[med-svn] [libbpp-seq] 01/05: New upstream version 2.3.2
Julien Dutheil
jdutheil-guest at moszumanska.debian.org
Mon Feb 5 19:47:55 UTC 2018
This is an automated email from the git hooks/post-receive script.
jdutheil-guest pushed a commit to branch master
in repository libbpp-seq.
commit 0dc6a7ed726ee743d7e1964c669209b93f1946d6
Author: Julien Y. Dutheil <dutheil at evolbio.mpg.de>
Date: Mon Feb 5 17:34:25 2018 +0100
New upstream version 2.3.2
---
Doxyfile | 477 +++++--------
src/Bpp/Seq/Alphabet/AlphabetTools.cpp | 1 +
src/Bpp/Seq/Alphabet/AlphabetTools.h | 5 +-
src/Bpp/Seq/Alphabet/CodonAlphabet.cpp | 163 +++--
src/Bpp/Seq/Alphabet/CodonAlphabet.h | 577 +++++++++++-----
src/Bpp/Seq/Alphabet/WordAlphabet.cpp | 14 +-
src/Bpp/Seq/Alphabet/WordAlphabet.h | 738 ++++++++++++---------
src/Bpp/Seq/CodonSiteTools.cpp | 13 +-
src/Bpp/Seq/CodonSiteTools.h | 2 +-
.../Container/VectorProbabilisticSiteContainer.cpp | 187 ------
.../Container/VectorProbabilisticSiteContainer.h | 123 ----
src/Bpp/Seq/SequenceTools.cpp | 22 +-
src/Bpp/Seq/StringSequenceTools.cpp | 8 +-
src/Bpp/Seq/SymbolListTools.cpp | 4 +-
test/CMakeLists.txt | 2 +
test/test_alphabets.cpp | 9 +
16 files changed, 1222 insertions(+), 1123 deletions(-)
diff --git a/Doxyfile b/Doxyfile
index 75faa98..b496a3c 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.11
+# Doxyfile 1.8.7
# This file describes the settings to be used by the documentation system
# doxygen (www.doxygen.org) for a project.
@@ -44,23 +44,23 @@ PROJECT_NUMBER = 2.3.0
# 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 =
+PROJECT_BRIEF =
-# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
-# in the documentation. The maximum height of the logo should not exceed 55
-# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
-# the logo to the output directory.
+# 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 =
+PROJECT_LOGO =
# 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 =
+OUTPUT_DIRECTORY =
-# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
+# 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
@@ -93,14 +93,14 @@ ALLOW_UNICODE_NAMES = NO
OUTPUT_LANGUAGE = English
-# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
+# 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, doxygen will prepend the brief
+# 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
@@ -118,7 +118,7 @@ REPEAT_BRIEF = YES
# the entity):The $name class, The $name widget, The $name file, is, provides,
# specifies, contains, represents, a, an and the.
-ABBREVIATE_BRIEF =
+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
@@ -135,7 +135,7 @@ ALWAYS_DETAILED_SEC = NO
INLINE_INHERITED_MEMB = YES
-# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
+# 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.
@@ -205,9 +205,9 @@ MULTILINE_CPP_IS_BRIEF = NO
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
@@ -228,13 +228,13 @@ TAB_SIZE = 2
# "Side Effects:". You can put \n's in the value part of an alias to insert
# newlines.
-ALIASES =
+ALIASES =
# This tag can be used to specify a number of word-keyword mappings (TCL only).
# A mapping has the form "name=value". For example adding "class=itcl::class"
# will allow you to use the command class in the itcl::class meaning.
-TCL_SUBST =
+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
@@ -276,12 +276,12 @@ OPTIMIZE_OUTPUT_VHDL = NO
# 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 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 =
+EXTENSION_MAPPING =
# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
# according to the Markdown format, which allows for more readable
@@ -295,8 +295,8 @@ 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 putting a % sign in front of the word or
-# globally by setting AUTOLINK_SUPPORT to NO.
+# 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
@@ -336,20 +336,13 @@ SIP_SUPPORT = NO
IDL_PROPERTY_SUPPORT = YES
# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
-# tag is set to YES then doxygen will reuse the documentation of the first
+# 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
-# If one adds a struct or class to a group and this option is enabled, then also
-# any nested class or struct is added to the same group. By default this option
-# is disabled and one has to add nested compounds explicitly via \ingroup.
-# The default value is: NO.
-
-GROUP_NESTED_COMPOUNDS = NO
-
# Set the SUBGROUPING tag to YES to allow class member groups of the same type
# (for instance a group of public functions) to be put as a subgroup of that
# type (e.g. under the Public Functions section). Set it to NO to prevent
@@ -408,7 +401,7 @@ LOOKUP_CACHE_SIZE = 0
# Build related configuration options
#---------------------------------------------------------------------------
-# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
+# 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.
@@ -418,35 +411,35 @@ LOOKUP_CACHE_SIZE = 0
EXTRACT_ALL = YES
-# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class will
# be included in the documentation.
# The default value is: NO.
EXTRACT_PRIVATE = YES
-# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
+# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal
# scope will be included in the documentation.
# The default value is: NO.
EXTRACT_PACKAGE = NO
-# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
+# 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,
+# 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. If set to YES, local methods,
+# 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 in the documentation. If set to NO only methods in the interface are
# included.
# The default value is: NO.
@@ -471,21 +464,21 @@ 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, these classes will be included in the various overviews. This option
-# has no effect if EXTRACT_ALL is enabled.
+# 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, these declarations will be
+# (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, these
+# 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.
@@ -499,7 +492,7 @@ HIDE_IN_BODY_DOCS = 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
+# 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.
@@ -508,19 +501,12 @@ INTERNAL_DOCS = NO
CASE_SENSE_NAMES = YES
# 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
+# 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 HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
-# append additional text to a page's title, such as Class Reference. If set to
-# YES the compound reference will be hidden.
-# The default value is: NO.
-
-HIDE_COMPOUND_REFERENCE= NO
-
# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
# the files that are included by a file in the documentation of that file.
# The default value is: YES.
@@ -548,14 +534,14 @@ INLINE_INFO = YES
# 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.
+# 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
# descriptions of file, namespace and class members alphabetically by member
-# name. If set to NO, the members will appear in declaration order. Note that
+# 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.
@@ -600,25 +586,27 @@ SORT_BY_SCOPE_NAME = 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
+# 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 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.
@@ -629,7 +617,7 @@ GENERATE_DEPRECATEDLIST= YES
# sections, marked by \if <section_label> ... \endif and \cond <section_label>
# ... \endcond blocks.
-ENABLED_SECTIONS =
+ENABLED_SECTIONS =
# 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
@@ -643,8 +631,8 @@ ENABLED_SECTIONS =
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.
+# 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
@@ -671,7 +659,7 @@ SHOW_NAMESPACES = YES
# by doxygen. Whatever the program writes to standard output is used as the file
# version. For an example see the documentation.
-FILE_VERSION_FILTER =
+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
@@ -684,7 +672,7 @@ FILE_VERSION_FILTER =
# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
# tag is left empty.
-LAYOUT_FILE =
+LAYOUT_FILE =
# 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
@@ -692,9 +680,10 @@ LAYOUT_FILE =
# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
# For LaTeX the style of the bibliography can be controlled using
# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
-# search path. See also \cite for info how to create references.
+# 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 =
+CITE_BIB_FILES =
#---------------------------------------------------------------------------
# Configuration options related to warning and progress messages
@@ -708,7 +697,7 @@ CITE_BIB_FILES =
QUIET = NO
# 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
+# 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.
@@ -716,7 +705,7 @@ QUIET = NO
WARNINGS = YES
-# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
+# 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.
@@ -733,18 +722,12 @@ WARN_IF_DOC_ERROR = YES
# 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.
+# 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
-# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
-# a warning is encountered.
-# The default value is: NO.
-
-WARN_AS_ERROR = NO
-
# The WARN_FORMAT tag determines the format of the warning messages that doxygen
# can produce. The string should contain the $file, $line, and $text tags, which
# will be replaced by the file and line number from which the warning originated
@@ -759,7 +742,7 @@ WARN_FORMAT = "$file:$line: $text"
# messages should be written. If left blank the output is written to standard
# error (stderr).
-WARN_LOGFILE =
+WARN_LOGFILE =
#---------------------------------------------------------------------------
# Configuration options related to the input files
@@ -768,7 +751,7 @@ WARN_LOGFILE =
# The INPUT tag is used to specify the files and/or directories that contain
# documented source files. You may enter file names like myfile.cpp or
# directories like /usr/src/myproject. Separate the files or directories with
-# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
+# spaces.
# Note: If this tag is empty the current directory is searched.
INPUT = src
@@ -784,17 +767,12 @@ 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 patterns (like *.cpp and
-# *.h) to filter out the source-files in the directories.
-#
-# Note that for custom extensions or not directly supported extensions you also
-# need to set EXTENSION_MAPPING for the extension otherwise the files are not
-# read by doxygen.
-#
-# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
-# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
-# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
-# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f, *.for, *.tcl,
-# *.vhd, *.vhdl, *.ucf, *.qsf, *.as and *.js.
+# *.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
@@ -812,7 +790,7 @@ RECURSIVE = YES
# Note that relative paths are relative to the directory from which doxygen is
# run.
-EXCLUDE =
+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
@@ -828,7 +806,7 @@ EXCLUDE_SYMLINKS = NO
# 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 =
+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
@@ -839,20 +817,20 @@ EXCLUDE_PATTERNS =
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories use the pattern */test/*
-EXCLUDE_SYMBOLS =
+EXCLUDE_SYMBOLS =
# The EXAMPLE_PATH tag can be used to specify one or more files or directories
# that contain example code fragments that are included (see the \include
# command).
-EXAMPLE_PATH =
+EXAMPLE_PATH =
# If the value of the EXAMPLE_PATH tag contains directories, you can use the
# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
# *.h) to filter out the source-files in the directories. If left blank all
# files are included.
-EXAMPLE_PATTERNS =
+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
@@ -865,7 +843,7 @@ EXAMPLE_RECURSIVE = NO
# that contain images that are to be included in the documentation (see the
# \image command).
-IMAGE_PATH =
+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
@@ -881,12 +859,8 @@ IMAGE_PATH =
# Note that the filter must not add or remove lines; it is applied before the
# code is scanned, but not when the output code is generated. If lines are added
# or removed, the anchors will not be placed correctly.
-#
-# Note that for custom extensions or not directly supported extensions you also
-# need to set EXTENSION_MAPPING for the extension otherwise the files are not
-# properly processed by doxygen.
-INPUT_FILTER =
+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
@@ -894,15 +868,11 @@ INPUT_FILTER =
# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
# patterns match the file name, INPUT_FILTER is applied.
-#
-# Note that for custom extensions or not directly supported extensions you also
-# need to set EXTENSION_MAPPING for the extension otherwise the files are not
-# properly processed by doxygen.
-FILTER_PATTERNS =
+FILTER_PATTERNS =
# 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
+# 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.
@@ -914,14 +884,14 @@ FILTER_SOURCE_FILES = NO
# *.ext= (so without naming a filter).
# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
-FILTER_SOURCE_PATTERNS =
+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 =
+USE_MDFILE_AS_MAINPAGE =
#---------------------------------------------------------------------------
# Configuration options related to source browsing
@@ -962,7 +932,7 @@ REFERENCED_BY_RELATION = YES
REFERENCES_RELATION = YES
# 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
+# 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.
@@ -1009,25 +979,6 @@ USE_HTAGS = NO
VERBATIM_HEADERS = YES
-# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
-# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the
-# cost of reduced performance. This can be particularly helpful with template
-# rich C++ code for which doxygen's built-in parser lacks the necessary type
-# information.
-# Note: The availability of this option depends on whether or not doxygen was
-# generated with the -Duse-libclang=ON option for CMake.
-# The default value is: NO.
-
-CLANG_ASSISTED_PARSING = NO
-
-# If clang assisted parsing is enabled you can provide the compiler with command
-# line options that you would normally use when invoking the compiler. Note that
-# the include paths will already be set by doxygen for the files and directories
-# specified with INPUT and INCLUDE_PATH.
-# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
-
-CLANG_OPTIONS =
-
#---------------------------------------------------------------------------
# Configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
@@ -1052,13 +1003,13 @@ COLS_IN_ALPHA_INDEX = 5
# while generating the index headers.
# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
-IGNORE_PREFIX =
+IGNORE_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the HTML output
#---------------------------------------------------------------------------
-# If the GENERATE_HTML tag is set to YES, 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
@@ -1096,7 +1047,7 @@ HTML_FILE_EXTENSION = .html
# of the possible markers and block names see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
-HTML_HEADER =
+HTML_HEADER =
# 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
@@ -1106,7 +1057,7 @@ HTML_HEADER =
# that doxygen normally uses.
# This tag requires that the tag GENERATE_HTML is set to YES.
-HTML_FOOTER =
+HTML_FOOTER =
# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
# sheet that is used by each HTML page. It can be used to fine-tune the look of
@@ -1118,20 +1069,18 @@ HTML_FOOTER =
# obsolete.
# This tag requires that the tag GENERATE_HTML is set to YES.
-HTML_STYLESHEET =
+HTML_STYLESHEET =
-# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
-# cascading style sheets that are included after the standard style sheets
+# 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 therefore more robust against future updates.
