Doxyfile

# Doxyfile 1.7.5.1

# This file describes the settings to be used by the documentation system
# doxygen (www.doxygen.org) for a project
#
# All text after a hash (#) is considered a comment and will be ignored
# The format is:
#       TAG = value [value, ...]
# For lists items can also be appended using:
#       TAG += value [value, ...]
# Values that contain spaces should be placed between quotes (" ")

#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------

# This tag specifies the encoding used for all characters in the config file 
# that follow. The default is UTF-8 which is also the encoding used for all 
# text before the first occurrence of this tag. Doxygen uses libiconv (or the 
# iconv built into libc) for the transcoding. See 
# http://www.gnu.org/software/libiconv for the list of possible encodings.

DOXYFILE_ENCODING      = UTF-8

# The PROJECT_NAME tag is a single word (or sequence of words) that should 
# identify the project. Note that if you do not use Doxywizard you need 
# to put quotes around the project name if it contains spaces.

PROJECT_NAME           = "Galosh: Profile to Alignment Profile"

# The PROJECT_NUMBER tag can be used to enter a project or revision number. 
# This could be handy for archiving the generated documentation or 
# if some version control system is used.

PROJECT_NUMBER         = 0.1

# Using the PROJECT_BRIEF tag one can provide an optional one line description 
# for a project that appears at the top of each page and should give viewer 
# a quick idea about the purpose of the project. Keep the description short.

PROJECT_BRIEF          = "Generate Alignment profiles from Galosh profiles + fasta files"

# 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           = g.jpg


# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
# base path where the generated documentation will be put. 
# If a relative path is entered, it will be relative to the location 
# where doxygen was started. If left blank the current directory will be used.

OUTPUT_DIRECTORY       = .

# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 
# 4096 sub-directories (in 2 levels) under the output directory of each output 
# format and will distribute the generated files over these directories. 
# Enabling this option can be useful when feeding doxygen a huge amount of 
# source files, where putting all generated files in the same directory would 
# otherwise cause performance problems for the file system.

CREATE_SUBDIRS         = NO

# The OUTPUT_LANGUAGE tag is used to specify the language in which all 
# documentation generated by doxygen is written. Doxygen will use this 
# information to generate all constant output in the proper language. 
# The default language is English, other supported languages are: 
# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, 
# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German, 
# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English 
# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, 
# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak, 
# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.

OUTPUT_LANGUAGE        = English

# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will 
# include brief member descriptions after the members that are listed in 
# the file and class documentation (similar to JavaDoc). 
# Set to NO to disable this.

BRIEF_MEMBER_DESC      = YES

# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend 
# the brief description of a member or function before the detailed description. 
# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the 
# brief descriptions will be completely suppressed.

REPEAT_BRIEF           = YES

# This tag implements a quasi-intelligent brief description abbreviator 
# that is used to form the text in various listings. Each string 
# in this list, if found as the leading text of the brief description, will be 
# stripped from the text and the result after processing the whole list, is 
# used as the annotated text. Otherwise, the brief description is used as-is. 
# If left blank, the following values are used ("$name" is automatically 
# replaced with the name of the entity): "The $name class" "The $name widget" 
# "The $name file" "is" "provides" "specifies" "contains" 
# "represents" "a" "an" "the"

ABBREVIATE_BRIEF       = "The $name class" \
                         "The $name widget" \
                         "The $name file" \
                         is \
                         provides \
                         specifies \
                         contains \
                         represents \
                         a \
                         an \
                         the

# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then 
# Doxygen will generate a detailed section even if there is only a brief 
# description.

ALWAYS_DETAILED_SEC    = YES

# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all 
# inherited members of a class in the documentation of that class as if those 
# members were ordinary class members. Constructors, destructors and assignment 
# operators of the base classes will not be shown.

INLINE_INHERITED_MEMB  = YES

# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full 
# path before files name in the file list and in the header files. If set 
# to NO the shortest path that makes the file name unique will be used.

FULL_PATH_NAMES        = YES

# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag 
# can be used to strip a user-defined part of the path. Stripping is 
# only done if one of the specified strings matches the left-hand part of 
# the path. The tag can be used to show relative paths in the file list. 
# If left blank the directory from which doxygen is run is used as the 
# path to strip.

STRIP_FROM_PATH        = 

# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of 
# the path mentioned in the documentation of a class, which tells 
# the reader which header file to include in order to use a class. 
# If left blank only the name of the header file containing the class 
# definition is used. Otherwise one should specify the include paths that 
# are normally passed to the compiler using the -I flag.

STRIP_FROM_INC_PATH    = 

# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter 
# (but less readable) file names. This can be useful if your file system 
# doesn't support long names like on DOS, Mac, or CD-ROM.

SHORT_NAMES            = NO

# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen 
# will interpret the first line (until the first dot) of a JavaDoc-style 
# comment as the brief description. If set to NO, the JavaDoc 
# comments will behave just like regular Qt-style comments 
# (thus requiring an explicit @brief command for a brief description.)

JAVADOC_AUTOBRIEF      = NO

# If the QT_AUTOBRIEF tag is set to YES then Doxygen will 
# interpret the first line (until the first dot) of a Qt-style 
# comment as the brief description. If set to NO, the comments 
# will behave just like regular Qt-style comments (thus requiring 
# an explicit \brief command for a brief description.)

QT_AUTOBRIEF           = NO

# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen 
# treat a multi-line C++ special comment block (i.e. a block of //! or /// 
# comments) as a brief description. This used to be the default behaviour. 
# The new default is to treat a multi-line C++ comment block as a detailed 
# description. Set this tag to YES if you prefer the old behaviour instead.

MULTILINE_CPP_IS_BRIEF = NO

# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented 
# member inherits the documentation from any documented member that it 
# re-implements.

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.

SEPARATE_MEMBER_PAGES  = NO

# The TAB_SIZE tag can be used to set the number of spaces in a tab. 
# Doxygen uses this value to replace tabs by spaces in code fragments.

TAB_SIZE               = 8

# This tag can be used to specify a number of aliases that acts 
# as commands in the documentation. An alias has the form "name=value". 
# For example adding "sideeffect=\par Side Effects:\n" will allow you to 
# put the command \sideeffect (or @sideeffect) in the documentation, which 
# will result in a user-defined paragraph with heading "Side Effects:". 
# You can put \n's in the value part of an alias to insert newlines.

# Several of the comments in seqan and galosh contain \symbols that generate
# errors or warnings in doxygen.  I'm using this section castrate them
ALIASES                = \
 Tag="" \
 Class="" \
 Metafunction="" \
 Adaption="" \
 Concept="" \
 Function="" \
 Internal="" \
 Memfunc="" \
 Shortcut="" \
 Spec="" \
 geq="" \
 glos=""\
 s=""
# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C 
# sources only. Doxygen will then generate output that is more tailored for C. 
# For instance, some of the names that are used will be different. The list 
# of all members will be omitted, etc.

