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add package to the repository

msa


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@102253 bc3139a8-67e5-0310-9ffc-ced21a209358

Sonali Arora authored on 10/04/2015 00:12:33
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+# Doxyfile 1.5.8
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+
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+# This file describes the settings to be used by the documentation system
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+# doxygen (www.doxygen.org) for a project
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+#
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+# All text after a hash (#) is considered a comment and will be ignored
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+# The format is:
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+#       TAG = value [value, ...]
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+# For lists items can also be appended using:
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+#       TAG += value [value, ...]
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+# Values that contain spaces should be placed between quotes (" ")
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+
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+#---------------------------------------------------------------------------
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+# Project related configuration options
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+#---------------------------------------------------------------------------
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+
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+# This tag specifies the encoding used for all characters in the config file 
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+# that follow. The default is UTF-8 which is also the encoding used for all 
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+# text before the first occurrence of this tag. Doxygen uses libiconv (or the 
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+# iconv built into libc) for the transcoding. See 
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+# http://www.gnu.org/software/libiconv for the list of possible encodings.
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+
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+DOXYFILE_ENCODING      = UTF-8
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+
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+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
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+# by quotes) that should identify the project.
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+
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+PROJECT_NAME           = "Clustal Omega"
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+
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+# The PROJECT_NUMBER tag can be used to enter a project or revision number. 
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+# This could be handy for archiving the generated documentation or 
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+# if some version control system is used.
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+
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+PROJECT_NUMBER         = 1.2.0
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+
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+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
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+# base path where the generated documentation will be put. 
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+# If a relative path is entered, it will be relative to the location 
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+# where doxygen was started. If left blank the current directory will be used.
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+
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+OUTPUT_DIRECTORY       = ./doc/doxygen/
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+
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+# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 
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+# 4096 sub-directories (in 2 levels) under the output directory of each output 
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+# format and will distribute the generated files over these directories. 
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+# Enabling this option can be useful when feeding doxygen a huge amount of 
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+# source files, where putting all generated files in the same directory would 
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+# otherwise cause performance problems for the file system.
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+
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+CREATE_SUBDIRS         = NO
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+
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+# The OUTPUT_LANGUAGE tag is used to specify the language in which all 
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+# documentation generated by doxygen is written. Doxygen will use this 
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+# information to generate all constant output in the proper language. 
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+# The default language is English, other supported languages are: 
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+# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, 
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+# Croatian, Czech, Danish, Dutch, Farsi, Finnish, French, German, Greek, 
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+# Hungarian, Italian, Japanese, Japanese-en (Japanese with English messages), 
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+# Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, Polish, 
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+# Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak, Slovene, 
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+# Spanish, Swedish, and Ukrainian.
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+
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+OUTPUT_LANGUAGE        = English
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+
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+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will 
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+# include brief member descriptions after the members that are listed in 
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+# the file and class documentation (similar to JavaDoc). 
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+# Set to NO to disable this.
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+
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+BRIEF_MEMBER_DESC      = YES
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+
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+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend 
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+# the brief description of a member or function before the detailed description. 
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+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the 
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+# brief descriptions will be completely suppressed.
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+
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+REPEAT_BRIEF           = YES
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+
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+# This tag implements a quasi-intelligent brief description abbreviator 
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+# that is used to form the text in various listings. Each string 
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+# in this list, if found as the leading text of the brief description, will be 
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+# stripped from the text and the result after processing the whole list, is 
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+# used as the annotated text. Otherwise, the brief description is used as-is. 
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+# If left blank, the following values are used ("$name" is automatically 
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+# replaced with the name of the entity): "The $name class" "The $name widget" 
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+# "The $name file" "is" "provides" "specifies" "contains" 
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+# "represents" "a" "an" "the"
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+
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+ABBREVIATE_BRIEF       = 
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+
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+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then 
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+# Doxygen will generate a detailed section even if there is only a brief 
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+# description.
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+
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+ALWAYS_DETAILED_SEC    = NO
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+
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+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all 
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+# inherited members of a class in the documentation of that class as if those 
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+# members were ordinary class members. Constructors, destructors and assignment 
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+# operators of the base classes will not be shown.
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+
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+INLINE_INHERITED_MEMB  = NO
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+
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+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full 
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+# path before files name in the file list and in the header files. If set 
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+# to NO the shortest path that makes the file name unique will be used.
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+
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+FULL_PATH_NAMES        = YES
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+
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+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag 
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+# can be used to strip a user-defined part of the path. Stripping is 
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+# only done if one of the specified strings matches the left-hand part of 
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+# the path. The tag can be used to show relative paths in the file list. 
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+# If left blank the directory from which doxygen is run is used as the 
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+# path to strip.
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+
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+STRIP_FROM_PATH        = 
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+
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+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of 
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+# the path mentioned in the documentation of a class, which tells 
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+# the reader which header file to include in order to use a class. 
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+# If left blank only the name of the header file containing the class 
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+# definition is used. Otherwise one should specify the include paths that 
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+# are normally passed to the compiler using the -I flag.
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+
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+STRIP_FROM_INC_PATH    = 
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+
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+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter 
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+# (but less readable) file names. This can be useful is your file systems 
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+# doesn't support long names like on DOS, Mac, or CD-ROM.
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+
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+SHORT_NAMES            = NO
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+
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+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen 
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+# will interpret the first line (until the first dot) of a JavaDoc-style 
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+# comment as the brief description. If set to NO, the JavaDoc 
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+# comments will behave just like regular Qt-style comments 
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+# (thus requiring an explicit @brief command for a brief description.)
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+
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+JAVADOC_AUTOBRIEF      = NO
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+
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+# If the QT_AUTOBRIEF tag is set to YES then Doxygen will 
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+# interpret the first line (until the first dot) of a Qt-style 
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+# comment as the brief description. If set to NO, the comments 
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+# will behave just like regular Qt-style comments (thus requiring 
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+# an explicit \brief command for a brief description.)
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+
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+QT_AUTOBRIEF           = NO
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+
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+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen 
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+# treat a multi-line C++ special comment block (i.e. a block of //! or /// 
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+# comments) as a brief description. This used to be the default behaviour. 
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+# The new default is to treat a multi-line C++ comment block as a detailed 
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+# description. Set this tag to YES if you prefer the old behaviour instead.
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+
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+MULTILINE_CPP_IS_BRIEF = NO
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+
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+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented 
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+# member inherits the documentation from any documented member that it 
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+# re-implements.
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+
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+INHERIT_DOCS           = YES
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+
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+# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce 
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+# a new page for each member. If set to NO, the documentation of a member will 
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+# be part of the file/class/namespace that contains it.
