#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: srsgen.i,v $
#    $Revision: 1.147 $
#    $Date: 2003/02/17 10:22:38 $
#    $Author: davies $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

## Note if you want to modify any of the settings in this file see the
## instructions in localApplicationOptions.i.

# syntaxes

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

$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
$EMBAPPL_LIBS=$LibGroup:['EMBOSS Results' short:bio]
$SEQUENCE_LIBS=$LibGroup:[Sequence short:SQ 
     printName:'Sequence databanks - 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 databanks - 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:['Tool 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]
$SRSDOC_LIBS=$LibGroup:['SRS Documentation' short:srsdoc search:all show:never]
 
# data field types
#$DF_AAmutType=$SrsField:[AAMutType short:amt guiInfo:$GI_CheckList]
#$DF_ACCNO=$SrsField:[AccNumber short:acc]
#$DF_AID=$SrsField:[AccID short:aid isGroup:yes type:str] 
$DF_ALL=$SrsField:[AllText short:all isGroup:yes type:str] 
$DF_ALLPOS=$SrsField:[AllPositive short:alp]
#$DF_ALLText=$SrsField:[AllText short:all] 
$DF_AUPDate=$SrsField:[LastAnnotationUpdate short:lau]
$DF_AaChange=$SrsField:[AaChange short:aac]
$DF_AccSurface=$SrsField:[AccSurface short:sur]
$DF_Accession=$SrsField:[AccNumber short:acc]
#$DF_AccessionKey=$SrsField:[AccessionKey short:ack]
#$DF_Age=$SrsField:[Age short:Age]
$DF_AliasProtein=$SrsField:[AliasProtein short:alp] 
$DF_AliasSymbol=$SrsField:[AliasSymbol short:als] 
#$DF_AlleleN=$SrsField:[NAlleles short:nal]
$DF_AlleleText=$SrsField:[AlleleText short:atx]
$DF_Alphabet=$SrsField:[Alphabet short:alf]
$DF_AltName=$SrsField:[AltName short:alt]	
$DF_Altern_Prom=$SrsField:[altern_prom short:ap]
$DF_AntiHb=$SrsField:[AntiHb short:ahb]
$DF_Assembly=$SrsField:[Assembly short:ass] 
$DF_AssignCode=$SrsField:[PatentAssigneeCode short:pac]
$DF_AssignName=$SrsField:[PatentAssignee short:pan]
$DF_Authors=$SrsField:[Authors short:aut]
#$DF_BAcc=$SrsField:[BlastHits short:BH]
$DF_BBridge=$SrsField:[BetaBridge short:bbr]
$DF_BINDFAC=$SrsField:[BindingFactor short:bf]
#$DF_BLAX=$SrsField:[Blast short:BX]
$DF_Beta=$SrsField:[Beta short:bet]
$DF_BindingFactor=$SrsField:[BindingFactor short:bf]
#$DF_BitScore=$SrsField:[BitScore short:bsc]
$DF_BookName=$SrsField:[BookName short:bkn]
$DF_Break=$SrsField:[Break short:bre]
$DF_CAS=$SrsField:[CASnumber short:cas]
$DF_CDD=$SrsField:[Matches short:mat] 
#$DF_CDnaChangePos=$SrsField:[cDnaChangePos short:cdp]
$DF_CEvidence=$SrsField:[ContigEvidence short:cevi] 
#$DF_CHUCKLES=$SrsField:[CHUCKLES short:chu]
$DF_CN=$SrsField:[CN short:cn]
#$DF_COMM=$SrsField:[Comment short:cc]
#$DF_COMMENT=$SrsField:[Comment short:cc]
#$DF_CRC=$SrsField:[crc short:crc]
$DF_CREDate=$SrsField:[DateCreated short:crd]
$DF_CS=$SrsField:[CS short:cs]
#$DF_CaseReference=$SrsField:[CaseRefrence short:cre]
$DF_CatActivity=$SrsField:[CatalyticActivity short:cat]	
$DF_Caveat=$SrsField:[Caveat short:cav]
$DF_CdsBegin=$SrsField:[CdsBegin short:cdb]
$DF_CdsEnd=$SrsField:[CdsEnd   short:cde]
#$DF_CdsLocation=$SrsField:[CDSLocation short:clc]
$DF_ChainN=$SrsField:[NChains short:chn]
$DF_ChainName=$SrsField:[ChainName short:chn  guiInfo:$GI_MultiSelectOver]
$DF_Checked=$SrsField:[Checked  short:chk]
$DF_Checksum=$SrsField:[Checksum short:cks]
$DF_ChrLocation=$SrsField:[ChrLocation short:clc]
$DF_Chromosome=$SrsField:[Chromosome short:chr]
$DF_ChrsNo=$SrsField:[ChromosomeNo short:chn]
$DF_Cispep=$SrsField:[Cispep short:cp]
$DF_Citation=$SrsField:[Citation short:cit]
$DF_Class=$SrsField:[Class short:cla]
$DF_ClassComment=$SrsField:[Comments short:ccm]
$DF_ClinicalSymptoms=$SrsField:[ClinicalSymptoms short:cls]
$DF_Clone=$SrsField:[Clone short:clo]
$DF_CloneEnd=$SrsField:[CloneEnd short:cle]
$DF_CloneIdType=$SrsField:[CloneIdType short:cit]