OPTIMIZE_OUTPUT_FOR_C  = NO

# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java 
# sources only. Doxygen will then generate output that is more tailored for 
# Java. For instance, namespaces will be presented as packages, qualified 
# scopes will look different, etc.

OPTIMIZE_OUTPUT_JAVA   = NO

# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran 
# sources only. Doxygen will then generate output that is more tailored for 
# Fortran.

OPTIMIZE_FOR_FORTRAN   = NO

# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL 
# sources. Doxygen will then generate output that is tailored for 
# VHDL.

OPTIMIZE_OUTPUT_VHDL   = NO

# Doxygen selects the parser to use depending on the extension of the files it 
# parses. With this tag you can assign which parser to use for a given extension. 
# Doxygen has a built-in mapping, but you can override or extend it using this 
# tag. The format is ext=language, where ext is a file extension, and language 
# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C, 
# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make 
# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C 
# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions 
# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.

EXTENSION_MAPPING      = 

# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want 
# to include (a tag file for) the STL sources as input, then you should 
# set this tag to YES in order to let doxygen match functions declarations and 
# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. 
# func(std::string) {}). This also makes the inheritance and collaboration 
# diagrams that involve STL classes more complete and accurate.

BUILTIN_STL_SUPPORT    = NO

# If you use Microsoft's C++/CLI language, you should set this option to YES to 
# enable parsing support.

CPP_CLI_SUPPORT        = NO

# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. 
# Doxygen will parse them like normal C++ but will assume all classes use public 
# instead of private inheritance when no explicit protection keyword is present.

SIP_SUPPORT            = NO

# For Microsoft's IDL there are propget and propput attributes to indicate getter 
# and setter methods for a property. Setting this option to YES (the default) 
# will make doxygen replace the get and set methods by a property in the 
# documentation. This will only work if the methods are indeed getting or 
# setting a simple type. If this is not the case, or you want to show the 
# methods anyway, you should set this option to NO.

IDL_PROPERTY_SUPPORT   = YES

# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC 
# tag is set to YES, then doxygen will reuse the documentation of the first 
# member in the group (if any) for the other members of the group. By default 
# all members of a group must be documented explicitly.

DISTRIBUTE_GROUP_DOC   = NO

# Set the SUBGROUPING tag to YES (the default) to allow class member groups of 
# the same type (for instance a group of public functions) to be put as a 
# subgroup of that type (e.g. under the Public Functions section). Set it to 
# NO to prevent subgrouping. Alternatively, this can be done per class using 
# the \nosubgrouping command.

SUBGROUPING            = YES

# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and 
# unions are shown inside the group in which they are included (e.g. using 
# @ingroup) instead of on a separate page (for HTML and Man pages) or 
# section (for LaTeX and RTF).

INLINE_GROUPED_CLASSES = NO

# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and 
# unions with only public data fields will be shown inline in the documentation 
# of the scope in which they are defined (i.e. file, namespace, or group 
# documentation), provided this scope is documented. If set to NO (the default), 
# structs, classes, and unions are shown on a separate page (for HTML and Man 
# pages) or section (for LaTeX and RTF).

INLINE_SIMPLE_STRUCTS  = NO

# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum 
# is documented as struct, union, or enum with the name of the typedef. So 
# typedef struct TypeS {} TypeT, will appear in the documentation as a struct 
# with name TypeT. When disabled the typedef will appear as a member of a file, 
# namespace, or class. And the struct will be named TypeS. This can typically 
# be useful for C code in case the coding convention dictates that all compound 
# types are typedef'ed and only the typedef is referenced, never the tag name.

TYPEDEF_HIDES_STRUCT   = NO

# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to 
# determine which symbols to keep in memory and which to flush to disk. 
# When the cache is full, less often used symbols will be written to disk. 
# For small to medium size projects (<1000 input files) the default value is 
# probably good enough. For larger projects a too small cache size can cause 
# doxygen to be busy swapping symbols to and from disk most of the time 
# causing a significant performance penalty. 
# If the system has enough physical memory increasing the cache will improve the 
# performance by keeping more symbols in memory. Note that the value works on 
# a logarithmic scale so increasing the size by one will roughly double the 
# memory usage. The cache size is given by this formula: 
# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, 
# corresponding to a cache size of 2^16 = 65536 symbols

SYMBOL_CACHE_SIZE      = 4

#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------

# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in 
# documentation are documented, even if no documentation was available. 
# Private class members and static file members will be hidden unless 
# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES

EXTRACT_ALL            = YES

# If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
# will be included in the documentation.

EXTRACT_PRIVATE        = YES                    

# If the EXTRACT_STATIC tag is set to YES all static members of a file 
# will be included in the documentation.

EXTRACT_STATIC         = YES

# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) 
# defined locally in source files will be included in the documentation. 
# If set to NO only classes defined in header files are included.

EXTRACT_LOCAL_CLASSES  = YES

# This flag is only useful for Objective-C code. When set to YES local 
# methods, which are defined in the implementation section but not in 
# the interface are included in the documentation. 
# If set to NO (the default) only methods in the interface are included.

EXTRACT_LOCAL_METHODS  = YES

# If this flag is set to YES, the members of anonymous namespaces will be 
# extracted and appear in the documentation as a namespace called 
# 'anonymous_namespace{file}', where file will be replaced with the base 
# name of the file that contains the anonymous namespace. By default 
# anonymous namespaces are hidden.

EXTRACT_ANON_NSPACES   = YES

# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all 
# undocumented members of documented classes, files or namespaces. 
# If set to NO (the default) these members will be included in the 
# various overviews, but no documentation section is generated. 
# This option has no effect if EXTRACT_ALL is enabled.

HIDE_UNDOC_MEMBERS     = NO

# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all 
# undocumented classes that are normally visible in the class hierarchy. 
# If set to NO (the default) these classes will be included in the various 
# overviews. This option has no effect if EXTRACT_ALL is enabled.

HIDE_UNDOC_CLASSES     = NO

# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all 
# friend (class|struct|union) declarations. 
# If set to NO (the default) these declarations will be included in the 
# documentation.

HIDE_FRIEND_COMPOUNDS  = NO

# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any 
# documentation blocks found inside the body of a function. 
# If set to NO (the default) these blocks will be appended to the 
# function's detailed documentation block.

HIDE_IN_BODY_DOCS      = NO

# The INTERNAL_DOCS tag determines if documentation 
# that is typed after a \internal command is included. If the tag is set 
# to NO (the default) then the documentation will be excluded. 
# Set it to YES to include the internal documentation.

INTERNAL_DOCS          = YES

# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate 
# file names in lower-case letters. If set to YES upper-case letters are also 
# allowed. This is useful if you have classes or files whose names only differ 
# in case and if your file system supports case sensitive file names. Windows 
# and Mac users are advised to set this option to NO.

CASE_SENSE_NAMES       = NO

# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen 
# will show members with their full class and namespace scopes in the 
# documentation. If set to YES the scope will be hidden.

