#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: srsgen.i,v $
#    $Revision: 1.114.2.2.2.11 $
#    $Date: 2003/11/20 14:52:39 $
#    $Author: hilbers $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

# syntaxes

$XML_SYNTAX=$Syntax:[name:xml file:"SRSICA:xml2obj.is"]

$SRSQUERY_SYNTAX = $Syntax:[file:"SRSICA:srsquery.i" name:srsquery 
  ignore:" \r\t\n"
]
$SRSQUERYTREE_SYNTAX = $Syntax:[file:"SRSICA:srsquerytree.i" name:srsquerytree
  ignore:" \r\t\n"
]
$MakeWild_Syntax = $Syntax:[file:"SRSICA:makewild.i" name:makeWild 
  ignore:" \r\t\n"
]
$ICARUS_SYNTAX=$Syntax:[name:icarus file:"SRSICA:icarus.i" 
  comment:"^#[^\n]*\n" name:icarus
  ignore:" \t\n"
]
$SRSQLANALYSE_SYNTAX = $Syntax:[file:"SRSICA:srsqlAnalyze.is" name:srsqlAnalyse
  ignore:" \r\t\n"
]

$ColIcarus_Syntax=$Syntax:[name:colicarus file:"SRSICA:colicarus.i" ignore:" \n\t"]
$SeqInput_Syntax=$Syntax:[name:seqinput file:"SRSDB:readseq.i"]
$ReadSeq_Syntax=$Syntax:[file:"SRSDB:readseq.i" name:readseq ignore:""]
$ftseq=$Syntax:[name:ftseq file:"SRSDB:ftseq.is" ignore:" \t\n"]

# data bank groups
$SEQUENCE_LIBS=$LibGroup:[Sequence short:SQ 
     printName:'Sequence libraries - complete'
     search:all show:y]
$FASTASEQ_LIBS=$LibGroup:[FastaSequences short:FSQ 
     printName:'FASTA formatted sequences'
     search:all show:y]
$SEQUENCESUB_LIBS=$LibGroup:[SequenceSub 
     short:SSQ printName:'Sequence libraries - subsections'
     search:all show:n]
$SEQRELATED_LIBS=$LibGroup:[SeqRelated]
$TRANSFAC_LIBS=$LibGroup:[TransFac short:'tf']
$USER_LIBS=$LibGroup:['User Owned Databanks' short:usr]
$APPLICATION_LIBS=$LibGroup:['Application Results' short:app]
$GQ_LIBS=$LibGroup:[GeneQuiz short:gq search:all]
$LITERATURE_LIBS=$LibGroup:[Literature short:lit]
$PROTSTRUCT_LIBS=$LibGroup:[Protein3DStruct short:'3d']
$GENOME_LIBS=$LibGroup:[Genome short:gen]
$MAP_LIBS=$LibGroup:[Mapping short:gen]
$MUTATION_LIBS=$LibGroup:['Mutations' short:'mut']
$SPMUTATION_LIBS=$LibGroup:['Locus Specific Mutations' short:'lsm']
$PATHWAY_LIBS=$LibGroup:['Metabolic Pathways' short:mpw]
$MISC_LIBS=$LibGroup:[Others]
$SYSTEM_LIBS=$LibGroup:[System]
$SNP_LIBS=$LibGroup:['SNP' short:'snp']
$BS_LIBS=$LibGroup:[bioSCOUT]
$BSF_LIBS=$LibGroup:[bSF short:bsf search:all]
$BSSUB_LIBS=$LibGroup:[bioSUB]
$GENCHEM_LIBS=$LibGroup:['GenChem' short:gc show:n]
$INTERPRO_LIBS=$LibGroup:['InterPro&Related' show:y]
$RDB_LIBS=$LibGroup:[Relational short:RDB search:all show:y]
$XML_LIBS=$LibGroup:['XML database' short:XML search:all show:y]
 
# data field types
$DF_Class=$SrsField:[Class short:cla]
$DF_Synonyms=$SrsField:[Synonyms short:SYM]
$DF_HeaderField=$SrsField:[HeaderField short:hd type:header]
$DF_ALL=$SrsField:[AllText short:all isGroup:yes type:str] 
$DF_ALLText=$SrsField:[AllText short:all] 
$DF_AID=$SrsField:[AccID short:aid isGroup:yes type:str group:$DF_ALL] 
$DF_ID=$SrsField:[ID short:id  group:$DF_ALL group:$DF_AID]
$DF_NID=$SrsField:[NID short:nid group:$DF_ALL]
$DF_GID=$SrsField:[GID short:gid group:$DF_ALL]
$DF_FtGID=$SrsField:[FeatureGID short:fgi group:$DF_ALL]
$DF_PID=$SrsField:[PID short:pid group:$DF_ALL]
$DF_ACCNO=$SrsField:[AccNumber short:acc group:$DF_ALL]
$DF_Accession=$SrsField:[AccNumber short:acc group:$DF_ALL]
$DF_PrimAccession=$SrsField:[PrimAccNumber short:pac]
$DF_SeqLength=$SrsField:[SeqLength short:sl]
$DF_Date=$SrsField:[Date short:dat]
$DF_CRC=$SrsField:[crc short:crc]
$DF_DBNAME=$SrsField:[dbname short:dbn]
$DF_CREDate=$SrsField:[DateCreated short:crd]
$DF_LUPDate=$SrsField:[LastUpdated short:crlu]
$DF_AUPDate=$SrsField:[LastAnnotationUpdate short:lau]
$DF_SUPDate=$SrsField:[LastSequenceUpdate short:lsu]
$DF_Description=$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]
$DF_TaxId=$SrsField:[NCBI_TaxId short:txi group:$DF_ALL]
$DF_GeneName=$SrsField:[GeneName short:gen group:$DF_ALL]
$DF_Molecule=$SrsField:[Molecule short:mol group:$DF_ALL guiInfo:$GI_CheckList]
$DF_MolWeight=$SrsField:[MolWeight short:mow]
$DF_Authors=$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]
$DF_RefJournal=$SrsField:[Journal short:jnl]
$DF_RefYear=$SrsField:[Year short:yr]
$DF_RefFirstPage=$SrsField:[FirstPage short:fp]
$DF_RefVolumeNo=$SrsField:[VolumeNo short:vol]
$DF_RefPos=$SrsField:[RefPosition short:rp]
$DF_RefComment=$SrsField:[RefComment short:rc]
$DF_RefCommentCode=$SrsField:[RefCommentCode short:rcc guiInfo:$GI_MultiSelectOver]
$DF_Division=$SrsField:[Division short:div  guiInfo:$GI_CheckList]
$DF_SubLibrary=$SrsField:[SubLibrary short:sublib  guiInfo:$GI_CheckList]
$DF_LINK=$SrsField:[Link short:lnk]
$DF_LINK_ENH=$SrsField:[Link_enh short:lnk_enh]
$DF_Type=$SrsField:[Type short: typ]
$DF_COMMENT=$SrsField:[Comment short:cc group:$DF_ALL]
$DF_Comment=$SrsField:[Comment short:cc group:$DF_ALL]
$DF_CommentType=$SrsField:[CommentType short:cct group:$DF_ALL
  guiInfo:$GI_MultiSelectOver
]
$DF_Consortium=$SrsField:[Consortium short:con]

