Changeset 3092 in Sophya for trunk/SophyaLib/Manual

Timestamp:

Oct 11, 2006, 6:47:06 PM (19 years ago)

Author:

ansari

Message:

petites corrections ds la doc (dont numero de version V_Sep2006) - Reza 11/10/2006

Location:

trunk/SophyaLib/Manual

Files:

• dox_sophya.conf (modified) (11 diffs)
• piapp.tex (modified) (1 diff)
• sophya.tex (modified) (2 diffs)

trunk/SophyaLib/Manual/dox_sophya.conf

@@ -1 @@
-# Doxyfile 1.1.1
-# The format is:       TAG = value [value, ...]
+# Doxyfile 1.4.3
+
+# 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 (" ")
 
 #---------------------------------------------------------------------------
-# General configuration options
-#---------------------------------------------------------------------------
-
-# The PROJECT_NAME tag is a single word (or a sequence of word surrounded
-# by quotes) that should identify the project. 
-
-PROJECT_NAME         = SOPHYA
-
-# The PROJECT_NUMBER tag can be used to enter a project or revision number.
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
+# by quotes) that should identify the project.
+
+PROJECT_NAME           = SOPHYA
+
+# 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       = 
+PROJECT_NUMBER         = 
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
@@ -23 +31 @@
 # where doxygen was started. If left blank the current directory will be used.
 
-OUTPUT_DIRECTORY     = .
-
-# 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.
+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: 
-# Dutch, French, Italian, Czech, Swedish, German and Japanese
-
-OUTPUT_LANGUAGE      = English
-
-# 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
-
-# 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
-
-# If the EXTRACT_ALL tag is set to YES all classes and functions will be
-# included in the documentation, even if no documentation was available.
-
-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      = NO
-
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
-# undocumented members inside documented classes or files.
-
-HIDE_UNDOC_MEMBERS   = NO
-
-# If the HIDE_UNDOC_CLASSESS tag is set to YES, Doxygen will hide all
-# undocumented classes.
-
-HIDE_UNDOC_CLASSES   = NO
-
-# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
+# 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
+
+# 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).
+
+USE_WINDOWS_ENCODING   = NO
+
+# 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).
+# 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.
+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
-
-# 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
+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.
 
-ALWAYS_DETAILED_SEC  = NO
-
-# 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
+ALWAYS_DETAILED_SEC    = NO
+
+# 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  = NO
+
+# 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      = 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
-# only done if one of the specified strings matches the left-hand part of
-# the path.
-
-STRIP_FROM_PATH      = 
-
-# The INTERNAL_DOCS tag determines if documentation
+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 
+# 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 is your file systems 
+# 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 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 
+# documentation.
+
+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 
+# 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
+
+# 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.
+
+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            = YES
+
+# 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  = NO
+
+# 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.
+# to NO (the default) then the documentation will be excluded. 
 # Set it to YES to include the internal documentation.
 
-INTERNAL_DOCS        = NO
-
-# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
-# generate a class diagram (in Html and LaTeX) for classes with base or
-# super classes. Setting the tag to NO turns the diagrams off.
-
-CLASS_DIAGRAMS       = YES
-
-# 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.
-
-SOURCE_BROWSER       = NO
-
-# 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  = YES
-
-# If the CASE_SENSE_NAMES tag is set to NO (the default) 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.
-
-CASE_SENSE_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
+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 
+# 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 JAVADOC_AUTOBRIEF tag is set to YES (the default) 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-style will
-# behave just like the Qt-style comments.
-
-JAVADOC_AUTOBRIEF    = 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.
-
-INHERIT_DOCS         = YES
-
-# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
+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.
 
-INLINE_INFO          = YES
-
-# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
+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
+# alphabetically by member name. If set to NO the members will appear in 
 # declaration order.
 
-SORT_MEMBER_DOCS     = YES
-
-# 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
+SORT_MEMBER_DOCS       = NO
+
+# 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_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
+
+# 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 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  = 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.
+
+SHOW_DIRECTORIES       = 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 progam writes to standard output 
+# is used as the file version. See the manual for examples.
+
+FILE_VERSION_FILTER    = 
+
+#---------------------------------------------------------------------------
+# 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
+
+# This WARN_NO_PARAMDOC option can be abled 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       = NO
+
+# 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           = 
 
 #---------------------------------------------------------------------------
@@ -191 +451 @@
 # with spaces.
 
