attribute a type definition name
  */
  
  if (refClass->gtyp_n == 0 || tokval == SDLxXOBJ)
    attr->tnam = refClass->tnam;
  else if (tokval != ODDxNULL) 
    attr->tnam = (refClass->gtypdef_nm)[tokval];

  return 1;
}


int OFInsertHeader (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
		    unsigned int **dest, char *tokstr, unsigned int tokval, 
		    int dflt_f)

{
#ifdef org
  ODDoHEAD *head;

  if (!dflt_f) {
    if ((head = (ODDoHEAD *) _SdlMalloc (sizeof (ODDoHEAD))) == 0) 
      _ErrRet2(e__allocfail, "object clone");
    memcpy (head, &ODD_headers[tokval], sizeof (ODDoHEAD));
  }
  else
    head = NULL;

  memcpy (*dest, &head, sizeof (int *)); 
  *dest += 1; 
#endif
  return 1;
}

int OFInherit (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
	       unsigned int **dest, char *tokstr, unsigned int tokval,
	       int dflt_f)
{
  SDLoOBJ *inherit_obj;
  void    *obj_p;

  inherit_obj = &(odd->oc[attr->dfltv]);
  if (tokval >= inherit_obj->gbl_n)
    _ErrRet4 (e__objnotfound, f->n, f->nam, tokstr);
  
  obj_p = (void *) (inherit_obj->s + tokval * inherit_obj->siz);
  memcpy (*dest, obj_p, inherit_obj->siz);
  if (odd->section_f)
    SdlSaveAddr (inherit_obj, (SDLoPTR) *dest);
  return 1;
}

int OFGeneric (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
	       void ***dest, char *tokstr, unsigned int tokval, 
	       int dflt_f)
{
  _ErrRet (SdlGenericNames (&(odd->oc[O_HEAD]), attr->typ, tokstr));
  return 1;
}


/******************************************************************************
******** group of functions for writing attribute value to header file ********
*******************************************************************************
**
**
**	INPUT:	    attribute object [R]
**		    destination string [W]
**		    address of source [W]
**	        IMPLICIT:
**
**	RETURNS:  
**		  
*/

int OFWrtInt (SDLoATTR *attr, char *s, int **source)
{
  sprintf (s, "%d", **source);
  (*source)++;
  return 1;
}

int OFWrtUChar (SDLoATTR *attr, char *s, unsigned char **source)
{
  sprintf (s, "%d", **source);
  (*source)++;
  return 1;
}

int OFWrtUInt (SDLoATTR *attr, char *s, unsigned int **source)
{
  sprintf (s, "%u", **source);
  (*source)++;
  return 1;
}

int OFWrtFloat (SDLoATTR *attr, char *s, float **source)
{
  sprintf (s, "%f", **source);
  (*source)++;
  return 1;
}

int OFWrtStr (SDLoATTR *attr, char *s, char ***source)
{
  static STRv str;
  if (!str)
    str = StrNew ();

  StrSetS (str, **source);
  StrEncode (str);
  sprintf (s, "\"%s\"", _Str (str));
  (*source)++;
  return 1;
}

int OFWrtName (SDLoATTR *attr, char *s, char ***source)
{
  sprintf (s, "%s", **source);
  (*source)++;
  return 1;
}

int OFWrtNULL (SDLoATTR *attr, char *s, void ***source)
{
  sprintf (s, "NULL");
  (*source)++;
  return 1;
}

int OFWrtAddr (SDLoATTR *attr, char *s, unsigned int **source)
{
  if (**source == ODDxNULL)
    sprintf(s, "NULL");
  else 
    sprintf(s, "&%s[%d]", attr->dflts, **source);

  (*source)++;
  return 1;
}

int OFWrtEBNF (SDLoATTR *attr, char *s, char ***source)
{
  sprintf(s, "&%s[0], %d", **source, ** (int **) (source+sizeof (char *)));
  (*source) += 8;
  return 1;
}


/******************************************************************************
******* group of functions for checking attribute values **********************
*******************************************************************************
** 
**
**	INPUT:	 
**		    address of attribute [R]
**		    address of value
**	        IMPLICIT:
**                 f (FILo *) [R]
**
**	RETURNS: 
**		    e__parnotok <ln nr., str> +
**		    1
*/ 


int OFCheckNum (SDLoATTR *attr, int v, char *s)
{
  char    errmsg[MSGxXLN];

  if (v > attr->max)
    sprintf(errmsg, "Attribute: %s, value: %d, max: %d", 
	    attr->nam, v, attr->max);
  else if (v < attr->min)
    sprintf(errmsg, "Attribute: %s, value: %d, min: %d",
	    attr->nam, v, attr->min);
  else 
    return 1;
  
  _ErrRet4 (e__parnotok, f->n, f->nam, errmsg);
  return 1;
}

int OFCheckStr (SDLoATTR *attr, int v, char *s)
{
  char    errmsg[MSGxXLN];
  int	    len;
  
  len = strlen (s);
  if (len > attr->max)
    sprintf (errmsg, "Attribute: %s, string: %s, maxlen: %d",
	     attr->nam, s, attr->max);
  else if (len < attr->min)
    sprintf (errmsg, "Attribute: %s, string: %s, minlen: %d", 
	     attr->nam, s, attr->min);
  else return 1;
  
  _ErrRet4 (e__parnotok, f->n, f->nam, errmsg);
  return 1;
}



/******************************************************************************
******* group of functions for generating generic types    ********************
*******************************************************************************
**
**
**	INPUT:	 
**		    address of attribute [R]
**		    address of value
**	        IMPLICIT:
**                  odd (SDLo *) [R]
**
**	RETURNS: 
**		    e__parnotok <ln nr., str> +
**		    1
*/ 

int OFGenSimple (SDLoOBJ * headobj, SDLoATTR *attr)
{
  SdlGenericNames (headobj, AT_GENERIC_TYP, odd->at[attr->typ].tnam);
  return 1;
}

int OFGenObject (SDLoOBJ * headobj, SDLoATTR *attr)
{
  SDLoOBJ	*ref_obj;
  char	gtyp_nm[SDLxXLSYM+1];
  
  ref_obj = &(odd->oc[attr->dfltv]);	
  sprintf (gtyp_nm, "struct %s *", ref_obj->tnam);
  SdlGenericNames (headobj, AT_GENERIC_TYP, gtyp_nm);
  return 1;
}




:
**                  odd (SDLo *) [R]
**
**	RETURNS: 
**		    e__parnotok <ln nr., str> +
**		    1
*/ 

int srs/src/oddfnctsnew.c
char oddfncts_ID[] = "$Id: oddfnctsnew.c,v 1.5 1997/03/12 16:17:44 srs Exp $";
/*
**
**    $RCSfile: oddfnctsnew.c,v $
**    $Revision: 1.5 $
**    $Date: 1997/03/12 16:17:44 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  Copyright by Thure Etzold
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include "message.h"
#include "sm.h"
#include "futil.h"
#include "strv.h"
#include "odd.h"
#define _SDL
#define _ODD
#include "oddclass.h"

typedef int (*SDLoFNCT)();
INT4 OddIsAttr (SDLoATTR *attr, char *option);
INT4 OddIsClass (SDLoOBJ *class, char *option);


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  object wide variables
*/

extern SDLo	    *odd;
extern SDLoFNCT	    SDL_fnct[];  
extern ODDoFNCT_P   function[SDLxXFNCT];
extern FILo	    *f; 


/******************************************************************************
****** Group of functions calculating object size *****************************
*******************************************************************************
**
**	INPUT:	    address of parent object [R]
**		    address of attribute [R]
**                  address of offset within structure [W]
**	        IMPLICIT:
**		    odd (SDLo *)
*/   

int OFInheritSize (SDLoOBJ *obj, SDLoATTR *attr, int *off)
{
  return 0;
} 

int OF4BArrSize (SDLoOBJ *obj, SDLoATTR *attr, int *off)
{
  _SdlAlignFour (*off);
  return 4 * attr->arrsz;
}

int OF4BSize (SDLoOBJ *obj, SDLoATTR *attr, int *off)
{
  _SdlAlignFour (*off);
  return 4;
}

int OFPtrArrSize (SDLoOBJ *obj, SDLoATTR *attr, int *off)
{
  _SdlAlignEight (*off);
  return (sizeof (char *) * attr->arrsz);
}

int OFPtrSize (SDLoOBJ *obj, SDLoATTR *attr, int *off)
{
  _SdlAlignEight (*off);
  return sizeof (char *);
}

int OFBNFSize (SDLoOBJ *obj, SDLoATTR *attr, int *off)
{
  _SdlAlignEight (*off);
  return (sizeof (char *) + sizeof (int));
}

int OFBArrSize (SDLoOBJ *obj, SDLoATTR *attr, int *off)
{
  return 1 * attr->arrsz;
}


/******************************************************************************
****** group of functions for posprocesssing attributes ***********************
*******************************************************************************
**
**	INPUT:	    address of parent object [R]
**		    address of attribute [R]
**		    address of header [W]
**		    address of current offset in target structure [W]
**	        IMPLICIT:
**		    odd (SDLo *) [R]
**
**	RETURNS:    e__icarequiredattr <ln_nr, file_name, attr_name> +
**		    1
*/ 
   
int OFMakeDefault (SDLoOBJ *obj, SDLoATTR *attr, SDLoPTR *off)
{
  int (*insert)();
  int l, rv;

  if (!(attr->isrd)) {
    if (attr->req)                                                 
      _ErrRet (e__icarequiredattr);
    else                                                           
      if ((insert = odd->at[attr->typ].insert) != NULL)
	for (l = 0;  l < attr->arrsz;  l++) {
	  rv = (*insert) (obj, attr, attr, off, 0, ODDxNULL, TRUE);
	  _ErrRet (rv);
	}
  }
  return 1;                                                             
}

int OFMakeNoDefault (SDLoOBJ *obj, SDLoATTR *attr, SDLoPTR *off)
{
  if (!(attr->isrd))                                                 
    _ErrRet (e__icarequiredattr);
  return 1;
}

int OFMakeChildN (SDLoOBJ *obj, SDLoATTR *attr, SDLoPTR *off)
{
  Int4 n;
  
  n = (attr->hasObjsN!=-1) ? attr->hasObjsN : odd->oc[attr->dfltv].loc_n;

  memcpy (*off, &n, sizeof (int));
  return 1;
}

int OFMakeAllObjN (SDLoOBJ *obj, SDLoATTR *attr, SDLoPTR *off)
{
  memcpy (*(int **) off, &((odd->oc)[attr->dfltv].gbl_n), sizeof (int)); 
  return 1;
}

int OFMakeChild (SDLoOBJ *obj, SDLoATTR *attr, SDLoPTR *off)
{
  SDLoOBJ  *refClass;
  SDLoPTR  tmp;
  int      rv, firstX, l, i;
  
  refClass = OddGetPartofClass (attr);
  firstX = refClass->gbl_n - refClass->loc_n; 
  if (attr->hasObjsN != -1)
    refClass->loc_n -= attr->hasObjsN; 
  
  attr->dflts = OddGetClassDeclName (refClass);
  attr->tnam = &(refClass->tnam[0]);
  
  if (odd->action != SDLxNOHDR && !odd->section_f)	    
    memcpy (*(int **) off, &firstX, sizeof (int));	
  else {
    SDLoPTR tmp;

    if (attr->hasObjsN == -1) 
      tmp = refClass->s + (refClass->siz * firstX);
    else 
      tmp = attr->hasFirstObj;
    memcpy (*off, &tmp, sizeof (SDLoPTR));
  }
  return 1;
}

int OFMakeAllObj (SDLoOBJ *obj, SDLoATTR *attr, SDLoPTR *off)
{
  SDLoOBJ *refClass;

  refClass = OddGetPartofClass (attr);

  if ((odd->action != SDLxNOHDR) && !odd->section_f)	    
    memset (*off, 0, sizeof (SDLoPTR)); 
  else
    memcpy (*off, &(refClass->s), sizeof (SDLoPTR));	
  attr->dflts = OddGetClassDeclName (refClass);
  attr->tnam = &(refClass->tnam[0]);
  return 1;
}



/****** OfArraySiz ***********************************************************/
/**
 **	returns string with array size for declaration of arrays
 **     if not array string is empty;
 **
 **	INPUT:	    attribute object [R]
 **	        IMPLICIT:
 **
 **	RETURNS:    address of string
**/ 
   
char *OFArraySiz (SDLoATTR *attr)
{
    static char    as[10];

    if (attr->arrsz > 1)	
	sprintf(as, "[%d]", attr->arrsz);
    else
	as[0] = '\0';
    return &as[0];
}


/******************************************************************************
***** group of functions for writing attribute definition to header file ******
*******************************************************************************
**
**
**	INPUT:	    attribute object [R]
**		    generic type [R]
**		    generic object type [R]
**	        IMPLICIT:
**                 odd (SDLo *) [R]
**
**	RETURNS:  
*/

char *OddRemark (SDLoATTR *attr)
{
  static char remark[550];

  if (!*attr->rem)
    remark[0] = '\0';
  else
    sprintf (remark, "  /*%s %s */", OddIsAttr (attr, "api") ? "API" : "",
	     attr->rem);
  return remark;
}

char *OddAddRemark (char *ln, SDLoATTR *attr)
{
  static char newLn[600];
  char remark[550];
  char *lastBlankPtr;
  int  l, k, lSave;

  if (!*attr->rem)
    return ln;
  else {
    sprintf (newLn, "%-40s ", ln);
    sprintf (remark, "/*%s %s */", OddIsAttr (attr, "api") ? "API" : "",
	     attr->rem);
    l = 0;
    while (1) {
      for (k=strlen (newLn); (k % 80) && remark[l]; k++, l++) {
	newLn[k] = remark[l];
	if (newLn[k] == ' ') {
	  lastBlankPtr = &newLn[k];
	  lSave = l;
	}
      }
      if (remark[l]) {  /* comment string is not yet finished */
	*lastBlankPtr = '\0'; 
	sprintf (newLn, "%s\n%43s", newLn, " ");
	l = lSave;
      }
      else {
	newLn[k] = '\0';
	break;
      }
    }
  }
  return newLn;
}


int OFDefSimple (FILE *fil, SDLoATTR *attr, char *gtyp_nm, char *typdef_nm)
{
  char l[133];

  sprintf(l, "  %-24s%s%s;", odd->at[attr->typ].tnam, 
	  OddGetAttrDeclName (attr), OFArraySiz (attr));
  fprintf (fil, "%s\n", OddAddRemark (l, attr));
  return 1;
}

int OFDefStr (FILE *fil, SDLoATTR *attr, char *gtyp_nm, char *typdef_nm)
{
  char l[133];

  sprintf (l, "  %-24s*%s%s;", "char", OddGetAttrDeclName (attr), 
	   OFArraySiz (attr));
  fprintf (fil, "%s\n", OddAddRemark (l, attr));
  return 1;
}

int OFDefFnct (FILE *fil, SDLoATTR *attr, char *gtyp_nm, char *typdef_nm)
{
  char l[133];
  char tnam[80], args[80], tmp[80];
  
  strcpy (args, attr->dflts); 
  
  if (gtyp_nm != NULL) {			 /* generic argument type   */
    if (typdef_nm != NULL) {
      sprintf (tmp, "struct %s", typdef_nm);
      SmSwapS (args, SDLxGTYPDEFNAM, tmp);
    }
    SmSwapS (args, SDLxGTYPNAM, gtyp_nm);
  }
  else	
    SmSwapS (args, SDLxGTYPDEFNAM, "void");
  
                                               /* generic return val type */
  if (strcmp (SDLxGTYPNAM, attr->tnam) == 0 && gtyp_nm != NULL)
    sprintf (tnam, "%-24s*", gtyp_nm);
  else
    strcpy (tnam, "INT4");
  
  sprintf (l, "  %-24s(*%s)%s;", tnam, attr->dnam, " ()" /*args*/ );
  fprintf (fil, "%s\n", OddAddRemark (l, attr));
  return 1;
}

int OFDefHeader (FILE *fil, SDLoATTR *attr, char *gtyp_nm, char *typdef_nm)
{
  char l[133];

  sprintf (l, "  %-24s*%s;", attr->tnam, attr->dnam);
  fprintf (fil, "%s\n", OddAddRemark (l, attr));
  return 1;
}

int OFDefStructPtr (FILE *fil, SDLoATTR *attr, char *gtyp_nm, char *typdef_nm)
{
  char l[133];
  char tnam[80];

  sprintf (tnam, "struct %s", odd->oc[attr->dfltv].tnam);
  sprintf (l, "  %-24s*%s%s;", tnam, OddGetAttrDeclName (attr), 
	   OFArraySiz (attr));
  fprintf (fil, "%s\n", OddAddRemark (l, attr));

  return 1;
}

int OFDefGenericTyp (FILE *fil, SDLoATTR *attr, char *gtyp_nm, char *typdef_nm)
{
  char l[133];

  if (gtyp_nm == NULL)
    sprintf (l, "  %-24s*%s;", "void", attr->dnam);
  else
    sprintf(l, "  %-24s*%s;", gtyp_nm, attr->dnam);

  fprintf (fil, "%s\n", OddAddRemark (l, attr));
  return 1;
}

int OFDefUser (FILE *fil, SDLoATTR *attr, char *gtyp_nm, char *typdef_nm)
{
  char l[133];
  int	    pp_f;
  
  pp_f = *(attr->sw_nm) != '\0' ? TRUE : FALSE;
  
  if (pp_f)					 /* if preprocessor switch  */
    fprintf(fil, "#ifdef %s\n", attr->sw_nm);
  
  sprintf (l, "  %-24s%s%s;", attr->tnam, attr->dnam, OFArraySiz (attr));
  fprintf (fil, "%s\n", OddAddRemark (l, attr));
  
  if (pp_f) {
    fprintf(fil, "#else\n");
    fprintf(fil, "  %-24s%s%s;%s\n", 
	    (*attr->alt_nm == '\0') ? "unsigned int" : attr->alt_nm, 
	    attr->dnam, OFArraySiz (attr), OddRemark (attr));
    fprintf(fil, "#endif\n");
  }			    
  return 1;
}

int OFDefEbnf (FILE *fil, SDLoATTR *attr, char *gtyp_nm, char *typdef_nm)
{
  fprintf(fil, "  %-24s%s;\n", "char", "**ebnfln");
  fprintf(fil, "  %-24s%s;\n", "INT4", "nebnfln");
  return 1;
} 


/******************************************************************************
****** group of functions for inserting attribute values **********************
*******************************************************************************
**
**
**	INPUT:	    address of parent object [R]
**		    address of attribute [R]
**		    address of header [W]
**		    address of current offset in target structure [W]
**	        IMPLICIT:
**		    odd (SDLo *) [R]
**                  f (FILo *) [R]
** 
**	RETURNS:    e__icarequiredattr <ln_nr, file_name, attr_name> +
**		    e__icaattrval +
**		    e__allocfail <name of item to be alloc> +
**		    e__objnotfound <filnam, linenr., obj-ID> +
**		    1
*/ 

   
int OFInsertFloat (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
		   float **dest, char *tokstr, unsigned int tokval, int dflt_f)
{
  float value;
  
  if (dflt_f) 
    value =  dfltattr->dfltvf;
  else
    sscanf (tokstr, "%f", &value);
  
  _ErrRet (SdlCheckPar (attr, 0, value));
  
  memcpy (*dest, &value, sizeof (float)); 
  *dest += 1;
  return 1;
}


int OFInsertInt (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, int **dest, 
                char *tokstr, unsigned int tokval, int dflt_f)
{
  int value;
  
  if (tokval == ODDxNULL)
    value = dflt_f ? dfltattr->dfltv : atoi(tokstr);
  else
    value = tokval;
  
  _ErrRet (SdlCheckPar (attr, 0, value));
  
  memcpy (*dest, &value, sizeof (int)); 
  *dest += 1;
  return 1;
}


int OFInsertUInt (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
               unsigned int **dest, char *tokstr, unsigned int tokval, 
               int dflt_f)
{
  unsigned int value;

  if (tokval == ODDxNULL)
    value = dflt_f ? dfltattr->dfltv : atoi(tokstr);
  else
    value = tokval;
  
  _ErrRet (SdlCheckPar (attr, 0, value));
  
  memcpy (*dest, &value, sizeof (unsigned int)); 
  *dest += 1;
  return 1;
}

int OFInsertUChar (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
                unsigned char **dest, 
                char *tokstr, unsigned int tokval, int dflt_f)
{
  unsigned char value;

  if (tokval == ODDxNULL)
    value = dflt_f ? dfltattr->dfltv : atoi(tokstr);
  else
    value = tokval;
  
  _ErrRet (SdlCheckPar (attr, 0, value));
  
  memcpy (*dest, &value, sizeof (char)); 
  *dest += 1;
  return 1;
}

int OFInsertUser (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
		  void ***dest, char *tokstr, unsigned int tokval, int dflt_f)
{
  memset (*dest, 0, sizeof (char *));
  *dest += 1; 
  return 1;
}

int OFInsertStr (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
		 char ***dest, char *tokstr, unsigned int tokval, int dflt_f)
{
  char	   *newvalue, *value = NULL;
  int	   rv;
  
  /*  if (tokval == ODDxNULL) ...does this ever happen? */
    value = dflt_f ? &((dfltattr->dflts)[0]) : tokstr;	    
    /*  else
    value += _SdlIsStr (tokval); */
  
  rv = SdlCheckPar (attr, value, 0);
  _ErrRet (rv);
  
  /* insert into user-object */
  if ((newvalue = (char *) _SdlMalloc (strlen (value) + 1)) == 0) 
    _ErrRet2(e__allocfail, "symbol string");
  memcpy (*dest, &newvalue, sizeof (char *));
  
  if (attr->typ == AT_PROTOFNCT)		 /* copy function to array  */
    OddAddFunction (*dest);
  
  *dest = *dest + 1;	

  strcpy (newvalue, value);
  /*  
  if (odd->action == SDLxNOHDR || odd->section_f)
    SmEdit (newvalue, SMxDECODE);
    */
  return 1;
}

int OFInsertFunction (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
		      unsigned int **dest, char *tokstr, unsigned int tokval, 
		      int dflt_f)
{
  unsigned int value;
  SDLoPTR  tmp=NULL;
  
  value = dflt_f ? SDLxNULLFNCT : atoi (tokstr);
  
  if (odd->action == SDLxNOHDR || odd->section_f) {
    if (odd->section_f)	{  /* function index */
      tmp += dflt_f ? SDLxXFNCT : value;
      memcpy (*dest, &tmp, sizeof (SDLoPTR));
    }
    else {  /* function address */
      tmp = dflt_f ? NULL : (SDLoPTR) SDL_fnct[value]; 
      memcpy (*dest, &tmp, sizeof (SDLoPTR));
    }
  }
  else {  /* function name	    */
    tmp = dflt_f ? "NULL" : *(function[value].nam);
     memcpy (*(char ***) dest, &tmp, sizeof (SDLoPTR));} 

  if (!dflt_f) 
    attr->dflts = *(function[value].args);
  *dest += 1; 
  return 1;
}

int OFInsertObject (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
       	    void ***dest, char *tokstr, unsigned int tokval, int dflt_f)
{
  SDLoOBJ  *refClass;
  SDLoPTR  obj_p;
  int	   rv, objX;
  
  refClass = OddGetPartofClass (attr);
  if (tokstr)
    objX = atoi (tokstr);
  else if (tokval == ODDxNULL)
    objX = -1;
  else
    objX = tokval; /* possibly never occurs */

  if (!dflt_f && objX != -1)  {
    obj_p = (void *) (refClass->s + refClass->siz * objX);
  }
  else
    obj_p = NULL;
  
  /* copy object address into output object */
  if (odd->action == SDLxNOHDR || odd->section_f)  
    memcpy (*dest, &obj_p, sizeof (SDLoPTR));	
  else
    memcpy (*dest, &objX, sizeof (SDLoPTR));
  (*dest)++; 
  attr->dflts = OddGetClassDeclName (refClass);  /* declaration name */
  
  /* give attribute a type definition name */
  attr->tnam = refClass->tnam;
  return 1;
}


int OFInsertHeader (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
		    unsigned int **dest, char *tokstr, unsigned int tokval, 
		    int dflt_f)
{
  return 1;
}

int OFInherit (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
	       unsigned int **dest, char *tokstr, unsigned int tokval,
	       int dflt_f)
{
  return 1;
}

int OFGeneric (SDLoOBJ *obj, SDLoATTR *attr, SDLoATTR *dfltattr, 
	       void ***dest, char *tokstr, unsigned int tokval, 
	       int dflt_f)
{
  return 1;
}


/******************************************************************************
******** group of functions for writing attribute value to header file ********
*******************************************************************************
**
**
**	INPUT:	    attribute object [R]
**		    destination string [W]
**		    address of source [W]
**	        IMPLICIT:
**
**	RETURNS:  
**		  
*/

int OFWrtInt (SDLoATTR *attr, char *s, int **source)
{
  sprintf (s, "%d", **source);
  (*source)++;
  return 1;
}

int OFWrtUChar (SDLoATTR *attr, char *s, unsigned char **source)
{
  sprintf (s, "%d", **source);
  (*source)++;
  return 1;
}

int OFWrtUInt (SDLoATTR *attr, char *s, unsigned int **source)
{
  sprintf (s, "%u", **source);
  (*source)++;
  return 1;
}

int OFWrtFloat (SDLoATTR *attr, char *s, float **source)
{
  sprintf (s, "%f", **source);
  (*source)++;
  return 1;
}

int OFWrtStr (SDLoATTR *attr, char *s, char ***source)
{
  static STRv str;
  if (!str)
    str = StrNew ();

  StrSetS (&str, **source);
  StrEncode (&str);
  sprintf (s, "\"%s\"", _Str (str));
  (*source)++;
  return 1;
}

int OFWrtName (SDLoATTR *attr, char *s, char ***source)
{
  sprintf (s, "%s", **source);
  (*source)++;
  return 1;
}

int OFWrtNULL (SDLoATTR *attr, char *s, void ***source)
{
  sprintf (s, "NULL");
  (*source)++;
  return 1;
}

int OFWrtAddr (SDLoATTR *attr, char *s, unsigned int **source)
{
  if (**source == ODDxNULL)
    sprintf(s, "NULL");
  else 
    sprintf(s, "&%s[%d]", attr->dflts, **source);

  (*source)++;
  return 1;
}

int OFWrtEBNF (SDLoATTR *attr, char *s, char ***source)
{
  return 1;
}


/******************************************************************************
******* group of functions for checking attribute values **********************
*******************************************************************************
** 
**	INPUT:	    address of attribute [R]
**		    address of value
**	        IMPLICIT:
**                 f (FILo *) [R]
**
**	RETURNS:    e__icaattrval +
**		    1
*/ 

int OFCheckNum (SDLoATTR *attr, int v, char *s)
{
  char    errmsg[MSGxXLN];

  if (v > attr->max)
    sprintf(errmsg, "Attribute: %s, value: %d, max: %d", 
	    attr->nam, v, attr->max);
  else if (v < attr->min)
    sprintf(errmsg, "Attribute: %s, value: %d, min: %d",
	    attr->nam, v, attr->min);
  else 
    return 1;
  
  _ErrRet2 (e__icaattrval, errmsg);
  return 1;
}

int OFCheckStr (SDLoATTR *attr, int v, char *s)
{
  char    errmsg[MSGxXLN];
  int	    len;
  
  len = strlen (s);
  if (len > attr->max)
    sprintf (errmsg, "Attribute: %s, string: %s, maxlen: %d",
	     attr->nam, s, attr->max);
  else if (len < attr->min)
    sprintf (errmsg, "Attribute: %s, string: %s, minlen: %d", 
	     attr->nam, s, attr->min);
  else return 1;
  
  _ErrRet2 (e__icaattrval, errmsg);
  return 1;
}




int OFGenSimple (SDLoOBJ * headobj, SDLoATTR *attr)
{
  return 1;
}

int OFGenObject (SDLoOBJ * headobj, SDLoATTR *attr)
{
  return 1;
}

r    errmsg[MSGxXLN];
  int	    len;
  
  len = strlen (s);
  if (len > attr->max)
    sprintf (errmsg, "Attribute: %s, string: %s, maxlen: %d",
	     attr->nam, s, attr->max);
  else if (len < attr->min)
    sprintf (errmsg, "Attribute: %s, string: %s, minlen: %d", 
	     attr->nam, s, attr->min);
  else return 1;
  
  srs/src/oddtools.c
char oddtools_srs_ID[] = "$Id: oddtools.c,v 1.1 1996/05/06 15:17:04 srs Exp $";
/*
**
**    $RCSfile: oddtools.c,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:17:04 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.x Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/


#include <stdio.h>
#include <stdlib.h>
#include "message.h"
#include "oddtools.h"

#ifndef TRUE
#define TRUE 1
#endif

#ifndef FALSE
#define FALSE 0
#endif

typedef struct ODDooQ_P {
  struct ODDooQ_P	*dn ,*up;
  int		data;
} ODDoQ_P;

typedef struct ODDooL_P {
  struct ODDooL_P	*dn;
  int		data;
} ODDoL_P;

typedef struct ODDooT_P {
  struct ODDooT_P	*left, *right;
  char            bal;
  int		data;
} ODDoT_P;

typedef struct ODDoHEAD_
    {
        void                    *dn;
        void                    *up;
        void                    *null;
        int                     cx;
        unsigned char           init_f;
        int                     n;
        void                    *current;
        void                    *new;
        unsigned char           off;
        int                     (*getnew)(struct ODDoHEAD *, int);
        int                     (*add)(struct ODDoHEAD *);
        int                     (*search)(struct ODDoHEAD *, void *, char *);
        int                     (*delete)(struct ODDoHEAD *);
        void                     *(*position)(struct ODDoHEAD *,int);
        int                     (*clear)(struct ODDoHEAD *);
    } ODDoHEAD;

/***********************************/
/****** OBJECT WIDE VARIABLES ******/
/***********************************/

extern char	*section;
extern int	section_z;



/****** OddQInit **************************************************************
**
**	inititalizes data-structure queue;
**
**	INPUT:	    queue-header [W]
**	        IMPLICIT:
**
**	RETURNS:    1
*/ 
   
int OddQInit (ODDoHEAD *hd)
{
  hd->null = (void *) &(hd->dn);
  hd->up = (void *) hd->null;
  hd->dn = (void *) hd->null;
  hd->n = 0;
  hd->init_f = TRUE;
  return 1;
}


/**api* OddLAdd ***************************************************************
**
**	adds new item to linked list;
**
**	INPUT:	    queue-dscr. [W]
**	        IMPLICIT:
**
**	RETURNS:    1 if success
**                  0 if head->new is NULL
*/ 
   
int OddLAdd (ODDoHEAD *hd)
{
  ODDoL_P    *new, *lst;
  
  if (!hd->init_f)
    OddQInit (hd);  /* use same function as for queue */
                                             
  if (hd->new == NULL)
    return 0;
  
  new = (ODDoL_P *) ((char *) hd->new - hd->off);
  new->dn = (ODDoL_P *) hd->null;
  lst = (ODDoL_P *) hd->up;
  lst->dn = new;
  hd->up = new;
  hd->n++;
  if (hd->n == 1) {			 /* first element	    */
    hd->cx = 0;
    hd->current = &(new->data);
  }
  hd->new = NULL;
  return 1;
}


/**api* OddNew ****************************************************************
**
**	allocates memory for new element and places address to i
**	into header->new;
**
**	INPUT:	    address of header [W] 
**                  size of item
**	        IMPLICIT:
**
**	RETURNS:    1 
**                  e__allocfail <item> +
*/ 
   
int OddNew (ODDoHEAD *hd, int size)
{
  if ((hd->new = (void *) malloc (size + hd->off)) == NULL)
    _ErrRet2(e__allocfail, "item by OddNew");
  
  hd->new = (char *) hd->new + hd->off; /* shift offset	    */
  return 1;
}




/**api* OddQAdd **************************************************************
**
**	places item that header->new points to at end of  queue;
**      initializes queue if necessary;
**
**	INPUT:	    queue-header [W]
**	        IMPLICIT:
**
**	RETURNS:    1 if success
**                  0 if header->new not defined
**                 
*/ 

int OddQAdd (ODDoHEAD *hd)
{
  ODDoQ_P    *new;
  
  if (!hd->init_f)
    OddQInit (hd);
  
  if (hd->new == NULL)
    return 0;
  
  new = (ODDoQ_P *) ((char *) hd->new - hd->off);
  new->up = (ODDoQ_P *) hd->up;
  new->dn = (ODDoQ_P *) hd->null;
  new->up->dn = new;
  new->dn->up = new;
  hd->n++;
  if (hd->n == 1) {
    hd->cx = 0;
    hd->current = &(new->data);
  }
  hd->new = NULL;
  return 1;
}



/**api* OddQPosition **********************************************************
**
**	positions cursor to element with specified number
**
**	INPUT:	    list-dscr. [W]
**		    index of item [R] first element has index 1 !!!
**                  or ODDxNEXT, ODDxPREV, ODDxFIRST, ODDxLAST
**	        IMPLICIT:
**
**	RETURNS:    pointer to object
**		    NULL if index larger than actual count or queue empty
*/ 

void *OddQPosition (ODDoHEAD *hd, int x)
{
  ODDoQ_P *nxt;
  int	    k;
  
  if (x > 0) x--;
  
  if (x == ODDxNEXT) x = hd->cx+1;
  if (x == ODDxPREV) x = hd->cx-1;
  
  if (x >= hd->n || x == -1 || hd->n == 0)
    return NULL;
  
  if (x == hd->cx)
    return hd->current;
  
  if (x != ODDxFIRST && x != ODDxLAST) {
    nxt = (ODDoQ_P *) ((char *) hd->current - hd->off);
    
    if (x > hd->cx)
      for (k=hd->cx; k < x;  nxt = nxt->dn, k++)
	;
    else 
      for (k=hd->cx; k > x; nxt = nxt->up, k--)
	;
  }
  else if (x == ODDxFIRST)
    nxt = hd->dn, x = 0;
  else if (x == ODDxLAST)
    nxt = hd->up, x = hd->n -1;
  
  hd->current = &(nxt->data);
  hd->cx = x;
  return hd->current;
}



/**api* OddLPosition **************************************************************
**
**	positions cursor to element with specified number in linked list;
**
**	INPUT:	    list-dscr. [W]
**		    index of item [R] first element has index 1 !!!
**                  or ODDxNEXT, ODDxPREV, ODDxFIRST, ODDxLAST
**	        IMPLICIT:
**
**	RETURNS:    pointer to object
**		    NULL if index larger than actual count or queue empty
*/ 
   
void *OddLPosition (ODDoHEAD *hd, int x)
{
  ODDoL_P *nxt;
  int	    k;
  
  if (x > 0) x--;
  
  if (x == ODDxNEXT) x = hd->cx+1;
  if (x == ODDxPREV) x = hd->cx-1;
  
  if (x >= hd->n || x == -1 || hd->n == 0)
    return NULL;
  
  if (x == hd->cx)
    return hd->current;
  
  if (x != ODDxFIRST && x != ODDxLAST) {
    if (x > hd->cx)
      k = hd->cx, nxt = (ODDoL_P *) ((char *) hd->current - hd->off);
    else
      k = 0, nxt = hd->dn;
    
    for (; k < x;  nxt = nxt->dn, k++)
      ;
  }
  else if (x == ODDxFIRST)
    nxt = hd->dn, x = 0;
  else 
    nxt = hd->up, x = hd->n - 1;
  
  hd->current = &(nxt->data);
  hd->cx = x;
  return hd->current;
}


/**api* OddLInsert ****************************************************************
**
**	inserts element in linked list either left or right of current;
**	new element becomes then current element;
**
**	INPUT:	    address of list header [W]
**		    ODDxLEFT or ODDxRIGHT [R]
**	        IMPLICIT: 
**
**	RETURNS:    1
*/ 

int OddLInsert (ODDoHEAD *hd, int pos)
{
  ODDoL_P    *tmp, *new;
  
  if (!hd->init_f || !hd->n) {
    OddLAdd (hd);	
    return 1;
  }
  else {
    new = (ODDoL_P *) ((char *) hd->new - hd->off);
    if (pos == ODDxRIGHT) {
      tmp = (ODDoL_P *) ((char *) hd->current - hd->off);
      hd->cx++;
    }
    else if (pos == ODDxLEFT) {
      if (hd->cx > 0) {
	OddLPosition (hd, hd->cx);
	hd->cx++;
	tmp = (ODDoL_P *) ((char *) hd->current - hd->off);
      }
      else {
	hd->cx = 0;
	tmp = (ODDoL_P *) hd;
      }
    }
    new->dn = tmp->dn;
    tmp->dn = new;
  }
  hd->n++;
  hd->current = &(new->data);
  return 1;
}


/**api* OddLDelete ****************************************************************
**
**	Deletes an entry from a list - current entry will be the one after
**	the deleted one;
**
**	INPUT:	    address of header-dsc. [W]
**	        IMPLICIT:
**
**	RETURNS:    1
**                  0 if list empty
*/ 
   
int OddLDelete (ODDoHEAD *hd)
{
  ODDoL_P *prev, *tmp;
  int     *rv, fst_f = FALSE;

  if (hd->n == 0)
    return 0;

  tmp = (ODDoL_P *) ((char *) hd->current - hd->off);
  
  if (hd->cx > 0) {
    OddLPosition (hd, hd->cx);
    prev = (ODDoL_P *) ((char *) hd->current - hd->off);
  }
  else
    prev = (ODDoL_P *) hd, fst_f = TRUE;
  
  prev->dn = tmp->dn; 
  OddFree (tmp);
  if (hd->n == 1)
    OddQInit (hd);    
  else {
    hd->n--;	
    if (hd->cx == hd->n)
      hd->current = &(prev->data);
    else {
      hd->current = &(prev->dn->data);
      if (!fst_f)
	hd->cx++;	
    }
  }
  return 1;
}


/****** OddFree *******************************************************************
**
**	frees memory - does it only if memory is not within the ODD-section;
**
**	INPUT:	    pointer to memory to be freed [W]
**	        IMPLICIT:
**		    section (void *) [R]
**		    section_z (int) [R]
**
**	RETURNS:    1 if freed
**		    0 if not
*/ 
   
int OddFree (char *p)
{
  if (p >= section && p <= section + section_z)
    return 0;
  else
    free (p);
  p = NULL;
  return 1;
}


->cx++;	
    }
  }
  return 1;
}


/****** OddFree *******************************************************************
**
**	frees memory - does it only if memory is not within the ODD-section;
**
**	INPUT:	    pointer to memory to be freed [W]
**	        IMPLICIT:
**		    section (void *) [R]
**		    section_z (int) [R]
**
**	RETURNS:    1 if freed
**		    0 if not
*/ 
   
int OddFree (char *p)
{
  if (p >= section && p <= section + section_z)
  srs/src/oddtools.h
**
**    $RCSfile: oddtools.h,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:17:05 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**                  SRS V3.0 Copyright by Thure Etzold
**
*/

#define ODDxNEXT    -2
#define ODDxPREV    -3
#define ODDxFIRST   -4
#define ODDxLAST    -5
#define ODDxRIGHT    0
#define ODDxLEFT     1
#define ODDxFORWARD  2	
#define ODDxREVERSE  4
#define ODDxCURRENT  8
à)
  srs/src/oldlistbuf.c
** C list management
*****************************************************************************/

#include <stdlib.h>
#include <string.h>

#include "def.h"
#include "oldlistbuf.h"


/* creation/deletion */

void  ListBufCreate(LISTBUFv* list, LISTBUFoINFO* i, int dim) {
   int memSize=sizeof(LISTBUFo)+(i->elemSize)*dim;
   *list=malloc(memSize);
   (*list)->info=i;
   (*list)->num=0;
   (*list)->size=memSize;
}

void  ListBufDelete(LISTBUFv* list) {
   free(*list); /* I know the size of it! */
   *list=NULL;
}


/* insertion/removal */

void  ListBufAppend(LISTBUFv* list, void* val) {
   Iter i=NULL; ListBufAdd(list, &i, val);
}


void  ListBufInsert(LISTBUFv* list, void* val) {
   Iter i=ListBufFirst(list); ListBufAdd(list,&i,val);
}

void  ListBufAdd   (LISTBUFv* list, Iter* i, void* val) {
   int num=((*list)->num++);
   int elemSize=(*list)->info->elemSize;
   int last=sizeof(LISTBUFo)+num*elemSize;
   int offset; num++;
   /* append if i invalid */
   if (!*i) *i=cast(*list,BYTE*)+last;
   offset=cast(*i,BYTE*)-cast(*list,BYTE*);
   if (last>=(*list)->size) {
      /* grow the list, copy elements inserting new */
      LISTBUFo* oldListBuf=*list;
      BYTE* oldIter=cast(*i,BYTE*);
      int newSize=sizeof(LISTBUFo)+2*num*elemSize;
      *list=malloc(newSize);
      *i=cast(*list,BYTE*)+offset;
      memcpy(cast(*list,BYTE*),cast(oldListBuf,BYTE*),offset);
      memcpy(cast(*i,BYTE*)+elemSize,oldIter,last-offset);
      memcpy(cast(*i,BYTE*),val,elemSize);
      (*list)->size=newSize;
      free(oldListBuf);
   }
   else {
      /* move the elements after (including) insertion point */
      memmove(cast(*i,BYTE*)+elemSize,cast(*i,BYTE*),last-offset);
      memcpy(*i,val,elemSize);
   }
}

void  ListBufRemove(LISTBUFv* list, Iter* i) {
   int num=(--(*list)->num);
   int elemSize= (*list)->info->elemSize;
   int last=sizeof(LISTBUFo)+num*elemSize;
   int offset;
   /* append if i invalid */
   ASSERT(*i,RemoveInvalid);
   offset=cast(*i,BYTE*)-cast(*list,BYTE*);
   if ((*list)->size>last+2*num*elemSize) {
      /* shrink the list, copy elements removing */
      LISTBUFv oldListBuf=*list;
      BYTE* oldIter=cast(*i,BYTE*);
      int newSize=sizeof(LISTBUFo)+num*elemSize;
      *list=malloc(newSize);
      *i=cast(*list,BYTE*)+offset;
      memcpy(cast(*list,BYTE*),cast(oldListBuf,BYTE*),offset);
      memcpy(cast(*i,BYTE*),oldIter+elemSize,last-offset);
      cast(*list,LISTBUFo*)->size=newSize;
      free(oldListBuf);
      if (cast(*i, BYTE*)>=cast(*list, BYTE*)+newSize) *i=NULL;
   }
   else {
      /* move the elements after removal point */
      memmove(cast(*i,BYTE*),cast(*i,BYTE*)+elemSize,last-offset);
   }
}

void  ListBufClear (LISTBUFv* list) {
   (*list)->num=0;
}

/* access */
void* ListBufAtPos  (LISTBUFv* list, int pos) {
   return ListBufAt(list,ListBufInPos(list,pos));
}

void* ListBufAt (LISTBUFv* list, Iter i) {
   ASSERT(i,InvalidIter);
   return i;
}

/* iterator support */
Iter  ListBufInPos(LISTBUFv* list, int pos) {
   if (pos<(*list)->num)
      return cast(*list,BYTE*)+sizeof(LISTBUFo)+
         pos*(*list)->info->elemSize;
   else return NULL;
}

int   ListBufPosAt(LISTBUFv* list, Iter i) {
   ASSERT(i,InvalidIter);
   return (cast(i,BYTE*)-(cast(*list,BYTE*)+sizeof(LISTBUFo)))/
      (*list)->info->elemSize;
}

Iter  ListBufFirst(LISTBUFv* list) {
   return ListBufInPos(list,0);
}

void*  ListBufNext (LISTBUFv* list, Iter* i) {
   if (!*i) *i=ListBufFirst(list);
   else {
      int elemSize=(*list)->info->elemSize;
      *i=cast(*i,BYTE*)+elemSize;
      if (cast(*i,BYTE*)>=cast(*list,BYTE*)+sizeof(LISTBUFo)+(*list)->num*elemSize) {
         *i=NULL; return NULL;
      }
   }
   return *i;
}

Iter  ListBufLast (LISTBUFv* list) {
   int num=(*list)->num;
   if (num) return cast(*list,BYTE*)+(*list)->info->elemSize*(num-1);
   else return NULL;
}

void* ListBufPrev (LISTBUFv* list, Iter* i) {
   if (!*i) i=ListBufLast(list);
   else {
      int elemSize=(*list)->info->elemSize;
      *i=cast(*i,BYTE*)-elemSize;
      if (cast(*i,BYTE*)<cast(*list,BYTE*)+sizeof(LISTBUFo)) {
         *i=NULL; return NULL;
      }
   }
   return *i;
}


/* information */

int   ListBufCard (LISTBUFv* list) {
   return (*list)->num;
}

BOOL  ListBufEmpty(LISTBUFv* list) {
   return (*list)->num==0;
}
(*list,BYTE*)+(*list)->info->elemSize*(num-1);
   else return NULL;
}

void* ListBufPrev (LISTBUFv* list, Iter* i) {
   if (!*i) i=ListBufLast(list);
   else {
      int elemSize=(*list)->info->elemSize;
      *i=cast(*i,BYTE*)-elemSisrs/src/oldlistbuf.h
#define _LISTBUF_H

/*******************************************************************************
** C generic ListBuf management
**/


/* will be class of value */
typedef struct LISTBUFoINFO {
   int elemSize;
} LISTBUFoINFO;

typedef struct LISTBUFo {
   LISTBUFoINFO*  info;
   int         size;
   int         num;
} LISTBUFo;

/* a list of values */
typedef LISTBUFo* LISTBUFv;

/************************************
** ITERATOR
**
** USE ONLY ONE iterator with add,remove:
** other iterators become invalid
** NULL iterator is position without value:
** access:  invalid
** add:     identifies position AFTER last element (append)
** next:    starts from first again
** prev:    starts from last again
*/


/************************************
** LISTBUF API
*/

/* creation/deletion */
void  ListBufCreate(LISTBUFv* list, LISTBUFoINFO* i, int dim);
void  ListBufDelete(LISTBUFv* list);

/* insertion/removal */
void  ListBufAppend(LISTBUFv* list, void* val);
void  ListBufInsert(LISTBUFv* list, void* val);
void  ListBufClear (LISTBUFv* list);
   /* iterator mantains position after operation */
void  ListBufAdd   (LISTBUFv* list, Iter* i, void* val);
void  ListBufRemove(LISTBUFv* list, Iter* i);

/* access */
void* ListBufAtPos  (LISTBUFv* list, int pos);
void* ListBufAt     (LISTBUFv* list, Iter i);

/* iterator support */
Iter  ListBufInPos  (LISTBUFv* list, int pos);
int   ListBufPosAt  (LISTBUFv* list, Iter i);

Iter  ListBufFirst(LISTBUFv* list);
void* ListBufNext (LISTBUFv* list, Iter* i);
Iter  ListBufLast (LISTBUFv* list);
void* ListBufPrev (LISTBUFv* list, Iter* i);

/* information */

int   ListBufCard (LISTBUFv* list);
BOOL  ListBufEmpty(LISTBUFv* list);

/************************************************************************
** specialized list declarations (good for debugging)
*/

typedef struct LISTBUFoChar {
   LISTBUFo head;
   char arr[100];
} LISTBUFoChar;

typedef LISTBUFoChar STRINGo;
 
typedef struct LISTBUFoInt {
   LISTBUFo head;
   int arr[10];
} LISTBUFoInt;

typedef struct LISTBUFoPtr {
   LISTBUFo head;
   BYTE* arr[10];
} LISTBUFoPtr;


#endif
i);

/* information */

int   ListBufCard (LISTBUFv* list);
BOOL  ListBufEmpty(LISTBUFv* list);

/************************************************************************
** specialized list declarations (good for debugging)
*/

typedef struct LISTBUFoChar {
   LISTBUFo head;
   char arr[100];
} LISTBUFoChar;

typedef LISTBUFoChar STRINGo;
 
typedef struct LISTBUFoInt {
   LISTBUFo head;
   int arr[10];
} LISTBUFoInt;

typedef strusrs/src/omtest/

	gcc -g -w -o try blub.c tryblub.c strv.c parse.c mi.c dict.c def.c

trygen: blub.c trygen.c mystr.c parse.c mi.c dict.c /home/srs/srs5/src/def.c
	gcc -g -w -o trygen -I/home/srs/srs5/src blub.c trygen.c mystr.c parse.c mi.c dict.c /home/srs/srs5/src/def.c

tryget: blub.c tryget.c mystr.c parse.c mi.c dict.c /home/srs/srs5/src/def.c
	gcc -O3 -w -o tryget -I/home/srs/srs5/src blub.c tryget.c mystr.c parse.c mi.c dict.c /home/srs/srs5/src/def.c

slist: slist.c tryslist.c
	cc -g -o try -I/home/srs/srs5/src slist.c tryslist.c mycomdef.c
yblub.c strv.c parse.c mi.c dict.c def.c

trygen: blub.c trygen.c mystr.c parse.c mi.c dict.c /home/srs/srs5/src/def.c
	gcc -g -w -o trygen -I/home/srs/srs5/src blub.c trygen.c mystr.c parse.c mi.c dict.c /home/srs/srs5/src/def.c

tryget: blub.c tryget.c mystr.c parse.c mi.c dict.c /home/srs/srs5/src/def.c
	gcc -O3 -w -o tryget -I/home/srs/srs5/src blub.c tryget.c mystr.c parse.c mi.c dict.c /home/srs/srs5/src/def.c

slistsrs/src/omtest/tryblub.c
#include "strv.h"
#include "blub.h"

typedef struct TRYOBJ {
  OBJo head;
  int a;
  STRv b;
  struct TRYOBJ* part;
} TRYOBJ;

typedef struct TRYMORE {
  TRYOBJ head;
  STRv more;
  ListAttr list;
  int arr[10];
} TRYMORE;


int main() {
    TRYOBJ* o=ObjCpy(Object);
    TRYOBJ* o1,*oc;
    TRYMORE* o2;
    void *r1, *r2, *r3,*a1; 
    AttrIter ai; Iter i;
    int* list;
    OBJpStream s;
    ObjInit();
    ObjAttrNew(&o, StrTemp("a"), int)=3;
    ObjAttrNew(&o, StrTemp("b"), STRv)=StrCpyS("ciao");
    ObjAttrNewRef(&o, StrTemp("part"),TRYOBJ*)=NULL;
    ObjPrint(o); printf("\n");
    ObjMakeClass(o,StrTemp("TRYOBJ"));
    o1=ObjCpy(o);
    ObjChange(&o1,TRYOBJ*);
    o1->part=ObjCpy(o);
    ObjChange(&ObjChange(&o1, TRYOBJ*)->part, TRYOBJ*)->a=10;
    o1->a=5;
    StrSetS(&o1->b,"containing");
    o2=ObjCpy(o1);
    ObjAttrNew(&o2,StrTemp("more"),STRv)=StrCpyS("someMore");
    list=&ObjListNew(&o2,4,int);
    *list++=1;
    *list++=2;
    *list++=3;
    *list++=4;
    ObjDebug(o);
    ObjDebug(o1); 
    ObjDebug(o2);
    ObjMakeClass(o2,StrTemp("TRYMORE"));
    ObjListApp(&o2,int)=6;
    ObjListApp(&o2,int)=7;
    ObjDebug(o2);
    ObjListCut((void**)&o2,ObjListWith(o2,1),3);
    ObjDebug(o2);
    /* try access by name */
    printf("%d %s\n", ObjAttr(o,StrTemp("a"),int),
	Str(ObjAttr(o,StrTemp("b"),STRv)));
    printf("%d %s\n", ObjAttr(o1,StrTemp("a"),int),
	Str(ObjAttr(o1,StrTemp("b"),STRv)));
    printf("%d %s\n", ObjAttr(o2,StrTemp("2"),int),
	Str(ObjAttr(o2,StrTemp("more"),STRv)));
    /* attribute iteration */
    printf("iterating:\n");
    for (ai=ObjAttrFirst(o2); ai; ObjAttrNext(o2,&ai)) {
        STRv name=ObjAttrName(o2,ai);
        printf("%s\n",Str(name));
	StrDel(name);
    }    
    /* testing list iteration */
    printf("list:\n");
    for (i=ObjListFirst(o2);i;ObjListNext(o2,&i)) {
        printf("%i:%i\n",ObjListPos(o2,i),ObjListIn(i,int));
    }
    printf("%d",ObjListCard(o2));
    
    PathInit();
    oc=ObjCpy(o1);
    r1=PathStaticImpl(theRoot,StrTemp("o"),&o,OBJvClass,NULL);
    r2=PathStaticImpl(theRoot,StrTemp("o1"),&o1,OBJvClass,NULL);
    r3=PathStaticImpl(theRoot,StrTemp("o2"),&o2,OBJvClass,NULL);
    a1=Path("o1.part.a"); PathCompileImpl(a1);
    PathChange(a1, int)=6;
    ObjDebug(o1); ObjDebug(oc);
    
    /* try stream output */
    printf("\n-----------------saving\n");
    ObjDebug(o); ObjDebug(o1); ObjDebug(o2); ObjDebug(oc);
    PathPrint(a1);
    s=ObjStreamOpen("blabla","wb",TRUE);
    ObjStore(o, s); 
    ObjStore(o1, s);
    ObjStore(o2, s);
    ObjStore(oc, s);
    RefStore(a1,s);
    ObjStreamClose(s);
    
    /* try stream input */
    s=ObjStreamOpen("blabla","rb",TRUE);
    ObjSet(&o, ObjLoad(s));
    ObjSet(&o1, ObjLoad(s));
    ObjSet(&o2, ObjLoad(s));
    ObjSet(&oc,ObjLoad(s));
    ObjSet(&a1,RefLoad(s));
    ObjStreamClose(s);
    ObjDebug(o); ObjDebug(o1); ObjDebug(o2); ObjDebug(oc);
    PathPrint(a1);

    /* release everything */
    ObjDel(o); ObjDel(o1); ObjDel(o2); 
    ObjDel(oc);
    ObjDel(a1); ObjDel(r1);
}

jStore(o2, s);
    ObjStorsrs/src/par.c
char parameter_srs_ID[] = "$Id: par.c,v 1.8 1997/03/18 18:45:32 srs Exp $";
/*
**    $RCSfile: par.c,v $
**    $Revision: 1.8 $
**    $Date: 1997/03/18 18:45:32 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: file, sm, message, rtl, sdl, sdlget, oddfncts 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**    Description
**    =========== 
**
**    management of user defined variables 
**    if the variable is a number or real then the value is 0 if undefined -
**    which means that every parameter has a default value of 0!
**                    
** 
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/


#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include <string.h>
#include "message.h"
#include "sm.h"
#include "strv.h"
#include "futil.h"
#include "sdlget.h"
#include "lst.h"
#include "regexp.h"
#include "par.h"


#include SRSINCLUDE


#define PARxXNAM 80
#define PARxXSTR 5000


/*
**  name of the ODD file with the user definitions
*/

#define SRSDEFAULTS "SRSDAT:srsparam.dat"
#ifdef VMS
#  define USERDEFAULTS "SYS$LOGIN:srsparam.dat"
#else
#  define USERDEFAULTS "HOME/.srsparam"
#endif

enum tableType {PARxPRIVATE=1,PARxLAYERED};



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  parameter list object (parameter table) 
*/

typedef struct PARoTABLE {
  char             *list;         /* for usage of module "list" only! */
  INT4             classId;      /* for "list" module */  
  char             name[132];     /* name of the parameter table */
  struct PARo     *par;          /* list of all predefined parameters */
  INT4             parN;          /* number of predefined parameters */
  struct PARoTYPE *parType;      /* list of all predefined parameter types */
  INT4             parTypeN;      /* number of predefined parameter types */
  INT4             parClassId;    /* for the /lst/ module */
  INT4             parTypeClassId; /* for the /lst/ module */
  char             isModified;    /* has one of the parameters in the
                                            table been modified? */
  struct PARoTABLE *up;          /* Upper or outer parameter list */
  enum tableType   type;          /* type of the table */
} PARoTABLE;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  global and module wide variables
*/

static PARoTABLE *parTable=NULL;

INT4       changepar_f; /* tells if any parameter in the list was changed */

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  internal functions
*/

int ParOCheckFunction (PARo *par, INT4 (*function) ());
int ParOCheckReal (PARo *par, float real);
int ParOCheckNum (PARo *par, int num);
int ParOCheckStr (PARo *par, char *str);
static INT4 ParODefBool (PARo *par, char *str);
static void ParTableNew (void *obj);
static void ParTableKill (void *obj);
static void ParNew (void *obj);
static void ParDump (FILE *file, void *obj);



/***** ParTableNew ************************************************************
**
**      Initializes a new parameter table object.
**
**	INPUT:	    pointer to memory location [W]
**	        IMPLICIT:
**
**	RETURNS: 
*/ 

static void ParTableNew (void *obj)
{
  static INT4 parClassId=0, parTypeClassId=0;
  PARoTABLE *table = (PARoTABLE *) obj;

  
  if (!parClassId) {
    LstManageClassFlex (&parClassId, sizeof (PARo), ParNew, NULL, ParDump);
    LstManageClassFlex (&parTypeClassId, sizeof (PARoTYPE), NULL, NULL, NULL);
  }
  table->parClassId = parClassId;
  table->parTypeClassId = parTypeClassId;

  table->parN = 0;
  table->parTypeN = 0;
  table->par = NULL;
  table->parType = NULL;

}


/***** ParTableKill ***********************************************************
**
**      Deletes a parameter table object.
**
**	INPUT:	    pointer to memory location [W]
**	        IMPLICIT:
**
**	RETURNS: 
*/ 

static void ParTableKill (void *obj)
{
  PARoTABLE *table = (PARoTABLE *) obj;

  if (table->par)
    LstDeleteAll ((void **)&table->par); 
  if (table->parType)
    LstDeleteAll ((void **)&table->parType); 
}

/**api* ParGetTable ***********************************************************
**
**      Returns table object for specified name.
**
**	INPUT:	    table name [R]
**	        IMPLICIT:
**                  parTable [W]
**
**	RETURNS: 
**                  address of parameter table object
*/ 

PARoTABLE *ParGetTable (char *name)
{
  PARoTABLE *tmp = parTable;

  if (!LstHashSearch ((void **) &tmp, name)) 
    _ErrExit3 (e__objectunknown, "parameter table", name);
  return tmp;
}


/***** ParSetTable ************************************************************
**
**
**	INPUT:	  o table name [R]
**                o table name of table that the new table is added to [R]
**                  if omitted then the currently active table is used
**                o option: "private", "layered" [R]
**	        IMPLICIT:
**                  parTable [W]
**
**	RETURNS: 
**                  address of parameter table object
*/ 

PARoTABLE *ParSetTable (char *name, char *upName, char *option)
{
  static INT4 classId=0;
  static PARoTABLE *table=NULL;
  PARoTABLE *upTable = parTable;

  if (!classId)
    LstManageClass (&classId, sizeof (PARoTABLE), 
		    ParTableNew, ParTableKill, NULL);

  if (upName) 
    if (!LstHashSearch ((void **) &upTable, upName)) 
      _ErrExit3 (e__objectunknown, "parameter table", upName);
  
  if (!LstHashSearch ((void **) &table, name)) {
    LstNewNamed ((void **) &table, classId, name);
   table->up = upTable;
    table->type = SmEqs (option, "private") ? PARxPRIVATE : PARxLAYERED;
  }
  parTable = table;
  return table;
}


/***** ParUnsetTable ************************************************************
**      Sets table that has been set prior to the current one.
**
**	INPUT:	    
**	        IMPLICIT:
**                  parTable [W]
**
**	RETURNS: 
**                  address of parameter table object
*/ 

PARoTABLE *ParUnsetTable ()
{
  if (parTable->up)
    parTable = parTable->up;
  return parTable;
}

void ParDeleteTable (char *name)
{
  PARoTABLE *table=parTable;

  if (!LstHashSearch ((void **) &table, name)) 
    _ErrExit3 (e__objectunknown, "table", name);

  if (parTable == table)
    parTable = table->up;

  LstDelete ((void **) &table);
}



/***** ParNew *****************************************************************
**
**      initializes parameter list; this is only necessary if predefined
**      parameter's + parameter types exists ...
**
**	INPUT:	    parameter name [R]
**	        IMPLICIT:
**                  parClassId (int) [W]
**                  parTypeClassId (int) [W]
**
**	RETURNS:    address of parameter object
*/ 

static void ParNew (void *obj)
{
  PARo *par=(PARo *) obj;

  memset (par, 0, sizeof (PARo));
  par->type = PARxNEW;
}


/***** ParDump ****************************************************************
**
**      initializes parameter list; this is only necessary if predefined
**      parameter's + parameter types exists ...
**
**	INPUT:	    file pointer [W] or NULL
**                  parameter name [R]
**	        IMPLICIT:
**                  parClassId (int) [W]
**                  parTypeClassId (int) [W]
**
**	RETURNS:    address of parameter object
*/ 

static void ParDump (FILE *file, void *obj)
{
  PARo *par=(PARo *) obj;

  if (!file)
    file = stderr;

  switch (par->type) {
  case PARxNUM:
  case PARxBOOL:
    fprintf (file, "#par /name=%s /num=%d\n", par->name, par->num);
    break;
  case PARxREAL:
    fprintf (file, "#par /name=%s /real=%f\n", par->name, par->real);
    break;
  case PARxSTR:
    fprintf (file, "#par /name=%s /str=%s\n", par->name, par->str);
    break;
  default:
    break;
  }
}

void ParDumpAll ()
{
  LstPrintAll ((void *) parTable->par);
}


/**api* ParInit ***************************************************************
**
**      Initializes parameter table with a predifined parameter table. 
**
**	INPUT:	    address of parameter list object [R]
**	        IMPLICIT:
**                  parTable (PARoTABLE *) [W]
**
**	RETURNS:    
*/ 

void ParInit (PARoLIST *parList)
{
  PARo     *par=NULL;
  PARoTYPE *parType=NULL;
  char     tmp[256];
  int      k, len;

  /*
  ** Copy parameters from the Parameter list (ODD) to the parameter table.
  */

  LstNewNamed ((void **) &par, parTable->parClassId, "__dummy__");
  for (k=0; k < parList->parN; k++) {
    parList->par[k].classId = parTable->parClassId;
    LstInsertObject ((void **) &par, &parList->par[k]);
  }
  parTable->par = par;

  /*
  ** Do the same for the list of parameter types.
  */

  LstNewNamed ((void **) &parType, parTable->parTypeClassId, "__dummy__");
  for (k=0; k < parList->parTypeN; k++) {
    parList->parType[k].classId = parTable->parTypeClassId;
    LstInsertObject ((void **) &parType, &parList->parType[k]); 
    if (*parType->charSet) { /* expand permissive character set */
      strcpy (tmp, parType->charSet);
      SmCharSet (tmp);
      parType->charSet = (char *) malloc (strlen (tmp) + 1);
      strcpy (parType->charSet, tmp);
    }
  }
  parTable->parType = parType;
  
}



/***** ParFind ****************************************************************
**
**     searches a parameter by name; if not found a new parameter is inserted 
**     in the list with parameter type PARxNEW and returned;
**
**	INPUT:	    parameter name [R]
**	        IMPLICIT:
**                  parTable (PARoTABLE *) [W]
**
**	RETURNS:    address of parameter object
*/ 

PARo *ParFind (char *parName)
{
  if (!parTable)
    ParInit (NULL);
  
  if (!LstHashSearch ((void **) &parTable->par, parName)) 
    LstNewNamed ((void **) &parTable->par, parTable->parClassId, parName);

  return parTable->par;
}


/**api* ParGetRead ************************************************************
**
**     Searches a parameter for read access.
**     If the table is not specified then the one currently active is used.
**
**	INPUT:	    parameter name [R]
**                  parameter table [R] or NULL
**	        IMPLICIT:
**                  parTable (PARoTABLE *) [W]
**
**	RETURNS:    address of parameter object
**                  NULL if not found
*/ 

PARo *ParGetRead (char *parName, PARoTABLE *table)
{
  PARo *getPar=NULL;

  if (!table)
    table = parTable;

  for (; table; table=table->up)
    if (LstHashSearch ((void **) &table->par, parName)) {
      getPar = table->par;
      break;
    }
  return getPar;
}


/**api* ParGetWrite ***********************************************************
**
**      Retrieves a parameter for write access.
**      If the table is not specified then the one currently active is used.
**
**	INPUT:	    parameter name [R]
**                  parameter table [W] or NULL
**	        IMPLICIT:
**                  parTable (PARoTABLE *) [W]
**
**	RETURNS:    address of parameter object
**                  NULL if not found
*/ 

PARo *ParGetWrite (char *parName, PARoTABLE *table)
{
  PARoTABLE *tmp;
  PARo      *getPar=NULL;
  char      *intern;

  if (!table)
    table = parTable;

  for (tmp=parTable; tmp; tmp=tmp->up) {
    if (LstHashSearch ((void **) &tmp->par, parName)) {
      /* if found in upper table than copy it to current table */
      if (tmp != table) {
	LstNewNamed ((void **) &table->par, table->parClassId, 
		     parName);
	getPar = table->par;
	intern = getPar->intern; /* save the pointer to the list */
	memcpy (getPar, tmp->par, sizeof (PARo));
	getPar->intern = intern;
	if (tmp->par->str) {
	  getPar->str = (char *) malloc (strlen (tmp->par->str) + 1); 
	  strcpy (getPar->str, tmp->par->str);
	}
      }
      else
	getPar = tmp->par;
      break;
    }	
  }

  /* create new parameter in current table if not found */
  if (!getPar) { 
    LstNewNamed ((void **) &table->par, table->parClassId, parName);
    getPar = table->par;
  }
  return getPar;
}



/**API* ParDelete *************************************************************
**
**      Deletes parameter with specified name.
**
**	INPUT:	    parameter name [R]
**	        IMPLICIT:
**                  parTable (PARoTABLE *) [W]
**
**	RETURNS:    1 if parameter was found and deleted
**                  0 if parameter was not found
*/ 

INT4 ParDelete (char *parName)
{
  PARo *par;

  if (!(par = ParGetRead (parName, parTable)))
    return 0;
  parTable->par = par;
  LstDelete ((void**) &parTable->par);
  return 1;
}


/**API* ParDeleteMatch ********************************************************
**
**      Searches all parameters for regular expression and delete all that 
**      match.
**
**	INPUT:	    regular expression [R]
**	        IMPLICIT:
**
**	RETURNS:    number of parameters deleted
*/ 

INT4 ParDeleteMatch (char *reStr)
{
  regexp *re;
  INT4   k=0;

  re = RegComp (reStr);
  LstFirst ((void **) &parTable->par);
  do {
    if (RegExec (re, parTable->par->name)) {
      LstDelete ((void**) &parTable->par);
      k++;
    }
    else LstNext ((void **) &parTable->par);
    
  } while (!LstIsLast ((void *) parTable->par));

  if (RegExec (re, parTable->par->name)) {
    LstDelete ((void**) &parTable->par);
    k++;
  }    

  free (re);
  return k;
}

INT4 ParDeleteAssign (char *s)
{
  if (*s)
    ParDeleteMatch (s);
}


/**API* ParDefNum *************************************************************
**
**     Inserts or modifies a "number" parameter.
**
**	INPUT:	    parameter name [R]
**		    parameter value [R]
**	        IMPLICIT:
**
**	RETURNS:    1 if parameter was found
**		    0 if it has been inserted
**                  invalid value: e__parnottype <parameter_name, type>+
*/ 
   
INT4 ParDefNum (char *parName, INT4 num)
{
  PARo  *par;

  par = ParGetWrite (parName, parTable);
  return ParODefNum (par, num);
}

/**API* ParDefBool **************************************************************
**     Inserts or modifies a "boolean" parameter.
**
**	INPUT:	    parameter name [R]
**		    parameter value [R]
**	        IMPLICIT:
**
**	RETURNS:    1 if parameter was found
**		    0 if it has been inserted
**                  invalid value: e__parnottype <parameter_name, type>+
*/ 
   
INT4 ParDefBool (char *parName, INT4 num)
{
  PARo  *par;

  par = ParGetWrite (parName, parTable);
  return ParODefNum (par, num);
}



/**API* ParDefReal ************************************************************
**
**     Inserts or modifies a "real" parameter.
**
**	INPUT:	    parameter name [R]
**		    parameter value [R]
**	        IMPLICIT:
**                  parTable (PARoTABLE *) [W]
**
**	RETURNS:    1 if parameter was found
**		    0 if it has been inserted
**                  invalid value: e__parnottype <parameter_name, type>+
*/ 
   
INT4 ParDefReal (char *parName, float real)
{
  PARo  *par;

  par = ParGetWrite (parName, parTable);
  return ParODefReal (par, real);
}


/**API* ParDefStr *************************************************************
**
**     Inserts or modifies a "string" parameter.
**
**	INPUT:	    parameter name [R]
**		    parameter value [R]
**	        IMPLICIT:
**                  parTable (PARoTABLE *) [W]
**
**	RETURNS:    1 if parameter was found
**		    0 if it has been inserted
**                  invalid value: e__parnottype <parameter_name, type>+
*/ 
   
INT4 ParDefStr (char *parName, char *str)
{
  PARo  *par;

  par = ParGetWrite (parName, parTable);
  return ParODefStr (par, str);
}


/**API* ParDefFunction ********************************************************
**
**     Inserts or modifies a "function" parameter.
**
**	INPUT:	    parameter name [R]
**		    parameter value [R]
**	        IMPLICIT:
**                  parTable (PARoTABLE *) [W]
**
**	RETURNS:    1 if parameter was found
**		    0 if it has been inserted
**                  invalid value: e__parnottype <parameter_name, type>+
*/ 
   
INT4 ParDefFunction (char *parName, INT4 (*function) ())
{
  PARo  *par;

  par = ParGetWrite (parName, parTable);
  return ParODefFunction (par, function);
}

/**api* ParGetNumF ************************************************************
**
**      Calls ParGetNum with variable length argument lists
**
**
**      INPUT: pointer to string
**
**
**      RETURNS: modified string
**
**/

INT4 ParIsDefinedF(char *strfmt, ...)
{
  char parName[200];
  va_list args;
  va_start(args,strfmt);
  vsprintf(parName,strfmt,args);
  va_end(args);
  return ParIsDefined (parName);
}  

/**api* ParGetNumF ************************************************************
**
**      Calls ParGetNum with variable length argument lists
**
**
**      INPUT: pointer to string
**
**
**      RETURNS: modified string
**
**/

INT4 ParGetNumF(char *strfmt, ...)
{
  char parName[200];
  va_list args;
  va_start(args,strfmt);
  vsprintf(parName,strfmt,args);
  va_end(args);
  return ParGetNum (parName);
}  

/**api* function **************************************************************
**
**   Does a ParGetStr with variable length argument lists
**
**      INPUT: pointer to string
**
**
**      RETURNS: modified string
**
**
*/

char *ParGetStrF (char *strfmt, ...)
{
  char parName[200];
  va_list args;
  va_start(args,strfmt);
  vsprintf(parName,strfmt,args);
  va_end(args);
  return ParGetStr(parName);
}

/** RParGetBool **********************************************************************
**
**   Does a ParGetBool with variable length argument lists
**
**      INPUT: pointer to string
**
**
**      RETURNS: modified string
**
**
**
**
*/

INT4 ParGetBoolF(char *strfmt, ...)
{
  char parName[200];
  va_list args;
  va_start(args,strfmt);
  vsprintf(parName,strfmt,args);
  va_end(args);
  return ParGetBool(parName);
}  


/**api* function **************************************************************
**
**   Does a variable format ParDefStr
**
**      INPUT: pointer to string
**
**
**      RETURNS: modified string
**
**
*/
INT4 ParDefStrF (char *str, char *parNameF, ...)
{
  char parName[200];
  va_list args;
  va_start (args, parNameF);
  vsprintf (parName, parNameF, args);
  va_end (args);
  return ParDefStr (parName, str);
}



/** RParDelete ***********************************************************
**
**    Variable format ParDelete 
**
**      INPUT: pointer to string
**
**      RETURNS: modified string
**
**
*/ 

INT4 ParDeleteF (char *strfmt, ...)
{
  char parName[200];
  va_list args;
  va_start(args,strfmt);
  vsprintf(parName,strfmt,args);
  va_end(args);
  return ParDelete(parName);
}


/**API* ParDefObject **********************************************************
**
**     Inserts or modifies an "object" parameter.
**
**	INPUT:	    parameter name [R]
**		    parameter value [R]
**	        IMPLICIT:
**                  parTable (PARoTABLE *) [W]
**
**	RETURNS:    1 if parameter was found
**		    0 if it has been inserted
**                  invalid value: e__parnottype <parameter_name, type>+
*/ 
   
INT4 ParDefObject (char *parName, void *object)
{
  PARo  *par;

  par = ParGetWrite (parName, parTable);
  return ParODefObject (par, object);
}




/**API* ParGetNum *************************************************************
**
**	Retrieves the value of a "number" parameter.
**
**	INPUT:	    parameter name [R]
**	        IMPLICIT:
**
**	RETURNS:    value if parameter found
**                  0 if not (default value)
*/ 
   
INT4 ParGetNum (char *parName)
{
  PARo *par;
  
  if ((par = ParGetRead (parName, parTable)))
    return ParOGetNum (par);
  else
    return 0;
}


/**API* ParGetBool ************************************************************
**
**	Retrieves the value of a "boolean" parameter.
**      parameter may be a number or string ("1", "yes", "ja", "on").
**
**	INPUT:	    parameter name [R]
**	        IMPLICIT:
**
**	RETURNS:    value if parameter found
**                  0 if not
*/ 
   
INT4 ParGetBool (char *parName)
{
  PARo *par;

  if ((par = ParGetRead (parName, parTable)))
    return ParOGetBool (par);
  else
    return 0;
}


/**API* ParGetReal ************************************************************
**
**	Retrieves the value of a "real" parameter.
**
**	INPUT:	    parameter name [R]
**	        IMPLICIT:
**
**	RETURNS:    value if parameter found
**                  0 if not (default value)
*/ 
   
float ParGetReal (char *parName)
{
  PARo *par;

  if ((par = ParGetRead (parName, parTable)))
    return ParOGetReal (par);
  else
    return 0;
}

   
/**API* ParGetStr *************************************************************
**
**	Retrieves the value of a "string" parameter.
**
**	INPUT:	    parameter name [R]
**	        IMPLICIT:
**
**	RETURNS:    value if parameter found
**                  address to empty string if not
*/ 
   
char *ParGetStr (char *parName)
{
  static char nullString[1]="";
  PARo *par;

  if ((par = ParGetRead (parName, parTable)))
    return ParOGetStr (par);
  else
    return nullString;
}
   
/**API* ParGetFunction ********************************************************
**
**	Retrieves the value of a "function" parameter.
**
**	INPUT:	    parameter name [R]
**	        IMPLICIT:
**
**	RETURNS:    value if parameter found
**                  NULL if not
*/ 
   
INT4 (*ParGetFunction (char *parName))()
{
  PARo *par;

  if ((par = ParGetRead (parName, parTable)))
    return ParOGetFunction (par);
  else
    return NULL;
}

/**API* ParGetObject **********************************************************
**
**	Retrieves the value of an "object" parameter.
**
**	INPUT:	    parameter name [R]
**	        IMPLICIT:
**
**	RETURNS:    value if parameter found
**                  NULL if not
*/ 
   
void *ParGetObject (char *parName)
{
  PARo *par;

  if ((par = ParGetRead (parName, parTable)))
    return ParOGetObject (par);
  else
    return NULL;
}



/**api* ParIsModified *********************************************************
**
**	returns TRUE if any of the parameters was changed since reading into
**      memory
**
**	INPUT:
**	        IMPLICIT:
**		    table (PARoTABLE *) [R]
**
**	RETURNS:    TRUE if at least one parameter is changed
**                  FALSE if not
*/ 

INT4 ParIsModified ()
{
  return parTable->isModified;
}

/**api* ParIsDefined **********************************************************
**
**	returns TRUE if the parameter exists already
**
**	INPUT:
**	        IMPLICIT:
**		    parTable (PARoTABLE *) [R]
**
**	RETURNS:    TRUE if exists
**                  FALSE if not
*/ 

INT4 ParIsDefined (char *parName)
{
  return ParGetRead (parName, parTable) ? 1 : 0;
}



/**api*************************************************************************
**
**	functions that get single descriptive values in the parameter object
**
**	INPUT:      address of parameter object [W]
**                  ...
**	        IMPLICIT:
**
**	RETURNS: 
*/ 


char *ParOGetHelpTopic (PARo *par)
{
  return par->helpTopic;
}

char *ParOGetComment (PARo *par)
{
  return par->comment;
}

char *ParOGetKey (PARo *par)
{
  return par->key;
}

char *ParOCharSet (PARo *par)
{
  return par->parType ? par->parType->charSet : NULL;
}

INT4 ParOGetNum (PARo *par)
{
  /* convert string to integer */
  if (par->type & PARxSTR && !(par->type & PARxNUM)) {
    par->num = atoi (par->str);
    par->type = par->type | PARxNUM;
  }
  if (!(par->type & PARxNUM || par->type & PARxBOOL))
    _ErrExit3 (e__parnottype, par->name, "number");  
  return par->num;
}

INT4 ParOGetBool (PARo *par)
{
  /* a boolean may be stored as a string parameter: "yes", "ja", "on" */
  if (par->type == PARxSTR) {
    if (strchr ("yj", tolower (par->str[0])) || 
	strchr ("n", tolower (par->str[1]))) {
      par->num = 1;
      par->type = par->type | PARxBOOL;
  }
  else if (!(par->type & PARxNUM || par->type & PARxBOOL))
    _ErrExit3 (e__parnottype, par->name, "number/boolean/string");  
  }
  return par->num;
}

float ParOGetReal (PARo *par)
{
  if (!(par->type & PARxREAL))
    _ErrExit3 (e__parnottype, par->name, "real");  
  return par->real;
}

char *ParOGetStr (PARo *par)
{
  char   s[20];

  if (!(par->type & PARxSTR) && par->type & PARxNUM) {
    sprintf (s, "%d", par->num);
    par->type = par->type | PARxSTR;
    ParODefStr (par, s);
  }
  else if (!(par->type & PARxSTR))
    _ErrExit3 (e__parnottype, par->name, "string");  
  return par->str;
}

INT4 (*ParOGetFunction (PARo *par))()
{
  if (par->type != PARxFUNCTION)
    _ErrExit3 (e__parnottype, par->name, "function");  
  return par->function;
}

void *ParOGetObject (PARo *par)
{
  if (par->type != PARxOBJECT)
    _ErrExit3 (e__parnottype, par->name, "object");  
  return par->object;
}


INT4 ParOGetType (PARo *par)
{
  return par->type;
}



/**api*************************************************************************
**
**	functions that set single descriptive values in the parameter object
**
**	INPUT:      address of parameter object [W]
**                  ...
**	        IMPLICIT:
**
**	RETURNS: 
*/ 


void ParODefHelpTopic (PARo *par, char *helpTopic)
{
  par->helpTopic = helpTopic;
}

void ParODefComment (PARo *par, char *comment)
{
  par->comment = comment;
}

void ParODefKey (PARo *par, char *key)
{
  par->key = key;
}

void ParODefCharSet (PARo *par, char *charSet)
{
  if (par->parType)
    par->parType->charSet = charSet;
}

void ParODefType (PARo *par, char *parTypeName)
{
  LstFirstNamed ((void **) &parTable->parType, parTypeName);
  par->parType = parTable->parType;
}


INT4 ParODefNum (PARo *par, INT4 num)
{
 /* _ErrRet (ParOCheckNum (par, num));  */

  if (par->isLocked)
    return 0;

  if (par->type & PARxSTR)
    par->type = PARxNUM; /* forces implicit conversion next time 
			    accessed as str */
  else
    par->type |= PARxNUM;

  if (!par->num != num) 
    parTable->isModified = 1;  /* record change */
  par->num = num;
  return 1;
}

INT4 ParODefStr (PARo *par, char *str)
{
  int rv;

  if (par->isLocked)
    return 0;
  if (!str)
    return 0;

  if (par->type == PARxNUM){ /* string should be tested if contains digits */
    return ParODefNum (par, atoi (str));
  }

  if (par->type == PARxBOOL)
    return ParODefBool (par, str);

  if (par->type & PARxNUM)
    par->type = PARxSTR; /* forces implicit conversion next time 
			    accessed as num */
  else
    par->type |= PARxSTR;

  if (par->set && *par->set) {
    char com[200];
    sprintf (com, par->set, str);
    IcaEval (NULL, com);
  }
  rv = ParOCheckStr (par, str); 
  _ErrRet (rv); 

  if (!par->str || strcmp (par->str, str)) { /** record change */
    parTable->isModified = 1;
    if (par->str && !OddIsInDepot (par->str))
      free (par->str);  /* delete ...new string could be larger */
    par->str = (char *) malloc (strlen (str) + 1); 
    strcpy (par->str, str);
  }
  return 1;
}

INT4 ParODefReal (PARo *par, float real)
{
  if (par->isLocked)
    return 0;
  par->type |= PARxREAL;
  par->real = real;
  return 1;
}

INT4 ParODefFunction (PARo *par, INT4 (*function)())
{
  if (par->isLocked)
    return 0;
  par->type |= PARxFUNCTION;
  par->function = function;
  return 1;
}

INT4 ParODefObject (PARo *par, void *object)
{
  if (par->isLocked)
    return 0;
  par->type = PARxOBJECT;
  par->object = object;
  return 1;
}

static INT4 ParODefBool (PARo *par, char *str)
{
  INT4 val;

  if (par->isLocked)
    return 0;
  if (strchr ("yj", tolower (str[0]))) /* yes, ja */
    val = 1;
  else if (strchr ("n", tolower (str[1]))) /* on */
    val = 1;
  else
    val = 0;

  par->type |= PARxBOOL;

  if (!par->num != val) 
    parTable->isModified = 1;  /* record change */
  ParODefNum (par, val);
  return 1;
}


/**API* ParSetVolatile ********************************************************
**
**	Sets the parameter so that it does not get saved by ParSave.
**
**	INPUT:      parameter name [R]
**	        IMPLICIT:
**
**	RETURNS: 
*/ 

void ParSetVolatile (char *parName)
{
  PARo *par;

  if ((par = ParGetRead (parName, parTable)))
    par->isVolatile = 1;
}

/**API* ParLock ***************************************************************
**
**	Locks a parameter to prevent modification until unlocked again.
**
**	INPUT:      parameter name [R]
**	        IMPLICIT:
**
**	RETURNS: 
*/ 

void ParLock (char *parName)
{
  PARo *par;

  if ((par = ParGetRead (parName, parTable)))
    par->isLocked = 1;
}

/**API* ParUnlock *************************************************************
**
**	Unlocks a parameter.
**
**	INPUT:      parameter name [R]
**	        IMPLICIT:
**
**	RETURNS: 
*/ 

void ParUnlock (char *parName)
{
  PARo *par;

  if ((par = ParGetRead (parName, parTable)))
    par->isLocked = 0;
}


/**api*************************************************************************
**
**	checks a 'string' value
**
**	INPUT:      parameter object [R]
**                  string [R]
**	        IMPLICIT:
**
**	RETURNS: 
**                 1 if value OK
**                 e__parnottype <parName, type> +
**                 e__checkfunctionerr <>
**                 e__strnotinset <num> +
**                 e__charnotallowed <char> +
*/ 

int ParOCheckStr (PARo *par, char *str)
{
  PARoTYPE *parType;
  int      isFound=0, len, k;

  if (!(par->type & PARxSTR || par->type & PARxBOOL))  /* parameter type */
    _ErrRet3 (e__parnottype, par->name, "string");  
  
  if ((parType = par->parType)) { /* now use parType object... */
    len = strlen (str);

    if (parType->charSet)   /* test character set */
      for (k=0; k < len; k++)
	if (!strchr (parType->charSet, str[k]))
	   _ErrRet3 (e__charnotallowed, str[k], par->name);

    if (parType->max) {
      if (len > parType->max || len < parType->min)   /* string length */
	_ErrRet3 (e__invalstr, parType->min, parType->max);
    }    

    if (parType->check)  /* user check function */
      if (!(*parType->check) (str))
	return e__checkerr;
  }
  return 1;
}

/**api*************************************************************************
**
**	checks a 'num' value
**
**	INPUT:      parameter object [R]
**                  number [R]
**	        IMPLICIT:
**
**	RETURNS: 
**                 1 if value OK
**                 e__parnottype <parName, type> +
**                 e__checkfunctionerr <>
**                 e__numnotinset <num> +
*/ 

int ParOCheckNum (PARo *par, int num)
{
  PARoTYPE *parType;
  int      isFound=0;

  if (par->type != PARxNUM && par->type != PARxBOOL)  /* parameter type */
    _ErrRet3 (e__parnottype, par->name, "number");  
  

  if ((parType = par->parType)) {
    if (num > parType->max || num < parType->min)   /* number range */
      _ErrRet3 (e__invalnumber, parType->min, parType->max);
    
    if (parType->check)  /* user check function */
      if (!(*parType->check) (num))
	return e__checkerr;
  }	  
  return 1;
} 

/**api*************************************************************************
**
**	checks a 'real' value
**
**	INPUT:      parameter object [R]
**                  real [R]
**	        IMPLICIT:
**
**	RETURNS: 
**                 1 if value OK
**                 e__parnottype <parName, type> +
**                 e__checkfunctionerr <>
**                 e__realnotinset <real> +
*/ 

int ParOCheckReal (PARo *par, float real)
{
  PARoTYPE *parType;
  int      isFound=0;

  if (par->type != PARxREAL)  /* parameter type */
    _ErrRet3 (e__parnottype, par->name, "real");  
  
  if ((parType = par->parType)) {
    if (real > parType->maxReal || real < parType->minReal)   /* range */
      _ErrRet5 (e__realnotinrange, real, parType->minReal, parType->maxReal, 
		par->name);
    
    if (!parType->check)  /* user check function */
      if (!(*parType->check) (real))
	return e__checkerr;
  }
  return 1;
} 


/**api*************************************************************************
**
**	checks a 'function' value
**
**	INPUT:      parameter object [R]
**                  function pionter [R]
**	        IMPLICIT:
**
**	RETURNS: 
**                 1 if value OK
**                 e__parnottype <parName, type> +
**                 e__checkfunctionerr <>
**                 e__functionnotinset <str> +
*/ 

int ParOCheckFunction (PARo *par, INT4 (*function) ())
{
  PARoTYPE *parType;
  int      isFound=0;

  if (par->type != PARxFUNCTION)  /* parameter type */
    _ErrRet3 (e__parnottype, par->name, "function");  
  
  if ((parType = par->parType)) {
    if (!parType->check)  /* user check function */
      if (!(*parType->check) (function))
	return e__checkerr;
  }

  return 1;
} 




/**api* ParSave ***************************************************************
**
**	saves parameters in ODD-file;
**
**	INPUT:      file name of output file [R]
**	        IMPLICIT:
**
**	RETURNS: 
*/ 
   
void ParSave (char *fileName)
{
  FILE *file;
  INT4  errCode, context;
  
  file  = (FILE *) FilOpenW (fileName, &errCode);
  _ErrExit2 (errCode, fileName);
  for (context=0; ParPrintNext (file, &context, "odd");)
    ;
  fclose (file);
}

/**api* ParIsVolatileName *****************************************************
**
**	Analyses if the name has the 'volatile' mark at the end, removes it 
**      and sets the parameter volatile.
**
**	INPUT:	    parameter name [W]
**	        IMPLICIT:
**
**	RETURNS:    1 or 0
*/ 
  
Int4 ParIsVolatileName (char *name)
{
  Int4 len=strlen(name);
  if (name[len-1] == '~') {
    name[len-1] = '\0';
    ParSetVolatile (name);
  }
}

 
/**api* ParRead ***************************************************************
**
**	reads user defined parameters from SRSPARAM in either the user's home
**      directory, or if it does not exist there in SRSDAT
**
**	INPUT:	    file of input file [R]
**	        IMPLICIT:
**
**	RETURNS:    1 if successful 
**                  e__filnotok <fileName> 
*/ 
  
INT4 ParRead (char *fileName)
{

  STRv  str=StrNew ();
  FILo  file;
  INT4  num, rv;
  float real;
  char  s[PARxXSTR+1], parName[PARxXNAM+1];

  rv = FilUOpen (&file, fileName, PARxXSTR+20, 0);
  _ErrRet (rv);
  while (!FilEof (&file)) {
    if (sscanf (file.ln, "#par /name=%[^ /] /num=%d", parName, &num) == 2) {
      ParIsVolatileName (parName);
      ParDefNum (parName, num);
    }
    else if (sscanf (file.ln, "#par /name=%[^ /] /bool=%d", parName, &num)==2){
      ParIsVolatileName (parName);
      ParDefBool (parName, num);
    }
    else if (sscanf (file.ln, "#par /name=%[^ /] /real=%f", parName,&real)==2){
      ParIsVolatileName (parName);
      ParDefReal (parName, real);
    }
    else if ((rv = (sscanf(file.ln, "#par /name=%[^ /] /str=%[^\n]", 
			  parName, s))) >= 1) {
      StrSetS (&str, s);
      StrDecode (&str);
      ParIsVolatileName (parName);
      if (rv == 2)
	ParDefStr (parName, _Str(str));
      else
	ParDefStr (parName, "");
    }
    else
      _ErrMsg2 (e__novalformat, file.ln);
    FilURead (&file);
  }
  FilUClose (&file); 
  return 1;
}


/**api* ParPrintNext **********************************************************
**
**	prints the next (or first if context=0) parameter in various formats;
**
**	INPUT:	    output file [W]
**                  address of context [W]
**	        IMPLICIT:
**
**	RETURNS:    1 if successful 
**                  0 if last parameter was reached
*/ 

INT4 ParPrintNext (FILE *file, INT4 *context, char *option)
{
  static PARo *par=NULL;
  static STRv str=NULL;

  if (!str)
    str = StrNew ();

  if (!*context || !par) {
    par = parTable->par;
    LstFirst ((void **) &par);
    *context = 1;
  }
  else if (!LstNext ((void **) &par)) {
    *context = 0; /* list is exhausted */
    par = NULL;
    return 0;
  }

  while (1) {

    if (par->isVolatile) 
      return 1;
    else if (par->type & PARxBOOL ) {
      fprintf (file, "#par /name=%s /bool=%d\n", par->name, par->num);
      break;
    }
    else if (par->type & PARxSTR ) {
      StrSetS (&str, par->str);
      StrEncode (&str);
      fprintf (file, "#par /name=%s /str=%s\n", par->name, _Str (str));
      break;
    }
    else if (par->type & PARxNUM  ) {
      fprintf (file, "#par /name=%s /num=%d\n", par->name, par->num);
      break;
    }
    else if (par->type & PARxREAL ) {
      fprintf (file, "#par /name=%s /real=%f\n", par->name, par->real);
      break;
    }
    else {
      if (!LstNext ((void **) &par)) {
	*context = NULL;
	par = NULL;
	return 0;
      }
    }
  }
  return 1;
}




, par->str);
      StrEncode (&str);
      fprintf (file, "#par /name=%s /str=%s\n", par->name, _Str (str));
      break;
    }
    else if (par->type & PARxNUM  ) {
      fprintf (file, "#par /name=%s /num=%d\n", par->name, par->num);
      break;
    }
    else if (par->type & PARxREAL ) {
      fprintf (file, "#par /name=%s /real=%f\n", par->nsrs/src/par.h
**
**    $RCSfile: par.h,v $
**    $Revision: 1.2 $
**    $Date: 1996/07/14 16:21:24 $
**    $Author: etzold $
**
**    $Locker:  $
**    $State: Exp $
**
*/

enum par_type {PARxNEW=0, PARxSTR=1, PARxNUM=2, PARxREAL=4, PARxFUNCTION=8, 
		 PARxBOOL=16, PARxOBJECT=32};

#define PARxPARNOTDEF 100000
#define PARxPARNULL   99999

#define PARxON        1
#define PARxOFF       0

#ifndef _PARoTABLE 
typedef struct PARoLIST *dummytointroducestructtagPARoLIST;
#endif

#ifndef PARoTABLE 
typedef struct PARoTABLE *dummytointroducestructtagPARoTABLE;
#endif

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of exported functions
*/


    /* acting on the parameter table */

void ParInit (struct PARoLIST *parList);
INT4 ParIsModified ();
void ParDumpAll ();
INT4 ParRead (char *fileName);
void ParSave (char *fileName);
INT4 ParPrintNext (FILE *file, INT4 *context, char *option);
INT4 ParDelete (char *parName);
INT4 ParDeleteMatch (char *reStr);

struct PARoTABLE *ParSetTable (char *name, char *upName, char *option);
void               ParDeleteTable (char *name);
struct PARoTABLE *ParUnsetTable ();
struct PARoTABLE *ParGetTable (char *name);

    /* define parameters */

INT4 ParDefNum (char *par_nm, INT4 num);
INT4 ParDefBool (char *par_nm, INT4 num);
INT4 ParDefReal (char *par_nm, float real);
INT4 ParDefStr (char *par_nm, char *str);
INT4 ParDefFunction (char *par_nm, INT4 (*function) ());
INT4 ParDefObject (char *par_nm, void *object);

    /* retrieve parameter values */

INT4 ParGetNum (char *par_nm);
INT4 ParGetBool (char *parName);
float ParGetReal (char *par_nm);
char *ParGetStr (char *par_nm);
INT4 (*ParGetFunction (char *par_nm))();
void *ParGetObject (char *par_nm);

INT4 ParIsDefinedF(char *strfmt, ...);
INT4 ParGetNumF(char *strfmt, ...);
INT4 ParGetBoolF(char *strfmt, ...);
char *ParGetStrF(char *strfmt, ...);
INT4 ParDeleteF (char *strfmt, ...);
INT4 ParDefStrF (char *parName, char *strfmt, ...);

    /* get a pointer to parameter of various types */

struct PARo *ParGetRead (char *parName, struct PARoTABLE *table);
struct PARo *ParGetWrite (char *parName, struct PARoTABLE *table);
struct PARo *ParFind (char *parName);
struct PARo *ParGetDefault (char *parName);
struct PARo *ParNextValue (struct PARo *par, INT4 *context);
struct PARo *ParGetNeighbour (char *parName);

   /* info from parameter using parameter pointer */

INT4 ParOGetState (struct PARo *par);
char *ParOGetHelpTopic (struct PARo *par);
char *ParOGetComment (struct PARo *par);
char *ParOGetKey (struct PARo *par);
char *ParOGetCharSet (struct PARo *par);
INT4 ParOGetType (struct PARo *par);

INT4 ParOGetNum (struct PARo *par);
char *ParOGetStr (struct PARo *par);
float ParOGetReal (struct PARo *par);
INT4 (*ParOGetFunction (struct PARo *par))();
void *ParOGetObject (struct PARo *par);

   /* manipulate parameter using parameter pointer */

void ParODefState (struct PARo *par, INT4 state);
void ParODefHelpTopic (struct PARo *par, char *helpTopic);
void ParODefComment (struct PARo *par, char *comment);
void ParODefKey (struct PARo *par, char *key);
void ParODefCharSet (struct PARo *par, char *charSet);
void ParODefType (struct PARo *par, char *parTypeName);
INT4 ParODefNeighbour (struct PARo *par, char *parName);
void ParODefValue (struct PARo *par, struct  PARo *valPar);

INT4 ParODefNum (struct PARo *par, INT4 num);
INT4 ParODefStr (struct PARo *par, char *str);
INT4 ParODefReal (struct PARo *par, float real);
INT4 ParODefFunction (struct PARo *par, INT4 (*function) ());
INT4 ParODefObject (struct PARo *par, void *object);

    /* others */

INT4 ParIsDefined (char *par_nm);
void ParUnlock (char *parName);
void ParLock (char *parName);
void ParSetVolatile (char *parName);
ghbour (struct PARo *par, char *parName);
void ParODefValue (struct PARo *par, struct  PARo *valPar);

INT4 ParODefNum (struct PARo *par, INT4 num);
INT4 ParODefStr (struct PARo *par, char *str);
INT4 ParODefReal (struct PARo *par, float real);
INT4 ParODefFunction (struct PARo srs/src/print.c
#include <stdarg.h>
#include <stdio.h>

#include "def.h"
#include "print.h"
#include "oldlistbuf.h"
#include "string.h"

/*****************************************************************
** IMPLEMENTATION utilities
*/

PRINTv	Active[20];
PRINTv* LastActive=Active;

PRINTv Printer=NULL;

void NoFormat(PRINTv out, char command, ...) {
    /* command does nothing */
}

void PushPrinter() { *(LastActive++)=Printer; }
void PopPrinter() { Printer=*(--LastActive); }

PRINTv CopyPrinter(PRINTv p) { p->usage++; return p; }

/*****************************************************************
** API functions - no context
*/

void xPrintBuf(PRINTv out, BYTE* buf, int n) {
    do {
	int want=n;
	BYTE* s=call(out->book)(out, &want); n-=want;
	while (want--) *s++=*buf++;
    } while (n);
}

void xPrintClose(PRINTv* out) {
    PRINTv p=*out;
    if (!--p->usage) {call (p->close) (p, NULL, 0); }
    *out=NULL;
}

void xPrintBufClose(PRINTv* out, BYTE* s, int n) {
    PRINTv p=*out;
    if (!--p->usage) call (p->close) (p, s, n); 
    *out=NULL;
}

void xPrintFormat(PRINTv out, char comm, ...) {
    va_list l;
    va_start(l, comm);
    call (out->format)(out, comm, l);
    va_end(l);
}

void xPrintInt(PRINTv out, int i) {
   char buf[20]; char* p=buf;
   xPrintFormat(out, '[');
   sprintf(buf, "%d", i);
   while (*p) xPrint(out, *p++);
   xPrintFormat(out, ']');
}

void xPrintS(PRINTv out, char* s) {
   xPrintFormat(out, '[');
   xPrintBuf(out, s, strlen(s));
   xPrintFormat(out, ']');
}

void xPrintStr(PRINTv out, STRv s) {
    xPrintS(out, Str(s));
}

/*****************************************************************
** API functions - contextual
*/

PRINTv PrintGet() { Printer->usage++; return Printer; }

void PrintClose() {
    xPrintClose(&Printer);
    PopPrinter();
}

void PrintBufClose(BYTE* s, int n) {
    xPrintBufClose(&Printer, s, n);
    PopPrinter();
}

void PrintBuf(BYTE* buf, int n) { xPrintBuf(Printer, buf, n); }
void PrintInt(int i)		{ xPrintInt(Printer, i); }
void PrintS(char* s)	        { xPrintS(Printer, s); }
void PrintStr(STRv s)           { xPrintStr(Printer, s); }

void PrintFormat(char comm, ...) {
    va_list l;
    va_start(l, comm);
    call (Printer->format)(Printer, comm, l);
    va_end(l);
}

/************************************************************
** output to STRING
*/

/* string writer */

#define PRINT_BUF_DIM 256

typedef struct PRINToBUF {
    BYTE	buf[PRINT_BUF_DIM];
    struct PRINToBUF* next;
} PRINToBUF;

/* buffered string writer */
typedef struct PRINToSTR {
    PRINTo     head;
    STRv*       dest;
    BYTE*	pos;
    BYTE*	stop;
    PRINToBUF* beg;
    PRINToBUF* buf;
    int		len;
} PRINToSTR;


/************************************************************
** BUFFERED output to string
*/

void PrintBufOverflow(PRINToSTR* out) {
    /* allocate new buffer */
    BYTE* s;
    PRINToBUF* buf=typeAlloc(PRINToBUF);
    buf->next=NULL;
    out->buf->next=buf;
    out->buf=buf;
    s=buf->buf; 
    out->pos=s;
    out->stop=s+PRINT_BUF_DIM;
    out->len+=PRINT_BUF_DIM;
}

void StrPrintBufPut(PRINToSTR* out, BYTE c) {
    if (out->pos!=out->stop) *(out->pos++)=c;
    else {
	PrintBufOverflow(out);
	*(out->pos++)=c;
    }
}

BYTE* StrPrintBufBook(struct PRINToSTR* out, int* n) {
    BYTE* s=out->pos;
    if (s+*n<out->stop) { out->pos+=*n; return s; }
    else if (s!=out->stop) {
	/* ask to fill buffer */
	*n=out->stop-s;
	out->pos=out->stop;
	return s;
    }
    else {
	PrintBufOverflow(out);
	return StrPrintBufBook(out, n);
    }
}

void StrPrintBufClose(struct PRINToSTR* out, BYTE* src, int n) {
    int lastLen=out->pos - out->buf->buf;
    int dlen=out->len+lastLen;
    STRv val=*out->dest;
    BYTE* s;
    PRINToBUF *buf, *next;
    /* reallocate the string */
    if (val) {
	int len=val->len;
	StrBufChange(&val,len,len+dlen);
	s=val->arr+len;
    }
    else {
	val=StrBufNew(dlen);
	val->len=dlen;
	s=val->arr;
	*(s+dlen)='\0';
    }
    *out->dest=val;
    /* now copy the BYTEs from the buffers */
    buf=out->beg;
    while ((next=buf->next)) {
	memcpy(s, buf->buf, PRINT_BUF_DIM);
	free(buf); buf=next;
	s+=PRINT_BUF_DIM;
    }
    /* copy last (not full) buffer */
    memcpy(s, buf->buf, lastLen);
    free(buf);
    /* kill myself */
    free(out);
}

/***************************************************************
** UNBUFFERED output to string
*/

void PrintStrOverflow(PRINToSTR* out) {
    /* string space exceeded: go to buffered management */
    BYTE* s;
    PRINToBUF* buf;
    STRv val=*out->dest;
    if (val) val->len=(char *)out->pos-val->arr;
    out->head.put=(Putter)StrPrintBufPut;
    out->head.book=(Booker)StrPrintBufBook;
    out->head.close=(Closer)StrPrintBufClose;
    buf=typeAlloc(PRINToBUF);
    buf->next=NULL;
    out->beg=out->buf=buf;
    s=buf->buf;
    out->pos=s;
    out->stop=s+PRINT_BUF_DIM;    
    out->len=0;
}

void PrintStrPut(PRINToSTR* out, BYTE c) {
    if (out->pos!=out->stop) *(out->pos++)=c;
    else {
	PrintStrOverflow(out);
	*(out->pos++)=c;
    }
}

BYTE* PrintStrBook(struct PRINToSTR* out, int* n) {
    BYTE* s=out->pos;
    if (s+*n<out->stop) { out->pos+=*n; return s; }
    else if (s!=out->stop && *out->dest) {
	/* ask to fill string */
	*n=out->stop-s;
	out->pos=out->stop;
	return s;
    }
    else {
	PrintStrOverflow(out);
	return StrPrintBufBook(out, n);
    }
}

void PrintStrClose(struct PRINToSTR* out, BYTE* src, int n) {
    BYTE* s=out->pos;
    STRv val=*out->dest;
    if (val) {
	int len;
	*s='\0'; len=val->len=(char *)s-val->arr;
	StrBufChange(&val, len, len+n);
	memcpy(val->arr+len, src, n);
    } 
    else { 
	val=StrBufNew(n); 
	val->len=n; 
	memcpy(val->arr, src, n);
    }
    *out->dest=val;
    free(out);
}

void PrintOpenStr(STRv* out) {
    PRINToSTR* s=typeAlloc(PRINToSTR);
    STRv val=*out;
    PushPrinter();
    Printer=(PRINTv)s;
    s->head.usage=1;
    s->dest=out;
    s->head.put=(Putter)PrintStrPut;
    s->head.book=(Booker)PrintStrBook;
    s->head.close=(Closer)PrintStrClose;
    s->head.format=(Formatter)NoFormat;
    if (val->usage==1 && val->len<val->dim) {
	s->pos=val->arr;
	s->stop=val->arr+val->dim;
    }
    else {
	StrDel(val); *out=NULL;
	s->pos=s->stop=NULL;
    }
}

/************************************************************
** output to FILE
*/

/* file writer */

#define PRINT_FILE_DIM 256

typedef struct PRINToFILE {
    PRINTo    head;
    FILE*      dest;
    BYTE       buf[PRINT_FILE_DIM];
    int	       num;
} PRINToFILE;


void PrintFilePut(struct PRINToFILE* out, BYTE c) {
    if (out->num) { 
	fwrite(out->buf, 1, out->num, out->dest);
	out->num=0;
    }
    putc(c, out->dest);
}

BYTE* PrintFileBook(struct PRINToFILE* out, int* n) {
    if (out->num) fwrite(out->buf, 1, out->num, out->dest);
    if ((out->num=*n)>PRINT_FILE_DIM) out->num=*n=PRINT_FILE_DIM;
    return out->buf;
}

void PrintFileClose(struct PRINToFILE* out, BYTE* src, int n) {
    if (out->num) fwrite(out->buf, 1, out->num, out->dest);
    fwrite(src, 1, n, out->dest);
    fclose(out->dest);
    free(out);   
}

void PrintOpenFileImpl(FILE* file) {
    PRINToFILE* s=typeAlloc(PRINToFILE);
    PushPrinter();
    Printer=(PRINTv)s;
    s->head.usage=1;
    s->dest=file;
    s->head.put=(Putter)PrintFilePut;
    s->head.book=(Booker)PrintFileBook;
    s->head.close=(Closer)PrintFileClose;
    s->head.format=(Formatter)NoFormat;
    s->num=0;
}

void PrintOpenFile(char* fileName) {
    PrintOpenFileImpl(fopen(fileName, "wb"));
}

void PrintStdoutClose(struct PRINToFILE* out, BYTE* src, int n) {
    if (out->num) fwrite(out->buf, 1, out->num, out->dest);
    fwrite(src, 1, n, out->dest);
    free(out);   
}

void PrintOpen() {
   PrintOpenFileImpl(stdout);
   Printer->close=(Closer)PrintStdoutClose;
}

/***************************************************************
** PRETTY PRINTING filter
*/

/* parses the result, pretty-printing it 
** breakAt suggests where to cut lines (no indentation) 
** indent, unindent are matching pairs 
*/

#define PRETTY_MASK 0xFF
#define PRETTY_BUF_SIZE (PRETTY_MASK+1)
#define PRETTY_NOEND  0x7FFF
 
typedef struct PRETTYoBLOCK {
   LISTBUFv comm;
   struct PRETTYoBLOCK* up;
   int   end;
   BOOL  broken;
} PRETTYoBLOCK;

typedef struct PRETTYoCOMMAND {
   char command;
   int start;
   struct PRETTYoBLOCK* block;
} PRINToCOMMAND;

LISTBUFoINFO PrettyCommandListInfo = { sizeof(PRINToCOMMAND) };


/*CLASSoLISTBUF PrettyCommandListInfo= {
    sizeof(PRINToCOMMAND), 
    sizeof(LISTBUFo),
    DefElemCopier, 
    DefElemDeleter, 
    0, 
    NoHeadCopier, 
    NoHeadDeleter, 
    0 
};*/

typedef struct PRINToPRETTY {
    /* global state */
    PRINTo head;
    PRINTv out;
    char line[256];
    int width;
    int minWidth;
    int step;    
    /* state of delayed output */
    int last;
    int lastIndent;
    int lastBreak;
    struct PRETTYoBLOCK* lastBlock;
    /* state of current output */
    int pos;
    struct PRETTYoBLOCK* currBlock;
} PRINToPRETTY;

PRINToPRETTY* PrettyCx;

/**********************************************************************
** the real printing.. 
*/

void PrettyIndent() {
    int num=PrettyCx->lastIndent;
    PRINTv out=PrettyCx->out;
    PrettyCx->lastBreak=PrettyCx->last+PrettyWidth()-PrettyCx->lastIndent;
    call (out->put)(out, '\n');
    do {
	int want=num;
	BYTE* s=call(out->book)(out, &want); num-=want;
	while (want--) *s++=' ';
    } while (num);
}

void PrettyOut(PRINTv out, char c) {
    if (c=='\n') PrettyIndent();
    else call(out->put)(out, c);
}


/**********************************************************************
** INDENTATION MANAGEMENT 
*/

int PrettyWidth() {
    if (PrettyCx->width-PrettyCx->lastIndent<PrettyCx->minWidth) 
        return PrettyCx->lastIndent+PrettyCx->minWidth;
    else return PrettyCx->width;
} 

BOOL PrettyInNextLine() {
    int nextWidth=PrettyWidth()-PrettyCx->lastIndent;
    if (PrettyCx->lastBlock->end-PrettyCx->last<=nextWidth) {
	PrettyIndent();
	return TRUE;
    }
    return FALSE;
}

void PrettyCommand(char command) {
    switch(command) {
	case 'N': {
	    PrettyIndent();
	} break;	
	case 'I': {
	    PrettyCx->lastIndent += PrettyCx->step;
	} break;
	case 'U': {
	    PrettyCx->lastIndent -= PrettyCx->step;		  
	} break;
    }
}


/***********************************************************************
** BLOCK PRINTING MANAGEMENT 
*/

void PrettySkip(PRETTYoBLOCK* bl) {
    Iter comm=bl->comm;
    PRINToCOMMAND* curr;
    while (curr=ListBufNext(&bl->comm, &comm)) {
	if (curr->command=='[') {
	    PrettySkip(curr->block);
	    free(curr->block);
	}
    }
}

BOOL PrettyBlock() {
   PRETTYoBLOCK* bl=PrettyCx->lastBlock;
   PRINTv out=PrettyCx->out;
   BOOL doBreak=TRUE;
   if (!bl->broken) {
        if (bl->end==PRETTY_NOEND) {
            if (PrettyCx->pos<PrettyCx->lastBreak) return FALSE;
        }
        else if (bl->end<PrettyCx->lastBreak || PrettyInNextLine()) doBreak=FALSE;
   }
   if (doBreak) {
       PRINToCOMMAND* curr; Iter comm=NULL;
       bl->broken=TRUE;
       comm=ListBufFirst(&bl->comm);
       while (comm) {
           curr=(PRINToCOMMAND*)ListBufAt(&bl->comm,comm);
           while (PrettyCx->last!=curr->start) {
               if (PrettyCx->last==PrettyCx->pos) return FALSE;
               if (PrettyCx->last==PrettyCx->lastBreak) PrettyIndent();
               PrettyOut(out,PrettyCx->line[PrettyCx->last++&PRETTY_MASK]);
           }
           if (curr->command=='[') {
               PrettyCx->lastBlock=curr->block;
               ListBufRemove(&bl->comm, &comm);
               if (!PrettyBlock()) return FALSE;
           }
           else {
               PrettyCommand(curr->command);
               ListBufRemove(&bl->comm, &comm);
           }
       }
       /* finish block */
       while (PrettyCx->last!=bl->end) {
           if (PrettyCx->last==PrettyCx->pos) return FALSE;
           if (PrettyCx->last==PrettyCx->lastBreak) PrettyIndent();
           PrettyOut(out, PrettyCx->line[PrettyCx->last++&PRETTY_MASK]);
       }
   }
   else {
        /* if new block fits in PrettyCx->line, print it all */
        while (PrettyCx->last<bl->end)
            PrettyOut(out, PrettyCx->line[PrettyCx->last++&PRETTY_MASK]);
        PrettySkip(bl);
   }
   PrettyCx->lastBlock=bl->up;
   ListBufDelete(&bl->comm); free(bl);
   return TRUE;
}

/****************************************************************
** PRINTING API
*/

void PrintPrettyPut(struct PRINToPRETTY* out, BYTE c) {
   if (out->pos>out->last+out->width) {
       /* print line, formatting it */
       PrettyCx=out; while (PrettyBlock());
   }
   out->line[out->pos++&PRETTY_MASK]=c;
}

BYTE* PrintPrettyBook(struct PRINToPRETTY* out, int* n) {
   int avail, pos, toBufEnd;
   if (out->pos>out->last+out->width) {
       /* print line, formatting it */
       PrettyCx=out; while (PrettyBlock());
   }
   avail=(out->last-out->pos)&PRETTY_MASK;
   if (!avail) avail=PRETTY_BUF_SIZE;
   toBufEnd=PRETTY_BUF_SIZE-(out->pos&PRETTY_MASK);
   if (avail>toBufEnd) avail=toBufEnd;
   if (*n<=avail) {
       pos=out->pos;
       out->pos+=*n;
       return out->line+(pos&PRETTY_MASK); 
   }
   else {
      *n=avail;
      pos=out->pos; out->pos+=avail;
      return out->line+(pos&PRETTY_MASK);
   }
}

void PrintPrettyFlush(struct PRINToPRETTY* out);

void PrintPrettyFormat(struct PRINToPRETTY* out, char command, ...) {
    PRINToCOMMAND c;
    switch (command) {
	case ']': {
	    out->currBlock->end=out->pos;
	    out->currBlock=out->currBlock->up;
	} break;
	case '[': {
	    PRETTYoBLOCK* bl=typeAlloc(PRETTYoBLOCK);
	    bl->up=out->currBlock;
	    ListBufCreate(&bl->comm,&PrettyCommandListInfo,5);
	    bl->end=PRETTY_NOEND;
	    bl->broken=FALSE;
	    c.command=command;
	    c.start=out->pos;
	    c.block=bl;
	    if (out->currBlock) ListBufAppend(&out->currBlock->comm, &c);
	    out->currBlock=c.block;
	} break;
	case 'I':
	case 'U':
	case 'N': {
	    c.command=command;
	    c.start=out->pos;
	    if (out->currBlock) ListBufAppend(&out->currBlock->comm, &c);
	} break;
	case 'F': {
	    PrintPrettyFlush(out);
	    PrintPrettyFormat(out, '[');
	    out->lastBlock=out->currBlock;
	} break;
	default: {
	    va_list l;
	    va_start(l, command);
	    call(out->out->format)(out->out,command, l);
	    va_end(l); 
	}
    }
}

void PrintPrettyFlush(struct PRINToPRETTY* out) {
    PrettyCx=out;
    while (out->currBlock) PrintPrettyFormat(out,']');
    while (out->lastBlock) PrettyBlock();
}    

void PrintPrettyClose(struct PRINToPRETTY* out, BYTE* src, int n) {
    while (n) {
	int want=n;
	BYTE* s=PrintPrettyBook(out, &want);
	n-=want;
    } 
    /* flush now */
    xPrintBuf((PRINTv)out, src, n);
    PrintPrettyFlush(out);
    xPrintClose(&out->out);
    free(out);
}

PRINToPRETTY* PrintPrettyImpl(int width, int minWidth, int step) {
    PRINToPRETTY* p=PrettyCx=typeAlloc(PRINToPRETTY);
    p->head.usage=1;
    p->head.put=(Putter)PrintPrettyPut;
    p->head.book=(Booker)PrintPrettyBook;
    p->head.close=(Closer)PrintPrettyClose;
    p->head.format=(Formatter)PrintPrettyFormat;
    p->width=width;
    p->minWidth=minWidth;
    p->step=step;
    p->pos=0; p->currBlock=NULL; PrintPrettyFormat(p,'[');
    p->last=0; p->lastIndent=0; p->lastBreak=p->width;
    p->lastBlock=p->currBlock;
    return p;
}

void PrintPretty(int width, int minWidth, int step) {
    PRINToPRETTY* p=PrintPrettyImpl(width, minWidth, step);
    p->out=Printer;
    Printer=(PRINTv)p;
}

void xPrintPretty(PRINTv* out, int width, int minWidth, int step) {
    PRINToPRETTY* p=PrintPrettyImpl(width, minWidth, step);
    p->out=*out;
    *out=(PRINTv)p;
}

/************************************************************************/

[');
    p->last=0; p->lastIndent=0; p->lastBreak=p->width;
    p->lastBlock=p->currBlock;
    return p;
}

void PrintPretty(int width, int minWidth, int step) {
    PRINToPRETTY* p=PrintPrettyImpl(widsrs/src/print.h
#define _MYSTREAM_H

#include "strv.h"

typedef struct PRINTo* PRINTv;
typedef void  (*Putter)(PRINTv out, BYTE c);
typedef BYTE* (*Booker)(PRINTv out, int* n);
typedef void  (*Closer)(PRINTv out, BYTE* src, int n);
typedef void  (*Formatter)(PRINTv out, char command, ...);

typedef struct PRINTo {
    int		usage;
    Putter	put;
    Booker	book;
    Closer      close;
    Formatter   format;
} PRINTo;

extern PRINTv Printer;


/* PUBLIC OPERATIONS */

/* stream management operations */
void PrintOpen();
void PrintOpenStr(STRv* out);
void PrintOpenFile(char* fileName);

/* gets an external copy of the current stream  */
PRINTv PrintGet();

/* contextual operations */
void PrintPretty(int width, int minWidth, int step);
void PrintClose();
void PrintBufClose(BYTE* s, int n);

void PrintFormat(char command, ...);
#define Print(char) call(Printer->put)(Printer,char)
void PrintBuf(BYTE* buf, int n);
void PrintS(char* s);
void PrintStr(STRv s);
void PrintInt(int i);

/* not contextual operations */
void xPrintPretty(PRINTv* out, int width, int minWidth, int step);
void xPrintClose(PRINTv* out);
void xPrintBufClose(PRINTv* out, BYTE* s, int n);

void xPrintFormat(PRINTv out, char comm, ...);
#define xPrint(out, char) call(out->put)(out, char)
void xPrintBuf(PRINTv out, BYTE* buf, int n);
void xPrintInt(PRINTv out, int i);
void xPrintS(PRINTv out, char* s);
void xPrintStr(PRINTv out, STRv s);

#endif
n);
void PrintS(char* s);
void PrintStr(STRv s);
void PrintInt(int i);

/* not contextual operationssrs/src/query.c
char query_srs_ID[] = "$Id: query.c,v 1.12 1997/03/03 18:20:45 srs Exp $";
/*
**
**    $RCSfile: query.c,v $
**    $Revision: 1.12 $
**    $Date: 1997/03/03 18:20:45 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**             Unix port by Lukas Rosenthaler and Reinhard
**
**             Author: Gerald Schaefer
**                     EMBL, Meyerhofstrasse 1
**                     D-69012 Heidelberg, Germany
**                     Tel: 06221 387372  
**                     Email: schaefer@embl-heidelberg.de
**
**
**    Requires: 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <stdarg.h>

#include "message.h"
#include "futil.h"
#include "sm.h"
#include "lst.h"
#include "strv.h"
#include "par.h"
#include "regexp.h"
#include "ids.h"
#include "btree.h" 
#include "tm.h"
#include "library.h"
#include "id.h"
#include "entry.h"
#include "set.h"
#include "link.h"
#include "seqlib.h"
#include "query.h"
#include "icarus.h"
#include "icaarg.h"

#define _CONSTANTS
#define _SRS
#define _SLB
#define _INDEX
#include SRSINCLUDE



#ifdef sun
extern INT4 printf ();
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  constants and enums
*/


#define	QRYxXFIL    10     /* max no of indices opened */
#define	QRYxXSNLN   255
#define	QRYxXSYM    300	  /* max no of tokens in token list */
#define	QRYxXST	    3000  /* max no of characters allocated for token list */

enum qry_tok {QRYxKEY=1, QRYxNAME, QRYxINDEX, QRYxLPAR, QRYxRPAR, QRYxLBRK, 
              QRYxRBRK, QRYxOP};  /* all token types in the query */

#define QRYxSETOP   32		       /* log op have 6th + 4th bit set	    */
#define QRYxLINK    16		       /* link op have 5th + 4th bit set    */
#define QRYxLLINK   24
#define QRYxRLINK   25
#define QRYxOR      40


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Describes the external parameter context which determines the 
**  'behaviour' of this module.
*/

typedef struct QUERYoInfo {
  char doReport;
  char doListValues;
  char doRetrieve;
  char doListFromMatch;
  char isErrWrongField;
  char isWWW;
  Int4 valN;
  Int4 maxValN;
  Int4 minValN;
  Int4 printValN;
  Int4 printFirstValN;
  /* retrieving subentries */
  SLBo *subEntryLib;
  Int4 subEntryNo;
} QUERYoInfo;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of static functions
*/

INT4 QueryRangeSearchIndex (SLBo *lib, SLBoFIELD *field,
		       INT4 low, INT4 high, double lowReal, double highReal,
		       INT4 isReal, INT4 isLE, INT4 isRE, 
		       INT4 isFirst, INT4 isLast, SETo *set);

static INT4  QueryGet ( LIBoINDEX *openinx, SETo *set_p, char *key);
static INT4  QueryGetWild (LIBoINDEX *libIndex, SETo *set, char *str, 
		       char *wildStr, INT4 cmpLen);
static INT4  QryCollectIds (SETo *set, LIBoINDEX *libInx, BTRoREC *record, 
		      FIP idFip);
static INT4  QryGoGcgDots (FILo *file);
static INT4  QrySetSearch (char *s);
static INT4  QryKey (char *set_nm);
static INT4  QryRetrieveRange (LIBoINDEX *libIndex, SETo *set);
static INT4  QryIndexRetrieve (SLBo *lib, SRSoFLD *fieldType, SETo *set);
static SETo* QueryDo (char *s, char *name, INT4 isRecursive);
static SETo *QueryGetWholeLib (char *libName, SETo *set);

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  external, global and module wide variables
*/

static SETo*       resultSet = NULL;
static QUERYoInfo  queryInfoBuff;
static QUERYoInfo* queryInfo=&queryInfoBuff;
static INT4        (*print)(char *, ...);
void  (*QueryPrintValue)()=NULL;




/* prints information if result_name is a set */
/* returns: 1 if set, 0 if none               */
int dump_info(char *result_name)
{
  SETo *set;
  set = (SETo*) SetGet(result_name);
  if (set) {
      printf("*** Set \"%s\": total of %d entries ***\n",
             result_name ,set->n);
      return 1;
  }

  return 0;
}


#define NAMELEN  40
typedef char FILENAME[FILxXNAM+1];
#define MAXNAMES 20


void QuerySetPrintValue (void  (*func)()) {
  if (func)
    QueryPrintValue = func;
}



static INT4 qryprintferr (char *ln,...)
{
    va_list ap;

    va_start (ap, ln);
    vfprintf (stderr, ln, ap);
    va_end (ap);
    return 1;
}




/****** QueryGet **************************************************************
**
** 	searches a key in index and retrieves block of pointers;
** 
** 	INPUT:	    index object [W]
** 		    set object [W]
** 		    search value [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if key found
** 		    0 if not
*/ 
   
static INT4 QueryGet ( LIBoINDEX *libInx, SETo *set, char *value)
{
  BTRoREC *record;
  FIP     idFip;

  if ((record = BtrSearch (libInx->btree, value, &idFip, 0))) {
      QryCollectIds (set, libInx, record, idFip); 
    return 1;
  }
  else
    return 0;    
}


/****** QueryGetWild ************************************************************
**
** 	same as QryGet but takes keys with wildcard at end;
** 
** 	INPUT:	    address of index-descriptor [W]
** 		    address of set-descriptor [W]
** 		    address of search key [R]
**                  length of string before wildcard [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if key found
** 		    0 if not
*/ 
   
static INT4 QueryGetWild (LIBoINDEX *libInx, SETo *set, char *str, 
			  char *regexpStr, INT4 cmpLen)
{
  regexp  *regExp;
  BTRoREC *record;
  FIP     idFip;
  SETo    *setTmp;
  char    tmpStr[133];
  char	  setName[SETxXNAM+1];
  INT4    rv, maxValN, valCount=0;

  /*
  ** compile the regular expression and get the first record to start
  ** the search
  */

  regExp = RegComp (regexpStr);
  if (regExp == NULL)
    _ErrRet2 (e__regerror, "regcomp failure");
  if ((--cmpLen)) {  /* is 1 if wildcard is at begin ...set to 0 */
    if (!(record = BtrSearch (libInx->btree, str, &idFip, cmpLen))) {
      if (queryInfo->doListFromMatch)
	record = BtrRecordGet (libInx->btree, BTRxCURR);
      else
	return 0;
    }
  }
  else
    if (!(record = BtrRecordGet (libInx->btree, BTRxFIRST))) 
      return 0;
    
  /*
  ** now iterate over this and following records and try to match 
  ** regular expression 
  */
  
  while (1) {
    strcpy (tmpStr, record->str);
    if (FieldIsKeyConvert (libInx->field))
      SmEdit (tmpStr, SMxLOWCASE);
    
    if (!queryInfo->doListFromMatch &&
	(cmpLen) && memcmp (tmpStr, str, cmpLen) != 0) 
      break;  /* string begin not found any more */
    
    if (queryInfo->valN > queryInfo->printValN)
      break;

    if (queryInfo->doListFromMatch || RegExec (regExp, tmpStr)) {
      if (queryInfo->doRetrieve)
	setTmp = SetNew (setName, "temp");

      QryCollectIds (setTmp, libInx, record, idFip);

      if (queryInfo->doRetrieve) {
	rv = SetOp (set, setTmp, NULL, QRYxOR);
	SetDelete (setName);
	_ErrRet(rv);  
      }
    }
    idFip++;  /* next entries idFip...if ID index */
    if (!(record = BtrRecordGet (libInx->btree, BTRxNEXT)))
      break;  /* no more records */
    
  }
  free (regExp);
  return 1;
}



/****** QryCollectIds *********************************************************
**
** 	retrieves id-descriptor in index-file, accesses the ids-file
** 	and retrieves all ids;
** 
** 	INPUT:	    library index object [R]
** 		    value record [R]
** 		    set object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if success
*/ 
   
static INT4 QryCollectIds (SETo *set, LIBoINDEX *libInx, BTRoREC *record, 
			  FIP idFip)
{
  BTRoVALUE *valRec;
  INT4       n;

  if (queryInfo->doListValues) {
    n = record->r.value.idN;
    if (queryInfo->minValN <= n) {
      if (++queryInfo->valN >= queryInfo->printFirstValN) {
	if (QueryPrintValue) 
	  QueryPrintValue (LibName (libInx->lib), 
			   LibGetFieldName (libInx->field),
			   record->str, 
			   queryInfo->valN - queryInfo->printFirstValN+1, n);
	else
	  TemplPrint ("value", record->str, n);
      }
    }
    if (!queryInfo->doRetrieve)
      return;
  }

  set->idType = libInx->field->indexId;
  valRec = &record->r.value;
  _ErrStop (SetAlloc (set, valRec->idN, set->idType));
  IdsGet (libInx->idsFile, set->id_p, valRec->firstIdFip, valRec->idN);
  set->n = valRec->idN;

  if (queryInfo->subEntryNo) {
    IDoENTRY id, idSub;

    SetRealloc (set, 2, NULL); /* double in size - enough for subentry-ID */
    SetGetID (set, 1, &id);
    IdBuildSub (&idSub, &id, queryInfo->subEntryNo);
    set->n = 0;
    set->idType = idSub.idType;
    SetAddID (set, &idSub);
  }
  return 1;
}

/****** QryCheckNam ***********************************************************
**
** 	checks a name within an expression
** 
** 	INPUT:	    address of name [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if ok
** 		    0 if not
*/ 
   
INT4 QryCheckNam (char *nam)
{
  return SetTestName (nam);
}



INT4 QryReadName (SETo *set, char *ln)
{
  return 1;
}


   
INT4 QryReadNames (char *fil_nm, char *set_nm)
{
  return 1;
}






/**API* QrySetToList **********************************************************
**
**      Prints a set as a list of entry names which can be read again 
**      by "QryReadNames". The format is compatible with the 
**      GCG file of names. If the global boolean parameter "fosnWithPos" 
**      is set to 1 and the set contains subentry-IDs (sequence features) 
**      then the begin and end positions within the parent entry's sequence 
**      are added.
**      function prints to STDOUT unless a print function is defined using
**      the global parameter "printf".
**
**	INPUT:	    set name [R]
**	        IMPLICIT:
**
** 	RETURNS:    no of entries printed 
** 		    e__novalnam <name> +
*/ 
   
INT4 QrySetToList (char *set_nm)
{
  SETo     *set;
  ENTRYv   entry;
  IDoENTRY id;
  char     hexnumstr[20], source_nm[40], ln[133];
  INT4     k,(*print)(char*, ...)=(INT4(*)(char*,...))ParGetFunction("printf");

  if ((set = SetGet (set_nm)) == NULL)
    _ErrRet2 (e__novalnam, set_nm);

  /*
  ** get for every ID in the set the logical name of the flat file (GCG) or the
  ** library ..or if not available just the library name, the entry name
  ** and the hexnum string of the entry ID and write them out; 
  */

  for (k=1; k <= set->n; k++) {
    SetGetID (set, k, &id);
    entry = EntryOpen (&id);
    IdToStr (&id, hexnumstr); 
    EntrySourceName (entry, source_nm);
    if (IdIsSub (EntryGetId (entry)) && ParGetBool ("fosnWithPos")) 
      ;/*SlbGetFeature (entry, NULL, NULL);*/
    else {
      sprintf (ln, "%s:%s ! ID: %s\n", source_nm, EntryGetName (entry),
	       hexnumstr);
      if (!(*print) (ln))
	break; 
    }
    EntryClose (&entry);
  }
  return k-1;
}


/**API* QryLinkOne ************************************************************
** 
**  	Links a single one entry-ID to a library.
**  
**  	INPUT:	  o address of ID object [R]
**                o library name [R]
**  		  o name of result set [W] if NULL string then a name is
**                  created and written into char array
**  	        IMPLICIT:
**  
**  	RETURNS:
**  		    1 
**                  output set name exists: e__namnotunique <set name> +
*/ 
   
INT4 QryLinkOne (IDoENTRY *id, char *lib_nm, char *out_nm)
{
  SETo *tmp, *outset;
  char    tmp_nm[QRYxXNAM+1];
  INT4     rv;
  
  /* 
  ** new set that contains the one ID to be linked
  */

  tmp = SetNew (tmp_nm, "temp");
  tmp->id_p = id->id;
  tmp->n = 1;
  rv = SetMakeOwn (tmp, id->idType);
  _ErrRet(rv);

  /*
  ** create output set - name can be optionally supplied but must be unique
  */

  if (*out_nm == '\0')
    outset = SetNew (out_nm, "temp");
  else if (!(outset = SetNew (out_nm, NULL)))
    return 0;
  
  /*
  ** do the link, delete temporary set and output set if link was not
  ** successful
  */ 

  LinkMap (lib_nm, tmp_nm, outset);
  SetDelete (tmp_nm);
  if (outset->n)
    return 1;
  else {
    SetDelete (out_nm);
    return 0;
  }
}

#ifdef xxx
/**API* QryFindID *************************************************************
**
**      Retrieves a single entry from specified library by searching a word
**      in the specified index.
**      Returns first ID of the set. This function should be only applied
**      where no more than one entry can be found (eg, searching entry names, 
**      primary accession numbers).
**
**	INPUT:	    name of library [R]
**                  name of data-field [R]
**                  search word [R]
**	        IMPLICIT:
**
**	RETURNS:  address of ID object
**                NULL if no success
*/      

IDoENTRY *QryFindID (char *libName, char *fieldName, char *word)
{
  static IDoENTRY id, *idPtr=NULL;
  char query[1024], *setName = "__fromQueryFindId__";

  if (!LibGetLibGroup (libName, NULL, NULL)) {
    _ErrMsg3 (e__unknownnam, "Library", libName );
    return NULL;
  }
  if (LibGetFieldType (libName, fieldName) == NULL) {
    _ErrMsg3 (e__namnotdef, "Index", fieldName);
    return NULL;
  }

  sprintf (query, "[%s-%s:%s]", libName, fieldName, word);
  if (QryDo (query, setName)) {
    SetGetID (SetGet (setName), 1, &id);
    idPtr = &id;
  }
  SetDelete (setName);
  return idPtr;
}
#endif

/*****************************************************************************/
/*****************************************************************************/
/*****************************************************************************/
/*****************************************************************************/


/***** QuerySetBehave *********************************************************
** 
**  	Populates the "queryInfo" object with flags determining the behaviour
**      of some of the functions in this module which is determined by
**      the global parameters (module "par"). 
**  
**  	INPUT:	
**  	        IMPLICIT:
**                  queryInfo (QUERYoInfo *) [W]
**  
*/ 

static void QuerySetBehave ()
{
  memset (queryInfo, 0, sizeof (QUERYoInfo));
  queryInfo->isWWW = ParGetBool ("isHTMLFormat") ? 1 : 0;
  
  if (ParGetBool ("queryDoReport"))
    queryInfo->doReport = 1;
  if (ParGetBool ("queryListValues") || ParGetBool ("queryListFromMatch")) {
    queryInfo->doListValues = 1;
    queryInfo->doRetrieve = 0;
  }
  else
    queryInfo->doRetrieve = 1;

  if (queryInfo->doListValues) {
    if (ParGetBool ("queryListFromMatch")) 
      queryInfo->doListFromMatch = 1;
      
    queryInfo->printFirstValN = ParGetNum ("printIndexFirstValN") ? 
      ParGetNum ("printIndexFirstValN") : 1;
    queryInfo->valN = 0;
    queryInfo->maxValN = ParGetNum ("maxIndexValN");
    queryInfo->minValN = ParGetNum ("minIndexValN");
    if (!ParGetNum ("printIndexValN"))
      queryInfo->printValN = 2000000000; /* max num will never be reached */
    else 
      queryInfo->printValN = ParGetNum ("printIndexValN") +
	queryInfo->printFirstValN;
  }
}

/**API* QueryMakeWild *********************************************************
**
** 	Adds wildcards ('*') to the search strings of the query if the
**      parameter "makeWild" is ON.
** 
** 	INPUT:	    STRv with query string [W]
** 
** 	RETURNS:    query string with wildcards added 
*/ 

char *QueryMakeWild (STRv *s)
{
  static ICAoSYNTAX *syntax=NULL;
  static ICAoJOB    *job=NULL;

  if (!syntax) {
    syntax = (ICAoSYNTAX *) LibObjByName ("syntax", "makeWild");
    job = IcaCreateJob (syntax);
  }
  
  IcaJobSetString (job, _Str(*s));
  IcaDoJob (job, "query");
  StrSetS (s, IcaGetInputString (job));
  IcaEndJob (job);
  return _Str (*s);
}


/**api* Query *****************************************************************
**
**      Performs the specified query. If no query name is specified a 
**      unique temporary name will be used.
** 
** 	INPUT:	    the SRS query string [R]
**                  the query name (or NULL) [R]
** 
** 	RETURNS:    
*/ 

SETo *Query (char *s, char *name)
{
  SETo *set;

  QuerySetBehave ();
  set = QueryDo (s, name, 0);
  return (set && set->n) ? set : NULL;
}


SETo *QueryRecursive (char *s, char *name)
{
  return QueryDo (s, name, 1);
}

static SETo *QueryDo (char *s, char *name, INT4 isRecursive)
{
  static ICAoSYNTAX *syntax=NULL;
  static ICAoJOB    *jobStatic=NULL;
  static INT4       uniqueSetN=0;
  SETo    *resultSetSave, *tmp;
  ICAoJOB *job;
  char    uniqueName[100];

  if (!syntax) {
    syntax = (ICAoSYNTAX *) LibObjByName ("syntax", "srsquery");
    jobStatic = IcaCreateJob (syntax);
  }

  if (isRecursive) {
    resultSetSave = resultSet;
    job = IcaCreateJob (syntax);
  }
  else
    job = jobStatic;
  
  if (!name) {
    sprintf (uniqueName, "Q_%d", ++uniqueSetN);
    name = uniqueName;
  }
  resultSet = SetNew (name, NULL);

  IcaJobSetString (job, s);
  if (queryInfo->doListValues)
    TemplPrint ("head");
  IcaDoJob (job, "query");
  IcaEndJob (job);

  tmp = resultSet; 

  if (queryInfo->doListValues)
    TemplPrint ("tail", SetGetQueryStr (name));
  if (isRecursive)
    resultSet = resultSetSave;
  return tmp;
}


static SETo *QueryGetWholeLib (char *libName, SETo *set)
{
  SETo      *tmp;
  SLBo      *lib;
  LIBoINDEX *libInx;
  IDoENTRY  id;
  Int4      entryN, libId, k;

  memset (&id, 0, sizeof (IDoENTRY));
  if ((tmp = SetGet (libName)) && !SetIsDB (tmp))
    return tmp;

  lib = (SLBo *) LibObjByName ("library", libName);
  libInx = LibIndexOpen (lib, LibGetIdField (lib), 0);
  entryN = BtrGetRecordN (libInx->btree);
  libId = LibToId (lib);

  SetAlloc (set, entryN, LibGetIdType (NULL, libId, 4));
  for (k=1; k<=entryN; k++) {
    IdBuild (&id, libId, k, 0);
    SetAddID (set, &id);
  }
  SetSetIsDB (set, 0);
  printf ("%s ------> %d\n", libName, set->n);
  return set;
}

void QuerySetGet ()
{
  LINKo *link;
  SLBo *lib;
  SETo *set;
  Int4 isLink, c;
  char name[132];

  IargGetArgs ("name", name);

  if (!(set = SetGet (name))) {
    if (!(lib = (SLBo *) LibObjByName ("library", name)) &&
	!SmEqs (name, "parent")) {
      for (c=0, isLink=0; (link=LibNextLink (&c));)
	if (SmEqs (name, LibGetLinkFromName (link)) ||
	    SmEqs (name, LibGetLinkToName (link))) {
	  isLink=1;
	  break;
	}
      if (!isLink)
	_ErrExit2 (e__nosetorlib, name);
    }
    set = SetNew (name, NULL);
    SetSetIsDB (set, 1);
  }
  IcaReturn ("set", set);
}

void QueryDBGroup ()
{
  SRSoGROUP *group, *tmp;
  SLBo      *lib;
  char      libName[132], groupName[132];

  IargGetArgs ("init|db|group", groupName, libName, &group);

  if (*groupName) { /* initialize new or already existing group */
    if (!(group = (SRSoGROUP *) LibObjByName ("group", groupName))) 
      group = LibGroupNew (groupName); 
    group->libraryN = 0; 
  }
  /* databank name could be a group name! */
  else if ((tmp = (SRSoGROUP*) LibObjByName ("group", libName)))
    group = tmp;

  else { /* add a new databank to the group */
    if (!(lib = (SLBo *) LibObjByName ("library", libName))) {
      _ErrMsg3 (e__objectunknown, "data bank", libName);
      return;
    }
    else 
      LibGroupAddDb (group, lib);
  }
  IcaReturn ("group", (void*) group);
} 

void QuerySaveResult (Int4 runTime, SETo *set, STRv q)
{
  if (runTime)
    IargGetArgs ("set|q", &set, &q);
  if (SetIsDB (set)) 
    set = QueryGetWholeLib (SetGetName (set), set);
  SetOp (resultSet, set, NULL, QRYxOR);
  resultSet->queryStr = q;
}



void QueryStrSearch ()
{
  SRSoGROUP *group;
  SRSoFLD   *fieldType;
  SLBoFIELD *field, *f;
  SLBo      *lib;
  SETo      *tmp, *tmpSub, *set;
  STRv      s;
  char      indexName[40];
  INT4      c, k;

  IargGetArgs ("group|index|s", &group, indexName, &s);
  set = SetNew (NULL, "temp");

  for (c=0; lib = LibNextLib (group, &c);) {
    if (queryInfo->doListValues)
      TemplPrint ("library", LibName (lib));
    if ((field = LibHasFieldNamed (lib, indexName))) {
      if (FieldIs (field, "group")) /* field is field group (eg, "all") */
	for (k=0; (f = LibNextFieldInGroup (lib, field, &k));) {
	  tmp = SetNew (NULL, "temp");
	  if (QueryStrSearchIndex (&s, lib, f, tmp)) {
	    if (SetIsSubEntry (SetGetName (tmp))) { /* set of subentries */
	      tmpSub = tmp;
	      tmp = SetNew (NULL, "temp");
	      LinkToParent ("PARENT", SetGetName (tmpSub), tmp);
	      SetDel (tmpSub);
	    }
	    SetOp (set, tmp, NULL, QRYxOR);
	  }
	  SetDel (tmp); 
	}	  

      else {
	tmp = SetNew (NULL, "temp");
	if (QueryStrSearchIndex (&s, lib, field, tmp)) 
	  SetOp (set, tmp, NULL, QRYxOR);
	SetDel (tmp); 
      }
    }  
  }
  IcaReturn ("set", set);
}




void QueryRangeSearch ()
{
  SRSoGROUP *group;
  SRSoFLD   *fieldType;
  SLBoFIELD *field;
  SLBo      *lib;
  SETo      *tmp, *set;
  char      indexName[40], l[40], h[40];
  INT4      c, le, re, rv, isFirst, isLast;

  IargGetArgs ("group|index|l|h|le|re", &group, indexName, l, h, &le, &re);
  set = SetNew (NULL, "temp");

  isFirst = SmEqs (l, "min") ? 1 : 0;
  isLast = SmEqs (h, "max") ? 1 : 0;
      

  for (c=0; lib = LibNextLib (group, &c);) {
    if ((field = LibHasFieldNamed (lib, indexName))) {
      tmp = SetNew (NULL, "temp");

      if (FieldIs (field, "real"))
	rv = QueryRangeSearchIndex (lib, field, 0, 0,
			       isFirst ? 0 : strtod (l, NULL), 
			       isLast ? 0 : strtod (h, NULL), 1, 
			       re, le, isFirst, isLast, tmp);
      else if (FieldIs (field, "num"))
	rv = QueryRangeSearchIndex (lib, field, 
			       isFirst ? 0 : atoi(l), 
			       isLast ? 0 : atoi(h), 
			       0, 0, 0, le, re, isFirst, isLast, tmp);
      else
	continue;
      if (rv)
	SetOp (set, tmp, NULL, QRYxOR);
      SetDel (tmp); 
    }  
  }
  IcaReturn ("set", set);
}

SETo *QuerySetAssign (Int4 runTime, STRv name, SETo *set)
{
  SETo *tmp;

  if (runTime)
    IargGetArgs ("name|s", &name, &set);
  if ((tmp = SetNew (_Str (name), NULL))) {
    if (SetIsDB (set)) 
      set = QueryGetWholeLib (SetGetName (set), set);
    SetOp (tmp, set, NULL, SETxOR);
  }
  if (runTime)
    IcaReturn ("set", tmp);
  else 
    return set;
}


void QueryLinkOp ()
{
  SETo *set, *s1, *s2;
  char op[10], s1Name[100], s2Name[100];

  
  IargGetArgs ("op|s1|s2", op, &s1, &s2);
  set = SetNew (NULL, "temp");
  switch (*op) {
  case '>':
    LinkMap (SetGetName (s1), SetGetName (s2), set);
    break;
  case '<':
    LinkMap (SetGetName (s2), SetGetName (s1), set);
    break;
  default:
    _ErrExit2 (e__unknownoption, "op in QuerySetOp");
  }
  IcaReturn ("set", set);
}

void QueryLogOp ()
{
  SETo *set, *s1, *s2;
  char op[10], s1Name[100], s2Name[100];

  
  IargGetArgs ("op|s1|s2", op, &s1, &s2);
  if (SetIsDB (s1)) 
    s1 = QueryGetWholeLib (SetGetName (s1), s1);
  if (SetIsDB (s2)) 
    s2 = QueryGetWholeLib (SetGetName (s2), s2);

  set = SetNew (NULL, "temp");
  switch (*op) {
  case '&':
    SetOp (s1, s2, set, SETxAND);
    break;
  case '|':
    SetOp (s1, s2, set, SETxOR);
    break;
  case '!':
    SetOp (s2, s1, set, SETxNOT);
    break;
  default:
    _ErrExit2 (e__unknownoption, "op in QuerySetOp");
  }
  IcaReturn ("set", set);
}


INT4 QueryStrSearchIndex (STRv *str, SLBo *lib, SLBoFIELD *field, SETo *set)
{  
  LIBoINDEX *libIndex;
  char      sWild[255];
  INT4      len;   

  if (!(libIndex = LibIndexOpen (lib, field, 0))) 
    return 0;

  if (LibIs (lib, "subentries")) {
    queryInfo->subEntryLib = lib;
    queryInfo->subEntryNo = QueryGetAndDeleteSubEntryNo (_Str(*str));
  }
  else {
    queryInfo->subEntryLib = NULL;
    queryInfo->subEntryNo = 0;
  }


  StrDecode (str);
  StrLower (str);
  StrTrim (str, NULL);
  if ((len = RegWildToRegexp (_Str(*str), sWild, 1))) {
    if (queryInfo->doReport)
      print ("        ...searching \"%s\"\n", _Str(*str));
    QueryGetWild (libIndex, set, _Str(*str), sWild, len);
  }
  else		    
    QueryGet (libIndex, set, _Str(*str));

  return SetGetSize (set);
}

Int4 QueryGetAndDeleteSubEntryNo (char *s)
{
  Int4 k;
  
  for (k=strlen(s)-1; k > 0 && s[k] != '_'; k--)
    ;

  if (s[k] == '_') {
    s[k] = '\0';

    return atoi (&s[k+1]);
  }
  else
    return 0;
}

STRv QueryOpMakeWild (INT4 runTime, STRv s)
{
  if (runTime)
    IargGetArgs ("s", &s);
    
  if (!strchr ("*", _Str(s)[StrLen(s)-1]) && StrLen (s) > 1)
    StrAppS (&s, "*");

  if (runTime)
    IcaReturn ("strv", s);
  return s;
}


INT4 QueryRangeSearchIndex (SLBo *lib, SLBoFIELD *field,
		       INT4 low, INT4 high, double lowReal, double highReal,
		       INT4 isReal, INT4 isLE, INT4 isRE, 
		       INT4 isFirst, INT4 isLast, SETo *set)
{
  BTRoVALUE begin, end, *val;
  LIBoINDEX *libIndex;
  BTRo      *btree;
  INT4      idN;

  if (!(libIndex = LibIndexOpen (lib, field, 0))) 
    return 0;
  btree = libIndex->btree;

  /*
  ** get record for low value in range
  */

  if (isFirst)
    begin = (BtrRecordGet(btree, BTRxFIRST))->r.value;
  else {
    val = isReal ? BtrSearchReal(btree, lowReal) : BtrSearchNum(btree, low);
    if (BtrIsSearchGreaterMaxVal (btree)) 
      return 0;
    if (val && isLE)
      begin = (BtrRecordGet (btree, BTRxNEXT))->r.value;
    else
      begin = (BtrRecordGet (btree, BTRxCURR))->r.value;
  }

  /*
  ** get record for high value in range
  */

  if (isLast)
    end = (BtrRecordGet(btree, BTRxLAST))->r.value;
  else {
    val = isReal ? BtrSearchReal(btree, highReal) : BtrSearchNum(btree, high);
    if (BtrIsSearchLessMinVal (btree)) 
      return 0;
    else if (BtrIsSearchGreaterMaxVal (btree)) 
      end = (BtrRecordGet(btree, BTRxLAST))->r.value;
    if (val && isRE)
      end = (BtrRecordGet (btree, BTRxPREV))->r.value;
    else
      end = (BtrRecordGet (btree, BTRxCURR))->r.value;
  }

  if (begin.firstIdFip > end.firstIdFip)
    return 0; /* nothing found */

  /*
  ** get the set of IDs
  */ 

  idN = IdsGetRange (libIndex->idsFile, (IDPTR) NULL, 
		     begin.firstIdFip, end.firstIdFip, begin.idN, end.idN);
  
  _ErrStop (SetAlloc (set, idN, libIndex->field->indexId)); /* alloc id-buff */
  /* read id's */
  set->n = IdsGet (libIndex->idsFile, set->id_p, begin.firstIdFip, idN);
  SetSort (set);  /* sorting is necessary for set operations */
}





void QuerySetFunctions ()
{
  IcaSetFunction ("QuerySetGet", (FUNC)QuerySetGet);
  IcaSetFunction ("QueryDBGroup", (FUNC)QueryDBGroup);
  IcaSetFunction ("QueryStrSearch", (FUNC)QueryStrSearch);
  IcaSetFunction ("QueryRangeSearch", (FUNC)QueryRangeSearch);
  IcaSetFunction ("QueryLogOp", (FUNC)QueryLogOp);
  IcaSetFunction ("QueryLinkOp", (FUNC)QueryLinkOp);
  IcaSetFunction ("QueryOpMakeWild", (FUNC)QueryOpMakeWild);
  IcaSetFunction ("QuerySaveResult", (FUNC)QuerySaveResult);
  IcaSetFunction ("QuerySetAssign", (FUNC)QuerySetAssign);
  IcaSetFunction ("QueryMakeWild", (FUNC)QueryMakeWild);
}
unction ("QueryDBGroup", (FUNC)QueryDBGroup);
  IcaSetFunction ("QueryStrSearch", (FUNC)QueryStrSearch);
  IcaSetFunction ("QueryRangeSearch", (FUNC)QueryRangeSearch);
  IcaSetFunction ("QueryLogOp", (FUNC)QueryLogOp);
  IcaSetFunction ("QueryLinkOp", (FUNC)QueryLinkOp);
  IcaSetFunction ("QueryOpMakeWild", (FUNC)QueryOpMakeWild);
  IcaSetFunction ("QuerySaveResult", (FUNC)QuerySaveResult);
  IcaSetFunction ("QuerySetAssign", (FUNC)QuerySetAssign);
  IcaSetFunction (srs/src/query.h
**
**    $RCSfile: query.h,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:17:10 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
*/

#define	QRYxXNAM    30     /* max length of names for ? */


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of exported functions
*/

#ifndef _PRSoST
typedef struct PRSoST *dummytointroducestructtagPRSoST;
#endif
#ifndef _SETo
typedef struct SETo *dummytointroducestructtagSETo;
#endif

    /* functions for retrieval */

struct SETo *Query (char *s, char *name);
struct SETo *QueryRecursive (char *s, char *name);

INT4 QryReadNames (char *fil_nm, char *set_nm);
INT4 QryListToSet (struct PRSoST *tokstack, FILo *file);
INT4 QryLinkOne (IDoENTRY *id, char *lib_nm, char *set_nm);
/* IDoENTRY *QryFindID (char *lib_nm, char *field_nm, char *value);*/

    /* check or transform query */


    /* others */

INT4 QrySetToList (char *set_nm);




f struct SETo *dummytointroducestructtagSETo;
#endif

    /* functions for retrieval */

struct SETo *Query (char *s, char *name);
struct SETo *QueryRecursive (char *s, char *name);

INT4 QryReadNames (char *fil_nm, char *set_nm);
INT4 QryListToSet (struct PRSoST *tokstack, FILo *file);
INT4 QryLinkOne (IDoENTRY *id, char *lib_nm, char *set_nm);
/* IDoENTRY *QryFindID (char *lib_nm, char *field_nsrs/src/queryass.c
char queryass_ID[] = "$Id: queryass.c,v 1.9 1997/03/03 18:20:46 srs Exp $";
/*
**
**    $Source: /homes/srs/cvsroot/srs/src/queryass.c,v $
**    $Revision: 1.9 $
**    $Date: 1997/03/03 18:20:46 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>

#include "message.h"
#include "futil.h"
#include "strv.h"
#include "library.h"
#include "queryass.h"

#define _CONSTANTS
#define _SRS
#define _SLB
#include "srs5.h"


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Describes a library or group to be queried.
*/

typedef struct QASoLibOrGroup {
  STRv      name;	
  SLBo      *lib;
  SRSoGROUP *group;
  Int4      isGroup;
} QASoLibOrGroup;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  describes a retrieve command from any index
**  + two functions for creating and deleting instances
*/

typedef struct QASoRETRIEVE {
  STRv fieldName;
  STRv search;	
  STRv query;	
  char rangeBegin[20];
  char rangeEnd[20];
  INT4 isRangeBeginExcl;
  INT4 isRangeEndExcl;
  INT4 isSubEntry;
  INT4 doSubEntry;
  INT4 isRange;
  Int4 isAll;
} QASoRETRIEVE;

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  The query 'object'. 
*/

typedef struct QASoQUERY {
  char           name[80];
  Int4           isMakeWild;
  Int4           isLink;
  Int4           tmpSetNum;     /* used to create set names */
  struct STRo    *linkWith[100];
  struct STRo    *queryToLink;
  Int4           linkWithN;
  QASeLinkType   linkType;
  char           subEntryType[80];
  enum QASeOP    op;
  char           opName[10];
  QASoRETRIEVE   *retrieve;
  Int4           retrieveN;
  Int4           retrieveAllocN;
  QASoLibOrGroup *lib;
  Int4           libN;
  Int4           libAllocN;
  struct SRSoFLD *subEntryFieldType;
  Int4           opndN;
  Int4           opndAllocN;
  STRv           *opnd;
} QASoQUERY;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**
**  static functions
*/

static Int4 QasIsSubentryLink (QASoQUERY *query);
static QASoRETRIEVE *QasSetRetrieve (QASoQUERY *query, char *fieldName); 
static STRv QasGetLibNames (QASoQUERY *query);
static Int4 QasMakeRetrievals (QASoQUERY *query, STRv libNames, INT4 doLink);
static STRv QasGetRetrieveString (QASoQUERY *qas);
static STRv QasGetOpString (QASoQUERY *qas);
static STRv QasGetLinkString (QASoQUERY *qas);
static Int4 QasIsSubEntry (QASoQUERY *qas, QASoRETRIEVE *r);
static void QasClear (QASoQUERY *qas);



static int QasInitRetrieve (QASoRETRIEVE *r)
{
  r->rangeBegin[0] = r->rangeEnd[0] = '\0';
  r->isRangeBeginExcl = r->isRangeEndExcl = 0;
  r->isSubEntry = r->doSubEntry = 0;
  r->search = StrNew (20);
  r->query = StrNew (20);
  r->isRange = 0;
}

static int QasDeleteRetrieve (QASoRETRIEVE *r)
{
  if (r->search)
    StrDel (r->search);
  if (r->query)
    StrDel (r->query);
}


/**API* QasNew ****************************************************************
**
**      Get a new query object.
**
**	INPUT:	    
**	        IMPLICIT:
**
**	RETURNS:    new query object
*/ 

QASoQUERY *QasNew ()
{
  QASoQUERY *query;  

  query = (QASoQUERY *) calloc (sizeof (QASoQUERY), 1);
  query->op = QASxAND;
  strcpy (query->opName, "&");
  return query;
}

/**API* QasNew ****************************************************************
**
**      Deletes a query object.
**
**	INPUT:	    query object [W] 
**	        IMPLICIT:
**
**	RETURNS:    NULL
*/ 

QASoQUERY *QasDelete (QASoQUERY *query)
{
  if (query) {
    QasClear (query);
    free (query);
  }
  return NULL;
}

/**API* QasInitLink ***********************************************************
**
** 	Sets the query to be a link from an arbitrary query expression 
**      to one or more
**      databanks. The query must be further defined with QasSetQueryToLink,
**      QasSetLinkLib, QasSetLinkType before obtaining the query string
**      from QasGetQueryString.
**      The input query object can be obtained from QasNew.
** 
** 	INPUT:	    query object [W]
**                  
*/ 

void QasInitLink (QASoQUERY *qas) 
{
  QasClear (qas);
  qas->isLink = 1;
  qas->linkWithN = 0;
}

/**API* QasSetTmpSetNum *******************************************************
**
** 	Sets the start number for the query assistant to use as part of
**      names generated for temporary sets.
** 
** 	INPUT:	    query object [W]
**                  the number [R]
**                  
*/ 

void QasSetTmpSetNum (QASoQUERY *qas, Int4 n)
{
  qas->tmpSetNum = n;
}


/**API* QasSetQueryToLink *****************************************************
**
** 	Sets the query expression to be linked with one or more libraries.
**      Query must be initialized with QasInitLink.
** 
** 	INPUT:	    link object [W]
**                  library name [R]
**                  
*/ 
void QasSetQueryToLink (QASoQUERY *query, char *s) 
{
  query->queryToLink = StrCpyS (s);
}

/**API* QasSetLinkWith ********************************************************
**
** 	Sets the library or expression to be linked with the linkQuery. Several
**      'with' expressions can be set. 
**      Query must be initialized with QasInitLink.
** 
** 	INPUT:	    link object [W]
**                  library name [R]
**                  
*/ 

void QasSetLinkWith (QASoQUERY *query, char *with)
{
  query->linkWith[query->linkWithN++] = StrCpyS (with);
}

/**API* QasSetLinkType ********************************************************
**
** 	Sets the type of the link query. Query must be initialized with
**      QasInitLink.
** 
** 	INPUT:	    link object [W]
**                  option: "toSet", "toLibs", "notToSet" [R]
**                  
*/ 

void QasSetLinkType (QASoQUERY *qas, char *option)
{
  switch (option[2]) {
  case 'S':
    qas->linkType = QASxToSet;
    break;
  case 'L':
    qas->linkType = QASxToLibs;
    break;
  case 't':
    qas->linkType = QASxToSetNot;
    break;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
}


/**API* QasReset *************************************************************
**
**      Resets a query object to initial state.
**
**	INPUT:	    query object [W]
**	        IMPLICIT:
**
**	RETURNS:
*/ 

void QasReset (QASoQUERY *query)
{
  QasClear (query);
  query->op = QASxAND;
  strcpy (query->opName, "&");
  query->isMakeWild = 0;
  query->subEntryFieldType = NULL;
}


/**API* QasSetRetrieveStr *****************************************************
**
**      Sets a databank to be searched. More than one can be set.
**
**	INPUT:	    query object [W]
**                  databank (library) name [R]
**	        IMPLICIT:
**
**	RETURNS:    1: success
**                  e__objectunknown+: databank name unknown
*/ 

INT4 QasSetLibrary (QASoQUERY *qas, char *libName)
{
  QASoLibOrGroup *tmp;
  SRSoGROUP      *group;
  SLBo           *lib;

  tmp = _addObj (qas->lib, qas->libN, qas->libAllocN, QASoLibOrGroup);

  if ((tmp->lib = (SLBo *) LibObjByName ("library", libName))) 
    tmp->name = StrCpyS (LibName (tmp->lib));
  else if ((tmp->group = (SRSoGROUP *) LibObjByName ("group", libName))) {
    tmp->name = StrCpyS (LibGetGroupName (group, "full"));
    tmp->isGroup = 1;
  }
  else
    _ErrRet3 (e__objectunknown, "databank (group)", libName);
  return 1;
}


/****** QasSetRetrieve ********************************************************
**
**      Returns a "retrieve" object or creates a new one.
**
**	INPUT:	    query object [W]
**                  field name [R]
**                  low boundary string (maybe int or real) [R]
**	        IMPLICIT:
**
**	RETURNS:    retrieve object if success
**                  NULL if field name unknown
*/ 

static QASoRETRIEVE *QasSetRetrieve (QASoQUERY *query, char *fieldName)
{
  SRSoFLD      *fieldType;
  QASoRETRIEVE *retrieve;

  if (!(fieldType = (SRSoFLD *) LibObjByName ("fieldtype", fieldName))) {
    _ErrMsg3 (e__objectunknown, "data-field", fieldName);
    return NULL;
  }
  fieldName = fieldType->nam;
  return _addObj (query->retrieve, query->retrieveN, query->retrieveAllocN, 
		  QASoRETRIEVE);

  return query->retrieve;
}


/**API* QasNewRetrieve *******************************************************
**
**      Creates a new 'Retrieval object' which can be used to further 
**      define an index search. The Retrieval object is managed by the 
**      query object and needs not to be deleted.
**
**	INPUT:	    query object [W]
**                  field name [R]
**	        IMPLICIT:
**
**	RETURNS:    a handle to the Retrieval object
*/ 

QASoRETRIEVE *QasNewRetrieve (QASoQUERY *query, char *fieldName)
{
  QASoRETRIEVE *r;

  r = QasSetRetrieve (query, fieldName);
  if (r->fieldName)
    StrDel (r->fieldName);
  r->fieldName = StrCpyS (fieldName);
  return r;
}

/**API* function **************************************************************
**
**      Creates an expression to retrieve all entries of all libraries
**      selected by QasSetLibrary.
**      <p>
**      function has not yet been tested!
**
**	INPUT:	    query object [W]
*/ 

void QasSetRetrieveAll (QASoQUERY *query)
{
  QASoRETRIEVE *r;
  Int4         k;

  r =  _addObj (query->retrieve, query->retrieveN, query->retrieveAllocN, 
	       QASoRETRIEVE);
  r->isAll = 1;
  r->search = StrCpyS ("(");
  for (k=0; k < query->libN; k++) 
    StrPrintf (&r->search, "%s |", _Str (query->lib[k].name));
  StrCut (&r->search, StrLen (r->search)-2, 2);
  StrAppS (&r->search, ")");
  StrLower (&r->search);
}



/**API* QasSetRetrieveStr *****************************************************
**
**      Sets a search string for specified index.
**
**	INPUT:	    query object [W]
**                  retrieval object [W]
**                  search string [R]
**	        IMPLICIT:
**
**	RETURNS:   
*/ 

void QasSetRetrieveStr (QASoQUERY *query, QASoRETRIEVE *retrieve, char *str)
{
  if (retrieve->search)
    StrDel (retrieve->search);
  retrieve->search = StrCpyS (str);
}


/**API* QasSetRangeBegin ******************************************************
**
**      Sets the lower boundary of a range retrieval.
**
**	INPUT:	    query object [W]
**                  retrieval object [W]
**                  low boundary string (maybe int or real) [R]
**	        IMPLICIT:
**
**	RETURNS:    number of query in history if success
**                  0 if not
*/ 

void QasSetRangeBegin (QASoQUERY *query, QASoRETRIEVE *retrieve, char *begin)
{
  strcpy (retrieve->rangeBegin, begin);
  retrieve->isRange = 1;
}

/**API* QasSetRangeEnd ********************************************************
**
**      Sets the upper boundary of a range retrieval.
**
**	INPUT:	    query object [W]
**                  retrieval object [W]
**                  low boundary string (maybe int or real) [R]
**	        IMPLICIT:
**
**	RETURNS:    number of query in history if success
**                  0 if not
*/ 

void QasSetRangeEnd (QASoQUERY *query, QASoRETRIEVE *retrieve, char *end)
{
  strcpy (retrieve->rangeEnd, end);
  retrieve->isRange = 1;
}

/**API* QasSetRangeBeginExcl **************************************************
**
**      Sets the lower boundary not to be included in range.
**
**	INPUT:	    query object [W]
**                  field name [R]
**                  low boundary string (maybe int or real) [R]
**	        IMPLICIT:
**
**	RETURNS:    number of query in history if success
**                  0 if not
*/ 

void QasSetRangeBeginExcl (QASoQUERY *query, QASoRETRIEVE *retrieve)
{
  retrieve->isRangeBeginExcl = 1;
  retrieve->isRange = 1;
}

/**API* QasSetRangeEndExcl ****************************************************
**
**      Sets the upper boundary not to be included in range.
**
**	INPUT:	    query object [W]
**                  field name [R]
**                  low boundary string (maybe int or real) [R]
**	        IMPLICIT:
**
**	RETURNS:    number of query in history if success
**                  0 if not
*/ 

void QasSetRangeEndExcl (QASoQUERY *query, QASoRETRIEVE *retrieve)
{
  retrieve->isRangeEndExcl = 1;
  retrieve->isRange = 1;
}


/**API* QasSetMakeWild *******************************************************
**
**      Sets the flag to add to all search words a terminal wildcard "*".
**
**	INPUT:	    query object [W]
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

void QasSetMakeWild (QASoQUERY *query)
{
  query->isMakeWild = 1;
}


/**API* QasSetSubEntries ******************************************************
**
**      Sets the query to return subentries found by specified field. This 
**      works only if the fields of different entry types are combined
**      with logical AND.
**     
**	INPUT:	    query object [W]
**                  field name [R]
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

void QasSetSubEntries (QASoQUERY *query, QASoRETRIEVE *retrieve)
{
  if (!(query->subEntryFieldType = 
	(SRSoFLD *) LibObjByName ("fieldtype", _Str (retrieve->fieldName)))) {
    _ErrMsg3 (e__objectunknown, "fieldType", _Str (retrieve->fieldName));
  }
  retrieve->doSubEntry = 1;
}


