[med-svn] [libbpp-qt] 01/06: Imported Upstream version 2.1.0
Andreas Tille
tille at debian.org
Sat Apr 23 17:49:16 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libbpp-qt.
commit fedbf4db98e37334f45ac396cf5dad1121df71ea
Author: Andreas Tille <tille at debian.org>
Date: Sat Apr 23 19:43:16 2016 +0200
Imported Upstream version 2.1.0
---
AUTHORS.txt | 0
CMakeLists.txt | 186 +++
COPYING.txt | 674 +++++++++++
ChangeLog | 19 +
Doxyfile | 1890 ++++++++++++++++++++++++++++++
INSTALL.txt | 12 +
NEWS | 0
bpp-qt.spec | 236 ++++
debian/changelog | 25 +
debian/compat | 1 +
debian/control | 28 +
debian/copyright | 66 ++
debian/docs | 0
debian/libbpp-qt-dev.install | 3 +
debian/libbpp-qt1.install | 1 +
debian/postinst | 43 +
debian/postrm | 45 +
debian/prerm | 27 +
debian/rules | 119 ++
debian/source/format | 1 +
src/Bpp/Qt/MouseListener.h | 155 +++
src/Bpp/Qt/MouseListeningWidget.h | 92 ++
src/Bpp/Qt/QtGraphicDevice.cpp | 160 +++
src/Bpp/Qt/QtGraphicDevice.h | 118 ++
src/Bpp/Qt/QtOutputStream.cpp | 58 +
src/Bpp/Qt/QtOutputStream.h | 123 ++
src/Bpp/Qt/QtTools.h | 113 ++
src/Bpp/Qt/Tree/TreeCanvas.cpp | 150 +++
src/Bpp/Qt/Tree/TreeCanvas.h | 212 ++++
src/Bpp/Qt/Tree/TreeCanvasControlers.cpp | 254 ++++
src/Bpp/Qt/Tree/TreeCanvasControlers.h | 200 ++++
src/Bpp/Qt/Tree/TreeStatisticsBox.cpp | 76 ++
src/Bpp/Qt/Tree/TreeStatisticsBox.h | 83 ++
src/CMakeLists.txt | 53 +
34 files changed, 5223 insertions(+)
diff --git a/AUTHORS.txt b/AUTHORS.txt
new file mode 100644
index 0000000..e69de29
diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000..5699949
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,186 @@
+# CMake script for Bio++ Qt
+# Author: Julien Dutheil
+# Created: 22/08/2009
+
+# Global parameters
+CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
+PROJECT(bpp-qt CXX C)
+IF(NOT CMAKE_BUILD_TYPE)
+ SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING
+ "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel."
+ FORCE)
+ENDIF(NOT CMAKE_BUILD_TYPE)
+
+SET(CMAKE_CXX_FLAGS "-Wall")
+IF(NOT NO_VIRTUAL_COV)
+ SET(NO_VIRTUAL_COV FALSE CACHE BOOL
+ "Disable covariant return type with virtual inheritance, for compilers that do not support it."
+ FORCE)
+ENDIF(NOT NO_VIRTUAL_COV)
+
+IF(NO_VIRTUAL_COV)
+ MESSAGE("-- Covariant return with virtual inheritance disabled.")
+ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DNO_VIRTUAL_COV=1")
+ENDIF(NO_VIRTUAL_COV)
+
+IF(NOT NO_DEP_CHECK)
+ SET(NO_DEP_CHECK FALSE CACHE BOOL
+ "Disable dependencies check for building distribution only."
+ FORCE)
+ENDIF(NOT NO_DEP_CHECK)
+
+IF(NO_DEP_CHECK)
+ MESSAGE("-- Dependencies checking disabled. Only distribution can be built.")
+ELSE(NO_DEP_CHECK)
+
+# Libtool-like version number
+# CURRENT:REVISION:AGE => file.so.(C-A).A.R
+# current: The most recent interface number that this library implements.
+# revision: The implementation number of the current interface.
+# age: The difference between the newest and oldest interfaces that this
+# library implements.
+# In other words, the library implements all the interface numbers in the
+# range from number current - age to current.
+SET(BPPQT_VERSION_CURRENT "1")
+SET(BPPQT_VERSION_REVISION "1")
+SET(BPPQT_VERSION_AGE "0")
+
+# Effective version number computation
+MATH(EXPR BPPQT_VERSION_MAJOR "${BPPQT_VERSION_CURRENT} - ${BPPQT_VERSION_AGE}")
+SET(BPPQT_VERSION_MINOR ${BPPQT_VERSION_AGE})
+SET(BPPQT_VERSION_PATCH ${BPPQT_VERSION_REVISION})
+SET(BPPQT_VERSION "${BPPQT_VERSION_MAJOR}.${BPPQT_VERSION_MINOR}.${BPPQT_VERSION_PATCH}")
+
+# Set the CMAKE_PREFIX_PATH for the find_library fonction when using non
+# standard install location
+IF(CMAKE_INSTALL_PREFIX)
+ SET(CMAKE_PREFIX_PATH "${CMAKE_INSTALL_PREFIX}" ${CMAKE_PREFIX_PATH})
+ENDIF(CMAKE_INSTALL_PREFIX)
+
+#here is a useful function:
+MACRO(IMPROVED_FIND_LIBRARY OUTPUT_LIBS lib_name include_to_find)
+ #start:
+ FIND_PATH(${lib_name}_INCLUDE_DIR ${include_to_find})
+ SET(${lib_name}_NAMES ${lib_name} ${lib_name}lib ${lib_name}dll)
+ FIND_LIBRARY(${lib_name}_LIBRARY NAMES ${${lib_name}_NAMES} PATH_SUFFIXES lib${LIB_SUFFIX})
+
+ IF(${lib_name}_LIBRARY)
+ MESSAGE("-- Library ${lib_name} found here:")
+ MESSAGE(" includes : ${${lib_name}_INCLUDE_DIR}")
+ MESSAGE(" libraries: ${${lib_name}_LIBRARY}")
+ ELSE(${lib_name}_LIBRARY)
+ MESSAGE(FATAL_ERROR "${lib_name} required but not found.")
+ ENDIF(${lib_name}_LIBRARY)
+
+ #add the dependency:
+ INCLUDE_DIRECTORIES(${${lib_name}_INCLUDE_DIR})
+ SET(${OUTPUT_LIBS} ${${OUTPUT_LIBS}} ${${lib_name}_LIBRARY})
+ENDMACRO(IMPROVED_FIND_LIBRARY)
+
+#Find the Bio++ libraries:
+IMPROVED_FIND_LIBRARY(LIBS bpp-phyl Bpp/Phyl/Tree.h)
+IMPROVED_FIND_LIBRARY(LIBS bpp-seq Bpp/Seq/Alphabet/Alphabet.h)
+IMPROVED_FIND_LIBRARY(LIBS bpp-core Bpp/Clonable.h)
+
+# Find the Qt installation
+FIND_PACKAGE(Qt4 REQUIRED)
+INCLUDE(${QT_USE_FILE})
+SET(LIBS ${LIBS} ${QT_LIBRARIES})
+
+# Subdirectories
+ADD_SUBDIRECTORY(src)
+
+# Doxygen
+FIND_PACKAGE(Doxygen)
+IF (DOXYGEN_FOUND)
+ ADD_CUSTOM_TARGET (apidoc cp Doxyfile ${CMAKE_BINARY_DIR}/Doxyfile-build
+ COMMAND echo "OUTPUT_DIRECTORY=${CMAKE_BINARY_DIR}" >> ${CMAKE_BINARY_DIR}/Doxyfile-build
+ COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/Doxyfile-build
+ WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
+ ADD_CUSTOM_TARGET (apidoc-stable cp Doxyfile ${CMAKE_BINARY_DIR}/Doxyfile-stable
+ COMMAND echo "OUTPUT_DIRECTORY=${CMAKE_BINARY_DIR}" >> ${CMAKE_BINARY_DIR}/Doxyfile-stable
+ COMMAND echo "HTML_HEADER=header.html" >> ${CMAKE_BINARY_DIR}/Doxyfile-stable
+ COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/Doxyfile-stable
+ WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
+ENDIF (DOXYGEN_FOUND)
+
+ENDIF(NO_DEP_CHECK)
+
+# Packager
+SET(CPACK_PACKAGE_NAME "libbpp-qt")
+SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
+SET(CPACK_PACKAGE_VERSION "2.1.0")
+SET(CPACK_PACKAGE_VERSION_MAJOR "2")
+SET(CPACK_PACKAGE_VERSION_MINOR "1")
+SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Qt graphic library")
+SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
+SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
+SET(CPACK_RESOURCE_FILE_INSTALL "${CMAKE_SOURCE_DIR}/INSTALL.txt")
+SET(CPACK_SOURCE_GENERATOR "TGZ")
+SET(CPACK_SOURCE_IGNORE_FILES
+ "CMakeFiles"
+ "Makefile"
+ "_CPack_Packages"
+ "CMakeCache.txt"
+ ".*\\\\.cmake"
+ ".*\\\\.git"
+ ".*\\\\.gz"
+ ".*\\\\.deb"
+ ".*\\\\.rpm"
+ ".*\\\\.dmg"
+ ".*\\\\.sh"
+ ".*\\\\..*\\\\.swp"
+ "src/\\\\..*"
+ "src/libbpp*"
+ ".*moc_.*"
+ "debian/tmp"
+ "debian/libbpp.*/"
+ "debian/libbpp.*\\\\.so.*"
+ "debian/libbpp.*\\\\.a"
+ "debian/libbpp.*\\\\.substvars"
+ "debian/libbpp.*\\\\.debhelper"
+ "debian/debhelper\\\\.log"
+ "html"
+ "Qt.tag"
+ "Testing"
+ "build-stamp"
+ "genIncludes.py"
+ "install_manifest.txt"
+ "DartConfiguration.tcl"
+ ${CPACK_SOURCE_IGNORE_FILES}
+)
+IF (MACOS)
+ SET(CPACK_GENERATOR "Bundle")
+ENDIF()
+
+SET(CPACK_SOURCE_PACKAGE_FILE_NAME "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
+SET(CPACK_DEBSOURCE_PACKAGE_FILE_NAME "lib${CMAKE_PROJECT_NAME}_${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}.orig")
+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)
+ENDIF()
+
+IF(NOT NO_DEP_CHECK)
+IF (UNIX)
+#This creates deb packages:
+ADD_CUSTOM_TARGET(origdist COMMAND cp ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz ../${CPACK_DEBSOURCE_PACKAGE_FILE_NAME}.tar.gz)
+ADD_DEPENDENCIES(origdist dist)
+ADD_CUSTOM_TARGET(deb dpkg-buildpackage -uc -us -i${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz)
+ADD_DEPENDENCIES(deb origdist)
+
+#This creates rpm packages:
+ADD_CUSTOM_TARGET(rpm rpmbuild -ta ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz)
+ADD_DEPENDENCIES(rpm dist)
+
+ENDIF()
+
+ENDIF(NOT NO_DEP_CHECK)
diff --git a/COPYING.txt b/COPYING.txt
new file mode 100644
index 0000000..94a9ed0
--- /dev/null
+++ b/COPYING.txt
@@ -0,0 +1,674 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
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+software and other kinds of works.
+
+ The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works. By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users. We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors. You can apply it to
+your programs, too.
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+ Notwithstanding any other provision of this License, for material you
+add to a covered work, you may (if authorized by the copyright holders of
+that material) supplement the terms of this License with terms:
+
+ a) Disclaiming warranty or limiting liability differently from the
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+
+ b) Requiring preservation of specified reasonable legal notices or
+ author attributions in that material or in the Appropriate Legal
+ Notices displayed by works containing it; or
+
+ c) Prohibiting misrepresentation of the origin of that material, or
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+ All other non-permissive additional terms are considered "further
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+received it, or any part of it, contains a notice stating that it is
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+a further restriction but permits relicensing or conveying under this
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+
+ Additional terms, permissive or non-permissive, may be stated in the
+form of a separately written license, or stated as exceptions;
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+ 8. Termination.
+
+ You may not propagate or modify a covered work except as expressly
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+modify it is void, and will automatically terminate your rights under
+this License (including any patent licenses granted under the third
+paragraph of section 11).
+
+ However, if you cease all violation of this License, then your
+license from a particular copyright holder is reinstated (a)
+provisionally, unless and until the copyright holder explicitly and
+finally terminates your license, and (b) permanently, if the copyright
+holder fails to notify you of the violation by some reasonable means
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+
+ Moreover, your license from a particular copyright holder is
+reinstated permanently if the copyright holder notifies you of the
+violation by some reasonable means, this is the first time you have
+received notice of violation of this License (for any work) from that
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+your receipt of the notice.
+
+ Termination of your rights under this section does not terminate the
+licenses of parties who have received copies or rights from you under
+this License. If your rights have been terminated and not permanently
+reinstated, you do not qualify to receive new licenses for the same
+material under section 10.
+
+ 9. Acceptance Not Required for Having Copies.
+
+ You are not required to accept this License in order to receive or
+run a copy of the Program. Ancillary propagation of a covered work
+occurring solely as a consequence of using peer-to-peer transmission
+to receive a copy likewise does not require acceptance. However,
+nothing other than this License grants you permission to propagate or
+modify any covered work. These actions infringe copyright if you do
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+covered work, you indicate your acceptance of this License to do so.
+
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+
+ Each time you convey a covered work, the recipient automatically
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+propagate that work, subject to this License. You are not responsible
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+ An "entity transaction" is a transaction transferring control of an
+organization, or substantially all assets of one, or subdividing an
+organization, or merging organizations. If propagation of a covered
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+transaction who receives a copy of the work also receives whatever
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+Corresponding Source of the work from the predecessor in interest, if
+the predecessor has it or can get it with reasonable efforts.
+
+ You may not impose any further restrictions on the exercise of the
+rights granted or affirmed under this License. For example, you may
+not impose a license fee, royalty, or other charge for exercise of
+rights granted under this License, and you may not initiate litigation
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+any patent claim is infringed by making, using, selling, offering for
+sale, or importing the Program or any portion of it.
+
+ 11. Patents.
+
+ A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based. The
+work thus licensed is called the contributor's "contributor version".
+
+ A contributor's "essential patent claims" are all patent claims
+owned or controlled by the contributor, whether already acquired or
+hereafter acquired, that would be infringed by some manner, permitted
+by this License, of making, using, or selling its contributor version,
+but do not include claims that would be infringed only as a
+consequence of further modification of the contributor version. For
+purposes of this definition, "control" includes the right to grant
+patent sublicenses in a manner consistent with the requirements of
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+
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+patent license under the contributor's essential patent claims, to
+make, use, sell, offer for sale, import and otherwise run, modify and
+propagate the contents of its contributor version.
+
+ In the following three paragraphs, a "patent license" is any express
+agreement or commitment, however denominated, not to enforce a patent
+(such as an express permission to practice a patent or covenant not to
+sue for patent infringement). To "grant" such a patent license to a
+party means to make such an agreement or commitment not to enforce a
+patent against the party.
+
+ If you convey a covered work, knowingly relying on a patent license,
+and the Corresponding Source of the work is not available for anyone
+to copy, free of charge and under the terms of this License, through a
+publicly available network server or other readily accessible means,
+then you must either (1) cause the Corresponding Source to be so
+available, or (2) arrange to deprive yourself of the benefit of the
+patent license for this particular work, or (3) arrange, in a manner
+consistent with the requirements of this License, to extend the patent
+license to downstream recipients. "Knowingly relying" means you have
+actual knowledge that, but for the patent license, your conveying the
+covered work in a country, or your recipient's use of the covered work
+in a country, would infringe one or more identifiable patents in that
+country that you have reason to believe are valid.
+
+ If, pursuant to or in connection with a single transaction or
+arrangement, you convey, or propagate by procuring conveyance of, a
+covered work, and grant a patent license to some of the parties
+receiving the covered work authorizing them to use, propagate, modify
+or convey a specific copy of the covered work, then the patent license
+you grant is automatically extended to all recipients of the covered
+work and works based on it.
+
+ A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License. You may not convey a covered
+work if you are a party to an arrangement with a third party that is
+in the business of distributing software, under which you make payment
+to the third party based on the extent of your activity of conveying
+the work, and under which the third party grants, to any of the
+parties who would receive the covered work from you, a discriminatory
+patent license (a) in connection with copies of the covered work
+conveyed by you (or copies made from those copies), or (b) primarily
+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+ Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+ 12. No Surrender of Others' Freedom.
+
+ If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+ 13. Use with the GNU Affero General Public License.
+
+ Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
+combined work, and to convey the resulting work. The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ <program> Copyright (C) <year> <name of author>
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/ChangeLog b/ChangeLog
new file mode 100644
index 0000000..9ceae9f
--- /dev/null
+++ b/ChangeLog
@@ -0,0 +1,19 @@
+08/03/13 -*- Version 2.1.0 -*-
+
+09/02/12 -*- Version 2.0.2 -*-
+
+11/06/11 -*- Version 2.0.1 -*-
+* Improved TreeCanvasControler.
+
+28/02/11 -*- Version 2.0.0 -*-
+
+05/02/2010 Julien Dutheil
+* New QtGraphicDevice, now uses QGraphicsScene => Works with layers, and
+faster rendering for TreeCanvas!
+
+30/12/09 Julien Dutheil
+* Improved QtGraphicDevice.
+* Added class QtTools.