HIDE_SCOPE_NAMES       = NO

# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen 
# will put a list of the files that are included by a file in the documentation 
# of that file.

SHOW_INCLUDE_FILES     = YES

# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen 
# will list include files with double quotes in the documentation 
# rather than with sharp brackets.

FORCE_LOCAL_INCLUDES   = YES

# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] 
# is inserted in the documentation for inline members.

INLINE_INFO            = YES

# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen 
# will sort the (detailed) documentation of file and class members 
# alphabetically by member name. If set to NO the members will appear in 
# declaration order.

SORT_MEMBER_DOCS       = YES

# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the 
# brief documentation of file, namespace and class members alphabetically 
# by member name. If set to NO (the default) the members will appear in 
# declaration order.

SORT_BRIEF_DOCS        = NO

# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen 
# will sort the (brief and detailed) documentation of class members so that 
# constructors and destructors are listed first. If set to NO (the default) 
# the constructors will appear in the respective orders defined by 
# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. 
# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO 
# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.

SORT_MEMBERS_CTORS_1ST = NO

# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the 
# hierarchy of group names into alphabetical order. If set to NO (the default) 
# the group names will appear in their defined order.

SORT_GROUP_NAMES       = NO

# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be 
# sorted by fully-qualified names, including namespaces. If set to 
# NO (the default), the class list will be sorted only by class name, 
# not including the namespace part. 
# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. 
# Note: This option applies only to the class list, not to the 
# alphabetical list.

SORT_BY_SCOPE_NAME     = NO

# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to 
# do proper type resolution of all parameters of a function it will reject a 
# match between the prototype and the implementation of a member function even 
# if there is only one candidate or it is obvious which candidate to choose 
# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen 
# will still accept a match between prototype and implementation in such cases.

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.

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.

GENERATE_TESTLIST      = YES

# 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.

GENERATE_BUGLIST       = YES

# 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.

GENERATE_DEPRECATEDLIST= YES

# The ENABLED_SECTIONS tag can be used to enable conditional 
# documentation sections, marked by \if sectionname ... \endif.

ENABLED_SECTIONS       = 

# The MAX_INITIALIZER_LINES tag determines the maximum number of lines 
# the initial value of a variable or macro consists of for it to appear in 
# the documentation. If the initializer consists of more lines than specified 
# here it will be hidden. Use a value of 0 to hide initializers completely. 
# The appearance of the initializer of individual variables and macros in the 
# documentation can be controlled using \showinitializer or \hideinitializer 
# command in the documentation regardless of this setting.

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.

SHOW_USED_FILES        = YES

# If the sources in your project are distributed over multiple directories 
# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy 
# in the documentation. The default is NO.

SHOW_DIRECTORIES       = YES

# Set the SHOW_FILES tag to NO to disable the generation of the Files page. 
# This will remove the Files entry from the Quick Index and from the 
# Folder Tree View (if specified). The default is YES.

SHOW_FILES             = YES

# Set the SHOW_NAMESPACES tag to NO to disable the generation of the 
# Namespaces page.  This will remove the Namespaces entry from the Quick Index 
# and from the Folder Tree View (if specified). The default is YES.

SHOW_NAMESPACES        = YES

# The FILE_VERSION_FILTER tag can be used to specify a program or script that 
# doxygen should invoke to get the current version for each file (typically from 
# the version control system). Doxygen will invoke the program by executing (via 
# popen()) the command <command> <input-file>, where <command> is the value of 
# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file 
# provided by doxygen. Whatever the program writes to standard output 
# is used as the file version. See the manual for examples.

FILE_VERSION_FILTER    = 

# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed 
# by doxygen. The layout file controls the global structure of the generated 
# output files in an output format independent way. The create the layout file 
# that represents doxygen's defaults, run doxygen with the -l option. 
# You can optionally specify a file name after the option, if omitted 
# DoxygenLayout.xml will be used as the name of the layout file.

LAYOUT_FILE            = 

# The CITE_BIB_FILES tag can be used to specify one or more bib files 
# containing the references data. This must be a list of .bib files. The 
# .bib extension is automatically appended if omitted. Using this command 
# requires the bibtex tool to be installed. See also 
# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style 
# of the bibliography can be controlled using LATEX_BIB_STYLE.

CITE_BIB_FILES         = 

#---------------------------------------------------------------------------
# configuration options related to warning and progress messages
#---------------------------------------------------------------------------

# The QUIET tag can be used to turn on/off the messages that are generated 
# by doxygen. Possible values are YES and NO. If left blank NO is used.

QUIET                  = NO

# The WARNINGS tag can be used to turn on/off the warning messages that are 
# generated by doxygen. Possible values are YES and NO. If left blank 
# NO is used.

WARNINGS               = YES

# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings 
# for undocumented members. If EXTRACT_ALL is set to YES then this flag will 
# automatically be disabled.

WARN_IF_UNDOCUMENTED   = YES

# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for 
# potential errors in the documentation, such as not documenting some 
# parameters in a documented function, or documenting parameters that 
# don't exist or using markup commands wrongly.

WARN_IF_DOC_ERROR      = YES

# The WARN_NO_PARAMDOC option can be enabled to get warnings for 
# functions that are documented, but have no documentation for their parameters 
# or return value. If set to NO (the default) doxygen will only warn about 
# wrong or incomplete parameter documentation, but not about the absence of 
# documentation.

WARN_NO_PARAMDOC       = YES

# The WARN_FORMAT tag determines the format of the warning messages that 
# doxygen can produce. The string should contain the $file, $line, and $text 
# tags, which will be replaced by the file and line number from which the 
# warning originated and the warning text. Optionally the format may contain 
# $version, which will be replaced by the version of the file (if it could 
# be obtained via FILE_VERSION_FILTER)

WARN_FORMAT            = "$file:$line: $text"

# The WARN_LOGFILE tag can be used to specify a file to which warning 
# and error messages should be written. If left blank the output is written 
# to stderr.

WARN_LOGFILE           = 

#---------------------------------------------------------------------------
# configuration options related to the input files
#---------------------------------------------------------------------------

# The INPUT tag can be used to specify the files and/or directories that contain 
# documented source files. You may enter file names like "myfile.cpp" or 
# directories like "/usr/src/myproject". Separate the files or directories 
# with spaces.

INPUT                  = .

# This tag can be used to specify the character encoding of the source files 
# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is 
# also the default input encoding. Doxygen uses libiconv (or the iconv built 
# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for 
# the list of possible encodings.

