[med-svn] [libbpp-core] 02/06: Imported Upstream version 2.2.0
Andreas Tille
tille at debian.org
Fri Apr 8 20:01:36 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libbpp-core.
commit 39df58f8491e1d4f5b3f7b2f393a2b78632c62d2
Author: Andreas Tille <tille at debian.org>
Date: Fri Apr 8 21:44:46 2016 +0200
Imported Upstream version 2.2.0
---
CMakeLists.txt | 5 +-
ChangeLog | 13 +
Doxyfile | 2531 ++++++++++++--------
bpp-core.spec | 7 +-
debian/changelog | 9 +
debian/control | 2 +-
debian/copyright | 6 +-
debian/postinst | 22 +-
debian/postrm | 26 +-
debian/prerm | 22 +-
debian/rules | 4 +-
debian/postinst => genIncludes.sh | 10 +-
src/Bpp/App/ApplicationTools.cpp | 126 +-
src/Bpp/App/ApplicationTools.h | 185 +-
src/Bpp/App/BppApplication.cpp | 11 +-
src/Bpp/App/BppApplication.h | 3 +-
src/Bpp/Exceptions.h | 1 +
src/Bpp/Graph/BasicONode.cpp | 4 +-
src/Bpp/Graph/BasicONode.h | 4 +-
src/Bpp/Graph/BasicTNode.cpp | 22 +-
src/Bpp/Graphics/AbstractGraphicDevice.h | 2 +-
src/Bpp/Graphics/ColorTools.cpp | 33 +-
src/Bpp/Graphics/Fig/XFigGraphicDevice.cpp | 2 +-
src/Bpp/Graphics/Fig/XFigGraphicDevice.h | 2 +-
src/Bpp/Graphics/RgbColor.h | 8 +-
src/Bpp/Io/BppOParametrizableFormat.cpp | 76 +-
src/Bpp/Io/FileTools.cpp | 12 +-
src/Bpp/Io/OutputStream.h | 18 +-
src/Bpp/Numeric/AbstractParameterAliasable.cpp | 128 +-
src/Bpp/Numeric/AbstractParameterAliasable.h | 318 ++-
src/Bpp/Numeric/AbstractParametrizable.h | 17 +-
.../Numeric/AdaptiveKernelDensityEstimation.cpp | 2 +-
src/Bpp/Numeric/Constraints.h | 108 +-
src/Bpp/Numeric/DataTable.cpp | 504 ++--
src/Bpp/Numeric/DataTable.h | 809 ++++---
.../Function/ConjugateGradientMultiDimensions.cpp | 10 +-
.../Function/FivePointsNumericalDerivative.cpp | 35 +-
.../Function/FivePointsNumericalDerivative.h | 149 +-
src/Bpp/Numeric/Function/GoldenSectionSearch.cpp | 8 +-
src/Bpp/Numeric/Function/MetaOptimizer.h | 22 +-
.../Function/OneDimensionOptimizationTools.cpp | 284 +--
.../Function/OneDimensionOptimizationTools.h | 230 +-
.../Function/ReparametrizationFunctionWrapper.cpp | 4 +-
.../Function/ReparametrizationFunctionWrapper.h | 2 +-
.../Function/ThreePointsNumericalDerivative.cpp | 180 +-
.../Function/ThreePointsNumericalDerivative.h | 143 +-
.../Function/TwoPointsNumericalDerivative.cpp | 32 +-
.../Function/TwoPointsNumericalDerivative.h | 150 +-
.../Hmm/AbstractHmmTransitionMatrix.cpp} | 60 +-
src/Bpp/Numeric/Hmm/AbstractHmmTransitionMatrix.h | 108 +
.../Hmm/AutoCorrelationTransitionMatrix.cpp | 113 +
.../Numeric/Hmm/AutoCorrelationTransitionMatrix.h | 118 +
src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.cpp | 155 ++
src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.h | 130 +
src/Bpp/Numeric/Hmm/HmmEmissionProbabilities.h | 133 +-
src/Bpp/Numeric/Hmm/HmmLikelihood.cpp | 90 +
src/Bpp/Numeric/Hmm/HmmLikelihood.h | 224 +-
src/Bpp/Numeric/Hmm/HmmStateAlphabet.h | 140 +-
src/Bpp/Numeric/Hmm/HmmTransitionMatrix.h | 73 +-
src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.cpp | 325 ++-
src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.h | 325 ++-
.../Numeric/Hmm/LowMemoryRescaledHmmLikelihood.cpp | 7 +-
.../Numeric/Hmm/LowMemoryRescaledHmmLikelihood.h | 41 +-
src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp | 298 ++-
src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.h | 324 ++-
src/Bpp/Numeric/Matrix/EigenValue.h | 364 +--
src/Bpp/Numeric/Matrix/Matrix.h | 114 +-
src/Bpp/Numeric/Matrix/MatrixTools.h | 2032 ++++++++--------
src/Bpp/Numeric/NumConstants.h | 2 +-
src/Bpp/Numeric/Number.h | 144 +-
src/Bpp/Numeric/Parameter.h | 1 -
src/Bpp/Numeric/ParameterAliasable.h | 118 +-
src/Bpp/Numeric/ParameterList.cpp | 66 +-
src/Bpp/Numeric/ParameterList.h | 21 +-
src/Bpp/Numeric/ParametrizableCollection.h | 356 +++
.../Numeric/Prob/AbstractDiscreteDistribution.cpp | 4 +-
src/Bpp/Numeric/Prob/ConstantDistribution.cpp | 12 +-
src/Bpp/Numeric/Prob/ConstantDistribution.h | 3 +-
.../Prob/InvariantMixedDiscreteDistribution.h | 256 +-
.../Numeric/Prob/SimpleDiscreteDistribution.cpp | 4 +-
src/Bpp/Numeric/Prob/Simplex.cpp | 165 +-
src/Bpp/Numeric/Prob/Simplex.h | 140 +-
src/Bpp/Numeric/Random/RandomTools.cpp | 9 +-
src/Bpp/Numeric/Random/RandomTools.h | 21 +-
src/Bpp/Numeric/Range.h | 4 +-
src/Bpp/Numeric/TransformedParameter.h | 12 +-
src/Bpp/Numeric/VectorTools.h | 1 +
src/Bpp/Text/KeyvalTools.cpp | 2 +
src/Bpp/Text/NestedStringTokenizer.cpp | 110 +-
src/Bpp/Text/NestedStringTokenizer.h | 116 +-
src/Bpp/Text/StringTokenizer.cpp | 2 +-
src/Bpp/Text/StringTokenizer.h | 160 +-
src/Bpp/Text/TextTools.cpp | 29 +-
src/Bpp/Text/TextTools.h | 7 +-
src/Bpp/Utils/AttributesTools.cpp | 229 +-
src/Bpp/Utils/AttributesTools.h | 304 ++-
src/CMakeLists.txt | 8 +
test/CMakeLists.txt | 12 +-
test/test_derivative1.cpp | 12 +-
test/test_reparametrization.cpp | 98 +
test/test_simplex.cpp | 117 +
101 files changed, 8948 insertions(+), 5072 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index fb9b712..8950551 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -67,9 +67,9 @@ ENDIF (DOXYGEN_FOUND)
# Packager
SET(CPACK_PACKAGE_NAME "libbpp-core")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.1.0")
+SET(CPACK_PACKAGE_VERSION "2.2.0")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
-SET(CPACK_PACKAGE_VERSION_MINOR "1")
+SET(CPACK_PACKAGE_VERSION_MINOR "2")
SET(CPACK_PACKAGE_VERSION_PATCH "0")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Core library")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
@@ -87,7 +87,6 @@ SET(CPACK_SOURCE_IGNORE_FILES
".*\\\\.deb"
".*\\\\.rpm"
".*\\\\.dmg"
- ".*\\\\.sh"
".*\\\\..*\\\\.swp"
"src/\\\\..*"
"src/libbpp*"
diff --git a/ChangeLog b/ChangeLog
index 8c8ed8d..26b8901 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,16 @@
+17/09/14 -*- Version 2.2.0 -*-
+
+16/09/14 Julien Dutheil
+* Fixed bug in transformed parameters!
+ Derivative of tanh was incorrectly set to 1/cosh(x^2) instead of 1 / cosh^2(x) :s
+* Bug #88 fixed.
+
+12/06/14 Julien Dutheil
+* Added --warning argument to BppApplication + new gestion of warnings.
+
+14/04/14 Julien Dutheil
+* Added --seed argument to BppApplication to set random seed.
+
04/03/13 -*- Version 2.1.0 -*-
06/02/13 Julien Dutheil
diff --git a/Doxyfile b/Doxyfile
index 338c654..75bf108 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -1,339 +1,388 @@
-# Doxyfile 1.7.6.1
+# Doxyfile 1.8.6
# 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-core
-# 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 = 2.1.0
+PROJECT_NUMBER = 2.2.0
-# 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 an logo or icon that is included in
+# the documentation. The maximum height of the logo should not exceed 55 pixels
+# and the maximum width should not exceed 200 pixels. Doxygen will copy the logo
+# to the output directory.
PROJECT_LOGO =
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
-# base path where the generated documentation will be put.
-# If a relative path is entered, it will be relative to the location
-# where doxygen was started. If left blank the current directory will be used.
+# 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, Lithuanian, Norwegian, Macedonian, Persian,
-# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak,
-# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
+# 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.
+# 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, 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 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 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 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);
+# 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.
+# 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 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
@@ -341,1110 +390,1492 @@ 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_STATIC tag is set to YES all static members of a file
-# will be included in the documentation.
+# 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.
+# 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. 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 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 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 sectionname ... \endif.
+# 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
-# list will mention the files that were used to generate the documentation.
+# 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
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES = 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. The 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.
+# 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. Do not use file names with spaces, bibtex cannot handle them. 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)
+# 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.
+# 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. 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, *.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.
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.
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_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 and C++ 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
#---------------------------------------------------------------------------
-# 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 the tag is left blank doxygen
-# will generate a default style sheet. Note that doxygen will try to copy
-# the style sheet file to the HTML output directory, so don't put your own
-# style sheet in the HTML output directory as well, or it will be erased!
+# 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_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_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. 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.
+# 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 stylesheet 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 NO can help when comparing the output of multiple runs.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_TIMESTAMP = YES
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS = YES
-
-# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
-# documentation will contain sections that can be hidden and shown after the
-# page has loaded. For this to work a browser that supports
-# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
-# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
+# 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
-# 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
+# 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 (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++ Core Library"
-# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
-# should uniquely identify the documentation set bundle. This should be a
-# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
-# will append .docset to the name.
+# This tag specifies a string that should uniquely identify the documentation
+# set bundle. This should be a reverse domain-name style string, e.g.
+# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_BUNDLE_ID = bpp.core
-# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
-# the documentation publisher. This should be a reverse domain-name style
+# 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.
+# 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 stylesheets (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
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES = NO
-
-# 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.
+# 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.
+# 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 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 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.
+# 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 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.org site, so you can quickly see the result without installing
-# MathJax, but it is strongly recommended to install a local copy of MathJax
-# before deployment.
+# 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.
+# 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://www.mathjax.org/mathjax
-# 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 PHP enabled web server instead of at the web client
-# using Javascript. Doxygen will generate the search PHP script and index
-# file to put on the web server. The advantage of the server
-# based approach is that it scales better to large projects and allows
-# full text search. The disadvantages are that it is more difficult to setup
-# and does not have live searching capabilities.
+# 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 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 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 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
+# 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
+# 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 = 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. To get the times font for
+# instance you can specify
+# EXTRA_PACKAGES=times
+# 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. Doxygen will
+# replace them by respectively the title of the page, the current date and time,
+# only the current date, the version number of doxygen, the project name (see
+# PROJECT_NAME), or the project number (see PROJECT_NUMBER).
+# 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.
+#
+# 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 =
-# 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.
+# 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 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 LATEX_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
#---------------------------------------------------------------------------
-# 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 =
#---------------------------------------------------------------------------
-# 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.
+# 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.
+# The XML_SCHEMA tag can be used to specify a XML schema, which can be used by a
+# validating XML parser to check the syntax of the XML files.
+# This tag requires that the tag GENERATE_XML is set to YES.
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.
+# The XML_DTD tag can be used to specify a XML DTD, which can be used by a
+# validating XML parser to check the syntax of the XML files.
+# This tag requires that the tag GENERATE_XML is set to YES.
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 for the AutoGen Definitions output
+# Configuration options related to the DOCBOOK 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_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.
+# The default directory is: docbook.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_OUTPUT = docbook
+
+#---------------------------------------------------------------------------
+# Configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES doxygen will generate an AutoGen
+# Definitions (see 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 =
@@ -1452,108 +1883,128 @@ 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 includes 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 refrences 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.
-# Optionally an initial location of the external documentation
-# can be added for each tagfile. 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. If a location is present for each tag, the installdox tool
-# does not have to be run to correct the links.
-# 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 an 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 =
-# 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 = BppCore.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
-# The PERL_PATH should be the absolute path and name of the perl script
-# interpreter (i.e. the result of `which perl').
+# 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 default file (with absolute path) is: /usr/bin/perl.
PERL_PATH = /usr/bin/perl
@@ -1561,213 +2012,293 @@ 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: NO.
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 n 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 set to YES, the inheritance and collaboration graphs will show the
-# relations between templates and their instances.
+# 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 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.
+# 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.
+# 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, SHOW_DIRECTORIES 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.
+# 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, jpg, gif and svg.
+# 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 =
+
+# 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 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/bpp-core.spec b/bpp-core.spec
index 06e8efd..38b3761 100644
--- a/bpp-core.spec
+++ b/bpp-core.spec
@@ -1,5 +1,5 @@
%define _basename bpp-core
-%define _version 2.1.0
+%define _version 2.2.0
%define _release 1
%define _prefix /usr
@@ -166,6 +166,11 @@ exit 0
%{_prefix}/include/*
%changelog
+* Wed Sep 17 2014 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.2.0-1
+- Reparametrization wrapper debugged
+- Improved and rationalized display of warning messages
+- Possibility to set random seed in applications
+- Code checked for compilation with CLang.
* Mon Mar 04 2013 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.1.0-1
- Extended range classes
- Improved initialization of static members
diff --git a/debian/changelog b/debian/changelog
index fb0eee0..d84c97f 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+libbpp-core (2.2.0-1) unstable; urgency=low
+
+ * Reparametrization wrapper debugged
+ * Improved and rationalized display of warning messages
+ * Possibility to set random seed in applications
+ * Code checked for compilation with CLang.
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Wed, 17 Sep 2014 14:00:00 +0100
+
libbpp-core (2.1.0-1) unstable; urgency=low
* Extended range classes
diff --git a/debian/control b/debian/control
index bc0ed01..8d6aa49 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ 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)
-Standards-Version: 3.9.1
+Standards-Version: 3.9.4
Package: libbpp-core-dev
Section: libdevel
diff --git a/debian/copyright b/debian/copyright
index 597cf01..c9da444 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,5 +1,5 @@
This package was debianized by Julien Dutheil <julien.dutheil at univ-montp2.fr> on
-Mon, 04 Mar 2013 14:30:00 +0100.
+Wed, 17 Sep 2014 14:00:00 +0100.
It was downloaded from <http://biopp.univ-montp2.fr/Repositories/sources>
@@ -9,7 +9,7 @@ Upstream Author:
Copyright:
- Copyright (C) 2013 Bio++ Development Team
+ Copyright (C) 2014 Bio++ Development Team
License:
@@ -30,7 +30,7 @@ License:
On Debian systems, the complete text of the GNU General
Public License can be found in `/usr/share/common-licenses/GPL'.
-The Debian packaging is (C) 2013, Julien Dutheil <julien.dutheil at univ-montp2.fr> and
+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:
diff --git a/debian/postinst b/debian/postinst
index cf9e925..cff89b1 100755
--- a/debian/postinst
+++ b/debian/postinst
@@ -35,9 +35,23 @@ createGeneric() {
done;
}
-if [ "$1" = "configure" ]; then
- # Actualize .all files
- createGeneric /usr/include/Bpp
-fi
+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
index 3931669..744f8b1 100755
--- a/debian/postrm
+++ b/debian/postrm
@@ -35,11 +35,25 @@ createGeneric() {
done;
}
-if [ "$1" = "remove" ]; then
- # Automatically added by dh_makeshlibs
- ldconfig
- # Actualize .all files
- createGeneric /usr/include/Bpp
-fi
+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
index 5aefd24..8fab52e 100755
--- a/debian/prerm
+++ b/debian/prerm
@@ -19,9 +19,23 @@ removeGeneric() {
done
}
-if [ "$1" = "remove" ]; then
- # Actualize .all files
- removeGeneric /usr/include/Bpp
-fi
+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
index 92c389e..34313ef 100755
--- a/debian/rules
+++ b/debian/rules
@@ -38,7 +38,9 @@ configure:
config.status: configure
dh_testdir
-build: build-stamp
+build: build-arch build-indep
+build-arch: build-stamp
+build-indep: build-stamp
build-stamp: config.status
dh_testdir
diff --git a/debian/postinst b/genIncludes.sh
similarity index 80%
copy from debian/postinst
copy to genIncludes.sh
index cf9e925..56710e9 100755
--- a/debian/postinst
+++ b/genIncludes.sh
@@ -1,8 +1,5 @@
#! /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:
@@ -35,9 +32,4 @@ createGeneric() {
done;
}
-if [ "$1" = "configure" ]; then
- # Actualize .all files
- createGeneric /usr/include/Bpp
-fi
-
-exit 0
+createGeneric $1
diff --git a/src/Bpp/App/ApplicationTools.cpp b/src/Bpp/App/ApplicationTools.cpp
index d449a53..3480e15 100644
--- a/src/Bpp/App/ApplicationTools.cpp
+++ b/src/Bpp/App/ApplicationTools.cpp
@@ -56,6 +56,7 @@ time_t ApplicationTools::startTime;
size_t ApplicationTools::terminalWidth = 80;
float ApplicationTools::terminalSplit = 0.5;
bool ApplicationTools::interactive = true;
+int ApplicationTools::warningLevel = 0;
/******************************************************************************/
@@ -65,18 +66,102 @@ bool ApplicationTools::parameterExists(
{
return (params.find(parameterName) != params.end() && !TextTools::isEmpty(params[parameterName]));
}
+
+bool ApplicationTools::parameterExists(
+ const std::string & parameterName,
+ std::vector<std::string>& params)
+{
+ for (size_t i = 0; i < params.size(); ++i)
+ if (params[i] == parameterName)
+ return true;
+
+ return false;
+}
+
+/******************************************************************************/
+std::vector<std::string> ApplicationTools::matchingParameters(const std::string& pattern, std::map<std::string, std::string>& params)
+{
+ vector<string> retv;
+
+ map<string, string>::iterator it;
+ for (it=params.begin(); it!=params.end(); it++)
+ {
+ StringTokenizer stj(pattern, "*", true, false);
+ size_t pos1, pos2;
+ string parn = it->first;
+ bool flag(true);
+ string g = stj.nextToken();
+ pos1 = parn.find(g);
+ if (pos1 != 0)
+ flag = false;
+ pos1 += g.length();
+ while (flag && stj.hasMoreToken())
+ {
+ g = stj.nextToken();
+ pos2 = parn.find(g, pos1);
+ if (pos2 == string::npos)
+ {
+ flag = false;
+ break;
+ }
+ pos1 = pos2 + g.length();
+ }
+ if (flag &&
+ ((g.length() == 0) || (pos1 == parn.length()) || (parn.rfind(g) == parn.length() - g.length())))
+ retv.push_back(parn);
+ }
+
+ return retv;
+}
+
+std::vector<std::string> ApplicationTools::matchingParameters(const std::string& pattern, std::vector<std::string>& params)
+{
+ vector<string> retv;
+
+ for (size_t i=0;i<params.size();i++)
+ {
+ StringTokenizer stj(pattern, "*", true, false);
+ size_t pos1, pos2;
+ string parn = params[i];
+ bool flag(true);
+ string g = stj.nextToken();
+ pos1 = parn.find(g);
+ if (pos1 != 0)
+ flag = false;
+ pos1 += g.length();
+ while (flag && stj.hasMoreToken())
+ {
+ g = stj.nextToken();
+ pos2 = parn.find(g, pos1);
+ if (pos2 == string::npos)
+ {
+ flag = false;
+ break;
+ }
+ pos1 = pos2 + g.length();
+ }
+ if (flag &&
+ ((g.length() == 0) || (pos1 == parn.length()) || (parn.rfind(g) == parn.length() - g.length())))
+ retv.push_back(parn);
+ }
+
+ return retv;
+}
+
/******************************************************************************/
-std::string ApplicationTools::getAFilePath(
- const std::string& parameter,
- std::map<std::string, std::string>& params,
+string ApplicationTools::getAFilePath(
+ const string& parameter,
+ map<string, string>& params,
bool isRequired,
bool mustExist,
- const std::string& suffix,
- bool suffixIsOptional) throw (Exception)
+ const string& suffix,
+ bool suffixIsOptional,
+ const string& defaultPath,
+ int warn) throw (Exception)
{
- string filePath = getStringParameter(parameter, params, "none", suffix, suffixIsOptional, false);
+ string filePath = getStringParameter(parameter, params, defaultPath, suffix, suffixIsOptional, warn);
if (filePath == "") filePath = "none";
if (filePath == "none" && isRequired)
{
@@ -93,12 +178,12 @@ std::string ApplicationTools::getAFilePath(
/******************************************************************************/
double ApplicationTools::getDoubleParameter(
- const std::string & parameterName,
- std::map<std::string, std::string> & params,
+ const std::string& parameterName,
+ std::map<std::string, std::string>& params,
double defaultValue,
- const std::string & suffix,
+ const std::string& suffix,
bool suffixIsOptional,
- bool warn)
+ int warn)
{
double dParam = defaultValue;
if (parameterExists(parameterName + suffix, params))
@@ -109,7 +194,7 @@ double ApplicationTools::getDoubleParameter(
{
dParam = TextTools::toDouble(params[parameterName]);
}
- else if(warn)
+ else if(warn <= warningLevel)
{
displayWarning("Parameter " + parameterName + suffix + " not specified. Default used instead: " + TextTools::toString(defaultValue));
}
@@ -124,14 +209,14 @@ int ApplicationTools::getIntParameter(
int defaultValue,
const std::string & suffix,
bool suffixIsOptional,
- bool warn)
+ int warn)
{
int iParam = defaultValue;
if (parameterExists(parameterName + suffix, params)) {
iParam = TextTools::toInt(params[parameterName + suffix]);
} else if(suffixIsOptional && parameterExists(parameterName, params)) {
iParam = TextTools::toInt(params[parameterName]);
- } else if (warn) {
+ } else if (warn <= warningLevel) {
displayWarning("Parameter " + parameterName + suffix + " not specified. Default used instead: " + TextTools::toString(defaultValue));
}
return iParam;
@@ -145,14 +230,14 @@ std::string ApplicationTools::getStringParameter(
const std::string& defaultValue,
const std::string& suffix,
bool suffixIsOptional,
- bool warn)
+ int warn)
{
string sParam = defaultValue;
if (parameterExists(parameterName + suffix, params)) {
sParam = params[parameterName + suffix];
} else if (suffixIsOptional && parameterExists(parameterName, params)) {
sParam = params[parameterName];
- } else if (warn) {
+ } else if (warn <= warningLevel) {
displayWarning("Parameter " + parameterName + " not specified. Default used instead: " + defaultValue);
}
return sParam;
@@ -166,7 +251,7 @@ bool ApplicationTools::getBooleanParameter(
bool defaultValue,
const std::string& suffix,
bool suffixIsOptional,
- bool warn)
+ int warn)
{
string sParam;
bool bParam = defaultValue;
@@ -179,7 +264,7 @@ bool ApplicationTools::getBooleanParameter(
sParam = params[parameterName];
}
else {
- if (warn)
+ if (warn <= warningLevel)
{
displayWarning("Parameter " + parameterName + " not specified. Default used instead: " + TextTools::toString(defaultValue));
}
@@ -239,14 +324,15 @@ void ApplicationTools::displayGauge(size_t iter, size_t total, char symbol, cons
size_t width = static_cast<size_t>(static_cast<float>(terminalWidth) * terminalSplit - 2);
string gauge = string(static_cast<size_t>((1. * static_cast<double>(iter) / static_cast<double>(total)) * static_cast<double>(width)), symbol);
string info = mes;
+ size_t step = static_cast<size_t>(ceil(1. * static_cast<double>(total) / static_cast<double>(width)));
+ size_t x = iter % step;
if (interactive)
{
string fill = string(width - gauge.length(), ' ');
gauge = "[" + gauge + fill + "] " + TextTools::resizeLeft(TextTools::toString(100 * iter / total), 3) + "%";
if (mes.size() > terminalWidth - gauge.size())
info = TextTools::resizeRight(mes, terminalWidth - gauge.size());
- *message << '\r' + info + gauge;
- message->flush();
+ if (x == 0 || iter == total) { *message << '\r' + info + gauge; message->flush(); }
}
else
{
@@ -256,7 +342,6 @@ void ApplicationTools::displayGauge(size_t iter, size_t total, char symbol, cons
message->flush();
return;
}
- size_t step = static_cast<size_t>(ceil(1. * static_cast<double>(total) / static_cast<double>(width)));
if (iter >= total)
{
size_t fill = static_cast<size_t>(static_cast<float>(terminalWidth) * terminalSplit) - (total - 1) / step - 1;
@@ -264,7 +349,6 @@ void ApplicationTools::displayGauge(size_t iter, size_t total, char symbol, cons
message->flush();
return;
}
- size_t x = iter % step;
if (x == 0) { *message << symbol; message->flush(); }
}
}
diff --git a/src/Bpp/App/ApplicationTools.h b/src/Bpp/App/ApplicationTools.h
index 272ca85..a9b40af 100644
--- a/src/Bpp/App/ApplicationTools.h
+++ b/src/Bpp/App/ApplicationTools.h
@@ -6,36 +6,36 @@
//
/*
-Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
-
-This software is a computer program whose purpose is to provide basal and
-utilitary classes. This file belongs to the Bio++ Project.
-
-This software is governed by the CeCILL license under French law and
-abiding by the rules of distribution of free software. You can use,
-modify and/ or redistribute the software under the terms of the CeCILL
-license as circulated by CEA, CNRS and INRIA at the following URL
-"http://www.cecill.info".
-
-As a counterpart to the access to the source code and rights to copy,
-modify and redistribute granted by the license, users are provided only
-with a limited warranty and the software's author, the holder of the
-economic rights, and the successive licensors have only limited
-liability.
-
-In this respect, the user's attention is drawn to the risks associated
-with loading, using, modifying and/or developing or reproducing the
-software by the user in light of its specific status of free software,
-that may mean that it is complicated to manipulate, and that also
-therefore means that it is reserved for developers and experienced
-professionals having in-depth computer knowledge. Users are therefore
-encouraged to load and test the software's suitability as regards their
-requirements in conditions enabling the security of their systems and/or
-data to be ensured and, more generally, to use and operate it in the
-same conditions as regards security.
-
-The fact that you are presently reading this means that you have had
-knowledge of the CeCILL license and that you accept its terms.
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide basal and
+ utilitary classes. This file belongs to the Bio++ Project.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
*/
#ifndef _APPLICATIONTOOLS_H_
@@ -47,6 +47,8 @@ knowledge of the CeCILL license and that you accept its terms.
#include "../Text/StringTokenizer.h"
#include "../Text/NestedStringTokenizer.h"
+#include "../Numeric/Matrix/Matrix.h"
+
// From the STL:
#include <map>
#include <vector>
@@ -87,8 +89,8 @@ namespace bpp
* containing the parameters (names are the keys of the map, and values are... the values of the map!).
* These map objects may be obtained from the AttributesTools utilitary class.
*/
-class ApplicationTools
-{
+ class ApplicationTools
+ {
public:
/**
@@ -123,7 +125,12 @@ class ApplicationTools
* @brief Tell if the program is interactive (typically run in foreground). Default to yes.
*/
static bool interactive;
-
+
+ /**
+ * @brief Specify the amount of warning to display.
+ */
+ static int warningLevel;
+
public:
ApplicationTools() {}
virtual ~ApplicationTools() {}
@@ -138,7 +145,22 @@ class ApplicationTools
* @return True is the parameter of specified name is in the list.
*/
static bool parameterExists(const std::string& parameterName, std::map<std::string, std::string>& params);
-
+
+ static bool parameterExists(const std::string& parameterName, std::vector<std::string>& params);
+
+ /**
+ * @brief Returns a vector of parameter names that match a given pattern.
+ *
+ * Only "*" wildcard is implemented now.
+ *
+ * @param pattern The pattern.
+ * @param params The parameter list.
+ * @return a vector of matching names.
+ */
+ static std::vector<std::string> matchingParameters(const std::string& pattern, std::map<std::string, std::string>& params);
+
+ static std::vector<std::string> matchingParameters(const std::string& pattern, std::vector<std::string>& params);
+
/**
* @brief Get a double parameter.
*
@@ -156,7 +178,7 @@ class ApplicationTools
double defaultValue,
const std::string& suffix = "",
bool suffixIsOptional = true,
- bool warn = true);
+ int warn = 0);
/**
* @brief Get an integer parameter.
@@ -175,7 +197,7 @@ class ApplicationTools
int defaultValue,
const std::string& suffix = "",
bool suffixIsOptional = true,
- bool warn = true);
+ int warn = 0);
/**
* @brief Get a string parameter.
@@ -194,7 +216,7 @@ class ApplicationTools
const std::string& defaultValue,
const std::string& suffix = "",
bool suffixIsOptional = true,
- bool warn = true);
+ int warn = 0);
/**
* @brief Get a boolean parameter.
@@ -213,7 +235,7 @@ class ApplicationTools
bool defaultValue,
const std::string& suffix = "",
bool suffixIsOptional = true,
- bool warn = true);
+ int warn = 0);
/**
* @brief Get a parameter.
@@ -232,17 +254,18 @@ class ApplicationTools
T defaultValue,
const std::string& suffix = "",
bool suffixIsOptional = true,
- bool warn = true)
+ int warn = 0)
{
T tParam = defaultValue;
- if(parameterExists(parameterName + suffix, params))
+ if (parameterExists(parameterName + suffix, params))
{
tParam = TextTools::to<T>(params[parameterName + suffix]);
}
- else if(suffixIsOptional && parameterExists(parameterName, params))
+ else if (suffixIsOptional && parameterExists(parameterName, params))
{
tParam = TextTools::to<T>(params[parameterName]);
- } else if(warn)
+ }
+ else if (warn <= warningLevel)
{
displayWarning("Parameter " + parameterName + suffix + " not specified. Default used instead: " + TextTools::toString(defaultValue));
}
@@ -261,6 +284,8 @@ class ApplicationTools
* @param mustExist Tell if the corresponding file must already exist.
* @param suffix A suffix to be applied to the parameter name.
* @param suffixIsOptional Tell if the suffix is absolutely required.
+ * @param defaultPath Path to use if no argument is provided.
+ * @param warn Tell if a warning must be sent in case the parameter is not found.
* @throw Exception If no file path is specified and isRequired is
* true, or the file does not exist and mustExist
* is set to true.
@@ -271,7 +296,9 @@ class ApplicationTools
bool isRequired = true,
bool mustExist = true,
const std::string& suffix = "",
- bool suffixIsOptional = false) throw (Exception);
+ bool suffixIsOptional = false,
+ const std::string& defaultPath = "none",
+ int warn = 0) throw (Exception);
/**
* @brief Get a vector.
@@ -292,7 +319,7 @@ class ApplicationTools
const std::string& defaultValue,
const std::string& suffix = "",
bool suffixIsOptional = true,
- bool warn = true)
+ int warn = 0)
{
std::string s = getStringParameter(parameterName, params, defaultValue, suffix, suffixIsOptional, warn);
if (TextTools::isEmpty(s)) return std::vector<T>(0);
@@ -338,6 +365,11 @@ class ApplicationTools
bool warn = true)
{
std::string s = getStringParameter(parameterName, params, defaultValue, suffix, suffixIsOptional, warn);
+ if (s[0] == '(' && s[s.size() - 1] == ')') {
+ //This is a delimited vector:
+ s = s.substr(1, s.size() - 2);
+ if (TextTools::isEmpty(s)) return std::vector<T>(0);
+ }
StringTokenizer st(s, TextTools::toString(separator));
size_t n = st.numberOfRemainingTokens();
std::vector<T> v;
@@ -360,7 +392,68 @@ class ApplicationTools
}
return v;
}
-
+
+ /**
+ * @brief Get a RowMatrix. The input is made of embedded
+ * parenthesis, such as ((1,2),(3,4)), where the matrix is filled by
+ * lines. Here, the matrix would be:
+ * \f[
+ * \begin{pmatrix}
+ * 1 & 2 \\
+ * 3 & 4 \\
+ * \end{pmatrix}
+ * \f]
+ *
+ * @param parameterName The name of the corresponding parameter.
+ * @param params The attribute map where options may be found.
+ * @param separator The character used to delimit values.
+ * @param defaultValue The default value to use if the parameter is not found.
+ * @param suffix A suffix to be applied to the parameter name.
+ * @param suffixIsOptional Tell if the suffix is absolutely required.
+ * @param warn Tell if a warning must be sent in case the parameter is not found.
+ * @return The corresponding value.
+ */
+
+ template<class T> static RowMatrix<T> getMatrixParameter(
+ const std::string& parameterName,
+ std::map<std::string, std::string>& params,
+ char separator,
+ const std::string& defaultValue,
+ const std::string& suffix = "",
+ bool suffixIsOptional = true,
+ bool warn = true)
+ {
+ RowMatrix<T> mat;
+
+ std::string s = getStringParameter(parameterName, params, defaultValue, suffix, suffixIsOptional, warn);
+ if (TextTools::isEmpty(s)) return RowMatrix<T>(0,0);
+ if (s[0] == '(' && s[s.size() - 1] == ')') {
+ //This is a delimited vector:
+ s = s.substr(1, s.size() - 2);
+ if (TextTools::isEmpty(s)) return RowMatrix<T>(0,0);
+ }
+
+ StringTokenizer st1(s, "()");
+
+ while (st1.hasMoreToken())
+ {
+ std::string si=st1.nextToken();
+ StringTokenizer st2(si, TextTools::toString(separator));
+ size_t n = st2.numberOfRemainingTokens();
+
+ std::vector<T> v(n);
+ for (size_t i = 0; i < n; i++)
+ {
+ v[i] = TextTools::fromString<T>(st2.nextToken());
+ }
+
+ if (v.size()!=0)
+ mat.addRow(v);
+ }
+ return mat;
+ }
+
+
/**
* @name Output methods.
*
@@ -506,7 +599,7 @@ class ApplicationTools
* @return The number of seconds from when timer was started.
*/
static double getTime();
-};
+ };
} //end of namespace bpp.
diff --git a/src/Bpp/App/BppApplication.cpp b/src/Bpp/App/BppApplication.cpp
index 5d10750..dfbc988 100644
--- a/src/Bpp/App/BppApplication.cpp
+++ b/src/Bpp/App/BppApplication.cpp
@@ -5,7 +5,7 @@
//
/*
-Copyright or © or Copr. CNRS, (November 17, 2004)
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
This software is a computer program whose purpose is to provide basal and
utilitary classes. This file belongs to the Bio++ Project.
@@ -39,6 +39,7 @@ knowledge of the CeCILL license and that you accept its terms.
#include "BppApplication.h"
#include "../Utils/AttributesTools.h"
+#include "../Numeric/Random/RandomTools.h"
#include "ApplicationTools.h"
// From the STL:
@@ -51,8 +52,14 @@ BppApplication::BppApplication(int argc, char* argv[], const std::string& name):
{
cout << "Parsing options:" << endl;
params_ = AttributesTools::parseOptions(argc, argv);
- bool noint = ApplicationTools::getBooleanParameter("--noninteractive", params_, false, "", true, false);
+ ApplicationTools::warningLevel = ApplicationTools::getIntParameter("--warning", params_, 0, "", true, 3);
+ bool noint = ApplicationTools::getBooleanParameter("--noninteractive", params_, false, "", true, 3);
ApplicationTools::interactive = !noint;
+ long seed = ApplicationTools::getParameter<long>("--seed", params_, -1, "", true, 3);
+ if (seed >= 0) {
+ RandomTools::setSeed(seed);
+ ApplicationTools::displayResult("Random seed set to", seed);
+ }
}
void BppApplication::startTimer()
diff --git a/src/Bpp/App/BppApplication.h b/src/Bpp/App/BppApplication.h
index 8798f17..78286f0 100644
--- a/src/Bpp/App/BppApplication.h
+++ b/src/Bpp/App/BppApplication.h
@@ -5,7 +5,7 @@
//
/*
-Copyright or © or Copr. CNRS, (November 17, 2004)
+Copyright or © or Copr. Development Team, (November 17, 2004)
This software is a computer program whose purpose is to provide basal and
utilitary classes. This file belongs to the Bio++ Project.
@@ -72,6 +72,7 @@ namespace bpp
}
std::string& getParam(const std::string& name) { return params_[name]; }
+
};
} //end of namespace bpp;
diff --git a/src/Bpp/Exceptions.h b/src/Bpp/Exceptions.h
index 2ac2c53..ce62920 100644
--- a/src/Bpp/Exceptions.h
+++ b/src/Bpp/Exceptions.h
@@ -44,6 +44,7 @@ knowledge of the CeCILL license and that you accept its terms.
#include <stdexcept>
#include <vector>
+#include <string>
namespace bpp
{
diff --git a/src/Bpp/Graph/BasicONode.cpp b/src/Bpp/Graph/BasicONode.cpp
index 97e0ec9..1ab3f09 100644
--- a/src/Bpp/Graph/BasicONode.cpp
+++ b/src/Bpp/Graph/BasicONode.cpp
@@ -5,7 +5,7 @@
//
/*
-Copyright or © or Copr. CNRS, (January 12, 2011)
+Copyright or © or Copr. Bio++ Development Team, (January 12, 2011)
This software is a computer program whose purpose is to provide utilitary
classes. This file belongs to the Bio++ Project.
@@ -41,3 +41,5 @@ knowledge of the CeCILL license and that you accept its terms.
using namespace bpp;
+BasicONode::BasicONode() {}
+
diff --git a/src/Bpp/Graph/BasicONode.h b/src/Bpp/Graph/BasicONode.h
index 535fd6a..2cf8bfb 100644
--- a/src/Bpp/Graph/BasicONode.h
+++ b/src/Bpp/Graph/BasicONode.h
@@ -5,7 +5,7 @@
//
/*
-Copyright or © or Copr. CNRS, (January 12, 2011)
+Copyright or © or Copr. Bio++ Development Team, (January 12, 2011)
This software is a computer program whose purpose is to provide utilitary
classes. This file belongs to the Bio++ Project.
@@ -53,6 +53,8 @@ namespace bpp {
* @author Sylvain Gaillard
*/
class BasicONode: public ONode {
+ public:
+ BasicONode();
};
}
diff --git a/src/Bpp/Graph/BasicTNode.cpp b/src/Bpp/Graph/BasicTNode.cpp
index 7033b40..0872f54 100644
--- a/src/Bpp/Graph/BasicTNode.cpp
+++ b/src/Bpp/Graph/BasicTNode.cpp
@@ -5,7 +5,7 @@
//
/*
-Copyright or © or Copr. CNRS, (January 12, 2011)
+Copyright or © or Copr. Bio++ Development Team, (January 12, 2011)
This software is a computer program whose purpose is to provide utilitary
classes. This file belongs to the Bio++ Project.
@@ -41,6 +41,10 @@ knowledge of the CeCILL license and that you accept its terms.
using namespace bpp;
+#include <cstddef>
+
+using namespace std;
+
BasicTNode::~BasicTNode() {
if (father_) {
father_->removeSon(this);
@@ -65,7 +69,7 @@ BasicTNode& BasicTNode::operator=(const BasicTNode& node) {
const BasicTNode* BasicTNode::getNeighbor(int pos) const {
if (pos < 0 || pos > static_cast<int>(sons_.size())) {
- throw IndexOutOfBoundsException("BasicTNode::getNeighbor() pos is out of bounds", pos, 0, static_cast<int>(sons_.size()));
+ throw IndexOutOfBoundsException("BasicTNode::getNeighbor() pos is out of bounds", static_cast<size_t>(pos), 0, sons_.size());
}
if (pos == 0)
return father_;
@@ -75,7 +79,7 @@ const BasicTNode* BasicTNode::getNeighbor(int pos) const {
BasicTNode* BasicTNode::getNeighbor(int pos) {
if (pos < 0 || pos > static_cast<int>(sons_.size())) {
- throw IndexOutOfBoundsException("BasicTNode::getNeighbor() pos is out of bounds", pos, 0, static_cast<int>(sons_.size()));
+ throw IndexOutOfBoundsException("BasicTNode::getNeighbor() pos is out of bounds", static_cast<size_t>(pos), 0, sons_.size());
}
if (pos == 0)
return father_;
@@ -103,14 +107,14 @@ BasicTNode* BasicTNode::operator[](int i) {
const BasicTNode* BasicTNode::getFather(int pos) const {
if (pos != 0) {
- throw IndexOutOfBoundsException("BasicTNode::getFather() pos must be 0 for TNode", pos, 0, 0);
+ throw IndexOutOfBoundsException("BasicTNode::getFather() pos must be 0 for TNode", static_cast<size_t>(pos), 0, 0);
}
return getFather();
}
BasicTNode* BasicTNode::getFather(int pos) {
if (pos != 0) {
- throw IndexOutOfBoundsException("BasicTNode::getFather() pos must be 0 for TNode", pos, 0, 0);
+ throw IndexOutOfBoundsException("BasicTNode::getFather() pos must be 0 for TNode", static_cast<size_t>(pos), 0, 0);
}
return getFather();
}
@@ -154,14 +158,14 @@ BasicTNode* BasicTNode::removeFather() {
const BasicTNode* BasicTNode::getSon(int pos) const {
if (pos < 0 || pos > static_cast<int>(sons_.size()) - 1) {
- throw IndexOutOfBoundsException("BasicTNode::getSon() pos out of range", pos, 0, sons_.size() - 1);
+ throw IndexOutOfBoundsException("BasicTNode::getSon() pos out of range", static_cast<size_t>(pos), 0, sons_.size() - 1);
}
return sons_[static_cast<size_t>(pos)];
}
BasicTNode* BasicTNode::getSon(int pos) {
if (pos < 0 || pos > static_cast<int>(sons_.size()) - 1) {
- throw IndexOutOfBoundsException("BasicTNode::getSon() pos out of range", pos, 0, sons_.size() - 1);
+ throw IndexOutOfBoundsException("BasicTNode::getSon() pos out of range", static_cast<size_t>(pos), 0, sons_.size() - 1);
}
return sons_[static_cast<size_t>(pos)];
}
@@ -188,7 +192,7 @@ void BasicTNode::removeSon(BasicTNode* node) {
throw NullPointerException("BasicTNode::removeSon() Empty node given as input.");
for (size_t i = 0 ; i < sons_.size() ; i++) {
if (sons_[i] == node) {
- sons_.erase(sons_.begin() + i);
+ sons_.erase(sons_.begin() + static_cast<ptrdiff_t>(i));
node->removeFather();
}
}
@@ -196,7 +200,7 @@ void BasicTNode::removeSon(BasicTNode* node) {
BasicTNode* BasicTNode::removeSon(int pos) {
if (pos < 0 || pos > static_cast<int>(sons_.size() - 1))
- throw IndexOutOfBoundsException("BasicTNode::removeSon() pos out of bound", pos, 0, sons_.size() - 1);
+ throw IndexOutOfBoundsException("BasicTNode::removeSon() pos out of bound", static_cast<size_t>(pos), 0, sons_.size() - 1);
BasicTNode* node = sons_[static_cast<size_t>(pos)];
sons_.erase(sons_.begin() + pos);
node->removeFather();
diff --git a/src/Bpp/Graphics/AbstractGraphicDevice.h b/src/Bpp/Graphics/AbstractGraphicDevice.h
index 961945f..6f2e629 100644
--- a/src/Bpp/Graphics/AbstractGraphicDevice.h
+++ b/src/Bpp/Graphics/AbstractGraphicDevice.h
@@ -5,7 +5,7 @@
//
/*
-Copyright or © or Copr. CNRS, (November 16, 2006)
+Copyright or © or Copr. Bio++ Development Team, (November 16, 2006)
This software is a computer program whose purpose is to provide utilitary
classes. This file belongs to the Bio++ Project.
diff --git a/src/Bpp/Graphics/ColorTools.cpp b/src/Bpp/Graphics/ColorTools.cpp
index 19ef7b7..87cb73a 100644
--- a/src/Bpp/Graphics/ColorTools.cpp
+++ b/src/Bpp/Graphics/ColorTools.cpp
@@ -5,7 +5,7 @@
//
/*
-Copyright or © or Copr. CNRS, (November 17, 2004)
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
This software is a computer program whose purpose is to provide utilitary
classes. This file belongs to the Bio++ Project.
@@ -54,14 +54,29 @@ const RGBColor ColorTools::ORANGE = RGBColor(255,127,0);
/******************************************************************************/
-std::vector<RGBColor> ColorTools::gradient(unsigned int n, const RGBColor & low, const RGBColor & high)
+std::vector<RGBColor> ColorTools::gradient(unsigned int n, const RGBColor& low, const RGBColor& high)
{
vector<RGBColor> colors(n);
- for(unsigned int i = 0; i < n-1; i++)
+ for (unsigned int i = 0; i < n - 1; ++i)
{
- colors[i][0] = low[0] + (int)floor((double)i*(double)((int)high[0] - (int)low[0])/(double)(n-1));
- colors[i][1] = low[1] + (int)floor((double)i*(double)((int)high[1] - (int)low[1])/(double)(n-1));
- colors[i][2] = low[2] + (int)floor((double)i*(double)((int)high[2] - (int)low[2])/(double)(n-1));
+ colors[i][0] = low[0] + static_cast<unsigned int>(
+ floor(
+ static_cast<double>(i) * static_cast<double>(static_cast<int>(high[0]) - static_cast<int>(low[0]))
+ / static_cast<double>(n - 1)
+ )
+ );
+ colors[i][1] = low[1] + static_cast<unsigned int>(
+ floor(
+ static_cast<double>(i) * static_cast<double>(static_cast<int>(high[1]) - static_cast<int>(low[1]))
+ / static_cast<double>(n - 1)
+ )
+ );
+ colors[i][2] = low[2] + static_cast<unsigned int>(
+ floor(
+ static_cast<double>(i) * static_cast<double>(static_cast<int>(high[2]) - static_cast<int>(low[2]))
+ / static_cast<double>(n - 1)
+ )
+ );
}
colors[n-1] = high;
return colors;
@@ -71,11 +86,11 @@ std::vector<RGBColor> ColorTools::gradient(unsigned int n, const RGBColor & low,
std::vector<RGBColor> ColorTools::gradient(unsigned int n, const RGBColor & low, const RGBColor & mid, const RGBColor & high)
{
- unsigned int lower = n/2;
+ unsigned int lower = n / 2;
unsigned int upper = n - lower;
vector<RGBColor> colors1 = gradient(lower, low, mid);
- vector<RGBColor> colors2 = gradient(upper+1, mid, high);
- for(unsigned int i = 1; i < colors2.size(); i++)
+ vector<RGBColor> colors2 = gradient(upper + 1, mid, high);
+ for (size_t i = 1; i < colors2.size(); i++)
{
colors1.push_back(colors2[i]);
}
diff --git a/src/Bpp/Graphics/Fig/XFigGraphicDevice.cpp b/src/Bpp/Graphics/Fig/XFigGraphicDevice.cpp
index c1c062c..fc0ce44 100644
--- a/src/Bpp/Graphics/Fig/XFigGraphicDevice.cpp
+++ b/src/Bpp/Graphics/Fig/XFigGraphicDevice.cpp
@@ -5,7 +5,7 @@
//
/*
-Copyright or © or Copr. CNRS, (November 17, 2004)
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
This software is a computer program whose purpose is to provide utilitary
classes. This file belongs to the Bio++ Project.
diff --git a/src/Bpp/Graphics/Fig/XFigGraphicDevice.h b/src/Bpp/Graphics/Fig/XFigGraphicDevice.h
index dd70748..de91f69 100644
--- a/src/Bpp/Graphics/Fig/XFigGraphicDevice.h
+++ b/src/Bpp/Graphics/Fig/XFigGraphicDevice.h
@@ -69,7 +69,7 @@ class XFigGraphicDevice:
int fontCode_;
unsigned int fontSize_;
unsigned int fontFlag_;
- unsigned int lineTypeCode_;
+ short lineTypeCode_;
public:
XFigGraphicDevice(std::ostream& out):
diff --git a/src/Bpp/Graphics/RgbColor.h b/src/Bpp/Graphics/RgbColor.h
index faeac00..5e0fdfd 100644
--- a/src/Bpp/Graphics/RgbColor.h
+++ b/src/Bpp/Graphics/RgbColor.h
@@ -5,7 +5,7 @@
//
/*
-Copyright or © or Copr. CNRS, (November 17, 2004)
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
This software is a computer program whose purpose is to provide utilitary
classes. This file belongs to the Bio++ Project.
@@ -140,12 +140,12 @@ class RGBColor:
std::string hex = "";
while (dec > 15)
{
- unsigned int tmp = dec - (int)floor((double)dec/16.)*16;
+ unsigned int tmp = dec - static_cast<unsigned int>(floor(static_cast<double>(dec)/16.)*16);
hex = hexa[tmp] + hex;
- dec=(int)floor((double)dec/16.);
+ dec = static_cast<unsigned int>(floor(static_cast<double>(dec)/16.));
}
hex = hexa[dec] + hex;
- if(hex.size() == 1) hex = "0" + hex;
+ if (hex.size() == 1) hex = "0" + hex;
return hex;
}
diff --git a/src/Bpp/Io/BppOParametrizableFormat.cpp b/src/Bpp/Io/BppOParametrizableFormat.cpp
index c5f9587..10fb470 100644
--- a/src/Bpp/Io/BppOParametrizableFormat.cpp
+++ b/src/Bpp/Io/BppOParametrizableFormat.cpp
@@ -54,22 +54,23 @@ void BppOParametrizableFormat::write(const Parametrizable* parametrizable,
bool printComma) const
{
ParameterList pl = parametrizable->getParameters();
- unsigned int p = out.getPrecision();
+ int p = out.getPrecision();
out.setPrecision(12);
- bool flag=printComma;
- for (unsigned int i = 0; i < pl.size(); i++)
+ bool flag = printComma;
+ for (size_t i = 0; i < pl.size(); ++i)
+ {
+ if (find(writtenNames.begin(), writtenNames.end(), pl[i].getName()) == writtenNames.end())
{
- if (find(writtenNames.begin(),writtenNames.end(),pl[i].getName())==writtenNames.end()){
- if (flag)
- out << ",";
- else
- flag=true;
- string pname = parametrizable->getParameterNameWithoutNamespace(pl[i].getName());
+ if (flag)
+ out << ",";
+ else
+ flag = true;
+ string pname = parametrizable->getParameterNameWithoutNamespace(pl[i].getName());
- (out << pname << "=").enableScientificNotation(false) << pl[i].getValue();
+ (out << pname << "=").enableScientificNotation(false) << pl[i].getValue();
- }
}
+ }
out.setPrecision(p);
}
@@ -82,37 +83,38 @@ void BppOParametrizableFormat::write(const ParameterAliasable* parametrizable,
bool printComma) const
{
ParameterList pl = parametrizable->getIndependentParameters().subList(names);
- unsigned int p = out.getPrecision();
+ int p = out.getPrecision();
out.setPrecision(12);
- bool flag=printComma;
- for (unsigned int i = 0; i < pl.size(); i++)
+ bool flag = printComma;
+ for (size_t i = 0; i < pl.size(); ++i)
+ {
+ if (find(writtenNames.begin(), writtenNames.end(), pl[i].getName()) == writtenNames.end())
{
- if (find(writtenNames.begin(),writtenNames.end(),pl[i].getName())==writtenNames.end()){
- if (flag)
- out << ",";
- else
- flag=true;
- string pname = parametrizable->getParameterNameWithoutNamespace(pl[i].getName());
+ if (flag)
+ out << ",";
+ else
+ flag = true;
+ string pname = parametrizable->getParameterNameWithoutNamespace(pl[i].getName());
- // Check for global aliases:
- if (globalAliases.find(pl[i].getName()) == globalAliases.end())
- {
- (out << pname << "=").enableScientificNotation(false) << pl[i].getValue();
- }
- else
- out << pname << "=" << globalAliases[pl[i].getName()];
+ // Check for global aliases:
+ if (globalAliases.find(pl[i].getName()) == globalAliases.end())
+ {
+ (out << pname << "=").enableScientificNotation(false) << pl[i].getValue();
+ }
+ else
+ out << pname << "=" << globalAliases[pl[i].getName()];
- // Now check for local aliases:
- if (printLocalAliases)
- {
- vector<string> aliases = parametrizable->getAlias(pname);
- for (unsigned int j = 0; aliases.size(); j++)
- {
- out << ", " << aliases[j] << "=" << pname;
- }
- }
- writtenNames.push_back(pl[i].getName());
+ // Now check for local aliases:
+ if (printLocalAliases)
+ {
+ vector<string> aliases = parametrizable->getAlias(pname);
+ for (size_t j = 0; j < aliases.size(); ++j)
+ {
+ out << ", " << aliases[j] << "=" << pname;
+ }
}
+ writtenNames.push_back(pl[i].getName());
}
+ }
out.setPrecision(p);
}
diff --git a/src/Bpp/Io/FileTools.cpp b/src/Bpp/Io/FileTools.cpp
index c6392f3..9dbf2f9 100644
--- a/src/Bpp/Io/FileTools.cpp
+++ b/src/Bpp/Io/FileTools.cpp
@@ -54,7 +54,7 @@ char FileTools::DIR_SEP = '/';
bool FileTools::fileExists(const std::string& filename)
{
ifstream file(filename.c_str());
- bool test = file;
+ bool test = file ? true : false; //needed for CLang.
file.close();
return test;
}
@@ -64,7 +64,7 @@ bool FileTools::fileExists(const std::string& filename)
bool FileTools::directoryExists(const std::string& path)
{
ifstream file(path.c_str());
- bool test = file;
+ bool test = file ? true : false; //needed for CLang.
file.close();
return test;
}
@@ -73,8 +73,8 @@ bool FileTools::directoryExists(const std::string& path)
std::string FileTools::getFileName(const std::string& path, char dirSep)
{
- size_t end = path.find_last_of(".");
- size_t begin = path.find_last_of(dirSep) + 1;
+ ptrdiff_t end = static_cast<ptrdiff_t>(path.find_last_of("."));
+ ptrdiff_t begin = static_cast<ptrdiff_t>(path.find_last_of(dirSep) + 1);
// Return an empty string if specified string isn't a path
if (begin > end) return "";
@@ -105,7 +105,7 @@ streampos FileTools::getFileSize(const std::string& filename)
std::string FileTools::getParent(const std::string& path, char dirSep)
{
// Position of file name:
- size_t begin = path.find_last_of(dirSep);
+ ptrdiff_t begin = static_cast<ptrdiff_t>(path.find_last_of(dirSep));
// Copy string and delte filename:
string result(path);
@@ -120,7 +120,7 @@ std::string FileTools::getParent(const std::string& path, char dirSep)
std::string FileTools::getExtension(const std::string& path)
{
size_t end = path.find_last_of(".");
- return path.substr(end+1);
+ return path.substr(end + 1);
}
/******************************************************************************/
diff --git a/src/Bpp/Io/OutputStream.h b/src/Bpp/Io/OutputStream.h
index 452bb07..5c6d363 100644
--- a/src/Bpp/Io/OutputStream.h
+++ b/src/Bpp/Io/OutputStream.h
@@ -1,5 +1,5 @@
//
-// File: BppStream.h
+// File: OutputStream.h
// Created by: Julien Dutheil
// Created on: Mon Jan 25 17:41 2010
//
@@ -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 _BPPSTREAM_H_
-#define _BPPSTREAM_H_
+#ifndef _OUTPUTSTREAM_H_
+#define _OUTPUTSTREAM_H_
#include "../Clonable.h"
@@ -77,8 +77,8 @@ public:
virtual OutputStream& operator<<(const bool& message) = 0;
virtual OutputStream& endLine() = 0;
virtual OutputStream& flush() = 0;
- virtual OutputStream& setPrecision(unsigned int digit) = 0;
- virtual unsigned int getPrecision() const = 0;
+ virtual OutputStream& setPrecision(int digit) = 0;
+ virtual int getPrecision() const = 0;
virtual OutputStream& enableScientificNotation(bool yn) = 0;
virtual bool isScientificNotationEnabled() const = 0;
@@ -105,19 +105,19 @@ class AbstractOutputStream :
public virtual OutputStream
{
private:
- unsigned int precision_;
+ int precision_;
bool scienceNotation_;
public:
AbstractOutputStream() : precision_(6), scienceNotation_(false) {}
public:
- OutputStream& setPrecision(unsigned int digit)
+ OutputStream& setPrecision(int digit)
{
precision_ = digit;
return *this;
}
- unsigned int getPrecision() const { return precision_; }
+ int getPrecision() const { return precision_; }
virtual OutputStream& enableScientificNotation(bool yn) { scienceNotation_ = yn; return *this; }
virtual bool isScientificNotationEnabled() const { return scienceNotation_; }
@@ -350,5 +350,5 @@ public:
} // end of namespace bpp;
-#endif //_BPPSTREAM_H_
+#endif //_OUTPUTSTREAM_H_
diff --git a/src/Bpp/Numeric/AbstractParameterAliasable.cpp b/src/Bpp/Numeric/AbstractParameterAliasable.cpp
index 98157bd..353cf8c 100644
--- a/src/Bpp/Numeric/AbstractParameterAliasable.cpp
+++ b/src/Bpp/Numeric/AbstractParameterAliasable.cpp
@@ -116,10 +116,12 @@ throw (ParameterNotFoundException, Exception)
string id = "__alias_" + p2 + "_to_" + p1;
string idCheck = "__alias_" + p1 + "_to_" + p2;
+
if (aliasListenersRegister_.find(idCheck) != aliasListenersRegister_.end())
throw Exception("AbstractParameterAliasable::aliasParameters. Trying to alias parameter " + p2 + " to " + p1 + ", but parameter " + p1 + " is already aliased to parameter " + p2 + ".");
Parameter* param1 = &getParameter_(p1);
Parameter* param2 = &getParameter_(p2);
+
if (!param1->hasConstraint())
{
if (param2->hasConstraint())
@@ -127,19 +129,72 @@ throw (ParameterNotFoundException, Exception)
}
else
// We use a small trick here, we test the constraints on the basis of their string description (C++ does not provide a default operator==() :( ).
- if (param2->hasConstraint() && (param1->getConstraint()->getDescription() != param2->getConstraint()->getDescription()))
- throw Exception("AbstractParameterAliasable::aliasParameters. Cannot alias parameter " + p2 + " to " + p1 + ", because the constraints attached to these two parameters are different.");
+ if (param2->hasConstraint() && (param1->getConstraint()->getDescription() != param2->getConstraint()->getDescription()))
+ throw Exception("AbstractParameterAliasable::aliasParameters. Cannot alias parameter " + p2 + " to " + p1 + ", because the constraints attached to these two parameters are different.");
// Every thing seems ok, let's create the listener and register it:
- AliasParameterListener* aliasListener = new AliasParameterListener(id, getParameters().whichParameterHasName(getNamespace() + p2), &getParameters_());
+
+ AliasParameterListener* aliasListener = new AliasParameterListener(id, getParameters().whichParameterHasName(getNamespace() + p2), &getParameters_(), p1);
+
+ ParameterList pl=getParameters_();
+
aliasListenersRegister_[id] = aliasListener;
+
// Now we add it to the appropriate parameter, that is p1.
// The parameter will not own the listener, the bookkeeping being achieved by the register:
param1->addParameterListener(aliasListener, false);
// Finally we remove p2 from the list of independent parameters:
independentParameters_.deleteParameter(getNamespace() + p2);
+
+}
+
+void AbstractParameterAliasable::aliasParameters(map<string, string>& unparsedParams, bool verbose)
+{
+ ParameterList plpars, pl=getParameters();
+
+ for (size_t i=0; i< pl.size(); i++)
+ {
+ if (unparsedParams.find(pl[i].getName())==unparsedParams.end())
+ plpars.addParameter(*pl[i].clone());
+ }
+
+ size_t unp_s=unparsedParams.size();
+ while (unp_s!=0)
+ {
+ map<string, string>::iterator it;
+ for (it=unparsedParams.begin(); it!=unparsedParams.end(); it++)
+ {
+ Parameter* pp=0;
+ try {
+ pp=&plpars.getParameter(it->second);
+ }
+ catch (ParameterNotFoundException& e){
+ if (!pl.hasParameter(it->second))
+ throw ParameterNotFoundException("Unknown aliasing parameter", it->second);
+ continue;
+ }
+ auto_ptr<Parameter> p2(pp->clone());
+ p2->setName(it->first);
+ plpars.addParameter(p2.release());
+ plpars.getParameter(it->first);
+ aliasParameters(it->second, it->first);
+ if (verbose)
+ ApplicationTools::displayResult("Parameter alias found", it->first + " -> " + it->second + " = " + TextTools::toString(pp->getValue()));
+ unparsedParams.erase(it);
+ }
+
+ if (unparsedParams.size()==unp_s)
+ throw Exception("Error, there is a cycle in aliasing");
+ else
+ unp_s=unparsedParams.size();
+ }
+
+ matchParametersValues(plpars);
}
+
+
+
void AbstractParameterAliasable::unaliasParameters(const std::string& p1, const std::string& p2)
throw (ParameterNotFoundException, Exception)
{
@@ -190,18 +245,79 @@ void AbstractParameterAliasable::setNamespace(const std::string& prefix)
vector<string> AbstractParameterAliasable::getAlias(const string& name) const
{
vector<string> aliases;
+
for (map<string, AliasParameterListener*>::const_iterator it = aliasListenersRegister_.begin();
it != aliasListenersRegister_.end();
it++)
{
- if (it->second->getName() == name)
+ if (it->second->getFrom() == name)
{
string alias = it->second->getAlias();
aliases.push_back(alias);
- vector<string> chainAliases = getAlias(alias);
- VectorTools::append(aliases, chainAliases);
+ if (alias!=name){
+ vector<string> chainAliases = getAlias(alias);
+ VectorTools::append(aliases, chainAliases);
+ }
}
}
return aliases;
}
+ParameterList AbstractParameterAliasable::getAliasedParameters(const ParameterList& pl) const
+{
+ ParameterList aliases;
+ bool b=false;
+
+ for (map<string, AliasParameterListener*>::const_iterator it = aliasListenersRegister_.begin();
+ it != aliasListenersRegister_.end();
+ it++)
+ {
+ if ((pl.hasParameter(it->second->getFrom()) ||
+ aliases.hasParameter(it->second->getFrom()))
+ && ! (aliases.hasParameter(it->second->getAlias()) ||
+ pl.hasParameter(it->second->getAlias())))
+ {
+ b=true;
+ aliases.addParameter(getParameter(it->second->getAlias()));
+ }
+ }
+
+ while (b)
+ {
+ b=false;
+
+ for (map<string, AliasParameterListener*>::const_iterator it = aliasListenersRegister_.begin();
+ it != aliasListenersRegister_.end();
+ it++)
+ {
+ if (aliases.hasParameter(it->second->getFrom())
+ && ! (aliases.hasParameter(it->second->getAlias()) ||
+ pl.hasParameter(it->second->getAlias())))
+ {
+ b=true;
+ aliases.addParameter(getParameter(it->second->getAlias()));
+ }
+ }
+ }
+
+ return aliases;
+}
+
+string AbstractParameterAliasable::getFrom(const string& name) const
+{
+ string from="";
+
+ for (map<string, AliasParameterListener*>::const_iterator it = aliasListenersRegister_.begin();
+ it != aliasListenersRegister_.end();
+ it++)
+ {
+ if (it->second->getName() == name)
+ {
+ from = it->second->getFrom();
+ break;
+ }
+ }
+
+ return from;
+}
+
diff --git a/src/Bpp/Numeric/AbstractParameterAliasable.h b/src/Bpp/Numeric/AbstractParameterAliasable.h
index 623161a..1fc4157 100644
--- a/src/Bpp/Numeric/AbstractParameterAliasable.h
+++ b/src/Bpp/Numeric/AbstractParameterAliasable.h
@@ -5,36 +5,36 @@
//
/*
-Copyright or © or Copr. Bio++ Development Team, (November 19, 2004)
-
-This software is a computer program whose purpose is to provide classes
-for numerical calculus.
-
-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.
+ Copyright or © or Copr. Bio++ Development Team, (November 19, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for numerical calculus.
+
+ 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 _ABSTRACTPARAMETERALIASABLE_H_
@@ -55,61 +55,67 @@ namespace bpp
class AliasParameterListener:
public ParameterListener
{
- private:
- std::string id_;
- size_t alias_;
- ParameterList *pl_;
- std::string name_;
-
- public:
- AliasParameterListener(const std::string& id, size_t alias, ParameterList* pl):
- id_(id),
- alias_(alias),
- pl_(pl),
- name_()
- {
- //This allow us to check if the parameter position have changed at some point...
- name_ = (*pl_)[alias].getName();
- }
-
- AliasParameterListener(const AliasParameterListener& apl):
- id_(apl.id_),
- alias_(apl.alias_),
- pl_(apl.pl_),
- name_(apl.name_)
- {}
-
- AliasParameterListener& operator=(const AliasParameterListener& apl)
- {
- id_ = apl.id_;
- alias_ = apl.alias_;
- pl_ = apl.pl_;
- name_ = apl.name_;
- return *this;
- }
-
- AliasParameterListener* clone() const { return new AliasParameterListener(*this); }
-
- public:
- const std::string& getId() const { return id_; }
-
- void setParameterList(ParameterList* pl) { pl_ = pl; }
+ private:
+ std::string id_;
+ size_t alias_;
+ ParameterList *pl_;
+ std::string name_;
+ std::string from_;
+
+ public:
+ AliasParameterListener(const std::string& id, size_t alias, ParameterList* pl, const std::string& from):
+ id_(id),
+ alias_(alias),
+ pl_(pl),
+ name_(),
+ from_(from)
+ {
+ //This allow us to check if the parameter position have changed at some point...