-# Doxygen will copy the style sheet files to the output directory.
-# Note: The order of the extra style sheet files is of importance (e.g. the last
-# style sheet in the list overrules the setting of the previous ones in the
-# list). For an example see the documentation.
+# 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 =
+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
@@ -1141,10 +1090,10 @@ HTML_EXTRA_STYLESHEET =
# 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 =
+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
+# 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
@@ -1175,9 +1124,8 @@ 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 YES can help to show when doxygen was last run and thus if the
-# documentation is up to date.
-# The default value is: NO.
+# 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
@@ -1270,31 +1218,31 @@ GENERATE_HTMLHELP = NO
# written to the html output directory.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
-CHM_FILE =
+CHM_FILE =
# 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,
+# 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 =
+HHC_LOCATION =
-# 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
-# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
+# 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 =
+CHM_INDEX_ENCODING =
-# The BINARY_TOC flag controls whether a binary table of contents is generated
-# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
+# The BINARY_TOC flag controls whether a binary table of contents is generated (
+# YES) or a normal table of contents ( NO) in the .chm file. Furthermore it
# enables the Previous and Next buttons.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
@@ -1322,7 +1270,7 @@ GENERATE_QHP = NO
# the HTML output folder.
# This tag requires that the tag GENERATE_QHP is set to YES.
-QCH_FILE =
+QCH_FILE =
# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
# Project output. For more information please see Qt Help Project / Namespace
@@ -1347,7 +1295,7 @@ QHP_VIRTUAL_FOLDER = doc
# filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
-QHP_CUST_FILTER_NAME =
+QHP_CUST_FILTER_NAME =
# 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
@@ -1355,21 +1303,21 @@ QHP_CUST_FILTER_NAME =
# filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
-QHP_CUST_FILTER_ATTRS =
+QHP_CUST_FILTER_ATTRS =
# 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 =
+QHP_SECT_FILTER_ATTRS =
# 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 =
+QHG_LOCATION =
# 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
@@ -1408,7 +1356,7 @@ DISABLE_INDEX = NO
# index structure (just like the one that is generated for HTML Help). For this
# to work a browser that supports JavaScript, DHTML, CSS and frames is required
# (i.e. any modern browser). Windows users are probably better off using the
-# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
+# 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
@@ -1436,7 +1384,7 @@ ENUM_VALUES_PER_LINE = 4
TREEVIEW_WIDTH = 250
-# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
+# 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.
@@ -1465,7 +1413,7 @@ 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 pre-rendered bitmaps. Use this if you do not have LaTeX
+# 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.
@@ -1502,7 +1450,7 @@ MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest
# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
# This tag requires that the tag USE_MATHJAX is set to YES.
-MATHJAX_EXTENSIONS =
+MATHJAX_EXTENSIONS =
# 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
@@ -1510,7 +1458,7 @@ MATHJAX_EXTENSIONS =
# example see the documentation.
# This tag requires that the tag USE_MATHJAX is set to YES.
-MATHJAX_CODEFILE =
+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
@@ -1551,7 +1499,7 @@ SERVER_BASED_SEARCH = NO
# 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
+# 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/).
#
@@ -1564,13 +1512,13 @@ 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
+# 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 =
+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
@@ -1586,7 +1534,7 @@ SEARCHDATA_FILE = searchdata.xml
# projects and redirect the results back to the right project.
# This tag requires that the tag SEARCHENGINE is set to YES.
-EXTERNAL_SEARCH_ID =
+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
@@ -1596,13 +1544,13 @@ EXTERNAL_SEARCH_ID =
# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
# This tag requires that the tag SEARCHENGINE is set to YES.
-EXTRA_SEARCH_MAPPINGS =
+EXTRA_SEARCH_MAPPINGS =
#---------------------------------------------------------------------------
# Configuration options related to the LaTeX output
#---------------------------------------------------------------------------
-# If the GENERATE_LATEX tag is set to YES, 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
@@ -1633,7 +1581,7 @@ LATEX_CMD_NAME = latex
MAKEINDEX_CMD_NAME = makeindex
-# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
+# 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.
@@ -1651,12 +1599,9 @@ COMPACT_LATEX = NO
PAPER_TYPE = a4wide
# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
-# that should be included in the LaTeX output. The package can be specified just
-# by its name or with the correct syntax as to be used with the LaTeX
-# \usepackage command. To get the times font for instance you can specify :
-# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
-# To use the option intlimits with the amsmath package you can specify:
-# EXTRA_PACKAGES=[intlimits]{amsmath}
+# 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.
@@ -1670,35 +1615,22 @@ EXTRA_PACKAGES = amsmath
#
# Note: Only use a user-defined header if you know what you are doing! The
# following commands have a special meaning inside the header: $title,
-# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
-# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
-# string, for the replacement values of the other commands the user is referred
-# to HTML_HEADER.
+# $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 =
+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. See
-# LATEX_HEADER for more information on how to generate a default footer and what
-# special commands can be used inside the footer.
+# 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 =
-
-# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
-# LaTeX style sheets that are included after the standard style sheets created
-# by doxygen. Using this option one can overrule certain style aspects. Doxygen
-# will copy the style sheet files to the output directory.
-# Note: The order of the extra style sheet files is of importance (e.g. the last
-# style sheet in the list overrules the setting of the previous ones in the
-# list).
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_EXTRA_STYLESHEET =
+LATEX_FOOTER =
# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
# other source files which should be copied to the LATEX_OUTPUT output
@@ -1706,7 +1638,7 @@ LATEX_EXTRA_STYLESHEET =
# markers available.
# This tag requires that the tag GENERATE_LATEX is set to YES.
-LATEX_EXTRA_FILES =
+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
@@ -1717,8 +1649,8 @@ LATEX_EXTRA_FILES =
PDF_HYPERLINKS = NO
-# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
-# the PDF file directly from the LaTeX files. Set this option to YES, to get a
+# 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.
@@ -1759,19 +1691,11 @@ LATEX_SOURCE_CODE = NO
LATEX_BIB_STYLE = plain
-# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
-# page will contain the date and time when the page was generated. Setting this
-# to NO can help when comparing the output of multiple runs.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_TIMESTAMP = NO
-
#---------------------------------------------------------------------------
# Configuration options related to the RTF output
#---------------------------------------------------------------------------
-# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
+# 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.
@@ -1786,7 +1710,7 @@ GENERATE_RTF = NO
RTF_OUTPUT = rtf
-# If the COMPACT_RTF tag is set to YES, doxygen generates more compact 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.
# The default value is: NO.
@@ -1814,30 +1738,20 @@ RTF_HYPERLINKS = NO
# default style sheet that doxygen normally uses.
# This tag requires that the tag GENERATE_RTF is set to YES.
-RTF_STYLESHEET_FILE =
+RTF_STYLESHEET_FILE =
# Set optional variables used in the generation of an RTF document. Syntax is
# similar to doxygen's config file. A template extensions file can be generated
# using doxygen -e rtf extensionFile.
# This tag requires that the tag GENERATE_RTF is set to YES.
-RTF_EXTENSIONS_FILE =
-
-# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
-# with syntax highlighting in the RTF output.
-#
-# Note that which sources are shown also depends on other settings such as
-# SOURCE_BROWSER.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_SOURCE_CODE = NO
+RTF_EXTENSIONS_FILE =
#---------------------------------------------------------------------------
# Configuration options related to the man page output
#---------------------------------------------------------------------------
-# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
+# If the GENERATE_MAN tag is set to YES doxygen will generate man pages for
# classes and files.
# The default value is: NO.
@@ -1866,7 +1780,7 @@ MAN_EXTENSION = .3
# MAN_EXTENSION with the initial . removed.
# This tag requires that the tag GENERATE_MAN is set to YES.
-MAN_SUBDIR =
+MAN_SUBDIR =
# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
# will generate one additional man file for each entity documented in the real
@@ -1881,7 +1795,7 @@ MAN_LINKS = NO
# Configuration options related to the XML output
#---------------------------------------------------------------------------
-# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
+# 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.
@@ -1895,7 +1809,7 @@ GENERATE_XML = NO
XML_OUTPUT = xml
-# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
+# 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.
@@ -1908,7 +1822,7 @@ XML_PROGRAMLISTING = YES
# Configuration options related to the DOCBOOK output
#---------------------------------------------------------------------------
-# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
+# If the GENERATE_DOCBOOK tag is set to YES doxygen will generate Docbook files
# that can be used to generate PDF.
# The default value is: NO.
@@ -1922,23 +1836,14 @@ GENERATE_DOCBOOK = NO
DOCBOOK_OUTPUT = docbook
-# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
-# program listings (including syntax highlighting and cross-referencing
-# information) to the DOCBOOK output. Note that enabling this will significantly
-# increase the size of the DOCBOOK output.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
-
-DOCBOOK_PROGRAMLISTING = NO
-
#---------------------------------------------------------------------------
# Configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------
-# 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.
+# 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
@@ -1947,7 +1852,7 @@ GENERATE_AUTOGEN_DEF = NO
# Configuration options related to the Perl module output
#---------------------------------------------------------------------------
-# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
+# 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.
@@ -1955,7 +1860,7 @@ GENERATE_AUTOGEN_DEF = NO
GENERATE_PERLMOD = NO
-# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
+# 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.
@@ -1963,9 +1868,9 @@ GENERATE_PERLMOD = NO
PERLMOD_LATEX = NO
-# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
+# 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
+# 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.
@@ -1979,20 +1884,20 @@ PERLMOD_PRETTY = YES
# overwrite each other's variables.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
-PERLMOD_MAKEVAR_PREFIX =
+PERLMOD_MAKEVAR_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------
-# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
+# 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, only conditional compilation will be
+# 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.
@@ -2008,7 +1913,7 @@ MACRO_EXPANSION = NO
EXPAND_ONLY_PREDEF = NO
-# If the SEARCH_INCLUDES tag is set to YES, the include files in the
+# 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.
@@ -2020,7 +1925,7 @@ SEARCH_INCLUDES = YES
# preprocessor.
# This tag requires that the tag SEARCH_INCLUDES is set to YES.
-INCLUDE_PATH =
+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
@@ -2028,7 +1933,7 @@ INCLUDE_PATH =
# used.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-INCLUDE_FILE_PATTERNS =
+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 e.g.
@@ -2038,7 +1943,7 @@ INCLUDE_FILE_PATTERNS =
# recursively expanded use the := operator instead of the = operator.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-PREDEFINED =
+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
@@ -2047,7 +1952,7 @@ PREDEFINED =
# definition found in the source code.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-EXPAND_AS_DEFINED =
+EXPAND_AS_DEFINED =
# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
# remove all references to function-like macros that are alone on a line, have
@@ -2084,21 +1989,20 @@ TAGFILES = ../bpp-core/BppCore.tag=../../bpp-core/html/
GENERATE_TAGFILE = BppSeq.tag
-# 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.
+# 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
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed in
+# the modules index. If set to NO, only the current project's groups will be
# listed.
# The default value is: YES.
EXTERNAL_GROUPS = YES
-# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in
+# 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.
@@ -2115,7 +2019,7 @@ PERL_PATH = /usr/bin/perl
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
-# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram
+# 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
@@ -2131,16 +2035,16 @@ CLASS_DIAGRAMS = YES
# the mscgen tool resides. If left empty the tool is assumed to be found in the
# default search path.
-MSCGEN_PATH =
+MSCGEN_PATH =
# 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 =
+DIA_PATH =
-# If set to YES the inheritance and collaboration graphs will hide inheritance
+# 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.
@@ -2165,7 +2069,7 @@ HAVE_DOT = YES
DOT_NUM_THREADS = 0
-# When you want a differently looking font in the dot files that doxygen
+# 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
@@ -2187,7 +2091,7 @@ DOT_FONTSIZE = 10
# the path where dot can find it using this tag.
# This tag requires that the tag HAVE_DOT is set to YES.
-DOT_FONTPATH =
+DOT_FONTPATH =
# 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.
@@ -2213,7 +2117,7 @@ COLLABORATION_GRAPH = YES
GROUP_GRAPHS = YES
-# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and
+# 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.
@@ -2265,8 +2169,7 @@ INCLUDED_BY_GRAPH = YES
#
# Note that enabling this option will significantly increase the time of a run.
# So in most cases it will be better to enable call graphs for selected
-# functions only using the \callgraph command. Disabling a call graph can be
-# accomplished by means of the command \hidecallgraph.
+# functions only using the \callgraph command.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
@@ -2277,8 +2180,7 @@ CALL_GRAPH = NO
#
# Note that enabling this option will significantly increase the time of a run.
# So in most cases it will be better to enable caller graphs for selected
-# functions only using the \callergraph command. Disabling a caller graph can be
-# accomplished by means of the command \hidecallergraph.
