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().