+ name_ = (*pl_)[alias].getName();
+ }
+
+ AliasParameterListener(const AliasParameterListener& apl):
+ id_(apl.id_),
+ alias_(apl.alias_),
+ pl_(apl.pl_),
+ name_(apl.name_),
+ from_(apl.from_)
+ {}
+
+ AliasParameterListener& operator=(const AliasParameterListener& apl)
+ {
+ id_ = apl.id_;
+ alias_ = apl.alias_;
+ pl_ = apl.pl_;
+ name_ = apl.name_;
+ from_ = apl.from_;
+ return *this;
+ }
+
+ AliasParameterListener* clone() const { return new AliasParameterListener(*this); }
+
+ public:
+ const std::string& getId() const { return id_; }
+
+ const std::string& getFrom() const { return from_; }
+
+ void setParameterList(ParameterList* pl) { pl_ = pl; }
- void parameterNameChanged(ParameterEvent& event) throw (Exception) {}
+ void parameterNameChanged(ParameterEvent& event) throw (Exception) {}
- void parameterValueChanged(ParameterEvent& event) throw (Exception)
- {
- Parameter* p = &(*pl_)[alias_];
- if (p->getName() != name_)
- throw Exception("AbstractParameterAliasable::AliasParameterListener::parameterValueChanged. Error, aliased parameter have change, maybe because it was renamed, or a parameter was removed?");
- p->setValue(event.getParameter()->getValue());
- }
+ void parameterValueChanged(ParameterEvent& event) throw (Exception)
+ {
+ Parameter* p = &(*pl_)[alias_];
+ if (p->getName() != name_)
+ throw Exception("AbstractParameterAliasable::AliasParameterListener::parameterValueChanged. Error, aliased parameter have change, maybe because it was renamed, or a parameter was removed?");
+ p->setValue(event.getParameter()->getValue());
+ }
- const std::string& getName() const { return name_; }
+ const std::string& getName() const { return name_; }
- void rename(const std::string& name) { name_ = name; }
+ void rename(const std::string& name) { name_ = name; }
- const std::string& getAlias() const { return (*pl_)[alias_].getName(); }
+ const std::string& getAlias() const { return (*pl_)[alias_].getName(); }
};
@@ -127,78 +133,124 @@ namespace bpp
public AbstractParametrizable,
public virtual ParameterAliasable
{
- private:
+ private:
- mutable ParameterList independentParameters_;
+ mutable ParameterList independentParameters_;
- /**
- * Contains all parameter listeners for maintening alias relationships.
- * The registry will be updated appropriately upon cloning and deleting.
- */
- std::map<std::string, AliasParameterListener *> aliasListenersRegister_;
+ /**
+ * Contains all parameter listeners for maintening alias relationships.
+ * The registry will be updated appropriately upon cloning and deleting.
+ */
+ std::map<std::string, AliasParameterListener *> aliasListenersRegister_;
- public:
- AbstractParameterAliasable(const std::string& prefix) :
- AbstractParametrizable(prefix),
- independentParameters_(),
- aliasListenersRegister_()
- {}
-
- AbstractParameterAliasable(const AbstractParameterAliasable& ap);
+ public:
+ AbstractParameterAliasable(const std::string& prefix) :
+ AbstractParametrizable(prefix),
+ independentParameters_(),
+ aliasListenersRegister_()
+ {}
+
+ AbstractParameterAliasable(const AbstractParameterAliasable& ap);
- AbstractParameterAliasable& operator=(const AbstractParameterAliasable& ap);
+ AbstractParameterAliasable& operator=(const AbstractParameterAliasable& ap);
- virtual ~AbstractParameterAliasable();
+ virtual ~AbstractParameterAliasable();
- public:
- void setNamespace(const std::string& prefix);
+ public:
+ void setNamespace(const std::string& prefix);
- const ParameterList& getIndependentParameters() const { return independentParameters_; }
+ const ParameterList& getIndependentParameters() const { return independentParameters_; }
- size_t getNumberOfIndependentParameters() const { return independentParameters_.size(); }
+ size_t getNumberOfIndependentParameters() const { return independentParameters_.size(); }
- void aliasParameters(const std::string& p1, const std::string& p2) throw (ParameterNotFoundException, Exception);
+ void aliasParameters(const std::string& p1, const std::string& p2) throw (ParameterNotFoundException, Exception);
- void unaliasParameters(const std::string& p1, const std::string& p2) throw (ParameterNotFoundException, Exception);
+ void unaliasParameters(const std::string& p1, const std::string& p2) throw (ParameterNotFoundException, Exception);
- /**
- * @return The list of names of the parameters that are aliased with a given parameter.
- * The implementation is recursive, which means that in the case of A->B->C, getalias(C) will return both A and B.
- * @param name The name of the parameter to look for.
- */
- std::vector<std::string> getAlias(const std::string& name) const;
+ /**
+ * @brief alias the parameters following the links described in a
+ * map, and update the object accordingly. Cycles in aliasing are
+ * detected and forbidden.
+ *
+ * @param unparsedParams the map of the links : <A,B> matches for A->B aliasing.
+ * @param verbose verbosity
+ *
+ **/
+
+ void aliasParameters(std::map<std::string, std::string>& unparsedParams, bool verbose);
- void fireParameterChanged(const ParameterList& parameters)
- {
- independentParameters_.matchParametersValues(getParameters());
- }
+ /**
+ * @brief Return the list of the names of the parameters that are
+ * aliased (directly or not) to one of the parameters of the list.
+ *
+ */
+
+ ParameterList getAliasedParameters(const ParameterList& pl) const;
+
+
+ /**
+ * @return The list of names of the parameters that are aliased with a given parameter.
+ * The implementation is recursive, which means that in the case of A->B->C, getalias(C) will return both A and B.
+ * @param name The name of the parameter to look for.
+ */
+
+ std::vector<std::string> getAlias(const std::string& name) const;
- protected:
- void addParameter_(Parameter* parameter)
- {
- AbstractParametrizable::addParameter_(parameter);
- independentParameters_.addParameter(parameter->clone());
- }
+ /**
+ * @return The name of the parameter from which a given parameter is aliased.
+ * @param name The name of the parameter to look for.
+ */
- void addParameters_(const ParameterList& parameters)
- {
- AbstractParametrizable::addParameters_(parameters);
- independentParameters_.addParameters(parameters);
- }
+ std::string getFrom(const std::string& name) const;
+
+ void fireParameterChanged(const ParameterList& parameters)
+ {
+ independentParameters_.matchParametersValues(getParameters());
+ }
+
+ protected:
+ void addParameter_(Parameter* parameter)
+ {
+ AbstractParametrizable::addParameter_(parameter);
+ independentParameters_.addParameter(parameter->clone());
+ }
+
+ void addParameters_(const ParameterList& parameters)
+ {
+ AbstractParametrizable::addParameters_(parameters);
+ independentParameters_.addParameters(parameters);
+ }
+
+ void deleteParameter_(size_t index) throw (IndexOutOfBoundsException)
+ {
+ std::string name = getParameter_(index).getName();
+ AbstractParametrizable::deleteParameter_(index);
+ if (independentParameters_.hasParameter(name))
+ independentParameters_.deleteParameter(name);
+ }
- void deleteParameter_(size_t index) throw (IndexOutOfBoundsException)
- {
- std::string name = getParameter_(index).getName();
- AbstractParametrizable::deleteParameter_(index);
- if (independentParameters_.hasParameter(name))
+ void deleteParameter_(std::string& name) throw (IndexOutOfBoundsException)
+ {
+ AbstractParametrizable::deleteParameter_(name);
+ if (independentParameters_.hasParameter(name))
independentParameters_.deleteParameter(name);
- }
+ }
- void resetParameters_()
+ void deleteParameters_(const std::vector<std::string>& names)
+ {
+ std::string x;
+ for (size_t i=0; i<names.size(); i++)
{
- AbstractParametrizable::resetParameters_();
- independentParameters_.reset();
+ x=names[i];
+ deleteParameter_(x);
}
+ }
+
+ void resetParameters_()
+ {
+ AbstractParametrizable::resetParameters_();
+ independentParameters_.reset();
+ }
};
diff --git a/src/Bpp/Numeric/AbstractParametrizable.h b/src/Bpp/Numeric/AbstractParametrizable.h
index ba52630..a023d83 100644
--- a/src/Bpp/Numeric/AbstractParametrizable.h
+++ b/src/Bpp/Numeric/AbstractParametrizable.h
@@ -111,9 +111,10 @@ class AbstractParametrizable:
bool matchParametersValues(const ParameterList& parameters)
throw (ConstraintException)
{
- bool test = parameters_.matchParametersValues(parameters);
+ std::auto_ptr< std::vector<size_t> >updatedParameters(new std::vector<size_t>());
+ bool test = parameters_.matchParametersValues(parameters, updatedParameters.get());
if (test)
- fireParameterChanged(parameters);
+ fireParameterChanged(parameters.subList(*updatedParameters));
return test;
}
@@ -144,13 +145,23 @@ class AbstractParametrizable:
parameters_.addParameters(parameters);
}
- void deleteParameter_(size_t index) throw (IndexOutOfBoundsException)
+ void deleteParameter_(size_t index) throw (IndexOutOfBoundsException)
{
if (index >= parameters_.size())
throw IndexOutOfBoundsException("AbstractParametrizable::deleteParameter_.", index, 0, parameters_.size() - 1);
parameters_.deleteParameter(index);
}
+ void deleteParameter_(std::string& name)
+ {
+ parameters_.deleteParameter(name);
+ }
+
+ void deleteParameters_(const std::vector<std::string>& names)
+ {
+ parameters_.deleteParameters(names);
+ }
+
void resetParameters_()
{
parameters_.reset();
diff --git a/src/Bpp/Numeric/AdaptiveKernelDensityEstimation.cpp b/src/Bpp/Numeric/AdaptiveKernelDensityEstimation.cpp
index c3fde70..86608e1 100644
--- a/src/Bpp/Numeric/AdaptiveKernelDensityEstimation.cpp
+++ b/src/Bpp/Numeric/AdaptiveKernelDensityEstimation.cpp
@@ -5,7 +5,7 @@
//
/*
-Copyright or © or Copr. CNRS, (November 17, 2004)
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
This software is a computer program whose purpose is to provide classes
for numerical calculus. This file is part of the Bio++ project.
diff --git a/src/Bpp/Numeric/Constraints.h b/src/Bpp/Numeric/Constraints.h
index 187ec4c..0202cbe 100644
--- a/src/Bpp/Numeric/Constraints.h
+++ b/src/Bpp/Numeric/Constraints.h
@@ -43,10 +43,12 @@
// From the STL:
#include <string>
#include <iostream>
+#include <typeinfo>
// From Utils:
#include "../Clonable.h"
#include "../Text/TextTools.h"
+#include "../Exceptions.h"
#include "NumConstants.h"
@@ -115,6 +117,12 @@ public:
* @return the intersection
*/
virtual Constraint* operator&(const Constraint& c) const = 0;
+
+ /**
+ * @brief Tells if this constraints defines an empty set
+ */
+
+ virtual bool isEmpty() const = 0;
};
/**
@@ -170,13 +178,30 @@ public:
* @param incl Tell if the finite bound is included or not.
* @param precision Parameter precision.
*/
+
IntervalConstraint(bool isPositive, double bound, bool incl, double precision = NumConstants::TINY()) :
lowerBound_(isPositive ? bound : NumConstants::MINF()),
upperBound_(isPositive ? NumConstants::PINF() : bound),
inclLowerBound_(isPositive ? incl : false),
inclUpperBound_(isPositive ? false : incl),
precision_(precision) {}
-
+
+ /**
+ * @brief Create an interval from a string description, using
+ * readDescription method.
+ *
+ **/
+
+ IntervalConstraint(std::string& desc) :
+ lowerBound_(NumConstants::MINF()),
+ upperBound_(NumConstants::PINF()),
+ inclLowerBound_(true),
+ inclUpperBound_(true),
+ precision_(NumConstants::TINY())
+ {
+ readDescription(desc);
+ }
+
virtual ~IntervalConstraint() {}
IntervalConstraint* clone() const { return new IntervalConstraint(*this); }
@@ -249,12 +274,41 @@ public:
{
return (inclLowerBound_ ? "[ " : "]")
+ (finiteLowerBound() ? TextTools::toString(lowerBound_) : "-inf")
- + ", "
+ + "; "
+ (finiteUpperBound() ? TextTools::toString(upperBound_) : "+inf")
+ (inclUpperBound_ ? "] " : "[");
}
/**
+ *
+ * @brief Sets the bounds of the interval from a string.
+ *
+ * @param desc the description in interval-like syntax, with signs
+ * "[", ";", "]" as well as floats and "-inf" and "inf".
+ *
+ **/
+
+ void readDescription(std::string& desc)
+ {
+ size_t pdp=desc.find(";");
+ size_t dc=desc.find_first_of("[]",1);
+
+ if (dc==std::string::npos || pdp==std::string::npos ||
+ (desc[0]!=']' && desc[0]!='[') || (pdp >=dc))
+ throw Exception("Constraints::readDescription. Wrong description:" + desc);
+
+ std::string deb=desc.substr(1,pdp-1);
+ std::string fin=desc.substr(pdp+1, dc-pdp-1);
+
+ inclLowerBound_=(desc[0]=='[');
+ inclUpperBound_=(desc[dc]==']');
+
+ lowerBound_ = (deb=="-inf")?NumConstants::MINF():TextTools::toDouble(deb);
+ upperBound_ = ((fin=="+inf") || (fin=="inf"))?NumConstants::PINF():TextTools::toDouble(fin);
+
+ }
+
+ /**
* @brief Intersect this IntervalConstraint with another one
*
* @param c the intersected IntervalConstraint
@@ -298,43 +352,31 @@ public:
}
/**
- * @brief Intersect this IntervalConstraint with another one
+ * @brief Intersect this IntervalConstraint with another constraint
*
- * @param c the intersected IntervalConstraint
+ * @param c the intersected constraint
* @return this IntervalConstraint modified, or not modified if c is not an
* IntervalConstraint. The precision is set to the maximum of bith precisions.
*/
-
IntervalConstraint& operator&=(const Constraint& c)
{
- const IntervalConstraint* pi = dynamic_cast<const IntervalConstraint*>(&c);
+ try {
+ const IntervalConstraint& pi = dynamic_cast<const IntervalConstraint&>(c);
- if (pi)
- {
- if (lowerBound_ <= pi->lowerBound_)
- {
- lowerBound_ = pi->lowerBound_;
- inclLowerBound_ = pi->inclLowerBound_;
- }
- else
+ if (lowerBound_ <= pi.lowerBound_)
{
- lowerBound_ = lowerBound_;
- inclLowerBound_ = inclLowerBound_;
+ lowerBound_ = pi.lowerBound_;
+ inclLowerBound_ = pi.inclLowerBound_;
}
- if (upperBound_ >= pi->upperBound_)
- {
- upperBound_ = pi->upperBound_;
- inclUpperBound_ = pi->inclUpperBound_;
- }
- else
+ if (upperBound_ >= pi.upperBound_)
{
- upperBound_ = upperBound_;
- inclUpperBound_ = inclUpperBound_;
+ upperBound_ = pi.upperBound_;
+ inclUpperBound_ = pi.inclUpperBound_;
}
- if (pi->getPrecision()>precision_)
- precision_=pi->getPrecision();
- }
+ if (pi.getPrecision() > precision_)
+ precision_ = pi.getPrecision();
+ } catch(std::bad_cast&) {}
return *this;
}
@@ -375,6 +417,18 @@ public:
return lowerBound_ >= i.lowerBound_
&& upperBound_ <= i.upperBound_;
}
+
+ /**
+ * @brief Tells if this interval is empty
+ */
+
+ bool isEmpty() const
+ {
+ return ((lowerBound_ > upperBound_) ||
+ ((lowerBound_ > upperBound_) &&
+ inclUpperBound_ && inclLowerBound_));
+ }
+
};
diff --git a/src/Bpp/Numeric/DataTable.cpp b/src/Bpp/Numeric/DataTable.cpp
index 7c0d8a8..5049655 100644
--- a/src/Bpp/Numeric/DataTable.cpp
+++ b/src/Bpp/Numeric/DataTable.cpp
@@ -5,37 +5,37 @@
//
/*
-Copyright or © or Copr. CNRS, (November 17, 2004)
-
-This software is a computer program whose purpose is to provide classes
-for numerical calculus.
-
-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.
-*/
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for numerical calculus.
+
+ 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 "DataTable.h"
#include "VectorTools.h"
@@ -49,42 +49,65 @@ using namespace std;
/******************************************************************************/
DataTable::DataTable(size_t nRow, size_t nCol) :
- nRow_(nRow), nCol_(nCol), data_(nCol), rowNames_(0), colNames_(0)
+ nRow_(nRow),
+ nCol_(nCol),
+ data_(nCol),
+ rowNames_(0),
+ colNames_(0)
{
- for(size_t i = 0; i < nCol; i++)
+ for (size_t i = 0; i < nCol; i++)
+ {
data_[i].resize(nRow);
+ }
}
-
+
DataTable::DataTable(size_t nCol) :
- nRow_(0), nCol_(nCol), data_(nCol), rowNames_(0), colNames_(0)
-{
-}
-
+ nRow_(0),
+ nCol_(nCol),
+ data_(nCol),
+ rowNames_(0),
+ colNames_(0)
+{}
+
DataTable::DataTable(const std::vector<std::string>& colNames) throw (DuplicatedTableColumnNameException) :
- nRow_(0), nCol_(colNames.size()), data_(colNames.size()), rowNames_(0), colNames_(0)
+ nRow_(0),
+ nCol_(colNames.size()),
+ data_(colNames.size()),
+ rowNames_(0),
+ colNames_(0)
{
- setColumnNames(colNames); //May throw an exception.
+ setColumnNames(colNames); // May throw an exception.
}
-
+
DataTable::DataTable(const DataTable& table) :
- nRow_(table.nRow_), nCol_(table.nCol_), data_(table.data_), rowNames_(0), colNames_(0)
+ nRow_(table.nRow_),
+ nCol_(table.nCol_),
+ data_(table.data_),
+ rowNames_(0),
+ colNames_(0)
{
- if(table.rowNames_) rowNames_ = new vector<string>(*table.rowNames_);
- if(table.colNames_) colNames_ = new vector<string>(*table.colNames_);
+ if (table.rowNames_)
+ rowNames_ = new vector<string>(*table.rowNames_);
+ if (table.colNames_)
+ colNames_ = new vector<string>(*table.colNames_);
}
-DataTable& DataTable::operator=(const DataTable & table)
+DataTable& DataTable::operator=(const DataTable& table)
{
nRow_ = table.nRow_;
nCol_ = table.nCol_;
data_ = table.data_;
- if(rowNames_) delete rowNames_;
- if(colNames_) delete colNames_;
+ if (rowNames_)
+ delete rowNames_;
+ if (colNames_)
+ delete colNames_;
rowNames_ = 0;
colNames_ = 0;
- if(table.rowNames_) rowNames_ = new vector<string>(*table.rowNames_);
- if(table.colNames_) colNames_ = new vector<string>(*table.colNames_);
+ if (table.rowNames_)
+ rowNames_ = new vector<string>(*table.rowNames_);
+ if (table.colNames_)
+ colNames_ = new vector<string>(*table.colNames_);
return *this;
}
@@ -92,93 +115,107 @@ DataTable& DataTable::operator=(const DataTable & table)
DataTable::~DataTable()
{
- if(rowNames_ != NULL) delete rowNames_;
- if(colNames_ != NULL) delete colNames_;
+ if (rowNames_ != NULL)
+ delete rowNames_;
+ if (colNames_ != NULL)
+ delete colNames_;
}
/******************************************************************************/
/* Cell access */
/******************************************************************************/
-string & DataTable::operator()(size_t rowIndex, size_t colIndex) throw (IndexOutOfBoundsException)
+string& DataTable::operator()(size_t rowIndex, size_t colIndex) throw (IndexOutOfBoundsException)
{
- if(colIndex >= nCol_) throw IndexOutOfBoundsException("DataTable::operator(size_t, size_t).", colIndex, 0, nCol_ - 1);
- if(rowIndex >= data_[colIndex].size()) throw IndexOutOfBoundsException("DataTable::operator(size_t, size_t).", rowIndex, 0, data_[colIndex].size() - 1);
+ if (colIndex >= nCol_)
+ throw IndexOutOfBoundsException("DataTable::operator(size_t, size_t).", colIndex, 0, nCol_ - 1);
+ if (rowIndex >= data_[colIndex].size())
+ throw IndexOutOfBoundsException("DataTable::operator(size_t, size_t).", rowIndex, 0, data_[colIndex].size() - 1);
return data_[colIndex][rowIndex];
}
-const string & DataTable::operator()(size_t rowIndex, size_t colIndex) const throw (IndexOutOfBoundsException)
+const string& DataTable::operator()(size_t rowIndex, size_t colIndex) const throw (IndexOutOfBoundsException)
{
- if(colIndex >= nCol_) throw IndexOutOfBoundsException("DataTable::operator(size_t, size_t).", colIndex, 0, nCol_ - 1);
- if(rowIndex >= data_[colIndex].size()) throw IndexOutOfBoundsException("DataTable::operator(size_t, size_t).", rowIndex, 0, data_[colIndex].size() - 1);
+ if (colIndex >= nCol_)
+ throw IndexOutOfBoundsException("DataTable::operator(size_t, size_t).", colIndex, 0, nCol_ - 1);
+ if (rowIndex >= data_[colIndex].size())
+ throw IndexOutOfBoundsException("DataTable::operator(size_t, size_t).", rowIndex, 0, data_[colIndex].size() - 1);
return data_[colIndex][rowIndex];
}
/******************************************************************************/
-string & DataTable::operator()(const string & rowName, const string & colName)
+string& DataTable::operator()(const string& rowName, const string& colName)
throw (NoTableRowNamesException, NoTableColumnNamesException, TableNameNotFoundException)
{
- if(rowNames_ == NULL) throw NoTableRowNamesException("DataTable::operator(const string &, const string &).");
- if(colNames_ == NULL) throw NoTableColumnNamesException("DataTable::operator(const string &, const string &).");
+ if (rowNames_ == NULL)
+ throw NoTableRowNamesException("DataTable::operator(const string &, const string &).");
+ if (colNames_ == NULL)
+ throw NoTableColumnNamesException("DataTable::operator(const string &, const string &).");
try
{
size_t rowIndex = VectorTools::which(*rowNames_, rowName);
size_t colIndex = VectorTools::which(*colNames_, colName);
return (*this)(rowIndex, colIndex);
}
- catch(ElementNotFoundException<string> & ex)
+ catch (ElementNotFoundException<string>& ex)
{
throw TableNameNotFoundException("DataTable::operator(const string &, const string &).", *ex.getElement());
}
}
-const string & DataTable::operator()(const string & rowName, const string & colName) const
+const string& DataTable::operator()(const string& rowName, const string& colName) const
throw (NoTableRowNamesException, NoTableColumnNamesException, TableNameNotFoundException)
{
- if(rowNames_ == NULL) throw NoTableRowNamesException("DataTable::operator(const string &, const string &).");
- if(colNames_ == NULL) throw NoTableColumnNamesException("DataTable::operator(const string &, const string &).");
+ if (rowNames_ == NULL)
+ throw NoTableRowNamesException("DataTable::operator(const string &, const string &).");
+ if (colNames_ == NULL)
+ throw NoTableColumnNamesException("DataTable::operator(const string &, const string &).");
try
{
size_t rowIndex = VectorTools::which(*rowNames_, rowName);
size_t colIndex = VectorTools::which(*colNames_, colName);
return (*this)(rowIndex, colIndex);
}
- catch(ElementNotFoundException<string> & ex)
+ catch (ElementNotFoundException<string>& ex)
{
throw TableNameNotFoundException("DataTable::operator(const string &, const string &).", *ex.getElement());
}
}
-
+
/******************************************************************************/
-string & DataTable::operator()(const string & rowName, size_t colIndex)
+string& DataTable::operator()(const string& rowName, size_t colIndex)
throw (NoTableRowNamesException, TableNameNotFoundException, IndexOutOfBoundsException)
{
- if(rowNames_ == NULL) throw NoTableRowNamesException("DataTable::operator(const string &, size_t).");
- if(colIndex >= nCol_) throw IndexOutOfBoundsException("DataTable::operator(const string &, size_t).", colIndex, 0, nCol_ - 1);
+ if (rowNames_ == NULL)
+ throw NoTableRowNamesException("DataTable::operator(const string &, size_t).");
+ if (colIndex >= nCol_)
+ throw IndexOutOfBoundsException("DataTable::operator(const string &, size_t).", colIndex, 0, nCol_ - 1);
try
{
size_t rowIndex = VectorTools::which(*rowNames_, rowName);
return (*this)(rowIndex, colIndex);
}
- catch(ElementNotFoundException<string> & ex)
+ catch (ElementNotFoundException<string>& ex)
{
throw TableNameNotFoundException("DataTable::operator(const string &, size_t).", *ex.getElement());
}
}
-const string & DataTable::operator()(const string & rowName, size_t colIndex) const
+const string& DataTable::operator()(const string& rowName, size_t colIndex) const
throw (NoTableRowNamesException, TableNameNotFoundException, IndexOutOfBoundsException)
{
- if(rowNames_ == NULL) throw NoTableRowNamesException("DataTable::operator(const string &, size_t).");
- if(colIndex >= nCol_) throw IndexOutOfBoundsException("DataTable::operator(const string &, size_t).", colIndex, 0, nCol_ - 1);
+ if (rowNames_ == NULL)
+ throw NoTableRowNamesException("DataTable::operator(const string &, size_t).");
+ if (colIndex >= nCol_)
+ throw IndexOutOfBoundsException("DataTable::operator(const string &, size_t).", colIndex, 0, nCol_ - 1);
try
{
size_t rowIndex = VectorTools::which(*rowNames_, rowName);
return (*this)(rowIndex, colIndex);
}
- catch(ElementNotFoundException<string> & ex)
+ catch (ElementNotFoundException<string>& ex)
{
throw TableNameNotFoundException("DataTable::operator(const string &, size_t).", *ex.getElement());
}
@@ -186,33 +223,37 @@ throw (NoTableRowNamesException, TableNameNotFoundException, IndexOutOfBoundsExc
/******************************************************************************/
-string & DataTable::operator()(size_t rowIndex, const string & colName)
+string& DataTable::operator()(size_t rowIndex, const string& colName)
throw (IndexOutOfBoundsException, NoTableColumnNamesException, TableNameNotFoundException)
{
- if(colNames_ == NULL) throw NoTableColumnNamesException("DataTable::operator(size_t, const string &).");
+ if (colNames_ == NULL)
+ throw NoTableColumnNamesException("DataTable::operator(size_t, const string &).");
try
{
size_t colIndex = VectorTools::which(*colNames_, colName);
- if(rowIndex >= data_[colIndex].size()) throw IndexOutOfBoundsException("DataTable::operator(size_t, const string &).", rowIndex, 0, data_[colIndex].size() - 1);
+ if (rowIndex >= data_[colIndex].size())
+ throw IndexOutOfBoundsException("DataTable::operator(size_t, const string &).", rowIndex, 0, data_[colIndex].size() - 1);
return (*this)(rowIndex, colIndex);
}
- catch(ElementNotFoundException<string> & ex)
+ catch (ElementNotFoundException<string>& ex)
{
throw TableNameNotFoundException("DataTable::operator(const string &, const string &).", *ex.getElement());
}
}
-const string & DataTable::operator()(size_t rowIndex, const string & colName) const
+const string& DataTable::operator()(size_t rowIndex, const string& colName) const
throw (IndexOutOfBoundsException, NoTableColumnNamesException, TableNameNotFoundException)
{
- if(colNames_ == NULL) throw NoTableColumnNamesException("DataTable::operator(size_t, const string &).");
+ if (colNames_ == NULL)
+ throw NoTableColumnNamesException("DataTable::operator(size_t, const string &).");
try
{
size_t colIndex = VectorTools::which(*colNames_, colName);
- if(rowIndex >= data_[colIndex].size()) throw IndexOutOfBoundsException("DataTable::operator(size_t, const string &).", rowIndex, 0, data_[colIndex].size() - 1);
+ if (rowIndex >= data_[colIndex].size())
+ throw IndexOutOfBoundsException("DataTable::operator(size_t, const string &).", rowIndex, 0, data_[colIndex].size() - 1);
return (*this)(rowIndex, colIndex);
}
- catch(ElementNotFoundException<string> & ex)
+ catch (ElementNotFoundException<string>& ex)
{
throw TableNameNotFoundException("DataTable::operator(const string &, const string &).", *ex.getElement());
}
@@ -222,145 +263,167 @@ throw (IndexOutOfBoundsException, NoTableColumnNamesException, TableNameNotFound
/* Work with names */
/******************************************************************************/
-void DataTable::setRowNames(const vector<string> & rowNames)
+void DataTable::setRowNames(const vector<string>& rowNames)
throw (DimensionException, DuplicatedTableRowNameException)
{
if (!VectorTools::isUnique(rowNames))
{
throw DuplicatedTableRowNameException("DataTable::setRowNames(...). Row names must be unique.");
}
- if (rowNames.size() != nRow_) throw DimensionException("DataTable::setRowNames.", rowNames.size(), nRow_);
+ if (rowNames.size() != nRow_)
+ throw DimensionException("DataTable::setRowNames.", rowNames.size(), nRow_);
else
{
- if(rowNames_ != NULL) delete rowNames_;
+ if (rowNames_ != NULL)
+ delete rowNames_;
rowNames_ = new vector<string>(rowNames.begin(), rowNames.end());
}
}
vector<string> DataTable::getRowNames() const throw (NoTableRowNamesException)
{
- if(rowNames_ == NULL) throw NoTableRowNamesException("DataTable::getRowNames().");
- return * rowNames_;
+ if (rowNames_ == NULL)
+ throw NoTableRowNamesException("DataTable::getRowNames().");
+ return *rowNames_;
}
string DataTable::getRowName(size_t index) const throw (NoTableRowNamesException, IndexOutOfBoundsException)
{
- if(rowNames_ == NULL) throw NoTableRowNamesException("DataTable::getRowName(size_t).");
- if(index >= nRow_) throw IndexOutOfBoundsException("DataTable::getRowName(size_t).", index, 0, nRow_ - 1);
- return (* rowNames_)[index];
+ if (rowNames_ == NULL)
+ throw NoTableRowNamesException("DataTable::getRowName(size_t).");
+ if (index >= nRow_)
+ throw IndexOutOfBoundsException("DataTable::getRowName(size_t).", index, 0, nRow_ - 1);
+ return (*rowNames_)[index];
}
/******************************************************************************/
-void DataTable::setColumnNames(const vector<string> & colNames)
+void DataTable::setColumnNames(const vector<string>& colNames)
throw (DimensionException, DuplicatedTableColumnNameException)
{
- if(!VectorTools::isUnique(colNames)) throw DuplicatedTableColumnNameException("DataTable::setColumnNames(...). Column names must be unique.");
- if(colNames.size() != nCol_) throw DimensionException("DataTable::setColumnNames.", colNames.size(), nCol_);
+ if (!VectorTools::isUnique(colNames))
+ throw DuplicatedTableColumnNameException("DataTable::setColumnNames(...). Column names must be unique.");
+ if (colNames.size() != nCol_)
+ throw DimensionException("DataTable::setColumnNames.", colNames.size(), nCol_);
else
{
- if(colNames_ != NULL) delete colNames_;
+ if (colNames_ != NULL)
+ delete colNames_;
colNames_ = new vector<string>(colNames.begin(), colNames.end());
}
}
vector<string> DataTable::getColumnNames() const throw (NoTableColumnNamesException)
{
- if(colNames_ == NULL) throw NoTableColumnNamesException("DataTable::getColumnNames().");
+ if (colNames_ == NULL)
+ throw NoTableColumnNamesException("DataTable::getColumnNames().");
return *colNames_;
}
string DataTable::getColumnName(size_t index) const throw (NoTableColumnNamesException, IndexOutOfBoundsException)
{
- if(colNames_ == NULL) throw NoTableColumnNamesException("DataTable::getColumnName(size_t).");
- if(index >= nCol_) throw IndexOutOfBoundsException("DataTable::getColumnName(size_t).", index, 0, nCol_ - 1);
- return (* colNames_)[index];
+ if (colNames_ == NULL)
+ throw NoTableColumnNamesException("DataTable::getColumnName(size_t).");
+ if (index >= nCol_)
+ throw IndexOutOfBoundsException("DataTable::getColumnName(size_t).", index, 0, nCol_ - 1);
+ return (*colNames_)[index];
}
/******************************************************************************/
/* Work on columns */
/******************************************************************************/
-vector<string> & DataTable::getColumn(size_t index)
- throw (IndexOutOfBoundsException)
+vector<string>& DataTable::getColumn(size_t index)
+throw (IndexOutOfBoundsException)
{
- if(index >= nCol_) throw IndexOutOfBoundsException("DataTable::getColumn(size_t).", index, 0, nCol_ - 1);
+ if (index >= nCol_)
+ throw IndexOutOfBoundsException("DataTable::getColumn(size_t).", index, 0, nCol_ - 1);
return data_[index];
}
-const vector<string> & DataTable::getColumn(size_t index) const
- throw (IndexOutOfBoundsException)
+const vector<string>& DataTable::getColumn(size_t index) const
+throw (IndexOutOfBoundsException)
{
- if(index >= nCol_) throw IndexOutOfBoundsException("DataTable::getColumn(size_t).", index, 0, nCol_ - 1);
+ if (index >= nCol_)
+ throw IndexOutOfBoundsException("DataTable::getColumn(size_t).", index, 0, nCol_ - 1);
return data_[index];
-}
+}
-vector<string> & DataTable::getColumn(const string & colName)
- throw (NoTableColumnNamesException, TableColumnNameNotFoundException)
+vector<string>& DataTable::getColumn(const string& colName)
+throw (NoTableColumnNamesException, TableColumnNameNotFoundException)
{
- if(colNames_ == NULL) throw NoTableColumnNamesException("DataTable::getColumn(const string &).");
+ if (colNames_ == NULL)
+ throw NoTableColumnNamesException("DataTable::getColumn(const string &).");
try
{
size_t colIndex = VectorTools::which(*colNames_, colName);
return data_[colIndex];
}
- catch(ElementNotFoundException<string> & ex)
+ catch (ElementNotFoundException<string>& ex)
{
throw TableColumnNameNotFoundException("DataTable::getColumn(const string &).", colName);
}
}
-const vector<string> & DataTable::getColumn(const string & colName) const
- throw (NoTableColumnNamesException, TableColumnNameNotFoundException)
+const vector<string>& DataTable::getColumn(const string& colName) const
+throw (NoTableColumnNamesException, TableColumnNameNotFoundException)
{
- if(colNames_ == NULL) throw NoTableColumnNamesException("DataTable::getColumn(const string &).");
+ if (colNames_ == NULL)
+ throw NoTableColumnNamesException("DataTable::getColumn(const string &).");
try
{
size_t colIndex = VectorTools::which(*colNames_, colName);
return data_[colIndex];
}
- catch(ElementNotFoundException<string> & ex)
+ catch (ElementNotFoundException<string>& ex)
{
throw TableColumnNameNotFoundException("DataTable::getColumn(const string &).", colName);
}
}
-bool DataTable::hasColumn(const string & colName) const
-{
- if(colNames_ == NULL) return false;
- for(size_t i = 0; i < colNames_->size(); i++)
- if((* colNames_)[i] == colName) return true;
+bool DataTable::hasColumn(const string& colName) const
+{
+ if (colNames_ == NULL)
+ return false;
+ for (size_t i = 0; i < colNames_->size(); i++)
+ {
+ if ((*colNames_)[i] == colName)
+ return true;
+ }
return false;
}
void DataTable::deleteColumn(size_t index)
- throw (IndexOutOfBoundsException)
+throw (IndexOutOfBoundsException)
{
- if(index >= nCol_) throw IndexOutOfBoundsException("DataTable::deleteColumn(size_t).", index, 0, nCol_ - 1);
- data_.erase(data_.begin() + index);
- if(colNames_ != NULL) colNames_->erase(colNames_->begin()+index);
+ if (index >= nCol_)
+ throw IndexOutOfBoundsException("DataTable::deleteColumn(size_t).", index, 0, nCol_ - 1);
+ data_.erase(data_.begin() + static_cast<ptrdiff_t>(index));
+ if (colNames_)
+ colNames_->erase(colNames_->begin() + static_cast<ptrdiff_t>(index));
nCol_--;
}
-void DataTable::deleteColumn(const string & colName)
- throw (NoTableColumnNamesException, TableColumnNameNotFoundException)
+void DataTable::deleteColumn(const string& colName)
+throw (NoTableColumnNamesException, TableColumnNameNotFoundException)
{
- if(colNames_ == NULL) throw NoTableColumnNamesException("DataTable::deleteColumn(const string &).");
+ if (!colNames_)
+ throw NoTableColumnNamesException("DataTable::deleteColumn(const string &).");
try
{
size_t colIndex = VectorTools::which(*colNames_, colName);
- data_.erase(data_.begin() + colIndex);
- colNames_->erase(colNames_->begin() + colIndex);
+ data_.erase(data_.begin() + static_cast<ptrdiff_t>(colIndex));
+ colNames_->erase(colNames_->begin() + static_cast<ptrdiff_t>(colIndex));
nCol_--;
}
- catch(ElementNotFoundException<string> & ex)
+ catch (ElementNotFoundException<string>& ex)
{
throw TableColumnNameNotFoundException("DataTable::deleteColumn(const string &).", colName);
}
}
void DataTable::addColumn(const vector<string>& newColumn)
- throw (DimensionException, TableColumnNamesException)
+throw (DimensionException, TableColumnNamesException)
{
if (colNames_)
throw TableColumnNamesException("DataTable::addColumn. Table has column names.");
@@ -371,12 +434,14 @@ void DataTable::addColumn(const vector<string>& newColumn)
}
void DataTable::addColumn(const string& colName, const vector<string>& newColumn)
- throw (DimensionException, NoTableColumnNamesException, DuplicatedTableColumnNameException)
+throw (DimensionException, NoTableColumnNamesException, DuplicatedTableColumnNameException)
{
- if(!colNames_)
+ if (!colNames_)
{
- if (nCol_ == 0) colNames_ = new vector<string>();
- else throw NoTableColumnNamesException("DataTable::addColumn. Table has column names.");
+ if (nCol_ == 0)
+ colNames_ = new vector<string>();
+ else
+ throw NoTableColumnNamesException("DataTable::addColumn. Table has column names.");
}
if (newColumn.size() != nRow_)
throw DimensionException("DataTable::addColumn.", newColumn.size(), nRow_);
@@ -392,101 +457,121 @@ void DataTable::addColumn(const string& colName, const vector<string>& newColumn
/******************************************************************************/
vector<string> DataTable::getRow(size_t index) const
- throw (IndexOutOfBoundsException)
+throw (IndexOutOfBoundsException)
{
- if(index >= nRow_) throw IndexOutOfBoundsException("DataTable::getRow(size_t).", index, 0, nRow_ - 1);
+ if (index >= nRow_)
+ throw IndexOutOfBoundsException("DataTable::getRow(size_t).", index, 0, nRow_ - 1);
vector<string> row;
- for (size_t i = 0 ; i < nCol_ ; i++)
+ for (size_t i = 0; i < nCol_; i++)
+ {
row.push_back(data_[i][index]);
+ }
return row;
}
vector<string> DataTable::getRow(const string& rowName) const
- throw (NoTableRowNamesException, TableRowNameNotFoundException)
+throw (NoTableRowNamesException, TableRowNameNotFoundException)
{
- if (!rowNames_) throw NoTableRowNamesException("DataTable::getRow(const string &).");
+ if (!rowNames_)
+ throw NoTableRowNamesException("DataTable::getRow(const string &).");
try
{
size_t rowIndex = VectorTools::which(*rowNames_, rowName);
vector<string> row;
- for (size_t i = 0 ; i < nCol_ ; i++)
+ for (size_t i = 0; i < nCol_; i++)
+ {
row.push_back(data_[i][rowIndex]);
+ }
return row;
}
- catch(ElementNotFoundException<string> & ex)
+ catch (ElementNotFoundException<string>& ex)
{
throw TableRowNameNotFoundException("DataTable::getRow(const string &).", rowName);
}
}
-bool DataTable::hasRow(const string & rowName) const
-{
- if(rowNames_ == NULL) return false;
- for(size_t i = 0; i < rowNames_->size(); i++)
+bool DataTable::hasRow(const string& rowName) const
+{
+ if (rowNames_ == NULL)
+ return false;
+ for (size_t i = 0; i < rowNames_->size(); i++)
{
- if((* rowNames_)[i] == rowName) return true;
+ if ((*rowNames_)[i] == rowName)
+ return true;
}
return false;
}
void DataTable::deleteRow(size_t index)
- throw (IndexOutOfBoundsException)
+throw (IndexOutOfBoundsException)
{
- for(size_t j = 0; j < nCol_; j++)
+ for (size_t j = 0; j < nCol_; j++)
{
- vector<string> * column = & data_[j];
- if(index >= column->size()) throw IndexOutOfBoundsException("DataTable::deleteRow(size_t).", index, 0, column->size() - 1);
- column->erase(column->begin()+index);
+ vector<string>* column = &data_[j];
+ if (index >= column->size())
+ throw IndexOutOfBoundsException("DataTable::deleteRow(size_t).", index, 0, column->size() - 1);
+ column->erase(column->begin() + static_cast<ptrdiff_t>(index));
}
- if(rowNames_ != NULL) rowNames_->erase(rowNames_->begin()+index);
+ if (rowNames_)
+ rowNames_->erase(rowNames_->begin() + static_cast<ptrdiff_t>(index));
nRow_--;
}
void DataTable::deleteRow(const string& rowName)
- throw (NoTableRowNamesException, TableRowNameNotFoundException)
+throw (NoTableRowNamesException, TableRowNameNotFoundException)
{
- if(rowNames_ == NULL) throw NoTableRowNamesException("DataTable::deleteRow(const string &).");
+ if (!rowNames_)
+ throw NoTableRowNamesException("DataTable::deleteRow(const string &).");
try
{
size_t rowIndex = VectorTools::which(*rowNames_, rowName);
- for(size_t j = 0; j < nCol_; j++)
+ for (size_t j = 0; j < nCol_; j++)
{
- vector<string> * column = & data_[j];
- column->erase(column->begin()+rowIndex);
+ vector<string>* column = &data_[j];
+ column->erase(column->begin() + static_cast<ptrdiff_t>(rowIndex));
}
- rowNames_->erase(rowNames_->begin()+rowIndex);
+ rowNames_->erase(rowNames_->begin() + static_cast<ptrdiff_t>(rowIndex));
nRow_--;
}
- catch(ElementNotFoundException<string> & ex)
+ catch (ElementNotFoundException<string>& ex)
{
throw TableRowNameNotFoundException("DataTable::deleteRow(const string &).", rowName);
}
}
void DataTable::addRow(const vector<string>& newRow)
- throw (DimensionException, TableRowNamesException)
+throw (DimensionException, TableRowNamesException)
{
- if (rowNames_) throw TableRowNamesException("DataTable::addRow. Table has row names.");
- if (newRow.size() != nCol_) throw DimensionException("DataTable::addRow.", newRow.size(), nCol_);
+ if (rowNames_)
+ throw TableRowNamesException("DataTable::addRow. Table has row names.");
+ if (newRow.size() != nCol_)
+ throw DimensionException("DataTable::addRow.", newRow.size(), nCol_);
for (size_t j = 0; j < nCol_; j++)
+ {
data_[j].push_back(newRow[j]);
+ }
nRow_++;
}
void DataTable::addRow(const string& rowName, const vector<string>& newRow)
- throw (DimensionException, NoTableRowNamesException, DuplicatedTableRowNameException)
+throw (DimensionException, NoTableRowNamesException, DuplicatedTableRowNameException)
{
if (!rowNames_)
{
- if (nRow_ == 0) rowNames_ = new vector<string>();
- else throw NoTableRowNamesException("DataTable::addRow. Table has row names.");
+ if (nRow_ == 0)
+ rowNames_ = new vector<string>();
+ else
+ throw NoTableRowNamesException("DataTable::addRow. Table has row names.");
}
- if (newRow.size() != nCol_) throw DimensionException("DataTable::addRow.", newRow.size(), nCol_);
+ if (newRow.size() != nCol_)
+ throw DimensionException("DataTable::addRow.", newRow.size(), nCol_);
if (nRow_ > 0 && find(rowNames_->begin(), rowNames_->end(), rowName) != rowNames_->end())
throw DuplicatedTableRowNameException("DataTable::addRow(const string &, const vector<string> &). Row names must be unique.");
rowNames_->push_back(rowName);
for (size_t j = 0; j < nCol_; j++)
+ {
data_[j].push_back(newRow[j]);
+ }
nRow_++;
}
@@ -495,7 +580,7 @@ void DataTable::addRow(const string& rowName, const vector<string>& newRow)
/******************************************************************************/
DataTable* DataTable::read(istream& in, const string& sep, bool header, int rowNames)
- throw (DimensionException, IndexOutOfBoundsException, DuplicatedTableRowNameException)
+throw (DimensionException, IndexOutOfBoundsException, DuplicatedTableRowNameException)
{
string firstLine = FileTools::getNextLine(in);
StringTokenizer st1(firstLine, sep, false, true);
@@ -505,12 +590,12 @@ DataTable* DataTable::read(istream& in, const string& sep, bool header, int rowN
vector<string> row2(st2.getTokens().begin(), st2.getTokens().end());
size_t nCol = row1.size();
bool hasRowNames;
- DataTable * dt;
- if(row1.size() == row2.size())
+ DataTable* dt;
+ if (row1.size() == row2.size())
{
dt = new DataTable(nCol);
- if(header)
- { //Use first line as header.
+ if (header)
+ { // Use first line as header.
dt->setColumnNames(row1);
}
else
@@ -520,25 +605,26 @@ DataTable* DataTable::read(istream& in, const string& sep, bool header, int rowN
dt->addRow(row2);
hasRowNames = false;
}
- else if(row1.size() == row2.size() - 1)
+ else if (row1.size() == row2.size() - 1)
{
dt = new DataTable(nCol);
dt->setColumnNames(row1);
string rowName = *row2.begin();
- dt->addRow(rowName, vector<string>(row2.begin()+1, row2.end()));
+ dt->addRow(rowName, vector<string>(row2.begin() + 1, row2.end()));
hasRowNames = true;
}
- else throw DimensionException("DataTable::read(...). Row 2 has not the correct number of columns.", row2.size(), nCol);
+ else
+ throw DimensionException("DataTable::read(...). Row 2 has not the correct number of columns.", row2.size(), nCol);
// Now read each line:
string line = FileTools::getNextLine(in);
- while(!TextTools::isEmpty(line))
+ while (!TextTools::isEmpty(line))
{
StringTokenizer st(line, sep, false, true);
- if(hasRowNames)
+ if (hasRowNames)
{
string rowName = *st.getTokens().begin();
- vector<string> row(st.getTokens().begin()+1, st.getTokens().end());
+ vector<string> row(st.getTokens().begin() + 1, st.getTokens().end());
dt->addRow(rowName, row);
}
else
@@ -550,15 +636,16 @@ DataTable* DataTable::read(istream& in, const string& sep, bool header, int rowN
}
// Row names:
- if(rowNames > -1)
+ if (rowNames > -1)
{
- if((size_t)rowNames >= nCol) throw IndexOutOfBoundsException("DataTable::read(...). Invalid column specified for row names.", rowNames, 0, nCol-1);
- vector<string> col = dt->getColumn((size_t)rowNames);
+ if (static_cast<size_t>(rowNames) >= nCol)
+ throw IndexOutOfBoundsException("DataTable::read(...). Invalid column specified for row names.", static_cast<size_t>(rowNames), 0, nCol - 1);
+ vector<string> col = dt->getColumn(static_cast<size_t>(rowNames));
dt->setRowNames(col);
- dt->deleteColumn(rowNames);
+ dt->deleteColumn(static_cast<size_t>(rowNames));
}
-
- return(dt);
+
+ return dt;
}
/******************************************************************************/
@@ -566,23 +653,27 @@ DataTable* DataTable::read(istream& in, const string& sep, bool header, int rowN
void DataTable::write(const DataTable& data, ostream& out, const string& sep, bool alignHeaders)
{
size_t n = data.getNumberOfColumns();
- if(n == 0) return;
- if(data.hasColumnNames())
- { //Write header
+ if (n == 0)
+ return;
+ if (data.hasColumnNames())
+ { // Write header
vector<string> colNames = data.getColumnNames();
- if (alignHeaders && data.hasRowNames()) out << sep;
+ if (alignHeaders && data.hasRowNames())
+ out << sep;
out << colNames[0];
- for(size_t i = 1; i < n; i++) {
+ for (size_t i = 1; i < n; i++)
+ {
out << sep << colNames[i];
}
out << endl;
}
- //Now write each row:
- for(size_t i = 0; i < data.getNumberOfRows(); i++)
+ // Now write each row:
+ for (size_t i = 0; i < data.getNumberOfRows(); i++)
{
- if(data.hasRowNames()) out << data.getRowName(i) << sep;
+ if (data.hasRowNames())
+ out << data.getRowName(i) << sep;
out << data(i, 0);
- for(size_t j = 1; j < n; j++)
+ for (size_t j = 1; j < n; j++)
{
out << sep << data(i, j);
}
@@ -590,5 +681,36 @@ void DataTable::write(const DataTable& data, ostream& out, const string& sep, bo
}
}
+void DataTable::write(const DataTable& data, bpp::OutputStream& out, const string& sep, bool alignHeaders)
+{
+ size_t n = data.getNumberOfColumns();
+ if (n == 0)
+ return;
+ if (data.hasColumnNames())
+ { // Write header
+ vector<string> colNames = data.getColumnNames();
+ if (alignHeaders && data.hasRowNames())
+ out << sep;
+ out << colNames[0];
+ for (size_t i = 1; i < n; i++)
+ {
+ out << sep << colNames[i];
+ }
+ out.endLine();
+ }
+ // Now write each row:
+ for (size_t i = 0; i < data.getNumberOfRows(); i++)
+ {
+ if (data.hasRowNames())
+ out << data.getRowName(i) << sep;
+ out << data(i, 0);
+ for (size_t j = 1; j < n; j++)
+ {
+ out << sep << data(i, j);
+ }
+ out.endLine();
+ }
+}
+
/******************************************************************************/
diff --git a/src/Bpp/Numeric/DataTable.h b/src/Bpp/Numeric/DataTable.h
index b720ccf..b9f55c8 100644
--- a/src/Bpp/Numeric/DataTable.h
+++ b/src/Bpp/Numeric/DataTable.h
@@ -5,37 +5,37 @@
//
/*
-Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
-
-This software is a computer program whose purpose is to provide classes
-for numerical calculus.
-
-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.
-*/
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for numerical calculus.
+
+ 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 _DataTable_H_
#define _DataTable_H_
@@ -48,12 +48,11 @@ knowledge of the CeCILL license and that you accept its terms.
// From the STL:
#include <string>
-#include<vector>
+#include <vector>
#include <map>
namespace bpp
{
-
/**
* @brief This class corresponds to a 'dataset', <i>i.e.</i> a table with data by rows
* and variable by columns.
@@ -62,382 +61,378 @@ namespace bpp
* A DataTable object is hence similar to a ColMatrix<string>.object.
* (NB: actually, ColMatrix does not exist yet...)
*/
-class DataTable:
+class DataTable :
public Clonable
{
-
- protected:
- size_t nRow_, nCol_;
- std::vector< std::vector<std::string> > data_;
- std::vector<std::string>* rowNames_;
- std::vector<std::string>* colNames_;
-
- public:
-
- /**
- * @brief Build a new void DataTable object with nRow rows and nCol columns.
- *
- * @param nRow The number of rows of the DataTable.
- * @param nCol The number of columns of the DataTable.
- */
- DataTable(size_t nRow, size_t nCol);
-
- /**
- * @brief Build a new void DataTable object with nCol columns.
- *
- * @param nCol The number of columns of the DataTable.
- */
- DataTable(size_t nCol);
-
- /**
- * @brief Build a new void DataTable object with named columns.
- *
- * @param colNames The names of the columns of the DataTable.
- * @throw DuplicatedTableColumnNameException If colnames contains identical names.
- */
- DataTable(const std::vector<std::string>& colNames) throw (DuplicatedTableColumnNameException);
-
- DataTable(const DataTable& table);
-
- DataTable& operator=(const DataTable& table);
-
- DataTable* clone() const { return new DataTable(*this); }
-
- virtual ~DataTable();
-
- public:
-
- /**
- * @return The element at a given position.
- * @param rowIndex Row number.
- * @param colIndex Column number.
- * @throw IndexOutOfBoundsException If one of the index is greater or equal to the corresponding number of columns/rows.
- */
- std::string& operator()(size_t rowIndex, size_t colIndex) throw (IndexOutOfBoundsException);
-
- /**
- * @return The element at a given position.
- * @param rowIndex Row number.
- * @param colIndex Column number.
- * @throw IndexOutOfBoundsException If one of the index is greater or equal to the corresponding number of columns/rows.
- */
- const std::string& operator()(size_t rowIndex, size_t colIndex) const throw (IndexOutOfBoundsException);
-
- /**
- * @return The element at a given position.
- * @param rowName Row name.
- * @param colName Column name.
- * @throw NoTableRowNamesException If the table does not have names associated to rows.
- * @throw NoTableColumnNamesException If the table does not have names associated to columns.
- * @throw TableNameNotFoundException If one of rowName or colName do not match existing names.
- */
- std::string& operator()(const std::string& rowName, const std::string& colName)
- throw (NoTableRowNamesException, NoTableColumnNamesException, TableNameNotFoundException);
-
- /**
- * @return The element at a given position.
- * @param rowName Row name.
- * @param colName Column name.
- * @throw NoTableRowNamesException If the table does not have names associated to rows.
- * @throw NoTableColumnNamesException If the table does not have names associated to columns.
- * @throw TableNameNotFoundException If one of rowName or colName do not match existing names.
- */
- const std::string& operator()(const std::string& rowName, const std::string& colName) const
- throw (NoTableRowNamesException, NoTableColumnNamesException, TableNameNotFoundException);
-
- /**
- * @return The element at a given position.
- * @param rowName Row name.
- * @param colIndex Column number.
- * @throw NoTableRowNamesException If the table does not have names associated to rows.
- * @throw IndexOutOfBoundsException If the index is greater or equal to the number of columns.
- * @throw TableNameNotFoundException If rowName do not match existing names.
- */
- std::string& operator()(const std::string& rowName, size_t colIndex)
- throw (NoTableRowNamesException, TableNameNotFoundException, IndexOutOfBoundsException);
-
- /**
- * @return The element at a given position.
- * @param rowName Row name.
- * @param colIndex Column number.
- * @throw NoTableRowNamesException If the table does not have names associated to rows.
- * @throw IndexOutOfBoundsException If the index is greater or equal to the number of columns.
- * @throw TableNameNotFoundException If rowName do not match existing names.
- */
- const std::string& operator()(const std::string& rowName, size_t colIndex) const
- throw (NoTableRowNamesException, TableNameNotFoundException, IndexOutOfBoundsException);
-
- /**
- * @return The element at a given position.
- * @param rowIndex Row number.
- * @param colName Column name.
- * @throw IndexOutOfBoundsException If the index is greater or equal to the number of rows.
- * @throw NoTableColumnNamesException If the table does not have names associated to columns.
- * @throw TableNameNotFoundException If colName do not match existing names.
- */
- std::string& operator()(size_t rowIndex, const std::string& colName)
- throw (IndexOutOfBoundsException, NoTableColumnNamesException, TableNameNotFoundException);
-
- /**
- * @return The element at a given position.
- * @param rowIndex Row number.
- * @param colName Column name.
- * @throw IndexOutOfBoundsException If the index is greater or equal to the number of rows.
- * @throw NoTableColumnNamesException If the table does not have names associated to columns.
- * @throw TableNameNotFoundException If colName do not match existing names.
- */
- const std::string& operator()(size_t rowIndex, const std::string& colName) const
- throw (IndexOutOfBoundsException, NoTableColumnNamesException, TableNameNotFoundException);
-
- /**
- * @name Work on columns.
- *
- * @{
- */
-
- /**
- * @return The number of columns in this table.
- */
- size_t getNumberOfColumns() const { return nCol_; }
-
- /**
- * @brief Set the column names of this table.
- *
- * @param colNames The row names.
- * @throw DimensionException If the number of names do not match the number of columns in the table.
- * @throw DuplicatedTableColumnNameException If names are not unique.
- */
- void setColumnNames(const std::vector<std::string>& colNames) throw (DimensionException, DuplicatedTableColumnNameException);
- /**
- * @brief Get the column names of this table.
- *
- * @return The column names of this table.
- * @throw NoTableColumnNamesException If no column names are associated to this table.
- */
- std::vector<std::string> getColumnNames() const throw (NoTableColumnNamesException);
- /**
- * @brief Get a given column name.
- *
- * @param index The index of the column.
- * @return The column name associated to the given column.
- * @throw NoTableColumnNamesException If no column names are associated to this table.
- * @throw IndexOutOfBoundsException If index is >= number of columns.
- */
- std::string getColumnName(size_t index) const throw (NoTableColumnNamesException, IndexOutOfBoundsException);
-
- /**
- * @return true If column names are associated to this table.
- */
- bool hasColumnNames() const { return colNames_!= 0; }
-
- /**
- * @return The values in the given column.
- * @param index The index of the column.
- * @throw IndexOutOfBoundsException If index is >= number of columns.
- */
- std::vector<std::string>& getColumn(size_t index) throw (IndexOutOfBoundsException);
- /**
- * @return The values in the given column.
- * @param index The index of the column.
- * @throw IndexOutOfBoundsException If index is >= number of columns.
- */
- const std::vector<std::string>& getColumn(size_t index) const throw (IndexOutOfBoundsException);
-
- /**
- * @return The values in the given column.
- * @param colName The name of the column.
- * @throw NoTableColumnNamesException If no column names are associated to this table.
- * @throw TableColumnNameNotFoundException If colName do not match existing column names.
- */
- std::vector<std::string>& getColumn(const std::string& colName) throw (NoTableColumnNamesException, TableColumnNameNotFoundException);
- /**
- * @return The values in the given column.
- * @param colName The name of the column.
- * @throw NoTableColumnNamesException If no column names are associated to this table.
- * @throw TableColumnNameNotFoundException If colName do not match existing column names.
- */
- const std::vector<std::string>& getColumn(const std::string& colName) const throw (NoTableColumnNamesException, TableColumnNameNotFoundException);
-
- /**
- * @brief Tell is a given column exists.
- *
- * @param colName The name of the column to look for.
- * @return true if the column was found, false if not or if there are no column names.
- */
- bool hasColumn(const std::string& colName) const;
-
- /**
- * @brief Delete the given column.
- *
- * @param index The index of the column.
- * @throw IndexOutOfBoundsException If index is >= number of columns.
- */
- void deleteColumn(size_t index) throw (IndexOutOfBoundsException);
-
- /**
- * @brief Delete the given column.
- *
- * @param colName The name of the column.
- * @throw NoTableColumnNamesException If no column names are associated to this table.
- * @throw TableColumnNameNotFoundException If colName do not match existing column names.
- */
- void deleteColumn(const std::string& colName) throw (NoTableColumnNamesException, TableColumnNameNotFoundException);
-
- /**
- * @brief Add a new column.
- *
- * @param newColumn The new column values.
- * @throw DimensionException If the number of values does not match the number of rows.
- * @throw TableColumnNamesException If the table has row names.
- */
- void addColumn(const std::vector<std::string>& newColumn) throw (DimensionException, TableColumnNamesException);
- /**
- * @brief Add a new column.
- *
- * @param colName The name of the column.
- * @param newColumn The new column values.
- * @throw DimensionException If the number of values does not match the number of rows.
- * @throw NoTableColumnNamesException If the table does not have row names.
- * @throw DuplicatedTableColumnNameException If colName is already used.
- */
- void addColumn(const std::string& colName, const std::vector<std::string>& newColumn) throw (DimensionException, NoTableColumnNamesException, DuplicatedTableColumnNameException);
- /** @} */
-
- /**
- * @name Work on rows.
- *
- * @{
- */
-
- /**
- * @return The number of rows in this table.
- */
- size_t getNumberOfRows() const { return nRow_; }
-
- /**
- * @brief Set the row names of this table.
- *
- * @param rowNames The row names.
- * @throw DimensionException If the number of names do not match the number of rows in the table.
- * @throw DuplicatedTableRowNameException If names are not unique.
- */
- void setRowNames(const std::vector<std::string>& rowNames) throw (DimensionException, DuplicatedTableRowNameException);
-
- /**
- * @brief Get the row names of this table.
- *
- * @return The row names of this table.
- * @throw NoTableRowNamesException If no row names are associated to this table.
- */
- std::vector<std::string> getRowNames() const throw (NoTableRowNamesException);
-
- /**
- * @brief Tell is a given row exists.
- *
- * @param rowName The name of the row to look for.
- * @return true if the row was found, false if not or if there are no row names.
- */
- bool hasRow(const std::string& rowName) const;
-
- /**
- * @brief Get a given row name.
- *
- * @param index The index of the row.
- * @return The row name associated to the given row.
- * @throw NoTableRowNamesException If no row names are associated to this table.
- * @throw IndexOutOfBoundsException If index is >= number of rows.
- */
- std::string getRowName(size_t index) const throw (NoTableRowNamesException, IndexOutOfBoundsException);
-
- /**
- * @return true If row names are associated to this table.
- */
- bool hasRowNames() const { return rowNames_!= 0; }
-
- /**
- * @return A vector which contains a copy in the given row.
- * @param index The index of the row.
- * @throw IndexOutOfBoundsException If index is >= number of rows.
- */
- std::vector<std::string> getRow(size_t index) const throw (IndexOutOfBoundsException);
-
- /**
- * @return A vector which contains a copy in the given row.
- * @param rowName The name of the row.
- * @throw NoTableRowNamesException If no row names are associated to this table.
- * @throw TableRowNameNotFoundException If rowName do not match existing row names.
- */
- std::vector<std::string> getRow(const std::string& rowName) const throw (NoTableRowNamesException, TableRowNameNotFoundException);
-
- /**
- * @brief Delete the given row.
- *
- * @param index The index of the row.
- * @throw IndexOutOfBoundsException If index is >= number of row.
- */
- void deleteRow(size_t index) throw (IndexOutOfBoundsException);
-
- /**
- * @brief Delete the given row.
- *
- * @param rowName The name of the row.
- * @throw NoTableRowNamesException If no row names are associated to this table.
- * @throw TableRowNameNotFoundException If rowName do not match existing column names.
- */
- void deleteRow(const std::string& rowName) throw (NoTableRowNamesException, TableRowNameNotFoundException);
-
- /**
- * @brief Add a new row.
- *
- * @param newRow The new row values.
- * @throw DimensionException If the number of values does not match the number of columns.
- * @throw TableRowNamesException If the table has column names.
- */
- void addRow(const std::vector<std::string>& newRow) throw (DimensionException, TableRowNamesException);
- /**
- * @brief Add a new row.
- *
- * @param rowName The name of the row.
- * @param newRow The new row values.
- * @throw DimensionException If the number of values does not match the number of columns.
- * @throw NoTableRowNamesException If the table does not have column names.
- * @throw DuplicatedTableRowNameException If rowName is already used.
- */
- void addRow(const std::string& rowName, const std::vector<std::string>& newRow) throw (DimensionException, NoTableRowNamesException, DuplicatedTableRowNameException);
- /** @} */
-
- public:
-
- /**
- * @brief Read a table form a stream in CSV-like format.
- *
- * The number of rows is given by the second line in the file.
- * By default, if the first line as one column less than the second one,
- * the first line is taken as column names, and the first column as row names.
- * Otherwise, no column names and no row names are specified, unless
- * explicitely precised by the user.
- *
- * @param in The input stream.
- * @param sep The column delimiter.
- * @param header Tell if the first line must be used as column names, otherwise use default.
- * @param rowNames Use a column as rowNames. If positive, use the specified column to compute rownames, otherwise use default;
- * @return A pointer toward a new DataTable object.
- */
- static DataTable* read(std::istream& in, const std::string& sep = "\t", bool header = true, int rowNames = -1)
- throw (DimensionException, IndexOutOfBoundsException, DuplicatedTableRowNameException);
-
- /**
- * @brief Write a DataTable object to stream in CVS-like format.
- *
- * @param data The table to write.
- * @param out The output stream.
- * @param sep The column delimiter.
- * @param alignHeaders If true, add a delimiter before the first column header if there is row names.
- */
- static void write(const DataTable& data, std::ostream& out, const std::string& sep = "\t", bool alignHeaders = false);
+protected:
+ size_t nRow_, nCol_;
+ std::vector< std::vector<std::string> > data_;
+ std::vector<std::string>* rowNames_;
+ std::vector<std::string>* colNames_;
+
+public:
+ /**
+ * @brief Build a new void DataTable object with nRow rows and nCol columns.
+ *
+ * @param nRow The number of rows of the DataTable.
+ * @param nCol The number of columns of the DataTable.
+ */
+ DataTable(size_t nRow, size_t nCol);
+
+ /**
+ * @brief Build a new void DataTable object with nCol columns.
+ *
+ * @param nCol The number of columns of the DataTable.
+ */
+ DataTable(size_t nCol);
+
+ /**
+ * @brief Build a new void DataTable object with named columns.
+ *
+ * @param colNames The names of the columns of the DataTable.
+ * @throw DuplicatedTableColumnNameException If colnames contains identical names.
+ */
+ DataTable(const std::vector<std::string>& colNames) throw (DuplicatedTableColumnNameException);
+
+ DataTable(const DataTable& table);
+
+ DataTable& operator=(const DataTable& table);
+
+ DataTable* clone() const { return new DataTable(*this); }
+
+ virtual ~DataTable();
+
+public:
+ /**
+ * @return The element at a given position.
+ * @param rowIndex Row number.
+ * @param colIndex Column number.
+ * @throw IndexOutOfBoundsException If one of the index is greater or equal to the corresponding number of columns/rows.
+ */
+ std::string& operator()(size_t rowIndex, size_t colIndex) throw (IndexOutOfBoundsException);
+
+ /**
+ * @return The element at a given position.
+ * @param rowIndex Row number.
+ * @param colIndex Column number.
+ * @throw IndexOutOfBoundsException If one of the index is greater or equal to the corresponding number of columns/rows.
+ */
+ const std::string& operator()(size_t rowIndex, size_t colIndex) const throw (IndexOutOfBoundsException);
+
+ /**
+ * @return The element at a given position.
+ * @param rowName Row name.
+ * @param colName Column name.
+ * @throw NoTableRowNamesException If the table does not have names associated to rows.
+ * @throw NoTableColumnNamesException If the table does not have names associated to columns.
+ * @throw TableNameNotFoundException If one of rowName or colName do not match existing names.
+ */
+ std::string& operator()(const std::string& rowName, const std::string& colName)
+ throw (NoTableRowNamesException, NoTableColumnNamesException, TableNameNotFoundException);
+
+ /**
+ * @return The element at a given position.
+ * @param rowName Row name.
+ * @param colName Column name.
+ * @throw NoTableRowNamesException If the table does not have names associated to rows.
+ * @throw NoTableColumnNamesException If the table does not have names associated to columns.
+ * @throw TableNameNotFoundException If one of rowName or colName do not match existing names.
+ */
+ const std::string& operator()(const std::string& rowName, const std::string& colName) const
+ throw (NoTableRowNamesException, NoTableColumnNamesException, TableNameNotFoundException);
+
+ /**
+ * @return The element at a given position.
+ * @param rowName Row name.
+ * @param colIndex Column number.
+ * @throw NoTableRowNamesException If the table does not have names associated to rows.
+ * @throw IndexOutOfBoundsException If the index is greater or equal to the number of columns.
+ * @throw TableNameNotFoundException If rowName do not match existing names.
