/* objalign.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: objalign.h * * Author: James Ostell * * Version Creation Date: 4/1/91 * * $Revision: 6.6 $ * * File Description: Object manager interface for module NCBI-Seqalign * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * $Log: objalign.h,v $ * Revision 6.6 1999/09/28 12:09:56 kans * added alignID field * * Revision 6.5 1999/09/27 17:48:37 kans * using GatherIndex structure * * Revision 6.4 1999/09/24 23:09:23 kans * adds EXTRA_OBJMGR_FIELDS to several objects * * Revision 6.3 1999/09/07 17:00:26 kans * added entityID, itemID, itemtype fields for new Alignment Indexing functions * * Revision 6.2 1999/07/29 15:49:58 ostell * added pointer and free for a SeqAlignIndex * * Revision 6.1 1999/07/26 20:41:01 ostell * added SAT_ and SAS_ defines, added master to SeqAlign * * Revision 6.0 1997/08/25 18:49:14 madden * Revision changed to 6.0 * * Revision 4.1 1997/06/19 18:40:41 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 3.5 1995/07/22 21:59:13 ostell * added support for ASN.1 spec 4.0 * * Revision 3.4 1995/06/21 17:17:50 epstein * *** empty log message *** * * Revision 3.3 95/05/15 21:22:00 ostell * added Log line * * * * * ========================================================================== */ #ifndef _NCBI_Seqalign_ #define _NCBI_Seqalign_ #ifndef _ASNTOOL_ #include #endif #ifndef _NCBI_General_ #include #endif #ifndef _NCBI_Seqloc_ #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 SeqAlignAsnLoad PROTO((void)); /***************************************************************************** * * internal structures for NCBI-Seqalign objects * *****************************************************************************/ /***************************************************************************** * * Score * NOTE: read, write, and free always process GROUPS of scores * *****************************************************************************/ typedef struct score { ObjectIdPtr id; Uint1 choice; /* 0=not set, 1=int, 2=real */ DataVal value; struct score PNTR next; /* for sets of scores */ } Score, PNTR ScorePtr; NLM_EXTERN ScorePtr LIBCALL ScoreNew PROTO((void)); NLM_EXTERN Boolean LIBCALL ScoreSetAsnWrite PROTO((ScorePtr sp, AsnIoPtr aip, AsnTypePtr settype)); NLM_EXTERN ScorePtr LIBCALL ScoreSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr settype)); NLM_EXTERN ScorePtr LIBCALL ScoreSetFree PROTO((ScorePtr anp)); /**************************************************************************** * * SeqAlignIndex * * This structure is the public face of a data structure which is * extended in AlignMgr for alignment indexing, alignment features * and other utilities. * * It is left as a limited structure "stub" here * ****************************************************************************/ /** the VoidPtr below should really be a SeqAlignIndexPtr **/ typedef Boolean (LIBCALLBACK * SeqAlignIndexFreeFunc)(VoidPtr); typedef struct seqalignindex { Uint1 indextype; SeqAlignIndexFreeFunc freefunc; } SeqAlignIndex, PNTR SeqAlignIndexPtr; NLM_EXTERN SeqAlignIndexPtr LIBCALL SeqAlignIndexFree (SeqAlignIndexPtr saip); /***************************************************************************** * * SeqAlign * type = type of alignment not-set (0) , global (1) , diags (2) , partial (3) , -- mapping pieces together other (255) } , segtype = type of segs structure not-set 0 dendiag 1 denseq 2 std 3 packed 4 disc 5 SeqAlignSet is used compseq 6 used by colombe * * *****************************************************************************/ /** SeqAlign.type values ***/ #define SAT_GLOBAL 1 /* ordered segments, over full length of seqs */ #define SAT_DIAGS 2 /* unordered, possibly overlapping segments */ #define SAT_PARTIAL 3 /* ordered segments, over part of sequence */ #define SAT_MASTERSLAVE 4 /* set of SeqAligns, all of which have one common */ /* sequence. Not in ASN.1 yet */ /** SeqAlign.segtype values ***/ #define SAS_DENDIAG 1 #define SAS_DENSEG 2 #define SAS_STD 3 #define SAS_PACKED 4 #define SAS_DISC 5 #define SAS_COMPSEQ 6 typedef struct seqalign { Uint1 type, segtype; Int2 dim; ScorePtr score; Pointer segs; struct seqalign PNTR next; SeqLocPtr bounds; /* sequence of SeqLocPtr */ SeqIdPtr master; /* for SAT_MASTERSLAVE */ SeqAlignIndexPtr saip; /* for added Alignment Indexing