sequence_viewer.hpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: sequence_viewer.hpp,v $
- * PRODUCTION Revision 1000.1 2004/04/12 17:33:35 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.33
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: sequence_viewer.hpp,v 1000.1 2004/04/12 17:33:35 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:
- * implementation of non-GUI part of main sequence/alignment viewer
- *
- * ===========================================================================
- */
- #ifndef CN3D_SEQUENCE_VIEWER__HPP
- #define CN3D_SEQUENCE_VIEWER__HPP
- #include <corelib/ncbistl.hpp>
- #include <list>
- #include "viewer_base.hpp"
- BEGIN_SCOPE(Cn3D)
- class Sequence;
- class AlignmentManager;
- class BlockMultipleAlignment;
- class SequenceViewerWindow;
- class SequenceDisplay;
- class SequenceViewer : public ViewerBase
- {
- friend class SequenceViewerWindow;
- friend class SequenceDisplay;
- friend class AlignmentManager;
- public:
- SequenceViewer(AlignmentManager *alnMgr);
- ~SequenceViewer(void);
- // to create displays from unaligned sequence(s), or multiple alignment
- typedef std::list < const Sequence * > SequenceList;
- void DisplaySequences(const SequenceList *sequenceList);
- void DisplayAlignment(BlockMultipleAlignment *multipleAlignment);
- // turn on the editor (if not already on)
- void TurnOnEditor(void);
- // functions to save edited data
- void SaveDialog(void);
- void SaveAlignment(void);
- // export current alignment
- enum eExportType {
- asFASTA, // plain FASTA with gaps and all uppercase
- asFASTAa2m, // a2m variant of FASTA, lowercase unaligned and '.' as unaligned gap
- asText, // plain text with id's and locations
- asHTML // HTML, like text but with color
- };
- void ExportAlignment(eExportType type);
- private:
- SequenceViewerWindow *sequenceWindow;
- void CreateSequenceWindow(bool showNow);
- };
- END_SCOPE(Cn3D)
- #endif // CN3D_SEQUENCE_VIEWER__HPP
- /*
- * ---------------------------------------------------------------------------
- * $Log: sequence_viewer.hpp,v $
- * Revision 1000.1 2004/04/12 17:33:35 gouriano
- * PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.33
- *
- * Revision 1.33 2004/02/19 17:05:08 thiessen
- * remove cn3d/ from include paths; add pragma to disable annoying msvc warning
- *
- * Revision 1.32 2003/10/13 14:16:31 thiessen
- * add -n option to not show alignment window
- *
- * Revision 1.31 2003/02/03 19:20:06 thiessen
- * format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros
- *
- * Revision 1.30 2002/12/06 17:07:15 thiessen
- * remove seqrow export format; add choice of repeat handling for FASTA export; export rows in display order
- *
- * Revision 1.29 2002/12/02 13:37:08 thiessen
- * add seqrow format export
- *
- * Revision 1.28 2002/09/09 13:38:23 thiessen
- * separate save and save-as
- *
- * Revision 1.27 2002/09/03 13:15:58 thiessen
- * add A2M export
- *
- * Revision 1.26 2002/06/05 14:28:40 thiessen
- * reorganize handling of window titles
- *
- * Revision 1.25 2002/04/22 14:27:28 thiessen
- * add alignment export
- *
- * Revision 1.24 2002/03/07 19:16:04 thiessen
- * don't auto-show sequence windows
- *
- * Revision 1.23 2001/12/06 23:13:45 thiessen
- * finish import/align new sequences into single-structure data; many small tweaks
- *
- * Revision 1.22 2001/10/01 16:03:58 thiessen
- * make CDD annotation window non-modal; add SetWindowTitle to viewers
- *
- * Revision 1.21 2001/04/05 22:54:51 thiessen
- * change bg color handling ; show geometry violations
- *
- * Revision 1.20 2001/04/04 00:27:22 thiessen
- * major update - add merging, threader GUI controls
- *
- * Revision 1.19 2001/03/19 15:47:37 thiessen
- * add row sorting by identifier
- *
- * Revision 1.18 2001/03/13 01:24:16 thiessen
- * working undo system for >1 alignment (e.g., update window)
- *
- * Revision 1.17 2001/03/09 15:48:43 thiessen
- * major changes to add initial update viewer
- *
- * Revision 1.16 2001/03/01 20:15:29 thiessen
- * major rearrangement of sequence viewer code into base and derived classes
- *
- */