Wrapper for all lookup tables used in BLAST. More...

#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_def.h>
#include <algo/blast/core/blast_options.h>
#include <algo/blast/core/blast_rps.h>
#include <algo/blast/core/blast_stat.h>
#include <algo/blast/core/blast_seqsrc.h>

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Classes
struct	LookupTableWrap
	Wrapper structure for different types of BLAST lookup tables. More...

Macros
#define	OFFSET_ARRAY_SIZE 4096
	Default size of offset arrays filled in a single ScanSubject call. More...

Typedefs
typedef struct LookupTableWrap	LookupTableWrap
	Wrapper structure for different types of BLAST lookup tables. More...

typedef Boolean(*	T_Lookup_Callback) (const LookupTableWrap *, Int4, Int4)
	Function pointer type to check the presence of index->q_off pair. More...

Functions
Int2	LookupTableWrapInit (BLAST_SequenceBlk query, const LookupTableOptions lookup_options, const QuerySetUpOptions query_options, BlastSeqLoc lookup_segments, BlastScoreBlk sbp, LookupTableWrap lookup_wrap_ptr, const BlastRPSInfo rps_info, Blast_Message *error_msg, BlastSeqSrc seqsrc)
	Create the lookup table for all query words. More...

Int2	LookupTableWrapInit_MT (BLAST_SequenceBlk query, const LookupTableOptions lookup_options, const QuerySetUpOptions query_options, BlastSeqLoc lookup_segments, BlastScoreBlk sbp, LookupTableWrap lookup_wrap_ptr, const BlastRPSInfo rps_info, Blast_Message *error_msg, BlastSeqSrc seqsrc, Uint4 num_threads)
	Create the lookup table for all query words (possibly multithreaded, depends on implementation). More...

LookupTableWrap *	LookupTableWrapFree (LookupTableWrap *lookup)
	Deallocate memory for the lookup table. More...

Int4	GetOffsetArraySize (LookupTableWrap *lookup)
	Determine the size of the offsets arrays to be filled by the ScanSubject function. More...

Detailed Description

Wrapper for all lookup tables used in BLAST.

Definition in file lookup_wrap.h.

Macro Definition Documentation

◆ OFFSET_ARRAY_SIZE

#define OFFSET_ARRAY_SIZE 4096

Default size of offset arrays filled in a single ScanSubject call.

Definition at line 119 of file lookup_wrap.h.

Typedef Documentation

◆ LookupTableWrap

typedef struct LookupTableWrap LookupTableWrap

Wrapper structure for different types of BLAST lookup tables.

◆ T_Lookup_Callback

typedef Boolean(* T_Lookup_Callback) (const LookupTableWrap *, Int4, Int4)

Function pointer type to check the presence of index->q_off pair.

Definition at line 66 of file lookup_wrap.h.

Function Documentation

◆ GetOffsetArraySize()

Int4 GetOffsetArraySize ( LookupTableWrap * lookup )

Determine the size of the offsets arrays to be filled by the ScanSubject function.

Definition at line 255 of file lookup_wrap.c.

References eAaLookupTable, eCompressedAaLookupTable, eMBLookupTable, eNaHashLookupTable, eNaLookupTable, eSmallNaLookupTable, lookup(), and OFFSET_ARRAY_SIZE.

Referenced by AascanTestFixture::AascanTestFixture(), BOOST_AUTO_TEST_CASE(), CompressedAascanTestFixture::CompressedAascanTestFixture(), CSeedTop::Run(), s_BlastSearchEngineOneContext(), s_BlastSetUpAuxStructures(), TestFixture::ScanCheckHitsCore(), TestFixture::ScanMaxHitsTestCore(), TestFixture::ScanOffsetTestCore(), TestFixture::SetUpLookupTable(), and TestFixture::SkipMaskedRangesCore().

◆ LookupTableWrapFree()

LookupTableWrap* LookupTableWrapFree ( LookupTableWrap * lookup )

Deallocate memory for the lookup table.

Definition at line 197 of file lookup_wrap.c.

References BlastAaLookupTableDestruct(), BlastCompressedAaLookupTableDestruct(), BlastMBLookupTableDestruct(), BlastNaHashLookupTableDestruct(), BlastNaLookupTableDestruct(), BlastSmallNaLookupTableDestruct(), eAaLookupTable, eCompressedAaLookupTable, eIndexedMBLookupTable, eMBLookupTable, eMixedMBLookupTable, eNaHashLookupTable, eNaLookupTable, ePhiLookupTable, ePhiNaLookupTable, eRPSLookupTable, eSmallNaLookupTable, lookup(), NULL, RPSLookupTableDestruct(), sfree, and SPHIPatternSearchBlkFree().