+# functions only using the \callergraph command.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
@@ -2301,17 +2203,13 @@ GRAPHICAL_HIERARCHY = YES
DIRECTORY_GRAPH = YES
# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
-# generated by dot. For an explanation of the image formats see the section
-# output formats in the documentation of the dot tool (Graphviz (see:
-# http://www.graphviz.org/)).
+# 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, png:cairo, png:cairo:cairo, png:cairo:gd, png:gd,
# png:gd:gd, jpg, jpg:cairo, jpg:cairo:gd, jpg:gd, jpg:gd:gd, gif, gif:cairo,
-# gif:cairo:gd, gif:gd, gif:gd:gd, svg, png:gd, png:gd:gd, png:cairo,
-# png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and
-# png:gdiplus:gdiplus.
+# gif:cairo:gd, gif:gd, gif:gd:gd and svg.
# The default value is: png.
# This tag requires that the tag HAVE_DOT is set to YES.
@@ -2333,39 +2231,26 @@ INTERACTIVE_SVG = NO
# 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 =
+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).
# This tag requires that the tag HAVE_DOT is set to YES.
-DOTFILE_DIRS =
+DOTFILE_DIRS =
# The MSCFILE_DIRS tag can be used to specify one or more directories that
# contain msc files that are included in the documentation (see the \mscfile
# command).
-MSCFILE_DIRS =
+MSCFILE_DIRS =
# The DIAFILE_DIRS tag can be used to specify one or more directories that
# contain dia files that are included in the documentation (see the \diafile
# command).
-DIAFILE_DIRS =
-
-# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
-# path where java can find the plantuml.jar file. If left blank, it is assumed
-# PlantUML is not used or called during a preprocessing step. Doxygen will
-# generate a warning when it encounters a \startuml command in this case and
-# will not generate output for the diagram.
-
-PLANTUML_JAR_PATH =
-
-# When using plantuml, the specified paths are searched for files specified by
-# the !include statement in a plantuml block.
-
-PLANTUML_INCLUDE_PATH =
+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
@@ -2403,7 +2288,7 @@ MAX_DOT_GRAPH_DEPTH = 0
DOT_TRANSPARENT = NO
-# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
+# 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.
@@ -2420,7 +2305,7 @@ DOT_MULTI_TARGETS = YES
GENERATE_LEGEND = YES
-# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate dot
+# 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.
diff --git a/src/Bpp/Seq/Alphabet/AlphabetTools.cpp b/src/Bpp/Seq/Alphabet/AlphabetTools.cpp
index 6585ab9..d0def5b 100644
--- a/src/Bpp/Seq/Alphabet/AlphabetTools.cpp
+++ b/src/Bpp/Seq/Alphabet/AlphabetTools.cpp
@@ -91,6 +91,7 @@ bool AlphabetTools::checkAlphabetCodingSize(const Alphabet& alphabet) throw (Alp
if (alphabet.getNumberOfChars() == 0)
return true; // Will this really happen?
size_t size = alphabet.intToChar(0).size();
+
for (int i = 1; i < static_cast<int>(alphabet.getNumberOfTypes()); ++i)
{
if (alphabet.intToChar(i).size() != size)
diff --git a/src/Bpp/Seq/Alphabet/AlphabetTools.h b/src/Bpp/Seq/Alphabet/AlphabetTools.h
index ed7f4af..c2cb310 100644
--- a/src/Bpp/Seq/Alphabet/AlphabetTools.h
+++ b/src/Bpp/Seq/Alphabet/AlphabetTools.h
@@ -45,6 +45,7 @@
#include "ProteicAlphabet.h"
#include "DefaultAlphabet.h"
#include "CodonAlphabet.h"
+#include "WordAlphabet.h"
#include "RNY.h"
#include "BinaryAlphabet.h"
#include <Bpp/Numeric/VectorTools.h>
@@ -168,7 +169,7 @@ public:
* @return True if the alphabet is an instanciation of the WordAlphabet class.
* @param alphabet The alphabet to check.
*/
- static bool isWordAlphabet(const Alphabet* alphabet) { return alphabetInheritsFrom<WordAlphabet>(alphabet); }
+ static bool isWordAlphabet(const Alphabet* alphabet) { return alphabetInheritsFrom<CoreWordAlphabet>(alphabet); }
/**
* @return True if the alphabet is an instanciation of the RNY class.
@@ -221,7 +222,7 @@ private:
try
{
const Y* t = dynamic_cast<const Y*>(alphabet);
- return t != 0; // Solves strange behavior in new gcc?
+ return t != nullptr;
}
catch (std::exception& e)
{
diff --git a/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp b/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp
index 9072c02..9f3241c 100644
--- a/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp
+++ b/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp
@@ -47,75 +47,156 @@ using namespace bpp;
using namespace std;
-/******************************************************************************/
-int CodonAlphabet::getCodon(int pos1, int pos2, int pos3) const
-throw (BadIntException)
+void CodonAlphabet::build_()
{
- vector<int> vint;
- vint.push_back(pos1);
- vint.push_back(pos2);
- vint.push_back(pos3);
-
- return getWord(vint);
-}
+ vector<AlphabetState*> states(66);
-/******************************************************************************/
+ states[0] = new AlphabetState(-1, "---", "gap");
+
+ size_t i=0;
+ for (int i1 = 0; i1 < 4; ++i1)
+ for (int i2 = 0; i2 < 4; ++i2)
+ for (int i3 = 0; i3 < 4; ++i3)
+ {
+ string s=nAlph_->intToChar(i1)+nAlph_->intToChar(i2)+nAlph_->intToChar(i3);
+ states[i+1] = new AlphabetState(static_cast<int>(i), s, s);
+ i++;
+ }
+
+
+ states[65] = new AlphabetState(static_cast<int>(64), "NNN", "Unresolved");
+
+ //Now register all states once for all:
+ for (i = 0; i < states.size(); ++i)
+ registerState(states[i]);
-string CodonAlphabet::getCodon(const string & pos1, const string & pos2, const string & pos3) const
-throw (BadCharException)
-{
- vector<string> vint;
- vint.push_back(pos1);
- vint.push_back(pos2);
- vint.push_back(pos3);
-
- return getWord(vint);
}
-/******************************************************************************/
+int CodonAlphabet::getGCinCodon(int codon) const
+{
+ int i=0;
+ int j=getFirstPosition(codon);
+ if (j==1 || j==2)
+ i++;
+ j=getSecondPosition(codon);
+ if (j==1 || j==2)
+ i++;
+ j=getThirdPosition(codon);
+ if (j==1 || j==2)
+ i++;
+
+ return i;
+}
-int CodonAlphabet::getFirstPosition (int codon) const throw (BadIntException)
+bool CodonAlphabet::containsUnresolved(const std::string& state) const
{
- return getNPosition(codon,0);
+ if (state.length() != 3)
+ throw BadCharException(state, "CodonAlphabet::containsUnresolved", this);
+
+ for (size_t i = 0; i < 3; i++)
+ {
+ if (nAlph_->isUnresolved(state.substr(i, 1)))
+ {
+ return true;
+ }
+ }
+ return false;
}
/******************************************************************************/
-int CodonAlphabet::getSecondPosition(int codon) const throw (BadIntException)
+bool CodonAlphabet::containsGap(const std::string& state) const
{
- return getNPosition(codon,1);
+ if (state.length() != 3)
+ throw BadCharException(state, "CodonAlphabet::containsGap", this);
+
+ for (size_t i = 0; i < 3; i++)
+ {
+ if (nAlph_->isGap(state.substr(i, 1)))
+ return true;
+ }
+
+ return false;
}
-/******************************************************************************/
-int CodonAlphabet::getThirdPosition (int codon) const throw (BadIntException)
+/****************************************************************************************/
+
+Sequence* CodonAlphabet::translate(const Sequence& sequence, size_t pos) const
{
- return getNPosition(codon,2);
+ vector<int> content;
+
+ size_t s = sequence.size();
+ size_t i = pos;
+
+ while (i + 3 <= s)
+ {
+ content.push_back(getWord(sequence, i));
+ i += 3;
+ }
+
+ return new BasicSequence(sequence.getName(), content, this);
}
-/******************************************************************************/
+/****************************************************************************************/
-string CodonAlphabet::getFirstPosition (const string & codon) const
-throw (BadCharException)
+Sequence* CodonAlphabet::reverse(const Sequence& sequence) const
{
- return getNPosition(codon,0);
+ Sequence* pseq = new BasicSequence(sequence.getName(), "", getNAlphabet(0));
+
+ size_t s = sequence.size();
+ for (size_t i = 0; i < s; i++)
+ {
+ pseq->append(getPositions(sequence[i]));
+ }
+
+ return pseq;
}
-/******************************************************************************/
+/****************************************************************************************/
-string CodonAlphabet::getSecondPosition(const string & codon) const
-throw (BadCharException)
+std::vector<int> CodonAlphabet::getAlias(int state) const throw (BadIntException)
{
- return getNPosition(codon,1);
+ if (!isIntInAlphabet(state))
+ throw BadIntException(state, "WordAlphabet::getAlias(int): Specified base unknown.");
+ vector<int> v;
+
+ if (state == 64)
+ {
+ v.resize(64);
+ for (size_t i = 0; i < 64; ++i)
+ {
+ v[i] = static_cast<int>(i);
+ }
+ }
+ else
+ {
+ v.resize(1); v[0] = state;
+ }
+ return v;
}
/******************************************************************************/
-string CodonAlphabet::getThirdPosition (const string & codon) const
-throw (BadCharException)
+std::vector<std::string> CodonAlphabet::getAlias(const std::string& state) const throw (BadCharException)
{
- return getNPosition(codon,2);
+ string locstate = TextTools::toUpper(state);
+ if (!isCharInAlphabet(locstate))
+ throw BadCharException(locstate, "CodonAlphabet::getAlias(string): Specified base unknown.");
+ vector<string> v;
+
+ if (locstate == "NNN")
+ {
+ v.resize(64);
+ for (size_t i = 0; i < 64; ++i)
+ {
+ v[i] = intToChar(static_cast<int>(i));
+ }
+ }
+ else
+ {
+ v.resize(1); v[0] = state;
+ }
+ return v;
}
-
-/******************************************************************************/
diff --git a/src/Bpp/Seq/Alphabet/CodonAlphabet.h b/src/Bpp/Seq/Alphabet/CodonAlphabet.h
index 5715bad..fa5a05c 100644
--- a/src/Bpp/Seq/Alphabet/CodonAlphabet.h
+++ b/src/Bpp/Seq/Alphabet/CodonAlphabet.h
@@ -5,47 +5,47 @@
//
/*
-Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
-
-This software is a computer program whose purpose is to provide classes
-for sequences analysis.
-
-This software is governed by the CeCILL license under French law and
-abiding by the rules of distribution of free software. You can use,
-modify and/ or redistribute the software under the terms of the CeCILL
-license as circulated by CEA, CNRS and INRIA at the following URL
-"http://www.cecill.info".
-
-As a counterpart to the access to the source code and rights to copy,
-modify and redistribute granted by the license, users are provided
-only with a limited warranty and the software's author, the holder of
-the economic rights, and the successive licensors have only limited
-liability.
-
-In this respect, the user's attention is drawn to the risks associated
-with loading, using, modifying and/or developing or reproducing the
-software by the user in light of its specific status of free software,
-that may mean that it is complicated to manipulate, and that also
-therefore means that it is reserved for developers and experienced
-professionals having in-depth computer knowledge. Users are therefore
-encouraged to load and test the software's suitability as regards
-their requirements in conditions enabling the security of their
-systems and/or data to be ensured and, more generally, to use and
-operate it in the same conditions as regards security.
-
-The fact that you are presently reading this means that you have had
-knowledge of the CeCILL license and that you accept its terms.
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided
+ only with a limited warranty and the software's author, the holder of
+ the economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards
+ their requirements in conditions enabling the security of their
+ systems and/or data to be ensured and, more generally, to use and
+ operate it in the same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
*/
#ifndef _CODONALPHABET_H_
#define _CODONALPHABET_H_
-#include "WordAlphabet.h"
#include "NucleicAlphabet.h"
-
+#include "WordAlphabet.h"
+
// From the STL:
#include <string>
-
+#include <memory>
namespace bpp
{
@@ -54,135 +54,412 @@ namespace bpp
* @brief Codon alphabet class.
* @author Laurent Guéguen, Julien Dutheil
*
- * A codon alphabet object is a particular case of WordAlphabet with three letters.
* Since codons are made of 3 nucleic bases (RNA or DNA), this class
* has a NucleicAlphabet field used to check char description. This
* nucleic alphabet is passed to the constructor. This class also adds
* some methods specific to codon manipulation.
*/
-class CodonAlphabet:
- public WordAlphabet
-{
-public: // Constructor and destructor.
+
+ class CodonAlphabet:
+ public virtual CoreWordAlphabet,
+ public AbstractAlphabet
+ {
+ protected:
+ const NucleicAlphabet* nAlph_;
+
+ public: // Constructor and destructor.
- /**
- * @brief Builds a new codon alphabet from a nucleic alphabet.
