Update documentation

1 files changed, 119 insertions, 122 deletions

diff --git a/Doxyfile b/Doxyfile
index ab0ead2..e69fa61 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -1,53 +1,55 @@
-# Doxyfile 1.5.1-KDevelop
+# Doxyfile 1.7.4
 
 #---------------------------------------------------------------------------
 # Project related configuration options
 #---------------------------------------------------------------------------
-PROJECT_NAME           = "The Osirion Project"
-PROJECT_NUMBER         = 0.0.1
+DOXYFILE_ENCODING      = UTF-8
+PROJECT_NAME           = Project::OSiRiON
+PROJECT_NUMBER         =
+PROJECT_BRIEF          =
+PROJECT_LOGO           =
 OUTPUT_DIRECTORY       = apidocs
 CREATE_SUBDIRS         = NO
 OUTPUT_LANGUAGE        = English
-USE_WINDOWS_ENCODING   = YES
 BRIEF_MEMBER_DESC      = YES
 REPEAT_BRIEF           = YES
-ABBREVIATE_BRIEF       = "The $name class" \
-                         "The $name widget" \
-                         "The $name file" \
-                         is \
-                         provides \
-                         specifies \
-                         contains \
-                         represents \
-                         a \
-                         an \
-                         the
+ABBREVIATE_BRIEF       =
 ALWAYS_DETAILED_SEC    = NO
 INLINE_INHERITED_MEMB  = NO
-FULL_PATH_NAMES        = NO
-STRIP_FROM_PATH        = /home/ingar/projects/osirion/osirion-work
-STRIP_FROM_INC_PATH    = 
+FULL_PATH_NAMES        = YES
+STRIP_FROM_PATH        =
+STRIP_FROM_INC_PATH    =
 SHORT_NAMES            = NO
 JAVADOC_AUTOBRIEF      = NO
+QT_AUTOBRIEF           = NO
 MULTILINE_CPP_IS_BRIEF = NO
-DETAILS_AT_TOP         = NO
 INHERIT_DOCS           = YES
 SEPARATE_MEMBER_PAGES  = NO
-TAB_SIZE               = 2
-ALIASES                = 
+TAB_SIZE               = 8
+ALIASES                =
 OPTIMIZE_OUTPUT_FOR_C  = NO
 OPTIMIZE_OUTPUT_JAVA   = NO
+OPTIMIZE_FOR_FORTRAN   = NO
+OPTIMIZE_OUTPUT_VHDL   = NO
+EXTENSION_MAPPING      =
 BUILTIN_STL_SUPPORT    = NO
+CPP_CLI_SUPPORT        = NO
+SIP_SUPPORT            = NO
+IDL_PROPERTY_SUPPORT   = YES
 DISTRIBUTE_GROUP_DOC   = NO
 SUBGROUPING            = YES
+INLINE_GROUPED_CLASSES = NO
+TYPEDEF_HIDES_STRUCT   = NO
+SYMBOL_CACHE_SIZE      = 0
 #---------------------------------------------------------------------------
 # Build related configuration options
 #---------------------------------------------------------------------------
 EXTRACT_ALL            = NO
 EXTRACT_PRIVATE        = NO
-EXTRACT_STATIC         = YES
+EXTRACT_STATIC         = NO
 EXTRACT_LOCAL_CLASSES  = YES
 EXTRACT_LOCAL_METHODS  = NO
+EXTRACT_ANON_NSPACES   = NO
 HIDE_UNDOC_MEMBERS     = NO
 HIDE_UNDOC_CLASSES     = NO
 HIDE_FRIEND_COMPOUNDS  = NO
@@ -56,145 +58,139 @@ INTERNAL_DOCS          = NO
 CASE_SENSE_NAMES       = YES
 HIDE_SCOPE_NAMES       = NO
 SHOW_INCLUDE_FILES     = YES
+FORCE_LOCAL_INCLUDES   = NO
 INLINE_INFO            = YES
 SORT_MEMBER_DOCS       = YES
 SORT_BRIEF_DOCS        = NO
+SORT_MEMBERS_CTORS_1ST = NO
+SORT_GROUP_NAMES       = NO
 SORT_BY_SCOPE_NAME     = NO
+STRICT_PROTO_MATCHING  = NO
 GENERATE_TODOLIST      = YES
 GENERATE_TESTLIST      = YES
 GENERATE_BUGLIST       = YES
 GENERATE_DEPRECATEDLIST= YES
-ENABLED_SECTIONS       = 
+ENABLED_SECTIONS       =
