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NCBI C++ ToolKit: src/algo/blast/core/blast_engine.c File Reference

Function calls to actually perform a BLAST search (high level). More...

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Function calls to actually perform a BLAST search (high level).

The hierarchy of function calls, starting from the top level in the BLAST core, is described below.

Preliminary stage of the BLAST search:

   Blast_RunPreliminarySearch
       BLAST_GapAlignSetUp
       BLAST_PreliminarySearchEngine
           if (RPS BLAST) {
               s_RPSPreliminarySearchEngine
                   s_BlastSearchEngineCore
           } else {
               for (all sequences in the database)
                   s_BlastSearchEngineCore
           }

Full BLAST search, including preliminary search and traceback:

   Blast_RunFullSearch
       BLAST_GapAlignSetUp
       BLAST_PreliminarySearchEngine
       BLAST_ComputeTraceback

Definition in file blast_engine.c.

Converts nucleotide coordinates to protein.

Definition at line 79 of file blast_engine.c.

Structure to be passed to s_BlastSearchEngineCore, containing pointers to various preallocated structures and arrays.

Structure used for subject sequence split.

Perform the preliminary stage of the BLAST search.

Parameters

program_number Type of BLAST program [in] query The query sequence [in] query_info Additional query information [in] seq_src Structure containing BLAST database [in] gap_align Structure containing scoring block and memory allocated for gapped alignment. [in] score_params Hit scoring parameters [in] lookup_wrap The lookup table, constructed earlier [in] word_options Options for processing initial word hits [in] ext_params Parameters for the gapped extension [in] hit_params Parameters for saving the HSPs [in] eff_len_params Parameters for setting effective lengths [in] psi_options Options specific to PSI-BLAST [in] db_options Options for handling BLAST database [in] hsp_stream Placeholder for saving HSP lists [in] diagnostics Return statistics containing numbers of hits on different stages of the search. Statistics saved only for the allocated parts of the structure. [in] [out] interrupt_search function callback to allow interruption of BLAST search [in, optional] progress_info contains information about the progress of the current BLAST search [in|out]

Definition at line 1335 of file blast_engine.c.

References ASSERT, BLAST_SequenceBlk::bases_offset, Blast_HSPListFree(), Blast_HSPListGetBitScores(), Blast_HSPListGetEvalues(), Blast_HSPListReapByQueryCoverage(), Blast_HSPListReapByRawScore(), Blast_HSPListReevaluateUngapped(), BLAST_LinkHsps(), BLAST_OneSubjectUpdateParameters(), Blast_ProgramIsMapping(), Blast_ProgramIsNucleotide(), Blast_ProgramIsRpsBlast(), BLAST_SEQSRC_EOF, BLAST_SEQSRC_ERROR, Blast_SubjectIsTranslated(), BLASTERR_INTERRUPTED, BLASTERR_SEQSRC, BlastHSPStreamWrite(), BlastInitialWordParametersFree(), BlastInitialWordParametersNew(), BlastLinkHSPParametersUpdate(), BlastSeqSrcGetAvgSeqLen(), BlastSeqSrcGetNumSeqs(), BlastSeqSrcGetSequence(), BlastSeqSrcGetTotLen(), BlastSeqSrcIteratorFree(), BlastSeqSrcIteratorNewEx(), BlastSeqSrcIteratorNext(), BlastSeqSrcReleaseSequence(), BlastSequenceBlkFree(), CalculateLinkHSPCutoffs(), LookupTableWrap::check_index_oid, CODON_LENGTH, BlastDiagnostics::cutoffs, DoAnchoredSearch(), eBlastEncodingProtein, BlastSeqSrcGetSeqArg::encoding, LookupTableWrap::end_search_indication, eNoResults, ePrelimSearch, FALSE, BlastScoringOptions::gapped_calculation, BLAST_SequenceBlk::gen_code_string, GenCodeSingletonFind(), BlastDatabaseOptions::genetic_code, BlastHitList::heapified, BlastHSPResults::hitlist_array, BlastHSPList::hspcnt, if(), LAST_VOL_IDX_INIT, BLAST_SequenceBlk::length, BlastHitSavingParameters::link_hsp_params, BlastHitList::low_score, BlastHitSavingParameters::low_score, BlastHitSavingOptions::low_score_perc, BlastScoreBlk::matrix_only_scoring, MAX, NULL, BlastHSPResults::num_queries, BlastSeqSrcGetSeqArg::oid, BlastExtensionParameters::options, BlastHitSavingParameters::options, BlastScoringParameters::options, query, BlastHSPStream::results, s_AdjustSubjectForSraSearch(), s_AdjustSubjectForTranslatedSraSearch(), s_Blast_HSPListReapByPrelimEvalue(), s_BlastCoreAuxStructFree(), s_BlastSearchEngineCore(), s_BlastSetUpAuxStructures(), s_FillReturnCutoffsInfo(), s_GetMinimumSubjSeqLen(), s_RPSPreliminarySearchEngine(), BlastGapAlignStruct::sbp, BlastSeqSrcGetSeqArg::seq, SBlastProgress::stage, and TRUE.

