#---------------------------------------------------------------------------

# Project related configuration options

#---------------------------------------------------------------------------

DOXYFILE_ENCODING      = UTF-8

PROJECT_NAME           = "Scythe MCMC"

PROJECT_NUMBER         = 0.1

OUTPUT_DIRECTORY       = /Users/tristanz/Data/ScytheMCMC/docs/wiki

CREATE_SUBDIRS         = NO

OUTPUT_LANGUAGE        = English

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

ALWAYS_DETAILED_SEC    = NO

INLINE_INHERITED_MEMB  = NO

FULL_PATH_NAMES        = YES

STRIP_FROM_PATH        = /Users/tristanz/Data/ScytheMCMC/src

STRIP_FROM_INC_PATH    = 

SHORT_NAMES            = NO

JAVADOC_AUTOBRIEF      = NO

QT_AUTOBRIEF           = NO

MULTILINE_CPP_IS_BRIEF = NO

INHERIT_DOCS           = YES

SEPARATE_MEMBER_PAGES  = NO

TAB_SIZE               = 4

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

TYPEDEF_HIDES_STRUCT   = NO

SYMBOL_CACHE_SIZE      = 0

#---------------------------------------------------------------------------

# Build related configuration options

#---------------------------------------------------------------------------

EXTRACT_ALL            = YES

EXTRACT_PRIVATE        = NO

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

HIDE_IN_BODY_DOCS      = NO

INTERNAL_DOCS          = NO

CASE_SENSE_NAMES       = NO

HIDE_SCOPE_NAMES       = NO

SHOW_INCLUDE_FILES     = YES

INLINE_INFO            = YES

SORT_MEMBER_DOCS       = YES

SORT_BRIEF_DOCS        = NO

SORT_GROUP_NAMES       = NO

SORT_BY_SCOPE_NAME     = NO

GENERATE_TODOLIST      = YES

GENERATE_TESTLIST      = YES

GENERATE_BUGLIST       = YES

GENERATE_DEPRECATEDLIST= YES

ENABLED_SECTIONS       = 

MAX_INITIALIZER_LINES  = 30

SHOW_DIRECTORIES       = NO

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   = YES

WARN_IF_DOC_ERROR      = YES

WARN_NO_PARAMDOC       = NO

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

WARN_LOGFILE           = 

#---------------------------------------------------------------------------

# configuration options related to the input files

#---------------------------------------------------------------------------

INPUT                  = /Users/tristanz/Data/ScytheMCMC/src

INPUT_ENCODING         = UTF-8

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 \

                         *.vhd \

                         *.vhdl

RECURSIVE              = YES

EXCLUDE                = CovertUTF.h \

						 SimpleIni.h \

						 SimpleOpt.h

EXCLUDE_SYMLINKS       = NO

EXCLUDE_PATTERNS       = *ConvertUTF* \

						 *SimpleIni* \

						 *SimpleOpt*

EXCLUDE_SYMBOLS        = 

EXAMPLE_PATH           = 

EXAMPLE_PATTERNS       = *

EXAMPLE_RECURSIVE      = NO

IMAGE_PATH             = 

INPUT_FILTER           = 

FILTER_PATTERNS        = 

FILTER_SOURCE_FILES    = NO

#---------------------------------------------------------------------------

# configuration options related to source browsing

#---------------------------------------------------------------------------

SOURCE_BROWSER         = NO

INLINE_SOURCES         = NO

STRIP_CODE_COMMENTS    = 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

COLS_IN_ALPHA_INDEX    = 5

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_ALIGN_MEMBERS     = YES

HTML_DYNAMIC_SECTIONS  = NO

GENERATE_DOCSET        = NO

DOCSET_FEEDNAME        = "Doxygen generated docs"

