#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: srsgen.i,v $
#    $Revision: 1.1.1.1 $
#    $Date: 1999/12/13 00:15:07 $
#    $Author: gilbertd $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


# 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]
MAP_LIBS:$libgroup:[Mapping short:gen]
TRANSFAC_LIBS:$libgroup:[TransFac short:'tf']
MUTATION_LIBS:$libgroup:['Mutations' short:'mut']
SPMUTATION_LIBS:$libgroup:['Locus Specific Mutations' short:'lsm']

APPLICATION_LIBS:$libgroup:[Application short:app]

# data field types
DF_Class: $srsfield:[Class short:cla group:@DF_ALL]
DF_Synonyms: $srsfield:[Synonyms short:syn group:@DF_ALL]  # was SYM ! dgg
DF_HeaderField:$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 group:@DF_ALL]
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 guiInfo:@GI_CheckList]
DF_Authors:$srsfield:[Authors short:aut group:@DF_ALL]
DF_Title:$srsfield:[Title short:tit group:@DF_ALL]
DF_Features:$srsfield:[Features short:fts group:@DF_ALL]
## drop Citation for Reference
DF_Citation:$srsfield:[Citation short:cit group:@DF_ALL]
DF_Division:$srsfield:[Division short:div guiInfo:@GI_CheckList]
DF_LINK:$srsfield:[Link short:lnk]
DF_COMMENT:$srsfield:[Comment short:cc group:@DF_ALL]
DF_Comment:$srsfield:[Comment short:cc group:@DF_ALL]
DF_CommentType:$srsfield:[CommentType short:cct group:@DF_ALL
  guiInfo:@GI_MultiSelectOver
]
DF_REF:$srsfield:[Reference short:ref]
DF_Reference:$srsfield:[Reference short:ref group:@DF_ALL]
DF_EnzymeCode:$srsfield:[EnzymeCode short:enz group:@DF_ALL]
DF_AccessionKey:$srsfield:[AccessionKey short:ack group:@DF_ALL]
DF_DBOrigin:$srsfield:[DBOrigin short:dbo]
DF_Genomic:$srsfield:[Genomic short:gno]  #dgg

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]
DF_NAlign:$srsfield:[NAlign short:nal]

# FlyBase definitions

DF_Headline:$srsfield:[Headline short:hed]  #no group; a print field
#-------- new ---
ACODE_FILE:$filetype:[text typename:acode maxline:1024]

# FlyBase definitions
  # text fields
DF_FBSymbol:$srsfield:[Symbol short:sym group:@DF_ALL]
DF_FBSymbolCS:$srsfield:[SymbolCaseSensitive short:Smc group:@DF_ALL]
DF_FBSynonymsCS:$srsfield:[SynonymsCaseSensitive short:Snc group:@DF_ALL] 
DF_FBGeneSymbol:$srsfield:[GeneSymbol short:gsm group:@DF_ALL]
DF_FBGeneSymbolCS:$srsfield:[GeneSymbolCaseSensitive short:Gsc group:@DF_ALL]
DF_FBSecAccession:$srsfield:[SecondaryAccNumber short:acs group:@DF_ALL]
DF_FBPhenotype:$srsfield:[Phenotype short:phe group:@DF_ALL]
DF_FBVector:$srsfield:[Vector short:vec group:@DF_ALL]
DF_FBTransposon:$srsfield:[Transposon short:trp group:@DF_ALL]
DF_FBAberration:$srsfield:[Aberration short:abr group:@DF_ALL]
DF_FBAlleleSymbol:$srsfield:[AlleleSymbol short:als group:@DF_ALL]
DF_FBAlleleSymbolCS:$srsfield:[AlleleSymbolCaseSensitive short:Asc group:@DF_ALL]
DF_FBStock:$srsfield:[Stock short:stk group:@DF_ALL]
DF_FBFunction:$srsfield:[Function short:fun group:@DF_ALL]

## dgg nov98 additions for more acode fields
DF_FBCytologicLoc:$srsfield:[CytologicLoc short:cyl group:@DF_ALL]
DF_FBGeneLoc:$srsfield:[GenotypicLoc short:gel group:@DF_ALL]
DF_FBKbLoc:$srsfield:[KilobaseLoc short:kbl group:@DF_ALL]

DF_FBCellLoc:$srsfield:[CellLocation short:cel group:@DF_ALL]
## use DF_EnzymeCode
##DF_FBEnzyme:$srsfield:[GenotypicLoc short:enz group:@DF_ALL]

