[med-svn] [libbpp-qt] 04/06: New upstream version 2.3.1

Andreas Tille tille at debian.org
Wed Jun 14 09:55:43 UTC 2017


This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository libbpp-qt.

commit 372e3a9ed617cde7cf124ed8d779d279ef10c2e3
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jun 14 10:58:32 2017 +0200

    New upstream version 2.3.1
---
 CMakeLists.txt                           |  170 +-
 ChangeLog                                |    4 +
 Doxyfile                                 | 2662 ++++++++++++++++++------------
 INSTALL.txt                              |   19 +-
 bpp-qt.spec                              |  116 +-
 debian/changelog                         |   31 -
 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                          |   57 -
 debian/postrm                            |   59 -
 debian/prerm                             |   41 -
 debian/rules                             |  121 --
 debian/source/format                     |    1 -
 genIncludes.sh                           |   35 -
 package.cmake.in                         |   30 +
 src/Bpp/Qt/QtGraphicDevice.cpp           |    9 +-
 src/Bpp/Qt/QtGraphicDevice.h             |    5 +-
 src/Bpp/Qt/QtTools.h                     |    4 +-
 src/Bpp/Qt/Tree/TreeCanvas.cpp           |    8 +-
 src/Bpp/Qt/Tree/TreeCanvas.h             |   20 +-
 src/Bpp/Qt/Tree/TreeCanvasControlers.cpp |    7 +-
 src/CMakeLists.txt                       |   70 +-
 26 files changed, 1797 insertions(+), 1771 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 0b41743..b0be31e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,28 +1,21 @@
 # CMake script for Bio++ Qt
-# Author: Julien Dutheil
+# Authors:
+#   Julien Dutheil
+#   Francois Gindraud (2017)
 # Created: 22/08/2009
 
-# Global parameters
-CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
-PROJECT(bpp-qt CXX C)
+cmake_minimum_required (VERSION 2.8.11)
+project (bpp-qt CXX)
+
+# Compile options
+set (CMAKE_CXX_FLAGS "-std=c++11 -Wall -Wshadow -Wconversion")
+
 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 "${CMAKE_CXX_FLAGS} -DNO_VIRTUAL_COV=1")
-ENDIF(NO_VIRTUAL_COV)
-
 IF(NOT NO_DEP_CHECK)
   SET(NO_DEP_CHECK FALSE CACHE BOOL
       "Disable dependencies check for building distribution only."
@@ -41,54 +34,52 @@ ELSE(NO_DEP_CHECK)
 #           library implements.
 # In other words, the library implements all the interface numbers in the
 # range from number current - age to current.
-SET(BPPQT_VERSION_CURRENT "1")
-SET(BPPQT_VERSION_REVISION "1")
-SET(BPPQT_VERSION_AGE "0")
+SET(${PROJECT_NAME}_VERSION_CURRENT "1")
+SET(${PROJECT_NAME}_VERSION_REVISION "1")
+SET(${PROJECT_NAME}_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)
+math(EXPR ${PROJECT_NAME}_VERSION_MAJOR "${${PROJECT_NAME}_VERSION_CURRENT} - ${${PROJECT_NAME}_VERSION_AGE}")
+SET(${PROJECT_NAME}_VERSION_MINOR ${${PROJECT_NAME}_VERSION_AGE})
+SET(${PROJECT_NAME}_VERSION_PATCH ${${PROJECT_NAME}_VERSION_REVISION})
+SET(${PROJECT_NAME}_VERSION "${${PROJECT_NAME}_VERSION_MAJOR}.${${PROJECT_NAME}_VERSION_MINOR}.${${PROJECT_NAME}_VERSION_PATCH}")
+
+set (PROJECT_VERSION ${${PROJECT_NAME}_VERSION})
+
+# Find dependencies (add install directory to search)
+if (CMAKE_INSTALL_PREFIX)
+  set (CMAKE_PREFIX_PATH "${CMAKE_INSTALL_PREFIX}" ${CMAKE_PREFIX_PATH})
+endif (CMAKE_INSTALL_PREFIX)
+
+include (GNUInstallDirs)
+find_package (bpp-phyl 11.0.0 REQUIRED)
 
 # Find the Qt installation
-FIND_PACKAGE(Qt4 REQUIRED)
-INCLUDE(${QT_USE_FILE})
-SET(LIBS ${LIBS} ${QT_LIBRARIES})
+set (QT_USE_IMPORTED_TARGETS TRUE)
+find_package (Qt4 COMPONENTS QtCore QtGui REQUIRED)
+include (${QT_USE_FILE})
+set (qt-libs ${QT_QTCORE_LIBRARY} ${QT_QTGUI_LIBRARY})
+
+# CMake package
+set (cmake-package-location ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME})
+include (CMakePackageConfigHelpers)
+configure_package_config_file (
+  package.cmake.in
+  ${CMAKE_CURRENT_BINARY_DIR}/package.cmake
+  INSTALL_DESTINATION ${cmake-package-location}
+  )
+write_basic_package_version_file (
+  ${CMAKE_CURRENT_BINARY_DIR}/package-version.cmake
+  VERSION ${PROJECT_VERSION}
+  COMPATIBILITY SameMajorVersion
+  )
+install (FILES ${CMAKE_CURRENT_BINARY_DIR}/package.cmake DESTINATION ${cmake-package-location}
+  RENAME ${PROJECT_NAME}-config.cmake)
+install (FILES ${CMAKE_CURRENT_BINARY_DIR}/package-version.cmake DESTINATION ${cmake-package-location}
+  RENAME ${PROJECT_NAME}-config-version.cmake)
 
-# Subdirectories
-ADD_SUBDIRECTORY(src)
+# Define the libraries
+add_subdirectory (src)
 
 # Doxygen
 FIND_PACKAGE(Doxygen)
@@ -109,49 +100,22 @@ ENDIF(NO_DEP_CHECK)
 # Packager
 SET(CPACK_PACKAGE_NAME "libbpp-qt")
 SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.2.0")
+SET(CPACK_PACKAGE_VERSION "2.3.1")
 SET(CPACK_PACKAGE_VERSION_MAJOR "2")
-SET(CPACK_PACKAGE_VERSION_MINOR "2")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_MINOR "3")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
 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"
- ".*\\\\..*\\\\.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()
+# /!\ This assumes that an external build is used
+SET(CPACK_SOURCE_IGNORE_FILES 
+       "/build/" 
+       "/\\\\.git/" 
+       "/\\\\.gitignore" 
+       ${CPACK_SOURCE_IGNORE_FILES}
+       )
 
 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")
@@ -159,27 +123,13 @@ 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/ChangeLog b/ChangeLog
index 7b2faf7..f8939a7 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,7 @@
+06/06/17 -*- Version 2.3.1 -*-
+
+10/05/17 -*- Version 2.3.0 -*-
+
 26/09/14 -*- Version 2.2.0 -*-
 
 08/03/13 -*- Version 2.1.0 -*-
diff --git a/Doxyfile b/Doxyfile
index d1d4583..19fb078 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -1,358 +1,406 @@
-# Doxyfile 1.8.3.1-20130209
+# Doxyfile 1.8.11
 
 # This file describes the settings to be used by the documentation system
-# doxygen (www.doxygen.org) for a project
+# doxygen (www.doxygen.org) for a project.
 #
-# All text after a hash (#) is considered a comment and will be ignored
+# All text after a double hash (##) is considered a comment and is placed in
+# front of the TAG it is preceding.
+#
+# All text after a single 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 (" ")
+# 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.
+# 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.
+# The default value is: UTF-8.
 
 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.
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
+# double-quotes, unless you are using Doxywizard) that should identify the
+# project for which the documentation is generated. This name is used in the
+# title of most generated pages and in a few other places.
+# The default value is: My Project.
 
 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.
+# 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         = 2.2.0
+PROJECT_NUMBER         = 2.3.0
 
-# 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.
+# 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.
+# With the PROJECT_LOGO tag one can specify a logo or an 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.
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
+# into which the generated documentation will be written. 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.
+# 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 causes
+# performance problems for the file system.
+# The default value is: NO.
 