/**API* QasSetOp **************************************************************
**
**      Sets the operator that combines the separate retrieval commands.
**
**	INPUT:	    query object [W]
**                  operator name: "or", "and", "butnot" [R]
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

void QasSetOp (QASoQUERY *query, char *opName)
{
  switch (tolower (opName[0])) {
  case '|':
  case 'o':  /* or */
    query->op = QASxOR;
    strcpy (query->opName, "|");
    break;
  case '!':
  case 'b':  /* butnot */
    query->op = QASxBUTNOT;
    strcpy (query->opName, "!");
    break;
  case '&':
  case 'a':  /* and */
    query->op = QASxAND;
    strcpy (query->opName, "&");
    break;
  default:
    _ErrExit2 (e__unknownoption, opName);
  }
}


/**API* QasMakeOperand *****************************************************
**
**      Creates the query string built sofar and makes it a single operand 
**      which can be used to create further queries using QasAddOperand
**      QasSetOp and QasGetQueryString.
**
**	INPUT:	    query object [W]
**
*/ 

void QasMakeOperand (QASoQUERY *qas) 
{
  STRv s, expr;
  s = StrCpyS (QasGetQueryString (qas));
  QasClear (qas);
  expr = StrNew (expr);
  StrPrintf (&expr, "(%s)", _Str (s));
  QasAddOperand (qas, _Str (expr));
  StrDel (s);
  StrDel (expr);
}

static void QasClear (QASoQUERY *qas)
{
  QASoRETRIEVE   *r;
  QASoLibOrGroup *l;
  Int4 k;

  if (qas->retrieveN) {
    for (k=0; k < qas->retrieveN; k++) {
      r = &qas->retrieve[k];
      StrDel (r->fieldName);
      StrDel (r->search);
      StrDel (r->query);
    }
    free (qas->retrieve);
    qas->retrieveN = 0;
    qas->retrieveAllocN = 0;
  }    

  if (qas->libN) {
    for (k=0; k < qas->libN; k++) {
      l = &qas->lib[k];
      StrDel (l->name);
    }
    free (qas->lib);
    qas->libN = 0;
    qas->libAllocN = 0;
  }    

  if (qas->opndN) {
    for (k=0; k < qas->opndN; k++) {
      StrDel (qas->opnd[k]);
    }
    free (qas->opnd);
    qas->opndN = 0;
    qas->opndAllocN = 0;
  }    
}


/**API* QasAddOperand *****************************************************
**
**      Adds a set name as operand to the current list of operands which 
**      will be combined using the operator specified by QasSetOp.
**
**	INPUT:	    query object [W]
**                  operand name (set name) [R]
**
*/ 

void QasAddOperand (QASoQUERY *query, char *name) 
{
  STRv s;

  s = StrCpyS (name);
  *(_addObj (query->opnd, query->opndN, query->opndAllocN, STRv)) = s;
}



/**API* QasGetQueryString *****************************************************
**
**      Build a query string from all the information accumulated so far.
**      This function can be called at any point during query building.
**      The function might generate names of intermediate sets for later
**      reference in the query, eg, "(L1=[a-b:c]) ! L1<d". The number added to
**      the L can be set by QasSetTmpSetNum.
**
**	INPUT:	    query object [W]
**
**	RETURNS:    query string 
**                  NULL: no complete query was specified
*/ 

char *QasGetQueryString (QASoQUERY *query) 
{
  if (query->retrieveN)
    return _Str (QasGetRetrieveString (query));
  else if (query->opndN)
    return _Str (QasGetOpString (query));
  else if (query->isLink) 
    return _Str (QasGetLinkString (query));
  else
    return NULL;
}

static STRv QasGetOpString (QASoQUERY *qas)
{
  STRv str=StrNew ();
  Int4 k;

  for (k=0; k < qas->opndN; k++) {
    if (!k)
      StrPrintf (&str, "%s", _Str (qas->opnd[k]));
    else 
      StrPrintf (&str, " %s %s", qas->opName,  _Str (qas->opnd[k]));
  }
  return str;
}

static STRv QasGetRetrieveString (QASoQUERY *qas)
{
  STRv         libNames, query, seQuery;
  QASoRETRIEVE *retrieve;
  Int4         rv, k, doLink=0, makeWildSave;

  libNames = QasGetLibNames (qas);
  doLink = QasIsSubentryLink (qas);
  if (!QasMakeRetrievals (qas, libNames, doLink)) {
    StrDel (libNames);
    return NULL;
  }
  query=StrNew ();
  seQuery=StrNew ();

  /* Now combine all retrievals to one big query string */
  if (doLink)
    StrAppS (&query, "(");
  
  for (k=0; k < qas->retrieveN; k++) {
    retrieve = &qas->retrieve[k];
    
    if (retrieve->doSubEntry && doLink) {
      if (StrLen (seQuery))
	StrPrintf (&seQuery, "%s %s ", qas->opName, _Str (retrieve->query));
      else
	StrPrintf (&seQuery, "%s ", _Str (retrieve->query));
    }
    else {
      if (StrLen (query) > 1)
	StrPrintf (&query, "%s %s ", qas->opName, _Str (retrieve->query));
      else
	StrPrintf (&query, "%s ", _Str (retrieve->query));
    }
  }
  
  /* if retrieval of subentries requires link */
  if (doLink) 
    StrPrintf (&query, ") > (%s)", _Str (seQuery));
  
  if (qas->isMakeWild) {
    Int4 save = ParGetNum ("makeWild");
    ParDefNum ("makeWild", 1);
    QueryMakeWild (&query);
    ParDefNum ("makeWild", save);
  }
  StrDel (seQuery);
  StrDel (libNames);
  return query;
}


static STRv QasGetLinkString (QASoQUERY *qas)
{
  static Int4 count;
  STRv query1, query2, str;
  Int4 k;

  count = qas->tmpSetNum;

  str = StrNew ();
  query1 = StrNew ();
  query2 = StrNew ();
  if (qas->linkWithN > 1 || qas->linkType == QASxToSetNot) {
    StrPrintf (&query1, "(L%d=%s)", ++count, _Str(qas->queryToLink));
    StrPrintf (&query2, "L%d", count); 
  }     
  else {
    StrPrintf (&query1, "(%s)", _Str(qas->queryToLink));
    StrPrintf (&query2, "(%s)", _Str(qas->queryToLink));
  }

  ASSERT (qas->linkType, "wrong link type");
  if (qas->linkType == QASxToSet) {
    for (k=0; k < qas->linkWithN; k++)
      if (!k)
	StrPrintf (&str, "(%s < %s)", _Str(query1), _Str(qas->linkWith[k]));
      else
	StrPrintf (&str, " & (%s < %s)", _Str(query2), _Str(qas->linkWith[k]));
  }
  else if (qas->linkType == QASxToLibs) {
    for (k=0; k < qas->linkWithN; k++)
      if (!k)
	StrPrintf (&str, "(%s > %s)", _Str(query1), _Str(qas->linkWith[k]));
      else
	StrPrintf (&str, " | (%s > %s)", _Str(query2), _Str(qas->linkWith[k]));
  }
  else if (qas->linkType == QASxToSetNot) {
    for (k=0; k < qas->linkWithN; k++) 
      if (!k)
	StrPrintf (&str, "%s ! (%s < %s)", _Str(query1), _Str(query2),
		   _Str(qas->linkWith[k]));
      else
	StrPrintf (&str, " ! (%s < %s)", _Str(query2), _Str(qas->linkWith[k]));
  }
  StrDel (query1);
  StrDel (query2);
  return str;
}

/****** QasIsSubentryLink *****************************************************
**
**      Finds out if the current query contains a mixture of subentry and
**      entry retrievals so that a link operation between the two will be
**      necessary.
**
**	INPUT:	    query object [W]
**
**	RETURNS:    1: link is necessary
**                  0: not
*/ 

static Int4 QasIsSubentryLink (QASoQUERY *qas)
{
  QASoRETRIEVE *retrieve;
  Int4         k, isSubentry=0, isEntry=0;

  for (k=0; k < qas->retrieveN; k++) {
    retrieve = &qas->retrieve[k];
    if (QasIsSubEntry (qas, retrieve) && retrieve->doSubEntry)
      isSubentry = 1;
    else
      isEntry = 1;
  }    
  return isSubentry && isEntry;
}

static Int4 QasIsSubEntry (QASoQUERY *qas, QASoRETRIEVE *r)
{
  SLBo           *lib;
  SLBoFIELD      *field;
  QASoLibOrGroup *tmp;
  Int4           k, c, isSubEntry=0;
  
  for (k=0; k < qas->libN; k++) {
    tmp = &qas->lib[k];
    if (tmp->isGroup) {
      for (c=0; (lib = LibNextLib (tmp->group, &c));)
	if (field = LibHasFieldNamed (lib, _Str (r->fieldName)))
	  if (FieldIs (field, "subentry"))
	    isSubEntry = 1;
    }
    else {
      if (field = LibHasFieldNamed (tmp->lib, _Str (r->fieldName)))
	if (FieldIs (field, "subentry"))
	  isSubEntry = 1;
    }
  }
  r->isSubEntry = isSubEntry;
  return isSubEntry;
}


/****** QasGetLibNames *******************************************************
**
**      Prints the list of selected databanks into a string using a 
**      space as separator.
**
**	INPUT:	    query object [W]
**
**	RETURNS:    library names list
*/ 

static STRv QasGetLibNames (QASoQUERY *query)
{
  STRv      libNames;
  SRSoGROUP *group;
  SLBo      *lib;
  char      *libName;
  INT4      k;

  libNames = StrNew ();
  for (k=0; k < query->libN; k++) 
    StrPrintf (&libNames, "%s ", _Str (query->lib[k].name));
  StrCut (&libNames, StrLen (libNames)-1, 1);
  StrLower (&libNames);
  return libNames;
}


/****** QasGetLibsAndDoLink ***************************************************
**
**      Writes the list of selected libraries and groups into a buffer
**      marks retrieval commands that lead to subentries and determines if
**      the desired ouput is a list of subentries and if a link to subentries
**      must be performed.
**
**	INPUT:	 o  query object [W]
**               o  string list of library names to be queried [W]
**               o  flag if a link between entries and subentries needs
**                  to be performed (QasIsSubentryLink)
**
**	RETURNS:    1: successful
**                  0: no retrieval was set
*/ 

static Int4 QasMakeRetrievals (QASoQUERY *query, STRv libNames, 
			       Int4 isSubentryLink)
{
  SRSoFLD      *fieldType;
  QASoRETRIEVE *r;
  INT4         k, isFirst;

  if (!query->retrieveN)
    return 0;

  for (isFirst=1, k=0; k < query->retrieveN; k++) {
    r = &query->retrieve[k];
    r->query = StrNew ();

    /* convert subentries to PARENT */
    if (r->isSubEntry && !r->doSubEntry)
      r->query = StrCpyS ("(");

    /* databank names */
    if (query->libN == 1)
      StrPrintf (&r->query, "[%s-", _Str (libNames));
    else if (isFirst && !(isSubentryLink && r->doSubEntry)) {
      StrPrintf (&r->query, "[libs={%s}-", _Str (libNames));
      isFirst=0;
    }
    else 
      StrAppS (&r->query, "[libs-");

    if (!(fieldType = 
	  (SRSoFLD *) LibObjByName ("fieldtype", _Str (r->fieldName)))) 
      _ErrExit3 (e__objectunknown, "data-field", _Str (r->fieldName));
    
    /* get all - string already exists */
    if (r->isAll)
      ;
    /* string search */
    else if (!r->isRange)
      StrPrintf (&r->query, "%s: %s]", 
		 _Str (r->fieldName),
		 _Str (r->search));

    /* range retrieval */
    else
      StrPrintf (&r->query, "%s# %s%s:%s%s]", 
		 _Str (r->fieldName),
		 r->isRangeBeginExcl ? "!" : "",
		 r->rangeBegin,
		 r->isRangeEndExcl ? "!" : "",
		 r->rangeEnd);

    /* convert subentries to PARENT */
    if (r->isSubEntry && !r->doSubEntry)
      StrAppS (&r->query, " > parent)");

  }
  return 1;
}


 if (r->isAll)
      ;
    /* string search */
    else if (!r->isRange)
 srs/src/queryass.h
**
**    $Source: /homes/srs/cvsroot/srs/src/queryass.h,v $
**    $Revision: 1.4 $
**    $Date: 1997/03/03 18:20:46 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**                  Copyright by Thure Etzold
**
*/


typedef enum QASeOP {QASxOR=1, QASxAND, QASxBUTNOT} QASeOP;
typedef enum QASeLinkType {QASxToSet=1, QASxToLibs, QASxToSetNot} QASeLinkType;

typedef struct QASoQUERY *QASvQUERY;
typedef struct QASoRETRIEVE *QASvRETRIEVE;

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of exported functions
*/

    /* construct and destruct */

QASvQUERY QasNew ();
QASvQUERY QasDelete (QASvQUERY query);
QASvRETRIEVE QasNewRetrieve (QASvQUERY query, char *fieldName);

    /* set attributes */

INT4 QasSetLibrary (QASvQUERY query, char *libName);
void QasSetRetrieveStr (QASvQUERY query, QASvRETRIEVE retrieve, char *str);
void QasSetRangeBegin (QASvQUERY query, QASvRETRIEVE retrieve, char *begin);
void QasSetRangeEnd (QASvQUERY query, QASvRETRIEVE retrieve, char *end);
void QasSetRangeBeginExcl (QASvQUERY query, QASvRETRIEVE retrieve);
void QasSetRangeEndExcl (QASvQUERY query, QASvRETRIEVE retrieve);
void QasSetOp (QASvQUERY query, char *opName);
void QasSetMakeWild (QASvQUERY query); 
void QasSetSubEntries (QASvQUERY query, QASvRETRIEVE retrieve);
void QasSetTmpSetNum (QASvQUERY qas, Int4 n);
void QasAddOperand (QASvQUERY query, char *name); 
void QasSetRetrieveAll (QASvQUERY query);

    /* get attributes */

char *QasGetQueryString (QASvQUERY query);

eve, char *end);
void QasSetRangeBeginExcl (QASvQUERY query, QASvRETRIEVE retrieve);
void QasSetRangeEndExcl (QASvQUERY query, QASvRETRIEVE retrieve);
void QasSetOp (QASvQUERY query, char *opName);
void QasSetMakeWild (QASvQUERY query); 
void QasSetSubEntries (QASvQUERY query, QASvRETRIEVE retrieve);
void QasSetTmpSetNum (QASvQUERY qas, Int4 n);
void QasAddOperand (QASvQUERY query, char *name); 
void QasSetRetrieveAll (QASvQUERY query);

srs/src/regexp.c
 * regcomp and regexec -- regsub and regerror are elsewhere
 * @(#)regexp.c	1.3 of 18 April 87
 *
 *	Copyright (c) 1986 by University of Toronto.
 *	Written by Henry Spencer.  Not derived from licensed software.
 *
 *	Permission is granted to anyone to use this software for any
 *	purpose on any computer system, and to redistribute it freely,
 *	subject to the following restrictions:
 *
 *	1. The author is not responsible for the consequences of use of
 *		this software, no matter how awful, even if they arise
 *		from defects in it.
 *
 *	2. The origin of this software must not be misrepresented, either
 *		by explicit claim or by omission.
 *
 *	3. Altered versions must be plainly marked as such, and must not
 *		be misrepresented as being the original software.
 *
 * Beware that some of this code is subtly aware of the way operator
 * precedence is structured in regular expressions.  Serious changes in
 * regular-expression syntax might require a total rethink.
 */

#include <stdio.h>
#include <string.h>
#include "regexp.h"
#include "regmagic.h"
#include "message.h"  /* added */

/*
 * The "internal use only" fields in regexp.h are present to pass info from
 * compile to execute that permits the execute phase to run lots faster on
 * simple cases.  They are:
 *
 * regstart	char that must begin a match; '\0' if none obvious
 * reganch	is the match anchored (at beginning-of-line only)?
 * regmust	string (pointer into program) that match must include, or NULL
 * regmlen	length of regmust string
 *
 * Regstart and reganch permit very fast decisions on suitable starting points
 * for a match, cutting down the work a lot.  Regmust permits fast rejection
 * of lines that cannot possibly match.  The regmust tests are costly enough
 * that regcomp() supplies a regmust only if the r.e. contains something
 * potentially expensive (at present, the only such thing detected is * or +
 * at the start of the r.e., which can involve a lot of backup).  Regmlen is
 * supplied because the test in regexec() needs it and regcomp() is computing
 * it anyway.
 */

/*
 * Structure for regexp "program".  This is essentially a linear encoding
 * of a nondeterministic finite-state machine (aka syntax charts or
 * "railroad normal form" in parsing technology).  Each node is an opcode
 * plus a "next" pointer, possibly plus an operand.  "Next" pointers of
 * all nodes except BRANCH implement concatenation; a "next" pointer with
 * a BRANCH on both ends of it is connecting two alternatives.  (Here we
 * have one of the subtle syntax dependencies:  an individual BRANCH (as
 * opposed to a collection of them) is never concatenated with anything
 * because of operator precedence.)  The operand of some types of node is
 * a literal string; for others, it is a node leading into a sub-FSM.  In
 * particular, the operand of a BRANCH node is the first node of the branch.
 * (NB this is *not* a tree structure:  the tail of the branch connects
 * to the thing following the set of BRANCHes.)  The opcodes are:
 */

/* definition	number	opnd?	meaning */
#define	END	0	/* no	End of program. */
#define	BOL	1	/* no	Match "" at beginning of line. */
#define	EOL	2	/* no	Match "" at end of line. */
#define	ANY	3	/* no	Match any one character. */
#define	ANYOF	4	/* str	Match any character in this string. */
#define	ANYBUT	5	/* str	Match any character not in this string. */
#define	BRANCH	6	/* node	Match this alternative, or the next... */
#define	BACK	7	/* no	Match "", "next" ptr points backward. */
#define	EXACTLY	8	/* str	Match this string. */
#define	NOTHING	9	/* no	Match empty string. */
#define	STAR	10	/* node	Match this (simple) thing 0 or more times. */
#define	PLUS	11	/* node	Match this (simple) thing 1 or more times. */
#define	OPEN	20	/* no	Mark this point in input as start of #n. */
			/*	OPEN+1 is number 1, etc. */
#define	CLOSE	30	/* no	Analogous to OPEN. */

/*
 * Opcode notes:
 *
 * BRANCH	The set of branches constituting a single choice are hooked
 *		together with their "next" pointers, since precedence prevents
 *		anything being concatenated to any individual branch.  The
 *		"next" pointer of the last BRANCH in a choice points to the
 *		thing following the whole choice.  This is also where the
 *		final "next" pointer of each individual branch points; each
 *		branch starts with the operand node of a BRANCH node.
 *
 * BACK		Normal "next" pointers all implicitly point forward; BACK
 *		exists to make loop structures possible.
 *
 * STAR,PLUS	'?', and complex '*' and '+', are implemented as circular
 *		BRANCH structures using BACK.  Simple cases (one character
 *		per match) are implemented with STAR and PLUS for speed
 *		and to minimize recursive plunges.
 *
 * OPEN,CLOSE	...are numbered at compile time.
 */

/*
 * A node is one char of opcode followed by two chars of "next" pointer.
 * "Next" pointers are stored as two 8-bit pieces, high order first.  The
 * value is a positive offset from the opcode of the node containing it.
 * An operand, if any, simply follows the node.  (Note that much of the
 * code generation knows about this implicit relationship.)
 *
 * Using two bytes for the "next" pointer is vast overkill for most things,
 * but allows patterns to get big without disasters.
 */
#define	OP(p)	(*(p))
#define	NEXT(p)	(((*((p)+1)&0377)<<8) + (*((p)+2)&0377))
#define	OPERAND(p)	((p) + 3)

/*
 * See regmagic.h for one further detail of program structure.
 */


/*
 * Utility definitions.
 */
#ifndef CHARBITS
#define	UCHARAT(p)	((int)*(unsigned char *)(p))
#else
#define	UCHARAT(p)	((int)*(p)&CHARBITS)
#endif

#define	FAIL(m)	{ regerror(m); return(NULL); }
#define	ISMULT(c)	((c) == '*' || (c) == '+' || (c) == '?')
#define	META	"^$.[()|?+*\\"

/*
 * Flags to be passed up and down.
 */
#define	HASWIDTH	01	/* Known never to match null string. */
#define	SIMPLE		02	/* Simple enough to be STAR/PLUS operand. */
#define	SPSTART		04	/* Starts with * or +. */
#define	WORST		0	/* Worst case. */

/*
 * Global work variables for regcomp().
 */
static char *regparse;		/* Input-scan pointer. */
static int regnpar;		/* () count. */
static char regdummy;
static char *regcode;		/* Code-emit pointer; &regdummy = don't. */
static long regsize;		/* Code size. */

/*
 * Forward declarations for regcomp()'s friends.
 */
#ifndef STATIC
#define	STATIC	static
#endif
STATIC char *reg();
STATIC char *regbranch();
STATIC char *regpiece();
STATIC char *regatom();
STATIC char *regnode();
STATIC char *regnext();
STATIC void regc();
STATIC void reginsert();
STATIC void regtail();
STATIC void regoptail();
#ifdef STRCSPN
STATIC int strcspn();
#endif

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
** the error reporting functions are located elsewhere in the original
** distribution.. the macro _ErrMsg replaces the original function "regerror"
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

int errreport = 0;		/* Report errors via errseen? */
char *errseen = NULL;		/* Error message. */

/*
void error (char *s1, char *s2)
{
  fprintf(stderr, "regexp: ");
  fprintf(stderr, s1, s2);
  fprintf(stderr, "\n");
  exit(1);
}*/

void regerror (char *s)
{
  if (errreport)
    errseen = s;
  else
    _ErrMsg2 (e__regerror, s);
} 

/*
 - regcomp - compile a regular expression into internal code
 *
 * We can't allocate space until we know how big the compiled form will be,
 * but we can't compile it (and thus know how big it is) until we've got a
 * place to put the code.  So we cheat:  we compile it twice, once with code
 * generation turned off and size counting turned on, and once "for real".
 * This also means that we don't allocate space until we are sure that the
 * thing really will compile successfully, and we never have to move the
 * code and thus invalidate pointers into it.  (Note that it has to be in
 * one piece because free() must be able to free it all.)
 *
 * Beware that the optimization-preparation code in here knows about some
 * of the structure of the compiled regexp.
 */
regexp *
RegComp(exp)  /* formerly "regcomp" */
char *exp;
{
  register regexp *r;
  register char *scan;
  register char *longest;
  register int len;
  int flags;
  extern char *malloc();
  
  if (exp == NULL)
    FAIL("NULL argument");
  
  /* First pass: determine size, legality. */
  regparse = exp;
  regnpar = 1;
  regsize = 0L;
  regcode = &regdummy;
  regc(MAGIC);
  if (reg(0, &flags) == NULL)
    return(NULL);
  
  /* Small enough for pointer-storage convention? */
  if (regsize >= 32767L)		/* Probably could be 65535L. */
    FAIL("regexp too big");
  
  /* Allocate space. */
  r = (regexp *)malloc(sizeof(regexp) + (unsigned)regsize);
  if (r == NULL)
    FAIL("out of space");
  
  /* Second pass: emit code. */
  regparse = exp;
  regnpar = 1;
  regcode = r->program;
  regc(MAGIC);
  if (reg(0, &flags) == NULL)
    return(NULL);
  
  /* Dig out information for optimizations. */
  r->regstart = '\0';	/* Worst-case defaults. */
  r->reganch = 0;
  r->regmust = NULL;
  r->regmlen = 0;
  scan = r->program+1;			/* First BRANCH. */
  if (OP(regnext(scan)) == END) {      /* Only one top-level choice. */
    scan = OPERAND(scan);
    
    /* Starting-point info. */
    if (OP(scan) == EXACTLY)
      r->regstart = *OPERAND(scan);
    else if (OP(scan) == BOL)
      r->reganch++;
    
    /*
     * If there's something expensive in the r.e., find the
     * longest literal string that must appear and make it the
     * regmust.  Resolve ties in favor of later strings, since
     * the regstart check works with the beginning of the r.e.
     * and avoiding duplication strengthens checking.  Not a
     * strong reason, but sufficient in the absence of others.
     */
    if (flags&SPSTART) {
      longest = NULL;
      len = 0;
      for (; scan != NULL; scan = regnext(scan))
	if (OP(scan) == EXACTLY && strlen(OPERAND(scan)) >= len) {
	  longest = OPERAND(scan);
	  len = strlen(OPERAND(scan));
	}
      r->regmust = longest;
      r->regmlen = len;
    }
  }

  return(r);
}


/*
 - reg - regular expression, i.e. main body or parenthesized thing
 *
 * Caller must absorb opening parenthesis.
 *
 * Combining parenthesis handling with the base level of regular expression
 * is a trifle forced, but the need to tie the tails of the branches to what
 * follows makes it hard to avoid.
 */
static char *
reg(paren, flagp)
int paren;			/* Parenthesized? */
int *flagp;
{
  register char *ret;
  register char *br;
  register char *ender;
  register int parno;
  int flags;
  
  *flagp = HASWIDTH;	/* Tentatively. */
  
  /* Make an OPEN node, if parenthesized. */
  if (paren) {
    if (regnpar >= NSUBEXP)
      FAIL("too many ()");
    parno = regnpar;
    regnpar++;
    ret = regnode(OPEN+parno);
  } else
    ret = NULL;
  
  /* Pick up the branches, linking them together. */
  br = regbranch(&flags);
  if (br == NULL)
    return(NULL);
  if (ret != NULL)
    regtail(ret, br);	/* OPEN -> first. */
  else
    ret = br;
  if (!(flags&HASWIDTH))
		*flagp &= ~HASWIDTH;
  *flagp |= flags&SPSTART;
  while (*regparse == '|') {
    regparse++;
    br = regbranch(&flags);
    if (br == NULL)
      return(NULL);
    regtail(ret, br);	/* BRANCH -> BRANCH. */
    if (!(flags&HASWIDTH))
      *flagp &= ~HASWIDTH;
    *flagp |= flags&SPSTART;
  }
  
  /* Make a closing node, and hook it on the end. */
  ender = regnode((paren) ? CLOSE+parno : END);	
  regtail(ret, ender);
  
  /* Hook the tails of the branches to the closing node. */
  for (br = ret; br != NULL; br = regnext(br))
    regoptail(br, ender);
  
  /* Check for proper termination. */
  if (paren && *regparse++ != ')') {
    FAIL("unmatched ()");
  } else if (!paren && *regparse != '\0') {
    if (*regparse == ')') {
      FAIL("unmatched ()");
    } else
      FAIL("junk on end");	/* "Can't happen". */
    /* NOTREACHED */
  }
  
  return(ret);
}

/*
 - regbranch - one alternative of an | operator
 *
 * Implements the concatenation operator.
 */
static char *
regbranch(flagp)
int *flagp;
{
  register char *ret;
  register char *chain;
  register char *latest;
  int flags;
  
  *flagp = WORST;		/* Tentatively. */
  
  ret = regnode(BRANCH);
  chain = NULL;
  while (*regparse != '\0' && *regparse != '|' && *regparse != ')') {
    latest = regpiece(&flags);
    if (latest == NULL)
      return(NULL);
    *flagp |= flags&HASWIDTH;
    if (chain == NULL)	/* First piece. */
      *flagp |= flags&SPSTART;
    else
      regtail(chain, latest);
    chain = latest;
  }
  if (chain == NULL)	/* Loop ran zero times. */
    (void) regnode(NOTHING);
  
  return(ret);
}

/*
 - regpiece - something followed by possible [*+?]
 *
 * Note that the branching code sequences used for ? and the general cases
 * of * and + are somewhat optimized:  they use the same NOTHING node as
 * both the endmarker for their branch list and the body of the last branch.
 * It might seem that this node could be dispensed with entirely, but the
 * endmarker role is not redundant.
 */
static char *
regpiece(flagp)
int *flagp;
{
	register char *ret;
	register char op;
	register char *next;
	int flags;

	ret = regatom(&flags);
	if (ret == NULL)
		return(NULL);

	op = *regparse;
	if (!ISMULT(op)) {
		*flagp = flags;
		return(ret);
	}

	if (!(flags&HASWIDTH) && op != '?')
		FAIL("*+ operand could be empty");
	*flagp = (op != '+') ? (WORST|SPSTART) : (WORST|HASWIDTH);

	if (op == '*' && (flags&SIMPLE))
		reginsert(STAR, ret);
	else if (op == '*') {
		/* Emit x* as (x&|), where & means "self". */
		reginsert(BRANCH, ret);			/* Either x */
		regoptail(ret, regnode(BACK));		/* and loop */
		regoptail(ret, ret);			/* back */
		regtail(ret, regnode(BRANCH));		/* or */
		regtail(ret, regnode(NOTHING));		/* null. */
	} else if (op == '+' && (flags&SIMPLE))
		reginsert(PLUS, ret);
	else if (op == '+') {
		/* Emit x+ as x(&|), where & means "self". */
		next = regnode(BRANCH);			/* Either */
		regtail(ret, next);
		regtail(regnode(BACK), ret);		/* loop back */
		regtail(next, regnode(BRANCH));		/* or */
		regtail(ret, regnode(NOTHING));		/* null. */
	} else if (op == '?') {
		/* Emit x? as (x|) */
		reginsert(BRANCH, ret);			/* Either x */
		regtail(ret, regnode(BRANCH));		/* or */
		next = regnode(NOTHING);		/* null. */
		regtail(ret, next);
		regoptail(ret, next);
	}
	regparse++;
	if (ISMULT(*regparse))
		FAIL("nested *?+");

	return(ret);
}

/*
 - regatom - the lowest level
 *
 * Optimization:  gobbles an entire sequence of ordinary characters so that
 * it can turn them into a single node, which is smaller to store and
 * faster to run.  Backslashed characters are exceptions, each becoming a
 * separate node; the code is simpler that way and it's not worth fixing.
 */
static char *
regatom(flagp)
int *flagp;
{
  register char *ret;
  int flags;
  
  *flagp = WORST;		/* Tentatively. */
  
  switch (*regparse++) {
  case '^':
    ret = regnode(BOL);
    break;
  case '$':
    ret = regnode(EOL);
    break;
  case '.':
    ret = regnode(ANY);
    *flagp |= HASWIDTH|SIMPLE;
    break;
  case '[': {
    register int class;
    register int classend;
    
    if (*regparse == '^') {	/* Complement of range. */
      ret = regnode(ANYBUT);
      regparse++;
    } else
      ret = regnode(ANYOF);
    if (*regparse == ']' || *regparse == '-')
      regc(*regparse++);
    while (*regparse != '\0' && *regparse != ']') {
      if (*regparse == '-') {
	regparse++;
	if (*regparse == ']' || *regparse == '\0')
	  regc('-');
	else {
	  class = UCHARAT(regparse-2)+1;
	  classend = UCHARAT(regparse);
	  if (class > classend+1)
	    FAIL("invalid [] range");
	  for (; class <= classend; class++)
	    regc(class);
	  regparse++;
	}
      } else
	regc(*regparse++);
    }
    regc('\0');
    if (*regparse != ']')
      FAIL("unmatched []");
    regparse++;
    *flagp |= HASWIDTH|SIMPLE;
  }
    break;
  case '(':
    ret = reg(1, &flags);
    if (ret == NULL)
      return(NULL);
    *flagp |= flags&(HASWIDTH|SPSTART);
    break;
  case '\0':
  case '|':
  case ')':
    FAIL("internal urp");	/* Supposed to be caught earlier. */
  case '?':
  case '+':
  case '*':
    FAIL("?+* follows nothing");
  case '\\':
    if (*regparse == '\0')
      FAIL("trailing \\");
    ret = regnode(EXACTLY);
    regc(*regparse++);
    regc('\0');
    *flagp |= HASWIDTH|SIMPLE;
    break;
  default: {
    register int len;
    register char ender;
    
    regparse--;
    len = strcspn(regparse, META);
    if (len <= 0)
      FAIL("internal disaster");
    ender = *(regparse+len);
    if (len > 1 && ISMULT(ender))
      len--; /* Back off clear of ?+* operand. */
    *flagp |= HASWIDTH;
    if (len == 1)
      *flagp |= SIMPLE;
    ret = regnode(EXACTLY);
    while (len > 0) {
      regc(*regparse++);
      len--;
    }
    regc('\0');
  }
    break;
  }
  
  return(ret);
}

/*
 - regnode - emit a node
 */
static char *			/* Location. */
regnode(op)
char op;
{
	register char *ret;
	register char *ptr;

	ret = regcode;
	if (ret == &regdummy) {
		regsize += 3;
		return(ret);
	}

	ptr = ret;
	*ptr++ = op;
	*ptr++ = '\0';		/* Null "next" pointer. */
	*ptr++ = '\0';
	regcode = ptr;

	return(ret);
}

/*
 - regc - emit (if appropriate) a byte of code
 */
static void
regc(b)
char b;
{
	if (regcode != &regdummy)
		*regcode++ = b;
	else
		regsize++;
}

/*
 - reginsert - insert an operator in front of already-emitted operand
 *
 * Means relocating the operand.
 */
static void
reginsert(op, opnd)
char op;
char *opnd;
{
	register char *src;
	register char *dst;
	register char *place;

	if (regcode == &regdummy) {
		regsize += 3;
		return;
	}

	src = regcode;
	regcode += 3;
	dst = regcode;
	while (src > opnd)
		*--dst = *--src;

	place = opnd;		/* Op node, where operand used to be. */
	*place++ = op;
	*place++ = '\0';
	*place++ = '\0';
}

/*
 - regtail - set the next-pointer at the end of a node chain
 */
static void
regtail(p, val)
char *p;
char *val;
{
	register char *scan;
	register char *temp;
	register int offset;

	if (p == &regdummy)
		return;

	/* Find last node. */
	scan = p;
	for (;;) {
		temp = regnext(scan);
		if (temp == NULL)
			break;
		scan = temp;
	}

	if (OP(scan) == BACK)
		offset = scan - val;
	else
		offset = val - scan;
	*(scan+1) = (offset>>8)&0377;
	*(scan+2) = offset&0377;
}

/*
 - regoptail - regtail on operand of first argument; nop if operandless
 */
static void
regoptail(p, val)
char *p;
char *val;
{
	/* "Operandless" and "op != BRANCH" are synonymous in practice. */
	if (p == NULL || p == &regdummy || OP(p) != BRANCH)
		return;
	regtail(OPERAND(p), val);
}

/*
 * regexec and friends
 */

/*
 * Global work variables for regexec().
 */
static char *reginput;		/* String-input pointer. */
static char *regbol;		/* Beginning of input, for ^ check. */
static char **regstartp;	/* Pointer to startp array. */
static char **regendp;		/* Ditto for endp. */

/*
 * Forwards.
 */
STATIC int regtry();
STATIC int regmatch();
STATIC int regrepeat();

#ifdef DEBUG
int regnarrate = 0;
void regdump();
STATIC char *regprop();
#endif

/*
 - regexec - match a regexp against a string
 */
int
RegExec(prog, string) /* formerly "regexec" */
register regexp *prog;
register char *string;
{
	register char *s;

	/* Be paranoid... */
	if (prog == NULL || string == NULL) {
		regerror("NULL parameter");
		return(0);
	}

	/* Check validity of program. */
	if (UCHARAT(prog->program) != MAGIC) {
		regerror("corrupted program");
		return(0);
	}

	/* If there is a "must appear" string, look for it. */
	if (prog->regmust != NULL) {
		s = string;
		while ((s = strchr(s, prog->regmust[0])) != NULL) {
			if (strncmp(s, prog->regmust, prog->regmlen) == 0)
				break;	/* Found it. */
			s++;
		}
		if (s == NULL)	/* Not present. */
			return(0);
	}

	/* Mark beginning of line for ^ . */
	regbol = string;

	/* Simplest case:  anchored match need be tried only once. */
	if (prog->reganch)
		return(regtry(prog, string));

	/* Messy cases:  unanchored match. */
	s = string;
	if (prog->regstart != '\0')
		/* We know what char it must start with. */
		while ((s = strchr(s, prog->regstart)) != NULL) {
			if (regtry(prog, s))
				return(1);
			s++;
		}
	else
		/* We don't -- general case. */
		do {
			if (regtry(prog, s))
				return(1);
		} while (*s++ != '\0');

	/* Failure. */
	return(0);
}

/*
 - regtry - try match at specific point
 */
static int			/* 0 failure, 1 success */
regtry(prog, string)
regexp *prog;
char *string;
{
	register int i;
	register char **sp;
	register char **ep;

	reginput = string;
	regstartp = prog->startp;
	regendp = prog->endp;

	sp = prog->startp;
	ep = prog->endp;
	for (i = NSUBEXP; i > 0; i--) {
		*sp++ = NULL;
		*ep++ = NULL;
	}
	if (regmatch(prog->program + 1)) {
		prog->startp[0] = string;
		prog->endp[0] = reginput;
		return(1);
	} else
		return(0);
}

/*
 - regmatch - main matching routine
 *
 * Conceptually the strategy is simple:  check to see whether the current
 * node matches, call self recursively to see whether the rest matches,
 * and then act accordingly.  In practice we make some effort to avoid
 * recursion, in particular by going through "ordinary" nodes (that don't
 * need to know whether the rest of the match failed) by a loop instead of
 * by recursion.
 */
static int			/* 0 failure, 1 success */
regmatch(prog)
char *prog;
{
  register char *scan;	/* Current node. */
  char *next;		/* Next node. */
  
  scan = prog;
#ifdef DEBUG
  if (scan != NULL && regnarrate)
    fprintf(stderr, "%s(\n", regprop(scan));
#endif
  while (scan != NULL) {
#ifdef DEBUG
    if (regnarrate)
      fprintf(stderr, "%s...\n", regprop(scan));
#endif
    next = regnext(scan);
    
    switch (OP(scan)) {
    case BOL:
      if (reginput != regbol)
	return(0);
      break;
    case EOL:
      if (*reginput != '\0')
	return(0);
      break;
    case ANY:
      if (*reginput == '\0')
	return(0);
      reginput++;
      break;
    case EXACTLY: {
      register int len;
      register char *opnd;
      
      opnd = OPERAND(scan);
      /* Inline the first character, for speed. */
      if (*opnd != *reginput)
	return(0);
      len = strlen(opnd);
      if (len > 1 && strncmp(opnd, reginput, len) != 0)
	return(0);
      reginput += len;
    }
      break;
    case ANYOF:
      if (*reginput == '\0' || strchr(OPERAND(scan), *reginput) == NULL)
	return(0);
      reginput++;
      break;
    case ANYBUT:
      if (*reginput == '\0' || strchr(OPERAND(scan), *reginput) != NULL)
	return(0);
      reginput++;
      break;
    case NOTHING:
      break;
    case BACK:
      break;
    case OPEN+1:
    case OPEN+2:
    case OPEN+3:
    case OPEN+4:
    case OPEN+5:
    case OPEN+6:
    case OPEN+7:
    case OPEN+8:
    case OPEN+9: {
      register int no;
      register char *save;
      
      no = OP(scan) - OPEN;
      save = reginput;
      
      if (regmatch(next)) {
	/*
	 * Don't set startp if some later
	 * invocation of the same parentheses
	 * already has.
	 */
	if (regstartp[no] == NULL)
	  regstartp[no] = save;
	return(1);
      } else
	return(0);
    }
    case CLOSE+1:
    case CLOSE+2:
    case CLOSE+3:
    case CLOSE+4:
    case CLOSE+5:
    case CLOSE+6:
    case CLOSE+7:
    case CLOSE+8:
    case CLOSE+9: {
      register int no;
      register char *save;
      
      no = OP(scan) - CLOSE;
      save = reginput;
      
      if (regmatch(next)) {
	/*
	 * Don't set endp if some later
	 * invocation of the same parentheses
	 * already has.
	 */
	if (regendp[no] == NULL)
	  regendp[no] = save;
	return(1);
      } else
	return(0);
    }
    case BRANCH: {
      register char *save;
      
      if (OP(next) != BRANCH)		/* No choice. */
	next = OPERAND(scan);	/* Avoid recursion. */
      else {
	do {
	  save = reginput;
	  if (regmatch(OPERAND(scan)))
	    return(1);
	  reginput = save;
	  scan = regnext(scan);
	} while (scan != NULL && OP(scan) == BRANCH);
	return(0);
	/* NOTREACHED */
      }
    }
      break;
    case STAR:
    case PLUS: {
      register char nextch;
      register int no;
      register char *save;
      register int min;
      
      /*
       * Lookahead to avoid useless match attempts
       * when we know what character comes next.
       */
      nextch = '\0';
      if (OP(next) == EXACTLY)
	nextch = *OPERAND(next);
      min = (OP(scan) == STAR) ? 0 : 1;
      save = reginput;
      no = regrepeat(OPERAND(scan));
      while (no >= min) {
	/* If it could work, try it. */
	if (nextch == '\0' || *reginput == nextch)
	  if (regmatch(next))
	    return(1);
	/* Couldn't or didn't -- back up. */
	no--;
	reginput = save + no;
      }
      return(0);
    }
    case END:
      return(1);	/* Success! */
    default:
      regerror("memory corruption");
      return(0);
    }
    
    scan = next;
  }
  
  /*
   * We get here only if there's trouble -- normally "case END" is
   * the terminating point.
   */
  regerror("corrupted pointers");
  return(0);
}

/*
 - regrepeat - repeatedly match something simple, report how many
 */
static int
regrepeat(p)
char *p;
{
  register int count = 0;
  register char *scan;
  register char *opnd;
  
  scan = reginput;
  opnd = OPERAND(p);
  switch (OP(p)) {
  case ANY:
    count = strlen(scan);
    scan += count;
    break;
  case EXACTLY:
    while (*opnd == *scan) {
      count++;
      scan++;
    }
    break;
  case ANYOF:
    while (*scan != '\0' && strchr(opnd, *scan) != NULL) {
      count++;
      scan++;
    }
    break;
  case ANYBUT:
    while (*scan != '\0' && strchr(opnd, *scan) == NULL) {
      count++;
      scan++;
    }
    break;
  default:		/* Oh dear.  Called inappropriately. */
    regerror("internal foulup");
    count = 0;	/* Best compromise. */
    break;
  }
  reginput = scan;
  
  return(count);
}

/*
 - regnext - dig the "next" pointer out of a node
 */
static char *
regnext(p)
register char *p;
{
	register int offset;

	if (p == &regdummy)
		return(NULL);

	offset = NEXT(p);
	if (offset == 0)
		return(NULL);

	if (OP(p) == BACK)
		return(p-offset);
	else
		return(p+offset);
}

#ifdef DEBUG

STATIC char *regprop();

/*
 - regdump - dump a regexp onto stdout in vaguely comprehensible form
 */
void
regdump(r)
regexp *r;
{
  register char *s;
  register char op = EXACTLY;	/* Arbitrary non-END op. */
  register char *next;
  extern char *strchr();
  
  
  s = r->program + 1;
  while (op != END) {	/* While that wasn't END last time... */
    op = OP(s);
    printf("%2d%s", s-r->program, regprop(s));	/* Where, what. */
    next = regnext(s);
    if (next == NULL)		/* Next ptr. */
      printf("(0)");
    else 
      printf("(%d)", (s-r->program)+(next-s));
    s += 3;
    if (op == ANYOF || op == ANYBUT || op == EXACTLY) {
      /* Literal string, where present. */
      while (*s != '\0') {
	putchar(*s);
	s++;
      }
      s++;
    }
    putchar('\n');
  }
  
  /* Header fields of interest. */
  if (r->regstart != '\0')
    printf("start `%c' ", r->regstart);
  if (r->reganch)
    printf("anchored ");
  if (r->regmust != NULL)
    printf("must have \"%s\"", r->regmust);
  printf("\n");
}

/*
 - regprop - printable representation of opcode
 */
static char *
regprop(op)
char *op;
{
	register char *p;
	static char buf[50];

	(void) strcpy(buf, ":");

	switch (OP(op)) {
	case BOL:
		p = "BOL";
		break;
	case EOL:
		p = "EOL";
		break;
	case ANY:
		p = "ANY";
		break;
	case ANYOF:
		p = "ANYOF";
		break;
	case ANYBUT:
		p = "ANYBUT";
		break;
	case BRANCH:
		p = "BRANCH";
		break;
	case EXACTLY:
		p = "EXACTLY";
		break;
	case NOTHING:
		p = "NOTHING";
		break;
	case BACK:
		p = "BACK";
		break;
	case END:
		p = "END";
		break;
	case OPEN+1:
	case OPEN+2:
	case OPEN+3:
	case OPEN+4:
	case OPEN+5:
	case OPEN+6:
	case OPEN+7:
	case OPEN+8:
	case OPEN+9:
		sprintf(buf+strlen(buf), "OPEN%d", OP(op)-OPEN);
		p = NULL;
		break;
	case CLOSE+1:
	case CLOSE+2:
	case CLOSE+3:
	case CLOSE+4:
	case CLOSE+5:
	case CLOSE+6:
	case CLOSE+7:
	case CLOSE+8:
	case CLOSE+9:
		sprintf(buf+strlen(buf), "CLOSE%d", OP(op)-CLOSE);
		p = NULL;
		break;
	case STAR:
		p = "STAR";
		break;
	case PLUS:
		p = "PLUS";
		break;
	default:
		regerror("corrupted opcode");
		break;
	}
	if (p != NULL)
		(void) strcat(buf, p);
	return(buf);
}
#endif

/*
 * The following is provided for those people who do not have strcspn() in
 * their C libraries.  They should get off their butts and do something
 * about it; at least one public-domain implementation of those (highly
 * useful) string routines has been published on Usenet.
 */
#ifdef STRCSPN
/*
 * strcspn - find length of initial segment of s1 consisting entirely
 * of characters not from s2
 */

static int
strcspn(s1, s2)
char *s1;
char *s2;
{
	register char *scan1;
	register char *scan2;
	register int count;

	count = 0;
	for (scan1 = s1; *scan1 != '\0'; scan1++) {
		for (scan2 = s2; *scan2 != '\0';)	/* ++ moved down. */
			if (*scan1 == *scan2++)
				return(count);
		count++;
	}
	return(count);
}
#endif



/****** RegWildToRegexp *******************************************************
**
**      converts a string containing wildcards into a regular expression; 
**      the world can contain
**      the wildcards '*' (any number of chars) and '?' (any single character);
**      the function returns the position of the first wildcard within the
**      word (first position is 1!);
**      "." is converted to "\."
**      expression will begin with '^' and end with '$';
**
**	INPUT:	 o  string containing wildcards [R]
**               o  pointer to output regular expression [R]
**               o  flag if wildcards (see above) are to be recognized as
**                  such and be replaced within a regular expression
**	        IMPLICIT:
**
**	RETURNS:  0 if word contains no wildcards
**                position of first wildcard in string (1=string begin)
*/      

int RegWildToRegexp (char *s, char *reStr, INT4 isWild)
{
  int firstWildLoc=0, k;
  char c, tmp[512];
  char *reStrPtr=tmp; /* tmp str so that output can be written
			 to input str */

  /*
  ** a full regular expression is given between two  '/' s
  */

  if (*s == '/' && *(s + strlen (s) - 1) == '/') {
    strcpy (tmp, s+1); /* remove left '/'*/
    tmp[ strlen (tmp) - 1 ] = '\0'; /* ...and right '/' */
    strcpy (reStr, tmp);
    return 1;
  }


  if (isWild) {
    *reStrPtr++ = '^';  /* begin of line */
    for (k=0; (c = s[k]); k++) {
      switch (c) {
      case '*':
      case '?':
	if (!firstWildLoc)
	  firstWildLoc = k+1;
	*reStrPtr++ = '.';
	if (c == '*') {
	  *reStrPtr++ = '*';
	}
	break;
      case '.':
      case '|':
      case '(':
      case ')':
      case '+':
      case '[':
	*reStrPtr++ = '\\';
	*reStrPtr++ = c;
	break;
      default:
	*reStrPtr++ = s[k];
      }
    }
    *reStrPtr++ = '$';  /* end of line */
    *reStrPtr = '\0';
    if (reStr)
      strcpy (reStr, tmp);
  }
  return firstWildLoc;
}

(c = s[k]); k++) {
      switch (c) {
      case '*':
      case '?':
	if (!firstWildLoc)
	  firstWildLoc = k+1;
	*reStrPtr++ = '.';
	if (c == '*') {
	  *reStrPtr++ = '*';
	}
	break;
      case '.':
      case '|':
      case '(':
      case ')':
      case '+':
      case '[':
	*reStrPtr++ = '\\';
	*reStrPtr++ = c;
	break;
      default:
	*reStrPtr++ = s[k];
      }
    }
    *reStrPtr++ = '$';  /* end of line */
    *reStrPtr = '\srs/src/regexp.h
 * Definitions etc. for regexp(3) routines.
 *
 * Caveat:  this is V8 regexp(3) [actually, a reimplementation thereof],
 * not the System V one.
 */
#define NSUBEXP  10
typedef struct regexp {
	char *startp[NSUBEXP];
	char *endp[NSUBEXP];
	char regstart;		/* Internal use only. */
	char reganch;		/* Internal use only. */
	char *regmust;		/* Internal use only. */
	int regmlen;		/* Internal use only. */
	char program[1];	/* Unwarranted chumminess with compiler. */
} regexp;

extern regexp *RegComp();
extern int RegExec();
extern void regsub();
extern void regerror();
extern int RegWildToRegexp (char *str, char *reStr, int isWild);
ot the System V one.
 */
#define NSUBEXP  10
typedef struct regexp {
	char *startp[NSUBEXP];
	char *endp[NSUBEXP];
	char regstart;		/* Internal use only. */
	char reganch;		/* Internal use only. */
	char *regmust;		/* Internal use only. */
	int regmlen;		/* Internal use only. */
	char program[1];	/* Unwarranted chumminess with compiler. */
} regexp;

extern regexp *RegComp();
externsrs/src/regmagic.h
 * The first byte of the regexp internal "program" is actually this magic
 * number; the start node begins in the second byte.
 */
#define	MAGIC	0234
define NSUBEXP  10
typedef struct regexp {
	char *startp[NSUBEXP];
	char *endp[NSUBEXP];
	char regstart;		/* Internal use only. */
	char reganch;		/* Internal use only. */
	char *regmust;		/* Internal use only. */
	int regmlen;		/* Internal use only. */
	char program[1];	/* Unwarranted chumminess with compiler. */
} regexp;

extern regexp *R¶ £¡Ü;
externsrs/src/regsub.c
 * regsub
 * @(#)regsub.c	1.3 of 2 April 86
 *
 *	Copyright (c) 1986 by University of Toronto.
 *	Written by Henry Spencer.  Not derived from licensed software.
 *
 *	Permission is granted to anyone to use this software for any
 *	purpose on any computer system, and to redistribute it freely,
 *	subject to the following restrictions:
 *
 *	1. The author is not responsible for the consequences of use of
 *		this software, no matter how awful, even if they arise
 *		from defects in it.
 *
 *	2. The origin of this software must not be misrepresented, either
 *		by explicit claim or by omission.
 *
 *	3. Altered versions must be plainly marked as such, and must not
 *		be misrepresented as being the original software.
 */
#include <stdio.h>
#include <regexp.h>
#include "regmagic.h"

#ifndef CHARBITS
#define	UCHARAT(p)	((int)*(unsigned char *)(p))
#else
#define	UCHARAT(p)	((int)*(p)&CHARBITS)
#endif

/*
 - regsub - perform substitutions after a regexp match
 */
void
regsub(prog, source, dest)
regexp *prog;
char *source;
char *dest;
{
	register char *src;
	register char *dst;
	register char c;
	register int no;
	register int len;
	extern char *strncpy();

	if (prog == NULL || source == NULL || dest == NULL) {
		regerror("NULL parm to regsub");
		return;
	}
	if (UCHARAT(prog->program) != MAGIC) {
		regerror("damaged regexp fed to regsub");
		return;
	}

	src = source;
	dst = dest;
	while ((c = *src++) != '\0') {
		if (c == '&')
			no = 0;
		else if (c == '\\' && '0' <= *src && *src <= '9')
			no = *src++ - '0';
		else
			no = -1;

		if (no < 0) {	/* Ordinary character. */
			if (c == '\\' && (*src == '\\' || *src == '&'))
				c = *src++;
			*dst++ = c;
		} else if (prog->startp[no] != NULL && prog->endp[no] != NULL) {
			len = prog->endp[no] - prog->startp[no];
			(void) strncpy(dst, prog->startp[no], len);
			dst += len;
			if (len != 0 && *(dst-1) == '\0') {	/* strncpy hit NUL. */
				regerror("damaged match string");
				return;
			}
		}
	}
	*dst++ = '\0';
}
&& '0' <= *src && *src <= '9')
			no = *src++ - '0';
		esrs/src/sdlget.c
char sdlget_ID[] = "\n$Id: sdlget.c,v 1.1 1996/05/06 15:17:15 srs Exp $";
/*
**
**    $RCSfile: sdlget.c,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:17:15 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.x Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>

#include "message.h"
#include "futil.h"
#include "odd.h"
#define _SDL	
#define _ODD	
#include "oddclass.h"

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  object wide variables
*/

#ifndef BOOTSTRAP 
typedef int (*SDLoFNCT)();
extern	SDLoFNCT    SDL_fnctx[];
#endif 

SDLoPTR section;
INT4	section_z;

/**api* SdlGetObjects *********************************************************
** 
** 	expands name to "SRSSEC:name.SEC" and "... .PTR" reads these files
** 	using block-IO into newly allocated memory; addresses in ref-list
** 	are corrected for the difference of location of section-block;
** 
** 	INPUT:	    address of array of array of objects [W]
** 		    address of array of sizes of above array  [W]
** 		    address of section name [R]
** 	        IMPLICIT:
**                  SDL_fnct (SDLoFNCT[]) [R]
** 		    section (void *) [W]
** 		    section_z (int) [W]
** 
** 	RETURNS:    1
*/ 
   
INT4 SdlGetObjects (long int **obj_n, void ***obj_p, char *sec_nm)
{
  FILE      *sec_fd, *ptr_fd;
  char      fil_nm[FILxXNAM+1];
  SDLoPTR   *ptr, *ptrlist, data, *addr, sec, *o_p, *ptr_p;
  long int  addr_n, *o_n;
  int       diff, k, objc_n, rv, sec_z, ptr_z;

  /*
  ** open file with the data (*.sec) and the file with a list of pointers
  ** int the data file to be updated (*.ptr)
  */

  sprintf (fil_nm, "SRSSEC:%s.sec", sec_nm);
  sec_fd = FilOpenR (fil_nm, &rv);
  _ErrExit2 (rv, fil_nm);
  
  sprintf (fil_nm, "SRSSEC:%s.ptr", sec_nm);
  ptr_fd = FilOpenR (fil_nm, &rv);
  _ErrExit2 (rv, fil_nm);
  
  /*
  ** get the sizes of both files, allocate memory accordingly and read the
  ** files in one go
  */

  rv = fread (&sec_z, sizeof(int), 1, sec_fd);
  if (sizeof (char *) != sizeof (int))
    fseek (sec_fd, sizeof (char *) - sizeof (int), 1);  /** 1 == SEEK_CUR */
  rv = fread (&ptr_z, sizeof(int), 1, ptr_fd);

  if ((sec = (SDLoPTR) malloc (sec_z)) == NULL) 
    _ErrExit2(e__allocfail, "section by SdlGetObjects");
  
  section = sec;  /** global variables	*/
  section_z = sec_z;
  
  if ((ptrlist = (SDLoPTR *) malloc (ptr_z)) == 0)
    _ErrExit2(e__allocfail, "pointer array by SdlGetObjects");

  fread (sec, 1, sec_z, sec_fd);
  fread (ptrlist, 1, ptr_z, ptr_fd);
  ptr = ptrlist;

  /*
  ** get the following info from begin of .ptr file:
  **   o address of section begin (at the time section was built)
  **   o number of object classes represented in the section
  **   o for each class the number of instances + offset of its array in 
  **     the section   
  */

  data = (char *) *ptr++;  /** addr of section begin */
  objc_n = (long) *ptr++;  /** number of objects */

  o_n = (long *) malloc (objc_n * sizeof (int *));
  o_p = (SDLoPTR *) malloc (objc_n * sizeof (unsigned int *));
  diff = (int) (sec - data);
  
  for (k=0;  k < objc_n;  k++) {
    o_p[k] = (SDLoPTR) (*ptr++) + diff;  /** address of obj-array */
    o_n[k] = (long) *ptr++;  /** size of obj-array */
  }
  
  /*
  ** then read the number of references
  */

  addr_n = (long) *ptr++;  /** number of references    */
  addr = ptr;  /** ref list */
  
  for (k=0;  k < addr_n;  k++) {
    ptr_p = (SDLoPTR *) (addr[k] + diff);
    if ((long) *ptr_p <= SDLxXFNCT) {
#ifndef BOOTSTRAP
      if ((long) *ptr_p < 0) 
	*ptr_p = 0;
      else 
	*ptr_p = (long) *ptr_p == SDLxXFNCT ? 
	  NULL : (SDLoPTR) SDL_fnctx[(long)*ptr_p];
#else 
      ; 
#endif
    }
    else 
      *ptr_p = *ptr_p + diff;
  }
  
  /*
  ** delete list of pointers to be relocated and return info to caller
  */
  
  free (ptrlist);
  
  *obj_p = (void **) o_p;
  *obj_n = o_n;
  return objc_n;
}


/**api* SdlGetObj *************************************************************
**
**	gets pointer to objects of a type and the number;
**
**	INPUT:	    address of SDL descr. [R]
**		    object-class ID [R]
**		    address of object pointer [W]
**		    address of object count [W]
**	        IMPLICIT:
**
**	RETURNS:    1
*/ 
   
INT4 SdlGetObj (SDLo *sdl, int class_x, void **obj_p, int *obj_n)
{
  *obj_p = (void *) (sdl->oc[class_x].s);
  *obj_n = sdl->oc[class_x].ns;
  return 1;
}


/**api* OddIsInDepot **********************************************************
**
**	returns 1 if pointer points within a depot with defined ODD objects
**      ...means that that 
**      cannot be freed because the whole depot is allocated as one big block
**
**	INPUT:	    address [R]
**	        IMPLICIT:
**
**	RETURNS:    1
*/ 
   
INT4 OddIsInDepot (char *p)
{
  return  (p >= section && p < section + section_z) ? 1 : 0;
}
= (void *) (sdl->oc[class_x].s);
  *obj_n = sdl->oc[class_x].ns;
  return 1;
}


/**api* OddIsInDepot **********************************************************
**
**	returns 1 if pointer posrs/src/sdlget.h
**
**    $RCSfile: sdlget.h,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:17:15 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**                  Copyright by Thure Etzold
**
*/

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  list of functions exported by module "seqlib"
*/

INT4 OddIsInDepot (char *p);
********************************************
**
**	returns¶ £¡Üinter posrs/src/sdlnew.c
char sdl_ID[] = "$Id: sdlnew.c,v 1.14 1997/03/18 22:52:32 srs Exp $";
/*
**
**    $RCSfile: sdlnew.c,v $
**    $Revision: 1.14 $
**    $Date: 1997/03/18 22:52:32 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  Copyright by Thure Etzold
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>

#include "message.h"
#include "futil.h"
#include "sm.h"
#include "strv.h"
#include "tm.h"
#include "map.h"
#include "par.h"
#include "templ.h"
#include "dict.h"
#include "variable.h"

#define _SDL
#define _ODD
#include "oddclass.h"
#include "odd.h"

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  macros and enums
*/

enum status {ODDxOBSOLETE=1, ODDxSYSTEM, ODDxAPI};
enum linebreak {SDLxFIRST=1, SDLxLAST=2, SDLxBREAK=4, SDLxBOUND=8};

typedef INT4 (*SDLoFNCT)();

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  object wide variables
*/

static int	    addr_n = 0;
static SDLoPTR      *addr;
static FILo	    file;
static int	    fnct_x;
SDLo                *odd=NULL;
ODDoFNCT_P	    function[SDLxXFNCT];
FILo		    *f = &file; 
static MAPo	    map;
ODDoCDEFINE         cDefine[100];
INT4                cDefineN=0;

#ifndef BOOTSTRAP 
extern SDLoFNCT     SDL_fnct[];
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of static functions
*/

static void OddSetFlags (int opt);
static int  OddObjSizes (void);
static int  SdlAlloc (void);
       int  SdlWrtHdr (SDLo *d, int opt);
static int  SdlCloseSec ();
static int  SdlObjInx (char *nam);
       int  OddRegisterObj (SDLoOBJ *obj);
static int  SdlIsChild (int p_x, int ch_x);
     void  *OddFinishObj (SDLoOBJ *obj);
static int  OddResetObj (SDLoOBJ *obj);
static int  OddGetValue (SDLoATTR *attr, char **tokstr, 
			 unsigned *tokval, VARo *value);
static int  SdlCopySec (char **s);
static int  SdlWrtTtl (FILE *f, char *in, char *out);
static int  SdlWrtTypDef (FILE *fil, SDLoOBJ *s, int ns);
static int  OddWrtInit (FILE *fil, SDLoOBJ *s, int ns);
static void OddWrtInitExtern (FILE *file, SDLoOBJ *class, int classN);
static int  SdlWrtAttr (FILE *fil, SDLoOBJ *obj, char *typdef_nm, 
		       char *gtyp_nm);
static int  SdlWrtFnct (FILE *f, SDLoOBJ *s);
void OddWriteClassInfo (SDLo *odd);

INT4 OddIsAttr (SDLoATTR *attr, char *option);
INT4 OddIsClass (SDLoOBJ *class, char *option);


/**api* OddInit ***************************************************************
**
**
**	INPUT:	    ODD data base object [W]
**
**		IMPLICIT:
**                  odd (SDLo *) [W]
**
**	RETURNS:    1 
*/ 

SDLo *OddInit (SDLo *oddBase, INT4 level)
{
  ODDoATYP *at;
  INT4     atN;

  if (level == 1) {
    odd = oddBase;
  }
  else if (level == 2) {
    at = oddBase->at;
    atN = oddBase->at_n;
    odd = (SDLo *) oddBase->oc[odd->oc_n-1].s;
    odd->at = at;
    odd->at_n = atN;
    odd->action |= SDLxHDR;
  }
  odd->pass_n = 1;
  OddSetFlags (level);
  OddObjSizes ();
  return odd;
}

Int4 OddIsActive ()
{
  return odd ? 1 : 0;
}


/**api* OddInit ***************************************************************
**
**
**	INPUT:	    ODD data base object [W]
**
**		IMPLICIT:
**                  odd (SDLo *) [W]
**
**	RETURNS:    1 
*/ 

void OddInitDepot ()
{
  if (odd->pass_n == 1) {
    odd->pass_n = 2;
    SdlAlloc (); 
  }
}


/****** SdlMalloc *************************************************************
**
**	same as malloc but creates a mapsection initially
**
**	INPUT:	    nr. of bytes to allocate [R]
**	        IMPLICIT:
**                  addr (unsigned int)
**		    odd (SDLo *)
**                  map (MAPo)
**
**	RETURNS:    address of allocated area
**		    NULL if none available
*/ 
   
void *SdlMalloc (int siz)
{
  static int init_f = FALSE;
  char       fil_nm[FILxXNAM+1];
  int        shiftalign, rv;

  if (!init_f) /* init_f is FALSE on first call, else TRUE */ {

    /*
    ** this part of the code is only execute the first time this
    ** function is called. It then allocates a map section of
    ** size given by odd->sec_z
    */

    sprintf (fil_nm, "SRSSEC:%s.sec", odd->sec_nm);
    rv = MapAlloc (&map, fil_nm, odd->sec_z);
    _ErrExit (rv);
    
    /*
    ** first int in section has the file offset after the last byte written
    ** to same section...this int + some bytes (for alignment) must be skipped
    ** before starting to write to the section
    */

    shiftalign = (sizeof (char *) - sizeof (unsigned int));	
    map.off += shiftalign;
    *(map.foff) += shiftalign;

    if ((addr = (SDLoPTR *) malloc (sizeof (SDLoPTR) * SDLxXADDR)) == NULL)
      _ErrExit2(e__allocfail, "array addr");
    init_f = TRUE;
  }
  return (void *) MapMalloc (&map, siz);
}


/****** OddSetFlags ***********************************************************
**
**	sets global flags;
**
**	INPUT:	    compilation level (1 or 2) [R] 
**	        IMPLICIT:
**                  odd (SDLo *) [W]
**
**	RETURNS:    1
*/ 
   
static void OddSetFlags (INT4 level)
{
  odd->error = FALSE;

  if (level == 1) {
    if (ParGetBool ("doMetaData"))
      odd->action = SDLxHDR;
    else 
      odd->action = SDLxNOHDR;
  }
  else if (level == 2) {
    if (ParGetBool ("doInitHeader"))
      odd->action = SDLxHDR;
    else if (ParGetBool ("doSection") && ParGetBool ("doHeader"))
      odd->action = SDLxHDRSEC;
    else if (ParGetBool ("doSection"))
      odd->action = SDLxSECTION;
    else if (ParGetBool ("doHeader"))
      odd->action = SDLxHDR2;
    else if (ParGetBool ("doClassInfo"))
      odd->action = SDLxHDR2;
  }
  odd->section_f = (odd->action == SDLxSECTION || odd->action == SDLxHDRSEC);
}



/**new* OddGetClass ***********************************************************
**
**      Returns the class object which has the specified name.
**
**	INPUT:	    name of the class [W]
**		IMPLICIT:
**                  odd (SDLo *)
**
**
**	RETURNS:
**		    class object
**                  NULL if specified class does not exist
*/ 
   
SDLoOBJ *OddGetClass (char *className)
{
  SDLoOBJ *class;
  INT4    classIndex;

  classIndex = SdlObjInx (className); 
  _ErrIf (classIndex)
    return NULL;
  else
    return &(odd->oc[classIndex]); 
}

void *OddGetCurrObj (SDLoOBJ *class)
{
  return class->uobj_coff;
}


char *OddGetClassName (SDLoOBJ *class)
{
  return class->nam;
}

SDLoOBJ *OddGetPartofClass (SDLoATTR *attr)
{
  return &(odd->oc[attr->dfltv]);
}


void *OddGetObjectPtr (SDLoOBJ *class, Int4 n)
{
  Int4 firstX;

  firstX =  (n < 0) ? class->gbl_n + n : n;
  return (void *) (class->s + (class->siz * firstX));

}

Int4 OddGetObjectN (SDLoOBJ *class)
{
  return (class->ns);

}

void OddSetObjListSize (SDLoOBJ *class, char *attrName, Int4 n)
{
  SDLoOBJ  *refClass;
  SDLoATTR *attr;
  char tmp[100];
  
  sprintf (tmp, "%sN", attrName);
  if ((attr = OddGetAttribute (class, tmp))) {
    attr->hasObjsN = n;
    if (!(attr = OddGetAttribute (class, attrName)))
      _ErrExit3 (e__icaunknownattr, OddGetClassName (class), attrName);
    attr->hasObjsN = n;
    refClass = OddGetPartofClass (attr);
    attr->hasFirstObj = OddGetObjectPtr (refClass, -n); 
  }
}


/****** OddFinishObj ***********************************************************
**
**	does post processing of object i.e. checks whether all required
**	attributes have been read, fills non read attributes with defaults;
**
**	INPUT:	    object ID [W]
**		IMPLICIT:
**                  odd (SDLo *) [W]
**                  f (FILo *) [R]
**
**	RETURNS:    1 if success
**		    e__icarequiredattr <ln nr. parnam> +
**		    e__parnotok <ln nr., str> +
**		    e__noss <ln nr. parnam> +
*/ 
   
void *OddFinishObj (SDLoOBJ *class)
{
  SDLoATTR *attr;        
  SDLoPTR  off;
  int      rv, k;
  int      (*make) (SDLoOBJ *, SDLoATTR *, SDLoPTR *);

  for (k = 0;  k < class->np;  k++) {
    attr = &(class->p[k]);
    off = class->uobj_coff + attr->off; /* off to place prmtr	    */
    if ((make = odd->at[attr->typ].make) != NULL) {
      rv = (*make) (class, attr, &off); 
    }
    _ErrIf (rv) {
      if (rv == e__icarequiredattr)
	_ErrMsg3(e__icarequiredattr, attr->nam, OddGetClassName (class));
      odd->error = TRUE;                                          
      continue;
    }
  }
  if (odd->section_f && class->typ != SDLxVIRTUAL)
    SdlSaveAddr (class, class->uobj_coff); /* save pointers */
  OddResetObj (class);
  return class->uobj_coff;
}


/****** OddResetObj **********************************************************
**
**	after a object has been read along with all child-objects
**	some attributes of SDLoOBJ and SDLoATTR have to be reset before
**	working on the next object on the same level; this is
**	what is done here;
**
**	INPUT:	    object ID [W]
**		IMPLICIT: 
**                 odd (SDLo *) [W]
**
**	RETURNS:    1 
*/ 
   
static int OddResetObj (SDLoOBJ *obj)
{
  SDLoOBJ  *tmp;
  SDLoATTR *attr;
  int      k;

  for (k = 0;  k < obj->np;  k++) {
    attr = &obj->p[k];
    attr->isrd = FALSE;
    attr->hasObjsN = -1;
  }  
  for (k = 0;  k < obj->nss;  k++) { /* child-objects	    */
    tmp = &odd->oc[ (obj->ss)[k] ];
    if (tmp != obj)
      tmp->loc_n = 0;
  }
  return 1;
}



/****** OddRegisterObj ********************************************************
**
**	increments counter for a specific object and calculates offset
**	of new target object;
**	counters gbl_n and loc_n must be initialized with 0
**
**	INPUT:	    address of object-descriptor (SDLoOBJ) [W]
**		IMPLICIT:
**                  odd (SDLo *)
**
**	RETURNS:    1 if success	
**		    e__toomanstrct <strct nr, nr. of strct alloc>
*/ 
   
int OddRegisterObj (SDLoOBJ *obj)
{
  (obj->gbl_n)++;
  (obj->loc_n)++;
  if (obj->gbl_n > obj->ns && odd->pass_n == 2)
    return e__toomanstrct;
  if (obj->gbl_n != 1)
    obj->uobj_coff += obj->siz;
  else
    obj->uobj_coff = obj->s;
  return 1;
}


/******************* odd ids ************************************************/

typedef struct ODDoID {
  char    name[80];
  SDLoOBJ *class;
  INT4    objX;
} ODDoID;

static void* OddIdToKey (DictElem* e)
{
  return (*(ODDoID **)e)->name;
}
static CLASSoDICT idDictClass = {
  (ValComparer)strequal, (ValHasher)strhash, (KeyAccessor)OddIdToKey, NULL, 0
};


static DICTv idDict=NULL;

void OddIdInit ()
{
  if (idDict)
    DictDestroy (idDict);

  idDict = DictCreate (&idDictClass);
}

int OddIdRetrieve (char *idName, INT4 isOptional)
{
  Iter   i;
  ODDoID *id;

  if (i = DictWith (idDict, idName)) {
    id = DictIn (i, ODDoID*);
    return id->objX;
  }      
  else {
    if (!isOptional)
      _ErrMsg3 (e__objectunknown, "object-ID", idName);
    return -1;
  }
}

void OddIdRegister (SDLoOBJ *class, char *idName)
{
  ODDoID *id;

  if ((id = (ODDoID *) malloc (sizeof (ODDoID))) == NULL)
    _ErrExit2 (e__allocfail, "object-Id");

  strcpy (id->name, idName);
  id->class = class;
  id->objX = class->gbl_n-1;

  if (!idDict)
    OddIdInit ();
  if (DictWith (idDict, idName))
    _ErrMsg2 (e__duplicatekey, idName);
  DictSet (&idDict, idName, ODDoID*) = id;
}


/****** OddObjSizes ***********************************************************
**
**	calculates offsets of attributes in all objects described 
**	in array of object definitions and calculates
**	the objects sizes; objects that inherit others get size of inherited 
**      object added - inherited objects are appended;
**
**	INPUT:	    
**		IMPLICIT:
**                  odd (SDLo *) [W]
**		    gblerr (int) [W]
**
**	RETURNS:    1 if success
**		    e__novalptyp <type value> +
*/ 
   
static int OddObjSizes (void)
{
  SDLoOBJ  *obj, *iobj;
  SDLoATTR *attr;
  int      n, k, attr_n, off, member_z, maxmember_z;
  int      (*calcsize) ();
  
  for (n = 0;  n < odd->oc_n;  n++) {
    obj = &((odd->oc)[n]);

    attr_n = obj->np;
    off = 0;
    for (k=0, maxmember_z=0;  k < attr_n;  k++) { 
      attr = &(obj->p)[k];

      /*
      ** calculate the size of the data member that will correspond
      ** to the attribute....assuming that the data structure itself is 
      ** optimally aligned some invidual members have to be aligned within the
      ** structure ...this is also done by the function "calcsize" which 
      ** sets the offset to the begin of the data member
      */

      if ((calcsize = odd->at[attr->typ].size) != NULL) {
	member_z = (*calcsize) (obj, attr, &off); 
	if (member_z > maxmember_z)
	  maxmember_z = member_z;
	attr->off = off;
	off += member_z;
      }
    }     

    /*
    ** calc. size of structure until begin of next ...this depends on the
    ** alignment which is to the size of the largest member; eg, on osf, a 
    ** structure that has a pointer (size 8byte) is always aligned to an 8 byte
    ** boundary  
    */

    if (maxmember_z >= 8)
      _SdlAlignEight (off);
    else if (maxmember_z >= 4)
      _SdlAlignFour (off);
    obj->siz = off;
    
  }
  return 1;
}


/****** SdlAlloc **************************************************************
**
**     allocates storage for all counted objects and sets counters back to 0;
**     if object is to be organized in a data structure (such as a list)
**     then the size has to be increased by the size of the pointers needed.
**     - the needed space is given by org->off.
**     This additional space is always at the beginning of a user block!
**     So by shifting the whole array of user-objects by org->off
**     obj->s points to the begin of the user-block as seen from the user
**     and so it can be treated as any other user-object.
**
**	INPUT:
**		IMPLICIT:
**		    odd (SDLo *) [W]
**
**	RETURNS:    1 if successfull
*/ 
   
static int SdlAlloc (void)
{
  SDLoOBJ *obj;	
  int     allsiz, k;

  for (k=0;  k < odd->oc_n;  k++) {
    obj = &(odd->oc[k]);
    if (obj->gbl_n == 0)
      continue;
    
    obj->ns = obj->gbl_n;
    allsiz = obj->siz * obj->ns;
    
    obj->s = _SdlMalloc (allsiz);
    if (!obj->s)
      _ErrExit2 (e__allocfail, "array of objects by SdlAlloc");
    
    obj->gbl_n = obj->loc_n = 0;		 /* reset counter	    */
  }
  return 1;
}


/****** SdlIsChild ************************************************************
**
**	finds out if object with second index is a child of object    
**	with first index;
**
**	INPUT:	    ID of parent object [R]
**		    ID of child object [R]
**		IMPLICIT:
**                  odd (SDLo *)
**
**	RETURNS:    1 if child
**		    0 if not
*/ 
   
static int SdlIsChild (int p_x, int ch_x)
{
  SDLoOBJ *obj = &(odd->oc[p_x]);
  int	  k;
  
  for (k = 0;  k < obj->nss;  k++)
    if (ch_x == obj->ss[k])
      return 1;
  return 0;
}



/****** SdlObjInx *************************************************************
**
**	takes a "DEFINE" name, checks whether this name corresponds to a 
**	object to be processed and returns the offset of the object
**	description in global array of SDLoOBJ;
**
**	INPUT:	    address of object name [R]
**		IMPLICIT:    
**                  odd (SDLo *)
**
**	RETURNS:    object ID (offset in array of object-descriptors) 
**		    e__novalsnam  <ln nr., name>
*/ 
   
static int SdlObjInx (char *nam)
{
  SDLoOBJ *obj;
  int	    k, inx;
  
  for (k = 0, inx = -1;  k < odd->oc_n;  k++) {
    obj = &(odd->oc)[k];	
    if (SmEqs (obj->nam, nam))
      inx = k;
  }
  if (inx == -1)
    return e__novalsnam;
  return inx;    
}


/****** OddGetAttribute *******************************************************
**
**      Returns the attribute description with specified name for specified 
**      class;
**
**	INPUT:	    class object [R]
**                  attribute name [R]
**
**	RETURNS:
**		    attribute type object
**                  NULL if attribute with specified name was not found
*/ 
   
SDLoATTR *OddGetAttribute (SDLoOBJ *class, char *name)
{
  SDLoATTR *attr;
  INT4 k;

  for (k = 0;  k < class->np;  k++) {
    attr = &class->p[k];
    /* unnamed attributes start with ':' */
    if (SmEqs (attr->nam, name) || (*name == ':' && attr->unnamed))
      return attr;
  }
  return NULL;    
}


INT4 OddIsPartOfList (SDLoOBJ *class, char *attrName) 
{
  SDLoATTR *attr;

  if (!(attr = OddGetAttribute (class, attrName)))
    _ErrRet3 (e__icaunknownattr, OddGetClassName (class), attrName);
  return attr->typ == AT_CHILD ? 1 : 0;
}

void OddInstallClasses () 
{
  odd = (SDLo *)odd->oc[odd->oc_n-1].s;
}


/****** OddObjAttribute ******************************************************
**
**      Replaces SdlAttribute;
**   
**	INPUT:	    class object [W]
**                  attribute name [R]
**		IMPLICIT:
**                  odd (SDLo *)
**
**	RETURNS:    e__icaunknownattr +
**		    e__parnotok <ln nr., str> +
**		    e__symnotuniq <ln nr., str> +
**                  e__novalid <ln nr. str> +
**                  e__bnfbuildfail <line nr.> +
**		    e__allocfail <name of item to be alloc> +
** 		    e__objnotfound <line nr., file, object> +
**		    e__objnotnhrt  <line nr., file, object> + 
**		    1 if successful
*/ 
   
INT4 OddObjAttribute (SDLoOBJ *class, char *attrName, VARo *value)
{
  VARo     *varList=NULL;
  char     *tokstr;
  SDLoATTR *attr, *defaultAttr;
  SDLoPTR  off;
  unsigned tokval;
  int      (*insert) (), k, rv, isDefault=0, c=0;
  
  if (!(attr = OddGetAttribute (class, attrName)))
    _ErrRet3 (e__icaunknownattr, OddGetClassName (class), attrName);
  defaultAttr = attr;
  
  off = ((SDLoPTR) class->uobj_coff + attr->off); 

  if (VarType (value) == VARxLIST) { /* first in list - if list */
    varList = value;
    value = AnyNextInList (varList, &c);
  }

  for (k=0; k < attr->arrsz; k++) {
    if (!isDefault) {
      rv = (k && !varList) ? 0 : OddGetValue (attr, &tokstr, &tokval, value); 
      if (!rv) 
	isDefault = 1; /* now enter default value */
      _ErrIf (rv) odd->error = TRUE;
    }
    if ((insert = odd->at[attr->typ].insert) != NULL) {
      rv =(*insert)(class, attr, defaultAttr, &off, tokstr, tokval, isDefault);
      _ErrIf (rv) odd->error = TRUE;	
    }
    
    if (varList && !isDefault) /* next in list - if list */
      if (!(value = AnyNextInList (varList, &c)))
	isDefault = 1;
    attr->isrd = TRUE; 
  }
  attr->isrd = TRUE; 
  return 1;
}


/****** SdlParTyp *************************************************************
**
**	checks whether ATTRIBUTE value type is one of declared types:
**     SDLxPNUM, SDLxPNAM, SDLxPTXT, SDLxPCNST; 
** 
**	INPUT:	    address of ATTRIBUTE name
**                  address of array of alowed types
**		    actual type
**		IMPLICIT:
**		    f (FILo *)
**
**	OUTPUT:
**		    returns:	1 if ok
**				e__wrongpartyp (line nr., msg-line) +
*/ 

int SdlParTyp (char *nam, unsigned char *ptyp, unsigned int typ)
{
  static char *typn[4] = {", number", ", name", ", text", ", constant"};
  char	      errs[MSGxXLN], errln[MSGxXLN];
  int	      k, err_f = FALSE;
  
  (void) strcpy (errs, "");
  for (k = 0; k < 4 && ptyp[k] != 0; k++)
    if (ptyp[k] == typ) {
      err_f = FALSE;
      break;
    }
    else {
      err_f = TRUE;
      strcat(errs, typn[ptyp[k] - SDLxPNUM]);
    }
  
  if (!err_f)
    return 1;
  errs[0] = ' ';       /* remove ',' */
  sprintf(errln, "ATTRIBUTE: %s, expected type: %s", nam, errs);
  _ErrRet4(e__wrongpartyp, f->n, f->nam, errln);
  return 1;
}


/****** OddIsOfVal ************************************************************
**
**	checks list of values if specified string is OK;
**
**	INPUT:	    address of attribute-dsc. [R]
**		    string read [R]
**		    address of value [W]
**	        IMPLICIT:
**
**	RETURNS:    1 if found
**		    0 else
*/ 
   
int OddIsOfVal (SDLoATTR *attr, char *tokstr, unsigned int *val)
{
  int k;
  
  SmEdit (tokstr, SMxLOWCASE);
  for (k=0;  k < attr->val_n && strcmp (tokstr, attr->val[k].nam) != 0;  k++)
    ;
  if (k==attr->val_n)
    return 0;
  else *val = attr->val[k].val;
  return 1;	   
}


/****** OddGetValue ***********************************************************
**
**	gets next value from the symbol table, tests it and gets symbol value
**	if it is a constant, or number if enumerated type;
**
**	INPUT:	    
**                  attribute descriptor [R]
**                  address of token string [W]
**		    address of token value [W]
**	        IMPLICIT:
**
**	RETURNS:    1 if value could be read
**		    0 there was no token in token table
**		    e__icaenumval <line nr., symbol> +
**		    e__symnotknown <line nr., symbol> +
**		    e__symnotuniq <symbol, symbol value> +
*/ 
   
static int OddGetValue (SDLoATTR *attr, char **tokstr, unsigned *tokval, 
			VARo *value)
{
  static STRv str=NULL;
  int rv;
  
  if (str)
    StrDel (str);

  *tokval = ODDxNULL;
  str = VarGetStrv (value);
  *tokstr = _Str(str);


  /*  rv = SdlParTyp (attr->nam, &attr->ptyp[0], *tokval);
  _ErrRet (rv);*/
  
  *tokval = ODDxNULL;
  
  if (attr->val_n)		       /* check if value is one of the list */
    if (!OddIsOfVal (attr, *tokstr, tokval))
      _ErrRet3(e__icaenumval, *tokstr, attr->nam);
  return 1;
}


/****** SdlSaveAddr ***********************************************************
**
**	Processes each attribute in a user-object and in case it is an
**	address saves it in global array
**
**	INPUT:	    object-descriptor [R]
**		    start address of user-object [W]
**	        IMPLICIT:
**		    addr_n (int) [W]
**		    addr (unsigned int *) [W]
**                  odd (SDLo *) [R]
**
**	RETURNS:    1
*/ 
   
int SdlSaveAddr (SDLoOBJ *obj, SDLoPTR uobj)
{
  SDLoATTR     *attr;
  SDLoPTR      **off;
  int          k, l;

  for (k=0;  k < obj->np;) {
    attr = &((obj->p)[k++]);
    off = (SDLoPTR **) (uobj + attr->off);
    
    if (odd->at[attr->typ].save_f)
      for (l=0;  l < attr->arrsz;  l++, off++)
	if (*off != 0 || attr->typ == AT_FNCT)
	  __SdlAddr ((SDLoPTR) off);
  }
  return 1;
}


/****** SdlCheckPar ***********************************************************
**
**	tests an attribute value;
**
**	INPUT:	    address of ATTRIBUTE description (SDLoATTR)	    
**		    address of string 0 if an int or char 
**		    int or char
**		IMPLICIT:
**
**	OUTPUT:
**		    returns:	1 if parameter ok
**				e__parnotok <ln nr., str> +
*/ 
   
int SdlCheckPar (SDLoATTR *attr, char *s, int v)
{
  int	(*check) (SDLoATTR *, int, char *);

  if ((check = odd->at[attr->typ].check) != NULL) {
    return (*check) (attr, v, s);
  }
  
  return 1;
}



/****** OddWriteCDefines ******************************************************
**
**	writes constant definitions into header
**
**	INPUT:	    address of file descriptor [W]
**
**	RETURNS:
*/ 

static void OddWriteCDefines (FILE *file)
{
  ODDoCDEFINE *tmp;
  INT4        k;

  for (k=0, tmp=cDefine; k < cDefineN; k++, tmp++)
    fprintf(file, "#define  %-16s   %d\n", tmp->name, tmp->n);
}



/****** SdlWrtHdr *************************************************************
**
**	writes a header file that contains constant definitions, type 
**	declarations, and declaration + init of OBJECT   s;
**
**	INPUT:	    address of SDLo
**		    option: SDLxHDR, SDLxHDR2
**
**	OUTPUT:
**		    returns:	1 if success
**				e__filopenerr, <file name>
*/ 
   
 int SdlWrtHdr (SDLo *d, int opt)
{
  FILE *fil;
  int  errCode;
    
  fil = FilOpenW (d->ofnam, &errCode);
  _ErrExit2 (errCode, d->ofnam);
  
  SdlWrtTtl(fil, d->ifnam, d->ofnam);
  OddWriteCDefines (fil);
  SdlWrtTypDef(fil, &(d->oc[0]), d->oc_n);
  if (opt == SDLxHDR) {
    OddWrtInitExtern (fil, &(d->oc[0]), d->oc_n);
    OddWrtInit (fil, &(d->oc[0]), d->oc_n);
  }  
  fclose(fil);
  return 1;
}


/****** OddGetAttrDeclName ****************************************************
**
**	Returns the name to be used for declaring a member of a C struct for
**      specified attribute object.
**
**	INPUT:	    attribute object [R]
**
**	RETURNS     declaration name [R]
*/ 
   
char *OddGetAttrDeclName (SDLoATTR *attr)
{
  return (*attr->dnam ? attr->dnam : attr->nam);
}

/****** OddGetClassDeclName ***************************************************
**
**	Returns the name to be used for declaring a C struct.
**
**	INPUT:	    class object [R]
**
**	RETURNS     declaration name [R]
*/ 
   
char *OddGetClassDeclName (SDLoOBJ *class)
{
  return (*class->dnam ? class->dnam : class->nam);
}


/****** SdlWrtTtl *************************************************************
**
**	writes a title to a header file;
**
**	INPUT:	    address of file descr. 
**		    name of DDL- language input file
**		    name of output file
**
**	OUTPUT:
**		    returns:	1
*/ 
   
static int SdlWrtTtl (FILE *f, char *in, char *out)
{
  char *time;

  SmEdit(in, SMxLOWCASE);
  SmEdit(out, SMxLOWCASE);
  time = SmTime (0);

  fprintf(f, 
"/******************************************************************************\n");
  fprintf(f,
"**\n\
**    $RCSfile: sdlnew.c,v $\n\
**    $Revision: 1.14 $\n\
**    $Date: 1997/03/18 22:52:32 $\n\
**    $Author: srs $\n\
**\n\
**    $Locker:  $\n\
**    $State: Exp $\n\
**\n");
  
  fprintf(f,"**             from ODD file: \"%s\"\n", in); 
  fprintf(f,"**   date of ODD compilation: %s\n", time);
  fprintf(f,"**\n"); 
  fprintf(f,"*/\n\n\n"); 
  return 1;
}



/****** SdlWrtTypDef **********************************************************
**
**	writes type definitions of all objects in header file;
**	puts typdefs with #ifndef-#endif clause this allows the OBJECT   
**	to be defined else where; the identifier is the same as in the 
**	typdef but in uppercase;
**      writes typdef only if at least one object of class has been
**      defined;
**
**	INPUT:	    address of file descr. [W]
**		    base address of array of strct defs. (SDLoOBJ) [R]
**		    number of strct defs. [R]
**
**	RETURNS:    1
*/ 
   
static int SdlWrtTypDef (FILE *fil, SDLoOBJ *s, int ns)
{
  SDLoOBJ *obj;
  char    *typdef_nm, *gtyp_nm = NULL;
  int     k, l, i, gentype_f;
  
  for (k = 1;  k < ns;  k++) {  /** for every object-class  */
    obj = &(s[k]);
    if (obj->typ == SDLxVIRTUAL)
      continue;
    else {
      gentype_f = obj->gtyp_n == 0 ? FALSE : TRUE;
      
      /*
      ** for every distinct generic type ...if any
      */

      for (l=gentype_f ? obj->gtyp_n-1 : 0;  l >= 0;  l--) {
	if (!gentype_f)  
	  typdef_nm = obj->tnam;
	else {
	  gtyp_nm = (obj->gtyp_nm)[l]; 
	  typdef_nm = (obj->gtypdef_nm)[l]; 
	  for (i=0; i < obj->gtyp_n; i++) {
	    if (strcmp ((obj->gtyp_nm)[i], gtyp_nm) == 0)
	      break;
	  }
	  if (i < l) continue;	 /* typedef was already	written */
	}		    

	/*
        ** write title: comment (if available) ...
        */

	if (*obj->rem) {
	  fprintf (fil, 
          "\n\n/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *\n");
	  fprintf (fil, "**  %s\n*/\n", obj->rem); 
	}


	if (*(obj->pp_nm) != '\0')	 /* preprocessor switch */
	  fprintf (fil, "\n#if defined(_%s) && !defined(_%s)\n", 
		   obj->pp_nm, typdef_nm);
	else
	  fprintf (fil, "\n#ifndef _%s\n", typdef_nm);
	
	fprintf(fil, "#define _%s\n", typdef_nm); /* ...to prevent redefinit */

	fprintf(fil, "typedef struct %s {\n", typdef_nm);
	SdlWrtAttr (fil, obj, typdef_nm, gtyp_nm);

	/*
	** process attribues of inherited objects 
	*/

	fprintf(fil, "} %s;\n#endif\n", typdef_nm);
      }
    }
  }

  /*
  ** print all funtion info at the end of all typdefs...function class - if
  ** present is the first of all classes (index=0) -> C compilers like
  ** that better...
  */

  obj = &(s[0]);
  if (obj->typ == SDLxFNCT)
    SdlWrtFnct (fil, obj);

  return 1;
}


/****** SdlWrtAttr ************************************************************
**
**	Writes declaration for all attributes within a struct typedef;
**
**	INPUT:	    address of file-dsc [W]
**		    address of object-dsc [R]
**                  address of typedef name [R]
**                  address of generic type [R] or NULL
**	        IMPLICIT:
**
**	RETURNS:    1
*/ 
   
static int SdlWrtAttr (FILE *fil, SDLoOBJ *obj, char *typdef_nm, char *gtyp_nm)
{
  SDLoATTR *attr;
  int      (*declare) (FILE *, SDLoATTR *, char *, char *);
  int      l;
  
  for (l = 0;  l < obj->np;  l++) {
    attr = &((obj->p)[l]);
    if ((declare = odd->at[attr->typ].declare) != NULL) {
      (*declare) (fil, attr, gtyp_nm, typdef_nm); 
    }
  }
  return 1;
}


/****** OddAddFunction ********************************************************
**
**	adds a new function to the list;
**
**	INPUT:	    address of location of object function [R]
**	        IMPLICIT:
**                  function (struct []) [W]
**
**	RETURNS:
*/ 
   
void OddAddFunction (char **loc)
{
  function[fnct_x].nam = loc;	     
  function[fnct_x].args = loc + 1;	     
  function[fnct_x].module = loc + 2;	     
  function[fnct_x++].isDone = 0;
}


/****** OddOutput *************************************************************
**
**	Performs selected output operations.
**
**	INPUT:	    odd base object [W]
**	        IMPLICIT:
**
**	RETURNS:
*/ 

void OddOut (SDLo *odd)
{
  if (odd->error)
    _ErrExit (e__procfail);

  if (ParGetBool ("doClassInfo")) {
    OddWriteClassInfo ((SDLo *) odd->oc[odd->oc_n-1].s );
  }
  else if (odd->action != SDLxNOHDR && odd->action != SDLxSECTION &&
      odd->action != SDLxPRESEC) {	
    SdlWrtHdr (odd, odd->action);
  }
  if (odd->section_f)       
    SdlCloseSec ();    
}


/****** SdlWrtVal *************************************************************
**
**	writes a single value in header file for init. arrays of OBJECTs;
**
**	INPUT:	    address of file descr.
**		    address of attribute object (SDLoATTR)
**                  address of current offset in target object   
**		    address of flag saying SDLxFIRST, SDLxLAST, SDLxNORMAL
**	OUTPUT:
**		    returns:	1
*/ 
   
int SdlWrtVal (FILE *fil, SDLoATTR *attr, SDLoPTR *off, int *item_f)
{
  static char  ln[SDLxXLN], str[SDLxXLN];
  int	       (*writeval) (); 

  if (*item_f & SDLxLAST) {
    fprintf(fil, "%s%s", ln, *item_f & SDLxBOUND ? "}" : ""); 
    *item_f = 0;
    return 1;
  }

  if ((writeval = odd->at[attr->typ].write) != NULL) {
    (*writeval) (attr, str, off); 
  }

  if (*item_f & SDLxFIRST) {  /* print first item */
    sprintf(ln, "    %s%s",  *item_f & SDLxBOUND ? "{" : "", str);
    *item_f = 0;
  }
  else {
    if (*item_f & SDLxBREAK) {
      fprintf(fil, "%s%s,\n", ln, *item_f & SDLxBOUND ? "}" : "");
      sprintf(ln, "    %s%s",  *item_f & SDLxBOUND ? "{" : "", str);
      *item_f = 0;
    }
    else if (strlen(ln) + strlen(str) + 2 >= SDLxXHLN) {
      fprintf(fil, "%s,\n", ln);
      sprintf(ln, "    %s", str);
    }
    else
      sprintf(ln, "%s, %s", ln, str);
  }
  return 1;
}


/****** SdlWrtFnct ************************************************************
**
**	writes typedef for function pointer, prototypes of functions 
**      and array of function pointers;
**
**	INPUT:	    output-file [W]
**		    Object-descriptor [R]
**	        IMPLICIT:
**                  function (struct *) [R]
**
**	RETURNS:    1
**                  0 if no functions defined
*/ 
   
static int SdlWrtFnct (FILE *f, SDLoOBJ *s)
{
  char args[132], *moduleName, *fnctName, tmp[80];
  char *tmpPtr = tmp, **tmpPPtr, *tmpFnctName[100];
  int  item_f, k, i, l, n;
  
  if (s->gbl_n == 0)
    return 0;				 /* nothing to initialize   */
  
  fprintf(f, "\n#ifdef _FUNCTION\n#undef _FUNCTION\n");
  
  /*
  ** define a constant with the function name - if module name is defined
  ** otherwise assign dummy function - defines are grouped by module name
  */

  if (1/*odd->action != SDLxHDR*/) {
    for (i=0;  i < s->gbl_n;  i++) {
      for (k=i, moduleName=NULL, l=0;  k < s->gbl_n;  k++) {
	if (!function[k].isDone) {
	  if (!moduleName) { /* new module name */
	    moduleName = *function[k].module;
	    if (*moduleName)
	      fprintf (f, "\n#ifdef %s_M\n", moduleName);
	    else
	      fprintf (f, "\n");
	  }

	  if (!(strcmp (moduleName, *function[k].module))) { 

	    /* 
	    ** write function prototype
	    */

	    fnctName = *function[k].nam;
	    strcpy (args, *(function[k].args));
	    SmSwapS (args, SDLxGTYPDEFNAM, "void");
	    SmSwapS (args, SDLxGTYPNAM, "void");
	    fprintf (f, "INT4 %s ", fnctName); 
	    fprintf (f, "%s;\n", args);

	    tmpFnctName[l++] = fnctName; /* save for "#else" */
	    fprintf (f, "#%sdefine %s_F (INT4(*)()) %s\n", 
		     *moduleName ? " " : "",
		     fnctName, fnctName);
	    function[k].isDone = 1;
	  }
	}
      }
      if (moduleName && *moduleName) {
	fprintf (f, "#else\n");
       fprintf (f,"void Dummy%s () {_ErrExit2 (e__fnctnotdefined, \"%s\");}\n",
		 moduleName, moduleName);
	for (n=0; n < l; n++)
	  fprintf (f, "# define %s_F (INT4(*)()) Dummy%s\n", 
		   tmpFnctName[n], moduleName);
	fprintf (f, "#endif\n");
      }
    }
  }

  /*
  ** write array of function pointers - or rather with the macros
  ** defined just above
  */

  if (1/*odd->action != SDLxHDR*/) {
    fprintf (f, "typedef INT4 (*SDLoFNCT)();\n\n");
    fprintf (f, "\nSDLoFNCT    SDL_fnct[] = {\n");
    item_f = SDLxFIRST;
    for (k=0;  k < s->gbl_n;  k++) {
     tmpPPtr = &tmpPtr;
      sprintf (*tmpPPtr, "%s_F", *function[k].nam);
      SdlWrtVal (f, &(s->p[0]), (SDLoPTR *) &tmpPPtr, &item_f);
    }

    item_f = SDLxLAST;
    SdlWrtVal (f, &(s->p[0]), NULL, &item_f);
    fprintf (f, "\n};\n");
  }
  fprintf (f, "#endif\n");
  return 1;
}



/****** function *****************************************************************
**
**	initializes arrays of objects with values;
**
**	INPUT:	    address of file descr.
**		    base address of array of strct defs. (SDLoOBJ)
**		    number of strct defs.
**
**	RETURNS:    1
*/ 

static int OddWrtInit (FILE *fil, SDLoOBJ *s, int ns)
{
  SDLoOBJ   *obj;
  SDLoATTR  *pptr;
  SDLoPTR  off, trgts;
  int       k, l, m, n, item_f;
  
  fprintf (fil, "\n#ifdef _INITOBJS\n");

  for (k = 0;  k < ns;  k++) {  /* all strct types */
    obj = &s[k];
    if (obj->gbl_n == 0)			 /* nothing to initialize   */
      continue;
    if (obj->typ == SDLxFNCT)
      continue;
    fprintf(fil, "\n%s    %s[] = {\n", obj->tnam, OddGetClassDeclName (obj));
    item_f = SDLxFIRST | SDLxBOUND;
    for (n = 0; n < obj->gbl_n; n++) {  /* all alloc. strct */
      trgts = obj->s + (n * obj->siz);  
      item_f |= SDLxBREAK | SDLxBOUND;
      for (l = 0;  l < obj->np;  l++) { /* all attributes */
	pptr = &(obj->p[l]);                            
	off = trgts + pptr->off;		
	for (m = 0;  m < pptr->arrsz;  m++) /* all vals. in par	    */
	  /* array		    */
	  SdlWrtVal(fil, pptr, &off, &item_f);         
      }                                                
    }
    item_f |= SDLxLAST | SDLxBOUND;
    SdlWrtVal(fil, pptr, &off, &item_f);         
    fprintf(fil, "\n};\n");
  }
  fprintf (fil, "\n#endif\n");
  return 1;
}

/****** function ****************************************************************
**
**	Lists names of arrays to be initialized as extern variables so that
**      they can be used for cross-referencing before they are actually 
**      initialized (forward references).
**
**	INPUT:	    file descr. [W]
**		    array of class descriptors [R]
**		    number of class descriptors [R]
**
*/ 

static void OddWrtInitExtern (FILE *file, SDLoOBJ *classList, int classN)
{
  SDLoOBJ *class;
  Int4    k;

  fprintf (file, "\n"); 
  for (k=0;  k < classN;  k++) { 
    class = &classList[k];
    if (class->gbl_n == 0 || class->typ == SDLxFNCT)
      continue;
    fprintf (file, "extern %s    %s[];\n", 
	     class->tnam, OddGetClassDeclName (class));
  }
}



/****** SdlListAddr ***********************************************************
**
**
**	INPUT:	    address to be put on list [R]
**	        IMPLICIT:
**		    addr_n (int)
**                  addr (unsigned int)
**
**	RETURNS:    1
*/ 
   
int SdlListAddr (SDLoPTR a)
{
  addr[addr_n++] = a;
  if (addr_n > SDLxXADDR)
    _ErrExit3 (e__exceedsize, "array addr", SDLxXADDR);
  return 1;
}


/****** SdlCopySec ************************************************************
**
**	copies string into map-section and outputs new address
**
**	INPUT:	    address of pointer to string [W]
**	        IMPLICIT:
**
**	RETURNS:    1
*/ 
   
static int SdlCopySec (char **s)
{
  char *p;

  p = (char *) SdlMalloc (strlen (*s) + 1); 
  strcpy (p, *s);
  *s = p;
  return 1;
}


/****** SdlCloseSec ***********************************************************
**
**	closes a map-section and writes out file of addresses;
**
**	INPUT:
**	        IMPLICIT:
**		    odd (SDLo *)
**                  map (MAPo)
**		    addr_n (int)
**                  addr (unsigned int)
**
**	RETURNS:    1
*/ 
   
static int SdlCloseSec ()
{
  FILE *fil;
  char ptr_nm[FILxXNAM+1], sec_nm[FILxXNAM+1];
  long tmp;
  int  rv, k, obj_n, size;

  sprintf (ptr_nm, "SRSSEC:%s.ptr", odd->sec_nm);
  sprintf (sec_nm, "SRSSEC:%s.sec", odd->sec_nm);
  fil = FilOpenW (ptr_nm, &rv);
  _ErrExit2 (rv, ptr_nm);
  size = (addr_n + (odd->oc_n*2) + 3) * sizeof (SDLoPTR) + sizeof (int);
  

  fwrite (&size, sizeof (int), 1, fil);            /* size of ptr file */
  tmp = (long) map.data + sizeof (char *);
  fwrite (&tmp, sizeof (SDLoPTR), 1, fil); /* addr of section begin */
  tmp = odd->oc_n;
  fwrite (&tmp, sizeof (long), 1, fil);    /* number of objects */
  
  /*
  ** for each class represented in the section, write the pointer to its
  ** array of instances within the section and the number of instances
  */

  for (k=0;  k < odd->oc_n;  k++) {
    fwrite (&((odd->oc)[k].s), sizeof (SDLoPTR), 1, fil); 
    tmp = odd->oc[k].ns;
    fwrite (&tmp, sizeof (long), 1, fil);   
  }
  
  tmp = addr_n;
  fwrite (&tmp, sizeof (long), 1, fil);  /* number of references */
  fwrite (addr, sizeof (SDLoPTR), addr_n, fil);           /* ref. list */
  fclose (fil);
  
  size = *(map.foff);
  rv = MapFree (&map);
  _ErrExit (rv);
  
  for (k=0, obj_n=0; k < odd->oc_n; obj_n += (odd->oc)[k++].ns)
    ; 
  Message (9, i__sdlreport, 0, sec_nm, size / 512, ptr_nm, addr_n / 512*4, 
	   odd->ifnam, obj_n, odd->oc_n);
  
  return 1;    
}


/****** OddWriteClassInfo *****************************************************
**
**	writes a text file with meta info about all defined classes;
**
**	INPUT:	    address of odd base [W]
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

void OddWriteClassInfo (SDLo *odd)
{
  TEMPLv   templ;
  SDLoOBJ  *class;
  SDLoATTR *attr;
  
  char     *typeName[30]={"real", "number", "number", "", 
			    "string", "", "list of", "", "", "pointer to", 
			    "", "function", "", "", "", "", "", "", "", 
			    "", "", "BNF-productions", "", "", "", "", "", 
			    "", "" };
  int      i, k, l, isPointer;
  
  /*
  ** open script and print first a directory of all classes 
  */

  templ = TemplOpen ("SRSICA:srswww.i", NULL);
  TemplWith (templ, "$classInfo");

  /*
  TemplPrint ("dir.head", TimeToString (0, "date"));
  for (k=0;  k < odd->oc_n; k++) { 
    class = &(odd->oc[k]);
    if (OddIsClass (class, "system") || OddIsClass (class, "obsolete"))
      continue;

    SmEdit (class->nam, SMxLOWCASE);
    class->nam[0] = toupper (class->nam[0]);
    TemplPrint ("dir.class", k, class->nam);
  }
  TemplPrint ("dir.tail");
  */

  /*
  ** then the classes + attributes
  */

  TemplPrint ("head", TimeToString (0, "date"));
  for (k=0;  k < odd->oc_n; k++) { 
    class = &(odd->oc[k]);
    if (OddIsClass (class, "system") || OddIsClass (class, "obsolete"))
      continue;

    
    TemplPrint ("class.head", k, class->nam);
    TemplPrint ("class.remark", class->rem);

    /*
    ** attribute information
    */
      
    TemplWith (templ, "class.attrib");
    for (l=0; l < class->np; l++) {
      attr = &(class->p[l]);
      if (*attr->nam 
	  && !OddIsAttr (attr, "obsolete") && ! OddIsAttr (attr, "system")) {

	SmEdit (attr->nam, SMxLOWCASE);
	TemplPrint ("head", attr->nam);

	/* print comment */
	
	TemplPrint (*attr->rem ? "remark" : "empty", attr->rem);

	/* unnamed */
	
	TemplPrint (attr->unnamed ? "unnamed" : "empty");

	/* required */

	TemplPrint (attr->req ? "required" : "empty");

	/* attribute type */
	
	isPointer = 0;
        TemplPrint ("typeHead");
	if (attr->val_n) { /* list of string values */
	  TemplPrint ("optionList.head");
	  for (i=0;  i < attr->val_n;  i++)
	    TemplPrint ("optionList.option", attr->val[i].nam);
	  TemplPrint ("optionList.tail");
	}

	else if (*typeName[attr->typ] == 'p') { /* pointer */
	  TemplPrint ("ptrType",typeName[attr->typ], odd->oc[attr->dfltv].nam);
	  isPointer = 1;
	}
	else if (*typeName[attr->typ] == 'l') {
	  TemplPrint ("listType", odd->oc[attr->dfltv].nam);
	  isPointer = 1;
	}
	else if (*typeName[attr->typ] == 'p') {
	  TemplPrint ("ptrType",typeName[attr->typ], odd->oc[attr->dfltv].nam);
	  isPointer = 1;
	}
        else if (*typeName[attr->typ])
	  TemplPrint ("type", typeName[attr->typ]);

	/* min + max */

	if (attr->min != -1000000000 && attr->max != 1000000000) {
	  if (attr->typ == 4)
	    TemplPrint ("minmaxStr", attr->min, attr->max);
	  else
	    TemplPrint ("minmaxNum", attr->min, attr->max);
	}

	/* array of max number of elements */
	if (attr->arrsz > 1)
	  TemplPrint ("arrSize", attr->arrsz);

        TemplPrint ("typeTail");


	/* default value */
	if (attr->val_n) {
	  for (i=0;  i < attr->val_n;  i++)
	    if (attr->val[i].val == attr->dfltv) {
	      TemplPrint ("default.option", attr->val[i].nam);
	      break;
            }
	  if (i >= attr->val_n)
	    TemplPrint ("empty");
	}
	else if (*attr->dflts)
	  TemplPrint ("default.string", attr->dflts); 
	else if (attr->dfltv != 0 && !isPointer)
	  TemplPrint ("default.num", attr->dfltv); 
	else if (attr->dfltvf != 0)
	  TemplPrint ("default.num", attr->dfltvf); 
	else
	  TemplPrint ("empty", attr->dfltvf); 


	TemplPrint ("tail");
	TemplPrint ("infoEnd");

      }
    }
    TemplEndWith ();
    TemplPrint ("class.tail");
  }
  TemplEndWith ();
}



/**api* OddIsAttr *************************************************************
**
** 	returns some boolean information about the attribute;
**
** 	INPUT:	    attribute object [R]
**                  option: "obsolete", "system", "api" [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 
**                  0 
*/ 

INT4 OddIsAttr (SDLoATTR *attr, char *option)
{
  int k;

  switch (tolower (option[0])) {
  case 'a':  /* api */
    for (k=0; k < 2; k++)
      if (attr->status[k] == (unsigned char) ODDxAPI)
	return 1;
    break;
  case 'o':  /* obsolete */
    for (k=0; k < 2; k++)
      if (attr->status[k] == (unsigned char) ODDxOBSOLETE)
	return 1;
    break;
  case 's':  /* system */
    for (k=0; k < 2; k++)
      if (attr->status[k] == (unsigned char)ODDxSYSTEM)
	return 1;
    break;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
  return 0;
}


/**api* OddIsClass ************************************************************
**
** 	returns some boolean information about the class;
**
** 	INPUT:	    class object [R]
**                  option: "obsolete", "system", "api" [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 
**                  0 
*/ 

INT4 OddIsClass (SDLoOBJ *class, char *option)
{
  int k;

  switch (tolower (option[0])) {
  case 'a':  /* api */
    for (k=0; k < 2; k++)
      if (class->status[k] == (unsigned char) ODDxAPI)
	return 1;
    break;
  case 'o':  /* obsolete */
    for (k=0; k < 2; k++)
      if (class->status[k] == (unsigned char) ODDxOBSOLETE)
	return 1;
    break;
  case 's':  /* system */
    for (k=0; k < 2; k++)
      if (class->status[k] == (unsigned char)ODDxSYSTEM)
	return 1;
    break;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
  return 0;
}
n)
{
  int k;

  switch (tolower (option[0])) {
  case 'a':  /* api */
    for (k=0; k < 2; k++)
      if (class->status[k] == (unsigned char) ODDxAPI)
	return 1;
    break;
  case 'o':  /* obsolete */
    for (ksrs/src/seq.c
/*****************************************************************************/
char seq_srs_ID[] = "$Id: seq.c,v 1.14 1997/03/20 12:08:04 srs Exp $";
/*
**
**    $RCSfile: seq.c,v $
**    $Revision: 1.14 $
**    $Date: 1997/03/20 12:08:04 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     D-69012 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: file, sm, message, list
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>

#include "message.h"
#include "sm.h"
#include "strv.h"
#include "futil.h"
#include "lst.h"
#include "par.h"
#include "icarus.h"
#include "icaarg.h"
#define _INITOBJS
#include "seq.h"


#ifdef sun
extern INT4 printf ();
#endif

typedef  char  TABLE[4][4][4];

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  static functions
*/

static char SeqTranslCodon (char *triplett, SEQoTranslTable *transTable,
			    INT4 isStartCodon);
static void SeqTranslTableEdit (SEQoTranslTable *tTable,
				SEQoTranslCodon *tCodon);
static void SeqTranslTableRevert (SEQoTranslTable *tTable);
static INT4 *SeqGetTranslNtOrder ();
static void SeqDump (FILE *file, void *obj);
static void SeqInit (void *obj);
static void SeqKill (void *obj);
static void SeqBinToAscii (SEQo *seq);
static INT4 SeqTest (FILo *file);
static INT4 SeqCopy (SEQo *seq, char *s, INT4 read_o);
static INT4 SeqReadPirSeq (SEQo **seq, FILo *file);
static INT4 SeqReadEMBLSeq (SEQo **seq, FILo *file);
static INT4 SeqReadGCGSeq (SEQo **seq, FILo *file);
static INT4 SeqReadMSFSeq (SEQo **seq, FILo *file);
static INT4 SeqMSFNam (char *name, char *file_nm, char *seq_nm);
static INT4 SeqGCGCheck(char *seq, INT4 len);
static INT4 SeqWrite (char *seq, INT4 len, INT4 line_n, INT4 block_n, 
		      INT4 format_o, INT4 (*print)(char*,...));
static void SeqAlloc (SEQo *seq, INT4 len);
static void SeqMakeOwn (SEQo *seq);

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  global variables
*/

INT4 global_before_f;
INT4 global_after_f;
static INT4 recordSeparatorLength=0;

/**api* SeqNew ***************************************************************
**
**	gets a new initialized sequence object;
**
**	INPUT:      pointer to address of sequence object [W]
**	        IMPLICIT:
**
**	RETURNS:    
*/ 
   
INT4 SeqNew (SEQo **seq)
{
  static INT4 seqtype_id=0;

  if (!seqtype_id) 
    LstManageClass (&seqtype_id, sizeof (SEQo), SeqInit, SeqKill, SeqDump);

  return LstNew ((void **) seq, seqtype_id);
}

/****** SeqDump **************************************************************
**
**      dumps all information belonging to the specified object.
**      This is the print function set through LstManageClass
**      for seq_type objects (see SeqNew).
**
**      INPUT:      address of an object [R]
**                  file pointer [W] or NULL
**              IMPLICIT:
**
**      RETURNS:    nothing
*/

static void SeqDump (FILE *file, void *obj)
{
  SEQo *tmp = (SEQo*)obj;

  if (!file)
    file = stderr;
  
  fprintf (file, "*%s*\n", tmp->name);
  fprintf (file, "......accno: %10s    bpos %d   epos %d   compl_f %d\n",
	  tmp->accno, tmp->bpos, tmp->epos, (INT4)tmp->compl_f);
  if (tmp->seq) printf ("......*%s*......\n", tmp->seq);
  /* print sublist, i.e. parameter list of function */
  if (tmp->sublist) {
    fprintf (file, "SUBLIST ");
    LstPrintAll ((void*) tmp->sublist);
  }
}

/****** SeqInit **************************************************************
**
**      initializes the specified object.
**      This is the init function set through LstManageClass
**      for seq_type objects (see SeqNew).
**
**      INPUT:      address of an object [R]
**              IMPLICIT:
**
**      RETURNS:    nothing
*/

static void SeqInit (void *obj)
{
    SEQo *tmp = (SEQo*) obj;

    strcpy(tmp->name, "");    /* dummy values */
    tmp->cmnt = NULL;
    tmp->seq = NULL;
    tmp->replace = NULL;
    tmp->len = 0;
    tmp->check = 0;
    tmp->bpos = 0;
    tmp->epos = 0;
    tmp->part_len = 0;
    strcpy(tmp->accno, "");  /* dummy values */
    tmp->keep_f = 0;
    tmp->compl_f = 0;
    tmp->cut_f = 0;
    tmp->before_f = 0;
    tmp->after_f = 0;
    tmp->sublist = NULL;
}

/****** SeqKill **************************************************************
**
**      deletes the specified object.
**      This is the delete function set through LstManageClass
**      for seq_type objects (see SeqNew).
**
**      INPUT:      address of an object [R]
**              IMPLICIT:
**
**      RETURNS:    nothing
*/

static void SeqKill (void *obj)
{
    SEQo *tmp = (SEQo*) obj;

    if (tmp->seq) 
      free(tmp->seq);
    if (tmp->cmnt) 
      StrDel (tmp->cmnt);
    if (tmp->replace) 
      free(tmp->replace);
    /* delete sublist ? */
    if (tmp->sublist) 
      LstDeleteAll((void**)&tmp->sublist);
}


/**API* function **************************************************************
**
**	Deletes a sequence object and resets the pointer to NULL.
**
**	INPUT:	    address of of pointer to sequence object [R]
*/ 
  
void SeqDel (SEQo **seq)
{
  SEQo *tmp = *seq;
  if (tmp->seq) 
    free(tmp->seq);
  if (tmp->cmnt) 
    StrDel (tmp->cmnt);
  if (tmp->replace) 
    free(tmp->replace);
  /* delete sublist ? */
  if (tmp->sublist) 
    LstDeleteAll((void**)&tmp->sublist);
  free (tmp);
  *seq=NULL;
}

/**API* function **************************************************************
**
**	Sets the name of a sequence.
**
**	INPUT:	    sequence object [W]
**                  new sequence name [R}
*/ 
  
void SeqSetName (SEQo *seq, char *name)
{
  strcpy (seq->name, name);
}

/**API* function **************************************************************
**
**	Sets a comment for the sequence.
**
**	INPUT:	    sequence object [W]
**                  new sequence name [R}
*/ 
  
void SeqSetComment (SEQo *seq, char *comment)
{
  if (!seq->cmnt)
    seq->cmnt = StrNew ();
  StrSetS (&seq->cmnt, comment);
}



/****** SeqBinToAscii *********************************************************
**
**	Converts sequence of 2-bit GATC to ASCII; corresponds to 
**	GCG procedures BinToSeq, BinToFilter and BinToGATC;
**
**	INPUT:	    address of sequence object 
*/ 
  
static void SeqBinToAscii (SEQo *seq)
{
  static char   nuc[] = "CTAG", fstcall_f = TRUE;
  static UINT4  tbl[256];
  UINT4         *seqPtr = (UINT4 *) seq->seq;
  unsigned char *binseq, *buff;
  INT4          i, k, l, m, n, x;


  if (fstcall_f) {

    /*	 
    ** make a table of translations from a byte with encoded sequence
    ** to an array of 4 ascii characters
    */	 

    fstcall_f = FALSE;
    for (k=0, x=0;  k < 4;  k++)
      for (l=0;  l < 4;  l++)
	for (m=0;  m < 4;  m++)
	  for (n=0;  n < 4;  n++)
	    tbl[x++] = nuc[k] + 256 * nuc[l] + 
	      65536 * nuc[m] + 16777216 * nuc[n];
  }						

  /*	 
  ** convert unsigned characters with 4 ecoded nucleotide names into
  ** unsigned ints (in reality an array of 4 ascii characters); start
  ** from the end of the sequence...then we can do the replacement
  ** "within" the string;
  ** the base address of array seq_p (=seq) must be aligned on 4 byte 
  ** boundary!!!
  **
  ** slightly more complicated since we have the little-big endian problem
  ** again...the 4 byte value in "tbl" (which is a four letter sequence) is
  ** LITTLE endian...it needs to be converted to platform dependent format
  ** which is done by the shifting;
  */	 

  i = ((seq->len+3)/4)-1; 
  binseq = (unsigned char *) seq->seq;
  for (; i >= 0; i--) {
    buff = (unsigned char *) &tbl[binseq[i]];
    seqPtr[i] = ((UINT4) ((unsigned char) buff[0])) + 
                ((UINT4) ((unsigned char) buff[1]) << 8) + 
	        ((UINT4) ((unsigned char) buff[2]) << 16) + 
	        ((UINT4) ((unsigned char) buff[3]) << 24); 
  }
  seq->seq[seq->len] = '\0';
}



/****** SeqRemoveStop *********************************************************
**
**      Removes trailing stop codon from sequence.
**
**      INPUT:      sequence object [W]
**              IMPLICIT:
**
**      RETURNS:  
*/

void SeqRemoveStop (SEQo *seq)
{
  if (seq->seq[seq->len-1] == '*') 
    seq->seq[ --(seq->len) ] = '\0';
}



/****** SeqTranslate *********************************************************
**
**      Translates a DNA sequence into protein;
**      The translation is controlled by the translation table, the list
**      of translation exceptions and the list of codon changes to be
**      applied to the translation table.
**
**      INPUT:    o address dna sequence object [R]
**                o start position (begin=1) [R]
**                o translation table [R]
**                o array of translation exception descriptions [R] or NULL
**                o array of codon changes to be applied to the 
**                  translation table [R] or NULL
**              IMPLICIT:
**
**      RETURNS:    translated protein sequence 
**                  NULL if there was a problem
*/

SEQo *SeqTranslate (SEQo *dna, INT4 start, SEQoTranslTable *tTable,
		    SEQoTranslExcept *tExcept, SEQoTranslCodon *tCodon)
{
  SEQoTranslExcept *tExceptNext;
  SEQo *prot=NULL;
  INT4 k, l, isFirst=1;
  char aa;
  
  if (dna->len - start + 1 < 3) {
    _ErrMsg3 (e__seqillegallength, start, dna->len);
    return NULL;
  }
  
  if (tCodon)
    SeqTranslTableEdit (tTable, tCodon);
  SeqNew (&prot);
  SeqAlloc (prot, (dna->len - start)/3 + 100);
  
  for (k=start-1, l=0, tExceptNext=tExcept; k < dna->len-1;) {

    /* deal with possible translation exception */
    if (tExceptNext && k == tExceptNext->begin-1) {
      isFirst=0;
      prot->seq[l++] = tExceptNext->aa;
      k += tExcept->length;
      tExceptNext->isDone = 1;
      tExceptNext = (++tExceptNext)->aa ? tExceptNext : NULL;
    }
    else if (isFirst) { /* first codon */
      isFirst = 0;
      if ((aa = SeqTranslCodon (&dna->seq[k], tTable, 1)) == 'M') {
	  prot->seq[l++] = aa;
	  k += 3;
      }
      else 
	global_before_f-- ; 
    }
    else {
      prot->seq[l++] = SeqTranslCodon (&dna->seq[k], tTable, 0);
      k += 3;
    }
  }
  prot->seq[l] = '\0';
  prot->len = l;
  if (tCodon) /* remove edited translation table again */
    SeqTranslTableRevert (tTable);

  SeqRemoveStop (prot);
  sprintf (prot->name, "%s_aa", dna->name);
  return prot;
}


/****** SeqTranslCodon ********************************************************
**
**      Translates a nucleotide triplett into an amino acid.
**      The triplett may contain ambiguity codes.
**      If the last nucleotide is missing an 'x' is assumed.
**
**      INPUT:      nucleotide triplett [R]
**                  the translation table [R]
**                  a flag if to translate the start codon [R]
**              IMPLICIT:
**
**      RETURNS:    the translated amino acid.
*/

char SeqTranslCodon (char *triplett, SEQoTranslTable *transTable, 
		     INT4 isStartCodon)
{
  static char *ntAmbigList[26]={ "A","CGT","C","AGT","","","G","ACT","", 
                                 "","GT","","AC","GATC","","","","AG",
                                 "CG","T","U","ACG","AT","ACGT","CT",""};
  INT4 k, l, m, *order;
  char b1, b2, b3, aa, aaPrev=0, *ntList[3], *aaTrans;

  order = SeqGetTranslNtOrder ();
  aaTrans = isStartCodon ? transTable->saa : transTable->aa;

  /* The triplett might contain ambiguity codes:
     assign to each base in the triplett the list of possible nucleotides 
     Make the last nucleotide an 'x' if it is missing
  */
  for (k=0; k<3; k++) {
    b1 = tolower(triplett[k]);
    ntList[k] = ntAmbigList[(b1 ? b1 : 'x') - 'a'];
  }

  /* get all indices into the aa transl list for all combinations */
  aa = 'X';
  for (k=0; (b1=ntList[0][k]); k++) 
    for (l=0; (b2=ntList[1][l]); l++) 
      for (m=0; (b3=ntList[2][m]); m++) {
	aa = aaTrans[order[b1]*16 + order[b2]*4 + order[b3]];
	if (aaPrev && aa != aaPrev) {
	  aa = 'X';
	  break;
	  aaPrev = aa;
	}
      }	
  return aa;
}


/****** SeqTranslTableEdit ****************************************************
**
**      Translates a nucleotide triplett into an amino acid.
**      The triplett may contain ambiguity codes.
**
**      INPUT:      nucleotide triplett [R]
**                  the translation table [R]
**                  a flag if to translate the start codon [R]
**              IMPLICIT:
**
**      RETURNS:    the translated amino acid.
*/

static void SeqTranslTableEdit (SEQoTranslTable *tTable,
				     SEQoTranslCodon *tCodon)
{
  SEQoTranslCodon *tmp;
  INT4            *order;
  char            *swap, *nt;

  order = SeqGetTranslNtOrder ();

  if (!tTable->aaAlt)
    tTable->aaAlt = (char *) malloc (strlen (tTable->aa) + 1);
  strcpy (tTable->aaAlt, tTable->aa);

  swap = tTable->aa;
  tTable->aa = tTable->aaAlt;
  tTable->aaAlt = swap;

  for (tmp = tCodon; tmp->aa; tmp++) {
    nt = tmp->codon;
    tTable->aa[ order[*nt++]*16 + order[*nt++]*4 + order[*nt] ] = tmp->aa;
  }
}

/****** SeqTranslTableRevert **************************************************
**
**      Reverts edited table to original version.
**
**      INPUT:      translation table [W]
**              IMPLICIT:
**
**      RETURNS:  
*/

static void SeqTranslTableRevert (SEQoTranslTable *tTable)
{
  char *swap;

  swap = tTable->aa;
  tTable->aa = tTable->aaAlt;
  tTable->aaAlt = swap;
}


/****** SeqTaxaToTranslTable **************************************************
**
**      Searches various taxa (case insensitive) to find the appropriate
**      translation table;
**
**      INPUT:      address of buffer with organism source information
**              IMPLICIT:
**
**      RETURNS:    the translation table
*/

SEQoTranslTable *SeqTaxaToTranslTable (SMoBUFF *org)
{
  INT4 id;

  if (BuffSearch(org,"Protozoa") && BuffSearch(org,"Cili")
      && !BuffSearch(org,"Mitoch"))
    id = 6;

  else if (BuffSearch(org,"Mitochond") && BuffSearch(org,"Yeast"))
    id = 3;

  else if (BuffSearch(org,"Mitochond")
      && (BuffSearch(org,"Podospora") || BuffSearch(org,"Protozoa"))
      || BuffSearch (org, "Mycoplasma"))
    id = 4;

  else if (BuffSearch(org,"Mitochond")
      && (BuffSearch(org,"Vertebrata") || BuffSearch(org,"Mammalia")))
    id = 2;

  else if (BuffSearch(org,"Mitochond") && BuffSearch(org,"Echinoderm"))
    id = 9;

  else if (BuffSearch(org,"Mitochond"))
    id = 5;

  else if (BuffSearch(org,"Bacteri") || BuffSearch(org,"Chloroplast") )
    id = 11;

  else if (BuffSearch(org,"Platyhelminthes"))
    id = 14;

  else
    id = 1; /* standard */

  return (SeqIdToTranslTable (id));
}

/****** SeqIdToTranslTable **************************************************
**
**      Returns the translation table with specified (numeric) ID.
**
**      INPUT:      the id (1 to ?) [R]
**              IMPLICIT:
**
**      RETURNS:    the translation table
**                  NULL if not found
*/

SEQoTranslTable *SeqIdToTranslTable (INT4 id)
{
  SEQoTranslTable *tmp=translTable;

  for (tmp=translTable; *tmp->name; tmp++)
    if (tmp->id == id)
      return tmp;
  return NULL;
}



/****** SeqGetTranslNtOrder **************************************************
**
**      Gets the order for the nucleotides to be used to correspond a codon
**      to an amino acid in the translation table
**
**      INPUT:     
**              IMPLICIT:
**
**      RETURNS:   an array where the nt character addresses the order
*/

static INT4 *SeqGetTranslNtOrder ()
{
  static INT4 isInit=0, order[300];

  if (!isInit) {
    order['T'] = 0;
    order['C'] = 1;
    order['A'] = 2;
    order['G'] = 3;
    isInit = 1;
  }
  return order;
}



/****** SeqComplement *********************************************************
**
**      reverse complements a dna sequence;
**      processes also GCG ambiguity codes;
**
**      INPUT:      address of dna sequence object [W]
**              IMPLICIT:
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 SeqComplement (SEQo *seq) 
{
  INT4 i,j;
  char c, *s=seq->seq;
  
  if (!s) return 0;

  /* swap flags */
  i = global_before_f;
  global_before_f = global_after_f;
  global_after_f = i;

  for (i=0, j=seq->len-1; i < j; i++, j--) {
    c = s[i];
    s[i] = s[j];
    s[j] = c;
  }

  for (i=0; i < seq->len; i++)
    switch (s[i]) {
    case 'A':  s[i] = 'T'; break;
    case 'C':  s[i] = 'G'; break;
    case 'G':  s[i] = 'C'; break;
    case 'T':  s[i] = 'A'; break;
    case 'U':  s[i] = 'A'; break;
    case 'M':  s[i] = 'K'; break;
    case 'R':  s[i] = 'Y'; break;
    case 'W':  s[i] = 'W'; break;
    case 'S':  s[i] = 'S'; break;
    case 'Y':  s[i] = 'R'; break;
    case 'K':  s[i] = 'M'; break;
    case 'V':  s[i] = 'B'; break;
    case 'H':  s[i] = 'D'; break;
    case 'D':  s[i] = 'H'; break;
    case 'B':  s[i] = 'V'; break;
    case 'X':  s[i] = 'X'; break;
    case 'N':  s[i] = 'N'; break;

    case 'a':  s[i] = 't'; break;
    case 'c':  s[i] = 'g'; break;
    case 'g':  s[i] = 'c'; break;
    case 't':  s[i] = 'a'; break;
    case 'u':  s[i] = 'a'; break;
    case 'm':  s[i] = 'k'; break;
    case 'r':  s[i] = 'y'; break;
    case 'w':  s[i] = 'w'; break;
    case 's':  s[i] = 's'; break;
    case 'y':  s[i] = 'r'; break;
    case 'k':  s[i] = 'm'; break;
    case 'v':  s[i] = 'b'; break;
    case 'h':  s[i] = 'd'; break;
    case 'd':  s[i] = 'h'; break;
    case 'b':  s[i] = 'v'; break;
    case 'x':  s[i] = 'x'; break;
    case 'n':  s[i] = 'n'; break;
    }
  
  return 1;
}


/**api** SeqClr ***************************************************************
**
**	deletes all sequence-descriptors
**	in the list;
**
**	INPUT:      pointer to address of sequence object [W]
**                  
**	        IMPLICIT:
**
**	RETURNS:    1
*/ 
   
void SeqClr (SEQo **seq)
{
  LstDeleteAll ((void **) seq);
  *seq = NULL;
}


/**api* SeqClean **************************************************************
**
**	removes sequences with seq->keep_f == FALSE; sets seq->keep_f
**      of kept sequences to FALSE; sets list pointer to the first element
**      in the set;
**
**	INPUT:
**	        IMPLICIT:
**
**	RETURNS:    1
*/ 
   
void SeqClean (SEQo **seq)
{
  LstFirst ((void **) seq);
  do {
    if (!(*seq)->keep_f)
      LstDelete ((void **) seq);
    else 
      (*seq)->keep_f = FALSE;
  } while (LstNext ((void **) seq));

  LstFirst ((void **) seq);
}



/****** SeqTest ***************************************************************
**
**     reads a file, tests line for any of the tokens described for 
**     TestSeqFormat, and returns if something is found;
**
**	INPUT:	     address of file-dsc. [W]
**	        IMPLICIT:
**
**	RETURNS:    token-value
*/ 
   
static INT4 SeqTest (FILo *file)
{
  INT4	x, lineNoSave=0;
  
  while (!file->eof) {
    if (file->l[0] == '>') {
      file->l++;
      return SEQxRANGLE;
    }

    if (file->l[2] == ';') {
      file->l++;
      return SEQxSEMICOLON;
    }
    if ((x = SmLoc (file->l, "Check:")) != -1) {
      file->l += x + 1;
      return SEQxCHECK;
    }
    
    if ((x = SmLoc (file->l, "..")) != -1) {
      file->l += x + 1;
      return SEQxDOTDOT;
    }
    
    /*
    ** recognize EMBL format by "SQ   Sequence" line followed by 
    ** line starting with "     ".
    */

    if (SmMixLoc (file->l, "SQ   Sequence", 1, 1) != -1) 
      lineNoSave = file->n;
    if (SmMixLoc (file->l, "     ", 1, 1) != -1) 
      if (file->n == lineNoSave + 1)
	return SEQxEMBL;

    FilURead (file);
  }
  return e__eof;
}


/**api* SeqGoGcgDots **********************************************************
**
**      searches for ".." and sets file pointer to following line - if not 
**      found file pointer is set at begin of file
**
**	INPUT:	     address of file-dsc. [W]
**	        IMPLICIT:
**
**	RETURNS:    1 if dots were found
**                  0 if not
*/ 

INT4 SeqGoGcgDots (FILo *file)
{
  FILoL_S savepos;

  FilUSave (file, &savepos);
  while (!file->eof) {
    if (SmLoc (file->l, "..") != -1) {
      FilURead (file);
      return 1;
    }
    FilURead (file);
  }
  FilUBack (file, &savepos);
  file->eof = 0;
  return 0;
}



/****** SeqTestFormat *********************************************************
**
**      takes an opened file, analyzes file for sequence format:
** 	o  GCG, if there is a line with a "Check:" followed by "..", either
** 	   on same or following line;
**      o  GCG-MSF, if "Check:", ".." is followed by "//" in first column; 
** 	o  PIR, if a line with '>' in first column followed by ';' with 
** 	   a distance of 3 columns
** 	o  PEARSON or FASTA if only the '>' is found;
**      if a format could be dtermined then file pointer is set at beginning
**      of sequence that is: GCG or GCG-MSF: line with ".."
**                          PIR, PEARSON: line with ">"
**
** 	INPUT:	    address of file-dsc [W]
** 	        IMPLICIT:
**
** 	RETURNS:    if format found: SEQxGCG, SEQxMSF, SEQxPIR, SEQxPEARSON
**                  else: 0 
*/ 
   
static INT4 SeqTestFormat (FILo *file)
{
  INT4	rv, format=0, gcg_f=0, check_f=0;

  do {
    rv = SeqTest (file);
    
    if (rv == SEQxEMBL) {
      format = SEQxEMBL;
      break;
    }

    if (rv == SEQxRANGLE)
      format = SEQxPIR;
    
    if (rv == SEQxPIRTOKENS)
      format = SEQxPIR;
    
    if (rv == SEQxCHECK) {
      if (gcg_f) {
	format = SEQxMSF;
	FilUBack2 (file);
      }
      else
	check_f = TRUE;	   
    }        
    
    if (rv == SEQxDOTDOT && check_f) {
      FilUSave2 (file);
      gcg_f = TRUE;
      check_f = FALSE;
    }
  }
  while (rv != e__eof && !format);
  
  if (gcg_f && !format) {
    format = SEQxGCG;
    FilUBack2 (file);
  }
  return format;   
}



/****** SeqCopy ***************************************************************
**
**	adds sequence to existing sequence
**	with or without filtering (i.e. copies only alphanums and ".', \"-")
**
**	INPUT:	    address of sequence descriptor [W]
**		    address of sequence string [R]
**		    copy option: SEQxFILTER, or 0 [R]
**	        IMPLICIT:
**
**	RETURNS:    1
**                  0 if sequence terminator was found ('*')
*/ 
   
static INT4 SeqCopy (SEQo *seq, char *stream, INT4 option)
{
  static SMoBUFF *buff=NULL;
  INT4 rv=1;
  
  if (!buff) 
    buff = BuffNew (1000);

  if (seq->seq == NULL)  /* begin of new sequence? */
    BuffReset (buff);
  
  /*
  ** process single characters...filter nonsequence characters out
  */
  
  if (option == SEQxFILTER) {
    for (; *stream != '\0'; stream++) {
      if (isalpha (*stream) || *stream == '-' || *stream == '.')
	BuffCopyChar (buff, *stream);
      else if (*stream == '*') {  /* terminator */
	rv = 0;
	break;
      }		
    }
    BuffCopyChar (buff, '\0');
    BuffShiftCurrPtr (buff, -1); /* 0 char will be overwritten by next call */
  }

  else { /* sequence is trustworthy...copy without looking at the content */
    BuffCopyString (buff, stream);
  }
  seq->len = BuffGetCurrOffset (buff);
  seq->seq = BuffGetPtr (buff); 
  return rv;
}


/****** SeqReadPirSeq *********************************************************
**
**      assumes that file->ln contains title line >...;
**	reads a sequence in PIR format from file;
**
**	INPUT:	    pointer to address of sequence object [R] 
**		    file object (opened for reading) [W]
**
**	        IMPLICIT:
**
**	RETURNS:    1 if success
**		    0 if either wrong format or EOF
*/ 
   
static INT4 SeqReadPirSeq (SEQo **seq, FILo *file)
{
  SeqNew (seq);
  sscanf (&file->ln[4], "%s", (*seq)->name);
  FilURead (file);
  StrSetS (&(*seq)->cmnt, file->ln);
  
  while (FilURead (file) != e__eof) 
    if (!SeqCopy (*seq, file->ln, SEQxFILTER))
      break;
  SeqMakeOwn (*seq);
  return 1;	        
}


/****** SeqReadEMBLSeq ********************************************************
**
**      Assumes that file pointer is at begin of sequence.
**	Reads a sequence in EMBL format from file;
**
**	INPUT:	    pointer to address of sequence object [R] 
**		    file object (opened for reading) [W]
**
**	        IMPLICIT:
**
**	RETURNS:    1 if success
**		    0 if either wrong format or EOF
*/ 
   
static INT4 SeqReadEMBLSeq (SEQo **seq, FILo *file)
{
  SeqNew (seq);
  
  do {
    if (!SeqCopy (*seq, file->ln, SEQxFILTER))
      break;
  } while (FilURead (file) != e__eof);
  SeqMakeOwn (*seq);
  return 1;	        
}



/****** SeqReaddGCGSeq ********************************************************
**
**	reads GCG -sequence from file; assumes that file->ln contains line
**	with >..<;
**
**	INPUT:	    pointer to address of sequence object [R] 
**		    file object (opened for reading) [W]
**	        IMPLICIT:
**
**	RETURNS:    1
*/ 
   
static INT4 SeqReadGCGSeq (SEQo **seq, FILo *file)
{
  SeqNew (seq);
  FilParse (file->nam, (*seq)->name, FILxNAME);
  
  while (FilURead (file) != e__eof) {
    if (!SeqCopy (*seq, file->ln, SEQxFILTER))
      break;
  } 
  SeqMakeOwn (*seq);
  return 1;	        
}



/****** SeqReadMSFSeq *********************************************************
**
**      assumes that file->ln contains line with /../;
**	reads all sequences from MSF-file;
**
**	INPUT:	    pointer to address of sequence object [R] 
**		    file object (opened for reading) [W]
**	        IMPLICIT:
**
**	RETURNS:    number of sequences read
*/ 
   
static INT4 SeqReadMSFSeq (SEQo **seq, FILo *file)
{
  char	 seq_nm[SEQxXNAM+1];
  INT4    seq_n, max_nmz, nam_z, seq_f, seq_z;

  for (seq_n=0, max_nmz=0, seq_f=FALSE; FilURead (file) != e__eof;) {

    /*
    ** after the two dots all sequences occuring in the msf file are listed
    ** one name per row, each row starts with "Name:"
    */

    if (!seq_f) {
      if (sscanf (file->ln, " Name: %s Len: %d", seq_nm, &seq_z) == 2) {
	SeqNew (seq);
	strcpy ((*seq)->name, seq_nm);
	SeqAlloc ((*seq), seq_n);  /** allocate sequence buffer */
	seq_n++;

	if ((nam_z = strlen (seq_nm)) > max_nmz)  
	  max_nmz = nam_z; /** size of longest name -> identation length */
      }
      else if (SmLoc (file->ln, "//") != -1)
	seq_f = TRUE;  /** sequences start after that */
    }

    /*
    ** block with sequences is being processed
    */

    else {

      /*
      ** read sequence name -> length is determined by longest name...
      ** if the string is not empty (line might be a number line ...)
      ** then the sequence must be copied -> get the sequence object
      ** by the name just read;
      */ 

      strncpy (seq_nm, file->ln, max_nmz);
      SmEdit (seq_nm, SMxTRIM);
      if (seq_nm[0] != ' ') {
	LstFirstNamed ((void **) seq, seq_nm);  /** assumes names are unique */
	SeqCopy (*seq, &file->ln[max_nmz], SEQxFILTER);  
      }
    }    	
  }

  return seq_n;
}



/**API* SeqReadAll ************************************************************
**
**	Opens file, tests format and reads sequence(s) if format could 
**      be determined.
**      The following formats are understood: PIR, FASTA, EMBL, GCG, MSF.
**
**	INPUT:	    address of pointer to sequence object [W] 
**		    file name [R]
**	        IMPLICIT:
**
**	RETURNS:    number of sequences read;
**		    e__novalseqform <fil_nm, format> +
**		    e__filnotok <fil_nm> +
*/ 
   
INT4 SeqReadAll (SEQo **seq, char *fil_nm)
{
  FILo    *file;
  INT4	  seq_n=0, rv;

  rv = FilUOpen2 (&file, fil_nm, SEQxXLN, FILxVAR);
  _ErrIf (rv) {
    _ErrMsg2 (rv, fil_nm);
    return 0;
  }

  rv = SeqTestFormat (file);
  
  switch (rv) {
  case SEQxGCG:
    seq_n = SeqReadGCGSeq (seq, file);
    break;
  case SEQxMSF:
    seq_n = SeqReadMSFSeq (seq, file);
    break;
  case SEQxPIR:
    do {
      SeqReadPirSeq (seq, file);
      seq_n++;
    } while (SeqTestFormat (file) == SEQxPIR);
    break;
  case SEQxPEARSON:
    break;
  case SEQxEMBL:
    seq_n = SeqReadEMBLSeq (seq, file);
    break;
  default:
    _ErrMsg3 (e__novalseqform, fil_nm, "GCG, GCG-MSF, PIR, FASTA, EMBL");
      
  }
  FilUClose2 (file);
  return seq_n;
}


SEQo *SeqReadString (char *s)
{
  SEQo *seq=NULL;

  SeqNew (&seq);
  SeqCopy (seq, s, SEQxFILTER);
  SeqMakeOwn (seq);
  return seq;	        
}


/**api* SeqReadPIR ************************************************************
**
**	reads a sequence in PIR format;
**
**	INPUT:	    pointer to address of sequence object [W] 
**		    file name [R]
**	        IMPLICIT:
**
**	RETURNS:    number of sequences read
**		    e__novalseqform <fil_nm, format> +
**                  e__filnotok <fil_nm> +
*/ 
   
INT4 SeqReadPIR (SEQo **seq, char *fil_nm)
{
  FILo *file;
  INT4  k, rv;

  rv = FilUOpen2 (&file, fil_nm, SEQxXLN, FILxVAR);
  _ErrRet2(rv, fil_nm);
  
  for (k=0; SeqTestFormat (file) == SEQxPIR;  k++)
    SeqReadPirSeq (seq, file);
  FilUClose2 (file);
  
  if (k==0)
    _ErrRet3 (e__novalseqform, fil_nm, "PIR");
  return k;
}


/**api* SeqReadGCG ************************************************************
** 
** 	reads either single GCG files or GCG-MSF-file or file-of-names;
** 
**	INPUT:	    pointer to address of sequence object [W] 
**		    name (GCG-file name)  [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
*/ 
   
INT4 SeqReadGCG (SEQo **seq, char *name)
{
#ifndef dos
  char	        file_nm[FILxXNAM];
  UINT4  context = 0;

  if (strchr (name, '{') != NULL) 
    SeqReadMSF (seq, name);

  else
    while (FilSearch (name, file_nm, &context) != 0) 
      SeqReadGCGFile (seq, file_nm);
#endif
  return 1;
}


/**api* SeqReadGCGFile ********************************************************
** 
** 	opens a sequence in GCG-format and reads sequence into global seqbuff;
** 	sequence-info goes into sequence-descriptor;
**      file-NAME is copied to sequence-name
** 
**	INPUT:	    pointer to address of sequence object [W] 
**		    name (GCG-file name)  [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if OK
** 		    e__allocfail <item> +
**                  e__novalseqform <file_nm, format> +
*/ 
   
INT4 SeqReadGCGFile (SEQo **seq, char *fil_nm)
{
  FILo *file;
  INT4  rv;

  rv = FilUOpen2 (&file, fil_nm, SEQxXLN, FILxVAR);
  _ErrRet2 (rv, fil_nm);
  
  if (SeqTestFormat (file) != SEQxGCG)
    _ErrRet3 (e__novalseqform, fil_nm, "GCG");
      
  rv = SeqReadGCGSeq (seq, file);
  FilUClose2 (file);
  return 1;
}


/****** SeqMSFNam *************************************************************
**
**	analyzes a name that specifies a set of sequences in MSF file
**      file name must have "{*}" at the end;
**
**	INPUT:	 o  address of input string [R]
**		 o  address that receives filename part [W]
**		 o  address that receives seqname part [W]
**	            wildcard will be removed
**	        IMPLICIT:
**
**	RETURNS:    0 if no wildcard
**		    1 if yes
*/ 
   
static INT4 SeqMSFNam (char *name, char *file_nm, char *seq_nm)
{
  char    *off;
  INT4	  l;
  
  for (l=0; *name != '{' && *name; name++, l++) 
    file_nm[l] = *name; 
  file_nm[l] = '\0';
  
  for (l=0; *(++name) != '}' && *name; l++) 
    seq_nm[l] = *name;
  seq_nm[l] = '\0';
  
  if ((off = (char *) strchr (seq_nm, '*')) == NULL)
    return 0;
  else
    *off = '\0';
  return 1;
}

/**api* SeqReadMSF ************************************************************
** 
** 	reads all sequences in an MSF file;
**      file name must have "{*}" at the end;
** 
**	INPUT:	    pointer to address of sequence object [W] 
**		    name of MSF file [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    number of sequences read 
** 		    e__novalseqform <fil_nm, format> +
**                  e__filnotok <fil_nm> +
*/ 
   
INT4 SeqReadMSF (SEQo **seq, char *msf_nm)
{
  FILo *file;
  char fil_nm[SEQxXNAM+1], seq_nm[SEQxXNAM+1];
  INT4  rv, seq_n;

  SeqMSFNam (msf_nm, fil_nm, seq_nm);
  
  seq_n = 0;
  rv = FilUOpen2 (&file, fil_nm, SEQxXLN, FILxVAR);
  _ErrRet2 (rv, fil_nm);
    
  if (SeqTestFormat (file) != SEQxMSF)	 
    _ErrRet3 (e__novalseqform, fil_nm, "GCG-MSF");
	
  seq_n = SeqReadMSFSeq (seq, file);
  FilUClose2 (file);
  return seq_n;
}



/**api* SeqSetRecordSeparator *************************************************
**
**	GCG 7.x format on VMS has a single char separating records.
**      SeqFromLib must ignore that.
**
**	INPUT:      length of separator [R]
**	        IMPLICIT:
**                  recordSeparatorLength (INT4) [W]
**
**	RETURNS:    
*/ 

void SeqSetRecordSeparator (INT4 i)
{
#ifdef VMS
  recordSeparatorLength = i;
#else
  recordSeparatorLength = 0;
#endif
}


/**api* SeqFromLib ************************************************************
**
**	reads sequence file from current position - assumes that the 
**      title line is just read in and reads comment plus sequence;
**
**	INPUT:	 o  address of sequence object [W]
**		 o  address of file-descriptor [W]
**               o  optional scanf format string to extract the name [R] or
**                  NULL 
**               o  string that marks the end of the sequence [R]
**               o  flag determines if first line after title is a comment line
**                  else the title line is read into comment [R]
**	        IMPLICIT:
**
**	RETURNS:    1
**                  e__eof
*/ 
   
INT4 SeqFromLib (SEQo **seq, FILo *file, char *findId, char *exitstr, INT4 options)
{
  INT4 k, l, off, len, seq_z, readchar_n, rv=1, 
      gcgascii_f = FALSE, gcgbin_f = FALSE;

  SeqNew (seq);

  /*	 
  **  edit first entry line and get entry name
  */	 

  SmEdit (file->ln, SMxUPCASE);
  SmXLoc (file->ln, exitstr, 1, 1);
  if (findId)
    sscanf (file->ln, findId, (*seq)->name); 
  else
    sscanf (file->ln, "%s", (*seq)->name); 

  /*	 
  **  if this is a gcg sequences then it has a length field and either 2BIT
  **  or ASCII
  */

  if ((off = SmLoc (file->ln, "LEN:")) != -1) {
    sscanf (&((file->ln)[off]), "LEN: %d", &seq_z);
    if (SmLoc (file->ln, "2BIT") != -1) 
      gcgbin_f = TRUE;
    if (SmLoc (file->ln, "ASCII") != -1) 
      gcgascii_f = TRUE;
  }

  /*	 
  **  read and copy second line of entry with comment to the sequence
  */	 

  if (options & 1) {
    if (FilURead (file) == e__eof)
      return e__eof;
  }
     /*  strcpy (seq->cmnt, file->ln); */

  /*
  ** read the binary encoded sequence (length = sequence len * 4 ...  some
  ** extra info is read if the last byte is not completely used; then
  ** convert the sequence to ascii format; seq->seq must be aligned to 4 byte
  ** boundary for SeqBinToAsci - SeqMalloc does this 
  */	 

  if (gcgbin_f || gcgascii_f) {
    readchar_n = gcgbin_f ? (seq_z+3)/4 : seq_z;
    SeqAlloc (*seq, seq_z+4+1);
    for (k=0, l=readchar_n; k < readchar_n; k += file->len, l -= file->len)
      fread ((*seq)->seq+k, 1, 
	     l > file->len ? file->len + recordSeparatorLength : l, 
	     file->fil);

    /*    if (gcgbin_f)
      SeqBinToAscii ((*seq)->seq, seq_z); */
    (*seq)->len = seq_z;

    file->l = file->ln; file->ln[0] = '\0';  /** wipe out file->ln...fread! */ 
  }

  /*
  ** if not gcg format read the sequence until exitstr is encountered
  */

  else {
    while (1) {
      if (FilURead (file) == e__eof) {
	rv = e__eof;
	break;
      }
      if (memcmp (file->ln, exitstr, strlen (exitstr))  == 0) 
	break;
      
      len = strlen (file->ln);
      if (file->ln[len-1] == '\n')
	file->ln[--len] = '\0';
      SeqCopy (*seq, file->ln, SEQxFILTER); 
    }
    if (options & 2)
      (*seq)->seq = NULL; /* prevents strange behaviour of srsbuild on osf1 ...
			     sequence is not needed anyway ..just the length */    else 
      SeqMakeOwn (*seq);
  }
  return rv;
}



/****** SeqGCGCheck ***********************************************************
**
**	is the equiv. to the GCG CheckSeq; calculates a check sum for the
**	input sequence; 
**
**	INPUT:	    address of array holding sequence
**		    length of seuqence 
**
**	RETURNS:    check sum if successful
**		    
*/

static INT4 SeqGCGCheck(char *seq, INT4 len)
{
  static INT4	    fstcall_f = 1;
  static char	    table[256];
  INT4		    k, check = 0, i = 0;

  if (fstcall_f) {
    for (k = 0;  k <= 255;  k++)
      table[k] = toupper(k);
    fstcall_f = 0;
  }

  for( i=0, check=0; i < len; i++, seq++)
    check += ((i % 57)+1) * table[ (INT4) *seq];
  return check % 10000;		
}


/****** SeqWrite **************************************************************
**
**	writes a sequence to file with specified characters per line and 
**	characters by block;
**
**	INPUT:	 o  address of file block [W]
**		 o  address of sequence [R]
**		 o  length of sequence [R]
**		 o  char per line [R]
**		 o  char per block [R]
**		 o  format option bitmask [R]
**                     using SEQxNUMBER, SEQxSTAR, SMxLOWCASE, SMxUPCASE or 0
**                           SEQxLMARGIN
**	        IMPLICIT:
**
**	RETURNS:    nr. of lines written
*/ 
   
static INT4 SeqWrite (char *seq, INT4 len, INT4 colN, INT4 blockColN, 
		      INT4 option, INT4 (*print)(char*,...))
{
  char    line[SEQxXLN+1], *tmp;
  INT4	  lineN = 0, k;

  if (!len)
    return 0;

  for (k=0;  k < len && *seq != '\0';  k++) {    
    if (k % colN == 0) { /* is end of line? */
      if (k != 0) {
	*tmp = '\0';
	if (option & SEQxEMBLNUMBER)
	  sprintf (line, "%-70s%10d", line, k);
	print ("%s\n", line);
      }
      if (option & SEQxNUMBER)
	sprintf (line, "%8d  ", k+1);
      else if (option & SEQxLMARGIN)
	sprintf (line, "     ");
      else
	strcpy (line, "");
      tmp = &(line[strlen (line)]);
    }
    else if (k % blockColN == 0) /* is end of block ? */
      *(tmp++) = ' ';	    
    
    *(tmp++) = seq[k];
  }
  
  if (option & SEQxSTAR) /* put star at the end of the sequence */
    *tmp++ = '*';
  *tmp = '\0';

  /* print last line feed */
  if (option & SEQxEMBLNUMBER)
    sprintf (line, "%-70s%10d", line, k);
  print ("%s\n", line);
  
  return ++lineN;
}


/**API* SeqWriteGCG ***********************************************************
** 
** 	Prints a sequence in GCG format.
**  
** 	INPUT:	  o address of sequence object [R]
**                o sequence name [R] or NULL
**                o function to be used for printing lines [R] prints to STDOUT
**                  if NULL
** 
** 	RETURNS:    no of lines printed
*/

INT4 SeqWriteGCG (SEQo *seq, char *nam, INT4 (*print)(char*,...))
{
  INT4 cksum;

  if (!print)
    print = (INT4 (*)(char*,...)) printf;
  
  cksum = SeqGCGCheck (seq->seq, seq->len);
  print ("%s  Length: %d  Check: %d  ..\n\n", 
	   nam == NULL ? seq->name : nam, seq->len, cksum);
  return SeqWrite (seq->seq, seq->len, 60, 10, SEQxNUMBER, print) + 2;
}


/**API* SeqWriteApplet **************************************************************
** 
** 	Prints a sequence in GCG format.
**  
** 	INPUT:	  o address of sequence object [R]
**                o sequence name [R] or NULL
**                o function to be used for printing lines [R] prints to STDOUT
**                  if NULL
** 
** 	RETURNS:    no of lines printed
*/

INT4 SeqWriteApplet (SEQo *seq, char *nam)
{
  printf ("<applet code=\"ChartApplet.class\" codebase=\"http://srs.ebi.ac.uk:5000/java/\"");
  printf (" width=400 height=200>\n");
  printf ("<param name=sequence value=\"%s\">\n", seq->seq);
  printf ("<param name=property value=\"");
  printf (" A:0.36  R:-0.52  N:-0.90  D:-1.09 C:0.70  Q:-1.05  E:-0.83  G:-0.82");
  printf (" H:0.16   I:2.17");
  printf (" L:1.18  K:-0.56  M:1.21   F:1.01  P:-0.06 S:-0.60  T:-1.20  W:1.31");
  printf (" Y:1.05   V:1.21\">");
  printf ("</applet>\n");
}



/**API* SeqWritePIR ***********************************************************
** 
** 	Prints a sequence in PIR format.
**  
** 	INPUT:	  o address of sequence object [R]
**                o sequence name [R] title line is omitted if NULL
**                o title line [R] or NULL
**                o function to be used for printing lines [R] prints to STDOUT
**                  if NULL
** 
** 	RETURNS:    no of lines printed
*/

INT4 SeqWritePIR (SEQo *seq, char *nam, char *cmnt, INT4 (*print)(char*,...))
{
  INT4 lncnt = 0;

  if (!print)
    print = (INT4 (*)(char*,...)) printf;

  if (!seq) return 0;
  print (">P1;%s\n", nam == NULL ? seq->name : nam);
  if (!seq->cmnt)
    print ("    Length: %d\n", seq->len);
  else
    print ("%s\n", _Str (seq->cmnt));

  lncnt = SeqWrite (seq->seq, seq->len, 60, 10, SEQxSTAR, print);
  print ("\n");
  return lncnt+2;
}

STRv Seq2Pretty (SEQo *seq, Int4 width)
{
  STRv s=StrNew ();
  char tmp[20];
  Int4 i, k, len=SeqGetLength (seq);
  
  for (i=1; i <= len; i+= width) {
    for (k=i; k < width+i && k <= len; k+= 10) {
      sprintf (tmp, "%d", k);
      StrPrintf (&s, "%-10s", tmp);
    }      
    StrAppS (&s, "\n");
    StrAppN (&s, seq->seq+i-1, width);
    StrAppS (&s, "\n");
  }
  return s;
}




/**API* SeqWriteEmbl **********************************************************
** 
** 	Prints a sequence in EMBL format.
**  
** 	INPUT:	  o address of sequence object [R]
**                o sequence name [R] title line is omitted if NULL
**                o function to be used for printing lines [R] prints to STDOUT
**                  if NULL
** 
** 	RETURNS:    no of lines printed
** 		    
*/

INT4 SeqWriteEMBL (SEQo *seq, char *nam, INT4 (*print)(char*,...))
{
  INT4 lncnt = 0;

  if (!print)
    print = (INT4 (*)(char*,...)) printf;

  if (!seq) return 0;
  if (nam && !ParGetBool ("printEntireEntry"))
    print ("SQ   Sequence%6d BP;\n", seq->len);
  lncnt = SeqWrite (seq->seq, seq->len, 60, 10, SEQxLMARGIN | SEQxEMBLNUMBER, 
		    print);
  print ("//\n");
  return lncnt+2;
}


/**Api* SeqWriteSwiss *********************************************************
** 
** 	writes sequence in Swissprot format to file
**  
** 	INPUT:	    sequence object [R]
**                  sequence name ...if NULL then the title line is omitted [R]
**                  print line function [R]
** 
** 	OUTPUT:
** 		    returns:	nr. of lines written to file
*/

INT4 SeqWriteSwiss (SEQo *seq, char *nam, INT4 (*print)(char*,...))
{
  INT4 lncnt = 0;
  if (!print)
    print = (INT4 (*)(char*,...)) printf;
  
  if (!seq) return 0;
  if (nam)
    if  (!ParGetBool ("printEntireEntry"))
      print ("SQ   Sequence%6d AA;\n", seq->len);
  lncnt = SeqWrite (seq->seq, seq->len, 60, 10, SEQxLMARGIN, 
		    print);
  print ("//\n");
  return lncnt+2;
}




/**api* SeqWriteGDE ***********************************************************
** 
** 	writes sequence in GDE format
** 
** 	INPUT:	    address of sequence object [R]
**                  file pointer of output file [W]
**                  name to appear in the title line [R] or NULL
** 
** 	RETURNS:    nr. of lines written to file
*/

INT4 SeqWriteGDE (SEQo *seq, char *nam, INT4 (*print)(char*,...)) 
{
  INT4 ln_n=0;

  if (!print)
    print = (INT4 (*)(char*,...)) printf;

  if (!seq) return 0;
  print ("%c%s\n", '%', nam == NULL ? seq->name : nam);
  ln_n = SeqWrite (seq->seq, seq->len, 60, 10, 0, print);
  print ("\n");
  return ln_n+1;
}


/**api* SeqWriteFasta *********************************************************
** 
** modified 3-may-95 by Peter Rice to cut out spaces
** 
** 	writes sequence in PIR format to file
**  
** 	INPUT:	    address of sequence object [R]
**                  file pointer of output file [W]
**                  name to appear in the title line [R] or NULL
** 
** 	RETURNS:	nr. of lines written to file
**
*/

INT4 SeqWriteFasta (SEQo *seq, char *nam, INT4 (*print)(char*,...))
{
  INT4 lncnt = 0;

  if (!print)
    print = (INT4 (*)(char*,...)) printf;

  if (!seq) return 0;
  print (">%s\n", nam == NULL ? seq->name : nam);
  lncnt = SeqWrite (seq->seq, seq->len, 60, 60, 0, print); /* block 10 to 60 */
/*  print ("\n");  commented out */
  return lncnt+1; /* was lncnt+2 */
}


/**API* SeqWrtMSF *************************************************************
** 
** 	Prints a list of sequences in MSF (GCG) format.
** 
** 	INPUT:	  o address of sequence object [R]
**                o function to be used for printing lines [R] prints to STDOUT
**                  if NULL
** 
** 	RETURNS:
*/ 
  
INT4 SeqWrtMSF (SEQo *seq, INT4 (*print)(char*,...))
{
  INT4 savepos, k, allcksum, ali_z, line_n = 60;

  if (!print)
    print = (INT4 (*)(char*,...)) printf;

  if (!seq) return 0;
  LstGetPosition (seq, &savepos);

  /*
  ** go through all sequences and find out the max length which will
  ** become the length of the alignment...and calculate the total check sum
  ** of the alignment; 
  */

  do {
    if (seq->len > ali_z) 
      ali_z = seq->len;
    allcksum += SeqGCGCheck (seq->seq, seq->len);
  } while (LstNext ((void **) &seq));
  allcksum = allcksum % 10000; 

  /*
  ** print title of alignment and the names of the sequences occurring
  ** in the MSF file;
  */

  print ("MSF: %d  Type: P  Check: %d  ..\n\n", ali_z, allcksum);
  LstSetPosition ((void **) &seq, savepos);
  do {
    print (" Name: %-12s  Len: %6d  Check: %4d  Weight: 1\n", 
	     seq->name, seq->len, SeqGCGCheck (seq->seq, seq->len));
  } while (LstNext ((void **) &seq));
  print ("\n//\n");

  /*
  ** print the sequence alignment
  */ 
  
  for (k=0;  k < ali_z;  k += line_n) {
    LstSetPosition ((void **) &seq, savepos);
    do {
      print ("%-12s ", seq->name);
      SeqWrite (&seq->seq[k], line_n, line_n, 10, 0, print);
    } while (LstNext ((void **) &seq));
    print ("\n");
  }

  return 1;
}


/**api** SeqAlloc ************************************************************
** 
** 	allocates memory for a sequence string with know length;
** 
** 	INPUT:	    address of sequence object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if OK
**                  0 else
*/ 

static void SeqAlloc (SEQo *seq, INT4 len)
{
  if (seq->seq) 
    fprintf(stderr, "*** MEMORY LEAK in SeqAlloc ***\n");

  if ((seq->seq = (char *) malloc (len + 1)) == NULL)
    _ErrExit2 (e__allocfail, "sequence");
}


/**api** SeqMakeOwn ***********************************************************
** 
** 	copies the sequence string from temporary to extra allocated memory;
** 
** 	INPUT:	    address of sequence object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:  
*/ 

static void SeqMakeOwn (SEQo *seq)
{
  char *tmp;

  if (seq->len) {
    if ((tmp = (char *) malloc (seq->len + 1)) == NULL)
      _ErrExit2 (e__allocfail, "sequence");
    memcpy (tmp, seq->seq, seq->len);
    tmp[seq->len] = '\0';
    seq->seq = tmp; 
  }
  else
    seq->seq = NULL;
}


/**api** SeqSubSeq ************************************************************
** 
** 	Makes a subsequence from sequence as specified. Does not change the
**      allocation
** 
** 	INPUT:	    address of sequence object [W]
** 		    begin of subsequence (first aa = 1) [R]
** 		    length of subsequence [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if OK
**                  0 else
*/ 
   
INT4 SeqSubSeq (SEQo *seq, INT4 beg, INT4 len)
{
  if (beg <= 0 || len <= 0)
    return 0;
  
  if (beg > seq->len)  /* begin */
    return 0;

  if (beg + len-1 > seq->len)  /* length */
    len = seq->len - beg + 1;

  memcpy (seq->seq, &seq->seq[beg-1], len);
  seq->len = len;
  seq->seq[len] = '\0';
  return 1;
}


/**api** SeqHead ************************************************************
** 
** 	makes a subsequence from start of sequence with length len
** 
** 	INPUT:	    address of sequence object [W]
** 		    length of subsequence [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if OK
**                  0 else
*/ 

INT4 SeqHead(SEQo *seq, INT4 len)
{
    /* 
    ** SeqSubSeq does no free allocated memory, so maybe 
    ** another implementation will be used later
    */
    return SeqSubSeq(seq, 1, len);
}


/**api** SeqTail ************************************************************
** 
** 	makes a subsequence from end of sequence with length len
** 
** 	INPUT:	    address of sequence object [W]
** 		    length of subsequence [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if OK
**                  0 else
*/ 

INT4 SeqTail(SEQo *seq, INT4 len)
{
    /* 
    ** SeqSubSeq does no free allocated memory, so maybe 
    ** another implementation will be used later
    */
    return SeqSubSeq(seq, seq->len - len + 1, len);
}


/**api** SeqCat ************************************************************
** 
** 	concatenates a subsequence (range) to another sequence (*seq)
** 
** 	INPUT:	    sequence object [R]
** 		    sequence object to be added to first  [R]
** 
*/ 

void SeqCat (SEQo *seq, SEQo *range)
{
  SEQo *result = seq;
  char *oldseq;
  
  /* look, if there was already a sequence before */
  oldseq = result->seq;
  
  /* make sure correct length is set */
  if (!oldseq)  {
    result->len = 0;
    oldseq = "";
  }
  else result->len = strlen(result->seq);
  
  result->len += strlen(range->seq);
  result->seq = (char*) malloc(result->len + 1);
  strcpy(result->seq, oldseq);
  strcat(result->seq, range->seq);
  
  if (*oldseq)
    free(oldseq);
}


/**api* SeqSwap ***************************************************************
** 
** 	swaps a character in all sequences;
** 
** 	INPUT:	    address of sequence object [W]
**                  old character [R]
** 		    new character [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
*/ 
   
INT4 SeqSwap (SEQo *seq, char a, char b)
{
  INT4 savepos;