+
+22/08/09 Julien Dutheil
+* Added CMake configuration files.
diff --git a/Doxyfile b/Doxyfile
new file mode 100644
index 0000000..0228a15
--- /dev/null
+++ b/Doxyfile
@@ -0,0 +1,1890 @@
+# Doxyfile 1.8.3.1-20130209
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project
+#
+# All text after a hash (#) is considered a comment and will be ignored
+# The format is:
+# TAG = value [value, ...]
+# For lists items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (" ")
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the config file
+# that follow. The default is UTF-8 which is also the encoding used for all
+# text before the first occurrence of this tag. Doxygen uses libiconv (or the
+# iconv built into libc) for the transcoding. See
+# http://www.gnu.org/software/libiconv for the list of possible encodings.
+
+DOXYFILE_ENCODING = UTF-8
+
+# The PROJECT_NAME tag is a single word (or sequence of words) that should
+# identify the project. Note that if you do not use Doxywizard you need
+# to put quotes around the project name if it contains spaces.
+
+PROJECT_NAME = bpp-qt
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number.
+# This could be handy for archiving the generated documentation or
+# if some version control system is used.
+
+PROJECT_NUMBER = 2.1.0
+
+# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# for a project that appears at the top of each page and should give viewer
+# a quick idea about the purpose of the project. Keep the description short.
+
+PROJECT_BRIEF =
+
+# With the PROJECT_LOGO tag one can specify an logo or icon that is
+# included in the documentation. The maximum height of the logo should not
+# exceed 55 pixels and the maximum width should not exceed 200 pixels.
+# Doxygen will copy the logo to the output directory.
+
+PROJECT_LOGO =
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
+# base path where the generated documentation will be put.
+# If a relative path is entered, it will be relative to the location
+# where doxygen was started. If left blank the current directory will be used.
+
+OUTPUT_DIRECTORY =
+
+# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
+# 4096 sub-directories (in 2 levels) under the output directory of each output
+# format and will distribute the generated files over these directories.
+# Enabling this option can be useful when feeding doxygen a huge amount of
+# source files, where putting all generated files in the same directory would
+# otherwise cause performance problems for the file system.
+
+CREATE_SUBDIRS = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# The default language is English, other supported languages are:
+# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
+# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
+# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
+# messages), Korean, Korean-en, Latvian, Lithuanian, Norwegian, Macedonian, Persian,
+# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak,
+# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
+
+OUTPUT_LANGUAGE = English
+
+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
+# include brief member descriptions after the members that are listed in
+# the file and class documentation (similar to JavaDoc).
+# Set to NO to disable this.
+
+BRIEF_MEMBER_DESC = YES
+
+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
+# the brief description of a member or function before the detailed description.
+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# brief descriptions will be completely suppressed.
+
+REPEAT_BRIEF = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator
+# that is used to form the text in various listings. Each string
+# in this list, if found as the leading text of the brief description, will be
+# stripped from the text and the result after processing the whole list, is
+# used as the annotated text. Otherwise, the brief description is used as-is.
+# If left blank, the following values are used ("$name" is automatically
+# replaced with the name of the entity): "The $name class" "The $name widget"
+# "The $name file" "is" "provides" "specifies" "contains"
+# "represents" "a" "an" "the"
+
+ABBREVIATE_BRIEF =
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# Doxygen will generate a detailed section even if there is only a brief
+# description.
+
+ALWAYS_DETAILED_SEC = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+# inherited members of a class in the documentation of that class as if those
+# members were ordinary class members. Constructors, destructors and assignment
+# operators of the base classes will not be shown.
+
+INLINE_INHERITED_MEMB = YES
+
+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
+# path before files name in the file list and in the header files. If set
+# to NO the shortest path that makes the file name unique will be used.
+
+FULL_PATH_NAMES = YES
+
+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
+# can be used to strip a user-defined part of the path. Stripping is
+# only done if one of the specified strings matches the left-hand part of
+# the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the
+# path to strip. Note that you specify absolute paths here, but also
+# relative paths, which will be relative from the directory where doxygen is
+# started.
+
+STRIP_FROM_PATH = ./src/
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
+# the path mentioned in the documentation of a class, which tells
+# the reader which header file to include in order to use a class.
+# If left blank only the name of the header file containing the class
+# definition is used. Otherwise one should specify the include paths that
+# are normally passed to the compiler using the -I flag.
+
+STRIP_FROM_INC_PATH = ./src/
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
+# (but less readable) file names. This can be useful if your file system
+# doesn't support long names like on DOS, Mac, or CD-ROM.
+
+SHORT_NAMES = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
+# will interpret the first line (until the first dot) of a JavaDoc-style
+# comment as the brief description. If set to NO, the JavaDoc
+# comments will behave just like regular Qt-style comments
+# (thus requiring an explicit @brief command for a brief description.)
+
+JAVADOC_AUTOBRIEF = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
+# interpret the first line (until the first dot) of a Qt-style
+# comment as the brief description. If set to NO, the comments
+# will behave just like regular Qt-style comments (thus requiring
+# an explicit \brief command for a brief description.)
+
+QT_AUTOBRIEF = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
+# treat a multi-line C++ special comment block (i.e. a block of //! or ///
+# comments) as a brief description. This used to be the default behaviour.
+# The new default is to treat a multi-line C++ comment block as a detailed
+# description. Set this tag to YES if you prefer the old behaviour instead.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
+# member inherits the documentation from any documented member that it
+# re-implements.
+
+INHERIT_DOCS = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
+# a new page for each member. If set to NO, the documentation of a member will
+# be part of the file/class/namespace that contains it.
+
+SEPARATE_MEMBER_PAGES = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab.
+# Doxygen uses this value to replace tabs by spaces in code fragments.
+
+TAB_SIZE = 2
+
+# This tag can be used to specify a number of aliases that acts
+# as commands in the documentation. An alias has the form "name=value".
+# For example adding "sideeffect=\par Side Effects:\n" will allow you to
+# put the command \sideeffect (or @sideeffect) in the documentation, which
+# will result in a user-defined paragraph with heading "Side Effects:".
+# You can put \n's in the value part of an alias to insert newlines.
+
+ALIASES =
+
+# This tag can be used to specify a number of word-keyword mappings (TCL only).
+# A mapping has the form "name=value". For example adding
+# "class=itcl::class" will allow you to use the command class in the
+# itcl::class meaning.
+
+TCL_SUBST =
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
+# sources only. Doxygen will then generate output that is more tailored for C.
+# For instance, some of the names that are used will be different. The list
+# of all members will be omitted, etc.
+
+OPTIMIZE_OUTPUT_FOR_C = NO
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
+# sources only. Doxygen will then generate output that is more tailored for
+# Java. For instance, namespaces will be presented as packages, qualified
+# scopes will look different, etc.
+
+OPTIMIZE_OUTPUT_JAVA = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources only. Doxygen will then generate output that is more tailored for
+# Fortran.
+
+OPTIMIZE_FOR_FORTRAN = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for
+# VHDL.
+
+OPTIMIZE_OUTPUT_VHDL = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it
+# parses. With this tag you can assign which parser to use for a given
+# extension. Doxygen has a built-in mapping, but you can override or extend it
+# using this tag. The format is ext=language, where ext is a file extension,
+# and language is one of the parsers supported by doxygen: IDL, Java,
+# Javascript, CSharp, C, C++, D, PHP, Objective-C, Python, Fortran, VHDL, C,
+# C++. For instance to make doxygen treat .inc files as Fortran files (default
+# is PHP), and .f files as C (default is Fortran), use: inc=Fortran f=C. Note
+# that for custom extensions you also need to set FILE_PATTERNS otherwise the
+# files are not read by doxygen.
+
+EXTENSION_MAPPING =
+
+# If MARKDOWN_SUPPORT is enabled (the default) then doxygen pre-processes all
+# comments according to the Markdown format, which allows for more readable
+# documentation. See http://daringfireball.net/projects/markdown/ for details.
+# The output of markdown processing is further processed by doxygen, so you
+# can mix doxygen, HTML, and XML commands with Markdown formatting.
+# Disable only in case of backward compatibilities issues.
+
+MARKDOWN_SUPPORT = YES
+
+# When enabled doxygen tries to link words that correspond to documented classes,
+# or namespaces to their corresponding documentation. Such a link can be
+# prevented in individual cases by by putting a % sign in front of the word or
+# globally by setting AUTOLINK_SUPPORT to NO.
+
+AUTOLINK_SUPPORT = YES
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should
+# set this tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
+# func(std::string) {}). This also makes the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+
+BUILTIN_STL_SUPPORT = YES
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# enable parsing support.
+
+CPP_CLI_SUPPORT = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
+# Doxygen will parse them like normal C++ but will assume all classes use public
+# instead of private inheritance when no explicit protection keyword is present.
+
+SIP_SUPPORT = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES (the
+# default) will make doxygen replace the get and set methods by a property in
+# the documentation. This will only work if the methods are indeed getting or
+# setting a simple type. If this is not the case, or you want to show the
+# methods anyway, you should set this option to NO.
+
+IDL_PROPERTY_SUPPORT = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES, then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+
+DISTRIBUTE_GROUP_DOC = NO
+
+# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
+# the same type (for instance a group of public functions) to be put as a
+# subgroup of that type (e.g. under the Public Functions section). Set it to
+# NO to prevent subgrouping. Alternatively, this can be done per class using
+# the \nosubgrouping command.
+
+SUBGROUPING = YES
+
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and
+# unions are shown inside the group in which they are included (e.g. using
+# @ingroup) instead of on a separate page (for HTML and Man pages) or
+# section (for LaTeX and RTF).
+
+INLINE_GROUPED_CLASSES = NO
+
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and
+# unions with only public data fields or simple typedef fields will be shown
+# inline in the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO (the default), structs, classes, and unions are shown on a separate
+# page (for HTML and Man pages) or section (for LaTeX and RTF).
+
+INLINE_SIMPLE_STRUCTS = NO
+
+# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
+# is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically
+# be useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+
+TYPEDEF_HIDES_STRUCT = NO
+
+# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
+# determine which symbols to keep in memory and which to flush to disk.
+# When the cache is full, less often used symbols will be written to disk.
+# For small to medium size projects (<1000 input files) the default value is
+# probably good enough. For larger projects a too small cache size can cause
+# doxygen to be busy swapping symbols to and from disk most of the time
+# causing a significant performance penalty.
+# If the system has enough physical memory increasing the cache will improve the
+# performance by keeping more symbols in memory. Note that the value works on
+# a logarithmic scale so increasing the size by one will roughly double the
+# memory usage. The cache size is given by this formula:
+# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
+# corresponding to a cache size of 2^16 = 65536 symbols.
+
+SYMBOL_CACHE_SIZE = 0
+
+# Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be
+# set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given
+# their name and scope. Since this can be an expensive process and often the
+# same symbol appear multiple times in the code, doxygen keeps a cache of
+# pre-resolved symbols. If the cache is too small doxygen will become slower.
+# If the cache is too large, memory is wasted. The cache size is given by this
+# formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0,
+# corresponding to a cache size of 2^16 = 65536 symbols.
+
+LOOKUP_CACHE_SIZE = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
+# documentation are documented, even if no documentation was available.
+# Private class members and static file members will be hidden unless
+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+
+EXTRACT_ALL = YES
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
+# will be included in the documentation.
+
+EXTRACT_PRIVATE = YES
+
+# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal
+# scope will be included in the documentation.
+
+EXTRACT_PACKAGE = NO
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file
+# will be included in the documentation.
+
+EXTRACT_STATIC = YES
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
+# defined locally in source files will be included in the documentation.
+# If set to NO only classes defined in header files are included.
+
+EXTRACT_LOCAL_CLASSES = YES
+
+# This flag is only useful for Objective-C code. When set to YES local
+# methods, which are defined in the implementation section but not in
+# the interface are included in the documentation.
+# If set to NO (the default) only methods in the interface are included.
+
+EXTRACT_LOCAL_METHODS = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base
+# name of the file that contains the anonymous namespace. By default
+# anonymous namespaces are hidden.
+
+EXTRACT_ANON_NSPACES = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
+# undocumented members of documented classes, files or namespaces.
+# If set to NO (the default) these members will be included in the
+# various overviews, but no documentation section is generated.
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy.
+# If set to NO (the default) these classes will be included in the various
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_CLASSES = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
+# friend (class|struct|union) declarations.
+# If set to NO (the default) these declarations will be included in the
+# documentation.
+
+HIDE_FRIEND_COMPOUNDS = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
+# documentation blocks found inside the body of a function.
+# If set to NO (the default) these blocks will be appended to the
+# function's detailed documentation block.
+
+HIDE_IN_BODY_DOCS = NO
+
+# The INTERNAL_DOCS tag determines if documentation
+# that is typed after a \internal command is included. If the tag is set
+# to NO (the default) then the documentation will be excluded.
+# Set it to YES to include the internal documentation.
+
+INTERNAL_DOCS = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
+# file names in lower-case letters. If set to YES upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+
+CASE_SENSE_NAMES = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
+# will show members with their full class and namespace scopes in the
+# documentation. If set to YES the scope will be hidden.
+
+HIDE_SCOPE_NAMES = NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
+# will put a list of the files that are included by a file in the documentation
+# of that file.
+
+SHOW_INCLUDE_FILES = YES
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
+# will list include files with double quotes in the documentation
+# rather than with sharp brackets.
+
+FORCE_LOCAL_INCLUDES = NO
+
+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
+# is inserted in the documentation for inline members.
+
+INLINE_INFO = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
+# will sort the (detailed) documentation of file and class members
+# alphabetically by member name. If set to NO the members will appear in
+# declaration order.
+
+SORT_MEMBER_DOCS = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
+# brief documentation of file, namespace and class members alphabetically
+# by member name. If set to NO (the default) the members will appear in
+# declaration order.
+
+SORT_BRIEF_DOCS = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen
+# will sort the (brief and detailed) documentation of class members so that
+# constructors and destructors are listed first. If set to NO (the default)
+# the constructors will appear in the respective orders defined by
+# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
+# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
+# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
+# hierarchy of group names into alphabetical order. If set to NO (the default)
+# the group names will appear in their defined order.
+
+SORT_GROUP_NAMES = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
+# sorted by fully-qualified names, including namespaces. If set to
+# NO (the default), the class list will be sorted only by class name,
+# not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the
+# alphabetical list.
+
+SORT_BY_SCOPE_NAME = NO
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
+# do proper type resolution of all parameters of a function it will reject a
+# match between the prototype and the implementation of a member function even
+# if there is only one candidate or it is obvious which candidate to choose
+# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen
+# will still accept a match between prototype and implementation in such cases.
+
+STRICT_PROTO_MATCHING = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or
+# disable (NO) the todo list. This list is created by putting \todo
+# commands in the documentation.
+
+GENERATE_TODOLIST = NO
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or
+# disable (NO) the test list. This list is created by putting \test
+# commands in the documentation.
+
+GENERATE_TESTLIST = NO
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or
+# disable (NO) the bug list. This list is created by putting \bug
+# commands in the documentation.
+
+GENERATE_BUGLIST = NO
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
+# disable (NO) the deprecated list. This list is created by putting
+# \deprecated commands in the documentation.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional
+# documentation sections, marked by \if section-label ... \endif
+# and \cond section-label ... \endcond blocks.
+
+ENABLED_SECTIONS =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
+# the initial value of a variable or macro consists of for it to appear in
+# the documentation. If the initializer consists of more lines than specified
+# here it will be hidden. Use a value of 0 to hide initializers completely.
+# The appearance of the initializer of individual variables and macros in the
+# documentation can be controlled using \showinitializer or \hideinitializer
+# command in the documentation regardless of this setting.
+
+MAX_INITIALIZER_LINES = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
+# at the bottom of the documentation of classes and structs. If set to YES the
+# list will mention the files that were used to generate the documentation.
+
+SHOW_USED_FILES = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
+# This will remove the Files entry from the Quick Index and from the
+# Folder Tree View (if specified). The default is YES.
+
+SHOW_FILES = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
+# Namespaces page. This will remove the Namespaces entry from the Quick Index
+# and from the Folder Tree View (if specified). The default is YES.
+
+SHOW_NAMESPACES = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command <command> <input-file>, where <command> is the value of
+# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
+# provided by doxygen. Whatever the program writes to standard output
+# is used as the file version. See the manual for examples.
+
+FILE_VERSION_FILTER =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option.
+# You can optionally specify a file name after the option, if omitted
+# DoxygenLayout.xml will be used as the name of the layout file.
+
+LAYOUT_FILE =
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files
+# containing the references data. This must be a list of .bib files. The
+# .bib extension is automatically appended if omitted. Using this command
+# requires the bibtex tool to be installed. See also
+# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style
+# of the bibliography can be controlled using LATEX_BIB_STYLE. To use this
+# feature you need bibtex and perl available in the search path. Do not use
+# file names with spaces, bibtex cannot handle them.
+
+CITE_BIB_FILES =
+
+#---------------------------------------------------------------------------
+# configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated
+# by doxygen. Possible values are YES and NO. If left blank NO is used.
+
+QUIET = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated by doxygen. Possible values are YES and NO. If left blank
+# NO is used.
+
+WARNINGS = YES
+
+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
+# automatically be disabled.
+
+WARN_IF_UNDOCUMENTED = YES
+
+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some
+# parameters in a documented function, or documenting parameters that
+# don't exist or using markup commands wrongly.