Referenced by Blast_RunFullSearch(), and Blast_RunPreliminarySearchWithInterrupt().

The high level function performing the BLAST search against a BLAST database after all the setup has been done.

Parameters

program_number Type of BLAST program [in] query The query sequence [in] query_info Additional query information [in] seq_src Structure containing BLAST database [in] sbp Scoring and statistical parameters [in] score_options Hit scoring options [in] lookup_wrap The lookup table, constructed earlier [in] word_options Options for processing initial word hits [in] ext_options Options and parameters for the gapped extension [in] hit_options Options for saving the HSPs [in] eff_len_options Options for setting effective lengths [in] psi_options Options specific to PSI-BLAST [in] db_options Options for handling BLAST database [in] hsp_stream Structure for streaming results [in] [out] rps_info RPS BLAST auxiliary data structure [in] diagnostics Return statistics containing numbers of hits on different stages of the search [out] results Results of the BLAST search [out] interrupt_search function callback to allow interruption of BLAST search [in, optional] progress_info contains information about the progress of the current BLAST search [in|out]

Definition at line 1727 of file blast_engine.c.

References BLAST_ComputeTraceback(), BLAST_GapAlignSetUp(), BLAST_PreliminarySearchEngine(), Blast_ProgramIsPhiBlast(), BlastHSPStreamClose(), BlastUngappedStats::lookup_hits, LookupTableWrap::lut, NULL, SPHIPatternSearchBlk::num_patterns_db, query, results, s_BlastRunFullSearchCleanUp(), and BlastDiagnostics::ungapped_stat.

The high level function performing the BLAST search against a BLAST database after all the setup has been done.

Parameters

program_number Type of BLAST program [in] query The query sequence [in] query_info Additional query information [in] seq_src Structure containing BLAST database [in] score_options Hit scoring options [in] sbp Scoring and statistical parameters [in] lookup_wrap The lookup table, constructed earlier [in] word_options Options for processing initial word hits [in] ext_options Options and parameters for the gapped extension [in] hit_options Options for saving the HSPs [in] eff_len_options Options for setting effective lengths [in] psi_options Options specific to PSI-BLAST [in] db_options Options for handling BLAST database [in] hsp_stream Structure for streaming results [in] [out] diagnostics Return statistics containing numbers of hits on different stages of the search [out]

Definition at line 1610 of file blast_engine.c.

References Blast_RunPreliminarySearchWithInterrupt(), NULL, and query.

Same as above, with support for user interrupt function.

Parameters

program_number Type of BLAST program [in] query The query sequence [in] query_info Additional query information [in] seq_src Structure containing BLAST database [in] score_options Hit scoring options [in] sbp Scoring and statistical parameters [in] lookup_wrap The lookup table, constructed earlier [in] word_options Options for processing initial word hits [in] ext_options Options and parameters for the gapped extension [in] hit_options Options for saving the HSPs [in] eff_len_options Options for setting effective lengths [in] psi_options Options specific to PSI-BLAST [in] db_options Options for handling BLAST database [in] hsp_stream Structure for streaming results [in] [out] diagnostics Return statistics containing numbers of hits on different stages of the search [out] interrupt_search User defined function to interrupt search [in] progress_info User supplied data structure to aid interrupt [in]

Definition at line 1633 of file blast_engine.c.

