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Sourcecode: bppphyview version File versions  Download package


// File: PhyView.h
// Created by: Julien Dutheil
// Created on: Tue Aug 05 14:59 2009

Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)

This software is a computer program whose purpose is to provide
graphic components to develop bioinformatics applications.

This software is governed by the CeCILL  license under French law and
abiding by the rules of distribution of free software.  You can  use, 
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL

As a counterpart to the access to the source code and  rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty  and the software's author,  the holder of the
economic rights,  and the successive licensors  have only  limited

In this respect, the user's attention is drawn to the risks associated
with loading,  using,  modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean  that it is complicated to manipulate,  and  that  also
therefore means  that it is reserved for developers  and  experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or 
data to be ensured and,  more generally, to use and operate it in the 
same conditions as regards security. 

The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.

#include "TreeSubWindow.h"
#include "TreeCommands.h"

//From Qt:
#include <QWidget>
#include <QPaintEvent>
#include <QMainWindow>
#include <QFileDialog>
#include <QMdiArea>
#include <QUndoGroup>
#include <QDialog>
#include <QListWidget>
#include <QRadioButton>
#include <QPrinter>
#include <QPrintDialog>

class QAction;
class QLabel;

#include <Bpp/Phyl/Graphics/TreeDrawing.h>
#include <Bpp/Phyl/Io/IoTreeFactory.h>
#include <Bpp/Qt/Tree/TreeCanvas.h>
#include <Bpp/Qt/Tree/TreeCanvasControlers.h>
#include <Bpp/Qt/Tree/TreeStatisticsBox.h>

using namespace bpp;

class PhyView;

00069 class MouseActionListener:
  public MouseAdapter
    PhyView* phyview_;
    QDialog* treeChooser_;
    QListWidget* treeList_;

    MouseActionListener(PhyView* phyview);

    MouseActionListener* clone() const { return new MouseActionListener(*this); }
    void mousePressEvent(QMouseEvent *event);

    bool isAutonomous() const { return false; }

    TreeTemplate<Node>* pickTree_();


00093 class TranslateNameChooser :
  public QDialog

    PhyView* phyview_;
    QFileDialog* fileDialog_;
    QStringList fileFilters_;
    QComboBox* fromList_, * toList_;
    QPushButton* ok_, *cancel_;

    TranslateNameChooser(PhyView* phyview);

      delete fileDialog_;

    void translateTree(TreeTemplate<Node>& tree);

00119 class DataLoader :
  public QDialog

    PhyView* phyview_;
    QRadioButton* idIndex_, * nameIndex_;
    QComboBox* indexCol_;
    QPushButton* ok_, * cancel_;

    DataLoader(PhyView* phyview);

    ~DataLoader() {}

    void load(const DataTable* data);

    void addProperties_(Node* node, const DataTable& data);

00144 class ImageExportDialog :
  public QDialog

    PhyView* phyview_;
    QLabel* path_;
    QSpinBox* width_, * height_;
    QCheckBox* transparent_, * keepAspectRatio_;
    QPushButton* ok_, * cancel_, * browse_;
    QFileDialog* imageFileDialog_;
    QStringList imageFileFilters_;

    ImageExportDialog(PhyView* phyview);

    ~ImageExportDialog() {}

    void process(QGraphicsScene* scene);

  public slots:
    void chosePath();


00174 class TypeNumberDialog :
  public QDialog

    QSpinBox* spinBox_;
    QPushButton* ok_, * cancel_;

    TypeNumberDialog(PhyView* phyview, const string& what, unsigned int min, unsigned int max);

    ~TypeNumberDialog() {}

    unsigned int getValue() const { return spinBox_->value(); }

00194 class PhyView :
  public QMainWindow,
  public TreeCanvasControlersListener

    QMenu* fileMenu_;
    QMenu* editMenu_;
    QMenu* viewMenu_;
    QMenu* helpMenu_;
    QAction* openAction_;
    QAction* saveAction_;
    QAction* saveAsAction_;
    QAction* closeAction_;
    QAction* printAction_;
    QAction* exportAction_;
    QAction* exitAction_;
    QAction* cascadeWinAction_;
    QAction* tileWinAction_;
    QAction* aboutAction_;
    QAction* aboutBppAction_;
    QAction* aboutQtAction_;
    QAction* undoAction_;
    QAction* redoAction_;

