sequence_display.hpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: sequence_display.hpp,v $
- * PRODUCTION Revision 1000.1 2004/04/12 17:33:23 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.28
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: sequence_display.hpp,v 1000.1 2004/04/12 17:33:23 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:
- * Classes to hold rows in a sequence/alignment display
- *
- * ===========================================================================
- */
- #ifndef CN3D_SEQUENCE_DISPLAY__HPP
- #define CN3D_SEQUENCE_DISPLAY__HPP
- #include <corelib/ncbistd.hpp>
- #include <corelib/ncbistl.hpp>
- #include <map>
- #include "viewable_alignment.hpp"
- #include "block_multiple_alignment.hpp"
- #include "sequence_set.hpp"
- BEGIN_SCOPE(Cn3D)
- typedef std::map < BlockMultipleAlignment *, BlockMultipleAlignment * > Old2NewAlignmentMap;
- ////////////////////////////////////////////////////////////////////////////////
- // The sequence view is composed of rows which can be from sequence, alignment,
- // or any string - anything derived from DisplayRow.
- ////////////////////////////////////////////////////////////////////////////////
- class DisplayRow
- {
- public:
- virtual int Width(void) const = 0;
- virtual bool GetCharacterTraitsAt(int column, BlockMultipleAlignment::eUnalignedJustification justification,
- char *character, Vector *color, bool *drawBackground, Vector *cellBackgroundColor) const = 0;
- virtual bool GetSequenceAndIndexAt(int column, BlockMultipleAlignment::eUnalignedJustification justification,
- const Sequence **sequence, int *index) const = 0;
- virtual const Sequence * GetSequence(void) const = 0;
- virtual void SelectedRange(int from, int to,
- BlockMultipleAlignment::eUnalignedJustification justification, bool toggle) const = 0;
- virtual DisplayRow * Clone(const Old2NewAlignmentMap& newAlignments) const = 0;
- };
- class DisplayRowFromAlignment : public DisplayRow
- {
- public:
- int row;
- BlockMultipleAlignment * const alignment;
- DisplayRowFromAlignment(int r, BlockMultipleAlignment *a) :
- row(r), alignment(a) { }
- int Width(void) const { return alignment->AlignmentWidth(); }
- DisplayRow * Clone(const Old2NewAlignmentMap& newAlignments) const
- { return new DisplayRowFromAlignment(row, newAlignments.find(alignment)->second); }
- bool GetCharacterTraitsAt(int column, BlockMultipleAlignment::eUnalignedJustification justification,
- char *character, Vector *color, bool *drawBackground, Vector *cellBackgroundColor) const;
- bool GetSequenceAndIndexAt(int column, BlockMultipleAlignment::eUnalignedJustification justification,
- const Sequence **sequence, int *index) const
- {
- bool ignore;
- return alignment->GetSequenceAndIndexAt(column, row, justification, sequence, index, &ignore);
- }
- const Sequence * GetSequence(void) const
- {
- return alignment->GetSequenceOfRow(row);
- }
- void SelectedRange(int from, int to,
- BlockMultipleAlignment::eUnalignedJustification justification, bool toggle) const
- {
- alignment->SelectedRange(row, from, to, justification, toggle);
- }
- };
- class DisplayRowFromSequence : public DisplayRow
- {
- public:
- const Sequence * const sequence;
- const int fromIndex, toIndex;
- DisplayRowFromSequence(const Sequence *s, int from, int to);
- int Width(void) const { return toIndex - fromIndex + 1; }
- DisplayRow * Clone(const Old2NewAlignmentMap& newAlignments) const
- { return new DisplayRowFromSequence(sequence, fromIndex, toIndex); }
- bool GetCharacterTraitsAt(int column, BlockMultipleAlignment::eUnalignedJustification justification,
- char *character, Vector *color, bool *drawBackground, Vector *cellBackgroundColor) const;
- bool GetSequenceAndIndexAt(int column, BlockMultipleAlignment::eUnalignedJustification justification,
- const Sequence **sequenceHandle, int *index) const;
- const Sequence * GetSequence(void) const
- { return sequence; }
- void SelectedRange(int from, int to,
- BlockMultipleAlignment::eUnalignedJustification justification, bool toggle) const;
- };
- class DisplayRowFromString : public DisplayRow
- {
- public:
- const std::string title;
- std::string theString;
- const Vector stringColor, backgroundColor;
- const bool hasBackgroundColor;
- BlockMultipleAlignment * const alignment;
- DisplayRowFromString(const std::string& s, const Vector color = Vector(0,0,0.5),
- const std::string& t = "", bool hasBG = false, Vector bgColor = Vector(1,1,1),
- BlockMultipleAlignment *a = NULL) :
- theString(s), stringColor(color), title(t),
- hasBackgroundColor(hasBG), backgroundColor(bgColor), alignment(a) { }
- int Width(void) const { return theString.size(); }
- DisplayRow * Clone(const Old2NewAlignmentMap& newAlignments) const
- { return new DisplayRowFromString(
- theString, stringColor, title, hasBackgroundColor, backgroundColor,
- alignment ? newAlignments.find(alignment)->second : NULL); }
- bool GetCharacterTraitsAt(int column, BlockMultipleAlignment::eUnalignedJustification justification,
- char *character, Vector *color, bool *drawBackground, Vector *cellBackgroundColor) const;
- bool GetSequenceAndIndexAt(int column, BlockMultipleAlignment::eUnalignedJustification justification,
- const Sequence **sequenceHandle, int *index) const { return false; }
- const Sequence * GetSequence(void) const { return NULL; }
- void SelectedRange(int from, int to,
- BlockMultipleAlignment::eUnalignedJustification justification, bool toggle) const
- { } // do nothing
- };
- ////////////////////////////////////////////////////////////////////////////////
- // The SequenceDisplay is the structure that holds the DisplayRows of the view.
- // It's also derived from ViewableAlignment, in order to be plugged into a
- // SequenceViewerWidget.
- ////////////////////////////////////////////////////////////////////////////////
- class SequenceViewer;
- class UpdateViewer;
- class ViewerWindowBase;
- class Molecule;
- class SequenceDisplay : public ViewableAlignment
- {
- friend class SequenceViewer;
- friend class UpdateViewer;
- public:
- SequenceDisplay(bool editable, ViewerWindowBase* const *parentViewerWindow);
- ~SequenceDisplay(void);
- // these functions add a row to the end of the display, from various sources
- void AddRowFromAlignment(int row, BlockMultipleAlignment *fromAlignment);
- void AddRowFromSequence(const Sequence *sequence, int from, int to);
- void AddRowFromString(const std::string& anyString);
- // 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
- *
- */
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