+
+WARN_IF_DOC_ERROR = YES
+
+# The WARN_NO_PARAMDOC option can be enabled to get warnings for
+# functions that are documented, but have no documentation for their parameters
+# or return value. If set to NO (the default) doxygen will only warn about
+# wrong or incomplete parameter documentation, but not about the absence of
+# documentation.
+
+WARN_NO_PARAMDOC = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that
+# doxygen can produce. The string should contain the $file, $line, and $text
+# tags, which will be replaced by the file and line number from which the
+# warning originated and the warning text. Optionally the format may contain
+# $version, which will be replaced by the version of the file (if it could
+# be obtained via FILE_VERSION_FILTER)
+
+WARN_FORMAT = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning
+# and error messages should be written. If left blank the output is written
+# to stderr.
+
+WARN_LOGFILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag can be used to specify the files and/or directories that contain
+# documented source files. You may enter file names like "myfile.cpp" or
+# directories like "/usr/src/myproject". Separate the files or directories
+# with spaces.
+
+INPUT = src
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
+# also the default input encoding. Doxygen uses libiconv (or the iconv built
+# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
+# the list of possible encodings.
+
+INPUT_ENCODING = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank the following patterns are tested:
+# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh
+# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
+# *.f90 *.f *.for *.vhd *.vhdl
+
+FILE_PATTERNS = *.h \
+ *.cpp
+
+# The RECURSIVE tag can be used to turn specify whether or not subdirectories
+# should be searched for input files as well. Possible values are YES and NO.
+# If left blank NO is used.
+
+RECURSIVE = YES
+
+# The EXCLUDE tag can be used to specify files and/or directories that should be
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
+
+EXCLUDE =
+
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
+# from the input.
+
+EXCLUDE_SYMLINKS = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories. Note that the wildcards are matched
+# against the file with absolute path, so to exclude all test directories
+# for example use the pattern */test/*
+
+EXCLUDE_PATTERNS =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+
+EXCLUDE_SYMBOLS =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or
+# directories that contain example code fragments that are included (see
+# the \include command).
+
+EXAMPLE_PATH =
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank all files are included.
+
+EXAMPLE_PATTERNS =
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude
+# commands irrespective of the value of the RECURSIVE tag.
+# Possible values are YES and NO. If left blank NO is used.
+
+EXAMPLE_RECURSIVE = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or
+# directories that contain image that are included in the documentation (see
+# the \image command).
+
+IMAGE_PATH =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command <filter> <input-file>, where <filter>
+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
+# input file. Doxygen will then use the output that the filter program writes
+# to standard output. If FILTER_PATTERNS is specified, this tag will be
+# ignored.
+
+INPUT_FILTER =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form:
+# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
+# info on how filters are used. If FILTER_PATTERNS is empty or if
+# non of the patterns match the file name, INPUT_FILTER is applied.
+
+FILTER_PATTERNS =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will be used to filter the input files when producing source
+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+
+FILTER_SOURCE_FILES = NO
+
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any)
+# and it is also possible to disable source filtering for a specific pattern
+# using *.ext= (so without naming a filter). This option only has effect when
+# FILTER_SOURCE_FILES is enabled.
+
+FILTER_SOURCE_PATTERNS =
+
+# If the USE_MD_FILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page (index.html).
+# This can be useful if you have a project on for instance GitHub and want reuse
+# the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE =
+
+#---------------------------------------------------------------------------
+# configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will
+# be generated. Documented entities will be cross-referenced with these sources.
+# Note: To get rid of all source code in the generated output, make sure also
+# VERBATIM_HEADERS is set to NO.
+
+SOURCE_BROWSER = YES
+
+# Setting the INLINE_SOURCES tag to YES will include the body
+# of functions and classes directly in the documentation.
+
+INLINE_SOURCES = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
+# doxygen to hide any special comment blocks from generated source code
+# fragments. Normal C, C++ and Fortran comments will always remain visible.
+
+STRIP_CODE_COMMENTS = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES
+# then for each documented function all documented
+# functions referencing it will be listed.
+
+REFERENCED_BY_RELATION = YES
+
+# If the REFERENCES_RELATION tag is set to YES
+# then for each documented function all documented entities
+# called/used by that function will be listed.
+
+REFERENCES_RELATION = YES
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
+# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
+# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
+# link to the source code. Otherwise they will link to the documentation.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code
+# will point to the HTML generated by the htags(1) tool instead of doxygen
+# built-in source browser. The htags tool is part of GNU's global source
+# tagging system (see http://www.gnu.org/software/global/global.html). You
+# will need version 4.8.6 or higher.
+
+USE_HTAGS = NO
+
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
+# will generate a verbatim copy of the header file for each class for
+# which an include is specified. Set to NO to disable this.
+
+VERBATIM_HEADERS = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
+# of all compounds will be generated. Enable this if the project
+# contains a lot of classes, structs, unions or interfaces.
+
+ALPHABETICAL_INDEX = NO
+
+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
+# in which this list will be split (can be a number in the range [1..20])
+
+COLS_IN_ALPHA_INDEX = 5
+
+# In case all classes in a project start with a common prefix, all
+# classes will be put under the same header in the alphabetical index.
+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
+# should be ignored while generating the index headers.
+
+IGNORE_PREFIX =
+
+#---------------------------------------------------------------------------
+# configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
+# generate HTML output.
+
+GENERATE_HTML = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `html' will be used as the default path.
+
+HTML_OUTPUT = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
+# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
+# doxygen will generate files with .html extension.
+
+HTML_FILE_EXTENSION = .html
+
+# The HTML_HEADER tag can be used to specify a personal HTML header for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard header. Note that when using a custom header you are responsible
+# for the proper inclusion of any scripts and style sheets that doxygen
+# needs, which is dependent on the configuration options used.
+# It is advised to generate a default header using "doxygen -w html
+# header.html footer.html stylesheet.css YourConfigFile" and then modify
+# that header. Note that the header is subject to change so you typically
+# have to redo this when upgrading to a newer version of doxygen or when
+# changing the value of configuration settings such as GENERATE_TREEVIEW!
+
+HTML_HEADER =
+
+# The HTML_FOOTER tag can be used to specify a personal HTML footer for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard footer.
+
+HTML_FOOTER =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
+# style sheet that is used by each HTML page. It can be used to
+# fine-tune the look of the HTML output. If left blank doxygen will
+# generate a default style sheet. Note that it is recommended to use
+# HTML_EXTRA_STYLESHEET instead of this one, as it is more robust and this
+# tag will in the future become obsolete.
+
+HTML_STYLESHEET =
+
+# The HTML_EXTRA_STYLESHEET tag can be used to specify an additional
+# user-defined cascading style sheet that is included after the standard
+# style sheets created by doxygen. Using this option one can overrule
+# certain style aspects. This is preferred over using HTML_STYLESHEET
+# since it does not replace the standard style sheet and is therefor more
+# robust against future updates. Doxygen will copy the style sheet file to
+# the output directory.
+
+HTML_EXTRA_STYLESHEET =
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that
+# the files will be copied as-is; there are no commands or markers available.
+
+HTML_EXTRA_FILES =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
+# Doxygen will adjust the colors in the style sheet and background images
+# according to this color. Hue is specified as an angle on a colorwheel,
+# see http://en.wikipedia.org/wiki/Hue for more information.
+# For instance the value 0 represents red, 60 is yellow, 120 is green,
+# 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
+# The allowed range is 0 to 359.
+
+HTML_COLORSTYLE_HUE = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
+# the colors in the HTML output. For a value of 0 the output will use
+# grayscales only. A value of 255 will produce the most vivid colors.
+
+HTML_COLORSTYLE_SAT = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
+# the luminance component of the colors in the HTML output. Values below
+# 100 gradually make the output lighter, whereas values above 100 make
+# the output darker. The value divided by 100 is the actual gamma applied,
+# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
+# and 100 does not change the gamma.
+
+HTML_COLORSTYLE_GAMMA = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting
+# this to NO can help when comparing the output of multiple runs.
+
+HTML_TIMESTAMP = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded.
+
+HTML_DYNAMIC_SECTIONS = YES
+
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files
+# will be generated that can be used as input for Apple's Xcode 3
+# integrated development environment, introduced with OSX 10.5 (Leopard).
+# To create a documentation set, doxygen will generate a Makefile in the
+# HTML output directory. Running make will produce the docset in that
+# directory and running "make install" will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
+# it at startup.
+# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# for more information.
+
+GENERATE_DOCSET = YES
+
+# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
+# feed. A documentation feed provides an umbrella under which multiple
+# documentation sets from a single provider (such as a company or product suite)
+# can be grouped.
+
+DOCSET_FEEDNAME = "Bio++ Qt Library"
+
+# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
+# should uniquely identify the documentation set bundle. This should be a
+# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
+# will append .docset to the name.
+
+DOCSET_BUNDLE_ID = bpp.Qt
+
+# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely
+# identify the documentation publisher. This should be a reverse domain-name
+# style string, e.g. com.mycompany.MyDocSet.documentation.
+
+DOCSET_PUBLISHER_ID = org.doxygen.Publisher
+
+# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
+
+DOCSET_PUBLISHER_NAME = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files
+# will be generated that can be used as input for tools like the
+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
+# be used to specify the file name of the resulting .chm file. You
+# can add a path in front of the file if the result should not be
+# written to the html output directory.
+
+CHM_FILE =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
+# be used to specify the location (absolute path including file name) of
+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
+# the HTML help compiler on the generated index.hhp.
+
+HHC_LOCATION =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
+# controls if a separate .chi index file is generated (YES) or that
+# it should be included in the master .chm file (NO).
+
+GENERATE_CHI = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
+# is used to encode HtmlHelp index (hhk), content (hhc) and project file
+# content.
+
+CHM_INDEX_ENCODING =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
+# controls whether a binary table of contents is generated (YES) or a
+# normal table of contents (NO) in the .chm file.
+
+BINARY_TOC = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members
+# to the contents of the HTML help documentation and to the tree view.
+
+TOC_EXPAND = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated
+# that can be used as input for Qt's qhelpgenerator to generate a
+# Qt Compressed Help (.qch) of the generated HTML documentation.
+
+GENERATE_QHP = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
+# be used to specify the file name of the resulting .qch file.
+# The path specified is relative to the HTML output folder.
+
+QCH_FILE =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#namespace
+
+QHP_NAMESPACE = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#virtual-folders
+
+QHP_VIRTUAL_FOLDER = doc
+
+# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to
+# add. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#custom-filters
+
+QHP_CUST_FILTER_NAME =
+
+# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see
+# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">
+# Qt Help Project / Custom Filters</a>.
+
+QHP_CUST_FILTER_ATTRS =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's
+# filter section matches.
+# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">
+# Qt Help Project / Filter Attributes</a>.
+
+QHP_SECT_FILTER_ATTRS =
+
+# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
+# be used to specify the location of Qt's qhelpgenerator.
+# If non-empty doxygen will try to run qhelpgenerator on the generated
+# .qhp file.
+
+QHG_LOCATION =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
+# will be generated, which together with the HTML files, form an Eclipse help
+# plugin. To install this plugin and make it available under the help contents
+# menu in Eclipse, the contents of the directory containing the HTML and XML
+# files needs to be copied into the plugins directory of eclipse. The name of
+# the directory within the plugins directory should be the same as
+# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before
+# the help appears.
+
+GENERATE_ECLIPSEHELP = NO
+
+# A unique identifier for the eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have
+# this name.
+
+ECLIPSE_DOC_ID = org.doxygen.Project
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs)
+# at top of each HTML page. The value NO (the default) enables the index and
+# the value YES disables it. Since the tabs have the same information as the
+# navigation tree you can set this option to NO if you already set
+# GENERATE_TREEVIEW to YES.
+
+DISABLE_INDEX = NO
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information.
+# If the tag value is set to YES, a side panel will be generated
+# containing a tree-like index structure (just like the one that
+# is generated for HTML Help). For this to work a browser that supports
+# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
+# Windows users are probably better off using the HTML help feature.
+# Since the tree basically has the same information as the tab index you
+# could consider to set DISABLE_INDEX to NO when enabling this option.
+
+GENERATE_TREEVIEW = YES
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values
+# (range [0,1..20]) that doxygen will group on one line in the generated HTML
+# documentation. Note that a value of 0 will completely suppress the enum
+# values from appearing in the overview section.
+
+ENUM_VALUES_PER_LINE = 4
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
+# used to set the initial width (in pixels) of the frame in which the tree
+# is shown.
+
+TREEVIEW_WIDTH = 250
+
+# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
+# links to external symbols imported via tag files in a separate window.
+
+EXT_LINKS_IN_WINDOW = NO
+
+# Use this tag to change the font size of Latex formulas included
+# as images in the HTML documentation. The default is 10. Note that
+# when you change the font size after a successful doxygen run you need
+# to manually remove any form_*.png images from the HTML output directory
+# to force them to be regenerated.
+
+FORMULA_FONTSIZE = 10
+
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are
+# not supported properly for IE 6.0, but are supported on all modern browsers.
+# Note that when changing this option you need to delete any form_*.png files
+# in the HTML output before the changes have effect.
+
+FORMULA_TRANSPARENT = YES
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax
+# (see http://www.mathjax.org) which uses client side Javascript for the
+# rendering instead of using prerendered bitmaps. Use this if you do not
+# have LaTeX installed or if you want to formulas look prettier in the HTML
+# output. When enabled you may also need to install MathJax separately and
+# configure the path to it using the MATHJAX_RELPATH option.
+
+USE_MATHJAX = NO
+
+# When MathJax is enabled you can set the default output format to be used for
+# thA MathJax output. Supported types are HTML-CSS, NativeMML (i.e. MathML) and
+# SVG. The default value is HTML-CSS, which is slower, but has the best
+# compatibility.
+
+MATHJAX_FORMAT = HTML-CSS
+
+# When MathJax is enabled you need to specify the location relative to the
+# HTML output directory using the MATHJAX_RELPATH option. The destination
+# directory should contain the MathJax.js script. For instance, if the mathjax
+# directory is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to
+# the MathJax Content Delivery Network so you can quickly see the result without
+# installing MathJax. However, it is strongly recommended to install a local
+# copy of MathJax from http://www.mathjax.org before deployment.
+
+MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest
+
+# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension
+# names that should be enabled during MathJax rendering.
+
+MATHJAX_EXTENSIONS =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box
+# for the HTML output. The underlying search engine uses javascript
+# and DHTML and should work on any modern browser. Note that when using
+# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets
+# (GENERATE_DOCSET) there is already a search function so this one should
+# typically be disabled. For large projects the javascript based search engine
+# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
+
+SEARCHENGINE = YES
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a web server instead of a web client using Javascript.
+# There are two flavours of web server based search depending on the
+# EXTERNAL_SEARCH setting. When disabled, doxygen will generate a PHP script for
+# searching and an index file used by the script. When EXTERNAL_SEARCH is
+# enabled the indexing and searching needs to be provided by external tools.
+# See the manual for details.
+
+SERVER_BASED_SEARCH = NO
+
+# When EXTERNAL_SEARCH is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain
+# the search results. Doxygen ships with an example indexer (doxyindexer) and
+# search engine (doxysearch.cgi) which are based on the open source search engine
+# library Xapian. See the manual for configuration details.
+
+EXTERNAL_SEARCH = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will returned the search results when EXTERNAL_SEARCH is enabled.
+# Doxygen ships with an example search engine (doxysearch) which is based on
+# the open source search engine library Xapian. See the manual for configuration
+# details.
+
+SEARCHENGINE_URL =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+
+SEARCHDATA_FILE = searchdata.xml
+
+# When SERVER_BASED_SEARCH AND EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+
+EXTERNAL_SEARCH_ID =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id
+# of to a relative location where the documentation can be found.
+# The format is: EXTRA_SEARCH_MAPPINGS = id1=loc1 id2=loc2 ...
+
+EXTRA_SEARCH_MAPPINGS =
+
+#---------------------------------------------------------------------------
+# configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
+# generate Latex output.
+
+GENERATE_LATEX = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `latex' will be used as the default path.
+
+LATEX_OUTPUT = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked. If left blank `latex' will be used as the default command name.
+# Note that when enabling USE_PDFLATEX this option is only used for
+# generating bitmaps for formulas in the HTML output, but not in the
+# Makefile that is written to the output directory.
+
+LATEX_CMD_NAME = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
+# generate index for LaTeX. If left blank `makeindex' will be used as the
+# default command name.
+
+MAKEINDEX_CMD_NAME = makeindex
+
+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
+# LaTeX documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_LATEX = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used
+# by the printer. Possible values are: a4, letter, legal and
+# executive. If left blank a4wide will be used.
+
+PAPER_TYPE = a4wide
+
+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
+# packages that should be included in the LaTeX output.
+
+EXTRA_PACKAGES = amsmath
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
+# the generated latex document. The header should contain everything until
+# the first chapter. If it is left blank doxygen will generate a
+# standard header. Notice: only use this tag if you know what you are doing!
+
+LATEX_HEADER =
+
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for
+# the generated latex document. The footer should contain everything after
+# the last chapter. If it is left blank doxygen will generate a
+# standard footer. Notice: only use this tag if you know what you are doing!
+
+LATEX_FOOTER =
+
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images
+# or other source files which should be copied to the LaTeX output directory.
+# Note that the files will be copied as-is; there are no commands or markers
+# available.