## use srs DF_Reference
## DF_FBGenReference:$srsfield:[GeneralReference short:grf group:@DF_ALL]
DF_FBPublisher:$srsfield:[Publisher short:pub group:@DF_ALL]
DF_FBJournal:$srsfield:[Journal short:jou group:@DF_ALL]
DF_FBAddress:$srsfield:[Address short:adr group:@DF_ALL]
DF_FBCity:$srsfield:[City short:cit group:@DF_ALL]
DF_FBState:$srsfield:[State short:sta group:@DF_ALL]
DF_FBCountry:$srsfield:[Country short:cou group:@DF_ALL]
DF_FBEMail:$srsfield:[EMail short:eml group:@DF_ALL]
DF_FBOtherFields:$srsfield:[AllOtherFields type:str short:xxx group:@DF_ALL] 
  # text fields with controlled vocabularies
DF_FBItemType:$srsfield:[ItemType short:typ]
DF_FBPhenClass:$srsfield:[PhenotypeClass short:phc]
DF_FBClassQualifier:$srsfield:[ClassQualifier short:phq]
DF_FBAssayMode:$srsfield:[AssayMode short:phm]
DF_FBOrigin:$srsfield:[Origin short:pho]
DF_FBBodyPart:$srsfield:[BodyPart short:phb]
DF_FBLanguage:$srsfield:[Language short:lng group:@DF_ALL]
DF_FBCharacteristics:$srsfield:[Characteristics short:chr group:@DF_ALL]
DF_FBUses:$srsfield:[Uses short:use group:@DF_ALL]
DF_FBProgenitor:$srsfield:[Progenitor short:prg group:@DF_ALL]
DF_FBDescendant:$srsfield:[Descendant short:dsc group:@DF_ALL]
  # numeric fields
DF_FBMinCytologicLoc:$srsfield:[MinCytologicLocation short:clm]
DF_FBMaxCytologicLoc:$srsfield:[MaxCytologicLocation short:clx]

## more
DF_FBSCLocation:$srsfield:[SubCelLocation short:loc group:@DF_ALL]
DF_FBMarker:$srsfield:[Marker short:mrk group:@DF_ALL]
DF_FBInsertion:$srsfield:[Insertion short:ins group:@DF_ALL]
DF_FBTranscript:$srsfield:[Transcript short:trs group:@DF_ALL]
DF_FBPolypeptide:$srsfield:[Polypeptide short:ppt group:@DF_ALL]

DF_FBHomologue:$srsfield:[Homologue short:hg group:@DF_ALL]
## used by other db == DF_Organism
DF_Species:$SrsField:[Species short:spc group:@DF_ALL]
#-----------



# for sequence features
DF_FtKey:$srsfield:[FeatureKey short:ftk guiInfo:@GI_MultiSelect]
DF_FtQualifier:$srsfield:[FeatureQualifier short:ftq 
  guiInfo:@GI_MultiSelectOver
]
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 group:@DF_ALL]
DF_FtMap:$srsfield:[MapLocation short:mpl]

DF_Chromosome:$srsfield:[Chromosome short:chr]
DF_Updated:$srsfield:[Updated short:upd]
DF_Entered:$srsfield:[Entered short:ent]
DF_Clone:$srsfield:[Clone short:clo]

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:[$token db:$EntryLib:$entry]]
      }@
    ]
    $fieldFormat:[location 
      eval:@{$Print:$token}@
    ]
    $fieldFormat:[fasta 
      eval:@{ $SeqPrint:[format:fasta 
                s:$SeqGetFt:[$token db:$EntryLib:$entry]]
           }@
    ]
    $fieldFormat:[plain
      eval:@{$SeqPrint:[format:plain 
               s:$SeqGetFt:[$token db:$EntryLib:$entry]]
           }@
    ]
    $fieldFormat:[pir 
      eval:@{$SeqPrint:[format:pir 
               s:$SeqGetFt:[$token db:$EntryLib:$entry]]
           }@
    ]
    $fieldFormat:[embl 
      eval:@{$SeqPrint:[format:embl 
               s:$SeqGetFt:[$token db:$EntryLib:$entry]]
           }@
    ]
  }
]
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:[swiss eval:@{
        $SeqPrint:[format:swiss s:$SeqGetFt:[$token db:swissprot]]
      }@
    ]
    $fieldFormat:[ProteinChart eval:@{
        $SeqPrint:[format:msf width:50 s:$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 mut dbs
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_ProteinDomain:$srsfield:[ProteinDomain short:dom guiInfo:@GI_CheckList]
DF_Sex:$srsfield:[Sex short:sex guiInfo:@GI_CheckList]

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 
  group:@DF_ALL guiInfo:@GI_MultiSelect]

DF_InEx:$srsfield:[IntronExon short:IE]
DF_CpG:$srsfield:[CpG short:cpg guiInfo:@GI_CheckList]
DF_Polymorphism:$srsfield:[Polymorphism short:plm guiInfo:@GI_CheckList]
DF_REChange:$srsfield:[REChange short:RE]
DF_FuncStudies:$srsfield:[FunctionalStudies short:fst guiInfo:@GI_CheckList]

DF_LabName:$srsfield:[LabName short:lan group:@DF_ALL]

DF_AlleleN:$srsfield:[NAlleles short:nal]
DF_Haplotype:$srsfield:[Haplotype short:hap]
DF_FamHist:$srsfield:[FamilyHistory short:fah]
DF_FamilyN:$srsfield:[NFamilies short:nfa]
DF_PatientN:$srsfield:[NPatients short:npa]
DF_Population:$srsfield:[Population short:pop group:@DF_ALL]

DF_CaseReference:$srsfield:[CaseRefrence short:cre]

# 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
]
Feature_Id:$idtype:[Feature size:6 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:1
]
Chain_Id:$idtype:[Chain size:6 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:1
]
Change_Id:$idtype:[Change size:6 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:1
]
Field_Id:$idtype:[Field 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]
#STAR_FILE:$filetype:[text typename:star maxline:1000 fipVar:entryFip]
RPT_FILE:$filetype:[text typename:rpt 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:$filetype:[seq typename:seq maxline:10000 fieldTokens:sequence 
  fipVar:seqFip]
PIRDAT_FILE:$filetype:[text typename:dat maxline:10000 fipVar:entryFip]


# 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}
#]

# Info type for representing fields in query forms

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