From 5adb8d9425a4662e790664faa82dce851efc577d Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Sat, 4 Feb 2006 00:38:24 +0000 Subject: [PATCH] massive code move mussa_gui_ was redundant so i moved all of those modules into gui/ Also I used the non-recursive gnu make style build system. And lastly there are some Doxygen compatible bits of doucmentation thrown in here. --- Doxyfile | 1228 +++++++++++++++++ Makefile | 128 +- flp.cc => flp.cxx | 0 flp.hh | 9 +- flp_seqcomp.cc => flp_seqcomp.cxx | 0 .../AnnotWindow.cxx | 2 +- .../AnnotWindow.hh | 2 +- mussa_gui_conn_view.cc => gui/ConnView.cxx | 6 +- mussa_gui_conn_view.hh => gui/ConnView.hh | 10 +- .../ConnWindow.cxx | 6 +- mussa_gui_conn_window.hh => gui/ConnWindow.hh | 19 +- .../MotifWindow.cxx | 2 +- .../MotifWindow.hh | 0 .../SeqTextWindow.cxx | 22 +- mussa_gui_seq_text.hh => gui/SeqTextWindow.hh | 9 +- mussa_gui_seq_view.cc => gui/SeqView.cxx | 3 +- mussa_gui_seq_view.hh => gui/SeqView.hh | 4 +- mussa_gui_seq.cc => gui/SeqWindow.cxx | 2 +- mussa_gui_seq.hh => gui/SeqWindow.hh | 2 +- .../SetupWindow.cxx | 4 +- .../SetupWindow.hh | 7 +- .../SubAnalysisWindow.cxx | 40 +- .../SubAnalysisWindow.hh | 10 +- gui/module.mk | 15 + module.mk | 16 + mussa.cc => mussa.cxx | 2 +- mussa_class.cc => mussa_class.cxx | 2 +- mussa_class.hh | 7 +- mussa_nway.cc => mussa_nway.cxx | 0 mussa_nway.hh | 3 - ..._nway_entropy.cc => mussa_nway_entropy.cxx | 0 mussa_nway_other.cc => mussa_nway_other.cxx | 0 mussa_nway_refine.cc => mussa_nway_refine.cxx | 0 seqcomp.cc => seqcomp.cxx | 3 + sequence.cc => sequence.cxx | 9 +- sequence.hh | 4 +- 36 files changed, 1386 insertions(+), 190 deletions(-) create mode 100644 Doxyfile rename flp.cc => flp.cxx (100%) rename flp_seqcomp.cc => flp_seqcomp.cxx (100%) rename mussa_gui_annot_window.cc => gui/AnnotWindow.cxx (99%) rename mussa_gui_annot_window.hh => gui/AnnotWindow.hh (97%) rename mussa_gui_conn_view.cc => gui/ConnView.cxx (99%) rename mussa_gui_conn_view.hh => gui/ConnView.hh (91%) rename mussa_gui_conn_window.cc => gui/ConnWindow.cxx (98%) rename mussa_gui_conn_window.hh => gui/ConnWindow.hh (80%) rename mussa_gui_motif_window.cc => gui/MotifWindow.cxx (99%) rename mussa_gui_motif_window.hh => gui/MotifWindow.hh (100%) rename mussa_gui_seq_text.cc => gui/SeqTextWindow.cxx (85%) rename mussa_gui_seq_text.hh => gui/SeqTextWindow.hh (86%) rename mussa_gui_seq_view.cc => gui/SeqView.cxx (99%) rename mussa_gui_seq_view.hh => gui/SeqView.hh (96%) rename mussa_gui_seq.cc => gui/SeqWindow.cxx (99%) rename mussa_gui_seq.hh => gui/SeqWindow.hh (98%) rename mussa_gui_load_window.cc => gui/SetupWindow.cxx (99%) rename mussa_gui_load_window.hh => gui/SetupWindow.hh (96%) rename mussa_gui_subana.cc => gui/SubAnalysisWindow.cxx (84%) rename mussa_gui_subana.hh => gui/SubAnalysisWindow.hh (90%) create mode 100644 gui/module.mk create mode 100644 module.mk rename mussa.cc => mussa.cxx (99%) rename mussa_class.cc => mussa_class.cxx (99%) rename mussa_nway.cc => mussa_nway.cxx (100%) rename mussa_nway_entropy.cc => mussa_nway_entropy.cxx (100%) rename mussa_nway_other.cc => mussa_nway_other.cxx (100%) rename mussa_nway_refine.cc => mussa_nway_refine.cxx (100%) rename seqcomp.cc => seqcomp.cxx (98%) rename sequence.cc => sequence.cxx (98%) diff --git a/Doxyfile b/Doxyfile new file mode 100644 index 0000000..1022908 --- /dev/null +++ b/Doxyfile @@ -0,0 +1,1228 @@ +# Doxyfile 1.4.4 + +# 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 (" ") + +#--------------------------------------------------------------------------- +# 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 = mussa + +# 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 = $Revision$ + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + +OUTPUT_DIRECTORY = doc + +# 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: +# 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). +# 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. