[med-svn] [bppphyview] 04/07: Import Upstream version 0.3.0
Andreas Tille
tille at debian.org
Wed Jun 14 11:49:21 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bppphyview.
commit e85adb0f7b5710587f502df51b9606864ccb032d
Author: Andreas Tille <tille at debian.org>
Date: Wed Jun 14 13:38:40 2017 +0200
Import Upstream version 0.3.0
---
AUTHORS.txt | 0
CMakeLists.txt | 65 +++-
COPYING.txt | 846 ++++++++++++++++++++++++++-----------------
ChangeLog | 5 +
NEWS | 0
README | 0
bppPhyView.spec | 59 ---
bppPhyView/PhyView.cpp | 19 +-
bppPhyView/PhyView.h | 1 +
bppPhyView/TreeSubWindow.cpp | 14 +-
bppphyview.spec | 124 +++++++
debian/changelog | 7 +
debian/control | 4 +-
debian/copyright | 8 +-
debian/rules | 12 +-
man/CMakeLists.txt | 2 +-
16 files changed, 728 insertions(+), 438 deletions(-)
diff --git a/AUTHORS.txt b/AUTHORS.txt
old mode 100755
new mode 100644
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 61b76e3..50c207c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -29,6 +29,18 @@ IF(NOT NO_DEP_CHECK)
FORCE)
ENDIF(NOT NO_DEP_CHECK)
+IF(NOT DOC_COMPRESS)
+ SET(DOC_COMPRESS gzip CACHE STRING
+ "Set program for compressing documentation."
+ FORCE)
+ENDIF(NOT DOC_COMPRESS)
+
+IF(NOT DOC_COMPRESS_EXT)
+ SET(DOC_COMPRESS_EXT gz CACHE STRING
+ "Set extension of compressed documentation."
+ FORCE)
+ENDIF(NOT DOC_COMPRESS_EXT)
+
IF(NO_DEP_CHECK)
MESSAGE("-- Dependencies checking disabled. Only distribution can be built.")
ELSE(NO_DEP_CHECK)
@@ -50,7 +62,23 @@ IF(NOT DEFINED MAN)
ENDIF(NOT DEFINED MAN)
#find executables for documentation
-FIND_PROGRAM(NROFF_EXE NAMES nroff)
+IF(MAN)
+ FIND_PROGRAM(NROFF_EXE NAMES nroff)
+ IF(NROFF_EXE)
+ MESSAGE("-- Found nroff here: ${NROFF_EXE}")
+ MESSAGE(" Adding targets: man")
+
+ ADD_CUSTOM_TARGET(man
+ ALL
+ COMMAND cp phyview.1.txt phyview.1
+ COMMAND ${DOC_COMPRESS} -f phyview.1
+ WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/man
+ )
+ SET_DIRECTORY_PROPERTIES(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES man/phyview.1.${DOC_COMPRESS_EXT})
+ ELSE()
+ MESSAGE(FATAL_ERROR "Program nroff required but not found.")
+ ENDIF()
+ENDIF(MAN)
#here is a useful function:
MACRO(IMPROVED_FIND_LIBRARY OUTPUT_LIBS lib_name include_to_find)
@@ -104,19 +132,6 @@ FIND_PACKAGE(Qt4 4.4.0 COMPONENTS QtCore QtGui REQUIRED)
INCLUDE(${QT_USE_FILE})
SET(LIBS ${LIBS} ${QT_LIBRARIES})
-IF(NROFF_EXE)
- MESSAGE("-- Found nroff here: ${NROFF_EXE}")
- MESSAGE(" Adding targets: man")
-
- ADD_CUSTOM_TARGET(man
- ALL
- COMMAND cp phyview.1.txt phyview.1
- COMMAND gzip -f phyview.1
- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/man
- )
- SET_DIRECTORY_PROPERTIES(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES man/phyview.1.gz)
-ENDIF(NROFF_EXE)
-
# Subdirectories
ADD_SUBDIRECTORY(bppPhyView)
ADD_SUBDIRECTORY(man)
@@ -126,10 +141,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "bppphyview")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "0.2.1")
+SET(CPACK_PACKAGE_VERSION "0.3.0")
SET(CPACK_PACKAGE_VERSION_MAJOR "0")
-SET(CPACK_PACKAGE_VERSION_MINOR "2")
-SET(CPACK_PACKAGE_VERSION_PATCH "1")
+SET(CPACK_PACKAGE_VERSION_MINOR "3")
+SET(CPACK_PACKAGE_VERSION_PATCH "0")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Phylogenetic Viewer")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
@@ -151,7 +166,7 @@ SET(CPACK_SOURCE_IGNORE_FILES
".*moc_.*"
"bppPhyView/\\\\..*"
"bppPhyView/phyview"
- "man/.*\\\\.1.gz"
+ "man/.*\\\\.1.${DOC_COMPRESS_EXT}"
"debian/tmp"
"debian/bppphyview/"
"debian/bppphyview\\\\.substvars"
@@ -171,6 +186,20 @@ INCLUDE(CPack)
#This adds the 'dist' target
ADD_CUSTOM_TARGET(dist COMMAND ${CMAKE_MAKE_PROGRAM} package_source)
+# 'clean' is not (yet) a first class target. However, we need to clean the directories before building the sources:
+IF("${CMAKE_GENERATOR}" MATCHES "Make")
+ ADD_CUSTOM_TARGET(make_clean
+ COMMAND ${CMAKE_MAKE_PROGRAM} clean
+ WORKING_DIRECTORY ${CMAKE_CURRENT_DIR}
+ )
+ ADD_DEPENDENCIES(dist make_clean)
+
+ ADD_CUSTOM_TARGET(make_clean_man
+ COMMAND rm -f *.${DOC_COMPRESS_EXT}
+ WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/man
+ )
+ ADD_DEPENDENCIES(dist make_clean_man)
