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The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# http://www.gnu.org/software/libiconv for the list of possible encodings. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or sequence of words) that should +# identify the project. Note that if you do not use Doxywizard you need +# to put quotes around the project name if it contains spaces. + +PROJECT_NAME = RNAlib-2.1.2 + +# 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 = + +# Using the PROJECT_BRIEF tag one can provide an optional one line description +# for a project that appears at the top of each page and should give viewer +# a quick idea about the purpose of the project. Keep the description short. + +PROJECT_BRIEF = + +# With the PROJECT_LOGO tag one can specify an logo or icon that is +# included in the documentation. The maximum height of the logo should not +# exceed 55 pixels and the maximum width should not exceed 200 pixels. +# Doxygen will copy the logo to the output directory. + +PROJECT_LOGO = + +# 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. 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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. 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This can be useful if your file system +# 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 regular Qt-style comments +# (thus requiring an explicit @brief command for a brief description.) + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will +# interpret the first line (until the first dot) of a Qt-style +# comment as the brief description. If set to NO, the comments +# will behave just like regular Qt-style comments (thus requiring +# an explicit \brief command for a brief description.) + +QT_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. 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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 = + +# This tag can be used to specify a number of word-keyword mappings (TCL only). +# A mapping has the form "name=value". For example adding +# "class=itcl::class" will allow you to use the command class in the +# itcl::class meaning. + +TCL_SUBST = + +# 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 = YES + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java +# sources only. 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The format is ext=language, where ext is a file extension, and language +# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C, +# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make +# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C +# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions +# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If MARKDOWN_SUPPORT is enabled (the default) then doxygen pre-processes all +# comments according to the Markdown format, which allows for more readable +# documentation. 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Alternatively, this can be done per class using +# the \nosubgrouping command. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and +# unions are shown inside the group in which they are included (e.g. using +# @ingroup) instead of on a separate page (for HTML and Man pages) or +# section (for LaTeX and RTF). + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and +# unions with only public data fields will be shown inline in the documentation +# of the scope in which they are defined (i.e. file, namespace, or group +# documentation), provided this scope is documented. If set to NO (the default), +# structs, classes, and unions are shown on a separate page (for HTML and Man +# pages) or section (for LaTeX and RTF). + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum +# is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically +# be useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. + +TYPEDEF_HIDES_STRUCT = YES + +# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to +# determine which symbols to keep in memory and which to flush to disk. +# When the cache is full, less often used symbols will be written to disk. +# For small to medium size projects (<1000 input files) the default value is +# probably good enough. For larger projects a too small cache size can cause +# doxygen to be busy swapping symbols to and from disk most of the time +# causing a significant performance penalty. +# If the system has enough physical memory increasing the cache will improve the +# performance by keeping more symbols in memory. Note that the value works on +# a logarithmic scale so increasing the size by one will roughly double the +# memory usage. The cache size is given by this formula: +# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, +# corresponding to a cache size of 2^16 = 65536 symbols. + +SYMBOL_CACHE_SIZE = 0 + +# Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be +# set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given +# their name and scope. Since this can be an expensive process and often the +# same symbol appear multiple times in the code, doxygen keeps a cache of +# pre-resolved symbols. If the cache is too small doxygen will become slower. +# If the cache is too large, memory is wasted. The cache size is given by this +# formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0, +# corresponding to a cache size of 2^16 = 65536 symbols. + +LOOKUP_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES + +EXTRACT_ALL = NO + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + +EXTRACT_PRIVATE = NO + +# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal scope will be included in the documentation. + +EXTRACT_PACKAGE = 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 this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base +# name of the file that contains the anonymous namespace. By default +# anonymous namespaces are hidden. + +EXTRACT_ANON_NSPACES = 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 = YES + +# 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 = NO + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen +# will list include files with double quotes in the documentation +# rather than with sharp brackets. + +FORCE_LOCAL_INCLUDES = NO + +# 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 = 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_MEMBERS_CTORS_1ST tag is set to YES then doxygen +# will sort the (brief and detailed) documentation of class members so that +# constructors and destructors are listed first. If set to NO (the default) +# the constructors will appear in the respective orders defined by +# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. +# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO +# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the +# hierarchy of group names into alphabetical order. If set to NO (the default) +# the group names will appear in their defined order. + +SORT_GROUP_NAMES = 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 + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to +# do proper type resolution of all parameters of a function it will reject a +# match between the prototype and the implementation of a member function even +# if there is only one candidate or it is obvious which candidate to choose +# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen +# will still accept a match between prototype and implementation in such cases. + +STRICT_PROTO_MATCHING = 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 macro 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 macros 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 + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. +# This will remove the Files entry from the Quick Index and from the +# Folder Tree View (if specified). The default is YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the +# Namespaces page. +# This will remove the Namespaces entry from the Quick Index +# and from the Folder Tree View (if specified). The default is YES. + +SHOW_NAMESPACES = 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 program writes to standard output +# is used as the file version. See the manual for examples. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. The create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. +# You can optionally specify a file name after the option, if omitted +# DoxygenLayout.xml will be used as the name of the layout file. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files +# containing the references data. This must be a list of .bib files. The +# .bib extension is automatically appended if omitted. Using this command +# requires the bibtex tool to be installed. See also +# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style +# of the bibliography can be controlled using LATEX_BIB_STYLE. To use this +# feature you need bibtex and perl available in the search path. + +CITE_BIB_FILES = viennarna.bib + +#--------------------------------------------------------------------------- +# 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 = YES + +# 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 + +# The WARN_NO_PARAMDOC option can be enabled 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 = mainpage.h ../H ../lib + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is +# also the default input encoding. Doxygen uses libiconv (or the iconv built +# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for +# the list of possible encodings. + +INPUT_ENCODING = UTF-8 + +# 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++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh +# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py +# *.f90 *.f *.for *.vhd *.vhdl + +FILE_PATTERNS = *.h + +# 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 be +# 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. +# Note that relative paths are relative to the directory from which doxygen is +# run. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or +# directories that are symbolic links (a Unix file system 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 EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# 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 or if +# non of the patterns match the file name, INPUT_FILTER is applied. + +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 + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) +# and it is also possible to disable source filtering for a specific pattern +# using *.ext= (so without naming a filter). This option only has effect when +# FILTER_SOURCE_FILES is enabled. + +FILTER_SOURCE_PATTERNS = + +#--------------------------------------------------------------------------- +# 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 +# then for each documented function all documented +# functions referencing it will be listed. + +REFERENCED_BY_RELATION = NO + +# If the REFERENCES_RELATION tag is set to YES +# then for each documented function all documented entities +# called/used by that function will be listed. + +REFERENCES_RELATION = NO + +# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) +# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from +# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will +# link to the source code. +# Otherwise they will link to the documentation. + +REFERENCES_LINK_SOURCE = 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 = 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. Note that when using a custom header you are responsible +# for the proper inclusion of any scripts and style sheets that doxygen +# needs, which is dependent on the configuration options used. +# It is advised to generate a default header using "doxygen -w html +# header.html footer.html stylesheet.css YourConfigFile" and then modify +# that header. Note that the header is subject to change so you typically +# have to redo this when upgrading to a newer version of doxygen or when +# changing the value of configuration settings such as GENERATE_TREEVIEW! + +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 +# style sheet in the HTML output directory as well, or it will be erased! + +HTML_STYLESHEET = + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that +# the files will be copied as-is; there are no commands or markers available. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. +# Doxygen will adjust the colors in the style sheet and background images +# according to this color. Hue is specified as an angle on a colorwheel, +# see http://en.wikipedia.org/wiki/Hue for more information. +# For instance the value 0 represents red, 60 is yellow, 120 is green, +# 180 is cyan, 240 is blue, 300 purple, and 360 is red again. +# The allowed range is 0 to 359. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of +# the colors in the HTML output. For a value of 0 the output will use +# grayscales only. A value of 255 will produce the most vivid colors. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to +# the luminance component of the colors in the HTML output. Values below +# 100 gradually make the output lighter, whereas values above 100 make +# the output darker. The value divided by 100 is the actual gamma applied, +# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2, +# and 100 does not change the gamma. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting +# this to NO can help when comparing the output of multiple runs. + +HTML_TIMESTAMP = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. For this to work a browser that supports +# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox +# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari). + +HTML_DYNAMIC_SECTIONS = YES + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of +# entries shown in the various tree structured indices initially; the user +# can expand and collapse entries dynamically later on. Doxygen will expand +# the tree to such a level that at most the specified number of entries are +# visible (unless a fully collapsed tree already exceeds this amount). +# So setting the number of entries 1 will produce a full collapsed tree by +# default. 0 is a special value representing an infinite number of entries +# and will result in a full expanded tree by default. + +HTML_INDEX_NUM_ENTRIES = 100 + +# If the GENERATE_DOCSET tag is set to YES, additional index files +# will be generated that can be used as input for Apple's Xcode 3 +# integrated development environment, introduced with OSX 10.5 (Leopard). +# To create a documentation set, doxygen will generate a Makefile in the +# HTML output directory. Running make will produce the docset in that +# directory and running "make install" will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find +# it at startup. +# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html +# for more information. + +GENERATE_DOCSET = NO + +# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the +# feed. A documentation feed provides an umbrella under which multiple +# documentation sets from a single provider (such as a company or product suite) +# can be grouped. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that +# should uniquely identify the documentation set bundle. This should be a +# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen +# will append .docset to the name. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher. + +DOCSET_PUBLISHER_NAME = Publisher + +# 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 compiled 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 = RNAlib-2.1.2.chm + +# 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 CHM_INDEX_ENCODING +# is used to encode HtmlHelp index (hhk), content (hhc) and project file +# content. + +CHM_INDEX_ENCODING = + +# 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 + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated +# that can be used as input for Qt's qhelpgenerator to generate a +# Qt Compressed Help (.qch) of the generated HTML documentation. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can +# be used to specify the file name of the resulting .qch file. +# The path specified is relative to the HTML output folder. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#namespace + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#virtual-folders + +QHP_VIRTUAL_FOLDER = doc + +# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to +# add. For more information please see +# http://doc.trolltech.com/qthelpproject.html#custom-filters + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see +# +# Qt Help Project / Custom Filters. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's +# filter section matches. +# +# Qt Help Project / Filter Attributes. + +QHP_SECT_FILTER_ATTRS = + +# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can +# be used to specify the location of Qt's qhelpgenerator. +# If non-empty doxygen will try to run qhelpgenerator on the generated +# .qhp file. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files +# will be generated, which together with the HTML files, form an Eclipse help +# plugin. To install this plugin and make it available under the help contents +# menu in Eclipse, the contents of the directory containing the HTML and XML +# files needs to be copied into the plugins directory of eclipse. The name of +# the directory within the plugins directory should be the same as +# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before +# the help appears. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have +# this name. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) +# at top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. Since the tabs have the same information as the +# navigation tree you can set this option to NO if you already set +# GENERATE_TREEVIEW to YES. + +DISABLE_INDEX = NO + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. +# If the tag value 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 (i.e. any modern browser). +# Windows users are probably better off using the HTML help feature. +# Since the tree basically has the same information as the tab index you +# could consider to set DISABLE_INDEX to NO when enabling this option. + +GENERATE_TREEVIEW = YES + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values +# (range [0,1..20]) that doxygen will group on one line in the generated HTML +# documentation. Note that a value of 0 will completely suppress the enum +# values from appearing in the overview section. + +ENUM_VALUES_PER_LINE = 4 + +# 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 + +# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open +# links to external symbols imported via tag files in a separate window. + +EXT_LINKS_IN_WINDOW = NO + +# Use this tag to change the font size of Latex formulas included +# as images in the HTML documentation. The default is 10. Note that +# when you change the font size after a successful doxygen run you need +# to manually remove any form_*.png images from the HTML output directory +# to force them to be regenerated. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are +# not supported properly for IE 6.0, but are supported on all modern browsers. +# Note that when changing this option you need to delete any form_*.png files +# in the HTML output before the changes have effect. + +FORMULA_TRANSPARENT = YES + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax +# (see http://www.mathjax.org) which uses client side Javascript for the +# rendering instead of using prerendered bitmaps. Use this if you do not +# have LaTeX installed or if you want to formulas look prettier in the HTML +# output. When enabled you may also need to install MathJax separately and +# configure the path to it using the MATHJAX_RELPATH option. + +USE_MATHJAX = NO + +# When MathJax is enabled you need to specify the location relative to the +# HTML output directory using the MATHJAX_RELPATH option. The destination +# directory should contain the MathJax.js script. For instance, if the mathjax +# directory is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to +# the MathJax Content Delivery Network so you can quickly see the result without +# installing MathJax. +# However, it is strongly recommended to install a local +# copy of MathJax from http://www.mathjax.org before deployment. + +MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest + +# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension +# names that should be enabled during MathJax rendering. + +MATHJAX_EXTENSIONS = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box +# for the HTML output. The underlying search engine uses javascript +# and DHTML and should work on any modern browser. Note that when using +# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets +# (GENERATE_DOCSET) there is already a search function so this one should +# typically be disabled. For large projects the javascript based search engine +# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution. + +SEARCHENGINE = NO + +# When the SERVER_BASED_SEARCH tag is enabled the search engine will be +# implemented using a PHP enabled web server instead of at the web client +# using Javascript. Doxygen will generate the search PHP script and index +# file to put on the web server. The advantage of the server +# based approach is that it scales better to large projects and allows +# full text search. The disadvantages are that it is more difficult to setup +# and does not have live searching capabilities. + +SERVER_BASED_SEARCH = NO + +#--------------------------------------------------------------------------- +# 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. +# Note that when enabling USE_PDFLATEX this option is only used for +# generating bitmaps for formulas in the HTML output, but not in the +# Makefile that is written to the output directory. + +LATEX_CMD_NAME = /usr/bin/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 = /usr/bin/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, letter, legal and +# executive. If left blank a4wide will be used. + +PAPER_TYPE = a4 + +# 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 = + +# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for +# the generated latex document. The footer should contain everything after +# the last chapter. If it is left blank doxygen will generate a +# standard footer. Notice: only use this tag if you know what you are doing! + +LATEX_FOOTER = + +# 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 = YES + +# 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 = YES + +# 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 = YES + +# 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 + +# If LATEX_SOURCE_CODE is set to YES then doxygen will include +# source code with syntax highlighting in the LaTeX output. +# Note that which sources are shown also depends on other settings +# such as SOURCE_BROWSER. + +LATEX_SOURCE_CODE = YES + +# The LATEX_BIB_STYLE tag can be used to specify the style to use for the +# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See +# http://en.wikipedia.org/wiki/BibTeX for more info. + +LATEX_BIB_STYLE = plain + +#--------------------------------------------------------------------------- +# 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 style sheet 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 = YES + +# 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_DEFINED tags. + +EXPAND_ONLY_PREDEF = YES + +# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files +# pointed to by INCLUDE_PATH will be searched when 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 that +# overrules the definition found in the source code. + +EXPAND_AS_DEFINED = DEPRECATED INLINE PUBLIC FLT_OR_DBL + +# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then +# doxygen's preprocessor will remove all references to function-like macros +# that are alone on a line, have an all uppercase name, and do not end with a +# semicolon, because these 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. For each +# tag file the location of the external documentation should be added. 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. 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 = RNAlib-2.1.2.tag + +# 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 also works with HAVE_DOT disabled, but it is recommended to +# install and use dot, since it yields more powerful graphs. + +CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see +# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the +# documentation. The MSCGEN_PATH tag allows you to specify the directory where +# the mscgen tool resides. If left empty the tool is assumed to be found in the +# default search path. + +MSCGEN_PATH = + +# 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 = YES + +# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is +# allowed to run in parallel. When set to 0 (the default) doxygen will +# base this on the number of processors available in the system. You can set it +# explicitly to a value larger than 0 to get control over the balance +# between CPU load and processing speed. + +DOT_NUM_THREADS = 0 + +# By default doxygen will use the Helvetica font for all dot files that +# doxygen generates. When you want a differently looking font you can specify +# the font name using DOT_FONTNAME. You need to make sure dot is able to find +# the font, which can be done by putting it in a standard location or by setting +# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the +# directory containing the font. + +DOT_FONTNAME = FreeSans + +# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. +# The default size is 10pt. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the Helvetica font. +# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to +# set the path where dot can find it. + +DOT_FONTPATH = + +# 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 +# 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 the UML_LOOK tag is enabled, the fields and methods are shown inside +# the class node. If there are many fields or methods and many nodes the +# graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS +# threshold limits the number of items for each type to make the size more +# managable. Set this to 0 for no limit. Note that the threshold may be +# exceeded by 50% before the limit is enforced. + +UML_LIMIT_NUM_FIELDS = 10 + +# 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 options 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 CALLER_GRAPH and HAVE_DOT tags are set to YES then +# doxygen will generate a caller 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 caller +# graphs for selected functions only using the \callergraph command. + +CALLER_GRAPH = NO + +# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen +# will generate a graphical hierarchy of all classes instead of a textual one. + +GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH 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 svg, png, jpg, or gif. +# If left blank png will be used. If you choose svg you need to set +# HTML_FILE_EXTENSION to xhtml in order to make the SVG files +# visible in IE 9+ (other browsers do not have this requirement). + +DOT_IMAGE_FORMAT = png + +# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to +# enable generation of interactive SVG images that allow zooming and panning. +# Note that this requires a modern browser other than Internet Explorer. +# Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you +# need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files +# visible. Older versions of IE do not have SVG support. + +INTERACTIVE_SVG = YES + +# 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 MSCFILE_DIRS tag can be used to specify one or more directories that +# contain msc files that are included in the documentation (see the +# \mscfile command). + +MSCFILE_DIRS = + +# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of +# nodes that will be shown in the graph. If the number of nodes in a graph +# becomes larger than this value, doxygen will truncate the graph, which is +# visualized by representing a node as a red box. Note that doxygen if the +# number of direct children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note +# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. + +DOT_GRAPH_MAX_NODES = 50 + +# 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 the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. + +MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not +# seem to support this out of the box. 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 = YES + +# 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 + diff --git a/binaries/src/ViennaRNA/doc/html/sync_off.png b/binaries/src/ViennaRNA/doc/html/sync_off.png new file mode 100644 index 0000000000000000000000000000000000000000..3b443fc62892114406e3d399421b2a881b897acc GIT binary patch literal 853 zcmV-b1FHOqP)oT|#XixUYy%lpuf3i8{fX!o zUyDD0jOrAiT^tq>fLSOOABs-#u{dV^F$b{L9&!2=9&RmV;;8s^x&UqB$PCj4FdKbh zoB1WTskPUPu05XzFbA}=KZ-GP1fPpAfSs>6AHb12UlR%-i&uOlTpFNS7{jm@mkU1V zh`nrXr~+^lsV-s1dkZOaI|kYyVj3WBpPCY{n~yd%u%e+d=f%`N0FItMPtdgBb@py; zq@v6NVArhyTC7)ULw-Jy8y42S1~4n(3LkrW8mW(F-4oXUP3E`e#g**YyqI7h-J2zK zK{m9##m4ri!7N>CqQqCcnI3hqo1I;Yh&QLNY4T`*ptiQGozK>FF$!$+84Z`xwmeMh zJ0WT+OH$WYFALEaGj2_l+#DC3t7_S`vHpSivNeFbP6+r50cO8iu)`7i%Z4BTPh@_m3Tk!nAm^)5Bqnr%Ov|Baunj#&RPtRuK& z4RGz|D5HNrW83-#ydk}tVKJrNmyYt-sTxLGlJY5nc&Re zU4SgHNPx8~Yxwr$bsju?4q&%T1874xxzq+_%?h8_ofw~(bld=o3iC)LUNR*BY%c0y zWd_jX{Y8`l%z+ol1$@Qa?Cy!(0CVIEeYpKZ`(9{z>3$CIe;pJDQk$m3p}$>xBm4lb zKo{4S)`wdU9Ba9jJbVJ0C=SOefZe%d$8=2r={nu<_^a3~>c#t_U6dye5)JrR(_a^E f@}b6j1K9lwFJq@>o)+Ry00000NkvXXu0mjfWa5j* literal 0 HcmV?d00001 diff --git a/binaries/src/ViennaRNA/doc/html/sync_on.png b/binaries/src/ViennaRNA/doc/html/sync_on.png new file mode 100644 index 0000000000000000000000000000000000000000..e08320fb64e6fa33b573005ed6d8fe294e19db76 GIT binary patch literal 845 zcmV-T1G4;yP)Y;xxyHF2B5Wzm| zOOGupOTn@c(JmBOl)e;XMNnZuiTJP>rM8<|Q`7I_))aP?*T)ow&n59{}X4$3Goat zgjs?*aasfbrokzG5cT4K=uG`E14xZl@z)F={P0Y^?$4t z>v!teRnNZym<6h{7sLyF1V0HsfEl+l6TrZpsfr1}luH~F7L}ktXu|*uVX^RG$L0`K zWs3j|0tIvVe(N%_?2{(iCPFGf#B6Hjy6o&}D$A%W%jfO8_W%ZO#-mh}EM$LMn7joJ z05dHr!5Y92g+31l<%i1(=L1a1pXX+OYnalY>31V4K}BjyRe3)9n#;-cCVRD_IG1fT zOKGeNY8q;TL@K{dj@D^scf&VCs*-Jb>8b>|`b*osv52-!A?BpbYtTQBns5EAU**$m zSnVSm(teh>tQi*S*A>#ySc=n;`BHz`DuG4&g4Kf8lLhca+zvZ7t7RflD6-i-mcK=M z!=^P$*u2)bkY5asG4gsss!Hn%u~>}kIW`vMs%lJLH+u*9<4PaV_c6U`KqWXQH%+Nu zTv41O(^ZVi@qhjQdG!fbZw&y+2o!iYymO^?ud3{P*HdoX83YV*Uu_HB=?U&W9%AU# z80}k1SS-CXTU7dcQlsm<^oYLxVSseqY6NO}dc`Nj?8vrhNuCdm@^{a3AQ_>6myOj+ z`1RsLUXF|dm|3k7s2jD(B{rzE>WI2scH8i1;=O5Cc9xB3^aJk%fQjqsu+kH#0=_5a z0nCE8@dbQa-|YIuUVvG0L_IwHMEhOj$Mj4Uq05 X8=0q~qBNan00000NkvXXu0mjfptF>5 literal 0 HcmV?d00001 diff --git a/binaries/src/ViennaRNA/doc/latex/1_88_84__epars_8h.tex b/binaries/src/ViennaRNA/doc/latex/1_88_84__epars_8h.tex new file mode 100644 index 0000000..bd0f092 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/1_88_84__epars_8h.tex @@ -0,0 +1,28 @@ +\hypertarget{1_88_84__epars_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/1.8.4\-\_\-epars.h File Reference} +\label{1_88_84__epars_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/1.\-8.\-4\-\_\-epars.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/1.\-8.\-4\-\_\-epars.\-h}} +} + + +Free energy parameters for parameter file conversion. + + + + +\subsection{Detailed Description} +Free energy parameters for parameter file conversion. This file contains the free energy parameters used in Vienna\-R\-N\-A\-Package 1.\-8.\-4. They are summarized in\-: + +D.\-H.\-Mathews, J. Sabina, M. Z\-Uker, D.\-H. Turner \char`\"{}\-Expanded sequence dependence of thermodynamic parameters improves +prediction of R\-N\-A secondary structure\char`\"{} J\-M\-B, 288, pp 911-\/940, 1999 + +Enthalpies taken from\-: + +A. Walter, D Turner, J Kim, M Lyttle, P M\char`\"{}uller, D Mathews, M Zuker +\char`\"{}Coaxial stckaing of helices enhances binding of oligoribonucleotides.." P\-N\-A\-S, 91, pp 9218-\/9222, 1994 + +D.\-H. Turner, N. Sugimoto, and S.\-M. Freier. \char`\"{}\-R\-N\-A Structure Prediction\char`\"{}, Ann. Rev. Biophys. Biophys. Chem. 17, 167-\/192, 1988. + +John A.\-Jaeger, Douglas H.\-Turner, and Michael Zuker. \char`\"{}\-Improved predictions of secondary structures for R\-N\-A\char`\"{}, P\-N\-A\-S, 86, 7706-\/7710, October 1989. + +L. He, R. Kierzek, J. Santa\-Lucia, A.\-E. Walter, D.\-H. Turner \char`\"{}\-Nearest-\/\-Neughbor Parameters for G\-U Mismatches....\char`\"{} Biochemistry 1991, 30 11124-\/11132 + +A.\-E. Peritz, R. Kierzek, N, Sugimoto, D.\-H. Turner \char`\"{}\-Thermodynamic Study of Internal Loops in Oligoribonucleotides...