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/* $Id: blast_engine.h,v 1.44 2004/09/07 17:20:01 dondosha Exp $
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* ===========================================================================
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* National Center for Biotechnology Information
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* This software/database is a "United States Government Work" under the
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* terms of the United States Copyright Act. It was written as part of
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* the author's official duties as a United States Government employee and
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* thus cannot be copyrighted. This software/database is freely available
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* to the public for use. The National Library of Medicine and the U.S.
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* Government have not placed any restriction on its use or reproduction.
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* Although all reasonable efforts have been taken to ensure the accuracy
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* and reliability of the software and data, the NLM and the U.S.
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* Government do not and cannot warrant the performance or results that
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* may be obtained by using this software or data. The NLM and the U.S.
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* Government disclaim all warranties, express or implied, including
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* warranties of performance, merchantability or fitness for any particular
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* Please cite the author in any work or product based on this material.
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* ===========================================================================
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* Author: Ilya Dondoshansky
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/** @file blast_engine.h
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* High level BLAST functions
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#ifndef __BLAST_ENGINE__
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#define __BLAST_ENGINE__
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#include <algo/blast/core/blast_def.h>
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#include <algo/blast/core/blast_extend.h>
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#include <algo/blast/core/blast_gapalign.h>
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#include <algo/blast/core/blast_hits.h>
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#include <algo/blast/core/blast_seqsrc.h>
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#include <algo/blast/core/blast_diagnostics.h>
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#include <algo/blast/core/blast_hspstream.h>
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/** The high level function performing the BLAST search against a BLAST
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* database after all the setup has been done.
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* @param program_number Type of BLAST program [in]
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* @param query The query sequence [in]
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* @param query_info Additional query information [in]
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* @param seq_src Structure containing BLAST database [in]
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* @param sbp Scoring and statistical parameters [in]
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* @param score_options Hit scoring options [in]
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* @param lookup_wrap The lookup table, constructed earlier [in]
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* @param word_options Options for processing initial word hits [in]
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* @param ext_options Options and parameters for the gapped extension [in]
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* @param hit_options Options for saving the HSPs [in]
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* @param eff_len_options Options for setting effective lengths [in]
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* @param psi_options Options specific to PSI-BLAST [in]
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* @param db_options Options for handling BLAST database [in]
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* @param hsp_stream Structure for streaming results [in] [out]
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* @param diagnostics Return statistics containing numbers of hits on
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* different stages of the search [out]
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* @param results Results of the BLAST search [out]
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BLAST_SearchEngine(EBlastProgramType program_number,
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BLAST_SequenceBlk* query, BlastQueryInfo* query_info,
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const BlastSeqSrc* seq_src, BlastScoreBlk* sbp,
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const BlastScoringOptions* score_options,
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LookupTableWrap* lookup_wrap,
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const BlastInitialWordOptions* word_options,
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const BlastExtensionOptions* ext_options,
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const BlastHitSavingOptions* hit_options,
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const BlastEffectiveLengthsOptions* eff_len_options,
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const PSIBlastOptions* psi_options,
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const BlastDatabaseOptions* db_options,
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BlastHSPStream* hsp_stream, BlastDiagnostics* diagnostics,
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BlastHSPResults** results);
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/** The high level function performing an RPS BLAST search
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* @param program_number Type of BLAST program [in]
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* @param query The query sequence [in]
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* @param query_info Additional query information [in]
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* @param seq_src Structure containing BLAST database [in]
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* @param sbp Scoring and statistical parameters [in]
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* @param score_options Hit scoring options [in]
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* @param lookup_wrap The lookup table, constructed earlier [in]
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* @param word_options Options for processing initial word hits [in]
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* @param ext_options Options and parameters for the gapped extension [in]
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* @param hit_options Options for saving the HSPs [in]
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* @param eff_len_options Options for setting effective lengths [in]
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* @param psi_options Options specific to PSI-BLAST [in]
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* @param db_options Options for handling BLAST database [in]
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* @param hsp_stream Placeholder for saving results [in]
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* @param diagnostics Return statistics containing numbers of hits on
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* different stages of the search [out]
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* @param results Structure holding all saved results [in] [out]
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BLAST_RPSSearchEngine(EBlastProgramType program_number,
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BLAST_SequenceBlk* query, BlastQueryInfo* query_info,
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const BlastSeqSrc* seq_src, BlastScoreBlk* sbp,
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const BlastScoringOptions* score_options,
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LookupTableWrap* lookup_wrap,
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const BlastInitialWordOptions* word_options,
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const BlastExtensionOptions* ext_options,
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const BlastHitSavingOptions* hit_options,
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const BlastEffectiveLengthsOptions* eff_len_options,
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const PSIBlastOptions* psi_options,
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const BlastDatabaseOptions* db_options,
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BlastHSPStream* hsp_stream, BlastDiagnostics* diagnostics,
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BlastHSPResults** results);
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/** Perform the preliminary stage of the BLAST search.
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* @param program_number Type of BLAST program [in]
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* @param query The query sequence [in]
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* @param query_info Additional query information [in]
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* @param seq_src Structure containing BLAST database [in]
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* @param gap_align Structure containing scoring block and memory allocated
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* for gapped alignment. [in]
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* @param score_params Hit scoring parameters [in]
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* @param lookup_wrap The lookup table, constructed earlier [in]
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* @param word_options Options for processing initial word hits [in]
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* @param ext_params Parameters for the gapped extension [in]
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* @param hit_params Parameters for saving the HSPs [in]
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* @param eff_len_params Parameters for setting effective lengths [in]
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* @param psi_options Options specific to PSI-BLAST [in]
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* @param db_options Options for handling BLAST database [in]
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* @param hsp_stream Placeholder for saving HSP lists [in]
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* @param diagnostics Return statistics containing numbers of hits on
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* different stages of the search. Statistics saved only
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* for the allocated parts of the structure. [in] [out]
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BLAST_PreliminarySearchEngine(EBlastProgramType program_number,
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BLAST_SequenceBlk* query, BlastQueryInfo* query_info,
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const BlastSeqSrc* seq_src, BlastGapAlignStruct* gap_align,
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BlastScoringParameters* score_params,
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LookupTableWrap* lookup_wrap,
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const BlastInitialWordOptions* word_options,
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BlastExtensionParameters* ext_params,
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BlastHitSavingParameters* hit_params,
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BlastEffectiveLengthsParameters* eff_len_params,
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const PSIBlastOptions* psi_options,
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const BlastDatabaseOptions* db_options,
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BlastHSPStream* hsp_stream, BlastDiagnostics* diagnostics);
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/** Gapped extension function pointer type */
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typedef Int2 (*BlastGetGappedScoreType)
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(EBlastProgramType, BLAST_SequenceBlk*, BlastQueryInfo* query_info,
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BLAST_SequenceBlk*, BlastGapAlignStruct*, const BlastScoringParameters*,
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const BlastExtensionParameters*, const BlastHitSavingParameters*,
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BlastInitHitList*, BlastHSPList**, BlastGappedStats*);
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/** Word finder function pointer type */
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typedef Int2 (*BlastWordFinderType)
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(BLAST_SequenceBlk*, BLAST_SequenceBlk*,
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LookupTableWrap*, Int4**, const BlastInitialWordParameters*,
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Blast_ExtendWord*, Uint4*, Uint4*, Int4, BlastInitHitList*,
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BlastUngappedStats*);
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#endif /* !__BLAST_ENGINE__ */
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removed
algo/blast/core/blast_engine.h