+ */
+ std::string& operator()(const std::string& rowName, size_t colIndex)
+ throw (NoTableRowNamesException, TableNameNotFoundException, IndexOutOfBoundsException);
+
+ /**
+ * @return The element at a given position.
+ * @param rowName Row name.
+ * @param colIndex Column number.
+ * @throw NoTableRowNamesException If the table does not have names associated to rows.
+ * @throw IndexOutOfBoundsException If the index is greater or equal to the number of columns.
+ * @throw TableNameNotFoundException If rowName do not match existing names.
+ */
+ const std::string& operator()(const std::string& rowName, size_t colIndex) const
+ throw (NoTableRowNamesException, TableNameNotFoundException, IndexOutOfBoundsException);
+
+ /**
+ * @return The element at a given position.
+ * @param rowIndex Row number.
+ * @param colName Column name.
+ * @throw IndexOutOfBoundsException If the index is greater or equal to the number of rows.
+ * @throw NoTableColumnNamesException If the table does not have names associated to columns.
+ * @throw TableNameNotFoundException If colName do not match existing names.
+ */
+ std::string& operator()(size_t rowIndex, const std::string& colName)
+ throw (IndexOutOfBoundsException, NoTableColumnNamesException, TableNameNotFoundException);
+
+ /**
+ * @return The element at a given position.
+ * @param rowIndex Row number.
+ * @param colName Column name.
+ * @throw IndexOutOfBoundsException If the index is greater or equal to the number of rows.
+ * @throw NoTableColumnNamesException If the table does not have names associated to columns.
+ * @throw TableNameNotFoundException If colName do not match existing names.
+ */
+ const std::string& operator()(size_t rowIndex, const std::string& colName) const
+ throw (IndexOutOfBoundsException, NoTableColumnNamesException, TableNameNotFoundException);
+
+ /**
+ * @name Work on columns.
+ *
+ * @{
+ */
+
+ /**
+ * @return The number of columns in this table.
+ */
+ size_t getNumberOfColumns() const { return nCol_; }
+
+ /**
+ * @brief Set the column names of this table.
+ *
+ * @param colNames The row names.
+ * @throw DimensionException If the number of names do not match the number of columns in the table.
+ * @throw DuplicatedTableColumnNameException If names are not unique.
+ */
+ void setColumnNames(const std::vector<std::string>& colNames) throw (DimensionException, DuplicatedTableColumnNameException);
+ /**
+ * @brief Get the column names of this table.
+ *
+ * @return The column names of this table.
+ * @throw NoTableColumnNamesException If no column names are associated to this table.
+ */
+ std::vector<std::string> getColumnNames() const throw (NoTableColumnNamesException);
+ /**
+ * @brief Get a given column name.
+ *
+ * @param index The index of the column.
+ * @return The column name associated to the given column.
+ * @throw NoTableColumnNamesException If no column names are associated to this table.
+ * @throw IndexOutOfBoundsException If index is >= number of columns.
+ */
+ std::string getColumnName(size_t index) const throw (NoTableColumnNamesException, IndexOutOfBoundsException);
+
+ /**
+ * @return true If column names are associated to this table.
+ */
+ bool hasColumnNames() const { return colNames_ != 0; }
+
+ /**
+ * @return The values in the given column.
+ * @param index The index of the column.
+ * @throw IndexOutOfBoundsException If index is >= number of columns.
+ */
+ std::vector<std::string>& getColumn(size_t index) throw (IndexOutOfBoundsException);
+ /**
+ * @return The values in the given column.
+ * @param index The index of the column.
+ * @throw IndexOutOfBoundsException If index is >= number of columns.
+ */
+ const std::vector<std::string>& getColumn(size_t index) const throw (IndexOutOfBoundsException);
+
+ /**
+ * @return The values in the given column.
+ * @param colName The name of the column.
+ * @throw NoTableColumnNamesException If no column names are associated to this table.
+ * @throw TableColumnNameNotFoundException If colName do not match existing column names.
+ */
+ std::vector<std::string>& getColumn(const std::string& colName) throw (NoTableColumnNamesException, TableColumnNameNotFoundException);
+ /**
+ * @return The values in the given column.
+ * @param colName The name of the column.
+ * @throw NoTableColumnNamesException If no column names are associated to this table.
+ * @throw TableColumnNameNotFoundException If colName do not match existing column names.
+ */
+ const std::vector<std::string>& getColumn(const std::string& colName) const throw (NoTableColumnNamesException, TableColumnNameNotFoundException);
+
+ /**
+ * @brief Tell is a given column exists.
+ *
+ * @param colName The name of the column to look for.
+ * @return true if the column was found, false if not or if there are no column names.
+ */
+ bool hasColumn(const std::string& colName) const;
+
+ /**
+ * @brief Delete the given column.
+ *
+ * @param index The index of the column.
+ * @throw IndexOutOfBoundsException If index is >= number of columns.
+ */
+ void deleteColumn(size_t index) throw (IndexOutOfBoundsException);
+
+ /**
+ * @brief Delete the given column.
+ *
+ * @param colName The name of the column.
+ * @throw NoTableColumnNamesException If no column names are associated to this table.
+ * @throw TableColumnNameNotFoundException If colName do not match existing column names.
+ */
+ void deleteColumn(const std::string& colName) throw (NoTableColumnNamesException, TableColumnNameNotFoundException);
+
+ /**
+ * @brief Add a new column.
+ *
+ * @param newColumn The new column values.
+ * @throw DimensionException If the number of values does not match the number of rows.
+ * @throw TableColumnNamesException If the table has row names.
+ */
+ void addColumn(const std::vector<std::string>& newColumn) throw (DimensionException, TableColumnNamesException);
+ /**
+ * @brief Add a new column.
+ *
+ * @param colName The name of the column.
+ * @param newColumn The new column values.
+ * @throw DimensionException If the number of values does not match the number of rows.
+ * @throw NoTableColumnNamesException If the table does not have row names.
+ * @throw DuplicatedTableColumnNameException If colName is already used.
+ */
+ void addColumn(const std::string& colName, const std::vector<std::string>& newColumn) throw (DimensionException, NoTableColumnNamesException, DuplicatedTableColumnNameException);
+ /** @} */
+
+ /**
+ * @name Work on rows.
+ *
+ * @{
+ */
+
+ /**
+ * @return The number of rows in this table.
+ */
+ size_t getNumberOfRows() const { return nRow_; }
+
+ /**
+ * @brief Set the row names of this table.
+ *
+ * @param rowNames The row names.
+ * @throw DimensionException If the number of names do not match the number of rows in the table.
+ * @throw DuplicatedTableRowNameException If names are not unique.
+ */
+ void setRowNames(const std::vector<std::string>& rowNames) throw (DimensionException, DuplicatedTableRowNameException);
+
+ /**
+ * @brief Get the row names of this table.
+ *
+ * @return The row names of this table.
+ * @throw NoTableRowNamesException If no row names are associated to this table.
+ */
+ std::vector<std::string> getRowNames() const throw (NoTableRowNamesException);
+
+ /**
+ * @brief Tell is a given row exists.
+ *
+ * @param rowName The name of the row to look for.
+ * @return true if the row was found, false if not or if there are no row names.
+ */
+ bool hasRow(const std::string& rowName) const;
+
+ /**
+ * @brief Get a given row name.
+ *
+ * @param index The index of the row.
+ * @return The row name associated to the given row.
+ * @throw NoTableRowNamesException If no row names are associated to this table.
+ * @throw IndexOutOfBoundsException If index is >= number of rows.
+ */
+ std::string getRowName(size_t index) const throw (NoTableRowNamesException, IndexOutOfBoundsException);
+
+ /**
+ * @return true If row names are associated to this table.
+ */
+ bool hasRowNames() const { return rowNames_ != 0; }
+
+ /**
+ * @return A vector which contains a copy in the given row.
+ * @param index The index of the row.
+ * @throw IndexOutOfBoundsException If index is >= number of rows.
+ */
+ std::vector<std::string> getRow(size_t index) const throw (IndexOutOfBoundsException);
+
+ /**
+ * @return A vector which contains a copy in the given row.
+ * @param rowName The name of the row.
+ * @throw NoTableRowNamesException If no row names are associated to this table.
+ * @throw TableRowNameNotFoundException If rowName do not match existing row names.
+ */
+ std::vector<std::string> getRow(const std::string& rowName) const throw (NoTableRowNamesException, TableRowNameNotFoundException);
+
+ /**
+ * @brief Delete the given row.
+ *
+ * @param index The index of the row.
+ * @throw IndexOutOfBoundsException If index is >= number of row.
+ */
+ void deleteRow(size_t index) throw (IndexOutOfBoundsException);
+
+ /**
+ * @brief Delete the given row.
+ *
+ * @param rowName The name of the row.
+ * @throw NoTableRowNamesException If no row names are associated to this table.
+ * @throw TableRowNameNotFoundException If rowName do not match existing column names.
+ */
+ void deleteRow(const std::string& rowName) throw (NoTableRowNamesException, TableRowNameNotFoundException);
+
+ /**
+ * @brief Add a new row.
+ *
+ * @param newRow The new row values.
+ * @throw DimensionException If the number of values does not match the number of columns.
+ * @throw TableRowNamesException If the table has column names.
+ */
+ void addRow(const std::vector<std::string>& newRow) throw (DimensionException, TableRowNamesException);
+ /**
+ * @brief Add a new row.
+ *
+ * @param rowName The name of the row.
+ * @param newRow The new row values.
+ * @throw DimensionException If the number of values does not match the number of columns.
+ * @throw NoTableRowNamesException If the table does not have column names.
+ * @throw DuplicatedTableRowNameException If rowName is already used.
+ */
+ void addRow(const std::string& rowName, const std::vector<std::string>& newRow) throw (DimensionException, NoTableRowNamesException, DuplicatedTableRowNameException);
+ /** @} */
+
+public:
+ /**
+ * @brief Read a table form a stream in CSV-like format.
+ *
+ * The number of rows is given by the second line in the file.
+ * By default, if the first line as one column less than the second one,
+ * the first line is taken as column names, and the first column as row names.
+ * Otherwise, no column names and no row names are specified, unless
+ * explicitely precised by the user.
+ *
+ * @param in The input stream.
+ * @param sep The column delimiter.
+ * @param header Tell if the first line must be used as column names, otherwise use default.
+ * @param rowNames Use a column as rowNames. If positive, use the specified column to compute rownames, otherwise use default;
+ * @return A pointer toward a new DataTable object.
+ */
+ static DataTable* read(std::istream& in, const std::string& sep = "\t", bool header = true, int rowNames = -1)
+ throw (DimensionException, IndexOutOfBoundsException, DuplicatedTableRowNameException);
+
+ /**
+ * @brief Write a DataTable object to stream in CVS-like format.
+ *
+ * @param data The table to write.
+ * @param out The output stream.
+ * @param sep The column delimiter.
+ * @param alignHeaders If true, add a delimiter before the first column header if there is row names.
+ */
+ static void write(const DataTable& data, std::ostream& out, const std::string& sep = "\t", bool alignHeaders = false);
+ static void write(const DataTable& data, bpp::OutputStream& out, const std::string& sep = "\t", bool alignHeaders = false);
};
+} // end of namespace bpp.
-} //end of namespace bpp.
-
-#endif //_DataTable_H_
+#endif // _DataTable_H_
diff --git a/src/Bpp/Numeric/Function/ConjugateGradientMultiDimensions.cpp b/src/Bpp/Numeric/Function/ConjugateGradientMultiDimensions.cpp
index 7e455ac..adc339e 100644
--- a/src/Bpp/Numeric/Function/ConjugateGradientMultiDimensions.cpp
+++ b/src/Bpp/Numeric/Function/ConjugateGradientMultiDimensions.cpp
@@ -101,10 +101,14 @@ double ConjugateGradientMultiDimensions::doStep() throw (Exception)
return f;
}
gam = dgg / gg;
- for(unsigned int j = 0; j < n; j++)
+
+ if (!(std::isnan(gam) || std::isinf(gam)))
{
- g_[j] = -xi_[j];
- xi_[j] = h_[j] = g_[j] + gam * h_[j];
+ for(unsigned int j = 0; j < n; j++)
+ {
+ g_[j] = -xi_[j];
+ xi_[j] = h_[j] = g_[j] + gam * h_[j];
+ }
}
return f;
diff --git a/src/Bpp/Numeric/Function/FivePointsNumericalDerivative.cpp b/src/Bpp/Numeric/Function/FivePointsNumericalDerivative.cpp
index 647ac90..ab6c02f 100644
--- a/src/Bpp/Numeric/Function/FivePointsNumericalDerivative.cpp
+++ b/src/Bpp/Numeric/Function/FivePointsNumericalDerivative.cpp
@@ -46,8 +46,10 @@ throw (ParameterNotFoundException, ConstraintException)
{
if (computeD1_ && variables_.size() > 0)
{
- if (function1_) function1_->enableFirstOrderDerivatives(false);
- if (function2_) function2_->enableSecondOrderDerivatives(false);
+ if (function1_)
+ function1_->enableFirstOrderDerivatives(false);
+ if (function2_)
+ function2_->enableSecondOrderDerivatives(false);
function_->setParameters(parameters);
f3_ = function_->getValue();
string lastVar;
@@ -57,7 +59,8 @@ throw (ParameterNotFoundException, ConstraintException)
for (unsigned int i = 0; i < variables_.size(); i++)
{
string var = variables_[i];
- if (!parameters.hasParameter(var)) continue;
+ if (!parameters.hasParameter(var))
+ continue;
if (!start)
{
vector<string> vars(2);
@@ -74,7 +77,7 @@ throw (ParameterNotFoundException, ConstraintException)
functionChanged = true;
double value = function_->getParameterValue(var);
double h = (1. + std::abs(value)) * h_;
- //Compute four other points:
+ // Compute four other points:
try
{
p[0].setValue(value - 2 * h);
@@ -85,7 +88,7 @@ throw (ParameterNotFoundException, ConstraintException)
p[0].setValue(value + 2 * h);
function_->setParameters(p);
f5_ = function_->getValue();
- //No limit raised, use central approximation:
+ // No limit raised, use central approximation:
p[0].setValue(value - h);
function_->setParameters(p);
f2_ = function_->getValue();
@@ -97,7 +100,7 @@ throw (ParameterNotFoundException, ConstraintException)
}
catch (ConstraintException& ce)
{
- //Right limit raised, use backward approximation:
+ // Right limit raised, use backward approximation:
p[0].setValue(value - h);
function_->setParameters(p);
f2_ = function_->getValue();
@@ -110,7 +113,7 @@ throw (ParameterNotFoundException, ConstraintException)
}
catch (ConstraintException& ce)
{
- //Left limit raised, use forward approximation:
+ // Left limit raised, use forward approximation:
p[0].setValue(value + h);
function_->setParameters(p);
f4_ = function_->getValue();
@@ -121,19 +124,23 @@ throw (ParameterNotFoundException, ConstraintException)
der2_[i] = (f5_ - 2. * f4_ + f3_) / (h * h);
}
}
- //Reset last parameter and compute analytical derivatives if any.
- if (function1_) function1_->enableFirstOrderDerivatives(computeD1_);
- if (function2_) function2_->enableSecondOrderDerivatives(computeD2_);
+ // Reset last parameter and compute analytical derivatives if any.
+ if (function1_)
+ function1_->enableFirstOrderDerivatives(computeD1_);
+ if (function2_)
+ function2_->enableSecondOrderDerivatives(computeD2_);
if (functionChanged)
function_->setParameters(parameters.subList(lastVar));
}
else
{
- //Reset initial value and compute analytical derivatives if any.
- if (function1_) function1_->enableFirstOrderDerivatives(computeD1_);
- if (function2_) function2_->enableSecondOrderDerivatives(computeD2_);
+ // Reset initial value and compute analytical derivatives if any.
+ if (function1_)
+ function1_->enableFirstOrderDerivatives(computeD1_);
+ if (function2_)
+ function2_->enableSecondOrderDerivatives(computeD2_);
function_->setParameters(parameters);
- //Just in case derivatives are not computed:
+ // Just in case derivatives are not computed:
f3_ = function_->getValue();
}
}
diff --git a/src/Bpp/Numeric/Function/FivePointsNumericalDerivative.h b/src/Bpp/Numeric/Function/FivePointsNumericalDerivative.h
index 77cb6f1..30c8388 100644
--- a/src/Bpp/Numeric/Function/FivePointsNumericalDerivative.h
+++ b/src/Bpp/Numeric/Function/FivePointsNumericalDerivative.h
@@ -5,37 +5,37 @@
//
/*
-Copyright or © or Copr. CNRS, (November 17, 2004)
-
-This software is a computer program whose purpose is to provide classes
-for numerical calculus.
-
-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.
-*/
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for numerical calculus.
+
+ 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 _FIVEPOINTSNUMERICALDERIVATIVE_H_
#define _FIVEPOINTSNUMERICALDERIVATIVE_H_
@@ -43,14 +43,13 @@ knowledge of the CeCILL license and that you accept its terms.
#include "Functions.h"
#include "AbstractNumericalDerivative.h"
-//From the STL:
+// From the STL:
#include <map>
#include <vector>
#include <string>
namespace bpp
{
-
/**
* @brief Five points numerical derivative function wrapper.
*
@@ -62,7 +61,7 @@ namespace bpp
* \dfrac{\partial f}{\partial x } &=& \dfrac{f_{-2}-8f_{-1}+8f_{+1}-f_{+2}}{12h}\\
* \dfrac{\partial^2 f}{\partial x^2} &=& \dfrac{-f_{-2}+16f_{-1}-30f_0+16f_{+1}-f_{+2}}{12h^2}\\
* @f}
- * In case of border limit (when @f$x_{-2}@f$ or @f$x_{+2}@f$ are not computable),
+ * In case of border limit (when @f$x_{-2}@f$ or @f$x_{+2}@f$ are not computable),
* the foreward and backward three points computations are performed, respectively:
* @f{eqnarray*}
* \dfrac{\partial f}{\partial x } &=& \dfrac{f_{+1}-f_0}{h}\\
@@ -83,43 +82,55 @@ namespace bpp
* @warning cross second order derivatives are not implemented with the five points method.
* @see AbstractNumericalDerivative
*/
-class FivePointsNumericalDerivative:
+class FivePointsNumericalDerivative :
public AbstractNumericalDerivative
{
- private:
- double f1_, f2_, f3_, f4_, f5_;
-
- public:
- FivePointsNumericalDerivative(Function* function) :
- AbstractNumericalDerivative(function), f1_(), f2_(), f3_(), f4_(), f5_() {}
- FivePointsNumericalDerivative(DerivableFirstOrder* function) :
- AbstractNumericalDerivative(function), f1_(), f2_(), f3_(), f4_(), f5_() {}
- FivePointsNumericalDerivative(DerivableSecondOrder* function) :
- AbstractNumericalDerivative(function), f1_(), f2_(), f3_(), f4_(), f5_() {}
- virtual ~FivePointsNumericalDerivative() {}
-
- FivePointsNumericalDerivative* clone() const { return new FivePointsNumericalDerivative(*this); }
-
- public:
-
- double getValue() const throw (Exception)
- {
- return f3_;
- }
-
- double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const
- throw (Exception)
- {
- throw Exception("Unimplemented cross derivative.");
- }
-
- protected:
- void updateDerivatives(const ParameterList parameters)
- throw (ParameterNotFoundException, ConstraintException);
-
+private:
+ double f1_, f2_, f3_, f4_, f5_;
+
+public:
+ FivePointsNumericalDerivative(Function* function) :
+ AbstractNumericalDerivative(function),
+ f1_(),
+ f2_(),
+ f3_(),
+ f4_(),
+ f5_() {}
+ FivePointsNumericalDerivative(DerivableFirstOrder* function) :
+ AbstractNumericalDerivative(function),
+ f1_(),
+ f2_(),
+ f3_(),
+ f4_(),
+ f5_() {}
+ FivePointsNumericalDerivative(DerivableSecondOrder* function) :
+ AbstractNumericalDerivative(function),
+ f1_(),
+ f2_(),
+ f3_(),
+ f4_(),
+ f5_() {}
+ virtual ~FivePointsNumericalDerivative() {}
+
+ FivePointsNumericalDerivative* clone() const { return new FivePointsNumericalDerivative(*this); }
+
+public:
+ double getValue() const throw (Exception)
+ {
+ return f3_;
+ }
+
+ double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const
+ throw (Exception)
+ {
+ throw Exception("Unimplemented cross derivative.");
+ }
+
+protected:
+ void updateDerivatives(const ParameterList parameters)
+ throw (ParameterNotFoundException, ConstraintException);
};
+} // end of namespace bpp.
-} //end of namespace bpp.
-
-#endif //_FIVEPOINTSNUMERICALDERIVATIVE_H_
+#endif // _FIVEPOINTSNUMERICALDERIVATIVE_H_
diff --git a/src/Bpp/Numeric/Function/GoldenSectionSearch.cpp b/src/Bpp/Numeric/Function/GoldenSectionSearch.cpp
index 840d48a..5ef7070 100644
--- a/src/Bpp/Numeric/Function/GoldenSectionSearch.cpp
+++ b/src/Bpp/Numeric/Function/GoldenSectionSearch.cpp
@@ -5,7 +5,7 @@
//
/*
-Copyright or © or Copr. CNRS, (November 17, 2004)
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
This software is a computer program whose purpose is to provide classes
for numerical calculus.
@@ -60,11 +60,7 @@ double GoldenSectionSearch::GSSStopCondition::getCurrentTolerance() const
{
// NRC Test for done:
const GoldenSectionSearch* gss = dynamic_cast<const GoldenSectionSearch*>(optimizer_);
- double x0 = gss->x0;
- double x1 = gss->x1;
- double x2 = gss->x2;
- double x3 = gss->x3;
- return NumTools::abs(x3 - x0) / (NumTools::abs(x1) + NumTools::abs(x2));
+ return NumTools::abs(gss->x3 - gss->x0) / (NumTools::abs(gss->x1) + NumTools::abs(gss->x2));
}
/******************************************************************************/
diff --git a/src/Bpp/Numeric/Function/MetaOptimizer.h b/src/Bpp/Numeric/Function/MetaOptimizer.h
index 228c769..c776911 100644
--- a/src/Bpp/Numeric/Function/MetaOptimizer.h
+++ b/src/Bpp/Numeric/Function/MetaOptimizer.h
@@ -8,7 +8,7 @@
//
/*
- Copyright or © or Copr. CNRS, (November 17, 2004)
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
This software is a computer program whose purpose is to provide classes
for phylogenetic data analysis.
@@ -116,7 +116,7 @@ namespace bpp
* @param derivatives 0, 1 or 2: does this parameter use no, first order or second order derivatives?
* @param type For each optimization step, shall we perform a full optimization with this optimizer or only one step?
*/
- virtual void addOptimizer(const std::string & name, Optimizer * optimizer, const std::vector<std::string> & params, const short derivatives = 0, const std::string & type = IT_TYPE_STEP)
+ virtual void addOptimizer(const std::string & name, Optimizer * optimizer, const std::vector<std::string> & params, unsigned short derivatives = 0, const std::string & type = IT_TYPE_STEP)
{
names_.push_back(name);
optimizers_.push_back(optimizer);
@@ -128,43 +128,43 @@ namespace bpp
/**
* @return The display name of the ith optimizer in the set.
*/
- virtual const std::string& getName(unsigned int i) const { return names_[i]; }
+ virtual const std::string& getName(size_t i) const { return names_[i]; }
/**
* @return The ith optimizer in the set.
*/
- virtual Optimizer* getOptimizer(unsigned int i) { return optimizers_[i]; }
+ virtual Optimizer* getOptimizer(size_t i) { return optimizers_[i]; }
/**
* @return The ith optimizer in the set.
*/
- virtual const Optimizer* getOptimizer(unsigned int i) const { return optimizers_[i]; }
+ virtual const Optimizer* getOptimizer(size_t i) const { return optimizers_[i]; }
/**
* @return The parameter names associated to the ith optimizer in the set.
*/
- virtual std::vector<std::string>& getParameterNames(unsigned int i) { return parameterNames_[i]; }
+ virtual std::vector<std::string>& getParameterNames(size_t i) { return parameterNames_[i]; }
/**
* @return The parameter names associated to the ith optimizer in the set.
*/
- virtual const std::vector<std::string>& getParameterNames(unsigned int i) const { return parameterNames_[i]; }
+ virtual const std::vector<std::string>& getParameterNames(size_t i) const { return parameterNames_[i]; }
/**
* @return The type of iteration to perform for the ith optimizer in the set.
*/
- virtual std::string& getIterationType(unsigned int i) { return itTypes_[i]; }
+ virtual std::string& getIterationType(size_t i) { return itTypes_[i]; }
/**
* @return The type of iteration to perform for the ith optimizer in the set.
*/
- virtual const std::string& getIterationType(unsigned int i) const { return itTypes_[i]; }
+ virtual const std::string& getIterationType(size_t i) const { return itTypes_[i]; }
/**
* @return True if the ith optimizer in the set requires first order derivatives.
*/
- virtual bool requiresFirstOrderDerivatives(unsigned int i) const { return derivatives_[i] > 0; }
+ virtual bool requiresFirstOrderDerivatives(size_t i) const { return derivatives_[i] > 0; }
/**
* @return True if the ith optimizer in the set requires second order derivatives.
*/
- virtual bool requiresSecondOrderDerivatives(unsigned int i) const { return derivatives_[i] > 1; }
+ virtual bool requiresSecondOrderDerivatives(size_t i) const { return derivatives_[i] > 1; }
/**
* @return The number of optimizers in the set.
diff --git a/src/Bpp/Numeric/Function/OneDimensionOptimizationTools.cpp b/src/Bpp/Numeric/Function/OneDimensionOptimizationTools.cpp
index ac707cb..238fe64 100644
--- a/src/Bpp/Numeric/Function/OneDimensionOptimizationTools.cpp
+++ b/src/Bpp/Numeric/Function/OneDimensionOptimizationTools.cpp
@@ -5,37 +5,37 @@
//
/*
- Copyright or © or Copr. CNRS, (November 17, 2004)
-
- This software is a computer program whose purpose is to provide classes
- for numerical calculus. This file is part of the Bio++ project.
-
- This software is governed by the CeCILL license under French law and
- abiding by the rules of distribution of free software. You can use,
- modify and/ or redistribute the software under the terms of the CeCILL
- license as circulated by CEA, CNRS and INRIA at the following URL
- "http://www.cecill.info".
-
- As a counterpart to the access to the source code and rights to copy,
- modify and redistribute granted by the license, users are provided only
- with a limited warranty and the software's author, the holder of the
- economic rights, and the successive licensors have only limited
- liability.
-
- In this respect, the user's attention is drawn to the risks associated
- with loading, using, modifying and/or developing or reproducing the
- software by the user in light of its specific status of free software,
- that may mean that it is complicated to manipulate, and that also
- therefore means that it is reserved for developers and experienced
- professionals having in-depth computer knowledge. Users are therefore
- encouraged to load and test the software's suitability as regards their
- requirements in conditions enabling the security of their systems and/or
- data to be ensured and, more generally, to use and operate it in the
- same conditions as regards security.
-
- The fact that you are presently reading this means that you have had
- knowledge of the CeCILL license and that you accept its terms.
-*/
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for numerical calculus. This file is part of the Bio++ project.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
#include "NewtonBacktrackOneDimension.h"
#include "BrentOneDimension.h"
@@ -47,26 +47,24 @@ using namespace bpp;
using namespace std;
/******************************************************************************
- * The Point class *
- ******************************************************************************/
-
-inline void BracketPoint::set(double xval, double fval) { this->x = xval; this->f = fval; }
+* The Point class *
+******************************************************************************/
+inline void BracketPoint::set(double xval, double fval) { this->x = xval; this->f = fval; }
/******************************************************************************
- * The Bracket class *
- ******************************************************************************/
-
+* The Bracket class *
+******************************************************************************/
inline void Bracket::setA(double xa, double fa) { a.set(xa, fa); }
inline void Bracket::setB(double xb, double fb) { b.set(xb, fb); }
inline void Bracket::setC(double xc, double fc) { c.set(xc, fc); }
/******************************************************************************/
-
+
Bracket OneDimensionOptimizationTools::bracketMinimum(
- double a,
- double b,
- Function * function,
- ParameterList parameters)
+ double a,
+ double b,
+ Function* function,
+ ParameterList parameters)
{
Bracket bracket;
// Copy the parameter to use.
@@ -75,96 +73,96 @@ Bracket OneDimensionOptimizationTools::bracketMinimum(
bracket.b.x = b;
parameters[0].setValue(bracket.b.x); bracket.b.f = function->f(parameters);
if (bracket.b.f > bracket.a.f)
- {
- // Switch roles of first and second point so that we can go downhill
- // in the direction from a to b.
- NumTools::swap<double>(bracket.a.x, bracket.b.x);
- NumTools::swap<double>(bracket.a.f, bracket.b.f);
- }
-
+ {
+ // Switch roles of first and second point so that we can go downhill
+ // in the direction from a to b.
+ NumTools::swap<double>(bracket.a.x, bracket.b.x);
+ NumTools::swap<double>(bracket.a.f, bracket.b.f);
+ }
+
// First guess for third point:
bracket.c.x = bracket.b.x + NumConstants::GOLDEN_RATIO_PHI() * (bracket.b.x - bracket.a.x);
parameters[0].setValue(bracket.c.x); bracket.c.f = function->f(parameters);
-
+
// Keep returning here until we bracket:
while (bracket.b.f > bracket.c.f)
+ {
+ // Compute xu by parabolic extrapolation from a, b, c. TINY is used to prevent
+ // any possible division by 0.
+ double r = (bracket.b.x - bracket.a.x) * (bracket.b.f - bracket.c.f);
+ double q = (bracket.b.x - bracket.c.x) * (bracket.b.f - bracket.a.f);
+
+ double xu = bracket.b.x - ((bracket.b.x - bracket.c.x) * q - (bracket.b.x - bracket.a.x) * r) /
+ (2.0 * NumTools::sign(NumTools::max(NumTools::abs(q - r), NumConstants::VERY_TINY()), q - r));
+ double xulim = (bracket.b.x) + GLIMIT * (bracket.c.x - bracket.b.x);
+ double fu;
+
+ // We don't go farther than this.
+ // Test various possibilities:
+ if ((bracket.b.x - xu) * (xu - bracket.c.x) > 0.0)
+ {
+ parameters[0].setValue(xu); fu = function->f(parameters);
+ if (fu < bracket.c.f)
+ {
+ bracket.setA(bracket.b.x, bracket.b.f);
+ bracket.setB(xu, fu);
+ return bracket;
+ }
+ else if (fu > bracket.b.f)
+ {
+ bracket.setC(xu, fu);
+ return bracket;
+ }
+ // Parabolic fit was no use.
+ // Use default magnification.
+ xu = bracket.c.x + NumConstants::GOLDEN_RATIO_PHI() * (bracket.c.x - bracket.b.x);
+ parameters[0].setValue(xu); fu = function->f(parameters);
+ }
+ else if ((bracket.c.x - xu) * (xu - xulim) > 0.0)
+ {
+ // Parabolic fit is between point 3 and its allowed limit.
+ parameters[0].setValue(xu); fu = function->f(parameters);
+ if (fu < bracket.c.f)
+ {
+ NumTools::shift<double>(bracket.b.x, bracket.c.x, xu, bracket.c.x + NumConstants::GOLDEN_RATIO_PHI() * (bracket.c.x - bracket.b.x));
+ parameters[0].setValue(xu);
+ NumTools::shift<double>(bracket.b.f, bracket.c.f, fu, function->f(parameters));
+ }
+ }
+ else if ((xu - xulim) * (xulim - bracket.c.x) >= 0.0)
{
- // Compute xu by parabolic extrapolation from a, b, c. TINY is used to prevent
- // any possible division by 0.
- double r = (bracket.b.x - bracket.a.x) * (bracket.b.f - bracket.c.f);
- double q = (bracket.b.x - bracket.c.x) * (bracket.b.f - bracket.a.f);
-
- double xu = bracket.b.x - ((bracket.b.x - bracket.c.x) * q - (bracket.b.x - bracket.a.x) * r) /
- (2.0 * NumTools::sign(NumTools::max(NumTools::abs(q - r), NumConstants::VERY_TINY()), q - r));
- double xulim = (bracket.b.x) + GLIMIT * (bracket.c.x - bracket.b.x);
- double fu;
-
- // We don't go farther than this.
- // Test various possibilities:
- if ((bracket.b.x - xu) * (xu - bracket.c.x) > 0.0)
- {
- parameters[0].setValue(xu); fu = function->f(parameters);
- if (fu < bracket.c.f)
- {
- bracket.setA(bracket.b.x, bracket.b.f);
- bracket.setB(xu, fu);
- return bracket;
- }
- else if (fu > bracket.b.f)
- {
- bracket.setC(xu, fu);
- return bracket;
- }
- // Parabolic fit was no use.
- // Use default magnification.
- xu = bracket.c.x + NumConstants::GOLDEN_RATIO_PHI() * (bracket.c.x - bracket.b.x);
- parameters[0].setValue(xu); fu = function->f(parameters);
- }
- else if ((bracket.c.x - xu) * (xu - xulim) > 0.0)
- {
- // Parabolic fit is between point 3 and its allowed limit.
- parameters[0].setValue(xu); fu = function->f(parameters);
- if (fu < bracket.c.f)
- {
- NumTools::shift<double>(bracket.b.x, bracket.c.x, xu, bracket.c.x + NumConstants::GOLDEN_RATIO_PHI() * (bracket.c.x - bracket.b.x));
- parameters[0].setValue(xu);
- NumTools::shift<double>(bracket.b.f, bracket.c.f, fu, function->f(parameters));
- }
- }
- else if ((xu - xulim) * (xulim - bracket.c.x) >= 0.0)
- {
- // Limit parabolic xu to maximum allowed value.
- xu = xulim;
- parameters[0].setValue(xu); fu = function->f(parameters);
- }
- else
- {
- // Reject parabolic xu, use default magnification.
- xu = bracket.c.x + NumConstants::GOLDEN_RATIO_PHI() * (bracket.c.x - bracket.b.x);
- parameters[0].setValue(xu); fu = function->f(parameters);
- }
- // Eliminate oldest point and continue.
- NumTools::shift<double>(bracket.a.x, bracket.b.x, bracket.c.x, xu);
- NumTools::shift<double>(bracket.a.f, bracket.b.f, bracket.c.f, fu);
+ // Limit parabolic xu to maximum allowed value.
+ xu = xulim;
+ parameters[0].setValue(xu); fu = function->f(parameters);
}
+ else
+ {
+ // Reject parabolic xu, use default magnification.
+ xu = bracket.c.x + NumConstants::GOLDEN_RATIO_PHI() * (bracket.c.x - bracket.b.x);
+ parameters[0].setValue(xu); fu = function->f(parameters);
+ }
+ // Eliminate oldest point and continue.
+ NumTools::shift<double>(bracket.a.x, bracket.b.x, bracket.c.x, xu);
+ NumTools::shift<double>(bracket.a.f, bracket.b.f, bracket.c.f, fu);
+ }
return bracket;
}
/******************************************************************************/
unsigned int OneDimensionOptimizationTools::lineMinimization(
- DirectionFunction& f1dim,
- ParameterList& parameters,
- std::vector<double>& xi,
- double tolerance,
- OutputStream* profiler,
- OutputStream* messenger,
- int verbose)
+ DirectionFunction& f1dim,
+ ParameterList& parameters,
+ std::vector<double>& xi,
+ double tolerance,
+ OutputStream* profiler,
+ OutputStream* messenger,
+ unsigned int verbose)
{
// Initial guess for brackets:
double ax = 0.;
double xx = 0.01;
-
+
f1dim.setConstraintPolicy(AutoParameter::CONSTRAINTS_AUTO);
f1dim.setMessageHandler(messenger);
f1dim.init(parameters, xi);
@@ -180,11 +178,11 @@ unsigned int OneDimensionOptimizationTools::lineMinimization(
singleParameter.addParameter(Parameter("x", 0.0));
bod.init(singleParameter);
bod.optimize();
- //Update parameters:
- //parameters.matchParametersValues(f1dim.getFunction()->getParameters());
-
+ // Update parameters:
+ // parameters.matchParametersValues(f1dim.getFunction()->getParameters());
+
double xmin = f1dim.getParameters()[0].getValue();
- for(size_t j = 0; j < parameters.size(); j++)
+ for (size_t j = 0; j < parameters.size(); j++)
{
xi[j] *= xmin;
parameters[j].setValue(parameters[j].getValue() + xi[j]);
@@ -200,29 +198,32 @@ unsigned int OneDimensionOptimizationTools::lineSearch(DirectionFunction& f1dim,
std::vector<double>& gradient,
OutputStream* profiler,
OutputStream* messenger,
- int verbose)
+ unsigned int verbose)
{
size_t size = xi.size();
-
+
f1dim.setConstraintPolicy(AutoParameter::CONSTRAINTS_AUTO);
f1dim.setMessageHandler(messenger);
f1dim.init(parameters, xi);
- double slope=0;
- for (unsigned int i=0;i<size;i++)
- slope+=xi[i]*gradient[i];
+ double slope = 0;
+ for (size_t i = 0; i < size; i++)
+ {
+ slope += xi[i] * gradient[i];
+ }
// if (slope>=0)
// throw Exception("Slope problem in OneDimensionOptimizationTools::lineSearch. Slope="+TextTools::toString(slope));
- double x, temp, test=0;
- for (unsigned int i=0;i<size;i++){
- x=abs(parameters[i].getValue());
- temp=abs(xi[i]);
- if (x>1.0)
- temp/=x;
- if (temp>test)
- test=temp;
+ double x, temp, test = 0;
+ for (size_t i = 0; i < size; ++i)
+ {
+ x = abs(parameters[i].getValue());
+ temp = abs(xi[i]);
+ if (x > 1.0)
+ temp /= x;
+ if (temp > test)
+ test = temp;
}
NewtonBacktrackOneDimension nbod(&f1dim, slope, test);
@@ -238,15 +239,15 @@ unsigned int OneDimensionOptimizationTools::lineSearch(DirectionFunction& f1dim,
singleParameter.addParameter(Parameter("x", 0.0));
nbod.init(singleParameter);
nbod.optimize();
- //Update parameters:
- //parameters.matchParametersValues(f1dim.getFunction()->getParameters());
-
+ // Update parameters:
+ // parameters.matchParametersValues(f1dim.getFunction()->getParameters());
+
double xmin = f1dim.getParameters()[0].getValue();
- for(unsigned int j = 0; j < parameters.size(); j++)
- {
- xi[j] *= xmin;
- parameters[j].setValue(parameters[j].getValue() + xi[j]);
- }
+ for (unsigned int j = 0; j < parameters.size(); j++)
+ {
+ xi[j] *= xmin;
+ parameters[j].setValue(parameters[j].getValue() + xi[j]);
+ }
return nbod.getNumberOfEvaluations();
}
@@ -256,4 +257,3 @@ unsigned int OneDimensionOptimizationTools::lineSearch(DirectionFunction& f1dim,
double OneDimensionOptimizationTools::GLIMIT = 100.0;
/******************************************************************************/
-
diff --git a/src/Bpp/Numeric/Function/OneDimensionOptimizationTools.h b/src/Bpp/Numeric/Function/OneDimensionOptimizationTools.h
index 75ab4aa..a064853 100644
--- a/src/Bpp/Numeric/Function/OneDimensionOptimizationTools.h
+++ b/src/Bpp/Numeric/Function/OneDimensionOptimizationTools.h
@@ -5,37 +5,37 @@
//
/*
- Copyright or © or Copr. CNRS, (November 17, 2004)
-
- This software is a computer program whose purpose is to provide classes
- for numerical calculus. This file is part of the Bio++ project.
-
- This software is governed by the CeCILL license under French law and
- abiding by the rules of distribution of free software. You can use,
- modify and/ or redistribute the software under the terms of the CeCILL
- license as circulated by CEA, CNRS and INRIA at the following URL
- "http://www.cecill.info".
-
- As a counterpart to the access to the source code and rights to copy,
- modify and redistribute granted by the license, users are provided only
- with a limited warranty and the software's author, the holder of the
- economic rights, and the successive licensors have only limited
- liability.
-
- In this respect, the user's attention is drawn to the risks associated
- with loading, using, modifying and/or developing or reproducing the
- software by the user in light of its specific status of free software,
- that may mean that it is complicated to manipulate, and that also
- therefore means that it is reserved for developers and experienced
- professionals having in-depth computer knowledge. Users are therefore
- encouraged to load and test the software's suitability as regards their
- requirements in conditions enabling the security of their systems and/or
- data to be ensured and, more generally, to use and operate it in the
- same conditions as regards security.
-
- The fact that you are presently reading this means that you have had
- knowledge of the CeCILL license and that you accept its terms.
-*/
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for numerical calculus. This file is part of the Bio++ project.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
#ifndef _ONEDIMENSIONOPTIMIZATIONTOOLS_H_
#define _ONEDIMENSIONOPTIMIZATIONTOOLS_H_
@@ -46,93 +46,93 @@
namespace bpp
{
+class BracketPoint
+{
+public:
+ double x;
+ double f;
+
+public:
+ // Constructor and destructor:
+ BracketPoint() : x(0),
+ f(0) {}
+ BracketPoint(double xval, double fval) : x(xval),
+ f(fval) {}
+ virtual ~BracketPoint() {}
+
+public:
+ void set(double x, double f);
+};
+
+class Bracket
+{
+public:
+ // Constructor and destructor::
+ Bracket() : a(),
+ b(),
+ c() {}
+ virtual ~Bracket() {}
+
+public:
+ // Methods:
+ void setA(double xa, double fa);
+ void setB(double xb, double fb);
+ void setC(double xc, double fc);
+
+public:
+ BracketPoint a, b, c;
+};
+
+/**
+ * @brief Tools of one parameter-functions optimizations.
+ *
+ * For now, contains only one method to bracket a minimum.
+ */
+class OneDimensionOptimizationTools
+{
+public:
+ OneDimensionOptimizationTools() {}
+ virtual ~OneDimensionOptimizationTools() {}
- class BracketPoint
- {
- public:
- double x;
- double f;
-
- public: // Constructor and destructor:
- BracketPoint(): x(0), f(0) {}
- BracketPoint(double xval, double fval): x(xval), f(fval) {}
- virtual ~BracketPoint() {}
-
- public:
- void set(double x, double f);
-
- };
-
- class Bracket
- {
- public: // Constructor and destructor::
- Bracket(): a(), b(), c() {}
- virtual ~Bracket() {}
-
- public: // Methods:
- void setA(double xa, double fa);
- void setB(double xb, double fb);
- void setC(double xc, double fc);
-
- public:
- BracketPoint a, b, c;
- };
+public:
+ /**
+ * @brief Bracket a minimum.
+ *
+ * Given a function func, and given distinct initial points x1 and x2,
+ * this routine searches in the downhill direction (defined by the function as
+ * evaluated at the initial points) and returns a Bracket object with new points
+ * a.x, b.x and c.x that bracket a minimum of the function. Also returned are the
+ * function values at the three points, a.f, b.f and c.f.
+ *
+ * @param a, b Two initial values for the parameter.
+ * @param function The function to bracket.
+ * @param parameters The parameter to use as a variable.
+ * @return A bracket object.
+ */
+ static Bracket bracketMinimum(double a, double b, Function* function, ParameterList parameters);
+
+ static unsigned int lineMinimization(DirectionFunction& f1dim, ParameterList& parameters, std::vector<double>& xi, double tolerance, OutputStream* profiler = 0, OutputStream* messenger = 0, unsigned int verbose = 2);
/**
- * @brief Tools of one parameter-functions optimizations.
+ * @brief Search a 'sufficiently low' value for a function in a given direction.
+ *
+ * This function performs a similar computation as the lnsrch function defined at page 385 of
+ *
+ * <pre>
+ * NUMERICAL RECIPES IN C: THE ART OF SCIENTIFIC COMPUTING
+ * (ISBN 0-521-43108-5)
+ * </pre>
*
- * For now, contains only one method to bracket a minimum.
+ * without the stpmax argument, since the steps are bounded in another way.
+ */
+ static unsigned int lineSearch(DirectionFunction& f1dim, ParameterList& parameters, std::vector<double>& xi, std::vector<double>& gradient, OutputStream* profiler = 0, OutputStream* messenger = 0, unsigned int verbose = 2);
+
+public:
+ /**
+ * @brief Maximum magnification allowed for a parabolic-fit step.
*/
- class OneDimensionOptimizationTools
- {
- public:
- OneDimensionOptimizationTools() {}
- virtual ~OneDimensionOptimizationTools() {}
-
- public:
-
- /**
- * @brief Bracket a minimum.
- *
- * Given a function func, and given distinct initial points x1 and x2,
- * this routine searches in the downhill direction (defined by the function as
- * evaluated at the initial points) and returns a Bracket object with new points
- * a.x, b.x and c.x that bracket a minimum of the function. Also returned are the
- * function values at the three points, a.f, b.f and c.f.
- *
- * @param a, b Two initial values for the parameter.
- * @param function The function to bracket.
- * @param parameters The parameter to use as a variable.
- * @return A bracket object.
- */
- static Bracket bracketMinimum(double a, double b, Function* function, ParameterList parameters);
-
- static unsigned int lineMinimization(DirectionFunction& f1dim, ParameterList& parameters, std::vector<double>& xi, double tolerance, OutputStream* profiler = 0, OutputStream* messenger = 0, int verbose = 2);
-
- /**
- * @brief Search a 'sufficiently low' value for a function in a given direction.
- *
- * This function performs a similar computation as the lnsrch function defined at page 385 of
- *
- * <pre>
- * NUMERICAL RECIPES IN C: THE ART OF SCIENTIFIC COMPUTING
- * (ISBN 0-521-43108-5)
- * </pre>
- *
- * without the stpmax argument, since the steps are bounded in another way.
- */
- static unsigned int lineSearch(DirectionFunction& f1dim, ParameterList& parameters, std::vector<double>& xi, std::vector<double>& gradient, OutputStream* profiler = 0, OutputStream* messenger = 0, int verbose = 2);
-
- public:
-
- /**
- * @brief Maximum magnification allowed for a parabolic-fit step.
- */
- static double GLIMIT;
-
- };
-
-} //end of namespace bpp.
-
-#endif //_ONEDIMENSIONOPTIMIZATIONTOOLS_H_
+ static double GLIMIT;
+};
+} // end of namespace bpp.
+#endif // _ONEDIMENSIONOPTIMIZATIONTOOLS_H_
diff --git a/src/Bpp/Numeric/Function/ReparametrizationFunctionWrapper.cpp b/src/Bpp/Numeric/Function/ReparametrizationFunctionWrapper.cpp
index 620da3d..4b8753d 100644
--- a/src/Bpp/Numeric/Function/ReparametrizationFunctionWrapper.cpp
+++ b/src/Bpp/Numeric/Function/ReparametrizationFunctionWrapper.cpp
@@ -45,7 +45,7 @@ using namespace std;
void ReparametrizationFunctionWrapper::init_(bool verbose)
{
- for (unsigned int i = 0; i < functionParameters_.size(); i++)
+ for (size_t i = 0; i < functionParameters_.size(); i++)
{
Parameter& p = functionParameters_[i];
Constraint* constraint = p.getConstraint();
@@ -177,7 +177,7 @@ void ReparametrizationFunctionWrapper::fireParameterChanged(const ParameterList&
// but that would implied a quick sort on parameter names (nlog(n))
// whereas using a loop over the set is in o(n). It should hence be
// more efficient in most cases.
- for (unsigned int i = 0; i < getNumberOfParameters(); i++)
+ for (size_t i = 0; i < getNumberOfParameters(); ++i)
{
double x = dynamic_cast<TransformedParameter&>(getParameter_(i)).getOriginalValue();
try
diff --git a/src/Bpp/Numeric/Function/ReparametrizationFunctionWrapper.h b/src/Bpp/Numeric/Function/ReparametrizationFunctionWrapper.h
index cc6ac1d..323b794 100644
--- a/src/Bpp/Numeric/Function/ReparametrizationFunctionWrapper.h
+++ b/src/Bpp/Numeric/Function/ReparametrizationFunctionWrapper.h
@@ -5,7 +5,7 @@
//
/*
-Copyright or © or Copr. CNRS, (November 17, 2004)
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
This software is a computer program whose purpose is to provide classes
for numerical calculus.
diff --git a/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.cpp b/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.cpp
index 732f9fd..341864c 100644
--- a/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.cpp
+++ b/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.cpp
@@ -47,26 +47,31 @@ throw (ParameterNotFoundException, ConstraintException)
{
if (computeD1_ && variables_.size() > 0)
{
- if (function1_) function1_->enableFirstOrderDerivatives(false);
- if (function2_) function2_->enableSecondOrderDerivatives(false);
+ if (function1_)
+ function1_->enableFirstOrderDerivatives(false);
+ if (function2_)
+ function2_->enableSecondOrderDerivatives(false);
function_->setParameters(parameters);
f2_ = function_->getValue();
- if ((abs(f2_) >= NumConstants::VERY_BIG()) || isnan(f2_)){
- for (unsigned int i = 0; i < variables_.size(); i++){
- der1_[i]=log(-1);
- der2_[i]=log(-1);
+ if ((abs(f2_) >= NumConstants::VERY_BIG()) || isnan(f2_))
+ {
+ for (size_t i = 0; i < variables_.size(); ++i)
+ {
+ der1_[i] = log(-1);
+ der2_[i] = log(-1);
}
return;
}
-
+
string lastVar;
bool functionChanged = false;
ParameterList p;
bool start = true;
- for (unsigned int i = 0; i < variables_.size(); i++)
+ for (size_t i = 0; i < variables_.size(); ++i)
{
string var = variables_[i];
- if (!parameters.hasParameter(var)) continue;
+ if (!parameters.hasParameter(var))
+ continue;
if (!start)
{
vector<string> vars(2);
@@ -83,91 +88,93 @@ throw (ParameterNotFoundException, ConstraintException)
functionChanged = true;
double value = function_->getParameterValue(var);
double h = -(1. + std::abs(value)) * h_;
- if (abs(h)<p[0].getPrecision())
- h=h<0?-p[0].getPrecision():p[0].getPrecision();
+ if (abs(h) < p[0].getPrecision())
+ h = h < 0 ? -p[0].getPrecision() : p[0].getPrecision();
double hf1(0), hf3(0);
- unsigned int nbtry=0;
-
- //Compute f1_
- while (hf1==0){
+ unsigned int nbtry = 0;
+
+ // Compute f1_
+ while (hf1 == 0)
+ {
try
+ {
+ p[0].setValue(value + h);
+ function_->setParameters(p); // also reset previous parameter...
+
+ p = p.subList(0);
+ f1_ = function_->getValue();
+ if ((abs(f1_) >= NumConstants::VERY_BIG()) || isnan(f1_))
+ throw ConstraintException("f1_ too large", &p[0], f1_);
+ else
+ hf1 = h;
+ }
+ catch (ConstraintException& ce)
+ {
+ if (++nbtry == 10) // no possibility to compute derivatives
+ break;
+ else if (h < 0)
+ h = -h; // try on the right
+ else
+ h /= -2; // try again on the left with smaller interval
+ }
+ }
+
+ if (hf1 != 0)
+ {
+ // Compute f3_
+ if (h < 0)
+ h = -h; // on the right
+ else
+ h /= 2; // on the left with smaller interval
+
+ nbtry = 0;
+ while (hf3 == 0)
+ {
+ try
{
p[0].setValue(value + h);
- function_->setParameters(p); //also reset previous parameter...
-
+ function_->setParameters(p); // also reset previous parameter...
+
p = p.subList(0);
- f1_ = function_->getValue();
- if ((abs(f1_) >= NumConstants::VERY_BIG()) || isnan(f1_))
- throw ConstraintException("f1_ too large", &p[0], f1_);
+ f3_ = function_->getValue();
+ if ((abs(f3_) >= NumConstants::VERY_BIG()) || isnan(f3_))
+ throw ConstraintException("f3_ too large", &p[0], f3_);
else
- hf1=h;
+ hf3 = h;
}
- catch (ConstraintException& ce)
+ catch (ConstraintException& ce)
{
- if (++nbtry==10) // no possibility to compute derivatives
+ if (++nbtry == 10) // no possibility to compute derivatives
break;
+ else if (h < 0)
+ h = -h; // try on the right
else
- if (h<0)
- h=-h; // try on the right
- else
- h/=-2; // try again on the left with smaller interval
+ h /= -2; // try again on the left with smaller interval
}
- }
-
- if (hf1!=0){
- //Compute f3_
- if (h<0)
- h=-h; // on the right
- else
- h/=2; // on the left with smaller interval
-
- nbtry=0;
- while (hf3==0){
- try
- {
- p[0].setValue(value + h);
- function_->setParameters(p); //also reset previous parameter...
-
- p = p.subList(0);
- f3_ = function_->getValue();
- if ((abs(f3_) >= NumConstants::VERY_BIG()) || isnan(f3_))
- throw ConstraintException("f3_ too large", &p[0], f3_);
- else
- hf3=h;
- }
- catch (ConstraintException& ce)
- {
- if (++nbtry==10) // no possibility to compute derivatives
- break;
- else
- if (h<0)
- h=-h; // try on the right
- else
- h/=-2; // try again on the left with smaller interval
- }
}
}
-
- if (hf3==0){
- der1_[i]=log(-1);
- der2_[i]=log(-1);
+
+ if (hf3 == 0)
+ {
+ der1_[i] = log(-1);
+ der2_[i] = log(-1);
}
- else {
- der1_[i] = (f1_ - f3_) / (hf1-hf3);
- der2_[i] = ((f1_ - f2_)/hf1 - (f3_ - f2_)/hf3)*2/(hf1-hf3);
+ else
+ {
+ der1_[i] = (f1_ - f3_) / (hf1 - hf3);
+ der2_[i] = ((f1_ - f2_) / hf1 - (f3_ - f2_) / hf3) * 2 / (hf1 - hf3);
}
}
-
-
if (computeCrossD2_)
{
string lastVar1, lastVar2;
for (unsigned int i = 0; i < variables_.size(); i++)
{
string var1 = variables_[i];
- if (!parameters.hasParameter(var1)) continue;
+ if (!parameters.hasParameter(var1))
+ continue;
for (unsigned int j = 0; j < variables_.size(); j++)
{
if (j == i)
@@ -176,15 +183,18 @@ throw (ParameterNotFoundException, ConstraintException)
continue;
}
string var2 = variables_[j];
- if (!parameters.hasParameter(var2)) continue;
+ if (!parameters.hasParameter(var2))
+ continue;
vector<string> vars(2);
vars[0] = var1;
vars[1] = var2;
if (i > 0 && j > 0)
{
- if (lastVar1 != var1 && lastVar1 != var2) vars.push_back(lastVar1);
- if (lastVar2 != var1 && lastVar2 != var2) vars.push_back(lastVar2);
+ if (lastVar1 != var1 && lastVar1 != var2)
+ vars.push_back(lastVar1);
+ if (lastVar2 != var1 && lastVar2 != var2)
+ vars.push_back(lastVar2);
}
p = parameters.subList(vars);
@@ -193,16 +203,16 @@ throw (ParameterNotFoundException, ConstraintException)
double h1 = (1. + std::abs(value1)) * h_;
double h2 = (1. + std::abs(value2)) * h_;
- //Compute 4 additional points:
+ // Compute 4 additional points:
try
{
p[0].setValue(value1 - h1);
p[1].setValue(value2 - h2);
- function_->setParameters(p); //also reset previous parameter...
+ function_->setParameters(p); // also reset previous parameter...
vector<size_t> tmp(2);
tmp[0] = 0;
tmp[1] = 1;
- p = p.subList(tmp); //removed the previous parameters.
+ p = p.subList(tmp); // removed the previous parameters.
f11_ = function_->getValue();
p[1].setValue(value2 + h2);
@@ -230,19 +240,23 @@ throw (ParameterNotFoundException, ConstraintException)
}
}
- //Reset last parameter and compute analytical derivatives if any.
- if (function1_) function1_->enableFirstOrderDerivatives(computeD1_);
- if (function2_) function2_->enableSecondOrderDerivatives(computeD2_);
+ // Reset last parameter and compute analytical derivatives if any.
+ if (function1_)
+ function1_->enableFirstOrderDerivatives(computeD1_);
+ if (function2_)
+ function2_->enableSecondOrderDerivatives(computeD2_);
if (functionChanged)
function_->setParameters(parameters.subList(lastVar));
}
else
{
- //Reset initial value and compute analytical derivatives if any.
- if (function1_) function1_->enableFirstOrderDerivatives(computeD1_);
- if (function2_) function2_->enableSecondOrderDerivatives(computeD2_);
+ // Reset initial value and compute analytical derivatives if any.
+ if (function1_)
+ function1_->enableFirstOrderDerivatives(computeD1_);
+ if (function2_)
+ function2_->enableSecondOrderDerivatives(computeD2_);
function_->setParameters(parameters);
- //Just in case derivatives are not computed:
+ // Just in case derivatives are not computed:
f2_ = function_->getValue();
}
}
diff --git a/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.h b/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.h
index 80a2bc1..e413494 100644
--- a/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.h
+++ b/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.h
@@ -5,37 +5,37 @@
//
/*
-Copyright or © or Copr. CNRS, (November 17, 2004)
-
-This software is a computer program whose purpose is to provide classes
-for numerical calculus.
-
-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.
-*/
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for numerical calculus.
+
+ 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 _THREEPOINTSNUMERICALDERIVATIVE_H_
#define _THREEPOINTSNUMERICALDERIVATIVE_H_
@@ -43,14 +43,13 @@ knowledge of the CeCILL license and that you accept its terms.
#include "Functions.h"
#include "AbstractNumericalDerivative.h"
-//From the STL:
+// From the STL:
#include <map>
#include <vector>
#include <string>
namespace bpp
{
-
/**
* @brief Three points numerical derivative function wrapper.
*
@@ -62,7 +61,7 @@ namespace bpp
* \dfrac{\partial f}{\partial x } &=& \dfrac{f_{+1}-f_{-1}}{2h}\\
* \dfrac{\partial^2 f}{\partial x^2} &=& \dfrac{f_{+1}-2f_0+f_{-1}}{h^2}\\
* @f}
- * In case of border limit (when @f$x_{-1}@f$ or @f$x_{+1}@f$ are not computable),
+ * In case of border limit (when @f$x_{-1}@f$ or @f$x_{+1}@f$ are not computable),
* the foreward and backward computations are performed, respectively:
* @f{eqnarray*}
* \dfrac{\partial f}{\partial x } &=& \dfrac{f_{+1}-f_0}{h}\\
@@ -82,37 +81,55 @@ namespace bpp
*
* @see AbstractNumericalDerivative
*/
-class ThreePointsNumericalDerivative:
+class ThreePointsNumericalDerivative :
public AbstractNumericalDerivative
{
- private:
- double f1_, f2_, f3_, f11_, f22_, f12_, f21_;
-
- public:
- ThreePointsNumericalDerivative (Function* function) :
- AbstractNumericalDerivative(function), f1_(), f2_(), f3_(), f11_(), f22_(), f12_(), f21_() {}
- ThreePointsNumericalDerivative (DerivableFirstOrder * function) :
- AbstractNumericalDerivative(function), f1_(), f2_(), f3_(), f11_(), f22_(), f12_(), f21_() {}
- ThreePointsNumericalDerivative (DerivableSecondOrder * function) :
- AbstractNumericalDerivative(function), f1_(), f2_(), f3_(), f11_(), f22_(), f12_(), f21_() {}
- virtual ~ThreePointsNumericalDerivative() {}
-
- ThreePointsNumericalDerivative* clone() const { return new ThreePointsNumericalDerivative(*this); }
-
- public:
-
- double getValue() const throw (Exception)
- {
- return f2_;
- }
-
- protected:
- void updateDerivatives(const ParameterList parameters)
- throw (ParameterNotFoundException, ConstraintException);
-
+private:
+ double f1_, f2_, f3_, f11_, f22_, f12_, f21_;
+
+public:
+ ThreePointsNumericalDerivative (Function* function) :
+ AbstractNumericalDerivative(function),
+ f1_(),
+ f2_(),
+ f3_(),
+ f11_(),
+ f22_(),
+ f12_(),
+ f21_() {}
+ ThreePointsNumericalDerivative (DerivableFirstOrder* function) :
+ AbstractNumericalDerivative(function),
+ f1_(),
+ f2_(),
+ f3_(),
+ f11_(),
+ f22_(),
+ f12_(),
+ f21_() {}
+ ThreePointsNumericalDerivative (DerivableSecondOrder* function) :
+ AbstractNumericalDerivative(function),
+ f1_(),
+ f2_(),
+ f3_(),
+ f11_(),
+ f22_(),
+ f12_(),
+ f21_() {}
+ virtual ~ThreePointsNumericalDerivative() {}
+
+ ThreePointsNumericalDerivative* clone() const { return new ThreePointsNumericalDerivative(*this); }
+
+public:
+ double getValue() const throw (Exception)
+ {
+ return f2_;
+ }
+
+protected:
+ void updateDerivatives(const ParameterList parameters)
+ throw (ParameterNotFoundException, ConstraintException);
};
+} // end of namespace bpp.
-} //end of namespace bpp.
-
-#endif //_THREEPOINTSNUMERICALDERIVATIVE_H_
+#endif // _THREEPOINTSNUMERICALDERIVATIVE_H_
diff --git a/src/Bpp/Numeric/Function/TwoPointsNumericalDerivative.cpp b/src/Bpp/Numeric/Function/TwoPointsNumericalDerivative.cpp
index 8970e59..295b7d7 100644
--- a/src/Bpp/Numeric/Function/TwoPointsNumericalDerivative.cpp
+++ b/src/Bpp/Numeric/Function/TwoPointsNumericalDerivative.cpp
@@ -47,8 +47,10 @@ throw (ParameterNotFoundException, ConstraintException)
{
if (computeD1_ && variables_.size() > 0)
{
- if (function1_) function1_->enableFirstOrderDerivatives(false);
- if (function2_) function2_->enableSecondOrderDerivatives(false);
+ if (function1_)
+ function1_->enableFirstOrderDerivatives(false);
+ if (function2_)
+ function2_->enableSecondOrderDerivatives(false);
function_->setParameters(parameters);
f1_ = function_->getValue();
string lastVar;
@@ -57,7 +59,8 @@ throw (ParameterNotFoundException, ConstraintException)
for (unsigned int i = 0; i < variables_.size(); i++)
{
string var = variables_[i];
- if (!parameters.hasParameter(var)) continue;
+ if (!parameters.hasParameter(var))
+ continue;
ParameterList p;
if (!start)
{
@@ -77,7 +80,7 @@ throw (ParameterNotFoundException, ConstraintException)
}
double value = function_->getParameterValue(var);
double h = (1 + std::abs(value)) * h_;
- //Compute one other point:
+ // Compute one other point:
try
{
p[0].setValue(value + h);
@@ -86,7 +89,7 @@ throw (ParameterNotFoundException, ConstraintException)
}
catch (ConstraintException& ce1)
{
- //Right limit raised, use backward approximation:
+ // Right limit raised, use backward approximation:
try
{
p[0].setValue(value - h);
@@ -96,24 +99,27 @@ throw (ParameterNotFoundException, ConstraintException)
}
catch (ConstraintException& ce2)
{
- //PB: can't compute derivative, because of a two narrow interval (lower than h)
+ // PB: can't compute derivative, because of a two narrow interval (lower than h)
throw ce2;
}
}
- //No limit raised, use forward approximation:
+ // No limit raised, use forward approximation:
der1_[i] = (f2_ - f1_) / h;
}
- //Reset last parameter and compute analytical derivatives if any:
- if (function1_) function1_->enableFirstOrderDerivatives(computeD1_);
+ // Reset last parameter and compute analytical derivatives if any:
+ if (function1_)
+ function1_->enableFirstOrderDerivatives(computeD1_);
if (functionChanged)
function_->setParameters(parameters.subList(lastVar));
}
else
{
- //Reset initial value and compute analytical derivatives if any.
- if (function1_) function1_->enableFirstOrderDerivatives(computeD1_);
- if (function2_) function2_->enableSecondOrderDerivatives(computeD2_);
- //Just in case derivatives are not computed:
+ // Reset initial value and compute analytical derivatives if any.
+ if (function1_)
+ function1_->enableFirstOrderDerivatives(computeD1_);
+ if (function2_)
+ function2_->enableSecondOrderDerivatives(computeD2_);
+ // Just in case derivatives are not computed:
function_->setParameters(parameters);
f1_ = function_->getValue();
}
diff --git a/src/Bpp/Numeric/Function/TwoPointsNumericalDerivative.h b/src/Bpp/Numeric/Function/TwoPointsNumericalDerivative.h
index 9b236bc..c871606 100644
--- a/src/Bpp/Numeric/Function/TwoPointsNumericalDerivative.h
+++ b/src/Bpp/Numeric/Function/TwoPointsNumericalDerivative.h
@@ -5,37 +5,37 @@
//
/*
-Copyright or © or Copr. CNRS, (November 17, 2004)
-
-This software is a computer program whose purpose is to provide classes
-for numerical calculus.
-
-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.
-*/
+ Copyright or © or Copr. CNRS, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for numerical calculus.
+
+ 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 _TWOPOINTSNUMERICALDERIVATIVE_H_
#define _TWOPOINTSNUMERICALDERIVATIVE_H_
@@ -43,14 +43,13 @@ knowledge of the CeCILL license and that you accept its terms.
#include "Functions.h"
#include "AbstractNumericalDerivative.h"
-//From the STL:
+// From the STL:
#include <map>
#include <vector>
#include <string>
namespace bpp
{
-
/**
* @brief Two points numerical derivative function wrapper.
*
@@ -72,50 +71,51 @@ namespace bpp
*
* @see AbstractNumericalDerivative, ThreePointsNumericalDerivative, FivePointsNumericalDerivative
*/
-class TwoPointsNumericalDerivative:
+class TwoPointsNumericalDerivative :
public AbstractNumericalDerivative
{
- private:
- double f1_, f2_;
-
- public:
- TwoPointsNumericalDerivative(Function* function) :
- AbstractNumericalDerivative(function), f1_(), f2_() {}
- TwoPointsNumericalDerivative(DerivableFirstOrder* function) :
- AbstractNumericalDerivative(function), f1_(), f2_() {}
- virtual ~TwoPointsNumericalDerivative() {}
-
- TwoPointsNumericalDerivative* clone() const { return new TwoPointsNumericalDerivative(*this); }
-
- public:
-
- double getValue() const throw (Exception) { return f1_; }
-
- /**
- * @name The DerivableSecondOrder interface
- *
- * @{
- */
- double getSecondOrderDerivative(const std::string & variable) const
- throw (Exception)
- {
- throw Exception("Second order derivative not avalaible with two points method.");
- }
-
- double getSecondOrderDerivative(const std::string & variable1, const std::string & variable2) const
- throw (Exception)
- {
- throw Exception("Unimplemented cross derivative.");
- }
- /** @} */
-
- protected:
- void updateDerivatives(const ParameterList parameters)
- throw (ParameterNotFoundException, ConstraintException);
-
+private:
+ double f1_, f2_;
+
+public:
+ TwoPointsNumericalDerivative(Function* function) :
+ AbstractNumericalDerivative(function),
+ f1_(),
+ f2_() {}
+ TwoPointsNumericalDerivative(DerivableFirstOrder* function) :
+ AbstractNumericalDerivative(function),
+ f1_(),
+ f2_() {}
+ virtual ~TwoPointsNumericalDerivative() {}
+
+ TwoPointsNumericalDerivative* clone() const { return new TwoPointsNumericalDerivative(*this); }
+
+public:
+ double getValue() const throw (Exception) { return f1_; }
+
+ /**
+ * @name The DerivableSecondOrder interface
+ *
+ * @{
+ */
+ double getSecondOrderDerivative(const std::string& variable) const
+ throw (Exception)
+ {
+ throw Exception("Second order derivative not avalaible with two points method.");
+ }
+
+ double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const
+ throw (Exception)
+ {
+ throw Exception("Unimplemented cross derivative.");
+ }
+ /** @} */
+
+protected:
+ void updateDerivatives(const ParameterList parameters)
+ throw (ParameterNotFoundException, ConstraintException);
};
+} // end of namespace bpp.
