Wrapper for different flavors of lookup tables allowing a uniform interface in the code. More...

#include <algo/blast/core/lookup_wrap.h>
#include <algo/blast/core/blast_aalookup.h>
#include <algo/blast/core/blast_nalookup.h>
#include <algo/blast/core/phi_lookup.h>
#include <algo/blast/core/blast_filter.h>
#include <algo/blast/core/lookup_util.h>
#include <algo/blast/core/blast_rps.h>
#include <algo/blast/core/blast_encoding.h>

Include dependency graph for lookup_wrap.c:

Go to the source code of this file.

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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 different flavors of lookup tables allowing a uniform interface in the code.

The wrapper (LookupTableWrap) contains an unsigned byte specifying the type of lookup table as well as a void pointer pointing to the actual lookup table. Examples of different types of lookup tables are those for protein queries, the "standard" nucleotide one, the megablast lookup table, etc.

Definition in file lookup_wrap.c.

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).