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + +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 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 = YES + +# 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 = NO + +# 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 = NO + +# 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 = YES + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + +EXTRACT_STATIC = YES + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. When set to YES local +# methods, which are defined in the implementation section but not in +# the interface are included in the documentation. +# If set to NO (the default) only methods in the interface are included. + +EXTRACT_LOCAL_METHODS = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + +HIDE_SCOPE_NAMES = NO + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + +SHOW_INCLUDE_FILES = YES + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + +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 +# declaration order. + +SORT_MEMBER_DOCS = YES + +# 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. The default is YES. + +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 , where is the value of +# the FILE_VERSION_FILTER tag, and 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 = + +#--------------------------------------------------------------------------- +# configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + +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 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 = + +# 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 +# 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 = + +# 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. Note that the wildcards are matched +# against the file with absolute path, so to exclude all test directories +# for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + +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 = + +# 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 +# directories that contain image that are included in the documentation (see +# the \image command). + +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 , where +# is the value of the INPUT_FILTER tag, and 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 = + +# 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 = NO + +# 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 = 5 + +# 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 = + +#--------------------------------------------------------------------------- +# configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# 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 + +# 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 +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +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. 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) +# of the generated HTML documentation. + +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 + +#--------------------------------------------------------------------------- +# configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# 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 +# put in front of it. If left blank `latex' will be used as the default path. + +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 +# 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 +# packages that should be included in the LaTeX output. + +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 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 +# This makes the output suitable for online browsing using a pdf viewer. + +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 + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + +LATEX_HIDE_INDICES = NO + +#--------------------------------------------------------------------------- +# configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is 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 +# 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 WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + +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 +# generate man pages + +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 +# the generated man pages (default is the subroutine's section .3) + +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 +# names in the source code. If set to NO (the default) only conditional +# 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 +# the preprocessor. + +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. 