-} //end of namespace bpp.
-
-#endif //_TWOPOINTSNUMERICALDERIVATIVE_H_
+#endif // _TWOPOINTSNUMERICALDERIVATIVE_H_
diff --git a/src/Bpp/App/BppApplication.cpp b/src/Bpp/Numeric/Hmm/AbstractHmmTransitionMatrix.cpp
similarity index 51%
copy from src/Bpp/App/BppApplication.cpp
copy to src/Bpp/Numeric/Hmm/AbstractHmmTransitionMatrix.cpp
index 5d10750..8362d12 100644
--- a/src/Bpp/App/BppApplication.cpp
+++ b/src/Bpp/Numeric/Hmm/AbstractHmmTransitionMatrix.cpp
@@ -1,14 +1,14 @@
//
-// File: BppApplication.cpp
-// Created by: Julien Dutheil
-// Created on: Sat Aug 08 08:21 2009
+// File: AbstractHmmTransitionMatrix.cpp
+// Created by: Laurent Guéguen
+// Created on: lundi 10 février 2014, à 10h 59
//
/*
-Copyright or © or Copr. CNRS, (November 17, 2004)
+Copyright or © or Copr. Bio++Development Team, (November 16, 2004)
-This software is a computer program whose purpose is to provide basal and
-utilitary classes. This file belongs to the Bio++ Project.
+This software is a computer program whose purpose is to provide classes
+for phylogenetic data 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,
@@ -37,34 +37,48 @@ 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 "BppApplication.h"
-#include "../Utils/AttributesTools.h"
-#include "ApplicationTools.h"
+#include "AbstractHmmTransitionMatrix.h"
-// From the STL:
-#include <iostream>
+#include "../Matrix/MatrixTools.h"
+#include "../VectorTools.h"
using namespace bpp;
using namespace std;
-BppApplication::BppApplication(int argc, char* argv[], const std::string& name): appName_(name), params_(), timerStarted_(false)
+AbstractHmmTransitionMatrix::AbstractHmmTransitionMatrix(const HmmStateAlphabet* alph, const string& prefix) :
+ alph_(alph),
+ pij_((size_t)alph->getNumberOfStates(), (size_t)alph->getNumberOfStates()),
+ tmpmat_((size_t)alph->getNumberOfStates(), (size_t)alph->getNumberOfStates()),
+ eqFreq_((size_t)alph->getNumberOfStates()),
+ upToDate_(false)
{
- cout << "Parsing options:" << endl;
- params_ = AttributesTools::parseOptions(argc, argv);
- bool noint = ApplicationTools::getBooleanParameter("--noninteractive", params_, false, "", true, false);
- ApplicationTools::interactive = !noint;
}
-void BppApplication::startTimer()
+AbstractHmmTransitionMatrix::AbstractHmmTransitionMatrix(const AbstractHmmTransitionMatrix& hptm) :
+ alph_(hptm.alph_),
+ pij_(hptm.pij_),
+ tmpmat_(hptm.tmpmat_),
+ eqFreq_(hptm.eqFreq_),
+ upToDate_(hptm.upToDate_)
{
- ApplicationTools::startTimer();
- timerStarted_ = true;
}
-void BppApplication::done()
+AbstractHmmTransitionMatrix& AbstractHmmTransitionMatrix::operator=(const AbstractHmmTransitionMatrix& hptm)
{
- cout << appName_ << "'s done. Bye." << endl;
- if (timerStarted_)
- ApplicationTools::displayTime("Total execution time:");
+ alph_=hptm.alph_;
+ pij_=hptm.pij_;
+ tmpmat_=hptm.tmpmat_;
+ eqFreq_=hptm.eqFreq_;
+ upToDate_=hptm.upToDate_;
+
+ return *this;
+}
+
+void AbstractHmmTransitionMatrix::setHmmStateAlphabet(const HmmStateAlphabet* stateAlphabet) throw (HmmUnvalidAlphabetException)
+{
+ if (stateAlphabet==NULL)
+ throw HmmUnvalidAlphabetException("Null alphabet in AbstractHmmTransitionMatrix::setHmmStateAlphabet");
+
+ alph_=stateAlphabet;
}
diff --git a/src/Bpp/Numeric/Hmm/AbstractHmmTransitionMatrix.h b/src/Bpp/Numeric/Hmm/AbstractHmmTransitionMatrix.h
new file mode 100644
index 0000000..9e6dee3
--- /dev/null
+++ b/src/Bpp/Numeric/Hmm/AbstractHmmTransitionMatrix.h
@@ -0,0 +1,108 @@
+//
+// File: AbstractHmmTransitionMatrix.h
+// Created by: Laurent Guéguen
+// Created on: lundi 10 février 2014, à 10h 55
+//
+
+/*
+Copyright or © or Copr. Bio++Development Team, (November 16, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for phylogenetic data 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 _ABSTRACTHMMTRANSITIONMATRIX_H_
+#define _ABSTRACTHMMTRANSITIONMATRIX_H_
+
+#include "HmmStateAlphabet.h"
+#include "HmmTransitionMatrix.h"
+
+#include "../VectorTools.h"
+
+namespace bpp
+{
+
+/**
+ * @brief Partial implementation of HmmTransitionMatrix.
+ *
+ */
+
+class AbstractHmmTransitionMatrix:
+ public virtual HmmTransitionMatrix
+{
+private:
+ const HmmStateAlphabet* alph_;
+
+protected:
+ mutable RowMatrix<double> pij_, tmpmat_;
+
+ mutable Vdouble eqFreq_;
+
+ mutable bool upToDate_;
+
+public:
+
+ AbstractHmmTransitionMatrix(const HmmStateAlphabet* alph, const std::string& prefix = "");
+
+ AbstractHmmTransitionMatrix(const AbstractHmmTransitionMatrix& hptm);
+
+ AbstractHmmTransitionMatrix& operator=(const AbstractHmmTransitionMatrix& hptm);
+
+ /**
+ * @return The hidden alphabet associated to this model.
+ */
+
+ const HmmStateAlphabet* getHmmStateAlphabet() const
+ {
+ return alph_;
+ }
+
+ /**
+ * @brief Set the new hidden state alphabet
+ * @param stateAlphabet The new state alphabet
+ * @throw UnvalidStateAlphabetException if the new alphabet is uncorrect (for instance is NULL pointer).
+ */
+
+ void setHmmStateAlphabet(const HmmStateAlphabet* stateAlphabet) throw (HmmUnvalidAlphabetException);
+
+ /**
+ * @return The number of states in the model.
+ */
+
+ size_t getNumberOfStates() const
+ {
+ return alph_->getNumberOfStates();
+ }
+
+};
+
+} //end of namespace bpp
+
+#endif //_ABSTRACTHMMTRANSITIONMATRIX_H_
+
diff --git a/src/Bpp/Numeric/Hmm/AutoCorrelationTransitionMatrix.cpp b/src/Bpp/Numeric/Hmm/AutoCorrelationTransitionMatrix.cpp
new file mode 100644
index 0000000..134eeb3
--- /dev/null
+++ b/src/Bpp/Numeric/Hmm/AutoCorrelationTransitionMatrix.cpp
@@ -0,0 +1,113 @@
+//
+// File: AutoCorrelationTransitionMatrix.cpp
+// Created by: Laurent Guéguen
+// Created on: lundi 10 février 2014, à 09h 56
+//
+
+/*
+Copyright or © or Copr. Bio++Development Team, (November 16, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for phylogenetic data 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 "AutoCorrelationTransitionMatrix.h"
+
+#include "../../Text/TextTools.h"
+
+#include "../Matrix/MatrixTools.h"
+#include "../VectorTools.h"
+
+using namespace bpp;
+using namespace std;
+
+AutoCorrelationTransitionMatrix::AutoCorrelationTransitionMatrix(const HmmStateAlphabet* alph, const string& prefix) :
+ AbstractHmmTransitionMatrix(alph),
+ AbstractParametrizable(prefix),
+ vAutocorrel_()
+{
+ size_t size=(size_t)getNumberOfStates();
+
+ for (size_t i=0; i<size; i++)
+ {
+ vAutocorrel_.push_back(1./(double)size);
+ addParameter_(new Parameter("lambda"+TextTools::toString(i+1), 1./(double)size, &Parameter::PROP_CONSTRAINT_EX));
+ }
+
+ for (size_t i = 0; i < size; i++)
+ eqFreq_[i] = 1./(double)size;
+}
+
+
+AutoCorrelationTransitionMatrix::AutoCorrelationTransitionMatrix(const AutoCorrelationTransitionMatrix& aptm) :
+ AbstractHmmTransitionMatrix(aptm),
+ AbstractParametrizable(aptm),
+ vAutocorrel_(aptm.vAutocorrel_)
+{
+}
+
+AutoCorrelationTransitionMatrix& AutoCorrelationTransitionMatrix::operator=(const AutoCorrelationTransitionMatrix& aptm)
+{
+ AbstractHmmTransitionMatrix::operator=(aptm);
+ AbstractParametrizable::operator=(aptm);
+
+ vAutocorrel_=aptm.vAutocorrel_;
+
+ return *this;
+}
+
+const Matrix<double>& AutoCorrelationTransitionMatrix::getPij() const
+ {
+ if (!upToDate_){
+ for (size_t i = 0; i < vAutocorrel_.size(); ++i)
+ for (size_t j = 0; j < vAutocorrel_.size(); ++j)
+ pij_(i,j) = (i==j) ? vAutocorrel_[i] : (1 - vAutocorrel_[i]) / static_cast<double>(getNumberOfStates()-1);
+
+ upToDate_ = true;
+ }
+
+ return pij_;
+ }
+
+const std::vector<double>& AutoCorrelationTransitionMatrix::getEquilibriumFrequencies() const
+{
+ return eqFreq_;
+}
+
+void AutoCorrelationTransitionMatrix::fireParameterChanged(const ParameterList& parameters)
+{
+ size_t salph=getNumberOfStates();
+
+ for (size_t i=0; i< salph; i++)
+ vAutocorrel_[i]=getParameterValue("lambda"+TextTools::toString(i+1));
+
+ upToDate_=false;
+}
+
+
diff --git a/src/Bpp/Numeric/Hmm/AutoCorrelationTransitionMatrix.h b/src/Bpp/Numeric/Hmm/AutoCorrelationTransitionMatrix.h
new file mode 100644
index 0000000..cb3ec80
--- /dev/null
+++ b/src/Bpp/Numeric/Hmm/AutoCorrelationTransitionMatrix.h
@@ -0,0 +1,118 @@
+//
+// File: AutoCorrelationTransitionMatrix.h
+// Created by: Laurent Guéguen
+// Created on: lundi 10 février 2014, à 09h 56
+//
+
+/*
+Copyright or © or Copr. Bio++Development Team, (November 16, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for phylogenetic data 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 _AUTOCORRELATIONTRANSITIONMATRIX_H_
+#define _AUTOCORRELATIONTRANSITIONMATRIX_H_
+
+#include "AbstractHmmTransitionMatrix.h"
+
+#include "../AbstractParameterAliasable.h"
+
+namespace bpp
+{
+
+/**
+ * @brief Describe the auto-correlation probabilities inside hidden
+ * states of a Hidden Markov Model.
+ *
+ * This modelling behaves like a HMM in which, from a given state,
+ * all transition probabilities to the other states are equal.
+ *
+ * The parameters are the within states transition probabilities,
+ * denoted as \c "lambaN" with N the number of the state (1 is the
+ * first).
+ */
+
+class AutoCorrelationTransitionMatrix:
+ public virtual AbstractHmmTransitionMatrix,
+ public AbstractParametrizable
+{
+private:
+ std::vector<double> vAutocorrel_;
+
+public:
+
+ AutoCorrelationTransitionMatrix(const HmmStateAlphabet* alph, const std::string& prefix = "");
+
+ AutoCorrelationTransitionMatrix(const AutoCorrelationTransitionMatrix& hptm);
+
+ AutoCorrelationTransitionMatrix& operator=(const AutoCorrelationTransitionMatrix& hptm);
+
+ AutoCorrelationTransitionMatrix* clone() const { return new AutoCorrelationTransitionMatrix(*this);}
+
+ /**
+ * @brief Get the transition probability between two states.
+ *
+ * @param i initial state.
+ * @param j final state.
+ * @return the transition probability between the two states.
+ */
+ double Pij(size_t i, size_t j) const
+ {
+ return (i == j) ? vAutocorrel_[i] : (1 - vAutocorrel_[i]) / static_cast<double>(getNumberOfStates() - 1);
+ }
+
+ /**
+ * @brief Get all transition probabilities as a matrix.
+ *
+ * @return A n*n matrix will all transition probabilities (n being the number of hidden states).
+ */
+
+ const Matrix<double>& getPij() const;
+
+ /**
+ * @return The vector of equilibrium frequencies of the Markov chain described by the matrix.
+ */
+
+ const std::vector<double>& getEquilibriumFrequencies() const;
+
+
+ /*
+ * @brief From AbstractParametrizable interface
+ *
+ */
+
+ void fireParameterChanged(const ParameterList& parameters);
+
+};
+
+} //end of namespace bpp
+
+#endif //_AUTOCORRELATIONTRANSITIONMATRIX_H_
+
diff --git a/src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.cpp b/src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.cpp
new file mode 100644
index 0000000..23f057c
--- /dev/null
+++ b/src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.cpp
@@ -0,0 +1,155 @@
+//
+// File: FullHmmTransitionMatrix.cpp
+// Created by: Laurent Guéguen
+// Created on: samedi 21 septembre 2013, à 14h 43
+//
+
+/*
+Copyright or © or Copr. Bio++Development Team, (November 16, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for phylogenetic data 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 "FullHmmTransitionMatrix.h"
+
+#include "../../Text/TextTools.h"
+
+#include "../Matrix/MatrixTools.h"
+#include "../VectorTools.h"
+
+using namespace bpp;
+using namespace std;
+
+FullHmmTransitionMatrix::FullHmmTransitionMatrix(const HmmStateAlphabet* alph, const string& prefix) :
+ AbstractHmmTransitionMatrix(alph),
+ AbstractParametrizable(prefix),
+ vSimplex_()
+{
+ size_t size=(size_t)getNumberOfStates();
+
+ for (size_t i=0; i<size; i++)
+ {
+ vSimplex_.push_back(Simplex(size,1));
+ ParameterList pl=vSimplex_[i].getParameters();
+ for (size_t j=0; j<pl.size(); j++)
+ {
+ Parameter* p=pl[j].clone();
+ p->setName(TextTools::toString(i+1)+"."+p->getName());
+ addParameter_(p);
+ }
+ }
+}
+
+FullHmmTransitionMatrix::FullHmmTransitionMatrix(const FullHmmTransitionMatrix& hptm) :
+ AbstractHmmTransitionMatrix(hptm),
+ AbstractParametrizable(hptm),
+ vSimplex_(hptm.vSimplex_)
+{
+}
+
+FullHmmTransitionMatrix& FullHmmTransitionMatrix::operator=(const FullHmmTransitionMatrix& hptm)
+{
+ AbstractHmmTransitionMatrix::operator=(hptm);
+ AbstractParametrizable::operator=(hptm);
+
+ return *this;
+}
+
+void FullHmmTransitionMatrix::setTransitionProbabilities(const Matrix<double>& mat)
+{
+ if (mat.getNumberOfRows()!=vSimplex_.size())
+ throw BadSizeException("FullHmmTransitionMatrix::setTransitionProbabilities: Wrong number of rows in given Matrix", mat.getNumberOfRows(), vSimplex_.size());
+
+ ParameterList pl;
+
+ for (size_t i=0; i<mat.getNumberOfRows();i++)
+ {
+ vSimplex_[i].setFrequencies(mat.row(i));
+ ParameterList pls=vSimplex_[i].getParameters();
+ for (size_t j=0; j<pls.size(); j++)
+ {
+ Parameter* p=pls[j].clone();
+ p->setName(TextTools::toString(i+1)+"."+p->getName());
+ pl.addParameter(p);
+ }
+ }
+
+ matchParametersValues(pl);
+}
+
+
+const Matrix<double>& FullHmmTransitionMatrix::getPij() const
+ {
+ if (!upToDate_){
+ for (size_t i=0; i<vSimplex_.size(); i++)
+ for (size_t j=0; j<vSimplex_[i].dimension(); j++)
+ pij_(i,j)=vSimplex_[i].prob(j);
+ upToDate_=true;
+ }
+
+ return pij_;
+ }
+
+const std::vector<double>& FullHmmTransitionMatrix::getEquilibriumFrequencies() const
+{
+ size_t salph=getNumberOfStates();
+
+ if (!upToDate_){
+ pij_=getPij();
+
+ MatrixTools::pow(pij_, 256, tmpmat_);
+
+ for (size_t i = 0; i < salph; i++)
+ eqFreq_[i] = tmpmat_(0,i);
+
+ upToDate_=true;
+ }
+
+ return eqFreq_;
+}
+
+void FullHmmTransitionMatrix::fireParameterChanged(const ParameterList& parameters)
+{
+ size_t salph=getNumberOfStates();
+
+ for (size_t i=0; i< salph; i++)
+ {
+ ParameterList pl=vSimplex_[i].getParameters();
+
+ for (size_t j=0; j<pl.size(); j++)
+ pl[j].setValue(getParameterValue(TextTools::toString(i+1)+"."+pl[j].getName()));
+
+ vSimplex_[i].matchParametersValues(pl);
+ }
+
+ upToDate_=false;
+}
+
+
diff --git a/src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.h b/src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.h
new file mode 100644
index 0000000..f0d4aca
--- /dev/null
+++ b/src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.h
@@ -0,0 +1,130 @@
+//
+// File: FullHmmTransitionMatrix.h
+// Created by: Laurent Guéguen
+// Created on: samedi 21 septembre 2013, à 00h 41
+//
+
+/*
+Copyright or © or Copr. Bio++Development Team, (November 16, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for phylogenetic data 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 _FULLHMMTRANSITIONMATRIX_H_
+#define _FULLHMMTRANSITIONMATRIX_H_
+
+#include "../Prob/Simplex.h"
+
+#include "AbstractHmmTransitionMatrix.h"
+
+#include "../AbstractParameterAliasable.h"
+
+namespace bpp
+{
+
+/**
+ * @brief Describe the transition probabilities between hidden states of a Hidden Markov Model.
+ *
+ *
+ * Transition probabilities are described through simplexes.
+ *
+ *
+ * Parameters are denoted \c "I.Simplex.thetaJ" where \c I is the line number
+ * of the transition matrix, and \c "thetaJ" is the matching parameter
+ * in the Ith Simplex.
+ *
+ * @see Simplex
+ */
+
+class FullHmmTransitionMatrix:
+ public virtual AbstractHmmTransitionMatrix,
+ public AbstractParametrizable
+{
+private:
+ std::vector<Simplex> vSimplex_;
+
+public:
+
+ FullHmmTransitionMatrix(const HmmStateAlphabet* alph, const std::string& prefix = "");
+
+ FullHmmTransitionMatrix(const FullHmmTransitionMatrix& hptm);
+
+ FullHmmTransitionMatrix& operator=(const FullHmmTransitionMatrix& hptm);
+
+ FullHmmTransitionMatrix* clone() const { return new FullHmmTransitionMatrix(*this);}
+
+ /**
+ * @brief Set the matrix of the transition probabilities.
+ *
+ */
+
+ void setTransitionProbabilities(const Matrix<double>& mat);
+
+ /**
+ * @brief Get the transition probability between two states.
+ *
+ * @param i initial state.
+ * @param j final state.
+ * @return the transition probability between the two states.
+ */
+
+ double Pij(size_t i, size_t j) const
+ {
+ return vSimplex_[i].prob(j);
+ }
+
+ /**
+ * @brief Get all transition probabilities as a matrix.
+ *
+ * @return A n*n matrix will all transition probabilities (n being the number of hidden states).
+ */
+
+ const Matrix<double>& getPij() const;
+
+ /**
+ * @return The vector of equilibrium frequencies of the Markov chain described by the matrix.
+ */
+
+ const std::vector<double>& getEquilibriumFrequencies() const;
+
+
+ /*
+ * @brief From AbstractParametrizable interface
+ *
+ */
+
+ void fireParameterChanged(const ParameterList& parameters);
+
+};
+
+} //end of namespace bpp
+
+#endif //_FULLHMMTRANSITIONMATRIX_H_
+
diff --git a/src/Bpp/Numeric/Hmm/HmmEmissionProbabilities.h b/src/Bpp/Numeric/Hmm/HmmEmissionProbabilities.h
index 5f8efeb..970c662 100644
--- a/src/Bpp/Numeric/Hmm/HmmEmissionProbabilities.h
+++ b/src/Bpp/Numeric/Hmm/HmmEmissionProbabilities.h
@@ -5,36 +5,36 @@
//
/*
-Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
-
-This software is a computer program whose purpose is to provide classes
-for phylogenetic data 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.
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data 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 _HMMEMISSIONPROBABILITIES_H_
@@ -61,9 +61,9 @@ namespace bpp
* @see HmmStateAlphabet
* @see HmmTransitionMatrix
*/
-class HmmEmissionProbabilities:
- public virtual Parametrizable
-{
+ class HmmEmissionProbabilities:
+ public virtual Parametrizable
+ {
public:
virtual HmmEmissionProbabilities* clone() const = 0;
@@ -77,31 +77,6 @@ class HmmEmissionProbabilities:
virtual void setHmmStateAlphabet(const HmmStateAlphabet* stateAlphabet) throw (HmmUnvalidAlphabetException) = 0;
/**
- * @name Access emission probabilities per site.
- *
- * This functions are handy, but might not be the most efficient way to retrieve the probabilities.
- * @{
- */
-
- /**
- * @param pos The position of the sequential data to consider.
- * @param stateIndex The index of the hidden state to consider, as defined by the HmmStateAlphabet object associated to this class.
- */
- virtual double getEmissionProbability(size_t pos, size_t stateIndex) const throw (Exception) = 0;
- virtual void getEmissionProbabilities(size_t pos, std::vector<double>& probs) const throw (Exception) = 0;
- virtual void getEmissionProbabilitiesForEachPosition(std::vector< std::vector<double> >& probs, bool append) const throw (Exception) = 0;
-
- /**
- * @param pos The position of the sequential data to consider.
- * @param stateIndex The index of the hidden state to consider, as defined by the HmmStateAlphabet object associated to this class.
- */
- virtual double getLogEmissionProbability(size_t pos, size_t stateIndex) const throw (Exception) = 0;
- virtual void getLogEmissionProbabilities(size_t pos, std::vector<double>& probs) const throw (Exception) = 0;
- virtual void getLogEmissionProbabilitiesForEachPosition(std::vector< std::vector<double> >& probs, bool append) const throw (Exception) = 0;
-
- /**@} */
-
- /**
* @brief Operator access to the emission probabilities.
*
* This is the fastest way to get the values, but no checking is performed on the indices.
@@ -110,8 +85,29 @@ class HmmEmissionProbabilities:
* @param pos The position of the sequential data to consider.
* @param state The index of the hidden state to consider, as defined by the HmmStateAlphabet object associated to this class.
*/
+
virtual double operator()(size_t pos, size_t state) const = 0;
+ virtual void computeDEmissionProbabilities(std::string& variable) const
+ {
+ throw (NotImplementedException("HmmEmissionProbabilities::computeDEmissionProbabilities is not overdefined."));
+ }
+
+ virtual void computeD2EmissionProbabilities(std::string& variable) const
+ {
+ throw (NotImplementedException("HmmEmissionProbabilities::computeD2EmissionProbabilities is not overdefined."));
+ }
+
+ virtual const std::vector<double>& getDEmissionProbabilities(size_t pos) const
+ {
+ throw (NotImplementedException("HmmEmissionProbabilities::getDEmissionProbability is not overdefined."));
+ }
+
+ virtual const std::vector<double>& getD2EmissionProbabilities(size_t pos) const
+ {
+ throw (NotImplementedException("HmmEmissionProbabilities::getD2EmissionProbability is not overdefined."));
+ }
+
/**
* @brief Operator access to the emission probabilities.
*
@@ -127,26 +123,7 @@ class HmmEmissionProbabilities:
* @return The number of positions in the data.
*/
virtual size_t getNumberOfPositions() const = 0;
-
- /**
- * @brief Get the index of a given state in the list of observed states.
- * The indexing if up to the implementation of this interface.
- *
- * @param pos The position of the observed state in the original sequence.
- * @return The index of the observed state in the list.
- */
- virtual size_t getObservedStateIndex(size_t pos) const = 0;
-
- /**
- * @brief Get all emission probabilities, in a compressed form.
- *
- * @return a 2-dimensions array E[i,j], where i is the index of the observed states (@see getObservedStateIndex), and j in the index of the hidden state.
- * @param probs a 2-dimensional array which is going to be resized and filled with the emission probabilities.
- */
- virtual void getEmissionProbabilities(std::vector< std::vector<double> >& probs) const = 0;
-
-
-};
+ };
} //end of namespace bpp.
diff --git a/src/Bpp/Numeric/Hmm/HmmLikelihood.cpp b/src/Bpp/Numeric/Hmm/HmmLikelihood.cpp
new file mode 100644
index 0000000..da9acb7
--- /dev/null
+++ b/src/Bpp/Numeric/Hmm/HmmLikelihood.cpp
@@ -0,0 +1,90 @@
+//
+// File: HmmLikelihood.cpp
+// Created by: Laurent Guéguen
+// Created on: jeudi 26 septembre 2013, à 13h 55
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data 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 "HmmLikelihood.h"
+
+using namespace bpp;
+using namespace std;
+
+AbstractHmmLikelihood::AbstractHmmLikelihood() :
+ dLogLik_(0),
+ dVariable_(""),
+ d2LogLik_(0),
+ d2Variable_("") {}
+
+AbstractHmmLikelihood::AbstractHmmLikelihood(const AbstractHmmLikelihood& adhlik) :
+ dLogLik_(adhlik.dLogLik_),
+ dVariable_(adhlik.dVariable_),
+ d2LogLik_(adhlik.d2LogLik_),
+ d2Variable_(adhlik.d2Variable_)
+{}
+
+AbstractHmmLikelihood& AbstractHmmLikelihood::operator=(const AbstractHmmLikelihood& adhlik)
+{
+ dLogLik_=adhlik.dLogLik_;
+ dVariable_=adhlik.dVariable_;
+ d2LogLik_=adhlik.d2LogLik_;
+ d2Variable_=adhlik.d2Variable_;
+
+ return *this;
+}
+
+double AbstractHmmLikelihood::getFirstOrderDerivative(const std::string& variable) const throw (Exception)
+{
+ if (variable!=dVariable_){
+ dVariable_=variable;
+
+ getHmmEmissionProbabilities().computeDEmissionProbabilities(dVariable_);
+ computeDLikelihood_();
+ }
+ return -dLogLik_;
+
+}
+
+double AbstractHmmLikelihood::getSecondOrderDerivative(const std::string& variable) const throw (Exception)
+{
+ if (variable!=d2Variable_){
+ d2Variable_=variable;
+
+ getHmmEmissionProbabilities().computeD2EmissionProbabilities(d2Variable_);
+ computeD2Likelihood_();
+ }
+ return -d2LogLik_;
+}
+
diff --git a/src/Bpp/Numeric/Hmm/HmmLikelihood.h b/src/Bpp/Numeric/Hmm/HmmLikelihood.h
index 20bf4a1..7306ecc 100644
--- a/src/Bpp/Numeric/Hmm/HmmLikelihood.h
+++ b/src/Bpp/Numeric/Hmm/HmmLikelihood.h
@@ -5,36 +5,36 @@
//
/*
-Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
-
-This software is a computer program whose purpose is to provide classes
-for phylogenetic data 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.
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data 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 _HMMLIKELIHOOD_H_
@@ -43,6 +43,8 @@ knowledge of the CeCILL license and that you accept its terms.
// From NumCalc:
#include "../Function/Functions.h"
+#include "../VectorTools.h"
+
#include "HmmStateAlphabet.h"
#include "HmmTransitionMatrix.h"
#include "HmmEmissionProbabilities.h"
@@ -50,30 +52,31 @@ knowledge of the CeCILL license and that you accept its terms.
namespace bpp
{
-/**
- * @brief Basal interface for Hidden Markov Models likelihood computation.
- *
- * HmmLikelihood classes compute the probability of data according to parameters (likelihood),
- * using the so-called forward recursion:
- *
- * - Initialisation: @f[ f_0({\cal A}_0), \ldots, f_0({\cal A}_n) @f] The initial frequencies, set to the equilibrium frequencies of the chain.
- * - Recursion (for i=1 to l, the length of the sequence data): @f[ f_i({\cal A}_y) = e_y(D_i) \sum_{x=1}^n f_{i-1}({\cal A}_x) \cdot p_{x,y} @f]
- * - Termination: @f[ \Pr(D) = \sum_{x=1}^n f_l({\cal A}_x) @f]
- * where @f$ {\cal A}_{1..n} @f$ denotes the hidden states of the alphabet, @f$ e_y(D_i) @f$ the
- * probability of the data at position i conditioned on hidden state y (emission probabilities)
- * and @f$ p_{x,y} @f$ is the probability of havving hidden state y at state i+1 knowing there
- * is hidden state x at position i (transition probabilities). These essential elements are given
- * respectively by the HmmEmissionProbabilities and HmmTransitionMatrix object associated to this
- * class. Both objects have to share the same HmmStateAlphabet instance, which describes all
- * allowed hidden states.
- *
- * The HmmLikelihood interface provides essentially two major methods:
- * - A method to retrieve the likelihood value (parameter estimation)
- * - Two methods to retrieve the posterio probabilities of each state using the forward and backward conditionnal likelihoods (posterior decoding).
- */
-class HmmLikelihood:
- public virtual Function
-{
+ /**
+ * @brief Basal interface for Hidden Markov Models likelihood computation.
+ *
+ * HmmLikelihood classes compute the probability of data according to parameters (likelihood),
+ * using the so-called forward recursion:
+ *
+ * - Initialisation: @f[ f_0({\cal A}_0), \ldots, f_0({\cal A}_n) @f] The initial frequencies, set to the equilibrium frequencies of the chain.
+ * - Recursion (for i=1 to l, the length of the sequence data): @f[ f_i({\cal A}_y) = e_y(D_i) \sum_{x=1}^n f_{i-1}({\cal A}_x) \cdot p_{x,y} @f]
+ * - Termination: @f[ \Pr(D) = \sum_{x=1}^n f_l({\cal A}_x) @f]
+ * where @f$ {\cal A}_{1..n} @f$ denotes the hidden states of the alphabet, @f$ e_y(D_i) @f$ the
+ * probability of the data at position i conditioned on hidden state y (emission probabilities)
+ * and @f$ p_{x,y} @f$ is the probability of havving hidden state y at state i+1 knowing there
+ * is hidden state x at position i (transition probabilities). These essential elements are given
+ * respectively by the HmmEmissionProbabilities and HmmTransitionMatrix object associated to this
+ * class. Both objects have to share the same HmmStateAlphabet instance, which describes all
+ * allowed hidden states.
+ *
+ * The HmmLikelihood interface provides essentially two major methods:
+ * - A method to retrieve the likelihood value (parameter estimation)
+ * - Two methods to retrieve the posterio probabilities of each state using the forward and backward conditionnal likelihoods (posterior decoding).
+ */
+
+ class HmmLikelihood:
+ public virtual DerivableSecondOrder
+ {
public:
#ifndef NO_VIRTUAL_COV
@@ -90,13 +93,118 @@ class HmmLikelihood:
virtual HmmEmissionProbabilities& getHmmEmissionProbabilities() = 0;
virtual void getHiddenStatesPosteriorProbabilities(std::vector< std::vector<double> >& probs, bool append) const throw (Exception) = 0;
-
+
+ virtual Vdouble getHiddenStatesPosteriorProbabilitiesForASite(size_t site) const = 0;
+
virtual double getLogLikelihood() const = 0;
-
+
+ virtual double getDLogLikelihood() const = 0;
+
+ virtual double getD2LogLikelihood() const = 0;
+
+ /**
+ * @brief Get the likelihood for a site.
+ *
+ * @param site The site index to analyse.
+ * @return The likelihood for site <i>site</i>.
+ */
+
+ virtual double getLikelihoodForASite(size_t site) const = 0;
+
+ /**
+ * @brief Get the likelihood for each site.
+ *
+ * @return A vector with all likelihoods for each site.
+ */
+ virtual Vdouble getLikelihoodForEachSite() const = 0;
+
virtual const std::vector<size_t>& getBreakPoints() const = 0;
+
virtual void setBreakPoints(const std::vector<size_t>& breakPoints) = 0;
-
-};
+
+ protected:
+
+ virtual void computeDLikelihood_() const = 0;
+
+ virtual void computeD2Likelihood_() const = 0;
+
+ };
+
+
+ /*
+ * @brief partial impmementation of Hmm Likelihoods.
+ *
+ */
+
+ class AbstractHmmLikelihood:
+ public virtual HmmLikelihood
+ {
+ protected:
+
+ mutable double dLogLik_;
+ mutable std::string dVariable_;
+
+ mutable double d2LogLik_;
+ mutable std::string d2Variable_;
+
+ public:
+ AbstractHmmLikelihood();
+
+ AbstractHmmLikelihood(const AbstractHmmLikelihood& adhlik);
+
+ AbstractHmmLikelihood& operator=(const AbstractHmmLikelihood& adhlik);
+
+ /* @{
+ *
+ * @brief From FirstOrder:
+ *
+ */
+
+ void enableFirstOrderDerivatives(bool yn) {};
+
+ bool enableFirstOrderDerivatives() const { return true;}
+
+ double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
+
+ double getDLogLikelihood() const
+ {
+ return dLogLik_;
+ }
+
+ /*
+ * @}
+ *
+ */
+
+ /* @{
+ *
+ * @brief From SecondOrder:
+ *
+ */
+
+ void enableSecondOrderDerivatives(bool yn) {};
+
+ bool enableSecondOrderDerivatives() const {return true;}
+
+ double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
+
+ double getD2LogLikelihood() const
+ {
+ return d2LogLik_;
+ }
+
+ double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) {
+ throw (NotImplementedException("AbstractHmmLikelihood::getSecondOrderDerivative is not defined for 2 variables."));
+ }
+
+ /*
+ * @}
+ *
+ */
+
+
+ };
+
} //end of namespace bpp.
diff --git a/src/Bpp/Numeric/Hmm/HmmStateAlphabet.h b/src/Bpp/Numeric/Hmm/HmmStateAlphabet.h
index 15e30f9..40442a6 100644
--- a/src/Bpp/Numeric/Hmm/HmmStateAlphabet.h
+++ b/src/Bpp/Numeric/Hmm/HmmStateAlphabet.h
@@ -5,36 +5,36 @@
//
/*
-Copyright or © or Copr. CNRS, (November 16, 2004)
-
-This software is a computer program whose purpose is to provide classes
-for phylogenetic data 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.
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data 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 _HMMSTATEALPHABET_H_
@@ -62,64 +62,58 @@ namespace bpp {
class HmmStateAlphabet:
public virtual Parametrizable
{
- public:
- HmmStateAlphabet() {}
- virtual ~HmmStateAlphabet() {}
-
- public:
- /**
- * @param stateIndex The index of a hidden state.
- * @return The corresponding hidden state.
- * @see getNumberOfStates
- */
- virtual const Clonable& getState(unsigned int stateIndex) const throw (HmmBadStateException) = 0;
-
- /**
- * @param stateIndex The index of a hidden state.
- * @return The corresponding hidden state.
- * @see getNumberOfStates
- */
- virtual Clonable& getState(unsigned int stateIndex) throw (HmmBadStateException) = 0;
-
- virtual unsigned int getNumberOfStates() const = 0;
-
- /**
- * @brief Tell if this instance can work with the instance of alphabet given as input.
- *
- * In many case, this will return true is the pointer provided as argument refers to this object.
- *
- * @param stateAlphabet The alphabet to check.
- * @return true if the matrix is compatible with the given alphabet.
- */
- virtual bool worksWith(const HmmStateAlphabet* stateAlphabet) const = 0;
+ public:
+ HmmStateAlphabet() {}
+ virtual ~HmmStateAlphabet() {}
+
+ public:
+ /**
+ * @param stateIndex The index of a hidden state.
+ * @return The corresponding hidden state.
+ * @see getNumberOfStates
+ */
+ virtual const Clonable& getState(size_t stateIndex) const throw (HmmBadStateException) = 0;
+
+
+ virtual size_t getNumberOfStates() const = 0;
+
+ /**
+ * @brief Tell if this instance can work with the instance of alphabet given as input.
+ *
+ * In many case, this will return true is the pointer provided as argument refers to this object.
+ *
+ * @param stateAlphabet The alphabet to check.
+ * @return true if the matrix is compatible with the given alphabet.
+ */
+ virtual bool worksWith(const HmmStateAlphabet* stateAlphabet) const = 0;
};
class StateListener
{
- public:
- StateListener() {}
- virtual ~StateListener() {}
+ public:
+ StateListener() {}
+ virtual ~StateListener() {}
- public:
- virtual void stateChanged(StateChangedEvent& event) = 0;
+ public:
+ virtual void stateChanged(StateChangedEvent& event) = 0;
};
class StateChangedEvent
{
- protected:
- std::vector<unsigned int> states_;
+ protected:
+ std::vector<unsigned int> states_;
- public:
- StateChangedEvent(unsigned int stateIndex): states_(1)
+ public:
+ StateChangedEvent(unsigned int stateIndex): states_(1)
{
states_[0] = stateIndex;
}
- StateChangedEvent(std::vector<unsigned int>& states): states_(states) {}
+ StateChangedEvent(std::vector<unsigned int>& states): states_(states) {}
- public:
- const std::vector<unsigned int>& getStates() const { return states_; }
- std::vector<unsigned int>& getStates() { return states_; }
+ public:
+ const std::vector<unsigned int>& getStates() const { return states_; }
+ std::vector<unsigned int>& getStates() { return states_; }
};
diff --git a/src/Bpp/Numeric/Hmm/HmmTransitionMatrix.h b/src/Bpp/Numeric/Hmm/HmmTransitionMatrix.h
index 72ddd80..34ab889 100644
--- a/src/Bpp/Numeric/Hmm/HmmTransitionMatrix.h
+++ b/src/Bpp/Numeric/Hmm/HmmTransitionMatrix.h
@@ -5,36 +5,36 @@
//
/*
-Copyright or © or Copr. Bio++Development Team, (November 16, 2004)
-
-This software is a computer program whose purpose is to provide classes
-for phylogenetic data 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.
+ Copyright or © or Copr. Bio++Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data 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 _HMMTRANSITIONMATRIX_H_
@@ -56,14 +56,15 @@ namespace bpp
*
* This class is part of the HMM framework.
*/
-class HmmTransitionMatrix:
- public virtual Parametrizable
-{
+ class HmmTransitionMatrix:
+ public virtual Parametrizable
+ {
public:
/**
* @return The hidden alphabet associated to this model.
*/
+
virtual const HmmStateAlphabet* getHmmStateAlphabet() const = 0;
/**
@@ -76,7 +77,7 @@ class HmmTransitionMatrix:
/**
* @return The number of states in the model.
*/
- virtual unsigned int getNumberOfStates() const = 0;
+ virtual size_t getNumberOfStates() const = 0;
/**
* @brief Get the transition probability between two states.
@@ -85,7 +86,7 @@ class HmmTransitionMatrix:
* @param j final state.
* @return the transition probability between the two states.
*/
- virtual double Pij(unsigned int i, unsigned int j) const = 0;
+ virtual double Pij(size_t i, size_t j) const = 0;
/**
* @brief Get all transition probabilities as a matrix.
@@ -99,7 +100,7 @@ class HmmTransitionMatrix:
*/
virtual const std::vector<double>& getEquilibriumFrequencies() const = 0;
-};
+ };
} //end of namespace bpp
diff --git a/src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.cpp b/src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.cpp
index a8aa7fd..3540f34 100644
--- a/src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.cpp
+++ b/src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.cpp
@@ -5,7 +5,7 @@
//
/*
-Copyright or © or Copr. CNRS, (November 16, 2004)
+Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
This software is a computer program whose purpose is to provide classes
for phylogenetic data analysis.
@@ -50,6 +50,7 @@ LogsumHmmLikelihood::LogsumHmmLikelihood(
HmmTransitionMatrix* transitionMatrix,
HmmEmissionProbabilities* emissionProbabilities,
const std::string& prefix) throw (Exception):
+ AbstractHmmLikelihood(),
AbstractParametrizable(prefix),
hiddenAlphabet_(hiddenAlphabet),
transitionMatrix_(transitionMatrix),
@@ -57,6 +58,12 @@ LogsumHmmLikelihood::LogsumHmmLikelihood(
logLikelihood_(),
partialLogLikelihoods_(),
logLik_(),
+ dLogLikelihood_(),
+ partialDLogLikelihoods_(),
+ d2LogLikelihood_(),
+ partialD2LogLikelihoods_(),
+ backLogLikelihood_(),
+ backLogLikelihoodUpToDate_(false),
breakPoints_(),
nbStates_(),
nbSites_()
@@ -85,6 +92,9 @@ LogsumHmmLikelihood::LogsumHmmLikelihood(
void LogsumHmmLikelihood::fireParameterChanged(const ParameterList& pl)
{
+ dVariable_="";
+ d2Variable_="";
+
bool alphabetChanged = hiddenAlphabet_->matchParametersValues(pl);
bool transitionsChanged = transitionMatrix_->matchParametersValues(pl);
bool emissionChanged = emissionProbabilities_->matchParametersValues(pl);
@@ -95,6 +105,7 @@ void LogsumHmmLikelihood::fireParameterChanged(const ParameterList& pl)
if (alphabetChanged && !emissionChanged) emissionProbabilities_->setParametersValues(emissionProbabilities_->getParameters());
computeForward_();
+ backLogLikelihoodUpToDate_=false;
}
/***************************************************************************************************************************/
@@ -109,15 +120,17 @@ void LogsumHmmLikelihood::computeForward_()
{
size_t ii = i * nbStates_;
for (size_t j = 0; j < nbStates_; j++)
- logTrans[ii + j] = log(transitionMatrix_->Pij(static_cast<int>(j), static_cast<int>(i)));
+ logTrans[ii + j] = log(transitionMatrix_->Pij(j, i));
}
//Initialisation:
const vector<double>* emissions = &(*emissionProbabilities_)(0);
+
for (size_t j = 0; j < nbStates_; j++)
{
size_t jj = j * nbStates_;
x = logTrans[jj] + log(transitionMatrix_->getEquilibriumFrequencies()[0]);
+
for (size_t k = 1; k < nbStates_; k++)
{
a = logTrans[k + jj] + log(transitionMatrix_->getEquilibriumFrequencies()[k]);
@@ -175,9 +188,10 @@ void LogsumHmmLikelihood::computeForward_()
else nextBrkPt = nbSites_;
}
}
+
//Termination:
double tmpLog = logLikelihood_[(nbSites_ - 1) * nbStates_];
- for (unsigned int k = 1; k < nbStates_; k++)
+ for (size_t k = 1; k < nbStates_; k++)
tmpLog = NumTools::logsum(tmpLog, logLikelihood_[(nbSites_ - 1) * nbStates_ + k]);
partialLogLikelihoods_.push_back(tmpLog);
@@ -191,13 +205,15 @@ void LogsumHmmLikelihood::computeForward_()
/***************************************************************************************************************************/
-void LogsumHmmLikelihood::computeBackward_(std::vector< std::vector<double> >& b) const
+void LogsumHmmLikelihood::computeBackward_() const
{
- b.resize(nbSites_);
- for (size_t i = 0; i < nbSites_; i++)
+ if (backLogLikelihood_.size()==0)
{
- b[i].resize(nbStates_);
+ backLogLikelihood_.resize(nbSites_);
+ for (size_t i=0;i<nbSites_;i++)
+ backLogLikelihood_[i].resize(nbStates_);
}
+
double x;
//Transition probabilities:
@@ -206,7 +222,7 @@ void LogsumHmmLikelihood::computeBackward_(std::vector< std::vector<double> >& b
{
size_t ii = i * nbStates_;
for (size_t j = 0; j < nbStates_; j++)
- logTrans[ii + j] = log(transitionMatrix_->Pij(static_cast<int>(i), static_cast<int>(j)));
+ logTrans[ii + j] = log(transitionMatrix_->Pij(i, j));
}
@@ -218,7 +234,7 @@ void LogsumHmmLikelihood::computeBackward_(std::vector< std::vector<double> >& b
for (size_t k = 0; k < nbStates_; k++)
{
- b[nbSites_ - 1][k] = 0.;
+ backLogLikelihood_[nbSites_ - 1][k] = 0.;
}
//Recursion:
@@ -230,29 +246,87 @@ void LogsumHmmLikelihood::computeBackward_(std::vector< std::vector<double> >& b
for (size_t j = 0; j < nbStates_; j++)
{
size_t jj = j * nbStates_;
- x = log((*emissions)[0]) + logTrans[jj] + b[i][0];
+ x = log((*emissions)[0]) + logTrans[jj] + backLogLikelihood_[i][0];
for (size_t k = 1; k < nbStates_; k++)
{
- x = NumTools::logsum(x, log((*emissions)[k]) + logTrans[jj + k] + b[i][k]);
+ x = NumTools::logsum(x, log((*emissions)[k]) + logTrans[jj + k] + backLogLikelihood_[i][k]);
}
- b[i - 1][j] = x;
+ backLogLikelihood_[i - 1][j] = x;
}
}
else //Reset markov chain
{
for (unsigned int j = 0; j < nbStates_; j++)
{
- b[i - 1][j] = 0.;
+ backLogLikelihood_[i - 1][j] = 0.;
}
bpIt++;
if (bpIt != breakPoints_.rend()) nextBrkPt = *bpIt;
else nextBrkPt = 0;
}
}
+
+ backLogLikelihoodUpToDate_=true;
}
+
/***************************************************************************************************************************/
+double LogsumHmmLikelihood::getLikelihoodForASite(size_t site) const
+{
+ Vdouble probs=getHiddenStatesPosteriorProbabilitiesForASite(site);
+ double x=0;
+ for (size_t i=0;i<nbStates_;i++)
+ x+=probs[i]*(*emissionProbabilities_)(site,i);
+
+ return x;
+}
+
+Vdouble LogsumHmmLikelihood::getLikelihoodForEachSite() const
+{
+ std::vector< std::vector<double> > vv;
+ getHiddenStatesPosteriorProbabilities(vv);
+
+ Vdouble ret(nbSites_);
+ for (size_t i=0;i<nbSites_;i++)
+ {
+ ret[i]=0;
+ for (size_t j=0;j<nbStates_;j++)
+ ret[i]+=vv[i][j]*(*emissionProbabilities_)(i,j);
+ }
+
+ return ret;
+}
+
+
+/***************************************************************************************************************************/
+
+Vdouble LogsumHmmLikelihood::getHiddenStatesPosteriorProbabilitiesForASite(size_t site) const
+{
+ if (!backLogLikelihoodUpToDate_)
+ computeBackward_();
+
+ Vdouble probs(nbStates_);
+
+ vector<size_t>::const_iterator bpIt = breakPoints_.begin();
+ vector<double>::const_iterator logLikIt = partialLogLikelihoods_.begin();
+ while (bpIt != breakPoints_.end())
+ {
+ if (site>=(*bpIt))
+ logLikIt++;
+ else
+ break;
+ bpIt++;
+ }
+
+ for (size_t j = 0; j < nbStates_; j++)
+ {
+ probs[j] = exp(logLikelihood_[site * nbStates_ + j] + backLogLikelihood_[site][j] - *logLikIt);
+ }
+
+ return probs;
+}
+
void LogsumHmmLikelihood::getHiddenStatesPosteriorProbabilities(std::vector< std::vector<double> >& probs, bool append) const throw (Exception)
{
size_t offset = append ? probs.size() : 0;
@@ -262,8 +336,8 @@ void LogsumHmmLikelihood::getHiddenStatesPosteriorProbabilities(std::vector< std
probs[offset + i].resize(nbStates_);
}
- vector< vector<double> > logB;
- computeBackward_(logB);
+ if (!backLogLikelihoodUpToDate_)
+ computeBackward_();
size_t nextBrkPt = nbSites_; //next break point
vector<size_t>::const_iterator bpIt = breakPoints_.begin();
@@ -282,10 +356,229 @@ void LogsumHmmLikelihood::getHiddenStatesPosteriorProbabilities(std::vector< std
size_t ii = i * nbStates_;
for (size_t j = 0; j < nbStates_; j++)
{
- probs[offset + i][j] = exp(logLikelihood_[ii + j] + logB[i][j] - *logLikIt);
+ probs[offset + i][j] = exp(logLikelihood_[ii + j] + backLogLikelihood_[i][j] - *logLikIt);
+ }
+ }
+}
+
+/***************************************************************************************************************************/
+
+void LogsumHmmLikelihood::computeDForward_() const
+{
+ //Init arrays:
+ if (dLogLikelihood_.size()==0){
+ dLogLikelihood_.resize(nbSites_);
+ for (size_t i=0;i<nbSites_;i++)
+ dLogLikelihood_[i].resize(nbStates_);
+ }
+
+ partialDLogLikelihoods_.clear();
+
+ double x;
+
+ vector<double> num(nbStates_);
+
+ //Transition probabilities:
+ const ColMatrix<double> trans(transitionMatrix_->getPij());
+
+ //Initialisation:
+ const vector<double>* emissions = &(*emissionProbabilities_)(0);
+ const vector<double>* dEmissions = &emissionProbabilities_->getDEmissionProbabilities(0);
+
+ for (size_t j = 0; j < nbStates_; j++)
+ dLogLikelihood_[0][j] = (*dEmissions)[j] / (*emissions)[j];
+
+ //Recursion:
+ size_t nextBrkPt = nbSites_; //next break point
+ vector<size_t>::const_iterator bpIt = breakPoints_.begin();
+ if (bpIt != breakPoints_.end()) nextBrkPt = *bpIt;
+ partialDLogLikelihoods_.clear();
+
+ for (size_t i = 1; i < nbSites_; i++)
+ {
+ size_t iip = (i - 1) * nbStates_;
+
+ emissions = &(*emissionProbabilities_)(i);
+ dEmissions = &emissionProbabilities_->getDEmissionProbabilities(i);
+
+ if (i < nextBrkPt)
+ {
+ for (size_t j = 0; j < nbStates_; j++)
+ {
+ x=(*dEmissions)[j]/(*emissions)[j];
+
+ for (size_t k = 0; k < nbStates_; k++)
+ {
+ for (size_t kp = 0; kp < nbStates_; kp++)
+ num[kp]=logLikelihood_[iip+kp]-logLikelihood_[iip+k];
+
+ x+=dLogLikelihood_[i-1][k]*trans(k,j)/VectorTools::sumExp(num,trans.getCol(j));
+ }
+
+ dLogLikelihood_[i][j] = x;
+ }
+ }
+ else //Reset markov chain:
+ {
+ //Termination of previous segment
+ x = 0;
+ for (size_t k = 0; k < nbStates_; k++)
+ {
+ for (size_t kp = 0; kp < nbStates_; kp++)
+ num[kp]=logLikelihood_[iip+kp]-logLikelihood_[iip+k];
+
+ x += dLogLikelihood_[i-1][k] / VectorTools::sumExp(num);
+ }
+
+ partialDLogLikelihoods_.push_back(x);
+
+ for (size_t j = 0; j < nbStates_; j++)
+ dLogLikelihood_[i][j] = (*dEmissions)[j] / (*emissions)[j];
+
+ bpIt++;
+ if (bpIt != breakPoints_.end())
+ nextBrkPt = *bpIt;
+ else
+ nextBrkPt = nbSites_;
}
}
+
+ //Termination:
+ x=0;
+ for (size_t k = 0; k < nbStates_; k++)
+ {
+ for (size_t kp = 0; kp < nbStates_; kp++)
+ num[kp]=logLikelihood_[nbStates_*(nbSites_-1)+kp]-logLikelihood_[nbStates_*(nbSites_-1)+k];
+
+ x += dLogLikelihood_[nbSites_-1][k] / VectorTools::sumExp(num);
+ }
+
+ partialDLogLikelihoods_.push_back(x);
+
+ //Compute dLogLikelihood
+
+ dLogLik_ = 0;
+ vector<double> copy = partialDLogLikelihoods_; //We need to keep the original order for posterior decoding.
+ sort(copy.begin(), copy.end());
+ for (size_t i = copy.size(); i > 0; --i)
+ dLogLik_ += copy[i - 1];
}
/***************************************************************************************************************************/
+void LogsumHmmLikelihood::computeD2Forward_() const
+{
+ // Make sure that Dlikelihoods are correctly computed
+ getFirstOrderDerivative(d2Variable_);
+
+ //Init arrays:
+ if (d2LogLikelihood_.size()==0){
+ d2LogLikelihood_.resize(nbSites_);
+ for (size_t i=0;i<nbSites_;i++)
+ d2LogLikelihood_[i].resize(nbStates_);
+ }
+
+ partialD2LogLikelihoods_.clear();
+
+ double x, z, snum;
+
+ vector<double> num(nbStates_);
+
+ //Transition probabilities:
+ const ColMatrix<double> trans(transitionMatrix_->getPij());
+
+ //Initialisation:
+ const vector<double>* emissions = &(*emissionProbabilities_)(0);
+ const vector<double>* dEmissions = &emissionProbabilities_->getDEmissionProbabilities(0);
+ const vector<double>* d2Emissions = &emissionProbabilities_->getD2EmissionProbabilities(0);
+
+ for (size_t j = 0; j < nbStates_; j++)
+ d2LogLikelihood_[0][j] = (*d2Emissions)[j] / (*emissions)[j] - pow((*dEmissions)[j] / (*emissions)[j],2);
+
+ //Recursion:
+ size_t nextBrkPt = nbSites_; //next break point
+ vector<size_t>::const_iterator bpIt = breakPoints_.begin();
+ if (bpIt != breakPoints_.end()) nextBrkPt = *bpIt;
+ partialDLogLikelihoods_.clear();
+
+ for (size_t i = 1; i < nbSites_; i++)
+ {
+ size_t iip = (i - 1) * nbStates_;
+
+ emissions = &(*emissionProbabilities_)(i);
+ dEmissions = &emissionProbabilities_->getDEmissionProbabilities(i);
+ d2Emissions = &emissionProbabilities_->getD2EmissionProbabilities(i);
+
+ if (i < nextBrkPt)
+ {
+ for (size_t j = 0; j < nbStates_; j++)
+ {
+ x=(*d2Emissions)[j] / (*emissions)[j] - pow((*dEmissions)[j] / (*emissions)[j],2);
+
+ for (size_t k = 0; k < nbStates_; k++)
+ {
+ for (size_t kp = 0; kp < nbStates_; kp++)
+ num[kp]=logLikelihood_[iip+kp]-logLikelihood_[iip+k];
+ snum=VectorTools::sumExp(num,trans.getCol(j));
+
+
+ z=d2LogLikelihood_[i-1][k]+pow(dLogLikelihood_[i-1][k],2)
+ - dLogLikelihood_[i-1][k] * VectorTools::sumExp(num, trans.getCol(j) * dLogLikelihood_[i-1])/snum;
+
+ x += z * trans(k,j) / snum;
+ }
+
+ d2LogLikelihood_[i][j] = x;
+ }
+ }
+ else //Reset markov chain:
+ {
+ x=0;
+
+ //Termination of previous segment:
+ for (size_t k = 1; k < nbStates_; k++)
+ {
+ for (size_t kp = 0; kp < nbStates_; kp++)
+ num[kp]=logLikelihood_[iip+kp]-logLikelihood_[iip+k];
+
+ snum=VectorTools::sumExp(num);
+
+ x += (d2LogLikelihood_[i-1][k]+pow(dLogLikelihood_[i-1][k],2)
+ - dLogLikelihood_[i-1][k] * VectorTools::sumExp(num, dLogLikelihood_[i-1])/snum)/snum;
+ }
+
+ partialD2LogLikelihoods_.push_back(x);
+
+ for (size_t j = 0; j < nbStates_; j++)
+ d2LogLikelihood_[i][j] = (*d2Emissions)[j] / (*emissions)[j] - pow((*dEmissions)[j] / (*emissions)[j],2);
+
+
+ bpIt++;
+ if (bpIt != breakPoints_.end()) nextBrkPt = *bpIt;
+ else nextBrkPt = nbSites_;
+ }
+ }
+
+ //Termination:
+ x=0;
+ for (size_t k = 0; k < nbStates_; k++)
+ {
+ for (size_t kp = 0; kp < nbStates_; kp++)
+ num[kp]=logLikelihood_[nbStates_*(nbSites_-1)+kp]-logLikelihood_[nbStates_*(nbSites_-1)+k];
+
+ snum=VectorTools::sumExp(num);
+
+ x += (d2LogLikelihood_[nbSites_-1][k]+pow(dLogLikelihood_[nbSites_-1][k],2)
+ - dLogLikelihood_[nbSites_-1][k] * VectorTools::sumExp(num, dLogLikelihood_[nbSites_-1])/snum)/snum;
+ }
+
+ partialD2LogLikelihoods_.push_back(x);
+
+ //Compute dLogLikelihood
+
+ d2LogLik_ = 0;
+ vector<double> copy = partialD2LogLikelihoods_; //We need to keep the original order for posterior decoding.
+ sort(copy.begin(), copy.end());
+ for (size_t i = copy.size(); i > 0; --i)
+ d2LogLik_ += copy[i - 1];
+}
diff --git a/src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.h b/src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.h
index 5501d85..b896044 100644
--- a/src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.h
+++ b/src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.h
@@ -5,36 +5,36 @@
//
/*
-Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
-
-This software is a computer program whose purpose is to provide classes
-for phylogenetic data 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.
+ Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data 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 _LOGSUMHMMLIKELIHOOD_H_
@@ -63,124 +63,187 @@ namespace bpp {
* @see RescaledHmmLikelihood
*/
class LogsumHmmLikelihood:
- public virtual HmmLikelihood,
+ public virtual AbstractHmmLikelihood,
public AbstractParametrizable
{
- private:
- /**
- * @brief The alphabet describing the hidden states.
- */
- std::auto_ptr<HmmStateAlphabet> hiddenAlphabet_;
- std::auto_ptr<HmmTransitionMatrix> transitionMatrix_;
- std::auto_ptr<HmmEmissionProbabilities> emissionProbabilities_;
-
- /**
- * @brief The likelihood array.
- *
- * logLikelihood_[i * nbStates_ + j] corresponds to Pr(x1...xi, yi=j),
- * where the x are the observed states, and y the hidden states.
- */
- std::vector<double> logLikelihood_;
- std::vector<double> partialLogLikelihoods_;
- double logLik_;
-
- std::vector<size_t> breakPoints_;
-
- size_t nbStates_, nbSites_;
-
- public:
- /**
- * @brief Build a new LogsumHmmLikelihood object.
- *
- * @warning the HmmTransitionMatrix and HmmEmissionProbabilities object passed as argument must be non-null
- * and point toward the same HmmStateAlphabet instance. The three object will be copied if needed, and
- * deleted when the hmm likelihood objet is deleted. You should secure a copy before if you don't want them to
- * be destroyed with this object.
- */
- LogsumHmmLikelihood(
- HmmStateAlphabet* hiddenAlphabet,
- HmmTransitionMatrix* transitionMatrix,
- HmmEmissionProbabilities* emissionProbabilities,
- const std::string& prefix) throw (Exception);
-
- LogsumHmmLikelihood(const LogsumHmmLikelihood& lik):
- AbstractParametrizable(lik),
- hiddenAlphabet_(dynamic_cast<HmmStateAlphabet*>(lik.hiddenAlphabet_->clone())),
- transitionMatrix_(dynamic_cast<HmmTransitionMatrix*>(lik.transitionMatrix_->clone())),
- emissionProbabilities_(dynamic_cast<HmmEmissionProbabilities*>(lik.emissionProbabilities_->clone())),
- logLikelihood_(lik.logLikelihood_),
- partialLogLikelihoods_(lik.partialLogLikelihoods_),
- logLik_(lik.logLik_),
- breakPoints_(lik.breakPoints_),
- nbStates_(lik.nbStates_),
- nbSites_(lik.nbSites_)
- {
- // Now adjust pointers:
- transitionMatrix_->setHmmStateAlphabet(hiddenAlphabet_.get());
- emissionProbabilities_->setHmmStateAlphabet(hiddenAlphabet_.get());
- }
-
- LogsumHmmLikelihood& operator=(const LogsumHmmLikelihood& lik)
- {
- AbstractParametrizable::operator =(lik);
- hiddenAlphabet_ = std::auto_ptr<HmmStateAlphabet>(dynamic_cast<HmmStateAlphabet*>(lik.hiddenAlphabet_->clone()));
- transitionMatrix_ = std::auto_ptr<HmmTransitionMatrix>(dynamic_cast<HmmTransitionMatrix*>(lik.transitionMatrix_->clone()));
- emissionProbabilities_ = std::auto_ptr<HmmEmissionProbabilities>(dynamic_cast<HmmEmissionProbabilities*>(lik.emissionProbabilities_->clone()));
- logLikelihood_ = lik.logLikelihood_;
- partialLogLikelihoods_ = lik.partialLogLikelihoods_;
- logLik_ = lik.logLik_;
- breakPoints_ = lik.breakPoints_;
- nbStates_ = lik.nbStates_;
- nbSites_ = lik.nbSites_;
-
- // Now adjust pointers:
- transitionMatrix_->setHmmStateAlphabet(hiddenAlphabet_.get());
- emissionProbabilities_->setHmmStateAlphabet(hiddenAlphabet_.get());
- return *this;
- }
-
- virtual ~LogsumHmmLikelihood() {}
+ protected:
+ /**
+ * @brief The alphabet describing the hidden states.
+ */
+ std::auto_ptr<HmmStateAlphabet> hiddenAlphabet_;
+ std::auto_ptr<HmmTransitionMatrix> transitionMatrix_;
+ std::auto_ptr<HmmEmissionProbabilities> emissionProbabilities_;
+
+ /**
+ * @brief The likelihood array.
+ *
+ * logLikelihood_[i * nbStates_ + j] corresponds to log(Pr(x1...xi, yi=j)),
+ * where the x are the observed states, and y the hidden states.
+ */
+ std::vector<double> logLikelihood_;
+ std::vector<double> partialLogLikelihoods_;
+ double logLik_;
+
+ /**
+ * @brief The DLogLikelihood arrays.
+ *
+ * dLogLikelihood_[i][j] corresponds to d(log(Pr(x1...xi, yi=j))),
+ * where the x are the observed states, and y the hidden states.
+ *
+ * d2LogLikelihood_[i][j] corresponds to d2(log(Pr(x1...xi, yi=j))),
+ * where the x are the observed states, and y the hidden states.
+ *
+ */
+
+ mutable std::vector< std::vector<double> > dLogLikelihood_;
+ mutable std::vector<double> partialDLogLikelihoods_;
+
+ mutable std::vector< std::vector<double> > d2LogLikelihood_;
+ mutable std::vector<double> partialD2LogLikelihoods_;
+
+ /**
+ * @brief backward logLikelihood
+ *
+ * backLogLikelihood_[i][j] corresponds to log(Pr(x_i+1...x_n | yi=j)),
+ * where the x are the observed states, and y the hidden states.
+ */
+
+ mutable std::vector<std::vector<double> > backLogLikelihood_;
+ mutable bool backLogLikelihoodUpToDate_;
+
+ std::vector<size_t> breakPoints_;
+
+ size_t nbStates_, nbSites_;
+
+ public:
+ /**
+ * @brief Build a new LogsumHmmLikelihood object.
+ *
+ * @warning the HmmTransitionMatrix and HmmEmissionProbabilities object passed as argument must be non-null
+ * and point toward the same HmmStateAlphabet instance. The three object will be copied if needed, and
+ * deleted when the hmm likelihood objet is deleted. You should secure a copy before if you don't want them to
+ * be destroyed with this object.
