[med-svn] [libbpp-seq-omics] 02/06: New upstream version 2.3.1
Andreas Tille
tille at debian.org
Tue Jun 13 21:31:03 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libbpp-seq-omics.
commit 7b9eb571a3f24cbd73f1f7f699882ddea9e5ba59
Author: Andreas Tille <tille at debian.org>
Date: Tue Jun 13 23:19:43 2017 +0200
New upstream version 2.3.1
---
BppSeqOmics.tag | 4984 --------------------
CMakeLists.txt | 172 +-
CTestConfig.cmake | 13 +
ChangeLog | 41 +
Doxyfile | 2662 ++++++-----
INSTALL.txt | 19 +-
bpp-seq-omics.spec | 137 +-
debian/changelog | 19 -
debian/compat | 1 -
debian/control | 25 -
debian/copyright | 66 -
debian/libbpp-seq-omics-dev.install | 3 -
debian/libbpp-seq-omics1.install | 1 -
debian/postinst | 57 -
debian/postrm | 59 -
debian/prerm | 41 -
debian/rules | 122 -
debian/source/format | 1 -
genIncludes.sh | 35 -
package.cmake.in | 26 +
src/Bpp/Seq/Feature/Bed/BedGraphFeatureReader.cpp | 105 +
.../BedGraphFeatureReader.h} | 57 +-
src/Bpp/Seq/Feature/Gff/GffFeatureReader.cpp | 4 +-
src/Bpp/Seq/Feature/Gff/GffFeatureReader.h | 8 +-
src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.cpp | 4 +-
src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.h | 8 +-
src/Bpp/Seq/Feature/SequenceFeature.h | 150 +-
src/Bpp/Seq/Feature/SequenceFeatureTools.cpp | 11 +
src/Bpp/Seq/Feature/SequenceFeatureTools.h | 14 +
src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp | 72 +-
src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.h | 105 +-
src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp | 4 +-
src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.cpp | 25 +-
src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.h | 11 +-
.../Seq/Io/Maf/CoordinateTranslatorMafIterator.cpp | 136 +
...terator.h => CoordinateTranslatorMafIterator.h} | 72 +-
.../Seq/Io/Maf/CoordinatesOutputMafIterator.cpp | 6 +
src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.h | 10 +-
src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp | 23 +-
src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.h | 4 +-
src/Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp | 6 +-
src/Bpp/Seq/Io/Maf/FullGapFilterMafIterator.cpp | 6 +-
src/Bpp/Seq/Io/Maf/IterationListener.h | 2 +-
src/Bpp/Seq/Io/Maf/MafParser.cpp | 51 +-
src/Bpp/Seq/Io/Maf/MafParser.h | 43 +-
src/Bpp/Seq/Io/Maf/MafSequence.h | 36 +-
src/Bpp/Seq/Io/Maf/MafStatistics.cpp | 159 +-
src/Bpp/Seq/Io/Maf/MafStatistics.h | 107 +-
src/Bpp/Seq/Io/Maf/MaskFilterMafIterator.cpp | 8 +-
src/Bpp/Seq/Io/Maf/MsmcOutputMafIterator.cpp | 113 +
...OutputMafIterator.h => MsmcOutputMafIterator.h} | 65 +-
src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp | 20 +-
src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h | 59 +-
src/Bpp/Seq/Io/Maf/OutputMafIterator.cpp | 2 +-
src/Bpp/Seq/Io/Maf/PlinkOutputMafIterator.cpp | 124 +
src/Bpp/Seq/Io/Maf/PlinkOutputMafIterator.h | 144 +
...tor.cpp => RemoveEmptySequencesMafIterator.cpp} | 40 +-
...terator.h => RemoveEmptySequencesMafIterator.h} | 50 +-
.../Seq/Io/Maf/SequenceLDhotOutputMafIterator.cpp | 139 +
...Iterator.h => SequenceLDhotOutputMafIterator.h} | 80 +-
src/Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.cpp | 2 +-
src/Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.h | 4 +-
src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp | 3 +
src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h | 10 +-
src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.cpp | 16 +-
src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.h | 7 +-
src/CMakeLists.txt | 148 +-
test/CMakeLists.txt | 66 +-
68 files changed, 3616 insertions(+), 7207 deletions(-)
diff --git a/BppSeqOmics.tag b/BppSeqOmics.tag
deleted file mode 100644
index 131b933..0000000
--- a/BppSeqOmics.tag
+++ /dev/null
@@ -1,4984 +0,0 @@
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- <file>SequenceFeatureTools.cpp</file>
- <file>SequenceFeatureTools.h</file>
- </compound>
- <compound kind="dir">
- <name>Bpp/Seq/Feature/Gff</name>
- <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Feature/Gff/</path>
- <filename>dir_c0bf08a5d2a47f401a6888f5e1d87c21.html</filename>
- <file>GffFeatureReader.cpp</file>
- <file>GffFeatureReader.h</file>
- </compound>
- <compound kind="dir">
- <name>Bpp/Seq/Feature/Gtf</name>
- <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Feature/Gtf/</path>
- <filename>dir_09373788d42d67ba1bb1b5a4c9d36ae2.html</filename>
- <file>GtfFeatureReader.cpp</file>
- <file>GtfFeatureReader.h</file>
- </compound>
- <compound kind="dir">
- <name>Bpp/Seq/Io</name>
- <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/</path>
- <filename>dir_5e67b57d7661860c73cf9ed56f8c6bb7.html</filename>
- <dir>Bpp/Seq/Io/Maf</dir>
- <file>Fastq.cpp</file>
- <file>Fastq.h</file>
- </compound>
- <compound kind="dir">
- <name>Bpp/Seq/Io/Maf</name>
- <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/Io/Maf/</path>
- <filename>dir_5cd58ecbcb201e183133cbca86be7628.html</filename>
- <file>AlignmentFilterMafIterator.cpp</file>
- <file>AlignmentFilterMafIterator.h</file>
- <file>BlockLengthMafIterator.h</file>
- <file>BlockMergerMafIterator.cpp</file>
- <file>BlockMergerMafIterator.h</file>
- <file>BlockSizeMafIterator.h</file>
- <file>ChromosomeMafIterator.cpp</file>
- <file>ChromosomeMafIterator.h</file>
- <file>ConcatenateMafIterator.cpp</file>
- <file>ConcatenateMafIterator.h</file>
- <file>CoordinatesOutputMafIterator.cpp</file>
- <file>CoordinatesOutputMafIterator.h</file>
- <file>DuplicateFilterMafIterator.cpp</file>
- <file>DuplicateFilterMafIterator.h</file>
- <file>EntropyFilterMafIterator.cpp</file>
- <file>EntropyFilterMafIterator.h</file>
- <file>FeatureExtractorMafIterator.cpp</file>
- <file>FeatureExtractorMafIterator.h</file>
- <file>FeatureFilterMafIterator.cpp</file>
- <file>FeatureFilterMafIterator.h</file>
- <file>FullGapFilterMafIterator.cpp</file>
- <file>FullGapFilterMafIterator.h</file>
- <file>IterationListener.cpp</file>
- <file>IterationListener.h</file>
- <file>MafBlock.h</file>
- <file>MafIterator.cpp</file>
- <file>MafIterator.h</file>
- <file>MafParser.cpp</file>
- <file>MafParser.h</file>
- <file>MafSequence.cpp</file>
- <file>MafSequence.h</file>
- <file>MafStatistics.cpp</file>
- <file>MafStatistics.h</file>
- <file>MaskFilterMafIterator.cpp</file>
- <file>MaskFilterMafIterator.h</file>
- <file>OrphanSequenceFilterMafIterator.cpp</file>
- <file>OrphanSequenceFilterMafIterator.h</file>
- <file>OutputAlignmentMafIterator.cpp</file>
- <file>OutputAlignmentMafIterator.h</file>
- <file>OutputMafIterator.cpp</file>
- <file>OutputMafIterator.h</file>
- <file>QualityFilterMafIterator.cpp</file>
- <file>QualityFilterMafIterator.h</file>
- <file>SequenceFilterMafIterator.cpp</file>
- <file>SequenceFilterMafIterator.h</file>
- <file>SequenceStatisticsMafIterator.cpp</file>
- <file>SequenceStatisticsMafIterator.h</file>
- <file>SequenceStreamToMafIterator.cpp</file>
- <file>SequenceStreamToMafIterator.h</file>
- <file>VcfOutputMafIterator.cpp</file>
- <file>VcfOutputMafIterator.h</file>
- <file>WindowSplitMafIterator.cpp</file>
- <file>WindowSplitMafIterator.h</file>
- </compound>
- <compound kind="dir">
- <name>Bpp/Seq</name>
- <path>/home/jdutheil/Devel/Cpp/Projects/bpp-seq-omics/src/Bpp/Seq/</path>
- <filename>dir_a6df4600355513c0d02be2734b44b033.html</filename>
- <dir>Bpp/Seq/Feature</dir>
- <dir>Bpp/Seq/Io</dir>
- </compound>
- <compound kind="page">
- <name>index</name>
- <title></title>
- <filename>index</filename>
- </compound>
-</tagfile>
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 75b241a..521cbb8 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,28 +1,22 @@
# CMake script for Bio++ Sequence-Omics library
-# Author: Sylvain Gaillard and Julien Dutheil
+# Authors:
+# Sylvain Gaillard
+# Julien Dutheil
+# Francois Gindraud (2017)
# Created: 30/07/2012
-# Global parameters
-CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
-PROJECT(bpp-seq-omics CXX)
+cmake_minimum_required (VERSION 2.8.11)
+project (bpp-seq-omics CXX)
+
+# Compile options
+set (CMAKE_CXX_FLAGS "-std=c++11 -Wall -Weffc++ -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 -Weffc++ -Wshadow -Wconversion")
-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 "${CMAKE_CXX_FLAGS} -DNO_VIRTUAL_COV=1")
-ENDIF(NO_VIRTUAL_COV)
-
IF(NOT NO_DEP_CHECK)
SET(NO_DEP_CHECK FALSE CACHE BOOL
"Disable dependencies check for building distribution only."
@@ -41,47 +35,46 @@ ELSE(NO_DEP_CHECK)
# library implements.
# In other words, the library implements all the interface numbers in the
# range from number current - age to current.
-SET(BPPSEQOMICS_VERSION_CURRENT "1")
-SET(BPPSEQOMICS_VERSION_REVISION "0")
-SET(BPPSEQOMICS_VERSION_AGE "0")
+SET(${PROJECT_NAME}_VERSION_CURRENT "2")
+SET(${PROJECT_NAME}_VERSION_REVISION "0")
+SET(${PROJECT_NAME}_VERSION_AGE "0")
# Effective version number computation
-math(EXPR BPPSEQOMICS_VERSION_MAJOR "${BPPSEQOMICS_VERSION_CURRENT} - ${BPPSEQOMICS_VERSION_AGE}")
-SET(BPPSEQOMICS_VERSION_MINOR ${BPPSEQOMICS_VERSION_AGE})
-SET(BPPSEQOMICS_VERSION_PATCH ${BPPSEQOMICS_VERSION_REVISION})
-SET(BPPSEQOMICS_VERSION "${BPPSEQOMICS_VERSION_MAJOR}.${BPPSEQOMICS_VERSION_MINOR}.${BPPSEQOMICS_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}" ${CMAKE_PREFIX_PATH})
-ENDIF(CMAKE_INSTALL_PREFIX)
-
-MACRO(IMPROVED_FIND_LIBRARY OUTPUT_LIBS lib_name include_to_find)
- #start:
- FIND_PATH(${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-core Bpp/Clonable.h)
-IMPROVED_FIND_LIBRARY(LIBS bpp-seq Bpp/Seq/Alphabet/Alphabet.h)
-
-# Subdirectories
-ADD_SUBDIRECTORY(src)
+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-seq 11.0.0 REQUIRED)
+
+# 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 ${PROJECT_NAME}-config-version.cmake)
+
+# Define the libraries
+add_subdirectory (src)
# Doxygen
FIND_PACKAGE(Doxygen)
@@ -102,47 +95,22 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "libbpp-seq-omics")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.2.0")
+SET(CPACK_PACKAGE_VERSION "2.3.1")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
-SET(CPACK_PACKAGE_VERSION_MINOR "2")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_MINOR "3")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Sequence-Omics library")
SET(CPACK_RESOURCE_FILE_LICENSE "${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*"
- "debian/tmp"
- "debian/libbpp.*/"
- "debian/libbpp.*\\\\.so.*"
- "debian/libbpp.*\\\\.a"
- "debian/libbpp.*\\\\.substvars"
- "debian/libbpp.*\\\\.debhelper"
- "debian/debhelper\\\\.log"
- "html"
- "Seq.tag"
- "Testing"
- "build-stamp"
- "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")
@@ -150,22 +118,9 @@ 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)
@@ -177,10 +132,11 @@ SET(CTEST_UPDATE_TYPE git)
SET(UPDATE_COMMAND "git")
SET(UPDATE_OPTIONS "")
-ENABLE_TESTING()
-INCLUDE(CTest)
-IF (BUILD_TESTING)
- ADD_SUBDIRECTORY(test)
-ENDIF(BUILD_TESTING)
+# Tests
+enable_testing ()
+include (CTest)
+if (BUILD_TESTING)
+ add_subdirectory (test)
+endif (BUILD_TESTING)
ENDIF(NOT NO_DEP_CHECK)
diff --git a/CTestConfig.cmake b/CTestConfig.cmake
new file mode 100644
index 0000000..d62749c
--- /dev/null
+++ b/CTestConfig.cmake
@@ -0,0 +1,13 @@
+## This file should be placed in the root directory of your project.
+## Then modify the CMakeLists.txt file in the root directory of your
+## project to incorporate the testing dashboard.
+## # The following are required to uses Dart and the Cdash dashboard
+## ENABLE_TESTING()
+## INCLUDE(CTest)
+set(CTEST_PROJECT_NAME "bpp-seq-omics")
+set(CTEST_NIGHTLY_START_TIME "00:00:00 CEST")
+
+set(CTEST_DROP_METHOD "http")
+set(CTEST_DROP_SITE "biopp.univ-montp2.fr")
+set(CTEST_DROP_LOCATION "/dashboard/submit.php?project=bpp-seq-omics")
+set(CTEST_DROP_SITE_CDASH TRUE)
diff --git a/ChangeLog b/ChangeLog
index e1885cb..92ca8b4 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,44 @@
+10/05/17 -*- Version 2.3.0 -*-
+
+03/04/17 Julien Dutheil
+* VCF export now can export all position, including non-variable ones.
+
+04/07/16 Julien Dutheil
+* Alignment filters now allow for relative proportions of gaps.
+
+24/05/16 Julien Dutheil
+* Added output for SequenceLDhot.
+* Added more statistics in SiteMafStatistics: constant, bi-, tri- and quadriallelic site counts.
+
+26/04/16 Julien Dutheil
+* Portage to c++11
+* Added RemoveEmptySequencesMafFilter class.
+
+10/02/16 Julien Dutheil
+* Fixed bug in AlignmentFilter2: also counts gaps at begining of window!
+
+04/02/16 Julien Dutheil
+* Added support for features in BedGraph format.
+* Added lift over filter as MafIterator.
+
+08/12/15 Julien Dutheil
+* Added Tajima's D computation.
+
+22/11/15 Julien Dutheil
+* Fix bug in FeatureFilter when two features are exactly following each other.
+
+23/04/15 Julien Dutheil
+* Fix another bug in feature extraction on negative strands.
+
+31/03/15 Julien Dutheil
+* OutputAlignments now allows to discard coordinates in output.
+
+13/01/15 Julien Dutheil
+* OutputAlignments can now use coordinates of ref species infile names.
+
+07/01/15 Julien Dutheil
+* Added export filter for MSMC.
+
22/09/14 -*- Version 2.2.0 -*-
22/08/13 Julien Dutheil
diff --git a/Doxyfile b/Doxyfile
index 5c2d0d1..dc1cf4d 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-seq-omics
-# 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 = YES
-# 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++ Sequence Library - Omics components"
-# 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.seq.omics
-# 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 =
@@ -1556,111 +1985,130 @@ 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
-# 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 = BppSeqOmics.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
@@ -1668,222 +2116,314 @@ 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-seq-omics.spec b/bpp-seq-omics.spec
index 3aab529..db513e1 100644
--- a/bpp-seq-omics.spec
+++ b/bpp-seq-omics.spec
@@ -1,5 +1,5 @@
%define _basename bpp-seq-omics
-%define _version 2.2.0
+%define _version 2.3.1
%define _release 1
%define _prefix /usr
@@ -17,11 +17,11 @@ Requires: bpp-core = %{_version}
Requires: bpp-seq = %{_version}
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-seq9 = %{_version}
+BuildRequires: libbpp-seq11 = %{_version}
BuildRequires: libbpp-seq-devel = %{_version}
AutoReq: yes
@@ -31,21 +31,21 @@ AutoProv: yes
This library contains the genomics components of the Bio++ sequence library.
It is part of the Bio++ project.
-%package -n libbpp-seq-omics1
+%package -n libbpp-seq-omics2
Summary: Bio++ Sequence library: genomics components
Group: Development/Libraries/C and C++
-%description -n libbpp-seq-omics1
+%description -n libbpp-seq-omics2
This library contains the genomics components of the Bio++ sequence library.
It is part of the Bio++ project.
%package -n libbpp-seq-omics-devel
Summary: Bio++ Sequence library: genomics components
Group: Development/Libraries/C and C++
-Requires: libbpp-seq-omics1 = %{_version}
-Requires: libbpp-seq9 = %{_version}
+Requires: libbpp-seq-omics2 = %{_version}
+Requires: libbpp-seq11 = %{_version}
Requires: libbpp-seq-devel = %{_version}
-Requires: libbpp-core2 = %{_version}
+Requires: libbpp-core3 = %{_version}
Requires: libbpp-core-devel = %{_version}
%description -n libbpp-seq-omics-devel
@@ -58,9 +58,6 @@ 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 $CMAKE_FLAGS .
make
@@ -70,103 +67,11 @@ make DESTDIR=$RPM_BUILD_ROOT install
%clean
rm -rf $RPM_BUILD_ROOT
-%post -n libbpp-seq-omics1 -p /sbin/ldconfig
-
-%post -n libbpp-seq-omics-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-seq-omics-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-seq-omics1 -p /sbin/ldconfig
-
-%postun -n libbpp-seq-omics-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-seq-omics1
+%post -n libbpp-seq-omics2 -p /sbin/ldconfig
+
+%postun -n libbpp-seq-omics2 -p /sbin/ldconfig
+
+%files -n libbpp-seq-omics2
%defattr(-,root,root)
%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
%{_prefix}/%{_lib}/lib*.so.*
@@ -174,11 +79,23 @@ exit 0
%files -n libbpp-seq-omics-devel
%defattr(-,root,root)
%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
+%dir %{_prefix}/%{_lib}/cmake/
+%dir %{_prefix}/%{_lib}/cmake/bpp-seq-omics
%{_prefix}/%{_lib}/lib*.so
%{_prefix}/%{_lib}/lib*.a
+%{_prefix}/%{_lib}/cmake/bpp-seq-omics/bpp-seq-omics*.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
+- Several bugs fixed and performance improvements
+- New Maf filters: LiftOver, RemoveEmptySequence
+- Support for BED features input
+- New output options: MSMC, PLINK
+- More options for Vcf and Alignment output
+- Upgrade to C++11
* Mon Sep 22 2014 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.2.0-1
- New statistics, including sequence diversity estimators
- Several bugs and memory leaks fixed.
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index b38ff21..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,19 +0,0 @@
-libbpp-seq-omics (2.2.0-1) unstable; urgency=low
-
- * New statistics, including sequence diversity estimators
- * Several bugs and memory leaks fixed.
-
- -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Mon, 22 Sep 2014 14:00:00 +0100
-
-libbpp-seq-omics (2.1.0-1) unstable; urgency=low
-
- * Maf to VCF tool added as a MafIterator.
-
- -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Wed, 06 Mar 2013 14:34:00 +0100
-
-libbpp-seq-omics (2.0.3-1) unstable; urgency=low
-
- * Initial release, forking from bpp-seq.
-
- -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Tue, 06 Nov 2012 14:05:00 +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 62aa8e5..0000000
--- a/debian/control
+++ /dev/null
@@ -1,25 +0,0 @@
-Source: libbpp-seq-omics
-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),
- libbpp-seq-dev (>= 2.2.0)
-Standards-Version: 3.9.4
-
-Package: libbpp-seq-omics-dev
-Section: libdevel
-Architecture: any
-Depends: libbpp-seq-omics1 (= ${binary:Version}), ${misc:Depends},
- libbpp-seq-dev (>= 2.2.0)
-Description: Bio++ Sequence library: genomics components.
- Contains the Bio++ sequence classes dedicated to genomics.
-
-Package: libbpp-seq-omics1
-Section: libs
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends},
- libbpp-seq9 (>= 2.2.0)
-Description: Bio++ Sequence library: genomics components.
- Contains the Bio++ sequence classes dedicated to genomics.
