Comment: This patch is deactivated but do NOT delete it.
         It enables compilation of the package but needs more work which is explained in
            https://lists.debian.org/debian-mentors/2017/12/msg00025.html
Author: Andreas Tille <tille@debian.org>
Last-Update: Sat, 02 Dec 2017 17:06:16 +0100
Description: Migration from Qt4 to Qt5

--- a/gui/mainwindowimpl.cpp
+++ b/gui/mainwindowimpl.cpp
@@ -1,9 +1,11 @@
 #include "mainwindowimpl.h"
 #include <QDBusConnection>
 #include <QDBusMessage>
-
+#include <QtPrintSupport/QPrinter>
+#include <QMessageBox>
+#include <QFileDialog>
 //
-MainWindowImpl::MainWindowImpl( QWidget * parent, Qt::WFlags f):QMainWindow(parent, f) {
+MainWindowImpl::MainWindowImpl( QWidget * parent, Qt::WindowFlags f):QMainWindow(parent, f) {
   param=new ParamQt();
   outputFile=NULL;
   data=NULL;
@@ -313,8 +315,8 @@ void MainWindowImpl::on_actionExtractIte
 {
   //Select iterations to combine
 	 bool ok;
-  int istart = QInputDialog::getInteger(this, tr("Start Sample Number"),tr("Enter the mininum sample number:"), 0, 0, 2147483647, 1, &ok);
-  int iend = QInputDialog::getInteger(this, tr("End Sample Number"),tr("Enter the maximum sample number:"), 0, 0, 2147483647, 1, &ok);
+  int istart = QInputDialog::getInt(this, tr("Start Sample Number"),tr("Enter the mininum sample number:"), 0, 0, 2147483647, 1, &ok);
+  int iend = QInputDialog::getInt(this, tr("End Sample Number"),tr("Enter the maximum sample number:"), 0, 0, 2147483647, 1, &ok);
   QString qstr = QFileDialog::getSaveFileName(this, tr("Save output file"),".","XML files (*.xml);;All files (*)");
   on_actionExtractIterations_activated(qstr,istart,iend);
 }
@@ -344,7 +346,7 @@ void MainWindowImpl::on_actionThinIterat
 {
   //Select iterations to combine
 	 bool ok;
-  int thin = QInputDialog::getInteger(this, tr("Thin Amount"),tr("Enter the thinning step:"), 0, 0, 2147483647, 1, &ok);
+  int thin = QInputDialog::getInt(this, tr("Thin Amount"),tr("Enter the thinning step:"), 0, 0, 2147483647, 1, &ok);
   QString qstr = QFileDialog::getSaveFileName(this, tr("Save output file"),".","XML files (*.xml);;All files (*)");
   on_actionThinIterations_activated(qstr,thin);
 }
@@ -362,7 +364,7 @@ void MainWindowImpl::on_actionOnly_one_g
 	actionAll_genes->setChecked(false);
 	actionOnly_one_gene->setChecked(true);
 	 bool ok;
-     int i = QInputDialog::getInteger(this, tr("Pick a gene"),tr("Show events for gene number:"), 1, 1, param->getData()->getB(), 1, &ok);
+     int i = QInputDialog::getInt(this, tr("Pick a gene"),tr("Show events for gene number:"), 1, 1, param->getData()->getB(), 1, &ok);
      if (ok) param->setGene(i);
      repaint();
 }
@@ -532,7 +534,7 @@ void MainWindowImpl::on_actionMajority_r
 {
   if (outputFile==NULL) {QMessageBox::about(0,"Information","Need some data first.");return;}
   bool ok=true;