$DF_SubmissionDate=$SrsField:[SubmissionDate short:sub]
$DF_Tissue=$SrsField:[Tissue short:tis group:$DF_ALL]
$DF_Strain=$SrsField:[Strain short:str]
$DF_Transposon=$SrsField:[Transposon short:tra]
$DF_Plasmid=$SrsField:[Plasmid short:pla]
$DF_Patent=$SrsField:[Patent short:pat group:$DF_ALL]
$DF_PatentDate=$SrsField:[PatentDate short:pdt group:$DF_ALL]
$DF_ReportType=$SrsField:[ReportType short:rty group:$DF_ALL]
$DF_dbref=$SrsField:[DBxref short:dr group:$DF_ALL]
$DF_dbnam=$SrsField:[DbName short:dbn guiInfo:$GI_MultiSelect]

$DF_Factor=$SrsField:[Factor short:tf 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 guiInfo:$GI_CheckList]
$DF_Size=$SrsField:[Size short:siz]
$DF_Protocol=$SrsField:[ExpProtocol short:ptc group:$DF_ALL]
$DF_Express=$SrsField:[ExpresRegul short:ess group:$DF_ALL]

$DF_SourceSTSid=$SrsField:[STSName short:sts]
$DF_Chromosome=$SrsField:[Chromosome short:chr]
$DF_MapLocation=$SrsField:[MapLocation short:mlc  group:$DF_ALL]
$DF_Library=$SrsField:[Library short:lib]
$DF_Alphabet=$SrsField:[Alphabet short:alf]
$DF_RF=$SrsField:[RF short:rf]
$DF_CS=$SrsField:[CS short:cs]
$DF_MP=$SrsField:[Map short:map]
$DF_Command=$SrsField:[Command short:com]
$DF_Checksum=$SrsField:[Checksum short:cks]

$DF_FtGene=$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]

$DF_SeqVersion=$SrsField:[SeqVersion short:sv]
$DF_Sequences=$SrsField:[Sequences short:nsq]

$DF_Compound=$SrsField:[Compound short:com group:$DF_ALL]
$DF_Header=$SrsField:[Header short:hdr group:$DF_ALL]
$DF_Source=$SrsField:[Source short:src group:$DF_ALL]
$DF_Substrate=$SrsField:[Substrate short:sub group:$DF_ALL]
$DF_WaterMols=$SrsField:[WaterMols short:wat]
$DF_Kind=$SrsField:[Kind short:kin]
$DF_Method=$SrsField:[Method short:met group:$DF_ALL]
$DF_Genbankid=$SrsField:[GenbankAcc short:gid]
$DF_Cloneid=$SrsField:[CloneID short:cid]
$DF_DNA=$SrsField:[DnaType short:typ]
$DF_CdsLocation=$SrsField:[CDSLocation short:clc]
$DF_GDB=$SrsField:[GDB short:gdb]
$DF_Text=$SrsField:[Text short:txt]
$DF_GenType=$SrsField:[GenType short:gtp]
$DF_Seq=$SrsField:[Sequence short:sq]
$DF_RHPanel=$SrsField:[RHPanel short:pan]

$DF_GeneProduct=$SrsField:[GeneProduct short:pro group:$DF_ALL]
$DF_IsoelectricPoint=$SrsField:[IsoelectricPoint short:iep]
$DF_NAlign=$SrsField:[NAlign short:nal]

$DF_JobName=  $SrsField:[ JobName      short:jnm group:$DF_ALL ]
$DF_JobSerial=$SrsField:[ JobSerial    short:jsr ]
$DF_PercSim=  $SrsField:[ PercentSimil short:psi ]
$DF_PercIdt=  $SrsField:[ PercentIdent short:piy ]
$DF_Len=$SrsField:[ Length short:len]
$DF_Map=$SrsField:[MapLocation short:mlc  group:$DF_ALL]

#taken from application .i files

$DF_BitScore=$SrsField:[ BitScore short:bsc ]
$DF_MatchLen=$SrsField:[ MatchLength short:mtl ]
$DF_SW_Score=$SrsField:[SW_Score      short:sws ]
$DF_E_Score=$SrsField:[E_Score  short:esc ]
$DF_Z_OptScore=$SrsField:[Z_OptScore    short:zsc ]
$DF_OptScore=$SrsField:[OptScore    short:osc]
$DF_Score=$SrsField:[Score short:sco ]
$DF_Eval=$SrsField:[Evalue short:eva ]
$DF_HMMhit=$SrsField:[HMMhit short:hmh ]
$DF_Init_n=$SrsField:[Init_n  short:inn ]
$DF_Init_1=$SrsField:[Init_1  short:in1 ]
$DF_Frame=$SrsField:[Frame short:fra guiInfo:$GI_MultiSelectOver]