\char`\"{} Biochemistry 1991, 30, 6428--6435 \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/1_88_84__epars_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/1_88_84__epars_8h_source.tex new file mode 100644 index 0000000..f3b9b55 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/1_88_84__epars_8h_source.tex @@ -0,0 +1,338 @@ +\hypertarget{1_88_84__epars_8h}{\section{1.8.4\-\_\-epars.h} +\label{1_88_84__epars_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/1.\-8.\-4\-\_\-epars.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/1.\-8.\-4\-\_\-epars.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_OLD\_EPARS\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_OLD\_EPARS\_\_} +00003 \textcolor{preprocessor}{} +00038 \textcolor{preprocessor}{#define K0 273.15} +00039 \textcolor{preprocessor}{}\textcolor{preprocessor}{#ifdef INF} +00040 \textcolor{preprocessor}{}\textcolor{preprocessor}{#undef INF} +00041 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif} +00042 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define INF 1000000} +00043 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define NBPAIRS 7} +00044 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define NST 0 }\textcolor{comment}{/* Energy for nonstandard stacked pairs */}\textcolor{preprocessor}{} +00045 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEF -50 }\textcolor{comment}{/* Default terminal mismatch, used for I */}\textcolor{preprocessor}{} +00046 \textcolor{preprocessor}{} \textcolor{comment}{/* and any non\_pairing bases */} +00047 \textcolor{preprocessor}{#define NSM 0 }\textcolor{comment}{/* terminal mismatch for non standard pairs */}\textcolor{preprocessor}{} +00048 \textcolor{preprocessor}{} +00049 PRIVATE \textcolor{keywordtype}{double} Tmeasure\_184 = 37 + \hyperlink{energy__const_8h_a307c72605e3713972b4f4fb2d53ea20e}{K0}; \textcolor{comment}{/* temperature of param measurements */} +00050 PRIVATE \textcolor{keywordtype}{double} lxc37\_184 = 107.856; \textcolor{comment}{/* parameter for logarithmic loop} +00051 \textcolor{comment}{ energy extrapolation */} +00052 +00053 PRIVATE \textcolor{keywordtype}{int} stack37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1] = +00054 \textcolor{comment}{/* CG GC GU UG AU UA */} +00055 \{ \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, +00056 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -240, -330, -210, -140, -210, -210, NST\}, +00057 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -330, -340, -250, -150, -220, -240, NST\}, +00058 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -210, -250, 130, -50, -140, -130, NST\}, +00059 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -140, -150, -50, 30, -60, -100, NST\}, +00060 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -210, -220, -140, -60, -110, -90, NST\}, +00061 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -210, -240, -130, -100, -90, -130, NST\}, +00062 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, NST, NST, NST, NST, NST, NST, NST\}\}; +00063 +00064 \textcolor{comment}{/* enthalpies (0.01*kcal/mol at 37 C) for stacked pairs */} +00065 \textcolor{comment}{/* different from mfold-2.3, which uses values from mfold-2.2 */} +00066 PRIVATE \textcolor{keywordtype}{int} enthalpies\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1] = +00067 \textcolor{comment}{/* CG GC GU UG AU UA */} +00068 \{ \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, +00069 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -1060, -1340, -1210, -560, -1050, -1040, NST\}, +00070 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -1340, -1490, -1260, -830, -1140, -1240, NST\}, +00071 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -1210, -1260, -1460, -1350, -880, -1280, NST\}, +00072 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -560, -830, -1350, -930, -320, -700, NST\}, +00073 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -1050, -1140, -880, -320, -940, -680, NST\}, +00074 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -1040, -1240, -1280, -700, -680, -770, NST\}, +00075 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, NST, NST, NST, NST, NST, NST, NST\}\}; +00076 +00077 +00078 \textcolor{comment}{/* old values are here just for comparison */} +00079 PRIVATE \textcolor{keywordtype}{int} oldhairpin37\_184[31] = \{ \textcolor{comment}{/* from ViennaRNA 1.3 */} +00080 \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 410, 490, 440, 470, 500, 510, 520, 531, +00081 542, 551, 560, 568, 575, 582, 589, 595, 601, 606, +00082 611, 616, 621, 626, 630, 634, 638, 642, 646, 650\}; +00083 +00084 PRIVATE \textcolor{keywordtype}{int} hairpin37\_184[31] = \{ +00085 \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 570, 560, 560, 540, 590, 560, 640, 650, +00086 660, 670, 678, 686, 694, 701, 707, 713, 719, 725, +00087 730, 735, 740, 744, 749, 753, 757, 761, 765, 769\}; +00088 +00089 PRIVATE \textcolor{keywordtype}{int} oldbulge37\_184[31] = \{ +00090 \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 390, 310, 350, 420, 480, 500, 516, 531, 543, 555, +00091 565, 574, 583, 591, 598, 605, 612, 618, 624, 630, +00092 635, 640, 645, 649, 654, 658, 662, 666, 670, 673\}; +00093 +00094 PRIVATE \textcolor{keywordtype}{int} bulge37\_184[31] = \{ +00095 \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 380, 280, 320, 360, 400, 440, 459, 470, 480, 490, +00096 500, 510, 519, 527, 534, 541, 548, 554, 560, 565, +00097 571, 576, 580, 585, 589, 594, 598, 602, 605, 609\}; +00098 +00099 PRIVATE \textcolor{keywordtype}{int} oldinternal\_loop37\_184[31] = \{ +00100 \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 410, 510, 490, 530, 570, 587, 601, 614, 625, +00101 635, 645, 653, 661, 669, 676, 682, 688, 694, 700, +00102 705, 710, 715, 720, 724, 728, 732, 736, 740, 744\}; +00103 +00104 PRIVATE \textcolor{keywordtype}{int} internal\_loop37\_184[31] = \{ +00105 \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 410, 510, 170, 180, 200, 220, 230, 240, 250, +00106 260, 270, 278, 286, 294, 301, 307, 313, 319, 325, +00107 330, 335, 340, 345, 349, 353, 357, 361, 365, 369\}; +00108 +00109 \textcolor{comment}{/* terminal mismatches */} +00110 \textcolor{comment}{/* mismatch free energies for interior loops at 37C */} +00111 PRIVATE \textcolor{keywordtype}{int} mismatchI37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5] = +00112 \{ \textcolor{comment}{/* @@ */} +00113 \{\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\}\}, +00114 \{ \textcolor{comment}{/* CG */} +00115 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00116 \{ 0, 0, 0, -110, 0\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00117 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00118 \{ 0, -110, 0, 0, 0\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00119 \{ 0, 0, 0, 0, -70\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00120 \{ \textcolor{comment}{/* GC */} +00121 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00122 \{ 0, 0, 0, -110, 0\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00123 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00124 \{ 0, -110, 0, 0, 0\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00125 \{ 0, 0, 0, 0, -70\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00126 \{ \textcolor{comment}{/* GU */} +00127 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00128 \{ 0, 70, 70, -40, 70\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00129 \{ 0, 70, 70, 70, 70\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00130 \{ 0, -40, 70, 70, 70\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00131 \{ 0, 70, 70, 70, 0\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00132 \{ \textcolor{comment}{/* UG */} +00133 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00134 \{ 0, 70, 70, -40, 70\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00135 \{ 0, 70, 70, 70, 70\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00136 \{ 0, -40, 70, 70, 70\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00137 \{ 0, 70, 70, 70, 0\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00138 \{ \textcolor{comment}{/* AU */} +00139 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00140 \{ 0, 70, 70, -40, 70\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00141 \{ 0, 70, 70, 70, 70\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00142 \{ 0, -40, 70, 70, 70\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00143 \{ 0, 70, 70, 70, 0\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00144 \{ \textcolor{comment}{/* UA */} +00145 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00146 \{ 0, 70, 70, -40, 70\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00147 \{ 0, 70, 70, 70, 70\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00148 \{ 0, -40, 70, 70, 70\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00149 \{ 0, 70, 70, 70, 0\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00150 \{ \textcolor{comment}{/* @@ */} +00151 \{ 90, 90, 90, 90, 90\},\{ 90, 90, 90, 90,-20\},\{ 90, 90, 90, 90, 90\}, +00152 \{ 90,-20, 90, 90, 90\},\{ 90, 90, 90, 90, 20\}\} +00153 \}; +00154 +00155 \textcolor{comment}{/* mismatch free energies for hairpins at 37C */} +00156 PRIVATE \textcolor{keywordtype}{int} mismatchH37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5] = +00157 \{ \textcolor{comment}{/* @@ */} +00158 \{\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\}\}, +00159 \{ \textcolor{comment}{/* CG */} +00160 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00161 \{ -90, -150, -150, -140, -180\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00162 \{ -90, -100, -90, -290, -80\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00163 \{ -90, -220, -200, -160, -110\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00164 \{ -90, -170, -140, -180, -200\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00165 \{ \textcolor{comment}{/* GC */} +00166 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00167 \{ -70, -110, -150, -130, -210\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00168 \{ -70, -110, -70, -240, -50\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00169 \{ -70, -240, -290, -140, -120\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00170 \{ -70, -190, -100, -220, -150\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00171 \{ \textcolor{comment}{/* GU */} +00172 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00173 \{ 0, 20, -50, -30, -30\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00174 \{ 0, -10, -20, -150, -20\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00175 \{ 0, -90, -110, -30, 0\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00176 \{ 0, -30, -30, -40, -110\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00177 \{ \textcolor{comment}{/* UG */} +00178 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00179 \{ 0, -50, -30, -60, -50\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00180 \{ 0, -20, -10, -170, 0\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00181 \{ 0, -80, -120, -30, -70\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00182 \{ 0, -60, -10, -60, -80\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00183 \{ \textcolor{comment}{/* AU */} +00184 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00185 \{ 0, -30, -50, -30, -30\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00186 \{ 0, -10, -20, -150, -20\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00187 \{ 0, -110, -120, -20, 20\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00188 \{ 0, -30, -30, -60, -110\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00189 \{ \textcolor{comment}{/* UA */} +00190 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00191 \{ 0, -50, -30, -60, -50\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00192 \{ 0, -20, -10, -120, -0\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00193 \{ 0, -140, -120, -70, -20\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00194 \{ 0, -30, -10, -50, -80\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00195 \{ \textcolor{comment}{/* @@ */} +00196 \{ 0, 0, 0, 0, 0\},\{ 0, 0, 0, 0, 0\},\{ 0, 0, 0, 0, 0\}, +00197 \{ 0, 0, 0, 0, 0\},\{ 0, 0, 0, 0, 0\}\} +00198 \}; +00199 +00200 \textcolor{comment}{/* mismatch energies in multiloops */} +00201 PRIVATE \textcolor{keywordtype}{int} mismatchM37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00202 +00203 \textcolor{comment}{/* these are probably junk */} +00204 \textcolor{comment}{/* mismatch enthalpies for temperature scaling */} +00205 PRIVATE \textcolor{keywordtype}{int} mism\_H\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5] = +00206 \{ \textcolor{comment}{/* no pair */} +00207 \{\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\}\}, +00208 \{ \textcolor{comment}{/* CG */} +00209 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00210 \{ DEF,-1030, -950,-1030,-1030\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00211 \{ DEF, -520, -450, -520, -670\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00212 \{ DEF, -940, -940, -940, -940\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00213 \{ DEF, -810, -740, -810, -860\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00214 \{ \textcolor{comment}{/* GC */} +00215 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00216 \{ DEF, -520, -880, -560, -880\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00217 \{ DEF, -720, -310, -310, -390\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00218 \{ DEF, -710, -740, -620, -740\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00219 \{ DEF, -500, -500, -500, -570\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00220 \{ \textcolor{comment}{/* GU */} +00221 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00222 \{ DEF, -430, -600, -600, -600\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00223 \{ DEF, -260, -240, -240, -240\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00224 \{ DEF, -340, -690, -690, -690\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00225 \{ DEF, -330, -330, -330, -330\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00226 \{ \textcolor{comment}{/* UG */} +00227 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00228 \{ DEF, -720, -790, -960, -810\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00229 \{ DEF, -480, -480, -360, -480\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00230 \{ DEF, -660, -810, -920, -810\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00231 \{ DEF, -550, -440, -550, -360\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00232 \{ \textcolor{comment}{/* AU */} +00233 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00234 \{ DEF, -430, -600, -600, -600\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00235 \{ DEF, -260, -240, -240, -240\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00236 \{ DEF, -340, -690, -690, -690\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00237 \{ DEF, -330, -330, -330, -330\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00238 \{ \textcolor{comment}{/* UA */} +00239 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */} +00240 \{ DEF, -400, -630, -890, -590\}, \textcolor{comment}{/* A@ AA AC AG AU */} +00241 \{ DEF, -430, -510, -200, -180\}, \textcolor{comment}{/* C@ CA CC CG CU */} +00242 \{ DEF, -380, -680, -890, -680\}, \textcolor{comment}{/* G@ GA GC GG GU */} +00243 \{ DEF, -280, -140, -280, -140\}\},\textcolor{comment}{/* U@ UA UC UG UU */} +00244 \{ \textcolor{comment}{/* nonstandard pair */} +00245 \{DEF,DEF,DEF,DEF,DEF\},\{DEF,DEF,DEF,DEF,DEF\},\{DEF,DEF,DEF,DEF,DEF\}, +00246 \{DEF,DEF,DEF,DEF,DEF\},\{DEF,DEF,DEF,DEF,DEF\}\} +00247 \}; +00248 +00249 \textcolor{comment}{/* 5' dangling ends (unpaird base stacks on first paired base) */} +00250 PRIVATE \textcolor{keywordtype}{int} dangle5\_37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5]= +00251 \{\textcolor{comment}{/* @ A C G U */} +00252 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* no pair */} +00253 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -50, -30, -20, -10\}, \textcolor{comment}{/* CG (stacks on C) */} +00254 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -20, -30, -0, -0\}, \textcolor{comment}{/* GC (stacks on G) */} +00255 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -30, -30, -40, -20\}, \textcolor{comment}{/* GU */} +00256 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -30, -10, -20, -20\}, \textcolor{comment}{/* UG */} +00257 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -30, -30, -40, -20\}, \textcolor{comment}{/* AU */} +00258 