-  if(cutoff<0) cutoff=QInputDialog::getInteger(this,"Enter cutoff","Enter value of cutoff for majority-rule consensus:",95,0,100,1,&ok);
+  if(cutoff<0) cutoff=QInputDialog::getInt(this,"Enter cutoff","Enter value of cutoff for majority-rule consensus:",95,0,100,1,&ok);
   if (!ok || cutoff>100) return;
   ParamTreeCons * paramtreecons=new ParamTreeCons();
   paramtreecons->setBlocks(outputFile->getBlocks());
@@ -715,7 +717,7 @@ void MainWindowImpl::on_actionPd_map_act
   if (outputFile==NULL) {QMessageBox::about(0,"Information","Need some data first.");return;}
 
   bool ok;
-  int sitejump=QInputDialog::getInteger(this,"Site Sample Rate","Enter gap between evaluated sites:",1,1,10000,1,&ok);
+  int sitejump=QInputDialog::getInt(this,"Site Sample Rate","Enter gap between evaluated sites:",1,1,10000,1,&ok);
   if(!ok) return;
   if(!param->displaySet()) param->newDisplayTree(param->getTree());
   outputFile->startOver();
@@ -831,7 +833,7 @@ void MainWindowImpl::on_actionPrev_site_
 void MainWindowImpl::on_actionSet_cutoff_activated()
 {
   bool ok;
-  int cutoff=QInputDialog::getInteger(this,"Enter cutoff","Enter value of cutoff:",explorerCutoff,0,100,1,&ok);
+  int cutoff=QInputDialog::getInt(this,"Enter cutoff","Enter value of cutoff:",explorerCutoff,0,100,1,&ok);
   if (!ok) return;
   explorerCutoff=cutoff;
   ((ParamMR*)param)->consensus(explorerCutoff,explorerSite);
@@ -841,7 +843,7 @@ void MainWindowImpl::on_actionSet_cutoff
 void MainWindowImpl::on_actionJump_to_site_activated()
 {
   bool ok;
-  int site=QInputDialog::getInteger(this,"Enter site","Enter number of site:",explorerSite,0,param->getData()->getL()-1,1,&ok);
+  int site=QInputDialog::getInt(this,"Enter site","Enter number of site:",explorerSite,0,param->getData()->getL()-1,1,&ok);
   if (!ok) return;
   jumpToSite(site);
 }
@@ -858,7 +860,7 @@ void MainWindowImpl::on_actionExport_mov
 {
   QString qstr = QFileDialog::getSaveFileName(this, tr("Save movie file"),".",tr("WMV files (*.wmv);;AVI files (*.avi)"));
   if (qstr==NULL) return;
-  bool ok;int step=QInputDialog::getInteger(this,"Enter step","Enter value of step:",1,1,100000,1,&ok);if (!ok) return;
+  bool ok;int step=QInputDialog::getInt(this,"Enter step","Enter value of step:",1,1,100000,1,&ok);if (!ok) return;
   QImage image(width(),height(),QImage::Format_ARGB32);
   explorerSite=0;
   QString time=QTime::currentTime().toString();
@@ -887,7 +889,7 @@ void MainWindowImpl::on_actionExport_CSV
 {
   QString qstr = QFileDialog::getSaveFileName(this, tr("Export to CSV"),".","CSV index files (*.csv);;All files (*)");
   if (qstr==NULL) return;
-  bool ok;int step=QInputDialog::getInteger(this,"Enter step","Enter value of step:",1,1,100000,1,&ok);if (!ok) return;
+  bool ok;int step=QInputDialog::getInt(this,"Enter step","Enter value of step:",1,1,100000,1,&ok);if (!ok) return;
   QFile file(qstr);
   if ( !file.open(QIODevice::WriteOnly)) return;
   QTextStream out(&file);
--- a/gui/gui.pro
