/* objfeat.h * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * File Name: objfeat.h * * Author: James Ostell * * Version Creation Date: 4/1/91 * * $Revision: 6.10 $ * * File Description: Object manager interface for module NCBI-SeqFeat * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * $Log: objfeat.h,v $ * Revision 6.10 2001/10/02 21:47:54 kans * added hooks for writing extra descriptors or features (JO) * * Revision 6.9 2000/09/28 11:40:19 ostell * added endogenous_virus (19) to MolInfo.genome * * Revision 6.8 2000/01/16 19:18:32 kans * added specialCleanupFlag field to SeqFeatXref structure * * Revision 6.7 1999/12/14 17:30:39 ostell * changed protoplast to proplastid * * Revision 6.6 1999/10/06 18:45:27 kans * fixed nested comment warning * * Revision 6.5 1999/10/05 20:23:17 kans * fixed typo * * Revision 6.4 1999/10/05 19:05:45 ostell * added comments on BioSource.genome * * Revision 6.3 1999/09/27 17:48:37 kans * using GatherIndex structure * * Revision 6.2 1999/09/24 23:09:23 kans * adds EXTRA_OBJMGR_FIELDS to several objects * * Revision 6.1 1998/06/29 20:31:30 kans * explicit defines for FEATDEF_MAX, SEQFEAT_MAX, and SEQDESCR_MAX Boolean array sizes * * Revision 6.0 1997/08/25 18:49:53 madden * Revision changed to 6.0 * * Revision 4.3 1997/08/20 19:17:06 madden * Version 6 of ASN.1 * * Revision 4.2 1997/06/19 18:41:18 vakatov * [WIN32,MSVC++] Adopted for the "NCBIOBJ.LIB" DLL'ization * * Revision 4.1 1996/05/20 19:43:50 ostell * added prot-ref.processed, virion, div * * Revision 4.0 1995/07/26 13:48:06 ostell * force revision to 4.0 * * Revision 3.6 1995/07/12 22:02:07 ostell * added comment on OrgRef.db * * Revision 3.5 1995/07/11 18:46:25 ostell * added dbxref to Seqfeat * added anticodon to tRNA * * Revision 3.4 1995/05/15 21:22:00 ostell * added Log line * * * * ========================================================================== */ #ifndef _NCBI_Seqfeat_ #define _NCBI_Seqfeat_ #ifndef _ASNTOOL_ #include #endif #ifndef _NCBI_General_ #include #endif #ifndef _NCBI_Seqloc_ #include #endif #ifndef _NCBI_Pub_ #include #endif #ifndef _NCBI_Pubdesc_ #include #endif #undef NLM_EXTERN #ifdef NLM_IMPORT #define NLM_EXTERN NLM_IMPORT #else #define NLM_EXTERN extern #endif #ifdef __cplusplus extern "C" { #endif /***************************************************************************** * * loader * *****************************************************************************/ NLM_EXTERN Boolean LIBCALL SeqFeatAsnLoad PROTO((void)); /***************************************************************************** * * GBQual * *****************************************************************************/ typedef struct gbqual { CharPtr qual, val; struct gbqual PNTR next; } GBQual, PNTR GBQualPtr; NLM_EXTERN GBQualPtr LIBCALL GBQualNew PROTO((void)); NLM_EXTERN Boolean LIBCALL GBQualAsnWrite PROTO((GBQualPtr gbp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN GBQualPtr LIBCALL GBQualAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN GBQualPtr LIBCALL GBQualFree PROTO((GBQualPtr gbp)); /***************************************************************************** * * SeqFeatXref * cross references between features * *****************************************************************************/ typedef struct seqfeatxref { Choice id; Choice data; struct seqfeatxref PNTR next; Boolean specialCleanupFlag; /* marks converted gbquals for extra checking within SeriousSeqEntryCleanup */ } SeqFeatXref, PNTR SeqFeatXrefPtr; NLM_EXTERN SeqFeatXrefPtr LIBCALL SeqFeatXrefNew PROTO((void)); NLM_EXTERN Boolean LIBCALL SeqFeatXrefAsnWrite PROTO((SeqFeatXrefPtr sfxp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqFeatXrefPtr LIBCALL SeqFeatXrefAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqFeatXrefPtr LIBCALL SeqFeatXrefFree PROTO((SeqFeatXrefPtr sfxp)); /* free frees whole chain of SeqFeatXref */ /***************************************************************************** * * SeqFeat * Feat-id is built into idtype/id * 1=gibb (in id.intvalue) * 2=gimm (id.ptrvalue) * 3=local (id.ptrvalue to Object-id) * 4=general (id.ptrvalue to Dbtag) * SeqFeatData is built into datatype/data * datatype gives type of SeqFeatData: * 0 = not set 1 = gene, data.value.ptrvalue = Gene-ref , 2 = org , data.value.ptrvalue = Org-ref , 3 = cdregion, data.value.ptrvalue = Cdregion , 4 = prot , data.value.ptrvalue = Prot-ref , 5 = rna, data.value.ptrvalue = RNA-ref , 6 = pub, data.value.ptrvalue = Pubdesc , -- publication applies to this seq 7 = seq, data.value.ptrvalue = Seq-loc , -- for tracking source of a seq. 8 = imp, data.value.ptrvalue = Imp-feat , 9 = region, data.value.ptrvalue= VisibleString, -- for a name 10 = comment, data.value.ptrvalue= NULL , -- just a comment 11 = bond, data.value.intvalue = ENUMERATED { disulfide (1) , thiolester (2) , xlink (3) , other (255) } , 12 = site, data.value.intvalue = ENUMERATED { active (1) , binding (2) , cleavage (3) , inhibit (4) , modified (5), other (255) } , 13 = rsite, data.value.ptrvalue = Rsite-ref 14 = user, data.value.ptrvalue = UserObjectPtr 15 = txinit, data.value.ptrvalue = TxinitPtr 16 = num, data.value.ptrvalue = NumberingPtr -- a numbering system 17 = psec-str data.value.intvalue = ENUMERATED { -- protein secondary structure helix (1) , -- any helix sheet (2) , -- beta sheet turn (3) } , -- beta or gamma turn 18 = non-std-residue data.value.ptrvalue = VisibleString , -- non-standard residue here in seq 19 = het data.value.ptrvalue=CharPtr Heterogen -- cofactor, prosthetic grp, etc, bound to seq 20 = biosrc, data.value.ptrvalue = BioSource * * *****************************************************************************/ typedef struct seqfeat { Choice id; Choice data; Boolean partial , excpt; /* except changed to excpt (Win32 reserved word) */ CharPtr comment; ValNodePtr product , location; GBQualPtr qual; CharPtr title; UserObjectPtr ext; ValNodePtr cit; /* citations (Pub-set) */ Uint1 exp_ev; SeqFeatXrefPtr xref; ValNodePtr dbxref; /* each vnp->data.ptrvalue is a DbtagPtr */ Boolean pseudo; /* pseudogene feature ? */ CharPtr except_text; /* explanation of biological exception */ struct seqfeat PNTR next; GatherIndex idx; /* internal gather/objmgr tracking fields */ } SeqFeat, PNTR SeqFeatPtr; NLM_EXTERN SeqFeatPtr LIBCALL SeqFeatNew PROTO((void)); NLM_EXTERN Boolean LIBCALL SeqFeatAsnWrite PROTO((SeqFeatPtr anp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqFeatPtr LIBCALL SeqFeatAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqFeatPtr LIBCALL SeqFeatFree PROTO((SeqFeatPtr anp)); /********************************************** * * the SeqFeat Labelling functions are quite complex and are all in * objfdef.[ch]. See FeatDefLabel() * ************************************************/ /* get a SeqFeatXref from a feature. Currently only Prot-ref and */ /* Gene-ref are supported */ NLM_EXTERN SeqFeatXrefPtr LIBCALL SeqFeatToXref PROTO((SeqFeatPtr sfp)); #define SEQFEAT_GENE 1 #define SEQFEAT_ORG 2 #define SEQFEAT_CDREGION 3 #define SEQFEAT_PROT 4 #define SEQFEAT_RNA 5 #define SEQFEAT_PUB 6 #define SEQFEAT_SEQ 7 #define SEQFEAT_IMP 8 #define SEQFEAT_REGION 9 #define SEQFEAT_COMMENT 10 #define SEQFEAT_BOND 11 #define SEQFEAT_SITE 12 #define SEQFEAT_RSITE 13 #define SEQFEAT_USER 14 #define SEQFEAT_TXINIT 15 #define SEQFEAT_NUM 16 #define SEQFEAT_PSEC_STR 17 #define SEQFEAT_NON_STD_RESIDUE 18 #define SEQFEAT_HET 19 #define SEQFEAT_BIOSRC 20 #define SEQFEAT_MAX 21 /* size of array needed for seqfeat filter parameters */ /***************************************************************************** * * SeqFeatId - used as parts of other things, so is not allocated itself * *****************************************************************************/ NLM_EXTERN void LIBCALL SeqFeatIdFree PROTO((ChoicePtr cp)); /* does NOT free cp itself */ NLM_EXTERN Boolean LIBCALL SeqFeatIdAsnWrite PROTO((ChoicePtr cp, AsnIoPtr aip, AsnTypePtr orig)); NLM_EXTERN Boolean