Referenced by BlastSetupPreliminarySearchEx(), BOOST_AUTO_TEST_CASE(), s_GetInitialWordParameters(), LinkHspTestFixture::setupCutoffScores(), TestFixture::TearDownLookupTable(), CBlastTracebackSearch::x_Init(), AalookupTestFixture::~AalookupTestFixture(), AascanTestFixture::~AascanTestFixture(), CompressedAalookupTestFixture::~CompressedAalookupTestFixture(), CompressedAascanTestFixture::~CompressedAascanTestFixture(), and NuclWordFinderTextFixture::~NuclWordFinderTextFixture().

◆ LookupTableWrapInit()

Int2 LookupTableWrapInit	(	BLAST_SequenceBlk *	query,
		const LookupTableOptions *	lookup_options,
		const QuerySetUpOptions *	query_options,
		BlastSeqLoc *	lookup_segments,
		BlastScoreBlk *	sbp,
		LookupTableWrap **	lookup_wrap_ptr,
		const BlastRPSInfo *	rps_info,
		Blast_Message **	error_msg,
		BlastSeqSrc *	seqsrc
	)

Create the lookup table for all query words.

Parameters

query	The query sequence [in]
lookup_options	What kind of lookup table to build? [in]
query_options	options for query setup [in]
lookup_segments	Locations on query to be used for lookup table construction [in]
sbp	Scoring block containing matrix [in]
lookup_wrap_ptr	The initialized lookup table [out]
rps_info	Structure containing RPS blast setup information [in]
error_msg	message with warning or errors [in\|out]
seqsrc	Database sequences [in]

Definition at line 47 of file lookup_wrap.c.

References LookupTableWrapInit_MT(), and query.

Referenced by AascanTestFixture::AascanTestFixture(), BOOST_AUTO_TEST_CASE(), CompressedAascanTestFixture::CompressedAascanTestFixture(), CompressedAalookupTestFixture::FillLookupTable(), AalookupTestFixture::FillLookupTable(), s_GetInitialWordParameters(), LinkHspTestFixture::setupCutoffScores(), TestFixture::SetUpLookupTable(), CPhiblastTestFixture::setUpLookupTable(), and CSeedTop::x_MakeLookupTable().

◆ LookupTableWrapInit_MT()

Int2 LookupTableWrapInit_MT	(	BLAST_SequenceBlk *	query,
		const LookupTableOptions *	lookup_options,
		const QuerySetUpOptions *	query_options,
		BlastSeqLoc *	lookup_segments,
		BlastScoreBlk *	sbp,
		LookupTableWrap **	lookup_wrap_ptr,
		const BlastRPSInfo *	rps_info,
		Blast_Message **	error_msg,
		BlastSeqSrc *	seqsrc,
		Uint4	num_threads
	)

Create the lookup table for all query words (possibly multithreaded, depends on implementation).

Parameters

query	The query sequence [in]
lookup_options	What kind of lookup table to build? [in]
query_options	options for query setup [in]
lookup_segments	Locations on query to be used for lookup table construction [in]
sbp	Scoring block containing matrix [in]
lookup_wrap_ptr	The initialized lookup table [out]
rps_info	Structure containing RPS blast setup information [in]
error_msg	message with warning or errors [in\|out]
seqsrc	Database sequences [in]
num_threads	Number of threads to use [in]

Definition at line 61 of file lookup_wrap.c.

References ASSERT, Blast_MaskUnsupportedAA(), BLASTAA_SIZE, BlastAaLookupFinalize(), BlastAaLookupIndexQuery(), BlastAaLookupTableNew(), BlastChooseNaLookupTable(), BlastCompressedAaLookupTableNew(), BlastMBLookupTableNew(), BlastNaHashLookupTableNew(), BlastNaLookupTableNew(), BlastSmallNaLookupTableNew(), calloc(), SBlastScoreMatrix::data, eAaLookupTable, eBackbone, eCompressedAaLookupTable, eIndexedMBLookupTable, eMBLookupTable, eMixedMBLookupTable, eNaHashLookupTable, eNaLookupTable, ePhiLookupTable, ePhiNaLookupTable, eRPSLookupTable, eSmallbone, eSmallNaLookupTable, EstimateNumTableEntries(), FALSE, INT2_MAX, lookup(), LookupTableWrap::lut, LookupTableOptions::lut_type, LookupTableWrap::lut_type, BlastScoreBlk::matrix, NULL, LookupTableOptions::phi_pattern, BlastScoreBlk::psi_matrix, SPsiBlastScoreMatrix::pssm, query, RPSLookupTableNew(), SPHIPatternSearchBlkNew(), and TRUE.

Referenced by CSetupFactory::CreateLookupTable(), and LookupTableWrapInit().

Classes

Macros

Typedefs

Functions