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/**
* @author Mark Larkin, Conway Institute, UCD. mark.larkin@ucd.ie
* This widget contains an AlignmentWidget, HistogramWidget and a SeqNamesWidget.
* This is the main widget for displaying the alignment
*
* Changes:
*
* 16-01-07,Nigel Brown(EMBL): Added Q_MOS_MAC preprocessor checks for Mac OS
* X port, which uses AlignmentWidgetScroll in place of AlignmentWidget, and
* HistogramWidgetScroll in place of HistogramWidget. This is to work around a
* scrolling limitation in Qt4 QScrollArea. THESE CHANGES SHOULD BE REMOVED
* WHEN QT4 QSCROLLAREA IS FIXED! *
* Mark: Jan 16th 2007
* I have added an access function hasSeqNameWidgetFocus().
*
* 31-01-07,Nigel Brown(EMBL): added defaultFontSize member.
*
* 12-4-07, Mark Larkin : Changed destructor. We dont need to delete QObjects.
*
* 04-05-07,Nigel Brown(EMBL): renamed hasSeqNameWidgetFocus() to hasFocus().
*
* 27-06-07,Nigel Brown(EMBL): For screen layout balancing: added
* recvNumSequencesChanged() and balanceNumSequences() slots, and
* numSequencesChanged() signal.
*
* 20-7-07, Mark, I added in the resizeEvent and moveNamesScrollBarToRight function.
****************************************************************************/
#ifndef ALIGNMENTVIEWERWIDGET_H
#define ALIGNMENTVIEWERWIDGET_H
//AW not needed anymore #include "compile.h" //nige
#include <vector>
#include <string>
#include "clustalW/alignment/Alignment.h"
#include "AlignmentWidget.h"
#include "HistogramWidget.h"
#include "SeqNameWidget.h"
#include "ColorParameters.h"
#include "PostscriptFileParams.h"
class QFont;
class QScrollArea;
class QScrollBar;
class QGroupBox;
class QGridLayout;
class QVBoxLayout;
/**
* This class is an extension of the widget QMainWindow. It contains an
* alignment widget, a histogram widget and a sequence name widget.
* It is currently used as an alignment viewer, but it will be possible to extend its
* functionality to an alignment editor.
*/
class AlignmentViewerWidget : public QWidget
{
Q_OBJECT
public:
AlignmentViewerWidget(QWidget *parent = 0);
~AlignmentViewerWidget();
void setAlignmentView(clustalw::Alignment* alignPtr, int fSeq, int lSeq);
void updateView(int fSeq, int lSeq);
void updateView();
void updateHistogram(int fSeq, int lSeq);
void showExceptionalRes(bool show);
void showLowScoringSegments(bool show, clustalw::Array2D<int>* _lowScoreRes);
int getFirstSeq(){return firstSeq;}
int getLastSeq(){return lastSeq;}
int getLengthLongestSeqInRange();
QScrollBar* getAlignmentScrollBar();
void setColorScheme(ColorParameters* colors);
void setPrintoutColorScheme(ColorParameters colors);
void setBlackAndWhite();
void setBackGroundColoring(bool backgroundColor);
void clearSequenceSelection();
void clearRangeSelection();
void selectAllSequences();
bool outputColumnScores();
void saveSequences(QString inputFileName, int type);
int getNumberOfSeqsSelected();
const std::vector<int>* getSelectedRows();
void setProfileNum(int prfNum){profileNum = prfNum;}
void writeToPSFile(PostscriptFileParams postscriptParams);
bool seqsLoaded();
ColorParameters* getPtrToCurrentColorScheme()
{return alignWidget->getPtrToCurrentColorScheme();}
int getFirstSelectedCol(){return alignWidget->getFirstSelectedCol();}
int getSecondSelectedCol(){return alignWidget->getSecondSelectedCol();}
bool hasFocus(); //- nige
protected:
//void paintEvent(QPaintEvent *event);
void resizeEvent ( QResizeEvent * event );
/*
* slots are functions, they can be linked to signals
*/
public slots:
void updateFontAndBoxes(const QString& font);
void recvNumSequencesChanged(int count); //nige
signals:
void numSequencesChanged(int count); //nige
private:
void createGridBox();
void sendInfoToAlignWidget();
void sendInfoToNameWidget();
int makeGapPenaltyData();
int makeSecStructData();
void moveNamesScrollBarToRight();
int firstSeq;
int lastSeq;
QGroupBox *gridGroupBox;
QGridLayout *layoutGridBox;
/*
* Widgets to display the alignent and the histogram.
*/
AlignmentWidget *alignWidget;
QScrollArea *alignmentScroll;
HistogramWidget *histWidget;
QScrollArea *conservationScroll;
QScrollArea *namesScroll;
QVBoxLayout *mainlayout;
/*
* Widget to display the sequence names
*/
SeqNameWidget *seqNames;
int defaultFontSize; //nige
int defaultBoxSize;
int defaultBoxWidth;
int alignLength;
/*
* The main font for the application
*/
QFont* displayFont;
clustalw::Alignment* alignmentToDisplay;
std::vector<int> histogram; // vector of column heights
clustalw::Array2D<int>* exRes; // Exceptional residues.
clustalw::Array2D<int>* lowScoreRes; // low scoring residues.
int profileNum;
QString secStructData;
QString ssName;
int nHead;
};
#endif
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