LIBCALL SeqFeatIdAsnRead PROTO((AsnIoPtr aip, AsnTypePtr orig, ChoicePtr cp)); /** NOTE: SeqFeatIdAsnRead() does NOT allocate cp ***/ NLM_EXTERN Boolean LIBCALL SeqFeatIdDup PROTO((ChoicePtr dest, ChoicePtr src)); /***************************************************************************** * * SeqFeatData - used as parts of other things, so is not allocated itself * *****************************************************************************/ NLM_EXTERN void LIBCALL SeqFeatDataFree PROTO((ChoicePtr cp)); /* does NOT free cp itself */ NLM_EXTERN Boolean LIBCALL SeqFeatDataAsnWrite PROTO((ChoicePtr cp, AsnIoPtr aip, AsnTypePtr orig)); NLM_EXTERN Boolean LIBCALL SeqFeatDataAsnRead PROTO((AsnIoPtr aip, AsnTypePtr orig, ChoicePtr cp)); /** NOTE: SeqFeatDataAsnRead() does NOT allocate cp ***/ /***************************************************************************** * * SeqFeatSet - sets of seqfeats * *****************************************************************************/ NLM_EXTERN Boolean LIBCALL SeqFeatSetAsnWrite PROTO((SeqFeatPtr anp, AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)); NLM_EXTERN SeqFeatPtr LIBCALL SeqFeatSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)); /** used only SeqAnnotAsnWriteExtra **/ NLM_EXTERN Boolean LIBCALL SeqFeatSetAsnWriteExtra PROTO((SeqFeatPtr anp, AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element, ValNodePtr extras)); /***************************************************************************** * * CodeBreak * *****************************************************************************/ typedef struct cb { SeqLocPtr loc; /* the Seq-loc */ Choice aa; /* 1=ncbieaa, 2=ncbi8aa, 3=ncbistdaa */ struct cb PNTR next; } CodeBreak, PNTR CodeBreakPtr; NLM_EXTERN CodeBreakPtr LIBCALL CodeBreakNew PROTO((void)); NLM_EXTERN Boolean LIBCALL CodeBreakAsnWrite PROTO((CodeBreakPtr cbp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN CodeBreakPtr LIBCALL CodeBreakAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN CodeBreakPtr LIBCALL CodeBreakFree PROTO((CodeBreakPtr cbp)); /***************************************************************************** * * CdRegion * *****************************************************************************/ typedef struct cdregion { Boolean orf; Uint1 frame; Boolean conflict; Uint1 gaps, /* 255 = any number > 254 */ mismatch, stops; ValNodePtr genetic_code; /* NULL = not set */ CodeBreakPtr code_break; } CdRegion, PNTR CdRegionPtr; NLM_EXTERN CdRegionPtr LIBCALL CdRegionNew PROTO((void)); NLM_EXTERN Boolean LIBCALL CdRegionAsnWrite PROTO((CdRegionPtr cdp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN CdRegionPtr LIBCALL CdRegionAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN CdRegionPtr LIBCALL CdRegionFree PROTO((CdRegionPtr cdp)); /***************************************************************************** * * GeneticCode * * ncbieaa, ncbi8aa, ncbistdaa * are arrays 64 cells long, where each cell gives the aa produced * by triplets coded by T=0, C=1, A=2, G=3 * TTT = cell[0] * TTC = cell[1] * TTA = cell[2] * TTG = cell[3] * TCT = cell[4] * ((base1 * 16) + (base2 * 4) + (base3)) = cell in table * * sncbieaa, sncbi8aa, sncbistdaa * are arrays same as above, except the AA's they code for are only for * the first AA of a peptide. This accomdates alternate start codes. * If a codon is not a valid start, the cell contains the "gap" symbol * instead of an AA. * * in both cases, IUPAC cannot be used because it has no symbol for * stop. * * * GeneticCode is a ValNodePtr so variable numbers of elements are * easily accomodated. A ValNodePtr with choice = 254 is the head * of the list. It's elements are a chain of ValNodes beginning with * the data.ptrvalue of the GeneticCode (head). GeneticCodeNew() * returns the head. * * Types in ValNodePtr->choice are: * 0 = not set * 1 = name (CharPtr in ptrvalue) * 2 = id (in intvalue) * 3 = ncbieaa (CharPtr in ptrvalue) * 4 = ncbi8aa (ByteStorePtr in ptrvalue) * 