NCBI C++ ToolKit
Functions
blast_kappa.h File Reference

Header file for composition-based statistics. More...

#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_def.h>
#include <algo/blast/core/blast_program.h>
#include <algo/blast/core/blast_query_info.h>
#include <algo/blast/core/blast_stat.h>
#include <algo/blast/core/blast_hits.h>
#include <algo/blast/core/blast_hspstream.h>
+ Include dependency graph for blast_kappa.h:
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Go to the source code of this file.

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Functions

Int2 Blast_RedoAlignmentCore (EBlastProgramType program_number, BLAST_SequenceBlk *queryBlk, const BlastQueryInfo *query_info, BlastScoreBlk *sbp, BLAST_SequenceBlk *subjectBlk, const BlastSeqSrc *seqSrc, Int4 db_genetic_code, BlastHSPList *thisMatch, BlastHSPStream *hsp_stream, BlastScoringParameters *scoringParams, const BlastExtensionParameters *extendParams, const BlastHitSavingParameters *hitParams, const PSIBlastOptions *psiOptions, BlastHSPResults *results)
 Top level routine to recompute alignments for each match found by the gapped BLAST algorithm (single-thread prototype) This prototype is an adapter to the multi-thread prototype with num_threads set to 1. More...
 
Int2 Blast_RedoAlignmentCore_MT (EBlastProgramType program_number, Uint4 num_threads, BLAST_SequenceBlk *queryBlk, const BlastQueryInfo *query_info, BlastScoreBlk *sbp, BLAST_SequenceBlk *subjectBlk, const BlastSeqSrc *seqSrc, Int4 db_genetic_code, BlastHSPList *thisMatch, BlastHSPStream *hsp_stream, BlastScoringParameters *scoringParams, const BlastExtensionParameters *extendParams, const BlastHitSavingParameters *hitParams, const PSIBlastOptions *psiOptions, BlastHSPResults *results)
 Top level routine to recompute alignments for each match found by the gapped BLAST algorithm (multi-thread prototype) A linked list of alignments is returned (param hitList); the alignments are sorted according to the lowest E-value of the best alignment for each matching sequence; alignments for the same matching sequence are in the list consecutively regardless of the E-value of the secondary alignments. More...
 

Detailed Description

Header file for composition-based statistics.

Definition in file blast_kappa.h.

Function Documentation

◆ Blast_RedoAlignmentCore()

Int2 Blast_RedoAlignmentCore ( EBlastProgramType  program_number,
BLAST_SequenceBlk queryBlk,
const BlastQueryInfo queryInfo,
BlastScoreBlk sbp,
BLAST_SequenceBlk subjectBlk,
const BlastSeqSrc seqSrc,
Int4  default_db_genetic_code,
BlastHSPList thisMatch,
BlastHSPStream hsp_stream,
BlastScoringParameters scoringParams,
const BlastExtensionParameters extendParams,
const BlastHitSavingParameters hitParams,
const PSIBlastOptions psiOptions,
BlastHSPResults results 
)

Top level routine to recompute alignments for each match found by the gapped BLAST algorithm (single-thread prototype) This prototype is an adapter to the multi-thread prototype with num_threads set to 1.

A linked list of alignments is returned (param hitList); the alignments are sorted according to the lowest E-value of the best alignment for each matching sequence; alignments for the same matching sequence are in the list consecutively regardless of the E-value of the secondary alignments. Ties in sorted order are much rarer than for the standard BLAST method, but are broken deterministically based on the index of the matching sequences in the database.

Parameters
program_numberthe type of blast search being performed [in]
queryBlkquery sequence [in]
query_infoquery information [in]
sbp(Karlin-Altschul) information for search [in]
subjectBlksubject sequence [in]
seqSrcused to fetch database/match sequences [in]
db_genetic_codeGenetic code to use if database sequences are translated, and there is no other guidance on which genetic code to use [in]
thisMatchhit for further processing [in]
hsp_streamused to fetch hits for further processing [in]
scoringParamsparameters used for scoring (matrix, gap costs etc.) [in]
extendParamsparameters used for extension [in]
hitParamsparameters used for saving hits [in]
psiOptionsoptions related to psi-blast [in]
resultsAll HSP results from previous stages of the search [in] [out]
Returns
0 on success, otherwise failure.