  LstGetPosition (seq, &savepos);
  LstFirst ((void **) &seq);
  do {
    SmSwap (seq->seq, a, b);
  } while (LstNext ((void **) &seq));
  LstSetPosition ((void **) &seq, savepos);

  return 1;
}
   

/**api* SeqRemoveGaps *********************************************************
** 
** 	removes gaps (either '-' or '.') from sequence
** 
** 	INPUT:	    address of sequence-dsc. [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
*/ 
   
INT4 SeqRemoveGaps (SEQo *seq)
{
  SmSwapS (seq->seq, ".", ""); 
  SmSwapS (seq->seq, "-", "");
  seq->len = strlen (seq->seq);
  return 1;
}


/**api* SeqGetLength **********************************************************
** 
** 	Returns the sequence's length
** 
** 	INPUT:	    sequence object
**
** 	RETURNS:    sequence length
*/ 

Int4 SeqGetLength (SEQo *seq)
{
  return seq->len;
}


/**api* SeqGet ***************************************************************
** 
** 	Gets sequence in sequence buffer by name;
** 
** 	INPUT:	    pointer to address of sequence object [W]
**                  name [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    number in list if found
** 		    0 if not
*/ 
   
INT4 SeqGet (SEQo **seq, char *seq_nm)
{
  INT4 pos;

  if (!LstFirstNamed ((void **) seq, seq_nm))
    return 0;

  LstGetPosition ((void *) *seq, &pos);
  return pos;
}


/*
    icarus functions
 */

static SEQo *seqCurr=NULL;


void SeqIopGet2Bit (Int4 runTime, SEQo *seq, FILEo *file, Int4 len)
{
  SEQo *tmp=NULL;
  Int4 byteN;

  if (runTime)
    IargGetArgs ("s|file|len", &seq, &file, &len);

  if (SeqGetLength (seq))
    SeqNew (&tmp);
  else 
    tmp = seq;

  byteN = (len+3)/4; /* sequence is stored in 4byte words */
  SeqAlloc (tmp, len+4+1);

  fread (tmp->seq, 1, byteN, FileGetFile (file));
  tmp->len = len;
  SeqBinToAscii (tmp);

  if (tmp != seq) {
    /* concatenate sequences */
    SeqCat (seq, tmp);
    SeqDel (&tmp);
  }
  
}

void SeqIopCut (Int4 runTime, SEQo *seq, Int4 from, Int4 len)
{
  if (runTime)
    IargGetArgs ("s|from|len", &seq, &from, &len);
}


void SeqIopNew ()
{
  SEQo *seq=NULL;
  STRv name;

  IargGetArgs ("name|list", &name, &seq);
  if (seqCurr) 
    SeqClean (&seqCurr);
  
  SeqNew (&seq);
  if (name) {
    SeqSetName (seq, _Str (name));
    StrDel (name);
  }
  seqCurr = seq;
  IcaReturn ("sequence", seq);
}


void SeqIopApp ()
{
  SEQo *seq;
  STRv s;

  IargGetArgs ("seq|s", &seq, &s);
  SeqCopy (seq, _Str(s), SEQxFILTER);  
  StrDel (s);
  IcaReturn ("sequence", seq);
}

void SeqIopLen ()
{
  SEQo *seq;
  STRv s;

  IargGetArgs ("seq", &seq);
  IcaReturn ("int", seq->len);
}

void SeqIopMake ()
{
  SEQo *seq;

  IargGetArgs ("seq", &seq);
  SeqMakeOwn (seq);
}

void SeqIopTrunc (Int4 runTime, SEQo *seq, Int4 l)
{
  Int4 len;

  IargGetArgs ("seq|len", &seq, &l);
  len = SeqGetLength (seq);
  if (!(len % l))
    SeqSubSeq (seq, 1, len-l);
}

void SeqIopPrint ()
{
  STRv s;
  SEQo *seq, tmp;
  INT4 format;

  IargGetArgs ("format|seq|s", &format, &seq, &s);
  if (s) {
    seq = &tmp;
    *tmp.name = '\0';
    tmp.len = StrLen (s);
    tmp.seq = _Str(s);
  }    
  else if (!seq)
    seq = seqCurr;

  /*  SeqFormatPrint (seq) */

  switch (format) {
  case SEQxGCG:
    SeqWriteGCG (seq, NULL, NULL);
    break;
  case SEQxPIR:
    SeqWritePIR (seq, seq->name, "", NULL);
    break;
  case SEQxFASTA:
    SeqWriteFasta (seq, seq->name, NULL);
    break;
  case SEQxEMBL:
    SeqWriteEMBL (seq, seq->name, NULL);
    break;
  case SEQxSWISS:
    SeqWriteSwiss (seq, seq->name, NULL);
    break;
  case SEQxMSF:
    SeqWriteApplet (seq, seq->name);
    break;
  default:
    _ErrExit2 (e__unknownoption, "format in SeqIopPrint");
  }
  if (s)
    StrDel (s);

}

SEQo* SeqGetCurrent() {
    SEQo* curr=seqCurr;
    seqCurr=NULL;
    return curr; 
}

void SeqSetCurrent(SEQo* seq) {
    /* cancel current sequence */
  if (seqCurr) SeqClr(&seqCurr);
    seqCurr=seq;
}









QxEMBL:
    SeqWriteEMBL (seq, seq->name, NULL);
    break;
  case SEQxSWISS:
    SeqWriteSwiss (seq, seq->name, NULL);
    break;
  case SEQxMSF:
    SeqWriteApplet (seq, seq->name);
    break;
  default:
    _ErrExit2 (e__unknownoption, "format in SeqIopPrint");
  }
  if (s)
    StrDel (s);

}

SEQo* SeqGetCurrent() {
    SEQo* curr=seqCurr;
    seqCurr=NULL;
    return curr; 
}

void SeqSetCurrent(SEQo* seq) {
    /* cancel current sequence */
  if (seqCurr) SeqClr(&seqCurr);
    seqCurr=seqsrs/src/seq.h
**
**    $RCSfile: seq.h,v $
**    $Revision: 1.3 $
**    $Date: 1997/03/03 18:20:49 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
*/

#include "transl.h"


#define SEQxXNAM	50      /* max size of sequence name */
#define SEQxXWIN	31      
#define SEQxXCMNT	512     /* max size of sequence comment */
#define SEQxXLN		255     
#define SEQxSEQBUFF	1000000  /* size of sequence buffer */

enum seqformat {SEQxGCG=1, SEQxMSF, SEQxPIR, SEQxPEARSON, SEQxFASTA, 
		  SEQxEMBL, SEQxSWISS, SEQxCLUSTAL};
enum formattoken {SEQxRANGLE=1, SEQxPIRTOKENS, SEQxCHECK, SEQxDOTDOT, 
		  SEQxSEMICOLON};

enum formatoption {SEQxFILTER=1, SEQxNUMBER=8, SEQxSTAR=16, SEQxLMARGIN=32, 
		     SEQxEMBLNUMBER=64};


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  description of a sequence
*/

typedef struct SEQo { 
  char  *intern;   /* the first three attributes are necessary  */
  INT4   type_id;   /* for all objects to be managed by the list */
  char  name[20]; 
  STRv  cmnt;     /* sequence description */
  char  *seq;      /* pointer to sequence string */
  char  *replace;  /* string to be replaced or inserted into sequence */
  INT4   len;	   /* length of sequence */
  INT4   check;	   /* GCG check sum */
  INT4   bpos;      /* begin position of range */
  INT4   epos;      /* end position of range */
  INT4   part_len;  /* 0: complete    <0: head    >0: tail */
  char  accno[10]; 
  char  keep_f;    /* flag if sequence should be kept */
  char  compl_f;   /* flag if sequence is to be reverse complemented */
  char  cut_f;     /* flag that replace sequence is to be inserted in range */
  char  before_f;  /* flag that shows whether the operator BEFORE exists */
  char  after_f;   /* flag that shows whether the operator AFTER exists */
  struct SEQo *sublist;
} SEQo;


typedef struct SEQoTranslExcept {
  char aa;
  INT4 begin;
  INT4 length;
  INT4 isDone;
} SEQoTranslExcept;


typedef struct SEQoTranslCodon {
  char aa;
  char codon[4];
} SEQoTranslCodon;



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of exported functions
*/

INT4 SeqNew (SEQo **seq);
void SeqClr (SEQo **seq);
void SeqClean (SEQo **seq);
void SeqDel (SEQo **seq);

    /* input from file in various formats */

INT4 SeqReadAll (SEQo **seq, char *fil_nm);
INT4 SeqReadPIR (SEQo **seq, char *fil_nm);
INT4 SeqReadGCG (SEQo **seq, char *nam);
INT4 SeqReadGCGFile (SEQo **seq, char *fil_nm);
INT4 SeqReadMSF (SEQo **seq, char *msf_nm);
INT4 SeqReadLib (SEQo **seq, FILo *file, char *exitstr);
INT4 SeqFromLib (SEQo **seq, FILo *file, char *scanId, char *exitstr, 
		 INT4 comment_f);
SEQo *SeqReadString (char *s);

    /* output to file in various formats */

INT4 SeqWriteGCG (SEQo *seq, char *nam, INT4 (*print)(char*,...));
INT4 SeqWritePIR (SEQo *seq, char *nam, char *cmnt, INT4 (*print)(char*,...));
INT4 SeqWriteFasta (SEQo *seq, char *nam, INT4 (*print)(char*,...));
INT4 SeqWriteEMBL (SEQo *seq, char *nam, INT4 (*print)(char*,...));
INT4 SeqWriteSwiss (SEQo *seq, char *nam, INT4 (*print)(char*,...));
INT4 SeqWriteMSF (SEQo *seq, INT4 (*print)(char*,...));

    /* conversion of sequence into various formats */

struct STRo *Seq2Pretty (SEQo *seq, Int4 width);

    /* sequence manipulation */

INT4 SeqSwap (SEQo *seq, char a, char b);
INT4 SeqSubSeq (SEQo *seq, INT4 beg, INT4 len);
INT4 SeqRemoveGaps (SEQo *seq);
INT4 SeqComplement (SEQo *seq);
INT4 SeqHead (SEQo *seq, INT4 len);
INT4 SeqTail (SEQo *seq, INT4 len);
void SeqCat (SEQo *seq1, SEQo *seq2);

    /* for translating DNA to protein */

SEQoTranslTable *SeqTaxaToTranslTable (SMoBUFF *org);
SEQoTranslTable *SeqIdToTranslTable (INT4 id);
struct SEQo *SeqTranslate (SEQo *dna, INT4 start, 
			   SEQoTranslTable *tTable,
			   SEQoTranslExcept *tExcept, 
			   SEQoTranslCodon *tCodon);

    /* others */

INT4 SeqGoGcgDots (FILo *file);
INT4 SeqGet (SEQo **seq, char *seq_nm);
void SeqSetRecordSeparator (INT4 i);
Int4 SeqGetLength (SEQo *seq);
void SeqSetName (SEQo *seq, char *name);

SEQo* SeqGetCurrent();
void SeqSetCurrent(SEQo* seq);
    



SEQoTranslTable *SeqTaxaToTranslTable (SMoBUFF *org);
SEQoTranslTable *SeqIdToTranslTable (INT4 id);
struct SEQo *SeqTranslate (SEQo *dna, INT4 start, 
			   SEQoTranslTable *tTable,
			   SEQoTranslExcept *tExcept, 
			   SEQoTranslCodon *tCodon);

    /* others */

INT4 SeqGoGcgDots (FILo *file);
INT4 SeqGet (SEQo **seq, srs/src/seqdb.c
char seqdb_ID[] = "$Id: seqdb.c,v 1.7 1997/03/03 18:20:50 srs Exp $";
/*
**
**    $RCSfile: seqdb.c,v $
**    $Revision: 1.7 $
**    $Date: 1997/03/03 18:20:50 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  Copyright by Thure Etzold
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <stdarg.h>
#include <ctype.h>

#include "message.h"
#include "sm.h"
#include "strv.h"
#include "futil.h"
#include "toklist.h"
#include "icarus.h"
#include "entry.h"
#include "id.h"
#include "set.h"
#include "query.h"
#include "library.h"
#include "field.h"
#include "seq.h"
#include "listv.h"

#define _SRS
#define _SLB
#include SRSINCLUDE

/*********************************************************
** ENTRY stack management
*********************************************************/

STRv SdbGetEntryField(STRv db, STRv acc, STRv fieldName) {
  SETo     *set;
  IDoENTRY id;
  ENTRYv   entry;
  int      n, entryN;
  char     query[100];
  static char qname[20]="SingleEntryQuery";
  STRv     res;
  SLBoFIELD* field; 
  SLBo*    lib;
  STRv     s;
  INT4 k; 
  
  /* build query string */
  sprintf(query,"[%s-acc:%s]",Str(db),Str(acc));

  if (Query (query, qname)) {
    set = SetGet (qname); 
    entryN = SetSize (qname);
    
    /* check one and only one entry */
    if (entryN>0) {
	if (entryN!=1) {
	    ENTRYv temp; INT4 e;
	    /* select the one with the primary accession num */
	    entry=NULL;
	    for (e=1; e<=entryN; e++) {
		SetGetID(set,e,&id); 
		temp = EntryOpen (&id);
		lib= EntryGetLib(temp);
		field = LibHasFieldNamed (lib, "acc");
		ASSERT(field,"NoAccession");
		/* first is primary acc *HOPE* */
		if (StrEqualS(acc,_Str(EntryGetField (temp, field, &k)))) {
		    if (!entry) entry=temp;
		    else printf("MultipleEntries: %s\n", Str(acc));
		}
		if (temp!=entry) EntryClose (&temp);
	    }
	}
	else {
	    /* get id */
	    SetGetID (set, 1, &id); 
	    entry = EntryOpen (&id);
	}
	lib=EntryGetLib(entry);

	/* retrieve field */
	field = LibHasFieldNamed (lib, Str(fieldName));
	ASSERT(field,"NoSuchField");

	/* concatenate all tokens of the field */
	res=StrNew();
	for (k=0; (s = (EntryGetField (entry, field, &k)));) {
	    StrApp(&res,s); 
	    StrDel (s);
	}

	EntryClose (&entry);
    }
    else res=NULL;
  }
  else res=NULL;
  SetDelete(qname);
  return res;
}

/***************************************************************
** ENTRY context
***************************************************************/
STRv currSeq=NULL;
STRv currDb=NULL;
BOOL exception=FALSE;

/*********************************************************
**  SEQUENCE CALCULATOR
*********************************************************/

enum SDB_ChunkConstants { 
	SDB_unbounded=-1, 
	SDB_optional=1,   /* chunk can be omitted */
	SDB_left=2,  	  /* chunk varies left^right to right^right */
	SDB_right=3, 	  /* chunk varies left^right to left^left */
	SDB_wrong=4       /* chunk contains an error */
};

typedef struct SDBoChunk {
    STRv seq;
    int  beg;
    int  end;
    int  uncertain;
} SDBoChunk;

INT4 ChunkLen(SDBoChunk* c) {
    INT4 len;
    len=c->end-c->beg;
    if (len<0) len=-len;
    return len;
}

BOOL ChunkUncertain(SDBoChunk* c) {
    int u=c->uncertain;
    return u==SDB_wrong || u==SDB_right || u==SDB_left;
}

BOOL ChunkCheck(SDBoChunk* c) {
    Int4 len=StrLen(c->seq);
    if (c->beg<=c->end) return c->beg>=0 && c->end<=len;
    else return c->end>=0 && c->beg<=len;
}


_List(SDBoChunk) calcStack[256];
_List(SDBoChunk) *calc=calcStack-1;

 STRv SdbEval(INT4 runTime);

/***********************************************************
** Pushes a given sequence on the calculator stack
***********************************************************/
   
BOOL chunkStart=TRUE;
INT4 chunkFrom;

void SdbPush() {
    *++calc=_ListNew(SDBoChunk,1);
    chunkStart=TRUE;
}

void SdbPop() {
    int i;
    for (i=0; i<_ListLen(*calc); i++) {
	SDBoChunk* sc=&(*calc)[i];
	/* delete sequence chunk */
	StrDel(sc->seq);
    }
    _ListDel(*calc); calc--;
}

STRv SdbRetrieve(INT4 runTime, STRv acc, STRv db) {
    STRv seq; 
    if (runTime) IargGetArgs("acc|db",&acc,&db);
    if (acc && !StrEqualS(acc,"")) {
	SEQo* curr=SeqGetCurrent();
	STRv res;
	if (!db || StrEqualS(db,"")) db=StrCpy(currDb);
	res=SdbGetEntryField(db,acc,StrTemp("sequence"));
	if (res) {
	    SEQo* tmp=SeqGetCurrent();
	    seq=StrCpyS(tmp->seq);
	    SeqSetCurrent(tmp);
	    StrDel(res);
	}
	else {
	    printf("!!!Entry not found:%s\n",Str(acc));
	    seq=StrNew();
	    exception=TRUE;
	}
	SeqSetCurrent(curr);
    }
    else seq=StrCpy(currSeq);
    StrDel(acc); StrDel(db);
    if (runTime) IcaReturn("strv",seq);
    return seq;
}

/************************************************************
**  Extracts a range from the current sequence
**  and pushes it on the calculator stack
************************************************************/

void SdbChunk (INT4 runTime, STRv seq, INT4 to, INT4 uncertain) {
    SDBoChunk* sc; INT4 len; BOOL out=FALSE;
    if (runTime)  IargGetArgs("seq|to|uncertain", &seq, &to, &uncertain);
    len=StrLen(seq);
    if (to==-2) to=len; /* apply default*/
    else if (to==-3) to=chunkFrom+1;
    if (!chunkStart)  {
	/* create chunk */
	sc=&_ListApp(calc);
	sc->seq=StrCpy(seq);
	sc->beg=chunkFrom;
	sc->end=to;
	/* check boundaries */
	if (to!=SDB_unbounded && (to<chunkFrom || to>len)) { 
	    sc->uncertain=SDB_wrong;
	    exception=TRUE;
	    printf("Out of bounds\n"); 
	}
	else sc->uncertain=uncertain;
    }
    chunkStart=FALSE; chunkFrom=to;
    StrDel(seq);
}

/************************************************************
**  Extracts a sequence calculating a feature of the current 
**  entry sequence, and pushes it on the calculator stack
************************************************************/

void SdbFeature(INT4 runTime,STRv feature) {
    if (runTime) IargGetArgs("feature", &feature);
    StrDel(feature);
}

/************************************************************
** Replaces the given range of the (current-1) entry sequence
** with the sequence at calc top, pushes result
************************************************************/ 

void SdbReplace () {
    int from, to;
    STRv repl=SdbEval(FALSE); 
    SDBoChunk *sc, *rng=*calc; /* replace range */
    if (_ListLen(rng)!=1) { printf("Complex range in replace\n"); exception=TRUE; }
    else if (ChunkUncertain(rng)) { printf("Uncertain range in replace\n"); exception=TRUE;}
    if (!exception) {
	*calc=_ListNew(SDBoChunk,1);
	sc=&_ListApp(calc);
	sc->seq=rng->seq; from=rng->beg; to=rng->end;
	if (from>=0 && from<StrLen(sc->seq)) StrSubst(&sc->seq,from,to-from,repl);
	else { printf("Replace Out of Bonds"); exception=TRUE; }
	sc->beg=0;
	sc->end=StrLen(sc->seq);
	sc->uncertain=exception?SDB_wrong:0;
    }
    StrDel(repl); StrDel(rng->seq); _ListDel(rng);
}

/************************************************************
** Complements the sequence on the top of the calculator stack
************************************************************/ 

void SdbComplement () {
    int i;
    _List(SDBoChunk) res=_ListNew(SDBoChunk,_ListLen(*calc));
    for (i=_ListLen(*calc)-1; i>=0; i--) {
	SDBoChunk* sc=&(*calc)[i];
	SDBoChunk* d=&_ListApp(&res);
	/* reverse beg and end to indicate complement */
	d->seq=sc->seq;
	d->beg=sc->end;
	d->end=sc->beg;
    }
    _ListDel(*calc); *calc=res;
}


/************************************************************
** Pops the top sequence on the calculator stack 
** and appends it to the one below
************************************************************/

void SdbJoin() {
    int i;
    SDBoChunk* d=_ListAppMany(calc-1,_ListLen(*calc));
    for (i=0; i<_ListLen(*calc); i++) {
	SDBoChunk* sc=&(*calc)[i];
	d->seq=sc->seq;
	d->beg=sc->beg;
	d->end=sc->end;
	d->uncertain=sc->uncertain;
	d++;
    }
    _ListDel(*calc--); 
}

/***********************************************************
** Applies shifts to the top of stack sequence
***********************************************************/
INT4 jobcnt=0;

enum SDBeShiftOrg { SDB_NoShift, SDB_Beg, SDB_Both, SDB_End };
BOOL moveCertain;
BOOL shiftedOut;

   
BOOL ChunkRight(_List(SDBoChunk) l, int* c, BOOL certain) {
    int ll=_ListLen(l); 
    int p=*c+1;
    if (p>=ll) return FALSE;
    if (certain) {
	if (p==ll-1 && ChunkUncertain(l+p)) return FALSE;
	while (ChunkUncertain(l+p)) {
	    moveCertain=FALSE;
	    p++; if (p>=ll-1) return FALSE;
	}
    }
    *c=p; return TRUE;
}
	    
BOOL ChunkLeft(_List(SDBoChunk) l, int* c, BOOL certain) {
    int p=*c-1;
    if (p<0) return FALSE;
    if (certain) {
	if (p==0 && ChunkUncertain(l)) return FALSE;
	while (ChunkUncertain(l+p)) {
	    moveCertain=FALSE;
	    p--; if (p<0) return FALSE;
	}
    }
    *c=p; return TRUE;
}

BOOL ChunkMove(_List(SDBoChunk) l, int* chunk, INT4* pos, BOOL certain) {
    INT4 chunkLen=0; int llen=_ListLen(l);
    int c=*chunk; INT4 p=*pos;
    if (c<=llen && p>=ChunkLen(l+c)) { 
	if (!ChunkRight(l,chunk,certain)) return FALSE;
	while (c<llen-1) {
	    chunkLen=ChunkLen(l+c);
	    if (p<chunkLen) break;
	    if (!ChunkRight(l,&c,certain)) {
		*chunk=c; *pos=p; return FALSE;
	    }
	    p-=chunkLen;
	}
    }
    else if (c>=0 && p<0) {
	if (!ChunkLeft(l,chunk,certain)) return FALSE;
	while (c>=0) {
	    chunkLen=ChunkLen(l+c);
	    if (p>=0) break;
	    if (!ChunkLeft(l,&c,certain)) {
		*chunk=c; *pos=p; return FALSE;
	    }
	    p+=chunkLen;
	}
    }
    *chunk=c; *pos=p; return moveCertain;    
}

BOOL ChunkFind(_List(SDBoChunk) l, BOOL fromBeg, int* chunk, INT4* pos, BOOL certain) {
    int llen=_ListLen(l);
    if (!llen) return FALSE;
    if (fromBeg) *chunk=0; 
    else {
	*chunk=llen; 
	if (!ChunkLeft(l,chunk,certain)) return FALSE;
	*pos+=ChunkLen(l+*chunk);
    }
    if (ChunkMove(l,chunk,pos,certain)) return TRUE;
    else return *chunk==0 || *chunk==llen-1;
}

void SdbShift(INT4 runTime, INT4 org, INT4 beg, INT4 end) {
    _List(SDBoChunk) l=*calc;
    SDBoChunk* c; BOOL out=FALSE;
    int begChunk,endChunk,i; INT4 len=0;
    BOOL begComplemented,endComplemented;
    if (runTime) IargGetArgs("org|beg|end",&org, &beg, &end);
    
    if (org==SDB_NoShift || _ListLen(l)==0) return;

    moveCertain=TRUE;
    if (!ChunkFind(l,org!=SDB_End,&begChunk,&beg, TRUE)) { shiftedOut=TRUE; return; }
    if (!ChunkFind(l,org==SDB_Beg,&endChunk,&end, TRUE)) { shiftedOut=TRUE; return; }
    if (!moveCertain) { shiftedOut=TRUE; return; }

    /* trim beg of list */
    i=begChunk; while (--i>=0) StrDel(l[i].seq);
    _ListCutMany(calc,0,begChunk); 
    l=*calc; 
    endChunk-=begChunk; 
    /* trim end of list */
    i=endChunk; while (++i<_ListLen(l)) StrDel(l[i].seq);
    _ListCutMany(calc,endChunk+1,_ListLen(l)-endChunk-1); 
    l=*calc; 
    
    /* store endchunk in case begChunk==endChunk */
    c=&_ListLast(l);
    endComplemented=c->end<c->beg;
    end-=ChunkLen(c); /* end is end-relative */
    
    /* trim begChunk */
    c=&_ListFirst(l);
    begComplemented=c->end<c->beg;
    if (!begComplemented) {
	c->beg+=beg;
	if (c->beg<0) { c->beg=0; out=TRUE; }
	else {
	    len=StrLen(c->seq);
	    if (c->beg>=len) c->beg=len;
	}
    }
    else {
	c->beg-=beg;
	len=StrLen(c->seq);
	if (c->beg>len) { c->beg=len; out=TRUE; }
	else if (c->beg<0) c->beg=0;
    }

    /* trim endChunk */
    c=&_ListLast(l);
    if (!endComplemented) {
	c->end+=end;
	len=StrLen(c->seq);
	if (c->end<c->beg) { c->end=c->beg; out=TRUE; }
	else if (c->end>len) { c->end=len; out=TRUE; }
    }
    else {
	c->end-=end;
	if (c->end>c->beg) { c->end=c->beg; out=TRUE; }
	else if (c->end<0) { c->end=0; out=TRUE; }
    }
	
 
    if (out) { 
	/*printf("Shifted out\n");*/
	shiftedOut=TRUE;
    }
}


/**********************************************************
** Pops the calculator stack, returning the popped
** sequence
**********************************************************/

void complement(char* dest, char* src, int n) {   
    static char complBase[] = {
    /*   a   b   c    d   e  f   g    h   i  j   k   l   m    n */
	't', 0, 'g', 'h', 0, 0, 'c', 'd', 0, 0, 'm', 0, 'k', 'n',
    /*  o  p  q   r    s    t    u    v    w    x    y   z */          
	0, 0, 0, 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 0
    };
    char* s=src+n-1;
    while (s>=src) {
	char c=*s--;
	if (c>'z') printf("!!!Not a nucleotide in sequence source");
	if (c<'a') {
	    if (c<'A'||c>'Z') printf("!!!Not a nucleotide in sequence source: %c\n",c);
	    *dest++=complBase[c-'A']+'A'-'a';
	}
	else *dest++=complBase[c-'a'];
    }
} 

STRv SdbEval(INT4 runTime) {
    /* interpret top of stack , creating actual sequence */
    STRv res=NULL; char* rs;
    int i; INT4 len=0; BOOL certain=TRUE; BOOL wrong=FALSE;
    /* pre-calculate sequence lenght */
    for (i=0; i<_ListLen(*calc); i++) {
	SDBoChunk* sc=*calc+i;
	if (ChunkUncertain(sc)) {
	  certain=FALSE;
	  if (i>0 && i<_ListLen(*calc)-1) {
	    /* if internal uncertain block*/
	    wrong=TRUE; break;
	  }
	  continue;
	} 
	else if (!ChunkCheck(sc)) { wrong=TRUE; break; }
	len+=ChunkLen(sc);
    }
    if (!wrong) {
	/* now compute sequence */
	res=StrBufNew(len); res->len=len; 
	rs=Str(res);
	for (i=0; i<_ListLen(*calc); i++) {
	    SDBoChunk* sc=&(*calc)[i];
	    INT4 lenAdd;
            if (!ChunkUncertain(sc)&& ChunkCheck(sc)){
	      lenAdd=sc->end-sc->beg;
	      if (lenAdd<0) {
		lenAdd=-lenAdd;
		complement(rs,Str(sc->seq)+sc->end,lenAdd);
	      }
	      else strncpy(rs,Str(sc->seq)+sc->beg,lenAdd);
	      rs+=lenAdd;
	    }
	    /* delete sequence chunk */
	    StrDel(sc->seq);
	}
	*rs='\0';
	_ListDel(*calc); calc--;
    }
    else {
        if (!certain) printf("!!!Uncertainty in the middle of the location");
	else printf("!!!Wrong location definition");
	SdbPop();
	res=StrNew();
    }
    if (runTime) IcaReturn("strv",res);
    else return res;
}

#ifdef XX

/****** SeqTranslate *********************************************************
**
**      Translates a DNA sequence into protein;
**      The translation is controlled by the translation table, the list
**      of translation exceptions and the list of codon changes to be
**      applied to the translation table.
**
**      INPUT:    * address dna sequence object [R]
**                * start position (begin=1) [R]
**                * translation table [R]
**                * array of translation exception descriptions [R] or NULL
**                * array of codon changes to be applied to the 
**                  translation table [R] or NULL
**              IMPLICIT:
**
**      RETURNS:    translated protein sequence 
**                  NULL if there was a problem
*/

SEQo *SdbTranslate (SEQo *ntSeq, INT4 start, SEQoTranslTable *translTable,
		    SEQoTranslExcept *translExcept,
		    SEQoTranslCodon *translCodon)
{
  SEQo *prot;
  INT4 k, l;
  
  dnaSeq = dnaseq->seq + startPos;
  peptlen = (dnaseq->len - startPos) / 3;

  if (peptlen <= 0) 
    _ErrRet3 (e__seqillegallength, seq->len, start);
  
  /* modify translation table, if codon list is not empty */
  if (tCodon)
    tTable = SeqTranslTableEdit (tTable, tCodon);

  SeqNew (protSeq);
  SeqAlloc (*protseq, (ntSeq->len - start)/3 + 100);
  
  for (k=start-1, l=0; k < dna->len;) {

    /* deal with possible translation exception */
    if (tExceptNext && k == tExceptNext->start) {
      prot->seq[l++] = tExceptNext->aa;
      k += tExcept->length;
      tExceptNext->isDone = 1;
      tExceptNext = (++tExceptNext)->aa ? tExceptNext : NULL;
    }
    else if (!k) { /* first codon */
      if ((aa = SeqTranslateCodon (seq, tTable, 1)) == 'M'
	  prot->seq[l++] = aa;
      else {
	global_before_f-- ; 
      }
    else 
      prot->seq[l++] = SeqTranslateCodon (&dna->seq[k], tTable, 0);
  }
  if (codon) /* remove edited translation table again */
    free (tTable);

  SeqRemoveStop (prot);
  sprintf prot->name, "%s_aa", dna->name);
  return prot;
}

SdbTranslate (char *triplett, INT4 isStartCodon, SEQoTRANSLTABLE *transTable)
{
  static char *ntAmbigList[26]={ "A","CGT","C","AGT","","","G","ACT","", 
                                 "","GT","","AC","GATC","","","","AG",
                                 "CG","T","U","ACG","AT","ACGT","CT",""};
  static INT4 isInit=0, order[26];
  INT4 k, l, m;
  char b1, b2, b3, aa, aaPrev, **ntList[3];

  if (isInit) {
    order['T'] = 0;
    order['C'] = 1;
    order['A'] = 2;
    order['G'] = 3;
    isInit = 1;
  }

  aaTrans = isStartCodon ? transTable->saa : transTable->aa;

  /* The triplett might contain ambiguity codes:
     assign to each base in the triplett the list of possible nucleotides */
  for (k=0; k<3; k++) {
    ntList[k] = ntAmbigList[triplett[k]];
  }

  /* get all indices into the aa transl list for all combinations */
  aa = 'X';
  for (i=0,k=0; (b1=ntList[k]); k++) 
    for (l=0; (b1=ntList[l]); l++) 
      for (m=0; (b1=ntList[m]); m++) {
	aa = aaTrans[order[b1]*16 + order[b1]*4 + order[b1]];
	if (aa != aaPrev) {
	  aa = 'X';
	  break;
	aaPrev = aa;
      }

  return aa;
}

#endif


STRv SdbGetFeatureSequence(INT4 runTime, STRv seqExpr, STRv db, INT4 shiftOrg, INT4 left, INT4 right) {
    STRv seq; SEQo* curr;
    static ICAoJOB* job=NULL;
    char *start;
    
    if (runTime) IargGetArgs("expr|db|shift|left|right",
			     &seqExpr, &db, &shiftOrg, &left, &right);

    if (jobcnt==20808) {
	printf("--------------------------------------here\n");
    }
    /* extract current sequence as STRv */
    curr=SeqGetCurrent();
    ASSERT (curr, "no curr sequence");
    currSeq=StrCpyS(curr->seq);
    currDb=StrCpy(db);
    SeqSetCurrent(curr);

    /* calculate feature expression */
    if (!job) {
	ICAoSYNTAX* syntax=(ICAoSYNTAX*)LibObjByName("syntax","ftseq");
	job=IcaCreateJob(syntax);
    }
    else IcaJobNext(job);
    IcaJobSetString(job,Str(seqExpr));
    start = SmEqs (_Str (db), "swissprot") ? "swissrange" : "sequence";
    exception|=!IcaDoJob(job, start);

    if (calc>calcStack) exception=TRUE;
    if (!exception) {
	shiftedOut=FALSE;
	SdbShift(FALSE,shiftOrg,left,right);
	exception=shiftedOut;
    }
    if (!exception) seq=SdbEval (FALSE);
    else {
	/* clean up */
	exception=FALSE;
	/*printf("%s", Str(seqExpr));*/
	while (calc>=calcStack) SdbPop();
	seq=StrNew(); 
    }
    if (runTime) IcaReturn ("strv", seq); 

    StrDel(seqExpr); StrDel(db);
    StrDel(currSeq); StrDel(currDb);
    jobcnt++;
    return seq;
}

/**API* function **************************************************************
**
**	returns the sequence of the entry as sequence object. The function
**      assumes that the sequence is represented by the data-field with 
**      the short name "seq".
**
**      INPUT:          [W] the entry object
**
**      RETURNS:        sequence object
**                      NULL: entry does not have the "seq" data-field
*/

SEQo *SdbGetEntrySeq (ENTRYv entry)
{
  SLBo   *lib;
  FIELDv field;
  Int4   k;

  lib = EntryGetLib (entry);
  for (k=0; (field=LibNextField (lib, &k));)
    if (SmEqs ("seq", FieldGetShortName (field)))
      break;
  if (!field)
    return NULL;
  EntryGetField (entry, field, NULL);
  return SeqGetCurrent();
}



INT4 SdbFunctions()
{
  IcaSetFunction("SdbEval", (FUNC)SdbEval);
  IcaSetFunction("SdbPop", (FUNC)SdbPop);
  IcaSetFunction("SdbPush", (FUNC)SdbPush);
  IcaSetFunction("SdbRetrieve", (FUNC)SdbRetrieve);  
  IcaSetFunction("SdbChunk",(FUNC) SdbChunk);
  IcaSetFunction("SdbFeature", (FUNC)SdbFeature);
  IcaSetFunction("SdbReplace", (FUNC)SdbReplace);
  IcaSetFunction("SdbComplement", (FUNC)SdbComplement);
  IcaSetFunction("SdbJoin", (FUNC)SdbJoin);
  IcaSetFunction("SdbGetFeatureSequence", (FUNC)SdbGetFeatureSequence);
  return 1;
}





unction("SdbEval", (FUNC)SdbEval);
  srs/src/seqdb.h
#define _SDB_H

struct SEQo *SdbGetEntrySeq (struct ENTRYo *entry);
void SdbFunctions();
STRv SdbGetFeatureSequence(INT4 runTime, STRv seqExpr,STRv db,INT4 shiftOrg,INT4 left, INT4 right);

#endif
", (FUNC)SdbFeature);
  IcaSetFunction("SdbReplace", (FUNC)SdbReplace);
  IcaSetFunction("SdbComplement", (FUNC)SdbComplement);
  IcaSetFunction("SdbJoin", (FUNC)SdbJoin);
  IcaSetFunction("SdbGetFeatureSequence", (FUNC)SdbGetFeatureSequence);
  return 1;
}





unction("SdbEval", (F¶ £¡Üval);
  srs/src/seqlib.c
char seqlib_srs_ID[] = "$Id: seqlib.c,v 1.2 1996/05/06 19:20:52 etzold Exp $";
/*
**
**    $RCSfile: seqlib.c,v $
**    $Revision: 1.2 $
**    $Date: 1996/05/06 19:20:52 $
**    $Author: etzold $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.x Copyright by Thure Etzold
**
**             Author: Gerald Schaefer
**                     EMBL, Meyerhofstrasse 1
**                     D-69012 Heidelberg, Germany
**                     Tel: 06221 387372  
**                     Email: schaefer@embl-heidelberg.de
**
**
**    Requires: list,expr,stack
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description    sequence computation using generic list
**    =========== 
**
**    Global Parameters:
**        "printf"
**        "writeFOSN"
**        "shiftbeginpos"
**        "shiftendpos"
**        "isshiftbeginrelend"
**        "isshiftendrelbegin"
**        "takeuncompletefeature"
**        "takeuncompleteshiftfeature"
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/


/*
#define TRACE
#define DUMMY
#define TRACE1
*/

#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <stdarg.h>
#include <ctype.h>

#include "message.h"
#include "sm.h"
#include "lst.h"
#include "futil.h"
#include "par.h"
#include "id.h"
#include "library.h"
#include "entry.h"
#include "seq.h"
#include "query.h"
#include "seqlib.h"

#define _SRS
#define _SLB
#define _CONSTANTS
#include SRSINCLUDE

#define vabs(x)  ((x)<0 ? -(x) : (x))
#define NAMELEN  40
enum slbfile_type {SLBxNORMAL=0, SLBxGCG7, SLBxGCG8, SLBxGCG8_1};

typedef struct STKo {
  void *a;
}STKo;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  external, global and module wide variables
*/

extern FILE        *protokoll;
ENTRYo             *global_entry; 
SEQo               *seqCurr = NULL;  /* remembers, if entry sequence was 
					  already read */
SEQo               *featureSeq = NULL;
SEQo               *seqRangeList = NULL;
static SLBoFEATURE feature = { 0, 0, 1, NULL, NULL, NULL, 0, NULL, NULL, NULL};
static FILE        *file=NULL;
static SMoBUFF     *featureBuff=NULL;
INT4               global_before_f = 0;
INT4               global_after_f = 0;

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  static functions
*/

static INT4 join(STKo *parameter_stack, STKo *eval_stack);
static INT4 complement(STKo *parameter_stack, STKo *eval_stack);
static INT4 replace(STKo *parameter_stack, STKo *eval_stack);
static INT4 one_of(STKo *parameter_stack, STKo *eval_stack);
static void SlbInitFeature (SLBoFEATURE *feature);

static void SlbJoinList();
static void SlbComplementList();
static void SlbReplaceList(char *replace);
static INT4 SlbInsert (INT4 bpos, INT4 epos);
static INT4 SlbSetAccno(char *acc);
static INT4 SlbShiftAndCheck();
static INT4 SlbEvaluate();
static void SlbWriteFosn (SEQo *seq);
static SEQo *SlbRetrieveAccNo (char *accno);
static char *SlbCurrEntryName ();


typedef struct FUNC_DESC_ {
           char func_name[20];
           INT4 (*func) ();
        } FUNC_DESC;
#define  MAXFUNC  4
FUNC_DESC func_table[MAXFUNC] = {
             { "join", join },
             { "complement", complement },
             { "replace", replace },
             { "one-of", one_of }
          };



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  default function for printing lines
*/

static INT4 SlbPrintF (char *formatStr, ...)
{
    va_list ap;

    va_start (ap, formatStr);
    vfprintf (file, formatStr, ap);
    va_end (ap);

    if (formatStr[strlen (formatStr) -1] != '\n')
    fprintf (file, "\n");

    return 1;
}



/****** SlbGetCurrEntryName ***************************************************
**
**      Prints name entry that is currently processed.
**
**      INPUT:      
**              IMPLICIT:
**                  global_entry (ENTRYo *) [R]
**
**      RETURNS:    
*/

static char *SlbGetCurrEntryName ()
{
  return EntryGetFullName (global_entry);
}

/****** SlbEntryPrint *********************************************************
**
**      prints a single sequence entry using various options; function needs
**      to know how many entries have to be printed and are currently printed
**      in order to decide if the output file (if any) has to be opened or
**      closed.
**
**      INPUT:      entry object [R]
**                  set Name (for constructing output file name) [R]
**                  number of entries to print in whole list [R]
**                  number of current entry [R]
**              IMPLICIT:
**
**      RETURNS:    
*/

void SlbEntryPrint (ENTRYo *entry, char *setName, int entryN, int entryCurrN)
{
  SLBoFEATURE *feature;
  SEQo        *seq = NULL;
  char        *fileExt;
  INT4        errCode, seqFormat, (*print)(char*,...);

  switch (tolower (ParGetStr ("seqFormat")[0])) {
  case 'p':
    seqFormat = SEQxPIR;
    fileExt = ".pir";
    break;
  case 'e':
    seqFormat = SEQxEMBL;
    fileExt = ".dat";
    break;
  case 's':
    seqFormat = SEQxSWISS;
    fileExt = ".dat";
    break;
  case 'g':
    seqFormat = SEQxGCG;
    fileExt = ".gcg";
    break;
  case 'f':
    seqFormat = SEQxFASTA;
    fileExt = ".fas";
    break;
  }
  
  /* 
  ** the next deals with the file name... part of which may be specified by 
  ** user and open the file ...if not already open
  */

  if (ParGetNum ("printToFile")) {
    char *tmp, *outFileName, outDirName[FILxXNAM+1], fileName[FILxXNAM+1];
    

    ParDefFunction ("printf", (INT4 (*)()) SlbPrintF);
    outFileName = ParGetStr ("outFileName");	  
    
    if ((tmp = ParGetStr ("outDirName")))
      sprintf (outDirName, "%s/", tmp);
    else
      *outDirName = '\0';
    
    if (!entryCurrN && seqFormat != SEQxGCG) {
      if (outFileName && *outFileName)
	sprintf (fileName, "%s%s", outDirName, outFileName);
      else
	sprintf (fileName, "%s%s%s", outDirName, setName, fileExt);
    }
    else if (seqFormat == SEQxGCG) {
      if (entryN == 1 && outFileName && *outFileName)
	sprintf (fileName, "%s%s", outDirName, outFileName);
      else
	sprintf (fileName, "%s%s%s", outDirName, entry->entry_nm, fileExt);
    }
    if (*fileName) {
      file = FilOpenW (fileName, &errCode);
      _ErrMsg2 (errCode, fileName);

    }
  }    

  /*  
  ** print text (annotation)
  */
  
  print = (INT4 (*)(char*,...)) ParGetFunction ("printf");
  if (ParGetNum ("printText")) 
    EntryPrint (entry); 
  else if (ParGetNum ("parSetFields")) {
    print ("entry: %s \n", entry->full_nm);
    EntryPrintFields (entry); 
  }
  else if (seqFormat != SEQxFASTA)
    print ("entry: %s \n", entry->full_nm);

  /* 
  ** print data (sequence)
  */

  if (ParGetNum ("printData")) {
    if (IdIsSub (entry->id)) 
      errCode = SlbGetFeature (entry, &seq, &feature);
    else
      errCode = SlbGetSequence (entry, &seq);
    
    _ErrIf (errCode) 
      _ErrMsg2 (e__failureinslbgetx, entry->full_nm);

    else {
      switch (seqFormat) {
      case SEQxPIR:
	SeqWritePIR (seq, entry->entry_nm, 0, print);
	break;
      case SEQxEMBL:
	SeqWriteEMBL (seq, 
		      ParGetNum ("printText") ? NULL : EntryGetName (entry), 
		      print);
	break;
      case SEQxSWISS:
	SeqWriteSwiss (seq, entry->entry_nm, print);
	break;
      case SEQxGCG:
	SeqWriteGCG (seq, entry->entry_nm, print);
	break;
      case SEQxFASTA:
	SeqWriteFasta (seq, entry->entry_nm, print);
	break;
      }
    }
  }

  /*
  ** close file 
  */

  if (file && (entryCurrN == entryN - 1 || seqFormat == SEQxGCG)) {
    fclose (file);
    file = NULL;  /* set back to default value /stdout/ */
  }
}


/****** SlbGetNamedFunction ***************************************************
**
**      looks for the named function in the local function table
**
**      INPUT:      address of function name [R]
**              IMPLICIT:
**
**      RETURNS:    address of function descriptor, if function exists,
**                  otherwise NULL
*/

static FUNC_DESC* SlbGetNamedFunction(char* name)
{
  INT4 i;
  for (i=0; i<MAXFUNC; i++)
      if (!strcmp(func_table[i].func_name, name)) return &func_table[i];

  return NULL; /* Function undefined */
}


/****** join ******************************************************************
**
**      implements the join function of a sequence expression.
**      As the parameter stack and evaluation stack is not used any more
**      SlbJoinList could be called directly.
**
**      INPUT:      address of parameter stack [R]
**                  address of evaluation stack [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success
*/

static INT4 join(STKo *parameter_stack, STKo *eval_stack)
{
#ifdef xxx
  if (!StkIsEmpty (parameter_stack)) 
    _ErrRet2 (e__joinillegalpar, "in stack");
  
  SlbJoinList();
#endif
  return 1;
}

/****** complement ************************************************************
**
**      implements the complement function of a sequence expression.
**      As the parameter stack and evaluation stack is not used any more
**      SlbComplementList could be called directly.
**
**      INPUT:      address of parameter stack [R]
**                  address of evaluation stack [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success
*/

static INT4 complement(STKo *parameter_stack, STKo *eval_stack)
{
    SlbComplementList();

    return 1;
}

/****** replace ***************************************************************
**
**      implements the replace function of a sequence expression.
**      The string "replace" has to be set in the last inserted
**      sequence object.
**
**      INPUT:      address of parameter stack [R]
**                  address of evaluation stack [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success
*/

static INT4 replace(STKo *parameter_stack, STKo *eval_stack)
{
#ifdef xxx
  char repstring[100];

  strcpy (repstring, "_ERROR_");
  ExpPopVarname(parameter_stack, repstring);
  SlbReplaceList(repstring);
#endif
  return 1;
}

/****** one_of ****************************************************************
**
**      implements the one_of function of a sequence expression.
**
**      INPUT:      address of parameter stack [R]
**                  address of evaluation stack [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success
**                  e__foundoneof <entry name>   
*/

static INT4 one_of(STKo *parameter_stack, STKo *eval_stack)
{
#ifdef xxx
    STKoSYM op;
    STKoSYM first;
    INT4 param_count = 0;
    INT4 rv=1;


    if (ParGetNum("discardoneof")) {
        _ErrRet(e__foundoneof);
    }

    /*
    ** auf dem Stack koennen Zahlen (pos) liegen oder es kann eine
    ** Parameterliste mit Ranges existieren !!
    */

    while (StkPop(parameter_stack, &op) != e__eostack)
    {
        param_count++;
        /* printf("Parameter: %d\n", param_count); */
        if (param_count==1) first = op;
    }

    if (param_count > 0) {
        rv = StkPush(eval_stack, first);
        _ErrRet2(rv, "when evaluating one-of");
    }
    else {   /* seqRangeList with ranges */
        LstFirst ((void**)&seqRangeList);
        if (LstNext ((void**)&seqRangeList)) 
            LstDeleteToEndOfList((void**)&seqRangeList);
    }
#endif
    return 1;
}

/****** SlbExe ****************************************************************
**
**      this function implements the operator EXE.
**      Symbols are popped from the evaluation stack until the next
**      function name is popped. If there are values on the stack,
**      the values are pushed into a private parameter stack. If the
**      function name is popped, the corresponding function is called
**      and supplied with the parameter stack.
**
**      INPUT:      address of evaluation stack [R]
**              IMPLICIT:
**                  reads the content of the evaluation stack
**                  writes the content of the parameter stack
**
**      RETURNS:    1 on success
**                  e__doesnotexistfunction
*/

INT4 SlbExe (STKo *eval_stack)
{
  /* pop symbols from eval_stack,
     if operator: execute them (not possible here!)
     if value: put it into private parameter_stack
     if variable: put it's value into private parameter_stack
     if functionname: execute function giving it a pointer
                      to the private parameter_stack
     if OP_SEQ: nothing to do
  */
#ifdef xxx
  STKo private_stack;
  STKoSYM sym;
  FUNC_DESC *func_desc_ptr;
  float float_val;
  INT4 int_flag=1, rv=1;

  if (!StkIniSym(&private_stack, 20)) {
      _ErrRet2(e__allocfail, 
               "in initialization of private parameter stack");
  }
   
  while (1) {
    rv = StkPop(eval_stack, &sym);

    if (sym.any.code == STKxFNAME) {
      /* get function_description pointer ... */
      func_desc_ptr = SlbGetNamedFunction(sym.var_name.name);
 /* ??? Should there be a number that decides what parameter list to use ? */
      if (func_desc_ptr)
	rv = (func_desc_ptr->func) (&private_stack, eval_stack);
      else rv = e__doesnotexistfunction;
      _ErrIf(rv) {
	StkDelSym(&private_stack);
	_ErrRet2(rv, sym.var_name.name);
      }
      break;
    }
    
    switch (sym.any.code) {
    case 0:
      break;
    case STKxNAME:
      rv = StkPush(&private_stack, sym);
      _ErrIf(rv) {
	StkDelSym(&private_stack);
	_ErrMsg(rv); /* because _ErrRet does not print message */
	_ErrRet(rv);
      }
      break;
      
    case STKxNUMBER:  /* put value into private parameter stack */
    case STKxFLOAT:
    case STKxINUM:
    case STKxFNUM:
      int_flag = 1;
      ExpGetVal(&sym,&float_val,&int_flag);

      ExpGetSym(&sym,float_val,int_flag);
      rv = StkPush(&private_stack, sym);
      _ErrIf(rv) {
	StkDelSym(&private_stack);
	_ErrMsg(rv); /* because _ErrRet does not print message */
	_ErrRet(rv);
      }
      break;
    }

  }

  StkDelSym(&private_stack);
#endif
  return 1;
}


/****** SlbOpAfter ************************************************************
**
**      this function implements the operator AFTER ( > ).
**      An integer value is popped from the evaluation stack. 
**      Negative positions are rejected.
**      Legal positions are made negative afterwards to mark the
**      existence of the 'after' operator.
**      The value is pushed onto the evaluation stack again. 
**
**      INPUT:      address of evaluation stack [R]
**              IMPLICIT:
**                  modifies the content of the evaluation stack
**
**      RETURNS:    1
*/

INT4 SlbOpAfter (STKo *eval_stack)
{
#ifdef xxx
  float val, ergval;
  INT4 int_flag=1;
  INT4 rv;


  if (!ParGetNum("takeuncompletefeature"))
      _ErrRet(e__operatorafternotallowed);
  else global_after_f = 1;

  rv = ExpPopVal(eval_stack, &val, &int_flag);
  if (!int_flag) 
      _ErrRet2(e__illegalvalueonstack, val);

  /* negative positions must not exist, parser should signal error before */
  if (val<0)
      _ErrRet(e__illegalposition);

  ergval = val>0 ? val : 1;  /* default */

  /*
  **  make ergval negative to use it later as a sign
  **  for the existence of after_f in range
  */

  ergval = -ergval;

  ExpPushVal(eval_stack, ergval, int_flag);
  return rv;
#endif
}


/****** SlbOpBefore ***********************************************************
**
**      this function implements the operator BEFORE ( < ).
**      An integer value is popped from the evaluation stack. 
**      Negative positions are rejected.
**      Legal positions are made negative afterwards to mark the
**      existence of the 'before' operator.
**      The value is pushed onto the evaluation stack again. 
**
**      INPUT:      address of evaluation stack [R]
**              IMPLICIT:
**                  modifies the content of the evaluation stack
**
**      RETURNS:    1
*/

INT4 SlbOpBefore (STKo *eval_stack)
{
#ifdef xxx
  float op1val, ergval;
  INT4 int_flag=1;
  INT4 rv;


  if (!ParGetNum("takeuncompletefeature"))
      _ErrRet(e__operatorbeforenotallowed);
  else global_before_f = 1;

  rv = ExpPopVal(eval_stack, &op1val, &int_flag);
  if (!int_flag)
      _ErrRet2(e__illegalvalueonstack, op1val);

  /* negative positions must not exist, parser should signal error before */
  if (op1val<0)
      _ErrRet(e__illegalposition);

  ergval = op1val>1 ? op1val : 1;  /* default */

  /*
  **  make ergval negative to use it later as a sign
  **  for the existence of before_f in range
  */
  ergval = -ergval;

  ExpPushVal(eval_stack, ergval, int_flag);
  return rv;
#endif
}

/****** SlbOpRange ************************************************************
**
**      this function implements the operator RANGE ( .. ).
**      Two integer values are popped from the evaluation stack.
**      A new sequence object is inserted into the seqRangeList, using
**      the popped value as begin and end position. The accession number
**      of the new sequence object is initially an empty string.
**      If a position is negative it means that an operator (before, after)
**      existed. Therefore a flag (before_f, after_f) is set TRUE in SlbInsert.
**
**      INPUT:      address of evaluation stack [R]
**              IMPLICIT:
**                  modifies the content of the evaluation stack
**                  inserts a new sequence object into seqRangeList
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 SlbOpRange (STKo *eval_stack)
{
#ifdef xxx
  float val1, val2;
  INT4 int_flag=1;
  INT4 rv;

  rv = ExpPopVals(eval_stack, &val1, &val2, &int_flag);
  if (!int_flag)
      _ErrRet3(e__illegalvaluesonstack, val1, val2);

  if (!val1 || !val2)
    _ErrRet (e__rangewithundefval);

  if (vabs (val1) > vabs(val2)) 
      _ErrRet(e__illegaldirectioninrange);

  /* Generate new range and insert it into list */
  rv = SlbInsert((INT4) val1, (INT4) val2);
  return rv;
#endif
}


/****** SlbOpMakeRange ********************************************************
**
**      this function implements the operator MAKERANGE ( .. ).
**      One integer value gets popped from the evaluation stack.
**      A new sequence object is inserted into the seqRangeList, using
**      the popped value as begin and end position. The accession number
**      of the new sequence object is initially an empty string.
**
**      INPUT:      address of evaluation stack [R]
**              IMPLICIT:
**                  modifies the content of the evaluation stack
**                  inserts a new sequence object into seqRangeList
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 SlbOpMakeRange (STKo *eval_stack)
{
  float op1val;
  INT4 int_flag=1;
  INT4 rv;

#ifdef xxx
#ifdef TRACE1
  printf("Function *SlbOpMakeRange* called\n");
#endif
  rv = ExpPopVal(eval_stack, &op1val, &int_flag);
  if (!int_flag)
      _ErrRet2(e__illegalvalueonstack, op1val);

  if (op1val<=0)
      _ErrRet(e__illegalposition);

#ifdef TRACE
  printf("computing range %d .. %d \n", (INT4)op1val, (INT4)op1val);
#endif

  /* Generate new range and insert it into list */
  rv = SlbInsert((INT4)op1val, (INT4)op1val);
  return rv;
#endif
}


/****** SlbOpSelect ***********************************************************
**
**      this function implements the operator SELECT ( . ).
**      Two integer values are popped from the evaluation stack.
**      The user is asked to specify a position between that positions.
**      The user-specified or default position is pushed onto stack again.
**
**      INPUT:      address of evaluation stack [R]
**              IMPLICIT:
**                  modifies the content of the evaluation stack
**
**      RETURNS:    1
*/

INT4 SlbOpSelect (STKo *eval_stack)
{
#ifdef xxx
  char answer[20];
  float op1val, op2val, ergval, userval;
  INT4 int_flag=1;
  INT4 rv;


  rv = ExpPopVals(eval_stack, &op1val, &op2val, &int_flag);
  if (!int_flag)
      _ErrRet3(e__illegalvaluesonstack, op1val, op2val);

  ergval = op1val;  /* default */

  if (ParGetNum("interactiveselect")) {
      printf("what position do you want BETWEEN %d and %d [%d]: ",
              (INT4)op1val, (INT4)op2val, (INT4)ergval);
      gets(answer);
      if (strlen(answer) > 0) {
         if (sscanf(answer, "%f", &userval) == 1) {
            if (userval < op1val || userval > op2val)
               printf("** position too low or too high: default used !!\n");
            else ergval = userval;
         }
         else printf("** illegal input: default used !!\n");
      }
  }

  ExpPushVal(eval_stack, ergval, int_flag);
  return rv;
#endif
}

/****** SlbOpCut **************************************************************
**
**      this function implements the operator CUT ( ^ ).
**      Two integer values are popped from the evaluation stack.
**      A new sequence object is inserted into the seqRangeList, using
**      the popped values as begin and end position. Because there should
**      be only a site specified, begin and end position must be adjacent.
**      At the moment the end position is set according to begin position.
**      The accession number of the new sequence object is initially an
**      empty string.
**
**      INPUT:      address of evaluation stack [R]
**              IMPLICIT:
**                  modifies the content of the evaluation stack
**                  inserts a new sequence object into seqRangeList
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 SlbOpCut (STKo *eval_stack)
{
#ifdef xxx
  char answer[20];
  float val1, val2, ergval, userval;
  INT4 int_flag=1;
  INT4 rv;

  rv = ExpPopVals (eval_stack, &val1, &val2, &int_flag);
  if (!int_flag)
      _ErrRet3(e__illegalvaluesonstack, val1, val2);

  ergval = val1;  /* default */

  if (val2-val1 > 1 && ParGetNum("interactivecut")) {
      printf("after what position do you want to CUT %d..%d [%d]: ",
              (INT4)val1, (INT4)val2, (INT4)ergval);
      gets(answer);
      if (strlen(answer) > 0) {
         if (sscanf(answer, "%f", &userval) == 1) {
            if (userval < val1 || userval > val2-1)
               printf("** position too low or too high: default used !!\n");
            else ergval = userval;
         }
         else printf("** illegal input: default used !!\n");
      }
  }

  val1 = ergval;
  val2 = val1 + 1;  /* the two positions must be adjacent */
  /* Generate new sequence object and insert it into list */
  rv = SlbInsert ((INT4)val1, (INT4)val2);
  if (rv) 
      seqRangeList->cut_f = 1; /* set flag (site_flag) */
  return rv;
#endif
}



/****** SlbOpSetAccno *********************************************************
**
**      this function implements the operator SET_ACCNO ( : ).
**      The accession number is popped from the evaluation stack.
**      Modifies (sets) the accession number of the sequence object,
**      that was last inserted into the seqRangeList.
**
**      INPUT:      address of evaluation stack [R]
**              IMPLICIT:
**                  modifies the content of the evaluation stack
**                  modifies last inserted sequence object in seqRangeList
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 SlbOpSetAccno (STKo *eval_stack)
{
#ifdef xxx
  char accno[NAMELEN];
  INT4 rv;

  rv = ExpPopVarname(eval_stack, accno);
  rv = SlbSetAccno (accno);
  return rv;
#endif
}


/****** SlbPrintFeature *******************************************************
**
**      this function is used to concatenate all lines belonging to
**      the same feature description in a database. After concatenating
**      all lines into one string, the resulting string will be parsed
**      and evaluated.
**
**      INPUT:      address of line in feature table [R]
**              IMPLICIT:
**                  modifies the global featureline
**
**      RETURNS:
*/

static void SlbPrintFeature(char *ln)
{
  INT4 len;

#if defined(TRACE)
  printf ("%s", ln);
#endif
  memcpy (ln, "  ", 2);   /* blank FT */
  len = strlen (ln);
  if (ln[ len-1 ] == '\n')
    ln[len-1] = '\0';
  BuffCopyString (featureBuff, ln);
}


/**api* SlbMakeFeature *****************************************************
**
**      accesses the feature table of an entry from the sequence library
**      and returns the evaluated sequence object; also returns a pointer
**      to the global feature object, wherein translation exceptions and
**      special codons may be stored.
**
**      INPUT:      buffer with the feature description [R]
**                  address of entry object [R]
**                  pointer to address of sequence object [W]
**                  pointer to address of feature description object [W]
**              IMPLICIT:
**                  featureBuff (SMoBUFF *) [W]
**
**      RETURNS:    1 on success, 0 otherwise
*/

INT4 SlbMakeFeature (SMoBUFF *featureBuff, ENTRYo *entry, SEQo *seq,
		     SEQo **res_seq, SLBoFEATURE **featurePtr)
{
#ifdef xxx
  static SMoBUFF *buff=NULL;

#ifdef xxx
  EXPo  *expression;
  INT4   rv;
  char  *tmp;

  if (!buff) 
    buff = BuffNew (100);
  else
    BuffReset (buff);

#ifdef xxx
  if (BuffSearch (featureBuff, "join("))
    return 0;
#endif

  global_entry = entry;   /* needed in SlbSeqFromAccNo to get library name */ 
  seqCurr = seq;  /* entry sequence already read */
  SlbInitFeature (&feature); 
  if (featurePtr)
    *featurePtr = &feature;

  expression = (EXPo*) LibObjByName("expression", "embl_feature");
  if (!expression)
    _ErrRet4(e__objnotfound, 5, "seqlib.c", "embl_feature");

  ExpInit(expression);
 
  SlbListReset();  /* maybe at another place ??? */

  /*
  **  ExpEval builds only a list structure (seqRangeList), that has
  **  to be evaluated later. The sequence of the entry was passed
  **  to SlbMakeFeature via the attribute "seq".
  **  After ExpEval parsing is already completely done and 
  **  feature.transl_except points to one of maybe many translation
  **  exception objects in a list, if there exists one.
  */

  BuffCopyString (buff, BuffGetPtr (featureBuff)+5); /* remove line code */
  while ((tmp = BuffSearch (buff,"\nFT")))
    strncpy(tmp,"   ",3);

  rv = ExpEval (BuffGetPtr (buff), "location", EXPxEVALUATE);
  if (rv == e__parsefail)
    rv = e__entryparsefail;
  _ErrRet2(rv, entry->entry_nm);
  rv = SlbShiftAndCheck();
  _ErrMsg2(rv, entry->entry_nm);
  _ErrRet(rv);

  rv = SlbEvaluate();
  _ErrRet2(rv, entry->entry_nm);
    
  /*
  **  the last inserted one is the RESULT
  **  move it to the result sequence list
  */

  seqCurr = NULL;  /* reset to initial state */

  if (featureSeq) {
    LstMove ((void**) res_seq, (void**)&featureSeq);
    return 1;
  }
  else 
#endif
    return 0;
#endif
}


/**API* SlbGetFeature *********************************************************
**
**      Retrives for the specified subentry, or sequence feature, the sequence
**      and the address of an object that contains parts of the feature
**      annotation. Function accesses the feature table of the 
**      original flat file and evaluates the feature location expression.
**
**      INPUT:      address of entry object [R]
**                  address of pointer to sequence object [W]
**                  address of pointer to feature description object [W]
**              IMPLICIT:
**
**      RETURNS:    1 if successful
**                  e__entryparsefail <entryName> +
**                  0 otherwise
*/

INT4 SlbGetFeature (ENTRYo *entry, SEQo **res_seq, SLBoFEATURE **featurePtr)
{
#ifdef xxx
  EXPo  *expression;
  INT4   rv, (*printSave)();
  
  SlbInitFeature (&feature);
  if (featurePtr)
    *featurePtr = &feature;
  expression = entry->lib->form->featureExpression;
  ExpInit(expression);
   SlbListReset(); 
  global_entry = entry; 
  
  /*
  ** goto begin of feature in entry
  */
  rv=EntryOpenText(entry);
  EntryBeginSub(entry);
  while ( (rv = EntryNextSub (entry)) < entry->id->subentry_n) 
    if (_ErrIs (rv) || rv == 0) 
      _ErrRet2 (e__entryparsefail, entry->entry_nm);

  /*
  ** print feature to the feature buffer
  */
  if (!featureBuff)
    featureBuff = BuffNew (1000);
  else
    BuffReset (featureBuff);
  printSave = ParGetFunction ("printf");
  ParDefFunction ("printf", (INT4(*)()) SlbPrintFeature);
  EntryPrintSub (entry);  /* copy feature to featureBuff */
  ParDefFunction ("printf", printSave);  /* reset print function */

  /*
  **  ExpEval builds only a list structure (seqRangeList), that has
  **  to be evaluated later. The sequence of the entry has not
  **  been read yet. After ExpEval parsing is already completely
  **  done and feature.transl_except points to one of maybe many
  **  translation exception objects in a list, if there exists one.
  */

  rv = ExpEval(BuffGetPtr (featureBuff), "location", EXPxEVALUATE);
  if (rv == e__parsefail)
    rv = e__entryparsefail;
  _ErrRet2(rv, entry->entry_nm);
  rv = SlbShiftAndCheck();
  _ErrRet(rv); 

  if (ParGetNum ("listFOSN") && !ParGetNum ("printData")) {
    SlbWriteFosn (seqRangeList);
  }	
  else {    
    rv = SlbEvaluate();
    _ErrRet(rv); 
    
    /*
    **  the last inserted one is the RESULT
    **  move it to the result sequence list
    */
    if (featureSeq) {
      LstMove ((void**) res_seq, (void**)&featureSeq);
      return 1;
    }
  }
#endif
  return 0;
}


/**api* SlbWriteFosn **********************************************************
**
**      writes list of features as extended FOSN file with begin and end
**      positions within parent sequence, complement...join
**
**      INPUT:      address of sequence object [R]
**              IMPLICIT:
**
**      RETURNS:    nothing
*/

static void SlbWriteFosn (SEQo *seq)
{
  SEQo *joinSeq;
  char hexNumStr[20], l[133];
  INT4  (*print)();

  IdToStr (global_entry->id, hexNumStr);
  
  print = ParGetFunction ("printf");
  
  /*
  ** check first if there is a sublist (-> join) and process that
  */ 

  if (seq->sublist && ParGetNum ("fosnWithPos")) {  
    joinSeq = seq->sublist;
    
    /*
    ** start with the last sequence if the WHOLE join must be complemented
    ** in that case all individual joined sequences must be complemented 
    */
    
    if (seq->compl_f) 
      LstLast ((void **) &joinSeq);
    else
      LstFirst ((void **) &joinSeq);
    
    do {
      if (seq->compl_f)
	joinSeq->compl_f = !joinSeq->compl_f;
      
      if (!*joinSeq->name)
	sprintf (l, "%s:%s", global_entry->lib->nam, 
		 global_entry->entry_nm);
      else {
	sprintf (l, "%s", joinSeq->name);
      }
      sprintf (l, "%s  Begin: %d End: %d", l, joinSeq->bpos, joinSeq->epos);
      if (LibIsDataType (global_entry->lib, "dna"))
	sprintf (l, "%s Strand: %c", l, joinSeq->compl_f ? '-' : '+');
      sprintf (l, "%s Join: %s_%d", l,  
	       global_entry->entry_nm, global_entry->id->subentry_n);
      sprintf (l, "%s !Id: %s\n", l, hexNumStr);
      print (l);
    } while (seq->compl_f ? LstPrev ((void **) &joinSeq) :
	     LstNext ((void **) &joinSeq));
  }
  
  /*
  ** normal sequence
  */

  else {
    sprintf (l, "%s", EntryGetGCGName (global_entry));
    if (ParGetNum ("fosnWithPos")) {

      if (seq->part_len > 0)
	seq->bpos = seq->epos - seq->part_len + 1;
      else if (seq->part_len < 0)
	seq->epos = seq->bpos + -seq->part_len - 1;

      sprintf (l, "%s  Begin: %d End: %d", l, seq->bpos, seq->epos);
      if (LibIsDataType (global_entry->lib, "dna"))
	sprintf (l, "%s Strand: %c", l, seq->compl_f ? '-' : '+');
      sprintf (l, "%s Join: %s_%d", l,  
	       EntryGetName (global_entry), global_entry->id->subentry_n);
    }
    sprintf (l, "%s !Id: %s\n", l, hexNumStr);
    print (l);
  }
}



/**API* SlbNextSequence *******************************************************
**
**      'Walks' to the next sequence in the file. Use "EntryOpenStream" to open
**      the flat file.
**
**      INPUT:      address of entry object [W]
**              IMPLICIT:
**
**      RETURNS:    1 on success
**                  0 if at the end of the file
*/

INT4 SlbNextSequence (ENTRYo *entry)
{
#ifdef xxx
  SRSoFILTYP *fileType=entry->lib->form->fil_t[1];
  FILo       *file=entry->file[1];
  INT4       k;

  while (1) {				     
    if (SmXLoc (file->l, fileType->fsts, fileType->fstl, fileType->fstr) != -1)
      break;
    if (FilURead (file) == e__eof)
      return 0;
  }
  
  /* 
  ** advance lines 
  */

  for (k=1; k < fileType->adv; k++) 
    FilURead (file);


  entry->isDataBegin = 1;
  entry->fip[1] = file->crfdd;
#endif
  return 1;
}


/**API* SlbGetSequence ********************************************************
**
**      Retrieves the sequence for specified entry.
**
**      INPUT:      address of entry object [R]
**                  address of pointer to sequence object [W]
**              IMPLICIT:
**
**      RETURNS:    1 on success
**                  0 otherwise
*/

INT4 SlbGetSequence (ENTRYo *entry, SEQo **seqPtr)
{
#ifdef xxx
  SEQo       *seq=NULL;
  SRSoFILTYP *fileType;
  FIP        fipSave;
  INT4       isGetSeqLenOnly = ParGetNum ("getSeqLenOnly"), splitN;
  char       name[50], dummy[10];

#if defined(TRACE)
  printf("SlbGetSequence: %d\n", sequence_count++);
#endif

  if (entry->isDataBegin)
    entry->isDataBegin = 0;  /* stream access - file pointer is positioned */
  else
    if (!EntryOpenData (entry))
      return 0;

  /*
  ** get the file type object and assume that the first line after the
  ** sequence title is a comment line only if a production "find" for
  ** the entry name is specified
  */

  fileType = entry->lib->form->fil_t[ENTxDATA];

  SeqSetRecordSeparator (fileType->type == SLBxGCG7 ? 1 : 0); /* gcg format 
								 for vms */
  SeqFromLib (seqPtr, entry->file[ENTxDATA],
	      (*fileType->find) ? fileType->find : NULL, /* scanf gets name */
	      fileType->exit, 
	      (*fileType->find ? 1 : 0) | /* no title line -> no comment ... */
	      (isGetSeqLenOnly ? 2 : 0));   

  /*
  ** GCG 8.1 if a sequence exceeds some size it is split into overlapping
  ** fragments, each 110000bp long with an overlap of 10000
  ** sequence which is the continuation - a file is considered to be split
  ** if it has exactly the split size.
  */

  if (fileType->type == SLBxGCG8_1 && 
      sscanf ((*seqPtr)->name, "%[A-Z0-9]_%[0]", name, dummy) == 2) {
    strcpy ((*seqPtr)->name, name);
    fipSave = entry->fip[1];

    if (isGetSeqLenOnly)
      (*seqPtr)->len -= 10000;
    else 
      SeqHead (*seqPtr, 100000);

    while (1) {
      SlbNextSequence (entry);
      SlbGetSequence (entry, &seq);
      if (seq->len == 110000) {
	if (isGetSeqLenOnly)
	  seq->len -= 10000;
	else 
	  SeqHead (seq, 100000);
      }
      if (isGetSeqLenOnly)
	(*seqPtr)->len += seq->len;
      else
	SeqCat (seqPtr, seq);

      if (seq->len != 100000)  /* the last of the split subentries */
	break;

    }
    entry->fip[1] = fipSave;
  }

  /*
  ** if the sequence is split into two files (GCG format) then get the next 
  ** sequence which is the continuation - a file is considered to be split
  ** if it has exactly the split size.
  */

  else if ((*seqPtr)->len && (*seqPtr)->len == fileType->gcgSplitSize) {
    fipSave = entry->fip[1];
    SlbNextSequence (entry);
    SlbGetSequence (entry, &seq);
    if (isGetSeqLenOnly)
      (*seqPtr)->len += seq->len;
    else
      SeqCat (seqPtr, seq);
    SeqClr (&seq);
    entry->fip[1] = fipSave;
  }

  if (!*fileType->find) /* no title line -> no name either */
    strcpy ((*seqPtr)->name, entry->entry_nm);
#endif
  return 1;
}


/****** SlbJoinList ***********************************************************
**
**      implements the join function of a sequence expression.
**      Creates a new function object as first member of a local list.
**      The current parameter list is assigned to the sublist pointer
**      of the new function object. As there is no parameter list any more,
**      the local list can be assigned to the (new) parameter list.
**
**      INPUT:
**              IMPLICIT:
**                  seqRangeList changes
**
**      RETURNS:    nothing
*/

static void SlbJoinList()
{
    SEQo *local_list = NULL;
    
    if (SeqNew(&local_list)) {
      /*sprintf (local_list->name, "%s", global_entry->entry_nm);*/
      strcpy(local_list->name, "JOIN");
      
      /* 
       **  no hashing  if LstHashSearch or LstDelete... is never used
       */
      LstAssign((void**)&local_list->sublist, (void**)&seqRangeList);
      LstAssign((void**)&seqRangeList, (void**)&local_list);
    }
    else printf("ERROR: JOIN object could not be created in SlbJoinList !\n");
}

/****** SlbComplementList *****************************************************
**
**      implements the complement function of a sequence expression.
**      Simply inverts the complement flag of the current sequence object
**      in the seqRangeList.
**
**      INPUT:
**              IMPLICIT:
**                  inverts the complement flag of the current sequence object
**
**      RETURNS:    nothing
*/

static void SlbComplementList()
{
    seqRangeList->compl_f = !seqRangeList->compl_f;
}

/****** SlbReplaceList ********************************************************
**
**      implements the replace function of a sequence expression.
**      Simply sets the replace string of the current sequence object
**      in the seqRangeList.
**
**      INPUT:
**                  address of replace string [R]
**              IMPLICIT:
**                  sets the replace string of the current sequence object
**
**      RETURNS:    nothing
*/

static void SlbReplaceList(char *replace)
{
    seqRangeList->replace = (char*) malloc(strlen(replace) + 1);
    strcpy(seqRangeList->replace, replace);
}

/****** SlbInsert *************************************************************
**
**      inserts a new (current) subsequence object (range) into the 
**      "seqRangeList".
**      The accession number of a sequence object is up to now initially
**      set to an empty string, i.e. the accession number equals the
**      accession number of the current entry.
**      In case of the CUT operator the cut_f flag has to be set afterwards.
**
**      INPUT:      start position of subsequence [R]
**                  end position of subsequence [R]
**              IMPLICIT:
**                  new sequence object in seqRangeList
**
**      RETURNS:    1 on success, 0 otherwise
*/

static INT4 SlbInsert (INT4 bpos, INT4 epos)
{
    if (!SeqNew(&seqRangeList))  
      return 0;

    if (bpos<0) {
        seqRangeList->before_f = 1;
        seqRangeList->bpos = -bpos;
    }
    else {
        seqRangeList->before_f = 0;
        seqRangeList->bpos = bpos;
    }

    if (epos<0) {
        seqRangeList->after_f = 1;
        seqRangeList->epos = -epos;
    }
    else {
        seqRangeList->after_f = 0;
        seqRangeList->epos = epos;
    }
    return 1;
}

/****** SlbSetAccno ***********************************************************
**
**      sets accession number of last (current) sequence object in the
**      seqRangeList. The accession number of a sequence object is initially
**      set to an empty string, i.e. the accession number equals the
**      accession number of the current entry.
**
**      INPUT:      address of accession number [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success, 0 otherwise
*/

static INT4 SlbSetAccno(char *acc)
{
  if (seqRangeList)
    strcpy(seqRangeList->accno, acc);
  else {
    _ErrMsg(e__noseqinlist);
    return 0;
  }
  return 1;
}

/****** SlbModifyBegin ********************************************************
**
**      modifies the begin positiom of the specified sequence object.
**      If an illegal position (<1) would result, an error is
**      reported.
**
**      INPUT:      address of a sequence object [R]
**                  delta for shift [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success, 0 otherwise
*/

static INT4 SlbModifyBegin(SEQo *range, INT4 delta)
{
  if (range)
    if (range->bpos + delta > 0)
      range->bpos += delta;
    else {
      if (!ParGetNum("takeuncompleteshiftfeature")) {
	_ErrRet2 (e__shiftseqisfrag, SlbGetCurrEntryName ());
      }
      else range->bpos = 1;
    }
  else {
    _ErrMsg(e__noseqinlist);
    return 0;
  }
  
  return 1;
}

/****** SlbModifyEnd **********************************************************
**
**      modifies the end positiom of the specified sequence object.
**      If an illegal position (<1) would result, an error is
**      reported.
**
**      INPUT:      address of a sequence object [R]
**                  delta for shift [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success, 0 otherwise
*/

static INT4 SlbModifyEnd(SEQo *range, INT4 delta)
{
  if (range)
    if (range->epos + delta > 0)
      range->epos += delta;
    else {
      if (!ParGetNum("takeuncompleteshiftfeature")) {
	_ErrRet2 (e__shiftseqisfrag, SlbGetCurrEntryName ());
      }
      else range->epos = 1;
    }
  else {
    _ErrMsg(e__noseqinlist);
    return e__noseqinlist;
  }
  
  return 1;
}


	  
/****** SlbSeqFromAccNo *******************************************************
**
**      gets the complete sequence string belonging to the entry with the
**      specified accession number. To retrieve the sequence string the
**      unique accession number is transformed into a unique id_name.
**      If the sequence string is not already in the global list (seq)
**      it will be retrieved by a query and the sequence object will be
**      inserted into the global list.
**
**      INPUT:      address of accession number [R]
**              IMPLICIT:
**                  global_entry (ENTRYo) [R]
**                  featureSeq (SEQo *) [W]
**
**      RETURNS:    address of the sequence object
**                  0, in case of an error (message already printed)
*/

static SEQo *SlbSeqFromAccNo (char *accno)
{
  ENTRYo   *entry = global_entry;
  IDoENTRY *id;
  SEQo     *seq = NULL;
  INT4     rv;
  char     libEntryName[80] = "", *tmp;
  
  /*
  ** use external program to fetch the sequence by accession number 
  */
  
  if (*accno && (tmp = ParGetStr ("findAccNoCommand")) && *tmp) {
    if (!(seq = SlbRetrieveAccNo (accno))) 
      return NULL;
    LstMove((void**)&featureSeq, (void**)&seq);
  }

  /* 
  ** retrieve sequence if accno is specified ...no accession number means
  ** sequence of current entry which may not be read yet 
  */

  else {
    if (*accno) {
#ifdef xx
      if (!(id = QryFindID (LibGetName (global_entry->lib, "full"), 
			    "acc", accno))) {
/*	_ErrMsg3(e__couldnotgetsequence,accno, global_entry->entry_nm); */
	return NULL;
      }
#endif
      entry = EntryOpen (id);
    }
    else if (seqCurr)
      return seqCurr;  /* for SlbMakeFeature */

    strcpy (libEntryName, EntryGetGCGName (entry));

    /*
    ** search in the current sequence list ...to check if current entry's 
    ** sequence is opened
    */
    
    if (!LstHashSearch((void**)&featureSeq, libEntryName))  {
      rv = SlbGetSequence (entry, &seq);
      if (entry != global_entry) {
	EntryClose (&entry);
      }

      if (!rv)  {
	LstDeleteAll ((void**)&seq);
	_ErrMsg2 (e__couldnotgetsequence, accno);
	return NULL;
      }
      LstMove((void**)&featureSeq, (void**)&seq);

      strcpy (featureSeq->name, libEntryName);
    }
  }

  return featureSeq;
}


/****** SlbRetrieveAccNo ******************************************************
**
**      Uses the command specified in "findAccNoCommand" to get entry by 
**      accession number.
**
**      INPUT:      address of accession number [R]
**              IMPLICIT:
**
**      RETURNS:    address of the complete sequence string
**                  0, in case of an error (message already printed)
*/

static SEQo *SlbRetrieveAccNo (char *accno)
{
  SEQo *seq=NULL;
  INT4 rv;
  char command[256], fileName[256];

  sprintf (command, ParGetStr ("findAccNoCommand"), accno, accno, accno);
  sprintf (fileName, ParGetStr ("inputSeqFile"), accno);
  system (command);

  rv = SeqReadAll (&seq, fileName);
  remove (fileName);
  return  (rv && !_ErrIs (rv) )? seq : NULL;
}


/****** SeqReplace ************************************************************
**
**
**      INPUT:      address of a sequence object [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success
**                  e__incorrectlength
*/

INT4 SeqReplace (SEQo *new, SEQo *seq, char *replace, 
		 INT4 begPos, INT4 endPos, INT4 doInsert)
{
  INT4 length;

  /* calculate length of output sequence */
  length = strlen (seq->seq) + strlen (replace);
  if (!doInsert)  
    length -= endPos - begPos + 1;

  new->seq = (char*) malloc (length + 1);
  new->len = length;
  
  if (doInsert) {
    strncpy (new->seq, seq->seq, begPos);
    new->seq[begPos] = '\0';
    strcat (new->seq, replace);
    strcat (new->seq, &seq->seq[begPos]); /* endPos = begPos +1 */
  }
  else {
    strncpy (new->seq, seq->seq, begPos - 1);
    new->seq[begPos - 1] = '\0';
    strcat (new->seq, replace);
    strcat (new->seq, &seq->seq[endPos]);
  }
  
  if (new->len != strlen (new->seq)) 
    _ErrRet1 (e__incorrectlength);
  return 1;
}


/****** SeqGetSubSeq **********************************************************
**
**
**      INPUT:      address of a sequence object [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success
**                  e__incorrectlength
*/

INT4 SeqGetSubSeq (SEQo *new, SEQo *seq, INT4 begPos, INT4 endPos)
{
  INT4 length;

  length = endPos - begPos + 1;
  if (length <= 0)  
    _ErrRet4 (e__seqwithneglen, SlbGetCurrEntryName (), begPos, endPos);

  new->seq = (char*) malloc (length + 1);
  strncpy (new->seq, &(seq->seq[ begPos-1 ]), length);
  new->seq[length] = '\0';
  new->len = length;
  return 1;
}


/****** SlbEvalSequence *******************************************************
**
**      gets the sequence string belonging to the specified sequence object.
**      If the sequence string is not already calculated the calculation
**      will be done here using the complete sequence of an entry with
**      an unique accession number and the begin and end of a partial
**      sequence. At last the sequence string may be complemented.
**
**      INPUT:      address of a sequence object [R]
**              IMPLICIT:
**
**      RETURNS:    1 on success
**                  e__error, in case of an already printed error message
**                  e__postoohigh, position is greater than length of sequence
*/

static INT4 SlbEvalSequence (SEQo *new)
{
  SEQoTranslExcept *tmp;
  SEQo *seq;
  INT4 rv;
  
  if (new->seq)
    return 1;
  
  /* fetch pointer (tmp) to complete sequence */
  if ((seq = SlbSeqFromAccNo (new->accno)) == NULL) {
    _ErrMsg2 (e__couldnotgetsequence, new->accno);
    _ErrRet (e__error);
  }  

  strcpy (new->name, seq->name);
  
  /*
  ** report error if begin and end positions are greater than sequence length  
  */


  /* to be fixed some time (te) */
  if (feature.tExceptN > 1) {
    for (tmp=feature.tExcept; tmp->aa; tmp++)
      if (tmp->begin >= new->bpos && tmp->begin < new->bpos + new->epos)
	tmp->begin = tmp->begin - new->bpos + 1;
  }

  if (new->bpos > seq->len)  {
    if (!ParGetNum ("takeuncompletefeature"))
      _ErrRet1 (e__postoohigh);
    else new->bpos = seq->len;
  }
  if (new->epos > seq->len)  {
    if (!ParGetNum ("takeuncompletefeature")) 
      _ErrRet1 (e__postoohigh);
    else new->epos = seq->len;
  }
  
  if (new->replace)
    rv = SeqReplace (new, seq, new->replace, new->epos, new->bpos, new->cut_f);
  else 
    rv = SeqGetSubSeq (new, seq, new->bpos, new->epos);
  
  _ErrRet (rv);

  if (new->compl_f)
    SeqComplement (new);
  return 1;
}




/****** SlbShiftAndCheck *****************************************************
**
**      looks for the current values of the modification parameters (shift) and
**      checks the global seqRangeList. In the seqRangeList there could be
**      one sequence object generated by an expression like "135 .. 177" or
**      one function object that has a sublist of sequence objects generated
**      by an expression like "join(135 .. 177, complement(23 .. 97))".
**
**      INPUT:
**              IMPLICIT:
**
**      RETURNS:    1 on success
**                  e__nothingtoevaluate
**                  e__invalidshift
**                  e__relbegandend
**
*/

static INT4 SlbShiftAndCheck()
{
  SEQo *range;
  INT4 begPos=0, endPos=0, isBegRelEnd=0, isEndRelBeg=0;
  INT4 head_len=0, tail_len=0;
  INT4 rv;

  if (!seqRangeList)  {
    _ErrRet2 (e__nothingtoevaluate, SlbGetCurrEntryName ());
  }

  begPos = ParGetNum ("shiftbeginpos");
  endPos = ParGetNum ("shiftendpos");
  isBegRelEnd = ParGetNum ("isshiftbeginrelend");
  isEndRelBeg = ParGetNum ("isshiftendrelbegin");

  /*
  ** return error message for all combinations of
  ** modification parameters that should not occur
  */

  if (isBegRelEnd && isEndRelBeg) 
    _ErrRet2 (e__relbegandend, SlbGetCurrEntryName ());
  else if (isBegRelEnd && begPos > endPos)
    _ErrRet5 (e__invalidshift, SlbGetCurrEntryName (), begPos, endPos, "end");
  else if (isEndRelBeg && begPos > endPos)
    _ErrRet5 (e__invalidshift, SlbGetCurrEntryName (), begPos, endPos, "beg");

  /*
  ** compute length of head or tail subsequence
  */

  if (isEndRelBeg)
    head_len = endPos - begPos + 1;
  if (isBegRelEnd)
    tail_len = endPos - begPos + 1;

  seqRangeList->part_len = 0;  /* whole sequence */
  if (head_len > 0) seqRangeList->part_len = -head_len;
  if (tail_len > 0) seqRangeList->part_len = tail_len;
  
  range = seqRangeList->sublist;  /* for shorter source code */
  
  if (!range) {
    if (begPos && !isBegRelEnd)
      rv = SlbModifyBegin (seqRangeList, begPos);
    else if (begPos && isBegRelEnd)
      rv = SlbModifyBegin (seqRangeList, endPos - begPos);
    else if (endPos && !isEndRelBeg)
      rv = SlbModifyEnd (seqRangeList, endPos);
    _ErrRet (rv);  /* already printed */
    
    rv = SlbEvalSequence(seqRangeList);
    _ErrRet (rv);  /* already printed */
  }
  else  {

    /*
    **  range is the sublist of a (Join-) function
    */

    if (begPos && !isBegRelEnd)
      if (LstFirst((void**)&range))
	rv = SlbModifyBegin (range, begPos);
    
    if (endPos && !isEndRelBeg)
      if (LstLast((void**)&range))
	rv = SlbModifyEnd (range, endPos);
    
    if (LstFirst((void**)&range)) {
      do  {
	rv = SlbEvalSequence(range);
	_ErrRet (rv);  /* already printed */
      }
      while (LstNext((void**)&range));
    }
    else {
      _ErrRet(e__noparamlist);
    }
  } 

  return 1;
}


/****** SlbEvaluate ***********************************************************
**
**      evaluates the global seqRangeList. In the seqRangeList there could be
**      one sequence object generated by an expression like "135 .. 177" or
**      one function object that has a sublist of sequence objects generated
**      by an expression like "join(135 .. 177, complement(23 .. 97))".
**
**      INPUT:
**              IMPLICIT:
**                  featureSeq (SEQo *) [W]
**
**      RETURNS:    1 on success, 0 otherwise
**
*/

static INT4 SlbEvaluate()
{
  SEQo *range;
  
  if (!seqRangeList)  {
    _ErrMsg(e__nothingtoevaluate);
    return 0;
  }
  
  range = seqRangeList->sublist;  /* for shorter source code */
  
  if (!range) {
    /* the single range (seqRangeList) has been evaluated already */
    SeqJoin (&featureSeq, seqRangeList);
  }
  else  {

    /*
    **  range is the sublist of a (Join-) function.
    **  Make sure that all ranges in this list
    **  are already evaluated (SlbEvalSequence)
    **  before joining them (see SlbShiftAndCheck)
    */
    
    if (LstFirst((void**)&range)) {
      SeqJoin (&featureSeq, range);
    }
    else {
      _ErrMsg(e__noparamlist);
      return 0;
    }
  }
  
  /*
  ** give sequence a name, and complement it if necessary
  */
  if (seqRangeList->compl_f && seqRangeList->sublist)
    SeqComplement (featureSeq);
  strcpy (featureSeq->name, "RESULT");
  strcpy (featureSeq->accno, "RESULT");
  
  if (seqRangeList->part_len < 0)
    SeqHead(featureSeq, -seqRangeList->part_len);
  if (seqRangeList->part_len > 0)
    SeqTail (featureSeq, seqRangeList->part_len);
  
  return 1;
}



/**api* SlbListReset **********************************************************
**
**      deletes all local lists (seq, seqRangeList) created during evaluation
**
**      INPUT:
**              IMPLICIT:
**                  featureSeq (SEQo *) [W]
**
**      RETURNS:    1
*/

INT4 SlbListReset()
{
  LstDeleteAll ((void**) &seqRangeList);
  if (featureSeq)
    LstDeleteAll ((void**) &featureSeq);
  return 1;
}




/****** SlbCitationDump ****************************************
**
**      dumps all information belonging to the specified object.
**      This is the print function set through LstManageClass
**      for citationtype objects (see SlbCitationNew).
**
**      INPUT:      address of an object [R]
**                  file pointer [W] or NULL
**              IMPLICIT:
**
**      RETURNS:    nothing
*/

static void SlbCitationDump (FILE *file, void *obj)
{
  CITATION *tmp = (CITATION*)obj;

  if (!file)
    file = stderr;
  fprintf (file, "*** /CITATION %d\n", tmp->citationNum);
}


/**api* SlbCitationNew *************************************************
**
**      gets a new initialized citation object.
**      The citationtype_id tells, if the class CITATION is already
**      registered by the list module (LstManageClass).
**
**      INPUT:      pointer to address of citation object [W]
**              IMPLICIT:
**
**      RETURNS:
*/

INT4 SlbCitationNew (CITATION **citation)
{
  static INT4 citationtype_id=0;

  if (!citationtype_id)
    LstManageClass (&citationtype_id, sizeof (CITATION),
		    NULL, NULL, SlbCitationDump);

  return LstNew ((void **) citation, citationtype_id);
}


/****** SlbInitFeature ********************************************************
**
**      initializes global feature object ...functions that modify it can
**      be called directly form the parser.     
**      For managing translation exceptions the list module has been used.
**      Therefore, when resetting the feature object, an already existing
**      list has to be destroyed.
**
**      INPUT:      feature object [W]
**              IMPLICIT:
**
**      RETURNS:   
*/

static void SlbInitFeature (SLBoFEATURE *feature)
{
  feature->tTableId = 0;       /* id of translation table to be used */
  feature->codonStartShifted = 0;  /* normally there should be no shifting */
  feature->codonStart = 1;         /* default start position */
  feature->isPseudo = 0;

  /*
  **  if lists of special treated codons, translation exceptions or 
  **  citations exist, free the lists
  */

  if (!feature->tCodon) {
    _addObj (feature->tCodon, feature->tCodonN, feature->tCodonAllocN,
	   SEQoTranslCodon);
  }
  else if (feature->tCodonN > 1)
    feature->tCodonN = 1;
  feature->tCodon->aa = 0;


  if (!feature->tExcept) {
    _addObj (feature->tExcept, feature->tExceptN, feature->tExceptAllocN,
	   SEQoTranslExcept);
  }
  else if (feature->tExceptN > 1)
    feature->tExceptN = 1;
  feature->tExcept->aa = 0;



  if (feature->citation)
    LstDeleteAll((void**)&feature->citation);
  feature->citation = NULL;        /* no list */

  if (!feature->gene) {
    feature->gene = BuffNew (20);
    feature->product = BuffNew (20);
    feature->note = BuffNew (20);
  }
  else {
    BuffReset (feature->gene);
    BuffReset (feature->product);
    BuffReset (feature->note);
  }
}


/**api* SlbSetCodonStart *****************************************************
**
**            
**
**      INPUT:
**              IMPLICIT:
**                  feature (SLBoFEATURE *) [W]
**
**      RETURNS:    1
*/

INT4 SlbSetCodonStart (PRSoST *tokList,  FILo *file)
{
#ifdef xxx
  UINT4 tokval;

  char  tokstr[20];

  PrsUnSym (tokList, tokstr, &tokval);
  feature.codonStart = atoi (tokstr);
#endif
  return 1;
}


/**api* SlbSetCodon **********************************************************
**
**            
**
**      INPUT:
**              IMPLICIT:
**                  feature (SLBoFEATURE *) [W]
**
**      RETURNS:    1
*/

INT4 SlbSetCodon (PRSoST *tokList,  FILo *file)
{
#ifdef xxx
  SEQoTranslCodon *tCodon=&feature.tCodon[feature.tCodonN-1];
  UINT4 tokval;
  char  tokstr[20];


  PrsUnSym (tokList, tokstr, &tokval);        
  PrsUnSym (tokList, tokstr, &tokval);   
  tCodon->aa = *tokstr;
  PrsUnSym (tokList, tCodon->codon, &tokval);


  _addObj (feature.tCodon, feature.tCodonN, feature.tCodonAllocN,
	   SEQoTranslCodon);
  (++tCodon)->aa = 0;

#endif
  return 1;
}


/**api* SlbSetTranslTable  ***************************************************
**
**            
**
**      INPUT:
**              IMPLICIT:
**                  feature (SLBoFEATURE *) [W]
**
**      RETURNS:    1
*/

INT4 SlbSetTranslTable(PRSoST *tokList,  FILo *file)
{
#ifdef xxx
  UINT4 tokval;
  char  tokstr[20];

  PrsUnSym (tokList, tokstr, &tokval);
  feature.tTableId = atoi (tokstr);

#endif
  return 1;
}


/**api* SlbSetTranslExcept ****************************************************
**
**            
**
**      INPUT:
**              IMPLICIT:
**                  feature (SLBoFEATURE *) [W]
**
**      RETURNS:    1
*/

INT4 SlbSetTranslExcept (PRSoST *tokList,  FILo *file)
{
#ifdef xxx
  SEQoTranslExcept *tExcept;
  UINT4 tokval;
  char  tokstr[20], end[20];

  tExcept = &feature.tExcept[feature.tExceptN-1];

  PrsUnSym (tokList, tokstr, &tokval);  /*  )  */
  PrsUnSym (tokList, tokstr, &tokval);  /* aa  */
  tExcept->aa = *tokstr;
  PrsUnSym (tokList, end, &tokval);  /* posend   */
  PrsUnSym (tokList, tokstr, &tokval);  /* posbegin */
  tExcept->begin = atoi (tokstr);
  tExcept->length = atoi (end) - tExcept->begin + 1;

  /* add new terminator */
  _addObj (feature.tExcept, feature.tExceptN, feature.tExceptAllocN,
	   SEQoTranslExcept);
  (++tExcept)->aa = 0;

#endif
  return 1;
}


/**api* SlbSetCitation *****************************************************
**
**            
**
**      INPUT:
**              IMPLICIT:
**                  feature (SLBoFEATURE *) [W]
**
**      RETURNS:    1
*/

INT4 SlbSetCitation (PRSoST *tokList,  FILo *file)
{
#ifdef xxx
  UINT4 tokval;
  char  tokstr[20];

  SlbCitationNew (&feature.citation);  /* get new object */
  PrsUnSym (tokList, tokstr, &tokval);
  feature.citation->citationNum = atoi (tokstr);
#endif
  return 1;
}


/**api* SlbSetPseudo **********************************************************
**
**       Called during feature parsing. Sets the "pseudo gene" flag.           
**
**      INPUT:
**              IMPLICIT:
**                  feature (SLBoFEATURE *) [W]
**
**      RETURNS:    1
*/

INT4 SlbSetPseudo (PRSoST *tokList,  FILo *file)
{
  feature.isPseudo = 1;
  return 1;
}

/**api* SlbSaveQualText *******************************************************
**
**      Called during feature parsing. Saves the text for certain qualifiers.
**
**      INPUT:
**              IMPLICIT:
**                  feature (SLBoFEATURE *) [W]
**
**      RETURNS:    1
*/

INT4 SlbSaveQualText (PRSoST *tokList,  FILo *file)
{
#ifdef xxx
  UINT4 tokval;
  char  text[500], qualName[30];

  PrsUnSym (tokList, text, &tokval);
  PrsUnSym (tokList, qualName, &tokval);

  switch (tolower (qualName[0])) {
  case 'g':  /* gene */
    BuffCopyString (feature.gene, text);
    break;
  case 'p':  /* product */
    BuffCopyString (feature.product, text);
    break;
  case 'n':  /* note */
    BuffCopyString (feature.note, text);
    break;
  default:
    _ErrExit2 (e__unknownoption, qualName);
  }

#endif
  return 1;
}


ist,  FILo *file)
{
#ifdef xxx
  UINT4 tokval;
  char  text[500], qualName[30];

  PrsUnSym (tokList, text, &tokval);
  PrsUnSym (tokList, qualName, &tokval);

  switch (tolower (qualName[0])) {
  case 'g':  /* gene */
    BuffCopyString (feature.gene, text);
    break;
  case 'p':  /* product */
    BuffCopyString (feature.product, text);
    break;
  case 'n':  /* note */
    srs/src/seqlib.h
**
**    $RCSfile: seqlib.h,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:17:19 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
*/


typedef struct {
    char *manager; /* the first two attributes are necessary  */
    INT4 type_id;  /* for all objects to be managed by the list module */
    INT4 citationNum;
} CITATION;

typedef struct SLBoFEATURE {
  INT4                    tTableId;
  INT4                    codonStartShifted; /* set during translation */
  INT4                    codonStart; /* from the databank */
  struct SEQoTranslCodon  *tCodon;    /* List of special codon translations */
  INT4                    tCodonN;
  INT4                    tCodonAllocN;
  struct SEQoTranslExcept *tExcept;   /* List of transl_except */
  INT4                    tExceptN;
  INT4                    tExceptAllocN;
  CITATION                *citation;  /* List of citations (numbers) */
  INT4                    isPseudo;   /* only for CDS features */
  SMoBUFF                 *gene;
  SMoBUFF                 *product;
  SMoBUFF                 *note;
} SLBoFEATURE;


#ifndef _SEQo
typedef struct SEQo *dummytointroducestructtagSEQoinseqlib;
typedef struct ENTRYo *dummytointroducestructtagENTRYoinseqlib;
#endif

INT4 SlbMakeFeature (SMoBUFF *featureBuff, struct ENTRYo *entry,
		     struct SEQo *entry_seq, struct SEQo **res_seq,
		     SLBoFEATURE **featurePtr);
INT4 SlbGetFeature (struct ENTRYo *entry, struct SEQo **res_seq, 
		    SLBoFEATURE **featurePtr);
INT4 SlbGetSequence(struct ENTRYo *entry, struct SEQo **res_seq);
INT4 SlbListReset();
INT4 SlbNextSequence (struct ENTRYo *entry);






ruct SEQo *dummytointroducestructtagSEQoinseqlib;
typedef struct ENTRYo *dummytointroducestructtagENTRYoinseqlib;
#endif

INT4 SlbMakeFeature (SMoBUFF *featureBuff, struct ENTRYo *entry,
		     struct SEQo *entry_seq, struct SEQo **res_seq,
		     SLBoFEATURE **featurePtr);
INT4 SlbGetFeature (struct ENTRYo *entry, struct SEsrs/src/set.c
char set_ID[] = "$Id: set.c,v 1.8 1997/03/03 18:20:51 srs Exp $";
/*
**
**    $RCSfile: set.c,v $
**    $Revision: 1.8 $
**    $Date: 1997/03/03 18:20:51 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     69012 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: file, sm, message 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    functions for manipulating sets of IDs
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include "message.h"
#include "lst.h"
#include "sm.h"
#include "strv.h"
#include "futil.h"
#include "id.h"
#include "entry.h"
#include "set.h"
#include "library.h"

#define _SRS
#define _SLB
#include SRSINCLUDE



#define SETxNOCPY	0
#define SETxNULL	4294967295U  /* long with all bits turned ON */


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  macro for comparing entry ID's - IDs are BIG-endian on all operating
**  systems! ie, last byte of IDs are compared first, then second last... 
*/

#define CMP(a,b,cmp,len) {\
			   register INT4 _i;\
			   for (_i = (len)-1; _i >= 0; _i--) {\
			     if (((cmp) = (a)[_i] - (b)[_i]) != 0) break;\
			   }}


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  macro to copy sets
*/

#define _SetCopyIds(b, a1, a2, len)\
        len = (unsigned long) a2 - (unsigned long) a1;\
        _BuffCopyNChars (b, a1, len) 

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  macro inits string buffer
*/

#define _SetInitBuff(b)\
  if (!buff) \
    buff = BuffNew (2000);\
  else\
    BuffReset (buff)


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of static functions
*/

static void SetInit (void *obj);
static void SetKill (void *obj);
static void SetDump (FILE *file, void *obj);
static IDPTR SetOr (IDPTR a, IDPTR b, INT4 an, INT4 bn, INT4 *cn, 
		    INT4 id_z);
static IDPTR SetNot (IDPTR a, IDPTR b, INT4 an, INT4 bn, INT4 *cn, 
		     INT4 id_z);
static IDPTR SetAnd (IDPTR a, IDPTR b, INT4 an, INT4 bn, INT4 *cn, 
		     INT4 id_z);


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  declaration of global or module wide variables
*/

static SMoBUFF *buff=NULL;
static SETo    *set=NULL;



/**api* SetDump **************************************************************
**
**      dumps all information belonging to the specified object.
**      This is the print function set through LstManageClass
**      for set_type objects (see SetNew).
**
**      INPUT:      address of an object [R]
**                  file pointer [W] or NULL
**              IMPLICIT:
**
**      RETURNS:    nothing
*/

static void SetDump (FILE *file, void *obj)
{
    SETo *tmp = (SETo*)obj;

    if (!file)
      file = stderr;
    fprintf (file, "set *%s* with %d entries\n", tmp->nam, tmp->n);
}

/****** SetInit **************************************************************
**
**      initializes the specified object.
**      This is the init function set through LstManageClass
**      for set_type objects (see SetNew).
**
**      INPUT:      address of an object [R]
**              IMPLICIT:
**
**      RETURNS:    nothing
*/

static void SetInit (void *obj)
{
  SETo *tmp = (SETo*)obj;

  tmp->id_p = NULL;   /* dummy values */
  tmp->queryStr = NULL;
  tmp->tmp_f = FALSE;
  tmp->anal_f = 0;
  tmp->n = 0;
  tmp->idType = NULL; 
  tmp->allocN = 0;
  tmp->isDb = 0;
}

/****** SetKill **************************************************************
**
**      deletes the specified object.
**      This is the delete function set through LstManageClass
**      for set_type objects (see SetNew).
**
**      INPUT:      address of an object [R]
**              IMPLICIT:
**
**      RETURNS:    nothing
*/

static void SetKill (void *obj)
{
  SETo *tmp = (SETo*)obj;
  
  if (tmp->id_p)
    free (tmp->id_p);
  if (tmp->queryStr)
    StrDel (tmp->queryStr);
}


/**api* SetNew ****************************************************************
**
** 	Creates a new set with a unique name used as identifier.
** 	If called with option "temp" then a unique name is created and 
**      in case the address of set name is not NULL copied there.
**      Issues a message if set with specified name exists already.
**      <P>
**      A set can be deleted with SetDelete. SetClean deletes all
**      sets created with "temp".
**      Use SetGet to obtain an existing set by name.
** 
** 	INPUT:	    set name [W] or NULL
**                  option: "temp" (or NULL) [R]
** 	        IMPLICIT:
** 		    set (SETo *) [W]
** 
** 	RETURNS:    address of new set
** 		    NULL: specified set name is alredy in use 
*/ 
   
SETo *SetNew (char *setName, char *opt)
{
  static INT4 setclass_id=0;
  static INT4 setN=0;
  char        tmpName[SETxXNAM]; 

  if (!setclass_id) {
    LstManageClass (&setclass_id, sizeof (SETo), SetInit, SetKill, SetDump);
  }

  if (opt && opt[0] == 't') { /* "temp" */
    sprintf (tmpName, "tmpset_%d", ++setN);
    if (setName)
      strcpy (setName, tmpName);
  }
  else if (setName) {
    strcpy (tmpName, setName);
    SmEdit (tmpName, SMxLOWCASE);
  }
  
  if (!SetTestName (tmpName)) {
    _ErrMsg2 (e__setnotuniqname, tmpName);
    return NULL;
  }  
  LstNewNamed ((void **) &set, setclass_id, tmpName);
  set->tmp_f = (opt && opt[0] == 't') ? TRUE : FALSE;

  return set;
}



/**api* SetTestName ***********************************************************
**
** 	checks if set-name has not been previously defined or if name is 
**      reserved - issues a message if the case;
** 
** 	INPUT:	    address of name [R]
** 	        IMPLICIT:
** 		    set (SETo *) [R]
** 
** 	RETURNS:    1 if new
** 		    0 if not
*/ 
   
INT4 SetTestName (char *setName)
{
  LINKo *link;
  INT4  context;
  char  tmpName[80];

  strcpy (tmpName, setName);
  SmEdit (tmpName, SMxLOWCASE);

  if (LstHashSearch ((void **) &set, tmpName))
    return 0;
  /*  
  for (context=0; (link = LibNextLink (&context)); ) 
    if (SmEqs (tmpName, link->nam1) || SmEqs (tmpName, link->nam2)) 
      return 0;
      */
  return 1;
}


/**api* SetSetIsDb ***********************************************************
**
** 	Sets a flag in the set objects that it now represents an entire data
**      bank.
** 
** 	INPUT:	    set object [W]
**                  flag: TRUE or FALSE [R]
** 	        IMPLICIT:
** 		    set (SETo *) [R]
** 
** 	RETURNS:    
*/ 
   
void SetSetIsDB (SETo *set, Int4 flag)
{
  set->isDb = flag;
}

/**api* SetIsDb ***********************************************************
**
** 	Returns 'true' if the set represents an entire databank.
**      bank.
** 
** 	INPUT:	    set object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 or 0
*/ 
   
INT4 SetIsDB (SETo *set)
{
  return set->isDb;
}

/**api* SetGetName ************************************************************
**
** 	Returns the name of the set.
** 
** 	INPUT:	    set object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    set name
*/ 
   
char *SetGetName (SETo *set)
{
  return set->nam;
}



/**API* SetGet *************************************************************
**
** 	Searches for a set with specified name and returns its address
**      (case insensitive).
** 
** 	INPUT:	    set name [R]
** 	        IMPLICIT:
** 		    set (SETo *) [R]
** 
** 	RETURNS:    address of set object
** 		    NULL if not found
*/ 
   
SETo *SetGet (char *setName)
{
  char tmpName[80];

  strcpy (tmpName, setName);
  SmEdit (tmpName, SMxLOWCASE);

  if (!LstHashSearch ((void **) &set, tmpName))
    return NULL;

  if (set->anal_f && set->idType != NULL)      /* list libraries    */
    SetLibStat (set); 
  return set;
}

/**API* SetSize *************************************************************
**
** 	Returns the size of the set (number of IDs) with the specified name.
** 
** 	INPUT:	    set name [R]
** 	        IMPLICIT:
**
** 	RETURNS:    number of entries in the set
*/ 
   
INT4 SetSize (char *nam)
{
  SETo *set;

  if (!(set = SetGet (nam)))
    return 0;
  else
    return set->n;
}

/**API* SetGetSize ************************************************************
**
** 	Returns the size of the set (number of IDs).
** 
** 	INPUT:	    set object [R]
** 	        IMPLICIT:
**
** 	RETURNS:    number of entries in the set
*/ 
   
INT4 SetGetSize (SETo *set)
{
  return set->n;
}


/**API* SetIsSubEntry *********************************************************
**
** 	Returns 1 if the set contains subentry IDs.
** 
** 	INPUT:	    set name [R]
** 	        IMPLICIT:
**
** 	RETURNS:    1  
**                  0 if not
*/ 
   
INT4 SetIsSubEntry (char *nam)
{
  SETo *set;

  if (!(set = SetGet (nam)) || !set->idType)
    return 0;
  else
    return set->idType->siz > 4 ? 1 : 0;
}


/**API* SetRename *************************************************************
**
** 	Renames a set.
** 
** 	INPUT:	    set object [W]
**                  new name for the set [R]
** 	        IMPLICIT:
** 		    set (SETo *) [W]
** 
** 	RETURNS:    1: success
** 		    0: set name is already in use
*/ 
   
Int4 SetRename (SETo *set, char *newSetName)
{
  SmEdit(newSetName,SMxLOWCASE);
  
  if (!SetTestName(newSetName)) {
    _ErrMsg2 (e__setnotuniqname, newSetName);
    return 0;
  }
  
  if (!LstChangeObjectName(set, newSetName)) {
    return 0;
  }
  return 1;
}


/**API* SetDelete *************************************************************
**
** 	Deletes a Set with specified name.
** 
** 	INPUT:	    set name [R]
** 	        IMPLICIT:
** 		    set (SETo *) [W]
** 
** 	RETURNS:    1 if success
** 		    set name does not exist: e__novalnam <name> 
*/ 
   
INT4 SetDelete (char *setName)
{
  char tmpName[80];

  strcpy (tmpName, setName);
  SmEdit (tmpName, SMxLOWCASE);

  if (!LstHashSearch ((void **) &set, tmpName))
    _ErrRet(e__novalnam);

  LstDelete ((void **) &set);
  return 1;
}

INT4 SetDel (SETo *setPtr)
{
  if (!LstHashSearch ((void **) &set, setPtr->nam))
    _ErrRet(e__novalnam);
  LstDelete ((void **) &set);
}



/**api* SetClean **************************************************************
**
** 	Deletes all temporary sets;
** 
** 	INPUT:	    
** 	        IMPLICIT:
** 		    set (SETo *) [W]
** 
** 	RETURNS:    number of sets deleted
*/ 
   
INT4 SetClean ()
{
  INT4 setDeletedN=0;

  if (!set)
    return 0;
  LstFirst ((void **) &set);
  do {
    if (set->tmp_f) {
      LstDelete ((void **) &set);
      setDeletedN++;
    }
  } while (LstNext ((void **) &set));

  return setDeletedN;;
}

/**api* SetPrintAll *********************************************************
**
** 	Prints information on all sets in global list;
** 
** 	INPUT:	    
** 	        IMPLICIT:
** 
** 	RETURNS:    nothing
*/ 
   
void  SetPrintAll()
{
  LstPrintAll((void*)set);
}

/**api* SetAlloc **************************************************************
**
** 	allocates memory for a set of pointers;
** 
** 	INPUT:	    address of set descriptor [W]
** 		    number of IDs [R]
**                  id-Type object [R] or NULL
** 
** 	RETURNS:    1
** 		    e__allocfail <item> +
*/ 

INT4 SetAlloc (SETo *set, INT4 n, IDoTYPE *idType)
{
  if (idType)
    set->idType = idType;

  if ((set->id_p = (IDPTR) malloc (n * set->idType->siz)) == 0)
    _ErrRet2(e__allocfail, "set->ids by SetAlloc");
  set->allocN = n;
  return 1;
}

/**api* SetGetIdBuff **************************************************************
**
** 	Returns the pointer to an ID buffer with the specified size. In case
**      the set's existing ID buffer is not large enough it will be increased.
** 
** 	INPUT:	    set object [W]
** 		    number of bytes [R]
** 
** 	RETURNS:    address of ID-buffer
*/ 

IDPTR SetGetIdBuff (SETo *set, INT4 n)
{
  if (n > set->allocBytesN) {
    if (!set->allocBytesN) {
      if (!(set->id_p = (IDPTR) malloc (n)))
	_ErrExit2 (e__allocfail, "set ID buffer");
    }
    else {
      if (!(set->id_p = (IDPTR) realloc ((void*) set->id_p, n)))
	_ErrExit2 (e__allocfail, "set ID buffer");
    }
    set->allocBytesN = n;
  }
  return set->id_p;
}



/**api* SetAlloc **************************************************************
**
** 	Reallocates memory for a set of pointers;
** 
** 	INPUT:	    address of set descriptor [W]
** 		    number of IDs [R]
**                  id-Type object [R] or NULL
** 	        IMPLICIT:
** 
** 	RETURNS:    1
** 		    e__allocfail <item> +
*/ 

INT4 SetRealloc (SETo *set, INT4 n, IDoTYPE *idType)
{
  if (idType)
    set->idType = idType;

  if ((set->id_p = (IDPTR) realloc ((void*) set->id_p, n*set->idType->siz)) == 0)
    _ErrRet2(e__allocfail, "set->ids by SetRealloc");
  set->allocN = n;
  return 1;
}


/**api* SetSetEntryN **************************************************************
**
** 	Sets the number of the entries in the set.
** 
** 	INPUT:	    set object [W]
** 		    entry number [R]
*/ 

void SetSetEntryN (SETo *set, INT4 n)
{
  set->n = n;
}

/**api* SetSetEntryN **************************************************************
**
** 	Sets the number of the entries in the set.
** 
** 	INPUT:	    set object [W]
** 		    ID-type object [R]
*/ 

void SetSetIdType (SETo *set, IDoTYPE *idType)
{
  set->idType = idType;
}


/**API* SetGetNextLibStat *****************************************************
**
** 	Returns next pair of library name and number of entries of set.
**      This is useful information if a set is composed of IDs from 
**      different libraries.
** 
** 	INPUT:	    name of set [R]
**                  pointer to address of library name [W]
**                  iteration context (must be initially set to 0) [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    number of entries from library 
**                  0 if no more value pairs exist
*/ 
   
INT4 SetGetNextLibStat (char *setName, char **libName, INT4 *context)
{
  SETo *set;

  if (!(set = SetGet (setName)))
    return 0;

  if (!set->anal_f)
    SetLibStat (set);

  if (*context < 0 || *context >= set->lib_n) {
    *context = 0;
    return 0;
  }

  *libName = set->lib_nm[*context];
  return set->lib_z[(*context)++];
}


/**api* SetLibStat ************************************************************
**
** 	forms an array of number of ID's per library in a set + library name
** 	and connects array to set-descrptor; note that all ID's of a certain
** 	library are always clustered since ID-block is sorted.
** 
** 	INPUT:	    address of set-descriptor [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    nr of different sets found
*/ 
   
INT4 SetLibStat (SETo *set)
{
  SLBo          *lib;
  unsigned char idPtrSave = 255;
  IDoENTRY      *id;{
  IDPTR         idPtr;
  INT4		k, n=0, siz, libN = 0;

  if (!set->n || set->anal_f)
    return 0;

  siz = set->idType->siz;

  for (k=0, idPtr=set->id_p+set->idType->lbxbeg; k < set->n; k++, idPtr += siz)
    if ((unsigned char ) *idPtr != idPtrSave) { 
      idPtrSave = *idPtr;

      /* if ID is subentry-ID find subentry lib */
      id = IdMakeFromBuff (idPtr, set->idType);
      lib = (SLBo *) LibObjById ("library", *idPtr);
      if (IdIsSub (id))
	lib = LibGetSubEntryLib (lib, IdGetSubN (id));
      
      set->lib_nm[libN] = LibName (lib);
      if (libN > 0) {
	set->lib_z[libN-1] = k-n;
	n = k;
      }	
      n = k;
      libN++;
    }
  
  set->lib_z[libN-1] = k-n;
  set->lib_n = libN;
  set->anal_f = 1;
  return 1;
  }
}


/**api* SetMakeOwn ************************************************************
**
** 	allocates storage for a set that is parked in global storage or some
**      other storage and copies it there.
** 
** 	INPUT:	    address of set-descriptor [W]
** 		    address of id-descr. set will receive [R] or NULL
** 	        IMPLICIT:
** 
** 	RETURNS:    1
** 		    e__allocfail <item> +
*/ 
   
INT4 SetMakeOwn (SETo *set, IDoTYPE *idType)
{
  IDPTR id_p;
  INT4 siz;
  
  if (idType)
    set->idType = idType;

  if (!set->idType)
    _ErrRet (e__error);

  siz = set->n * set->idType->siz; /*PURIFY*/ 

  if (siz) {
    if ((id_p = (IDPTR) malloc (siz)) == 0)
      _ErrRet2(e__allocfail, "ids-block by SetMakeOwn");
    memcpy (id_p, set->id_p, set->n * set->idType->siz);
  }
  else
    id_p = NULL;

  set->id_p = id_p;
  return 1;
}


/**api* SetSort ***************************************************************
**
** 	heapsort the IDs in a set
** 
** 	INPUT:	    set object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
** 		    e__allocfail <item> +
*/ 

INT4 SetSort (SETo *set)
{
  SetHeapSort (set->id_p, set->n, set->idType->siz, 0, set->idType->siz);
  SetRemoveDouble (set->id_p, set->n, set->idType->siz, &set->n);
  return 1;
}



/**api* SetOp *****************************************************************
**
** 	Performs logical operations AND, OR, NOT with sets of same type;
** 	if addres of resultant set is NULL then set a is replaced by resultant
** 	set "a" and memory held previously by set a is freed.
** 
** 	INPUT:	    address of set a [W]
** 		    address of set b [R]
** 		    address of result set [W] (or NULL)
** 		    operator: SETxAND, SETxOR, SETxNOT [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1 if success
**                  0 i both sets empty
** 		    invalid set types: e__novalsettyp <type A, type B-names> +
** 		    invalid set operator: e__novalopt <opt, optnam> +
*/ 

INT4 SetOp (SETo *a, SETo *b, SETo *resultSet, INT4 op)
{
  IDPTR   idPtr;
  INT4    n;

  /*
  ** both sets are empty ...might not even have
  ** ID descriptors since, if from unsuccessful index search, were never set.
  */

  if (a->n == 0 && b->n == 0)
    return 0;

  /* 
  ** get the id descriptor from either of the two sets - it might not be
  ** defined for either;
  */

  if (!b->idType)
    b->idType = a->idType;
  if (!a->idType)
    a->idType = b->idType;
  if (a->idType != b->idType)
    _ErrRet3 (e__novalsettyp, a->idType->nam, b->idType->nam);


  switch (op) {
  case SETxOR:
    idPtr = SetOr (a->id_p, b->id_p, a->n, b->n, &n, a->idType->siz);
    break;
  case SETxAND:
    idPtr = SetAnd (a->id_p, b->id_p, a->n, b->n, &n, a->idType->siz);
    break;
  case SETxNOT:
    idPtr = SetNot (a->id_p, b->id_p, a->n, b->n, &n, a->idType->siz);
    break;
  default:
    _ErrRet3(e__novalopt, op, "logical operator");
  }  

  if (!resultSet) {
    if (a->id_p && (a->id_p != b->id_p))
      free (a->id_p);
    resultSet = a;
  }

  resultSet->n = n;
  resultSet->id_p = idPtr;
  SetMakeOwn (resultSet, a->idType);
  return 1;
}




/**API* SetGetID **************************************************************
**
** 	Retrieves the ID with the specified number from the specified set.
**      The first ID in set has the number 1. See also SetNextId.
** 
** 	INPUT:	    address of set object [R]
**                  ID number within set [R]
**                  address of output id-object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
**                  0 if the ID number is out of range
*/ 

INT4 SetGetID (SETo *set, INT4 n, IDoENTRY *id)
{
  if (n < 1 || n > set->n)
    return 0;

  id->idType = set->idType;
  id->siz = set->idType->siz;

  memcpy (id->id, set->id_p + --n * id->siz, id->siz);
  IdSplit (id);
  return 1;
}

/**API* SetNextId **************************************************************
**
** 	Iterates over all IDs in the set. 
**      See also SetGetID.
** 
** 	INPUT:	    address of set [R]
**                  address of output ID object [W]
**                  address of iterator (must be set to 0 to start) [W]
** 
** 	RETURNS:    the ID object
**                  NULL: set exhausted
*/ 

IDoENTRY *SetNextId (SETo *set, IDoENTRY *id, INT4 *i)
{
  if (*i < set->n) {
    id->idType = set->idType;
    id->siz = set->idType->siz;
    memcpy (id->id, set->id_p + *i * id->siz, id->siz);
    IdSplit (id);
    (*i)++;
    return id;
  }
  else {
    *i = 0;
    return NULL;
  }
}

ENTRYv SetGetEntry (SETo *set, Int4 i)
{
  IDoENTRY id;
  ENTRYv entry;

  SetGetID (set, i, &id);
  entry = EntryOpen (&id);
  return entry;
}



/**API* SetAddID **************************************************************
**
**      Adds an entry ID to an existing set.	
** 
** 	INPUT:	    address of set object [W]
**                  address of id-object describing the ID to be added [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
** 		    allocation error: e__allocfail <item> +
*/ 

INT4 SetAddID (SETo *set, IDoENTRY *id)
{
  IDoTYPE *idType;

  /*
  ** get the ID-descriptor and copy it to the set if it doesn't have one
  */

  if (set->idType)
    idType = set->idType;
  else if (id->idType) {
    idType = id->idType;
    set->idType = idType;
  }
  else 
    return 0;

  /*
  ** allocate more space if needed
  */

  if (set->allocN == set->n)
    if (set->n == 0)
      _ErrStop (SetAlloc (set, 1, set->idType));
  else {
    set->allocN = set->allocN * 2;
    set->id_p = (IDPTR) realloc (set->id_p, (set->allocN) * idType->siz);
  }
  memcpy (set->id_p + (set->n++ * idType->siz), id->id, idType->siz);

  return 1;
}


/**API* SetGetQueryStr ********************************************************
**
** 	Returns the query string that is associated to the specified set.
** 
** 	INPUT:	    set name [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    query string
**                  NULL if the set could not be found
*/ 

char *SetGetQueryStr (char *setName)
{
  SETo *set;
  char *tmp;

  if (!(set = SetGet (setName)))
    return NULL;

  return _Str(set->queryStr);
}


/**API* SetGetQuery ***********************************************************
**
** 	Returns the query string that is associated to the specified set.
** 
** 	INPUT:	    set name [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    query string
**                  NULL if the set could not be found
*/ 

char *SetGetQuery (SETo *set)
{
  return "does not work yet";
}





/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */





/***** SetOr *****************************************************************
**
**	does logical OR operation between to sets and writes a third set;
**
**	INPUT:	    address of first element of first set [R]
**	            address of first element of second set [R]
**		    number of elements in a [R]
**		    number of elements in b [R]
**		    location that will receive number of elements in c [W]
**		    element size in bytes [R]
**	        IMPLICIT:
**                  buff (SMoBUFF *) [W]
**
**	RETURNS:
*/ 
   
static IDPTR SetOr (IDPTR a, IDPTR b, INT4 an, INT4 bn,  INT4 *resultN, 
		    INT4 idSize)
{
  IDPTR a_p=a, b_p=b, a_low=a, b_low=b;		    
  IDPTR a_end=a_p + an * idSize, b_end=b_p + bn * idSize;
  INT4  len, cmp, k, inc = idSize-1;

  _SetInitBuff (buff);

  while (a_p < a_end && b_p < b_end) {
    for (k = inc; k >= 0; k--) {
      if ((cmp = a_p[k] - b_p[k]) != 0)
	break;
    }
	
    if (cmp == 0) {  /* equal */
      if (b_low != SETxNOCPY) {
	_SetCopyIds (buff, b_low, b_p, len)
	b_low = SETxNOCPY;
	a_low = a_p;
      }
      a_p += idSize;
      b_p += idSize;
    }
    else if (cmp < 1) {  /* smaller */
      if (b_low != SETxNOCPY) {
	_SetCopyIds (buff, b_low, b_p, len)
	b_low = SETxNOCPY;
	a_low = a_p;
      }
      a_p += idSize;
    }
    else {  /* bigger */
      if (a_low != SETxNOCPY) {
	_SetCopyIds (buff, a_low, a_p, len)
	a_low = SETxNOCPY;
	b_low = b_p;
      }
      b_p += idSize;
    }
  }

  if (a_low != SETxNOCPY) {  /* collect the rest */
    _SetCopyIds (buff, a_low, a_end, len)
    if (b_p != b_end) {
      _SetCopyIds (buff, b_p, b_end, len)
    }
  }
  else {
    _SetCopyIds (buff, b_low, b_end, len)
    if (a_p != a_end) {
      _SetCopyIds (buff, a_p, a_end, len)
    }
  }
  *resultN = BuffGetCurrOffset (buff) / idSize;
  return (IDPTR) BuffGetPtr (buff);
}



/****** SetNot ****************************************************************
**
**	does logical AND NOT operation between to sets and writes a third set;
**
**	INPUT:	    address of first element of first set [R]
**	      	    address of first element of second set [R]
**		    number of elements in a [R]
**		    number of elements in b [R]
**		    location that will receive number of elements in c [W]
**		    element size in bytes [R]
**	        IMPLICIT:
**                  buff (SMoBUFF *) [W]
**
**	RETURNS:    1
*/ 
   
static IDPTR SetNot (IDPTR a, IDPTR b, INT4 an, INT4 bn, INT4 *resultN, 
		     INT4 idSize)
{
  IDPTR a_p= a, b_p=b, a_low=a, b_low=b;		    
  IDPTR a_end=a_p + an * idSize, b_end=b_p + bn * idSize;
  INT4  len, cmp, k, inc=idSize-1;

  _SetInitBuff (buff);

  while (a_p < a_end && b_p < b_end) {
    for (k = inc; k >= 0; k--) {
      if ((cmp = a_p[k] - b_p[k]) != 0)
	break;
    }
	
    if (cmp == 0) {  /* equal */
      if (a_low != SETxNOCPY) {
	_SetCopyIds (buff, a_low, a_p, len)
	a_low = SETxNOCPY;
	b_low = b_p;
      }
      a_p += idSize;
      b_p += idSize;
    }
    else if (cmp < 1) {  /* smaller */
      if (b_low != SETxNOCPY) {
	b_low = SETxNOCPY;
	a_low = a_p;
      }
      a_p += idSize;
    }
    else {  /* bigger */
      if (b_low != SETxNOCPY) {
	b_low = SETxNOCPY;
	a_low = a_p;
      }
      b_p += idSize;
    }
  }
  
  if (a_low != SETxNOCPY) { /* collect rest */
    _SetCopyIds (buff, a_low, a_end, len)
  }
  else {
    _SetCopyIds (buff, a_p, a_end, len)
  }
  *resultN = BuffGetCurrOffset (buff) / idSize;
  return (IDPTR) BuffGetPtr (buff);
}



/****** SetAnd ****************************************************************
**
**	Does logical AND operation between to sets and writes into third set.
**
**	INPUT:	    address of first element of first set [R]
**	            address of first element of second set [R]
**		    number of elements in a [R]
**		    number of elements in b [R]
**		    location that will receive number of elements in c [W]
**		    element size in bytes [R]
**	        IMPLICIT:
**                  buff (SMoBUFF *) [W]
**
**	RETURNS:    
*/ 
   
static IDPTR SetAnd (IDPTR a, IDPTR b, INT4 an, INT4 bn, INT4 *resultN, 
		     INT4 idSize)
{
  IDPTR a_p=a, b_p=b, a_low=a, b_low=b;		    
  IDPTR a_end=a_p+an*idSize, b_end=b_p+bn*idSize;
  INT4  len, cmp, k, inc=idSize-1;

  _SetInitBuff (buff);

  while (a_p < a_end && b_p < b_end) {
    for (k = inc; k >= 0; k--) {
      if ((cmp = a_p[k] - b_p[k]) != 0)
	break;
    }
    
    if (cmp == 0) {  /* equal */
      if (b_low != SETxNOCPY) {
	b_low = SETxNOCPY;
	a_low = a_p;
      }
      a_p += idSize;
      b_p += idSize;
    }
    else if (cmp < 1) {  /* less */
      if (a_low != SETxNOCPY) {
	_SetCopyIds (buff, a_low, a_p, len)
	a_low = SETxNOCPY;
	b_low = a_p;
      }
      a_p += idSize;
    }
    else {  /* bigger */
      if (a_low != SETxNOCPY) {
	_SetCopyIds (buff, a_low, a_p, len)
	a_low = SETxNOCPY;
	b_low = b_p;
      }
      b_p += idSize;
    }
  }

  if (a_low != SETxNOCPY) {  /* get rest */
    _SetCopyIds (buff, a_low, a_p, len)
  }

  *resultN = BuffGetCurrOffset (buff) / idSize;
  return (IDPTR) BuffGetPtr (buff);
}




/**api* SetMapIds *************************************************************
**
**	similar to SetAnd but more general -> 
**      copies all elements from set "a" that have a map-region owned
**      by at least one element in set "b"; resultant set "c" will
**      therefore contain a subset of set "a"
**      though part of ID used for mapping is variable it defaults to 4 bytes
**      here -> modify the "cmp =..." line so that the compared values
**      are shifted by (4-mlen)*8 bits to the right -> 4 byte would then
**      be the largest map-length,
**
**	INPUT:	    address of first element of first set [R]
**	            address of first element of second set [R]
**		    number of elements in a [R]
**		    number of elements in b [R]
**		    location that will receive number of elements in c [W]
**		    ID-size in bytes of first set [R]
**		    ID-size in bytes of second set [R]
**                  offset of join region in first set's ID [R]
**                  offset of join region in second set's ID [R]
**                  length of join region [R]
**	        IMPLICIT:
**                  buff (SMoBUFF *) [W]
**
**	RETURNS: 
*/ 
   
IDPTR SetMapIds (IDPTR a, IDPTR b, INT4 an, INT4 bn, INT4 *resultN, 
             INT4 aidSize, INT4 bidSize, INT4 amoff, INT4 bmoff, INT4 mlen)
{
  IDPTR a_p=a, b_p=b;
  IDPTR a_end=a_p+an*aidSize, b_end=b_p+bn*bidSize;
  INT4  cmp;
  
  _SetInitBuff (buff);

  while (a_p < a_end && b_p < b_end) {
    CMP (a_p + amoff, b_p + bmoff, cmp, 4)
    if (cmp == 0) {  /* equal */
      _BuffCopyNChars (buff, a_p, aidSize) 
      a_p += aidSize;
    }
    else if (cmp < 1) /* less */
      a_p += aidSize;
    else  /* bigger */
      b_p += bidSize;
  }
  *resultN = BuffGetCurrOffset (buff) / aidSize;
  return (IDPTR) BuffGetPtr (buff);
}


/**api* SetMapToParent ********************************************************
**
** 	Takes a set of subentry IDs, removes the subentry-no and removes
** 	redundant elements;
**      length of PARENT-ID should be variable but is here always 4 byte!
** 
** 	INPUT:	    address of ID-block [R]
** 		    nr of IDs [R]
** 		    adress of nr of IDs in resultant set [W]
**                  size of CHILD-ID [R]
** 		    offset of PARENT-ID [R]
** 		    length of PARENT-ID [R]
** 	        IMPLICIT:
**                  buff (SMoBUFF *) [W]
** 
** 	RETURNS:    1
*/ 
   
IDPTR SetMapToParent (IDPTR a, INT4 a_n, INT4 *resultN, INT4 siz, INT4 off, 
		      INT4 len)
{
  UINT4 id_s, id;
  IDPTR id_p;
  INT4  k, cmp;

  _SetInitBuff (buff);

  id_s = SETxNULL;
  for (k=0, id_p=a;  k < a_n;  k++, id_p = id_p + siz) {
    memcpy (&id, (id_p + off), sizeof (UINT4));
    if (k > 0) {
      CMP ((IDPTR) &id, (IDPTR) &id_s, cmp, 4);
    }
    else {
      cmp = -1;
    }
    if (cmp != 0) {
      id_s = id;
      _BuffCopyNChars (buff, &id, sizeof (UINT4)) 
    }
  }
  *resultN = BuffGetCurrOffset (buff) / sizeof (UINT4);
  return (IDPTR) BuffGetPtr (buff);
}


/**api* SetLink ***************************************************************
**
**     similar to SetMapIds but more specialized -> 
**     compares entry-ID with link ID and creates a sorted set of 
**     linked ID's (the part of the link ID that was not used for
**     comparison);
**
**	INPUT:	    address of first element of first set [R]
**	            address of first element of second set [R]
**		    address of buffer reserved for third set [W]
**		    number of elements in a [R]
**		    number of elements in b [R]
**		    location that will receive number of elements in c [W]
**                 1 or 2 copare
**	        IMPLICIT:
**                  buff (SMoBUFF *) [W]
**
**	RETURNS:    1
*/ 
   
IDPTR SetLink (IDPTR a, INT4 a_n, IDPTR b, INT4 b_n, INT4 *resultN, INT4 rev_f)
{
  IDPTR aPtr=a, bPtr, aEnd, bEnd;
  INT4	cmp, shift;

  _SetInitBuff (buff);

  bPtr = b + (rev_f ? 4 : 0);
  aEnd = a +  a_n*4; 
  bEnd = b + (b_n * 2)*4;
  shift = rev_f ? -4 : 4;
  
  while (aPtr < aEnd && bPtr < bEnd) {
    CMP (aPtr, bPtr, cmp, 4);
    if (cmp == 0) {  /* equal */
      _BuffCopyNChars (buff, (bPtr + shift), 4) 
      bPtr += 2*4;
    }
    else if (cmp < 1) /* less */
      aPtr += 4;
    else  /* bigger */
      bPtr += 2*4;
  }

  *resultN = BuffGetCurrOffset (buff) / 4;
  SetHeapSort ((IDPTR) BuffGetPtr (buff), *resultN, 4, 0, 4); 
  return (IDPTR) BuffGetPtr (buff);
}


/**api* SetCutLink ************************************************************
**
**	Cuts either first or second ID from each link ID and writes it
**	into result set. Set is always sorted.
**      Function assumes that entry ID's within link-ID's are always 4 byte 
**      long (will have to be changed as soon as subentry-IDs will be involved
**      in links!!)
**
**	INPUT:	    address of set with link-IDs [R]
**		    number of ID's in set [R]
**		    address of number of IDs in result set [W]
**                  reverse flag [R]
**	        IMPLICIT:
**                  buff (SMoBUFF *) [W]
**
**	RETURNS:    1
*/ 
   
IDPTR SetCutLink (IDPTR a, INT4 a_n, INT4 *resultN, INT4 rev_f)
{
  IDPTR aPtr, aEnd;

  _SetInitBuff (buff);

  aPtr = a + (rev_f ? 0 : 4); 
  aEnd = 8 * a_n + a;
  for (;  aPtr < aEnd;  aPtr+=8)
    _BuffCopyNChars (buff, aPtr, 4) 

  *resultN = BuffGetCurrOffset (buff) / 4;
  return (IDPTR) BuffGetPtr (buff);
}


/**api* SetRemoveDouble *******************************************************
**
** 	removes duplicates from a set of IDs;
** 
** 	INPUT:	    address of input set [R/W]
** 		    address of output set [W] may be the same as input set
** 		    size of input set [R]
** 		    address to place size of output set [W]
** 		    ID-size [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
**/ 
   
INT4 SetRemoveDouble (IDPTR idPtr, INT4 idN, INT4 idSize, INT4 *resultN)
{
  IDPTR off, last, out;
    
  if (idN == 0) {
    *resultN = 0;
    return 0;
  }
  off = idPtr + idSize;
  last = idPtr + idN * idSize;
  out = idPtr + idSize;
  for (;  off < last;  off += idSize)
    if (memcmp (off, out-idSize, idSize) != 0) {
      memcpy (out, off, idSize);
      out += idSize;
    }
  *resultN = (out - idPtr) / idSize;
  return 1;
}


/**api* SetCountKey **********************************************************
**
** 	counts the number of unique keys within ID ...assumes that the set
**      is sorted after the key to be counted;
** 
** 	INPUT:	    address of input set [R]
** 		    size of input set [R]
** 		    size of ID [R]
** 		    size of key [R]
** 		    offset of key within set [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
**/ 
   
INT4 SetCountKey (IDPTR idPtr, INT4 idN, INT4 idSize, INT4 keyOff, 
		  INT4 keySize)
{
  INT4 keyN=0;
  char *tmp, *tmpSave=NULL;

  for (tmp = (char*)(idPtr + idSize * (idN-1) + keyOff); tmp >= (char*) idPtr; 
       tmp -= idSize) 
    if (!keyN || memcmp (tmp, tmpSave, keySize) != 0) {
      keyN++;
      tmpSave = tmp;
    }    
  return keyN;
}

/**api* SetHeapSort ***********************************************************
**
** 	uses "sort" from Numerical Recipies in C, p 247;
** 	sorts an array of ID's using a key-number within the ID with specified
** 	begin and length;
**      Note that the base of array is shifted by one element to make the
**      first element the element with index=1;
** 
** 	INPUT:	    base address of array [W]
** 		    number of elements [R]
** 		    size of ID [R]
** 		    offset of sorting key in ID [R]
** 		    length of sorting key [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
*/ 
   
INT4 SetHeapSort (IDPTR ra, INT4 n, INT4 siz, INT4 beg, INT4 len)
{
  INT4		k, l, j, ir, i, cmp;
  unsigned char rra[SETxXID];
  IDPTR         a_p, b_p;

  if (n <= 1)
    return 0;  /* nothing to sort */
  
  ra = ra - siz; /* num recipies start with "1" as first index in array */

  l = (n >> 1) + 1;
  ir = n;
  
  for (;;) {
    if (l > 1)
      memcpy (rra, ra + --l * siz, siz);
    else {
      memcpy (rra, ra + ir * siz, siz);
      memcpy (ra + ir * siz, ra + 1 * siz, siz);
      if (--ir == 1) {
	memcpy (ra + 1 * siz, rra, siz);
	return 1;
      }
    }
    i = l;
    j = l << 1;
    while (j <= ir) {
      for (k=beg+len-1, a_p = ra + j*siz, b_p = ra + (j+1)*siz; 
	   k >= beg; k--) {
	if ((cmp = a_p[k] - b_p[k]) != 0)
	  break;
      }
      if (j < ir && cmp < 0)
	++j;
      
      for (k=beg+len-1, a_p = rra,  b_p = ra + j*siz; k >= beg; k--) {
	if ((cmp = a_p[k] - b_p[k]) != 0)
	  break;
      }
      if (cmp < 0) {
	memcpy (ra + i*siz, ra+j*siz, siz);
	j += (i = j);
      }
      else
	j = ir + 1;
    }
    memcpy (ra + i * siz, rra, siz);
  }
}				












   j = l << 1;
    while (j <= ir) {
      for (k=beg+len-1, a_p = ra + j*siz, b_p = ra + (j+1)*siz; 
	   k >= beg; k--) {
	if ((cmp = a_p[k] - b_p[k]) != 0)
	  break;
      }
      if (j < ir && cmp < 0)
	++j;
      
      for (k=beg+len-1, a_p = rra,  b_p = ra + j*siz; k >= beg; k--) {
	if ((cmp = a_p[k] - b_p[k]) != 0)
	  break;
      }
      if (cmp < 0) {
	memcpy (ra + i*siz, ra+j*siz, siz);
	j += (i = j);
      }
      else
	j = ir + 1;
    }
    memcpy (ra + i * siz, rrasrs/src/set.h
**
**    $RCSfile: set.h,v $
**    $Revision: 1.7 $
**    $Date: 1997/03/03 18:20:52 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
*/


#define SETxXKEY	80    /* max key size */
#define SETxXNAM	20    /* max size of set name */
#define SETxXCMNT	132   /* max size of set description */
#define SETxXID		12    /* max len of ID */
#define SETxXLIBS	64    /* max no of source libraries of a set */

enum set_op {SETxOR=40, SETxAND, SETxNOT};


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Description of a set.
*/

typedef struct SETo {
  char            *list;              /* for usage of module "list" only! 
					 should be (void *) but the gdb... */
  INT4            class_id;           /* for "list" module */  
  char	          nam[SETxXNAM];      /* (API) name of set */
  char	          cmnt[SETxXCMNT];    /* set description */
  struct STRo     *queryStr;          /* query string used to generate set*/
  char	          time[SETxXNAM];     /* (API) creation time */
  INT4	          n;		      /* number of IDs */
  struct IDoTYPE *idType;              /* pointer to ID descriptor */
  IDPTR	          id_p;	              /* array of IDs */
  INT4	          lib_n;              /* no of different source libraries */
  char	          *lib_nm[SETxXLIBS]; /* names of these libraries */
  INT4	          lib_z[SETxXLIBS];   /* how many IDs of each library? */
  INT4	          anal_f;             /* flag if libraries were counted */ 
  INT4            tmp_f;              /* flag if set is for temporary use */
  INT4            allocN;             /* allocated space for n Ids */
  INT4            isDb;               /* flag if set represents a databank */
  Int4            allocBytesN;        /* number of allocated bytes */
} SETo;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of exported functions
*/

    /* operations on sets */

SETo *SetNew (char *nam, char *opt);
SETo *SetGet (char *nam);
INT4 SetDelete (char *nam);
INT4 SetSort (SETo *set);
Int4 SetRename (SETo *set, char *newSetName);
INT4 SetClean ();
void SetPrintAll ();
INT4 SetOp (SETo *a, SETo *b, SETo *c, INT4 op);

  /* info about set */

INT4 SetSize (char *setName);
INT4 SetIsSubEntry (char *setName);
INT4 SetGetNextLibStat (char *setName, char **libName, INT4 *context);
char *SetGetQueryStr (char *setName);
char *SetGetQuery (SETo *set);
char *SetGetName (SETo *set);
INT4 SetGetSize (SETo *set);
struct ENTRYo *SetGetEntry (SETo *set, Int4 i);
 
  /* modify set */

void SetSetIdType (SETo *set, struct IDoTYPE *idType);
void SetSetEntryN (SETo *set, INT4 n);
IDPTR SetGetIdBuff (SETo *set, INT4 n);

    /* allocation */

INT4 SetAlloc (SETo *set, INT4 n, struct IDoTYPE *idType);
INT4 SetRealloc (SETo *set, INT4 n, struct IDoTYPE *idType);
INT4 SetMakeOwn (SETo *set, struct IDoTYPE *idType);

    /* handling IDs in sets */

INT4 SetGetID (SETo *set, INT4 n, struct IDoENTRY *id);
struct IDoENTRY *SetNextId (SETo *set, struct IDoENTRY *id, INT4 *i);
INT4 SetAddID (SETo *set, struct IDoENTRY *id);

    /* others ... */

void SetSetIsDB (SETo*, Int4);
INT4 SetIsDB (SETo *set);
INT4 SetLibStat (SETo *set);
INT4 SetTestName (char *nam);
IDPTR SetMapIds (IDPTR a, IDPTR b, INT4 an, INT4 bn, INT4 *cn, 
		 INT4 aid_z, INT4 bid_z, INT4 amoff, INT4 bmoff, INT4 mlen);
IDPTR SetMapToParent (IDPTR a, INT4 a_n, INT4 *c_n, INT4 siz, INT4 off, 
		      INT4 len);
IDPTR SetLink (IDPTR a, INT4 a_n, IDPTR b, INT4 b_n, INT4 *resultN,INT4 rev_f);
IDPTR SetCutLink (IDPTR a, INT4 a_n, INT4 *resultN, INT4 rev_f);
INT4 SetRemoveDouble (IDPTR a, INT4 a_n, INT4 id_z, INT4 *b_n);
INT4 SetHeapSort (IDPTR ra, INT4 n, INT4 siz, INT4 beg, INT4 len);
INT4 SetCountKey (IDPTR idPtr, INT4 idN, INT4 idSize, INT4 keyOff, 
		  INT4 keySize);
4 aid_z, INT4 bid_z, INT4 amoff, INT4 bmoff, INT4 mlen);
IDPTR SetMapToParent (IDPTR a, INT4 a_nsrs/src/sm.c
char sm__ID[] = "$Id: sm.c,v 1.5 1996/11/27 19:45:26 weare Exp $";
/*
**
**    $RCSfile: sm.c,v $
**    $Revision: 1.5 $
**    $Date: 1996/11/27 19:45:26 $
**    $Author: weare $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     D-69012 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: file, sm, message 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    contains functions for string manipulation
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#define DEBUGNOT

#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include <string.h>
/*#include <stdarg.h>*/
#include <time.h>

#include "message.h"
#include "sm.h"
#include "lst.h"
#include "regexp.h"


#define _BuffIncWrite(buff,len)   (buff)->writePtr += (len)
#define _BuffIncRead(buff,len)   (buff)->readPtr += (len)

 void SmMemMove (char *to, char *from, int len);


/****** SmCharSet *************************************************************
**
**	decodes strings used to describe character set;
**     "A-Da-d" -> "ABCDabcd"
**     "\-" -> "-" 
**
**	INPUT:	    address of string [W]
**	        IMPLICIT:
**
**	RETURNS:    address of expanded charset string
**                  
*/ 
   
char *SmCharSet (char *s)
{
  char *loc, tmpa[512+1], tmpb[512+1];
  INT4 k;

  for (loc=s; (loc = strchr (loc, '-')) != NULL; loc++) {
    if (*(loc-1) == '\\') 
      continue;
    
    if (loc == s || *(loc+1) == '\0' || *(loc-1) >= *(loc+1))
      _ErrExit (e__novalterm);
	
	memcpy (tmpa, loc-1, 3);	    
    tmpa[3] = '\0';
    for (k=1, tmpb[0] = *(loc-1);  tmpb[k-1] < *(loc+1);  k++)
      tmpb[k] = tmpb[k-1] + 1;
    tmpb[k] = '\0';
    SmSwapS (s, tmpa, tmpb);
  }	    
  while (SmSwapS (s, "\\-", "-"))
    ;
  return s;
}




/**api* SmFill ****************************************************************
**
**
**  	writes the specified number specified character into string address
**  
**  	INPUT:	    address of string [W]
**  		    number of characters to write [R]
**  		    character to write [R]
**  
**  	RETURNS:    1
*/

char *SmFill (char *str, INT4 n, char c)
{
  INT4 k;

  for (k = 0;  k < n;  str[k++] = c)
    ;
  str[k] = '\0';
  return str;
} 



/**api* SmLoc *****************************************************************
**
**  	return index of string t in string s, -1 if none;
**  
**  	INPUT:	    address of string1 [R]
**  		    address of string2 that is searched in string1 [R]
**  
**  	RETURNS:    index of string2 in string1
**  		    -1 if not there
*/

INT4 SmLoc(char *str1, char *str2)
{
  INT4	i, j, k;

  for (i = 0;  str1[i] != '\0';  i++) {
    for (j = i, k = 0;  str2[k] != '\0' && str1[j] == str2[k];  j++, k++)
      ;
    if (k > 0 && (str2[k] == '\0' || *str2 == '\0'))
      return i;
  }
  return -1;
}


/****** SmXLoc ****************************************************************
**
**	searches string1 for occ. of string2 starting from first index
**	until the second; if found then string2 is replaced by blanks in 
**	string1;
**
**	INPUT:	    address of string1
**		    address of string2 that is searched in string1
**		    index where to start (first in string is 1)
**		    index where to stop (first in string is 1)
**
**	RETURNS:    index of string2 in string1
**		    -1 if not there
*/

INT4 SmXLoc(char *str1, char *str2, INT4 l, INT4 r)
{
  INT4	i, j, k;

  for (i = --l;  str1[i] != '\0' && i < r;  i++) {
    for (j = i, k = 0;  str2[k] != '\0' && str1[j] == str2[k];  j++, k++)
      ;
    if (k > 0 && (!str2[k] || !*str2)) {
      while (j > i)
	str1[--j] = ' ';
      return i;
    }
  }
  return -1;
}

/****** SmMixLoc **************************************************************
**
**	same as SmXLoc but case insensitive; does no blotting out
**
**	INPUT:	    address of string1
**		    address of string2 that is searched in string1
**		    index where to start (first in string is 1)
**		    index where to stop (first in string is 1)
** 
**	RETURNS:    index of string2 in string1
**		    -1 if not there
*/

INT4 SmMixLoc(char *str1, char *str2, INT4 l, INT4 r)
{
  INT4	i, j, k;
  
  for (i = --l;  str1[i] != '\0' && i < r;  i++) {
    for (j = i, k = 0;  str2[k] != '\0' && 
	 (isalpha (str1[j]) ? toupper (str1[j]) : str1[j]) == 
	 (isalpha (str2[k]) ? toupper (str2[k]) : str2[k]);  j++, k++)
      ;
    if (k > 0 && (str2[k] == '\0' || *str2 == '\0'))
      return i;
  }
  return -1;
}


/**api* SmStrCmp **************************************************************
**
**  	same as strcmp - but case insensitive 
**      
**  
**  	INPUT:	    string 1 [R]
**  		    string 2 [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    difference of first characters that differ 
**                  0 if equal
**  		    
*/ 
   
INT4 SmStrCmp (char *a, char *b)
{
  for (; *a && *b; a++, b++)
    if (tolower (*a) != tolower (*b))
      break;
  return (tolower (*a) - tolower (*b));
}


/**api* SmStrCmpLen ***********************************************************
**
**  	same as SmStrCmp but continues comparison until specified length
**      is reached;
**  
**  	INPUT:	    string 1 [R]
**  		    string 2 [R]
**                  comparison length [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    difference of first characters that differ 
**                  0 if equal
*/ 
   
INT4 SmStrCmpLen (char *a, char *b, INT4 len)
{
  for (; *a && *b && len; a++, b++, len--)
    if (tolower (*a) != tolower (*b))
      break;
  return !len ? 0 : (tolower (*a) - tolower (*b));
}



/**api* SmRStrCmp *************************************************************
**
**  	same as strcmp - but case insensitive (strings are converted to
**      uppercase first)
**      once above replacement is done then SmRStrCmp may be called SmStrCmp
**  
**  	INPUT:	    string 1 [R]
**  		    string 2 [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    positive no if string 1 is greater (alphab.)
**  		    negative if string 2 is less
**                  0 if both strings are equal
*/ 
   
INT4 SmRStrCmp (char *a, char *b)
{
  INT4 cmp; 

  while (1) {
    if ((cmp = toupper (*a) - toupper (*b)) != 0)
      return cmp;
    if (!*a && !*b)
      return 0;
    a++, b++;
  }
}

/**api* SmRStrCmpLen **********************************************************
**
**  	same as SmRStrCmpLen - but a length can be set where string comparison
**      should stop; if the two strings are identical until length the
**      0 is returned;
**
**  	INPUT:	    string 1 [R]
**  		    string 2 [R]
**                  length - comparison stops after length is reached [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    positive no if string 1 is greater (alphab.)
**  		    negative if string 2 is less
**                  0 if both strings are equal
*/ 
   
INT4 SmRStrCmpLen (char *a, char *b, INT4 len)
{
  INT4 cmp; 

  while (len--) {
    if ((cmp = toupper (*a) - toupper (*b)) != 0)
      return cmp;
    if (!*a && !*b)
      return 0;
    a++, b++;
  }
  return 0;
}



/****** SmBinLoc **************************************************************
**
**	return index of string t in string s, -1 if none;
**      as Smloc except that it searches any bytes (not only ascii)
**
**	INPUT:	    address of string1
**		    address of string2 that is searched in string1
**                  length of string 1
**                  length of string 2
**
**	RETURNS:	index of string2 in string1
**				-1 if not there
*/

INT4 SmBinLoc(char *str1, char *str2, INT4 len1, INT4 len2)
{
  INT4	i, j, k;
  
  for (i = 0;  i < len1;  i++) {
    for (j = i, k = 0; k < len2 && str1[j] == str2[k];  j++, k++)
      ;
    if (k == len2)
      return i;
  }
  return -1;
}

/*#define _SmUpper(c)  (c >= 'a' & c <= 'z') ? (223 & c) : c */




#define _SmUpper(c)  charTbl [(int) c]  
	    

/**api* SmEdit ****************************************************************
**
**  	mofifies a string:
**  	SMxTRIM:     cuts of leading and trailing " \n\t"
**  	SMxTRIM2:    cuts of leading and trailing " \n\t"
**      SMxLEAD:     only leader is trimmed
**      SMxTRAIL:    only trailer is trimmed
**  	SMxUPCASE:   converts to upper case
**  	SMxLOWCASE:  converts to lower case
**  	SMxDECODE:   replaces \n, \b by proper character values
**  	SMxDETAB:    replaces \t by ' '
**  
**  	modified:    9-OCT-1992 strcmp->strcpy (remc...)
**  
**  	INPUT:	    address of string [W]
**  		    bit mask containing constants (see above) [R]
**  
**  	RETURNS:    address of modified string
*/ 
   
char *SmEdit (char *s, UINT4 bm)
{
  static char charTbl[255];
  static INT4  isInit;
  char remc[10], remc2[10], *remc_p;
  INT4 code, k, l, slen;
  
  if (!isInit) {
    for (k=0; k < 255; k++)
      charTbl[k] = toupper (k);
    isInit = 1;
  }


  strcpy (remc, " \n\t\"");
  strcpy (remc2, " \n\t");
  
  slen = strlen(s);
  if (bm & SMxTRIM || bm & SMxTRIM2) { 
    remc_p = bm & SMxTRIM ? &(remc[0]) : &(remc2[0]);
    
    if (!(bm & SMxTRAIL)) {			 /* trim beginning	    */
      for (k = 0;  s[k] != 0 && (strchr(remc_p, s[k]) != 0);  k++) 
	;
      if (bm & SMxTRIM2 && s[k] == '\"') /* " */
	k++;
      slen -= k;
      if (k > 0)
	memcpy(s, &s[k], slen+1);
    }
    if (!(bm & SMxLEAD)) {			 /* trim end		    */
      for (k = slen - 1; k >= 0 &&  (strchr(remc_p, s[k]) != 0);  k--)
	;
      if (bm & SMxTRIM2 && s[k] == '\"') /* " ..emacs colors */
	k--;
      if (s[++k]) /* modify only if necess..string might be protected */
	s[k] = '\0';
      slen = k;
    }
  }
  
  if (bm & SMxDECODE) {
    for (k = 0, l = 0;  k < slen; k++)
      if (s[k] != '\\')
	s[l++] = s[k];
      else
	switch (s[++k]) {
        case '0':
        case '1':
        case '2':
        case '3':
        case '4':
        case '5':
        case '6':
        case '7':
        case '8':
        case '9':
	  code = s[k] - '0';
	  while (isdigit (s[k+1])) {
            k++;
	    code = code*10 + (s[k] - '0');
          }
	  s[l++] = code;
          break;
	case 'n':
	  s[l++] = 10;
	  break;
	case 'a':
	  s[l++] = 7;
	  break;
	case 't':
	  s[l++] = 9;
	  break;
	case 'b':
	  s[l++] = 7;
	  break;
	case 'r':
	  s[l++] = 13;
	  break;
	case '\"':  /* " ...emacs colors */
	  s[l++] = 34;
	  break;
	case '\\':
	  s[l++] = 92;
	  break;
	case '-':
	  s[l++] = '\\'; /* see PrsDecode */
	  s[l++] = '-';
	  break;
	default:
	  s[l++] = s[k];
	  break;
	}
    s[l] = '\0';
  }
  
  if (bm & SMxUPCASE)
    for (k = slen-1;  k>=0;  k--)
      s[k] = _SmUpper (s[k]);
/*       s[k] = toupper(s[k]); */
  
  if (bm & SMxLOWCASE)
    for (k = 0;  k < slen;  k++)
      s[k] = tolower(s[k]);
  
  if (bm & SMxDETAB)
    for (k = 0;  k < slen;  k++)
      if (s[k] == '\t') s[k] = ' ';
  return s;
}




/**api* SmTime ****************************************************************
**
**      should become OBSOLETE
**  	writes current date and time in the input string address in the format:
**  	" 9-OCT-1989  9:12\0";
**  
**  	INPUT:	    time value (seconds) [R] or 0
**  
**  	RETURNS:    pointer to time string
*/

char *SmTime (unsigned long usertime_val)
{
    time_t      time_val = usertime_val;
    struct tm   *t_s;
    char	min[3];

    static char timstr[30];    
    static char *month[12] = {"JAN","FEB","MAR","APR","MAY","JUN","JUL",
			      "AUG","SEP","OCT","NOV","DEC"};

    if (time_val == 0)
	time (&time_val); 
    t_s = localtime (&time_val);

    sprintf(min, "%2d", t_s->tm_min);		 /* min may need leading '0' */
    if (t_s->tm_min < 10)
	min[0] = 48;

    sprintf (timstr, "%2d-%s-19%d %2d:%s", t_s->tm_mday, 
					  month[t_s->tm_mon], 
					  t_s->tm_year, 
					  t_s->tm_hour,  
					  min);
    return &timstr[0]; 
}


/**api* SmSwap ****************************************************************
**
**  	replaces all occurances of a character in a string by another character
**  
**  	INPUT:	    address of string [W]
**  		    character to be replaced [R]
**  		    replacement character [R]
**  
**  		    returns:	1
*/ 
   
INT4 SmSwap (char *s, char a, char b)
{
  char    *loc;
  
  while ((loc = strchr (s, a)) != NULL)
    *loc = b;
  return 1;
}

/**api* SmSwapFirst ***********************************************************
**
**  	swaps only first occurrence of string;
**  
**  	INPUT:	    string to be searched and modified [W]
**  		    string to be searched [R]
**  		    replacement string [R]
**  
**  	RETURNS:    1 if swap
**  		    0 if no swap
*/ 

INT4 SmSwapFirst (char *str, char *search, char *replace)
{
  char *tmp, *loc;
  INT4 sLen, rLen, diff;

  if (!(loc = strstr (str, search)))
    return 0;

  sLen = strlen (search);
  rLen = strlen (replace);
  if (sLen > rLen) {  /* move chars AFTER searchstring from left to right */
    diff = sLen - rLen;
    for (tmp=loc+sLen; *tmp; tmp++)
      *(tmp - diff) = *tmp;
  }
  else if (sLen < rLen) {  /* move chars AFTER searchstring from right */
    diff = rLen - sLen;
    for (tmp=str+strlen(str); tmp >= loc + sLen; tmp--)
      *(tmp + diff) = *tmp;
  }
  memcpy (loc, replace, rLen);
  return 1;
}

/****** SmReplace *************************************************************
**
**
**	INPUT:	    address of string [W]
**                  pointer inside the buff to the substring to be replaced [W]
**                  length of string to be replaced [R]
**                  replacement string [R]
**                  length of that substring [R]
**	        IMPLICIT:
**
**	RETURNS:  
**		 pointer to the beginning of the replaced string
*/      

char *SmReplace (char *buff, char *target, INT4 targetLen, char *s,
                   INT4 lenS)
{
  char *endPtr;
  INT4  off, shift;

  off = (Int4)(target - buff) + targetLen; 
  shift = lenS - targetLen;
    
  if (shift != 0) {
    endPtr = buff + off;
    SmMemMove (endPtr + shift, endPtr, strlen(buff) - off + 1);
    memcpy (endPtr - targetLen, s, lenS);
  }
  return endPtr-targetLen;
}


/**api* SmSwapS ***************************************************************
**
**  	swap all occurrances of old string against new string; goes from left
**  	to right;
**  
**  	INPUT:	    address of input string [W]
**  		    address of old string (to be searched in string) [R]
**  		    address of new string [R]
**  
**  	RETURNS:    1 if swap
**  		    0 if no swap
*/ 

INT4 SmSwapS (char *str, char *a, char *b)
{
  INT4	    off=0, strLen, a_z, b_z, swap_f, rv;
#ifdef sun
    char *tmp;
#endif

  swap_f = FALSE;
  strLen = strlen (str);
  a_z = strlen (a);
  b_z = strlen (b);
  while ((rv = SmLoc (str+off, a)) != -1) {
    off += rv;
    swap_f = TRUE;
#ifdef sun
    tmp = (char *) malloc (strLen - a_z - off + 1);
    memcpy (tmp, &str[off+a_z], strLen - a_z - off + 1);
    memcpy (&str[off+b_z], tmp, strLen - a_z - off + 1);
    free (tmp);
#else
    memmove (&str[off+b_z], &str[off+a_z], strLen-a_z-off+1);
#endif
    memcpy (&str[off], b, b_z); 
    strLen += b_z - a_z;  /* string size changes	    */
    off += b_z;
  }
  return swap_f;
}


 void SmMemMove (char *to, char *from, int len)  
{

#ifdef sun
  char *tmp;

  tmp = (char *) malloc (len);
  memcpy (tmp, from, len);
  memcpy (to, tmp, len);
  free (tmp);
#else
  memmove (to, from, len);
#endif
}



/****** SmFLen ****************************************************************
**
**	replaces in format-string for printf '#' against width (neg. or pos)
**
**	INPUT:	    address of format-string [W]
**		    any number of width numbers [R]
**	        IMPLICIT:
**
**	RETURNS:    address of modified string
*/ 
   
char *SmFLen (char *s,...)
{
  static char tmps[SMxXTMP];
  va_list ap;
  char    tmp[5];
  INT4	  wid;

  strcpy (tmps, s);
  va_start (ap, s);				
  while (strchr (tmps, '#') != NULL) {
    wid = va_arg (ap, INT4);
    sprintf (tmp, "%d", wid);	
    SmSwapS (tmps, "#", tmp);
  }
  va_end (ap);
  return tmps;
}


/**api* SmElement *************************************************************
**
**  	extracts string element with specified number bordered by begin, or end
**  	of string or specified character; first element has number 1;
**  
**  	INPUT:	    address of input string [R]
**  		    address of output string [W]
**                  delimiter character [R]
**  		    element number [R]
**                  option SMxSKIP or SMxNOSKIP [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    1 if success 
**  		    0 if specified element not found
*/ 
   
INT4 SmElement (char *a, char *b, char tok, INT4 n, INT4 skip_o)
{
  INT4	k, l, beg, len;
  
  for (k=0, l=0;  k < n -1;  k++) {		 /* goto element begin	    */
    while (a[l] != tok && a[l] != '\0')
      l++;
    if (a[l++] == '\0')
      return 0;
  }
  
  beg = l;
  if (skip_o == SMxNOSKIP && beg != 0)
    beg--;
  
  while (a[l] != tok && a[l] != '\0')		 /* goto element's end	    */
    l++;
  
  if (beg == l)
    return 0;
  
  len = l-beg;
  memcpy (b, &(a[beg]), len);
  b[len] = '\0';
  return 1;
}

/**api* SmStrTok **************************************************************
**
**  	inspired from strtok, ...tok is a separator STRING with one or more
**      characters; function returns next substring bordered by tok; the 
**      context is reset when called with a different string ...or when
**      an iteration is complete and there are no more substrings ...this 
**      means that it must be always iterated until the function returns NULL;
**      function put '\0's into the input string;
**  
**  	INPUT:	    string  [W]
**  		    string token [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    pointer to next substring
**   		    NULL if there are no more
*/ 

char *SmStrTok (char *str, char *tok)
{
  static char *strSave, *strPtr=NULL, *tokPtr, *tmpPtr;

  if (strSave != str || !strPtr)
    strSave = str, strPtr = str;
  
  if (!*strPtr) { /* at end of string */
    strPtr = NULL;
    return NULL;
  }

  if ((tokPtr = strstr (strPtr, tok))) {
    *tokPtr = '\0';
    tmpPtr = strPtr;
    strPtr = tokPtr + strlen (tok);
    return tmpPtr;
  }
  else {  /* no token found */
    tmpPtr = strPtr;
    strPtr = str + strlen (str);
    return tmpPtr;
  }
}


/**api* SmEqs ****************************************************************
**
**  	compares to strings case insensitive;
**  
**  	INPUT:	    string a [R]
**  		    string b [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    1 if equal
**   		    0 if not
*/ 
   
INT4 SmEqs (char *a, char *b)
{
  for (; *a && *b; a++, b++)
    if (toupper (*a) != toupper (*b))
      break;
  return (!*a && !*b) ? 1 : 0;
}






static Int4 buffAllocN, buffAllocByte, buffFreedN, buffFreedByte;

/**api* BuffNew ***************************************************************
**
**  	Creates a new buffer object with the specified initial size which 
**      will double as needed;
**  
**  	INPUT:	    initial size in bytes [R]
**  
**  	RETURNS:    buffer object
*/ 
   
