cn3d_ba_interface.hpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: cn3d_ba_interface.hpp,v $
- * PRODUCTION Revision 1000.0 2003/10/29 18:30:23 gouriano
- * PRODUCTION PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.10
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: cn3d_ba_interface.hpp,v 1000.0 2003/10/29 18:30:23 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:
- * Interface to Alejandro's block alignment algorithm
- *
- * ===========================================================================
- */
- #ifndef CN3D_BA_INTERFACE__HPP
- #define CN3D_BA_INTERFACE__HPP
- #include <corelib/ncbistl.hpp>
- #include <list>
- class wxWindow;
- BEGIN_SCOPE(Cn3D)
- class BlockMultipleAlignment;
- class BlockAligner
- {
- public:
- BlockAligner(void);
- ~BlockAligner(void) { }
- 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.
- bool CreateNewPairwiseAlignmentsByBlockAlignment(BlockMultipleAlignment *multiple,
- const AlignmentList& toRealign, AlignmentList *newAlignments, int *nRowsAddedToMultiple,
- bool canMerge);
- // brings up a dialog that lets the user set block aligner ; returns false if cancelled
- bool SetOptions(wxWindow* parent);
- typedef struct {
- double loopPercentile;
- int loopExtension;
- int loopCutoff;
- bool globalAlignment;
- bool keepExistingBlocks;
- bool mergeAfterEachSequence;
- } BlockAlignerOptions;
- private:
- BlockAlignerOptions currentOptions;
- };
- END_SCOPE(Cn3D)
- #endif // CN3D_BA_INTERFACE__HPP
- /*
- * ---------------------------------------------------------------------------
- * $Log: cn3d_ba_interface.hpp,v $
- * Revision 1000.0 2003/10/29 18:30:23 gouriano
- * PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.10
- *
- * Revision 1.10 2003/08/23 22:26:23 thiessen
- * switch to new dp block aligner, remove Alejandro's
- *
- * Revision 1.9 2003/03/27 18:46:00 thiessen
- * update blockaligner code
- *
- * Revision 1.8 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 1.7 2002/09/30 17:13:02 thiessen
- * change structure import to do sequences as well; change cache to hold mimes; change block aligner vocabulary; fix block aligner dialog bugs
- *
- * Revision 1.6 2002/09/23 19:12:32 thiessen
- * add option to allow long gaps between frozen blocks
- *
- * Revision 1.5 2002/09/16 21:24:58 thiessen
- * add block freezing to block aligner
- *
- * Revision 1.4 2002/08/13 20:46:36 thiessen
- * add global block aligner
- *
- * Revision 1.3 2002/08/01 01:59:26 thiessen
- * fix type syntax error
- *
- * Revision 1.2 2002/08/01 01:55:16 thiessen
- * add block aligner options dialog
- *
- * Revision 1.1 2002/07/26 15:28:45 thiessen
- * add Alejandro's block alignment algorithm
- *
- */