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -30, -10, -20, -20\}, \textcolor{comment}{/* UA */} +00259 \{ 0, 0, 0, 0, 0\} \textcolor{comment}{/* @ */} +00260 \}; +00261 +00262 \textcolor{comment}{/* 3' dangling ends (unpaired base stacks on second paired base */} +00263 PRIVATE \textcolor{keywordtype}{int} dangle3\_37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5]= +00264 \{\textcolor{comment}{/* @ A C G U */} +00265 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* no pair */} +00266 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -110, -40, -130, -60\}, \textcolor{comment}{/* CG (stacks on G) */} +00267 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -170, -80, -170, -120\}, \textcolor{comment}{/* GC */} +00268 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -70, -10, -70, -10\}, \textcolor{comment}{/* GU */} +00269 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -80, -50, -80, -60\}, \textcolor{comment}{/* UG */} +00270 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -70, -10, -70, -10\}, \textcolor{comment}{/* AU */} +00271 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -80, -50, -80, -60\}, \textcolor{comment}{/* UA */} +00272 \{ 0, 0, 0, 0, 0\} \textcolor{comment}{/* @ */} +00273 \}; +00274 +00275 \textcolor{comment}{/* enthalpies for temperature scaling */} +00276 PRIVATE \textcolor{keywordtype}{int} dangle3\_H\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5] = +00277 \{\textcolor{comment}{/* @ A C G U */} +00278 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* no pair */} +00279 \{ 0, -740, -280, -640, -360\}, +00280 \{ 0, -900, -410, -860, -750\}, +00281 \{ 0, -740, -240, -720, -490\}, +00282 \{ 0, -490, -90, -550, -230\}, +00283 \{ 0, -570, -70, -580, -220\}, +00284 \{ 0, -490, -90, -550, -230\}, +00285 \{ 0, 0, 0, 0, 0\} +00286 \}; +00287 +00288 PRIVATE \textcolor{keywordtype}{int} dangle5\_H\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5] = +00289 \{\textcolor{comment}{/* @ A C G U */} +00290 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* no pair */} +00291 \{ 0, -240, 330, 80, -140\}, +00292 \{ 0, -160, 70, -460, -40\}, +00293 \{ 0, 160, 220, 70, 310\}, +00294 \{ 0, -150, 510, 10, 100\}, +00295 \{ 0, 160, 220, 70, 310\}, +00296 \{ 0, -50, 690, -60, -60\}, +00297 \{ 0, 0, 0, 0, 0\} +00298 \}; +00299 +00300 +00301 \textcolor{comment}{/* constants for linearly destabilizing contributions for multi-loops} +00302 \textcolor{comment}{ F = ML\_closing + ML\_intern*k + ML\_BASE*u */} +00303 \textcolor{comment}{/* old versions erroneously used ML\_intern*(k-1) */} +00304 PRIVATE \textcolor{keywordtype}{int} ML\_BASE37\_184 = 0; +00305 PRIVATE \textcolor{keywordtype}{int} ML\_closing37\_184 = 340; +00306 PRIVATE \textcolor{keywordtype}{int} ML\_intern37\_184 = 40; +00307 +00308 \textcolor{comment}{/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */} +00309 \textcolor{comment}{/* ninio\_energy = min\{max\_ninio, |n1-n2|*F\_ninio[min\{4.0, n1, n2\}] \} */} +00310 PRIVATE \textcolor{keywordtype}{int} MAX\_NINIO\_184 = 300; \textcolor{comment}{/* maximum correction */} +00311 PRIVATE \textcolor{keywordtype}{int} F\_ninio37\_184[5] = \{ 0, 40, 50, 20, 10 \}; \textcolor{comment}{/* only F[2] used */} +00312 +00313 \textcolor{comment}{/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */} +00314 +00315 PRIVATE \textcolor{keywordtype}{char} Tetraloops\_184[1400] = \textcolor{comment}{/* place for up to 200 tetra loops */} +00316 \textcolor{stringliteral}{"GGGGAC "} +00317 \textcolor{stringliteral}{"GGUGAC "} +00318 \textcolor{stringliteral}{"CGAAAG "} +00319 \textcolor{stringliteral}{"GGAGAC "} +00320 \textcolor{stringliteral}{"CGCAAG "} +00321 \textcolor{stringliteral}{"GGAAAC "} +00322 \textcolor{stringliteral}{"CGGAAG "} +00323 \textcolor{stringliteral}{"CUUCGG "} +00324 \textcolor{stringliteral}{"CGUGAG "} +00325 \textcolor{stringliteral}{"CGAAGG "} +00326 \textcolor{stringliteral}{"CUACGG "} +00327 \textcolor{stringliteral}{"GGCAAC "} +00328 \textcolor{stringliteral}{"CGCGAG "} +00329 \textcolor{stringliteral}{"UGAGAG "} +00330 \textcolor{stringliteral}{"CGAGAG "} +00331 \textcolor{stringliteral}{"AGAAAU "} +00332 \textcolor{stringliteral}{"CGUAAG "} +00333 \textcolor{stringliteral}{"CUAACG "} +00334 \textcolor{stringliteral}{"UGAAAG "} +00335 \textcolor{stringliteral}{"GGAAGC "} +00336 \textcolor{stringliteral}{"GGGAAC "} +00337 \textcolor{stringliteral}{"UGAAAA "} +00338 \textcolor{stringliteral}{"AGCAAU "} +00339 \textcolor{stringliteral}{"AGUAAU "} +00340 \textcolor{stringliteral}{"CGGGAG "} +00341 \textcolor{stringliteral}{"AGUGAU "} +00342 \textcolor{stringliteral}{"GGCGAC "} +00343 \textcolor{stringliteral}{"GGGAGC "} +00344 \textcolor{stringliteral}{"GUGAAC "} +00345 \textcolor{stringliteral}{"UGGAAA "} +00346 ; +00347 +00348 PRIVATE \textcolor{keywordtype}{int} TETRA\_ENERGY37\_184[200] = \{ +00349 -300, -300, -300, -300, -300, -300, -300, -300, -300, -250, -250, -250, +00350 -250, -250, -200, -200, -200, -200, -200, -150, -150, -150, -150, -150, +00351 -150, -150, -150, -150, -150, -150\}; +00352 +00353 PRIVATE \textcolor{keywordtype}{int} TETRA\_ENTH37\_184 = -400; +00354 +00355 PRIVATE \textcolor{keywordtype}{char} Triloops\_184[241] = \textcolor{stringliteral}{""}; +00356 +00357 PRIVATE \textcolor{keywordtype}{int} Triloop\_E37\_184[40]; +00358 +00359 \textcolor{comment}{/* penalty for AU (or GU) terminating helix) */} +00360 \textcolor{comment}{/* mismatches already contain these */} +00361 PRIVATE \textcolor{keywordtype}{int} TerminalAU\_184 = 50; +00362 +00363 \textcolor{comment}{/* penalty for forming a bi-molecular duplex */} +00364 PRIVATE \textcolor{keywordtype}{int} DuplexInit\_184 = 410; +00365 +00366 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/1_88_84__intloops_8h.tex b/binaries/src/ViennaRNA/doc/latex/1_88_84__intloops_8h.tex new file mode 100644 index 0000000..04186a3 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/1_88_84__intloops_8h.tex @@ -0,0 +1,12 @@ +\hypertarget{1_88_84__intloops_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/1.8.4\-\_\-intloops.h File Reference} +\label{1_88_84__intloops_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/1.\-8.\-4\-\_\-intloops.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/1.\-8.\-4\-\_\-intloops.\-h}} +} + + +Free energy parameters for interior loop contributions needed by the parameter file conversion functions. + + + + +\subsection{Detailed Description} +Free energy parameters for interior loop contributions needed by the parameter file conversion functions. \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/1_88_84__intloops_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/1_88_84__intloops_8h_source.tex new file mode 100644 index 0000000..94fae06 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/1_88_84__intloops_8h_source.tex @@ -0,0 +1,12791 @@ +\hypertarget{1_88_84__intloops_8h}{\section{1.8.4\-\_\-intloops.h} +\label{1_88_84__intloops_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/1.\-8.\-4\-\_\-intloops.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/1.\-8.\-4\-\_\-intloops.\-h}} +} + +\begin{DoxyCode} +00001 +00005 PRIVATE \textcolor{keywordtype}{int} int11\_37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5] = +00006 \{ \textcolor{comment}{/* noPair */} \{\{\{0\}\}\}, +00007 \{ \textcolor{comment}{/* noPair */} \{\{0\}\}, +00008 \textcolor{comment}{/* CG..CG */} +00009 \{\{ 110, 110, 110, 110, 110\}, +00010 \{ 110, 110, 40, 40, 40\}, +00011 \{ 110, 40, 40, 40, 40\}, +00012 \{ 110, 40, 40, -140, 40\}, +00013 \{ 110, 40, 40, 40, 40\} +00014 \}, +00015 \textcolor{comment}{/* CG..GC */} +00016 \{\{ 110, 110, 110, 110, 110\}, +00017 \{ 110, 40, -40, 40, 40\}, +00018 \{ 110, 30, 50, 40, 50\}, +00019 \{ 110, -10, 40, -170, 40\}, +00020 \{ 110, 40, 0, 40, -30\} +00021 \}, +00022 \textcolor{comment}{/* CG..GU */} +00023 \{\{ 110, 110, 110, 110, 110\}, +00024 \{ 110, 110, 110, 110, 110\}, +00025 \{ 110, 110, 110, 110, 110\}, +00026 \{ 110, 110, 110, -100, 110\}, +00027 \{ 110, 110, 110, 110, 110\} +00028 \}, +00029 \textcolor{comment}{/* CG..UG */} +00030 \{\{ 110, 110, 110, 110, 110\}, +00031 \{ 110, 110, 110, 110, 110\}, +00032 \{ 110, 110, 110, 110, 110\}, +00033 \{ 110, 110, 110, -100, 110\}, +00034 \{ 110, 110, 110, 110, 110\} +00035 \}, +00036 \textcolor{comment}{/* CG..AU */} +00037 \{\{ 110, 110, 110, 110, 110\}, +00038 \{ 110, 110, 110, 110, 110\}, +00039 \{ 110, 110, 110, 110, 110\}, +00040 \{ 110, 110, 110, -100, 110\}, +00041 \{ 110, 110, 110, 110, 110\} +00042 \}, +00043 \textcolor{comment}{/* CG..UA */} +00044 \{\{ 110, 110, 110, 110, 110\}, +00045 \{ 110, 110, 110, 110, 110\}, +00046 \{ 110, 110, 110, 110, 110\}, +00047 \{ 110, 110, 110, -100, 110\}, +00048 \{ 110, 110, 110, 110, 110\} +00049 \}, +00050 \textcolor{comment}{/* CG..?? */} +00051 \{\{ 110, 110, 110, 110, 110\}, +00052 \{ 110, 110, 110, 110, 110\}, +00053 \{ 110, 110, 110, 110, 110\}, +00054 \{ 110, 110, 110, 110, 110\}, +00055 \{ 110, 110, 110, 110, 110\} +00056 \} +00057 \}, +00058 \{ \textcolor{comment}{/* noPair */} \{\{0\}\}, +00059 \textcolor{comment}{/* GC..CG */} +00060 \{\{ 110, 110, 110, 110, 110\}, +00061 \{ 110, 40, 30, -10, 40\}, +00062 \{ 110, -40, 50, 40, 0\}, +00063 \{ 110, 40, 40, -170, 40\}, +00064 \{ 110, 40, 50, 40, -30\} +00065 \}, +00066 \textcolor{comment}{/* GC..GC */} +00067 \{\{ 110, 110, 110, 110, 110\}, +00068 \{ 110, 80, 40, 40, 40\}, +00069 \{ 110, 40, 40, 40, 40\}, +00070 \{ 110, 40, 40, -210, 40\}, +00071 \{ 110, 40, 40, 40, -70\} +00072 \}, +00073 \textcolor{comment}{/* GC..GU */} +00074 \{\{ 110, 110, 110, 110, 110\}, +00075 \{ 110, 110, 110, 110, 110\}, +00076 \{ 110, 110, 110, 110, 110\}, +00077 \{ 110, 110, 110, -100, 110\}, +00078 \{ 110, 110, 110, 110, 110\} +00079 \}, +00080 \textcolor{comment}{/* GC..UG */} +00081 \{\{ 110, 110, 110, 110, 110\}, +00082 \{ 110, 110, 110, 110, 110\}, +00083 \{ 110, 110, 110, 110, 110\}, +00084 \{ 110, 110, 110, -100, 110\}, +00085 \{ 110, 110, 110, 110, 110\} +00086 \}, +00087 \textcolor{comment}{/* GC..AU */} +00088 \{\{ 110, 110, 110, 110, 110\}, +00089 \{ 110, 110, 110, 110, 110\}, +00090 \{ 110, 110, 110, 110, 110\}, +00091 \{ 110, 110, 110, -100, 110\}, +00092 \{ 110, 110, 110, 110, 100\} +00093 \}, +00094 \textcolor{comment}{/* GC..UA */} +00095 \{\{ 110, 110, 110, 110, 110\}, +00096 \{ 110, 110, 110, 110, 110\}, +00097 \{ 110, 110, 110, 110, 110\}, +00098 \{ 110, 110, 110, -100, 110\}, +00099 \{ 110, 110, 110, 110, 110\} +00100 \}, +00101 \textcolor{comment}{/* GC..?? */} +00102 \{\{ 110, 110, 110, 110, 110\}, +00103 \{ 110, 110, 110, 110, 110\}, +00104 \{ 110, 110, 110, 110, 110\}, +00105 \{ 110, 110, 110, 110, 110\}, +00106 \{ 110, 110, 110, 110, 110\} +00107 \} +00108 \}, +00109 \{ \textcolor{comment}{/* noPair */} \{\{0\}\}, +00110 \textcolor{comment}{/* GU..CG */} +00111 \{\{ 110, 110, 110, 110, 110\}, +00112 \{ 110, 110, 110, 110, 110\}, +00113 \{ 110, 110, 110, 110, 110\}, +00114 \{ 110, 110, 110, -100, 110\}, +00115 \{ 110, 110, 110, 110, 110\} +00116 \}, +00117 \textcolor{comment}{/* GU..GC */} +00118 \{\{ 110, 110, 110, 110, 110\}, +00119 \{ 110, 110, 110, 110, 110\}, +00120 \{ 110, 110, 110, 110, 110\}, +00121 \{ 110, 110, 110, -100, 110\}, +00122 \{ 110, 110, 110, 110, 110\} +00123 \}, +00124 \textcolor{comment}{/* GU..GU */} +00125 \{\{ 170, 170, 170, 170, 170\}, +00126 \{ 170, 170, 170, 170, 170\}, +00127 \{ 170, 170, 170, 170, 170\}, +00128 \{ 170, 170, 170, -40, 170\}, +00129 \{ 170, 170, 170, 170, 170\} +00130 \}, +00131 \textcolor{comment}{/* GU..UG */} +00132 \{\{ 170, 170, 170, 170, 170\}, +00133 \{ 170, 170, 170, 170, 170\}, +00134 \{ 170, 170, 170, 170, 170\}, +00135 \{ 170, 170, 170, -40, 170\}, +00136 \{ 170, 170, 170, 170, 170\} +00137 \}, +00138 \textcolor{comment}{/* GU..AU */} +00139 \{\{ 170, 170, 170, 170, 170\}, +00140 \{ 170, 170, 170, 170, 170\}, +00141 \{ 170, 170, 170, 170, 170\}, +00142 \{ 170, 170, 170, -40, 170\}, +00143 \{ 170, 170, 170, 170, 170\} +00144 \}, +00145 \textcolor{comment}{/* GU..UA */} +00146 \{\{ 170, 170, 170, 170, 170\}, +00147 \{ 170, 170, 170, 170, 170\}, +00148 \{ 170, 170, 170, 170, 170\}, +00149 \{ 170, 170, 170, -40, 170\}, +00150 \{ 170, 170, 170, 170, 170\} +00151 \}, +00152 \textcolor{comment}{/* GU..?? */} +00153 \{\{ 170, 170, 170, 170, 170\}, +00154 \{ 170, 170, 170, 170, 170\}, +00155 \{ 170, 170, 170, 170, 170\}, +00156 \{ 170, 170, 170, 170, 170\}, +00157 \{ 170, 170, 170, 170, 170\} +00158 \} +00159 \}, +00160 \{ \textcolor{comment}{/* noPair */} \{\{0\}\}, +00161 \textcolor{comment}{/* UG..CG */} +00162 \{\{ 110, 110, 110, 110, 110\}, +00163 \{ 110, 110, 110, 110, 110\}, +00164 \{ 110, 110, 110, 110, 110\}, +00165 \{ 110, 110, 110, -100, 110\}, +00166 \{ 110, 110, 110, 110, 110\} +00167 \}, +00168 \textcolor{comment}{/* UG..GC */} +00169 \{\{ 110, 110, 110, 110, 110\}, +00170 \{ 110, 110, 110, 110, 110\}, +00171 \{ 110, 110, 110, 110, 110\}, +00172 \{ 110, 110, 110, -100, 110\}, +00173 \{ 110, 110, 110, 110, 110\} +00174 \}, +00175 \textcolor{comment}{/* UG..GU */} +00176 \{\{ 170, 170, 170, 170, 170\}, +00177 \{ 170, 170, 170, 170, 170\}, +00178 \{ 170, 170, 170, 170, 170\}, +00179 \{ 170, 170, 170, -40, 170\}, +00180 \{ 170, 170, 170, 170, 170\} +00181 \}, +00182 \textcolor{comment}{/* UG..UG */} +00183 \{\{ 170, 170, 170, 170, 170\}, +00184 \{ 170, 170, 170, 170, 170\}, +00185 \{ 170, 170, 170, 170, 170\}, +00186 \{ 170, 170, 170, -40, 170\}, +00187 \{ 170, 170, 170, 170, 170\} +00188 \}, +00189 \textcolor{comment}{/* UG..AU */} +00190 \{\{ 170, 170, 170, 170, 170\}, +00191 \{ 170, 170, 170, 170, 170\}, +00192 \{ 170, 170, 170, 170, 170\}, +00193 \{ 170, 170, 170, -40, 170\}, +00194 \{ 170, 170, 170, 170, 170\} +00195 \}, +00196 \textcolor{comment}{/* UG..UA */} +00197 \{\{ 170, 170, 170, 170, 170\}, +00198 \{ 170, 170, 170, 170, 170\}, +00199 \{ 170, 170, 170, 170, 170\}, +00200 \{ 170, 170, 170, -40, 170\}, +00201 \{ 170, 170, 170, 170, 170\} +00202 \}, +00203 \textcolor{comment}{/* UG..?? */} +00204 \{\{ 170, 170, 170, 170, 170\}, +00205 \{ 170, 170, 170, 170, 170\}, +00206 \{ 170, 170, 170, 170, 170\}, +00207 \{ 170, 170, 170, 170, 170\}, +00208 \{ 170, 170, 170, 170, 170\} +00209 \} +00210 \}, +00211 \{ \textcolor{comment}{/* noPair */} \{\{0\}\}, +00212 \textcolor{comment}{/* AU..CG */} +00213 \{\{ 110, 110, 110, 110, 110\}, +00214 \{ 110, 110, 110, 110, 110\}, +00215 \{ 110, 110, 110, 110, 110\}, +00216 \{ 110, 110, 110, -100, 110\}, +00217 \{ 110, 110, 110, 110, 110\} +00218 \}, +00219 \textcolor{comment}{/* AU..GC */} +00220 \{\{ 110, 110, 110, 110, 110\}, +00221 \{ 110, 110, 110, 110, 110\}, +00222 \{ 110, 110, 110, 110, 110\}, +00223 \{ 110, 110, 110, -100, 110\}, +00224 \{ 110, 110, 110, 110, 100\} +00225 \}, +00226 \textcolor{comment}{/* AU..GU */} +00227 \{\{ 170, 170, 170, 170, 170\}, +00228 \{ 170, 170, 170, 170, 170\}, +00229 \{ 170, 170, 170, 170, 170\}, +00230 \{ 170, 170, 170, -40, 170\}, +00231 \{ 170, 170, 170, 170, 170\} +00232 \}, +00233 \textcolor{comment}{/* AU..UG */} +00234 \{\{ 170, 170, 170, 170, 170\}, +00235 \{ 170, 170, 170, 170, 170\}, +00236 \{ 170, 170, 170, 170, 170\}, +00237 \{ 170, 170, 170, -40, 170\}, +00238 \{ 170, 170, 170, 170, 170\} +00239 \}, +00240 \textcolor{comment}{/* AU..AU */} +00241 \{\{ 170, 170, 170, 170, 170\}, +00242 \{ 170, 170, 170, 170, 170\}, +00243 \{ 170, 170, 170, 170, 170\}, +00244 \{ 170, 170, 170, -40, 170\}, +00245 \{ 170, 170, 170, 170, 120\} +00246 \}, +00247 \textcolor{comment}{/* AU..UA */} +00248 \{\{ 170, 170, 170, 170, 170\}, +00249 \{ 170, 170, 170, 170, 170\}, +00250 \{ 170, 170, 170, 170, 170\}, +00251 \{ 170, 170, 170, -40, 170\}, +00252 \{ 170, 170, 170, 170, 150\} +00253 \}, +00254 \textcolor{comment}{/* AU..?? */} +00255 \{\{ 170, 170, 170, 170, 170\}, +00256 \{ 170, 170, 170, 170, 170\}, +00257 \{ 170, 170, 170, 170, 170\}, +00258 \{ 170, 170, 170, 170, 170\}, +00259 \{ 170, 170, 170, 170, 170\} +00260 \} +00261 \}, +00262 \{ \textcolor{comment}{/* noPair */} \{\{0\}\}, +00263 \textcolor{comment}{/* UA..CG */} +00264 \{\{ 110, 110, 110, 110, 110\}, +00265 \{ 110, 110, 110, 110, 110\}, +00266 \{ 110, 110, 110, 110, 110\}, +00267 \{ 110, 110, 110, -100, 110\}, +00268 \{ 110, 110, 110, 110, 110\} +00269 \}, +00270 \textcolor{comment}{/* UA..GC */} +00271 \{\{ 110, 110, 110, 110, 110\}, +00272 \{ 110, 110, 110, 110, 110\}, +00273 \{ 110, 110, 110, 110, 110\}, +00274 \{ 110, 110, 110, -100, 110\}, +00275 \{ 110, 110, 110, 110, 110\} +00276 \}, +00277 \textcolor{comment}{/* UA..GU */} +00278 \{\{ 170, 170, 170, 170, 170\}, +00279 \{ 170, 170, 170, 170, 