$DF_Cloneid=$SrsField:[CloneID short:cid]
$DF_CmpChains=$SrsField:[CmpChains short:cch]
$DF_CmpDesc=$SrsField:[CmpDesc short:cde]
$DF_CmpEng=$SrsField:[CmpEng short:cen]
$DF_CmpFrag=$SrsField:[CmpFrag short:cfr]
$DF_CmpMut=$SrsField:[CmpMut short:cmu]
$DF_CmpOther=$SrsField:[CmpOther short:cot]
$DF_CmpSynon=$SrsField:[CmpSynon short:csy]
$DF_CmpUnit=$SrsField:[CmpUnit short:cun]
#$DF_Code=$SrsField:[Code short:cod]
#$DF_CodonChange=$SrsField:[CodonChange short:coc]
#$DF_CodonNo=$SrsField:[CodonNo short:cdn]
#$DF_CodonPos=$SrsField:[CodonPos short:cdp guiInfo:$GI_CheckList]
$DF_Cofactor=$SrsField:[Cofactor short:cof]
#$DF_Com=$SrsField:[Comment short:com]
$DF_Command=$SrsField:[Command short:com]
#$DF_Commands=$SrsField:[Commands  short:com]
$DF_Comment=$SrsField:[Comment short:cc]
$DF_CommentType=$SrsField:[CommentType short:cct  guiInfo:$GI_MultiSelectOver]
#$DF_Comp=$SrsField:[CompMapLink   short:cml] 
$DF_CompMap=$SrsField:[CompMap short:cmp] 
$DF_Compound=$SrsField:[Compound short:com]
#$DF_CompoundName=$SrsField:[CompoundName short:na]
$DF_Contents=$SrsField:[Contents short:cnt]
$DF_Contig=$SrsField:[Contig short:cont] 
$DF_ConvergeStatus=$SrsField:[ConvergeStatus short:cmp]
#$DF_Coords3d=$SrsField:[Coords3d short:coo]
$DF_CounterItem=$SrsField:[CountedItem short:cti guiInfo:$GI_Menu]
$DF_CounterN=$SrsField:[CountedN short:ctn]
#$DF_CpG=$SrsField:[CpG short:cpg guiInfo:$GI_CheckList]
$DF_CurrentId=$SrsField:[CurrentId   short:cid] 
$DF_Cytoband=$SrsField:[Cytoband short:CB]
$DF_DBLinks=$SrsField:[OtherDBlinks short:dbl]
$DF_DBNAME=$SrsField:[dbname short:dbn]
$DF_DBOrigin=$SrsField:[DBOrigin short:dbo guiInfo:$GI_CheckList]
$DF_DBXn=$SrsField:[EMBLxref short:dbxn]
$DF_DBXp=$SrsField:[SWALLxref short:dbxp]
$DF_DComment=$SrsField:[BuildInfo short:bi]
$DF_DNA=$SrsField:[DnaType short:typ]
#$DF_DNAChange=$SrsField:[NucleotideChange short:nuc]
$DF_DNAmutType=$SrsField:[DNAMutType short:dmt guiInfo:$GI_CheckList]
#$DF_DSeg=$SrsField:[GDBDSeq short:GDB]
$DF_DWPI=$SrsField:[DWPIAccessionNumber short:dwpi]
$DF_Database=$SrsField:[Database short:qdb]
$DF_Date=$SrsField:[Date short:dat]
$DF_Dbref=$SrsField:[Dbref short:dr]
$DF_DefineFirstPos=$SrsField:[DefineFirstPos short:dfp]
$DF_Depend=$SrsField:[depend  short:dep]
$DF_Description=$SrsField:[Description short:des]
$DF_Detection=$SrsField:[DetectionMethod short:met ]
#$DF_Determination=$SrsField:[Determination short:det]
$DF_Diameter=$SrsField:[Diameter_PAM short:dia]
$DF_Division=$SrsField:[Division short:div  guiInfo:$GI_CheckList]
#$DF_DnaChangePos=$SrsField:[DnaChangePos short:dcp]
$DF_Doc=$SrsField:[doc short:doc]
$DF_EC=$SrsField:[EC short:ec]
$DF_ECNumber=$SrsField:[ECNumber short:ecn]
$DF_EVDlambda=$SrsField:[EVDlambda short:ela]
$DF_EVDmu=$SrsField:[EVDmu short:emu]
$DF_EXP_METHOD=$SrsField:[ExpMethod short:exp  guiInfo:$GI_CheckList] 
$DF_E_Score=$SrsField:[E_Score  short:esc]
$DF_EcNum=$SrsField:[EcNum short:ecn] 
$DF_Effector=$SrsField:[Effector short:eff]
$DF_ElemDenom=$SrsField:[ElementDenomination short:eld]
$DF_End2=$SrsField:[End2 short:e2]
$DF_End=$SrsField:[End short:end]
$DF_Entered=$SrsField:[Entered short:ent]
$DF_EntryAuthors=$SrsField:[EntryAuthors short:eat]
#$DF_EnzAct=$SrsField:[EnzymeActivity short:EAc]
$DF_Enzyme=$SrsField:[LENZYMElinks short:len]
$DF_EnzymeCode=$SrsField:[EnzymeCode short:enz]
$DF_Equivalences=$SrsField:[Equivalences short:eqv]
$DF_ErrorCode=$SrsField:[ErrorCode short:erc]
$DF_ErrorDetail=$SrsField:[ErrorDetail short:edt]
$DF_ErrorExplanation=$SrsField:[ErrorExplanation short:ere]
$DF_ErrorFix=$SrsField:[ErrorFix short:efx]
$DF_ErrorGroup=$SrsField:[ErrorGroup short:grp]
$DF_ErrorShortMsg=$SrsField:[ErrorShortMsg short:esm]
$DF_Eval=$SrsField:[Evalue short:eva]
$DF_Evidence=$SrsField:[Evidence short:evi] 
#$DF_Exon=$SrsField:[Exon_Number short:Exn  guiInfo:$GI_CheckList]