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+
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+SEPARATE_MEMBER_PAGES  = NO
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+
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+# The TAB_SIZE tag can be used to set the number of spaces in a tab. 
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+# Doxygen uses this value to replace tabs by spaces in code fragments.
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+
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+TAB_SIZE               = 4
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+
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+# This tag can be used to specify a number of aliases that acts 
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+# as commands in the documentation. An alias has the form "name=value". 
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+# For example adding "sideeffect=\par Side Effects:\n" will allow you to 
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+# put the command \sideeffect (or @sideeffect) in the documentation, which 
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+# will result in a user-defined paragraph with heading "Side Effects:". 
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+# You can put \n's in the value part of an alias to insert newlines.
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+
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+ALIASES                = 
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+
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+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C 
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+# sources only. Doxygen will then generate output that is more tailored for C. 
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+# For instance, some of the names that are used will be different. The list 
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+# of all members will be omitted, etc.
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+
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+OPTIMIZE_OUTPUT_FOR_C  = YES
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+
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+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java 
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+# sources only. Doxygen will then generate output that is more tailored for 
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+# Java. For instance, namespaces will be presented as packages, qualified 
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+# scopes will look different, etc.
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+
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+OPTIMIZE_OUTPUT_JAVA   = NO
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+
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+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran 
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+# sources only. Doxygen will then generate output that is more tailored for 
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+# Fortran.
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+
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+OPTIMIZE_FOR_FORTRAN   = NO
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+
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+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL 
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+# sources. Doxygen will then generate output that is tailored for 
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+# VHDL.
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+
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+OPTIMIZE_OUTPUT_VHDL   = NO
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+
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+# Doxygen selects the parser to use depending on the extension of the files it parses. 
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+# With this tag you can assign which parser to use for a given extension. 
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+# Doxygen has a built-in mapping, but you can override or extend it using this tag. 
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+# The format is ext=language, where ext is a file extension, and language is one of 
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+# the parsers supported by doxygen: IDL, Java, Javascript, C#, C, C++, D, PHP, 
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+# Objective-C, Python, Fortran, VHDL, C, C++. For instance to make doxygen treat 
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+# .inc files as Fortran files (default is PHP), and .f files as C (default is Fortran), 
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+# use: inc=Fortran f=C
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+
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+EXTENSION_MAPPING      = 
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+
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+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want 
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+# to include (a tag file for) the STL sources as input, then you should 
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+# set this tag to YES in order to let doxygen match functions declarations and 
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+# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. 
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+# func(std::string) {}). This also make the inheritance and collaboration 
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+# diagrams that involve STL classes more complete and accurate.
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+
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+BUILTIN_STL_SUPPORT    = NO
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+
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+# If you use Microsoft's C++/CLI language, you should set this option to YES to 
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+# enable parsing support.
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+
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+CPP_CLI_SUPPORT        = NO
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+
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+# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. 
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+# Doxygen will parse them like normal C++ but will assume all classes use public 
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+# instead of private inheritance when no explicit protection keyword is present.
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+
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+SIP_SUPPORT            = NO
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+
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+# For Microsoft's IDL there are propget and propput attributes to indicate getter 
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+# and setter methods for a property. Setting this option to YES (the default) 
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+# will make doxygen to replace the get and set methods by a property in the 
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+# documentation. This will only work if the methods are indeed getting or 
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+# setting a simple type. If this is not the case, or you want to show the 
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+# methods anyway, you should set this option to NO.
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+
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+IDL_PROPERTY_SUPPORT   = YES
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+
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+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC 
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+# tag is set to YES, then doxygen will reuse the documentation of the first 
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+# member in the group (if any) for the other members of the group. By default 
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+# all members of a group must be documented explicitly.
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+
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+DISTRIBUTE_GROUP_DOC   = NO
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+
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+# Set the SUBGROUPING tag to YES (the default) to allow class member groups of 
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+# the same type (for instance a group of public functions) to be put as a 
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+# subgroup of that type (e.g. under the Public Functions section). Set it to 
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+# NO to prevent subgrouping. Alternatively, this can be done per class using 
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+# the \nosubgrouping command.
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+
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+SUBGROUPING            = YES
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+
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+# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum 
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+# is documented as struct, union, or enum with the name of the typedef. So 
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+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct 
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+# with name TypeT. When disabled the typedef will appear as a member of a file, 
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+# namespace, or class. And the struct will be named TypeS. This can typically 
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+# be useful for C code in case the coding convention dictates that all compound 
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+# types are typedef'ed and only the typedef is referenced, never the tag name.
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+
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+TYPEDEF_HIDES_STRUCT   = NO
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+
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+# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to 
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+# determine which symbols to keep in memory and which to flush to disk. 
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+# When the cache is full, less often used symbols will be written to disk. 
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+# For small to medium size projects (<1000 input files) the default value is 
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+# probably good enough. For larger projects a too small cache size can cause 
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+# doxygen to be busy swapping symbols to and from disk most of the time 
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+# causing a significant performance penality. 
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+# If the system has enough physical memory increasing the cache will improve the 
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+# performance by keeping more symbols in memory. Note that the value works on 
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+# a logarithmic scale so increasing the size by one will rougly double the 
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+# memory usage. The cache size is given by this formula: 
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+# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, 
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+# corresponding to a cache size of 2^16 = 65536 symbols
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+
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+SYMBOL_CACHE_SIZE      = 0
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+
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+#---------------------------------------------------------------------------
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+# Build related configuration options
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+#---------------------------------------------------------------------------
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+
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+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in 
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+# documentation are documented, even if no documentation was available. 
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+# Private class members and static file members will be hidden unless 
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+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
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+
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+EXTRACT_ALL            = YES
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+
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+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
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+# will be included in the documentation.
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+
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+EXTRACT_PRIVATE        = NO
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+
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+# If the EXTRACT_STATIC tag is set to YES all static members of a file 
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+# will be included in the documentation.
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+
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+EXTRACT_STATIC         = NO
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+
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+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) 
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+# defined locally in source files will be included in the documentation. 
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+# If set to NO only classes defined in header files are included.
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+
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+EXTRACT_LOCAL_CLASSES  = YES
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+
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+# This flag is only useful for Objective-C code. When set to YES local 
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+# methods, which are defined in the implementation section but not in 
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+# the interface are included in the documentation. 
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+# If set to NO (the default) only methods in the interface are included.
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+
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+EXTRACT_LOCAL_METHODS  = NO
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+
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+# If this flag is set to YES, the members of anonymous namespaces will be 
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+# extracted and appear in the documentation as a namespace called 
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+# 'anonymous_namespace{file}', where file will be replaced with the base 
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+# name of the file that contains the anonymous namespace. By default 
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+# anonymous namespace are hidden.