 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.
+# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
+# characters to appear in the names of generated files. If set to NO, non-ASCII
+# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
+# U+3044.
+# The default value is: NO.
+
+ALLOW_UNICODE_NAMES    = 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.
+# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
+# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
+# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
+# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
+# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
+# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
+# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
+# Ukrainian and Vietnamese.
+# The default value is: English.
 
 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.
+# If the BRIEF_MEMBER_DESC tag is set to YES, 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.
+# The default value is: YES.
 
 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 
+# If the REPEAT_BRIEF tag is set to YES, 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.
+# The default value is: YES.
 
 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 $name file" "is" "provides" "specifies" "contains" 
-# "represents" "a" "an" "the"
+# This tag implements a quasi-intelligent brief description abbreviator that is
+# used to form the text in various listings. Each string in this list, if found
+# as the leading text of the brief description, will be stripped from the text
+# and the result, after processing the whole list, is used as the annotated
+# text. Otherwise, the brief description is used as-is. If left blank, the
+# following values are used ($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 and 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 
+# 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.
+# The default value is: NO.
 
 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 
+# 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.
+# The default value is: NO.
 
 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.
+# If the FULL_PATH_NAMES tag is set to YES, 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
+# The default value is: YES.
 
 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.
+# 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 can specify absolute paths here, but also relative paths, which
+# will be relative from the directory where doxygen is started.
+# This tag requires that the tag FULL_PATH_NAMES is set to YES.
 
 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.
+# 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 list of 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.
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
+# less readable) file names. This can be useful is your file systems doesn't
+# support long names like on DOS, Mac, or CD-ROM.
+# The default value is: NO.
 
 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.)
+# 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-style will behave just like regular Qt-
+# style comments (thus requiring an explicit @brief command for a brief
+# description.)
+# The default value is: NO.
 
 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.)
+# 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 Qt-style will behave just like regular Qt-style comments (thus
+# requiring an explicit \brief command for a brief description.)
+# The default value is: NO.
 
 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.
+# 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 behavior. 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 behavior instead.
+#
+# Note that setting this tag to YES also means that rational rose comments are
+# not recognized any more.
+# The default value is: NO.
 
 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.
+# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
+# documentation from any documented member that it re-implements.
+# The default value is: YES.
 
 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.
+# 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.
+# The default value is: NO.
 
 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.
+# 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.
+# Minimum value: 1, maximum value: 16, default value: 4.
 
 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.
+# This tag can be used to specify a number of aliases that act 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.
+# 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.
+# 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.
+# The default value is: NO.
 
 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.
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
+# Python sources only. Doxygen will then generate output that is more tailored
+# for that language. For instance, namespaces will be presented as packages,
+# qualified scopes will look different, etc.
+# The default value is: NO.
 
 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.
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources. Doxygen will then generate output that is tailored for Fortran.
+# The default value is: NO.
 
 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.
+# 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.
+# The default value is: NO.
 
 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.
+# 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,
+# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran:
+# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran:
+# Fortran. In the later case the parser tries to guess whether the code is fixed
+# or free formatted code, this is the default for Fortran type files), VHDL. 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: For files without extension you can use no_extension as a placeholder.
+#
+# 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.
+# If the MARKDOWN_SUPPORT tag is enabled 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.
+# The default value is: YES.
 
 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 
+# 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 putting a % sign in front of the word or
 # globally by setting AUTOLINK_SUPPORT to NO.
+# The default value is: YES.
 
 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 
+# 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);
+# versus func(std::string) {}). This also make the inheritance and collaboration
 # diagrams that involve STL classes more complete and accurate.
+# The default value is: NO.
 
 BUILTIN_STL_SUPPORT    = YES
 
-# If you use Microsoft's C++/CLI language, you should set this option to YES to 
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
 # enable parsing support.
+# The default value is: NO.
 
 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.
+# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
+# http://www.riverbankcomputing.co.uk/software/sip/intro) 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.
+# The default value is: NO.
 
 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.
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES will make
+# doxygen to 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.
+# The default value is: YES.
 
 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 
+# 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.
+# The default value is: NO.
 
 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.
+# If one adds a struct or class to a group and this option is enabled, then also
+# any nested class or struct is added to the same group. By default this option
+# is disabled and one has to add nested compounds explicitly via \ingroup.
+# The default value is: NO.
+
+GROUP_NESTED_COMPOUNDS = NO
+
+# Set the SUBGROUPING tag to YES 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.
+# The default value is: YES.
 
 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).
+# 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).
+#
+# Note that this feature does not work in combination with
+# SEPARATE_MEMBER_PAGES.
+# The default value is: NO.
 
 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).
+# 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, structs, classes, and unions are shown on a separate page (for HTML and
+# Man pages) or section (for LaTeX and RTF).
+# The default value is: NO.
 
 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 
+# When TYPEDEF_HIDES_STRUCT tag 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.
+# The default value is: NO.
 
 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.
+# 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 appears 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. At the end of a run doxygen will report the cache usage and suggest
+# the optimal cache size from a speed point of view.
+# Minimum value: 0, maximum value: 9, default value: 0.
 
 LOOKUP_CACHE_SIZE      = 0
 
@@ -360,1195 +408,1576 @@ 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
+# 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 respectively EXTRACT_STATIC tags are set to YES.
+# Note: This will also disable the warnings about undocumented members that are
+# normally produced when WARNINGS is set to YES.
+# The default value is: NO.
 
 EXTRACT_ALL            = YES
 
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
-# will be included in the documentation.
+# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
+# be included in the documentation.
+# The default value is: NO.
 
 EXTRACT_PRIVATE        = YES
 
-# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal 
+# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
 # scope will be included in the documentation.
+# The default value is: NO.
 
 EXTRACT_PACKAGE        = NO
 
-# If the EXTRACT_STATIC tag is set to YES all static members of a file 
-# will be included in the documentation.
+# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
+# included in the documentation.
+# The default value is: NO.
 
 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.
+# 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. Does not have any effect
+# for Java sources.
+# The default value is: YES.
 
 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.
+# This flag is only useful for Objective-C code. If 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, only methods in the interface are
+# included.
+# The default value is: NO.
 
 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.
+# 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 namespace
+# are hidden.
+# The default value is: NO.
 
 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.
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
+# undocumented members inside documented classes or files. If set to NO 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.
+# The default value is: NO.
 
 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.
+# 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, these classes will be included in the various overviews. This option
+# has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
 
 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.
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
+# (class|struct|union) declarations. If set to NO, these declarations will be
+# included in the documentation.
+# The default value is: NO.
 
 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.
+# 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, these
+# blocks will be appended to the function's detailed documentation block.
+# The default value is: NO.
 
 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.
+# The INTERNAL_DOCS tag determines if documentation that is typed after a
+# \internal command is included. If the tag is set to NO then the documentation
+# will be excluded. Set it to YES to include the internal documentation.
+# The default value is: NO.
 
 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 
+# 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.
+# The default value is: system dependent.
 
 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.
+# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
+# their full class and namespace scopes in the documentation. If set to YES, the
+# scope will be hidden.
+# The default value is: NO.
 
 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.
+# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
+# append additional text to a page's title, such as Class Reference. If set to
+# YES the compound reference will be hidden.
+# The default value is: NO.
+
+HIDE_COMPOUND_REFERENCE= NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
 
 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.
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC  = NO
+
+# 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.
+# The default value is: NO.
 
 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.
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
 
 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.
+# If the SORT_MEMBER_DOCS tag is set to YES 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.
+# The default value is: YES.
 
 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.
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
 
 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.
+# 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 constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: 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.
+# 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 group names will
+# appear in their defined order.
+# The default value is: NO.
 
 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.
+# 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 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.
+# The default value is: NO.
 
 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.
+# 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.
+# The default value is: NO.
 