- *
- * @param alpha The nucleic alphabet to be used.
- */
- CodonAlphabet(const NucleicAlphabet* alpha) :
- WordAlphabet(alpha, 3) {}
+ /**
+ * @brief Builds a new codon alphabet from a nucleic alphabet.
+ *
+ * @param alpha The nucleic alphabet to be used.
+ */
+ CodonAlphabet(const NucleicAlphabet* alpha) :
+ AbstractAlphabet(),
+ nAlph_(alpha)
+ {
+ build_();
+ }
- CodonAlphabet(const CodonAlphabet& bia) : WordAlphabet(bia) {}
+ CodonAlphabet(const CodonAlphabet& bia) :
+ AbstractAlphabet(bia),
+ nAlph_(bia.nAlph_)
+ {}
- CodonAlphabet& operator=(const CodonAlphabet& bia)
- {
- WordAlphabet::operator=(bia);
- return *this;
- }
+ CodonAlphabet& operator=(const CodonAlphabet& bia)
+ {
+ AbstractAlphabet::operator=(bia);
+ nAlph_ = bia.nAlph_;
+
+ return *this;
+ }
- CodonAlphabet* clone() const
- {
- return new CodonAlphabet(*this);
- }
+ CodonAlphabet* clone() const
+ {
+ return new CodonAlphabet(*this);
+ }
- virtual ~CodonAlphabet() {}
+ virtual ~CodonAlphabet() {}
- std::string getAlphabetType() const
- {
- return "Codon(letter="+ vAbsAlph_[0]->getAlphabetType() + ")";
- }
-
-
-public:
-
- /**
- * @name Codon specific methods
- *
- * @{
- */
-
- /**
- * @brief Get the int code for a codon given the int code of the three underlying positions.
- *
- * The int code of each position must match the nucleic alphabet specified for this alphabet.
- * @param pos1 Int description for position 1.
- * @param pos2 Int description for position 2.
- * @param pos3 Int description for position 3.
- * @return The int code of the codon.
- */
- virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
-
- /**
- * @brief Get the char code for a codon given the char code of the three underlying positions.
- *
- * The char code of each position must match the nucleic alphabet specified for this alphabet.
- * NB: This performs pos1 + pos2 + pos3 after checking for each position validity.
- * @param pos1 Char description for position 1.
- * @param pos2 Char description for position 2.
- * @param pos3 Char description for position 3.
- * @return The Char code of the codon.
- */
- virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
-
- /**
- * @brief Get the int code of the first position of a codon given its int description.
- *
- * @param codon The int description of the codon.
- * @return The int description of the first position of the codon.
- */
- virtual int getFirstPosition(int codon) const throw (BadIntException);
-
- /**
- * @brief Get the int code of the second position of a codon given its int description.
- *
- * @param codon The int description of the codon.
- * @return The int description of the second position of the codon.
- */
- virtual int getSecondPosition(int codon) const throw (BadIntException);
-
- /**
- * @brief Get the int code of the third position of a codon given its int description.
- *
- * @param codon The int description of the codon.
- * @return The int description of the third position of the codon.
- */
- virtual int getThirdPosition(int codon) const throw (BadIntException);
-
- /**
- * @brief Get the char code of the first position of a codon given its char description.
- *
- * @param codon The char description of the codon.
- * @return The char description of the first position of the codon.
- */
- virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
-
- /**
- * @brief Get the char code of the second position of a codon given its char description.
- *
- * @param codon The char description of the codon.
- * @return The char description of the second position of the codon.
- */
- virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
-
- /**
- * @brief Get the char code of the third position of a codon given its char description.
- *
- * @param codon The char description of the codon.
- * @return The char description of the third position of the codon.
- */
- virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
-
- /**
- * @return The nucleic alphabet associated to this codon alphabet.
- */
- virtual const NucleicAlphabet* const getNucleicAlphabet() const
- {
- return dynamic_cast<const NucleicAlphabet*>(vAbsAlph_[0]);
- }
+ std::string getAlphabetType() const
+ {
+ return "Codon(letter="+ nAlph_->getAlphabetType() + ")";
+ }
+
+ private:
+ /**
+ * @name Inner utilitary functions
+ *
+ * @{
+ */
+ bool containsUnresolved(const std::string& state) const;
+
+ bool containsGap(const std::string& state) const;
+
+ void build_();
+
+ /** @} */
+
+ public:
+
+ /**
+ * @name From AbstractAlphabet
+ *
+ * @{
+ */
+
+ unsigned int getNumberOfTypes() const {return 65;}
+
+ unsigned int getSize() const
+ {
+ return 64;
+ }
+
+ int getUnknownCharacterCode() const
+ {
+ return 64;
+ }
+
+ bool isUnresolved(int state) const
+ {
+ return state>=64;
+ }
+
+ bool isUnresolved(const std::string& state) const
+ {
+ return isUnresolved(charToInt(state));
+ }
+
+ std::vector<int> getAlias(int state) const throw (BadIntException);
+
+ std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
+
+ int getGeneric(const std::vector<int>& states) const throw (BadIntException)
+ {
+ return states[0];
+ }
+
+ std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException)
+ {
+ return states[0];
+ }
+
+ int charToInt(const std::string& state) const throw (BadCharException)
+ {
+ if (state.size() != 3)
+ throw BadCharException(state, "CodonAlphabet::charToInt", this);
+ if (containsUnresolved(state))
+ return static_cast<int>(getSize());
+ if (containsGap(state))
+ return -1;
+ else return AbstractAlphabet::charToInt(state);
+ }
+
+ /**
+ * @name Codon specific methods
+ *
+ * @{
+ */
+
+ /**
+ * @brief Get the int code for a codon given the int code of the three underlying positions.
+ *
+ * The int code of each position must match the nucleic alphabet specified for this alphabet.
+ * @param pos1 Int description for position 1.
+ * @param pos2 Int description for position 2.
+ * @param pos3 Int description for position 3.
+ * @return The int code of the codon.
+ */
+
+ int getCodon(int pos1, int pos2, int pos3) const
+ {
+ return (nAlph_->isUnresolved(pos1)
+ || nAlph_->isUnresolved(pos2)
+ || nAlph_->isUnresolved(pos3))? getUnknownCharacterCode()
+ : pos3 + 4*pos2 + 16 * pos1;
+ }
+
+ /**
+ * @brief Get the char code for a codon given the char code of the
+ * three underlying positions.
+ *
+ * The char code of each position must match the nucleic alphabet
+ * specified for this alphabet.
+ *
+ * NB: This performs pos1 + pos2 + pos3 after checking for each
+ * position validity.
+ *
+ * @param pos1 Char description for position 1.
+ * @param pos2 Char description for position 2.
+ * @param pos3 Char description for position 3.
+ * @return The Char code of the codon.
+ */
+
+ std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const
+ {
+ return pos1+pos2+pos3;
+ }
+
+ /**
+ * @brief Get the int code of the first position of a codon given its int description.
+ *
+ * @param codon The int description of the codon.
+ * @return The int description of the first position of the codon.
+ */
+
+ int getFirstPosition(int codon) const
+ {
+ return isUnresolved(codon)?nAlph_->charToInt("N"):codon / 16;
+ }
- /** @} */
-};
+ /**
+ * @brief Get the int code of the second position of a codon given its int description.
+ *
+ * @param codon The int description of the codon.
+ * @return The int description of the second position of the codon.
+ */
+
+ int getSecondPosition(int codon) const
+ {
+ return isUnresolved(codon)?nAlph_->charToInt("N"):(codon / 4) % 4;
+ }
+
+
+ /**
+ * @brief Get the int code of the third position of a codon given its int description.
+ *
+ * @param codon The int description of the codon.
+ * @return The int description of the third position of the codon.
+ */
+
+ int getThirdPosition(int codon) const
+ {
+ return isUnresolved(codon)?nAlph_->charToInt("N"):codon % 4;
+ }
+
+ /**
+ * @brief Get the char code of the first position of a codon given its char description.
+ *
+ * @param codon The char description of the codon.
+ * @return The char description of the first position of the codon.
+ */
+
+ std::string getFirstPosition (const std::string& codon) const
+ {
+ return codon.substr(0,1);
+ }
+
+
+ /**
+ * @brief Get the char code of the second position of a codon given its char description.
+ *
+ * @param codon The char description of the codon.
+ * @return The char description of the second position of the codon.
+ */
+
+ std::string getSecondPosition(const std::string& codon) const
+ {
+ return codon.substr(1,1);
+ }
+
+
+ /**
+ * @brief Get the char code of the third position of a codon given its char description.
+ *
+ * @param codon The char description of the codon.
+ * @return The char description of the third position of the codon.
+ */
+
+ std::string getThirdPosition(const std::string& codon) const
+ {
+ return codon.substr(2,1);
+ }
+
+
+ /**
+ * @name From CoreWordAlphabet
+ *
+ * @{
+ */
+
+ unsigned int getLength() const
+ {
+ return 3;
+ }
+
+ bool hasUniqueAlphabet() const
+ {
+ return true;
+ }
+
+ const Alphabet* getNAlphabet(size_t n) const
+ {
+ return nAlph_;
+ }
+
+ int getWord(const Sequence& seq, size_t pos = 0) const
+ {
+ if (seq.size() < pos + 3)
+ throw IndexOutOfBoundsException("CodonAlphabet::getWord", pos, 0, seq.size() - 3);
+ return getCodon(seq[pos], seq[pos+1], seq[pos+2]);
+ }
+
+ /**
+ * @brief Get the char code for a word given the char code of the
+ * underlying positions.
+ *
+ * The char code of each position must match the corresponding alphabet specified at this position.
+ * @param vpos vector description for all the positions.
+ * @param pos the start position to match in the vector.
+ * @return The string of the word.
+ * @throw IndexOutOfBoundsException In case of wrong position.
+ */
+
+ std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const
+ {
+ if (vpos.size() < pos + 3)
+ throw IndexOutOfBoundsException("CodonAlphabet::getWord", pos, 0, vpos.size() - 3);
+
+ return getCodon(vpos[pos], vpos[pos+1], vpos[pos+2]);
+ }
+
+ int getWord(const std::vector<int>& vpos, size_t pos = 0) const
+ {
+ if (vpos.size() < pos + 3)
+ throw IndexOutOfBoundsException("CodonAlphabet::getWord", pos, 0, vpos.size() - 3);
+
+ return getCodon(vpos[pos], vpos[pos+1], vpos[pos+2]);
+ }
+
+
+ int getNPosition(int codon, size_t pos) const
+ {
+ if (isUnresolved(codon))
+ return nAlph_->getUnknownCharacterCode();
+ else
+ return (pos==0 ? codon/16:
+ (pos==1? (codon/4)%4
+ : codon%4));
+ }
+
+ /**
+ * @brief Get the int codes of each position of a word given its int description.
+ *
+ * @param word The int description of the word.
+ * @return The int description of the positions of the codon.
+ */
+
+ std::vector<int> getPositions(int word) const
+ {
+ if (isUnresolved(word))
+ {
+ int n=nAlph_->getUnknownCharacterCode();
+ return std::vector<int>{n,n,n};
+ }
+ else
+ return std::vector<int>{word / 16, (word/4)%4, word%4};
+ }
+
+
+ /**
+ * @brief Get the char code of the Nth position of a codon given its char description.
+ *
+ * @param codon The char description of the codon.
+ * @param pos the position in the codon (starting at 0)
+ * @return The char description of the position of the codon.
+ */
+
+ std::string getNPosition(const std::string& codon, size_t pos) const
+ {
+ return codon.substr(pos,1);
+ }
+
+ /**
+ * @brief Get the char codes of each position of a word given its char description.
+ *
+ * @param word The char description of the word.
+ * @return The char description of the three positions of the word.
+ */
+
+ std::vector<std::string> getPositions(const std::string& word) const
+ {
+ return std::vector<std::string>{word.substr(0,1), word.substr(1,1), word.substr(2,1)};
+ }
+
+ /**
+ * @brief Translate a whole sequence from letters alphabet to words alphabet.
+ *
+ * @param sequence A sequence in letters alphabet.
+ * @param pos the start postion (default 0)
+ * @return The corresponding sequence in words alphabet.
+ * @throw AlphabetMismatchException If the sequence alphabet do not match the source alphabet.
+ * @throw Exception Other kind of error, depending on the implementation.
+ */
+
+ Sequence* translate(const Sequence &sequence, size_t = 0) const;
+
+ /**
+ * @brief Translate a whole sequence from words alphabet to letters alphabet.
+ *
+ * @param sequence A sequence in words alphabet.
+ * @return The corresponding sequence in letters alphabet.
+ * @throw AlphabetMismatchException If the sequence alphabet do not match the target alphabet.
+ * @throw Exception Other kind of error, depending on the implementation.
+ */
+
+ Sequence* reverse(const Sequence& sequence) const;
+
+ /*
+ *
+ * @}
+ */
+
+ /**
+ * @brief Get the number of G+C in codon
+ * @param codon The int description of the codon.
