NCBI C++ ToolKit
blast_sw.h File Reference

Smith-Waterman alignment for use within the infrastructure of BLAST. More...

#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_def.h>
#include <algo/blast/core/blast_program.h>
#include <algo/blast/core/blast_query_info.h>
#include <algo/blast/core/blast_parameters.h>
#include <algo/blast/core/blast_gapalign.h>
#include <algo/blast/core/blast_hits.h>
#include <algo/blast/core/blast_diagnostics.h>
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void SmithWatermanScoreWithTraceback (EBlastProgramType program_number, const Uint1 *A, Int4 a_size, const Uint1 *B, Int4 b_size, BlastHSP *template_hsp, BlastHSPList *hsp_list, const BlastScoringParameters *score_params, const BlastHitSavingParameters *hit_params, BlastGapAlignStruct *gap_align, Int4 start_shift, Int4 cutoff)
 Find all local alignments between two (unpacked) sequences, using the Smith-Waterman algorithm, then save the list of alignments found. More...
Int2 BLAST_SmithWatermanGetGappedScore (EBlastProgramType program_number, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, BLAST_SequenceBlk *subject, BlastGapAlignStruct *gap_align, const BlastScoringParameters *score_params, const BlastExtensionParameters *ext_params, const BlastHitSavingParameters *hit_params, BlastInitHitList *init_hitlist, BlastHSPList **hsp_list_ptr, BlastGappedStats *gapped_stats, Boolean *fence_hit)
 Performs score-only Smith-Waterman gapped alignment of the subject sequence with all contexts in the query. More...

Detailed Description

Smith-Waterman alignment for use within the infrastructure of BLAST.

Definition in file blast_sw.h.

Modified on Sun Apr 21 03:43:13 2024 by rev. 669887