 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.
+# 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.
+# The default value is: YES.
 
 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.
+# 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.
+# The default value is: YES.
 
 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.
+# 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.
+# The default value is: YES.
 
 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.
+# 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.
+# The default value is: YES.
 
 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.
+# 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.
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have 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 value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
 
 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 
+# 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.
+# The default value is: YES.
 
 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.
+# 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 value 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.
+# 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 value 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.
+# 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. For an example see the documentation.
 
 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.
+# 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.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
 
 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.
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This 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. See also \cite for info how to create references.
 
 CITE_BIB_FILES         = 
 
 #---------------------------------------------------------------------------
-# configuration options related to warning and progress messages
+# 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.
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
 
 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.
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
 
 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.
+# If the WARN_IF_UNDOCUMENTED tag 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.
+# The default value is: YES.
 
 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.
+# If the WARN_IF_DOC_ERROR tag 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.
+# The default value is: YES.
 
 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.
+# This 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, doxygen will only warn about wrong or incomplete
+# parameter documentation, but not about the absence of documentation.
+# The default value is: NO.
 
 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)
+# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
+# a warning is encountered.
+# The default value is: NO.
+
+WARN_AS_ERROR          = 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)
+# The default value is: $file:$line: $text.
 
 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.
+# 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 standard
+# error (stderr).
 
 WARN_LOGFILE           = 
 
 #---------------------------------------------------------------------------
-# configuration options related to the input files
+# 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.
+# The INPUT tag is 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. See also FILE_PATTERNS and EXTENSION_MAPPING
+# Note: If this tag is empty the current directory is searched.
 
 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.
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
+# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
+# documentation (see: http://www.gnu.org/software/libiconv) for the list of
+# possible encodings.
+# The default value is: UTF-8.
 
 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
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
+# *.h) to filter out the source-files in the directories.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# read by doxygen.
+#
+# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
+# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
+# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
+# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f, *.for, *.tcl,
+# *.vhd, *.vhdl, *.ucf, *.qsf, *.as and *.js.
 
 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.
+# The RECURSIVE tag can be used to specify whether or not subdirectories should
+# be searched for input files as well.
+# The default value is: NO.
 
 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 
+# 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 
+# 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.
+# The default value is: NO.
 
 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/*
+# 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, 
+# 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
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories use the pattern */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).
+# 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.
+# 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.
+# 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.
+# The default value is: NO.
 
 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).
+# The IMAGE_PATH tag can be used to specify one or more files or directories
+# that contain images that are to be 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.
+# 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.
+#
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
 
 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.
+# 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 information on how
+# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
+# patterns match the file name, INPUT_FILTER is applied.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
 
 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).
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will also be used to filter the input files that are used for
+# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The default value is: NO.
 
 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.
+# 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 tag requires that the tag FILTER_SOURCE_FILES is set to YES.
 
 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.
+# If the USE_MDFILE_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 to reuse the introduction page also for the doxygen output.
 
 USE_MDFILE_AS_MAINPAGE = 
 
 #---------------------------------------------------------------------------
-# configuration options related to source browsing
+# 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.
+# 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 that
+# also VERBATIM_HEADERS is set to NO.
+# The default value is: NO.
 
 SOURCE_BROWSER         = YES
 
-# Setting the INLINE_SOURCES tag to YES will include the body 
-# of functions and classes directly in the documentation.
+# Setting the INLINE_SOURCES tag to YES will include the body of functions,
+# classes and enums directly into the documentation.
+# The default value is: NO.
 
 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.
+# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
+# special comment blocks from generated source code fragments. Normal C, C++ and
+# Fortran comments will always remain visible.
+# The default value is: YES.
 
 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.
+# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
+# function all documented functions referencing it will be listed.
+# The default value is: NO.
 
 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.
+# 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.
+# The default value is: NO.
 
 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.
+# If the REFERENCES_LINK_SOURCE tag is set to YES 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.
+# The default value is: YES.
 
 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.
+# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
+# source code will show a tooltip with additional information such as prototype,
+# brief description and links to the definition and documentation. Since this
+# will make the HTML file larger and loading of large files a bit slower, you
+# can opt to disable this feature.
+# The default value is: YES.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+SOURCE_TOOLTIPS        = 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.
+#
+# To use it do the following:
+# - Install the latest version of global
+# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
+# - Make sure the INPUT points to the root of the source tree
+# - Run doxygen as normal
+#
+# Doxygen will invoke htags (and that will in turn invoke gtags), so these
+# tools must be available from the command line (i.e. in the search path).
+#
+# The result: instead of the source browser generated by doxygen, the links to
+# source code will now point to the output of htags.
+# The default value is: NO.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
 
 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.
+# If the VERBATIM_HEADERS tag is set the YES 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.
+# See also: Section \class.
+# The default value is: YES.
 
 VERBATIM_HEADERS       = YES
 
+# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
+# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the
+# cost of reduced performance. This can be particularly helpful with template
+# rich C++ code for which doxygen's built-in parser lacks the necessary type
+# information.
+# Note: The availability of this option depends on whether or not doxygen was
+# generated with the -Duse-libclang=ON option for CMake.
+# The default value is: NO.
+
+CLANG_ASSISTED_PARSING = NO
+
+# If clang assisted parsing is enabled you can provide the compiler with command
+# line options that you would normally use when invoking the compiler. Note that
+# the include paths will already be set by doxygen for the files and directories
+# specified with INPUT and INCLUDE_PATH.
+# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
+
+CLANG_OPTIONS          = 
+
 #---------------------------------------------------------------------------
-# configuration options related to the alphabetical class index
+# 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.
+# 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.
+# The default value is: YES.
 
 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])
+# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
+# which the alphabetical index list will be split.
+# Minimum value: 1, maximum value: 20, default value: 5.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
 
 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.
+# 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 a prefix (or a list of prefixes) that should be ignored
+# while generating the index headers.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
 
 IGNORE_PREFIX          = 
 
 #---------------------------------------------------------------------------
-# configuration options related to the HTML output
+# Configuration options related to the HTML output
 #---------------------------------------------------------------------------
 
-# If the GENERATE_HTML tag is set to YES (the default) Doxygen will 
-# generate HTML output.
+# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
+# The default value is: YES.
 
 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.
+# 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.
+# The default directory is: html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
+# generated HTML page (for example: .htm, .php, .asp).
+# The default value is: .html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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!
+# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
+# each generated HTML page. If the tag is left blank doxygen will generate a
+# standard header.
+#
+# To get valid HTML the header file that includes any scripts and style sheets
+# that doxygen needs, which is dependent on the configuration options used (e.g.
+# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
+# default header using
+# doxygen -w html new_header.html new_footer.html new_stylesheet.css
+# YourConfigFile
+# and then modify the file new_header.html. See also section "Doxygen usage"
+# for information on how to generate the default header that doxygen normally
+# uses.
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. For a description
+# of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+# generated HTML page. If the tag is left blank doxygen will generate a standard
+# footer. See HTML_HEADER for more information on how to generate a default
+# footer and what special commands can be used inside the footer. See also
+# section "Doxygen usage" for information on how to generate the default footer
+# that doxygen normally uses.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# 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.
+# See also section "Doxygen usage" for information on how to generate the style
+# sheet that doxygen normally uses.
+# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
+# it is more robust and this tag (HTML_STYLESHEET) will in the future become
+# obsolete.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# cascading style sheets that are 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 therefore more robust against future updates.
+# Doxygen will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list). For an example see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# 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.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# 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.
+# Minimum value: 0, maximum value: 359, default value: 220.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# 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.
+# Minimum value: 0, maximum value: 255, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# 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.
+# Minimum value: 40, maximum value: 240, default value: 80.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# 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 YES can help to show when doxygen was last run and thus if the
+# documentation is up to date.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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 
+# 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.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# 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.
+# Minimum value: 0, maximum value: 9999, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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 
+# 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 (see: http://developer.apple.com/tools/xcode/), 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.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# This tag determines the name of the docset 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.
+# The default value is: Doxygen generated docs.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
 
 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.
+# 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.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
 
 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.
+# The DOCSET_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.
+# The default value is: org.doxygen.Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
 
 DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
 
-# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
+# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
+# The default value is: Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
 
 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.
+# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
+# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
+# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
+# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
+# Windows.
+#
+# The HTML Help Workshop contains a compiler that can convert all HTML output
+# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
+# files are now used as the Windows 98 help format, and will replace the old
+# Windows help format (.hlp) on all Windows platforms in the future. Compressed
+# HTML files also contain an index, a table of contents, and you can search for
+# words in the documentation. The HTML workshop also contains a viewer for
+# compressed HTML files.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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 
+# 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.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
 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.
+# 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.
+# The file has to be specified with full path.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
 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).
+# 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).
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
 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.
+# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
+# and project file content.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
 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.
+# 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. Furthermore it
+# enables the Previous and Next buttons.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
 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.
+# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# the table of contents of the HTML help documentation and to the tree view.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
 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.
+# 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.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# 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.
+# This tag requires that the tag GENERATE_QHP is set to YES.
 