+ *
+ * @return The number of G+C in codon
+ */
+
+ int getGCinCodon(int codon) const;
+
+ /**
+ * @return The nucleic alphabet associated to this codon alphabet.
+ */
+
+ const NucleicAlphabet* const getNucleicAlphabet() const
+ {
+ return nAlph_;
+ }
+
+ /**
+ * @name Overloaded AbstractAlphabet methods.
+ * @{
+ */
+
+ unsigned int getStateCodingSize() const { return 3; }
+ /** @} */
+ };
} //end of namespace bpp.
diff --git a/src/Bpp/Seq/Alphabet/WordAlphabet.cpp b/src/Bpp/Seq/Alphabet/WordAlphabet.cpp
index 862584a..2a26792 100644
--- a/src/Bpp/Seq/Alphabet/WordAlphabet.cpp
+++ b/src/Bpp/Seq/Alphabet/WordAlphabet.cpp
@@ -157,7 +157,7 @@ bool WordAlphabet::hasUniqueAlphabet() const
return true;
}
-bool WordAlphabet::containsUnresolved(const std::string& state) const throw (BadCharException)
+bool WordAlphabet::containsUnresolved(const std::string& state) const
{
size_t s = vAbsAlph_.size();
if (state.length() != s)
@@ -175,7 +175,7 @@ bool WordAlphabet::containsUnresolved(const std::string& state) const throw (Bad
/******************************************************************************/
-bool WordAlphabet::containsGap(const std::string& state) const throw (BadCharException)
+bool WordAlphabet::containsGap(const std::string& state) const
{
size_t s = vAbsAlph_.size();
if (state.length() != s)
@@ -276,7 +276,7 @@ std::string WordAlphabet::getGeneric(const std::vector<std::string>& states) con
/******************************************************************************/
-int WordAlphabet::getWord(const Sequence& seq, size_t pos) const throw (IndexOutOfBoundsException)
+int WordAlphabet::getWord(const Sequence& seq, size_t pos) const
{
if (seq.size() < pos + vAbsAlph_.size())
throw IndexOutOfBoundsException("WordAlphabet::getWord", pos, 0, seq.size() - vAbsAlph_.size());
@@ -293,7 +293,7 @@ int WordAlphabet::getWord(const Sequence& seq, size_t pos) const throw (IndexOut
/******************************************************************************/
-int WordAlphabet::getWord(const std::vector<int>& vint, size_t pos) const throw (IndexOutOfBoundsException)
+int WordAlphabet::getWord(const std::vector<int>& vint, size_t pos) const
{
if (vint.size() < pos + vAbsAlph_.size())
throw IndexOutOfBoundsException("WordAlphabet::getWord", pos, 0, vint.size() - vAbsAlph_.size());
@@ -309,7 +309,7 @@ int WordAlphabet::getWord(const std::vector<int>& vint, size_t pos) const throw
/****************************************************************************************/
-std::string WordAlphabet::getWord(const std::vector<string>& vpos, size_t pos) const throw (IndexOutOfBoundsException, BadCharException)
+std::string WordAlphabet::getWord(const std::vector<string>& vpos, size_t pos) const
{
if (vpos.size() < pos + vAbsAlph_.size())
throw IndexOutOfBoundsException("WordAlphabet::getWord", pos, 0, vpos.size() - vAbsAlph_.size());
@@ -326,7 +326,7 @@ std::string WordAlphabet::getWord(const std::vector<string>& vpos, size_t pos) c
/****************************************************************************************/
-Sequence* WordAlphabet::translate(const Sequence& sequence, size_t pos) const throw (AlphabetMismatchException, Exception)
+Sequence* WordAlphabet::translate(const Sequence& sequence, size_t pos) const
{
if ((!hasUniqueAlphabet()) or
(sequence.getAlphabet()->getAlphabetType() != vAbsAlph_[0]->getAlphabetType()))
@@ -349,7 +349,7 @@ Sequence* WordAlphabet::translate(const Sequence& sequence, size_t pos) const th
/****************************************************************************************/
-Sequence* WordAlphabet::reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception)
+Sequence* WordAlphabet::reverse(const Sequence& sequence) const
{
if ((!hasUniqueAlphabet()) or
(sequence.getAlphabet()->getAlphabetType() != getAlphabetType()))
diff --git a/src/Bpp/Seq/Alphabet/WordAlphabet.h b/src/Bpp/Seq/Alphabet/WordAlphabet.h
index 94141a3..9dd63b2 100644
--- a/src/Bpp/Seq/Alphabet/WordAlphabet.h
+++ b/src/Bpp/Seq/Alphabet/WordAlphabet.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 sequences analysis.
-
- This software is governed by the CeCILL license under French law and
- abiding by the rules of distribution of free software. You can use,
- modify and/ or redistribute the software under the terms of the CeCILL
- license as circulated by CEA, CNRS and INRIA at the following URL
- "http://www.cecill.info".
-
- As a counterpart to the access to the source code and rights to copy,
- modify and redistribute granted by the license, users are provided
- only with a limited warranty and the software's author, the holder of
- the economic rights, and the successive licensors have only limited
- liability.
-
- In this respect, the user's attention is drawn to the risks associated
- with loading, using, modifying and/or developing or reproducing the
- software by the user in light of its specific status of free software,
- that may mean that it is complicated to manipulate, and that also
- therefore means that it is reserved for developers and experienced
- professionals having in-depth computer knowledge. Users are therefore
- encouraged to load and test the software's suitability as regards
- their requirements in conditions enabling the security of their
- systems and/or data to be ensured and, more generally, to use and
- operate it in the same conditions as regards security.
-
- The fact that you are presently reading this means that you have had
- knowledge of the CeCILL license and that you accept its terms.
- */
+ Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
+
+ This software is a computer program whose purpose is to provide classes
+ for sequences analysis.
+
+ This software is governed by the CeCILL license under French law and
+ abiding by the rules of distribution of free software. You can use,
+ modify and/ or redistribute the software under the terms of the CeCILL
+ license as circulated by CEA, CNRS and INRIA at the following URL
+ "http://www.cecill.info".
+
+ As a counterpart to the access to the source code and rights to copy,
+ modify and redistribute granted by the license, users are provided
+ only with a limited warranty and the software's author, the holder of
+ the economic rights, and the successive licensors have only limited
+ liability.
+
+ In this respect, the user's attention is drawn to the risks associated
+ with loading, using, modifying and/or developing or reproducing the
+ software by the user in light of its specific status of free software,
+ that may mean that it is complicated to manipulate, and that also
+ therefore means that it is reserved for developers and experienced
+ professionals having in-depth computer knowledge. Users are therefore
+ encouraged to load and test the software's suitability as regards
+ their requirements in conditions enabling the security of their
+ systems and/or data to be ensured and, more generally, to use and
+ operate it in the same conditions as regards security.
+
+ The fact that you are presently reading this means that you have had
+ knowledge of the CeCILL license and that you accept its terms.
+*/
#ifndef _WORDALPHABET_H_
#define _WORDALPHABET_H_
@@ -50,6 +50,133 @@
namespace bpp
{
+
+/**
+ * @brief The interface class for word alphabets.
+ *
+ */
+
+ class CoreWordAlphabet
+ {
+ public:
+ CoreWordAlphabet() {}
+
+ virtual ~CoreWordAlphabet() {}
+
+ virtual unsigned int getLength() const = 0;
+
+ virtual unsigned int getSize() const = 0;
+
+ virtual bool hasUniqueAlphabet() const = 0;
+
+ virtual const Alphabet* getNAlphabet(size_t n) const = 0;
+
+ virtual int getWord(const Sequence& seq, size_t pos = 0) const = 0;
+
+
+ /**
+ * @brief Get the int code for a word given the int code of the underlying positions.
+ *
+ * The int code of each position must match the corresponding alphabet specified at this position.
+ * @param vint description for all the positions.
+ * @param pos the start position to match in the vector.
+ * @return The int code of the word.
+ * @throw IndexOutOfBoundsException In case of wrong position.
+ */
+
+ virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const = 0;
+
+ /**
+ * @brief Get the char code for a word given the char code of the
+ * underlying positions.
+ *
+ * The char code of each position must match the corresponding alphabet specified at this position.
+ * @param vpos vector description for all the positions.
+ * @param pos the start position to match in the vector.
+ * @return The string of the word.
+ * @throw IndexOutOfBoundsException In case of wrong position.
+ */
+
+ virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const = 0;
+
+ /**
+ * @brief Get the int code of the n-position of a word given its int description.
+ *
+ * @param word The int description of the word.
+ * @param n The position in the word (starting at 0).
+ * @return The int description of the n-position of the word.
+ */
+
+ virtual int getNPosition(int word, size_t n) const = 0;
+
+ /**
+ * @brief Get the int codes of each position of a word given its int description.
+ *
+ * @param word The int description of the word.
+ * @return The int description of the positions of the codon.
+ */
+
+ virtual std::vector<int> getPositions(int word) const = 0;
+
+ /**
+ * @brief Get the char code of the n-position of a word given its char description.
+ *
+ * @param word The char description of the word.
+ * @param n The position in the word (starting at 0).
+ * @return The char description of the n-position of the word.
+ */
+
+ virtual std::string getNPosition(const std::string& word, size_t n) const = 0;
+
+ /**
+ * @brief Get the char codes of each position of a word given its char description.
+ *
+ * @param word The char description of the word.
+ * @return The char description of the three positions of the word.
+ */
+
+ virtual std::vector<std::string> getPositions(const std::string& word) const = 0;
+
+ /**
+ * @brief Translate a whole sequence from letters alphabet to words alphabet.
+ *
+ * @param sequence A sequence in letters alphabet.
+ * @param pos the start postion (default 0)
+ * @return The corresponding sequence in words alphabet.
+ * @throw AlphabetMismatchException If the sequence alphabet do not match the source alphabet.
+ * @throw Exception Other kind of error, depending on the implementation.
+ */
+
+ virtual Sequence* translate(const Sequence &sequence, size_t pos = 0) const = 0;
+
+ /**
+ * @brief Translate a whole sequence from words alphabet to letters alphabet.
+ *
+ * @param sequence A sequence in words alphabet.
+ * @return The corresponding sequence in letters alphabet.
+ * @throw AlphabetMismatchException If the sequence alphabet do not match the target alphabet.
+ * @throw Exception Other kind of error, depending on the implementation.
+ */
+
+ virtual Sequence* reverse(const Sequence& sequence) const = 0;
+
+ private:
+
+ /**
+ * @name Inner utilitary functions
+ *
+ * @{
+ */
+
+ virtual bool containsUnresolved(const std::string& state) const = 0;
+
+ virtual bool containsGap(const std::string& state) const = 0;
+
+ /** @} */
+
+ };
+
+
/**
* @brief The base class for word alphabets.
*
@@ -63,294 +190,307 @@ namespace bpp
* of the Alphabets. They are made from the resolved letters of the
* Alphabets.
*/
-class WordAlphabet :
- public AbstractAlphabet
-{
-protected:
- std::vector<const Alphabet* > vAbsAlph_;
-
-public:
- // Constructor and destructor.
- /**
- * @brief Builds a new word alphabet from a vector of Alphabets.
- *
- * The unit alphabets are not owned by the world alphabet, and won't
- * be destroyed when this instance is destroyed.
- *
- * @param vAlpha The vector of Alphabets to be used.
- */
- WordAlphabet(const std::vector<const Alphabet*>& vAlpha);
-
- /**
- * @brief Builds a new word alphabet from a pointer to number of
- * Alphabets.
- *
- * @param pAlpha The Pointer to the Alphabet to be used.
- * @param num the length of the words.
- */
- WordAlphabet(const Alphabet* pAlpha, size_t num);
-
- WordAlphabet(const WordAlphabet& bia) : AbstractAlphabet(bia), vAbsAlph_(bia.vAbsAlph_) {}
-
- WordAlphabet& operator=(const WordAlphabet& bia)
- {
- AbstractAlphabet::operator=(bia);
- vAbsAlph_=bia.vAbsAlph_;
- return *this;
- }
- WordAlphabet* clone() const
+
+ class WordAlphabet :
+ public virtual CoreWordAlphabet,
+ public AbstractAlphabet
{
- return new WordAlphabet(*this);
- }
-
- virtual ~WordAlphabet() {}
-
-public:
- /**
- * @name Methods redefined from Alphabet
- *
- * @{
- */
- /**
- * @brief Get the complete name of a state given its string description.
- *
- * In case of undefined characters (i.e. N and X for nucleic alphabets),
- * this method will return the name of the undefined word.
- *
- * @param state The string description of the given state.
- * @return The name of the state.
- * @throw BadCharException When state is not a valid char description.
- */
- std::string getName(const std::string& state) const throw (BadCharException);
-
- int charToInt(const std::string& state) const throw (BadCharException)
- {
- if (state.size() != vAbsAlph_.size())
- throw BadCharException(state, "WordAlphabet::charToInt", this);
- if (containsUnresolved(state))
- return static_cast<int>(getSize());
- if (containsGap(state))
- return -1;
- else return AbstractAlphabet::charToInt(state);
- }
+ protected:
+ std::vector<const Alphabet* > vAbsAlph_;
+
+ public:
+ // Constructor and destructor.