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 +# will be listed. + +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 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 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 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 + +# 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 +#--------------------------------------------------------------------------- + +# The SEARCHENGINE tag specifies whether or not a search engine should be +# used. If set to NO the values of all tags below this one will be ignored. + +SEARCHENGINE = NO diff --git a/Makefile b/Makefile index 9c4282b..2315302 100644 --- a/Makefile +++ b/Makefile @@ -1,121 +1,31 @@ -# may the coders of gcc be infested with the fleas of ten thousand camels... +BASEDIR := ./ -CFLAGS=-ftemplate-depth-25 -#CFLAGS= -ftemplate-depth-25 -ggdb -#-Winline +CXXFLAGS := +LDFLAGS := -lfltk -OFLAG= -O +# each module will add to this, .os are derived from it +SRC := -# this is sufficient on debian machines -#LDFLAGS= -lfltk +include module.mk +include gui/module.mk -# this is what's needed on redhat machines -#LDFLAGS= -lfltk -L/usr/X11R6/lib -lX11 -# this is what's needed on fedora machines -#LDFLAGS= -lfltk -L/usr/X11R6/lib -lX11 -lXft +# process what the module.mks defined +OBJ := $(patsubst %.cxx,%.o, $(filter %.cxx,$(SRC))) +DEPS := $(OBJ:.o=.d) -# this is what's needed on gentoo machines -LDFLAGS= -L/usr/lib/fltk-1.1/ -lfltk -L/usr/X11R6/lib -lX11 -lXft - -# needed for apple/OS X -#LDFLAGS= -framework Carbon -framework ApplicationServices -lfltk - -# needed for cygwin/mingw32 -#CFLAGS=-ftemplate-depth-25 -mno-cygwin -#LDFLAGS= -lfltk -L/usr/lib/w32lib -lgdi32 -lws2_32 -luuid -lole32 +mussa: $(OBJ) + g++ -o $@ $(CXXFLAGS) $(LDFLAGS) $^ -# to check for memory leaks -MEMFLAG= -lefence +%.d: %.cxx + makedepend -o.d $(dirname $^) $(CFLAGS) $(CXXFILAGS) $^ -f- > $@ -all: mussa +%.o: %.cxx + g++ -c -o $@ $(CXXFLAGS) $^ -sequence.o : sequence.cc sequence.hh - $(CXX) $(CFLAGS) $(OFLAG) -c sequence.cc +include $(DEPS) -flp.o : flp.cc flp.hh - $(CXX) $(CFLAGS) $(OFLAG) -c flp.cc +clean: + -rm $(OBJ) $(DEPS) -flp_seqcomp.o : flp_seqcomp.cc flp.hh - $(CXX) $(CFLAGS) $(OFLAG) -c flp_seqcomp.cc -seqcomp : seqcomp.cc flp.o flp_seqcomp.o sequence.o - $(CXX) $(CFLAGS) $(OFLAG) -o seqcomp seqcomp.cc flp.o flp_seqcomp.o sequence.o - -mussa_nway.o : mussa_nway.cc mussa_nway.hh - $(CXX) $(CFLAGS) $(OFLAG) -c mussa_nway.cc - -mussa_nway_other.o : mussa_nway_other.cc mussa_nway.hh - $(CXX) $(CFLAGS) $(OFLAG) -c mussa_nway_other.cc - -mussa_nway_entropy.o : mussa_nway_entropy.cc mussa_nway.hh - $(CXX) $(CFLAGS) $(OFLAG) -c mussa_nway_entropy.cc - -mussa_class.o : mussa_class.cc mussa_class.hh - $(CXX) $(CFLAGS) -c mussa_class.cc - -mussan : sequence.o flp.o flp_seqcomp.o mussa_nway.o mussa_class.o \ - mussa_overlord.o mussa.cc - $(CXX) $(CFLAGS) -o mussa mussa.cc mussa_overlord.o \ - mussa_class.o mussa_nway.o flp_seqcomp.o flp.o sequence.o $(LDFLAGS) - -mussa_gui_seq_view.o : mussa_gui_seq_view.cc mussa_gui_seq_view.hh - $(CXX) $(CFLAGS) -c mussa_gui_seq_view.cc - -mussa_gui_seq.o : mussa_gui_seq.cc mussa_gui_seq.hh - $(CXX) $(CFLAGS) -c mussa_gui_seq.cc - -mussa_gui_seq_text.o : mussa_gui_seq_text.cc mussa_gui_seq_text.hh - $(CXX) $(CFLAGS) -c mussa_gui_seq_text.cc - -mussa_gui_motif_window.o : mussa_gui_motif_window.cc mussa_gui_motif_window.hh - $(CXX) $(CFLAGS) -c mussa_gui_motif_window.cc - -mussa_gui_annot_window.o : mussa_gui_annot_window.cc mussa_gui_annot_window.hh - $(CXX) $(CFLAGS) -c mussa_gui_annot_window.cc - -mussa_gui_load_window.o : mussa_gui_load_window.cc mussa_gui_load_window.hh - $(CXX) $(CFLAGS) -c mussa_gui_load_window.cc - -mussa_gui_subana.o : mussa_gui_subana.cc mussa_gui_subana.hh - $(CXX) $(CFLAGS) -c mussa_gui_subana.cc - -mussa_gui_conn_view.o : mussa_gui_conn_view.cc mussa_gui_conn_view.hh - $(CXX) $(CFLAGS) -O -c mussa_gui_conn_view.cc - -mussa_gui_conn_window.o : mussa_gui_conn_window.cc mussa_gui_conn_window.hh - $(CXX) $(CFLAGS) -c mussa_gui_conn_window.cc - -mussa : sequence.o flp.o flp_seqcomp.o \ - mussa_nway.o mussa_nway_other.o \ - mussa_nway_entropy.o mussa_class.o \ - mussa_gui_seq.o mussa_gui_seq_view.o \ - mussa_gui_motif_window.o mussa_gui_annot_window.o \ - mussa_gui_load_window.o mussa_gui_subana.o \ - mussa_gui_seq_text.o \ - mussa_gui_conn_view.o mussa_gui_conn_window.o \ - mussa.cc - $(CXX) $(CFLAGS) -o mussa mussa.cc \ - mussa_gui_conn_view.o mussa_gui_conn_window.o \ - mussa_gui_seq_text.o \ - mussa_gui_subana.o mussa_gui_load_window.o \ - mussa_gui_motif_window.o mussa_gui_annot_window.o \ - mussa_gui_seq.o mussa_gui_seq_view.o \ - mussa_class.o mussa_nway.o \ - mussa_nway_entropy.o mussa_nway_other.o \ - flp_seqcomp.o flp.o sequence.o $(LDFLAGS) - - -clean : - rm *.o - -cleaner : - rm *~ - -#mussa_overlord.o : mussa_overlord.cc mussa_overlord.hh -# $(CXX) $(CFLAGS) -c mussa_overlord.cc - - - -annot_test : sequence.o annot_test.cc - $(CXX) $(CFLAGS) -o annot_test annot_test.cc sequence.o diff --git a/flp.cc b/flp.cxx similarity index 100% rename from flp.cc rename to flp.cxx diff --git a/flp.hh b/flp.hh index 0929bd1..a34b51a 100644 --- a/flp.hh +++ b/flp.hh @@ -18,13 +18,16 @@ #include #include - -// FLP = Fixed Length Pairs (Data) -// vector of linked lists of the match type struct +//! FLP = Fixed Length Pairs (Data) +/*! + * vector of linked lists of the match type struct + */ class FLPs { private: + //! the number of base pairs used to compute this sliding window int window_size; + //! the minimum tnumber of base pairs need for this window to be saved. int hard_threshold; int seq1_length, seq2_length, seq1_win_num, seq2_win_num; std::string ana_type; diff --git a/flp_seqcomp.cc b/flp_seqcomp.cxx similarity index 100% rename from flp_seqcomp.cc rename to flp_seqcomp.cxx diff --git a/mussa_gui_annot_window.cc b/gui/AnnotWindow.cxx similarity index 99% rename from mussa_gui_annot_window.cc rename to gui/AnnotWindow.cxx index daa6a0f..e82a51a 100644 --- a/mussa_gui_annot_window.cc +++ b/gui/AnnotWindow.cxx @@ -8,7 +8,7 @@ // file for more information, or contact Tristan directly. -#include "mussa_gui_annot_window.hh" +#include "AnnotWindow.hh" #include #include diff --git a/mussa_gui_annot_window.hh b/gui/AnnotWindow.hh similarity index 97% rename from mussa_gui_annot_window.hh rename to gui/AnnotWindow.hh index bd1a60c..0303139 100644 --- a/mussa_gui_annot_window.hh +++ b/gui/AnnotWindow.hh @@ -20,7 +20,7 @@ #include #include -#include "mussa_gui_motif_window.hh" +#include "MotifWindow.hh" struct annot_color { diff --git a/mussa_gui_conn_view.cc b/gui/ConnView.cxx similarity index 99% rename from mussa_gui_conn_view.cc rename to gui/ConnView.cxx index 2c91da7..15cc250 100644 --- a/mussa_gui_conn_view.cc +++ b/gui/ConnView.cxx @@ -8,10 +8,14 @@ // file for more information, or contact Tristan directly. -#include "mussa_gui_conn_view.hh" +#include "ConnView.hh" #include #include + +#include +#include + using namespace std; void diff --git a/mussa_gui_conn_view.hh b/gui/ConnView.hh similarity index 91% rename from mussa_gui_conn_view.hh rename to gui/ConnView.hh index 75d5b5b..cf28ff7 100644 --- a/mussa_gui_conn_view.hh +++ b/gui/ConnView.hh @@ -14,10 +14,16 @@ #include #include -#include "mussa_gui_annot_window.hh" -#include "mussa_gui_subana.hh" +#include "sequence.hh" +#include "SeqView.hh" +#include "SeqWindow.hh" +#include "MotifWindow.hh" +#include "AnnotWindow.hh" // aparently for annot_color +#include "mussa_nway.hh" +#include +class Nway_Paths; class ConnView : public Fl_Box { public: diff --git a/mussa_gui_conn_window.cc b/gui/ConnWindow.cxx similarity index 98% rename from mussa_gui_conn_window.cc rename to gui/ConnWindow.cxx index 4574372..6a99cdc 100644 --- a/mussa_gui_conn_window.cc +++ b/gui/ConnWindow.cxx @@ -8,7 +8,7 @@ // file for more information, or contact Tristan directly. -#include "mussa_gui_conn_window.hh" +#include "ConnWindow.hh" #include using namespace std; @@ -155,7 +155,7 @@ ConnWindow::real_subana_cb() string subana_name; sub_analysis = new Mussa(); - subana_win = new SubanaWindow(500,400,"Sub Analysis Setup", sub_analysis, + subana_win = new SubAnalysisWindow(500,400,"Sub Analysis Setup", sub_analysis, an_analysis->the_Seqs); while(subana_win->visible()) @@ -184,7 +184,7 @@ seq_show_cb(Fl_Button* o, void* v) void ConnWindow::real_seq_show_cb() { - show_seq_win = new SeqTextWin(500,400,"Seq Show", an_analysis->the_Seqs); + show_seq_win = new SeqTextWindow(500,400,"Seq Show", an_analysis->the_Seqs); } void diff --git a/mussa_gui_conn_window.hh b/gui/ConnWindow.hh similarity index 80% rename from mussa_gui_conn_window.hh rename to gui/ConnWindow.hh index 5a1044f..35c9e05 100644 --- a/mussa_gui_conn_window.hh +++ b/gui/ConnWindow.hh @@ -12,14 +12,16 @@ #include -#include -#include +#include +#include +#include -#include "mussa_gui_conn_view.hh" -#include "mussa_gui_load_window.hh" -#include "mussa_gui_subana.hh" -#include "mussa_gui_seq_text.hh" +#include "ConnView.hh" +#include "SetupWindow.hh" +#include "SubAnalysisWindow.hh" +#include "SeqTextWindow.hh" +//! Window for showing the lines connecting the various sequences together class ConnWindow : public Fl_Double_Window { private: @@ -28,13 +30,14 @@ class ConnWindow : public Fl_Double_Window Fl_Menu_Button *file_menu; Fl_Menu_Button *view_menu; + Fl_Menu_Bar *menu_bar; Fl_Input *bar_input; Fl_Input *line_input; Fl_Input *thres_input; ConnView *conn_box; SetupWindow *setup_win; - SubanaWindow *subana_win; - SeqTextWin *show_seq_win; + SubAnalysisWindow *subana_win; + SeqTextWindow *show_seq_win; int padding, name_pad; std::string window_name; diff --git a/mussa_gui_motif_window.cc b/gui/MotifWindow.cxx similarity index 99% rename from mussa_gui_motif_window.cc rename to gui/MotifWindow.cxx index 302ab74..7667ec1 100644 --- a/mussa_gui_motif_window.cc +++ b/gui/MotifWindow.cxx @@ -8,7 +8,7 @@ // file for more information, or contact Tristan directly. -#include "mussa_gui_motif_window.hh" +#include "MotifWindow.hh" #include diff --git a/mussa_gui_motif_window.hh b/gui/MotifWindow.hh similarity index 100% rename from mussa_gui_motif_window.hh rename to gui/MotifWindow.hh diff --git a/mussa_gui_seq_text.cc b/gui/SeqTextWindow.cxx similarity index 85% rename from mussa_gui_seq_text.cc rename to gui/SeqTextWindow.cxx index 45554f6..4f1d059 100644 --- a/mussa_gui_seq_text.cc +++ b/gui/SeqTextWindow.cxx @@ -8,19 +8,19 @@ // file for more information, or contact Tristan directly. -#include "mussa_gui_seq_text.hh" +#include "SeqTextWindow.hh" #include using namespace std; void get_seq_cb(Fl_Button* o, void* v) { - SeqTextWin* T=(SeqTextWin*)v; + SeqTextWindow* T=(SeqTextWindow*)v; T->real_get_seq_cb(); } void -SeqTextWin::real_get_seq_cb() +SeqTextWindow::real_get_seq_cb() { string sub_seq_formatted; int seq_len, i, line_len; @@ -52,12 +52,12 @@ SeqTextWin::real_get_seq_cb() void set_seq_id_cb(Fl_Input* o, void* v) { - SeqTextWin* T=(SeqTextWin*)v; + SeqTextWindow* T=(SeqTextWindow*)v; T->real_set_seq_id_cb(o); } void -SeqTextWin::real_set_seq_id_cb(Fl_Input* o) +SeqTextWindow::real_set_seq_id_cb(Fl_Input* o) { seq_id = atoi(o->value()) - 1; // -1 since arrays start at 0 } @@ -68,12 +68,12 @@ SeqTextWin::real_set_seq_id_cb(Fl_Input* o) void set_seq_start_cb(Fl_Input* o, void* v) { - SeqTextWin* T=(SeqTextWin*)v; + SeqTextWindow* T=(SeqTextWindow*)v; T->real_set_seq_start_cb(o); } void -SeqTextWin::real_set_seq_start_cb(Fl_Input* o) +SeqTextWindow::real_set_seq_start_cb(Fl_Input* o) { seq_start = atoi(o->value()); } @@ -83,18 +83,18 @@ SeqTextWin::real_set_seq_start_cb(Fl_Input* o) void set_seq_end_cb(Fl_Input* o, void* v) { - SeqTextWin* T=(SeqTextWin*)v; + SeqTextWindow* T=(SeqTextWindow*)v; T->real_set_seq_end_cb(o); } void -SeqTextWin::real_set_seq_end_cb(Fl_Input* o) +SeqTextWindow::real_set_seq_end_cb(Fl_Input* o) { seq_end = atoi(o->value()); } -SeqTextWin::SeqTextWin(int w, int h, const char* title, +SeqTextWindow::SeqTextWindow(int w, int h, const char* title, vector