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+
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+EXTRACT_ANON_NSPACES   = NO
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+
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+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all 
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+# undocumented members of documented classes, files or namespaces. 
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+# If set to NO (the default) these members will be included in the 
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+# various overviews, but no documentation section is generated. 
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+# This option has no effect if EXTRACT_ALL is enabled.
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+
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+HIDE_UNDOC_MEMBERS     = NO
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+
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+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all 
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+# undocumented classes that are normally visible in the class hierarchy. 
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+# If set to NO (the default) these classes will be included in the various 
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+# overviews. This option has no effect if EXTRACT_ALL is enabled.
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+
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+HIDE_UNDOC_CLASSES     = NO
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+
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+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all 
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+# friend (class|struct|union) declarations. 
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+# If set to NO (the default) these declarations will be included in the 
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+# documentation.
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+
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+HIDE_FRIEND_COMPOUNDS  = NO
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+
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+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any 
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+# documentation blocks found inside the body of a function. 
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+# If set to NO (the default) these blocks will be appended to the 
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+# function's detailed documentation block.
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+
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+HIDE_IN_BODY_DOCS      = NO
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+
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+# The INTERNAL_DOCS tag determines if documentation 
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+# that is typed after a \internal command is included. If the tag is set 
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+# to NO (the default) then the documentation will be excluded. 
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+# Set it to YES to include the internal documentation.
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+
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+INTERNAL_DOCS          = NO
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+
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+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate 
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+# file names in lower-case letters. If set to YES upper-case letters are also 
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+# allowed. This is useful if you have classes or files whose names only differ 
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+# in case and if your file system supports case sensitive file names. Windows 
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+# and Mac users are advised to set this option to NO.
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+
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+CASE_SENSE_NAMES       = YES
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+
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+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen 
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+# will show members with their full class and namespace scopes in the 
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+# documentation. If set to YES the scope will be hidden.
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+
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+HIDE_SCOPE_NAMES       = NO
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+
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+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen 
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+# will put a list of the files that are included by a file in the documentation 
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+# of that file.
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+
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+SHOW_INCLUDE_FILES     = YES
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+
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+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] 
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+# is inserted in the documentation for inline members.
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+
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+INLINE_INFO            = YES
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+
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+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen 
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+# will sort the (detailed) documentation of file and class members 
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+# alphabetically by member name. If set to NO the members will appear in 
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+# declaration order.
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+
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+SORT_MEMBER_DOCS       = YES
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+
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+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the 
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+# brief documentation of file, namespace and class members alphabetically 
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+# by member name. If set to NO (the default) the members will appear in 
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+# declaration order.
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+
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+SORT_BRIEF_DOCS        = NO
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+
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+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the 
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+# hierarchy of group names into alphabetical order. If set to NO (the default) 
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+# the group names will appear in their defined order.
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+
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+SORT_GROUP_NAMES       = NO
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+
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+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be 
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+# sorted by fully-qualified names, including namespaces. If set to 
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+# NO (the default), the class list will be sorted only by class name, 
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+# not including the namespace part. 
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+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. 
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+# Note: This option applies only to the class list, not to the 
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+# alphabetical list.
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+
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+SORT_BY_SCOPE_NAME     = NO
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+
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+# The GENERATE_TODOLIST tag can be used to enable (YES) or 
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+# disable (NO) the todo list. This list is created by putting \todo 
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+# commands in the documentation.
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+
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+GENERATE_TODOLIST      = YES
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+
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+# The GENERATE_TESTLIST tag can be used to enable (YES) or 
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+# disable (NO) the test list. This list is created by putting \test 
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+# commands in the documentation.
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+
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+GENERATE_TESTLIST      = YES
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+
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+# The GENERATE_BUGLIST tag can be used to enable (YES) or 
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+# disable (NO) the bug list. This list is created by putting \bug 
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+# commands in the documentation.
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+
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+GENERATE_BUGLIST       = YES
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+
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+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or 
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+# disable (NO) the deprecated list. This list is created by putting 
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+# \deprecated commands in the documentation.
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+
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+GENERATE_DEPRECATEDLIST= YES
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+
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+# The ENABLED_SECTIONS tag can be used to enable conditional 
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+# documentation sections, marked by \if sectionname ... \endif.
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+
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+ENABLED_SECTIONS       = 
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+
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+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines 
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+# the initial value of a variable or define consists of for it to appear in 
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+# the documentation. If the initializer consists of more lines than specified 
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+# here it will be hidden. Use a value of 0 to hide initializers completely. 
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+# The appearance of the initializer of individual variables and defines in the 
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+# documentation can be controlled using \showinitializer or \hideinitializer 
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+# command in the documentation regardless of this setting.
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+
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+MAX_INITIALIZER_LINES  = 30
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+
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+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated 
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+# at the bottom of the documentation of classes and structs. If set to YES the 
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+# list will mention the files that were used to generate the documentation.
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+
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+SHOW_USED_FILES        = YES
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+
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+# If the sources in your project are distributed over multiple directories 
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+# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy 
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+# in the documentation. The default is NO.
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+
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+SHOW_DIRECTORIES       = NO
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+
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+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. 
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+# This will remove the Files entry from the Quick Index and from the 
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+# Folder Tree View (if specified). The default is YES.
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+
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+SHOW_FILES             = YES
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+
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+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the 
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+# Namespaces page. 
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+# This will remove the Namespaces entry from the Quick Index 
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+# and from the Folder Tree View (if specified). The default is YES.
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+
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+SHOW_NAMESPACES        = YES
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+
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+# The FILE_VERSION_FILTER tag can be used to specify a program or script that 
489
+# doxygen should invoke to get the current version for each file (typically from 
490
+# the version control system). Doxygen will invoke the program by executing (via 
491
+# popen()) the command <command> <input-file>, where <command> is the value of 
492
+# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file 
493
+# provided by doxygen. Whatever the program writes to standard output 
494
+# is used as the file version. See the manual for examples.
495
+
496
+FILE_VERSION_FILTER    = 
497
+
498
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed by 
499
+# doxygen. The layout file controls the global structure of the generated output files 
500
+# in an output format independent way. The create the layout file that represents 
501
+# doxygen's defaults, run doxygen with the -l option. You can optionally specify a 
502
+# file name after the option, if omitted DoxygenLayout.xml will be used as the name 
503
+# of the layout file.
504
+
505
+LAYOUT_FILE            = 
506
+
507
+#---------------------------------------------------------------------------
508
+# configuration options related to warning and progress messages
509
+#---------------------------------------------------------------------------
510
+
511
+# The QUIET tag can be used to turn on/off the messages that are generated 
512
+# by doxygen. Possible values are YES and NO. If left blank NO is used.
