NCBI C++ ToolKit
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mb_indexed_lookup.h File Reference

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>
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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
subjectThe subject sequence [in]
queryIgnored
query_infoIgnored
lookup_wrapPointer to the (wrapper) lookup table structure [in]
matrixIgnored
word_paramsIgnored
ewpIgnored
offset_pairsIgnored
max_hitsIgnored
init_hitlistStructure to hold all hits information. Has to be allocated up front [out]
ungapped_statsIgnored

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().

Modified on Wed Apr 17 13:08:55 2024 by modify_doxy.py rev. 669887