 MAX_INITIALIZER_LINES  = 30
 SHOW_USED_FILES        = YES
 SHOW_DIRECTORIES       = NO
-FILE_VERSION_FILTER    = 
+SHOW_FILES             = YES
+SHOW_NAMESPACES        = YES
+FILE_VERSION_FILTER    =
+LAYOUT_FILE            =
 #---------------------------------------------------------------------------
 # configuration options related to warning and progress messages
 #---------------------------------------------------------------------------
 QUIET                  = NO
 WARNINGS               = YES
-WARN_IF_UNDOCUMENTED   = NO
+WARN_IF_UNDOCUMENTED   = YES
 WARN_IF_DOC_ERROR      = YES
 WARN_NO_PARAMDOC       = NO
 WARN_FORMAT            = "$file:$line: $text"
-WARN_LOGFILE           = 
+WARN_LOGFILE           =
 #---------------------------------------------------------------------------
 # configuration options related to the input files
 #---------------------------------------------------------------------------
 INPUT                  = src/
-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 \
-                         *.C \
-                         *.CC \
-                         *.C++ \
-                         *.II \
-                         *.I++ \
-                         *.H \
-                         *.HH \
-                         *.H++ \
-                         *.CS \
-                         *.PHP \
-                         *.PHP3 \
-                         *.M \
-                         *.MM \
-                         *.PY \
-                         *.C \
-                         *.H \
-                         *.tlh \
-                         *.diff \
-                         *.patch \
-                         *.moc \
-                         *.xpm \
-                         *.dox
+INPUT_ENCODING         = UTF-8
+FILE_PATTERNS          = *.cc *.h
 RECURSIVE              = YES
-EXCLUDE                = 
+EXCLUDE                =
 EXCLUDE_SYMLINKS       = NO
-EXCLUDE_PATTERNS       = 
-EXAMPLE_PATH           = 
-EXAMPLE_PATTERNS       = *
+EXCLUDE_PATTERNS       =
+EXCLUDE_SYMBOLS        =
+EXAMPLE_PATH           =
+EXAMPLE_PATTERNS       =
 EXAMPLE_RECURSIVE      = NO
-IMAGE_PATH             = 
-INPUT_FILTER           = 
-FILTER_PATTERNS        = 
+IMAGE_PATH             =
+INPUT_FILTER           =
+FILTER_PATTERNS        =
 FILTER_SOURCE_FILES    = NO
+FILTER_SOURCE_PATTERNS =
 #---------------------------------------------------------------------------
 # configuration options related to source browsing
 #---------------------------------------------------------------------------
 SOURCE_BROWSER         = NO
 INLINE_SOURCES         = NO
 STRIP_CODE_COMMENTS    = YES
-REFERENCED_BY_RELATION = YES
-REFERENCES_RELATION    = YES
+REFERENCED_BY_RELATION = NO
+REFERENCES_RELATION    = NO
 REFERENCES_LINK_SOURCE = YES
 USE_HTAGS              = NO
 VERBATIM_HEADERS       = YES
 #---------------------------------------------------------------------------
 # configuration options related to the alphabetical class index
 #---------------------------------------------------------------------------
-ALPHABETICAL_INDEX     = NO
+ALPHABETICAL_INDEX     = YES
 COLS_IN_ALPHA_INDEX    = 5
-IGNORE_PREFIX          = 
+IGNORE_PREFIX          =
 #---------------------------------------------------------------------------