structures */ GatherIndex idx; /* internal gather/objmgr tracking fields */ Uint2 alignID; /* unique number assigned to alignment */ } SeqAlign, PNTR SeqAlignPtr; NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignNew PROTO((void)); NLM_EXTERN Boolean LIBCALL SeqAlignAsnWrite PROTO((SeqAlignPtr anp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignFree PROTO((SeqAlignPtr anp)); NLM_EXTERN Int2 LIBCALL SeqAlignLabel PROTO((SeqAlignPtr sap, CharPtr buffer, Int2 buflen, Uint1 content)); /***************************************************************************** * * SeqAlignSet * *****************************************************************************/ NLM_EXTERN Boolean LIBCALL SeqAlignSetAsnWrite PROTO((SeqAlignPtr anp, AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)); NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)); NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignSetFree PROTO((SeqAlignPtr sap)); NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignSetNew PROTO((void)); NLM_EXTERN SeqAlignPtr LIBCALL SpecialSeqAlignSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr set)); NLM_EXTERN Boolean LIBCALL SpecialSeqAlignSetAsnWrite PROTO((SeqAlignPtr sap, AsnIoPtr aip, AsnTypePtr set)); /***************************************************************************** * * DenseDiag * * *****************************************************************************/ typedef struct dendiag { Int2 dim; /* this is a convenience, not in asn1 */ SeqIdPtr id; Int4Ptr starts; Int4 len; Uint1Ptr strands; ScorePtr scores; struct dendiag PNTR next; } DenseDiag, PNTR DenseDiagPtr; NLM_EXTERN DenseDiagPtr LIBCALL DenseDiagNew PROTO((void)); NLM_EXTERN Boolean LIBCALL DenseDiagAsnWrite PROTO((DenseDiagPtr ddp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN DenseDiagPtr LIBCALL DenseDiagAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN DenseDiagPtr LIBCALL DenseDiagFree PROTO((DenseDiagPtr ddp)); /***************************************************************************** * * DenseSeg * * *****************************************************************************/ typedef struct denseg { Int2 dim, numseg; SeqIdPtr ids; /* dimension is dim */ Int4Ptr starts; /* dimension is dim * numseg */ Int4Ptr lens; /* dimension is numseg */ Uint1Ptr strands; /* dimension is dim * numseg */ ScorePtr scores; /* dimension is numseg */ } DenseSeg, PNTR DenseSegPtr; NLM_EXTERN DenseSegPtr LIBCALL DenseSegNew PROTO((void)); NLM_EXTERN Boolean LIBCALL DenseSegAsnWrite PROTO((DenseSegPtr dsp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN DenseSegPtr LIBCALL DenseSegAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN DenseSegPtr LIBCALL DenseSegFree PROTO((DenseSegPtr dsp)); /***************************************************************************** * * PackSeg * * *****************************************************************************/ typedef struct packseg { Int2 dim, numseg; SeqIdPtr ids; /* dimension is dim */ Int4Ptr starts; /* dimension is dim */ ByteStorePtr present; /* dimension is dim * numseg booleans */ Int4Ptr lens; /* dimension is numseg */ Uint1Ptr strands; /* dimension is dim */ ScorePtr scores; /* dimension is numseg */ } PackSeg, PNTR PackSegPtr; NLM_EXTERN PackSegPtr LIBCALL PackSegNew PROTO((void)); NLM_EXTERN Boolean LIBCALL PackSegAsnWrite PROTO((PackSegPtr psp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN PackSegPtr LIBCALL PackSegAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN PackSegPtr LIBCALL PackSegFree PROTO((PackSegPtr psp)); /***************************************************************************** * * StdSeg * * *****************************************************************************/ typedef struct stdseg { Int2 dim; SeqIdPtr ids; /* SeqId s */ SeqLocPtr loc; /* SeqLoc s */ ScorePtr scores; struct stdseg PNTR next; } StdSeg, PNTR StdSegPtr; NLM_EXTERN StdSegPtr LIBCALL StdSegNew PROTO((void)); NLM_EXTERN Boolean LIBCALL StdSegAsnWrite PROTO((StdSegPtr ssp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN StdSegPtr LIBCALL StdSegAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN StdSegPtr LIBCALL StdSegFree PROTO((StdSegPtr ssp)); #ifdef __cplusplus } #endif #undef NLM_EXTERN #ifdef NLM_EXPORT #define NLM_EXTERN NLM_EXPORT #else #define NLM_EXTERN #endif #endif