# counting things subentry

$DF_CounterItem=$SrsField:[CountedItem short:cti guiInfo:$GI_Menu]
$DF_CounterN=$SrsField:[CountedN short:ctn]

# for sequence features
$DF_FtKey=$SrsField:[FtKey short:ftk guiInfo:$GI_MultiSelectOver]
$DF_FtQualifier=$SrsField:[FtQualifier short:ftq 
  guiInfo:$GI_MultiSelectOver
]
$DF_FtSource=$SrsField:[FtSource short:fts]
$DF_FtDescription=$SrsField:[FtDescription short:ftd]
$DF_FtLength=$SrsField:[FtLength short:ftl]
$DF_FtLocation=$SrsField:[FtLocation short:flo]
$DF_ChrsNo=$SrsField:[ChromosomeNo short:chn]
$DF_FtMap=$SrsField:[MapLocation short:mpl]

$DF_Updated=$SrsField:[Updated short:upd]
$DF_Entered=$SrsField:[Entered short:ent]
$DF_Clone=$SrsField:[Clone short:clo]

$DF_Sequence=$SrsField:[Sequence short:seq]
$DF_Medline=$SrsField:[MedlineID short:mid group:$DF_ALL]
$DF_PubMed=$SrsField:[PubMedID short:pmd group:$DF_ALL]
 
$DF_HMM=$SrsField:[HMM short:hmm is:$HMM_DATA]
$DF_XT=$SrsField:[XT short:xt]
$DF_NulT=$SrsField:[NulT short:nut]
$DF_NulE=$SrsField:[NulE short:nue]
$DF_EVDmu=$SrsField:[EVDmu short:emu]
$DF_EVDlambda=$SrsField:[EVDlambda short:ela]


$DF_ProtSequence=$SrsField:[Sequence short:seq
  parameter:seqFormat is:$PROTSEQ_DATA
  format:{
    $FieldFormat:[fasta eval:@{$token.obj:[].str:fasta}] 
    $FieldFormat:[gcg eval:@{$token.obj:[].str:gcg}] 
    $FieldFormat:[pir eval:@{$token.obj:[].str:pir}] 
    $FieldFormat:[swiss eval:@{$token.obj:[].str:swiss}] 
    $FieldFormat:[genbank eval:@{$token.obj:[].str:genbank}] 
    $FieldFormat:[plain eval:@{$token.obj:[].str:plain}]
    $FieldFormat:[pretty eval:@{$token.obj:[].str:pretty}] 
    $FieldFormat:[string eval:@{$token.obj:[].str:string}]
    $FieldFormat:[not]
    $FieldFormat:[ProteinChart tableFormat:left eval:@{
        $tl=$entry.tokens:[field:seq]
        |<applet code="ChartApplet.class" 
        |  codebase="($ParStr:docdir)/java"
        |  width=400 height=200>
        |<param name=sequence 
        |  value="($tl.first.obj:[].str:string)">
        |</applet>
      }
    ]
  }
]

$DF_Peptide=$SrsField:[Sequence short:seq
  parameter:seqFormat is:$PEPTIDE_DATA
  format:{
    $FieldFormat:[fasta eval:@{$token.obj:[].str:fasta}] 
    $FieldFormat:[gcg eval:@{$token.obj:[].str:gcg}] 
    $FieldFormat:[pir eval:@{$token.obj:[].str:pir}] 
    $FieldFormat:[swiss eval:@{$token.obj:[].str:swiss}] 
    $FieldFormat:[genbank eval:@{$token.obj:[].str:genbank}] 
    $FieldFormat:[plain eval:@{$token.obj:[].str:plain}]
    $FieldFormat:[pretty eval:@{$token.obj:[].str:pretty}] 
    $FieldFormat:[string eval:@{$token.obj:[].str:string}]
    $FieldFormat:[not]
    $FieldFormat:[ProteinChart tableFormat:left eval:@{
        $tl=$entry.tokens:[field:seq]
        |<applet code="ChartApplet.class" 
        |  codebase="($ParStr:docdir)/java"
        |  width=400 height=200>
        |<param name=sequence 
        |  value="($tl.first.obj:[].str:string)">
        |</applet>
      }
    ]
  }
]


$DF_DNASequence=$SrsField:[Sequence short:seq
  parameter:seqFormat is:$DNASEQ_DATA
  format:{
    $FieldFormat:[fasta   eval:@{$token.obj:[].str:fasta}] 
    $FieldFormat:[gcg     eval:@{$token.obj:[].str:gcg}] 
    $FieldFormat:[pir     eval:@{$token.obj:[].str:pir}] 
    $FieldFormat:[embl    eval:@{$token.obj:[].str:embl}] 
    $FieldFormat:[genbank eval:@{$token.obj:[].str:genbank}] 
    $FieldFormat:[plain   eval:@{$token.obj:[].str:plain}]
    $FieldFormat:[string eval:@{$token.obj:[].str:string}]
    $FieldFormat:[not]
  }
]

$DF_OligoSequence=$SrsField:[Sequence short:seq
  parameter:seqFormat is:$OLIGOSEQ_DATA
  format:{
    $FieldFormat:[fasta   eval:@{$token.obj:[].str:fasta}] 
    $FieldFormat:[gcg     eval:@{$token.obj:[].str:gcg}] 
    $FieldFormat:[pir     eval:@{$token.obj:[].str:pir}] 
    $FieldFormat:[embl    eval:@{$token.obj:[].str:embl}] 
    $FieldFormat:[genbank eval:@{$token.obj:[].str:genbank}] 
    $FieldFormat:[plain   eval:@{$token.obj:[].str:plain}]
    $FieldFormat:[string eval:@{$token.obj:[].str:string}]
    $FieldFormat:[not]
  }
]

