sequence_display.hpp

ncbi源码

/*
 * ===========================================================================
 * 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);