+ENDIF()
IF(NOT NO_DEP_CHECK)
IF (UNIX)
diff --git a/COPYING.txt b/COPYING.txt
old mode 100755
new mode 100644
index d60c31a..d424827
--- a/COPYING.txt
+++ b/COPYING.txt
@@ -1,340 +1,506 @@
- GNU GENERAL PUBLIC LICENSE
- Version 2, June 1991
-
- Copyright (C) 1989, 1991 Free Software Foundation, Inc.
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+3.2 One copy of the Agreement, containing a notice relating to the
+characteristics of the Software, to the limited warranty, and to the
+fact that its use is restricted to experienced users has been provided
+to the Licensee prior to its acceptance as set forth in Article 3.1
+hereinabove, and the Licensee hereby acknowledges that it has read and
+understood it.
+
+
+ Article 4 - EFFECTIVE DATE AND TERM
+
+
+ 4.1 EFFECTIVE DATE
+
+The Agreement shall become effective on the date when it is accepted by
+the Licensee as set forth in Article 3.1.
+
+
+ 4.2 TERM
+
+The Agreement shall remain in force for the entire legal term of
+protection of the economic rights over the Software.
+
+
+ Article 5 - SCOPE OF RIGHTS GRANTED
+
+The Licensor hereby grants to the Licensee, who accepts, the following
+rights over the Software for any or all use, and for the term of the
+Agreement, on the basis of the terms and conditions set forth hereinafter.
+
+Besides, if the Licensor owns or comes to own one or more patents
+protecting all or part of the functions of the Software or of its
+components, the Licensor undertakes not to enforce the rights granted by
+these patents against successive Licensees using, exploiting or
+modifying the Software. If these patents are transferred, the Licensor
+undertakes to have the transferees subscribe to the obligations set
+forth in this paragraph.
+
+
+ 5.1 RIGHT OF USE
+
+The Licensee is authorized to use the Software, without any limitation
+as to its fields of application, with it being hereinafter specified
+that this comprises:
+
+ 1. permanent or temporary reproduction of all or part of the Software
+ by any or all means and in any or all form.
+
+ 2. loading, displaying, running, or storing the Software on any or
+ all medium.
+
+ 3. entitlement to observe, study or test its operation so as to
+ determine the ideas and principles behind any or all constituent
+ elements of said Software. This shall apply when the Licensee
+ carries out any or all loading, displaying, running, transmission
+ or storage operation as regards the Software, that it is entitled
+ to carry out hereunder.
+
+
+ 5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
+
+The right to make Contributions includes the right to translate, adapt,
+arrange, or make any or all modifications to the Software, and the right
+to reproduce the resulting software.
+
+The Licensee is authorized to make any or all Contributions to the
+Software provided that it includes an explicit notice that it is the
+author of said Contribution and indicates the date of the creation thereof.
+
+
+ 5.3 RIGHT OF DISTRIBUTION
+
+In particular, the right of distribution includes the right to publish,
+transmit and communicate the Software to the general public on any or
+all medium, and by any or all means, and the right to market, either in
+consideration of a fee, or free of charge, one or more copies of the
+Software by any means.
+
+The Licensee is further authorized to distribute copies of the modified
+or unmodified Software to third parties according to the terms and
+conditions set forth hereinafter.
+
+
+ 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
+
+The Licensee is authorized to distribute true copies of the Software in
+Source Code or Object Code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+ 1. a copy of the Agreement,
+
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+
+and that, in the event that only the Object Code of the Software is
+redistributed, the Licensee allows future Licensees unhindered access to
+the full Source Code of the Software by indicating how to access it, it
+being understood that the additional cost of acquiring the Source Code
+shall not exceed the cost of transferring the data.