+ /**
+ * @brief Builds a new word alphabet from a vector of Alphabets.
+ *
+ * The unit alphabets are not owned by the world alphabet, and won't
+ * be destroyed when this instance is destroyed.
+ *
+ * @param vAlpha The vector of Alphabets to be used.
+ */
+ WordAlphabet(const std::vector<const Alphabet*>& vAlpha);
+
+ /**
+ * @brief Builds a new word alphabet from a pointer to number of
+ * Alphabets.
+ *
+ * @param pAlpha The Pointer to the Alphabet to be used.
+ * @param num the length of the words.
+ */
+ WordAlphabet(const Alphabet* pAlpha, size_t num);
+
+ WordAlphabet(const WordAlphabet& bia) : AbstractAlphabet(bia), vAbsAlph_(bia.vAbsAlph_) {}
+
+ WordAlphabet& operator=(const WordAlphabet& bia)
+ {
+ AbstractAlphabet::operator=(bia);
+ vAbsAlph_=bia.vAbsAlph_;
+ return *this;
+ }
- unsigned int getSize() const
- {
- return getNumberOfChars() - 2;
- }
-
- /** @} */
-
- /**
- * @brief Returns True if the Alphabet of the letters in the word
- * are the same type.
- *
- */
- bool hasUniqueAlphabet() const;
-
- /**
- * @brief Returns the length of the word
- *
- */
- unsigned int getLength() const
- {
- return static_cast<unsigned int>(vAbsAlph_.size());
- }
+ WordAlphabet* clone() const
+ {
+ return new WordAlphabet(*this);
+ }
+ virtual ~WordAlphabet() {}
+
+ public:
+ /**
+ * @name Methods redefined from Alphabet
+ *
+ * @{
+ */
+ /**
+ * @brief Get the complete name of a state given its string description.
+ *
+ * In case of undefined characters (i.e. N and X for nucleic alphabets),
+ * this method will return the name of the undefined word.
+ *
+ * @param state The string description of the given state.
+ * @return The name of the state.
+ * @throw BadCharException When state is not a valid char description.
+ */
+ std::string getName(const std::string& state) const throw (BadCharException);
+
+ int charToInt(const std::string& state) const throw (BadCharException)
+ {
+ if (state.size() != vAbsAlph_.size())
+ throw BadCharException(state, "WordAlphabet::charToInt", this);
+ if (containsUnresolved(state))
+ return static_cast<int>(getSize());
+ if (containsGap(state))
+ return -1;
+ else return AbstractAlphabet::charToInt(state);
+ }
- /**
- * @brief Returns the number of resolved states + one for unresolved
- *
- */
- unsigned int getNumberOfTypes() const
- {
- return getNumberOfChars() - 1;
- }
+ unsigned int getSize() const
+ {
+ return getNumberOfChars() - 2;
+ }
- std::string getAlphabetType() const;
+ /** @} */
- int getUnknownCharacterCode() const
- {
- return static_cast<int>(getSize());
- }
-
- bool isUnresolved(int state) const { return state == getUnknownCharacterCode(); }
- bool isUnresolved(const std::string& state) const { return charToInt(state) == getUnknownCharacterCode(); }
-
- std::vector<int> getAlias(int state) const throw (BadIntException);
- std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
- int getGeneric(const std::vector<int>& states) const throw (BadIntException);
- std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
-
-private:
- /**
- * @name Inner utilitary functions
- *
- * @{
- */
- bool containsUnresolved(const std::string& state) const throw (BadCharException);
- bool containsGap(const std::string& state) const throw (BadCharException);
- void build_();
- /** @} */
-
-public:
- /**
- * @name Word specific methods
- *
- * @{
- */
-
- /**
- * @brief Get the pointer to the Alphabet of the n-position.
- *
- * @param n The position in the word (starting at 0).
- * @return The pointer to the Alphabet of the n-position.
- */
- const Alphabet* getNAlphabet(size_t n) const
- {
- if (n >= vAbsAlph_.size())
- throw IndexOutOfBoundsException("WordAlphabet::getNPosition", n, 0, vAbsAlph_.size());
-
- return vAbsAlph_[n];
- }
-
- /**
- * @brief Get the int code for a word given the int code of the underlying positions.
- *
- * The int code of each position must match the corresponding alphabet specified at this position.
- * @param seq description for all the positions as a Sequence object.
- * @param pos the start position to match in the vector.
- * @return The int code of the word.
- * @throw IndexOutOfBoundsException In case of wrong position.
- */
- virtual int getWord(const Sequence& seq, size_t pos = 0) const throw (IndexOutOfBoundsException);
-
-
- /**
- * @brief Get the int code for a word given the int code of the underlying positions.
- *
- * The int code of each position must match the corresponding alphabet specified at this position.
- * @param vint description for all the positions.
- * @param pos the start position to match in the vector.
- * @return The int code of the word.
- * @throw IndexOutOfBoundsException In case of wrong position.
- */
- virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);
-
- /**
- * @brief Get the char code for a word given the char code of the
- * underlying positions.
- *
- * The char code of each position must match the corresponding alphabet specified at this position.
- * @param vpos vector description for all the positions.
- * @param pos the start position to match in the vector.
- * @return The string of the word.
- * @throw IndexOutOfBoundsException In case of wrong position.
- */
- virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);
-
- /**
- * @brief Get the int code of the n-position of a word given its int description.
- *
- * @param word The int description of the word.
- * @param n The position in the word (starting at 0).
- * @return The int description of the n-position of the word.
- */
- int getNPosition(int word, size_t n) const throw (BadIntException)
- {
- if (n >= vAbsAlph_.size())
- throw IndexOutOfBoundsException("WordAlphabet::getNPosition", n, 0, vAbsAlph_.size());
+ /**
+ * @brief Returns True if the Alphabet of the letters in the word
+ * are the same type.
+ *
+ */
+ bool hasUniqueAlphabet() const;
- std::string s = intToChar(word);
- return vAbsAlph_[n]->charToInt(s.substr(n, 1));
- }
+ /**
+ * @brief Returns the length of the word
+ *
+ */
+ unsigned int getLength() const
+ {
+ return static_cast<unsigned int>(vAbsAlph_.size());
+ }
- /**
- * @brief Get the int codes of each position of a word given its int description.
- *
- * @param word The int description of the word.
- * @return The int description of the positions of the codon.
- */
- std::vector<int> getPositions(int word) const throw (BadIntException)
- {
- std::string s = intToChar(word);
- std::vector<int> positions;
- for (size_t i = 0; i < s.size(); i++)
+ /**
+ * @brief Returns the number of resolved states + one for unresolved
+ *
+ */
+ unsigned int getNumberOfTypes() const
{
- positions.push_back(vAbsAlph_[i]->charToInt(s.substr(i, 1)));
+ return getNumberOfChars() - 1;
}
- return positions;
- }
- /**
- * @brief Get the char code of the n-position of a word given its char description.
- *
- * @param word The char description of the word.
- * @param n The position in the word (starting at 0).
- * @return The char description of the n-position of the word.
- */
- std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
- {
- if (n > vAbsAlph_.size())
- throw BadCharException("", "WordAlphabet::getNPosition", this);
- // Test:
- charToInt(word);
+ std::string getAlphabetType() const;
- return "" + word.substr(n, 1);
- }
+ int getUnknownCharacterCode() const
+ {
+ return static_cast<int>(getSize());
+ }
+ bool isUnresolved(int state) const { return state == getUnknownCharacterCode(); }
+ bool isUnresolved(const std::string& state) const { return charToInt(state) == getUnknownCharacterCode(); }
+
+ std::vector<int> getAlias(int state) const throw (BadIntException);
+
+ std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
+
+ int getGeneric(const std::vector<int>& states) const throw (BadIntException);
+
+ std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);
+
+ private:
+ /**
+ * @name Inner utilitary functions
+ *
+ * @{
+ */
+ bool containsUnresolved(const std::string& state) const;
+ bool containsGap(const std::string& state) const;
+ void build_();
+ /** @} */
+
+ public:
+ /**
+ * @name Word specific methods
+ *
+ * @{
+ */
+
+ /**
+ * @brief Get the pointer to the Alphabet of the n-position.
+ *
+ * @param n The position in the word (starting at 0).
+ * @return The pointer to the Alphabet of the n-position.
+ */
+ const Alphabet* getNAlphabet(size_t n) const
+ {
+ if (n >= vAbsAlph_.size())
+ throw IndexOutOfBoundsException("WordAlphabet::getNPosition", n, 0, vAbsAlph_.size());
- /**
- * @brief Get the char codes of each position of a word given its char description.
- *
- * @param word The char description of the word.
- * @return The char description of the three positions of the word.
- */
+ return vAbsAlph_[n];
+ }
- std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
- {
- charToInt(word);
- std::vector<std::string> positions;
- for (size_t i = 0; i < word.size(); i++)
+ /**
+ * @brief Get the int code for a word given the int code of the underlying positions.
+ *
+ * The int code of each position must match the corresponding alphabet specified at this position.
+ * @param seq description for all the positions as a Sequence object.
+ * @param pos the start position to match in the vector.
+ * @return The int code of the word.
+ * @throw IndexOutOfBoundsException In case of wrong position.
+ */
+
+ virtual int getWord(const Sequence& seq, size_t pos = 0) const;
+
+
+ /**
+ * @brief Get the int code for a word given the int code of the underlying positions.
+ *
+ * The int code of each position must match the corresponding alphabet specified at this position.
+ * @param vint description for all the positions.
+ * @param pos the start position to match in the vector.
+ * @return The int code of the word.
+ * @throw IndexOutOfBoundsException In case of wrong position.
+ */
+
+ virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const;
+
+ /**
+ * @brief Get the char code for a word given the char code of the
+ * underlying positions.
+ *
+ * The char code of each position must match the corresponding alphabet specified at this position.
+ * @param vpos vector description for all the positions.
+ * @param pos the start position to match in the vector.
+ * @return The string of the word.
+ * @throw IndexOutOfBoundsException In case of wrong position.
+ */
+
+ virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const;
+
+ /**
+ * @brief Get the int code of the n-position of a word given its int description.
+ *
+ * @param word The int description of the word.
+ * @param n The position in the word (starting at 0).
+ * @return The int description of the n-position of the word.
+ */
+
+ int getNPosition(int word, size_t n) const
+ {
+ if (n >= vAbsAlph_.size())
+ throw IndexOutOfBoundsException("WordAlphabet::getNPosition", n, 0, vAbsAlph_.size());
+
+ std::string s = intToChar(word);
+ return vAbsAlph_[n]->charToInt(s.substr(n, 1));
+ }
+
+ /**
+ * @brief Get the int codes of each position of a word given its int description.
+ *
+ * @param word The int description of the word.
+ * @return The int description of the positions of the codon.
+ */
+
+ std::vector<int> getPositions(int word) const
+ {
+ std::string s = intToChar(word);
+ std::vector<int> positions;
+ for (size_t i = 0; i < s.size(); i++)
+ {
+ positions.push_back(vAbsAlph_[i]->charToInt(s.substr(i, 1)));
+ }
+
+ return positions;
+ }
+ /**
+ * @brief Get the char code of the n-position of a word given its char description.
+ *
+ * @param word The char description of the word.
+ * @param n The position in the word (starting at 0).
+ * @return The char description of the n-position of the word.
+ */
+
+ std::string getNPosition(const std::string& word, size_t n) const
+ {
+ if (n > vAbsAlph_.size())
+ throw BadCharException("", "WordAlphabet::getNPosition", this);
+ // Test:
+ charToInt(word);
+
+ return "" + word.substr(n, 1);
+ }
+
+
+ /**
+ * @brief Get the char codes of each position of a word given its char description.
+ *
+ * @param word The char description of the word.
+ * @return The char description of the three positions of the word.
+ */
+
+ std::vector<std::string> getPositions(const std::string& word) const
{
- positions.push_back(word.substr(i, 1));
+ charToInt(word);
+ std::vector<std::string> positions;
+ for (size_t i = 0; i < word.size(); i++)
+ {
+ positions.push_back(word.substr(i, 1));
+ }
+
+ return positions;
}
- return positions;
- }
-
- /**
- * @brief Translate a whole sequence from letters alphabet to words alphabet.
- *
- * @param sequence A sequence in letters alphabet.
- * @param pos the start postion (default 0)
- * @return The corresponding sequence in words alphabet.
- * @throw AlphabetMismatchException If the sequence alphabet do not match the source alphabet.
- * @throw Exception Other kind of error, depending on the implementation.
- */
- Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);
-
- /**
- * @brief Translate a whole sequence from words alphabet to letters alphabet.
- *
- * @param sequence A sequence in words alphabet.
- * @return The corresponding sequence in letters alphabet.
- * @throw AlphabetMismatchException If the sequence alphabet do not match the target alphabet.
- * @throw Exception Other kind of error, depending on the implementation.
- */
- Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);
-
- /** @} */
-
- /**
- * @name Overloaded AbstractAlphabet methods.