References Blast_DiagnosticsFree(), Blast_DiagnosticsInit(), Blast_DiagnosticsUpdate(), BLAST_GapAlignSetUp(), BLAST_GapAlignStructFree(), BLAST_PreliminarySearchEngine(), BlastEffectiveLengthsParametersFree(), BlastExtensionParametersFree(), BlastHitSavingParametersFree(), BlastScoringParametersFree(), NULL, query, and BlastGapAlignStruct::sbp.

Referenced by Blast_RunPreliminarySearch(), and CPrelimSearchRunner::operator()().

Definition at line 1209 of file blast_engine.c.

References CODON_LENGTH, BlastSeg::end, FALSE, BlastSeg::frame, BlastSeg::gapped_start, BlastHSPList::hsp_array, BlastHSPList::hspcnt, i, BlastSeg::offset, offset, BlastHSP::query, BlastHSP::subject, and TRUE.

Referenced by BLAST_PreliminarySearchEngine().

Definition at line 145 of file blast_engine.c.

References SubjectSplitStruct::allocated, ASSERT, eHardSubjMasking, eSoftSubjMasking, SubjectSplitStruct::full_range, SubjectSplitStruct::hard_ranges, SubjectSplitStruct::hm_index, SSeqRange::left, SubjectSplitStruct::next, SubjectSplitStruct::num_hard_ranges, SubjectSplitStruct::num_seq_ranges, SubjectSplitStruct::num_soft_ranges, SubjectSplitStruct::offset, SSeqRange::right, SubjectSplitStruct::seq_ranges, SubjectSplitStruct::sequence, SubjectSplitStruct::sm_index, SubjectSplitStruct::soft_ranges, and subject.

Referenced by s_BlastSearchEngineCore(), and s_BlastSearchEngineOneContext().

The core of the BLAST search: comparison between the (concatenated) query against one subject sequence.

Translation of the subject sequence into 6 frames is done inside, if necessary. If subject sequence is too long, it can be split into several chunks.

Parameters

program_number BLAST program type [in] query Query sequence structure [in] query_info_in Query information [in] subject Subject sequence structure [in] lookup Lookup table [in] gap_align Structure for gapped alignment information [in] score_params Scoring parameters [in] word_params Initial word finding and ungapped extension parameters [in] ext_params Gapped extension parameters [in] hit_params Hit saving parameters [in] db_options Database options [in] diagnostics Hit counts and other diagnostics [in] [out] aux_struct Structure containing different auxiliary data and memory for the preliminary stage of the BLAST search [in] hsp_list_out_ptr List of HSPs found for a given subject sequence [in] interrupt_search function callback to allow interruption of BLAST search [in, optional] progress_info contains information about the progress of the current BLAST search [in|out]

Definition at line 702 of file blast_engine.c.

References BLAST_ContextToFrame(), BLAST_GetAllTranslations(), Blast_HSPListAppend(), Blast_HSPListFree(), Blast_HSPListGetEvalues(), Blast_HSPListReapByRawScore(), BLAST_LinkHsps(), Blast_ProgramIsNucleotide(), Blast_ProgramIsPhiBlast(), Blast_ProgramIsRpsBlast(), Blast_SubjectIsTranslated(), BLASTERR_INTERRUPTED, BlastHspNumMax(), BlastQueryInfoNew(), context, ContextOffsetsToOffsetArray(), CONV_NUCL2PROT_COORDINATES, eBlastEncodingNcbi2na, eBlastTypeBlastx, eBlastTypeMapping, eBlastTypeRpsBlast, eBlastTypeRpsTblastn, eNoSubjMasking, FALSE, SubjectSplitStruct::full_range, BlastScoringOptions::gapped_calculation, BlastDiagnostics::gapped_stat, BlastScoreBlk::gbp, BlastGappedStats::good_extensions, BlastHSPList::hspcnt, i, BlastScoringOptions::is_ooframe, SSeqRange::left, BlastHitSavingParameters::link_hsp_params, lookup(), BlastScoreBlk::matrix_only_scoring, NULL, BlastRPSLookupTable::num_profiles, SubjectSplitStruct::num_seq_ranges, BlastGappedStats::num_seqs_passed, BlastHitSavingParameters::options, BlastScoringParameters::options, query, SSeqRange::right, BlastRPSLookupTable::rps_seq_offsets, s_AllocateSeqRange(), s_BackupSubject(), s_Blast_HSPListReapByPrelimEvalue(), s_BlastSearchEngineCoreCleanUp(), s_BlastSearchEngineOneContext(), s_RestoreSubject(), s_RPSOffsetArrayToContextOffsets(), BlastGapAlignStruct::sbp, BlastScoringParameters::scale_factor, SubjectSplitStruct::seq_ranges, SubjectSplitStruct::sequence, subject, and TRUE.