-
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index 9eb55d6..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,66 +0,0 @@
-This package was debianized by Julien Dutheil <julien.dutheil at univ-montp2.fr> on
-Wed, 22 Sep 2014 14:00:00 +0100.
-
-It was downloaded from <http://biopp.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/libbpp-seq-omics-dev.install b/debian/libbpp-seq-omics-dev.install
deleted file mode 100644
index 7d74f2b..0000000
--- a/debian/libbpp-seq-omics-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-seq-omics1.install b/debian/libbpp-seq-omics1.install
deleted file mode 100644
index c45ebcf..0000000
--- a/debian/libbpp-seq-omics1.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 34313ef..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,122 +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;
- [ ! -f test/Makefile ] || rm test/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 $1
diff --git a/package.cmake.in b/package.cmake.in
new file mode 100644
index 0000000..05c1027
--- /dev/null
+++ b/package.cmake.in
@@ -0,0 +1,26 @@
+# CMake package file for Bio++ Sequence Omics
+# Authors:
+# Francois Gindraud (2017)
+# Created: 16/03/2017
+ at PACKAGE_INIT@
+
+if (NOT @PROJECT_NAME at _FOUND)
+ # Deps
+ find_package (bpp-seq @bpp-seq_VERSION@ REQUIRED)
+ # Add targets
+ include ("${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/Seq/Feature/Bed/BedGraphFeatureReader.cpp b/src/Bpp/Seq/Feature/Bed/BedGraphFeatureReader.cpp
new file mode 100644
index 0000000..c641d92
--- /dev/null
+++ b/src/Bpp/Seq/Feature/Bed/BedGraphFeatureReader.cpp
@@ -0,0 +1,105 @@
+//
+// File: BedGraphFeatureReader.cpp
+// Created by: Julien Dutheil
+// Created on: Tue Feb 2 2016
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "BedGraphFeatureReader.h"
+
+//From bpp-core:
+#include <Bpp/Text/StringTokenizer.h>
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Text/KeyvalTools.h>
+#include <Bpp/Numeric/VectorTools.h>
+
+//From the STL:
+#include <string>
+#include <iostream>
+
+using namespace bpp;
+using namespace std;
+
+const std::string BedGraphFeatureReader::BED_VALUE = "BedValue";
+
+
+void BedGraphFeatureReader::getNextLine_() {
+ nextLine_ = "";
+ while (TextTools::isEmpty(nextLine_) || nextLine_.size() < 2 || nextLine_[0] == '#') {
+ if (input_.eof()) {
+ nextLine_ = "";
+ return;
+ }
+ getline(input_, nextLine_);
+ }
+}
+
+const BasicSequenceFeature BedGraphFeatureReader::nextFeature() throw (Exception)
+{
+ if (!hasMoreFeature())
+ throw Exception("BedGraphFeatureReader::nextFeature(). No more feature in file.");
+
+ //Parse current line:
+ StringTokenizer st(nextLine_, "\t");
+ if (st.numberOfRemainingTokens() != 4)
+ throw Exception("BedGraphFeatureReader::nextFeature(). Wrong BedGraph file format: should have 4 tab delimited columns.");
+
+ //if ok, we can parse each column:
+ string seqId = st.nextToken();
+ unsigned int start = TextTools::to<unsigned int>(st.nextToken());
+ unsigned int end = TextTools::to<unsigned int>(st.nextToken());
+ string value = st.nextToken();
+ string id = "bed" + TextTools::toString(++id_);
+ BasicSequenceFeature feature(id, seqId, "bed_graph", "", start, end, '.', -1);
+
+ //Set value attributes:
+ if (value != ".") feature.setAttribute(BED_VALUE, value);
+
+ //Read the next line:
+ getNextLine_();
+
+ return feature;
+}
+
+std::string BedGraphFeatureReader::toString(const bpp::SequenceFeature& f) {
+ std::vector< std::string > v;
+ v.push_back(f.getSequenceId());
+ v.push_back(bpp::TextTools::toString(f.getStart()));
+ v.push_back(bpp::TextTools::toString(f.getEnd()));
+ string value = f.getAttribute(BED_VALUE);
+ v.push_back(bpp::TextTools::toString(value == "" ? "." : value));
+ return bpp::VectorTools::paste(v, "\t");
+}
+
diff --git a/src/Bpp/Seq/Feature/Gff/GffFeatureReader.h b/src/Bpp/Seq/Feature/Bed/BedGraphFeatureReader.h
similarity index 71%
copy from src/Bpp/Seq/Feature/Gff/GffFeatureReader.h
copy to src/Bpp/Seq/Feature/Bed/BedGraphFeatureReader.h
index 3400e68..ea3a545 100644
--- a/src/Bpp/Seq/Feature/Gff/GffFeatureReader.h
+++ b/src/Bpp/Seq/Feature/Bed/BedGraphFeatureReader.h
@@ -1,7 +1,7 @@
//
-// File: GffFeatureReader.h
+// File: BedGraphFeatureReader.h
// Created by: Julien Dutheil
-// Created on: Mon Nov 21 2011
+// Created on: Tue Feb 2 2016
//
/*
@@ -37,8 +37,8 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/
-#ifndef _GFFFEATUREREADER_H_
-#define _GFFFEATUREREADER_H_
+#ifndef _BEDGRAPHFEATUREREADER_H_
+#define _BEDGRAPHFEATUREREADER_H_
#include "../SequenceFeature.h"
#include "../FeatureReader.h"
@@ -53,48 +53,43 @@ knowledge of the CeCILL license and that you accept its terms.
namespace bpp {
/**
- * @brief A simple reader implementing the Gene Finding Feature format.
+ * @brief A simple reader for features in the BedGraph format.
*
- * The reference norm in use is the one of GFF3 http://www.sequenceontology.org/gff3.shtml .
- * This class is a "beta" class, and may undeavour interface changes in the future.
+ * Format desciption at UCSC: https://genome.ucsc.edu/goldenpath/help/bedgraph.html
*
- * Note that in GFF, coordinates are [a, b] 1-based. They will therefore be converted to [a, b[ 0-based,
- * as specified for the SequenceFeature object.
+ * Note: The value associated to each feature is stored as a string attribute, using
+ * tag BegGraphFeatureReader::BED_VALUE. No check is performed regarding its value.
+ * An automatic id is generated, and the source tag is set to "beg_graph".
*
- * @author Julien Dutheil, Sylvain Gaillard
+ * @author Julien Dutheil
*/
-class GffFeatureReader:
+class BedGraphFeatureReader:
public virtual FeatureReader
{
public:
- static const std::string GFF_STRAND;
- static const std::string GFF_PHASE;
- static const std::string GFF_NAME;
- static const std::string GFF_ALIAS;
- static const std::string GFF_PARENT;
- static const std::string GFF_TARGET;
- static const std::string GFF_GAP;
- static const std::string GFF_DERIVES_FROM;
- static const std::string GFF_NOTE;
- static const std::string GFF_DBXREF;
- static const std::string GFF_ONTOLOGY_TERM;
- static const std::string GFF_IS_CIRCULAR;
+ static const std::string BED_VALUE;
private:
- std::istream* input_;
+ std::istream& input_;
std::string nextLine_;
+ unsigned int id_;
public:
- GffFeatureReader(std::istream& input):
- input_(&input), nextLine_()
+ BedGraphFeatureReader(std::istream& input):
+ input_(input), nextLine_(), id_(0)
{
+ bool start = false;
+ do {
+ getNextLine_();
+ if (nextLine_.size() >= 5 && nextLine_.substr(0, 5) == "track") {
+ start = true;
+ }
+ } while(!start && !input_.eof());
+ if (input_.eof())
+ throw Exception("BedGraphFeatureReader::constructor: Invalid BedGraph file, missing proper header.");
getNextLine_();
}
- private:
- GffFeatureReader(const GffFeatureReader& reader): input_(0), nextLine_() {}
- GffFeatureReader& operator=(const GffFeatureReader& reader) { return *this; }
-
public:
bool hasMoreFeature() const { return nextLine_ != ""; }
const BasicSequenceFeature nextFeature() throw (Exception);
@@ -150,5 +145,5 @@ class GffFeatureReader:
} //end of namespace bpp
-#endif //_GFFFEATUREREADER_H_
+#endif //_BEDGRAPHFEATUREREADER_H_
diff --git a/src/Bpp/Seq/Feature/Gff/GffFeatureReader.cpp b/src/Bpp/Seq/Feature/Gff/GffFeatureReader.cpp
index 9031e68..7e049de 100644
--- a/src/Bpp/Seq/Feature/Gff/GffFeatureReader.cpp
+++ b/src/Bpp/Seq/Feature/Gff/GffFeatureReader.cpp
@@ -68,11 +68,11 @@ const std::string GffFeatureReader::GFF_IS_CIRCULAR = "Is_circular";
void GffFeatureReader::getNextLine_() {
nextLine_ = "";
while (TextTools::isEmpty(nextLine_) || nextLine_.size() < 2 || nextLine_[0] == '#') {
- if (input_->eof()) {
+ if (input_.eof()) {
nextLine_ = "";
return;
}
- getline(*input_, nextLine_);
+ getline(input_, nextLine_);
}
}
diff --git a/src/Bpp/Seq/Feature/Gff/GffFeatureReader.h b/src/Bpp/Seq/Feature/Gff/GffFeatureReader.h
index 3400e68..d6e2917 100644
--- a/src/Bpp/Seq/Feature/Gff/GffFeatureReader.h
+++ b/src/Bpp/Seq/Feature/Gff/GffFeatureReader.h
@@ -81,20 +81,16 @@ class GffFeatureReader:
static const std::string GFF_IS_CIRCULAR;
private:
- std::istream* input_;
+ std::istream& input_;
std::string nextLine_;
public:
GffFeatureReader(std::istream& input):
- input_(&input), nextLine_()
+ input_(input), nextLine_()
{
getNextLine_();
}
- private:
- GffFeatureReader(const GffFeatureReader& reader): input_(0), nextLine_() {}
- GffFeatureReader& operator=(const GffFeatureReader& reader) { return *this; }
-
public:
bool hasMoreFeature() const { return nextLine_ != ""; }
const BasicSequenceFeature nextFeature() throw (Exception);
diff --git a/src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.cpp b/src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.cpp
index 1bb0c94..7c62ce1 100644
--- a/src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.cpp
+++ b/src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.cpp
@@ -62,11 +62,11 @@ void GtfFeatureReader::getNextLine_() {
todo: remove characters between # and end-of-line taking care of double quotes
*/
while (TextTools::isEmpty(nextLine_) || nextLine_.size() < 2 || nextLine_[0] == '#') {
- if (input_->eof()) {
+ if (input_.eof()) {
nextLine_ = "";
return;
}
- getline(*input_, nextLine_);
+ getline(input_, nextLine_);
}
}
diff --git a/src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.h b/src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.h
index 9600dc4..7e4a797 100644
--- a/src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.h
+++ b/src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.h
@@ -72,20 +72,16 @@ class GtfFeatureReader:
static const std::string GTF_TRANSCRIPT_ID;
private:
- std::istream* input_;
+ std::istream& input_;
std::string nextLine_;
public:
GtfFeatureReader(std::istream& input):
- input_(&input), nextLine_()
+ input_(input), nextLine_()
{
getNextLine_();
}
- private:
- GtfFeatureReader(const GtfFeatureReader& reader): input_(0), nextLine_() {}
- GtfFeatureReader& operator=(const GtfFeatureReader& reader) { return *this; }
-
public:
bool hasMoreFeature() const { return nextLine_ != ""; }
const BasicSequenceFeature nextFeature() throw (Exception);
diff --git a/src/Bpp/Seq/Feature/SequenceFeature.h b/src/Bpp/Seq/Feature/SequenceFeature.h
index b652a0f..754419b 100644
--- a/src/Bpp/Seq/Feature/SequenceFeature.h
+++ b/src/Bpp/Seq/Feature/SequenceFeature.h
@@ -90,6 +90,16 @@ class SeqRange:
strand_ = '.';
}
+ /**
+ * @param range A range object
+ * @param strand The strand information. Can take one of the four values: '+' for positive strand, '-' for negative, '.' if not stranded or '?' if strandedness is relevant but unknown.
+ */
+ SeqRange(const Range<size_t> range, char strand = '.'):
+ Range<size_t>(range), strand_(strand) {
+ if (strand != '+' && strand != '-' && strand != '?' && strand != '.')
+ strand_ = '.';
+ }
+
SeqRange* clone() const { return new SeqRange(*this); }
public:
@@ -180,6 +190,13 @@ class SequenceFeature:
virtual const size_t getEnd() const = 0;
/**
+ * @return The size of the feature.
+ */
+ virtual const size_t size() const {
+ return getEnd() - getStart();
+ };
+
+ /**
* @return True if the feature is stranded.
*/
virtual bool isStranded() const = 0;
@@ -200,11 +217,36 @@ class SequenceFeature:
virtual SeqRange getRange() const = 0;
/**
+ * @return Check if the feature is empty (start == end)
+ */
+ virtual bool isEmpty() const { return size() == 0; }
+
+ /**
+ * @return Check if the feature is a point annotation (start + 1 == end)
+ */
+ virtual bool isPoint() const { return size() == 1; }
+
+ /**
* @return True if the features overlap.
*/
virtual bool overlap(const SequenceFeature& feat) const = 0;
/**
+ * @return True if the feature overlap with the given range (non-null intersection).
+ */
+ virtual bool overlap(const SeqRange& range) const = 0;
+
+ /**
+ * @return True if the feature fully contains the given range.
+ */
+ virtual bool includes(const SeqRange& range) const = 0;
+
+ /**
+ * @return True if the feature is fully contained in the given range.
+ */
+ virtual bool isIncludedIn(const SeqRange& range) const = 0;
+
+ /**
* @return The score associated to the feature (eg, an E-value or a P-value).
*/
virtual const double& getScore() const = 0;
@@ -264,6 +306,8 @@ class BasicSequenceFeature:
//SequenceFeatureSet subFeatures_;
public:
+ BasicSequenceFeature(): id_(""), sequenceId_(""), source_(""), type_(""), range_(0, 0, '.'), score_(-1), attributes_() {}
+
BasicSequenceFeature(
const std::string& id,
const std::string& seqId,
@@ -342,7 +386,19 @@ class BasicSequenceFeature:
return false;
}
- //const SequenceFeatureSet& getSubFeatures() const { return subFeatures; }
+ bool overlap(const SeqRange& range) const {
+ return range_.overlap(range);
+ }
+
+ virtual bool includes(const SeqRange& range) const {
+ return range_.contains(range);
+ }
+
+ virtual bool isIncludedIn(const SeqRange& range) const {
+ return range.contains(range_);
+ }
+
+ //const SequenceFeatureSet& getSubFeatures() const { return subFeatures; }
//SequenceFeatureSet& getSubFeatures() { return subFeatures; }
};
@@ -425,6 +481,11 @@ class SequenceFeatureSet
size_t getNumberOfFeatures() const { return features_.size(); }
/**
+ * @return True if the set contains no feature.
+ */
+ bool isEmpty() const { return features_.size() == 0; }
+
+ /**
* @brief Add a feature to the container. The feature will be copied and the copy owned by the container.
*
* @param feature The feature to add to the container.
@@ -460,6 +521,19 @@ class SequenceFeatureSet
}
/**
+ * @brief Get all coordinates of features.
+ * All ranges are added to a RangeCollection container, as SeqRange objects.
+ * @param coords [out] a container where to add the coordinates of each feature.
+ */
+ void fillRangeCollection(RangeCollection<size_t>& coords) const {
+ for (std::vector<SequenceFeature*>::const_iterator it = features_.begin();
+ it != features_.end();
+ ++it) {
+ coords.addRange((**it).getRange());
+ }
+ }
+
+ /**
* @brief Get all coordinates of features for a given source.
* All ranges are added to a RangeCollection container, as SeqRange objects.
* @param seqId The name of the sequence id to consider.
@@ -476,10 +550,26 @@ class SequenceFeatureSet
}
/**
- * @param types The feature type.
+ * @param type The feature type.
* @return A new set with all features of a given type.
*/
- SequenceFeatureSet* getSubsetForType(const std::vector<std::string>& types) const {
+ SequenceFeatureSet* getSubsetForType(const std::string& type) const {
+ SequenceFeatureSet* subset = new SequenceFeatureSet();
+ for (std::vector<SequenceFeature*>::const_iterator it = features_.begin();
+ it != features_.end();
+ ++it) {
+ if ((**it).getType() == type) {
+ subset->addFeature(**it);
+ }
+ }
+ return subset;
+ }
+
+ /**
+ * @param types The feature types.
+ * @return A new set with all features of given types.
+ */
+ SequenceFeatureSet* getSubsetForTypes(const std::vector<std::string>& types) const {
SequenceFeatureSet* subset = new SequenceFeatureSet();
for (std::vector<SequenceFeature*>::const_iterator it = features_.begin();
it != features_.end();
@@ -491,6 +581,60 @@ class SequenceFeatureSet
return subset;
}
+ /**
+ * @param id The sequence id to look for.
+ * @return A new set with all features for a given sequence id.
+ */
+ SequenceFeatureSet* getSubsetForSequence(const std::string& id) const {
+ SequenceFeatureSet* subset = new SequenceFeatureSet();
+ for (std::vector<SequenceFeature*>::const_iterator it = features_.begin();
+ it != features_.end();
+ ++it) {
+ if ((**it).getSequenceId() == id) {
+ subset->addFeature(**it);
+ }
+ }
+ return subset;
+ }
+
+ /**
+ * @param ids The sequence ids to look for.
+ * @return A new set with all features of given sequence ids.
+ */
+ SequenceFeatureSet* getSubsetForSequences(const std::vector<std::string>& ids) const {
+ SequenceFeatureSet* subset = new SequenceFeatureSet();
+ for (std::vector<SequenceFeature*>::const_iterator it = features_.begin();
+ it != features_.end();
+ ++it) {
+ if (std::find(ids.begin(), ids.end(), (**it).getSequenceId()) != ids.end()) {
+ subset->addFeature(**it);
+ }
+ }
+ return subset;
+ }
+
+ /**
+ * @param range The range of features to look for.
+ * @param complete If true, only return features fully included in the given range.
+ * Otherwise returns features overlapping with the range.
+ * @return A new set with all features included in the given range.
+ */
+ SequenceFeatureSet* getSubsetForRange(const SeqRange& range, bool complete) const {
+ SequenceFeatureSet* subset = new SequenceFeatureSet();
+ for (std::vector<SequenceFeature*>::const_iterator it = features_.begin();
+ it != features_.end();
+ ++it) {
+ if (complete) {
+ if ((**it).isIncludedIn(range))
+ subset->addFeature(**it);
+ } else {
+ if ((**it).overlap(range))
+ subset->addFeature(**it);
+ }
+ }
+ return subset;
+ }
+
};
} //end of namespace bpp
diff --git a/src/Bpp/Seq/Feature/SequenceFeatureTools.cpp b/src/Bpp/Seq/Feature/SequenceFeatureTools.cpp
index f90a2c9..427eb99 100644
--- a/src/Bpp/Seq/Feature/SequenceFeatureTools.cpp
+++ b/src/Bpp/Seq/Feature/SequenceFeatureTools.cpp
@@ -65,6 +65,17 @@ Sequence* SequenceFeatureTools::extract(const Sequence& seq, const SeqRange& ran
/******************************************************************************/
+void SequenceFeatureTools::extract(const Sequence& seq, const SeqRange& range, Sequence& output) {
+ if (range.end() > seq.size())
+ throw IndexOutOfBoundsException ("SequenceTools::extract: Invalid upper bound", range.end(), 0, seq.size());
+ SequenceTools::subseq(seq, range.begin(), range.end() - 1, output);
+ if (range.isNegativeStrand()) {
+ SequenceTools::invertComplement(output);
+ }
+}
+
+/******************************************************************************/
+
unsigned int SequenceFeatureTools::getOrfs(const Sequence& seq, SequenceFeatureSet& featSet, const GeneticCode& gCode)
{
if (! AlphabetTools::isNucleicAlphabet(seq.getAlphabet())) {
diff --git a/src/Bpp/Seq/Feature/SequenceFeatureTools.h b/src/Bpp/Seq/Feature/SequenceFeatureTools.h
index 7bbb152..228b30e 100644
--- a/src/Bpp/Seq/Feature/SequenceFeatureTools.h
+++ b/src/Bpp/Seq/Feature/SequenceFeatureTools.h
@@ -64,6 +64,20 @@ class SequenceFeatureTools
* @author Sylvain Gaillard
*/
static Sequence* extract(const Sequence& seq, const SeqRange& range);
+
+ /**
+ * @brief Extract a sub-sequence given a SeqRange.
+ *
+ * The sub-sequence is revese-complemented if SeqRange is in negative
+ * strand.
+ *
+ * @param seq The Sequence to trunc.
+ * @param range The SeqRange to extract.
+ * @param output The Sequence object to be filled with the given subsequence
+ * oriented according to the SeqRange.