- * @{
- */
- unsigned int getStateCodingSize() const { return static_cast<unsigned int>(vAbsAlph_.size()); }
- /** @} */
-};
+ /**
+ * @brief Translate a whole sequence from letters alphabet to words alphabet.
+ *
+ * @param sequence A sequence in letters alphabet.
+ * @param pos the start postion (default 0)
+ * @return The corresponding sequence in words alphabet.
+ * @throw AlphabetMismatchException If the sequence alphabet do not match the source alphabet.
+ * @throw Exception Other kind of error, depending on the implementation.
+ */
+
+ Sequence* translate(const Sequence &sequence, size_t = 0) const;
+
+ /**
+ * @brief Translate a whole sequence from words alphabet to letters alphabet.
+ *
+ * @param sequence A sequence in words alphabet.
+ * @return The corresponding sequence in letters alphabet.
+ * @throw AlphabetMismatchException If the sequence alphabet do not match the target alphabet.
+ * @throw Exception Other kind of error, depending on the implementation.
+ */
+
+ Sequence* reverse(const Sequence& sequence) const;
+
+ /** @} */
+
+ /**
+ * @name Overloaded AbstractAlphabet methods.
+ * @{
+ */
+ unsigned int getStateCodingSize() const { return static_cast<unsigned int>(vAbsAlph_.size()); }
+ /** @} */
+ };
} // end of namespace bpp.
#endif // _WORDALPHABET_H_
diff --git a/src/Bpp/Seq/CodonSiteTools.cpp b/src/Bpp/Seq/CodonSiteTools.cpp
index 9ec992a..decb720 100644
--- a/src/Bpp/Seq/CodonSiteTools.cpp
+++ b/src/Bpp/Seq/CodonSiteTools.cpp
@@ -232,6 +232,7 @@ size_t CodonSiteTools::numberOfDifferences(int i, int j, const CodonAlphabet& ca
double CodonSiteTools::numberOfSynonymousDifferences(int i, int j, const GeneticCode& gCode, bool minchange)
{
const CodonAlphabet* ca = dynamic_cast<const CodonAlphabet*>(gCode.getSourceAlphabet());
+
vector<int> ci = ca->getPositions(i);
vector<int> cj = ca->getPositions(j);
@@ -250,10 +251,12 @@ double CodonSiteTools::numberOfSynonymousDifferences(int i, int j, const Genetic
return 2;
vector<double> path(2, 0); // Vector of number of synonymous changes per path (2 here)
vector<double> weight(2, 1); // Weight to exclude path through stop codon
+
if (ci[0] == cj[0])
{
int trans1 = ca->getCodon(ci[0], cj[1], ci[2]); // transitory codon between NcNiNi et NcNjNj: NcNjNi, Nc = identical site
int trans2 = ca->getCodon(ci[0], ci[1], cj[2]); // transitory codon between NcNiNi et NcNjNj: NcNiNj, Nc = identical site
+
if (!gCode.isStop(trans1))
{
if (gCode.areSynonymous(i, trans1))
@@ -462,14 +465,17 @@ double CodonSiteTools::piSynonymous(const Site& site, const GeneticCode& gCode,
// General polymorphism checking
if (SiteTools::isConstant(site))
return 0;
+
// Computation
map<int, double> freq;
+
SiteTools::getFrequencies(site, freq);
double pi = 0;
for (map<int, double>::iterator it1 = freq.begin(); it1 != freq.end(); it1++)
{
for (map<int, double>::iterator it2 = freq.begin(); it2 != freq.end(); it2++)
{
+
pi += (it1->second) * (it2->second) * (numberOfSynonymousDifferences(it1->first, it2->first, gCode, minchange));
}
}
@@ -509,6 +515,7 @@ double CodonSiteTools::piNonSynonymous(const Site& site, const GeneticCode& gCod
pi += (it1->second) * (it2->second) * (nbtot - nbsyn);
}
}
+
size_t n = site.size();
return pi * static_cast<double>(n / (n - 1));
}
@@ -580,14 +587,14 @@ double CodonSiteTools::meanNumberOfSynonymousPositions(const Site& site, const G
/******************************************************************************/
-size_t CodonSiteTools::numberOfSubsitutions(const Site& site, const GeneticCode& gCode, double freqmin)
+size_t CodonSiteTools::numberOfSubstitutions(const Site& site, const GeneticCode& gCode, double freqmin)
{
// Alphabet checking
if (!AlphabetTools::isCodonAlphabet(site.getAlphabet()))
- throw AlphabetException("CodonSiteTools::numberOfSubsitutions: alphabet is not CodonAlphabet", site.getAlphabet());
+ throw AlphabetException("CodonSiteTools::numberOfSubstitutions: alphabet is not CodonAlphabet", site.getAlphabet());
// Empty site checking
if (site.size() == 0)
- throw EmptySiteException("CodonSiteTools::numberOfSubsitutions: Incorrect specified site", &site);
+ throw EmptySiteException("CodonSiteTools::numberOfSubstitutions: Incorrect specified site", &site);
if (SiteTools::isConstant(site))
return 0;
diff --git a/src/Bpp/Seq/CodonSiteTools.h b/src/Bpp/Seq/CodonSiteTools.h
index 9f0b85c..f4e92df 100644
--- a/src/Bpp/Seq/CodonSiteTools.h
+++ b/src/Bpp/Seq/CodonSiteTools.h
@@ -226,7 +226,7 @@ class CodonSiteTools:
* @param gCode a GeneticCode
* @param freqmin a double To exclude snp in frequency strictly lower than freqmin (by default freqmin = 0)
*/
- static size_t numberOfSubsitutions(const Site& site, const GeneticCode& gCode, double freqmin = 0.);
+ static size_t numberOfSubstitutions(const Site& site, const GeneticCode& gCode, double freqmin = 0.);
/**
* @brief Return the number of Non Synonymous subsitutions per codon site.
diff --git a/src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.cpp b/src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.cpp
deleted file mode 100644
index b40a379..0000000
--- a/src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.cpp
+++ /dev/null
@@ -1,187 +0,0 @@
-//
-// File: VectorProbabilisticSiteContainer.cpp
-// Created by: Murray Patterson
-// Created on: Mon Oct 19 2015
-//
-
-/*
- Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
-
- This software is a computer program whose purpose is to provide classes
- for sequences analysis.
-
- This software is governed by the CeCILL license under French law and
- abiding by the rules of distribution of free software. You can use,
- modify and/ or redistribute the software under the terms of the CeCILL
- license as circulated by CEA, CNRS and INRIA at the following URL
- "http://www.cecill.info".
-
- As a counterpart to the access to the source code and rights to copy,
- modify and redistribute granted by the license, users are provided only
- with a limited warranty and the software's author, the holder of the
- economic rights, and the successive licensors have only limited
- liability.
-
- In this respect, the user's attention is drawn to the risks associated
- with loading, using, modifying and/or developing or reproducing the
- software by the user in light of its specific status of free software,
- that may mean that it is complicated to manipulate, and that also
- therefore means that it is reserved for developers and experienced
- professionals having in-depth computer knowledge. Users are therefore
- encouraged to load and test the software's suitability as regards their
- requirements in conditions enabling the security of their systems and/or
- data to be ensured and, more generally, to use and operate it in the
- same conditions as regards security.
-
- The fact that you are presently reading this means that you have had
- knowledge of the CeCILL license and that you accept its terms.
-*/
-
-#include "VectorProbabilisticSiteContainer.h"
-
-#include <Bpp/Text/TextTools.h>
-#include <Bpp/Numeric/DataTable.h>
-
-using namespace bpp;
-
-/********************************************************************************/
-
-VectorProbabilisticSiteContainer::VectorProbabilisticSiteContainer(const Alphabet * alpha) :
- VectorSiteContainer(alpha),
- p_sites_(0),
- p_sequences_(0)
-{}
-
-/********************************************************************************/
-
-const ProbabilisticSite & VectorProbabilisticSiteContainer::getProbabilisticSite(std::size_t i) const throw (IndexOutOfBoundsException)
-{
- if(i >= getNumberOfProbabilisticSites())
- throw IndexOutOfBoundsException("VectorProbabilisticSiteContainer::getProbabilisticSite.", i, 0, getNumberOfProbabilisticSites() - 1);
-
- return *p_sites_[i];
-}
-
-/********************************************************************************/
-
-void VectorProbabilisticSiteContainer::addSite(const ProbabilisticSite & site, bool checkPosition) throw (Exception)
-{
- // check size :
- if(site.size() != getNumberOfProbabilisticSequences())
- throw Exception("VectorProbabilisticSiteContainer::addSite. Site does not have the appropriate length: " + TextTools::toString(site.size()) + ", should be " + TextTools::toString(getNumberOfProbabilisticSequences()) + ".");
-
- // new site's alphabet and site container's alphabet must match :
- if(site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
- throw AlphabetMismatchException("VectorProbabilisticSiteContainer::addSite.", getAlphabet(), site.getAlphabet());
-
- // check position :
- if(checkPosition) {
-
- int position = site.getPosition();
- // for all positions in vector : throw exception if position already exists
- for(std::size_t i = 0; i < p_sites_.size(); ++i)
- if(p_sites_[i]->getPosition() == position)
- throw Exception("VectorSiteContainer::addSite. Site position: " + TextTools::toString(position) + ", already exists in container.");
- }
-
- p_sites_.push_back(dynamic_cast<ProbabilisticSite *>(site.clone()));
-}
-
-/********************************************************************************/
-
-const ProbabilisticSequence & VectorProbabilisticSiteContainer::getProbabilisticSequence(std::size_t i) const throw (IndexOutOfBoundsException)
-{
-
- if(i >= getNumberOfProbabilisticSequences())
- throw IndexOutOfBoundsException("VectorProbabilisticSiteContainer::getProbabilisticSequence.", i, 0, getNumberOfProbabilisticSequences() - 1);
-
- // main loop : for all sites
- std::size_t n = getNumberOfProbabilisticSites();
- DataTable sequence(getAlphabet()->getResolvedChars());
- for(std::size_t j = 0; j < n; ++j)
- sequence.addRow(p_sites_[j]->getContent().getRow(i));
-
- if(p_sequences_[i])
- delete p_sequences_[i];
-
- p_sequences_[i] = new BasicProbabilisticSequence(names_[i], sequence, *comments_[i], getAlphabet());
-
- return *p_sequences_[i];
-}
-
-/********************************************************************************/
-
-void VectorProbabilisticSiteContainer::addSequence(const ProbabilisticSequence & sequence, bool checkName) throw (Exception)
-{
-
- // if the container has no sequence, we set the size to the size of this sequence :
- if(getNumberOfProbabilisticSequences() == 0)
- pRealloc(sequence.size());
-
- // new sequence's alphabet and site container's alphabet must match :
- if(sequence.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
- throw AlphabetMismatchException("VectorProbabilisticSiteContainer::addSequence.", getAlphabet(), sequence.getAlphabet());
-
- if(sequence.size() != p_sites_.size())
- throw Exception("VectorProbabilisticSiteContainer::addSequence. Sequence does not have the appropriate length: " + TextTools::toString(sequence.size()) + ", should be " + TextTools::toString(p_sites_.size()) + ".");
-
- // check name :
- if(checkName)
- for(std::size_t i = 0; i < names_.size(); ++i)
- if(sequence.getName() == names_[i])
- throw Exception("VectorProbabilisticSiteContainer::addSequence. Name: " + sequence.getName() + ", already exists in the container.");
-
- // append name :
- names_.push_back(sequence.getName());
-
- // append elements at each site :
- for(size_t i = 0; i < p_sites_.size(); ++i)
- p_sites_[i]->addElement(sequence.getContent().getRow(i));
-
- // append comments :
- comments_.push_back(new Comments(sequence.getComments()));
-
- // sequence pointers :
- p_sequences_.push_back(0);
-}
-
-/********************************************************************************/
-
-void VectorProbabilisticSiteContainer::pClear()
-{
- clear(); // call VectorSiteContainer clear
-
- // now clear all probabilistic sites / sequences
- for(std::size_t i = 0; i < p_sites_.size(); ++i)
- delete p_sites_[i];
-
- for(std::size_t i = 0; i < p_sequences_.size(); ++i)
- delete p_sequences_[i];
-
- // and delete the corresponding pointers
- p_sites_.clear();
- p_sequences_.clear();
-}
-
-/********************************************************************************/
-
-void VectorProbabilisticSiteContainer::reindexpSites()
-{
- int pos = 1; // start at position 1
- std::vector<ProbabilisticSite *>::iterator i = p_sites_.begin();
- for(; i != p_sites_.end(); ++i)
- (*i)->setPosition(++pos);
-}
-
-/********************************************************************************/
-
-void VectorProbabilisticSiteContainer::pRealloc(std::size_t n)
-{
- pClear();
- p_sites_.resize(n);
-
- for(std::size_t i = 0; i < n; ++i)
- p_sites_[i] = new BasicProbabilisticSite(getAlphabet());
-
- reindexpSites();
-}
diff --git a/src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.h b/src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.h
deleted file mode 100644
index 5f93474..0000000
--- a/src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.h
+++ /dev/null
@@ -1,123 +0,0 @@
-//
-// File: VectorProbabilisticSiteContainer.h
-// Created by: Murray Patterson
-// Created on: Mon Oct 19 2015
-//
-
-/*
- Copyright or © or Copr. CNRS, (November 17, 2004)
-
- This software is a computer program whose purpose is to provide classes
- for sequences analysis.
