CMakeLists.txt

@@ -60,7 +60,8 @@ else ()
   # Generate command line args (always add -c to output compressed file to stdout)
   if (${COMPRESS_PROGRAM} STREQUAL "gzip")
     # -n for no timestamp in files (reproducible builds)
-    set (COMPRESS_ARGS -c -n)
+    # -9 for maximal compression (lintian warning)
+    set (COMPRESS_ARGS -c -9 -n)
   else ()
     set (COMPRESS_ARGS -c)
   endif ()
@@ -73,13 +74,15 @@ if (CMAKE_INSTALL_PREFIX)
 endif (CMAKE_INSTALL_PREFIX)
 
 include (GNUInstallDirs)
-find_package (bpp-qt 1.0.1 REQUIRED)
+find_package (bpp-qt 2.0.0 REQUIRED)
 
 # Find the Qt installation
-set (QT_USE_IMPORTED_TARGETS TRUE)
-find_package (Qt4 4.4.0 COMPONENTS QtCore QtGui REQUIRED)
-include (${QT_USE_FILE})
-set (qt-libs ${QT_QTCORE_LIBRARY} ${QT_QTGUI_LIBRARY})
+set(CMAKE_AUTOMOC ON)
+find_package (Qt5Widgets)
+find_package (Qt5Core)
+find_package (Qt5Gui)
+find_package (Qt5PrintSupport)
+set (qt-libs Qt5::Core Qt5::Gui Qt5::Widgets Qt5::PrintSupport)
 
 # Subdirectories
 add_subdirectory (bppPhyView)
@@ -90,10 +93,10 @@ ENDIF(NO_DEP_CHECK)
 # Packager
 SET(CPACK_PACKAGE_NAME "bppphyview")
 SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "0.5.1")
+SET(CPACK_PACKAGE_VERSION "0.6.0")
 SET(CPACK_PACKAGE_VERSION_MAJOR "0")
-SET(CPACK_PACKAGE_VERSION_MINOR "5")
-SET(CPACK_PACKAGE_VERSION_PATCH "1")
+SET(CPACK_PACKAGE_VERSION_MINOR "6")
+SET(CPACK_PACKAGE_VERSION_PATCH "0")
 SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Phylogenetic Viewer")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
 SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")

ChangeLog

+25/02/18 -*- Version 0.6.0 -*-
+
+27/12/17 Julien Dutheil
+* Added "removeAllLengths" command.
+
+13/09/17 Julien Dutheil
+* Ported to Qt5.
+
 10/05/17 -*- Version 0.5.0 -*-
 * Compatibility update with Bio++ 2.3.0.
 

bppPhyView/CMakeLists.txt

@@ -13,10 +13,9 @@ set (H_MOC_FILES
   PhyView.h
   TreeSubWindow.h
   )
-qt4_wrap_cpp (CPP_MOC_FILES ${H_MOC_FILES})
 
 # Phyview
-add_executable (phyview ${CPP_FILES} ${CPP_MOC_FILES})
+add_executable (phyview ${CPP_FILES} ${CPP_FILES})
 if (BUILD_STATIC)
   target_link_libraries (phyview ${BPP_LIBS_STATIC} ${qt-libs})
 else (BUILD_STATIC)

bppPhyView/PhyView.cpp

@@ -43,6 +43,18 @@ knowledge of the CeCILL license and that you accept its terms.
 
 #include <QApplication>
 #include <QtGui>
+#include <QVBoxLayout>
+#include <QFormLayout>
+#include <QPushButton>
+#include <QMessageBox>
+#include <QButtonGroup>
+#include <QDockWidget>
+#include <QUndoView>
+#include <QLineEdit>
+#include <QAction>
+#include <QMenuBar>
+#include <QInputDialog>
+#include <QGraphicsTextItem>
 
 #include <Bpp/Qt/QtGraphicDevice.h>
 
@@ -79,8 +91,9 @@ TranslateNameChooser::TranslateNameChooser(PhyView* phyview) :
   fileFilters_ << "Coma separated columns (*.txt *.csv)"
                << "Tab separated columns (*.txt *.csv)";
   fileDialog_->setNameFilters(fileFilters_);
+  fileDialog_->setOptions(QFileDialog::DontUseNativeDialog);
   hasHeader_ = new QCheckBox(tr("File has header line"));
-  QGridLayout *dlayout = dynamic_cast<QGridLayout*>(fileDialog_->layout());
+  QGridLayout *dlayout = dynamic_cast<QGridLayout*>(fileDialog_->layout()); //Check that here!!
   dlayout->addWidget(hasHeader_, 4, 0);
   QFormLayout* layout = new QFormLayout;
   fromList_ = new QComboBox;
@@ -555,6 +568,11 @@ void PhyView::createBrlenPanel_()
   
   brlenLayout->addWidget(brlenSetLengthsBox);
 
