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/* $Id: blast_engine.h,v 1.24 2003/09/10 19:41:02 dondosha Exp $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's offical duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================*/
/*****************************************************************************
File name: blast_engine.h
Author: Ilya Dondoshansky
Contents: High level BLAST functions
******************************************************************************
* $Revision: 1.24 $
* */
#ifndef __BLAST_ENGINE__
#define __BLAST_ENGINE__
#ifdef __cplusplus
extern "C" {
#endif
#include <algo/blast/core/blast_def.h>
#include <algo/blast/core/blast_extend.h>
#include <algo/blast/core/blast_gapalign.h>
#include <algo/blast/core/blast_hits.h>
#include <algo/blast/core/blast_seqsrc.h>
/** The high level function performing the BLAST search against a BLAST
* database after all the setup has been done.
* @param program_number Type of BLAST program [in]
* @param query The query sequence [in]
* @param query_info Additional query information [in]
* @param rdfp Structure containing BLAST database [in]
* @param sbp Scoring and statistical parameters [in]
* @param score_options Hit scoring options [in]
* @param lookup_wrap The lookup table, constructed earlier [in]
* @param word_options Options for processing initial word hits [in]
* @param ext_options Options and parameters for the gapped extension [in]
* @param hit_options Options for saving the HSPs [in]
* @param eff_len_options Options for setting effective lengths [in]
* @param psi_options Options specific to PSI-BLAST [in]
* @param db_options Options for handling BLAST database [in]
* @param results Structure holding all saved results [in] [out]
* @param return_stats Return statistics containing numbers of hits on
* different stages of the search [out]
*/
Int4
BLAST_DatabaseSearchEngine(Uint1 program_number,
BLAST_SequenceBlk* query, BlastQueryInfo* query_info,
const BlastSeqSrc* bssp, BlastScoreBlk* sbp,
const BlastScoringOptions* score_options,
LookupTableWrap* lookup_wrap,
const BlastInitialWordOptions* word_options,
const BlastExtensionOptions* ext_options,
const BlastHitSavingOptions* hit_options,
const BlastEffectiveLengthsOptions* eff_len_options,
const PSIBlastOptions* psi_options,
const BlastDatabaseOptions* db_options,
BlastResults* results, BlastReturnStat* return_stats);
/** The high level function performing BLAST comparison of two sequences,
* after all the setup has been done.
* @param program_number Type of BLAST program [in]
* @param query Query sequence [in]
* @param query_info Query information structure [in]
* @param subject Subject sequence [in]
* @param sbp Scoring and statistical parameters [in]
* @param score_options Hit scoring options [in]
* @param lookup_wrap The lookup table, constructed earlier [in]
* @param word_options Options for processing initial word hits [in]
* @param ext_options Options and parameters for the gapped extension [in]
* @param hit_options Options for saving the HSPs [in]
* @param eff_len_options Options for setting effective lengths [in]
* @param psi_options Options specific to PSI-BLAST [in]
* @param db_options Options for handling BLAST database [in]
* @param results Structure holding all saved results [in] [out]
* @param return_stats Return statistics containing numbers of hits on
* different stages of the search [out]
*/
Int4
BLAST_TwoSequencesEngine(Uint1 program_number,
BLAST_SequenceBlk* query, BlastQueryInfo* query_info,
BLAST_SequenceBlk* subject,
BlastScoreBlk* sbp, const BlastScoringOptions* score_options,
LookupTableWrap* lookup_wrap,
const BlastInitialWordOptions* word_options,
const BlastExtensionOptions* ext_options,
const BlastHitSavingOptions* hit_options,
const BlastEffectiveLengthsOptions* eff_len_options,
const PSIBlastOptions* psi_options,
const BlastDatabaseOptions* db_options,
BlastResults* results, BlastReturnStat* return_stats);
/** Function to calculate effective query length and db length as well as
* effective search space.
* @param program_number blastn, blastp, blastx, etc. [in]
* @param scoring_options options for scoring. [in]
* @param eff_len_options used to calc. effective lengths [in]
* @param sbp Karlin-Altschul parameters [out]
* @param query_info The query information block, which stores the effective
* search spaces for all queries [in] [out]
*/
Int2 BLAST_CalcEffLengths (Uint1 program_number,
const BlastScoringOptions* scoring_options,
const BlastEffectiveLengthsOptions* eff_len_options,
const BlastScoreBlk* sbp, BlastQueryInfo* query_info);
/** Gapped extension function pointer type */
typedef Int2 (*BlastGetGappedScoreType)
(Uint1, BLAST_SequenceBlk*, BLAST_SequenceBlk*,
BlastGapAlignStruct*, const BlastScoringOptions*,
BlastExtensionParameters*, BlastHitSavingParameters*,
BlastInitHitList*, BlastHSPList**);
/** Word finder function pointer type */
typedef Int4 (*BlastWordFinderType)
(BLAST_SequenceBlk*, BLAST_SequenceBlk*,
LookupTableWrap*, Int4**, BlastInitialWordParameters*,
BLAST_ExtendWord*, Uint4*, Uint4*, Int4, BlastInitHitList*);
/** Structure to be passed to BLAST_SearchEngineCore, containing pointers
to various preallocated structures and arrays. */
typedef struct BlastCoreAuxStruct {
BLAST_ExtendWord* ewp; /**< Structure for keeping track of diagonal
information for initial word matches */
BlastWordFinderType WordFinder; /**< Word finder function pointer */
BlastGetGappedScoreType GetGappedScore; /**< Gapped extension function
pointer */
BlastInitHitList* init_hitlist; /**< Placeholder for HSPs after
ungapped extension */
BlastHSPList* hsp_list; /**< Placeholder for HSPs after gapped
extension */
Uint4* query_offsets; /**< Placeholder for initial word match query
offsets */
Uint4* subject_offsets; /**< Placeholder for initial word match
subject offsets */
Uint1* translation_buffer; /**< Placeholder for translated subject
sequences */
Uint1* translation_table; /**< Translation table for forward strand */
Uint1* translation_table_rc; /**< Translation table for reverse
strand */
} BlastCoreAuxStruct;
#ifdef __cplusplus
}
#endif
#endif /* !__BLAST_ENGINE__ */
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