Update Doxygen file to 1.8.1

doc/Doxyfile.in

@@ -1,4 +1,4 @@
-# Doxyfile 1.7.4
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -22,8 +22,9 @@
 
 DOXYFILE_ENCODING      = UTF-8
 
-# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
-# by quotes) that should identify the project.
+# 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           = dmmlib
 
@@ -194,6 +195,13 @@ TAB_SIZE               = 8
 
 ALIASES                =
 
+# This tag can be used to specify a number of word-keyword mappings (TCL only).
+# A mapping has the form "name=value". For example adding
+# "class=itcl::class" will allow you to use the command class in the
+# itcl::class meaning.
+
+TCL_SUBST              =
+
 # 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
@@ -232,6 +240,15 @@ OPTIMIZE_OUTPUT_VHDL   = NO
 
 EXTENSION_MAPPING      =
 
+# If MARKDOWN_SUPPORT is enabled (the default) then doxygen pre-processes all
+# comments according to the Markdown format, which allows for more readable
+# documentation. See http://daringfireball.net/projects/markdown/ for details.
+# The output of markdown processing is further processed by doxygen, so you
+# can mix doxygen, HTML, and XML commands with Markdown formatting.
+# Disable only in case of backward compatibilities issues.
+
+MARKDOWN_SUPPORT       = YES
+
 # If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
 # to include (a tag file for) the STL sources as input, then you should
 # set this tag to YES in order to let doxygen match functions declarations and
@@ -283,6 +300,15 @@ SUBGROUPING            = YES
 
 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
@@ -305,10 +331,21 @@ TYPEDEF_HIDES_STRUCT   = NO
 # 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
+# corresponding to a cache size of 2^16 = 65536 symbols.
 
 SYMBOL_CACHE_SIZE      = 0
 
+# Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be
+# set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given
+# their name and scope. Since this can be an expensive process and often the
+# same symbol appear multiple times in the code, doxygen keeps a cache of
+# pre-resolved symbols. If the cache is too small doxygen will become slower.
+# If the cache is too large, memory is wasted. The cache size is given by this
+# formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0,
+# corresponding to a cache size of 2^16 = 65536 symbols.
+
+LOOKUP_CACHE_SIZE      = 0
+
 #---------------------------------------------------------------------------
 # Build related configuration options
 #---------------------------------------------------------------------------
@@ -325,6 +362,10 @@ EXTRACT_ALL            = NO
 
 EXTRACT_PRIVATE        = NO
 
+# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal scope will be included in the documentation.
+
+EXTRACT_PACKAGE        = NO
+
 # If the EXTRACT_STATIC tag is set to YES all static members of a file
 # will be included in the documentation.
 
@@ -512,12 +553,6 @@ MAX_INITIALIZER_LINES  = 30
 
 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       = NO
-
 # 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.
@@ -550,6 +585,16 @@ FILE_VERSION_FILTER    =
 
 LAYOUT_FILE            =
 
+# The CITE_BIB_FILES tag can be used to specify one or more bib files
+# containing the references data. This must be a list of .bib files. The
+# .bib extension is automatically appended if omitted. Using this command
+# requires the bibtex tool to be installed. See also
+# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style
+# of the bibliography can be controlled using LATEX_BIB_STYLE. To use this
+# feature you need bibtex and perl available in the search path.
+
+CITE_BIB_FILES         =
+
 #---------------------------------------------------------------------------
 # configuration options related to warning and progress messages
 #---------------------------------------------------------------------------
@@ -628,7 +673,8 @@ INPUT_ENCODING         = UTF-8
 # *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
 # *.f90 *.f *.for *.vhd *.vhdl
 
-FILE_PATTERNS          = *.c *.h
+FILE_PATTERNS          = *.c \
+                         *.h
 
 # 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.
@@ -636,13 +682,17 @@ FILE_PATTERNS          = *.c *.h
 
 RECURSIVE              = YES
 
-# The EXCLUDE tag can be used to specify files and/or directories that should
+# The EXCLUDE tag can be used to specify files and/or directories that should be
 # excluded from the INPUT source files. This way you can easily exclude a
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
 
-EXCLUDE                = test.c lran2.h larson.c
+EXCLUDE                = test.c \
+                         lran2.h \
+                         larson.c
 
-# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
 # from the input.
 
@@ -654,7 +704,7 @@ EXCLUDE_SYMLINKS       = NO
 # against the file with absolute path, so to exclude all test directories
 # for example use the pattern */test/*
 
-				       EXCLUDE_PATTERNS       =
+EXCLUDE_PATTERNS       =
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -829,12 +879,13 @@ 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
+#  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
+# It is advised to generate a default header using "doxygen -w html
 # header.html footer.html stylesheet.css YourConfigFile" and then modify
 # that header. Note that the header is subject to change so you typically
-# have to redo this when upgrading to a newer version of doxygen or when changing the value of configuration settings such as GENERATE_TREEVIEW!
+# 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            =
 
@@ -849,7 +900,7 @@ HTML_FOOTER            =
 # 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!
+# style sheet in the HTML output directory as well, or it will be erased!
 