Referenced by BLAST_PreliminarySearchEngine(), and s_RPSPreliminarySearchEngine().

Clean up function for s_BlastSearchEngineCore.

Parameters

program_number BLAST program type [in] query_info Query information structure local to s_BlastSearchEngineCore, which may or may not be deallocated [in] query_info_in Query information [in] translation_buffer buffer containing translated sequence data [in] frame_offsets_a FIXME

Definition at line 613 of file blast_engine.c.

References BlastQueryInfoFree(), eBlastTypeRpsTblastn, and sfree.

Referenced by s_BlastSearchEngineCore().

Searches only one context of a database sequence, but does all chunks if it is split.

Parameters

program_number BLAST program type [in] query Query sequence structure [in] query_info Query information [in] subject Subject sequence structure [in] orig_length original length of query before translation [in] lookup Lookup table [in] gap_align Structure for gapped alignment information [in] score_params Scoring parameters [in] word_params Initial word finding and ungapped extension parameters [in] ext_params Gapped extension parameters [in] hit_params Hit saving parameters [in] diagnostics Hit counts and other diagnostics [in] [out] aux_struct Structure containing different auxiliary data and memory for the preliminary stage of the BLAST search [in] hsp_list_out_ptr List of HSPs found for a given subject sequence [out] interrupt_search function callback to allow interruption of BLAST search [in, optional] progress_info contains information about the progress of the current BLAST search [in|out]

Definition at line 423 of file blast_engine.c.

References ASSERT, BLAST_GetUngappedHSPList(), Blast_HSPListAdjustOddBlastnScores(), Blast_HSPListAdjustOffsets(), Blast_HSPListFree(), Blast_HSPListPurgeHSPsWithCommonEndpoints(), Blast_HSPListsMerge(), Blast_HSPListSortByScore(), Blast_HSPListSubjectBestHit(), Blast_ProgramIsMapping(), Blast_ProgramIsNucleotide(), Blast_SubjectIsTranslated(), BLASTERR_INTERRUPTED, BlastHspNumMax(), BlastInitHitListReset(), SBlastScoreMatrix::data, DBSEQ_CHUNK_OVERLAP, eBlastTypeRpsTblastn, BlastCoreAuxStruct::ewp, BlastScoringOptions::gapped_calculation, BlastDiagnostics::gapped_stat, BlastCoreAuxStruct::GetGappedScore, GetOffsetArraySize(), SubjectSplitStruct::hard_ranges, SubjectSplitStruct::hm_index, BlastHitSavingOptions::hsp_filt_opt, BlastHSPList::hspcnt, BlastCoreAuxStruct::init_hitlist, INT4_MIN, BlastScoringOptions::is_ooframe, BlastCoreAuxStruct::JumperGapped, SSeqRange::left, lookup(), BlastCoreAuxStruct::mapper_wordhits, BlastScoreBlk::matrix, BlastQueryInfo::max_length, NULL, SubjectSplitStruct::offset, BlastCoreAuxStruct::offset_pairs, BlastHSPList::oid, BlastHitSavingParameters::options, BlastScoringParameters::options, BlastGapAlignStruct::positionBased, BlastScoreBlk::psi_matrix, SPsiBlastScoreMatrix::pssm, query, s_BackupSubject(), s_GetNextSubjectChunk(), s_RestoreSubject(), s_TranslateHSPsToDNAPCoord(), BlastGapAlignStruct::sbp, SubjectSplitStruct::sequence, subject, BlastHSPFilteringOptions::subject_besthit_opts, SUBJECT_SPLIT_DONE, SUBJECT_SPLIT_NO_RANGE, SUBJECT_SPLIT_OK, BlastInitHitList::total, TRUE, BlastDiagnostics::ungapped_stat, and BlastCoreAuxStruct::WordFinder.