170\}, +00280 \{ 170, 170, 170, 170, 170\}, +00281 \{ 170, 170, 170, -40, 170\}, +00282 \{ 170, 170, 170, 170, 170\} +00283 \}, +00284 \textcolor{comment}{/* UA..UG */} +00285 \{\{ 170, 170, 170, 170, 170\}, +00286 \{ 170, 170, 170, 170, 170\}, +00287 \{ 170, 170, 170, 170, 170\}, +00288 \{ 170, 170, 170, -40, 170\}, +00289 \{ 170, 170, 170, 170, 170\} +00290 \}, +00291 \textcolor{comment}{/* UA..AU */} +00292 \{\{ 170, 170, 170, 170, 170\}, +00293 \{ 170, 170, 170, 170, 170\}, +00294 \{ 170, 170, 170, 170, 170\}, +00295 \{ 170, 170, 170, -40, 170\}, +00296 \{ 170, 170, 170, 170, 150\} +00297 \}, +00298 \textcolor{comment}{/* UA..UA */} +00299 \{\{ 170, 170, 170, 170, 170\}, +00300 \{ 170, 170, 170, 170, 170\}, +00301 \{ 170, 170, 170, 170, 170\}, +00302 \{ 170, 170, 170, -40, 170\}, +00303 \{ 170, 170, 170, 170, 180\} +00304 \}, +00305 \textcolor{comment}{/* UA..?? */} +00306 \{\{ 170, 170, 170, 170, 170\}, +00307 \{ 170, 170, 170, 170, 170\}, +00308 \{ 170, 170, 170, 170, 170\}, +00309 \{ 170, 170, 170, 170, 170\}, +00310 \{ 170, 170, 170, 170, 170\} +00311 \} +00312 \}, +00313 \{ \textcolor{comment}{/* noPair */} \{\{0\}\}, +00314 \textcolor{comment}{/* ??..CG */} +00315 \{\{ 110, 110, 110, 110, 110\}, +00316 \{ 110, 110, 110, 110, 110\}, +00317 \{ 110, 110, 110, 110, 110\}, +00318 \{ 110, 110, 110, 110, 110\}, +00319 \{ 110, 110, 110, 110, 110\} +00320 \}, +00321 \textcolor{comment}{/* ??..GC */} +00322 \{\{ 110, 110, 110, 110, 110\}, +00323 \{ 110, 110, 110, 110, 110\}, +00324 \{ 110, 110, 110, 110, 110\}, +00325 \{ 110, 110, 110, 110, 110\}, +00326 \{ 110, 110, 110, 110, 110\} +00327 \}, +00328 \textcolor{comment}{/* ??..GU */} +00329 \{\{ 170, 170, 170, 170, 170\}, +00330 \{ 170, 170, 170, 170, 170\}, +00331 \{ 170, 170, 170, 170, 170\}, +00332 \{ 170, 170, 170, 170, 170\}, +00333 \{ 170, 170, 170, 170, 170\} +00334 \}, +00335 \textcolor{comment}{/* ??..UG */} +00336 \{\{ 170, 170, 170, 170, 170\}, +00337 \{ 170, 170, 170, 170, 170\}, +00338 \{ 170, 170, 170, 170, 170\}, +00339 \{ 170, 170, 170, 170, 170\}, +00340 \{ 170, 170, 170, 170, 170\} +00341 \}, +00342 \textcolor{comment}{/* ??..AU */} +00343 \{\{ 170, 170, 170, 170, 170\}, +00344 \{ 170, 170, 170, 170, 170\}, +00345 \{ 170, 170, 170, 170, 170\}, +00346 \{ 170, 170, 170, 170, 170\}, +00347 \{ 170, 170, 170, 170, 170\} +00348 \}, +00349 \textcolor{comment}{/* ??..UA */} +00350 \{\{ 170, 170, 170, 170, 170\}, +00351 \{ 170, 170, 170, 170, 170\}, +00352 \{ 170, 170, 170, 170, 170\}, +00353 \{ 170, 170, 170, 170, 170\}, +00354 \{ 170, 170, 170, 170, 170\} +00355 \}, +00356 \textcolor{comment}{/* ??..?? */} +00357 \{\{ 170, 170, 170, 170, 170\}, +00358 \{ 170, 170, 170, 170, 170\}, +00359 \{ 170, 170, 170, 170, 170\}, +00360 \{ 170, 170, 170, 170, 170\}, +00361 \{ 170, 170, 170, 170, 170\} +00362 \} +00363 \} +00364 \}; +00365 +00366 PRIVATE \textcolor{keywordtype}{int} int11\_H\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5] = +00367 \textcolor{comment}{/* GC..GC */} +00368 \{ \textcolor{comment}{/* noPair */} \{\{\{0\}\}\}, +00369 \{ \textcolor{comment}{/* noPair */} \{\{0\}\}, +00370 \{ \{ 0, 0, 0, 0, 0\}, +00371 \{ 0, 0, 0, 0, 0\}, +00372 \{ 0, 0, 0, 0, 0\}, +00373 \{ 0, 0, 0, 0, 0\}, +00374 \{ 0, 0, 0, 0, 0\}\}, +00375 \textcolor{comment}{/* GC..CG */} +00376 \{ \{ 0, 0, 0, 0, 0\}, +00377 \{ 0, 0, 0, 0, 0\}, +00378 \{ 0, 0, 0, 0, 0\}, +00379 \{ 0, 0, 0, 0, 0\}, +00380 \{ 0, 0, 0, 0, 0\}\}, +00381 \textcolor{comment}{/* GC..GU */} +00382 \{ \{ 0, 0, 0, 0, 0\}, +00383 \{ 0, 0, 0, 0, 0\}, +00384 \{ 0, 0, 0, 0, 0\}, +00385 \{ 0, 0, 0, 0, 0\}, +00386 \{ 0, 0, 0, 0, 0\}\}, +00387 \textcolor{comment}{/* GC..UG */} +00388 \{ \{ 0, 0, 0, 0, 0\}, +00389 \{ 0, 0, 0, 0, 0\}, +00390 \{ 0, 0, 0, 0, 0\}, +00391 \{ 0, 0, 0, 0, 0\}, +00392 \{ 0, 0, 0, 0, 0\}\}, +00393 \textcolor{comment}{/* GC..AU */} +00394 \{ \{ 0, 0, 0, 0, 0\}, +00395 \{ 0, 0, 0, 0, 0\}, +00396 \{ 0, 0, 0, 0, 0\}, +00397 \{ 0, 0, 0, 0, 0\}, +00398 \{ 0, 0, 0, 0, 0\}\}, +00399 \textcolor{comment}{/* GC..UA */} +00400 \{ \{ 0, 0, 0, 0, 0\}, +00401 \{ 0, 0, 0, 0, 0\}, +00402 \{ 0, 0, 0, 0, 0\}, +00403 \{ 0, 0, 0, 0, 0\}, +00404 \{ 0, 0, 0, 0, 0\}\}, +00405 \textcolor{comment}{/* GC.. @ */} +00406 \{ \{ 0, 0, 0, 0, 0\}, +00407 \{ 0, 0, 0, 0, 0\}, +00408 \{ 0, 0, 0, 0, 0\}, +00409 \{ 0, 0, 0, 0, 0\}, +00410 \{ 0, 0, 0, 0, 0\}\}\}, +00411 \textcolor{comment}{/* CG..GC */} +00412 \{ \textcolor{comment}{/* noPair */} \{\{0\}\}, +00413 \{ \{ 0, 0, 0, 0, 0\}, +00414 \{ 0, 0, 0, 0, 0\}, +00415 \{ 0, 0, 0, 0, 0\}, +00416 \{ 0, 0, 0, 0, 0\}, +00417 \{ 0, 0, 0, 0, 0\}\}, +00418 \textcolor{comment}{/* CG..CG */} +00419 \{ \{ 0, 0, 0, 0, 0\}, +00420 \{ 0, 0, 0, 0, 0\}, +00421 \{ 0, 0, 0, 0, 0\}, +00422 \{ 0, 0, 0, 0, 0\}, +00423 \{ 0, 0, 0, 0, 0\}\}, +00424 \textcolor{comment}{/* CG..GU */} +00425 \{ \{ 0, 0, 0, 0, 0\}, +00426 \{ 0, 0, 0, 0, 0\}, +00427 \{ 0, 0, 0, 0, 0\}, +00428 \{ 0, 0, 0, 0, 0\}, +00429 \{ 0, 0, 0, 0, 0\}\}, +00430 \textcolor{comment}{/* CG..UG */} +00431 \{ \{ 0, 0, 0, 0, 0\}, +00432 \{ 0, 0, 0, 0, 0\}, +00433 \{ 0, 0, 0, 0, 0\}, +00434 \{ 0, 0, 0, 0, 0\}, +00435 \{ 0, 0, 0, 0, 0\}\}, +00436 \textcolor{comment}{/* CG..AU */} +00437 \{ \{ 0, 0, 0, 0, 0\}, +00438 \{ 0, 0, 0, 0, 0\}, +00439 \{ 0, 0, 0, 0, 0\}, +00440 \{ 0, 0, 0, 0, 0\}, +00441 \{ 0, 0, 0, 0, 0\}\}, +00442 \textcolor{comment}{/* CG..UA */} +00443 \{ \{ 0, 0, 0, 0, 0\}, +00444 \{ 0, 0, 0, 0, 0\}, +00445 \{ 0, 0, 0, 0, 0\}, +00446 \{ 0, 0, 0, 0, 0\}, +00447 \{ 0, 0, 0, 0, 0\}\}, +00448 \textcolor{comment}{/* CG.. @ */} +00449 \{ \{ 0, 0, 0, 0, 0\}, +00450 \{ 0, 0, 0, 0, 0\}, +00451 \{ 0, 0, 0, 0, 0\}, +00452 \{ 0, 0, 0, 0, 0\}, +00453 \{ 0, 0, 0, 0, 0\}\}\}, +00454 \textcolor{comment}{/* GU..GC */} +00455 \{ \textcolor{comment}{/* noPair */} \{\{0\}\}, +00456 \{ \{ 0, 0, 0, 0, 0\}, +00457 \{ 0, 0, 0, 0, 0\}, +00458 \{ 0, 0, 0, 0, 0\}, +00459 \{ 0, 0, 0, 0, 0\}, +00460 \{ 0, 0, 0, 0, 0\}\}, +00461 \textcolor{comment}{/* GU..CG */} +00462 \{ \{ 0, 0, 0, 0, 0\}, +00463 \{ 0, 0, 0, 0, 0\}, +00464 \{ 0, 0, 0, 0, 0\}, +00465 \{ 0, 0, 0, 0, 0\}, +00466 \{ 0, 0, 0, 0, 0\}\}, +00467 \textcolor{comment}{/* GU..GU */} +00468 \{ \{ 0, 0, 0, 0, 0\}, +00469 \{ 0, 0, 0, 0, 0\}, +00470 \{ 0, 0, 0, 0, 0\}, +00471 \{ 0, 0, 0, 0, 0\}, +00472 \{ 0, 0, 0, 0, 0\}\}, +00473 \textcolor{comment}{/* GU..UG */} +00474 \{ \{ 0, 0, 0, 0, 0\}, +00475 \{ 0, 0, 0, 0, 0\}, +00476 \{ 0, 0, 0, 0, 0\}, +00477 \{ 0, 0, 0, 0, 0\}, +00478 \{ 0, 0, 0, 0, 0\}\}, +00479 \textcolor{comment}{/* GU..AU */} +00480 \{ \{ 0, 0, 0, 0, 0\}, +00481 \{ 0, 0, 0, 0, 0\}, +00482 \{ 0, 0, 0, 0, 0\}, +00483 \{ 0, 0, 0, 0, 0\}, +00484 \{ 0, 0, 0, 0, 0\}\}, +00485 \textcolor{comment}{/* GU..UA */} +00486 \{ \{ 0, 0, 0, 0, 0\}, +00487 \{ 0, 0, 0, 0, 0\}, +00488 \{ 0, 0, 0, 0, 0\}, +00489 \{ 0, 0, 0, 0, 0\}, +00490 \{ 0, 0, 0, 0, 0\}\}, +00491 \textcolor{comment}{/* GU.. @ */} +00492 \{ \{ 0, 0, 0, 0, 0\}, +00493 \{ 0, 0, 0, 0, 0\}, +00494 \{ 0, 0, 0, 0, 0\}, +00495 \{ 0, 0, 0, 0, 0\}, +00496 \{ 0, 0, 0, 0, 0\}\}\}, +00497 \textcolor{comment}{/* UG..GC */} +00498 \{ \textcolor{comment}{/* noPair */} \{\{0\}\}, +00499 \{ \{ 0, 0, 0, 0, 0\}, +00500 \{ 0, 0, 0, 0, 0\}, +00501 \{ 0, 0, 0, 0, 0\}, +00502 \{ 0, 0, 0, 0, 0\}, +00503 \{ 0, 0, 0, 0, 0\}\}, +00504 \textcolor{comment}{/* UG..CG */} +00505 \{ \{ 0, 0, 0, 0, 0\}, +00506 \{ 0, 0, 0, 0, 0\}, +00507 \{ 0, 0, 0, 0, 0\}, +00508 \{ 0, 0, 0, 0, 0\}, +00509 \{ 0, 0, 0, 0, 0\}\}, +00510 \textcolor{comment}{/* UG..GU */} +00511 \{ \{ 0, 0, 0, 0, 0\}, +00512 \{ 0, 0, 0, 0, 0\}, +00513 \{ 0, 0, 0, 0, 0\}, +00514 \{ 0, 0, 0, 0, 0\}, +00515 \{ 0, 0, 0, 0, 0\}\}, +00516 \textcolor{comment}{/* UG..UG */} +00517 \{ \{ 0, 0, 0, 0, 0\}, +00518 \{ 0, 0, 0, 0, 0\}, +00519 \{ 0, 0, 0, 0, 0\}, +00520 \{ 0, 0, 0, 0, 0\}, +00521 \{ 0, 0, 0, 0, 0\}\}, +00522 \textcolor{comment}{/* UG..AU */} +00523 \{ \{ 0, 0, 0, 0, 0\}, +00524 \{ 0, 0, 0, 0, 0\}, +00525 \{ 0, 0, 0, 0, 0\}, +00526 \{ 0, 0, 0, 0, 0\}, +00527 \{ 0, 0, 0, 0, 0\}\}, +00528 \textcolor{comment}{/* UG..UA */} +00529 \{ \{ 0, 0, 0, 0, 0\}, +00530 \{ 0, 0, 0, 0, 0\}, +00531 \{ 0, 0, 0, 0, 0\}, +00532 \{ 0, 0, 0, 0, 0\}, +00533 \{ 0, 0, 0, 0, 0\}\}, +00534 \textcolor{comment}{/* UG.. @ */} +00535 \{ \{ 0, 0, 0, 0, 0\}, +00536 \{ 0, 0, 0, 0, 0\}, +00537 \{ 0, 0, 0, 0, 0\}, +00538 \{ 0, 0, 0, 0, 0\}, +00539 \{ 0, 0, 0, 0, 0\}\}\}, +00540 \textcolor{comment}{/* AU..GC */} +00541 \{ \textcolor{comment}{/* noPair */} \{\{0\}\}, +00542 \{ \{ 0, 0, 0, 0, 0\}, +00543 \{ 0, 0, 0, 0, 0\}, +00544 \{ 0, 0, 0, 0, 0\}, +00545 \{ 0, 0, 0, 0, 0\}, +00546 \{ 0, 0, 0, 0, 0\}\}, +00547 \textcolor{comment}{/* AU..CG */} +00548 \{ \{ 0, 0, 0, 0, 0\}, +00549 \{ 0, 0, 0, 0, 0\}, +00550 \{ 0, 0, 0, 0, 0\}, +00551 \{ 0, 0, 0, 0, 0\}, +00552 \{ 0, 0, 0, 0, 0\}\}, +00553 \textcolor{comment}{/* AU..GU */} +00554 \{ \{ 0, 0, 0, 0, 0\}, +00555 \{ 0, 0, 0, 0, 0\}, +00556 \{ 0, 0, 0, 0, 0\}, +00557 \{ 0, 0, 0, 0, 0\}, +00558 \{ 0, 0, 0, 0, 0\}\}, +00559 \textcolor{comment}{/* AU..UG */} +00560 \{ \{ 0, 0, 0, 0, 0\}, +00561 \{ 0, 0, 0, 0, 0\}, +00562 \{ 0, 0, 0, 0, 0\}, +00563 \{ 0, 0, 0, 0, 0\}, +00564 \{ 0, 0, 0, 0, 0\}\}, +00565 \textcolor{comment}{/* AU..AU */} +00566 \{ \{ 0, 0, 0, 0, 0\}, +00567 \{ 0, 0, 0, 0, 0\}, +00568 \{ 0, 0, 0, 0, 0\}, +00569 \{ 0, 0, 0, 0, 0\}, +00570 \{ 0, 0, 0, 0, 0\}\}, +00571 \textcolor{comment}{/* AU..UA */} +00572 \{ \{ 0, 0, 0, 0, 0\}, +00573 \{ 0, 0, 0, 0, 0\}, +00574 \{ 0, 0, 0, 0, 0\}, +00575 \{ 0, 0, 0, 0, 0\}, +00576 \{ 0, 0, 0, 0, 0\}\}, +00577 \textcolor{comment}{/* AU.. @ */} +00578 \{ \{ 0, 0, 0, 0, 0\}, +00579 \{ 0, 0, 0, 0, 0\}, +00580 \{ 0, 0, 0, 0, 0\}, +00581 \{ 0, 0, 0, 0, 0\}, +00582 \{ 0, 0, 0, 0, 0\}\}\}, +00583 \textcolor{comment}{/* UA..GC */} +00584 \{ \textcolor{comment}{/* noPair */} \{\{0\}\}, +00585 \{ \{ 0, 0, 0, 0, 0\}, +00586 \{ 0, 0, 0, 0, 0\}, +00587 \{ 0, 0, 0, 0, 0\}, +00588 \{ 0, 0, 0, 0, 0\}, +00589 \{ 0, 0, 0, 0, 0\}\}, +00590 \textcolor{comment}{/* UA..CG */} +00591 \{ \{ 0, 0, 0, 0, 0\}, +00592 \{ 0, 0, 0, 0, 0\}, +00593 \{ 0, 0, 0, 0, 0\}, +00594 \{ 0, 0, 0, 0, 0\}, +00595 \{ 0, 0, 0, 0, 0\}\}, +00596 \textcolor{comment}{/* UA..GU */} +00597 \{ \{ 0, 0, 0, 0, 0\}, +00598 \{ 0, 0, 0, 0, 0\}, +00599 \{ 0, 0, 0, 0, 0\}, +00600 \{ 0, 0, 0, 0, 0\}, +00601 \{ 0, 0, 0, 0, 0\}\}, +00602 \textcolor{comment}{/* UA..UG */} +00603 \{ \{ 0, 0, 0, 0, 0\}, +00604 \{ 0, 0, 0, 0, 0\}, +00605 \{ 0, 0, 0, 0, 0\}, +00606 \{ 0, 0, 0, 0, 0\}, +00607 \{ 0, 0, 0, 0, 0\}\}, +00608 \textcolor{comment}{/* UA..AU */} +00609 \{ \{ 0, 0, 0, 0, 0\}, +00610 \{ 0, 0, 0, 0, 0\}, +00611 \{ 0, 0, 0, 0, 0\}, +00612 \{ 0, 0, 0, 0, 0\}, +00613 \{ 0, 0, 0, 0, 0\}\}, +00614 \textcolor{comment}{/* UA..UA */} +00615 \{ \{ 0, 0, 0, 0, 0\}, +00616 \{ 0, 0, 0, 0, 0\}, +00617 \{ 0, 0, 0, 0, 0\}, +00618 \{ 0, 0, 0, 0, 0\}, +00619 \{ 0, 0, 0, 0, 0\}\}, +00620 \textcolor{comment}{/* UA.. @ */} +00621 \{ \{ 0, 0, 0, 0, 0\}, +00622 \{ 0, 0, 0, 0, 0\}, +00623 \{ 0, 0, 0, 0, 0\}, +00624 \{ 0, 0, 0, 0, 0\}, +00625 \{ 0, 0, 0, 0, 0\}\}\}, +00626 \textcolor{comment}{/* @..GC */} +00627 \{ \textcolor{comment}{/* noPair */} \{\{0\}\}, +00628 \{ \{ 0, 0, 0, 0, 0\}, +00629 \{ 0, 0, 0, 0, 0\}, +00630 \{ 0, 0, 0, 0, 0\}, +00631 \{ 0, 0, 0, 0, 0\}, +00632 \{ 0, 0, 0, 0, 0\}\}, +00633 \textcolor{comment}{/* @..CG */} +00634 \{ \{ 0, 0, 0, 0, 0\}, +00635 \{ 0, 0, 0, 0, 0\}, +00636 \{ 0, 0, 0, 0, 0\}, +00637 \{ 0, 0, 0, 0, 0\}, +00638 \{ 0, 0, 0, 0, 0\}\}, +00639 \textcolor{comment}{/* @..GU */} +00640 \{ \{ 0, 0, 0, 0, 0\}, +00641 \{ 0, 0, 0, 0, 0\}, +00642 \{ 0, 0, 0, 0, 0\}, +00643 \{ 0, 0, 0, 0, 0\}, +00644 \{ 0, 0, 0, 0, 0\}\}, +00645 \textcolor{comment}{/* @..UG */} +00646 \{ \{ 0, 0, 0, 0, 0\}, +00647 \{ 0, 0, 0, 0, 0\}, +00648 \{ 0, 0, 0, 0, 0\}, +00649 \{ 0, 0, 0, 0, 0\}, +00650 \{ 0, 0, 0, 0, 0\}\}, +00651 \textcolor{comment}{/* @..AU */} +00652 \{ \{ 0, 0, 0, 0, 0\}, +00653 \{ 0, 0, 0, 0, 0\}, +00654 \{ 0, 0, 0, 0, 0\}, +00655 \{ 0, 0, 0, 0, 0\}, +00656 \{ 0, 0, 0, 0, 0\}\}, +00657 \textcolor{comment}{/* @..UA */} +00658 \{ \{ 0, 0, 0, 0, 0\}, +00659 \{ 0, 0, 0, 0, 0\}, +00660 \{ 0, 0, 0, 0, 0\}, +00661 \{ 0, 0, 0, 0, 0\}, +00662 \{ 0, 0, 0, 0, 0\}\}, +00663 \textcolor{comment}{/* @.. @ */} +00664 \{ \{ 0, 0, 0, 0, 0\}, +00665 \{ 0, 0, 0, 0, 0\}, +00666 \{ 0, 0, 0, 0, 0\}, +00667 \{ 0, 0, 0, 0, 0\}, +00668 \{ 0, 0, 0, 0, 0\}\}\}\}; +00669 +00670 PRIVATE \textcolor{keywordtype}{int} int21\_37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5] = +00671 \{ \textcolor{comment}{/* noPair */} \{\{\{\{0\}\}\}\}, +00672 \{ \textcolor{comment}{/* noPair */} \{\{\{0\}\}\}, +00673 \{ +00674 \textcolor{comment}{/* CG.@..GC */} +00675 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00676 \textcolor{comment}{/* CG.A..GC */} +00677 \{\{ 550, 550, 550, 550, 550\},\{ 550, 240, 220, 160, 400\},\{ 550, 210, 170, 160, 400\},\{ 550, 100, 60, 40, 400 + \},\{ 550, 400, 400, 400, 400\}\}, +00678 \textcolor{comment}{/* CG.C..GC */} +00679 \{\{ 550, 550, 550, 550, 550\},\{ 550, 230, 220, 400, 220\},\{ 550, 220, 250, 400, 220\},\{ 550, 400, 400, 400, 400 + \},\{ 550, 250, 190, 400, 220\}\}, +00680 \textcolor{comment}{/* CG.G..GC */} +00681 \{\{ 550, 550, 550, 550, 550\},\{ 550, 170, 400, 80, 400\},\{ 550, 400, 400, 400, 400\},\{ 550, 80, 400, 220, 400 + \},\{ 550, 400, 400, 400, 400\}\}, +00682 \textcolor{comment}{/* CG.U..GC */} +00683 \{\{ 550, 550, 550, 550, 550\},\{ 550, 400, 400, 400, 400\},\{ 550, 400, 220, 400, 130\},\{ 550, 400, 400, 400, 400 + \},\{ 550, 400, 170, 400, 120\}\} +00684 \}, +00685 \{ +00686 \textcolor{comment}{/* CG.@..CG */} +00687 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00688 \textcolor{comment}{/* CG.A..CG */} +00689 \{\{ 550, 550, 550, 550, 550\},\{ 550, 230, 220, 110, 400\},\{ 550, 210, 170, 160, 400\},\{ 550, 80, 60, 40, 400 + \},\{ 550, 400, 400, 400, 400\}\}, +00690 \textcolor{comment}{/* CG.C..CG */} +00691 \{\{ 550, 550, 550, 550, 550\},\{ 550, 230, 220, 400, 220\},\{ 550, 220, 250, 400, 220\},\{ 550, 400, 400, 400, 400 + \},\{ 550, 250, 190, 400, 220\}\}, +00692 \textcolor{comment}{/* CG.G..CG */} +00693 \{\{ 550, 550, 550, 550, 550\},\{ 550, 170, 400, 80, 400\},\{ 550, 400, 400, 400, 400\},\{ 550, 80, 400, 220, 400 + \},\{ 550, 400, 400, 400, 400\}\}, +00694 \textcolor{comment}{/* CG.U..CG */} +00695 \{\{ 550, 550, 550, 550, 550\},\{ 550, 400, 400, 400, 400\},\{ 550, 400, 220, 400, 150\},\{ 550, 400, 400, 400, 400 + \},\{ 550, 400, 170, 400, 120\}\} +00696 \}, +00697 \{ +00698 \textcolor{comment}{/* CG.@..UG */} +00699 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00700 \textcolor{comment}{/* CG.A..UG */} +00701 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 300, 240, 480\},\{ 550, 290, 250, 240, 480\},\{ 550, 180, 140, 120, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00702 \textcolor{comment}{/* CG.C..UG */} +00703 \{\{ 550, 550, 550, 550, 550\},\{ 550, 310, 300, 480, 300\},\{ 550, 300, 330, 480, 300\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 330, 270, 480, 300\}\}, +00704 \textcolor{comment}{/* CG.G..UG */} +00705 \{\{ 550, 550, 550, 550, 550\},\{ 550, 250, 480, 160, 480\},\{ 550, 480, 480, 480, 480\},\{ 550, 160, 480, 300, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00706 \textcolor{comment}{/* CG.U..UG */} +00707 \{\{ 550, 550, 550, 550, 550\},\{ 550, 480, 480, 480, 480\},\{ 550, 480, 300, 480, 210\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 480, 250, 480, 200\}\} +00708 \}, +00709 \{ +00710 \textcolor{comment}{/* CG.@..GU */} +00711 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00712 \textcolor{comment}{/* CG.A..GU */} +00713 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 300, 240, 480\},\{ 550, 290, 250, 240, 480\},\{ 550, 180, 140, 120, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00714 \textcolor{comment}{/* CG.C..GU */} +00715 \{\{ 550, 550, 550, 550, 550\},\{ 550, 310, 300, 480, 300\},\{ 550, 300, 330, 480, 300\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 330, 270, 480, 300\}\}, +00716 \textcolor{comment}{/* CG.G..GU */} +00717 \{\{ 550, 550, 550, 550, 550\},\{ 550, 250, 480, 160, 480\},\{ 550, 480, 480, 480, 480\},\{ 550, 160, 480, 300, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00718 \textcolor{comment}{/* CG.U..GU */} +00719 \{\{ 550, 550, 550, 550, 550\},\{ 550, 480, 480, 480, 480\},\{ 550, 480, 300, 480, 210\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 480, 250, 480, 200\}\} +00720 \}, +00721 \{ +00722 \textcolor{comment}{/* CG.