INPUT_ENCODING         = UTF-8

# If the value of the INPUT tag contains directories, you can use the 
# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
# and *.h) to filter out the source-files in the directories. If left 
# blank the following patterns are tested: 
# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh 
# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py 
# *.f90 *.f *.for *.vhd *.vhdl

FILE_PATTERNS          = *.c \
                         *.cc \
                         *.cxx \
                         *.cpp \
                         *.c++ \
                         *.d \
                         *.java \
                         *.ii \
                         *.ixx \
                         *.ipp \
                         *.i++ \
                         *.inl \
                         *.h \
                         *.hh \
                         *.hxx \
                         *.hpp \
                         *.h++ \
                         *.idl \
                         *.odl \
                         *.cs \
                         *.php \
                         *.php3 \
                         *.inc \
                         *.m \
                         *.mm \
                         *.dox \
                         *.py \
                         *.f90 \
                         *.f \
                         *.for \
                         *.vhd \
                         *.vhdl

# The RECURSIVE tag can be used to turn specify whether or not subdirectories 
# should be searched for input files as well. Possible values are YES and NO. 
# If left blank NO is used.

RECURSIVE              = YES

# The EXCLUDE tag can be used to specify files and/or directories that should 
# excluded from the INPUT source files. This way you can easily exclude a 
# subdirectory from a directory tree whose root is specified with the INPUT tag. 
# Note that relative paths are relative to directory from which doxygen is run.

EXCLUDE                = /usr/local \
                         /usr/local/include \
                         /usr/local/include/boost \
                         boost-include\
                         boost-lib\
                         ../boost_1_47_0\
                         ../SeqAn_1.2
 
# The EXCLUDE_SYMLINKS tag can be used select whether or not files or 
# directories that are symbolic links (a Unix file system feature) are excluded 
# from the input.

EXCLUDE_SYMLINKS       = NO

# If the value of the INPUT tag contains directories, you can use the 
# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude 
# certain files from those directories. Note that the wildcards are matched 
# against the file with absolute path, so to exclude all test directories 
# for example use the pattern */test/*

EXCLUDE_PATTERNS       = /usr/local/* \
                         *.profile \
                         *.fasta \
                         */boost-include/* \
                         */seqan/* \
                         */hmmer/*
 
# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names 
# (namespaces, classes, functions, etc.) that should be excluded from the 
# output. The symbol name can be a fully qualified name, a word, or if the 
# wildcard * is used, a substring. Examples: ANamespace, AClass, 
# AClass::ANamespace, ANamespace::*Test

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           = 

# If the value of the EXAMPLE_PATH tag contains directories, you can use the 
# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
# and *.h) to filter out the source-files in the directories. If left 
# blank all files are included.

EXAMPLE_PATTERNS       =

# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be 
# searched for input files to be used with the \include or \dontinclude 
# commands irrespective of the value of the RECURSIVE tag. 
# Possible values are YES and NO. If left blank NO is used.

EXAMPLE_RECURSIVE      = NO

# The IMAGE_PATH tag can be used to specify one or more files or 
# directories that contain image that are included in the documentation (see 
# the \image command).

IMAGE_PATH             = 

# The INPUT_FILTER tag can be used to specify a program that doxygen should 
# invoke to filter for each input file. Doxygen will invoke the filter program 
# by executing (via popen()) the command <filter> <input-file>, where <filter> 
# is the value of the INPUT_FILTER tag, and <input-file> is the name of an 
# input file. Doxygen will then use the output that the filter program writes 
# to standard output.  If FILTER_PATTERNS is specified, this tag will be 
# ignored.

INPUT_FILTER           = 

# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern 
# basis.  Doxygen will compare the file name with each pattern and apply the 
# filter if there is a match.  The filters are a list of the form: 
# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further 
# info on how filters are used. If FILTER_PATTERNS is empty or if 
# non of the patterns match the file name, INPUT_FILTER is applied.

FILTER_PATTERNS        = 

# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using 
# INPUT_FILTER) will be used to filter the input files when producing source 
# files to browse (i.e. when SOURCE_BROWSER is set to YES).

FILTER_SOURCE_FILES    = NO

# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file 
# pattern. A pattern will override the setting for FILTER_PATTERN (if any) 
# and it is also possible to disable source filtering for a specific pattern 
# using *.ext= (so without naming a filter). This option only has effect when 
# FILTER_SOURCE_FILES is enabled.

FILTER_SOURCE_PATTERNS = 

#---------------------------------------------------------------------------
# configuration options related to source browsing
#---------------------------------------------------------------------------

# If the SOURCE_BROWSER tag is set to YES then a list of source files will 
# be generated. Documented entities will be cross-referenced with these sources. 
# Note: To get rid of all source code in the generated output, make sure also 
# VERBATIM_HEADERS is set to NO.

SOURCE_BROWSER         = YES

# Setting the INLINE_SOURCES tag to YES will include the body 
# of functions and classes directly in the documentation.

INLINE_SOURCES         = NO

# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct 
# doxygen to hide any special comment blocks from generated source code 
# fragments. Normal C and C++ comments will always remain visible.

STRIP_CODE_COMMENTS    = NO

# If the REFERENCED_BY_RELATION tag is set to YES 
# then for each documented function all documented 
# functions referencing it will be listed.

REFERENCED_BY_RELATION = YES

# If the REFERENCES_RELATION tag is set to YES 
# then for each documented function all documented entities 
# called/used by that function will be listed.

REFERENCES_RELATION    = YES

# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) 
# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from 
# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will 
# link to the source code.  Otherwise they will link to the documentation.

REFERENCES_LINK_SOURCE = YES

# If the USE_HTAGS tag is set to YES then the references to source code 
# will point to the HTML generated by the htags(1) tool instead of doxygen 
# built-in source browser. The htags tool is part of GNU's global source 
# tagging system (see http://www.gnu.org/software/global/global.html). You 
# will need version 4.8.6 or higher.

USE_HTAGS              = NO

# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen 
# will generate a verbatim copy of the header file for each class for 
# which an include is specified. Set to NO to disable this.

VERBATIM_HEADERS       = YES

#---------------------------------------------------------------------------
# configuration options related to the alphabetical class index
#---------------------------------------------------------------------------

# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index 
# of all compounds will be generated. Enable this if the project 
# contains a lot of classes, structs, unions or interfaces.

ALPHABETICAL_INDEX     = YES

# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then 
# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns 
# in which this list will be split (can be a number in the range [1..20])

COLS_IN_ALPHA_INDEX    = 5

# In case all classes in a project start with a common prefix, all 
# classes will be put under the same header in the alphabetical index. 
# The IGNORE_PREFIX tag can be used to specify one or more prefixes that 
# should be ignored while generating the index headers.

IGNORE_PREFIX          = 

#---------------------------------------------------------------------------
# configuration options related to the HTML output
#---------------------------------------------------------------------------

# If the GENERATE_HTML tag is set to YES (the default) Doxygen will 
# generate HTML output.

GENERATE_HTML          = YES

# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. 
# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
# put in front of it. If left blank `html' will be used as the default path.

HTML_OUTPUT            = html

# The HTML_FILE_EXTENSION tag can be used to specify the file extension for 
# each generated HTML page (for example: .htm,.php,.asp). If it is left blank 
# doxygen will generate files with .html extension.

