Declarations for functions that extract hits from indexed blast databases (specialized for megablast) More...

#include <algo/blast/core/blast_parameters.h>
#include <algo/blast/core/blast_extend.h>

Include dependency graph for mb_indexed_lookup.h:

This graph shows which files directly or indirectly include this file:

Macros
#define	LAST_VOL_IDX_INIT (-1)

#define	LAST_VOL_IDX_NULL (-2)

Typedefs
typedef unsigned long(*	T_MB_IdbGetResults) (Int4 oid, Int4 chunk, BlastInitHitList *init_hitlist)
	Function pointer type to retrieve hits from an indexed database. More...

typedef int(*	T_MB_IdbCheckOid) (Int4 oid, Int4 *last_vol_id)
	Function pointer type to check index seeds availability for oid. More...

typedef void(*	T_MB_IdxEndSearchIndication) (Int4 last_vol_id)
	Function pointer type to indicate end of preliminary search by the thread to the indexing library. More...

Enumerations
enum	EOidState { eNoResults = 0 , eHasResults , eNotIndexed }

Functions
Int2	MB_IndexedWordFinder (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)
	Finds all runs of a specified number of exact matches between two nucleotide sequences. More...

Detailed Description

Declarations for functions that extract hits from indexed blast databases (specialized for megablast)

Definition in file mb_indexed_lookup.h.

Macro Definition Documentation

◆ LAST_VOL_IDX_INIT

#define LAST_VOL_IDX_INIT (-1)

Definition at line 45 of file mb_indexed_lookup.h.

◆ LAST_VOL_IDX_NULL

#define LAST_VOL_IDX_NULL (-2)

Definition at line 46 of file mb_indexed_lookup.h.

Typedef Documentation

◆ T_MB_IdbCheckOid

typedef int(* T_MB_IdbCheckOid) (Int4 oid, Int4 *last_vol_id)

Function pointer type to check index seeds availability for oid.

Definition at line 59 of file mb_indexed_lookup.h.

◆ T_MB_IdbGetResults

typedef unsigned long(* T_MB_IdbGetResults) (Int4 oid, Int4 chunk, BlastInitHitList *init_hitlist)

Function pointer type to retrieve hits from an indexed database.

Definition at line 55 of file mb_indexed_lookup.h.

◆ T_MB_IdxEndSearchIndication

typedef void(* T_MB_IdxEndSearchIndication) (Int4 last_vol_id)

Function pointer type to indicate end of preliminary search by the thread to the indexing library.

Definition at line 64 of file mb_indexed_lookup.h.

Enumeration Type Documentation

◆ EOidState

enum EOidState

Enumerator
eNoResults
eHasResults
eNotIndexed

Definition at line 48 of file mb_indexed_lookup.h.

Function Documentation

◆ MB_IndexedWordFinder()

Int2 MB_IndexedWordFinder	(	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
	)

Finds all runs of a specified number of exact matches between two nucleotide sequences.

Assumes the subject sequence is part of a previously indexed database

Parameters

subject	The subject sequence [in]
query	Ignored
query_info	Ignored
lookup_wrap	Pointer to the (wrapper) lookup table structure [in]
matrix	Ignored
word_params	Ignored
ewp	Ignored
offset_pairs	Ignored
max_hits	Ignored
init_hitlist	Structure to hold all hits information. Has to be allocated up front [out]
ungapped_stats	Ignored

Definition at line 1697 of file na_ungapped.c.

References ASSERT, Blast_InitHitListSortByScore(), BlastNaWordFinder(), BSearchContextInfo(), LookupTableWrap::check_index_oid, context, BlastUngappedCutoffs::cutoff_score, BlastInitialWordParameters::cutoffs, ir_diag_data_::diag, ir_hash_entry_::diag_data, eNotIndexed, get_results(), BlastInitHitList::init_hsp_array, IR_DIAG, ir_hash_create(), ir_hash_destroy(), IR_KEY, IR_LOCATE, ncbi::grid::netcache::search::fields::key, LAST_VOL_IDX_NULL, BlastUngappedData::length, malloc(), BlastInitialWordParameters::nucl_score_table, BlastInitHSP::offsets, BlastOffsetPair::q_off, BlastUngappedData::q_start, ir_diag_data_::qend, BlastOffsetPair::qs_offsets, query, LookupTableWrap::read_indexed_db, BlastUngappedCutoffs::reduced_nucl_cutoff_score, s_NuclUngappedExtend(), BlastOffsetPair::s_off, BlastUngappedData::score, subject, BlastInitHitList::total, BlastInitHSP::ungapped_data, BlastInitialWordParameters::ungapped_extension, and BlastUngappedCutoffs::x_dropoff.

Referenced by s_BlastSetUpAuxStructures().

Macros

Typedefs

Enumerations

Functions