@..UA */} +00723 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00724 \textcolor{comment}{/* CG.A..UA */} +00725 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 300, 240, 480\},\{ 550, 290, 250, 240, 480\},\{ 550, 180, 140, 120, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00726 \textcolor{comment}{/* CG.C..UA */} +00727 \{\{ 550, 550, 550, 550, 550\},\{ 550, 310, 300, 480, 300\},\{ 550, 300, 330, 480, 300\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 330, 270, 480, 300\}\}, +00728 \textcolor{comment}{/* CG.G..UA */} +00729 \{\{ 550, 550, 550, 550, 550\},\{ 550, 250, 480, 160, 480\},\{ 550, 480, 480, 480, 480\},\{ 550, 160, 480, 300, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00730 \textcolor{comment}{/* CG.U..UA */} +00731 \{\{ 550, 550, 550, 550, 550\},\{ 550, 480, 480, 480, 480\},\{ 550, 480, 300, 480, 210\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 480, 250, 480, 200\}\} +00732 \}, +00733 \{ +00734 \textcolor{comment}{/* CG.@..AU */} +00735 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00736 \textcolor{comment}{/* CG.A..AU */} +00737 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 300, 240, 480\},\{ 550, 290, 250, 240, 480\},\{ 550, 180, 140, 120, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00738 \textcolor{comment}{/* CG.C..AU */} +00739 \{\{ 550, 550, 550, 550, 550\},\{ 550, 310, 300, 480, 300\},\{ 550, 300, 330, 480, 300\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 330, 270, 480, 300\}\}, +00740 \textcolor{comment}{/* CG.G..AU */} +00741 \{\{ 550, 550, 550, 550, 550\},\{ 550, 250, 480, 160, 480\},\{ 550, 480, 480, 480, 480\},\{ 550, 160, 480, 300, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00742 \textcolor{comment}{/* CG.U..AU */} +00743 \{\{ 550, 550, 550, 550, 550\},\{ 550, 480, 480, 480, 480\},\{ 550, 480, 300, 480, 210\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 480, 250, 480, 200\}\} +00744 \}, +00745 \{ +00746 \textcolor{comment}{/* CG.@..?? */} +00747 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00748 \textcolor{comment}{/* CG.A..?? */} +00749 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00750 \textcolor{comment}{/* CG.C..?? */} +00751 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00752 \textcolor{comment}{/* CG.G..?? */} +00753 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00754 \textcolor{comment}{/* CG.U..?? */} +00755 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\} +00756 \} +00757 \}, +00758 \{ \textcolor{comment}{/* noPair */} \{\{\{0\}\}\}, +00759 \{ +00760 \textcolor{comment}{/* GC.@..GC */} +00761 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00762 \textcolor{comment}{/* GC.A..GC */} +00763 \{\{ 550, 550, 550, 550, 550\},\{ 550, 250, 220, 210, 400\},\{ 550, 210, 170, 160, 400\},\{ 550, 120, 60, 40, 400 + \},\{ 550, 400, 400, 400, 400\}\}, +00764 \textcolor{comment}{/* GC.C..GC */} +00765 \{\{ 550, 550, 550, 550, 550\},\{ 550, 230, 220, 400, 220\},\{ 550, 220, 250, 400, 220\},\{ 550, 400, 400, 400, 400 + \},\{ 550, 250, 190, 400, 220\}\}, +00766 \textcolor{comment}{/* GC.G..GC */} +00767 \{\{ 550, 550, 550, 550, 550\},\{ 550, 170, 400, 80, 400\},\{ 550, 400, 400, 400, 400\},\{ 550, 80, 400, 220, 400 + \},\{ 550, 400, 400, 400, 400\}\}, +00768 \textcolor{comment}{/* GC.U..GC */} +00769 \{\{ 550, 550, 550, 550, 550\},\{ 550, 400, 400, 400, 400\},\{ 550, 400, 220, 400, 120\},\{ 550, 400, 400, 400, 400 + \},\{ 550, 400, 170, 400, 120\}\} +00770 \}, +00771 \{ +00772 \textcolor{comment}{/* GC.@..CG */} +00773 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00774 \textcolor{comment}{/* GC.A..CG */} +00775 \{\{ 550, 550, 550, 550, 550\},\{ 550, 240, 220, 160, 400\},\{ 550, 210, 170, 160, 400\},\{ 550, 100, 60, 40, 400 + \},\{ 550, 400, 400, 400, 400\}\}, +00776 \textcolor{comment}{/* GC.C..CG */} +00777 \{\{ 550, 550, 550, 550, 550\},\{ 550, 230, 220, 400, 220\},\{ 550, 220, 250, 400, 220\},\{ 550, 400, 400, 400, 400 + \},\{ 550, 250, 190, 400, 220\}\}, +00778 \textcolor{comment}{/* GC.G..CG */} +00779 \{\{ 550, 550, 550, 550, 550\},\{ 550, 170, 400, 80, 400\},\{ 550, 400, 400, 400, 400\},\{ 550, 80, 400, 220, 400 + \},\{ 550, 400, 400, 400, 400\}\}, +00780 \textcolor{comment}{/* GC.U..CG */} +00781 \{\{ 550, 550, 550, 550, 550\},\{ 550, 400, 400, 400, 400\},\{ 550, 400, 220, 400, 130\},\{ 550, 400, 400, 400, 400 + \},\{ 550, 400, 170, 400, 120\}\} +00782 \}, +00783 \{ +00784 \textcolor{comment}{/* GC.@..UG */} +00785 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00786 \textcolor{comment}{/* GC.A..UG */} +00787 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 300, 240, 480\},\{ 550, 290, 250, 240, 480\},\{ 550, 180, 140, 120, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00788 \textcolor{comment}{/* GC.C..UG */} +00789 \{\{ 550, 550, 550, 550, 550\},\{ 550, 310, 300, 480, 300\},\{ 550, 300, 330, 480, 300\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 330, 270, 480, 300\}\}, +00790 \textcolor{comment}{/* GC.G..UG */} +00791 \{\{ 550, 550, 550, 550, 550\},\{ 550, 250, 480, 160, 480\},\{ 550, 480, 480, 480, 480\},\{ 550, 160, 480, 300, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00792 \textcolor{comment}{/* GC.U..UG */} +00793 \{\{ 550, 550, 550, 550, 550\},\{ 550, 480, 480, 480, 480\},\{ 550, 480, 300, 480, 210\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 480, 250, 480, 200\}\} +00794 \}, +00795 \{ +00796 \textcolor{comment}{/* GC.@..GU */} +00797 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00798 \textcolor{comment}{/* GC.A..GU */} +00799 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 300, 240, 480\},\{ 550, 290, 250, 240, 480\},\{ 550, 180, 140, 120, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00800 \textcolor{comment}{/* GC.C..GU */} +00801 \{\{ 550, 550, 550, 550, 550\},\{ 550, 310, 300, 480, 300\},\{ 550, 300, 330, 480, 300\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 330, 270, 480, 300\}\}, +00802 \textcolor{comment}{/* GC.G..GU */} +00803 \{\{ 550, 550, 550, 550, 550\},\{ 550, 250, 480, 160, 480\},\{ 550, 480, 480, 480, 480\},\{ 550, 160, 480, 300, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00804 \textcolor{comment}{/* GC.U..GU */} +00805 \{\{ 550, 550, 550, 550, 550\},\{ 550, 480, 480, 480, 480\},\{ 550, 480, 300, 480, 210\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 480, 250, 480, 200\}\} +00806 \}, +00807 \{ +00808 \textcolor{comment}{/* GC.@..UA */} +00809 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00810 \textcolor{comment}{/* GC.A..UA */} +00811 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 300, 240, 480\},\{ 550, 290, 250, 240, 480\},\{ 550, 180, 140, 120, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00812 \textcolor{comment}{/* GC.C..UA */} +00813 \{\{ 550, 550, 550, 550, 550\},\{ 550, 310, 300, 480, 300\},\{ 550, 300, 330, 480, 300\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 330, 270, 480, 300\}\}, +00814 \textcolor{comment}{/* GC.G..UA */} +00815 \{\{ 550, 550, 550, 550, 550\},\{ 550, 250, 480, 160, 480\},\{ 550, 480, 480, 480, 480\},\{ 550, 160, 480, 300, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00816 \textcolor{comment}{/* GC.U..UA */} +00817 \{\{ 550, 550, 550, 550, 550\},\{ 550, 480, 480, 480, 480\},\{ 550, 480, 300, 480, 210\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 480, 250, 480, 200\}\} +00818 \}, +00819 \{ +00820 \textcolor{comment}{/* GC.@..AU */} +00821 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00822 \textcolor{comment}{/* GC.A..AU */} +00823 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 300, 240, 480\},\{ 550, 290, 250, 240, 480\},\{ 550, 180, 140, 120, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00824 \textcolor{comment}{/* GC.C..AU */} +00825 \{\{ 550, 550, 550, 550, 550\},\{ 550, 310, 300, 480, 300\},\{ 550, 300, 330, 480, 300\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 330, 270, 480, 300\}\}, +00826 \textcolor{comment}{/* GC.G..AU */} +00827 \{\{ 550, 550, 550, 550, 550\},\{ 550, 250, 480, 160, 480\},\{ 550, 480, 480, 480, 480\},\{ 550, 160, 480, 300, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00828 \textcolor{comment}{/* GC.U..AU */} +00829 \{\{ 550, 550, 550, 550, 550\},\{ 550, 480, 480, 480, 480\},\{ 550, 480, 300, 480, 210\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 480, 250, 480, 200\}\} +00830 \}, +00831 \{ +00832 \textcolor{comment}{/* GC.@..?? */} +00833 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00834 \textcolor{comment}{/* GC.A..?? */} +00835 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00836 \textcolor{comment}{/* GC.C..?? */} +00837 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00838 \textcolor{comment}{/* GC.G..?? */} +00839 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00840 \textcolor{comment}{/* GC.U..?? */} +00841 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\} +00842 \} +00843 \}, +00844 \{ \textcolor{comment}{/* noPair */} \{\{\{0\}\}\}, +00845 \{ +00846 \textcolor{comment}{/* GU.@..GC */} +00847 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00848 \textcolor{comment}{/* GU.A..GC */} +00849 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 300, 240, 480\},\{ 550, 290, 250, 240, 480\},\{ 550, 180, 140, 120, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00850 \textcolor{comment}{/* GU.C..GC */} +00851 \{\{ 550, 550, 550, 550, 550\},\{ 550, 310, 300, 480, 300\},\{ 550, 300, 330, 480, 300\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 330, 270, 480, 300\}\}, +00852 \textcolor{comment}{/* GU.G..GC */} +00853 \{\{ 550, 550, 550, 550, 550\},\{ 550, 250, 480, 160, 480\},\{ 550, 480, 480, 480, 480\},\{ 550, 160, 480, 300, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00854 \textcolor{comment}{/* GU.U..GC */} +00855 \{\{ 550, 550, 550, 550, 550\},\{ 550, 480, 480, 480, 480\},\{ 550, 480, 300, 480, 210\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 480, 250, 480, 200\}\} +00856 \}, +00857 \{ +00858 \textcolor{comment}{/* GU.@..CG */} +00859 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00860 \textcolor{comment}{/* GU.A..CG */} +00861 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 300, 240, 480\},\{ 550, 290, 250, 240, 480\},\{ 550, 180, 140, 120, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00862 \textcolor{comment}{/* GU.C..CG */} +00863 \{\{ 550, 550, 550, 550, 550\},\{ 550, 310, 300, 480, 300\},\{ 550, 300, 330, 480, 300\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 330, 270, 480, 300\}\}, +00864 \textcolor{comment}{/* GU.G..CG */} +00865 \{\{ 550, 550, 550, 550, 550\},\{ 550, 250, 480, 160, 480\},\{ 550, 480, 480, 480, 480\},\{ 550, 160, 480, 300, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00866 \textcolor{comment}{/* GU.U..CG */} +00867 \{\{ 550, 550, 550, 550, 550\},\{ 550, 480, 480, 480, 480\},\{ 550, 480, 300, 480, 210\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 480, 250, 480, 200\}\} +00868 \}, +00869 \{ +00870 \textcolor{comment}{/* GU.@..UG */} +00871 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00872 \textcolor{comment}{/* GU.A..UG */} +00873 \{\{ 550, 550, 550, 550, 550\},\{ 550, 390, 370, 310, 550\},\{ 550, 360, 320, 310, 550\},\{ 550, 250, 210, 190, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00874 \textcolor{comment}{/* GU.C..UG */} +00875 \{\{ 550, 550, 550, 550, 550\},\{ 550, 380, 370, 550, 370\},\{ 550, 370, 400, 550, 370\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 400, 340, 550, 370\}\}, +00876 \textcolor{comment}{/* GU.G..UG */} +00877 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 550, 230, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 230, 550, 370, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00878 \textcolor{comment}{/* GU.U..UG */} +00879 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 370, 550, 280\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 320, 550, 270\}\} +00880 \}, +00881 \{ +00882 \textcolor{comment}{/* GU.@..GU */} +00883 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00884 \textcolor{comment}{/* GU.A..GU */} +00885 \{\{ 550, 550, 550, 550, 550\},\{ 550, 390, 370, 310, 550\},\{ 550, 360, 320, 310, 550\},\{ 550, 250, 210, 190, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00886 \textcolor{comment}{/* GU.C..GU */} +00887 \{\{ 550, 550, 550, 550, 550\},\{ 550, 380, 370, 550, 370\},\{ 550, 370, 400, 550, 370\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 400, 340, 550, 370\}\}, +00888 \textcolor{comment}{/* GU.G..GU */} +00889 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 550, 230, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 230, 550, 370, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00890 \textcolor{comment}{/* GU.U..GU */} +00891 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 370, 550, 280\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 320, 550, 270\}\} +00892 \}, +00893 \{ +00894 \textcolor{comment}{/* GU.@..UA */} +00895 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00896 \textcolor{comment}{/* GU.A..UA */} +00897 \{\{ 550, 550, 550, 550, 550\},\{ 550, 390, 370, 310, 550\},\{ 550, 360, 320, 310, 550\},\{ 550, 250, 210, 190, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00898 \textcolor{comment}{/* GU.C..UA */} +00899 \{\{ 550, 550, 550, 550, 550\},\{ 550, 380, 370, 550, 370\},\{ 550, 370, 400, 550, 370\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 400, 340, 550, 370\}\}, +00900 \textcolor{comment}{/* GU.G..UA */} +00901 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 550, 230, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 230, 550, 370, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00902 \textcolor{comment}{/* GU.U..UA */} +00903 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 370, 550, 280\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 320, 550, 270\}\} +00904 \}, +00905 \{ +00906 \textcolor{comment}{/* GU.@..AU */} +00907 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00908 \textcolor{comment}{/* GU.A..AU */} +00909 \{\{ 550, 550, 550, 550, 550\},\{ 550, 390, 370, 310, 550\},\{ 550, 360, 320, 310, 550\},\{ 550, 250, 210, 190, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00910 \textcolor{comment}{/* GU.C..AU */} +00911 \{\{ 550, 550, 550, 550, 550\},\{ 550, 380, 370, 550, 370\},\{ 550, 370, 400, 550, 370\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 400, 340, 550, 370\}\}, +00912 \textcolor{comment}{/* GU.G..AU */} +00913 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 550, 230, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 230, 550, 370, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00914 \textcolor{comment}{/* GU.U..AU */} +00915 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 370, 550, 280\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 320, 550, 270\}\} +00916 \}, +00917 \{ +00918 \textcolor{comment}{/* GU.@..?? */} +00919 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00920 \textcolor{comment}{/* GU.A..?? */} +00921 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00922 \textcolor{comment}{/* GU.C..?? */} +00923 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00924 \textcolor{comment}{/* GU.G..?? */} +00925 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00926 \textcolor{comment}{/* GU.U..?? */} +00927 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\} +00928 \} +00929 \}, +00930 \{ \textcolor{comment}{/* noPair */} \{\{\{0\}\}\}, +00931 \{ +00932 \textcolor{comment}{/* UG.@..GC */} +00933 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00934 \textcolor{comment}{/* UG.A..GC */} +00935 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 300, 240, 480\},\{ 550, 290, 250, 240, 480\},\{ 550, 180, 140, 120, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00936 \textcolor{comment}{/* UG.C..GC */} +00937 \{\{ 550, 550, 550, 550, 550\},\{ 550, 310, 300, 480, 300\},\{ 550, 300, 330, 480, 300\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 330, 270, 480, 300\}\}, +00938 \textcolor{comment}{/* UG.G..GC */} +00939 \{\{ 550, 550, 550, 550, 550\},\{ 550, 250, 480, 160, 480\},\{ 550, 480, 480, 480, 480\},\{ 550, 160, 480, 300, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00940 \textcolor{comment}{/* UG.U..GC */} +00941 \{\{ 550, 550, 550, 550, 550\},\{ 550, 480, 480, 480, 480\},\{ 550, 480, 300, 480, 210\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 480, 250, 480, 200\}\} +00942 \}, +00943 \{ +00944 \textcolor{comment}{/* UG.