 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
+# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
+# Project output. For more information please see Qt Help Project / Namespace
+# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_QHP is set to YES.
 
 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
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
+# Help Project output. For more information please see Qt Help Project / Virtual
+# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
+# folders).
+# The default value is: doc.
+# This tag requires that the tag GENERATE_QHP is set to YES.
 
 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
+# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
+# filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
 
 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>.
+# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
 
 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>.
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's filter section matches. Qt Help Project / Filter Attributes (see:
+# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
+# This tag requires that the tag GENERATE_QHP is set to YES.
 
 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.
+# 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.
+# This tag requires that the tag GENERATE_QHP is set to YES.
 
 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.
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
+# generated, together with the HTML files, they 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.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# 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. Each documentation set should have its own identifier.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
 
 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.
+# If you want full control over the layout of the generated HTML pages it might
+# be necessary to disable the index and replace it with your own. The
+# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
+# of each HTML page. A value of NO enables the index and the value YES disables
+# it. Since the tabs in the index contain the same information as the navigation
+# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set 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.
+# 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. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
+# further fine-tune the look of the index. As an example, the default style
+# sheet generated by doxygen has an example that shows how to put an image at
+# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
+# the same information as the tab index, you could consider setting
+# DISABLE_INDEX to YES when enabling this option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values 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.
+# Minimum value: 0, maximum value: 20, default value: 4.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# 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.
+# Minimum value: 0, maximum value: 1500, default value: 250.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# If 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.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# Use this tag to change the font size of LaTeX formulas included as images in
+# the HTML documentation. 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.
+# Minimum value: 8, maximum value: 50, default value: 10.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# 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 directory before the changes have effect.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# 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 pre-rendered 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.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. See the MathJax site (see:
+# http://docs.mathjax.org/en/latest/output.html) for more details.
+# Possible values are: HTML-CSS (which is slower, but has the best
+# compatibility), NativeMML (i.e. MathML) and SVG.
+# The default value is: HTML-CSS.
+# This tag requires that the tag USE_MATHJAX is set to YES.
 
 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.
+# 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.
+# The default value is: http://cdn.mathjax.org/mathjax/latest.
+# This tag requires that the tag USE_MATHJAX is set to YES.
 
 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.
+# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
+# extension names that should be enabled during MathJax rendering. For example
+# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# This tag requires that the tag USE_MATHJAX is set to YES.
 
 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.
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
+# of code that will be used on startup of the MathJax code. See the MathJax site
+# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
+# example see the documentation.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_CODEFILE       = 
+
+# 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. It is possible to
+# search using the keyboard; to jump to the search box use <access key> + S
+# (what the <access key> is depends on the OS and browser, but it is typically
+# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
+# key> to jump into the search results window, the results can be navigated
+# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
+# the search. The filter options can be selected when the cursor is inside the
+# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
+# to select a filter and <Enter> or <escape> to activate or cancel the filter
+# option.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
 
 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.
+# 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 flavors of web server based searching 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 section
+# "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
 
 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.
+# When EXTERNAL_SEARCH tag 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: http://xapian.org/).
+#
+# See the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
 
 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.
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will return the search results when EXTERNAL_SEARCH is enabled.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/). See the section "External Indexing and
+# Searching" for details.
+# This tag requires that the tag SEARCHENGINE is set to YES.
 
 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 
+# 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.
+# The default file is: searchdata.xml.
+# This tag requires that the tag SEARCHENGINE is set to YES.
 
 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 
+# 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.
+# This tag requires that the tag SEARCHENGINE is set to YES.
 
 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 ...
+# 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 = tagname1=loc1 tagname2=loc2 ...
+# This tag requires that the tag SEARCHENGINE is set to YES.
 
 EXTRA_SEARCH_MAPPINGS  = 
 
 #---------------------------------------------------------------------------
-# configuration options related to the LaTeX output
+# Configuration options related to the LaTeX output
 #---------------------------------------------------------------------------
 
-# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will 
-# generate Latex output.
+# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
+# The default value is: YES.
 
 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.
+# 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.
+# The default directory is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 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.
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked.
+#
+# 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.
+# The default file is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 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.
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
+# index for LaTeX.
+# The default file is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 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.
+# 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.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 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.
+# The PAPER_TYPE tag can be used to set the paper type that is used by the
+# printer.
+# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
+# 14 inches) and executive (7.25 x 10.5 inches).
+# The default value is: a4.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 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.
+# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
+# that should be included in the LaTeX output. The package can be specified just
+# by its name or with the correct syntax as to be used with the LaTeX
+# \usepackage command. To get the times font for instance you can specify :
+# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
+# To use the option intlimits with the amsmath package you can specify:
+# EXTRA_PACKAGES=[intlimits]{amsmath}
+# If left blank no extra packages will be included.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 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!
+# 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. See
+# section "Doxygen usage" for information on how to let doxygen write the
+# default header to a separate file.
+#
+# Note: Only use a user-defined header if you know what you are doing! The
+# following commands have a special meaning inside the header: $title,
+# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
+# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
+# string, for the replacement values of the other commands the user is referred
+# to HTML_HEADER.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 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!
+# 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. See
+# LATEX_HEADER for more information on how to generate a default footer and what
+# special commands can be used inside the footer.
+#
+# Note: Only use a user-defined footer if you know what you are doing!
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 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.
+# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# LaTeX style sheets that are included after the standard style sheets created
+# by doxygen. Using this option one can overrule certain style aspects. Doxygen
+# will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list).
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_STYLESHEET = 
+
+# 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 output
+# directory. Note that the files will be copied as-is; there are no commands or
+# markers available.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 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.
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
+# prepared for conversion to PDF (using ps2pdf or pdflatex). 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.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 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 
+# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
+# the PDF file directly from the LaTeX files. Set this option to YES, to get a
 # higher quality PDF documentation.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 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.
+# 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.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 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.
+# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
+# index chapters (such as File Index, Compound Index, etc.) in the output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 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.
+# If the LATEX_SOURCE_CODE tag 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.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 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.
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. See
+# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
+# The default value is: plain.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_BIB_STYLE        = plain
 
+# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
+# 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.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_TIMESTAMP        = NO
+
 #---------------------------------------------------------------------------
-# configuration options related to the RTF output
+# 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.
+# 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 too pretty with other RTF
+# readers/editors.
+# The default value is: NO.
 
 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.
+# 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.
+# The default directory is: rtf.
+# This tag requires that the tag GENERATE_RTF is set to YES.
 
 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.
+# 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.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
 
 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.
+# 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 some other Word compatible readers that support those
+# fields.
+#
+# Note: WordPad (write) and others do not support links.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
 
 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.
+# Load stylesheet 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.
+#
+# See also section "Doxygen usage" for information on how to generate the
+# default style sheet that doxygen normally uses.
+# This tag requires that the tag GENERATE_RTF is set to YES.
 