SMoBUFF *BuffNew (INT4 size)
{
  SMoBUFF *buff;
  
  if (size < 10) /* minimum size of buffer */
    size = 10;

  if ((buff = (SMoBUFF *) malloc (sizeof (SMoBUFF))) == NULL)
    _ErrExit2 (e__allocfail, "buff object");
  if ((buff->buff = (char *) malloc (size)) == NULL)
    _ErrExit2 (e__allocfail, "buff string");

  buff->writePtr = buff->buff;
  buff->readPtr = buff->buff;
  buff->size = size;
  *buff->buff = '\0';

#ifdef DEBUG
  buffAllocN++;
  if (!(buffAllocN%1000))
    fprintf (stderr, "BUFFERS: allocN: %d, freedN, %d\n",
	     buffAllocN, buffFreedN);
#endif
  return buff;
}

/**api* BuffInit **************************************************************
**
**  	Creates a new buffer object if the buffer object's address is NULL
**      otherwise just resets the buffer.
**  
**  	INPUT:	    address of buffer object [R] (initially NULL)
**                  initial size in bytes [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    buffer object
*/ 
   
SMoBUFF *BuffInit (SMoBUFF *buff, INT4 size)
{
  if (!buff)
    buff = BuffNew (size);
  else
    BuffReset (buff);
  return buff;
}


/**api* BuffReset *************************************************************
**
**  	Resets a buffer object, ie, resets the "current" pointer to the buffer
**      begin.
**  
**  	INPUT:	    address of buffer object [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    
*/ 
   
void BuffReset (SMoBUFF *buff)
{
  buff->writePtr = buff->buff;
  buff->readPtr = buff->buff;
  *buff->buff = '\0';
}

/**api* BuffResetRead *********************************************************
**
**  	Resets a the read pointer of a buffer object,
**  
**  	INPUT:	    address of buffer object [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    
*/ 
   
void BuffResetRead (SMoBUFF *buff)
{
  buff->readPtr = buff->buff;
}


/**api* BuffGetCurrOffset *****************************************************
**
**  	Returns the offset of the current pointer from the buffer begin.
**  
**  	INPUT:	    address of buffer object [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    offset
*/ 
   
INT4 BuffGetCurrOffset (SMoBUFF *buff)
{
  return (INT4) (buff->writePtr - buff->buff);
}
/**api* BuffLength ************************************************************
**
**  	Returns the offset of the current pointer from the buffer begin.
**  
**  	INPUT:	    address of buffer object [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    offset
*/ 
   
INT4 BuffLength (SMoBUFF *buff)
{
  return (INT4) (buff->writePtr - buff->buff);
}

/**api* BuffGetCurrPtr ********************************************************
**
**  	Returns the current pointer, pointing to the current location in
**      the buffer.
**  
**  	INPUT:	    address of buffer object [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    current pointer
*/ 
   
char *BuffGetCurrPtr (SMoBUFF *buff)
{
  return buff->writePtr;
}

/**api* BuffGetPtr ************************************************************
**
**  	Returns the pointer to the buffer begin - this may change during buffer
**      growth.
**  
**  	INPUT:	    address of buffer object [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    current pointer
*/ 
   
char *BuffGetPtr (SMoBUFF *buff)
{
  return buff->buff;
}


/**api* BuffCopyChar **********************************************************
**
**  	Copies a single character to the buffer and advances current pointer.
**      Doubles the buffer if the end of buffer is reached. Does NOT put
**      a NULL character at the end!
**  
**  	INPUT:	    address of buffer object [W]
**                  character value [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    
*/ 
   
void BuffCopyChar (SMoBUFF *buff, char c)
{
  if ((INT4) (buff->writePtr - buff->buff) == buff->size) 
    BuffGrow (buff, 1);
  *(buff->writePtr++) = c;
}

/**API* BuffCopyNChar *******************************************************
**
**      Copies exactly n characters to the buffer and advances current
**      pointer. Doubles the buffer if the end of buffer is reached.
**      Does NOT put a NULL character at the end. All the string will be
**      copied if the length of s is n or more.
**  
**      INPUT:      address of buffer object [W]
**                  string to be copied [R]
**              IMPLICIT:
**  
**      RETURNS:    
*/ 
   
void BuffCopyNChar (SMoBUFF *buff, char *s, INT4 n)
{
  if(n > 0) {
    if ((INT4) (buff->writePtr - buff->buff + n) >= buff->size) 
      BuffGrow (buff, n+1);
    strncpy (buff->writePtr, s, n);
    buff->writePtr += n;
  }
}

/**api* BuffCopyString ********************************************************
**
**  	Copies a string to the buffer and advances current pointer.
**      Doubles the buffer if the end of buffer is reached.
**  
**  	INPUT:	    address of buffer object [W]
**                  string to be copied [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    
*/ 
   
void BuffCopyString (SMoBUFF *buff, char *s)
{
  INT4 len;

  len = strlen (s);

  if ((INT4) (buff->writePtr - buff->buff + len) >= buff->size) 
    BuffGrow (buff, len+1);
  strcpy (buff->writePtr, s);
  buff->writePtr += len;
}

/**api* BuffCat ***************************************************************
**
**  	Copies contents of second buffer to first buffer
**      (analogous to 'strcat'). If the 'read pointer' is not at the
**      buffer begin then that is used as begin of the buffer to
**      be copied from.
**  
**  	INPUT:	    address of buffer [W]
**                  address of buffer [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    
*/ 
   
void BuffCat (SMoBUFF *a, SMoBUFF *b)
{
  INT4 len;

  len = b->writePtr - b->readPtr;
  _BuffCopyNChars (a, b->readPtr, len);
  *(a->writePtr) = '\0'; /* add NULL terminator */
}


/**api* BuffPrintF ************************************************************
**
**  	Copies a string to the buffer that is previously formatted (in a 
**      printf fashion.
**      Doubles the buffer if the end of buffer is reached.
**  
**  	INPUT:	    address of buffer object [W]
**                  string to be copied [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    
*/ 
   
void BuffPrintF (SMoBUFF *buff, char *formatStr, ...)
{
  va_list ap;
  char    s[2000];

  va_start (ap, formatStr);
  vsprintf (s, formatStr, ap);
  va_end (ap);

  BuffCopyString (buff, s);
}

/**api* BuffVPrintF ***********************************************************
**
**  	Copies a string to the buffer that is previously formatted (in a 
**      printf fashion.
**      Doubles the buffer if the end of buffer is reached.
**  
**  	INPUT:	    address of buffer object [W]
**                  string to be copied [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    
*/ 
   
void BuffVPrintF (SMoBUFF *buff, char *formatStr, va_list ap)
{
  char    s[50000];

  vsprintf (s, formatStr, ap);
  BuffCopyString (buff, s);
}



/****** BuffGrow **************************************************************
**
**  	'Grows' the buffer to double size or if this is not sufficient,
**      by the specified size.
**  
**  	INPUT:	    address of buffer object [W]
**                  minimum size by which to grow [W]
**  	        IMPLICIT:
**  
**  	RETURNS:    
*/ 
   
void BuffGrow (SMoBUFF *buff, INT4 size)
{
  INT4 off1, off2;

  if (buff->size < size) /* check if doubling is not enough */
    buff->size += size;
  else
    buff->size = buff->size * 2;

  off1 = (INT4) (buff->writePtr - buff->buff);
  off2 = (INT4) (buff->readPtr - buff->buff);
  if ((buff->buff = (char *) realloc (buff->buff, buff->size)) == NULL)
    _ErrExit2 (e__allocfail, "buff string");
  buff->writePtr = buff->buff + off1;
  buff->readPtr = buff->buff + off2;
}


/**api* BuffShiftCurrPtr ******************************************************
**
**  	Shifts the current pointer by requested amont back (negative) or 
**      forward.
**  
**  	INPUT:	    address of buffer object [W]
**  	        IMPLICIT:
**  
**  	RETURNS:    
*/ 
   
void BuffShiftCurrPtr (SMoBUFF *buff, INT4 n)
{
  buff->writePtr += n; /* should do some checking */
}

/**api* BuffFill **************************************************************
**
**  	Writes the specified number of times specified character into buffer.
**  
**  	INPUT:	    address of buffer object [W]
**  		    number of characters to write [R]
**  		    character to write [R]
**  
**  	RETURNS:    1
*/

void BuffFill (SMoBUFF *buff, INT4 n, char c)
{
  INT4 k;

  for (k=0; k < n; k++) {
    if ((INT4) (buff->writePtr - buff->buff + 1) >= buff->size) /* the 1 for the
								  NULL char */ 
      BuffGrow (buff, 1);
    *(buff->writePtr++) = c;
  }
  *(buff->writePtr) = '\0'; /* add NULL terminator - safer! */
} 

/**api* BuffTrim **************************************************************
**
**  	Trims the buffer from begin and/or end
**  
**  	INPUT:	    address of buffer object [W]
**  		    option: "lf" trims line feed from end
**  		    option: "continue" trims line feed from end
**  
**  	RETURNS:    1
*/

void BuffTrim (SMoBUFF *buff, char *option)
{
  char *tmp;

  switch (tolower (option[0])) {
  case 'l':  /* lf */
    tmp = buff->writePtr;
    while (*(--tmp) == '\n') {
      *tmp = '\0';
      buff->writePtr = tmp;
    }  
    break;
  case 'c':  /* continue */
    tmp = buff->writePtr - 2;
    if (*tmp == '\\') {
      *tmp = '\0';
      buff->writePtr -= 2;
    }
    break;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
}

/**api* BuffToUpper ***********************************************************
**
**  
**  	INPUT:	    address of buffer object [W]
**  
**  	RETURNS:    address of string 
*/

char *BuffToUpper (SMoBUFF *buff)
{
  SmEdit (buff->buff, SMxUPCASE);
  return buff->buff;
}

/**api* BuffToLower ***********************************************************
**
**  
**  	INPUT:	    address of buffer object [W]
**  
**  	RETURNS:    address of string 
*/

char *BuffToLower (SMoBUFF *buff)
{
  SmEdit (buff->buff, SMxLOWCASE);
  return buff->buff;
}


/**api* BuffSearchSensitive *********************************************
**
**      Searches a string and returns pointer to string if found.
**      Search is case sensitive.
**  
**      INPUT:      buffer object [R]
**                  address of string [R]
**  
**      RETURNS:    pointer to location if found
**                  NULL if not
*/

char *BuffSearchSensitive (SMoBUFF *buff, char *s)
{
  BuffCopyChar (buff, '\0'); /* make sure there is a NULL terminator */
  BuffShiftCurrPtr (buff, -1); 

  return strstr (buff->buff, s);
}

/**api* BuffSearch ************************************************************
**
**      Searches a string and returns pointer to string if found.
**      Search is case insensitive.
**  
**      INPUT:      buffer object [R]
**                  address of string [R]
**  
**      RETURNS:    pointer to location if found
**                  NULL if not
*/

char *BuffSearch (SMoBUFF *buff, char *s)
{
  char *buf;
  INT4 len = strlen(s);

  BuffCopyChar (buff, '\0'); /* make sure there is a NULL terminator */
  BuffShiftCurrPtr (buff, -1); 

  for (buf = buff->buff; *buf; buf++)
    if (!SmStrCmpLen(buf, s, len)) {
      return buf;
    } 
  return NULL;
}


/**api* BuffDuplicate ****************************************************
**
**      Creates a new buffer object with the necessary initial size 
**      and copies the existing buffer to it.
**  
**      INPUT:      address of buffer object [R]
**              IMPLICIT:
**  
**      RETURNS:    buffer object
*/ 
   
SMoBUFF *BuffDuplicate(SMoBUFF *oldBuff)
{
  SMoBUFF *buff;
  INT4 size;
  
  size = strlen(oldBuff->buff) + 1;
  
  if ((buff = (SMoBUFF *) malloc (sizeof (SMoBUFF))) == NULL)
    _ErrExit2 (e__allocfail, "buff object");
  if ((buff->buff = (char *) malloc (size)) == NULL)
    _ErrExit2 (e__allocfail, "buff string");
  
  strcpy(buff->buff, oldBuff->buff); /* copy content of buffer */
  buff->writePtr = buff->buff+size-1;
  buff->size = size;
  return buff;
}

/**api* BuffIsEmpty *****************************************************
**
**      Returns TRUE if buffer object is empty, FALSE otherwise
**  
**      INPUT:      address of buffer object [R]
**              IMPLICIT:
**  
**      RETURNS:    1     if buffer object empty
**                  0     otherwise
*/ 

INT4 BuffIsEmpty(SMoBUFF *buff)
{
  if  (buff->writePtr == buff->buff)
    return 1;
  else
    return 0;
}

/**api* BuffDelete *******************************************************
**
**      Deletes a buffer object and frees the allocated memory.
**  
**      INPUT:      address of buffer object [R]
**              IMPLICIT:
**  
**      RETURNS:    nothing
*/ 

void BuffDelete(SMoBUFF **buff)
{
#ifdef DEBUG
  buffFreedN++;
#endif

  free((*buff)->buff);
  free(*buff);
  *buff = NULL;
}

/**api* BuffPrint *******************************************************
**
**      Prints the string contained in a buffer object.
**  
**      INPUT:      address of buffer object [R]
**              IMPLICIT:
**  
**      RETURNS:    nothing
*/ 

void BuffPrint (FILE *file, SMoBUFF *buff)
{
  if (file) 
    fprintf (file, "%s", buff->buff);
  else
    printf ("%s", buff->buff);

}

/**api* BuffReadFile **********************************************************
**
**      Prints the string contained in a buffer object.
**  
**      INPUT:      address of buffer object [R]
**              IMPLICIT:
**  
**      RETURNS:    nothing
*/ 

void BuffReadFile (SMoBUFF *buff, FILE *file, INT4 size)
{
  _BuffReserve (buff, size);
  fread (buff->writePtr, 1, size, file);
  _BuffIncWrite (buff, size);
}


/**api* BuffReadLine **********************************************************
**
**      Reads a line from file into the buffer;
**  
**      INPUT:      address of buffer object [R]
**              IMPLICIT:
**  
**      RETURNS:    nothing
*/ 

int BuffReadLine (SMoBUFF *buff, FILE *file, int maxLen)
{
  char *tmp;
  int  len;

  _BuffReserve (buff, maxLen);
  if (!(tmp = fgets (buff->writePtr, maxLen, file)))
    return 0;
  else {
    len = strlen (tmp);
    _BuffIncWrite (buff, len);
    return 1;
  }
}


/**api* BuffCollapse **********************************************************
**
**      Replaces a stretch of whitespace chars by single blankl
**  
**      INPUT:      address of buffer object [R]
**              IMPLICIT:
**  
**      RETURNS:    pointer to string
*/ 

char *BuffCollapse (SMoBUFF *buff)
{
  char *w, *r;

  *buff->writePtr = '\0';

  for (w=r=buff->buff; *r != '\0'; r++) {
    if (*r == ' ') {
      *w++ = ' ';
      while (*r == ' ')
	r++;
      r--;
    }
    else
      *w++ = *r;
  }
  *w = *r;
  buff->writePtr = buff->buff + strlen (buff->buff);
  return buff->buff;
}


/**api* BuffFormat ***********************************************************
**
**  	Returns the formatted string; string returned 'owned' by the function
**      so make sure you do something with it before calling the function
**      again.
**  
**  	INPUT:	    address of buffer object [W]
**                  maximum length of the output line [R]
**                  identation of first line [R] or 0
**                  identation of all/following line [R]
**                  text to be printed in front of each line [R] or NULL
**  	        IMPLICIT:
**  
**  	RETURNS:    current pointer
*/ 
   
char *BuffFormat (SMoBUFF *buff, INT4 lineSize, 
		  INT4 firstIdent, INT4 allIdent, char *leftText)
{
  static SMoBUFF *tmp=NULL;
  char    *p, *pSave;
  INT4    k, lineLen;

  if (leftText)
    allIdent = strlen (leftText);

  if (!tmp)
    tmp = BuffNew (lineSize);
  else
    BuffReset (tmp);
  
  /* text or ident to the left of first line */
  if (leftText)
    BuffCopyString (tmp, leftText);
  else if (firstIdent)
    BuffFill (tmp, firstIdent, ' ');
  
  lineLen = BuffGetCurrOffset(tmp);
  p = buff->buff;
  k = lineLen + (buff->writePtr - p); 
  while (k >= lineSize) {
    pSave = p;
    p += lineSize - lineLen;
    while (*p != ' ' && p > pSave) /* find the next ' ' backwards */
      p--;

    if (p == pSave) /* if no space was found break at line end */
      p += lineSize - lineLen;

    *(p++) = '\0';
  
    BuffCopyString (tmp, pSave);
    BuffCopyChar (tmp, '\n');

    /* text or ident to the left of following lines */
    if (leftText)
      BuffCopyString (tmp, leftText);
    else
      BuffFill (tmp, allIdent, ' ');

    lineLen = allIdent;
    k = lineLen + (buff->writePtr - p); 
  }
  BuffCopyString (tmp, p);

  return tmp->buff;
}



char *SmScanNumber (char *s, INT4 *num)
{
  *num = 0;
  while (isdigit (*s))
    *num = *num * 10 + (*s++ - '0');

  return s; /* points to first character after number */
}

char *BuffExpandTemplate (char *template)
{
  static char newTemplate[100];
  char *tmp;
  INT4 k, l;

  for (k=0, tmp=template; *tmp;) {
    if (!isdigit (*tmp))
      newTemplate[k++] = *tmp++;
    else {
      if (strchr ("aA", *(tmp-1)) == NULL) {
	tmp = SmScanNumber (tmp, &l);
	while (--l) {
	  newTemplate[k] = newTemplate[k-1];
	  k++;
	}    
      }
      else
	while (isdigit (*tmp))
	  newTemplate[k++] = *tmp++;
    }
  }
  newTemplate[k] = '\0';
  return newTemplate;
}


#define BYTE1   0xFFUL
#define BYTE2   0xFF00UL
#define BYTE3   0xFF0000UL
#define BYTE4   0xFF000000UL

/**api* BuffPack **************************************************************
**
**  	Returns the formatted string; string returned 'owned' by the function
**      so make sure you do something with it before calling the function
**      again.
**  
**  	INPUT:	    address of buffer object [W]
**                  maximum length of the output line [R]
**                  identation of first line [R] or 0
**                  identation of all/following line [R]
**                  text to be printed in front of each line [R] or NULL
**  	        IMPLICIT:
**  
**  	RETURNS:    current pointer
*/ 

void BuffPack (SMoBUFF *buff, char *template, ...)
{
  va_list ap;
  char *s, *tmp;
  INT4 n, len;

  va_start (ap, template);

  for (tmp=template; *tmp; tmp++) {
    switch (*tmp) {

    case 'a': /* ASCII string */
      s = va_arg (ap, char *);

      if (isdigit (tmp[1]))
	tmp = SmScanNumber (tmp+1, &len) - 1;
      else 
	len = strlen (s) + 1;
      _BuffReserve (buff, len);
      strncpy (buff->writePtr, s, len); 
      _BuffIncWrite (buff, len);
      break;

    case 'i': /* signed integer */
      n = va_arg (ap, INT4);

      _BuffReserve (buff, 4);
      buff->writePtr[0] = n & BYTE1; 
      buff->writePtr[1] = (n & BYTE2) >> 8; 
      buff->writePtr[2] = (n & BYTE3) >> 16; 
      buff->writePtr[3] = (n & BYTE4) >> 24; 
      _BuffIncWrite (buff, 4);
      break;

    default: /* digit ...or whitespace */
      if (isdigit (*tmp)) {
	int diff;

	diff = tmp - template;
	tmp = BuffExpandTemplate (template);
	tmp += diff -1;
      }	
    }
  }
  va_end (ap);

}

/**api* BuffUnPack ************************************************************
**
**      Unpacks items from buffer, a number after the item means
**      repetition, except after 'a' or 'z' where it means length.
**
**      a: copy of ASCII string 
**      z: pointer to ASCII string
**      i: 4 byte signed integer
**  
**  	INPUT:	    address of buffer object [W]
**                  template string [R]
**                  list of pointers to receive unpacked values
**  	        IMPLICIT:
**  
**  	RETURNS:    1 if successful
**                  0 if not all items could be read
*/ 

INT4 BuffUnpack (SMoBUFF *buff, char *template, ...)
{
  va_list ap;
  char *s, **sPtr, *tmp;
  INT4 *n, len;

  va_start (ap, template);

  for (tmp=template; *tmp; tmp++) {
    if (buff->readPtr >= buff->writePtr)
      return 0;

    switch (*tmp) {

    case 'a': /* ASCII string */
      s = va_arg (ap, char *);
      if (isdigit (tmp[1])) {
	tmp = SmScanNumber (tmp+1, &len) - 1;
	strncpy (s, buff->readPtr, len); 
	s[len] = '\0';
      }
      else {
	strcpy (s, buff->readPtr); 
	len = strlen (s) + 1;
      }
      _BuffIncRead (buff, len);
      break;

    case 'z': /* pointer to ASCII string */
      sPtr = va_arg (ap, char **);
      *sPtr = buff->readPtr; 
      if (isdigit (tmp[1]))
	tmp = SmScanNumber (tmp+1, &len) - 1;
      else 
	len = strlen (*sPtr) + 1;
      _BuffIncRead (buff, len);
      break;

    case 'i': /* signed integer */
      n = va_arg (ap, INT4 *);
     *n = ((UINT4) ((unsigned char) buff->readPtr[0])) + 
          ((UINT4) ((unsigned char) buff->readPtr[1]) << 8) + 
	  ((UINT4) ((unsigned char) buff->readPtr[2]) << 16) + 
	  ((UINT4) ((unsigned char) buff->readPtr[3]) << 24); 
      _BuffIncRead (buff, 4);
      break;

    default: /* digit ...or whitespace */
      if (isdigit (*tmp)) {
	int diff;

	diff = tmp - template;
	tmp = BuffExpandTemplate (template);
	tmp += diff -1;
      }	
    }
  }
  va_end (ap);
  return 1;
}

static regexp *regCurr=NULL;
/****** BuffMatch *************************************************************
**
**      Matches a string against a regular expression.
**      Use RegGetField to extract fields denoted by parentheses or the
**      entire match.
**
**	INPUT:	    buffer object to be searched [R]
**                  string with regular expression [R]
**	        IMPLICIT:
**
**	RETURNS:  1 if string matches
**                0 if not
*/      

int BuffMatch (SMoBUFF *buff, char *reStr)
{
  static int classId = 0;
  static struct SMoRE {
    char   *list;    /* for usage of module "list" only!  */
    INT4   class_id; /* for "list" module */  
    char   nam[100];
    regexp *re;
  } *re=NULL;

  if (!classId) 
    LstManageClass (&classId, sizeof (struct SMoRE), NULL, NULL, NULL);

  if (!LstHashSearch ((void **) &re, reStr)) {
    LstNewNamed ((void **) &re, classId, reStr);
    re->re = RegComp (reStr);
  }
  regCurr = re->re;
  return RegExec (re->re, buff->buff) ? 1 : 0;
}


/****** RegGetMatch ***********************************************************
**
**      Extracts entire match (field number 0) or subfield from previous 
**      regular expression match by RegMatch.
**
**	INPUT:	    number of match to be returned [R]
**	        IMPLICIT:
**                  regCurr (regexp *)
**
**	RETURNS:    string 
**                  NULL if invalid number specified
*/      

char *BuffGetMatch (int n)
{
  static SMoBUFF *b[10]={NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
  static INT4 cnt=0;
  SMoBUFF *buff=b[cnt++%10];
  char *endp, *startp;
  int  len;

  if (!buff)
    buff = BuffNew(100);
  else 
    BuffReset (buff);

  if (n >= 0 && n <= 9 && regCurr) {
    startp = regCurr->startp[n];
    endp = regCurr->endp[n];
    len = endp - startp;

    _BuffCopyNChars (buff, startp, len);
    BuffCopyChar (buff, '\0');
    return buff->buff;
  }
  return NULL;
}

/****** BuffSubstMatch **************************************************************
**
**      Replaces match by previous regular expression with specified number
**      by specified string.
**
**	INPUT:	    address of buffer object [W]
**                  number of match to be replaced [R]
**                  replacement string [R]
**	        IMPLICIT:
**                  regCurr (regexp *)
**
**	RETURNS:  
*/      

char *BuffSubstMatch (SMoBUFF *buff, int n, char *s)
{
  char *endp, *startp;
  int  lenMatch, lenS, shift;

  if (n >= 0 && n <= 9 && regCurr) {
    startp = regCurr->startp[n];
    endp = regCurr->endp[n];
    lenMatch = endp - startp;
    lenS = strlen (s);

    shift = lenS - lenMatch;
    if (shift > 0)
     _BuffReserve (buff, shift);
    
    if (shift != 0)
      SmMemMove (endp+shift, endp, buff->writePtr - endp+1);

    memcpy (startp, s, lenS);
  }
  _BuffIncWrite (buff, shift);

  return buff->buff;
}

/****** BuffReplace ***********************************************************
**
**
**	INPUT:	    address of buffer object [W]
**                  pointer inside the buff to the substring to be replaced [W]
**                  length of string to be replaced [R]
**                  replacement string [R]
**                  length of that substring [R]
**	        IMPLICIT:
**
**	RETURNS:  
**		 pointer to the beginning of the target into the buffer
*/      

char *BuffReplace (SMoBUFF *buff, char *target, INT4 targetLen, char *s,
                   INT4 lenS)
{
  char *endPtr;
  INT4  off, shift;

  off = (INT4)(target - buff->buff) + targetLen; 
  shift = lenS - targetLen;
  if (shift > 0)
    _BuffReserve (buff, shift);
    
  if (shift != 0) {
    endPtr = buff->buff + off;
    SmMemMove (endPtr + shift, endPtr, buff->writePtr - endPtr + 1);
    memcpy (endPtr - targetLen, s, lenS);
  }
  _BuffIncWrite (buff, shift);
  return endPtr-targetLen;
}

#ifdef MAIN
INT4 SDL_fnct(){}
main() {

  SMoBUFF *test;
  char    *ptr;


	test = BuffInit(NULL, 1000);
	BuffCopyString(test, "1234567890abcdefghi");
	ptr = BuffGetPtr(test) + 5;
	ptr = BuffReplace(test, ptr, 3, "XXXXX", 5);
	printf("%s %s\n", BuffGetPtr(test), ptr);
	ptr = BuffReplace(test, BuffGetPtr(test), 5, "YYxxx", 2);
	printf("%s %s\n", BuffGetPtr(test), ptr);
}
#endif

/**api* SmIsSeparator *******************************************************
**
**   Determines whether the input contains trivial character or not
**
**   INPUT:   address of input string
**           separator character
**
**   RETURNS:  true   if all the chars of input string are same
**            false otherwise
*/

INT4 SmIsSeperator(char *s, char c)
{

  while(*s)
    if( *s++ != c) return -1;
  return 1;
}

est, BuffGetPtr(test), 5, "YYxxx", 2);
	printf("%s %s\n", BuffGetPtr(test), ptr);
}
#endif

/**api* SmIsSeparator *******************************************************
**
**   Determines whether the input contains trivial character or not
**
**   INPUT:   address of input string
**           separator character
**
**   RETURNS:  true   if all the chars of input string are same
**            falsrs/src/sm.h
**
**    $RCSfile: sm.h,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:17:22 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
*/

#include <stdarg.h>

#ifndef TRUE
#define TRUE 1
#endif

#ifndef FALSE
#define FALSE 0
#endif

#ifndef MAX
#define MAX(a,b) ((a)<(b) ? (b) : (a))
#endif

#ifndef MIN
#define MIN(a,b) ((a)<(b) ? (a) : (b))
#endif

#define SMxXTMP		512
#define SMxXITEML	80

#define SMxSKIP 	0
#define SMxNOSKIP	1

#define SMxMIXCASE	0
#define SMxTRIM         1
#define SMxUPCASE	2
#define SMxLOWCASE	4
#define SMxDECODE	8
#define SMxDETAB	16
#define SMxLEAD		32
#define SMxTRAIL	64
#define SMxTRIM2        128


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  buffer object;
*/

typedef struct SMoBUFF { 
  char *buff;
  char *writePtr;
  char *readPtr;
  INT4 size;
} SMoBUFF, *SMpBUFF;

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of functions to be exported
*/

char *SmFLen (char *s,...);
char *SmFill (char *str, INT4 n, char c);
char *SmEdit (char *s, UINT4 bm);
char *SmTime (unsigned long time_val);
INT4 SmSwap (char *s, char a, char b);
INT4 SmSwapS (char *s, char *a, char *b);
INT4 SmElement (char *a, char *b, char tok, INT4 n, INT4 skip_o);
char *SmCharSet (char *s);
char *SmStrTok (char *str, char *tok);
INT4 SmSwapFirst (char *str, char *search, char *replace);

    /* string comparison */

INT4 SmEqs (char *a, char *b);
INT4 SmMixLoc(char *str1, char *str2, INT4 l, INT4 r);
INT4 SmXLoc(char *str1, char *str2, INT4 l, INT4 r);
INT4 SmLoc(char *str1, char *str2);
INT4 SmStrCmp (char *a, char *b);
INT4 SmStrCmpLen (char *a, char *b, INT4 len);
INT4 SmRStrCmp (char *a, char *b);
INT4 SmRStrCmpLen (char *a, char *b, INT4 len);
INT4 SmBinLoc(char *str1, char *str2, INT4 len1, INT4 len2);

    /* buffer Management */

struct SMoBUFF *BuffNew (INT4 initSize);
void BuffReset (struct SMoBUFF *buff);
struct SMoBUFF *BuffInit (struct SMoBUFF *buff, INT4 initSize);
void BuffResetRead (SMoBUFF *buff);
void BuffGrow (SMoBUFF *buff, INT4 size);

INT4 BuffLength (struct SMoBUFF *buff);
INT4 BuffGetCurrOffset (struct SMoBUFF *buff);
char *BuffGetCurrPtr (struct SMoBUFF *buff);
char *BuffGetPtr (struct SMoBUFF *buff);


void BuffCopyChar (struct SMoBUFF *buff, char c);
void BuffCopyString (struct SMoBUFF *buff, char *s);
void BuffPrintF (SMoBUFF *buff, char *formatStr, ...);
void BuffVPrintF (SMoBUFF *buff, char *formatStr, va_list ap);
void BuffShiftCurrPtr (SMoBUFF *buff, INT4 n);
void BuffFill (SMoBUFF *buff, INT4 n, char c);

    /* buffer editing */ 

void BuffCat (SMoBUFF *a, SMoBUFF *b);
void BuffTrim (SMoBUFF *buff, char *option);
char *BuffToUpper (SMoBUFF *buff);
char *BuffToLower (SMoBUFF *buff);

char *BuffSearchSensitive (SMoBUFF *buff, char *s);
char *BuffSearch (SMoBUFF *buff, char *s);
SMoBUFF *BuffDuplicate(SMoBUFF *oldBuff);
INT4 BuffIsEmpty(SMoBUFF *buff);
void BuffDelete(SMoBUFF **buff);
void BuffPrint (FILE *file, SMoBUFF *buff);
void BuffReadFile (SMoBUFF *buff, FILE *file, int size);
int BuffReadLine (SMoBUFF *buff, FILE *file, int maxLen);

char *BuffCollapse (SMoBUFF *buff);
char *BuffReplace (SMoBUFF *buff, char *target, INT4 targetLen, char *s,
                   INT4 lenS);
char *BuffFormat (SMoBUFF *buff, INT4 lineSize, 
		  INT4 firstIdent, INT4 allIdent, char *leftText);
void BuffPack (SMoBUFF *buff, char *template, ...);
INT4 BuffUnpack (SMoBUFF *buff, char *template, ...);

    /* regular expressions */

int BuffMatch (SMoBUFF *buff, char *reStr);
char *BuffGetMatch (int n);
char *BuffSubstMatch (SMoBUFF *buff, int n, char *s);


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  BuffCopyNChar as macro
*/

#define _BuffCopyNChars(b, s, len) \
{\
  if ((INT4) ((b)->writePtr - (b)->buff + (len)) >= (b)->size) \
    BuffGrow ((b), (len));\
  memcpy ((b)->writePtr, (s), (len));\
  (b)->writePtr += (len);\
}

#define _BuffReserve(buffer,len) \
  if ((INT4) ((buffer)->writePtr - (buffer)->buff + (len)) >= (buffer)->size) \
    BuffGrow ((buffer), len+1)


int n);
char *BuffSubstMatch (SMoBUFF *buff, int n, char *s);


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  BuffCopyNChar as macro
*/

#define _BuffCopyNChars(b, s, len) \
{\
  if ((INT4) ((b)->writePtr - (b)->buff + (len)) >= (b)->size) \
    BuffGrow ((b), (len));\
  memcpy ((b)->writePtr, (s), (len));\
  (b)->writePtr += (lesrs/src/srs.h
**
**    $RCSfile: srs.h,v $
**    $Revision: 1.6 $
**    $Date: 1997/03/12 16:17:46 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**    This file must be included by applications that bind to the SRS library
**
*/

#include "def.h"
#include "message.h"
#include "futil.h"
#include "sm.h"
#include "tm.h"
#include "strv.h"
#include "dict.h"
#include "idx.h"
#include "seq.h"
#include "par.h"
#include "variable.h"
#include "arglist.h"
#include "id.h"
#include "set.h"
#include "entry.h"
#include "seqdb.h"
#include "library.h"
#include "seqlib.h"
#include "query.h"
#include "queryass.h"
#include "templ.h"
#include "link.h"
#include "toklist.h"
#include "cursor.h"
#include "icarus.h"
#include "icabnf.h"
#include "view.h"
#include "appl.h"

# define _CONSTANTS
# define _SRS      
# define _SLB      
# define _SYNTAX

#ifndef DECLARE_ONLY
# define _FUNCTION
# define QUERY_M
# define XQUERY_M
# define SEQLIB_M
#endif
#include "srs5.h"

#ifndef DECLARE_ONLY
# ifndef NO_ENVIRONMENT
#  ifndef VMS
#   include "srsenv.h"
#  endif
# endif
# include "odd.h"
# define _INITOBJS
# define _CONSTANTS
# define _SDL
# define _ODD
# define _FUNCTION 
# include "oddclass.h"
#endif
.h"
#include "icarus.h"
#include "icabnf.h"
#include "view.h"
#include "appl.h"

# define _CONSTANTS
# define _SRS      
# define _SLB      
# define _SYNTAX

#ifndef DECLARE_ONLY
# define _FUNCTION
# define QUERY_M
# define XQUERY_M
# define SEQLIB_M
#endif
#isrs/src/srs5.h
**
**    $RCSfile: srs5.h,v $
**    $Revision: 1.20 $
**    $Date: 1997/03/13 19:40:06 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**             from ODD file: "srsica:srs.i"
**   date of ODD compilation: 13-MAR-1997 19:09
**
*/


#define  O_SRSDB            12
#define  LIBxFILE           1
#define  LIBxNAME           2
#define  LIBxPATH           3

#if defined(_SRS) && !defined(_ICAoSYNTAX)
#define _ICAoSYNTAX
typedef struct ICAoSYNTAX {
  char                    *name;         /* Name of the syntax. */
  char                    *fileName;     /* Name of the Icarus file with the
                                            production list. */
  char                    *rules;        /* Pointer to the production list. */
  struct SMoBUFF_         *buff;         /* Name of the file with ICA rules */
  struct ICAoSYNTAX       *commandSyntax; /* The syntax of for the commands */
  struct ICAoNAMELIST     *prodList;     /* List of productions */
  struct ICAoCOMMAND      *userCommand;
  struct taskList         *taskList;
  char                    *ign;          /* 
String containing characters to be
                                            ignored or skipped during 
parsing
                                            (white space).
 */
  char                    *lf;           /* A regular expression to skip
                                            comments. */
  unsigned char           linkFlag;
  struct VARo             *prod;
  struct VARoSCOPE        *scope;
  struct regexp           *cmntRe;
  char                    *ignAlt;
} ICAoSYNTAX;
#endif

#ifndef _PARo
#define _PARo
typedef struct PARo {
  char                    *intern;       /* for internal use for the list
                                            manager */
  INT4                    classId;       /* for internal use for the list
                                            manager */
  char                    *name;         /* name of associated global parameter
                                            */
  char                    *str;          /* Value of 'string' parameter. */
  INT4                    num;           /* Value of 'number' parameter. */
  float                   real;          /* Value of 'real' parameter. */
  INT4                    (*function) (); /* Value of 'function' parameter. */
  void                    *object;       /* Value of 'object' parameter. */
  unsigned char           isVolatile;
  unsigned char           type;          /* Parameter type. */
  char                    *comment;      /* Short description of parameter. */
  char                    *helpTopic;    /* help topic associated to parameter
                                            */
  char                    *key;          /* keystroke associated to parameter
                                            or value */
  struct PARoTYPE         *parType;      /* Object 'partype' for validating the
                                            parameter value. */
  struct PARoTYPE         *check;        /* Object 'partype' for validating the
                                            parameter value. */
  INT4                    isLocked;      /* internal use... */
  char                    *set;          /* Icarus command to set the current
                                            value. */
  char                    *get;          /* Icarus command to get the current
                                            value. */
} PARo;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Describes further a parameter type by specifying constraints or a function for checking the parameter value.
*/

#ifndef _PARoTYPE
#define _PARoTYPE
typedef struct PARoTYPE {
  char                    *intern;       /* for internal use for the list
                                            manager */
  INT4                    classId;       /* for internal use for the list
                                            manager */
  char                    *name;         /* Name of associated global
                                            parameter. */
  INT4                    (*check) ();   /* Function that checks parameter
                                            value. */
  INT4                    max;           /* Max value, or max length. */
  INT4                    min;           /* Mmin value, or min length. */
  float                   maxReal;       /* Max real value. */
  float                   minReal;       /* Min real value. */
  char                    *charSet;      /* Permissible set of chars for
                                            parameter value string. */
} PARoTYPE;
#endif

#ifndef _PARoLIST
#define _PARoLIST
typedef struct PARoLIST {
  struct PARo             *par;          /* List of all predefined parameters.
                                            */
  INT4                    parN;          /* Number of predefined parameters. */
  struct PARoTYPE         *parType;      /* List of all predefined parameter
                                            types. */
  INT4                    parTypeN;      /* Number of predefined parameter
                                            types. */
} PARoLIST;
#endif

#ifndef _arg_t
#define _arg_t
typedef struct arg_t {
  char                    *name;
  INT4                    type;
  char                    *parameter;
  char                    *comment;
  INT4                    (*check) ();
  INT4                    defaultNum;
  char                    *defaultStr;
  float                   defaultReal;
} arg_t;
#endif

#ifndef _ARGoLIST
#define _ARGoLIST
typedef struct ARGoLIST {
  char                    *name;
  char                    *usage;
  struct arg_t            *arg;
  INT4                    argN;
} ARGoLIST;
#endif

#if defined(_SRS) && !defined(_SLBoFIL)
#define _SLBoFIL
typedef struct SLBoFIL {
  char                    *nam;          /* File name without extension and
                                            directory name. */
  char                    *lnam;         /* Logical name (meaningful only for
                                            GCG programs)/ */
  INT4                    isBad;         /* This flag will be set upon failure
                                            to open this file */
} SLBoFIL;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Top level object of the databank (library) description.
*/

#if defined(_SRS) && !defined(_SLBo)
#define _SLBo
typedef struct SLBo {
  char                    *nam;          /*API Name of library. */
  char                    *shortName;    /*API Short name for library - needed
                                            for DOS file names. */
  char                    *lnam[3];      /* Logical name(s) for the library
                                            (GCG). */
  struct SRSoGROUP        *group;        /* Library group this library belongs
                                            to. */
  struct SLBo             *parent;       /* Library can be a virtual library of
                                            subentries. In that case
                                            this
attribute must point to the library of
                                            parent entries.
 */
  struct SLBoFORM         *form;         /* Pointer to the format description.
                                            */
  char                    *dirName[3];   /* Address of Name of directory with
                                            all flat files. */
  char                    *cmnt;         /* One line comment on library. */
  char                    *ifiles;       /* Name of the Icarus file(s) with the
                                            databank description. */
  INT4                    idNum;
  INT4                    maxNameLen;    /* max length of unique entry name -
                                            important for ID-index */
  INT4                    maxIndexSizeKb;
  INT4                    csiz;
  struct SLBoFIL          *fil;          /* list of pointers to file
                                            descriptions */
  INT4                    nfil;          /* number of file descriptions */
  unsigned char           skey;
  unsigned char           isFromUser;
  unsigned char           dataType;
  char                    *indexDirName; /* Address of the name of the
                                            directory with the SRS indices. */
  INT4                    pargroup;
  unsigned char           upd_f;
  unsigned char           updlink_f;
  unsigned char           isActive;      /* Flag if library is active. */
  unsigned char           isInit;        /* Flag if library is initiated. */
  struct FILo             *file[4];
  INT4                    allEntryCnt;
  INT4                    newEntryCnt;
  INT4                    updEntryCnt;
  char                    *entryNam;
  struct IDoENTRY         *idCurr;
  struct TOKoLIST         *tokList;
  struct ICAoJOB          *job;
  unsigned char           partFiles;     /* Single flat files are to be indexed
                                            as separate parts for later
                                            
merging.
 */
  struct SLBo             *subEntries[10]; /* List of all $library objects that
                                            represent subentry types.
 */
  INT4                    partSize;      /* Size of the databank part in number
                                            of entries to be indexed
                                            
separately for later merging.
 */
} SLBo;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Associates a number between 1 and 255 (library-ID) and a library 
(databank).

*/

#if defined(_SRS) && !defined(_LIBoID)
#define _LIBoID
typedef struct LIBoID {
  struct SLBo             *library;      /* Library object.  */
  INT4                    n;             /* Library-ID to be associated to the
                                            library */
} LIBoID;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  List of active libraries together with their directory names. 
A particular environment can be selected by defining the 
parameter 'environment'

*/

#if defined(_SRS) && !defined(_LIBoENV)
#define _LIBoENV
typedef struct LIBoENV {
  char                    *name;         /* Name of the environment. */
  struct LIBoLIBENV       *libenv;       /* List of active libraries. */
  INT4                    libenvN;       /* Number of libraries in that list. */
} LIBoENV;
#endif

#if defined(_SRS) && !defined(_LIBoLIBENV)
#define _LIBoLIBENV
typedef struct LIBoLIBENV {
  struct SLBo             *lib;          /* Library object. */
  char                    *dirName[3];   /* List of directory names with the
                                            library's flat files. 
The files will
                                            be searched in the directories in
                                            the same order as of 
the list.
 */
  char                    *indexDirName; /* Name of the directory with the SRS
                                            indices. */
} LIBoLIBENV;
#endif

#if defined(_SRS) && !defined(_SRSoDB)
#define _SRSoDB
typedef struct SRSoDB {
  struct LIBoID           *libId;
  INT4                    libIdN;
  struct LIBoENV          *environment;  /* List of defined library
                                            environments. */
  INT4                    environmentN;  /* Number of defined library
                                            environments. */
  struct SLBo             *slb;
  INT4                    nslb;
  struct SRSoGROUP        *group;
  INT4                    ngroup;
  struct SRSoFLD          *fld;
  INT4                    nfld;
  struct IDoTYPE          *iddsc;
  INT4                    niddsc;
  struct SRSoFILTYP       *filtyp;
  INT4                    nfiltyp;
  struct LINKo            *lnk;
  INT4                    nlnk;
  struct ICAoSYNTAX       *syntax;
  INT4                    syntaxN;
  struct ARGoLIST         *command;
  INT4                    commandN;
  struct APPLo            *application;
  INT4                    applicationN;
  struct PARoLIST         *parTable;     /* table of predefined global
                                            parameters */
  struct VIEWo            *view;
  INT4                    viewN;
  struct LIBoHREF         *href;
  INT4                    hrefN;
  INT4                    xcopy_n;
  INT4                    xlist_n;
  INT4                    copy_fst;
  INT4                    list_fst;
  struct SLBo             **libTable;
} SRSoDB;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Description of a library (databank) group.
*/

#if defined(_SRS) && !defined(_SRSoGROUP)
#define _SRSoGROUP
typedef struct SRSoGROUP {
  char                    *key;
  char                    *com;          /*API Name of library group. */
  char                    *short_nm;     /*API Short name (abbreviation) of
                                            library group. */
  char                    *cmnt;         /* A single line of text describing
                                            the group. */
  char                    *help;
  unsigned char           single_f;      /* This flag determines if all
                                            libraries in the group can be
                                            searched
simultaneously or one at a time (this is
                                            advisable if the libraries 
differ
                                            greatly in their data-fields.
 */
  struct SLBo             *library[50];  /* Pointers to the libraries in the
                                            group */
  INT4                    libraryN;
  struct SLBoFIELD        *field[500];
  INT4                    fieldN;
  char                    *fieldCount;
  unsigned char           upd_f;
} SRSoGROUP;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Description of a data-field within a library.
*/

#ifndef _SLBoFIELD
#define _SLBoFIELD
typedef struct SLBoFIELD {
  unsigned char           index;         /* Index type - 'show' means that the
                                            field can be displayed only;
                                            
'group' points to a group of indices.
 */
  char                    *name;
  char                    *code;         /* Code of the token in the 'fields'
                                            token list that contains the
                                            
data-field.
 */
  INT4                    fieldTokCode;
  char                    *token;        /* If the data-field is not contained
                                            in the 'fields' token list the 
full
                                            name 'tokenList|code' must be
                                            specified here.
 */
  struct IDoTYPE          *indexId;      /* The ID-type description for the IDs
                                            that will be put into the index.
 */
  char                    *indexToken[5]; /* The name of the token list that
                                            supplies the values for indexing. 
The
                                            list name may be followed by a
                                            token code separated by ':'.
 */
  INT4                    indexTokCode[5];
  unsigned char           isSystem;      /* A 'system' data field is only for
                                            internal use and should be 
ignored
                                            by a user interface.
 */
  unsigned char           keyConvert;    /* Directs conversion of index
                                            strings.
 */
  struct SRSoFLD          *type;         /*API Object that describes the
                                            data-field type. */
  struct SRSoFLD          *replace;      /*API Field type of corresponding
                                            field object from parent entry in
                                            case
it is not the same.
 */
  struct SLBoFIELD        *parent;       /* Indicates if the field definition
                                            of the parent entry library should
be
                                            taken instead.
 */
  struct IDXo             *idx;
  struct INXo             *inx;
  struct BTRo             *btree;
  struct IDSoFILE         *idFile;
  unsigned char           do_f;
  INT4                    *on_fp;
  INT4                    pargroup;
  unsigned char           done_f;
  unsigned char           noerrmsg_f;    /* Supresses printing of parsing error
                                            messages. */
  char                    *format;       /* Name of default format of the
                                            contents of a 
field (see $srsfield).
 */
  char                    *tableToken;   /* Name of the table and the token
                                            code. */
  INT4                    tableTokCode;
  unsigned char           tableFormat;   /* The format of the default as
                                            displayed inside a 'table view'.
If left
                                            unspecified then the same attribute
                                            of the 'format'
object is read.
 */
} SLBoFIELD;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Specifies the parser to be used for parsing all data-fields of a library, 
its flat file format and has a list of all data-field descriptions.

*/

#if defined(_SLB) && !defined(_SLBoFORM)
#define _SLBoFORM
typedef struct SLBoFORM {
  struct SLBoFIELD        *f;
  INT4                    nf;
  unsigned char           access_f;
  struct ICAoSYNTAX       *syntax;       /* The syntax of the flat file entry.
                                            */
  struct SRSoFILTYP       *fil_t[4];     /* List of flat file types. There can
                                            be more than (eg, the sequence 
and
                                            annotation are stored in two
                                            different files).
 */
  unsigned char           tableFormat;
  unsigned char           printFormat;
  struct DICTo            *tokenDict;
  INT4                    isInit;
  struct LIBoDataType     *contains[5];  /* List of types of data contained in
                                            the databank described.
 */
} SLBoFORM;
#endif

#ifndef _LIBoFieldFormat
#define _LIBoFieldFormat
typedef struct LIBoFieldFormat {
  char                    *name;
  char                    *eval;
  INT4                    isSelected;
} LIBoFieldFormat;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Description of a data-field Type (eg, 'Authors').
*/

#if defined(_SRS) && !defined(_SRSoFLD)
#define _SRSoFLD
typedef struct SRSoFLD {
  char                    *shortn;       /*API Short name (abbreviation) of
                                            data-field type */
  char                    *nam;          /*API Short name of data-field type */
  char                    *cmnt;
  INT4                    pargroup;
  unsigned char           ityp;          /* The type of the field type. At the
                                            moment only 'header' is used.
The
                                            other types should be used to enforce
                                            a certain type on all
the library
                                            fields referencing them.
 */
  unsigned char           isGroup;       /* field type: single or group (of
                                            other field types) */
  struct SRSoFLD          *group;        /* pointer to the field type group */
  struct LIBoFieldFormat  *format;
  INT4                    formatN;
} SRSoFLD;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Every entry of every databank indexed in SRS is represented by an 
entry-ID which uniquely identifies it. Several ID types are defined 
(eg, entry-ID, seq-ID, 3D-ID). Only the subentry-ID is structurally 
different from the others.

*/

#if defined(_SRS) && !defined(_IDoTYPE)
#define _IDoTYPE
typedef struct IDoTYPE {
  char                    *nam;          /* Name of Id-type. */
  INT4                    siz;           /* Size of ID in number of bytes. */
  INT4                    fddbeg;        /* Offset of fadd (file address within
                                            IDX file) within ID. */
  INT4                    fddlen;        /* Size of fadd in bytes. */
  INT4                    lbxbeg;        /* Offset of databank-ID within ID. */
  INT4                    lbxlen;        /* Size of databank-ID in bytes. */
  INT4                    lxbeg;         /* Offset of subentry number within
                                            ID. */
  INT4                    lxlen;         /* Size of subentry number in bytes. */
  INT4                    (*cpy) ();     /* Function for printing an individual
                                            entry represented by  ID. */
} IDoTYPE;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Describes a flat file type. Databanks may have more than one flat file
type, eg, databanks in PIR or GCG with 'ref'-files containing the 
sequence annotation and 'seq'-files with the sequence.

*/

#if defined(_SRS) && !defined(_SRSoFILTYP)
#define _SRSoFILTYP
typedef struct SRSoFILTYP {
  char                    *name;         /* Symbolic name of the file. */
  char                    *typ_nm;       /* File extension name. */
  char                    *searchName;   /* A search string used for finding
                                            all files in the specified 
directory
                                            (only for file per entry databanks).
                                            Any number of 
wildcards ('*' -
                                            matches all, '?' matches all single
                                            character) may 
be used.
 */
  INT4                    ln_z;
  UINT4                   context;
  char                    *fipVar;       /* Name of the Icarus variable
                                            containing the file address of the
entry
                                            begin.
 */
  struct SRSoFILTYP       *shareWith;    /* The file type can be only logical
                                            and the actual file object
shared
                                            with another file type. It is to
                                            pretend that input comes
from two
                                            different files where in fact it doesn't.
 */
  char                    *fieldTokens;  /* Name of the token table that has
                                            one token for each data-field of
the
                                            entry.
 */
  INT4                    saveName;      /* For databanks where each entry
                                            resides in a separate file where
                                            the
file name cannot be inferred from the
                                            entry name. Option
to request the
                                            whole or part of the file name to be
                                            saved in the
IDX index.
 */
  INT4                    saveNameLength; /* Max. length of the name saved
                                            according to 'saveName'.
 */
  unsigned char           sngl_f;        /* Selects a file has only one single
                                            entry. */
  char                    *pipe;         /* Format string (printf style) to
                                            create a command for processing the
                                            
entry file before reading (eg,
                                            'uncompress %%s'). 
 */
} SRSoFILTYP;
#endif

#ifndef _LIBoSUBENTRY
#define _LIBoSUBENTRY
typedef struct LIBoSUBENTRY {
  char                    *name;
  struct IDoTYPE          *idType;
  struct SRSoFLD          *first;
  struct SLBoFIELD        *fields;       /* The Definition of the fields of the
                                            subentry. Each field must
                                            
correspond to a field in the parent entry.
                                            Part of the definition
(such as
                                            'token' can 'shadow' the definition of
                                            the parent).
 */
  INT4                    fieldsN;
} LIBoSUBENTRY;
#endif

#ifndef _LIBoHREF
#define _LIBoHREF
typedef struct LIBoHREF {
  char                    *name;
  char                    *link;
} LIBoHREF;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Specifies a link between two libraries. A link can be built by using two
indices built from one data-field of each library ('type=index') or by
reading one library and processing cross-reference data ('type=read').

*/

#if defined(_SRS) && !defined(_LINKo)
#define _LINKo
typedef struct LINKo {
  INT4                    val;           /* The weight attached to a link can
                                            be used to eliminate
                                            ambiguities
during path resolution, or to force a
                                            certain path.
 */
  char                    *token;
  INT4                    tokCode;
  INT4                    codeNum;
  char                    *nam1;         /* Name of the first library - in case
                                            not the library name itself. */
  char                    *nam2;         /* Name of the first library - in case
                                            not the library name itself. */
  struct IDoTYPE          *id1_d;        /* Object describing the first
                                            library's ID's to be linked. */
  struct IDoTYPE          *id2_d;        /* Object describing the second
                                            library's ID's to be linked. */
  struct SLBo             *lib1;         /* Object desribing the first library.
                                            */
  struct SLBo             *lib2;         /* Object desribing the second
                                            library. */
  struct SRSoFLD          *fromField;    /* Object describing the data-field of
                                            first library providing
                                            link
information (only for index links).
 */
  struct SRSoFLD          *toField;      /* Object describing the data-field of
                                            second library providing link
                                            
information (for both index- and
                                            read-links).
 */
  unsigned char           rev_f;
  unsigned char           init_f;
  unsigned char           isActive;
  unsigned char           do_f;
  INT4                    goodRefN;
  INT4                    badRefN;       /* count of unsuccessful links */
  INT4                    lib1EntryN;    /* number of entries from library 1
                                            linked */
  INT4                    lib2EntryN;    /* number of entries from library 2
                                            linked */
  INT4                    linkIdN;
  IDPTR                   id_p;
  char                    *idWrtOff;
  struct FILEo            *toFile;
  struct FILEo            *fromFile;
  struct BTRo             *btree1;
  struct BTRo             *btree2;
  struct IDSoFILE         *ids1;
  struct IDSoFILE         *ids2;
  struct LINKo            *use;          /* Reference to the link object to be
                                            used to resolve the link.
 */
  INT4                    isOpen;
  unsigned char           typ;           /* Type of the link. 'read': first
                                            library must be read to find
                                            
cross-references to second library; 'index':
                                            two indices, one from
each library
                                            will be used to build the link;
                                            'parent': link between 
entry and
                                            subentry.
 */
} LINKo;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Description of individual data-fields of both root and leaf databanks
of a view.

*/

#ifndef _VIEWoFIELD
#define _VIEWoFIELD
typedef struct VIEWoFIELD {
  struct SRSoFLD          *type;         /* Reference the object describing the
                                            field type.
 */
  char                    *format;       /* If the field type has additional
                                            format options a format can
                                            be
specified for the field, otherwise the
                                            default will be taken.
 */
} VIEWoFIELD;
#endif

#ifndef _VIEWoLIB
#define _VIEWoLIB
typedef struct VIEWoLIB {
  struct SLBo             *lib;
  struct VIEWoFIELD       *fields;
  INT4                    fieldsN;
  INT4                    fieldsAllocN;
  char                    *query;
  char                    *viewName;
  unsigned char           printOnlyEntryN;
} VIEWoLIB;
#endif

#ifndef _VIEWo
#define _VIEWo
typedef struct VIEWo {
  char                    *name;
  INT4                    format;
  unsigned char           isEntryNamePrinting;
  unsigned char           useShortFieldNames;
  struct VIEWoLIB         *root;
  INT4                    rootN;
  INT4                    rootAllocN;
  struct VIEWoFIELD       *rootFields;
  INT4                    rootFieldsN;
  INT4                    rootFieldsAllocN;
  struct VIEWoLIB         *leaves;
  INT4                    leavesN;
  INT4                    leavesAllocN;
  INT4                    n;
  INT4                    isNascent;
  INT4                    isDeleted;
  char                    *templateFile;
  struct TEMPLo           *templ;
  void                    (*entryNamePrint)();
  void                    (*entryNPrint)();
} VIEWo;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Description of a data type which can be linked to applications.

*/

#ifndef _LIBoDataType
#define _LIBoDataType
typedef struct LIBoDataType {
  char                    *name;         /* Symbolic name of the data-type, eg,
                                            "DNASequence"
 */
  struct APPLo            *applications[20]; /* List of applications that can
                                            be called with data of this type.
 */
} LIBoDataType;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Description of an application to be called on data of a certain type.

*/

#ifndef _APPLo
#define _APPLo
typedef struct APPLo {
  char                    *name;         /* Symbolic name of the application.

                                            */
  char                    *title;        /* Short description of the program
                                            that can be used in a title line.
 */
  INT4                    type[5];       /* Type of the application.
 */
  INT4                    inSeqFormat;   /* Format of the input sequence(s)
 */
  struct APPLoOpt         *options;      /* List of command line options.
 */
  INT4                    optionsN;
  char                    *command;      /* Icarus script used to defined the
                                            command line to call the 
application
                                            program.
 */
  char                    *launch;       /* Icarus script used to launch the
                                            program. The script relies
                                            on
$opt.command being defined
 */
  struct ICAoJOB          *interp;
  struct STRo             *com;
} APPLo;
#endif

#ifndef _APPLoOpt
#define _APPLoOpt
typedef struct APPLoOpt {
  char                    *name;
  struct APPLoOptGroup    *group;
  char                    *prompt;
  INT4                    type;
  INT4                    guiType;
  struct APPLoOptVal      *values;       /* List of option values.
 */
  INT4                    valuesN;
  char                    *defStr;
  INT4                    defInt;
  float                   defReal;
} APPLoOpt;
#endif

#ifndef _APPLoOptVal
#define _APPLoOptVal
typedef struct APPLoOptVal {
  char                    *name;
  char                    *prompt;
  char                    *valStr;
  INT4                    valInt;
  float                   valReal;
  INT4                    on;
} APPLoOptVal;
#endif

#ifndef _APPLoOptGroup
#define _APPLoOptGroup
typedef struct APPLoOptGroup {
  char                    *name;
} APPLoOptGroup;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Value in an enumeration
*/

#ifndef _ODDoVALUE
#define _ODDoVALUE
typedef struct ODDoVALUE {
  char                    *name;         /* Name of value. */
  INT4                    n;             /* Number value. */
  char                    *rem;          /* Comment field. */
} ODDoVALUE;
#endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Argument of Icarus command.
*/

#ifndef _IARGoVALUE
#define _IARGoVALUE
typedef struct IARGoVALUE {
  char                    *name;         /* Name of the argument in an Icarus
                                            program. */
  char                    *rem;          /* Comment field. */
  unsigned char           isUnnamed;     /* Defines if parameter may be
                                            unnamed. */
  unsigned char           isRequired;    /* Defines if parameter is required. */
  unsigned char           type;          /* Type of the argument */
  char                    *className;
  INT4                    defInt;        /* Default value of type 'int'
                                            arguments. */
  char                    *defaultStr;   /* Default value of type 'string'
                                            arguments. */
  struct ODDoVALUE        *vals;
  INT4                    valsN;
  unsigned char           isSet;
  struct VARo             *val;
} IARGoVALUE;
#endif

#ifndef _IARGoCOM
#define _IARGoCOM
typedef struct IARGoCOM {
  char                    *name;         /* Name of command in Icarus programs.
                                            */
  char                    *functionName; /* C function that implements the
                                            command. */
  INT4                    isShow;        /* Determines whether the command
                                            should appear in the 
Icarus functions
                                            reference list.
 */
  char                    *rem;          /* Comment field. */
  unsigned char           returnType;    /* Type of value to be returned (if
                                            any). */
  INT4                    time;          /* Execution time of command. */
  char                    *returnClass;
  unsigned char           isDirectCall;  /* Call function directly or via
                                            C-interface. */
  char                    *methodOf;     /* The class of which this function is
                                            a method otherwise treated
                                            as
normal function.
 */
  struct IARGoVALUE       *args;
  INT4                    argsN;
  INT4                    (*function)(); /* Function to be executed for
                                            command. */
  INT4                    orderN;        /* Number of arguments ordered from C
                                            function (via 'IargGetArgs'). */
  INT4                    orderAllocN;   /* Number of orders currently
                                            allocated. */
  struct IARGoVALUE       **order;       /* Array with a list of argument
                                            orders. */
} IARGoCOM;
#endif

#ifdef _FUNCTION
#undef _FUNCTION

INT4 LibParSetFields (char *);
#define LibParSetFields_F (INT4(*)()) LibParSetFields
INT4 LibParSetLibs (char *);
#define LibParSetLibs_F (INT4(*)()) LibParSetLibs
INT4 LibParSetLinkLibs (char *);
#define LibParSetLinkLibs_F (INT4(*)()) LibParSetLinkLibs
INT4 LibSetEnvironment (char *);
#define LibSetEnvironment_F (INT4(*)()) LibSetEnvironment
INT4 LibParSetLibsViewRoot (char *);
#define LibParSetLibsViewRoot_F (INT4(*)()) LibParSetLibsViewRoot
INT4 LibParSetLibsViewLeaf (char *);
#define LibParSetLibsViewLeaf_F (INT4(*)()) LibParSetLibsViewLeaf
typedef INT4 (*SDLoFNCTx)();


SDLoFNCTx    SDL_fnctx[] = {
    LibParSetFields_F, LibParSetLibs_F, LibParSetLinkLibs_F,
    LibSetEnvironment_F, LibParSetLibsViewRoot_F, LibParSetLibsViewLeaf_F
};
#endif
tLinkLibs
INT4 LibSetEnvironment (char *);
#define LibSetEnvironment_F (INT4(*)()) LibSetEnvironment
INT4 LibParSetLibsViewRoot (char *);
#define LibParSetLibsViewRoot_F (INT4(*)()) LibParSetLibsViewRoot
INT4 LibParSetLibsViewLeaf (char *);srs/src/srsbuild.c
char srsbuild_srs_ID[] = "$Id: srsbuild.c,v 1.18 1997/03/13 19:40:08 srs Exp $";
/*
**
**    $RCSfile: srsbuild.c,v $
**    $Revision: 1.18 $
**    $Date: 1997/03/13 19:40:08 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**           Unix port: Lukas Rosenthaler and Reinhard Doelz
**
**            Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires:  
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
** 
**  
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdarg.h>
#include <string.h>

#include "srs.h"
#include "merge.h"
#include "btree.h"
#include "index.h"
#include "ids.h"

#define BLDxMAXTMPSETSIZE 10000

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of static functions
*/

static void BldLibIndex (char *libName);
static void BldLibRelocate (char *libName);
static void BldCompress (char *libName);
static void BldSetReleaseName (char *libName);
static void BldIndexTouch (char *libName);
static void BldIndexLink (char *lib1Name, char *lib2Name);
static void BldReadLink (char *libName);
static void BldIndicesOpen (ENTRYv entry);
static void BldIndicesClose (SLBo *lib);
static void BldEntryFinish (ENTRYv entry);
static void BldShowWords (ENTRYv entry, SLBoFIELD *field);
static int BldIndexOpen (SLBo *lib, SLBoFIELD *field, Int4 partNo);
static INT4 BldEntryId (ENTRYv entry);
static LINKo *BldLinkFind (INT4 code);
static void BldMakeLinkDict (SLBo *lib);
static void BldIndexMerge (char *libName);


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  function used by module "message" for printing error messages
*/

static int PrintMessage (MSGo *msg) 
{ 

  if (!ParGetNum ("showWarnings")) {
    switch (msg->msg_code) {
    case e__parsefail:
    case e__novalreference:
    case e__namnotuniq:
    case e__bldparsefail:
    case e__parsererror1:
    case e__parsererror2:
    case e__parsererror3:
      return 0;
    }
  }

  IcaPrintMessage (msg);
  return 1;
}




/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  main section...
*/


int main (int argc, char **argv)
{
  ARGoLIST *arglist;
  char     *tmpStr;

  LibOpen ("srs5");
  arglist = (ARGoLIST *) LibObjByName ("arglist", "srsbuild");
  argc = ArgGet (arglist, argc, argv);
  MsgSetFnct ((FUNC)IcaPrintMessage);

  IcaInitSyntax (LibObjByName ("syntax", "icarus"));
  
  if (ParGetNum ("indexLink") && argc == 3) {
    MsgSetFnct ((Func)PrintMessage);
    BldIndexLink (argv[1], argv[2]);
  }
  else if (ParGetNum ("compress") && argc == 2) 
    BldCompress (argv[1]);
  else if (ParGetNum ("touchIndex") && argc == 2) 
    BldIndexTouch (argv[1]);
  else if ((tmpStr = ParGetStr ("releaseName")) && *tmpStr && argc == 2) 
    BldSetReleaseName (argv[1]);
  else if (ParGetNum ("printLibInfo") && argc == 2) 
    LibPrintInfo (argv[1]);
  else if (ParGetNum ("relocateLib") && argc == 2) 
    BldLibRelocate (argv[1]);	  
  else if (ParGetNum ("readLink") && argc == 2) 
    BldReadLink (argv[1]);	  
  else if (ParGetNum ("mergeIndex") && argc == 2)
    BldIndexMerge (argv[1]);
  else if (ParGetNum ("buildIndex") && argc == 2) 
    BldLibIndex (argv[1]);	  
  else
    ArgUsage (arglist);

  exit (0);
}


/****** BldLibIndex ***********************************************************
** 
** 	do the indexing of a library;
** 
** 	INPUT:	    name of library
** 		IMPLICIT:
** 		    convert (int) [W]
**                  global parameter "fieldList" [R]
**                  global parameter "newId" [W]
** 
** 	RETURNS:
*/ 

static void BldLibIndex (char *libName)
{
  SLBo   *lib;
  char   *fieldList, *fieldName;
  ENTRYv entry;
  Int4   k;

  if (!(lib = (SLBo *) LibObjByName ("library", libName)))
    _ErrExit3 (e__objectunknown, "library", libName);
  _ErrMsg2 (i__processing, lib->nam);
  
  /* select data-fields for processing */
  LibSetField (libName, 0, "xinit");
  if ((fieldList = ParGetStr ("fieldList")) && *fieldList)
    while ((fieldName = strtok (fieldList, " "))) {
      fieldList = NULL;
      LibSetField (libName, fieldName, "set");
      /* if an ID field is among the selected the "newId" flag must be set */
      if (LibIsIdField (libName, fieldName))
	ParDefNum ("newId", 1);  /* new ID index must be build  */
    }
  else {
    LibSetField (libName, 0, "allindex");
    ParDefNum ("newId", 1);  /* new ID index must be build  */
  }

  entry = EntryOpenStream (lib);
  MsgSetFnct ((Func)PrintMessage);
  for (k=0; EntryNext (entry); k++) {
    if (EntryIsPartBegin (entry)) {
      if (k)
	BldIndicesClose (lib);
      BldIndicesOpen (entry);	      
    }
    BldEntryFinish (entry);
  }
  BldIndicesClose (lib);	      
}

static void BldActivateFields (char *libName, char *option)
{
  char *fieldList, *fieldName;

  /* set the fields (indices to be processed */
  LibSetField (libName, 0, "init");
  if ((fieldList = ParGetStr ("fieldList")) && *fieldList) {
    ParDefNum ("parSetFields", 1);
    while ((fieldName = strtok (fieldList, " "))) {
      fieldList = NULL;
      LibSetField (libName, fieldName, "set");
    }
  }
  else 
    LibSetField (libName, 0, "compress"); /*compress is the same as allIndex*/
}

/****** BldCompress ***********************************************************
** 
** 
** 	INPUT:	    name of library
** 		IMPLICIT:
** 		    convert (int) [W]
**                  global parameter "fieldList" [R]
**                  global parameter "newId" [W]
** 
** 	RETURNS:
*/ 

static void BldCompress (char *libName)
{
  SLBo      *lib;
  SLBoFIELD *field;
  char      fileName[FILxXNAM+1];
  int       c, partNo;

  if (!(lib = (SLBo *) LibObjByName ("library", libName)))
    _ErrExit3 (e__objectunknown, "library", libName);
  BldActivateFields (libName, "compress"); 

  /* iterate over active fields (indices) */
  
  for (partNo=0; MergeNextPartNo (lib, &partNo); ) {
    for (c=0; (field = (LibNextField (lib, &c))); ) 
      if (FieldIs (field, "active")) { 
	if (FieldIs (field, "index")) {
	  if (partNo != -1) 
	    MergeGetIndexPartName (lib, field, partNo, "write", fileName);
	  else 
	    LibGetIndexName (lib, field, fileName, "write");
	  BtrCompress (fileName);
	}
	else
	  _ErrMsg2 (e__inxnotcompress, field->type->nam);
      }
  }
}

/****** BldIndexMerge *********************************************************
** 
** 	Merges all index partitions to single index.
** 
** 	INPUT:	    name of library
**
*/ 

static void BldIndexMerge (char *libName)
{
  SLBo      *lib;
  SLBoFIELD *field;
  MERGEvSet merge;
  char      fileName[FILxXNAM+1];
  Int4      c;
  
  if (!(lib = (SLBo *) LibObjByName ("library", libName)))
    _ErrExit3 (e__objectunknown, "library", libName);
  if (!LibIs (lib, "partitioned"))
    _ErrExit2 (e__bldLibNotMerge, libName);
  BldActivateFields (libName, "compress");

  merge = MergeInit (lib);
  ParDefNum ("buildIndex", 1); /* for BldIndexOpen */
  for (c=0; (field = (LibNextField (lib, &c))); ) 
    if (FieldIs (field, "active")) {
      MergeIndex (merge, field);
    }
  BldIndicesClose (lib);	      
}

/****** BldIndexTouch *********************************************************
** 
**      sets internal index date to current date ...this is necessary if
**      the original flat files are moved after index building; 
**
** 	INPUT:	    name of library
** 		IMPLICIT:
** 		    convert (int) [W]
**                  global parameter "fieldList" [R]
**                  global parameter "newId" [W]
** 
** 	RETURNS:
*/ 

static void BldIndexTouch (char *libName)
{
  SLBo      *lib;
  SLBoFIELD *field;
  char      *fieldList, *fieldName, fileName[FILxXNAM+1];
  int       c;

  if (!(lib = (SLBo *) LibObjByName ("library", libName)))
    _ErrExit3 (e__objectunknown, "library", libName);
  BldActivateFields (libName, "touch"); 

  for (c=0; (field = LibNextField (lib, &c)); ) 
    if (FieldIs (field, "active")) {
      LibGetIndexName (lib, field, fileName, "read");
      BtrTouch (fileName);
      if (FieldIs (field, "id")) 
	IdxTouch (fileName);
    }
}

/****** BldLibRelocate ********************************************************
** 
** 	processes a file of a sequence library;
** 
** 	INPUT:	    library object [W]
** 		IMPLICIT:
** 
** 	OUTPUT:
** 		    returns:	
*/ 
   
static void BldLibRelocate (char *libName)
{
  SLBo      *lib;
  SLBoFIELD *field;
  ENTRYv    entry;

  if (!(lib = (SLBo *) LibObjByName ("library", libName)))
    _ErrExit3 (e__objectunknown, "library", libName);

  LibSetField (libName, 0, "xinit"); /* activate ID-index */
  BldIndexOpen (lib, LibGetIdField (lib), 0);

  entry = EntryOpenStream (lib);
  MsgSetFnct ((Func)PrintMessage);
  while (EntryNext (entry)) {
    BldEntryId (entry);
  }
  BldIndicesClose (lib);	      

}

/****** BldSetReleaseName *****************************************************
** 
** 	associates a release name to the library's indices
** 
** 	INPUT:	    library name [W]
** 		IMPLICIT:
** 
** 	OUTPUT:
** 		    returns:	
*/ 
   
static void BldSetReleaseName (char *libName)
{
  SLBo         *lib;
  SLBoFIELD    *field;
  struct IDXo *idx;
  char         indexName[133];
  INT4         errCode;

  lib = (SLBo *) LibObjByName ("library", libName);
  if (!lib) 
    _ErrExit3 (e__objectunknown, "library", libName);
  
  field = LibGetIdField (lib);
  LibGetIndexName (lib, field, indexName, "read");
  
  idx = IdxOpen (indexName, "update", 0, &errCode);
  _ErrExit2 (errCode, indexName);

  IdxSetReleaseName (idx, ParGetStr ("releaseName"));
  IdxClose (idx);
}



/****** BldIndicesOpen *******************************************************
** 
** 	Opens all indices for index building
** 
** 	INPUT:	    library object [W]
** 
*/ 

static void BldIndicesOpen (ENTRYv entry)
{
  SLBo      *lib=EntryGetLib (entry);
  SLBoFIELD *field;
  Int4      c, partNo;

  if (LibIs (lib, "partitioned")) 
    partNo = EntryGetPartNo (entry);
  else
    partNo = 0;

  if (!ParGetNum ("parseTest")) {
    for (c=0; (field = LibNextField (lib, &c));)
      if (FieldIs (field, "active"))
	BldIndexOpen (lib, field, partNo);
  }
}

/****** BldIndicesClose *******************************************************
** 
** 	prepares a library for indexing
** 
** 	INPUT:	    library object [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
*/ 

static void BldIndicesClose (SLBo *lib)
{
  LINKo     *link;
  SLBoFIELD *field;
  int	    context;

  for (context=0; (field = LibNextField (lib, &context)); ) {
    if (!field->do_f)
      continue;
    
    if (field->idx)
      IdxClose (field->idx);
    if (field->inx)
      InxClose (field->inx);
    if (field->btree)
      BtrClose (field->btree);
  }
}




/****** BldIndexLink **********************************************************
** 
** 	links two libraries using two selected indices
** 
** 	INPUT:	    name of one library [R]
** 		    name of other library [R]
** 	        IMPLICIT:
** 
** 	RETURNS:    1
*/ 
   
static void BldIndexLink (char *lib1Name, char *lib2Name)
{
  LINKo    *link;
  BTRoREC  *record1, *record2;
  SETo     *set1, *set2;
  FIP      idFip1, idFip2;
  int      opt;

  if (!(link = LibGetLink (lib1Name, lib2Name)))
    _ErrExit3 (e__novallink, lib1Name, lib2Name);
  if (!(link = LinkOpen (link, "writeindex")))
    exit (0);

  set1 = SetNew (NULL, "temp");
  set2 = SetNew (NULL, "temp");
  SetAlloc (set1, BLDxMAXTMPSETSIZE, link->id1_d);
  SetAlloc (set2, BLDxMAXTMPSETSIZE, link->id2_d);

  for (idFip1=1, opt=BTRxFIRST; (record1 = BtrRecordGet (link->btree1, opt));
       idFip1++, opt=BTRxNEXT) {
    if ((record2 = BtrSearch (link->btree2, record1->str, &idFip2, 0))) {
      LinkCollectSet (set1, record1, link->ids1);
      LinkCollectSet (set2, record2, link->ids2);
      LinkSets (link, set1, set2);
      link->goodRefN++;
    }
    else {
      _ErrMsg4 (e__novalreference, link->lib1->nam, link->lib2->nam, 
		   record1->str);
      link->badRefN++;
    }
  }
  if (link->linkIdN)
    LinkClose (link);
}


void BldPrintProgress (ENTRYv entry)
{
  SLBo *lib=EntryGetLib (entry);

  if (lib->allEntryCnt % 300 == 0) 
    _ErrMsg3 (i__processingentry, lib->allEntryCnt, EntryGetName (entry)); 
}


/**api* BldReadLink *****************************************************************
** 
** 	Processes all 'read links' for specified databank. Opens the flat file,
**      reads entries one by one and builds link indices.
** 
** 	INPUT:	    library name [R]
*/ 
   
static void BldReadLink (char *libName)
{
  SLBo      *lib;
  SLBoFIELD *field;
  ENTRYv    entry;
  LINKo     *link;
  TOKoLIST  *tokList;
  TOKoTOKEN *tok;
  char      *tokListName, *tokStr;
  Int4      i, j, k, code, isTest=ParGetBool ("parseTest");

  if (!(lib = (SLBo *) LibObjByName ("library", libName)))
    _ErrExit3 (e__objectunknown, "library", libName);

  if (!isTest)
    BldIndexOpen (lib, LibGetIdField (lib), 0);
  for (i=0, k=0; (link = LinkNext (lib, "read", &i)); k++) {
    _ErrMsg2 (i__bldReadLink, LibGetLinkToName (link)); 
    if (!isTest)
      link = LinkOpen (link, "writeread");
  }
  if (!k) {
    _ErrMsg2 (e__bldNoReadLinks, libName);
    return;
  }
    
  entry = EntryOpenStream (lib);
  MsgSetFnct ((Func)PrintMessage);
  while (EntryNext (entry)) {
    BldEntryId (entry);
    for (i=0; (link = LinkNext (lib, "read", &i));) {
      for (k=0; (tokListName = LinkNextToken (link, &code, &k));) {
	tokList = IcaGetTokenList (EntryGetJob (entry), tokListName);
	for (j=0; (tok = TokNextWithCode (tokList, code, &j));) {
	  tokStr = TokGetStringCopy (tokList, tok);
	  if (isTest) 
	    printf (" code: %d, %s -> %s\n", 
		    code, tokStr, LibGetLinkToName (link)); 
	  else if (!LinkIdWithString (link, EntryGetId (entry), tokStr)) 
	    _ErrMsg4 (e__novalreference, LibGetLinkFromName (link),
		      LibGetLinkToName (link), tokStr);
	}	  
      }
    }
  }
  if (!isTest)
    for (i=0; (link = LinkNext (lib, "read", &i));) 
      LinkClose (link);
}



/****** BldIndexOpen **********************************************************
** 
** 	opens an index and links it to the data-field;
** 
** 	INPUT:	    library object [R]
**                  data-field object [R]
**                  number of library part [R] or 0
** 	        IMPLICIT:
**                  global parameter "newId" [R]
**                  global parameter "buildIndex" [R]
** 
** 	RETURNS:    1
*/ 
   
static int BldIndexOpen (SLBo *lib, SLBoFIELD *field, Int4 partNo)
{
  INXo *index=NULL;
  char readIndexName[133], writeIndexName[133];
  Int4  errCode;

  /*
  ** two different file names...input directory is not necessarily
  ** the output directory
  */

  if (partNo) {
    MergeGetIndexPartName (lib, field, partNo, "read", readIndexName);
    MergeGetIndexPartName (lib, field, partNo, "write", writeIndexName);
  }
  else {
    LibGetIndexName (lib, field, readIndexName, "read");
    LibGetIndexName (lib, field, writeIndexName, "write");
  }

  /*
  ** open index for writing
  */
 
  if (ParGetNum ("relocateLib")) {
    field->idx = IdxOpen (writeIndexName, "write", 
			  LibGetIdRecordSize (lib), &errCode);
    _ErrExit2 (errCode, writeIndexName);
  }

  else if (ParGetNum ("buildIndex")) {
    if (FieldIs (field, "id") && !ParGetNum ("newId")) {
      field->btree = BtrOpen (readIndexName, "read", &errCode);
      _ErrExit2 (errCode, FileGetName (field->btree->file, "path"));
      if (!(field->idFile = IdsOpen (readIndexName, "read", 0, NULL,&errCode)))
	_ErrExit (e__error);
    }
    else {
      if (FieldIs (field, "index")) { 
	index = InxOpen (writeIndexName, "new");

	if (FieldIs (field, "num")) 
	  InxSetType (index, "num");
	else if (FieldIs (field, "real")) 
	  InxSetType (index, "real");
	else
	  InxSetType (index, "string");

	InxSetCache (index, lib->csiz);
	if (FieldIs (field, "id")) {
	  field->idx = IdxOpen (writeIndexName, "write", 
				LibGetIdRecordSize (lib), &errCode);
	  _ErrExit2 (errCode, writeIndexName);
	  if (LibHasNoFiles (lib) && !LibIsFilePerEntry (lib))
	    LibSetLibFlatFiles (lib, field->idx); 
	}
      }
      else 
	_ErrExit2 (e__fieldnotindex, field->type->nam);
    }
  }
  field->inx = index;
  return 1;
}


/****** BldEntryId ************************************************************
** 
**      Gets the entry-ID and places it into the ID index if appropriate.
** 
** 	INPUT:	    entry object [w]
** 
** 	RETURNS:    1: normal completion
**                  0: no valid entry-id token could be obtained 
*/ 

static INT4 BldEntryId (ENTRYv entry)
{
  SLBoFIELD *field;
  TOKoLIST  *tokList;
  TOKoTOKEN *tok;
  SLBo      *lib=EntryGetLib (entry);
  char      *tokStr, *buff;

  EntryParse (entry);

  field = LibGetIdField (EntryGetLib (entry));
  tokList = EntryGetTokList (entry, field->indexToken[0]);
  if (!(tok = TokGetFirst (tokList)))
    return 0;
  tokStr = TokGetStringCopy (tokList, tok);
  strcpy (EntryGetName (entry), tokStr);

  /* get entry ID and insert into index */

  if ((ParGetBool ("newId") || ParGetBool ("relocateLib"))
      && !ParGetBool ("parseTest")) {
    if (FieldIsKeyConvert (field))
      SmEdit (tokStr, SMxLOWCASE);
    EntryIdRecordPack (entry, IdxRecordNew (field->idx));
    if (ParGetNum ("newId")) {
      SmEdit (tokStr, SMxLOWCASE);
      IdBuild (EntryGetId (entry), LibToId (lib), lib->allEntryCnt, 0); 
      InxInsertStr (field->inx, tokStr, EntryGetId (entry));
    }
  }
  else
    IdBuild (EntryGetId (entry), LibToId (lib), lib->allEntryCnt, 0); 

  BldPrintProgress (entry);
  return 1;
}


/****** BldEntryFinish ********************************************************
** 
** 	INPUT:	    entry object [R]
** 		IMPLICIT:
** 
** 	RETURNS:
*/ 
   
static void BldEntryFinish (ENTRYv entry)
{
  SLBoFIELD *field;
  INT4      c;

  if (BldEntryId (entry)) {
    for (c=0; (field = LibNextField (EntryGetLib (entry), &c)); ) {
      if (FieldIs (field, "active")) {
	if (ParGetNum ("parseTest"))
	  BldShowWords (entry, field);
	else if (FieldIs (field, "index") && !FieldIs (field, "id"))
	  BldSaveKey (entry, field);
      }
    }
  }
}



/****** BldSaveKey ************************************************************
** 
** 
** 	INPUT:	    entry object [R]
** 		    field object [R]
** 		IMPLICIT
** 		    toklist (PRSoST *)
*/ 
   
INT4 BldSaveKey (ENTRYv entry, SLBoFIELD *field)
{
  TOKoLIST  *tokList;
  TOKoTOKEN *tok;
  IDoENTRY  id, *idPtr;
  char      *tokStr;
  INT4      c, isSubEntry, code, wantedCode;
 
  idPtr = (isSubEntry=FieldIs (field, "subEntry")) ? &id : EntryGetId (entry);

  tokList = IcaGetTokenList (EntryGetJob (entry), field->indexToken[0]);
  for (c=0; (tok = TokNext (tokList, &c));) {
    tokStr = TokGetStringCopy (tokList, tok);
    code = TokGetCode (tok);
    wantedCode = field->indexTokCode[0];
    if (isSubEntry)
      IdBuildSub (&id, EntryGetId (entry), TokGetCode (tok));
    else if (wantedCode != ICAxUNDEFCODE && code != wantedCode)
      continue;
    InxInsertStr (field->inx, SmEdit (tokStr, SMxLOWCASE|SMxTRIM), idPtr);
  }
  return 1;
}



/****** BldShowWords **********************************************************
** 
**      Displays for specified data-field all words that could be extracted 
**      from the current entry.
** 
** 	INPUT:	    entry object[R]
**                  data-field object [R]
** 		IMPLICIT:
** 
** 	RETURNS:    
*/ 
   
static void BldShowWords (ENTRYv entry, SLBoFIELD *field)
{
  TOKoLIST  *tokList;
  TOKoTOKEN *tok;
  INT4      c, code, wantedCode;

  if (FieldIs (field, "id")) {
    printf ("---------------------------------------\n");
    printf ("Entry no: %d, fip1: %d fip2: %d\n", 
	    (EntryGetLib (entry))->allEntryCnt,
	    EntryGetFip (entry, 0), EntryGetFip (entry, 1));
  }	       
  printf ("  %s:\n", LibGetFieldName (field)); 
  tokList = IcaGetTokenList (EntryGetJob (entry), field->indexToken[0]);
  for (c=0; (tok = TokNext (tokList, &c));) {
    code = TokGetCode (tok);
    wantedCode = field->indexTokCode[0];
    if (wantedCode == ICAxUNDEFCODE || code == wantedCode)
      printf ("       code: %d, %s\n", 
	      TokGetCode (tok), TokGetStringCopy (tokList, tok)); 
  }
}

 
	    (EntryGetLib (entry))->alsrs/src/srscheck.c
char srscheck_ID[] = "$Id: srscheck.c,v 1.14 1997/03/15 14:15:10 srs Exp $";
/*
**
**    $RCSfile: srscheck.c,v $
**    $Revision: 1.14 $
**    $Date: 1997/03/15 14:15:10 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    checks if all indexes are up to date and writes 
**    out a DCL file to keep system up to date        
**
**    still to be done:
**    o do "srsbuild -r" if the IDX index is not of the correct version
**    o compress index if date is ok but index is not compressed
**    o check ALL indices for the dates ...not just the Id index 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>

#define NO_ENVIRONMENT 1
#include "srs.h"


typedef struct CHECKoInfo {
  SLBo  *lib;
  UINT4 libCreTime;
} CHECKoInfo;

static DICTv compressFieldsDict=NULL;
 
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  static functions
*/

static int CheckLink (LINKo *link);
int CheckIsBigLib (SLBo *lib);
static void CheckBuildLinks ();
static void CheckPrintSrsEnvHeader (char **envPtr);
static void CheckSingleIndices (CHECKoInfo *ci);
static int CheckOperateIndices (SLBo *lib);
static void CheckBuildAllIndices (SLBo *lib);
static int CheckIsNewLibrary (CHECKoInfo *ci);
static CHECKoInfo *CheckInfoNew (SLBo *lib);
static void CheckInfoDel (CHECKoInfo **ci);


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  main section
*/

int main(int argc, char *argv[], char *envp[])
{
  CHECKoInfo *ci;
  ARGoLIST   *arglist;
  SRSoGROUP  *group;
  SLBo       *lib;
  TEMPLv     templ;
  char       *tok, *tokList, etcDirName[FILxXNAM+1];
  int        rv, context1, context2, isLibSelect=0, isLibUnSelect=0;
  char       *tmp;
#ifndef VMS
  char       *scriptName = "SRSETC:srsupdate";
#else
  char       *scriptName = "SRSETC:srsupdate.com";
#endif

  strcpy (etcDirName, "");

  /*
  ** open the resource file and get pointer to all library objects
  */

  LibOpen ("srs5");
  IcaInitSyntax (LibObjByName ("syntax", "icarus"));
  
  arglist = (ARGoLIST *) LibObjByName ("arglist", "srscheck");
  argc = ArgGet (arglist, argc, argv);
  if (argc > 2) {
    ArgUsage (arglist);
    _ErrorExit ();
  }
  
  if (ParGetNum ("srsEnvHeader")) {
    CheckPrintSrsEnvHeader (envp);
    exit (0);
  }
  else if (ParGetNum ("printLibInfo") && argc == 2) { /* print only info ? */
    LibPrintInfo (argv[1]);
    exit (0);
  }
  

  if (!((tmp = ParGetStr ("updateScriptName")) && *tmp))
    tmp = scriptName;
  templ = TemplOpen ("SRSICA:srscheck.i", tmp);
  FileSetMode (TemplGetOutFile (templ), "rwxr-xr-x");
  TemplWith (templ, "$srscheck");

  
  strcpy (etcDirName, getenv ("SRSETC"));
  if (!*etcDirName)
    strcpy (etcDirName, ParGetStr ("etcDir"));
  TemplPrint ("head.unix", etcDirName);
  
  
  /*
  ** process list of libraries to be checked...if specified
  */

  if (*(tokList = ParGetStr ("checkLibList")))
    isLibSelect = 1;
  else if (*(tokList = ParGetStr ("notCheckLibList")))
    isLibUnSelect = 1;
  
  for (context1=0; (group = LibNextLibGroup (&context1)); )  /* set all libs */
    for (context2=0; (lib = LibNextLib (group, &context2)); ) 
      ParDefNum (lib->nam, isLibSelect ? 0 : 1);
  
  if (isLibSelect || isLibUnSelect) /* set libs specified in list */
    while ((tok = strtok (tokList, " "))) {  /** set the databases of "SQ" */
      tokList = NULL;
      if (!(lib = (SLBo *) LibObjByName ("library", tok)))
	_ErrExit3 (e__objectunknown, "library", tok);
      ParDefNum (lib->nam, isLibUnSelect ? 0 : 1);
    }
  
  /*
  ** now iterate over all selected libs that are not user defined libraries
  */

  for (context1=0; (group = LibNextLibGroup (&context1)); ) {
    for (context2=0; (lib = LibNextLib (group, &context2)); ) {
      if (LibIs (lib, "user") || !LibIs (lib, "selected") || 
	  LibIs (lib, "subentries"))
	continue;
      _ErrMsg2 (i__checkinglib, lib->nam);
      ci = CheckInfoNew (lib);
      rv = CheckIsNewLibrary (ci);
      _ErrIf (rv) {  /* if there is something wrong with library */
	_ErrMsg2 (i__givinguplib, lib->nam);
	ParDefNum (lib->nam, 0);  /* turn lib OFF ...nothing can be done */
        continue;
      }
      if (!rv) { 
	CheckBuildAllIndices (lib);
        lib->upd_f = TRUE;
      }
      else {
	lib->upd_f = FALSE;
        CheckSingleIndices (ci);
      }
      CheckOperateIndices (lib);
      CheckInfoDel (&ci);
    }
  }
  
  CheckBuildLinks ();
  TemplEndWith (templ);
  TemplClose (templ);
  exit (0);
}


static CHECKoInfo *CheckInfoNew (SLBo *lib)
{
  CHECKoInfo *ci;

  ci = calloc (sizeof (CHECKoInfo), 1);
  ci->lib = lib;
  return ci;
}

static void CheckInfoDel (CHECKoInfo **ci)
{
  if (*ci)
    free (*ci);
  *ci = NULL;
}

/*******************************************************************************
**
** Set of functions to set flags of different types for the field object.
** Utilizes flags in the field objects that are normally used in other contexts.
**
*/

static void CheckSetFieldIsDone (SLBoFIELD *field)
{
  field->done_f =1;
}
static void CheckSetFieldDoBuild (SLBoFIELD *field)
{
  field->do_f =1;
}
static void CheckSetFieldDoCompress (SLBoFIELD *field)
{
  if (!compressFieldsDict)
    compressFieldsDict = 
      DictCreate(DictCreateClassSelfPtrKey (FALSE));
  DictSet (&compressFieldsDict, field, SLBoFIELD*) = field;
}

static INT4 CheckGetFieldIsDone (SLBoFIELD *field)
{
  return field->done_f;
}
static INT4 CheckGetFieldDoBuild (SLBoFIELD *field)
{
  return field->do_f;
}
static INT4 CheckGetFieldDoCompress (SLBoFIELD *field)
{
  if (compressFieldsDict && DictWith (compressFieldsDict, field))
    return 1;
  else  
    return 0;
}




/****** CheckIdIndex **********************************************************
**
**      Creates "checkindex" objects for all indexable fields and sets
**      both create and compress flags.
**
**	INPUT:	    address of library object [W]
**              IMPLICIT:
**
**	RETURNS:    1
*/ 

static void CheckBuildAllIndices (SLBo *lib)
{
  SLBoFIELD   *field;
  INT4        c;

  for (c=0; (field = LibNextField (lib, &c)); ) {
    if (FieldIs (field, "index")) {
      CheckSetFieldDoBuild (field);
      CheckSetFieldDoCompress (field);
    }
  }
  _ErrMsg2 (i__mustbuildinx, lib->nam);
}


/****** CheckSingleIndices ****************************************************
**
**      Checks every individual index if up to date. The index will be 
**      rebuilt if it is:
**       o older than the idx file
**       o does not exist
**       o is busy (which should mean it was never completed because of a 
**         crash)  
**       It will be just compressed if it is not compressed and fine otherwise.
**  
**
**	INPUT:      address of library object [W]
**              IMPLICIT:
**
**	RETURNS:    1
*/ 

static void CheckSingleIndices (CHECKoInfo *ci)
{
  SLBo        *lib=ci->lib;
  LIBoINDEX   *libInx;
  SLBoFIELD   *field;
  int         c;
  UINT4       idInxCreTime;

  /* creation date of ID index */
  if ((libInx = LibIndexOpen (lib, LibGetIdField (lib), 0)))
    idInxCreTime = IdxGetTimeCreated (libInx->idx);

  for (c=0; (field = LibNextField (lib, &c)); ) {

    if (FieldIs (field, "index")) {

      /* index not found */
      if (!(libInx = LibIndexOpen (lib, field, 1))) {
	CheckSetFieldDoBuild (field);
	CheckSetFieldDoCompress (field);
	_ErrMsg3 (i__indexnotexist, LibGetFieldName (field),
		  LibGetName (lib, "full"));
      }
      /* index not completed - rebuild! */
      else if (BtrIsBusy (libInx->btree))  {
	CheckSetFieldDoBuild (field);
	CheckSetFieldDoCompress (field);
	_ErrMsg3 (i__indexnotcompleted, LibGetFieldName (field),
		  LibGetName (lib, "full"));
      }
      /* library more recent as index */
      else if (ci->libCreTime > BtrGetTimeCreated (libInx->btree)) {
	CheckSetFieldDoBuild (field);
	CheckSetFieldDoCompress (field);
	_ErrMsg3 (i__indexnotuptodate, LibGetFieldName (field),
		  LibGetName (lib, "full"));
      }
      /* index not compressed */
      else if (!IdsIsCompressed (libInx->idsFile)) {
	CheckSetFieldDoCompress (field);
	_ErrMsg3 (i__indexnotcompressed, LibGetFieldName (field), 
		  LibGetName (lib, "full"));
      }
    }
  }
}


/****** CheckOperateIndices *************************************************
**
**      Write the commands to build and compress all indices
**      of the library.
**
**	INPUT:	    address of library object [W]
**                  address of template object [W]
**	        IMPLICIT:
**
**	RETURNS:    1
*/ 

static int CheckOperateIndices (SLBo *lib)
{
  SLBoFIELD   *field;
  int         context, procIndexSize, procSize, indexSize;
  char        *indexDirName, *outDirName, fieldList[512];

  indexDirName = ParGetStr ("indexDirName");
  outDirName = ParGetStr ("outDirName");
  TemplPrint ("build.head", LibName (lib));
  
  /*	 
  **  commands for index compression: if ids files are regarded as
  **  being large then the files are built and compressed by
  **  independent srsbuild calls;
  */	 
  
  procIndexSize = ParGetNum ("procIndexSize");
  while (1) {
    for (context=0, procSize=0, fieldList[0]='\0'; 
	 (field = LibNextField (lib, &context)); ) {
      
      if (FieldIs (field, "index") && !CheckGetFieldIsDone (field) &&
	  CheckGetFieldDoBuild (field)) {
	indexSize = 1 /*field->relIndexSize*/ * lib->maxIndexSizeKb;
	
	/*
	** add index to list if ..list is still empty ...or if there
	** is still space in "process memory" ...set the "on" flag of
	** the field object
	*/
	
	if (!procSize || procSize + indexSize <= procIndexSize) {
	  sprintf (fieldList, "%s %s", fieldList, field->type->shortn);
	  procSize += indexSize;
	  CheckSetFieldIsDone (field);
	}
      }	    
    }
    if (!procSize && indexSize)
      break;
    TemplPrint ("build.indexList", LibName (lib), fieldList, indexDirName, 
		                   outDirName, ParGetStr ("env"));
    if (!indexSize) /* index sizes were not specified */
      break;
  } 
  
  /* compress indices one by one */
  for (context=0; (field = LibNextField (lib, &context)); )
    if (FieldIs (field, "index") && CheckGetFieldDoCompress (field)) {
      TemplPrint ("compress.index", LibName (lib), field->type->shortn, 
		  indexDirName, outDirName, ParGetStr ("env")); 
      if (LibIs (lib, "partitioned")) {
	static FILEo *file=NULL;
	if (!file)
	  file = FileNew (NULL);
	FileSetName (file, "full", LibGetIndexName (lib, field, NULL, "read"));
	TemplPrint ("merge.index", LibName (lib), field->type->shortn, 
		    indexDirName, outDirName, ParGetStr ("env")); 
	if (!FieldIs (field, "id"))
	  TemplPrint ("merge.deleteIndex", FileGetName (file, "path"));
      }
    }	    

  /*TemplPrint ("tail");*/
  return 1;
}


/****** CheckBuildLinks *******************************************************
**
**      processes all "index" and "read" links
**
**	INPUT:	    
**	        IMPLICIT:
**
**	RETURNS:    1
*/ 

static void CheckBuildLinks ()
{
  SRSoGROUP *group;
  SLBo      *lib;
  LINKo     *link;
  char      *indexDirName, *outDirName;
  int       i, j, isFirstReadLink=1, isFirstIndexLink=1;

  indexDirName = ParGetStr ("indexDirName");
  outDirName = ParGetStr ("outDirName");

  /*	 
  **  analyze all pairwise links ...first "index" links
  */	 

  for (i=0; (link = LibNextLink (&i)); ) {
    if (LinkIs (link, "using"))
      continue;
    if (!CheckLink (link)) {
      _ErrMsg3 (i__mustbuildlink, LibGetLinkFromName (link),
		LibGetLinkToName (link));
      if (LinkIs (link, "index")) {
	if (isFirstIndexLink) {
	  TemplPrint ("link.indexLink.head");
	  isFirstIndexLink = 0;
	}
	TemplPrint ("link.indexLink.do", LibGetLinkFromName (link), 
		    LibGetLinkToName (link),
		    indexDirName, outDirName, ParGetStr ("env")); 
      }	    
    }
  }  
  
  /*
  **  then "read" links
  */

  for (i=0; (group = LibNextLibGroup (&i)); ) {
    for (j=0; (lib = LibNextLib (group, &j)); ) {
      if (!lib->updlink_f)
	continue;
      if (isFirstReadLink) {
	TemplPrint ("link.readLink.head");
	isFirstReadLink = 0;
      }
      TemplPrint ("link.readLink.do", LibName (lib), indexDirName, 
		  outDirName, ParGetStr ("env")); 
    }	
  }
}


/****** CheckIsNewLibrary *****************************************************
**
**	checks if libaries indices are OK and puts the library's 
**      creation time into the info object.  
**
**	INPUT:	    address of info object [W]
**
**	RETURNS:    TRUE: indices are up to date
**		    FALSE: must be built
*/ 
   
static int CheckIsNewLibrary (CHECKoInfo *ci)
{
  SLBo      *lib=ci->lib;
  LIBoINDEX *libInx;
  FILEo      *file;
  int       k, rv;
  UINT4     creTime, context;
  char      searchName[132], fileName[FILxXNAM+1];

  libInx = LibIndexOpen (lib, LibGetIdField (lib), 1);  /* open ID index */
  
  if (!LibIsFilePerEntry (lib)) {
    for (k=0, ci->libCreTime=0; k < lib->nfil; k++) {
      if (!(file = LibOpenFlatFile (lib, k, LibGetFileType 
				    (lib, NULL, NULL), &rv))){
	_ErrMsg2 (e__checkInvalidLibInfo, 
		  LibGetIcarusFileName (lib, "structure"));
	return 0;
      }
      creTime = FileGetTime (file, "create");
      if (ci->libCreTime < creTime)
	ci->libCreTime = creTime;
    }
    if (!libInx || ci->libCreTime > BtrGetTimeCreated (libInx->btree))
      return 0;
  }
  
  /*
  ** each entry resides in a separate file, count all these files and
  ** compare the number of files with the number of keys in the ID index -
  ** for that the ID index must be opened - but first check if the index
  ** exists;
  */

  else {
    if (*lib->form->fil_t[0]->searchName)
      sprintf (searchName, "%s%s", lib->dirName[0], 
	       lib->form->fil_t[0]->searchName);
    else
      sprintf (searchName, "%s*.%s", lib->dirName[0], 
	       lib->form->fil_t[0]->typ_nm);
    for (k=0, context=0; 
	 FilSearch (_FilTempLN (searchName), fileName, &context); k++)
      ;
    
    /* flag lib to be reindexed but allow 2 entries tolerance (fssp, hssp)*/
    if (!libInx || (k < BtrGetRecordN (libInx->btree)-2) ||
	(k > BtrGetRecordN (libInx->btree) + 2)) {
      if (libInx)
	_ErrMsg4 (i__diffentrynum, lib->nam, BtrGetRecordN (libInx->btree), k);
      return 0;
    }
  }
  return 1;  /* indices are OK */
}


/****** CheckLink *************************************************************
**
**	checks if link index is up to date;
**
**	INPUT:	    address of link descriptor [R]
**	        IMPLICIT:
**
**	RETURNS:   1 if link OK
**                 0 if update needed
*/ 
   
static int CheckLink (LINKo *link)
{
  FILE      *file;
  SLBo      *lib1 = link->lib1, *lib2 = link->lib2;
  LIBoINDEX *libInx;
  UINT4     indexTime1, indexTime2, linkTime;
  char      fileName[FILxXNAM+1];

  if (!LinkIs (link, "libs"))
    return 1;  
  if (LinkIs (link, "user"))
    return 1;  /* links to user libs have not to be updated */
  if (!LibIs (lib1, "selected") || !LibIs (lib2, "selected"))
	return 1; /* one of the 2 libs is not selected for updating */

  if (!lib1->upd_f && !lib2->upd_f) {

    libInx = LibIndexOpen (lib1, LibGetIdField (lib1), 1); 
    indexTime1 = libInx ? BtrGetTimeCreated (libInx->btree) : 0;

    libInx = LibIndexOpen (lib2, LibGetIdField (lib2), 1); 
    indexTime2 = libInx ? BtrGetTimeCreated (libInx->btree) : 0;

    /* time = LinkGetCreTime (link); !!!te */
    LibGetLinkName (link, 0, fileName, "read");
    file = fopen (_FilTempLN (fileName), "r");
    linkTime = file ? TimeFileCreate (file) : 0;
    fclose (file);

    if (!(linkTime <= indexTime1 || linkTime <= indexTime2)) 
      return 1;
  }

  /* 
  ** if link is of type INDEX then it is build by reading the library's
  ** flatfile (-> extract the crossreferences)
  */ 

  if (!LinkIs (link, "index"))
    lib1->updlink_f = TRUE;
  return 0;
}


/****** CheckIsBigLib *********************************************************
**
**	checks if library is big
**
**	INPUT:	    address of library object[R]
**	        IMPLICIT:
**
**	RETURNS:   1 if big
**             0 if not 
*/ 

int CheckIsBigLib (SLBo *lib)
{
  SLBoFIELD *field;
  int       context, totalIndexSize;

  if (!lib->maxIndexSizeKb)
	return 0;

  for (context=0, totalIndexSize=0; (field = LibNextField (lib, &context)); )
	if (FieldIs (field, "index")) {
	  totalIndexSize += lib->maxIndexSizeKb * /*field->relIndexSize*/ 1;
	}	    
  return (totalIndexSize > ParGetNum ("procIndexSize")) ? 1 : 0;
}


/****** CheckPrintSrsEnvHeader ************************************************
**
**	    prints a C-language header file that defines all SRS environment 
**      variables as they are currently defined;
**
**	    INPUT:	
**	            IMPLICIT:
**                  envp (char **) [R]
**
**	    RETURNS:
*/ 

static void CheckPrintSrsEnvHeader (char **envPtr)
{
  TEMPLv  templ;
  char    var[800], val[3000];

  templ = TemplOpen ("SRSICA:srsenv.i", "SRSEXE:srsenv.h");
  TemplWith (templ, "srsenv.unix");
  TemplPrint ("head");
  for (; *envPtr; envPtr++) {
    val[0] = '\0';  /* there might be no defined value */
    sscanf (*envPtr, "%[^=]=%[^:]", var, val);
    if ((SmStrCmpLen (var, "SRS", 3) == 0) && *val) 
      TemplPrint ("name", var, var, val);
  }
  TemplPrint ("tail");
  TemplEndWith (templ);
  TemplClose (templ);
}

ckPrintSrsEnvHeader (char **envPtr)
{
  TEMPLv  templ;
  char    var[800], val[3000];

  templ = TemplOpen ("SRSICA:srsenv.i", "SRSEXE:srsenv.h");
  TemplWith (templ, "srsenv.unix");
  TemplPrint ("head");
  for (; *envPtr; envPtr++) {
    val[0] = '\0';  /* there might be no defined value */
    sscanf (*envPtr, "%[^=]=%[^:]"srs/src/srspict.c
char srsnet_ID[] = "$Id: srspict.c,v 1.1 1996/05/06 15:17:26 srs Exp $";
/*
**
**    $RCSfile: srspict.c,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:17:26 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  Copyright by Thure Etzold
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     69012 Heidelberg, Germany
**                     Tel: 06221 387372  
**                     Email: etzold@embl-heidelberg.de
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    program takes a list of coordinates (databank nodes in a graph)
**    of the form: 'coord:' databankName x y and produces a GIF file
**    and a image map file for the WWW server
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/


#include <stdio.h>
#include "gd.h"
#include "srs.h"

#define brown             165,  42,  42
#define darkorange        255, 140,   0
#define rosybrown         188, 143, 143
#define seagreen           46, 139,  87
#define darkred           152,  20,   0
#define olivegreen         76,  39,   0
#define steelblue          57, 127, 145
#define maize             220, 185,  22
#define mediumaquamarine  102, 205, 170             
#define cornflowerblue    100, 149, 237            
#define mediumvioletred   199,  21, 133 



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  structure describing a databank node in the image;
*/

typedef struct PICToNODE {
    char name[20];
    int  x;
    int  y;
    int  fg, bg;
    int  isOnGraph;
  } PICToNODE;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  external, global and module wide variables
*/

static SCRIPTo    *script;
static gdImagePtr bullet=NULL;
static int        light, shade, red, grey, white, black, 
                  transparent, fg[10], bg[10];
;

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  static functions
*/

static void PictClose (gdImagePtr im, char *fileName);
static void PictPrintDB (gdImagePtr im, char *name, int color1, int color2, 
			 int x, int y);
static void PictPrintLegend (gdImagePtr im, int left, int upper);
static void PictNetwork (gdImagePtr im);
static void PictInit (gdImagePtr im);
static void PictPrintLinkBox (gdImagePtr im, int x, int y, int linkN);
static void PictRelocateNodes (PICToNODE *node, float width, float height);



void PictLinkInfo (char *s1, char *s2, int x1, int y1, int x2, int y2) 
{
  ScriptWriteFrom (script, "PIC-LINKINFO", _s(s1), _s(s2), 
		   _d(x1), _d(y1), _d(x2), _d(y2));
}

void PictLibInfo (char *s, int x1, int y1, int x2, int y2) 
{
  ScriptWriteFrom (script, "PIC-LIBINFO", _s(s), 
		   _d(x1), _d(y1), _d(x2), _d(y2));
}


/****** PictPrintNetwork *****************************************************
**
**      Initialises colors and other things that other functions need;
**      works on global variables ...not nice ...pragmatic solution!
**
**      INPUT:      
**              IMPLICIT:
**                  all variables are global
**
**      RETURNS:
*/

static void PictPrintNetwork ()
{
  SRSoGROUP  *group;
  SLBo       *lib;
  LINKo      *link;
  INT4       k, l, i, c1, c2, c, rv, x, y; 
  PICToNODE  dbNode[100], *node, *tmp;
  gdImagePtr im;


  im = gdImageCreate (750,  600);
  PictInit (im);

  script = ScriptOpen ("SRSWWW:wgetz.script", "SRSWWW:srsnet.map");

  fg[0] = gdImageColorAllocate (im, black);
  fg[1] = gdImageColorAllocate (im, black);
  fg[2] = gdImageColorAllocate (im, black);
  fg[3] = gdImageColorAllocate (im, black);
  fg[4] = gdImageColorAllocate (im, black);
  fg[5] = gdImageColorAllocate (im, black);
  fg[6] = gdImageColorAllocate (im, black);

  bg[0] = white; 
  bg[1] = white;
  bg[2] = white;
  bg[3] = white;
  bg[4] = white;
  bg[5] = white;
  bg[6] = white;



  /*
  ** assign databank names and background and foreground colors to 
  ** the nodes
  */

  for (k=0, l=0, c1=0; (group = LibNextLibGroup (&c1));) {
    for (c2=0, i=0; (lib = LibNextLib (group, &c2)); k++, i++) {
      node = &dbNode[k];
      strcpy (node->name, LibGetName (lib, "full"));
      node->fg = fg[l];
      node->bg = bg[l];
      node->isOnGraph = 0;
    }
    if (i) /* if group is not empty */
      l++;
  }
  dbNode[k].name[0] = '\0'; /* terminating node */

  /*
  ** read the file with the coordinates and assign x and y coordinates
  ** to the nodes
  */

  {
    FILo file;
    char libName[80];
     
    rv = FilUOpen (&file, "SRSWWW:srsnet.dat", 512, 0);
    _ErrExit2 (rv, "SRSWWW:srsnet.dat");
    do {
      if (sscanf (file.ln, "coord: %s %d %d", libName, &x, &y) == 3) {
	for (k=0; *dbNode[k].name; k++) {
	  node = &dbNode[k];
	  if (SmEqs (libName, node->name)) {
	    node->x = x;
	    node->y = y;
	    node->isOnGraph = 1;
	  }
	}
      }
      FilURead (&file);
    } while (!FilEof (&file));
  }

  /*
  ** find default positions for databanks not listed in the coordinate
  ** file
  */

  for (tmp=dbNode, y=0; *(tmp->name); tmp++)
    if (!tmp->isOnGraph) {
      tmp->x = 0;
      tmp->y = y;
      tmp->isOnGraph = 1;
      y += 50;
    }


  PictRelocateNodes (dbNode, 750, 530);

  /*
  ** paint the all links between nodes
  */

  for (c=0; (link = LibNextLink (&c)); ) 
    if (link->lib1 && link->lib2)
      PictLinkDBs (im, black, dbNode, 
		  LibGetName (link->lib1, "full"),
		  LibGetName (link->lib2, "full"));
  
  /*
  ** paint the nodes
  */

  for (k=0; *dbNode[k].name; k++) {
    PictPrintDB (im, dbNode[k].name, dbNode[k].fg, dbNode[k].bg, 
		dbNode[k].x, dbNode[k].y);
  }

  /* figure lengend */
/*  PictPrintLegend (im, 40, 540);*/

  /* default action for the clickable WWW map */

  ScriptWriteFrom (script, "PIC-LIBINFO", _s("points_to_nothing"), 
		   _d(0), _d(0), _d(im->sx), _d(im->sy));

  ScriptClose (script);
  PictClose (im, "SRSWWW:srsnet.gif");

}


/****** PictRelocateNodes *****************************************************
**
**
**      INPUT:      
**              IMPLICIT:
**
**      RETURNS:
*/

static void PictRelocateNodes (PICToNODE *node, float width, float height)
{
  PICToNODE *tmp;
  INT4      k, hrim=40, vrim=30;
  float     minx=1000, maxx=0, miny=1000, maxy=0;
  float     relx, rely;

  width -= 2*hrim;
  height -= 2*vrim;

  for (k=0; *node[k].name; k++) {
    tmp = &node[k];
    if (tmp->x < minx)
      minx = tmp->x;
    if (tmp->x > maxx)
      maxx = tmp->x;
    if (tmp->y < miny)
      miny = tmp->y;
    if (tmp->y > maxy)
      maxy = tmp->y;
  }

  maxx -= minx;
  maxy -= miny;

  relx = width / maxx;
  rely = height / maxy;

  for (k=0; *node[k].name; k++) {
    tmp = &node[k];
    tmp->x = (tmp->x - minx) * relx + hrim ;
    tmp->y = (tmp->y - miny) * rely + vrim ;
  }
}


/****** PictPrintGraphTable ***************************************************
**
**      Prints a picture that represents the databank network in a tabular
**      form.
**
**      INPUT:      
**              IMPLICIT:
**                  script (SCRIPTo *) [W]
**
**      RETURNS:
*/

static void PictPrintGraphTable ()
{
  gdImagePtr im;

  im = gdImageCreate (560, 620);
  script = ScriptOpen ("SRSWWW:wgetz.script", "SRSWWW:srslink.map");
  PictInit (im);

  fg[0] = gdImageColorAllocate (im, 210, 210, 250);
  fg[1] = gdImageColorAllocate (im, 190, 190, 230);
  fg[2] = gdImageColorAllocate (im, 170, 170, 210);
  fg[3] = gdImageColorAllocate (im, 140, 140, 190);
  fg[4] = gdImageColorAllocate (im, 110, 110, 170);
  fg[5] = gdImageColorAllocate (im, 80, 80,   150);
  fg[6] = gdImageColorAllocate (im, 50, 50,   130);

  bg[0] = black; 
  bg[1] = black;
  bg[2] = black;
  bg[3] = white;
  bg[4] = white;
  bg[5] = white;
  bg[6] = white;


  PictNetwork (im);
  PictPrintLegend (im, 20, 560);
  PictClose (im, "SRSWWW:srslink.gif");
  ScriptClose (script);
}


#define HRIM       4
#define VRIM       0
#define BOXLEN     (12+2*VRIM)
#define BOXHEIGHT  (12+2*VRIM)

static void PictNetwork (gdImagePtr im)
{
  SRSoGROUP *group, *group2;
  SLBo      *lib, *lib2;
  struct LINKoNOD *path;
  INT4      maxLen, len, textLen;
  INT4      c1, c2, c3, c4, i, k, x, y;
  char      *libName, *lib2Name;


  /* find maximum length of databank names */
  maxLen = 0;
  for (c1=0; (group = LibNextLibGroup (&c1)); )
    for (c2=0; (lib = LibNextLib (group, &c2)); ) {
      len = strlen (LibGetName (lib, "full"));
      if (maxLen < len)
	maxLen = len;
    }
  textLen = maxLen*6;

  /* print databank names horizontally */

  x=10;
  y=10;

  for (k=0, c1=0; (group = LibNextLibGroup (&c1));) {
    for (c2=0, i=0; (lib = LibNextLib (group, &c2)); i++) {
      gdImageFilledRectangle (im, x, y, x+textLen+2*HRIM, y+12+2*VRIM, fg[k]);
      gdImageString (im, gdFontSmall, x+HRIM, y+VRIM, 
		     LibGetName (lib, "full"), bg[k]);

      PictLibInfo (LibGetName (lib, "full"), x, y, 
		  x+textLen+2*HRIM, y+12+2*VRIM); 

      y += 12 + 2 * VRIM + 1;
    }
    if (i)
      k++;
  }

  /* print databank names vertically */

  x += textLen + 2* HRIM ;

  for (k=0, c1=0; (group = LibNextLibGroup (&c1));) {
    for (c2=0, i=0; (lib = LibNextLib (group, &c2)); i++) {
      gdImageFilledRectangle (im, x, y, x+12+2*VRIM, y+textLen+2*HRIM, fg[k]);
      gdImageStringUp (im, gdFontSmall, x+VRIM, y+HRIM+textLen, 
		     LibGetName (lib, "full"), bg[k]);

      PictLibInfo (LibGetName (lib, "full"), 
		  x, y, x+12+2*VRIM, y+textLen+2*HRIM);

      x += 12 + 2 * VRIM + 1;
    }
    if (i)
      k++;
  }

  y = 10;

  for (c1=0; (group = LibNextLibGroup (&c1)); )
    for (c2=0; (lib = LibNextLib (group, &c2)); ) {

      x = 10+textLen+2*HRIM+1;
      
      libName = (LibGetName (lib, "full"));
      for (c3=0; (group2 = LibNextLibGroup (&c3)); )
	for (c4=0; (lib2 = LibNextLib (group2, &c4)); ) {

	  lib2Name = LibGetName (lib2, "full");
	  if (lib == lib2)
	    goto endofline;  /* proceed until diagonal is reached */
	  if ((LibGetLink (libName, lib2Name))){ /* direct link */
	    PictPrintLinkBox (im, x, y, 1);
	    PictLinkInfo (libName, lib2Name, x, y, x+BOXLEN, y+BOXHEIGHT); 
	  }
	  else {
	    if ((path = LinkSearchPath (libName, lib2Name))) {
	      PictPrintLinkBox (im, x, y, LinkGetPathLength (path));
	      PictLinkInfo (libName, lib2Name, x, y, x+BOXLEN, y+BOXHEIGHT); 
	    }
	  }
	  x += BOXLEN+1;
	}	    
    endofline:
      y += BOXHEIGHT+1;
    }



}


static void PictPrintLinkBox (gdImagePtr im, int x, int y, int linkN)
{
  static int grey[4];
  char tmp[5];

  if (!grey[0] && ! grey[1]) {
    grey[0] = white;
    grey[1] = gdImageColorAllocate (im, 255, 240, 240);
    grey[2] = gdImageColorAllocate (im, 255, 220, 220);
    grey[3] = gdImageColorAllocate (im, 255, 200, 200);
  }
  gdImageFilledRectangle (im, x, y, x+BOXLEN, y+BOXHEIGHT, grey[linkN-1]);
  sprintf (tmp, "%d", linkN);
  gdImageString (im, gdFontSmall, x+HRIM, y+VRIM, tmp, 
		 linkN == 1 ? red : black);

}



static void PictClose (gdImagePtr im, char *fileName)
{
  FILE *file;
  int  rv;
  

  /* Make output image interlaced (allows "fade in" in some viewers,
     and in the latest web browsers) */
  gdImageInterlace (im, 1);
    
  /* set transparent color */
  transparent = gdImageColorExact (im, 190, 190, 190);
  gdImageColorTransparent(im, transparent); 

  file = FilOpenW (fileName, &rv);
  _ErrExit2 (rv, fileName);
  gdImageGif (im, file);
  fclose (file);
  gdImageDestroy (im);
}



/****** PictInit ***************************************************************
**
**      Initialises colors and other things that other functions need;
**      works on global variables ...not nice ...pragmatic solution!
**
**      INPUT:      pointer to image [W]
**              IMPLICIT:
**                  all variables are global
**
**      RETURNS:
*/

static void PictInit (gdImagePtr im)
{
  FILE *file;
  int  rv;

  /* First color allocated is background. */
  white = gdImageColorAllocate (im, 255, 255, 255);
  grey  = gdImageColorAllocate(im, 190, 190, 190);


  light = gdImageColorAllocate (im, 255, 240, 255); 
  shade = gdImageColorAllocate (im, 80, 80, 100);
  black = gdImageColorAllocate (im, 0, 0, 0);
  red   = gdImageColorAllocate (im, 255, 0, 0);

  file = FilOpenR ("SRSWWW:bullet.gif", &rv);
  _ErrExit2 (rv, "SRSWWW:bullet.gif");

  bullet = gdImageCreateFromGif(file);
}


/****** PictLinkDBs ************************************************************
**
**      
**      
**
**      INPUT:      pointer to image [W]
**              IMPLICIT:
**
**      RETURNS:    1 if success
**                  0 if name could not be found or if no coordinates exist
*/

int PictLinkDBs (gdImagePtr im, int color, PICToNODE *node, 
		char *libName1, char *libName2)
{
  FILE *in;
  PICToNODE *node1, *node2;
  int x, y, h, l;

  /*
  ** Search both databank names and exchange for a "node" object
  ** and connect them by a line
  */

  for (node1=node; *(node1->name); node1++)
    if (SmEqs (node1->name, libName1))
      break;
  for (node2=node; *(node2->name); node2++)
    if (SmEqs (node2->name, libName2))
      break;

  if (!node1->isOnGraph || !node2->isOnGraph || !*node1->name || !*node2->name)
    return 0;

  gdImageLine (im, node1->x, node1->y, node2->x, node2->y, color);	

  /*
  ** find the center of that line for drawing a bullet (for clicking)
  */ 

  if (node1->y < node2->y) 
    h = node2->y, l = node1->y;
  else
    l = node2->y, h = node1->y;
  y = l + (h - l) /2;

  if (node1->x < node2->x) 
    h = node2->x, l = node1->x;
  else
    l = node2->x, h = node1->x;
  x = l + (h - l) /2;

  /*
  ** paste the bullet and print its coordinates into the WWW image map file
  */

  x -= bullet->sx/2;
  y -= bullet->sy/2;
  gdImageCopy (im, bullet, x, y, 0, 0, bullet->sx, bullet->sy);

  ScriptWriteFrom (script, "PIC-LINKINFO", 
		   _s(node1->name), 
		   _s(node2->name), 
		   _d(x), 
		   _d(y), 
		   _d(x+bullet->sx), 
		   _d(y+bullet->sy));
  return 1;
}



/****** PictPrintDB ************************************************************
**
**      Initialises colors and other things that other functions need;
**      works on global variables ...not nice ...pragmatic solution!
**
**      INPUT:      pointer to image [W]
**              IMPLICIT:
**
**      RETURNS:
*/

static void PictPrintDB (gdImagePtr im, char *name, int color1, int color2, 
		 int x, int y)
{
  /* Points for polygon */
  gdPoint points[10];
  int x1, y1, x2, y2, len, xrel, yrel, margin=4, outRim=2, diff;

  /*
  ** calculate size of text, and of the whole box in points 
  */

  len = strlen (name);
  x1 = 1;
  y1 = 1;
  x2 = x1 + len*8 + margin*2; /* font is 8*16 */
  y2 = y1 + 16 + margin*2;

  /*
  ** calculate positions of that box on the image 
  */

  xrel = (x2 - x1) / 2;
  yrel = (y2 - y1) / 2;
  x1 = x-xrel;
  y1 = y-yrel;
  x2 = x+xrel;
  y2 = y+yrel;

  /*
  ** paste an even bigger box in "light" ...for the 3d aspect
  */
  
/*  gdImageFilledRectangle (im, x1-outRim, y1-outRim, x2+outRim, y2+outRim, 
			  light);
*/
  /*
  ** now paste over the "light" box a "shade" polygon ...together they will
  ** be ligth and shadow ...node that the polygon drawing is a bit buggy
  */

  diff = (y2-y1)/2;
  points[0].x = x2 + outRim;
  points[0].y = y2 + outRim;
  points[1].x = x2 + outRim;
  points[1].y = y1 - outRim;	
  points[2].x = x2 - diff - 1;
  points[2].y = y1 + diff - 1; /* the +1 prevents some bug ...a white line */
  points[3].x = x1 + diff;
  points[3].y = y1 + diff;	
  points[4].x = x1 - outRim;
  points[4].y = y2 + outRim;	
/*  gdImageFilledPolygon(im, points, 5, shade);
*/
  /*
  ** now print the rectangle with the databank name and write a 
  ** "rect" statement into the WWW image map file
  */

  gdImageFilledRectangle (im, x1, y1, x2, y2, color1);
  gdImageString(im, gdFontLarge, x1+margin, y1+margin, name, color2);

  ScriptWriteFrom (script, "PIC-LIBINFO", _s(name),
		   _d(x1), _d(y1), _d(x2), _d(y2));
}

/****** PictPrintLegend ********************************************************
**
**      Prints the legend with the color codes for the databank groups.
**
**      INPUT:      pointer to image [W]
**              IMPLICIT:
**                  bullet
**                  fg
**                  black
**
**      RETURNS:
*/

static void PictPrintLegend (gdImagePtr im, int left, int upper)
{
  SRSoGROUP *group;
  int x,y, probeSize=12, space=5, bigSpace=10;
  int k, i, c1, c2;
  char tmp[132];

  /*
  ** print the creation time and explain the bullet 
  */

  x = left;
  y = upper;
    
  sprintf (tmp, "Creation Date: %s\n", TimeToString (0, "date"));
  gdImageString(im, gdFontSmall, x, y, tmp, black);

  x+= 180;

  if (ParGetNum ("doNetworkPict")) {
    gdImageCopy (im, bullet, x, y, 0, 0, bullet->sx, bullet->sy); 
    x += bullet->sy + space;
  }
  else if (ParGetNum ("doGraphTablePict")) {
    PictPrintLinkBox (im, x, y, 1);
    x+= BOXLEN;
    PictPrintLinkBox (im, x, y, 2);
    x+= BOXLEN;
    PictPrintLinkBox (im, x, y, 3);
    x+= BOXLEN;
    PictPrintLinkBox (im, x, y, 4);
    x+= BOXLEN + space;
  }  

  gdImageString (im, gdFontSmall, x, y, 
		 "Press to get link information", black);
  
  /*
  ** print on next line a color probe and the databank group name
  */

  x = left;
  y = upper+20;


  for (k=0, c1=0; (group = LibNextLibGroup (&c1));) {
    for (c2=0, i=0; (LibNextLib (group, &c2)); i++) 
      ;
    if (i) { /* if group is not empty */

      gdImageFilledRectangle (im, x, y, x+probeSize, y+probeSize, fg[k++]);
      x += probeSize + space;
      gdImageString(im, gdFontSmall, x, y, group->com, black);
      x += strlen (group->com) * 6 + bigSpace;
    }
  }

  gdImageRectangle (im, left-bigSpace, upper-bigSpace, 
		    x+bigSpace, upper+30+bigSpace, black);
}


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  The main thing
*/

INT4 main (INT4 argc, char *argv[], char *envp[])
{
  ARGoLIST   *arglist;
  gdImagePtr im_out;
  

  SrsEnv ();
  LibOpen ("srswin");

  arglist = (ARGoLIST *) LibObjByName ("arglist", "srspict");
  argc = ArgGet (arglist, argc, argv);

  if (ParGetNum ("doNetworkPict"))
    PictPrintNetwork ();
  if (ParGetNum ("doGraphTablePict"))
    PictPrintGraphTable ();
  return 0;
}

x+bigSpace, upper+30+bigSpace, black);
}


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  The main thing
*/

INT4 msrs/src/srswww.c
char srswww_ID[] = "$Id: srswww.c,v 1.26 1997/03/15 14:14:22 srs Exp $";
/*
**
**    $Source: /homes/srs/cvsroot/srs/src/srswww.c,v $
**    $Revision: 1.26 $
**    $Date: 1997/03/15 14:14:22 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     69012 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    Modified to fit the new SRS WWW interface
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include <string.h>
#include <stdarg.h>

/*
#include <sys/types.h>
#include <sys/stat.h>
*/

#include "message.h"
#include "sm.h"
#include "tm.h"
#include "strv.h"
#include "lst.h"
#include "futil.h"
#include "templ.h"
#include "par.h"
#include "id.h"
#include "set.h"

#include "library.h"
#include "appl.h"
#include "btree.h"
#include "idx.h"
#include "entry.h"
#include "link.h"
#include "seq.h"
#include "query.h"
#include "queryass.h"
#include "seqdb.h"
#include "icarus.h"
#include "icaarg.h"
#include "variable.h"
#include "view.h"
#include "srswww.h"


#define	_SRS      
#define _SLB      
#define _WWW    
#include "srs5.h"

#define WWWxMAXLINESIZE 500000

typedef struct SCRIPTo{
    void *x;
}SCRIPTo;

INT4 SmRemoveChar(char remoteAddr[],char c);
INT4 LibShufflebuff(char s[]);
void LibRevStr(char s[]);
INT4 LibPower(int base, int n);

extern char *ScriptFile;
extern char *RParGetStr(char *strfmt, ...);
/* * * * * * * * stuff from HTTP server's "util.c" * * * * * * * * * */

#define LF 10
#define CR 13

static char *makeword(char *line, char stop) 
{
  int x = 0,y;
  char *word = (char *) malloc(sizeof(char) * (strlen(line) + 1));
  
  for(x=0;((line[x]) && (line[x] != stop));x++)
    word[x] = line[x];
  
  word[x] = '\0';
  if(line[x]) ++x;
  y=0;
  
  while ((line[y++] = line[x++]));
  return word;
}

static char *fmakeword(char **buffPtr, char *buffEnd, char stop, int *cl) 
{
  int wsize;
  char *word;
  int ll;
  
  wsize = 132;
  ll=0;
  word = (char *) malloc(sizeof(char) * (wsize + 1));
  
  while(1) {
    word[ll] = *(*buffPtr)++;
    if(ll==wsize) {
      word[ll+1] = '\0';
      wsize+=102400;
      word = (char *)realloc(word,sizeof(char)*(wsize+1));
    }
    --(*cl);
    if((word[ll] == stop) || (*buffPtr >= buffEnd) || (!(*cl))) {
      if(word[ll] != stop) ll++;
      word[ll] = '\0';
      return word;
    }
    ++ll;
  }
}

static char x2c(char *what) 
{
  register char digit;
  
  digit = (what[0] >= 'A' ? ((what[0] & 0xdf) - 'A')+10 : (what[0] - '0'));
  digit *= 16;
  digit += (what[1] >= 'A' ? ((what[1] & 0xdf) - 'A')+10 : (what[1] - '0'));
  return(digit);
}

static void unescape_url(char *url) {
  register int x,y;
  
  for(x=0,y=0;url[y];++x,++y) {
    if((url[x] = url[y]) == '%') {
      url[x] = x2c(&url[y+1]);
      y+=2;
    }
  }
  url[x] = '\0';
}

static void plustospace(char *str) 
{
  register int x;
  
  for(x=0;str[x];x++) if(str[x] == '+') str[x] = ' ';
}


/* * * * * * * * end stuff from HTTP server's "util.c" * * * * * * * * * */


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  external, global and module wide variables
*/

VIEWo  *wwwView=NULL;
char   buff[WWWxMAXLINESIZE+1];
ENTRYv entryCurr;

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of static functions
*/

static INT4 WwwViewEntryInTable (TEMPLv templ, ENTRYv entry, VIEWoLIB *vlib,
				 Int4 entryNum, Int4 isRoot, Int4 rowN);
static void WwwViewEntryInList (TEMPLv templ, ENTRYv entry, VIEWoLIB *vlib,
				Int4 entryNum, Int4 isRoot);
static void WwwPrintTableEmptyEntry (VIEWoLIB *vlib, Int4 rowN);
static void WwwPresentSkipChunkSet (TEMPLv templ, INT4 setSize, INT4 queryN);
static void WwwDeleteQuery ();
static void WwwViewTableHeader (TEMPLv templ, VIEWo *view);
static Int4 WwwIsViewForQuery (VIEWo *view, char *setName);
static void WwwViewPrintEntryN (VIEWo *view, VIEWoLEAFSET *leaf, ENTRYv entry, Int4 rowN);
static void WwwViewSave (VIEWo *view, char *option);
static void WwwApplOptPrint (APPLo *appl, APPLoOpt *opt);


char *WwwReadInput (int byteN, char *fileName)
{ 
  static char buff[10000];
  FILE *file;

  fread (buff, 1, byteN, stdin);
  if (ParGetBool ("debugSRSWWW")) { /* file with form input for debugging */
    file = fopen (fileName, "w");
    fwrite (buff, 1, byteN, file);
    fclose (file);
    chmod (fileName, 00777);  
  }
  return buff;
}


Int4 WwwPrintContentType (char *s)
{
  static Int4 isPrinted=0;
  char *tmp;

  if (*(tmp = ParGetStr ("mimeType")))
    s = tmp;

  if (!isPrinted) {
    isPrinted=1;
    if (s && SmEqs (s, "none"))
      ;
    else if (s) {
      /*printf ("Pragma: no-cache\r\n");*/
      printf ("%s\r\n", s);
      /*printf ("Expires: Thu, 01 Dec 1994 16:00:00 GMT\r\n");*/
      /* date see internet RFC-1945! */
      printf ("\r\n");
    }
    else {
      /*printf ("Pragma: no-cache\r\n");*/
      printf ("Content-type: text/html\r\n");
      /*printf ("Expires: Thu, 01 Dec 1994 16:00:00 GMT\r\n");*/
    printf ("\r\n");
    }
    return 1;
  }
  return 0;
}

INT4 WwwPrintMessage (MSGo *msg) 
{ 
  static TEMPLv templ=NULL;
  
  MsgSetFnct ((Func)IcaPrintMessage); /* avoid recursion in error printing! */
  if (!(templ = TemplGet ())) {
    templ = TemplOpen ("SRSICA:srswww.i", NULL);
  }
  TemplWith (templ, "$messages");
  WwwSetColorScheme (templ);
  if (WwwPrintContentType (NULL)) {
    TemplPrint ("head");
  }

  switch (msg->msg_code) {
  case i__wroteset:
    break;
  case e__parsererror3:
    TemplPrint ("parseError", msg->primsg, msg->secmsg);
    break;
  default:
    if (msg->msg_t == MSGxINFO) 
      TemplPrint ("info", msg->primsg, msg->secmsg);
    else 
      TemplPrint ("error", msg->primsg, msg->secmsg);
    break;
  }
  TemplEndWith ();
  MsgSetFnct (WwwPrintMessage);
}



int WwwParInput (int byteN, char *buff)
{
  struct {
    char *name;
    char *val;
  } entry[1000];
  int  k, len, entryN=0, isDebug=ParGetBool ("isDebug");
  char *name, *val;

  if (isDebug) 
    printf ("Content-type: text/html\n\n");


  /*
  ** the for loop contains code from the "post-query.c" shipped with Mosaic
  ** collect all pairs entry name and value from stdin
  */

  for (k=0; byteN && (buff < buff+byteN); k++) {
    entry[k].val = fmakeword (&buff, buff+byteN, '&',&byteN);
    plustospace (entry[k].val);
    unescape_url (entry[k].val);
    entry[k].name = makeword (entry[k].val,'=');
  }

  entryN = k;
  
  /*
  ** now process these pairs into pairs of parameter name and value
  */

  for (k=0; k < entryN; k++) {
    name = entry[k].name;
    val = entry[k].val;
    SmEdit (val, SMxTRIM);  /* macintotsh client */
    if (isDebug) 
      printf ("#par /name=%s /str=%s<BR>\n", name, val);

    ParIsVolatileName (name);
    ParDefStr (name, val);
  }
  if (isDebug) 
    printf("<HR>\n");
  return entryN;
}


INT4 WwwPrintF (char *formatStr, ...)
{
  static char *ln = NULL;
  va_list ap;

  if (!ln)
    if (!(ln = (char *) malloc (WWWxMAXLINESIZE+1)))
      _ErrExit2 (e__allocfail, "WWW output line");
    

 /*[WWWxMAXLINESIZE+1]*/;
  
  va_start (ap, formatStr);
  vsprintf (ln, formatStr, ap);
  va_end (ap);
  
  printf ("%s", ln); 
  if (ln[strlen (ln) -1] != '\n')
    printf ("\n");
  
  return 1;

}

char *WwwChecked (Int4 flag)
{
  return flag ? "CHECKED" : "";
}
char *WwwSelected (Int4 flag)
{
  return flag ? "SELECTED" : "";
}



/****** WwwStringEncode *******************************************************
**
**      Replaces special characters by HTML codes;
**
**	INPUT:	  string [W]
**	        IMPLICIT:
**
**	RETURNS:  modified string
*/ 

char *WwwStringEncode (char *str)
{
  static STRv s=NULL;

  if (!s)
    s = StrNew ();
  else 
    StrClear (&s);
  StrAppS (&s, str);
  StrReplace (&s, "&", "&");
  StrReplace (&s, "|", "|"); 
  StrReplace (&s, "<", "&lt;");
  StrReplace (&s, ">", "&gt;");
  return _Str (s);
}


INT4 WwwIndexValueLink (char *formatStr, ...)
{
  static char *libName, *fieldName;
  va_list ap;
  char    *value, tmp[80], queryStr[132];
  INT4    entryN;

  if (!formatStr) { /* init */
    libName = ParGetStr ("libName");
    fieldName = ParGetStr ("listIndex");
    return 1;
  }    

  va_start (ap, formatStr);
  value = va_arg (ap, char *);
  entryN = va_arg (ap, INT4);
  va_end (ap);

  sprintf (tmp, "%s</A>", value);
  sprintf (queryStr, "[%s-%s:%s]", libName, fieldName, value);

  printf ("<A HREF=\"/srs/srsc?-viv+%s+-f+%s\">%-55s %6d entries\n",
	  WwwTransform ("encode", queryStr), fieldName, tmp, entryN);

  return 1;
}




/**api* WwwViewFeature ********************************************************
**
**      views a sequence feature 
**
**	INPUT:	    name of set [R]
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

void WwwViewFeature (char *queryStr, INT4 subEntryN)
{
#ifdef script
  SETo      *set, *setSub;
  IDoENTRY  id, idSub;
  SCRIPTo   *script;

  script = ScriptOpen (ScriptFile, NULL);

  if (QryDo (queryStr, "Q")) { 
    set = SetGet ("Q");
    SetGetID (set, 1, &id); 
    setSub = SetNew ("QSUB", NULL);
    idSub.id_d =  (IDoTYPE *) LibObjByName ("idtype", "seq-ft-id");
    IdBuildSub (&idSub, &id, subEntryN);
    SetAddID (setSub, &idSub);

    ParDefBool ("parSetFields", 1);
    ParDefBool ("Features", 1);
    ParDefBool ("Definition", 1);
    ParDefBool ("ID", 1);
    ParDefBool ("takeuncompletefeature", 1);
    WwwPrintSet ("QSUB", 1, 1, script);
  }
#endif
}

/**api* WwwPresentLaunchAppls *************************************************
**
**     In case they are available list all applications that can be launched
**     for the specified query.
**
**     INPUT:     query number
*/

void WwwPresentLaunchAppls (Int4 queryNo, ENTRYv entry)
{
  WWWoQUERY       *query;
  SLBo            *lib;
  LIBoDataType    *dataType;
  APPLo           **appl=NULL, *tmp;
  Int4            applN=0, applAllocN=0, k, i, c1, c2;

  if (!entry)
    query=WwwGetQuery (queryNo);
  else 
    lib = EntryGetLib (entry);

  for (k=0; entry || query->lib[k].entryN; k++) {
    if (!entry)
      lib = (SLBo*) LibObjByName ("library", query->lib[k].name);
    for (c1=0; (dataType = LibNextDataType (lib, &c1));)
      for (c2=0; (tmp = ApplNextInDataType (dataType, &c2));) {
	for (i=0; i < applN; i++)
	  if (tmp == appl[i])
	    break;
	if (i == applN && (!entry || ApplIs (tmp, "single"))) {
	  *_addObj (appl, applN, applAllocN, APPLo*) = tmp;
	}
      }
    if (entry)
      break;
  }
  if (applN) {
    TemplPrint ("launch.head");
    for (k=0; k < applN; k++)
      TemplPrint ("launch.appl", ApplGetName (appl[k]));
    TemplPrint ("launch.tail");
  }
  free (appl);
  if (!entry)
    WwwDelQuery (query);
}


/**api* function ***********************************************************
**
**     Presents all view where all libraries in the group  
**     are contained as root libraries.
**
**     INPUT:     library group object (or NULL) [R]
*/

void WwwPresentActiveViews (SRSoGROUP *group, SLBo *lib, WWWoQUERY *query,
			    TEMPLv templ, Int4 isOptional)
{
  VIEWo    *view;
  VIEWoLIB *vlib;
  Int4     currViewNo=0, j, i, c, k, isPrinted=0;

  WwwInitViews (templ);
  if (ViewGetViewsN () > 0) {
    currViewNo = ParGetNum ("viewNumber");
    if (!isOptional)
      TemplPrint ("selectView.head");
    for (c=0,j=1; (view = ViewNext (&c));j++) { 
      if (ViewIs (view, "forAll") && !isOptional)
	TemplPrint ("selectView.name", j, WwwSelected (j == currViewNo), 
		    ViewGetName (view));
      else  
	for (k=0; (vlib=ViewGetNextRootLib (view, &k));) {
	  for (i=0; lib || (group && (lib = LibNextLib (group, &i))) ||
(query && (lib = (SLBo*) LibObjByName ("library", query->lib[i++].name)));){
	    if (vlib->lib == lib) {
	      if (!isPrinted && isOptional) {
		TemplPrint ("selectView.head");
		isPrinted = 1;
	      }
	      TemplPrint ("selectView.name", j, 
			  WwwSelected (j == currViewNo), 
			  ViewGetName (view));
            }
	    if (!group) 
	      break;
	    else 
	      lib=NULL;

	  }
	}
    }
    if (!isOptional || isPrinted)
      TemplPrint ("selectView.tail");
  }
}

/**api* WwwPresentViewsForLeaf ***********************************************
**
**     As WwwPresentViewForLibs but for a single leaf library.
**
**     INPUT:     view object [R]
**                leaf object [R]
*/

void WwwPresentViewsForLeaf (VIEWo *view, VIEWoLIB *vlib, TEMPLv templ)
{
  VIEWoLIB *rootVlib;
  Int4     c, j, k;
  char     *tmp, *viewName;

  WwwInitViews (templ);
  viewName = ViewGetLeafView (vlib);
  if (ViewGetViewsN () > 0) {
    TemplPrint ("selectView.head", view->n, LibName (vlib->lib),
		WwwSelected (!*viewName));

    for (c=0,j=1; (view = ViewNext (&c));j++) { 
      tmp = ViewGetName (view);
      if (ViewIs (view, "forAll"))
	TemplPrint ("selectView.name",
		    WwwSelected (SmEqs (viewName, tmp)), tmp);
      else  
	for (k=0; (rootVlib=ViewGetNextRootLib (view, &k));) 
	  if (vlib->lib == rootVlib->lib) 
	    TemplPrint ("selectView.name",
			WwwSelected (SmEqs (viewName, tmp)), tmp);
    }
    TemplPrint("selectView.tail");
  }
}


/****** WwwPresentViewList ****************************************************
**
**      Print a menu with list all the views for selection.
**      Requires that the template context is already set to a list
**      with the "view labels" by TemplWith.
**
**      INPUT:         option: "reset", "current" [R]
**
*/

void WwwPresentViewList (char *option, TEMPLv templ)
{
  VIEWo *view;
  char  *tmp;
  Int4  k, i, currentViewNumber = ParGetNum("viewNumber");

  WwwInitViews (templ);
  if (option[0] == 'r') /* reset */
    currentViewNumber = 0;

  /*Int4 WwwIsViewForQuery (VIEWo *view, char *setName)*/
  TemplPrint("head");
  for (k=0, i=1; (view = ViewNext (&k)); i++) 
    TemplPrint ("name", i, WwwSelected (k==currentViewNumber), 
		ViewGetName (view));
  TemplPrint("tail");
}


/**api* WwwViewPartI **********************************************************
**
**      Lets user create or edit a view, part I, which is the selection of
**      the leaf and root libraries.
**
**      INPUT:         view number [R]
**                     flag whether to edit an existing view [R]
**
*/

void WwwViewPartI (INT4 viewNo,INT4 isEdit, TEMPLv templ)
{
  VIEWo         *view;
  VIEWoLIB      *vlib;
  SLBo          *lib;
  SLBoFIELD     *field;
  SRSoGROUP     *group;
  INT4          i,c1,c2,c3, isFound;
  char          *libName, *viewName;

  if(!isEdit)
    TemplPrint("create.logo");
  else
    ParDefNum("nascentViewN", viewNo); 

  view = WwwViewGet (viewNo, templ);
  if (view && WwwIsViewInternal (view))
    WwwViewSave (view, "");
  TemplPrint("create.head",viewNo,viewNo,viewNo,viewNo);
  TemplPrint("rootHeader", viewNo, 
	     view ? ViewGetName (view) : "", viewNo, 
	     WwwChecked (!view || ViewIsTable (view)), viewNo, viewNo,
	     WwwChecked (view && ViewIsShortNames (view)), viewNo);

  if (!view)
    TemplPrint ("nascentName", viewNo);
  for(c1=0; (group = LibNextLibGroup(&c1)); ) {
    if( ! LibNofGroups(group) ) continue;
    TemplPrint("separator");
    for(c2=0; (lib= LibNextLib(group,&c2)); ) {
      libName = LibGetName(lib,"full");
      isFound=0;
      if (view)
	for (c3=0; (vlib=ViewGetNextRootLib (view, &c3));)
	  if (vlib->lib == lib) {
	    isFound = 1;
	    break;
	  }
      TemplPrint("rootLibsSelect",viewNo,libName, WwwSelected (isFound), 
		 libName);
    }
  }

  TemplPrint("rootTrailer");
  TemplPrint("leafHeader");
  for(c1=0; (group = LibNextLibGroup(&c1)); ) {
    if( !LibNofGroups(group) ) continue;
    TemplPrint("separator");
    for(c2=0; (lib= LibNextLib(group,&c2)); ) {
      libName = LibName (lib);
      isFound=0;
      if (view)
	for (c3=0; (vlib=ViewGetNextLeafLib (view, &c3));)
	  if (vlib->lib == lib) {
	    isFound = 1;
	    break;
	  }
      TemplPrint("leafLibsSelect", viewNo, libName, WwwSelected (isFound),
		 libName);
    }
  }
  TemplPrint("leafTrailer");
}


char *WwwEntryQuery (ENTRYv entry, char *entryName, char *libName)
{
  static STRv s=NULL;
  SLBo *lib;

  if (!s)
    s=StrNew ();
  else
    StrClear (&s);

  if (entry) {
    entryName = EntryGetName (entry);
    libName = LibName (EntryGetLib (entry));
    lib = EntryGetLib (entry);
  }
  else
    lib = (SLBo*) LibObjByName ("library", libName);

  StrPrintf (&s, "[%s-%s:'%s']", libName,
	     FieldGetName (LibGetIdField (lib)), entryName);
  return WwwTransform ("encode", _Str (s));
}


/**api* WwwEntryPrint *********************************************************
**
**      Prints a single entry in various forms.
**
**	INPUT:	    entry object [R]
**                  script object [W]
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

void WwwEntryPrint (TEMPLv templ, ENTRYv entry)
{
  static int  entryNum=0;
  SEQo        *seq=NULL, *protseq=NULL;
  char        *entryName, *libName;

  TemplWith (templ, "$entry.inList");
  if (ParGetBool ("printEntireEntry")){ /* print the complete entry */

    /* print a few buttons */
    TemplWith (templ, "envelope.head");
    TemplPrint ("head", 
		LibName (EntryGetLib (entry)),
		EntryGetName (entry), EntryGetFullName (entry));
    WwwPresentLaunchAppls (0, entry);
    WwwPresentActiveViews (NULL, EntryGetLib (entry), NULL, templ, 1);
    TemplPrint ("tail");
    TemplEndWith ();

    EntryViewPrintEnvelope (entry, "head");
    EntryPrint (entry, NULL);
    EntryViewPrintEnvelope (entry, "tail");
  }
  else if (ParGetBool ("downloadEntireEntry")){ /* download complete entry */
    EntryPrint (entry, NULL);
  }
  else { /* entry within entry list */
    entryName = EntryGetName (entry);
    libName = LibName (EntryGetLib (entry));
    if (*ParGetStr ("userIdOpt")) {
      TemplPrint ("entry.rootName", 
		  ++entryNum, EntryGetFullName (entry),
		  WwwEntryQuery (entry, NULL, NULL), 
		  EntryGetFullName (entry));
      
    }
    else 
      TemplPrint ("entry.inListNoId", WwwEntryQuery (entry, NULL, NULL), 
		  libName, entryName); 

    if (LibIsAnyFieldActive (libName)) {
      EntryViewPrintEnvelope (entry, "head");
      ParDefBool ("isHTMLFormat", 1);
      EntryPrintFields (entry, NULL);  
      EntryViewPrintEnvelope (entry, "tail");
    }
  }
  TemplEndWith ();
}



/**api* WwwPrintHelpTopic *****************************************************
**
**	prints help topic
**
**	INPUT:	    name of help topic [R]
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

void WwwPrintHelpTopic (char *helpTopic)
{
  TEMPLv   templ;

  templ = TemplOpen ("SRSDB:general.it", NULL);
  TemplWith (templ, "$main.fields");
  WwwPrintContentType (NULL);
  TemplPrint(helpTopic);
  TemplEndWith();
}




/****** WwwLinkStat ***********************************************************
**
**
**
*/

INT4 WwwLinkStat (char *setName)
{
  TEMPLv templ;
  SLBo      *lib;
  SRSoGROUP *group;
  char      queryStr[512], *libName;
  INT4      k=0, context1, context2, context3, doSkipLib, isSelected=0;
  Int4 entryN =0,linkLibsN =0;

  templ = TemplOpen ("SRSICA:srswww.i", NULL);
  WwwPrintContentType(NULL);

  WwwQueryRepeat (ParGetNum ("linkSetNumber"));

  TemplWith(templ,"$linkSet");
  TemplPrint("head");
  WwwPrintButtons (templ);
  TemplPrint("tableHead", setName);

  for (context1=0; (group = LibNextLibGroup (&context1));) 
    for (context2=0; (lib = LibNextLib (group, &context2));)
      if (LibIs (lib, "linkTarget")) {
        TemplPrint("newRow");
	doSkipLib=0;
	for (context3=0; (SetGetNextLibStat (setName, &libName, &context3));)
	  if (SmEqs (lib->nam, libName))
	    doSkipLib = 1;  /* don't link to libs contained in the set */
	if (!doSkipLib) {
	  isSelected = 1; 
	  linkLibsN++;
	  TemplPrint("libName",linkLibsN,lib->nam,lib->nam);
	  sprintf (queryStr, "%s > %s", setName, lib->nam);
          WwwQueryLinkDo(queryStr);

	  sprintf (queryStr, "%s < %s", setName, lib->nam); 
          WwwQueryLinkDo(queryStr);	  

	  sprintf (queryStr, "%s ! (%s < %s)", setName, setName, lib->nam); 
          WwwQueryLinkDo(queryStr);
          TemplPrint("endRow");
	}
      }
  if (!isSelected)
    _ErrMsg2 (e__nolinklibselected, "LINK");
  TemplPrint("tail",linkLibsN);
  TemplEndWith();
  return k;
}


/****** WwwQueryLinkDo  ***************************************************
**
**
**
**
**
**
**
*/

WwwQueryLinkDo(char *queryStr)
{
  WWWoQUERY *query;
  Int4      entryN, k;

  k = WwwQueryDo (queryStr, "link");
  if( k ) {
    query = WwwGetQuery(k);
    TemplPrint("libEntriesH",ParGetStr("userId"),k,query->entryN);
    WwwDelQuery(query);
  } 
  else {
    TemplPrint("libEntries",0);
  }
}

/****** WwwWriteFile  ***************************************************
**
*/

INT4 WwwWriteFile (char *formatStr, ...)
{
  FILE *file;
  va_list ap;
  
  va_start (ap, formatStr);
  vfprintf (file, formatStr, ap);
  va_end (ap);
  
  if (formatStr[strlen (formatStr) -1] != '\n')
    fprintf (file, "\n");
  return 1;
}


/****** WwwGrowQuery **********************************************************
**
**       new query string is constructed from the selected 
**       entry names from result page
**
**       INPUT:   query string [W] 
**                Entry name [R]
**
*/

void  WwwGrowQuery(char *queryString, char *fullEntry)
{
  static char oldLibName[30] ="";
  char         entryName[30],libName[30];
   
  if(!*fullEntry)
    _ErrMsg2 (i__invalidentry, fullEntry);

  sscanf(fullEntry,"%[^:]:%[^@]",libName,entryName);

  if(!*queryString) {  /* head part */
      sprintf(queryString,"[%s-id:%s",libName,entryName);
  }
  else {              /* tail parts */
    if( SmEqs(oldLibName,libName))
      sprintf(queryString,"%s | %s",queryString,entryName);
    else {
      sprintf(queryString,"%s] | [%s-id:%s",queryString,libName,entryName);
    }
  }
  strcpy(oldLibName,libName);
}

/****** WwwNextSelectedQuery **************************************************
**
**      Returns the number of the next query selected in the query manager.
**
**	INPUT:	  the address of iterator (set to 0 to get the first) [W]
**                address of pointer to the query name (or NULL) [W]
**
**      RETURNS:  the number of the next selected query.
**                0: no query was selected
**
*/

Int4 WwwNextSelectedQuery (Int4 *c, char **name)
{
  static Int4 queryN=0;
  char *tmp;

  if (!*c) {
    *c = 1;
    queryN = ParGetNum ("numberOfQueries");
  }  
  else
    (*c)++;
  while (!*(tmp = ParGetStrF ("qmstr%d", *c)) && *c <= queryN)
    (*c)++;

  if (*c > queryN)
    return (*c = 0);
  if (name)
    *name = tmp;
  return (*c);
}


/****** WwwQuerySelectedEntries ***********************************************
**
**      Make a set with selected entries from the query result page and 
**      do the query.
**
**      RETURNS:  the number of the resulting query/set
**                0: no entry was selected
**
*/

Int4 WwwQuerySelectedEntries ()
{
  char     *entryName,queryString[5000];
  Int4     i, entryN, queryN=0, last=ParGetNum ("viewEntriesChunkSize");

  queryString[0] ='\0';

  for(i=1, entryN=0; i <= last; i++){
    entryName = ParGetStrF("EntryNum_%d",i);
    if(*entryName) {
      WwwGrowQuery(queryString,entryName);
      entryN++;
    }
  }
  if (entryN) {
    sprintf(queryString,"%s]",queryString);
    queryN = WwwQueryDo(queryString,"select");
  }
  return queryN;
}

/**api* WwwQueryPrint ********************************************************
**
**	Prints the page with the results of a query. The entry list can
**      be printed either as a normal list or as a table.
**
**	INPUT:	    the query number in the "query history" [R]
**
*/ 

void WwwQueryPrint (INT4 queryN)
{
  WWWoQUERY *query;
  TEMPLv    templ;
  Int4      startN=ParGetNum ("viewEntriesStartN"), 
            chunkSize=ParGetNum ("viewEntriesChunkSize");

  templ = WwwInit ();
  WwwInitViews (templ);

  TemplWith (templ, "$queryResult");
  TemplPrint ("head");
  WwwPrintButtons (templ);
  
  /* get the query and print the header of result list*/
  query = WwwGetQuery (queryN);
  TemplPrint ("title", WwwStringEncode (query->queryStr),
	      query->entryN,query->entryN);
  TemplPrint ("options.head", queryN, chunkSize, queryN);
  TemplWith (templ, "options");
  WwwPresentLaunchAppls (queryN, NULL);
  TemplEndWith ();
  TemplPrint ("options.download");
  TemplWith (templ, "options");
  WwwPresentActiveViews (NULL, NULL, query, templ, 0);
  TemplEndWith ();
  TemplPrint ("options.tail");
  TemplPrint ("entriesStart");

  /* print entry list */
  if (ParGetNum ("viewNumber") > 1) 
    WwwPrintSetView (templ, query->name, startN, chunkSize);
  else 
    WwwPrintSet (templ, query->name, startN, chunkSize);

  WwwDelQuery (query);
  WwwPresentSkipChunkSet (templ, query->entryN, queryN);
  TemplPrint ("tail");
  TemplEndWith ();
}


char *WwwRootLibNames (VIEWo *view)
{
  static char s[500];
  VIEWoLIB *vlib;
  Int4 k;

  for (k=0, s[0]='\0'; (vlib = ViewGetNextRootLib (view, &k));)
    sprintf (s, "%s%s ", s, LibName (vlib->lib));
  s[strlen(s)-1] = '\0';
  return s;
}


/****** WwwPrintSelectField ***************************************************
**
**      Prints a field name in the list fields to be selected for view.
**
**      INPUT:      view object  [R]
**                  number of view [R]
**                  field object [R]
**                  view library object [R] or NULL if field from root library
**                  number of columns per row [R]
**                  address of count of fields in the current row [R]
**
*/

void WwwPrintSelectField (VIEWo *view, Int4 viewNum, SLBoFIELD *field, 
			  VIEWoLIB *vlib, Int4 numCol, Int4 *count)
{
  LIBoFieldFormat *format;
  char            *fieldName,*tmp, *libNames;
  Int4            c;

  fieldName = LibGetFieldName (field);
  if (!vlib)
    libNames = WwwRootLibNames (view);
  else
    libNames = LibName (vlib->lib);

  if (FieldIs (field, "header")) {
    if (*count>0) 
      TemplPrint ("newRow");
    TemplPrint ("fieldHeader", numCol, fieldName);
    *count = 0;
  }
  else {
    if (!((*count)++ % numCol)) 
      TemplPrint ("newRow");

    if (vlib)  /* field of leaf library */
      TemplPrint ("field", viewNum, LibName (vlib->lib), fieldName,
		  WwwChecked (ViewIsLeafField (view, vlib, field)), 
		  fieldName, libNames, fieldName, "");
    else 
      TemplPrint ("field", viewNum, fieldName,
		  WwwChecked (ViewIsRootField (view, field)), 
		  fieldName, libNames, fieldName, "");

    /* if field has format option print the menu with all options */    
    if (field->type->formatN) {
      
      if (vlib) {
	TemplPrint ("format.head", viewNum, LibName (vlib->lib), fieldName);
	for (c=0; (format=LibNextFieldFormat (field->type, &c));){
	  tmp = ParGetStrF("v%d_LF_%s_%s_format", viewNum,
			   LibName (vlib->lib), fieldName);
	  TemplPrint ("format.name",SmEqs(tmp,format->name) ? "SELECTED" : "",
		      format->name);
	}
      }
      else {
	TemplPrint ("format.head", viewNum, fieldName);
	for (c=0; (format=LibNextFieldFormat (field->type, &c));){
	  tmp = ParGetStrF("v%d_RF_%s_format",viewNum,fieldName);
	  TemplPrint ("format.name",SmEqs(tmp,format->name) ? "SELECTED" : "",
		      format->name);
	}
      }
      TemplPrint ("format.tail");
    }
    TemplPrint ("fieldTail");
  }
} 



/**api* WwwPrintSetView *******************************************************
**
**      Equivalent to WwwPrintSet (calls WwwPrintSet) but prints the list of 
**      entries using a view.
**
**      INPUT:      the template object [W]
**                  the query name [R]
**                  the start entry number [R]
**                  the chunk size [R]
**           IMPLICIT:
**                  wwwView (VIEWo *)
**
*/

void WwwPrintSetView (TEMPLv templ, char *queryName, 
                      Int4 startN, Int4 chunkSize)
{
  Int4 viewNo = 0;

  ParDefBool ("isHTMLFormat", 1);
  if (!(viewNo = ParGetNum("viewNumber")))
    viewNo = ViewGetViewsN ();
  wwwView = ViewGetWithNo (viewNo);
  
  if (!WwwIsViewForQuery (wwwView, queryName)) {
    _ErrMsg3 (e__wwwnomatchingview, queryName, ViewGetName (wwwView));
    WwwPrintSet (templ, queryName, startN, chunkSize);
  }
  else {
    ParDefBool ("isView", 1);
    ParSetVolatile ("isView");
    if (ViewIsTable (wwwView)) {
      TemplWith (templ, "$entry.inTable");
      WwwViewTableHeader (templ, wwwView);
      ParDefBool("isTable", 1);
      ParSetVolatile ("isTable");
    }
    WwwPrintSet (templ, queryName, startN, chunkSize);
    if (ViewIsTable (wwwView)) {
      TemplPrint ("tail");
      TemplEndWith ();
    }
  }
  ViewDelete (wwwView);
}

/****** WwwViewTableHeader ****************************************************
**
**      Prints the header of the table containing a view of one or more
**      entries.
**
**      INPUT:     template object [W]
**
*/

static void WwwViewTableHeader (TEMPLv templ, VIEWo *view)
{
  SLBoFIELD *field;
  VIEWoLIB  *tmp, *vlib;
  char      *libName;
  Int4      k, l, m;

  TemplPrint ("head");

  for (k=0, l=0; (tmp=ViewGetNextRootLib (view, &k)); l++)
    vlib = tmp;
  libName = l>1 ? "RootLibs" : LibName (vlib->lib);
  TemplPrint ("title.library", libName);
  
  for (m=0; (field=ViewGetNextField (vlib, &m));)
    TemplPrint ("title.field", 
		LibName (vlib->lib), LibGetFieldName (field),
		ViewIsShortNames (view) ?
		LibGetFieldShortName (field) : LibGetFieldName (field));

  /* ... and view leaf fields names */
  for (k=0; (vlib=ViewGetNextLeafLib (view, &k));) {
    TemplPrint ("title.library", LibName (vlib->lib));
    if (!ViewLeafIsOnlyEntryN (vlib)) 
      for(m=0; (field=ViewGetNextField (vlib, &m));)
	TemplPrint ("title.field", 
		    LibName (vlib->lib), LibGetFieldName (field),
		    ViewIsShortNames (view) ?
		    LibGetFieldShortName (field) : LibGetFieldName (field));
  }
  TemplPrint ("title.tail");
}


/****** WwwViewPrintEntryN ***************************************************
**
**      Prints an entry view inside a table.
**     
** 	INPUT:	  leaf object [R]
**                the root entry object [R]
**                number of rows to extend [R]
**
**      RETURNS:  number of fields printed for the entry
*/

static void WwwViewPrintEntryN (VIEWo *view, VIEWoLEAFSET *leaf, ENTRYv entry, Int4 rowN)
{
  char *viewName, *queryStr;
  Int4 viewN;
  viewName = ViewGetLeafView (leaf->vlib);
  viewN = *viewName ? ViewGetViewNumber (viewName) : 0;
  if (*viewName);
  queryStr = ViewGetLeafQuery (leaf->vlib, entry);
  TemplPrint ("onlyEntryN", rowN, viewN, WwwTransform ("encode", queryStr), 
	      leaf->entryN);
}


/**api* WwwPrintSet ***********************************************************
**
**      Prints a list of entries in various formats.
**
**	INPUT:	  o template object [W]
**                o name of set/query [R]
**                o number of first entry to be printed, first is 1...if 0 
**                  then is set to 1 [R]
**                o number of entries to print, if 0 then size of set is
**                  assumed [R]
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

void WwwPrintSet (TEMPLv templ, char *setName, int firstN, int printN)
{
  ENTRYv   entry;
  SETo     *set;
  IDoENTRY id;
  char     *tmp;
  INT4     setEntryN, k, lastN, moreN;
  
  if (!firstN) 
    firstN = 1;

  set = SetGet (setName);
  setEntryN = SetSize (setName);
  if (!printN)
    printN = setEntryN;

  lastN = firstN + printN - 1; 

  for (k=firstN;  k <= lastN && k <= setEntryN;  k++) {
    SetGetID (set, k, &id); 
    entry = EntryOpen (&id);
    if (entry) { 
      if (LibIs (EntryGetLib (entry), "user")) 
	chdir (_FilTempLN (ParGetStrF ("%sDirName", 
				       LibName (EntryGetLib (entry)))));
      
      if(ParGetBool("isView"))
	EntryView (entry, wwwView);
      else
	WwwEntryPrint (templ, entry);
      EntryClose (&entry);
    }
  }
}


void WwwViewEntryNamePrint (VIEWo *view, ENTRYv entry, 
			    Int4 entryNo, Int4 rowN, Int4 isRoot)
{
  if (ViewIsTable (view)) {
    if (isRoot)
      TemplPrint ("rootNameManyLibs", rowN,  entryNo, 
		  EntryGetFullName (entry),
		  WwwEntryQuery (entry, NULL, NULL), 
		  LibName (EntryGetLib (entry)), EntryGetName(entry));
    else
      TemplPrint ("leafName", rowN, WwwEntryQuery (entry, NULL, NULL), 
		  EntryGetName (entry));
  }
  else {
    if (isRoot)
      TemplPrint ("rootName", entryNo, EntryGetFullName (entry),
		  WwwEntryQuery (entry, NULL, NULL),
		  EntryGetFullName(entry));
    else
      TemplPrint ("leafName", WwwEntryQuery (entry, NULL, NULL), 
		  EntryGetFullName (entry));
  }
}


/**api* WwwViewGet **************************************************************
**
**      Retrieves a view object from user context. The view number can
**      be obtained by ViewGetViewNumber. Delete the object with ViewDelete.
**      A view can also be logically deleted by user 
**      - check with ViewIsDeleted.
**
**      INPUT:  view number [R]
*               the template used for printing entries [R]
**
**      RETURNS: view object               
**
**
*/