+
+LATEX_EXTRA_FILES =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
+# is prepared for conversion to pdf (using ps2pdf). The pdf file will
+# contain links (just like the HTML output) instead of page references
+# This makes the output suitable for online browsing using a pdf viewer.
+
+PDF_HYPERLINKS = NO
+
+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
+# plain latex in the generated Makefile. Set this option to YES to get a
+# higher quality PDF documentation.
+
+USE_PDFLATEX = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
+# command to the generated LaTeX files. This will instruct LaTeX to keep
+# running if errors occur, instead of asking the user for help.
+# This option is also used when generating formulas in HTML.
+
+LATEX_BATCHMODE = NO
+
+# If LATEX_HIDE_INDICES is set to YES then doxygen will not
+# include the index chapters (such as File Index, Compound Index, etc.)
+# in the output.
+
+LATEX_HIDE_INDICES = NO
+
+# If LATEX_SOURCE_CODE is set to YES then doxygen will include
+# source code with syntax highlighting in the LaTeX output.
+# Note that which sources are shown also depends on other settings
+# such as SOURCE_BROWSER.
+
+LATEX_SOURCE_CODE = NO
+
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See
+# http://en.wikipedia.org/wiki/BibTeX for more info.
+
+LATEX_BIB_STYLE = plain
+
+#---------------------------------------------------------------------------
+# configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
+# The RTF output is optimized for Word 97 and may not look very pretty with
+# other RTF readers or editors.
+
+GENERATE_RTF = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `rtf' will be used as the default path.
+
+RTF_OUTPUT = rtf
+
+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
+# RTF documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_RTF = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
+# will contain hyperlink fields. The RTF file will
+# contain links (just like the HTML output) instead of page references.
+# This makes the output suitable for online browsing using WORD or other
+# programs which support those fields.
+# Note: wordpad (write) and others do not support links.
+
+RTF_HYPERLINKS = NO
+
+# Load style sheet definitions from file. Syntax is similar to doxygen's
+# config file, i.e. a series of assignments. You only have to provide
+# replacements, missing definitions are set to their default value.
+
+RTF_STYLESHEET_FILE =
+
+# Set optional variables used in the generation of an rtf document.
+# Syntax is similar to doxygen's config file.
+
+RTF_EXTENSIONS_FILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
+# generate man pages
+
+GENERATE_MAN = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `man' will be used as the default path.
+
+MAN_OUTPUT = man
+
+# The MAN_EXTENSION tag determines the extension that is added to
+# the generated man pages (default is the subroutine's section .3)
+
+MAN_EXTENSION = .3
+
+# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
+# then it will generate one additional man file for each entity
+# documented in the real man page(s). These additional files
+# only source the real man page, but without them the man command
+# would be unable to find the correct page. The default is NO.
+
+MAN_LINKS = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES Doxygen will
+# generate an XML file that captures the structure of
+# the code including all documentation.
+
+GENERATE_XML = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `xml' will be used as the default path.
+
+XML_OUTPUT = xml
+
+# The XML_SCHEMA tag can be used to specify an XML schema,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_SCHEMA =
+
+# The XML_DTD tag can be used to specify an XML DTD,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_DTD =
+
+# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
+# dump the program listings (including syntax highlighting
+# and cross-referencing information) to the XML output. Note that
+# enabling this will significantly increase the size of the XML output.
+
+XML_PROGRAMLISTING = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_DOCBOOK tag is set to YES Doxygen will generate DOCBOOK files
+# that can be used to generate PDF.
+
+GENERATE_DOCBOOK = NO
+
+# The DOCBOOK_OUTPUT tag is used to specify where the DOCBOOK pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it. If left blank docbook will be used as the default path.
+
+DOCBOOK_OUTPUT = docbook
+
+#---------------------------------------------------------------------------
+# configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
+# generate an AutoGen Definitions (see autogen.sf.net) file
+# that captures the structure of the code including all
+# documentation. Note that this feature is still experimental
+# and incomplete at the moment.
+
+GENERATE_AUTOGEN_DEF = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES Doxygen will
+# generate a Perl module file that captures the structure of
+# the code including all documentation. Note that this
+# feature is still experimental and incomplete at the
+# moment.
+
+GENERATE_PERLMOD = NO
+
+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
+# the necessary Makefile rules, Perl scripts and LaTeX code to be able
+# to generate PDF and DVI output from the Perl module output.
+
+PERLMOD_LATEX = NO
+
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
+# nicely formatted so it can be parsed by a human reader. This is useful
+# if you want to understand what is going on. On the other hand, if this
+# tag is set to NO the size of the Perl module output will be much smaller
+# and Perl will parse it just the same.
+
+PERLMOD_PRETTY = YES
+
+# The names of the make variables in the generated doxyrules.make file
+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
+# This is useful so different doxyrules.make files included by the same
+# Makefile don't overwrite each other's variables.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
+# evaluate all C-preprocessor directives found in the sources and include
+# files.
+
+ENABLE_PREPROCESSING = YES
+
+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
+# names in the source code. If set to NO (the default) only conditional
+# compilation will be performed. Macro expansion can be done in a controlled
+# way by setting EXPAND_ONLY_PREDEF to YES.
+
+MACRO_EXPANSION = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
+# then the macro expansion is limited to the macros specified with the
+# PREDEFINED and EXPAND_AS_DEFINED tags.
+
+EXPAND_ONLY_PREDEF = NO
+
+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
+# pointed to by INCLUDE_PATH will be searched when a #include is found.
+
+SEARCH_INCLUDES = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by
+# the preprocessor.
+
+INCLUDE_PATH =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will
+# be used.
+
+INCLUDE_FILE_PATTERNS =
+
+# The PREDEFINED tag can be used to specify one or more macro names that
+# are defined before the preprocessor is started (similar to the -D option of
+# gcc). The argument of the tag is a list of macros of the form: name
+# or name=definition (no spaces). If the definition and the = are
+# omitted =1 is assumed. To prevent a macro definition from being
+# undefined via #undef or recursively expanded use the := operator
+# instead of the = operator.
+
+PREDEFINED =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
+# this tag can be used to specify a list of macro names that should be expanded.
+# The macro definition that is found in the sources will be used.
+# Use the PREDEFINED tag if you want to use a different macro definition that
+# overrules the definition found in the source code.
+
+EXPAND_AS_DEFINED =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
+# doxygen's preprocessor will remove all references to function-like macros
+# that are alone on a line, have an all uppercase name, and do not end with a
+# semicolon, because these will confuse the parser if not removed.
+
+SKIP_FUNCTION_MACROS = YES
+
+#---------------------------------------------------------------------------
+# Configuration::additions related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES option can be used to specify one or more tagfiles. For each
+# tag file the location of the external documentation should be added. The
+# format of a tag file without this location is as follows:
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where "loc1" and "loc2" can be relative or absolute paths
+# or URLs. Note that each tag file must have a unique name (where the name does
+# NOT include the path). If a tag file is not located in the directory in which
+# doxygen is run, you must also specify the path to the tagfile here.
+
+TAGFILES = ../bpp-core/BppCore.tag=../../bpp-core/html \
+ ../bpp-seq/BppSeq.tag=../../bpp-seq/html \
+ ../bpp-phyl/BppPhyl.tag=../../bpp-phyl/html
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create
+# a tag file that is based on the input files it reads.
+
+GENERATE_TAGFILE = BppQt.tag
+
+# If the ALLEXTERNALS tag is set to YES all external classes will be listed
+# in the class index. If set to NO only the inherited external classes
+# will be listed.
+
+ALLEXTERNALS = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will
+# be listed.
+
+EXTERNAL_GROUPS = YES
+
+# If the EXTERNAL_PAGES tag is set to YES all external pages will be listed
+# in the related pages index. If set to NO, only the current project's
+# pages will be listed.
+
+EXTERNAL_PAGES = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of `which perl').
+
+PERL_PATH = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
+# or super classes. Setting the tag to NO turns the diagrams off. Note that
+# this option also works with HAVE_DOT disabled, but it is recommended to
+# install and use dot, since it yields more powerful graphs.
+
+CLASS_DIAGRAMS = YES
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see
+# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# default search path.
+
+MSCGEN_PATH =
+
+# If set to YES, the inheritance and collaboration graphs will hide
+# inheritance and usage relations if the target is undocumented
+# or is not a class.
+
+HIDE_UNDOC_RELATIONS = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz, a graph visualization
+# toolkit from AT&T and Lucent Bell Labs. The other options in this section
+# have no effect if this option is set to NO (the default)
+
+HAVE_DOT = YES
+
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is
+# allowed to run in parallel. When set to 0 (the default) doxygen will
+# base this on the number of processors available in the system. You can set it
+# explicitly to a value larger than 0 to get control over the balance
+# between CPU load and processing speed.
+
+DOT_NUM_THREADS = 0
+
+# By default doxygen will use the Helvetica font for all dot files that
+# doxygen generates. When you want a differently looking font you can specify
+# the font name using DOT_FONTNAME. You need to make sure dot is able to find
+# the font, which can be done by putting it in a standard location or by setting
+# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the
+# directory containing the font.
+
+DOT_FONTNAME = FreeSans
+
+# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
+# The default size is 10pt.
+
+DOT_FONTSIZE = 10
+
+# By default doxygen will tell dot to use the Helvetica font.
+# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to
+# set the path where dot can find it.
+
+DOT_FONTPATH =
+
+# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect inheritance relations. Setting this tag to YES will force the
+# CLASS_DIAGRAMS tag to NO.
+
+CLASS_GRAPH = YES
+
+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect implementation dependencies (inheritance, containment, and
+# class references variables) of the class with other documented classes.
+
+COLLABORATION_GRAPH = YES
+
+# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for groups, showing the direct groups dependencies
+
+GROUP_GRAPHS = YES
+
+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# Language.
+
+UML_LOOK = NO
+
+# If the UML_LOOK tag is enabled, the fields and methods are shown inside
+# the class node. If there are many fields or methods and many nodes the
+# graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS
+# threshold limits the number of items for each type to make the size more
+# managable. Set this to 0 for no limit. Note that the threshold may be
+# exceeded by 50% before the limit is enforced.
+
+UML_LIMIT_NUM_FIELDS = 10
+
+# If set to YES, the inheritance and collaboration graphs will show the
+# relations between templates and their instances.
+
+TEMPLATE_RELATIONS = YES
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
+# tags are set to YES then doxygen will generate a graph for each documented
+# file showing the direct and indirect include dependencies of the file with
+# other documented files.
+
+INCLUDE_GRAPH = YES
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
+# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
+# documented header file showing the documented files that directly or
+# indirectly include this file.
+
+INCLUDED_BY_GRAPH = YES
+
+# If the CALL_GRAPH and HAVE_DOT options are set to YES then
+# doxygen will generate a call dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable call graphs
+# for selected functions only using the \callgraph command.
+
+CALL_GRAPH = NO
+
+# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
+# doxygen will generate a caller dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable caller
+# graphs for selected functions only using the \callergraph command.
+
+CALLER_GRAPH = NO
+
+# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
+# will generate a graphical hierarchy of all classes instead of a textual one.
+
+GRAPHICAL_HIERARCHY = YES
+
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
+# then doxygen will show the dependencies a directory has on other directories
+# in a graphical way. The dependency relations are determined by the #include
+# relations between the files in the directories.
+
+DIRECTORY_GRAPH = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot. Possible values are svg, png, jpg, or gif.
+# If left blank png will be used. If you choose svg you need to set
+# HTML_FILE_EXTENSION to xhtml in order to make the SVG files
+# visible in IE 9+ (other browsers do not have this requirement).
+
+DOT_IMAGE_FORMAT = png
+
+# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
+# enable generation of interactive SVG images that allow zooming and panning.
+# Note that this requires a modern browser other than Internet Explorer.
+# Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you
+# need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files
+# visible. Older versions of IE do not have SVG support.
+
+INTERACTIVE_SVG = NO
+
+# The tag DOT_PATH can be used to specify the path where the dot tool can be
+# found. If left blank, it is assumed the dot tool can be found in the path.
+
+DOT_PATH =
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that
+# contain dot files that are included in the documentation (see the
+# \dotfile command).
+
+DOTFILE_DIRS =
+
+# The MSCFILE_DIRS tag can be used to specify one or more directories that
+# contain msc files that are included in the documentation (see the
+# \mscfile command).
+
+MSCFILE_DIRS =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
+# nodes that will be shown in the graph. If the number of nodes in a graph
+# becomes larger than this value, doxygen will truncate the graph, which is
+# visualized by representing a node as a red box. Note that doxygen if the
+# number of direct children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
+# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+
+DOT_GRAPH_MAX_NODES = 50
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
+# graphs generated by dot. A depth value of 3 means that only nodes reachable
+# from the root by following a path via at most 3 edges will be shown. Nodes
+# that lay further from the root node will be omitted. Note that setting this
+# option to 1 or 2 may greatly reduce the computation time needed for large
+# code bases. Also note that the size of a graph can be further restricted by
+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+
+MAX_DOT_GRAPH_DEPTH = 0
+
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
+# background. This is disabled by default, because dot on Windows does not
+# seem to support this out of the box. Warning: Depending on the platform used,
+# enabling this option may lead to badly anti-aliased labels on the edges of
+# a graph (i.e. they become hard to read).
+
+DOT_TRANSPARENT = NO
+
+# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10)
+# support this, this feature is disabled by default.
+
+DOT_MULTI_TARGETS = YES
+
+# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
+# generate a legend page explaining the meaning of the various boxes and
+# arrows in the dot generated graphs.
+
+GENERATE_LEGEND = YES
+
+# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
+# remove the intermediate dot files that are used to generate
+# the various graphs.
+
+DOT_CLEANUP = YES
diff --git a/INSTALL.txt b/INSTALL.txt
new file mode 100644
index 0000000..c8859da
--- /dev/null
+++ b/INSTALL.txt
@@ -0,0 +1,12 @@
+This software needs cmake >= 2.6 to build.
+
+After installing cmake, run it with the following command:
+cmake -DCMAKE_INSTALL_PREFIX=[where to install, for instance /usr/local or $HOME/.local] .
+
+If available, you can also use ccmake instead of cmake for a more user-friendly interface.
+
+Then compile and install the software with
+make install
+
+You may also consider installing and using the software checkinstall for easier system administration.
+
diff --git a/NEWS b/NEWS
new file mode 100644
index 0000000..e69de29
diff --git a/bpp-qt.spec b/bpp-qt.spec
new file mode 100644
index 0000000..cf63ff6
--- /dev/null
+++ b/bpp-qt.spec
@@ -0,0 +1,236 @@
+%define _basename bpp-qt
+%define _version 2.1.0
+%define _release 1
+%define _prefix /usr
+
+URL: http://biopp.univ-montp2.fr/
+
+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++ Qt graphic library
+Group: Development/Libraries/C and C++
+Requires: bpp-core = 2.0.3
+Requires: bpp-phyl = 2.0.3
+%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: 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
+
+%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
+
+%description
+This library contains graphic classes developed in Qt.
+It is part of the Bio++ project.
+
+%package -n libbpp-qt1
+Summary: Bio++ Qt graphic library
+Group: Development/Libraries/C and C++
+
+%description -n libbpp-qt1
+This library contains graphic classes developed in Qt.
+It is part of the Bio++ project.
+
+%package -n libbpp-qt-devel
+Summary: Libraries, includes to develop applications with %{_basename}
+Group: Development/Libraries/C and C++
+Requires: libbpp-qt1 = %{_version}
+Requires: libbpp-phyl9 = 2.1.0
+Requires: libbpp-phyl-devel = 2.1.0
+Requires: libbpp-core2 = 2.1.0
+Requires: libbpp-core-devel = 2.1.0
+%if 0%{?fedora} || 0%{?rhel_version} || 0%{?centos_version}
+Requires: qt >= 4.6.0
+Requires: qt-devel >= 4.6.0
+%endif
+%if 0%{?suse_version}
+Requires: libqt4 >= 4.6.0
+Requires: libqt4-devel >= 4.6.0
+%endif
+%if 0%{?mdkversion}
+%ifarch x86_64
+Requires: lib64qtgui4 >= 4.6.0
+Requires: lib64qt4-devel >= 4.6.0
+%else
+Requires: libqtgui4 >= 4.6.0
+Requires: libqt4-devel >= 4.6.0
+%endif
+%endif
+
+%description -n libbpp-qt-devel
+The libbpp-qt-devel package contains the header files and static libraries for
+building applications which use %{_basename}.
+
+%prep
+%setup -q
+
+%build
+CFLAGS="$RPM_OPT_FLAGS"
+CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=%{_prefix} -DBUILD_TESTING=OFF"
+if [ %{_lib} == 'lib64' ] ; then
+ CMAKE_FLAGS="$CMAKE_FLAGS -DLIB_SUFFIX=64"
+fi
+cmake $CMAKE_FLAGS .