$DF_Name=$SrsField:[Name short:nam group:$DF_ALL]
$DF_Alignment=$SrsField:[Alignment short:ali
  parameter:aliFormat is:$PROTALI_DATA
  format:{
    $FieldFormat:[msf eval:@{$entry.tokens:[ali].first:[].obj:[].str:msf}]
    $FieldFormat:[clustal eval:@{$entry.tokens:[ali].first:[].obj:[].str:clustal}]
    $FieldFormat:[color eval:@{$entry.tokens:[ali].first:[].obj:[].str:color}]
    $FieldFormat:[fasta eval:@{$entry.tokens:[ali].first:[].obj:[].str:fasta}]
    $FieldFormat:[pir eval:@{$entry.tokens:[ali].first:[].obj:[].str:pir}]
    $FieldFormat:[not]
    $FieldFormat:[jalView eval:@{
	$tl=$entry.tokens:ali
	$ali=$tl.first:[].obj
	$s=|<APPLET archive="($ParStr:docdir)/java/jalview.jar"
	   | code="jalview.ButtonAlignApplet.class" width = 100 height = 35>   
	   |<PARAM name=type value=url>                                        
	   |<PARAM name=format value=msf>                                      
	   |<PARAM name="numseqs" value=($ali.seqList.len:[])>                 
	$i=0
	foreach:[$seq in:$ali.seqList] {
	  $i++
	  $s.app:|<PARAM name=seq($i) value="($seq.seq)">
      		 |<PARAM name=id($i) value="($seq.name)">
	}
        $s.app:|</APPLET>
      }
    ]
#    $FieldFormat:[alignChart eval:@{
#	  $tl=$entry.tokens:ali	 
#	  |<applet code="AlignChartApplet.class" 
#	  |  width=600 height=400 codebase="http://www.ebi.ac.uk/~verde">
#	  |<param name=seq value="
#	  |($tl.first:[].obj:[].str:fasta)
#	  |">
#	  |</applet>
#      }
#    ]
    $FieldFormat:[alignScroll 
      eval:@{ |<TEXTAREA ROWS=10 COLS=70>
              |($entry.tokens:[ali].first:[].obj:[].str:clustal)
              |</TEXTAREA>
            }
    ]
  }
]
$DF_DnaAlignment=$SrsField:[Alignment short:ali
  parameter:aliFormat is:$DNAALI_DATA  format:{
    $FieldFormat:[msf eval:@{$entry.tokens:[ali].first:[].obj:[].str:msf}]
    $FieldFormat:[clustal eval:@{$entry.tokens:[ali].first:[].obj:[].str:clustal}]
    $FieldFormat:[color eval:@{$entry.tokens:[ali].first:[].obj:[].str:color}]
    $FieldFormat:[fasta eval:@{$entry.tokens:[ali].first:[].obj:[].str:fasta}]
    $FieldFormat:[pir eval:@{$entry.tokens:[ali].first:[].obj:[].str:pir}]
    $FieldFormat:[not]
    $FieldFormat:[jalView eval:@{
	$tl=$entry.tokens:ali
	$ali=$tl.first:[].obj
	$s=|<APPLET archive="($ParStr:docdir)/java/jalview.jar"
	   | code="jalview.ButtonAlignApplet.class" width = 100 height = 35>   
	   |<PARAM name=type value=url>                                        
	   |<PARAM name=format value=msf>                                      
	   |<PARAM name="numseqs" value=($ali.seqList.len:[])>                 
	$i=0
	foreach:[$seq in:$ali.seqList] {
	  $i++
	  $s.app:|<PARAM name=seq($i) value="($seq.seq)">
      		 |<PARAM name=id($i) value="($seq.name)">
	}
        $s.app:|</APPLET>
      }
    ]
#    $FieldFormat:[alignChart eval:@{
#	  $tl=$entry.tokens:ali	 
#	  |<applet code="AlignChartApplet.class" 
#	  |  width=600 height=400 codebase="http://www.ebi.ac.uk/~verde">
#	  |<param name=seq value="
#	  |($tl.first:[].obj:[].str:fasta)
#	  |">
#	  |</applet>
#      }
#    ]
    $FieldFormat:[alignScroll 
      eval:@{ |<TEXTAREA ROWS=10 COLS=70>
              |($entry.tokens:[ali].first:[].obj:[].str:clustal)
              |</TEXTAREA>
            }
    ]
  }
]
#apps

$DF_MatchLen=$SrsField:[MatchLength short:mtl]
$DF_QueryBeg=$SrsField:[QueryMatchBeginPos short:qbp]
$DF_QueryEnd=$SrsField:[QueryMatchEndPos short:qep]
$DF_PercIdt=$SrsField:[PercentIdentity short:pci]
$DF_Query=$SrsField:[Query short:qry]
$DF_Database=$SrsField:[Database short:qdb]

#added from hmmpfam.i by DS 17.08.00

$DF_Score=$SrsField:[Score short:sco ]
$DF_Eval=$SrsField:[Evalue short:eva ]

# structure

$DF_Resolution=$SrsField:[Resolution short:res group:$DF_ALL] 
$DF_EXP_METHOD=$SrsField:[ExpMethod short:exp group:$DF_ALL 
  guiInfo:$GI_CheckList] 
$DF_R_FACTOR=$SrsField:[RFactor short:rfa group:$DF_ALL] 
$DF_EntryAuthors=$SrsField:[EntryAuthors short:eat group:$DF_ALL]
$DF_DNALocation=$SrsField:[Sequence short:seq
  parameter:seqFormat is:$DNASEQ_DATA
  format:{
    $FieldFormat:[gcg eval:@{
        $SeqGetFt:[$token.str entry:$entry].str:gcg
      }
    ]
    $FieldFormat:[location 
      eval:@{$token.str:[]}
    ]
    $FieldFormat:[fasta 
      eval:@{ 
        $SeqGetFt:[$token.str:[] entry:$entry].str:fasta
      }
    ]
    $FieldFormat:[plain
      eval:@{
        $SeqGetFt:[$token.str:[] entry:$entry].str:plain
      }
    ]
    $FieldFormat:[pir 
      eval:@{ 
        $SeqGetFt:[$token.str:[] entry:$entry].str:pir
      }
    ]
    $FieldFormat:[embl 
      eval:@{
        $SeqGetFt:[$token.str:[] entry:$entry].str:embl
      }
    ]
    $FieldFormat:[genbank
      eval:@{
        $SeqGetFt:[$token.str:[] entry:$entry].str:genbank
      }
    ]
  }
]