#$DF_Express=$SrsField:[ExpresRegul short:ess]
$DF_Expression=$SrsField:[Expression short:exp]
$DF_FF=$SrsField:[FuncFeature short:ff]
$DF_Factor=$SrsField:[Factor short:tf]
$DF_FactorSource=$SrsField:[FactorSource short:so]
#$DF_FamHist=$SrsField:[FamilyHistory short:fah guiInfo:$GI_CheckList ]
#$DF_FamilyN=$SrsField:[NFamilies short:nfa]
#$DF_Features=$SrsField:[Features short:fts]
$DF_FilingCountry=$SrsField:[FilingCountry short:pfc]
$DF_FilingDate=$SrsField:[FilingDate short:pfd]
$DF_FilingNumber=$SrsField:[FilingNumber short:pfn]
$DF_Flag=$SrsField:[Flag short:flg]
#$DF_Formul=$SrsField:[Formul short:fo]
$DF_Formula=$SrsField:[Formula short:frm]
$DF_Frame=$SrsField:[Frame short:fra guiInfo:$GI_MultiSelectOver]
$DF_FtDescription=$SrsField:[FtDescription short:ftd]
$DF_FtGID=$SrsField:[FeatureGID short:fgi]
#$DF_FtGene=$SrsField:[Gene short:gen]
$DF_FtKey=$SrsField:[FtKey short:ftk guiInfo:$GI_MultiSelectOver]
$DF_FtLength=$SrsField:[FtLength short:ftl]
$DF_FtLocation=$SrsField:[FtLocation short:flo]
#$DF_FtMap=$SrsField:[MapLocation short:mpl]
$DF_FtNumASNexp=$SrsField:[Asparagines short:asn]
$DF_FtNumASNpred=$SrsField:[AsparaginesPredicted short:asnp]
$DF_FtNumSERexp=$SrsField:[Serines short:ser]
$DF_FtNumSERpred=$SrsField:[SerinesPredicted short:serp]
$DF_FtNumTHRexp=$SrsField:[Threonines short:thr]
$DF_FtNumTHRpred=$SrsField:[ThreoninesPredicted short:thrp]
$DF_FtNumber=$SrsField:[Number short:num]
#$DF_FtPartial=$SrsField:[Partial short:par]
#$DF_FtProduct=$SrsField:[Product short:pro]
#$DF_FtPseudo=$SrsField:[Pseudo short:pse]
$DF_FtQualifier=$SrsField:[FtQualifier short:ftq guiInfo:$GI_MultiSelectOver]
#$DF_FtSource=$SrsField:[FtSource short:fts]
$DF_Ftnote=$SrsField:[Ftnote short:ft]
$DF_FullLength=$SrsField:[FullLength short:fln]
$DF_Fullname=$SrsField:[FullName short:ffn]
#$DF_FuncStudies=$SrsField:[FunctionalStudies short:fst guiInfo:$GI_CheckList]
$DF_FunctCat=$SrsField:[FuctionCategory short:fuca] 
$DF_Function=$SrsField:[Fuction short:fun] 
$DF_GDB=$SrsField:[GDB short:gdb]
$DF_GID=$SrsField:[GID short:gid]
$DF_GN=$SrsField:[GnmTeminus short:gn]
$DF_GenType=$SrsField:[GenType short:gtp]
$DF_Genbank=$SrsField:[GenbankAccession short:gba] 
$DF_Genbankid=$SrsField:[GenbankAcc short:gid]
$DF_Gene=$SrsField:[Gene short:GE]
$DF_GeneName=$SrsField:[GeneName short:gen]
#$DF_GeneProduct=$SrsField:[GeneProduct short:pro]
$DF_GeneSymbol=$SrsField:[GeneSymbol short:symb]
$DF_Genes=$SrsField:[GENESlinks short:gen]
$DF_GeneticCode=$SrsField:[GeneticCode short:gc  guiInfo:$GI_CheckList]
$DF_Glycoprotein=$SrsField:[Glycoprotein short:gly]
$DF_HMM=$SrsField:[HMM short:hmm is:$HMM_DATA]
$DF_HMMhit=$SrsField:[HMMhit short:hmh]
#$DF_Haplotype=$SrsField:[Haplotype short:hap]
$DF_Header=$SrsField:[Header short:hdr]
$DF_HeaderField=$SrsField:[HeaderField short:hd type:header]
$DF_Helix=$SrsField:[Helix short:hel]
$DF_Hetero=$SrsField:[Hetero short:het]
$DF_Histograms=$SrsField:[Histograms short:his]
$DF_History=$SrsField:[History short:his]
$DF_HydBondsAntiP=$SrsField:[NHBondsAntiParBridge short:hab]
$DF_HydBondsJN=$SrsField:[NHydBondsJ short:hb]
$DF_HydBondsParaP=$SrsField:[NHBondsParaBridge short:hpb]
$DF_ID=$SrsField:[ID short:id]
$DF_II3=$SrsField:[II3 short:ii3]
$DF_II5=$SrsField:[II5 short:ii5]
#$DF_InEx=$SrsField:[IntronExon short:IE guiInfo:$GI_MultiSelect]
$DF_Inhibitor=$SrsField:[Inhibitor short:ihb]
$DF_InitFrequency=$SrsField:[InitialFrequency short:if]
$DF_Init_1=$SrsField:[Init_1  short:in1]
$DF_Init_n=$SrsField:[Init_n  short:inn]
$DF_Interaction=$SrsField:[Interaction short:ia]
#$DF_Intron=$SrsField:[Intron_Number short:Irn  guiInfo:$GI_CheckList]
$DF_Inventors=$SrsField:[Inventors short:inv]
$DF_IsoelectricPoint=$SrsField:[IsoelectricPoint short:iep]
$DF_Iterations=$SrsField:[Iterations short:ite]
$DF_JobName=  $SrsField:[JobName      short:jnm ]
#$DF_JobSerial=$SrsField:[JobSerial    short:jsr]
