sequence_viewer.hpp

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/*  $Id: sequence_viewer.hpp 64773 2014-10-08 13:59:20Z thiessen $
* ===========================================================================
*
*                            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);
 
    // put in a new alignment (undoable)
    bool ReplaceAlignment(const BlockMultipleAlignment *origAln, BlockMultipleAlignment *newAln);
 
    // functions to save edited data
    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
        asPSSM      // asn PssmWithParameters
    };
    void ExportAlignment(eExportType type);
 
private:
 
    SequenceViewerWindow *sequenceWindow;
 
    void CreateSequenceWindow(bool showNow);
};
 
END_SCOPE(Cn3D)
 
#endif // CN3D_SEQUENCE_VIEWER__HPP