$DF_ProtLocation=$SrsField:[ProtLocation short:seq group:$DF_ALL
  parameter:seqFormat is:$PROTSEQ_DATA
  format:{
    $FieldFormat:[gcg eval:@{
        $SeqGetFt:[$token.str entry:$entry].str:gcg
      }
    ]
    $FieldFormat:[location eval:@{$token.str}
    ]
    $FieldFormat:[fasta eval:@{ 
        $SeqGetFt:[$token.str entry:$entry].str:fasta
      }
    ]
    $FieldFormat:[plain eval:@{
        $SeqGetFt:[$token.str entry:$entry].str:plain
      }
    ]
    $FieldFormat:[pir eval:@{
        $SeqGetFt:[$token.str entry:$entry].str:pir
      }
    ]
    $FieldFormat:[swiss eval:@{
        $SeqGetFt:[$token.str entry:$entry].str:swiss
      }
    ]
    $FieldFormat:[pretty eval:@{
        $SeqGetFt:[$token.str entry:$entry].str:pretty
      }
    ]
    $FieldFormat:[ProteinChart eval:@{
        $SeqGetFt:[$token.str entry:$entry].str:msf
      }
    ]
    $FieldFormat:[genbank
      eval:@{
        $SeqGetFt:[$token.str:[] entry:$entry].str:genbank
      }
    ]
  }
]
#
# Taxonomy
#

$DF_Taxon=$SrsField:[Taxon short:tax group:$DF_ALL]
$DF_Species=$SrsField:[Species short:spc group:$DF_ALL]
$DF_ParentId=$SrsField:[ParentId short:pid]
$DF_Rank=$SrsField:[Rank short:rnk guiInfo:$GI_MultiSelect]

#
# Mutation db
#

# Identification
$DF_SystName=$SrsField:['SystematicName' short:sNa  group:$DF_ALL]
$DF_TrivName=$SrsField:['TrivialName' short:tNa  group:$DF_ALL]
$DF_Code=$SrsField:[Code short:cod group:$DF_ALL]
$DF_OriCode=$SrsField:[OriginalCode short:oco group:$DF_ALL]
$DF_PatientID=$SrsField:[PatientID short:PT group:$DF_ALL]
# $DF_Accession

#Mutation classification
$DF_DNAmutType=$SrsField:[DNAMutType short:dmt guiInfo:$GI_CheckList]
$DF_RNAmutType=$SrsField:[RNAMutType short:rmt guiInfo:$GI_CheckList]
$DF_AAmutType=$SrsField:[AAMutType short:amt guiInfo:$GI_CheckList ]
   # if division is not possible:
$DF_MutType=$SrsField:[MutationType short:mty guiInfo:$GI_MultiSelectOver]
$DF_TranslEffect=$SrsField:[TranslationEffect short:tre 
  group:$DF_ALL guiInfo:$GI_MultiSelect]

#Mutation
$DF_DNAChange=$SrsField:[NucleotideChange short:nuc]
  #genomic or cDNA unless DF_CDnaChangePos defined
$DF_DnaChangePos=$SrsField:[DnaChangePos short:dcp]
$DF_MutLength=$SrsField:[DnaChangeLength  short:LE group:$DF_ALL]
$DF_CDnaChangePos=$SrsField:[cDnaChangePos short:cdp]
$DF_RNAChange=$SrsField:[RnaChange short:rna]
$DF_RNAChangePos=$SrsField:[RnaChangePos short:rcp]
$DF_AaChange=$SrsField:[AaChange short:aac]
$DF_ProtChangePos=$SrsField:[ProteinChangePos short:acp]
$DF_ProtID=$SrsField:[ProteinID short:prd]

#Mutation context
#DF_GeneName

$DF_Exon=$SrsField:[Exon_Number short:Exn group:$DF_ALL 
  guiInfo:$GI_CheckList]
$DF_Intron=$SrsField:[Intron_Number short:Irn group:$DF_ALL 
  guiInfo:$GI_CheckList]
$DF_InEx=$SrsField:[IntronExon short:IE guiInfo:$GI_MultiSelect]
$DF_Location=$SrsField:[Location short:loc  guiInfo:$GI_CheckList]

$DF_CodonChange=$SrsField:[CodonChange short:coc]
$DF_CodonNo=$SrsField:[CodonNo short:cdn]
$DF_CodonPos=$SrsField:[CodonPos short:cdp guiInfo:$GI_CheckList]

$DF_CpG=$SrsField:[CpG short:cpg guiInfo:$GI_CheckList]
$DF_Polymorphism=$SrsField:[Polymorphism short:plm guiInfo:$GI_CheckList]
$DF_REChange=$SrsField:[REChange short:RE group:$DF_ALL]

$DF_ProteinDomain=$SrsField:[ProteinDomain short:dom guiInfo:$GI_CheckList]

$DF_Detection=$SrsField:[DetectionMethod short:met group:$DF_ALL ]
$DF_Region=$SrsField:[RegionStudied short:reg group:$DF_ALL ]

$DF_Evidence=$SrsField:[Evidence short:evi group:$DF_ALL] 
$DF_Function=$SrsField:[Fuction short:fun group:$DF_ALL] 
$DF_FunctCat=$SrsField:[FuctionCategory short:fuca group:$DF_ALL] 

