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Viewing changes to algo/blast/core/blast_gapalign.h

  • Committer: Bazaar Package Importer
  • Author(s): Aaron M. Ucko
  • Date: 2009-08-11 22:03:47 UTC
  • mfrom: (1.4.1 upstream)
  • mto: This revision was merged to the branch mainline in revision 10.
  • Revision ID: james.westby@ubuntu.com-20090811220347-g4b6lzdvphvvbpiu
* New upstream release.
* debian/libncbi6.symbols: update accordingly.
* debian/control: clean up obsolete or redundant relationship declarations.

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algo/blast/core/blast_gapalign.h
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/* $Id: blast_gapalign.h,v 1.69 2009/01/05 16:54:38 kazimird Exp $
 
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/* $Id: blast_gapalign.h,v 1.70 2009/03/26 14:34:31 kazimird Exp $
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 * ===========================================================================
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 *
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 *                            PUBLIC DOMAIN NOTICE
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 * @param sbp The scoring information block [in]
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 * @param gap_align_ptr The BlastGapAlignStruct structure [out]
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*/
 
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NCBI_XBLAST_EXPORT
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Int2
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BLAST_GapAlignStructNew(const BlastScoringParameters* score_params, 
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   const BlastExtensionParameters* ext_params, 
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 * @param gapped_stats Return statistics (not filled if NULL) [out]
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 * @param fence_hit True is returned here if overrun is detected. [in]
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 */
 
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NCBI_XBLAST_EXPORT
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Int2 BLAST_GetGappedScore (EBlastProgramType program_number, 
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            BLAST_SequenceBlk* query, BlastQueryInfo* query_info, 
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              BLAST_SequenceBlk* subject,
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 * @param subject_length Maximal allowed extension in subject [in]
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 * @param fence_hit True is returned here if overrun is detected. [in]
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 */
 
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NCBI_XBLAST_EXPORT
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Int2 BLAST_GappedAlignmentWithTraceback(EBlastProgramType program, 
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        const Uint1* query, const Uint1* subject, 
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        BlastGapAlignStruct* gap_align, 
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 * @param do_traceback Should traceback be saved? [in]
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 * @param fence_hit True is returned here if overrun is detected. [in]
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 */
 
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NCBI_XBLAST_EXPORT
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Int2 
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BLAST_GreedyGappedAlignment(const Uint1* query, const Uint1* subject, 
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   Int4 query_length, Int4 subject_length, BlastGapAlignStruct* gap_align,
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 * @param hit_options Hit saving options [in]
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 * @param hsp_list_ptr HSPs in the final form [out]
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 */
 
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NCBI_XBLAST_EXPORT
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Int2 BLAST_GetUngappedHSPList(BlastInitHitList* init_hitlist, 
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        BlastQueryInfo* query_info, BLAST_SequenceBlk* subject, 
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        const BlastHitSavingOptions* hit_options, 
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 * @param start_shift The offset by which the output range is shifted with
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 *                    respect to the full subject sequence [out]
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 */
 
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NCBI_XBLAST_EXPORT
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void 
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AdjustSubjectRange(Int4* subject_offset_ptr, Int4* subject_length_ptr, 
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                   Int4 query_offset, Int4 query_length, Int4* start_shift);
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 * @param s_length Length of HSP in subject [in]
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 * @return The offset at which alignment should be started [out]
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*/
 
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NCBI_XBLAST_EXPORT
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Int4 
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BlastGetStartForGappedAlignment (const Uint1* query, const Uint1* subject,
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   const BlastScoreBlk* sbp, Uint4 q_start, Uint4 q_length,