+  //Remove all branch lengths:
+  QPushButton* brlenRemoveAll = new QPushButton(tr("Remove all lengths"));
+  connect(brlenRemoveAll, SIGNAL(clicked(bool)), this, SLOT(deleteAllLengths()));
+  brlenLayout->addWidget(brlenRemoveAll);
+
   //Grafen method:
   QPushButton* brlenInitGrafen = new QPushButton(tr("Init"));
   connect(brlenInitGrafen, SIGNAL(clicked(bool)), this, SLOT(initLengthsGrafen()));
@@ -1020,15 +1038,15 @@ void PhyView::exit()
 void PhyView::aboutBpp()
 {
   QMessageBox msgBox;
-  msgBox.setText("Bio++ 2.3.0.");
-  msgBox.setInformativeText("bpp-core 2.3.0\nbpp-seq 2.3.0.\nbpp-phyl 2.3.0.\nbpp-qt 2.3.0");
+  msgBox.setText("Bio++ 2.4.0.");
+  msgBox.setInformativeText("bpp-core 2.4.0\nbpp-seq 2.4.0.\nbpp-phyl 2.4.0.\nbpp-qt 2.4.0");
   msgBox.exec();
 }
 
 void PhyView::about()
 {
   QMessageBox msgBox;
-  msgBox.setText("This is Bio++ Phylogenetic Viewer version 0.5.0.");
+  msgBox.setText("This is Bio++ Phylogenetic Viewer version 0.6.0.");
   msgBox.setInformativeText("Julien Dutheil <dutheil@evolbio.mpg.de>.");
   msgBox.exec();
 }
@@ -1071,6 +1089,13 @@ void PhyView::midpointRooting()
     }
 }
 
+void PhyView::deleteAllLengths()
+{
+  if (hasActiveDocument())
+    submitCommand(new DeleteLengthCommand(getActiveDocument()));
+}
+
+
 void PhyView::unresolveUncertainNodes()
 {
   if (hasActiveDocument()) {
@@ -1302,7 +1327,7 @@ int main(int argc, char *argv[])
   //Parse command line arguments:
   QStringList args = app.arguments();
   string format = IOTreeFactory::NEWICK_FORMAT;
-  QTextCodec* codec = QTextCodec::codecForLocale();
+  //QTextCodec* codec = QTextCodec::codecForLocale(); Not supported in Qt5...
   for (int i = 1; i < args.size(); ++i) {
     if (args[i] == "--nhx") {
       format = IOTreeFactory::NHX_FORMAT;
@@ -1310,18 +1335,17 @@ int main(int argc, char *argv[])
       format = IOTreeFactory::NEWICK_FORMAT;
     } else if (args[i] == "--newick") {
       format = IOTreeFactory::NEWICK_FORMAT;
-    } else if (args[i] == "--enc") {
-      if (i == args.size() - 1) {
-        cerr << "You must specify a text encoding after --enc tag." << endl;
-        exit(1);
-      }
-      ++i;
-      codec = QTextCodec::codecForName(args[i].toStdString().c_str());
+    //} else if (args[i] == "--enc") {
+    //  if (i == args.size() - 1) {
+    //    cerr << "You must specify a text encoding after --enc tag." << endl;
+    //    exit(1);
+    //  }
+    //  ++i;
+    //  codec = QTextCodec::codecForName(args[i].toStdString().c_str());
     } else {
       phyview->readTree(args[i], format);
     }
   }
-  QTextCodec::setCodecForCStrings(codec);
   return app.exec();
 }
 

bppPhyView/PhyView.h

@@ -369,6 +369,7 @@ class PhyView :
     void computeLengthsGrafen();
     void convertToClockTree();
     void midpointRooting();
+    void deleteAllLengths();
     void unresolveUncertainNodes();
     void translateNames();
 

bppPhyView/TreeCommands.h

@@ -45,7 +45,7 @@ knowledge of the CeCILL license and that you accept its terms.
 #include <Bpp/Text/TextTools.h>
 #include <Bpp/Numeric/DataTable.h>
 
