NCBI C++ ToolKit
phi_extend.c File Reference

Word finder functions for PHI-BLAST. More...

#include <algo/blast/core/phi_lookup.h>
#include <algo/blast/core/phi_extend.h>
+ Include dependency graph for phi_extend.c:

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static Int2 s_PHISaveInitialHit (BlastInitHitList *init_hitlist, BlastOffsetPair *offset_pair)
 Saves a pattern hit in a BlastInitHitList. More...
Int2 PHIBlastWordFinder (BLAST_SequenceBlk *subject, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, LookupTableWrap *lookup_wrap, Int4 **matrix, const BlastInitialWordParameters *word_params, Blast_ExtendWord *ewp, BlastOffsetPair *offset_pairs, Int4 max_hits, BlastInitHitList *init_hitlist, BlastUngappedStats *ungapped_stats)
 WordFinder type function for PHI BLAST. More...

Detailed Description

Word finder functions for PHI-BLAST.

Definition in file phi_extend.c.

Function Documentation

◆ PHIBlastWordFinder()

Int2 PHIBlastWordFinder ( BLAST_SequenceBlk subject,
BLAST_SequenceBlk query,
BlastQueryInfo query_info,
LookupTableWrap lookup_wrap,
Int4 **  matrix,
const BlastInitialWordParameters word_params,
Blast_ExtendWord ewp,
BlastOffsetPair offset_pairs,
Int4  max_hits,
BlastInitHitList init_hitlist,
BlastUngappedStats ungapped_stats 

WordFinder type function for PHI BLAST.

subjectSubject sequence [in]
queryQuery sequence [in]
query_infoConcatenated query information [in]
lookup_wrapWrapper for the lookup table with pattern information [in]
matrixScoring matrix (not used)
word_paramsInitial word parameters (not used)
ewpWord extension structure (not used)
offset_pairsAllocated array of offset pairs for storing subject pattern hits in [in] [out]
max_hitsMaximal number of hits allowed in the offset_pairs array. Not used - array is always allocated to fit all pattern hits.
init_hitlistStructure for saving initial hits. [in]
ungapped_statsStructure for saving hit counts [in] [out]
always zero

Definition at line 53 of file phi_extend.c.

References Blast_UngappedStatsUpdate(), PHIBlastScanSubject(), query, s_PHISaveInitialHit(), and subject.

Referenced by s_BlastSetUpAuxStructures().

◆ s_PHISaveInitialHit()

static Int2 s_PHISaveInitialHit ( BlastInitHitList init_hitlist,
BlastOffsetPair offset_pair 

Saves a pattern hit in a BlastInitHitList.

offset_pairPattern start and stop in subject [in]
init_hitlistInitial hit list structure to save the hit in. [in] [out]

Definition at line 42 of file phi_extend.c.

References BLAST_SaveInitialHit(), NULL, BlastOffsetPair::phi_offsets, BlastOffsetPair::s_end, and BlastOffsetPair::s_start.

Referenced by PHIBlastWordFinder().

Modified on Thu Apr 11 15:03:53 2024 by rev. 669887