+ * @author Sylvain Gaillard
+ */
+ static void extract(const Sequence& seq, const SeqRange& range, Sequence& output);
/**
* @brief Get ORF features for a Sequence.
diff --git a/src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp b/src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
index a5c4d21..7daed34 100644
--- a/src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
@@ -75,16 +75,18 @@ MafBlock* AlignmentFilterMafIterator::analyseCurrentBlock_() throw (Exception)
}
} else {
vector<string> speciesSet = VectorTools::vectorIntersection(species_, block->getSpeciesList());
- nr = speciesSet.size();
- aln.resize(nr);
- for (size_t i = 0; i < nr; ++i) {
- aln[i] = block->getSequenceForSpecies(species_[i]).getContent();
+ for (size_t i = 0; i < species_.size(); ++i) {
+ if (block->hasSequenceForSpecies(species_[i])) {
+ aln.push_back(block->getSequenceForSpecies(species_[i]).getContent());
+ } else {
+ if (!relative_) {
+ throw Exception("AlignmentFilterMafIterator::analyseCurrentBlock_. Block does not include selected species '" + species_[i] + "' and threshold are absolutes, leading to an undefined behavior. Consider selecting blocks first, or use relative thresholds.");
+ }
+ }
}
+ nr = aln.size();
}
-
-
-
//First we create a mask:
vector<size_t> pos;
vector<int> col(nr);
@@ -121,12 +123,19 @@ MafBlock* AlignmentFilterMafIterator::analyseCurrentBlock_() throw (Exception)
}
sumEnt += VectorTools::shannonDiscrete<int, double>(col) / log(5.);
}
- if (sumGap > maxGap_ && (sumEnt / static_cast<double>(windowSize_)) > maxEnt_) {
+ bool test = (sumEnt / static_cast<double>(windowSize_)) > maxEnt_;
+ if (relative_) {
+ double propGap = static_cast<double>(sumGap) / static_cast<double>(nr * nc);
+ test = test && (propGap > maxPropGap_);
+ } else {
+ test = test && (sumGap > maxGap_);
+ }
+ if (test) {
if (pos.size() == 0) {
pos.push_back(i - windowSize_);
pos.push_back(i);
} else {
- if (i - windowSize_ < pos[pos.size() - 1]) {
+ if (i - windowSize_ <= pos[pos.size() - 1]) {
pos[pos.size() - 1] = i; //Windows are overlapping and we extend previous region
} else { //This is a new region
pos.push_back(i - windowSize_);
@@ -159,7 +168,14 @@ MafBlock* AlignmentFilterMafIterator::analyseCurrentBlock_() throw (Exception)
}
sumEnt += VectorTools::shannonDiscrete<int, double>(col) / log(5.);
}
- if (sumGap > maxGap_ && (sumEnt / static_cast<double>(windowSize_)) > maxEnt_) {
+ bool test = (sumEnt / static_cast<double>(windowSize_)) > maxEnt_;
+ if (relative_) {
+ double propGap = static_cast<double>(sumGap) / static_cast<double>(nr);
+ test = test && (propGap > maxPropGap_);
+ } else {
+ test = test && (sumGap > maxGap_);
+ }
+ if (test) {
if (pos.size() == 0) {
pos.push_back(i - windowSize_);
pos.push_back(i);
@@ -283,12 +299,18 @@ MafBlock* AlignmentFilter2MafIterator::analyseCurrentBlock_() throw (Exception)
}
} else {
vector<string> speciesSet = VectorTools::vectorIntersection(species_, block->getSpeciesList());
- nr = speciesSet.size();
- aln.resize(nr);
- for (size_t i = 0; i < nr; ++i) {
- aln[i] = block->getSequenceForSpecies(species_[i]).getContent();
+ for (size_t i = 0; i < species_.size(); ++i) {
+ if (block->hasSequenceForSpecies(species_[i])) {
+ aln.push_back(block->getSequenceForSpecies(species_[i]).getContent());
+ } else {
+ if (!relative_) {
+ throw Exception("AlignmentFilter2MafIterator::analyseCurrentBlock_. Block does not include selected species '" + species_[i] + "' and threshold are absolutes, leading to an undefined behavior. Consider selecting blocks first, or use relative thresholds.");
+ }
+ }
}
+ nr = aln.size();
}
+
//First we create a mask:
vector<size_t> pos;
vector<bool> col(nr);
@@ -312,13 +334,19 @@ MafBlock* AlignmentFilter2MafIterator::analyseCurrentBlock_() throw (Exception)
ApplicationTools::displayGauge(i - windowSize_, nc - windowSize_ - 1, '>');
//Evaluate current window:
unsigned int count = 0;
- bool posIsGap = true;
+ bool posIsGap = false;
for (size_t u = 0; u < window_.size(); ++u) {
unsigned int partialCount = 0;
if (!posIsGap || (u > 0 && window_[u] != window_[u - 1])) {
for (size_t v = 0; v < window_[u].size(); ++v)
if (window_[u][v]) partialCount++;
- if (partialCount > maxGap_) {
+ bool test;
+ if (relative_) {
+ test = (static_cast<double>(partialCount) / static_cast<double>(nr) > maxPropGap_);
+ } else {
+ test = (partialCount > maxGap_);
+ }
+ if (test) {
count++;
posIsGap = true;
} else {
@@ -331,7 +359,7 @@ MafBlock* AlignmentFilter2MafIterator::analyseCurrentBlock_() throw (Exception)
pos.push_back(i - windowSize_);
pos.push_back(i);
} else {
- if (i - windowSize_ < pos[pos.size() - 1]) {
+ if (i - windowSize_ <= pos[pos.size() - 1]) {
pos[pos.size() - 1] = i; //Windows are overlapping and we extend previous region
} else { //This is a new region
pos.push_back(i - windowSize_);
@@ -353,13 +381,19 @@ MafBlock* AlignmentFilter2MafIterator::analyseCurrentBlock_() throw (Exception)
//Evaluate last window:
unsigned int count = 0;
- bool posIsGap = true;
+ bool posIsGap = false;
for (size_t u = 0; u < window_.size(); ++u) {
unsigned int partialCount = 0;
if (!posIsGap || (u > 0 && window_[u] != window_[u - 1])) {
for (size_t v = 0; v < window_[u].size(); ++v)
if (window_[u][v]) partialCount++;
- if (partialCount > maxGap_) {
+ bool test;
+ if (relative_) {
+ test = (static_cast<double>(partialCount) / static_cast<double>(nr) > maxPropGap_);
+ } else {
+ test = (partialCount > maxGap_);
+ }
+ if (test) {
count++;
posIsGap = true;
} else {
diff --git a/src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.h b/src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.h
index 2f83f70..ba56ae5 100644
--- a/src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.h
@@ -69,14 +69,30 @@ class AlignmentFilterMafIterator:
unsigned int windowSize_;
unsigned int step_;
unsigned int maxGap_;
+ double maxPropGap_;
double maxEnt_;
std::deque<MafBlock*> blockBuffer_;
std::deque<MafBlock*> trashBuffer_;
std::deque< std::vector<int> > window_;
bool keepTrashedBlocks_;
bool missingAsGap_;
+ bool relative_;
public:
+
+ /**
+ * @brief Create a new AlignmentFilterMafIterator with absolute thresholds.
+ *
+ * @param iterator Input iterator
+ * @param species Selection of species on which filtering criteria are applied.
+ * Results of filtering will be applied to all species.
+ * @param windowSize Size of the sliding window (nt).
+ * @param step Step by which windows are moved (nt).
+ * @param maxGap Maximum number of gaps allowed in the window.
+ * @param maxEnt Maximum entropy allowed in the window.
+ * @param keepTrashedBlocks Removed windows are kept as separate blocks.
+ * @param missingAsGap Add missing species as gap sequences where needed.
+ */
AlignmentFilterMafIterator(MafIterator* iterator,
const std::vector<std::string>& species,
unsigned int windowSize,
@@ -90,14 +106,53 @@ class AlignmentFilterMafIterator:
windowSize_(windowSize),
step_(step),
maxGap_(maxGap),
+ maxPropGap_(),
maxEnt_(maxEnt),
blockBuffer_(),
trashBuffer_(),
window_(species.size()),
keepTrashedBlocks_(keepTrashedBlocks),
- missingAsGap_(missingAsGap)
+ missingAsGap_(missingAsGap),
+ relative_(false)
{}
+ /**
+ * @brief Create a new AlignmentFilterMafIterator with relative thresholds.
+ *
+ * @param iterator Input iterator
+ * @param species Selection of species on which filtering criteria are applied.
+ * Results of filtering will be applied to all species.
+ * @param windowSize Size of the sliding window (nt).
+ * @param step Step by which windows are moved (nt).
+ * @param maxPropGap Maximum proportion of gaps allowed in the window.
+ * @param maxEnt Maximum entropy allowed in the window.
+ * @param keepTrashedBlocks Removed windows are kept as separate blocks.
+ * @param missingAsGap Add missing species as gap sequences where needed.
+ */
+ AlignmentFilterMafIterator(MafIterator* iterator,
+ const std::vector<std::string>& species,
+ unsigned int windowSize,
+ unsigned int step,
+ double maxPropGap,
+ double maxEnt,
+ bool keepTrashedBlocks,
+ bool missingAsGap) :
+ AbstractFilterMafIterator(iterator),
+ species_(species),
+ windowSize_(windowSize),
+ step_(step),
+ maxGap_(),
+ maxPropGap_(maxPropGap),
+ maxEnt_(maxEnt),
+ blockBuffer_(),
+ trashBuffer_(),
+ window_(species.size()),
+ keepTrashedBlocks_(keepTrashedBlocks),
+ missingAsGap_(missingAsGap),
+ relative_(true)
+ {}
+
+
public:
MafBlock* nextRemovedBlock() throw (Exception) {
if (trashBuffer_.size() == 0) return 0;
@@ -127,26 +182,72 @@ class AlignmentFilter2MafIterator:
unsigned int windowSize_;
unsigned int step_;
unsigned int maxGap_;
+ double maxPropGap_;
unsigned int maxPos_;
std::deque<MafBlock*> blockBuffer_;
std::deque<MafBlock*> trashBuffer_;
std::deque< std::vector<bool> > window_;
bool keepTrashedBlocks_;
bool missingAsGap_;
+ bool relative_;
public:
+ /**
+ * @brief Create a new AlignmentFilter2MafIterator with absolute thresholds.
+ *
+ * @param iterator Input iterator
+ * @param species Selection of species on which filtering criteria are applied.
+ * Results of filtering will be applied to all species.
+ * @param windowSize Size of the sliding window (nt).
+ * @param step Step by which windows are moved (nt).
+ * @param maxGap Maximum number of gaps allowed in the window.
+ * @param maxPos Maximum number of gaps "events" allowed.
+ * @param keepTrashedBlocks Removed windows are kept as separate blocks.
+ * @param missingAsGap Add missing species as gap sequences where needed.
+ */
AlignmentFilter2MafIterator(MafIterator* iterator, const std::vector<std::string>& species, unsigned int windowSize, unsigned int step, unsigned int maxGap, unsigned int maxPos, bool keepTrashedBlocks, bool missingAsGap) :
AbstractFilterMafIterator(iterator),
species_(species),
windowSize_(windowSize),
step_(step),
maxGap_(maxGap),
+ maxPropGap_(),
+ maxPos_(maxPos),
+ blockBuffer_(),
+ trashBuffer_(),
+ window_(species.size()),
+ keepTrashedBlocks_(keepTrashedBlocks),
+ missingAsGap_(missingAsGap),
+ relative_(false)
+ {}
+
+ /**
+ * @brief Create a new AlignmentFilterMafIterator with relative thresholds.
+ *
+ * @param iterator Input iterator
+ * @param species Selection of species on which filtering criteria are applied.
+ * Results of filtering will be applied to all species.
+ * @param windowSize Size of the sliding window (nt).
+ * @param step Step by which windows are moved (nt).
+ * @param maxPropGap Maximum proportion of gaps allowed in the window.
+ * @param maxPos Maximum number of gaps "events" allowed.
+ * @param keepTrashedBlocks Removed windows are kept as separate blocks.
+ * @param missingAsGap Add missing species as gap sequences where needed.
+ */
+ AlignmentFilter2MafIterator(MafIterator* iterator, const std::vector<std::string>& species, unsigned int windowSize, unsigned int step, double maxPropGap, unsigned int maxPos, bool keepTrashedBlocks, bool missingAsGap) :
+ AbstractFilterMafIterator(iterator),
+ species_(species),
+ windowSize_(windowSize),
+ step_(step),
+ maxGap_(),
+ maxPropGap_(maxPropGap),
maxPos_(maxPos),
blockBuffer_(),
trashBuffer_(),
window_(species.size()),
keepTrashedBlocks_(keepTrashedBlocks),
- missingAsGap_(missingAsGap)
+ missingAsGap_(missingAsGap),
+ relative_(true)
{}
public:
diff --git a/src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp b/src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp
index 9bb3886..e713e59 100644
--- a/src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp
@@ -108,13 +108,13 @@ MafBlock* BlockMergerMafIterator::analyseCurrentBlock_() throw (Exception)
//Now fill the new block:
for (size_t i = 0; i < allSp.size(); ++i) {
- auto_ptr<MafSequence> seq;
+ unique_ptr<MafSequence> seq;
try {
seq.reset(new MafSequence(currentBlock_->getSequenceForSpecies(allSp[i])));
//Check is there is a second sequence:
try {
- auto_ptr<MafSequence> tmp(new MafSequence(incomingBlock_->getSequenceForSpecies(allSp[i])));
+ unique_ptr<MafSequence> tmp(new MafSequence(incomingBlock_->getSequenceForSpecies(allSp[i])));
string ref1 = seq->getDescription(), ref2 = tmp->getDescription();
//Add spacer if needed:
if (globalSpace > 0) {
diff --git a/src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.cpp b/src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.cpp
index 933b6b1..534c889 100644
--- a/src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.cpp
@@ -45,6 +45,9 @@ using namespace bpp;
#include <string>
#include <numeric>
+//From bpp-core:
+#include <Bpp/App/ApplicationTools.h>
+
using namespace std;
MafBlock* ConcatenateMafIterator::analyseCurrentBlock_() throw (Exception)
@@ -52,10 +55,26 @@ MafBlock* ConcatenateMafIterator::analyseCurrentBlock_() throw (Exception)
if (!incomingBlock_) return 0;
currentBlock_ = incomingBlock_;
incomingBlock_ = iterator_->nextBlock();
- while (incomingBlock_) {
+ size_t count = 1;
+ if (verbose_)
+ ApplicationTools::displayMessage("Concatenating new block...");
+ while (incomingBlock_ &&
+ (refSpecies_ == "" ||
+ (incomingBlock_->hasSequenceForSpecies(refSpecies_) &&
+ currentBlock_->hasSequenceForSpecies(refSpecies_) &&
+ incomingBlock_->getSequenceForSpecies(refSpecies_).getChromosome() ==
+ currentBlock_->getSequenceForSpecies(refSpecies_).getChromosome()
+ )
+ )
+ )
+ {
if (currentBlock_->getNumberOfSites() >= minimumSize_) {
return currentBlock_;
}
+ if (verbose_) {
+ ApplicationTools::displayUnlimitedGauge(count++, "Concatenating...");
+ }
+
//We merge the two blocks:
vector<string> sp1 = currentBlock_->getSpeciesList();
vector<string> sp2 = incomingBlock_->getSpeciesList();
@@ -74,13 +93,13 @@ MafBlock* ConcatenateMafIterator::analyseCurrentBlock_() throw (Exception)
//Now fill the new block:
for (size_t i = 0; i < allSp.size(); ++i) {
- auto_ptr<MafSequence> seq;
+ unique_ptr<MafSequence> seq;
try {
seq.reset(new MafSequence(currentBlock_->getSequenceForSpecies(allSp[i])));
//Check is there is a second sequence:
try {
- auto_ptr<MafSequence> tmp(new MafSequence(incomingBlock_->getSequenceForSpecies(allSp[i])));
+ unique_ptr<MafSequence> tmp(new MafSequence(incomingBlock_->getSequenceForSpecies(allSp[i])));
string ref1 = seq->getDescription(), ref2 = tmp->getDescription();
if (seq->getChromosome() != tmp->getChromosome()) {
seq->setChromosome("fus");
diff --git a/src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.h b/src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.h
index 6c35619..7729390 100644
--- a/src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.h
@@ -55,6 +55,7 @@ namespace bpp {
* Blocks are appended regardless of their coordinates, to form concatenated blocks of at least a given number of positions.
* The scores, if any, will be averaged for the block, weighted by the corresponding block sizes.
* The pass value will be removed if it is different for the blocks.
+ * If a reference species is given, only block with identical chr tag will be concatenated.
*/
class ConcatenateMafIterator:
public AbstractFilterMafIterator
@@ -62,12 +63,14 @@ class ConcatenateMafIterator:
private:
MafBlock* incomingBlock_;
unsigned int minimumSize_;
+ std::string refSpecies_;
public:
- ConcatenateMafIterator(MafIterator* iterator, unsigned int minimumSize) :
+ ConcatenateMafIterator(MafIterator* iterator, unsigned int minimumSize, std::string refSpecies = "") :
AbstractFilterMafIterator(iterator),
incomingBlock_(0),
- minimumSize_(minimumSize)
+ minimumSize_(minimumSize),
+ refSpecies_(refSpecies)
{
incomingBlock_ = iterator->nextBlock();
}
@@ -76,13 +79,15 @@ class ConcatenateMafIterator:
ConcatenateMafIterator(const ConcatenateMafIterator& iterator) :
AbstractFilterMafIterator(0),
incomingBlock_(iterator.incomingBlock_),
- minimumSize_(iterator.minimumSize_)
+ minimumSize_(iterator.minimumSize_),
+ refSpecies_(iterator.refSpecies_)
{}
ConcatenateMafIterator& operator=(const ConcatenateMafIterator& iterator)
{
incomingBlock_ = iterator.incomingBlock_;
minimumSize_ = iterator.minimumSize_;
+ refSpecies_ = iterator.refSpecies_;
return *this;
}
diff --git a/src/Bpp/Seq/Io/Maf/CoordinateTranslatorMafIterator.cpp b/src/Bpp/Seq/Io/Maf/CoordinateTranslatorMafIterator.cpp
new file mode 100644
index 0000000..9e6f93c
--- /dev/null
+++ b/src/Bpp/Seq/Io/Maf/CoordinateTranslatorMafIterator.cpp
@@ -0,0 +1,136 @@
+//
+// File: CoordinateTranslatorMafIterator.cpp
+// Authors: Julien Dutheil
+// Created: Thu Jan 28 2016
+//
+
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (2010)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "CoordinateTranslatorMafIterator.h"
+
+//From bpp-seq:
+#include <Bpp/Seq/SequenceWalker.h>
+
+using namespace bpp;
+
+//From the STL:
+#include <string>
+#include <numeric>
+
+using namespace std;
+
+MafBlock* CoordinateTranslatorMafIterator::analyseCurrentBlock_() throw (Exception)
+{
+ unique_ptr<MafBlock> block(iterator_->nextBlock());
+ if (!block.get()) return 0; //No more block.