+make
+
+%install
+make DESTDIR=$RPM_BUILD_ROOT install
+
+%clean
+rm -rf $RPM_BUILD_ROOT
+
+%post -n libbpp-qt1 -p /sbin/ldconfig
+
+%post -n libbpp-qt-devel
+createGeneric() {
+ echo "-- Creating generic include file: $1.all"
+ #Make sure we run into subdirectories first:
+ dirs=()
+ for file in "$1"/*
+ do
+ if [ -d "$file" ]
+ then
+ # Recursion:
+ dirs+=( "$file" )
+ fi
+ done
+ for dir in ${dirs[@]}
+ do
+ createGeneric $dir
+ done
+ #Now list all files, including newly created .all files:
+ if [ -f $1.all ]
+ then
+ rm $1.all
+ fi
+ dir=`basename $1`
+ for file in "$1"/*
+ do
+ if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] )
+ then
+ file=`basename $file`
+ echo "#include \"$dir/$file\"" >> $1.all
+ fi
+ done;
+}
+# Actualize .all files
+createGeneric %{_prefix}/include/Bpp
+exit 0
+
+%preun -n libbpp-qt-devel
+removeGeneric() {
+ if [ -f $1.all ]
+ then
+ echo "-- Remove generic include file: $1.all"
+ rm $1.all
+ fi
+ for file in "$1"/*
+ do
+ if [ -d "$file" ]
+ then
+ # Recursion:
+ removeGeneric $file
+ fi
+ done
+}
+# Actualize .all files
+removeGeneric %{_prefix}/include/Bpp
+exit 0
+
+%postun -n libbpp-qt1 -p /sbin/ldconfig
+
+%postun -n libbpp-qt-devel
+createGeneric() {
+ echo "-- Creating generic include file: $1.all"
+ #Make sure we run into subdirectories first:
+ dirs=()
+ for file in "$1"/*
+ do
+ if [ -d "$file" ]
+ then
+ # Recursion:
+ dirs+=( "$file" )
+ fi
+ done
+ for dir in ${dirs[@]}
+ do
+ createGeneric $dir
+ done
+ #Now list all files, including newly created .all files:
+ if [ -f $1.all ]
+ then
+ rm $1.all
+ fi
+ dir=`basename $1`
+ for file in "$1"/*
+ do
+ if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] )
+ then
+ file=`basename $file`
+ echo "#include \"$dir/$file\"" >> $1.all
+ fi
+ done;
+}
+# Actualize .all files
+createGeneric %{_prefix}/include/Bpp
+exit 0
+
+%files -n libbpp-qt1
+%defattr(-,root,root)
+%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
+%{_prefix}/%{_lib}/lib*.so.*
+
+%files -n libbpp-qt-devel
+%defattr(-,root,root)
+%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
+%{_prefix}/%{_lib}/lib*.so
+%{_prefix}/%{_lib}/lib*.a
+%{_prefix}/include/*
+
+%changelog
+* Fri Mar 08 2013 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.1.0-1
+- Compatibility update with other libraries.
+* Thu Feb 09 2012 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.0.2-1
+* Thu Jun 09 2011 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.0.1-1
+* Mon Feb 28 2011 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.0.0-1
+- First draft of the spec file
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..a5be0a6
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,25 @@
+libbpp-qt (2.1.0-1) unstable; urgency=low
+
+ * Compatibility update.
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Fri, 08 Mar 2013 09:44:00 +0100
+
+libbpp-qt (2.0.2-1) unstable; urgency=low
+
+ * Compatibility update.
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Thu, 09 Feb 2012 21:27:00 +0100
+
+libbpp-qt (2.0.1-1) unstable; urgency=low
+
+ * RFP: Bio++ -- The Bio++ bioinformatics libraries. (Closes: #616373).
+ * Packages are now non-native.
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Thu, 09 Jun 2011 11:00:00 +0100
+
+libbpp-qt (2.0.0) unstable; urgency=low
+
+ * Initial release
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Mon, 28 Feb 2011 09:00:00 +0100
+
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..7ed6ff8
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+5
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..b8726c6
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,28 @@
+Source: libbpp-qt
+Section: libs
+Priority: optional
+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-phyl-dev (>= 2.1.0),
+Standards-Version: 3.9.1
+
+Package: libbpp-qt-dev
+Section: libdevel
+Architecture: any
+Depends: libbpp-qt1 (= ${binary:Version}), ${misc:Depends},
+ libbpp-phyl-dev (>= 2.1.0), libqt4-dev (>= 4.6.0)
+Description: Bio++ Qt Graphic classes library development files.
+ Contains the Bio++ graphical classes developed with Qt.
+
+Package: libbpp-qt1
+Section: libs
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ libbpp-phyl9 (>= 2.1.0),
+ libqtcore4 (>= 4.6.0), libqtgui4 (>= 4.6.0)
+Description: Bio++ Qt Graphic classes library.
+ Contains the Bio++ graphical classes developed with Qt.
+
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..d481687
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,66 @@
+This package was debianized by Julien Dutheil <julien.dutheil at univ-montp2.fr> on
+Fri, 08 Mar 2013 09:44:00 +0100
+
+It was downloaded from <http://kimura.univ-montp2.fr/Repositories/sources>
+
+Upstream Author:
+
+ Julien Dutheil <julien.dutheil at univ-montp2.fr>
+
+Copyright:
+
+ Copyright (C) 2013 Bio++ Development Team
+
+License:
+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL'.
+
+The Debian packaging is (C) 2013, Julien Dutheil <julien.dutheil at univ-montp2.fr> and
+is licensed under the GPL, see above.
+
+The provided software is distributed under the CeCILL license:
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+
+The complete text of the license may be found here:
+http://www.cecill.info/licences/Licence_CeCILL_V2-en.html
+
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..e69de29
diff --git a/debian/libbpp-qt-dev.install b/debian/libbpp-qt-dev.install
new file mode 100644
index 0000000..7d74f2b
--- /dev/null
+++ b/debian/libbpp-qt-dev.install
@@ -0,0 +1,3 @@
+debian/tmp/usr/include/*
+debian/tmp/usr/lib/lib*.a
+debian/tmp/usr/lib/lib*.so
diff --git a/debian/libbpp-qt1.install b/debian/libbpp-qt1.install
new file mode 100644
index 0000000..c45ebcf
--- /dev/null
+++ b/debian/libbpp-qt1.install
@@ -0,0 +1 @@
+debian/tmp/usr/lib/lib*.so.*
diff --git a/debian/postinst b/debian/postinst
new file mode 100755
index 0000000..cf9e925
--- /dev/null
+++ b/debian/postinst
@@ -0,0 +1,43 @@
+#! /bin/bash
+
+# Abort if any command returns an error value
+set -e
+
+createGeneric() {
+ echo "-- Creating generic include file: $1.all"
+ #Make sure we run into subdirectories first:
+ dirs=()
+ for file in "$1"/*
+ do
+ if [ -d "$file" ]
+ then
+ # Recursion:
+ dirs+=( "$file" )
+ fi
+ done
+ for dir in ${dirs[@]}
+ do
+ createGeneric $dir
+ done
+ #Now list all files, including newly created .all files:
+ if [ -f $1.all ]
+ then
+ rm $1.all
+ fi
+ dir=`basename $1`
+ for file in "$1"/*
+ do
+ if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] )
+ then
+ file=`basename $file`
+ echo "#include \"$dir/$file\"" >> $1.all
+ fi
+ done;
+}
+
+if [ "$1" = "configure" ]; then
+ # Actualize .all files
+ createGeneric /usr/include/Bpp
+fi
+
+exit 0
diff --git a/debian/postrm b/debian/postrm
new file mode 100755
index 0000000..3931669
--- /dev/null
+++ b/debian/postrm
@@ -0,0 +1,45 @@
+#! /bin/bash
+
+# Abort if any command returns an error value
+set -e
+
+createGeneric() {
+ echo "-- Creating generic include file: $1.all"
+ #Make sure we run into subdirectories first:
+ dirs=()
+ for file in "$1"/*
+ do
+ if [ -d "$file" ]
+ then
+ # Recursion:
+ dirs+=( "$file" )
+ fi
+ done
+ for dir in ${dirs[@]}
+ do
+ createGeneric $dir
+ done
+ #Now list all files, including newly created .all files:
+ if [ -f $1.all ]
+ then
+ rm $1.all
+ fi
+ dir=`basename $1`
+ for file in "$1"/*
+ do
+ if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] )
+ then
+ file=`basename $file`
+ echo "#include \"$dir/$file\"" >> $1.all
+ fi
+ done;
+}
+
+if [ "$1" = "remove" ]; then
+ # Automatically added by dh_makeshlibs
+ ldconfig
+ # Actualize .all files
+ createGeneric /usr/include/Bpp
+fi
+
+exit 0
diff --git a/debian/prerm b/debian/prerm
new file mode 100755
index 0000000..5aefd24
--- /dev/null
+++ b/debian/prerm
@@ -0,0 +1,27 @@
+#! /bin/bash
+
+# Abort if any command returns an error value
+set -e
+
+removeGeneric() {
+ if [ -f $1.all ]
+ then
+ echo "-- Remove generic include file: $1.all"
+ rm $1.all
+ fi
+ for file in "$1"/*
+ do
+ if [ -d "$file" ]
+ then
+ # Recursion:
+ removeGeneric $file
+ fi
+ done
+}
+
+if [ "$1" = "remove" ]; then
+ # Actualize .all files
+ removeGeneric /usr/include/Bpp
+fi
+
+exit 0
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..b38bb97
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,119 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# 24/01/10 Modification for use with CMake by Julien Dutheil.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+# These are used for cross-compiling and for saving the configure script
+# from having to guess our platform (since we know it already)
+DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
+DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+# shared library versions
+version=`ls src/lib*.so.* | \
+ awk '{if (match($$0,/[0-9]+\.[0-9]+\.[0-9]+$$/)) print substr($$0,RSTART)}'`
+major=`ls src/lib*.so.* | \
+ awk '{if (match($$0,/\.so\.[0-9]+$$/)) print substr($$0,RSTART+4)}'`
+
+configure:
+ cmake -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_TESTING=OFF .
+
+config.status: configure
+ dh_testdir
+
+build: build-stamp
+build-stamp: config.status
+ dh_testdir
+
+ # Add here commands to compile the package.
+ $(MAKE)
+
+ touch $@
+
+clean:
+ dh_testdir
+ dh_testroot
+
+ # Add here commands to clean up after the build process.
+ [ ! -f Makefile ] || $(MAKE) clean;
+ [ ! -f Makefile ] || rm Makefile;
+ [ ! -f src/Makefile ] || rm src/Makefile;
+ rm -f config.sub config.guess
+ rm -f build-stamp
+ rm -f CMakeCache.txt
+ rm -f *.cmake
+ rm -f src/*.cmake
+ #rm -f test/*.cmake
+ rm -rf CMakeFiles
+ rm -rf src/CMakeFiles
+ #rm -rf test/CMakeFiles
+ rm -rf _CPack_Packages
+ #rm -rf Testing
+ #rm -f DartConfiguration.tcl
+
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_prep
+ dh_installdirs
+
+ # Add here commands to install the package into debian/tmp
+ $(MAKE) DESTDIR=$(CURDIR)/debian/tmp install
+
+
+# Build architecture-independent files here.
+binary-indep: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs ChangeLog
+ dh_installdocs
+ dh_installexamples
+ dh_install
+# dh_installmenu
+# dh_installdebconf
+# dh_installlogrotate
+# dh_installemacsen
+# dh_installpam
+# dh_installmime
+# dh_installinit
+# dh_installcron
+# dh_installinfo
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+# dh_perl
+# dh_python
+ dh_makeshlibs
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/src/Bpp/Qt/MouseListener.h b/src/Bpp/Qt/MouseListener.h
new file mode 100644
index 0000000..df4b7d5
--- /dev/null
+++ b/src/Bpp/Qt/MouseListener.h
@@ -0,0 +1,155 @@
+//
+// File: MouseListener.h
+// Created by: Julien Dutheil
+// Created on: Tue May 11 13:04 2010
+//
+
+/*
+Copyright or © or Copr. Bio++ Develomment Team, (2010)
+
+This software is a computer program whose purpose is to provide
+graphic components to develop bioinformatics applications.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _MOUSELISTENER_H_
+#define _MOUSELISTENER_H_
+
+#include <Bpp/Clonable.h>
+
+//From the STL:
+#include <vector>
+
+//From Qt:
+#include <QMouseEvent>
+
+namespace bpp {
+
+/**
+ * @brief a general interface to grab mouse events associated to a widget.
+ */
+class MouseListener:
+ public virtual Clonable
+{
+ public:
+#ifndef NO_VIRTUALCOV
+ MouseListener* clone() const = 0;
+#endif
+
+ public:
+ virtual void mouseDoubleClickEvent(QMouseEvent* event) = 0;
+ virtual void mouseMoveEvent(QMouseEvent* event) = 0;
+ virtual void mousePressEvent(QMouseEvent *event) = 0;
+ virtual void mouseReleaseEvent(QMouseEvent *event) = 0;
+
+ virtual bool isAutonomous() const = 0;
+};
+
+/**
+ * @brief an empty implementation of the MouseListener interface.
+ */
+class MouseAdapter:
+ public virtual MouseListener
+{
+ public:
+ void mouseDoubleClickEvent(QMouseEvent* event) {}
+ void mouseMoveEvent(QMouseEvent* event) {}
+ void mousePressEvent(QMouseEvent *event) {}
+ void mouseReleaseEvent(QMouseEvent *event) {}
+};
+
+/**
+ * @brief a helper class that deal with several MouseListener classes.
+ */
+class MouseListenerGroup
+{
+ private:
+ std::vector<MouseListener*> mouseListeners_;
+
+ public:
+ MouseListenerGroup(): mouseListeners_() {}
+
+ MouseListenerGroup(const MouseListenerGroup& mlg):
+ mouseListeners_(mlg.mouseListeners_)
+ {
+ for (unsigned int i = 0; i < mlg.mouseListeners_.size(); i++)
+ if (!mlg.mouseListeners_[i]->isAutonomous())
+ mouseListeners_[i] = dynamic_cast<MouseListener*>(mlg.mouseListeners_[i]->clone());
+ }
+
+ MouseListenerGroup& operator=(const MouseListenerGroup& mlg)
+ {
+ mouseListeners_ = mlg.mouseListeners_;
+ for (unsigned int i = 0; i < mlg.mouseListeners_.size(); i++)
+ if (!mlg.mouseListeners_[i]->isAutonomous())
+ mouseListeners_[i] = dynamic_cast<MouseListener*>(mlg.mouseListeners_[i]->clone());
+ return *this;
+ }
+
+ virtual ~MouseListenerGroup()
+ {
+ for (unsigned int i = 0; i < mouseListeners_.size(); i++)
+ if (!mouseListeners_[i]->isAutonomous())
+ delete mouseListeners_[i];
+ }
+
+ public:
+ void addMouseListener(MouseListener* listener)
+ {
+ mouseListeners_.push_back(listener);
+ }
+
+ void processMouseDoubleClickEvent(QMouseEvent* event)
+ {
+ for (unsigned int i = 0; i < mouseListeners_.size(); i++)
+ mouseListeners_[i]->mouseDoubleClickEvent(event);
+ }
+
+ void processMouseMoveEvent(QMouseEvent* event)
+ {
+ for (unsigned int i = 0; i < mouseListeners_.size(); i++)
+ mouseListeners_[i]->mouseMoveEvent(event);
+ }
+ void processMousePressEvent(QMouseEvent* event)
+ {
+ for (unsigned int i = 0; i < mouseListeners_.size(); i++)
+ mouseListeners_[i]->mousePressEvent(event);
+ }
+
+ void processMouseReleaseEvent(QMouseEvent* event)
+ {
+ for (unsigned int i = 0; i < mouseListeners_.size(); i++)
+ mouseListeners_[i]->mouseReleaseEvent(event);
+ }
+
+};
+
+} //end of namespace bpp.
+
+#endif //_MOUSELISTENER_H_
+
diff --git a/src/Bpp/Qt/MouseListeningWidget.h b/src/Bpp/Qt/MouseListeningWidget.h
new file mode 100644
index 0000000..ae45a4e
--- /dev/null
+++ b/src/Bpp/Qt/MouseListeningWidget.h
@@ -0,0 +1,92 @@
+//
+// File: MouseListeningWidget.h
+// Created by: Julien Dutheil
+// Created on: Tue May 11 13:22 2010
+//
+
+/*
+Copyright or © or Copr. Bio++ Develomment Team, (2010)
+
+This software is a computer program whose purpose is to provide
+graphic components to develop bioinformatics applications.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _MOUSELISTENINGWIDGET_H_
+#define _MOUSELISTENINGWIDGET_H_
+
+#include "MouseListener.h"
+
+//From Qt:
+#include <QWidget>
+
+namespace bpp {
+
+/**
+ * @brief A simple QWidget object which adds support for mouse listeners.
+ */
+class MouseListeningWidget:
+ public QWidget
+{
+ Q_OBJECT
+
+ private:
+ MouseListenerGroup mouseListenerGroup_;
+
+ public:
+ void addMouseListener(MouseListener* listener)
+ {
+ mouseListenerGroup_.addMouseListener(listener);
+ }
+
+ protected:
+
+ void mouseDoubleClickEvent(QMouseEvent* event)
+ {
+ mouseListenerGroup_.processMouseDoubleClickEvent(event);
+ }
+
+ void mouseMoveEvent(QMouseEvent* event)
+ {
+ mouseListenerGroup_.processMouseMoveEvent(event);
+ }
+ void mousePressEvent(QMouseEvent* event)
+ {
+ mouseListenerGroup_.processMousePressEvent(event);
+ }
+
+ void mouseReleaseEvent(QMouseEvent* event)
+ {
+ mouseListenerGroup_.processMouseReleaseEvent(event);
+ }
+};
+
+} //end of namespace bpp.