HTML_FILE_EXTENSION    = .html

# The HTML_HEADER tag can be used to specify a personal HTML header for 
# each generated HTML page. If it is left blank doxygen will generate a 
# standard header. Note that when using a custom header you are responsible  
# for the proper inclusion of any scripts and style sheets that doxygen 
# needs, which is dependent on the configuration options used. 
# It is adviced to generate a default header using "doxygen -w html 
# header.html footer.html stylesheet.css YourConfigFile" and then modify 
# that header. Note that the header is subject to change so you typically 
# have to redo this when upgrading to a newer version of doxygen or when 
# changing the value of configuration settings such as GENERATE_TREEVIEW!

HTML_HEADER            = 

# The HTML_FOOTER tag can be used to specify a personal HTML footer for 
# each generated HTML page. If it is left blank doxygen will generate a 
# standard footer.

HTML_FOOTER            = 

# The HTML_STYLESHEET tag can be used to specify a user-defined cascading 
# style sheet that is used by each HTML page. It can be used to 
# fine-tune the look of the HTML output. If the tag is left blank doxygen 
# will generate a default style sheet. Note that doxygen will try to copy 
# the style sheet file to the HTML output directory, so don't put your own 
# stylesheet in the HTML output directory as well, or it will be erased!

HTML_STYLESHEET        = 

# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or 
# other source files which should be copied to the HTML output directory. Note 
# that these files will be copied to the base HTML output directory. Use the 
# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these 
# files. In the HTML_STYLESHEET file, use the file name only. Also note that 
# the files will be copied as-is; there are no commands or markers available.

HTML_EXTRA_FILES       = 

# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. 
# Doxygen will adjust the colors in the stylesheet and background images 
# according to this color. Hue is specified as an angle on a colorwheel, 
# see http://en.wikipedia.org/wiki/Hue for more information. 
# For instance the value 0 represents red, 60 is yellow, 120 is green, 
# 180 is cyan, 240 is blue, 300 purple, and 360 is red again. 
# The allowed range is 0 to 359.

HTML_COLORSTYLE_HUE    = 220

# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of 
# the colors in the HTML output. For a value of 0 the output will use 
# grayscales only. A value of 255 will produce the most vivid colors.

HTML_COLORSTYLE_SAT    = 100

# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to 
# the luminance component of the colors in the HTML output. Values below 
# 100 gradually make the output lighter, whereas values above 100 make 
# the output darker. The value divided by 100 is the actual gamma applied, 
# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2, 
# and 100 does not change the gamma.

HTML_COLORSTYLE_GAMMA  = 80

# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML 
# page will contain the date and time when the page was generated. Setting 
# this to NO can help when comparing the output of multiple runs.

HTML_TIMESTAMP         = YES

# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, 
# files or namespaces will be aligned in HTML using tables. If set to 
# NO a bullet list will be used.

HTML_ALIGN_MEMBERS     = YES

# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML 
# documentation will contain sections that can be hidden and shown after the 
# page has loaded. For this to work a browser that supports 
# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox 
# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).

HTML_DYNAMIC_SECTIONS  = YES

# If the GENERATE_DOCSET tag is set to YES, additional index files 
# will be generated that can be used as input for Apple's Xcode 3 
# integrated development environment, introduced with OSX 10.5 (Leopard). 
# To create a documentation set, doxygen will generate a Makefile in the 
# HTML output directory. Running make will produce the docset in that 
# directory and running "make install" will install the docset in 
# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find 
# it at startup. 
# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html 
# for more information.

GENERATE_DOCSET        = NO

# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the 
# feed. A documentation feed provides an umbrella under which multiple 
# documentation sets from a single provider (such as a company or product suite) 
# can be grouped.

DOCSET_FEEDNAME        = "Doxygen generated docs"

# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that 
# should uniquely identify the documentation set bundle. This should be a 
# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen 
# will append .docset to the name.

DOCSET_BUNDLE_ID       = org.doxygen.Project

# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify 
# the documentation publisher. This should be a reverse domain-name style 
# string, e.g. com.mycompany.MyDocSet.documentation.

DOCSET_PUBLISHER_ID    = org.doxygen.Publisher

# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.

DOCSET_PUBLISHER_NAME  = Publisher

# If the GENERATE_HTMLHELP tag is set to YES, additional index files 
# will be generated that can be used as input for tools like the 
# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) 
# of the generated HTML documentation.

GENERATE_HTMLHELP      = YES

# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can 
# be used to specify the file name of the resulting .chm file. You 
# can add a path in front of the file if the result should not be 
# written to the html output directory.

CHM_FILE               = 

# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can 
# be used to specify the location (absolute path including file name) of 
# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run 
# the HTML help compiler on the generated index.hhp.

HHC_LOCATION           = 

# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag 
# controls if a separate .chi index file is generated (YES) or that 
# it should be included in the master .chm file (NO).

GENERATE_CHI           = NO

# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING 
# is used to encode HtmlHelp index (hhk), content (hhc) and project file 
# content.

CHM_INDEX_ENCODING     = 

# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag 
# controls whether a binary table of contents is generated (YES) or a 
# normal table of contents (NO) in the .chm file.

BINARY_TOC             = NO

# The TOC_EXPAND flag can be set to YES to add extra items for group members 
# to the contents of the HTML help documentation and to the tree view.

TOC_EXPAND             = NO

# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and 
# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated 
# that can be used as input for Qt's qhelpgenerator to generate a 
# Qt Compressed Help (.qch) of the generated HTML documentation.

GENERATE_QHP           = NO

# If the QHG_LOCATION tag is specified, the QCH_FILE tag can 
# be used to specify the file name of the resulting .qch file. 
# The path specified is relative to the HTML output folder.

QCH_FILE               = 

# The QHP_NAMESPACE tag specifies the namespace to use when generating 
# Qt Help Project output. For more information please see 
# http://doc.trolltech.com/qthelpproject.html#namespace

QHP_NAMESPACE          = org.doxygen.Project

# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating 
# Qt Help Project output. For more information please see 
# http://doc.trolltech.com/qthelpproject.html#virtual-folders

QHP_VIRTUAL_FOLDER     = doc

# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to 
# add. For more information please see 
# http://doc.trolltech.com/qthelpproject.html#custom-filters

QHP_CUST_FILTER_NAME   = 

# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the 
# custom filter to add. For more information please see 
# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters"> 
# Qt Help Project / Custom Filters</a>.

QHP_CUST_FILTER_ATTRS  = 

# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this 
# project's 
# filter section matches. 
# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes"> 
# Qt Help Project / Filter Attributes</a>.

QHP_SECT_FILTER_ATTRS  = 

# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can 
# be used to specify the location of Qt's qhelpgenerator. 
# If non-empty doxygen will try to run qhelpgenerator on the generated 
# .qhp file.

QHG_LOCATION           = 

# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files  
# will be generated, which together with the HTML files, form an Eclipse help 
# plugin. To install this plugin and make it available under the help contents 
# menu in Eclipse, the contents of the directory containing the HTML and XML 
# files needs to be copied into the plugins directory of eclipse. The name of 
# the directory within the plugins directory should be the same as 
# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before 
# the help appears.