@..CG */} +00945 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00946 \textcolor{comment}{/* UG.A..CG */} +00947 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 300, 240, 480\},\{ 550, 290, 250, 240, 480\},\{ 550, 180, 140, 120, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00948 \textcolor{comment}{/* UG.C..CG */} +00949 \{\{ 550, 550, 550, 550, 550\},\{ 550, 310, 300, 480, 300\},\{ 550, 300, 330, 480, 300\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 330, 270, 480, 300\}\}, +00950 \textcolor{comment}{/* UG.G..CG */} +00951 \{\{ 550, 550, 550, 550, 550\},\{ 550, 250, 480, 160, 480\},\{ 550, 480, 480, 480, 480\},\{ 550, 160, 480, 300, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +00952 \textcolor{comment}{/* UG.U..CG */} +00953 \{\{ 550, 550, 550, 550, 550\},\{ 550, 480, 480, 480, 480\},\{ 550, 480, 300, 480, 210\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 480, 250, 480, 200\}\} +00954 \}, +00955 \{ +00956 \textcolor{comment}{/* UG.@..UG */} +00957 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00958 \textcolor{comment}{/* UG.A..UG */} +00959 \{\{ 550, 550, 550, 550, 550\},\{ 550, 390, 370, 310, 550\},\{ 550, 360, 320, 310, 550\},\{ 550, 250, 210, 190, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00960 \textcolor{comment}{/* UG.C..UG */} +00961 \{\{ 550, 550, 550, 550, 550\},\{ 550, 380, 370, 550, 370\},\{ 550, 370, 400, 550, 370\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 400, 340, 550, 370\}\}, +00962 \textcolor{comment}{/* UG.G..UG */} +00963 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 550, 230, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 230, 550, 370, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00964 \textcolor{comment}{/* UG.U..UG */} +00965 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 370, 550, 280\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 320, 550, 270\}\} +00966 \}, +00967 \{ +00968 \textcolor{comment}{/* UG.@..GU */} +00969 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00970 \textcolor{comment}{/* UG.A..GU */} +00971 \{\{ 550, 550, 550, 550, 550\},\{ 550, 390, 370, 310, 550\},\{ 550, 360, 320, 310, 550\},\{ 550, 250, 210, 190, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00972 \textcolor{comment}{/* UG.C..GU */} +00973 \{\{ 550, 550, 550, 550, 550\},\{ 550, 380, 370, 550, 370\},\{ 550, 370, 400, 550, 370\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 400, 340, 550, 370\}\}, +00974 \textcolor{comment}{/* UG.G..GU */} +00975 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 550, 230, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 230, 550, 370, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00976 \textcolor{comment}{/* UG.U..GU */} +00977 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 370, 550, 280\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 320, 550, 270\}\} +00978 \}, +00979 \{ +00980 \textcolor{comment}{/* UG.@..UA */} +00981 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00982 \textcolor{comment}{/* UG.A..UA */} +00983 \{\{ 550, 550, 550, 550, 550\},\{ 550, 390, 370, 310, 550\},\{ 550, 360, 320, 310, 550\},\{ 550, 250, 210, 190, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00984 \textcolor{comment}{/* UG.C..UA */} +00985 \{\{ 550, 550, 550, 550, 550\},\{ 550, 380, 370, 550, 370\},\{ 550, 370, 400, 550, 370\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 400, 340, 550, 370\}\}, +00986 \textcolor{comment}{/* UG.G..UA */} +00987 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 550, 230, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 230, 550, 370, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00988 \textcolor{comment}{/* UG.U..UA */} +00989 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 370, 550, 280\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 320, 550, 270\}\} +00990 \}, +00991 \{ +00992 \textcolor{comment}{/* UG.@..AU */} +00993 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00994 \textcolor{comment}{/* UG.A..AU */} +00995 \{\{ 550, 550, 550, 550, 550\},\{ 550, 390, 370, 310, 550\},\{ 550, 360, 320, 310, 550\},\{ 550, 250, 210, 190, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +00996 \textcolor{comment}{/* UG.C..AU */} +00997 \{\{ 550, 550, 550, 550, 550\},\{ 550, 380, 370, 550, 370\},\{ 550, 370, 400, 550, 370\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 400, 340, 550, 370\}\}, +00998 \textcolor{comment}{/* UG.G..AU */} +00999 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 550, 230, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 230, 550, 370, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01000 \textcolor{comment}{/* UG.U..AU */} +01001 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 370, 550, 280\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 320, 550, 270\}\} +01002 \}, +01003 \{ +01004 \textcolor{comment}{/* UG.@..?? */} +01005 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01006 \textcolor{comment}{/* UG.A..?? */} +01007 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01008 \textcolor{comment}{/* UG.C..?? */} +01009 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01010 \textcolor{comment}{/* UG.G..?? */} +01011 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01012 \textcolor{comment}{/* UG.U..?? */} +01013 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\} +01014 \} +01015 \}, +01016 \{ \textcolor{comment}{/* noPair */} \{\{\{0\}\}\}, +01017 \{ +01018 \textcolor{comment}{/* AU.@..GC */} +01019 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01020 \textcolor{comment}{/* AU.A..GC */} +01021 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 300, 240, 480\},\{ 550, 290, 250, 240, 480\},\{ 550, 180, 140, 120, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +01022 \textcolor{comment}{/* AU.C..GC */} +01023 \{\{ 550, 550, 550, 550, 550\},\{ 550, 310, 300, 480, 300\},\{ 550, 300, 330, 480, 300\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 330, 270, 480, 300\}\}, +01024 \textcolor{comment}{/* AU.G..GC */} +01025 \{\{ 550, 550, 550, 550, 550\},\{ 550, 250, 480, 160, 480\},\{ 550, 480, 480, 480, 480\},\{ 550, 160, 480, 300, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +01026 \textcolor{comment}{/* AU.U..GC */} +01027 \{\{ 550, 550, 550, 550, 550\},\{ 550, 480, 480, 480, 480\},\{ 550, 480, 300, 480, 210\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 480, 250, 480, 200\}\} +01028 \}, +01029 \{ +01030 \textcolor{comment}{/* AU.@..CG */} +01031 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01032 \textcolor{comment}{/* AU.A..CG */} +01033 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 300, 240, 480\},\{ 550, 290, 250, 240, 480\},\{ 550, 180, 140, 120, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +01034 \textcolor{comment}{/* AU.C..CG */} +01035 \{\{ 550, 550, 550, 550, 550\},\{ 550, 310, 300, 480, 300\},\{ 550, 300, 330, 480, 300\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 330, 270, 480, 300\}\}, +01036 \textcolor{comment}{/* AU.G..CG */} +01037 \{\{ 550, 550, 550, 550, 550\},\{ 550, 250, 480, 160, 480\},\{ 550, 480, 480, 480, 480\},\{ 550, 160, 480, 300, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +01038 \textcolor{comment}{/* AU.U..CG */} +01039 \{\{ 550, 550, 550, 550, 550\},\{ 550, 480, 480, 480, 480\},\{ 550, 480, 300, 480, 210\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 480, 250, 480, 200\}\} +01040 \}, +01041 \{ +01042 \textcolor{comment}{/* AU.@..UG */} +01043 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01044 \textcolor{comment}{/* AU.A..UG */} +01045 \{\{ 550, 550, 550, 550, 550\},\{ 550, 390, 370, 310, 550\},\{ 550, 360, 320, 310, 550\},\{ 550, 250, 210, 190, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01046 \textcolor{comment}{/* AU.C..UG */} +01047 \{\{ 550, 550, 550, 550, 550\},\{ 550, 380, 370, 550, 370\},\{ 550, 370, 400, 550, 370\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 400, 340, 550, 370\}\}, +01048 \textcolor{comment}{/* AU.G..UG */} +01049 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 550, 230, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 230, 550, 370, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01050 \textcolor{comment}{/* AU.U..UG */} +01051 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 370, 550, 280\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 320, 550, 270\}\} +01052 \}, +01053 \{ +01054 \textcolor{comment}{/* AU.@..GU */} +01055 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01056 \textcolor{comment}{/* AU.A..GU */} +01057 \{\{ 550, 550, 550, 550, 550\},\{ 550, 390, 370, 310, 550\},\{ 550, 360, 320, 310, 550\},\{ 550, 250, 210, 190, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01058 \textcolor{comment}{/* AU.C..GU */} +01059 \{\{ 550, 550, 550, 550, 550\},\{ 550, 380, 370, 550, 370\},\{ 550, 370, 400, 550, 370\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 400, 340, 550, 370\}\}, +01060 \textcolor{comment}{/* AU.G..GU */} +01061 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 550, 230, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 230, 550, 370, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01062 \textcolor{comment}{/* AU.U..GU */} +01063 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 370, 550, 280\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 320, 550, 270\}\} +01064 \}, +01065 \{ +01066 \textcolor{comment}{/* AU.@..UA */} +01067 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01068 \textcolor{comment}{/* AU.A..UA */} +01069 \{\{ 550, 550, 550, 550, 550\},\{ 550, 390, 370, 310, 550\},\{ 550, 360, 320, 310, 550\},\{ 550, 250, 210, 190, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01070 \textcolor{comment}{/* AU.C..UA */} +01071 \{\{ 550, 550, 550, 550, 550\},\{ 550, 380, 370, 550, 370\},\{ 550, 370, 400, 550, 370\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 400, 340, 550, 370\}\}, +01072 \textcolor{comment}{/* AU.G..UA */} +01073 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 550, 230, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 230, 550, 370, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01074 \textcolor{comment}{/* AU.U..UA */} +01075 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 370, 550, 280\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 320, 550, 270\}\} +01076 \}, +01077 \{ +01078 \textcolor{comment}{/* AU.@..AU */} +01079 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01080 \textcolor{comment}{/* AU.A..AU */} +01081 \{\{ 550, 550, 550, 550, 550\},\{ 550, 390, 370, 310, 550\},\{ 550, 360, 320, 310, 550\},\{ 550, 250, 210, 190, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01082 \textcolor{comment}{/* AU.C..AU */} +01083 \{\{ 550, 550, 550, 550, 550\},\{ 550, 380, 370, 550, 370\},\{ 550, 370, 400, 550, 370\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 400, 340, 550, 370\}\}, +01084 \textcolor{comment}{/* AU.G..AU */} +01085 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 550, 230, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 230, 550, 370, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01086 \textcolor{comment}{/* AU.U..AU */} +01087 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 370, 550, 280\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 320, 550, 270\}\} +01088 \}, +01089 \{ +01090 \textcolor{comment}{/* AU.@..?? */} +01091 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01092 \textcolor{comment}{/* AU.A..?? */} +01093 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01094 \textcolor{comment}{/* AU.C..?? */} +01095 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01096 \textcolor{comment}{/* AU.G..?? */} +01097 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01098 \textcolor{comment}{/* AU.U..?? */} +01099 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\} +01100 \} +01101 \}, +01102 \{ \textcolor{comment}{/* noPair */} \{\{\{0\}\}\}, +01103 \{ +01104 \textcolor{comment}{/* UA.@..GC */} +01105 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01106 \textcolor{comment}{/* UA.A..GC */} +01107 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 300, 240, 480\},\{ 550, 290, 250, 240, 480\},\{ 550, 180, 140, 120, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +01108 \textcolor{comment}{/* UA.C..GC */} +01109 \{\{ 550, 550, 550, 550, 550\},\{ 550, 310, 300, 480, 300\},\{ 550, 300, 330, 480, 300\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 330, 270, 480, 300\}\}, +01110 \textcolor{comment}{/* UA.G..GC */} +01111 \{\{ 550, 550, 550, 550, 550\},\{ 550, 250, 480, 160, 480\},\{ 550, 480, 480, 480, 480\},\{ 550, 160, 480, 300, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +01112 \textcolor{comment}{/* UA.U..GC */} +01113 \{\{ 550, 550, 550, 550, 550\},\{ 550, 480, 480, 480, 480\},\{ 550, 480, 300, 480, 210\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 480, 250, 480, 200\}\} +01114 \}, +01115 \{ +01116 \textcolor{comment}{/* UA.@..CG */} +01117 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01118 \textcolor{comment}{/* UA.A..CG */} +01119 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 300, 240, 480\},\{ 550, 290, 250, 240, 480\},\{ 550, 180, 140, 120, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +01120 \textcolor{comment}{/* UA.C..CG */} +01121 \{\{ 550, 550, 550, 550, 550\},\{ 550, 310, 300, 480, 300\},\{ 550, 300, 330, 480, 300\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 330, 270, 480, 300\}\}, +01122 \textcolor{comment}{/* UA.G..CG */} +01123 \{\{ 550, 550, 550, 550, 550\},\{ 550, 250, 480, 160, 480\},\{ 550, 480, 480, 480, 480\},\{ 550, 160, 480, 300, 480 + \},\{ 550, 480, 480, 480, 480\}\}, +01124 \textcolor{comment}{/* UA.U..CG */} +01125 \{\{ 550, 550, 550, 550, 550\},\{ 550, 480, 480, 480, 480\},\{ 550, 480, 300, 480, 210\},\{ 550, 480, 480, 480, 480 + \},\{ 550, 480, 250, 480, 200\}\} +01126 \}, +01127 \{ +01128 \textcolor{comment}{/* UA.@..UG */} +01129 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01130 \textcolor{comment}{/* UA.A..UG */} +01131 \{\{ 550, 550, 550, 550, 550\},\{ 550, 390, 370, 310, 550\},\{ 550, 360, 320, 310, 550\},\{ 550, 250, 210, 190, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01132 \textcolor{comment}{/* UA.C..UG */} +01133 \{\{ 550, 550, 550, 550, 550\},\{ 550, 380, 370, 550, 370\},\{ 550, 370, 400, 550, 370\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 400, 340, 550, 370\}\}, +01134 \textcolor{comment}{/* UA.G..UG */} +01135 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 550, 230, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 230, 550, 370, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01136 \textcolor{comment}{/* UA.U..UG */} +01137 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 370, 550, 280\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 320, 550, 270\}\} +01138 \}, +01139 \{ +01140 \textcolor{comment}{/* UA.@..GU */} +01141 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01142 \textcolor{comment}{/* UA.A..GU */} +01143 \{\{ 550, 550, 550, 550, 550\},\{ 550, 390, 370, 310, 550\},\{ 550, 360, 320, 310, 550\},\{ 550, 250, 210, 190, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01144 \textcolor{comment}{/* UA.C..GU */} +01145 \{\{ 550, 550, 550, 550, 550\},\{ 550, 380, 370, 550, 370\},\{ 550, 370, 400, 550, 370\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 400, 340, 550, 370\}\}, +01146 \textcolor{comment}{/* UA.G..GU */} +01147 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 550, 230, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 230, 550, 370, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01148 \textcolor{comment}{/* UA.U..GU */} +01149 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 370, 550, 280\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 320, 550, 270\}\} +01150 \}, +01151 \{ +01152 \textcolor{comment}{/* UA.@..UA */} +01153 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01154 \textcolor{comment}{/* UA.A..UA */} +01155 \{\{ 550, 550, 550, 550, 550\},\{ 550, 390, 370, 310, 550\},\{ 550, 360, 320, 310, 550\},\{ 550, 250, 210, 190, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01156 \textcolor{comment}{/* UA.C..UA */} +01157 \{\{ 550, 550, 550, 550, 550\},\{ 550, 380, 370, 550, 370\},\{ 550, 370, 400, 550, 370\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 400, 340, 550, 370\}\}, +01158 \textcolor{comment}{/* UA.G..UA */} +01159 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 550, 230, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 230, 550, 370, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01160 \textcolor{comment}{/* UA.U..UA */} +01161 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 370, 550, 280\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 320, 550, 270\}\} +01162 \}, +01163 \{ +01164 \textcolor{comment}{/* UA.