Referenced by s_BlastSearchEngineCore().

Setup of the auxiliary BLAST structures; also calculates internally used parameters from options.

Parameters

seq_src Sequence source information, with callbacks to get sequences, their lengths, etc. [in] lookup_wrap Lookup table, already constructed. [in] word_params Parameters for initial word finding and ungapped extension. [in] ext_options options for gapped extension. [in] hit_options options for saving hits. [in] query The query sequence block [in] aux_struct_ptr Placeholder joining various auxiliary memory structures [out]

Definition at line 971 of file blast_engine.c.

References ASSERT, BLAST_GetGappedScore(), BLAST_InitHitListNew(), BLAST_SmithWatermanGetGappedScore(), BlastAaWordFinder(), BlastChooseNaExtend(), BlastChooseNucleotideScanSubject(), BlastChooseProteinScanSubject(), BlastExtendWordNew(), BlastNaWordFinder(), BlastRPSWordFinder(), calloc(), eAaLookupTable, eCompressedAaLookupTable, eIndexedMBLookupTable, eJumperWithTraceback, ePhiLookupTable, ePhiNaLookupTable, BlastExtensionOptions::ePrelimGapExt, eRPSLookupTable, eSmithWatermanScoreOnly, BlastCoreAuxStruct::ewp, BlastCoreAuxStruct::GetGappedScore, GetOffsetArraySize(), BlastCoreAuxStruct::init_hitlist, BlastCoreAuxStruct::JumperGapped, JumperNaWordFinder(), LookupTableWrap::lut_type, malloc(), BlastCoreAuxStruct::mapper_wordhits, MapperWordHitsNew(), MB_IndexedWordFinder(), NULL, BlastQueryInfo::num_queries, BlastCoreAuxStruct::offset_pairs, PHI_MAX_HIT, PHIBlastWordFinder(), PHIGetGappedScore(), query, LookupTableWrap::read_indexed_db, ShortRead_IndexedWordFinder(), and BlastCoreAuxStruct::WordFinder.

Referenced by BLAST_PreliminarySearchEngine().

Fills the output information about the cutoffs uses in a BLAST search.

Parameters

return_cutoffs Structure for saving cutoffs information [in] [out] score_params Scoring parameters, containing the scaling factor [in] word_params Initial word parameters [in] ext_params Gapped extension parameters [in] hit_params Hit saving parameters [in]

Definition at line 928 of file blast_engine.c.

References BlastRawCutoffs::cutoff_score, BlastInitialWordParameters::cutoff_score_min, BlastHitSavingParameters::cutoff_score_min, BlastExtensionParameters::gap_x_dropoff, BlastExtensionParameters::gap_x_dropoff_final, if(), BlastScoringParameters::scale_factor, BlastRawCutoffs::ungapped_cutoff, BlastRawCutoffs::x_drop_gap, BlastRawCutoffs::x_drop_gap_final, BlastRawCutoffs::x_drop_ungapped, and BlastInitialWordParameters::x_dropoff_max.

Referenced by BLAST_PreliminarySearchEngine(), and s_RPSPreliminarySearchEngine().

Definition at line 221 of file blast_engine.c.