513
+
514
+QUIET                  = YES
515
+
516
+# The WARNINGS tag can be used to turn on/off the warning messages that are 
517
+# generated by doxygen. Possible values are YES and NO. If left blank 
518
+# NO is used.
519
+
520
+WARNINGS               = YES
521
+
522
+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings 
523
+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will 
524
+# automatically be disabled.
525
+
526
+WARN_IF_UNDOCUMENTED   = YES
527
+
528
+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for 
529
+# potential errors in the documentation, such as not documenting some 
530
+# parameters in a documented function, or documenting parameters that 
531
+# don't exist or using markup commands wrongly.
532
+
533
+WARN_IF_DOC_ERROR      = YES
534
+
535
+# This WARN_NO_PARAMDOC option can be abled to get warnings for 
536
+# functions that are documented, but have no documentation for their parameters 
537
+# or return value. If set to NO (the default) doxygen will only warn about 
538
+# wrong or incomplete parameter documentation, but not about the absence of 
539
+# documentation.
540
+
541
+WARN_NO_PARAMDOC       = YES
542
+
543
+# The WARN_FORMAT tag determines the format of the warning messages that 
544
+# doxygen can produce. The string should contain the $file, $line, and $text 
545
+# tags, which will be replaced by the file and line number from which the 
546
+# warning originated and the warning text. Optionally the format may contain 
547
+# $version, which will be replaced by the version of the file (if it could 
548
+# be obtained via FILE_VERSION_FILTER)
549
+
550
+WARN_FORMAT            = "$file:$line: $text"
551
+
552
+# The WARN_LOGFILE tag can be used to specify a file to which warning 
553
+# and error messages should be written. If left blank the output is written 
554
+# to stderr.
555
+
556
+WARN_LOGFILE           = 
557
+
558
+#---------------------------------------------------------------------------
559
+# configuration options related to the input files
560
+#---------------------------------------------------------------------------
561
+
562
+# The INPUT tag can be used to specify the files and/or directories that contain 
563
+# documented source files. You may enter file names like "myfile.cpp" or 
564
+# directories like "/usr/src/myproject". Separate the files or directories 
565
+# with spaces.
566
+
567
+INPUT                  = ./src/clustal ./src/clustal-omega.h ./src/clustal-omega.c
568
+
569
+# This tag can be used to specify the character encoding of the source files 
570
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is 
571
+# also the default input encoding. Doxygen uses libiconv (or the iconv built 
572
+# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for 
573
+# the list of possible encodings.
574
+
575
+INPUT_ENCODING         = UTF-8
576
+
577
+# If the value of the INPUT tag contains directories, you can use the 
578
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
579
+# and *.h) to filter out the source-files in the directories. If left 
580
+# blank the following patterns are tested: 
581
+# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx 
582
+# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
583
+
584
+FILE_PATTERNS          = *.h *.c
585
+
586
+# The RECURSIVE tag can be used to turn specify whether or not subdirectories 
587
+# should be searched for input files as well. Possible values are YES and NO. 
588
+# If left blank NO is used.
589
+
590
+RECURSIVE              = NO
591
+
592
+# The EXCLUDE tag can be used to specify files and/or directories that should 
593
+# excluded from the INPUT source files. This way you can easily exclude a 
594
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
595
+
596
+EXCLUDE                = ./src/config.h
597
+
598
+# The EXCLUDE_SYMLINKS tag can be used select whether or not files or 
599
+# directories that are symbolic links (a Unix filesystem feature) are excluded 
600
+# from the input.
601
+
602
+EXCLUDE_SYMLINKS       = NO
603
+
604
+# If the value of the INPUT tag contains directories, you can use the 
605
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude 
606
+# certain files from those directories. Note that the wildcards are matched 
607
+# against the file with absolute path, so to exclude all test directories 
608
+# for example use the pattern */test/*
609
+
610
+EXCLUDE_PATTERNS       = 
611
+
612
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names 
613
+# (namespaces, classes, functions, etc.) that should be excluded from the 
614
+# output. The symbol name can be a fully qualified name, a word, or if the 
615
+# wildcard * is used, a substring. Examples: ANamespace, AClass, 
616
+# AClass::ANamespace, ANamespace::*Test
617
+
618
+EXCLUDE_SYMBOLS        = 
619
+
620
+# The EXAMPLE_PATH tag can be used to specify one or more files or 
621
+# directories that contain example code fragments that are included (see 
622
+# the \include command).
623
+
624
+EXAMPLE_PATH           = ./src/
625
+
626
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the 
627
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
628
+# and *.h) to filter out the source-files in the directories. If left 
629
+# blank all files are included.
630
+
631
+EXAMPLE_PATTERNS       = 
632
+
633
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be 
634
+# searched for input files to be used with the \include or \dontinclude 
635
+# commands irrespective of the value of the RECURSIVE tag. 
636
+# Possible values are YES and NO. If left blank NO is used.
637
+
638
+EXAMPLE_RECURSIVE      = NO
639
+
640
+# The IMAGE_PATH tag can be used to specify one or more files or 
641
+# directories that contain image that are included in the documentation (see 
642
+# the \image command).
643
+
644
+IMAGE_PATH             = 
645
+
646
+# The INPUT_FILTER tag can be used to specify a program that doxygen should 
647
+# invoke to filter for each input file. Doxygen will invoke the filter program 
648
+# by executing (via popen()) the command <filter> <input-file>, where <filter> 
649
+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an 
650
+# input file. Doxygen will then use the output that the filter program writes 
651
+# to standard output. 
652
+# If FILTER_PATTERNS is specified, this tag will be 
653
+# ignored.
654
+
655
+INPUT_FILTER           = 
656
+
657
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern 
658
+# basis. 
659
+# Doxygen will compare the file name with each pattern and apply the 
660
+# filter if there is a match. 
661
+# The filters are a list of the form: 
662
+# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further 
663
+# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER 
664
+# is applied to all files.
665
+
666
+FILTER_PATTERNS        = 
667
+
668
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using 
669
+# INPUT_FILTER) will be used to filter the input files when producing source 
670
+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
671
+
672
+FILTER_SOURCE_FILES    = NO
673
+
674
+#---------------------------------------------------------------------------
675
+# configuration options related to source browsing
676
+#---------------------------------------------------------------------------
677
+
678
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will 
679
+# be generated. Documented entities will be cross-referenced with these sources. 
680
+# Note: To get rid of all source code in the generated output, make sure also 
681
+# VERBATIM_HEADERS is set to NO.
682
+
683
+SOURCE_BROWSER         = NO
684
+
685
+# Setting the INLINE_SOURCES tag to YES will include the body 
686
+# of functions and classes directly in the documentation.