+ */
+ LogsumHmmLikelihood(
+ HmmStateAlphabet* hiddenAlphabet,
+ HmmTransitionMatrix* transitionMatrix,
+ HmmEmissionProbabilities* emissionProbabilities,
+ const std::string& prefix) throw (Exception);
+
+ LogsumHmmLikelihood(const LogsumHmmLikelihood& lik):
+ AbstractHmmLikelihood(lik),
+ AbstractParametrizable(lik),
+ hiddenAlphabet_(dynamic_cast<HmmStateAlphabet*>(lik.hiddenAlphabet_->clone())),
+ transitionMatrix_(dynamic_cast<HmmTransitionMatrix*>(lik.transitionMatrix_->clone())),
+ emissionProbabilities_(dynamic_cast<HmmEmissionProbabilities*>(lik.emissionProbabilities_->clone())),
+ logLikelihood_(lik.logLikelihood_),
+ partialLogLikelihoods_(lik.partialLogLikelihoods_),
+ logLik_(lik.logLik_),
+ dLogLikelihood_(lik.dLogLikelihood_),
+ partialDLogLikelihoods_(lik.partialDLogLikelihoods_),
+ d2LogLikelihood_(lik.d2LogLikelihood_),
+ partialD2LogLikelihoods_(lik.partialD2LogLikelihoods_),
+ backLogLikelihood_(lik.backLogLikelihood_),
+ backLogLikelihoodUpToDate_(lik.backLogLikelihoodUpToDate_),
+ breakPoints_(lik.breakPoints_),
+ nbStates_(lik.nbStates_),
+ nbSites_(lik.nbSites_)
+ {
+ // Now adjust pointers:
+ transitionMatrix_->setHmmStateAlphabet(hiddenAlphabet_.get());
+ emissionProbabilities_->setHmmStateAlphabet(hiddenAlphabet_.get());
+ }
+
+ LogsumHmmLikelihood& operator=(const LogsumHmmLikelihood& lik)
+ {
+ AbstractHmmLikelihood::operator=(lik);
+ AbstractParametrizable::operator =(lik);
+ hiddenAlphabet_ = std::auto_ptr<HmmStateAlphabet>(dynamic_cast<HmmStateAlphabet*>(lik.hiddenAlphabet_->clone()));
+ transitionMatrix_ = std::auto_ptr<HmmTransitionMatrix>(dynamic_cast<HmmTransitionMatrix*>(lik.transitionMatrix_->clone()));
+ emissionProbabilities_ = std::auto_ptr<HmmEmissionProbabilities>(dynamic_cast<HmmEmissionProbabilities*>(lik.emissionProbabilities_->clone()));
+ logLikelihood_ = lik.logLikelihood_;
+ partialLogLikelihoods_ = lik.partialLogLikelihoods_;
+ dLogLikelihood_ = lik.dLogLikelihood_;
+ partialDLogLikelihoods_= lik.partialDLogLikelihoods_;
+ d2LogLikelihood_ = lik.d2LogLikelihood_;
+ partialD2LogLikelihoods_ = lik.partialD2LogLikelihoods_;
+ backLogLikelihood_ = lik.backLogLikelihood_;
+ backLogLikelihoodUpToDate_= lik.backLogLikelihoodUpToDate_;
+ logLik_ = lik.logLik_;
+ breakPoints_ = lik.breakPoints_;
+ nbStates_ = lik.nbStates_;
+ nbSites_ = lik.nbSites_;
+
+ // Now adjust pointers:
+ transitionMatrix_->setHmmStateAlphabet(hiddenAlphabet_.get());
+ emissionProbabilities_->setHmmStateAlphabet(hiddenAlphabet_.get());
+ return *this;
+ }
+
+ virtual ~LogsumHmmLikelihood() {}
#ifndef NO_VIRTUAL_COV
- LogsumHmmLikelihood*
+ LogsumHmmLikelihood*
#else
- Clonable*
+ Clonable*
#endif
- clone() const { return new LogsumHmmLikelihood(*this); }
+ clone() const { return new LogsumHmmLikelihood(*this); }
- public:
- const HmmStateAlphabet& getHmmStateAlphabet() const { return *hiddenAlphabet_; }
- HmmStateAlphabet& getHmmStateAlphabet() { return *hiddenAlphabet_; }
+ public:
+ const HmmStateAlphabet& getHmmStateAlphabet() const { return *hiddenAlphabet_; }
+ HmmStateAlphabet& getHmmStateAlphabet() { return *hiddenAlphabet_; }
- const HmmTransitionMatrix& getHmmTransitionMatrix() const { return *transitionMatrix_; }
- HmmTransitionMatrix& getHmmTransitionMatrix() { return *transitionMatrix_; }
+ const HmmTransitionMatrix& getHmmTransitionMatrix() const { return *transitionMatrix_; }
+ HmmTransitionMatrix& getHmmTransitionMatrix() { return *transitionMatrix_; }
- const HmmEmissionProbabilities& getHmmEmissionProbabilities() const { return *emissionProbabilities_; }
- HmmEmissionProbabilities& getHmmEmissionProbabilities() { return *emissionProbabilities_; }
+ const HmmEmissionProbabilities& getHmmEmissionProbabilities() const { return *emissionProbabilities_; }
+ HmmEmissionProbabilities& getHmmEmissionProbabilities() { return *emissionProbabilities_; }
- void setBreakPoints(const std::vector<size_t>& breakPoints) {
- breakPoints_ = breakPoints;
- computeForward_();
- }
+ void setBreakPoints(const std::vector<size_t>& breakPoints) {
+ breakPoints_ = breakPoints;
+ computeForward_();
+ backLogLikelihoodUpToDate_=false;
+ }
- const std::vector<size_t>& getBreakPoints() const { return breakPoints_; }
+ const std::vector<size_t>& getBreakPoints() const { return breakPoints_; }
- void setParameters(const ParameterList& pl) throw (Exception)
- {
- setParametersValues(pl);
- }
+ void setParameters(const ParameterList& pl) throw (Exception)
+ {
+ setParametersValues(pl);
+ }
- double getValue() const throw (Exception) { return -logLik_; }
+ double getValue() const throw (Exception) { return -logLik_; }
- double getLogLikelihood() const { return logLik_; }
+ double getLogLikelihood() const { return logLik_; }
- void fireParameterChanged(const ParameterList& pl);
+ double getLikelihoodForASite(size_t site) const;
- void getHiddenStatesPosteriorProbabilities(std::vector< std::vector<double> >& probs, bool append = false) const throw (Exception);
+ Vdouble getLikelihoodForEachSite() const;
- protected:
- void computeForward_();
- void computeBackward_(std::vector< std::vector<double> >& b) const;
+ virtual void fireParameterChanged(const ParameterList& pl);
+
+ Vdouble getHiddenStatesPosteriorProbabilitiesForASite(size_t site) const;
+
+ void getHiddenStatesPosteriorProbabilities(std::vector< std::vector<double> >& probs, bool append = false) const throw (Exception);
+
+ protected:
+ void computeForward_();
+ void computeBackward_() const;
+
+ void computeDLikelihood_() const
+ {
+ computeDForward_();
+ }
+
+ void computeD2Likelihood_() const
+ {
+ computeD2Forward_();
+ }
+
+ void computeDForward_() const;
+
+ void computeD2Forward_() const;
+
};
diff --git a/src/Bpp/Numeric/Hmm/LowMemoryRescaledHmmLikelihood.cpp b/src/Bpp/Numeric/Hmm/LowMemoryRescaledHmmLikelihood.cpp
index 6caf388..21639b8 100644
--- a/src/Bpp/Numeric/Hmm/LowMemoryRescaledHmmLikelihood.cpp
+++ b/src/Bpp/Numeric/Hmm/LowMemoryRescaledHmmLikelihood.cpp
@@ -51,6 +51,7 @@ LowMemoryRescaledHmmLikelihood::LowMemoryRescaledHmmLikelihood(
HmmEmissionProbabilities* emissionProbabilities,
const std::string& prefix,
size_t maxSize) throw (Exception) :
+ AbstractHmmLikelihood(),
AbstractParametrizable(prefix),
hiddenAlphabet_(hiddenAlphabet),
transitionMatrix_(transitionMatrix),
@@ -115,7 +116,7 @@ void LowMemoryRescaledHmmLikelihood::computeForward_()
size_t ii = i * nbStates_;
for (size_t j = 0; j < nbStates_; j++)
{
- trans[ii + j] = transitionMatrix_->Pij(static_cast<int>(j), static_cast<int>(i));
+ trans[ii + j] = transitionMatrix_->Pij(j, i);
}
}
@@ -124,7 +125,7 @@ void LowMemoryRescaledHmmLikelihood::computeForward_()
const vector<double>* emissions = &(*emissionProbabilities_)(0);
for (size_t j = 0; j < nbStates_; j++)
{
- size_t jj = j * nbStates_;
+ size_t jj = j * nbStates_;
x = 0;
for (size_t k = 0; k < nbStates_; k++)
{
@@ -233,7 +234,7 @@ void LowMemoryRescaledHmmLikelihood::computeForward_()
offset += maxSize_;
}
}
- sort(lScales.begin(), lScales.begin() + nbSites_ - offset, cmp);
+ sort(lScales.begin(), lScales.begin() + static_cast<ptrdiff_t>(nbSites_ - offset), cmp);
double partialLogLik = 0;
for (size_t i = 0; i < nbSites_ - offset; ++i)
{
diff --git a/src/Bpp/Numeric/Hmm/LowMemoryRescaledHmmLikelihood.h b/src/Bpp/Numeric/Hmm/LowMemoryRescaledHmmLikelihood.h
index 06d49ad..a9e797a 100644
--- a/src/Bpp/Numeric/Hmm/LowMemoryRescaledHmmLikelihood.h
+++ b/src/Bpp/Numeric/Hmm/LowMemoryRescaledHmmLikelihood.h
@@ -56,11 +56,15 @@ namespace bpp
* This implementation is similar to the one used in the RescaledHmmLikelihood class,
* but does not store the full likelihood array. The benefit of it is a significantly reduced
* memory usage, allowing to compute likelihood for very large data sets.
- * The drawback is that this class can't compute posterior probabilities, and can hence only
- * be used to estimate parameters.
+ *
+ * The drawback is that this class can't compute posterior
+ * probabilities, neither derivatives of the likelihoods, and can
+ * hence only be used to compute likelihoods.
+ *
*/
+
class LowMemoryRescaledHmmLikelihood :
- public virtual HmmLikelihood,
+ public AbstractHmmLikelihood,
public AbstractParametrizable
{
private:
@@ -109,6 +113,7 @@ public:
size_t maxSize = 1000000) throw (Exception);
LowMemoryRescaledHmmLikelihood(const LowMemoryRescaledHmmLikelihood& lik) :
+ AbstractHmmLikelihood(lik),
AbstractParametrizable(lik),
hiddenAlphabet_(dynamic_cast<HmmStateAlphabet*>(lik.hiddenAlphabet_->clone())),
transitionMatrix_(dynamic_cast<HmmTransitionMatrix*>(lik.transitionMatrix_->clone())),
@@ -128,6 +133,7 @@ public:
LowMemoryRescaledHmmLikelihood& operator=(const LowMemoryRescaledHmmLikelihood& lik)
{
+ AbstractHmmLikelihood::operator=(lik);
AbstractParametrizable::operator=(lik);
hiddenAlphabet_ = std::auto_ptr<HmmStateAlphabet>(dynamic_cast<HmmStateAlphabet*>(lik.hiddenAlphabet_->clone()));
transitionMatrix_ = std::auto_ptr<HmmTransitionMatrix>(dynamic_cast<HmmTransitionMatrix*>(lik.transitionMatrix_->clone()));
@@ -183,6 +189,23 @@ public:
void fireParameterChanged(const ParameterList& pl);
+
+ double getLikelihoodForASite(size_t site) const
+ {
+ throw (NotImplementedException("LowMemoryRescaledHmmLikelihood::getLikelihoodForASite. This class can't compute posterior probabilities, use RescaledHmmLikelihood instead."));
+ }
+
+
+ Vdouble getLikelihoodForEachSite() const
+ {
+ throw (NotImplementedException("LowMemoryRescaledHmmLikelihood::getLikelihoodForEachSite. This class can't compute posterior probabilities, use RescaledHmmLikelihood instead."));
+ }
+
+ Vdouble getHiddenStatesPosteriorProbabilitiesForASite(size_t site) const
+ {
+ throw (NotImplementedException("LowMemoryRescaledHmmLikelihood::getHiddenStatesPosteriorProbabilitiesForASite. This class can't compute posterior probabilities, use RescaledHmmLikelihood instead."));
+ }
+
void getHiddenStatesPosteriorProbabilities(std::vector< std::vector<double> >& probs, bool append = false) const throw (NotImplementedException)
{
throw (NotImplementedException("LowMemoryRescaledHmmLikelihood::getHiddenStatesPosteriorProbabilities. This class can't compute posterior probabilities, use RescaledHmmLikelihood instead."));
@@ -190,9 +213,19 @@ public:
protected:
void computeForward_();
+
+ void computeDLikelihood_() const
+ {
+ // computeDForward_();
+ }
+
+ void computeD2Likelihood_() const
+ {
+ // computeD2Forward_();
+ }
};
}
-#endif // _RESCALEDHMMLIKELIHOOD_H_
+#endif // _LOWMEMORYRESCALEDHMMLIKELIHOOD_H_
diff --git a/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp b/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp
index cc7350f..5cb884d 100644
--- a/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp
+++ b/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp
@@ -52,12 +52,19 @@ RescaledHmmLikelihood::RescaledHmmLikelihood(
HmmTransitionMatrix* transitionMatrix,
HmmEmissionProbabilities* emissionProbabilities,
const std::string& prefix) throw (Exception):
+ AbstractHmmLikelihood(),
AbstractParametrizable(prefix),
hiddenAlphabet_(hiddenAlphabet),
transitionMatrix_(transitionMatrix),
emissionProbabilities_(emissionProbabilities),
likelihood_(),
+ dLikelihood_(),
+ d2Likelihood_(),
+ backLikelihood_(),
+ backLikelihoodUpToDate_(false),
scales_(),
+ dScales_(),
+ d2Scales_(),
logLik_(),
breakPoints_(),
nbStates_(),
@@ -80,6 +87,7 @@ RescaledHmmLikelihood::RescaledHmmLikelihood(
//Init arrays:
likelihood_.resize(nbSites_ * nbStates_);
+
scales_.resize(nbSites_);
//Compute:
@@ -98,6 +106,7 @@ void RescaledHmmLikelihood::fireParameterChanged(const ParameterList& pl)
if (alphabetChanged && !emissionChanged) emissionProbabilities_->setParametersValues(emissionProbabilities_->getParameters());
computeForward_();
+ backLikelihoodUpToDate_=false;
}
/***************************************************************************************************************************/
@@ -114,7 +123,7 @@ void RescaledHmmLikelihood::computeForward_()
{
size_t ii = i * nbStates_;
for (size_t j = 0; j < nbStates_; j++) {
- trans[ii + j] = transitionMatrix_->Pij(static_cast<int>(j), static_cast<int>(i));
+ trans[ii + j] = transitionMatrix_->Pij(j, i);
if (isnan(trans[ii + j]))
throw Exception("RescaledHmmLikelihood::computeForward_. NaN transition probability");
if (trans[ii + j] < 0)
@@ -228,13 +237,15 @@ void RescaledHmmLikelihood::computeForward_()
/***************************************************************************************************************************/
-void RescaledHmmLikelihood::computeBackward_(std::vector< std::vector<double> >& b) const
+void RescaledHmmLikelihood::computeBackward_() const
{
- b.resize(nbSites_);
- for (size_t i = 0; i < nbSites_; i++)
- {
- b[i].resize(nbStates_);
- }
+ if (backLikelihood_.size()==0)
+ {
+ backLikelihood_.resize(nbSites_);
+ for (size_t i=0;i<nbSites_;i++)
+ backLikelihood_[i].resize(nbStates_);
+ }
+
double x;
//Transition probabilities:
@@ -243,7 +254,7 @@ void RescaledHmmLikelihood::computeBackward_(std::vector< std::vector<double> >&
{
size_t ii = i * nbStates_;
for (size_t j = 0; j < nbStates_; j++)
- trans[ii + j] = transitionMatrix_->Pij(static_cast<int>(i), static_cast<int>(j));
+ trans[ii + j] = transitionMatrix_->Pij(i, j);
}
@@ -256,7 +267,7 @@ void RescaledHmmLikelihood::computeBackward_(std::vector< std::vector<double> >&
for (size_t j = 0; j < nbStates_; j++)
{
x = 0;
- b[nbSites_ - 1][j] = 1.;
+ backLikelihood_[nbSites_ - 1][j] = 1.;
}
//Recursion:
@@ -271,47 +282,296 @@ void RescaledHmmLikelihood::computeBackward_(std::vector< std::vector<double> >&
size_t jj = j * nbStates_;
for (size_t k = 0; k < nbStates_; k++)
{
- x += (*emissions)[k] * trans[jj + k] * b[i][k];
+ x += (*emissions)[k] * trans[jj + k] * backLikelihood_[i][k];
}
- b[i-1][j] = x / scales_[i];
+ backLikelihood_[i-1][j] = x / scales_[i];
}
}
else //Reset markov chain
{
for (size_t j = 0; j < nbStates_; j++)
{
- b[i-1][j] = 1.;
+ backLikelihood_[i-1][j] = 1.;
}
bpIt++;
if (bpIt != breakPoints_.rend()) nextBrkPt = *bpIt;
else nextBrkPt = 0;
}
}
+
+ backLikelihoodUpToDate_=true;
+}
+
+/***************************************************************************************************************************/
+
+double RescaledHmmLikelihood::getLikelihoodForASite(size_t site) const
+{
+ Vdouble probs=getHiddenStatesPosteriorProbabilitiesForASite(site);
+ double x=0;
+ for (size_t i=0;i<nbStates_;i++)
+ x+=probs[i]*(*emissionProbabilities_)(site,i);
+
+ return x;
+}
+
+Vdouble RescaledHmmLikelihood::getLikelihoodForEachSite() const
+{
+ std::vector< std::vector<double> > vv;
+ getHiddenStatesPosteriorProbabilities(vv);
+
+ Vdouble ret(nbSites_);
+ for (size_t i=0;i<nbSites_;i++)
+ {
+ ret[i]=0;
+ for (size_t j=0;j<nbStates_;j++)
+ ret[i]+=vv[i][j]*(*emissionProbabilities_)(i,j);
+ }
+
+ return ret;
}
/***************************************************************************************************************************/
+Vdouble RescaledHmmLikelihood::getHiddenStatesPosteriorProbabilitiesForASite(size_t site) const
+{
+ if (!backLikelihoodUpToDate_)
+ computeBackward_();
+
+ Vdouble probs(nbStates_);
+
+ for (size_t j = 0; j < nbStates_; j++)
+ {
+ probs[j] = likelihood_[site * nbStates_ + j] * backLikelihood_[site][j];
+ }
+
+ return probs;
+}
+
+
void RescaledHmmLikelihood::getHiddenStatesPosteriorProbabilities(std::vector< std::vector<double> >& probs, bool append) const throw (Exception)
{
size_t offset = append ? probs.size() : 0;
probs.resize(offset + nbSites_);
for (size_t i = 0; i < nbSites_; i++)
+ {
+ probs[offset + i].resize(nbStates_);
+ }
+
+ if (!backLikelihoodUpToDate_)
+ computeBackward_();
+
+ for (size_t i = 0; i < nbSites_; i++)
+ {
+ size_t ii = i * nbStates_;
+ for (size_t j = 0; j < nbStates_; j++)
+ {
+ probs[offset + i][j] = likelihood_[ii + j] * backLikelihood_[i][j];
+ }
+ }
+}
+
+/***************************************************************************************************************************/
+
+void RescaledHmmLikelihood::computeDForward_() const
+{
+ //Init arrays:
+ if (dLikelihood_.size()==0){
+ dLikelihood_.resize(nbSites_);
+ for (size_t i=0;i<nbSites_;i++)
+ dLikelihood_[i].resize(nbStates_);
+ }
+ if (dScales_.size()==0)
+ dScales_.resize(nbSites_);
+
+ double x;
+ vector<double> tmp(nbStates_), dTmp(nbStates_);
+ vector<double> dLScales(nbSites_);
+
+ //Transition probabilities:
+ const ColMatrix<double> trans(transitionMatrix_->getPij());
+
+ //Initialisation:
+ dScales_[0] = 0;
+ const vector<double>* emissions = &(*emissionProbabilities_)(0);
+ const vector<double>* dEmissions = &emissionProbabilities_->getDEmissionProbabilities(0);
+
+ for (size_t j = 0; j < nbStates_; j++)
{
- probs[offset + i].resize(nbStates_);
+ dTmp[j] = (*dEmissions)[j] * transitionMatrix_->getEquilibriumFrequencies()[j];
+ tmp[j] = (*emissions)[j] * transitionMatrix_->getEquilibriumFrequencies()[j];
+
+ dScales_[0] += dTmp[j];
}
- vector< vector<double> > b;
- computeBackward_(b);
+ dLScales[0]=dScales_[0]/scales_[0];
+
- for (size_t i = 0; i < nbSites_; i++)
+ for (size_t j = 0; j < nbStates_; j++)
+ dLikelihood_[0][j] = (dTmp[j] * scales_[0] - tmp[j] * dScales_[0]) / pow(scales_[0],2);
+
+ //Recursion:
+
+ size_t nextBrkPt = nbSites_; //next break point
+ vector<size_t>::const_iterator bpIt = breakPoints_.begin();
+ if (bpIt != breakPoints_.end()) nextBrkPt = *bpIt;
+
+ for (size_t i = 1; i < nbSites_; i++)
{
- size_t ii = i * nbStates_;
- for (size_t j = 0; j < nbStates_; j++)
+ size_t iip = (i - 1) * nbStates_;
+
+ dScales_[i] = 0 ;
+
+ emissions = &(*emissionProbabilities_)(i);
+ dEmissions = &emissionProbabilities_->getDEmissionProbabilities(i);
+
+ if (i < nextBrkPt)
{
- probs[offset + i][j] = likelihood_[ii + j] * b[i][j];
+ for (size_t j = 0; j < nbStates_; j++)
+ {
+ x = 0;
+ for (size_t k = 0; k < nbStates_; k++)
+ x += trans(k,j) * likelihood_[iip + k];
+
+ tmp[j] = (*emissions)[j] * x;
+ dTmp[j] = (*dEmissions)[j] * x + (*emissions)[j] * VectorTools::sum(trans.getCol(j) * dLikelihood_[i-1]);
+
+ dScales_[i] += dTmp[j];
+ }
+ }
+ else //Reset markov chain:
+ {
+ for (size_t j = 0; j < nbStates_; j++)
+ {
+ dTmp[j] = (*dEmissions)[j] * transitionMatrix_->getEquilibriumFrequencies()[j];
+ tmp[j] = (*emissions)[j] * transitionMatrix_->getEquilibriumFrequencies()[j];
+
+ dScales_[i] += dTmp[j];
+ }
+
+ bpIt++;
+ if (bpIt != breakPoints_.end()) nextBrkPt = *bpIt;
+ else nextBrkPt = nbSites_;
}
+
+ dLScales[i]=dScales_[i]/scales_[i];
+
+ for (size_t j = 0; j < nbStates_; j++)
+ dLikelihood_[i][j] = (dTmp[j] * scales_[i] - tmp[j] * dScales_[i]) / pow(scales_[i],2);
+ }
+
+ greater<double> cmp;
+ sort(dLScales.begin(), dLScales.end(), cmp);
+ dLogLik_ = 0;
+ for (size_t i = 0; i < nbSites_; ++i)
+ {
+ dLogLik_ += dLScales[i];
}
}
/***************************************************************************************************************************/
+
+void RescaledHmmLikelihood::computeD2Forward_() const
+{
+ //Init arrays:
+ if (d2Likelihood_.size()==0){
+ d2Likelihood_.resize(nbSites_);
+ for (size_t i=0;i<nbSites_;i++)
+ d2Likelihood_[i].resize(nbStates_);
+ }
+ if (d2Scales_.size()==0)
+ d2Scales_.resize(nbSites_);
+
+ double x;
+ vector<double> tmp(nbStates_), dTmp(nbStates_), d2Tmp(nbStates_);
+ vector<double> d2LScales(nbSites_);
+
+ //Transition probabilities:
+ const ColMatrix<double> trans(transitionMatrix_->getPij());
+
+ //Initialisation:
+ d2Scales_[0] = 0;
+ const vector<double>* emissions = &(*emissionProbabilities_)(0);
+ const vector<double>* dEmissions = &emissionProbabilities_->getDEmissionProbabilities(0);
+ const vector<double>* d2Emissions = &emissionProbabilities_->getD2EmissionProbabilities(0);
+
+ for (size_t j = 0; j < nbStates_; j++)
+ {
+ tmp[j] = (*emissions)[j] * transitionMatrix_->getEquilibriumFrequencies()[j];
+ dTmp[j] = (*dEmissions)[j] * transitionMatrix_->getEquilibriumFrequencies()[j];
+ d2Tmp[j] = (*d2Emissions)[j] * transitionMatrix_->getEquilibriumFrequencies()[j];
+
+ d2Scales_[0] += d2Tmp[j];
+ }
+
+ d2LScales[0]=d2Scales_[0]/scales_[0]-pow(dScales_[0]/scales_[0],2);
+
+ for (size_t j = 0; j < nbStates_; j++)
+ d2Likelihood_[0][j] = d2Tmp[j] / scales_[0] - (d2Scales_[0] * tmp[j] + 2 * dScales_[0] * dTmp[j]) / pow(scales_[0],2)
+ + 2 * pow(dScales_[0],2) * tmp[j] / pow(scales_[0],3);
+
+ //Recursion:
+
+ size_t nextBrkPt = nbSites_; //next break point
+ vector<size_t>::const_iterator bpIt = breakPoints_.begin();
+ if (bpIt != breakPoints_.end()) nextBrkPt = *bpIt;
+
+ for (size_t i = 1; i < nbSites_; i++)
+ {
+ dScales_[i] = 0 ;
+
+ emissions = &(*emissionProbabilities_)(i);
+ dEmissions = &emissionProbabilities_->getDEmissionProbabilities(i);
+ d2Emissions = &emissionProbabilities_->getD2EmissionProbabilities(i);
+
+ if (i < nextBrkPt)
+ {
+ size_t iip = (i - 1) * nbStates_;
+
+ for (size_t j = 0; j < nbStates_; j++)
+ {
+ x = 0;
+ for (size_t k = 0; k < nbStates_; k++)
+ x += trans(k,j) * likelihood_[iip + k];
+
+ tmp[j] = (*emissions)[j] * x;
+ dTmp[j] = (*dEmissions)[j] * x + (*emissions)[j] * VectorTools::sum(trans.getCol(j) * dLikelihood_[i-1]);
+ d2Tmp[j] = (*d2Emissions)[j] * x + 2 * (*dEmissions)[j] * VectorTools::sum(trans.getCol(j) * dLikelihood_[i-1])
+ + (*emissions)[j] * VectorTools::sum(trans.getCol(j) * d2Likelihood_[i-1]);
+
+ d2Scales_[i] += d2Tmp[j];
+ }
+ }
+ else //Reset markov chain:
+ {
+ for (size_t j = 0; j < nbStates_; j++)
+ {
+ tmp[j] = (*emissions)[j] * transitionMatrix_->getEquilibriumFrequencies()[j];
+ dTmp[j] = (*dEmissions)[j] * transitionMatrix_->getEquilibriumFrequencies()[j];
+ d2Tmp[j] = (*d2Emissions)[j] * transitionMatrix_->getEquilibriumFrequencies()[j];
+
+ d2Scales_[i] += d2Tmp[j];
+ }
+
+ bpIt++;
+ if (bpIt != breakPoints_.end()) nextBrkPt = *bpIt;
+ else nextBrkPt = nbSites_;
+ }
+
+ d2LScales[i]=d2Scales_[i]/scales_[i]-pow(dScales_[i]/scales_[i],2);
+
+ for (size_t j = 0; j < nbStates_; j++)
+ d2Likelihood_[i][j] = d2Tmp[j] / scales_[i] - (d2Scales_[i] * tmp[j] + 2 * dScales_[i] * dTmp[j]) / pow(scales_[i],2)
+ + 2 * pow(dScales_[i],2) * tmp[j] / pow(scales_[i],3);
+ }
+
+ greater<double> cmp;
+ sort(d2LScales.begin(), d2LScales.end(), cmp);
+ dLogLik_ = 0;
+ for (size_t i = 0; i < nbSites_; ++i)
+ {
+ d2LogLik_ += d2LScales[i];
+ }
+}
+
+/***************************************************************************************************************************/
diff --git a/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.h b/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.h
index c775c5b..93f6ea9 100644
--- a/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.h
+++ b/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.h
@@ -5,36 +5,36 @@
//
/*
-Copyright or © or Copr. CNRS, (November 16, 2004)
-
-This software is a computer program whose purpose is to provide classes
-for phylogenetic data 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.
+ Copyright or © or Copr. CNRS, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data 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 _RESCALEDHMMLIKELIHOOD_H_
@@ -57,125 +57,199 @@ namespace bpp {
* It also offer the possibility to specify "breakpoints", where the chain will be reset to the equilibrium frequencies.
*/
class RescaledHmmLikelihood:
- public virtual HmmLikelihood,
+ public virtual AbstractHmmLikelihood,
public AbstractParametrizable
{
- private:
- /**
- * @brief The alphabet describing the hidden states.
- */
- std::auto_ptr<HmmStateAlphabet> hiddenAlphabet_;
- std::auto_ptr<HmmTransitionMatrix> transitionMatrix_;
- std::auto_ptr<HmmEmissionProbabilities> emissionProbabilities_;
-
- /**
- * @brief The likelihood array.
- *
- * likelihood_[i * nbStates_ + j] corresponds to Pr(x1...xi, yi=j),
- * where the x are the observed states, and y the hidden states.
- */
- std::vector<double> likelihood_;
- std::vector<double> scales_;
- double logLik_;
-
- std::vector<size_t> breakPoints_;
-
- size_t nbStates_, nbSites_;
-
- public:
- /**
- * @brief Build a new RescaledHmmLikelihood object.
- *
- * @warning the HmmTransitionMatrix and HmmEmissionProbabilities object passed as argument must be non-null
- * and point toward the same HmmStateAlphabet instance. The three object will be copied if needed, and
- * deleted when the hmm likelihood objet is deleted. You should secure a copy before if you don't want them to
- * be destroyed with this object.
- */
- RescaledHmmLikelihood(
- HmmStateAlphabet* hiddenAlphabet,
- HmmTransitionMatrix* transitionMatrix,
- HmmEmissionProbabilities* emissionProbabilities,
- const std::string& prefix) throw (Exception);
-
- RescaledHmmLikelihood(const RescaledHmmLikelihood& lik):
- AbstractParametrizable(lik),
- hiddenAlphabet_(dynamic_cast<HmmStateAlphabet*>(lik.hiddenAlphabet_->clone())),
- transitionMatrix_(dynamic_cast<HmmTransitionMatrix*>(lik.transitionMatrix_->clone())),
- emissionProbabilities_(dynamic_cast<HmmEmissionProbabilities*>(lik.emissionProbabilities_->clone())),
- likelihood_(lik.likelihood_),
- scales_(lik.scales_),
- logLik_(lik.logLik_),
- breakPoints_(lik.breakPoints_),
- nbStates_(lik.nbStates_),
- nbSites_(lik.nbSites_)
+ private:
+ /**
+ * @brief The alphabet describing the hidden states.
+ */
+ std::auto_ptr<HmmStateAlphabet> hiddenAlphabet_;
+ std::auto_ptr<HmmTransitionMatrix> transitionMatrix_;
+ std::auto_ptr<HmmEmissionProbabilities> emissionProbabilities_;
+
+ /**
+ * @brief The likelihood arrays.
+ *
+ */
+
+ /**
+ * @brief forward likelihood
+ *
+ * likelihood_[i * nbStates_ + j] corresponds to Pr(x_1...x_i, y_i=j)/Pr(x_1...x_i),
+ * where the x are the observed states, and y the hidden states.
+ */
+
+ std::vector<double> likelihood_;
+
+ /**
+ * @brief derivatec of forward likelihood
+ *
+ * dlikelihood_[i][j] corresponds to d(Pr(x_1...x_i, y_i=j))/Pr(x_1...x_i)),
+ * where the x are the observed states, and y the hidden states.
+ */
+
+ mutable std::vector<std::vector<double> > dLikelihood_;
+ mutable std::vector<std::vector<double> > d2Likelihood_;
+
+ /**
+ * @brief backward likelihood
+ *
+ * backLikelihood_[i][j] corresponds to Pr(x_i+1...x_n | yi=j),
+ * where the x are the observed states, and y the hidden states.
+ */
+
+ mutable std::vector<std::vector<double> > backLikelihood_;
+ mutable bool backLikelihoodUpToDate_;
+
+ /**
+ * @brief scales for likelihood computing
+ *
+ * scales_[i * nbStates_ + j] corresponds to Pr(x_1...x_i)/Pr(x_1...x_{i-1})
+ * where the x are the observed states.
+ */
+
+ std::vector<double> scales_;
+
+ mutable std::vector<double> dScales_;
+ mutable std::vector<double> d2Scales_;
+ double logLik_;
+
+ std::vector<size_t> breakPoints_;
+
+ size_t nbStates_, nbSites_;
+
+ public:
+ /**
+ * @brief Build a new RescaledHmmLikelihood object.
+ *
+ * @warning the HmmTransitionMatrix and HmmEmissionProbabilities object passed as argument must be non-null
+ * and point toward the same HmmStateAlphabet instance. The three object will be copied if needed, and
+ * deleted when the hmm likelihood objet is deleted. You should secure a copy before if you don't want them to
+ * be destroyed with this object.
+ */
+ RescaledHmmLikelihood(
+ HmmStateAlphabet* hiddenAlphabet,
+ HmmTransitionMatrix* transitionMatrix,
+ HmmEmissionProbabilities* emissionProbabilities,
+ const std::string& prefix) throw (Exception);
+
+ RescaledHmmLikelihood(const RescaledHmmLikelihood& lik):
+ AbstractHmmLikelihood(lik),
+ AbstractParametrizable(lik),
+ hiddenAlphabet_(dynamic_cast<HmmStateAlphabet*>(lik.hiddenAlphabet_->clone())),
+ transitionMatrix_(dynamic_cast<HmmTransitionMatrix*>(lik.transitionMatrix_->clone())),
+ emissionProbabilities_(dynamic_cast<HmmEmissionProbabilities*>(lik.emissionProbabilities_->clone())),
+ likelihood_(lik.likelihood_),
+ dLikelihood_(lik.dLikelihood_),
+ d2Likelihood_(lik.d2Likelihood_),
+ backLikelihood_(lik.backLikelihood_),
+ backLikelihoodUpToDate_(lik.backLikelihoodUpToDate_),
+ scales_(lik.scales_),
+ dScales_(lik.dScales_),
+ d2Scales_(lik.d2Scales_),
+ logLik_(lik.logLik_),
+ breakPoints_(lik.breakPoints_),
+ nbStates_(lik.nbStates_),
+ nbSites_(lik.nbSites_)
{
// Now adjust pointers:
transitionMatrix_->setHmmStateAlphabet(hiddenAlphabet_.get());
emissionProbabilities_->setHmmStateAlphabet(hiddenAlphabet_.get());
}
- RescaledHmmLikelihood& operator=(const RescaledHmmLikelihood& lik)
- {
- AbstractParametrizable::operator =(lik);
- hiddenAlphabet_ = std::auto_ptr<HmmStateAlphabet>(dynamic_cast<HmmStateAlphabet*>(lik.hiddenAlphabet_->clone()));
- transitionMatrix_ = std::auto_ptr<HmmTransitionMatrix>(dynamic_cast<HmmTransitionMatrix*>(lik.transitionMatrix_->clone()));
- emissionProbabilities_ = std::auto_ptr<HmmEmissionProbabilities>(dynamic_cast<HmmEmissionProbabilities*>(lik.emissionProbabilities_->clone()));
- likelihood_ = lik.likelihood_;
- scales_ = lik.scales_;
- logLik_ = lik.logLik_;
- breakPoints_ = lik.breakPoints_;
- nbStates_ = lik.nbStates_;
- nbSites_ = lik.nbSites_;
-
- // Now adjust pointers:
- transitionMatrix_->setHmmStateAlphabet(hiddenAlphabet_.get());
- emissionProbabilities_->setHmmStateAlphabet(hiddenAlphabet_.get());
- return *this;
- }
-
- virtual ~RescaledHmmLikelihood() {}
+ RescaledHmmLikelihood& operator=(const RescaledHmmLikelihood& lik)
+ {
+ AbstractHmmLikelihood::operator=(lik);
+ AbstractParametrizable::operator=(lik);
+ hiddenAlphabet_ = std::auto_ptr<HmmStateAlphabet>(dynamic_cast<HmmStateAlphabet*>(lik.hiddenAlphabet_->clone()));
+ transitionMatrix_ = std::auto_ptr<HmmTransitionMatrix>(dynamic_cast<HmmTransitionMatrix*>(lik.transitionMatrix_->clone()));
+ emissionProbabilities_ = std::auto_ptr<HmmEmissionProbabilities>(dynamic_cast<HmmEmissionProbabilities*>(lik.emissionProbabilities_->clone()));
+ likelihood_ = lik.likelihood_;
+ dLikelihood_ = lik.dLikelihood_;
+ d2Likelihood_ = lik.d2Likelihood_;
+ backLikelihood_ = lik.backLikelihood_;
+ backLikelihoodUpToDate_= lik.backLikelihoodUpToDate_;
+ scales_ = lik.scales_;
+ dScales_ = lik.dScales_;
+ d2Scales_ = lik.d2Scales_;
+ logLik_ = lik.logLik_;
+ breakPoints_ = lik.breakPoints_;
+ nbStates_ = lik.nbStates_;
+ nbSites_ = lik.nbSites_;
+
+ // Now adjust pointers:
+ transitionMatrix_->setHmmStateAlphabet(hiddenAlphabet_.get());
+ emissionProbabilities_->setHmmStateAlphabet(hiddenAlphabet_.get());
+ return *this;
+ }
+
+ virtual ~RescaledHmmLikelihood() {}
#ifndef NO_VIRTUAL_COV
- RescaledHmmLikelihood*
+ RescaledHmmLikelihood*
#else
- Clonable*
+ Clonable*
#endif
- clone() const { return new RescaledHmmLikelihood(*this); }
+ clone() const { return new RescaledHmmLikelihood(*this); }
- public:
- const HmmStateAlphabet& getHmmStateAlphabet() const { return *hiddenAlphabet_; }
- HmmStateAlphabet& getHmmStateAlphabet() { return *hiddenAlphabet_; }
+ public:
+ const HmmStateAlphabet& getHmmStateAlphabet() const { return *hiddenAlphabet_; }
+ HmmStateAlphabet& getHmmStateAlphabet() { return *hiddenAlphabet_; }
- const HmmTransitionMatrix& getHmmTransitionMatrix() const { return *transitionMatrix_; }
- HmmTransitionMatrix& getHmmTransitionMatrix() { return *transitionMatrix_; }
+ const HmmTransitionMatrix& getHmmTransitionMatrix() const { return *transitionMatrix_; }
+ HmmTransitionMatrix& getHmmTransitionMatrix() { return *transitionMatrix_; }
- const HmmEmissionProbabilities& getHmmEmissionProbabilities() const { return *emissionProbabilities_; }
- HmmEmissionProbabilities& getHmmEmissionProbabilities() { return *emissionProbabilities_; }
+ const HmmEmissionProbabilities& getHmmEmissionProbabilities() const { return *emissionProbabilities_; }
+ HmmEmissionProbabilities& getHmmEmissionProbabilities() { return *emissionProbabilities_; }
- void setBreakPoints(const std::vector<size_t>& breakPoints) {
- breakPoints_ = breakPoints;
- computeForward_();
- }
+ void setBreakPoints(const std::vector<size_t>& breakPoints) {
+ breakPoints_ = breakPoints;
+ computeForward_();
+ backLikelihoodUpToDate_=false;
+ }
- const std::vector<size_t>& getBreakPoints() const { return breakPoints_; }
+ const std::vector<size_t>& getBreakPoints() const { return breakPoints_; }
- void setParameters(const ParameterList& pl) throw (Exception)
- {
- setParametersValues(pl);
- }
+ void setParameters(const ParameterList& pl) throw (Exception)
+ {
+ setParametersValues(pl);
+ }
- double getValue() const throw (Exception) { return -logLik_; }
+ double getValue() const throw (Exception) { return -logLik_; }
- double getLogLikelihood() const { return logLik_; }
+ double getLogLikelihood() const { return logLik_; }
- void fireParameterChanged(const ParameterList& pl);
+ double getLikelihoodForASite(size_t site) const;
- void getHiddenStatesPosteriorProbabilities(std::vector< std::vector<double> >& probs, bool append = false) const throw (Exception);
+ Vdouble getLikelihoodForEachSite() const;
- protected:
- void computeForward_();
- void computeBackward_(std::vector< std::vector<double> >& b) const;
+ void fireParameterChanged(const ParameterList& pl);
+
+ Vdouble getHiddenStatesPosteriorProbabilitiesForASite(size_t site) const;
+
+ void getHiddenStatesPosteriorProbabilities(std::vector< std::vector<double> >& probs, bool append = false) const throw (Exception);
+
+
+ protected:
+ void computeForward_();
+ void computeBackward_() const;
+
+
+ void computeDLikelihood_() const
+ {
+ computeDForward_();
+ }
+
+ void computeD2Likelihood_() const
+ {
+ computeD2Forward_();
+ }
+ void computeDForward_() const;
+
+ void computeD2Forward_() const;
+
};
}
diff --git a/src/Bpp/Numeric/Matrix/EigenValue.h b/src/Bpp/Numeric/Matrix/EigenValue.h
index 17050c1..c294761 100644
--- a/src/Bpp/Numeric/Matrix/EigenValue.h
+++ b/src/Bpp/Numeric/Matrix/EigenValue.h
@@ -41,6 +41,7 @@ knowledge of the CeCILL license and that you accept its terms.
#ifndef _EIGENVALUE_H_
#define _EIGENVALUE_H_
+#define TOST(i) static_cast<size_t>(i)
#include <algorithm>
// for min(), max() below
@@ -168,36 +169,36 @@ class EigenValue
// Householder reduction to tridiagonal form.
- for (int i = static_cast<int>(n_)-1; i > 0; i--)
+ for (size_t i = n_-1; i > 0; i--)
{
// Scale to avoid under/overflow.
Real scale = 0.0;
Real h = 0.0;
- for (int k = 0; k < i; k++)
+ for (size_t k = 0; k < i; ++k)
{
scale = scale + NumTools::abs<Real>(d_[k]);
}
if (scale == 0.0)
{
e_[i] = d_[i-1];
- for (int j = 0; j < i; j++)
+ for (size_t j = 0; j < i; ++j)
{
- d_[j] = V_(i-1,j);
- V_(i,j) = 0.0;
- V_(j,i) = 0.0;
+ d_[j] = V_(i - 1, j);
+ V_(i, j) = 0.0;
+ V_(j, i) = 0.0;
}
}
else
{
// Generate Householder vector.
- for (int k = 0; k < i; k++)
+ for (size_t k = 0; k < i; ++k)
{
d_[k] /= scale;
h += d_[k] * d_[k];
}
- Real f = d_[i-1];
+ Real f = d_[i - 1];
Real g = sqrt(h);
if (f > 0)
{
@@ -206,19 +207,19 @@ class EigenValue
e_[i] = scale * g;
h = h - f * g;
d_[i-1] = f - g;
- for (int j = 0; j < i; j++)
+ for (size_t j = 0; j < i; ++j)
{
e_[j] = 0.0;
}
// Apply similarity transformation to remaining columns.
- for (int j = 0; j < i; j++)
+ for (size_t j = 0; j < i; ++j)
{
f = d_[j];
V_(j,i) = f;
g = e_[j] + V_(j,j) * f;
- for (int k = j+1; k <= i-1; k++)
+ for (size_t k = j + 1; k <= i - 1; k++)
{
g += V_(k,j) * d_[k];
e_[k] += V_(k,j) * f;
@@ -226,21 +227,21 @@ class EigenValue
e_[j] = g;
}
f = 0.0;
- for (int j = 0; j < i; j++)
+ for (size_t j = 0; j < i; ++j)
{
e_[j] /= h;
f += e_[j] * d_[j];
}
Real hh = f / (h + h);
- for (int j = 0; j < i; j++)
+ for (size_t j = 0; j < i; ++j)
{
e_[j] -= hh * d_[j];
}
- for (int j = 0; j < i; j++)
+ for (size_t j = 0; j < i; ++j)
{
f = d_[j];
g = e_[j];
- for (int k = j; k <= i-1; k++)
+ for (size_t k = j; k <= i-1; ++k)
{
V_(k,j) -= (f * e_[k] + g * d_[k]);
}
@@ -303,22 +304,22 @@ class EigenValue
{
for (size_t i = 1; i < n_; i++)
{
- e_[i-1] = e_[i];
+ e_[i - 1] = e_[i];
}
- e_[n_-1] = 0.0;
+ e_[n_ - 1] = 0.0;
Real f = 0.0;
Real tst1 = 0.0;
Real eps = pow(2.0,-52.0);
- for (int l = 0; l < static_cast<int>(n_); l++)
+ for (size_t l = 0; l < n_; ++l)
{
// Find small subdiagonal element
tst1 = std::max(tst1, NumTools::abs<Real>(d_[l]) + NumTools::abs<Real>(e_[l]));
- int m = l;
+ size_t m = l;
// Original while-loop from Java code
- while (m < static_cast<int>(n_))
+ while (m < n_)
{
if (NumTools::abs<Real>(e_[m]) <= eps*tst1)
{
@@ -340,17 +341,17 @@ class EigenValue
// Compute implicit shift
Real g = d_[l];
- Real p = (d_[l+1] - g) / (2.0 * e_[l]);
+ Real p = (d_[l + 1] - g) / (2.0 * e_[l]);
Real r = hypot(p,1.0);
if (p < 0)
{
r = -r;
}
d_[l] = e_[l] / (p + r);
- d_[l+1] = e_[l] * (p + r);
- Real dl1 = d_[l+1];
+ d_[l + 1] = e_[l] * (p + r);
+ Real dl1 = d_[l + 1];
Real h = g - d_[l];
- for (size_t i = l+2; i < n_; i++)
+ for (size_t i = l + 2; i < n_; ++i)
{
d_[i] -= h;
}
@@ -362,30 +363,32 @@ class EigenValue
Real c = 1.0;
Real c2 = c;
Real c3 = c;
- Real el1 = e_[l+1];
+ Real el1 = e_[l + 1];
Real s = 0.0;
Real s2 = 0.0;
- for (int i = m-1; i >= l; i--)
+ //for (size_t i = m - 1; i >= l; --i)
+ for (size_t ii = m; ii > l; --ii)
{
+ size_t i = ii - 1; //to avoid infinite loop!
c3 = c2;
c2 = c;
s2 = s;
g = c * e_[i];
h = c * p;
- r = hypot(p,e_[i]);
- e_[i+1] = s * r;
+ r = hypot(p, e_[i]);
+ e_[i + 1] = s * r;
s = e_[i] / r;
c = p / r;
p = c * d_[i] - s * g;
- d_[i+1] = h + s * (c * g + s * d_[i]);
+ d_[i + 1] = h + s * (c * g + s * d_[i]);
// Accumulate transformation.
for (size_t k = 0; k < n_; k++)
{
- h = V_(k,i+1);
- V_(k,i+1) = s * V_(k,i) + c * h;
- V_(k,i) = c * V_(k,i) - s * h;
+ h = V_(k, i + 1);
+ V_(k, i + 1) = s * V_(k, i) + c * h;
+ V_(k, i) = c * V_(k, i) - s * h;
}
}
p = -s * s2 * c3 * el1 * e_[l] / dl1;
@@ -394,7 +397,7 @@ class EigenValue
// Check for convergence.
- } while (NumTools::abs<Real>(e_[l]) > eps*tst1);
+ } while (NumTools::abs<Real>(e_[l]) > eps * tst1);
}
d_[l] = d_[l] + f;
e_[l] = 0.0;
@@ -420,8 +423,8 @@ class EigenValue
d_[i] = p;
for (size_t j = 0; j < n_; j++)
{
- p = V_(j,i);
- V_(j,i) = V_(j,k);
+ p = V_(j, i);
+ V_(j,i) = V_(j, k);
V_(j,k) = p;
}
}
@@ -436,28 +439,29 @@ class EigenValue
* Vol.ii-Linear Algebra, and the corresponding
* Fortran subroutines in EISPACK.
*/
- void orthes ()
+ void orthes()
{
- int low = 0;
- int high = static_cast<int>(n_)-1;
+ if (n_ == 0) return;
+ size_t low = 0;
+ size_t high = n_-1;
- for (int m = low+1; m <= high-1; m++)
+ for (size_t m = low + 1; m <= high - 1; ++m)
{
// Scale column.
Real scale = 0.0;
- for (int i = m; i <= high; i++)
+ for (size_t i = m; i <= high; ++i)
{
- scale = scale + NumTools::abs<Real>(H_(i,m-1));
+ scale = scale + NumTools::abs<Real>(H_(i, m - 1));
}
if (scale != 0.0)
{
// Compute Householder transformation.
Real h = 0.0;
- for (int i = high; i >= m; i--)
+ for (size_t i = high; i >= m; --i)
{
- ort_[i] = H_(i,m-1)/scale;
+ ort_[i] = H_(i, m - 1)/scale;
h += ort_[i] * ort_[i];
}
Real g = sqrt(h);
@@ -471,35 +475,35 @@ class EigenValue
// Apply Householder similarity transformation
// H = (I-u*u'/h)*H*(I-u*u')/h)
- for (int j = m; j < static_cast<int>(n_); j++)
+ for (size_t j = m; j < n_; ++j)
{
Real f = 0.0;
- for (int i = high; i >= m; i--)
+ for (size_t i = high; i >= m; --i)
{
- f += ort_[i]*H_(i,j);
+ f += ort_[i] * H_(i, j);
}
f = f/h;
- for (int i = m; i <= high; i++)
+ for (size_t i = m; i <= high; ++i)
{
H_(i,j) -= f*ort_[i];
}
}
- for (int i = 0; i <= high; i++)
+ for (size_t i = 0; i <= high; ++i)
{
Real f = 0.0;
- for (int j = high; j >= m; j--)
+ for (size_t j = high; j >= m; --j)
{
- f += ort_[j]*H_(i,j);
+ f += ort_[j] * H_(i, j);
}
f = f/h;
- for (int j = m; j <= high; j++)
+ for (size_t j = m; j <= high; ++j)
{
- H_(i,j) -= f*ort_[j];
+ H_(i,j) -= f * ort_[j];
}
}
- ort_[m] = scale*ort_[m];
- H_(m,m-1) = scale*g;
+ ort_[m] = scale * ort_[m];
+ H_(m, m - 1) = scale * g;
}
}
@@ -513,26 +517,26 @@ class EigenValue
}
}
- for (int m = high-1; m >= low+1; m--)
+ for (size_t m = high - 1; m >= low + 1; --m)
{
- if (H_(m,m-1) != 0.0)
+ if (H_(m, m - 1) != 0.0)
{
- for (int i = m+1; i <= high; i++)
+ for (size_t i = m + 1; i <= high; ++i)
{
- ort_[i] = H_(i,m-1);
+ ort_[i] = H_(i, m - 1);
}
- for (int j = m; j <= high; j++)
+ for (size_t j = m; j <= high; ++j)
{
Real g = 0.0;
- for (int i = m; i <= high; i++)
+ for (size_t i = m; i <= high; i++)
{
- g += ort_[i] * V_(i,j);
+ g += ort_[i] * V_(i, j);
}
// Double division avoids possible underflow
- g = (g / ort_[m]) / H_(m,m-1);
- for (int i = m; i <= high; i++)
+ g = (g / ort_[m]) / H_(m, m - 1);
+ for (size_t i = m; i <= high; ++i)
{
- V_(i,j) += g * ort_[i];
+ V_(i, j) += g * ort_[i];
}
}
}
@@ -589,12 +593,12 @@ class EigenValue
{
if ((i < low) || (i > high))
{
- d_[i] = H_(i,i);
- e_[i] = 0.0;
+ d_[TOST(i)] = H_(TOST(i),TOST(i));
+ e_[TOST(i)] = 0.0;
}
for (int j = std::max(i-1,0); j < nn; j++)
{
- norm = norm + NumTools::abs<Real>(H_(i,j));
+ norm = norm + NumTools::abs<Real>(H_(TOST(i),TOST(j)));
}
}
@@ -608,12 +612,12 @@ class EigenValue
int l = n;
while (l > low)
{
- s = NumTools::abs<Real>(H_(l-1,l-1)) + NumTools::abs<Real>(H_(l,l));
+ s = NumTools::abs<Real>(H_(TOST(l-1),TOST(l-1))) + NumTools::abs<Real>(H_(TOST(l),TOST(l)));
if (s == 0.0)
{
s = norm;
}
- if (NumTools::abs<Real>(H_(l,l-1)) < eps * s)
+ if (NumTools::abs<Real>(H_(TOST(l),TOST(l-1))) < eps * s)
{
break;
}
@@ -625,9 +629,9 @@ class EigenValue
if (l == n)
{
- H_(n,n) = H_(n,n) + exshift;
- d_[n] = H_(n,n);
- e_[n] = 0.0;
+ H_(TOST(n),TOST(n)) = H_(TOST(n),TOST(n)) + exshift;
+ d_[TOST(n)] = H_(TOST(n),TOST(n));
+ e_[TOST(n)] = 0.0;
n--;
iter = 0;
@@ -636,13 +640,13 @@ class EigenValue
}
else if (l == n-1)
{
- w = H_(n,n-1) * H_(n-1,n);
- p = (H_(n-1,n-1) - H_(n,n)) / 2.0;
+ w = H_(TOST(n),TOST(n-1)) * H_(TOST(n-1),TOST(n));
+ p = (H_(TOST(n-1),TOST(n-1)) - H_(TOST(n),TOST(n))) / 2.0;
q = p * p + w;
z = sqrt(NumTools::abs<Real>(q));
- H_(n,n) = H_(n,n) + exshift;
- H_(n-1,n-1) = H_(n-1,n-1) + exshift;
- x = H_(n,n);
+ H_(TOST(n),TOST(n)) = H_(TOST(n),TOST(n)) + exshift;
+ H_(TOST(n-1),TOST(n-1)) = H_(TOST(n-1),TOST(n-1)) + exshift;
+ x = H_(TOST(n),TOST(n));
// Real pair
@@ -656,15 +660,15 @@ class EigenValue
{
z = p - z;
}
- d_[n-1] = x + z;
- d_[n] = d_[n-1];
+ d_[TOST(n - 1)] = x + z;
+ d_[TOST(n)] = d_[TOST(n - 1)];
if (z != 0.0)
{
- d_[n] = x - w / z;
+ d_[TOST(n)] = x - w / z;
}
- e_[n-1] = 0.0;
- e_[n] = 0.0;
- x = H_(n,n-1);
+ e_[TOST(n - 1)] = 0.0;
+ e_[TOST(n)] = 0.0;
+ x = H_(TOST(n),TOST(n-1));
s = NumTools::abs<Real>(x) + NumTools::abs<Real>(z);
p = x / s;
q = z / s;
@@ -676,27 +680,27 @@ class EigenValue
for (int j = n-1; j < nn; j++)
{
- z = H_(n-1,j);
- H_(n-1,j) = q * z + p * H_(n,j);
- H_(n,j) = q * H_(n,j) - p * z;
+ z = H_(TOST(n-1),TOST(j));
+ H_(TOST(n-1),TOST(j)) = q * z + p * H_(TOST(n),TOST(j));
+ H_(TOST(n),TOST(j)) = q * H_(TOST(n),TOST(j)) - p * z;
}
// Column modification
for (int i = 0; i <= n; i++)
{
- z = H_(i,n-1);
- H_(i,n-1) = q * z + p * H_(i,n);
- H_(i,n) = q * H_(i,n) - p * z;
+ z = H_(TOST(i),TOST(n-1));
+ H_(TOST(i),TOST(n-1)) = q * z + p * H_(TOST(i),TOST(n));
+ H_(TOST(i),TOST(n)) = q * H_(TOST(i),TOST(n)) - p * z;
}
// Accumulate transformations
for (int i = low; i <= high; i++)
{
- z = V_(i,n-1);
- V_(i,n-1) = q * z + p * V_(i,n);
- V_(i,n) = q * V_(i,n) - p * z;
+ z = V_(TOST(i),TOST(n-1));
+ V_(TOST(i),TOST(n-1)) = q * z + p * V_(TOST(i),TOST(n));
+ V_(TOST(i),TOST(n)) = q * V_(TOST(i),TOST(n)) - p * z;
}
// Complex pair
@@ -704,10 +708,10 @@ class EigenValue
}
else
{
- d_[n-1] = x + p;
- d_[n] = x + p;
- e_[n-1] = z;
- e_[n] = -z;
+ d_[TOST(n - 1)] = x + p;
+ d_[TOST(n)] = x + p;
+ e_[TOST(n-1)] = z;
+ e_[TOST(n)] = -z;
}
n = n - 2;
iter = 0;
@@ -719,13 +723,13 @@ class EigenValue
{
// Form shift
- x = H_(n,n);
+ x = H_(TOST(n),TOST(n));
y = 0.0;
w = 0.0;
if (l < n)
{
- y = H_(n-1,n-1);
- w = H_(n,n-1) * H_(n-1,n);
+ y = H_(TOST(n-1),TOST(n-1));
+ w = H_(TOST(n),TOST(n-1)) * H_(TOST(n-1),TOST(n));
}
// Wilkinson's original ad hoc shift
@@ -735,9 +739,9 @@ class EigenValue
exshift += x;
for (int i = low; i <= n; i++)
{
- H_(i,i) -= x;
+ H_(TOST(i),TOST(i)) -= x;
}
- s = NumTools::abs<Real>(H_(n,n-1)) + NumTools::abs<Real>(H_(n-1,n-2));
+ s = NumTools::abs<Real>(H_(TOST(n),TOST(n-1))) + NumTools::abs<Real>(H_(TOST(n-1),TOST(n-2)));
x = y = 0.75 * s;
w = -0.4375 * s * s;
}
@@ -757,7 +761,7 @@ class EigenValue
s = x - w / ((y - x) / 2.0 + s);
for (int i = low; i <= n; i++)
{
- H_(i,i) -= s;
+ H_(TOST(i),TOST(i)) -= s;
}
exshift += s;
x = y = w = 0.964;
@@ -771,12 +775,12 @@ class EigenValue
int m = n-2;
while (m >= l)
{
- z = H_(m,m);
+ z = H_(TOST(m),TOST(m));
r = x - z;
s = y - z;
- p = (r * s - w) / H_(m+1,m) + H_(m,m+1);
- q = H_(m+1,m+1) - z - r - s;
- r = H_(m+2,m+1);
+ p = (r * s - w) / H_(TOST(m+1),TOST(m)) + H_(TOST(m),TOST(m+1));
+ q = H_(TOST(m+1),TOST(m+1)) - z - r - s;
+ r = H_(TOST(m+2),TOST(m+1));
s = NumTools::abs<Real>(p) + NumTools::abs<Real>(q) + NumTools::abs<Real>(r);
p = p / s;
q = q / s;
@@ -785,9 +789,9 @@ class EigenValue
{
break;
}
- if (NumTools::abs<Real>(H_(m,m-1)) * (NumTools::abs<Real>(q) + NumTools::abs<Real>(r)) <
- eps * (NumTools::abs<Real>(p) * (NumTools::abs<Real>(H_(m-1,m-1)) + NumTools::abs<Real>(z) +
- NumTools::abs<Real>(H_(m+1,m+1)))))
+ if (NumTools::abs<Real>(H_(TOST(m),TOST(m-1))) * (NumTools::abs<Real>(q) + NumTools::abs<Real>(r)) <
+ eps * (NumTools::abs<Real>(p) * (NumTools::abs<Real>(H_(TOST(m-1),TOST(m-1))) + NumTools::abs<Real>(z) +
+ NumTools::abs<Real>(H_(TOST(m+1),TOST(m+1))))))
{
break;
}
@@ -796,10 +800,10 @@ class EigenValue
for (int i = m+2; i <= n; i++)
{
- H_(i,i-2) = 0.0;
+ H_(TOST(i),TOST(i-2)) = 0.0;
if (i > m+2)
{
- H_(i,i-3) = 0.0;
+ H_(TOST(i),TOST(i-3)) = 0.0;
}
}
@@ -810,9 +814,9 @@ class EigenValue
int notlast = (k != n-1);
if (k != m)
{
- p = H_(k,k-1);
- q = H_(k+1,k-1);
- r = (notlast ? H_(k+2,k-1) : 0.0);
+ p = H_(TOST(k),TOST(k-1));
+ q = H_(TOST(k+1),TOST(k-1));
+ r = (notlast ? H_(TOST(k+2),TOST(k-1)) : 0.0);
x = NumTools::abs<Real>(p) + NumTools::abs<Real>(q) + NumTools::abs<Real>(r);
if (x != 0.0)
{
@@ -834,11 +838,11 @@ class EigenValue
{
if (k != m)
{
- H_(k,k-1) = -s * x;
+ H_(TOST(k),TOST(k-1)) = -s * x;
}
else if (l != m)
{
- H_(k,k-1) = -H_(k,k-1);
+ H_(TOST(k),TOST(k-1)) = -H_(TOST(k),TOST(k-1));
}
p = p + s;
x = p / s;
@@ -851,42 +855,42 @@ class EigenValue
for (int j = k; j < nn; j++)
{
- p = H_(k,j) + q * H_(k+1,j);
+ p = H_(TOST(k),TOST(j)) + q * H_(TOST(k+1),TOST(j));
if (notlast)
{
- p = p + r * H_(k+2,j);
- H_(k+2,j) = H_(k+2,j) - p * z;
+ p = p + r * H_(TOST(k+2),TOST(j));
+ H_(TOST(k+2),TOST(j)) = H_(TOST(k+2),TOST(j)) - p * z;
}
- H_(k,j) = H_(k,j) - p * x;
- H_(k+1,j) = H_(k+1,j) - p * y;
+ H_(TOST(k),TOST(j)) = H_(TOST(k),TOST(j)) - p * x;
+ H_(TOST(k+1),TOST(j)) = H_(TOST(k+1),TOST(j)) - p * y;
}
// Column modification
for (int i = 0; i <= std::min(n,k+3); i++)
{
- p = x * H_(i,k) + y * H_(i,k+1);
+ p = x * H_(TOST(i),TOST(k)) + y * H_(TOST(i),TOST(k+1));
if (notlast)
{
- p = p + z * H_(i,k+2);
- H_(i,k+2) = H_(i,k+2) - p * r;
+ p = p + z * H_(TOST(i),TOST(k+2));
+ H_(TOST(i),TOST(k+2)) = H_(TOST(i),TOST(k+2)) - p * r;
}
- H_(i,k) = H_(i,k) - p;
- H_(i,k+1) = H_(i,k+1) - p * q;
+ H_(TOST(i),TOST(k)) = H_(TOST(i),TOST(k)) - p;
+ H_(TOST(i),TOST(k+1)) = H_(TOST(i),TOST(k+1)) - p * q;
}
// Accumulate transformations
for (int i = low; i <= high; i++)
{
- p = x * V_(i,k) + y * V_(i,k+1);
+ p = x * V_(TOST(i),TOST(k)) + y * V_(TOST(i),TOST(k+1));
if (notlast)
{
- p = p + z * V_(i,k+2);
- V_(i,k+2) = V_(i,k+2) - p * r;
+ p = p + z * V_(TOST(i),TOST(k+2));
+ V_(TOST(i),TOST(k+2)) = V_(TOST(i),TOST(k+2)) - p * r;
}
- V_(i,k) = V_(i,k) - p;
- V_(i,k+1) = V_(i,k+1) - p * q;
+ V_(TOST(i),TOST(k)) = V_(TOST(i),TOST(k)) - p;
+ V_(TOST(i),TOST(k+1)) = V_(TOST(i),TOST(k+1)) - p * q;
}
} // (s != 0)
} // k loop
@@ -902,24 +906,24 @@ class EigenValue
for (n = nn-1; n >= 0; n--)
{
- p = d_[n];
- q = e_[n];
+ p = d_[TOST(n)];
+ q = e_[TOST(n)];
// Real vector
if (q == 0)
{
int l = n;
- H_(n,n) = 1.0;
+ H_(TOST(n),TOST(n)) = 1.0;
for (int i = n-1; i >= 0; i--)
{
- w = H_(i,i) - p;
+ w = H_(TOST(i),TOST(i)) - p;
r = 0.0;
for (int j = l; j <= n; j++)
{
- r = r + H_(i,j) * H_(j,n);
+ r = r + H_(TOST(i),TOST(j)) * H_(TOST(j),TOST(n));
}
- if (e_[i] < 0.0)
+ if (e_[TOST(i)] < 0.0)
{
z = w;
s = r;
@@ -927,15 +931,15 @@ class EigenValue
else
{
l = i;
- if (e_[i] == 0.0)
+ if (e_[TOST(i)] == 0.0)
{
if (w != 0.0)
{
- H_(i,n) = -r / w;
+ H_(TOST(i),TOST(n)) = -r / w;
}
else
{
- H_(i,n) = -r / (eps * norm);
+ H_(TOST(i),TOST(n)) = -r / (eps * norm);
}
// Solve real equations
@@ -943,29 +947,29 @@ class EigenValue
}
else
{
- x = H_(i,i+1);
- y = H_(i+1,i);
- q = (d_[i] - p) * (d_[i] - p) + e_[i] * e_[i];
+ x = H_(TOST(i),TOST(i+1));
+ y = H_(TOST(i+1),TOST(i));
+ q = (d_[TOST(i)] - p) * (d_[TOST(i)] - p) + e_[TOST(i)] * e_[TOST(i)];
t = (x * s - z * r) / q;
- H_(i,n) = t;
+ H_(TOST(i),TOST(n)) = t;
if (NumTools::abs<Real>(x) > NumTools::abs<Real>(z))
{
- H_(i+1,n) = (-r - w * t) / x;
+ H_(TOST(i+1),TOST(n)) = (-r - w * t) / x;
}
else
{
- H_(i+1,n) = (-s - y * t) / z;
+ H_(TOST(i+1),TOST(n)) = (-s - y * t) / z;
}
}
// Overflow control
- t = NumTools::abs<Real>(H_(i,n));
+ t = NumTools::abs<Real>(H_(TOST(i),TOST(n)));
if ((eps * t) * t > 1)
{
for (int j = i; j <= n; j++)
{
- H_(j,n) = H_(j,n) / t;
+ H_(TOST(j),TOST(n)) = H_(TOST(j),TOST(n)) / t;
}
}
}
@@ -980,19 +984,19 @@ class EigenValue
// Last vector component imaginary so matrix is triangular
- if (NumTools::abs<Real>(H_(n,n-1)) > NumTools::abs<Real>(H_(n-1,n)))
+ if (NumTools::abs<Real>(H_(TOST(n),TOST(n-1))) > NumTools::abs<Real>(H_(TOST(n-1),TOST(n))))
{
- H_(n-1,n-1) = q / H_(n,n-1);
- H_(n-1,n) = -(H_(n,n) - p) / H_(n,n-1);
+ H_(TOST(n-1),TOST(n-1)) = q / H_(TOST(n),TOST(n-1));
+ H_(TOST(n-1),TOST(n)) = -(H_(TOST(n),TOST(n)) - p) / H_(TOST(n),TOST(n-1));
}
else
{
- cdiv(0.0,-H_(n-1,n),H_(n-1,n-1)-p,q);
- H_(n-1,n-1) = cdivr;
- H_(n-1,n) = cdivi;
+ cdiv(0.0,-H_(TOST(n-1),TOST(n)),H_(TOST(n-1),TOST(n-1))-p,q);
+ H_(TOST(n-1),TOST(n-1)) = cdivr;
+ H_(TOST(n-1),TOST(n)) = cdivi;
}
- H_(n,n-1) = 0.0;
- H_(n,n) = 1.0;
+ H_(TOST(n),TOST(n-1)) = 0.0;
+ H_(TOST(n),TOST(n)) = 1.0;
for (int i = n-2; i >= 0; i--)
{
Real ra,sa,vr,vi;
@@ -1000,12 +1004,12 @@ class EigenValue
sa = 0.0;
for (int j = l; j <= n; j++)
{
- ra = ra + H_(i,j) * H_(j,n-1);
- sa = sa + H_(i,j) * H_(j,n);
+ ra = ra + H_(TOST(i),TOST(j)) * H_(TOST(j),TOST(n-1));
+ sa = sa + H_(TOST(i),TOST(j)) * H_(TOST(j),TOST(n));
}
- w = H_(i,i) - p;
+ w = H_(TOST(i),TOST(i)) - p;
- if (e_[i] < 0.0)
+ if (e_[TOST(i)] < 0.0)
{
z = w;
r = ra;
@@ -1014,49 +1018,49 @@ class EigenValue
else
{
l = i;
- if (e_[i] == 0)
+ if (e_[TOST(i)] == 0)
{
cdiv(-ra,-sa,w,q);
- H_(i,n-1) = cdivr;
- H_(i,n) = cdivi;
+ H_(TOST(i),TOST(n-1)) = cdivr;
+ H_(TOST(i),TOST(n)) = cdivi;
}
else
{
// Solve complex equations
- x = H_(i,i+1);
- y = H_(i+1,i);
- vr = (d_[i] - p) * (d_[i] - p) + e_[i] * e_[i] - q * q;
- vi = (d_[i] - p) * 2.0 * q;
+ x = H_(TOST(i),TOST(i+1));
+ y = H_(TOST(i+1),TOST(i));
+ vr = (d_[TOST(i)] - p) * (d_[TOST(i)] - p) + e_[TOST(i)] * e_[TOST(i)] - q * q;
+ vi = (d_[TOST(i)] - p) * 2.0 * q;
if ((vr == 0.0) && (vi == 0.0))
{
vr = eps * norm * (NumTools::abs<Real>(w) + NumTools::abs<Real>(q) +
NumTools::abs<Real>(x) + NumTools::abs<Real>(y) + NumTools::abs<Real>(z));
}
cdiv(x*r-z*ra+q*sa,x*s-z*sa-q*ra,vr,vi);
- H_(i,n-1) = cdivr;
- H_(i,n) = cdivi;
+ H_(TOST(i),TOST(n-1)) = cdivr;
+ H_(TOST(i),TOST(n)) = cdivi;
if (NumTools::abs<Real>(x) > (NumTools::abs<Real>(z) + NumTools::abs<Real>(q)))
{
- H_(i+1,n-1) = (-ra - w * H_(i,n-1) + q * H_(i,n)) / x;
- H_(i+1,n) = (-sa - w * H_(i,n) - q * H_(i,n-1)) / x;
+ H_(TOST(i+1),TOST(n-1)) = (-ra - w * H_(TOST(i),TOST(n-1)) + q * H_(TOST(i),TOST(n))) / x;
+ H_(TOST(i+1),TOST(n)) = (-sa - w * H_(TOST(i),TOST(n)) - q * H_(TOST(i),TOST(n-1))) / x;
}
else
{
- cdiv(-r-y*H_(i,n-1),-s-y*H_(i,n),z,q);
- H_(i+1,n-1) = cdivr;
- H_(i+1,n) = cdivi;
+ cdiv(-r-y*H_(TOST(i),TOST(n-1)),-s-y*H_(TOST(i),TOST(n)),z,q);
+ H_(TOST(i+1),TOST(n-1)) = cdivr;
+ H_(TOST(i+1),TOST(n)) = cdivi;
}
}
// Overflow control
- t = std::max(NumTools::abs<Real>(H_(i,n-1)),NumTools::abs<Real>(H_(i,n)));
+ t = std::max(NumTools::abs<Real>(H_(TOST(i),TOST(n-1))),NumTools::abs<Real>(H_(TOST(i),TOST(n))));
if ((eps * t) * t > 1)
{
for (int j = i; j <= n; j++)
{
- H_(j,n-1) = H_(j,n-1) / t;
- H_(j,n) = H_(j,n) / t;
+ H_(TOST(j),TOST(n-1)) = H_(TOST(j),TOST(n-1)) / t;
+ H_(TOST(j),TOST(n)) = H_(TOST(j),TOST(n)) / t;
}
}
}
@@ -1072,7 +1076,7 @@ class EigenValue
{
for (int j = i; j < nn; j++)
{
- V_(i,j) = H_(i,j);
+ V_(TOST(i),TOST(j)) = H_(TOST(i),TOST(j));
}
}
}
@@ -1086,9 +1090,9 @@ class EigenValue
z = 0.0;
for (int k = low; k <= std::min(j,high); k++)
{
- z = z + V_(i,k) * H_(k,j);
+ z = z + V_(TOST(i),TOST(k)) * H_(TOST(k),TOST(j));
}
- V_(i,j) = z;
+ V_(TOST(i),TOST(j)) = z;
}
}
}
diff --git a/src/Bpp/Numeric/Matrix/Matrix.h b/src/Bpp/Numeric/Matrix/Matrix.h
index 42d2f32..dac0a53 100644
--- a/src/Bpp/Numeric/Matrix/Matrix.h
+++ b/src/Bpp/Numeric/Matrix/Matrix.h
@@ -63,12 +63,14 @@ public:
virtual ~Matrix() {}
public:
+
/**
* @return \f$m_{i,j}\f$.