$DF_KChain=$SrsField:[KChain short:kch]
$DF_Keywords=$SrsField:[Keywords short:key]
$DF_Kind=$SrsField:[Kind short:kin]
$DF_LINK=$SrsField:[Link short:lnk]
$DF_LUPDate=$SrsField:[LastUpdated short:crlu]
#$DF_LabName=$SrsField:[LabName short:lan]
$DF_Len=$SrsField:[Length short:len]
$DF_LibId=$SrsField:[LibraryID short:lid]
$DF_LibLevel=$SrsField:[LibLevel short:ll]
$DF_Library=$SrsField:[Library short:lib]
$DF_Links=$SrsField:[Links   short:lnk] 
#$DF_Location=$SrsField:[Location short:loc  guiInfo:$GI_CheckList]
$DF_LocusLink=$SrsField:[LocusLink short:loc]
$DF_Lod=$SrsField:[LodScore short:lod]
$DF_MGC=$SrsField:[CDScompleteness short:mgc]
$DF_MN=$SrsField:[MN short:mn]
#$DF_MP=$SrsField:[Map short:map]
$DF_Map=$SrsField:[MapLocation short:mlc ]
$DF_MapLink=$SrsField:[MapLink short:mli] 
$DF_MapLocation=$SrsField:[MapLocation short:mlc ]
$DF_MapNo=$SrsField:[MapNo short:map]
$DF_Marker=$SrsField:[Marker short:mkr]
$DF_MatchLen=$SrsField:[MatchLength short:mtl]
$DF_Matrices=$SrsField:[Matrices short:mat]
#$DF_MaxRepeat=$SrsField:[MaxRepeat short:max]
$DF_Medianscore=$SrsField:[Medianscore short:med]
$DF_Medline=$SrsField:[MedlineID short:mid]
$DF_Method=$SrsField:[Method short:met]
$DF_MethodComment=$SrsField:[Comments short:mcm]
$DF_MethodProto=$SrsField:[Prototype short:pto]
$DF_MissBB=$SrsField:[MissBB short:mbb]
$DF_MissSC=$SrsField:[MissSC short:msc]
$DF_MitoCode=$SrsField:[MitochondrialCode short:mgc  guiInfo:$GI_CheckList]
$DF_Modres=$SrsField:[Modres short:mr]
$DF_MolWeight=$SrsField:[MolWeight short:mow]
$DF_Molecule=$SrsField:[Molecule short:mol  guiInfo:$GI_CheckList]
$DF_MoleculeType=$SrsField:[MoleculeType short:mot  guiInfo:$GI_CheckList]
$DF_MoreLinks=$SrsField:[MoreLinks   short:mlnk] 
$DF_Motif=$SrsField:[Motif  short:mot]
#$DF_MutLength=$SrsField:[DnaChangeLength  short:LE]
$DF_MutType=$SrsField:[MutationType short:mty guiInfo:$GI_MultiSelectOver]
$DF_NAlign=$SrsField:[NAlign short:nal]
$DF_NChain=$SrsField:[NChain short:nch]
$DF_NG =$SrsField:[RefSeq_Genome short:ng] 
$DF_NID=$SrsField:[NID short:nid]
#$DF_NWaterMols=$SrsField:[NWaterMols short:nwm]
$DF_N_AMINOACIDS=$SrsField:[AminoAcids short:aa]
$DF_N_HET_GROUPS=$SrsField:[NoHetGroups short:het]
$DF_N_HSSP_ALIGN=$SrsField:[NoHSSPAlign short:nha] 
$DF_N_NUCLACIDS=$SrsField:[NucleicAcids short:nuc]
$DF_Navigate=$SrsField:[Navigate short:nav]
#$DF_Neighb_Prom=$SrsField:[neighb_prom short:np]
$DF_Nmodel=$SrsField:[Nmodel short:nmdl]
$DF_Nmol=$SrsField:[Nmol short:nmol]
$DF_NulE=$SrsField:[NulE short:nue]
$DF_NulT=$SrsField:[NulT short:nut]
$DF_NumAlign=$SrsField:[NumAlignments short:nal]
$DF_NumHSPs=$SrsField:[NumHSPs short:nhs]
$DF_OMIM=$SrsField:[OMIMlinks short:omm]
$DF_Omim=$SrsField:[Omim short:omim] 
$DF_OptScore=$SrsField:[OptScore    short:osc]
$DF_Organelle=$SrsField:[Organelle short:ogn]
$DF_Organism=$SrsField:[Organism short:org]
$DF_OriCode=$SrsField:[OriginalCode short:oc]
$DF_PATTERN=$SrsField:[Patterns short:pat]
$DF_PDBDATA=$SrsField:[PDB short:pdb is:$STRUCTURE_DATA]
$DF_PDBchain=$SrsField:[Chain short:ch]
$DF_PDBsite=$SrsField:[Site short:sit]
$DF_PID=$SrsField:[PID short:pid]
#$DF_PVal=$SrsField:[BlastScore short:SC]
$DF_ParaHb=$SrsField:[ParaHb short:phb]
$DF_ParentId=$SrsField:[ParentId short:pid]
#$DF_Patent=$SrsField:[Patent short:pat]
$DF_PatentCountry=$SrsField:[PatentCountry short:ptc]
$DF_PatentDate=$SrsField:[PatentDate short:pdt]
$DF_PatentLanguage=$SrsField:[Language short:lng]
$DF_PatentNumber=$SrsField:[PatentNumber short:pnu]
$DF_PatentSection=$SrsField:[Section short:sec]
$DF_PatentTitle=$SrsField:[DerwentPatentTitle short:pat]
$DF_Pathway=$SrsField:[PATHWAYlinks short:pth]
#$DF_PatientID=$SrsField:[PatientID short:PT]
#$DF_PatientN=$SrsField:[NPatients short:npa]
$DF_PercIdt=$SrsField:[PercentIdent short:piy]
$DF_PercSim=$SrsField:[PercentSimil short:psi]