#Expression
$DF_FuncStudies=$SrsField:[FunctionalStudies short:fst guiInfo:$GI_CheckList]
$DF_mRNAlevel=$SrsField:[mRNAlevel short:mRN  guiInfo:$GI_MultiSelectOver]
$DF_EnzAct=$SrsField:[EnzymeActivity short:EAc ]
$DF_ProtLevel=$SrsField:[protLevel short:prl   ]
  # most fields are db specific

#Inheritance and Phenotype
$DF_Sex=$SrsField:[Sex short:sex guiInfo:$GI_CheckList group:$DF_ALL]
$DF_Age=$SrsField:[Age short:Age]
$DF_AlleleN=$SrsField:[NAlleles short:nal group:$DF_ALL]
$DF_Haplotype=$SrsField:[Haplotype short:hap group:$DF_ALL]
$DF_FamHist=$SrsField:[FamilyHistory short:fah guiInfo:$GI_CheckList  group:$DF_ALL]
$DF_FamilyN=$SrsField:[NFamilies short:nfa group:$DF_ALL]
$DF_PatientN=$SrsField:[NPatients short:npa group:$DF_ALL]
$DF_Relative=$SrsField:[Relative short:Rel group:$DF_ALL]
$DF_Population=$SrsField:[Population short:pop group:$DF_ALL]

# pathways
$DF_ECNumber=$SrsField:[ECNumber short:ecn group:$DF_ALL]
$DF_Pathway=$SrsField:[PATHWAYlinks short:pth group:$DF_ALL]
$DF_Product=$SrsField:[Product short:pro group:$DF_ALL]
$DF_Cofactor=$SrsField:[Cofactor short:cof group:$DF_ALL]
$DF_Inhibitor=$SrsField:[Inhibitor short:ihb group:$DF_ALL]
$DF_Effector=$SrsField:[Effector short:eff group:$DF_ALL]
$DF_Sysname=$SrsField:[SystematicName short:syn group:$DF_ALL]
$DF_Com=$SrsField:[Comment short:com group:$DF_ALL]
$DF_OMIM=$SrsField:[OMIMlinks short:omm group:$DF_ALL]
$DF_Genes=$SrsField:[GENESlinks short:gen group:$DF_ALL]
$DF_Motif=$SrsField:[Motif  short:mot group:$DF_ALL]
$DF_Structure=$SrsField:[PDBlinks short:stt group:$DF_ALL]
$DF_DBLinks=$SrsField:[OtherDBlinks short:dbl group:$DF_ALL]
$DF_Fullname=$SrsField:[FullName short:ffn group:$DF_ALL]
$DF_Formula=$SrsField:[Formula short:frm group:$DF_ALL]
$DF_Enzyme=$SrsField:['LENZYMElinks' short:len group:$DF_ALL]
$DF_CAS=$SrsField:['CASnumber' short:cas group:$DF_ALL]
$DF_Reaction=$SrsField:['Reaction' short:react group:$DF_ALL]

#Reference
$DF_LabName=$SrsField:[LabName short:lan group:$DF_ALL]
$DF_CaseReference=$SrsField:[CaseRefrence short:cre group:$DF_ALL]
$DF_PatentNumber=$SrsField:[PatentNumber short:pnu group:$DF_ALL]
#DF_Reference

$DF_Release=$SrsField:[Release short:rel]
$DF_Status=$SrsField:[status  short:sta]

# Chemistry
$DF_Formula=$SrsField:[Formula short:frm group:$DF_ALL]   # the # of each atom in molecule
$DF_CAS=$SrsField:['CASnumber' short:cas group:$DF_ALL]   # CAS number for compound
$DF_CompoundName=$SrsField:[CompoundName short:na group:$DF_ALL]
$DF_SLN=$SrsField:[SLN short:tln group:$DF_ALL            # inline representation of molecule topology
  is:$COMPOUND_DATA]
$DF_SMILES=$SrsField:[SMILES short:sml group:$DF_ALL]     # inline representation of molecule topology
$DF_CHUCKLES=$SrsField:[CHUCKLES short:chu group:$DF_ALL] # inline representation of molecule topology
$DF_Coords3d=$SrsField:[Coords3d short:coo group:$DF_ALL] # 3D coords of atoms in molecule
$DF_SimIdx=$SrsField:[SimIdx short:sim group:$DF_ALL]     # Similarity index of search reult compared to query

# ID types
$SRSxSEQID=$IdType:['Seq-ID' size:5 fipBeg:0 fipLen:3 libIdBeg:3 libIdLen:2]
$ENTRY_ID=$IdType:['Entry-ID' size:5 fipBeg:0 fipLen:3 libIdBeg:3 libIdLen:2] 
$ENTRYNAME_ID=$IdType:['EntryName-ID' names:y size:22 fipBeg:2 fipLen:20 libIdBeg:0 libIdLen:2]
$BIGENTRY_ID=$IdType:['BigEntry-ID' size:5 fipBeg:0 fipLen:4 libIdBeg:4 libIdLen:1 shareName:'Entry-ID']
$STRUCTENT_ID=$IdType:['3D-ID' size:5 fipBeg:0 fipLen:3 libIdBeg:3 libIdLen:2] 
$SUBENTRY_ID=$IdType:['SubEntry-ID' size:6 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:1
]
$Revision_Id=$IdType:[Revision size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:2 from:41000 to:50000
]
$Feature_Id=$IdType:[Feature size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:2 from:1 to:10000
]
$BigFeature_Id=$IdType:[Features size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:4 libIdBeg:6 libIdLen:1 from:1 to:10000 shareName:Feature
]
$Sim_Id=$IdType:[Similarity size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:2 from:10001 to:20000
]
$Reference_Id=$IdType:[Reference size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:2 from:30001 to:40000
]
$BigReference_Id=$IdType:[References size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:4 libIdBeg:6 libIdLen:1 from:30001 to:40000 shareName:Reference
]
$Comment_Id=$IdType:[Comment size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:2 from:20001 to:21000
]
$BigComment_Id=$IdType:[Comments size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:4 libIdBeg:6 libIdLen:2 from:20001 to:21000
]
$Counter_Id=$IdType:[Counter size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:2 from:10001 to:11000
]
$BigCounter_Id=$IdType:[Counters size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:4 libIdBeg:6 libIdLen:2 from:10001 to:11000 shareName:Counter
]
$Chain_Id=$IdType:[Chain size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:2
]
$Change_Id=$IdType:[Change size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:2
]
$Allele_Id=$IdType:[Allele size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:2
]
$Field_Id=$IdType:[Field size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:2
]
$Command_Id=$IdType:[Command size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:2
]
$HSP_Id=$IdType:[HSP size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:2
]
$Sequence_Id=$IdType:[Sequence size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:2
]