GENERATE_ECLIPSEHELP   = NO

# A unique identifier for the eclipse help plugin. When installing the plugin 
# the directory name containing the HTML and XML files should also have 
# this name.

ECLIPSE_DOC_ID         = org.doxygen.Project

# The DISABLE_INDEX tag can be used to turn on/off the condensed index at 
# top of each HTML page. The value NO (the default) enables the index and 
# the value YES disables it.

DISABLE_INDEX          = NO

# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values 
# (range [0,1..20]) that doxygen will group on one line in the generated HTML 
# documentation. Note that a value of 0 will completely suppress the enum 
# values from appearing in the overview section.

ENUM_VALUES_PER_LINE   = 4

# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index 
# structure should be generated to display hierarchical information. 
# If the tag value is set to YES, a side panel will be generated 
# containing a tree-like index structure (just like the one that 
# is generated for HTML Help). For this to work a browser that supports 
# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). 
# Windows users are probably better off using the HTML help feature.

GENERATE_TREEVIEW      = NO

# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories, 
# and Class Hierarchy pages using a tree view instead of an ordered list.

USE_INLINE_TREES       = NO

# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be 
# used to set the initial width (in pixels) of the frame in which the tree 
# is shown.

TREEVIEW_WIDTH         = 250

# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open 
# links to external symbols imported via tag files in a separate window.

EXT_LINKS_IN_WINDOW    = NO

# Use this tag to change the font size of Latex formulas included 
# as images in the HTML documentation. The default is 10. Note that 
# when you change the font size after a successful doxygen run you need 
# to manually remove any form_*.png images from the HTML output directory 
# to force them to be regenerated.

FORMULA_FONTSIZE       = 10

# Use the FORMULA_TRANPARENT tag to determine whether or not the images 
# generated for formulas are transparent PNGs. Transparent PNGs are 
# not supported properly for IE 6.0, but are supported on all modern browsers. 
# Note that when changing this option you need to delete any form_*.png files 
# in the HTML output before the changes have effect.

FORMULA_TRANSPARENT    = YES

# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax 
# (see http://www.mathjax.org) which uses client side Javascript for the 
# rendering instead of using prerendered bitmaps. Use this if you do not 
# have LaTeX installed or if you want to formulas look prettier in the HTML 
# output. When enabled you also need to install MathJax separately and 
# configure the path to it using the MATHJAX_RELPATH option.

USE_MATHJAX            = NO

# When MathJax is enabled you need to specify the location relative to the 
# HTML output directory using the MATHJAX_RELPATH option. The destination 
# directory should contain the MathJax.js script. For instance, if the mathjax 
# directory is located at the same level as the HTML output directory, then 
# MATHJAX_RELPATH should be ../mathjax. The default value points to the 
# mathjax.org site, so you can quickly see the result without installing 
# MathJax, but it is strongly recommended to install a local copy of MathJax 
# before deployment.

MATHJAX_RELPATH        = http://www.mathjax.org/mathjax

# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension 
# names that should be enabled during MathJax rendering.

MATHJAX_EXTENSIONS     = 

# When the SEARCHENGINE tag is enabled doxygen will generate a search box 
# for the HTML output. The underlying search engine uses javascript 
# and DHTML and should work on any modern browser. Note that when using 
# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets 
# (GENERATE_DOCSET) there is already a search function so this one should 
# typically be disabled. For large projects the javascript based search engine 
# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.

SEARCHENGINE           = NO

# When the SERVER_BASED_SEARCH tag is enabled the search engine will be 
# implemented using a PHP enabled web server instead of at the web client 
# using Javascript. Doxygen will generate the search PHP script and index 
# file to put on the web server. The advantage of the server 
# based approach is that it scales better to large projects and allows 
# full text search. The disadvantages are that it is more difficult to setup 
# and does not have live searching capabilities.

SERVER_BASED_SEARCH    = NO

#---------------------------------------------------------------------------
# configuration options related to the LaTeX output
#---------------------------------------------------------------------------

# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will 
# generate Latex output.

GENERATE_LATEX         = NO

# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. 
# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
# put in front of it. If left blank `latex' will be used as the default path.

LATEX_OUTPUT           = latex

# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be 
# invoked. If left blank `latex' will be used as the default command name. 
# Note that when enabling USE_PDFLATEX this option is only used for 
# generating bitmaps for formulas in the HTML output, but not in the 
# Makefile that is written to the output directory.

LATEX_CMD_NAME         = /sw/bin/latex

# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to 
# generate index for LaTeX. If left blank `makeindex' will be used as the 
# default command name.

MAKEINDEX_CMD_NAME     = makeindex

# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact 
# LaTeX documents. This may be useful for small projects and may help to 
# save some trees in general.

COMPACT_LATEX          = NO

# The PAPER_TYPE tag can be used to set the paper type that is used 
# by the printer. Possible values are: a4, letter, legal and 
# executive. If left blank a4wide will be used.

PAPER_TYPE             = a4

# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX 
# packages that should be included in the LaTeX output.

EXTRA_PACKAGES         = 

# The LATEX_HEADER tag can be used to specify a personal LaTeX header for 
# the generated latex document. The header should contain everything until 
# the first chapter. If it is left blank doxygen will generate a 
# standard header. Notice: only use this tag if you know what you are doing!

LATEX_HEADER           = 

# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for 
# the generated latex document. The footer should contain everything after 
# the last chapter. If it is left blank doxygen will generate a 
# standard footer. Notice: only use this tag if you know what you are doing!

LATEX_FOOTER           = 

# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated 
# is prepared for conversion to pdf (using ps2pdf). The pdf file will 
# contain links (just like the HTML output) instead of page references 
# This makes the output suitable for online browsing using a pdf viewer.

PDF_HYPERLINKS         = YES

# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of 
# plain latex in the generated Makefile. Set this option to YES to get a 
# higher quality PDF documentation.

USE_PDFLATEX           = YES

# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. 
# command to the generated LaTeX files. This will instruct LaTeX to keep 
# running if errors occur, instead of asking the user for help. 
# This option is also used when generating formulas in HTML.

LATEX_BATCHMODE        = NO

# If LATEX_HIDE_INDICES is set to YES then doxygen will not 
# include the index chapters (such as File Index, Compound Index, etc.) 
# in the output.

LATEX_HIDE_INDICES     = NO

# If LATEX_SOURCE_CODE is set to YES then doxygen will include 
# source code with syntax highlighting in the LaTeX output. 
# Note that which sources are shown also depends on other settings 
# such as SOURCE_BROWSER.

LATEX_SOURCE_CODE      = NO

# The LATEX_BIB_STYLE tag can be used to specify the style to use for the 
# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See 
# http://en.wikipedia.org/wiki/BibTeX for more info.