    QUndoGroup manager_;

    QMdiArea* mdiArea_;
    QFileDialog* treeFileDialog_;
    QStringList treeFileFilters_;
    QFileDialog* dataFileDialog_;
    QStringList dataFileFilters_;
    IOTreeFactory ioTreeFactory_;
    QPrinter* printer_;
    QPrintDialog* printDialog_;
    TreeCanvasControlers* treeControlers_;
    QWidget* displayPanel_;
    TreeStatisticsBox* statsBox_;
    QWidget* statsPanel_;
    QWidget* brlenPanel_;
    QWidget* mouseControlPanel_;
    QWidget* dataPanel_;
    QWidget* searchPanel_;

    QDockWidget* statsDockWidget_; 
    QDockWidget* displayDockWidget_;
    QDockWidget* undoDockWidget_;
    //Branch lengths operations:
    QDockWidget* brlenDockWidget_;
    QDoubleSpinBox* brlenSetLengths_;
    QDoubleSpinBox* brlenComputeGrafen_;

    //Mouse actions change:
    QDockWidget* mouseControlDockWidget_;
    QComboBox* leftButton_;
    QComboBox* middleButton_;
    QComboBox* rightButton_;

    //Data operations:
    QDockWidget* dataDockWidget_;
    QPushButton* translateNames_;
    QPushButton* loadData_;
    QPushButton* saveData_;
    QPushButton* addData_;
    QPushButton* removeData_;
    QPushButton* renameData_;
    QPushButton* duplicateDownSelection_;
    QPushButton* snapData_;

    QDockWidget* searchDockWidget_;
    QLineEdit*   searchText_;
    QListWidget* searchResults_;

    LabelCollapsedNodesTreeDrawingListener collapsedNodesListener_;

    TranslateNameChooser* translateNameChooser_;

    DataLoader* dataLoader_;

    ImageExportDialog* imageExportDialog_;

    QList<QGraphicsTextItem*> searchResultsItems_;


    bool hasActiveDocument() const
      return mdiArea_->currentSubWindow() != 0;

    TreeDocument* getActiveDocument()
      return dynamic_cast<TreeSubWindow*>(mdiArea_->currentSubWindow())->getDocument();

    QList<TreeDocument*> getNonActiveDocuments();

    TreeSubWindow* getActiveSubWindow()
      return dynamic_cast<TreeSubWindow*>(mdiArea_->currentSubWindow());

    void submitCommand(QUndoCommand* cmd)

    TreeDocument* createNewDocument(Tree* tree);

    MouseActionListener* getMouseActionListener()
      return new MouseActionListener(this);

    QString getMouseLeftButtonActionType() const { return leftButton_->currentText(); }
    QString getMouseMiddleButtonActionType() const { return middleButton_->currentText(); }
    QString getMouseRightButtonActionType() const { return rightButton_->currentText(); }

    void controlerTakesAction();
    void readTree(const QString& path, const string& format);

    void closeEvent(QCloseEvent* event);

  private slots:
    void openTree();
    bool saveTree();
    bool saveTreeAs();
    void closeTree();
    void exportTree();
    void printTree();
    void exit();
    void about();
    void aboutBpp();
    void updateStatusBar();
    void setCurrentSubWindow(TreeSubWindow* tsw);
    void setCurrentSubWindow(QMdiSubWindow *msw)
      TreeSubWindow* tsw = dynamic_cast<TreeSubWindow*>(msw);
      if (tsw) setCurrentSubWindow(tsw);

    void updateStatistics()
    void setLengths();
    void initLengthsGrafen();
    void computeLengthsGrafen();
    void convertToClockTree();
    void midpointRooting();
    void translateNames();

    void attachData();
    void saveData();
    void addData();
    void removeData();
    void renameData();
    void duplicateDownSelection();
    void snapData();
    void searchText();
    void searchResultSelected();

    void clearSearchResults() {

    void initGui_();
    void createActions_();
    void createMenus_();
    void createStatusBar_();

    void createStatsPanel_();
    void createDisplayPanel_();
    void createBrlenPanel_();
    void createMouseControlPanel_();
    void createDataPanel_();
    void createSearchPanel_();


int main(int argc, char *argv[]);

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