* @param i row index.
* @param j column index.
*/
virtual const Scalar& operator()(size_t i, size_t j) const = 0;
+
/**
* @return \f$m_{i,j}\f$.
* @param i row index.
@@ -116,6 +118,7 @@ public:
virtual void resize(size_t nRows, size_t nCols) = 0;
};
+
/**
* @brief Matrix storage by row.
*
@@ -190,6 +193,11 @@ public:
return r;
}
+ const std::vector<Scalar>& getRow(size_t i) const
+ {
+ return m_[i];
+ }
+
std::vector<Scalar> col(size_t j) const
{
std::vector<Scalar> c(getNumberOfRows());
@@ -208,12 +216,116 @@ public:
void addRow(const std::vector<Scalar>& newRow) throw (DimensionException)
{
- if (newRow.size() != getNumberOfColumns()) throw DimensionException("RowMatrix::addRow: invalid row dimension", newRow.size(), getNumberOfColumns());
+ if (getNumberOfColumns()!=0 && newRow.size() != getNumberOfColumns())
+ throw DimensionException("RowMatrix::addRow: invalid row dimension", newRow.size(), getNumberOfColumns());
m_.push_back(newRow);
}
};
/**
+ * @brief Matrix storage by column.
+ *
+ * This matrix is a vector of vector of Scalar.
+ * Column access is in \f$O(1)\f$ while row access is in \f$O(nCol)\f$.
+ */
+ template<class Scalar>
+ class ColMatrix :
+ public Matrix<Scalar>
+ {
+ private:
+ std::vector< std::vector<Scalar> > m_;
+
+ public:
+ ColMatrix() : m_() {}
+
+ ColMatrix(size_t nRow, size_t nCol) : m_(nCol)
+ {
+ for (size_t i = 0; i < nCol; i++)
+ {
+ m_[i].resize(nRow);
+ }
+ }
+
+ ColMatrix(const Matrix<Scalar>& m) : m_(m.getNumberOfColumns())
+ {
+ size_t nr = m.getNumberOfRows();
+ size_t nc = m.getNumberOfColumns();
+ for (size_t i = 0; i < nc; i++)
+ {
+ m_[i].resize(nr);
+ for (size_t j = 0; j < nr; j++)
+ {
+ m_[i][j] = m(j, i);
+ }
+ }
+ }
+
+ ColMatrix& operator=(const Matrix<Scalar>& m)
+ {
+ size_t nc = m.getNumberOfColumns();
+ m_.resize(nc);
+ size_t nr = m.getNumberOfRows();
+ for (size_t i = 0; i < nc; i++)
+ {
+ m_[i].resize(nr);
+ for (size_t j = 0; j < nr; j++)
+ {
+ m_[i][j] = m(j, i);
+ }
+ }
+ return *this;
+ }
+
+ virtual ~ColMatrix() {}
+
+ public:
+ ColMatrix* clone() const { return new ColMatrix(*this); }
+
+ const Scalar& operator()(size_t i, size_t j) const { return m_[j][i]; }
+
+ Scalar& operator()(size_t i, size_t j) { return m_[j][i]; }
+
+ size_t getNumberOfColumns() const { return m_.size(); }
+
+ size_t getNumberOfRows() const { return m_.size() == 0 ? 0 : m_[0].size(); }
+
+ std::vector<Scalar> row(size_t i) const
+ {
+ std::vector<Scalar> r(getNumberOfColumns());
+ for (size_t j = 0; j < getNumberOfColumns(); j++) { r[j] = operator()(i, j); }
+ return r;
+ }
+
+ const std::vector<Scalar>& getCol(size_t i) const
+ {
+ return m_[i];
+ }
+
+ std::vector<Scalar> col(size_t j) const
+ {
+ std::vector<Scalar> c(getNumberOfRows());
+ for (size_t i = 0; i < getNumberOfRows(); i++) { c[i] = operator()(i, j); }
+ return c;
+ }
+
+ void resize(size_t nRows, size_t nCols)
+ {
+ m_.resize(nCols);
+ for (size_t i = 0; i < nCols; i++)
+ {
+ m_[i].resize(nRows);
+ }
+ }
+
+ void addCol(const std::vector<Scalar>& newCol) throw (DimensionException)
+ {
+ if (getNumberOfRows()!=0 && newCol.size() != getNumberOfRows())
+ throw DimensionException("ColMatrix::addCol: invalid column dimension", newCol.size(), getNumberOfRows());
+ m_.push_back(newCol);
+ }
+ };
+
+/**
* @brief Matrix storage in one vector.
*
* This Matrix is a simple vector of Scalar of size n x m.
diff --git a/src/Bpp/Numeric/Matrix/MatrixTools.h b/src/Bpp/Numeric/Matrix/MatrixTools.h
index b1a62e8..c988f29 100644
--- a/src/Bpp/Numeric/Matrix/MatrixTools.h
+++ b/src/Bpp/Numeric/Matrix/MatrixTools.h
@@ -5,37 +5,37 @@
//
/*
- Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
-
- This software is a computer program whose purpose is to provide classes
- for numerical calculus. This file is part of the Bio++ project.
-
- This software is governed by the CeCILL license under French law and
- abiding by the rules of distribution of free software. You can use,
- modify and/ or redistribute the software under the terms of the CeCILL
- license as circulated by CEA, CNRS and INRIA at the following URL
- "http://www.cecill.info".
-
- As a counterpart to the access to the source code and rights to copy,
- modify and redistribute granted by the license, users are provided only
- with a limited warranty and the software's author, the holder of the
- economic rights, and the successive licensors have only limited
- liability.
-
- In this respect, the user's attention is drawn to the risks associated
- with loading, using, modifying and/or developing or reproducing the
- software by the user in light of its specific status of free software,
- that may mean that it is complicated to manipulate, and that also
- therefore means that it is reserved for developers and experienced
- professionals having in-depth computer knowledge. Users are therefore
- encouraged to load and test the software's suitability as regards their
- requirements in conditions enabling the security of their systems and/or
- data to be ensured and, more generally, to use and operate it in the
- same conditions as regards security.
-
- The fact that you are presently reading this means that you have had
- knowledge of the CeCILL license and that you accept its terms.
- */
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for numerical calculus. This file is part of the Bio++ project.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
#ifndef _MATRIXTOOLS_H_
#define _MATRIXTOOLS_H_
@@ -44,6 +44,7 @@
#include "Matrix.h"
#include "LUDecomposition.h"
#include "EigenValue.h"
+#include "../../Io/OutputStream.h"
#include <cstdio>
#include <iostream>
@@ -53,1162 +54,1191 @@ namespace bpp
/**
* @brief Functions dealing with matrices.
*/
-class MatrixTools
-{
-public:
- MatrixTools() {}
- ~MatrixTools() {}
-
-public:
- /**
- * @brief Copy operation. This function supplies the lack of inheritence of the assigment operator :D .
- *
- * @param A [in] Original matrix.
- * @param O [out] A copy of the given matrix.
- */
- template<class MatrixA, class MatrixO>
- static void copy(const MatrixA& A, MatrixO& O)
+ class MatrixTools
{
- O.resize(A.getNumberOfRows(), A.getNumberOfColumns());
- for (size_t i = 0; i < A.getNumberOfRows(); i++)
+ public:
+ MatrixTools() {}
+ ~MatrixTools() {}
+
+ public:
+ /**
+ * @brief Copy operation. This function supplies the lack of inheritence of the assigment operator :D .
+ *
+ * @param A [in] Original matrix.
+ * @param O [out] A copy of the given matrix.
+ */
+ template<class MatrixA, class MatrixO>
+ static void copy(const MatrixA& A, MatrixO& O)
{
- for (size_t j = 0; j < A.getNumberOfColumns(); j++)
+ O.resize(A.getNumberOfRows(), A.getNumberOfColumns());
+ for (size_t i = 0; i < A.getNumberOfRows(); i++)
{
- O(i, j) = A(i, j);
+ for (size_t j = 0; j < A.getNumberOfColumns(); j++)
+ {
+ O(i, j) = A(i, j);
+ }
}
}
- }
-
- /**
- * @brief Get a identity matrix of a given size.
- *
- * @param n the size of the matrix.
- * @param O [out] A identity matrix of size n.
- */
- template<class Matrix>
- static void getId(size_t n, Matrix& O)
- {
- O.resize(n, n);
- for (size_t i = 0; i < n; i++)
+
+ /**
+ * @brief Get a identity matrix of a given size.
+ *
+ * @param n the size of the matrix.
+ * @param O [out] A identity matrix of size n.
+ */
+ template<class Matrix>
+ static void getId(size_t n, Matrix& O)
{
- for (size_t j = 0; j < n; j++) {
- O(i, j) = (i == j) ? 1 : 0;
+ O.resize(n, n);
+ for (size_t i = 0; i < n; i++)
+ {
+ for (size_t j = 0; j < n; j++) {
+ O(i, j) = (i == j) ? 1 : 0;
+ }
}
}
- }
-
- /**
- * @param D [in] A vector of diagonal elements.
- * @param O [out] A diagonal matrix with diagonal elements taken from a vector.
- */
- template<class Scalar>
- static void diag(const std::vector<Scalar>& D, Matrix<Scalar>& O)
- {
- size_t n = D.size();
- O.resize(n, n);
- for (size_t i = 0; i < n; i++)
+
+ /**
+ * @param D [in] A vector of diagonal elements.
+ * @param O [out] A diagonal matrix with diagonal elements taken from a vector.
+ */
+ template<class Scalar>
+ static void diag(const std::vector<Scalar>& D, Matrix<Scalar>& O)
{
- for (size_t j = 0; j < n; j++) { O(i, j) = (i == j) ? D[i] : 0;}
+ size_t n = D.size();
+ O.resize(n, n);
+ for (size_t i = 0; i < n; i++)
+ {
+ for (size_t j = 0; j < n; j++) { O(i, j) = (i == j) ? D[i] : 0;}
+ }
}
- }
-
- /**
- * @param x [in] A scalar
- * @param n [in] the dimension of the output matrix
- * @param O [out] A diagonal matrix with diagonal elements equal to x
- */
- template<class Scalar>
- static void diag(const Scalar x, size_t n, Matrix<Scalar>& O)
- {
- O.resize(n, n);
- for (size_t i = 0; i < n; i++)
+
+ /**
+ * @param x [in] A scalar
+ * @param n [in] the dimension of the output matrix
+ * @param O [out] A diagonal matrix with diagonal elements equal to x
+ */
+ template<class Scalar>
+ static void diag(const Scalar x, size_t n, Matrix<Scalar>& O)
+ {
+ O.resize(n, n);
+ for (size_t i = 0; i < n; i++)
{
for (size_t j = 0; j < n; j++) { O(i, j) = (i == j) ? x : 0;}
}
- }
-
- /**
- * @param M [in] The matrix.
- * @param O [out] The diagonal elements of a square matrix as a vector.
- * @throw DimensionException If M is not a square matrix.
- */
- template<class Scalar>
- static void diag(const Matrix<Scalar>& M, std::vector<Scalar>& O) throw (DimensionException)
- {
- size_t nc = M.getNumberOfColumns();
- size_t nr = M.getNumberOfRows();
- if (nc != nr) throw DimensionException("MatrixTools::diag(). M must be a square matrix.", nr, nc);
- O.resize(nc);
- for (size_t i = 0; i < nc; i++) { O[i] = M(i, i);}
- }
-
- /**
- * @brief Set all elements in M to value x.
- * @param M A matrix.
- * @param x The value to use.
- */
- template<class Matrix, class Scalar>
- static void fill(Matrix& M, Scalar x)
- {
- for (size_t i = 0; i < M.getNumberOfRows(); i++)
+ }
+
+ /**
+ * @param M [in] The matrix.
+ * @param O [out] The diagonal elements of a square matrix as a vector.
+ * @throw DimensionException If M is not a square matrix.
+ */
+ template<class Scalar>
+ static void diag(const Matrix<Scalar>& M, std::vector<Scalar>& O) throw (DimensionException)
{
- for (size_t j = 0; j < M.getNumberOfColumns(); j++)
+ size_t nc = M.getNumberOfColumns();
+ size_t nr = M.getNumberOfRows();
+ if (nc != nr) throw DimensionException("MatrixTools::diag(). M must be a square matrix.", nr, nc);
+ O.resize(nc);
+ for (size_t i = 0; i < nc; i++) { O[i] = M(i, i);}
+ }
+
+ /**
+ * @brief Set all elements in M to value x.
+ * @param M A matrix.
+ * @param x The value to use.
+ */
+ template<class Matrix, class Scalar>
+ static void fill(Matrix& M, Scalar x)
+ {
+ for (size_t i = 0; i < M.getNumberOfRows(); i++)
{
- M(i, j) = x;
+ for (size_t j = 0; j < M.getNumberOfColumns(); j++)
+ {
+ M(i, j) = x;
+ }
}
}
- }
-
- /**
- * @brief Multiply all elements of a matrix by a given value, and add a constant.
- *
- * Performs \f$\forall i \forall j m_{i,j} = a.m_{i,j}+b\f$.
- *
- * @param A A matrix.
- * @param a Multiplicator.
- * @param b Constant.
- */
- template<class Matrix, class Scalar>
- static void scale(Matrix& A, Scalar a, Scalar b = 0)
- {
- for (size_t i = 0; i < A.getNumberOfRows(); i++)
+
+ /**
+ * @brief Multiply all elements of a matrix by a given value, and add a constant.
+ *
+ * Performs \f$\forall i \forall j m_{i,j} = a.m_{i,j}+b\f$.
+ *
+ * @param A A matrix.
+ * @param a Multiplicator.
+ * @param b Constant.
+ */
+ template<class Matrix, class Scalar>
+ static void scale(Matrix& A, Scalar a, Scalar b = 0)
{
- for (size_t j = 0; j < A.getNumberOfColumns(); j++)
+ for (size_t i = 0; i < A.getNumberOfRows(); i++)
{
- A(i, j) = a * A(i, j) + b;
+ for (size_t j = 0; j < A.getNumberOfColumns(); j++)
+ {
+ A(i, j) = a * A(i, j) + b;
+ }
}
}
- }
-
- /**
- * @param A [in] First matrix.
- * @param B [in] Second matrix.
- * @param O [out] The dot product of two matrices.
- */
- template<class Scalar>
- static void mult(const Matrix<Scalar>& A, const Matrix<Scalar>& B, Matrix<Scalar>& O) throw (DimensionException)
- {
- size_t ncA = A.getNumberOfColumns();
- size_t nrA = A.getNumberOfRows();
- size_t nrB = B.getNumberOfRows();
- size_t ncB = B.getNumberOfColumns();
- if (ncA != nrB) throw DimensionException("MatrixTools::mult(). nrows B != ncols A.", nrB, ncA);
- O.resize(nrA, ncB);
- for (size_t i = 0; i < nrA; i++)
+
+ /**
+ * @param A [in] First matrix.
+ * @param B [in] Second matrix.
+ * @param O [out] The dot product of two matrices.
+ */
+ template<class Scalar>
+ static void mult(const Matrix<Scalar>& A, const Matrix<Scalar>& B, Matrix<Scalar>& O) throw (DimensionException)
{
- for (size_t j = 0; j < ncB; j++)
+ size_t ncA = A.getNumberOfColumns();
+ size_t nrA = A.getNumberOfRows();
+ size_t nrB = B.getNumberOfRows();
+ size_t ncB = B.getNumberOfColumns();
+ if (ncA != nrB) throw DimensionException("MatrixTools::mult(). nrows B != ncols A.", nrB, ncA);
+ O.resize(nrA, ncB);
+ for (size_t i = 0; i < nrA; i++)
{
- O(i, j) = 0;
- for (size_t k = 0; k < ncA; k++)
+ for (size_t j = 0; j < ncB; j++)
{
- O(i, j) += A(i, k) * B(k, j);
+ O(i, j) = 0;
+ for (size_t k = 0; k < ncA; k++)
+ {
+ O(i, j) += A(i, k) * B(k, j);
+ }
}
}
}
- }
-
- /**
- * @brief Compute A . D . B where D is a diagonal matrix in O(n^3).
- *
- * Since D is a diagonal matrix, this function is more efficient than doing
- * mult(mult(A, diag(D)), B), which involves two 0(n^3) operations.
- *
- * @param A [in] The first matrix.
- * @param D [in] The diagonal matrix (only diagonal elements in a vector)
- * @param B [in] The second matrix.
- * @param O [out] The result matrix.
- * @throw DimensionException If matrices have not the appropriate size.
- */
- template<class Scalar>
- static void mult(const Matrix<Scalar>& A, const std::vector<Scalar>& D, const Matrix<Scalar>& B, Matrix<Scalar>& O) throw (DimensionException)
- {
- size_t ncA = A.getNumberOfColumns();
- size_t nrA = A.getNumberOfRows();
- size_t nrB = B.getNumberOfRows();
- size_t ncB = B.getNumberOfColumns();
- if (ncA != nrB) throw DimensionException("MatrixTools::mult(). nrows B != ncols A.", nrB, ncA);
- if (ncA != D.size()) throw DimensionException("MatrixTools::mult(). Vector size is not equal to matrix size.", D.size(), ncA);
- O.resize(nrA, ncB);
- for (size_t i = 0; i < nrA; i++)
+
+ /**
+ * @brief Compute A . D . B where D is a diagonal matrix in O(n^3).
+ *
+ * Since D is a diagonal matrix, this function is more efficient than doing
+ * mult(mult(A, diag(D)), B), which involves two 0(n^3) operations.
+ *
+ * @param A [in] The first matrix.
+ * @param D [in] The diagonal matrix (only diagonal elements in a vector)
+ * @param B [in] The second matrix.
+ * @param O [out] The result matrix.
+ * @throw DimensionException If matrices have not the appropriate size.
+ */
+ template<class Scalar>
+ static void mult(const Matrix<Scalar>& A, const std::vector<Scalar>& D, const Matrix<Scalar>& B, Matrix<Scalar>& O) throw (DimensionException)
{
- for (size_t j = 0; j < ncB; j++)
+ size_t ncA = A.getNumberOfColumns();
+ size_t nrA = A.getNumberOfRows();
+ size_t nrB = B.getNumberOfRows();
+ size_t ncB = B.getNumberOfColumns();
+ if (ncA != nrB) throw DimensionException("MatrixTools::mult(). nrows B != ncols A.", nrB, ncA);
+ if (ncA != D.size()) throw DimensionException("MatrixTools::mult(). Vector size is not equal to matrix size.", D.size(), ncA);
+ O.resize(nrA, ncB);
+ for (size_t i = 0; i < nrA; i++)
{
- O(i, j) = 0;
- for (size_t k = 0; k < ncA; k++)
+ for (size_t j = 0; j < ncB; j++)
{
- O(i, j) += A(i, k) * B(k, j) * D[k];
+ O(i, j) = 0;
+ for (size_t k = 0; k < ncA; k++)
+ {
+ O(i, j) += A(i, k) * B(k, j) * D[k];
+ }
}
}
}
- }
-
- /**
- * @brief Compute A . (U+D+L) . B where D is a diagonal matrix, U
- * (resp. L) is a matrix in which the only non-zero terms are on the
- * diagonal that is over (resp. under) the main diagonal, in O(n^3).
- *
- * Since D is a diagonal matrix, this function is more efficient than doing
- * mult(mult(A, diag(D)), B), which involves two 0(n^3) operations.
- *
- * @param A [in] The first matrix.
- * @param D [in] The diagonal matrix (only diagonal elements in a vector)
- * @param U [in] The upper diagonal matrix (only upper diagonal elements in a vector)
- * @param L [in] The lower diagonal matrix (only lower diagonal elements in a vector)
- * @param B [in] The second matrix.
- * @param O [out] The result matrix.
- * @throw DimensionException If matrices have not the appropriate size.
- */
- template<class Scalar>
- static void mult(const Matrix<Scalar>& A, const std::vector<Scalar>& D, const std::vector<Scalar>& U, const std::vector<Scalar>& L, const Matrix<Scalar>& B, Matrix<Scalar>& O) throw (DimensionException)
- {
- size_t ncA = A.getNumberOfColumns();
- size_t nrA = A.getNumberOfRows();
- size_t nrB = B.getNumberOfRows();
- size_t ncB = B.getNumberOfColumns();
- if (ncA != nrB) throw DimensionException("MatrixTools::mult(). nrows B != ncols A.", nrB, ncA);
- if (ncA != D.size()) throw DimensionException("MatrixTools::mult(). Vector size is not equal to matrix size.", D.size(), ncA);
- if (ncA != U.size()+1) throw DimensionException("MatrixTools::mult(). Vector size is not equal to matrix size-1.", U.size(), ncA);
- if (ncA != L.size()+1) throw DimensionException("MatrixTools::mult(). Vector size is not equal to matrix size-1.", L.size(), ncA);
- O.resize(nrA, ncB);
- for (size_t i = 0; i < nrA; i++)
+
+ /**
+ * @brief Compute A . (U+D+L) . B where D is a diagonal matrix, U
+ * (resp. L) is a matrix in which the only non-zero terms are on the
+ * diagonal that is over (resp. under) the main diagonal, in O(n^3).
+ *
+ * Since D is a diagonal matrix, this function is more efficient than doing
+ * mult(mult(A, diag(D)), B), which involves two 0(n^3) operations.
+ *
+ * @param A [in] The first matrix.
+ * @param D [in] The diagonal matrix (only diagonal elements in a vector)
+ * @param U [in] The upper diagonal matrix (only upper diagonal elements in a vector)
+ * @param L [in] The lower diagonal matrix (only lower diagonal elements in a vector)
+ * @param B [in] The second matrix.
+ * @param O [out] The result matrix.
+ * @throw DimensionException If matrices have not the appropriate size.
+ */
+ template<class Scalar>
+ static void mult(const Matrix<Scalar>& A, const std::vector<Scalar>& D, const std::vector<Scalar>& U, const std::vector<Scalar>& L, const Matrix<Scalar>& B, Matrix<Scalar>& O) throw (DimensionException)
+ {
+ size_t ncA = A.getNumberOfColumns();
+ size_t nrA = A.getNumberOfRows();
+ size_t nrB = B.getNumberOfRows();
+ size_t ncB = B.getNumberOfColumns();
+ if (ncA != nrB) throw DimensionException("MatrixTools::mult(). nrows B != ncols A.", nrB, ncA);
+ if (ncA != D.size()) throw DimensionException("MatrixTools::mult(). Vector size is not equal to matrix size.", D.size(), ncA);
+ if (ncA != U.size()+1) throw DimensionException("MatrixTools::mult(). Vector size is not equal to matrix size-1.", U.size(), ncA);
+ if (ncA != L.size()+1) throw DimensionException("MatrixTools::mult(). Vector size is not equal to matrix size-1.", L.size(), ncA);
+ O.resize(nrA, ncB);
+ for (size_t i = 0; i < nrA; i++)
{
for (size_t j = 0; j < ncB; j++)
+ {
+ O(i, j) = A(i, 0) * D[0] * B(0, j);
+ if (nrB>1)
+ O(i, j) += A(i,0) * U[0] * B(1,j);
+ for (size_t k = 1; k < ncA-1; k++)
{
- O(i, j) = A(i, 0) * D[0] * B(0, j);
- if (nrB>1)
- O(i, j) += A(i,0) * U[0] * B(1,j);
- for (size_t k = 1; k < ncA-1; k++)
- {
- O(i, j) += A(i, k) * (L[k-1] * B(k-1, j) + D[k] * B(k, j) + U[k] * B(k+1,j));
- }
- if (ncA>=2)
- O(i, j) += A(i, ncA-1) * L[ncA-2] * B(ncA-2, j);
- O(i,j) += A(i, ncA-1) * D[ncA-1] * B(ncA-1, j);
+ O(i, j) += A(i, k) * (L[k-1] * B(k-1, j) + D[k] * B(k, j) + U[k] * B(k+1,j));
}
+ if (ncA>=2)
+ O(i, j) += A(i, ncA-1) * L[ncA-2] * B(ncA-2, j);
+ O(i,j) += A(i, ncA-1) * D[ncA-1] * B(ncA-1, j);
+ }
}
- }
-
- /**
- * @brief Add matrix B to matrix A.
- *
- * @param A [in] Matrix A
- * @param B [in] Matrix B
- * @throw DimensionException If A and B have note the same size.
- */
- template<class MatrixA, class MatrixB>
- static void add(MatrixA& A, const MatrixB& B) throw (DimensionException)
- {
- size_t ncA = A.getNumberOfColumns();
- size_t nrA = A.getNumberOfRows();
- size_t nrB = B.getNumberOfRows();
- size_t ncB = B.getNumberOfColumns();
- if (ncA != ncB) throw DimensionException("MatrixTools::operator+(). A and B must have the same number of colums.", ncB, ncA);
- if (nrA != nrB) throw DimensionException("MatrixTools::operator+(). A and B must have the same number of rows.", nrB, nrA);
- for (size_t i = 0; i < A.getNumberOfRows(); i++)
+ }
+
+ /**
+ * @brief Add matrix B to matrix A.
+ *
+ * @param A [in] Matrix A
+ * @param B [in] Matrix B
+ * @throw DimensionException If A and B have note the same size.
+ */
+ template<class MatrixA, class MatrixB>
+ static void add(MatrixA& A, const MatrixB& B) throw (DimensionException)
{
- for (size_t j = 0; j < A.getNumberOfColumns(); j++)
+ size_t ncA = A.getNumberOfColumns();
+ size_t nrA = A.getNumberOfRows();
+ size_t nrB = B.getNumberOfRows();
+ size_t ncB = B.getNumberOfColumns();
+ if (ncA != ncB) throw DimensionException("MatrixTools::operator+(). A and B must have the same number of colums.", ncB, ncA);
+ if (nrA != nrB) throw DimensionException("MatrixTools::operator+(). A and B must have the same number of rows.", nrB, nrA);
+ for (size_t i = 0; i < A.getNumberOfRows(); i++)
{
- A(i, j) += B(i, j);
+ for (size_t j = 0; j < A.getNumberOfColumns(); j++)
+ {
+ A(i, j) += B(i, j);
+ }
}
}
- }
-
- /**
- * @brief Add matrix x.B to matrix A.
- *
- * @param A [in,out] Matrix A
- * @param x [in] Scalar x
- * @param B [in] Matrix B
- * @throw DimensionException If A and B have note the same size.
- */
- template<class MatrixA, class MatrixB, class Scalar>
- static void add(MatrixA& A, Scalar& x, const MatrixB& B) throw (DimensionException)
- {
- size_t ncA = A.getNumberOfColumns();
- size_t nrA = A.getNumberOfRows();
- size_t nrB = B.getNumberOfRows();
- size_t ncB = B.getNumberOfColumns();
- if (ncA != ncB) throw DimensionException("MatrixTools::operator+(). A and B must have the same number of colums.", ncB, ncA);
- if (nrA != nrB) throw DimensionException("MatrixTools::operator+(). A and B must have the same number of rows.", nrB, nrA);
- for (size_t i = 0; i < A.getNumberOfRows(); i++)
+
+ /**
+ * @brief Add matrix x.B to matrix A.
+ *
+ * @param A [in,out] Matrix A
+ * @param x [in] Scalar x
+ * @param B [in] Matrix B
+ * @throw DimensionException If A and B have note the same size.
+ */
+ template<class MatrixA, class MatrixB, class Scalar>
+ static void add(MatrixA& A, Scalar& x, const MatrixB& B) throw (DimensionException)
+ {
+ size_t ncA = A.getNumberOfColumns();
+ size_t nrA = A.getNumberOfRows();
+ size_t nrB = B.getNumberOfRows();
+ size_t ncB = B.getNumberOfColumns();
+ if (ncA != ncB) throw DimensionException("MatrixTools::operator+(). A and B must have the same number of colums.", ncB, ncA);
+ if (nrA != nrB) throw DimensionException("MatrixTools::operator+(). A and B must have the same number of rows.", nrB, nrA);
+ for (size_t i = 0; i < A.getNumberOfRows(); i++)
{
for (size_t j = 0; j < A.getNumberOfColumns(); j++)
- {
- A(i, j) += x*B(i, j);
- }
- }
- }
-
- /**
- * @brief Compute the power of a given matrix.
- *
- * @param A [in] The matrix.
- * @param p The number of multiplications.
- * @param O [out]\f$ A^p \f$ computed recursively:
- * \f$ A^{2n} = (A^n)^2 \f$
- * \f$ A^{2n+1} = A*(A^n)^2 \f$
- * If p = 0, sends the identity matrix.
- * @throw DimensionException If m is not a square matrix.
- */
- template<class Matrix>
- static void pow(const Matrix& A, size_t p, Matrix& O) throw (DimensionException)
- {
- size_t n = A.getNumberOfRows();
- if (n != A.getNumberOfColumns()) throw DimensionException("MatrixTools::pow(). nrows != ncols.", A.getNumberOfColumns(), A.getNumberOfRows());
- switch(p){
- case 0:
- getId<Matrix>(n, O);
- break;
- case 1:
- copy(A,O);
- break;
- case 2:
- mult(A,A,O);
- break;
- default:
- Matrix tmp;
- if (p%2){
- pow(A,p/2,tmp);
- pow(tmp,2,O);
+ {
+ A(i, j) += x*B(i, j);
+ }
}
- else{
- pow(A,(p-1)/2,tmp);
- pow(tmp,2,O);
- mult(A,O,tmp);
- copy(tmp,O);
+ }
+
+ /**
+ * @brief Compute the power of a given matrix.
+ *
+ * @param A [in] The matrix.
+ * @param p The number of multiplications.
+ * @param O [out]\f$ A^p \f$ computed recursively:
+ * \f$ A^{2n} = (A^n)^2 \f$
+ * \f$ A^{2n+1} = A*(A^n)^2 \f$
+ * If p = 0, sends the identity matrix.
+ * @throw DimensionException If m is not a square matrix.
+ */
+ template<class Matrix>
+ static void pow(const Matrix& A, size_t p, Matrix& O) throw (DimensionException)
+ {
+ size_t n = A.getNumberOfRows();
+ if (n != A.getNumberOfColumns()) throw DimensionException("MatrixTools::pow(). nrows != ncols.", A.getNumberOfColumns(), A.getNumberOfRows());
+ switch(p){
+ case 0:
+ getId<Matrix>(n, O);
+ break;
+ case 1:
+ copy(A,O);
+ break;
+ case 2:
+ mult(A,A,O);
+ break;
+ default:
+ Matrix tmp;
+ if (p%2){
+ pow(A,p/2,tmp);
+ pow(tmp,2,O);
+ }
+ else{
+ pow(A,(p-1)/2,tmp);
+ pow(tmp,2,O);
+ mult(A,O,tmp);
+ copy(tmp,O);
+ }
}
}
- }
-
- /**
- * @brief Compute the power of a given matrix, using eigen value decomposition.
- *
- * @param A [in] The matrix.
- * @param p The power of the matrix.
- * @param O [out]\f$\prod_{i=1}^p m\f$.
- * If p = 0, sends the identity matrix.
- * @throw DimensionException If m is not a square matrix.
- */
- template<class Scalar>
- static void pow(const Matrix<Scalar>& A, double p, Matrix<Scalar>& O) throw (DimensionException)
- {
- size_t n = A.getNumberOfRows();
- if (n != A.getNumberOfColumns()) throw DimensionException("MatrixTools::pow(). nrows != ncols.", A.getNumberOfColumns(), A.getNumberOfRows());
- EigenValue<Scalar> eigen(A);
- RowMatrix<Scalar> rightEV, leftEV;
- rightEV = eigen.getV();
- inv(rightEV, leftEV);
- mult(rightEV, VectorTools::pow(eigen.getRealEigenValues(), p), leftEV, O);
- }
-
- /**
- * @brief Perform matrix exponentiation using diagonalization.
- *
- * @warning This method currently relies only on diagonalization, so it won't work if your matrix is not diagonalizable.
- * The function may be extended later to deal with other cases.
- *
- * @param A [in] The matrix.
- * @param O [out]\f$\prod_{i=1}^p m\f$.
- * @throw DimensionException If m is not a square matrix.
- */
- template<class Scalar>
- static void exp(const Matrix<Scalar>& A, Matrix<Scalar>& O) throw (DimensionException)
- {
- size_t n = A.getNumberOfRows();
- if (n != A.getNumberOfColumns()) throw DimensionException("MatrixTools::exp(). nrows != ncols.", A.getNumberOfColumns(), A.getNumberOfRows());
- EigenValue<Scalar> eigen(A);
- RowMatrix<Scalar> rightEV, leftEV;
- rightEV = eigen.getV();
- inv(rightEV, leftEV);
- mult(rightEV, VectorTools::exp(eigen.getRealEigenValues()), leftEV, O);
- }
-
- /**
- * @brief Compute a vector of the first powers of a given matrix.
- *
- * @param A [in] The matrix.
- * @param p The number of powers.
- * @param vO [out] the vector of the powers (from 0 to p)
- *
- * @throw DimensionException If m is not a square matrix.
- */
+
+ /**
+ * @brief Compute the power of a given matrix, using eigen value decomposition.
+ *
+ * @param A [in] The matrix.
+ * @param p The power of the matrix.
+ * @param O [out]\f$\prod_{i=1}^p m\f$.
+ * If p = 0, sends the identity matrix.
+ * @throw DimensionException If m is not a square matrix.
+ */
+ template<class Scalar>
+ static void pow(const Matrix<Scalar>& A, double p, Matrix<Scalar>& O) throw (DimensionException)
+ {
+ size_t n = A.getNumberOfRows();
+ if (n != A.getNumberOfColumns()) throw DimensionException("MatrixTools::pow(). nrows != ncols.", A.getNumberOfColumns(), A.getNumberOfRows());
+ EigenValue<Scalar> eigen(A);
+ RowMatrix<Scalar> rightEV, leftEV;
+ rightEV = eigen.getV();
+ inv(rightEV, leftEV);
+ mult(rightEV, VectorTools::pow(eigen.getRealEigenValues(), p), leftEV, O);
+ }
+
+ /**
+ * @brief Perform matrix exponentiation using diagonalization.
+ *
+ * @warning This method currently relies only on diagonalization, so it won't work if your matrix is not diagonalizable.
+ * The function may be extended later to deal with other cases.
+ *
+ * @param A [in] The matrix.
+ * @param O [out]\f$\prod_{i=1}^p m\f$.
+ * @throw DimensionException If m is not a square matrix.
+ */
+ template<class Scalar>
+ static void exp(const Matrix<Scalar>& A, Matrix<Scalar>& O) throw (DimensionException)
+ {
+ size_t n = A.getNumberOfRows();
+ if (n != A.getNumberOfColumns()) throw DimensionException("MatrixTools::exp(). nrows != ncols.", A.getNumberOfColumns(), A.getNumberOfRows());
+ EigenValue<Scalar> eigen(A);
+ RowMatrix<Scalar> rightEV, leftEV;
+ rightEV = eigen.getV();
+ inv(rightEV, leftEV);
+ mult(rightEV, VectorTools::exp(eigen.getRealEigenValues()), leftEV, O);
+ }
+
+ /**
+ * @brief Compute a vector of the first powers of a given matrix.
+ *
+ * @param A [in] The matrix.
+ * @param p The number of powers.
+ * @param vO [out] the vector of the powers (from 0 to p)
+ *
+ * @throw DimensionException If m is not a square matrix.
+ */
- template<class Matrix, class Scalar>
- static void Taylor(const Matrix& A, size_t p, std::vector< RowMatrix<Scalar> > & vO) throw (DimensionException)
- {
- size_t n = A.getNumberOfRows();
- if (n != A.getNumberOfColumns())
- throw DimensionException("MatrixTools::pow(). nrows != ncols.", A.getNumberOfColumns(), A.getNumberOfRows());
- vO.resize(p+1);
- getId<Matrix>(n, vO[0]);
- copy(A,vO[1]);
+ template<class Matrix, class Scalar>
+ static void Taylor(const Matrix& A, size_t p, std::vector< RowMatrix<Scalar> > & vO) throw (DimensionException)
+ {
+ size_t n = A.getNumberOfRows();
+ if (n != A.getNumberOfColumns())
+ throw DimensionException("MatrixTools::pow(). nrows != ncols.", A.getNumberOfColumns(), A.getNumberOfRows());
+ vO.resize(p+1);
+ getId<Matrix>(n, vO[0]);
+ copy(A,vO[1]);
- for (size_t i = 1; i < p; i++)
+ for (size_t i = 1; i < p; i++)
{
mult(vO[i], A, vO[i+1]);
}
- }
-
- /**
- * @return The position of the maximum value in the matrix.
- * @param m The matrix.
- */
- template<class Matrix>
- static std::vector<size_t> whichMax(const Matrix& m)
- {
- size_t nrows = m.getNumberOfRows();
- size_t ncols = m.getNumberOfColumns();
- std::vector<size_t> pos(2);
- size_t imax = 0;
- size_t jmax = 0;
- double currentMax = log(0.);
- for (size_t i = 0; i < nrows; i++)
+ }
+
+ /**
+ * @return The position of the maximum value in the matrix.
+ * @param m The matrix.
+ */
+ template<class Matrix>
+ static std::vector<size_t> whichMax(const Matrix& m)
{
- for (size_t j = 0; j < ncols; j++)
+ size_t nrows = m.getNumberOfRows();
+ size_t ncols = m.getNumberOfColumns();
+ std::vector<size_t> pos(2);
+ size_t imax = 0;
+ size_t jmax = 0;
+ double currentMax = log(0.);
+ for (size_t i = 0; i < nrows; i++)
{
- double currentValue = m(i, j);
- // cout << currentValue << "\t" << (currentValue > currentMax) << endl;
- if (currentValue > currentMax)
+ for (size_t j = 0; j < ncols; j++)
{
- imax = i;
- jmax = j;
- currentMax = currentValue;
+ double currentValue = m(i, j);
+ // cout << currentValue << "\t" << (currentValue > currentMax) << endl;
+ if (currentValue > currentMax)
+ {
+ imax = i;
+ jmax = j;
+ currentMax = currentValue;
+ }
}
}
+ pos[0] = imax;
+ pos[1] = jmax;
+ return pos;
}
- pos[0] = imax;
- pos[1] = jmax;
- return pos;
- }
-
- /**
- * @return The position of the minimum value in the matrix.
- * @param m The matrix.
- */
- template<class Matrix>
- static std::vector<size_t> whichMin(const Matrix& m)
- {
- size_t nrows = m.getNumberOfRows();
- size_t ncols = m.getNumberOfColumns();
- std::vector<size_t> pos(2);
- size_t imin = 0;
- size_t jmin = 0;
- double currentMin = -log(0.);
- for (size_t i = 0; i < nrows; i++)
+
+ /**
+ * @return The position of the minimum value in the matrix.
+ * @param m The matrix.
+ */
+ template<class Matrix>
+ static std::vector<size_t> whichMin(const Matrix& m)
{
- for (size_t j = 0; j < ncols; j++)
+ size_t nrows = m.getNumberOfRows();
+ size_t ncols = m.getNumberOfColumns();
+ std::vector<size_t> pos(2);
+ size_t imin = 0;
+ size_t jmin = 0;
+ double currentMin = -log(0.);
+ for (size_t i = 0; i < nrows; i++)
{
- double currentValue = m(i, j);
- if (currentValue < currentMin)
+ for (size_t j = 0; j < ncols; j++)
{
- imin = i;
- jmin = j;
- currentMin = currentValue;
+ double currentValue = m(i, j);
+ if (currentValue < currentMin)
+ {
+ imin = i;
+ jmin = j;
+ currentMin = currentValue;
+ }
}
}
+ pos[0] = imin;
+ pos[1] = jmin;
+ return pos;
}
- pos[0] = imin;
- pos[1] = jmin;
- return pos;
- }
-
- /**
- * @return The maximum value in the matrix.
- * @param m The matrix.
- */
- template<class Real>
- static Real max(const Matrix<Real>& m)
- {
- size_t nrows = m.getNumberOfRows();
- size_t ncols = m.getNumberOfColumns();
- Real currentMax = log(0.);
- for (size_t i = 0; i < nrows; i++)
+
+ /**
+ * @return The maximum value in the matrix.
+ * @param m The matrix.
+ */
+ template<class Real>
+ static Real max(const Matrix<Real>& m)
{
- for (size_t j = 0; j < ncols; j++)
+ size_t nrows = m.getNumberOfRows();
+ size_t ncols = m.getNumberOfColumns();
+ Real currentMax = log(0.);
+ for (size_t i = 0; i < nrows; i++)
{
- Real currentValue = m(i, j);
- // cout << currentValue << "\t" << (currentValue > currentMax) << endl;
- if (currentValue > currentMax)
+ for (size_t j = 0; j < ncols; j++)
{
- currentMax = currentValue;
+ Real currentValue = m(i, j);
+ // cout << currentValue << "\t" << (currentValue > currentMax) << endl;
+ if (currentValue > currentMax)
+ {
+ currentMax = currentValue;
+ }
}
}
+ return currentMax;
}
- return currentMax;
- }
- /**
- * @return The minimum value in the matrix.
- * @param m The matrix.
- */
- template<class Real>
- static Real min(const Matrix<Real>& m)
- {
- size_t nrows = m.getNumberOfRows();
- size_t ncols = m.getNumberOfColumns();
- Real currentMin = -log(0.);
- for (size_t i = 0; i < nrows; i++)
+ /**
+ * @return The minimum value in the matrix.
+ * @param m The matrix.
+ */
+ template<class Real>
+ static Real min(const Matrix<Real>& m)
{
- for (size_t j = 0; j < ncols; j++)
+ size_t nrows = m.getNumberOfRows();
+ size_t ncols = m.getNumberOfColumns();
+ Real currentMin = -log(0.);
+ for (size_t i = 0; i < nrows; i++)
{
- Real currentValue = m(i, j);
- if (currentValue < currentMin)
+ for (size_t j = 0; j < ncols; j++)
{
- currentMin = currentValue;
+ Real currentValue = m(i, j);
+ if (currentValue < currentMin)
+ {
+ currentMin = currentValue;
+ }
}
}
+ return currentMin;
}
- return currentMin;
- }
-
- /**
- * @brief Print a matrix to a stream.
- *
- * @param m The matrix to print.
- * @param out The stream to use.
- */
- template<class Matrix>
- static void print(const Matrix& m, std::ostream& out = std::cout)
- {
- out << m.getNumberOfRows() << "x" << m.getNumberOfColumns() << std::endl;
- out << "[" << std::endl;
- for (size_t i = 0; i < m.getNumberOfRows(); i++)
+
+ /**
+ * @brief Print a matrix to a stream.
+ *
+ * @param m The matrix to print.
+ * @param out The stream to use.
+ */
+ template<class Matrix>
+ static void print(const Matrix& m, std::ostream& out = std::cout)
{
- out << "[";
- for (size_t j = 0; j < m.getNumberOfColumns() - 1; j++)
+ out << m.getNumberOfRows() << "x" << m.getNumberOfColumns() << std::endl;
+ out << "[" << std::endl;
+ for (size_t i = 0; i < m.getNumberOfRows(); i++)
{
- out << m(i, j) << ", ";
+ out << "[";
+ for (size_t j = 0; j < m.getNumberOfColumns() - 1; j++)
+ {
+ out << m(i, j) << ", ";
+ }
+ if (m.getNumberOfColumns() > 0) out << m(i, m.getNumberOfColumns() - 1) << "]" << std::endl;
}
- if (m.getNumberOfColumns() > 0) out << m(i, m.getNumberOfColumns() - 1) << "]" << std::endl;
+ out << "]" << std::endl;
}
- out << "]" << std::endl;
- }
-
- /**
- * @brief Print a matrix to a stream, so that it is read by R.
- *
- * @param m The matrix to print.
- * @param variableName The name of the R variable handeling the matrix
- * @param out The stream to use.
- */
- template<class Matrix>
- static void printForR(const Matrix& m, const std::string& variableName = "x", std::ostream& out = std::cout)
- {
- out.precision(12);
- out << variableName << "<-matrix(c(";
- for (size_t i = 0; i < m.getNumberOfRows(); i++)
+
+ /**
+ * @brief Print a matrix to a stream.
+ *
+ * @param m The matrix to print.
+ * @param out The stream to use.
+ * @param pIn left delimiter (default: "(")
+ * @param pOut right delimiter (default: ")")
+ */
+ template<class Matrix>
+ static void print(const Matrix& m, bpp::OutputStream& out, char pIn = '(', char pOut = ')')
{
- for (size_t j = 0; j < m.getNumberOfColumns(); j++)
+ out << pIn;
+
+ for (size_t i = 0; i < m.getNumberOfRows(); i++)
{
- if (i > 0 || j > 0)
- out << ", ";
- out << m(i, j);
+ if (i!=0)
+ out << ",";
+
+ out << pIn;
+ for (size_t j = 0; j < m.getNumberOfColumns() - 1; j++)
+ {
+ out << m(i, j) << ", ";
+ }
+ if (m.getNumberOfColumns() > 0) out << m(i, m.getNumberOfColumns() - 1) << pOut;
}
+ out << pOut;
}
- out << "), nrow=" << m.getNumberOfRows() << ", byrow=TRUE)" << std::endl;
- }
-
-
- /**
- * @brief Print a vector to a stream.
- *
- * @param v The vector to print.
- * @param out The stream to use.
- */
- template<class Real>
- static void print(const std::vector<Real>& v, std::ostream& out = std::cout)
- {
- out << v.size() << std::endl;
- out << "[";
- for (size_t i = 0; i < v.size() - 1; i++)
- {
- out << v[i] << ", ";
- }
- if (v.size() > 0) out << v[v.size() - 1];
- out << "]" << std::endl;
- }
-
- /**
- * @return True if the matrix is a square matrix.
- * @param A A matrix.
- */
- template<class Matrix>
- static bool isSquare(const Matrix& A) { return A.getNumberOfRows() == A.getNumberOfColumns(); }
-
- /**
- * @param A [in] The matrix to inverse.
- * @param O [out] The inverse matrix of A.
- * @return x the minimum absolute value of the diagonal of the LU decomposition
- * @throw DimensionException If A is not a square matrix.
- */
- template<class Scalar>
- static Scalar inv(const Matrix<Scalar>& A, Matrix<Scalar>& O) throw (DimensionException, ZeroDivisionException)
- {
- if (!isSquare(A)) throw DimensionException("MatrixTools::inv(). Matrix A is not a square matrix.", A.getNumberOfRows(), A.getNumberOfColumns());
- LUDecomposition<Scalar> lu(A);
- RowMatrix<Scalar> I;
- getId(A.getNumberOfRows(), I);
- return lu.solve(I, O);
- }
-
- /**
- * @brief Get determinant of a square matrix.
- *
- * This implementation is in @f$o(n^3)@f$ and uses the LU decomposition method.
- *
- * @param A [in] The input matrix.
- * @return The determinant of A.
- * @throw DimensionException If A is not a square matrix.
- */
- template<class Scalar>
- static double det(const Matrix<Scalar>& A) throw (DimensionException)
- {
- if (!isSquare(A)) throw DimensionException("MatrixTools::det(). Matrix A is not a square matrix.", A.getNumberOfRows(), A.getNumberOfColumns());
- LUDecomposition<Scalar> lu(A);
- return lu.det();
- }
-
- /**
- * @param A [in] The matrix to transpose.
- * @param O [out] The transposition of A.
- */
- template<class MatrixA, class MatrixO>
- static void transpose(const MatrixA& A, MatrixO& O)
- {
- O.resize(A.getNumberOfColumns(), A.getNumberOfRows());
- for (size_t i = 0; i < A.getNumberOfColumns(); i++)
+
+ /**
+ * @brief Print a matrix to a stream, so that it is read by R.
+ *
+ * @param m The matrix to print.
+ * @param variableName The name of the R variable handeling the matrix
+ * @param out The stream to use.
+ */
+ template<class Matrix>
+ static void printForR(const Matrix& m, const std::string& variableName = "x", std::ostream& out = std::cout)
{
- for (size_t j = 0; j < A.getNumberOfRows(); j++)
+ out.precision(12);
+ out << variableName << "<-matrix(c(";
+ for (size_t i = 0; i < m.getNumberOfRows(); i++)
{
- O(i, j) = A(j, i);
+ for (size_t j = 0; j < m.getNumberOfColumns(); j++)
+ {
+ if (i > 0 || j > 0)
+ out << ", ";
+ out << m(i, j);
+ }
}
+ out << "), nrow=" << m.getNumberOfRows() << ", byrow=TRUE)" << std::endl;
}
- }
-
- /**
- * @brief Compute the variance-covariance matrix of an input matrix.
- *
- * The input matrix represent a n-sample of a random vector of dimension r.
- * It is assumed to have r rows and n columns.
- * The variance matrix is then computed as @f[ V = A\cdot A^T - \mu\cdot\mu^T at f],
- * where @f$\mu at f$ is the mean vector of the sample.
- * the output matrix is a square matrix of size r.
- *
- * @param A [in] The intput matrix.
- * @param O [out] The resulting variance covariance matrix.
- */
- template<class Scalar>
- static void covar(const Matrix<Scalar>& A, Matrix<Scalar>& O)
- {
- size_t r = A.getNumberOfRows();
- size_t n = A.getNumberOfColumns();
- O.resize(r, r);
- RowMatrix<Scalar> tA;
- transpose(A, tA);
- mult(A, tA, O);
- scale(O, 1. / static_cast<double>(n));
- RowMatrix<Scalar> mean(r, 1);
- for (size_t i = 0; i < r; i++)
+
+
+ /**
+ * @brief Print a vector to a stream.
+ *
+ * @param v The vector to print.
+ * @param out The stream to use.
+ */
+ template<class Real>
+ static void print(const std::vector<Real>& v, std::ostream& out = std::cout)
{
- for (size_t j = 0; j < n; j++)
+ out << v.size() << std::endl;
+ out << "[";
+ for (size_t i = 0; i < v.size() - 1; i++)
{
- mean(i, 0) += A(i, j);
+ out << v[i] << ", ";
}
- mean(i, 0) /= static_cast<double>(n);
+ if (v.size() > 0) out << v[v.size() - 1];
+ out << "]" << std::endl;
}
- RowMatrix<Scalar> tMean;
- transpose(mean, tMean);
- RowMatrix<Scalar> meanMat;
- mult(mean, tMean, meanMat);
- scale(meanMat, -1.);
- add(O, meanMat);
- }
-
- /**
- * @brief Compute the Kronecker product of two row matrices.
- *
- * @param A [in] The first row matrix.
- * @param B [in] The second row matrix.
- * @param O [out] The product \f$A \otimes B\f$.
- */
- template<class Scalar>
- static void kroneckerMult(const Matrix<Scalar>& A, const Matrix<Scalar>& B, Matrix<Scalar>& O)
- {
- size_t ncA = A.getNumberOfColumns();
- size_t nrA = A.getNumberOfRows();
- size_t nrB = B.getNumberOfRows();
- size_t ncB = B.getNumberOfColumns();
- O.resize(nrA * nrB, ncA * ncB);
- for (size_t ia = 0; ia < nrA; ia++)
+
+ /**
+ * @return True if the matrix is a square matrix.
+ * @param A A matrix.
+ */
+ template<class Matrix>
+ static bool isSquare(const Matrix& A) { return A.getNumberOfRows() == A.getNumberOfColumns(); }
+
+ /**
+ * @param A [in] The matrix to inverse.
+ * @param O [out] The inverse matrix of A.
+ * @return x the minimum absolute value of the diagonal of the LU decomposition
+ * @throw DimensionException If A is not a square matrix.
+ */
+ template<class Scalar>
+ static Scalar inv(const Matrix<Scalar>& A, Matrix<Scalar>& O) throw (DimensionException, ZeroDivisionException)
+ {
+ if (!isSquare(A)) throw DimensionException("MatrixTools::inv(). Matrix A is not a square matrix.", A.getNumberOfRows(), A.getNumberOfColumns());
+ LUDecomposition<Scalar> lu(A);
+ RowMatrix<Scalar> I;
+ getId(A.getNumberOfRows(), I);
+ return lu.solve(I, O);
+ }
+
+ /**
+ * @brief Get determinant of a square matrix.
+ *
+ * This implementation is in @f$o(n^3)@f$ and uses the LU decomposition method.
+ *
+ * @param A [in] The input matrix.
+ * @return The determinant of A.
+ * @throw DimensionException If A is not a square matrix.
+ */
+ template<class Scalar>
+ static double det(const Matrix<Scalar>& A) throw (DimensionException)
{
- for (size_t ja = 0; ja < ncA; ja++)
+ if (!isSquare(A)) throw DimensionException("MatrixTools::det(). Matrix A is not a square matrix.", A.getNumberOfRows(), A.getNumberOfColumns());
+ LUDecomposition<Scalar> lu(A);
+ return lu.det();
+ }
+
+ /**
+ * @param A [in] The matrix to transpose.
+ * @param O [out] The transposition of A.
+ */
+ template<class MatrixA, class MatrixO>
+ static void transpose(const MatrixA& A, MatrixO& O)
+ {
+ O.resize(A.getNumberOfColumns(), A.getNumberOfRows());
+ for (size_t i = 0; i < A.getNumberOfColumns(); i++)
{
- Scalar aij = A(ia, ja);
- for (size_t ib = 0; ib < nrB; ib++)
+ for (size_t j = 0; j < A.getNumberOfRows(); j++)
{
- for (size_t jb = 0; jb < ncB; jb++)
- {
- O(ia * nrB + ib, ja * ncB + jb) = aij * B(ib, jb);
- }
+ O(i, j) = A(j, i);
}
}
}
- }
-
- /**
- * @brief Compute the Hadamard product of two row matrices with same dimensions.
- *
- * @param A [in] The first row matrix.
- * @param B [in] The second row matrix.
- * @param O [out] The Hadamard product.
- */
- template<class Scalar>
- static void hadamardMult(const Matrix<Scalar>& A, const Matrix<Scalar>& B, Matrix<Scalar>& O)
- {
- size_t ncA = A.getNumberOfColumns();
- size_t nrA = A.getNumberOfRows();
- size_t nrB = B.getNumberOfRows();
- size_t ncB = B.getNumberOfColumns();
- if (nrA != nrB) throw DimensionException("MatrixTools::hadamardMult(). nrows A != nrows B.", nrA, nrB);
- if (ncA != ncB) throw DimensionException("MatrixTools::hadamardMult(). ncols A != ncols B.", ncA, ncB);
- O.resize(nrA, ncA);
- for (size_t i = 0; i < nrA; i++)
+
+ /**
+ * @brief Compute the variance-covariance matrix of an input matrix.
+ *
+ * The input matrix represent a n-sample of a random vector of dimension r.
+ * It is assumed to have r rows and n columns.
+ * The variance matrix is then computed as @f[ V = A\cdot A^T - \mu\cdot\mu^T at f],
+ * where @f$\mu at f$ is the mean vector of the sample.
+ * the output matrix is a square matrix of size r.
+ *
+ * @param A [in] The intput matrix.
+ * @param O [out] The resulting variance covariance matrix.
+ */
+ template<class Scalar>
+ static void covar(const Matrix<Scalar>& A, Matrix<Scalar>& O)
{
- for (size_t j = 0; j < ncA; j++)
+ size_t r = A.getNumberOfRows();
+ size_t n = A.getNumberOfColumns();
+ O.resize(r, r);
+ RowMatrix<Scalar> tA;
+ transpose(A, tA);
+ mult(A, tA, O);
+ scale(O, 1. / static_cast<double>(n));
+ RowMatrix<Scalar> mean(r, 1);
+ for (size_t i = 0; i < r; i++)
{
- O(i, j) = A(i, j) * B(i, j);
+ for (size_t j = 0; j < n; j++)
+ {
+ mean(i, 0) += A(i, j);
+ }
+ mean(i, 0) /= static_cast<double>(n);
}
+ RowMatrix<Scalar> tMean;
+ transpose(mean, tMean);
+ RowMatrix<Scalar> meanMat;
+ mult(mean, tMean, meanMat);
+ scale(meanMat, -1.);
+ add(O, meanMat);
}
- }
-
- /**
- * @brief Compute the "Hadamard" product of a row matrix and a vector containing weights, according to rows or columns.
- *
- * @param A [in] The row matrix.
- * @param B [in] The vector of row or column weights.
- * @param O [out] The 'Hadamard' product.
- * @param row Boolean. If row is set to 'true', the vector contains weights for rows. Otherwise the vector contains weights for columns.
- */
- template<class Scalar>
- static void hadamardMult(const Matrix<Scalar>& A, const std::vector<Scalar>& B, Matrix<Scalar>& O, bool row = true)
- {
- size_t ncA = A.getNumberOfColumns();
- size_t nrA = A.getNumberOfRows();
- size_t sB = B.size();
- if (row == true && nrA != sB) throw DimensionException("MatrixTools::hadamardMult(). nrows A != size of B.", nrA, sB);
- if (row == false && ncA != sB) throw DimensionException("MatrixTools::hadamardMult(). ncols A != size of B.", ncA, sB);
- O.resize(nrA, ncA);
- if (row)
+
+ /**
+ * @brief Compute the Kronecker product of two row matrices.
+ *
+ * @param A [in] The first row matrix.
+ * @param B [in] The second row matrix.
+ * @param O [out] The product \f$A \otimes B\f$.
+ */
+ template<class Scalar>
+ static void kroneckerMult(const Matrix<Scalar>& A, const Matrix<Scalar>& B, Matrix<Scalar>& O)
{
- for (size_t i = 0; i < nrA; i++)
+ size_t ncA = A.getNumberOfColumns();
+ size_t nrA = A.getNumberOfRows();
+ size_t nrB = B.getNumberOfRows();
+ size_t ncB = B.getNumberOfColumns();
+ O.resize(nrA * nrB, ncA * ncB);
+ for (size_t ia = 0; ia < nrA; ia++)
{
- for (size_t j = 0; j < ncA; j++)
+ for (size_t ja = 0; ja < ncA; ja++)
{
- O(i, j) = A(i, j) * B[i];
+ Scalar aij = A(ia, ja);
+ for (size_t ib = 0; ib < nrB; ib++)
+ {
+ for (size_t jb = 0; jb < ncB; jb++)
+ {
+ O(ia * nrB + ib, ja * ncB + jb) = aij * B(ib, jb);
+ }
+ }
}
}
}
- else
+
+ /**
+ * @brief Compute the Hadamard product of two row matrices with same dimensions.
+ *
+ * @param A [in] The first row matrix.
+ * @param B [in] The second row matrix.
+ * @param O [out] The Hadamard product.
+ */
+ template<class Scalar>
+ static void hadamardMult(const Matrix<Scalar>& A, const Matrix<Scalar>& B, Matrix<Scalar>& O)
{
+ size_t ncA = A.getNumberOfColumns();
+ size_t nrA = A.getNumberOfRows();
+ size_t nrB = B.getNumberOfRows();
+ size_t ncB = B.getNumberOfColumns();
+ if (nrA != nrB) throw DimensionException("MatrixTools::hadamardMult(). nrows A != nrows B.", nrA, nrB);
+ if (ncA != ncB) throw DimensionException("MatrixTools::hadamardMult(). ncols A != ncols B.", ncA, ncB);
+ O.resize(nrA, ncA);
for (size_t i = 0; i < nrA; i++)
{
for (size_t j = 0; j < ncA; j++)
{
- O(i, j) = A(i, j) * B[j];
+ O(i, j) = A(i, j) * B(i, j);
}
}
}
- }
-
- /**
- * @brief Compute the Kronecker sum of two row matrices.
- *
- * @param A [in] The first row matrix.
- * @param B [in] The second row matrix.
- * @param O [out] The product \f$A \oplus B\f$.
- */
- template<class Scalar>
- static void kroneckerSum(const Matrix<Scalar>& A, const Matrix<Scalar>& B, Matrix<Scalar>& O)
- {
- size_t ncA = A.getNumberOfColumns();
- size_t nrA = A.getNumberOfRows();
- size_t nrB = B.getNumberOfRows();
- size_t ncB = B.getNumberOfColumns();
- O.resize(nrA + nrB, ncA + ncB);
- for (size_t ia = 0; ia < nrA; ia++)
+
+ /**
+ * @brief Compute the "Hadamard" product of a row matrix and a vector containing weights, according to rows or columns.
+ *
+ * @param A [in] The row matrix.
+ * @param B [in] The vector of row or column weights.
+ * @param O [out] The 'Hadamard' product.
+ * @param row Boolean. If row is set to 'true', the vector contains weights for rows. Otherwise the vector contains weights for columns.
+ */
+ template<class Scalar>
+ static void hadamardMult(const Matrix<Scalar>& A, const std::vector<Scalar>& B, Matrix<Scalar>& O, bool row = true)
{
- for (size_t ja = 0; ja < ncA; ja++)
+ size_t ncA = A.getNumberOfColumns();
+ size_t nrA = A.getNumberOfRows();
+ size_t sB = B.size();
+ if (row == true && nrA != sB) throw DimensionException("MatrixTools::hadamardMult(). nrows A != size of B.", nrA, sB);
+ if (row == false && ncA != sB) throw DimensionException("MatrixTools::hadamardMult(). ncols A != size of B.", ncA, sB);
+ O.resize(nrA, ncA);
+ if (row)
{
- O(ia, ja) = A(ia, ja);
+ for (size_t i = 0; i < nrA; i++)
+ {
+ for (size_t j = 0; j < ncA; j++)
+ {
+ O(i, j) = A(i, j) * B[i];
+ }
+ }
}
- }
- for (size_t ib = 0; ib < nrB; ib++)
- {
- for (size_t jb = 0; jb < nrB; jb++)
+ else
{
- O(nrA + ib, ncA + jb) = B(ib, jb);
+ for (size_t i = 0; i < nrA; i++)
+ {
+ for (size_t j = 0; j < ncA; j++)
+ {
+ O(i, j) = A(i, j) * B[j];
+ }
+ }
}
}
- }
-
- /**
- * @brief Compute the Kronecker sum of n row matrices.
- *
- * @param vA [in] A vector of row matrices of any size.
- * @param O [out] The product \f$\bigoplus_i A_i\f$.
- */
- template<class Scalar>
- static void kroneckerSum(const std::vector< Matrix<Scalar>*>& vA, Matrix<Scalar>& O)
- {
- size_t nr = 0;
- size_t nc = 0;
- for (size_t k = 0; k < vA.size(); k++)
- {
- nr += vA[k]->getNumberOfRows();
- nc += vA[k]->getNumberOfColumns();
- }
- O.resize(nr, nc);
- size_t rk = 0; // Row counter
- size_t ck = 0; // Col counter
- for (size_t k = 0; k < vA.size(); k++)
+
+ /**
+ * @brief Compute the Kronecker sum of two row matrices.
+ *
+ * @param A [in] The first row matrix.
+ * @param B [in] The second row matrix.
+ * @param O [out] The product \f$A \oplus B\f$.
