cn3d_blast.hpp
上传用户:yhdzpy8989
上传日期:2007-06-13
资源大小:13604k
文件大小:4k
- /*
- * ===========================================================================
- * PRODUCTION $Log: cn3d_blast.hpp,v $
- * PRODUCTION Revision 1000.0 2003/10/29 18:30:40 gouriano
- * PRODUCTION PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.9
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: cn3d_blast.hpp,v 1000.0 2003/10/29 18:30:40 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.
- *
- * ===========================================================================
- *
- * Authors: Paul Thiessen
- *
- * File Description:
- * module for aligning with BLAST and related algorithms
- *
- * ===========================================================================
- */
- #ifndef CN3D_BLAST__HPP
- #define CN3D_BLAST__HPP
- #include <corelib/ncbistl.hpp>
- #include <list>
- BEGIN_SCOPE(Cn3D)
- class Sequence;
- class BlockMultipleAlignment;
- class BLASTer
- {
- public:
- BLASTer(void) { }
- ~BLASTer(void) { }
- static const std::string BLASTResidues;
- typedef std::list < BlockMultipleAlignment * > AlignmentList;
- // creates new pairwise alignments (as two-row BlockMultipleAlignments), each of which has
- // the given master and one of the given sequences. If the alignment algorithm fails to
- // align the new sequence, it will include a null-alignment for that sequence. If usePSSM is
- // true, will do BLAST/PSSM, otherwise, BlastTwoSequences. In both cases, alignment is restricted
- // to locations based on the multiple and alignTo/From values.
- void CreateNewPairwiseAlignmentsByBlast(const BlockMultipleAlignment *multiple,
- const AlignmentList& toRealign, AlignmentList *newAlignments, bool usePSSM);
- // calculate the self-hits for the given alignment - e.g., the score of each row when
- // aligned with the multiple using BLAST/PSSM. The scores will be placed in each row, -1.0
- // if no significant alignment is found.
- void CalculateSelfHitScores(const BlockMultipleAlignment *multiple);
- };
- // utility functions
- extern int LookupBLASTResidueNumberFromCharacter(char r);
- extern int LookupBLASTResidueNumberFromThreaderResidueNumber(char r);
- END_SCOPE(Cn3D)
- #endif // CN3D_BLAST__HPP
- /*
- * ---------------------------------------------------------------------------
- * $Log: cn3d_blast.hpp,v $
- * Revision 1000.0 2003/10/29 18:30:40 gouriano
- * PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.9
- *
- * Revision 1.9 2003/02/03 19:20:02 thiessen
- * format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros
- *
- * Revision 1.8 2003/01/22 14:47:30 thiessen
- * cache PSSM in BlockMultipleAlignment
- *
- * Revision 1.7 2002/08/01 12:51:36 thiessen
- * add E-value display to block aligner
- *
- * Revision 1.6 2002/06/13 13:32:39 thiessen
- * add self-hit calculation
- *
- * Revision 1.5 2002/05/22 17:17:09 thiessen
- * progress on BLAST interface ; change custom spin ctrl implementation
- *
- * Revision 1.4 2002/05/17 19:10:27 thiessen
- * preliminary range restriction for BLAST/PSSM
- *
- * Revision 1.3 2002/03/28 14:06:02 thiessen
- * preliminary BLAST/PSSM ; new CD startup style
- *
- * Revision 1.2 2001/09/27 15:36:47 thiessen
- * decouple sequence import and BLAST
- *
- * Revision 1.1 2001/09/18 03:09:38 thiessen
- * add preliminary sequence import pipeline
- *
- */