+
+ //Check if the block contains the reference and target species:
+ if (!block->hasSequenceForSpecies(referenceSpecies_))
+ return block.release();
+ if (!block->hasSequenceForSpecies(targetSpecies_))
+ return block.release();
+
+ //Get the feature ranges for this block:
+ const MafSequence& refSeq = block->getSequenceForSpecies(referenceSpecies_);
+ const MafSequence& targetSeq = block->getSequenceForSpecies(targetSpecies_);
+
+ //first check if there is one (for now we assume that features refer to the chromosome or contig name, with implicit species):
+ std::map<std::string, SequenceFeatureSet*>::iterator mr = inputFeaturesPerChr_.find(refSeq.getChromosome());
+ if (mr == inputFeaturesPerChr_.end())
+ return block.release();
+
+ //second get only features within this block:
+ unique_ptr<SequenceFeatureSet> selectedFeatures(mr->second->getSubsetForRange(SeqRange(refSeq.getRange(true)), true));
+
+ //test if there are some features to translate here:
+ if (selectedFeatures->isEmpty())
+ return block.release();
+
+ //Get coordinate range sets:
+ RangeSet<size_t> ranges;
+ selectedFeatures->fillRangeCollection(ranges);
+
+ //If the reference sequence is on the negative strand, then we have to correct the coordinates:
+ if (refSeq.getStrand() == '-') {
+ RangeSet<size_t> cRanges;
+ for (set<Range<size_t>*>::iterator it = ranges.getSet().begin();
+ it != ranges.getSet().end();
+ ++it)
+ {
+ cRanges.addRange(SeqRange(refSeq.getSrcSize() - (**it).end(), refSeq.getSrcSize() - (**it).begin(), dynamic_cast<SeqRange*>(*it)->getStrand()));
+ }
+ ranges = cRanges;
+ }
+
+ //We will need to convert to alignment positions, using a sequence walker:
+ SequenceWalker referenceWalker(refSeq);
+ SequenceWalker targetWalker(targetSeq);
+
+ //Now creates all blocks for all ranges:
+ if (verbose_) {
+ ApplicationTools::message->endLine();
+ ApplicationTools::displayTask("Extracting annotations", true);
+ }
+ if (logstream_) {
+ (*logstream_ << "COORDINATE CONVERTOR: lifting over " << ranges.getSet().size() << " features from block " << block->getDescription() << ".").endLine();
+ }
+
+ size_t i = 0;
+ for (set<Range<size_t>*>::iterator it = ranges.getSet().begin();
+ it != ranges.getSet().end();
+ ++it)
+ {
+ if (verbose_) {
+ ApplicationTools::displayGauge(i++, ranges.getSet().size() - 1, '=');
+ }
+ size_t a = referenceWalker.getAlignmentPosition((**it).begin() - refSeq.start());
+ size_t b = referenceWalker.getAlignmentPosition((**it).end() - refSeq.start() - 1);
+ size_t a2 = targetWalker.getSequencePosition(a) + targetSeq.start();
+ size_t b2 = targetWalker.getSequencePosition(b) + targetSeq.start() + 1;
+ if (targetSeq.getStrand() == '-') {
+ a2 = targetSeq.getSrcSize() - a2;
+ b2 = targetSeq.getSrcSize() - b2;
+ }
+ output_ << refSeq.getChromosome() << "\t" << refSeq.getStrand() << "\t" << (**it).begin() << "\t" << (**it).end() << "\t";
+ output_ << targetSeq.getChromosome() << "\t" << targetSeq.getStrand() << "\t" << a2 << "\t" << b2 << endl;
+ }
+
+ if (verbose_)
+ ApplicationTools::displayTaskDone();
+
+ //Block is simply forwarded:
+ return block.release();
+}
+
diff --git a/src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.h b/src/Bpp/Seq/Io/Maf/CoordinateTranslatorMafIterator.h
similarity index 52%
copy from src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.h
copy to src/Bpp/Seq/Io/Maf/CoordinateTranslatorMafIterator.h
index 48e9f74..7350090 100644
--- a/src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/CoordinateTranslatorMafIterator.h
@@ -1,7 +1,7 @@
//
-// File: FeatureExtractorMafIterator.h
+// File: CoordinateTranslatorMafIterator.h
// Authors: Julien Dutheil
-// Created: Tue Sep 07 2010
+// Created: Thu Jan 28 2016
//
/*
@@ -37,8 +37,8 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/
-#ifndef _FEATUREEXTRACTORMAFITERATOR_H_
-#define _FEATUREEXTRACTORMAFITERATOR_H_
+#ifndef _COORDINATETRANSLATORMAFITERATOR_H_
+#define _COORDINATETRANSLATORMAFITERATOR_H_
#include "MafIterator.h"
@@ -47,53 +47,67 @@ knowledge of the CeCILL license and that you accept its terms.
#include <string>
#include <deque>
+//From bpp-core:
+#include <Bpp/Numeric/DataTable.h>
+
namespace bpp {
/**
- * @brief Extract alignments corresponding to sequence features given as a vector of SequenceFeature objects.
+ * @brief Translate features coordinates from one species to another, based on the alignment.
*
- * The resulting blocks will contain the specified annotated regions.
- * Note that this iterator is not the opposite of FeatureFilterMafIterator,
- * as overlapping features will all be extracted. This iterator may therefore results
- * in duplication of original data.
+ * This filter is similar in principle to the UCSC "liftOver" utility and software alike.
+ * For now, only write a text file with all coordinates from reference and corresponding target sequence.
*/
-class FeatureExtractor:
+class CoordinateTranslatorMafIterator:
public AbstractFilterMafIterator
{
private:
- std::string refSpecies_;
- bool completeOnly_;
- bool ignoreStrand_;
- std::deque<MafBlock*> blockBuffer_;
- std::map<std::string, RangeSet<size_t> > ranges_;
+ std::string referenceSpecies_;
+ std::string targetSpecies_;
+ std::map<std::string, SequenceFeatureSet*> inputFeaturesPerChr_;
+ std::ostream& output_;
public:
/**
- * @brief Build a new FeatureExtractor iterator.
+ * @brief Build a new CoordinateTranslator iterator.
*
* @param iterator The input iterator
- * @param refSpecies The reference species for feature coordinates
- * @param complete Tell if features should be extracted only if they can be extracted in full
- * @param features The set of features to extract
- * @param ignoreStrand If true, features will be extracted 'as is', without being reversed in case they are on the negative strand.
+ * @param referenceSpecies The reference species for feature coordinates
+ * @param targetSpecies The target species for which features coordinates should be translated
+ * @param features The set of features to lift over
+ * @param output Output stream for translated coordinates
*/
- FeatureExtractor(MafIterator* iterator, const std::string& refSpecies, const SequenceFeatureSet& features, bool complete = false, bool ignoreStrand = false) :
+ CoordinateTranslatorMafIterator(
+ MafIterator* iterator,
+ const std::string& referenceSpecies,
+ const std::string& targetSpecies,
+ const SequenceFeatureSet& features,
+ std::ostream& output) :
AbstractFilterMafIterator(iterator),
- refSpecies_(refSpecies),
- completeOnly_(complete),
- ignoreStrand_(ignoreStrand),
- blockBuffer_(),
- ranges_()
+ referenceSpecies_(referenceSpecies),
+ targetSpecies_(targetSpecies),
+ inputFeaturesPerChr_(),
+ output_(output)
{
- //Build ranges:
+ //Sort features per chromosome for a faster access:
std::set<std::string> seqIds = features.getSequences();
for (std::set<std::string>::iterator it = seqIds.begin();
it != seqIds.end();
++it) {
{
- features.fillRangeCollectionForSequence(*it, ranges_[*it]);
+ inputFeaturesPerChr_[*it] = features.getSubsetForSequence(*it);
}
}
+ output_ << "chr.ref\tstrand.ref\tbegin.ref\tend.ref\tchr.target\tstrand.target\tbegin.target\tend.target" << std::endl;
+ }
+
+ virtual ~CoordinateTranslatorMafIterator() {
+ //Clean sorted features.
+ for (std::map<std::string, SequenceFeatureSet*>::iterator it = inputFeaturesPerChr_.begin();
+ it != inputFeaturesPerChr_.end();
+ it++) {
+ delete it->second;
+ }
}
private:
@@ -103,4 +117,4 @@ class FeatureExtractor:
} // end of namespace bpp.
-#endif //_FEATUREEXTRACTORMAFITERATOR_H_
+#endif //_COORDINATETRANSLATORMAFITERATOR_H_
diff --git a/src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.cpp b/src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.cpp
index 305a60f..3c52a6a 100644
--- a/src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.cpp
@@ -48,6 +48,8 @@ void CoordinatesOutputMafIterator::writeHeader_(ostream& out) const
if (i > 0) out << "\t";
string sp = species_[i];
out << sp << ".chr\t" << sp << ".strand\t" << sp << ".start\t" << sp << ".stop";
+ if (includeSrcSize_)
+ out << "\t" << sp << ".src";
}
out << endl;
}
@@ -63,8 +65,12 @@ MafBlock* CoordinatesOutputMafIterator::analyseCurrentBlock_() throw (Exception)
throw Exception("CoordinatesOutputMafIterator::analyseCurrentBlock_(). There is more than one sequence for species '" + species_[i] + "' in current block.");
else if (seqs.size() == 0) {
*output_ << "NA\tNA\tNA\tNA";
+ if (includeSrcSize_)
+ *output_ << "\tNA";
} else {
*output_ << seqs[0]->getChromosome() << "\t" << seqs[0]->getStrand() << "\t" << seqs[0]->start() << "\t" << seqs[0]->stop();
+ if (includeSrcSize_)
+ *output_ << "\t" << seqs[0]->getSrcSize();
}
}
*output_ << endl;
diff --git a/src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.h b/src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.h
index 0ae520c..aefa95c 100644
--- a/src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.h
@@ -61,6 +61,7 @@ class CoordinatesOutputMafIterator:
private:
std::ostream* output_;
std::vector<std::string> species_;
+ bool includeSrcSize_;
public:
/**
@@ -69,9 +70,10 @@ class CoordinatesOutputMafIterator:
* @param iterator The input iterator.
* @param out A pointer toward the output stream. The stream will not be own by this instance, and will not be copied neither destroyed.
* @param species A vector of species names for which coordinates should be output. In case of missing species for one block, NA will be produced.
+ * @param includeSrcSize Tell if source size should also be written (useful to convert coordinates on the negative strand).
*/
- CoordinatesOutputMafIterator(MafIterator* iterator, std::ostream* out, const std::vector<std::string>& species):
- AbstractFilterMafIterator(iterator), output_(out), species_(species)
+ CoordinatesOutputMafIterator(MafIterator* iterator, std::ostream* out, const std::vector<std::string>& species, bool includeSrcSize = false):
+ AbstractFilterMafIterator(iterator), output_(out), species_(species), includeSrcSize_(includeSrcSize)
{
if (output_)
writeHeader_(*output_);
@@ -81,13 +83,15 @@ class CoordinatesOutputMafIterator:
CoordinatesOutputMafIterator(const CoordinatesOutputMafIterator& iterator) :
AbstractFilterMafIterator(0),
output_(iterator.output_),
- species_(iterator.species_)
+ species_(iterator.species_),
+ includeSrcSize_(iterator.includeSrcSize_)
{}
CoordinatesOutputMafIterator& operator=(const CoordinatesOutputMafIterator& iterator)
{
output_ = iterator.output_;
species_ = iterator.species_;
+ includeSrcSize_ = iterator.includeSrcSize_;
return *this;
}
diff --git a/src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp b/src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp
index 721dae0..0a928ff 100644
--- a/src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp
@@ -50,11 +50,11 @@ using namespace bpp;
using namespace std;
-MafBlock* FeatureExtractor::analyseCurrentBlock_() throw (Exception)
+MafBlock* FeatureExtractorMafIterator::analyseCurrentBlock_() throw (Exception)
{
while (blockBuffer_.size() == 0) {
//Unless there is no more block in the buffer, we need to parse more:
- auto_ptr<MafBlock> block;
+ unique_ptr<MafBlock> block;
START:
block.reset(iterator_->nextBlock());
if (!block.get()) return 0; //No more block.
@@ -79,13 +79,14 @@ MafBlock* FeatureExtractor::analyseCurrentBlock_() throw (Exception)
goto START;
//If the reference sequence is on the negative strand, then we have to correct the coordinates:
+ (*logstream_ << "Strand: " << refSeq.getStrand()).endLine();
if (refSeq.getStrand() == '-') {
RangeSet<size_t> cRanges;
for (set<Range<size_t>*>::iterator it = ranges.getSet().begin();
- it != ranges.getSet().end();
+ it != ranges.getSet().end();
++it)
{
- cRanges.addRange(Range<size_t>(refSeq.getSrcSize() - (**it).end(), refSeq.getSrcSize() - (**it).begin()));
+ cRanges.addRange(SeqRange(refSeq.getSrcSize() - (**it).end(), refSeq.getSrcSize() - (**it).begin(), dynamic_cast<SeqRange*>(*it)->getStrand()));
}
ranges = cRanges;
}
@@ -109,20 +110,24 @@ MafBlock* FeatureExtractor::analyseCurrentBlock_() throw (Exception)
{
if (verbose_) {
ApplicationTools::displayGauge(i++, ranges.getSet().size() - 1, '=');
- }
+ }
+ //This does not go after i=0, problem with ranges?????
MafBlock* newBlock = new MafBlock();
newBlock->setScore(block->getScore());
newBlock->setPass(block->getPass());
+ size_t a = walker.getAlignmentPosition((**it).begin() - refSeq.start());
+ size_t b = walker.getAlignmentPosition((**it).end() - refSeq.start() - 1);
for (size_t j = 0; j < block->getNumberOfSequences(); ++j) {
- auto_ptr<MafSequence> subseq;
- size_t a = walker.getAlignmentPosition((**it).begin() - refSeq.start());
- size_t b = walker.getAlignmentPosition((**it).end() - refSeq.start() - 1);
+ unique_ptr<MafSequence> subseq;
subseq.reset(block->getSequence(j).subSequence(a, b - a + 1));
if (!ignoreStrand_) {
- if (dynamic_cast<SeqRange*>(*it)->isNegativeStrand()) {
+ if ((dynamic_cast<SeqRange*>(*it)->isNegativeStrand() && refSeq.getStrand() == '+') ||
+ (!dynamic_cast<SeqRange*>(*it)->isNegativeStrand() && refSeq.getStrand() == '-'))
+ {
SequenceTools::invertComplement(*subseq);
}
}
+ (*logstream_ << subseq->getName()).endLine();
newBlock->addSequence(*subseq);
}
blockBuffer_.push_back(newBlock);
diff --git a/src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.h b/src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.h
index 48e9f74..48c3501 100644
--- a/src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.h
@@ -57,7 +57,7 @@ namespace bpp {
* as overlapping features will all be extracted. This iterator may therefore results
* in duplication of original data.
*/
-class FeatureExtractor:
+class FeatureExtractorMafIterator:
public AbstractFilterMafIterator
{
private:
@@ -77,7 +77,7 @@ class FeatureExtractor:
* @param features The set of features to extract
* @param ignoreStrand If true, features will be extracted 'as is', without being reversed in case they are on the negative strand.
*/
- FeatureExtractor(MafIterator* iterator, const std::string& refSpecies, const SequenceFeatureSet& features, bool complete = false, bool ignoreStrand = false) :
+ FeatureExtractorMafIterator(MafIterator* iterator, const std::string& refSpecies, const SequenceFeatureSet& features, bool complete = false, bool ignoreStrand = false) :
AbstractFilterMafIterator(iterator),
refSpecies_(refSpecies),
completeOnly_(complete),
diff --git a/src/Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp b/src/Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp
index 1e4e674..0417104 100644
--- a/src/Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp
@@ -110,11 +110,11 @@ MafBlock* FeatureFilterMafIterator::analyseCurrentBlock_() throw (Exception)
}
for (size_t alnPos = 0; alnPos < refSeq.size() && refBounds.size() > 0; ++alnPos) {
if (verbose_)
- ApplicationTools::displayGauge(alnPos, refBounds.back(), '>');
+ ApplicationTools::displayGauge(static_cast<size_t>(refPos + 1), refBounds.back() + 1, '>');
if (refSeq[alnPos] != gap) {
refPos++;
//check if this position is a bound:
- if (refBounds.front() == static_cast<size_t>(refPos)) {
+ while (refBounds.front() == static_cast<size_t>(refPos)) {
pos.push_back(alnPos);
refBounds.pop_front();
}
@@ -134,7 +134,7 @@ MafBlock* FeatureFilterMafIterator::analyseCurrentBlock_() throw (Exception)
throw Exception("FeatureFilterMafIterator::nextBlock(). An error occurred here, " + TextTools::toString(refBounds.size()) + " coordinates are left, in sequence " + refSeq.getDescription() + "... this is most likely a bug, please report!");
}
- //Next step is simply to split the black according to the translated coordinates:
+ //Next step is simply to split the block according to the translated coordinates:
if (pos.size() == 2 && pos.front() == 0 && pos.back() == block->getNumberOfSites()) {
//Everything is removed:
if (logstream_) {
diff --git a/src/Bpp/Seq/Io/Maf/FullGapFilterMafIterator.cpp b/src/Bpp/Seq/Io/Maf/FullGapFilterMafIterator.cpp
index ca0297d..e7b5264 100644
--- a/src/Bpp/Seq/Io/Maf/FullGapFilterMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/FullGapFilterMafIterator.cpp
@@ -59,8 +59,12 @@ MafBlock* FullGapFilterMafIterator::analyseCurrentBlock_() throw (Exception)
//We create a copy of the ingroup alignement for better efficiency:
VectorSiteContainer vsc(&AlphabetTools::DNA_ALPHABET);
for (size_t i = 0; i < species_.size(); ++i) {
- vsc.addSequence(block->getSequence(i));
+ if (block->hasSequenceForSpecies(species_[i])) {
+ vsc.addSequence(block->getSequenceForSpecies(species_[i]));
+ }
}
+ if (vsc.getNumberOfSequences() == 0) return block; //Block ignored as it does not contain any of the focus species.
+
//Now check the positions that are only made of gaps:
if (verbose_) {
ApplicationTools::message->endLine();
diff --git a/src/Bpp/Seq/Io/Maf/IterationListener.h b/src/Bpp/Seq/Io/Maf/IterationListener.h
index a6e2b9e..b0fa172 100644
--- a/src/Bpp/Seq/Io/Maf/IterationListener.h
+++ b/src/Bpp/Seq/Io/Maf/IterationListener.h
@@ -46,7 +46,7 @@ knowledge of the CeCILL license and that you accept its terms.
namespace bpp {
/**
- * @brief Listener which enable to catch events when parsing a Maf file.
+ * @brief Listener which enables to catch events when parsing a Maf file.
*/
class IterationListener
{
diff --git a/src/Bpp/Seq/Io/Maf/MafParser.cpp b/src/Bpp/Seq/Io/Maf/MafParser.cpp
index 8720977..8a9b74b 100644
--- a/src/Bpp/Seq/Io/Maf/MafParser.cpp
+++ b/src/Bpp/Seq/Io/Maf/MafParser.cpp
@@ -43,6 +43,8 @@ knowledge of the CeCILL license and that you accept its terms.
#include <Bpp/Text/TextTools.h>
#include <Bpp/Text/KeyvalTools.h>
+#include <algorithm>
+
using namespace std;
using namespace bpp;
@@ -52,10 +54,13 @@ MafBlock* MafParser::analyseCurrentBlock_() throw (Exception)
string line;
bool test = true;
- MafSequence* currentSequence = 0;
+ unique_ptr<MafSequence> currentSequence;
+
while (test)
{
- if (stream_->eof()) return 0;
+ if (stream_->eof()) {
+ break;
+ }
getline(*stream_, line, '\n');
if (TextTools::isEmpty(line))
{
@@ -64,7 +69,7 @@ MafBlock* MafParser::analyseCurrentBlock_() throw (Exception)
if (currentSequence) {
//Add previous sequence:
block->addSequence(*currentSequence); //The sequence is copied in the container.
- delete currentSequence;
+ currentSequence.reset();
}
//end of paragraph
@@ -75,7 +80,7 @@ MafBlock* MafParser::analyseCurrentBlock_() throw (Exception)
if (currentSequence) {
//Add previous sequence:
block->addSequence(*currentSequence); //The sequence is copied in the container.
- delete currentSequence;
+ currentSequence.reset();
}
//New block.
@@ -111,17 +116,29 @@ MafBlock* MafParser::analyseCurrentBlock_() throw (Exception)
if (currentSequence) {
//Add previous sequence:
block->addSequence(*currentSequence); //The sequence is copied in the container.
- delete currentSequence;
+ currentSequence.reset();
+ }
+ string seq = st.nextToken();
+ if (dotOption_ == DOT_ASGAP) {
+ std::replace(seq.begin(), seq.end(), '.', '-');
+ }
+ if (dotOption_ == DOT_ASUNRES) {
+ std::replace(seq.begin(), seq.end(), '.', 'N');
+ }
+ currentSequence.reset(new MafSequence(src, seq, start, strand, srcSize));
+ if (currentSequence->getGenomicSize() != size) {
+ if (checkSequenceSize_)
+ throw Exception("MafAlignmentParser::nextBlock. Sequence found (" + src + ") does not match specified size: " + TextTools::toString(currentSequence->getGenomicSize()) + ", should be " + TextTools::toString(size) + ".");
+ else {
+ if (verbose_) {
+ ApplicationTools::displayWarning("MafAlignmentParser::nextBlock. Sequence found (" + src + ") does not match specified size: " + TextTools::toString(currentSequence->getGenomicSize()) + ", should be " + TextTools::toString(size) + ".");
+ }
+ }
}
- const string seq = st.nextToken();
- currentSequence = new MafSequence(src, seq, start, strand, srcSize);
- if (currentSequence->getGenomicSize() != size)
- throw Exception("MafAlignmentParser::nextBlock. Sequence found (" + src + ") does not match specified size: " + TextTools::toString(currentSequence->getGenomicSize()) + ", should be " + TextTools::toString(size) + ".");
-
//Add mask:
if (mask_) {
vector<bool> mask(currentSequence->size());
- for (unsigned int i = 0; i < mask.size(); ++i) {
+ for (size_t i = 0; i < mask.size(); ++i) {
mask[i] = cmAlphabet_.isMasked(seq[i]);
}
currentSequence->addAnnotation(new SequenceMask(mask));
@@ -139,7 +156,7 @@ MafBlock* MafParser::analyseCurrentBlock_() throw (Exception)
string qstr = st.nextToken();
//Now parse the score string:
SequenceQuality* seqQual = new SequenceQuality(qstr.size());
- for (unsigned int i = 0; i < qstr.size(); ++i) {
+ for (size_t i = 0; i < qstr.size(); ++i) {
char c = qstr[i];
if (c == '-') {
seqQual->setScore(i, -1);
@@ -156,6 +173,16 @@ MafBlock* MafParser::analyseCurrentBlock_() throw (Exception)
currentSequence->addAnnotation(seqQual);
}
}
+ //// Final check and passing by results
+
+ //In case last line in not empty:
+ if (currentSequence) {
+ //Add previous sequence:
+ block->addSequence(*currentSequence); //The sequence is copied in the container.
