/* =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information (NCBI) * * 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 do not place any restriction on its use or reproduction. * We would, however, appreciate having the NCBI and the author cited in * any work or product based on this material * * 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. * * =========================================================================== * * File Name: salsap.h * * Author: Colombe Chappey * * Version Creation Date: 1/27/96 * * $Revision: 6.5 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * $Log: salsap.h,v $ * Revision 6.5 2006/07/13 17:06:39 bollin * use Uint4 instead of Uint2 for itemID values * removed unused variables * resolved compiler warnings * * Revision 6.4 2006/01/10 22:27:06 bollin * added function SeqAlignInsertByLoc, to be used when nucleotides are inserted * into a sequence that is in an alignment. An extra segment, where all functions * except the one with the insertion are gapped, is created. * * Revision 6.3 1999/11/24 21:24:28 vakatov * Fixed for the C++ and/or MSVC DLL compilation * * ========================================================================== */ #ifndef _SALSAP_ #define _SALSAP_ #include #include /* Put in all the transfered Functions */ #include /* For prototype for SeqAlignGapCount Function */ #include #undef NLM_EXTERN #ifdef NLM_IMPORT #define NLM_EXTERN NLM_IMPORT #else #define NLM_EXTERN extern #endif #ifdef __cplusplus extern "C" { #endif NLM_EXTERN SeqIdPtr LIBCALL SeqAlignIDList (SeqAlignPtr salp); /* Used in salsa.c .. mapped to Find SeqIdInSeqAlign*/ NLM_EXTERN Int2 LIBCALL position_inIdlist(SeqIdPtr sip, ValNodePtr list); NLM_EXTERN Boolean LIBCALL FindSeqIdinSeqAlign (SeqAlignPtr salphead, SeqIdPtr sip); NLM_EXTERN SeqAlignPtr LIBCALL build_seqalign_fromstart (Int2 dim, Int2 numseg, SeqIdPtr sip, Int4Ptr starts, Int4Ptr lens); NLM_EXTERN SeqAlignPtr LIBCALL SeqLocToFastaSeqAlign (ValNodePtr vnp); NLM_EXTERN SeqAnnotPtr LIBCALL LocalAlignToSeqAnnotDimn (ValNodePtr seqvnp, SeqIdPtr seqsip, ValNodePtr fromp, Int2 nbseq, Int4 lens, ValNodePtr strands, Boolean trunc_emptyends); NLM_EXTERN DenseDiagPtr LIBCALL DenseDiagCreate (Int4 dim, SeqIdPtr id, Int4Ptr starts, Int4 len, Uint1Ptr strands, ScorePtr scores); NLM_EXTERN Pointer LIBCALL FindSeqAlignInSeqEntry (SeqEntryPtr sep, Uint1 choice); NLM_EXTERN SeqAlignPtr LIBCALL is_salp_in_sap (SeqAnnotPtr sap, Uint1 choice); NLM_EXTERN Boolean LIBCALL is_dim1seqalign (SeqAlignPtr salp); NLM_EXTERN Boolean LIBCALL is_dim2seqalign (SeqAlignPtr salp); NLM_EXTERN Boolean LIBCALL SeqAlignSeqLocComp (SeqAlignPtr salphead, ValNodePtr vnp); NLM_EXTERN Boolean LIBCALL get_pos_from_salp (SeqAlignPtr salp, Int4 pos, Int4 PNTR offset, Int4Ptr PNTR startp, Int4Ptr PNTR lenp, Int4 PNTR numseg); /**SeqLoc**/ NLM_EXTERN ValNodePtr LIBCALL SeqLocListFromSeqAlign (SeqAlignPtr salp); NLM_EXTERN SeqLocPtr LIBCALL SeqLocFromSeqAlign (SeqAlignPtr salp, SeqIdPtr sip); NLM_EXTERN SeqLocPtr LIBCALL SeqLocMixFromSeqAlign (SeqAlignPtr salp, SeqIdPtr sip); NLM_EXTERN ValNodePtr LIBCALL SeqLocListOfBioseqsFromSeqAlign (SeqAlignPtr salp); /**Alignment Score**/ NLM_EXTERN Int4 LIBCALL SeqAlignBestScore (SeqAlignPtr salp); /**Sequence**/ NLM_EXTERN Int4 LIBCALL readbuff_fromseqalign (SeqPortPtr spp, SeqAlignPtr salp, Int2 index, CharPtr buffer, Int4 from, Int4 to, Int4 offset, Boolean strand); /**misc**/ NLM_EXTERN Boolean LIBCALL is_fasta_seqalign (SeqAlignPtr salp); /** *Functions taking a SeqAlign and returning a pointer to the "same" SeqAlign **/ NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignMerge (SeqAlignPtr salp1, SeqAlignPtr salp2, Boolean return_salp); NLM_EXTERN SeqAnnotPtr LIBCALL SeqAnnotMerge (SeqAnnotPtr sap1, SeqAnnotPtr sap2, Boolean return_salp); NLM_EXTERN DenseDiagPtr LIBCALL DenseDiagLink (DenseDiagPtr *ddp_head, DenseDiagPtr ddp); NLM_EXTERN DenseDiagPtr LIBCALL DenseDiagInsert (DenseDiagPtr ddp_before, DenseDiagPtr ddp); NLM_EXTERN DenseDiagPtr LIBCALL DenseDiagPrecede (DenseDiagPtr ddp_after, DenseDiagPtr *ddp); NLM_EXTERN DenseDiagPtr LIBCALL DenseDiagLinkSort (DenseDiagPtr *ddp_head, DenseDiagPtr ddp); /**Sort**/ NLM_EXTERN SeqAlignPtr LIBCALL SortSeqAlign (SeqAlignPtr PNTR salp); NLM_EXTERN SeqAlignPtr LIBCALL SortSeqAlignFromList (SeqAlignPtr salp, Int2Ptr sortlst); /**SeqId**/ NLM_EXTERN Boolean LIBCALL SeqAlignIDCache (SeqAlignPtr salphead, SeqIdPtr sip); NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignIDUncache (SeqAlignPtr salphead, SeqIdPtr sip); NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignIDUncacheAll (SeqAlignPtr salphead); /**Extend**/ NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignEndExtend (SeqAlignPtr sap, Int4 start1, Int4 start2, Int4 stop1, Int4 stop2, Int4 x1, Int4 y1, Int4 x2, Int4 y2, Uint1 strand1, Uint1 strand2); NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignInsertByLoc (SeqLocPtr slp, SeqAlignPtr salp); /**Delete, Truncate**/ NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignDeleteByLoc (SeqLocPtr slp, SeqAlignPtr salp); NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignTrunc (SeqAlignPtr salp, Int4 from, Int4 to); NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignTrunc2 (SeqAlignPtr salp, Int4 from, Int4 to); NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignMapOnFirstSeq (SeqAlignPtr salp); /**Clean**/ NLM_EXTERN SeqAlignPtr LIBCALL CleanStrandsSeqAlign (SeqAlignPtr salp); /** *Functions taking a SeqAlign and returning a new SeqAlign **/ /**Duplicate**/ NLM_EXTERN DenseDiagPtr LIBCALL DenseDiagDup (DenseDiagPtr ddp); /**Transfer of Format**/ NLM_EXTERN SeqAlignPtr LIBCALL DenseSegToDenseDiag (SeqAlignPtr salp); /**Nuc/AA**/ NLM_EXTERN SeqAlignPtr LIBCALL aaSeqAlign_to_dnaSeqAlign (SeqAlignPtr salp, ValNodePtr vnp, ValNodePtr framep); NLM_EXTERN SeqAnnotPtr aaSeqAnnot_to_dnaSeqAnnotFunc (SeqAnnotPtr PNTR sapnahead, SeqAlignPtr salpnew, ValNodePtr vnp, ValNodePtr framep); /** *SeqAlign and SeqEntry **/ NLM_EXTERN void LIBCALL ReplaceSeqAlignInSeqEntry (Uint2 entityID, Uint4 itemID, SeqAlignPtr salp); /*******************************************************/ NLM_EXTERN SeqAnnotPtr LIBCALL CompSeqAnnotFree (SeqAnnotPtr sap); NLM_EXTERN SeqAlignPtr LIBCALL CompSeqAlignFree (SeqAlignPtr salp); NLM_EXTERN SeqAnnotPtr LIBCALL SeqAlignBoolSegCpy (SeqAnnotPtr sap, Int4 from, Int4 to); NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignDenseSegToBoolSeg (SeqAlignPtr salp); NLM_EXTERN SeqAnnotPtr LIBCALL SeqAnnotDenseSegToBoolSeg (SeqAnnotPtr sap); NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignBoolSegToDenseSeg (SeqAlignPtr salp); NLM_EXTERN SeqAnnotPtr LIBCALL SeqAnnotBoolSegToDenseSeg (SeqAnnotPtr sap); NLM_EXTERN void LIBCALL CompSeqAlignPrint (SeqAlignPtr salp); NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignDupRegion (SeqAlignPtr salp, Int2 to_numseg, Int4 subseg, Boolean first_part); NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignDupAdd (SeqAlignPtr *salp_head, SeqAlignPtr salp, Int2 to_numseg, Int4 subseg, Boolean first_part); NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignExtend (SeqAlignPtr salp1, SeqAlignPtr salp2); NLM_EXTERN SeqAlignPtr LIBCALL DeleteRegion (SeqIntPtr sip, SeqAlignPtr salp); NLM_EXTERN SeqAlignPtr LIBCALL DenseDiagToDenseSegFunc (SeqAlignPtr salp, Boolean add_ends); NLM_EXTERN SeqAlignPtr LIBCALL DenseDiagToDenseSeg (SeqAlignPtr salp, Boolean add_ends); NLM_EXTERN SeqAnnotPtr multseqalign_from_pairseqalign (SeqAlignPtr salp); NLM_EXTERN SeqAlignPtr PairSeqAlign2MultiSeqAlign (SeqAlignPtr salp); NLM_EXTERN Int2 LIBCALLBACK MultSeqAlignFromPairSeqAlign (Pointer data); NLM_EXTERN SeqAlignPtr LIBCALL multseqalign_to_pairseqalign (SeqAlignPtr salp); #ifdef __cplusplus } #endif #undef NLM_EXTERN #ifdef NLM_EXPORT #define NLM_EXTERN NLM_EXPORT #else #define NLM_EXTERN #endif #endif