5 = ncbistdaa (ByteStorePtr in ptrvalue) * 6 = sncbieaa (CharPtr in ptrvalue) * 7 = sncbi8aa (ByteStorePtr in ptrvalue) * 8 = sncbistdaa (ByteStorePtr in ptrvalue) * 255 = read unrecognized type, but passed ASN.1 * *****************************************************************************/ typedef ValNode GeneticCode, FAR *GeneticCodePtr; NLM_EXTERN GeneticCodePtr LIBCALL GeneticCodeNew PROTO((void)); NLM_EXTERN Boolean LIBCALL GeneticCodeAsnWrite PROTO((GeneticCodePtr gcp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN GeneticCodePtr LIBCALL GeneticCodeAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN GeneticCodePtr LIBCALL GeneticCodeFree PROTO((GeneticCodePtr gcp)); NLM_EXTERN Boolean LIBCALL GeneticCodeTableAsnWrite PROTO((GeneticCodePtr gcp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN GeneticCodePtr LIBCALL GeneticCodeTableAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN GeneticCodePtr LIBCALL GeneticCodeFind PROTO((Int4 id, CharPtr name)); NLM_EXTERN GeneticCodePtr LIBCALL GeneticCodeTableLoad PROTO((void)); /***************************************************************************** * * ImpFeat * *****************************************************************************/ typedef struct impfeat { CharPtr key, loc, descr; } ImpFeat, PNTR ImpFeatPtr; NLM_EXTERN ImpFeatPtr LIBCALL ImpFeatNew PROTO((void)); NLM_EXTERN Boolean LIBCALL ImpFeatAsnWrite PROTO((ImpFeatPtr ifp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN ImpFeatPtr LIBCALL ImpFeatAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN ImpFeatPtr LIBCALL ImpFeatFree PROTO((ImpFeatPtr ifp)); /***************************************************************************** * * RnaRef * Choice used for extensions * 0 = no extension * 1 = name, ext.value.ptrvalue = CharPtr * 2 = trna, ext.value.ptrvalue = tRNA * *****************************************************************************/ typedef struct rnaref { Uint1 type; Boolean pseudo; Choice ext; } RnaRef, PNTR RnaRefPtr; NLM_EXTERN RnaRefPtr LIBCALL RnaRefNew PROTO((void)); NLM_EXTERN Boolean LIBCALL RnaRefAsnWrite PROTO((RnaRefPtr rrp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN RnaRefPtr LIBCALL RnaRefAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN RnaRefPtr LIBCALL RnaRefFree PROTO((RnaRefPtr rrp)); /***************************************************************************** * * tRNA * *****************************************************************************/ typedef struct trna { Uint1 aatype, /* 0=not set, 1=iupacaa, 2=ncbieaa, 3=ncbi8aa 4=ncbistdaa */ aa; /* the aa transferred in above code */ Uint1 codon[6]; /* codons recognized, coded as for Genetic-code */ SeqLocPtr anticodon; /* location of anticodon */ } tRNA, PNTR tRNAPtr; /* 0-63 = codon, 255=no data in cell */ /***************************************************************************** * * GeneRef * *****************************************************************************/ typedef struct generef { CharPtr locus, allele, desc, maploc; Boolean pseudo; ValNodePtr db; /* ids in other databases */ ValNodePtr syn; /* synonyms for locus */ } GeneRef, PNTR GeneRefPtr; NLM_EXTERN GeneRefPtr LIBCALL GeneRefNew PROTO((void)); NLM_EXTERN Boolean LIBCALL GeneRefAsnWrite PROTO((GeneRefPtr grp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN GeneRefPtr LIBCALL GeneRefAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN GeneRefPtr LIBCALL GeneRefFree PROTO((GeneRefPtr grp)); NLM_EXTERN GeneRefPtr LIBCALL GeneRefDup PROTO((GeneRefPtr grp)); /***************************************************************************** * * OrgRef * *****************************************************************************/ typedef struct taxelement { Uint1 fixed_level; /* controlled levels, 0=other,1=family,2=order,3=class */ CharPtr level, /* level name, if "other" */ name; /* tax name at this level */ struct taxelement PNTR next; } TaxElement, PNTR TaxElementPtr; NLM_EXTERN TaxElementPtr