 # configuration options related to the HTML output
 #---------------------------------------------------------------------------
 GENERATE_HTML          = YES
 HTML_OUTPUT            = html
 HTML_FILE_EXTENSION    = .html
-HTML_HEADER            = 
-HTML_FOOTER            = 
-HTML_STYLESHEET        = 
+HTML_HEADER            =
+HTML_FOOTER            =
+HTML_STYLESHEET        =
+HTML_EXTRA_FILES       =
+HTML_COLORSTYLE_HUE    = 220
+HTML_COLORSTYLE_SAT    = 100
+HTML_COLORSTYLE_GAMMA  = 80
+HTML_TIMESTAMP         = YES
 HTML_ALIGN_MEMBERS     = YES
+HTML_DYNAMIC_SECTIONS  = NO
+GENERATE_DOCSET        = NO
+DOCSET_FEEDNAME        = "Doxygen generated docs"
+DOCSET_BUNDLE_ID       = org.doxygen.Project
+DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
+DOCSET_PUBLISHER_NAME  = Publisher
 GENERATE_HTMLHELP      = NO
-CHM_FILE               = 
-HHC_LOCATION           = 
+CHM_FILE               =
+HHC_LOCATION           =
 GENERATE_CHI           = NO
+CHM_INDEX_ENCODING     =
 BINARY_TOC             = NO
 TOC_EXPAND             = NO
+GENERATE_QHP           = NO
+QCH_FILE               =
+QHP_NAMESPACE          = org.doxygen.Project
+QHP_VIRTUAL_FOLDER     = doc
+QHP_CUST_FILTER_NAME   =
+QHP_CUST_FILTER_ATTRS  =
+QHP_SECT_FILTER_ATTRS  =
+QHG_LOCATION           =
+GENERATE_ECLIPSEHELP   = NO
+ECLIPSE_DOC_ID         = org.doxygen.Project
 DISABLE_INDEX          = NO
 ENUM_VALUES_PER_LINE   = 4
 GENERATE_TREEVIEW      = NO
+USE_INLINE_TREES       = NO
 TREEVIEW_WIDTH         = 250
+EXT_LINKS_IN_WINDOW    = NO
+FORMULA_FONTSIZE       = 10
+FORMULA_TRANSPARENT    = YES
+USE_MATHJAX            = NO
+MATHJAX_RELPATH        = http://www.mathjax.org/mathjax
+SEARCHENGINE           = YES
+SERVER_BASED_SEARCH    = NO
 #---------------------------------------------------------------------------
 # configuration options related to the LaTeX output
 #---------------------------------------------------------------------------
-GENERATE_LATEX         = NO
+GENERATE_LATEX         = YES
 LATEX_OUTPUT           = latex
 LATEX_CMD_NAME         = latex
 MAKEINDEX_CMD_NAME     = makeindex
 COMPACT_LATEX          = NO
-PAPER_TYPE             = a4wide
-EXTRA_PACKAGES         = 
-LATEX_HEADER           = 
-PDF_HYPERLINKS         = NO
-USE_PDFLATEX           = NO
+PAPER_TYPE             = a4
+EXTRA_PACKAGES         =
+LATEX_HEADER           =
+LATEX_FOOTER           =
+PDF_HYPERLINKS         = YES
+USE_PDFLATEX           = YES
 LATEX_BATCHMODE        = NO
 LATEX_HIDE_INDICES     = NO
+LATEX_SOURCE_CODE      = NO
 #---------------------------------------------------------------------------
 # configuration options related to the RTF output
 #---------------------------------------------------------------------------
@@ -202,8 +198,8 @@ GENERATE_RTF           = NO
 RTF_OUTPUT             = rtf
 COMPACT_RTF            = NO
 RTF_HYPERLINKS         = NO
-RTF_STYLESHEET_FILE    = 
-RTF_EXTENSIONS_FILE    = 
+RTF_STYLESHEET_FILE    =
+RTF_EXTENSIONS_FILE    =
 #---------------------------------------------------------------------------
 # configuration options related to the man page output
 #---------------------------------------------------------------------------
@@ -216,9 +212,9 @@ MAN_LINKS              = NO
 #---------------------------------------------------------------------------