# 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
    
# these should be or become obsolete
$parentLink1=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$SUBENTRY_ID idtype2:$ENTRY_ID]
$parentLink2=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$Revision_Id idtype2:$ENTRY_ID]
$parentLink3=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$Feature_Id idtype2:$ENTRY_ID]
$parentLink3B=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$BigFeature_Id idtype2:$BIGENTRY_ID]
$parentLink4=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$Reference_Id idtype2:$ENTRY_ID]
$parentLink4B=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$BigReference_Id idtype2:$BIGENTRY_ID]
$parentLink5=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$Comment_Id idtype2:$ENTRY_ID]
$parentLink5B=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$BigComment_Id idtype2:$BIGENTRY_ID]
$parentLink6=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$Counter_Id idtype2:$ENTRY_ID]
$parentLink6B=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$BigCounter_Id idtype2:$BIGENTRY_ID]
$parentLink7=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$Chain_Id idtype2:$ENTRY_ID]
$parentLink8=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$Change_Id idtype2:$ENTRY_ID]
$parentLink9=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$Allele_Id idtype2:$ENTRY_ID]
$parentLink10=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$Field_Id idtype2:$ENTRY_ID]
$parentLink11=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$Command_Id idtype2:$ENTRY_ID]
$parentLink12=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$HSP_Id idtype2:$ENTRY_ID]
$parentLink13=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$Sequence_Id idtype2:$ENTRY_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
#################################################################################


$DNASEQ_DATA=$DataType:
[ DNASequence
  dataClass:$CLASS.Seq
  bioType:NA
  applications:
  { 
     $CPG_APP
#     $OLIGOBLAST_APP
     $BLASTN_APP
     $BLASTX_APP
     $TBLASTX_APP
     $NFASTA_APP
     $FASTX_APP
     $FASTY_APP
     $NCLUSTALW_APP
     $TACG_APP
     $RESTRICTIONMAP_APP
  }
   print:@{$obj.str:[$format useStream:y]}
]
$OLIGOSEQ_DATA=$DataType:
[ OligoSequence
  dataClass:$CLASS.Seq
  applications:
  { 
     $OLIGOBLAST_APP
  }
   print:@{$obj.str:[$format useStream:y]}
]


$BIOSCOUT_DATA=$DataType:
[ bioSCOUT
  dataClass:$CLASS.Entry
#   print:@{$Print:["($obj.libName):($obj.name)\n" useStream:y]}
  applications:
  { $ORTHOLOGY_APP }
  ext:'.bS'
]


$PROTSEQ_DATA=$DataType:[ProteinSequence 
  dataClass:$CLASS.Seq
  bioType:AA
  applications: {  
     $BLASTP_APP 
     $PSIBLAST_APP 
     $TBLASTN_APP 
     $SW_APP 
     $FASTA_APP 
     $TFASTA_APP 
     $TFASTX_APP 
     $TFASTY_APP 
     $SSEARCH_APP 
     $CLUSTALW_APP 
     $PROSITESEARCH_APP 
     $HMMPFAM_APP 
     $PRINTSCAN_APP
     $PPSEARCH_APP
  }
  print:@{$obj.str:[$format useStream:y]}
]

$PEPTIDE_DATA=$DataType:[Peptide 
  dataClass:$CLASS.Seq
  bioType:AA
  applications:{  
     $FASTS_APP 
  }
   print:@{$obj.str:[$format useStream:y]}
]

$DNAALI_DATA=$DataType:[DNAAlignment  # applications:{}
  bioType:NA
  print:   @{      $applOpt.printSeqAli:   [ $obj entry:$entry ] }
]

$PROTALI_DATA=$DataType:[ProteinAlignment
  dataClass:$CLASS.SeqAli
  bioType:AA
  applications:{ 
     $HMMBUILD_APP
     $HMMALIGN_APP
  }
   print:@{$obj.str:[$format useStream:y]}
]

$HMM_DATA=$DataType:[ Hmm
  print:@{$obj.str:[useStream:y]}
  dataClass:$CLASS.Entry
  applications:{ $HMMSEARCH_APP }
]


$COMPOUND_DATA=$DataType:[ChemicalCompound
  dataClass:$CLASS.Entry
  applications:{
    $UNITY_CHEM_SIM_SEARCH_APP
  }
  print:@{$obj.str:[useStream:y]}
  applications:{ 
    $HMMSEARCH_APP
    $HMMALIGN_APP
  }
]



#################################################################################
# APPLICATION OPTION GROUPS
#################################################################################

$GENERAL_OPTS=$OptGroup:['General Options'   format:table]
$MIN_OPTS    =$OptGroup:['Minimum Options'               ]
$PRIM_OPTS   =$OptGroup:['Primary Options'   format:normal]
$SEARCH_OPTS =$OptGroup:['Search Parameters' format:table]
$OUTPUT_OPTS =$OptGroup:['Output Options'    format:table]
$ALG_OPTS    =$OptGroup:['Algorithm Options' format:table]
$OTHER_OPTS  =$OptGroup:['Others'            format:table]
$DATA_OPTS   =$OptGroup:[]

##############################################################
# Applicatio options commonly used
##############################################################

