/* objloc.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 loclic 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: objloc.h * * Author: James Ostell * * Version Creation Date: 4/1/91 * * $Revision: 6.3 $ * * File Description: Object manager interface for module NCBI-Seqloc * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * $Log: objloc.h,v $ * Revision 6.3 2001/08/06 20:07:26 ostell * added SEQID_TPG, TPE, TPD types * * Revision 6.2 2001/01/31 15:24:20 kans * PatentSeqId.seqid is now an Int4 (JO) * * Revision 6.1 2000/04/05 18:11:41 dondosha * Moved SeqIdSetDup from mblast.h * * Revision 6.0 1997/08/25 18:50:07 madden * Revision changed to 6.0 * * Revision 4.1 1997/06/19 18:41:32 vakatov * [WIN32,MSVC++] Adopted for the "NCBIOBJ.LIB" DLL'ization * * Revision 4.0 1995/07/26 13:48:06 ostell * force revision to 4.0 * * Revision 3.3 1995/05/09 18:04:44 ostell * added NUM_SEGID to define how many SeqId classes there are * * * * ========================================================================== */ #ifndef _NCBI_Seqloc_ #define _NCBI_Seqloc_ #ifndef _ASNTOOL_ #include #endif #ifndef _NCBI_General_ #include #endif #ifndef _NCBI_Biblio_ #include #endif typedef ValNode SeqId, FAR *SeqIdPtr; typedef ValNode SeqLoc, FAR *SeqLocPtr; #ifndef _NCBI_Seqfeat_ #include /* after Seqloc to avoid cycles */ #endif #undef NLM_EXTERN #ifdef NLM_IMPORT #define NLM_EXTERN NLM_IMPORT #else #define NLM_EXTERN extern #endif #ifdef __cplusplus extern "C" { #endif /***************************************************************************** * * Seqloc loader * *****************************************************************************/ NLM_EXTERN Boolean LIBCALL SeqLocAsnLoad PROTO((void)); /***************************************************************************** * * internal structures for NCBI-Seqloc objects * *****************************************************************************/ /***************************************************************************** * * SeqId is a choice using an ValNode, most types in data.ptrvalue * except integers, in data.intvalue * choice: * 0 = not set 1 = local Object-id , -- local use 2 = gibbsq INTEGER , -- Geninfo backbone seqid 3 = gibbmt INTEGER , -- Geninfo backbone moltype 4 = giim Giimport-id , -- Geninfo import id 5 = genbank Textseq-id , 6 = embl Textseq-id , 7 = pir Textseq-id , 8 = swissprot Textseq-id , 9 = patent Patent-seq-id , 10 = other Textseq-id , -- catch all 11 = general Dbtag -- for other databases 12 = gi INTEGER -- GenInfo Integrated Database 13 = ddbj Textseq-id 14 = prf Textseq-id , -- PRF SEQDB 15 = pdb PDB-seq-id -- PDB sequence 16 = tpg Textseq-id , -- Third Party Annot/Seq Genbank 17 = tpe Textseq-id , -- Third Party Annot/Seq EMBL 18 = tpd Textseq-id } -- Third Party Annot/Seq DDBJ WARNING: Some routines in sequtil.c (e.g. SeqIdPrint, SeqIdParse) and tofasta.c use arrays of size NUM_SEQID to set certain behaviors. They should be changed when SeqIds are added or changed. * *****************************************************************************/ #define NUM_SEQID 19 /* total number of SeqId types */ #define SEQID_NOT_SET ( (Uint1)0) #define SEQID_LOCAL ( (Uint1)1) #define SEQID_GIBBSQ ( (Uint1)2) #define SEQID_GIBBMT ( (Uint1)3) #define SEQID_GIIM ( (Uint1)4) #define SEQID_GENBANK ( (Uint1)5) #define SEQID_EMBL ( (Uint1)6) #define SEQID_PIR ( (Uint1)7) #define SEQID_SWISSPROT ( (Uint1)8) #define SEQID_PATENT ( (Uint1)9) #define SEQID_OTHER ( (Uint1)10) #define SEQID_GENERAL ( (Uint1)11) #define SEQID_GI ( (Uint1)12) #define SEQID_DDBJ ((Uint1)13) #define SEQID_PRF ((Uint1)14) #define SEQID_PDB ((Uint1)15) #define SEQID_TPG ((Uint1)16) #define SEQID_TPE ((Uint1)17) #define SEQID_TPD ((Uint1)18) NLM_EXTERN Boolean LIBCALL SeqIdAsnWrite PROTO((SeqIdPtr anp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqIdPtr LIBCALL SeqIdAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqIdPtr LIBCALL SeqIdFree PROTO((SeqIdPtr anp)); NLM_EXTERN SeqIdPtr LIBCALL SeqIdDup PROTO((SeqIdPtr oldid)); NLM_EXTERN SeqIdPtr LIBCALL SeqIdSetDup PROTO((SeqIdPtr seqid)); NLM_EXTERN Int2 LIBCALL SeqIdLabel PROTO(( SeqIdPtr sip, CharPtr buffer, Int2 buflen, Uint1 content)); /***************************************************************************** * * These routines process sets or sequences of SeqId's * *****************************************************************************/ NLM_EXTERN Boolean LIBCALL SeqIdSetAsnWrite PROTO((SeqIdPtr