+ currentSequence.reset();
+ }
+
+ //Returning block:
return block;
}
diff --git a/src/Bpp/Seq/Io/Maf/MafParser.h b/src/Bpp/Seq/Io/Maf/MafParser.h
index 54475a2..eb9b59a 100644
--- a/src/Bpp/Seq/Io/Maf/MafParser.h
+++ b/src/Bpp/Seq/Io/Maf/MafParser.h
@@ -64,21 +64,56 @@ class MafParser:
private:
std::istream* stream_;
bool mask_;
+ bool checkSequenceSize_;
CaseMaskedAlphabet cmAlphabet_;
bool firstBlock_;
+ short dotOption_;
public:
- MafParser(std::istream* stream, bool parseMask = false) :
- stream_(stream), mask_(parseMask), cmAlphabet_(&AlphabetTools::DNA_ALPHABET), firstBlock_(true) {}
+ /**
+ * @brief Create a new instance of MafParser
+ *
+ * @param stream The input stream to read text from
+ * @param parseMask Tell is masking (lower case) should be kept
+ * @param checkSize Tell if the size of sequence found should be
+ * compared to the specified one. An exception is thrown
+ * in case of mismatch (default). If set to no, a warning
+ * will be displayed if verbose is set to true.
+ * @param dotOption (one of DOT_ERROR, DOT_ASGAP or DOT_ASUNRES)
+ * tells how dot should be treated. DOT_ERROR, the default,
+ * will return an exception. DOT_ASGAP will convert all dots
+ * to gaps and DOT_ASUNRES will convert them to 'N', which
+ * will increase parsing time.
+ */
+ MafParser(std::istream* stream, bool parseMask = false, bool checkSize = true, short dotOption = DOT_ERROR) :
+ stream_(stream), mask_(parseMask), checkSequenceSize_(checkSize), cmAlphabet_(&AlphabetTools::DNA_ALPHABET),
+ firstBlock_(true), dotOption_(dotOption) {}
private:
//Recopy is forbidden!
- MafParser(const MafParser& maf): stream_(0), mask_(maf.mask_), cmAlphabet_(&AlphabetTools::DNA_ALPHABET), firstBlock_(maf.firstBlock_) {}
- MafParser& operator=(const MafParser& maf) { stream_ = 0; mask_ = maf.mask_; firstBlock_ = maf.firstBlock_; return *this; }
+ MafParser(const MafParser& maf):
+ stream_(0), mask_(maf.mask_), checkSequenceSize_(maf.checkSequenceSize_),
+ cmAlphabet_(&AlphabetTools::DNA_ALPHABET), firstBlock_(maf.firstBlock_),
+ dotOption_(maf.dotOption_) {}
+
+ MafParser& operator=(const MafParser& maf) {
+ stream_ = 0;
+ mask_ = maf.mask_;
+ checkSequenceSize_ = maf.checkSequenceSize_;
+ firstBlock_ = maf.firstBlock_;
+ dotOption_ = maf.dotOption_;
+ return *this;
+ }
private:
MafBlock* analyseCurrentBlock_() throw (Exception);
+ public:
+ static constexpr short DOT_ERROR = 0;
+ static constexpr short DOT_ASGAP = 1;
+ static constexpr short DOT_ASUNRES = 2;
+ //static constexpr short DOT_RESOLVE = 3; // not yet supported
+
};
} // end of namespace bpp.
diff --git a/src/Bpp/Seq/Io/Maf/MafSequence.h b/src/Bpp/Seq/Io/Maf/MafSequence.h
index c5278e8..bcd6458 100644
--- a/src/Bpp/Seq/Io/Maf/MafSequence.h
+++ b/src/Bpp/Seq/Io/Maf/MafSequence.h
@@ -72,30 +72,34 @@ class MafSequence:
size_t srcSize_;
public:
- MafSequence():
- SequenceWithAnnotation(&AlphabetTools::DNA_ALPHABET), hasCoordinates_(false), begin_(0), species_(""), chromosome_(""), strand_(0), size_(0), srcSize_(0)
- {
- size_ = 0;
- }
+ MafSequence(const Alphabet* alphabet = &AlphabetTools::DNA_ALPHABET):
+ SequenceWithAnnotation(alphabet), hasCoordinates_(false), begin_(0), species_(""), chromosome_(""), strand_(0), size_(0), srcSize_(0)
+ {}
- MafSequence(const std::string& name, const std::string& sequence, bool parseName = true):
- SequenceWithAnnotation(name, sequence, &AlphabetTools::DNA_ALPHABET), hasCoordinates_(false), begin_(0), species_(""), chromosome_(""), strand_(0), size_(0), srcSize_(0)
+ MafSequence(const std::string& name, const std::string& sequence, bool parseName = true, const Alphabet* alphabet = &AlphabetTools::DNA_ALPHABET):
+ SequenceWithAnnotation(name, sequence, alphabet), hasCoordinates_(false), begin_(0), species_(""), chromosome_(""), strand_(0), size_(0), srcSize_(0)
{
size_ = SequenceTools::getNumberOfSites(*this);
if (parseName)
splitNameIntoSpeciesAndChromosome(name, species_, chromosome_);
}
- MafSequence(const std::string& name, const std::string& sequence, size_t begin, char strand, size_t srcSize, bool parseName = true) :
- SequenceWithAnnotation(name, sequence, &AlphabetTools::DNA_ALPHABET), hasCoordinates_(true), begin_(begin), species_(""), chromosome_(""), strand_(strand), size_(0), srcSize_(srcSize)
+ MafSequence(const std::string& name, const std::string& sequence, size_t begin, char strand, size_t srcSize, bool parseName = true, const Alphabet* alphabet = &AlphabetTools::DNA_ALPHABET) :
+ SequenceWithAnnotation(name, sequence, alphabet), hasCoordinates_(true), begin_(begin), species_(""), chromosome_(""), strand_(strand), size_(0), srcSize_(srcSize)
{
size_ = SequenceTools::getNumberOfSites(*this);
if (parseName)
splitNameIntoSpeciesAndChromosome(name, species_, chromosome_);
}
- MafSequence* clone() const { return new MafSequence(*this); }
-
+ MafSequence* clone() const {
+ return new MafSequence(*this);
+ }
+
+ MafSequence* cloneMeta() const {
+ return new MafSequence(getName(), std::string(), begin_, strand_, srcSize_, true);
+ }
+
~MafSequence() {}
public:
@@ -103,7 +107,7 @@ class MafSequence:
void removeCoordinates() { hasCoordinates_ = false; begin_ = 0; }
- size_t start() const throw (Exception) {
+ size_t start() const throw (Exception) {
if (hasCoordinates_) return begin_;
else throw Exception("MafSequence::start(). Sequence " + getName() + " does not have coordinates.");
}
@@ -114,11 +118,11 @@ class MafSequence:
}
/**
- * @return A range with cooridinates from this sequence.
- * @param origin Tell if coorinates according to original sequence should be used.
- * If 'yes' and the sequence is on the negative strand, the returned rang will be computed as [SrcSize-Stop, SrcSize-Start[
+ * @return A range with coordinates from this sequence.
+ * @param origin Tell if coordinates according to original sequence should be used.
+ * If 'yes' and the sequence is on the negative strand, the returned range will be computed as [SrcSize-Stop, SrcSize-Start[
*/
- Range<size_t> getRange(bool origin=true) const {
+ Range<size_t> getRange(bool origin = true) const {
if (hasCoordinates_) {
if (origin && strand_ == '-') {
return Range<size_t>(srcSize_ - stop(), srcSize_ - start());
diff --git a/src/Bpp/Seq/Io/Maf/MafStatistics.cpp b/src/Bpp/Seq/Io/Maf/MafStatistics.cpp
index 01b2367..49b9802 100644
--- a/src/Bpp/Seq/Io/Maf/MafStatistics.cpp
+++ b/src/Bpp/Seq/Io/Maf/MafStatistics.cpp
@@ -40,6 +40,7 @@ knowledge of the CeCILL license and that you accept its terms.
#include "MafStatistics.h"
#include <Bpp/Seq/Container/SequenceContainerTools.h>
#include <Bpp/Seq/Container/VectorSiteContainer.h>
+#include <Bpp/Seq/Container/SiteContainerTools.h>
#include <Bpp/Seq/SiteTools.h>
//From bpp-core:
@@ -64,36 +65,12 @@ void PairwiseDivergenceMafStatistics::compute(const MafBlock& block)
result_.setValue(100. - SequenceTools::getPercentIdentity(*seqs1[0], *seqs2[0], true));
}
-vector<string> CharacterCountsMafStatistics::getSupportedTags() const
-{
- vector<string> tags;
- for (int i = 0; i < static_cast<int>(alphabet_->getSize()); ++i) {
- tags.push_back(alphabet_->intToChar(i));
- }
- tags.push_back("Gap");
- tags.push_back("Unresolved");
-
- return tags;
-}
-
-void CharacterCountsMafStatistics::compute(const MafBlock& block)
-{
- std::map<int, int> counts;
- SequenceContainerTools::getCounts(block.getAlignment(), counts);
- for (int i = 0; i < static_cast<int>(alphabet_->getSize()); ++i) {
- result_.setValue(alphabet_->intToChar(i), counts[i]);
- }
- result_.setValue("Gap", counts[alphabet_->getGapCharacterCode()]);
- double countUnres = 0;
- for (map<int, int>::iterator it = counts.begin(); it != counts.end(); ++it) {
- if (alphabet_->isUnresolved(it->first))
- countUnres += it->second;
- }
- result_.setValue("Unresolved", countUnres);
-}
-
SiteContainer* AbstractSpeciesSelectionMafStatistics::getSiteContainer_(const MafBlock& block)
{
+ if (noSpeciesMeansAllSpecies_ && species_.size() == 0) {
+ return new VectorSiteContainer(block.getAlignment());
+ }
+ //Otherwise, we select species:
VectorSiteContainer* alignment = new VectorSiteContainer(block.getAlignment().getAlphabet());
for (size_t i = 0; i < species_.size(); ++i) {
if (block.hasSequenceForSpecies(species_[i])) {
@@ -135,6 +112,35 @@ vector<SiteContainer*> AbstractSpeciesMultipleSelectionMafStatistics::getSiteCon
return alignments;
}
+vector<string> CharacterCountsMafStatistics::getSupportedTags() const
+{
+ vector<string> tags;
+ for (int i = 0; i < static_cast<int>(alphabet_->getSize()); ++i) {
+ tags.push_back(alphabet_->intToChar(i));
+ }
+ tags.push_back("Gap");
+ tags.push_back("Unresolved");
+
+ return tags;
+}
+
+void CharacterCountsMafStatistics::compute(const MafBlock& block)
+{
+ std::map<int, int> counts;
+ unique_ptr<SiteContainer> sites(getSiteContainer_(block));
+ SequenceContainerTools::getCounts(*sites, counts);
+ for (int i = 0; i < static_cast<int>(alphabet_->getSize()); ++i) {
+ result_.setValue(alphabet_->intToChar(i), counts[i]);
+ }
+ result_.setValue("Gap", counts[alphabet_->getGapCharacterCode()]);
+ double countUnres = 0;
+ for (map<int, int>::iterator it = counts.begin(); it != counts.end(); ++it) {
+ if (alphabet_->isUnresolved(it->first))
+ countUnres += it->second;
+ }
+ result_.setValue("Unresolved", countUnres);
+}
+
vector<string> SiteFrequencySpectrumMafStatistics::getSupportedTags() const
{
vector<string> tags;
@@ -156,7 +162,7 @@ void SiteFrequencySpectrumMafStatistics::compute(const MafBlock& block)
int state;
bool hasOutgroup = (outgroup_ != "");
bool isAnalyzable;
- auto_ptr<SiteContainer> alignment;
+ unique_ptr<SiteContainer> alignment;
const Sequence* outgroupSeq = 0;
if (hasOutgroup) {
isAnalyzable = (block.hasSequenceForSpecies(outgroup_) && block.getNumberOfSequences() > 1);
@@ -259,7 +265,7 @@ vector<string> FourSpeciesPatternCountsMafStatistics::getSupportedTags() const
void FourSpeciesPatternCountsMafStatistics::compute(const MafBlock& block)
{
counts_.assign(6, 0);
- auto_ptr<SiteContainer> alignment(getSiteContainer_(block));
+ unique_ptr<SiteContainer> alignment(getSiteContainer_(block));
if (alignment->getNumberOfSequences() == 4) {
unsigned int nbIgnored = 0;
for (size_t i = 0; i < block.getNumberOfSites(); ++i) {
@@ -298,28 +304,50 @@ vector<string> SiteMafStatistics::getSupportedTags() const
vector<string> tags;
tags.push_back("NbWithoutGap");
tags.push_back("NbComplete");
+ tags.push_back("NbConstant");
+ tags.push_back("NbBiallelic");
+ tags.push_back("NbTriallelic");
+ tags.push_back("NbQuadriallelic");
tags.push_back("NbParsimonyInformative");
return tags;
}
void SiteMafStatistics::compute(const MafBlock& block)
{
- auto_ptr<SiteContainer> alignment(getSiteContainer_(block));
+ unique_ptr<SiteContainer> alignment(getSiteContainer_(block));
unsigned int nbNg = 0;
unsigned int nbCo = 0;
unsigned int nbPi = 0;
+ unsigned int nbP1 = 0;
+ unsigned int nbP2 = 0;
+ unsigned int nbP3 = 0;
+ unsigned int nbP4 = 0;
if (alignment->getNumberOfSequences() > 0) {
for (size_t i = 0; i < alignment->getNumberOfSites(); ++i) {
if (!SiteTools::hasGap(alignment->getSite(i)))
nbNg++;
- if (SiteTools::isComplete(alignment->getSite(i)))
+ if (SiteTools::isComplete(alignment->getSite(i))) {
nbCo++;
+ map<int, size_t> counts;
+ SiteTools::getCounts(alignment->getSite(i), counts);
+ switch (counts.size()) {
+ case 1: nbP1++; break;
+ case 2: nbP2++; break;
+ case 3: nbP3++; break;
+ case 4: nbP4++; break;
+ default: throw Exception("The impossible happened. Probably a distortion in the Minkowski space.");
+ }
+ }
if (SiteTools::isParsimonyInformativeSite(alignment->getSite(i)))
nbPi++;
}
}
result_.setValue("NbWithoutGap", nbNg);
result_.setValue("NbComplete", nbCo);
+ result_.setValue("NbConstant", nbP1);
+ result_.setValue("NbBiallelic", nbP2);
+ result_.setValue("NbTriallelic", nbP3);
+ result_.setValue("NbQuadriallelic", nbP4);
result_.setValue("NbParsimonyInformative", nbPi);
}
@@ -445,33 +473,62 @@ vector<string> SequenceDiversityMafStatistics::getSupportedTags() const
vector<string> tags;
tags.push_back("NbSeggregating");
tags.push_back("WattersonTheta");
+ tags.push_back("TajimaPi");
+ tags.push_back("TajimaD");
return tags;
}
void SequenceDiversityMafStatistics::compute(const MafBlock& block)
{
- auto_ptr<SiteContainer> alignment(getSiteContainer_(block));
- unsigned int nbSeg = 0;
- unsigned int nbTot = 0;
- if (alignment->getNumberOfSequences() > 0) {
- for (size_t i = 0; i < alignment->getNumberOfSites(); ++i) {
- const Site& site = alignment->getSite(i);
- if (SiteTools::isComplete(site)) {
- nbTot++;
- if (!SiteTools::isConstant(site))
- nbSeg++;
- }
+ unique_ptr<SiteContainer> alignment(getSiteContainer_(block));
+ //Get only complete sites:
+ unique_ptr<SiteContainer> alignment2(SiteContainerTools::getCompleteSites(*alignment));
+ double S = 0;
+ size_t nbTot = alignment2->getNumberOfSites();
+ size_t n = alignment2->getNumberOfSequences();
+ if (n > 0) {
+ for (size_t i = 0; i < alignment2->getNumberOfSites(); ++i) {
+ const Site& site = alignment2->getSite(i);
+ if (!SiteTools::isConstant(site))
+ S++;
}
}
- double wt = 0;
- if (nbSeg > 0) {
- size_t n = alignment->getNumberOfSequences();
- double hf = 0;
- for (double i = 1; i < n; ++i)
- hf += 1. / i;
- wt = static_cast<double>(nbSeg) / (static_cast<double>(nbTot) * hf);
+
+ double a1 = 0;
+ double a2 = 0;
+ double dn = static_cast<double>(n);
+ for (double i = 1; i < dn; ++i) {
+ a1 += 1. / i;
+ a2 += 1. / (i * i);
+ }
+ double wt = S / (static_cast<double>(nbTot) * a1);
+ double b1 = (dn + 1) / (3 * (dn - 1));
+ double b2 = 2 * (dn * dn + dn + 3) / (9 * dn * (dn - 1));
+ double c1 = b1 - 1. / a1;
+ double c2 = b2 - (dn + 2) / (a1 * dn) + a2 / (a1 * a1);
+ double e1 = c1 / a1;
+ double e2 = c2 / (a1 * a1 + a2);
+
+ //Compute pairwise heterozigocity:
+ double pi = 0;
+ for (size_t i = 0; i < n - 1; ++i) {
+ for (size_t j = i + 1; j < n; ++j) {
+ pi += SiteContainerTools::computeSimilarity(
+ alignment2->getSequence(i),
+ alignment2->getSequence(j),
+ true,
+ SiteContainerTools::SIMILARITY_ALL,
+ false);
+ }
}
- result_.setValue("NbSeggregating", nbSeg);
+ pi /= static_cast<double>((n - 1) * n / 2);
+
+ //Compute Tajima's D:
+ double tajd = static_cast<double>(nbTot) * (pi - wt) / sqrt(e1 * S + e2 * S * (S - 1));
+
+ result_.setValue("NbSeggregating", S);
result_.setValue("WattersonTheta", wt);
+ result_.setValue("TajimaPi", pi);
+ result_.setValue("TajimaD", tajd);
}
diff --git a/src/Bpp/Seq/Io/Maf/MafStatistics.h b/src/Bpp/Seq/Io/Maf/MafStatistics.h
index 3c89894..b5805d6 100644
--- a/src/Bpp/Seq/Io/Maf/MafStatistics.h
+++ b/src/Bpp/Seq/Io/Maf/MafStatistics.h
@@ -155,7 +155,7 @@ class SimpleMafStatisticsResult:
virtual ~SimpleMafStatisticsResult() {}
public:
- virtual const BppNumberI& getValue(const std::string& tag) const throw (Exception) { return SimpleMafStatisticsResult::getValue(tag); }
+ virtual const BppNumberI& getValue(const std::string& tag) const throw (Exception) { return MafStatisticsResult::getValue(tag); }
virtual const BppNumberI& getValue() const { return *values_[name_]; }
@@ -365,42 +365,6 @@ class AlignmentScoreMafStatistics:
}
};
-/**
- * @brief Compute the base frequencies of a maf block.
- *
- * For each block, provides the following numbers (with their corresponding tags):
- * - A: total counts of A
- * - C: total counts of C
- * - G: total counts of G
- * - T [or U]: total counts of T/U
- * - Gap: total counts of gaps
- * - Unresolved: total counts of unresolved characters
- * The sum of all characters should equal BlockSize x BlockLength
- */
-class CharacterCountsMafStatistics:
- public AbstractMafStatistics
-{
- private:
- const Alphabet* alphabet_;
-
- public:
- CharacterCountsMafStatistics(const Alphabet* alphabet): AbstractMafStatistics(), alphabet_(alphabet) {}
- CharacterCountsMafStatistics(const CharacterCountsMafStatistics& stats):
- AbstractMafStatistics(stats), alphabet_(stats.alphabet_) {}
- CharacterCountsMafStatistics& operator=(const CharacterCountsMafStatistics& stats) {
- AbstractMafStatistics::operator=(stats);
- alphabet_ = stats.alphabet_;
- return *this;
- }
-
- virtual ~CharacterCountsMafStatistics() {}
-
- public:
- std::string getShortName() const { return "Count"; }
- std::string getFullName() const { return "Character counts."; }
- void compute(const MafBlock& block);
- std::vector<std::string> getSupportedTags() const;
-};
/**
@@ -413,10 +377,20 @@ class AbstractSpeciesSelectionMafStatistics:
{
private:
std::vector<std::string> species_;
+ bool noSpeciesMeansAllSpecies_;
+
+ protected:
+ std::string suffix_;
public:
- AbstractSpeciesSelectionMafStatistics(const std::vector<std::string>& species):
- species_(species) {}
+ AbstractSpeciesSelectionMafStatistics(
+ const std::vector<std::string>& species,
+ bool noSpeciesMeansAllSpecies = false,
+ const std::string& suffix = ""):
+ species_(species),
+ noSpeciesMeansAllSpecies_(noSpeciesMeansAllSpecies),
+ suffix_(suffix)
+ {}
protected:
SiteContainer* getSiteContainer_(const MafBlock& block);
@@ -444,6 +418,55 @@ class AbstractSpeciesMultipleSelectionMafStatistics:
};
+
+/**
+ * @brief Compute the base frequencies of a maf block.