+
+
+ 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
+
+When the Licensee makes a Contribution to the Software, the terms and
+conditions for the distribution of the resulting Modified Software
+become subject to all the provisions of this Agreement.
+
+The Licensee is authorized to distribute the Modified Software, in
+source code or object code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+ 1. a copy of the Agreement,
+
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+
+and that, in the event that only the object code of the Modified
+Software is redistributed, the Licensee allows future Licensees
+unhindered access to the full source code of the Modified Software by
+indicating how to access it, it being understood that the additional
+cost of acquiring the source code shall not exceed the cost of
+transferring the data.
+
+
+ 5.3.3 DISTRIBUTION OF EXTERNAL MODULES
+
+When the Licensee has developed an External Module, the terms and
+conditions of this Agreement do not apply to said External Module, that
+may be distributed under a separate license agreement.
+
+
+ 5.3.4 COMPATIBILITY WITH THE GNU GPL
+
+The Licensee can include a code that is subject to the provisions of one
+of the versions of the GNU GPL in the Modified or unmodified Software,
+and distribute that entire code under the terms of the same version of
+the GNU GPL.
+
+The Licensee can include the Modified or unmodified Software in a code
+that is subject to the provisions of one of the versions of the GNU GPL,
+and distribute that entire code under the terms of the same version of
+the GNU GPL.
+
+
+ Article 6 - INTELLECTUAL PROPERTY
+
+
+ 6.1 OVER THE INITIAL SOFTWARE
+
+The Holder owns the economic rights over the Initial Software. Any or
+all use of the Initial Software is subject to compliance with the terms
+and conditions under which the Holder has elected to distribute its work
+and no one shall be entitled to modify the terms and conditions for the
+distribution of said Initial Software.
+
+The Holder undertakes that the Initial Software will remain ruled at
+least by this Agreement, for the duration set forth in Article 4.2.
+
+
+ 6.2 OVER THE CONTRIBUTIONS
+
+The Licensee who develops a Contribution is the owner of the
+intellectual property rights over this Contribution as defined by
+applicable law.
+
+
+ 6.3 OVER THE EXTERNAL MODULES
+
+The Licensee who develops an External Module is the owner of the
+intellectual property rights over this External Module as defined by
+applicable law and is free to choose the type of agreement that shall
+govern its distribution.
+
+
+ 6.4 JOINT PROVISIONS
+
+The Licensee expressly undertakes:
+
+ 1. not to remove, or modify, in any manner, the intellectual property
+ notices attached to the Software;
+
+ 2. to reproduce said notices, in an identical manner, in the copies
+ of the Software modified or not.
+
+The Licensee undertakes not to directly or indirectly infringe the
+intellectual property rights of the Holder and/or Contributors on the
+Software and to take, where applicable, vis-à-vis its staff, any and all
+measures required to ensure respect of said intellectual property rights
+of the Holder and/or Contributors.
+
+
+ Article 7 - RELATED SERVICES
+
+7.1 Under no circumstances shall the Agreement oblige the Licensor to
+provide technical assistance or maintenance services for the Software.
+
+However, the Licensor is entitled to offer this type of services. The
+terms and conditions of such technical assistance, and/or such
+maintenance, shall be set forth in a separate instrument. Only the
+Licensor offering said maintenance and/or technical assistance services
+shall incur liability therefor.
+
+7.2 Similarly, any Licensor is entitled to offer to its licensees, under
+its sole responsibility, a warranty, that shall only be binding upon
+itself, for the redistribution of the Software and/or the Modified
+Software, under terms and conditions that it is free to decide. Said
+warranty, and the financial terms and conditions of its application,
+shall be subject of a separate instrument executed between the Licensor
+and the Licensee.
+
+
+ Article 8 - LIABILITY
+
+8.1 Subject to the provisions of Article 8.2, the Licensee shall be
+entitled to claim compensation for any direct loss it may have suffered
+from the Software as a result of a fault on the part of the relevant
+Licensor, subject to providing evidence thereof.
+
+8.2 The Licensor's liability is limited to the commitments made under
+this Agreement and shall not be incurred as a result of in particular:
+(i) loss due the Licensee's total or partial failure to fulfill its
+obligations, (ii) direct or consequential loss that is suffered by the
+Licensee due to the use or performance of the Software, and (iii) more
+generally, any consequential loss. In particular the Parties expressly
+agree that any or all pecuniary or business loss (i.e. loss of data,
+loss of profits, operating loss, loss of customers or orders,
+opportunity cost, any disturbance to business activities) or any or all
+legal proceedings instituted against the Licensee by a third party,
+shall constitute consequential loss and shall not provide entitlement to
+any or all compensation from the Licensor.