-//From PhylLib:
+//From bpp-phyl:
 #include <Bpp/Phyl/TreeTools.h>
 
 //From Qt:
@@ -105,6 +105,17 @@ class SetLengthCommand: public AbstractCommand
     }
 };
 
+class DeleteLengthCommand: public AbstractCommand
+{
+  public:
+    DeleteLengthCommand(TreeDocument* doc):
+      AbstractCommand(QtTools::toQt("Delete all branch length."), doc)
+    {
+      new_ = new TreeTemplate<Node>(*old_);
+      TreeTemplateTools::deleteBranchLengths(*new_->getRootNode());
+    }
+};
+
 class InitGrafenCommand: public AbstractCommand
 {
   public:

bppphyview.spec

-%define _basename bppphyview
-%define _version 0.5.1
-%define _release 1
 %define _prefix /usr
 
-URL: http://biopp.univ-montp2.fr/forge/bppphyview
+URL: https://github.com/BioPP/bppphyview
 
-Name: %{_basename}
-Version: %{_version}
-Release: %{_release}
+Name: bppphyview
+Version: 0.6.0
+Release: 1%{?dist}
 License: CECILL-2.0
 Vendor: The Bio++ Project
-Source: http://biopp.univ-montp2.fr/repos/sources/%{_basename}-%{_version}.tar.gz
+Source: %{name}-%{version}.tar.gz
 Summary: Bio++ Phylogenetic Viewer
 Group: Productivity/Scientific/Other
 
-Requires: libbpp-phyl11 = 2.3.1
-Requires: libbpp-core3 = 2.3.1
-Requires: libbpp-qt1 = 2.3.1
-%if 0%{?fedora} || 0%{?rhel_version} || 0%{?centos_version}
-Requires: qt >= 4.6.0
+Requires: libbpp-phyl12 = 2.4.0
+Requires: libbpp-core4 = 2.4.0
+Requires: libbpp-qt2 = 2.4.0
+
+%if 0%{?fedora} || 0%{?rhel_version} || 0%{?centos_version} || 0%{?scientificlinux_version}
+Requires: libqt5core5 >= 5.0.0
+Requires: libqt5gui5 >= 5.0.0
+Requires: libqt5widgets5 >= 5.0.0
 %endif
 %if 0%{?suse_version}
-Requires: libqt4 >= 4.6.0
+Requires: libQt5Core5 >= 5.0.0
+Requires: libQt5Gui5 >= 5.0.0
+Requires: libQt5Widgets5 >= 5.0.0
 %endif
-%if 0%{?mdkversion}
+%if 0%{?mageia} || 0%{?mdkversion}
 %ifarch x86_64
-Requires: lib64qtgui4 >= 4.6.0
+Requires: lib64proxy-webkit >= 0.4.14
+Requires: lib64qt5core5 >= 5.0.0
+Requires: lib64qt5gui5 >= 5.0.0
+Requires: lib64qt5widgets5 >= 5.0.0
+Requires: qt5-qtdeclarative >= 5.0.0
+Requires: qt5-qtbase >= 5.0.0
 %else
-Requires: libqtgui4 >= 4.6.0
+Requires: libproxy-webkit >= 0.4.14
+Requires: libqt5core5 >= 5.0.0
+Requires: libqt5gui5 >= 5.0.0
+Requires: libqt5widgets5 >= 5.0.0
+Requires: qt5-qtdeclarative >= 5.0.0
+Requires: qt5-qtbase >= 5.0.0
 %endif
 %endif
 