 RTF_STYLESHEET_FILE    = 
 
-# Set optional variables used in the generation of an rtf document. 
-# Syntax is similar to doxygen's config file.
+# Set optional variables used in the generation of an RTF document. Syntax is
+# similar to doxygen's config file. A template extensions file can be generated
+# using doxygen -e rtf extensionFile.
+# This tag requires that the tag GENERATE_RTF is set to YES.
 
 RTF_EXTENSIONS_FILE    = 
 
+# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
+# with syntax highlighting in the RTF output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_SOURCE_CODE        = NO
+
 #---------------------------------------------------------------------------
-# configuration options related to the man page output
+# Configuration options related to the man page output
 #---------------------------------------------------------------------------
 
-# If the GENERATE_MAN tag is set to YES (the default) Doxygen will 
-# generate man pages
+# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
+# classes and files.
+# The default value is: NO.
 
 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.
+# 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. A directory man3 will be created inside the directory specified by
+# MAN_OUTPUT.
+# The default directory is: man.
+# This tag requires that the tag GENERATE_MAN is set to YES.
 
 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)
+# The MAN_EXTENSION tag determines the extension that is added to the generated
+# man pages. In case the manual section does not start with a number, the number
+# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
+# optional.
+# The default value is: .3.
+# This tag requires that the tag GENERATE_MAN is set to YES.
 
 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.
+# The MAN_SUBDIR tag determines the name of the directory created within
+# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
+# MAN_EXTENSION with the initial . removed.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_SUBDIR             = 
+
+# 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 value is: NO.
+# This tag requires that the tag GENERATE_MAN is set to YES.
 
 MAN_LINKS              = NO
 
 #---------------------------------------------------------------------------
-# configuration options related to the XML output
+# 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.
+# 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.
+# The default value is: NO.
 
 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.
+# 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.
+# The default directory is: xml.
+# This tag requires that the tag GENERATE_XML is set to YES.
 
 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.
+# 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.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_XML is set to YES.
 
 XML_PROGRAMLISTING     = YES
 
 #---------------------------------------------------------------------------
-# configuration options related to the DOCBOOK output
+# Configuration options related to the DOCBOOK output
 #---------------------------------------------------------------------------
 
-# If the GENERATE_DOCBOOK tag is set to YES Doxygen will generate DOCBOOK files 
+# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
 # that can be used to generate PDF.
+# The default value is: NO.
 
 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.
+# 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.
+# The default directory is: docbook.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
 
 DOCBOOK_OUTPUT         = docbook
 
+# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
+# program listings (including syntax highlighting and cross-referencing
+# information) to the DOCBOOK output. Note that enabling this will significantly
+# increase the size of the DOCBOOK output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_PROGRAMLISTING = NO
+
 #---------------------------------------------------------------------------
-# configuration options for the AutoGen Definitions output
+# 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.
+# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
+# AutoGen Definitions (see http://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.
+# The default value is: NO.
 
 GENERATE_AUTOGEN_DEF   = NO
 
 #---------------------------------------------------------------------------
-# configuration options related to the Perl module output
+# 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.
+# 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.
+# The default value is: NO.
 
 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.
+# 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.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
 
 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.
+# 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.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
 
 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.
+# 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.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
 
 PERLMOD_MAKEVAR_PREFIX = 
 
@@ -1556,112 +1985,131 @@ 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.
+# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
+# C-preprocessor directives found in the sources and include files.
+# The default value is: YES.
 
 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.
+# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
+# in the source code. If set to NO, only conditional compilation will be
+# performed. Macro expansion can be done in a controlled way by setting
+# EXPAND_ONLY_PREDEF to YES.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set 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.
+# 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.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
 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.
+# If the SEARCH_INCLUDES tag is set to YES, the include files in the
+# INCLUDE_PATH will be searched if a #include is found.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
 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.
+# 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.
+# This tag requires that the tag SEARCH_INCLUDES is set to YES.
 
 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.
+# 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.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
 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.
+# 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 e.g.
+# 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.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
 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.
+# 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.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
 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.
+# If the SKIP_FUNCTION_MACROS tag is set to YES 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. Such function macros
+# are typically used for boiler-plate code, and will confuse the parser if not
+# removed.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
 SKIP_FUNCTION_MACROS   = YES
 
 #---------------------------------------------------------------------------
-# Configuration::additions related to external references
+# Configuration options 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.
+# The TAGFILES tag can be used to specify one or more tag files. 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. See the
+# section "Linking to external documentation" for more information about the use
+# of tag files.
+# Note: 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.
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
+# tag file that is based on the input files it reads. See section "Linking to
+# external documentation" for more information about the usage of tag files.
 
 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.
+# If the ALLEXTERNALS tag is set to YES, all external class will be listed in
+# the class index. If set to NO, only the inherited external classes will be
+# listed.
+# The default value is: NO.
 
 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.
+# 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.
+# The default value is: YES.
 
 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.
+# 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.
+# The default value is: YES.
 
 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').
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of 'which perl').
+# The default file (with absolute path) is: /usr/bin/perl.
 
 PERL_PATH              = /usr/bin/perl
 
@@ -1669,222 +2117,314 @@ 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.
+# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram
+# (in HTML 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.
+# The default value is: YES.
 
 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 
+# 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.
+# You can include diagrams made with dia in doxygen documentation. Doxygen will
+# then run dia to produce the diagram and insert it in the documentation. The
+# DIA_PATH tag allows you to specify the directory where the dia binary resides.
+# If left empty dia is assumed to be found in the default search path.
+
+DIA_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.
+# The default value is: YES.
 
 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)
+# 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 (see:
+# http://www.graphviz.org/), 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 value is: YES.
 
 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.
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
+# to run in parallel. When set to 0 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.
+# Minimum value: 0, maximum value: 32, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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.
+# When you want a differently looking font in the dot files that doxygen
+# generates 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.
+# The default value is: Helvetica.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
-DOT_FONTNAME           = FreeSans
+DOT_FONTNAME           = Helvetica
 
-# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. 
-# The default size is 10pt.
+# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
+# dot graphs.
+# Minimum value: 4, maximum value: 24, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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.
+# By default doxygen will tell dot to use the default font as specified with
+# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
+# the path where dot can find it using this tag.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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.
+# If the CLASS_GRAPH tag is 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.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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.
+# If the COLLABORATION_GRAPH tag is 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.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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
+# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
+# groups, showing the direct groups dependencies.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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 
+# 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.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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.
+# 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 manageable. Set this to 0
+# for no limit. Note that the threshold may be exceeded by 50% before the limit
+# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
+# but if the number exceeds 15, the total amount of fields shown is limited to
+# 10.
+# Minimum value: 0, maximum value: 100, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 UML_LIMIT_NUM_FIELDS   = 10
 
-# If set to YES, the inheritance and collaboration graphs will show the 
-# relations between templates and their instances.
+# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
+# collaboration graphs will show the relations between templates and their
+# instances.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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.
+# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES 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.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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.
+# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES 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.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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.
+# If the CALL_GRAPH tag is 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. Disabling a call graph can be
+# accomplished by means of the command \hidecallgraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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.
+# If the CALLER_GRAPH tag is 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. Disabling a caller graph can be
+# accomplished by means of the command \hidecallergraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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.
+# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
+# hierarchy of all classes instead of a textual one.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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.
+# If the DIRECTORY_GRAPH tag is 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.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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).
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot. For an explanation of the image formats see the section
+# output formats in the documentation of the dot tool (Graphviz (see:
+# http://www.graphviz.org/)).
+# Note: 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).
+# Possible values are: png, png:cairo, png:cairo:cairo, png:cairo:gd, png:gd,
+# png:gd:gd, jpg, jpg:cairo, jpg:cairo:gd, jpg:gd, jpg:gd:gd, gif, gif:cairo,
+# gif:cairo:gd, gif:gd, gif:gd:gd, svg, png:gd, png:gd:gd, png:cairo,
+# png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and
+# png:gdiplus:gdiplus.
+# The default value is: png.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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.
+# 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.
+# Note: 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.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 INTERACTIVE_SVG        = NO
 
