fix documentation, fix PanamaMAC, fix algorithm names

1 files changed, 374 insertions, 178 deletions

diff --git a/Doxyfile b/Doxyfile
index fbe685a5..635f5a07 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -1,4 +1,4 @@
-# Doxyfile 1.2.15-20020512
+# Doxyfile 1.3.7
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project
@@ -11,7 +11,7 @@
 # Values that contain spaces should be placed between quotes (" ")
 
 #---------------------------------------------------------------------------
-# General configuration options
+# Project related configuration options
 #---------------------------------------------------------------------------
 
 # The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
@@ -32,54 +32,35 @@ PROJECT_NUMBER         =
 
 OUTPUT_DIRECTORY       = doc
 
+# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 
+# 2 levels of 10 sub-directories 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: 
-# Brazilian, Chinese, Chinese-Traditional, Croatian, Czech, Danish, Dutch, 
-# Finnish, French, German, Greek, Hungarian, Italian, Japanese, Korean, 
-# Norwegian, Polish, Portuguese, Romanian, Russian, Slovak, Slovene, 
-# Spanish, Swedish and Ukrainian.
+# Brazilian, Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish, Dutch, 
+# Finnish, French, German, Greek, Hungarian, Italian, Japanese, Japanese-en 
+# (Japanese with English messages), Korean, Korean-en, Norwegian, Polish, Portuguese, 
+# Romanian, Russian, Serbian, Slovak, Slovene, Spanish, Swedish, and Ukrainian.
 
 OUTPUT_LANGUAGE        = English
 
-# 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            = NO
-
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
-# will be included in the documentation.
-
-EXTRACT_PRIVATE        = NO
-
-# If the EXTRACT_STATIC tag is set to YES all static members of a file 
-# will be included in the documentation.
-
-EXTRACT_STATIC         = NO
-
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) 
-# defined locally in source files will be included in the documentation. 
-# If set to NO only classes defined in header files are included.
-
-EXTRACT_LOCAL_CLASSES  = 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 class will be included in the various 
-# overviews. This option has no effect if EXTRACT_ALL is enabled.
+# This tag can be used to specify the encoding used in the generated output. 
+# The encoding is not always determined by the language that is chosen, 
+# but also whether or not the output is meant for Windows or non-Windows users. 
+# In case there is a difference, setting the USE_WINDOWS_ENCODING tag to YES 
+# forces the Windows encoding (this is the default for the Windows binary), 
+# whereas setting the tag to NO uses a Unix-style encoding (the default for 
+# all platforms other than Windows).
 
-HIDE_UNDOC_CLASSES     = No
+USE_WINDOWS_ENCODING   = YES
 
 # 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 
@@ -95,6 +76,17 @@ BRIEF_MEMBER_DESC      = YES
 
 REPEAT_BRIEF           = YES
 
+# This tag implements a quasi-intelligent brief description abbreviator 
+# that is used to form the text in various listings. Each string 
+# in this list, if found as the leading text of the brief description, will be 
+# stripped from the text and the result after processing the whole list, is used 
+# as the annotated text. Otherwise, the brief description is used as-is. If left 
+# blank, the following values are used ("$name" is automatically replaced with the 
+# name of the entity): "The $name class" "The $name widget" "The $name file" 
+# "is" "provides" "specifies" "contains" "represents" "a" "an" "the"
+
+ABBREVIATE_BRIEF       = 
+
 # If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then 
 # Doxygen will generate a detailed section even if there is only a brief 
 # description.
@@ -115,32 +107,22 @@ INLINE_INHERITED_MEMB  = YES
 FULL_PATH_NAMES        = NO
 
 # 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 
+# 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. It is allowed to use relative paths in the argument list.
+# 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 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          = 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 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 
-# users are adviced to set this option to NO.
+# 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.
 
