phi_extend.h File Reference

Word finder for PHI-BLAST. 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/lookup_wrap.h>
#include <algo/blast/core/blast_hits.h>
#include <algo/blast/core/blast_extend.h>
#include <algo/blast/core/blast_diagnostics.h>

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Functions
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 for PHI-BLAST.

Definition in file phi_extend.h.

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.

Parameters

subject	Subject sequence [in]
query	Query sequence [in]
query_info	Concatenated query information [in]
lookup_wrap	Wrapper for the lookup table with pattern information [in]
matrix	Scoring matrix (not used)
word_params	Initial word parameters (not used)
ewp	Word extension structure (not used)
offset_pairs	Allocated array of offset pairs for storing subject pattern hits in [in] [out]
max_hits	Maximal number of hits allowed in the offset_pairs array. Not used - array is always allocated to fit all pattern hits.
init_hitlist	Structure for saving initial hits. [in]
ungapped_stats	Structure for saving hit counts [in] [out]

Returns

always zero

Definition at line 53 of file phi_extend.c.

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

Referenced by s_BlastSetUpAuxStructures().