-BuildRoot: %{_builddir}/%{_basename}-root
+BuildRoot: %{_builddir}/%{name}-root
 BuildRequires: cmake >= 2.8.11
 BuildRequires: gcc-c++ >= 4.7.0
 BuildRequires: groff
-BuildRequires: libbpp-core3 = 2.3.1
-BuildRequires: libbpp-core-devel = 2.3.1
-BuildRequires: libbpp-phyl11 = 2.3.1
-BuildRequires: libbpp-phyl-devel = 2.3.1
-BuildRequires: libbpp-qt1 = 2.3.1
-BuildRequires: libbpp-qt-devel = 2.3.1
-
-%if 0%{?fedora} || 0%{?rhel_version} || 0%{?centos_version}
-BuildRequires: qt >= 4.6.0
-BuildRequires: qt-devel >= 4.6.0
+BuildRequires: libbpp-core4 = 2.4.0
+BuildRequires: libbpp-core-devel = 2.4.0
+BuildRequires: libbpp-phyl12 = 2.4.0
+BuildRequires: libbpp-phyl-devel = 2.4.0
+BuildRequires: libbpp-qt2 = 2.4.0
+BuildRequires: libbpp-qt-devel = 2.4.0
+
+%if 0%{?fedora} || 0%{?rhel_version} || 0%{?centos_version} || 0%{?scientificlinux_version}
+BuildRequires: qt >= 5.0.0
+BuildRequires: qt-devel >= 5.0.0
 %endif
 %if 0%{?suse_version}
-BuildRequires: libqt4 >= 4.6.0
-BuildRequires: libqt4-devel >= 4.6.0
+BuildRequires: libQt5Core5 >= 5.0.0
+BuildRequires: libQt5Gui5 >= 5.0.0
+BuildRequires: libQt5Widgets5 >= 5.0.0
+BuildRequires: libqt5-qtdeclarative-devel >= 5.0.0
+BuildRequires: libqt5-qtbase-devel >= 5.0.0
 %endif
-%if 0%{?mdkversion}
+%if 0%{?mageia} || 0%{?mdkversion}
 %ifarch x86_64
-BuildRequires: lib64qtgui4 >= 4.6.0
-BuildRequires: lib64qt4-devel >= 4.6.0
+BuildRequires: lib64proxy-webkit >= 0.4.14
+BuildRequires: lib64qt5core5 >= 5.0.0
+BuildRequires: lib64qt5gui5 >= 5.0.0
+BuildRequires: lib64qt5widgets5 >= 5.0.0
+BuildRequires: lib64qt5base5-devel >= 5.0.0
 %else
-BuildRequires: libqtgui4 >= 4.6.0
-BuildRequires: libqt4-devel >= 4.6.0
+BuildRequires: libproxy-webkit >= 0.4.14
+BuildRequires: libqt5core5 >= 5.0.0
+BuildRequires: libqt5gui5 >= 5.0.0
+BuildRequires: libqt5widgets5 >= 5.0.0
+BuildRequires: libqt5base5-devel >= 5.0.0
 %endif
 %endif
 
@@ -72,7 +93,7 @@ BuildRequires: lzma
 %define compress_program lzma
 %endif
 %else
-%if 0%{?distribution:1} && "%{distribution}" == "Mageia"
+%if 0%{?mageia}
 BuildRequires: xz
 %define compress_program xz
 %else
@@ -111,6 +132,9 @@ rm -rf $RPM_BUILD_ROOT
 %{_prefix}/share/man/man1/phyview.1*
 
 %changelog
+* Mon Mar 12 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 0.6.0-1
+- Compatibility update with Bio++ 2.4.0.
+- More options in branch lengths panel.
 * Thu Jun 8 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 0.5.1-1
 - Compatibility update with Bio++ 2.3.1.
 * Wed May 10 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 0.5.0-1

debian/changelog

+bppphyview (0.6.0-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * Added full text of CeCILL license.
+  * Compiles with -DCMAKE_BUILD_TYPE=RelWithDebInfo to generate debug info
+  * Point Vcs-fields to salsa.debian.org
+  * Standards-Version: 4.1.4
+  * debhelper 11
+
+ -- Julien Dutheil <julien.dutheil@univ-montp2.fr>  Wed, 18 Apr 2018 21:03:35 +0200
+
 bppphyview (0.5.1-1) unstable; urgency=medium
 
   * New upstream version

debian/control

@@ -4,14 +4,14 @@ Uploaders: Julien Dutheil <julien.dutheil@univ-montp2.fr>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                cmake,
-               qt4-qmake,
-               libqt4-dev,
-               libbpp-qt-dev (>= 2.3.1)
-Standards-Version: 4.1.0
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bppphyview.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/bppphyview.git
+               qt5-qmake,
+               qtdeclarative5-dev,
+               libbpp-qt-dev (>= 2.4.0)
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/bppphyview.git
+Vcs-Git: https://salsa.debian.org/med-team/bppphyview.git
 Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
 
 Package: bppphyview

debian/rules

@@ -6,3 +6,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 %:
 	dh $@
+
+override_dh_auto_configure:
+	dh_auto_configure -- -DCMAKE_BUILD_TYPE=RelWithDebInfo
+