-CASE_SENSE_NAMES       = NO
+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 is your file systems 
@@ -148,32 +130,22 @@ CASE_SENSE_NAMES       = NO
 
 SHORT_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 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
-
-# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen 
-# will put list of the files that are included by a file in the documentation 
-# of that file.
-
-SHOW_INCLUDE_FILES     = YES
-
 # 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 the Qt-style comments (thus requiring an 
-# explict @brief command for a brief description.
+# comments will behave just like the Qt-style comments (thus requiring an 
+# explicit @brief command for a brief description.
 
 JAVADOC_AUTOBRIEF      = YES
 
+# 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 DETAILS_AT_TOP tag is set to YES then Doxygen 
 # will output the detailed description near the top, like JavaDoc.
 # If set to NO, the detailed description appears after the member 
@@ -183,10 +155,143 @@ DETAILS_AT_TOP         = Yes
 
 # If the INHERIT_DOCS tag is set to YES (the default) then an undocumented 
 # member inherits the documentation from any documented member that it 
-# reimplements.
+# re-implements.
 
 INHERIT_DOCS           = 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
+
+# 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.
+
+ALIASES                = 
+
+# 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 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
+
+#---------------------------------------------------------------------------
+# 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            = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
+# will be included in the documentation.
+
+EXTRACT_PRIVATE        = NO
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file 
+# will be included in the documentation.
+
+EXTRACT_STATIC         = NO
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) 
+# defined locally in source files will be included in the documentation. 
+# If set to NO only classes defined in header files are included.
+
+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  = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all 
+# undocumented members of documented classes, files or namespaces. 
+# If set to NO (the default) these members will be included in the 
+# various overviews, but no documentation section is generated. 
+# This option has no effect if EXTRACT_ALL is enabled.
+
+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          = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate 
+# file names in lower-case letters. If set to YES upper-case letters are also 
+# allowed. This is useful if you have classes or files whose names only differ 
+# in case and if your file system supports case sensitive file names. Windows 
+# 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 INLINE_INFO tag is set to YES (the default) then a tag [inline] 
 # is inserted in the documentation for inline members.
 
@@ -199,17 +304,22 @@ INLINE_INFO            = YES
 
 SORT_MEMBER_DOCS       = NO
 
-# 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.
+# 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.
 
-DISTRIBUTE_GROUP_DOC   = NO
+SORT_BRIEF_DOCS        = 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.
+# 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.
 
-TAB_SIZE               = 8
+SORT_BY_SCOPE_NAME     = NO
 
 # The GENERATE_TODOLIST tag can be used to enable (YES) or 
 # disable (NO) the todo list. This list is created by putting \todo 
@@ -229,14 +339,11 @@ GENERATE_TESTLIST      = YES
 
 GENERATE_BUGLIST       = YES
 
-# 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.
+# 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.
 
-ALIASES                = 
+GENERATE_DEPRECATEDLIST= YES
 
 # The ENABLED_SECTIONS tag can be used to enable conditional 
 # documentation sections, marked by \if sectionname ... \endif.
@@ -244,28 +351,14 @@ ALIASES                =
 ENABLED_SECTIONS       = 
 
 # The MAX_INITIALIZER_LINES tag determines the maximum number of lines 
-# the initial value of a variable or define consist of for it to appear in 
+# the initial value of a variable or define 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 defines in the 
 # documentation can be controlled using \showinitializer or \hideinitializer 
 # command in the documentation regardless of this setting.
 
-MAX_INITIALIZER_LINES  = 
-
-# 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
+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 
@@ -294,6 +387,13 @@ WARNINGS               = No
 
 WARN_IF_UNDOCUMENTED   = No
 
+# 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_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 
@@ -323,7 +423,7 @@ INPUT                  = .
 # and *.h) to filter out the source-files in the directories. If left 
 # blank the following patterns are tested: 
 # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx *.hpp 
-# *.h++ *.idl *.odl
+# *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm
 
 FILE_PATTERNS          = *.h \
                          *.cpp
@@ -338,7 +438,7 @@ RECURSIVE              = NO
 # 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.
 