-
- This software is governed by the CeCILL license under French law and
- abiding by the rules of distribution of free software. You can use,
- modify and/ or redistribute the software under the terms of the CeCILL
- license as circulated by CEA, CNRS and INRIA at the following URL
- "http://www.cecill.info".
-
- As a counterpart to the access to the source code and rights to copy,
- modify and redistribute granted by the license, users are provided only
- with a limited warranty and the software's author, the holder of the
- economic rights, and the successive licensors have only limited
- liability.
-
- In this respect, the user's attention is drawn to the risks associated
- with loading, using, modifying and/or developing or reproducing the
- software by the user in light of its specific status of free software,
- that may mean that it is complicated to manipulate, and that also
- therefore means that it is reserved for developers and experienced
- professionals having in-depth computer knowledge. Users are therefore
- encouraged to load and test the software's suitability as regards their
- requirements in conditions enabling the security of their systems and/or
- data to be ensured and, more generally, to use and operate it in the
- same conditions as regards security.
-
- The fact that you are presently reading this means that you have had
- knowledge of the CeCILL license and that you accept its terms.
-*/
-
-#ifndef _VECTORPROBABILISTICSITECONTAINER_H_
-#define _VECTORPROBABILISTICSITECONTAINER_H_
-
-#include "VectorSiteContainer.h"
-
-#include "../ProbabilisticSite.h"
-#include "../ProbabilisticSequence.h"
-
-// From the STL :
-#include <vector>
-
-namespace bpp
-{
-
-/**
- * @brief The VectorProbabilisticSiteContainer class.
- *
- * ProbabilisticSites are stored in a std::vector of pointers.
- * ProbabilisticSite access is hence in \f$O(1)\f$, and sequence
- * access in \f$O(l)\f$, where \f$l\f$ is the number of sites in the
- * container.
- *
- * This is a modified copy of VectorSiteContainer with the minimum
- * changes necessary for it to work with bppML and bppAncestor
- *
- * @see ProbabilisticSequence, ProbabilisticSite, VectorSiteContainer
- */
-class VectorProbabilisticSiteContainer :
- public VectorSiteContainer
-{
-
- protected :
-
- std::vector<ProbabilisticSite *> p_sites_;
- mutable std::vector<ProbabilisticSequence *> p_sequences_;
-
- public :
-
- /**
- * @brief Build a new emtpy container.
- *
- * @param alpha The alphabet for this container.
- */
- VectorProbabilisticSiteContainer(const Alphabet * alpha);
-
- /**
- * @name The Clonable interface.
- *
- * @{
- */
- VectorSiteContainer* clone() const { return new VectorSiteContainer(*this); }
-
- /**
- * @}
- */
-
- // class destructor
- virtual ~VectorProbabilisticSiteContainer() { pClear(); }
-
- public :
-
- const ProbabilisticSite & getProbabilisticSite(std::size_t i) const throw (IndexOutOfBoundsException);
-
- void addSite(const ProbabilisticSite & site, bool checkPosition = true) throw (Exception);
-
- const ProbabilisticSequence & getProbabilisticSequence(std::size_t i) const throw (IndexOutOfBoundsException);
-
- void addSequence(const ProbabilisticSequence & sequence, bool checkName = true) throw (Exception);
-
- std::size_t getNumberOfProbabilisticSites() const { return p_sites_.size(); }
- std::size_t getNumberOfProbabilisticSequences() const { return p_sequences_.size(); }
-
- void pClear();
- void reindexpSites();
-
- protected :
-
- // create n void probabilistic sites :
- void pRealloc(std::size_t n);
-};
-
-} // end of namespace bpp
-
-#endif // _VECTORPROBABILISTICSITECONTAINER_H_
diff --git a/src/Bpp/Seq/SequenceTools.cpp b/src/Bpp/Seq/SequenceTools.cpp
index c483f72..6156f8a 100644
--- a/src/Bpp/Seq/SequenceTools.cpp
+++ b/src/Bpp/Seq/SequenceTools.cpp
@@ -109,11 +109,11 @@ Sequence& SequenceTools::complement(Sequence& seq) throw (AlphabetException)
{
// Alphabet type checking
NucleicAcidsReplication* NAR;
- if (seq.getAlphabet()->getAlphabetType() == "DNA alphabet")
+ if (AlphabetTools::isDNAAlphabet(seq.getAlphabet()))
{
NAR = &DNARep_;
}
- else if (seq.getAlphabet()->getAlphabetType() == "RNA alphabet")
+ else if (AlphabetTools::isRNAAlphabet(seq.getAlphabet()))
{
NAR = &RNARep_;
}
@@ -134,11 +134,11 @@ Sequence* SequenceTools::getComplement(const Sequence& sequence) throw (Alphabet
{
// Alphabet type checking
NucleicAcidsReplication* NAR;
- if (sequence.getAlphabet()->getAlphabetType() == "DNA alphabet")
+ if (AlphabetTools::isDNAAlphabet(sequence.getAlphabet()))
{
NAR = &DNARep_;
}
- else if (sequence.getAlphabet()->getAlphabetType() == "RNA alphabet")
+ else if (AlphabetTools::isRNAAlphabet(sequence.getAlphabet()))
{
NAR = &RNARep_;
}
@@ -155,7 +155,7 @@ Sequence* SequenceTools::getComplement(const Sequence& sequence) throw (Alphabet
Sequence* SequenceTools::transcript(const Sequence& sequence) throw (AlphabetException)
{
// Alphabet type checking
- if (sequence.getAlphabet()->getAlphabetType() != "DNA alphabet")
+ if (AlphabetTools::isDNAAlphabet(sequence.getAlphabet()))
{
throw AlphabetException ("SequenceTools::transcript : Sequence must be DNA", sequence.getAlphabet());
}
@@ -168,7 +168,7 @@ Sequence* SequenceTools::transcript(const Sequence& sequence) throw (AlphabetExc
Sequence* SequenceTools::reverseTranscript(const Sequence& sequence) throw (AlphabetException)
{
// Alphabet type checking
- if (sequence.getAlphabet()->getAlphabetType() != "RNA alphabet")
+ if (AlphabetTools::isRNAAlphabet(sequence.getAlphabet()))
{
throw AlphabetException ("SequenceTools::reverseTranscript : Sequence must be RNA", sequence.getAlphabet());
}
@@ -208,17 +208,17 @@ Sequence& SequenceTools::invertComplement(Sequence& seq)
{
// Alphabet type checking
NucleicAcidsReplication* NAR;
- if (seq.getAlphabet()->getAlphabetType() == "DNA alphabet")
+ if (AlphabetTools::isDNAAlphabet(seq.getAlphabet()))
{
NAR = &DNARep_;
}
- else if (seq.getAlphabet()->getAlphabetType() == "RNA alphabet")
+ else if (AlphabetTools::isRNAAlphabet(seq.getAlphabet()))
{
NAR = &RNARep_;
}
else
{
- throw AlphabetException("SequenceTools::complement: Sequence must be nucleic.", seq.getAlphabet());
+ throw AlphabetException("SequenceTools::invertComplement: Sequence must be nucleic.", seq.getAlphabet());
}
// for (size_t i = 0 ; i < seq.size() ; i++) {
// seq.setElement(i, NAR->translate(seq.getValue(i)));
@@ -577,7 +577,7 @@ Sequence* SequenceTools::subtractHaplotype(const Sequence& s, const Sequence& h,
Sequence* SequenceTools::RNYslice(const Sequence& seq, int ph) throw (AlphabetException)
{
// Alphabet type checking
- if (seq.getAlphabet()->getAlphabetType() != "DNA alphabet")
+ if (AlphabetTools::isDNAAlphabet(seq.getAlphabet()))
{
throw AlphabetException ("SequenceTools::transcript : Sequence must be DNA", seq.getAlphabet());
}
@@ -619,7 +619,7 @@ Sequence* SequenceTools::RNYslice(const Sequence& seq, int ph) throw (AlphabetEx
Sequence* SequenceTools::RNYslice(const Sequence& seq) throw (AlphabetException)
{
// Alphabet type checking
- if (seq.getAlphabet()->getAlphabetType() != "DNA alphabet")
+ if (AlphabetTools::isDNAAlphabet(seq.getAlphabet()))
{
throw AlphabetException ("SequenceTools::transcript : Sequence must be DNA", seq.getAlphabet());
}
diff --git a/src/Bpp/Seq/StringSequenceTools.cpp b/src/Bpp/Seq/StringSequenceTools.cpp
index fb29e48..6fab544 100644
--- a/src/Bpp/Seq/StringSequenceTools.cpp
+++ b/src/Bpp/Seq/StringSequenceTools.cpp
@@ -272,7 +272,13 @@ double StringSequenceTools::getGCcontent(const string& sequence, size_t pos, siz
vector<int> StringSequenceTools::codeSequence(const string& sequence, const Alphabet* alphabet)
throw (BadCharException)
{
- unsigned int size = AlphabetTools::getAlphabetCodingSize(alphabet); // Warning, an exception may be casted here!
+ unsigned int size = AlphabetTools::getAlphabetCodingSize(alphabet); // Warning,
+ // an
+ // exception
+ // may
+ // be
+ // casted
+ // here!
vector<int> code(static_cast<size_t>(floor(static_cast<double>(sequence.size()) / static_cast<double>(size))));
size_t pos = 0;
size_t count = 0;
diff --git a/src/Bpp/Seq/SymbolListTools.cpp b/src/Bpp/Seq/SymbolListTools.cpp
index 8e67127..561d1a1 100644
--- a/src/Bpp/Seq/SymbolListTools.cpp
+++ b/src/Bpp/Seq/SymbolListTools.cpp
@@ -91,7 +91,7 @@ void SymbolListTools::getCounts(const SymbolList& list1, const SymbolList& list2
void SymbolListTools::getFrequencies(const SymbolList& list, map<int, double>& frequencies, bool resolveUnknowns)
{
- double n = (double)list.size();
+ double n = (double)list.size();
map<int, double> counts;
getCounts(list, counts, resolveUnknowns);
for (map<int, double>::iterator i = counts.begin(); i != counts.end(); i++)
@@ -102,7 +102,7 @@ void SymbolListTools::getFrequencies(const SymbolList& list, map<int, double>& f
void SymbolListTools::getFrequencies(const SymbolList& list1, const SymbolList& list2, map<int, map<int, double> >& frequencies, bool resolveUnknowns) throw (DimensionException)
{
- double n2 = (double)list1.size() * (double)list1.size();
+ double n2 = (double)list1.size() * (double)list1.size();
map<int, map<int, double> > counts;
getCounts(list1, list2, counts, resolveUnknowns);
for (map<int, map<int, double> >::iterator i = counts.begin(); i != counts.end(); i++)
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index 2e19f7d..ab9b0aa 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -16,9 +16,11 @@ foreach (test_cpp_file ${test_cpp_files})
get_filename_component (test_name ${test_cpp_file} NAME_WE)
add_executable (${test_name} ${test_cpp_file})
target_link_libraries (${test_name} ${PROJECT_NAME}-shared)
+ set_target_properties (${test_name} PROPERTIES POSITION_INDEPENDENT_CODE TRUE)
add_test (
NAME ${test_name}
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
COMMAND ${test_name}
)
+ set_tests_properties (${test_name} PROPERTIES TIMEOUT 60000)
endforeach (test_cpp_file)
diff --git a/test/test_alphabets.cpp b/test/test_alphabets.cpp
index bf5b346..8773c5d 100644
--- a/test/test_alphabets.cpp
+++ b/test/test_alphabets.cpp
@@ -42,6 +42,7 @@ knowledge of the CeCILL license and that you accept its terms.
#include <Bpp/Seq/Alphabet/ProteicAlphabet.h>
#include <Bpp/Seq/Alphabet/DefaultAlphabet.h>
#include <Bpp/Seq/Alphabet/CodonAlphabet.h>
+#include <Bpp/Seq/Alphabet/AlphabetTools.h>
#include <iostream>
using namespace bpp;
@@ -55,6 +56,14 @@ int main() {
Alphabet* def = new DefaultAlphabet;
Alphabet* cdn = new CodonAlphabet(rna);
+ //Testing functions:
+ if (!AlphabetTools::isDNAAlphabet(dna)) return 1;
+ if (!AlphabetTools::isRNAAlphabet(rna)) return 1;
+ if (!AlphabetTools::isNucleicAlphabet(dna)) return 1;
+ if (!AlphabetTools::isNucleicAlphabet(rna)) return 1;
+ if (!AlphabetTools::isProteicAlphabet(pro)) return 1;
+ if (!AlphabetTools::isCodonAlphabet(cdn)) return 1;
+
delete dna;
delete rna;
delete pro;
--
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