$DF_Pfam=$SrsField:[PfamID short:pf]
$DF_PfamAcc=$SrsField:[PfamAcc short:pfa]
$DF_Phenotype=$SrsField:[Phenotype short:phe]
#$DF_Plasmid=$SrsField:[Plasmid short:pla]
#$DF_Polymorphism=$SrsField:[Polymorphism short:plm guiInfo:$GI_CheckList]
#$DF_Population=$SrsField:[Population short:pop]
$DF_PrimAccession=$SrsField:[PrimAccNumber short:pac]
$DF_PriorityCountry=$SrsField:[PriorityCountry short:prc]
$DF_PriorityDate=$SrsField:[PriorityDate short:prd]
$DF_PriorityNumber=$SrsField:[PriorityNumber short:prn]
$DF_Product=$SrsField:[Product short:pro]
$DF_ProtChangePos=$SrsField:[ProteinChangePos short:acp]
$DF_ProtGI=$SrsField:[ProtGI short:pgi]
$DF_ProtID=$SrsField:[ProteinID short:prd]
#$DF_ProtLevel=$SrsField:[protLevel short:prl  ]
$DF_Protein=$SrsField:[GenbankProtein short:gbp] 
#$DF_ProteinDomain=$SrsField:[ProteinDomain short:dom guiInfo:$GI_CheckList]
$DF_Proto=$SrsField:[Prototype short:pro]
$DF_Protocol=$SrsField:[ExpProtocol short:ptc]
$DF_Protsim=$SrsField:[Protsim short:ps]
$DF_PubMed=$SrsField:[PubMedID short:pmd]
$DF_PubmedComment=$SrsField:[PubMedComment short:pmc] 
$DF_Query=$SrsField:[Query short:qry]
$DF_QueryBeg=$SrsField:[QueryMatchBeginPos short:qbp]
$DF_QueryEnd=$SrsField:[QueryMatchEndPos short:qep]
#$DF_REChange=$SrsField:[REChange short:RE]
$DF_REF=$SrsField:[Reference short:ref]
#$DF_REFTITLE=$SrsField:[Title short:tit]
$DF_RF=$SrsField:[RF short:rf]
$DF_RHPanel=$SrsField:[RHPanel short:pan]
#$DF_RNAChange=$SrsField:[RnaChange short:rna]
#$DF_RNAChangePos=$SrsField:[RnaChangePos short:rcp]
$DF_RNAmutType=$SrsField:[RNAMutType short:rmt guiInfo:$GI_CheckList]
$DF_RStatus=$SrsField:[RStatus  short:rst]
$DF_R_FACTOR=$SrsField:[RFactor short:rfa] 
$DF_Radius=$SrsField:[radius_PAM short:rad]
$DF_Rank=$SrsField:[Rank short:rnk guiInfo:$GI_MultiSelect]
$DF_Rawscore=$SrsField:[Rawscore short:raw]
$DF_Reaction=$SrsField:[Reaction short:react]
$DF_RefComment=$SrsField:[RefComment short:rc]
$DF_RefCommentCode=$SrsField:[RefCommentCode short:rcc guiInfo:$GI_MultiSelectOver]
$DF_RefFirstPage=$SrsField:[FirstPage short:fp]
$DF_RefJournal=$SrsField:[Journal short:jnl]
$DF_RefModel=$SrsField:[RefseqModelId short:rsmi] 
$DF_RefPos=$SrsField:[RefPosition short:rp]
$DF_RefVolumeNo=$SrsField:[VolumeNo short:vol]
$DF_RefYear=$SrsField:[Year short:yr]
$DF_Reference=$SrsField:[Reference short:ref]
$DF_Refseq=$SrsField:[RefseqId short:rsi] 
$DF_Reftitl=$SrsField:[Reftitl short:rt]
#$DF_Region=$SrsField:[RegionStudied short:reg ]
$DF_RelatedLocus=$SrsField:[RelatedLoxus short:rell] 
#$DF_Relative=$SrsField:[Relative short:Rel]
$DF_Release=$SrsField:[Release short:rel]
$DF_Remark=$SrsField:[Remark short:rem]
#$DF_ReportType=$SrsField:[ReportType short:rty]
$DF_Residues=$SrsField:[Residues short:res]
$DF_ResiduesN=$SrsField:[NResiduesN short:rsn]
$DF_Resol=$SrsField:[Resol short:res]
$DF_Resolution=$SrsField:[Resolution short:res] 
$DF_Rfree=$SrsField:[Rfree short:rf]
$DF_Run=$SrsField:[run  short:run]
$DF_Rwork=$SrsField:[Rwork short:rw]
$DF_SA=$SrsField:[SA short:sa]
$DF_SCount=$SrsField:[SeqCount short:SC]
#$DF_SLN=$SrsField:[SLN short:tln  is:$COMPOUND_DATA]
#$DF_SMILES=$SrsField:[SMILES short:sml]    
$DF_SSbond=$SrsField:[SSbond short:ss]
$DF_STATBAS=$SrsField:[StatisticBasis short:stb]
#$DF_STRDES=$SrsField:[StrDescrip short:sd]
#$DF_STS=$SrsField:[STS short:sts]
$DF_SUPDate=$SrsField:[LastSequenceUpdate short:lsu]
$DF_SW_Score=$SrsField:[SW_Score      short:sws]
$DF_Score=$SrsField:[Score short:sco]
$DF_SecStruc=$SrsField:[SecStruc short:ss]
$DF_Secondary=$SrsField:[Secondary short:sec]
$DF_Seq=$SrsField:[Sequence short:sq]
$DF_SeqAcc=$SrsField:[SequenceAcc short:acc]
$DF_SeqLength=$SrsField:[SeqLength short:sl]
$DF_SeqList=$SrsField:[SeqList short:sql]
$DF_SeqVersion=$SrsField:[SeqVersion short:sv]
$DF_Seqadv=$SrsField:[Seqadv short:sa]
$DF_Seqres=$SrsField:[Seqres short:sr]