VIEWo *WwwViewGet (INT4 viewN, TEMPLv templ)
{
  VIEWo      *view;
  VIEWoLIB   *vlib;  
  VIEWoFIELD *vfield;
  SLBo       *lib, *rootLib;
  SLBoFIELD  *field;
  SRSoGROUP  *group;
  char       *libName, *fieldName, *viewName;
  INT4       c1,c2,c3;

  if (!*(viewName = ParGetStrF ("view%d_Name", viewN)))
    return ViewGetWithNo (viewN); /* might be internally known */
  view = ViewNew (viewN, viewName);
  ViewSetTemplate (view, templ);
  ViewSetEntryNamePrint (view, WwwViewEntryNamePrint);
  ViewSetEntryNamePrinting (view, 1);
  ViewSetEntryNPrint (view, (Func) WwwViewPrintEntryN);

  if (ParGetNumF("view%d_isTable", viewN))
    ViewSetFormat (view, "table"); 
  ViewSetUseShortNames (view, ParGetNumF ("view%d_isShortNames", viewN));
  if (ParGetNumF ("ViewDeleted_%d", viewN))
    ViewMarkDeleted (view); 

  /* process root databanks */
  for (c1=0; (group = LibNextLibGroup(&c1));) {
    for (c2=0; (lib = LibNextLib (group, &c2));) {
      if (ParGetNumF ("v%d_R_%s", viewN, LibName (lib))) {
	rootLib = lib;
	vlib = ViewAddRootLib (view, lib);
      }
    }
  }
  for (c3=0; (field = LibNextField (rootLib, &c3));) {
    fieldName = LibGetFieldName (field);
    if (ParGetNumF ("v%d_RF_%s", viewN, fieldName)) {
      vfield = ViewAddRootField (view, LibFieldType (field));
      ViewSetFieldFormat (vfield, ParGetStrF ("v%d_RF_%s_format",
					      viewN, fieldName));
    }
  }

  /* process leaf databanks */
  for (c1=0; (group = LibNextLibGroup (&c1));) {
    for (c2=0; (lib = LibNextLib (group, &c2));) {
      libName = LibGetName (lib, "full");
      if (ParGetNumF ("v%d_L_%s", viewN, libName)) {
        vlib = ViewAddLeafLib (view, lib);
	ViewSetLeafQuery (vlib, ParGetStrF ("v%d_Lextra_%s_query", 
					    viewN, libName)); 
	ViewSetLeafPrintN (vlib, ParGetNumF ("v%d_Lextra_%s_onlyEntryN",
					     viewN, libName));
        ViewSetLeafView (vlib, ParGetStrF ("v%d_Lextra_%s_view", 
					   viewN, libName));
	for(c3=0; (field = LibNextField (lib, &c3));) {
	  fieldName = LibGetFieldName (field);
	  if(ParGetNumF("v%d_LF_%s_%s", viewN, libName, fieldName)) {
	    vfield = ViewAddField (vlib, LibFieldType (field));
	    ViewSetFieldFormat (vfield, ParGetStrF ("v%d_LF_%s_%s_format",
						    viewN, libName,fieldName));
	  }
	}
      }
    }
  }
  return view;
}

Int4 WwwIsViewInternal (VIEWo *view)
{
  return *ParGetStrF ("view%d_Name", ViewGetNo (view)) ? 0 : 1;
}

static void WwwViewSave (VIEWo *view, char *option)
{
  VIEWoLIB *vlib;
  SLBoFIELD *field;
  Int4 n=ViewGetNo (view), k, c, c2;

  ParDefStrF (ViewGetName (view), "view%d_Name", n);
  if (ViewIsShortNames (view))
    ParDefStrF ("1", "view%d_isShortNames", n);
  if (ViewIsTable (view))
    ParDefStrF ("1", "view%d_isTable", n);
  
  for(c=0, k=0; (vlib = ViewGetNextRootLib (view, &c)); k++) {
    ParDefStrF ("1", "v%d_R_%s", n, LibName (vlib->lib));
    if (!k)
      for(c2=0; (field = ViewGetNextField (vlib, &c2));) {
	ParDefStrF ("1", "v%d_RF_%s", n, FieldGetName (field));
      }    
  }
  for(c=0, k=0; (vlib = ViewGetNextLeafLib (view, &c)); k++) {
    ParDefStrF ("1", "v%d_L_%s", n, LibName (vlib->lib));
      for(c2=0; (field = ViewGetNextField (vlib, &c2));) {
	ParDefStrF ("1", "v%d_LF_%s_%s", n, LibName (vlib->lib), 
		    FieldGetName (field));
      }    
  }


}


void WwwInitViews (TEMPLv templ)
{
  static int isInit=0;
  VIEWo *view;
  Int4  c, viewNo;
  
  if (isInit)
    return;

  for (c=0; (view = ViewNext (&c));) { 
    /* get modified version if exists */
    viewNo = ViewGetNo (view);
    if (!ViewIs (view, "forAll") && *ParGetStrF ("view%d_Name", viewNo)) {
      view = WwwViewGet (viewNo, templ);
      ViewSetWithNo (view, viewNo);
    }
    else {
      ViewSetTemplate (view, templ);
      ViewSetEntryNamePrint (view, WwwViewEntryNamePrint);
      ViewSetEntryNPrint (view, (Func) WwwViewPrintEntryN);
      ViewSetEntryNamePrinting (view, 1);
    }
  }
  ViewSetUserList (WwwViewGet, templ);
  isInit=1;
}


/**api* WwwQueryGetSet ********************************************************
**
**      This is SRSWWW's version of 'QueryGetSet' of the query module.
**      The difference is that queries represented with names inside
**      the query are evaluated by submitting the query associated to 
**      a set name.
**      Evaluation of the overall query is a recursive process.
**
*/ 

INT4 WwwQuerySetGet ()
{
  WWWoQUERY *query;
  SLBo      *lib;
  SETo      *set;
  char      name[132];

  IargGetArgs ("name", name);

  if (!(set = SetGet (name))) {
    if ((lib = (SLBo *) LibObjByName ("library", name)) 
	|| SmEqs (name, "parent")) {
      set = SetNew (name, NULL);
      SetSetIsDB (set, 1);
    }
    else if ((query = WwwGetQueryName (name))) {
      set = QueryRecursive (query->queryStr, name);
    }
    else
      _ErrExit2 (e__nosetorlib, name);
  }
  IcaReturn ("set", set);
}



/**api* WwwQueryDo ************************************************************
**
**      evaluates a query in a recursive way ...whenever a set name is
**      encountered that set is reconstructed by repeating the 
**      associated query (if not already done).
**
**	INPUT:	    query expression string [R]
**                  query type: "link", "query" [R]
**	        IMPLICIT:
**
**	RETURNS:    number of query in history if success
**                  0 if not
*/ 

INT4 WwwQueryDo (char *queryStr, char *queryType)
{
  static INT4 isInit=0;
  char queryName[80];
  INT4 queryN=ParGetNum ("numberOfQueries");
  
  if (!isInit) /* set SRSWWW's own function */
    IcaSetFunction ("QuerySetGet", WwwQuerySetGet);

  sprintf (queryName, "Q%d", queryN + 1);

  if (Query (queryStr, queryName)) {
    WwwRegisterQuery (queryName, SetGetQueryStr (queryName), queryType);
    return queryN + 1;
  }
  return 0;
}



/**api* WwwQueryRepeat ********************************************************
**
**      Repeats a query already recorded in history which is identified
**      by the query number.
**
**	INPUT:	    
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

INT4 WwwQueryRepeat (INT4 queryN)
{
  static INT4 isInit=0;
  WWWoQUERY *query=NULL;

  if (!isInit) /* set SRSWWW's own function */
    IcaSetFunction ("QuerySetGet", WwwQuerySetGet);

  query = WwwGetQuery (queryN);
  Query (query->queryStr, query->name);
  WwwDelQuery (query);  
  return 1;
}    



/**api* WwwQueryExpression ****************************************************
**
**	Evaluates a query expression and prints the result;
**
**	INPUT:	  o the type of the result set: "expression", "query", 
                    ... [R]
**                o the query string [R]
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

void WwwQueryExpression (char *queryType, char *queryStr)
{
  char *s;

  s= WwwTransform ("decode", queryStr); 

  if (WwwQueryDo (s, queryType)) 
    WwwQueryPrint (ParGetNum ("numberOfQueries"));
  else
   _ErrMsg2 (i__querynegative, queryStr);
}



/**api* WwwLinkSet ************************************************************
**
**	links a set from history to selected libraries using various options;
**
**	INPUT:	    number of query to be linked [R]
**	        IMPLICIT:
**
**	RETURNS:    number of result query in history
**                  0: no library was selected for linking 
*/ 

Int4 WwwLinkSet (Int4 queryN)
{
  QASvQUERY qas;
  WWWoQUERY *query;
  SLBo      *lib;
  SRSoGROUP *group;
  Int4      k, c1, c2;

  qas = QasNew ();
  QasInitLink (qas);
  query = WwwGetQuery (queryN);
  QasSetQueryToLink (qas, query->queryStr);
  WwwDelQuery (query);  
  QasSetLinkType (qas, ParGetStr ("linkSetType"));
  QasSetTmpSetNum (qas, queryN);
  
  for (k=0, c1=0; (group = LibNextLibGroup (&c1));) 
    for (c2=0; (lib = LibNextLib (group, &c2));)
      if (LibIs (lib, "linkTarget")) {
	QasSetLinkWith (qas, LibName (lib));
	k++;
      }  
  if (!k) {
    _ErrRet2 (e__nolinklibselected, "[S+L]");
    return 0;
  }
  else 
    queryN = WwwQueryDo (QasGetQueryString (qas), "link");
  QasDelete (qas);
  return queryN;
}


Int4 WwwLinkEntry (char *libName, char *entryName)
{
  QASvQUERY qas;
  SLBo      *lib;
  SRSoGROUP *group;
  Int4      k, c1, c2, queryN;

  qas = QasNew ();
  QasInitLink (qas);
  QasSetQueryToLink (qas, WwwEntryQuery (NULL, entryName, libName));
  QasSetLinkType (qas, "toLibs");
  QasSetTmpSetNum (qas, 555);
  
  for (k=0, c1=0; (group = LibNextLibGroup (&c1));) 
    for (c2=0; (lib = LibNextLib (group, &c2));)
      if (LibIs (lib, "linkTarget")) {
	QasSetLinkWith (qas, LibName (lib));
	k++;
      }  
  if (!k) {
    _ErrRet2 (e__nolinklibselected, "[S+L]");
    return 0;
  }
  else 
    queryN = WwwQueryDo (QasGetQueryString (qas), "link");
  QasDelete (qas);
  return queryN;
}



/**api* WwwTransform *********************************************************
**
**	if a query string is put as parameter value in html script then
**      <> chars are recognized as syntactic elements;
**
**	INPUT:	    option "decode" and "encode" [R]
**                  string to be transformed [R]
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

char *WwwTransform (char *option, char *s)
{
  static char tmp[1000];

  strcpy (tmp, s);
  if (option[0] == 'e') {
    SmSwapS (tmp, ">", "&gt;");
    SmSwapS (tmp, "<", "&lt;"); 
    SmSwapS (tmp, "+", "_PL_"); 
    SmSwapS (tmp, " ", "_SP_"); 
  }
  else {
    SmSwapS (tmp, "&gt;", ">");
    SmSwapS (tmp, "&lt;", "<"); 
    SmSwapS (tmp, "_PL_", "+"); 
    SmSwapS (tmp, "_SP_", " "); 
  }
  return tmp;
}


/**api* WwwRegisterQuery ******************************************************
**
**	records a query description as a list of parameters;
**      these parameter's will be saved in the user file;
**
**	INPUT:	    name of successful query [R]
**                  query expression [R]
**                  query type: "query", "link"
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

void WwwRegisterQuery (char *queryName, char *queryStr, char *queryType)
{
  char *libName, parName[80];
  INT4 c, k, libN, queryN, entryN;
  
  entryN = SetSize (queryName);
  if ((SmEqs (queryType, "expression") || SmEqs (queryType, "query")
       || SmEqs(queryType,"link") || SmEqs (queryType, "select")) && entryN) {
    queryN = ParGetNum ("numberOfQueries");
    ParDefNum ("numberOfQueries", ++queryN);
    sprintf (parName, "QueryStr%d", queryN); 
    ParDefStr (parName, queryStr);
    sprintf (parName, "QuerySize%d", queryN); 
    ParDefNum (parName, entryN);
    sprintf (parName, "QueryType%d", queryN); 
    ParDefStr (parName, queryType);
    sprintf (parName, "isSubEntry%d", queryN);
    ParDefNum (parName, SetIsSubEntry (queryName));
    
    sprintf(parName,"QueryDeleted_%d",queryN);  /* added: Ramu */
    ParDefNum(parName,ParGetNum(parName));   /* for query manager function */

    sprintf(parName,"QueryComm%d",queryN);
    ParDefStr(parName,ParGetStr(parName));
    
    for (c=0, k=1;
	 (libN=SetGetNextLibStat (queryName, &libName, &c)); k++) {
      sprintf (parName, "QueryLibrary%d_%d", queryN, k); 
      ParDefStr (parName, libName);
      sprintf (parName, "QueryLibraryN%d_%d", queryN, k); 
      ParDefNum (parName, libN);
    }
  }
}


/**api* WwwDeleteQuery ******************************************************
**
**	deletes last query in history;
**
**	INPUT:	    
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

static void WwwDeleteQuery ()
{
  char parName[80];
  INT4 queryN, k;
  
  queryN = ParGetNum ("numberOfQueries");
  sprintf (parName, "QueryStr%d", queryN); 
  ParDelete (parName);
  sprintf (parName, "QuerySize%d", queryN); 
  ParDelete (parName);
  sprintf (parName, "QueryType%d", queryN); 
  ParDelete (parName);
  sprintf (parName, "isSubEntry%d", queryN);
  ParDelete (parName);
  
  for (k=0; ; k++) {
    sprintf (parName, "QueryLibrary%d_%d", queryN, k); 
    if (!ParDelete (parName))
      break; /* no more items */
    sprintf (parName, "QueryLibraryN%d_%d", queryN, k); 
    ParDelete (parName);
  }
  ParDefNum ("numberOfQueries", --queryN);
}

/**api* WwwGetQueryName *********************************************************
**
**	Returns descriptor of query with specified name.
**
**	INPUT:	    query name [R]
**	        IMPLICIT:
**
**	RETURNS:    query descriptor object
*/ 

WWWoQUERY *WwwGetQueryName (char *name)
{
  INT4 queryN;

  if (!(sscanf (name, "Q%d", &queryN) || sscanf (name, "q%d", &queryN)))
    _ErrExit3 (e__objectunknown, "set", name);
  
  return WwwGetQuery (queryN);
}

/**api* WwwGetQuery ***********************************************************
**
**	Creates a query object with all information about it from the user 
**      file - this object must be deleted with WwwDelQuery after use.
**
**	INPUT:	    address of query object [W]
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

WWWoQUERY *WwwGetQuery(int queryN)
{
  WWWoQUERY *query;
  char parName[132];
  int  k;

  if (queryN > ParGetNum ("numberOfQueries")) {
    _ErrExit3 (e__objectunknown, "query" , "number?");
  }  
  query = malloc (sizeof (WWWoQUERY));
  query->queryN = queryN;
  sprintf (query->name, "Q%d", queryN);
  sprintf (parName, "QueryStr%d", queryN); 


 /* better copy query string since it will have to be encoded for
    printing on HTML and therefore needs some extraspace */

  strcpy (query->queryStr, ParGetStr (parName));

  sprintf(parName,"QueryComm%d",queryN);
  strcpy(query->comment,ParGetStr(parName));

  sprintf (parName, "QuerySize%d", queryN); 
  query->entryN = ParGetNum (parName);

  sprintf (parName, "QueryType%d", queryN); 
  query->type = ParGetStr (parName);

  sprintf (parName, "isSubEntry%d", queryN);
  query->isSubEntry = ParGetBool (parName);

  sprintf(parName, "QueryDeleted_%d",queryN);
  query->isDeleted = ParGetNum(parName);

  for (k=0;; k++) {
    sprintf (parName, "QueryLibrary%d_%d", queryN, k+1); 
    if (!*(query->lib[k].name = ParGetStr (parName)))
      break;
    sprintf (parName, "QueryLibraryN%d_%d", queryN, k+1); 
    query->lib[k].entryN = ParGetNum (parName);
  }
  query->lib[k].entryN = 0; /* end marker ..."name" is also NULL! */

  return query;
}


/**api* WwwDelQuery *********************************************************
**
**	Deletes a query object created with WwwGetQuery or WwwGetQueryName.
**
**	INPUT:	    address of query object [W]
**
*/ 

void WwwDelQuery (WWWoQUERY *query)
{
  if (query)
    free (query);
}


void WwwPrintValue (char *libName, char *fieldName, char *value, 
		    Int4 n, Int4 entryN)
{
  TemplPrint ("value", n, libName, fieldName, value, fieldName, libName,
	      fieldName, WwwTransform ("encode", value), value, entryN);
}


/**api* WwwParRead ***********************************************************
**
**	reads parameters from user-context file
**
**	INPUT:	userID [R]
**              true if failure to read parameter file is fatal;    
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

void WwwParRead (char *userId, INT4 doInsist)
{
  INT4 rv;

  if (!userId || !*userId) {
    if (doInsist)
      _ErrExit (e__filnotok);
    else 
      return;
  }

  rv = ParRead (WwwGetName (userId, "context"));
   if (_ErrIs (rv) && doInsist)
    _ErrExit2 (rv, userId);
}


/**api* WwwParWrite ***********************************************************
**
**	reads parameters from user-context file
**
**	INPUT:	userID [R]
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

void WwwParWrite (char *userId)
{
  ParSave (WwwGetName (userId, "context"));
}

/**api* WwwNewUserId ***********************************************************
**
**	reads parameters from user-context file
**
**	INPUT:	userID [R]
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

char *WwwNewUserId ()
{
  static char userId[80];
  char tmp1[30];
  char tmp2[30];
  char *remoteAddr = getenv ("REMOTE_ADDR"), *dirName, command[255];
  int  k;

  if (!remoteAddr)
    remoteAddr = "local";
  ParDefStr("remoteAddress",remoteAddr);
  SmRemoveChar(remoteAddr,'.');

  /* trim to 8 characters */
  for (k=strlen (remoteAddr) - 8; k > 0; k--)
    remoteAddr[k-1] = ' ';

  LibBaseConv(atoi(remoteAddr),60,tmp1);
  LibBaseConv(TimeGet(),60,tmp2);

  sprintf (userId, "%s%s",tmp1, tmp2 );
  dirName = WwwGetName (userId, "directory");
  
  if (mkdir (dirName, 00777) != 0)
    _ErrExit2 (e__filnotok, dirName);
  sprintf (command, "chmod 777 %s", dirName);
  system (command); 
  ParDefStr ("userId", userId);
  return userId;
}


/**api* WwwFileName **********************************************************
**
**	returns a file or directory name
**
**	INPUT:	userID [R]
**              option: "context", "directory" [R]
**	    IMPLICIT:
**
**	RETURNS:    file name
*/ 

char *WwwGetName (char *userId, char *option)
{
  static char name[255], rootDirName[80]="SRSWWWTMP";

  switch (tolower (option[0])) {
  case 'c':  /* context */ 
    sprintf (name, "%s/%s/user.par", rootDirName, userId);
    break;
  case 'd':  /* directory */
    sprintf (name, "%s/%s", rootDirName, userId);
    break;
  case 's':  /* status */
    sprintf (name, "%s/%s/busy", rootDirName, userId);
    break;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
  return  _FilLN (name);
} 


/**api* WwwGetIdParam *********************************************************
**
**	builds the Id parameter for calling wgetz via command line
**
**	INPUT:	
**	    IMPLICIT:
**
**	RETURNS:    parameter for command line
*/ 

char *WwwGetIdParam ()
{
  static char parStr[80];
  char *userId;

  userId = ParGetStr ("userId");
  if (!userId || !*userId) {
    parStr[0] = '\0';
    return parStr;
  }
  else {
    sprintf (parStr, "-id+%s+", userId);
    return parStr;
  }
} 




/**api* WwwGetODDFile *********************************************************
**
**	Gets, if available, the ODD file for the library;
**
**	INPUT:	
**	    IMPLICIT:
**
**	RETURNS:    
*/ 

void WwwGetODDFile (char *libName)
{
#ifdef xxx
  SLBo *lib;
  FILEo file;
  INT4 rv;
  char fileName[132];


  if (SmEqs (libName, "hyperlink"))
    strcpy (fileName, "SRSICA:hyperlink.sdl");
  else {
    if (!(lib = (SLBo*) LibObjByName ("library", libName)))
      _ErrExit3 (e__objectunknown, "library", libName);

    if (*lib->oddfile) 
      sprintf (fileName, "SRSICA:%s", lib->oddfile);
    else 
      return;
  }

  rv = FilUOpen (&file, fileName, 255, 0);
  _ErrExit2 (rv, fileName);
  printf ("<PRE>");
  do {
    fputs (WwwStringEncode (file.ln), stdout);
    rv = FilURead (&file);
  }
  while (rv != e__eof);
  printf ("</PRE>");
  FilUClose (&file);
#endif
}




/***LibBaseConv*************************************************************
**             Author: Chenna Ramu
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387372  
**                     Email: chenna@embl-heidelberg.de
**
**   Base Conversion to any base less than the number of characters
**   available in symbol table.
**
**
**   INPUT:  num : Decimal number to be converted
**           base : 
**           temp : converted number as string
**
*/

int LibBaseConv( int num, int base, char *temp)
{
  char abuf[]=
  {"0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ_abcdefghijklmnopqrstuvxyz" };
  Int4 i = 0, r = 0, iret = 0;

  temp[0] = '\0';

/*  LibShuffleBuff(abuf); */

  if (base > strlen(abuf) ) {
    _ErrMsg2 (e__illegalbaseconv,strlen(abuf)+1);
    base = strlen(abuf); /* assume the maximum possible base */
  }

  for(i=0; num >= base; i++) {
    r = num%base;    
    iret = iret + LibPower(10,i) * r;
    num = (num-r)/base ;
    temp[i] = abuf[r];
  }

  iret = iret + LibPower(10,i) * num;
  temp[i] = abuf[num];
  temp[i+1] = '\0';
  LibRevStr(temp);
  return (iret);
}

/** LibPower *************************************************
**
**
**
**  raise base to the power n  and return the result
**
**
**/

INT4 LibPower(int base, int n)
{

  int i = 0;
  for( i = 1; n > 0; --n)
    i = i * base;
  return i;
}


/** LibRevStr *******************************************************************
**
**
**
**   Reverse given string
**
**
**
**/
void LibRevStr(char s[])
{
  int c,i,j;

  for(i=0, j = strlen(s)-1; i <j; i++,j--) {
    c = s[i];
    s[i] = s[j];
    s[j] = c;
  }
}

/** SmRemoveChar *******************************************************
**
**
**  Removes all the occurrences of a char in a string.
**
**
**  INPUT :
**         string to be modified
**         char to remove
**
**  RETURN: Length of the modified string.
**
**
**  Ramu C
**
*/

INT4 SmRemoveChar(char s[],char c)
{
  INT4 i = 0, j = 0;
  while(s[i]) {
    if(!(s[i] == c) ) s[j++] = s[i];
    i++;
  }
  s[j]='\0';
  return j;
}
     

/*** WwwPresentSkipChunkSet *****************************************************
**
**   Presents chunk sets to skip when there is more than one 
**   result page. 
**
**
**   INPUT: script object [R]
**          set size [R]
**          query Number [R]
**
**
**   RETURNS: 
**
*/

void WwwPresentSkipChunkSet(TEMPLv templ,INT4 setSize,INT4 queryN)
{
  INT4 windowSize = 5;
  INT4 chunkStart = ParGetNum("chunkStart");
  INT4 chunkSize = ParGetNum("viewEntriesChunkSize");
  INT4 startN = ParGetNum ("viewEntriesStartN");
  INT4 k, chunkEnd = setSize-chunkSize;

  if( chunkSize >= setSize) 
    return; /* do not show skip set when there is only one result page */
  if( !startN) 
    startN = 1;
  TemplWith (templ, "$chunkSet");
  TemplPrint ("head", WwwGetIdParam(),queryN, chunkSize,ParGetNum("viewNumber"));
  if( ParGetNum("viewEntriesStartN") > windowSize * chunkSize)
    chunkStart = startN/chunkSize; 
  
  if( chunkStart-5 > 0) /* slide window size */
    chunkStart = chunkStart - 5 ;
  
  for( k=chunkStart; k < windowSize+chunkStart+5 ;  k++) {
    if( (k*chunkSize+1) > setSize) break;
    if (startN == (k*chunkSize+1))
      TemplPrint ("current",WwwGetIdParam(),queryN,k*chunkSize+1,
		  (setSize < chunkSize) ? setSize:chunkSize,
		  ParGetNum("viewNumber"),k+1);
    else
      TemplPrint ("other", WwwGetIdParam(), queryN,k*chunkSize+1,
		  (setSize < chunkSize) ? setSize:chunkSize,
		  ParGetNum("viewNumber"),k+1);
  }
  if( chunkEnd < 1 ) chunkEnd = 1; 
  TemplPrint ("tail", WwwGetIdParam(),queryN,chunkEnd, 
	      (setSize < chunkSize) ? setSize:chunkSize,ParGetNum("viewNumber"));
  TemplEndWith ();
}


/**api* WwwIsViewForQuery ****************************************************
**
**	Determines if the view is really suitable for a particular query.
**      If the query has elements from more than one databank then all of
**      these must be root libraries in the view.
**
**	INPUT:	    the view object [R]
**                  the query object [R}
**	        IMPLICIT:
**
**	RETURNS:    1: view is suitable
**                  0: not
*/ 

static Int4 WwwIsViewForQuery (VIEWo *view, char *setName)
{
  VIEWoLIB *vlib;
  char     *libName;
  Int4     isFound, c, h, n;

  if (ViewIs (view, "forAll"))
    return 1;

  for (c=0; (n = SetGetNextLibStat (setName, &libName, &c));) {
    for (h=0, isFound=0; (vlib = ViewGetNextRootLib (view, &h));)
      if (SmEqs (libName, LibName (vlib->lib)))
	isFound++;
    if (!isFound)
      return 0;
  }
  return 1;
}


/**api* WwwPresentChunkSizes **************************************************
**
**	Prints the chunk sizes for listing and viewing entries;
**
**	INPUT:	    script object [R]
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

Int4 WwwPresentChunkSizes (TEMPLv templ)
{
  INT4 viewChunk[20] = {5, 10, 20, 30, 40, 50, 100, 200, 500, 1000, 2000, 
			5000, 10000},
       viewChunkCurr = ParGetNum ("viewEntriesChunkSize"), k;

  TemplPrint("head");
  for (k=0; viewChunk[k]; k++) {
    TemplPrint ("size", viewChunk[k] == viewChunkCurr ? "SELECTED" : "",
		viewChunk[k]);
  }
  TemplPrint("tail");
  
}

/**api* WwwPresentChunkSizesMime **********************************************
**
**	prints the chunk sizes for exporting entries;
**
**	INPUT:	    script object [R]
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

void WwwPresentChunkSizesMime (TEMPLv templ, Int4 queryN)
{
  WWWoQUERY *query = WwwGetQuery (queryN);
  INT4      entryN=query->entryN, k, l, 
            chunkSize = ParGetNum ("viewEntriesChunkSize");

  TemplWith (templ,"mime");
  TemplPrint ("head");
  for (k=entryN, l=0; k > 0 && l < 50 /*max menu size*/; k -= chunkSize, l++)
    TemplPrint ("size", WwwSelected (!l), l*chunkSize+1, 
		k < chunkSize ? entryN : (l+1)*chunkSize );

  TemplPrint ("tail");
  TemplEndWith ();
  WwwDelQuery (query);
}


/**api* WwwSetColorScheme *****************************************************
**
**	Sets the color scheme for the current page. The color is specified
**      by the parameter "wwwColorScheme"
**
*/ 

void WwwSetColorScheme (TEMPLv templ)
{
  char *color, tmp[200];

  color = ParGetStr ("wwwColorScheme");
  if (color && *color && !(SmEqs (color, "plain"))) {
    TemplWith (templ, "$colorScheme");
    TemplWith (templ, color);
    ParDefStr ("pageColor", TemplSPrint (tmp, "page"));
    ParDefStr ("cellColor", TemplSPrint (tmp, "cell"));
    ParSetVolatile ("pageColor");
    ParSetVolatile ("cellColor");
    TemplEndWith ();
    TemplEndWith ();
  }
}

/* ought to disappear soon */
void WwwPresentColorMenu  ()
{
  char *color, *colorSelected;
  struct VARo *any, *tmp;
  Int4   i;

  colorSelected = ParGetStr ("wwwColorScheme");
  if (!*colorSelected)
    colorSelected = "plain";

  TemplPrint ("head");
  any = TemplExists (NULL, "$colorScheme");
  for (i=0; (tmp = AnyNextInList (any, &i));) {
    color = VarGetName (tmp);
    TemplPrint ("color", SmEqs (colorSelected, color) ?"SELECTED" :"", color);
  }    
  TemplPrint ("tail");
}



TEMPLv WwwInit ()
{
  TEMPLv templ;

  templ = TemplOpen ("SRSICA:srswww.i", NULL);
  WwwSetColorScheme (templ);
  WwwPrintContentType(NULL);
  return templ;
}


void WwwApplOpt (APPLo *appl)
{
  TEMPLv        templ;
  APPLoOpt      *opt;
  APPLoOptGroup *group, *groupPrev;
  WWWoQUERY     *query;
  SETo          *set;
  SEQo          *seq;
  STRv          s;
  ENTRYv        entry;
  IDoENTRY      id;
  char          *applName;
  Int4          queryNo, i;
  
  applName = ApplGetName (appl);
  templ = WwwInit ();
  TemplWith (templ, "applOpt");
  TemplPrint ("head", applName, applName);
  WwwPrintButtons (templ);
  TemplPrint ("title", applName, applName, ApplGetTitle (appl));

  if (ApplIs (appl, "search") && (opt = ApplOptNamed (appl, "search")))
    WwwApplOptPrint (appl, opt);
    

  /* display input sequence(s) */
  TemplPrint ("sequence.head");
  if ((queryNo=WwwQuerySelectedEntries ())) {
    query = WwwGetQuery (queryNo);
    set = SetGet (query->name);
    for (i=1; i <= set->n; i++) {
      SetGetID (set, i, &id);
      entry = EntryOpen (&id);
      seq=SdbGetEntrySeq (entry);
      s = Seq2Pretty (seq, 60);
      if (ApplIs (appl, "multi"))
	TemplPrint ("sequence.multi", WwwEntryQuery (entry, NULL, NULL),
		    EntryGetFullName (entry), i, _Str (s), seq->len, 
		    i, EntryGetName (entry), 
		    i, EntryGetFullName (entry), seq->len);
      else
	TemplPrint ("sequence.single", _Str (s));

      EntryClose (&entry);
      StrDel (s);
      if (!ApplIs (appl, "multi"))
	break;
    }    
    WwwDelQuery (query);
  }
  /* submit button */
  TemplPrint ("submit");
  if (opt = ApplOptNamed (appl, "output"))
    WwwApplOptPrint (appl, opt);

  /* list of options */
  TemplPrint ("options.head");
  for (groupPrev=NULL, i=0; (opt=ApplNextOpt (appl, &i));) {
    group = ApplOptGetGroup (opt);
    if (!group) continue;
    if (group != groupPrev) {
      TemplPrint ("options.group.head", 
		  ApplOptGroupGetSize (appl, group),
		  ApplOptGroupGetName (group));
      groupPrev = group;
    }
    else
      TemplPrint ("options.group.next");

    WwwApplOptPrint (appl, opt);
  }
  TemplPrint ("options.tail");
  TemplPrint ("tail");

}


static void WwwApplOptPrint (APPLo *appl, APPLoOpt *opt)
{
  APPLoOptVal *val;
  char        *applName;
  Int4        l;

  applName = ApplGetName (appl);

  TemplPrint ("options.group.option.head");
  TemplPrint ("options.group.option.prompt", ApplOptGetPrompt (opt));
  if (ApplOptIs (opt, "menu")) {
    TemplPrint ("options.group.option.menu.head", 
		applName, ApplOptGetName (opt));
    for (l=0; (val=ApplOptNextVal (opt, &l)); ) {
      if (ApplOptValIs (val, "named"))
	  TemplPrint ("options.group.option.menu.valNamed",
		      ApplOptValGetValue (opt, val), 
		      WwwSelected (ApplOptValIs (val, "on")),
		      ApplOptValGetName (val));
      else 
	  TemplPrint ("options.group.option.menu.val",
		      WwwSelected (ApplOptValIs (val, "on")),
		      ApplOptValGetValue (opt, val)); 
    }
    TemplPrint ("options.group.option.menu.tail");
  }
  
  else if (ApplOptIs (opt, "radio"))
    for (l=0; (val=ApplOptNextVal (opt, &l)); )
      TemplPrint ("options.group.option.radio.val", applName, 
		  ApplOptGetName (opt), ApplOptValGetValue (opt, val),
                  WwwChecked (ApplOptValIs (val, "on")),
		  ApplOptValGetPrompt (val));
  
  else if (ApplOptIs (opt, "multi"))
    for (l=0; (val=ApplOptNextVal (opt, &l)); )
      TemplPrint ("options.group.option.multi.val", applName, 
		  ApplOptGetName (opt), 
		  WwwChecked (ApplOptValGetInt (opt, val)),
		  ApplOptValGetPrompt (val));
  
  else if (ApplOptIs (opt, "real"))
    TemplPrint ("options.group.option.real", ApplOptGetDefValue (opt),
		applName, ApplOptGetName (opt));
  
  else if (ApplOptIs (opt, "int"))
    TemplPrint ("options.group.option.int", ApplOptGetDefValue (opt),
		applName, ApplOptGetName (opt));
  else if (ApplOptIs (opt, "bool"))
    TemplPrint ("options.group.option.bool", 
		WwwChecked (ApplOptGetDefInt (opt)),
		applName, ApplOptGetName (opt));
  else if (ApplOptIs (opt, "string"))
    TemplPrint ("options.group.option.string", 
		ApplOptGetDefValue (opt),
		applName, ApplOptGetName (opt));

  TemplPrint ("options.group.option.tail");

}








(opt));srs/src/srswww.h

typedef struct WWWoQUERY {
  char name[80];
  char queryStr[5000];
  char comment[300];
  char *type;
  INT4 entryN;
  INT4 queryN;
  INT4 isSubEntry;
  struct {
    char *name;
    int  entryN;
  } lib[20];
  char linkLib[30];
  char linkType[30];
  int isDeleted;
} WWWoQUERY;

typedef struct ENTRYo *dummytointroducestructtagENTRYo;


    /* parameters, userId, messages */

INT4 WwwPrintMessage (MSGo *msg); 
char *WwwReadInput (int byteN, char *fileName);
INT4 WwwParInput (int byteN, char *buff);
void WwwParWrite (char *userId);
void WwwParRead (char *userId, INT4 doInsist);
char *WwwNewUserId ();
char *WwwGetName (char *userId, char *option);
INT4 WwwPrintF (char *formatStr, ...);

INT4 WwwLinkSet (Int4 queryN);
/*void WwwLinkToLibs (char *queryStr);*/
void WwwLibInfo (char *libName, char *userId);
void WwwLinkInfo (TEMPLv templ, char *libName1, char *libName2);
void WwwPrintHelpTopic (char *helpTopic);
void WwwDoBlastSearch ();
void WwwQueryExpression (char *queryType, char *queryStr);
void WwwListIndex (char *userId);
void WwwGetMessage ();
void WwwSendMessage ();
void WwwPrintLinkOptions (char *query);
void WwwPrintLibNetwork ();
void WwwGetODDFile (char *libName);

    /* retrieval, query */

void WwwInitRetrieve ();
INT4 WwwQueryDo (char *expr, char *queryType);
char *WwwRetrieve ();
INT4 WwwQueryDoRecursive (INT4 queryN, char *queryStr);
void WwwRegisterQuery (char *queryName, char *queryStr, char *queryType);
struct WWWoQUERY *WwwGetQuery (int queryN);
struct WWWoQUERY *WwwGetQueryName (char *name);
void WwwDelQuery (struct WWWoQUERY *query);
char *WwwTransformQuery (char *option, char *queryStr);

    /* others */

void WwwEntryPrint (struct TEMPLo *templ, struct ENTRYo *entry);
char *WwwGetIdParam ();
void WwwViewFeature (char *queryStr, INT4 subEntryN);
char *WwwStringEncode (char *);
char *WwwTransform (char *option, char *str);

  /* helpers for printing HTML pages */

TEMPLv WwwInit ();
INT4 WwwPresentChunkSizes (struct TEMPLo *templ);
void WwwPresentChunkSizesMime (struct TEMPLo *templ, Int4 entryN);
void WwwPrintButtons (struct TEMPLo *templ);
char *WwwChecked (Int4 flag);
char *WwwSelected (Int4 flag);

  
  /* printing entries */ 

void WwwPrintSet     (struct TEMPLo *templ, char *setName, 
		      int firstN, int printN);
void WwwPrintSetView (struct TEMPLo *templ, char *setName, 
		      int firstN, int printN);
void WwwQueryPrint   (INT4 queryN);
void WwwPrintValue (char *libName, char *fieldName, char *value, 
		    Int4 n, Int4 entryN);


  /* dealing with  views */ 

void WwwInitViews (TEMPLv templ);
struct VIEWo *WwwViewGet (INT4 viewN, struct TEMPLo *templ);
void WwwPrintSelectField (struct VIEWo *view, Int4 viewNum, 
                          struct SLBoFIELD *field, 
			  struct VIEWoLIB *vlib, Int4 numCol, Int4 *count);
void WwwPresentViewList (char *option, TEMPLv templ);
void WwwPresentActiveViews (struct SRSoGROUP*, struct SLBo*, 
			    struct WWWoQUERY*, TEMPLv, Int4);
void WwwPresentViewsForLeaf (struct VIEWo *view, struct VIEWoLIB *vlib, 
			     TEMPLv templ);
void WwwViewPartI (INT4 viewNumber,INT4 isEdit, TEMPLv templ);

void WwwSetColorScheme (struct TEMPLo *templ);






struct VIEWo *view, Int4 viewNum, 
                          struct SLBoFIELD *field, 
			  struct VIEWoLIB *vlib, Int4 numCol, Int4 *count);
void WwwPresentViewList (char *option, TEMPLv templ);
void WwwPresentActiveViews (struct SRSoGROUP*, struct SLBo*, 
			    struct WWWoQUERY*, TEMPLv, Int4);
void WwwPresentViewsForLeaf (struct VIEWo *view, struct VIEWoLIB *vlib, 
			     TEMPLv templ);
void WwwViewPartIsrs/src/strv.c
**
**  MODULE for management of virtually-copied strings
**  
**            Authors: Giorgio Verde
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387451
**                     Email: verde@embl-heidelberg.de
**
*************************************************************************/

#include <stdio.h>
#include <stdarg.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>

#include "def.h"
#include "message.h"
#include "strv.h"

#define DEBUGnot
static Int4 strAllocN, strAllocByte, strFreedN, strFreedByte;

/****** StrBufNew *********************************************************
** 
**	Creates a STRv buffer with space for a string of lenght dim
**	The string length must be manually set by the user
**
**      INPUT:          the maximum lenght of the contained string
**	RETURNS:	a new STRv with the uninitialized buffer
*/

STRv StrBufNew(int dim) {
    STRv s=(STRv)malloc(sizeof(STRo)+dim);
#ifdef DEBUG
  strAllocByte += dim;
  strAllocN++;
  if (!(strAllocN%10000))
    fprintf (stderr, "allocN: %d, allocByte:  %d, freedN, %d, freedByte: %d\n",
	     strAllocN, strAllocByte, strFreedN, strFreedByte);
#endif
    s->usage=1;
    s->dim=dim; 
    return s;
}

/****** StrBufChange *********************************************************
** 
**	Vanilla function for string modification
**	Moves all characters of the string after position beg ("cut" position)
**	to position end ("paste" position)
**	<BR> if end>beg this results in the creation of space for end-beg 
**	characters in position beg
**	<BR> if end<beg the beg-end characters in position beg are dropped
**	<BR> a new STRv buffer is created only if:
**	<BR>- the STRv buffer has usage>1 (2 or more STRv's share a virtual copy)
**	<BR>- the STRv buffer needs to be grown
**
**      INPUT:          the pointer to the STRv to be modified
**			the cut position
**			the paste position 
*/

void StrBufChange(STRv* val, int beg, int end) {
    STRv s=*val;
    int len=s->len;
    int dlen=end-beg;
    if (s->dim<len+dlen || s->usage>1) {
	STRv old=s;
	s=StrBufNew(len+dlen);
	memcpy(s->arr+end, old->arr+beg, len-beg+1);
	if (dlen>0) memcpy(s->arr, old->arr, beg);
	else memcpy(s->arr, old->arr, end);
	StrDel (old);
    }
    else MemMove(s->arr+end, s->arr+beg, len-beg+1);
    s->len=len+dlen;
    *val=s;
}

#define STRTEMP_NUM 10

STRo StrNULLObj = { 1+STRTEMP_NUM, 0, 1, '\0' };
STRv StrNULL=&StrNULLObj;

STRv StrTemporary[STRTEMP_NUM]= {
    &StrNULLObj, &StrNULLObj, 
    &StrNULLObj, &StrNULLObj, 
    &StrNULLObj, &StrNULLObj, 
    &StrNULLObj, &StrNULLObj, 
    &StrNULLObj, &StrNULLObj
};


/**API* StrNew *********************************************************
**
**	Creates a new STRv containing the empty string (virtually copied)
**      <BR>See STRv creators: StrNew, StrCpy, StrCpyS, StrTemp
**
**      RETURNS:        a new STRv		    
*/

STRv StrNew() {
    return StrCpy(StrNULL);
}

/**API* StrCpy *********************************************************
**
**	creates a new STRv containing a 
**	virtual copy of the given STRv
**      <BR>See STRv creators: StrNew, StrCpy, StrCpyS, StrTemp
**
**      INPUT:          a STRv (can be NULL)
**      RETURNS:        a copy of input
**		        NULL if input is NULL
*/


STRv StrCpy(STRv val) {
    if (val) val->usage++;
    return val;
}

/**API* StrDel *********************************************************
**
**	Deletes a STRv (a virtual copy of the value).
**	If the given STRv was the only instance of the value in
**	use, the value buffer is freed.
**	Must be used whenever an assigned STRv goes out of scope
**
**      INPUT:          a STRv (can be NULL)
*/

void StrDel(STRv val) {
  if (val && !--(val->usage)) {
#ifdef DEBUG
    { 
	if (val->len!=strlen(val->arr)) {
	    printf("SuspectSTRv\n");
	}
	strFreedByte += val->dim;
	strFreedN++;
    }
#endif
    free(val);
  }
}

/**API* StrGrow *********************************************************
**
**	Reserves space so that following operations on the STRv
**	can modify it's value to a longer string. This is just
**	an optimization, as STRv's grow automatically if the
**	value lenght exceeds the allocated buffer
**	<BR>See STRv optimizers: StrGrow, StrShrink
**
**      INPUT:          o [W] pointer to the STRv to be grown
**			o the number of characters to be reserved for growth
*/


void StrGrow(STRv* val, int dlen) {
    STRv s=*val;
    int len=s->len;
    if (s->dim<len+dlen || s->usage>1) {
	STRv old=s;
	s=StrBufNew(len+dlen);
	s->len=len;
	memcpy(s->arr, old->arr, len+1);
	if (!--(old->usage)) {
#ifdef DEBUG
  strFreedByte += old->dim;
  strFreedN++;
#endif
	  free(old); 
        }
	*val=s;    
    }
}

/**API* StrShrink *********************************************************
**
**	Optimizes the value buffer to have exactly the lenght   
**	needed to contain the string value
**	See STRv optimizers: StrGrow, StrShrink
**
**      INPUT:          [W] pointer to the STRv to be trimmed 
*/


void StrShrink(STRv* val) {
    STRv s=*val;
    int len=s->len;
    if (s->dim>len) {
	STRv old=s;
	s=StrBufNew(len);
	s->len=len;
	memcpy(s->arr, old->arr, len+1);
#ifdef DEBUG
  strFreedByte += old->dim;
  strFreedN++;
#endif
	free(old); 
	*val=s;    
    }
}

/**API* StrClear *********************************************************
**
**	if the STRv buffer is unique, resets the content of the STRv to
**	"" without freeing the buffer
**
**      INPUT:          [W] the STRv to be cleard
*/

void StrClear(STRv* sp) {
    STRv s=*sp;
    if (s->usage==1) {
	s->len=0;
	s->arr[0]='\0';
    }
    else StrSet(sp, StrNULL);
}

/* operations */


/**API* StrSet *********************************************************
**
**	Assignes to one STRv the value of another STRv (virtual copy)
**	The old value of the STRv is released
**	<BR>See STRv modifiers: StrSet, StrIns, StrApp, StrAdd, StrCut
**	<BR>To assign instead a char* value, see StrSetS
**
**      INPUT:          o [W] pointer to the STRv to be modified 
**			o STRv value to be assigned
*/


void StrSet(STRv* dest, STRv src) {
    if (*dest!=src) { 
	StrDel(*dest); 
	*dest=StrCpy(src);
    }
}

/**API* StrIns *********************************************************
**
**	Inserts in one STRv the value of another STRv at the beginning
**	of the string. The destination STRv buffer is grown if needed.
**	The old value of the STRv is released
**	<BR>See STRv modifiers: StrSet, StrIns, StrApp, StrAdd, StrCut
**	<BR>To insert instead a char* value, see StrInsS
**
**      INPUT:          o [W] pointer to the STRv to be modified 
**			o STRv value to be inserted
*/

void StrIns(STRv* dest, STRv src) {
    int len=src->len;
    StrBufChange(dest, 0, len);
    memcpy((*dest)->arr, src->arr, len);
}

/**API* StrApp *********************************************************
**
**	Appends to one STRv the value of another STRv.
**	The destination STRv buffer is grown if needed.
**	The old value of the STRv is released
**	<BR>See STRv modifiers: StrSet, StrIns, StrApp, StrAdd, StrCut
**	<BR>To append instead a char* value, see StrAppS
**
**      INPUT:          o [W] pointer to the STRv to be modified 
**			o STRv value to be appended
*/

void StrApp(STRv* dest, STRv src) {
    int dlen=(*dest)->len;
    int len=src->len;
    StrBufChange(dest, dlen, dlen+len);
    memcpy((*dest)->arr+dlen, src->arr, len);    
}

/**API* StrAdd *********************************************************
**
**	Inserts in one STRv the value of another STRv at a certain
**	position. The position must be between 0 (works like StrIns)
**	and the lenght of the string (works like StrApp). If outside
**	this range,  a PosOutOfBounds exception is thrown.
**	The destination STRv buffer is grown if needed.
**	The old value of the STRv is released
**	<BR>See STRv modifiers: StrSet, StrIns, StrApp, StrAdd, StrCut
**	<BR>To append instead a char* value, see StrAddS
**
**      INPUT:          o [W] pointer to the STRv to be modified 
**			o the position of insertion.
**			o STRv value to be added
*/


void StrAdd(STRv* dest, int pos, STRv src) {
    int dlen=(*dest)->len;
    int len=src->len;
    ASSERT(pos<=dlen, "PosOutOfBounds");
    StrBufChange(dest, pos, pos+len);
    memcpy((*dest)->arr+pos, src->arr, len);        
}

/**API* StrCut *********************************************************
**
**	Cuts in one STRv the characters starting at a certain
**	position and for a given lenght. 
**	The position must be between 0 and the length of the string. 
**	If outside this range, a PosOutOfBounds exception is thrown.
**	The given length can be longer then the length of the string;
**	in that case it is adjusted to the string length
**	The destination STRv buffer keeps its lenght, and must be 
**	explicitly trimmed with StrShrink if needed. 
**	The old value of the STRv is released
**	<BR>See STRv modifiers: StrSet, StrIns, StrApp, StrAdd, StrCut
**
**      INPUT:          o [W] pointer to the STRv to be modified 
**			o the cutting position
**			o the cutting length
*/


void StrCut(STRv* dest, int pos, int len) {
    int dlen=(*dest)->len;
    ASSERT(pos<=dlen, "PosOutOfBounds");
    if (len>dlen-pos) len=dlen-pos;
    StrBufChange(dest, pos+len, pos);
}

/**API* StrSub *********************************************************
**
**	creates a new STRv containing a 
**	substring of the given STRv
**      <BR>See STRv creators: StrNew, StrCpy, StrCpyS, StrTemp
**
**      INPUT:          a STRv
**                      the postition of the substring
**                      the length of the substring
**      RETURNS:        the substring
*/

STRv StrSub(STRv s, int pos, int len) {
    if (pos>s->len) pos=s->len;
    if (pos+len>s->len) len=s->len-pos;
    return StrNCpyS(s->arr+pos, len);
}

/**API* StrRight *********************************************************
**
**	creates a new STRv containing the characters of the given STRv 
**      on the right of the given position (including the one at the position)
**      <BR>See STRv creators: StrNew, StrCpy, StrCpyS, StrTemp
**
**      INPUT:          a STRv
**                      the cut position
**      RETURNS:        the substring
*/

STRv StrRight(STRv s, int pos) {
    if (pos>s->len) pos=s->len;    
    return StrNCpyS(s->arr+pos, s->len-pos);
}

/**API* StrLeft *********************************************************
**
**	creates a new STRv containing the characters of the given STRv 
**      on the left of the given position (excluding the one at the position)
**      <BR>See STRv creators: StrNew, StrCpy, StrCpyS, StrTemp
**
**      INPUT:          a STRv
**                      the cut position
**      RETURNS:        the substring
*/

STRv StrLeft(STRv s, int pos) {
    if (pos>s->len) pos=s->len;    
    return StrNCpyS(s->arr, pos);
}

/**API* StrSubst *********************************************************
** 
**	Substitutes a range of characters in one STRv in a given 
**	position and of a certain lenght with the value of a given STRv.
**
**
**      INPUT:          o [W] pointer to the STRv to be modified 
** 			o position of replacement (0<=pos<=len)
**			o num char to replace in the original string
**			  if bigger, it's adjusted to string lenght
**			o value to replace
*/

void StrSubst(STRv* dest, int pos, int len, STRv subst) {
    int dlen=(*dest)->len; int slen=subst->len;
    ASSERT (pos<=dlen, "PosOutOfBounds");
    if (len>dlen-pos) len=dlen-pos;
    StrBufChange(dest, pos+len, pos+slen);
    memcpy((*dest)->arr+pos, subst->arr, slen);
}

/**API* StrDebug *********************************************************
** 
**	Debug function to print the status of a STRv on stdout
**
**      INPUT:          the STRv to be displayed
*/

void StrDebug(STRv s) {
    printf("STRv:%p ", s);
    if (s) {
	char *p=s->arr, *stop;
	if (s->usage!=1) printf("usage:%d ", s->usage);
	printf("len:%d ", s->len);
	if (s->dim!=s->len) printf("grow:%d ",s->dim-s->len);
	/* check if the string is printable 
	stop=p+s->len;
	while (p<stop) {
	    
	}*/
	printf("\"%s\"\n",p);
    }
}

/**API* StrUpper *********************************************************
** 
**	Converts a STRv into upper case
**
**      INPUT:          a ponter to STRv
*/

void StrUpper(STRv* sp) {
    STRv s=*sp;
    char* p=s->arr;
    char c;
    if (s->usage==1) {
	while (c=*p) *p++=_ToUpper(c);
    }
    else {
	STRv d=StrBufNew(s->len);
	char* dp=d->arr;
	d->len=s->len;
	while (c=*p++) *dp++=_ToUpper(c);
	s->usage--;
	*sp=d;
    }
}

/**API* StrLower *********************************************************
** 
**	Converts a STRv into lower case
**
**      INPUT:          a ponter to STRv
*/

void StrLower(STRv* sp) {
    STRv s=*sp;
    char* p=s->arr;
    char c;
    if (s->usage==1) {
	while (c=*p) *p++=_ToLower(c);
    }
    else {
	STRv d=StrBufNew(s->len);
	char* dp=d->arr;
	d->len=s->len;
	while (c=*p++) *dp++=_ToLower(c);
	s->usage--;
	*sp=d;
    }
}

/**API* StrTrim ***************************************************************
** 
**	Removes leading and trailing spaces or, if specified, other 
**      characters.
**
**      INPUT:          a pointer to STRv [W]
**                      a set of characters to be removed [R] or NULL
*/

void StrTrim (STRv* str, char *skipSet) {

  static char ws[10]=" \n\t";
  STRv tStr;
  char *s;
  Int4 k, l, len;

  len = StrLen (*str);
  if (!skipSet) 
    skipSet = ws;

  s = _Str (*str);
  for (k=0; k < len && strchr (skipSet, s[k]); k++)
    ;
  for (l=len-1; l>0 && strchr (skipSet, s[l]); l--)
    ;

  len = l-k+1;
  tStr = StrSub (*str, k, len < 0 ? 0 : len); 
  StrSet (str, tStr);
}

/* queries */

/**API* StrEmpty *********************************************************
** 
**	returns if the string is empty
**
**
**      INPUT:          the STRv (must be not NULL)
**	RETURNS:	TRUE if the STRv is the empty string	
*/


BOOL StrEmpty(STRv str) {
    return !str->len;
}

/**API* StrLen *********************************************************
** 
**	returns the length of the string value
**
**
**      INPUT:          the STRv (must be not NULL)
**	RETURNS:	length in chars
*/

int StrLen(STRv str) {
    return str->len;
}

/**API* StrEqual *********************************************************
** 
**	compares 2 STRv's for equal values
**
**
**      INPUT:          o STRv (must be not NULL)
**			o STRv (must be not NULL)
**	RETURNS:	TRUE if equal
*/


BOOL StrEqual(STRv s1, STRv s2)  {
    if (s1==s2) return TRUE;
    else if (s1->len==s2->len) return strcmp(s1->arr, s2->arr)==0;
    else return FALSE;    
}

/**API* StrCmp *********************************************************
** 
**	compares 2 STRv's for lexicographic ordering
**
**
**      INPUT:          o s1:STRv (must be not NULL)
**			o s2:STRv (must be not NULL)
**	RETURNS:	o <0 if s1<s2
**			o =0 if s1=s2
**			o >0 if s1>s2 
*/

int StrCmp(STRv s1, STRv s2) {
    if (s1==s2) return 0;
    else return strcmp(s1->arr, s2->arr);
}

/**API* StrHash *********************************************************
** 
**	calculates a hash value for a STRv. 
**
**
**      INPUT:          o STRv (must be not NULL)
**			o upper bound for the result
**	RETURNS:	an integer 0<= i < max
*/


int StrHash(STRv val, int max) {
    return StrHashS(val->arr, max);    
}

/* user */

/**API* StrConst *********************************************************
** 
**	Defines a STRv value to become a constant to be never released.
**	The returned char* cannot be used for modifying the string, 
**	and it is guaranteed to be stable.
**
**      INPUT:          STRv (must be not NULL)
**	RETURNS:	the STRv value as char*
*/

char* StrConst(STRv val) {
    val->usage++;
    return val->arr;    
}

/**API* StrVal *********************************************************
** 
**	Returns a C string containing a (real) copy of the STRv value
**	The user can do everything with it and has the reponsability
**	of freeing it.
**
**      INPUT:          STRv (must be not NULL)
**	RETURNS:	the STRv value as char*
*/

char* StrVal(STRv val) {
    int len=val->len+1;
    char* s=malloc(len);
    memcpy(s, val->arr, len);
    return s;
}

/**API* StrGet *********************************************************
** 
**	Writes the STRv value into an allocated C char buffer of a 
**      given size. If there is enough space in the buffer, string
**	will be NULL-terminated, else only the portion which fits 
**	is copied.   
**
**      INPUT:          o [W] the pointer to the buffer
**			o the length of the buffer
**			o the STRv to be copied (must be not NULL)
**	RETURNS:	o a pointer to the first unused char in the buffer
**			  if the value fitted
**			o NULL otherwhise
*/

char* StrGet(char* dest, int sz, STRv src) {
    int len=src->len+1;
    if (len<=sz) {
	memcpy(dest, src->arr, len);
	return dest+len;
    }
    else {
	memcpy(dest, src->arr, sz);
	return NULL;
    }
}

/**API* StrShared *********************************************************
** 
**      Returns the number of virtual copies of the given STRv 
**      (not counting the given copy)
**
**      INPUT:          a STRv
**	RETURNS:	o 0 if this is the only instance of the value
**                      o >0 if the buffer is shared by other STRv's
*/


int StrShared(STRv s) {
    return s->usage-1;
}


/* c string operations */

/**API* StrTemp *********************************************************
** 
**	Creates a temporary STRv from a C string. This STRv does'nt
**      need to be deleted with StrDel, but the user is not entitled
**	to perform modifying operations on this string 
**      (for example StrAppS(&StrTemp("bla"),"alb") is unlegal)
**	Basically,  the only legal operation is to use StrTemp where
**	the STRv is not modified. 
**	The maximum number of active temporary STRv is defined by
**	the macro STRTEMP_NUM
**
**      INPUT:          a pointer to a C string
**	RETURNS:	a temporary STRv
*/

STRv StrTemp(char* src) {
    static int currTemp=0;
    STRv* s=&StrTemporary[currTemp];
    StrSetS(s, src);
    currTemp=(currTemp+1)%STRTEMP_NUM;
    return *s;
}

/**API* StrCpyS *********************************************************
**
**	Creates a new STRv from a C string (char*)
**
**      INPUT:          the C string 
**	RETURNS:	a STRv
*/

STRv StrCpyS(char* src) {
    int len=strlen(src);
    STRv s=StrBufNew(len);
    s->len=len;
    memcpy(s->arr, src, len+1);
    return s;
}

/**API* StrSetS *********************************************************
**
**	Assignes to a STRv the value of a C string (char*)
**	The old value of the STRv is released
**
**      INPUT:          [W] pointer to the STRv to be assigned 
**			the C string 
*/

void StrSetS(STRv* dest, char* src) {
    int len=strlen(src);
    int dlen=(*dest)->len;
    StrBufChange(dest, dlen, len);
    memcpy((*dest)->arr, src, len+1); 
}

/**API* StrInsS *********************************************************
**
**	Inserts at the beginning of a STRv the value of a C string (char*)
**	The old value of the STRv is released
**
**      INPUT:          [W] pointer to the STRv to be assigned 
**			the C string 
*/

void StrInsS(STRv* dest, char* src) {
    int len=strlen(src);
    StrBufChange(dest, 0, len);
    memcpy((*dest)->arr, src, len);
}

/**API* StrAppS *********************************************************
**
**	Appends to a STRv the value of a C string (char*)
**	The old value of the STRv is released
**
**      INPUT:          [W] pointer to the STRv to be assigned 
**			the C string 
*/

void StrAppS(STRv* dest, char* src) {
    int dlen=(*dest)->len;
    int len=strlen(src);
    StrBufChange(dest, dlen, dlen+len);
    memcpy((*dest)->arr+dlen, src, len);    
}

/**API* StrFill **********************************************************
**
**	Appends a certain number of fill characters to a STRv.
**
**      INPUT:          [W] pointer to the STRv to be assigned 
**			the fill character [R]
**                      number of characters to be added [R]
*/

void StrFill(STRv* dest, char c, Int4 len) {
    int dlen=(*dest)->len, k;
    StrBufChange(dest, dlen, dlen+len);
    for (k=0; k<len; k++)
      (*dest)->arr[dlen+k] = c;
    (*dest)->arr[dlen+k] = '\0';
}

/**api* StrReplace *********************************************************
**
**	Replaces all occurrences of the "from" substring with the "to"
**      string. 
**
**      INPUT:          [W] pointer to the STRv to be assigned 
**			"from" substring to be searched [R}
**                      "to" string to be inserted [R]
*/

STRv StrReplace (STRv* dest, char *from, char *to)
{
  char *p;
  int  len=(*dest)->len, pos,
       fromLen=strlen(from), toLen=strlen(to);

  p=_Str (*dest);
  while ((p=strstr (p, from))) {
    pos = p - _Str(*dest);
    StrBufChange (dest, pos+fromLen, pos+toLen);
    p = _Str (*dest) + pos;
    memcpy (p, to, toLen);
    p += toLen;
  }
}



/**API* StrAppN *********************************************************
**
**	Appends to a STRv a given number of chars of a C string (char*) 
**	if the string is shorter,  then the number of chars is the length
**	of the source string
**	The old value of the STRv is released
**
**      INPUT:          [W] pointer to the STRv to be assigned 
**			the C string 
**			the number of chars
*/

void StrAppN(STRv* dest, char* src, int len) {
    int dlen=(*dest)->len;
    /* copy until \0 is found */
    char* p=src;
    while (p<src+len) {
	if (!*p) { len=p-src; break; }
	p++;
    }
    StrBufChange(dest, dlen, dlen+len);
    memcpy((*dest)->arr+dlen, src, len);    
}

/**API* StrNSetS *********************************************************
**
**	returns a STRv containing the first 'len' characters 
**      of a C string (char*)
**
**      INPUT:          the C string 
**                      len=the number of chars 
**      RETURNS:        the STRv
*/

STRv StrNCpyS(char* src, int len) {
    STRv s=StrBufNew(len);
    s->len=len;
    memcpy(s->arr, src, len);
    s->arr[len]='\0';
    return s;   
}

/**API* StrNSetS *********************************************************
**
**	Assignes to a STRv the first 'len' characters of a C string (char*)
**	The old value of the STRv is released
**
**      INPUT:          [W] pointer to the STRv to be assigned 
**			the C string 
**                      len=the number of chars 
*/

void StrNSetS(STRv* dest, char* src, int len) {
    int dlen=(*dest)->len;
    StrBufChange(dest, dlen, len);
    memcpy((*dest)->arr, src, len);
    (*dest)->arr[len]='\0';    
}


/**API* StrAddS *********************************************************
**
**	Inserts in a STRv the value of a C string (char*) at 
**	a given position
**	The old value of the STRv is released
**
**      INPUT:          [W] pointer to the STRv to be assigned 
**			the position of insertion (see StrAdd)
**			the C string 
*/

void StrAddS(STRv* dest, int pos, char* src) {
    int dlen=(*dest)->len;
    int len=strlen(src);
    ASSERT(pos<=dlen, "OutOfBounds");
    StrBufChange(dest, pos, pos+len);
    memcpy((*dest)->arr+pos, src, len);                
}


/**API* StrEqualS *********************************************************
**
**	Compares the value of a STRv with the value of a C string (char*)
**
**      INPUT:          the STRv to be compared 
**			the C string 
**	RETURNS:	TRUE if they are equal
*/


BOOL StrEqualS(STRv s1, char* s2) {
    return strcmp(s1->arr, s2)==0;
}
 
/**API* StrCmpS *********************************************************
**
**	Compares the value of a STRv with the value of a C string (char*)
**	for lexicographic ordering
**
**      INPUT:          s1:the STRv to be compared 
**			s2:the C string 
**	RETURNS:	<0 if s1<s2
**			=0 if s1=s2
**			>0 if s1>s2 
*/

int StrCmpS(STRv s1, char* s2) {
    return strcmp(s1->arr, s2);
}

/**API* StrHashS *********************************************************
** 
**	calculates a hash value for a C string 
**
**
**      INPUT:          the C string (char*)
**	RETURNS:	an integer 0<= i < max
*/

int StrHashS (char* s, int max) {
    WORD h=0, g;
    while (*s) {
      h=(h << 4 | (h&0xf0000000L)>>28) ^ *s++;
    }
    return h%max;
}


/* for string initialization */

void StrInitStatic(STRv s,int sz, int num) {
    while (num--) {
	s->usage=1;
	s->len=strlen(s->arr);
	s->dim=s->len+1;
	s=offset(s,sz,STRv);
    }
}

/* conversions */

/**API* StrFromInt *********************************************************
** 
**	Creates a STRv from an int value
**
**      INPUT:          the integer
**	RETURNS:	a new STRv with the value of the integer
*/

STRv  StrFromInt(int i) {
    char buf[20];
    sprintf(buf, "%d", i);
    return StrCpyS(buf);
}

/**API* StrToInt *********************************************************
** 
**	Converts a STRv to an integer
**	The function uses atoi for the conversion
**
**      INPUT:          the STRv
**	RETURNS:	a new STRv with the value of the integer
*/

int   StrToInt(STRv s) {
    return atoi(s->arr);
}


STRv  StrFromPtr(void* p) {return NULL;}
void* StrToPtr(STRv s) {return NULL;}

/* functions needed for use in icarus */

/**API* StrPrintf *********************************************************
** 
**	formatted print into a STRv
**
**      INPUT:          o [W] pointer to the STRv to be assigned (if NULL, the 
**                        function returns the result string)
**                      the format string
**                      the print items
**      RETURNS:        o the result string (if the str pointer was assigned, the 
**                        return value is just a pointer to the result, not a copy)
*/

STRv StrPrintf (STRv* str, char *format, ...)
{
  va_list ap;
  char    s[2000];
  STRv res;

  va_start (ap, format);
  vsprintf (s, format, ap);
  va_end (ap);

  if (str) { StrAppS (str, s); res=*str; } /* returns just a pointer!! don't delete! */
  else  res=StrCpyS(s);
  return res;
}

/**API* StrEncode *********************************************************
** 
**	Changes all non-printable characters into printable 
**      excape expressions, in C format (like \n -> "\n")
**
**      <BR>See also: StrDecode, StrTranslate
**
**      INPUT:          [W] pointer to the STRv to be converted
*/

STRv StrEncode (STRv *str)
{
  char codeStr[10], *code, *s;
  INT4 k;

  for (k = 0;  k < StrLen (*str);) {
    s = _Str (*str);
    switch (s[k]) {
    case '\n':
      code = "\\n"; 
      break;
    case 7:
      code = "\\b";
      break;
    case '\t':
      code = "\\t";
      break;
    case '\r':
      code = "\\r";
      break;
    case '"': 
      code = "\\\"";  /* " ...emacs colors;-( */
      break;
    case '\\':
      code = "\\\\";
      break;
    default:
      if (s[k] < 8) {
	sprintf (codeStr, "\\%d", s[k]);
	code = codeStr;
      }
      else {
	code = NULL;
	k++;
      }
      break;
    }
    if (code) {
      StrSubst (str, k, 1, StrTemp (code));
      k += strlen (code);
    }
  }
  return *str;
}

/**API* StrDecode *********************************************************
** 
**	Converts C format escape expressions into ASCII codes (like "\n"->\n)
**
**      <BR>See also: StrEncode, StrTranslate
**
**      INPUT:          [W] pointer to the STRv to be converted
*/


void StrDecode (STRv* str)
{
  char *s;
  INT4 k,l, slen, code;

  StrBufChange(str,0,0);
  s = _Str (*str);
  slen = StrLen (*str);
  for (k = 0, l = 0;  k < slen; k++)
    if (s[k] != '\\')
      s[l++] = s[k];
    else
      switch (s[++k]) {
      case '0': case '1': case '2': case '3':
      case '4': case '5': case '6': case '7':
      case '8': case '9':
	code = s[k] - '0';
	while (isdigit (s[k+1])) {
	  k++;
	  code = code*10 + (s[k] - '0');
	}
	s[l++] = code;
          break;
      case 'n':
	s[l++] = 10;
	break;
      case 'a':
	s[l++] = 7;
	  break;
      case 't':
	s[l++] = 9;
	break;
      case 'b':
	  s[l++] = 7;
	  break;
      case 'r':
	s[l++] = 13;
	break;
      case '\"':  /* " ...emacs colors;-( */
	s[l++] = 34;
	  break;
      case '\\':
	s[l++] = 92;
	break;
      case '-':
	s[l++] = '\\'; /* see PrsDecode */
	s[l++] = '-';
	break;
      default:
	s[l++] = s[k];
	break;
      }
  s[l] = '\0';
  (*str)->len = l;
}

/**api* function **************************************************************
** 
**      Formats a string so that it fits on a device with fixed line size. 
**      Additional arguments control identation and prefix.
**
**  	INPUT:	    address of STRv [W]
**                  maximum length of the output line [R]
**                  identation of first line [R] or 0
**                  identation of all/following lines [R] or 0
**                  text to be printed in front of each line [R] or NULL
**
**      RETURNS:  o A new STRv with the input string reformatted. Deletion is 
**                  client responsability
**  
*/

STRv StrFormat (STRv str, INT4 lineSize, 
		INT4 firstIdent, INT4 allIdent, char *leftText)
{
  STRv tmp=NULL;
  char *p, *pSave, cSave;
  INT4 k, lineLen;

  if (leftText)
    allIdent = strlen (leftText);

  tmp = StrNew ();
  
  /* text or ident to the left of first line */
  if (leftText)
    StrAppS (&tmp, leftText);
  else if (firstIdent)
    StrFill (&tmp, ' ', firstIdent);

  for (lineLen=StrLen (tmp), k=lineLen + StrLen (str), p=_Str(str); 
       k >= lineSize; 
       lineLen=allIdent, k=lineLen + StrLen (str) - (p - _Str(str))) {

    pSave = p;
    p += lineSize - lineLen;
    while (*p != ' ' && p > pSave) /* find the next ' ' backwards */
      p--;
    if (p == pSave) /* if no space was found break at line end */
      p += lineSize - lineLen;
    cSave = *p;
    *p = '\0';
    StrPrintf (&tmp, "%s\n", pSave);
    *(p++) = cSave;

    /* text or ident to the left of following lines */
    if (leftText)
      StrAppS (&tmp, leftText);
    else
      StrFill (&tmp, ' ', allIdent);

  }
  StrAppS (&tmp, p);
  return tmp;
}



/**api* function **************************************************************
** 
**	Removes a line feed at the end of the string.
**
**      INPUT:          [W] pointer to the STRv to be modified
**
*/

void StrCutLF (STRv *s)
{
  Int4 l=StrLen (*s);
  char *tmp=_Str (*s);

  if (tmp[l-1] == '\n')
    StrCut (s, l-1, 1);
}

/**API* StrTranslate *********************************************************
** 
**	Changes all characters of the string which are contained 
**      in the 'from' character set into
**      the corresponding character in the 'to' charcter set. 
**      The 2 character sets must have the same lenght 
**
**      <BR>See also: StrEncode, StrDecode
**
**      INPUT:          [W] pointer to the STRv to be converted
*/

void StrTranslate(STRv* s, char* from, char* to) {
    char* p;
    StrBufChange(s,0,0); p=Str(*s);
    p+=strcspn(p,from);
    /* substitute to end string */
    while (*p) {
      *p++=to[strchr(from,*p)-from];
      p+=strcspn(p,from); 
    }
}

 'from' character set into
**      the corresponding character in the 'to' charcter set. 
**      The 2 character sets must have the same lenght 
**
**      <BR>See also: StrEncode, StrDecode
**
**      INPUT:          [W] pointer to the STRv to be converted
*/

void StrTranslate(STRvsrs/src/strv.h
#define _STRV_H


typedef struct STRo {
    int usage;
    int len;
    int dim;
    char arr[1];
} STRo;

typedef STRo* STRv;

extern STRv StrNULL;

/* allocation */
STRv StrNew();
STRv StrCpy(STRv src);
void StrDel(STRv val);
void StrGrow(STRv* val, int dlen);
void StrShrink(STRv* val);
void StrClear(STRv* s);
STRv StrSub(STRv s, int pos, int len);
STRv StrLeft(STRv s, int pos);
STRv StrRight(STRv s, int pos);

/* operations */
void StrSet(STRv* dest, STRv src);
void StrIns(STRv* dest, STRv src);
void StrApp(STRv* dest, STRv src);
void StrAdd(STRv* dest, int pos, STRv src);
void StrCut(STRv* dest, int pos, int len);
void StrSubst(STRv* dest, int pos, int len, STRv subst);
void StrDebug(STRv s);
void StrUpper(STRv* s);
void StrLower(STRv* s);

/* queries */
BOOL StrEmpty(STRv str);
int  StrLen(STRv str);
BOOL StrEqual(STRv s1, STRv s2); 
int  StrCmp(STRv s1, STRv s2); 
int  StrHash(STRv val, int max);

/* user */
char* StrConst(STRv val);
char* StrVal(STRv val);
char* StrGet(char* dest, int sz, STRv src);
#define Str(val) ((val)->arr)
#define _Str(val) ((val)->arr)
int StrShared(STRv s);

/* c string operations */
STRv StrTemp(char* src);
STRv StrCpyS(char* src);
void StrSetS(STRv* dest, char* src);
void StrInsS(STRv* dest, char* src);
void StrAppS(STRv* dest, char* src);
void StrAppN(STRv* dest, char* src, int len);
void StrAddS(STRv* dest, int pos, char* src);
BOOL StrEqualS(STRv s1, char* s2); 
int  StrCmpS(STRv s1, char* s2); 
int  StrHashS (char* val, int dim);
STRv StrNCpyS(char* s, int len);
void StrNSetS(STRv* dest, char* s, int len);

/* low-level */

STRv StrBufNew(int dim);
void StrBufChange(STRv* val, int beg, int end);

/* conversions */

STRv  StrFromInt(int i);
int   StrToInt(STRv s);
STRv  StrPtr(void* p);
void* PtrStr(STRv s);

/* functions similar to Buff... */

void StrCutLF (STRv *s);
STRv StrPrintf (STRv* str, char *format, ...);
STRv StrEncode (STRv *str);
void StrDecode (STRv* str);
void StrTranslate(STRv* s, char* from, char* to);
void StrFill(STRv* dest, char c, Int4 len);
void StrTrim (STRv *s, char *skipSet);
STRv StrFormat (STRv str, INT4 lineSize, 
		INT4 firstIdent, INT4 allIdent, char *leftText);

/* for string initialization */

typedef struct {
    struct { int u; int l; int d; } DontInitalize;
    char arr[20];
} STRoStatic_20;

typedef struct {
    struct { int u; int l; int d; } DontInitalize;
    char arr[100];
} STRoStatic_100;

typedef struct {
    struct { int u; int l; int d; } DontInitalize;
    char arr[1000];
} STRoStatic_1000;

void StrInitStatic(STRv list, int size, int num);
#define _StrInitStatic(list,num) StrInitStatic((STRv)(list),sizeof((list)[0]),num) 

#endif
 char *leftText);

/* for string initialization */

typedef struct {
    struct { int u; int l; int d; } DontInitalize;
    char arr[20];
} STRoStatic_20;

typedef struct {
    struct { int u; int l; int d; } DontInitalize;
    char arr[100];
} STRoStatic_100;

typedef struct {
    struct { int u; int l; int d; } DontInitalize;
    char arr[1000];
} STRoStatic_1000;

void StrInitStatic(STRv lisrs/src/templ.c
char template_ID[] = "$Id: templ.c,v 1.22 1997/03/18 22:52:33 srs Exp $";
/*
**
**    $Source: /homes/srs/cvsroot/srs/src/templ.c,v $
**    $Revision: 1.22 $
**    $Date: 1997/03/18 22:52:33 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
** 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    facility for writing any type of command procedure within a program
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include "def.h"
#include "message.h"
#include "sm.h"
#include "futil.h"
#include "library.h"
#include "strv.h"
#include "lst.h"
#include "par.h"
#include "dict.h"
#include "variable.h"
#include "templ.h"
#include "icarus.h"
#include "icaarg.h"

#define TEMPLxMaxContextN 20

typedef struct TEMPLo {
  FILEo              *inFile;
  FILEo              *outFile;
  STRv               outString;
  VARo               *varList;
  ICAoJOB            *job;
  struct TEMPLoLABEL *label;
  DICTv              labelDict;
  INT4               labelN;
  INT4               labelAllocN;
} TEMPLo;

typedef struct TEMPLoCONTEXT {
  TEMPLo *templ;
  STRv   name;
  VARo   *var;
  Int4   isRoot;
} TEMPLoCONTEXT;

typedef struct TEMPLoLABEL {
  char *name;
  FIP  fip;
} TEMPLoLABEL;

static TEMPLo        *templCurr=NULL;
static ICAoJOB       *templJob=NULL;
static TEMPLoCONTEXT *templContext=NULL;




void TemplIcaAddLabel ();
static void TemplIcaAddTemplate ();
static void TemplInit ();
static char *TemplContext (char *option, TEMPLo *templ, VARo *var, 
			   Int4 isRoot);
static struct VARo *TemplGetTemplate (TEMPLv templ, char *name);
static Int4 TemplWithImpl (TEMPLo *templ, char *label);

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  for the variable dictionary
*/

static void* TemplToKey (DictElem* e)
{
  return offset(templContext->templ->label, 
		(WORD)*e - 555, TEMPLoLABEL*)->name;
}
static CLASSoDICT dictClass = {
  (ValComparer)strequal, (ValHasher)strhash, (KeyAccessor)TemplToKey, NULL, 0
};



void TemplIcaAddLabel (Int4 runTime, STRv name, Int4 fip)
{
  TEMPLo      *templ = templContext->templ;
  TEMPLoLABEL *tmp;

  if (runTime)
    IargGetArgs ("name|fip", &name, &fip);
  tmp = _addObj (templ->label, templ->labelN, templ->labelAllocN, TEMPLoLABEL);
  tmp->name = (char *) malloc (StrLen(name)+1);
  strcpy (tmp->name, _Str (name));
  tmp->fip = fip;
  DictSet (&templ->labelDict, tmp->name, TEMPLoLABEL*) = 
    (void *) (displ(tmp,templ->label) + 555); 
    /* add 555 since NULL not allowed */
}


static void TemplIcaAddTemplate ()
{
  VARo *var;

  IargGetArgs ("var", &var);
}

static void TemplInit ()
{
  ICAoSYNTAX *syntax;
    
  if (!templJob) {
    syntax = (ICAoSYNTAX*)LibObjByName ("syntax", "icarus");
    templJob = IcaCreateJob (syntax);

    IcaSetFunction("TemplIcaAddLabel",    (FUNC) TemplIcaAddLabel);
    IcaSetFunction("TemplIcaAddTemplate", (FUNC) TemplIcaAddTemplate);
  }
}

/**API* TemplOpen *************************************************************
**
**      Opens the template file and the output stream.
**      TemplWith must be used before the first call of TemplPrint.
**
**	INPUT:	    name of template file [R]
**                  name of output file (opens 'stdout' if NULL) [R]
**	        IMPLICIT:
**                  templJob (JOBo*)
**
**	RETURNS: 
**                  the new template object
**		    NULL if read file could not open
*/ 

TEMPLo *TemplOpen (char *inFileName, char *outFileName)
{
  TEMPLo   *templ;

  TemplInit ();

  /* new templ object */
  if (!(templ = (TEMPLo *) calloc (1, sizeof (TEMPLo))))
    _ErrExit2 (e__allocfail, "templ object");

  /* open files, init label dictionary and variable list*/
  templ->inFile = FileNew (inFileName);
  if (!FileOpen (templ->inFile))
    return(NULL);

  templ->outFile = FileNew (outFileName);
  if (!FileOpen (FileSetWrite(templ->outFile)))
    _ErrExit2 (e__filnotok, FileGetName (templ->outFile, "full"));

  templ->labelDict = 
    DictCreate (&dictClass);
  /*DictCreateClassStrKey (NULL, mPtr(TEMPLoLABEL, name), 0));*/
  templ->varList = VarNew ();

  /* scan the templ input file for variable names and insert in dictionary */
  TemplWith (templ, NULL);
  IcaJobSetFile (templJob, templ->inFile);
  IcaDoJob (templJob, "scan");
  if (templJob->prog)
    VarExec (templJob->prog); 
  TemplEndWith ();

  return templ;
}


static VARo *TemplGetTemplate (TEMPLo *templ, char *name)
{
  TEMPLoLABEL *label;
  VARo        *var;
  Iter        i;

  TemplContext ("push", templ, NULL, 0);
  var = AnyGetListAssoc (templ->varList, name);
  if (!VarType (var)) {
    if ((i = DictWith (templ->labelDict, name)))
      label = (TEMPLoLABEL*) ((char *)templ->label + 
	 ((Word) DictIn (i, TEMPLoLABEL*) - 555));
    else
      _ErrExit3 (e__labelnotfound, name, FileGetName (templ->inFile, "full"));

    FileSeek (templ->inFile, label->fip);
    IcaJobNext (templJob);
    IcaJobSetFile (templJob, templ->inFile);
    IcaDoJob (templJob, "template");
    IcaExecProg (templJob);
    AnySetList (var, VarGet (&templJob->scope, name));
  }
  TemplContext ("pop", NULL, NULL, 0);
  return var;
}

/**API* TemplGet **************************************************************
**
**      Returns the template object set by the last TemplWith call.
**
**      RETURNS:    the template object
**                  NULL: no template open
**
*/ 

TEMPLv TemplGet ()
{
  return templContext ? templContext->templ : NULL; 
}

FILEo *TemplGetOutFile (TEMPLv templ)
{
  return templ->outFile;
}


/**API* TemplPrint ************************************************************
**
**      Prints the text contained by specified label. Additional arguments
**      are required if the text contains '%' metacharacters.
**
**	INPUT:	    o label name starting from current template context
**                    (see TemplWith). Instead of the name the position of
**                    the label within the list can be used by specifying the
**                    number in square brackets (eg, [2]). The first label
**                    in the list has number 1. [R]
**                  o additional arguments to be inserted into text [R]
**	        IMPLICIT:
**                  templJob (JOBo*)
**
*/ 

void TemplPrint (char *name, ...)
{

  TEMPLo   *templ=templContext->templ;
  STRv     str;
  char     s[90000];
  va_list  ap;

  TemplWith (templ, name);
  va_start (ap, name);
  str = VarGetStrv (templContext->var);
  vsprintf (s, _Str(str), ap);
  StrDel (str);
  va_end (ap);
  fprintf (templ->outFile->file, "%s", s);
  TemplEndWith ();
}

/**API* TemplPrintAll *********************************************************
**
**      Prints all elements of the list specified by the name argument.
**
**	INPUT:	    o label name starting from current template context
**                    (see TemplWith). Instead of the name the position of
**                    the label within the list can be used by specifying the
**                    number in square brackets (eg, [2]). The first label
**                    in the list has number 1. [R]
**	        IMPLICIT:
**                  templJob (JOBo*)
**
*/ 

ANYv TemplPrintAll (char *name)
{
  TEMPLo *templ=templContext->templ;
  ANYv   any, anyList;
  INT4   errCode, k, i;

  anyList = TemplExists (templ, "command");
  TemplWith (templ, "command");
  for (i=0, k=1; (any=AnyNextInList (anyList, &i)); k++)
    TemplPrint (TemplN (k, NULL));
  TemplEndWith ();
}

ANYv TemplSPrintAll (STRv *str, char *name)
{
  TEMPLo *templ=templContext->templ;
  ANYv   any, anyList;
  INT4   errCode, k, i;
  char   tmp[1000];

  anyList = TemplExists (templ, "command");
  TemplWith (templ, "command");
  for (i=0, k=1; (any=AnyNextInList (anyList, &i)); k++) {
    TemplSPrint (tmp, TemplN (k, NULL));
    StrAppS (str, tmp);
  }
  TemplEndWith ();
}


/**API* TemplExists ***********************************************************
**
**      This function is useful for asserting that the specified label exists
**      before using it for printing. The function returns the Any object
**      containing the label name as well as the text or an Any list in
**      case the name specifies an internal label. 
**
**	INPUT:      the template object (or NULL) [R]
**                  label name (see TemplWith) [R]
**	        IMPLICIT:
**                  templJob (JOBo*)
**      RETURNS:
**                  address of Any object
**                  NULL: label does not exist
**
*/ 

VARo *TemplExists (TEMPLv templ, char *name)
{
  VARo *var=NULL;
  if (TemplWithImpl (templ, name)) {
    var = templContext->var;
    TemplEndWith ();
  }
  return var;
}

/**API* TemplSPrint ***********************************************************
**
**      Same as TemplPrint except that it prints into the string with
**      specified address rather than the output stream.
**
**	INPUT:	    address of output string [W]
**                  label name (see TemplWith) [R]
**                  additional arguments to be inserted into text [R]
**	        IMPLICIT:
**                  templJob (JOBo*)
**      RETURNS:
**                  address of output string (same as first argument)
**
*/ 

char *TemplSPrint (char *s, char *name, ...)
{
  TEMPLo   *templ=templContext->templ;
  STRv     str;
  va_list  ap;

  TemplWith(templ, name);
  va_start(ap, name);
  str = VarGetStrv (templContext->var);
  vsprintf(s, _Str(str), ap);
  StrDel (str);
  va_end(ap);
  TemplEndWith();
  return(s);
}

/**API* TemplWith ************************************************************
**
**      Sets the template context to a new list. The context can
**      be either a list contained in the list represented by the current
**      context (relative name) or in another variable which may be 
**      forced by prefixing
**      the label name with a '$' (absolute name). 
**      <P>
**      The label name can contain indices for specifiying elements in
**      the list which must then be inclosed in square brackets (eg, [1], 
**      TemplN assists in generating labels with an index).
**      After printing with the 'template' context TemplEndWith must be
**      called to restore to the previous context (The contexts are 
**      maintained as a stack where TemplWith pushes and TemplEndWith pops).
**
**	INPUT:	    template object (or NULL) [W]
**                  label name [R]
**
*/ 

void TemplWith (TEMPLo *templ, char *label)
{
  char path[200];
  if (!TemplWithImpl (templ, label)) {
    sprintf (path, "%s.%s", 
	     TemplContext ("root", NULL, NULL, 0), label);
    _ErrExit3 (e__objectunknown, "label", path);
  }
}


static Int4 TemplWithImpl (TEMPLo *templ, char *label)
{
  VARo *var=NULL, *tmp;
  Int4     isRoot=0, index;
  char *name, path[200], *context;
  
  if (!templ) {
    if (!templContext)
      _ErrExit (e__templNoCurrTemplate);
    templ = templContext->templ;
  }
  if (label && *label == '$') { /* start with root */
    isRoot=1;
    label++;
  }
  else if (templContext && templ == templContext->templ) 
    var = templContext->var; /* take root from prev context */
  
  if (label) {
    strcpy (path, label);
    context = path;
    while ((name = strtok (context, ".["))) {
      context = NULL;
      if (sscanf (name, "%d]", &index)) { /* access by index */
	if (!var || !(var = AnyGetListIndex (var, index-1)))
	  return 0;
      }	  
      else if (var && !isRoot) { /* access by name */
	if (!(tmp = AnyFindListAssoc (var, name))) 
	  return 0;
	else 
	  var = tmp;
      }
      else { /* root or variable name */
	var = TemplGetTemplate (templ, name);
	isRoot = 0; /* prevents treatment of next name compononent as root */
      }
    }
  }
  TemplContext ("push", templ, var, isRoot);
  return 1;
}

/**API* TemplEndWith **********************************************************
**
**      Destroys the current template context set by the most recent
**      call of TemplWith and reinstalls the previous context.
**
**	INPUT:	
**	        IMPLICIT:
**                  templJob (JOBo*)
**
*/ 

void TemplEndWith ()
{
  TemplContext ("pop", NULL, NULL, 0);
}


static char *TemplContext (char *option, TEMPLo *templ, VARo *var, Int4 isRoot)
{
  static TEMPLoCONTEXT contexts[TEMPLxMaxContextN];
  static INT4 contextN=0;
  static char path[200];
  char tmp[200];
  Int4 k;
  
  switch (tolower (option[2])) {
  case 's':  /* push */
    if (contextN == TEMPLxMaxContextN)
      _ErrExit3 (f__limitexceeded, "templ contexts", TEMPLxMaxContextN);
    templContext = &contexts[++contextN];
    templContext->templ = templ;
    templContext->var = var;
    templContext->isRoot = isRoot;
    break;
  case 'p':  /* pop */
    if (contextN)
      templContext = &contexts[--contextN];
    else
      _ErrExit (e__templEndOfHistory);
    break;
  case 'o': /* root */ /* get the entire path from history */
    for (k=contextN, path[0]='\0'; k >= 0; k--) {
      if ((var = contexts[k].var)) { 
	strcpy (tmp, path);
	sprintf (path, ".%s%s", VarGetName (var), tmp);
      }
      else
	break;
      if (contexts[k].isRoot)
	break;
    }
    if (*path)
      path[0] = '$';
    return path;
  }
}

void TemplClose (TEMPLv templ)
{
  FileClose (templ->outFile);
  FileClose (templ->inFile);
  free (templ);
  /* should also 'unwind' the context if there is some left */
}

static char line[999];

/**API* TemplN ****************************************************************
**
**      Assists in creating a label name used when calling, eg, TemplPrint
**      The generated label name's first component is an
**      index number rather than a name. The specified name is added to
**      the number, eg, if the index is 5 and the name is "head" then the
**      generated string is "[5].head".
**      <BR>
**      This function 
**
**	INPUT:	    the index number [R]
**                  the name to go after the index (NULL if not desired) [R]
**
**      RETURNS:    the string containing the label name
**
*/ 

char *TemplN (INT4 index, char *name)
{
  static char line[999];
  if (name)
    sprintf(line, "[%d].%s", index, name);
  else
    sprintf(line, "[%d]", index);
  return(line);
}
**      the number, eg, if the index is 5 and the name is "head" then the
**      generated string is "[5].head".
**      <BR>
**      This function 
**
**	INPUT:	    the index number [R]
**                  the name to srs/src/templ.h
**
**    $RCSfile: templ.h,v $
**    $Revision: 1.8 $
**    $Date: 1996/08/12 20:24:30 $
**    $Author: etzold $
**
**    $Locker:  $
**    $State: Exp $
**
**
*/

typedef struct TEMPLo *TEMPLv;

TEMPLv        TemplOpen       (char *inFileName, char *outFileName);
TEMPLv        TemplGet        ();
char*         TemplSPrint     (char *s, char *name, ...);
char*         TemplN          (INT4 index, char *name);
void          TemplPrint      (char *name, ...);
void          TemplWith       (TEMPLv templ, char *name);
struct VARo*  TemplExists     (TEMPLv templ, char *name);
void          TemplEndWith    ();
void          TemplClose      (TEMPLv templ);  
struct FILEo* TemplGetOutFile (TEMPLv templ);


#define _s(x)  (x)
#define _d(x)  (x)
nFileName, char *outFileName);
TEMPLv        TemplGet        ();
char*         TemplSPrint     (char *s, char *name, ...);
char*         TemplN          (INT4 index, char *name);
void          Templsrs/src/termio.c
char termio_ID[] = "$Id: termio.c,v 1.2 1996/10/11 18:16:54 etzold Exp $"; 
/*               
**  
**    $RCSfile: termio.c,v $ 
**    $Revision: 1.2 $
**    $Date: 1996/10/11 18:16:54 $
**    $Author: etzold $
**
**
**                  Copyright by Thure Etzold
**
**             Authors: Lukas Rosenthaler and Thure Etzold
**
**                      Thure Etzold
**                      EMBL, Meyerhofstrasse 1
**                      W-69012 Heidelberg, Germany
**                      Tel: 06221 387529
**                      Email: etzold@embl-heidelberg.de
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**
**    Description
**    =========== 
**  
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*/  

#include <stdio.h>
#include <string.h>

#ifdef VMS
#  include <ssdef.h>
#  include <rmsdef.h>
#  include <jpidef.h>
#  include <libdef.h>
#  include <descrip.h>
#  include <iodef.h>
#  include <unixlib.h>
#  include <ctype.h>
#else
#  include <stdlib.h>
/*#  include <sys/ttychars.h> linux doesn't have that - is in bsd/sys */
#  include <sys/termio.h>
#endif  

#include "message.h"
#include "strv.h"
#include "termio.h"


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  some typedefs for VMS
*/

# ifdef VMS
typedef struct {                /* I/O status block     */
        short i_cond;           /* Condition value      */
        short i_xfer;           /* Transfer count     */
        long  i_info;           /* Device information     */
} iosb;
 
typedef struct {                /* Terminal characteristics   */
        char  t_class;          /* Terminal class     */
        char  t_type;           /* Terminal type      */
        short t_width;          /* Terminal width in characters   */
        long  t_mandl;          /* Terminal's mode and length   */
        long  t_extend;         /* Extended terminal characteristics  */
}  termchar;                    

short TTY_CHANNEL_GLOBAL;
# else
#   ifdef BSD
#     include <sgtty.h>
      struct ltchars  OLDTTY_LC;
      struct tchars   OLDTTY_TC;
      struct sgttyb   OLDTTY;
#   else
     struct termio   OLDTTY;
#   endif
# endif


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  Describes a line for the line editor in this module
*/
#define TERMxHistorySize 100

typedef struct TERMoLine {
  Int4 cursPos;
  Int4 editN;
  Int4 backN;
  STRv line[TERMxHistorySize];
} TERMoLine;


/**api* TermInitTty **********************************************************
**
**      Initializes either "/dev/tty" (unix) or "TT:" (VMS) for single 
**      character input.
**
**      Keyboard characteristics may have changed such that normal
**      input is no longer possible until TermResetTty is called.
**      Therefore TermResetTty *MUST* be called before the
**      program terminates, even in case of catastrophic events
**      such as exceptions caused by SIG_SEGV or SIG_BUS!
*/

void TermInitTty (void)
{
#ifdef VMS  
  $DESCRIPTOR ( Term, "TT:" ); 
  (void) sys$assign ( &Term, &TTY_CHANNEL_GLOBAL, 0, 0 );
#else    
#ifdef BSD
  struct sgttyb  newtty;
  struct tchars tc;
  struct ltchars lc;

  ioctl(TTY_DESCR, TIOCGLTC,&OLDTTY_LC);
  ioctl(TTY_DESCR, TIOCGETC,&OLDTTY_TC);
  ioctl(TTY_DESCR, TIOCGETP, &OLDTTY);
  newtty = OLDTTY;
  newtty.sg_flags |= CBREAK;
  newtty.sg_flags &= ~(ECHO | XTABS);
  newtty.sg_erase = 0;
  newtty.sg_kill = 0;
  tc.t_intrc = 0;
  tc.t_quitc = 0;
  lc.t_suspc = 0;
  lc.t_dsuspc = 0;
  ioctl(TTY_DESCR, TIOCSETP, &newtty);
  ioctl(TTY_DESCR, TIOCSLTC,&lc);
  ioctl(TTY_DESCR, TIOCSETC,&tc);

#else /* for non-BSD systems */

  struct termio   newtty;
	  
  ioctl(TTY_DESCR, TCGETA, &OLDTTY);
  ioctl(TTY_DESCR, TCGETA, &newtty);
  newtty.c_iflag |= CBREAK;  
  newtty.c_iflag &= ~(ECHO);  
  newtty.c_iflag &= ~(IGNCR);  
  newtty.c_iflag &= ~(ICRNL);  
  newtty.c_iflag &= ~(INLCR);  
  newtty.c_lflag = 0; 
  newtty.c_cc[VMIN]  = 1; 
  newtty.c_cc[VTIME] = 0;
  newtty.c_cc[VEOF]  = 1; 
  
  ioctl(TTY_DESCR, TCSETA, &newtty);

#endif
#endif
}


/**api* TermResetTty **********************************************************
**
**      Resets the keyboard characterstics of either "/dev/tty" (unix) or "TT:"
**      (VMS) to default values.
**
*/

void TermResetTty (void)
{
#ifndef VMS
#ifdef BSD
  ioctl(TTY_DESCR, TIOCSETP, &OLDTTY);
  ioctl(TTY_DESCR, TIOCSLTC, &OLDTTY_LC);
  ioctl(TTY_DESCR, TIOCSETC, &OLDTTY_TC);
#else        
  ioctl(TTY_DESCR, TCSETA, &OLDTTY);
#endif
#endif
}


/**api* TermGetChar **********************************************************
**
**      Wait until next keyboard event, then returns the key pressed. Requires
**      that TermInitTty has been called before.
**      check the cursor position, if it at the beginning of the line do
**      pre/post-parsing action.
**
**      RETURNS:        ascii code of pressed key
*/

char TermGetChar (void)
{
  char c;
    
#ifndef VMS
  read(TTY_DESCR, &c, 1); 
#else
  int status, trmmsk [2] = { 0, 0 };
  short iosb [4];
  
  status = sys$qiow (0, TTY_CHANNEL_GLOBAL,
		     IO$_READVBLK + IO$M_NOECHO | IO$_TTYREADALL,
		     iosb, 0, 0,
		     &c, 1, 0, trmmsk, 0, 0 );
#endif
  return(c); 
}


/**api* TermGetDimensions *****************************************************
**
**      Get dimensions of terminal screen.
**
**    int *cols : number of columns [returned]
**    int *rows : number of rows [returned]
**
*/

void TermGetDimensions (int *cols, int *rows)
{
#ifdef VMS
  short fd;
  int status;
  iosb iostatus;
  static termchar tc; /* Terminal characteristics   */
  $DESCRIPTOR(devnam, "SYS$COMMAND");
    
  /* Assign input to a channel */
  status = sys$assign(&devnam, &fd, 0, 0);
  if ((status & 1) == 0)
    exit(status);

  /* Get current terminal characteristics */
  status = sys$qiow(                 /* Queue and wait   */
		    0,               /* Wait on event flag zero  */
		    fd,              /* Channel to input terminal  */
		    IO$_SENSEMODE,   /* Get current characteristic */
		    &iostatus,       /* Status after operation */
		    0, 0,            /* No AST service   */
		    &tc,             /* Terminal characteristics buf */
		    sizeof(tc),      /* Size of the buffer   */
		    0, 0, 0, 0);     /* P3-P6 unused     */


  /*  The next few lines from Mats Akerberg <mats@efd.lth.se> */
  
  /* De-assign the input device: */
  if ((sys$dassgn(fd) & 1) == 0) {
    exit(status);
  }

  /* Jump out if bad status */
  if ((status & 1) == 0) {
    exit(status);
  }
  if ((iostatus.i_cond & 1) == 0) {
    exit(iostatus.i_cond);
  }
  *cols = (int) tc.t_width;
  *rows = (int) ((unsigned int) tc.t_mandl >> 24);

#else 
   
  /* this may need work on other unix-- works for sun4 */
  struct winsize wind_struct;
      
  ioctl(2,TIOCGWINSZ,&wind_struct);
  if (((int) wind_struct.ws_col < 1) || ((int) wind_struct.ws_row < 1)) {
    *cols = 80;
    *rows = 24;
  }
  else {
    *cols = (int) wind_struct.ws_col;
    *rows = (int) wind_struct.ws_row;
  }
    
#endif
}

/**api* TermGetChar **********************************************************
**
**      Returns either an ASCII code (single character) or a TERM code for a
**      function key which produces an escape sequence.
**
**      RETURNS:        ASCII code or TERM code of pressed key 
*/

int TermGetKey (void)
{
  char c;
  int key;

  c = TermGetChar ();
  switch (c) {
  case ESC : 
    c = TermGetChar();
    if (c == '[') {
      c = TermGetChar();
      switch (c) {
      case 'A' : 
	key = TERMxUp;
	break;
      case 'B' : 
	key = TERMxDown;
	break;
      case 'C' : 
	key = TERMxRight;
	break;
      case 'D' : 
	key = TERMxLeft;
	break;
      case '2' : 
	c = TermGetChar();
	if (isdigit(c)) {
	  c = TermGetChar();
	  switch (c) {
	  case '1' : 
	    key = TERMxF10;
	    break;
	  case '9' : 
	    key = TERMxDo;
	    break;
	  }
	  TermGetChar();
	}
	break;
      case '5' : 
	key = TERMxPrevScreen;
	(void) TermGetChar();
	break;
      case '6' : 
	key = TERMxNextScreen;
	(void) TermGetChar();
	break;
      }
    }
    else if (c == 'O') {
      c = TermGetChar();
      switch (c) {
      case 'A' : 
	key = TERMxUp;
	break;
      case 'B' : 
	key = TERMxDown;
	break;
      case 'C': 
	key = TERMxRight;
	break;
      case 'D' : 
	key = TERMxLeft;
	break;
      case 'P' : 
	key = TERMxPF1;
	break;
      case 'Q' : 
	key = TERMxPF2;
	break;
      case 'R' : 
	key = TERMxPF3;
	break;
      case 'S' : 
	key = TERMxPF4;
	break;
      }
    }
    break;
  case TERMxCtrl_P : 
    key = TERMxPrevScreen;
    break;
  case TERMxCtrl_N : 
    key = TERMxNextScreen;
    break;
  case 13 : 
    key = TERMxReturn;
    break;
  default: 
    key = (int) c;
  }
  return (key);
}


/**api* TermNewLineEditor *****************************************************
**
**      Creates a new terminal line editor.
**
**      RETURNS:        line edit object
*/

TERMvLine TermNewLineEditor ()
{
  TERMvLine led=NULL;

  if ((led = (TERMoLine *) calloc (sizeof(TERMoLine), 1)) == NULL)
    _ErrExit2 (e__allocfail, "line editor");

  return led;
}

/**api* TermLineEdit **********************************************************
**
**      Simple line editor. Returns the line submitted with the 
**      Return key.
**
**      RETURNS:        current line
*/

STRv TermLineEdit (TERMvLine led, char *prompt)
{
  STRv ln, *tmp, t;
  Int4 key, doSubmit=0;
  char s[2]="*";
  
  TermInitTty ();
  ln = StrNew ();
  if (prompt) {
    printf (prompt);  
    fflush (stdout);
  }
  led->cursPos = 0;
  led->backN = led->editN;

  /* iterate over keyboard input */
  while ((key = TermGetKey ())) {
    if (_TermIsTypeChar (key)) {
      s[0] = (char) key;
      StrAddS (&ln, led->cursPos, s);
      CURSOR_SAVE (stdout);
      if (led->cursPos)
	CURSOR_LEFT (led->cursPos, stdout);
      fputs (_Str (ln), stdout);
      CURSOR_RESTORE (stdout);
      CURSOR_RIGHT (1, stdout);
      led->cursPos++;
    }    
    else
      switch (key) {
      case TERMxCtrl_A:
	CURSOR_LEFT (led->cursPos, stdout);
	led->cursPos = 0;
	break;
      case TERMxCtrl_E:
	CURSOR_RIGHT (StrLen (ln) - led->cursPos, stdout);
	led->cursPos = StrLen (ln);
	break;
      case TERMxCtrl_K:
	DELETE_CURSPOS_EOL (stdout);
	StrCut (&ln, led->cursPos, StrLen (ln) - led->cursPos);
	break;
      case TERMxCtrl_C:
      case TERMxCtrl_Y:
      case TERMxCtrl_Z:
	exit (0);
      case TERMxLeft:
	if (led->cursPos>0) {
	  CURSOR_LEFT (1, stdout);
	  led->cursPos--;
	}
	break;
      case TERMxRight:
	if (led->cursPos < StrLen (ln)) {
	  CURSOR_RIGHT (1, stdout);
	  led->cursPos++;
        }
	break;
      case TERMxUp:
	if (led->backN>0) {
	  if ((t = led->line[(led->backN-1) % TERMxHistorySize])) {
	    ln = StrCpy (t);
	    led->backN--;
	    if (led->cursPos)
	      CURSOR_LEFT (led->cursPos, stdout);
	    DELETE_CURSPOS_EOL (stdout);
	    fputs (_Str (ln), stdout);
	    led->cursPos = StrLen (ln);
	  }
	}
	break;
      case TERMxDown:
	if (led->backN < led->editN-1) {
	  ln = StrCpy (led->line[(++led->backN) % TERMxHistorySize]);
	  if (led->cursPos)
	    CURSOR_LEFT (led->cursPos, stdout);
	  DELETE_CURSPOS_EOL (stdout);
	  fputs (_Str (ln), stdout);
	  led->cursPos = StrLen (ln);
	}
	else if (led->backN == led->editN-1) {
	  led->backN++;
	  ln = StrNew ();
	  if (led->cursPos)
	    CURSOR_LEFT (led->cursPos, stdout);
	  DELETE_CURSPOS_EOL (stdout);
	  fputs (_Str (ln), stdout);
	  led->cursPos = StrLen (ln);
	}
	  
	break;
      case TERMxDelete:
	if (led->cursPos>0) {
	  CURSOR_LEFT (1, stdout);
	  DELETE_CURSPOS_EOL (stdout);
	  StrCut (&ln, --led->cursPos, 1);
	  CURSOR_SAVE (stdout);
	  CURSOR_LEFT (led->cursPos, stdout);
          fputs (_Str (ln), stdout);
	  CURSOR_RESTORE (stdout);
	}
	break;
      case TERMxCtrl_J:
      case TERMxReturn:
	doSubmit = 1;
	fputs ("\n", stdout);
	break;
      }
    fflush (stdout);
    if (doSubmit) {
      /* save line in history */
      if (StrLen (ln)) {
	tmp = &led->line[led->editN++ % TERMxHistorySize];
	if (*tmp)
	  StrDel (*tmp);
	*tmp = ln;
      }
      break;
    }
  }
  TermResetTty ();
  return ln;
}
cursPos, 1);
	  CURSOR_SAVE (stdout);
	  CURSOR_LEFT (led->cursPos, stdout);
          fputs (_Str (ln), stdousrs/src/termio.h
 * $Header: /homes/srs/cvsroot/srs/src/termio.h,v 1.2 1996/10/11 18:16:55 etzold Exp $
 *----------------------------------------------------------------------------
 *
 *                  SRS V3.0 Copyright by Thure Etzold
 *
 *    Author of this module: Lukas Rosenthaler and Reinhard Doelz
 * Copyright granted to Thure Etzold for distribution withing the SRS package
 *                Use outside the SRS is strictly prohibited
 *
 *****************************************************************************
 */

#define TTY_DESCR 2
#ifdef CBRK
# ifndef CBREAK
#  define CBREAK CBRK
# endif
#else
#define CBREAK BRKINT
#endif
#define ESC '\033'
#define BS  '\010'

enum TERMxKey  {TERMxCtrl_SP=0, TERMxCtrl_A, TERMxCtrl_B, TERMxCtrl_C, 
		TERMxCtrl_D, TERMxCtrl_E, TERMxCtrl_F, TERMxCtrl_G, 
		TERMxCtrl_H, TERMxCtrl_I, TERMxCtrl_J, TERMxCtrl_K, 
		TERMxCtrl_L, TERMxCtrl_M, TERMxCtrl_N, TERMxCtrl_O, 
		TERMxCtrl_P, TERMxCtrl_Q, TERMxCtrl_R, TERMxCtrl_S, 
		TERMxCtrl_T, TERMxCtrl_U, TERMxCtrl_V, TERMxCtrl_W, 
		TERMxCtrl_X, TERMxCtrl_Y, TERMxCtrl_Z, 
		TERMxDelete=127, TERMxUp=300, 
		TERMxDown, TERMxRight, TERMxLeft};

#define _TermIsTypeChar(x) ((x) >= 30 && (x) <= 126)


#define TERMxPrevScreen 304
#define TERMxNextScreen 305
#define TERMxF10         310
#define TERMxF16         316
#define TERMxDo          316
#define TERMxPF1         316 /* SPECIAL FOR SRS, otherwise 331 */
#define TERMxPF2         332
#define TERMxPF3         333
#define TERMxPF4         310 /* SPECIAL FOR SRS, otherwise 334 */

#define TERMxReturn      13
#define TERMxDelete      127

#define RENDITION_OFF_STR        "\033[0m"
#define RENDITION_BOLD_STR       "\033[1m"
#define RENDITION_UNDERSCORE_STR "\033[4m"
#define RENDITION_BLINK_STR      "\033[5m"
#define RENDITION_REVERSE_STR    "\033[7m"

#define DELETE_CURSPOS_EOL_STR   "\033[0K"
#define DELETE_BOL_CURSPOS_STR   "\033[1K"
#define DELETE_LINE_STR          "\033[2K"
#define DELETE_CURSPOS_EOS_STR   "\033[0J"
#define DELETE_BOS_CURSPOS_STR   "\033[1J"
#define DELETE_SCREEN_STR        "\033[2J"

#define CURSOR_UP_STR            "\033[%dA"
#define CURSOR_DOWN_STR          "\033[%dB"
#define CURSOR_RIGHT_STR         "\033[%dC"
#define CURSOR_LEFT_STR          "\033[%dD"
#define CURSOR_POSITION_STR      "\033[%d;%dH"
#define CURSOR_SAVE_STR          "\0337"
#define CURSOR_RESTORE_STR       "\0338"

/*
#define SET_SCROLL_STR           "\033[%d;%dr\033[?6h"
#define RESET_SCROLL_STR         "\033[;r\033[?6l"
*/
#define SET_SCROLL_STR           "\033[%d;%dr"
#define RESET_SCROLL_STR         "\033[;r"
#define SCROLL_UP_STR            "\033D"
#define SCROLL_DOWN_STR          "\033M"

#define SET_RENDITION_OFF(f)        (void) fputs (RENDITION_OFF_STR, f)
#define SET_RENDITION_BOLD(f)       (void) fputs (RENDITION_BOLD_STR, f)
#define SET_RENDITION_UNDERSCORE(f) (void) fputs (RENDITION_UNDERSCORE_STR, f)
#define SET_RENDITION_BLINK(f)      (void) fputs (RENDITION_BLINK_STR, f)
#define SET_RENDITION_REVERSE(f)    (void) fputs (RENDITION_REVERSE_STR, f)

#define DELETE_CURSPOS_EOL(f)       (void) fputs (DELETE_CURSPOS_EOL_STR, f)
#define DELETE_BOL_CURSPOS(F)       (void) fputs (DELETE_BOL_CURSPOS_STR, f)
#define DELETE_LINE(f)              (void) fputs (DELETE_LINE_STR, f)
#define DELETE_CURSPOS_EOS(f)       (void) fputs (DELETE_CURSPOS_EOS_STR, f)
#define DELETE_BOS_CURSPOS(f)       (void) fputs (DELETE_BOS_CURSPOS_STR, f)
#define DELETE_SCREEN(f)            (void) fputs (DELETE_SCREEN_STR, f)

#define CURSOR_UP(n,f)              (void) fprintf (f, CURSOR_UP_STR, n)
#define CURSOR_DOWN(n,f)            (void) fprintf (f, CURSOR_DOWN_STR, n)
#define CURSOR_RIGHT(n,f)           (void) fprintf (f, CURSOR_RIGHT_STR, n)
#define CURSOR_LEFT(n,f)            (void) fprintf (f, CURSOR_LEFT_STR, n)
#define CURSOR_POSITION(x,y,f)      (void) fprintf (f, CURSOR_POSITION_STR,y,x)
#define CURSOR_SAVE(f)              (void) fputs (CURSOR_SAVE_STR, f)
#define CURSOR_RESTORE(f)           (void) fputs (CURSOR_RESTORE_STR, f);

#define SCROLL_REGION(s,e,f)        (void) fprintf (f, SET_SCROLL_STR, (s),(e))
#define RESET_SCROLL(f)             (void) fputs (RESET_SCROLL_STR, f)
#define SCROLL_UP(f)                (void) fputs (SCROLL_UP_STR, f)
#define SCROLL_DOWN(f)              (void) fputs (SCROLL_DOWN_STR, f)

#define VIDEO_OFF        0
#define VIDEO_BOLD       1
#define VIDEO_REVERSE    2
#define VIDEO_BLINK      4
#define VIDEO_UNDERSCORE 8


typedef struct TERMoLine *TERMvLine;

void      TermInitTty       (void);
void      TermResetTty      (void);
char      TermGetChar       (void);
void      TermGetDimensions (int *cols, int *rows);
int       TermGetKey        (void);
TERMvLine TermNewLineEditor ();
STRv      TermLineEdit      (TERMvLine led, char *prompt);




           (void) fputs (SCROLL_DOWN_STR, f)

#define VIDEO_OFF        0
#define VIDEO_BOLD       1
#define VIDEO_REVERSE    2
#define VIDEO_BLINK      4
#define VIDEO_UNDERSCORE 8


typedef struct TERMoLine *TERMvLine;

void      TermInitTty       (void);
void      TermResetTty      (void)srs/src/tm.c
char time_srs_ID[] = "$Id: tm.c,v 1.1 1996/05/06 15:17:31 srs Exp $";
/*
**
**    $RCSfile: tm.c,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:17:31 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**             Unix port by Lukas Rosenthaler and Reinhard
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: time
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <time.h>
#include <ctype.h>

#ifdef VMS
#include <types.h>
#include <stat.h>
#else
#include <sys/types.h>
#include <sys/stat.h>
#endif

#include "message.h"
#include "tm.h"

/**api* TimeGet ***************************************************************
**  
**  	gets the time elapsed since 1-jan-1970 00:00 in seconds;
**  
**  	        IMPLICIT:
**  
**  	RETURNS:    1
*/ 
   
UINT4 TimeGet ()
{
  time_t seconds;
  
  time (&seconds);
  return (UINT4) seconds;
}


/**api* TimeToString *********************************************************
**  
**  	converts time into a string;
**  
**  	INPUT:	    time value [R]
**                  option: "short", "long", "date"
**  	        IMPLICIT:
**  
**  	RETURNS:    pointer to static string 
*/ 

char *TimeToString (UINT4 userTimeVal, char *opt)
{
  static char timeStr[30];
  static char *month[12] = {"Jan","Feb","Mar","Apr","May","Jun","Jul",
			      "Aug","Sep","Oct","Nov","Dec"};
  time_t    timeVal = (time_t) userTimeVal;
  struct tm *timeRec;

  if (timeVal == 0)
    time (&timeVal); 
  timeRec = localtime (&timeVal);

  switch (tolower (opt[0])) {
  case 's':  /* short */
    sprintf (timeStr, "%0d/%0d/%0d", timeRec->tm_mon+1, 
	                          timeRec->tm_mday,
                                  timeRec->tm_year);
    break;
  case 'l':  /* long */
    sprintf (timeStr, "%02d-%s-19%0d %02d:%02d", timeRec->tm_mday, 
	     month[timeRec->tm_mon], 
	     timeRec->tm_year, 
	     timeRec->tm_hour,  
	     timeRec->tm_min);
    break;
  case 'd':  /* date */
    sprintf (timeStr, "%02d-%s-19%0d", timeRec->tm_mday, 
	     month[timeRec->tm_mon], 
	     timeRec->tm_year); 
    break;
  default:
    _ErrExit2 (e__unknownoption, opt);
  }
  return timeStr;
}


/**api* TimeFileCreate ********************************************************
**
**  	retrieves files creation and last modification date;
**  
**  	INPUT:	    address of file descriptor [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    file creation time
**                  0 if file could not be opened
*/ 

   
UINT4 TimeFileCreate (FILE *file)
{
  struct stat buff;
  INT4         fileNo;

  if (!file)
    return 0;

  fileNo = fileno (file);
  fstat (fileNo, &buff);
  
  return buff.st_ctime;
}




}


/**api* TimeFileCreate ********************************************************
**
**  	retrieves files creation and last modification date;
**  
**  	INPUT:	    address of file descriptor [R]
**  	        IMPLICIT:
**  
**  	RETURNS:    file creation time
**                  0 if file could not be opened
*/ 

   
UINT4 TimeFileCreate (FILE *file)
{
  struct stat buff;
  INT4         fileNo;

  if (!fisrs/src/tm.h
**
**    $RCSfile: tm.h,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:17:31 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**                  SRS V3.x Copyright by Thure Etzold
**
*/

UINT4 TimeGet ();
char *TimeToString (UINT4 time, char *option);
UINT4 TimeFileCreate (FILE *file);
 could not be opened
*/ 

   
UINT4 Tim¶ £¡@ate (FILE *file)
{
  struct stat buff;
  INT4         fi¶ £¡Ü’¨(!fisrs/src/toklist.c
char toklist__ID[] = "$Id: toklist.c,v 1.17 1997/03/19 20:41:41 srs Exp $"; 
/*               
**  
**    $RCSfile: toklist.c,v $ 
**    $Revision: 1.17 $
**    $Date: 1997/03/19 20:41:41 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  Copyright by Thure Etzold
**
**             Author: Anatoly Ulyanov
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387451
**                     Email: ulyanov@embl-heidelberg.de
**
*/  

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>

#include "message.h"
#include "futil.h"
#include "sm.h"
#include "dict.h"
#include "strv.h"
#include "lst.h"
#include "toklist.h"

/* * * * * * * * * * Private Domain  * * * * * * * * * * * * * * * */

static TOKoLIST *tokListGbl;


static void ListDump(FILE *file, void *obj)
{
  TOKoLIST *t = (TOKoLIST *)obj;
  printf("List/%d %s\n", t->isActive, t->name);
}

static void ListKill(void *obj)
{
  TOKoLIST *tokList = (TOKoLIST *)obj;
  if (tokList->dict)
    DictDestroy (tokList->dict);
  free(tokList->first);
  if(tokList->buff)
    free(tokList->buff);
}

/****** TokGrowList *********************************************************
** 
**      This function implements growing of number of allocated tokens
**      into token list class object when number of required tokens
**      exceed maximum.
**
**      INPUT:      address of token list object [R]
** 
**              IMPLICIT:
** 
**      RETURNS:
*/

static void TokGrowList(TOKoLIST *tokList)
{
  TOKoTOKEN *tokenSave;
  INT4 offsetRead,
       offsetWrite;

  tokList->size *= 2;
  offsetRead = (INT4) (tokList->currTokenRead - tokList->first);
  offsetWrite = (INT4) (tokList->currTokenWrite - tokList->first);
  tokenSave=tokList->first;
  tokList->first = (TOKoTOKEN *)
                   realloc(tokList->first, tokList->size*sizeof(TOKoTOKEN));
  if(!tokList->first)
    _ErrExit2 (e__allocfail, "tokList list");
  if (tokList->first != tokenSave && tokList->dict)
    DictOffset (tokList->dict, displ (tokList->first, tokenSave));

  tokList->currTokenRead = tokList->first + offsetRead;
  tokList->currTokenWrite = tokList->first + offsetWrite;
  tokList->last = tokList->first + tokList->size;
}

/* * * * * * * * * * Public Domain  * * * * * * * * * * * * * * * */

/**api* TokGetList **********************************************************
** 
**      Create and initialise a new token list object if the name is not
**      in the list otherwise return pointer to existing token list.
**      If token list class object's address is NULL it would be created. 
** 
**      INPUT:      name of token list [R]
**                  address of token list object [R] (initially NULL)
** 
**              IMPLICIT:
** 
**      RETURNS:    token list object
*/

TOKoLIST *TokGetList(char *name, TOKoLIST **tokList)
{
  static INT4  TokListClassId = 0;
  TOKoLIST *tmp;

  if(!TokListClassId)
    LstManageClass(&TokListClassId, sizeof(TOKoLIST), NULL, ListKill,ListDump);

  if (!LstHashSearch((void **) tokList, name)) {
    LstNewNamed((void **) tokList, TokListClassId, name);
    tmp = *tokList;
    tmp->first = 
      (TOKoTOKEN *) calloc(1, TOKxMAXLISTSIZE * sizeof(TOKoTOKEN));
    if (!tmp->first)
      _ErrExit2 (e__allocfail, "tokList list");
    tmp->isActive = FALSE;
    tmp->size = TOKxMAXLISTSIZE;
    tmp->style =  TOKxANY;
    tmp->buff = NULL;
    tmp->currTokenWrite = tmp->first;
    tmp->currTokenRead = tmp->first;
    tmp->last = tmp->first + tmp->size;
  }
  return *tokList;
}

/**api* TokFindList **********************************************************
** 
**      Return pointer to token list object if the name is not
**      in the list exit program with error
** 
**      INPUT:      name of token list [R]
**                  address of token list object [R]
** 
**              IMPLICIT:
** 
**      RETURNS:    token list object
*/

TOKoLIST *TokFindList(char *name, TOKoLIST **tokList)
{
  if( !LstHashSearch((void **) tokList, name) )
   _ErrExit2(e__toklistFind, name);
  return (*tokList);
}

/**api* TokIsListActive *****************************************************
** 
**      Return "isActive" attribute of token list object. Token list is
**      "active" when read/write operations are allowed with this token
**      list
** 
**      INPUT:      address of token list object [R]
** 
**              IMPLICIT:
** 
**      RETURNS:    isActive attribute
*/

INT4 TokIsListActive(TOKoLIST *tokList)
{
  return(tokList->isActive);
}

/**api* TokIsListEmpty ******************************************************
** 
**      Check presence of token(s) in token list object.
** 
**      INPUT:      address of token list object [R]
** 
**              IMPLICIT:
** 
**      RETURNS:    TRUE
**                  FALSE
*/

INT4 TokIsListEmpty(TOKoLIST *tokList)
{
  return(tokList->first == tokList->currTokenWrite);
}

/**api* TokIsListStart ******************************************************
** 
**      Check if the current token to read is the first in token list object.
** 
**      INPUT:      address of token list object [R]
** 
**              IMPLICIT:
** 
**      RETURNS:    TRUE
**                  FALSE
*/

INT4 TokIsListStart(TOKoLIST *tokList)
{
  return(tokList->first == tokList->currTokenRead);
}

/**api* TokSetStyle *********************************************************
**
**      Set style attribute for the token list object.
** 
**      INPUT:      address of token list object [R]
**		    type of token list [R]
** 
**              IMPLICIT:
** 
**      RETURNS:
*/

void TokSetStyle(TOKoLIST *tokList, char *style)

{
  if(tokList->style == TOKxANY) {
    switch(tolower(style[0])) {
    case 'c': /* copy */
      tokList->style =  TOKxCOPY;
      tokList->buff = BuffInit(tokList->buff, TOKxMAXTOKBUFFSIZE);
      break;
    case 'e': /* echo */
      tokList->style =  TOKxECHO;
      break;
    case 'f': /* file */
      tokList->style =  TOKxFILE;
      break;
    default:
      _ErrExit2 (e__unknownoption, style);
    }
  }
}

/**api* TokSetFile **********************************************************
**
**      Initialize attributes for the token list object in special case
**      when token list is associated with standard input stream (file).
** 
**      INPUT:      address of token list object [R]
**		    address of file object [R]
** 
**              IMPLICIT:
** 
**      RETURNS:
*/

void TokSetFile(TOKoLIST *tokList, FILEo *file)
{
  tokList->file = file;
  tokList->isActive = TRUE;
  tokList->first->code= TOKxUNDEFCODE;
  tokList->first->isTerminal = FALSE;
  tokList->currTokenRead = tokList->first;
  tokList->currTokenWrite = tokList->first + 1;
  tokList->first->length = 0;
  tokList->style = TOKxFILE;
}

/**api* TokResetList ********************************************************
**
**      Deactivate the token list object.
** 
**      INPUT:      address of token list object [R]
** 
**              IMPLICIT:
** 
**      RETURNS:
*/

void TokResetList(TOKoLIST *tokList)
{
  tokList->isActive = FALSE;
  if (tokList->dict)
    DictClear (&tokList->dict);
  if(tokList->buff)
    BuffReset(tokList->buff);
  tokList->currTokenWrite = tokList->first;
  tokList->currTokenRead = tokList->first;
}

/**api* TokResetAllLists ****************************************************
**
**      Deactivate all token list objects.
** 
**      INPUT:      address of token list object [R]
** 
**              IMPLICIT:
** 
**      RETURNS:
*/

void TokResetAllLists(TOKoLIST *tokList)
{
  if (tokList) {
    LstFirst((void **) &tokList);
    do {
      TokResetList(tokList);
    }while(LstNext((void **) &tokList));
  }
}

/**api* TokRewindList *******************************************************
**
**      Set current input token in the token list objects at the beginning.
** 
**      INPUT:      address of token list object [R]
** 
**              IMPLICIT:
** 
**      RETURNS:
*/

void TokRewindList(TOKoLIST *tokList)
{
  tokList->currTokenRead = tokList->first;
}

/**api* TokDeleteList *******************************************************
**
**      Delete the token list object.
** 
**      INPUT:      address of token list object [R]
** 
**              IMPLICIT:
** 
**      RETURNS:
*/

void TokDeleteList(TOKoLIST *tokList)
{
  LstDelete((void **) &tokList);
}

/**api* TokDeleteAllLists ***************************************************
**
**      Delete all token list objects.
** 
**      INPUT:      address of token list object [R]
** 
**              IMPLICIT:
** 
**      RETURNS:
*/

void TokDeleteAllLists(TOKoLIST *tokList)
{
  LstDeleteAll((void **) &tokList);
}

/**api* TokAdd **************************************************************
**
**      Add a new token to the token list objects.
** 
**      INPUT:      address of the token list object [R]
** 		    address of the token [R]
** 		    length of the token [R]
** 		    code of the token [R]
** 
**      RETURNS:    new token
*/

TOKoTOKEN *TokAdd(TOKoLIST *tokList, char* tokStr, INT4 length, INT4 code)

{
  TOKoTOKEN *token;

  if(tokList->style == TOKxANY || tokList->style == TOKxFILE)
    _ErrExit2 (e__toktablenotwritable, tokList->name);
  tokList->isActive = TRUE;
  if(tokList->currTokenWrite >= tokList->last)
     TokGrowList(tokList);
   token = tokList->currTokenWrite;
   if(tokList->style == TOKxCOPY) {
     token->buffOffset = BuffGetCurrOffset(tokList->buff);
     BuffCopyNChar(tokList->buff, tokStr, length); 
     token->tokStr = NULL;
   }
   else
     token->tokStr = tokStr;
   token->isTerminal = TRUE;
   token->length = length;
   token->code = code;
   tokList->currTokenWrite++;
   return token;
} 


static int TokHash (TOKoTOKEN *tok, int max)
{
  UINT4 sum;

  sum = CharHashLen (TokGetString (tokListGbl, tok), TokGetLength (tok));
  _hash (sum, (UINT4) TokGetCode (tok));
  return sum%max;
}

static Int4 TokEqual (TOKoTOKEN *a, TOKoTOKEN *b)
{
  Int4 len, k;
  char *as, *bs;

  if ((len = TokGetLength (a)) == TokGetLength (b) &&
       TokGetCode (a) == TokGetCode (b)) {
    for (k=0, as=TokGetString (tokListGbl, a), 
	   bs=TokGetString (tokListGbl, b); k<len; k++)
      if (tolower(as[k]) != tolower(bs[k]))
	return 0;
    return 1;
  }
  else
    return 0;
}




/**api* TokAddUniq **********************************************************
**
**      Same as TokAdd except adds only if string does not exist in 
**      the token table.
** 
**      INPUT:      address of the token list object [R]
** 		    address of the token [R]
** 		    length of the token [R]
** 		    code of the token [R]
** 
**              IMPLICIT:
** 
**      RETURNS:    TRUE if token was added
**                  FALSE otherwise
*/

TOKoTOKEN *TokAddUniq (TOKoLIST *tokList, char* tokStr, INT4 length, INT4 code)
{
  static CLASSoDICT cl={(ValComparer)TokEqual, 
			(ValHasher)TokHash, 
			(KeyAccessor)KeyItself, 0, TRUE};
  TOKoTOKEN token, **tmp;

  if (!tokList->dict)
    tokList->dict = DictCreate (&cl);

  tokListGbl = tokList;
  memset (&token, 0, sizeof (TOKoTOKEN));
  token.tokStr = tokStr;
  token.isTerminal = TRUE;
  token.length = length;
  token.code = code;
  if (!DictWith (tokList->dict, &token)) {
    tmp = &DictAdd (&tokList->dict, &token, TOKoTOKEN*);
    *tmp = TokAdd (tokList, tokStr, length, code);
    return *tmp;
  }
  return NULL;
} 




/**api* TokAppend ***********************************************************
**
**      Append a token to the current output token in the token list objects.
** 
**      INPUT:      address of the token list object [R]
** 		    address of the token [R]
** 		    length of the token [R]
** 		    code of the token [R]
** 
**              IMPLICIT:
** 
**      RETURNS:    TRUE if token was appended
**                  FALSE otherwise
*/

INT4 TokAppend(TOKoLIST *tokList, char* tokStr, INT4 length)

{
   if(tokList->isActive == FALSE)
     return(FALSE);
   if(tokList->style == TOKxECHO) {
     (tokList->currTokenWrite-1)->isTerminal = FALSE;
     TokAdd(tokList, tokStr, length, (tokList->currTokenWrite-1)->code);
   }
   else {
     (tokList->currTokenWrite-1)->length += length;
     BuffCopyNChar(tokList->buff, tokStr, length);
   }
   return(TRUE);
} 


/**api* TokReplaceIn ********************************************************
** 
**      Replace a part of the current output token on target string
** 
**      INPUT:      address of the token list object [R]
** 		    start position of the replacement in the token [R]
** 		    length of the replacement [R]
** 		    replacement string [R]
** 
**              IMPLICIT:
** 
**	RETURN:     shift between new and old buffers, if new was reallocated
*/

INT4 TokReplaceIn(TOKoLIST *tokList, char *tag, INT4 tagLen, char *repStr,
                   INT4 repLen)
{
  TOKoTOKEN *token;
  char      *saveBuffPtr;
  INT4       shift, diff;

  if (tokList->style == TOKxFILE) {
    SmReplace (tokList->file->ln, tag, tagLen, repStr, repLen);
    return 0;
  }
  else if (tokList->style == TOKxCOPY) {
    saveBuffPtr = BuffGetPtr(tokList->buff);
    BuffReplace(tokList->buff, tag, tagLen, repStr, repLen);
    shift = repLen - tagLen;
    if(shift) {
      /* the token where the replacement takes place is not the current but
	 one prior! */
      (tokList->currTokenRead-1)->length += shift;
      token = tokList->currTokenRead-1;
      while(token++ < tokList->currTokenWrite)
	token->buffOffset += shift;
    }
    diff = (Int4)(BuffGetPtr(tokList->buff)-saveBuffPtr);
    return diff;
  }
  else {
    _ErrExit2(e__toklistReplace, tokList->name);
  }
}

/**api* TokCurrent *********************************************************
**
**      Return pointer to the current input token
** 
**      INPUT:      address of token list object [R]
** 
**              IMPLICIT:
** 
**      RETURNS:    address of the current input token
*/

TOKoTOKEN *TokCurrent(TOKoLIST *tokList)
{
  return(tokList->currTokenRead);
}

/**api* TokGet ************************************************************** 
**  
**      Return pointer to the current input token
** 
**      INPUT:      address of token list object [R]
** 
**              IMPLICIT:
** 
**      RETURNS:   pointer to the next token if it exists
**                 NULL otherwise
*/  
      
TOKoTOKEN *TokGet(TOKoLIST *tokList)
{
  TOKoTOKEN *token;

  if(!tokList->isActive)
    return(NULL);
  token = tokList->currTokenRead;
  if(tokList->style == TOKxFILE) {
    if (!tokList->file || FileReadLn(tokList->file) == NULL)
      return(NULL);
    token->tokStr = tokList->file->ln;
    token->length = strlen(tokList->file->ln);
    return(token);
  }
  if(token < tokList->currTokenWrite) {
    tokList->currTokenRead = token + 1;
    return(token);
  }
  else
    return(NULL);
}

/**api* TokGet2 ************************************************************** 
**  
**      Return pointer to the current input token.
**      If token list object associated with standard input stream
**      new line will be read if current is empty.
** 
**      INPUT:      address of token list object [R]
** 
**              IMPLICIT:
** 
**      RETURNS:   pointer to the next token if it exists
**                 NULL otherwise
*/  
      
TOKoTOKEN *TokGet2(TOKoLIST *tokList)
{
  TOKoTOKEN *token;

  if(!tokList->isActive)
    return(NULL);
  token = tokList->currTokenRead;
  if(tokList->style == TOKxFILE && tokList->file) {
    if (!(*tokList->file->ln))
      if(FileReadLn(tokList->file) == NULL)
	return(NULL);
    token->tokStr = tokList->file->ln;
    token->length = strlen(tokList->file->ln);
    return(token);
  }
  if(token < tokList->currTokenWrite) {
    tokList->currTokenRead = token + 1;
    return(token);
  }
  else
    return(NULL);
}

/**api* TokGetMore ********************************************************** 
**  
**      Return pointer to the next input token when current token
**      consist of more that one fragment.
**
**      INPUT:      address of token list object [R]
** 
**              IMPLICIT:
** 
**      RETURNS:    pointer to the next fragment of Multioken if it exists
**                  NULL otherwise
*/  
      
INT4 TokGetMore(TOKoLIST *tokList, char **ptr, INT4 *length)
{
  TOKoTOKEN *token;

  if( TokIsMultiTok(tokList) ) {
    if((token = TokGet(tokList))){
      *length = token->length;
      *ptr = token->tokStr;
      return(TRUE);
    }
  }
  return(FALSE);
}

/**api* TokGetFirst *********************************************************
**
**      Return pointer to the first input token
** 
**      INPUT:      address of token list object [R]
** 
**              IMPLICIT:
** 
**      RETURNS:   pointer to the first token
*/

TOKoTOKEN *TokGetFirst(TOKoLIST *tokList)
{
  tokList->currTokenRead = tokList->first;
  return(TokGet2(tokList));
}

/**api* TokNext *************************************************************
** 
**      Return pointer to the next input token. If counter equals to zero
**      return address of the first token
**
**      INPUT:      address of token list object [R]
** 		    address of counter [W]
** 
**              IMPLICIT:
** 
**      RETURNS:   pointer to the next(first) token
*/

TOKoTOKEN *TokNext(TOKoLIST *tokList, INT4 *count)
{
  
  (*count)++;
  if(*count == 1)
    return(TokGetFirst(tokList));
  else 
    return(TokGet(tokList));
} 

/**api* TokNextWithCode *****************************************************
** 
**      Return pointer to the next input token that has required code.
**      If counter equals to zero start search form the first token.
**
**      INPUT:      address of token list object [R]
** 		    address of counter [W]
** 		    code of input token [R]
** 
**              IMPLICIT:
** 
**      RETURNS:   pointer to the next token if it exists
**                 NULL otherwise
*/

TOKoTOKEN *TokNextWithCode(TOKoLIST *tokList, INT4 code, INT4 *count)
{
  TOKoTOKEN *token;

  if(*count == 0)
    token = TokGetFirst(tokList);
  else 
    token = TokGet(tokList);
  (*count)++;
  while( token ) {
    if(token->code == code || code == TOKxUNDEFCODE)
      return(token);
    else
      token = TokGet(tokList);
  }
  return(NULL);
} 

/**api* TokGetString ********************************************************
** 
**      Return pointer to the string content of the token
**
**      INPUT:      address of token list object [R]
** 		    address of token [R]
** 
**              IMPLICIT:
** 
**      RETURNS:   pointer to the string
*/

char *TokGetString(TOKoLIST *tokList, TOKoTOKEN *tokenRead)
{
  if (tokenRead->tokStr)
    return tokenRead->tokStr;

  else if(tokList->style == TOKxCOPY)
    return(BuffGetPtr(tokList->buff)+tokenRead->buffOffset);
  else
    return NULL;
}

/**api* TokGetStringCopy ****************************************************
** 
**      Return copy to the string content of the token.
**      Space for the copy of the string allocated in static buffer object.
**      The content of the string is stable until next call of the function.
**
**      INPUT:      address of token list object [R]
** 		    address of token [R]
** 
**              IMPLICIT:
** 
**      RETURNS:   pointer to the string
*/

char *TokGetStringCopy(TOKoLIST *tokList, TOKoTOKEN *token)
{
 
  static SMoBUFF *buffTokStr = NULL;
  
  buffTokStr = BuffInit(buffTokStr, TOKxMAXTOKBUFFSIZE);

  if(tokList->style == TOKxCOPY) {
    BuffCopyNChar(buffTokStr,
       BuffGetPtr(tokList->buff)+token->buffOffset, token->length);
    BuffCopyChar(buffTokStr, '\0');
  }
  else {
    BuffCopyNChar(buffTokStr, token->tokStr, token->length);
    while( !token->isTerminal ) {
      token++;
      BuffCopyNChar(buffTokStr, token->tokStr, token->length);
    }
    BuffCopyChar(buffTokStr, '\0');
  }
  return(BuffGetPtr(buffTokStr));
}

/**api* function *************************************************************
** 
**      Returns a string value with content of the token which must be
**      deleted by the user. 
**
**      INPUT:      address of token list object [R]
** 		    address of token [R]
** 
**      RETURNS:    new STRv with token
*/

STRv TokGetStrv (TOKoLIST *tokList, TOKoTOKEN *tok)
{
  STRv s;

  if (tokList->style == TOKxCOPY)
    s = StrNCpyS (BuffGetPtr(tokList->buff)+tok->buffOffset, tok->length);
  else {
    s = StrNCpyS (tok->tokStr, tok->length);
    while (!tok->isTerminal) {
      tok++;
      StrAppN (&s, tok->tokStr, tok->length);
    }
  }
  return s;
}

/**api* TokGetCode **********************************************************
** 
**      Get the code of the current output token
**
**      INPUT:      address of token [R]
** 
**              IMPLICIT:
** 
**      RETURNS:    value of the token code
*/

INT4 TokGetCode(TOKoTOKEN *tokenRead)
{
  return(tokenRead->code);
}

/**api* TokGetLength ********************************************************
** 
**      Get the length of the current output token
**
**      INPUT:      address of token [R]
** 
**              IMPLICIT:
** 
**      RETURNS:    value of the token length
*/

INT4 TokGetLength(TOKoTOKEN *tokenRead)
{
  return(tokenRead->length);
}

/**api* TokIsMultiTok ********************************************************
** 
**      Check, does specified token consist of fragments
**
**      INPUT:      address of token [R]
** 
**              IMPLICIT:
** 
**      RETURNS:    TRUE if token consists from fragment
**                  FALSE otherwise
*/ 

INT4 TokIsMultiTok(TOKoLIST *tokList)
{
  if(tokList->style == TOKxFILE)
    return(TRUE);
  if(tokList->currTokenRead < tokList->currTokenWrite)
    return(!(tokList->currTokenRead-1)->isTerminal);
  else
    return(FALSE);
}

/**api* TokIsUniq ***********************************************************
** 
**      Check, does specified token is unique
**
**      INPUT:      address of token [R]
** 
**              IMPLICIT:
** 
**      RETURNS:    TRUE if string is unique in tokList
**                  FALSE otherwise
*/ 

INT4 TokIsUniq(TOKoLIST *tokList, char *string, INT4 len, INT4 code)
{
  TOKoTOKEN *token;                                     
  INT4       count;

  if(tokList->style == TOKxFILE)
    _ErrExit2(e__toklistIsUniq, tokList->name);
  count = 0;
  while( (token = TokNextWithCode(tokList, code, &count)) )
    if( len == token->length &&
    strncmp(TokGetString(tokList, token), string, len) == 0)
      return(FALSE);
  return(TRUE);
}

/**api* TokPrintList ********************************************************
**
** 
**      Print out all tokens with particular code from specify token list
**      object
**
**      INPUT:      address of token list object [R]
** 		    token code [R]
** 
**              IMPLICIT:
** 
**      RETURNS:
*/

void TokPrintList(TOKoLIST *tokList, INT4 code)
{
  TOKoTOKEN *token;
  INT4       count;

  printf("TokList: %s\n", tokList->name);
  count = 0;
  while( (token = TokNextWithCode(tokList, code, &count)) )
    printf("TOKEN%2d: |%s| -- CODE: %d\n", count, 
      TokGetStringCopy(tokList, token),
      TokGetCode(token) );
}

static SMoBUFF* buff=NULL;

static void* BuffToKey(DictElem* e) {
    Word offs=cast(*e, Word)-TOKxCODESHIFT;
    return BuffGetPtr(buff)+offs;
}

static CLASSoDICT CodeDictClass = {
    (ValComparer)strequal,
    (ValHasher)strhash, 
    (KeyAccessor)BuffToKey, 
    NULL, 
    FALSE
};

/**api* TokStrToCode ********************************************************
**
**      Token list class has global dictionary of token codes defined as
**      names. Function converts name to integer and stores unique names
**      in dictionary object.
** 
**      INPUT:      name of token code [R]
** 
**              IMPLICIT:
** 
**      RETURNS:    integer value of the code
*/

INT4 TokStrToCode(char* str) {

  static DICTv codeNames=0;

  IntOrPtr code;
  char** p;

  if (!codeNames) {
    codeNames=DictCreate(&CodeDictClass);
    buff=BuffInit(buff, 512);
  }
  p=&DictSet(&codeNames, str, char*);
  if (*p) 
    code=(IntOrPtr)*p; /* the string is already in dictionary */
  else {
    code=BuffGetCurrOffset(buff)+TOKxCODESHIFT; /* new string */
    *p=(DictElem)code;
    BuffCopyString(buff, str);
    BuffCopyChar(buff,'\0');
  }
  return(code);
}


/**api* TokStrToCode ********************************************************
**
**      Token list class has global dictionary of token codes defined as
**      names. Function converts integer to name of the code using the
**      dictionary.
** 
**      INPUT:      integer value of the code [R]
** 
**              IMPLICIT:
** 
**      RETURNS:    name of token code 
*/

char* TokCodeToStr(INT4 code) {
  return(BuffGetPtr(buff)+(code-TOKxCODESHIFT));
}

/**api* TokGetBuff ***********************************************************
**
**      Returns the start address of the buffer of the token table.
**      Useful to memorize in order to keep track of possible reallocation
**      events.
** 
**      INPUT:      the token list object [R]
** 
**              IMPLICIT:
** 
**      RETURNS:    start address of token list buffer 
*/

char* TokGetBuff (TOKoLIST *tokList) {
  return tokList->buff ? BuffGetPtr(tokList->buff) : NULL;
}

/**api* function **************************************************************
**
**      Returns the address of the token list name.
**
**      INPUT:      the token list object [R]
** 
**      RETURNS:    address of the token list name
*/

char *TokListGetName (TOKoLIST *tokList)
{
  return tokList->name;
}


/**api* function **************************************************************
**
**      Returns the address of the token list name.
**
**      INPUT:      the token list object [R]
** 
**      RETURNS:    address of the token list name
*/

char *TokListPtrGetName (TOKoLIST **tokList)
{
  return (*tokList)->name;
}

n list name.
**
**      INPUT:      the token list object [R]
** 
**      RETURNS:    address of the token list name
*/

char *TokListGetName (TOKoLIST *tokList)
{
  return tokList->name;
}


/**api* function ****************************************srs/src/toklist.h
**    
**    $RCSfile: toklist.h,v $
**    $Revision: 1.8 $
**    $Date: 1997/03/17 23:24:03 $
**    $Author: srs $
**    
**    $Locker:  $ 
**    $State: Exp $
**                  
**                  
**                  Copyright by Thure Etzold
**             
**             Author: Anatoly Ulyanov
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387451
**                     Email: ulyanov@embl-heidelberg.de
**
*/

#define TOKxCODESHIFT       1000001
#define TOKxMAXNAMESIZE     40
#define TOKxMAXTOKBUFFSIZE  20
#define TOKxMAXHASHSIZE     10000
#define TOKxMAXLISTSIZE     512

#define TOKxUNDEFCODE       -1

enum style      {TOKxANY, TOKxECHO, TOKxCOPY, TOKxFILE};

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

typedef struct TOKoTOKEN {
  char               *tokStr;
  INT4                buffOffset;
  INT4                isTerminal;
  INT4                length;
  INT4                code;
  char               *codeName;                 /* name of the code */
} TOKoTOKEN;

typedef struct TOKoLIST   {
  char               *list;
  int                 listId;
  char                name[TOKxMAXNAMESIZE];
  INT4                isActive;                 /* FALSE if empty */
  INT4                size;
  enum style          style;                    /* TOKxCOPY or TOKxECHO */
  struct TOKoTOKEN   *first;
  struct TOKoTOKEN   *currTokenRead;
  struct TOKoTOKEN   *currTokenWrite;
  struct TOKoTOKEN   *last;
  struct DICTo       *dict;
  FILEo              *file;
  SMoBUFF            *buff;
} TOKoLIST;


TOKoLIST  *TokGetList(char *name, TOKoLIST **tokList);
TOKoLIST  *TokFindList(char *name, TOKoLIST **tokList);
TOKoTOKEN *TokCurrent(TOKoLIST *tokList);
TOKoTOKEN *TokGet(TOKoLIST *tokList);
TOKoTOKEN *TokGetFirst(TOKoLIST *tokList);
TOKoTOKEN *TokNext(TOKoLIST *tokList, INT4 *count);
TOKoTOKEN *TokNextWithCode(TOKoLIST *tokList, INT4 code, INT4 *count);
TOKoTOKEN *TokAdd(TOKoLIST *tokList, char* tokStr, INT4 length, INT4 code);
TOKoTOKEN *TokAddUniq(TOKoLIST *tokList, char* tokStr, INT4 length, 
		      INT4 code);
INT4       TokAppend(TOKoLIST *tokList, char* tokStr, INT4 length);
INT4       TokGetCode(TOKoTOKEN *tokenRead);
INT4       TokGetLength(TOKoTOKEN *tokenRead);
INT4       TokGetMore(TOKoLIST *tokList, char **ptr, INT4 *len);
INT4       TokIsListActive(TOKoLIST *tokList);
INT4       TokIsListEmpty(TOKoLIST *tokList);
INT4       TokIsListStart(TOKoLIST *tokList);
INT4       TokIsUniq(TOKoLIST *tokList, char *string, INT4 len, INT4 code);
INT4       TokIsMultiTok(TOKoLIST *tokList);
INT4       TokReplaceIn(TOKoLIST *tokList, char *s, INT4 l, char *s1, INT4 l1);
INT4       TokStrToCode(char *codeStr);
char      *TokCodeToStr(INT4 code);
char      *TokGetString(TOKoLIST *tokList, TOKoTOKEN *tokenRead);
char      *TokGetStringCopy(TOKoLIST *tokList, TOKoTOKEN *tokenRead);
struct STRo* TokGetStrv (TOKoLIST *tokList, TOKoTOKEN *tok);
void       TokDeleteAllLists(TOKoLIST *tokList);
void       TokDeleteList(TOKoLIST *tokList);
void       TokPrintList(TOKoLIST *tokList, INT4 code);
char*      TokListGetName (TOKoLIST *tokList);
char*      TokListPtrGetName (TOKoLIST **tokList);
void       TokResetAllLists(TOKoLIST *tokList);
void       TokResetList(TOKoLIST *tokList);
void       TokRewindList(TOKoLIST *tokList);
void       TokSetFile(TOKoLIST *tokList, FILEo *file);
void       TokSetStyle(TOKoLIST *tokList, char *style);
char*      TokGetBuff (TOKoLIST *tokList);



TOKoLIST *tokList);
void       TokDeleteLisrs/src/transl.h
**
**    $RCSfile: transl.h,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:17:33 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**             from ODD file: "srssdl:srswin.sdl"
**   date of ODD compilation: 12-JAN-1996 18:16
**
*/



#ifndef _SEQoTranslTable
#define _SEQoTranslTable
typedef struct SEQoTranslTable {
  char                    *name;         /* Name of translation table. */
  char                    *code;         /* Short name of translation table. */
  INT4                    id;            /* Numeric id. */
  char                    *aa;           /* Amino acid encoded by triplett. */
  char                    *aaAlt;        /* Alternative (edited) Amino acid
                                            encoded by triplett. */
  char                    *saa;          /* Amino acid encoded by triplett at
                                            translation start. */
} SEQoTranslTable;
#endif

#ifdef _INITOBJS

SEQoTranslTable    translTable[] = {
    {"Standard", "SGC0", 1,
    "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "",
    "-----------------------------------M----------------------------"},
    {"Vertebrate Mitochondrial", "SGC1", 2,
    "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG", "",
    "--------------------------------MMMM---------------M------------"},
    {"Yeast Mitochondrial", "SGC2", 3,
    "FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "",
    "-----------------------------------M----------------------------"},
    {"Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma",
    "SGC3", 4,
    "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "",
    "--MM---------------M------------MMMM---------------M------------"},
    {"Invertebrate Mitochondrial", "SGC4", 5,
    "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG", "",
    "---M----------------------------M-MM---------------M------------"},
    {"Ciliate Macronuclear; Dasycladacean Nuclear", "SGC5", 6,
    "FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "",
    "-----------------------------------M----------------------------"},
    {"Echinoderm Mitochondrial", "SGC8", 9,
    "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "",
    "-----------------------------------M----------------------------"},
    {"Euplotid Macronuclear", "SGC9", 10,
    "FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "",
    "-----------------------------------M----------------------------"},
    {"Bacterial", "", 11,
    "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "",
    "---M---------------M------------M--M---------------M------------"},
    {"Alternative Yeast Nuclear", "", 12,
    "FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "",
    "-------------------M---------------M----------------------------"},
    {"Ascidian Mitochondrial", "", 13,
    "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG", "",
    "-----------------------------------M----------------------------"},
    {"Flatworm Mitochondrial", "", 14,
    "FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "",
    "-----------------------------------M----------------------------"},
    {"Blepharisma Macronuclear", "", 15,
    "FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "",
    "-----------------------------------M----------------------------"}
};

#endif
PPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG", "",
    "-----------------------------------M----------------------------"},
    {"Flatworm Mitochondrial", "", 14,
    "FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "",
    "-----------------------------------M----------------------------"},
    {"Blepharisma Macronuclear", "", 15,
    "FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "",
    "---------------srs/src/trembl.c
char trembl_ID[] = "$Id: trembl.c,v 1.1 1996/05/06 15:17:34 srs Exp $";
/*
**
**    $Source: /homes/srs/cvsroot/srs/src/trembl.c,v $
**    $Revision: 1.1 $
**    $Date: 1996/05/06 15:17:34 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  Copyright by Thure Etzold
**
**             Author: Gerald Schaefer + Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     69012 Heidelberg, Germany
**                     Tel: 06221 387372  
**                     Email: schaefer@embl-heidelberg.de
**                            etzold@embl-heidelberg.de
**
**
**    Requires: 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    program translates all CDS features of EMBL sequences.
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/


#include <stdio.h>
#include <stdarg.h>
#include "srs.h"
#include "lst.h"
#define _INITOBJS
#include "transl.h"

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**
**  Object that contains the text of a complete data-field.
**  The first two attributes are initialized and maintained by
**  the list module. The third attribute must be initialized
**  by the application modules. If the application module never
**  uses a search by name this attribute may be skipped.
*/

typedef struct {
    char *internal;   /* the first three attributes are necessary  */
    INT4 type_id;     /* for all objects to be managed by the list */
    char *name;       /* dynamic (flexible) name */
/*    char name[20];    /* feature name or refnumber */
    SMoBUFF *buff;    /* pointer to description */
} FIELDo;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**
**  Object with all information from entry that is needed to generate 
**  a trembl entry.
*/

typedef struct {
  ENTRYo *entry;
  SMoBUFF *id, *accession, *definition, *organism, *featureCurr, *refCurr;
  FIELDo *links;         /* managed by List Module */
  FIELDo *features;      /* managed by List Module */
  FIELDo *references;    /* managed by List Module */
  SEQo *entrySeq;        /* complete entry sequence */
  SEQo *resultSeq;       /* CDS sequence */
  SEQo *protSeq;         /* AA sequence  */
  SLBoFEATURE *feature;  /* feature description */
  INT4 genCode;
  char *errorMessage;
} CDSoSTORE;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  external or module wide variables
*/

static INT4 cnt_syntaxerror=0, cnt_trerr=0, 
            cnt_firstcodonerror=0, cnt_correct=0;
extern INT4 global_before_f;
static char *geneticCodeTable[] = {
  "Standard",                     /* id 1 */
  "Vertebrate Mitochondrial",     /* id 2 */
  "Yeast Mitochondrial",          /* id 3 */
  "Mold Mitochondrial and Mycoplasma",  /* id 4 */
  "Invertebrate Mitochondrial",         /* id 5 */
  "Ciliate Macronuclear and Daycladacean",  /* id 6 */
  "Protozoan Mitochondrial",      /* id 7 */
  "obsolete",                     /* id 8 */
  "Echinoderm Mitochondrial",     /* id 9 */
  "Euplotid Macronuclear",        /* id 10 */
  "Eubacterial",                  /* id 11 */
  "Group II yeasts"               /* id 12 */
};


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  static functions
*/

static void FieldDump (FILE *file, void *obj);
static void FieldInit (void *obj);
static void FieldKill (void *obj);
static FILE *outFile=NULL;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  default function for printing lines
*/

static INT4 CDSPrintF (char *formatStr, ...)
{
    va_list ap;

    va_start (ap, formatStr);
    vfprintf (outFile, formatStr, ap);
    va_end (ap);

    if (formatStr[strlen (formatStr) -1] != '\n')
    fprintf (outFile, "\n");

    return 1;
}


/**api* FieldCopyList *********************************************************
**
**      gets a new initialized feature object;
**
**      INPUT:      pointer to address of feature object [W]
**                  pointer to buffer object [R]
**              IMPLICIT:
**
**      RETURNS:
*/

INT4 FieldCopyList (FIELDo **fieldList, SMoBUFF *field)
{
  static INT4 fieldClass_id=0;
  char name[40];
  int rv=0;

  if (!fieldClass_id)
    LstManageClassFlex (&fieldClass_id, sizeof(FIELDo), FieldInit, FieldKill, 
		    FieldDump);

  rv = LstNew ((void**) fieldList, fieldClass_id);
  (*fieldList)->buff = BuffDuplicate (field);

  /* get the first word after the line code: feature name or reference no */
  *name = '\0';  /* reset name */
  sscanf (field->buff, "%*[^ ] %s", name);
 
  if (name[strlen(name)-1] == ';')
    name[strlen(name)-1] = '\0'; /* remove ; at the end */
  LstChangeObjectName(*fieldList, name);

  return rv;
}


/****** FieldDump ***********************************************************
**
**      dumps all information belonging to the specified object.
**      This is the print function set through LstManageClass
**      for ftstype objects (see FtsNew).
**
**      INPUT:      address of an object [R]
**              IMPLICIT:
**
**      RETURNS:    nothing
*/

static void FieldDump (FILE *file, void *obj)
{
  FIELDo *tmp = (FIELDo*)obj;

  if (tmp->buff)
    BuffPrint (file, tmp->buff);
}


/****** FieldInit **********************************************************
**
**      initializes the specified object.
**      This is the init function set through LstManageClass
**      for ftstype objects (see FtsNew).
**
**      INPUT:      address of an object [R]
**              IMPLICIT:
**
**      RETURNS:    nothing
*/

static void FieldInit (void *obj)
{
  FIELDo *tmp = (FIELDo*) obj;
  
  tmp->buff = NULL;
}


/****** FieldKill **********************************************************
**
**      deletes the specified object.
**      This is the delete function set through LstManageClass
**      for ftstype objects (see FtsNew).
**
**      INPUT:      address of an object [R]
**              IMPLICIT:
**
**      RETURNS:    nothing
*/

static void FieldKill(void *obj)
{
  FIELDo *tmp = (FIELDo*) obj;
    
  if (tmp->buff)
    BuffDelete(tmp->buff);
}


INT4 CheckTranslationErrors (char *pseq)
{
  INT4 trerr=0;
  for ( ; *pseq; pseq++)
    if (*pseq == '*') trerr++;

  return trerr;
}


INT4 PrintMessage (MSGo *msg) 
{ 
  if (msg->msg_code == i__readingname)
    putc ('.', stderr); 

  switch (msg->msg_code) {
  case i__wroteset:
    return 0;
    
  default:
    if (msg->msg_t != MSGxINFO) 
      fprintf (stderr, "ERROR: %s, %s\n", msg->primsg, msg->secmsg);
    else
      fprintf (stderr, "%s\n", msg->secmsg);
    return 1;
  }
}

static INT4 PrintLine (char *formatStr, ...)
{
  va_list ap;

  va_start (ap, formatStr);
  vfprintf (stderr, formatStr, ap);
  va_end (ap);

  if (formatStr[strlen (formatStr) -1] != '\n')
    fprintf (stderr, "\n");
  
  return 1;
}


/****** TremblErrorPrint ******************************************************
**
**      prints information about entry that was rejected;
**
**      INPUT:      address of an entry object [R]
**              IMPLICIT:
**
**      RETURNS:    nothing
*/

static void TremblErrorPrint (CDSoSTORE *val)
{
  INT4 featureNumber=0;
  char id[20]="", accno[20]="";

  LstFirst((void**) &val->protSeq);  /* print first translation */

  /*
  ** get the entry-ID and accession number 
  ** and print the ID line and the link to the EMBL parent entry
  */

  sscanf (val->id->buff, "%*[^ ] %[A-Z0-9]", id);
  sscanf (val->accession->buff, "%*[^ ] %[A-Z0-9]", accno);
  LstGetPosition((void*)val->features, &featureNumber);
  featureNumber++;  /* 1 .. n */
  if (val->protSeq)
    fprintf(stderr, "\nID   %s_%d  standard; PRT; %d AA.\n",
	    accno, featureNumber, val->protSeq->len);
  else
    fprintf(stderr, "\nID   %s_%d  standard; PRT; 0 AA.\n",
	    accno, featureNumber);
  fprintf(stderr, "DR   EMBL; %s; %s.\n", accno, id);

  /*
  ** print "definition", "organism", "CDS-feature" data-fields
  */

  fprintf(stderr, "%s", val->definition->buff);
  fprintf(stderr, "%s", val->organism->buff);
  fprintf(stderr, "%s", val->features->buff->buff); /* print current feature */

  /*
  ** some error statement and both DNA and protein sequences
  */

  fprintf(stderr, "CC   ERROR: no valid translation with table \"%s\"\n",
	  geneticCodeTable[val->genCode - 1]);

  if (val->protSeq && val->resultSeq && val->feature)
  {
    char *start, *curr, *illegal_codon;
    start = curr = val->protSeq->seq;
    fprintf(stderr, "CC   REASON: ");
    while (curr = strchr(curr, (int)'*')) {
      illegal_codon = val->resultSeq->seq + (curr-start)*3
	              + val->feature->codonStart - 1;
      fprintf(stderr, " '%.3s'", illegal_codon);
      curr++;  /* skip '*' */
    }
    fprintf(stderr, " is an illegal codon\n");
  }
  
  SeqWriteEMBL (val->protSeq, val->entry->entry_nm, PrintLine); 
  SeqWriteEMBL (val->resultSeq, val->entry->entry_nm, PrintLine); 
}


/****** TremblPrint **********************************************************
**
**      Prints TREMBL entry;
**
**      INPUT:      address of an entry object [R]
**                  number of CDS feature in entry [R]
**              IMPLICIT:
**                  outFile (FILE *) [W}
**
**      RETURNS:    nothing
*/

static void TremblPrint (CDSoSTORE *store, int cdsN)
{
  FILE *file;
  static SMoBUFF *buff=NULL;
  char id[20]="", accno[20]="";
  char refName[20]="", fileName[200], *tmp;
  INT4 rv;

  sscanf (store->id->buff, "%*[^ ] %[A-Z0-9]", id);

  /*
  ** Open output file: one file for each entry, or only a single file
  ** or stdout.
  */

  if (ParGetNum ("printSeparateFiles")) {
    sprintf (fileName, "%s_%d.seq", id, cdsN);
    file = FilOpenW (fileName, &rv);
    _ErrExit2 (rv, fileName);
  }
  else if ((tmp = ParGetStr ("outputFileName")) && *tmp) {
    if (!outFile) {
      file = FilOpenW (tmp, &rv);
      _ErrExit2 (rv, tmp);
    }
    else
      file = outFile;
  }
  else
    file = stdout; /* print to stdout */



  if (!buff) 
    buff = BuffNew (100);

  if (!store->protSeq->len)
    return;

  /*
  ** print the ID line: accession number with the feature number
  ** appended, a DR line that links to the parent EMBL entry 
  */

  sscanf (store->id->buff, "%*[^ ] %[A-Z0-9]", id);
  sscanf (store->accession->buff, "%*[^ ] %[A-Z0-9]", accno);
/*  LstGetPosition ((void*)store->features, &featureNumber);
  featureNumber++;*/  /* 1 .. n */ 
  fprintf (file, "ID   %s_%d  standard; PRT; %d AA.\n",
	 id, cdsN, store->protSeq->len);
  fprintf (file, "AC   %s;\n", accno);
  fprintf (file, "DR   EMBL; %s; %s.\n", accno, id);

  /*
  ** print the DE line ...but the DE from DNA entry at the end!
  ** print some selected qualifiers from the feature first
  */

  BuffReset (buff);
  if (BuffLength (store->feature->gene))
    BuffPrintF (buff, "gene: %s; ", BuffGetPtr (store->feature->gene));
  if (BuffLength (store->feature->product))
    BuffPrintF (buff, "product: %s; ", BuffGetPtr(store->feature->product));
/*  if (BuffLength (store->feature->note))
    BuffPrintF (buff, "note: %s; ", BuffGetPtr(store->feature->note)); */
  BuffCollapse (buff); 


  fprintf (file, "%s\n", BuffFormat (buff, 80, 0, 0, "DE   "));
  BuffPrint (file, store->definition);

  if (!BuffLength (store->feature->gene) &&
      !BuffLength (store->feature->product) &&
      !BuffLength (store->feature->note)) 
   BuffCopyString (buff, "unnamed ORF;"); 

  BuffPrint (file, store->organism);
  

  /*
  ** print literature references if explicitly listed by "citation"
  ** qualifier in the feature annotation
  */

  if (store->feature->citation) {
    LstFirst((void**)&store->feature->citation);
    do {
      sprintf(refName, "[%d]", store->feature->citation->citationNum);
      if (LstFirstNamed ((void**)&store->references, refName))
	LstPrint (file, (void*)store->references);
      else 
	printf("CC   ERROR: reference *%s* not found.\n", refName);
    } while (LstNext((void**)&store->feature->citation));
  }
  
  LstPrint (file, (void*)store->features);  /* print current feature */


  /*
  ** print additional information obtained during evaluation of the
  ** feature and some warnings 
  */

  fprintf (file, "CC   translated using genetic code table \"%s\"\n",
	  geneticCodeTable[store->genCode - 1]);
  if (store->feature->codonStartShifted > 0)
    fprintf (file, "CC   Warning: codon start shifted by %d\n",
	    store->feature->codonStartShifted);
  if (global_before_f < 0) {
    fprintf (file, "CC   Warning: illegal start codon\n");
    cnt_firstcodonerror++;
  }
  else
    cnt_correct++;

  outFile = file;
  SeqWriteEMBL (store->protSeq, store->entry->entry_nm, CDSPrintF);

  if (ParGetNum ("printSeparateFiles")) 
    fclose (file);

}


/****** TaxaToTranslTable *****************************************************
**
**      Searches various taxa (case insensitive) to find the appropriate
**      translation table;
**
**      INPUT:      address of buffer with organism source information
**              IMPLICIT:
**
**      RETURNS:    the translation table id number
*/

INT4 TaxaToTranslTable (SMoBUFF *org)
{
  if (BuffSearch(org,"Protozoa") && BuffSearch(org,"Cili")
      && !BuffSearch(org,"Mitoch"))
    return 6;
  if (BuffSearch(org,"Mitochond") && BuffSearch(org,"Yeast"))
    return 3;
  if (BuffSearch(org,"Mitochond")
      && (BuffSearch(org,"Podospora") || BuffSearch(org,"Protozoa")))
    return 7;
  if (BuffSearch(org,"Mitochond")
      && (BuffSearch(org,"Vertebrata") || BuffSearch(org,"Mammalia")))
    return 2;
  if (BuffSearch(org,"Mitochond") && BuffSearch(org,"Echinoderm"))
    return 9;
  if (BuffSearch(org,"Mitochond"))
    return 5;

  return 1; /* default table */
}

/****** CDSTranslate *********************************************************
**
**      INPUT:      entry store [W]
**              IMPLICIT:
**
**      RETURNS:
*/

INT4 CDSTranslate (CDSoSTORE *store)
{
  INT4 i, trerr=1;
  for (i=0; i<=2; i++) {
    if (SeqTranslate(store->resultSeq, &store->protSeq,
		     store->feature->codonStart+i,
		     store->feature->codon,
		     store->feature->transl_except,
		     store->genCode - 1)) {
      trerr = CheckTranslationErrors(store->protSeq->seq);
      if (!trerr) break;
    }
  }

  if (trerr)
    return 0;

  store->feature->codonStartShifted = i;
  return 1;
}


/****** CDSStoreInit **********************************************************
**
**      INPUT:      entry store [W]
**                  entry [R] or NULL
**              IMPLICIT:
**
**      RETURNS:
*/