LIBCALL TaxElementNew PROTO((void)); NLM_EXTERN Boolean LIBCALL TaxElementAsnWrite PROTO((TaxElementPtr tep, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN TaxElementPtr LIBCALL TaxElementAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN TaxElementPtr LIBCALL TaxElementFree PROTO((TaxElementPtr tep)); NLM_EXTERN Boolean LIBCALL TaxElementSetAsnWrite PROTO((TaxElementPtr tep, AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)); NLM_EXTERN TaxElementPtr LIBCALL TaxElementSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)); NLM_EXTERN TaxElementPtr LIBCALL TaxElementSetFree PROTO((TaxElementPtr tep)); typedef struct binomialorgname { CharPtr genus, species, subspecies; } BinomialOrgName, PNTR BinomialOrgNamePtr; NLM_EXTERN BinomialOrgNamePtr LIBCALL BinomialOrgNameNew PROTO((void)); NLM_EXTERN Boolean LIBCALL BinomialOrgNameAsnWrite PROTO((BinomialOrgNamePtr bop, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN BinomialOrgNamePtr LIBCALL BinomialOrgNameAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN BinomialOrgNamePtr LIBCALL BinomialOrgNameFree PROTO((BinomialOrgNamePtr bop)); typedef struct orgmod { Uint1 subtype; CharPtr subname, attrib; struct orgmod PNTR next; } OrgMod, PNTR OrgModPtr; NLM_EXTERN OrgModPtr LIBCALL OrgModNew PROTO((void)); NLM_EXTERN Boolean LIBCALL OrgModAsnWrite PROTO((OrgModPtr omp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN OrgModPtr LIBCALL OrgModAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN OrgModPtr LIBCALL OrgModFree PROTO((OrgModPtr omp)); NLM_EXTERN Boolean LIBCALL OrgModSetAsnWrite PROTO((OrgModPtr omp, AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)); NLM_EXTERN OrgModPtr LIBCALL OrgModSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)); NLM_EXTERN OrgModPtr LIBCALL OrgModSetFree PROTO((OrgModPtr omp)); typedef struct orgname { Uint1 choice; /* 1=binomial, 2=virus, 3=hybrid, 4=namedhybrid, 5=partial */ Pointer data; /* depends on choice */ CharPtr attrib; /* attribution for this name */ OrgModPtr mod; /* OrgMods */ CharPtr lineage; /* lineage to this org */ Uint1 gcode, /* genetic code using GenBank keys */ mgcode; /* mitochondrial genetic code using GenBank keys..0=none */ CharPtr div; /* GenBank division code */ struct orgname PNTR next; /* for MultiOrgName */ } OrgName, PNTR OrgNamePtr; NLM_EXTERN OrgNamePtr LIBCALL OrgNameNew PROTO((void)); NLM_EXTERN Boolean LIBCALL OrgNameAsnWrite PROTO((OrgNamePtr onp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN OrgNamePtr LIBCALL OrgNameAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN OrgNamePtr LIBCALL OrgNameFree PROTO((OrgNamePtr onp)); NLM_EXTERN Boolean LIBCALL OrgNameSetAsnWrite PROTO((OrgNamePtr onp, AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)); NLM_EXTERN OrgNamePtr LIBCALL OrgNameSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)); NLM_EXTERN OrgNamePtr LIBCALL OrgNameSetFree PROTO((OrgNamePtr onp)); typedef struct orgref { CharPtr taxname, /* preferred full formal name */ common; /* preferred common name */ ValNodePtr mod; /* unstructured modifiers (Obsolete) */ ValNodePtr db; /* ids in other databases (set of Dbtag pointers)*/ ValNodePtr syn; /* synonyms for taxname and/or common */ OrgNamePtr orgname; /* structured names and components */ } OrgRef, PNTR OrgRefPtr; NLM_EXTERN OrgRefPtr LIBCALL OrgRefNew PROTO((void)); NLM_EXTERN Boolean LIBCALL OrgRefAsnWrite PROTO((OrgRefPtr orp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN OrgRefPtr LIBCALL OrgRefAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN OrgRefPtr LIBCALL OrgRefFree PROTO((OrgRefPtr orp)); /***************************************************************************** * * BioSource * *****************************************************************************/ typedef struct subsource { Uint1 subtype; CharPtr name, attrib; struct subsource PNTR next; } SubSource, PNTR SubSourcePtr; NLM_EXTERN SubSourcePtr LIBCALL SubSourceNew PROTO((void)); NLM_EXTERN