NCBI C++ ToolKit
|
Function prototypes used for PHI BLAST gapped extension and gapped extension with traceback. More...
#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_def.h>
#include <algo/blast/core/blast_query_info.h>
#include <algo/blast/core/blast_parameters.h>
#include <algo/blast/core/gapinfo.h>
#include <algo/blast/core/blast_hits.h>
#include <algo/blast/core/blast_gapalign.h>
#include <algo/blast/core/pattern.h>
Go to the source code of this file.
Go to the SVN repository for this file.
Functions | |
Int2 | PHIGappedAlignmentWithTraceback (Uint1 *query, Uint1 *subject, BlastGapAlignStruct *gap_align, const BlastScoringParameters *score_params, Int4 q_start, Int4 s_start, Int4 query_length, Int4 subject_length, Int4 q_pat_length, Int4 s_pat_length, SPHIPatternSearchBlk *pattern_blk) |
Perform a gapped alignment with traceback for PHI BLAST. More... | |
Int2 | PHIGetGappedScore (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, const BlastInitialWordParameters *word_params, BlastInitHitList *init_hitlist, BlastHSPList **hsp_list_ptr, BlastGappedStats *gapped_stats, Boolean *fence_hit) |
Preliminary gapped alignment for PHI BLAST. More... | |
Function prototypes used for PHI BLAST gapped extension and gapped extension with traceback.
Definition in file phi_gapalign.h.
Int2 PHIGappedAlignmentWithTraceback | ( | Uint1 * | query, |
Uint1 * | subject, | ||
BlastGapAlignStruct * | gap_align, | ||
const BlastScoringParameters * | score_params, | ||
Int4 | q_start, | ||
Int4 | s_start, | ||
Int4 | query_length, | ||
Int4 | subject_length, | ||
Int4 | q_pat_length, | ||
Int4 | s_pat_length, | ||
SPHIPatternSearchBlk * | pattern_blk | ||
) |
Perform a gapped alignment with traceback for PHI BLAST.
query | The query sequence [in] |
subject | The subject sequence [in] |
gap_align | The gapped alignment structure [in] [out] |
score_params | Scoring parameters [in] |
q_start | Offset in query where to start alignment [in] |
s_start | Offset in subject where to start alignment [in] |
query_length | Maximal allowed extension in query [in] |
subject_length | Maximal allowed extension in subject [in] |
q_pat_length | Length of this pattern in query. [in] |
s_pat_length | Length of this pattern in subject. [in] |
pattern_blk | Detailed pattern information. [in] |
Definition at line 837 of file phi_gapalign.c.
References Blast_PrelimEditBlockToGapEditScript(), Blast_SemiGappedAlign(), BlastGapAlignStruct::edit_script, FALSE, BlastGapAlignStruct::fwd_prelim_tback, GapPrelimEditBlockAppend(), GapPrelimEditBlockFree(), GapPrelimEditBlockNew(), GapPrelimEditBlockReset(), BlastScoreBlk::matrix, NULL, BlastScoringParameters::options, query, BlastGapAlignStruct::query_start, BlastGapAlignStruct::query_stop, BlastGapAlignStruct::rev_prelim_tback, s_PHIBlastAlignPatterns(), BlastGapAlignStruct::sbp, BlastGapAlignStruct::score, subject, BlastGapAlignStruct::subject_start, BlastGapAlignStruct::subject_stop, and TRUE.
Referenced by BOOST_AUTO_TEST_CASE(), and s_PHITracebackFromHSPList().
Int2 PHIGetGappedScore | ( | 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, | ||
const BlastInitialWordParameters * | word_params, | ||
BlastInitHitList * | init_hitlist, | ||
BlastHSPList ** | hsp_list_ptr, | ||
BlastGappedStats * | gapped_stats, | ||
Boolean * | fence_hit | ||
) |
Preliminary gapped alignment for PHI BLAST.
program_number | Type of BLAST program [in] |
query | The query sequence block [in] |
query_info | Query information structure, containing offsets into the concatenated sequence [in] |
subject | The subject sequence block [in] |
gap_align | The auxiliary structure for gapped alignment [in] |
score_params | Parameters related to scoring [in] |
ext_params | Parameters related to extensions (not used) [in] |
hit_params | Parameters related to saving hits [in] |
word_params | Options related to ungapped alignments [in] |
init_hitlist | List of initial HSPs, including offset pairs and pattern match lengths [in] |
hsp_list_ptr | Structure containing all saved HSPs [out] |
gapped_stats | Return statistics (not filled if NULL) [out] |
fence_hit | Not curently supported for PHI-blast but here for compatiability. Normally true here indicates that an overrun was detected. [out] |
Definition at line 739 of file phi_gapalign.c.
References ASSERT, Blast_HSPInit(), Blast_HSPListNew(), Blast_HSPListSaveHSP(), Blast_HSPListSortByScore(), BlastHspNumMax(), BlastQueryInfo::contexts, BlastHitSavingParameters::cutoff_score_min, BlastGapAlignStruct::edit_script, BlastGappedStats::extensions, BlastContextInfo::frame, BlastScoringOptions::gapped_calculation, SPHIHspInfo::index, BlastInitHitList::init_hsp_array, SPHIPatternInfo::length, SPHIHspInfo::length, malloc(), NULL, SPHIQueryInfo::num_patterns, SPHIQueryInfo::occurrences, SPHIPatternInfo::offset, BlastInitHSP::offsets, BlastHitSavingParameters::options, BlastScoringParameters::options, BlastHSP::pat_info, BlastQueryInfo::pattern_info, BlastOffsetPair::phi_offsets, query, BlastGapAlignStruct::query_start, BlastGapAlignStruct::query_stop, BlastOffsetPair::s_end, s_PHIGappedAlignment(), BlastOffsetPair::s_start, BlastGapAlignStruct::score, subject, BlastGapAlignStruct::subject_start, BlastGapAlignStruct::subject_stop, and BlastInitHitList::total.
Referenced by s_BlastSetUpAuxStructures().