NCBI C++ ToolKit
Functions
phi_gapalign.h File Reference

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>
+ Include dependency graph for phi_gapalign.h:
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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, BlastInitHitList *init_hitlist, BlastHSPList **hsp_list_ptr, BlastGappedStats *gapped_stats, Boolean *fence_hit)
 Preliminary gapped alignment for PHI BLAST. More...
 

Detailed Description

Function prototypes used for PHI BLAST gapped extension and gapped extension with traceback.

Definition in file phi_gapalign.h.

Function Documentation

◆ PHIGappedAlignmentWithTraceback()

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.

Parameters
queryThe query sequence [in]
subjectThe subject sequence [in]
gap_alignThe gapped alignment structure [in] [out]
score_paramsScoring parameters [in]
q_startOffset in query where to start alignment [in]
s_startOffset in subject where to start alignment [in]
query_lengthMaximal allowed extension in query [in]
subject_lengthMaximal allowed extension in subject [in]
q_pat_lengthLength of this pattern in query. [in]
s_pat_lengthLength of this pattern in subject. [in]
pattern_blkDetailed pattern information. [in]
Returns
Status, 0 on success, -1 on failure.

Definition at line 836 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().

◆ PHIGetGappedScore()

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,
BlastInitHitList init_hitlist,
BlastHSPList **  hsp_list_ptr,
BlastGappedStats gapped_stats,
Boolean fence_hit 
)

Preliminary gapped alignment for PHI BLAST.

Parameters
program_numberType of BLAST program [in]
queryThe query sequence block [in]
query_infoQuery information structure, containing offsets into the concatenated sequence [in]
subjectThe subject sequence block [in]
gap_alignThe auxiliary structure for gapped alignment [in]
score_paramsParameters related to scoring [in]
ext_paramsParameters related to extensions (not used) [in]
hit_paramsParameters related to saving hits [in]
init_hitlistList of initial HSPs, including offset pairs and pattern match lengths [in]
hsp_list_ptrStructure containing all saved HSPs [out]
gapped_statsReturn statistics (not filled if NULL) [out]
fence_hitNot curently supported for PHI-blast but here for compatiability. Normally true here indicates that an overrun was detected. [out]
Returns
Status, 0 on success, -1 on failure.

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().

Modified on Sun Apr 21 03:37:30 2024 by modify_doxy.py rev. 669887