+
+#endif //_MOUSELISTENINGWIDGET_H_
+
diff --git a/src/Bpp/Qt/QtGraphicDevice.cpp b/src/Bpp/Qt/QtGraphicDevice.cpp
new file mode 100644
index 0000000..89afea5
--- /dev/null
+++ b/src/Bpp/Qt/QtGraphicDevice.cpp
@@ -0,0 +1,160 @@
+//
+// File: QtGraphicDevice.cpp
+// Created by: Julien Dutheil
+// Created on: Thu Jul 16 2009
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 16, 2006)
+
+This software is a computer program whose purpose is to provide
+graphical components using the Qt library.
+This file belongs to the Bio++ Project.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "QtGraphicDevice.h"
+#include "QtTools.h"
+
+//From Qt:
+#include <QGraphicsLineItem>
+#include <QGraphicsRectItem>
+#include <QGraphicsTextItem>
+#include <QTextDocument>
+#include <QFontInfo>
+
+//From the STL:
+#include <iostream>
+using namespace std;
+
+using namespace bpp;
+
+QtGraphicDevice::QtGraphicDevice() :
+ scene_(0), supportedLineTypes_(), currentPen_(), currentBrush_(Qt::SolidPattern), currentFont_()
+{
+ supportedLineTypes_[GraphicDevice::LINE_SOLID] = Qt::SolidLine;
+ supportedLineTypes_[GraphicDevice::LINE_DASHED] = Qt::DashLine;
+ supportedLineTypes_[GraphicDevice::LINE_DOTTED] = Qt::DotLine;
+ setXUnit(1.);
+ setYUnit(1.);
+}
+
+QtGraphicDevice::~QtGraphicDevice() {}
+
+void QtGraphicDevice::begin() throw (Exception)
+{
+ if (scene_) delete scene_;
+ scene_ = new QGraphicsScene();
+}
+
+void QtGraphicDevice::end()
+{
+}
+
+void QtGraphicDevice::setCurrentForegroundColor(const RGBColor& color)
+{
+ AbstractGraphicDevice::setCurrentForegroundColor(color);
+ currentPen_.setColor(QtTools::toQt(color));
+}
+
+void QtGraphicDevice::setCurrentBackgroundColor(const RGBColor& color)
+{
+ AbstractGraphicDevice::setCurrentBackgroundColor(color);
+ currentBrush_.setColor(QtTools::toQt(color));
+}
+
+void QtGraphicDevice::setCurrentFont(const Font& font)
+{
+ AbstractGraphicDevice::setCurrentFont(font);
+ currentFont_ = QtTools::toQt(font);
+}
+
+void QtGraphicDevice::setCurrentPointSize(unsigned int size)
+{
+ AbstractGraphicDevice::setCurrentPointSize(size);
+ currentPen_.setWidth(static_cast<uint>(size));
+}
+
+void QtGraphicDevice::setCurrentLineType(short type) throw (Exception)
+{
+ AbstractGraphicDevice::setCurrentLineType(type);
+ currentPen_.setStyle(supportedLineTypes_[type]);
+}
+
+//void QtGraphicDevice::setCurrentLayer(int layerIndex)
+//{
+//
+//}
+
+void QtGraphicDevice::drawLine(double x1, double y1, double x2, double y2)
+{
+ QGraphicsLineItem* item = scene_->addLine(xpos(x1), ypos(y1), xpos(x2), ypos(y2), currentPen_);
+ item->setZValue(-qreal(getCurrentLayer()));
+}
+
+
+void QtGraphicDevice::drawRect(double x, double y, double width, double height, short fill)
+{
+ QGraphicsRectItem* item = scene_->addRect(xpos(x), ypos(y), width * getXUnit(), height * getYUnit(), currentPen_, currentBrush_);
+ item->setZValue(-qreal(getCurrentLayer()));
+}
+
+void QtGraphicDevice::drawCircle(double x, double y, double radius, short fill)
+{
+
+}
+
+void QtGraphicDevice::drawText(double x, double y, const std::string& text, short hpos, short vpos, double angle) throw (UnvalidFlagException)
+{
+ int xset = 0, yset = 0;
+ QString qtext = text.c_str();
+ QGraphicsTextItem* item = scene_->addText(qtext, currentFont_);
+ QSizeF fsize = item->document()->size();
+ QFontInfo fi(currentFont_);
+ double mar = (fsize.rheight() - fi.pixelSize()) / 2;
+ if (hpos == TEXT_HORIZONTAL_LEFT)
+ xset = 0;
+ else if (hpos == TEXT_HORIZONTAL_RIGHT)
+ xset = -fsize.rwidth();
+ else if (hpos == TEXT_HORIZONTAL_CENTER)
+ xset = -fsize.rwidth() / 2;
+ else throw UnvalidFlagException("QtGraphicDevice::drawText(). Unvalid horizontal alignment option.");
+
+ if (vpos == TEXT_VERTICAL_TOP) {
+ yset = mar;
+ } else if (vpos == TEXT_VERTICAL_BOTTOM) {
+ yset = fi.pixelSize() + mar;
+ } else if (vpos == TEXT_VERTICAL_CENTER) {
+ yset = fi.pixelSize() / 2 + mar;
+ } else throw UnvalidFlagException("QtGraphicDevice::drawText(). Unvalid vertical alignment option.");
+
+ item->setPos(xpos(x) + xset, ypos(y) - yset);
+ item->setDefaultTextColor(currentPen_.color());
+ item->setZValue(-qreal(getCurrentLayer()));
+}
+
diff --git a/src/Bpp/Qt/QtGraphicDevice.h b/src/Bpp/Qt/QtGraphicDevice.h
new file mode 100644
index 0000000..fec7365
--- /dev/null
+++ b/src/Bpp/Qt/QtGraphicDevice.h
@@ -0,0 +1,118 @@
+//
+// File: QtGraphicDevice.h
+// Created by: Julien Dutheil
+// Created on: Thu Jul 16 2009
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 16, 2006)
+
+This software is a computer program whose purpose is to provide
+graphical components using the Qt library.
+This file belongs to the Bio++ Project.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _QTGRAPHICDEVICE_H_
+#define _QTGRAPHICDEVICE_H_
+
+#include <Bpp/Graphics/AbstractGraphicDevice.h>
+
+//From Qt:
+#include <QGraphicsScene>
+#include <Qt>
+
+//From the STL:
+#include <map>
+
+/**
+ * @mainpage
+ *
+ * @par
+ * This library provides graphic classes for Bio++ developed using the Qt library.
+ * The class QtGraphicDevice implements the GraphicDevice interface of the bpp-core library, allowing output in a Qt widget.
+ * Similarly, the QtOutputStream implemente the OutputStream interface, and allows to redirect outputs to a widget.
+ *
+ * @par
+ * For now, only phylogeny-oriented widgets are available. Sequence-oriented widgets will be developed in the future.
+ */
+
+namespace bpp
+{
+
+/**
+ * @brief Bio++ wrapper for the QPainter class.
+ *
+ * This class implements the GraphicDevice interface from the bio++ core library, and calls the corresponding QPainter methods.
+ */
+class QtGraphicDevice:
+ public AbstractGraphicDevice
+{
+ private:
+ QGraphicsScene* scene_;
+ std::map<short int, Qt::PenStyle> supportedLineTypes_;
+ QPen currentPen_;
+ QBrush currentBrush_;
+ QFont currentFont_;
+
+ public:
+ QtGraphicDevice();
+ virtual ~QtGraphicDevice();
+
+ public:
+ QGraphicsScene& getScene() { return *scene_; }
+
+ void begin() throw (Exception);
+ void end();
+
+ void setCurrentForegroundColor(const RGBColor& color);
+ void setCurrentBackgroundColor(const RGBColor& color);
+ void setCurrentFont(const Font& font);
+ void setCurrentPointSize(unsigned int size);
+ void setCurrentLineType(short type) throw (Exception);
+
+ void drawLine(double x1, double y1, double x2, double y2);
+ void drawRect(double x, double y, double width, double height, short fill = FILL_EMPTY);
+ void drawCircle(double x, double y, double radius, short fill = FILL_EMPTY);
+ void drawText(double x, double y, const std::string& text, short hpos = TEXT_HORIZONTAL_LEFT, short vpos = TEXT_VERTICAL_BOTTOM, double angle = 0) throw (UnvalidFlagException);
+
+ void comment(const std::string& comment) {}
+
+ public:
+ int xpos(double x) const { return static_cast<int>(round(x_(x))); }
+ int ypos(double y) const { return static_cast<int>(round(y_(y))); }
+ double revx(int xpos) const { return revx_(static_cast<double>(xpos)); }
+ double revy(int ypos) const { return revy_(static_cast<double>(ypos)); }
+
+
+};
+
+} //end of namespace bpp
+
+#endif //_QTGRAPHICDEVICE_H_
+
diff --git a/src/Bpp/Qt/QtOutputStream.cpp b/src/Bpp/Qt/QtOutputStream.cpp
new file mode 100644
index 0000000..be1d197
--- /dev/null
+++ b/src/Bpp/Qt/QtOutputStream.cpp
@@ -0,0 +1,58 @@
+// File: QtOutputStream.h
+// Created by: Julien Dutheil
+// Created on: Mon Jan 25 2010
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 16, 2006)
+
+This software is a computer program whose purpose is to provide
+graphical components using the Qt library.
+This file belongs to the Bio++ Project.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "QtOutputStream.h"
+
+using namespace bpp;
+
+void QtOutputStream::checkNumberOfLines()
+{
+ QString text = toPlainText();
+ unsigned int nbLines = static_cast<unsigned int>(text.count('\n'));
+ if (nbLines > maxNbLines_)
+ {
+ unsigned int rm = nbLines - maxNbLines_;
+ for (unsigned int i = 0; i < rm; i++)
+ {
+ text.remove(0, text.indexOf('\n') + 1);
+ }
+ setPlainText(text);
+ }
+}
+
diff --git a/src/Bpp/Qt/QtOutputStream.h b/src/Bpp/Qt/QtOutputStream.h
new file mode 100644
index 0000000..0264bb6
--- /dev/null
+++ b/src/Bpp/Qt/QtOutputStream.h
@@ -0,0 +1,123 @@
+//
+// File: QtOutputStream.h
+// Created by: Julien Dutheil
+// Created on: Mon Jan 25 2010
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 16, 2006)
+
+This software is a computer program whose purpose is to provide
+graphical components using the Qt library.
+This file belongs to the Bio++ Project.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _QTOUTPUTSTREAM_H_
+#define _QTOUTPUTSTREAM_H_
+
+#include "QtTools.h"
+
+#include <Bpp/Io/OutputStream.h>
+
+//From Qt:
+#include <QPainter>
+#include <Qt>
+#include <QTextEdit>
+
+//From the STL:
+#include <map>
+#include <iostream>
+
+namespace bpp
+{
+
+/**
+ * @brief Qt output stream: Qt widget that implements the OutputStream interface.
+ *
+ * The stream is printed as a read-only text. The number of lines to display can be set.
+ */
+class QtOutputStream :
+ public AbstractOutputStream,
+ public QTextEdit
+{
+private:
+ unsigned int maxNbLines_;
+ QString buffer;
+
+public:
+ QtOutputStream(QWidget* parent = 0) :
+ QTextEdit(parent),
+ maxNbLines_(100)
+ {
+ setReadOnly(true);
+ }
+
+private:
+ QtOutputStream(const QtOutputStream& outputstream) {}
+ QtOutputStream& operator=(const QtOutputStream& outputstream) { return *this; }
+
+public:
+ QtOutputStream& operator<<(const QString& message) { buffer.append(message); return *this; }
+ QtOutputStream& operator<<(const std::string& message) { buffer.append(QtTools::toQt(message)); return *this; }
+ QtOutputStream& operator<<(const char* message) { buffer.append(QString(message)); return *this; }
+ QtOutputStream& operator<<(const char& message) { buffer.append(QtTools::toQt(TextTools::toString(message))); return *this; }
+ QtOutputStream& operator<<(const int& message) { buffer.append(QtTools::toQt(TextTools::toString(message))); return *this; }
+ QtOutputStream& operator<<(const unsigned int& message) { buffer.append(QtTools::toQt(TextTools::toString(message))); return *this; }
+ QtOutputStream& operator<<(const long int& message) { buffer.append(QtTools::toQt(TextTools::toString(message))); return *this; }
+ QtOutputStream& operator<<(const unsigned long int& message) { buffer.append(QtTools::toQt(TextTools::toString(message))); return *this; }
+ QtOutputStream& operator<<(const double& message) { buffer.append(QtTools::toQt(TextTools::toString(message, getPrecision()))); return *this; }
+ QtOutputStream& operator<<(const long double& message) { buffer.append(QtTools::toQt(TextTools::toString(message, getPrecision()))); return *this; }
+ QtOutputStream& operator<<(const bool& message) { buffer.append(QtTools::toQt(TextTools::toString(message))); return *this; }
+ QtOutputStream& endLine()
+ {
+ buffer.append("\n");
+ return flush();
+ }
+ QtOutputStream& flush()
+ {
+ insertPlainText(buffer);
+ buffer.fill(' ', 0);
+ checkNumberOfLines();
+ update();
+ return *this;
+ }
+
+ QtOutputStream* clone() const { return new QtOutputStream(*this); }
+
+private:
+ void checkNumberOfLines();
+
+};
+
+
+
+} //end of namespace bpp
+
+#endif //_QTOUTPUTSTREAM_H_
+
diff --git a/src/Bpp/Qt/QtTools.h b/src/Bpp/Qt/QtTools.h
new file mode 100644
index 0000000..ca6269e
--- /dev/null
+++ b/src/Bpp/Qt/QtTools.h
@@ -0,0 +1,113 @@
+//
+// File: QtTools.h
+// Created by: Julien Dutheil
+// Created on: Wed Dec 30 2009
+//
+
+/*
+Copyright or © or Copr. CNRS, (November 16, 2006)
+
+This software is a computer program whose purpose is to provide
+graphical components using the Qt library.
+This file belongs to the Bio++ Project.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _QTTOOLS_H_
+#define _QTTOOLS_H_
+
+#include <Bpp/Graphics/RgbColor.h>
+#include <Bpp/Graphics/Font/Font.h>
+#include <Bpp/BppString.h>
+#include <Bpp/Numeric/Number.h>
+
+//From Qt:
+#include <QColor>
+#include <QFont>
+
+namespace bpp
+{
+
+/**
+ * @brief Utilitary functions for working with Qt.
+ *
+ * Contains mostly conversion tools.
+ */
+class QtTools
+{
+public:
+
+ static QString toQt(const char* str)
+ {
+ return QString(str);
+ }
+
+ static QString toQt(const std::string& str)
+ {
+ return QString(str.c_str());
+ }
+
+ static QString toQt(const BppString& str)
+ {
+ return QString(str.toSTL().c_str());
+ }
+
+ template<class T>
+ static QString toQt(const Number<T>& number)
+ {
+ return toQt(TextTools::toString(number.getValue()));
+ }
+
+ static QColor toQt(const RGBColor& color)
+ {
+ return QColor(color[0], color[1], color[2]);
+ }
+
+ static QFont toQt(const Font& font)
+ {
+ QFont qFont(toQt(font.getFamily()), static_cast<int>(font.getSize()));
+
+ if (font.getStyle() == Font::STYLE_NORMAL)
+ qFont.setStyle(QFont::StyleNormal);
+ else if(font.getStyle() == Font::STYLE_ITALIC)
+ qFont.setStyle(QFont::StyleItalic);
+
+ if (font.getWeight() == Font::WEIGHT_NORMAL)
+ qFont.setWeight(QFont::Normal);
+ else if (font.getWeight() == Font::WEIGHT_BOLD)
+ qFont.setWeight(QFont::Bold);
+
+ return qFont;
+ }
+
+};
+
+} //end of namespace bpp;
+
+#endif //_QTTOOLS_H_
+
diff --git a/src/Bpp/Qt/Tree/TreeCanvas.cpp b/src/Bpp/Qt/Tree/TreeCanvas.cpp
new file mode 100644
index 0000000..ea8b9d7
--- /dev/null
+++ b/src/Bpp/Qt/Tree/TreeCanvas.cpp
@@ -0,0 +1,150 @@
+//
+// File: TreeCanvas.cpp
+// Created by: Julien Dutheil
+// Created on: Tue Oct 4 09:20 2006
+//
+
+/*
+Copyright or � or Copr. Bio++ Development Team, (November 16, 2004)
+
+This software is a computer program whose purpose is to provide
+graphic components to develop bioinformatics applications.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "TreeCanvas.h"
+#include <QGraphicsItem>
+
+//From PhyLib:
+#include <Bpp/Phyl/Graphics/CladogramPlot.h>
+
+using namespace bpp;
+
+#include <iostream>
+using namespace std;
+
+NodeMouseEvent::NodeMouseEvent(const TreeCanvas& treeCanvas, const QMouseEvent& event):
+ QMouseEvent(event), hasNode_(false), nodeId_(0)
+{
+ QPointF scenePos = treeCanvas.mapToScene(event.pos());
+ Point2D<double> pos(
+ treeCanvas.getDevice().revx(scenePos.x()),
+ treeCanvas.getDevice().revy(scenePos.y()));
+ try {
+ nodeId_ = treeCanvas.getTreeDrawing()->getNodeAt(pos);
+ hasNode_ = true;
+ } catch (std::exception& e) {
+ hasNode_ = false;
+ }
+}
+
+TreeCanvas::TreeCanvas(QWidget* parent) :
+ QGraphicsView(parent),
+ currentTree_(0),
+ device_(),
+ drawingWidth_(600),
+ drawingHeight_(800),
+ mouseListenerGroup_()
+{
+ defaultTreeDrawing_ = new CladogramPlot();
+ treeDrawing_ = defaultTreeDrawing_;
+}
+
+void TreeCanvas::redraw()
+{
+ if (treeDrawing_ && treeDrawing_->hasTree())
+ {
+ QPointF p = mapToScene(contentsRect().center());
+ device_.begin();
+ treeDrawing_->setXUnit(static_cast<double>(drawingWidth()) / treeDrawing_->getWidth());
+ treeDrawing_->setYUnit(static_cast<double>(drawingHeight()) / treeDrawing_->getHeight());
+ treeDrawing_->plot(device_);
+ device_.end();
+ QGraphicsScene* scene = &device_.getScene();
+
+ //Need to do that because line have can have a bounding box with null dimension.