+
+
+ Article 9 - WARRANTY
+
+9.1 The Licensee acknowledges that the scientific and technical
+state-of-the-art when the Software was distributed did not enable all
+possible uses to be tested and verified, nor for the presence of
+possible defects to be detected. In this respect, the Licensee's
+attention has been drawn to the risks associated with loading, using,
+modifying and/or developing and reproducing the Software which are
+reserved for experienced users.
+
+The Licensee shall be responsible for verifying, by any or all means,
+the suitability of the product for its requirements, its good working
+order, and for ensuring that it shall not cause damage to either persons
+or properties.
+
+9.2 The Licensor hereby represents, in good faith, that it is entitled
+to grant all the rights over the Software (including in particular the
+rights set forth in Article 5).
+
+9.3 The Licensee acknowledges that the Software is supplied "as is" by
+the Licensor without any other express or tacit warranty, other than
+that provided for in Article 9.2 and, in particular, without any warranty
+as to its commercial value, its secured, safe, innovative or relevant
+nature.
+
+Specifically, the Licensor does not warrant that the Software is free
+from any error, that it will operate without interruption, that it will
+be compatible with the Licensee's own equipment and software
+configuration, nor that it will meet the Licensee's requirements.
+
+9.4 The Licensor does not either expressly or tacitly warrant that the
+Software does not infringe any third party intellectual property right
+relating to a patent, software or any other property right. Therefore,
+the Licensor disclaims any and all liability towards the Licensee
+arising out of any or all proceedings for infringement that may be
+instituted in respect of the use, modification and redistribution of the
+Software. Nevertheless, should such proceedings be instituted against
+the Licensee, the Licensor shall provide it with technical and legal
+assistance for its defense. Such technical and legal assistance shall be
+decided on a case-by-case basis between the relevant Licensor and the
+Licensee pursuant to a memorandum of understanding. The Licensor
+disclaims any and all liability as regards the Licensee's use of the
+name of the Software. No warranty is given as regards the existence of
+prior rights over the name of the Software or as regards the existence
+of a trademark.
+
+
+ Article 10 - TERMINATION
+
+10.1 In the event of a breach by the Licensee of its obligations
+hereunder, the Licensor may automatically terminate this Agreement
+thirty (30) days after notice has been sent to the Licensee and has
+remained ineffective.
+
+10.2 A Licensee whose Agreement is terminated shall no longer be
+authorized to use, modify or distribute the Software. However, any
+licenses that it may have granted prior to termination of the Agreement
+shall remain valid subject to their having been granted in compliance
+with the terms and conditions hereof.
+
+
+ Article 11 - MISCELLANEOUS
+
+
+ 11.1 EXCUSABLE EVENTS
+
+Neither Party shall be liable for any or all delay, or failure to
+perform the Agreement, that may be attributable to an event of force
+majeure, an act of God or an outside cause, such as defective
+functioning or interruptions of the electricity or telecommunications
+networks, network paralysis following a virus attack, intervention by
+government authorities, natural disasters, water damage, earthquakes,
+fire, explosions, strikes and labor unrest, war, etc.
+
+11.2 Any failure by either Party, on one or more occasions, to invoke
+one or more of the provisions hereof, shall under no circumstances be
+interpreted as being a waiver by the interested Party of its right to
+invoke said provision(s) subsequently.
+
+11.3 The Agreement cancels and replaces any or all previous agreements,
+whether written or oral, between the Parties and having the same
+purpose, and constitutes the entirety of the agreement between said
+Parties concerning said purpose. No supplement or modification to the
+terms and conditions hereof shall be effective as between the Parties
+unless it is made in writing and signed by their duly authorized
+representatives.
+
+11.4 In the event that one or more of the provisions hereof were to
+conflict with a current or future applicable act or legislative text,
+said act or legislative text shall prevail, and the Parties shall make
+the necessary amendments so as to comply with said act or legislative
+text. All other provisions shall remain effective. Similarly, invalidity
+of a provision of the Agreement, for any reason whatsoever, shall not
+cause the Agreement as a whole to be invalid.
+
+
+ 11.5 LANGUAGE
+
+The Agreement is drafted in both French and English and both versions
+are deemed authentic.
+
+
+ Article 12 - NEW VERSIONS OF THE AGREEMENT
+
+12.1 Any person is authorized to duplicate and distribute copies of this
+Agreement.
+
+12.2 So as to ensure coherence, the wording of this Agreement is
+protected and may only be modified by the authors of the License, who
+reserve the right to periodically publish updates or new versions of the
+Agreement, each with a separate number. These subsequent versions may
+address new issues encountered by Free Software.