References ASSERT, COMPRESSION_RATIO, DBSEQ_CHUNK_OVERLAP, eSoftSubjMasking, SubjectSplitStruct::full_range, SubjectSplitStruct::hard_ranges, SubjectSplitStruct::hm_index, i, SSeqRange::left, len, MAX_DBSEQ_LEN, SubjectSplitStruct::next, SubjectSplitStruct::num_hard_ranges, SubjectSplitStruct::num_soft_ranges, SubjectSplitStruct::offset, SSeqRange::right, s_AllocateSeqRange(), SubjectSplitStruct::sequence, SubjectSplitStruct::sm_index, SubjectSplitStruct::soft_ranges, subject, SUBJECT_SPLIT_DONE, SUBJECT_SPLIT_NO_RANGE, and SUBJECT_SPLIT_OK.

Referenced by s_BlastSearchEngineOneContext().

Set up context offsets for the auxiliary BlastQueryInfo structure that is created for the concatenated database in RPS BLAST search.

Calls the public function OffsetArrayToContextOffsets with a blastp program, because subjects are protein sequences. This guarantees that all frames are set to 0.

Parameters

info The preallocated structure [in] [out] new_offsets The array context offsets to fill [in]

Definition at line 392 of file blast_engine.c.

References eBlastTypeBlastp, info, and OffsetArrayToContextOffsets().

Referenced by s_BlastSearchEngineCore().

Performs the preliminary stage of an RPS BLAST search, after all set up has already been done.

Parameters

program_number Type of BLAST program [in] query The query sequence [in] query_info Additional query information [in] seq_src Structure containing BLAST database [in] score_params Hit scoring parameters [in] lookup_wrap The lookup table, constructed earlier [in] aux_struct Wrapper for auxiliary structures used in preliminary search [in] word_params Parameters for processing initial word hits [in] ext_params Parameters for the gapped extension [in] gap_align Structure containing scoring block and memory allocated for gapped alignment. [in] hit_params Parameters for saving the HSPs [in] hsp_stream Placeholder for saving HSP lists [in] diagnostics Return statistics containing numbers of hits on different stages of the search. Statistics saved only for the allocated parts of the structure. [in] [out] interrupt_search function callback to allow interruption of BLAST search [in, optional] progress_info contains information about the progress of the current BLAST search [in|out]

Definition at line 1096 of file blast_engine.c.

References Blast_GetOneQueryStructs(), Blast_HSPListFree(), Blast_ProgramIsRpsBlast(), BLASTERR_INTERRUPTED, BlastExtendWordFree(), BlastExtendWordNew(), BlastHSPStreamWrite(), BlastQueryInfoFree(), BlastSeqSrcGetNumSeqs(), BlastSeqSrcGetTotLen(), BlastSequenceBlkFree(), BlastDiagnostics::cutoffs, BlastCoreAuxStruct::ewp, FALSE, BlastHSPList::hspcnt, if(), INT4_MAX, lookup(), LookupTableWrap::lut, NULL, BlastQueryInfo::num_queries, BlastGapAlignStruct::positionBased, query, BlastHSPList::query_index, RPSPsiMatrixAttach(), RPSPsiMatrixDetach(), s_BlastSearchEngineCore(), s_FillReturnCutoffsInfo(), BlastGapAlignStruct::sbp, and TRUE.

Referenced by BLAST_PreliminarySearchEngine().

Adjust HSP coordinates for out-of-frame gapped extension.

Parameters

program One of blastx or tblastn [in] init_hitlist List of hits after ungapped extension [in] query_info Query information containing context offsets; needed for blastx only [in] subject_frame Frame of the subject sequence; tblastn only [in] subject_length Length of the original nucleotide subject sequence; tblastn only [in] offset Shift in the subject sequence protein coordinates [in]

Definition at line 324 of file blast_engine.c.

References Blast_InitHitListSortByScore(), BSearchContextInfo(), CODON_LENGTH, BlastQueryInfo::contexts, eBlastTypeBlastx, BlastInitHitList::init_hsp_array, offset, BlastInitHSP::offsets, BlastOffsetPair::q_off, BlastUngappedData::q_start, BlastOffsetPair::qs_offsets, BlastContextInfo::query_offset, BlastOffsetPair::s_off, BlastUngappedData::s_start, BlastInitHitList::total, and BlastInitHSP::ungapped_data.

Referenced by s_BlastSearchEngineOneContext().

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