Boolean LIBCALL SubSourceAsnWrite PROTO((SubSourcePtr ssp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SubSourcePtr LIBCALL SubSourceAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SubSourcePtr LIBCALL SubSourceFree PROTO((SubSourcePtr ssp)); NLM_EXTERN Boolean LIBCALL SubSourceSetAsnWrite PROTO((SubSourcePtr ssp, AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)); NLM_EXTERN SubSourcePtr LIBCALL SubSourceSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)); NLM_EXTERN SubSourcePtr LIBCALL SubSourceSetFree PROTO((SubSourcePtr ssp)); /****************************** * BioSource current values for genome are: */ /* 0 unknown */ /* 1 genomic */ /* 2 chloroplast */ /* 3 chromoplast */ /* 4 kinteoplast */ /* 5 mitochondrion */ /* 6 plastid */ /* 7 macronuclear */ /* 8 extrachrom */ /* 9 plasmid */ /* 10 transposon */ /* 11 insertion_seq */ /* 12 cyanelle */ /* 13 proviral */ /* 14 virion */ /* Below are new in ASN.1 spec */ /* 15 nucleomorph */ /* 16 apicoplast */ /* 17 leucoplast */ /* 18 proplastid */ /* 19 endogenous_virus */ typedef struct biosource { Uint1 genome, origin; OrgRefPtr org; SubSourcePtr subtype; Boolean is_focus; /* is main BioSource for molecule (when multiple) */ } BioSource, PNTR BioSourcePtr; NLM_EXTERN BioSourcePtr LIBCALL BioSourceNew PROTO((void)); NLM_EXTERN Boolean LIBCALL BioSourceAsnWrite PROTO((BioSourcePtr bsp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN BioSourcePtr LIBCALL BioSourceAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN BioSourcePtr LIBCALL BioSourceFree PROTO((BioSourcePtr bsp)); /***************************************************************************** * * ProtRef * *****************************************************************************/ typedef struct protref { ValNodePtr name; CharPtr desc; ValNodePtr ec, activity; ValNodePtr db; /* ids in other databases */ Uint1 processed; /* 0=not-set, 1=preprotein, 2=mature protein, 3=signal peptide, 4=transit peptide */ } ProtRef, PNTR ProtRefPtr; NLM_EXTERN ProtRefPtr LIBCALL ProtRefNew PROTO((void)); NLM_EXTERN Boolean LIBCALL ProtRefAsnWrite PROTO((ProtRefPtr orp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN ProtRefPtr LIBCALL ProtRefAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN ProtRefPtr LIBCALL ProtRefFree PROTO((ProtRefPtr orp)); NLM_EXTERN ProtRefPtr LIBCALL ProtRefDup PROTO((ProtRefPtr orp)); /***************************************************************************** * * RsiteRef * uses an ValNode * choice = 1 = str * 2 = db * *****************************************************************************/ typedef ValNode RsiteRef, FAR *RsiteRefPtr; NLM_EXTERN Boolean LIBCALL RsiteRefAsnWrite PROTO((RsiteRefPtr orp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN RsiteRefPtr LIBCALL RsiteRefAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN RsiteRefPtr LIBCALL RsiteRefFree PROTO((RsiteRefPtr orp)); /***************************************************************************** * * Txinit * Transcription initiation site * *****************************************************************************/ typedef struct txevidence { Uint1 exp_code , exp_sys ; Boolean low_prec_data , from_homolog; struct txevidence PNTR next; } TxEvidence, PNTR TxEvidencePtr; typedef struct txinit { CharPtr name; ValNodePtr syn , gene , protein , rna ; CharPtr expression; Uint1 txsystem; CharPtr txdescr; OrgRefPtr txorg; Boolean mapping_precise, location_accurate; Uint1 inittype; /* 255 if not set */ TxEvidencePtr evidence; } Txinit, PNTR TxinitPtr; NLM_EXTERN TxinitPtr LIBCALL TxinitNew PROTO((void)); NLM_EXTERN Boolean LIBCALL TxinitAsnWrite PROTO((TxinitPtr txp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN TxinitPtr LIBCALL TxinitAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN TxinitPtr LIBCALL TxinitFree PROTO((TxinitPtr txp)); #ifdef __cplusplus } #endif #undef NLM_EXTERN #ifdef NLM_EXPORT #define NLM_EXTERN NLM_EXPORT #else #define NLM_EXTERN #endif #endif