NCBI C++ ToolKit
Functions
phi_lookup.h File Reference

Pseudo lookup table structure and database scanning functions used in PHI-BLAST. More...

#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_def.h>
#include <algo/blast/core/blast_stat.h>
#include <algo/blast/core/pattern.h>
#include <algo/blast/core/lookup_wrap.h>
+ Include dependency graph for phi_lookup.h:
+ This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Go to the SVN repository for this file.

Functions

Int2 SPHIPatternSearchBlkNew (char *pattern, Boolean is_dna, BlastScoreBlk *sbp, SPHIPatternSearchBlk **pattern_blk, Blast_Message **error_msg)
 Initialize the pattern items structure, serving as a "pseudo" lookup table in a PHI BLAST search. More...
 
SPHIPatternSearchBlkSPHIPatternSearchBlkFree (SPHIPatternSearchBlk *pattern_blk)
 Deallocate memory for the PHI BLAST lookup table. More...
 
Int4 PHIBlastScanSubject (const LookupTableWrap *lookup_wrap, const BLAST_SequenceBlk *query_blk, const BLAST_SequenceBlk *subject, Int4 *offset, BlastOffsetPair *offset_pairs, Int4 array_size)
 Scans the subject sequence from "offset" to the end of the sequence. More...
 

Detailed Description

Pseudo lookup table structure and database scanning functions used in PHI-BLAST.

Definition in file phi_lookup.h.

Function Documentation

◆ PHIBlastScanSubject()

Int4 PHIBlastScanSubject ( const LookupTableWrap lookup_wrap,
const BLAST_SequenceBlk query_blk,
const BLAST_SequenceBlk subject_blk,
Int4 offset_ptr,
BlastOffsetPair offset_pairs,
Int4  array_size 
)

Scans the subject sequence from "offset" to the end of the sequence.

Copies at most array_size hits. Returns the number of hits found. If there isn't enough room to copy all the hits, return early, and update "offset".

Parameters
lookup_wrapcontains the pseudo lookup table with offsets of pattern occurrences in query [in]
query_blkthe query sequence [in]
subjectthe subject sequence [in]
offsetthe offset in the subject at which to begin scanning [in/out]
offset_pairsArray of start and end positions of pattern in subject [out]
array_sizelength of the offset arrays [in]
Returns
The number of hits found.

Scans the subject sequence from "offset" to the end of the sequence.

Parameters
lookup_wrapPHI BLAST lookup table [in]
query_blkQuery sequence [in]
subject_blkSubject sequence [in]
offset_ptrNext offset in subject - set to end of sequence [out]
offset_pairsStarts and stops for pattern occurrences in subject [out]
array_sizeNot used.
Returns
Number of pattern occurrences found.

Definition at line 725 of file phi_lookup.c.

References ASSERT, ePhiLookupTable, ePhiNaLookupTable, FindPatternHits(), BLAST_SequenceBlk::length, LookupTableWrap::lut, LookupTableWrap::lut_type, PHI_MAX_HIT, BLAST_SequenceBlk::sequence, and subject.

Referenced by BOOST_AUTO_TEST_CASE(), PHIBlastWordFinder(), and CSeedTop::Run().

◆ SPHIPatternSearchBlkFree()

SPHIPatternSearchBlk* SPHIPatternSearchBlkFree ( SPHIPatternSearchBlk pattern_blk)

◆ SPHIPatternSearchBlkNew()

Int2 SPHIPatternSearchBlkNew ( char *  pattern,
Boolean  is_dna,
BlastScoreBlk sbp,
SPHIPatternSearchBlk **  pattern_blk,
Blast_Message **  error_msg 
)
Modified on Wed Apr 17 13:10:37 2024 by modify_doxy.py rev. 669887