Top level routine to recompute alignments for each match found by the gapped BLAST algorithm (single-thread prototype) This prototype is an adapter to the multi-thread prototype with num_threads set to 1.

Single-thread adapter to Blast_RedoAlignmentCore_MT.

Definition at line 2942 of file blast_kappa.c.

References Blast_RedoAlignmentCore_MT().

Referenced by CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), and s_RPSComputeTraceback().

◆ Blast_RedoAlignmentCore_MT()

Int2 Blast_RedoAlignmentCore_MT ( EBlastProgramType  program_number,
Uint4  num_threads,
BLAST_SequenceBlk queryBlk,
const BlastQueryInfo queryInfo,
BlastScoreBlk sbp,
BLAST_SequenceBlk subjectBlk,
const BlastSeqSrc seqSrc,
Int4  default_db_genetic_code,
BlastHSPList thisMatch,
BlastHSPStream hsp_stream,
BlastScoringParameters scoringParams,
const BlastExtensionParameters extendParams,
const BlastHitSavingParameters hitParams,
const PSIBlastOptions psiOptions,
BlastHSPResults results 
)

Top level routine to recompute alignments for each match found by the gapped BLAST algorithm (multi-thread prototype) A linked list of alignments is returned (param hitList); the alignments are sorted according to the lowest E-value of the best alignment for each matching sequence; alignments for the same matching sequence are in the list consecutively regardless of the E-value of the secondary alignments.

Ties in sorted order are much rarer than for the standard BLAST method, but are broken deterministically based on the index of the matching sequences in the database.

Parameters
program_numberthe type of blast search being performed [in]
num_threadsnumber of OpenMP threads to be used [in]
queryBlkquery sequence [in]
query_infoquery information [in]
sbp(Karlin-Altschul) information for search [in]
subjectBlksubject sequence [in]
seqSrcused to fetch database/match sequences [in]
db_genetic_codeGenetic code to use if database sequences are translated, and there is no other guidance on which genetic code to use [in]
thisMatchhit for further processing [in]
hsp_streamused to fetch hits for further processing [in]
scoringParamsparameters used for scoring (matrix, gap costs etc.) [in]
extendParamsparameters used for extension [in]
hitParamsparameters used for saving hits [in]
psiOptionsoptions related to psi-blast [in]
resultsAll HSP results from previous stages of the search [in] [out]
Returns
0 on success, otherwise failure.

Top level routine to recompute alignments for each match found by the gapped BLAST algorithm (multi-thread prototype) A linked list of alignments is returned (param hitList); the alignments are sorted according to the lowest E-value of the best alignment for each matching sequence; alignments for the same matching sequence are in the list consecutively regardless of the E-value of the secondary alignments.

Definition at line 2981 of file blast_kappa.c.