+ *
+ * For each block, provides the following numbers (with their corresponding tags):
+ * - A: total counts of A
+ * - C: total counts of C
+ * - G: total counts of G
+ * - T [or U]: total counts of T/U
+ * - Gap: total counts of gaps
+ * - Unresolved: total counts of unresolved characters
+ * The sum of all characters should equal BlockSize x BlockLength
+ */
+class CharacterCountsMafStatistics:
+ public AbstractMafStatistics,
+ public AbstractSpeciesSelectionMafStatistics
+{
+ private:
+ const Alphabet* alphabet_;
+
+ public:
+ CharacterCountsMafStatistics(const Alphabet* alphabet, const std::vector<std::string>& species, const std::string suffix):
+ AbstractMafStatistics(),
+ AbstractSpeciesSelectionMafStatistics(species, true, suffix),
+ alphabet_(alphabet) {}
+
+ CharacterCountsMafStatistics(const CharacterCountsMafStatistics& stats):
+ AbstractMafStatistics(stats),
+ AbstractSpeciesSelectionMafStatistics(stats),
+ alphabet_(stats.alphabet_) {}
+
+ CharacterCountsMafStatistics& operator=(const CharacterCountsMafStatistics& stats) {
+ AbstractMafStatistics::operator=(stats);
+ AbstractSpeciesSelectionMafStatistics::operator=(stats);
+ alphabet_ = stats.alphabet_;
+ return *this;
+ }
+
+ virtual ~CharacterCountsMafStatistics() {}
+
+ public:
+ std::string getShortName() const { return "Counts" + suffix_; }
+ std::string getFullName() const { return "Character counts (" + suffix_ + ")."; }
+ void compute(const MafBlock& block);
+ std::vector<std::string> getSupportedTags() const;
+};
+
+
+
/**
* @brief Compute the Site Frequency Spectrum of a maf block.
*
@@ -590,6 +613,10 @@ class FourSpeciesPatternCountsMafStatistics:
* Computed statistics include:
* - Number of sites without gaps
* - Number of complete sites (no gap, no unresolved)
+ * - Number of complete sites with only one state (constant sites)
+ * - Number of complete biallelic sites
+ * - Number of complete triallelic sites
+ * - Number of complete Quadriallelic sites
* - Number of parsimony informative sites
*/
class SiteMafStatistics:
@@ -656,6 +683,8 @@ class PolymorphismMafStatistics:
*
* - Number of segregating sites
* - Watterson's theta (per site)
+ * - Tajima's pi (average pairwise differences)
+ * - Tajima's D
*
* Only fully resolved sites are analyzed (no gap, no generic character).
*/
diff --git a/src/Bpp/Seq/Io/Maf/MaskFilterMafIterator.cpp b/src/Bpp/Seq/Io/Maf/MaskFilterMafIterator.cpp
index 0f1f02c..9a888bb 100644
--- a/src/Bpp/Seq/Io/Maf/MaskFilterMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/MaskFilterMafIterator.cpp
@@ -61,9 +61,11 @@ MafBlock* MaskFilterMafIterator::analyseCurrentBlock_() throw (Exception)
//Parse block.
vector< vector<bool> > aln;
for (size_t i = 0; i < species_.size(); ++i) {
- const MafSequence* seq = &block->getSequenceForSpecies(species_[i]);
- if (seq->hasAnnotation(SequenceMask::MASK)) {
- aln.push_back(dynamic_cast<const SequenceMask&>(seq->getAnnotation(SequenceMask::MASK)).getMask());
+ if (block->hasSequenceForSpecies(species_[i])) {
+ const MafSequence* seq = &block->getSequenceForSpecies(species_[i]);
+ if (seq->hasAnnotation(SequenceMask::MASK)) {
+ aln.push_back(dynamic_cast<const SequenceMask&>(seq->getAnnotation(SequenceMask::MASK)).getMask());
+ }
}
}
size_t nr = aln.size();
diff --git a/src/Bpp/Seq/Io/Maf/MsmcOutputMafIterator.cpp b/src/Bpp/Seq/Io/Maf/MsmcOutputMafIterator.cpp
new file mode 100644
index 0000000..d83ca70
--- /dev/null
+++ b/src/Bpp/Seq/Io/Maf/MsmcOutputMafIterator.cpp
@@ -0,0 +1,113 @@
+//
+// File: MsmcOutputMafIterator.cpp
+// Authors: Julien Dutheil
+// Created: Tue Jan 06 2015
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (2015)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "MsmcOutputMafIterator.h"
+
+//From bpp-seq:
+#include <Bpp/Seq/SequenceWithAnnotationTools.h>
+#include <Bpp/Seq/SequenceWithQuality.h>
+#include <Bpp/Seq/Container/VectorSiteContainer.h>
+#include <Bpp/Seq/SiteTools.h>
+#include <Bpp/Seq/SequenceWalker.h>
+
+using namespace bpp;
+
+//From the STL:
+#include <string>
+#include <numeric>
+#include <ctime>
+
+using namespace std;
+
+void MsmcOutputMafIterator::writeBlock_(std::ostream& out, const MafBlock& block)
+{
+ //Preliminary stuff...
+
+ VectorSiteContainer sites(&AlphabetTools::DNA_ALPHABET);
+ for (size_t i = 0; i < species_.size(); ++i) {
+ if (block.hasSequenceForSpecies(species_[i])) {
+ sites.addSequence(block.getSequenceForSpecies(species_[i]));
+ //Note: in case of duplicates, this takes the first sequence.
+ } else {
+ //Block with missing species are ignored.
+ return;
+ }
+ }
+ //Get the reference species for coordinates:
+ if (! block.hasSequenceForSpecies(refSpecies_))
+ return;
+ const MafSequence& refSeq = block.getSequenceForSpecies(refSpecies_);
+ string chr = refSeq.getChromosome();
+ if (chr != currentChr_) {
+ currentChr_ = chr;
+ nbOfCalledSites_ = 0; //Reset count of called sites.
+ lastPosition_ = 0;
+ } else {
+ //Check that block are ordered according to reference sequence:
+ if (refSeq.start() < lastPosition_)
+ throw Exception("MsmcOutputMafIterator: blocks are not projected according to reference sequence: " + refSeq.getDescription() + "<!>" + TextTools::toString(lastPosition_) + ".");
+ lastPosition_ = refSeq.stop();
+ }
+
+ SequenceWalker walker(refSeq);
+ size_t offset = refSeq.start();
+ int gap = refSeq.getAlphabet()->getGapCharacterCode();
+
+ //Now we shall scan all sites for SNPs:
+ for (size_t i = 0; i < sites.getNumberOfSites(); i++) {
+ if (refSeq[i] == gap)
+ continue;
+
+ //We call SNPs only at position without gap or unresolved characters:
+ if (SiteTools::isComplete(sites.getSite(i))) {
+ nbOfCalledSites_++;
+
+ if (!SiteTools::isConstant(sites.getSite(i))) {
+ string pos = "NA";
+ if (refSeq[i] != gap) {
+ pos = TextTools::toString(offset + walker.getSequencePosition(i) + 1);
+ }
+ out << chr << "\t" << pos << "\t" << nbOfCalledSites_ << "\t" << sites.getSite(i).toString() << endl;
+ //Reset number of called sites
+ nbOfCalledSites_ = 0;
+ }
+ }
+ }
+}
+
diff --git a/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h b/src/Bpp/Seq/Io/Maf/MsmcOutputMafIterator.h
similarity index 56%
copy from src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h
copy to src/Bpp/Seq/Io/Maf/MsmcOutputMafIterator.h
index 572ebbe..eb5cd52 100644
--- a/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/MsmcOutputMafIterator.h
@@ -1,11 +1,11 @@
//
-// File: VcfOutputMafIterator.h
+// File: MsmcOutputMafIterator.h
// Authors: Julien Dutheil
-// Created: Tue Jan 05 2013
+// Created: Tue Jan 06 2015
//
/*
-Copyright or © or Copr. Bio++ Development Team, (2010)
+Copyright or © or Copr. Bio++ Development Team, (2015)
This software is a computer program whose purpose is to provide classes
for sequences analysis.
@@ -37,8 +37,8 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/
-#ifndef _VCFOUTPUTMAFITERATOR_H_
-#define _VCFOUTPUTMAFITERATOR_H_
+#ifndef _MSMCOUTPUTMAFITERATOR_H_
+#define _MSMCOUTPUTMAFITERATOR_H_
#include "MafIterator.h"
@@ -50,47 +50,61 @@ knowledge of the CeCILL license and that you accept its terms.
namespace bpp {
/**
- * @brief This iterator performs a simple SNP call from the MAF blocks, and outputs the results in the Variant Call Format (VCF).
+ * @brief This iterator outputs all SNPs in the format readable by MSMC
*
- * Only substitutions are supported for now.
+ * See https://github.com/stschiff/msmc for a format description.
*/
-class VcfOutputMafIterator:
+class MsmcOutputMafIterator:
public AbstractFilterMafIterator
{
private:
std::ostream* output_;
+ std::vector<std::string> species_;
std::string refSpecies_;
- std::vector<std::string> genotypes_;
+ std::string currentChr_;
+ size_t lastPosition_;
+ unsigned int nbOfCalledSites_;
public:
/**
- * @brief Build a new VcfOutputMafIterator object.
+ * @brief Build a new MsmcOutputMafIterator object.
*
* @param iterator The input iterator.
- * @param out The output stream where to write the VCF file.
- * @param reference The species to use as a reference.
- * @param genotypes A list of species for which genotype information should be written in the VCF file. There will be one extra column per genotype, +1 format column.
+ * @param out The output stream where to write the MSMC file.
+ * @param species A list of at least two species to compute SNPs.
+ * Only blocks containing at least these two species will be used.
+ * In case one species is duplicated in a block, the first sequence will be used.
+ * @param reference The species to use as a reference for coordinates.
+ * It does not have to be one of the selected species on which SNPs are computed.
*/
- VcfOutputMafIterator(MafIterator* iterator, std::ostream* out, const std::string& reference, const std::vector<std::string>& genotypes) :
- AbstractFilterMafIterator(iterator), output_(out), refSpecies_(reference), genotypes_(genotypes)
- {
- if (output_)
- writeHeader_(*output_);
- }
+ MsmcOutputMafIterator(MafIterator* iterator,
+ std::ostream* out,
+ const std::vector<std::string>& species,
+ const std::string& reference) :
+ AbstractFilterMafIterator(iterator),
+ output_(out), species_(species), refSpecies_(reference),
+ currentChr_(""), lastPosition_(0), nbOfCalledSites_(0)
+ {}
private:
- VcfOutputMafIterator(const VcfOutputMafIterator& iterator) :
+ MsmcOutputMafIterator(const MsmcOutputMafIterator& iterator) :
AbstractFilterMafIterator(0),
output_(iterator.output_),
+ species_(iterator.species_),
refSpecies_(iterator.refSpecies_),
- genotypes_(iterator.genotypes_)
+ currentChr_(iterator.currentChr_),
+ lastPosition_(iterator.lastPosition_),
+ nbOfCalledSites_(iterator.nbOfCalledSites_)
{}
- VcfOutputMafIterator& operator=(const VcfOutputMafIterator& iterator)
+ MsmcOutputMafIterator& operator=(const MsmcOutputMafIterator& iterator)
{
output_ = iterator.output_;
+ species_ = iterator.species_;
refSpecies_ = iterator.refSpecies_;
- genotypes_ = iterator.genotypes_;
+ currentChr_ = iterator.currentChr_;
+ lastPosition_ = iterator.lastPosition_;
+ nbOfCalledSites_ = iterator.nbOfCalledSites_;
return *this;
}
@@ -104,10 +118,9 @@ class VcfOutputMafIterator:
}
private:
- void writeHeader_(std::ostream& out) const;
- void writeBlock_(std::ostream& out, const MafBlock& block) const;
+ void writeBlock_(std::ostream& out, const MafBlock& block);
};
} // end of namespace bpp.
-#endif //_VCFOUTPUTMAFITERATOR_H_
+#endif //_MSMCOUTPUTMAFITERATOR_H_
diff --git a/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp b/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp
index a8c4228..44a3a4c 100644
--- a/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp
@@ -57,9 +57,22 @@ MafBlock* OutputAlignmentMafIterator::analyseCurrentBlock_() throw (Exception)
if (output_) {
writeBlock(*output_, *block);
} else {
+ string chr = "ChrNA";
+ string start = "StartNA";
+ string stop = "StopNA";
+ if (block->hasSequenceForSpecies(refSpecies_)) {
+ const MafSequence& refseq = block->getSequenceForSpecies(refSpecies_);
+ chr = refseq.getChromosome();
+ start = TextTools::toString(refseq.start());
+ stop = TextTools::toString(refseq.stop());
+ }
string file = file_;
TextTools::replaceAll(file, "%i", TextTools::toString(++currentBlockIndex_));
+ TextTools::replaceAll(file, "%c", chr);
+ TextTools::replaceAll(file, "%b", start);
+ TextTools::replaceAll(file, "%e", stop);
std::ofstream output(file.c_str(), ios::out);
+
writeBlock(output, *block);
}
}
@@ -69,18 +82,21 @@ MafBlock* OutputAlignmentMafIterator::analyseCurrentBlock_() throw (Exception)
void OutputAlignmentMafIterator::writeBlock(std::ostream& out, const MafBlock& block) const {
//First get alignment:
AlignedSequenceContainer aln(&AlphabetTools::DNA_ALPHABET);
- //We cannot copy directly the container because we want to convert from MafSequence to BasicSequence (needed for renaiming):
+ //We cannot copy directly the container because we want to convert from MafSequence to BasicSequence (needed for renaming):
SequenceContainerTools::convertContainer<AlignedSequenceContainer, AlignedSequenceContainer, BasicSequence>(block.getAlignment(), aln);
//Format sequence names:
vector<string> names(aln.getNumberOfSequences());
for (size_t i = 0; i < aln.getNumberOfSequences(); ++i) {
const MafSequence& mafseq = block.getSequence(i);
- if (mafseq.hasCoordinates())
+ cout << mafseq.getSpecies() << "\t" << mafseq.getChromosome() << endl;
+ if (mafseq.hasCoordinates() && outputCoordinates_)
names[i] = mafseq.getSpecies() + "-" + mafseq.getChromosome() + "(" + mafseq.getStrand() + ")/" + TextTools::toString(mafseq.start() + 1) + "-" + TextTools::toString(mafseq.stop() + 1);
else
names[i] = mafseq.getSpecies();
}
aln.setSequencesNames(names);
+ if (addLDHatHeader_)
+ out << aln.getNumberOfSequences() << " " << aln.getNumberOfSites() << " 1" << endl; //We here assume sequences are haploid.
writer_->writeAlignment(out, aln);
}
diff --git a/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h b/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h
index 2954665..9ab34c7 100644
--- a/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h
@@ -63,8 +63,11 @@ class OutputAlignmentMafIterator:
std::ostream* output_;
std::string file_;
bool mask_;
- std::auto_ptr<OAlignment> writer_;
+ bool outputCoordinates_;
+ bool addLDHatHeader_;
+ std::unique_ptr<OAlignment> writer_;
unsigned int currentBlockIndex_;
+ std::string refSpecies_;
public:
/**
@@ -77,9 +80,28 @@ class OutputAlignmentMafIterator:
* @param writer A pointer toward an alignment writer object which specifies the format to use when writing sequences.
* The underlying object will be own by this instance, and destroyed when this object is deleted.
* @param mask Tell if sequences should be printed masked (if applicable).
+ * @param outputCoordinates Tell if coordinates should be written in sequence headers, if any.
+ * @param addLDHatHeader Tell if first line of file should contain number and lenght of sequences (for instance for use with LDhat/convert).
+ * @param reference [optional] specify a reference species which can be used to configure file names
+ * (for instance using coordinates information).
*/
- OutputAlignmentMafIterator(MafIterator* iterator, std::ostream* out, OAlignment* writer, bool mask = true) :
- AbstractFilterMafIterator(iterator), output_(out), file_(), mask_(mask), writer_(writer), currentBlockIndex_(0)
+ OutputAlignmentMafIterator(
+ MafIterator* iterator,
+ std::ostream* out,
+ OAlignment* writer,
+ bool mask = true,
+ bool outputCoordinates = true,
+ bool addLDHatHeader = false,
+ const std::string& reference = "") :
+ AbstractFilterMafIterator(iterator),
+ output_(out),
+ file_(),
+ mask_(mask),
+ outputCoordinates_(outputCoordinates),
+ addLDHatHeader_(addLDHatHeader),
+ writer_(writer),
+ currentBlockIndex_(0),
+ refSpecies_(reference)
{
if (!writer)
throw Exception("OutputAlignmentMafIterator (constructor 1): sequence writer should not be a NULL pointer!");
@@ -96,9 +118,28 @@ class OutputAlignmentMafIterator:
* @param writer A pointer toward an alignment writer object which specifies the format to use when writing sequences.
* The underlying object will be own by this instance, and destroyed when this object is deleted.
* @param mask Tell if sequences should be printed masked (if applicable).
+ * @param outputCoordinates Tell if coordinates should be written in sequence headers, if any.
+ * @param addLDHatHeader Tell if first line of file should contain number and lenght of sequences (for instance for use with LDhat/convert).
+ * @param reference [optional] specify a reference species which can be used to configure file names
+ * (for instance using coordinates information).
*/
- OutputAlignmentMafIterator(MafIterator* iterator, const std::string& file, OAlignment* writer, bool mask = true) :
- AbstractFilterMafIterator(iterator), output_(0), file_(file), mask_(mask), writer_(writer), currentBlockIndex_(0)
+ OutputAlignmentMafIterator(
+ MafIterator* iterator,
+ const std::string& file,
+ OAlignment* writer,
+ bool mask = true,
+ bool outputCoordinates = true,
+ bool addLDHatHeader = false,
+ const std::string& reference = "") :
+ AbstractFilterMafIterator(iterator),
+ output_(0),
+ file_(file),
+ mask_(mask),
+ outputCoordinates_(outputCoordinates),
+ addLDHatHeader_(addLDHatHeader),
+ writer_(writer),
+ currentBlockIndex_(0),
+ refSpecies_(reference)
{
if (!writer)
throw Exception("OutputAlignmentMafIterator (constructor 2): sequence writer should not be a NULL pointer!");
@@ -112,8 +153,11 @@ class OutputAlignmentMafIterator:
output_(iterator.output_),
file_(iterator.file_),
mask_(iterator.mask_),
+ outputCoordinates_(iterator.outputCoordinates_),
+ addLDHatHeader_(iterator.addLDHatHeader_),
writer_(),
- currentBlockIndex_(iterator.currentBlockIndex_)
+ currentBlockIndex_(iterator.currentBlockIndex_),
+ refSpecies_(iterator.refSpecies_)
{}
OutputAlignmentMafIterator& operator=(const OutputAlignmentMafIterator& iterator)
@@ -121,8 +165,11 @@ class OutputAlignmentMafIterator:
output_ = iterator.output_;
file_ = iterator.file_;
mask_ = iterator.mask_;
+ outputCoordinates_ = iterator.outputCoordinates_;
+ addLDHatHeader_ = iterator.addLDHatHeader_;
writer_.release();
currentBlockIndex_ = iterator.currentBlockIndex_;
+ refSpecies_ = iterator.refSpecies_;
return *this;
}
diff --git a/src/Bpp/Seq/Io/Maf/OutputMafIterator.cpp b/src/Bpp/Seq/Io/Maf/OutputMafIterator.cpp
index 6c9d305..07b8d41 100644
--- a/src/Bpp/Seq/Io/Maf/OutputMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/OutputMafIterator.cpp
@@ -60,7 +60,7 @@ void OutputMafIterator::writeHeader(std::ostream& out) const
void OutputMafIterator::writeBlock(std::ostream& out, const MafBlock& block) const
{
out << "a";
- if (! isinf(block.getScore()))
+ if (! std::isinf(block.getScore()))
out << " score=" << block.getScore();
if (block.getPass() > 0)
out << " pass=" << block.getPass();
diff --git a/src/Bpp/Seq/Io/Maf/PlinkOutputMafIterator.cpp b/src/Bpp/Seq/Io/Maf/PlinkOutputMafIterator.cpp
new file mode 100644
index 0000000..9e0d51f
--- /dev/null
+++ b/src/Bpp/Seq/Io/Maf/PlinkOutputMafIterator.cpp
@@ -0,0 +1,124 @@
+//
+// File: PlinkOutputMafIterator.cpp
+// Authors: Julien Dutheil
+// Created: Tue Dec 10 2015
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (2015)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "PlinkOutputMafIterator.h"
+
+//From bpp-seq:
+#include <Bpp/Seq/SequenceWithAnnotationTools.h>
+#include <Bpp/Seq/Container/VectorSiteContainer.h>
+#include <Bpp/Seq/SiteTools.h>
+#include <Bpp/Seq/SequenceWalker.h>
+
+using namespace bpp;
+
+//From the STL:
+#include <string>
+#include <numeric>
+#include <ctime>
+
+using namespace std;
+
+void PlinkOutputMafIterator::init_() {
+ for (size_t i = 0; i < species_.size(); ++i) {
+ ped_[i] = "FAM001\t" + TextTools::toString(i + 1) + "\t0\t0\t0\t0";
+ }
+}
+
+
+void PlinkOutputMafIterator::parseBlock_(std::ostream& out, const MafBlock& block)
+{
+ //Preliminary stuff...