CDSStoreInit (CDSoSTORE *store, ENTRYo *entry)
{
  if (!entry) {
    store->id = BuffNew(20);
    store->accession = BuffNew(20);
    store->definition = BuffNew(20);
    store->organism = BuffNew(20);
    store->featureCurr = BuffNew(20);
    store->refCurr = BuffNew(20);

    store->links = NULL;
    store->features = NULL;
    store->references = NULL;
    store->entrySeq = NULL;
    store->resultSeq = NULL;
    store->protSeq = NULL;
    store->feature = NULL;   /* feature description */
    store->genCode = 1;      /* id of default translation table */
  }
  else {
    store->entry = entry;
    BuffReset(store->id);
    BuffReset(store->accession);
    BuffReset(store->definition);
    BuffReset(store->organism);
    BuffReset(store->featureCurr);
    BuffReset(store->refCurr);

    if (store->links)
      LstDeleteAll((void**)&store->links);
    if (store->features)
      LstDeleteAll((void**)&store->features);
    if (store->references)
      LstDeleteAll((void**)&store->references);
    if (store->entrySeq)
      LstDeleteAll((void**)&store->entrySeq);
    if (store->resultSeq)
      LstDeleteAll((void**)&store->resultSeq);
    if (store->protSeq)
      LstDeleteAll((void**)&store->protSeq);
    store->feature = NULL;   /* feature description */
    store->genCode = 1;      /* id of default translation table */
  }
}


/****** CDSStoreEntry *********************************************************
**
**      INPUT:      entry store [W]
**                  entry [R] or NULL
**              IMPLICIT:
**
**      RETURNS:
*/

CDSStoreEntry (CDSoSTORE *store, ENTRYo *entry) 
{
  SMoBUFF   *buff = NULL;
  SLBoFIELD *field;
  char      *name, *ln;

  while ((field = EntryToNextField (entry))) {
    name = LibGetFieldName (field);
    buff = NULL;
    if (SmEqs(name, "ID"))
      buff = store->id;
    else if (SmEqs(name, "Accession"))
      buff = store->accession;
    else if (SmEqs(name, "Definition"))
      buff = store->definition;
    else if (SmEqs(name, "Organism"))
      buff = store->organism;
    else if (SmEqs(name, "RefNumber")) {
      buff = store->refCurr;
      if (!BuffIsEmpty (buff))
	FieldCopyList (&store->references, buff);
      BuffReset (buff);
    }
    else if (SmEqs(name, "Authors"))
      buff = store->refCurr;
    else if (SmEqs(name, "Title"))
      buff = store->refCurr;
    else if (SmEqs(name, "Reference"))
      buff = store->refCurr;
    else if (SmEqs(name, "Features")) {
      buff = store->featureCurr;
    }
    
    if (buff) {
      while ((ln = EntryFieldNextLine(entry)))
	BuffCopyString (buff, ln);
      if (buff == store->featureCurr) {
	FieldCopyList (&store->features, buff);
	BuffReset (buff);
      }
    }
    else	
      EntrySkipField (entry);
  }
  
  /* save the last reference in entry */
  
  if (!BuffIsEmpty (store->refCurr))
    FieldCopyList (&store->references, store->refCurr);
}


/****** CDSMakeEntry **********************************************************
**
**      INPUT:      entry store [W]
**                  entry [R] 
**                  file position [R]
**                  number of CDS feature in entry [R]
**              IMPLICIT:
**
**      RETURNS:
*/

CDSMakeEntry (CDSoSTORE *store, ENTRYo *entry, FILoL_S *fileSave, int cdsN) 
{
  INT4 rv=0;
     
  if (store->resultSeq)
    LstDeleteAll((void**)&store->resultSeq);
  if (store->protSeq)
    LstDeleteAll((void**)&store->protSeq);

  store->feature = NULL;
  store->genCode = 1; /* id of default translation table */
  store->errorMessage = NULL;
  global_before_f = 0; /* reset flag for next feature */


  rv = SlbMakeFeature (store->features->buff, entry,       
		       store->entrySeq, &store->resultSeq, &store->feature);
  FilUBack (entry->file[1], fileSave);
  if (!rv) 
    return 0;
  
  if (_ErrIs (rv) && (rv != e__operatorafternotallowed &&
		      rv != e__operatorbeforenotallowed)) {
    _ErrMsg (rv);
    cnt_syntaxerror++;
    return 0;
  }

  if (store->feature->isPseudo) /* pseudo gene */
    return 0;
  
  /*
  ** if the sequence - for some reason - is not empty, then do the 
  ** translation and, if all is correct, print the 
  ** TREMBL entry, otherwise an error report
  */
  
  if (!store->resultSeq) 
    return 0;
  
  store->genCode = TaxaToTranslTable(store->organism);
  if (store->feature->codeTableNum>0)  /* transl_table = .. */
    if (store->genCode != store->feature->codeTableNum) {
      fprintf(stderr, "\nCC   WARNING: used code table id %d instead of %d\n",
	      store->feature->codeTableNum, store->genCode);
      store->genCode = store->feature->codeTableNum;
    }
  
  if (CDSTranslate (store)) {
    TremblPrint (store, cdsN); /* print value structure */
    return 0;
  }
  else {
    TremblErrorPrint (store); /* print value structure */
    cnt_trerr++;
    return 0;
  }
  return 1;
} 



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  main section...
*/

int main (int argc, char **argv)
{
  ARGoLIST  *arglist;
  SLBo      *lib;
  ENTRYo    *entry;
  CDSoSTORE store;
  INT4      n=0, cdsN;
  char      *libraryName, *fileName;
  FILoL_S   fileSave;

  SrsEnv ();
  LibOpen ("srswin");
  MsgSetFnct (PrintMessage);
  CDSStoreInit (&store, NULL);

  /*
  ** process command line
  */

  arglist = (ARGoLIST *) LibObjByName ("arglist", "trembl");
  argc = ArgGet (arglist, argc, argv);
  
  libraryName = ParGetStr ("libName");
  if (!(lib = (SLBo *) LibObjByName ("library", libraryName)))
    _ErrExit3 (e__objectunknown, "library", libraryName);

  /*
  ** if a file name is specified then supersede the one defined 
  ** in ODD
  */

  if (*(fileName = ParGetStr ("tremblInFile"))) {
    char dirName[80], name[80];

    FilParse (fileName, dirName, FILxDEST);
  /*  strcat (dirName, "/"); */  /* must be added */
    FilParse (fileName, name, FILxNAME);
    LibSetFlatFileDir (lib, dirName);
    LibSetFlatFileName (lib, name);
  }

  /*
  ** open databank and iterate over all entries
  */

  entry = EntryOpenStream (lib);
  while (EntryNext (entry)) {
    CDSStoreInit (&store, entry);

    if (SlbNextSequence (entry)) {
      SlbGetSequence (entry, &store.entrySeq);
      FilUSave (entry->file[1], &fileSave);
    }

    CDSStoreEntry (&store, entry);

    /*
    ** if the entry has any features, iterate and process CDS
    ** features
    */

    if (store.features) {
      cdsN = 0;
      LstFirst ((void**) &store.features);

      do {
	if (!strncmp (store.features->name, "CDS", 3)) 
	  CDSMakeEntry (&store, entry, &fileSave, ++cdsN);
      } while (LstNext ((void**) &store.features));
    } 
      
    /* print progress */
    if (!(++n % 1000)) 
      fprintf(stderr, "...%d\n", n);
  }


  /*
  ** print final report if not translating a single file
  */

  if (!*ParGetStr ("tremblInFile")) {
    fprintf (stderr, "\n*********  Program correctly finished  ******\n\n");
    fprintf (stderr, "syntax errors:       %d\n", cnt_syntaxerror);
    fprintf (stderr, "translation errors:  %d\n", cnt_trerr);
    fprintf (stderr, "illegal start codon: %d\n", cnt_firstcodonerror);
    fprintf (stderr, "correct:             %d\n", cnt_correct);
  }
  exit(0);
}
) 
      fprintf(stderr, "...%d\n", n);
  }


  /*
  ** print final report if not translating a single file
  */

  if (!*ParGetStr ("tremblInFile")) {
    fprintf (stderr, "\n*********  Program correctly finished  ******\n\n");
    fprintf (stderr, "synsrs/src/try.c

#include <stdio.h>
#include <stdlib.h>
#include <stdarg.h>
#include "srs.h"


#include "odd.h"
#define _INITOBJS
#define _CONSTANTS
#define _SDL
#define _FUNCTION 
#include "oddclass.h"

ICAoSYNTAX *IcaInitSyntax (ICAoSYNTAX *);

static INT4 PrintMessage (MSGo *msg);

void ReadBuiltin (ICAoSYNTAX *syntax)
{
  FILEo   *file;
  ICAoJOB *job;
  SDLo    *odd;
  Int4    opt;

  /* never write C-conversion */
  opt = ParGetBool("ica2C");
  ParDefBool("ica2C", 0);
  ParDefBool ("doSection", 1); /* pointers instead of numbers */

  job = IcaCreateJob (syntax);

  /* process class information */
  odd = OddInit (def, 1);
  file = FileNew ("SRSSDL:builtin.ic");
  if (!FileOpen (file))
    _ErrExit2 (e__filnotok, "SRSSDL:builtin.ic");
  IcaNewJob (job, file, NULL);
  IcaGetTokenList (job, "prog");
  IcaEndJob (job);
  VarExec (job->prog);

  /* process objects */
  odd = OddInit (odd, 2); 
  file = FileNew ("SRSSDL:builtin.i");
  if (!FileOpen (file))
    _ErrExit2 (e__filnotok, "SRSSDL:builtin.i");
  IcaNewJob (job, file, NULL);
  IcaGetTokenList (job, "prog");
  IcaEndJob (job);
  FileClose (job->file);
  job->file = NULL;
  VarExec (job->prog);

  ParDefBool ("ica2C", opt);
}


main(int argc, char **argv)
{
  SDLo         *odd;
  ARGoLIST     *arglist;
  FILEo        *file;
  ICAoJOB      *job; 
  ICAoSYNTAX   *syntax;
  char         line[MAXLINESIZE], *tokStr, *name;
  INT4	       printAll, tokCode, c, rv;
  
  SrsEnv ();
  LibOpen ("srs5");
  MsgSetFnct ((FUNC)IcaPrintMessage);
  
  arglist = LibObjByName ("arglist", "try");
  argc = ArgGet (arglist, argc, argv);

  if (!ParGetBool ("useIni"))
    syntax = IcaInitSyntax ((ICAoSYNTAX*)LibObjByName ("syntax", "icarus"));
  else
    syntax  = (ICAoSYNTAX*)LibObjByName ("syntax", "icarus");
  odd = OddInit (def, 1); 

  if (ParGetBool ("doCommandInfo")) {
    IargPrintInfo ();
    exit (0);
  }

  if (argc != 2) {
    ArgUsage (arglist);
    _ErrorExit ();
  }

  job = IcaCreateJob (syntax);


  file = FileNew(argv[1]);
  if (!FileOpen (file))
    _ErrExit2 (e__filnotok, argv[1]);

  IcaNewJob (job, file, NULL);
  IcaGetTokenList (job, "prog");
  IcaEndJob (job);
  FileClose (job->file);
  job->file = NULL;

  if (job->prog) {
    if (ParGetBool ("readBuiltin"))
      ReadBuiltin (syntax);
    VarExec (job->prog); 
  }  

  if (ParGetBool ("doClassInfo")) {
    odd = OddInit (odd, 2);
    OddWriteClassInfo (odd);
  }
}  



sage (arglist);
    _ErrorExit ();
  }

  job = IcaCreateJob (syntax);

srs/src/tryblub.c
#include "strv.h"
#include "blub.h"
#include "objstream.h"

typedef struct TRYOBJ {
  OBJo head;
  int a;
  STRv b;
  struct TRYOBJ* part;
} TRYOBJ;

typedef struct TRYMORE {
  TRYOBJ head;
  STRv more;
  ListAttr list;
  int arr[10];
} TRYMORE;


int main() {
    TRYOBJ* o=ObjCpy(Object);
    TRYOBJ* o1;
    TRYMORE* o2;
    void* streamList,**streamElem;
    void *r1, *r2, *r3,*a1; 
    AttrIter ai; Iter i;
    int* list;
    OBJpStream s;
    ObjInit();
    ObjAttrNew(&o, StrTemp("a"), int)=3;
    ObjAttrNew(&o, StrTemp("b"), STRv)=StrCpyS("ciao");
    ObjAttrNewRef(&o, StrTemp("part"),TRYOBJ*)=NULL;
    ObjPrint(o); printf("\n");
    ObjMakeClass(o,StrTemp("TRYOBJ"));
    o1=ObjCpy(o);
    ObjChange(&o1,TRYOBJ*);
    o1->part=ObjCpy(o);
    ObjChange(&ObjChange(&o1, TRYOBJ*)->part, TRYOBJ*)->a=10;
    o1->a=5;
    StrSetS(&o1->b,"containing");
    o2=ObjCpy(o1);
    ObjAttrNew(&o2,StrTemp("more"),STRv)=StrCpyS("someMore");
    list=&ObjListNew(&o2,4,int);
    *list++=1;
    *list++=2;
    *list++=3;
    *list++=4;
    ObjDebug(o);
    ObjDebug(o1); 
    ObjDebug(o2);
    ObjMakeClass(o2,StrTemp("TRYMORE"));
    ObjListApp(&o2,int)=6;
    ObjListApp(&o2,int)=7;
    ObjDebug(o2);
    ObjListCut((void**)&o2,ObjListWith(o2,1),3);
    ObjDebug(o2);
    /* try access by name */
    printf("%d %s\n", ObjAttr(o,StrTemp("a"),int),
	Str(ObjAttr(o,StrTemp("b"),STRv)));
    printf("%d %s\n", ObjAttr(o1,StrTemp("a"),int),
	Str(ObjAttr(o1,StrTemp("b"),STRv)));
    printf("%d %s\n", ObjAttr(o2,StrTemp("2"),int),
	Str(ObjAttr(o2,StrTemp("more"),STRv)));
    /* attribute iteration */
    printf("iterating:\n");
    for (ai=ObjAttrFirst(o2); ai; ObjAttrNext(o2,&ai)) {
        STRv name=ObjAttrName(o2,ai);
        printf("%s\n",Str(name));
	StrDel(name);
    }    
    /* testing list iteration */
    printf("list:\n");
    for (i=ObjListFirst(o2);i;ObjListNext(o2,&i)) {
        printf("%i:%i\n",ObjListPos(o2,i),ObjListIn(i,int));
    }
    printf("%d",ObjListCard(o2));
    
    
    /* try stream output */
    streamList=ObjCpy(Object);
    streamElem=&ObjListNew(&streamList,3,OBJv);
    *streamElem++=ObjCpy(o);
    *streamElem++=ObjCpy(o1);
    *streamElem++=ObjCpy(o2);
    
    printf("\n-----------------saving\n");
    ObjDebug(o); ObjDebug(o1); ObjDebug(o2); 
    s=ObjStreamOpen("blabla","wb");
    ObjStore(streamList, s); 
    /*ObjStore(o1, s);
    ObjStore(o2, s);*/
    ObjStreamClose(s);
    ObjDel(streamList); streamList=NULL;
    
    /* try stream input */
    s=ObjStreamOpen("blabla","rb");
    ObjSet(&streamList,ObjLoad(s));
    /*ObjSet(&o, ObjLoad(s));
    ObjSet(&o1, ObjLoad(s));
    ObjSet(&o2, ObjLoad(s));*/
    ObjStreamClose(s);
    ObjDebug(streamList); /*ObjDebug(o1); ObjDebug(o2);*/

    /* release everything */
    ObjDel(streamList);
    ObjDel(o); ObjDel(o1); ObjDel(o2); 
    return 0;
}

treamList, s); 
    /*ObjStore(o1, s);
    ObjStore(o2, s);*/
    ObjStreamClose(s);
    ObjDel(streamList); streamList=NULL;
    
    /* try stream input */
    s=ObjStreamOpen("blabla","rb");
    ObjSetsrs/src/unix_map.c
char unix_map_srs_ID[] = "$Id: unix_map.c,v 1.5 1996/12/14 16:31:48 etzold Exp $";
/*
**
**    $RCSfile: unix_map.c,v $
**    $Revision: 1.5 $
**    $Date: 1996/12/14 16:31:48 $
**    $Author: etzold $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  SRS V3.0 Copyright by Thure Etzold
**        Unix port: This module has been modified in major parts
**                   by Lukas Rosenthaler and Reinhard
**
**             Author: Thure Etzold
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**    Requires: sm, message 
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**
**    Description
**    =========== 
**
**    maps a file to memory and provides functions for
**    writing to the file, saving and delteing the mapped 
**    memory; Either a file can be created with specified 
**    nr. of blocks or existing file can be extended by 
**    nr. of blocks.
**    before deleting the mapsection the memory is saved to
**    the file and the unused space of it is deleted;
**    the output file is a 
**    Two functions for writing are provided for assuring
**    that the map section is written to in a sequential 
**    manner.
**
**    map-section-file:
**	 1) LF-stream file (C-stream-file)
**	 2) first longword contains number of bytes written to file  
**  
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <unistd.h>

#include "message.h"
#include "futil.h"
#include "map.h"

#define PAGE_SIZE (512*sizeof (char))

#ifndef TRUE
#define TRUE 1
#endif

#ifndef FALSE
#define FALSE 0
#endif

#define TMPSTR_LEN 256

/*****************************************************************************
 *
 * create a map secion. This function is a dummy function which is not used
 * in the unix version ! It's solely included for compatibilty with the VMS
 * code. It should be removed later !!
 *
 *----------------------------------------------------------------------------
 *
 * Returns        : INT4
 *                  success code
 *
 * Parameters     :
 *    MAPo *m     : no meaning
 *    void *buff  : no meaning
 *    INT4  buff_z : no meaning
 *
 * side effects   : none
 *-
 *****************************************************************************
 */
 
INT4 MapCreSec (MAPo *m, void *buff, INT4 buff_z)
{
  _ErrRet2 (e__nonounix, "MapCreSec");
  return 1;
}


/*****************************************************************************
 *
 * <...>
 *
 *----------------------------------------------------------------------------
 *
 * Returns  : INT4
 *            perform page arithmetic
 *
 * Parameters :
 *    INT4 a : dividend
 *    INT4 b : divisor
 *
 * side effects : none
 *-
 *****************************************************************************
 */
 
INT4 MapMOD (INT4 a, INT4 b)
{
  INT4 quot;

  quot = a/b;
  return ((a == (quot * b)) ? quot : ++quot);
}



/*****************************************************************************
 *
 * Opens a file and reads it into core memory. The mechanism is read only,
 * that is, the core memory contents will *NOT* be updated in the file !
 *
 *----------------------------------------------------------------------------
 *
 * Returns        : INT4
 *                  success code
 *
 * Parameters     :
 *    MAPo *m     : address of map-descriptor
 *    char *fil_n : address of filename
 *    void *buff  : address of buffer or NULL. If NULL is supplied, then
 *                  the appropriate amount of core is allocated inside the
 *                  routine
 *    INT4  buff_z : amount of core which is to be "mapped". IF "buff" is not
 *                  NULL, "buff_z" must *NOT* be larger than the size of the
 *                  "buff" !
 *
 * side effects   : none
 *-
 *****************************************************************************
 */
 
INT4 MapMem (MAPo *m, char *fil_n, void *buff, INT4 buff_z)
{
  char *tmp, t_fil_n[TMPSTR_LEN];
  INT4 page_n;
  INT4 fid, n, nn;

  strcpy (t_fil_n, fil_n);

  /*
  ** open the file, readonly
  */

  if ((fid = open (_FilLN (t_fil_n), O_RDONLY, 0666)) == -1) {
    _ErrRet (e__filopenerr);
  }

  /*
  ** check, if buffer memory is supplied. If so, pray that it's enough
  ** memory to hold the data to be read. Otherwise, a friendly core dump...
  ** If no buffer is supplied, detemine the amount of memory used (given by
  ** the file size, and allocate the memory.
  **/

  if (buff == NULL) {

    /*
    ** get file size
    */

    if ((buff_z = lseek (fid, 0, SEEK_END)) == -1) {
      _ErrRet2 (e__seekfail, t_fil_n);
    }

    /*
    ** set file pointer back to beginning of file
    */

    if (lseek (fid, 0, SEEK_SET) == -1) {
      _ErrRet2 (e__seekfail, t_fil_n);
    }

    page_n = buff_z / 512 + ((buff_z % 512 > 0) ? 1 : 0);

    /*
    ** allocate "page_n" bytes of core
    */

    if ((tmp = (char *) malloc (page_n * PAGE_SIZE)) == NULL) {
      _ErrRet2 (e__allocfail, "MapMem");
    }
    m->isAllocBuff=1;
  }
  else {

    /*
    ** calculate the amount of memory. This calculations are remains from
    ** VMS ...                    
    */

    page_n = buff_z / 512 + ((buff_z % 512 > 0) ? 1 : 0);
    m->isAllocBuff=0;
    tmp = buff;
  }

  /*
  ** now we read in the data from the file, which has been opened
  ** before, and the file_id is in m->chan...
  */

  m->chan = fid;
  n = 0;
  while (n < page_n*PAGE_SIZE) {
    nn = read (fid, tmp + n, page_n*PAGE_SIZE - n);
    if (nn == -1) {
      _ErrRet2 (e__readerr, "MapMem");
    }
    if (nn == 0) { /* EOF detected */

      /*
      ** jump out of loop, we have EOF !!
      */

      goto eof_detected;
    }
    n += nn;
  }

 eof_detected:

  if (close ((INT4) m->chan) == -1) {
    _ErrRet2 (e__filcloseerr, t_fil_n);
  }

  /*
  ** update "m" struct (VMS compatibilty...)
  */

  m->data   = tmp;     /* pointer to allocated core memory */
  m->xbyt   = n;       /* number of bytes read */
  m->wrt_f  = FALSE;   /* we don't want to write to the file ! */
  m->trnc_f = TRUE;    /* doesn't matter... */
  m->foff   = (UINT4 *) m->data;
/*  m->off    = m->data +  *(m->foff); not needed and crashes on some sunos */

  (void) strncpy (m->filn, t_fil_n, FILxXNAM);
  
  return 1;
}


/*****************************************************************************
 *
 * allocates "nbloc" pages (a 512 bytes) of memory and marks them for
 * "mapping" which means that upon closure/flushing the contents will be
 * written to a file.
 *
 *----------------------------------------------------------------------------
 *
 * Returns       : INT4
 *                 success code
 *
 * Parameters    :
 *    MAPo *m    : address of map-descriptor
 *    char *filn : address of filename
 *    INT4  nbloc : number of 512 byte pages which are to be allocated and
 *                 marked for mapping
 *
 * side effects  : none
 *-
 *****************************************************************************
 */
 
INT4 MapAlloc (MAPo *m, char *filn, INT4 nbloc)
{
  char *tmp;

  /*
  ** allocate "nbloc" pages of memory
  */

  if ((tmp = (char *) malloc (nbloc * PAGE_SIZE)) == NULL) {
    _ErrRet2 (e__allocfail, "MapAlloc");
  }

  /*
  ** initialize allocated memory to zero.
  */

  (void) memset (tmp, 0, nbloc*PAGE_SIZE);

  /*
  ** update "m" struct (VMS compatibilty...)
  */

  m->data    = tmp;
  m->xbyt    = nbloc*PAGE_SIZE;
  m->trnc_f  = TRUE;  /* truncate on closure/flushing */
  m->wrt_f   = TRUE;  /* contents of allocated memory is written */
  m->off     = m->data + 4;
  m->foff    = (UINT4 *) m->data;
  *(m->foff) = 4;
  (void) strncpy(m->filn, _FilTempLN (filn), FILxXNAM);
  
  return 1;
}


/*****************************************************************************
 *+ INT4 MapExtend (MAPo *m, char *filn, INT4 nbloc)
 *----------------------------------------------------------------------------
 *
 * Description of MapExtend:
 *
 * adds "nbloc" 512 byte pages of core to existing "mapped" memory region.
 * In effect, adding core is done in junks of 64 pages. So "nbloc" is rounded
 * to be a multiple of 64!
 *
 *----------------------------------------------------------------------------
 *
 * Returns       : INT4
 *                 success code
 *
 * Parameters    :
 *    MAPo *m    : address of map-descriptor
 *    char *filn : address of filename
 *    INT4  nbloc : number of 512 byte pages to add to existing "mapped"
 *                 memory.
 *
 * side effects  : none
 *-
 *****************************************************************************
 */
 
INT4 MapExtend (MAPo *m, char *filn, INT4 nbloc)
{
  INT4 size, orig_size;
  char *tmp, t_filn[TMPSTR_LEN];
  INT4 fid, n, nn;

  /*
  ** get size of existing map-file to be extended
  */

  if ((fid = open (_FilLN (filn), O_RDONLY)) == -1) {
    _ErrRet2 (e__filopenerr, t_filn);
  }

  /*
  ** determine size of file
  */

  if ((size = lseek (fid, 0, SEEK_END)) == -1) {
    _ErrRet2 (e__seekfail, t_filn);
  }
  orig_size = size;

  /*
  ** set file pointer back to beginning of file
  */

  if (lseek (fid, 0, SEEK_SET) == -1) {
    _ErrRet2 (e__seekfail, t_filn);
  }


  /*
  ** calculate new size (multiple of 64  512 byte pages
  */

  size += 64*PAGE_SIZE;
  size += (MapMOD (nbloc, 64)*PAGE_SIZE);  /* add at least nbloc of core */

  /*
  ** 
  */

  if ((tmp = (char *) malloc (size)) == NULL) {
    _ErrRet2 (e__allocfail, "MapExtend");
  }


  n = 0;
  while (n < orig_size) {
    if ((nn = read (fid, tmp + n, orig_size - n)) == -1) {
      _ErrRet2 (e__readerr, "MapExtend");
    }
    if (nn == 0) break;
    n += nn;
  }

  if (close (fid) == -1) {
    _ErrRet2 (e__filcloseerr, "MapExtend");
  }
  fid = 0;

  /*
  ** update map-descriptor with new values
  */

  m->data = tmp;
  m->trnc_f = TRUE;
  m->xbyt  = size; /* new size */
  m->foff  = (UINT4 *) m->data;
  m->off   = m->data +  *(m->foff);
/*  m->fid   = fid; */
  strcpy(m->filn, t_filn);
  
  return 1;
}


/*****************************************************************************
 *+ INT4 MapFree (MAPo *m)
 *----------------------------------------------------------------------------
 *
 * Description of MapFree:
 *
 * If "mapped" core memory is readonly, then the allocated memory is just
 * released. Otherwise, the memory content is written to the file with the
 * filename given in the map-descriptor. Possibly the file is truncated to
 * the length actually used. This is controlled by the flag "m->trnc_f" of the
 * map-descriptor.
 *
 *----------------------------------------------------------------------------
 *
 * Returns    : INT4
 *              success code
 *
 * Parameters :
 *    MAPo *m : address of map-descriptor
 *
 * side effects : none
 *-
 *****************************************************************************
 */
 
INT4 MapFree (MAPo *m)
{
  INT4 fid;
  unsigned long n, nn, size;

  /*
  ** if "mapped" core memory  contents will be written to file, close last
  ** record by '\n' !
  */

  if (m->wrt_f) {
    *(m->off) = '\n';
    *(m->off + 1) = '\n';
  }

  /*
  ** test, if file should be written
  */

  if (m->wrt_f) {

    /*
    ** first we have to open the file. We will generate a new file,
    ** even if a file with the same name already exists !
    */

#ifndef dos
    if ((fid = open (m->filn, (O_WRONLY | O_CREAT | O_TRUNC), 0666)) == -1) {
#else
    if ((fid = open (m->filn, (O_WRONLY | O_CREAT | O_BINARY | O_TRUNC), 0666)) == -1) {
#endif
      _ErrRet2 (e__filopenerr, m->filn);
    }

    /*
    ** let's calculate the number of bytes to write.
    ** ATTENTION: This code possibly has to be changed:
    **            to my knowlegde, VMS mapped files are written always
    **            in PAGE_SIZE junks (also "MapMem" reads PAGE_SIZE junks...).
    **
    ** if the file is to be truncated to the length actually memory has been
    ** used, then we calculate the file size by the difference of the start
    ** address and the offset of the last write access to the "mapped" core
    ** memory. This is possible since all access is (should be !) done by
    ** routines which update "m->off".
    */

    if (m->trnc_f) {
      size = (unsigned long) (m->off - m->data) + 1;
    }
    else {
      size = m->xbyt;
    }
    n = 0;
    while (n < size) {
      if ((nn = write (fid, m->data + n, size - n)) == 0) {
	_ErrRet3 (e__filwriteerr, m->filn, (size - n));
      }
      n += nn;
    }

    /*
    ** close the file
    */

    if (close (fid) == -1) {
      _ErrRet2 (e__filcloseerr, m->filn);
    }
  }

  /*
  ** now we will free the allocated memory 
  */

  if (m->isAllocBuff)
    free (m->data); /* free allocated memory */
  m->data = NULL; /* set pointer to NIL */
  m->xbyt = 0;   /* set size to 0 */

  return 1;
}


/*****************************************************************************
 *+ INT4 MapTruncate (MAPo *m)
 *----------------------------------------------------------------------------
 *
 * Description of MapTruncate:
 *
 * Truncate a file which was mapped. This function is a dummy function
 * which is not used in the unix version ! It's solely included for
 * compatibilty with the VMS code. It should be removed later !!
 *
 *----------------------------------------------------------------------------
 *
 * Returns    : INT4
 *              success code
 *
 * Parameters :
 *    MAPo *m : address of map-descriptor
 *
 * side effects : none
 *-
 *****************************************************************************
 */
 
INT4 MapTruncate (MAPo *m)
{
  _ErrRet2 (e__nonounix, "MapTruncate");

  return 1;
}



/*****************************************************************************
 *+ INT4 MapNew (MAPo *m, UINT4 *fadd)
 *----------------------------------------------------------------------------
 *
 * Description of MapNew:
 *
 * Returns relative section file's address of begin of unused space.
 * Only MapPutS and MapWrite may be used for writing to the map-section
 *
 *----------------------------------------------------------------------------
 *
 * Returns               : INT4
 *                         success code
 *
 * Parameters            :
 *    MAPo         *m    : address of map-descriptor
 *    UINT4 *fadd : address of address where to put file address (???)
 *                         ( too many recursive addresses for me...  ;-)  )
 *
 * side effects          : none
 *-
 *****************************************************************************
 */

INT4 MapNew (MAPo *m, UINT4 *fadd)
{
  long int ptr_diff;

#ifndef dos
  /*
  ** the map-memory we return should be aligned at least to the pointer type
  */ 

  ptr_diff = (long int) m->off % sizeof (char *);
  if (ptr_diff != 0) {
    m->off += (sizeof (char *) - ptr_diff);
    *(m->foff) += (sizeof (char *) - ptr_diff);
  }
#endif

  *fadd = *(m->foff);
  return 1;
}


/*****************************************************************************
 *+ INT4 MapCNew (MAPoCCH *c, UINT4 *fadd)
 *----------------------------------------------------------------------------
 *
 * Description of MapCNew:
 *
 * Returns relative file address of begin of unused space in cache.
 * Only MapCWrite may be used for writing to the cache.
 *
 *----------------------------------------------------------------------------
 *
 * Returns               : INT4
 *                         success code
 *
 * Parameters            :
 *    MAPoCCH      *c    : address of cache-descriptor
 *    UINT4 *fadd : address of address where to put file address
 *                         (same comment as above...)
 *
 * side effects          : none
 *-
 *****************************************************************************
 */
 
INT4 MapCNew (MAPoCCH *cache, UINT4 *fadd)
{
#ifdef xxx
  long int ptr_diff;


  /*
  ** the map-memory we return should be aligned at least to the pointer type
  */ 

  ptr_diff = (long int) cache->off % sizeof (char *);
  if (ptr_diff != 0) {
    cache->off += (sizeof (char *) - ptr_diff);
    *(cache->foff) += (sizeof (char *) - ptr_diff);
  }
#endif
  *fadd = *(cache->foff);
  return 1;
}


/*****************************************************************************
 *+ INT4 MapPutS (MAPo *m, char *s)
 *----------------------------------------------------------------------------
 *
 * Description of MapPutS:
 *
 * Puts a 0-terminated string at the end of used space in map-section.
 * map->off and map->foff are updated according to string length.
 *
 *----------------------------------------------------------------------------
 *
 * Returns    : INT4
 *              success code
 *
 * Parameters :
 *    MAPo *m : address of map-descriptor
 *    char *s : string to add
 *
 * side effects : none
 *-
 *****************************************************************************
 */
 
INT4 MapPutS (MAPo *m, char *s)
{
  INT4	len;
    
  len = strlen(s);
  if (*m->foff + len + 1 > m->xbyt)
    return (e__eom);
  strcpy(m->off, s);
  m->off = m->off + len + 1;
  *(m->foff) = *(m->foff) + len + 1;

  return 1;
}


/*****************************************************************************
 *+ INT4 MapWrite (MAPo *m, char *s, INT4 n)
 *----------------------------------------------------------------------------
 *
 * Description of MapWrite:
 *
 * appends "n" bytes to "mapped" core memory
 *
 *----------------------------------------------------------------------------
 *
 * Returns    : INT4
 *              success code
 *
 * Parameters :
 *    MAPo *m : address of map-descriptor
 *    char *s : address of data to add
 *    INT4  n  : number of bytes to add
 *
 * side effects : none
 *-
 *****************************************************************************
 */
 
INT4 MapWrite (MAPo *m, char *s, INT4 n)
{
  long int ptr_diff;


#ifndef dos
 /*
  * the map-memory we return should be aligned at least to the pointer type
  */ 
  ptr_diff = (long int) m->off % sizeof (char *);
  if (ptr_diff != 0) {
    m->off += (sizeof (char *) - ptr_diff);
    *(m->foff) += (sizeof (char *) - ptr_diff);
  }
#endif

  if (*m->foff + n > m->xbyt)
    return (e__eom);
  (void) memcpy(m->off, s, n);
  m->off += n;
  *(m->foff) +=  n;

  return 1;
}


/*****************************************************************************
 *+ INT4 MapMalloc (MAPo *m, INT4 n)
 *----------------------------------------------------------------------------
 *
 * Description of MapMalloc:
 *
 * allocates memory in a "mapped" core memory region. The returned pointer
 * is aligned to the pointer type (char *).
 *
 *----------------------------------------------------------------------------
 *
 * Returns    : char *
 *              address of allocated "mapped" memory region
 *
 * Parameters :
 *    MAPo *m : address of map-descriptor
 *    INT4  n  : number of bytes to reserve
 *
 * side effects : none
 *-
 *****************************************************************************
 */
 
char *MapMalloc (MAPo *m, INT4 n)
{
  char    *off_s;
  long int ptr_diff;

#ifndef dos
  /*
  ** the map-memory we return should be aligned at least to the pointer type
  */ 

  ptr_diff = (long int) m->off % sizeof (char *);
  if (ptr_diff != 0) {
    m->off += (sizeof (char *) - ptr_diff);
    *(m->foff) += (sizeof (char *) - ptr_diff);
  }
#endif
  if (*(m->foff) + n > m->xbyt)
    return NULL;
  off_s = m->off;
  m->off += n;
  *(m->foff) +=  n;

  return (off_s) ;
}



/*****************************************************************************
 *
 * Description of MapFOpen:
 *
 * Open a file for reading/writing
 *
 *----------------------------------------------------------------------------
 *
 * Returns          : INT4
 *                    success code
 *
 * Parameters       :
 *    MAPoCCH *c    : address of cache-descriptor
 *    INT4     acc_o : access mode (MAPxREAD or MAPxWRITE), is ignored !!
 *
 * side effects     : none
 *-
 *****************************************************************************
 */
 
INT4 MapFOpen (MAPoCCH *cache, INT4 acc_o)
{
#ifndef dos
  if ((cache->fid = open (cache->filn, (O_RDWR | O_CREAT), 0666)) == -1) {
#else
  if ((cache->fid = open (cache->filn, (O_RDWR | O_CREAT | O_BINARY), 0666)) == -1) {
#endif
    _ErrRet2 (e__filopenerr, cache->filn);
  }
  return 1;
}




/****** function **************************************************************
**
**      Opens file for block-IO and writes specified number of blocks to 
**      block offset and closes file.
**
**      INPUT:        o address of cache-descriptor 
**                    o number of 512 byte pages to write
**                    o offset in file (in 512 byte pages) where to start
**                   	writing data
**      RETURNS:      1: success
*/
 
INT4 MapWriteBlk (MAPoCCH *cache, INT4 nbloc, INT4 off)
{
  INT4 size, wtotbytes_n, wbytes_n;

  if (cache->fid == 0) MapFOpen (cache, MAPxWRITE);

  /*
  ** first we skip "off" blocks
  */

  if (off > 0) {
    if (lseek (cache->fid, (off - 1)*PAGE_SIZE, SEEK_SET) == -1) {
      _ErrRet2 (e__seekfail, cache->filn);
    }
  }

  /*
  ** now let's write nbloc * PAGE_SIZE bytes
  */

  size = nbloc * PAGE_SIZE;
  wtotbytes_n = 0;
  while (wtotbytes_n < size) {
    if ((wbytes_n = write (cache->fid, cache->buff + wtotbytes_n, 
			   size - wtotbytes_n)) == -1) {
      _ErrRet3 (e__filwriteerr, cache->filn, (size - wtotbytes_n));
    }
    if (wbytes_n == 0) break;
    wtotbytes_n += wbytes_n;
  }

  return 1;
}



/*****************************************************************************
 *
 * closes file theat was opend for read/update access (for fseek)
 * writes 1st half of cache to file, shifts 2nd half of cache to begin
 * and opens file again for read/upd access (no sharing possible);
 *
 * REMARK : This routine has *NOT* been undestood. Some more comment would
 *          be appreciated (Dr. L. Rosenthaler, 30-dec-1992).
 *
 *----------------------------------------------------------------------------
 *
 * Returns       : INT4
 *                 success code
 *
 * Parameters    :
 *    MAPoCCH *c : addresss of cache-descriptor
 *
 * side effects  : none
 *-
 *****************************************************************************
 */
 
INT4 MapFlush (MAPoCCH *cache)
{
  Int4 shift = cache->hbloc * 512;
    
  MapWriteBlk (cache, cache->hbloc+1, cache->fstbloc);
  (void) memcpy (cache->buff, cache->buff + shift, shift); 

  cache->fstbloc += cache->hbloc; 
  cache->off  -= shift;
  cache->coff = cache->coff + shift;

  return 1;
}


 
/**api* MapCWrite *************************************************************
** 
** 	appends specified nr. of bytes to end of used cache;
** 
** 	INPUT:	    cache object [W]
** 		    source buffer [R]
**                  number of bytes to be written [R]
** 
** 	RETURNS:    1
**
*/ 
   
INT4 MapCWrite (MAPoCCH *cache, char *s, INT4 n)
{
  memcpy ((void *) cache->off, (void *) s, n); 
  cache->off = cache->off + n; 
  *(cache->foff) = *(cache->foff) + n;

  if (cache->off >  cache->buff + (cache->nbloc - 1) * 512)
    MapFlush (cache);
  return 1;
}


/*****************************************************************************
 *+ INT4 MapCWriteNA (MAPoCCH *c, char *s, INT4 n)
 *----------------------------------------------------------------------------
 *
 * Description of MapCWriteNA:
 *
 * appned "n" bytes of data to cache region, NOT ALIGNED !!!
 *
 *----------------------------------------------------------------------------
 *
 * Returns       : INT4
 *                 success code
 *
 * Parameters    :
 *    MAPoCCH *c : address of cache-descriptor
 *    char    *s : address of data to add
 *    INT4     n  : number of bytes to add
 *
 * side effects  : none
 *-
 *****************************************************************************
 */
 
INT4 MapCWriteNA (MAPoCCH *cache, char *s, INT4 n)
{

  (void) memcpy( (void *) cache->off, (void *) s, n);
  cache->off = cache->off + n; 
  *(cache->foff) = *(cache->foff) + n;

  if (cache->off >  cache->buff + (cache->nbloc - 1) * 512)
    MapFlush (cache);
  return 1;
}



/*****************************************************************************
 *+ INT4 MapReadBlk (MAPoCCH *c, INT4 nbloc, INT4 off)
 *----------------------------------------------------------------------------
 *
 * Description of MapReadBlk:
 *
 * Opens file for block-IO and reads specified number of blocks from 
 * block offset and closes file.
 *
 *----------------------------------------------------------------------------
 *
 * Returns          : INT4
 *                    success code
 *
 * Parameters       :
 *    MAPoCCH *c    : address of cache-descriptor
 *    INT4     nbloc : number of 512 byte pages to read
 *    INT4     off   : offset (in 512 byte pages) where to start reading
 *                    (first block is equal 1 !!)
 *
 * side effects     : none
 *-
 *****************************************************************************
 */

INT4 MapReadBlk (MAPoCCH *c, INT4 nbloc, INT4 off)
{               
  INT4 size, n, nn;

  size = nbloc * PAGE_SIZE;
  
  if (c->fid == 0) MapFOpen (c, MAPxWRITE);

  /*
  ** first we skip "off" blocks
  */

  if (off > 0) {
    if (lseek (c->fid, (off - 1)*PAGE_SIZE, SEEK_SET) == -1) {
      _ErrRet2 (e__seekfail, c->filn);
    }
  }

  /*
  ** now let's read nbloc*PAGE_SIZE bytes
  */

  size = nbloc * PAGE_SIZE;
  n = 0;
  while (n < size) {
    if ((nn = read (c->fid, c->buff + n, size - n)) == -1) {
      _ErrRet2 (e__readerr, c->filn);
    }
    if (nn == 0) break;
    n += nn;
  }


  return 1;
}


void *MapCacheBuff (char *option, void *buff, Int4 size)
{
  static int freeN=0, allocN=0;
  static void *freeList=NULL;
  void *tmp;

  if (option[0] == 'a') /* alloc */ {
    allocN++;
    if (freeList) {
      buff = freeList;
      freeList = *(void **) buff;
    }      
    else {
      if (!(buff = (char *) malloc (size)))
	_ErrExit2 (e__allocfail, "cache buffer");
    }
    return buff;
  }
  else if (option[0] == 'f') {
    freeN++;
    tmp = freeList;
    freeList = buff;
    *(void **) buff = tmp;
  }
  else if (option[0] == 'p') 
    printf ("alloc: %d, free: %d\n", allocN, freeN);
}

/*****************************************************************************
 *
 * initialize cache, that is allocate memory, open files etc. .
 * MAPoCCH->foff must be set before calling (0 = no existing file)
 *
 *----------------------------------------------------------------------------
 *
 * Returns             : INT4
 *                       success code
 *
 * Parameters          :
 *    MAPoCCH  *c      : address of cache-descriptor
 *    char     *fil_nm : filename
 *    unsigned *foff   : address of offset in file
 *    INT4      new_f   : flag. If set, a new file will be opened
 *
 * side effects        : none
 *-
 *****************************************************************************
 */
 
INT4 MapInitCache (MAPoCCH *cache, char *fil_nm, unsigned *foff, INT4 new_f)
{
  INT4	    nbloc;
  
  if ((cache->filn = (char *) malloc (strlen(_FilTempLN (fil_nm)) + 1))==NULL){
    _ErrRet2 (e__allocfail, "cache buffer");
  }
  
  (void) strcpy (cache->filn, _FilTempLN (fil_nm));
  
  cache->foff = foff;
  if (new_f)
    *foff = 0;
  
  cache->hbloc = MapMOD (cache->nbloc, 2);
  cache->nbloc = cache->hbloc * 2;  /* even number */
  
  cache->buff = MapCacheBuff ("alloc", NULL, cache->nbloc*512);
  cache->fid = 0;
  
  if (*(cache->foff) == 0) {
    cache->new_f = TRUE;
    cache->off = cache->buff;
    cache->fstbloc = 1;
    cache->coff = 0;
  }
  else {
    cache->new_f = FALSE;
    nbloc = MapMOD(*(cache->foff), 512);  
    if ((cache->fstbloc = nbloc - cache->hbloc + 1) <= 1) {
      cache->fstbloc = 1;
      cache->coff = 0;
    }
    else {
      nbloc = cache->hbloc;

      cache->coff = NULL;
      cache->coff = cache->coff + cache->fstbloc-1 * 512;
    }
    cache->off = cache->buff + (*cache->foff - cache->coff); 
    MapReadBlk (cache, nbloc, cache->fstbloc);
  }
  
  return 1;
}





/*****************************************************************************
 *
 * flushes cache to file and frees allocated memory
 *
 *----------------------------------------------------------------------------
 *
 * Returns       : INT4
 *                 sucess code
 *
 * Parameters    :
 *    MAPoCCH *c : address of cache-descriptor
 *
 * side effects  : none
 *-
 *****************************************************************************
 */

INT4 MapCloseCache (MAPoCCH *cache)
{
  INT4	nbloc;

  nbloc = MapMOD (*(cache->foff) - cache->coff, PAGE_SIZE);
  MapWriteBlk (cache, nbloc, cache->fstbloc);

  /*
  ** close file...set file descriptor to 0 to indicate that cache has been
  ** deleted and free allocated memory
  */

  if (close (cache->fid) == -1) {
    _ErrRet2 (e__filcloseerr, cache->filn);
  }
  cache->fid = 0; 
  free (cache->filn);
  MapCacheBuff ("free", cache->buff, 0);
  return 1;
}

/****** function *************************************************************
**
**      Read a cache file into a private area of core memory.
**
**      INPUT:      file name [R]
**                  pointer to address of allocated memory [W]
**
**      RETURNS:    1: success
*/
 
INT4 MapRdMem (char *fil_nm, void **p)
{
  MAPoCCH *c;
  char	  *data;
  INT4     n, nn, size;

  /* allocate cache struct */
  if ((c = (MAPoCCH *) calloc (1, sizeof (MAPoCCH))) == NULL) {
    _ErrRet2 (e__allocfail, "MapRdMem");
  }
  c->fid = 0;

  if ((c->filn = (char *) malloc (strlen (_FilTempLN (fil_nm)) + 1)) == NULL) {
    _ErrRet2 (e__allocfail, "MapRdMem");
  }

  /* open file */
  (void) strcpy (c->filn, _FilTempLN (fil_nm));
  MapFOpen(c, MAPxREAD);

  /* determine size of file*/
  if ((size = lseek (c->fid, 0, SEEK_END)) == -1) {
    _ErrRet2 (e__seekfail, c->filn);
  }

  /* set file pointer back to beginning of file */
  if (lseek (c->fid, 0, SEEK_SET) == -1) {
    _ErrRet2 (e__seekfail, c->filn);
  }

  /* allocate core memory to hold file contents */
  if ((data = (char *) malloc (size)) == NULL) {
    _ErrRet2 (e__allocfail, "MapRdMem");
  }

  *p = data;

  n = 0;
  while (n < size) {
    if ((nn = read (c->fid, data + n, size - n)) == -1) {
      _ErrRet2 (e__readerr, c->filn);
    }
    if (nn == 0) break;
    n += nn;
  }

  if (close (c->fid) == -1) {
    _ErrRet2 (e__filcloseerr, c->filn);
  }
  c->fid = 0;
  free (c->filn);

  return 1;
}


/*****************************************************************************
 *
 * write a 4 byte integer to a specified location in file
 *
 *----------------------------------------------------------------------------
 *
 * Returns              : INT4
 *                        success code
 *
 * Parameters           :
 *    MAPoCCH      *c   : address of cache-descriptor
 *    UINT4 fadd : offset in file where to wwrite integer
 *    UINT4 val  : integer to write to file
 *
 * side effects         : none
 *-
 *****************************************************************************
 */
 
INT4 MapCUpdate (MAPoCCH *c, UINT4 fadd, char *fip)
{

  /*
  ** set file pointer at position given by "fadd"
  */

  if (lseek (c->fid, fadd, SEEK_SET) == -1) {
    _ErrRet2 (e__seekfail, c->filn);
  }

  /*
  ** now write 4 bytes
  */

  if (write (c->fid, fip, 4) != 4) {
    _ErrRet3 (e__filwriteerr, c->filn, 4);
  }

  return (1);
}



/*****************************************************************************
 *
 * Translates relative byte offset in file into cache address if referring
 * to location in cache.
 *
 *----------------------------------------------------------------------------
 *
 * Returns              : INT4
 *                        success code
 *
 * Parameters           :
 *    MAPoCCH      *c   : address of cache-descriptor
 *    UINT4 fadd : offset in file
 *    UINT4 *ptr : address in cache memory
 *
 * side effects         : none
 *-
 *****************************************************************************
 */
 
INT4 MapInCache (MAPoCCH *c, UINT4 fip, void **ptr)
{
  if (fip < c->coff) {
    return 0;
  }
  else {
    *ptr = fip - c->coff + c->buff;
  }

  return 1;
}

/**api* MapDuplicateOverlap ***************************************************
** 
**      Addresses that need updating may be exactly on the boundary between
**      file and memory cache ...in that case both locations need updating.
**      This function updates in the cache only those bytes that overlaps.
**
** 	INPUT:	    address of IDS-file object [R]
**                  file pointer to first ID in the list [W]
** 	        IMPLICIT:
** 
** 	RETURNS:    length of overlap
**                  0 if no overlap exists
*/ 

INT4 MapDuplicateOverlap  (MAPoCCH *cache, UINT4 fip, void *buff, INT4 size)
{
  INT4 overlapLen;

  overlapLen = size - (cache->coff - fip);
  if ((cache->coff > fip) && overlapLen > 0) {
    memcpy (cache->buff, (char *) buff + size - overlapLen, overlapLen);
    return overlapLen;
  }
  else
    return 0;
}




ess of IDSsrs/src/variable.c
char variable_ID[] = "$Id: variable.c,v 1.23 1997/03/18 22:52:34 srs Exp $";
/*
**    $RCSfile: variable.c,v $
**    $Revision: 1.23 $
**    $Date: 1997/03/18 22:52:34 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  Copyright by Thure Etzold
**
**            Authors: Thure Etzold
**                     Anatoly Ulyanov
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387529  
**                     Email: etzold@embl-heidelberg.de
**
**
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
**    Description
**    =========== 
**
**    functions for manipulating 'any' objects which are used to build
**    the icarus 'execution tree'
** 
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 
*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include "message.h"
#include "sm.h"
#include "strv.h"
#include "listv.h"
#include "dict.h"
#include "variable.h"

/* more arguments */
#define _mA 0,0,0,0,0,0,0,0,0,0,0,0

#define _VarHandleTypeEval(x) \
  if ((x)->isDelayedType) { \
    if (!(x)->isTypeEval)  \
      VarGetType (x);  \
    (x)->isTypeEval = 0; \
  }


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  global and module wide variables
*/

extern VARoSCOPE *globalScope;
static VARo *VarNewIn (VARoSCOPE **scopePtr, char *name);
static char *AnyGetTypeName (INT4 type);


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  for the variable dictionary
*/

static void* VarToKey (DictElem* e)
{
  return (*(VARo **)e)->name;
}
static CLASSoDICT dictClass = {
  (ValComparer)strequal, (ValHasher)strhash, (KeyAccessor)VarToKey, NULL, 0
};



VARo *VarUnalias (VARo *alias)
{
  if (alias->code == 1)
    return (alias->v.alias);
  else if (!alias->isReadFunction) {
    if (!globalScope)
      _ErrExit (f__noVarScope);
    return (VARo*) ((ULONG)globalScope->var + (ULONG)alias->v.alias);
  }
  else 
    return (*alias->v.varGet)(alias);
}



/***** VarGetType *************************************************************
**
**      Return the type of argument variable
**
**	INPUT:	    variable pointer
**	        IMPLICIT:
**
**	RETURNS:    the type of argument variable
*/ 

char VarGetType (VARo *var)
{
  _VarUnalias(var);

  if (!var->isTypeEval && var->isDelayedType) {
    (*var->typeGet)(var,_mA);
    var->isTypeEval = 1;
  }
  return (var->type);
}

/***** AnyGetTypeName *********************************************************
**
**      Converts a type (list) into a readable string (mainly used for printing
**      error messages).
**      Function returns the string and make sure that for at least three
**      successive calls different bufferes will be used.
**
**	INPUT:	    one or combination of types [R]
**	        IMPLICIT:
**
**	RETURNS:    string with readable type name(s)
*/ 

static char *AnyGetTypeName (INT4 type)
{
  switch (type) {
  case VARxSTRING:
    return "string";
  case VARxSTRV:
    return "strv";
  case VARxINT:
    return "int";
  case VARxREAL:
    return "real";
  case VARxOBJECT:
    return "object";
  case VARxLIST:
    return "list";
  case VARxVAR:
    return "var";
  case VARxALIAS:
    return "alias";
  case VARxUNKNOWN:
    return "unknown";
  default:
    _ErrExit2 (e__unknownoption, "type in VarError");
    
  }
}

/***** VarError ***************************************************************
**
**	Common error message call
**
**      INPUT:      variable object [R]
**                  expected variable type [R]
**		    message line [R]
**              
**              IMPLICIT:
**
**      RETURNS:
*/

static void VarError(VARo *var, char *type, char *message)
{
  char *name;

  if (!(name = VarGetName (var)))
    name = "unnamed";
  _ErrExit4 (e__icavartype, message, type, AnyDebugStr (var));
  return;
}
/***** VarDestroy *************************************************************
**
**      Called from the list management functions. Deletes a variable.
**
**	INPUT:	    pointer to the object
**	        IMPLICIT:
**
**	RETURNS: 
*/ 

void VarDestroy (void *obj)
{
  VARo *tmp = (VARo*)obj;
  ANYv *list, *e;

  if (tmp) {
    if (tmp->type == VARxSTRV && !tmp->isReadFunction)
      StrDel (tmp->v.strv);
    else if (tmp->type == VARxSTRING && !tmp->isReadFunction && tmp->v.buff)
      BuffDelete (&tmp->v.buff);
    else if (tmp->type == VARxLIST) {
      DictDestroy (tmp->v.list.index);
      list = tmp->v.list.val;
      if (!_ListShared (list)) {
	for (e=list;e<list+_ListLen(list); e++) VarDestroy(*e); 
      }
      _ListDel (list);
    }
    free (tmp);
  } 
}


/***** VarDestroy2 *************************************************************
**
**      Called from the list management functions. Deletes a variable.
**
**	INPUT:	    pointer to the object
**	        IMPLICIT:
**
**	RETURNS: 
*/ 

void VarDestroy2 (void *obj)
{
  VARo *tmp = (VARo*)obj;
  ANYv *list, *e;

  if (tmp) {
    if (tmp->type == VARxSTRV && !tmp->isReadFunction)
      StrDel (tmp->v.strv);
    else if (tmp->type == VARxSTRING && !tmp->isReadFunction && tmp->v.buff)
      BuffDelete (&tmp->v.buff);
    else if (tmp->type == VARxLIST) {
      DictDestroy (tmp->v.list.index);
      list = tmp->v.list.val;
      _ListDel (list);
    }
    free (tmp);
  } 
}

/***** VarInit ****************************************************************
**
**      Called from the list management functions. Initializes a variable.
**
**	INPUT:	    pointer to the object
**	        IMPLICIT:
**
**	RETURNS: 
*/ 

static void VarInit (void *obj)
{
  VARo *tmp = (VARo*)obj;

  memset (tmp, 0, sizeof (VARo));
  tmp->isTypeEval = 1;
}



/***** VarReset ***************************************************************
**
**      Called from the list management functions. Initializes a variable.
**
**	INPUT:	    pointer to the object
**	        IMPLICIT:
**
**	RETURNS: 
*/ 

void VarReset (VARo *var)
{
  if (var->type == VARxSTRING && !var->isReadFunction && var->v.buff)
    BuffDelete (&var->v.buff);
  if (var->type == VARxSTRV && !var->isReadFunction && var->v.strv)
    StrDel (var->v.strv);
      
  memset (var, 0, sizeof (VARo));
  var->isTypeEval = 1;
}

/***** VarNew ****************************************************************
**
**      Creates a new variable object.
**
**	INPUT:	   
**	        IMPLICIT:
**
**	RETURNS: 
*/ 

VARo *VarNew ()
{
  VARo *var;

  if (!(var = (VARo *) calloc (sizeof(VARo), 1)))
    _ErrExit2 (e__allocfail, "variable object");

  var->isTypeEval = 1;
  return var;
}



/**api* function **************************************************************
**
**      Returns the predefined ANY with the empty list value.
**
**	RETURNS:    static ANY with empty list and dictionary
*/ 

ANYv AnyNewList ()
{
  static ANYv emptyList=NULL;
  if (!emptyList) {
    emptyList = VarNew ();
    emptyList->type = VARxLIST;
    emptyList->v.list.val = _ListNew (ANYv, 3);
    emptyList->v.list.index = DictCreate (&dictClass);
  }
  return emptyList;
}


/***** VarGet *****************************************************************
**
**      Searches for variable with specified name and creates a new one if
**      not found.
**
**	INPUT:	    variable object that represents the variable list [W]
**                  variable name [R]
**	        IMPLICIT:
**
**	RETURNS:    address of variable object
*/ 

VARo *VarGet (VARoSCOPE **scope, char *name)
{
  Iter i;
  VARo *var;

  if (*scope && (i = DictWith ((*scope)->dict, name)))
    var =  DictIn (i, VARo*);
  
  else {
    var = VarNewIn (scope, name);
    if (!(*scope)->dict)
      (*scope)->dict = DictCreate (&dictClass);
    DictSet (&((*scope)->dict), var->name, VARo*) = var;
  }
  return var;
}

/***** VarTemp *****************************************************************
**
**      Returns 1 of 10 variables for temporary use.
**
**	INPUT:	    
**	        IMPLICIT:
**
**	RETURNS:    variable for temporary use
*/ 

VARo *VarTemp ()
{
  static INT4 count=0;
  static VARo var[10];
  VARo *tmp;

  tmp = &var[ count++ % 10 ];
  VarReset (tmp);
  return tmp;
}


/***** VarNewIn ***************************************************************
**
**      Creates a new variable in the specified scope.
**
**	INPUT:	    scope object [W]
**                  name of new variable [R]
**	        IMPLICIT:
**
**	RETURNS:    initialized variable object 
*/ 

static VARo *VarNewIn (VARoSCOPE **scopePtr, char *name)
{
  VARoSCOPE *scope;
  VARo      *tmp, *varSave;
  INT4      initSize = 1000; /* initial size of scope */

  /* scope does not yet exist */
  if (!*scopePtr) {
    if (!(scope = (VARoSCOPE *) calloc (sizeof (VARoSCOPE), 1)))
      _ErrExit2 (e__allocfail, "variable stack");
    if (!(scope->var = (VARo *) malloc (sizeof(VARo) * initSize)))
      _ErrExit2 (e__allocfail, "icarus stack array");
    
    scope->varN = 0;
    scope->varAllocN = initSize;
    *scopePtr = scope;
  }
  else 
    scope = *scopePtr;

  /* check if scope can receive a new variable ...grow if not */
  if (scope->varN >= scope->varAllocN) {
    scope->varAllocN *= 2;
    
    varSave = scope->var;
    if ((scope->var = (void *) realloc
	 (scope->var, scope->varAllocN * sizeof (VARo))) == NULL)
      _ErrExit2 (e__allocfail, "variable scope");
    DictOffset (scope->dict, (char *) scope->var - (char *) varSave);
   
  }    

  tmp = &scope->var[scope->varN++];
  VarInit (tmp);
  tmp->name = (char *) malloc (strlen (name) + 1);
  strcpy (tmp->name, name);
  return tmp;
}

VARoSCOPE *VarCopyScope (VARoSCOPE *scope)
{
  VARoSCOPE *tmp;
  INT4      k;

  if (!scope)
    return NULL;

  if (!(tmp = (VARoSCOPE *) calloc (sizeof (VARoSCOPE), 1))) 
    _ErrExit2 (e__allocfail, "variable stack"); 
  if (!(tmp->var = (VARo *) malloc (sizeof(VARo) * (scope->varN+1)))) 
    _ErrExit2 (e__allocfail, "icarus stack array"); 
  memcpy (tmp->var, scope->var, sizeof (VARo) * scope->varN);
  
  tmp->varN = scope->varN;
  tmp->varAllocN = tmp->varN;
  
  tmp->dict = DictCreate (&dictClass);
  for (k=0; k < tmp->varN; k++)
    DictSet (&(tmp->dict), tmp->var[k].name, VARo*) = &tmp->var[k];

  return tmp;
}

void VarScopeDestroy (VARoSCOPE **scope)
{
  VARoSCOPE *tmp;

  if (scope && *scope) {
    tmp = *scope;
    if (tmp->dict)
      DictDestroy (tmp->dict);
    if (tmp->varN)
      free (tmp->var);
    free (tmp);
    *scope = NULL;
  }
}	





/***** VarSetStr **************************************************************
**
**	xx
**
**	INPUT:	    xx
**	        IMPLICIT:
**
**	RETURNS:    xx
*/ 

VARo *VarSetStr (VARo *var, char *s)
{
  _VarUnalias(var);

  if (var->isReadFunction)
    _ErrExit2 (e__varisreadonly, var->name);

  if (!var->type) {
    var->type = VARxSTRING;
    /*    var->v.buff = BuffInit (var->v.buff, 0);*/
  }

  if (var->type == VARxSTRING) {
    var->v.buff = BuffInit (var->v.buff, 0);
    BuffCopyString (var->v.buff, s);
  }
  else if (var->type == VARxINT)
    var->v.num = atoi (s);
  else if (var->type == VARxREAL)
    var->v.real = atof (s);
  else if (var->type == VARxSTRV)
    StrSetS (&var->v.strv, s);
  else 
    VarError(var, "string/int", "set");
  return var;
}

/**api* function **************************************************************
**
**	Copies the list contained in the second any in the argument list to
**      the first.
**
**	INPUT:	    'any' object [W]
**                  'any' object with the list to be copied [R]
*/ 

void AnyDeleteList (ANYv list)
{
  _VarUnalias (list);
  if (list->isReadFunction)
    return;

  if (list->type == VARxLIST) {
    DictDestroy (list->v.list.index);
    _ListDel (list->v.list.val);
    list->v.list.index = NULL;
    list->v.list.val = NULL;
  }
  else
    VarError (list, "list", "delete");
  return;
}

/**api* function **************************************************************
**
**	Copies the list contained in the second any in the argument list to
**      the first.
**
**	INPUT:	    'any' object [W]
**                  'any' object with the list to be copied [R]
*/ 

void AnySetList (ANYv any, ANYv list)
{
  _VarUnalias (any);
  _VarUnalias (list);
  if (any->isReadFunction)
    _ErrExit2 (e__varisreadonly, any->name);

  if (!any->type) {
    any->type = VARxLIST;
  }
  if (any->type == VARxLIST) {
    if (any->v.list.val)
      AnyDeleteList (any);
    if (list->isReadFunction)
      list = (*list->v.listGet)(list,_mA);
    any->v.list.val = _ListCpy (list->v.list.val);
    any->v.list.index = DictCopy (list->v.list.index);
  }
  else 
    VarError (any, "list", "set");
}

/**api* function **************************************************************
**
**	Creates a new ANY with the copy of the list in another ANY.
**      If the input ANY is not a list it is appended to the list of the
**      output ANY. This allows also normal ANYs to be treated as lists.
**
**	INPUT:	    ANY object containg a list [R]
**
**      RETURN:     a new ANY object (use VarDestroy after use)
*/ 

ANYv AnyListCpy (ANYv list)
{
  ANYv any;

  _VarUnalias (list);
  any = VarNew ();
  any->type = VARxLIST;
  VarSetName (any, VarGetName (list));
  if (!(list->type == VARxLIST)) {
    AnySetList (any, AnyNewList ());
    AnyListApp (any, list);
  }
  else {
    if (list->isReadFunction)
      list = (*list->v.listGet)(list,_mA);
    any->v.list.val = _ListCpy (list->v.list.val);
    any->v.list.index = DictCopy (list->v.list.index);
  }
  return any;
}

INT4 AnyIsWrite (ANYv any)
{
  return any->isWrite;
}

void AnySetWrite (ANYv any)
{
  any->isWrite = 1;
}

INT4 VarIsAlias (VARo *var)
{
  return var->type == VARxALIAS ? 1 : 0;
}

/**api* VarGetAlias **************************************************************
**
**      Returns the aliased variable.
**
**	INPUT:	    alias any object  [W]
**                  scope object [R]
**
**      RETURNS:    Any object 
*/ 

VARo *VarGetAlias (VARo *alias, VARoSCOPE *scope)
{
  if (alias->code == 1)
    return (alias->v.alias);
  else if (!alias->isReadFunction) {
    if (!scope)
      _ErrExit (f__noVarScope);
    return (VARo*) ((ULONG)scope->var + (ULONG)alias->v.alias);
  }
  else 
    return (*alias->v.varGet)(alias);
}

/**api* VarSetAlias **************************************************************
**
**      Sets an variable with a pointer to a named variable.
**      If the variable with the specified name is not found it is newly
**      created. An alias is either automatically 'unaliased' or can be
**      explicitly unaliased with VarGetAlias.
**
**	INPUT:	    alias any object  [W]
**                  any object which is to be aliased [W]
**                  scope object [R]
*/ 

void VarSetAlias (VARo *alias, VARo *var, VARoSCOPE *scope)
{
  if (!alias->type) {
    alias->type = VARxALIAS;
  }
  if (alias->type == VARxALIAS) {
    alias->v.alias = (VARo*) ((char *) var - (char *) scope->var);
  }
  else 
    VarError(alias, "alias", "set");
}


/***** VarSetSubStr ***********************************************************
**
**	xx
**
**	INPUT:	    xx
**	        IMPLICIT:
**
**	RETURNS:    xx
*/ 

void VarSetSubStr (VARo *var, char *s, INT4 len)
{
  _VarUnalias(var);

  if (!var->type) {
    var->type = VARxSTRING;
    var->v.buff = BuffInit (var->v.buff, 0);
  }

  if (var->type == VARxSTRING) {
    BuffReset (var->v.buff);
    BuffCopyNChar(var->v.buff, s, len);
    BuffCopyNChar(var->v.buff, "\0", 1);
  }
  else 
    VarError(var, "string", "set");
}

/***** VarSetReadStr **********************************************************
**
**	xx
**
**	INPUT:	    xx
**	        IMPLICIT:
**
**	RETURNS:    xx
*/ 

void VarSetReadStr (VARo *var, SMoBUFF *(*getStr)(char *))
{
  _VarUnalias(var);
  var->type = VARxSTRING;
  var->v.buffGet = getStr;
  var->isReadFunction = 1;
}

/***** function **************************************************************
**
**	Sets a function to create the list when reading from the variable.
**
**	INPUT:	    'any' object 
**                  address of function returning a list
**
*/ 

void VarSetReadList (VARo *var, VARo *(*listGet)(char *))
{
  _VarUnalias(var);
  var->type = VARxLIST;
  var->v.listGet = listGet;
  var->isReadFunction = 1;
}

/***** VarSetReadStr **********************************************************
**
**	xx
**
**	INPUT:	    xx
**	        IMPLICIT:
**
**	RETURNS:    xx
*/ 

void VarSetReadStrv (VARo *var, STRv (*strVGet)(char *))
{
  _VarUnalias(var);
  var->type = VARxSTRV;
  var->v.strVGet = strVGet;
  var->isReadFunction = 1;
}

/***** VarSetReadVar **********************************************************
**
**	Sets a function for evaluating an alias.
**
**	INPUT:	    xx
**	        IMPLICIT:
**
**	RETURNS:    xx
*/ 

void VarSetReadVar (VARo *var, VARo *(*varGet)(char *))
{
  _VarUnalias(var);
  var->type = VARxALIAS;
  var->v.varGet = varGet;
  var->isReadFunction = 1;
}

/***** VarSetReadType *********************************************************
**
**	xx
**
**	INPUT:	    xx
**	        IMPLICIT:
**
**	RETURNS:    xx
*/ 

void VarSetReadType (VARo *var, void (*getType)(char *))
{
  _VarUnalias(var);
  var->type = 0;
  var->typeGet = getType;
  var->isDelayedType = 1;
  var->isTypeEval = 0;
}


/***** VarSetReadInt **********************************************************
**
**	xx
**
**	INPUT:	    xx
**	        IMPLICIT:
**
**	RETURNS:    xx
*/ 

void VarSetReadInt (VARo *var, INT4 (*getInt)(char *))
{
  _VarUnalias(var);
  var->type = VARxINT;
  var->v.intGet = getInt;
  var->isReadFunction = 1;
}


/***** VarSetReadReal *********************************************************
**
**	xx
**
**	INPUT:	    xx
**	        IMPLICIT:
**
**	RETURNS:    xx
*/ 

void VarSetReadReal (VARo *var, double (*getReal)(char *))
{
  _VarUnalias(var);
  var->type = VARxREAL;
  var->v.realGet = getReal;
  var->isReadFunction = 1;
}

/***** VarSetType *************************************************************
**
**	xx
**
**	INPUT:	    xx
**	        IMPLICIT:
**
**	RETURNS:    xx
*/ 

void VarSetType (VARo *var, enum VAReTYPE type)
{
  var->type = type;
}


/**api* function **************************************************************
**
**	Prints summary information about the 'any' object.
**
**	INPUT:	    'any' object [R]
*/ 

void AnyDebug (VARo *var)
{
  STRv s;
  char *tmp;

  printf ("name: \"%s\"\n", (tmp=VarGetName (var)) ? tmp : "unknown");
  printf ("type: %s\n", AnyGetTypeName (var->type));
  if (var->isReadFunction)
    printf ("evaluate: value\n");
  else if (var->isDelayedType)
    printf ("evaluate: value+type\n");
  else 
    printf ("evaluate: no\n");
  if (var->type == VARxLIST && var->v.list.val && !var->isReadFunction) {
    ListPtrDebug ((void**)var->v.list.val);
    DictDebug (var->v.list.index);
  }
  else if (var->type == VARxSTRV || var->type == VARxSTRING) {
    s = VarGetStrv (var);
    printf ("string value: |%s|\n", _Str (s));
    StrDel (s);
  }
  else if (var->type == VARxINT)
    printf ("string value: |%d|\n", VarGetInt (var));

  if (var->lineN)
    printf ("line no: %d\n", var->lineN);

  if (var->type == VARxALIAS) {
    _VarUnalias(var);
    printf ("-------------------------\naliased ANY:\n");
    AnyDebug (var);
  }
}


char *AnyDebugStr (ANYv any)
{
  static STRv str=NULL;
  STRv s;
  char *tmp;

  if (!str)
    str = StrNew ();
  else
    StrClear (&str);

  StrPrintf (&str, "name: \"%s\"", (tmp=VarGetName (any)) ? tmp : "unknown");
  StrPrintf (&str, ", type: \"%s\"", AnyGetTypeName (any->type));

  if (any->isReadFunction)
    StrPrintf (&str, ", evaluate: value");
  else if (any->isDelayedType)
    StrPrintf (&str, ", evaluate: value+type");

  if (any->type == VARxSTRV || any->type == VARxSTRING) {
    s = VarGetStrv (any);
    StrPrintf (&str, ", value: \"%s\"", _Str (s));
    StrDel (s);
  }
  else if (any->type == VARxINT)
    StrPrintf (&str, ", value: %d", VarGetInt (any));

  if (any->lineN)
    StrPrintf (&str, ", line No: %d", any->lineN);

  return _Str (str);
}


/***** VarDefName *************************************************************
**
**	Sets the name of the variable. String must be allocated outside and
**      will not be copied.
**
**	INPUT:	    variable object [W]
**                  name
**	        IMPLICIT:
**
**	RETURNS:    xx
*/ 

void VarDefName (VARo *var, char *name)
{
  var->name = (char *) malloc (strlen (name) + 1); 
  strcpy (var->name, name); /* te!!!*/
}

/***** VarSetName *************************************************************
**
**	Sets the name of the variable. String must be allocated outside and
**      will not be copied.
**
**	INPUT:	    variable object [W]
**                  name
**	        IMPLICIT:
**
**	RETURNS:    xx
*/ 

void VarSetName (VARo *var, char *name)
{
  if (var->name)
    free (var->name);
  if (name) {
    var->name = (char *)malloc (strlen (name)+1); 
    strcpy (var->name, name); /*!!!tesafety measure case var gets deleted */
  }
  else
    var->name = 0;
}

/***** VarSetFunction *********************************************************
**
**	xx
**
**	INPUT:	    xx
**	        IMPLICIT:
**
**	RETURNS:    xx
*/ 

void VarSetFunction (VARo *var, FUNC function)
{
  _VarUnalias(var);
  var->v.operator.function = function;
}

/***** VarSetInt **************************************************************
**
**	xx
**
**	INPUT:	    xx
**	        IMPLICIT:
**
**	RETURNS:    xx
*/ 

VARo *VarSetInt (VARo *var, INT4 i)
{
  _VarUnalias (var);
  if (var->isReadFunction)
    _ErrExit2 (e__varisreadonly, var->name);

  if (!var->type)
    var->type = VARxINT;

  if (var->type == VARxINT) {
    var->v.num = i;
  }
  else if (var->type == VARxSTRING) {
    BuffReset (var->v.buff);
    BuffPrintF (var->v.buff, "%d", i);
  }
  else if (var->type == VARxSTRV) {
    StrClear (&var->v.strv);
    StrPrintf (&var->v.strv, "%d", i);
  }
  else
    VarError(var, "string/int", "set");

  return var;
}

/***** VarSetReal *************************************************************
**
**	xx
**
**	INPUT:	    xx
**	        IMPLICIT:
**
**	RETURNS:    xx
*/ 

VARo *VarSetReal (VARo *var, double r)
{
  _VarUnalias (var);
  if (var->isReadFunction)
    _ErrExit2 (e__varisreadonly, var->name);

  if (!var->type)
    var->type = VARxINT;

  if (var->type == VARxINT) {
    var->v.real = r;
  }
  else if (var->type == VARxSTRING) {
    BuffReset (var->v.buff);
    BuffPrintF (var->v.buff, "%f", r);
  }
  else 
    VarError(var, "string/real", "set");
  return var;
}


VARo *VarSetVar (VARo *var, VARo *ptr)
{
  static char className[]="var";

  if (!var->type) {
    var->type = VARxVAR;
    var->v.object.className = className;
  }
  if (var->type == VARxVAR) {
    var->v.object.ptr = ptr;
  }
  else 
    VarError(var, "var", "set");
  return var;
}

VARo *VarGetVar (VARo *var, Int4 doEval)
{
  if (doEval) 
    _VarHandleTypeEval (var);

  if (var->type == VARxVAR) {
    return var->v.object.ptr;
  }
  else 
    return var;
}

VARo *VarFreeze (VARo *var)
{
  var->isTypeEval = 1;
  return var;
}


/***** VarSetObject ***********************************************************
**
**      Sets an object pointer variable. The class name is optional and
**      will be used for comparison if available.
**      The class name will not be copied and must be allocated by the 
**      caller.
**
**	INPUT:	    address of class name [R] or NULL
**                  variable object [W]
**                  object pointer [R]
**	        IMPLICIT:
**
**	RETURNS: 
*/ 

VARo *VarSetObject (char *className, VARo *var, void *ptr)
{
  _VarUnalias(var);
  if (!var->type)
    var->type = VARxOBJECT;

  if (var->type == VARxOBJECT) {
    if (className) {
      if (var->v.object.className)
	if (var->v.object.className && 
	    !SmEqs (var->v.object.className, className))
	  _ErrExit4 (e__varwrongclass, 
		    var->name, var->v.object.className, className);
      var->v.object.className = className;
    }
    var->v.object.ptr = ptr;
  }
  else 
    VarError(var, "object", "set");
  return var;
}


/**api* function **************************************************************
**
**      Iterates over all elements in the list. The context set to 0 starts
**      the iteration with the first element.
**      If the variable is not a list then the variable itself is returned.
**      The next call using the same variable will return a NULL pointer.
**      Thus, a list with one element is mimicked.
**
**      INPUT:   o  variable object of "list" type [W]
**               o  address of void pointer with the address of the 
**                  iterator [W]
**              IMPLICIT:
**
**      RETURNS:    the variable at current list position
**                  NULL if the list is exhausted
*/  

ANYv AnyNextInList (ANYv list, Int4 *i)
{
  ANYv elem=NULL;

  _VarUnalias (list);
  if (*i >= AnyListLen (list))
    *i = 0;
  else
    elem = list->v.list.val[(*i)++];
  return elem;
}

/**api* function **************************************************************
**
**      Returns the length of the list.
**
**      INPUT:      ANY object [R]
**
**      RETURNS:    length of the list
*/  

Int4 AnyListLen (ANYv list)
{
  return _ListLen (list->v.list.val);
}


/**api* function **************************************************************
**
**      Inserts a new element into a list. Use VarListAddAssoc to insert
**      a new element together with the name.
**
**      INPUT:      the variable representing the list [W]
**                  the new element to be added [R}
*/  

void AnyListApp (ANYv list, ANYv any)
{
  ANYv *anyPtr,**listVal;

  _VarUnalias (list);

  if (!list->type) {
    AnySetList (list, AnyNewList ());
  }
  if (list->type != VARxLIST) 
    VarError (list, "list", "add");

  listVal=&list->v.list.val;
  _ListApp (listVal)=any;
  if (any->name) {
    anyPtr = &DictSet (&list->v.list.index, any->name, ANYv);
    if (*anyPtr)
      _ErrExit2 (e__duplicatekey, any->name);
    else
      *anyPtr = any;
  }
}


/**api* function **************************************************************
**
**      Returns the list element with specified index. Index of 0 returns
**      the first element. 
**
**      INPUT:      any object [W]
**                  index [R]
**
**      RETURNS:    ANY object 
*/

ANYv AnyGetListIndex (ANYv any, INT4 index)
{
  _VarUnalias (any);
  if (any->type != VARxLIST)
    VarError (any, "list", "get");
 
  if (index < 0 || index >= AnyListLen (any))
    return VarNew ();
  else
    return any->v.list.val[index];
}

/**api* function **************************************************************
**
**      Gets the element with specified name from the list; creates a
**      new element if it is not found
**
**      INPUT:      the variable holding the list [W]
**                  the name of the element [R]
**              IMPLICIT:
**
**      RETURNS:    the element with specified name
*/

ANYv AnyGetListAssoc (ANYv list, char *name)
{
  Iter i;
  ANYv elem;

  _VarUnalias (list);

  if (!list->type)
    AnySetList (list, AnyNewList ());
  if (list->type == VARxLIST) {
    if ((i = DictWith (list->v.list.index, name)))
      elem =  DictIn (i, ANYv);
    else {
      elem = VarNew ();
      VarSetName (elem, name);
      AnyListApp (list, elem);
    }
  }
  else
    _ErrExit3 (e__icainvalidselect, name, VarGetName (list));
  return elem;
}

/**api* AnyFindListAssoc ******************************************************
**
**      Searches the element with specified name from the list; 
**
**      INPUT:      the variable holding the list [W]
**                  the name of the element [R]
**              IMPLICIT:
**
**      RETURNS:    the element with specified name
**                  NULL if not found
*/

ANYv AnyFindListAssoc (ANYv list, char *name)
{
  Iter i;
  ANYv elem=NULL;

  _VarUnalias (list);

  if (!list->type)
    AnySetList (list, AnyNewList ());
  if (list->type == VARxLIST) {
    if ((i = DictWith (list->v.list.index, name)))
      elem = DictIn (i, ANYv);
  }
  else
    _ErrExit3 (e__icainvalidselect, name, VarGetName (list));
  return elem;
}


/***** VarGetStr **************************************************************
**
**      Retrieves a "buffer" object from variable. If its type is 'int' or
**      'real' then a buffer is created with value represented as ASCII string.
**      If the variable pointer is NULL or the varible is existent but
**      undefined then a 'default' buffer with a NULL string is returned
**
**	INPUT:	    variable object [R]
**	        IMPLICIT:
**
**	RETURNS:    buffer object containing a string value
*/ 

char *VarGetStr (VARo *var)
{
  static SMoBUFF *buff[50]={NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL};
  static INT4 c=0;
  STRv   str;
  SMoBUFF *tmp;

  _VarUnalias (var);
  _VarHandleTypeEval (var);


  if (var->type == VARxSTRING)
    tmp = (var->isReadFunction ? (*var->v.buffGet)(var,_mA) : var->v.buff);
  else {
    tmp = (buff[c%10] = BuffInit (buff[c%10], 10));
    c++;
    if (var->type == VARxSTRV) {
      str = VarGetStrv (var);
      BuffCopyString (tmp, _Str (str));
      StrDel (str);
    }
    else if (var->type == VARxINT) {
      BuffPrintF (tmp, "%d", 
		  var->isReadFunction ? (*var->v.intGet)(var,_mA): var->v.num);
    }
    else if (var->type == VARxREAL) {
      BuffPrintF (tmp, "%f", 
		  var->isReadFunction ? (*var->v.realGet)(var,_mA): var->v.real);
    }
    else if (var->type) 
      VarError(var, "string/int", "get");
  }    
  return (BuffGetPtr(tmp));
}


/**api* VarDuplicate **********************************************************
**
**     Duplicates specified Any. Note that duplication is not the same
**     as creation of a copy with VarCopy.
**
**	INPUT:	    Any object to be duplicated [R]
**
**	RETURNS:    the duplicate
*/ 

VARo *VarDuplicate (VARo *var)
{
  VARo *new;

  new = VarNew ();
  memcpy (new, var, sizeof (VARo));
  return new;
}

/**api* VarCopy ***************************************************************
**
**     Copies a value inside an Any into some other. The other Any
**     can be supplied by the client or if left unspecified will be created.
**     This function will not simply duplicate the Any as VarDuplicate
**     but retrieve values in a standard fashion which can execute evaluation
**     functions.
**
**	INPUT:	    Any object to be copied [R]
**                  the Any which will receive the copy (or NULL) [W]
**
**	RETURNS:    the Any object with the copy
*/ 

VARo *VarCopy (VARo *from, VARo *to)
{
  STRv str;
  Int4 type;

  _VarUnalias (from);

  if (!to)
    to = VarNew ();
  else {
    _VarUnalias (to);
    VarReset (to);
  }
  _VarGetType (from, type); 
  switch (type) {
  case VARxINT:
    VarSetInt (to, VarGetInt (from));
    break;
  case VARxSTRING:
    VarSetStr (to, VarGetStr (from));
    break;
  case VARxSTRV:
    str = VarGetStrv (from);
    VarSetStrv (to, str); 
    break;
  case VARxLIST:
    AnySetList (to, from);
    break;
  case VARxOBJECT:
    VarSetObject (NULL, to, VarGetObject (NULL, from));
    break;
  case VARxUNKNOWN:
    break; /* do nothing */
  default:
    _ErrExit2 (e__unknownoption, "type in IopAss");
  }
  return to;
}



/***** VarExec ****************************************************************
**
**     Executes associated 'get' or 'type' function regardless of the type.
**
**	INPUT:	    variable object [R]
**	        IMPLICIT:
**
**	RETURNS:
*/ 

void VarExec (VARo *var)
{
  if (!var->isTypeEval) {
    VarGetType (var); 
    var->isTypeEval = 0;
  }

  else if (var->isReadFunction) {
    switch (var->type) {
    case VARxINT:
      (*var->v.intGet)(var,_mA);
      break;
    case VARxREAL:
      (*var->v.realGet)(var,_mA);
      break;
    case VARxSTRING:
      (*var->v.buffGet)(var,_mA);
      break;
    }      
  }
}


/**api* VarGetInt *************************************************************
**
**      Returns an integer value contained in the Any. Does implicit 
**      conversions from "string", "strv" and "real" Anys.
**
**	INPUT:	    Any object [R]
**	        IMPLICIT:
**
**	RETURNS:    the integer contained in the Any
*/ 

INT4 VarGetInt (VARo *var)
{
  INT4 num;

  _VarUnalias (var);
  _VarHandleTypeEval (var);

  if (var->type == VARxINT)
    num = var->isReadFunction ? (*var->v.intGet)(var,_mA) : var->v.num;
  else if (var->type == VARxREAL)
    num = var->v.real;
  else if (var->type == VARxSTRING)
    num = (atoi(BuffGetPtr (var->isReadFunction ? 
			    (*var->v.buffGet)(var,_mA) : var->v.buff)));
  else if (var->type == VARxSTRV) {
    STRv str;

    if (var->isReadFunction) {
      str = (*var->v.strVGet)(var,_mA);
      num = atoi(_Str (str));
      StrDel (str);
    }
    else 
      num = atoi (_Str (var->v.strv));
  }
  else if (!var->type)
    num = 0;
  else
    VarError(var, "string/int", "get");
  return(num);
}

/***** VarGetReal *************************************************************
**
**
**	INPUT:	    variable object [R]
**	        IMPLICIT:
**
**	RETURNS:    buffer object containing a string value
*/ 

double VarGetReal (VARo *var)
{
  double real;

  _VarUnalias (var);
  _VarHandleTypeEval (var);

  if (!var || !var->type) 
    return 0;

  if (var->type == VARxSTRING)
    real = (atof(BuffGetPtr (var->isReadFunction ? 
			    (*var->v.buffGet)(var,_mA) : var->v.buff)));
  else if (var->type == VARxREAL)
    real = var->v.real;
  else if (var->type == VARxINT)
    real = var->v.num;
  else 
    VarError(var, "string/real", "get");
  return(real);
}

/***** VarGetObject ***********************************************************
**
**      Returns the object pointer from variable. The class name is optional
**      and will be used for checking the compatibility if supplied.
**
**	INPUT:	    class name [R]
**                  variable object [R]
**	        IMPLICIT:
**
**	RETURNS:    the object pointer
*/ 

void *VarGetObject (char *className, VARo *var)
{
  _VarUnalias (var);
  _VarHandleTypeEval (var);

  if (var->type == VARxOBJECT) {
    if (className) {
      if (var->v.object.className)
	if (!SmEqs (var->v.object.className, className))
	  _ErrExit4 (e__varwrongclass, 
		    var->name, var->v.object.className, className);
      var->v.object.className = className;
    }
  }
  else 
    VarError(var, "object", "get");

  return var->v.object.ptr;
}



/***** VarGetFunction *********************************************************
**
**	xx
**
**	INPUT:	    xx
**	        IMPLICIT:
**
**	RETURNS:    xx
*/ 

FUNC VarGetFunction (VARo *var)
{
  _VarUnalias (var);
  return(var->v.operator.function);
}

/***** VarType ****************************************************************
**
**      Return the type of argument variable
**
**	INPUT:	    variable pointer
**	        IMPLICIT:
**
**	RETURNS:    the type of argument variable
*/ 

char VarType(VARo *var)
{
  _VarUnalias (var);
  return(var->type);
}




/**api* VarGetCode ************************************************************
**
**      Return the code of argument variable
**
**	INPUT:	    variable pointer
**	        IMPLICIT:
**
**	RETURNS:    the type of argument variable
*/ 

char VarGetCode(VARo *var)
{
  /*  _VarUnalias(var); */
  return(var->code);
}


/**api* VarSetCode ************************************************************
**
**      Set the code of argument variable
**
**	INPUT:	    variable pointer
**	        IMPLICIT:
**
**	RETURNS:    the type of argument variable
*/ 

void VarSetCode(VARo *var, char code)
{
  _VarUnalias(var);
  var->code = code;
}

/**api* VarSetClassName *******************************************************
**
**      Sets the class name of a variable of type 'object'.
**
**	INPUT:	    variable pointer
**	        IMPLICIT:
**
**	RETURNS:    the type of argument variable
*/ 

void VarSetClassName (VARo *var, char *className)
{
  var->v.object.className = className;
}

char *VarGetClassName (VARo *var)
{
  return var->v.object.className;
}

void VarSetLineN (VARo *var, INT4 lineN)
{
  var->lineN = lineN;
}

INT4 VarGetLineN (VARo *var)
{
  return var->lineN;
}


/**api* VarGetName *********************************************************
**
**      Returns the name of the any object. Returns the name
**      of the aliased any if input is an alias.
**
**	INPUT:	    any object
**	        IMPLICIT:
**
**	RETURNS:    the name of the any
*/ 

char *VarGetName(VARo *var)
{
  _VarUnalias(var);
  return(var->name);
}
/**api* VarGetRealName ********************************************************
**
**      Return the real name of the variable. Does not, in contrast to
**      VarGetName follow a link to an alias.
**
**	INPUT:	    variable object [R]
**	        IMPLICIT:
**
**	RETURNS:    the var object's real name
*/ 

char *VarGetRealName(VARo *var)
{
  return(var->name);
}

/***** VarGetPriority *********************************************************
**
**      Return the type of argument variable
**
**	INPUT:	    variable pointer
**	        IMPLICIT:
**
**	RETURNS:    the type of argument variable
*/ 

char VarGetPriority(VARo *var)
{
  _VarUnalias (var);
  return(var->v.operator.priority);
}

/***** VarSetPriority *********************************************************
**
**      Return the type of argument variable
**
**	INPUT:	    variable pointer
**	        IMPLICIT:
**
**	RETURNS:    the type of argument variable
*/ 

void VarSetPriority(VARo *var, char priority)
{
  var->v.operator.priority = priority;
}


/***** VarStackNew ************************************************************
**
**
**	INPUT:	    initial size of the stack [R]
**
**	RETURNS:    stack object 
*/ 

VARoSTACK *VarStackNew (INT4 size)
{
  VARoSTACK *stack;

  size = MAX(10, size);
  if (!(stack = (VARoSTACK *) malloc (sizeof(VARoSTACK))))
    _ErrExit2 (e__allocfail, "variable stack");
  if (!(stack->var = (VARo *) calloc (size*sizeof(VARo), 1)))
    _ErrExit2 (e__allocfail, "icarus stack array");
  
  stack->varN = 0;
  stack->varAllocN = size;
  return (stack);
}

/***** VarStackClose **********************************************************
**
**      Return the stack size
**
**      INPUT:      stack object [R]
**              IMPLICIT:
**
**      RETURNS:    numer of symbols in the stack
*/ 

void VarStackClose (VARoSTACK *stack)
{
  VARo *var;
  INT4 c;

  if (stack) {
    
    for (c=0; (var = VarInStackNext (stack, &c)); )
#ifdef buff
      if (var->type == VARxSTRING)
	  BuffDelete (&var->v.buff);
#endif
    if (stack->var)
      free (stack->var);
    free (stack);
  }
}

/***** VarStackReset **********************************************************
**
**      Return the stack size
**
**      INPUT:      stack object [R]
**              IMPLICIT:
**
**      RETURNS:    numer of symbols in the stack
*/ 

void VarStackReset (VARoSTACK *stack)
{
  VARo *var;
  INT4 c;

  for (c=0; (var = VarInStackNext (stack, &c)); ) {
#ifdef buff
    if (var->type == VARxSTRING) 
      BuffDelete (&var->v.buff);
#endif
    memset (var, 0, sizeof (VARo));
  }
  stack->varN = 0;
}


/***** VarStackSize ***********************************************************
**
**      Return the stack size
**
**      INPUT:      stack object [R]
**              IMPLICIT:
**
**      RETURNS:    numer of symbols in the stack
*/ 

INT4 VarStackSize (VARoSTACK *stack)
{
  return (stack->varN);
}

/***** VarStackIsEmpty ********************************************************
**
**      Check the stack size
**
**      INPUT:      stack object [R]
**              IMPLICIT:
**
**      RETURNS:    TRUE - stack id empty;
**		    FALSE - otherwise
*/ 

INT4 VarStackIsEmpty (VARoSTACK *stack)
{
  return stack->varN ? 0 : 1;
}




/***** VarStackDouble *********************************************************
**
**      Doubles the size of the stack.
**
**	INPUT:	    initial size of the stack [R]
**	        IMPLICIT:
**
**	RETURNS:    stack object 
*/ 

static void VarStackDouble (VARoSTACK *stack)
{
  stack->varAllocN *= 2;

  if ((stack->var = (void *) realloc
       (stack->var, stack->varAllocN * sizeof (VARo))) == NULL)
    _ErrExit2 (e__allocfail, "variable stack var list");
  
  memset (&stack->var[stack->varN], 0, 
	  (stack->varAllocN - stack->varN) * sizeof (VARo));
}

/***** VarPushCopy ************************************************************
**
**      Pushes a copy of the variable onto the stack.
**
**	INPUT:	    initial size of the stack [R]
**	        IMPLICIT:
**
**	RETURNS:    stack object 
*/ 

void VarPushCopy (VARoSTACK *stack, VARo *var)
{
  VARo *tmp;

  if (stack->varN >= stack->varAllocN)
    VarStackDouble (stack);

  tmp = &stack->var[stack->varN++];

  /* make sure a string from a previously stored var is freed */
#ifdef buff
  if (tmp->type == VARxSTRING)
    BuffDelete (&tmp->v.buff);
#endif  

  *tmp = *var;
}

/***** VarPushNew *************************************************************
**
**      Pushes a 'new' element onto the stack and returns a pointer to it.
**
**	INPUT:	    stack object [W]
**	        IMPLICIT:
**
**	RETURNS:    variable object 
*/ 

VARo *VarPushNew (VARoSTACK *stack)
{
  VARo *tmp;

  if (stack->varN >= stack->varAllocN)
    VarStackDouble (stack);

  tmp = &stack->var[stack->varN++];

  /* make sure a string from a previously stored var is freed */
  if (tmp->type == VARxSTRING) 
    BuffDelete (&tmp->v.buff);
  
  memset (tmp, 0, sizeof (VARo));
  return tmp;
}


/***** VarPushAlias ***********************************************************
**
**      Pushes an alias of the variable onto the stack.
**
**	INPUT:	    initial size of the stack [R]
**	        IMPLICIT:
**
**	RETURNS:    stack object 
*/ 

void VarPushAlias (VARoSTACK *stack, VARo *var)
{
  VARo *tmp;

  if (stack->varN >= stack->varAllocN)
    VarStackDouble (stack);

  tmp = &stack->var[stack->varN++];

  /* make sure a string from a previously stored var is freed */
  if (tmp->type == VARxSTRING)
    BuffDelete (&tmp->v.buff);

  tmp->type = VARxALIAS;
  tmp->v.alias = var;
}


/***** VarPop *****************************************************************
**
**      Pops last top element in stack into user variable.
**
**	INPUT:	    stack object [W]
**	        IMPLICIT:
**
**	RETURNS:    stack object 
*/ 

VARo *VarPop (VARoSTACK *stack)
{
  VARo *var;

  if (stack->varN > 0) {
    var = &stack->var[--stack->varN];
    return var;
  }
  else
    return NULL;
}

/***** VarInStackNext *********************************************************
**
**      Pops last bottom element in stack into user variable.
**
**	INPUT:	    stack object [W]
**	        IMPLICIT:
**
**	RETURNS:    stack object 
*/ 

VARo *VarInStackNext (VARoSTACK *stack, INT4 *count)
{
  if (*count >= stack->varN) {
    *count = 0;
    return NULL;
  }
  else 
    return &stack->var[(*count)++];
}


/***** VarStackPrint **********************************************************
**
**      xx
**
**      INPUT:      xx
**              IMPLICIT:
**
**      RETURNS:    xx
*/

static void VarStackPrintOne(VARo *var)
{
  printf("%-10s: ", AnyGetTypeName(VarType(var)));

  switch(VarType(var)) {
  case VARxINT:
    printf("%d", VarGetInt(var));
    break;
  case VARxREAL:
    printf("%f", VarGetReal(var));
    break;
  case VARxSTRING:
    printf("\"%s\"", VarGetStr(var));
    break;
  case VARxALIAS:
    printf("%s", VarGetName(var));
    break;
  case VARxOPERATOR:
    if(VarGetPriority(var))
      printf("%s(%d)", IcaFunctionName(var->v.operator.function),
                       VarGetPriority(var));
    else
      printf(">>>SEPARATOR<<<");
  default:
    break;
  }
  printf("\n");
}


void VarStackPrint(VARoSTACK *stack)
{
  INT4 i;

  for (i=0; i < stack->varN; i++) {
    printf("SYMBOL %d:  ", i);
    VarStackPrintOne(&stack->var[i]);
  }
  if(!stack->varN)
    printf("symbolstack empty !\n");
}


/****** VarNextArg ***********************************************************
**
**      Returns next argument in the stack.
**
**	INPUT:	    program object [R]
**	        IMPLICIT:
**
**	RETURNS:    
**		    variable object
**		    argument name,
**		    number of elements in argument if it is a list
**		    (0 in case of scalar argument)
**                  
*/ 

VARo *VarNextArg (VARoSTACK *stack, STRv *name, INT4 *listSize)
{
  static STRv unnamed;
  static STRv str=NULL;
  VARo *arg;
  INT4 k=0, code;
  
  if (!unnamed)
    unnamed = StrCpyS ("::::::::::");
  if (str)
    StrDel (str);

  if (!stack->varN) 
    arg = NULL;
  else {
    *listSize = 0;
    arg = VarPop (stack);
    if ((code = VarGetCode (arg)) == 111) /* end of the argument list */
      arg = NULL;
    else if (code == 114) { /* end of user argument list */
      VarPop (stack); /* delete function name */
      arg = NULL;
    }
    else {
      if (code == 113) { /* a list between curly braces */
	while (stack->var[stack->varN-k].code != 112)
	  k++;
	*listSize = k-1;
	str = VarGetStrv (&stack->var[stack->varN-1-k]);
	VarPop (stack); /* pop first parent */
      }      
      else if (stack->var[stack->varN-1].code == 110) { /* argument name */
	str = VarGetStrv (&stack->var[stack->varN-1-k]);
	VarPop (stack); /* pop arg name */
      }
      else
	str = StrCpy(unnamed);
    }
  }
  *name = str;
  return arg;
}

/**api* VarNextListItem *******************************************************
**
**
**	INPUT:	    program object [R]
**                  current execution time [R]
**	        IMPLICIT:
**
**	RETURNS:    
**                  
*/ 

VARo *VarNextListItem (VARoSTACK *stack, INT4 *listSize)
{
  (*listSize)--;
  return(&stack->var[stack->varN-*listSize]);
}

/****** VarPopList ************************************************************
**
**
**	INPUT:	    program object [R]
**	        IMPLICIT:
**
**	RETURNS:    
**                  
*/ 

void VarPopList (VARoSTACK *stack)
{
    while( VarGetCode(VarPop(stack)) != 112)
      ;
    if (stack->var[stack->varN-1].code == 110)
      VarPop (stack);
}

/****** VarGetUserCommand ****************************************************
**
**      This function gets the name of the user command which is 
**      unfortunately below its arguments on the bottom of the stack.
**
**	INPUT:	    program object [R]
**	        IMPLICIT:
**
**	RETURNS:    
**                  
*/ 

VARo *VarGetUserCommand (VARoSTACK *stack)
{
  VARo *var;
  INT4 k;

  for (k=stack->varN-1; k >= 0; k--) {
    var = &stack->var[k];
    if (VarGetCode (var) == 114)
      return &stack->var[k-1];
  }
  return NULL;
}



void VarSetArgs (VARo *var, VARo **args)
{
  var->args = args;
}

VARo **VarGetArgs (VARo *var)
{
  return var->args;
}


/***** VarPrintf **************************************************************
**
**      Formats a string with printf type format directives.
**      '%' characters must be written '%%' if they should appear in the
**      formatted string.
**      If the input variable does not a list then simply the string value
**      is returned.
**
**	INPUT:	    variable object (list or others) [R]
**
**	RETURNS:    formatted string
**                  empty string if there was a problem 
*/ 

STRv VarPrintf (VARo *list)
{   
  STRv str;
  VARo *var;
  Int4 c=0;
  STRv t, string;
  char *s, *tmp, saveChar;

  if (VarGetType (list) != VARxLIST) 
    return VarGetStrv (list);


  str = StrNew ();
  list = AnyListCpy (list);
  var = AnyNextInList (list, &c);
  string = VarGetStrv (var);
  s = tmp = _Str (string);

  while (1) {
    while (*s && *s != '%') {
      if (*s++ == '%' && *s == '%') { /* skip %% */
	s++;
	continue;
      }
    }      
    if (!*s) {
      StrAppS (&str, tmp);
      break;
    }
    s += strcspn (s, "sdfxc");
    saveChar = s[1];
    s[1] = '\0';
    if (!(var = AnyNextInList (list, &c))) {
      _ErrMsg2 (e__missingarg, "format print");
      VarDestroy2 (list);
      StrDel (string);
      return str;
    }
    switch (*s) {
    case 's':
      t = VarGetStrv (var);
      StrPrintf (&str, tmp, _Str (t)); 
      StrDel (t);
      break;
    case 'd':
      StrPrintf (&str, tmp, VarGetInt (var)); 
      break;
    default:
      _ErrMsg3 (e__novalchar, "format directive",  *s); 
      return str;
    }
    s[1] = saveChar;
    tmp = &s[1];
  }
  VarDestroy2 (list);
  StrDel (string);
  return  str;
}


/**api* function *************************************************************
**
**      Gets the string value held by an 'any' object.
**
**	INPUT:	    'any' object [R]
**
**	RETURNS:    a new copy of the string value
*/ 

STRv VarGetStrv (VARo *var)
{
  STRv tmp;

  _VarUnalias (var);
  _VarHandleTypeEval (var);

  if (var->type == VARxSTRV)
    tmp = (var->isReadFunction ? (*var->v.strVGet)(var,_mA) : 
	   StrCpy(var->v.strv));
  else if (var->type == VARxSTRING) {
    tmp = StrNew ();
    StrSetS (&tmp, (BuffGetPtr ((var->isReadFunction ? 
				 (*var->v.buffGet)(var,_mA) : var->v.buff))));
  }
  else if (var->type == VARxINT) {
    tmp = StrNew ();
    StrPrintf (&tmp, "%d", var->isReadFunction ? 
	       (*var->v.intGet)(var,_mA) : var->v.num);
  }
  else if (var->type == VARxREAL) {
    tmp = StrNew ();
    StrPrintf (&tmp, "%f", 
	       var->isReadFunction ? (*var->v.realGet)(var,_mA): var->v.real);
  }
  else if (!var->type)
    tmp = StrNew ();
  else 
    VarError(var, "string/int", "get");

  return tmp;
}

VARo *VarSetStrvS (VARo *var, char *s)
{
  _VarUnalias(var);
  
  if (var->isReadFunction)
    _ErrExit2 (e__varisreadonly, var->name);

  if (!var->type) {
    var->type = VARxSTRV;
    var->v.strv = StrNew ();
  }

  if (var->type == VARxSTRV) {
    StrSetS (&var->v.strv, s);
  }
  else if (var->type == VARxINT)
    var->v.num = atoi (s);
  else 
    VarError(var, "string/int", "set");

  return var;
}

/**api* function *************************************************************
**
**      Sets an 'any' object to contain a string value. The string value
**      will not be copied, so don't delete the string value after calling
**      with it this function.
**
**	INPUT:	    'any' object [W]
**                  string value [R]
**
**	RETURNS:    the 'any' object itself
*/ 

VARo *VarSetStrv (VARo *var, STRv str)
{
  _VarUnalias(var);
  
  if (var->isReadFunction)
    _ErrExit2 (e__varisreadonly, var->name);

  if (!var->type) {
    var->type = VARxSTRV;
  }
  if (var->type == VARxSTRV) {
    if (var->v.strv)
      StrDel (var->v.strv);
    var->v.strv = str;
  }
  else if (var->type == VARxINT) {
    var->v.num = atoi (_Str (str));
    StrDel (str);
  }
  else if (var->type == VARxREAL) {
    var->v.real = atof (_Str (str));
    StrDel (str);
  }
  else if (var->type == VARxSTRING) {
    var->v.buff = BuffInit (var->v.buff, 0);
    BuffCopyString (var->v.buff, _Str (str));
    StrDel (str);
  }    
  else 
    VarError(var, "string/int", "set");

  return var;
}

/**api* function *************************************************************
**
**      Appends a string value to the one held by the 'any' object.
**      argument string value will not be copied, 
**      so don't delete the string value after calling with it this function.
**
**	INPUT:	    'any' object [W]
**                  string value to be appended [R]
**
**	RETURNS:    the 'any' object itself
*/ 

VARo *VarAppStrv (VARo *var, STRv str)
{
  _VarUnalias(var);
  
  if (var->isReadFunction)
    _ErrExit2 (e__varisreadonly, var->name);

  if (var->type == VARxSTRV) 
    StrApp (&var->v.strv, str);
  else 
    VarSetStrv (var, str);

  return var;
}
*      argument string value will not be copied, 
**      so don't delete the string value after calling with it this function.
**
**	INPUT:	    'any' object [W]
**                  string value to be appended [R]
**
**	RETURNS:    the 'any' object itself
*/ 

VARo *VarAppSsrs/src/variable.h
**
**    $RCSfile: variable.h,v $
**    $Revision: 1.11 $
**    $Date: 1997/03/18 22:52:35 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**                  Copyright by Thure Etzold
**
*/

enum VAReTYPE {VARxUNKNOWN, VARxINT, VARxSTRING, VARxOBJECT, VARxREAL, VARxALIAS,
	       VARxVAR, VARxANY, VARxOPERATOR, VARxSTRV, VARxLIST=16};

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  object pointer
*/

typedef struct VARoOBJECT {
  void *ptr;
  char *className;
} VARoOBJECT;

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  operator
*/

typedef struct VARoOPERATOR {
  FUNC function;
  char priority;
} VARoOPERATOR;


/* for irix 64 - it needs the largest item in the begin of a union -
   the first member 'intGet' is used for initialization in icainit.c */

typedef struct DUMMY {
  INT4         (*intGet)();
  char         *some;
} DUMMY;

typedef struct VARo *VARv;
typedef struct VARo *ANYv;

typedef struct ANYoLIST {
  ANYv         *val;
  struct DICTo *index;
} ANYoLIST;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  the variable object
*/

typedef struct VARo {
  char *name;
  char type;
  char code;
  char isReadFunction;
  char isTypeEval;
  char isDelayedType;
  char isWrite;
  short lineN;
  union {
    DUMMY        dummy;
    INT4         (*intGet)();
    double       (*realGet)();
    SMoBUFF      *(*buffGet)();
    struct VARo  *(*varGet)();
    struct VARo  *(*listGet)();
    STRv         (*strVGet)();

    VARoOBJECT   object;
    VARoOPERATOR operator;
    INT4         num;
    STRv         strv;
    SMoBUFF      *buff;
    double       real;
    struct ANYoLIST list;
    struct VARo  *alias;
  } v;
  struct VARo **args;
  void         (*typeGet)();

#ifdef xxx
  struct info {
    unsigned int 
    type:4
    code:8
    isReadFunction:1
    isTypeEval:1
    isDelayedType:1
    lineN:14 
    fileX:3
  }
#endif
} VARo;



/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  var scope - defines a space for contiguous allocation for variables
*/

typedef struct VARoSCOPE {
  struct DICTo *dict;
  VARo *var;
  INT4 varAllocN;
  INT4 varN;
} VARoSCOPE;


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  stack object
*/

typedef struct VARoSTACK {
  VARo *var;

  INT4 varAllocN;
  INT4 varN;
} VARoSTACK;

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  stack object for icarus level 4
*/

typedef struct VARoStack {
  VARo **ptr;
  Int4 n;
  Int4 allocN;
} VARoStack;


#define _VarGetType(var,x) \
  if ((var)->type == VARxALIAS) {\
     (x) = VarGetType (var);} \
  else if (!(var)->isTypeEval && (var)->isDelayedType) { \
    (*(var)->typeGet)(var); \
    (var)->isTypeEval = 1; \
    (x) = var->type; \
  } else  (x) = var->type


    /* general functions */

VARv  VarGet (struct VARoSCOPE **scope, char *varName);
VARv  VarTemp ();
VARv  VarNew ();
void  VarReset (VARv var);
VARv  VarGetUserCommand (VARoSTACK *stack);
void  VarSetType (VARv var, enum VAReTYPE type);
char  VarType(VARv var);
char* VarGetName(VARv var);
char* VarGetRealName(VARv var);
void  VarSetAlias (VARv alias, VARv var, VARoSCOPE *scope);
VARv  VarGetAlias (VARv alias, VARoSCOPE *scope);
VARv  VarGetVar (VARv var, Int4 doEval);
VARv  VarCopy (VARv from, VARv to);
VARv  VarDuplicate (VARv var);
VARv  VarGet (VARoSCOPE **scope, char *name);
char *AnyDebugStr (ANYv any);


    /* work on 'string' variables */

VARv  VarSetStr (VARv var, char *s);
void  VarSetSubStr (VARv var, char *s, INT4 len);
char* VarGetStr (VARv var);
void  VarSetReadStr (VARv var, SMoBUFF *(*getStr)(char *));
STRv  VarPrintf (VARv list);

    /* work on 'STRv' variables */

void VarSetReadStrv (VARo *var, STRv (*strVGet)(char *));
STRv VarGetStrv (VARv var);
VARv VarSetStrvS (VARv var, char *s);
VARv VarSetStrv (VARv var, STRv str);
VARo *VarAppStrv (VARo *var, STRv str);

    /* work on 'real' variables */

struct VARo  *VarSetReal (VARv var, double real); 
double VarGetReal (VARv var); 
void   VarSetReadReal (VARv var, double (*getReal)());

    /* work on 'object' variables */

VARv  VarSetObject (char *className, VARv var, void *object); 
void* VarGetObject (char *className, VARv var);
void  VarSetReadObject (VARv var, void (*getObject)(char *));

    /* work on 'num' variables */

VARv VarSetInt (VARv var, INT4);
INT4 VarGetInt (VARv var);
void VarSetReadInt (VARv var, INT4 (*getInt)(char *));

    /* work on 'operator' variables */

void VarSetFunction (VARv var, FUNC function);
FUNC VarGetFunction (VARv var);
void VarSetPriority(VARv var, char priority);
char VarGetPriority(VARv var);
void VarSetCode(VARv var, char code);
char VarGetCode(VARv var);

    /* work on 'list' variables */


void VarSetReadList (VARo *var, VARo *(*listGet)(char *));
ANYv AnyNextInList (VARv var, Int4 *i);
ANYv AnyNextInList (VARv var, Int4 *i);
void AnyListApp (VARv list, VARv any);
ANYv AnyNewList ();
ANYv AnyListCpy (VARv list);
ANYv AnyGetListIndex (VARv var, INT4 index);
ANYv AnyGetListAssoc (VARv var, char *name);
ANYv AnyFindListAssoc (VARv var, char *name);
Int4 AnyListLen (ANYv list);

    /* functions for variable stack management */ 

void       VarStackClose (VARoSTACK *stack);
void       VarStackReset (VARoSTACK *stack);
void       VarStackPrint (VARoSTACK *stack);
INT4       VarStackSize (VARoSTACK *stack);
VARoSTACK *VarStackCopy (VARoSTACK *stack);
VARoSTACK *VarStackNew (INT4 size);
VARo      *VarInStackNext (VARoSTACK *stack, INT4 *c);
VARo      *VarPop (VARoSTACK *stack);
VARo      *VarPushNew (VARoSTACK *stack);
void       VarPushAlias (VARoSTACK *stack, VARv var);
void       VarPushCopy (VARoSTACK *stack, VARv var);

    /* functions to treat stack object */

VARv VarNextArg(VARoSTACK *stack, struct STRo **name, INT4 *ListSize);
VARv VarNextListItem(VARoSTACK *stack, INT4 *ListSize);
void         VarPopList(VARoSTACK *stack);

    /* icarus level 4 stack functions */

struct VARoStack *VarStackInit (struct VARoStack *stack);
void VarPush2 (struct VARoStack *stack, VARv var);
VARv VarPop2 (struct VARoStack *stack);


    /* others */

INT4 VarIsAlias (VARv var);
void VarSetArgs (VARv var, VARv *args);
void VarSetName (VARv var, char *name);
VARv *VarGetArgs (VARv var);
char *VarGetClassName (VARv var);
struct VARoSCOPE *VarCopyScope (struct VARoSCOPE *scope);
INT4 VarGetLineN (VARv var);
void VarSetLineN (VARv var, INT4 lineN);
VARv VarSetVar (VARv out, VARv in);
VARv VarFreeze (VARv var);


VARo *VarUnalias (VARo *alias);
#define _VarUnalias(x)  if ((x)->type == VARxALIAS) (x) = VarUnalias(x)
ruct VARoStack *stack);


    /* others */

INT4 VarIsAlias (VARv var);
void VarSetArgs (VARv var, VARv *args);
void VarSetName (VARv var, char *name);
VARv *VarGetArgs (VARv var);
char *VarGetClassName (VARv var);
struct VARoSCOPE *VarCopyScope (struct VARoSCOPE *scope);
INT4 VarGetLineN (VARv var);
void VarSetLineN (VARv var, INT4 lineN);
VARv VarSetVar (VARv out, VARv in);
VARv VarFreeze (VARv var);


VARo *VarUnalias (VARo *alias);
#define _VarUnalias(x)  if ((x)->typesrs/src/view.c
#include <stdlib.h>
#include <string.h>

#include "message.h"
#include "sm.h"
#include "strv.h"
#include "dict.h"
#include "futil.h"
#include "templ.h"
#include "library.h"
#include "par.h"
#include "entry.h"

#define	_SRS      
#define _SLB      
#include "srs5.h"
#include "view.h"

enum VIEWeFormat {VIEWxTable=1, VIEWxList};

typedef struct VIEWoLIST {
  VIEWo  **views;
  Int4   viewsN;
  Int4   viewsAllocN;
  DICTv  dict;
  VIEWo  *(*getUserView)(Int4, TEMPLv);
  Int4   userViewN;
  TEMPLv userTempl;
} VIEWoLIST;


static void ViewUpdateRootLib (VIEWo *view, VIEWoLIB *vlib);


static VIEWoLIST staticViewList;
static VIEWoLIST *viewList = &staticViewList;




static void ViewAddList (VIEWoLIST *list, VIEWo *view)
{
  DictAddPtr (&list->dict, view);
  *(_addObj (list->views, list->viewsN, 
	     list->viewsAllocN, VIEWo*)) = view;
}

/**api* ViewGetViewsN ******************************************************
**
**       Returns the number of views defined.
**
**       RETURNS:   the number of views defined
**
*/

Int4 ViewGetViewsN ()
{
  return viewList->viewsN;
}


/**api* ViewInitDefined ******************************************************
**
**       Initializes all views defined in Icarus programs.
**
**       INPUT:    array with views defined in Icarus [W]
**                 number of views in the array [R]
**
*/

void ViewInitDefined (VIEWo *views, Int4 viewN)
{
  VIEWo    *view;
  VIEWoLIB *vlib;
  Int4     k, l;

  if (!viewList->dict)
    viewList->dict = 
      DictCreate (DictCreateClassStrZKey (NULL, mPtr (VIEWo, name), 0));
  for (k=0,l=0; k < viewN; k++) {
    view = &views[k];
    vlib = ViewGetNextRootLib (view, &l);
    for(l=0; (vlib = ViewGetNextRootLib (view, &l));)
      ViewUpdateRootLib (view, vlib);
    ViewAddList (viewList, view);
  }
}





/**api* ViewMarkDeleted ******************************************************
**
**       Mark deleted view to be logically deleted.
**       Check if a view is deleted with ViewIsDeleted.
**
**       INPUT:   Address of view Object [R]
**
*/

void ViewMarkDeleted (VIEWo *view)
{
  char par[80], *tmp;
  view->isDeleted = 1; /* set the status flag */
  sprintf(par,"ViewDeleted_%d", view->n);
  if (*(tmp = ParGetStrF ("selectedViewNo_%d", view->n)))
    ParDelete (tmp);
  ParDefNum (par,1);
}

/**api* ViewMarkNascent ******************************************************
**
**       Mark view to be nascent.
**
**       INPUT:    Address of view Object (or NULL) [W]
**                 view number [R]
**
*/

void ViewMarkNascent (VIEWo *view, INT4 viewN)
{
  char par[80];
  if (view)
    view->isNascent = 1; 
  sprintf(par,"v%d_isNascent", viewN);
  ParDefNum (par, 1);
}

/****** ViewIsDeleted *********************************************************
**
**      Checks for the logical deletion of a view object with ViewMarkDeleted.
**
**      INPUT:   Address of view object [R]
**           IMPLICIT
**
**      RETURNS: delete flag
*/

INT4 ViewIsDeleted(VIEWo *view)
{
  return(view->isDeleted);
}

/**API* ViewGetEntryNamePrinting **********************************************
**
**      Returns if the printing of the entry name before the selected 
**      information from entry is selected
**
**      INPUT:    view object [R]
**
**      RETURNS:  flag if entry name should be printed
*/

Int4 ViewIsEntryNamePrinting (VIEWo *view)
{
  return view->isEntryNamePrinting;
}

/**api* ViewIsTable ***********************************************************
**
**      Checks if view is to be displayed as a table
**
**      INPUT:   view object [R]
**
**      RETURNS: TRUE or FALSE
*/

INT4 ViewIsTable (VIEWo *view)
{
  return (view->format == VIEWxTable);
}


/**api* ViewIsShortNames ******************************************************
**
**      Checks whether field names in the table header are abbreviations 
**      rather than the full names.
**
**      INPUT:   view object [R]
**
**      RETURNS: TRUE or FALSE
*/

INT4 ViewIsShortNames (VIEWo *view)
{
  return(view->useShortFieldNames);
}

/**api* ViewIs ****************************************************************
**
**      Returns TRUE if specified characteristic applies to view.
**
**      INPUT:   view object [R]
**               option: "selected", "nascent", "forAll" [R]
**
**      RETURNS: TRUE or FALSE
*/

Int4 ViewIs (VIEWo *view, char *option)
{
  switch (option[0]) {
  case 's':
    return (*ParGetStrF ("selectedViewNo_%d", view->n) ? 1 : 0);
  case 'n':
    return ParGetNumF ("v%d_isNascent", view->n);
  case 'f': /* forAll */
    return view->rootN == 0 ? 1 : 0;
  default:
    _ErrExit2 (e__unknownoption, option);
  }
  return 0;
}


Int4 ViewIsRootField (VIEWo *view, SLBoFIELD *field)
{
  SLBoFIELD *tmp;
  VIEWoLIB  *vlib;
  Int4      c1=0, c2;
  
  vlib = ViewGetNextRootLib (view, &c1);
  for (c2=0; (tmp = ViewGetNextField (vlib, &c2));)
    if (field == tmp)
      return 1;
  return 0;
}

Int4 ViewIsLeafField (VIEWo *view, VIEWoLIB *vlib, SLBoFIELD *field)
{
  SLBoFIELD *tmp;
  VIEWoLIB  *tmpVlib;
  Int4      c1, c2;
  
  for (c1=0; (tmpVlib = ViewGetNextLeafLib (view, &c1));)
    if (vlib == tmpVlib)
      for (c2=0; (tmp = ViewGetNextField (vlib, &c2));)
	if (field == tmp)
	  return 1;
  return 0;
}


/**api* ViewNew ***************************************************************
**
**      Creates a new empty view which can be later identified by the
**      specified number or name.
**
**      INPUT:    view number [R]
**                view name [R] or NULL
**              IMPLICIT:
**                viewList [W]
**
**      RETURNS:  the view library object [R]
*/

VIEWo *ViewNew (Int4 n, char *name)
{
  VIEWo *view;

  if (!(view = (VIEWo *) calloc (1, sizeof (VIEWo))))
    _ErrExit2 (e__allocfail, "view object");
  view->n = n;
  if (name && *name)
    ViewSetName (view, name);
  return view;
}

/**api* ViewAddRootField ******************************************************
**
**      Adds a field to the root library(s).
**
**      INPUT:    view object [W]
**                field type object [R}
**
**      RETURNS:  the view field object [R]
*/

VIEWoFIELD *ViewAddRootField (VIEWo *view, SRSoFLD *fieldType) 
{
  VIEWoFIELD *vfield;
  VIEWoLIB   *vlib;

  if (!view->rootN)
    /*    _ErrExit (e__viewMissingRootLib);*/

  vlib = &view->root[0]; /* add all fields to the FIRST root library */

  vfield = _addObj (view->rootFields, view->rootFieldsN,
		    view->rootFieldsAllocN, VIEWoFIELD);
  memset (vfield, 0, sizeof (VIEWoFIELD));
  vfield->type = fieldType;
  return vfield;
}

void ViewSetUserList (VIEWo *(*getView)(Int4 n, TEMPLv templ), 
		      TEMPLv templ)
{
  VIEWo *view;
  Int4  k;

  viewList->getUserView = getView;
  viewList->userTempl = templ;

  for (k=viewList->viewsN+1; (view = (*viewList->getUserView) (k, templ)); k++) {
    ViewAddList (viewList, view);
  }
}

/**api* function **************************************************************
**
**      Returns view with specified name.
**
**      INPUT:    name of view [R]
**
**      RETURNS:  the first view with that name 
**                NULL: view with name has not been found
*/

VIEWo *ViewGetNamed (char *name)
{
  VIEWo *view;
  Int4 k;

  for (k=0; (view=ViewNext (&k));)
    if (SmEqs (name, ViewGetName (view)))
      return view;
  return NULL;
}



/**api* ViewNext **************************************************************
**
**      Iterates over all views. Assignes a view number which can be obtained
**      with ViewGetNo.
**
**      INPUT:    address of iterator [W]
**
**      RETURNS:  the next view object
**                NULL: end of list
*/

VIEWo *ViewNext (Int4 *c)
{
  VIEWo *view;
  Int4  userViewN;

  if (*c < viewList->viewsN) {
    view = viewList->views[(*c)++];
    if (!view->n)
      view->n = *c;
    return view;
  }
  else {
    *c = 0;
    return NULL;
  }
}

/**api* ViewSetWithNo *********************************************************
**
**      Sets or replaces view with specified number.
**
**      INPUT:    view object [R]
**                view number [R]
**
*/

void ViewSetWithNo (VIEWo *view, Int4 viewNo)
{
  viewList->views[viewNo-1] = view;
}


/**API* ViewGetWithNo *********************************************************
**
**      Returns view with a certain number.
**
**      INPUT:    view number [R]
**
**      RETURNS:  the view object
**                NULL: view with number was not found
*/

VIEWo *ViewGetWithNo (Int4 n)
{
  if (n <= viewList->viewsN && n > 0)
    return viewList->views[n-1];
  else 
    return NULL;
}



/**API* ViewAddField **********************************************************
**
**      Adds a field to a view library. Use ViewSetFieldFormat to set
**      its format, if applicable and ViewAddRootField to add a field to
**      the view root library(s).
**
**      INPUT:    view library object [W]
**                field type object [R}
**
**      RETURNS:  the view library object [R]
*/

VIEWoFIELD *ViewAddField (VIEWoLIB *vlib, SRSoFLD *fieldType) 
{
  VIEWoFIELD *vfield;

  vfield= _addObj (vlib->fields, vlib->fieldsN, vlib->fieldsAllocN,VIEWoFIELD);
  memset (vfield, 0, sizeof (VIEWoFIELD));
  vfield->type = fieldType;
  return vfield;
}

/**api* ViewAddRootLib ********************************************************
**
**      Adds a new root library to the view. 
**
**      INPUT:    view object [W]
**                query string [R}
**
**      RETURNS:  the view library object [R]
*/

VIEWoLIB *ViewAddRootLib (VIEWo *v, SLBo *lib)
{
  VIEWoLIB *vlib;

  vlib = _addObj (v->root, v->rootN, v->rootAllocN, VIEWoLIB);
  memset (vlib, 0, sizeof (VIEWoLIB));
  vlib->lib = lib;
  return vlib;
}

/**api* ViewAddLeafLib ********************************************************
**
**      Adds a new root library to the view. 
**
**      INPUT:    view object [W]
**                query string [R}
**
**      RETURNS:  the view library object [R]
*/

VIEWoLIB *ViewAddLeafLib (VIEWo *v, SLBo *lib)
{
  VIEWoLIB *vlib;

  vlib = _addObj (v->leaves, v->leavesN, v->leavesAllocN, VIEWoLIB);
  memset (vlib, 0, sizeof (VIEWoLIB));
  vlib->lib = lib;
  return vlib;
}

/**api* ViewSetLeafQuery *****************************************************
**
**      Sets the query string to be used for linking from the root library
**      to specified leaf library.
**
**      INPUT:    view library object [W]
**                query string [R}
*/

void ViewSetLeafQuery (VIEWoLIB *vlib, char *query)
{
  if (vlib->query)
    free (vlib->query);
  vlib->query = (char *) malloc (strlen (query)+1);
  strcpy (vlib->query, query);
}

/**api* ViewSetFormat *********************************************************
**
**      Sets the view to be in table format or not
**
**      INPUT:   view object [R]
**               format option: "table", "list" [R]
*/

void ViewSetFormat (VIEWo *view, char *format)
{
  if (format[0] == 't')
    view->format = VIEWxTable;
  else 
    view->format = VIEWxList;
}

/**api* ViewSetUseShortNames **************************************************
**
**      Sets whether or not to use short field names in the header of 
**      table views.
**
**      INPUT:   view object [W]
**               flag [R]
*/

void ViewSetUseShortNames (VIEWo *view, Int4 flag)
{
  view->useShortFieldNames = flag;
}

/**api* ViewSetLeafView ******************************************************
**
**      Sets a view from entries of the specified leaf library.
**
**      INPUT:    view library object [W]
**                view Name [R}
*/

void ViewSetLeafView (VIEWoLIB *vlib, char *viewName)
{
  if (vlib->viewName)
    free (vlib->viewName);
  vlib->viewName = (char *) malloc (strlen (viewName)+1);
  strcpy (vlib->viewName, viewName);
}

/**api* ViewSetLeafPrintN *****************************************************
**
**      Sets flag that only the number of linked entries is printed for a
**      leaf library.
**
**      INPUT:    view library object [W]
**                flag [R]
*/

void ViewSetLeafPrintN (VIEWoLIB *vlib, Int4 flag)
{
  vlib->printOnlyEntryN = flag; 
}

/**api* ViewSetFieldFormat ****************************************************
**
**      Sets for both root and leaf library fields the format. The address
**      of string argument must be static. This address can be obtained
**      by LibFieldFormat.
**
**      INPUT:    view field object [W]
**                address of format name [R]
*/

void ViewSetFieldFormat (VIEWoFIELD *vfield, char *format)
{
  if (format && *format)
    vfield->format = format;
}

/**api* ViewGetNextField ******************************************************
**
**      Returns the next field in the view object.
**
**      INPUT: address of view object [R]
**             address of context [W]
**
**      RETURNS:  next field object 
**                NULL: end of list
**
*/

SLBoFIELD *ViewGetNextField(VIEWoLIB *vlib, INT4  *context)
{
  SLBoFIELD *field;
  SRSoFLD *type;

  if (!vlib)
    return NULL;
  if (vlib->fieldsN > *context) {
    type = vlib->fields[(*context)++].type;
    if (!(field = LibHasField (vlib->lib, type)))
      _ErrExit3 (e__dbhasnotfield, LibName (vlib->lib), 
		 LibGetFieldTypeName (type)); 
    return field;
  }
  else {
    *context = 0;
    return NULL;
  }
}

VIEWoFIELD *ViewGetNextVfield(VIEWoLIB *vlib, INT4  *context)
{
  if (vlib->fieldsN > *context)
    return &vlib->fields[(*context)++];
  else {
    *context = 0;
    return NULL;
  }
}

/****** ViewGetNumOfLeafFields ************************************************
**
**      Counts number of leaf fields defined
**
**      INPUT:    address of view object [R]
**           IMPLICIT
**
**      RETURNS:  number of fields defined
**
**
*/

INT4  ViewGetNumOfLeafFields(VIEWo *view)
{
  INT4 m,k;

  for (m=0, k=0; k < view->leavesN; k++) 
    m += view->leaves[k].fieldsN;

  return m;
}

/****** ViewGetNumOfLeafFields ************************************************
**
**      Counts number of root fields defined
**
**      INPUT:    address of view object 
**
**      RETURNS:  number of fields defined
**
*/

INT4 ViewGetNumOfRootFields(VIEWo *view)
{
  INT4 m,k;
  
  return view->rootFieldsN;
}

/**api*  ViewSetName *********************************************************
**
**       Sets the name of a view. The name is entered into 
**       both the view object and the user context 
**
**       INPUT:  address of view object [W]
**               the name [R]
**
**       RETURNS:  view name
**
*/

void ViewSetName (VIEWo *view, char *name)
{
  char parName[100];

  sprintf (parName,"view%d_Name", view->n);
  ParDefStr (parName, name);
  view->name = ParGetStr (parName);
}


/**api*  ViewGetName ********************************************************
**
**       returns the name of the view
**
**       INPUT:  address of view object [R]
**
**       RETURNS:  view name
**
*/

char *ViewGetName(VIEWo *view)
{
  return(view->name);
}

/**api* ViewDelete ***********************************************************
**
**      Deletes the view object obtained with ViewGet.
**
**      INPUT:     address of view object [W]
**
*/

void ViewDelete (VIEWo *view)
{
  if (view) {
    free (view);
  }
}

/**api* ViewGetViewNumber ***************************************************
**
**      Gets the number of the view with the specified name.
**      See also ViewGet, ViewGetLeafView.
**
**      INPUT:   the name of the view [R] 
**
**      RETURN:  the number of the view
**
**
*/

INT4  ViewGetViewNumber (char *viewName)
{
  VIEWo *view;
  INT4  c, l;

  for (c=0,l=1; (view=ViewNext (&c)); l++) {
    if (SmEqs (viewName, ViewGetName (view)))
      return l;
  }
  return 0;
}

Int4 ViewGetNo (VIEWo *view)
{
  return view->n;
}

static void ViewUpdateRootLib (VIEWo *view, VIEWoLIB *vlib)
{
  vlib->fields = view->rootFields;
  vlib->fieldsN = view->rootFieldsN;
}


/**api* ViewGetNextRootLib ***************************************************
**
**     Returns next view root library. context must be initially 
**     set to 0;
**
**     INPUT:   address of the view object [R]
**              address of the context [W]
**
**     RETURNS: the view lib object
**              NULL: end of list
*/

VIEWoLIB *ViewGetNextRootLib(VIEWo *view, INT4   *context)
{
  VIEWoLIB *tmp = &view->root[(*context)++];

  if (*context <= view->rootN) {
    ViewUpdateRootLib (view, tmp);
    return tmp;
  }
  else {
    *context = 0; /* reset for reuse */
    return NULL;
  }
}

/**api* ViewGetNextLeafLib ***************************************************
**
**     Returns next view root library. context must be initially 
**     set to 0;
**
**     INPUT:   address of the view object 
**              address of the context
**
**     RETURNS: name of the view leaf library
**              NULL if no more leaflibrary
*/

VIEWoLIB *ViewGetNextLeafLib(VIEWo *view, INT4 *context)
{
  VIEWoLIB *tmp = &view->leaves[(*context)++];
  
  if (*context <= view->leavesN)
    return tmp;
  else {
    *context = 0; /* reset for reuse */
    return NULL;
  }
}

/**api* ViewLeafIsOnlyEntryN **************************************************
**
**     Returns TRUE if only the number of linked entries should be displayed.
**
**     INPUT:   leaf library object [R]
**
**     RETURNS: 1: yes
**              0: no
*/

Int4 ViewLeafIsOnlyEntryN (VIEWoLIB *vlib)
{
  return vlib->printOnlyEntryN;
}

/**api* ViewGetLeafView *******************************************************
**
**     Returns the name of the view associated with the leaf.
**     Use ViewGetViewNumber and ViewGet to obtain the view object.
**
**     INPUT:   leaf library object [R]
**
**     RETURNS: the view name
**              Null string: no view associated with leaf
*/

char *ViewGetLeafView (VIEWoLIB *vlib)
{
  static char empty[]="";
  return vlib->viewName ? vlib->viewName : empty;
}

/**api* ViewLeafQuery ********************************************************
**
**     Returns the query string associated with the leaf query. See also
**     ViewGetLeafQuery.
**     root entry.
**
**     INPUT:   leaf library object [R]
**
**     RETURNS: query string
*/

char *ViewGetLeafQueryStr (VIEWoLIB *vlib)
{
  static char empty[]="";
  return vlib->query ? vlib->query : empty;
}

/**api* ViewLeafQuery ********************************************************
**
**     Returns the query with which to get the leaf entry set for specified 
**     root entry.
**
**     INPUT:   leaf library object [R]
**              entry object [R]
**
**     RETURNS: query string
*/

char *ViewGetLeafQuery (VIEWoLIB *vlib, ENTRYv entry)
{
  SLBo *lib=EntryGetLib (entry);
  static char queryStr[500];
  char *tmp, entryStr[200];

  if (*(tmp = ViewGetLeafQueryStr (vlib))) {
    strcpy (queryStr , tmp);
    sprintf (entryStr, "[%s-%s:%s]", 
	     LibName (lib), 
	     FieldGetName (LibGetIdField (lib)),
	     EntryGetName (entry));
    SmSwapFirst (queryStr, "entry", entryStr);
  }
  else 
    sprintf (queryStr, "[%s-%s:%s] > %s", 
	     LibName (lib), FieldGetName (LibGetIdField (lib)),
	     EntryGetName (entry), LibName (vlib->lib));

  return queryStr;
}



LIBoFieldFormat *ViewGetFieldFormat (VIEWoLIB *vlib, SLBoFIELD *field)
{
  SRSoFLD    *type=LibFieldType (field);
  VIEWoFIELD *vfield;
  Int4       c;

  for (c=0; (vfield = ViewGetNextVfield (vlib, &c));)
    if (vfield->type == type)
      return LibFieldFormat (field, vfield->format);
  return NULL;
}



/****** ViewCountRootLib **************************************************
**
**     Returns next view root library. context must be initially 
**     set to 0;
**
**     INPUT :  address of the view object 
**              address of the context
**
**     RETURNS: name of the view root library
**              NULL if no more root library
**
**
**
*/

Int4 ViewCountRootLibs(VIEWo *view)
{
  Int4 k,j;

  for(k=0,j=0; ViewGetNextRootLib(view,&k) ;j++ )
    ;
    return j;
}


/****** ViewCountLeafLib **************************************************
**
**
**
*/

Int4 ViewCountLeafLibs(VIEWo *view)
{
  Int4 k,j;

  for(k=0,j=0; ViewGetNextLeafLib(view,&k) ;j++ )
    ;
    return j;

}


void ViewSetTemplate (VIEWo *view, TEMPLv templ)
{
  view->templ = templ;
}

TEMPLv ViewGetTemplate (VIEWo *view)
{
  return view->templ;
}


void ViewSetTemplateFile (VIEWo *view, char *fileName)
{
  if (view->templateFile)
    free (view->templateFile);
  view->templateFile = (char *) malloc (strlen (fileName)+1);
  strcpy (view->templateFile, fileName);
}


void ViewTemplateBegin (VIEWo *view)
{
  char *fileName;

  if (!view->templ) {
    if (view->templateFile && *view->templateFile)
      fileName = view->templateFile;
    else
      fileName = "SRSICA:ascii.it";
    view->templ = TemplOpen (fileName, NULL);
  }
  if (ViewIsTable (view))
    TemplWith (view->templ, "$entry.inTable.entry");
  else
    TemplWith (view->templ, "$entry.inList.entry");
}


void ViewTemplateEnd (VIEWo *view)
{
  TemplEndWith ();
}

/**API* ViewSetEntryNamePrinting **********************************************
**
**      Sets the printing of the entry name before the selected information
**      from entry is printed.
**
**      INPUT:    view object [R]
**
*/

void ViewSetEntryNamePrinting (VIEWo *view, Int4 flag)
{
  view->isEntryNamePrinting = flag;
}

void ViewSetEntryNamePrint (VIEWo *view, void (*func)())
{
  view->entryNamePrint = func;
}
void ViewSetEntryNPrint (VIEWo *view, void (*func)())
{
  view->entryNPrint = func;
}
void ViewEntryNamePrint (VIEWo *view, ENTRYv entry, Int4 entryNo, 
		    Int4 rowN, Int4 isRoot)
{
  (*view->entryNamePrint) (view, entry, entryNo, rowN, isRoot);
}

void ViewLeafEntryNPrint (VIEWo *view, VIEWoLEAFSET *leaf, ENTRYv entry, 
			  Int4 rowN)
{
  (*view->entryNPrint) (view, leaf, entry, rowN);
}

amePrinting = flag;
}

void ViewSetEntryNamePrint (VIEWo *view, void (*func)())
{
  view->entryNamePrint = func;
}
void ViewSetEntryNPrint (VIEWo *view, void (*func)())
{
  view->entryNPrint = func;
}
void ViewEntryNamePrint (VIEWo *view, ENsrs/src/view.h
**
**    $RCSfile: view.h,v $
**    $Revision: 
**    $Date: 1997/03/17 23:18:39 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**              SRS V5.x Copyright by Thure Etzold
**
**
**                    Author: Chenna Ramu
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387372
**                     Email: chenna@embl-heidelberg.de
**
**
*/


typedef struct VIEWoFIELD *VIEWvFIELD;
typedef struct VIEWoLIB *VIEWvLIB;
typedef struct VIEWo *VIEWv;

typedef struct VIEWoLEAFSET {
  struct VIEWoLIB *vlib;
  struct SETo     *set;
  INT4            entryN;
} VIEWoLEAFSET;

#ifndef _SLBoFORM
typedef struct SLBoFORM *dummytointroducestructtagSLBoFORM;
#endif


/* prototypes for view module */


struct VIEWo *ViewGet(int viewN);
struct VIEWo *ViewGetForLib(char *libName);
struct VIEWoLIB *ViewGetNextRootLib(struct VIEWo *view, INT4 *context);
struct VIEWoLIB *ViewGetNextLeafLib(struct VIEWo *view, INT4 *context);
struct SLBoFIELD *ViewGetNextField(struct VIEWoLIB *vlib, INT4 *context);

void ViewSetName (struct VIEWo *view, char *name);

void ViewMarkDeleted(struct VIEWo *query);
void ViewDel(struct VIEWo *v );
struct VIEWo *ViewNext (Int4 *c);
struct VIEWo *ViewGetWithNo (Int4 n);

  /* view creation */

struct VIEWo *ViewNew (Int4 n, char *name);
struct VIEWoFIELD *ViewAddRootField (struct VIEWo *view, 
				     struct SRSoFLD *type) ;
struct VIEWoFIELD *ViewAddField (struct VIEWoLIB *vlib, 
				 struct SRSoFLD *fieldType);
struct VIEWoLIB *ViewAddRootLib (struct VIEWo *view, struct SLBo *lib);
struct VIEWoLIB *ViewAddLeafLib (struct VIEWo *view, struct SLBo *lib);
void ViewSetLeafQuery (struct VIEWoLIB *vlib, char *query);
void ViewSetFieldFormat (struct VIEWoFIELD *vfield, char *format);
void ViewSetLeafView (struct VIEWoLIB *vlib, char *viewName);
void ViewSetLeafPrintN (struct VIEWoLIB *vlib, Int4 flag);
void ViewSetFormat (struct VIEWo *view, char *format);
void ViewSetTemplate (struct VIEWo *view, TEMPLv templ);

  /* view info */

struct VIEWo *ViewGetNamed (char *name);

Int4  ViewGetViewsN ();
INT4  ViewIsDeleted(struct VIEWo *v);
INT4  ViewIsTable (struct VIEWo *view);
Int4  ViewIsShortNames (struct VIEWo *view);
INT4  ViewGetNumOfRootFields(struct VIEWo *view);
INT4  ViewGetNumOfLeafFields(struct VIEWo *view);
char* ViewGetName(struct VIEWo *view);
INT4  ViewGetViewNumber( char *viewName);
char* ViewGetLeafQuery (struct VIEWoLIB *vlib, struct ENTRYo *entry);
char* ViewGetLeafQueryStr (struct VIEWoLIB *vlib);
char* ViewGetLeafView (struct VIEWoLIB *vlib);
Int4  ViewLeafIsOnlyEntryN (struct VIEWoLIB *vlib);
struct LIBoFieldFormat *ViewGetFieldFormat (struct VIEWoLIB *vlib, 
					    struct SLBoFIELD *field);
struct TEMPLo *ViewGetTemplate (struct VIEWo *view);

Int4 ViewCountRootLibs(struct VIEWo *view);
Int4 ViewCountLeafLibs(struct VIEWo *view);








4  ViewGetViewNumber( char *viewName);
char* ViewGetLeafQuery (struct VIEWoLIB *srs/src/wgetz.c
char wgetz_ID[] = "$Id: wgetz.c,v 1.37 1997/03/19 20:41:42 srs Exp $";
/*
**
**    $Source: /homes/srs/cvsroot/srs/src/wgetz.c,v $
**    $Revision: 1.37 $
**    $Date: 1997/03/19 20:41:42 $
**    $Author: srs $
**
**    $Locker:  $
**    $State: Exp $
**
**
**                  Copyright by Thure Etzold
**
**             Author: Chenna Ramu
**                     EMBL, Meyerhofstrasse 1
**                     W-6900 Heidelberg, Germany
**                     Tel: 06221 387372  
**                     Email: chenna@embl-heidelberg.de
**
**
**    Requires: message, file, sm
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**
**    Description
**    =========== 
**
**    call getz from within WWW ...entries are fortified by hypertext links
**
** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */  

#include <stdio.h>
#include <stdlib.h>
#include <stdarg.h>
#include <string.h>

#include "srs.h"
#include "srswww.h"


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  prototypes of static functions
*/

static void PageStart ();
static void PageSelectLibrary ();
static void PageQueryForm ();
static void PageDownloadSetOpt ();
static void PageDownloadSet ();
static void PageConstructQuery ();
static void PageReinspectQuery ();
static void PageConstructQuery ();
static void PageQueryManager ();
static void PageViewCreate ();
static void PageViewMgrCreate ();
static void PageViewSelectFields ();
static void PageViewManager ();
static void PageViewEdit ();
static void PageViewSelectedEntries ();
static void PageEntry ();
static void PageLaunchAppl ();
static void PageSearchOpt ();
static void PageDoSearch ();
static void PageDoAppl ();
static void PageQueryExpression ();
static void PageCombineQueries ();
static void PageIndexBrowseOpt ();
static void PageIndexBrowse ();
static void PageValues2Query ();
static void PageLinkOpt ();
static void PageLinkToLibs ();
static void PageLinkEntryOpt ();
static void PageMoreEntries ();
static void PageLibList ();
static void PageLibNetwork ();
static void PageLibInfo ();
static void PageLinkInfo ();
static void PageIcarusFile ();

void WwwGetOddFile();
void WwwMarkDeletedQuery(WWWoQUERY *query, INT4 queryN);
INT4 WwwisQueryDeleted(WWWoQUERY *query);
char *SmTrimAt (char *s, Int4 n);
char *SmFillFrom(char *s, Int4 n, char *fill);
INT4 GetEnvp(char **envPtr);
void GetEnv();


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  declaration of global or module wide variables
*/

char pageQuery[3000];
char **envPtr;

static struct functions {
  char name[80];
  void (*function) ();
} functions[] = {
  "PageStart",               PageStart,
  "PageReinspectQuery",      PageReinspectQuery,
  "PageDownloadSetOpt",      PageDownloadSetOpt,
  "PageDownloadSet",         PageDownloadSet,
  "PageQueryForm",           PageQueryForm,
  "PageQueryManager",        PageQueryManager,
  "PageConstructQuery",      PageConstructQuery,
  "PageSelectLibrary",       PageSelectLibrary,
  "PageViewCreate",          PageViewCreate,
  "PageViewMgrCreate",       PageViewMgrCreate,
  "PageViewSelectFields",    PageViewSelectFields,
  "PageViewManager",         PageViewManager,
  "PageViewEdit",            PageViewEdit,
  "PageEntry",               PageEntry,
  "PageViewSelectedEntries", PageViewSelectedEntries,
  "PageLaunchAppl",          PageLaunchAppl,
  "PageSearchOpt",           PageSearchOpt,
  "PageDoSearch",            PageDoSearch,
  "PageDoAppl",              PageDoAppl,
  "PageQueryExpression",     PageQueryExpression,
  "PageCombineQueries",      PageCombineQueries,
  "PageIndexBrowseOpt",      PageIndexBrowseOpt,
  "PageIndexBrowse",         PageIndexBrowse,
  "PageValues2Query",        PageValues2Query,
  "PageLinkOpt",             PageLinkOpt,
  "PageLinkEntryOpt",        PageLinkEntryOpt,
  "PageLinkToLibs",          PageLinkToLibs,
  "PageMoreEntries",         PageMoreEntries,
  "PageLibList",             PageLibList,
  "PageLibNetwork",          PageLibNetwork,
  "PageLibInfo",             PageLibInfo,
  "PageLinkInfo",            PageLinkInfo,
  "PageIcarusFile",          PageIcarusFile,
  "WwwGetOddFile",           WwwGetOddFile,
  "GetEnv",                  GetEnv,
  "",                        NULL
};


/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**  default function for module "arglist" for printing lines
*/


static INT4 WwwArgPrint (char *formatStr, ...)
{
  static  INT4 isFirst=1, isFirstOption=1;
  TEMPLv templ;

  va_list ap;
  char    line[2000], tmp[2000], *p;

  if (isFirst) {
    printf ("<PRE>\n");
    isFirst=0;
    templ = TemplOpen ("SRSICA:srswww.i", NULL);
    TemplWith(templ,"$argListOption");
  }
  va_start (ap, formatStr);
  vsprintf (line, formatStr, ap);
  va_end (ap);

  for (p=line; *p != '\0' && *p == ' '; p++)
    ;
  if (*p == '-') {
    if (isFirstOption) {
      TemplPrint("header");
      isFirstOption = 0;
    }
    line[22] = '\0';
    strcpy (tmp, &line[23]);
    TemplPrint("option",WwwStringEncode (line),  WwwStringEncode (tmp));
  }
  else
    printf ("%s", WwwStringEncode (line));
  return 1;
}

INT4 WwwGetInput (INT4 argc, char *argv[])
{
  ARGoLIST *arglist;
  char     *buff, *tmp;
  char     *tmp1, *userId, opt[100];
  INT4     byteN, k, j, argC, isInput=0;
  INT4 funDefined = 0;
  /*
  ** check if input from form 
  */


  if ((tmp = getenv ("REQUEST_METHOD")) && SmEqs (tmp,"POST")) {
    byteN = atoi (getenv ("CONTENT_LENGTH"));
    buff = WwwReadInput (byteN, _FilTempLN ("SRSWWWTMP:buff"));
    WwwParInput (byteN, buff);
    isInput = 1;
  }

  /*
  ** input from command line
  */

  else if (argc > 1) {
    arglist = (ARGoLIST *) LibObjByName ("arglist", "wgetz");
    for (k=0; k < argc; k++)
      SmEdit (argv[k], SMxDECODE);
    argC = ArgGet (arglist, argc, argv); 
    isInput = 1;
  }
  
  /*
  ** if the userId was specified by either the form or command line
  ** input then we read the user parameters file ...after that we
  ** must read the form or command line again to give those parameters
  ** the priority they deserve
  */

  userId = ParGetStr("userId");
  if (userId && *userId) {
    sprintf (opt, "-id+%s+", userId);
    ParDefStr ("userIdOpt", opt);
    WwwParRead (userId, 1);
    if ((tmp = getenv ("REQUEST_METHOD")) && SmEqs (tmp,"POST"))  {
      WwwParInput (byteN, buff);
    }
    else 
      argC = ArgGet (arglist, argc, argv); 
  }
  
  /*
  ** determine the function to be executed after returning from here
  ** ..set as function parameter "wwwFunction"
  */

  if ((tmp = ParGetStr ("wwwFunctionName")) && *tmp) { 
    for (k=0; functions[k].function; k++)
      if (SmEqs (tmp, functions[k].name))
	ParDefFunction ("wwwFunction", (INT4(*)()) functions[k].function);
    }
/*
   When no wwwFunction is defined, look for wwwFunctionName1, ...
   which might be defined. get ParGetStr(ParGetStr(wwwFunctionName1)) which 
   is a function name whose value is "submitted" through submit button.
   check for its existence and define wwwFunction
*/

  if (!ParGetFunction ("wwwFunction")) { 
    funDefined = 0;
    for( j =0; functions[j].function; j++) {
      if( funDefined ) break;
      if( (tmp = ParGetStrF("wwwFunctionName%d",j)) && *tmp ) { 
	if(*ParGetStr(tmp)) {
	  ParDelete (tmp);
	  ParDeleteF("wwwFunctionName%d",j);
	  for (k=0; functions[k].function; k++) 
	    if (SmEqs (tmp, functions[k].name)) {
	      ParDefFunction ("wwwFunction", (FUNC)functions[k].function);
	      funDefined = 1; break;
	    }
	}
      }
    }
  }

  if(!ParGetFunction("wwwFunction"))
    ParDefFunction ("wwwFunction", (FUNC) PageEntry)
 
    ; /*_ErrExit2 (e__functionnotexist, tmp); */ /* take default function!*/
   
  if (ParGetBool ("isHtml3"))
    ParDefStr ("HTML", "H3-");
  else
    ParDefStr ("HTML", "");
  
  if (SmEqs (ParGetStr ("style"),"fancy"))
    ParDefStr("FANCY","FANCY-");
  else
    ParDefStr("FANCY","");
  
  return isInput;
}

/****** main *******************************************************************
**
**      check wwwFunction defined, if,  then call appropriate function
**      and delete the function parameter name, save the user context.
**
**      INPUT:  function name with the arguments defined in arglist under
**              rwgetz 
**
**
*/

main (INT4 argc, char *argv[], char *envp[])
{
  INT4 (*function) ();
  char *userId=NULL, *tmp;

  SrsEnv ();
  LibOpen ("srs5");
  IcaInitSyntax (LibObjByName ("syntax", "icarus"));

  MsgSetFnct (WwwPrintMessage);
  setbuf (stdout,NULL); 
  envPtr = envp;
  ParDefStr("view0_Name", "* No View *");
  if (WwwGetInput (argc, argv)) {
    LibInitHyperLinks ();
    if (argv[1] && *argv[1]) {
      strcpy (pageQuery, WwwTransform ("decode", argv[1]));  
    }
    else if (*(tmp=ParGetStr ("pageQuery")))
      strcpy (pageQuery, tmp);  
      

    /* might create a new user id */
    userId = ParGetStr("userId");
    if (!( userId && *userId) && ParGetBool ("makeNewUserId")) {
      userId = WwwNewUserId();
      ParDefNum("makeWild",1); /* new user should have this */
    }
    if ((function = ParGetFunction ("wwwFunction")))
      (*function)();
  }

  userId = ParGetStr ("userId"); /* may be defined by 'page' function */
  if (userId && *userId)  {
    ParDeleteMatch("wwwFunctionName.+");
    WwwParWrite (userId);
  }
  exit (0);
}


/**api* PageStart *************************************************************
**
**      Prints the start page
**
*/

static void PageStart()
{
  TEMPLv templ;

  templ = WwwInit ();
  TemplWith(templ,"$startPage");
  TemplPrint ("head");
  TemplEndWith ();
  TemplClose (templ);
}



/**api* PageSelectLibrary *****************************************************
**
**      Lists all databanks that can be searched.
**
*/

static void PageSelectLibrary()
{
  TEMPLv    templ;
  SLBo      *lib;
  SRSoGROUP *group;
  char      *libName, *userId, *tmp;
  char      label[40];
  Int4      c1, c2, ngroups, nlib, numCol;

  /* create a new user if not already existent */
  userId = ParGetStr("userId");
  if (!( userId && *userId)) {
    userId = WwwNewUserId();
    ParDefNum("makeWild",1); /* new user should have this */
  }

  templ = WwwInit ();
  TemplWith(templ,"$selectLibrary");
  TemplPrint("head");
  WwwPrintButtons (templ);
  TemplPrint("submit");
  
  TemplWith (templ, ParGetBool("isHtml3") ? "libs.html3" : "libs.html2");
  for (c1=0; (group = LibNextLibGroup (&c1)); ) {
    /* calculate number of colums */
    numCol = 70 / (LibGetMaxNameSize (group, NULL, "library") + 2);
    if (!(ngroups = LibNofGroups(group))) continue;
    tmp = LibGetGroupName (group, "full");
    if (SmEqs (tmp,"Application")) 
      TemplPrint ("libGroupNameSearch", tmp);     
    else
      TemplPrint ("libGroupName", tmp);     

    for (c2=0, nlib=0; (lib = LibNextLib (group, &c2));) {
      if (LibIs (lib, "subentries"))
	continue;
      libName = LibGetName(lib,"full");
      if (nlib && !(nlib%numCol)) TemplPrint("newRow");
      TemplPrint ("library", libName, WwwChecked (0), 
		 libName, libName, "");
      nlib++;
    }
    TemplPrint("tail"); 
  }
  TemplEndWith ();
  TemplPrint("tail");
  TemplWith (templ, "colorScheme");
  WwwPresentColorMenu();
  TemplEndWith ();
  TemplEndWith ();
}

/****** LibNofGroups **************************************************
**
**      Counts number of databanks in a group
**
**      INPUT:    group object 
**           IMPLICIT
**
**      RETURNS: number of databanks in the group
**     
**
**
*/

INT4 LibNofGroups( SRSoGROUP *group)
{
  INT4 i,j;
  for( i = 0, j=0; LibNextLib(group,&i) ; j++)
    ;
  return(j);
}


/**api* PageIcarusFile *******************************************************
**
**      Prints an icarus file
**
*/

static void PageIcarusFile ()
{
  TEMPLv templ;
  SLBo  *lib;
  FILEo *file;
  char  *ln, *fileName, *libName, *type;

  templ = WwwInit ();
  TemplWith (templ, "$icarusFile");
  TemplPrint ("head");

  libName = ParGetStr ("libList");
  if (!(lib = (SLBo *) LibObjByName ("library", libName)))
    _ErrExit3 (e__objectunknown, "library", libName);
  type = ParGetStr ("icarusFileType");

  /* find the Icarus file name */
  if (SmEqs (type, "i"))
    if (!*(fileName = (LibGetIcarusFileName (lib, "structure"))))
      _ErrExit3 (e__objectunknown, "Icarus file", "structure");
  if (SmEqs (type, "is"))
    if (!*(fileName = (LibGetIcarusFileName (lib, "syntax"))))
      _ErrExit3 (e__objectunknown, "Icarus file", "syntax");
  if (SmEqs (type, "it"))
    if (!*(fileName = (LibGetIcarusFileName (lib, "info"))))
      _ErrExit3 (e__objectunknown, "Icarus file", "info");

  file = FileNew (fileName);
  if (!FileOpen (file))
    _ErrExit2 (e__filnotok, FileGetName (file, "full"));
  while ((ln = FileReadLn (file))) {
    ln = WwwStringEncode (ln);
    fwrite (ln, strlen (ln), 1, stdout);
  }
  TemplPrint ("tail");
  FileClose (file);
}



/**api* PageQueryForm ********************************************************
**
**      Builds a queryform page for the selected databanks.
**
*/

static void PageQueryForm ()
{
  TEMPLv   templ;
  SLBo      *lib, *libSave;
  SRSoGROUP *group, *groupCurr;
  SLBoFIELD *field;
  char      *tmp, *tmp1, *fieldName, *userId;
  INT4      max, c1, c2, i, currentViewNumber=0;

  ParDefNum("listEntriesStartN",1);
  ParDefNum("viewEntriesStartN",1);

  /* create a new user if not already existent */
  userId = ParGetStr("userId");
  if (!( userId && *userId)) {
    userId = WwwNewUserId();
    ParDefNum("makeWild",1); /* new user should have this */
  }

  templ = WwwInit ();
  TemplWith(templ, "$queryForm");
  TemplPrint("head");
  WwwPrintButtons (templ);
 
  /* loop over selected databanks */
  TemplPrint("searchInfo");
  groupCurr = LibGroupNew (NULL);
  for (c1=0; (group = LibNextLibGroup (&c1)); ) 
    for (c2=0; (lib = LibNextLib (group, &c2));) { 
      if (LibIs (lib, "selected")) {
	libSave = lib;
	LibGroupAddDb (groupCurr, lib);
        TemplPrint("listLibs",LibName (lib), LibName (lib));
      }
    }
  if (!groupCurr->libraryN) 
    _ErrExit (e__nolibslct); /* no databanks were selectect */
  TemplPrint("submit");
  TemplWith (templ, "chunkSize");
  WwwPresentChunkSizes (templ);  
  TemplEndWith ();
  WwwPresentActiveViews (groupCurr, NULL, NULL, templ, 0);
  TemplPrint ("searchOptions", WwwChecked (ParGetNum("makeWild")));
  TemplWith(templ, ParGetBool("isHtml3") ? 
	    "queryInput.html3" : "queryInput.html2");
  TemplPrint("head");


  max = LibGetMaxNameSize (groupCurr, NULL, "field")+1;

  for (c1=0; (field = LibNextGroupField (groupCurr, 
			 ParGetBool ("isOnlyCommonFields"), &c1));) {
    fieldName = LibGetFieldName (field);

    ParDefNum ("l", max-strlen (fieldName));
    if (FieldIs (field, "header")) {
      if (LibFieldHeaderHasWith (libSave, field, "doQuery"))
	TemplPrint ("fieldHeader", fieldName);
    }
    else if (FieldIs (field, "num") || FieldIs (field, "real")) {
      tmp = ParGetStrF("query_%s_begmod",fieldName);
      tmp1 = ParGetStrF("query_%s_endmod",fieldName);
      TemplPrint("fieldNum",
		 fieldName, fieldName, "", fieldName,
		 WwwSelected (SmEqs (tmp,">=")), WwwSelected (SmEqs (tmp,">")),
		 fieldName, fieldName,
		 WwwSelected (SmEqs (tmp1,"<=")),WwwSelected (SmEqs(tmp1,"<")),
		 fieldName, fieldName);
    } 
    else if (FieldIs (field, "doQuery")) 
      TemplPrint("fieldText", fieldName,fieldName,"",fieldName,fieldName); 
    if (FieldIs (field, "subEntry")) {
      tmp = ParGetStrF("%s",fieldName);
      TemplPrint("subEntry",fieldName,WwwChecked (*tmp));
    }
    TemplPrint("rowEnd");
  }
  TemplPrint("tail"); 
  TemplEndWith ();
  TemplPrint("tail");  
}


void WwwPrintFieldGroupInfo (SLBo *lib, SLBoFIELD *fieldGroup)
{
  SLBoFIELD *field;
  Int4 c;

  TemplPrint ("group.lib", LibName (lib));
  for (c=0; (field=LibNextFieldInGroup (lib, fieldGroup, &c));)
    TemplPrint ("group.member", LibGetFieldName (field), LibName (lib), 
		LibGetFieldName (field));
  TemplPrint ("group.tail");
}


void WwwPrintFieldInfo (SLBo *lib, SLBoFIELD *fieldSelect, Int4 count)
{
  LIBoINDEX *libInx;
  SLBoFIELD *field;
  STRv name=StrNew(), shrt=StrNew(), type=StrNew(), valN=StrNew(), 
       refN=StrNew(), date=StrNew(), status=StrNew();
  char tmp[500];
  Int4 c, isOk;

  if (!count)
    TemplPrint ("head");
  for (c=0; (field = fieldSelect) || (field = LibNextField (lib, &c));) {
    if (FieldIs (field, "group") || FieldIs (field, "header"))
      continue;
    
    StrAppS (&name, TemplSPrint (tmp, "name", LibGetFieldName (field), 
				 LibName (lib), LibGetFieldName (field)));
    StrAppS (&shrt, TemplSPrint (tmp, "short", LibGetFieldShortName (field)));
    
    if (FieldIs (field, "id"))
      TemplSPrint (tmp, "type", "ID");
    else if (FieldIs (field, "real"))
      TemplSPrint (tmp, "type", "real");
    else if (FieldIs (field, "num"))
      TemplSPrint (tmp, "type", "int");
    else if (FieldIs (field, "index"))
      TemplSPrint (tmp, "type", "string");
    else if (FieldIs (field, "link"))
      TemplSPrint (tmp, "type", "link");
    else if (FieldIs (field, "show"))
      TemplSPrint (tmp, "type", "show");
    StrAppS (&type, tmp);
    
    isOk = FieldIs (field, "index")&&
           (libInx = LibIndexOpen (lib, field, 1)) ? 1:0;
    if (isOk) {
      StrAppS (&valN, TemplSPrint(tmp, "valN", BtrGetRecordN(libInx->btree))); 
      StrAppS (&refN, TemplSPrint(tmp, "refN", IdsGetIdN (libInx->idsFile))); 
    }
    else {
      StrAppS (&valN, TemplSPrint(tmp, "empty"));
      StrAppS (&refN, TemplSPrint(tmp, "empty"));
    }
    StrAppS (&date, TemplSPrint(tmp, "date", isOk ? 
           TimeToString (BtrGetTimeCreated (libInx->btree), "short") : "")); 
    
    if (!isOk)
      StrAppS (&status, TemplSPrint (tmp, "status", "not indexed"));
    else if (BtrIsBusy (libInx->btree))
      StrAppS (&status, TemplSPrint (tmp, "status", "busy"));
    else if (!IdsIsCompressed (libInx->idsFile))
      StrAppS (&status, TemplSPrint (tmp, "status", "not compressed"));
    else
      StrAppS (&status, TemplSPrint (tmp, "status", "ok"));

    if (fieldSelect)
      break;
  }
  if (!count)
    TemplPrint ("tail", _Str (name), _Str (shrt), _Str (type), _Str (valN), 
		_Str (refN), _Str (date), _Str (status));
  else
    TemplPrint ("data", LibName (lib), _Str (name), _Str (shrt), _Str (type), 
                _Str (valN), _Str (refN), _Str (date), _Str (status));

  StrDel (name); 
  StrDel (shrt); 
  StrDel (type); 
  StrDel (valN); 
  StrDel (refN);
  StrDel (date);
  StrDel (status);
}

/****** PageIndexBrowseOpt ****************************************************
**
**      Presents the options of browsing an index.
**
*/

static void PageIndexBrowseOpt ()
{
  TEMPLv    templ, libTempl, genTempl;
  SLBo      *lib;
  SLBoFIELD *field;
  SRSoGROUP *group, *groupCurr;
  char      libList[200]="", path[999], *fieldName, *infoName, *tmp, label[200];
  INT4      c1,c2;

  templ = WwwInit ();

  TemplWith(templ,"$dataField");
  TemplPrint ("head");
  WwwPrintButtons (templ);

  /* make string with library list */
  groupCurr = LibGroupNew (NULL);
  if (*(tmp = ParGetStr ("libName"))) {
    if (!(lib = (SLBo *) LibObjByName ("library", tmp)))
      _ErrExit3 (e__objectunknown, "library", tmp);
    LibGroupAddDb (groupCurr, lib);
    strcpy (libList, tmp);
  }
  else {
    for (c1=0; (group=LibNextLibGroup (&c1)); ) 
      for (c2=0; (lib=LibNextLib (group, &c2));) {
	if (LibIs(lib, "selected")) {
	  sprintf (libList, "%s%s ", libList, LibName (lib));
	  LibGroupAddDb (groupCurr, lib);
	}
      }
    libList[strlen(libList)-1] = '\0';
  }

  fieldName = ParGetStr("browseIndex");
  TemplPrint ("title", fieldName);

  /* general description */
  if ((genTempl = TemplOpen ("SRSDB:general.it", NULL))) {
    TemplWith (genTempl, "$main");
    if (TemplExists (genTempl, fieldName)) 
      WwwPrintInfoChapter (templ, genTempl, 
			   "$dataField.description", fieldName);
    TemplEndWith ();
  }

  /* description from a single databank */
  for (c2=0; (lib=LibNextLib (groupCurr, &c2));) {
    if ((libTempl = TemplOpen (LibGetIcarusFileName (lib, "info"), NULL))) {
      TemplWith (libTempl, "$dbInfo");
      sprintf (label, "fields.%s", fieldName);
      if (TemplExists (libTempl, label)) {
	TemplWith (templ, "$dataField.description");
	TemplPrint ("headFrom", LibName (lib));
	TemplEndWith ();
	TemplPrint (label);
	TemplWith (templ, "$dataField.description");
	TemplPrint ("tail");
	TemplEndWith ();
      }
      TemplEndWith ();
    }
  }  

