nw_spliced_aligner.hpp
上传用户:yhdzpy8989
上传日期:2007-06-13
资源大小:13604k
文件大小:5k
- /*
- * ===========================================================================
- * PRODUCTION $Log: nw_spliced_aligner.hpp,v $
- * PRODUCTION Revision 1000.2 2004/06/01 18:02:29 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.10
- * PRODUCTION
- * ===========================================================================
- */
- #ifndef ALGO_ALIGN___NW_SPLICED_ALIGNER__HPP
- #define ALGO_ALIGN___NW_SPLICED_ALIGNER__HPP
- /* $Id: nw_spliced_aligner.hpp,v 1000.2 2004/06/01 18:02:29 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:
- * Base class for spliced aligners.
- *
- */
- #include "nw_aligner.hpp"
- /** @addtogroup AlgoAlignSpliced
- *
- * @{
- */
- BEGIN_NCBI_SCOPE
- class NCBI_XALGOALIGN_EXPORT CSplicedAligner: public CNWAligner
- {
- public:
- // Setters and getters
- void SetWi(unsigned char splice_type, TScore value);
- TScore GetWi(unsigned char splice_type);
- void SetIntronMinSize(size_t s) {
- m_IntronMinSize = s;
- }
- size_t GetIntronMinSize(void) const {
- return m_IntronMinSize;
- }
- static size_t GetDefaultIntronMinSize (void) {
- return 30;
- }
- virtual size_t GetSpliceTypeCount(void) = 0;
- // A naive pattern generator-use cautiously.
- // Do not use on sequences with repeats or error.
- size_t MakePattern(const size_t hit_size = 30);
- protected:
- CSplicedAligner();
- CSplicedAligner( const char* seq1, size_t len1,
- const char* seq2, size_t len2);
- size_t m_IntronMinSize;
- virtual TScore* x_GetSpliceScores() = 0;
-
- // Guides
- unsigned char x_CalcFingerPrint64( const char* beg,
- const char* end,
- size_t& err_index );
- const char* x_FindFingerPrint64( const char* beg,
- const char* end,
- unsigned char fingerprint,
- size_t size,
- size_t& err_index );
- };
- END_NCBI_SCOPE
- /* @} */
- /*
- * ===========================================================================
- * $Log: nw_spliced_aligner.hpp,v $
- * Revision 1000.2 2004/06/01 18:02:29 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.10
- *
- * Revision 1.10 2004/04/23 14:39:22 kapustin
- * Add Splign librry and other changes
- *
- * Revision 1.6 2003/12/12 19:41:46 kapustin
- * Valuable comments added
- *
- * Revision 1.5 2003/10/27 20:56:50 kapustin
- * Move static GetDefaultWi to descendants
- *
- * Revision 1.4 2003/09/30 19:49:32 kapustin
- * Make use of standard score matrix interface
- *
- * Revision 1.3 2003/09/26 14:43:01 kapustin
- * Remove exception specifications
- *
- * Revision 1.2 2003/09/10 20:12:47 kapustin
- * Update Doxygen tags
- *
- * Revision 1.1 2003/09/02 22:27:44 kapustin
- * Initial revision
- *
- * ===========================================================================
- */
- #endif /* ALGO_ALIGN___SPLICED_ALIGNER__HPP */