+
+12.3 Any Software distributed under a given version of the Agreement may
+only be subsequently distributed under the same version of the Agreement
+or a subsequent version, subject to the provisions of Article 5.3.4.
+
+
+ Article 13 - GOVERNING LAW AND JURISDICTION
+
+13.1 The Agreement is governed by French law. The Parties agree to
+endeavor to seek an amicable solution to any disagreements or disputes
+that may arise during the performance of the Agreement.
+
+13.2 Failing an amicable solution within two (2) months as from their
+occurrence, and unless emergency proceedings are necessary, the
+disagreements or disputes shall be referred to the Paris Courts having
+jurisdiction, by the more diligent Party.
+
+
+Version 2.0 dated 2006-09-05.
+
diff --git a/ChangeLog b/ChangeLog
old mode 100755
new mode 100644
index bf64b02..5a4091b
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,8 @@
+08/03/12 -*- Version 0.3.0 -*-
+
+04/06/12 Julien Dutheil
+* Added option for header line in name translation.
+
09/02/12 -*- Version 0.2.1 -*-
11/06/11 -*- Version 0.2.0 -*-
diff --git a/NEWS b/NEWS
old mode 100755
new mode 100644
diff --git a/README b/README
old mode 100755
new mode 100644
diff --git a/bppPhyView.spec b/bppPhyView.spec
deleted file mode 100644
index b65eccf..0000000
--- a/bppPhyView.spec
+++ /dev/null
@@ -1,59 +0,0 @@
-%define name bppphyview
-%define version 0.2.1
-%define release 1
-%define _prefix /usr
-
-Summary: The Bio++ Phylogenetic Viewer.
-Name: %{name}
-Version: %{version}
-Release: %{release}
-Vendor: Julien Dutheil
-Source: http://download.gna.org/bppsuite/%{name}-%{version}.tar.gz
-License: CeCILL 2
-Group: System Environment/Libraries
-BuildRoot: %{_builddir}/%{name}-root
-Packager: Julien Dutheil
-Prefix: %{_prefix}
-AutoReq: yes
-AutoProv: yes
-
-%description
-Bio++ Phylogenetic Viewer, using the Qt library.
-
-%prep
-%setup -q
-
-%build
-CFLAGS="-I%{_prefix}/include $RPM_OPT_FLAGS"
-CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=%{_prefix}"
-if [ %{_lib} == 'lib64' ] ; then
- CMAKE_FLAGS="$CMAKE_FLAGS -DLIB_SUFFIX=64"
-fi
-cmake $CMAKE_FLAGS .
-make
-
-%install
-rm -rf $RPM_BUILD_ROOT
-make DESTDIR=$RPM_BUILD_ROOT install
-
-%clean
-rm -rf $RPM_BUILD_ROOT
-
-%post -p /sbin/ldconfig
-
-%postun -p /sbin/ldconfig
-
-%files
-%defattr(-,root,root)
-%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
-%{_prefix}/bin/phyview
-%{_prefix}/share/man/man1/phyview.1.gz
-
-%changelog
-* Thu Feb 09 2012 Julien Dutheil <julien.dutheil at univ-montp2.fr>
-- PhyView 0.2.1 release. Compatibility update.
-* Thu Jun 09 2011 Julien Dutheil <julien.dutheil at univ-montp2.fr>
-- PhyView 0.2.0 release
-* Mon Feb 28 2011 Julien Dutheil <julien.dutheil at univ-montp2.fr>
-- PhyView 0.1.0 release
-
diff --git a/bppPhyView/PhyView.cpp b/bppPhyView/PhyView.cpp
index 8a6e0b0..f251ae6 100644
--- a/bppPhyView/PhyView.cpp
+++ b/bppPhyView/PhyView.cpp
@@ -79,7 +79,9 @@ TranslateNameChooser::TranslateNameChooser(PhyView* phyview) :
fileFilters_ << "Coma separated columns (*.txt *.csv)"
<< "Tab separated columns (*.txt *.csv)";
fileDialog_->setNameFilters(fileFilters_);
-
+ hasHeader_ = new QCheckBox(tr("File has header line"));
+ QGridLayout *dlayout = dynamic_cast<QGridLayout*>(fileDialog_->layout());
+ dlayout->addWidget(hasHeader_, 4, 0);
QFormLayout* layout = new QFormLayout;
fromList_ = new QComboBox;
toList_ = new QComboBox;
