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>

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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...
SPHIPatternSearchBlk *	SPHIPatternSearchBlkFree (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_wrap	contains the pseudo lookup table with offsets of pattern occurrences in query [in]
query_blk	the query sequence [in]
subject	the subject sequence [in]
offset	the offset in the subject at which to begin scanning [in/out]
offset_pairs	Array of start and end positions of pattern in subject [out]
array_size	length 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_wrap	PHI BLAST lookup table [in]
query_blk	Query sequence [in]
subject_blk	Subject sequence [in]
offset_ptr	Next offset in subject - set to end of sequence [out]
offset_pairs	Starts and stops for pattern occurrences in subject [out]
array_size	Not used.

Returns

Number of pattern occurrences found.

Definition at line 725 of file phi_lookup.c.

References ASSERT, count, 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

)

Deallocate memory for the PHI BLAST lookup table.

Parameters

pattern_blk

The structure to deallocate [in]

Returns

NULL.

Definition at line 690 of file phi_lookup.c.

References SShortPatternItems::dna_items, SLongPatternItems::dna_items, eVeryLong, SLongPatternItems::extra_long_items, SPHIPatternSearchBlk::flagPatternLength, SPHIPatternSearchBlk::multi_word_items, NULL, SPHIPatternSearchBlk::one_word_items, SPHIPatternSearchBlk::pattern, sfree, and SShortPatternItems::whichPositionPtr.

Referenced by LookupTableWrapFree(), and CMultiAligner::x_FindPatternHits().

SPHIPatternSearchBlkNew()

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.

Parameters

pattern	String describing the pattern to search for [in]
is_dna	boolean describing whether the strings are DNA or protein [in]
sbp	Scoring block with statistical parameters [in]
pattern_blk	The initialized structure [out]
error_msg	Error message, if any.

Returns

0 on success, -1 on failure.

Definition at line 388 of file phi_lookup.c.

References AMINOACID_TO_NCBISTDAA, Blast_MessageWrite(), Blast_ResFreqFree(), Blast_ResFreqNew(), Blast_ResFreqStdComp(), BLASTAA_SIZE, calloc(), eBlastSevWarning, eMultiWord, eVeryLong, SLongPatternItems::extra_long_items, SPHIPatternSearchBlk::flagPatternLength, SExtraLongPatternItems::highestPlace, if(), SLongPatternItems::inputPatternMasked, int, IUPACNA_TO_NCBI4NA, kBlastMessageNoContext, kMaskAaAlphabetBits, malloc(), SShortPatternItems::match_mask, SPHIPatternSearchBlk::minPatternMatchLength, SPHIPatternSearchBlk::multi_word_items, NULL, SPHIPatternSearchBlk::one_word_items, SPHIPatternSearchBlk::pattern, SPHIPatternSearchBlk::patternProbability, PHI_ASCII_SIZE, PHI_BITS_PACKED_PER_WORD, PHI_MAX_PATTERN_LENGTH, Blast_ResFreq::prob, s_ExpandPattern(), s_InitDNAPattern(), s_MakePatternUpperCase(), s_PackLongPattern(), s_PackPattern(), s_PackVeryLongPattern(), s_PatternSearchItemsInit(), and SShortPatternItems::whichPositionPtr.

Referenced by LookupTableWrapInit_MT(), and CMultiAligner::x_FindPatternHits().