  /* status of field/index */
  TemplWith (templ, "fields");
  if (SmEqs (fieldName, "all") || SmEqs (fieldName, "alltext")) {
    TemplPrint ("group.head");
    for (c2=0; (lib=LibNextLib (groupCurr, &c2));) {
      if (field = LibHasFieldNamed (lib, fieldName))
	WwwPrintFieldGroupInfo (lib, field); 
    }
  }
  else {
    TemplPrint ("head");
    for (c2=0; (lib=LibNextLib (groupCurr, &c2));) {
      field = LibHasFieldNamed (lib, fieldName);
      WwwPrintFieldInfo (lib, field, 1); 
    }
  }
  TemplPrint ("tail");
  TemplEndWith ();
  TemplPrint ("browse", fieldName, libList);
  TemplPrint ("tail");
}

/****** PageIndexBrowse *******************************************************
**
**      Prints all or some values of an index.
**
*/

static void PageIndexBrowse ()
{
  TEMPLv templ;
  char   *libList, *fieldName, queryStr[200];

  templ = WwwInit ();
  TemplWith(templ,"$browseList");
  TemplPrint ("head");
  WwwPrintButtons (templ);
  
  libList = ParGetStr ("browseLibs");
  fieldName = ParGetStr ("browseIndex");
  sprintf (queryStr, "[{%s}-%s:%s]", libList, fieldName, 
	   ParGetStr ("browseMatch"));
  TemplPrint ("title", fieldName, fieldName, libList, 
	      ParGetNum("printIndexValN") + ParGetNum ("printIndexFirstValN"));

  ParDefNum ("queryListValues", 1);
  ParDefNum ("isHTMLFormat", 1);
  /* Query prints the values!*/
  QuerySetPrintValue (WwwPrintValue);
  TemplWith (templ, "values");
  Query (queryStr, "");
  TemplEndWith ();
  TemplEndWith ();
}



/**api* PageValues2Query *****************************************************
**
**      Collects all selected values and combines them to a query.
**  
*/

static void PageValues2Query ()
{
  STRv str=NULL;
  char *tmp;
  Int4 valN = ParGetNum ("printIndexValN"), k;

  for (k=1; k<=valN; k++)
    if (*(tmp = ParGetStrF ("value_%d", k))) {
      tmp = WwwTransform ("decode", tmp);
      if (!str) 
	str = StrCpyS (tmp);
      else
	StrPrintf (&str, " | %s", tmp);
    }
  
  if (str) {
    WwwQueryExpression ("query", _Str (str));
    StrDel (str);
  }
}



/**api* PageQueryManager *****************************************************
**
**      Shows all successful queries and allows various operations on them.
**  
*/

static void PageQueryManager()
{
  WWWoQUERY *query ;
  TEMPLv templ;
  char      *tmp, *par, *userId;
  INT4      Nqueries, k, j, currentViewNumber=0;

/* initialize the parameters */
  ParDefStr("expr","");
  ParDefNum("listEntriesStartN",1);
  ParDefStr ("fieldList", "reset"); 
  Nqueries = ParGetNum("numberOfQueries");

  templ = WwwInit ();
  TemplWith(templ,"$queryManager");
  TemplPrint("head");
  WwwPrintButtons (templ);
  if( ParGetBool("isHtml3"))
    TemplWith(templ,"queryOptions.html3");
  else
    TemplWith(templ,"queryOptions.html2");
  TemplPrint("head");
  TemplEndWith();
  TemplWith(templ,"chunkSize");
  WwwPresentChunkSizes (templ);
  TemplEndWith();
  TemplWith(templ,"selectView");
  WwwPresentViewList ("current", templ);
  TemplEndWith();
  if(ParGetBool("isHtml3")) 
    TemplWith(templ,"queryOptions.html3.queryInfo");
  else
    TemplWith(templ,"queryOptions.html2.queryInfo");
  TemplPrint("head"); 
  for ( k = 1; k <= Nqueries; k++) {
    query = WwwGetQuery (k);
    if (SmEqs (query->type, "singleentry") || 
	SmEqs (query->type, "linkentry"))continue;
    if(WwwisQueryDeleted(query)) continue;
    
    if(*(ParGetStrF("qmstr%d",k))){
      WwwMarkDeletedQuery(query,k);
      continue;
    }
    if (!(ParGetBool("isHtml3"))) {
      TemplPrint("title", k,query->name,query->name,query->type,
		 WwwStringEncode(query->queryStr),query->entryN);
      for(j=0; query->lib[j].entryN;j++) {
	TemplPrint("entryN", query->lib[j].entryN, query->lib[j].name);
	if( query->isSubEntry)
	  TemplPrint("subEntry");
      }
    }
    else {
      TemplPrint("title",k,query->name,query->name,
		 query->type,query->entryN);
      TemplPrint("libAlign");
      for(j=0; query->lib[j].entryN; j++) {
	TemplPrint("library",(query->lib[j].name));
      }
      TemplPrint("numAlign");
      for(j=0; query->lib[j].entryN;j++) {
        TemplPrint("entryN",(query->lib[j].entryN));
      }
      TemplPrint("queryStr",WwwStringEncode(query->queryStr),
		 k,query->comment);
      if( query->isSubEntry)
        TemplPrint("subEntry");
      TemplPrint("rowEnd");
    }
    WwwDelQuery(query);
  }
  TemplEndWith();
  TemplPrint("tail");
}



/****** PageQueryExpression ***************************************************
**
**      Does an query expression.
**
*/

static void PageQueryExpression()
{
  WwwQueryExpression ("expression", ParGetStr ("expr"));
}

/****** PageCombineQueries ****************************************************
**
**      Combines several queries with a single set operator.
**
*/

static void  PageCombineQueries ()
{
  WWWoQUERY *query;
  STRv str;
  INT4 k,j;
  char *tmp, op;

  tmp = ParGetStr("operator");
  if (SmEqs(tmp,"AND"))
    op = '&';
  else if (SmEqs(tmp,"OR"))
    op = '|';
  else if (SmEqs(tmp,"BUTNOT"))
    op = '!';
  else 
    return;

  for (j=0, k=0; WwwNextSelectedQuery (&j, &tmp); k++) {
    if (!k)
      str = StrCpyS (tmp);
    else
      StrPrintf (&str, " %c %s", op, tmp);
  }
  if (!k)
    _ErrExit (e__wwwNoQueryOrEntriesSelected);
  else
    WwwQueryExpression ("expression", _Str (str));
}

/**api* PageReinspectQuery ****************************************************
**
**      Repeats a query selected in the QueryManager form.
**
*/

static void PageReinspectQuery ()
{
  INT4 j=0;

  if ((j=WwwNextSelectedQuery (&j, NULL))) {
    WwwQueryRepeat (j);
    WwwQueryPrint (j);
  }
  else 
    _ErrExit (e__wwwNoQueryOrEntriesSelected);
}

/****** PageSearchOpt *********************************************************
**
**      Displays the input form to launch a search program
**
*/

static void  PageSearchOpt ()
{
#ifdef xxx
  TEMPLv          templ;
  LIBoApplication *appl;
  WWWoQUERY       *query;
  SETo            *set;
  SEQo            *seq;
  STRv            s;
  ENTRYv          entry;
  IDoENTRY        id;
  Int4            queryNo;
  char            *tmp;

  if (!*(tmp = ParGetStr ("applicationName")))
    tmp = ParGetStr ("libList");
  if (!(appl = (LIBoApplication*) LibObjByName ("application", tmp)))
    _ErrExit3 (e__objectunknown, "application", tmp);

  templ = WwwInit ();
  TemplWith (templ, LibGetApplTemplate (appl));
  TemplPrint ("head");
  WwwPrintButtons (templ);

  if ((queryNo=WwwQuerySelectedEntries ())) {
    query = WwwGetQuery (queryNo);
    set = SetGet (query->name);
    SetGetID (set, 1, &id);
    entry = EntryOpen (&id);
    seq=SdbGetEntrySeq (entry);
    s = Seq2Pretty (seq, 60);
    TemplPrint ("tail", _Str (s));
    EntryClose (&entry);
    StrDel (s);
    WwwDelQuery (query);
  }
  else 
    TemplPrint ("tail", "");
#endif
}

static void PageLaunchAppl ()
{
  APPLo *appl;
  char  *applName;

  applName = ParGetStr ("applicationName");
  if (!(appl = ApplNamed (applName)))
    _ErrExit3 (e__objectunknown, "application", applName);
  WwwApplOpt (appl);
}





FILE *file;
INT4 wwwWriteFile (char *formatStr, ...)
{
  va_list ap;
  
  va_start (ap, formatStr);
  vfprintf (file, formatStr, ap);
  va_end (ap);
  
  if (formatStr[strlen (formatStr) -1] != '\n')
    fprintf (file, "\n");
  
}


/****** function **************************************************************
**
**         Prepares a c-shell for launching a sequence search 
**
*/ 

static void PageDoSearch()
{
  TEMPLv templ, cshTempl;
  SLBo   *lib;
  SEQo   *seq;
  INT4   errCode;
  STRv   searchCom;
  char   *userId = ParGetStr("userId"), *libName=ParGetStr ("libList");
  char   seqFile[200], cshFile[200], s[100], command[200]="", *tmp;

  if (!(lib = (SLBo *) LibObjByName ("library", libName)))
    _ErrExit3 (e__objectunknown, "library", libName);

  /* write out sequence file */
  seq = SeqReadString (ParGetStr ("inputSequence"));
  sprintf (seqFile, "%s/%s/tmp.seq", "SRSWWWTMP", userId);
  file = FilOpenW (seqFile, &errCode);
  _ErrExit2 (errCode, seqFile);
  if (SmEqs (ParGetStr ("searchSeqFormat"), "gcg"))
    SeqWriteGCG (seq, "tmp", (INT4(*)(char*,...)) wwwWriteFile);
  else
    SeqWriteFasta (seq, "tmp", (INT4(*)(char*,...)) wwwWriteFile);
  fclose (file);

  /* prepare a blast c-shell file*/
  sprintf (cshFile,"SRSWWWTMP:%s/script", userId);
  if (!(cshTempl = TemplOpen ("SRSICA:srswww.i", cshFile)))
    _ErrExit2 (errCode, cshFile);
  TemplWith (cshTempl, ParGetStr ("scriptTemplate"));
  TemplPrint ("head");
  TemplSPrint (command, "launch");
  
  /* print the blast command */
  TemplPrintAll ("command");
  searchCom=StrNew ();
  TemplSPrintAll (&searchCom, "command");
  TemplPrint ("tail");
  TemplEndWith ();
  TemplClose (cshTempl);

  /* print result page and execute script */
  templ = WwwInit ();
  TemplWith (templ, "$searchResult");
  TemplPrint ("head", libName, libName, libName, libName);
  TemplWith (templ, "chunkSize");
  WwwPresentChunkSizes (templ);  
  TemplEndWith ();
  WwwPresentActiveViews (NULL, lib, NULL, templ, 0);
  TemplPrint ("tail", _Str (searchCom));

  fflush (stdout);
  FilChMod (cshFile,"X"); /* there is no 'X' mode opt., but changes */
  system (command);

  sprintf (s, "SRSWWWTMP:%s/",userId); 
  ParDefStr ("libGroup", lib->group->com);
  ParDefStr ("libList", lib->nam);
  ParDefStrF (s, "%sDirName", lib->nam); 
}

static void PageDoAppl ()
{
  APPLo    *appl;
  APPLoOpt *opt;
  STRv     str;
  TEMPLv   templ;
  SEQo     *seq;
  SLBo     *lib;
  INT4     errCode, i;
  char     *userId = ParGetStr("userId");
  char     seqFile[200], *applName, *optName,  *tmp, s[100];

  applName = ParGetStr ("applName");
  appl = ApplNamed (applName);

  /* write out sequence file */
  sprintf (seqFile, "SRSWWWTMP/%s/tmp.seq", userId);
  file = FilOpenW (seqFile, &errCode);
  _ErrExit2 (errCode, seqFile);

  if (ApplIs (appl, "multi"))
    for (i=1; 1; i++) {
      if (*(tmp=ParGetStrF ("inputSequence%d", i))) {
	seq = SeqReadString (tmp);
	SeqSetName (seq, ParGetStrF ("inputSequenceName%d", i));
	SeqSetComment (seq, ParGetStrF ("inputSequenceComment%d", i));
	SeqWritePIR (seq, NULL, NULL, (INT4(*)(char*,...)) wwwWriteFile);
	SeqDel (&seq);
      }
      else break;
    }
  else {
    seq = SeqReadString (ParGetStr ("inputSequence"));
    if (ApplIsInSeq (appl, "gcg"))
      SeqWriteGCG (seq, "tmp", (INT4(*)(char*,...)) wwwWriteFile);
    else if (ApplIsInSeq (appl, "fasta"))
      SeqWriteFasta (seq, "tmp", (INT4(*)(char*,...)) wwwWriteFile);
  }
  fclose (file);

  /* create and run a script to init option variables of the appl */
  str = StrNew ();
  StrPrintf (&str, "$userId = $ParStr:userId\n"); 
  for (i=0; (opt=ApplNextOpt (appl, &i)); ) {
    optName = ApplOptGetName (opt);
    StrPrintf (&str, "$opt.%s = $ParStr:%s_%s\n", optName, 
	       ApplGetName (appl), optName);
  }
  ApplInit (appl);
  ApplEval (appl, _Str (str));
  StrDel (str);
   

  /* print result page and execute script */
  templ = WwwInit ();
  TemplWith (templ, "$applResult");
  TemplPrint ("head", applName, applName);
  WwwPrintButtons (templ);
  TemplPrint ("title", applName);

  if (ApplIs (appl, "search")) {
    TemplPrint ("search.head", applName, applName);
    TemplWith (templ, "search.chunkSize");
    WwwPresentChunkSizes (templ);  
    TemplEndWith ();
    TemplWith (templ, "search");
    WwwPresentActiveViews (NULL, LibObjByName ("library", applName), 
			   NULL, templ, 0);
    TemplEndWith ();
    TemplPrint ("search.tail");
  }
  TemplPrint ("tail", ApplGetCommand (appl));

  /* create script and execute */
  fflush (stdout);
  ApplLaunch (appl);

  /* 'remember' the clustalw directory */
  if (!(lib = (SLBo *) LibObjByName ("library", applName)))
    _ErrExit3 (e__objectunknown, "library", applName);
  sprintf (s, "SRSWWWTMP:%s/", userId); 
  ParDefStr ("libGroup", lib->group->com);
  ParDefStr ("libList", lib->nam);
  ParDefStrF (s, "%sDirName", lib->nam); 
}



/****** WwwMarkDeletedQuery *********************************************
**
**      Mark deleted query. 
**
**      INPUT :   Address of query Object [W]
**                 query number (INT)
**
**      RETURNS:   none
**
*/
void WwwMarkDeletedQuery(WWWoQUERY *query, INT4 queryN)
{
  char par[80];

  query->isDeleted = 1; /* set the status flag */
  sprintf(par,"QueryDeleted_%d",queryN);
  ParDefNum(par,query->isDeleted);
}

/****** WwwisQueryDeleted *********************************************
**
**      Checks whether a query marked deleted or not.
**
**      INPUT :   Address of query Object [R]
**
**      RETURNS:   query status flag.
**
*/
INT4 WwwisQueryDeleted(  WWWoQUERY *query)
{
  return(query->isDeleted);
}


/**api* PageConstructQuery ***************************************************
**
**      Constructs a valid query from form input, performs it and 
**      displays the result.
**
*/
static void PageConstructQuery()
{
  SLBo         *lib;
  SLBoFIELD    *field;
  SRSoGROUP    *group, *groupCurr;
  QASvQUERY    query;
  QASvRETRIEVE r;
  char         *fieldName, *tmp;
  INT4         c1,c2;
  
  query = QasNew ();
  QasSetOp (query, ParGetStr ("query_operator"));
  
  /* set selected libraries */
  groupCurr = LibGroupNew (NULL);
  for (c1=0; (group = LibNextLibGroup (&c1)); ) 
    for (c2=0; (lib = LibNextLib (group, &c2));) {
      if (!(LibIs(lib, "selected"))) 
	continue;
      QasSetLibrary(query, LibGetName(lib,"full"));
      LibGroupAddDb (groupCurr, lib);
    }

  /* set index queries */
  for (c1=0; (field = LibNextGroupField (groupCurr, 1, &c1));) {
    fieldName = LibGetFieldName(field) ;
    r = NULL;
    if(FieldIs(field,"num") || FieldIs (field, "real")) {
      if (*(tmp = ParGetStrF("query_%s_begin",fieldName))) {
	r = QasNewRetrieve (query, fieldName);
	QasSetRangeBegin (query, r, tmp);
      }
      if (*(tmp = ParGetStrF("query_%s_end",fieldName))) {
	if (!r) 
	  r = QasNewRetrieve (query, fieldName);
	QasSetRangeEnd (query, r, tmp); 
      }
      if (SmEqs (ParGetStrF("query_%s_beginmod",fieldName), ">"))
	QasSetRangeBeginExcl (query, r);
      if (SmEqs (ParGetStrF("query_%s_endmod",fieldName), "<"))
	QasSetRangeEndExcl (query, r);
    }
    else
      if( *(ParGetStrF ("query_%s", fieldName))) {
	r = QasNewRetrieve (query, fieldName);
	QasSetRetrieveStr (query, r, ParGetStrF ("query_%s", fieldName));
      }
    if (r && FieldIs (field,"subEntry") &&
	ParGetBoolF ("subEntry_%s", fieldName))
      QasSetSubEntries (query, r);
  } 
  if(ParGetNum("makeWild"))
    QasSetMakeWild (query);

  ParDeleteMatch ("^query_");
  if (QasGetQueryString(query))
    WwwQueryExpression ("query", QasGetQueryString(query));
  else 
    _ErrExit (e__wwwNoQuerySpecified);
  
}


/****** PageMoreEntries ************************************************
**
**      Lists entries of already existing query.
**
*/

static void  PageMoreEntries ()
{
  WwwQueryRepeat (ParGetNum ("listSetNumber"));
  WwwQueryPrint (ParGetNum ("listSetNumber"));
}



/****** PageLinkOpt ***********************************************************
**
**       Lets the user link an entire set or an entry selection to other
**       databanks.
**
*/

static void PageLinkOpt ()
{
  TEMPLv    templ;
  SLBo      *lib;
  SRSoGROUP *group;
  char *querystr, *opt; 
  Int4  ngroups = 0, num[10], c1=0, c2,setN;
  Int4  nlib = 0, numCol, queryN;

  templ = WwwInit ();
  TemplWith (templ, "$linkPage");
  querystr = ParGetStr("queryString");

  /* get either set selected from query manager or the list of
     selected entries */
  if ((queryN=WwwNextSelectedQuery (&c1, NULL)) ||
      (queryN=WwwQuerySelectedEntries ()))
    ParDefNum("linkSetNumber",queryN);
  else
    _ErrExit (e__wwwNoQueryOrEntriesSelected);
  setN = ParGetNum("linkSetNumber");

  TemplPrint ("head", querystr);
  WwwPrintButtons (templ);
  opt = ParGetStr ("linkSetType");
  TemplPrint ("linkType", setN);

  TemplWith(templ,"$queryManager.chunkSize");
  WwwPresentChunkSizes (templ);
  TemplEndWith();
  TemplWith(templ,"$queryManager.selectView");
  WwwPresentViewList ("reset", templ);
  TemplEndWith();


  TemplWith (templ, ParGetBool("isHtml3") ? "html3" : "html2");
  for (c1=0; (group = LibNextLibGroup (&c1)); ) {
    /* adjust number of columns */
    numCol = 70 / (LibGetMaxNameSize (group, NULL, "library") + 2);
    if (!(ngroups = LibNofGroups(group))) 
      continue;
    TemplPrint ("dbGroup", group->com);     
    for (c2=0, nlib = 0; (lib = LibNextLib (group, &c2));) {
      if (LibIs (lib, "subentries")) continue;
      if (!(nlib%numCol)) 
	TemplPrint ("newRow");
      TemplPrint ("library", LibGetName (lib,"full"),
		  WwwChecked (LibIs (lib,"linkTarget")),
		  LibGetName(lib,"full"), LibGetName(lib,"full"), "");
      nlib++;
    }
    TemplPrint ("tail");
  }
  TemplEndWith ();
  TemplPrint ("tail");
}

/****** PageLinkEntryOpt ******************************************************
**
**       Lets the user link an entire set or an entry selection to other
**       databanks.
**
*/

static void PageLinkEntryOpt ()
{
  TEMPLv    templ;
  SLBo      *lib;
  SRSoGROUP *group;
  char *querystr, *opt; 
  Int4  ngroups = 0, num[10], c1=0, c2,setN;
  Int4  nlib = 0, numCol, queryN;

  templ = WwwInit ();
  TemplWith (templ, "$linkPage");
  querystr = ParGetStr("queryString");

  TemplPrint ("head", querystr);
  WwwPrintButtons (templ);
  opt = ParGetStr ("linkSetType");
  TemplPrint ("linkEntry", 
              ParGetStr ("libName"), 
	      ParGetStr ("entryName"),
              ParGetStr ("libName"), 
	      ParGetStr ("entryName"));

  /* now the same as PageLinkEntryOpt */

  TemplWith(templ,"$queryManager.chunkSize");
  WwwPresentChunkSizes (templ);
  TemplEndWith();
  TemplWith(templ,"$queryManager.selectView");
  WwwPresentViewList ("reset", templ);
  TemplEndWith();


  TemplWith (templ, ParGetBool("isHtml3") ? "html3" : "html2");
  for (c1=0; (group = LibNextLibGroup (&c1)); ) {
    /* adjust number of columns */
    numCol = 70 / (LibGetMaxNameSize (group, NULL, "library") + 2);
    if (!(ngroups = LibNofGroups(group))) 
      continue;
    TemplPrint ("dbGroup", group->com);     
    for (c2=0, nlib = 0; (lib = LibNextLib (group, &c2));) {
      if (LibIs (lib, "subentries")) continue;
      if (!(nlib%numCol)) 
	TemplPrint ("newRow");
      TemplPrint ("library", LibGetName (lib,"full"),
		  WwwChecked (LibIs (lib,"linkTarget")),
		  LibGetName(lib,"full"), LibGetName(lib,"full"), "");
      nlib++;
    }
    TemplPrint ("tail");
  }
  TemplEndWith ();
  TemplPrint ("tail");
}



/****** PageLibNetwork ********************************************************
**
**	Prints the library network in a tabular representation;
**
*/ 

void PageLibNetwork ()
{
  TEMPLv    templ;
  SRSoGROUP *fromGroup, *toGroup;
  SLBo      *fromLib, *toLib;
  LINKo     *link;
  LINKvNode path;
  Int4      c1, c2, c3, c4;
  char      *fromLibName, *toLibName, *letter;

  templ = WwwInit ();
  TemplWith (templ, "$libNetwork");
  TemplPrint ("head");
  WwwPrintButtons (templ);
  TemplPrint ("title");

  /* iterate over all 'from' libs */
  for (c1=0; (fromGroup = LibNextLibGroup (&c1)); )
    for (c2=0; (fromLib = LibNextLib (fromGroup, &c2)); ) {
      if (LibIs (fromLib, "subentries")) continue;
      fromLibName = LibName (fromLib);
      TemplPrint ("fromLib", fromLibName, fromLibName);
      /* iterate over all 'to' libs */
      for (c3=0; (toGroup = LibNextLibGroup (&c3)); ) {
	for (c4=0; (toLib = LibNextLib (toGroup, &c4)); ) {
	  if (LibIs (toLib, "subentries")) continue;
	  toLibName = LibName (toLib);
	  if (fromLib == toLib)
	    break; /* link with 'self' - diagonal is reached */
	  else { 
	    if ((link = LibGetLink (fromLibName, toLibName))) 
	      TemplPrint ("link.direct", fromLibName, toLibName);
	    else {
	      if ((path = LinkSearchPath (fromLibName, toLibName))) 
		TemplPrint ("link.indirect", fromLibName, toLibName,
			    LinkGetPathLength (path));
	      else
		TemplPrint ("link.none");
	    }
	  }
	}
	if (fromLib == toLib)
	  break;
      }
      TemplPrint ("rowEnd");
    }
  
  /* print all databank names vertically */
  TemplPrint ("toLibs");
  for (c1=0; (toGroup = LibNextLibGroup (&c1)); )
    for (c2=0; (toLib = LibNextLib (toGroup, &c2)); ) {
      if (LibIs (toLib, "subentries")) continue;
      toLibName = LibName (toLib);
      TemplPrint ("toLib.head");
      for (letter=toLibName; *letter; letter++)
	TemplPrint (*(letter+1) ? "toLib.letter" : "toLib.last", *letter);
      TemplPrint ("toLib.tail");
    }

  TemplPrint ("tail");
  TemplEndWith ();
  TemplClose (templ);
}


/****** PageLinkInfo *********************************************************
**
**	Prints information about a link between two data banks.
**
*/ 

void PageLinkInfo ()
{
  TEMPLv    templ;
  LINKo     *link;
  LINKvNode path, p;
  char      *from, *to, *tmp;
  Int4      isReverse, toN, fromN, totalN;

  templ = WwwInit ();
  TemplWith (templ, "$linkInfo");
  TemplPrint ("head");
  WwwPrintButtons (templ);
  TemplPrint ("title");

  to = ParGetStr ("toLibName");
  from = ParGetStr ("fromLibName");

  if (!(path = LinkSearchPath (to, from)))
    TemplPrint ("noLink", from, to);
  else {
    if (LinkGetPathLength (path) == 1) /* direct link */
      TemplPrint ("direct", from, to);
    else { /* indirect link */
      TemplPrint ("indirect.head", WwwGetLinkedEntriesN (to, from), from,
		  WwwGetLinkedEntriesN (from, to), to, from);
      for (tmp=NULL, p=path; (p = LinkBackTrack (p, &link, &isReverse));
	   tmp=isReverse? LibName (link->lib1) : LibName (link->lib2))
	if (tmp)
	  TemplPrint ("indirect.pathLib", tmp);
      TemplPrint ("indirect.lastLib", tmp);
    }

    TemplWith (templ, "table");
    TemplPrint ("head");
    while ((path = LinkBackTrack (path, &link, &isReverse))) {
      to = LibName (link->lib2);
      from = LibName (link->lib1);

      if (LinkOpen (link, "read")) {
	toN = LinkGetEntryN (link, 1);
	fromN = LinkGetEntryN (link, 0);
	totalN = LinkGetLinkN (link);
      }
      else 
	toN=0, fromN=0, totalN=0;
	
      if (isReverse)
	TemplPrint ("names", to, to, toN, from, from, fromN);
      else
	TemplPrint ("names", from, from, fromN, to, to, toN);
      
      TemplPrint("total", totalN);
      if (link->typ == LNKxREAD)
	TemplPrint("read", from, link->toField->nam, to);
      else 
	TemplPrint("index", link->fromField->nam, to, link->toField->nam,from);

      /* creation time */
      if (toN)
	TemplPrint ("creTime", TimeToString (LinkGetCreTime (link), "long"));
      else 
	TemplPrint ("notCreated");

      TemplPrint ("rowEnd");
    }
  }
  TemplEndWith ();
  TemplPrint ("tail");
  TemplClose (templ);
}


Int4 WwwGetLinkedEntriesN (char *from, char *to)
{
  SETo *set;
  STRv str;
  Int4  n;

  str = StrNew ();
  if ((set = Query (_Str (StrPrintf (&str, "%s>%s", from, to)),"linkN"))) 
    n = SetGetSize (set);
  else 
    n = 0;
  SetDelete ("linkN");
  StrDel (str);
  return n;
}



/****** PageLibList **********************************************************
**
**      Displays information about available databanks
**
*/

void PageLibList ()
{
  TEMPLv    templ;
  SLBo      *lib;
  SRSoGROUP *group;
  LIBoINDEX *libInx;
  INT4      c1, c2; 
  char      *tmp, *libName;

  templ = WwwInit ();
  TemplWith (templ, "$libList");
  TemplPrint ("head");
  WwwPrintButtons (templ);
  TemplPrint ("title", TimeToString (0, "long"));

  for (c1=0; (group = LibNextLibGroup (&c1)); )
    for (c2=0; (lib = LibNextLib (group, &c2)); ) {
      if (LibIs (lib, "subentries"))
	continue;
      libName = LibName (lib);
      if ((libInx = LibIndexOpen (lib, LibGetIdField (lib), 1))) 
	TemplPrint ("libraryGood", WwwGetIdParam (), libName, libName,
		    tmp && *(tmp = IdxGetReleaseName (libInx->idx)) ? 
		    tmp : "&nbsp;",
		    BtrGetRecordN (libInx->btree),  
		    TimeToString (BtrGetTimeCreated (libInx->btree), "date"),
		    LibGetGroupName (group, "full"));
      else 
	TemplPrint ("libraryBad", WwwGetIdParam (), libName, libName,
		    LibGetGroupName (group, "full"));
    }
  TemplPrint ("tail");
  TemplEndWith ();
}

Int4 WwwPrintInfoChapter (TEMPLv templ, TEMPLv libTempl,
			  char *label, char *libLabel)
{
  if (TemplExists (libTempl, libLabel)) {
    TemplWith (templ, label);
    TemplPrint ("head");
    TemplEndWith ();
    TemplPrint (libLabel);
    TemplWith (templ, label);
    TemplPrint ("tail");
    TemplEndWith ();
  }
}



/****** PageLibInfo **********************************************************
**
**      Displays information about a databank.
**
*/

void PageLibInfo ()
{
  TEMPLv    templ, libTempl;
  SLBo      *lib;
  SLBoFIELD *field;
  LINKo     *link;
  LIBoINDEX *libInx;
  INT4      c, count; 
  char      *tmp, *libName, entryName[200];

  templ = WwwInit ();
  TemplWith (templ, "$libInfo");
  TemplPrint ("head");

  if (*WwwGetIdParam ())
    WwwPrintButtons (templ);

  libName = ParGetStr ("libInfo");
  if (!(lib = (SLBo *) LibObjByName ("library", libName)))
    _ErrExit3 (e__objectunknown, "library", libName);
  libName = LibName (lib);

  TemplPrint ("title", libName, libName, libName);
  if ((libInx = LibIndexOpen (lib, LibGetIdField (lib), 1))) {
    tmp = IdxGetReleaseName (libInx->idx);
    if (tmp && *tmp)
      TemplPrint ("release", tmp, BtrGetRecordN (libInx->btree),
		  TimeToString (BtrGetTimeCreated (libInx->btree), "date"));
    else 
      TemplPrint ("noRelease", BtrGetRecordN (libInx->btree),
		  TimeToString (BtrGetTimeCreated (libInx->btree), "date"));
  }
  else 
    TemplPrint ("notIndexed");

  /* print some general information */  
  if ((libTempl = TemplOpen (LibGetIcarusFileName (lib, "info"), NULL))) {
    TemplPrint ("t.head");
    TemplWith (libTempl, "$dbInfo");
    WwwPrintInfoChapter (templ, libTempl, "$libInfo.t.description",
			 "description");
    WwwPrintInfoChapter (templ, libTempl,"$libInfo.t.literature","literature");
    WwwPrintInfoChapter (templ, libTempl, "$libInfo.t.literature", "citation");
    WwwPrintInfoChapter (templ, libTempl, "$libInfo.t.www", "www");
    WwwPrintInfoChapter (templ, libTempl, "$libInfo.t.ftp", "ftp");
    WwwPrintInfoChapter (templ, libTempl, "$libInfo.t.email", "email");
    WwwPrintInfoChapter (templ, libTempl, "$libInfo.t.address", "address");
    WwwPrintInfoChapter (templ, libTempl, "$libInfo.t.contact", "contact");
    WwwPrintInfoChapter (templ, libTempl, "$libInfo.t.updates", "updates");

    /* example entry */
    if (TemplExists (libTempl, "example")) {
      TemplSPrint (entryName, "example");
      TemplWith (templ, NULL);
      SmEdit (entryName, SMxTRIM);
      TemplPrint ("$libInfo.example", libName, entryName, entryName);
      TemplEndWith ();
    }
    TemplEndWith ();
    TemplPrint ("t.tail");
  }


  /* print information about the fields */  

  TemplWith (templ, "fields");
  WwwPrintFieldInfo (lib, NULL, 0);
  TemplEndWith ();

  /* links to other databanks */

  TemplPrint ("links.to");
  for (c=0, count=0; (link = LibNextLink (&c));) 
    if (lib == link->lib1) {
      TemplPrint ("links.toLib", LibName (link->lib1), LibName (link->lib2), 
                  LibName (link->lib2));
      count++;
    }
  if (!count)
    TemplPrint ("links.none");
  TemplPrint ("links.from");
  for (c=0, count=0; (link = LibNextLink (&c)); ) 
    if (lib == link->lib2) {
      TemplPrint ("links.fromLib", LibName (link->lib2), LibName (link->lib1), 
                  LibName (link->lib1));
      count++;
    }
  if (!count)
    TemplPrint ("links.none");
  TemplPrint ("links.tail");

  /* list of Icarus files */

  TemplPrint ("icarusFiles.head");
  if (*(tmp = (LibGetIcarusFileName (lib, "structure"))))
    TemplPrint ("icarusFiles.structure", libName);
  if (*(tmp = (LibGetIcarusFileName (lib, "syntax"))))
    TemplPrint ("icarusFiles.syntax", libName);
  if (*(tmp = (LibGetIcarusFileName (lib, "info"))))
    TemplPrint ("icarusFiles.information", libName);
  TemplPrint ("icarusFiles.tail");

  TemplPrint ("tail");
  TemplEndWith ();
}






/****** WwwGetOddFile *******************************************************
**
**      Display odd description of a databank
**
**       INPUT:
**
**
*/

void  WwwGetOddFile()
{
  char *tmp = ParGetStr("getOddFile");
  if (tmp)
    WwwGetODDFile(tmp);
  
}



/****** PageEntry *************************************************************
**
**      Prints single entry. if the userId is defined AND option -sl
**      used then a within a session context normal entry list is printed.
**
*/

static void PageEntry ()
{
  TEMPLv   templ;

  templ = WwwInit ();

  ParDefBool ("isHTMLFormat", 1);
  if (ParGetBool ("makeNewUserId") || ParGetBool ("wwwSessionEntryList")) {
    ParSetVolatile ("wwwSessionEntryList");
    WwwQueryExpression ("query", pageQuery);
  }
  else if (Query (pageQuery, "Q")) { 
    WwwPrintSet (templ, "Q", 1, 0);
  }
  else
   _ErrExit2 (i__querynegative, pageQuery);
}


/****** WwwDeleteQueryByNum ******************************************************
**
**	deletes the selected query from history;
**
**	INPUT:	    
**	        IMPLICIT:
**
**	RETURNS:    
*/ 

INT4 WwwDeleteQueryByNum(INT4 j)
{
  char parName[80];
  INT4 queryN, k;
  
  queryN = ParGetNum ("numberOfQueries");
  sprintf (parName, "QueryStr%d", j); 
  ParDelete (parName);
  sprintf (parName, "QuerySize%d", j); 
  ParDelete (parName);
  sprintf (parName, "QueryType%d", j); 
  ParDelete (parName);
  sprintf (parName, "isSubEntry%d", j);
  ParDelete (parName);

  for (k=1; ; k++) {
    sprintf (parName, "QueryLibrary%d_%d", j, k); 
    if (!ParDelete (parName))
      break; /* no more items */
    sprintf (parName, "QueryLibraryN%d_%d", j, k); 
    ParDelete (parName);
  }
  ParDefNum ("numberOfQueries", --queryN);
}


/****** GetEnv **************************************************************
**
**      Get the environment variables
**
**	INPUT:	    
**	        IMPLICIT:
**
**	RETURNS:    
**
**
*/
void  GetEnv()
{

  GetEnvp(envPtr);
  
}

/****** GetEnvp **************************************************************
**
**
**
**
**	INPUT:	    
**	        IMPLICIT:
**
**	RETURNS:    
**
*/

INT4 GetEnvp(char **envPtr)
{
#ifdef script
  INT4 i=0;
  char *tmp;
  char name[80], value[80];

  SCRIPTo *script;

  script = ScriptOpen (ScriptFile,NULL);

  ScriptCopyFrom(script,"ENVIRONMENT-VAR");
  for (i=0;*envPtr; envPtr++) {
    sscanf (*envPtr, "%[^=]=%[^:]", name,value);
    ScriptWriteFrom(script,"LIST-ENV-VAR",name,++i,value);
  }
  ScriptCopyFrom(script,"ENV-END");
  return 1;
#endif
}

/*** GetEnvByName ***************************************************************
**
**     Returns Environment variable values referred.
**
**
**     INPUT : 
**               
**    RETURNS:
**               
**
*/

char *GetEnvByName(char *ename)
{
  static char value[80];
  INT4 i=0;
  char name[80];
  value[0] = name[0] = '\0';
  for (i=0;*envPtr; envPtr++) {
    sscanf (*envPtr, "%[^=]=%[^:]", name,value);
    if(SmEqs(ename,name) == 1) 
      return(value);
  }
  return(NULL);
}


/**api* PageDownloadSet ******************************************************
**
**      Refine the output with more options like alter flanking 
**      regions, sequence format etc., 
**
**	INPUT:	    
**
**	RETURNS:    
**
*/ 

static void PageDownloadSetOpt()
{
  TEMPLv templ;
  WWWoQUERY *query;
  char *tmp,  *tmp1, *tmp2, *tmp3;
  INT4 queryN, queryNo=0, c=0;

  if ((queryNo=WwwNextSelectedQuery (&c, NULL)) ||
      (queryNo=WwwQuerySelectedEntries ()))
    ParDefNum("queryNumber",queryNo);
  else
    _ErrExit (e__wwwNoQueryOrEntriesSelected);
  query = WwwGetQuery(queryNo);

  templ = WwwInit ();
  TemplWith (templ, "$downloadSet");
  TemplPrint("head");
  WwwPrintButtons (templ);

  TemplWith(templ, "inputInfo.html3");
  if (query->isSubEntry) {
    tmp = ParGetStr("shiftbeginpos");
    tmp1 = ParGetStr("shiftendpos");
    tmp2 = ParGetStr("checkbegin");
    tmp3 = ParGetStr("checkend");
    
    ParDefBool("isshiftendrelbegin",0);   /* default, keep as it is */
    ParDefBool("isshiftbeginrelend",0);

    if( (SmLoc(tmp2,"begin") != -1) &&  (SmLoc(tmp3,"begin") != -1) )
      ParDefBool("isshiftendrelbegin",1);
    
    if( (SmLoc(tmp2,"end") != -1) &&  (SmLoc(tmp3,"end") != -1) )
      ParDefBool("isshiftbeginrelend",1);
    
    TemplPrint("shift",(*tmp ? tmp : ""),(*tmp1 ? tmp1 : "" ));
    TemplEndWith();
    TemplPrint("unComplete");
  }
  else
    TemplEndWith();

  WwwPresentChunkSizesMime (templ, queryNo);
  WwwPresentActiveViews (NULL, NULL, query, templ, 0);

  tmp1  = ParGetStr ("localDirName");
  TemplPrint("useMime", (WwwChecked(ParGetBool("useMime"))),
	     (*tmp1 ? tmp1 : "" ));
  TemplPrint("tail", queryNo);
  WwwDelQuery(query);
}

/**api* PageDownloadSet *******************************************************
**
**      Saves the selected set to the user's directory.
**
*/

static void PageDownloadSet()
{

  TEMPLv  templ;

  WWWoQUERY *query;
  char *dirName;
  INT4 queryN;
  INT4 startNo = 0;
  INT4 entryN = 0;
  char *viewBlock = ParGetStr ("viewEntriesBlock");

  if( *viewBlock) {
    sscanf(viewBlock, "%d - %d",&startNo,&entryN);
    entryN = entryN - startNo + 1;
  }
  query = WwwGetQuery (ParGetNum ("listSetNumber"));
  if (!ParGetBool("useMime")) {
    WwwPrintContentType ("Content-type: binary");
    templ = WwwInit ();
    ParDefBool ("downloadEntireEntry", 1);
    WwwQueryRepeat (ParGetNum ("listSetNumber"));
    if (ParGetNum ("viewNumber") > 1) 
      WwwPrintSetView (templ, query->name, startNo, entryN);
    else 
      WwwPrintSet (templ, query->name, startNo, entryN);
  }
  else {
    templ = WwwInit ();
    dirName = ParGetStr("localDirName");
    if(!(*dirName))
     dirName = "trash" ;
    TemplPrint ("head");
    TemplPrint ("start","tempfile",dirName,"Ver1","copy",
	       ParGetStr("seqFormat"));

    queryN = ParGetNum ("queryNumber");
    WwwQueryRepeat (queryN);
    ParDefBool ("isHTMLFormat", 0);
    WwwPrintSet(templ,query->name,startNo,entryN);
    ParDefBool ("isHTMLFormat", 1);
    WwwDelQuery(query);
    ParDelete("useMime");
    TemplEndWith();
  }
}



/**api*  PageViewEdit *********************************************************
**
**      Lets the user edit an existing view.
**
*/

static void PageViewEdit ()
{
  TEMPLv templ;
  VIEWo  *view;
  INT4   j, k, viewNo;

  templ = WwwInit ();
  TemplWith (templ, "$viewCreate");
  TemplPrint ("head");

  WwwInitViews (templ);
  for (j=0, k=1, viewNo=0; (view = ViewNext (&j)); k++) {
    if (SmEqs (ViewGetName (view), ParGetStrF ("selectedViewNo_%d", j))) {
      viewNo = j;
      break;
    }
  }
  if(!viewNo)
    _ErrExit (e__noviewselect);

  WwwViewPartI (viewNo, 1, templ);
}

/**api* PageViewCreate ********************************************************
**
**      Lets the user create a new view.
**
*/

static void PageViewCreate ()
{
  TEMPLv templ;
  INT4   viewNo; 

  templ = WwwInit ();
  TemplWith (templ, "$viewCreate");
  TemplPrint ("head");

  WwwInitViews (templ);
  viewNo = ViewGetViewsN () + 1;
  WwwViewPartI (viewNo, 0, NULL);
  ViewMarkNascent (NULL, viewNo);
}

/**api*  PageViewMgrCreate ****************************************************
**
**       Create a new view from  from view manager.
**
*/

void  PageViewMgrCreate ()
{
  TEMPLv templ;
  INT4   viewNo;

  templ = WwwInit ();
  TemplWith (templ, "$viewCreate");
  TemplPrint ("head");

  WwwInitViews (templ);
  viewNo = ViewGetViewsN () + 1;
  WwwViewPartI (viewNo, 0, templ); 
  ViewMarkNascent (NULL, viewNo);
}


/**api* PageViewSelectFields **************************************************
**
**      View creation part II - selection of fields for 'root' and 'leaf'
**      libraries
**
*/

static void PageViewSelectFields ()
{
  TEMPLv          templ;
  SRSoGROUP       *group;
  SLBoFIELD       *field;
  VIEWo           *view;
  VIEWoLIB        *vlib;
  INT4            k, c, c2, viewNo, isOnlyCommon, numCol;
  char            viewName[100], *libName;

  templ = WwwInit ();

  viewNo = ParGetNum ("viewNumber");
  WwwInitViews (templ);
  view = ViewGetWithNo (viewNo);
  ParDelete ("isNewView");
  if (SmEqs (ViewGetName (view), "nascent")) {
    c=0;
    if (!(vlib = ViewGetNextRootLib (view, &c)))
      _ErrExit (e__nolibslct);
    sprintf (viewName, "%s_view%d", LibName (vlib->lib), viewNo);
    ViewSetName (view, viewName);
  }

  TemplWith(templ, "$viewSelectFields");
  TemplPrint ("head", viewNo, viewNo, viewNo, viewNo, ViewGetName (view), 
	      ParGetStrF ("view%d_Name",viewNo));

  /* print all root libraries and fields */
  TemplWith (templ, "root");
  group = LibGroupNew (NULL);
  TemplPrint ("lib.head");
  for (c=0; (vlib = ViewGetNextRootLib (view, &c));) {
    numCol = 60 / LibGetMaxNameSize (NULL, vlib->lib, "formatted")+1;
    LibGroupAddDb (group, vlib->lib);
    TemplPrint ("lib.name", LibName (vlib->lib), LibName (vlib->lib));
  }
  TemplPrint ("lib.tail");

  isOnlyCommon = ParGetBool ("isOnlyCommonFields");
  for ( c=0, k=0; (field = LibNextGroupField (group, isOnlyCommon, &c));) {
    if (FieldIs(field, "show") || FieldIs (field, "header"))
      WwwPrintSelectField (view, viewNo, field, NULL, numCol, &k);
  }
  TemplPrint ("tail");
  TemplEndWith ();

  /* iterate over leaf libraries */
  TemplWith (templ, "leaf");
  for(c=0; (vlib = ViewGetNextLeafLib (view, &c)); ) {
    numCol = 60 / LibGetMaxNameSize (NULL, vlib->lib, "formatted")+1;
    libName = LibName (vlib->lib);
    TemplPrint ("head", libName, "", libName, libName, viewNo, libName);
    for(c2=0, k=0; (field = LibNextField (vlib->lib, &c2));) {
      if (FieldIs(field,"show") || FieldIs (field, "header"))
	WwwPrintSelectField (view, viewNo, field, vlib, numCol, &k);
    }
    TemplPrint ("extraOptions", viewNo, libName, 
		WwwStringEncode (ViewGetLeafQueryStr (vlib)));
    WwwPresentViewsForLeaf (view, vlib, templ);
    TemplPrint ("tail", viewNo, libName, 
		WwwChecked (ViewLeafIsOnlyEntryN (vlib)));
  }
  TemplEndWith ();
  TemplPrint ("tail");
  TemplEndWith ();

}



/****** PageViewManager ***************************************************
**
**      Displays all defined views and some operations on them.
**
*/

static void PageViewManager()
{
  VIEWo           *view;
  TEMPLv          templ;
  SLBoFIELD       *field;
  VIEWoLIB        *vlib;
  LIBoFieldFormat *format;
  char            *tmp, *formatName;
  Int4            j, k, m, l, 
                  viewsN, nfield=0 ,nlibs=0;
  Int4            leafLibsN = 0, f;

  templ = WwwInit ();
  TemplWith(templ,"$viewManager");
  TemplPrint("head");
  WwwPrintButtons (templ);
  TemplPrint("actions");
  TemplWith(templ,"viewList");

  WwwInitViews (templ);
  viewsN = ViewGetViewsN ();
  for (j=0; (view = ViewNext (&j));) {
    if (ViewIs (view, "forAll"))
      continue;
    if (ViewIs (view, "nascent") || ViewIs (view, "selected")) {
      ViewMarkDeleted (view);
      continue;
    }
    leafLibsN = ViewCountLeafLibs(view);
    TemplPrint("head",leafLibsN,j,ViewGetName(view),
	       ViewGetName (view), leafLibsN,
               (ViewIsTable (view) ? "table" : "list"), leafLibsN);
    TemplPrint (ViewIsShortNames (view) ? "shortNames" : "longNames", 
		leafLibsN);

    for(k=0; (vlib = ViewGetNextRootLib(view,&k));) { 
      TemplPrint("root",LibName(vlib->lib));
    }
    TemplPrint("tableData",leafLibsN);
    if ((vlib = ViewGetNextRootLib(view,&k)))
      for(m=0;(field=ViewGetNextField(vlib,&m));) {
	TemplPrint("rootField",LibGetFieldName (field));
	formatName = ParGetStrF("v%d_RF_%s_format",j,LibGetFieldName(field));
	if(*formatName)
	  TemplPrint("format",formatName);
      }
    TemplPrint("tableDataEnd");

    /* leaf */
    for(k=0, l=0; ( vlib = ViewGetNextLeafLib(view,&k)); l++) {
      if (l) 
	TemplPrint("rowEnd");
      TemplPrint("leaf.lib",LibName (vlib->lib));
      for(m=0;(field=ViewGetNextField(vlib,&m));) {
	TemplPrint("leaf.field", LibGetFieldName (field));
	formatName  = ParGetStrF("v%d_LF_%s_%s_format",j,LibName(vlib->lib),
			 LibGetFieldName(field)); 
	if(*formatName)
	   TemplPrint("leaf.format",formatName);
      }
      tmp=ViewGetLeafQueryStr (vlib);
      TemplPrint (*tmp? "leaf.query" : "emptyCell", WwwStringEncode (tmp)); 
      tmp=ViewGetLeafView (vlib);
      TemplPrint (*tmp? "leaf.view" : "emptyCell", tmp); 
      TemplPrint (ViewLeafIsOnlyEntryN (vlib) ? 
		  "leaf.onlyEntryN" : "emptyCell");
    }
    TemplPrint("tail");
  }
  TemplEndWith();
  TemplPrint("tail");
  ViewDelete(view);
}




/**api* PageViewSelectedEntries **********************************************
**
**      Views selected entries.
**
*/

static void PageViewSelectedEntries ()
{
  TEMPLv    templ;
  INT4      queryN;

  templ = WwwInit ();
  queryN = WwwQuerySelectedEntries ();
  if(!queryN) { /* when no entries then do query for "queryNumber" */
    queryN = ParGetNum("queryNumber"); 
    WwwQueryRepeat (queryN); 
  }
  WwwQueryPrint (queryN);
}


/*** API* SmTrimAt ****************************************************************
**
**
**  	INPUT:	address of string [W]
**  		position to truncate
**  
**  	RETURNS:   
**
**
*/

char *SmTrimAt (char *s, Int4 n)
{
  if(strlen(s) >= n)
    s[n] = '\0';
  return s;
}

/*** API* SmFillFrom ****************************************************************
**
**  	INPUT:	address of string [W]
**  		position to fill from
**              address of the string to fill
**  
**  	RETURNS:  modified string
**
**
*/

char *SmFillFrom(char *s, Int4 n, char *fill)
{
  Int4 m = strlen(s)+strlen(fill),k=0;

  if( (m) > n ) {
    for(k=n; *fill ; k++) 
      s[k] = *fill++;
    s[k] = '\0';
  }
  return s;
}


/****** PageLinkToLibs ********************************************************
**
**
**
*/

static void PageLinkToLibs ()
{
  INT4 queryN;

  if ((queryN = ParGetNum ("linkSetNumber"))) {
    if (SmEqs ("linkStat", ParGetStr ("linkSetType"))) 
      WwwLinkStat (queryN);
    if ((queryN = WwwLinkSet (queryN)))
      WwwQueryPrint (queryN);
    else
      _ErrMsg (i__noentriesfound);
  }
  else if (*ParGetStr ("entryName")) {
    queryN = WwwLinkEntry (ParGetStr ("libName"), ParGetStr ("entryName"));
    WwwQueryPrint (queryN);
  }
}


/**api* WwwPrintButtons ******************************************************
**
**      Prints buttons at the top of the page.
**      The function finds out the current page by looking at what function
**      is defined.
**      The function assumes that the "templ" object is already opened.
**
*/

void WwwPrintButtons (TEMPLv templ)
{
  Func function;
  char *userId;

  if (!*(userId = ParGetStr ("userId")))
    return;


  TemplWith (templ, "$buttons");
  TemplPrint ("head");
#ifdef async
  if (FileOpen (FileNew (WwwGetName (userId, "status"))))
    TemplPrint ("busy");
  else if (ParGetBool ("isPendingJob")) {
    TemplPrint ("completed");
    ParDelete ("isPendingJob");
  }
#endif
  TemplPrint ("selectDatabanks");
  TemplPrint ("queryForm");
  TemplPrint ("queryManager");
  TemplPrint ("views");
  TemplPrint ("databank");
  TemplPrint ("help.head");

  function = ParGetFunction ("wwwFunction");
  if (function == (Func)PageSelectLibrary)
    TemplPrint ("help.top");
  else if (function == (Func)PageQueryForm)
    TemplPrint ("help.query");
  else if (function == (Func)PageViewCreate)
    TemplPrint ("help.viewLibs");
  else if (function == (Func)PageViewSelectFields)
    TemplPrint ("help.viewField");
  else if (function == (Func)PageViewManager)
    TemplPrint ("help.viewManager");
  else if (function == (Func)PageQueryManager)
    TemplPrint ("help.queryManager");
  else if (function == (Func)PageLibList)
    TemplPrint ("help.databanks");
  else if (function == (Func)PageLibNetwork)
    TemplPrint ("help.databanks");
  else if (function == (Func)PageLinkOpt)
    TemplPrint ("help.links");

  else
    TemplPrint ("help.default");
  TemplPrint ("help.tail");

  TemplPrint ("tail");
  TemplEndWith ();
}

 else if (function == (Func)PageViewManager)
    TemplPrint ("help.viewManager");
  else if (function == (Func)PageQueryManager)
    TemplPrint ("help.qusrs/srs.relnotes
Version 5.0.3 had still problems with EMBL in flat file format. This
problem is hopefully fixed now. We added also an improved set of files
for DSSP and IMGT done by Peter Rice.

The file is at ftp://ftp.ebi.ac.uk/pub/software/unix/srs/srs5.0.4.tar.gz


Release notes:



SRS version 5.0.4
=================

1) Fixed a memory leak in srsbuild, EMBL should index without problems
2) SRS supports compressed files again, in particular PDB. pdb.i contains
   2 alternatives of PDB_FILE for compressed and uncompressed files
3) Some internal changes should make srsbuild slightly faster
4) Improved descriptions for IMGT and DSSP 
 

--
Thure Etzold,   etzold@ebi.ac.uk
Giorgio Verde, verde@ebi.ac.uk
19. March, 1997

===============================================================================



SRS version 5.0.3
=================

SRS 5.0.3 has been compiled and tested on IRIX 5.x, 6.x (32-bit binary),
OSF1 4.x, Solaris.
It should work on SunOS, Ultrix and could work on AIX, HP-UX.


The numerous problems of version 5.0.2 concerning indexing and entry access
should all be fixed.
The main differences to the previous release are the addition of an 'option bar'
in the entry display and the incorporation of analysis tools (BLAST, FASTA,
Smith and Waterman search with the Bioccelerator and Clustalw). 
The way the applications are defined is still new and needs to be documented.


Differences in detail:

1)  Many bugs concerning indexing and access to entries have been removed.
    Indexing of GCG formatted databanks is now stable.
2)  The databank descriptions for many databanks, esp. the Transfacs and 
    Genbank has improved. 
3)  A few Icarus bugs have been fixed and also the error messages are 
    more informative. Both nodd and icarus should not dump core anymore.
4)  The example C programs in SRSDEMO have been revised and should all work.
5)  The regular expressions have been reintroduced into the SRS query language.
    (the documentation for the query language is still for version 4 but has been
    extended for version 5 considerably).
6)  The chapter "SRS Server Maintenance" has been added to the online
    documentation system. It describes in detail how to set up a separate WWW server
    that runs wgetz under its own account.
7)  in SRSWWW each single entry display contains an additional 'tool bar'
    for linking the entry to other databanks, viewing the entry and launching
    applications. 
8)  The applications BLAST, FASTA, SW (Smith & Waterman search with 
    Bioccelerator) and CLUSTALW have been added to SRS and can be called from
    a the page containing a list of entries and a single entry. Documentation of
    how to customize these applications and how to add more is still lacking but 
    please have a look into SRSDB/genes.i. Every application is described by an object
    $application. It has an Icarus command to build the command line and one for launching
    the application. All the customization happens there.
    
10) The "SRS group" has moved to the EBI in Hinxton!;-)

Known problems with this release:

1) The "Save" option in SRSWWW does still not work properly.
2) Customization of the applications is easy but still not documented.
4) The $application objects in appl.i for the four applications BLAST, FASTA, CLUSTALW
   and SW have been rewritten several times. It is possible that some default
   values don't make much sense or are missing - please check and let us know if you
   find bugs.
3) getz and wgetz can extract feature sequences but it is still not possible
   to modify their begin and end positions as in SRS4.


--
Thure Etzold,   etzold@ebi.ac.uk
Giorgio Verde, verde@ebi.ac.uk
13. March, 1997

===============================================================================




SRS version 5.0.2
=================


SRS 5.0.2 has been compiled and tested on IRIX 4.05, 5.x, 6.x (32-bit binary),
OSF1 2.x, 3.x, 4.x, Linux 2.x, ULTRIX 4.x, SunOS (gcc), Solaris.
It could also work on AIX, HP-UX.

Now the new things:
-------------------

1) The .is files can now run as an independent script and used by
   SRS without changing the script.
   So in 'tfsite.is' the 'entry' production must always have $In:[file:text]
   
   entry:   ~ {$In:[file:text] $Out}
   	      ('AC' {$Not} ln)*
   	      ('AC  ' {$entryFip=$Fip $Wrt} ln {$App} 
   	       ('AC' {$Not} ln {$App})+)?
   	    ~
   
   and the code for testing at the end must use "$TestMode" 
   
   
   if:$TestMode {
     $job = $JobNew:[prod:$rules skip:" " fileName:'/data/transfac/site.dat']
     while:$JobTokens:[$job name:id print:1] {
       $JobNext:$job
       $print:"-------->entry\n" 
     }
   }
   
2) There is now a very simple Icarus debugger. It is by no means ready but
   even at this stage really useful. It is documented in chapter 6 in the
   WWW manual. 
   
3) I modified the information pages for databanks and data-fields in 
   SRSWWW. Have a look at .it files in 'SRSDB:' which have the description
   about the databanks and fields which is placed into these pages.
   The library information page has the links to the .i, .it, .is
   files for each databank (btw, our test server is 
   'http://kappa.embl-heidelberg.de:8000/srs/'). The idea is that every 
   databank should be documented by a .it file.
   
4) There is an emacs lisp file in 'SRSETC:' which defines an Icarus mode -
   defines only coloring with fontlock. I don't know enough emacs lisp to write
   a proper mode with automatic indentation etc. - any volunteers?
   
5) The indexing of databank partitions runs stable now. This means that
   big databanks like genbank and EMBL can be indexed in chunks of eg, 
   100000 entries and then later merged. srscheck takes care of all
   necessary commands. Have a look in embl.i: attribute 'partSize' of 
   $library sets the partitioning. With a part size of 100000 the indexing
   of EMBL on an alpha takes less than 50mbyte memory.

Known problems with this release
--------------------------------
1) high optimisation on OSF1 2.x, 3.x might give problems.

2) On Solaris cc or gcc can now be used. When using gcc a warning message
   gcc: unrecognized option `-Xa' is now given and should be ignored.

3) There is a minor parsing error when installing the documentation - for us it
   is an old friend, but I guess it might be worrying if you haven't been
   introduced to it.....

man_capi.i:928: error: syntax error, production `l_proto' :
|INT4 (*ParGetFunction (char *parName))()|
.....^
  no match with |^[a-zA-Z0-9_*]+|


--
Thure Etzold,   etzold@embl-heidelberg.de
Johnathon Weare, weare@embl-heidelberg.de
22. January, 1997













gcsrs/srsinstall
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#    $RCSFile: /home/etzold/srs/RCS/srsinstall,v $
#    $Revision: 1.21 $
#    $Date: 1997/03/12 16:26:52 $
#    $Author: srs $
# 
# installs an srs release 
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

#set -e
# -e flag is used to immediately halt installation if a problem occurs

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# analyse command line and print usage if wrong
#
ERR='srsinstall: Stopping due to Error'

if [ "$#" = 0 ]; then
  option="usage"
elif [ "$1" = "make" ]; then
  option="make"
  cd etc
elif [ "$1" = "commands" ]; then
  option="commands"
  cd etc
elif [ "$1" = "all" ]; then
  option="all"
elif [ "$1" = "www" ]; then
  option="www"
elif [ "$1" = "doc" ]; then
  option="doc"
elif [ "$1" = "clean" ]; then
  option="clean"
elif [ "$1" = "cleanall" ]; then
  option="cleanall"
else
  option="usage"
  echo "unknown option '$1'"
fi

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# print "usage"
#
if [ "$option" = 'usage' ]; then
  cat << END

  Usage: ./srsinstall option

  Options:

  all        does a complete installation
  www        install SRS WWW server ...on the SRS side
  doc        installs the SRS documentation on the WWW
  make       compiles all programs
  commands   replaces the "cc", "make" commands by something else
  clean      removes the object and library files for this architecture
  cleanall   removes the bin directory for this architecture

  NOTE: Use "./srsinstall all" the first time you run srsinstall
  -----
  
END
  exit 1
fi

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# insert the correct root into prep_srs and prep_srs.sh
#

if [ "$option" = 'all' ]; then
  echo "...updating file 'prep_srs'"

  rootdir="`pwd`"
  cd etc

  sed "s:setenv SRSROOT .*:setenv SRSROOT "$rootdir":" prep_srs > tmp
  mv tmp prep_srs
  chmod +x prep_srs

  echo "...updating file 'prep_srs.sh'"
  sed "s:SRSROOT=.*:SRSROOT="$rootdir":" prep_srs.sh > tmp
  mv tmp prep_srs.sh
  chmod +x prep_srs.sh
fi

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# put correct "make" and "cc" commands into srsmake
#

OS=`uname`

if [ "$OS" = "SunOS" ]; then
    case "`uname -r`" in
	[56]*)   OS='Solaris' ;;
    esac
fi

# some echo commands do not support -n
# generally /usr/bin/echo doesn't but /usr/ucb/echo does, so one can hardwire
# to be independent of users path.
if [ -r /usr/ucb/echo ]; then
  ECHON="/usr/ucb/echo -n"
else
  ECHON="echo -n"
fi

# OSF/1 v4.0 /usr/ucb is symlink to /usr/bin, but /bin/sh has builtin -n
if [ "$OS" = "OSF1" ]; then
  case "`uname -r`" in
    V[4]*)  ECHON="echo -n"
	    # or can
	    #CMD_ENV=bsd ; export CMD_ENV
    ;;
  esac
fi

# we did our best, but now let's test
ECHONT="`$ECHON | wc -c`"
if [ $ECHONT != 0 ]; then
  ECHONEND="\c"
  ECHON=echo
else
  ECHONEND=""
fi


if [ "$option" = 'all' -o "$option" = 'commands' ]; then

  $ECHON "enter the make command [make]: $ECHONEND"
  read makeCom
  if [ "$makeCom" = "" ]; then makeCom='make' ; fi

  # for OSF1 need to know if it is osf1 make or gnu make
  if [ "$OS" = "OSF1" ]; then
	$ECHON "is this OSF1 make [y]: $ECHONEND"
	read OSFmake
	if [ "$OSFmake" = "" ]; then OSFmake='y' ; fi
  fi

  if [ "$OS" = "SunOS" -o "$OS" = "Solaris" ]; then
    ccComDef='gcc'
  else
    ccComDef='cc'    
  fi

  $ECHON "enter the cc command [${ccComDef}]: $ECHONEND"
  read ccCom

  if [ "$ccCom" = "" ]; then ccCom="$ccComDef" ; fi

  echo 'choose between optimised code, or code for debugging'
  #echo "or you can have no optimisation if you enter 'noopt'"
  $ECHON "optimised code [y]: $ECHONEND"
  read optimCom

  if [ "$optimCom" = "" ]; then optimCom="y" ; fi

  # for OSF1 currently use no optimisation
  if [ "$OS" = "OSF1" ]; then
    case "`uname -r`" in
	V[23]*)   if [ "$optimCom" = "y" ]; then optimCom="noopt" ; fi
	;;
    esac
  fi

  #
  # Possibility for Correction ????
  #

  echo "...inserting commands '$makeCom' and '$ccCom' into srsmake for '$OS'"

  sed "/  $OS)/,/;;/s@MAKE='[^ '][^ ']*@MAKE='$makeCom@" srsmake> tmp
  mv tmp srsmake
  sed "/  $OS)/,/;;/s@CCOMP=[^ '][^ ']*@CCOMP=$ccCom@" srsmake> tmp
  mv tmp srsmake
  # set another make flag for osf1 make
  if [ "$OS" = "OSF1" ]; then
    if [ "$OSFmake" = "y" ]; then
      echo '...inserting OSF1 make command'
      # use this with the make from OSF1
      OSFmake_flag='\\$\@'
    else
      echo '...inserting GNU make command'
      # use this with the make from GNU
      OSFmake_flag='\\$\%'
    fi
    sed "/  $OS)/,/;;/s@TO=[^ '][^ ']*@TO=$OSFmake_flag@" srsmake> tmp
    mv tmp srsmake
  fi

  chmod +x srsmake

  echo "...inserting optimisation choice into srsmakefile for '$OS'"
  if [ "$optimCom" = "y" ]; then
    sed -e "/# CFLAGS Optimised/,/CFLAGS     =/s@^#CFLAGS     =@CFLAGS     =@" -e "/# CFLAGS Not Optimised/,/CFLAGS     =/s@^CFLAGS     =@#CFLAGS     =@" -e "/# CFLAGS Debug/,/CFLAGS     =/s@^CFLAGS     =@#CFLAGS     =@" srsmakefile> tmp
  elif [ "$optimCom" = "noopt" ]; then
    sed -e "/# CFLAGS Optimised/,/CFLAGS     =/s@^CFLAGS     =@#CFLAGS     =@" -e "/# CFLAGS Not Optimised/,/CFLAGS     =/s@^#CFLAGS     =@CFLAGS     =@" -e "/# CFLAGS Debug/,/CFLAGS     =/s@^CFLAGS     =@#CFLAGS     =@" srsmakefile> tmp
  else
    sed -e "/# CFLAGS Optimised/,/CFLAGS     =/s@^CFLAGS     =@#CFLAGS     =@" -e "/# CFLAGS Not Optimised/,/CFLAGS     =/s@^CFLAGS     =@#CFLAGS     =@" -e "/# CFLAGS Debug/,/CFLAGS     =/s@^#CFLAGS     =@CFLAGS     =@"  srsmakefile> tmp
  fi
  mv tmp srsmakefile
fi


#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# now prepare the environment and compile
#


if [ "$option" = 'all' -o "$option" = 'make' ]; then

  . ./prep_srs.sh || { echo "$ERR $?" ; exit 1 ; }

  if [ "$option" = 'all' ]; then
    srsmake msgdef || { echo "$ERR $?" ; exit 1 ; }
  fi

  cd "$SRSSOU"
  msgdef || { echo "$ERR $?" ; exit 1 ; }

  # make a dummy srsenv.h file
  touch ${SRSEXE}/srsenv.h 

  echo '...making ODD-Compiler'
  srsmake nodd || { echo "$ERR $?" ; exit 1 ; }

  echo '...compiling Icarus files to object base'
  srssection || { echo "$ERR $?" ; exit 1 ; }

  echo '...make srsbuild'
  srsmake srsbuild || { echo "$ERR $?" ; exit 1 ; }

  echo '...make srscheck'
  srsmake srscheck || { echo "$ERR $?" ; exit 1 ; }

  echo "...make header file 'srsenv.h'"
  ${SRSEXE}/srscheck -header || { echo "$ERR $?" ; exit 1 ; }

  echo '...make getz'
  srsmake getz || { echo "$ERR $?" ; exit 1 ; }

  echo '...make icarus'
  srsmake icarus || { echo "$ERR $?" ; exit 1 ; }



  cat << END

  srsinstall: make has completed

END

fi

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Installs the SRS documentation
#

if [ "$option" = 'doc' ]; then
  echo '...Creating and installing the SRS documentation for the WWW'
  . etc/prep_srs.sh || { echo "$ERR $?" ; exit 1 ; }
  makedoc || { echo "$ERR $?" ; exit 1 ; }

  cat << END

  srsinstall: doc has completed

END
fi

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# installs WWW server
#

if [ "$option" = "www" ]; then
  . etc/prep_srs.sh || { echo "$ERR $?" ; exit 1 ; }

  docRootDef='/srs5/'
  $ECHON "enter httpd alias for doc root of SRSWWW [${docRootDef}]: $ECHONEND"
  read docRoot
  if [ "$docRoot" = "" ]; then docRoot="$docRootDef" ; fi
  docRoot="`echo $docRoot | sed -e 's/\/$//'`"

  binRootDef='/srs5bin/cgi-bin/'
  $ECHON "enter httpd alias for bin root or SRSWWW [${binRootDef}]: $ECHONEND"
  read binRoot
  if [ "$binRoot" = "" ]; then binRoot="$binRootDef" ; fi
  binRoot="`echo $binRoot | sed -e 's/\/$//'`"

  siteNameEG='EMBL, Heidelberg'
  siteNameDef='unknown'
  $ECHON "enter short name for your institution (eg, '$siteNameEG' ): $ECHONEND"
  read siteName
  if [ "$siteName" = "" ]; then siteName="$siteNameDef" ; fi

  srsAdminDef='unknown'
  srsAdminEG='srs@inst.org'
  $ECHON "E-mail address of SRS administrator (eg, '$srsAdminEG' ): $ECHONEND"
  read srsAdmin
  if [ "$srsAdmin" = "" ]; then srsAdmin="$srsAdminDef" ; fi

  # do replacement

  sed "s#docdir set:'[^']*'#docdir set:'"$docRoot"'#" $SRSICA/srswww.i > tmpsed
  mv tmpsed $SRSICA/srswww.i
  sed "s#cgidir set:'[^']*'#cgidir set:'"$binRoot"'#" $SRSICA/srswww.i > tmpsed
  mv tmpsed $SRSICA/srswww.i
  sed "s#siteName set:'[^']*'#siteName set:'""$siteName""'#" $SRSICA/srswww.i > tmpsed
  mv tmpsed ${SRSICA}/srswww.i
  sed "s#srsAdmin set:'[^']*'#srsAdmin set:'""$srsAdmin""'#" $SRSICA/srswww.i > tmpsed
  mv tmpsed ${SRSICA}/srswww.i

  srscheck -header || { echo "$ERR $?" ; exit 1 ; }

  srsmake wgetz || { echo "$ERR $?" ; exit 1 ; }

  chmod 777 "$SRSWWWTMP"
  ${SRSEXE}/wgetz -top -color yellowWeave -mime none > ${SRSWWW}/index.html || { echo "$ERR $?" ; exit 1 ; }

  cat << END

  srsinstall: www has completed

  Now you must edit the file 'srm.conf' of the httpd.
  Add the two aliases:
 
  -------------------------------------------------------
  ScriptAlias ${binRoot}/ ${SRSROOT}/www/bin/
  Alias ${docRoot}/ ${SRSROOT}/www/
  -------------------------------------------------------

  Then restart the server.

END

fi

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# cleans the SRS object and lib files for this architecture
#

if [ "$option" = 'clean' ]; then
  echo '...cleaning the SRS object files and libraries for this architecture'
  . etc/prep_srs.sh || { echo "$ERR $?" ; exit 1 ; }
  cd "$SRSSOU"
  echo '...make clean'
  srsmake clean || { echo "$ERR $?" ; exit 1 ; }

fi
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# cleans the SRS bin directory for this architecture
#

if [ "$option" = 'cleanall' ]; then
  echo '...cleaning the SRS bin directory for this architecture'
  . etc/prep_srs.sh || { echo "$ERR $?" ; exit 1 ; }
  cd "$SRSSOU"
  echo '...make cleanall'
  srsmake cleanall || { echo "$ERR $?" ; exit 1 ; }

fi
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~srs/tmp/

<TITLE>about SRS 5.0.3</TITLE>
<BODY background="images/yellow_weave.gif">
<H3><I>This</i> Browser for Databanks in Molecular Biology <I>was created by</I>
</H3>
<UL>
<LI><A HREF="http://www.embl-heidelberg.de/~etzold/"> Thure Etzold </A>, EMBL Heidelberg</LI>
<LI><A HREF="http://www.embl-heidelberg.de/~verde/"> Giorgio Verde </A>, EMBL Heidelberg</LI>
<LI><A HREF="http://www.embl-heidelberg.de/~weare/"> Johnathon Weare </A>, EMBL Heidelberg</LI>
<LI><A HREF="http://www.embl-heidelberg.de/~chenna/"> Ramu Chenna </A>, EMBL Heidelberg</LI>
<LI><A HREF="http://www.embl-heidelberg.de/~ulyanov/"> Anatoly Ulyanov </A>, EMBL Heidelberg</LI>
<LI>Gerald Sch&auml;fer</LI>
</UL>
This work has been financially supported in part by a European Union Biomed II
grant, and by the EMBnet.
<P>
We would also like to thank a long list of people who have provided
support and help, in particular those who suffered our beta releases.

<P>
The SRS WWW server can be easily configured to use a different set of 
databanks; in fact, almost all HTML files are produced dynamically. 
The server is layered over the SRS system and both will be
released as a software package in the near future.
<P>

<H3> References:</H3>
<UL>
<LI>
Thure Etzold, Anatoly Ulyanov, and Patrick Argos, SRS: Information Retrieval System for Molecular Biology Data Banks. Methods in Enzymology v. 266, p. 114, 1996.
</LI>
<LI>
Thure Etzold and Patrick Argos, SRS an indexing and retrieval tool for flat 
file data libraries. Comput. Appl. Biosci. 9:49-57, 1993 
</LI>

<LI>
Thure Etzold and Patrick Argos, Transforming a set of biological flat file 
libraries to a fast access network. Appl. Biosci. 9:59-64, 1993 
</LI>
</UL>

<P>

...if you have comments or questions you can send a mail to<BR>
<BLOCKQUOTE><I>etzold@embl-heidelberg.de</I>,<BR>
<I>verde@embl-heidelberg.de</I>,<BR>
<I>weare@embl-heidelberg.de</I><P></BLOCKQUOTE>
  <HR>
 Release SRS 5.0.4 is now available. It includes a command line
 interface and the SRSWWW server program. The central part of the release is
 the SRS function library (written in C) that lets you do queries and 
 access and link entries inside of your program. 
  <P>
<A HREF="file://ftp.ebi.ac.uk/pub/software/unix/srs/srs5.0.4.tar.gz"> 
 srs5.0.4.tar.gz</A>
 <P>
 <HR>
BLOCKQUOTE><I>etzold@embl-heidelberg.de</I>,<BR>
<I>verde@embl-heidelberg.de</I>,<BR>
<I>weare@embl-heidelberg.de</I><P></BLOCKQUOTE>
  <HR>
 Release SRS 5.0.4 is now available. It includes a command line
 interface and the SRSWWW server program. The central part of the release issrs/www/bin/

<title>Blast help</title>
<body text="#000000" bgcolor="#FFFFF0" link="#0000FF" vlink="#FF0000" alink="#FF0000">
<H1>BLAST</H1>
<H2> DESCRIPTION</H2>
     This document describes the BLAST version 1.4 programs.
     BLAST (Basic Local Alignment Search Tool) is  the  heuristic
     search  algorithm  employed  by the programs blastp, blastn,
     blastx, tblastn, and tblastx; these programs ascribe  significance 
 to  their findings using the statistical methods of
     Karlin and Altschul (1990, 1993) with  a  few  enhancements.
     The  BLAST  programs  were  tailored for sequence similarity
     searching -- for example to identify  homologs  to  a  query
     sequence.   The programs are not generally useful for motifstyle
 searching.  For a discussion of basic issues in  similarity 
 searching of sequence databases, see Altschul et al.
     (1994).
<P>
     The five BLAST programs described here perform the following
     tasks:

<DL>
<DT>     blastp  <DD>  compares an amino acid query  sequence  against  a
               protein sequence database;

<DT>     blastn <DD>   compares a nucleotide  query  sequence  against  a
               nucleotide sequence database;

<DT>     blastx <DD>   compares  the  six-frame  conceptual   translation
               products  of  a  nucleotide  query  sequence (both
               strands) against a protein sequence database;

<DT>     tblastn <DD>  compares  a  protein  query  sequence  against   a
               nucleotide     sequence    database    dynamically
               translated  in  all  six  reading   frames   (both
               strands).

<DT>     tblastx <DD>  compares the six-frame translations of  a  nucleotide
         query sequence against the six-frame translations
      of a nucleotide sequence database.
</DL>
<P>
     The fundamental unit of BLAST algorithm output is the  Highscoring
     Segment Pair (HSP).  An HSP consists of two sequence
     fragments of arbitrary but equal length whose  alignment  is
     locally  maximal  and for which the alignment score meets or
     exceeds a threshold or cutoff score.  A set of HSPs is  thus
     defined  by  two  sequences,  a scoring system, and a cutoff
     score; this set may be empty if the cutoff score  is  suffi-
     ciently  high.   In  the programmatic implementations of the
     BLAST algorithm described here, each HSP consists of a  seg-
     ment  from  the  query  sequence  and  one  from  a database
     sequence.  The sensitivity and speed of the programs can  be
     adjusted  via  the standard BLAST algorithm parameters W, T,
     and X (Altschul et al., 1990); selectivity of  the  programs
     can be adjusted via the cutoff score.
<P>
     A Maximal-scoring Segment  Pair  (MSP)  is  defined  by  two
     sequences and a scoring system and is the highest-scoring of
     all possible segment pairs that can be produced from the two
     sequences.   The  statistical methods of Karlin and Altschul
     (1990, 1993) are applicable to determining the  significance
     of MSP scores in the limit of long sequences, under a random
     sequence model that assumes independent and identically dis-
     tributed  choices  for  the residues at each position in the
     sequences.  In the programs described here,  Karlin-Altschul
     statistics  have  been extrapolated to the task of assessing
     the significance of HSP scores obtained from comparisons  of
     potentially short, biological sequences.

<H2>SEARCH STRATEGY</H2>
     The approach to similarity searching taken by the BLAST pro-
     grams  is  first to look for similar segments (HSPs) between
     the query sequence and a database sequence, then to evaluate
     the statistical significance of any matches that were found,
     and finally to report only  those  matches  that  satisfy  a
     user-selectable threshold of significance.  Findings of mul-
     tiple HSPs involving the query sequence and a  single  data-
     base  sequence  may be treated statistically in a variety of
     ways.  By default the programs use "Sum" statistics  (Karlin
     and  Altschul, 1993).  As such, the statistical significance
     ascribed to a set of HSPs may be higher than  that  ascribed
     to any individual member of the set.  Only when the ascribed
     significance  satisfies  the  user-selectable  threshold  (E
     parameter) will the match be reported to the user.
<P>
     The task of finding HSPs begins with identifying short words
     of  length  W  in  the  query  sequence that either match or
     satisfy some positive-valued threshold score T when  aligned
     with a word of the same length in a database sequence.  T is
     referred  to  as  the  neighborhood  word  score   threshold
     (Altschul  et  al.,  1990).  These initial neighborhood word
     hits act as seeds for initiating  searches  to  find  longer
     HSPs  containing  them.   The word hits are extended in both
     directions along each sequence for as far as the  cumulative
     alignment  score  can  be  increased.  Extension of the word
     hits in each direction  are  halted  when:   the  cumulative
     alignment score falls off by the quantity X from its maximum
     achieved value; the cumulative score goes to zero or  below,
     due  to  the  accumulation  of  one or more negative-scoring
     residue  alignments;  or  the  end  of  either  sequence  is
     reached.

<H2>SETTING PARAMETERS</H2>
     Many of the BLAST program parameters have one- or two-letter
     names  and  default  values  that  can  be  modified using a
     name=value syntax on  the  command  line,  e.g.,  E=0.05  or
     S2=35.   Other  command  line  options are flags that appear
     alone on the command line (e.g., - span).   Parameter  names
     are  expected  to be followed by a new value, separated from
     the parameter name by white space,  as  in  - filter seg  or
     -dbrecmax 10500.  An alternative parameter-value syntax sup-
     ported by the programs is  illustrated  in  these  examples:
     filter=seg and dbrecmax=10500.

<H2>SELECTIVITY IN REPORTING MATCHES</H2>
<A NAME=e></A>
     The  parameter  E  establishes  a  statistical  significance
     threshold  for  reporting  database  sequence matches.  E is
     interpreted as the upper bound on the expected frequency  of
     chance occurrence of an HSP (or set of HSPs) within the con-
     text of the entire database search.  Any  database  sequence
     whose  matching  satisfies E is subject to being reported in
     the program output.  If  the  query  sequence  and  database
     sequences  follow  the  random  sequence model of Karlin and
     Altschul (1990), and if sufficiently sensitive  BLAST  algo-
     rithm  parameters  are used, then E may be thought of as the
     number of matches one expects to  observe  by  chance  alone
     during  the database search.  The default value for E is 10,
     while the permitted range for this Real valued parameter  is
     0 < E <= 1000.
<P>
<A NAME=s></A>
     The parameter S represents the score at which a  single  HSP
     would  by  itself  satisfy  the  significance  threshold  E.
     Higher scores --  higher  values  for  S  --  correspond  to
     increasing  statistical  significance  (lower probability of
     chance occurrence).  Unless S is explicitly set on the  com-
     mand line, its default value is calculated from the value of
     E.  If both S and E are set on the  command  line,  the  one
     which is the most restrictive is used.  When neither parame-
     ter is specified on the command line, the default value  for
     E is used to calculate S.
<P>
     The values for E and S are interconvertible, given the  con-
     text  of the search, which includes:  the length and residue
     composition of the query sequence; the length of  the  data-
     base;  a  fixed,  hypothetical  residue  composition for the
     database; and the scoring system employed.  The scoring sys-
     tem used by the BLAST programs consists of a scoring matrix,
     wherein a score is ascribed to the alignment of each  letter
     (residue)  in  the  alphabet  with every other letter in the
     alphabet as well as to itself.
<P>
     The significance of an alignment  score  depends  intimately
     upon the specific scoring matrix employed and the length and
     residue composition of the query sequence and database,  all
     of  which  may  vary with each search performed.  Instead of
     the having the user guess at an appropriate  value  for  the
     cutoff score S for each search, an intuitive, general way to
     set thresholds for reporting matches is via the E parameter,
     which  has  the  direct statistical interpretation mentioned
     above.

<H3>     KARLIN-ALTSCHUL STATISTICS</H3>

     From Karlin and  Altschul  (1990),  the  principal  equation
     relating  the  score  of an HSP to its expected frequency of
     chance occurrence is:
<PRE>
                        E = K N exp(-Lambda S)
</PRE>
     where E is the expected frequency of chance occurrence of an
     HSP having score S (or one scoring higher); K and Lambda are
     Karlin-Altschul parameters; N is the product  of  the  query
     and  database  sequence  lengths,  or the size of the search
     space; and exp is the exponentiation function.
<P>
     Lambda may be thought of as the expected increase in  relia-
     bility  of  an  alignment associated with a unit increase in
     alignment score.  Reliability in this case is  expressed  in
     units  of  information,  such  as bits or nats, with one nat
     being equivalent to 1/log(2) (roughly 1.44) bits.
<P>
     The expectation E (range 0 to infinity)  calculated  for  an
     alignment between the query sequence and a database sequence
     can be  extrapolated  to  an  expectation  over  the  entire
     database search, by converting the pairwise expectation to a
     probability (range 0-1) and multiplying the  result  by  the
     ratio of the entire database size (expressed in residues) to
     the length of the matching database sequence.  In detail:
<PRE>
                   E_database = (1 - exp(-E)) D / d
</PRE>
     where D is the size of the database; d is the length of  the
     matching  database  sequence; and the quantity (1 - exp(-E))
     is the probability, P, corresponding to  the  expectation  E
     for  the  pairwise  sequence  comparison.   Note that in the
     limit of infinite E, P approaches 1; and in the limit  as  E
     approaches  0, E and P approach equality.  Due to inaccuracy
     in the statistical methods as they are applied in the  BLAST
     programs, whenever E and P are less than about 0.05, the two
     values can be practically treated as being equal.
<P>
     In contrast to the random sequence  model  used  by  Karlin-
     Altschul statistics, biological sequences are often short in
     length -- an HSP may involve a relatively large fraction  of
     the  query or database sequence, which reduces the effective
     size of the 2-dimensional search space defined  by  the  two
     sequences.   To obtain more accurate significance estimates,
     the BLAST programs compute effective lengths for  the  query
     and database sequences that are their real lengths minus the
     expected length of the HSP, where the expected length for an
     HSP is computed from its score.  In no event is an effective
     length for the query or database sequence  permitted  to  go
     below  1.  Thus, the effective length of either the query or
     the database sequence is computed according to  the  follow-
     ing:
<PRE>
          Length_eff = MAX( Length_real - Lambda S / H , 1)
</PRE>
     where H is the relative entropy of the target and background
     residue  frequencies (Karlin and Altschul, 1990), one of the
     statistics reported by the BLAST programs.  H may be thought
     of as the information expected to be obtained from each pair
     of aligned residues in a real alignment  that  distinguishes
     the alignment from a random one.

<H3>HSP SCORE THRESHOLDS</H3>
     Using the default  parameters,  many  more  aligned  segment
     pairs  are  typically  found  by the BLAST programs than are
     ultimately reported.  First, only those segment pairs  scor-
     ing  at or above a selectable cutoff score are saved as bona
     fide HSPs for further  consideration  of  their  statistical
     significance.   And  second, any HSPs that are found may not
     satisfy the significance threshold for reporting.
<P><a name=s2></a>
<P><a name=e2></a>
     The cutoff score which defines HSPs is parameterized as  S2.
     A  value for S2 can be set on the command line, or its value
     can be set indirectly via the command line parameter E2.  E2
     is  interpreted  as the expected number of HSPs that will be
     found when comparing two sequences that each have  the  same
     length -- either 300 amino acids or 1000 nucleotides, which-
     ever is appropriate for the particular program  being  used.
     S2  may  be  thought  of  as  the score expected for the MSP
     between two such sequences.  The default  value  for  E2  is
     typically about 0.15 but may vary from version to version of
     each program.  The default value for S2 will  be  calculated
     from  E2  and,  like  the  relationship  between E and S, is
     dependent on the residue composition of the  query  sequence
     and  the scoring system employed, as conveyed by the Karlin-
     Altschul K and Lambda statistics.

<H3>SEARCH SENSITIVITY</H3>
     Sensitivity of the BLAST programs should  be  considered  in
     two  areas.   First,  there  is  the  question  of  how well
     ungapped alignments (HSPs)  can  capture  or  represent  the
     similarity  between  two  biological sequences that may have
     evolved  independently  and/or  contain  sequencing  errors.
     Particularly  in  the  presence  of  insertions/deletions or
     frameshifts, it may be necessary to increase  E2  (or  lower
     S2), in order to detect the remnants of extended similarity.
     The  amount  of  evidence  or  information  to  support  the
     hypothesis  that  a  given  alignment is real and not random
     decreases with each mutation or sequencing error (States  et
     al.,  1991; Gish and States, 1993).  As a corollary of this,
     the expected  length  of  a  statistically  significant  HSP
     increases  with  each mutation or sequencing error.  At some
     point, accumulated mutations and errors  completely  obscure
     the  presence  of  a relationship between two sequences; the
     BLAST programs' focus on ungapped alignments will  sometimes
     cause  this point to be reached sooner than for other align-
     ment methods.
<P>
     The second area where sensitivity may be of  concern  is  in
     the  heuristic nature of the BLAST algorithm for finding HSP
     alignments.  Using this algorithm, the lower the score of an
     HSP  is,  the higher is the probability that the HSP will go
     undetected.  At the user's  discretion,  the  speed  of  the
     BLAST  algorithm  and  the  programs  can  be  sacrificed in
     exchange for increased sensitivity of detecting these  lower
     significance  HSPs,  and  vice  versa;  however, the default
     parameters for  all  of  the  programs  except  blastn  have
     already  been  chosen  to generally obtain moderate (blastx,
     tblastn, and tblastx) or high (blastp) sensitivity.  If sen-
     sitivity  is not an issue but speed is, then one should con-
     sider adjusting the BLAST algorithm  parameters  to  achieve
     higher speed (e.g., increase W by one and T by 10-50%).
<P>
     Raising E2 or lowering S2 can improve  the  apparent  sensi-
     tivity  of the BLAST programs by reducing their selectivity,
     permitting the programs to assess larger sets  of  HSPs  for
     statistical  significance.  Lower-scoring HSPs are more dif-
     ficult for the BLAST algorithm to detect,  however,  due  to
     its  heuristic  nature.  Therefore, merely increasing E2 (or
     lowering S2) may  not  significantly  increase  sensitivity,
     without  also  adjusting  the  BLAST algorithm's W, T, and X
     parameters to increase the true sensitivity of the programs.
<P>
     If E2 and S2 are adjusted much from their default values  to
     observe  even  lower-scoring  HSPs,  search speed may suffer
     significantly because the computational  complexity  of  the
     statistical  methods is nonlinear in the number of HSPs that
     are found.  For Sum statistics, the  complexity  is  a  qua-
     dratic  function  of the number of HSPs; for Poisson statis-
     tics, the  complexity  is  even  worse,  a  cubic  function.
     Furthermore,  as  more HSPs are considered, fuzziness in the
     HSP consistency rules yield more reports of false positives.
<P>
     Without varying the scoring scheme employed, the probability
     that  the  BLAST algorithm can detect an HSP having any par-
     ticular score can be increased by:  lowering  the  neighbor-
     hood  word  score threshold, T, while keeping the word size,
     W, constant;  lowering  both  W  and  T  appropriately  (see
     Altschul  et  al., 1990); and/or raising the word hit exten-
     sion drop-off score X (described earlier).
<P><a name=w></a>
     The default value for W is 3 amino acids for blastp, blastx,
     tblastn,  and  tblastx,  and 11 nucleotides for blastn.  For
     the first 4 BLAST programs,  which  perform  comparisons  of
     amino  acid  sequences,  W  should  usually be restricted to
     values less than 5, unless the  value  for  T  is  specified
     disproportionately  larger,  to  avoid  consuming  too  much
     memory  for  the  neighborhood  word  list  (see  below  and
     Altschul et al., 1990).
<p>
     X is a positive integer representing the maximum permissible
     decay of the cumulative segment score during word hit exten-
     sion.  Raising X may decrease  the  chance  that  the  BLAST
     algorithm   overlooks  an  HSP,  but  it  may  significantly
     increase the search time, as well.  If computation  time  is
     of  little  concern,  X might be increased a few points from
     its default value, but often little or no increase in sensi-
     tivity  is  observed  by  increasing this parameter from its
     default value.
<p>
     For blastp, blastx, tblastn, and tblastx, the default  value
     for  X  is  calculated  to  be  the  minimum  integral score
     representing 10 bits of information, or a decay in the  sta-
     tistical  significance  of the alignment by a factor of 2 to
     the tenth power (or about 1,000).  Since the X parameter  is
     used  to  terminate  extensions independently in both direc-
     tions,  about  1  in  500  alignments  are  expected  to  be
     terminated  prematurely  that  would  have attained a higher
     score had termination not come so soon.
<p>
     For blastn, the default value of X is the  minimum  integral
     score  that represents at least 20 bits of information, or a
     reduction in the statistical significance of  the  alignment
     by  a  factor of 2 to the twentieth power (or about one mil-
     lion).

<h3>THE NEIGHBORHOOD</h3>
     T is the neighborhood word score  threshold  for  generating
     all  words of length W that yield a score of at least T when
     aligned with some word of length W from the query  sequence.
     The  list  of  words so generated is called the neighborhood
     (Altschul et al., 1990).  The size of the  neighborhood  can
     be  increased,  thus  improving  sensitivity, by lowering T.
     Conversely, raising the value of T decreases the size of the
     neighborhood and decreases the likelihood of detecting HSPs.
     Generally, the larger the neighborhood (the lower T is), the
     slower the programs run, as well.
<P>

     The default value for the neighborhood word score  threshold
     is  calculated  at run-time from the residue composition and
     length  of  the  query  sequence  and  the  scoring   matrix
     employed,  using  an  ad  hoc equation that is a function of
     Lambda and H. Occasionally it may be necessary  to  manually
     set  the  neighborhood  word score threshold via the command
     line, for which 13 may be a good value to try,  but  a  good
     choice  is highly dependent on the particular scoring matrix
     and word length used.
<P>

     The PAM120 amino acid scoring matrix supplied with the BLAST
     programs,  produced  to  a scale of Natural log(2)/2, yields
     values for Lambda that are expected to be close to 0.5  bits
     per unit score for query sequences of typical residue compo-
     sitions.  Under these conditions, an increase in  an  align-
     ment  score by 2 units is expected to increase the reliabil-
     ity or informativeness of the alignment by 2 times 0.5  =  1
     bit,  corresponding to an increase in its statistical signi-
     ficance by a factor of 2.  The supplied  PAM250  matrix  was
     produced  to a scale of Natural log(2)/3, suggesting that an
     increase in alignment score by 3 units will be  required  to
     increase  statistical  significance by a factor of 2.  These
     are rules of thumb for the matrices  mentioned.   Generally,
     the  significance  of  an  alignment  score is indeterminate
     without specific knowledge of the scoring  matrix  employed.
     If  one communicates scores in a report, it may be useful to
     attach the values for the Karlin-Altschul parameters  Lambda
     and  K,  so  that  statistical  significance can be properly
     ascribed to the scores.

<h3>MORE OPTIONS</h3>
     Except where noted, all of the  BLAST  programs  accept  the
     following command line options:
<DL>

<DT><A NAME=matrix><b>-matrix matrixfile</b></A><DD>
             This option is used to specify the name  of  a  file
             containing  an  alternate  or  user-defined  scoring
             matrix.  Most of the programs will only accept one -
             matrix  option  at  a  time,  but  blastp  currently
             accepts as many as eight (8)  on  a  single  command
             line,  all  of  which are used simultaneously during
             the database search for increased sensitivity.

<DT><A NAME=qtype><b>-qtype</b></A><dd> 
             This option causes the BLAST programs to exit  non-
             zero  if  the  query  sequence  appears to be of the
             wrong type (either amino acid or nucleic  acid)  for
             the particular program invoked.

<DT><A NAME=qres><b>     -qres</b> </a><dd>
            This option causes the BLAST programs to exit  non-
             zero  if  the  query  sequence  contains  an invalid
             letter code for the type of query sequence  expected
             (amino acid or nucleic acid).

<DT><A NAME=dbrecmin><b>     -dbrecmin first_record_number</b></A><dd>
             By default the  BLAST  programs  search  the  entire
             database.   Using  the  -dbrecmin option, the record
             number of the database sequence where the search  is
             to  begin can be specified.  Record numbers are one-
             based (i.e., 1 is the first record, 2 is the  second
             record,  and  so on).  Statistics are computed using
             the complete database length, not the length of  the
             subset selected.  See also the -dbrecmax option.

<DT><A NAME=matrix><b>     -dbrecmax last_record_number</b></A><dd>
             By default the  BLAST  programs  search  the  entire
             database.   Using  the  -dbrecmax option, the record
             number of the database sequence where the search  is
             to  end  can  be  specified.  See also the -dbrecmin
             option.

<DT><A NAME=gi><b>-gi</b></A><DD>
             When GenInfo gi identifiers are available  for  the
             database  sequences (in their deflines), this option
             can be specified to have these identifiers  reported
             in the program output.
<DT><A NAME=span2><b> -span2</b></A><dd>
             While examining each database  sequence,  the  pro-
             grams use a greedy algorithm to discard any HSP they
             find which is spanned from start to end by a  previ-
             ously  found  HSP.  When this option is invoked (the
             default), an HSP is deemed to  be  spanning  another
             when  both  the query and database segments from the
             first  HSP  completely   cover   the   corresponding
             segments  in  the  other  HSP.   When  an  HSP spans
             another, the higher scoring one is retained and  the
             lower  scoring one is discarded; if their scores are
             equal, the longer,  less  information-dense  HSP  is
             discarded.  Note:  this option was previously called
             -overlap2 in the BLAST version 1.3 programs.
<DT><A NAME=span1><b>-span1</b></A><dd>
             This  option  relaxes  the  criteria  for  judging
             whether  an  HSP  spans another, prior to discarding
             one of them if  spanning  is  detected.   With  this
             option,  it  is  merely a matter of either the query
             segment or the database segment (or both) spans  the
             corresponding  segment(s)  in the other HSP, whereas
             the -span2 option requires  that  both  segments  be
             spanned.   The  - span1  option  may  be  useful  in
             suppressing reports of HSPs  when  the  query  or  a
             database  sequence contains internal repeats.  Note:
             this option was previously called -overlap1  in  the
             BLAST version 1.3 programs.
<DT><A NAME=span><b>-span</b></a><dd>
             This option  turns  off  entirely  the  feature  of
             detecting  and  discarding spanned HSPs.  Voluminous
             output often results  from  its  use.   Note:   this
             option  was  previously called -overlap in the BLAST
             version 1.3 programs.

<DT><A NAME=filter><b>-filter filtermethod</b></a><dd>
             This option activates filtering or masking  of  seg-
             ments  of  the query sequence based on a potentially
             wide variety  of  criteria.   The  usual  intent  of
             filtering  is  to mask regions that are non-specific
             for protein identification using  sequence  similar-
             ity.  For instance, it may be desired to mask acidic
             or  basic  segments  that  would   otherwise   yield
             overwhelming  amounts of uninteresting, non-specific
             matches against a wide  array  of  protein  families
             from  a  comprehensive  database  search.  The BLAST
             programs  have  internally-coded  knowledge  of  the
             specific  command  line options needed to invoke the
             SEG and XNU programs as query sequence filters,  but
             these  two  filter  programs are not included in the
             BLAST software distribution  and  must  be  indepen-
             dently  installed.   All filter programs must reside
             in  the  /usr/ncbi/blast/filter  directory,  or  the
             BLASTFILTER  environment  variable  must  be  set to
             point to the directory containing the desired filter
             programs.   The  SEG  program (Wootton and Federhen,
             1993) masks low  compositional  complexity  regions,
             while  XNU (Claverie and States, 1993) masks regions
             containing short-periodicity internal repeats.   The
             BLAST programs can pipe the filtered output from one
             program into  another.   For  instance,  XNU+SEG  or
             SEG+XNU can be specified as the filtermethod to have
             each program filter the query  sequence  in  succes-
             sion.  Note that neither SEG nor XNU is suitable for
             filtering untranslated nucleotide sequences for  use
             by blastn.
<DT><A NAME=echofilter><b>-echofilter</B></a><dd>
             This option causes the filtered query sequence to be
             displayed  in  the  output.   Any masked letters are
             typically  indicated  with  X's  (protein)  or   N's
             (nucleic acid).
<DT><A NAME=consistency><B>-consistency </B></a><dd>
             This option turns off both the determination of  the
             number  of  HSPs that are consistent with each other
             in a gapped alignment and an adjustment that is made
             to the Sum and Poisson statistics to account for the
             consistency.
<DT><A NAME=qoffset><B>     -qoffset offset</B></a><dd>
             This  option  permits  query   sequence   coordinate
             numbers  to  be  adjusted  by  the  value of offset,
             through simple addition.  This  may  useful  when  a
             query sequence must be split into short, overlapping
             segments in order to  complete  individual  searches
             within a restrictive time period.

<DT><A NAME=codoninfo><B>     -codoninfo codoninfofile</b></a><dd>
             This (blastx version 1.3 only)  option  is  used  to
             specify  a file containing codon usage or codon bias
             information to be used in concert with a traditional
             scoring  matrix  to score alignments.  The file con-
             taining codon usage information  must  have  a  .cdi
             extension  on its name, but this extension should be
             omitted from the codoninfofile argument specified on
             the command line.  Codon usage information should be
             expressed in units that coincide with the  scale  of
             the  scoring matrix employed, and the scoring matrix
             employed must also have  a  .cdi  extension  to  its
             name.   A few such pairs of scoring matrix and codon
             usage files are provided in the BLAST software  dis-
             tribution.   blastx  expects to find the codon usage
             files in the /usr/ncbi/blast/cdi directory,  or  the
             program can be directed to look in another directory
             by setting the BLASTCDI environment variable.  NOTE:
             this  option is presently supported only by the pre-
             vious version 1.3 of blastx.

<DT><A NAME=gapdecayrate><B>     -gapdecayrate rate</b></a><dd>
             This parameter defines the common ratio of the terms
             in  a geometric progression used in normalizing pro-
             babilities across  all  numbers  of  Poisson  events
             (typically  the  number  of  "consistent"  HSPs).  A
             Poisson probability for N segments  is  weighted  by
             the  reciprocal  of the Nth term in the progression,
             where the first term has a value  of  (1-rate),  the
             second  term is (1-rate)*rate, the third term is (1-
             rate)*rate*rate, and so on.   The  default  rate  is
             0.5,  such that the probability assigned to a single
             HSP is discounted by a factor of 2, the Poisson pro-
             bability  of  2 HSPs is discounted by a factor of 4,
             for 3 HSPs the discount factor is 8, and so on.  The
             rate  essentially  defines  a penalty imposed on the
             gap between each HSP, where the default  penalty  is
             equivalent  to 1 bit of information.  The suggestion
             to normalize Poisson probabilities was made by  Phil
             Green (University of Washington, Seattle, WA).

<DT><A NAME=top><B>     -top     </b></a><dd>
             Whenever  a  nucleotide  query  sequence  is  used
             (blastn,  blastx and tblastx), both strands or all 6
             reading frames are searched by default.  The   - top
             and -bottom options may be used to restrict a search
             to the specified strand or set of 3 reading  frames.
             If both -top and -bottom are specified, both strands
             will be searched.  In the case of the  tblastx  pro-
             gram,  which translates both the query and the data-
             base, the -top and -bottom options refer to  strands
             in  the query sequence only.  See -dbtop and -dbbot-
             tom.

<DT><A NAME=bottom><B>     -bottom  </b></a><dd>
             See the -top option.

<DT><A NAME=dbtop><B>     -dbtop   </b></a><dd>
       For those  programs  that  translate  a  nucleotide
             sequence  database (tblastn and tblastx), the -dbtop
             and -dbbottom options can be specified  to  restrict
             the  search  to a particular strand of each database
             sequence.  The top strand consists of  the  database
             sequence  as  stored  in  the  database;  the bottom
             strand refers to the reverse complement of the data-
             base sequence.

<DT><A NAME=dbbottom><B>     -dbbottom</b></a><dd>
             See -dbtop.

<DT><A NAME=gcode><B>     -gcode genetic_code_ID</b></a><dd>
             This parameter permits  the  genetic  code  used  in
             translating nucleotide query sequences to be changed
             from its default value of the Standard genetic  code
             (sometimes   erroneously   called   the  "Universal"
             genetic code).  See the available  list  of  genetic
             code identifiers below.  Note:  the C parameter is a
             synonym for the -gcode parameter.

<DT><A NAME=dbgcode><B>     -dbgcode genetic_code_ID</b></a><dd>
             For the tblastx program, which translates  both  the
             query sequence and the database, this option permits
             the particular genetic code used  to  translate  the
             database  to be set separately from the genetic code
             used to translate the query sequence.   This  option
             may  also  be  used  to set the genetic code used by
             tblastn to translate the database.  See  the  avail-
             able list of genetic code identifiers below.

<DT><A NAME=olfraction><B>     -olfraction overlap_fraction</b></a><dd>
             This parameter (with default value of 0.125)  allows
             the  user to define the maximum fractional length of
             an HSP that can overlap another HSP and  still  have
             the two HSPs be considered to be consistent with one
             another.

<DT><A NAME=sump><B>     -sump </b></a><dd>
      This option (the  default)  causes  Karlin-Altschul
             (1993)  "Sum" statistics to be used in assessing the
             statistical significance of multiple HSPs.

<DT><A NAME=poisson><B>      -poissonp</b></a><dd>
             This option causes Poisson  statistics,  instead  of
             the  default Sum statistics, to be used in assessing
             the statistical significance of multiple HSPs.

<DT><A NAME=prune><B>     -prune</b></a><dd>
             This option causes HSPs that are  not  involved  in
             achieving  statistical significance to be eliminated
             from the program output.  When  Sum  statistics  are
             used, the pruning is robust; when Poisson statistics
             are used, some HSPs may be reported  that  were  not
             involved in achieving statistical significance.
<DT><A NAME=hspmax><B>    -hspmax max_hsps_per_dbseq </b></a><dd>
             This option can be used to limit the number of  HSPs
             reported  per  database sequence.  The default limit
             is 100, which is ample  leeway  for  most  searches.
             Notable  exceptions  are  when numerous, significant
             repetitive regions exist in the  query  or  database
             sequences,  such  as the hundreds of copies of human
             Alu repeats  that  exist  in  some  longer  database
             sequences.

<DT><A NAME=nwstart><B>     -nwstart start_coord</b></a><dd>
             blastp and blastx support this option and the -nwlen
             option, for restricting BLAST neighborhood word gen-
             eration to a specific segment of the query  sequence
             that  begins at start_coord and continues for length
             residues or until the end of the query  sequence  is
             reached.   HSP  alignments  may  extend  outside the
             region  of  neighborhood  word  generation  but  the
             alignments can only be seeded by word hits occurring
             within  the  region.   Through  the  use  of   these
             options,  a very long query sequence can be searched
             piecemeal, using short,  overlapping  segments  each
             time.   The  amount of overlap from one neighborhood
             region to the next need only be the BLAST wordlength
             W  minus  1, in order to be assured of detecting all
             HSPs; however, in  order  to  interpret  adjacent  -
             s1HSPs in a single database match using Sum or Pois-
             son statistics, more overlapping of the  regions  is
             recommended.

<DT><A NAME=nwlen><B>     -nwlen length</b></a><dd>
             See -nwstart.

<DT><A NAME=asn1><B>     -asn1    </b></a><dd>
             This option causes the programs to  produce  print-
             able,  structured output (not for human consumption,
             but for accurate automated parsing)  in  conformance
             with specifications written in the ISO 8824 standard
             ASN.1 language.

<DT><A NAME=asn1bin><B>     -asn1bin</b></a><dd>
             This option causes the programs to  produce  binary-
             encoded,  structured  output (not for human consump-
             tion, but for accurate automated parsing) in confor-
             mance  with  specifications  written in the ISO 8824
             standard ASN.1 language and encoded according to the
             rules established by ISO 8825.

<DT><A NAME=outblk><B>     -outblk  </b></a><dd>
             This option causes ASN.1 output to be  encapsulated
             in  a BLAST0-Outblk structure.  For a description of
             this structure, see the ASN.1 message specifications
             accompanying the BLAST program source code.

<DT><A NAME=warnings><B>     -warnings</b></a><dd>
             This option turns off the reporting of  all  WARNING
             messages.

<DT><A NAME=compat><B>     -compat1.3</b></a><dd>
             This option is used  to  invoke  behavior  from  the
             BLAST  version  1.4 programs that is very similar to
             that of the previous  version  1.3  programs.   This
             option  affects  the  -poissonp, -span1, -olfraction
             0.5, -ctxfactor, E and E2 options.

</dl>
<H3><a name=sorting>SORT OPTIONS</A></H3>
     The default sort order for reporting database  sequences  is
     by  increasing  probability  (P-value).   The following sort
     options are available and may be combined  together  in  the
     same search:
<DL>
<DT><A NAME=sortByPvalue><b>  -sort_by_pvalue</B></a><dd>
                         Sort from most  statistically  signifi-
                         cant (lowest P-value) to least statisti-
                         cally significant (highest P-value), the
                         default sort order.

<DT><A NAME=sortByCount><B>     -sort_by_count</B></a><dd>
                         Sort from  highest  to  lowest  by  the
                         number  of  HSPs found for each database
                         sequence.

<DT><A NAME=sortByHighScore><B>     -sort_by_highscore</B></a><dd>
                         Sort from  highest  to  lowest  by  the
                         score  of  the  highest  scoring HSP for
                         each database sequence.

<DT><A NAME=sortByTotalScore><B>     -sort_by_totalscore</B></a><dd>
                         Sort from the highest to the lowest  by
                         the sum total score of all HSPs for each
                         database sequence.
</dl>
<H2>SCORING SCHEMES</h2>
     The default scoring matrix used by blastp, blastx,  tblastn,
     and  tblastx  is the BLOSUM62 matrix (Henikoff and Henikoff,
     1992).  The -matrix option can be used to select  an  alter-
     nate  scoring  matrix  file  (e.g.,  one of the PAM matrices
     described below).  In version 1.4, the - matrix  option  can
     also  be  used  with  blastn  to define a scoring matrix, in
     addition to supporting the traditional M and N parameters of
     this program.
<p>
     Several PAM (point  accepted  mutations  per  100  residues)
     amino  acid  scoring  matrices  are  provided  in  the BLAST
     software distribution,  including  the  PAM40,  PAM120,  and
     PAM250.  While the BLOSUM62 matrix is a good general purpose
     scoring matrix and is the default matrix used by  the  BLAST
     programs,  if  one  is  restricted to using only PAM scoring
     matrices, then the PAM120 is recommended for general protein
     similarity  searches  (Altschul,  1991).  The pam(1) program
     can be used to produce PAM matrices of any desired iteration
     from  2  to  511.   Each matrix is most sensitive at finding
     similarities at  its  particular  PAM  distance.   For  more
     thorough searches, particularly when the mutational distance
     between potential homologs is unknown and  the  significance
     of  their  similarity  may be only marginal, Altschul (1991,
     1992) recommends performing at  least  three  searches,  one
     each with the PAM40, PAM120 and PAM250 matrices.
<p>
     When multiple scoring matrices are used in searches with the
     same  query  sequence,  additional  degrees  of  freedom for
     optimizing alignment scores  are  available,  which  reduces
     each score's statistical significance.  The reduction may be
     by a factor that is as  large  as  the  number  of  matrices
     employed;  however,  the  potential loss of sensitivity from
     using a suboptimal matrix is typically  much  greater,  sug-
     gesting  that  the use of multiple matrices remains advanta-
     geous (Altschul, 1992).  Altschul  (1992)  has  shown  that,
     because  PAM  matrices  are related to one another through a
     common mutational  model  and  set  of  initial  conditions,
     statistical  significance  is reduced by a factor of no more
     than 4.6 (just over 2 bits of information) regardless of how
     many PAM matrices are employed.
<p>
     In blastn, the M parameter sets the reward score for a  pair
     of matching residues; the N parameter sets the penalty score
     for mismatching residues.  M and  N  must  be  positive  and
     negative integers, respectively.  The relative magnitudes of
     M and N determines the number of nucleic  acid  PAMs  (point
     accepted mutations per 100 residues) for which they are most
     sensitive  at  finding  homologs.   Higher  ratios  of   M:N
     correspond to increasing nucleic acid PAMs (increased diver-
     gence).  The default values for M and N, respectively 5  and
     -4,  having  a ratio of 1.25, correspond to about 47 nucleic
     acid PAMs, or about 58 amino acid PAMs; an M:N  ratio  of  1
     corresponds  to  30 nucleic acid PAMs or 38 amino acid PAMs.
     At higher than about 40 nucleic acid PAMs, or 50 amino  acid
     PAMs,  better  sensitivity at detecting similarities between
     coding regions is expected by performing comparisons at  the
     amino  acid  level (States et al., 1991), using conceptually
     translated nucleotide sequences (re:  blastx,  tblastn,  and
     tblastx).
<p>
     Independent of the values chosen for M and  N,  the  default
     wordlength  W=11  used  by  blastn  restricts the program to
     finding sequences that share at least an 11-mer  stretch  of
     100%  identity  with  the  query.  Under the random sequence
     model, stretches of 11  consecutive  matching  residues  are
     unlikely  to  occur  merely  by  chance  even  between  only
     moderately diverged homologs.  Thus, blastn with its default
     parameter  settings is poorly suited to finding anything but
     very similar sequences.  If better  sensitivity  is  needed,
     one should use a smaller value for W.
<p>
     For the blastn program, it may be easy to see how  multiply-
     ing both M and N by some large number will yield proportion-
     ally larger alignment scores with their statistical signifi-
     cance  remaining  unchanged.  This scale-independence of the
     statistical significance estimates from blastn has its  ana-
     log  in  the  scoring  matrices used by the other BLAST pro-
     grams:  multiplying all elements in a scoring matrix  by  an
     arbitrary  factor  will  proportionally  alter the alignment
     scores but will not  alter  their  statistical  significance
     (assuming  numerical precision is maintained).  From this it
     should be clear that raw alignment  scores  are  meaningless
     without  specific  knowledge  of the scoring matrix that was
     used.

<H2>SCORING REQUIREMENTS</h2>
     Regardless of the scoring  scheme  employed,  two  stringent
     criteria  must  be  met in order to be able to calculate the
     Karlin-Altschul parameters Lambda and K.  First,  given  the
     residue  composition  for the query sequence and the residue
     composition assumed for the database,  the  alignment  score
     expected  for  any  randomly  selected pair of residues (one
     from the query sequence and one from the database)  must  be
     negative.   Second,  given the sequence residue compositions
     and the scoring scheme, a positive score must be possible to
     achieve.   For  instance,  the  match reward score of blastn
     must have a positive value; and given the assumption made by
     blastn  that the 4 nucleotides A, C, G and T are represented
     at equal 25% frequencies in the database, a  wide  range  of
     value  combinations  for  M  and N are precluded from use --
     namely those combinations where the magnitude of  the  ratio
     M:N is greater than or equal to 3.

<h2>SEQUENCE LENGTH AND STATISTICAL SIGNIFICANCE</h2>
     For the purpose of calculating significance levels, Y is the
     effective  length  of the query sequence and Z is the effec-
     tive length of the database, both measured in residues.  The
     default  values  for these parameters are the actual lengths
     of the query sequence and  database,  respectively.   Larger
     values  signify  more  degrees  of  freedom for aligning the
     sequences and reduced statistical significance for an align-
     ment  of  any  given  score.   To  normalize  the statistics
     reported when databases of different lengths  are  searched,
     the parameter Z may be set to a constant value for all data-
     base searches.  Similarly, when querying with  sequences  of
     different  lengths, the parameter Y can be used to normalize
     over all searches.

<h2>GENETIC CODES</h2>
     The parameter C can be set to a positive integer  to  select
     the  genetic code that will be used by blastx and tblastx to
     translate the query sequence.  The -dbgcode parameter can be
     used  to select an alternate genetic code for translation of
     the database by the programs tblastn and tblastx.   In  each
     case,  the  default genetic code is the so-called "Standard"
     or "Universal" genetic code.  To obtain  a  listing  of  the
     genetic codes available and their associated numerical iden-
     tifiers, invoke blastx or  tblastx  with  the  command  line
     parameter C=list. Note:  the numerical identifiers used here
     for  genetic  codes  parallel  those  defined  in  the  NCBI
     software  Toolbox;  hence  some  numerical  values  will  be
     skipped as genetic codes are updated.
<p>
     The list of genetic codes  available  and  their  associated
     values for the parameters C and -dbgcode are:
<ol>
     <li> Standard or Universal

     <li> Vertebrate Mitochondrial

     <li> Yeast Mitochondrial

     <li>   Mold,   Protozoan,   Coelenterate   Mitochondrial    and
     Mycoplasma/Spiroplasma

     <li> Invertebrate Mitochondrial

     <li> Ciliate Macronuclear

     <li> Echinodermate Mitochondrial

     <li> Alternative Ciliate Macronuclear

     <li> Eubacterial

     <li> Alternative Yeast

     <li> Ascidian Mitochondrial

     <li> Flatworm Mitochondrial
</ol>
<H2>SUM STATISTICS</h2>
     Whereas the version 1.3 BLAST programs use  Poisson  statis-
     tics  to  ascribe significance to multiple HSPs, the version
     1.4 programs retain Poisson statistics as an option, but use
     Karlin  and  Altschul  (1993)  "Sum"  statistics  by default
     instead.  Sum statistics tends to rank database matches in a
     more  intuitive  order  than Poisson statistics and, in many
     cases, yields markedly increased sensitivity.   The  Sum  P-
     value  for  a  set  of  HSPs is a function of the sum of the
     information scores of the HSPs (expressed in bits)  and  the
     number of HSPs in the set.
<H3>POISSON STATISTICS</H3>
     The occurrence of two  or  more  HSPs  involving  the  query
     sequence  and the same database sequence can be modeled as a
     Poisson process by specifying the   - poissonp  option.   An
     important  result  of applying Poisson statistics is that an
     HSP having a low score and high Expect value (low  statisti-
     cal  significance)  may be ascribed a statistically signifi-
     cant Poisson P-value when the HSP appears in the context  of
     additional match(es) of equal or greater score with the same
     database sequence.

     The Poisson P-value for any given HSP is a function  of  its
     expected  frequency  of  occurrence  and  the number of HSPs
     observed against the same database sequence with  scores  at
     least  as  high.   The  Poisson  P-value  for a group of HSP
     events is the probability that at least as many  HSPs  would
     occur by chance alone, each with a score at least as high as
     the lowest-scoring member of the group.  HSPs  which  appear
     on  opposite  strands  of  a  nucleotide  query  or database
     sequence are considered to be  independent,  distinguishable
     events, and are counted separately.
<h2>P-VALUES, ALIGNMENT SCORES, AND INFORMATION</h2>
     The Expect and P-values reported for HSPs are  dependent  on
     several factors including:  the scoring system employed, the
     residue composition of the query sequence, an assumed  resi-
     due  composition for a typical database sequence, the length
     of the query sequence, and the total length of the database.
     HSP  scores from different program invocations are appropri-
     ate for comparison even if the  databases  searched  are  of
     different  lengths,  as  long as the other factors mentioned
     here do  not  vary.   For  example,  alignment  scores  from
     searches  with  the  default  BLOSUM62  matrix should not be
     directly compared  with  scores  obtained  with  the  PAM120
     matrix;  and  scores produced using two versions of the same
     PAM matrix, each created to different  scales  (see  above),
     can  not  be meaningfully compared without conversion to the
     same scale.
<p>
     Some isolation from the many factors involved  in  assessing
     the  statistical  significance  of  HSPs  can be attained by
     observing the information content reported (in bits) for the
     alignments.   While  the  information  content of an HSP may
     change when different scoring systems are used  (e.g.,  with
     different  PAM matrices), the number of bits reported for an
     HSP will at least be independent of the scale to  which  the
     scoring  matrix was generated.  (In practice, this statement
     is not quite true, because the alignment scores used by  the
     BLAST  programs  are integers that lack much precision).  In
     other words, when conveying the statistical significance  of
     an  alignment,  the  alignment  score  itself  is not useful
     unless the specific scoring matrix that was employed is also
     provided, but the informativeness of an alignment is a mean-
     ingful statistic that can be  used  to  ascribe  statistical
     significance  (a  P-value)  to  the  match  independently of
     specific knowledge about the scoring matrix.

<h2>GOVERNING OUTPUT</h2>
     BLAST program output is organized into  three  independently
     governed  sections:  a histogram of the statistical signifi-
     cance of the matches found;  one-line  descriptions  of  the
     database  sequences  that satisfied the statistical signifi-
     cance threshold (E parameter); and the high-scoring  segment
     pairs  themselves.  Each section of the output can be selec-
     tively suppressed by setting the parameters H, V, and B to 0
     (zero).

<p>
<a name=h></a>
     The H parameter regulates the display of a histogram of  the
     expected  frequency  of  chance  occurrence  of the database
     matches found.  If H is assigned a non-zero value, a  histo-
     gram  will  be  displayed.  The default value for H is 0 (no
     histogram displayed).

<p>
<a name=v></a>
     Parameter V is the maximum number of database sequences  for
     which  one-line  descriptions will be reported.  The default
     value for V is 500.  A bold warning message is displayed  at
     the  end of the one-line descriptions section when more than
     V sequences yield HSPs satisfying  the  significance  thres-
     hold.  When V is zero, no one-line descriptions are reported
     and no warning is given.  Negative values for  V  are  unde-
     fined and disallowed.
<p>

     As an example of how V can be used advantageously, if a high
     value for E is desired to virtually assure in all cases that
     at least one HSP will be found, selecting a small value  for
     V will ensure that the output will not be overly voluminous;
     only the most  statistically  significant  matches  will  be
     reported.
<p>
<a name=b></a>
     Parameter B regulates the display of the  high-scoring  seg-
     ment pairs (alignments).  For positive values, B is the max-
     imum number of database  sequences  for  which  high-scoring
     segment  pairs  will  be reported.  This may be much smaller
     than  the  actual  number  of  high-scoring  segment   pairs
     reported,  since  any  given  database  sequence  may  yield
     several HSPs.  The default value for  B  is  250.   Negative
     values for B are undefined and disallowed.

<h2>ENVIRONMENT VARIABLES</h2>
     The environment variables  BLASTDB,  BLASTMAT,  BLASTFILTER,
     and  BLASTCDI may be set by the user to override the default
     directories in which the  programs  look  to  find  database
     files,  scoring  matrix files, filtering programs, and codon
     usage information files, respectively.  The  default  direc-
     tories   are   /usr/ncbi/blast/db,   /usr/ncbi/blast/matrix,
     /usr/ncbi/blast/filter, and /usr/ncbi/blast/cdi.

<h2>SUPPORT UTILITIES</h2>
     Databases to be searched by the BLAST programs must first be
     formatted  by  the  setdb program for protein sequence data-
     bases (re: blastp and blastx) or  the  pressdb  program  for
     nucleotide sequence databases (re: blastn and tblastn).  The
     input database files read by setdb and pressdb  must  be  in
     FASTA/Pearson  format.   For  each  input file, three output
     files are created for searching by the BLAST programs.
<p>

     Point accepted mutation (PAM) matrices  of  various  generations
      can  be  produced automatically with the pam program.
     The output can be saved in a file whose  name  can  then  be
     specified  in  the M=filename option of a blastp, blastx, or
     tblastn query.

<h2>SAMPLE OUTPUT</h2>
     The BLAST programs all provide information  in  roughly  the
     same  format.   First  comes (A) an introduction to the pro-
     gram; (B) a histogram of expectations (see above) if one was
     requested; (C) a series of one-line descriptions of matching
     database sequences; (D) the actual sequence alignments;  and
     finally  the parameters and other statistics gathered during
     the search.
<p>
     Sample blastp output from comparing pir|A01243|DXCH  against
     the SWISS-PROT database is presented below.

<h3>  A. Program Introduction</h3>
     The introductory output provides the program name (BLASTP in
     this  case),  the version number (1.4.6MP in this case), the
     date the program  source  code  last  changed  substantially
     (June  13,  1994), the date the program was built (Sept. 22,
     1994), and a description of the query sequence and  database
     to be searched.  These may all be important pieces of infor-
     mation if a  bug  is  suspected  or  if  reproducibility  of
     results is important.
<p>

     The "Searching..." indicator  indicates  progress  that  the
     program made in searching the database.  A complete database
     search will yield 50 periods (.), or one period per database
     sequence,  whichever  number  is  smaller.  When searching a
     database consisting of 50 sequences or more, if  fewer  than
     50  periods  are  displayed and the program aborted for some
     reason, dividing the number of periods by 0.5 will yield the
     approximate  percentage  (0-100%)  of  the database that was
     searched before the program died.  If the program had diffi-
     culty  making  progress  through  the  database, one or more
     asterisks (*) may be interspersed  between  the  periods  at
     one-minute intervals.

<h3>  B. Histogram of Expectations</h3>
     Shown in the output below is a histogram of the lowest (most
     significant)  Expect  values  obtained  with  each  database
     sequence.  This information is  useful  in  determining  the
     numbers  of  database  sequences  that achieved a particular
     level of statistical significance.  It indicates the  number
     of database matches that would be reportable at various set-
     tings for the expectation threshold (E parameter).

<h3>  C. One-line Summaries</h3>
     The one-line sequence descriptions and summaries of  results
     are useful for identifying biologically interesting database
     matches and correlating this interest with  the  statistical
     significance  estimates.   Unless  otherwise  requested, the
     database sequences are sorted by increasing P-value  (proba-
     bility).   Identifiers  for the database sequences appear in
     the first column;  then  come  brief  descriptions  of  each
     sequence,  which may need to be truncated in order to fit in
     the available space.  The "High Score" column  contains  the
     score  of  the  highest-scoring HSP found with each database
     sequence.  The "P(N)" column  contains  the  lowest  P-value
     ascribed  to any set of HSPs for each database sequence; and
     the "N" column displays the number of HSPs in the set  which
     was  ascribed  the lowest P-value.  The P-values are a func-
     tion of N, as used in Karlin-Altschul  "Sum"  statistics  or
     Poisson  statistics, to treat situations where multiple HSPs
     are found.  It should be noted that the highest-scoring  HSP
     whose  score  is  reported in the "High Score" column is not
     necessarily a member of the set of  HSPs  which  yields  the
     lowest P-value; the highest-scoring HSP may be excluded from
     this set on the basis of  consistency  rules  governing  the
     grouping  of HSPs (see the -consistency option).  Numbers of
     the form "7.7e-160" are in  scientific  notation.   In  this
     particular  example,  the  number  being  represented is 7.7
     times 10 to the minus 160th power.  which is  astronomically
     close to zero.

<h3>  D. Alignments</h3>
     Alignments found with  the  BLAST  algorithm  are  ungapped.
     Several  statistics  are used to describe each HSP:  the raw
     alignment Score; the raw score converted to bits of information 
 by  multiplying by Lambda (see the Statistics output);
     the number of times one might Expect to see such a match (or
     a  better one) merely by chance; the P-value (probability in
     the range 0-1) of observing such a  match;  the  number  and
     fraction  of  total residues in the HSP which are identical;
     the number and fraction of residues for which the  alignment
     scores  have positive values.  When Sum statistics have been
     used to calculate the Expect and P-values,  the  P-value  is
     qualified  with  the  word "Sum" and the N parameter used in
     the Sum statistics is provided in  parentheses  to  indicate
     the  number of HSPs in the set; when Poisson statistics have
     been used to calculate the Expect and P-values, the  P-value
     is qualified with the word "Poisson".  Between the two lines
     of Query and Subject (database) sequence is a line  indicating
  the  specific  residues which are identical, as well as
     those which are non-identical but nevertheless have positive
     alignment scores defined in the scoring matrix that was used
     (the BLOSUM62 matrix in this case).   Identical  letters  or
     residues,  when  paired with each other, are not highlighted
     if their alignment score is negative or zero.   Examples  of
     this  would  be  an X juxtaposed with an X in two amino acid
     sequences, or an N juxtaposed with another N in two  nucleotide 
sequences.  Such ambiguous residue-residue pairings may
     be uninformative and thus lend no  support  to  the  overall
     alignment being either real or random; however, the informativeness
     of these pairings is left up to  the  user  of  the
     BLAST  programs to decide, because any values desired can be
     specified in a scoring matrix of the user's own making.
<PRE>
     BLASTP 1.4.6MP [13-Jun-94] [Build 13:58:36 Sep 22 1994]

     Reference:  Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers,
     and David J. Lipman (1990).  Basic local alignment search tool.  J. Mol. Biol.
     215:403-10.

     Query=  pir|A01243|DXCH  232 Gene X protein - Chicken (fragment)
             (232 letters)

     Database:  SWISS-PROT Release 29.0
                38,303 sequences; 13,464,008 total letters.
     Searching..................................................done

          Observed Numbers of Database Sequences Satisfying
         Various EXPECTation Thresholds (E parameter values)

             Histogram units:      = 31 Sequences     : less than 31 sequences

      EXPECTation Threshold
      (E parameter)
         |
         V   Observed Counts-->
       10000 4863 1861 |============================================================
        6310 3002  782 |=========================
        3980 2220  812 |==========================
        2510 1408  303 |=========
        1580 1105  393 |============
        1000  712  179 |=====
         631  533  161 |=====
         398  372   80 |==
         251  292   73 |==
         158  219   50 |=
         100  169   32 |=
        63.1  137   18 |:
        39.8  119    9 |:
        25.1  110    6 |:
        15.8  104    9 |:
      >>>>>>>>>>>>>>>>>>>>>  Expect = 10.0, Observed = 95<<<<<<<<<<<<<<<<<
        10.0   95    4 |:
        6.31   91    3 |:
        3.98   88    1 |:
        2.51   87    3 |:
        1.58   84    0 |
        1.00   84    2 |:

                                                                          Smallest
                                                                            Sum
                                                                   High  Probability
     Sequences producing High-scoring Segment Pairs:              Score  P(N)      N

     sp|P01013|OVAX_CHICK GENE X PROTEIN (OVALBUMIN-RELATED) (...  1191  7.7e-160  1
     sp|P01014|OVAY_CHICK GENE Y PROTEIN (OVALBUMIN-RELATED).       949  7.0e-127  1
     sp|P01012|OVAL_CHICK OVALBUMIN (PLAKALBUMIN).                  645  3.4e-100  2
     sp|P19104|OVAL_COTJA OVALBUMIN.                                626  1.2e-96   2
     sp|P05619|ILEU_HORSE LEUKOCYTE ELASTASE INHIBITOR (LEI).       216  3.7e-71   3
     sp|P80229|ILEU_PIG   LEUKOCYTE ELASTASE INHIBITOR (LEI) (...   325  4.0e-71   2
     sp|P29508|SCCA_HUMAN SQUAMOUS CELL CARCINOMA ANTIGEN (SCC...   439  3.5e-70   2
     sp|P30740|ILEU_HUMAN LEUKOCYTE ELASTASE INHIBITOR (LEI) (...   211  1.3e-66   3
     sp|P05120|PAI2_HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2, P...   176  1.8e-65   4
     sp|P35237|PTI_HUMAN  PLACENTAL THROMBIN INHIBITOR.             473  1.3e-61   1
     sp|P12388|PAI2_MOUSE PLASMINOGEN ACTIVATOR INHIBITOR-2, M...   179  1.8e-60   4
     sp|P36952|MASP_HUMAN MASPIN PRECURSOR.                         198  2.6e-58   4
     sp|P32261|ANT3_MOUSE ANTITHROMBIN-III PRECURSOR (ATIII).       142  4.0e-48   5
     sp|P01008|ANT3_HUMAN ANTITHROMBIN-III PRECURSOR (ATIII).       122  7.5e-48   5

     WARNING:  Descriptions of 80 database sequences were not reported due to the
               limiting value of parameter V = 15.

       ... alignments with the top 8 database sequences deleted ...

     >sp|P05120|PAI2_HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2, PLACENTAL (PAI-2)
                 (MONOCYTE ARG- SERPIN).
                 Length = 415

      Score = 176 (80.2 bits), Expect = 1.8e-65, Sum P(4) = 1.8e-65
      Identities = 38/89 (42%), Positives = 50/89 (56%)

     Query:     1 QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNN 60
                  +I +LL   S D DT +VLVNA+YFKG WKT F  +     PF V   +  PVQMM +
     Sbjct:   180 KIPNLLPEGSVDGDTRMVLVNAVYFKGKWKTPFEKKLNGLYPFRVNSAQRTPVQMMYLRE 239

     Query:    61 SFNVATLPAEKMKILELPFASGDLSMLVL 89
                    N+  +   K +ILELP+A      L+L
     Sbjct:   240 KLNIGYIEDLKAQILELPYAGDVSMFLLL 268

      Score = 165 (75.2 bits), Expect = 1.8e-65, Sum P(4) = 1.8e-65
      Identities = 33/78 (42%), Positives = 47/78 (60%)

     Query:   155 ANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHPFLFL 214
                  AN +G+S    L +S+  H A ++++E+G E A  TG +   +      QF ADHPFLFL
     Sbjct:   338 ANFSGMSERNDLFLSEVFHQAMVDVNEEGTEAAAGTGGVMTGRTGHGGPQFVADHPFLFL 397

     Query:   215 IKHNPTNTIVYFGRYWSP 232
                  I H  T  I++FGR+ SP
     Sbjct:   398 IMHKITKCILFFGRFCSP 415

      Score = 144 (65.6 bits), Expect = 1.8e-65, Sum P(4) = 1.8e-65
      Identities = 26/62 (41%), Positives = 41/62 (66%)

     Query:    90 LPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTSVLMALGMTD
                  + D  + LE +E  I ++KL +WT+ + M +  V+VY+PQ K+EE Y L S+L ++GM D
     Sbjct:   272 IADVSTGLELLESEITYDKLNKWTSKDKMAEDEVEVYIPQFKLEEHYELRSILRSMGMED 331

     Query:   150 LF 151
                   F
     Sbjct:   332 AF 333

      Score = 61 (27.8 bits), Expect = 1.8e-65, Sum P(4) = 1.8e-65
      Identities = 10/17 (58%), Positives = 16/17 (94%)

     Query:    81 SGDLSMLVLLPDEVSDL 97
                  +GD+SM +LLPDE++D+
     Sbjct:   259 AGDVSMFLLLPDEIADV 275

     WARNING:  HSPs involving 86 database sequences were not reported due to the               limiting value of parameter B = 9.

     Parameters:
       V=15
       B=9
       H=1

       -ctxfactor=1.00
       E=10

       Query                        -----  As Used  -----    -----  Computed  ----
       Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H

       Query
       Frame  MatID  Length  Eff.Length   E    S W   T  X     E2  S2
        +0      0      232       232      10. 57 3  11 22    0.22 33

     Statistics:
       Query          Expected         Observed           HSPs       HSPs
       Frame  MatID  High Score       High Score       Reportable  Reported
        +0      0    62 (28.2 bits)  1191 (542.5 bits)     330         24

       Query         Neighborhd  Word      Excluded    Failed   Successful  Overlaps
       Frame  MatID   Words      Hits        Hits    Extensions Extensions  Excluded
        +0      0      4988     5661199     1146395     4504598    10187        13

       Database:  SWISS-PROT Release 29.0
         Release date:  June 1994
         Posted date:  1:29 PM EDT Jul 28, 1994
       # of letters in database:  13,464,008
       # of sequences in database:  38,303
       # of database sequences satisfying E:  95
       No. of states in DFA:  561 (55 KB)
       Total size of DFA:  110 KB (128 KB)
       Time to generate neighborhood:  0.03u 0.01s 0.04t  Real: 00:00:00
       No. of processors used:  8
       Time to search database:  32.27u 0.78s 33.05t  Real: 00:00:04
       Total cpu time:  32.33u 0.91s 33.24t  Real: 00:00:05

     WARNINGS ISSUED:  2
</pre>
<h2>BUGS</h2>
     The statistics are not fully worked out yet for blastp  when
     multiple -matrix options are specified in a single command.
<p>

     blastn  by  default  uses  a  large  value  of  11  for  the
     wordlength,  W,  which severely reduces the program's sensi-
     tivity but provides for high speed searches.   Consequently,
     the program with its default parameter values is well suited
     to finding nearly identical sequences  rapidly,  but  poorly
     suited   to   finding   moderately-   or   distantly-related
     sequences.  The value for W may be reduced to  increase  the
     sensitivity  (at the expense of speed), but to identify weak
     similarity between coding regions,  greater  sensitivity  is
     obtained  by  comparing translation products (States et al.,
     1991); one should use blastx, tblastn, or  tblastx.   blastn
     is poorly suited to characterizing PCR primers.
<p>
<a name=w></a>
     In the protein-comparing programs blastp,  blastx,  tblastn,
     and  tblastx,  ad  hoc  equations  are  used  to calculate a
     default value for the neighborhood word  score  threshold  T
     when  the word length W has a value of 3 (the default) or 4.
     Equations  have  not  been  implemented  for  calculating  a
     default value of T when W has any value other than 3 or 4.
<p>

     When  nucleotide  sequence  databases  are  compressed  into
     searchable  form  by  the  pressdb  program, IUPAC ambiguity
     letters are replaced by an appropriate random selection from
     the  list A, C, G and T. For example, an R (purine) would be
     replaced on the average half of the time by an A (adenosine)
     and  the  remainder  of the time by a G (guanosine).  If the
     original database in FASTA format is not available to blastn
     and  tblastn  at  the  time of the search, then the original
     locations and identities of the ambiguity codes can  not  be
     determined  by  these programs and the alignments and align-
     ment scores may be in error with  respect  to  the  original
     sequences.
<p>

     tblastn and tblastx use only one genetic code  to  translate
     the  entire  nucleotide sequence database, although the code
     that is used is selectable via the -dbgcode option.
<p>

     blastn, blastx, tblastn, and tblastx treat U and T  residues
     in  nucleotide  sequences  as  being the same residue (i.e.,
     they match  perfectly  or  translate  in  exactly  the  same
     manner).
<p>

     The amino acid alphabet used by the BLAST programs  consists
     of   the   IUB   and   IUPAC   amino   acid  codes  (ABCDEF-
     GHIKLMNPQRSTVWXYZ), plus asterisk (*) and  hyphen  (-).   An
     asterisk  signifies  a  stop codon; and a hyphen signifies a
     gap of indeterminate length through which  BLAST  alignments
     are  never  permitted  to extend.  Any letter which is not a
     member of this alphabet will be stripped from an amino  acid
     query sequence on input and will not contribute to the query
     sequence coordinate numbers displayed in program output.  In
     protein  sequence  databases that are processed into search-
     able form by the setdb program, any  non-alphabetic  letters
     are also stripped.
<p>

     The nucleotide alphabet used by the BLAST programs  consists
     of  the  IUB  and IUPAC nucleotide codes (ACGTRYMKWSBDHVNU),
     plus hyphen (-) to signify a gap of indeterminate length.  U
     (uracil)  is  treated  like  a  T  (thymidine).   When  non-
     alphabetical codes appear in the FASTA-format input database
     to  the  pressdb  program, the program complains about their
     appearance and then halts with a non-zero exit status.
<p>

     Unlike its version 1.3 predecessor, blastn version  1.4  can
     employ  a concept of partial matching, such as might be used
     when two Rs (purines) are aligned with each other.  When the
     blastn  scoring  system is defined using the M and N parame-
     ters, the scoring matrix constructed by the program accounts
     for partial matching of nucleotide ambiguity codes.  If the
     -matrix option is used instead, the user has complete  free-
     dom  to  decide  how to score alignments involving ambiguity
     codes.
<p>

     When calculating the Sum and Poisson statistics,  some  HSPs
     may  be inconsistent or incompatible with one another in the
     same gapped alignment, and yet the programs will count  them
     as  independent,  consistent  events, leading to false posi-
     tives being reported in the output.  See  the   - olfraction
     option.  (However, HSPs appearing on opposite strands of the
     query or database sequence, or in reading frames on opposite
     strands, are considered separately in all cases).
<p>

     The nucleotide composition of a  blastn  query  sequence  is
     irrelevant  to  the  values reported for the Karlin-Altschul
     Lambda and K parameters.  This is due to  the  equi-probable
     0.25/0.25/0.25/0.25  A/C/G/T residue distribution assumed by
     blastn for  the  database  sequences.   The  values  of  the
     Karlin-Altschul parameters are still affected by the scoring
     system employed (defined by the parameters M and N, or the -
     matrix option).
<p>
     On multiprocessor  platforms,  blastn  restricts  itself  by
     default to using 3 processors maximum, due to the relatively
     high initialization cost per  processor  when  the  database
     contains  long  sequences, as compared to the brief cpu time
     required for searches that use the default wordlength of 11.
     More  than 3 processors can be recruited using the P command
     line option.

<h2>SEE ALSO</h2>
     blast3(1).

<H2>COPYRIGHT</h2>
     This work is in the public domain.

<H2>REFERENCES</H2>
     Altschul,  Stephen  F.  (1991).   Amino  acid   substitution
     matrices  from an information theoretic perspective. J. Mol.
     Biol.  219:555-65.
<p>

     Altschul, S. F. (1993).  A protein alignment scoring  system
     sensitive  at  all  evolutionary  distances.  J.  Mol. Evol.
     36:290-300.
<p>

     Altschul, S. F., M. S. Boguski, W. Gish and  J.  C.  Wootton
     (1994).   Issues  in searching molecular sequence databases.
     Nature Genetics 6:119-129.
<p>

     Altschul, Stephen F., Warren Gish, Webb  Miller,  Eugene  W.
     Myers,  and  David  J. Lipman (1990).  Basic local alignment
     search tool. J. Mol. Biol.  215:403-10.
<p>

     Claverie,  J.-M.  and  D.  J.  States  (1993).   Information
     enhancement  methods for large scale sequence analysis. Computers 
     in Chemistry 17:191-201.
<p>

     Gish, W. and D. J. States (1993).  Identification of protein
     coding  regions by database similarity search. Nature Genetics
     3:266-72.
<p>

     Henikoff, Steven and Jorga G. Henikoff (1992).   Amino  acid
     substitution matrices from protein blocks. Proc. Natl. Acad.
     Sci. USA 89:10915-19.
<p>

     Karlin, Samuel and Stephen F. Altschul (1990).  Methods  for
     assessing the statistical significance of molecular sequence
     features by using general scoring schemes. Proc. Natl. Acad.
     Sci. USA 87:2264-68.
<p>

     Karlin, Samuel and Stephen F. Altschul (1993).  Applications
     and statistics for multiple high-scoring segments in molecular
       sequences. Proc. Natl. Acad. Sci. USA 90:5873-7.
<p>

     States, D. J. and W. Gish (1994).  Combined use of  sequence
     similarity  and codon bias for coding region identification.
     J. Comput. Biol.  1:39-50.
<p>

     States, D. J., W. Gish and S. F. Altschul (1991).   Improved
     sensitivity  of  nucleic  acid  database similarity searches
     using application specific scoring matrices. Methods: A companion
       to Methods in Enzymology 3:66-70.
<p>
     Wootton, J. C. and S. Federhen (1993).  Statistics of  local
     complexity  in  amino acid sequences and sequence databases.
     Computers in Chemistry 17:149-163.
<hr>


</body>
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r coding region identification.
     J. Comput. Biol.  1:39-50.
<p>

     States, D. J., W. Gish and S. F. Altschul (1991).   Improved
     sensitivity  of  nucleic  acid  database similarity searches
     using application specific scoring matrices. Methods: A companion
       to Methods isrs/www/doc/contents.html
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<H1><A NAME="intro">The Icarus Debugger</H1>
<P>
The Icarus debugger supports unconditional and conditional breakpoints. For
example, by setting one or more breakpoints in the syntax file, one
can start the debugger and jump through the parsing procedure from one
breakpoint to the next. One can step through every step of the parsing
procedure, or a mixture of both of these. At the debugger prompt, the current
values of variables can be printing and altered, and even new variables
initialized.
<P>
The debugger uses the Icarus interpreter, and so the debugging environment is
and extension of the Icarus code being debugged. Multiple Icarus commands can
be given on the debugger command line, and command line editing is supported.
<P>
It is important to remember that because Icarus implements lazy parsing,
breakpoints must be placed in parts of the code that are used to produce the
requested output.

<H2><A NAME="starting">Starting Debugger Mode</A></H2>
<P>
There are three ways to invoke the Icarus debugger. To take the example from
the Guided Tour:
<PRE>
% genes.is -debug
% getz '[genes-id:HSU07616]' -e -debug
% srsbuild genes -d -debug
</PRE>
<P>
and here's another example
<PRE>
% tfsite.is -debug
% getz '[tfsite-id:hbv$hbve_03]' -e -debug
% srsbuild tfsite -d -debug
</PRE>

<H2><A NAME="breaks">Setting Debugger Breaks</A></H2>
<P>
The command $Break (or $break) sets a breakpoint at the current position in
the syntax definition and is evaluated at &quot;pre&quot; execution time.
<P>
Taking the example from the Guided Tour, a break point can be added
to the file &quot;SRSDEMO:genes.is&quot; using $Break at, say, this point
<PRE>
  # the data-fields
  fields:    ~ {$In:entry $Out $Skip:1 $Break} id date def cit seq ~
</PRE>
<P>
Or a conditional breakpoint can be set like this
<PRE>
  # the data-fields
  fields:    ~ {$In:entry $Out $Skip:1 $Break:[cond:$entry='HSU07616']} id date def cit seq ~
</PRE>

<H2><A NAME="commands">Debugger Commands</A></H2>
<P>
For convenience when debugging, all debugger commands are in lowercase, and are
therefore exceptions to the convention that Icarus functions start with an
uppercase character.

The following commands can be used at the debugger prompt &quot;>&quot;
<P>
Although the Icarus function $Print can be used for printing values of
variables, there is also a debugger print function which does the same but
formats the output for the debugging environment, and in keeping with the other
debugger commands, is lowercase:
<PRE>
> $dp
</PRE>
<P>
Inside the debugger, printing the values of the special scalar variables
$Ct, $It, $Fip, $1,$2...$9, $0, where $1 $2 etc are from the last regular
expression matches is simple.
<PRE>
> $dp:$Ct
> $dp:$It
> $dp:$1
> $dp:$Fip
</PRE>
To continue execution of the code until the next node:
<PRE>
> $next
</PRE>
To continue execution of the code until the next break point:
<PRE>
> $cont
</PRE>
To print a hierarchical view of the syntax tree. This can be used when
&quot;Prod&quot; is displayed.
<PRE>
> $tree
</PRE>
<P>
By typing the return key instead of giving a debugger command, the debugger
repeats the last command line given (which could be several commands).
<P>
<P>
When you are finished with the debugging session, you can exit the debugger by
typing
<PRE>
> $exit
</PRE>
<H2><A NAME="example">Debugger Example</A></H2>
Using the example above in "SRSDEMO:genes.is"
<PRE>
% genes.is -debug
[- Prod       fields]> $tree
====================================
    Production: fields  { *3 -2 +1 }
        Term 
            ProdName: id 
            ProdName: date 
            ProdName: def 
            ProdName: cit 
            ProdName: seq 
====================================
[- Prod       fields]> $next
[- ProdName   id]> $dp:$Ct
[- ProdName   id]> $dp:$It
LOCUS       HSU07616
DATE        02-FEB-1995
DEFINITION  Human amphiphysin mRNA, complete cds.
CITATION    YAMAR95
SEQUENCE  
        1 ccaggtgcct actgactcct tcagaaatgt cagttcctgt cccatgccct taatatttcc
       61 cacatgcagg gctctgtgca caatgcgtga caatggcttt tagat

//
[- ProdName   id]> $exit
% 
</PRE>
At this moment, one must be careful about entering debugging commands because
Icarus will terminate if there is a problem:
<PRE>
% genes.is -debug
<...>
[- Lit        'LOCUS']> $dp $Ct
Segmentation fault
%
</PRE>
<H2><A NAME="output">Debugger Output</A></H2>
<P>
The node of the syntax tree that has just been parsed is shown inside the
brackets &quot;[&quot; and &quot;]&quot; (as in the example shown above).
<P>
Shown inside these brackets from left to right are the execution time with
respect to the symbol comparison:
<P>
&quot;*&quot; refers to the execution time of init<P>
&quot;-&quot; refers to the execution time of pre, and <P>
&quot;+&quot; refers to the execution time of post <P>
Then the type of node is shown. By example &quot;Prod&quot; means a production
<P>
&quot;ProdName&quot; means a production name etc<P>
<P>
Then the value of the node is shown, in this case &quot;'LOCUS'&quot;.