some_Seqs):Fl_Window(w,h,title) { string a_name; @@ -136,7 +136,7 @@ SeqTextWin::SeqTextWin(int w, int h, const char* title, } -SeqTextWin::~SeqTextWin(){} +SeqTextWindow::~SeqTextWindow(){} /* cout << "fee\n"; diff --git a/mussa_gui_seq_text.hh b/gui/SeqTextWindow.hh similarity index 86% rename from mussa_gui_seq_text.hh rename to gui/SeqTextWindow.hh index 48b84b6..0000ec8 100644 --- a/mussa_gui_seq_text.hh +++ b/gui/SeqTextWindow.hh @@ -17,14 +17,15 @@ #include #include #include +#include -#include "mussa_gui_seq.hh" +#include "sequence.hh" -class SeqTextWin : public Fl_Window +class SeqTextWindow : public Fl_Window { public: - SeqTextWin(int w, int h, const char* title, std::vector some_Seqs); - ~SeqTextWin(); + SeqTextWindow(int w, int h, const char* title, std::vector some_Seqs); + ~SeqTextWindow(); Fl_Button* get_seq_but; Fl_Multiline_Output* seq_display; diff --git a/mussa_gui_seq_view.cc b/gui/SeqView.cxx similarity index 99% rename from mussa_gui_seq_view.cc rename to gui/SeqView.cxx index f4c83f2..1d1b547 100644 --- a/mussa_gui_seq_view.cc +++ b/gui/SeqView.cxx @@ -8,7 +8,8 @@ // file for more information, or contact Tristan directly. -#include "mussa_gui_seq.hh" +#include "SeqView.hh" +#include #include #include diff --git a/mussa_gui_seq_view.hh b/gui/SeqView.hh similarity index 96% rename from mussa_gui_seq_view.hh rename to gui/SeqView.hh index c66d368..a728d82 100644 --- a/mussa_gui_seq_view.hh +++ b/gui/SeqView.hh @@ -15,8 +15,8 @@ #include -#include "mussa_gui_motif_window.hh" -#include "mussa_gui_load_window.hh" +#include "MotifWindow.hh" +#include "SetupWindow.hh" class SeqView : public Fl_Box { diff --git a/mussa_gui_seq.cc b/gui/SeqWindow.cxx similarity index 99% rename from mussa_gui_seq.cc rename to gui/SeqWindow.cxx index a2cb19d..3e2c5bd 100644 --- a/mussa_gui_seq.cc +++ b/gui/SeqWindow.cxx @@ -8,7 +8,7 @@ // file for more information, or contact Tristan directly. -#include "mussa_gui_seq.hh" +#include "SeqWindow.hh" #include diff --git a/mussa_gui_seq.hh b/gui/SeqWindow.hh similarity index 98% rename from mussa_gui_seq.hh rename to gui/SeqWindow.hh index eaf1cc0..9ae346a 100644 --- a/mussa_gui_seq.hh +++ b/gui/SeqWindow.hh @@ -14,7 +14,7 @@ #include #include -#include "mussa_gui_seq_view.hh" +#include "SeqView.hh" #include #include diff --git a/mussa_gui_load_window.cc b/gui/SetupWindow.cxx similarity index 99% rename from mussa_gui_load_window.cc rename to gui/SetupWindow.cxx index 9f93525..0487628 100644 --- a/mussa_gui_load_window.cc +++ b/gui/SetupWindow.cxx @@ -8,8 +8,8 @@ // file for more information, or contact Tristan directly. -#include "mussa_gui_load_window.hh" - +#include "SetupWindow.hh" +#include "mussa_class.hh" #include #include diff --git a/mussa_gui_load_window.hh b/gui/SetupWindow.hh similarity index 96% rename from mussa_gui_load_window.hh rename to gui/SetupWindow.hh index 02e7727..42eccb7 100644 --- a/mussa_gui_load_window.hh +++ b/gui/SetupWindow.hh @@ -10,13 +10,16 @@ // under the GNU Public License; please see the included LICENSE.txt // file for more information, or contact Tristan directly. +#include +#include + #include #include #include #include -#include "mussa_class.hh" -#include "mussa_gui_load_window.hh" +class Mussa; +#include "SetupWindow.hh" class SetupWindow : public Fl_Window { diff --git a/mussa_gui_subana.cc b/gui/SubAnalysisWindow.cxx similarity index 84% rename from mussa_gui_subana.cc rename to gui/SubAnalysisWindow.cxx index cd29299..4831f93 100644 --- a/mussa_gui_subana.cc +++ b/gui/SubAnalysisWindow.cxx @@ -8,7 +8,7 @@ // file for more information, or contact Tristan directly. -#include "mussa_gui_subana.hh" +#include "SubAnalysisWindow.hh" #include using namespace std; @@ -16,14 +16,14 @@ using namespace std; void do_subana_cb(Fl_Button* o, void* v) { - SubanaWindow* T=(SubanaWindow*)v; + SubAnalysisWindow* T=(SubAnalysisWindow*)v; T->real_do_subana(); } // passes the parameters to the mussa class object and orders it to run void -SubanaWindow::real_do_subana() +SubAnalysisWindow::real_do_subana() { int i; string a_sequence, err_msg; @@ -68,12 +68,12 @@ void