New upstream version 0.6.0 (67019a0f) · Commits · Debian Med / bppphyview

CMakeLists.txt

+12 −9

Original line number	Diff line number	Diff line
		@@ -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

+8 −0

Original line number	Diff line number	Diff line
		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

+1 −2

Original line number	Diff line number	Diff line
		@@ -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

+37 −13

Original line number	Diff line number	Diff line
		@@ -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

+1 −0

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