db_traceback.hpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: db_traceback.hpp,v $
- * PRODUCTION Revision 1000.1 2004/06/01 18:03:00 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.5
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: db_traceback.hpp,v 1000.1 2004/06/01 18:03:00 gouriano 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 official 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.
- *
- * ===========================================================================
- *
- * Author: Ilya Dondoshansky
- *
- * File Description:
- * Class interface for performing BLAST traceback only, when preliminary
- * BLAST results have already been found.
- *
- */
- #ifndef ALGO_BLAST_API___DBTRACEBACK__HPP
- #define ALGO_BLAST_API___DBTRACEBACK__HPP
- #include <algo/blast/api/db_blast.hpp>
- #include <algo/blast/core/blast_gapalign.h>
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(blast)
- class NCBI_XBLAST_EXPORT CDbBlastTraceback : public CDbBlast
- {
- public:
- CDbBlastTraceback(const TSeqLocVector& queries, BlastSeqSrc* seq_src,
- EProgram p, BlastHSPResults* results);
- CDbBlastTraceback(const TSeqLocVector& queries, BlastSeqSrc* seq_src,
- CBlastOptionsHandle& opts, BlastHSPResults* results);
- void PartialRun();
- protected:
- int SetupSearch();
- void RunSearchEngine();
- void x_ResetQueryDs();
- private:
- BlastScoringParameters* m_ipScoringParams;
- BlastExtensionParameters* m_ipExtParams;
- BlastHitSavingParameters* m_ipHitParams;
- BlastEffectiveLengthsParameters* m_ipEffLenParams;
- BlastGapAlignStruct* m_ipGapAlign;
- };
- inline void CDbBlastTraceback::PartialRun()
- {
- // Don't need this method!
- }
- END_SCOPE(blast)
- END_NCBI_SCOPE
- /*
- * ===========================================================================
- *
- * $Log: db_traceback.hpp,v $
- * Revision 1000.1 2004/06/01 18:03:00 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.5
- *
- * Revision 1.5 2004/05/07 15:40:19 papadopo
- * add BlastScoringParameters private member
- *
- * Revision 1.4 2004/03/16 23:30:25 dondosha
- * Changed mi_ to m_i in member field names
- *
- * Revision 1.3 2004/03/09 18:41:31 dondosha
- * Added effective lengths parameters member
- *
- * Revision 1.2 2004/02/24 20:38:53 dondosha
- * Removed irrelevant CVS log comments
- *
- * Revision 1.1 2004/02/24 18:20:40 dondosha
- * Class derived from CDbBlast to do only traceback, given precomputed HSP results
- * ===========================================================================
- */
- #endif /* ALGO_BLAST_API___DBBLAST__HPP */