 HTML_STYLESHEET        =
 
@@ -863,7 +914,7 @@ HTML_STYLESHEET        =
 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
+# Doxygen will adjust the colors in the style sheet and background images
 # according to this color. Hue is specified as an angle on a colorwheel,
 # see http://en.wikipedia.org/wiki/Hue for more information.
 # For instance the value 0 represents red, 60 is yellow, 120 is green,
@@ -893,12 +944,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 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
@@ -907,6 +952,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = NO
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1058,19 +1114,14 @@ GENERATE_ECLIPSEHELP   = NO
 
 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.
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs)
+# at top of each HTML page. The value NO (the default) enables the index and
+# the value YES disables it. Since the tabs have the same information as the
+# navigation tree you can set this option to NO if you already set
+# GENERATE_TREEVIEW to YES.
 
 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
@@ -1078,13 +1129,17 @@ ENUM_VALUES_PER_LINE   = 4
 # is generated for HTML Help). For this to work a browser that supports
 # JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
 # Windows users are probably better off using the HTML help feature.
+# Since the tree basically has the same information as the tab index you
+# could consider to set DISABLE_INDEX to NO when enabling this option.
 
 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.
+# 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.
 
-USE_INLINE_TREES       = NO
+ENUM_VALUES_PER_LINE   = 4
 
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
@@ -1117,7 +1172,7 @@ FORMULA_TRANSPARENT    = YES
 # (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
+# output. When enabled you may also need to install MathJax separately and
 # configure the path to it using the MATHJAX_RELPATH option.
 
 USE_MATHJAX            = NO
@@ -1126,13 +1181,19 @@ USE_MATHJAX            = NO
 # 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 should be ../mathjax. The default value points to
+# the MathJax Content Delivery Network so you can quickly see the result without
+# installing MathJax.
+# However, it is strongly recommended to install a local
+# copy of MathJax from http://www.mathjax.org before deployment.
 
 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
@@ -1246,6 +1307,12 @@ LATEX_HIDE_INDICES     = NO
 
 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
 #---------------------------------------------------------------------------
@@ -1277,7 +1344,7 @@ COMPACT_RTF            = NO
 
 RTF_HYPERLINKS         = NO
 
-# Load stylesheet definitions from file. Syntax is similar to doxygen's
+# Load style sheet definitions from file. Syntax is similar to doxygen's
 # config file, i.e. a series of assignments. You only have to provide
 # replacements, missing definitions are set to their default value.
 
@@ -1468,22 +1535,18 @@ 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:
+# The TAGFILES option can be used to specify one or more tagfiles. For each
+# tag file the location of the external documentation should be added. The
+# format of a tag file without this location is as follows:
 #
 # TAGFILES = file1 file2 ...
 # Adding location for the tag files is done as follows:
 #
 # TAGFILES = file1=loc1 "file2 = loc2" ...
-# where "loc1" and "loc2" can be relative or absolute paths or
-# URLs. 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.
+# where "loc1" and "loc2" can be relative or absolute paths
+# or URLs. Note that each tag file must have a unique name (where the name does
+# NOT include the path). If a tag file is not located in the directory in which
+# doxygen is run, you must also specify the path to the tagfile here.
 
 TAGFILES               =
 
@@ -1551,13 +1614,12 @@ HAVE_DOT               = YES
 
 DOT_NUM_THREADS        = 0
 
-# By default doxygen will write a font called Helvetica to the output
-# directory and reference it in 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.
+# 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
 
@@ -1566,17 +1628,16 @@ DOT_FONTNAME           = Helvetica
 
 DOT_FONTSIZE           = 10
 
-# By default doxygen will tell dot to use the output directory to look for the
-# FreeSans.ttf font (which doxygen will put there itself). If you specify a
-# different font using DOT_FONTNAME you can set the path where dot
-# can find it using this tag.
+# 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_DIAGRAMS tag to NO.
 
 CLASS_GRAPH            = YES
 
@@ -1598,6 +1659,15 @@ GROUP_GRAPHS           = YES
 
 UML_LOOK               = NO
 
+# If the UML_LOOK tag is enabled, the fields and methods are shown inside
+# the class node. If there are many fields or methods and many nodes the
+# graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS
+# threshold limits the number of items for each type to make the size more
+# managable. Set this to 0 for no limit. Note that the threshold may be
+# exceeded by 50% before the limit is enforced.
+
+UML_LIMIT_NUM_FIELDS   = 10
+
 # If set to YES, the inheritance and collaboration graphs will show the
 # relations between templates and their instances.
 
@@ -1638,7 +1708,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = YES
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
@@ -1647,10 +1717,21 @@ 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 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.