LATEX_BIB_STYLE        = plain

#---------------------------------------------------------------------------
# configuration options related to the RTF output
#---------------------------------------------------------------------------

# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output 
# The RTF output is optimized for Word 97 and may not look very pretty with 
# other RTF readers or editors.

GENERATE_RTF           = NO

# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. 
# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
# put in front of it. If left blank `rtf' will be used as the default path.

RTF_OUTPUT             = rtf

# If the COMPACT_RTF tag is set to YES Doxygen generates more compact 
# RTF documents. This may be useful for small projects and may help to 
# save some trees in general.

COMPACT_RTF            = NO

# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated 
# will contain hyperlink fields. The RTF file will 
# contain links (just like the HTML output) instead of page references. 
# This makes the output suitable for online browsing using WORD or other 
# programs which support those fields. 
# Note: wordpad (write) and others do not support links.

RTF_HYPERLINKS         = NO

# Load stylesheet definitions from file. Syntax is similar to doxygen's 
# config file, i.e. a series of assignments. You only have to provide 
# replacements, missing definitions are set to their default value.

RTF_STYLESHEET_FILE    = 

# Set optional variables used in the generation of an rtf document. 
# Syntax is similar to doxygen's config file.

RTF_EXTENSIONS_FILE    = 

#---------------------------------------------------------------------------
# configuration options related to the man page output
#---------------------------------------------------------------------------

# If the GENERATE_MAN tag is set to YES (the default) Doxygen will 
# generate man pages

GENERATE_MAN           = YES

# The MAN_OUTPUT tag is used to specify where the man pages will be put. 
# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
# put in front of it. If left blank `man' will be used as the default path.

MAN_OUTPUT             = man

# The MAN_EXTENSION tag determines the extension that is added to 
# the generated man pages (default is the subroutine's section .3)

MAN_EXTENSION          = .3

# If the MAN_LINKS tag is set to YES and Doxygen generates man output, 
# then it will generate one additional man file for each entity 
# documented in the real man page(s). These additional files 
# only source the real man page, but without them the man command 
# would be unable to find the correct page. The default is NO.

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 captures the structure of 
# the code including all documentation.

GENERATE_XML           = NO

# The XML_OUTPUT tag is used to specify where the XML pages will be put. 
# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
# put in front of it. If left blank `xml' will be used as the default path.

XML_OUTPUT             = xml

# The XML_SCHEMA tag can be used to specify an XML schema, 
# which can be used by a validating XML parser to check the 
# syntax of the XML files.

XML_SCHEMA             = 

# The XML_DTD tag can be used to specify an XML DTD, 
# which can be used by a validating XML parser to check the 
# syntax of the XML files.

XML_DTD                = 

# If the XML_PROGRAMLISTING tag is set to YES Doxygen will 
# dump the program listings (including syntax highlighting 
# and cross-referencing information) to the XML output. Note that 
# enabling this will significantly increase the size of the XML output.

XML_PROGRAMLISTING     = YES

#---------------------------------------------------------------------------
# configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------

# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will 
# generate an AutoGen Definitions (see autogen.sf.net) file 
# that captures the structure of the code including all 
# documentation. Note that this feature is still experimental 
# and incomplete at the moment.

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 file that captures the structure of 
# the code including all documentation. Note that this 
# feature is still experimental and incomplete at the 
# moment.

GENERATE_PERLMOD       = NO

# If the PERLMOD_LATEX tag is set to YES Doxygen will generate 
# the necessary Makefile rules, Perl scripts and LaTeX code to be able 
# to generate PDF and DVI output from the Perl module output.

PERLMOD_LATEX          = NO

# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be 
# nicely formatted so it can be parsed by a human reader.  This is useful 
# if you want to understand what is going on.  On the other hand, if this 
# tag is set to NO the size of the Perl module output will be much smaller 
# and Perl will parse it just the same.

PERLMOD_PRETTY         = YES

# The names of the make variables in the generated doxyrules.make file 
# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. 
# This is useful so different doxyrules.make files included by the same 
# Makefile don't overwrite each other's variables.

PERLMOD_MAKEVAR_PREFIX = 

#---------------------------------------------------------------------------
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------

# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will 
# evaluate all C-preprocessor directives found in the sources and include 
# files.

ENABLE_PREPROCESSING   = YES

# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro 
# names in the source code. If set to NO (the default) only conditional 
# compilation will be performed. Macro expansion can be done in a controlled 
# way by setting EXPAND_ONLY_PREDEF to YES.

MACRO_EXPANSION        = YES

# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES 
# then the macro expansion is limited to the macros specified with the 
# PREDEFINED and EXPAND_AS_DEFINED tags.

EXPAND_ONLY_PREDEF     = NO

# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files 
# pointed to by INCLUDE_PATH will be searched when a #include is found.

SEARCH_INCLUDES        = YES

# The INCLUDE_PATH tag can be used to specify one or more directories that 
# contain include files that are not input files but should be processed by 
# the preprocessor.

INCLUDE_PATH           = 

# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard 
# patterns (like *.h and *.hpp) to filter out the header-files in the 
# directories. If left blank, the patterns specified with FILE_PATTERNS will 
# be used.

INCLUDE_FILE_PATTERNS  = 

# The PREDEFINED tag can be used to specify one or more macro names that 
# are defined before the preprocessor is started (similar to the -D option of 
# gcc). The argument of the tag is a list of macros of the form: name 
# or name=definition (no spaces). If the definition and the = are 
# omitted =1 is assumed. To prevent a macro definition from being 
# undefined via #undef or recursively expanded use the := operator 
# instead of the = operator.

PREDEFINED             = 

# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then 
# this tag can be used to specify a list of macro names that should be expanded. 
# The macro definition that is found in the sources will be used. 
# Use the PREDEFINED tag if you want to use a different macro definition that 
# overrules the definition found in the source code.

EXPAND_AS_DEFINED      = 

# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then 
# doxygen's preprocessor will remove all references to function-like macros 
# that are alone on a line, have an all uppercase name, and do not end with a 
# semicolon, because these will confuse the parser if not removed.

SKIP_FUNCTION_MACROS   = YES

#---------------------------------------------------------------------------
# Configuration::additions related to external references
#---------------------------------------------------------------------------

# The TAGFILES option can be used to specify one or more tagfiles. 
# Optionally an initial location of the external documentation 
# can be added for each tagfile. The format of a tag file without 
# this location is as follows: 
#   TAGFILES = file1 file2 ... 
# Adding location for the tag files is done as follows: 
#   TAGFILES = file1=loc1 "file2 = loc2" ... 
# where "loc1" and "loc2" can be relative or absolute paths or 
# URLs. If a location is present for each tag, the installdox tool 
# does not have to be run to correct the links. 
# Note that each tag file must have a unique name 
# (where the name does NOT include the path) 
# If a tag file is not located in the directory in which doxygen 
# is run, you must also specify the path to the tagfile here.

TAGFILES               = 

# When a file name is specified after GENERATE_TAGFILE, doxygen will create 
# a tag file that is based on the input files it reads.