-# The tag DOT_PATH can be used to specify the path where the dot tool can be 
+# The DOT_PATH tag 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.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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).
+# 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).
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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).
+# 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.
+# The DIAFILE_DIRS tag can be used to specify one or more directories that
+# contain dia files that are included in the documentation (see the \diafile
+# command).
+
+DIAFILE_DIRS           = 
+
+# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
+# path where java can find the plantuml.jar file. If left blank, it is assumed
+# PlantUML is not used or called during a preprocessing step. Doxygen will
+# generate a warning when it encounters a \startuml command in this case and
+# will not generate output for the diagram.
+
+PLANTUML_JAR_PATH      = 
+
+# When using plantuml, the specified paths are searched for files specified by
+# the !include statement in a plantuml block.
+
+PLANTUML_INCLUDE_PATH  = 
+
+# 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.
+# Minimum value: 0, maximum value: 10000, default value: 50.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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 
+# 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.
+# Minimum value: 0, maximum value: 1000, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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).
+# 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).
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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.
+# Set the DOT_MULTI_TARGETS tag to YES to 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.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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.
+# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
+# explaining the meaning of the various boxes and arrows in the dot generated
+# graphs.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 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.
+# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate dot
+# files that are used to generate the various graphs.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 DOT_CLEANUP            = YES
diff --git a/INSTALL.txt b/INSTALL.txt
index c8859da..8c499db 100644
--- a/INSTALL.txt
+++ b/INSTALL.txt
@@ -1,12 +1,23 @@
-This software needs cmake >= 2.6 to build.
+This software needs cmake >= 2.8.11 and a C++11 capable compiler to build
 
 After installing cmake, run it with the following command:
-cmake -DCMAKE_INSTALL_PREFIX=[where to install, for instance /usr/local or $HOME/.local] .
+$ 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
+Then compile and install the software with:
+$ make install
 
 You may also consider installing and using the software checkinstall for easier system administration.
 
+If you install Bio++ in a non standard path (not /usr/), remember that:
+-> if you compile your project with CMake, give it the path with -DCMAKE_PREFIX_PATH=<path>
+-> if you compile with something else, give the path to the compiler (-I / -L options)
+-> if you use shared libraries, you must also tell programs where to find them at startup:
+  -> either by adding the path to LD_LIBRARY_PATH environment variable.
+  -> or by using RPATHs to hard code the path in the executable (generates NON PORTABLE executables !)
+    -> with CMake, see documentation in bpp-core/cmake/project-template
+    -> or see your compiler documentation ("-Wl,-rpath,<path>" for clang/gcc)
+    -> consider installing Bio++ with the "-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE" option
+
+Detailed documentation for using Bio++ with CMake are available in bpp-core/cmake/
diff --git a/bpp-qt.spec b/bpp-qt.spec
index 3a9f3b9..9074ef2 100644
--- a/bpp-qt.spec
+++ b/bpp-qt.spec
@@ -1,5 +1,5 @@
 %define _basename bpp-qt
-%define _version 2.2.0
+%define _version 2.3.1
 %define _release 1
 %define _prefix /usr
 
@@ -30,11 +30,11 @@ Requires: libqtgui4 >= 4.6.0
 %endif
 
 BuildRoot: %{_builddir}/%{_basename}-root
-BuildRequires: cmake >= 2.6.0
-BuildRequires: gcc-c++ >= 4.0.0
-BuildRequires: libbpp-core2 = %{_version}
+BuildRequires: cmake >= 2.8.11
+BuildRequires: gcc-c++ >= 4.7.0
+BuildRequires: libbpp-core3 = %{_version}
 BuildRequires: libbpp-core-devel = %{_version}
-BuildRequires: libbpp-phyl9 = %{_version}
+BuildRequires: libbpp-phyl11 = %{_version}
 BuildRequires: libbpp-phyl-devel = %{_version}
 
 %if 0%{?fedora} || 0%{?rhel_version} || 0%{?centos_version}
@@ -74,9 +74,9 @@ It is part of the Bio++ project.
 Summary: Libraries, includes to develop applications with %{_basename}
 Group: Development/Libraries/C and C++
 Requires: libbpp-qt1 = %{_version}
-Requires: libbpp-phyl9 = %{_version}
+Requires: libbpp-phyl11 = %{_version}
 Requires: libbpp-phyl-devel = %{_version}
-Requires: libbpp-core2 = %{_version}
+Requires: libbpp-core3 = %{_version}
 Requires: libbpp-core-devel = %{_version}
 %if 0%{?fedora} || 0%{?rhel_version} || 0%{?centos_version}
 Requires: qt >= 4.6.0
@@ -106,9 +106,6 @@ building applications which use %{_basename}.
 %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
 
@@ -120,100 +117,8 @@ 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
@@ -222,11 +127,18 @@ exit 0
 %files -n libbpp-qt-devel
 %defattr(-,root,root)
 %doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
+%dir %{_prefix}/%{_lib}/cmake/
+%dir %{_prefix}/%{_lib}/cmake/bpp-qt
 %{_prefix}/%{_lib}/lib*.so
 %{_prefix}/%{_lib}/lib*.a
+%{_prefix}/%{_lib}/cmake/bpp-qt/bpp-qt*.cmake
 %{_prefix}/include/*
 
