[med-svn] [Git][med-team/bppphyview][upstream] New upstream version 0.6.0
Julien Y. Dutheil
gitlab at salsa.debian.org
Wed Apr 18 20:10:15 BST 2018
Julien Y. Dutheil pushed to branch upstream at Debian Med / bppphyview
Commits:
67019a0f by Julien Y. Dutheil at 2018-04-18T20:58:18+02:00
New upstream version 0.6.0
- - - - -
7 changed files:
- CMakeLists.txt
- ChangeLog
- bppPhyView/CMakeLists.txt
- bppPhyView/PhyView.cpp
- bppPhyView/PhyView.h
- bppPhyView/TreeCommands.h
- bppphyview.spec
Changes:
=====================================
CMakeLists.txt
=====================================
--- a/CMakeLists.txt
+++ b/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
=====================================
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,11 @@
+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
=====================================
--- a/bppPhyView/CMakeLists.txt
+++ b/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
=====================================
--- a/bppPhyView/PhyView.cpp
+++ b/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 at 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
=====================================
--- a/bppPhyView/PhyView.h
+++ b/bppPhyView/PhyView.h
@@ -369,6 +369,7 @@ class PhyView :
void computeLengthsGrafen();
void convertToClockTree();
void midpointRooting();
+ void deleteAllLengths();
void unresolveUncertainNodes();
void translateNames();
=====================================
bppPhyView/TreeCommands.h
=====================================
--- a/bppPhyView/TreeCommands.h
+++ b/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
=====================================
--- a/bppphyview.spec
+++ b/bppphyview.spec
@@ -1,62 +1,83 @@
-%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 at 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 at univ-montp2.fr> 0.5.1-1
- Compatibility update with Bio++ 2.3.1.
* Wed May 10 2017 Julien Dutheil <julien.dutheil at univ-montp2.fr> 0.5.0-1
View it on GitLab: https://salsa.debian.org/med-team/bppphyview/commit/67019a0facb1d0f4bb2da2a75a28e35f088fcdd3
---
View it on GitLab: https://salsa.debian.org/med-team/bppphyview/commit/67019a0facb1d0f4bb2da2a75a28e35f088fcdd3
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