<H2><A NAME="more">More Information</H2>
Further information can be found in the manual chapter &quot;Adding Databanks - A Guided Tour&quot; in the section &quot;Additional Tricks for Debugging a 
Syntax&quot;
</BODY>
</HTML>
ime of pre, and <P>
&quot;+&quot; refers to the execution time of post <P>
Then the type of node is shown. By example &quot;Prod&quot; means a production
<P>
&quot;ProdName&quot; means a production name etc<P>
<P>
Then the value of the node is shown, in this casesrs/www/doc/icarus.html
<HTML>
<HEAD>
   <TITLE>The Icarus Language</TITLE>
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<H1><A NAME="_Toc359130261"></A>The Icarus Language </H1>

<P>The Icarus language was originally designed to parse flat file databanks.
The syntax of these databanks can be often described in layers: the syntax
of the entry within the databank, the data-fields within the entry and
the syntax of each data-field. The full layered syntax we call incremental
or recursive. </P>

<P>A syntax definition alone is not enough. During the parsing process
it is necessary to save certain information or to modify or reformat the
tokens found. An example is the date in the data-field &quot;DATE&quot;
which might look like &quot;12-APR-88&quot; and for the purpose of indexing
needs to be reformatted to the number &quot;19880412&quot;. This is one
of many tasks that are conveniently executed during the parsing process.
</P>

<P>The name Icarus stands for Interpreter of Commands And RecUrsive Syntax.
Initially, it was used to attach commands to syntax descriptions. In fact,
the 'command part' became so powerful that Icarus can be seen as a 'normal'
interpreted language such as Perl or Tcl with the added capability of syntax
specification. </P>

<P>The current Icarus is not yet a general purpose language, since functions
can still not be implemented in Icarus and since a few operators like <TT>%</TT>
and <TT>-- </TT>are still missing. We developed Icarus mainly to meet the
demands of the SRS system.</P>

<H2><A NAME="gettingstarted"></A>Getting Started: a first Icarus program</H2>

<P>Use your favorite text editor to write the program &quot;first&quot;
with the line </P>

<PRE>$Print:&quot;hello world\n&quot;</PRE>

<P>then start the Icarus program with the command </P>

<PRE>% icarus first</PRE>

<P>This program should print the string &quot;hello world&quot; on your terminal </P>

<H2><A NAME="getstarted"></A>Getting Started: setting up your environment</H2>

<P>On systems that support &quot;magic numbers&quot; you can set up the
system so that you can directly execute icarus scripts without explicitly
call icarus. To do this you can add a line at the top of the program so
that the operating system knows what program to interpret your file with,
like this: </P>

<PRE>#!/bin/env icarus
$Print:&quot;hello world\n&quot;</PRE>

<P>To use the above format, the <TT>icarus</TT> executable must be defined
in your <B>$PATH</B> environment variable. To accomplish this, you can
also simply execute the command:</P>

<PRE>source prep_srs</PRE>

<P>before starting to work. This command defines everything that is necessary
to work with SRS.</P>

<P>An alternative and less flexible way is to hard-wire the path of the
icarus interpreter into your program:</P>

<PRE>#!/usr/local/bin/icarus
$Print:&quot;hello world\n&quot;</PRE>

<P>Before 'executing' program &quot;first&quot; you must also set the executable
permission on the file with</P>

<PRE>% chmod +x first</PRE>

<P>Once this is done, all you have to type is: </P>

<PRE>% first</PRE>

<H2><A NAME="icarusstructure"></A>The structure of an Icarus program</H2>

<P>An Icarus program is a list of statements, in which each statement is:</P>

<UL>
<LI>an assignment, in which a variable is assigned the value of an expression</LI>

<LI>an Icarus command, which can have parameters initialized with expressions</LI>

<LI>a flow control directive</LI>
</UL>

<P>Comments are delimited by the <TT># </TT>sign and continue to the end
of the line. The first line of the program must be the &quot;magic number&quot;
(!/bin/env/icarus) that tells to the operating system to use Icarus to
execute the program.</P>

<P><B><I>Example:</I></B></P>

<PRE>#!/bin/env icarus
#this is my first icarus program
$sum = (1 + 2) * 3   # an assignment 
$Print:&quot;hello world&quot; # a command</PRE>

<P>Almost all statements have expressions: the next paragraph explains
them in more detail.</P>

<H2><A NAME="Expressions"></A>Expressions </H2>

<P>Any Icarus expression consists of operands and operators. </P>

<P>Operands can be </P>

<UL>
<LI>literals or basic types: values which can directly be expressed in
the icarus language</LI>

<LI>variables</LI>

<LI>function calls</LI>

<LI>expressions within parentheses</LI>
</UL>

<P>Operators are binary, if they have two operands, such as the <TT>*</TT>
for multiplication, or unary if they act on one operand, such as the <TT>++</TT>
for incrementing the value of the operand. An expression with more than
one operation is executed by a certain order. The order depends on the
precedence of the operators, the order within the expression (since they
are normally evaluated left to right), and the grouping by parentheses.
Each basic type accepts a certain set of operators.</P>

<P><B><I>Example:</I></B> </P>

<PRE>$sum = (1 + 2) * 3 * $a</PRE>

<P>The result from the expression, the number 9, is stored in the variable
<B><TT>$sum</TT>.</B></P>

<P>All identifiers in Icarus are preceded by a <TT>$</TT>. Identifiers
are case sensitive, and can be both function or variable names. So the
identifier <B>$a </B>in the expression can refer to a variable or call
a function, depending on how <B>$a</B> is defined before. The convention
is to let function names start with uppercase letters and variables with
lowercase letters. Variables and function will be explained later in more
detail.</P>

<P>The following sections will explain the operands and operators of Icarus
expressions in detail. </P>

<H3><A NAME="_Toc359130264"></A>Basic Types</H3>

<P><A NAME="_Toc359130265"></A>Icarus provides a set of predefined types:</P>

<UL>
<LI>signed integers (32bit integers), </LI>

<LI>real numbers (implemented as the C language <TT>double</TT>, a 64bit
floating point number), </LI>

<LI>productions (rule), useful for parsing which will be explained later,
</LI>

<LI>strings.</LI>

<LI>lists.</LI>
</UL>

<H4><A NAME="strings">Strings</A></H4>

<P>Icarus knows four types of strings: </P>

<UL>
<LI>names: a name consists of one or more characters. The first must be
an alphabetical letter and the others alpha numerical characters including
the underscore (&quot;<TT>_</TT>&quot;). </LI>

<LI>single quoted strings: a string that must begin and end in the same
program line, but can contain spaces.</LI>

<LI>double quoted strings: as single quoted strings, but perform string
interpretation (see below)..</LI>

<LI>barstrings - The barstring may consist of more than one line and is
identified by a vertical bar <TT>|</TT> at the beginning of every line
which belongs to the string. The <TT>| </TT>at the begin of lines that
continue a barstring may be only preceded by blanks or tab characters.
Every character after the vertical bar to the end of the line, including
the carriage return is part of the string. Also barstrings perform string
interpretation.</LI>
</UL>

<P><B><I>Examples:</I></B> </P>

<PRE>$name      = Hello
$sqstring  = 'Hello World'
$dqstring  = &quot;Hello World&quot;
$barstring = |Hello
             |World.</PRE>

<P>Icarus defines a special syntax (escape sequences) for non-printing
and special characters. These are very similar to the ones defined for
the C language, i.e. a backslash <TT>\</TT> followed by the character code:</P>

<DL>
<DT><B><TT>\n</TT></B> </DT>

<DD>a new line character or line break </DD>

<DT><B><TT>\t</TT></B> </DT>

<DD>a tab character </DD>

<DT><B><TT>\a</TT></B> </DT>

<DD>an alert (beep) </DD>

<DT><B><TT>\</TT></B>decimal number </DT>

<DD>any ASCII character specified by a decimal number, e.g., <TT>\10</TT>
is the same as <TT>\n</TT> </DD>

<DT><B>\\ </B></DT>

<DD>the \ itself </DD>

<DT><B><TT>\</TT></B>any other character the character itself. 
</DL>
<P>Depending on the type of strings, other characters must be escaped.</P>
<UL>
<LI>in single quoted strings the ' and all non-printing characters must
be escaped</LI>

<LI>in double quoted strings the &quot; and all non-printing characters
must be escaped. In some cases which will be explained in the string interpretation
paragraph, the $ must also be escaped.</LI>

<LI>in barstrings characters normally don't need to be escaped: the string
can normally be written exactly as it will be printed. The carriage return
can be excluded from the string with an backslash <TT>\</TT> at the end
of the line. All the escapes can still be used if needed.</LI>
</UL>

<P><B><I>Examples:</I></B> </P>

<PRE>$name      = Hello
$sqstring  = '&quot;Hello&quot; \\World\\\n\t'Again\'.'
$dqstring  = &quot;\&quot;Hello\&quot; \\World\\\n\t'Again'.&quot;
$barstring = |&quot;Hello&quot; \
             |\\World\\
             |        'Again'.
              </PRE>

<P>prints in all 3 cases:</P>

<PRE>&quot;Hello&quot; \World\
        'Again'</PRE>

<P>For string management, Icarus provides the functions: </P>

<UL>
<P>$StrLen which returns the length of a string</P>

<P>$StrApp which appends a string to another</P>

<P>$StrTrans which translates a set of characters in a string into another
set of characters</P>

<P>$StrPad which pads a string with a certain character up to a certain
length</P>
</UL>

<H4><A NAME="_Toc359130266"></A>Lists and associative lists </H4>

<P>Icarus has flexible lists where several or all of its elements can be
associated with a name. This association of elements with a name is a property
of elements in associative arrays and can be also found in other programming
languages. The difference here is that the elements in the list are always
ordered and hence can always be accessed by position. Lists can have elements
of mixed types (e.g., strings and integers in the same list) and any basic
type can be inserted, including other lists that can be nested to any degree.
In the Icarus syntax members of a list must appear within curly braces
(e.g., <TT>{1 2 3}</TT>). </P>

<P>Elements can be accessed by position where the first element (list head)
has position 1. The number must appear in square brackets after the list
variable name. If a name is associated with the element it can be used
by adding the name to the list variable name using a dot (<TT>.</TT>) as
separator. </P>

<P><B><I>Examples:</I></B> </P>

<P>Initialize or reset a list: </P>

<PRE>$list = {}</PRE>

<P>Define a list with 5 elements of type string: </P>

<PRE>$list = {aa ee ii oo uu}</PRE>

<P>Access members in a list by position: </P>

<PRE>$a = $list[2]
  $Print:$a</PRE>

<P>will give the output </P>

<PRE>  ee</PRE>

<P>Define a nested associative list: </P>

<PRE>$list2 = {
  a: {aa: 1 bb: 2}
  b: 2
  c: 'Hello world'
  d: {1 2 3}
}</PRE>

<P>In this example &quot;list2&quot; has 4 elements where the first and
the last are lists themselves. </P>

<P>The following shows four ways of accessing the same element in &quot;list2&quot;:</P>

<UL>
<LI>Access by associated name: </LI>

<PRE>$list2.a.aa </PRE>

<P>If a name isn't defined, an empty variable will be returned (see below
in Program Variables).</P>

<LI>Access by associated name using the name &quot;a&quot; stored in the
variable <B>$selector</B>. Note that <B>$selector </B>must be put in parentheses;
otherwise the name &quot;aa&quot; would refer to an element in <B>$selector</B>:</LI>

<PRE>$selector = &quot;a&quot;
$list2.($selector).aa</PRE>

<LI>Access by list position: </LI>

<PRE>$list2[1][1]</PRE>

<LI>Access by list position where the position numbers are stored in variables
</LI>

<PRE>$i = 1
$j = 1
$list2[$i][$j]</PRE>
</UL>

<P>A list can be changed in two ways:</P>

<UL>
<LI>New list elements can be appended to the list using the <TT>+=</TT>
operator: </LI>

<PRE>$list2+=5</PRE>

<P>The new appended elements don't have an associated name</P>

<LI>Named elements can be reassigned or created simply by naming them:</LI>

<PRE>$list2.b=|Again</PRE>

<P>assigns a new string to the element b</P>

<PRE>$list2.e='Goodbye All'</PRE>

<P>appends the new element named <B>.e</B> to the list and initializes
it with a string</P>
</UL>

<P>For list management, Icarus provides the function $Key which takes a
list element as argument and returns the name of it in the list.</P>

<UL></UL>

<H3><A NAME="variablesandfunctions"></A>Variables</H3>

<P>In an Icarus program, variables can store any basic type. They can be
assigned using the <TT>=</TT> operator.</P>

<P>A variable can have any name that doesn't collide with a function name.
Conventionally, variable names start lower case.</P>

<P>A variable is undefined until it is assigned a value for the first time.
An unassigned variable, if used in an expression, returns the empty string.
After the first assignment the type of the variable is fixed and cannot
be changed any more, while instead the value can be changed at any time.
This is also true for list elements. </P>

<H3><A NAME="functions">Functions</A></H3>

<P>Icarus functions are all predefined in the Icarus parser during execution.
To define new functions, see chapter &quot;<A HREF="#newicaruscom">Creating
New Icarus Commands</A>&quot;. </P>

<P>In the function definition it is specified (together with other things):</P>

<UL>
<LI>name and type of the arguments. The function can have zero or more
arguments. Only one of the arguments can be unnamed. All arguments can
be defined with a default value.</LI>

<LI>type of the return value</LI>
</UL>

<P>Functions may be called with zero or more arguments which are enclosed
in square brackets <TT>([ ])</TT> and separated from the function name
by a colon <TT>(:)</TT>. Each argument must be preceded by the argument
name with the exception of the eventual unnamed argument. For example,
the following calls the function <B>$Print</B> which receives the unnamed
argument &quot;hello world&quot; and the argument <B>.f</B> (file) which
is assigned the contents of the variable <B>$output,</B> containing the
file name:</P>

<PRE>$Print:[&quot;hello world&quot; f:$output]</PRE>

<P>Most arguments have default values. In this case, they normally don't
need to be specified unless they need to be assigned a value different
from the default. For example, the <B>.f</B> argument defaults to standard
output.The function can the be written as:</P>

<PRE>$Print:&quot;hello world&quot;</PRE>

<P>If the argument list consists only of the unnamed attribute, as in the
above example, the square brackets can be omitted. </P>

<P>A function called without any argument and returning a value is indistinguishable
from a variable. The only difference is that a value cannot be assigned
to it.</P>

<P>An example is the function $Ct, which will be explained in the parsing
section:</P>

<PRE>$Print:$Ct</PRE>

<P> </P>

<H3><A NAME="interpretedstrings"></A>Interpreted Strings</H3>

<P>Double quoted and bar strings can perform substitution of the values
of variables and even functions every time they are evaluated. All <TT>$</TT>
characters followed by a letter or digit or _ (underscore) are interpreted
as Icarus identifiers and substituted. To avoid substitution, the <TT>$</TT>
character must be escaped as <TT>\$</TT> .</P>

<P>For instance the variable <B>$x</B> which is assigned the value &quot;World&quot;
in the example can be used within a string:</P>

<PRE>$x =  'world'
$Print:&quot;hello $x\n&quot;</PRE>

<P>The <B>$Print</B> call will produce the output</P>

<PRE>hello world</PRE>

<P>A problem arises if the variable name inside a text must be followed
by letters or digits. Here it is necessary to enclose the variable in parentheses
as in the next example. </P>

<PRE>$x = 'llo wo'
$Print:&quot;he($x)rld\n&quot;</PRE>

<P>The parentheses are not printed if the open parentheses is immediately
followed by the $, so to print then they must be escaped:</P>

<PRE>$x = Moon
$Print:&quot;hello\($x)\n&quot;</PRE>

<P>prints:</P>

<PRE>hello(Moon)</PRE>

<P>If enclosed in parentheses also more complex constructs that access elements
in lists by name or index, or function calls with full argument lists can
be inserted . The example</P>

<PRE>$list = {a: &quot;hello&quot; b: &quot;world&quot;}
$Print:|&quot;($list.a) ($list[2])&quot;: ($StrLen:&quot;($list.a) ($list[2])&quot;) characters</PRE>

<P>will produce the output</P>

<PRE>&quot;hello world&quot;, 11 characters</PRE>

<P>Note that in a bar strings double quotes need not be represented by
escape sequences. The argument of <B>$StrLen</B> is a string which is interpreted
itself. Icarus allows an indefinite amount of recursion in interpreted
strings!</P>

<H3><A NAME="printform"></A>Printing with Format Directives </H3>

<P>The <B>$Print</B> function has the same functionality as the C language
function &quot;printf&quot; if given a list of arguments as in</P>

<PRE>$Print:{&quot;\&quot;%s %s\&quot;, %3d\n&quot; 'hello' 'world' 11} </PRE>

<P>In that case the first element in the list must be the format string
which contains directives (starting with a <TT>%</TT>) where to insert
the items that follow next in the list. The syntax and type of the directives
is exactly as in the C language &quot;printf&quot;. Please consult a C
manual for further information.</P>

<H2><A NAME="objectdefinition"></A>Object Definition</H2>

<P>The Icarus language can be used for the definition of data. This feature
is still in a very preliminary stage of limited use and historically emerged
from the old ODD language. The main limitation is that single attributes
of the defined objects cannot be accessed within Icarus. They must be exported
first to C functions and can then be accessed there as normal C structures.
Also objects are now defined in a file separated from the main icarus program.</P>

<P>Here data are regarded as a series of object definitions. An object
comprises of attributes such as an integer, a character string, a list
of objects or a reference to another object. The object definition requires
knowledge of the object type or class which &quot;knows&quot; the type
and name of all attributes of the object. This knowledge, or meta information,
can be specified in objects as well which are then of the type &quot;class&quot;.
In Icarus both objects and object classes can be specified using the same
syntax which is equivalent to function calls where the class name is the
equivalent of the function name. The example defines an object of the class
<B>$shopping_list</B>: </P>

<PRE>$shopping_list:[budget:20 buy:{bread butter cheese milk}]</PRE>

<P>The attribute<B> .budget</B> is assigned the number 20 and the attribute
<B>.buy</B> a list of character strings. An object can reference other
objects by two ways. One way is the nested object definition. The next
example defines instances of the class <B>$item</B> within the instance
of <B>$Shopping_list</B>.</P>

<PRE>$shopping_list:[budget:20 
  buy:{
    $item:[name:bread weight:1000]
    $item:[name:butter weight:250]
    $item:[name:cheese weight:200]
    $item:[name:milk weight:1000]
  }
]</PRE>

<P>The difference to the previous example is that the values assigned to
attribute <B>.buy </B>have been 'promoted' from single strings to objects.
In the present implementation the defined instances of <B>$item</B> are
only referenced by the object of type <B>$shopping_list</B>, they are not
part of it. </P>

<P>The other way of referencing other objects, the direct reference, makes
use of name association which is equivalent to that in Icarus lists. object-IDs.
An name given to an object can be used from anywhere within the programs
to create a reference to it. In a reference the object name must be prefixed
with a <TT>@</TT>. The next example creates the same objects as the previous
but uses references instead of nested definition. Note that in the example
all references are all created before the objects themselves.</P>

<PRE>$shopping_list:[budget:20 buy:{@Item1 @Item2 @Item3 @Item4}]
 
Item1:$item:[name:bread weight:1000]
Item2:$item:[name:butter weight:250]
Item3:$item:[name:cheese weight:200]
Item4:$item:[name:milk weight:1000]</PRE>

<H2><A NAME="flowcontrol"></A>Flow Control</H2>

<P>Statements such as if-then-else, control the flow of a program. In Icarus
all control statements have a common syntax which is similar to function
calls. It begins with a name, e.g., &quot;for&quot; or &quot;while&quot;,
which as in function calls may be followed by one or more arguments and
must have a body, or list of statements at the end. The body can consist
of a single statement or a list which then must be enclosed in curly braces.
A simple example is the <B>init </B>which selects a list of statements
to be executed at the program initialization time:</P>

<PRE>init {$m=5}</PRE>

<P>The while statement receives an additional argument</P>

<PRE>while:($k &lt; 10)
  $Print:|$k</PRE>

<H3><A NAME="ifstatement"></A>The if-then-else statement </H3>

<P>The if statement may consists of three different parts: The <B>if</B>
part can be followed by one or more <B>elif</B> parts and then by an optional
<B>else</B> part. </P>

<H5>Example: </H5>

<PRE>if:($count&lt;$min)
  $Print:|$count is below $min
elif:($count&gt;$max)
  $Print:|$count is above $max
else
  $Print:|$count is in the range of $min to $max</PRE>

<H3><A NAME="_Toc359130273"></A>The while statement </H3>

<P>Begins with the name &quot;while&quot; followed by the condition and
a statement body. </P>

<H5>Example: </H5>

<PRE>while:($k &gt; 1)
  $Print:$k</PRE>

<H3><A NAME="_Toc359130274"></A>The for Statement</H3>

<P>The for statement is very similar to its equivalent in C. It receives
a list of three statements: The initialization before entering the loop,
the condition examined before each iteration and the update command executed
after each iteration. Since these three statements constitute a list they
must be enclosed in curly braces.</P>

<H5>Example: </H5>

<PRE>for:{$i=1 $i&lt;10 $i+=1} {
  $Print:&quot; $i &quot;
}</PRE>

<H3><A NAME="foreachstatement"></A>The<B> foreach </B>Statement</H3>

<P>This statement allows looping over the elements in a list. It takes
two arguments, the iteration variable and the list of elements.</P>

<H5>Example: </H5>

<PRE>foreach:[$i in:{1 2 3 4 5}]
  $Print:&quot; $i &quot;</PRE>

<P>Sometimes it is not clear whether a variable contains a list or a single
element. The <B>foreach</B> statement allows also iteration over a variable
of a simple type as, e.g., an integer. The example shows two nested <B>foreach</B>
statements where the outer loops over all elements of <B>$list</B> which
hold either a list again or a single integer. </P>

<PRE>$list={{1 2 3 4} 22 {5 6 7 8} 33 {9 10 11 12}}
foreach:[$i in:$list]
  foreach:[$j in:$i]
    $Print:&quot; $j &quot;</PRE>

<H2><A NAME="parsing"></A>Parsing</H2>

<P>This chapter describes the part Icarus was originally designed for -
the parsing of files with a defined format. Two types of syntax or pattern
description are available: </P>

<UL>
<LI>an extended version of the Backus-Naur format for specifying a context
free grammar which naturally describes the hierarchical structure of, e.g.,
programming language constructs; </LI>

<LI>regular expressions for specifying lexemes or patterns; regular expressions
are treated as part of the extended Backus-Naur format;</LI>
</UL>

<H3><A NAME="prod"></A>Productions </H3>

<P>Icarus has a special data type, the production, which is delimited by
a '~' reminiscent of delimiting strings by quotation marks. A production
derives or 'produces' all sentences with a certain syntax, e.g., </P>

<PRE>~ '1' '2'? '3' ~</PRE>

<P>derives the string &quot;<TT>123</TT>&quot; or &quot;<TT>13</TT>&quot;.
If the input string to be parsed is within the set of derived strings it
matches with the production. Parsing of all other input strings will generate
a parsing error. The <TT>?</TT> after the second symbol ('2') indicates
the occurrence of the &quot;<TT>2</TT>&quot; to be optional. A syntax or
grammar, can be formed by grouping one or more productions into an associative
list. The following defines the same syntax as the above but uses for each
of the literals '1', '2' and '3' a separate production. </P>

<PRE>$rules={
  a:     ~ one two? three ~
  one:   ~ '1' ~
  two:   ~ '2' ~
  three: ~ '3' ~
}
$Parse:['123' prod:$rules start:a]</PRE>

<P>The variable <B>$rules</B> is assigned a list with four productions
named &quot;<TT>a</TT>&quot;, &quot;one&quot;, &quot;two&quot; and &quot;three&quot;.
The production named &quot;a&quot; refers to the other productions by using
their name. Parsing of &quot;a&quot; begins with the evaluation of &quot;one&quot;
which is a <I>nonterminal</I> since it forwards evaluation to production
&quot;one&quot; which consists of the literal '1', a <I>terminal</I>, since
the string &quot;1&quot; can be directly compared with the input. Both
<I>terminals</I> and <I>nonterminals</I> are called <I>symbols</I>. </P>

<P>The <B>$Parse</B> command receives as arguments the input string to
be parsed ('123'), the production list stored in the variable <B>$rules</B>
and the name of the production (&quot;a&quot;) to start with. This production,
also called <I>start symbol,</I> or goal, represents the syntax of the
input string. It can be seen as the top of the syntax tree that can be
built from the productions stored in <B>$rules</B>. Note that <B>$Parse</B>
could also be called with &quot;one&quot; as the start symbol; in that
case the parser would try to match a single '1' against the input stream.
</P>

<P>A production can be seen as an expression with operands and operators
which are detailed below. </P>

<H4><A NAME="opnds"></A>Operands</H4>

<P>Symbols (see above) are operands within productions and will be matched
with the input in the same order as they occur in the expression. </P>

<DL>
<DT><B>Literal:</B> </DT>

<DD>A string in single quotes, e.g., <TT>'1'</TT> must directly match the
input. The <TT>'</TT> character within a literal must be escaped by a <TT>\</TT>
as in <TT>'\'hello\''.</TT> </DD>

<DT><B>Regular Expression:</B> </DT>

<DD>A pattern to be matched with the input. A regular expression must be
enclosed in forward slashes, e.g., <TT>/[123]/ </TT>which matches one of
'1' or '2' or '3'. Regular expression are explained in detail in a separate
section below<TT>. </TT></DD>

<DT><B>Production Name:</B> </DT>

<DD>The name forwards parsing to a production which must exist in the same
production list as the referring production. The reference can be also
recursive as in '<TT>a: ~ '1' a? ~</TT>' which describes a run of ones.
</DD>

<DT><B>Sub Expression:</B> </DT>

<DD>An expression contained in parentheses. </DD>
</DL>

<H4><A NAME="op"></A>Operators </H4>

<P>Only one binary but several unary operators exist. All unary operators
must be placed after a symbol, e.g., &quot;<TT>'2'?</TT>&quot;. </P>

<DL>
<DT><B>| </B>(binary) </DT>

<DD>Separates alternative operands, or symbols, that can match. The alternatives
are evaluated from left to right, e.g., <BR>
&quot;<TT>'1' | '2' | '3'</TT>&quot; matches either '1', '2', or '3'. </DD>

<DT><B>?</B> (unary)</DT>

<DD>Makes the occurrence of a symbol optional. </DD>

<DT><B>*</B> (unary)</DT>

<DD>Asks for zero or more instances of a symbol. </DD>

<DT><B>+</B> (unary)</DT>

<DD>Asks for one or more instances of a symbol. </DD>
</DL>

<H4><A NAME="regexp"></A>Regular Expressions</H4>

<P>Regular expressions are a powerful way to describe patterns.The patterns
that they can recognize are simpler than the languages that can be specified
in BNF form, but they are faster and more compact. They have very similar
operators as productions. Regular expressions are terminals in productions
and must appear within forward slashes (<TT>/</TT>). The characters <TT>^$.[]()?+*</TT>
have a special meaning and must be prefixed with a double backslash (<TT>\\</TT>)
if they should be matched literally. This includes also the forward slash
that must be escaped with a single backslash (\).</P>

<DL>
<DT><B>. </B></DT>

<DD>matches any character. </DD>

<DT><B><TT>[...]</TT></B> </DT>

<DD>indicates a set of characters to match, e.g. <TT>[0123456789]</TT>
matches a single digit or <TT>[()]</TT> matches an opening or closing parenthesis.
Character ranges can be specified by using a hyphen <TT>-</TT>, e.g. <TT>[0-9]</TT>
matches any digit. A caret <TT>^</TT> in front of the character set (after
the opening square bracket) negates the character set, e.g., <TT>[^0-9]</TT>
matches any non digit character. </DD>

<DT><B><TT>(...)</TT></B> </DT>

<DD>Groups a series of pattern elements to a single element. </DD>

<DT><B><TT>| </TT></B></DT>

<DD>Separates two alternative patterns. </DD>

<DT><B><TT>* </TT></B></DT>

<DD>The preceding group may be repeated zero or more times. </DD>

<DT><B><TT>+</TT></B> </DT>

<DD>The preceding group may be repeated one or more time. </DD>

<DT><B><TT>?</TT></B> </DT>

<DD>The preceding group may or may not occur. </DD>
</DL>

<H4><A NAME="exampleProd"></A>Examples of Productions</H4>

<P>The easiest way of learning how to write a production is by looking
at examples. The production &quot;expr&quot; consists of three terminals,
two regular expressions that describe a number with one or more digits
and a literal describing the operator &quot;+&quot;</P>

<PRE>expr:  ~ /[0-9]+/ '+' /[0-9]+/ ~</PRE>

<P>The production matches an expression as, e.g., &quot;1+10&quot;. To
allow more complex expressions, the literal &quot;+&quot; can be converted
to a regular expression matching both &quot;+&quot; and &quot;-&quot;.
In addition to that, the next production has the operator and second operand
enclosed in parentheses and followed by a star to let the expression consist
of a single number or an indefinite number of terms.</P>

<PRE>expr:  ~ /[0-9]+/ (/(+|-)/ /[0-9]+/)* ~</PRE>

<P>The last example allows the two operators &quot;+&quot; and &quot;-&quot;
as well as &quot;*&quot; and &quot;/&quot;. The convention to give operators
&quot;+&quot; and &quot;-&quot; lower priority over &quot;*&quot; and &quot;/&quot;
is reflected in the parsing process. The production &quot;expr&quot; starts
with the nonterminal &quot;term&quot; which matches first a factor optionally
followed by one or more operations using the &quot;*&quot; or &quot;/&quot;
operators. After finding a &quot;+&quot; or &quot;-&quot; or the end of
the input control is returned to production &quot;expr&quot; which then
tries matching a &quot;+&quot; or &quot;-&quot; operator and another term.
This means that the parser tries first to parse operations with &quot;*&quot;
or &quot;/&quot; operators, a fact, that will be used later to write a
simple calculator for arithmetic expressions.</P>

<PRE>expr:   ~ term (/(+|-)/ term)* ~
term:   ~ factor (/\\*|\/) factor)*
factor: ~ /(-|+)?[0-9]+/ | '(' expr ')'</PRE>

<P>Note that the syntax is recursive since &quot;factor&quot; can be either
a number or an &quot;expr&quot; which must occur within parentheses. The
recursion allows expressions to be arbitrarily nested, as e.g. &quot;(4+13/((5+7)*12))*10&quot;.</P>

<H4><A NAME="useProd"></A>Using Productions </H4>

<P>Productions are evaluated by a recursive descent or predictive parser.
This means that the parser can deal with uncertainty expressed in rules
like, &quot;a symbol may or may not be there&quot;, or, &quot;either of
two symbols can be found&quot;. The limitation here is that when trying
an &quot;uncertain&quot; symbol, the first terminal in it must make a decision
whether the symbol matches or not. This is of course not a problem if the
&quot;uncertain&quot; symbol has only one terminal but consider the example
</P>

<PRE>expr:   ~ plusop | multop ~
plusop: ~ num &quot;+&quot; num ~
multop: ~&nbsp;num &quot;*&quot; num ~
num:    ~ /[0-9]+/ ~</PRE>

<P>The production &quot;expr&quot; is invalid since &quot;plusop&quot;
and &quot;multop&quot; start with the same symbol which is the terminal
in &quot;num&quot;. Given the input expression &quot;4*10&quot;, the parser
will first try production &quot;plusop&quot; which initially matches the
input with &quot;num&quot;. Once it finds disagreement between the &quot;+&quot;
that must follow &quot;num&quot; and the &quot;*&quot; in the input it
is already too late for backtracking to &quot;expr&quot; in order to try
&quot;multop&quot;, and the parser must signal a parsing error. This lack
of &quot;look ahead&quot; can be a problem. It can be solved by designing
productions that branch to alternatives as late as possible. Another possibility
is to use regular expressions which do not have that problem. In particular,
it can be useful to have a look ahead using terminal as probes using commands
<B>$Not </B>or <B>$Probe</B>.</P>

<P>In general, it is both easy and difficult to write productions. Easy
because only a limited number of operators and operands exist, and difficult
since a syntax can be written in many ways with varying degrees of robustness
and efficiency. In addition, it is important to avoid a number of pitfalls
which are detailed below.&nbsp;</P>

<H5>Avoid left recursion</H5>

<P>As mentioned above productions can be recursive. If the first symbol
in the expression is the nonterminal defined by he production itself, it
is said to be left recursive. Consider the example </P>

<PRE>a: ~ a b c ~</PRE>

<P>During parsing <TT>a</TT> will be replaced by the expression &quot;<TT>a
b c</TT>&quot;. Since the first symbol of the expression is again <TT>a</TT>,
<TT>a</TT> will be replaced by <TT>a</TT> ....which will be replaced by
<TT>a</TT> which will... never end! </P>

<H5>Only the last alternative in the list may start with a symbol that
is optional (postfixed with * or ?). </H5>

<P>In a list of alternatives the first (!) symbol must decide whether or
not a subexpression is applied. Consider the example </P>

<PRE>a: ~ x? a | y? b ~</PRE>

<P>The first symbol <TT>x?</TT> of the term <TT>'x? a'</TT> will always
match since it is optional which means that control is never transferred
to the following term <TT>'y? b'</TT>. </P>

<H5>Within a list of alternative sub expressions a first symbol must not
be a superset of the first symbol of the sub expression that follows. </H5>

<P>A list of alternatives is evaluated from left to right; the next sub
expression is only evaluated if the first symbol of the preceding sub expression
fails. Using the production </P>

<PRE>a: ~ /[a-z]/ | 'abc' ~</PRE>

<P>the literal <TT>'abc'</TT> will never be found since it is a subset
of <TT>/[a-z]/</TT>. If the order of the alternatives is reversed first
the string <TT>'abc'</TT> and then the presence of any other string composed
of characters between <TT>a</TT> and <TT>z</TT> will be tested. </P>

<H3><A NAME="actions"></A>Actions</H3>

<P>The examples in the previous sections only disseminate the input string,
but nothing is returned and no action invoked after and during the parsing
process. It is possible to let productions &quot;do&quot; something by
adding <I>actions</I> to the symbols of a production. An action is a list
of Icarus statements within curly braces that must be associated to a terminal
or nonterminal by placing it on its right side, e.g., </P>

<PRE>num: ~ /[0-9]+/ {$Print:&quot;matched a number\n&quot;} ~  </PRE>

<P>Normally the list of Icarus statements is executed after the symbol
has been successfully matched against the input. This means that in the
example above &quot;matched a number&quot; is printed to the screen as
soon as the regular expression <TT>/[0-9]+/</TT> has been successfully
evaluated. If the production starts with an action it is associated with
the entire production.</P>

<PRE>num: ~ {$Print:&quot;matched a number\n&quot;} /[0-9]+/ ~ </PRE>

<P>will appear to do exactly the same as the previous example but the action
is executed after the evaluation of the production &quot;num&quot; instead
of the regular expression. Action are only invoked if the associated symbol
matches the input. Consider the example</P>

<PRE>opnd: ~ (/[a-z]+/ {$Print:&quot;letters\n&quot;} | /[0-9]+/ {$Print:&quot;digits\n})+ ~ </PRE>

<P>Parsing the input &quot;12abc&quot; the production will print</P>

<PRE>letters
digits</PRE>

<P>Within the actions it is of course desirable to access information regarding
the parsing process such as the input region that matches the current symbol.
For that a number of special functions exist, each of which returns a string:</P>

<DL>
<P><B>$Ct</B> </P>

<DD>returns the region of the input that matches the current symbol which
can be a terminal or nonterminal.</DD>

<DT><B>$It</B></DT>

<DD>returns the input string or input token from the current parsing position
to the end. The size of the returned string can be limited by an additional
unnamed argument, eg, &quot;$It:50&quot; returns the first 50 characters
of the input token.</DD>

<DT><B>$Itc</B></DT>

<DD>returns the code of the input token (see the chapter &quot;<A HREF="#tokandtoktbl">Tokens
and Token Tables</A>&quot; for further explanation).</DD>

<DT><B>$1</B>,<B>$2</B>...<B>$9</B>,<B>$0</B> </DT>

<DD>Return matching regions from the most recent evaluation of a regular
expression. <B>$0</B> returns the entire match which is equivalent to <B>$Ct</B>.
<B>$1 </B>until <B>$9 </B>return a sub-match that must be indicated by parentheses
within the regular expression itself where the opening parenthesis is used
for counting, eg, the regular expression &quot;/([0-9]+), ([0-9]+)/&quot;
describes a pattern like &quot;123, 456&quot;, here <B>$1</B> would return
&quot;123&quot; and <B>$2</B>, &quot;456&quot;.</DD>
</DL>

<H5>Example: </H5>

<PRE>expr:  ~ {$Print:&quot;expr: |$Ct|\n&quot;} num op num ~
num:   ~ /[0-9]+/ {$Print:&quot;num: |$Ct|\n&quot;} ~
op:    ~ '+' {$Print:&quot;op: |$Ct|\n&quot;} ~</PRE>

<P>if applied to the input </P>

<PRE>3+7</PRE>

<P>will print </P>

<PRE>num:  |3|
op:   |+|
num:  |7|
expr: |3+7|</PRE>

<P>Using a regular expression the example can be written as</P>

<PRE>expr: ~  /([0-9]+)(\\+)([0-9]+)/ 
         {$Print:&quot;num:  |$1|\nop:    |$2|\nnum:   |$3|\nexpr: |$0|\n&quot;} ~</PRE>

<H4><A NAME="exedTime"></A>Execution Times</H4>

<P>Statements within actions, as mentioned before, are normally executed
after the symbol comparison. There are, however, situations where one would
like to execute statements before the matching, e.g., initializing variables
or printing the input stream. This can be achieved by grouping those statements
into a <B>pre </B>clause. Syntactically, <B>pre</B> is a flow control statement
like <B>while</B> and <B>for,</B> but without additional arguments. The
example prints the input stream before and after matching the regular expression
<TT>/[0-9]+/</TT> </P>

<PRE>num: ~ /[0-9]+/ {pre{$Print:&quot;before:$It&quot;} $Print:&quot;after:$It&quot;} ~ </PRE>

<P>The <B>pre</B> statement may only occur in symbol actions and not in
'normal' Icarus programs. </P>

<P>Icarus, like Perl, precompiles the program before execution. It is possible
to schedule statements for execution during this initialization phase with
the <B>init</B> clause. This is useful for initializing program variables
and very much resembles the initialization of static variables in the C
language. The following example converts a date such as &quot;1|12|95&quot;
into the form &quot;1. January, 1995&quot;. It makes use of a list of month
names which is created only once before the main program starts. If a <B>pre</B>
clause were used instead of the <B>init, </B>the list would be created
before every evaluation of the production &quot;date&quot; which is inefficient.
The following complete example program uses the function <B>$Parse </B>which
receives the input string, the production list and the name of the start
symbol.</P>

<PRE>$dateConvert={
  dateList: ~ date+ ~
  date:     ~ { init $monthNames={January February March April May June July
                                  August September October November December}
              } 
              (/([0-9]+)|([0-9]+)|([0-9]+)/ 
              { $day=$1 $month=$monthNames[$2] $year=&quot;19$3&quot;
                $Print:&quot;$day. $monthName. year\n&quot;
              } / */)+
            ~
}</PRE>

<PRE>$Parse:['1|12|96 5|7|95 1|1|89' prod:$dateConvert start:dateList]</PRE>

<P>The output of the program is </P>

<PRE>1. December, 1996
5. July, 1995
1. January, 1989 </PRE>

<H4><A NAME="actionSymbol"></A>Action Symbol</H4>

<P>Actions can be only associated to terminals and nonterminals. This restriction
is overcome by introducing a 'dummy' symbol, the <I>action symbol</I>,
which is denoted &quot;x&quot; and can be inserted anywhere in the production.
</P>

<H5>Example: </H5>

<PRE>sum: ~ num {$sum=$Ct} 
       ('+' num {$sum+=$Ct})+ 
       x{$Print:&quot;The sum is: $sum&quot;} ~</PRE>

<H3><A NAME="inputOutput"></A>Input/Output</H3>

<P>A parsing process requires a syntax description and an input stream.
In Icarus this process may produce an output which can be used to start
a second process with a different syntax which is very useful to parse text
incrementally where one syntax breaks the stream in large components which
are subsequently fed to a second process for more detailed parsing. This
chapter describes the input and output of parsing processes in detail and
and describes the two possibilities of how they can call each other (lazy
and forced parsing).</P>

<H4><A NAME="tokandtoktbl"></A>Tokens and Token Tables</H4>

<P>A common task for a parser is to recognize and extract parts of the
input stream. A program language compiler, for instance, converts the input
stream, a stream of characters into another stream of groups of characters
which are called <I>tokens</I>. An expression such as &quot;10 + 2&quot;,
will yield the three tokens &quot;10&quot;, &quot;+&quot; and &quot;2&quot;.
The tokens &quot;10&quot; and &quot;2&quot; are integers and &quot;+&quot;
a plus operator. To facilitate further processing the three tokens can
be labeled according to syntactical meaning, e.g., the tokens &quot;10&quot;
and &quot;2&quot; could be labeled &quot;integer&quot; and &quot;+&quot;
could be labeled &quot;operator&quot;. Thus a token consists of a <I>token
string</I> and a label also called <I>token code</I>. </P>

<P>In Icarus tokens formed during the parsing process can be stored in
token tables. A token table must be given a name and be associated with
a production. The command <B>$Out</B>, which must appear within an <I>node
action</I> creates a new token table which by default has the name of the
production within which it is created. The execution time of <B>$Out</B>
is always before matching time. The command <B>$Wrt</B> can be used to
write a token into the most recently created token table. If called without
further arguments the current match ($Ct) is written without token code
attached. In the example production &quot;num&quot;&nbsp;creates a new
token with the same name. The production consists of a single terminal
which matches one or more numbers each of which is written to the token
table &quot;num&quot;.</P>

<PRE>num: ~ {$Out} /[0-9]+/+ {$Wrt} ~</PRE>

<P>If the <B>$Wrt</B> command is used in a production that does not create
a token table itself, the one most recently opened will be selected. In
the next example production &quot;expr&quot; creates a token table with
the same name. The <B>$Wrt</B> commands in productions &quot;num&quot;&nbsp;and
&quot;op&quot; write to that table adding the token codes &quot;operand&quot;
and &quot;operator&quot; respectively.</P>

<PRE>expr:  ~ {$Out} num op num ~
num:   ~ /[0-9]+/ {$Wrt:operand} ~
op:    ~ '+' {$Wrt:integer} ~</PRE>

<P>After parsing of the expression &quot;10 + 2&quot; the token table &quot;expr&quot;
will contain the following three tokens: </P>

<TABLE>
<TR>
<TD><B>token string</B></TD>

<TD><B>token code</B> </TD>
</TR>

<TR>
<TD>12</TD>

<TD>integer</TD>
</TR>

<TR>
<TD>+</TD>

<TD>operator</TD>
</TR>

<TR>
<TD>2</TD>

<TD>integer</TD>
</TR>
</TABLE>

<H4><A NAME="usingtokens"></A>Using Tokens as Parser Input</H4>

<P>Icarus extends the concept of a token so that also the input string
is regarded as a single token. This has the advantage that parsing processes
can be chained, i.e., tokens of a token table produced by one parser can
be used as input for another parser. If the input token table contains
more than one token the parser must iterate over each. The input for the
next example is a list of equations, each contained in a separate line.
</P>

<PRE>a = 10 + 2
a = 34 + 23
b = 23 + 7 + 66
b = 17 + 15 + 8
a = 103 + 85 + 1</PRE>

<P>The input can be processed in two parsing steps. First the production
&quot;line&quot; processes the list of equations and writes every line
as a single token into the token table &quot;line&quot;. Then production
&quot;equation&quot; takes the token table &quot;line&quot; as input and
parses each equation. The iteration over all tokens in token table &quot;line&quot;&nbsp;is
implicit. The command <B>$In</B> in the action of production &quot;equation&quot;
requests the token table &quot;line&quot; for input.</P>

<PRE>line:     ~ {$Out} /[^\n]+\n/ ~
equation: ~ {$In:line} variable '=' expr ~
expr:     ~ /[0-9]+/ ('+' /[0-9]+/)* ~
variable: ~ /[a-z]/ ~</PRE>

<P>The token code can be used to restrict the input to a subset of all
tokens in the input token table. The following example shows how to modify
the <I>line</I> and <I>equation</I> productions to select only equations
assigning variable &quot;a&quot; for parsing. The production &quot;line&quot;
parses now the variable name at the begin of the line and uses the name
stored in <B>$Ct</B> as the token code. The command <B>$App</B> attached
to the regular expression that follows appends the rest of the line to
the variable name already in the token table. The production &quot;equation&quot;
restricts its input to all tokens with the code &quot;a&quot; which is
specified as argument &quot;c&quot; for the command <B>$In</B>. </P>

<PRE>line:     ~ {$Out} /[a-z]/ {$Wrt:$Ct} /[^\n]+\n/ {$App} ~
equation: ~ {$In:[line c:a]} variable '=' expr ~</PRE>

<P>In general, production &quot;equation&quot; is a <I>consumer,</I> since
it processes the output of a <I>producer</I>, the production &quot;line&quot;.
Both &quot;equation&quot; and &quot;line&quot;&nbsp;represent different
parsing processes which can be coordinated in two ways: production &quot;equation&quot;
invokes production &quot;line&quot; in order to obtain its input or production
&quot;line&quot; invokes &quot;equation to further process the output it
created. Both models have been implemented in Icarus and are called &quot;lazy
parsing&quot; and &quot;forced parsing&quot; and can be generally defined:
</P>

<UL>
<LI>the consumer starts the producer and waits until he receives the input
token table (lazy parsing). </LI>

<LI>Upon completion of the output token table, the producer starts the
consumer (forced parsing).</LI>
</UL>

<P>Using these to invocation models the overall parsing process can be
separated into layers which call each other. This makes the overall parsing
task much more manageable and has the advantage that using the layers parsers
for different purposes can be written which can share components.</P>

<H4><A NAME="lazyparsing"></A>Lazy Parsing</H4>

<P>If the parser is called with the command <B>$Parse</B> as described
above, a start symbol, or goal, must be specified and the parser will immediately
start reading the input. In the lazy parsing mode the process is started
by asking for an output token table that is created by one of the productions
in the syntax. We call this process &quot;lazy&quot;, since nothing happens
unless somebody asks explicitly for the output, also, as will be shown
later, since the parser minimizes its effort to produce the requested token
table. </P>

<P>After the request of a token table the Icarus execution system must
find and call the <I>producer </I>that can creates the output token table
with the specified name. Any production that declares an output token table
with command <B>$Out</B> is a <I>producer</I> and its output can be requested.
The following example demonstrates that a producer can have more than one
<I>consumer</I>. Each of the four productions &quot;a&quot;, &quot;b&quot;,
&quot;c&quot; and &quot;d&quot;&nbsp;produces an output token table with
the respective name. Production &quot;b&quot; and &quot;c&quot; both take
their input from production &quot;a&quot; and production &quot;d&quot;
from &quot;c&quot;. </P>

<PRE>a: ~ {$Out} ... ~
b: ~ {$In:a $Out} ... ~
c: ~ {$In:a $Out} ... ~
d: ~ {$In:c $Out} ... ~ </PRE>

<P>A request for output token table &quot;d&quot; will create the following
chain of events: production &quot;d&quot; is identified as the producer
of token table &quot;d&quot;, but needs input token table &quot;c&quot;,
so production &quot;c&quot; must be called first. &quot;c&quot; in turn
needs input &quot;a&quot; and starts production &quot;a&quot;. &quot;a&quot;
can directly start processing a primary input source (file or buffer) and
upon completion hands over token table &quot;a&quot; to production &quot;c&quot;
which upon completion hands over its output token table to &quot;d&quot;
which will finally return token table &quot;d&quot; to the caller. Note
that the event chain the order of invocation (d =&gt; c =&gt; a) is inverse
to the order of execution (a =&gt; c =&gt; d).</P>

<P>All four productions in the example declare an output token table and
they can be all requested. A call for each will result in an event chain
like the one described for token table &quot;d&quot; where several token
tables may have to be created. Once a token table is created it stays alive
and can be used later. If the request for token table &quot;d&quot; is
followed by one for &quot;c&quot; the following will happen: production
&quot;c&quot; is identified as the producer of token table &quot;c&quot;
and invoked. Since the input for &quot;c&quot;, token table &quot;a&quot;
already exists from a previous request it can be directly handed to production
&quot;c&quot; which can immediately start execution.</P>

<P>Lazy parsing requires a context that manages token tables and handles
requests for token tables. In Icarus such a context is called &quot;job&quot;.
With the command <B>$JobNew</B> a new <I>job </I>can be created and associated
with the syntax and the parsing input which can be a file or a buffer.
<B>$JobTokens</B> returns a token table with a certain name and optionally
prints its contents. <B>$JobNext</B> resets the job context so that parsing
can continue to the next item in the input. <B>$JobHasInput</B> can be
called after <B>$JobNext</B> to verify that the input input is still available
for the next job.<B>$JobEnd</B> deletes the <I>job </I>again. </P>

<P>The example with the equations can be rewritten by using the lazy parsing
mode.</P>

<PRE>$rules={
  line:     ~ {$Out} /[^\n]+\n/ {$Wrt} ~
  equation: ~ {$In:line $Out:result $Wrt:[s:$sum]} 
              variable '=' expr ~
  expr:     ~ /[0-9]+/ {$sum=$Ct} ('+' /[0-9]+/ {$sum+=$Ct})* ~
  variable: ~ /[a-z]/ ~
}
$job=$JobNew:[$rules skip:' ' s:
  |a = 10 + 2
  |a = 34 + 23
  |b = 23 + 7 + 66
  |b = 17 + 15 + 8
  |a = 103 + 85 + 1
]
while:$JobHasInput:$job {
  $JobTokens:[$job name:line print:y]
  $JobTokens:[$job name:result print:y]
  $JobNext:$job
}
$JobEnd:$job</PRE>

<P>The syntax is modified so that production &quot;equation&quot; declares
the output token table &quot;result&quot; into which it writes the contents
of the variable <B>$sum</B>. <B>$sum </B>is computed by production &quot;expr&quot;
by adding all numbers of the right hand side of the equation. The call
of <B>$JobNew</B> creates a new job variable, associates it with the syntax
stored in <B>$rules</B>, with the input specified directly in the command
(attribute <B>.s</B>), and sets the space character to be skipped as white
space. Note that the input string contains several equations, whereas production
&quot;line&quot; which 'feeds' production&quot; equation reads only one
equation at a time. When <B>$JobTokens</B> is called to print the contents
of the table &quot;result&quot;, one line in the equation list will be
processed and a single token with the computed sum printed. To process
the entire list it is necessary to iterate using the function <B>$JobNext</B>.
This function resets all token tables and marks them 'non existent' so
that a request to token table &quot;line&quot;&nbsp;will result in the
parsing of the next equation. <B>$JobTokens</B> which 'does' the actual
parsing returns value 0 at the end of input which will exit the <B>while</B>
loop.</P>

<H4><A NAME="forcedParsing"></A>Forced Parsing</H4>

<P>Lazy parsing is a model in which the <I>consumer </I>asks the <I>producer
</I>for input and thereby activates it. Forced parsing is simply the reverse
in which the <I>producer </I>upon completion finds a <I>consumer </I>who
is willing to further process the output token table. A forced parsing
link between productions must be associated with a certain &quot;task&quot;.
A task has a name and a state which can be <I>active </I>or <I>inactive.
</I>The state determines if a production associated with the task is invoked
or not. Forced parsing is useful for modifying the contents of a token
table. </P>

<P>In the example with the equation we might want to multiply all numbers
in the equation with a constant value before its evaluation. This can be
achieved by adding the production &quot;mult&quot;&nbsp;which parses and
modifies the contents of the token table &quot;line&quot;.</P>

<PRE>mult: ~ {$In:[line task:mult100]} 
        (/[0-9]+/ {$Rep:($Ct*100)} | /[^0-9]+/)+ ~</PRE>

<P>It is again the consumer, in this case the production &quot;mult&quot;
which must request the link by using function <B>$In</B>. The only difference
to defining a lazy parsing link is that the argument <B>.task</B> must
be assigned a name, in this case &quot;mult100&quot;. The production itself
replaces any number in the input with the result of that number multiplied
by 100. The function <B>$Rep</B> replaces the match of the symbol (current
token) in the input stream with what is specified as argument. In order
to execute task &quot;mult100&quot; it must be activated with the function
<B>$JobTask</B> which can precede the while loop in the example. </P>

<PRE>$JobTask:[mult100 set:on]
while:$JobTokens:[$job name:line print:y]{
  $JobTokens:[$job name:result print:y]
  $JobNext:$job
}</PRE>

<P>The request of token table will trigger production &quot;line&quot;
to read the line which will be handed over to &quot;mult&quot; for modification
and finally given to &quot;expression&quot; which computes the sum of all
integers on the right hand side of the equation. </P>

<P>It is possible that several consumer productions request forced parse
links to the same producer production. If more than one task is activated
the consumer productions will be invoked in the same order as they requested
the link. Both lazy and forced parsing can be used to create a multi-functional
and multi-layered parser that performs different actions depending on which
tasks are active and which output token table is requested.</P>

<H3><A NAME="skipwhite"></A>Skipping Whitespace</H3>

<P>An important part of parsing is the treatment of filling characters
like a space, a tab or a new line. These characters, also called <I>white
space</I>, are used for text formatting, as for example indentation, but
have usually no syntactic meaning. In Icarus the construct </P>

<PRE>foreach:[$a in:{1 2 3}] {
  $Print:$a * 100
}</PRE>

<P>can be also written as </P>

<PRE>foreach:[$a in:{1 2 3}]{$Print:$a*100}</PRE>

<P>The few remaining spaces are needed to delimit the variable name &quot;$a&quot;
or the numbers 1 and 2. In general white space characters can be ignored
which greatly simplifies the parsing process and the syntax specification.
A set of white space characters can be specified when calling the parser
with function <B>$Parse</B></P>

<PRE>$Parse:[$input prod:$rules skip:&quot;\n\t &quot;]</PRE>

<P>which parses the string stored in the variable <B>$input</B> with the
syntax rules stored in <B>$rules</B> and skipping the line feed, the tab
and the space characters. Sometimes, however, whitespace characters do play
a syntactic role and should not be skipped as is typically the case when
parsing tables stored in ASCII format where records are often separated
by line feeds and cells by tab characters. The following example is a parser
for a list of literature citations which are separated by empty lines.
Parsing is made complicated by the fact that the citations can contain
new line characters themselves. The problem can be solved by dividing the
task into two steps: </P>

<OL>
<LI>Extracting the citations delimited by the empty lines </LI>

<LI>Parsing the isolated citations </LI>
</OL>

<P>At step (1) line feed characters must not be skipped whereas at step
(2) they should be skipped. </P>

<PRE>$rules={
  item:     ~ {$Out pre $Skip:0} ln {$Wrt} empty {$Not} ln {$App} ~
  ln:       ~ /[^\n]+\n/ ~
  empty:    ~ '\n' ~
  citation: ~ {$In:item $Out pre $Skip:1} authors journal vol pp year ~
}</PRE>

<PRE>$Parse:[file:&quot;reflist.doc&quot; prod:$rules skip:&quot; \t\n &quot; start:citation]</PRE>

<P>The decision of whether or not to skip white space can be left to the
productions themselves. Productions &quot;item&quot; starts with </P>

<PRE>item:     ~ {pre $Skip:0} </PRE>

<P>which turns skipping off before the parsing of the &quot;item&quot;
starts and </P>

<PRE>citation: ~ {$In:item pre $Skip:1}</PRE>

<P>turns it on again before parsing each citation. Skipping is turned on
by default. </P>

<H2><A NAME="newicaruscom"></A>Creating New Icarus Commands</H2>

<P>Currently all Icarus commands are implemented as C functions. A special
interface makes it convenient to add new commands and to let Icarus exchange
information with the C functions. A new Icarus command is created in three
steps: </P>

<OL>
<LI>Declaration of the command, its arguments and the return value in an
Icarus program using commands <B>$Com</B> and <B>$Var</B>. </LI>

<LI>Creation of the C language implementation </LI>

<LI>Association of the C function with the Icarus command name using the
C function IcaSetFunction. </LI>
</OL>

<P>The following example creates the command <B>$Toupper</B> that converts
all lowercase characters in a string to uppercase. The command can be defined
using <B>$Com</B> which must receive the name of the new Icarus command,
the name of the C function that implements if, the list of arguments and
a description of the return value. </P>

<PRE>$Com:[Toupper f:MyToupper
  args:$Var:[s t:string unnamed:y]
  returnType:string
]</PRE>

<P><B>$Toupper</B> has the single argument of the type &quot;string&quot;
named &quot;s&quot; that may optionally be given without name (the unnamed
argument). The value returned is also of type &quot;string&quot;. After
being defined the command can be used, e.g. in a <B>$Print</B> statement
</P>

<PRE>$Print:$Toupper:&quot;hello world\n&quot;</PRE>

<P>The command definition can be put into the script which also uses the
new command, however, care must be taken that the definition is executed
before the command itself. If the command is likely to be used by more
than one script it can be 'promoted' to a built in command by placing the
definition into the Icarus file &quot;builtin.i&quot; that comes with the
Icarus distribution. After the insertion the file must be compiled with
the command </P>

<PRE>% builtin</PRE>

<P>which must be followed by rebuilding the Icarus interpreter, but before
doing that the new command should be implement in C. </P>

<P>All 'local' command implementations must be put into the file &quot;local.c&quot;.
This file already contains at least one example of a command implementation.
The implementation function needs support from Icarus for receiving arguments
and returning a value. IcaGetArgs retrieves the arguments with which the
Icarus was called by their names which are separated by bars in the first
argument which is followed by the addresses where the values should be
stored. One specialty of Icarus is that it can be converted to a C language
program. In that case the functions that implement Icarus commands are
called directly with their arguments. To provide for that the first argument
of MyToupper must be of type Int4 which will have the value 1 if called
from the normal interpreter or 0 if called from a compiled C program. The
arguments for both calling modes are declared then in the argument list.
</P>

<PRE>STRv MyToupper (Int4 runTime, STRv s)
{
  if (runTime)
  IcaGetArgs (&quot;s&quot;, &amp;s);

  StrToupper (&amp;s);
  if (runTime)
    IcaReturn (&quot;string&quot;, s);
  else
    return (s)
}</PRE>

<P>The function can return values back to the Icarus interpreter using
IcaReturn or if called from a compiled interpreter by directly returning
the value. The first argument of IcaReturn is the type name which is used
to allow type checking which becomes more useful when pointers to C structures
are returned. </P>

<P>At the bottom of local.c you will find the function <B>LocalInitFunctions</B>.
In its body insert the statement </P>

<P><B>IcaSetFunction (&quot;MyToupper&quot;, (Func)MyToupper);</B> </P>

<P>The type casting of &quot;MyUpper&quot; casts it to a standard function
prototype. </P>

<P>To create a new Icarus interpreter run the command </P>

<P><B>srsmake icarus</B> </P>

<P>which will compile the file local.c and link it to the interpreter.
In case the new command was declared in &quot;builtin.i&quot; this will
also recompile the interpreter itself. </P>

<H1><A NAME="_Toc359130292"></A>Glossary </H1>

<H3><A NAME="attribute"></A>Attribute</H3>

<P>Property, data member, or method of an <A HREF="#object">object</A>.
Members and methods can be interchangeable to some extent: e.g. the sequence
length instead of being stored in the object can also be calculated each
time it is requested. An attribute has a value, such as &quot;5&quot; or
&quot;Jack&quot; and a type, such as &quot;integer&quot; or &quot;string&quot;.</P>

<H3><A NAME="class"></A>Class</H3>

<P>A class is a blueprint or prototype that defines the attributes and
methods common to all <A HREF="#object">objects </A>of a certain kind.
A class can also be said to define a data type. </P>

<H3><A NAME="expression"></A>Expression</H3>

<P>A meaningful combination of operands and operators, e.g., &quot;2 +
3 * 6&quot;.</P>

<H3><A NAME="grammaticrule"></A>Grammatic Rule </H3>

<P>See <A HREF="#production">production</A>. </P>

<H3><A NAME="_Toc359130297"></A>Instance </H3>

<P>One of possibly many actual <A HREF="#object">objects</A> that exist
for a given <A HREF="#class">class</A> </P>

<H3><A NAME="_Toc359130298"></A>Lexeme </H3>

<P>A lexeme is a sequence of characters in the source program that is matched
by the pattern for a token. </P>

<H3><A NAME="_Toc359130299"></A>Link </H3>

<P>A link is an pointer to any structured data. </P>

<H3><A NAME="_Toc359130300"></A>Match </H3>

<P>A match is an agreement between a symbol and the input stream. </P>

<H3><A NAME="nonterminal"></A>Nonterminal </H3>

<P>A nonterminal is a syntax element defined by a production. </P>

<H3><A NAME="object"></A>Object </H3>

<P>a physical and logical unit containing attributes (data members) and
behaviour (methods) each object of the same class or type has the same
set of attributes and behaviour. </P>

<P>OR ? </P>

<P>Objects are software bundles of data and related procedures. Software
objects are often used to model real-world objects you find in everyday
life. </P>

<H3><A NAME="_Toc359130304"></A>Parsing</H3>

<P>Parsing or syntax analysis, as it sometimes known, is a process in which
the string of tokens is examined to determine whether the string obeys
certain structural conventions explicit in the syntactic definition of
the language. </P>

<H3><A NAME="pattern"></A>Pattern </H3>

<P>A pattern is a production describing the set of lexemes that can represent
a particular token in source programs. </P>

<H3><A NAME="production"></A>Production </H3>

<P>same as (grammatic) rule, production has a name and a list of symbols
to be matched against the input stream </P>

<H3><A NAME="_Toc359130307"></A>Recursion </H3>

<P>A recursive function or production includes, as one of its steps, the
invocation of itself. </P>

<H3><A NAME="regularexpression"></A>Regular Expression </H3>

<P>Regular expressions are an important notation for specifying patterns.
Each pattern matches a set of strings. </P>

<H3><A NAME="rule"></A>Rule </H3>

<P>Same as <A HREF="#production">Production</A>. </P>

<H3><A NAME="symbol"></A>Symbol </H3>

<P>terminal or nonterminal </P>

<H3><A NAME="terminal"></A>Terminal </H3>

<P>A terminal defines a lexical element of a syntax (literal or <A HREF="regularexpression">regular
expression</A>). During the parsing process it is directly compared with
the input.</P>

<H3><A NAME="token"></A>Token</H3>

<P>A token has a code and a string. The string is often the part of the
parsing input that matches against a <A HREF="#terminal">terminal </A>or
nonterminal. </P>

<H3><A NAME="tokentable"></A>Token Table </H3>

<P>A token table contains one or more <A HREF="#token">tokens </A>and a
name. It can be both input and output of a parsing process.</P>

</BODY>
</HTML>
arexpression">regular
expression</A>). During the parsing process it is directly compared with
the input.</P>

<H3><A NAME="token"></A>Token</H3>

<P>A token has a code and a string. The string is often the part of the
parsing input that matches against a <A HREF="#terminal">terminal </A>or
nonterminal. </P>

<H3><A NAME="tokentable"></A>Token Table </H3>

<P>A token table contains one or more <A HREF="#token">tokens </A>and a
name. It can be both input and output of a parsinsrs/www/doc/install.html
<!-- $Revision: 1.1 $ -->
<!-- $Date: 1997/03/04 10:50:08 $ -->
<!-- $Author: srs $ -->
<HTML>
<BODY>
<H1><A NAME="install"></A>Installation of SRS</A></H1>


The following is for the release SRS4.05 and later. 
If you have any suggestions or problems with
the installation please contact me.
<BLOCKQUOTE>
<B>e-mail:</B> etzold@embl-heidelberg.de
</BLOCKQUOTE>
 <P>
<H2><A NAME="instruct"></A>Instructions</H2>

Before you compile any of the programs edit the file "srs4_0/odd/srsdb.sdl".
You must customize the object 'environment' with the name "unix" 
("vms" on VMS).
Add or modify a 'libenv' definition for each databank that you would like to 
index with SRS. Remove or outcomment all 'libenv' definitions of databanks you
don't have. Each databank must be associated with the name of the directory
with the flatfiles.
<H5>Example:</H5>
<PRE>   #libenv /lib=@EMBLNEW_DB    /dir="/data/emnew/"
</PRE>

<P>
Some sequence databanks have a special format when used under GCG 
(EMBL, GenBank, SwissProt). For each of these edit the respective files
("embl.sdl", "genbank.sdl", "swissprot.sdl"). 
<OL>
<LI>You must change the
file name(s) defined in 'file' objects; eg, the EMBL file "fun" is usually
called "em_fun" under GCG. 
<LI>In the 'libformat' definition for these databanks change the 'file_type'
attribute so that it points to 'GCGREF_FILE' and 'GCGSEQ_FILE'. It is all
there - all you have to do is move the begin-of-comment character ('!'). 

</UL>


Now 'go' to the root directory of SRS ("srs4_0") and invoke "srsinstall":
<PRE>&gt; srsinstall all</PRE>
This script asks you for the 'make' and 'cc' commands, compiles
all the programs and, using the ODD compiler, creates a new
binary file with all data defined by the files in the 'odd' directory.
 <P>
To build the indices 'source' the file "etc/prep_srs" and 
issue the command
<PRE>&gt; srscheck</PRE>
If it complains then, if a path or file name is at fault, edit the appropriate
file in the directory "odd" (eg, "srsdb.sdl") and run "srssection" to 
recompile the ODD files.
 <P>
If anything went well, build the indices with

<PRE>&gt; srsbuild</PRE>

"srsbuild" invokes the script that was generated by "srscheck". You can create a crontab file
with these two commands to keep the indices up to date automatically.
 <P>
The only program you can use for searching is the command line interface "getz". You can invoke
it in two ways: Either prepare the SRS environment with
<PRE>&gt; source srs4_0b/prep_srs</PRE>
or copy the file "$SRSEXE/getz" ("SRSEXE" is by running "prep_srs") to a directory that is 
included in your path (eg, "/usr/bin").
Try the following commands:


<BLOCKQUOTE>
<DL>
<DT> 
<PRE>&gt; getz -help </PRE> 
<DD> prints all command options (the same is true for "srsbuild", "srscheck") 
<DT> 
<PRE>&gt; getz -libs </PRE> 
<DD>prints status of all indexed libraries
<DT> 
<PRE>&gt; getz -info swissprot </PRE> <DD>  prints more information on a single databank
<DT> 
<PRE>&gt; getz '[swissprot-def:elastase]' -f 'id def'</PRE>
 <DD> searches all "elastases" in swissprot and
prints the "ID" and "Definition" fields of all found entries
</DL>
</BLOCKQUOTE>


 <HR>

<H2><A NAME="WWWinst"></A>Additional Steps to Install the SRSWWW Server</H2>
<UL>

<LI> Run the "srsinstall" again with option "www"

<PRE>&gt; srsinstall www</PRE>

<LI> 
The executables and the document files are, at least to the knowledge of the 
server,  situated in two different 
directories 'srs' and 'srsdoc' respectively.
Add the script alias 'srs' in the file 'srm.conf': 
<PRE>ScriptAlias /srs/ /usr/local/srs/www/</PRE>
and the alias 'srsdoc' in the same file:
<PRE>Alias /srsdoc/ /usr/local/srs/www/</PRE>
or add the symbolic link 'srsdoc' into the httpd's document root.
 <P>
<I>If for some reason the names 'srs' and 'srsdoc' are not acceptable you
can change them (eg, if you want to run two different SRSWWW servers in 
parallel). 
<BR>
To change the directory name with the executable, 'srs', replace the 
string '/srs/' in 'odd/hyperlink.sdl' and if you 
you don't make your own network images (see below) 'www/srswww.map'. 
Edit the file 'www/wgetz.script' and change the assignment to 'cgidir'.
 <BR>
To change the directory name 'srsdoc' edit the files www/wgetz.script' and
'www/wgetz_text.script' and change the assignments to 'docdir'.
</I>  
 <P>
<LI> For the clickable map the location of the program 'imagemap' must be
defined in the file 'www/wgetz.script' (assignment to the variable 'imagemap').
This file contains also variables with the path of the file with the 
icon link to your homepage ('homePageIcon') and your 
homepage's URL ('homePageURL') that will both be used in the top page of 
SRSWWW.
 <P>
<LI> You can now access the with the URL "http://serverAddress/srs/srsc"
 <P>
<LI> Each user of the server will get his own directory in "srs4_0b/www/tmp". The directory and
the file "user.par" don't take much space but will have to be deleted occasionally. A "crontab"
job can handle that.
 <P>
<LI> SRSWWW inserts many hypertext links into the entries before display.
These often request SRSWWW to 
retrieve an entry from a databank installed locally. 
You must change the configuration of the hypertext links if one or more of the
databanks addressed are missing.
<BR>
Edit the file "hyperlink.sdl". There you find definitions of 'linkcall' 
objects. The first link to medline already suggests a the alternative of
a link directly 
to medline. In other cases you may address SRSWWW servers installed
on other nodes; eg, replace "/srs/srsc" by "www.embl-heidelberg.de/srs/srsc".
After the changes you must run the command "srssection" to recompile the
ODD files!



</UL>


<H2><A NAME="optional"></A>Optional</H2>
<UL>
<LI> SRSWWW builds almost every HTML page during run-time. You can, to 
some extent, change their layout and content. <BR>
Edit the file 
"srs4_0b/www/wgetz.script". You find here the templates for all pages. 
The file contains 
labels that start with "@@" and directives for the insertion of
 numbers ("%d") and strings ("%s").  You can change anything except the
order and content of labels and directives.
<P>
<LI> You can create your own network image! This is a new feature and the
following procedure has been tested only at the EMBL:
 <P>
 <UL>
 <LI> Set the default to the directory 'www' and run the program 'srsnet.tcl'.
It is a tcl script that requires 'wish' with a tk version 3.x or 4.0.
Use command 'load' to load all databank icons onto the canvas. At the first
time the file 'srsnet.dat'with coordinates is missing and all the databanks
will be put into a vertical row. Now move all databank icons around until
you are satisfied (use left mouse button) and save the databank's coordinates
with the 'save' option.
<P>
<I> If some time later you add new databanks they will appear at the left top
corner of your network picture - simply drag them to a more appropriate
location.
</I> 
 <P>
<LI> 
Make the program 'srspict' with
<PRE>
srsmake srspict
</PRE>
 <P>
<LI> 
Run the command
<PRE>
srspict -n
</PRE>
to create the network picture. This will read the coordinates you saved 
within 'srspict.tcl' and produce a GIF file and the map file for the httpd. 
 <P>
 <LI>
Run the command 
<PRE>
srspict -t
</PRE>
to produce both the GIF file with the network as tabular diagram and the map file (This does not require the coordinates).
 <P>
 <LI>
Tell SRSWWW to use your own GIF files by editing the file 'www/wgetz.script'.
Just flip around the comment character ('#') so that 'NEWNETWORK' is defined:
<PRE>
@@# OLDNETWORK = 'NETWORK'
@@ NEWNETWORK = 'NETWORK'
</PRE>


</UL>
</UL>
<HR>
</BODY>
</HTML>
srspict.tcl' ansrs/www/doc/internal.html
<head>
   <title>Identification Convention </title>
   <meta name="GENERATOR" content="Mozilla/3.0b4Gold (Unix)">
</head>
<body>

<h1><a name=internal>Internal Documentation</A></h1>
The following is intendend for SRS developers only.

<h2><a name=idconv>Identification Convention</a></h2>
This defines naming conventions to be used in all C-language modules

<h3><a name=general>1. General</A></h3>

<p>All identifiers should be in <i>NameName</i> format. If identifier name
has more that one tag, every tag (except the first) starts from a capital
letter. </p>

<h5>Example:</h5>

<pre>tokenListName</pre>

<h3><a name=public>2. Public</A></h3>

<h4><a name=func>2.1 Function names: </A></h4>

<p>Function names should start from (short) capitalized module tag followed
by a function name in <i>NameName</i> format. </p>

<h5>Example:</h5>

<pre>IcaFunctionCall 
</pre>

<h4><A NAME="variable">2.2 Variable Names: </A></h4>

<p>Variable names (external and static) should start from a module tag
and a name in <i>NameName</i> format. </p>

<h5>Example:</h5>

<pre>icaGlobalScope
</pre>

<h4><A NAME="macroname">2.3 Names of Macro Functions:</A> </h4>

<p>Macro names should start from the underscore character, a capitalized
module tag and a name in <i>NameName</i> format. </p>

<h5>Example:</h5>

<pre>#define _IcaPrintError(x) printf(&quot;%d\n&quot;, (x))
</pre>

<h4><A NAME="macroandenum">2.4 Names Macro and Enumeration:</A> </h4>

<p>Macro names should start from all capitalized module tag plus &quot;x&quot;
and a name in <i>NameName</i> format. </p>

<h5>Example:</h5>


<pre>#define ICAxMaxNameSize 32
enum repeat {BNXxOne, BNXxZeroOrMore, BNXxZeroOrOne, BNXxOneOrMore};
</pre>

<h4><A NAME="typenames">2.5 Type Names: </A></h4>

<p>Type names should start from all capitalized module tag plus &quot;o&quot;
and a name in <i>NameName</i> format. For pointer to the structure instead
&quot;o&quot; should be &quot;p&quot;, for counted pointer it changes to
&quot;v&quot;. </p>

<h5>Example:</h5>

<pre>typedef struct ICAoProdName { ... }  ICAoProdName,
                                    *ICApProdName,
                                    *ICAvProdName;
</pre>

<h3><A NAME="exceptions">3. Exceptions</A></h3>

<h4><A NAME="defc">3.1 def.h and def.c:</A> </h4>

<p>There are several constants, variables and functions that have common
meaning like maximum or minimum macros. All this stuff should be placed
in def.h and def.c files. Those file have &quot;personal sections&quot;
where every person of SRS team should put his own variables. All variables
in those files do not have module tag and start from a capital letter.
</p>

<h5>Example:</h5>


<pre>#define True 0
typedef Int4 int;
</pre>

<h3><A NAME="functionhead">4. Function Head Description</A></h3>

<p>Function head has a format represented bellow: </p>

<pre>/****** RegWildToRegexp *************************************************
**
**      converts a string containing wildcards into a regular
**      expression; the world can contain the wildcards '*' (any number
**      of chars) and '?' (any single character); the function returns
**      the position of the first wildcard within the word (first
**      position is 1!); &quot;.&quot; is converted to &quot;\.&quot;
**      expression will begin with '^' and end with '$';
**
**      INPUT:   o string containing wildcards [R]
**               o pointer to output regular expression [R]
**               o flag if wildcards (see above) are to be recognized as
**                 such and be replaced within a regular expression [R]
**
**      RETURNS:  0 if word contains no wildcards
**                position of the first wildcard in string (1=string begin)
*/      
</pre>

<p>The first line has the format &quot;/****** FunctionName ********&quot;
than a description of the function. The &quot;INPUT&quot; and &quot;RETURNS&quot;
are essential part of the head. If argument description too long to fit
in one line all the argument descriptions should have a prefix &quot;o&quot;
as in the example above. The last line has a format &quot;*/&quot; </p>

<p>
<hr size=12 width="100%" ></p>

<h2><a name=docconvent>Documentation Convention</A></h2>

<h3><a name=names>1. Names</A></h3>

<table border=1 cellpadding=5 >
<tr>
<td>Icarus Functions, Icarus Variables</td>

<td><b>$name</b> </td>
</tr>

<tr>
<td>SRS&nbsp;classes</td>

<td><b>$name</b></td>
</tr>

<tr>
<td>attributes of SRS classes</td>

<td><b>.name</b></td>
</tr>

<tr>
<td>names</td>

<td>'string'</td>
</tr>

<tr>
<td>characters</td>

<td><tt>courier</tt></td>
</tr>

<tr>
<td>value </td>

<td>&quot;string&quot;</td>
</tr>

<tr>
<td>C Functions</td>

<td><b>name</b></td>
</tr>

<tr>
<td>C structures</td>

<td><tt>name</tt></td>
</tr>

<tr>
<td>C variable names</td>

<td><i>name</i></td>
</tr>

<tr>
<td>examples</td>

<td><tt>courier</tt>
<p>short one in quotes</p>
</td>
</tr>
</table>

</body>
</html>
>
<td>attributes of SRS classes</td>

<td><b>.name</b></td>
</tr>

<tr>
<td>names</td>

<td>'string'</td>
</tr>

<tr>
<td>characters</td>

<td><tt>courier</tt></td>
</tr>

<tr>
<td>value </td>

<tdsrs/www/doc/prog.html
<head>
   <title>t</title>
   <meta name="GENERATOR" content="Mozilla/3.0b4Gold (Unix)">
</head>
<body text="#000000" bgcolor="#FFFFF0" link="#0000FF" vlink="#FF0000" alink="#FF0000">
<h1><a name="progamming"></a>Programming in SRS</h1>

<h2><a name="intro"></a>Introduction</h2>

<p>It is very easy to write programs that use all of SRS's power to retrieve,
link and access entries from all indexed databanks. Just link your program
to the SRS library (written in C, documentation will be available). The
file &quot;srs4_0b/src/try.c&quot; is an example of such a program: </p>

<pre>#include &lt;stdio.h&gt;
#include &quot;srs.h&quot;

int main ()
{
  SrsEnv ();
  LibOpen ();

  if (Query (&quot;[swissprot-def:elastase]&quot;, &quot;Q1&quot;))
    printf (&quot;query Q1 found %d entries\n&quot;, SetSize (&quot;Q1&quot;));
}
</pre>

<p>The program must (in that order) </p>

<ul>
<li>include the file &quot;srs.h&quot; (in the directory &quot;$SRSROOT/src&quot;);
</li>

<li>call the function SrsEnv (without arguments) that defines all SRS directory
names; </li>

<li>call the function LibOpen with the name of the binary file containing
all run time data, eg, all information about the indexed libraries. </li>
</ul>

<p>The program can be compiled (and run) anywhere: </p>

<pre>&gt; cc -I$SRSSOU -I$SRSEXE try.c $SRSEXE/libsrs.a $SRSEXE/local.o -o try
</pre>

<p>The variable &quot;SRSEXE&quot; is defined by executing (sourcing) the
C-shell script &quot;prep_srs&quot; (or for Bourne-shell
&quot;prep_srs.sh&quot;) (see above). </p>

<p>Note that modules without a &quot;main&quot; section must define the
macro &quot;DECLARE_ONLY&quot; before including &quot;srs.h&quot;. </p>

<h5>Example:</h5>

<pre>#define DECLARE_ONLY
#include &quot;srs.h&quot;
</pre>

<p>
<hr></p>

<h2><a name="examples"></a>Programming Examples</h2>

<p>All program examples given are complete. Each example can be compiled
as shown for the program &quot;try.c&quot; in the <a href="http://www/srsdoc/srsman_prog.html#introduction">introduction</a>.
</p>

<h3><a name="PROG_1"></a>Performing queries </h3>

<p>The function Query lets you submit any <a href="http://www/srsdoc/srsman_query.html">SRS
query language</a> expression. Each query must be associated with a name.
If successful, that name lets you access the resulting set or can be used
within further query expressions. The following retrieves all &quot;receptor&quot;
sequences from EMBL and, using SetSize, prints the size of the resultant
set. The next query searches &quot;acetylchol*&quot; and performs an AND
operation with &quot;Q1&quot; from the previous query. The last two queries
link &quot;Q2&quot; to SwissProt by both <a href="http://www/srsdoc/srsman_query.html#linkop">link
operators</a>.</p>

<p>INCLUDE EXAMPLE:query.c</p>

<h3><a name="PROG_2"></a>Printing Entries </h3>

<p>Three steps are required to access a single entry from a successful
query: </p>

<ul>
<li><font COLOR="#000000">SetGet</font> uses the query name to retrieve
the set object (<tt><font COLOR="#000000">SETo</font></tt>). </li>

<li><font COLOR="#000000">SetGetID</font> retrieves the nth ID-object (<tt><font COLOR="#000000">IDoENTRY</font></tt>)
from the set object. </li>

<li>EntryOpen uses the ID-object to create an entry object (<tt><font COLOR="#000000">ENTRYo</font></tt>).
Use EntryClose to delete this object after use. </li>
</ul>

<p>Once the entry is opened the annotation and, if exists, the sequence
can be obtained. Here only the &quot;ID&quot; and the &quot;Definition&quot;
data-fields are extracted from the entry and printed by EntryPrintFields.
The two fields are selected using the function ParDefStr to successively
assign the global parameter &quot;fieldList&quot; the values &quot;Definition&quot;
and &quot;ID&quot;. This method to define global parameters accessible
by all functions in the library is commonly used. &quot;fieldList&quot;
can be reset by assigning the value &quot;reset&quot;. You will see more
examples of that in other programs where even functions are assigned as
parameter values. </p>

<p>INCLUDE EXAMPLE:prfields.c</p>

<h3><a name="PROG_4"></a>Accessing Information About the Databanks </h3>

<p>This program accesses information about the databanks seen from SRS.
The run-time-library provides iterators to access library group, library,
and respective data-field information ( <font COLOR="#000000">LibNextLibGroup</font>,
<font COLOR="#000000">LibNextLib</font>, <font COLOR="#000000">LibNextField</font>).
For iterating over all libraries (databanks) one must first iterate over
the group and then descend to the libraries. The function <font COLOR="#000000">LibIsField</font>
can be used to obtain more information about the data-field. </p>

<p>INCLUDE EXAMPLE:libinfo.c</p>

<h3><a name="PROG_4b"></a>Accessing Information About a Single Databank</h3>

<p>The example accesses for the databank "Swissprot" information that is
stored in its indices. The function LibIndexOpen can be used to open all
index files pertaining to a certain data-field, in this case the ID-field.
The indices of the ID-field contain information about the databank such as
release name or number of entries.

<P>
INCLUDE EXAMPLE:libinfo2.c</p>

<h3><a name="PROG_6"></a>Redefining Message Processing</h3>

<p>SRS prints quite a few error messages, warnings and informational messages
to &quot;stderr&quot;. The function <font COLOR="#000000">MsgSetFnct</font>
allows you to redefine the function that prints these messages. When called
it receives a pointer to the message object <tt><font COLOR="#000000">MSGo</font></tt>
as argument and must always return 1. </p>

<p>The message object <tt><font COLOR="#000000">MSGo</font></tt> contains
several fields with the message type, the message name, etc. The message
name (eg, &quot;e__objectunknown&quot;) is defined as macro, so it can
be directly used for comparisons (see <i>switch</i> statement below). </p>

<p>The example performs three queries, where only the last is successful
since the first two specify incorrect databank and data-field names. The
assignment to the global parameter &quot;libList&quot; is also incorrect
since the data-field name is misspelt. </p>

<p>INCLUDE EXAMPLE:msguse.c </p>

<h3><a name="constrquery"></a>Constructing an SRS query expression</h3>

<p>If you write a user interface to SRS you might create a form displaying
all the searchable indices plus some more search options. The user input
would have to be collected and combined to an SRS query string which can
be submitted to the function Query. The functions in the &quot;queryassist&quot;
module help you to construct that query expression. It is possible to construct
a query step by step and at the end ask for the complete expression. The
example first constructs a query with a string search and a range search
in two databanks. The resulting string is then used to generated a link
expression.</p>

<p>INCLUDE EXAMPLE:qasuse.c</p>

<h3><a name="views"></a>Printing Entries with Views</h3>

This prints a set of SWISS-PROT entries with a view defined in the program.

<p>INCLUDE EXAMPLE:views.c</p>

</body>
</html>
construct that query exsrs/www/doc/query.html
<HEAD>
<TITLE>SRS functions list</TITLE>
</HEAD>
<BODY BGCOLOR="#fffff0" LINK="#0000ff" VLINK="#ff0000" 
	ALINK="#ff0000" TEXT="#000000">
<BASE TARGET="text">
<!doctype html public "-//IETF//DTD HTML//EN">
<HTML>


<H1><A NAME="srsquerylang"></A>The SRS Query Language </H1>

<P>
In SRS any retrieval command, logical operations with sets that
were obtained by previous queries, links between sets of different
databanks, or a combination of all can be expressed by the SRS
query <A NAME=language></A>language. This chapter describes the language and gives
examples of its use.<HR>

<H2><A NAME="syntax"></A>General Syntax</H2>

<P>
A query is an <A NAME=expression></A>expression with operands and operators. In this
chapter queries are sometimes shown as equations in the form
<BLOCKQUOTE>
<I> queryName = expression</I> 
</BLOCKQUOTE>

<P>
The query name will be associated with the resultant set of entries.
Expressions can specify index searches, logical operations between
sets and link operations or a combination of all.
<H3><A NAME="ListOfOp"></A>List of Operators</H3>

<DL>
<DT>|
<DD>Logical OR.
<DT>&amp;
<DD>Logical AND.
<DT>!
<DD>Logical AND NOT, or in colloquial English, BUT NOT.
<DT>&gt;
<DD>Link to the right operand.
<DT>&lt;
<DD>Link to the left operand.
</DL>

<P>
The link operators have precedence over logical operators.
<H3><A NAME="ListOfOpnd"></A>List of Operands</H3>

<DL>
<DT>Name of a Databank
<DD>In SRS only one name for each databank is used (eg, &quot;EMBL&quot;).
Currently only the link operators accept the databank name as
a valid operand.
<DT>Set Name
<DD>Each query must be given a name (eg, &quot;Q1&quot;) which
can be later used to operate on the set that results from that
query.
<DT>Index Search
<DD>A command to search in one or more indices of one or more
libraries.
<DT>Expression
<DD>An <A NAME=expression></A>expression is treated as an operand if it occurs within
parentheses (eg, &quot;(Q1&amp;Q2)&gt;EMBL&quot;). Parentheses
can be nested to any degree.
<DT><TT><B>parent</B></TT> 
<DD>Special operand that allows the conversion of a set of subentries
(eg, sequence features) into a set of entries (sequence entries).
This is achieved by linking the set with the subentries to &quot;parent&quot;
(eg, &quot;Q1 &gt; parent&quot;).
</DL>

<P>
A query can be minimally a single operand excluding databank names
and the &quot;parent&quot; keyword.<HR>

<H2><A NAME="index_search"></A>Searching in Indices</H2>

<P>
This command specifies a search in a single index or a group of
indices of one or more databanks. An index search must specify
within square brackets the databank or databank group name, the
index or index group name, and a search <A NAME=expression></A>expression. The two names
must be separated by a hyphen ('-') and be separated from the
search expression by a ':' (string search) or a '#' (range search).
Both the field name (eg, &quot;Definition&quot;) and its abbreviation
(&quot;DEF&quot;) can be used as index name. All <A NAME=strings></A>strings, including
the search words, are treated case insensitive.
<H5>Example:</H5>

<DL>
<DT><TT><B> [pir-def:elastase]</B></TT> 
<DD>searches &quot;elastase&quot; in the DEFinition field of the
protein databank PIR.
</DL>

<P>
As indicated above two different types of searches, the string
search and the range search exist. A string search <A NAME=expression></A>expression
starts with a colon (':') after the index name whereas the range
search starts with a hash ('#'). Range searches can be performed
only in indices of the types &quot;num&quot; and &quot;real&quot;
<H3><A NAME="string_search"></A>Searching Strings</H3>

<P>
A search <A NAME=expression></A>expression is a single search word or several words separated
by a logical operator. Parentheses may be used for grouping.
<H5>Examples:</H5>

<PRE>
[embl-key:insulin]
[medline-aut:needleman,*!wunsch,*]
[embl-def:(acetylchol*&amp;receptor)!muscarinic]
</PRE>

<P>
Wildcards are useful for searching a group of words or whenever
it is unclear how a word is spelt in the databank. You can use
two different types of wildcards:
<DL>
<DT>*
<DD>Matches one or more characters of any value;
<DT>?
<DD>Matches a single character of any value,
</DL>

<P>
Any number of wildcards can be placed anywhere in the search word.
If you place one at the beginning you might have a slightly longer
response time since then <B>all</B> words of the index have to
be searched. But don't worry too much about that - it is still
quite fast!
<H4><A NAME="regExp"></A>Regular Expressions</H4>

<P>
Since search words with wildcards are translated into <A NAME=regular></A>regular
expressions, it is of course possible to enter regular expressions
directly. They must appear within forward slashes ('/'). Some
characters (&quot;^$.[]()?+*&quot;) have a special meaning. They
must be prefixed with a backslash ('\') if to be matched literally.
<DL>
<DT>^
<DD>marks the begin of a string, eg, &quot;/^phos/&quot; will
find all words beginning with &quot;phos&quot;, eg, &quot;phosphate&quot;.
<DT>$
<DD>marks the end of a string, eg, &quot;/ase$&quot; will find
all words ending with &quot;ase&quot;, eg, &quot;kinase&quot;.
<DT>.
<DD>means any character.
<DT>[...]
<DD>indicates a set of characters to match, eg &quot;[()]&quot;
matches an opening or closing parenthesis. Character ranges can
be specified by using a hyphen ('-'), eg &quot;[0-9]&quot; matches
a digit. A caret ('^') in front of the character set (after the
opening square bracket) negates the character set, eg, &quot;[^0-9]&quot;
matches any non-digit character.
<DT>(...)
<DD>Groups a series of pattern elements to a single <A NAME=element></A>element.
<DT>*
<DD>The preceding group may be repeated zero or more times.
<DT>+
<DD>The preceding group may be repeated one or more time.
<DT>?
<DD>The preceding group may or may not occur.
</DL>

<H5>Examples:</H5>

<DL>
<DT><TT><B>/^j..$/</B></TT> 
<DD>finds all 3 character strings with a j at the begining;
<DT><TT><B>/^5[0-9][0-9][0-9]$/</B></TT> 
<DD>finds all 4 digit numbers with a five at the begining;
<DT><TT><B>/^nif[a-e]$/</B></TT> 
<DD>finds the gene names &quot;nifa&quot;, &quot;nifb&quot;, &quot;nifc&quot;,
&quot;nifd&quot;, &quot;nife&quot;;
<DT><TT><B>/^mue?ller$/</B></TT> 
<DD>finds both &quot;muller&quot; and &quot;mueller&quot;.
</DL>

<P>
Note that searches with <A NAME=regular></A>regular expressions can be slow since
<B>all</B> words in the index have to be searched.
<H3><A NAME="range_search"></A>Searching Numeric Ranges</H3>

<P>
In a numeric index (integers, reals) it is possible to search
numeric ranges. The number index is only applicable where there
is a one to one relationship of entry and value (eg, sequence
length, creation date, resolution)
<P>
A range can be specified by a single value or two values separated
by a colon (':') where the left value must be smaller than the
right value. To exclude a boundary value from the range put a
'!' in front. A missing number on the left means the minimum,
and on the right the maximum value in the index.
<H5>Examples: </H5>

<BLOCKQUOTE>
The following are queries in an index of the sequence length.
</BLOCKQUOTE>

<DL>
<DT><TT><B>400</B></TT> 
<DD>selects all sequences with the length of 400
<DT><TT><B>400:500</B></TT> 
<DD>selects all sequences from 400 to 500 residues
<DT><TT><B>400:</B></TT> 
<DD>selects all sequences longer than 400 residues
<DT><TT><B>:500</B></TT> 
<DD>selects all sequences up to 500 residues
<DT><TT><B>400:!500</B></TT> 
<DD>selects all sequences between 400 and 500 residues excluding
500
<DT>:
<DD>is also valid and retrieves ...<B>all</B> sequences
</DL>

<P>
Note that ranges can be combined by logical operators.
<H5>Example: </H5>

<DL>
<DT><TT><B>300:!500 | !600:700<BR>
</B></TT> 
<DD>or
<DT><TT><B>300:700 ! 500:600</B></TT> 
<DD>retrieve the same set of sequences, namely all sequences from
300 to 500, excluding 500, plus all sequences from 600 to 700
where the 600 is excluded.
</DL>
<HR>

<H2><A NAME="logop"></A>Using Logical Operators</H2>

<P>
The three logical operators OR ('|'), AND ('&amp;') and BUTNOT
('!') can be used to combine search words in an index search,
or sets in a query expressions. The figure illustrates the effect
of the three operators in an <A NAME=expression></A>expression of the form &quot;A operator
B&quot;
<P>
<IMG align=top src="../images/logop.gif"> 
<P>
Within expressions, parentheses with any degree of nesting are
allowed.
<H5>Examples:</H5>

<PRE>
[medline-authors:(wu* &amp; rice*) ! (smith* | jones*)]
(q2 &amp; q2) ! (q3 &amp; q4)
</PRE>

<P>
Logical operations can be only performed between two sets of the
same type. It is not possible to combine a set of entries and
a set of subentries (see below). In those cases an additional
link operation must be specified.<HR>

<H2><A NAME="linkop"></A>Using Link Operators</H2>

<P>
The powerful <B>link</B> operators are unique in the SRS query
<A NAME=language></A>language. They to some extent resemble the <B>join</B> in relational
databank systems. The two link operators '&lt;' and '&gt;' combine
two sets from different databanks.
<P>
The figure shows two databanks &quot;A&quot; and &quot;B&quot;
where some entries in &quot;A&quot; have cross references to entries
in &quot;B&quot; as indicated by red lines. These cross references
are processed to build link indices which provide the basis for
the link operation.
<DL>
<DT><TT><B>A &gt; B</B></TT> 
<DD>gives those entries in &quot;B&quot; that <B>are referenced</B>
by entries in &quot;A&quot;
<DT><TT><B>A &lt; B</B></TT> 
<DD>gives those entries in &quot;A&quot; that reference entries
in &quot;B&quot;
</DL>

<P>
<IMG align=top src="../images/linkop.gif"> 
<P>
References are by nature not bidirectional, that is, there is
no guarantee that entries in &quot;B&quot; that are referenced
by entries in &quot;A&quot; have references back to &quot;A&quot;.
The link indices in SRS, however, can be always used bidirectionally.
The two link <A NAME=expression></A>expression can now be seen as:
<DL>
<DT><TT><B>A &gt; B</B></TT> 
<DD>gives those entries in &quot;B&quot; that <B>are linked</B>
to entries in &quot;A&quot;
<DT><TT><B>A &lt; B</B></TT> 
<DD>gives those entries in &quot;A&quot; that are linked to entries
in &quot;B&quot;
</DL>

<P>
In this context it is irrelevant which databank contributed the
information for building the link index.
<H5>Example:</H5>

<DL>
<DT><TT><B>[swissprot-def:kinase] &gt; PDB</B></TT> 
<DD>The index search retrieves all kinase sequences from the SwissProt
protein sequence databank which are then linked to the PDB databank
of solved tertiary protein structures. The result is all the PDB
entries with atomic coordinates for all kinases for which the
tertiary structure has been determined.
</DL>

<P>
In SRS all the pairwise links are combined to generate a network
of databanks. Within this network a link can be performed from
any databank to any other. If two databanks are not directly connected
by a link then a series of links is performed. The following rules
are applied resolve links:
<UL>
<LI>The same pairwise link index is used for both directions.
<LI>SRS tries to find the shortest possible way for linking entries
from two libraries. Ideally this is the direct link as, eg, between
EMBL and SwissProt; if no direct link is available (eg, EMBL &gt;
PDB) then automatically the optimal or cheapest succession of
links is performed (eg, EMBL &gt; SwissProt &gt; PDB).
<LI>If a set contains entries from different databanks (eg, from
EMBL and SwissProt) then the subsets of all libraries found in
the set are linked independently.
</UL>

<H5>Examples:</H5>

<DL>
<DT><TT><B>enzyme &lt; pdb </B></TT>
<DD>The Enzyme databank contains all known reactions catalyzed
by enzymes. The number of entries retrieved by the query is the
number of different reactions catalyzed by proteins with known
structure.<BR>
[swissprot-id: acha_human] &gt; prosite &gt; swissprot
<DT>
<DD>The index search retrieves the SwissProt entry &quot;ACHA_HUMAN&quot;.
This entry is then linked to the Prosite entry(s) that documents
the protein family where &quot;ACHA_HUMAN&quot; is a member, in
this case the family of neuronal acetylcholine receptors. The
next link retrieves all SwissProt entries that belong to that
family. In Effect, the entry &quot;ACHA_HUMAN&quot; is amplified
to all members of the protein family or families it belongs to.
the example shows that it is possible to navigate over the databank
network with an explicit succession of links that is evaluated
from left to right.
<DT><TT><B> [swissprot-id:tdt_human] &gt; prodom &gt; pdb </B></TT>
<DD>This example shows how the amplification by homologous entries
in the same databank can be used to find related information in
another databank to which the single entry itself is not linked.
The query retrieves a DNA polymerase from Swissprot, expands it
by related proteins as documented in Prodom (databank of protein
domains, another possibility would be Prosite or HSSP) and links
these entries to PDB. The result is the set of PDB tertiary protein
structures that are homologous to the SwissProt entry &quot;TDT_HUMAN&quot;.
<DT><TT><B> q = [sequence-def: kinase] q ! (q &lt; swissprot)
</B></TT>
<DD>Most protein or DNA databanks overlap to a great extend which
creates a lot of redundancy. The annotation of equivalent entries
in different databanks can be quite different which ban be very
useful for string searching since the probability of finding a
certain enzyme name is much greater if you search all sequence
databanks. After the search the links come in handy to remove
the overlap. The first query in the example searches &quot;kinase&quot;
in all sequence databanks (eg, EMBL, PIR, SwissProt, GenBank).
The second query removes the overlap. The goal is to have SwissProt
entries plus those in other databanks that do not have equivalents
in SwissProt. This is achieved by subtracting all entries from
&quot;q&quot; that are linked to SwissProt. SwissProt entries
in &quot;q&quot; are not linked to SwissProt and won't be removed!.
Just change &quot;SwissProt&quot; to &quot;PIR&quot; if you would
rather have PIR entries.<BR>

</DL>
<HR>

<H2><A NAME="subentry"></A>Entries and Subentries</H2>

<P>
Sets originating from the same databank may have different set
types. Consider the two queries:
<DL>
<DT><TT><B>[swissprot-keywords: transmembrane]</B></TT>
<DT><TT><B>[swissprot-features: transmem]</B></TT> 
</DL>

<P>
The first query retrieves all SwissProt entries that have transmembrane
segments, the second finds all transmembrane <B>features</B> contained
in SwissProt entries. The second query will retrieve many more
entries since most transmembrane proteins have more than one membrane
spanning segment. If you requested the sequences for entries in
the second set you would get the transmembrane segments and not
the parent entry's sequence. The first query returns a set of
<B>entries</B> whereas the second returns a set of <B>subentries</B>.
The &quot;features&quot; index has a special type: searches in
that index will for all sequence databanks result in sets of subentries.
Sets of entries and subentries can not be combined with logical
operators! Only the link operators may be used between them, ie,
it is always possible to link subentries to their respective parent
entries.
<H5>Example:</H5>

<DL>
<DT><TT><B>[swissprot-org:human] &gt; [swissprot-features:transmem]</B></TT>

<DD>returns all transmembrane segments found in human proteins.
<DT><TT><B>[swissprot-org:human] &lt; [swissprot-features:transmem]
</B></TT>
<DD>returns all human proteins that have transmembrane segments.
</DL>

<P>
Sometimes it is necessary to do an explicit conversion from subentries
to entries. This can be done with a link to &quot;parent&quot;.
<H5>Example:</H5>

<DL>
<DT><TT><B>[swissprot-features:transmem] &gt; parent | [swissprot-key:transmembrane]</B></TT>

<DD>returns all entries that have the &quot;transmembrane&quot;
keyword or &quot;transmem&quot; sequence features. This may be
necessary to ensure all entries with a certain property are retrieved
- the annotation is often not complete!
<DT><TT><B>[swissprot-features:transmem] &gt; parent &gt; pdb</B></TT>

<DD>finds all PDB entries of proteins that have transmembrane
segments (even though the known structure may not yet include
the transmembrane region).
</DL>

<P>

</BODY>

</HTML>
ansmembrane]</B></TT>

<DD>returns all entries that have the &quot;transmembrane&quot;
keyword or &quot;transmem&quot; sequence features. This may be
necessary to ensure all entries with a certain property are retrieved
- the annotation is often not complete!
<DT><TT><B>[swissprot-features:transmem] &gt; parent &gt; pdb</B></TT>

<DD>finds all PDB entries of proteins that have transmembrane
segments (even though the known structure may not yet include
the srs/www/doc/srsmaint.html
<HTML>
<HEAD>
   <TITLE>SRS Maintenance</TITLE>
   <META NAME="Description" CONTENT="Selected Chapters about SRS Server Maintenance">
   <META NAME="AUTHOR" CONTENT="Johnathon Weare">
   <META NAME="GENERATOR" CONTENT="Mozilla/4.0b1 (Win95; I) [Netscape]">
   <META NAME="Author" CONTENT="Thure Etzold">
</HEAD>
<BODY>

<H1><A NAME="tour"></A>SRS Server Maintenance&nbsp;</H1>

<P>This section explains in detail some aspects of SRS server maintenance.
The chapters that follow are in a loose order and more will be added as
soon as possible.</P>

<H2><A NAME="sepwwwserver"></A>Installing a Dedicated WWW&nbsp;</H2>

<P>It is possible to call SRSWWW with any httpd provided that the correct
Aliases are set. This worked fine with SRS4 and early versions of SRS5.
With the possibility of adding applications to the retrieval engine, however,
life has become more complicated for the following reasons:</P>

<UL>
<LI>The server, apart from the user context file &quot;user.par&quot; needs
to store the results of application programs and their input. Since on
a general server these data are owned by user &quot;nobody&quot; or &quot;www&quot;
any cgi script can access these data which creates a security problem.</LI>

<LI>The applications are often not available on the machine that hosts
the WWW server or to balance the workload should be run on other machines
and thus 'rsh's are needed.</LI>

<LI>Applications may take a lot of cpu time and sometimes do not terminate
properly.</LI>

<LI>Some applications require environment variables.</LI>
</UL>

<P>An immediate improvement towards solving these problems is the installation
of a dedicated SRSWWW server which runs under a special account.&nbsp;If
you want to set up an SRSWWW server and you do not have root privileges
then it also spares you a great deal of frustration for both you and the
system manager! In fact, the following procedure was suggested by Rodrigo
Lopez who was at that time a system administrator at the EMBL-EBI.</P>

<H3><A NAME="servinstallsteps"></A>Steps to create a dedicated SRSWWW server
running under its own account</H3>

<OL>
<LI>Create an account &quot;srs&quot; or &quot;srswww&quot; that may also
own the SRS distribution directory and the indices.&nbsp;</LI>

<LI>Log in as user &quot;srswww&quot;&nbsp;and install an httpd or copy
the &quot;conf&quot; directory from an existing server.</LI>

<LI>Edit the file &quot;httpd.conf&quot; in the httpd's &quot;conf&quot;
directory. There you need to specify a port number for the server since
it will not be run with root privilege. We try to use numbers with 5's
(SrS5!), eg, 5000 or 5555. Check the&nbsp; file &quot;/etc/services&quot;
of the machine hosting the server to see if the port number is free.</LI>

<LI>Edit the file &quot;srm.conf&quot; in the httpd's &quot;conf&quot;
directory. You can define the SRS directory &quot;srs/www&quot;&nbsp;as
document root so that no directory name is needed in the URL of the SRSWWW
server, eg, &quot;http://machine:5000/&quot;. Likewise the ScriptAlias
&quot;cgi-bin&quot; can be set to &quot;/srs/www/bin&quot;.</LI>

<DT>You need to think of where to run the applications you want to be launched
by SRSWWW. Edit the file &quot;.rhosts&quot; in the login directory of
user &quot;srswww&quot; and add an entry for the SRSWWW host machine, e.g.,&nbsp;</DT>

<PRE>croma.ebi.ac.uk srswww
croma&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; srswww&nbsp;</PRE>

<LI>Install SRS. If the SRS distribution directory is not visible from
all &quot;application hosts&quot; then you must move the directory &quot;srs/tmp&quot;
to some place that can be seen from all. This directory must be owned by
user &quot;srswww&quot; (srsinstall www)</LI>
</OL>

<DT>&nbsp;</DT>

<H2><A NAME="automhouse"></A>Automizing Housekeeping</H2>

<DT>Certain 'housekeeping' tasks for maintaining an SRS server can be automized
and started as cron jobs. These are</DT>

<UL>
<LI>keeping indices up to date;</LI>

<LI>deleting the temporary user directories created for each SRSWWW session;</LI>

<LI>killing run away jobs started by the SRSWWW server.</LI>
</UL>

<DT>Each of these task can be done either by a script or a single command.
The scripts that are provided with the SRS release</DT>

<DT>is what we use at our home site and not very portable. You are welcome
to change them to your needs and would be very grateful if you could send
them to us once you found a more general solution.&nbsp;</DT>

<DT>There is one last thing that could be done using cron, namely the automatic
restart of the SRSWWW httpd after a reboot of the host machine. The job
could check every half hour or so if the httpd process exists and restart
it if not. Up to this point we do it manually - if you write a script that
does that please send it to us and we will include it into our distribution.</DT>

<DT>&nbsp;</DT>

<H3><A NAME="indexupdate"></A>Keeping Indices up to Date</H3>

<DT>As mentioned in the &quot;Guided Tour&quot; the command <B>srscheck</B>
examines all indices of all databanks and writes a shell script with the
commands to create indices for all databanks that have changed. In our
experience we found it useful to separate the tasks of updating or mirroring
the databanks and the indexing. To this end we set up a cron job that calls
srscheck every half hour and runs the generated script. This means that
once a new databank arrived it will take a maximum of 30 minutes until
SRS notices that new indices should be built. The SRS release comes with
the Perl script &quot;SRSETC/srscronupdate&quot; that first checks if srscheck
or</DT>

<DT>srsbuild are already running. You can use it and call it as a cron
job</DT>

<PRE>10,40 * * * * /usr/local/srs/etc/srscronupdate&nbsp;</PRE>

<H3><A NAME="deldirs"></A>Deletion of Session Directories</H3>

<DT>Every SRSWWW session creates a new directory in &quot;SRSWWWTMP&quot;.
In SRS5 these directories will also contain files like Blast output, indices,
multiple alignments, so it is important to clean them up regularly. The
policy at our site is to keep directories after their last modification
date for a certain number of days. This gives people the chance to keep
their session going for many days or even weeks if they regularly 'touch'
their session files. The following crontab entry deletes any directory
that wasn't modified for more than 2 days.</DT>

<PRE>0 1 * * * find /home/srswww/tmp -mtime +2 -type d -depth -name '*' -exec rm -rf {} \;</PRE>

<H3><A NAME="killjobs"></A>Killing Runaway Jobs</H3>

<DT>It occasionally happens that processes created by the httpd are not
terminated and run for ever. This affects the programs <B>wgetz&nbsp;</B>and
<B>srsbuild</B>. The shell script &quot;SRSETC/killrunaway&quot; checks
for processes running either of the two for longer than 15 minutes and
kills them. You will have to change the script which has four variables
holding the name of the user running the SRSWWW server, the names of the
programs that need to be checked, the maximum time these programs may take
and optionally a mail address of where to send a report in case a process
is terminated. The script reads the output of the UNIX&nbsp;command <B>ps</B>&nbsp;
on IRIX so you might have to modify it for other platforms. The following
crontab entry runs the script every 30 minutes. &nbsp;</DT>

<PRE>5,35 * * * * /usr/local/srs/etc/killrunaway</PRE>

<PRE>Make sure that you set it on the machine hosting the WWW server and under the user &quot;srswww&quot;.</PRE>

<H2><A NAME="launchapps"></A>Launching Applications from SRSWWW</H2>

<DT>The Applications that can be launched from SRSWWW are divided into
several categories. The assumption is that a common</DT>

<DT>way can be used to treat applications from the same category. The &quot;Search
Application&quot; is currently the only generalization. It contains programs
such as BLAST, FASTA or the Smith and Waterman search with the Bioccelerator.&nbsp;</DT>

<DT>&nbsp;</DT>

<DT>In order to add a new application you need to&nbsp;</DT>

<OL>
<LI>Edit &quot;SRSICA:srsgen.i&quot; and add an object <B>$Application</B>
and let one or more <B>$ContentType</B> objects point to it.</LI>

<LI>Edit &quot;SRSICA:srswww.i&quot; and add two templates, one for to
create the HTML form that prompts the user for the program parameters and
the other that generates the shell script which launches the application
program</LI>

<LI>If the application program's output should not just be displayed but
indexed as an SRS databank then an .i, .is and .it file must be created
in the &quot;SRSDB&quot; directory. The databank with the application name
needs also to be declared in the &quot;SRSDB/srsdb.i&quot;</LI>
</OL>

<H3><A NAME="addsearchapps"></A>Adding or Modifying Search Applications</H3>

<DT>&nbsp;</DT>

<H2><A NAME="parsesequence"></A>Parsing and Processing a Protein and DNA
Sequence Field</H2>

<DT>Still missing.</DT>

<H2><A NAME="subentries"></A>Definition of Subentries</H2>

<DT>Still missing.</DT>

<H2><A NAME="javaapplets"></A>Adding Java Applets to Display Entries</H2>

<DT>Still missing.</DT>

<H2><A NAME="inernallinks"></A>Defining Internal Links</H2>

<DT>Still missing.</DT>

<H2><A NAME="origgcgformat"></A>Switching Between Original and GCG Sequence
Format</H2>

<P>In order to make a sequence databank acceptable for GCG&nbsp;programs
it needs to be reformatted. GCG has also its own conventions about file
names. SRS supports sequence databanks both in the distribution and the
GCG&nbsp;formats. The SRS distribution describes the databanks normally
to be in the distribution format so that the description needs to be modified
if a databank should be indexed in GCG format. Normally it is enough to
modify the .i file of a databank and change</P>

<UL>
<LI>the file name(s)</LI>

<LI>the .fileType attribute of $libformat</LI>

<LI>the .token attribute of the $field object describing the sequence data-field</LI>
</UL>

<P>&nbsp;In all files this three places have separate lines for both formats
which are marked '# orig format' and '# GCG format' where one alternative
is always outcommented. To switch between formats search the string 'GCG
format' and flip around the comment character ('#') so that, eg,&nbsp;</P>

<PRE>&nbsp;&nbsp;&nbsp; EMBLSeq:$field:[@DF_DNASequence token:gcgseq format:embl] #GCG format&nbsp;
#&nbsp;&nbsp;&nbsp; EMBLSeq:$field:[@DF_DNASequence token:sequence format:embl] #orig format</PRE>

<DT>becomes</DT>

<PRE>#&nbsp;&nbsp;&nbsp; EMBLSeq:$field:[@DF_DNASequence token:gcgseq format:embl] #GCG format&nbsp;
&nbsp;&nbsp;&nbsp; EMBLSeq:$field:[@DF_DNASequence token:sequence format:embl] #orig format</PRE>

<P>&nbsp;Make sure that you find all three locations!&nbsp;</P>

</BODY>
</HTML>
,&nbsp;</P>

<PRE>&nbsp;&nbsp;&nbsp; EMBLSeq:$field:[@DF_DNASequence token:gcgseq format:embl] #GCG format&nbsp;
#&nbsp;&nbsp;&nbsp; EMBLSeq:$field:[@DF_DNASequence token:sequence format:embl] #orig format</PRE>

<DT>becomes</DT>

<PRE>#&nbsp;&nbsp;&nbsp; EMBLSeq:$field:[@DF_DNASequence token:gcgseq format:embl] #GCG format&nbsp;
&nbsp;&nbsp;&nbsp; EMBLSeq:$field:[@DF_DNASequence token:sequence format:embl] #orig format</PRE>

<P>&nbsp;Make sure that you fsrs/www/doc/srsman.html
<HEAD>
<TITLE>Icarus Documentation </TITLE>
</HEAD>



<FRAMESET Cols="18%,82%">
<FRAME SRC="contents.html">
<FRAMESET Rows="70%,30%">
<FRAME NAME=text SRC="m_icarus.html">

<FRAMESET Cols="55%,45%">
<FRAME NAME=toc   SRC="mtoc_icarus.html">
<FRAME NAME=index SRC="m_inx.html">
</frameset>
</frameset>
</frameset>
</html>
NASequence token:gcgseq format:embl] #GCG format&nbsp;
&nbsp;&nbsp;&nbsp; EMBLSeq:$field:[@DF_DNASequence token:sequence format:embl] #orig format</PRE>

<P>&nbsp;Make¶ £¡Üat you fsrs/www/doc/srswww.html
<HEAD>
<TITLE>Untitled</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFF0" LINK="#0000ff" VLINK="#ff0000"   ALINK="#ff0000" TEXT="#000000">
<H1><A NAME="srswww">SRSWWW </A></H1>
&nbsp;
<H2><A NAME="intro">Introduction </A></H2>
<P>
SRSWWW is a World Wide Web interface to the Sequence Retrieval
System (SRS). Compared with other SRS interfaces SRSWWW has more
users because of the widespread use of web browsers, its easiness
to handle and its user friendly interface. It supports HTML3 and
lesser versions of HTML. Since HTTP is stateless, a user ID is
created to keep the state for the whole session. </P>
<P>
A SRS session is started by clicking on the 'Start' button in
the SRS home page. The page appearing next is the 'Select Libraries
Page' also referred to as 'Top Page'. 
<P>
Most pages in the SRSWWW have six header buttons which contain
links to other SRSWWW pages. One header button is the <A HREF="#Top" >'Top Page'</A>
which links to the start page of the SRSWWW. The other buttons
point to the <A HREF="#QueryForm" >'Query Form'</A> page, the
<A HREF="#QueryManager" >'Query Manager'</A> page, the <A HREF="#ViewManager" >'View Manager'</A>
page, the <A HREF="#Databanks" >'Databanks'</A> page and the <A HREF="#helppage" >'Help'</A>
page.</P> 
<P>
<CENTER><A HREF="/cgi-bin/imagemap/srs5/images/srswww.map"><IMG ISMAP SRC="../images/srswww.gif" BORDER=0 HEIGHT=295 WIDTH=506></A></P>
</CENTER>
<HR size=10>
<P>
<TABLE CELLPADDING=5>
<TR><TD VALIGN=TOP><A HREF=#intro>SRSWWW</A></TD><TD>
<H3><A NAME="Top">The Top Page</A></H3>

</TD></TR>
<TR><TD COLSPAN=2>The 'Top Page' is used to select the one or more databank(s) to be searched. Selecting databank(s) can be done by clicking the check boxes. In all cases, the databank names are linked to an information page ('Information about &#133;' page). It provides some information about the indices of the respective databank. The data fields of the databank can be browsed directly (see the <A HREF="#BrowseIndex" >'Browse Index'</A> page).
<P>
If you want to change databases for another search you have to go to the 'Top Page'.</P>
</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="continue">Continue &amp; Reset Button </A></H4>

</TD><TD>The 'Reset' button can be used to deselect all selections done so far. Each databank can individually be deselected by clicking again their checkboxes. Clicking the 'Continue' button finishes the 'Top page' and brings up the 'Query Form' page.
</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="commonFields">Common Fields selection</A></H4>
</TD><TD valign=top>Some fields in the databanks are common (e.g., ID field). The check box 'Show only fields that selected databanks have in common' is used to list only the common fields in the 'Query Form' page. 
</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="groupingdbs">Grouping the Databanks</A></H4>

</TD><TD VALIGN=TOP>
In the 'Top Page' all available databanks are collected in groups defined by SRS.
</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="userdefined">User defined Databases</A></H4>

</TD><TD>There is a possibility to include user defined databanks. For example with the search engine FASTA or BLAST special databanks can be created. Before such a databank can be selected it has to be created with a search (for instance with  BLAST). An existing sequence can be inserted in the 'Enter query sequence' field by &quot;cut and paiste&quot;.
</TD></TR>
</TABLE>
<HR size=10>
<P>
<TABLE CELLPADDING=5>
<TR><TD VALIGN=TOP><A HREF=#intro>SRSWWW</A></TD><TD>
<H3><A NAME="QueryForm">The Query Form Page</A></H3>

</TD></TR>
<TR><TD COLSPAN=2>With the 'Query Form' page the databank query can be defined. The selected databank(s) is/are listed at the top of the page. Which fields are listed depends on the 'Show only fields that selected databanks have in common ' check box from the <A HREF="#Top">Top Page</A> and the searchable fields of the databank(s). </P>
</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="doquery">Do Query &amp; Reset Button </A></H4>

</TD><TD>The 'Reset' button can be used to deselect all selections done so far. Each selection can be deselected individually by clicking again the check box. Clicking on the 'Do Query' button starts the query and brings up the <A HREF="#QueryResult" >'Query Result'</A> page.
</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="fieldname">FIELD NAME, QUERY, INCLUDE IN LIST &amp; RETRIEVE SUBETNTRIES columns</A></H4>

</TD><TD>The main query form has four columns. The column 'Field Name' lists all data fields of the selected databank which are linked to an information page. By clicking on a 'Field Name' one moves to the <A HREF="#BrowseIndex" >'Browse Index'</A> page. The 'Query' column is the input field for the query. By using the operators &quot;&amp;&quot; (= AND), &quot;!&quot; (= NOT), &quot;|&quot; (= OR) one can use more than one search expression in every 'Query' input field. The 'Include in List' column is a check box for inclusion of the corresponding field in the query result. The 'Retrieve Subentries' column is a check box for the inclusion of subentries in the query result.</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="addmenus">Additional Menus</A></H4>

</TD><TD>Some fields can have additional menus with &quot;greater than&quot; and &quot;greater than or equal to&quot; and &quot;less than&quot; and &quot;less than or equal to&quot; symbols (e.g., SeqLength) for their range selection. (e.g., seqLength &gt; 100 &amp;&amp; seqLength &lt; 500). </P>
</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="combinesearch">Combine Searches with</A></H4>

</TD><TD>If more than one data field is to be searched the 'Query' input fields can be combined with the boolean operators 'AND', 'OR' and 'NOT'. Optionally, a wildcard is appended to every search string to enhance the possibility to find a match. </P>
</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="chunksize">Chunk Size &amp; Use view</A></H4>

</TD><TD>Additional options are 'Entry list in chunks of' to define the number of entries shown per page and 'Use view' to select a predefined view with which the query result is shown (see the <A HREF="#CreateView" >'Create a new view'</A> page for more information on 'Views'). A new view can be defined before doing a query. All the 'Views' which are applicable to the selected databanks are listed in the 'Use view' box and one of them can be selected. Note: only the 'Views' are listed which can be used with the selected databank(s). The default is 'Names Only' (i.e. without a special 'View'). </TD></TR>
</TABLE>
<HR SIZE=10>
<P>
<TABLE CELLPADDING=5>
<TR>
<TD VALIGN=TOP><A HREF=#intro>SRSWWW</A></TD>
<TD>
<H3><A NAME="BrowseIndex">Browse Index Page</A></H3>
</TD></TR>
<TR><TD COLSPAN=2>From the 'Query Form' page the 'Browse Index' page is opened by clicking on a 'Field Name' (e.g., the 'ID' field). 
</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="listvalue">List Values Button</A></H4>
</TD>
<TD>Submits a search string typed in the open box marked with a wildcard (the wildcard can be used in the string or deleted). The result of any matches (referred to as &quot;values&quot;) of the search string in the indicated 'Field Name' is listed in the 'Values in the index of the ... field' page. In this list 'Values' can be selected and with the 'Make Query' button a query can be started immediately with the selected 'Value(s)'. 
</TD></TR>
</TABLE>
<HR SIZE=10>
<P>
<TABLE CELLPADDING=5>
<TR><TD VALIGN=TOP><A HREF=#intro>SRSWWW</A></TD><TD>
<H3><A NAME="QueryResult">The Query Result Page</A></H3>

</TD></TR>
<TR><TD COLSPAN=2>The 'Query Result' page shows the result of a submitted query. The query string, the number of &quot;hits&quot; and found entries with check boxes and included fields (if selected in the 'Query Form' page or in the view definition) are indicated. The found entries are listed by the searched databank and the entry ID. Clicking on the entry opens the <A HREF="#SingleEntry" >'Single Entry'</A> page. In addition, entries can be selected with the checkboxes. The 'Reset' button can be used to deselect all selections done so far. With the 'Link', 'Receive' and 'View' buttons further manipulations can be performed with the selected entries. </TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="linkbuton">Link Button</A></H4>

</TD><TD>With this button the whole/selected result entries can be checked whether they are linked to other databanks (see the <A HREF="#Link" >'Link Page'</A> for more information).</P>
</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="receivebutton">Receive Button</A></H4>

</TD><TD VALIGN=TOP>With the 'Receive' button the selected entries can be downloaded.</P>
</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="viewbutton">View Button</A></H4>

</TD><TD>With this button the result entries can be viewed with predefined 'View' definitions. The 'View' definitions can be selected out of the 'View' box.</P>
</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="chunklinks">Chunk Hypertext Links</A></H4>

</TD><TD>The last line are hypertext links for any additional chunk set(s). These links are only present if the number of entries found is bigger than the number of the defined chunk size. The chunk set numbers starts from 1 to &quot;number of hits&quot; divided by &quot;entry list chunk size&quot; (selected in the 'Query Form' page). The user can jump to any additional chunkset by the hypertext link. The current chunk set is shown within braces. The left anglebracket hyperlink moves to the first chunkset whereas the right anglebracket hyperlink moves to the last chunkset. </TD></TR>
</TABLE>
<HR size=10>
<P>
<TABLE CELLPADDING=5>
<TR><TD VALIGN=TOP><A HREF=#intro>SRSWWW</A></TD><TD>
<H3><A NAME="SingleEntry">Single Entry Page</A></H3>

</TD></TR>
<TR><TD COLSPAN=2>Every entry found and listed in the 'Query Result' page has a link to the complete entry in the databank. By clicking onto a entry, the 'Single Entry' page comes up and shows the complete entry. The complete entry can be saved or printed (refer to the documentation of your web browser).</P>
</TD></TR>
</TABLE>
<HR size=10>
<P>
<TABLE CELLPADDING=5>
<TR><TD VALIGN=TOP><A HREF=#intro>SRSWWW</A></TD><TD>
<H3><A NAME="Link">Link Page</A></H3>

</TD></TR>
<TR><TD COLSPAN=2>From the 'Query Result' page one can go to the 'Link' page by pressing the 'Link' button. The 'Link' page is used to find the links between the found entries (the set) and the selected databanks. The user can choose one of three options to display the different entries. The 'Link' page lists all the databanks like the top page. The user should select the databanks which are different from the databanks selected for the query search and should select one of three options of the 'Find all entries' field. Clicking on the 'Continue' button shows the 'Query Result' page. A link can also be done in the <A HREF="#QueryManager" >'Query Manager'</A> page.</P> <P>
(For more information about <A HREF="mi_query.html#linkop" >links</A> refer to the SRS manual)</P> 
</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="findall">Find all entries:</A></H4>

</TD><TD></TD></TR>
<TR><TD><H4><A NAME="l1">in the selected DATABANKS which are linked to the current set</A></H4>

</TD><TD>the result are entries out of the selected Databanks, which are linked with the set.</P>
</TD></TR>
<TR><TD>
<H4><A NAME="l2">in the current SET which are linked to all selected databanks</A></H4>

</TD><TD>the result are entries out of the set, which have links to the selected databanks.</P>
</TD></TR>
<TR><TD>
<H4><A NAME="l3">in the current set which are not linked to any of the selected databanks</A></H4>

</TD><TD>the result are entries out of the set, which contain NO&nbsp;links to the selected databanks.</P>
</TD></TR>
</TABLE>
<HR size=10>
<P>
<TABLE CELLPADDING=5>
<TR><TD VALIGN=TOP><A HREF=#intro>SRSWWW</A></TD><TD>
<H3><A NAME="QueryManager">Query Manager Page</A></H3>

</TD></TR>
<TR><TD COLSPAN=2>The 'Query Manager' has two functions: one is to store the queries done so far. The queries are listed in a table. Every query is listed with a check box, the query name in the form 'Qn' (e.g., Q1, Q2, ..), a type (e.g., 'query' , 'link' ), the total number of entries found, the library name(s), the number of entries for each library, the query expression (SRS query syntax) and a comment. The user may add own commentary to the query. Users working in HTML3 mode get a table with all these descriptors. In versions below HTML3  the same information is available in different style and in different order.<P>The second function of the 'Query Manager' is to make further queries and links.<P>
There are three functions to control the queries and three functions to do further queries and links.</P>
</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="control">Control Functions</A></H4>

</TD><TD></TD></TR>
<TR><TD VALIGN=TOP><B>Receive </B></TD><TD>With the 'Receive' function the selected queries can be downloaded.
</TD></TR>
<TR><TD VALIGN=TOP><B>Delete </B></TD><TD>The 'Delete' function deletes selected queries.
</TD></TR>
<TR><TD VALIGN=TOP><B>View </B></TD><TD>The 'View' function can be used to inspect a single query again or with a different 'View' (choose a 'View' from the 'Using the view' field).
</TD></TR>
<TR><TD COLSPAN=2>
<H4> <A NAME="querylink">Query/Link Functions</A></H4>

</TD></TR>
<TR><TD VALIGN=TOP><B>Link </B></TD><TD>The 'Link' function is exactly the same as in the 'Query Result' page, see detailed information in the chapter <A HREF="#QueryResult" >'The Query Result Page'</A>.
</TD></TR>
<TR><TD VALIGN=TOP><B>Combine </B></TD><TD>With this function it is possible to combine one or more queries with the logical operators AND, OR or NOT.
</TD></TR>
<TR><TD VALIGN=TOP><B>Expression </B></TD><TD>With this function the user can directly enter a query like &quot;(Q1 &amp; Q2) ! (Q3 | Q4) &gt; PDB&quot; (i.e. query 1 AND query 2 but NOT query 3 OR query 4 linked to the PDB database). In contrast to the 'Combine' function it allows to build more complex queries. 
<P>
For more information in using <A HREF="mi_query.html#logop" >logical operators</A> and <A HREF="mi_query.html#linkop" >link operators</A> see the SRS manual.
</TD></TR>
<TR><TD COLSPAN=2>
<H4><A NAME="resultdisplay">Result Display Options</A></H4>

</TD></TR>
<TR><TD COLSPAN=2>The 'Query Manager' offers two options to manipulate the 'Query Result' page:
</TD></TR>
<TR><TD VALIGN=TOP><B>Entry list in chunks of... &amp; Using the view&#133;</B>
</TD><TD>The options 'Entry list in chunks of ' and 'Using the view' are already described in the chapter about the <A HREF="#QueryForm" >'Query Form'</A> page.
</TD></TR>
</TABLE>
<P>
The queries done so far will be lost after closing the SRS session.
However, it is quite useful sometimes (especially in the case
of complex query runs) to store a useful query set in a file (referred
to as &quot;history&quot;) though it can be loaded and used again
in a new SRS session. This task is accomplished by activating
one or more checkboxes on the bottom 'Save in histories queries
of type' line. </P>
<HR size=10>
<P>
<TABLE CELLPADDING=5>
<TR><TD VALIGN=TOP><A HREF=#intro>SRSWWW</A></TD><TD>
<H3><A NAME="ViewManager">View Manager Page</A></H3>

</TD></TR>
<TR><TD COLSPAN=2>The extraction of information from the databank(s) is done with a query created in the 'Query Form' page. In the 'View Manager' you can define how to look at the query results. You can use predefined 'Views' or create your own 'Views'. You can apply them on new created queries or already existing queries. A set of 'Views' can be defined before any query has been performed. But of course, a 'View' can only be used after a query has been created.<P>
But the 'View Manager' can do a lot more than only to provide a special service on query sets as described above. The 'View Manager' works independently from the 'Query Form' routine. Thus, you can start complex queries within the 'View Manager' to investigate different relations between databanks and/or query sets. <P>
The following options are offered in the 'View Manager' page: 'Create a new view', 'Edit selected view' or 'Delete selected view'. The 'View Manager' lists all the 'Views' defined so far in a table with View Name, Format, Root Libs, Root Fields, Leaf Libs and Leaf Fields. After doing a query on the selected database(s) the user gets a set of entries as a result. 'Views' can help to recognize whether these entries may have e.g., links to other databases. 'Views' can be configured to see the fields of interest from the set and from the linked database entries. There exist already predefined 'Views' which can be used directly or modified for your own purpose.</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="vieweditor">independent View Manager</A></H4>

</TD><TD>Click on the link 'independent View Editor' with the middle or right mouse button; choose 'Open in New Window' in the appearing context menue. A new browser window is opened. By this way one can define several 'Views' at a time or edit a 'View' in one window and use it at once in the 'Query Result' page in the second window.
</TD></TR>
</TABLE>
<HR size=10>
<P>
<TABLE CELLPADDING=5>
<TR><TD VALIGN=TOP><A HREF=#intro>SRSWWW</A></TD><TD>
<H3><A NAME="CreateView">Create A New View Page</A></H3>

</TD></TR>
<TR><TD COLSPAN=2>In the 'Create A&nbsp;New View Page' the available databanks are listed in two columns. The databanks in the first column are called <U>root databanks</U>. The databanks in the second column are called <U>leaf databanks</U>. The root databanks refer to the databanks used for a particular query search. The leaf databank refer to the databanks which will be linked by the result set of the query search done with the root databanks. For example the user can define a view with SWISSPROT as root databank and prosite as leaf databank. In the 'View Select' page the fields which have to be displayed from both databanks have to be selected. Choose this as a current view and make a query on SWISSPROT (which is the root databank). The result will be swissprot entries and for entries with a link to PROSITE the PROSITE entries.</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="nameview">Name of new view</A></H4>

</TD><TD>In the 'Name of view' field you can assign a name to the new 'View'. Leaving this field blank a 'View' name is created automatically, prefixed by the first root databank name and a viewnumber at the end (e.g., Swissprot_view1, Prosite_view5 etc.).
</TD></TR>
<TR><TD VALIGN=TOP>
<H4> <A NAME="astable">Display view as table</A></H4>

</TD><TD  VALIGN=TOP>With selecting the 'Display view as table' checkbox the result is displayed in a table form instead of a list form.
</TD></TR>
<TR><TD VALIGN=TOP>
<H4> <A NAME="shortfields">Print short field names in header</A></H4>

</TD><TD VALIGN=TOP>With this checkbox it is possible to place the short field names as the header of the table columns.
</TD></TR>
<TR><TD VALIGN=TOP><A NAME="commonfields"><B> Show only fields common to selected root databanks</B></A>
</TD><TD VALIGN=TOP>This checkbox is selected by default. So only common fields of the root databanks are listed.
</TD></TR>
<TR><TD VALIGN=TOP>
<H4> <A NAME="x55">Continue &amp; Reset Button</A></H4>

</TD><TD  VALIGN=TOP>The 'Reset' button can be used to deselect all selections done so far. Each field and checkbox can individually be deselected by clicking again. Clicking on the 'Continue' button finishes the 'Create new view' page and brings up the <A HREF="#ViewField" >'View Field Select'</A> page. 
</TD></TR>
</TABLE>
<HR size=10>
<P>
<TABLE CELLPADDING=5>
<TR><TD VALIGN=TOP><A HREF=#intro>SRSWWW</A></TD><TD>
<H3><A NAME="EditView">Edit Existing View Page</A></H3>

</TD></TR>
<TR><TD COLSPAN=2>In this page a predefined 'View' can be edited. The 'Edit existing view' page offers the same editing options as the 'Create a new view' page.
</TD></TR>
</TABLE>
<HR size=10>
<P>
<TABLE CELLPADDING=5>
<TR><TD VALIGN=TOP><A HREF=#intro>SRSWWW</A></TD><TD>
<H3><A NAME="ViewField">View Field Select Page</A></H3>

</TD></TR>
<TR><TD COLSPAN=2>Lists the fields of all selected root and leaf databanks. Fields can be selected by their checkboxes and are displayed in the query. The display format of the sequence field can be selected by the format menu selection (e.g., FASTA, PIR, EMBL, Protein Chart etc.). <P>
The leaf databank selection has additional options:
</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="usequery">Use query instead link</A></H4>

</TD><TD>A query string can be inserted to search for special relations between the root and leaf databank. </P>
</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="useview">Use view to display entries</A></H4>

</TD><TD  VALIGN=TOP>
The result of the 'View' can be shown by another 'View'.</P>
</TD></TR>
<TR><TD VALIGN=TOP>
<H4><A NAME="onlynumber">Display only number of linked entries</A></H4>

</TD><TD  VALIGN=TOP>
Displays only the number of links which exist, not the links itself.</P> 
</TD></TR>
<TR><TD COLSPAN=2>To submit the view one of the four options ('Top page', 'Query form', 'Query manager' or 'View manager') must be clicked.</P>
</TD></TR>
</TABLE>
<P>
<H3><A NAME="Databanks">Databanks Page </A></H3>
<P>
The 'Databanks' page lists all available databases in a table
form. Every databank is listed as a hypertext link and shown with
the release version number, the number of entries, the indexing
date, the group (e.g., HomolSearch, Sequence etc.) and a availability
flag. This flag indicates whether the respective databank is available
(<I>ok</I>) or not (&nbsp;&nbsp;) for searches.</P> 
<H3><A NAME="helppage">Help Page </A></H3>
<P>
Most of the information about the databanks and their fields description
are available through hypertext links. Help is provided wherever
possible in a context sensitive way. In addition to providing
information, the data fields can be browsed directly (see the
<A HREF="#BrowseIndex" >'Browse Index'</A> page). </P>
</BODY>
</HTML>
ability
flag. This flag indicates whether the respective databank isrs/www/doc/tour.html
<HEAD>
<TITLE>Guided Tour</TITLE>

<META name="Description" content="How to add new DB in SRS">
<META NAME="AUTHOR" CONTENT="Johnathon Weare">
<META NAME="GENERATOR" CONTENT="emacs">
</HEAD>
<BODY>
<H1><A NAME="tour">Adding Databanks - A Guided Tour </H1>
<P>
This chapter is an introduction to SRS seen from the maintenance
side and requires knowledge of the basic principles of SRS and,
to a lesser degree, the Icarus language. It describes the integration
of two 'demo' databanks into SRS. There have to be two databanks
in this guided tour in order to demonstrate the specification
of links.
<H2><A NAME="TheDatabanks">The Databanks </A></H2>
<P>
The first databank which we call Genes is in a 'Genbank like'
format. Every entry of this databank consists of an annotation
and a DNA sequence part. The annotation has the four data-fields:
&quot;LOCUS&quot;, &quot;DATE&quot;, &quot;DEFINITION&quot;, and
&quot;CITATION&quot;. The &quot;CITATION&quot; field in Genes
links the name of an entry from the other example databank - RefList.
The RefList databank has an 'EMBL like' format and is a compilation
of literature citations which are referenced in Genes. Every entry
of RefList has four data-fields: The unique entry name (&quot;ID&quot;)
and the lines starting with &quot;RT&quot;, &quot;RA&quot; and
&quot;RL&quot; that describe the title, the author names and bibliographical
reference of the literature citation respectively. Samples of the two databanks
can be found in the directory &quot;SRSDEMO:&quot; in the files
&quot;genes.dat&quot; and &quot;reflist.dat&quot;.
<P>
<I>Example of a Genes entry:</I> 
<PRE>
LOCUS       HSAMCC
DATE        07-JUN-1960
DEFINITION  Human amphiphysin mRNA, complete cds.
CITATION    YAMAR95
SEQUENCE  
        1 ccaggtgcct actgactcct tcagaaatgt cagttcctgt cccatgccct taatatttcc
       61 cacatgcagg gctctgtgca caatgcgtga caatggcttt tagat
//
</PRE>
<P>
<I>Example of a RefList entry: </I>
<PRE>
ID   YAMAR95
RA   Yamamoto R., Li X., Winter S., Francke U., Kilimann M.W.;
RT   Primary structure of human amphiphysin, the dominant autoantigen
RT   of paraneoplastic Stiff-Man syndrome, and mapping of its gene
RT   (AMPH) to chromosome 7
RL   Hum. Mol. Genet. 4:265-268(1995).
//
</PRE>
<H2><A NAME="SyntaxDescr">The Syntax Description </A></H2>
<P>
To add a new databank to SRS you need to write two files, with a
third file being optional:
<OL>
<LI>a file with the syntax of the entry and the data-fields (file
extension &quot;.is&quot;)
<LI>a file describing the logical structure of the databank -
the name and type of the databank and its fields, how to index
field contents, links to other databanks etc. (file extension
&quot;.i&quot;) 
<LI>a optional file with text that extends the SRSWWW server -
see the section &quot;Extensions for the SRSWWW Server&quot; for more details (file extension
&quot;.it&quot;) 
</OL>
<P>
Both files must be written in the Icarus language and should be
stored in the directory &quot;SRSDB:&quot;. The best strategy is
to start with the syntax file since, as it will be shown later,
it can be tested independently from the SRS system. 
<P>
Before starting with the details a few terms need to be introduced
(See chapter &quot;The Icarus language&quot; for more information).
A <I>production</I> is a syntax rule that during parsing must
match with at least a part of the input stream. A <I>token</I>
is a part of the input string identified as syntactic element
by the parser, eg, the part that matches with a production. During
the parsing process <I>tokens</I> can be written to a <I>token
table</I>. To allow identification of an individual <I>token</I>
it can be assigned a <I>token code</I>, which is normally a name
like &quot;id&quot;. The token table can also have a name, eg,
&quot;fields&quot;. 
<P>
The following describes incrementally the creation of the syntax
file &quot;genes.is&quot; for the databank Genes. Essentially,
the file is an Icarus program with only one statement, an assignment
of a list of productions to the variable <B>$rules</B>.
<P>
The productions in the list can be grouped into the those with the
syntax of an entry in the flat file (production &quot;entry&quot;),
and the those defining the syntax of the data-fields within the
entry (production &quot;fields&quot;). The production &quot;entry&quot;
starts with a list of Icarus commands within curly braces. The
command <B>$Out </B>declares that parsing of &quot;entry&quot;
will produce an output token table. By default, the output token
table will be named after the production, in this case &quot;entry&quot;.
The <B>$Wrt</B> command used later deposits parts of the input
stream which we call tokens into an output token table. By default
the parser skips line feeds, tabs and spaces (&quot;white space&quot;)
which is convenient when parsing, eg, an author list. However,
in this example we need to keep the white space since it is part
of the entry. As we will see later it is also of syntactical importance,
eg, for parsing &quot;SEQUENCE&quot; data-field which spans the
first line starting with &quot;SEQUENCE&quot; and all following
lines that start with two blanks. The command &quot;<TT>$Skip:0</TT>&quot;
turns the white space skipping off. By default actions associated
to symbols, here the production &quot;entry&quot;, are executed
AFTER the nodes matched with the input stream. The <TT><B><FONT SIZE=2 FACE="Courier New">pre</FONT></B></TT>
directive ensures that the <B>$Skip</B> command is executed BEFORE
the parsing starts.
<PRE>
$rules={

  # the entry
  entry:     ~ {$In:[file:text] $Out pre{$Skip:0}} 
                ('LOCUS' {$Wrt} ln {$App}
                ('LOCUS' {$Not} ln {$App})*)?
             ~
  ln:        ~ /[^\n]*\n/ ~

  # the data-fields
  fields:    ~ {$In:entry $Out} id date def cit seq  ~
  id:        ~ {$wrt:id}   'LOCUS'      ln ~
  date:      ~ {$wrt:date} 'DATE'       ln ~
  def:       ~ {$wrt:def}  'DEFINITION' ln ('  ' ln)* ~
  cit:       ~ {$wrt:cit}  'CITATION'   ln ~
  seq:       ~ {$wrt:seq}  'SEQUENCE'   ln ('  ' ln)* ~
}
</PRE>
<P>
The entry itself starts with the literal 'LOCUS' which is written
into the token table &quot;entry&quot; by <B>$Wrt</B>. Of course
this is not enough and we want the entire entry, so we need to
continue and add more to the token we just wrote. The function
<B>$App</B> appends the current match to the last token written.
The production &quot;<TT>ln</TT>&quot; is a regular expression
and matches the rest of the line. We continue adding lines to
the one token we have in the output token table if the beginning of
the line does NOT match 'LOCUS' which is specified with the <B>$Not</B>
command attached to the literal 'LOCUS'. The production &quot;entry&quot;
gets the input directly from the flat file which means that we
need to process the input line by line. This will be easier afterwards
when the entire entry resides as a single string in memory.
<P>
The other productions are used to divide the entry into its data-fields.
The production &quot;fields&quot;, like production &quot;entry&quot;,
has an <B>$Out</B> directive which means that parsing of &quot;fields&quot;
will produce a token table with the name &quot;fields&quot;. The
input for parsing &quot;fields&quot; is not the flat file but
the token in the table &quot;entry&quot; which is described by
the command &quot;<TT>$In:entry</TT>&quot;. The relationship of
&quot;entry&quot; and &quot;fields&quot; exemplifies a very important
concept in Icarus and can be used to build <I>lazy</I> and <I>forced</I>
parsers as will be shown later.
<P>
The &quot;fields&quot; production describes the order of all data-fields
in the entry which are represented by the productions &quot;id&quot;,
&quot;def&quot; etc. The production &quot;def&quot; specifies
that the first line of the field starts with &quot;DEFINITION&quot;
but may be continued by lines beginning with two blanks. Note
that all data-field productions start with the command <B>$Wrt</B>
followed by the production name itself. If the production starts
with a command or action it applies to the entire production and
is, as mentioned already, executed after the matching of the production
with the input. This means that the entire data-field is written
to the token table &quot;fields&quot;. The name supplied will
be attached to each token so that later all tokens in the table
&quot;fields&quot; can be distinguished by their <I>token code</I>.
<P>
The general syntax of Genes is now completed and can be immediately
tested. For this we need to append the following lines to &quot;genes.is&quot;
<PRE>
if: $TestMode {
  $job = $JobNew:[prod:$rules skip:'\t ' fileName:"SRSDEMO:genes.dat"]
  while:$JobHasInput:$job {
    $JobTokens:[$job name:fields print:1]
    $JobNext:$job
  }
}
</PRE>
and add the following line to the top of &quot;genes.is&quot; as explained in
the section 'The Icarus Language'.
<PRE>
#!/bin/env icarus
</PRE>
<P>
and also set the executable permission using
<PRE>
% chmod +x genes.is
</PRE>
Then to test, simply type
<PRE>
% genes.is
</PRE>
<P>
This opens the flat file and creates a new parsing job with the
productions we have defined above (<B>$JobNew</B>). The parser
needs to iterate over all entries in &quot;Genes&quot; and parse
them one by one. The whole process can be viewed as a series of
parsing jobs for each entry. <B>$JobNext</B> resets the tables
&quot;entry&quot; and &quot;fields&quot; for the next job. The
command <B>$JobTokens</B> introduces the concept of <I>lazy parsing</I>,
it asks for all tokens in the table &quot;fields&quot; which by
default are printed to your screen together with the token codes.
It is important to understand that <B>$JobTokens</B> 'does' all
the parsing. This is what happens:
<P>
<B>$JobNext</B> associates the file with the parsing job. When
<B>$JobTokens</B> is called the file is still at the start and
nothing has really happened. However, asking for the token table
&quot;fields&quot; triggers a whole chain of events. The parser cannot
return the table &quot;fields&quot; since it does not exist yet; in order
to produce it it 'knows' it should use the production &quot;fields&quot;
which in turn needs the token table &quot;entry&quot; as input.
This token table does not exist either but its producer, the production
&quot;entry&quot;, can directly read from the file. Once parsing
the file with production &quot;entry&quot; is completed the output
token table can be handed over to production &quot;fields&quot;
which produces the token table &quot;fields&quot; which <B>$JobTokens</B>
finally prints it to the screen. We call this process &quot;lazy
parsing&quot; since nothing happens unless somebody asks for an
output token table. Also the parser is 'smart' enough to do the
minimum amount of work required to return the desired table. If you
replaced the name &quot;fields&quot; by &quot;entry&quot;
in the call of <B>$JobTokens</B>, the production &quot;entry&quot;
is triggered directly and parsing &quot;fields&quot; is not necessary.
<P>
Having defined &quot;entry&quot; and &quot;fields&quot; we can
proceed to add productions that extract words for indexing from
individual data-fields.
<PRE>
  # indexing
  word:   ~ /[a-zA-Z0-9_]+/ ~
  i_id:   ~ {$In:[fields c:id] $out:id} word word {$Wrt} ~
  i_date: ~ {$In:[fields c:date] $out:date 
  	     init{$month={JAN:1 FEB:2 MAR:3 APR:4 MAY:5 JUN:6 JUL:7 AUG:8 
  			  SEP:9 OCT:10 NOV:11 DEC:12}
  		 }
  	    } word
  	    /([0-9]+)-([A-Z][A-Z][A-Z])-([0-9]+)/ 
  	    {$Wrt:[s:$3 * 10000 + $month.$2 * 100 + $1]}
  	  ~ 
  i_def:  ~ {$In:[fields c:def] $out:def} word
  	    ( '('? /[^)., \n]+/ {$Wrt} /[).,\n]+/? )* ~
  i_cit:  ~ {$In:[fields c:cit] $out:cit} word word {$Wrt} ~
</PRE>
<P>
For each of four data-fields a production is specified. On top
of the parsing levels &quot;entry&quot; and &quot;fields&quot;
we build another level which consumes tokens from &quot;fields&quot;
as input. However, for extracting, (eg the entry name) we do not
have to parse all fields, the &quot;LOCUS&quot; line is quite enough!
So apart from the table name, the code of the desired token is
specified as in &quot;<TT>$In:[fields c:id]</TT>&quot;. Note that
supplying more than one argument to an Icarus function, in this
case <B>$In</B>, requires them to be enclosed in square brackets.
Each production declares its own output token table. In this case
we decided not to use the production names that start with &quot;i_&quot;
to make them disctinct from the ones parsing the entire fields,
but explicitly name them &quot;id&quot;, &quot;def&quot;, etc.
Note that the <B>$Wrt</B> command is used only for the parts of
the fields which should be put into the index. After adding the
above to &quot;genes.is&quot; we can test each production by replacing
the argument &quot;fields&quot; for <B>$JobTokens</B> with &quot;id&quot;,
&quot;date&quot;,&quot;def&quot;,&quot;cit&quot;.
<P>
The first symbol in all four productions is &quot;word&quot; which
is used to skip the field name. The most complicated production
is &quot;i_date&quot; which converts the date in a string form
such as &quot;02-FEB-1995&quot; into the number &quot;19950202&quot;.
This conversion is necessary for allowing range queries like all
entries later than the 1. January, 1995. The production shows
that <B>$Wrt</B> can write any string into the token table which
then needs to be specified as argument &quot;s&quot; since by
default it writes the current match. The three components of the
string date are parsed in one regular expression and extracted
as submatches afterwards. The variables <B>$1</B>, <B>$2</B>,
<B>$3</B> refer to whatever matches within the respective pair
of parentheses in the regular expression. Conversion of the month
name to a month number uses an associative list defined in an
<B>init </B>clause which executes the list definition only once
just after the precompilation phase of the Icarus program (See
the Icarus Manual for more information).
<P>
The file &quot;genes.is&quot; is now almost ready but one additional
command must be added that SRS needs for the indexing process.
The indexer needs to know the location, or file address, of the
entry in the flat file. This number can be obtained by the command
<B>$Fip </B>(Fip stands for File PoInter). The result must be
assigned to the Icarus variable <B>$entryFip</B> which is accessed
by the indexer. The change affects only the production &quot;entry&quot;
which is shown below again. 
<PRE>
  # the entry
  entry:     ~ {$In:[file:text] $Out pre{$Skip:0}} 
                ('LOCUS' {$entryFip=$Fip $Wrt} ln {$App}
                ('LOCUS' {$Not} ln {$App})*)?
             ~
</PRE>
<P>
The assignment &quot;<TT>$entryFip=$Fip</TT>&quot; is added to
the action of the first token of the entry, the name &quot;LOCUS&quot;.
The complete file &quot;genes.is&quot; is contained in the directory
&quot;SRSDEMO:&quot;.
<P>
The format of RefList is simpler than that of Genes and is defined
in an analogue manner. The difficult parts here are the parsing
of the single author names and the reference line for indexing.
The production &quot;entry&quot; allows the flat file to start
with some documentation or status information since the production
starts by skipping all lines that do not contain the literal &quot;ID&quot;
at the begin of the line.<I><B> </B></I>
<PRE>
#!/bin/env icarus

$rules={

  # the entry
  entry:     ~ {$In:[file:text] $Out}
               ('ID' {$Not} ln)*
               ('ID   ' {$entryFip=$Fip $Wrt} ln {$App}
               ('ID' {$Not} ln {$App})*)?
             ~

  # the data-fields
  fields:    ~ {$In:entry $Out} id ra? rt? rl?
             ~
  id:        ~ {$Wrt:id}   'ID   ' ln   ~ 
  ra:        ~ {$Wrt:ra}  ('RA   ' ln)+ ~
  rt:        ~ {$Wrt:rt}  ('RT   ' ln)+ ~
  rl:        ~ {$Wrt:rl}  ('RL   ' ln)+ ~

  # indexing
  i_id:      ~ {$In:[fields c:id] $Out:id} 
               'ID' /[A-Z0-9_]+/ {$Wrt} ~
  authors:   ~ {$In:[fields c:ra] $Out} 
               ('RA' ( author {$Wrt} /[,;]/ )* )* ~
  title:     ~ {$In:[fields c:rt] $Out} 
               ('RT' /[";]/? /[^ .,";\n]+/* {$Wrt} ln )* ~
  ref:       ~ {$In:[fields c:rl] $Out} 
               unpubl | journal ~
  author:    ~ name /[^,;]+/ ~
  unpubl:    ~ 'RL   Unpublished' ln ~
  address:   ~ ( 'RL' ( /[^ .,\n]+/ {$Wrt:adr} /[.,]+/? )* ln )*
             ~
  journal:   ~ 'RL' /[^0-9]+/ {$Wrt:jrn}
               /([0-9]+):([0-9]+)-([0-9]+)\\(([0-9]+)\\)/
               {$Wrt:[vol s:$1] $Wrt:[pg1 s:$2] $Wrt:[pg2 s:$3] $Wrt:[year s:$4]}
             ~

  # useful
  name:      ~ /[a-zA-Z0-9_'-]+/ ~
  num:       ~ /[0-9]+/ ~
  ln:        ~ /[^\n]*\n/ ~
}

if: $TestMode {
  $job =  $JobNew:[prod:$rules skip:'\t ' fileName:"SRSDEMO:reflist.dat"]
  while:$JobHasInput:$job {
    $JobTokens:[$job name:entry print:1]
    $JobNext:$job
  }
}
</PRE>
which can also be tested using
<PRE>
% chmod +x reflist.is
% genes.is
</PRE>
<H3><A NAME="AdditTricks">Additional Tricks for Debugging a Syntax
</A></H3>
<P>
Above, a few lines of Icarus were appended to the production list
for testing the syntax on the flat file. If the command <B>$JobTokens</B>
does not print the desired result we can use a number of tricks
to find out what is wrong. The main strategy is to use special
Icarus variables to print out information about the parsing process.
Theses variables are:
<DL>
<DT>$Ct 
<DD>the match of the current symbol
<DT>$It 
<DD>the input stream from the current position onwards 
</DL>
<P>
We can add additional <B>$Print</B> commands to any symbol in
the syntax. By default the commands are executed after the symbol
matched. The <B>pre</B> directive lets us print before the symbol
is parsed. The example shows again the &quot;fields&quot; production
from &quot;genes.is&quot; but 'embellished' with <B>$Print</B>
statements 'around' production &quot;id&quot; 
<PRE>
fields:    ~ {$In:entry $Out} 
             id {pre{$Print:&quot;...before: $It\n&quot;} $Print:&quot;...after: $It\n&quot;}
             def cit ref seq  ~
</PRE>
<P>
To compare the diagnostics with the input from the file itself
you could add <B>$Print</B> commands to the production &quot;ln&quot;:
<PRE>
ln:      ~ /[^\n]*\n/ {$Print:&quot;...the line is |$Ct|\n&quot;} ~
</PRE>
<P>
Icarus is an interpreted language, so debugging with diagnostic
messages can be quite rapid since no compilation is required.
<P>
Further information can be found in the section describing the Icarus debugger.
<H2><A NAME="StructDescript">The Structure Description </A></H2>
<P>
You are probably quite happy using Icarus up until this point, but now you
shall use the same Icarus syntax in a very different way - completely changing
it's symantics. Hold tight!
<P>
SRS needs to have more information about the databank than just the syntax :
the number and type of its data-fields, which tokens
should be put into which type of index and, how to establish links
to other databanks. This section describes the creation of the
other Icarus file for each Genes and RefList. In contrast to the
syntax file, it must be compiled before use and after any modification
with the command
<PRE>
% srssection
</PRE>
<P>
We start with &quot;genes.i&quot; which consists entirely of object
definitions of various predefined classes such as <B>$library</B>,
<B>$libformat</B>, <B>$field</B>, <B>$link</B>. Objects can be
associated with a name. In the example below, the object created
by <B>$library</B> is named &quot;GENES_DB&quot;. The name can
be used as a reference to the associated object by prefixing it
with a <TT>@.</TT>
<PRE>
GENES_DB:$library:[GENES group:@SEQUENCE_LIBS 
  format:@GENES_FORMAT maxNameLen:10 files:{
    $file:genes
  }
]
</PRE>
We define first the object of type <B>$library. </B>It is the
top level object in the hierarchically organized description of
Genes and represents it to SRS. The name &quot;GENES&quot;, defined
as the unnamed attribute of <B>$library</B>, is used by all SRS
programs, e.g., in the list of active databanks created by the
SRSWWW server. 
<P>
The three attributes <B>.group</B>, <B>.format</B> and <B>.file</B>
reference other objects: <B>.group</B> points to the library group
object (<B>$libgroup</B>) &quot;SEQUENCE_LIBS&quot; which is defined
in the file &quot;SRSICA:srsgen.i&quot;. Every databank must belong
to a group - you can let the new databank be a member of an already
existing group or of a new group which you define. <B>.file</B>
contains a list of <B>$file</B> objects which name all flat files
of the databank, in our case there is only the one named &quot;genes&quot;.
Note that the file name is given without directory name and file
extension which will be defined later inside the objects <B>$libloc</B>
and <B>$filetype</B> respectively. Attribute <B>.format</B> points
to the object &quot;GENES_FORMAT&quot; of type <B>$libformat </B>with
the format description which we define next:
<PRE>
GENES_FORMAT:$libformat:[fileType:@SEQ_FILE syntax:@GENES_SYNTAX
  fields:{
    $field:[@DF_ID code:id index:id indexToken:id]    
    $field:[@DF_Description code:def index:str indexToken:def]
    $field:[@DF_Date code:date index:int indexToken:date]
    $field:[@DF_Citation code:cit]
  }
]
</PRE>
<P>
Here, <B>.fileType</B> and <B>.syntax </B>reference objects described
later and <B>.fields</B> is a list of <B>$field</B> objects, one
for each data-field in Genes. The unnamed attribute for <B>$field</B>
is the pointer to the description of an abstract field type (<B>$srsfield</B>).
Attribute <B>.code</B> is very special in our guided tour since
it links to information in the file &quot;genes.i&quot;; eg, the
first <B>$field</B> object which represents the ID or locus line
has the <B>.code</B> &quot;id&quot; which means that in order
to obtain the ID line from the entry we must ask for the token
table &quot;fields&quot; and get the token with code &quot;id&quot;.
This, of course, requires for every databank that the production
with the ouput list &quot;fields&quot; must be defined. If the
contents of the data-field should be indexed attribute <B>.index</B>
must specify one of the 5 index types &quot;id&quot;, &quot;str&quot;,
&quot;int&quot;, &quot;real&quot; and &quot;link&quot;. Each databank
must have exactly one index of type &quot;id&quot; where a unique
name represents each entry. All other indices are optional. Attribute
<B>.indexToken</B> is another link to the syntax and specifies
the name of the token table which contains the words to be indexed
for each data-field. As a reminder the production to extract the
index token for the &quot;ID&quot; field from &quot;genes.is&quot;
is repeated:
<PRE>
i_id: ~ {$In:[fields c:id] $Out:id} word word {$Wrt} ~
</PRE>
<P>
The production writes into the token table &quot;id&quot; and
reads the token with the code &quot;id&quot; from the &quot;fields&quot;
table. The name of the syntax file is defined in a separate object
of the class <B>$syntax</B>:
<PRE>
GENES_SYNTAX:$syntax:[file:&quot;SRSDB:genes.is&quot;]
</PRE>
<P>
To allow queries and the presentation of query forms a data-field
needs to have a name. the class <B>$srsfield</B> allows the definition
of short and long names. If two fields from different databanks
are very similar, eg, the creation date or the short description,
the <B>$srsfield</B> object should be shared by both data-fields.
The file &quot;SRSDB:srsgen.i has a list of 'shareable' data-field
types - more can be added. Below are the two field type definitions
for the data-fields &quot;Date&quot; and &quot;Description&quot;
of the databank Genes:
<PRE>
DF_Date:$srsfield:[Date short:dat]
DF_Description:$srsfield:[Description short:des]
</PRE>
<P>
This means that later, when making a query, we can use either the long or the
short names of the two data-fields to search all kinase genes that were entered
into Genes after the 1.January, 1995 like this: 
<PRE>
getz -s -demo "[genes-description:kinase] &amp; [genes-dat# 1-jan-1995:]"
</PRE>
<P>
An important part of the databank structure is the description
of the flat file where the databank is stored.
<PRE>
SEQ_FILE:$filetype:[typename:dat maxline:100]
</PRE>
<P>
The definition contains the file extension name &quot;dat&quot;
which will be added to the name in $file defined above. Attribute
<B>.maxline </B>contains the maximum line length of the flat file
- be generous, it does not add much to storage requirements.
<P>
The last object in &quot;genes.i&quot; defines the link between
Genes and Reflist.
<PRE>
$link:[@GENES_DB to:@?REFLIST_DB fromField:@DF_Citation toField:@DF_ID
  token:cit]
</PRE>
<P>
SRS links two databanks usually by comparing the contents of a
certain data-field from one data-bank with those from another
data-field from the other databank. In this case the name listed
in the &quot;Citation&quot; field (<B>.fromField</B>) of Genes
must match a name in the &quot;ID&quot; field (<B>.toField</B>)
of RefList to link the Genes entry to one from RefList. The attribute
<B>.token</B> specifies the name of the token table with the names
(see also production 'i_cit' above) to be used for comparison.
Note that the reference assigned to <B>.fromField</B> has a ?
after the @. This means that the object named &quot;REFLIST_DB&quot;
may be absent which will invalidate the link. This feature facilitates
exchange of the file &quot;genes.i&quot;. If it is used on another
site that has the Genes databank but not RefList the <B>$link</B>
definition can be left in the file. 
<P>
The file &quot;genes.i&quot; is now complete and can be stored
in the directory &quot;SRSDEMO:&quot;. The file &quot;reflist.i&quot;
can be created in an analogous manner. It does not contain a  $link
definition since that would duplicate the one in &quot;genes.i&quot;.
<PRE>
REFLIST_DB:$library:[REFLIST group:@SEQUENCE_LIBS 
  format:@REFLIST_FORMAT cachesize:512 maxNameLen:10 files:{
    $file:reflist
  }
]
REFLIST_FORMAT:$libformat:[fileType:@SEQ_FILE syntax:@REFLIST_SYNTAX
  fields:{
    $field:[@DF_ID code:id index:id indexToken:id]    
    $field:[@DF_AUTHORS code:refaut index:str indexToken:authors]
    $field:[@DF_Title code:title index:str indexToken:title]
    $field:[@DF_Reference code:ref index:str indexToken:ref]
  }
]

DF_Reference:$srsfield:[SeqReference short:rff group:@DF_ALL]
DF_Citation:$srsfield:[Citation short:cit] group:@DF_ALL]
REFLIST_SYNTAX:$syntax:[file:&quot;SRSDB:reflist.is&quot; level3:1]
</PRE>
<H2><A NAME="AddingGenes">Adding Genes and Reflist to the System
</A></H2>
<P>
The next step is to tell SRS that the two new databanks exist
and where they physically reside. Within the file &quot;SRSDB:srsdb.i&quot;
all databanks are declared and assigned a location and a <I>library
ID</I>. At the beginning of the file there is a long list of include
statements, eg, <TT>file:&quot;SRSDB:swissprot.i&quot;</TT> which
includes a &quot;.i&quot; for databanks installed. For Genes and
RefList you must add
<PRE>
file:&quot;SRSDEMO:genes.i&quot;
file:&quot;SRSDEMO:reflist.i&quot;
</PRE>
<P>
For each databank a library -ID must be defined. The library ID
is a number between 1 and 255 and is used to unambigously identify
the databank source within an entry-ID which SRS stores as representative
of a retrieved entry. We chose the numbers 254 and 255 for Genes
and RefList respectively.
<P>
The two <B>$libid</B> definitions must be inserted in the list
<B>.libIds</B> of the <B>$srsdb</B> definition. 
<PRE>
$srsdb:[ 
  libIds:{
    $libid:[254 lib:@?GENES_DB] 
    $libid:[255 lib:@?REFLIST_DB]
  } 
]
</PRE>
<P>
Finally two objects of class <B>$libloc</B> must be inserted in
the list <B>.libs</B> of the <B>$site</B> definition. 
<PRE>
$site:[name:unix
  libs:{
    $libloc:[@GENES_DB dir:&quot;SRSDEMO:&quot;]
    $libloc:[@REFLIST_DB dir:&quot;SRSDEMO:&quot;]
  }
]
</PRE>
<P>
The directory name &quot;SRSDEMO:&quot; refers to the environment
variable (UNIX) or logical name (VMS) defined by the command
script &quot;SRSETC:prep_srs&quot; for UNIX C-shell users 
(&quot;SRSETC:prep_srs.sh&quot; for UNIX Bourne shell users,
&quot;SRSETC:prep_srs.com&quot; for VMS). Names like
that are always separated from the file name with a colon.
<P>
We are now finished with the modifications to the file &quot;srsdb.i&quot;
and can save it. To bring the changes into effect, the file &quot;srs.i&quot;
which includes among other files &quot;srsdb.i&quot; must be compiled
with the command
<PRE>
srssection
</PRE>
<P>
If the compiler reports errors you must correct them and run the command
again.</A>
<H2><A NAME="TestandDebug">Testing and Debugging Phase </H2>
<P>
Before indexing Genes and RefList we should convince ourselves
that the information in the &quot;.i&quot; is correct and that
it properly connects to the token tables defined in the &quot;.is&quot;
files. The command
<PRE>
srsbuild -s demo -info genes
</PRE>
<P>
displays the information SRS has about Genes. The &quot;-s&quot;
option tell <B>srsbuild</B> to select the site demo (and not the main site
containing all the databanks). This allows the demo site to be kept separate
but switchable.
<P>
After checking their
correctness run
<PRE>
srsbuild -s demo -d genes
</PRE>
<P>
This parses the databank for indexing all data-fields but instead
of putting the extracted words into the index it prints them onto
the screen. If printing to the screen is slow, one can redirect the output
to a file like so:
<PRE>
srsbuild -s demo -d genes> genes.debug
</PRE>
<P>
It is possible to run the command for individual data-fields.
<PRE>
srsbuild -s demo -d genes -f 'id date'
</PRE>
<P>
prints only the contents of the &quot;ID&quot; and the &quot;Date&quot;
fields. If you find errors then either the name of the index token
specified in &quot;genes.i&quot; or one or more syntax rules in
&quot;genes.is&quot; can be incorrect. Again, after  corrections
in the &quot;genes.i&quot; the command &quot;<TT>srssection</TT>&quot;
must be run whereas after corrections in &quot;genes.is&quot;
you can immediately try again.
<P>
Links must be built separately from the indices. The &quot;-l&quot;
option directs <B>srsbuild</B> to process link information only.
The command 
<PRE>
srsbuild -l -d genes -s demo
</PRE>
<P>
should display the references in the &quot;Citation&quot; field
of Genes.
<P>
If everything is well build all indices manually with the &quot;-w&quot;
option added. This will inform you of any syntax errors found
and of any cross-reference that could not effectively used for
building a link. The following commands build all indices for
both Genes and RefList and then the link between Genes and RefList.
The &quot;-c&quot; option directs <B>srsbuild</B> to compress
the indexes.
<PRE>
srsbuild -s demo -w genes
srsbuild -s demo -c genes
srsbuild -s demo -w reflist
srsbuild -s demo -c reflist
srsbuild -s demo -w -l genes
</PRE>
<P>
One final check you can do is to analyse the contents of individual
indices. The command
<PRE>
getz '[reflist-authors:*]' -lv -s demo
</PRE>
<P>
searches all values in the &quot;authors&quot; index of RefList
that match the wildcard '*' and prints them alphabetically sorted
to the screen.
<H2><A NAME="IndexBuild">Databank Maintenance </A></H2>
<P>
Indices must be built separately for each databank which needs
to be done whenever a new release of that databank is installed.
For instance the EMBL nucleotide sequence library is released
about every 3 months. New entries that come in between releases
can be accumulated in a separate file which can be updated daily
together with the indices. For both tasks which are normally handled
by scripts an <B>srsbuild </B>command for the generation of indices
could be easily added.
<P>
However, besides the search indices, the link indices must be
built as well. These are a bit more complex since they depend
on two databanks. Once either partner changes a new link index
is required. So when a new release of, e.g., the EMBL nucleotide
databank is installed, all the link indices from or to EMBL must
be recreated. To do that we need the knowledge about all links
and their types.
<P>
The good news is that there is a program that can deal with all
these complications and manage the entire task of updating indices:
<B>srscheck</B>, once called, examines the status of each installed
databank and writes a script with all the commands to build new
indices. By default this script is called <B>srsupdate</B>. It
is advisable to set up a periodical job that minimally has the
following three commands (if you are using a C-shell or equivalent):
<PRE>
source etc/prep_srs
srscheck
srsupdate
</PRE>
(or if you are using Bourne-shell or equivalent): 
<PRE>
. etc/prep_srs.sh
srscheck
srsupdate
</PRE>
<P>
Such a job could run every hour or even on a shorter period -
of course it should check if the index updating is already under
way.
<H3><A NAME="MemControl">Controlling Memory Requirements </A>
</H3>
<P>
During building of a search index, all of the index must be kept
in memory until it is finished, when it will be saved into the file with the
&quot;inx&quot; extension. If this becomes too heavy a burden
on your computer system, the indexing process can be configured
so that instead of building the index all at once, it will build it
in several iterations over the databank.
<P>
To do this, you must first modify the Icarus programs of the databanks that
you cannot build in one round. Edit the attribute .<B>maxindexsizekb</B>
of the <B>$library </B>object which sets an estimation size of
the largest index file (with the &quot;inx&quot; extension) of
the databank. You can obtain it by looking at the files in the
SRS index directory - a rough estimate should work! The attribute
.<B>relindexsize</B> in the <B>$field </B>object allows to specify
relative to the global maximum size of an index. This number ranges
from 0 to 1. The default value for this number is 1.
<P>
Having specified those number you can now call <B>srscheck</B>
with the option &quot;-s&quot; which specifies the maximum number
of kilobytes you want to let the indexing process use for allocating
the indices. 
<PRE>
srscheck -s 20000 
</PRE>
<P>
<B>srscheck</B> takes this number and then for each databank with
a total index size above 20 megabyte issues several <B>srsbuild
</B>commands.
<H3><A NAME="AssignRel">Assigning Release Numbers </A></H3>
<P>
Often biologists need to specify a release number if they publish
results that were obtained from analysis involving a particular
databank (e.g., homology search). In SRS it is possible to assign
a release number, or name, to a set of indices with the command:
<PRE>
srsbuild -s demo -rel &quot;22&quot; genes
</PRE>
<P>
This assigns the current release of Genes the release number &quot;22&quot;.
Unfortunately this must be done by hand for most if not all databanks
since there is no commonly accepted way of specifying the current
release number (e.g. in the first line of the flat file or in
a special file called &quot;release&quot;).
<H2><A NAME="ExtSRSWWW">Extensions for the SRSWWW Server </A>
</H2>
<P>
If you have an SRSWWW server installed there are a few optional
additions for the two databanks Genes and RefList you should consider
to do:
<P>
Add a description of a databank to be included into the databank
information page.
<P>
Tell the system how to add hypertext links into entries to be
displayed.<BR>
<H3><A NAME="AddDBInfo">Adding Text to the Databank Information
Page </A></H3>
<P>
The databank information page in the SRSWWW server lists all indices
and links for a given databank. This information is generated
automatically; however, the page can also contain handwritten
text which may even have hypertext links to, e.g., the site producing
that databank.
<P>
Those texts are contained in the &quot;.it&quot; file in $SRSDB
directory, For Genes and RefList databaks there are &quot;genes.it&quot;
and &quot;reflist.it&quot; files. Every &quot;.it&quot; file has
only one Icarus list variable - <B>$main</B>. The <B>$main </B>list
has several elements : <B>.description, .more, .citation, .ftpSite,
.fields, .signature</B> and <B>.date</B>. The meaning of every
element is obvious. The <B>.fields </B>element<B> </B>usualy is
a list also and contains information about entry fields. You may
take a look at &quot;general.it&quot; file in $SRSDB directory
that contains desctiptions of most common fields in SRS.
<H3><A NAME="HypertextLinks">Specifying Hypertext Links </A></H3>
<P>
The entries of Genes and RefList are linked by SRS links. For
a single Genes entry the related RefList entries can be obtained
with a single SRS query. Since the link to RefList is actually
shown in the &quot;Citation&quot; field of Genes it can be converted
into a hypertext link that on clicking calls the RefList entry
identified by the highlighted name. SRS supports the insertion
of hypertext links into entries before they are displayed to the
user. First, the hypertext link to RefList needs to be declared
in the file &quot;srsdb.i&quot; as an object of class <B>$href</B>.
<PRE>
$href:[reflistR link:&quot;&lt;A HREF=wgetz?[reflist-id:%s]&gt;%s&lt;/A&gt;&quot;]
</PRE>
<P>
This defines the HTML code with wich a RefList name should be
replaced and associates it with the name &quot;reflistR&quot;.
Within string assigned to <B>.link</B> all places where the actual
RefList entry name must be inserted is indicated by a &quot;%s&quot;.
This link uses the local &quot;wgetz&quot; program to search and
display the RefList entry with the specified &quot;ID&quot;. It
is also possible to use SRSWWW servers installed or to point to
completely different systems, eg, Medline or GDB.
<P>
SRS needs to be instructed where and how to insert the hypertext
links. This information is added to the syntax in &quot;genes.i&quot;
as a separate production
<PRE>
h_cit: ~ {$In:[fields c:cit t:html]} 
         word word {$Rep:{$ParStr:reflistR $Ct $Ct}} ~ 
</PRE>
<P>
This example introduces  <I>forced parsing</I>. The command &quot;$In:[field
c:cit t:html]&quot; asks for tokens with the code &quot;cit&quot;
from the token table&quot;fields&quot;. The additional argument
&quot;t:html&quot; specifies that the production &quot;h_cit&quot;
should be only called if the task &quot;html&quot; is active.
This means that after production &quot;fields&quot; has successfully
completed it checks if the task &quot;html&quot; is active and
then calls the production &quot;h_cit&quot; which is in contrast
to lazy parsing where, eg, the consumer &quot;i_cit&quot; activates
the producer &quot;fields&quot;. 
<P>
The <B>$Rep</B> command replaces the current match (&quot;word&quot;)
with the hypertext link which is specified as a list of the print
format define in the <B>$href</B> object above followed by instances
of <B>$Ct</B> which are the entry names to be inserted at the
positions marked with &quot;%s&quot;. <B>$ParStr</B> returns the
string value of the global variable &quot;reflistR&quot; which
is a way in which the the parts in SRS written in Icarus can communicate
the the ones written in C.
<P>
You can check the correctness of hypertext link insertion with
the SRSWWW server or with the program getz. The following command
extracts the the &quot;Citation&quot; field from a single entry.
The second does the same but activates the task &quot;html&quot;
with the additional &quot;-html&quot; on the command line 
<PRE>
getz -s -demo '[genes-id:?] -f cit
getz -s -demo '[genes-id:?] -f cit -html 
</PRE>
</BODY>
</HTML>
h the the parts in SRS written in Icarus can communicate
the the ones written in C.
<P>
You can check the correctness of hypertext link insertion with
the SRSWWW server or with the program getz. The following command
extracts the the &quot;Citation&quot; field from a single entry.
The second does the same but activates the task &quot;html&quot;
with the additional &quot;-html&quot; on the command line 
<PRE>
getz -s -demo '[genes-id:?] -f cit
getz -s -demo '[genes-id:?] -f cit -html srs/www/doc/usage.html
<HTML>

<HEAD>

<META NAME="GENERATOR" CONTENT="Internet Assistant for Word 1.0Z">
<META NAME="AUTHOR" CONTENT="egal">
</HEAD>

<BODY>

<H1><A NAME="progdes"></A>Program Descriptions</H1>

<H2><A NAME="getz"></A>GETZ</H2>

<P>
<B>getz</B> is the command line interface to the SRS query system.
It offers access to all the functionality that there is in SRS
albeit lengthy command lines must be typed.
<P>
The most complicated part of a <B>getz</B> command is the query
expression which is explained in the chapter &quot;The SRS Query
Language&quot; on page 0. The command line options mostly influence
the output you get after a successful query. With GETZ you usually
make a query and you get back a set of entries in some form:
<UL>
<LI>only entry names and entry-IDs; 
<LI>the entry annotation;
<LI>the sequence selected data-fields;
<LI>complete features;
<LI>features with their begin and/or end positions redefined.
</UL>
It is also possible to obtain a list of all accessible databanks
or information about individual databanks.
<H3><A NAME="getzsum"></A>Command Line Summary</H3>
<B>getz</B> was originally written as a workbench for testing
new functionality within SRS which means that new options will
be added all the time. Some options might have been added since
this documentation was written!
<P>
INCLUDE OPTIONS getz
<P>
<H3><A NAME="getzex"></A>Examples</H3>
<PRE>
getz -libs
</PRE>

<P>
Lists all available databanks.
<PRE>
getz -info swissprot
</PRE>

<P>
Displays information about SwissProt: the data-fields and their
index types and the links. Note that for retrieval both the short
and the long names can be used.
<PRE>
getz '[swissprot-id:acha_human]' -t
</PRE>

<P>
Retrieves the SwissProt entry &quot;Acha_human&quot; and displays
the annotation part.
<PRE>
getz '[embl-def:insulin&amp;receptor]' -td -sf gcg -fil
</PRE>

<P>
Searches all insulin receptor sequences from EMBL as defined by
the definition field and displays for each entry both text and
sequence part in the GCG sequence format. The entries are written
into separate file with the name of the entry and a &quot;.gcg&quot;
appended.
<PRE>
getz '[medline-authors:smith,j.]' -f 'id aut ref'
</PRE>

<P>
Searches all articles in Medline where J. Smith is an author and
displays for each entry the ID line, the author names and the
reference line. The example shows that both short and long data-field
names can be used (Use the option &quot;-info&quot; to obtain
the list of all data-fields available for searching).
<PRE>
getz '[embl-key:*glu*]' -rep -pmin 100
</PRE>

<P>
Searches all words containing &quot;glu&quot; in the keyword index
of the EMBL databank. As a result of the query only the strings
that represent at least 100 entries will be listed. 
<PRE>
getz '[prosite-def:protease]' &gt; q.dat
getz '@q.dat &gt; swissprot'
</PRE>

<P>
The first query retrieves all &quot;protease&quot; entries in
Prosite and writes the resulting entry list into the file &quot;q.dat&quot;.
The second query accesses the list stored in &quot;q.dat&quot;
and links the set of Prosite entries to SwissProt. Note that any
file of entry names can be used as input.
<PRE>
getz '[embl-org:escherichia]' -link ecdc -f def
</PRE>

<P>
Retrieves all EMBL sequences from E.coli and prints for each entry,
if available, the corresponding entry from ECDC. Prints for both
entries the definition line.
<PRE>
getz '[sequence-all:homeobox]' -libs 'swissprot pir trembl'
</PRE>

<P>
Searches &quot;homeobox&quot; in all text fields of the databanks
SwissProt, PIR and TREMBL. 
<PRE>
getz '[embl-features:cds]&amp;[embl-org:yeast]' -f 'id fts' -d
</PRE>

<P>
Retrieves all CDS features (coding sequences) from yeast as a
list of entries that contain the ID line of the parent entry,
the feature description and its sequence.  
<PRE>
getz '[embl-features:cds]&amp;[embl-org:yeast]' -pos
</PRE>

<P>
Returns the same set of features as a GCG compatible list of names.
The begin and end positions of each CDS feature are given together
with the name of the parent entry. &quot;joins&quot; are converted
into separate lists of subentries.
<PRE>
getz '[embl-fts:cds]&amp;[embl-org:yeast]' -d \
     -fbegs 50 -fends 50 -fendsrbeg
</PRE>

<P>
Searches all introns from yeast and extracts for each intron found
the sequences 50 bp upstream and 50 bp downstream of the intron
begin, that is, all exon-intron boundaries. 

<H2><A NAME="wgetz"></A>WGETZ</H2>

<H3><A NAME="wgetzsum"></A>Command Line Summary</H3>
INCLUDE OPTIONS wgetz

<H2><A NAME="srsbuild"></A>SRSBUILD</H2>

<P>
The program srsbuild builds the indices in SRS. It must be called
separately for every databank. For building the indices it is
not really necessary to invoke srsbuild directly. The program
srscheck checks for each databank if indices have to be built
and writes a script with the srsbuild commands necessary to get
the index system up to date. 
<P>
However, there are a few occasions such as testing a newly written
ODD file for a new databank or for assigning a release name/number
to the set of indices of a databank where srsbuild must be used
directly.

<H3><A NAME="srsbuildsum"></A>Command Line Summary</H3>
INCLUDE OPTIONS srsbuild
<P>
<H3><A NAME="srsbuildex"></A>Examples</H3>
<PRE>
srsbuild swissprot 
</PRE>

<P>
Builds all search indices (not the link indices!) for the SwissProt
databank.
<PRE>
srsbuild swissprot -c
</PRE>

<P>
Compresses the indices build by above command. Compression means
here not just a reduction in space but a reorganization of the
index that makes its use more efficient.
<PRE>
srsbuild swissprot -d -f -w 'aut tit ref'
</PRE>

<P>
This command is very useful for testing new databank formats written
in ODD. It displays all words to be indexed for the <B>authors</B>,
<B>title </B>and <B>reference </B>fields of SwissProt. The &quot;-w&quot;
option turns on the printing of syntax errors found by the parser.
 These errors may reflect errors in the databank as well as errors
in the grammar written in EBNF.
<PRE>
srsbuild swissprot -l -d
</PRE>

<P>
Displays cross-references read from the databank without creating
the link index.
<PRE>
srsbuild swissprot -rel &quot;23.1&quot;
</PRE>

<P>
Assigns a release number to a set of indices.
<PRE>
srsbuild swissprot -t
</PRE>

<P>
Sets the time stamp within the indices to the current data. This
becomes necessary after the databank files have been moved to
another location which changes the modification data of these
files. SRS will think the indices out of date since the file date
is now more recent than the indexing time stamp.

<H2><A NAME="srscheck"></A>SRSCHECK</H2>

<P>
When maintaining indices for a large number of flat file databanks
a huge number of indices has to be created and maintained. Whenever
a new release of a databank supercedes an old file the indices
for that databank have to be build again. But also all link indices
to or from the new databank must be rebuild. This might inolve
reading cross-reference information from databanks other than
the new one. 
<P>
The program srscheck relieves you of having which indices have
to be build at a given time. It compares the status of indices
and the databank files and writes a command procedure with all
srsbuild calls necessary to rebuild the indices that are out of
date. 
<P>
Using srscheck the maintenance of indices can be completely automized.
You can write a script to be executed daily, or even hourly that
has to commands:
<PRE>
srscheck
srsupdate
</PRE>

<P>
The latter command invokes the script produced by srscheck.

<P>
<H3><A NAME="srschecksum"></A>Command Line Summary</H3>
INCLUDE OPTIONS srscheck
<P>
<H3><A NAME="srscheckex"></A>Examples</H3>
<PRE>
srscheck
srscheck -l 'swissprot embl'
</PRE>



<H2><A NAME="icarusComm"></A>ICARUS</H2>

<P>

<H3><A NAME="icarussum"></A>Command Line Summary</H3>
<P>
INCLUDE OPTIONS icarus
<P>
<H2><A NAME="odd"></A>NODD</H2>

<P>
The ODD compiler processes all information stored in the files
in the &quot;odd&quot; directory and produces a binary file that
is not platform independent at the moment. After every change
in one of the files in the &quot;odd&quot; directory the this
section file must be produced again. 
<P>
It is normally not necessary to know more details about the command
line interface since the alias
<PRE>
srssection
</PRE>

<P>
takes care of the recompilation
<H3><A NAME="oddsum"></A>Command Line Summary</H3>
INCLUDE OPTIONS nodd
<P>
<H3><A NAME="oddex"></A>Examples</H3>
<PRE>
odd -ds srswin
</PRE>

<P>
Compiles all files that pertain to the &quot;srswin&quot; collection
of ODD files. This command is defined by the alias <B>srssection</B>




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February 12, 1996

This GIF file was assembled with GIF Construction Set from:

Alchemy Mindworks Inc.
P.O. Box 500
Beeton, Ontario
L0G 1A0
CANADA.

This comment block will not appear in files created with- a registered version of GIF Construction Set

Alchemy Mindworks Inc.
P.O. Box 500
Beeton, Ontario
L0G 1A0
CANADA.

This comment block will not appear in files created with a registered version of GIF Construction Set
February 12, 1996

This GIF file was assembled with GIF Construction Set from:

Alchemy Mindworks Inc.
P.O. Box 500
Beeton, Ontario
L0G 1A0
CANADA.

This comment block will not appear in files created with- a registered version of srs/www/images/gray_aluminum.gif
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