 %changelog
+* Tue Jun 06 2017 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.3.1-1
+- Increased interface number
+* Wed May 10 2017 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.3.0-1
+- Upgrade to C++11
 * Fri Sep 26 2014 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.2.0-1
 - Removed CLang warnings.
 * Fri Mar 08 2013 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.1.0-1
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index 1de1322..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,31 +0,0 @@
-libbpp-qt (2.2.0-1) unstable; urgency=low
-
-   * Removed CLang warnings.
-
- -- Julien Dutheil <julien.dutheil at univ-montp2.fr>  Fri, 26 Sep 2014 14:00:00 +0100
-
-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
deleted file mode 100644
index 7ed6ff8..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-5
diff --git a/debian/control b/debian/control
deleted file mode 100644
index d941c96..0000000
--- a/debian/control
+++ /dev/null
@@ -1,28 +0,0 @@
-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: 3.9.4
-
-Package: libbpp-qt-dev
-Section: libdevel
-Architecture: any
-Depends: libbpp-qt1 (= ${binary:Version}), ${misc:Depends},
-  libbpp-phyl-dev (>= 2.2.0), 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 (>= 2.2.0),
-  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
deleted file mode 100644
index e11e6ac..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,66 +0,0 @@
-This package was debianized by Julien Dutheil <julien.dutheil at univ-montp2.fr> on
-Fri, 26 Sep 2014 14:00:00 +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) 2014 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) 2014, 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
deleted file mode 100644
index e69de29..0000000
diff --git a/debian/libbpp-qt-dev.install b/debian/libbpp-qt-dev.install
deleted file mode 100644
index 7d74f2b..0000000
--- a/debian/libbpp-qt-dev.install
+++ /dev/null
@@ -1,3 +0,0 @@
-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
deleted file mode 100644
index c45ebcf..0000000
--- a/debian/libbpp-qt1.install
+++ /dev/null
@@ -1 +0,0 @@
-debian/tmp/usr/lib/lib*.so.*
diff --git a/debian/postinst b/debian/postinst
deleted file mode 100755
index cff89b1..0000000
--- a/debian/postinst
+++ /dev/null
@@ -1,57 +0,0 @@
-#! /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;
-}
-
-case "$1" in
-  configure)
-    # Actualize .all files
-    createGeneric /usr/include/Bpp
-  ;;
-  abort-upgrade|abort-remove|abort-deconfigure)
-    echo "$1"
-  ;;
-  *)
-    echo "postinst called with unknown argument \`\$1'" >&2
-    exit 0
-  ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
diff --git a/debian/postrm b/debian/postrm
deleted file mode 100755
index 744f8b1..0000000
--- a/debian/postrm
+++ /dev/null
@@ -1,59 +0,0 @@
-#! /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;
-}
-
-case "$1" in
-  remove)
-    # Automatically added by dh_makeshlibs
-    ldconfig
-    # Actualize .all files
-    createGeneric /usr/include/Bpp
-  ;;
-  purge|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
-    echo $1
-  ;;
-  *)
-    echo "postrm called with unknown argument \`\$1'" >&2
-    exit 0
-  ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
diff --git a/debian/prerm b/debian/prerm
deleted file mode 100755
index 8fab52e..0000000
--- a/debian/prerm
+++ /dev/null
@@ -1,41 +0,0 @@
-#! /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
-}
-
-case "$1" in
-  remove|upgrade|deconfigure)
-    # Actualize .all files
-    removeGeneric /usr/include/Bpp
-  ;;
-  failed-upgrade)
-    echo "$1"
-  ;;
-  *)
-    echo "prerm called with unknown argument \`$1'" >&2
-    exit 1
-  ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index c4539d2..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,121 +0,0 @@
-#!/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-arch build-indep
-build-arch: build-stamp
-build-indep: 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
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/genIncludes.sh b/genIncludes.sh
deleted file mode 100755
index 56710e9..0000000
--- a/genIncludes.sh
+++ /dev/null
@@ -1,35 +0,0 @@
-#! /bin/bash
-
-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;
-}
-
-createGeneric $1
diff --git a/package.cmake.in b/package.cmake.in
new file mode 100644
index 0000000..497a69a
--- /dev/null
+++ b/package.cmake.in
@@ -0,0 +1,30 @@
+# CMake package file for Bio++ Qt
+# Authors:
+#   Francois Gindraud (2017)
+# Created: 17/03/2017
+ at PACKAGE_INIT@
+
+if (NOT @PROJECT_NAME at _FOUND)
+  # Deps
+  find_package (bpp-phyl @bpp-phyl_VERSION@ REQUIRED)
+  # QT dep (pull imported target required by bpp-qt)
+  set (QT_USE_IMPORTED_TARGETS TRUE)
+  find_package (Qt4 COMPONENTS QtCore QtGui REQUIRED)
+  include (${QT_USE_FILE})
+  # Add targets
+  include ("${CMAKE_CURRENT_LIST_DIR}/@PROJECT_NAME at -targets.cmake")
+  # Append targets to convenient lists
+  set (BPP_LIBS_STATIC "${BPP_LIBS_STATIC}" @PROJECT_NAME at -static)
+  set (BPP_LIBS_SHARED "${BPP_LIBS_SHARED}" @PROJECT_NAME at -shared)
+  # Print some path info for targets
+  get_property (static-location TARGET @PROJECT_NAME at -static PROPERTY LOCATION)
+  get_property (shared-location TARGET @PROJECT_NAME at -shared PROPERTY LOCATION)
+  get_property (header-location TARGET @PROJECT_NAME at -static PROPERTY INTERFACE_INCLUDE_DIRECTORIES)
+  message (STATUS "@PROJECT_NAME@ @PROJECT_VERSION@ found:")
+  message (STATUS "  static lib: ${static-location}")
+  message (STATUS "  shared lib: ${shared-location}")
+  message (STATUS "  includes: ${header-location}")
+  unset (static-location)
+  unset (shared-location)
+  unset (header-location)
+endif (NOT @PROJECT_NAME at _FOUND)
diff --git a/src/Bpp/Qt/QtGraphicDevice.cpp b/src/Bpp/Qt/QtGraphicDevice.cpp
index 89afea5..4690248 100644
--- a/src/Bpp/Qt/QtGraphicDevice.cpp
+++ b/src/Bpp/Qt/QtGraphicDevice.cpp
@@ -55,7 +55,7 @@ using namespace std;
 using namespace bpp;
 
 QtGraphicDevice::QtGraphicDevice() :
-  scene_(0), supportedLineTypes_(), currentPen_(), currentBrush_(Qt::SolidPattern), currentFont_()
+  scene_(), supportedLineTypes_(), currentPen_(), currentBrush_(Qt::SolidPattern), currentFont_()
 {
   supportedLineTypes_[GraphicDevice::LINE_SOLID] = Qt::SolidLine;
   supportedLineTypes_[GraphicDevice::LINE_DASHED] = Qt::DashLine;
@@ -68,8 +68,7 @@ QtGraphicDevice::~QtGraphicDevice() {}
 
 void QtGraphicDevice::begin() throw (Exception)
 {
-  if (scene_) delete scene_;
-  scene_ = new QGraphicsScene();
+  scene_.reset(new QGraphicsScene());
 }
 
 void QtGraphicDevice::end()
@@ -97,7 +96,7 @@ void QtGraphicDevice::setCurrentFont(const Font& font)
 void QtGraphicDevice::setCurrentPointSize(unsigned int size)
 {
   AbstractGraphicDevice::setCurrentPointSize(size);
-  currentPen_.setWidth(static_cast<uint>(size));
+  currentPen_.setWidth(static_cast<int>(size));
 }
 
 void QtGraphicDevice::setCurrentLineType(short type) throw (Exception)
@@ -131,7 +130,7 @@ 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;
+  qreal xset = 0, yset = 0;
   QString qtext = text.c_str();
   QGraphicsTextItem* item = scene_->addText(qtext, currentFont_);
   QSizeF fsize = item->document()->size();
diff --git a/src/Bpp/Qt/QtGraphicDevice.h b/src/Bpp/Qt/QtGraphicDevice.h
index fec7365..86c8ce9 100644
--- a/src/Bpp/Qt/QtGraphicDevice.h
+++ b/src/Bpp/Qt/QtGraphicDevice.h
@@ -49,6 +49,7 @@ knowledge of the CeCILL license and that you accept its terms.
 
 //From the STL:
 #include <map>
+#include <memory>
 
 /**
  * @mainpage
@@ -74,7 +75,7 @@ class QtGraphicDevice:
   public AbstractGraphicDevice
 {
   private:
-    QGraphicsScene* scene_;
+    std::unique_ptr<QGraphicsScene> scene_;
     std::map<short int, Qt::PenStyle> supportedLineTypes_;
     QPen currentPen_;
     QBrush currentBrush_;
@@ -108,6 +109,8 @@ class QtGraphicDevice:
     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)); }
+    double revx(double xpos) const { return revx_(xpos); }
+    double revy(double ypos) const { return revy_(ypos); }
 
  
 };
diff --git a/src/Bpp/Qt/QtTools.h b/src/Bpp/Qt/QtTools.h
index ca6269e..84dc92c 100644
--- a/src/Bpp/Qt/QtTools.h
+++ b/src/Bpp/Qt/QtTools.h
@@ -85,7 +85,9 @@ public:
 
   static QColor toQt(const RGBColor& color)
   {
-    return QColor(color[0], color[1], color[2]);
+    return QColor(static_cast<int>(color[0]),
+		  static_cast<int>(color[1]),
+		  static_cast<int>(color[2]));
   }
 
   static QFont toQt(const Font& font)
diff --git a/src/Bpp/Qt/Tree/TreeCanvas.cpp b/src/Bpp/Qt/Tree/TreeCanvas.cpp
index ea8b9d7..be76efa 100644
--- a/src/Bpp/Qt/Tree/TreeCanvas.cpp
+++ b/src/Bpp/Qt/Tree/TreeCanvas.cpp
@@ -66,12 +66,14 @@ NodeMouseEvent::NodeMouseEvent(const TreeCanvas& treeCanvas, const QMouseEvent&
 TreeCanvas::TreeCanvas(QWidget* parent) :
   QGraphicsView(parent),
   currentTree_(0),
+  treeDrawing_(),
+  defaultTreeDrawing_(new CladogramPlot()),
   device_(),
   drawingWidth_(600),
   drawingHeight_(800),
-  mouseListenerGroup_()
+  mouseListenerGroup_(),
+  nodeCollapsed_()
 {
-  defaultTreeDrawing_ = new CladogramPlot();
   treeDrawing_ = defaultTreeDrawing_;
 }
 
