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>
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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_number the type of blast search being performed [in] queryBlk query sequence [in] query_info query information [in] sbp (Karlin-Altschul) information for search [in] subjectBlk subject sequence [in] seqSrc used to fetch database/match sequences [in] db_genetic_code Genetic code to use if database sequences are translated, and there is no other guidance on which genetic code to use [in] thisMatch hit for further processing [in] hsp_stream used to fetch hits for further processing [in] scoringParams parameters used for scoring (matrix, gap costs etc.) [in] extendParams parameters used for extension [in] hitParams parameters used for saving hits [in] psiOptions options related to psi-blast [in] results All 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_number the type of blast search being performed [in] num_threads number of OpenMP threads to be used [in] queryBlk query sequence [in] query_info query information [in] sbp (Karlin-Altschul) information for search [in] subjectBlk subject sequence [in] seqSrc used to fetch database/match sequences [in] db_genetic_code Genetic code to use if database sequences are translated, and there is no other guidance on which genetic code to use [in] thisMatch hit for further processing [in] hsp_stream used to fetch hits for further processing [in] scoringParams parameters used for scoring (matrix, gap costs etc.) [in] extendParams parameters used for extension [in] hitParams parameters used for saving hits [in] psiOptions options related to psi-blast [in] results All 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().