@@ -102,13 +104,20 @@ void TranslateNameChooser::translateTree(TreeTemplate<Node>& tree)
if (fileDialog_->selectedNameFilter() == fileFilters_[1])
sep = "\t";
ifstream file(path[0].toStdString().c_str(), ios::in);
- DataTable* table = DataTable::read(file, sep);
+ DataTable* table = DataTable::read(file, sep, hasHeader_->isChecked());
//Clean button groups:
fromList_->clear();
toList_->clear();
//Now add the new ones:
+ if (!hasHeader_->isChecked()) {
+ vector<string> names;
+ for (unsigned int i = 0; i < table->getNumberOfColumns(); ++i) {
+ names.push_back("Col" + TextTools::toString(i + 1));
+ }
+ table->setColumnNames(names);
+ }
for (unsigned int i = 0; i < table->getNumberOfColumns(); ++i) {
fromList_->addItem(QtTools::toQt(table->getColumnName(i)));
toList_->addItem(QtTools::toQt(table->getColumnName(i)));
@@ -940,15 +949,15 @@ void PhyView::exit()
void PhyView::aboutBpp()
{
QMessageBox msgBox;
- msgBox.setText("Bio++ 2.0.1.");
- msgBox.setInformativeText("bpp-core 2.0.2\nbpp-seq 2.0.2.\nbpp-phyl 2.0.2.\nbpp-qt 2.0.1");
+ msgBox.setText("Bio++ 2.1.0.");
+ msgBox.setInformativeText("bpp-core 2.1.0\nbpp-seq 2.1.0.\nbpp-phyl 2.1.0.\nbpp-qt 2.1.0");
msgBox.exec();
}
void PhyView::about()
{
QMessageBox msgBox;
- msgBox.setText("This is Bio++ Phy View version 0.2.0.");
+ msgBox.setText("This is Bio++ Phy View version 0.3.0.");
msgBox.setInformativeText("Julien Dutheil <julien.dutheil at univ-montp2.fr>.");
msgBox.exec();
}
diff --git a/bppPhyView/PhyView.h b/bppPhyView/PhyView.h
index 75f926f..0e56e3d 100644
--- a/bppPhyView/PhyView.h
+++ b/bppPhyView/PhyView.h
@@ -100,6 +100,7 @@ class TranslateNameChooser :
QFileDialog* fileDialog_;
QStringList fileFilters_;
QComboBox* fromList_, * toList_;
+ QCheckBox* hasHeader_;
QPushButton* ok_, *cancel_;
public:
diff --git a/bppPhyView/TreeSubWindow.cpp b/bppPhyView/TreeSubWindow.cpp
index 7475cca..9b05399 100644
--- a/bppPhyView/TreeSubWindow.cpp
+++ b/bppPhyView/TreeSubWindow.cpp
@@ -111,16 +111,18 @@ void TreeSubWindow::updateTable()
labels.append(tr("Id"));
labels.append(tr("Name"));
labels.append(tr("Branch length"));
- for (unsigned int i = 0; i < nodeProperties.size(); ++i)
+ for (size_t i = 0; i < nodeProperties.size(); ++i)
labels.append(QtTools::toQt(nodeProperties[i]));
- for (unsigned int i = 0; i < branchProperties.size(); ++i)
+ for (size_t i = 0; i < branchProperties.size(); ++i)
labels.append(QtTools::toQt(branchProperties[i]));
nodeEditor_->setColumnCount(labels.size());
nodeEditor_->setHorizontalHeaderLabels(labels);
- for (unsigned int i = 0; i < nodes_.size(); ++i) {
+ for (size_t i = 0; i < nodes_.size(); ++i) {
QTableWidgetItem* idItem = new QTableWidgetItem(QtTools::toQt(TextTools::toString(nodes_[i]->getId())));
- idItem->setFlags(!Qt::ItemIsEditable);
+ Qt::ItemFlags flags = idItem->flags();
+ flags &= ~Qt::ItemIsEditable;
+ idItem->setFlags(flags);
nodeEditor_->setItem(i, 0, idItem);
QTableWidgetItem* nameItem = new QTableWidgetItem();
@@ -131,7 +133,7 @@ void TreeSubWindow::updateTable()
if (nodes_[i]->hasDistanceToFather()) brlenItem->setText(QtTools::toQt(TextTools::toString(nodes_[i]->getDistanceToFather())));
nodeEditor_->setItem(i, 2, brlenItem);
- for (unsigned int j = 0; j < nodeProperties.size(); ++j) {
+ for (size_t j = 0; j < nodeProperties.size(); ++j) {
QTableWidgetItem* item = 0;
if (nodes_[i]->hasNodeProperty(nodeProperties[j])) {