-EXCLUDE                = 
+EXCLUDE                = adhoc.cpp
 
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or directories 
 # that are symbolic links (a Unix filesystem feature) are excluded from the input.
@@ -355,7 +455,7 @@ EXCLUDE_PATTERNS       =
 # directories that contain example code fragments that are included (see 
 # the \include command).
 
-EXAMPLE_PATH           = 
+EXAMPLE_PATH           = .
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the 
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
@@ -388,7 +488,7 @@ INPUT_FILTER           =
 
 # 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.
+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
 
 FILTER_SOURCE_FILES    = NO
 
@@ -397,7 +497,9 @@ FILTER_SOURCE_FILES    = NO
 #---------------------------------------------------------------------------
 
 # If the SOURCE_BROWSER tag is set to YES then a list of source files will 
-# be generated. Documented entities will be cross-referenced with these sources.
+# 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
 
@@ -406,6 +508,12 @@ SOURCE_BROWSER         = YES
 
 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 (the default) 
 # then for each documented function all documented 
 # functions referencing it will be listed.
@@ -418,6 +526,12 @@ REFERENCED_BY_RELATION = YES
 
 REFERENCES_RELATION    = YES
 
+# 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
 #---------------------------------------------------------------------------
@@ -474,10 +588,12 @@ HTML_HEADER            =
 
 HTML_FOOTER            = 
 
-# The HTML_STYLESHEET tag can be used to specify a user defined cascading 
+# 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
+# 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        = 
 
@@ -494,6 +610,20 @@ HTML_ALIGN_MEMBERS     = YES
 
 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).
@@ -507,7 +637,7 @@ GENERATE_CHI           = NO
 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.
+# to the contents of the HTML help documentation and to the tree view.
 
 TOC_EXPAND             = NO
 
@@ -525,10 +655,9 @@ ENUM_VALUES_PER_LINE   = 4
 # If the GENERATE_TREEVIEW tag 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 and frames is required (for instance Mozilla, Netscape 4.0+, 
-# or Internet explorer 4.0+). Note that for large projects the tree generation 
-# can take a very long time. In such cases it is better to disable this feature. 
-# Windows users are probably better off using the HTML help feature.
+# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, 
+# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are 
+# probably better off using the HTML help feature.
 
 GENERATE_TREEVIEW      = NO
 
@@ -553,7 +682,8 @@ GENERATE_LATEX         = NO
 
 LATEX_OUTPUT           = 
 
-# 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.
+# 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.
 
 LATEX_CMD_NAME         = latex
 
@@ -607,12 +737,18 @@ USE_PDFLATEX           = NO
 
 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
+
 #---------------------------------------------------------------------------
 # 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 optimised for Word 97 and may not look very pretty with 
+# The RTF output is optimized for Word 97 and may not look very pretty with 
 # other RTF readers or editors.
 
 GENERATE_RTF           = NO
@@ -639,7 +775,7 @@ COMPACT_RTF            = NO
 RTF_HYPERLINKS         = NO
 
 # Load stylesheet definitions from file. Syntax is similar to doxygen's 
-# config file, i.e. a series of assigments. You only have to provide 
+# 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    = 
@@ -683,12 +819,35 @@ MAN_LINKS              = NO
 
 # 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. Note that this 
-# feature is still experimental and incomplete at the 
-# moment.
+# 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
 #---------------------------------------------------------------------------
@@ -702,6 +861,39 @@ GENERATE_XML           = NO
 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   
 #---------------------------------------------------------------------------
 
@@ -754,7 +946,7 @@ PREDEFINED             = _WIN32 \
                          __FreeBSD__ \
                          CRYPTOPP_DOXYGEN_PROCESSING
 
-# If the MACRO_EXPANSION and EXPAND_PREDEF_ONLY tags are set to YES then 
+# 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.
@@ -763,16 +955,30 @@ EXPAND_AS_DEFINED      =
 
 # If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then 
 # doxygen's preprocessor will remove all function-like macros that are alone 
-# on a line and do not end with a semicolon. Such function macros are typically 
-# used for boiler-plate code, and will confuse the parser if not removed.
+# on a line, have an all uppercase name, and do not end with a semicolon. Such 
+# function macros are typically used for boiler-plate code, and will confuse the 
+# parser if not removed.
 