+++ b/gui/gui.pro
@@ -3,7 +3,9 @@ QT = gui \
  core \
  xml \
  svg \
- dbus
+ dbus \
+ printsupport \
+ widgets
 CONFIG += qt \
  warn_on \
  console \
--- a/gui/colouredimpl.cpp
+++ b/gui/colouredimpl.cpp
@@ -1,6 +1,6 @@
 #include "colouredimpl.h"
 //
-ColouredImpl::ColouredImpl( QWidget * parent, Qt::WFlags f) 
+ColouredImpl::ColouredImpl( QWidget * parent, Qt::WindowFlags f) 
 	: QDialog(parent, f)
 {
 	setAttribute(Qt::WA_DeleteOnClose);
--- a/gui/colouredimpl.h
+++ b/gui/colouredimpl.h
@@ -9,7 +9,7 @@ class ColouredImpl : public QDialog, pub
 {
 Q_OBJECT
 public:
-	ColouredImpl( QWidget * parent = 0, Qt::WFlags f = 0 );
+	ColouredImpl( QWidget * parent = 0, Qt::WindowFlags f = 0 );
 private:
     void closeEvent(QCloseEvent * event);
 private slots:
--- a/gui/gelmanrubinimpl.cpp
+++ b/gui/gelmanrubinimpl.cpp
@@ -1,6 +1,7 @@
 #include "gelmanrubinimpl.h"
+#include <QFileDialog>
 //
-GelmanRubinImpl::GelmanRubinImpl( QWidget * parent, Qt::WFlags f)
+GelmanRubinImpl::GelmanRubinImpl( QWidget * parent, Qt::WindowFlags f)
     : QDialog(parent, f) {
   setupUi(this);
   param=NULL;
--- a/gui/gelmanrubinimpl.h
+++ b/gui/gelmanrubinimpl.h
@@ -23,7 +23,7 @@ class GelmanRubinImpl : public QDialog,
 {
 Q_OBJECT
 public:
-	GelmanRubinImpl( QWidget * parent = 0, Qt::WFlags f = 0 );
+	GelmanRubinImpl( QWidget * parent = 0, Qt::WindowFlags f = 0 );
 	void compute(ParamQt*param,OutputFile*outputFile,QStringList*others, ostream* out=NULL,bool getparams=true,bool getnumedges=true,bool getpairwisedists=false);
 	void computeTree(ParamQt*,QStringList*,ostream* out=NULL);
 	void outputTracer(ParamQt*param,OutputFile*outputfile,QString*qstr,bool csv=false,bool getparams=true,bool getnumedges=true,bool getpairwisedists=false);
--- a/gui/heatimpl.cpp
+++ b/gui/heatimpl.cpp
@@ -1,6 +1,8 @@
 #include "heatimpl.h"
+#include <QtPrintSupport/QPrinter>
+#include <QFileDialog>
 //
-HeatImpl::HeatImpl(int n, QWidget * parent, Qt::WFlags f)
+HeatImpl::HeatImpl(int n, QWidget * parent, Qt::WindowFlags f)
     : QMainWindow(parent, f) {
   this->n=n;
   states=vector<vector<double> >(n,vector<double>(n,0.0));
--- a/gui/heatimpl.h
+++ b/gui/heatimpl.h
@@ -13,7 +13,7 @@ class HeatImpl : public QMainWindow, pub
 {
 Q_OBJECT
 public:
-	HeatImpl(int n, QWidget * parent = 0, Qt::WFlags f = 0 );
+	HeatImpl(int n, QWidget * parent = 0, Qt::WindowFlags f = 0 );
 	void account(ParamQt * p);
 	void compute();
 	void compute_correct(int mode);
--- a/gui/mainwindowimpl.h
+++ b/gui/mainwindowimpl.h
@@ -14,11 +14,12 @@
 #include "heatimpl.h"
 #include "pdimpl.h"
 #include "pheatimpl.h"
+#include <QFileDialog>
 //
 class MainWindowImpl : public QMainWindow, public Ui::MainWindow {
       Q_OBJECT
     public:
-      MainWindowImpl( QWidget * parent = 0, Qt::WFlags f = 0 );
+      MainWindowImpl( QWidget * parent = 0, Qt::WindowFlags f = 0 );
       virtual ~MainWindowImpl();