687
+
688
+INLINE_SOURCES         = NO
689
+
690
+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct 
691
+# doxygen to hide any special comment blocks from generated source code 
692
+# fragments. Normal C and C++ comments will always remain visible.
693
+
694
+STRIP_CODE_COMMENTS    = YES
695
+
696
+# If the REFERENCED_BY_RELATION tag is set to YES 
697
+# then for each documented function all documented 
698
+# functions referencing it will be listed.
699
+
700
+REFERENCED_BY_RELATION = NO
701
+
702
+# If the REFERENCES_RELATION tag is set to YES 
703
+# then for each documented function all documented entities 
704
+# called/used by that function will be listed.
705
+
706
+REFERENCES_RELATION    = NO
707
+
708
+# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) 
709
+# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from 
710
+# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will 
711
+# link to the source code. 
712
+# Otherwise they will link to the documentation.
713
+
714
+REFERENCES_LINK_SOURCE = YES
715
+
716
+# If the USE_HTAGS tag is set to YES then the references to source code 
717
+# will point to the HTML generated by the htags(1) tool instead of doxygen 
718
+# built-in source browser. The htags tool is part of GNU's global source 
719
+# tagging system (see http://www.gnu.org/software/global/global.html). You 
720
+# will need version 4.8.6 or higher.
721
+
722
+USE_HTAGS              = NO
723
+
724
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen 
725
+# will generate a verbatim copy of the header file for each class for 
726
+# which an include is specified. Set to NO to disable this.
727
+
728
+VERBATIM_HEADERS       = YES
729
+
730
+#---------------------------------------------------------------------------
731
+# configuration options related to the alphabetical class index
732
+#---------------------------------------------------------------------------
733
+
734
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index 
735
+# of all compounds will be generated. Enable this if the project 
736
+# contains a lot of classes, structs, unions or interfaces.
737
+
738
+ALPHABETICAL_INDEX     = NO
739
+
740
+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then 
741
+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns 
742
+# in which this list will be split (can be a number in the range [1..20])
743
+
744
+COLS_IN_ALPHA_INDEX    = 5
745
+
746
+# In case all classes in a project start with a common prefix, all 
747
+# classes will be put under the same header in the alphabetical index. 
748
+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that 
749
+# should be ignored while generating the index headers.
750
+
751
+IGNORE_PREFIX          = 
752
+
753
+#---------------------------------------------------------------------------
754
+# configuration options related to the HTML output
755
+#---------------------------------------------------------------------------
756
+
757
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will 
758
+# generate HTML output.
759
+
760
+GENERATE_HTML          = YES
761
+
762
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. 
763
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
764
+# put in front of it. If left blank `html' will be used as the default path.
765
+
766
+HTML_OUTPUT            = html
767
+
768
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for 
769
+# each generated HTML page (for example: .htm,.php,.asp). If it is left blank 
770
+# doxygen will generate files with .html extension.
771
+
772
+HTML_FILE_EXTENSION    = .html
773
+
774
+# The HTML_HEADER tag can be used to specify a personal HTML header for 
775
+# each generated HTML page. If it is left blank doxygen will generate a 
776
+# standard header.
777
+
778
+HTML_HEADER            = 
779
+
780
+# The HTML_FOOTER tag can be used to specify a personal HTML footer for 
781
+# each generated HTML page. If it is left blank doxygen will generate a 
782
+# standard footer.
783
+
784
+HTML_FOOTER            = 
785
+
786
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading 
787
+# style sheet that is used by each HTML page. It can be used to 
788
+# fine-tune the look of the HTML output. If the tag is left blank doxygen 
789
+# will generate a default style sheet. Note that doxygen will try to copy 
790
+# the style sheet file to the HTML output directory, so don't put your own 
791
+# stylesheet in the HTML output directory as well, or it will be erased!
792
+
793
+HTML_STYLESHEET        = 
794
+
795
+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, 
796
+# files or namespaces will be aligned in HTML using tables. If set to 
797
+# NO a bullet list will be used.
798
+
799
+HTML_ALIGN_MEMBERS     = YES
800
+
801
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML 
802
+# documentation will contain sections that can be hidden and shown after the 
803
+# page has loaded. For this to work a browser that supports 
804
+# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox 
805
+# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
806
+
807
+HTML_DYNAMIC_SECTIONS  = NO
808
+
809
+# If the GENERATE_DOCSET tag is set to YES, additional index files 
810
+# will be generated that can be used as input for Apple's Xcode 3 
811
+# integrated development environment, introduced with OSX 10.5 (Leopard). 
812
+# To create a documentation set, doxygen will generate a Makefile in the 
813
+# HTML output directory. Running make will produce the docset in that 
814
+# directory and running "make install" will install the docset in 
815
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find 
816
+# it at startup. 
817
+# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information.
818
+
819
+GENERATE_DOCSET        = NO
820
+
821
+# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the 
822
+# feed. A documentation feed provides an umbrella under which multiple 
823
+# documentation sets from a single provider (such as a company or product suite) 
824
+# can be grouped.
825
+
826
+DOCSET_FEEDNAME        = "Doxygen generated docs"
827
+
828
+# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that 
829
+# should uniquely identify the documentation set bundle. This should be a 
830
+# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen 
831
+# will append .docset to the name.
832
+
833
+DOCSET_BUNDLE_ID       = org.doxygen.Project
834
+
835
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files 
836
+# will be generated that can be used as input for tools like the 
837
+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) 
838
+# of the generated HTML documentation.
839
+
840
+GENERATE_HTMLHELP      = NO
841
+
842
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can 
843
+# be used to specify the file name of the resulting .chm file. You 
844
+# can add a path in front of the file if the result should not be 
845
+# written to the html output directory.
846
+
847
+CHM_FILE               = 
848
+
849
+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can 
850
+# be used to specify the location (absolute path including file name) of 
851
+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run 
852
+# the HTML help compiler on the generated index.hhp.
853
+
854
+HHC_LOCATION           = 
855
+
856
+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag 
857
+# controls if a separate .chi index file is generated (YES) or that 
858
+# it should be included in the master .chm file (NO).
859
+
860
+GENERATE_CHI           = NO
861
+
862
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING 
863
+# is used to encode HtmlHelp index (hhk), content (hhc) and project file 
864
+# content.
865
+
866
+CHM_INDEX_ENCODING     = 
867
+
868
+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag 
869
+# controls whether a binary table of contents is generated (YES) or a 
870
+# normal table of contents (NO) in the .chm file.
871
+
872
+BINARY_TOC             = NO
873
+
874
+# The TOC_EXPAND flag can be set to YES to add extra items for group members 
875
+# to the contents of the HTML help documentation and to the tree view.