+ QRectF rect;
+ QList<QGraphicsItem*> items = scene->items();
+ for (int i = 0; i < items.size(); i++) {
+ QRectF bb = items[i]->boundingRegion(items[i]->sceneTransform()).boundingRect();
+ if (i == 0) rect = bb;
+ else {
+ rect.setLeft(min(rect.left(), bb.left()));
+ rect.setRight(max(rect.right(), bb.right()));
+ rect.setBottom(max(rect.bottom(), bb.bottom()));
+ rect.setTop(min(rect.top(), bb.top()));
+ }
+ }
+ rect.setLeft(rect.left() - 5);
+ rect.setRight(rect.right() + 5);
+ rect.setBottom(rect.bottom() + 5);
+ rect.setTop(rect.top() - 5);
+ scene->setSceneRect(rect);
+ setScene(scene);
+ centerOn(p);
+ emit drawingChanged();
+ }
+}
+
+void TreeCanvas::setTree(const Tree* tree)
+{
+ currentTree_ = tree;
+ treeDrawing_->setTree(tree);
+ nodeCollapsed_.clear();
+ redraw();
+}
+
+void TreeCanvas::setTreeDrawing(const TreeDrawing& treeDrawing, bool repaint)
+{
+ if (treeDrawing_ != defaultTreeDrawing_)
+ delete treeDrawing_;
+ treeDrawing_ = dynamic_cast<TreeDrawing*>(treeDrawing.clone());
+ treeDrawing_->setTree(currentTree_);
+ vector<int> ids = currentTree_->getNodesId();
+ for (unsigned int i = 0; i < ids.size(); i++) {
+ treeDrawing_->collapseNode(ids[i], nodeCollapsed_[ids[i]]);
+ }
+ if (repaint) {
+ this->repaint();
+ }
+}
+
+QList<QGraphicsTextItem*> TreeCanvas::searchText(const QString& text)
+{
+ QList<QGraphicsTextItem*> match;
+ QList<QGraphicsItem*> items = device_.getScene().items();
+ for (int i = 0; i < items.size(); ++i) {
+ QGraphicsTextItem* item = dynamic_cast<QGraphicsTextItem*>(items[i]);
+ if (item) {
+ if (item->toPlainText().indexOf(text) > -1) {
+ match.append(item);
+ }
+ } //Else not a text item
+ }
+ return match;
+}
diff --git a/src/Bpp/Qt/Tree/TreeCanvas.h b/src/Bpp/Qt/Tree/TreeCanvas.h
new file mode 100644
index 0000000..49e4508
--- /dev/null
+++ b/src/Bpp/Qt/Tree/TreeCanvas.h
@@ -0,0 +1,212 @@
+//
+// File: TreeCanvas.h
+// Created by: Julien Dutheil
+// Created on: Tue Oct 4 09:20 2006
+//
+
+/*
+Copyright or � or Copr. Bio++ Development Team, (November 16, 2004)
+
+This software is a computer program whose purpose is to provide
+graphic components to develop bioinformatics applications.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _TREECANVAS_H_
+#define _TREECANVAS_H_
+
+#include "../QtGraphicDevice.h"
+#include "../MouseListener.h"
+
+//From the STL:
+#include <vector>
+#include <map>
+#include <string>
+#include <algorithm>
+
+//From PhylLib:
+#include <Bpp/Phyl/Tree.h>
+#include <Bpp/Phyl/Graphics/TreeDrawing.h>
+#include <Bpp/Phyl/Graphics/AbstractTreeDrawing.h>
+
+//From Qt:
+#include <QGraphicsView>
+
+namespace bpp
+{
+
+class TreeCanvas;
+
+/**
+ * @brief A simple mouse event.
+ */
+class NodeMouseEvent:
+ public QMouseEvent
+{
+ private:
+ bool hasNode_;
+ int nodeId_;
+
+ public:
+ NodeMouseEvent(const TreeCanvas& treeCanvas, const QMouseEvent& event);
+
+ bool hasNodeId() const { return hasNode_; }
+
+ int getNodeId() const throw (NodeNotFoundException)
+ {
+ if (!hasNode_)
+ throw NodeNotFoundException("NodeMouseEvent::getNodeId().", "");
+ else
+ return nodeId_;
+ }
+
+};
+
+/**
+ * @brief Panel for plotting phylogenetic trees.
+ *
+ * The graphe used for plotting the tree depends on the TreeDrawing object used.
+ * This panel can also capture event when a node is clicked on the tree.
+ */
+class TreeCanvas:
+ public QGraphicsView
+{
+ Q_OBJECT
+
+ private:
+ const Tree* currentTree_;
+ TreeDrawing* treeDrawing_;
+ TreeDrawing* defaultTreeDrawing_;
+ mutable QtGraphicDevice device_;
+ unsigned int drawingWidth_;
+ unsigned int drawingHeight_;
+ MouseListenerGroup mouseListenerGroup_;
+ mutable std::map<int, bool> nodeCollapsed_;
+
+ public:
+ TreeCanvas(QWidget* parent = 0);
+ virtual ~TreeCanvas()
+ {
+ delete defaultTreeDrawing_;
+ }
+
+ public:
+ virtual void setTree(const Tree* tree);
+
+ virtual const Tree* getTree() const { return currentTree_; }
+
+ virtual void setTreeDrawing(const TreeDrawing& treeDrawing, bool repaint = true);
+
+ virtual TreeDrawing* getTreeDrawing() { return treeDrawing_; }
+ virtual const TreeDrawing* getTreeDrawing() const { return treeDrawing_; }
+
+ virtual QtGraphicDevice& getDevice() { return device_; }
+ virtual const QtGraphicDevice& getDevice() const { return device_; }
+
+ virtual void setDrawingSize(unsigned int width, unsigned int height)
+ {
+ drawingWidth_ = width;
+ drawingHeight_ = height;
+ redraw();
+ }
+
+ virtual unsigned int drawingWidth() const { return drawingWidth_; }
+ virtual unsigned int drawingHeight() const { return drawingHeight_; }
+
+ void collapseNode(int nodeId, bool tf) throw (NodeNotFoundException)
+ {
+ if (!currentTree_) return;
+ if (!currentTree_->hasNode(nodeId))
+ throw NodeNotFoundException("TreeCanvas::collapseNode.", nodeId);
+ if (treeDrawing_)
+ treeDrawing_->collapseNode(nodeId, tf);
+ nodeCollapsed_[nodeId] = tf;
+ }
+
+ bool isNodeCollapsed(int nodeId) const throw (NodeNotFoundException)
+ {
+ if (!currentTree_) return false;
+ if (!currentTree_->hasNode(nodeId))
+ throw NodeNotFoundException("TreeCanvas::isNodeCollapsed.", nodeId);
+ return nodeCollapsed_[nodeId];
+ }
+
+ /**
+ * @brief Loop for some text in the drawing and get the corresponding coordinates.
+ *
+ * @todo We might want to use some proper indexing for this function to work properly...
+ */
+ QList<QGraphicsTextItem*> searchText(const QString& text);
+
+ /**
+ * @name Mouse handling functions.
+ *
+ * @{
+ */
+ void addMouseListener(MouseListener* listener)
+ {
+ mouseListenerGroup_.addMouseListener(listener);
+ }
+
+ virtual void redraw();
+
+ protected:
+
+ void mouseDoubleClickEvent(QMouseEvent* event)
+ {
+ std::auto_ptr<NodeMouseEvent> newEvent(new NodeMouseEvent(*this, *event));
+ mouseListenerGroup_.processMouseDoubleClickEvent(newEvent.get());
+ }
+
+ void mouseMoveEvent(QMouseEvent* event)
+ {
+ std::auto_ptr<NodeMouseEvent> newEvent(new NodeMouseEvent(*this, *event));
+ mouseListenerGroup_.processMouseMoveEvent(newEvent.get());
+ }
+ void mousePressEvent(QMouseEvent* event)
+ {
+ std::auto_ptr<NodeMouseEvent> newEvent(new NodeMouseEvent(*this, *event));
+ mouseListenerGroup_.processMousePressEvent(newEvent.get());
+ }
+
+ void mouseReleaseEvent(QMouseEvent* event)
+ {
+ std::auto_ptr<NodeMouseEvent> newEvent(new NodeMouseEvent(*this, *event));
+ mouseListenerGroup_.processMouseReleaseEvent(newEvent.get());
+ }
+ /** @} */
+
+ signals:
+ void drawingChanged();
+
+};
+
+} //end of namespace bpp.
+
+#endif //_TREECANVAS_H_
+
diff --git a/src/Bpp/Qt/Tree/TreeCanvasControlers.cpp b/src/Bpp/Qt/Tree/TreeCanvasControlers.cpp
new file mode 100644
index 0000000..8e4372d
--- /dev/null
+++ b/src/Bpp/Qt/Tree/TreeCanvasControlers.cpp
@@ -0,0 +1,254 @@
+//
+// File: TreeCanvasControlers.cpp
+// Created by: Julien Dutheil
+// Created on: Sun Oct 24 16:31 2006
+//
+
+/*
+Copyright or � or Copr. Bio++ Development Team, (November 16, 2004)
+
+This software is a computer program whose purpose is to provide
+graphic components to develop bioinformatics applications.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "TreeCanvasControlers.h"
+
+//From Qt:
+#include <QtGui>
+#include <QRadioButton>
+
+using namespace bpp;
+
+void NodeClickableAreasTreeDrawingListener::afterDrawNode(const DrawNodeEvent& event)
+{
+ const TreeDrawing* td = event.getTreeDrawing();
+ double r = td->getDisplaySettings().pointArea;
+ GraphicDevice* gd = event.getGraphicDevice();
+ Cursor cursor = event.getCursor();
+ gd->drawRect(cursor.getX() - r, cursor.getY() - r, 2 * r, 2 * r);
+}
+
+const int TreeCanvasControlers::ID_WIDTH_CTRL = 1;
+const int TreeCanvasControlers::ID_HEIGHT_CTRL = 2;
+const int TreeCanvasControlers::ID_DRAWING_CTRL = 3;
+const int TreeCanvasControlers::ID_ORIENTATION_CTRL = 4;
+const int TreeCanvasControlers::ID_DRAW_CLICKABLE_AREAS_CTRL = 5;
+const int TreeCanvasControlers::ID_DRAW_NODE_IDS_CTRL = 6;
+const int TreeCanvasControlers::ID_DRAW_LEAF_NAMES_CTRL = 7;
+const int TreeCanvasControlers::ID_DRAW_BRANCH_LENGTHS_CTRL = 8;
+const int TreeCanvasControlers::ID_DRAW_BOOTSTRAP_VALUES_CTRL = 9;
+const std::string TreeCanvasControlers::PROPERTY_CLICKABLE_AREA = "Clickable area";
+
+TreeCanvasControlers::TreeCanvasControlers(QWidget* parent): treeCanvas_(0)
+{
+ //Drawing algorithms and controler:
+ tdSettings_ = new TreeDrawingSettings();
+ phylogram_ = new PhylogramPlot();
+ cladogram_ = new CladogramPlot();
+ phylogram_->setDisplaySettings(tdSettings_);
+ cladogram_->setDisplaySettings(tdSettings_);
+ availableTreeDrawings_.append(QString(cladogram_->getName().c_str()));
+ availableTreeDrawings_.append(QString(phylogram_->getName().c_str()));
+ tdDisplayControler_ = new BasicTreeDrawingDisplayControler(tdSettings_);
+ tdDisplayControler_->addListener(PROPERTY_CLICKABLE_AREA, reinterpret_cast<TreeDrawingListener*>(new NodeClickableAreasTreeDrawingListener(true)));
+ tdDisplayControler_->registerTreeDrawing(phylogram_);
+ tdDisplayControler_->registerTreeDrawing(cladogram_);
+
+ //TreeDrawing algorithm choice and options:
+ widthCtrl_ = new QSpinBox(parent);
+ widthCtrl_->setRange(100, 100000);
+ connect(widthCtrl_, SIGNAL(valueChanged(int)), this, SLOT(treeDrawingUnitChanged()));
+ heightCtrl_ = new QSpinBox(parent);
+ heightCtrl_->setRange(100, 100000);
+ connect(heightCtrl_, SIGNAL(valueChanged(int)), this, SLOT(treeDrawingUnitChanged()));
+ drawingCtrl_ = new QComboBox(parent);
+ drawingCtrl_->addItems(availableTreeDrawings_);
+ connect(drawingCtrl_, SIGNAL(currentIndexChanged(int)), this, SLOT(treeDrawingChanged()));
+
+ orientationCtrl_ = new QGroupBox(parent);
+ QRadioButton* leftButton = new QRadioButton(QString("L"), orientationCtrl_);
+ QRadioButton* rightButton = new QRadioButton(QString("R"), orientationCtrl_);
+ QRadioButton* upButton = new QRadioButton(QString("U"), orientationCtrl_);
+ QRadioButton* downButton = new QRadioButton(QString("D"), orientationCtrl_);
+ QHBoxLayout *hbox = new QHBoxLayout;
+ hbox->addWidget(leftButton);
+ hbox->addWidget(rightButton);
+ hbox->addWidget(upButton);
+ hbox->addWidget(downButton);
+ orientationCtrl_->setLayout(hbox);
+ orientationLeftRight_ = new QButtonGroup;
+ connect(orientationLeftRight_, SIGNAL(buttonClicked(int)), this, SLOT(treeDrawingChanged()));
+ orientationUpDown_ = new QButtonGroup;
+ connect(orientationUpDown_, SIGNAL(buttonClicked(int)), this, SLOT(treeDrawingChanged()));
+ orientationLeftRight_->addButton(leftButton, 1);
+ orientationLeftRight_->addButton(rightButton, 2);
+ orientationUpDown_->addButton(upButton, 3);
+ orientationUpDown_->addButton(downButton, 4);
+ leftButton->setChecked(true);
+ upButton->setChecked(true);
+
+ //Display options:
+ drawClickableAreas_ = new QCheckBox("Clickable areas", parent);
+ drawNodesId_ = new QCheckBox("Nodes id", parent);
+ drawLeavesNames_ = new QCheckBox("Leaves names", parent);
+ drawBranchLengthValues_ = new QCheckBox("Branch lengths", parent);
+ drawBootstrapValues_ = new QCheckBox("Boostrap values", parent);
+ connect(drawClickableAreas_ , SIGNAL(stateChanged(int)), this, SLOT(treeDrawingChanged()));
+ connect(drawNodesId_ , SIGNAL(stateChanged(int)), this, SLOT(treeDrawingChanged()));
+ connect(drawLeavesNames_ , SIGNAL(stateChanged(int)), this, SLOT(treeDrawingChanged()));
+ connect(drawBranchLengthValues_, SIGNAL(stateChanged(int)), this, SLOT(treeDrawingChanged()));
+ connect(drawBootstrapValues_ , SIGNAL(stateChanged(int)), this, SLOT(treeDrawingChanged()));
+ drawLeavesNames_->setChecked(true);
+
+ blockSignal_ = false;
+ actualizeOptions();
+}
+
+TreeCanvasControlers::~TreeCanvasControlers()
+{
+ delete widthCtrl_;
+ delete heightCtrl_;
+ delete drawingCtrl_;
+ delete orientationCtrl_;
+ delete drawClickableAreas_;
+ delete drawNodesId_;
+ delete drawLeavesNames_;
+ delete drawBranchLengthValues_;
+ delete drawBootstrapValues_;
+ delete phylogram_;
+ delete cladogram_;
+ delete tdSettings_;
+ delete tdDisplayControler_;
+}
+
+
+
+void TreeCanvasControlers::setTreeCanvas(TreeCanvas* canvas, bool updateOptions)
+{
+ treeCanvas_ = canvas;
+ if (updateOptions) actualizeOptions();
+ else applyOptions(treeCanvas_);
+}
+
+
+
+void TreeCanvasControlers::applyOptions(TreeCanvas* canvas)
+{
+ QString selection = drawingCtrl_->currentText();
+ if (QString(canvas->getTreeDrawing()->getName().c_str()) != selection)
+ {
+ if (selection == QString(cladogram_->getName().c_str()))
+ {
+ canvas->setTreeDrawing(*cladogram_, false);
+ }
+ else if (selection == QString(phylogram_->getName().c_str()))
+ {
+ canvas->setTreeDrawing(*phylogram_, false);
+ }
+ }
+ AbstractDendrogramPlot* treeDrawing = dynamic_cast<AbstractDendrogramPlot*>(canvas->getTreeDrawing());
+
+ treeDrawing->setHorizontalOrientation(orientationLeftRight_->checkedId() == 1 ? AbstractDendrogramPlot::ORIENTATION_LEFT_TO_RIGHT : AbstractDendrogramPlot::ORIENTATION_RIGHT_TO_LEFT);
+ treeDrawing->setVerticalOrientation(orientationUpDown_->checkedId() == 3 ? AbstractDendrogramPlot::ORIENTATION_TOP_TO_BOTTOM : AbstractDendrogramPlot::ORIENTATION_BOTTOM_TO_TOP);
+
+ tdDisplayControler_->enableListener(PROPERTY_CLICKABLE_AREA, drawClickableAreas_->isChecked());
+ tdDisplayControler_->enableListener(BasicTreeDrawingDisplayControler::PROPERTY_NODE_IDS, drawNodesId_->isChecked());
+ tdDisplayControler_->enableListener(BasicTreeDrawingDisplayControler::PROPERTY_LEAF_NAMES, drawLeavesNames_->isChecked());
+ tdDisplayControler_->enableListener(BasicTreeDrawingDisplayControler::PROPERTY_BRANCH_LENGTHS, drawBranchLengthValues_->isChecked());
+ tdDisplayControler_->enableListener(BasicTreeDrawingDisplayControler::PROPERTY_BOOTSTRAP_VALUES, drawBootstrapValues_->isChecked());
+
+ //Refresh the drawing(s):
+ fireActionEvent_();
+}
+
+
+
+void TreeCanvasControlers::treeDrawingChanged()
+{
+ if (!treeCanvas_) return;
+ if (! blockSignal_) applyOptions(treeCanvas_);
+}
+
+
+void TreeCanvasControlers::treeDrawingUnitChanged()
+{
+ if (!treeCanvas_) return;
+ if (! blockSignal_)
+ {
+ treeCanvas_->setDrawingSize(widthCtrl_->value(), heightCtrl_->value());
+ }
+}
+
+void TreeCanvasControlers::actualizeOptions()
+{
+ if (!treeCanvas_) return;
+ AbstractDendrogramPlot* current = dynamic_cast<AbstractDendrogramPlot*>(treeCanvas_->getTreeDrawing());
+ blockSignal_ = true; //Dirty trick but no choice!