GENERATE_TAGFILE       = 

# If the ALLEXTERNALS tag is set to YES all external classes will be listed 
# in the class index. If set to NO only the inherited external classes 
# will be listed.

ALLEXTERNALS           = NO

# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed 
# in the modules index. If set to NO, only the current project's groups will 
# be listed.

EXTERNAL_GROUPS        = YES

# The PERL_PATH should be the absolute path and name of the perl script 
# interpreter (i.e. the result of `which perl').

PERL_PATH              = /usr/bin/perl

#---------------------------------------------------------------------------
# Configuration options related to the dot tool
#---------------------------------------------------------------------------

# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will 
# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base 
# or super classes. Setting the tag to NO turns the diagrams off. Note that 
# this option also works with HAVE_DOT disabled, but it is recommended to 
# install and use dot, since it yields more powerful graphs.

CLASS_DIAGRAMS         = YES

# You can define message sequence charts within doxygen comments using the \msc 
# command. Doxygen will then run the mscgen tool (see 
# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the 
# documentation. The MSCGEN_PATH tag allows you to specify the directory where 
# the mscgen tool resides. If left empty the tool is assumed to be found in the 
# default search path.

MSCGEN_PATH            = 

# If set to YES, the inheritance and collaboration graphs will hide 
# inheritance and usage relations if the target is undocumented 
# or is not a class.

HIDE_UNDOC_RELATIONS   = NO

# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is 
# available from the path. This tool is part of Graphviz, a graph visualization 
# toolkit from AT&T and Lucent Bell Labs. The other options in this section 
# have no effect if this option is set to NO (the default)

HAVE_DOT               = YES

# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is 
# allowed to run in parallel. When set to 0 (the default) doxygen will 
# base this on the number of processors available in the system. You can set it 
# explicitly to a value larger than 0 to get control over the balance 
# between CPU load and processing speed.

DOT_NUM_THREADS        = 0

# By default doxygen will use the Helvetica font for all dot files that 
# doxygen generates. When you want a differently looking font you can specify 
# the font name using DOT_FONTNAME. You need to make sure dot is able to find 
# the font, which can be done by putting it in a standard location or by setting 
# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the 
# directory containing the font.

DOT_FONTNAME           = Helvetica

# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. 
# The default size is 10pt.

DOT_FONTSIZE           = 12

# By default doxygen will tell dot to use the Helvetica font. 
# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to 
# set the path where dot can find it.

DOT_FONTPATH           = 

# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen 
# will generate a graph for each documented class showing the direct and 
# indirect inheritance relations. Setting this tag to YES will force the 
# the CLASS_DIAGRAMS tag to NO.

CLASS_GRAPH            = YES

# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen 
# will generate a graph for each documented class showing the direct and 
# indirect implementation dependencies (inheritance, containment, and 
# class references variables) of the class with other documented classes.

COLLABORATION_GRAPH    = YES

# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen 
# will generate a graph for groups, showing the direct groups dependencies

GROUP_GRAPHS           = YES

# If the UML_LOOK tag is set to YES doxygen will generate inheritance and 
# collaboration diagrams in a style similar to the OMG's Unified Modeling 
# Language.

UML_LOOK               = NO

# If set to YES, the inheritance and collaboration graphs will show the 
# relations between templates and their instances.

TEMPLATE_RELATIONS     = YES

# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT 
# tags are set to YES then doxygen will generate a graph for each documented 
# file showing the direct and indirect include dependencies of the file with 
# other documented files.

INCLUDE_GRAPH          = YES

# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and 
# HAVE_DOT tags are set to YES then doxygen will generate a graph for each 
# documented header file showing the documented files that directly or 
# indirectly include this file.

INCLUDED_BY_GRAPH      = YES

# If the CALL_GRAPH and HAVE_DOT options are set to YES then 
# doxygen will generate a call dependency graph for every global function 
# or class method. Note that enabling this option will significantly increase 
# the time of a run. So in most cases it will be better to enable call graphs 
# for selected functions only using the \callgraph command.

CALL_GRAPH             = YES

# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then 
# doxygen will generate a caller dependency graph for every global function 
# or class method. Note that enabling this option will significantly increase 
# the time of a run. So in most cases it will be better to enable caller 
# graphs for selected functions only using the \callergraph command.

CALLER_GRAPH           = YES

# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen 
# will generate a graphical hierarchy of all classes instead of a textual one.

GRAPHICAL_HIERARCHY    = YES

# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES 
# then doxygen will show the dependencies a directory has on other directories 
# in a graphical way. The dependency relations are determined by the #include 
# relations between the files in the directories.

DIRECTORY_GRAPH        = YES

# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images 
# generated by dot. Possible values are svg, png, jpg, or gif. 
# If left blank png will be used. If you choose svg you need to set 
# HTML_FILE_EXTENSION to xhtml in order to make the SVG files 
# visible in IE 9+ (other browsers do not have this requirement).

DOT_IMAGE_FORMAT       = png

# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to 
# enable generation of interactive SVG images that allow zooming and panning. 
# Note that this requires a modern browser other than Internet Explorer. 
# Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you 
# need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files 
# visible. Older versions of IE do not have SVG support.

INTERACTIVE_SVG        = NO

# The tag DOT_PATH can be used to specify the path where the dot tool can be 
# found. If left blank, it is assumed the dot tool can be found in the path.

DOT_PATH               = /sw/bin

# 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).

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           = 

# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of 
# nodes that will be shown in the graph. If the number of nodes in a graph 
# becomes larger than this value, doxygen will truncate the graph, which is 
# visualized by representing a node as a red box. Note that doxygen if the 
# number of direct children of the root node in a graph is already larger than 
# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note 
# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.

DOT_GRAPH_MAX_NODES    = 1000

# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the 
# graphs generated by dot. A depth value of 3 means that only nodes reachable 
# from the root by following a path via at most 3 edges will be shown. Nodes 
# that lay further from the root node will be omitted. Note that setting this 
# option to 1 or 2 may greatly reduce the computation time needed for large 
# code bases. Also note that the size of a graph can be further restricted by 
# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.

MAX_DOT_GRAPH_DEPTH    = 0

# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent 
# background. This is disabled by default, because dot on Windows does not 
# seem to support this out of the box. Warning: Depending on the platform used, 
# enabling this option may lead to badly anti-aliased labels on the edges of 
# a graph (i.e. they become hard to read).

DOT_TRANSPARENT        = NO

# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output 
# files in one run (i.e. multiple -o and -T options on the command line). This 
# makes dot run faster, but since only newer versions of dot (>1.8.10) 
# support this, this feature is disabled by default.

DOT_MULTI_TARGETS      = NO

# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will 
# generate a legend page explaining the meaning of the various boxes and 
# arrows in the dot generated graphs.

GENERATE_LEGEND        = YES

# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will 
# remove the intermediate dot files that are used to generate 
# the various graphs.

DOT_CLEANUP            = YES