+ */
+ template<class Scalar>
+ static void kroneckerSum(const Matrix<Scalar>& A, const Matrix<Scalar>& B, Matrix<Scalar>& O)
{
- const Matrix<Scalar>* Ak = vA[k];
- for (size_t i = 0; i < Ak->getNumberOfRows(); i++)
+ size_t ncA = A.getNumberOfColumns();
+ size_t nrA = A.getNumberOfRows();
+ size_t nrB = B.getNumberOfRows();
+ size_t ncB = B.getNumberOfColumns();
+ O.resize(nrA + nrB, ncA + ncB);
+ for (size_t ia = 0; ia < nrA; ia++)
{
- for (size_t j = 0; j < Ak->getNumberOfColumns(); j++)
+ for (size_t ja = 0; ja < ncA; ja++)
{
- O(rk + i, ck + j) = (*Ak)(i, j);
+ O(ia, ja) = A(ia, ja);
}
}
- rk += Ak->getNumberOfRows();
- ck += Ak->getNumberOfColumns();
- }
- }
-
- /**
- * @brief Convert to a vector of vector.
- *
- * @param M [in] A matrix object.
- * @param vO [out] The output vector of vector (will be resized accordingly).
- */
- template<class Scalar>
- static void toVVdouble(const Matrix<Scalar>& M, std::vector< std::vector<Scalar> >& vO)
- {
- size_t n = M.getNumberOfRows();
- size_t m = M.getNumberOfColumns();
- vO.resize(n);
- for (size_t i = 0; i < n; i++)
- {
- vO[i].resize(m);
- for (size_t j = 0; j < m; j++)
+ for (size_t ib = 0; ib < nrB; ib++)
{
- vO[i][j] = M(i, j);
+ for (size_t jb = 0; jb < nrB; jb++)
+ {
+ O(nrA + ib, ncA + jb) = B(ib, jb);
+ }
}
}
- }
-
- /**
- * @brief Sum all elements in M.
- * @param M A matrix.
- * @return The sum of all elements.
- */
- template<class Scalar>
- static Scalar sumElements(const Matrix<Scalar>& M)
- {
- Scalar sum = 0;
- for (size_t i = 0; i < M.getNumberOfRows(); i++)
+
+ /**
+ * @brief Compute the Kronecker sum of n row matrices.
+ *
+ * @param vA [in] A vector of row matrices of any size.
+ * @param O [out] The product \f$\bigoplus_i A_i\f$.
+ */
+ template<class Scalar>
+ static void kroneckerSum(const std::vector< Matrix<Scalar>*>& vA, Matrix<Scalar>& O)
{
- for (size_t j = 0; j < M.getNumberOfColumns(); j++)
+ size_t nr = 0;
+ size_t nc = 0;
+ for (size_t k = 0; k < vA.size(); k++)
{
- sum += M(i, j);
+ nr += vA[k]->getNumberOfRows();
+ nc += vA[k]->getNumberOfColumns();
}
- }
- return sum;
- }
-
-
-
- /**
- * @brief Linear Assignment Problem
- *
- * The algorithm coded here is described in
- * * A Shortest Augmenting Path Algorithm for Dense and Sparse Linear Assignment Problems, Computing 38, 325-340, 1987
- * by R. Jonker and A. Volgenant, University of Amsterdam.
- *
- * @param assignCost [input/output] Cost matrix
- * @param rowSol [output] Column assigned to row in solution
- * @param colSol [output] Row assigned to column in solution
- * @param u [output] Dual variables, row reduction numbers
- * @param v [output] Dual variables, column reduction numbers
- * @return The optimal cost.
- */
- template<class Scalar>
- static Scalar lap(Matrix<Scalar>& assignCost,
- std::vector<int> &rowSol,
- std::vector<int> &colSol,
- std::vector<Scalar> &u,
- std::vector<Scalar> &v) throw (Exception)
- {
- size_t dim = assignCost.getNumberOfRows();
- if (assignCost.getNumberOfColumns() != dim)
- throw Exception("MatrixTools::lap. Cost matrix should be scare.");
-
- bool unassignedFound;
- size_t i, iMin;
- size_t numFree = 0, previousNumFree, f, i0, k, freeRow;
- std::vector<size_t> free(dim); // list of unassigned rows.
- std::vector<size_t> pred(dim); // row-predecessor of column in augmenting/alternating path.
- size_t j, j1, j2, endOfPath, last, low, up;
- std::vector<size_t> colList(dim); // list of columns to be scanned in various ways.
- std::vector<short int> matches(dim, 0); // counts how many times a row could be assigned.
- Scalar min;
- Scalar h;
- size_t uMin, uSubMin;
- Scalar v2;
- std::vector<Scalar> d(dim); // 'cost-distance' in augmenting path calculation.
-
- // Column reduction
- for (j = dim; j > 0; j--) // reverse order gives better results.
- {
- // find minimum cost over rows.
- min = assignCost(0, j - 1);
- iMin = 0;
- for (i = 1; i < dim; ++i) {
- if (assignCost(i, j - 1) < min)
- {
- min = assignCost(i, j - 1);
- iMin = i;
+ O.resize(nr, nc);
+ size_t rk = 0; // Row counter
+ size_t ck = 0; // Col counter
+ for (size_t k = 0; k < vA.size(); k++)
+ {
+ const Matrix<Scalar>* Ak = vA[k];
+ for (size_t i = 0; i < Ak->getNumberOfRows(); i++)
+ {
+ for (size_t j = 0; j < Ak->getNumberOfColumns(); j++)
+ {
+ O(rk + i, ck + j) = (*Ak)(i, j);
+ }
}
+ rk += Ak->getNumberOfRows();
+ ck += Ak->getNumberOfColumns();
}
- v[j - 1] = min;
-
- if (++matches[iMin] == 1)
- {
- // init assignment if minimum row assigned for first time.
- rowSol[iMin] = j - 1;
- colSol[j - 1] = iMin;
- }
- else
- colSol[j - 1] = -1; // row already assigned, column not assigned.
}
- // Reduction tranfer
- for (i = 0; i < dim; i++) {
- if (matches[i] == 0) // fill list of unassigned 'free' rows.
- free[numFree++] = i;
- else {
- if (matches[i] == 1) // transfer reduction from rows that are assigned once.
+ /**
+ * @brief Convert to a vector of vector.
+ *
+ * @param M [in] A matrix object.
+ * @param vO [out] The output vector of vector (will be resized accordingly).
+ */
+ template<class Scalar>
+ static void toVVdouble(const Matrix<Scalar>& M, std::vector< std::vector<Scalar> >& vO)
+ {
+ size_t n = M.getNumberOfRows();
+ size_t m = M.getNumberOfColumns();
+ vO.resize(n);
+ for (size_t i = 0; i < n; i++)
+ {
+ vO[i].resize(m);
+ for (size_t j = 0; j < m; j++)
{
- j1 = rowSol[i];
- min = -log(0);
- for (j = 0; j < dim; j++)
- if (j != j1)
- if (assignCost(i, j - 1) - v[j] < min)
- min = assignCost(i, j - 1) - v[j - 1];
- v[j1] = v[j1] - min;
+ vO[i][j] = M(i, j);
}
}
}
- // Augmenting row reduction
- short loopcnt = 0; // do-loop to be done twice.
- do
+ /**
+ * @brief Sum all elements in M.
+ * @param M A matrix.
+ * @return The sum of all elements.
+ */
+ template<class Scalar>
+ static Scalar sumElements(const Matrix<Scalar>& M)
{
- loopcnt++;
-
- // scan all free rows.
- // in some cases, a free row may be replaced with another one to be scanned next.
- k = 0;
- previousNumFree = numFree;
- numFree = 0; // start list of rows still free after augmenting row reduction.
- while (k < previousNumFree)
+ Scalar sum = 0;
+ for (size_t i = 0; i < M.getNumberOfRows(); i++)
{
- i = free[k];
- k++;
-
- // find minimum and second minimum reduced cost over columns.
- uMin = assignCost(i, 0) - v[0];
- j1 = 0;
- uSubMin = -log(0);
- for (j = 1; j < dim; j++)
+ for (size_t j = 0; j < M.getNumberOfColumns(); j++)
{
- h = assignCost(i, j) - v[j];
- if (h < uSubMin) {
- if (h >= uMin)
- {
- uSubMin = h;
- j2 = j;
- }
- else
- {
- uSubMin = uMin;
- uMin = h;
- j2 = j1;
- j1 = j;
- }
- }
+ sum += M(i, j);
}
+ }
+ return sum;
+ }
- i0 = colSol[j1];
- if (uMin < uSubMin) {
- // change the reduction of the minimum column to increase the minimum
- // reduced cost in the row to the subminimum.
- v[j1] = v[j1] - (uSubMin - uMin);
- } else { // minimum and subminimum equal.
- if (i0 >= 0) // minimum column j1 is assigned.
+
+
+ /**
+ * @brief Linear Assignment Problem
+ *
+ * The algorithm coded here is described in
+ * * A Shortest Augmenting Path Algorithm for Dense and Sparse Linear Assignment Problems, Computing 38, 325-340, 1987
+ * by R. Jonker and A. Volgenant, University of Amsterdam.
+ *
+ * @param assignCost [input/output] Cost matrix
+ * @param rowSol [output] Column assigned to row in solution
+ * @param colSol [output] Row assigned to column in solution
+ * @param u [output] Dual variables, row reduction numbers
+ * @param v [output] Dual variables, column reduction numbers
+ * @return The optimal cost.
+ */
+ template<class Scalar>
+ static Scalar lap(Matrix<Scalar>& assignCost,
+ std::vector<int> &rowSol,
+ std::vector<int> &colSol,
+ std::vector<Scalar> &u,
+ std::vector<Scalar> &v) throw (Exception)
+ {
+ size_t dim = assignCost.getNumberOfRows();
+ if (assignCost.getNumberOfColumns() != dim)
+ throw Exception("MatrixTools::lap. Cost matrix should be scare.");
+
+ bool unassignedFound;
+ size_t i, iMin;
+ size_t numFree = 0, previousNumFree, f, k, freeRow;
+ int i0;
+ std::vector<size_t> free(dim); // list of unassigned rows.
+ std::vector<size_t> pred(dim); // row-predecessor of column in augmenting/alternating path.
+ size_t j, j1, j2, endOfPath, last, low, up;
+ std::vector<size_t> colList(dim); // list of columns to be scanned in various ways.
+ std::vector<short int> matches(dim, 0); // counts how many times a row could be assigned.
+ Scalar min;
+ Scalar h;
+ size_t uMin, uSubMin;
+ Scalar v2;
+ std::vector<Scalar> d(dim); // 'cost-distance' in augmenting path calculation.
+
+ // Column reduction
+ for (j = dim; j > 0; j--) // reverse order gives better results.
+ {
+ // find minimum cost over rows.
+ min = assignCost(0, j - 1);
+ iMin = 0;
+ for (i = 1; i < dim; ++i) {
+ if (assignCost(i, j - 1) < min)
{
- // swap columns j1 and j2, as j2 may be unassigned.
- j1 = j2;
- i0 = colSol[j2];
+ min = assignCost(i, j - 1);
+ iMin = i;
}
}
+ v[j - 1] = min;
- // (re-)assign i to j1, possibly de-assigning an i0.
- rowSol[i] = j1;
- colSol[j1] = i;
-
- if (i0 >= 0) { // minimum column j1 assigned earlier.
- if (uMin < uSubMin) {
- // put in current k, and go back to that k.
- // continue augmenting path i - j1 with i0.
- free[--k] = i0;
- } else {
- // no further augmenting reduction possible.
- // store i0 in list of free rows for next phase.
- free[numFree++] = i0;
- }
+ if (++matches[iMin] == 1)
+ {
+ // init assignment if minimum row assigned for first time.
+ rowSol[iMin] = static_cast<int>(j - 1);
+ colSol[j - 1] = static_cast<int>(iMin);
}
+ else
+ colSol[j - 1] = -1; // row already assigned, column not assigned.
}
- }
- while (loopcnt < 2); // repeat once.
- // Augment solution for each free row.
- for (f = 0; f < numFree; f++)
- {
- freeRow = free[f]; // start row of augmenting path.
-
- // Dijkstra shortest path algorithm.
- // runs until unassigned column added to shortest path tree.
- for (j = 0; j < dim; j++)
- {
- d[j] = assignCost(freeRow, j) - v[j];
- pred[j] = freeRow;
- colList[j] = j; // init column list.
+ // Reduction tranfer
+ for (i = 0; i < dim; i++) {
+ if (matches[i] == 0) // fill list of unassigned 'free' rows.
+ free[numFree++] = i;
+ else {
+ if (matches[i] == 1) // transfer reduction from rows that are assigned once.
+ {
+ j1 = static_cast<size_t>(rowSol[i]); //rowSol[i] is >= 0 here
+ min = -log(0);
+ for (j = 0; j < dim; j++)
+ if (j != j1)
+ if (assignCost(i, j - 1) - v[j] < min)
+ min = assignCost(i, j - 1) - v[j - 1];
+ v[j1] = v[j1] - min;
+ }
+ }
}
- low = 0; // columns in 0..low-1 are ready, now none.
- up = 0; // columns in low..up-1 are to be scanned for current minimum, now none.
- // columns in up..dim-1 are to be considered later to find new minimum,
- // at this stage the list simply contains all columns
- unassignedFound = false;
+ // Augmenting row reduction
+ short loopcnt = 0; // do-loop to be done twice.
do
{
- if (up == low) // no more columns to be scanned for current minimum.
+ loopcnt++;
+
+ // scan all free rows.
+ // in some cases, a free row may be replaced with another one to be scanned next.
+ k = 0;
+ previousNumFree = numFree;
+ numFree = 0; // start list of rows still free after augmenting row reduction.
+ while (k < previousNumFree)
{
- last = low - 1;
-
- // scan columns for up..dim-1 to find all indices for which new minimum occurs.
- // store these indices between low..up-1 (increasing up).
- min = d[colList[up++]];
- for (k = up; k < dim; k++)
+ i = free[k];
+ k++;
+
+ // find minimum and second minimum reduced cost over columns.
+ uMin = assignCost(i, 0) - v[0];
+ j1 = 0;
+ uSubMin = static_cast<size_t>(-log(0));
+ for (j = 1; j < dim; j++)
{
- j = colList[k];
- h = d[j];
- if (h <= min)
- {
- if (h < min) // new minimum.
+ h = assignCost(i, j) - v[j];
+ if (h < uSubMin) {
+ if (h >= uMin)
{
- up = low; // restart list at index low.
- min = h;
+ uSubMin = h;
+ j2 = j;
+ }
+ else
+ {
+ uSubMin = uMin;
+ uMin = h;
+ j2 = j1;
+ j1 = j;
}
- // new index with same minimum, put on undex up, and extend list.
- colList[k] = colList[up];
- colList[up++] = j;
}
}
- // check if any of the minimum columns happens to be unassigned.
- // if so, we have an augmenting path right away.
- for (k = low; k < up; k++) {
- if (colSol[colList[k]] < 0)
- {
- endOfPath = colList[k];
- unassignedFound = true;
- break;
+ i0 = colSol[j1];
+ if (uMin < uSubMin) {
+ // change the reduction of the minimum column to increase the minimum
+ // reduced cost in the row to the subminimum.
+ v[j1] = v[j1] - (uSubMin - uMin);
+ } else { // minimum and subminimum equal.
+ if (i0 >= 0) // minimum column j1 is assigned.
+ {
+ // swap columns j1 and j2, as j2 may be unassigned.
+ j1 = j2;
+ i0 = colSol[j2];
+ }
+ }
+
+ // (re-)assign i to j1, possibly de-assigning an i0.
+ rowSol[i] = static_cast<int>(j1);
+ colSol[j1] = static_cast<int>(i);
+
+ if (i0 >= 0) { // minimum column j1 assigned earlier.
+ if (uMin < uSubMin) {
+ // put in current k, and go back to that k.
+ // continue augmenting path i - j1 with i0.
+ free[--k] = static_cast<size_t>(i0);
+ } else {
+ // no further augmenting reduction possible.
+ // store i0 in list of free rows for next phase.
+ free[numFree++] = static_cast<size_t>(i0);
}
}
}
+ }
+ while (loopcnt < 2); // repeat once.
- if (!unassignedFound)
- {
- // update 'distances' between freerow and all unscanned columns, via next scanned column.
- j1 = colList[low];
- low++;
- i = colSol[j1];
- h = assignCost(i, j1) - v[j1] - min;
+ // Augment solution for each free row.
+ for (f = 0; f < numFree; f++)
+ {
+ freeRow = free[f]; // start row of augmenting path.
- for (k = up; k < dim; k++)
+ // Dijkstra shortest path algorithm.
+ // runs until unassigned column added to shortest path tree.
+ for (j = 0; j < dim; j++)
+ {
+ d[j] = assignCost(freeRow, j) - v[j];
+ pred[j] = freeRow;
+ colList[j] = j; // init column list.
+ }
+
+ low = 0; // columns in 0..low-1 are ready, now none.
+ up = 0; // columns in low..up-1 are to be scanned for current minimum, now none.
+ // columns in up..dim-1 are to be considered later to find new minimum,
+ // at this stage the list simply contains all columns
+ unassignedFound = false;
+ do
+ {
+ if (up == low) // no more columns to be scanned for current minimum.
{
- j = colList[k];
- v2 = assignCost(i, j) - v[j] - h;
- if (v2 < d[j])
+ last = low - 1;
+
+ // scan columns for up..dim-1 to find all indices for which new minimum occurs.
+ // store these indices between low..up-1 (increasing up).
+ min = d[colList[up++]];
+ for (k = up; k < dim; k++)
{
- pred[j] = i;
- if (v2 == min) { // new column found at same minimum value
- if (colSol[j] < 0)
- {
- // if unassigned, shortest augmenting path is complete.
- endOfPath = j;
- unassignedFound = true;
- break;
- }
- // else add to list to be scanned right away.
- else
+ j = colList[k];
+ h = d[j];
+ if (h <= min)
+ {
+ if (h < min) // new minimum.
{
- colList[k] = colList[up];
- colList[up++] = j;
+ up = low; // restart list at index low.
+ min = h;
}
+ // new index with same minimum, put on undex up, and extend list.
+ colList[k] = colList[up];
+ colList[up++] = j;
+ }
+ }
+
+ // check if any of the minimum columns happens to be unassigned.
+ // if so, we have an augmenting path right away.
+ for (k = low; k < up; k++) {
+ if (colSol[colList[k]] < 0)
+ {
+ endOfPath = colList[k];
+ unassignedFound = true;
+ break;
}
- d[j] = v2;
}
}
- }
- }
- while (!unassignedFound);
- // update column prices.
- for (k = 0; k <= last; k++)
- {
- j1 = colList[k];
- v[j1] = v[j1] + d[j1] - min;
+ if (!unassignedFound)
+ {
+ // update 'distances' between freerow and all unscanned columns, via next scanned column.
+ j1 = colList[low];
+ low++;
+ i = static_cast<size_t>(colSol[j1]);
+ h = assignCost(i, j1) - v[j1] - min;
+
+ for (k = up; k < dim; k++)
+ {
+ j = colList[k];
+ v2 = assignCost(i, j) - v[j] - h;
+ if (v2 < d[j])
+ {
+ pred[j] = i;
+ if (v2 == min) { // new column found at same minimum value
+ if (colSol[j] < 0)
+ {
+ // if unassigned, shortest augmenting path is complete.
+ endOfPath = j;
+ unassignedFound = true;
+ break;
+ }
+ // else add to list to be scanned right away.
+ else
+ {
+ colList[k] = colList[up];
+ colList[up++] = j;
+ }
+ }
+ d[j] = v2;
+ }
+ }
+ }
+ }
+ while (!unassignedFound);
+
+ // update column prices.
+ for (k = 0; k <= last; k++)
+ {
+ j1 = colList[k];
+ v[j1] = v[j1] + d[j1] - min;
+ }
+
+ // reset row and column assignments along the alternating path.
+ do
+ {
+ i = pred[endOfPath];
+ colSol[endOfPath] = static_cast<int>(i);
+ j1 = endOfPath;
+ endOfPath = static_cast<size_t>(rowSol[i]);
+ rowSol[i] = static_cast<int>(j1);
+ }
+ while (i != freeRow);
}
- // reset row and column assignments along the alternating path.
- do
+ // calculate optimal cost.
+ Scalar lapCost = 0;
+ for (i = 0; i < dim; i++)
{
- i = pred[endOfPath];
- colSol[endOfPath] = i;
- j1 = endOfPath;
- endOfPath = rowSol[i];
- rowSol[i] = j1;
+ j = static_cast<size_t>(rowSol[i]);
+ u[i] = assignCost(i, j) - v[j];
+ lapCost = lapCost + assignCost(i, j);
}
- while (i != freeRow);
- }
- // calculate optimal cost.
- Scalar lapCost = 0;
- for (i = 0; i < dim; i++)
- {
- j = rowSol[i];
- u[i] = assignCost(i, j) - v[j];
- lapCost = lapCost + assignCost(i, j);
+ return lapCost;
}
- return lapCost;
- }
-
-};
+ };
/* DEPRECATED
namespace MatrixOperators {
@@ -1274,7 +1304,7 @@ public:
}
};
- */
+*/
} // end of namespace bpp.
#endif // _MATRIXTOOLS_H_
diff --git a/src/Bpp/Numeric/NumConstants.h b/src/Bpp/Numeric/NumConstants.h
index fd8c809..18d95a2 100644
--- a/src/Bpp/Numeric/NumConstants.h
+++ b/src/Bpp/Numeric/NumConstants.h
@@ -90,7 +90,7 @@ namespace bpp {
static double INF() { return std::numeric_limits<double>::has_infinity ? -log(0) : std::numeric_limits<double>::max(); }
static double PINF() { return std::numeric_limits<double>::has_infinity ? -log(0) : std::numeric_limits<double>::max(); }
static double MINF() { return std::numeric_limits<double>::has_infinity ? log(0) : std::numeric_limits<double>::min(); }
- static double NaN() { return 3./0.; }
+ static double NaN() { return NAN; }
/** @} */
static double PI() { return 3.141593; }
diff --git a/src/Bpp/Numeric/Number.h b/src/Bpp/Numeric/Number.h
index dbd3906..7078d11 100644
--- a/src/Bpp/Numeric/Number.h
+++ b/src/Bpp/Numeric/Number.h
@@ -6,7 +6,7 @@
/*
-Copyright or © or Copr. CNRS, (November 17, 2004)
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
This software is a computer program whose purpose is to provide utilitary
classes. This file belongs to the Bio++ Project.
@@ -43,19 +43,63 @@ knowledge of the CeCILL license and that you accept its terms.
#include "../Clonable.h"
+#include <string>
+
namespace bpp
{
+/**
+ * @brief The Number interface.
+ *
+ * This template class may be used to deal with number in an object way.
+ */
+class BppNumberI: public Clonable
+{
+ public:
+
+ BppNumberI() {}
+
+ virtual ~BppNumberI() {}
+
+ public:
+
+ virtual BppNumberI* clone() const = 0;
+
+ public:
+
+ virtual std::string toString() const = 0;
+
+};
+
+
+class BppNotANumber: public virtual BppNumberI
+{
+ public:
+
+ BppNotANumber() {}
+
+ virtual ~BppNotANumber() {}
+
+ public:
+
+ virtual BppNotANumber* clone() const { return new BppNotANumber(); }
+
+ public:
+
+ virtual std::string toString() const { return "NaN"; }
+
+};
+
/**
* @brief The Number object template class.
*
* This template class may be used to deal with number in an object way.
*/
-template<class T> class Number: public Clonable
+template<class T> class Number: public virtual BppNumberI
{
protected:
/** @brief The value of this parameter. */
- T _value;
+ T value_;
public:
@@ -64,13 +108,13 @@ template<class T> class Number: public Clonable
*
* @param value The value that the Number must have.
*/
- Number(const T & value = 0): _value(value) {}
+ Number(const T& value = 0): value_(value) {}
virtual ~Number() {}
Number<T> & operator=(const T & t)
{
- _value = t;
+ value_ = t;
return *this;
}
@@ -81,7 +125,7 @@ template<class T> class Number: public Clonable
*
* @{
*/
- Number<T> * clone() const { return new Number<T>(_value); }
+ Number<T>* clone() const { return new Number<T>(value_); }
/** @} */
public:
@@ -91,7 +135,93 @@ template<class T> class Number: public Clonable
*
* @return The value of this number.
*/
- T getValue() const { return _value; }
+ T getValue() const { return value_; }
+
+ std::string toString() const { return TextTools::toString(value_); }
+};
+
+/**
+ * @brief An object wrapper for double values.
+ */
+class BppDouble: public virtual Number<double>
+{
+ public:
+
+ /**
+ * @brief Build a new BppDouble number object with a specific value.
+ *
+ * @param value The value that the Number must have.
+ */
+ BppDouble(double value = 0): Number<double>(value) {}
+
+ virtual ~BppDouble() {}
+
+ public:
+
+ /**
+ * @name The Clonable interface.
+ *
+ * @{
+ */
+ BppDouble* clone() const { return new BppDouble(*this); }
+ /** @} */
+
+};
+
+/**
+ * @brief An object wrapper for integer values.
+ */
+class BppInteger: public virtual Number<int>
+{
+ public:
+
+ /**
+ * @brief Build a new BppInteger number object with a specific value.
+ *
+ * @param value The value that the Number must have.
+ */
+ BppInteger(int value = 0): Number<int>(value) {}
+
+ virtual ~BppInteger() {}
+
+ public:
+
+ /**
+ * @name The Clonable interface.
+ *
+ * @{
+ */
+ BppInteger* clone() const { return new BppInteger(*this); }
+ /** @} */
+
+};
+
+/**
+ * @brief An object wrapper for unsigned integer values.
+ */
+class BppUnsignedInteger: public virtual Number<unsigned int>
+{
+ public:
+
+ /**
+ * @brief Build a new BppUnsignedInteger number object with a specific value.
+ *
+ * @param value The value that the Number must have.
+ */
+ BppUnsignedInteger(unsigned int value = 0): Number<unsigned int>(value) {}
+
+ virtual ~BppUnsignedInteger() {}
+
+ public:
+
+ /**
+ * @name The Clonable interface.
+ *
+ * @{
+ */
+ BppUnsignedInteger* clone() const { return new BppUnsignedInteger(*this); }
+ /** @} */
+
};
} //end of namespace bpp.
diff --git a/src/Bpp/Numeric/Parameter.h b/src/Bpp/Numeric/Parameter.h
index 1b0b74f..1ed95d2 100644
--- a/src/Bpp/Numeric/Parameter.h
+++ b/src/Bpp/Numeric/Parameter.h
@@ -282,7 +282,6 @@ namespace bpp
*
* @param constraint a pointer to the constraint (may be null)
* @param attach says if the constraint is attached to the Parameter (default: false).
- * @return A pointer toward the formerly used contraint.
*/
virtual void setConstraint(Constraint* constraint, bool attach = false);
diff --git a/src/Bpp/Numeric/ParameterAliasable.h b/src/Bpp/Numeric/ParameterAliasable.h
index 2ba444a..c634f96 100644
--- a/src/Bpp/Numeric/ParameterAliasable.h
+++ b/src/Bpp/Numeric/ParameterAliasable.h
@@ -5,36 +5,36 @@
//
/*
-Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
-
-This software is a computer program whose purpose is to provide classes
-for numerical calculus.
-
-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.
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for numerical calculus.
+
+ 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 _PARAMETERALIASABLE_H_
@@ -46,6 +46,7 @@ knowledge of the CeCILL license and that you accept its terms.
//From the STL:
#include <string>
+#include <map>
namespace bpp
{
@@ -79,9 +80,9 @@ namespace bpp
* @endcode
* is equivallent to the previous example.
*/
-class ParameterAliasable :
- public virtual Parametrizable
-{
+ class ParameterAliasable :
+ public virtual Parametrizable
+ {
public:
ParameterAliasable() {}
virtual ~ParameterAliasable() {}
@@ -108,6 +109,19 @@ class ParameterAliasable :
virtual void aliasParameters(const std::string & p1, const std::string & p2) throw (ParameterNotFoundException, Exception) = 0;
/**
+ * @brief alias the parameters following the links described in a
+ * map, and update the object accordingly. Cycles in aliasing are
+ * detected and forbidden.
+ *
+ * @param unparsedParams the map of the links : <A,B> matches for A->B aliasing.
+ * @param verbose verbosity
+ *
+ **/
+
+ virtual void aliasParameters(std::map<std::string, std::string>& unparsedParams, bool verbose) = 0;
+
+
+ /**
* @brief Detach two parameters previously set as 'aliased'.
*
* The values of the two parameters will now be independent.
@@ -115,7 +129,7 @@ class ParameterAliasable :
* @param p2 Aliased parameter.
* @throw ParameterNotFoundException if p1 or p2 do not correspond to existing parameters.
* @throw Exception when trying to perform non-valid dissociation.
- */
+ */
virtual void unaliasParameters(const std::string & p1, const std::string & p2) throw (ParameterNotFoundException, Exception) = 0;
/**
@@ -133,7 +147,7 @@ class ParameterAliasable :
* @param name The name of the parameter to look for.
*/
virtual std::vector<std::string> getAlias(const std::string& name) const = 0;
-};
+ };
@@ -143,28 +157,28 @@ class ParameterAliasable :
*
* @see Parameter, ParameterList, ParameterAliasable
*/
-class ParameterAliasableAdapter:
- public ParametrizableAdapter
-{
- public:
- ParameterAliasableAdapter() {}
- virtual ~ParameterAliasableAdapter() {}
-
- public:
-
- /**
- * @name The ParameterAliasable interface.
- *
- * @{
- */
- const ParameterList & getIndependentParameters() const { return getParameters(); }
+ class ParameterAliasableAdapter:
+ public ParametrizableAdapter
+ {
+ public:
+ ParameterAliasableAdapter() {}
+ virtual ~ParameterAliasableAdapter() {}
+
+ public:
+
+ /**
+ * @name The ParameterAliasable interface.
+ *
+ * @{
+ */
+ const ParameterList & getIndependentParameters() const { return getParameters(); }
void aliasParameters(const std::string & p1, const std::string & p2) throw (ParameterNotFoundException, Exception) {}
void unaliasParameters(const std::string & p1, const std::string & p2) throw (ParameterNotFoundException, Exception) {}
unsigned int getNumberOfIndependentParameters() const{ return 0; }
std::vector<std::string> getAlias(const std::string& name) const { return std::vector<std::string>(); }
- /** @} */
+ /** @} */
-};
+ };
} // end of namespace bpp.
diff --git a/src/Bpp/Numeric/ParameterList.cpp b/src/Bpp/Numeric/ParameterList.cpp
index 27651aa..0143376 100644
--- a/src/Bpp/Numeric/ParameterList.cpp
+++ b/src/Bpp/Numeric/ParameterList.cpp
@@ -5,7 +5,7 @@
//
/*
- Copyright or © or Copr. Julien Dutheil, (November 19, 2004)
+ Copyright or © or Copr. Bio++ Development Team, (November 19, 2004)
This software is a computer program whose purpose is to provide classes
for numerical calculus.
@@ -38,6 +38,7 @@
*/
#include "ParameterList.h"
+#include "../Text/StringTokenizer.h"
using namespace bpp;
@@ -184,6 +185,40 @@ std::vector<std::string> ParameterList::getParameterNames() const
return pNames;
}
+/****************************************************************************/
+
+vector<string> ParameterList::getMatchingParameterNames(const string& pattern) const
+{
+ vector<string> pNames;
+ for (unsigned int i = 0; i < size(); i++)
+ {
+ string name = parameters_[i]->getName();
+
+ StringTokenizer stj(pattern, "*", true, false);
+ size_t pos1, pos2;
+ bool flag(true);
+ string g=stj.nextToken();
+ pos1=name.find(g);
+ if (pos1!=0)
+ flag=false;
+ pos1+=g.length();
+ while (flag && stj.hasMoreToken()){
+ g=stj.nextToken();
+ pos2=name.find(g,pos1);
+ if (pos2 == string::npos){
+ flag=false;
+ break;
+ }
+ pos1=pos2+g.length();
+ }
+ if (flag &&
+ ((g.length()==0) || (pos1==name.length()) || (name.rfind(g)==name.length()-g.length())))
+ pNames.push_back(name);
+ }
+
+ return pNames;
+}
+
/******************************************************************************/
void ParameterList::addParameter(const Parameter& param) throw (ParameterException)
@@ -325,7 +360,7 @@ bool ParameterList::testParametersValues(const ParameterList& params) const
/******************************************************************************/
-bool ParameterList::matchParametersValues(const ParameterList& params)
+bool ParameterList::matchParametersValues(const ParameterList& params, vector<size_t>* updatedParameters)
throw (ConstraintException)
{
// First we check if all values are correct:
@@ -342,15 +377,20 @@ throw (ConstraintException)
// If all values are ok, we set them:
bool ch = 0;
+ size_t pos = 0;
for (vector<Parameter*>::const_iterator it = params.parameters_.begin(); it < params.parameters_.end(); it++)
{
if (hasParameter((*it)->getName()))
{
Parameter* p = &getParameter((*it)->getName());
- if (p->getValue() != (*it)->getValue())
+ if (p->getValue() != (*it)->getValue()) {
ch |= 1;
- p->setValue((*it)->getValue());
+ p->setValue((*it)->getValue());
+ if (updatedParameters)
+ updatedParameters->push_back(pos);
+ }
}
+ pos++;
}
return ch;
}
@@ -419,11 +459,21 @@ void ParameterList::deleteParameter(const std::string& name) throw (ParameterNot
}
/******************************************************************************/
-void ParameterList::deleteParameters(const std::vector<std::string>& names) throw (ParameterNotFoundException)
+void ParameterList::deleteParameters(const std::vector<std::string>& names, bool mustExist) throw (ParameterNotFoundException)
{
for (unsigned int i = 0; i < names.size(); i++)
{
- deleteParameter(names[i]);
+ try
+ {
+ deleteParameter(names[i]);
+ }
+ catch (ParameterNotFoundException& e)
+ {
+ if (mustExist)
+ throw ParameterNotFoundException(e);
+ else
+ continue;
+ }
}
}
@@ -433,7 +483,7 @@ void ParameterList::deleteParameter(size_t index) throw (IndexOutOfBoundsExcepti
if (index >= size()) throw IndexOutOfBoundsException("ParameterList::deleteParameter.", index, 0, size());
Parameter* p = parameters_[index];
delete p;
- parameters_.erase(parameters_.begin() + index);
+ parameters_.erase(parameters_.begin() + static_cast<ptrdiff_t>(index));
}
/******************************************************************************/
@@ -447,7 +497,7 @@ void ParameterList::deleteParameters(const std::vector<size_t>& indices) throw (
if (index >= size()) throw IndexOutOfBoundsException("ParameterList::deleteParameter.", index, 0, size());
Parameter* p = parameters_[index];
delete p;
- parameters_.erase(parameters_.begin() + index);
+ parameters_.erase(parameters_.begin() + static_cast<ptrdiff_t>(index));
}
}
diff --git a/src/Bpp/Numeric/ParameterList.h b/src/Bpp/Numeric/ParameterList.h
index da93029..57c6086 100644
--- a/src/Bpp/Numeric/ParameterList.h
+++ b/src/Bpp/Numeric/ParameterList.h
@@ -174,6 +174,16 @@ public:
virtual std::vector<std::string> getParameterNames() const;
/**
+ * @brief Get all parameter names matching with the given name. Up
+ * to now, only "*" jokers are available.
+ *
+ * @param pattern a pattern of name
+ * @return A vector of matching names
+ */
+
+ virtual std::vector<std::string> getMatchingParameterNames(const std::string& pattern) const;
+
+ /**
* @brief Add a new parameter at the end of the list.
*
* @param param The parameter to add to the list.
@@ -274,10 +284,14 @@ public:
* Only common parameters with <i>params</i> will be updated.
*
* @param params A list of parameters.
+ * @param updatedParameters An optional pointer toward a vector which will
+ * store the indices of parameters for which a value has changed.
+ * Indices are relative on the input parameter list "params".
* @return true iff a least one parameter value has been changed.
* @see setParameters(), setAllParameters()
*/
- virtual bool matchParametersValues(const ParameterList& params)
+
+ virtual bool matchParametersValues(const ParameterList& params, std::vector<size_t>* updatedParameters = 0)
throw (ConstraintException);
/**
@@ -324,8 +338,11 @@ public:
* @brief Delete several parameters from the list.
*
* @param names The names of the parameters to delete from the list.
+ * @param mustExist If true, an exception is thrown if a name does
+ * not match an extant parameter.
*/
- virtual void deleteParameters(const std::vector<std::string>& names) throw (ParameterNotFoundException);
+
+ virtual void deleteParameters(const std::vector<std::string>& names, bool mustExist = true) throw (ParameterNotFoundException);
/**
* @brief Delete a parameter from the list.
diff --git a/src/Bpp/Numeric/ParametrizableCollection.h b/src/Bpp/Numeric/ParametrizableCollection.h
new file mode 100644
index 0000000..e677d7b
--- /dev/null
+++ b/src/Bpp/Numeric/ParametrizableCollection.h
@@ -0,0 +1,356 @@
+//
+// File: ParametrizableCollection.h
+// Created by: Laurent Guéguen
+// Created on: mercredi 12 juin 2013, à 14h 24
+//
+
+/*
+ Copyright or (c) or Copr. Bio++ Development Team, (November 16, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for phylogenetic data 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 _PARAMETRIZABLECOLLECTION_H_
+#define _PARAMETRIZABLECOLLECTION_H_
+
+#include "Parametrizable.h"
+#include "AbstractParameterAliasable.h"
+
+// From the STL:
+#include <map>
+#include <memory>
+
+namespace bpp
+{
+ /**
+ * @brief Plain collection of parametrizable objects
+ *
+ * The collection is a map from unsigned integers to Parametrizables.
+ *
+ * The access to the parameters of the objects will be done through
+ * this collection.
+ *
+ */
+
+ template <class N>
+ class ParametrizableCollection :
+ public AbstractParameterAliasable
+ {
+ protected:
+ /**
+ * @brief Contains all objects used.
+ */
+
+ std::map<size_t, N* > objectsSet_;
+
+ /**
+ * @brief A vector of the numbers of objects that have changed
+ * during the last fireParameterChanged.
+ *
+ */
+
+ std::vector<size_t> vChanged_;
+
+ public:
+ /**
+ * @brief Create an empty object set.
+ *
+ */
+
+ ParametrizableCollection():
+ AbstractParameterAliasable(""),
+ objectsSet_(),
+ vChanged_()
+ {
+ }
+
+ ParametrizableCollection(const ParametrizableCollection<N>& set) :
+ AbstractParameterAliasable(set),
+ objectsSet_(),
+ vChanged_(set.vChanged_)
+ {
+ // Duplicate all objects:
+ typename std::map<size_t, N* >::const_iterator it;
+ for (it=set.objectsSet_.begin(); it!=set.objectsSet_.end(); it++)
+ objectsSet_[it->first]=it->second->clone();
+ }
+
+ ParametrizableCollection<N>& operator=(const ParametrizableCollection<N>& set)
+ {
+ clear();
+
+ AbstractParameterAliasable::operator=(set);
+ vChanged_ = set.vChanged_;
+
+ // Duplicate all objects:
+ typename std::map<size_t, N* >::const_iterator it;
+ for (it=set.objectsSet_.begin(); it!=set.objectsSet_.end(); it++)
+ objectsSet_[it->first]=it->second->clone();
+
+ return *this;
+ }
+
+ /**
+ * @brief Resets all the information contained in this object.
+ *
+ */
+
+ void clear()
+ {
+ resetParameters_();
+
+ typename std::map<size_t, N*>::const_iterator it;
+ for (it=objectsSet_.begin(); it!=objectsSet_.end(); it++)
+ delete it->second;
+ objectsSet_.clear();
+ vChanged_.empty();
+ }
+
+ ~ParametrizableCollection()
+ {
+ clear();
+ }
+
+ ParametrizableCollection<N>* clone() const { return new ParametrizableCollection<N>(*this); }
+
+ public:
+ /**
+ * To be called when a parameter has changed.
+ * Depending on parameters, this will actualize the corresponding objects in the set.
+ * @param parameters The modified parameters.
+ */
+
+ void fireParameterChanged(const ParameterList& parameters)
+ {
+ vChanged_.clear();
+
+ std::vector<size_t> vCh;
+
+ std::map<size_t, ParameterList > mNumPl;
+
+ for (size_t i=0; i<parameters.size(); i++)
+ {
+ std::string n=parameters[i].getName();
+ size_t t=n.rfind("_");
+ if (t==std::string::npos)
+ continue;
+ size_t num=(size_t)atoi(n.substr(t+1).c_str());
+ mNumPl[num].addParameter(Parameter(n.substr(0,t),parameters[i].getValue()));
+ }
+
+ std::map<size_t, ParameterList >::iterator it;
+
+ // Then we update all objects in the set:
+ for (it=mNumPl.begin(); it!=mNumPl.end(); it++){
+ if (hasObject(it->first) && objectsSet_[it->first]->matchParametersValues(it->second))
+ vChanged_.push_back(it->first);
+ }
+ }
+
+ std::vector<size_t> hasChanged() const
+ {
+ return vChanged_;
+ }
+
+ void clearChanged()
+ {
+ vChanged_.clear();
+ }
+
+ /**
+ * @return The current number of distinct discrete objects in this set.
+ */
+
+ size_t getNumberOfObjects() const { return objectsSet_.size(); }
+
+ /**
+ * @brief Says if there is a object with a given index.
+ *
+ * @param objectIndex Index of the object in the set.
+ * @return true or false.
+ */
+
+ const bool hasObject(size_t objectIndex) const
+ {
+ return (objectsSet_.find(objectIndex)!=objectsSet_.end());
+ }
+
+ /**
+ * @brief Returns the keys of the set.
+ *
+ */
+
+ const std::vector<size_t> keys() const
+ {
+ std::vector<size_t> vkeys;
+ typename std::map<size_t, N*>::const_iterator it;
+
+ for (it=objectsSet_.begin(); it!=objectsSet_.end(); it++)
+ vkeys.push_back(it->first);
+
+ return vkeys;
+ }
+
+
+ /**
+ * @brief Get one object from the set knowing its index.
+ *
+ * @param objectIndex Index of the object in the set.
+ * @return A pointer toward the corresponding object.
+ */
+
+ const N* operator[](size_t objectIndex) const
+ {
+ typename std::map<size_t, N*>::const_iterator it=objectsSet_.find(objectIndex);
+ if (it==objectsSet_.end())
+ throw BadIntegerException("ParametrizableCollection::getObject().", (int)objectIndex);
+
+ return dynamic_cast<const N*>(it->second);
+ }
+
+ N* operator[](size_t objectIndex)
+ {
+ typename std::map<size_t, N*>::iterator it=objectsSet_.find(objectIndex);
+ if (it==objectsSet_.end())
+ throw BadIntegerException("ParametrizableCollection::getObject().", (int)objectIndex);
+
+ return it->second;
+ }
+
+ /**
+ * @brief Add a new object to the set with a given number.
+ *
+ * @throw Exception if the number is already used. See replace function instead.
+ *
+ * @param object A pointer toward an object, that will added to the set.
+ *
+ * WARNING! The set will now be the owner of the pointer, and will destroy it if needed!
+ * Copy the object first if you don't want it to be lost!
+ *
+ * @param objectIndex The number of the object in the Collection
+ *
+ */
+
+ void addObject(N* object, size_t objectIndex)
+ {
+ typename std::map<size_t, N*>::iterator it=objectsSet_.find(objectIndex);
+ if (it!=objectsSet_.end())
+ throw BadIntegerException("ParametrizableCollection<N>::addObject. Object objectIndex already used", (int)objectIndex);
+
+ objectsSet_[objectIndex]=object;
+
+ // Associate parameters:
+ std::string pname;
+ std::vector<std::string> nplm;
+ nplm=object->getParameters().getParameterNames();
+
+ for (size_t i = 0; i < nplm.size(); i++)
+ {
+ pname = nplm[i];
+ Parameter* p = new Parameter(object->getParameters().getParameter(pname));
+ p->setName(pname + "_" + TextTools::toString(objectIndex));
+ addParameter_(p);
+ }
+
+ if (dynamic_cast<ParameterAliasable*>(object)){
+ ParameterAliasable* ppa=dynamic_cast<ParameterAliasable*>(object);
+ for (size_t i = 0; i < nplm.size(); i++)
+ {
+ std::vector<std::string> va=ppa->getAlias(nplm[i]);
+ for (size_t j=0;j<va.size();j++)
+ aliasParameters(nplm[i] + "_" + TextTools::toString(objectIndex), va[j] + "_" + TextTools::toString(objectIndex));
+ }
+ }
+ }
+
+ /**
+ * @brief Remove a object from the set, and all corresponding
+ * parameters.
+ *
+ * @param objectIndex The index of the object in the set.
+ * @return the removed N*.
+ */
+
+ N* removeObject(size_t objectIndex)
+ {
+ if (objectsSet_.find(objectIndex)==objectsSet_.end())
+ throw BadIntegerException("ParametrizableCollection<N>::removeObject. None Object at this objectIndex", (int)objectIndex);
+
+ N* pm=objectsSet_[objectIndex];
+ objectsSet_.erase(objectIndex);
+
+ // Erase all parameter references to this object and translate other indices...
+
+ ParameterList pl=getParameters();
+
+ for (size_t i = pl.size(); i>0; i--)
+ {
+ std::string pn=pl[i-1].getName();
+
+ size_t pu=pn.rfind("_");
+ int nm=atoi(pn.substr(pu+1).c_str());
+ if (nm==(int)objectIndex){
+ std::vector<std::string> alpn=getAlias(pn);
+ for (unsigned j=0; j<alpn.size(); j++)
+ try {
+ unaliasParameters(alpn[j],pn);
+ }
+ catch (Exception& e)
+ {
+ continue;
+ }
+ deleteParameter_(i-1);
+ }
+ }
+
+ return pm;
+ }
+
+ /**
+ * @brief Replace a object in the set, and returns the replaced one.
+ *
+ * @param objectIndex The index of the object to be replaced in the set.
+ * @param object the replacing N
+ * @return the replaced N*.
+ */
+
+ N* replaceObject(N* object, size_t objectIndex)
+ {
+ N* pm=removeObject(objectIndex);
+ addObject(object, objectIndex);
+ return pm;
+ }
+
+
+ };
+} // end of namespace bpp.
+
+#endif // _PARAMETRIZABLECOLLECTION_H_
+
diff --git a/src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.cpp b/src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.cpp
index 3d25976..1dc4c40 100644
--- a/src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.cpp
+++ b/src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.cpp
@@ -158,7 +158,7 @@ Vdouble AbstractDiscreteDistribution::getCategories() const
Vdouble AbstractDiscreteDistribution::getProbabilities() const
{
Vdouble result(distribution_.size());
- int i = 0;
+ size_t i = 0;
for (map<double, double>::const_iterator it = distribution_.begin();
it != distribution_.end();
it++)
@@ -425,7 +425,7 @@ void AbstractDiscreteDistribution::discretize()
{
if (distribution_.find(values[i]) != distribution_.end())
{
- unsigned int j = 1;
+ int j = 1;
int f = ((values[i] + NumConstants::TINY()) >= intMinMax_.getUpperBound()) ? -1 : 1;
while (distribution_.find(values[i] + f * j * precision()) != distribution_.end())
{
diff --git a/src/Bpp/Numeric/Prob/ConstantDistribution.cpp b/src/Bpp/Numeric/Prob/ConstantDistribution.cpp
index 5dc0cd5..600f19b 100644
--- a/src/Bpp/Numeric/Prob/ConstantDistribution.cpp
+++ b/src/Bpp/Numeric/Prob/ConstantDistribution.cpp
@@ -76,12 +76,10 @@ ConstantDistribution& ConstantDistribution::operator=(const ConstantDistribution
void ConstantDistribution::fireParameterChanged(const ParameterList& parameters)
{
AbstractDiscreteDistribution::fireParameterChanged(parameters);
-
- if (hasParameter("value")) {
- value_=getParameterValue("value");
- distribution_.clear();
- distribution_[value_] = 1; //One single class of rate 1 with probability 1.
- }
+
+ value_=getParameterValue("value");
+ distribution_.clear();
+ distribution_[value_] = 1; //One single class of rate 1 with probability 1.
}
/******************************************************************************/
@@ -102,4 +100,4 @@ void ConstantDistribution::restrictToConstraint(const Constraint& c)
Parameter& p=getParameter_("value");
p.setConstraint(intMinMax_.clone(),true);
-}
+ }
diff --git a/src/Bpp/Numeric/Prob/ConstantDistribution.h b/src/Bpp/Numeric/Prob/ConstantDistribution.h
index aa7cbcc..75d9e9b 100644
--- a/src/Bpp/Numeric/Prob/ConstantDistribution.h
+++ b/src/Bpp/Numeric/Prob/ConstantDistribution.h
@@ -56,7 +56,7 @@ namespace bpp
private:
double value_;
-
+
public:
/**
* @brief Builds a new ConstantDistribution object from a
@@ -65,6 +65,7 @@ namespace bpp
* @param value The value of the distribution.
*
*/
+
ConstantDistribution(double value);
ConstantDistribution(const ConstantDistribution&);
diff --git a/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.h b/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.h
index f807a0f..7742ac1 100644
--- a/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.h
+++ b/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.h
@@ -5,37 +5,37 @@
//
/*
- Copyright or © or Copr. CNRS, (November 17, 2004)
-
- This software is a computer program whose purpose is to provide classes
- for numerical calculus.
-
- 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.
-*/
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for numerical calculus.
+
+ 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 _INVARIANTMIXEDDISCRETEDISTRIBUTION_H_
#define _INVARIANTMIXEDDISCRETEDISTRIBUTION_H_
@@ -44,119 +44,119 @@
namespace bpp
{
+/**
+ * @brief Discrete mixed distribution, with a one-category fixed value (called "invariant") and a user-specified multi-categories distribution.
+ *
+ * The term "invariant" comes from the use of such distributions in phylogenetics:
+ * the fixed category corresponds to a value of 0 and describes invariant positions in an alignment.
+ */
+class InvariantMixedDiscreteDistribution :
+ public AbstractDiscreteDistribution
+{
+private:
+ DiscreteDistribution* dist_;
+ double invariant_, p_;
+ std::string nestedPrefix_;
+public:
/**
- * @brief Discrete mixed distribution, with a one-category fixed value (called "invariant") and a user-specified multi-categories distribution.
+ * @brief Build a new InvariantMixedDiscreteDistribution object.
*
- * The term "invariant" comes from the use of such distributions in phylogenetics:
- * the fixed category corresponds to a value of 0 and describes invariant positions in an alignment.
+ * @param dist The distribution to use. The mixed distribution will "own" this distribution object.
+ * This means that the distribution will be cloned in case of copy of this instance, and will be
+ * deleted with this instance.
+ * @param p The probability of being in the invariant category.
+ * @param invariant The value of the invariant category (typically 0, but other values may be specified).
*/
- class InvariantMixedDiscreteDistribution:
- public AbstractDiscreteDistribution
+ InvariantMixedDiscreteDistribution(DiscreteDistribution* dist, double p, double invariant = 0.);
+
+ virtual ~InvariantMixedDiscreteDistribution()
{
- private:
- DiscreteDistribution* dist_;
- double invariant_, p_;
- std::string nestedPrefix_;
-
- public:
- /**
- * @brief Build a new InvariantMixedDiscreteDistribution object.
- *
- * @param dist The distribution to use. The mixed distribution will "own" this distribution object.
- * This means that the distribution will be cloned in case of copy of this instance, and will be
- * deleted with this instance.
- * @param p The probability of being in the invariant category.
- * @param invariant The value of the invariant category (typically 0, but other values may be specified).
- */
- InvariantMixedDiscreteDistribution(DiscreteDistribution* dist, double p, double invariant = 0.);
-
- virtual ~InvariantMixedDiscreteDistribution()
- {
- delete dist_;
- }
-
- InvariantMixedDiscreteDistribution(const InvariantMixedDiscreteDistribution& imdd):
- AbstractParameterAliasable(imdd),
- AbstractDiscreteDistribution(imdd),
- dist_(dynamic_cast<DiscreteDistribution *>(imdd.dist_->clone())),
- invariant_(imdd.invariant_), p_(imdd.p_),
- nestedPrefix_(imdd.nestedPrefix_)
- {}
-
- InvariantMixedDiscreteDistribution& operator=(const InvariantMixedDiscreteDistribution& imdd)
- {
- AbstractParameterAliasable::operator=(imdd);
- AbstractDiscreteDistribution::operator=(imdd);
- dist_ = dynamic_cast<DiscreteDistribution *>(imdd.dist_->clone());
- invariant_ = imdd.invariant_;
- p_ = imdd.p_;
- nestedPrefix_ = imdd.nestedPrefix_;
- return *this;
- }
+ delete dist_;
+ }
+
+ InvariantMixedDiscreteDistribution(const InvariantMixedDiscreteDistribution& imdd) :
+ AbstractParameterAliasable(imdd),
+ AbstractDiscreteDistribution(imdd),
+ dist_(dynamic_cast<DiscreteDistribution*>(imdd.dist_->clone())),
+ invariant_(imdd.invariant_),
+ p_(imdd.p_),
+ nestedPrefix_(imdd.nestedPrefix_)
+ {}
+
+ InvariantMixedDiscreteDistribution& operator=(const InvariantMixedDiscreteDistribution& imdd)
+ {
+ AbstractParameterAliasable::operator=(imdd);
+ AbstractDiscreteDistribution::operator=(imdd);
+ dist_ = dynamic_cast<DiscreteDistribution*>(imdd.dist_->clone());
+ invariant_ = imdd.invariant_;
+ p_ = imdd.p_;
+ nestedPrefix_ = imdd.nestedPrefix_;
+ return *this;
+ }
- InvariantMixedDiscreteDistribution* clone() const { return new InvariantMixedDiscreteDistribution(*this); }
+ InvariantMixedDiscreteDistribution* clone() const { return new InvariantMixedDiscreteDistribution(*this); }
- public:
+public:
+ std::string getName() const {return "Invariant"; }
- std::string getName() const {return("Invariant");}
+ void fireParameterChanged(const ParameterList& parameters);
- void fireParameterChanged(const ParameterList & parameters);
+ void setNamespace(const std::string& prefix);
- void setNamespace(const std::string& prefix);
+ /**
+ * @ brief Sets the number of categories of the embedded
+ * distribution. The number of categories of this class equals this
+ * plus one if the invariant_ is not in the embedded distribution
+ * values.
+ */
+ void setNumberOfCategories(size_t nbClasses)
+ {
+ dist_->setNumberOfCategories(nbClasses);
+ updateDistribution();
+ }
- /*
- *@ brief Sets the number of categories of the embedded
- *distribution. The number of categories of this class equals this
- *plus one if the invariant_ is not in the embedded distribution
- *values.
- *
- */
-
- void setNumberOfCategories(unsigned int nbClasses) {
- dist_->setNumberOfCategories(nbClasses);
- updateDistribution();
- }
-
- /**
- * @return The nested, conditional, sub-distribution.
- */
- const DiscreteDistribution * getVariableSubDistribution() const { return dist_; }
-
- double qProb(double x) const{
- return (x>=p_+(1-p_)*dist_->pProb(invariant_))?dist_->qProb((x-p_)/(1-p_)):dist_->qProb(x/(1-p_));
- }
-
- double pProb(double x) const{
- return (1-p_)*dist_->pProb(x)+(x<invariant_)?0:p_;
- }
-
- double Expectation(double a) const{
- return (1-p_)*dist_->Expectation(a)+(a<invariant_?0:p_);
- }
+ /**
+ * @return The nested, conditional, sub-distribution.
+ */
+ const DiscreteDistribution* getVariableSubDistribution() const { return dist_; }
- void setMedian(bool median){
- if (median_!=median){
- median_=median;
- dist_->setMedian(median);
- updateDistribution();
- }
- }
-
- void discretize(){
- dist_->discretize();
- updateDistribution();
- }
+ double qProb(double x) const
+ {
+ return (x >= p_ + (1 - p_) * dist_->pProb(invariant_)) ? dist_->qProb((x - p_) / (1 - p_)) : dist_->qProb(x / (1 - p_));
+ }
- void restrictToConstraint(const Constraint& c);
+ double pProb(double x) const
+ {
+ return (1 - p_) * dist_->pProb(x) + (x < invariant_ ? 0 : p_);
+ }
- protected:
- void updateDistribution();
+ double Expectation(double a) const
+ {
+ return (1 - p_) * dist_->Expectation(a) + (a < invariant_ ? 0 : p_);
+ }
+ void setMedian(bool median)
+ {
+ if (median_ != median)
+ {
+ median_ = median;
+ dist_->setMedian(median);
+ updateDistribution();
+ }
+ }
- };
+ void discretize()
+ {
+ dist_->discretize();
+ updateDistribution();
+ }
-} //end of namespace bpp.
+ void restrictToConstraint(const Constraint& c);
-#endif //_INVARIANTMIXEDDISCRETEDISTRIBUTION_H_
+protected:
+ void updateDistribution();
+};
+} // end of namespace bpp.
+#endif // _INVARIANTMIXEDDISCRETEDISTRIBUTION_H_
diff --git a/src/Bpp/Numeric/Prob/SimpleDiscreteDistribution.cpp b/src/Bpp/Numeric/Prob/SimpleDiscreteDistribution.cpp
index f7faf38..8fc0145 100644
--- a/src/Bpp/Numeric/Prob/SimpleDiscreteDistribution.cpp
+++ b/src/Bpp/Numeric/Prob/SimpleDiscreteDistribution.cpp
@@ -222,7 +222,7 @@ void SimpleDiscreteDistribution::fireParameterChanged(const ParameterList& param
v = getParameterValue("V" + TextTools::toString(i + 1));
if (distribution_.find(v) != distribution_.end())
{
- unsigned int j = 1;
+ int j = 1;
int f = ((v + precision()) >= intMinMax_.getUpperBound()) ? -1 : 1;
while (distribution_.find(v + f * j * precision()) != distribution_.end())
{
@@ -240,7 +240,7 @@ void SimpleDiscreteDistribution::fireParameterChanged(const ParameterList& param
v = getParameterValue("V" + TextTools::toString(size));
if (distribution_.find(v) != distribution_.end())
{
- unsigned int j = 1;
+ int j = 1;
int f = ((v + precision()) >= intMinMax_.getUpperBound()) ? -1 : 1;
while (distribution_.find(v + f * j * precision()) != distribution_.end())
{
diff --git a/src/Bpp/Numeric/Prob/Simplex.cpp b/src/Bpp/Numeric/Prob/Simplex.cpp
index 29bb5f5..b07591f 100644
--- a/src/Bpp/Numeric/Prob/Simplex.cpp
+++ b/src/Bpp/Numeric/Prob/Simplex.cpp
@@ -45,81 +45,131 @@
using namespace bpp;
using namespace std;
-Simplex::Simplex(const std::vector<double>& probas, unsigned short method, const std::string& name) : AbstractParameterAliasable(name),
+Simplex::Simplex(const std::vector<double>& probas, unsigned short method, bool allowNull, const std::string& name) : AbstractParameterAliasable(name),
dim_(probas.size()),
method_(method),
vProb_(),
valpha_()
{
+ if (dim_==0)
+ return;
+
double sum = VectorTools::sum(probas);
if (fabs(1. - sum) > NumConstants::SMALL())
throw Exception("Simplex. Probabilities must equal 1 (sum =" + TextTools::toString(sum) + ").");
+ const Constraint* pc = (allowNull ? &Parameter::PROP_CONSTRAINT_IN : &Parameter::PROP_CONSTRAINT_EX);
+
for (unsigned int i = 0; i < dim_; i++)
{
vProb_.push_back(probas[i]);
}
+ double y = 1;
switch (method_)
{
+ case 1:
+ for (unsigned int i = 0; i < dim_ - 1; i++)
+ {
+ addParameter_(new Parameter(name + "theta" + TextTools::toString(i + 1), vProb_[i] / y, pc));
+ y -= vProb_[i];
+ }
+ break;
case 2:
for (unsigned int i = 0; i < dim_ - 1; i++)
{
- addParameter_(new Parameter(name + "theta" + TextTools::toString(i + 1), vProb_[i] / (vProb_[i] + vProb_[i + 1]), &Parameter::PROP_CONSTRAINT_IN));
+ addParameter_(new Parameter(name + "theta" + TextTools::toString(i + 1), vProb_[i] / (vProb_[i] + vProb_[i + 1]), pc));
}
for (unsigned int i = 0; i < dim_ - 1; i++)
{
valpha_.push_back(vProb_[i + 1] / vProb_[i]);
}
break;
- case 1:
- double y = 1;
- for (unsigned int i = 0; i < dim_ - 1; i++)
+ case 3:
+ for (size_t i = 1; i < dim_; i++)
{
- addParameter_(new Parameter(name + "theta" + TextTools::toString(i + 1), vProb_[i] / y, &Parameter::PROP_CONSTRAINT_IN));
- y -= vProb_[i];
+ size_t o = i;
+ size_t li2 = 0; // rank of the strongest bit
+ while (o)
+ {
+ li2++;
+ o = o >> 1;
+ }
+
+ double i1 = 0, i0 = 0;
+ size_t j = 0;
+ size_t pi = i & ~(1 << (li2 - 1));
+ while (j < dim_)
+ {
+ size_t t = (j << li2) + pi;
+ if (t >= dim_)
+ break;
+ else
+ i0 += vProb_[t];
+ t += (1 << (li2 - 1));
+ if (t < dim_)
+ i1 += vProb_[t];
+ j++;
+ }
+ addParameter_(new Parameter(name + "theta" + TextTools::toString(i), i1 / (i0 + i1), pc));
}
break;
}
}
-Simplex::Simplex(size_t dim, unsigned short method, const std::string& name) :
+Simplex::Simplex(size_t dim, unsigned short method, bool allowNull, const std::string& name) :
AbstractParameterAliasable(name),
dim_(dim),
method_(method),
vProb_(),
valpha_()
{
+ if (dim_==0)
+ return;
+
for (size_t i = 0; i < dim_; i++)
{
vProb_.push_back(1. / static_cast<double>(dim_));
}
+ const Constraint* pc = (allowNull ? &Parameter::PROP_CONSTRAINT_IN : &Parameter::PROP_CONSTRAINT_EX);
+
+ double y = 1;
switch (method_)
{
+ case 1:
+ for (unsigned int i = 0; i < dim_ - 1; i++)
+ {
+ addParameter_(new Parameter(name + "theta" + TextTools::toString(i + 1), vProb_[i] / y, pc));
+ y -= vProb_[i];
+ }
+ break;
case 2:
for (unsigned int i = 0; i < dim_ - 1; i++)
{
- addParameter_(new Parameter(name+ "theta" + TextTools::toString(i + 1), 0.5, &Parameter::PROP_CONSTRAINT_IN));
+ addParameter_(new Parameter(name + "theta" + TextTools::toString(i + 1), 0.5, pc));
}
for (unsigned int i = 0; i < dim_ - 1; i++)
{
valpha_.push_back(1.);
}
break;
- case 1:
- double y = 1;
+ case 3:
for (unsigned int i = 0; i < dim_ - 1; i++)
{
- addParameter_(new Parameter(name+"theta" + TextTools::toString(i + 1), vProb_[i] / y, &Parameter::PROP_CONSTRAINT_IN));
- y -= vProb_[i];
+ addParameter_(new Parameter(name + "theta" + TextTools::toString(i + 1), 0.5, pc));
}
+ setFrequencies(vProb_);
+
break;
}
}
void Simplex::fireParameterChanged(const ParameterList& parameters)
{
+ if (dim_==0)
+ return;
+
AbstractParameterAliasable::fireParameterChanged(parameters);
double x = 1.0;
@@ -151,15 +201,47 @@ void Simplex::fireParameterChanged(const ParameterList& parameters)
x += vProb_[i + 1];
}
for (unsigned int i = 0; i < dim_; i++)
+ {
vProb_[i] /= x;
+ }
break;
+ case 3:
+ size_t o = dim_;
+ size_t ld2 = 0; // rank of the strongest bit
+ while (o)
+ {
+ ld2++;
+ o = o >> 1;
+ }
+ for (size_t i = 0; i < dim_; i++)
+ {
+ x = 1;
+ size_t ld = ld2;
+ size_t k = i;
+ while (ld)
+ {
+ if (k >> (ld - 1))
+ x *= getParameterValue("theta" + TextTools::toString(k));
+ else
+ {
+ if ((k + (1 << (ld - 1))) < dim_)
+ x *= 1 - getParameterValue("theta" + TextTools::toString(k + (1 << (ld - 1))));
+ }
+ k &= ~(1 << (--ld));
+ }
+ vProb_[i] = x;
+ }
+ break;
}
}
void Simplex::setFrequencies(const std::vector<double>& probas)
{
+ if (dim_==0)
+ return;
+
double sum = VectorTools::sum(probas);
if (fabs(1. - sum) > NumConstants::SMALL())
throw Exception("Simplex::setFrequencies. Probabilities must equal 1 (sum =" + TextTools::toString(sum) + ").");
@@ -168,22 +250,51 @@ void Simplex::setFrequencies(const std::vector<double>& probas)
ParameterList pl;
switch (method_)
+ {
+ case 1:
+ for (unsigned int i = 0; i < dim_ - 1; i++)
{
- case 1:
- for (unsigned int i = 0; i < dim_ - 1; i++)
- {
- pl.addParameter(Parameter(getNamespace()+"theta" + TextTools::toString(i + 1), probas[i] / y));
- y -= probas[i];
- }
- break;
- case 2:
- for (unsigned int i = 0; i < dim_ - 1; i++)
- {
- pl.addParameter(Parameter(getNamespace()+"theta" + TextTools::toString(i + 1), probas[i] / (probas[i] + probas[i + 1])));
- valpha_[i]=probas[i + 1] / probas[i];
- }
- break;
+ pl.addParameter(Parameter(getNamespace() + "theta" + TextTools::toString(i + 1), probas[i] / y));
+ y -= probas[i];
+ }
+ break;
+ case 2:
+ for (unsigned int i = 0; i < dim_ - 1; i++)
+ {
+ pl.addParameter(Parameter(getNamespace() + "theta" + TextTools::toString(i + 1), probas[i] / (probas[i] + probas[i + 1])));
+ valpha_[i] = probas[i + 1] / probas[i];
}
+ break;
+ case 3:
+ for (size_t i = 1; i < dim_; i++)
+ {
+ size_t o = i;
+ size_t li2 = 0; // rank of the strongest bit
+ while (o)
+ {
+ li2++;
+ o = o >> 1;
+ }
+
+ double i1 = 0, i0 = 0;
+ size_t j = 0;
+ size_t pi = i & ~(1 << (li2 - 1));
+ while (j < dim_)
+ {
+ size_t t = (j << li2) + pi;
+ if (t >= dim_)
+ break;
+ else
+ i0 += vProb_[t];
+ t += (1 << (li2 - 1));
+ if (t < dim_)
+ i1 += vProb_[t];
+ j++;
+ }
+ pl.addParameter(Parameter(getNamespace() + "theta" + TextTools::toString(i), i1 / (i0 + i1)));
+ }
+ break;
+ }
matchParametersValues(pl);
}
diff --git a/src/Bpp/Numeric/Prob/Simplex.h b/src/Bpp/Numeric/Prob/Simplex.h
index 20c1f66..cf93cb4 100644
--- a/src/Bpp/Numeric/Prob/Simplex.h
+++ b/src/Bpp/Numeric/Prob/Simplex.h
@@ -5,37 +5,37 @@
//
/*
-Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
-
-This software is a computer program whose purpose is to provide classes
-for numerical calculus.
