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#ifndef MAINWINDOWIMPL_H
#define MAINWINDOWIMPL_H
//
#include "ui_mainwindow.h"
#include "plotimpl.h"
#include "gelmanrubinimpl.h"
#include "paramcons.h"
#include "paramconsmult.h"
#include <QtSvg>
#include "outputfile.h"
#include "parammr.h"
#include "paramtreecons.h"
#include "colouredimpl.h"
#include "heatimpl.h"
#include "pdimpl.h"
#include "pheatimpl.h"
//
class MainWindowImpl : public QMainWindow, public Ui::MainWindow {
Q_OBJECT
public:
MainWindowImpl( QWidget * parent = 0, Qt::WFlags f = 0 );
virtual ~MainWindowImpl();
void openXMLFile(QStringList qstrs);
void doColourPlot(QStringList*nodes,QStringList*colors,bool denDep,bool colDep);
void on_actionExport_in_CSV_format_activated(QString qstr,int grmode=2);
void on_actionScore_against_true_tree_activated(QString qstr,QString dest);
void on_actionTest_convergence_of_trees_activated(QStringList files,QString dest);
void on_actionHeat_map_activated(int correctforprior,QString dest);
void on_actionPd_map_activated(int correctforprior,QString dest);
void on_actionPheat_map_activated(int correctforprior,QString dest,bool reldists=true);
void on_actionGelman_Rubin_test_activated(QStringList files,QString dest,int grmode=2);
void on_actionMajority_rule_consensus_of_trees_activated(int p,QString dest);
void on_actionExtended_consensus_of_trees_activated(QString dest);
void on_actionCombine_output_files_activated(QStringList files,QString dest);
void on_actionThinIterations_activated(QString outputfile,int thin);
void on_actionExtractIterations_activated(QString outputfile,int istart,int iend);
void jumpToSite(int site);
inline void setRecView(int i){param->setRecView(i);}
signals:
void wasDbClicked(int node,QMouseEvent * event);
private slots:
void computeAfterDbClick(int id,QMouseEvent * event);
void on_actionGelman_Rubin_test_activated();
void on_actionShowComment_activated();
void on_actionExit_activated();
void on_actionSave_picture_activated();
void on_actionReOpen_output_file_activated();
void on_actionOpen_output_file_activated();
void on_actionAbout_activated();
void on_menuPlot_triggered(QAction* action);
void on_menuVisualisation_triggered(QAction* action);
void on_actionCombine_output_files_activated();
void on_actionExtractIterations_activated();
void on_actionThinIterations_activated();
void on_actionCompute_prior_corrected_activated();
void on_actionExport_to_Artemis_activated();
void on_actionExport_CSV_activated();
void on_actionExport_movie_activated();
void on_actionJump_to_site_activated();
void on_actionSet_cutoff_activated();
void on_actionPrev_site_activated();
void on_actionNext_site_activated();
void on_actionAll_genes_activated();
void on_actionOnly_one_gene_activated();
void on_actionSave_movie_activated();
void on_actionToggleView_activated();
void on_actionShowCF_activated();
void on_actionDeparture_arrival_density_activated();
void on_actionMajority_rule_Consensus_activated();
void on_actionExport_as_Tracer_file_activated();
void on_actionSave_tree_to_Newick_file_activated();
void on_actionSave_trees_to_Nexus_file_activated();
void on_actionMajority_rule_Density_activated();
void on_actionRelative_Departure_Arrival_density_activated();
void on_actionColour_density_plot_activated();
void on_actionHeat_map_activated();
void on_actionPd_map_activated();
void on_actionPheat_map_activated();
void on_actionPheat_map_rel_activated();
void on_actionNameFormatm1_activated();
void on_actionNameFormat0_activated();
void on_actionNameFormat1_activated();
void on_actionNameFormat2_activated();
inline void on_actionMajority_rule_consensus_of_trees_activated(){
on_actionMajority_rule_consensus_of_trees_activated(-1,QString());
}
inline void on_actionExtended_consensus_of_trees_activated(){
on_actionExtended_consensus_of_trees_activated(QString());
}
inline void on_actionExport_in_CSV_format_activated(){
on_actionExport_in_CSV_format_activated(QString());
}
inline void on_actionScore_against_true_tree_activated(){
on_actionScore_against_true_tree_activated(QString(),QString());
}
inline void on_actionTest_convergence_of_trees_activated(){
on_actionTest_convergence_of_trees_activated(QStringList(),QString());
};
int doDeparture_arrival_density(ParamCons * paramcons,bool relative=false);
ParamTreeCons * newExtConsTree();///<returns a pointer to a new extended consensus tree
void computeExplorer(bool correct);
inline void checkDataLoaded(){
if(data==NULL) {QStringList qstrs = QFileDialog::getOpenFileNames(this, tr("Open data file"),".","XMFA files (*.xmfa);;All files (*)");
data=new Data(qstrs[0].toStdString()); // we have to keep reloading the data
WargXml infile(outputfilenames[0].toStdString());
data->subset(outputFile->getRegions(),-1);
param->setData(data);
}
}
protected:
QStringList outputfilenames;
ParamQt * param;
ParamQt * ioparam;
int explorerSite;
int explorerCutoff;
//QDomDocument * domDoc;
//QDomNodeList its;
OutputFile * outputFile;
Data * data;
//int currentIteration;
//int maxIteration;
void paintEvent(QPaintEvent*);
void loadIteration(bool startOver=false);
void mouseDoubleClickEvent ( QMouseEvent * event );
void displayStatus(QString str=tr(""));
};
#endif
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