       void openXMLFile(QStringList qstrs);
       void doColourPlot(QStringList*nodes,QStringList*colors,bool denDep,bool colDep);
--- a/gui/pdimpl.cpp
+++ b/gui/pdimpl.cpp
@@ -1,6 +1,8 @@
 #include "pdimpl.h"
+#include <QtPrintSupport/QPrinter>
+#include <QFileDialog>
 //
-PdImpl::PdImpl(int n, int dist, QWidget * parent, Qt::WFlags f)
+PdImpl::PdImpl(int n, int dist, QWidget * parent, Qt::WindowFlags f)
     : QMainWindow(parent, f) {
   this->n=n;
   sitedist=dist;
--- a/gui/pdimpl.h
+++ b/gui/pdimpl.h
@@ -13,7 +13,7 @@ class PdImpl : public QMainWindow, publi
 {
 Q_OBJECT
 public:
-	PdImpl(int n, int dist=1, QWidget * parent = 0, Qt::WFlags f = 0 );
+	PdImpl(int n, int dist=1, QWidget * parent = 0, Qt::WindowFlags f = 0 );
 	void account(ParamQt * p);
 	void compute(int mode);
 	void print(ostream* f_out);
--- a/gui/pheatimpl.cpp
+++ b/gui/pheatimpl.cpp
@@ -1,6 +1,8 @@
 #include "pheatimpl.h"
+#include <QtPrintSupport/QPrinter>
+#include <QFileDialog>
 //
-PHeatImpl::PHeatImpl(int n, bool reldists, QWidget * parent, Qt::WFlags f)
+PHeatImpl::PHeatImpl(int n, bool reldists, QWidget * parent, Qt::WindowFlags f)
     : QMainWindow(parent, f) {
   this->n=n;
   this->reldists=reldists;
--- a/gui/pheatimpl.h
+++ b/gui/pheatimpl.h
@@ -13,7 +13,7 @@ class PHeatImpl : public QMainWindow, pu
 {
 Q_OBJECT
 public:
-	PHeatImpl(int n, bool reldists=true, QWidget * parent = 0, Qt::WFlags f = 0 );
+	PHeatImpl(int n, bool reldists=true, QWidget * parent = 0, Qt::WindowFlags f = 0 );
 	void account(ParamQt * p);
 	void compute(int mode);
 	void print(ostream* f_out);
--- a/gui/plotimpl.cpp
+++ b/gui/plotimpl.cpp
@@ -1,6 +1,8 @@
 #include "plotimpl.h"
+#include <QtPrintSupport/QPrinter>
+#include <QFileDialog>
 //
-PlotImpl::PlotImpl( QWidget * parent, Qt::WFlags f)
+PlotImpl::PlotImpl( QWidget * parent, Qt::WindowFlags f)
     : QDialog(parent, f) {
   mode=0;
   setupUi(this);
--- a/gui/plotimpl.h
+++ b/gui/plotimpl.h
@@ -14,7 +14,7 @@ using namespace std;
 class PlotImpl : public QDialog, public Ui::Plot {
       Q_OBJECT
     public:
-      PlotImpl( QWidget * parent = 0, Qt::WFlags f = 0 );
+      PlotImpl( QWidget * parent = 0, Qt::WindowFlags f = 0 );
       ~PlotImpl();
       //void extractValues(QDomDocument * domDoc,string str);
       //void extractStat(QDomDocument * domDoc,string str,int b=1,int L=1);
--- a/gui/paramcons.h
+++ b/gui/paramcons.h
@@ -1,5 +1,6 @@
 #ifndef PARAMCONS_H
 #define PARAMCONS_H
+#include <QMessageBox>
 //
 #include "paramqt.h"
 #include "densityontree.h"
--- a/gui/paramconsmult.h
+++ b/gui/paramconsmult.h
@@ -3,6 +3,7 @@
 //
 #include "paramqt.h"
 #include "densityontree.h"
+#include <QMessageBox>
 //
 class ParamConsMult  : public ParamQt
 {
--- a/gui/gui.cpp
+++ b/gui/gui.cpp
@@ -5,6 +5,7 @@
 #include "../warg/src/mpiutils.h"
 #include "mainapplicationdbusadaptor.h"
 #include <QDBusConnection>
+#include <getopt.h>
 
 bool verbose=false;