item = getTableWigetItem_(nodes_[i]->getNodeProperty(nodeProperties[j]));
@@ -141,7 +143,7 @@ void TreeSubWindow::updateTable()
nodeEditor_->setItem(i, 3 + j, item);
}
- for (unsigned int j = 0; j < branchProperties.size(); ++j) {
+ for (size_t j = 0; j < branchProperties.size(); ++j) {
QTableWidgetItem* item = 0;
if (nodes_[i]->hasBranchProperty(branchProperties[j])) {
item = getTableWigetItem_(nodes_[i]->getBranchProperty(branchProperties[j]));
diff --git a/bppphyview.spec b/bppphyview.spec
new file mode 100644
index 0000000..93058ce
--- /dev/null
+++ b/bppphyview.spec
@@ -0,0 +1,124 @@
+%define _basename bppphyview
+%define _version 0.3.0
+%define _release 1
+%define _prefix /usr
+
+URL: http://biopp.univ-montp2.fr/forge/bppphyview
+
+Name: %{_basename}
+Version: %{_version}
+Release: %{_release}
+License: CECILL-2.0
+Vendor: The Bio++ Project
+Source: http://biopp.univ-montp2.fr/repos/sources/%{_basename}-%{_version}.tar.gz
+Summary: Bio++ Phylogenetic Viewer
+Group: Productivity/Scientific/Other
+
+Requires: libbpp-phyl9 = 2.1.0
+Requires: libbpp-core2 = 2.1.0
+Requires: libbpp-qt1 = 2.1.0
+%if 0%{?fedora} || 0%{?rhel_version} || 0%{?centos_version}
+Requires: qt >= 4.6.0
+%endif
+%if 0%{?suse_version}
+Requires: libqt4 >= 4.6.0
+%endif
+%if 0%{?mdkversion}
+%ifarch x86_64
+Requires: lib64qtgui4 >= 4.6.0
+%else
+Requires: libqtgui4 >= 4.6.0
+%endif
+%endif
+
+BuildRoot: %{_builddir}/%{_basename}-root
+BuildRequires: cmake >= 2.6.0
+BuildRequires: gcc-c++ >= 4.0.0
+BuildRequires: groff
+BuildRequires: libbpp-core2 = 2.1.0
+BuildRequires: libbpp-core-devel = 2.1.0
+BuildRequires: libbpp-phyl9 = 2.1.0
+BuildRequires: libbpp-phyl-devel = 2.1.0
+BuildRequires: libbpp-qt1 = 2.1.0
+BuildRequires: libbpp-qt-devel = 2.1.0
+
+%if 0%{?fedora} || 0%{?rhel_version} || 0%{?centos_version}
+BuildRequires: qt >= 4.6.0
+BuildRequires: qt-devel >= 4.6.0
+%endif
+%if 0%{?suse_version}
+BuildRequires: libqt4 >= 4.6.0
+BuildRequires: libqt4-devel >= 4.6.0
+%endif
+%if 0%{?mdkversion}
+%ifarch x86_64
+BuildRequires: lib64qtgui4 >= 4.6.0
+BuildRequires: lib64qt4-devel >= 4.6.0
+%else
+BuildRequires: libqtgui4 >= 4.6.0
+BuildRequires: libqt4-devel >= 4.6.0
+%endif
+%endif
+
+AutoReq: yes
+AutoProv: yes
+%if 0%{?mdkversion}
+%if 0%{?mdkversion} >= 201100
+BuildRequires: xz
+%define zipext xz
+%else
+BuildRequires: lzma
+%define zipext lzma
+%endif
+%else
+BuildRequires: gzip
+%define zipext gz
+%endif
+
+%description
+Bio++ Phylogenetic Viewer, using the Qt library.
+
+%prep
+%setup -q
+
+%build
+CFLAGS="-I%{_prefix}/include $RPM_OPT_FLAGS"
+CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=%{_prefix}"
+if [ %{_lib} == 'lib64' ] ; then
+ CMAKE_FLAGS="$CMAKE_FLAGS -DLIB_SUFFIX=64"
+fi
+if [ %{zipext} == 'lzma' ] ; then
+ CMAKE_FLAGS="$CMAKE_FLAGS -DDOC_COMPRESS=lzma -DDOC_COMPRESS_EXT=lzma"
+fi
+if [ %{zipext} == 'xz' ] ; then
+ CMAKE_FLAGS="$CMAKE_FLAGS -DDOC_COMPRESS=xz -DDOC_COMPRESS_EXT=xz"
+fi
+
+cmake $CMAKE_FLAGS .
+make
+
+%install
+make DESTDIR=$RPM_BUILD_ROOT install
+
+%clean
+rm -rf $RPM_BUILD_ROOT
+
+%post -p /sbin/ldconfig
+
+%postun -p /sbin/ldconfig
+
+%files
+%defattr(-,root,root)
+%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
+%{_prefix}/bin/phyview
+%{_prefix}/share/man/man1/phyview.1.%{zipext}
+
+%changelog
+* Fri Mar 08 2013 Julien Dutheil <julien.dutheil at univ-montp2.fr> 0.3.0-1
+- Compatibility update.