sub_start_in_cb1(Fl_Input* o, void* v) { sub_seq_data_instance * blah = (sub_seq_data_instance *) v; - SubanaWindow* T= blah->sw_ptr; + SubAnalysisWindow* T= blah->sw_ptr; T->real_sub_start_in_cb(o,blah->index); } void -SubanaWindow::real_sub_start_in_cb(Fl_Input* o, int i) +SubAnalysisWindow::real_sub_start_in_cb(Fl_Input* o, int i) { sub_seq_starts[i] = atoi(o->value()); } @@ -84,12 +84,12 @@ void sub_end_in_cb1(Fl_Input* o, void* v) { sub_seq_data_instance * blah = (sub_seq_data_instance *) v; - SubanaWindow* T= blah->sw_ptr; + SubAnalysisWindow* T= blah->sw_ptr; T->real_sub_end_in_cb(o,blah->index); } void -SubanaWindow::real_sub_end_in_cb(Fl_Input* o, int i) +SubAnalysisWindow::real_sub_end_in_cb(Fl_Input* o, int i) { sub_seq_ends[i] = atoi(o->value()); @@ -100,12 +100,12 @@ SubanaWindow::real_sub_end_in_cb(Fl_Input* o, int i) void set_ana_name_cb1(Fl_Input* o, void* v) { - SubanaWindow* T=(SubanaWindow*)v; + SubAnalysisWindow* T=(SubAnalysisWindow*)v; T->real_set_ana_name_cb(o); } void -SubanaWindow::real_set_ana_name_cb(Fl_Input* o) +SubAnalysisWindow::real_set_ana_name_cb(Fl_Input* o) { ana_name = o->value(); } @@ -115,12 +115,12 @@ SubanaWindow::real_set_ana_name_cb(Fl_Input* o) void set_win_size_cb1(Fl_Input* o, void* v) { - SubanaWindow* T=(SubanaWindow*)v; + SubAnalysisWindow* T=(SubAnalysisWindow*)v; T->real_set_win_size_cb(o); } void -SubanaWindow::real_set_win_size_cb(Fl_Input* o) +SubAnalysisWindow::real_set_win_size_cb(Fl_Input* o) { window = atoi(o->value()); } @@ -130,25 +130,25 @@ SubanaWindow::real_set_win_size_cb(Fl_Input* o) void set_threshold_cb1(Fl_Input* o, void* v) { - SubanaWindow* T=(SubanaWindow*)v; + SubAnalysisWindow* T=(SubAnalysisWindow*)v; T->real_set_threshold_cb(o); } void -SubanaWindow::real_set_threshold_cb(Fl_Input* o) +SubAnalysisWindow::real_set_threshold_cb(Fl_Input* o) { threshold = atoi(o->value()); } bool -SubanaWindow::done() +SubAnalysisWindow::done() { return all_done; } -SubanaWindow::SubanaWindow(int w, int h, const char* title,Mussa *the_analysis, +SubAnalysisWindow::SubAnalysisWindow(int w, int h, const char* title,Mussa *the_analysis, vector some_Seqs):Fl_Window(w,h,title) { string a_name; @@ -218,11 +218,11 @@ SubanaWindow::SubanaWindow(int w, int h, const char* title,Mussa *the_analysis, } -SubanaWindow::~SubanaWindow(){} +SubAnalysisWindow::~SubAnalysisWindow(){} void -SubanaWindow::add_seq_input(int i, string a_name) +SubAnalysisWindow::add_seq_input(int i, string a_name) { Fl_Input *start_input, *end_input; @@ -255,14 +255,14 @@ SubanaWindow::add_seq_input(int i, string a_name) cout << "fum\n"; */ -void SubanaWindow::print_cb(Fl_Button* o, void* v) +void SubAnalysisWindow::print_cb(Fl_Button* o, void* v) { - SubanaWindow* T=(SubanaWindow*)v; + SubAnalysisWindow* T=(SubAnalysisWindow*)v; T->print_cb_real(o,v); } -void SubanaWindow::print_cb_real(Fl_Button* , void*) +void SubAnalysisWindow::print_cb_real(Fl_Button* , void*) { cout << "ana_name: " << ana_name << endl; cout << "win: " << window << endl; diff --git a/mussa_gui_subana.hh b/gui/SubAnalysisWindow.hh similarity index 90% rename from mussa_gui_subana.hh rename to gui/SubAnalysisWindow.hh index e86e777..e4a9e2d 100644 --- a/mussa_gui_subana.hh +++ b/gui/SubAnalysisWindow.hh @@ -19,14 +19,14 @@ #include #include "mussa_class.hh" -#include "mussa_gui_seq_text.hh" +#include "SeqTextWindow.hh" -class SubanaWindow : public Fl_Window +class SubAnalysisWindow : public Fl_Window { public: - SubanaWindow(int w, int h, const char* title, Mussa *an_analysis, + SubAnalysisWindow(int w, int h, const char* title, Mussa *an_analysis, std::vector some_Seqs); - ~SubanaWindow(); + ~SubAnalysisWindow(); bool done(); @@ -75,7 +75,7 @@ class SubanaWindow : public Fl_Window struct sub_seq_data_instance { - SubanaWindow * sw_ptr; + SubAnalysisWindow * sw_ptr; int index; }; #endif diff --git a/gui/module.mk b/gui/module.mk new file mode 100644 index 0000000..31e1286 --- /dev/null +++ b/gui/module.mk @@ -0,0 +1,15 @@ +CURDIR := $(BASEDIR)gui/ + +SOURCES.cxx := AnnotWindow.cxx \ + ConnView.cxx \ + ConnWindow.cxx \ + MotifWindow.cxx \ + SeqTextWindow.cxx \ + SeqView.cxx \ + SeqWindow.cxx \ + SetupWindow.cxx \ + SubAnalysisWindow.cxx + +SRC += $(addprefix $(CURDIR), $(SOURCES.cxx)) +CXXFLAGS += -I$(CURDIR) + diff --git a/module.mk b/module.mk new file mode 100644 index 0000000..b86e711 --- /dev/null +++ b/module.mk @@ -0,0 +1,16 @@ +CURDIR := $(BASEDIR) + +SOURCES.cxx := flp.cxx \ + flp_seqcomp.cxx \ + mussa.cxx \ + mussa_class.cxx \ + mussa_nway.cxx \ + mussa_nway_entropy.cxx \ + mussa_nway_other.cxx \ + sequence.cxx + #seqcomp.cxx \ #(old seqcomp) + #mussa_nway_refine.cxx \ (broken code) + +SRC += $(addprefix $(CURDIR), $(SOURCES.cxx)) +CXXFLAGS += -I$(CURDIR) + diff --git a/mussa.cc b/mussa.cxx similarity index 99% rename from mussa.cc rename to mussa.cxx index d3d48f5..1ee7ae6 100644 --- a/mussa.cc +++ b/mussa.cxx @@ -8,7 +8,7 @@ // file for more information, or contact Tristan directly. -#include "mussa_gui_conn_window.hh" +#include "ConnWindow.hh" #include using namespace std; diff --git a/mussa_class.cc b/mussa_class.cxx similarity index 99% rename from mussa_class.cc rename to mussa_class.cxx index a6597ed..b571516 100644 --- a/mussa_class.cc +++ b/mussa_class.cxx @@ -13,7 +13,7 @@ // ---------------------------------------- #include "mussa_class.hh" - +#include "flp.hh" #include #include #include diff --git a/mussa_class.hh b/mussa_class.hh index efa6e91..334f10f 100644 --- a/mussa_class.hh +++ b/mussa_class.hh @@ -23,7 +23,6 @@ std::string int_to_str(int an_int); - class Mussa { friend class MussaOverlord; @@ -41,11 +40,11 @@ class Mussa bool win_override, thres_override; bool win_append, thres_append; - // sequence data + //! sequence data std::vector the_Seqs; - // the seqcomp data + //! the seqcomp data std::vector > all_comps; - // N-way data, ie the mussa results + //! N-way data, ie the mussa results Nway_Paths the_paths; diff --git a/mussa_nway.cc b/mussa_nway.cxx similarity index 100% rename from mussa_nway.cc rename to mussa_nway.cxx diff --git a/mussa_nway.hh b/mussa_nway.hh index 645a069..32209c4 100644 --- a/mussa_nway.hh +++ b/mussa_nway.hh @@ -20,7 +20,6 @@ #include "flp.hh" - class Nway_Paths { friend class ConnView; @@ -37,8 +36,6 @@ class Nway_Paths std::list > pathz; std::list > refined_pathz; - - public: Nway_Paths(); void setup(int sp_num, int w, int t); diff --git a/mussa_nway_entropy.cc b/mussa_nway_entropy.cxx similarity index 100% rename from mussa_nway_entropy.cc rename to mussa_nway_entropy.cxx diff --git a/mussa_nway_other.cc b/mussa_nway_other.cxx similarity index 100% rename from mussa_nway_other.cc rename to mussa_nway_other.cxx diff --git a/mussa_nway_refine.cc b/mussa_nway_refine.cxx similarity index 100% rename from mussa_nway_refine.cc rename to mussa_nway_refine.cxx diff --git a/seqcomp.cc b/seqcomp.cxx similarity index 98% rename from seqcomp.cc rename to seqcomp.cxx index f2bc843..c9c953e 100644 --- a/seqcomp.cc +++ b/seqcomp.cxx @@ -9,9 +9,12 @@ #include "flp.hh" +#include "sequence.hh" #include #include +using namespace std; + int main(int argc, char **argv) { Sequence seqA, seqB; diff --git a/sequence.cc b/sequence.cxx similarity index 98% rename from sequence.cc rename to sequence.cxx index 62025aa..d6f363e 100644 --- a/sequence.cc +++ b/sequence.cxx @@ -31,7 +31,14 @@ Sequence::Sequence() { } - +//! load a fasta file into a sequence +/*! + * \param file_path the location of the fasta file in the filesystem + * \param seq_num which sequence in the file to load + * \param start_index starting position in the fasta sequence, 0 for beginning + * \param end_index ending position in the fasta sequence, 0 for end + * \return error message, empty string if no error. (gag!) + */ string Sequence::load_fasta(string file_path, int seq_num, int start_index, int end_index) diff --git a/sequence.hh b/sequence.hh index 11a50cc..3bdc75a 100644 --- a/sequence.hh +++ b/sequence.hh @@ -22,14 +22,14 @@ // Sequence data class -using namespace std; - +//! Attach annotation information to a sequence track struct annot { int start, end; std::string name, type; }; +//! sequence track for mussa. class Sequence { friend class ConnView; -- 2.30.2