+ VectorSiteContainer sites(&AlphabetTools::DNA_ALPHABET);
+ for (size_t i = 0; i < species_.size(); ++i) {
+ if (block.hasSequenceForSpecies(species_[i])) {
+ sites.addSequence(block.getSequenceForSpecies(species_[i]));
+ //Note: in case of duplicates, this takes the first sequence.
+ } else {
+ //Block with missing species are ignored.
+ return;
+ }
+ }
+ //Get the reference species for coordinates:
+ if (! block.hasSequenceForSpecies(refSpecies_))
+ return;
+ const MafSequence& refSeq = block.getSequenceForSpecies(refSpecies_);
+ string chr = refSeq.getChromosome();
+ if (chr != currentChr_) {
+ currentChr_ = chr;
+ lastPosition_ = 0;
+ } else {
+ //Check that block are ordered according to reference sequence:
+ if (refSeq.start() < lastPosition_)
+ throw Exception("MsmcOutputMafIterator: blocks are not projected according to reference sequence: " + refSeq.getDescription() + "<!>" + TextTools::toString(lastPosition_) + ".");
+ lastPosition_ = refSeq.stop();
+ }
+
+ SequenceWalker walker(refSeq);
+ size_t offset = refSeq.start();
+ int gap = refSeq.getAlphabet()->getGapCharacterCode();
+
+ //Now we shall scan all sites for SNPs:
+ for (size_t i = 0; i < sites.getNumberOfSites(); i++) {
+ if (refSeq[i] == gap)
+ continue;
+
+ //We call SNPs only at position without gap or unresolved characters, and for biallelic sites:
+ if (SiteTools::isComplete(sites.getSite(i)) && SiteTools::getNumberOfDistinctCharacters(sites.getSite(i)) == 2) {
+ string pos = "NA";
+ if (refSeq[i] != gap) {
+ pos = TextTools::toString(offset + walker.getSequencePosition(i) + 1);
+ }
+ string alleles = sites.getSite(i).toString();
+ for (size_t j = 0; j < alleles.size(); ++j) {
+ ped_[j] += "\t" + TextTools::toString(alleles[j]) + " " + alleles[j];
+ }
+ // SNP identifier are built as <chr>.<pos>
+ out << chr << "\t" << chr << "." << pos << "\t";
+ if (!map3_)
+ out << "0\t"; //Add null genetic distance
+ out << pos << endl;
+ }
+ }
+}
+
+void PlinkOutputMafIterator::writePedToFile_(ostream& out) {
+ for (size_t i = 0; i < ped_.size(); ++i)
+ out << ped_[i] << endl;
+}
+
diff --git a/src/Bpp/Seq/Io/Maf/PlinkOutputMafIterator.h b/src/Bpp/Seq/Io/Maf/PlinkOutputMafIterator.h
new file mode 100644
index 0000000..a2be2bf
--- /dev/null
+++ b/src/Bpp/Seq/Io/Maf/PlinkOutputMafIterator.h
@@ -0,0 +1,144 @@
+//
+// File: PlinkOutputMafIterator.h
+// Authors: Julien Dutheil
+// Created: Tue Dec 10 2015
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (2015)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _PLINKOUTPUTMAFITERATOR_H_
+#define _PLINKOUTPUTMAFITERATOR_H_
+
+#include "MafIterator.h"
+
+//From the STL:
+#include <iostream>
+#include <string>
+#include <deque>
+
+namespace bpp {
+
+/**
+ * @brief This iterator outputs all biallelic SNPs in the PLINK format (ped and map files).
+ */
+class PlinkOutputMafIterator:
+ public AbstractFilterMafIterator
+{
+ private:
+ std::ostream* outputPed_;
+ std::ostream* outputMap_;
+ std::vector<std::string> species_;
+ std::string refSpecies_;
+ bool map3_;
+ std::vector<std::string> ped_;
+ std::string currentChr_;
+ size_t lastPosition_;
+
+ public:
+ /**
+ * @brief Build a new PlinkOutputMafIterator object.
+ *
+ * @warning In the current implementation, there is no way to deal with diploid individuals.
+ * Each sequence is therefore considered as a haploid genome and will be written has a homozygous SNP
+ * in the Ped file.
+ *
+ * @param iterator The input iterator.
+ * @param outPed The output stream where to write the Ped file.
+ * @param outMap The output stream where to write the Map file.
+ * @param species A list of at least two species to compute SNPs.
+ * Only blocks containing at least these two species will be used.
+ * In case one species is duplicated in a block, the first sequence will be used.
+ * @param reference The species to use as a reference for coordinates.
+ * It does not have to be one of the selected species on which SNPs are computed.
+ * @param map3 Tell if genetic distance column should be ommited in the map file. Otherwise set to 0.
+ */
+ PlinkOutputMafIterator(MafIterator* iterator,
+ std::ostream* outPed,
+ std::ostream* outMap,
+ const std::vector<std::string>& species,
+ const std::string& reference,
+ bool map3 = false) :
+ AbstractFilterMafIterator(iterator),
+ outputPed_(outPed), outputMap_(outMap), species_(species), refSpecies_(reference), map3_(map3),
+ ped_(species.size()), currentChr_(""), lastPosition_(0)
+ {
+ init_();
+ }
+
+ private:
+ PlinkOutputMafIterator(const PlinkOutputMafIterator& iterator) :
+ AbstractFilterMafIterator(0),
+ outputPed_(iterator.outputPed_),
+ outputMap_(iterator.outputMap_),
+ species_(iterator.species_),
+ refSpecies_(iterator.refSpecies_),
+ map3_(iterator.map3_),
+ ped_(iterator.ped_),
+ currentChr_(iterator.currentChr_),
+ lastPosition_(iterator.lastPosition_)
+ {}
+
+ PlinkOutputMafIterator& operator=(const PlinkOutputMafIterator& iterator)
+ {
+ outputPed_ = iterator.outputPed_;
+ outputMap_ = iterator.outputMap_;
+ species_ = iterator.species_;
+ refSpecies_ = iterator.refSpecies_;
+ map3_ = iterator.map3_;
+ ped_ = iterator.ped_;
+ currentChr_ = iterator.currentChr_;
+ lastPosition_ = iterator.lastPosition_;
+ return *this;
+ }
+
+
+ public:
+ MafBlock* analyseCurrentBlock_() throw (Exception) {
+ currentBlock_ = iterator_->nextBlock();
+ if (outputMap_ && currentBlock_)
+ parseBlock_(*outputMap_, *currentBlock_);
+ if (outputMap_ && outputPed_ && !currentBlock_)
+ writePedToFile_(*outputPed_); //Note we currently can output Map and no Ped, but not Ped without Map.
+ return currentBlock_;
+ }
+
+ private:
+ void init_();
+ void parseBlock_(std::ostream& out, const MafBlock& block);
+ void writePedToFile_(std::ostream& out);
+};
+
+} // end of namespace bpp.
+
+#endif //_PLINKOUTPUTMAFITERATOR_H_
diff --git a/src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.cpp b/src/Bpp/Seq/Io/Maf/RemoveEmptySequencesMafIterator.cpp
similarity index 62%
copy from src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.cpp
copy to src/Bpp/Seq/Io/Maf/RemoveEmptySequencesMafIterator.cpp
index 305a60f..3475dd8 100644
--- a/src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/RemoveEmptySequencesMafIterator.cpp
@@ -1,7 +1,7 @@
//
-// File: CoordinatesOutputMafIterator.cpp
+// File: RemoveEmptySequencesMafIterator.cpp
// Authors: Julien Dutheil
-// Created: Mon Jun 02 2014
+// Created: Tue Apr 26 2016
//
/*
@@ -37,37 +37,31 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/
-#include "CoordinatesOutputMafIterator.h"
+#include "RemoveEmptySequencesMafIterator.h"
using namespace bpp;
using namespace std;
-void CoordinatesOutputMafIterator::writeHeader_(ostream& out) const
-{
- for (size_t i = 0; i < species_.size(); ++i) {
- if (i > 0) out << "\t";
- string sp = species_[i];
- out << sp << ".chr\t" << sp << ".strand\t" << sp << ".start\t" << sp << ".stop";
- }
- out << endl;
-}
-
-MafBlock* CoordinatesOutputMafIterator::analyseCurrentBlock_() throw (Exception)
+MafBlock* RemoveEmptySequencesMafIterator::analyseCurrentBlock_() throw (Exception)
{
currentBlock_ = iterator_->nextBlock();
if (currentBlock_) {
- for (size_t i = 0; i < species_.size(); ++i) {
- if (i > 0) *output_ << "\t";
- vector<const MafSequence*> seqs = currentBlock_->getSequencesForSpecies(species_[i]);
- if (seqs.size() > 1)
- throw Exception("CoordinatesOutputMafIterator::analyseCurrentBlock_(). There is more than one sequence for species '" + species_[i] + "' in current block.");
- else if (seqs.size() == 0) {
- *output_ << "NA\tNA\tNA\tNA";
+ for (size_t i = currentBlock_->getNumberOfSequences(); i > 0; --i) {
+ const MafSequence& seq = currentBlock_->getSequence(i - 1);
+ bool isEmpty = true;
+ if (unresolvedAsGaps_) {
+ for (size_t j = 0; isEmpty && j < currentBlock_->getNumberOfSites(); ++j) {
+ if (!AlphabetTools::DNA_ALPHABET.isUnresolved(seq[j]) && !AlphabetTools::DNA_ALPHABET.isGap(seq[j])) isEmpty = false;
+ }
} else {
- *output_ << seqs[0]->getChromosome() << "\t" << seqs[0]->getStrand() << "\t" << seqs[0]->start() << "\t" << seqs[0]->stop();
+ for (size_t j = 0; isEmpty && j < currentBlock_->getNumberOfSites(); ++j) {
+ if (!AlphabetTools::DNA_ALPHABET.isGap(seq[j])) isEmpty = false;
+ }
+ }
+ if (isEmpty) {
+ currentBlock_->getAlignment().deleteSequence(i - 1);
}
}
- *output_ << endl;
}
return currentBlock_;
}
diff --git a/src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.h b/src/Bpp/Seq/Io/Maf/RemoveEmptySequencesMafIterator.h
similarity index 60%
copy from src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.h
copy to src/Bpp/Seq/Io/Maf/RemoveEmptySequencesMafIterator.h
index bce9a87..0dbdd95 100644
--- a/src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/RemoveEmptySequencesMafIterator.h
@@ -1,11 +1,11 @@
//
-// File: WindowSplitMafIterator.h
+// File: RemoveEmptySequencesMafIterator.h
// Authors: Julien Dutheil
-// Created: Tue Sep 07 2010
+// Created: Tue Apr 26 2016
//
/*
-Copyright or © or Copr. Bio++ Development Team, (2010)
+Copyright or © or Copr. Bio++ Development Team, (2014)
This software is a computer program whose purpose is to provide classes
for sequences analysis.
@@ -37,43 +37,47 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/
-#ifndef _WINDOWSPLITMAFITERATOR_H_
-#define _WINDOWSPLITMAFITERATOR_H_
+#ifndef _REMOVEEMPTYSEQUENCESMAFITERATOR_H_
+#define _REMOVEEMPTYSEQUENCESMAFITERATOR_H_
#include "MafIterator.h"
//From the STL:
#include <iostream>
#include <string>
-#include <deque>
namespace bpp {
/**
- * @brief Splits block into windows of given sizes.
+ * @brief Remove ga-only or unresolved and gap-only sequences in each block.
*/
-class WindowSplitMafIterator:
+class RemoveEmptySequencesMafIterator:
public AbstractFilterMafIterator
{
private:
- unsigned int windowSize_;
- short align_;
- std::deque<MafBlock*> blockBuffer_;
+ bool unresolvedAsGaps_;
public:
- static const short RAGGED_LEFT;
- static const short RAGGED_RIGHT;
- static const short CENTER;
- static const short ADJUST;
+ /**
+ * @brief Creates a new RemoveEmptySequencesMafIterator object.
+ *
+ * @param iterator The input iterator.
+ * @param unresolvedAsGaps Tell if unresolved characters (e.g. 'N') should be treated as gaps.
+ */
+ RemoveEmptySequencesMafIterator(MafIterator* iterator, bool unresolvedAsGaps = false):
+ AbstractFilterMafIterator(iterator), unresolvedAsGaps_(unresolvedAsGaps)
+ {}
- public:
- WindowSplitMafIterator(MafIterator* iterator, unsigned int windowSize, short splitOption = CENTER) throw (Exception):
- AbstractFilterMafIterator(iterator),
- windowSize_(windowSize), align_(splitOption), blockBuffer_()
+ private:
+ RemoveEmptySequencesMafIterator(const RemoveEmptySequencesMafIterator& iterator) :
+ AbstractFilterMafIterator(nullptr),
+ unresolvedAsGaps_(iterator.unresolvedAsGaps_)
+ {}
+
+ RemoveEmptySequencesMafIterator& operator=(const RemoveEmptySequencesMafIterator& iterator)
{
- if (splitOption != RAGGED_LEFT && splitOption != RAGGED_RIGHT
- && splitOption != CENTER && splitOption != ADJUST)
- throw Exception("WindowSplitMafIterator: unvalid split option: " + TextTools::toString(splitOption));
+ unresolvedAsGaps_ = iterator.unresolvedAsGaps_;
+ return *this;
}
private:
@@ -83,4 +87,4 @@ class WindowSplitMafIterator:
} // end of namespace bpp.
-#endif //_WINDOWSPLITMAFITERATOR_H_
+#endif //_REMOVEEMPTYSEQUENCESMAFITERATOR_H_
diff --git a/src/Bpp/Seq/Io/Maf/SequenceLDhotOutputMafIterator.cpp b/src/Bpp/Seq/Io/Maf/SequenceLDhotOutputMafIterator.cpp
new file mode 100644
index 0000000..5ae70c6
--- /dev/null
+++ b/src/Bpp/Seq/Io/Maf/SequenceLDhotOutputMafIterator.cpp
@@ -0,0 +1,139 @@
+//
+// File: OutputSequenceLDHotMafIterator.cpp
+// Authors: Julien Dutheil
+// Created: Thr May 12 2016
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (2016)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "SequenceLDhotOutputMafIterator.h"
+
+//From bpp-seq:
+#include <Bpp/Seq/Container/SequenceContainerTools.h>
+#include <Bpp/Seq/Container/VectorSiteContainer.h>
+#include <Bpp/Seq/SiteTools.h>
+
+using namespace bpp;
+
+//From the STL:
+#include <string>
+#include <numeric>
+
+using namespace std;
+
+MafBlock* SequenceLDhotOutputMafIterator::analyseCurrentBlock_() throw (Exception)
+{
+ MafBlock* block = iterator_->nextBlock();
+ if (block) {
+ string chr = "ChrNA";
+ string start = "StartNA";
+ string stop = "StopNA";
+ if (block->hasSequenceForSpecies(refSpecies_)) {
+ const MafSequence& refseq = block->getSequenceForSpecies(refSpecies_);
+ chr = refseq.getChromosome();
+ start = TextTools::toString(refseq.start());
+ stop = TextTools::toString(refseq.stop());
+ }
+ string file = file_;
+ TextTools::replaceAll(file, "%i", TextTools::toString(++currentBlockIndex_));
+ TextTools::replaceAll(file, "%c", chr);
+ TextTools::replaceAll(file, "%b", start);
+ TextTools::replaceAll(file, "%e", stop);
+ std::ofstream output(file.c_str(), ios::out);
+ writeBlock(output, *block);
+ }
+ return block;
+}
+
+void SequenceLDhotOutputMafIterator::writeBlock(std::ostream& out, const MafBlock& block) const {
+ //First get alignment:
+ const SiteContainer& aln = block.getAlignment();
+ unique_ptr<VectorSiteContainer> variableSites(new VectorSiteContainer(aln.getSequencesNames(), &AlphabetTools::DNA_ALPHABET));
+
+ //We first preparse the data:
+ //We assume all sequences are distinct:
+ size_t nbDistinct = aln.getNumberOfSequences();
+ size_t nbGenes = aln.getNumberOfSequences();
+ size_t nbLoci = 0;
+
+ string positions = "";
+ for (size_t i = 0; i < aln.getNumberOfSites(); ++i) {
+ const Site& s = aln.getSite(i);
+ if (completeOnly_ && !SiteTools::isComplete(s)) {
+ continue;
+ }
+ unsigned int count = 0;
+ int x = -1;
+ for (size_t j = 0; j < s.size() && count < 2; ++j) {
+ if (!AlphabetTools::DNA_ALPHABET.isGap(s[j]) && !AlphabetTools::DNA_ALPHABET.isUnresolved(s[j])) {
+ if (count == 0) {
+ //First state found
+ count++;
+ //We record the state
+ x = s[j];
+ } else {
+ if (s[j] != x) {
+ //New state found
+ count++;
+ }
+ //Otherwise, same state as before.
+ }
+ }
+ }
+ if (count == 2) {
+ //At least two alleles (non-gap, non-unresolved) found in this position, so we record it
+ positions += " " + TextTools::toString(i + 1);
+ nbLoci++;
+ variableSites->addSite(aln.getSite(i));
+ }
+ }
+
+ //Write header:
+ out << "Distinct = " << nbDistinct << endl;
+ out << "Genes = " << nbGenes << endl;
+ out << "Loci = " << nbLoci << endl;
+ out << "K = -4 %4-allele model with Haplotype Alleles specified by A,C,G,T" << endl;
+
+ out << "Positions of loci:" << endl;
+ out << positions << endl;
+
+ out << "Haplotypes" << endl;
+
+ for (size_t i = 0; i < aln.getNumberOfSequences(); ++i) {
+ out << variableSites->getSequence(i).toString() << " 1" << endl;
+ }
+
+ out << "#" << endl;
+}
+
diff --git a/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h b/src/Bpp/Seq/Io/Maf/SequenceLDhotOutputMafIterator.h
similarity index 50%
copy from src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h
copy to src/Bpp/Seq/Io/Maf/SequenceLDhotOutputMafIterator.h
index 572ebbe..b21fce2 100644
--- a/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/SequenceLDhotOutputMafIterator.h
@@ -1,7 +1,7 @@
//
-// File: VcfOutputMafIterator.h
+// File: SequenceLDhotOutputMafIterator.h
// Authors: Julien Dutheil
-// Created: Tue Jan 05 2013
+// Created: Thr May 12 2016
//
/*
@@ -37,11 +37,14 @@ The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/
-#ifndef _VCFOUTPUTMAFITERATOR_H_
-#define _VCFOUTPUTMAFITERATOR_H_
+#ifndef _SEQUENCELDHOTOUTPUTMAFITERATOR_H_
+#define _SEQUENCELDHOTOUTPUTMAFITERATOR_H_
#include "MafIterator.h"
+//From bpp-seq:
+#include <Bpp/Seq/Io/OSequence.h>
+
//From the STL:
#include <iostream>
#include <string>
@@ -50,64 +53,69 @@ knowledge of the CeCILL license and that you accept its terms.
namespace bpp {
/**
- * @brief This iterator performs a simple SNP call from the MAF blocks, and outputs the results in the Variant Call Format (VCF).
- *
- * Only substitutions are supported for now.
+ * @brief This iterator forward the iterator given as input after having printed its content to an alignment file.
*/
-class VcfOutputMafIterator:
+class SequenceLDhotOutputMafIterator:
public AbstractFilterMafIterator
{
private:
- std::ostream* output_;
+ std::string file_;
std::string refSpecies_;
- std::vector<std::string> genotypes_;
+ unsigned int currentBlockIndex_;
+ bool completeOnly_;
public:
+
/**
- * @brief Build a new VcfOutputMafIterator object.
+ * @brief Creates a SequenceLDhotOutputMafIterator
*
- * @param iterator The input iterator.
- * @param out The output stream where to write the VCF file.
- * @param reference The species to use as a reference.
- * @param genotypes A list of species for which genotype information should be written in the VCF file. There will be one extra column per genotype, +1 format column.
+ * @param iterator The input iterator
+ * @param file A string describing the path to the output files. Each block will be written to a distinct file.
+ * @param completeOnly Only export complete sites (no gap, no unresolved character)
+ * If "file" is a fixed string, it will only contain the last block. Using the %i code in the file name allows to generate one file per block, %i denoting the block index.