876
+
877
+TOC_EXPAND             = NO
878
+
879
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER 
880
+# are set, an additional index file will be generated that can be used as input for 
881
+# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated 
882
+# HTML documentation.
883
+
884
+GENERATE_QHP           = NO
885
+
886
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can 
887
+# be used to specify the file name of the resulting .qch file. 
888
+# The path specified is relative to the HTML output folder.
889
+
890
+QCH_FILE               = 
891
+
892
+# The QHP_NAMESPACE tag specifies the namespace to use when generating 
893
+# Qt Help Project output. For more information please see 
894
+# http://doc.trolltech.com/qthelpproject.html#namespace
895
+
896
+QHP_NAMESPACE          = 
897
+
898
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating 
899
+# Qt Help Project output. For more information please see 
900
+# http://doc.trolltech.com/qthelpproject.html#virtual-folders
901
+
902
+QHP_VIRTUAL_FOLDER     = doc
903
+
904
+# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to add. 
905
+# For more information please see 
906
+# http://doc.trolltech.com/qthelpproject.html#custom-filters
907
+
908
+QHP_CUST_FILTER_NAME   = 
909
+
910
+# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the custom filter to add.For more information please see 
911
+# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">Qt Help Project / Custom Filters</a>.
912
+
913
+QHP_CUST_FILTER_ATTRS  = 
914
+
915
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this project's 
916
+# filter section matches. 
917
+# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">Qt Help Project / Filter Attributes</a>.
918
+
919
+QHP_SECT_FILTER_ATTRS  = 
920
+
921
+# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can 
922
+# be used to specify the location of Qt's qhelpgenerator. 
923
+# If non-empty doxygen will try to run qhelpgenerator on the generated 
924
+# .qhp file.
925
+
926
+QHG_LOCATION           = 
927
+
928
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index at 
929
+# top of each HTML page. The value NO (the default) enables the index and 
930
+# the value YES disables it.
931
+
932
+DISABLE_INDEX          = NO
933
+
934
+# This tag can be used to set the number of enum values (range [1..20]) 
935
+# that doxygen will group on one line in the generated HTML documentation.
936
+
937
+ENUM_VALUES_PER_LINE   = 4
938
+
939
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index 
940
+# structure should be generated to display hierarchical information. 
941
+# If the tag value is set to FRAME, a side panel will be generated 
942
+# containing a tree-like index structure (just like the one that 
943
+# is generated for HTML Help). For this to work a browser that supports 
944
+# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, 
945
+# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are 
946
+# probably better off using the HTML help feature. Other possible values 
947
+# for this tag are: HIERARCHIES, which will generate the Groups, Directories, 
948
+# and Class Hierarchy pages using a tree view instead of an ordered list; 
949
+# ALL, which combines the behavior of FRAME and HIERARCHIES; and NONE, which 
950
+# disables this behavior completely. For backwards compatibility with previous 
951
+# releases of Doxygen, the values YES and NO are equivalent to FRAME and NONE 
952
+# respectively.
953
+
954
+GENERATE_TREEVIEW      = NONE
955
+
956
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be 
957
+# used to set the initial width (in pixels) of the frame in which the tree 
958
+# is shown.
959
+
960
+TREEVIEW_WIDTH         = 250
961
+
962
+# Use this tag to change the font size of Latex formulas included 
963
+# as images in the HTML documentation. The default is 10. Note that 
964
+# when you change the font size after a successful doxygen run you need 
965
+# to manually remove any form_*.png images from the HTML output directory 
966
+# to force them to be regenerated.
967
+
968
+FORMULA_FONTSIZE       = 10
969
+
970
+#---------------------------------------------------------------------------
971
+# configuration options related to the LaTeX output
972
+#---------------------------------------------------------------------------
973
+
974
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will 
975
+# generate Latex output.
976
+
977
+GENERATE_LATEX         = YES
978
+
979
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. 
980
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
981
+# put in front of it. If left blank `latex' will be used as the default path.
982
+
983
+LATEX_OUTPUT           = latex
984
+
985
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be 
986
+# invoked. If left blank `latex' will be used as the default command name.
987
+
988
+LATEX_CMD_NAME         = latex
989
+
990
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to 
991
+# generate index for LaTeX. If left blank `makeindex' will be used as the 
992
+# default command name.
993
+
994
+MAKEINDEX_CMD_NAME     = makeindex
995
+
996
+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact 
997
+# LaTeX documents. This may be useful for small projects and may help to 
998
+# save some trees in general.
999
+
1000
+COMPACT_LATEX          = NO
1001
+
1002
+# The PAPER_TYPE tag can be used to set the paper type that is used 
1003
+# by the printer. Possible values are: a4, a4wide, letter, legal and 
1004
+# executive. If left blank a4wide will be used.
1005
+
1006
+PAPER_TYPE             = a4wide
1007
+
1008
+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX 
1009
+# packages that should be included in the LaTeX output.
1010
+
1011
+EXTRA_PACKAGES         = 
1012
+
1013
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for 
1014
+# the generated latex document. The header should contain everything until 
1015
+# the first chapter. If it is left blank doxygen will generate a 
1016
+# standard header. Notice: only use this tag if you know what you are doing!
1017
+
1018
+LATEX_HEADER           = 
1019
+
1020
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated 
1021
+# is prepared for conversion to pdf (using ps2pdf). The pdf file will 
1022
+# contain links (just like the HTML output) instead of page references 
1023
+# This makes the output suitable for online browsing using a pdf viewer.
1024
+
1025
+PDF_HYPERLINKS         = YES
1026
+
1027
+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of 
1028
+# plain latex in the generated Makefile. Set this option to YES to get a 
1029
+# higher quality PDF documentation.
1030
+
1031
+USE_PDFLATEX           = YES
1032
+
1033
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. 
1034
+# command to the generated LaTeX files. This will instruct LaTeX to keep 
1035
+# running if errors occur, instead of asking the user for help. 
1036
+# This option is also used when generating formulas in HTML.
1037
+
1038
+LATEX_BATCHMODE        = NO
1039
+
1040
+# If LATEX_HIDE_INDICES is set to YES then doxygen will not 
1041
+# include the index chapters (such as File Index, Compound Index, etc.) 
1042
+# in the output.
1043
+
1044
+LATEX_HIDE_INDICES     = NO
1045
+
1046
+#---------------------------------------------------------------------------
1047
+# configuration options related to the RTF output
1048
+#---------------------------------------------------------------------------
1049
+
1050
+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output 
1051
+# The RTF output is optimized for Word 97 and may not look very pretty with 
1052
+# other RTF readers or editors.