-INPUT = 
+INPUT                  = 
 
 # 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 all files are included.
-
-FILE_PATTERNS        = *.h *.cc *.c *.f *.cc *.C
-
-# 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.
+# blank the following patterns are tested: 
+# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx 
+# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm
+
+FILE_PATTERNS          = *.h \
+                         *.cc \
+                         *.c \
+                         *.f \
+                         *.cc \
+                         *.C
+
+# 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            = NO
-
-# The EXCLUDE tag can be used to specify files and/or directories that should
+RECURSIVE              = NO
+
+# 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.
 
-EXCLUDE              = 
-
-# 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
+EXCLUDE                = 
+
+# 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.
+
+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.
 
-EXCLUDE_PATTERNS     = 
+EXCLUDE_PATTERNS       = 
 
 # The EXAMPLE_PATH tag can be used to specify one or more files or 
@@ -222 +495 @@
 # the \include command).
 
-EXAMPLE_PATH         = 
-
-# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+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     = 
+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 
@@ -235 +515 @@
 # the \image command).
 
-IMAGE_PATH           = 
-
-# The INPUT_FILTER tag can be used to specify a program that doxygen should
+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.
-
-INPUT_FILTER = ./dox_filter
+# 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           = ./dox_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, INPUT_FILTER 
+# is applied to all files.
+
+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
+
+#---------------------------------------------------------------------------
+# 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         = NO
+
+# 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    = YES
+
+# 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.
+
+REFERENCED_BY_RELATION = YES
+
+# If the REFERENCES_RELATION tag is set to YES (the default) 
+# then for each documented function all documented entities 
+# called/used by that function will be listed.
+
+REFERENCES_RELATION    = 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    = 3
+
+# 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          = SOPHYA::
 
 #---------------------------------------------------------------------------
@@ -250 +617 @@
 #---------------------------------------------------------------------------
 
-# 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
+# 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
+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 
@@ -265 +638 @@
 # standard header.
 
-HTML_HEADER          = 
+HTML_HEADER            = 
 
 # The HTML_FOOTER tag can be used to specify a personal HTML footer for 
@@ -271 +644 @@
 # standard footer.
 
-HTML_FOOTER          = 
-
-# The HTML_STYLESHEET tag can be used to specify a user defined cascading
+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
-
-HTML_STYLESHEET      = 
-
-# 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
+# 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        = 
+
+# 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 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 compressed HTML help file (.chm)
+HTML_ALIGN_MEMBERS     = YES
+
+# 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 compressed HTML help file (.chm) 
 # of the generated HTML documentation.
 
-GENERATE_HTMLHELP    = NO
-
-#---------------------------------------------------------------------------
-# 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  = 3
-
-# 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        = SOPHYA::
+GENERATE_HTMLHELP      = NO
+
+# 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 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
+
+# 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
+
+# This tag can be used to set the number of enum values (range [1..20]) 
+# that doxygen will group on one line in the generated HTML documentation.
+
+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, 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
+
+# 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
 
 #---------------------------------------------------------------------------
@@ -320 +729 @@
 #---------------------------------------------------------------------------
 
-# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will 
 # generate Latex output.
 
-GENERATE_LATEX       = YES
-
-# 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
+GENERATE_LATEX         = YES
+
+# 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
-
-# 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
+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.
+
+LATEX_CMD_NAME         = 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
+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, a4wide, letter, legal and 
 # executive. If left blank a4wide will be used.
 
-PAPER_TYPE           = a4wide
-
-# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
+PAPER_TYPE             = a4wide
+
+# 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       = 
+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 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         = 
-
-# 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
+LATEX_HEADER           = 
+
+# 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       = NO
-
-# 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.
+PDF_HYPERLINKS         = NO
+
+# 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           = NO
+
+# 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
+
+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
 
 #---------------------------------------------------------------------------
@@ -372 +805 @@
 #---------------------------------------------------------------------------
 
-# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
-# For now this is experimental and is disabled by default. The RTF output
-# is optimised for Word 97 and may not look too pretty with other readers
-# or editors.
-
-#GENERATE_RTF         = YES
-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
+# 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
+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 a WORD or other.
-# programs which support those fields.
+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
+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
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will 
 # generate man pages
 