$DF_Sequence=$SrsField:[Sequence short:seq]
$DF_SequenceType=$SrsField:[SequenceType short:st]
$DF_Sequences=$SrsField:[Sequences short:nsq]
#$DF_Sex=$SrsField:[Sex short:sex guiInfo:$GI_CheckList]
$DF_Shortaccession=$SrsField:[Shortaccession short:sac]
#$DF_SimIdx=$SrsField:[SimIdx short:sim]
$DF_Site=$SrsField:[Site short:sit]
$DF_SiteFirstPos=$SrsField:[SiteFirstPos short:sfp]
$DF_SiteLastPos=$SrsField:[SiteLastPos short:slp]
$DF_SiteLen=$SrsField:[SiteLen short:len]
$DF_Size=$SrsField:[Size short:siz]
$DF_SkipFlag=$SrsField:[SkipFlag short:skf]
$DF_Source=$SrsField:[Source short:src]
$DF_SourceESTid=$SrsField:[ESTName short:est]
$DF_SourceSTSid=$SrsField:[STSName short:sts]
$DF_Species=$SrsField:[Species short:spc]
$DF_SsBridgeInterN=$SrsField:[NSsBridgeInter short:ern]
$DF_SsBridgeIntraN=$SrsField:[NSsBridgeIntra short:ran]
$DF_SsBridgeTotN=$SrsField:[NSsBridgeTot short:ssn]
$DF_StartTime=$SrsField:[StartTime short:stt]
$DF_Status=$SrsField:[status  short:sta]
$DF_Stderr=$SrsField:[Stderr  short:err]
$DF_Stdout=$SrsField:[Stdout  short:out]
#$DF_Strain=$SrsField:[Strain short:str]
$DF_Structure=$SrsField:[PDBlinks short:stt]
$DF_Sts=$SrsField:[Sts short:sts] 
#$DF_SubLibrary=$SrsField:[SubLibrary short:sublib  guiInfo:$GI_CheckList]
#$DF_SubmissionDate=$SrsField:[SubmissionDate short:sub]
$DF_Substrate=$SrsField:[Substrate short:sub]
$DF_SummFunc=$SrsField:[SummFunc short:sfu] 
$DF_Summary=$SrsField:[Summary short:sum]
$DF_SuperFamily=$SrsField:[SuperFamily short:sfa]
$DF_Supersedes=$SrsField:[Supersedes short:sps]
#$DF_Synonyms=$SrsField:[Synonyms short:SYM]
$DF_SysTime=$SrsField:[SysTime short:st]
$DF_Sysname=$SrsField:[SystematicName short:syn]
#$DF_SystName=$SrsField:[SystematicName short:sNa]
$DF_TWaterMols=$SrsField:[TotWaterMols short:twm] 
$DF_TXmap=$SrsField:[TXmap short:txm]
#$DF_T_FRAC_BETA=$SrsField:[TotFractBeta short:tfb] 
$DF_T_NRES_PROT=$SrsField:[TotNResProt short:tnp] 
$DF_Target=$SrsField:[Target short:trg]
$DF_TargetPos=$SrsField:[TargetPosition short:tpo]
$DF_TaxId=$SrsField:[NCBI_TaxId short:txi]
$DF_Taxo=$SrsField:[taxo short:tx]
#$DF_TaxoRange=$SrsField:[TaxoRange short:tax]
$DF_Taxon=$SrsField:[Taxon short:tax]
$DF_Text=$SrsField:[Text short:txt]
#$DF_Tissue=$SrsField:[Tissue short:tis]
$DF_Title=$SrsField:[Title short:tit]
$DF_TopScore=$SrsField:[TopScore short:tsc]  # need this for searchdb-views?
$DF_TransProd=$SrsField:[TranscriptProduct short:trpr] 
#$DF_TranslEffect=$SrsField:[TranslationEffect short:tre  guiInfo:$GI_MultiSelect]
#$DF_Transposon=$SrsField:[Transposon short:tra]
#$DF_TrivName=$SrsField:[TrivialName short:tNa]
$DF_Type=$SrsField:[Type short: typ]
$DF_UTR=$SrsField:[UTR   short:utr]
$DF_UniGeneId=$SrsField:[UniGeneId short:ugi]
$DF_Unigene=$SrsField:[Unigene short:uni] 
$DF_Updated=$SrsField:[Updated short:upd]
#$DF_Varcomm=$SrsField:[VariantComment short:vac]
$DF_Variant=$SrsField:[Variant short:var] 
$DF_VariantName=$SrsField:[VariantName short:vnm]
$DF_Vendor=$SrsField:[Vendor short:ven]
$DF_WallTime=$SrsField:[WallTime short:wt]
$DF_Hostname=$SrsField:[Hostname short:host]
$DF_WaterMols=$SrsField:[WaterMols short:wat]
$DF_Width=$SrsField:[Width short:wid]
$DF_XCDD=$SrsField:[ModelMatches short:xmat] 
$DF_XT=$SrsField:[XT short:xt]
$DF_Z_OptScore=$SrsField:[Z_OptScore    short:zsc]
$DF_a=$SrsField:[a short:a]
$DF_alpha=$SrsField:[alpha short:al]
$DF_b=$SrsField:[b short:b]
$DF_beta =$SrsField:[beta  short:be]
$DF_c=$SrsField:[c short:c]
$DF_dbnam=$SrsField:[DbName short:dbn guiInfo:$GI_MultiSelect]
$DF_dbref=$SrsField:[DBxref short:dr]
$DF_gamma=$SrsField:[gamma short:ga]
#$DF_mRNAlevel=$SrsField:[mRNAlevel short:mRN  guiInfo:$GI_MultiSelectOver]
$DF_spgrp=$SrsField:[spgrp short:sg]
$DF_stsAcc=$SrsField:[stsAcc short:SA]
$DF_stsName=$SrsField:[stsName short:SN]
$DF_tFracHelix=$SrsField:[TotFractHelix short:tfh] 
# fields for sequences/alignments