anp, AsnIoPtr aip, AsnTypePtr settype, AsnTypePtr elementtype)); NLM_EXTERN SeqIdPtr LIBCALL SeqIdSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr settype, AsnTypePtr elementtype)); NLM_EXTERN SeqIdPtr LIBCALL SeqIdSetFree PROTO((SeqIdPtr anp)); /***************************************************************************** * * PatentSeqId * *****************************************************************************/ typedef struct patentseqid { Int4 seqid; IdPatPtr cit; } PatentSeqId, PNTR PatentSeqIdPtr; NLM_EXTERN PatentSeqIdPtr LIBCALL PatentSeqIdNew PROTO((void)); NLM_EXTERN Boolean LIBCALL PatentSeqIdAsnWrite PROTO((PatentSeqIdPtr psip, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN PatentSeqIdPtr LIBCALL PatentSeqIdAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN PatentSeqIdPtr LIBCALL PatentSeqIdFree PROTO((PatentSeqIdPtr psip)); /***************************************************************************** * * TextSeqId * *****************************************************************************/ typedef struct textseqid { CharPtr name, accession, release; Int2 version; /* INT2_MIN (ncbilcl.h) = not set */ } TextSeqId, PNTR TextSeqIdPtr; NLM_EXTERN TextSeqIdPtr LIBCALL TextSeqIdNew PROTO((void)); NLM_EXTERN Boolean LIBCALL TextSeqIdAsnWrite PROTO((TextSeqIdPtr tsip, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN TextSeqIdPtr LIBCALL TextSeqIdAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN TextSeqIdPtr LIBCALL TextSeqIdFree PROTO((TextSeqIdPtr tsip)); /***************************************************************************** * * Giim * *****************************************************************************/ typedef struct giim { Int4 id; CharPtr db, release; } Giim, PNTR GiimPtr; NLM_EXTERN GiimPtr LIBCALL GiimNew PROTO((void)); NLM_EXTERN Boolean LIBCALL GiimAsnWrite PROTO((GiimPtr gip, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN GiimPtr LIBCALL GiimAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN GiimPtr LIBCALL GiimFree PROTO((GiimPtr gip)); /***************************************************************************** * * PDBSeqId * *****************************************************************************/ typedef struct pdbseqid { CharPtr mol; Uint1 chain; /* 0 = no chain set. default = 32 */ DatePtr rel; } PDBSeqId, PNTR PDBSeqIdPtr; NLM_EXTERN PDBSeqIdPtr LIBCALL PDBSeqIdNew PROTO((void)); NLM_EXTERN Boolean LIBCALL PDBSeqIdAsnWrite PROTO((PDBSeqIdPtr tsip, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN PDBSeqIdPtr LIBCALL PDBSeqIdAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN PDBSeqIdPtr LIBCALL PDBSeqIdFree PROTO((PDBSeqIdPtr tsip)); /***************************************************************************** * * SeqLoc * SeqLoc is a choice using an ValNode, most types in data.ptrvalue * except integers, in data.intvalue * choice: 1 = null NULL , -- not placed 2 = empty Seq-id , -- to NULL one Seq-id in a collection 3 = whole Seq-id , -- whole sequence 4 = int Seq-interval , -- from to 5 = packed-int Packed-seqint , 6 = pnt Seq-point , 7 = packed-pnt Packed-seqpnt , 8 = mix SEQUENCE OF Seq-loc , 9 = equiv SET OF Seq-loc , -- equivalent sets of locations 10 = bond Seq-bond 11 = feat Feat-id -- indirect through a feature * *****************************************************************************/ #define SEQLOC_NULL ( (Uint1)1) #define SEQLOC_EMPTY ( (Uint1)2) #define SEQLOC_WHOLE ( (Uint1)3) #define SEQLOC_INT ( (Uint1)4) #define SEQLOC_PACKED_INT ( (Uint1)5) #define SEQLOC_PNT ( (Uint1)6) #define SEQLOC_PACKED_PNT ( (Uint1)7) #define SEQLOC_MIX ( (Uint1)8) #define SEQLOC_EQUIV ( (Uint1)9) #define SEQLOC_BOND ( (Uint1)10) #define SEQLOC_FEAT ( (Uint1)11) NLM_EXTERN Boolean LIBCALL SeqLocAsnWrite PROTO((SeqLocPtr anp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqLocPtr LIBCALL SeqLocAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqLocPtr LIBCALL SeqLocFree PROTO((SeqLocPtr anp)); NLM_EXTERN Int2 LIBCALL SeqLocLabel PROTO((SeqLocPtr slp, CharPtr buffer, Int2 buflen, Uint1 content)); /***************************************************************************** * * these routines work on set/seq of SeqLoc * *****************************************************************************/ NLM_EXTERN Boolean LIBCALL SeqLocSetAsnWrite PROTO((SeqLocPtr anp, AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)); NLM_EXTERN SeqLocPtr LIBCALL SeqLocSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr orig, AsnTypePtr element)); NLM_EXTERN SeqLocPtr LIBCALL SeqLocSetFree PROTO((SeqLocPtr anp)); /***************************************************************************** * * SeqInt * *****************************************************************************/ typedef struct seqint { Int4 from, to; Uint1 strand; SeqIdPtr id; /* seq-id */ IntFuzzPtr if_from, if_to; } SeqInt, PNTR SeqIntPtr; NLM_EXTERN SeqIntPtr LIBCALL SeqIntNew PROTO((void)); NLM_EXTERN Boolean LIBCALL SeqIntAsnWrite PROTO((SeqIntPtr sip, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqIntPtr LIBCALL SeqIntAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqIntPtr LIBCALL SeqIntFree PROTO((SeqIntPtr sip)); /***************************************************************************** * * Packed-int * *****************************************************************************/ NLM_EXTERN Boolean LIBCALL PackSeqIntAsnWrite PROTO((SeqLocPtr sip, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqLocPtr LIBCALL PackSeqIntAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); /***************************************************************************** * * SeqLocMix * *****************************************************************************/ NLM_EXTERN Boolean LIBCALL SeqLocMixAsnWrite PROTO((SeqLocPtr anp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqLocPtr LIBCALL SeqLocMixAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); /***************************************************************************** * * SeqLocEquiv * *****************************************************************************/ NLM_EXTERN Boolean LIBCALL SeqLocEquivAsnWrite PROTO((SeqLocPtr anp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqLocPtr LIBCALL SeqLocEquivAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); /***************************************************************************** * * SeqPnt * *****************************************************************************/ typedef struct seqpoint { Int4 point; Uint1 strand; SeqIdPtr id; /* seq-id */ IntFuzzPtr fuzz; } SeqPnt, PNTR SeqPntPtr; NLM_EXTERN SeqPntPtr LIBCALL SeqPntNew PROTO((void)); NLM_EXTERN Boolean LIBCALL SeqPntAsnWrite PROTO((SeqPntPtr spp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqPntPtr LIBCALL SeqPntAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqPntPtr LIBCALL SeqPntFree PROTO((SeqPntPtr spp)); /***************************************************************************** * * PackSeqPnt * *****************************************************************************/ #define PACK_PNT_NUM 100 /* number of points per block */ typedef struct packseqpnt { SeqIdPtr id; /* seq-id */ IntFuzzPtr fuzz; Uint1 strand, used; /* number of pnts used */ Int4 pnts[PACK_PNT_NUM]; struct packseqpnt PNTR next; /* builds up chain of points */ } PackSeqPnt, PNTR PackSeqPntPtr; NLM_EXTERN PackSeqPntPtr LIBCALL PackSeqPntNew PROTO((void)); NLM_EXTERN Boolean LIBCALL PackSeqPntAsnWrite PROTO((PackSeqPntPtr pspp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN PackSeqPntPtr LIBCALL PackSeqPntAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN PackSeqPntPtr LIBCALL PackSeqPntFree PROTO((PackSeqPntPtr pspp)); NLM_EXTERN Int4 LIBCALL PackSeqPntGet PROTO((PackSeqPntPtr pspp, Int4 index)); NLM_EXTERN Boolean LIBCALL PackSeqPntPut PROTO((PackSeqPntPtr pspp, Int4 point)); NLM_EXTERN Int4 LIBCALL PackSeqPntNum PROTO((PackSeqPntPtr pspp)); /***************************************************************************** * * SeqBond * *****************************************************************************/ typedef struct seqbond { SeqPntPtr a, b; } SeqBond, PNTR SeqBondPtr; NLM_EXTERN SeqBondPtr LIBCALL SeqBondNew PROTO((void)); NLM_EXTERN Boolean LIBCALL SeqBondAsnWrite PROTO((SeqBondPtr sbp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqBondPtr LIBCALL SeqBondAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqBondPtr LIBCALL SeqBondFree PROTO((SeqBondPtr sbp)); /***************************************************************************** * * strand types * *****************************************************************************/ #define Seq_strand_unknown 0 #define Seq_strand_plus 1 #define Seq_strand_minus 2 #define Seq_strand_both 3 #define Seq_strand_both_rev 4 #define Seq_strand_other 255 #ifdef __cplusplus } #endif #undef NLM_EXTERN #ifdef NLM_EXPORT #define NLM_EXTERN NLM_EXPORT #else #define NLM_EXTERN #endif #endif