1053
+
1054
+GENERATE_RTF           = NO
1055
+
1056
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. 
1057
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
1058
+# put in front of it. If left blank `rtf' will be used as the default path.
1059
+
1060
+RTF_OUTPUT             = rtf
1061
+
1062
+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact 
1063
+# RTF documents. This may be useful for small projects and may help to 
1064
+# save some trees in general.
1065
+
1066
+COMPACT_RTF            = NO
1067
+
1068
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated 
1069
+# will contain hyperlink fields. The RTF file will 
1070
+# contain links (just like the HTML output) instead of page references. 
1071
+# This makes the output suitable for online browsing using WORD or other 
1072
+# programs which support those fields. 
1073
+# Note: wordpad (write) and others do not support links.
1074
+
1075
+RTF_HYPERLINKS         = NO
1076
+
1077
+# Load stylesheet definitions from file. Syntax is similar to doxygen's 
1078
+# config file, i.e. a series of assignments. You only have to provide 
1079
+# replacements, missing definitions are set to their default value.
1080
+
1081
+RTF_STYLESHEET_FILE    = 
1082
+
1083
+# Set optional variables used in the generation of an rtf document. 
1084
+# Syntax is similar to doxygen's config file.
1085
+
1086
+RTF_EXTENSIONS_FILE    = 
1087
+
1088
+#---------------------------------------------------------------------------
1089
+# configuration options related to the man page output
1090
+#---------------------------------------------------------------------------
1091
+
1092
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will 
1093
+# generate man pages
1094
+
1095
+GENERATE_MAN           = NO
1096
+
1097
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. 
1098
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
1099
+# put in front of it. If left blank `man' will be used as the default path.
1100
+
1101
+MAN_OUTPUT             = man
1102
+
1103
+# The MAN_EXTENSION tag determines the extension that is added to 
1104
+# the generated man pages (default is the subroutine's section .3)
1105
+
1106
+MAN_EXTENSION          = .3
1107
+
1108
+# If the MAN_LINKS tag is set to YES and Doxygen generates man output, 
1109
+# then it will generate one additional man file for each entity 
1110
+# documented in the real man page(s). These additional files 
1111
+# only source the real man page, but without them the man command 
1112
+# would be unable to find the correct page. The default is NO.
1113
+
1114
+MAN_LINKS              = NO
1115
+
1116
+#---------------------------------------------------------------------------
1117
+# configuration options related to the XML output
1118
+#---------------------------------------------------------------------------
1119
+
1120
+# If the GENERATE_XML tag is set to YES Doxygen will 
1121
+# generate an XML file that captures the structure of 
1122
+# the code including all documentation.
1123
+
1124
+GENERATE_XML           = NO
1125
+
1126
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. 
1127
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
1128
+# put in front of it. If left blank `xml' will be used as the default path.
1129
+
1130
+XML_OUTPUT             = xml
1131
+
1132
+# The XML_SCHEMA tag can be used to specify an XML schema, 
1133
+# which can be used by a validating XML parser to check the 
1134
+# syntax of the XML files.
1135
+
1136
+XML_SCHEMA             = 
1137
+
1138
+# The XML_DTD tag can be used to specify an XML DTD, 
1139
+# which can be used by a validating XML parser to check the 
1140
+# syntax of the XML files.
1141
+
1142
+XML_DTD                = 
1143
+
1144
+# If the XML_PROGRAMLISTING tag is set to YES Doxygen will 
1145
+# dump the program listings (including syntax highlighting 
1146
+# and cross-referencing information) to the XML output. Note that 
1147
+# enabling this will significantly increase the size of the XML output.
1148
+
1149
+XML_PROGRAMLISTING     = YES
1150
+
1151
+#---------------------------------------------------------------------------
1152
+# configuration options for the AutoGen Definitions output
1153
+#---------------------------------------------------------------------------
1154
+
1155
+# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will 
1156
+# generate an AutoGen Definitions (see autogen.sf.net) file 
1157
+# that captures the structure of the code including all 
1158
+# documentation. Note that this feature is still experimental 
1159
+# and incomplete at the moment.
1160
+
1161
+GENERATE_AUTOGEN_DEF   = NO
1162
+
1163
+#---------------------------------------------------------------------------
1164
+# configuration options related to the Perl module output
1165
+#---------------------------------------------------------------------------
1166
+
1167
+# If the GENERATE_PERLMOD tag is set to YES Doxygen will 
1168
+# generate a Perl module file that captures the structure of 
1169
+# the code including all documentation. Note that this 
1170
+# feature is still experimental and incomplete at the 
1171
+# moment.
1172
+
1173
+GENERATE_PERLMOD       = NO
1174
+
1175
+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate 
1176
+# the necessary Makefile rules, Perl scripts and LaTeX code to be able 
1177
+# to generate PDF and DVI output from the Perl module output.
1178
+
1179
+PERLMOD_LATEX          = NO
1180
+
1181
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be 
1182
+# nicely formatted so it can be parsed by a human reader. 
1183
+# This is useful 
1184
+# if you want to understand what is going on. 
1185
+# On the other hand, if this 
1186
+# tag is set to NO the size of the Perl module output will be much smaller 
1187
+# and Perl will parse it just the same.
1188
+
1189
+PERLMOD_PRETTY         = YES
1190
+
1191
+# The names of the make variables in the generated doxyrules.make file 
1192
+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. 
1193
+# This is useful so different doxyrules.make files included by the same 
1194
+# Makefile don't overwrite each other's variables.
1195
+
1196
+PERLMOD_MAKEVAR_PREFIX = 
1197
+
1198
+#---------------------------------------------------------------------------
1199
+# Configuration options related to the preprocessor   
1200
+#---------------------------------------------------------------------------
1201
+
1202
+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will 
1203
+# evaluate all C-preprocessor directives found in the sources and include 
1204
+# files.
1205
+
1206
+ENABLE_PREPROCESSING   = YES
1207
+
1208
+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro 
1209
+# names in the source code. If set to NO (the default) only conditional 
1210
+# compilation will be performed. Macro expansion can be done in a controlled 
1211
+# way by setting EXPAND_ONLY_PREDEF to YES.
1212
+
1213
+MACRO_EXPANSION        = NO
1214
+
1215
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES 
1216
+# then the macro expansion is limited to the macros specified with the 
1217
+# PREDEFINED and EXPAND_AS_DEFINED tags.
1218
+
1219
+EXPAND_ONLY_PREDEF     = NO
1220
+
1221
+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files 
1222
+# in the INCLUDE_PATH (see below) will be search if a #include is found.
1223
+
1224
+SEARCH_INCLUDES        = YES
1225
+
1226
+# The INCLUDE_PATH tag can be used to specify one or more directories that 
1227
+# contain include files that are not input files but should be processed by 
1228
+# the preprocessor.