-
-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.
-*/
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for numerical calculus.
+
+ 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 _SIMPLEX_H_
#define _SIMPLEX_H_
@@ -48,7 +48,6 @@ knowledge of the CeCILL license and that you accept its terms.
namespace bpp
{
-
/**
* @brief A Simplex object, used to define sets of probabilities that
* sum 1.
@@ -76,41 +75,57 @@ namespace bpp
* In the reverse if we denote @f$\alpha_i=\frac{1-\theta_i}{\theta_i}@f$,
* @f$p_i=\frac{\alpha_1...\alpha_{i-1}}{1+\sum_{k=1}^{n-1}\alpha_1...\alpha_k}@f$.
*
+ * Binary:
+ *
+ * This parametrization is based on the binary coding.
+ *
+ * Given @f$a_b...a_1 at f$ the writing of i in binary, we denote
+ * @f$i_k=a_k...a_1 at f$.
+ *
+ * Given @f$a_b...a_1 at f$ the writing of i in binary where @f$a_b=1 at f$,
+ * we denote @f$1_i=\sum\{p_{j+1} \text{ such that } j_b=i_b=1i_{b-1}\}@f$ and
+ * @f$0_i=\sum\{p_{j+1} \text{ such that } j_b=0i_{b-1}\}@f$, and then we define:
+ *
+ *
+ * @f$\theta_i=\frac{1_i}{1_i+0_i}@f$
+ *
+ * and on the reverse, we denote @f$\theta'_{0i_{b-1}}=1-\theta_i at f$
+ * and @f$\theta'_{1i_{b-1}}=\theta_i at f$.
+ *
+ * Then, if @f$c=ceil(log_2(n))@f$, for @f$i \in <0,n-1>@f$.
+ *
+ * @f$p_{i+1}=\theta'_{i_c}....\theta'_{i_1} @f$
+ *
*/
-
- class Simplex:
- public AbstractParameterAliasable
+class Simplex :
+ public AbstractParameterAliasable
{
private:
- /*
- *@brief The dimension+1 of the space simplex (ie the number of probabilities).
+
+ /**
+ * @brief The dimension+1 of the space simplex (ie the number of probabilities).
*
*/
-
size_t dim_;
- /*
- *@brief the method of parametrization.
+ /**
+ * @brief the method of parametrization.
*
* 0: No parametrization
* 1: Global ratio
* 2: Local ratio
- *
+ * 3: Binary
*/
unsigned short method_;
-
+
std::vector<double> vProb_;
- /*
- *@brief just used with local ratio (method 2)
- *
+ /**
+ * @brief just used with local ratio (method 2)
*/
-
std::vector<double> valpha_;
-
-
-public:
+public:
/**
* @brief Builds a new Simplex object from a number of
* probabilities. They are initialized equal.
@@ -120,11 +135,12 @@ public:
* 0: No parametrization
* 1: Global ratio
* 2: Local ratio
+ * 3: Binary
+ * @param allowNull if null probabilites are allowed (default: false)
* @param name The name passed to AbstractParameterAliasable constructor.
*
*/
-
- Simplex(size_t dim, unsigned short method = 0, const std::string& name = "Simplex.");
+ Simplex(size_t dim, unsigned short method = 0, bool allowNull = false, const std::string& name = "Simplex.");
/**
* @brief Builds a new Simplex object from a vector of probabilities
@@ -134,29 +150,33 @@ public:
* 0: No parametrization
* 1: Global ratio
* 2: Local ratio
+ * 3: Binary
+ * @param allowNull if null probabilites are allowed (default: false)
* @param name The name passed to AbstractParameterAliasable constructor.
*
*/
+ Simplex(const std::vector<double>& probas, unsigned short method = 0, bool allowNull = false, const std::string& name = "Simplex.");
- Simplex(const std::vector<double>& probas, unsigned short method = 0, const std::string& name = "Simplex.");
-
virtual ~Simplex() {}
Simplex* clone() const { return new Simplex(*this); }
public:
- void fireParameterChanged(const ParameterList & parameters);
+ void fireParameterChanged(const ParameterList& parameters);
size_t dimension() const { return dim_; }
void setFrequencies(const std::vector<double>&);
-
- double prob(size_t i) const { return vProb_[i];}
- unsigned short getMethod() const { return method_;}
-};
+ const std::vector<double>& getFrequencies() const { return vProb_;}
-} //end of namespace bpp.
+ std::vector<double>& getFrequencies() { return vProb_;}
+
+ double prob(size_t i) const { return vProb_[i]; }
+
+ unsigned short getMethod() const { return method_; }
+};
+} // end of namespace bpp.
-#endif //_SIMPLEDISCRETEDISTRIBUTION_H_
+#endif // _SIMPLEDISCRETEDISTRIBUTION_H_
diff --git a/src/Bpp/Numeric/Random/RandomTools.cpp b/src/Bpp/Numeric/Random/RandomTools.cpp
index 42e7516..e470001 100644
--- a/src/Bpp/Numeric/Random/RandomTools.cpp
+++ b/src/Bpp/Numeric/Random/RandomTools.cpp
@@ -72,13 +72,6 @@ bool RandomTools::flipCoin(const RandomFactory& generator)
return (RandomTools::giveRandomNumberBetweenZeroAndEntry(1.0, generator) - 0.5) > 0;
}
-// Method to get a integer random value (between 0 and specified range)
-// Note : the number you get is between 0 and entry not including entry !
-int RandomTools::giveIntRandomNumberBetweenZeroAndEntry(int entry, const RandomFactory& generator)
-{
- return static_cast<int>(giveRandomNumberBetweenZeroAndEntry(entry, generator));
-}
-
double RandomTools::randGaussian(double mean, double variance, const RandomFactory& generator)
{
return RandomTools::qNorm(generator.drawNumber(), mean, sqrt(variance));
@@ -256,7 +249,7 @@ double RandomTools::lnGamma (double alpha)
double RandomTools::incompleteGamma (double x, double alpha, double ln_gamma_alpha)
{
- int i;
+ size_t i;
double p = alpha, g = ln_gamma_alpha;
double accurate = 1e-8, overflow = 1e30;
double factor, gin = 0, rn = 0, a = 0, b = 0, an = 0, dif = 0, term = 0;
diff --git a/src/Bpp/Numeric/Random/RandomTools.h b/src/Bpp/Numeric/Random/RandomTools.h
index 04ba6eb..77bb820 100644
--- a/src/Bpp/Numeric/Random/RandomTools.h
+++ b/src/Bpp/Numeric/Random/RandomTools.h
@@ -117,7 +117,10 @@ namespace bpp
* @param entry Max number to reach.
* @param generator Random number generator to use.
*/
- static int giveIntRandomNumberBetweenZeroAndEntry(int entry, const RandomFactory& generator = *DEFAULT_GENERATOR);
+ template<class intType>
+ static intType giveIntRandomNumberBetweenZeroAndEntry(intType entry, const RandomFactory& generator = *DEFAULT_GENERATOR) {
+ return static_cast<intType>(giveRandomNumberBetweenZeroAndEntry(static_cast<double>(entry), generator));
+ }
/**
* @brief Set the default generator seed.
@@ -155,7 +158,6 @@ namespace bpp
* @param beta The beta parameter.
* @param generator The uniform generator to use.
*/
-
static double randBeta(double alpha, double beta, const RandomFactory& generator = *DEFAULT_GENERATOR);
/**
@@ -181,7 +183,7 @@ namespace bpp
static T pickOne(std::vector<T>& v, bool replace = false) throw (EmptyVectorException<T>) {
if (v.empty())
throw EmptyVectorException<T>("RandomTools::pickOne: input vector is empty", &v);
- size_t pos = static_cast<size_t>(RandomTools::giveIntRandomNumberBetweenZeroAndEntry(static_cast<int>(v.size())));
+ size_t pos = RandomTools::giveIntRandomNumberBetweenZeroAndEntry<size_t>(v.size());
if (replace)
return v[pos];
else {
@@ -192,6 +194,14 @@ namespace bpp
}
}
+ template<class T>
+ static T pickOne(const std::vector<T>& v) throw (EmptyVectorException<T>) {
+ if (v.empty())
+ throw EmptyVectorException<T>("RandomTools::pickOne: input vector is empty", &v);
+ size_t pos = RandomTools::giveIntRandomNumberBetweenZeroAndEntry<size_t>(v.size());
+ return v[pos];
+ }
+
/**
* @brief Sample a vector.
*
@@ -273,7 +283,7 @@ namespace bpp
* the result is a shuffle of the original vector.
*
* It has to be noted that in case of sampling without replacement,
- * the effect of the weighting scheme will be lower as the sampe size becomes
+ * the effect of the weighting scheme will be weaker as the sample size becomes
* close to the population size. In case the two are equal (pure permutations),
* the weigths have no effect at all.
*
@@ -285,7 +295,8 @@ namespace bpp
* @throw IndexOutOfBoundException if the sample size exceeds the original
* size when sampling without replacement.
* @throw EmptyVectorException if the vector is empty.
- *
+ * @warning: For large sampling with replacement, the function is not efficient,
+ * as it recomputes the some of weights for each element picked.
* @author Julien Dutheil
*/
template<class T>
diff --git a/src/Bpp/Numeric/Range.h b/src/Bpp/Numeric/Range.h
index 81cf091..bb4a669 100644
--- a/src/Bpp/Numeric/Range.h
+++ b/src/Bpp/Numeric/Range.h
@@ -47,8 +47,8 @@
#include <string>
#include <set>
#include <algorithm>
-
#include <iostream>
+#include <cstddef>
namespace bpp {
@@ -428,7 +428,7 @@ template<class T> class MultiRange:
ranges_[overlappingPositions[0]]->expandWith(*ranges_[overlappingPositions[i]]);
//Then removes this range:
delete ranges_[overlappingPositions[i]];
- ranges_.erase(ranges_.begin() + overlappingPositions[i]);
+ ranges_.erase(ranges_.begin() + static_cast<ptrdiff_t>(overlappingPositions[i]));
}
}
clean_();
diff --git a/src/Bpp/Numeric/TransformedParameter.h b/src/Bpp/Numeric/TransformedParameter.h
index 3360b36..88ae8e7 100644
--- a/src/Bpp/Numeric/TransformedParameter.h
+++ b/src/Bpp/Numeric/TransformedParameter.h
@@ -5,7 +5,7 @@
//
/*
-Copyright or © or Copr. CNRS, (November 19, 2004)
+Copyright or © or Copr. Bio++ Development Team, (November 19, 2004)
This software is a computer program whose purpose is to provide classes
for numerical calculus.
@@ -195,7 +195,7 @@ class RTransformedParameter:
* @f[
* x' = s\tan\left(\pi\frac{x-a}{b-a} - \frac{\pi}{2}\right)
* @f]
- * The 'a' and 'b' parameters are the lower and upper bounds and 's' is a sclaing factor set to 1 by default.
+ * The 'a' and 'b' parameters are the lower and upper bounds and 's' is a scaling factor set to 1 by default.
* If the hyperbolic option is set to true (the default), then the following transformation is used instead:
* @f[
* x' = s\,\text{atanh}\left(2\frac{x-a}{b-a} - 1\right)
@@ -221,7 +221,7 @@ class IntervalTransformedParameter:
* @param lowerBound the inerval lower bound to use.
* @param upperBound the inerval lower bound to use.
* @param scale the scaling factor.
- * @param hyper tell if the hyberboic function should be used (true by default).
+ * @param hyper tell if the hyberbolic function should be used (true by default).
*/
IntervalTransformedParameter(const std::string& name, double value, double lowerBound = 0, double upperBound = 1, double scale = 1, bool hyper = true):
TransformedParameter(name, hyper ?
@@ -242,7 +242,7 @@ class IntervalTransformedParameter:
if (value <= lowerBound_ || value >= upperBound_) throw ConstraintException("IntervalTransformedParameter::setValue", this, value);
setValue(hyper_ ?
scale_ * atanh(2. * (value - lowerBound_) / (upperBound_ - lowerBound_) - 1.) :
- scale_ * tan(NumConstants::PI() * (value - lowerBound_)/(upperBound_ - lowerBound_) - NumConstants::PI() / 2.));
+ scale_ * std::tan(NumConstants::PI() * (value - lowerBound_)/(upperBound_ - lowerBound_) - NumConstants::PI() / 2.));
}
double getOriginalValue() const
@@ -259,7 +259,7 @@ class IntervalTransformedParameter:
{
double x = getValue();
double x2 = hyper_ ?
- 1. / (cosh(pow(x / scale_, 2))) * (upperBound_ - lowerBound_) / (2. * scale_) :
+ 1. / (pow(cosh(x / scale_), 2)) * (upperBound_ - lowerBound_) / (2. * scale_) :
(upperBound_ - lowerBound_) / (NumConstants::PI() * scale_ * (pow(x / scale_, 2) + 1.));
return x2;
}
@@ -267,7 +267,7 @@ class IntervalTransformedParameter:
{
double x = getValue();
double x2 = hyper_ ?
- - 1. / (cosh(pow(x / scale_, 2))) * tanh(x / scale_) *(upperBound_ - lowerBound_) / (scale_ * scale_) :
+ - 1. / (pow(cosh(x / scale_), 2)) * tanh(x / scale_) * (upperBound_ - lowerBound_) / (scale_ * scale_) :
-2. * x * (upperBound_ - lowerBound_) / (NumConstants::PI() * pow(scale_, 3) * pow((pow(x / scale_, 2) + 1.), 2));
return x2;
}
diff --git a/src/Bpp/Numeric/VectorTools.h b/src/Bpp/Numeric/VectorTools.h
index 8c4ea51..8967d26 100644
--- a/src/Bpp/Numeric/VectorTools.h
+++ b/src/Bpp/Numeric/VectorTools.h
@@ -839,6 +839,7 @@ public:
static std::string paste(const std::vector<T>& v, const std::string& delim = " ")
{
std::ostringstream out;
+ out.precision(12);
for (size_t i = 0; i < v.size(); i++)
{
out << v[i];
diff --git a/src/Bpp/Text/KeyvalTools.cpp b/src/Bpp/Text/KeyvalTools.cpp
index 1b8f78b..396db5e 100644
--- a/src/Bpp/Text/KeyvalTools.cpp
+++ b/src/Bpp/Text/KeyvalTools.cpp
@@ -89,6 +89,8 @@ void KeyvalTools::multipleKeyvals(const std::string& desc, std::map<std::string,
for (vector<string>::iterator it = tokens.begin(); it != tokens.end(); it++)
{
singleKeyval(*it, key, val);
+ key=TextTools::removeSurroundingWhiteSpaces(key);
+ val=TextTools::removeSurroundingWhiteSpaces(val);
keyvals[key] = val;
}
}
diff --git a/src/Bpp/Text/NestedStringTokenizer.cpp b/src/Bpp/Text/NestedStringTokenizer.cpp
index bff6bc6..b51b7e5 100644
--- a/src/Bpp/Text/NestedStringTokenizer.cpp
+++ b/src/Bpp/Text/NestedStringTokenizer.cpp
@@ -5,36 +5,36 @@
//
/*
-Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
-This software is a computer program whose purpose is to map data onto
-a sequence or a phylogenetic tree.
+ This software is a computer program whose purpose is to map data onto
+ a sequence or a phylogenetic tree.
-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".
+ 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.
+ 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.
+ 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 fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
*/
#include "NestedStringTokenizer.h"
@@ -49,29 +49,29 @@ using namespace std;
NestedStringTokenizer::NestedStringTokenizer(const std::string& s, const std::string& open, const std::string& end, const std::string& delimiters, bool solid)
throw (Exception):
- StringTokenizer()
+ StringTokenizer()
{
int blocks = 0;
string cache = "";
- if (!solid)
+ if (!solid)
{
string::size_type index = s.find_first_not_of(delimiters, 0);
- while (index != s.npos)
+ while (index != s.npos)
{
string::size_type newIndex = s.find_first_of(delimiters, index);
bool endBlockFound = false;
while (!endBlockFound)
{
- if (newIndex != s.npos)
+ if (newIndex != s.npos)
{
- string token = s.substr(index, newIndex - index);
+ string token = s.substr(index, newIndex - index);
blocks += static_cast<int>(TextTools::count(token, open)) - static_cast<int>(TextTools::count(token, end));
- if (blocks == 0)
+ if (blocks == 0)
{
tokens_.push_back(cache + token);
cache = ""; //reset cache.
- index = s.find_first_not_of(delimiters, newIndex);
+ index = s.find_first_not_of(delimiters, newIndex);
endBlockFound = true;
}
else
@@ -81,42 +81,42 @@ NestedStringTokenizer::NestedStringTokenizer(const std::string& s, const std::st
index = newIndex + 1;
newIndex = s.find_first_of(delimiters, index);
}
- }
+ }
else
{
- string token = s.substr(index);
+ string token = s.substr(index);
blocks += static_cast<int>(TextTools::count(token, open)) - static_cast<int>(TextTools::count(token, end));
- if (blocks == 0)
+ if (blocks == 0)
{
- tokens_.push_back(cache + token);
+ tokens_.push_back(cache + token);
cache = ""; //reset cache.
- index = newIndex;
+ index = newIndex;
endBlockFound = true;
}
else throw Exception("NestedStringTokenizer (constructor). Unclosed block.");
- }
+ }
}
- }
- }
- else
+ }
+ }
+ else
{
string::size_type index = 0;
- while (index != s.npos)
+ while (index != s.npos)
{
string::size_type newIndex = s.find(delimiters, index);
bool endBlockFound = false;
while (!endBlockFound)
{
- if (newIndex != s.npos)
+ if (newIndex != s.npos)
{
- string token = s.substr(index, newIndex - index);
+ string token = s.substr(index, newIndex - index);
blocks += static_cast<int>(TextTools::count(token, open)) - static_cast<int>(TextTools::count(token, end));
if (blocks == 0)
{
tokens_.push_back(cache + token);
cache = ""; //reset cache.
- index = newIndex + delimiters.size();
+ index = newIndex + delimiters.size();
endBlockFound = true;
}
else
@@ -126,28 +126,28 @@ NestedStringTokenizer::NestedStringTokenizer(const std::string& s, const std::st
index = newIndex + 1;
newIndex = s.find(delimiters, index);
}
- }
+ }
else
{
- string token = s.substr(index);
+ string token = s.substr(index);
blocks += static_cast<int>(TextTools::count(token, open)) - static_cast<int>(TextTools::count(token, end));
- if (blocks == 0)
+ if (blocks == 0)
{
- tokens_.push_back(cache + token);
+ tokens_.push_back(cache + token);
cache = ""; //reset cache.
- index = newIndex;
+ index = newIndex;
endBlockFound = true;
}
else throw Exception("Unclosed block.");
- }
- }
- }
+ }
+ }
+ }
}
}
const std::string& NestedStringTokenizer::nextToken() throw (Exception)
{
- if (!hasMoreToken()) throw Exception("No more token in nested tokenizer.");
- return tokens_[currentPosition_++];
+ if (!hasMoreToken()) throw Exception("No more token in nested tokenizer.");
+ return tokens_[currentPosition_++];
}
diff --git a/src/Bpp/Text/NestedStringTokenizer.h b/src/Bpp/Text/NestedStringTokenizer.h
index 0a4dd36..9ba5f8b 100644
--- a/src/Bpp/Text/NestedStringTokenizer.h
+++ b/src/Bpp/Text/NestedStringTokenizer.h
@@ -5,36 +5,36 @@
//
/*
-Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
-
-This software is a computer program whose purpose is to map data onto
-a sequence or a phylogenetic tree.
-
-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.
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to map data onto
+ a sequence or a phylogenetic tree.
+
+ 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 _NESTEDSTRINGTOKENIZER_H_
@@ -50,39 +50,39 @@ knowledge of the CeCILL license and that you accept its terms.
namespace bpp
{
-/**
- * @brief An improved tokenizer for strings.
- *
- * Splits a string according to a given (set of) delimiter(s).
- * Delimiters in certains blocks ({}, [], etc) are ignored.
- */
-class NestedStringTokenizer:
- public StringTokenizer
-{
- public:
+ /**
+ * @brief An improved tokenizer for strings.
+ *
+ * Splits a string according to a given (set of) delimiter(s).
+ * Delimiters in certains blocks ({}, [], etc) are ignored.
+ */
+ class NestedStringTokenizer:
+ public StringTokenizer
+ {
+ public:
- /**
- * @brief Build a new StringTokenizer from a string.
- *
- * @param s The string to parse.
+ /**
+ * @brief Build a new StringTokenizer from a string.
+ *
+ * @param s The string to parse.
* @param open Opening block.
* @param end Ending block.
- * @param delimiters Chars that must be considered as delimiters.
- * @param solid If true, delimiters is considered as a single bloc delimiter.
- */
- NestedStringTokenizer(const std::string& s, const std::string& open, const std::string& end, const std::string& delimiters = " \t\n\f\r", bool solid = false) throw (Exception);
+ * @param delimiters Chars that must be considered as delimiters.
+ * @param solid If true, delimiters is considered as a single bloc delimiter.
+ */
+ NestedStringTokenizer(const std::string& s, const std::string& open, const std::string& end, const std::string& delimiters = " \t\n\f\r", bool solid = false) throw (Exception);
- virtual ~NestedStringTokenizer() {}
+ virtual ~NestedStringTokenizer() {}
- public:
+ public:
- /**
- * @brief Get the next available token.
- * If no token is availbale, throw an Exception.
- *
- * @return The next token if there is one.
- */
- const std::string& nextToken() throw (Exception);
+ /**
+ * @brief Get the next available token.
+ * If no token is availbale, throw an Exception.
+ *
+ * @return The next token if there is one.
+ */
+ const std::string& nextToken() throw (Exception);
/**
@@ -91,7 +91,7 @@ class NestedStringTokenizer:
* @return An empty string.
*/
std::string unparseRemainingTokens() const { return ""; }
-};
+ };
} //end of namespace bpp;
diff --git a/src/Bpp/Text/StringTokenizer.cpp b/src/Bpp/Text/StringTokenizer.cpp
index 51389a9..ac2caa3 100644
--- a/src/Bpp/Text/StringTokenizer.cpp
+++ b/src/Bpp/Text/StringTokenizer.cpp
@@ -105,7 +105,7 @@ void StringTokenizer::removeEmptyTokens()
{
for (size_t i = tokens_.size(); i > currentPosition_; i--)
{
- if (tokens_[i-1] == "") tokens_.erase(tokens_.begin() + i - 1);
+ if (tokens_[i - 1] == "") tokens_.erase(tokens_.begin() + static_cast<ptrdiff_t>(i - 1));
}
}
diff --git a/src/Bpp/Text/StringTokenizer.h b/src/Bpp/Text/StringTokenizer.h
index 3e96097..a7061e0 100644
--- a/src/Bpp/Text/StringTokenizer.h
+++ b/src/Bpp/Text/StringTokenizer.h
@@ -6,36 +6,36 @@
//
/*
-Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
-
-This software is a computer program whose purpose is to provide utilitary
-classes. This file belongs to the Bio++ Project.
-
-This software is governed by the CeCILL license under French law and
-abiding by the rules of distribution of free software. You can use,
-modify and/ or redistribute the software under the terms of the CeCILL
-license as circulated by CEA, CNRS and INRIA at the following URL
-"http://www.cecill.info".
-
-As a counterpart to the access to the source code and rights to copy,
-modify and redistribute granted by the license, users are provided only
-with a limited warranty and the software's author, the holder of the
-economic rights, and the successive licensors have only limited
-liability.
-
-In this respect, the user's attention is drawn to the risks associated
-with loading, using, modifying and/or developing or reproducing the
-software by the user in light of its specific status of free software,
-that may mean that it is complicated to manipulate, and that also
-therefore means that it is reserved for developers and experienced
-professionals having in-depth computer knowledge. Users are therefore
-encouraged to load and test the software's suitability as regards their
-requirements in conditions enabling the security of their systems and/or
-data to be ensured and, more generally, to use and operate it in the
-same conditions as regards security.
-
-The fact that you are presently reading this means that you have had
-knowledge of the CeCILL license and that you accept its terms.
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide utilitary
+ classes. This file belongs to the Bio++ Project.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
*/
#ifndef _STRINGTOKENIZER_H_
@@ -55,75 +55,75 @@ namespace bpp
*
* Splits a string according to a given (set of) delimiter(s).
*/
-class StringTokenizer
-{
- protected:
+ class StringTokenizer
+ {
+ protected:
- /** @brief Where the tokens are stored. */
+ /** @brief Where the tokens are stored. */
std::deque<std::string> tokens_;
std::deque<std::string> splits_;
- /** @brief the current position in the token list. */
- size_t currentPosition_;
+ /** @brief the current position in the token list. */
+ size_t currentPosition_;
- public:
+ public:
- /**
- * @brief Build a new StringTokenizer from a string.
- *
- * @param s The string to parse.
- * @param delimiters Chars that must be considered as delimiters.
- * @param solid If true, delimiters is considered as a single bloc delimiter.
+ /**
+ * @brief Build a new StringTokenizer from a string.
+ *
+ * @param s The string to parse.
+ * @param delimiters Chars that must be considered as delimiters.
+ * @param solid If true, delimiters is considered as a single bloc delimiter.
* @param allowEmptyTokens Tell if empty tokens are allowed or should be ignored.
- */
- StringTokenizer(const std::string& s, const std::string& delimiters = " \t\n\f\r", bool solid = false, bool allowEmptyTokens = false);
+ */
+ StringTokenizer(const std::string& s, const std::string& delimiters = " \t\n\f\r", bool solid = false, bool allowEmptyTokens = false);
- virtual ~StringTokenizer() {}
+ virtual ~StringTokenizer() {}
public:
StringTokenizer(): tokens_(), splits_(), currentPosition_(0) {}
- public:
+ public:
- /**
- * @brief Get the next available token.
- * If no token is availbale, throw an Exception.
- *
- * @return The next token if there is one.
- */
+ /**
+ * @brief Get the next available token.
+ * If no token is availbale, throw an Exception.
+ *
+ * @return The next token if there is one.
+ */
const std::string& nextToken() throw (Exception);
- /**
- * @brief Tell if some tokens are still available.
- * @return True if some tokens are still available.
- */
- bool hasMoreToken() const {
+ /**
+ * @brief Tell if some tokens are still available.
+ * @return True if some tokens are still available.
+ */
+ bool hasMoreToken() const {
return currentPosition_ < tokens_.size();
}
- /**
- * @brief Tell how many tokens are available.
- *
- * @return the number of tokens available.
- */
- size_t numberOfRemainingTokens() const { return tokens_.size() - currentPosition_; }
-
- /**
- * @brief Get a particular token.
- *
- * Do not move the iterator.
- *
- * @param pos The index of the token.
- * @return the token at position 'pos'.
- */
+ /**
+ * @brief Tell how many tokens are available.
+ *
+ * @return the number of tokens available.
+ */
+ size_t numberOfRemainingTokens() const { return tokens_.size() - currentPosition_; }
+
+ /**
+ * @brief Get a particular token.
+ *
+ * Do not move the iterator.
+ *
+ * @param pos The index of the token.
+ * @return the token at position 'pos'.
+ */
const std::string& getToken(size_t pos) const { return tokens_[pos]; }
- /**
- * @brief Retrieve all tokens.
- *
- * @return A reference toward the vector of tokens.
- */
- const std::deque<std::string>& getTokens() const { return tokens_; }
+ /**
+ * @brief Retrieve all tokens.
+ *
+ * @return A reference toward the vector of tokens.
+ */
+ const std::deque<std::string>& getTokens() const { return tokens_; }
/**
* @brief remove all empty token from the current position.
@@ -134,7 +134,7 @@ class StringTokenizer
* @return The remaining tokens as if the original corresponding string was not parsed.
*/
std::string unparseRemainingTokens() const;
-};
+ };
} //end of namespace bpp.
diff --git a/src/Bpp/Text/TextTools.cpp b/src/Bpp/Text/TextTools.cpp
index f187f7e..b531b8a 100644
--- a/src/Bpp/Text/TextTools.cpp
+++ b/src/Bpp/Text/TextTools.cpp
@@ -215,6 +215,9 @@ bool TextTools::isDecimalNumber(char c)
bool TextTools::isDecimalNumber(const std::string& s, char dec, char scientificNotation)
{
+ if (isEmpty(s))
+ return false;
+
size_t sepCount = 0;
size_t sciCount = 0;
size_t i = 0;
@@ -228,7 +231,7 @@ bool TextTools::isDecimalNumber(const std::string& s, char dec, char scientificN
sciCount++;
if (i == s.size() - 1) return false; //Must be sthg after scientific notation.
c = s[i + 1];
- if (c == '-') i++;
+ if (c == '-' || c == '+') i++;
if (i == s.size() - 1) return false; //Must be sthg after scientific notation.
if (sepCount == 0) sepCount = 1; //We do not want any dec in the exponent.
} else if (!isDecimalNumber(c))
@@ -243,6 +246,9 @@ bool TextTools::isDecimalNumber(const std::string& s, char dec, char scientificN
bool TextTools::isDecimalInteger(const std::string& s, char scientificNotation)
{
+ if (isEmpty(s))
+ return false;
+
size_t sciCount = 0;
size_t i = 0;
if (s[0] == '-') i = 1;
@@ -254,6 +260,8 @@ bool TextTools::isDecimalInteger(const std::string& s, char scientificNotation)
if (i == s.size() - 1) return false; //Must be sthg after scientific notation.
c = s[i + 1];
if (c == '-') return false; //Not an integer then!
+ if (c == '+') i++;
+ if (i == s.size() - 1) return false; //Must be sthg after scientific notation.
} else if (!isDecimalNumber(c))
return false;
if (sciCount > 1)
@@ -291,9 +299,9 @@ std::string TextTools::toString(double d, int precision)
/******************************************************************************/
-int TextTools::toInt(const std::string& s) throw (Exception)
+int TextTools::toInt(const std::string& s, char scientificNotation) throw (Exception)
{
- if (!isDecimalInteger(s)) throw Exception("TextTools::toInt(). Invalid number specification: " + s);
+ if (!isDecimalInteger(s, scientificNotation)) throw Exception("TextTools::toInt(). Invalid number specification: " + s);
istringstream iss(s);
int i;
iss >> i;
@@ -302,9 +310,9 @@ int TextTools::toInt(const std::string& s) throw (Exception)
/******************************************************************************/
-double TextTools::toDouble(const std::string& s) throw (Exception)
+double TextTools::toDouble(const std::string& s, char dec, char scientificNotation) throw (Exception)
{
- if (!isDecimalNumber(s)) throw Exception("TextTools::toDouble(). Invalid number specification: " + s);
+ if (!isDecimalNumber(s, dec, scientificNotation)) throw Exception("TextTools::toDouble(). Invalid number specification: " + s);
istringstream iss(s);
double d;
iss >> d;
@@ -353,8 +361,8 @@ throw (Exception)
{
string t = "";
int blockCount = 0;
- int begPos = 0;
- for (unsigned int i = 0; i < s.size(); i++)
+ size_t begPos = 0;
+ for (size_t i = 0; i < s.size(); i++)
{
char current = s[i];
if (current == blockBeginning)
@@ -512,12 +520,11 @@ void TextTools::replaceAll(std::string& target, const std::string& query, const
{
if (query.empty())
return;
- size_t pos = 0;
+ size_t pos = target.find(query);
while (pos != string::npos) {
- pos = target.find(query, pos);
target.replace(pos, query.length(), replacement);
- pos += replacement.length(); //We prevent recursivity!
-
+ pos += replacement.length(); //We prevent recursivity!
+ pos = target.find(query, pos);
}
}
diff --git a/src/Bpp/Text/TextTools.h b/src/Bpp/Text/TextTools.h
index 423d8fd..9ce50d8 100644
--- a/src/Bpp/Text/TextTools.h
+++ b/src/Bpp/Text/TextTools.h
@@ -251,19 +251,22 @@ namespace bpp
* @brief Convert from string to int.
*
* @param s The string to parse.
+ * @param scientificNotation character to use for scientific notation (typically 'e' or 'E').
* @return The integer corresponding to s.
* @throw Exception if the string does not specify a valid number.
*/
- static int toInt(const std::string& s) throw (Exception);
+ static int toInt(const std::string& s, char scientificNotation = 'e') throw (Exception);
/**
* @brief Convert from string to double.
*
* @param s The string to parse.
+ * @param dec The decimal separator.
+ * @param scientificNotation character to use for scientific notation (typically 'e' or 'E').
* @return The double corresponding to s.
* @throw Exception if the string does not specify a valid number.
*/
- static double toDouble(const std::string& s) throw (Exception);
+ static double toDouble(const std::string& s, char dec = '.', char scientificNotation = 'e') throw (Exception);
/**
* @brief Template to string conversion.
diff --git a/src/Bpp/Utils/AttributesTools.cpp b/src/Bpp/Utils/AttributesTools.cpp
index d2cd916..11e8915 100644
--- a/src/Bpp/Utils/AttributesTools.cpp
+++ b/src/Bpp/Utils/AttributesTools.cpp
@@ -5,43 +5,44 @@
//
/*
-Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
-
-This software is a computer program whose purpose is to provide basal and
-utilitary classes. This file belongs to the Bio++ Project.
-
-This software is governed by the CeCILL license under French law and
-abiding by the rules of distribution of free software. You can use,
-modify and/ or redistribute the software under the terms of the CeCILL
-license as circulated by CEA, CNRS and INRIA at the following URL
-"http://www.cecill.info".
-
-As a counterpart to the access to the source code and rights to copy,
-modify and redistribute granted by the license, users are provided only
-with a limited warranty and the software's author, the holder of the
-economic rights, and the successive licensors have only limited
-liability.
-
-In this respect, the user's attention is drawn to the risks associated
-with loading, using, modifying and/or developing or reproducing the
-software by the user in light of its specific status of free software,
-that may mean that it is complicated to manipulate, and that also
-therefore means that it is reserved for developers and experienced
-professionals having in-depth computer knowledge. Users are therefore
-encouraged to load and test the software's suitability as regards their
-requirements in conditions enabling the security of their systems and/or
-data to be ensured and, more generally, to use and operate it in the
-same conditions as regards security.
-
-The fact that you are presently reading this means that you have had
-knowledge of the CeCILL license and that you accept its terms.
-*/
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide basal and
+ utilitary classes. This file belongs to the Bio++ Project.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
// From the STL:
#include <cstdlib>
#include <string>
#include <iostream>
#include <fstream>
+#include <algorithm>
using namespace std;
@@ -54,19 +55,23 @@ using namespace bpp;
/******************************************************************************/
-std::vector<std::string> AttributesTools::getVector( int argc, char * argv[])
+std::vector<std::string> AttributesTools::getVector(int argc, char* argv[])
{
- vector<string> result(argc);
- for(int i = 1; i < argc; i++) result[i] = string(argv[i]);
- //Ignore first argc which is the program name!
+ size_t n = static_cast<size_t>(argc);
+ vector<string> result(n);
+ for (size_t i = 1; i < n; ++i)
+ {
+ result[i] = string(argv[i]);
+ }
+ // Ignore first argc which is the program name!
return result;
}
/******************************************************************************/
std::map<std::string, std::string> AttributesTools::getAttributesMap(
- const std::vector<std::string> & argv,
- const std::string & delimiter)
+ const std::vector<std::string>& argv,
+ const std::string& delimiter)
{
map<string, string> am;
getAttributesMap(argv, am, delimiter);
@@ -76,49 +81,51 @@ std::map<std::string, std::string> AttributesTools::getAttributesMap(
/******************************************************************************/
void AttributesTools::getAttributesMap(
- const std::vector<std::string> & argv,
- std::map<std::string, std::string> & am,
- const std::string & delimiter)
+ const std::vector<std::string>& argv,
+ std::map<std::string, std::string>& am,
+ const std::string& delimiter)
{
vector<string> argv2(argv.size());
- //First make a few cleaning:
- for(unsigned int i = 0; i < argv.size(); i++)
+ // First make a few cleaning:
+ for (size_t i = 0; i < argv.size(); i++)
{
- //Make a few corrections first:
- string arg = removeComments(argv[i], string("#"), string("\n"));//remove shell comments.
- arg = removeComments(arg, string("//"), string("\n"));//remove C simple comments.
- arg = removeComments(arg, string("/*"), string("*/"));//remove C multiple comments.
+ // Make a few corrections first:
+ string arg = removeComments(argv[i], string("#"), string("\n")); // remove shell comments.
+ arg = removeComments(arg, string("//"), string("\n")); // remove C simple comments.
+ arg = removeComments(arg, string("/*"), string("*/")); // remove C multiple comments.
arg = TextTools::removeWhiteSpaces(arg);
argv2[i] = arg;
}
- //Now parse arguments:
- for(unsigned int i = 0; i < argv.size(); i++)
+ // Now parse arguments:
+ for (size_t i = 0; i < argv.size(); i++)
{
string arg = argv2[i];
- if(arg == "") continue; //Skipping void line.
- while(arg[arg.size()-1] == '\\')
+ if (arg == "")
+ continue; // Skipping void line.
+ while (arg[arg.size() - 1] == '\\')
{
- //Splitted line
+ // Splitted line
i++;
- arg = arg.substr(0, arg.length()-1) + argv2[i];
+ arg = arg.substr(0, arg.length() - 1) + argv2[i];
}
- //Parsing:
+ // Parsing:
string::size_type limit = arg.find(delimiter, 0);
- if(limit == string::npos)
+ if (limit == string::npos)
{
- //Invalid parameter
+ // Invalid parameter
(*ApplicationTools::warning << "WARNING!!! Parameter '" << arg << "' has been ignored.").endLine();
}
else
{
- string name = string(arg.begin(), arg.begin() + limit);
- string value = string(arg.begin() + limit + delimiter.size(), arg.end());
- if(name == "param")
- {
- //Recursive inclusion:
- getAttributesMapFromFile(value, am, delimiter);
- }
- else am[name] = value;
+ string name = string(arg.begin(), arg.begin() + static_cast<ptrdiff_t>(limit));
+ string value = string(arg.begin() + static_cast<ptrdiff_t>(limit + delimiter.size()), arg.end());
+ // if ((name == "param") || (name == "params"))
+ // {
+ // //Recursive inclusion:
+ // getAttributesMapFromFile(value, am, delimiter);
+ // }
+ // else
+ am[name] = value;
}
}
}
@@ -126,9 +133,9 @@ void AttributesTools::getAttributesMap(
/******************************************************************************/
void AttributesTools::getAttributesMapFromFile(
- const std::string & file,
- std::map<std::string, std::string> & params,
- const std::string & delimiter)
+ const std::string& file,
+ std::map<std::string, std::string>& params,
+ const std::string& delimiter)
{
cout << "Parsing file " << file << " for options." << endl;
ifstream input(file.c_str(), ios::in);
@@ -139,8 +146,8 @@ void AttributesTools::getAttributesMapFromFile(
/******************************************************************************/
std::map<std::string, std::string> AttributesTools::getAttributesMapFromFile(
- const std::string & file,
- const std::string & delimiter)
+ const std::string& file,
+ const std::string& delimiter)
{
map<string, string> params;
getAttributesMapFromFile(file, params, delimiter);
@@ -150,25 +157,26 @@ std::map<std::string, std::string> AttributesTools::getAttributesMapFromFile(
/******************************************************************************/
void AttributesTools::actualizeAttributesMap(
- std::map<std::string, std::string> & attMap,
- const std::map<std::string, std::string> & atts)
+ std::map<std::string, std::string>& attMap,
+ const std::map<std::string, std::string>& atts)
{
- for(map<string, string>::const_iterator i = atts.begin(); i != atts.end(); i++)
+ for (map<string, string>::const_iterator i = atts.begin(); i != atts.end(); i++)
{
- attMap[i->first] = i->second;
+ if ((i->first != "param") && (i->first != "params"))
+ attMap[i->first] = i->second;
}
}
/******************************************************************************/
void AttributesTools::resolveVariables(
- std::map<std::string, std::string> & am,
+ std::map<std::string, std::string>& am,
char varCode,
char varBeg,
char varEnd)
throw (Exception)
{
- //Now resolve any variable:
+ // Now resolve any variable:
for (map<string, string>::iterator it = am.begin(); it != am.end(); it++)
{
string value = it->second;
@@ -181,7 +189,7 @@ throw (Exception)
string varName = value.substr(index1 + 2, index2 - index1 - 2);
map<string, string>::iterator varIt = am.find(varName);
string varValue = "";
- if (varIt == am.end())
+ if (varIt == am.end())
{
if (ApplicationTools::error)
(*ApplicationTools::error << "Variable '" << varName << "' is undefined and was ignored.").endLine();
@@ -190,7 +198,7 @@ throw (Exception)
{
varValue = varIt->second;
}
- //Modify original field:
+ // Modify original field:
string newValue = value.substr(0, index1) + varValue + value.substr(index2 + 1);
it->second = newValue;
}
@@ -205,33 +213,35 @@ throw (Exception)
/******************************************************************************/
std::string AttributesTools::removeComments(
- const std::string & s,
- const std::string & begin,
- const std::string & end)
+ const std::string& s,
+ const std::string& begin,
+ const std::string& end)
{
string r = s;
string::size_type last = 0;
do
{
string::size_type first = r.find(begin, last);
- if(first == string::npos) return r; //No shell comment.
- //else:
+ if (first == string::npos)
+ return r; // No shell comment.
+ // else:
last = r.find(end, first);
- if(last == string::npos)
+ if (last == string::npos)
{
- r.erase(r.begin() + first, r.end());
+ r.erase(r.begin() + static_cast<ptrdiff_t>(first), r.end());
}
else
{
- r.erase(r.begin() + first, r.begin() + last);
+ r.erase(r.begin() + static_cast<ptrdiff_t>(first), r.begin() + static_cast<ptrdiff_t>(last));
}
- } while(last != string::npos);
+ }
+ while (last != string::npos);
return r;
}
/******************************************************************************/
-std::map<std::string, std::string> AttributesTools::parseOptions(int args, char ** argv) throw (Exception)
+std::map<std::string, std::string> AttributesTools::parseOptions(int args, char** argv) throw (Exception)
{
// Get the parameters from command line:
map<string, string> cmdParams = AttributesTools::getAttributesMap(
@@ -239,10 +249,12 @@ std::map<std::string, std::string> AttributesTools::parseOptions(int args, char
// Look for a specified file with parameters:
map<string, string> params;
- if(cmdParams.find("param") != cmdParams.end())
+ std::map<std::string, std::string>::iterator it;
+
+ if (cmdParams.find("param") != cmdParams.end())
{
string file = cmdParams["param"];
- if(!FileTools::fileExists(file))
+ if (!FileTools::fileExists(file))
{
throw Exception("AttributesTools::parseOptions(). Parameter file not found.");
}
@@ -259,8 +271,47 @@ std::map<std::string, std::string> AttributesTools::parseOptions(int args, char
}
// Resolve variables:
resolveVariables(params);
+
+ std::vector<string> mapfile;
+ std::vector<string>::iterator imapfile;
+ string file;
+
+ while (true)
+ {
+ it = params.find("param");
+ if (it != params.end())
+ {
+ file = it->second;
+ if (std::find(mapfile.begin(), mapfile.end(), file) == mapfile.end())
+ {
+ params.erase(it);
+ mapfile.push_back(file);
+ getAttributesMapFromFile(file, params, "=");
+ resolveVariables(params);
+ continue;
+ }
+ else
+ throw Exception("parsing error : Already used file " + file);
+ }
+ it = params.find("params");
+ if (it != params.end())
+ {
+ file = it->second;
+ if (find(mapfile.begin(), mapfile.end(), file) == mapfile.end())
+ {
+ params.erase(it);
+ mapfile.push_back(file);
+ getAttributesMapFromFile(file, params, "=");
+ resolveVariables(params);
+ continue;
+ }
+ else
+ throw Exception("parsing error : Already used file " + file);
+ }
+ break;
+ }
+
return params;
}
/******************************************************************************/
-
diff --git a/src/Bpp/Utils/AttributesTools.h b/src/Bpp/Utils/AttributesTools.h
index e83390a..a73c0b4 100644
--- a/src/Bpp/Utils/AttributesTools.h
+++ b/src/Bpp/Utils/AttributesTools.h
@@ -5,37 +5,37 @@
//
/*
-Copyright or © or Copr. Bio++ Development Tools, (November 17, 2004)
-
-This software is a computer program whose purpose is to provide basal and
-utilitary classes. This file belongs to the Bio++ Project.
-
-This software is governed by the CeCILL license under French law and
-abiding by the rules of distribution of free software. You can use,
-modify and/ or redistribute the software under the terms of the CeCILL
-license as circulated by CEA, CNRS and INRIA at the following URL
-"http://www.cecill.info".
-
-As a counterpart to the access to the source code and rights to copy,
-modify and redistribute granted by the license, users are provided only
-with a limited warranty and the software's author, the holder of the
-economic rights, and the successive licensors have only limited
-liability.
-
-In this respect, the user's attention is drawn to the risks associated
-with loading, using, modifying and/or developing or reproducing the
-software by the user in light of its specific status of free software,
-that may mean that it is complicated to manipulate, and that also
-therefore means that it is reserved for developers and experienced
-professionals having in-depth computer knowledge. Users are therefore
-encouraged to load and test the software's suitability as regards their
-requirements in conditions enabling the security of their systems and/or
-data to be ensured and, more generally, to use and operate it in the
-same conditions as regards security.
-
-The fact that you are presently reading this means that you have had
-knowledge of the CeCILL license and that you accept its terms.
-*/
+ Copyright or © or Copr. Bio++ Development Tools, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide basal and
+ utilitary classes. This file belongs to the Bio++ Project.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
#ifndef _ATTRIBUTES_TOOLS_H_
#define _ATTRIBUTES_TOOLS_H_
@@ -48,9 +48,8 @@ knowledge of the CeCILL license and that you accept its terms.
#include <string>
#include <vector>
-namespace bpp
+namespace bpp
{
-
/**
* @brief Some functions to deal with attributes, i.e. parameters passed to a program/method.
*
@@ -72,7 +71,7 @@ namespace bpp
* @code
* optionfile=/home/foo/bar.txt
* @endcode
- *
+ *
* Attributes are stored as a map<string, string>, with attributes names as keys,
* and arguments as values.
*
@@ -104,10 +103,10 @@ namespace bpp
* @endcode
* These pieces of code does the following:
* - get all parameters from the command line and store them in a map,
- * - check if some parameter is called 'param'. If so, look for the file
+ * - check if some parameter is called 'param' or 'params'. If so, look for the file
* given as value and try to read some parameters from it.
* - If an parameter file was found, update the parameter in it with those from
- * the command line. This implies that when a parameter is found in bothe the
+ * the command line. This implies that when a parameter is found in both the
* command line and the option file, the value from the command line will be
* retained.
*
@@ -127,125 +126,120 @@ namespace bpp
*/
class AttributesTools
{
-
- public:
-
- AttributesTools() {}
- virtual ~AttributesTools() {}
-
- /**
- * @brief Get attributes a vector of strings from command line arguments.
- *
- * @param argc The number of arguments.
- * @param argv The array with all arguments.
- * @return A vector with all arguments as strings.
- */
- static std::vector<std::string> getVector(int argc, char * argv[]);
-
- /**
- * @brief Get an attribute map from a vector of arguments.
- *
- * This method also resolve all variable calls.
- *
- * @param argv The vector of arguments.
- * @param delimiter The string that separates attribute names from arguments (for instance '=').
- * @return The attribute map.
- */
- static std::map<std::string, std::string> getAttributesMap(
- const std::vector<std::string> & argv,
- const std::string & delimiter = "=");
-
- /**
- * @brief Get an attribute map from a vector of arguments.
- *
- * This method also resolve all variable calls.
- *
- * @param argv The vector of arguments.
- * @param am The attribute map to fill.
- * @param delimiter The string that separates attribute names from arguments (for instance '=').
- */
- static void getAttributesMap(
- const std::vector<std::string> & argv,
- std::map<std::string, std::string> & am,
- const std::string & delimiter = "=");
-
- /**
- * @brief Get an attribute map from a file.
- *
- * @param file The file with all arguments.
- * @param delimiter The string that separates attribute names from arguments (for instance '=').
- * @return An attribute map.
- */
- static std::map<std::string, std::string> getAttributesMapFromFile(
- const std::string & file,
- const std::string & delimiter);
-
- /**
- * @brief Get an attribute map from a file.
- *
- * @param file The file with all arguments.
- * @param params An attribute map to fill.
- * @param delimiter The string that separates attribute names from arguments (for instance '=').
- */
- static void getAttributesMapFromFile(
- const std::string & file,
- std::map<std::string, std::string> & params,
- const std::string & delimiter);
-
- /**
- * @brief Actualizes an attribute map with another.
- *
- * All fields in map 2 will be added to map 1.
- * If two attributes have the same name, then map 1 value will be overwritten.
- *
- * @param attMap The attributes map.
- * @param atts The attributes to add to the map.
- */
- static void actualizeAttributesMap(
- std::map<std::string, std::string> & attMap,
- const std::map<std::string, std::string> & atts);
-
- /**
- * @brief Resolve the variables.
- *
- * If used prior to the actualizeAttributesMap, this function will make the
- * variables 'local', whereas using them after will make them 'global'.
- *
- * @param am The attributes map.
- * @param varCode The code that defines variable recalls.
- * @param varBeg Variables begin name code.
- * @param varEnd Variables end name code.
- * @throw Exception If there is a syntax error.
- */
- static void resolveVariables(std::map<std::string, std::string> & am,
- char varCode = '$',
- char varBeg = '(',
- char varEnd = ')') throw (Exception);
-
- /**
- * @brief Global function that reads all parameters from command line and files,
- * and set the values in a map.
- *
- * @param args Number of arguments, as passed to the main function.
- * @param argv Array of values, as passed to the main function.
- * @return An attributes map.
- * @throw Exception in case an option file is not found.
- */
- static std::map<std::string, std::string> parseOptions(int args, char ** argv) throw (Exception);
-
- private:
-
- /**
- * @brief Remove comments from a string.
- *
- * @param s The string to parse.
- * @param begin Comments front delimiter.
- * @param end Comments end delimiter.
- */
- static std::string removeComments(const std::string & s, const std::string & begin, const std::string & end);
+public:
+ AttributesTools() {}
+ virtual ~AttributesTools() {}
+
+ /**
+ * @brief Get attributes a vector of strings from command line arguments.
+ *
+ * @param argc The number of arguments.
+ * @param argv The array with all arguments.
+ * @return A vector with all arguments as strings.
+ */
+ static std::vector<std::string> getVector(int argc, char* argv[]);
+
+ /**
+ * @brief Get an attribute map from a vector of arguments.
+ *
+ * This method also resolve all variable calls.
+ *
+ * @param argv The vector of arguments.
+ * @param delimiter The string that separates attribute names from arguments (for instance '=').
+ * @return The attribute map.
+ */
+ static std::map<std::string, std::string> getAttributesMap(
+ const std::vector<std::string>& argv,
+ const std::string& delimiter = "=");
+
+ /**
+ * @brief Get an attribute map from a vector of arguments.
+ *
+ * This method also resolve all variable calls.
+ *
+ * @param argv The vector of arguments.
+ * @param am The attribute map to fill.
+ * @param delimiter The string that separates attribute names from arguments (for instance '=').
+ */
+ static void getAttributesMap(
+ const std::vector<std::string>& argv,
+ std::map<std::string, std::string>& am,
+ const std::string& delimiter = "=");
+
+ /**
+ * @brief Get an attribute map from a file.
+ *
+ * @param file The file with all arguments.
+ * @param delimiter The string that separates attribute names from arguments (for instance '=').
+ * @return An attribute map.
+ */
+ static std::map<std::string, std::string> getAttributesMapFromFile(
+ const std::string& file,
+ const std::string& delimiter);
+
+ /**
+ * @brief Get an attribute map from a file.
+ *
+ * @param file The file with all arguments.
+ * @param params An attribute map to fill.
+ * @param delimiter The string that separates attribute names from arguments (for instance '=').
+ */
+ static void getAttributesMapFromFile(
+ const std::string& file,
+ std::map<std::string, std::string>& params,
+ const std::string& delimiter);
+
+ /**
+ * @brief Actualizes an attribute map with another.
+ *
+ * All fields in map 2 will be added to map 1.
+ * If two attributes have the same name, then map 1 value will be overwritten.
+ *
+ * @param attMap The attributes map.
+ * @param atts The attributes to add to the map.
+ */
+ static void actualizeAttributesMap(
+ std::map<std::string, std::string>& attMap,
+ const std::map<std::string, std::string>& atts);
+
+ /**
+ * @brief Resolve the variables.
+ *
+ * If used prior to the actualizeAttributesMap, this function will make the
+ * variables 'local', whereas using them after will make them 'global'.
+ *
+ * @param am The attributes map.
+ * @param varCode The code that defines variable recalls.
+ * @param varBeg Variables begin name code.
+ * @param varEnd Variables end name code.
+ * @throw Exception If there is a syntax error.
+ */
+ static void resolveVariables(std::map<std::string, std::string>& am,
+ char varCode = '$',
+ char varBeg = '(',
+ char varEnd = ')') throw (Exception);
+
+ /**
+ * @brief Global function that reads all parameters from command line and files,
+ * and set the values in a map.
+ *
+ * @param args Number of arguments, as passed to the main function.
+ * @param argv Array of values, as passed to the main function.
+ * @return An attributes map.
+ * @throw Exception in case an option file is not found.
+ */
+ static std::map<std::string, std::string> parseOptions(int args, char** argv) throw (Exception);
+
+private:
+ /**
+ * @brief Remove comments from a string.
+ *
+ * @param s The string to parse.
+ * @param begin Comments front delimiter.
+ * @param end Comments end delimiter.
+ */
+ static std::string removeComments(const std::string& s, const std::string& begin, const std::string& end);
};
-
-} //end of namespace bpp.
+} // end of namespace bpp.
#endif // _ATTRIBUTES_TOOLS_H_
-
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index f3006b1..7ae06c6 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -66,6 +66,10 @@ SET(CPP_FILES
Bpp/Numeric/Function/SimpleNewtonMultiDimensions.cpp
Bpp/Numeric/Function/ThreePointsNumericalDerivative.cpp
Bpp/Numeric/Function/TwoPointsNumericalDerivative.cpp
+ Bpp/Numeric/Hmm/HmmLikelihood.cpp
+ Bpp/Numeric/Hmm/AbstractHmmTransitionMatrix.cpp
+ Bpp/Numeric/Hmm/FullHmmTransitionMatrix.cpp
+ Bpp/Numeric/Hmm/AutoCorrelationTransitionMatrix.cpp
Bpp/Numeric/Hmm/LogsumHmmLikelihood.cpp
Bpp/Numeric/Hmm/LowMemoryRescaledHmmLikelihood.cpp
Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp
@@ -135,6 +139,7 @@ SET(H_FILES
Bpp/Numeric/Parameter.h
Bpp/Numeric/ParameterList.h
Bpp/Numeric/Parametrizable.h
+ Bpp/Numeric/ParametrizableCollection.cpp
Bpp/Numeric/TransformedParameter.h
Bpp/Numeric/Random/RandomFactory.h
Bpp/Numeric/Random/RandomTools.h
@@ -189,6 +194,9 @@ SET(H_FILES
Bpp/Numeric/Hmm/HmmLikelihood.h
Bpp/Numeric/Hmm/HmmStateAlphabet.h
Bpp/Numeric/Hmm/HmmTransitionMatrix.h
+ Bpp/Numeric/Hmm/AbstractHmmTransitionMatrix.h
+ Bpp/Numeric/Hmm/FullHmmTransitionMatrix.h
+ Bpp/Numeric/Hmm/AutoCorrelationTransitionMatrix.h
Bpp/Numeric/Hmm/LogsumHmmLikelihood.h
Bpp/Numeric/Hmm/LowMemoryRescaledHmmLikelihood.h
Bpp/Numeric/Hmm/RescaledHmmLikelihood.h
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index af83f96..40a3b87 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -40,6 +40,10 @@ ADD_EXECUTABLE(test_derivative1 test_derivative1.cpp)
TARGET_LINK_LIBRARIES(test_derivative1 ${LIBS})
ADD_TEST(test_derivative1 "test_derivative1")
+ADD_EXECUTABLE(test_reparametrization test_reparametrization.cpp)
+TARGET_LINK_LIBRARIES(test_reparametrization ${LIBS})
+ADD_TEST(test_reparametrization "test_reparametrization")
+
ADD_EXECUTABLE(test_downhill test_downhill.cpp)
TARGET_LINK_LIBRARIES(test_downhill ${LIBS})
ADD_TEST(test_downhill "test_downhill")
@@ -60,6 +64,10 @@ ADD_EXECUTABLE(test_distributions test_distributions.cpp)
TARGET_LINK_LIBRARIES(test_distributions ${LIBS})
ADD_TEST(test_distributions "test_distributions")
+ADD_EXECUTABLE(test_simplex test_simplex.cpp)
+TARGET_LINK_LIBRARIES(test_simplex ${LIBS})
+ADD_TEST(test_simplex "test_simplex")
+
ADD_EXECUTABLE(test_stats test_stats.cpp)
TARGET_LINK_LIBRARIES(test_stats ${LIBS})
ADD_TEST(test_stats "test_stats")
@@ -81,11 +89,11 @@ TARGET_LINK_LIBRARIES(test_text_tools ${LIBS})
ADD_TEST(test_text_tools "test_text_tools")
IF(UNIX)
- SET_PROPERTY(TEST test_numconstants test_eigen test_matrices test_derivative1 test_downhill test_powell test_gradient test_bfgs test_distributions test_stats test_mva test_sample test_range test_text_tools PROPERTY ENVIRONMENT "LD_LIBRARY_PATH=$ENV{LD_LIBRARY_PATH}:../src")
+ SET_PROPERTY(TEST test_numconstants test_eigen test_matrices test_derivative1 test_reparametrization test_downhill test_powell test_gradient test_bfgs test_distributions test_stats test_mva test_sample test_range test_text_tools test_simplex PROPERTY ENVIRONMENT "LD_LIBRARY_PATH=$ENV{LD_LIBRARY_PATH}:../src")
ENDIF()
IF(APPLE)
- SET_PROPERTY(TEST test_numconstants test_eigen test_matrices test_derivative1 test_downhill test_powell test_gradient test_bfgs test_distributions test_stats test_mva test_sample test_range test_text_tools PROPERTY ENVIRONMENT "DYLD_LIBRARY_PATH=$ENV{DYLD_LIBRARY_PATH}:../src")
+ SET_PROPERTY(TEST test_numconstants test_eigen test_matrices test_derivative1 test_reparametrization test_downhill test_powell test_gradient test_bfgs test_distributions test_stats test_mva test_sample test_range test_text_tools test_simplex PROPERTY ENVIRONMENT "DYLD_LIBRARY_PATH=$ENV{DYLD_LIBRARY_PATH}:../src")
ENDIF()
IF(WIN32)
diff --git a/test/test_derivative1.cpp b/test/test_derivative1.cpp
index 77cb089..e2e7fb1 100644
--- a/test/test_derivative1.cpp
+++ b/test/test_derivative1.cpp
@@ -57,33 +57,33 @@ int main() {
FivePointsNumericalDerivative nd5pt(&f) ; nd5pt.setParametersToDerivate(pl.getParameterNames());
for (unsigned int repeat = 0; repeat < 10000; ++repeat) {
- for (unsigned int i = 0; i < pl.size(); ++i) {
+ for (size_t i = 0; i < pl.size(); ++i) {
double val = RandomTools::giveRandomNumberBetweenZeroAndEntry(100) - 50;
pl[i].setValue(val);
}
nd2pt.setParameters(pl);
vector<double> derivativesNum2pt(pl.size());
- for (unsigned int i = 0; i < pl.size(); ++i) {
+ for (size_t i = 0; i < pl.size(); ++i) {
derivativesNum2pt[i] = nd2pt.getFirstOrderDerivative(pl.getParameterNames()[i]);
}
nd3pt.setParameters(pl);
vector<double> derivativesNum3pt(pl.size());
- for (unsigned int i = 0; i < pl.size(); ++i) {
+ for (size_t i = 0; i < pl.size(); ++i) {
derivativesNum3pt[i] = nd3pt.getFirstOrderDerivative(pl.getParameterNames()[i]);
}
nd5pt.setParameters(pl);
vector<double> derivativesNum5pt(pl.size());
- for (unsigned int i = 0; i < pl.size(); ++i) {
+ for (size_t i = 0; i < pl.size(); ++i) {
derivativesNum5pt[i] = nd5pt.getFirstOrderDerivative(pl.getParameterNames()[i]);
}
vector<double> derivativesAna(pl.size());
f1.setParameters(pl);
bool test = true;
- for (unsigned int i = 0; i < pl.size(); ++i) {
+ for (size_t i = 0; i < pl.size(); ++i) {
derivativesAna[i] = f1.getFirstOrderDerivative(pl.getParameterNames()[i]);
if (abs(derivativesAna[i] - derivativesNum2pt[i]) > std::sqrt(nd2pt.getInterval())) test = false;
if (abs(derivativesAna[i] - derivativesNum3pt[i]) > std::sqrt(nd2pt.getInterval())) test = false;
@@ -93,7 +93,7 @@ int main() {
//Test:
if (!test) {
//Failure!
- for (unsigned int i = 0; i < pl.size(); ++i) {
+ for (size_t i = 0; i < pl.size(); ++i) {
cout << setprecision(20) << pl[i].getName() << "=" << pl[i].getValue() << endl;
cout << setprecision(20) << "Ana. Der. =" << derivativesAna[i] << endl;
cout << setprecision(20) << "Num. Der. 2pts=" << derivativesNum2pt[i] << endl;
diff --git a/test/test_reparametrization.cpp b/test/test_reparametrization.cpp
new file mode 100644
index 0000000..c503ca8
--- /dev/null
+++ b/test/test_reparametrization.cpp
@@ -0,0 +1,98 @@
+//
+// File: test_derivative1.cpp
+// Created by: Julien Dutheil
+// Created on: Thu Oct 28 12:49 2010
+//
+
+/*
+Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+This software is a computer program whose purpose is to provide classes
+for numerical calculus. This file is part of the Bio++ project.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include <Bpp/Numeric/Random/RandomTools.h>
+#include <Bpp/Numeric/Function/PowellMultiDimensions.h>
+#include <Bpp/Numeric/Function/ReparametrizationFunctionWrapper.h>
+#include <vector>
+#include <iostream>
+
+using namespace bpp;
+using namespace std;
+
+class MyFunction:
+ public virtual Function,
+ public AbstractParametrizable
+{
+ private:
+ double fval_;
+
+ public:
+ MyFunction() : AbstractParametrizable(""), fval_(0) {
+ //We declare parameters here:
+ addParameter_(new Parameter("x", 0, new IntervalConstraint(-1, 7, true, true), true));
+ addParameter_(new Parameter("y", 0, new IntervalConstraint(-4, 4, true, true), true));
+ fireParameterChanged(getParameters());
+ }
+
+ MyFunction* clone() const { return new MyFunction(*this); }
+
+ public:
+ void setParameters(const ParameterList& pl)
+ throw (ParameterNotFoundException, ConstraintException, Exception)
+ {
+ matchParametersValues(pl);
+ }
+ double getValue() const throw (Exception) { return fval_; }
+
+ void fireParameterChanged(const ParameterList& pl) {
+ double x = getParameterValue("x");
+ double y = getParameterValue("y");
+ fval_ = cos(x) + sin(y);
+ }
+};
+
+int main() {
+ MyFunction f;
+ ReparametrizationFunctionWrapper fw(&f);
+ ParameterList pl = fw.getParameters();
+ PowellMultiDimensions optimizer(&fw);
+ optimizer.init(pl);
+ optimizer.optimize();
+ double minf = f.getValue();
+ double x = f.getParameterValue("x");
+ double y = f.getParameterValue("y");
+ cout << "x=" << x << endl;
+ cout << "y=" << y << endl;
+ cout << "f=" << minf << endl;
+
+ cout << setprecision(20) << (abs(x - 3.141593) + abs(y + 1.570796)) << endl;
+ bool test = (abs(x - 3.141593) + abs(y + 1.570796)) < optimizer.getStopCondition()->getTolerance();
+ return (test ? 0 : 1);
+}
diff --git a/test/test_simplex.cpp b/test/test_simplex.cpp
new file mode 100644
index 0000000..6c82e30
--- /dev/null
+++ b/test/test_simplex.cpp
@@ -0,0 +1,117 @@
+//
+// File: test_simplex.cpp
+// Created by: Laurent Guéguen
+// Created on: vendredi 5 juillet 2013, à 11h 08
+//
+
+/*
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for numerical calculus. This file is part of the Bio++ project.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards their
+ requirements in conditions enabling the security of their systems and/or
+ data to be ensured and, more generally, to use and operate it in the
+ same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+ */
+
+#include <Bpp/Numeric/Prob/Simplex.h>
+#include <Bpp/Text/TextTools.h>
+
+#include <iostream>
+#include <limits>
+
+using namespace bpp;
+using namespace std;
+
+int main()
+{
+ try
+ {
+ vector<double> prob;
+ prob.push_back(0.1);
+ prob.push_back(0.2);
+ prob.push_back(0.3);
+ prob.push_back(0.15);
+ prob.push_back(0.1);
+ prob.push_back(0.05);
+ prob.push_back(0.1);
+
+ vector<Simplex*> vpsi;
+ vpsi.push_back(new Simplex(prob, 1));
+ vpsi.push_back(new Simplex(prob, 2));
+ vpsi.push_back(new Simplex(prob, 3));
+
+ for (size_t i = 0; i < 3; i++)
+ {
+ cout << "Method " << i + 1 << endl;
+ for (size_t j = 0; j < prob.size() - 1; j++)
+ {
+ cout << vpsi[i]->getParameterValue("theta" + TextTools::toString(j + 1)) << "\t";
+ }
+ cout << endl;
+ }
+
+
+ cout << "Prob:";
+ for (size_t j = 0; j < prob.size(); j++)
+ {
+ cout << prob[j] << "\t";
+ }
+ cout << endl;
+ for (size_t i = 0; i < 3; i++)
+ {
+ for (size_t j = 0; j < prob.size() - 1; j++)
+ {
+ vpsi[i]->setParameterValue("theta" + TextTools::toString(j + 1),
+ vpsi[i]->getParameterValue("theta" + TextTools::toString(j + 1)) + 0.1);
+ }
+ for (size_t j = 0; j < prob.size() - 1; j++)
+ {
+ vpsi[i]->setParameterValue("theta" + TextTools::toString(j + 1),
+ vpsi[i]->getParameterValue("theta" + TextTools::toString(j + 1)) - 0.1);
+ }
+ cout << "Method " << i + 1 << endl;
+ cout << "prob\t";
+ for (size_t j = 0; j < prob.size(); j++)
+ {
+ cout << vpsi[i]->prob(j) << "\t";
+ }
+ cout << endl;
+ }
+
+ for (size_t i = 0; i < 3; i++)
+ {
+ delete vpsi[i];
+ }
+ return 0;
+ }
+ catch (Exception& ex)
+ {
+ cout << "failed :(" << endl;
+ return 1;
+ }
+}
+
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libbpp-core.git
More information about the debian-med-commit
mailing list