 GENERATE_XML           = NO
 XML_OUTPUT             = xml
-XML_SCHEMA             = 
-XML_DTD                = 
-XML_PROGRAMLISTING     = NO
+XML_SCHEMA             =
+XML_DTD                =
+XML_PROGRAMLISTING     = YES
 #---------------------------------------------------------------------------
 # configuration options for the AutoGen Definitions output
 #---------------------------------------------------------------------------
@@ -229,38 +225,43 @@ GENERATE_AUTOGEN_DEF   = NO
 GENERATE_PERLMOD       = NO
 PERLMOD_LATEX          = NO
 PERLMOD_PRETTY         = YES
-PERLMOD_MAKEVAR_PREFIX = 
+PERLMOD_MAKEVAR_PREFIX =
 #---------------------------------------------------------------------------
-# Configuration options related to the preprocessor   
+# Configuration options related to the preprocessor
 #---------------------------------------------------------------------------
 ENABLE_PREPROCESSING   = YES
 MACRO_EXPANSION        = NO
 EXPAND_ONLY_PREDEF     = NO
 SEARCH_INCLUDES        = YES
-INCLUDE_PATH           = 
-INCLUDE_FILE_PATTERNS  = 
-PREDEFINED             = 
-EXPAND_AS_DEFINED      = 
+INCLUDE_PATH           =
+INCLUDE_FILE_PATTERNS  =
+PREDEFINED             =
+EXPAND_AS_DEFINED      =
 SKIP_FUNCTION_MACROS   = YES
 #---------------------------------------------------------------------------
-# Configuration::additions related to external references   
+# Configuration::additions related to external references
 #---------------------------------------------------------------------------
-TAGFILES               = 
-GENERATE_TAGFILE       = osirion.tag
+TAGFILES               =
+GENERATE_TAGFILE       =
 ALLEXTERNALS           = NO
 EXTERNAL_GROUPS        = YES
 PERL_PATH              = /usr/bin/perl
 #---------------------------------------------------------------------------
-# Configuration options related to the dot tool   
+# Configuration options related to the dot tool
 #---------------------------------------------------------------------------
 CLASS_DIAGRAMS         = YES
+MSCGEN_PATH            =
 HIDE_UNDOC_RELATIONS   = YES
-HAVE_DOT               = YES
+HAVE_DOT               = NO
+DOT_NUM_THREADS        = 0
+DOT_FONTNAME           = Helvetica
+DOT_FONTSIZE           = 10
+DOT_FONTPATH           =
 CLASS_GRAPH            = YES
 COLLABORATION_GRAPH    = YES
 GROUP_GRAPHS           = YES
 UML_LOOK               = NO
-TEMPLATE_RELATIONS     = YES
+TEMPLATE_RELATIONS     = NO
 INCLUDE_GRAPH          = YES
 INCLUDED_BY_GRAPH      = YES
 CALL_GRAPH             = NO
@@ -268,16 +269,12 @@ CALLER_GRAPH           = NO
 GRAPHICAL_HIERARCHY    = YES
 DIRECTORY_GRAPH        = YES
 DOT_IMAGE_FORMAT       = png
-DOT_PATH               = 
-DOTFILE_DIRS           = 
-MAX_DOT_GRAPH_WIDTH    = 1024
-MAX_DOT_GRAPH_HEIGHT   = 1024
+DOT_PATH               =
+DOTFILE_DIRS           =
+MSCFILE_DIRS           =
+DOT_GRAPH_MAX_NODES    = 50
 MAX_DOT_GRAPH_DEPTH    = 0
 DOT_TRANSPARENT        = NO
 DOT_MULTI_TARGETS      = NO
 GENERATE_LEGEND        = YES
 DOT_CLEANUP            = YES
-#---------------------------------------------------------------------------
-# Configuration::additions related to the search engine   
-#---------------------------------------------------------------------------
-SEARCHENGINE           = NO