+ * @param reference [optional] specify a reference species which can be used to configure file names
+ * (for instance using coordinates information).
*/
- VcfOutputMafIterator(MafIterator* iterator, std::ostream* out, const std::string& reference, const std::vector<std::string>& genotypes) :
- AbstractFilterMafIterator(iterator), output_(out), refSpecies_(reference), genotypes_(genotypes)
+ SequenceLDhotOutputMafIterator(
+ MafIterator* iterator,
+ const std::string& file,
+ bool completeOnly = true,
+ const std::string& reference = "") :
+ AbstractFilterMafIterator(iterator),
+ file_(file),
+ refSpecies_(reference),
+ currentBlockIndex_(0),
+ completeOnly_(completeOnly)
{
- if (output_)
- writeHeader_(*output_);
}
+ ~SequenceLDhotOutputMafIterator() {}
+
private:
- VcfOutputMafIterator(const VcfOutputMafIterator& iterator) :
+ SequenceLDhotOutputMafIterator(const SequenceLDhotOutputMafIterator& iterator) :
AbstractFilterMafIterator(0),
- output_(iterator.output_),
+ file_(iterator.file_),
refSpecies_(iterator.refSpecies_),
- genotypes_(iterator.genotypes_)
+ currentBlockIndex_(iterator.currentBlockIndex_),
+ completeOnly_(iterator.completeOnly_)
{}
- VcfOutputMafIterator& operator=(const VcfOutputMafIterator& iterator)
+ SequenceLDhotOutputMafIterator& operator=(const SequenceLDhotOutputMafIterator& iterator)
{
- output_ = iterator.output_;
+ file_ = iterator.file_;
refSpecies_ = iterator.refSpecies_;
- genotypes_ = iterator.genotypes_;
+ currentBlockIndex_ = iterator.currentBlockIndex_;
+ completeOnly_ = iterator.completeOnly_;
return *this;
}
- public:
- MafBlock* analyseCurrentBlock_() throw (Exception) {
- currentBlock_ = iterator_->nextBlock();
- if (output_ && currentBlock_)
- writeBlock_(*output_, *currentBlock_);
- return currentBlock_;
- }
-
private:
- void writeHeader_(std::ostream& out) const;
- void writeBlock_(std::ostream& out, const MafBlock& block) const;
+ MafBlock* analyseCurrentBlock_() throw (Exception);
+
+ void writeBlock(std::ostream& out, const MafBlock& block) const;
};
} // end of namespace bpp.
-#endif //_VCFOUTPUTMAFITERATOR_H_
+#endif //_SEQUENCEOUTPUTLDHOTMAFITERATOR_H_
diff --git a/src/Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.cpp b/src/Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.cpp
index 1c722dd..de5d50b 100644
--- a/src/Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.cpp
@@ -46,7 +46,7 @@ using namespace bpp;
MafBlock* SequenceStreamToMafIterator::analyseCurrentBlock_() throw (Exception)
{
- auto_ptr<MafBlock> block(new MafBlock());
+ unique_ptr<MafBlock> block(new MafBlock());
MafSequence mafSeq;
if (stream_->eof()) return 0;
diff --git a/src/Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.h b/src/Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.h
index b2c5cd5..51f25c9 100644
--- a/src/Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.h
@@ -61,7 +61,7 @@ class SequenceStreamToMafIterator:
public AbstractMafIterator
{
private:
- std::auto_ptr<ISequenceStream> seqStream_;
+ std::unique_ptr<ISequenceStream> seqStream_;
std::istream* stream_;
bool zeroBasedCoords_;
bool firstBlock_;
@@ -73,7 +73,7 @@ class SequenceStreamToMafIterator:
private:
//Recopy is forbidden!
SequenceStreamToMafIterator(const SequenceStreamToMafIterator& ss2mi):
- seqStream_(0), stream_(0), zeroBasedCoords_(ss2mi.zeroBasedCoords_), firstBlock_(ss2mi.firstBlock_) {}
+ seqStream_(), stream_(0), zeroBasedCoords_(ss2mi.zeroBasedCoords_), firstBlock_(ss2mi.firstBlock_) {}
SequenceStreamToMafIterator& operator=(const SequenceStreamToMafIterator& ss2mi) {
seqStream_.reset(); stream_ = 0; zeroBasedCoords_ = ss2mi.zeroBasedCoords_; firstBlock_ = ss2mi.firstBlock_;
return *this;
diff --git a/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp b/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp
index 54f8397..3b6af62 100644
--- a/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp
@@ -131,6 +131,9 @@ void VcfOutputMafIterator::writeBlock_(std::ostream& out, const MafBlock& block)
snps[x] = 0;
}
}
+ if (ac == "" && outputAll_) {
+ ac = TextTools::toString(counts[ref]);
+ }
if (ac != "") {
out << chr << "\t" << (offset + walker.getSequencePosition(i) + 1) << "\t.\t" << chars[refSeq[i]] << "\t" << alt << "\t.\t" << filter << "\tAC=" << ac;
//Write genotpyes:
diff --git a/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h b/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h
index 572ebbe..75e7873 100644
--- a/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h
@@ -61,6 +61,7 @@ class VcfOutputMafIterator:
std::ostream* output_;
std::string refSpecies_;
std::vector<std::string> genotypes_;
+ bool outputAll_;
public:
/**
@@ -70,9 +71,10 @@ class VcfOutputMafIterator:
* @param out The output stream where to write the VCF file.
* @param reference The species to use as a reference.
* @param genotypes A list of species for which genotype information should be written in the VCF file. There will be one extra column per genotype, +1 format column.
+ * @param outputAll If true, also output non-variable positions.
*/
- VcfOutputMafIterator(MafIterator* iterator, std::ostream* out, const std::string& reference, const std::vector<std::string>& genotypes) :
- AbstractFilterMafIterator(iterator), output_(out), refSpecies_(reference), genotypes_(genotypes)
+ VcfOutputMafIterator(MafIterator* iterator, std::ostream* out, const std::string& reference, const std::vector<std::string>& genotypes, bool outputAll = false) :
+ AbstractFilterMafIterator(iterator), output_(out), refSpecies_(reference), genotypes_(genotypes), outputAll_(outputAll)
{
if (output_)
writeHeader_(*output_);
@@ -83,7 +85,8 @@ class VcfOutputMafIterator:
AbstractFilterMafIterator(0),
output_(iterator.output_),
refSpecies_(iterator.refSpecies_),
- genotypes_(iterator.genotypes_)
+ genotypes_(iterator.genotypes_),
+ outputAll_(iterator.outputAll_)
{}
VcfOutputMafIterator& operator=(const VcfOutputMafIterator& iterator)
@@ -91,6 +94,7 @@ class VcfOutputMafIterator:
output_ = iterator.output_;
refSpecies_ = iterator.refSpecies_;
genotypes_ = iterator.genotypes_;
+ outputAll_ = iterator.outputAll_;
return *this;
}
diff --git a/src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.cpp b/src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.cpp
index b06536d..62c1c91 100644
--- a/src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.cpp
@@ -68,14 +68,13 @@ MafBlock* WindowSplitMafIterator::analyseCurrentBlock_() throw (Exception)
case (CENTER) : { pos = (bSize % windowSize_) / 2; break; }
case (ADJUST) : {
size_t x = bSize / windowSize_;
- if (x == 0) size = bSize;
- else size = bSize / x;
+ if (x > 0) size = bSize / x;
break;
}
default : { }
}
//cout << "Effective size: " << size << endl;
- for(size_t i = pos; i + size < bSize; i += size) {
+ for(size_t i = pos; i + size <= bSize; i += size) {
MafBlock* newBlock = new MafBlock();
newBlock->setScore(block->getScore());
newBlock->setPass(block->getPass());
@@ -87,13 +86,18 @@ MafBlock* WindowSplitMafIterator::analyseCurrentBlock_() throw (Exception)
//cout << " => new size: " << size << endl;
}
}
- for (unsigned int j = 0; j < block->getNumberOfSequences(); ++j) {
- auto_ptr<MafSequence> subseq(block->getSequence(j).subSequence(i, size));
+ for (size_t j = 0; j < block->getNumberOfSequences(); ++j) {
+ unique_ptr<MafSequence> subseq(block->getSequence(j).subSequence(i, size));
newBlock->addSequence(*subseq);
}
blockBuffer_.push_back(newBlock);
}
- delete block;
+
+ if (align_ == ADJUST && keepSmallBlocks_ && bSize < windowSize_) {
+ blockBuffer_.push_back(block);
+ } else {
+ delete block;
+ }
}
MafBlock* nxtBlock = blockBuffer_.front();
diff --git a/src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.h b/src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.h
index bce9a87..ed7ca2c 100644
--- a/src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.h
+++ b/src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.h
@@ -56,9 +56,10 @@ class WindowSplitMafIterator:
public AbstractFilterMafIterator
{
private:
- unsigned int windowSize_;
+ size_t windowSize_;
short align_;
std::deque<MafBlock*> blockBuffer_;
+ bool keepSmallBlocks_;
public:
static const short RAGGED_LEFT;
@@ -67,9 +68,9 @@ class WindowSplitMafIterator:
static const short ADJUST;
public:
- WindowSplitMafIterator(MafIterator* iterator, unsigned int windowSize, short splitOption = CENTER) throw (Exception):
+ WindowSplitMafIterator(MafIterator* iterator, size_t windowSize, short splitOption = CENTER, bool keepSmallBlocks = false) throw (Exception):
AbstractFilterMafIterator(iterator),
- windowSize_(windowSize), align_(splitOption), blockBuffer_()
+ windowSize_(windowSize), align_(splitOption), blockBuffer_(), keepSmallBlocks_(keepSmallBlocks)
{
if (splitOption != RAGGED_LEFT && splitOption != RAGGED_RIGHT
&& splitOption != CENTER && splitOption != ADJUST)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 084c00d..8621bd8 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,101 +1,85 @@
-# CMake script for Bio++ Sequence Library
-# Author: Sylvain Gaillard and Julien Dutheil
+# CMake script for Bio++ Sequence Omics Library
+# Authors:
+# Sylvain Gaillard
+# Julien Dutheil
+# Francois Gindraud (2017)
# Created: 30/07/2012
# File list
-SET(CPP_FILES
+set (CPP_FILES
+ Bpp/Seq/Feature/Bed/BedGraphFeatureReader.cpp
+ Bpp/Seq/Feature/Gff/GffFeatureReader.cpp
+ Bpp/Seq/Feature/Gtf/GtfFeatureReader.cpp
+ Bpp/Seq/Feature/SequenceFeature.cpp
+ Bpp/Seq/Feature/SequenceFeatureTools.cpp
Bpp/Seq/Io/Fastq.cpp
- Bpp/Seq/Io/Maf/MafParser.cpp
- Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.cpp
- Bpp/Seq/Io/Maf/MafIterator.cpp
- Bpp/Seq/Io/Maf/SequenceFilterMafIterator.cpp
- Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.cpp
- Bpp/Seq/Io/Maf/ChromosomeMafIterator.cpp
- Bpp/Seq/Io/Maf/DuplicateFilterMafIterator.cpp
+ Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp
+ Bpp/Seq/Io/Maf/ChromosomeMafIterator.cpp
Bpp/Seq/Io/Maf/ConcatenateMafIterator.cpp
- Bpp/Seq/Io/Maf/FullGapFilterMafIterator.cpp
- Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
+ Bpp/Seq/Io/Maf/CoordinateTranslatorMafIterator.cpp
+ Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.cpp
+ Bpp/Seq/Io/Maf/DuplicateFilterMafIterator.cpp
Bpp/Seq/Io/Maf/EntropyFilterMafIterator.cpp
- Bpp/Seq/Io/Maf/MaskFilterMafIterator.cpp
- Bpp/Seq/Io/Maf/QualityFilterMafIterator.cpp
- Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp
Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp
- Bpp/Seq/Io/Maf/OutputMafIterator.cpp
+ Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp
+ Bpp/Seq/Io/Maf/FullGapFilterMafIterator.cpp
+ Bpp/Seq/Io/Maf/IterationListener.cpp
+ Bpp/Seq/Io/Maf/MafIterator.cpp
+ Bpp/Seq/Io/Maf/MafParser.cpp
+ Bpp/Seq/Io/Maf/MafSequence.cpp
+ Bpp/Seq/Io/Maf/MafStatistics.cpp
+ Bpp/Seq/Io/Maf/MaskFilterMafIterator.cpp
+ Bpp/Seq/Io/Maf/MsmcOutputMafIterator.cpp
+ Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.cpp
Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp
- Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp
- Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.cpp
+ Bpp/Seq/Io/Maf/OutputMafIterator.cpp
+ Bpp/Seq/Io/Maf/PlinkOutputMafIterator.cpp
+ Bpp/Seq/Io/Maf/QualityFilterMafIterator.cpp
+ Bpp/Seq/Io/Maf/RemoveEmptySequencesMafIterator.cpp
+ Bpp/Seq/Io/Maf/SequenceFilterMafIterator.cpp
+ Bpp/Seq/Io/Maf/SequenceLDhotOutputMafIterator.cpp
Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.cpp
+ Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.cpp
+ Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp
Bpp/Seq/Io/Maf/WindowSplitMafIterator.cpp
- Bpp/Seq/Io/Maf/MafSequence.cpp
- Bpp/Seq/Io/Maf/MafStatistics.cpp
- Bpp/Seq/Io/Maf/IterationListener.cpp
- Bpp/Seq/Feature/SequenceFeature.cpp
- Bpp/Seq/Feature/SequenceFeatureTools.cpp
- Bpp/Seq/Feature/Gff/GffFeatureReader.cpp
- Bpp/Seq/Feature/Gtf/GtfFeatureReader.cpp
- )
-
-SET(H_FILES
- Bpp/Seq/Io/Fastq.h
- Bpp/Seq/Io/Maf/MafSequence.h
- Bpp/Seq/Io/Maf/MafParser.h
- Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.h
- Bpp/Seq/Io/Maf/MafIterator.h
- Bpp/Seq/Io/Maf/BlockLengthMafIterator.h
- Bpp/Seq/Io/Maf/BlockSizeMafIterator.h
- Bpp/Seq/Io/Maf/SequenceFilterMafIterator.h
- Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.h
- Bpp/Seq/Io/Maf/ChromosomeMafIterator.h
- Bpp/Seq/Io/Maf/DuplicateFilterMafIterator.h
- Bpp/Seq/Io/Maf/BlockMergerMafIterator.h
- Bpp/Seq/Io/Maf/ConcatenateMafIterator.h
- Bpp/Seq/Io/Maf/FullGapFilterMafIterator.h
- Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.h
- Bpp/Seq/Io/Maf/EntropyFilterMafIterator.h
- Bpp/Seq/Io/Maf/MaskFilterMafIterator.h
- Bpp/Seq/Io/Maf/QualityFilterMafIterator.h
- Bpp/Seq/Io/Maf/FeatureFilterMafIterator.h
- Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.h
- Bpp/Seq/Io/Maf/OutputMafIterator.h
- Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h
- Bpp/Seq/Io/Maf/VcfOutputMafIterator.h
- Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.h
- Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.h
- Bpp/Seq/Io/Maf/WindowSplitMafIterator.h
- Bpp/Seq/Io/Maf/MafStatistics.h
- Bpp/Seq/Io/Maf/IterationListener.h
- Bpp/Seq/Feature/SequenceFeature.h
- Bpp/Seq/Feature/SequenceFeatureTools.h
- Bpp/Seq/Feature/FeatureReader.h
- Bpp/Seq/Feature/Gff/GffFeatureReader.h
- Bpp/Seq/Feature/Gtf/GtfFeatureReader.h
)
# Build the static lib
-ADD_LIBRARY(bppseqomics-static STATIC ${CPP_FILES})
-SET_TARGET_PROPERTIES(bppseqomics-static
- PROPERTIES OUTPUT_NAME bpp-seq-omics
- CLEAN_DIRECT_OUTPUT 1
+add_library (${PROJECT_NAME}-static STATIC ${CPP_FILES})
+target_include_directories (${PROJECT_NAME}-static PUBLIC
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
+ $<INSTALL_INTERFACE:$<INSTALL_PREFIX>/${CMAKE_INSTALL_INCLUDEDIR}>
)
-TARGET_LINK_LIBRARIES(bppseqomics-static ${LIBS})
+set_target_properties (${PROJECT_NAME}-static PROPERTIES OUTPUT_NAME ${PROJECT_NAME})
+target_link_libraries (${PROJECT_NAME}-static ${BPP_LIBS_STATIC})
# Build the shared lib
-ADD_LIBRARY(bppseqomics-shared SHARED ${CPP_FILES})
-SET_TARGET_PROPERTIES(bppseqomics-shared
- PROPERTIES OUTPUT_NAME bpp-seq-omics
- CLEAN_DIRECT_OUTPUT 1
- VERSION ${BPPSEQOMICS_VERSION}
- SOVERSION ${BPPSEQOMICS_VERSION_MAJOR}
+add_library (${PROJECT_NAME}-shared SHARED ${CPP_FILES})
+target_include_directories (${PROJECT_NAME}-shared PUBLIC
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
+ $<INSTALL_INTERFACE:$<INSTALL_PREFIX>/${CMAKE_INSTALL_INCLUDEDIR}>
)
-TARGET_LINK_LIBRARIES(bppseqomics-shared ${LIBS})
-
-# Install libs
-INSTALL(TARGETS bppseqomics-static bppseqomics-shared DESTINATION lib${LIB_SUFFIX})
-
-# Install headers
-INSTALL(DIRECTORY Bpp/ DESTINATION include/Bpp FILES_MATCHING PATTERN "*.h")
-
-# Generate generic include files (.all)
-INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${CMAKE_SOURCE_DIR}/genIncludes.sh ${CMAKE_PREFIX_PATH}/include/Bpp)")
+set_target_properties (${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})
+# 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 ${cmake-package-location})
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index ede9d50..adba586 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -1,46 +1,24 @@
-# CMake script for bpp-seq unit tests
-# Author: Julien Dutheil
+# CMake script for bpp-seq-omics unit tests
+# Authors:
+# Julien Dutheil
+# Francois Gindraud (2017)
# Created: 30/07/2012
-MACRO(TEST_FIND_LIBRARY OUTPUT_LIBS lib_name include_to_find)
- #start:
- FIND_PATH(${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})
- IF(${lib_name}_LIBRARY)
- MESSAGE("-- Library ${lib_name} found here:")
- MESSAGE(" includes: ${${lib_name}_INCLUDE_DIR}")
- MESSAGE(" dynamic libraries: ${${lib_name}_LIBRARY}")
- MESSAGE(WARNING "Library ${lib_name} is already installed in the system tree. Test will be built against it. This may lead to unexpected results. You may want to do 'make install' before 'make test', or remove the installed version.")
- ELSE()
- SET(${lib_name}_LIBRARY "-L../src -lbpp-seq-omics")
- SET(${lib_name}_INCLUDE_DIR "../src/")
- ENDIF()
- INCLUDE_DIRECTORIES(${${lib_name}_INCLUDE_DIR})
- SET(${OUTPUT_LIBS} ${${OUTPUT_LIBS}} ${${lib_name}_LIBRARY})
-ENDMACRO(TEST_FIND_LIBRARY)
-
-#Find the bpp-seq(-omics) library library:
-TEST_FIND_LIBRARY(LIBS bpp-seq-omics Bpp/Seq/Feature/SequenceFeature.h)
-
-ADD_EXECUTABLE(test_gff test_gff.cpp)
-TARGET_LINK_LIBRARIES(test_gff ${LIBS})
-ADD_TEST(test_gff "test_gff")
-
-ADD_EXECUTABLE(test_fastq test_fastq.cpp)
-TARGET_LINK_LIBRARIES(test_fastq ${LIBS})
-ADD_TEST(test_fastq "test_fastq")
-
-IF(UNIX)
- SET_PROPERTY(TEST test_gff test_fastq PROPERTY ENVIRONMENT "LD_LIBRARY_PATH=$ENV{LD_LIBRARY_PATH}:../src")
-ENDIF()
-
-IF(APPLE)
- SET_PROPERTY(TEST test_gff test_fastq PROPERTY ENVIRONMENT "DYLD_LIBRARY_PATH=$ENV{DYLD_LIBRARY_PATH}:../src")
-ENDIF()
-
-IF(WIN32)
- SET(ENV{PATH} "$ENV{PATH};..\\src")
-ENDIF()
-
+# Add all tests.
+# Any .cpp file in test/ is considered to be a test.
+# It will be compiled as a standalone program (must contain a main()).
+# A test is considered to succeed if it returns EXIT_SUCCESS (usually 0).
+# Tests are linked to the the shared library target.
+
+file (GLOB test_cpp_files RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.cpp)
+foreach (test_cpp_file ${test_cpp_files})
+ # Add each test (named as the filename without extension)
+ get_filename_component (test_name ${test_cpp_file} NAME_WE)
+ add_executable (${test_name} ${test_cpp_file})
+ target_link_libraries (${test_name} ${PROJECT_NAME}-shared)
+ add_test (
+ NAME ${test_name}
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+ COMMAND ${test_name}
+ )
+endforeach (test_cpp_file)
--
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