mm_aligner.hpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: mm_aligner.hpp,v $
- * PRODUCTION Revision 1000.0 2003/10/29 19:22:14 gouriano
- * PRODUCTION PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.14
- * PRODUCTION
- * ===========================================================================
- */
- #ifndef ALGO___MM_ALIGNER__HPP
- #define ALGO___MM_ALIGNER__HPP
- /* $Id: mm_aligner.hpp,v 1000.0 2003/10/29 19:22:14 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: Yuri Kapustin
- *
- * File Description:
- * CMMAligner class definition
- *
- * CMMAligner encapsulates the Hirschberg's divide-and-conquer
- * algorithm (also credited to Myers and Miller) featuring
- * affine gap penalty model and running in linear space
- *
- * E.W. Myers and W. Miller
- * Optimal alignment in linear space
- * Comp. Appl. Biosciences, 4:11-17, 1988
- *
- */
- #include "nw_aligner.hpp"
- #include <list>
- #include <corelib/ncbithr.hpp>
- /** @addtogroup AlgoAlignMM
- *
- * @{
- */
- BEGIN_NCBI_SCOPE
- struct SCoordRect; // auxiliary structure, see below
- class NCBI_XALGOALIGN_EXPORT CMMAligner: public CNWAligner
- {
- public:
- CMMAligner();
- CMMAligner(const char* seq1, size_t len1,
- const char* seq2, size_t len2,
- const SNCBIPackedScoreMatrix* scoremat = 0);
- virtual ~CMMAligner() {}
- void EnableMultipleThreads(bool enable = true);
- protected:
- list<ETranscriptSymbol> m_TransList;
- bool m_mt; // multiple threads
- unsigned int m_maxthreads;
- virtual TScore x_Run();
-
- void x_DoSubmatrix(const SCoordRect& submatr,
- list<ETranscriptSymbol>::iterator translist_pos,
- bool left_top, bool right_bottom);
- void x_RunTop(const SCoordRect& rect,
- vector<TScore>& vE, vector<TScore>& vF, vector<TScore>& vG,
- vector<unsigned char>& trace, bool lt) const;
- void x_RunBtm(const SCoordRect& rect,
- vector<TScore>& vE, vector<TScore>& vF, vector<TScore>& vG,
- vector<unsigned char>& trace, bool rb) const;
- TScore x_RunTerm(const SCoordRect& rect,
- bool left_top, bool right_bottom,
- list<ETranscriptSymbol>& subpath);
-
- enum ETransitionType {
- eII = 0, eDI, eGI,
- eID, eDD, eGD,
- eIG, eDG, eGG
- };
- TScore x_FindBestJ( const vector<TScore>& vEtop,
- const vector<TScore>& vFtop,
- const vector<TScore>& vGtop,
- const vector<TScore>& vEbtm,
- const vector<TScore>& vFbtm,
- const vector<TScore>& vGbtm,
- size_t& pos,
- ETransitionType& trans_type ) const;
-
- size_t x_ExtendSubpath(vector<unsigned char>::const_iterator trace_it,
- bool direction,
- list<ETranscriptSymbol>& subpath) const;
- virtual bool x_CheckMemoryLimit();
- friend class CThreadRunOnTop;
- friend class CThreadDoSM;
- };
- // auxiliary structure
-
- struct NCBI_XALGOALIGN_EXPORT SCoordRect {
- size_t i1, j1, i2, j2;
- SCoordRect() {};
- SCoordRect(size_t l, size_t t, size_t r, size_t b):
- i1(l), j1(t), i2(r), j2(b) {}
- unsigned int GetArea() {
- return (i2 - i1 + 1)*(j2 - j1 + 1);
- }
- };
- END_NCBI_SCOPE
- /* @} */
- /*
- * ===========================================================================
- * $Log: mm_aligner.hpp,v $
- * Revision 1000.0 2003/10/29 19:22:14 gouriano
- * PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.14
- *
- * Revision 1.14 2003/09/30 19:49:32 kapustin
- * Make use of standard score matrix interface
- *
- * Revision 1.13 2003/09/26 14:43:01 kapustin
- * Remove exception specifications
- *
- * Revision 1.12 2003/09/02 22:29:19 kapustin
- * Add default constructor
- *
- * Revision 1.10 2003/06/17 17:20:28 kapustin
- * CNWAlignerException -> CAlgoAlignException
- *
- * Revision 1.9 2003/04/14 18:56:56 kapustin
- * Run() --> x_Run()
- *
- * Revision 1.8 2003/04/10 19:12:07 kapustin
- * Modify algorithm's description
- *
- * Revision 1.7 2003/04/10 19:04:28 siyan
- * Added doxygen support
- *
- * Revision 1.6 2003/03/18 15:11:22 kapustin
- * Declare virtual memory limit checking function
- *
- * Revision 1.5 2003/02/21 16:41:11 dicuccio
- * Added Win32 export specifier
- *
- * Revision 1.4 2003/01/28 12:34:53 kapustin
- * Move m_score to the base class
- *
- * Revision 1.3 2003/01/22 13:29:11 kapustin
- * CMMAligner: thread classes declared as friends
- *
- * Revision 1.2 2003/01/21 16:36:22 kapustin
- * Support multi-thread interface
- *
- * Revision 1.1 2003/01/21 12:33:10 kapustin
- * Initial revision
- *
- * ===========================================================================
- */
- #endif /* ALGO___MM_ALIGNER__HPP */
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