+- New option for header line in names translation.
+* Thu Feb 09 2012 Julien Dutheil <julien.dutheil at univ-montp2.fr> 0.2.1-1
+- Compatibility update.
+* Thu Jun 09 2011 Julien Dutheil <julien.dutheil at univ-montp2.fr> 0.2.0-1
+* Mon Feb 28 2011 Julien Dutheil <julien.dutheil at univ-montp2.fr> 0.1.0-1
+
diff --git a/debian/changelog b/debian/changelog
index 299fa38..0b396cc 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+bppphyview (0.3.0-1) unstable; urgency=low
+
+ * Compatibility update.
+ * New option for header line in names translation.
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Fri, 08 Mar 2013 14:55:00 +0100
+
bppphyview (0.2.1-1) unstable; urgency=low
* Compatibility update.
diff --git a/debian/control b/debian/control
index bfa8962..0b721bb 100644
--- a/debian/control
+++ b/debian/control
@@ -5,13 +5,13 @@ Maintainer: Loic Dachary <loic at dachary.org>
Uploaders: Julien Dutheil <julien.dutheil at univ-montp2.fr>
Build-Depends: debhelper (>= 5), cmake (>= 2.6),
qt4-qmake (>= 4.6.0), libqt4-dev (>= 4.6.0),
- libbpp-qt-dev (>= 2.0.2)
+ libbpp-qt-dev (>= 2.1.0)
Standards-Version: 3.9.1
Package: bppphyview
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends},
- libbpp-qt1 (>= 2.0.2), libqtcore4 (>= 4.6.0), libqtgui4 (>= 4.6.0)
+ libbpp-qt1 (>= 2.1.0), libqtcore4 (>= 4.6.0), libqtgui4 (>= 4.6.0)
Description: Bio++ Phylogenetic Viewer
A phylogenetic tree editor developed using Bio++ and Qt.
diff --git a/debian/copyright b/debian/copyright
index c724823..5caf87f 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,15 +1,15 @@
This package was debianized by Julien Dutheil <julien.dutheil at univ-montp2.fr> on
-Mon, 28 Feb 2011 09:00:00 +0100.
+Fri, 08 Mar 2013 14:55:00 +0100
It was downloaded from <http://biopp.univ-montp2.fr/Repositories/sources>
-Upstream Author(s):
+Upstream Author:
Julien Dutheil <julien.dutheil at univ-montp2.fr>
Copyright:
- Copyright (C) 2011 Bio++ Development Team
+ Copyright (C) 2013 Bio++ Development Team
License:
@@ -27,7 +27,7 @@ License:
along with this package; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-The Debian packaging is (C) 2011, Julien Dutheil <julien.dutheil at univ-montp2.fr> and
+The Debian packaging is (C) 2013, Julien Dutheil <julien.dutheil at univ-montp2.fr> and
is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
The provided software is distributed under the CeCILL license:
diff --git a/debian/rules b/debian/rules
index 0cefd6d..453d4e1 100755
--- a/debian/rules
+++ b/debian/rules
@@ -64,16 +64,22 @@ clean:
# Add here commands to clean up after the build process.
[ ! -f Makefile ] || $(MAKE) clean;
[ ! -f Makefile ] || rm Makefile;
- [ ! -f Makefile ] || rm bppphyview/Makefile;
+ [ ! -f bppPhyView/Makefile ] || rm bppPhyView/Makefile;
+ [ ! -f man/Makefile ] || rm man/Makefile;
+ rm -f man/*.gz;
rm -f config.sub config.guess
rm -f build-stamp
rm -f CMakeCache.txt
rm -f *.cmake
- rm -f src/*.cmake
+ rm -f bppPhyView/*.cmake
#rm -f test/*.cmake
+ rm -f man/*.cmake
+ #rm -f doc/*.cmake
rm -rf CMakeFiles
- rm -rf src/CMakeFiles
+ rm -rf bppPhyView/CMakeFiles
#rm -rf test/CMakeFiles
+ rm -rf man/CMakeFiles
+ #rm -rf doc/CMakeFiles
rm -rf _CPack_Packages
#rm -rf Testing
#rm -f DartConfiguration.tcl
diff --git a/man/CMakeLists.txt b/man/CMakeLists.txt
index 4235389..bea4e00 100644
--- a/man/CMakeLists.txt
+++ b/man/CMakeLists.txt
@@ -3,5 +3,5 @@
# Created: 22/08/2009
IF(MAN)
- INSTALL(FILES phyview.1.gz DESTINATION share/man/man1)
+ INSTALL(FILES phyview.1.${DOC_COMPRESS_EXT} DESTINATION share/man/man1)
ENDIF(MAN)
--
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