$DF_ProtSequence=$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]
  }
]
# commented by fmalusa@ist.unige.it on 2003 08 11 
# $DF_Name=$SrsField:[Name short:nam ]

$DF_Alignment=$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>
            }
    ]
  }
]
$DF_DNALocation=$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 
  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
      }
    ]
  }
]
$DF_PDBseq=$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]
    }
]


# 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 from:10001 to:20000
]
$Allele_Id=$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
]
$Command_Id=$IdType:[Command size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:2
]
$Block_Id=$IdType:[Block size:6 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:1
]
$Refseq_Id=$IdType:[Refseq size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:2 from:1 to:10000
]
$Function_Id=$IdType:[Function size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:2 from:1 to:10000
]
$Model_Id=$IdType:[Model size:7 subNBeg:0 subNLen:2 fipBeg:2 
  fipLen:3 libIdBeg:5 libIdLen:2 from:1 to:10000
]



# 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]
$DATA_FILE=$FileType:[text typeName:data maxline:10000 fipVar:entryFip]
$ESTDATA_FILE=$FileType:[text typeName:all maxline:10000 fipVar:entryFip]
$SEQ_FILE=$FileType:[seq shareWith:$DAT_FILE fieldTokens:sequence fipVar:seqFip]
$HTML_FILE=$FileType:[text typeName:html maxline:10000]
$TXT_FILE=$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]
$GBREF_FILE=$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]
# GENESEQ datafiles
$UDAT_FILE=$FileType:[text typeName:DAT maxline:1000 fipVar:entryFip]
$USEQ_FILE=$FileType:[seq shareWith:$UDAT_FILE fieldTokens:sequence fipVar:seqFip]
$FASTA_FILE=$FileType:[maxline:500]
$FastaRun_File=$FileType:[run maxline:200 fipVar:runFip fieldTokens:run]
$FastaHit_File=$FileType:[hits maxline:200 fipVar:hitFip fieldTokens:hfs]
$BLAST_FILE=$FileType:[maxline:200 ]
$BlastRun_File=$FileType:[run maxline:200 fipVar:runFip fieldTokens:run]
$BlastHit_File=$FileType:[hits maxline:200 fipVar:hitFip fieldTokens:hf]
$BlastTail_File=$FileType:[tail maxline:200 fipVar:tailFip fieldTokens:tail]


