sequence_display.hpp

ncbi源码

    // adds a string row to the alignment, that contains block boundary indicators
    DisplayRowFromString * FindBlockBoundaryRow(const BlockMultipleAlignment *forAlignment) const;
    void UpdateBlockBoundaryRow(const BlockMultipleAlignment *forAlignment) const;
    void AddBlockBoundaryRow(BlockMultipleAlignment *forAlignment);  // adds to end of display!
    void AddBlockBoundaryRows(void);
    void RemoveBlockBoundaryRows(void);

    // returns a list of all sequences in the display (in order) for the given alignment
    typedef std::vector < const Sequence * > SequenceList;
    void GetSequences(const BlockMultipleAlignment *forAlignment, SequenceList *seqs) const;

    // returns a list of all protein sequences in the display (in order)
    void GetProteinSequences(SequenceList *seqs) const;

    // fills the vector with the current row ordering for the given alignment
    void GetRowOrder(const BlockMultipleAlignment *forAlignment, std::vector < int > *slaveRowOrder) const;

    // to inform the display that new rows have been added to or removed from the multiple
    void RowsAdded(int nRowsAddedToMultiple, BlockMultipleAlignment *multiple, int where = -1);
    void RowsRemoved(const std::vector < int >& rowsRemoved, const BlockMultipleAlignment *multiple);

    // row scoring and sorting functions - only for single-alignment displays!
    // sorting necessarily always leaves master at the top
    bool CalculateRowScoresWithThreader(double weightPSSM);
    void SortRowsByIdentifier(void);
    void SortRowsByThreadingScore(double weightPSSM);
    void SortRowsBySelfHit(void);
    void FloatPDBRowsToTop(void);
    void FloatHighlightsToTop(void);
    void FloatGVToTop(void);

    // a sort of clustering of similar sequences around a particular row
    bool ProximitySort(int displayRow);

    // create a new copy of this object
    SequenceDisplay * Clone(const Old2NewAlignmentMap& newAlignments) const;

    // clear out all rows from this display
    void Empty(void);

private:
    const bool isEditable;

    // generic row manipulation functions
    void AddRow(DisplayRow *row);
    BlockMultipleAlignment * GetAlignmentForRow(int row) const;
    void UpdateBlockBoundaryRow(DisplayRowFromString *blockBoundaryRow) const;

    ViewerWindowBase* const *viewerWindow;

    int startingColumn;
    typedef std::vector < DisplayRow * > RowVector;
    RowVector rows;

    int maxRowWidth;
    void UpdateMaxRowWidth(void);
    void UpdateAfterEdit(const BlockMultipleAlignment *forAlignment);

    bool shiftDown, controlDown;

    void SortRows(void);

public:

    int NRows(void) const { return rows.size(); }
    bool IsEditable(void) const { return isEditable; }
    const Sequence * GetSequenceForRow(int row) const
    {
        if (row >= 0 && row < NRows())
            return rows[row]->GetSequence();
        else
            return NULL;
    }

    // redraw all molecules associated with the SequenceDisplay
    void RedrawAlignedMolecules(void) const;

    // find coordinates of this residue in the display; returns false if not found
    bool GetDisplayCoordinates(const Molecule *molecule, int seqIndex,
        BlockMultipleAlignment::eUnalignedJustification justification, int *column, int *row);

    // column to scroll to when this display is first shown
    void SetStartingColumn(int column) { startingColumn = column; }
    int GetStartingColumn(void) const { return startingColumn; }

    // methods required by ViewableAlignment base class
    void GetSize(int *setColumns, int *setRows) const
        { *setColumns = maxRowWidth; *setRows = rows.size(); }
    bool GetRowTitle(int row, wxString *title, wxColour *color) const;
    bool GetCharacterTraitsAt(int column, int row,              // location
        char *character,										// character to draw
        wxColour *color,                                        // color of this character
        bool *drawBackground,                                   // special background color?
        wxColour *cellBackgroundColor
    ) const;

    // callbacks for ViewableAlignment
    void MouseOver(int column, int row) const;
    bool MouseDown(int column, int row, unsigned int controls);
    void SelectedRectangle(int columnLeft, int rowTop, int columnRight, int rowBottom);
    void DraggedCell(int columnFrom, int rowFrom, int columnTo, int rowTo);
};

END_SCOPE(Cn3D)

#endif // CN3D_SEQUENCE_DISPLAY__HPP

/*
* ---------------------------------------------------------------------------
* $Log: sequence_display.hpp,v $
* Revision 1000.1  2004/04/12 17:33:23  gouriano
* PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.28
*
* Revision 1.28  2004/02/19 17:05:06  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.27  2003/10/20 13:17:15  thiessen
* add float geometry violations sorting
*
* Revision 1.26  2003/02/03 19:20:05  thiessen
* format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros
*
* Revision 1.25  2003/01/29 01:41:06  thiessen
* add merge neighbor instead of merge near highlight
*
* Revision 1.24  2002/09/05 18:38:57  thiessen
* add sort by highlights
*
* Revision 1.23  2002/06/13 14:54:07  thiessen
* add sort by self-hit
*
* Revision 1.22  2002/04/26 19:01:00  thiessen
* fix display delete bug
*
* Revision 1.21  2002/02/28 19:11:52  thiessen
* wrap sequences in single-structure mode
*
* Revision 1.20  2002/02/05 18:53:25  thiessen
* scroll to residue in sequence windows when selected in structure window
*
* Revision 1.19  2001/11/27 16:26:09  thiessen
* major update to data management system
*
* Revision 1.18  2001/07/23 20:08:38  thiessen
* add regex pattern search
*
* Revision 1.17  2001/07/10 16:39:34  thiessen
* change selection control keys; add CDD name/notes dialogs
*
* Revision 1.16  2001/06/21 02:01:07  thiessen
* major update to molecule identification and highlighting ; add toggle highlight (via alt)
*
* Revision 1.15  2001/06/15 14:52:30  thiessen
* fix minor syntax errors
*
* Revision 1.14  2001/06/04 14:33:54  thiessen
* add proximity sort; highlight sequence on browser launch
*
* Revision 1.13  2001/06/01 18:07:38  thiessen
* fix display clone bug
*
* Revision 1.12  2001/06/01 14:04:54  thiessen
* add float PDB sort
*
* Revision 1.11  2001/05/11 02:10:04  thiessen
* add better merge fail indicators; tweaks to windowing/taskbar
*
* Revision 1.10  2001/05/03 14:38:32  thiessen
* put ViewableAlignment in its own (non-wx) header
*
* Revision 1.9  2001/04/04 00:27:21  thiessen
* major update - add merging, threader GUI controls
*
* Revision 1.8  2001/03/30 14:43:11  thiessen
* show threader scores in status line; misc UI tweaks
*
* Revision 1.7  2001/03/30 03:07:08  thiessen
* add threader score calculation & sorting
*
* Revision 1.6  2001/03/22 00:32:36  thiessen
* initial threading working (PSSM only); free color storage in undo stack
*
* Revision 1.5  2001/03/19 15:47:37  thiessen
* add row sorting by identifier
*
* Revision 1.4  2001/03/13 01:24:15  thiessen
* working undo system for >1 alignment (e.g., update window)
*
* Revision 1.3  2001/03/09 15:48:43  thiessen
* major changes to add initial update viewer
*
* Revision 1.2  2001/03/06 20:20:43  thiessen
* progress towards >1 alignment in a SequenceDisplay ; misc minor fixes
*
* Revision 1.1  2001/03/01 20:15:29  thiessen
* major rearrangement of sequence viewer code into base and derived classes
*
*/