DOCSET_BUNDLE_ID       = org.doxygen.Project

GENERATE_HTMLHELP      = NO

CHM_FILE               = 

HHC_LOCATION           = 

GENERATE_CHI           = NO

CHM_INDEX_ENCODING     = 

BINARY_TOC             = NO

TOC_EXPAND             = NO

GENERATE_QHP           = NO

QCH_FILE               = 

QHP_NAMESPACE          = 

QHP_VIRTUAL_FOLDER     = doc

QHP_CUST_FILTER_NAME   = 

QHP_CUST_FILTER_ATTRS  = 

QHP_SECT_FILTER_ATTRS  = 

QHG_LOCATION           = 

DISABLE_INDEX          = NO

ENUM_VALUES_PER_LINE   = 4

GENERATE_TREEVIEW      = NONE

TREEVIEW_WIDTH         = 250

FORMULA_FONTSIZE       = 10

#---------------------------------------------------------------------------

# configuration options related to the LaTeX output

#---------------------------------------------------------------------------

GENERATE_LATEX         = NO

LATEX_OUTPUT           = latex

LATEX_CMD_NAME         = latex

MAKEINDEX_CMD_NAME     = makeindex

COMPACT_LATEX          = NO

PAPER_TYPE             = a4wide

EXTRA_PACKAGES         = 

LATEX_HEADER           = 

PDF_HYPERLINKS         = YES

USE_PDFLATEX           = YES

LATEX_BATCHMODE        = NO

LATEX_HIDE_INDICES     = NO

LATEX_SOURCE_CODE      = NO

#---------------------------------------------------------------------------

# configuration options related to the RTF output

#---------------------------------------------------------------------------

GENERATE_RTF           = NO

RTF_OUTPUT             = rtf

COMPACT_RTF            = NO

RTF_HYPERLINKS         = NO

RTF_STYLESHEET_FILE    = 

RTF_EXTENSIONS_FILE    = 

#---------------------------------------------------------------------------

# configuration options related to the man page output

#---------------------------------------------------------------------------

GENERATE_MAN           = NO

MAN_OUTPUT             = man

MAN_EXTENSION          = .3

MAN_LINKS              = NO

#---------------------------------------------------------------------------

# configuration options related to the XML output

#---------------------------------------------------------------------------

GENERATE_XML           = NO

XML_OUTPUT             = xml

XML_SCHEMA             = 

XML_DTD                = 

XML_PROGRAMLISTING     = YES

#---------------------------------------------------------------------------

# configuration options for the AutoGen Definitions output

#---------------------------------------------------------------------------

GENERATE_AUTOGEN_DEF   = NO

#---------------------------------------------------------------------------

# configuration options related to the Perl module output

#---------------------------------------------------------------------------

GENERATE_PERLMOD       = NO

PERLMOD_LATEX          = NO

PERLMOD_PRETTY         = YES

PERLMOD_MAKEVAR_PREFIX = 

#---------------------------------------------------------------------------

# 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      = 

SKIP_FUNCTION_MACROS   = YES

#---------------------------------------------------------------------------

# Configuration::additions related to external references   

#---------------------------------------------------------------------------

TAGFILES               = 

GENERATE_TAGFILE       = 

ALLEXTERNALS           = NO

EXTERNAL_GROUPS        = YES

PERL_PATH              = /usr/bin/perl

#---------------------------------------------------------------------------

# Configuration options related to the dot tool   

#---------------------------------------------------------------------------

CLASS_DIAGRAMS         = NO

MSCGEN_PATH            = 

HIDE_UNDOC_RELATIONS   = YES

HAVE_DOT               = YES

DOT_FONTNAME           = FreeSans

DOT_FONTSIZE           = 10

DOT_FONTPATH           = 

CLASS_GRAPH            = YES

COLLABORATION_GRAPH    = YES

GROUP_GRAPHS           = YES

UML_LOOK               = NO

TEMPLATE_RELATIONS     = NO

INCLUDE_GRAPH          = YES

INCLUDED_BY_GRAPH      = YES

CALL_GRAPH             = NO

CALLER_GRAPH           = NO

GRAPHICAL_HIERARCHY    = YES

DIRECTORY_GRAPH        = YES

DOT_IMAGE_FORMAT       = png

DOT_PATH               = /usr/local/graphviz-2.14/bin

DOTFILE_DIRS           = 

DOT_GRAPH_MAX_NODES    = 50

MAX_DOT_GRAPH_DEPTH    = 0

DOT_TRANSPARENT        = NO

DOT_MULTI_TARGETS      = NO

GENERATE_LEGEND        = YES

DOT_CLEANUP            = YES

#---------------------------------------------------------------------------

# Options related to the search engine

#---------------------------------------------------------------------------

SEARCHENGINE           = NO