# 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]
$parentLink14=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$Block_Id idtype2:$ENTRY_ID]
$parentLinkRS=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$Refseq_Id idtype2:$ENTRY_ID]
$parentLinkRSF=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$Function_Id idtype2:$ENTRY_ID]
$parentLinkRMO=$Link:[fromName:subentry toName:parent type:parent
  idtype1:$Model_Id idtype2:$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.trim:[] $obj.str:[$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.trim:[] $obj.str:[$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 ] }
#]
$DNAALI_DATA=$DataType:[DNAAlignment
  dataClass:$CLASS.SeqAli
  bioType:NA
# applications:{}
   print:@{$obj.str:[$format useStream:y]}
]

$PROTALI_DATA=$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
  }
]

$STRUCTURE_DATA = $DataType: [Structure
  dataClass:$CLASS.Entry
  print:@{$obj.str:[useStream:y]}
  applications:{$WhatCheckApp}
]



#################################################################################
# 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:['Data Options']

##############################################################
# Application options commonly used
##############################################################

$jobName_Option=$AppOpt:[jobName group:$PRIM_OPTS
  prompt:'Name of <!>job<!>:'
  comment:
   |This option is a name for the current tool launch job.
   |It is used as part of the name of the tool 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 tool 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 tool requires a DNA
	  |sequence as input.
  prompt:'Query DNA sequence' pos:left outFormat:fasta
  mandatory:yes
]
# Note: the BLAST and FASTA database defintions are now in
# $SRSSITE/localApplicationOptions.i

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

$GI_CheckList=$GuiField:[CheckList type:checklist]
$GI_Menu=$GuiField:[Menu type:menu maxKeys:500]
$GI_MultiSelect=$GuiField:[MultiSelect type:multiselect visListHeight:7]
$GI_MultiSelectOver=$GuiField:[MultiSelectOver type:multiselect visListHeight:7 valOverlap:y]

$LSF=$BatchQueueSystem:[
  name:LSF
  sub_command:
   |bsub  \
  interactive_sub_command:
   |bsub -I  \
  del_command:
   |bkill \
  stat_command:
   |bjobs
  acct_command:
   |bacct \
  #-----------------
  #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)"
]
DF_IDE
$DQS=$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)"
]
DF_IDE
$CODINE=$BatchQueueSystem:[
  name:CODINE
  sub_command:
   |CODINE_ROOT=/software/codine; export CODINE_ROOT; qsub  -cwd \
  interactive_sub_command:
   |CODINE_ROOT=/software/codine; export CODINE_ROOT; qsh \
  del_command:
   |CODINE_ROOT=/software/codine; export CODINE_ROOT; qdel \
  stat_command:
   |CODINE_ROOT=/software/codine; export CODINE_ROOT; qstat
  acct_command:
   |CODINE_ROOT=/software/codine; export CODINE_ROOT; qacct -j \
  #-----------------
  #Option specifiers
  #-----------------
  job_name_spec:N
  priority_spec:p
  queue_name_spec:qDF_IDE
  #--------------------------------------------
  #Regular expressions for state identification
  #--------------------------------------------
  runStateIndicatorRE:"( r | t )"
  waitStateIndicatorRE:"( w | h | S | s | T | qw )"
]

# For local settings.
file:"SRSSITE:localApplicationOptions.i"
$ObjSave:[$blastList fileName:"SRSOM:blastList.om" saveNS:0]
$Print:|Wrote BLAST parser object file "SRSOM:blastList.om"

$DAT_FILE=$FileType:[text typeName:dat maxline:10000 fipVar:entryFip]