+ widthCtrl_->setValue(treeCanvas_->drawingWidth());
+ heightCtrl_->setValue(treeCanvas_->drawingHeight());
+ drawingCtrl_->setCurrentIndex(availableTreeDrawings_.indexOf(QString(current->getName().c_str())));
+ if (current->getHorizontalOrientation() == AbstractDendrogramPlot::ORIENTATION_LEFT_TO_RIGHT)
+ orientationLeftRight_->buttons()[0]->setChecked(true);
+ else
+ orientationLeftRight_->buttons()[1]->setChecked(true);
+ if (current->getVerticalOrientation() == AbstractDendrogramPlot::ORIENTATION_TOP_TO_BOTTOM)
+ orientationUpDown_->buttons()[0]->setChecked(true);
+ else
+ orientationUpDown_->buttons()[1]->setChecked(true);
+
+ //Not needed as all canvasses share the same controler:
+ //drawClickableAreas_ ->setChecked(tdDisplayControler_->isListenerEnabled(PROPERTY_CLICKABLE_AREA));
+ //drawNodesId_ ->setChecked(tdDisplayControler_->isListenerEnabled(BasicTreeDrawingDisplayControler::PROPERTY_NODE_IDS));
+ //drawLeavesNames_ ->setChecked(tdDisplayControler_->isListenerEnabled(BasicTreeDrawingDisplayControler::PROPERTY_LEAF_NAMES));
+ //drawBranchLengthValues_->setChecked(tdDisplayControler_->isListenerEnabled(BasicTreeDrawingDisplayControler::PROPERTY_BRANCH_LENGTHS));
+ //drawBootstrapValues_ ->setChecked(tdDisplayControler_->isListenerEnabled(BasicTreeDrawingDisplayControler::PROPERTY_BOOTSTRAP_VALUES));
+ blockSignal_ = false;
+}
+
+QWidget* TreeCanvasControlers::getControlerById(int id)
+{
+ if (id == ID_WIDTH_CTRL) return widthCtrl_;
+ if (id == ID_HEIGHT_CTRL) return heightCtrl_;
+ if (id == ID_DRAWING_CTRL) return drawingCtrl_;
+ if (id == ID_ORIENTATION_CTRL) return orientationCtrl_;
+ if (id == ID_DRAW_CLICKABLE_AREAS_CTRL) return drawClickableAreas_;
+ if (id == ID_DRAW_NODE_IDS_CTRL) return drawNodesId_;
+ if (id == ID_DRAW_LEAF_NAMES_CTRL) return drawLeavesNames_;
+ if (id == ID_DRAW_BRANCH_LENGTHS_CTRL) return drawBranchLengthValues_;
+ if (id == ID_DRAW_BOOTSTRAP_VALUES_CTRL) return drawBootstrapValues_;
+ return 0;
+}
+
+TreeDrawing* TreeCanvasControlers::getTreeDrawing(unsigned int i)
+{
+ if (i == 0) return cladogram_;
+ if (i == 1) return phylogram_;
+ return 0;
+}
+
diff --git a/src/Bpp/Qt/Tree/TreeCanvasControlers.h b/src/Bpp/Qt/Tree/TreeCanvasControlers.h
new file mode 100644
index 0000000..3e52bf7
--- /dev/null
+++ b/src/Bpp/Qt/Tree/TreeCanvasControlers.h
@@ -0,0 +1,200 @@
+//
+// File: TreeCanvasControls.h
+// Created by: Julien Dutheil
+// Created on: Sun Oct 24 16:31 2006
+//
+
+/*
+Copyright or � or Copr. Bio++ Development Team, (November 16, 2004)
+
+This software is a computer program whose purpose is to provide
+graphic components to develop bioinformatics applications.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _TREECANVASCONTROLERS_H_
+#define _TREECANVASCONTROLERS_H_
+
+
+#include "TreeCanvas.h"
+
+//From Phylib:
+#include <Bpp/Phyl/Graphics/CladogramPlot.h>
+#include <Bpp/Phyl/Graphics/PhylogramPlot.h>
+#include <Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h>
+
+//From Qt:
+#include <QSpinBox>
+#include <QComboBox>
+#include <QCheckBox>
+#include <QSpinBox>
+#include <QGroupBox>
+
+namespace bpp
+{
+
+/**
+ * @brief A TreeDrawingListener implementation that draw the clickable areas around nodes.
+ *
+ * This listener works with TreeDrawing classes, but is more efficient when used with a class that fires DrawINodeEvent events.
+ */
+class NodeClickableAreasTreeDrawingListener :
+ public TreeDrawingListenerAdapter
+{
+public:
+ NodeClickableAreasTreeDrawingListener(bool autonomous = false) :
+ TreeDrawingListenerAdapter(autonomous) {}
+
+ NodeClickableAreasTreeDrawingListener* clone() const { return new NodeClickableAreasTreeDrawingListener(*this); }
+
+public :
+ void afterDrawNode(const DrawNodeEvent& event);
+
+};
+
+
+
+/**
+ * @brief Listener interface for TreeCanvasControlers.
+ */
+class TreeCanvasControlersListener
+{
+ public:
+ virtual ~TreeCanvasControlersListener() {}
+
+ public:
+ virtual void controlerTakesAction() = 0;
+};
+
+/**
+ * @brief Manage controlers widgets to interact with a tree canvas.
+ */
+class TreeCanvasControlers:
+ public QObject
+{
+ Q_OBJECT
+
+ private:
+ TreeCanvas* treeCanvas_;
+ QSpinBox* widthCtrl_;
+ QSpinBox* heightCtrl_;
+ QComboBox* drawingCtrl_;
+ QGroupBox* orientationCtrl_;
+
+ QButtonGroup* orientationLeftRight_;
+ QButtonGroup* orientationUpDown_;
+
+
+ QCheckBox* drawClickableAreas_;
+ QCheckBox* drawNodesId_;
+ QCheckBox* drawLeavesNames_;
+ QCheckBox* drawBranchLengthValues_;
+ QCheckBox* drawBootstrapValues_;
+
+ CladogramPlot* cladogram_;
+ PhylogramPlot* phylogram_;
+ QStringList availableTreeDrawings_;
+ TreeDrawingSettings* tdSettings_;
+ TreeDrawingDisplayControler* tdDisplayControler_;
+
+ // Other controls may be added later.
+
+ std::vector<TreeCanvasControlersListener*> listeners_;
+
+ bool blockSignal_;
+
+ public:
+ /**
+ * @param parent The parent widget to pass to all controlers.
+ * This should be set to null if you do not intend to use all the controlers,
+ * or intend to use them witht different parent windows.
+ */
+ TreeCanvasControlers(QWidget* parent = 0);
+ virtual ~TreeCanvasControlers();
+
+ public:
+
+ /**
+ * @brief Actualize the controls according to the current tree canvas.
+ */
+ void actualizeOptions();
+
+ /**
+ * @brief Get a specific control according to its id.
+ *
+ * @param id The id of the control.
+ * @return The specified control, or NULL if no control corresponds to the specified id.
+ */
+ QWidget* getControlerById(int id);
+
+ void setTreeCanvas(TreeCanvas* canvas, bool updateOptions = true);
+ TreeCanvas* getTreeCanvas() { return treeCanvas_; }
+ const TreeCanvas* getTreeCanvas() const { return treeCanvas_; }
+
+ TreeDrawing* getTreeDrawing(unsigned int i);
+
+ TreeDrawing* getSelectedTreeDrawing() { return getTreeDrawing(static_cast<unsigned int>(drawingCtrl_->currentIndex())); }
+
+ unsigned int getNumberOfTreeDrawings() const { return 2; }
+
+ void applyOptions(TreeCanvas* canvas);
+
+ void addActionListener(TreeCanvasControlersListener* listener)
+ {
+ listeners_.push_back(listener);
+ }
+
+ protected:
+ void fireActionEvent_()
+ {
+ for (unsigned int i = 0; i < listeners_.size(); ++i)
+ listeners_[i]->controlerTakesAction();
+ }
+
+ private slots:
+ void treeDrawingChanged();
+ void treeDrawingUnitChanged();
+
+ public:
+ static const int ID_WIDTH_CTRL;
+ static const int ID_HEIGHT_CTRL;
+ static const int ID_DRAWING_CTRL;
+ static const int ID_ORIENTATION_CTRL;
+ static const int ID_DRAW_CLICKABLE_AREAS_CTRL;
+ static const int ID_DRAW_NODE_IDS_CTRL;
+ static const int ID_DRAW_LEAF_NAMES_CTRL;
+ static const int ID_DRAW_BRANCH_LENGTHS_CTRL;
+ static const int ID_DRAW_BOOTSTRAP_VALUES_CTRL;
+ static const std::string PROPERTY_CLICKABLE_AREA;
+
+};
+
+} //end of namespace bpp.
+
+#endif // _TREECANVASCONTROLERS_H_
+
diff --git a/src/Bpp/Qt/Tree/TreeStatisticsBox.cpp b/src/Bpp/Qt/Tree/TreeStatisticsBox.cpp
new file mode 100644
index 0000000..82db2d3
--- /dev/null
+++ b/src/Bpp/Qt/Tree/TreeStatisticsBox.cpp
@@ -0,0 +1,76 @@
+//
+// File: TreeStatisticsBox.cpp
+// Created by: Julien Dutheil
+// Created on: Sun Aug 9 12:27 2009
+//
+
+/*
+Copyright or � or Copr. CNRS, (November 16, 2004)
+
+This software is a computer program whose purpose is to provide
+graphic components to develop bioinformatics applications.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "TreeStatisticsBox.h"
+
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Numeric/VectorTools.h>
+
+//From Qt:
+#include <QFormLayout>
+
+using namespace bpp;
+
+TreeStatisticsBox::TreeStatisticsBox(QWidget* parent):
+ QGroupBox(parent),
+ leavesNumber_(this),
+ ancestorsNumber_(this),
+ maxFurcation_(this),
+ depth_(this),
+ height_(this)
+{
+ QFormLayout* layout = new QFormLayout();
+ layout->addRow(tr("# Leaves:"), &leavesNumber_);
+ layout->addRow(tr("# Ancestors:"), &ancestorsNumber_);
+ layout->addRow(tr("Max n-furcation:"), &maxFurcation_);
+ layout->addRow(tr("Depth:"), &depth_);
+ layout->addRow(tr("Height:"), &height_);
+ setLayout(layout);
+}
+
+void TreeStatisticsBox::updateTree(const Tree& tree)
+{
+ stats_.setTree(tree);
+ leavesNumber_.setText(tr(TextTools::toString(stats_.getNumberOfLeaves()).c_str()));
+ ancestorsNumber_.setText(tr(TextTools::toString(stats_.getNumberOfAncestors()).c_str()));
+ maxFurcation_.setText(tr(TextTools::toString(VectorTools::max(stats_.getNodeNumberOfSons())).c_str()));
+ depth_.setText(tr(TextTools::toString(*stats_.getNodeDepths().rbegin()).c_str()));
+ height_.setText(tr(TextTools::toString(*stats_.getNodeHeights().rbegin()).c_str()));
+}
+
diff --git a/src/Bpp/Qt/Tree/TreeStatisticsBox.h b/src/Bpp/Qt/Tree/TreeStatisticsBox.h
new file mode 100644
index 0000000..ab10780
--- /dev/null
+++ b/src/Bpp/Qt/Tree/TreeStatisticsBox.h
@@ -0,0 +1,83 @@
+//
+// File: TreeStatisticsBox.h
+// Created by: Julien Dutheil
+// Created on: Sun Aug 9 12:27 2009
+//
+
+/*
+Copyright or � or Copr. CNRS, (November 16, 2004)
+
+This software is a computer program whose purpose is to provide
+graphic components to develop bioinformatics applications.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _TREESTATISTICSBOX_H_
+#define _TREESTATISTICSBOX_H_
+
+
+//From PhylLib:
+#include <Bpp/Phyl/PhyloStatistics.h>
+
+//From Qt:
+#include <QWidget>
+#include <QGroupBox>
+#include <QLabel>
+
+namespace bpp
+{
+
+/**
+ * @brief Panel that display a few statistics on a tree.
+ */
+class TreeStatisticsBox:
+ public QGroupBox
+{
+ Q_OBJECT
+
+ protected:
+ PhyloStatistics stats_;
+ QLabel leavesNumber_;
+ QLabel ancestorsNumber_;
+ QLabel maxFurcation_;
+ QLabel depth_;
+ QLabel height_;
+
+ public:
+ TreeStatisticsBox(QWidget* parent = 0);
+ virtual ~TreeStatisticsBox() {}
+
+ public:
+ virtual void updateTree(const Tree& tree);
+
+};
+
+} //end of namespace bpp.
+
+#endif //_TREESTATISTICSBOX_H_
+
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
new file mode 100644
index 0000000..4e6e83b
--- /dev/null
+++ b/src/CMakeLists.txt
@@ -0,0 +1,53 @@
+# CMake script for Bio++ Qt
+# Author: Julien Dutheil
+# Created: 22/08/2009
+
+# File list
+set(CPP_FILES
+ Bpp/Qt/QtGraphicDevice.cpp
+ Bpp/Qt/QtOutputStream.cpp
+ Bpp/Qt/Tree/TreeCanvas.cpp
+ Bpp/Qt/Tree/TreeCanvasControlers.cpp
+ Bpp/Qt/Tree/TreeStatisticsBox.cpp
+ )
+set(H_FILES
+ Bpp/Qt/QtGraphicDevice.h
+ Bpp/Qt/QtTools.h
+ Bpp/Qt/QtOutputStream.h
+ Bpp/Qt/MouseListener.h
+ Bpp/Qt/MouseListeningWidget.h
+ Bpp/Qt/Tree/TreeCanvas.h
+ )
+set(H_MOC_FILES
+ Bpp/Qt/Tree/TreeCanvas.h
+ Bpp/Qt/Tree/TreeCanvasControlers.h
+ Bpp/Qt/Tree/TreeStatisticsBox.h
+ )
+qt4_wrap_cpp(CPP_MOC_FILES ${H_MOC_FILES})
+
+# Build the static lib
+add_library(bppqt-static STATIC ${CPP_FILES} ${CPP_MOC_FILES})
+set_target_properties(bppqt-static
+ PROPERTIES OUTPUT_NAME bpp-qt
+ CLEAN_DIRECT_OUTPUT 1
+ )
+target_link_libraries(bppqt-static ${LIBS})
+
+# Build the shared lib
+add_library(bppqt-shared SHARED ${CPP_FILES} ${CPP_MOC_FILES})
+set_target_properties(bppqt-shared
+ PROPERTIES OUTPUT_NAME bpp-qt
+ CLEAN_DIRECT_OUTPUT 1
+ VERSION ${BPPQT_VERSION}
+ SOVERSION ${BPPQT_VERSION_MAJOR}
+ )
+target_link_libraries(bppqt-shared ${LIBS})
+
+# Install libs
+install(TARGETS bppqt-static bppqt-shared DESTINATION lib${LIB_SUFFIX})
+
+# Install headers
+install(DIRECTORY Bpp/ DESTINATION include/Bpp FILES_MATCHING PATTERN "*.h")
+
+# Generate generic include files (.all)
+INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${CMAKE_SOURCE_DIR}/genIncludes.sh ${CMAKE_PREFIX_PATH}/include/Bpp)")
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libbpp-qt.git
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