update_viewer.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: update_viewer.hpp,v $
 * PRODUCTION Revision 1000.1  2004/04/12 17:34:36  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.25
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: update_viewer.hpp,v 1000.1 2004/04/12 17:34:36 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 update viewer
*
* ===========================================================================
*/

#ifndef CN3D_UPDATE_VIEWER__HPP
#define CN3D_UPDATE_VIEWER__HPP

#include <corelib/ncbistl.hpp>

#include <objects/mmdb1/Biostruc.hpp>
#include <objects/mmdb3/Biostruc_feature.hpp>

#include <list>

#include "viewer_base.hpp"


BEGIN_SCOPE(Cn3D)

class UpdateViewerWindow;
class BlockMultipleAlignment;
class AlignmentManager;
class Sequence;
class StructureSet;

class UpdateViewer : public ViewerBase
{
    friend class UpdateViewerWindow;
    friend class SequenceDisplay;

public:

    UpdateViewer(AlignmentManager *alnMgr);
    ~UpdateViewer(void);

    void CreateUpdateWindow(void);  // (re)creates the window

    // add new pairwise alignments to the update window
    typedef std::list < BlockMultipleAlignment * > AlignmentList;
    void AddAlignments(const AlignmentList& alignmentList);

    // replace contents of update window with given alignments
    void ReplaceAlignments(const AlignmentList& alignmentList);

    // delete a single alignment
    void DeleteAlignment(BlockMultipleAlignment *toDelete);

    // import
    void ImportSequences(void);
    void ImportStructure(void);

    // turns the current alignments+display into the "initial state" (the bottom) of the undo stack
    void SetInitialState(void);

    // functions to save edited data
    void SaveDialog(bool prompt);
    void SaveAlignments(void);

    // run BLAST on given pairwise alignment - if BLAST is successful, then alignment will be
    // replaced with the result, otherwise the alignment is left unchanged
    void BlastUpdate(BlockMultipleAlignment *alignment, bool usePSSMFromMultiple);

    // find alignment of nearest BLAST-2-sequences neighbor in the multiple, and use this as
    // a guide alignment to align this update with the multiple's master
    void BlastNeighbor(BlockMultipleAlignment *update);

    // save pending structures
    void SavePendingStructures(void);

    // sort updates
    void SortByIdentifier(void);

private:
    UpdateViewerWindow *updateWindow;

    const Sequence * GetMasterSequence(void) const;
    typedef std::list < const Sequence * > SequenceList;
    void FetchSequencesViaHTTP(SequenceList *newSequences, StructureSet *sSet) const;
    void ReadSequencesFromFile(SequenceList *newSequences, StructureSet *sSet) const;
    void FetchSequences(StructureSet *sSet, SequenceList *newSequences) const;

    void SortUpdates(void);
    void MakeEmptyAlignments(const SequenceList& newSequences,
        const Sequence *master, AlignmentList *newAlignments) const;

    typedef std::list < ncbi::CRef < ncbi::objects::CBiostruc > > BiostrucList;
    BiostrucList pendingStructures;
    typedef struct {
        ncbi::CRef < ncbi::objects::CBiostruc_feature > structureAlignment;
        int masterDomainID, slaveDomainID;
    } StructureAlignmentInfo;
    typedef std::list < StructureAlignmentInfo > PendingStructureAlignments;
    PendingStructureAlignments pendingStructureAlignments;

    void GetVASTAlignments(const SequenceList& newSequences,
        const Sequence *master, AlignmentList *newAlignments,
		PendingStructureAlignments *structureAlignments,
        int masterFrom = -1, int masterTo = -1) const;  // -1 means unrestricted
};

END_SCOPE(Cn3D)

#endif // CN3D_UPDATE_VIEWER__HPP

/*
* ---------------------------------------------------------------------------
* $Log: update_viewer.hpp,v $
* Revision 1000.1  2004/04/12 17:34:36  gouriano
* PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.25
*
* Revision 1.25  2004/02/19 17:05:21  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.24  2003/03/14 19:48:51  thiessen
* allow multiple gi's in network sequence import dialog
*
* Revision 1.23  2003/02/03 19:20:08  thiessen
* format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros
*
* Revision 1.22  2003/01/23 20:03:05  thiessen
* add BLAST Neighbor algorithm
*
* Revision 1.21  2002/10/27 22:23:51  thiessen
* save structure alignments from vastalign.cgi imports
*
* Revision 1.20  2002/10/25 19:00:02  thiessen
* retrieve VAST alignment from vastalign.cgi on structure import
*
* Revision 1.19  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 1.18  2002/09/16 21:24:58  thiessen
* add block freezing to block aligner
*
* Revision 1.17  2002/09/09 13:38:23  thiessen
* separate save and save-as
*
* Revision 1.16  2002/08/13 20:46:37  thiessen
* add global block aligner
*
* Revision 1.15  2002/07/26 15:28:48  thiessen
* add Alejandro's block alignment algorithm
*
* Revision 1.14  2002/06/05 14:28:41  thiessen
* reorganize handling of window titles
*
* Revision 1.13  2002/03/28 14:06:02  thiessen
* preliminary BLAST/PSSM ; new CD startup style
*
* Revision 1.12  2002/02/13 14:53:30  thiessen
* add update sort
*
* Revision 1.11  2002/02/12 17:19:23  thiessen
* first working structure import
*
* Revision 1.10  2001/10/01 16:03:58  thiessen
* make CDD annotation window non-modal; add SetWindowTitle to viewers
*
* Revision 1.9  2001/09/27 15:36:48  thiessen
* decouple sequence import and BLAST
*
* Revision 1.8  2001/09/18 03:09:38  thiessen
* add preliminary sequence import pipeline
*
* Revision 1.7  2001/05/02 13:46:15  thiessen
* major revision of stuff relating to saving of updates; allow stored null-alignments
*
* Revision 1.6  2001/04/19 12:58:25  thiessen
* allow merge and delete of individual updates
*
* Revision 1.5  2001/04/05 22:54:51  thiessen
* change bg color handling ; show geometry violations
*
* Revision 1.4  2001/04/04 00:27:22  thiessen
* major update - add merging, threader GUI controls
*
* Revision 1.3  2001/03/22 00:32:36  thiessen
* initial threading working (PSSM only); free color storage in undo stack
*
* Revision 1.2  2001/03/13 01:24:16  thiessen
* working undo system for >1 alignment (e.g., update window)
*
* Revision 1.1  2001/03/09 15:48:44  thiessen
* major changes to add initial update viewer
*
*/