 SKIP_FUNCTION_MACROS   = YES
 
 #---------------------------------------------------------------------------
-# Configuration::addtions related to external references   
+# Configuration::additions related to external references   
 #---------------------------------------------------------------------------
 
-# The TAGFILES tag can be used to specify one or more tagfiles.
+# 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               = 
 
@@ -803,10 +1009,10 @@ PERL_PATH              = /usr/bin/perl
 #---------------------------------------------------------------------------
 
 # 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 
+# 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 is superceded by the HAVE_DOT option below. This is only a fallback. It is 
-# recommended to install and use dot, since it yield more powerful graphs.
+# option is superseded by the HAVE_DOT option below. This is only a fallback. It is 
+# recommended to install and use dot, since it yields more powerful graphs.
 
 CLASS_DIAGRAMS         = YES
 
@@ -837,6 +1043,12 @@ CLASS_GRAPH            = YES
 
 COLLABORATION_GRAPH    = 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.
 
@@ -856,6 +1068,14 @@ INCLUDE_GRAPH          = YES
 
 INCLUDED_BY_GRAPH      = YES
 
+# If the CALL_GRAPH and HAVE_DOT tags 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             = NO
+
 # If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen 
 # will graphical hierarchy of all classes instead of a textual one.
 
@@ -894,6 +1114,17 @@ MAX_DOT_GRAPH_WIDTH    = 1024
 
 MAX_DOT_GRAPH_HEIGHT   = 1024
 
+# 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 a graph may be further truncated if the graph's image dimensions are 
+# not sufficient to fit the graph (see MAX_DOT_GRAPH_WIDTH and MAX_DOT_GRAPH_HEIGHT). 
+# If 0 is used for the depth value (the default), the graph is not depth-constrained.
+
+MAX_DOT_GRAPH_DEPTH    = 0
+
 # 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.
@@ -901,51 +1132,16 @@ MAX_DOT_GRAPH_HEIGHT   = 1024
 GENERATE_LEGEND        = YES
 
 # If the DOT_CLEANUP tag is set to YES (the default) Doxygen will 
-# remove the intermedate dot files that are used to generate 
+# remove the intermediate dot files that are used to generate 
 # the various graphs.
 
 DOT_CLEANUP            = YES
 
 #---------------------------------------------------------------------------
-# Configuration::addtions related to the search engine   
+# Configuration::additions related to the search engine   
 #---------------------------------------------------------------------------
 
 # The SEARCHENGINE tag specifies whether or not a search engine should be 
 # used. If set to NO the values of all tags below this one will be ignored.
 
 SEARCHENGINE           = NO
-
-# The CGI_NAME tag should be the name of the CGI script that 
-# starts the search engine (doxysearch) with the correct parameters. 
-# A script with this name will be generated by doxygen.
-
-CGI_NAME               = search.cgi
-
-# The CGI_URL tag should be the absolute URL to the directory where the 
-# cgi binaries are located. See the documentation of your http daemon for 
-# details.
-
-CGI_URL                = 
-
-# The DOC_URL tag should be the absolute URL to the directory where the 
-# documentation is located. If left blank the absolute path to the 
-# documentation, with file:// prepended to it, will be used.
-
-DOC_URL                = 
-
-# The DOC_ABSPATH tag should be the absolute path to the directory where the 
-# documentation is located. If left blank the directory on the local machine 
-# will be used.
-
-DOC_ABSPATH            = 
-
-# The BIN_ABSPATH tag must point to the directory where the doxysearch binary 
-# is installed.
-
-BIN_ABSPATH            = /usr/local/bin/
-
-# The EXT_DOC_PATHS tag can be used to specify one or more paths to 
-# documentation generated for other projects. This allows doxysearch to search 
-# the documentation for these projects as well.
-
-EXT_DOC_PATHS          =