References BlastScoreBlk::alphabet_code, ASSERT, b, BlastHSPList::best_evalue, Blast_CompositionWorkspaceFree(), Blast_CompositionWorkspaceInit(), Blast_CompositionWorkspaceNew(), Blast_ForbiddenRangesInitialize(), Blast_ForbiddenRangesRelease(), Blast_FrequencyDataIsAvailable(), BLAST_GapAlignStructFree(), BLAST_GapAlignStructNew(), Blast_HitListFree(), Blast_HSPListFree(), Blast_HSPListNew(), Blast_HSPListSwap(), Blast_HSPResultsFree(), Blast_HSPResultsNew(), Blast_RedoAlignParamsFree(), Blast_RedoOneMatch(), Blast_RedoOneMatchSmithWaterman(), BLAST_SetupPartialFetching(), BLASTAA_SIZE, BlastCompo_AlignmentsFree(), BlastCompo_EarlyTermination(), BlastCompo_HeapInitialize(), BlastCompo_HeapInsert(), BlastCompo_HeapRelease(), BlastCompo_HeapWouldInsert(), BlastHSPStreamRead(), BlastHSPStreamTBackClose(), BlastSeqSrcCopy(), BlastSeqSrcFree(), BlastSeqSrcGetMaxSeqLen(), BlastSeqSrcGetSupportsPartialFetching(), Boolean, calloc(), BlastExtensionOptions::compositionBasedStats, SBlastScoreMatrix::data, eBlastTypeBlastp, eBlastTypeBlastx, eBlastTypePsiBlast, eBlastTypeRpsBlast, eBlastTypeRpsTblastn, eBlastTypeTblastn, eCompositionBasedStats, eNoCompositionBasedStats, eSmithWatermanTbck, BlastExtensionOptions::eTbackExt, FALSE, BlastKappa_GappingParamsContext::gap_align, GenCodeSingletonFind(), head, SThreadLocalData::hit_params, BlastHSPResults::hitlist_array, BlastHitSavingOptions::hitlist_size, BlastHSPList::hsp_array, BlastHSPList::hspcnt, i, PSIBlastOptions::inclusion_ethresh, BlastCompo_MatchingSequence::index, kBlastHSPStream_Eof, BlastScoreBlk::kbp_gap, Blast_KarlinBlk::Lambda, BlastQueryInfo::last_context, BlastCompo_MatchingSequence::length, BLAST_SequenceBlk::length, BlastCompo_MatchingSequence::local_data, BlastKappa_GappingParamsContext::localScalingFactor, Blast_KarlinBlk::logK, match(), BlastScoringOptions::matrix, BlastScoreBlk::matrix, BlastQueryInfo::max_length, SBlastScoreMatrix::ncols, next(), NULL, BlastHSPResults::num_queries, BlastQueryInfo::num_queries, BlastScoreBlk::number_of_contexts, BlastHSPList::oid, BlastExtensionParameters::options, BlastHitSavingParameters::options, BlastScoringParameters::options, BlastKappa_GappingParamsContext::prog_number, PSI_INCLUSION_ETHRESH, BlastScoreBlk::psi_matrix, SPsiBlastScoreMatrix::pssm, BlastHSPList::query_index, SThreadLocalData::results, s_BlastGapAlignStruct_Copy(), s_BlastGapAlignStruct_Free(), s_BlastScoreBlk_Copy(), s_BlastScoreBlk_Free(), s_ClearHeap(), s_ComputeNumIdentities(), s_FillResultsFromCompoHeaps(), s_FreeBlastCompo_QueryInfoArray(), s_FreeEditScript(), s_GetAlignParams(), s_GetQueryInfo(), s_HitlistEvaluateAndPurge(), s_HitlistReapContained(), s_HSPListFromDistinctAlignments(), s_HSPListNormalizeScores(), s_MatchingSequenceInitialize(), s_MatchingSequenceRelease(), s_RecordInitialSearch(), s_RescaleSearch(), s_RestoreSearch(), s_ResultHspToDistinctAlign(), s_SavedParametersFree(), s_SavedParametersNew(), BlastGapAlignStruct::sbp, BlastKappa_GappingParamsContext::sbp, SCALING_FACTOR, BlastKappa_GappingParamsContext::scoringParams, BLAST_SequenceBlk::sequence, sfree, SThreadLocalDataArrayConsolidateResults(), SThreadLocalDataArrayNew(), SThreadLocalDataFree(), util::strcmp(), SThreadLocalDataArray::tld, TRUE, and BlastExtensionOptions::unifiedP.

Referenced by BLAST_ComputeTraceback_MT(), and Blast_RedoAlignmentCore().

Modified on Mon Apr 22 04:01:29 2024 by modify_doxy.py rev. 669887