@@ -126,7 +128,7 @@ void TreeCanvas::setTreeDrawing(const TreeDrawing& treeDrawing, bool repaint)
   treeDrawing_ = dynamic_cast<TreeDrawing*>(treeDrawing.clone());
   treeDrawing_->setTree(currentTree_);
   vector<int> ids = currentTree_->getNodesId();
-  for (unsigned int i = 0; i < ids.size(); i++) {
+  for (size_t i = 0; i < ids.size(); i++) {
     treeDrawing_->collapseNode(ids[i], nodeCollapsed_[ids[i]]);
   }
   if (repaint) {
diff --git a/src/Bpp/Qt/Tree/TreeCanvas.h b/src/Bpp/Qt/Tree/TreeCanvas.h
index 49e4508..3e286b1 100644
--- a/src/Bpp/Qt/Tree/TreeCanvas.h
+++ b/src/Bpp/Qt/Tree/TreeCanvas.h
@@ -90,7 +90,7 @@ class NodeMouseEvent:
 /**
  * @brief Panel for plotting phylogenetic trees.
  *
- * The graphe used for plotting the tree depends on the TreeDrawing object used.
+ * The graph 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:
@@ -110,6 +110,16 @@ class TreeCanvas:
 
   public:
     TreeCanvas(QWidget* parent = 0);
+
+  private:
+    //No copy allowed
+    TreeCanvas(const TreeCanvas& tc):
+      currentTree_(), treeDrawing_(), defaultTreeDrawing_(), device_(),
+      drawingWidth_(), drawingHeight_(), mouseListenerGroup_(), nodeCollapsed_()
+    {}
+    TreeCanvas& operator=(const TreeCanvas& tc) { return *this; }
+      
+  public:
     virtual ~TreeCanvas()
     {
       delete defaultTreeDrawing_;
@@ -179,24 +189,24 @@ class TreeCanvas:
   
     void mouseDoubleClickEvent(QMouseEvent* event)
     {
-      std::auto_ptr<NodeMouseEvent> newEvent(new NodeMouseEvent(*this, *event));
+      std::unique_ptr<NodeMouseEvent> newEvent(new NodeMouseEvent(*this, *event));
       mouseListenerGroup_.processMouseDoubleClickEvent(newEvent.get());
     }
 
     void mouseMoveEvent(QMouseEvent* event)
     {
-      std::auto_ptr<NodeMouseEvent> newEvent(new NodeMouseEvent(*this, *event));
+      std::unique_ptr<NodeMouseEvent> newEvent(new NodeMouseEvent(*this, *event));
       mouseListenerGroup_.processMouseMoveEvent(newEvent.get());
     }
     void mousePressEvent(QMouseEvent* event)
     {
-      std::auto_ptr<NodeMouseEvent> newEvent(new NodeMouseEvent(*this, *event));
+      std::unique_ptr<NodeMouseEvent> newEvent(new NodeMouseEvent(*this, *event));
       mouseListenerGroup_.processMousePressEvent(newEvent.get());
     }
 
     void mouseReleaseEvent(QMouseEvent* event)
     {
-      std::auto_ptr<NodeMouseEvent> newEvent(new NodeMouseEvent(*this, *event));
+      std::unique_ptr<NodeMouseEvent> newEvent(new NodeMouseEvent(*this, *event));
       mouseListenerGroup_.processMouseReleaseEvent(newEvent.get());
     }
     /** @} */
diff --git a/src/Bpp/Qt/Tree/TreeCanvasControlers.cpp b/src/Bpp/Qt/Tree/TreeCanvasControlers.cpp
index d42734c..a75e00e 100644
--- a/src/Bpp/Qt/Tree/TreeCanvasControlers.cpp
+++ b/src/Bpp/Qt/Tree/TreeCanvasControlers.cpp
@@ -201,7 +201,8 @@ void TreeCanvasControlers::treeDrawingUnitChanged()
   if (!treeCanvas_) return;
   if (! blockSignal_)
   {
-    treeCanvas_->setDrawingSize(widthCtrl_->value(), heightCtrl_->value());
+    treeCanvas_->setDrawingSize(static_cast<unsigned int>(widthCtrl_->value()),
+		                static_cast<unsigned int>(heightCtrl_->value()));
   }
 }
 
@@ -210,8 +211,8 @@ 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());
+  widthCtrl_->setValue(static_cast<int>(treeCanvas_->drawingWidth()));
+  heightCtrl_->setValue(static_cast<int>(treeCanvas_->drawingHeight()));
   drawingCtrl_->setCurrentIndex(availableTreeDrawings_.indexOf(QString(current->getName().c_str())));
   if (current->getHorizontalOrientation() == AbstractDendrogramPlot::ORIENTATION_LEFT_TO_RIGHT)
     orientationLeftRight_->buttons()[0]->setChecked(true);
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 4e6e83b..65f32d7 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,53 +1,59 @@
 # CMake script for Bio++ Qt
-# Author: Julien Dutheil
+# Authors:
+#   Julien Dutheil
+#   Francois Gindraud (2017)
 # Created: 22/08/2009
 
 # File list
-set(CPP_FILES
+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
+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})
+qt4_wrap_cpp (CPP_MOC_FILES ${H_MOC_FILES})
 
 # Build the static lib
-add_library(bppqt-static STATIC ${CPP_FILES} ${CPP_MOC_FILES})
-set_target_properties(bppqt-static
-  PROPERTIES OUTPUT_NAME bpp-qt
-  CLEAN_DIRECT_OUTPUT 1
+add_library (${PROJECT_NAME}-static STATIC ${CPP_FILES} ${CPP_MOC_FILES})
+target_include_directories (${PROJECT_NAME}-static PUBLIC
+  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
+  $<INSTALL_INTERFACE:$<INSTALL_PREFIX>/${CMAKE_INSTALL_INCLUDEDIR}>
   )
-target_link_libraries(bppqt-static ${LIBS})
+set_target_properties (${PROJECT_NAME}-static PROPERTIES OUTPUT_NAME ${PROJECT_NAME})
+target_link_libraries (${PROJECT_NAME}-static ${BPP_LIBS_STATIC} ${qt-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 ${BPPQT_VERSION_MAJOR}
+add_library (${PROJECT_NAME}-shared SHARED ${CPP_FILES} ${CPP_MOC_FILES})
+target_include_directories (${PROJECT_NAME}-shared PUBLIC
+  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
+  $<INSTALL_INTERFACE:$<INSTALL_PREFIX>/${CMAKE_INSTALL_INCLUDEDIR}>
   )
-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")
+set_target_properties (${PROJECT_NAME}-shared
+  PROPERTIES OUTPUT_NAME ${PROJECT_NAME}
+  MACOSX_RPATH 1
+  VERSION ${${PROJECT_NAME}_VERSION}
+  SOVERSION ${${PROJECT_NAME}_VERSION_MAJOR}
+  )
+target_link_libraries (${PROJECT_NAME}-shared ${BPP_LIBS_SHARED} ${qt-libs})
 
-# Generate generic include files (.all)
-INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${CMAKE_SOURCE_DIR}/genIncludes.sh ${CMAKE_PREFIX_PATH}/include/Bpp)")
+# Install libs and headers
+install (
+  TARGETS ${PROJECT_NAME}-static ${PROJECT_NAME}-shared
+  EXPORT ${PROJECT_NAME}-targets
+  LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+  ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+  RUNTIME DESTINATION ${CMAKE_INSTALL_LIBDIR}
+  )
+install (
+  DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/Bpp
+  DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+  FILES_MATCHING PATTERN "*.h"
+  )
+# Install cmake file representing targets
+install (EXPORT ${PROJECT_NAME}-targets DESTINATION ${cmake-package-location})

-- 
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