-# GENERATE_MAN         = YES
-GENERATE_MAN         = NO
-
-# 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
+GENERATE_MAN           = NO
+
+# 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
+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
-
-#---------------------------------------------------------------------------
-# 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
+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
+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      = NO
-
-# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
+# compilation will be performed. Macro expansion can be done in a controlled 
+# way by setting EXPAND_ONLY_PREDEF to YES.
+
+MACRO_EXPANSION        = NO
+
+# 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_PREDEFINED tags.
+
+EXPAND_ONLY_PREDEF     = NO
+
+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files 
 # in the INCLUDE_PATH (see below) will be search if 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
+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         = 
-
-# 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
+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.
-
-PREDEFINED           = 
-
-# 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 tag.
-
-EXPAND_ONLY_PREDEF   = NO
-
-#---------------------------------------------------------------------------
-# Configuration options related to external references 
-#---------------------------------------------------------------------------
-
-# The TAGFILES tag can be used to specify one or more tagfiles. 
-
-TAGFILES             = 
-
-# When a file name is specified after GENERATE_TAGFILE, doxygen will create
+# 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.
+
+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, 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::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
+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
-
-# The PERL_PATH should be the absolute path and name of the perl script
+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 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
+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 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
+
+# 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   = YES
+
+# 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             = NO
-
-# 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
+HAVE_DOT               = NO
+
+# 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 ENABLE_PREPROCESSING, 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 GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
+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     = NO
+
+# 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 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.
 
-GRAPHICAL_HIERARCHY  = YES
-
-#---------------------------------------------------------------------------
-# Configuration options related to the search engine 
+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 png, jpg, or gif
+# If left blank png will be used.
+
+DOT_IMAGE_FORMAT       = png
+
+# 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               = 
+
+# 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 MAX_DOT_GRAPH_WIDTH tag can be used to set the maximum allowed width 
+# (in pixels) of the graphs generated by dot. If a graph becomes larger than 
+# this value, doxygen will try to truncate the graph, so that it fits within 
+# the specified constraint. Beware that most browsers cannot cope with very 
+# large images.
+
+MAX_DOT_GRAPH_WIDTH    = 1024
+
+# The MAX_DOT_GRAPH_HEIGHT tag can be used to set the maximum allows height 
+# (in pixels) of the graphs generated by dot. If a graph becomes larger than 
+# this value, doxygen will try to truncate the graph, so that it fits within 
+# the specified constraint. Beware that most browsers cannot cope with very 
+# large images.
+
+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
+
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent 
+# background. This is disabled by default, which results in a white background. 
+# 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
+
+#---------------------------------------------------------------------------
+# Configuration::additions related to the search engine   
 #---------------------------------------------------------------------------
 
@@ -523 +1229 @@
 # 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          = 
-
-# 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        = 
+SEARCHENGINE           = NO

trunk/SophyaLib/Manual/piapp.tex

@@ -72 +72 @@
 \vspace{1cm}
 \begin{center}
-{\bf \Large piapp Version: 4.0 (V\_Jul2006) } 
+{\bf \Large piapp Version: 4.0 (V\_Sep2006) } 
 \end{center}
 \titrebp{5}

trunk/SophyaLib/Manual/sophya.tex

@@ -49 +49 @@
 \vspace{1cm}
 \begin{center}
-{\bf \Large Sophya Version: 2.0 (V\_Jul2006) }
+{\bf \Large Sophya Version: 2.0 (V\_Sep2006) }
 \end{center}
 \titrebp{1}
@@ -2012 +2012 @@
 OS & compiler \\
 \hline
-Linux           &     g++  (3.x 4.0)  \\
+Linux           &     g++  (3.x \, 4.0)  \\
 Linux  (SCL)          &     icc - Intel compiler (9.0)   \\
-MacOSX/Darwin 10.3 \, 10.4  &         g++ (3.3  4.0)\\
+MacOSX/Darwin (PowerPC) 10.3 \, 10.4  &         g++ (3.3  \, 4.0)\\
+MacOSX/Darwin (Intel) 10.4  &         g++ (4.0)\\
 HP/Compaq/DEC Tru64 ( OSF1)  &     cxx  (6.1  6.3)  \\
 SGI IRIX64       &     CC   (7.3)   \\