$jobName_Option=$AppOpt:[jobName group:$PRIM_OPTS
  prompt:'Name of <!>job<!>:'
  comment:
   |This option is a name for the current application launch job.
   |It is used as part of the name of the application result files.
   |If you think to use or return to current jobs results later, \
   |it is better to give a related name.
  defStr:temp cols:12
]
$ProtSeqInput_Option=$AppOpt:[in group:$MIN_OPTS dataType:$PROTSEQ_DATA 
  source:selection cardinality:1 includeDbInName:y
  comment:|This option indicates that this application requires a protein
	  |sequence as input.
  prompt:'Query protein sequence' pos:left outFormat:fasta
  mandatory:yes
]
$DNASeqInput_Option=$AppOpt:[in group:$MIN_OPTS dataType:$DNASEQ_DATA 
  source:selection cardinality:1 includeDbInName:y
  comment:|This option indicates that this application requires a DNA
	  |sequence as input.
  prompt:'Query DNA sequence' pos:left outFormat:fasta
  mandatory:yes
]
# fasta formatted databases
$BdbRoot = "/srsdata/flatfiles/blast"
$FastaProtDB_Option=$AppOpt:[search  guiType:menu pos:next group:$PRIM_OPTS
  prompt:'<!>Database<!> to search:'
  comment:
   |This option lets you to select a protein database to be searched.
  values:{
    $OptVal:['SWALL' valStr:'$BdbRoot/swall']
    # $OptVal:['SWALL' valStr:"$BdbRoot/swall"]
    $OptVal:['SWISSNEW' valStr:"$BdbRoot/swissnew" on:y]
    $OptVal:['SWISSPROT' valStr:"$BdbRoot/swissprot"]
    # $OptVal:['PIR' valStr:"$BdbRoot/pir"]
    # $OptVal:['GENPEPT' valStr:"$BdbRoot/genpept"]
    # $OptVal:['PDB' valStr:"$BdbRoot/pdb"]
    # $OptVal:['PRINTS' valStr:"$BdbRoot/prints"]
  }
]
# DNA databases available for all fasta programs
$FastaDnaDB_Option=$AppOpt:[search  guiType:menu pos:next group:$PRIM_OPTS
  prompt:'Database to search:' values:{
    $OptVal:['EMBL'    valStr:"$BdbRoot/embl"]
    $OptVal:['EMBLNEW' valStr:"$BdbRoot/emblnew" on:y]
    $OptVal:['GENBANK' valStr:"$BdbRoot/genbank"]
    #$OptVal:['EST_HUM' valStr:"$BdbRoot/est_hum"]
    #$OptVal:['EST_INV' valStr:"$BdbRoot/est_inv"]
    #$OptVal:['EST_MAM' valStr:"$BdbRoot/est_mam"]
    #$OptVal:['EST_PLN' valStr:"$BdbRoot/est_pln"]
    #$OptVal:['EST_PRO' valStr:"$BdbRoot/est_pro"]
    #$OptVal:['EST_ROD' valStr:"$BdbRoot/est_rod"]
    #$OptVal:['EST_VRT' valStr:"$BdbRoot/est_vrt"]
    #$OptVal:['HTG' valStr:"$BdbRoot/htg"]
    #$OptVal:['GSS' valStr:"$BdbRoot/gss"]
    #$OptVal:['STS' valStr:"$BdbRoot/sts"]
    
  }
]

#############################################################
# Info type for representing fields in query forms
#############################################################

$GI_CheckList=$GuiField:[checklist]
$GI_Menu=$GuiField:[menu maxKeys:500]
$GI_MultiSelect=$GuiField:[multiselect visListHeight:7]
$GI_MultiSelectOver=$GuiField:[multiselect visListHeight:7 valOverlap:y]

$LSF=$BatchQueueSystem:[
  name:LSF
  sub_command:
   |bsub  \
  interactive_sub_command:
   |bsub -I  \
  del_command:
   |del \
  stat_command:
   |bjobs
  #-----------------
  #Option specifiers
  #-----------------
  job_name_spec:J
  priority_spec:sp
  queue_name_spec:q
  #--------------------------------------------
  #Regular expressions for state identification
  #--------------------------------------------
  runStateIndicatorRE:"(RUN)"
  waitStateIndicatorRE:"(PEND|PSUSP|USUSP|SSUSP)"
  doneStateIndicatorRE:"(DONE|EXIT)"
]

$DQS=$BatchQueueSystem:[
  name:DQS
  sub_command:
   |/usr/local/DQS32/bin/qsub32  -cwd -F \
  del_command:
   |/usr/local/DQS32/bin/qdel32 \
  stat_command:
   |/usr/local/DQS32/bin/qstat32
  #-----------------
  #Option specifiers
  #-----------------
  job_name_spec:N
  priority_spec:p
  queue_name_spec:q
  #--------------------------------------------
  #Regular expressions for state identification
  #--------------------------------------------
  runStateIndicatorRE:"(RUNNING)"
  waitStateIndicatorRE:"(QUEUED)"
]

$CODINE=$BatchQueueSystem:[
  name:CODINE
  sub_command:
   |setenv CODINE_ROOT /software/codine
   |/software/codine/bin/irix6/qsub  -cwd \
  interactive_sub_command:
   |setenv CODINE_ROOT /software/codine
   |#!/bin..../qsh
   |
  del_command:
   |setenv CODINE_ROOT /software/codine
   |/software/codine/bin/irix6/qdel \
  stat_command:
   |CODINE_ROOT=/software/codine; export CODINE_ROOT
   |/software/codine/bin/irix6/qstat
  #-----------------
  #Option specifiers
  #-----------------
  job_name_spec:N
  priority_spec:p
  queue_name_spec:q
  #--------------------------------------------
  #Regular expressions for state identification
  #--------------------------------------------
  runStateIndicatorRE:"( r | t )"
  waitStateIndicatorRE:"( w | h | S | s | T | qw )"
]

# To enable localApplicationOptions.i uncomment the following line:
#file:"SRSSITE:localApplicationOptions.i"