1229
+
1230
+INCLUDE_PATH           = 
1231
+
1232
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard 
1233
+# patterns (like *.h and *.hpp) to filter out the header-files in the 
1234
+# directories. If left blank, the patterns specified with FILE_PATTERNS will 
1235
+# be used.
1236
+
1237
+INCLUDE_FILE_PATTERNS  = 
1238
+
1239
+# The PREDEFINED tag can be used to specify one or more macro names that 
1240
+# are defined before the preprocessor is started (similar to the -D option of 
1241
+# gcc). The argument of the tag is a list of macros of the form: name 
1242
+# or name=definition (no spaces). If the definition and the = are 
1243
+# omitted =1 is assumed. To prevent a macro definition from being 
1244
+# undefined via #undef or recursively expanded use the := operator 
1245
+# instead of the = operator.
1246
+
1247
+PREDEFINED             = 
1248
+
1249
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then 
1250
+# this tag can be used to specify a list of macro names that should be expanded. 
1251
+# The macro definition that is found in the sources will be used. 
1252
+# Use the PREDEFINED tag if you want to use a different macro definition.
1253
+
1254
+EXPAND_AS_DEFINED      = 
1255
+
1256
+# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then 
1257
+# doxygen's preprocessor will remove all function-like macros that are alone 
1258
+# on a line, have an all uppercase name, and do not end with a semicolon. Such 
1259
+# function macros are typically used for boiler-plate code, and will confuse 
1260
+# the parser if not removed.
1261
+
1262
+SKIP_FUNCTION_MACROS   = YES
1263
+
1264
+#---------------------------------------------------------------------------
1265
+# Configuration::additions related to external references   
1266
+#---------------------------------------------------------------------------
1267
+
1268
+# The TAGFILES option can be used to specify one or more tagfiles. 
1269
+# Optionally an initial location of the external documentation 
1270
+# can be added for each tagfile. The format of a tag file without 
1271
+# this location is as follows: 
1272
+#  
1273
+# TAGFILES = file1 file2 ... 
1274
+# Adding location for the tag files is done as follows: 
1275
+#  
1276
+# TAGFILES = file1=loc1 "file2 = loc2" ... 
1277
+# where "loc1" and "loc2" can be relative or absolute paths or 
1278
+# URLs. If a location is present for each tag, the installdox tool 
1279
+# does not have to be run to correct the links. 
1280
+# Note that each tag file must have a unique name 
1281
+# (where the name does NOT include the path) 
1282
+# If a tag file is not located in the directory in which doxygen 
1283
+# is run, you must also specify the path to the tagfile here.
1284
+
1285
+TAGFILES               = 
1286
+
1287
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create 
1288
+# a tag file that is based on the input files it reads.
1289
+
1290
+GENERATE_TAGFILE       = 
1291
+
1292
+# If the ALLEXTERNALS tag is set to YES all external classes will be listed 
1293
+# in the class index. If set to NO only the inherited external classes 
1294
+# will be listed.
1295
+
1296
+ALLEXTERNALS           = NO
1297
+
1298
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed 
1299
+# in the modules index. If set to NO, only the current project's groups will 
1300
+# be listed.
1301
+
1302
+EXTERNAL_GROUPS        = YES
1303
+
1304
+# The PERL_PATH should be the absolute path and name of the perl script 
1305
+# interpreter (i.e. the result of `which perl').
1306
+
1307
+PERL_PATH              = /usr/bin/perl
1308
+
1309
+#---------------------------------------------------------------------------
1310
+# Configuration options related to the dot tool   
1311
+#---------------------------------------------------------------------------
1312
+
1313
+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will 
1314
+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base 
1315
+# or super classes. Setting the tag to NO turns the diagrams off. Note that 
1316
+# this option is superseded by the HAVE_DOT option below. This is only a 
1317
+# fallback. It is recommended to install and use dot, since it yields more 
1318
+# powerful graphs.
1319
+
1320
+CLASS_DIAGRAMS         = YES
1321
+
1322
+# You can define message sequence charts within doxygen comments using the \msc 
1323
+# command. Doxygen will then run the mscgen tool (see 
1324
+# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the 
1325
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where 
1326
+# the mscgen tool resides. If left empty the tool is assumed to be found in the 
1327
+# default search path.
1328
+
1329
+MSCGEN_PATH            = 
1330
+
1331
+# If set to YES, the inheritance and collaboration graphs will hide 
1332
+# inheritance and usage relations if the target is undocumented 
1333
+# or is not a class.
1334
+
1335
+HIDE_UNDOC_RELATIONS   = YES
1336
+
1337
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is 
1338
+# available from the path. This tool is part of Graphviz, a graph visualization 
1339
+# toolkit from AT&T and Lucent Bell Labs. The other options in this section 
1340
+# have no effect if this option is set to NO (the default)
1341
+
1342
+HAVE_DOT               = YES
1343
+
1344
+# By default doxygen will write a font called FreeSans.ttf to the output 
1345
+# directory and reference it in all dot files that doxygen generates. This 
1346
+# font does not include all possible unicode characters however, so when you need 
1347
+# these (or just want a differently looking font) you can specify the font name 
1348
+# using DOT_FONTNAME. You need need to make sure dot is able to find the font, 
1349
+# which can be done by putting it in a standard location or by setting the 
1350
+# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory 
1351
+# containing the font.
1352
+
1353
+DOT_FONTNAME           = FreeSans
1354
+
1355
+# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. 
1356
+# The default size is 10pt.
1357
+
1358
+DOT_FONTSIZE           = 10
1359
+
1360
+# By default doxygen will tell dot to use the output directory to look for the 
1361
+# FreeSans.ttf font (which doxygen will put there itself). If you specify a 
1362
+# different font using DOT_FONTNAME you can set the path where dot 
1363
+# can find it using this tag.
1364
+
1365
+DOT_FONTPATH           = 
1366
+
1367
+# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen 
1368
+# will generate a graph for each documented class showing the direct and 
1369
+# indirect inheritance relations. Setting this tag to YES will force the 
1370
+# the CLASS_DIAGRAMS tag to NO.
1371
+
1372
+CLASS_GRAPH            = YES
1373
+
1374
+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen 
1375
+# will generate a graph for each documented class showing the direct and 
1376
+# indirect implementation dependencies (inheritance, containment, and 
1377
+# class references variables) of the class with other documented classes.
1378
+
1379
+COLLABORATION_GRAPH    = YES
1380
+
1381
+# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen 
1382
+# will generate a graph for groups, showing the direct groups dependencies
1383
+
1384
+GROUP_GRAPHS           = YES