@..AU */} +01165 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01166 \textcolor{comment}{/* UA.A..AU */} +01167 \{\{ 550, 550, 550, 550, 550\},\{ 550, 390, 370, 310, 550\},\{ 550, 360, 320, 310, 550\},\{ 550, 250, 210, 190, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01168 \textcolor{comment}{/* UA.C..AU */} +01169 \{\{ 550, 550, 550, 550, 550\},\{ 550, 380, 370, 550, 370\},\{ 550, 370, 400, 550, 370\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 400, 340, 550, 370\}\}, +01170 \textcolor{comment}{/* UA.G..AU */} +01171 \{\{ 550, 550, 550, 550, 550\},\{ 550, 320, 550, 230, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 230, 550, 370, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01172 \textcolor{comment}{/* UA.U..AU */} +01173 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 370, 550, 280\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 320, 550, 270\}\} +01174 \}, +01175 \{ +01176 \textcolor{comment}{/* UA.@..?? */} +01177 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01178 \textcolor{comment}{/* UA.A..?? */} +01179 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01180 \textcolor{comment}{/* UA.C..?? */} +01181 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01182 \textcolor{comment}{/* UA.G..?? */} +01183 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01184 \textcolor{comment}{/* UA.U..?? */} +01185 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\} +01186 \} +01187 \}, +01188 \{ \textcolor{comment}{/* noPair */} \{\{\{0\}\}\}, +01189 \{ +01190 \textcolor{comment}{/* ??.@..GC */} +01191 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01192 \textcolor{comment}{/* ??.A..GC */} +01193 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01194 \textcolor{comment}{/* ??.C..GC */} +01195 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01196 \textcolor{comment}{/* ??.G..GC */} +01197 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01198 \textcolor{comment}{/* ??.U..GC */} +01199 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\} +01200 \}, +01201 \{ +01202 \textcolor{comment}{/* ??.@..CG */} +01203 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01204 \textcolor{comment}{/* ??.A..CG */} +01205 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01206 \textcolor{comment}{/* ??.C..CG */} +01207 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01208 \textcolor{comment}{/* ??.G..CG */} +01209 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01210 \textcolor{comment}{/* ??.U..CG */} +01211 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\} +01212 \}, +01213 \{ +01214 \textcolor{comment}{/* ??.@..UG */} +01215 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01216 \textcolor{comment}{/* ??.A..UG */} +01217 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01218 \textcolor{comment}{/* ??.C..UG */} +01219 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01220 \textcolor{comment}{/* ??.G..UG */} +01221 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01222 \textcolor{comment}{/* ??.U..UG */} +01223 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\} +01224 \}, +01225 \{ +01226 \textcolor{comment}{/* ??.@..GU */} +01227 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01228 \textcolor{comment}{/* ??.A..GU */} +01229 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01230 \textcolor{comment}{/* ??.C..GU */} +01231 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01232 \textcolor{comment}{/* ??.G..GU */} +01233 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01234 \textcolor{comment}{/* ??.U..GU */} +01235 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\} +01236 \}, +01237 \{ +01238 \textcolor{comment}{/* ??.@..UA */} +01239 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01240 \textcolor{comment}{/* ??.A..UA */} +01241 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01242 \textcolor{comment}{/* ??.C..UA */} +01243 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01244 \textcolor{comment}{/* ??.G..UA */} +01245 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01246 \textcolor{comment}{/* ??.U..UA */} +01247 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\} +01248 \}, +01249 \{ +01250 \textcolor{comment}{/* ??.@..AU */} +01251 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01252 \textcolor{comment}{/* ??.A..AU */} +01253 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01254 \textcolor{comment}{/* ??.C..AU */} +01255 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01256 \textcolor{comment}{/* ??.G..AU */} +01257 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01258 \textcolor{comment}{/* ??.U..AU */} +01259 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\} +01260 \}, +01261 \{ +01262 \textcolor{comment}{/* ??.@..?? */} +01263 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01264 \textcolor{comment}{/* ??.A..?? */} +01265 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01266 \textcolor{comment}{/* ??.C..?? */} +01267 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01268 \textcolor{comment}{/* ??.G..?? */} +01269 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\}, +01270 \textcolor{comment}{/* ??.U..?? */} +01271 \{\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550\},\{ 550, 550, 550, 550, 550 + \},\{ 550, 550, 550, 550, 550\}\} +01272 \} +01273 \} +01274 \}; +01275 +01276 PRIVATE \textcolor{keywordtype}{int} int21\_H\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5] = +01277 \{ \textcolor{comment}{/* noPair */} \{\{\{\{0\}\}\}\}, +01278 \{ \textcolor{comment}{/* noPair */} \{\{\{0\}\}\}, +01279 \{ +01280 \textcolor{comment}{/* CG.@..CG */} +01281 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01282 \textcolor{comment}{/* CG.A..CG */} +01283 \{\{ DEF,-1029, -949,-1029,-1029\},\{-1079,-2058,-1978,-2058,-2058\},\{ -569,-1548,-1468,-1548,-1548\},\{ -989,- + 1968,-1888,-1968,-1968\},\{ -859,-1838,-1758,-1838,-1838\}\}, +01284 \textcolor{comment}{/* CG.C..CG */} +01285 \{\{ DEF, -519, -449, -519, -669\},\{ -999,-1468,-1398,-1468,-1618\},\{ -499, -968, -898, -968,-1118\},\{ -989,- + 1458,-1388,-1458,-1608\},\{ -789,-1258,-1188,-1258,-1408\}\}, +01286 \textcolor{comment}{/* CG.G..CG */} +01287 \{\{ DEF, -939, -939, -939, -939\},\{-1079,-1968,-1968,-1968,-1968\},\{ -569,-1458,-1458,-1458,-1458\},\{ -989,- + 1878,-1878,-1878,-1878\},\{ -859,-1748,-1748,-1748,-1748\}\}, +01288 \textcolor{comment}{/* CG.U..CG */} +01289 \{\{ DEF, -809, -739, -809, -859\},\{-1079,-1838,-1768,-1838,-1888\},\{ -719,-1478,-1408,-1478,-1528\},\{ -989,- + 1748,-1678,-1748,-1798\},\{ -909,-1668,-1598,-1668,-1718\}\} +01290 \}, +01291 \{ +01292 \textcolor{comment}{/* CG.@..GC */} +01293 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01294 \textcolor{comment}{/* CG.A..GC */} +01295 \{\{ DEF,-1029, -949,-1029,-1029\},\{ -569,-1548,-1468,-1548,-1548\},\{ -769,-1748,-1668,-1748,-1748\},\{ -759,- + 1738,-1658,-1738,-1738\},\{ -549,-1528,-1448,-1528,-1528\}\}, +01296 \textcolor{comment}{/* CG.C..GC */} +01297 \{\{ DEF, -519, -449, -519, -669\},\{ -929,-1398,-1328,-1398,-1548\},\{ -359, -828, -758, -828, -978\},\{ -789,- + 1258,-1188,-1258,-1408\},\{ -549,-1018, -948,-1018,-1168\}\}, +01298 \textcolor{comment}{/* CG.G..GC */} +01299 \{\{ DEF, -939, -939, -939, -939\},\{ -609,-1498,-1498,-1498,-1498\},\{ -359,-1248,-1248,-1248,-1248\},\{ -669,- + 1558,-1558,-1558,-1558\},\{ -549,-1438,-1438,-1438,-1438\}\}, +01300 \textcolor{comment}{/* CG.U..GC */} +01301 \{\{ DEF, -809, -739, -809, -859\},\{ -929,-1688,-1618,-1688,-1738\},\{ -439,-1198,-1128,-1198,-1248\},\{ -789,- + 1548,-1478,-1548,-1598\},\{ -619,-1378,-1308,-1378,-1428\}\} +01302 \}, +01303 \{ +01304 \textcolor{comment}{/* CG.@..GU */} +01305 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01306 \textcolor{comment}{/* CG.A..GU */} +01307 \{\{ DEF,-1029, -949,-1029,-1029\},\{ -479,-1458,-1378,-1458,-1458\},\{ -309,-1288,-1208,-1288,-1288\},\{ -389,- + 1368,-1288,-1368,-1368\},\{ -379,-1358,-1278,-1358,-1358\}\}, +01308 \textcolor{comment}{/* CG.C..GU */} +01309 \{\{ DEF, -519, -449, -519, -669\},\{ -649,-1118,-1048,-1118,-1268\},\{ -289, -758, -688, -758, -908\},\{ -739,- + 1208,-1138,-1208,-1358\},\{ -379, -848, -778, -848, -998\}\}, +01310 \textcolor{comment}{/* CG.G..GU */} +01311 \{\{ DEF, -939, -939, -939, -939\},\{ -649,-1538,-1538,-1538,-1538\},\{ -289,-1178,-1178,-1178,-1178\},\{ -739,- + 1628,-1628,-1628,-1628\},\{ -379,-1268,-1268,-1268,-1268\}\}, +01312 \textcolor{comment}{/* CG.U..GU */} +01313 \{\{ DEF, -809, -739, -809, -859\},\{ -649,-1408,-1338,-1408,-1458\},\{ -289,-1048, -978,-1048,-1098\},\{ -739,- + 1498,-1428,-1498,-1548\},\{ -379,-1138,-1068,-1138,-1188\}\} +01314 \}, +01315 \{ +01316 \textcolor{comment}{/* CG.@..UG */} +01317 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01318 \textcolor{comment}{/* CG.A..UG */} +01319 \{\{ DEF,-1029, -949,-1029,-1029\},\{ -769,-1748,-1668,-1748,-1748\},\{ -529,-1508,-1428,-1508,-1508\},\{ -709,- + 1688,-1608,-1688,-1688\},\{ -599,-1578,-1498,-1578,-1578\}\}, +01320 \textcolor{comment}{/* CG.C..UG */} +01321 \{\{ DEF, -519, -449, -519, -669\},\{ -839,-1308,-1238,-1308,-1458\},\{ -529, -998, -928, -998,-1148\},\{ -859,- + 1328,-1258,-1328,-1478\},\{ -489, -958, -888, -958,-1108\}\}, +01322 \textcolor{comment}{/* CG.G..UG */} +01323 \{\{ DEF, -939, -939, -939, -939\},\{-1009,-1898,-1898,-1898,-1898\},\{ -409,-1298,-1298,-1298,-1298\},\{ -969,- + 1858,-1858,-1858,-1858\},\{ -599,-1488,-1488,-1488,-1488\}\}, +01324 \textcolor{comment}{/* CG.U..UG */} +01325 \{\{ DEF, -809, -739, -809, -859\},\{ -859,-1618,-1548,-1618,-1668\},\{ -529,-1288,-1218,-1288,-1338\},\{ -859,- + 1618,-1548,-1618,-1668\},\{ -409,-1168,-1098,-1168,-1218\}\} +01326 \}, +01327 \{ +01328 \textcolor{comment}{/* CG.@..AU */} +01329 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01330 \textcolor{comment}{/* CG.A..AU */} +01331 \{\{ DEF,-1029, -949,-1029,-1029\},\{ -479,-1458,-1378,-1458,-1458\},\{ -309,-1288,-1208,-1288,-1288\},\{ -389,- + 1368,-1288,-1368,-1368\},\{ -379,-1358,-1278,-1358,-1358\}\}, +01332 \textcolor{comment}{/* CG.C..AU */} +01333 \{\{ DEF, -519, -449, -519, -669\},\{ -649,-1118,-1048,-1118,-1268\},\{ -289, -758, -688, -758, -908\},\{ -739,- + 1208,-1138,-1208,-1358\},\{ -379, -848, -778, -848, -998\}\}, +01334 \textcolor{comment}{/* CG.G..AU */} +01335 \{\{ DEF, -939, -939, -939, -939\},\{ -649,-1538,-1538,-1538,-1538\},\{ -289,-1178,-1178,-1178,-1178\},\{ -739,- + 1628,-1628,-1628,-1628\},\{ -379,-1268,-1268,-1268,-1268\}\}, +01336 \textcolor{comment}{/* CG.U..AU */} +01337 \{\{ DEF, -809, -739, -809, -859\},\{ -649,-1408,-1338,-1408,-1458\},\{ -289,-1048, -978,-1048,-1098\},\{ -739,- + 1498,-1428,-1498,-1548\},\{ -379,-1138,-1068,-1138,-1188\}\} +01338 \}, +01339 \{ +01340 \textcolor{comment}{/* CG.@..UA */} +01341 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01342 \textcolor{comment}{/* CG.A..UA */} +01343 \{\{ DEF,-1029, -949,-1029,-1029\},\{ -449,-1428,-1348,-1428,-1428\},\{ -479,-1458,-1378,-1458,-1458\},\{ -429,- + 1408,-1328,-1408,-1408\},\{ -329,-1308,-1228,-1308,-1308\}\}, +01344 \textcolor{comment}{/* CG.C..UA */} +01345 \{\{ DEF, -519, -449, -519, -669\},\{ -679,-1148,-1078,-1148,-1298\},\{ -559,-1028, -958,-1028,-1178\},\{ -729,- + 1198,-1128,-1198,-1348\},\{ -189, -658, -588, -658, -808\}\}, +01346 \textcolor{comment}{/* CG.G..UA */} +01347 \{\{ DEF, -939, -939, -939, -939\},\{ -939,-1828,-1828,-1828,-1828\},\{ -249,-1138,-1138,-1138,-1138\},\{ -939,- + 1828,-1828,-1828,-1828\},\{ -329,-1218,-1218,-1218,-1218\}\}, +01348 \textcolor{comment}{/* CG.U..UA */} +01349 \{\{ DEF, -809, -739, -809, -859\},\{ -639,-1398,-1328,-1398,-1448\},\{ -229, -988, -918, -988,-1038\},\{ -729,- + 1488,-1418,-1488,-1538\},\{ -190, -949, -879, -949, -999\}\} +01350 \}, +01351 \{ +01352 \textcolor{comment}{/* CG.@.. @ */} +01353 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01354 \textcolor{comment}{/* CG.A.. @ */} +01355 \{\{ -100,-1079, -999,-1079,-1079\},\{ -100,-1079, -999,-1079,-1079\},\{ -100,-1079, -999,-1079,-1079\},\{ -100,- + 1079, -999,-1079,-1079\},\{ -100,-1079, -999,-1079,-1079\}\}, +01356 \textcolor{comment}{/* CG.C.. @ */} +01357 \{\{ -100, -569, -499, -569, -719\},\{ -100, -569, -499, -569, -719\},\{ -100, -569, -499, -569, -719\},\{ -100, - + 569, -499, -569, -719\},\{ -100, -569, -499, -569, -719\}\}, +01358 \textcolor{comment}{/* CG.G.. @ */} +01359 \{\{ -100, -989, -989, -989, -989\},\{ -100, -989, -989, -989, -989\},\{ -100, -989, -989, -989, -989\},\{ -100, - + 989, -989, -989, -989\},\{ -100, -989, -989, -989, -989\}\}, +01360 \textcolor{comment}{/* CG.U.. @ */} +01361 \{\{ -100, -859, -789, -859, -909\},\{ -100, -859, -789, -859, -909\},\{ -100, -859, -789, -859, -909\},\{ -100, - + 859, -789, -859, -909\},\{ -100, -859, -789, -859, -909\}\} +01362 \} +01363 \}, +01364 \{ \textcolor{comment}{/* noPair */} \{\{\{0\}\}\}, +01365 \{ +01366 \textcolor{comment}{/* GC.@..CG */} +01367 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01368 \textcolor{comment}{/* GC.A..CG */} +01369 \{\{ DEF, -519, -879, -559, -879\},\{-1079,-1548,-1908,-1588,-1908\},\{ -569,-1038,-1398,-1078,-1398\},\{ -989,- + 1458,-1818,-1498,-1818\},\{ -859,-1328,-1688,-1368,-1688\}\}, +01370 \textcolor{comment}{/* GC.C..CG */} +01371 \{\{ DEF, -719, -309, -309, -389\},\{ -999,-1668,-1258,-1258,-1338\},\{ -499,-1168, -758, -758, -838\},\{ -989,- + 1658,-1248,-1248,-1328\},\{ -789,-1458,-1048,-1048,-1128\}\}, +01372 \textcolor{comment}{/* GC.G..CG */} +01373 \{\{ DEF, -709, -739, -619, -739\},\{-1079,-1738,-1768,-1648,-1768\},\{ -569,-1228,-1258,-1138,-1258\},\{ -989,- + 1648,-1678,-1558,-1678\},\{ -859,-1518,-1548,-1428,-1548\}\}, +01374 \textcolor{comment}{/* GC.U..CG */} +01375 \{\{ DEF, -499, -499, -499, -569\},\{-1079,-1528,-1528,-1528,-1598\},\{ -719,-1168,-1168,-1168,-1238\},\{ -989,- + 1438,-1438,-1438,-1508\},\{ -909,-1358,-1358,-1358,-1428\}\} +01376 \}, +01377 \{ +01378 \textcolor{comment}{/* GC.@..GC */} +01379 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01380 \textcolor{comment}{/* GC.A..GC */} +01381 \{\{ DEF, -519, -879, -559, -879\},\{ -569,-1038,-1398,-1078,-1398\},\{ -769,-1238,-1598,-1278,-1598\},\{ -759,- + 1228,-1588,-1268,-1588\},\{ -549,-1018,-1378,-1058,-1378\}\}, +01382 \textcolor{comment}{/* GC.C..GC */} +01383 \{\{ DEF, -719, -309, -309, -389\},\{ -929,-1598,-1188,-1188,-1268\},\{ -359,-1028, -618, -618, -698\},\{ -789,- + 1458,-1048,-1048,-1128\},\{ -549,-1218, -808, -808, -888\}\}, +01384 \textcolor{comment}{/* GC.G..GC */} +01385 \{\{ DEF, -709, -739, -619, -739\},\{ -609,-1268,-1298,-1178,-1298\},\{ -359,-1018,-1048, -928,-1048\},\{ -669,- + 1328,-1358,-1238,-1358\},\{ -549,-1208,-1238,-1118,-1238\}\}, +01386 \textcolor{comment}{/* GC.U..GC */} +01387 \{\{ DEF, -499, -499, -499, -569\},\{ -929,-1378,-1378,-1378,-1448\},\{ -439, -888, -888, -888, -958\},\{ -789,- + 1238,-1238,-1238,-1308\},\{ -619,-1068,-1068,-1068,-1138\}\} +01388 \}, +01389 \{ +01390 \textcolor{comment}{/* GC.@..GU */} +01391 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01392 \textcolor{comment}{/* GC.A..GU */} +01393 \{\{ DEF, -519, -879, -559, -879\},\{ -479, -948,-1308, -988,-1308\},\{ -309, -778,-1138, -818,-1138\},\{ -389, - + 858,-1218, -898,-1218\},\{ -379, -848,-1208, -888,-1208\}\}, +01394 \textcolor{comment}{/* GC.C..GU */} +01395 \{\{ DEF, -719, -309, -309, -389\},\{ -649,-1318, -908, -908, -988\},\{ -289, -958, -548, -548, -628\},\{ -739,- + 1408, -998, -998,-1078\},\{ -379,-1048, -638, -638, -718\}\}, +01396 \textcolor{comment}{/* GC.G..GU */} +01397 \{\{ DEF, -709, -739, -619, -739\},\{ -649,-1308,-1338,-1218,-1338\},\{ -289, -948, -978, -858, -978\},\{ -739,- + 1398,-1428,-1308,-1428\},\{ -379,-1038,-1068, -948,-1068\}\}, +01398 \textcolor{comment}{/* GC.U..GU */} +01399 \{\{ DEF, -499, -499, -499, -569\},\{ -649,-1098,-1098,-1098,-1168\},\{ -289, -738, -738, -738, -808\},\{ -739,- + 1188,-1188,-1188,-1258\},\{ -379, -828, -828, -828, -898\}\} +01400 \}, +01401 \{ +01402 \textcolor{comment}{/* GC.@..UG */} +01403 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01404 \textcolor{comment}{/* GC.A..UG */} +01405 \{\{ DEF, -519, -879, -559, -879\},\{ -769,-1238,-1598,-1278,-1598\},\{ -529, -998,-1358,-1038,-1358\},\{ -709,- + 1178,-1538,-1218,-1538\},\{ -599,-1068,-1428,-1108,-1428\}\}, +01406 \textcolor{comment}{/* GC.C..UG */} +01407 \{\{ DEF, -719, -309, -309, -389\},\{ -839,-1508,-1098,-1098,-1178\},\{ -529,-1198, -788, -788, -868\},\{ -859,- + 1528,-1118,-1118,-1198\},\{ -489,-1158, -748, -748, -828\}\}, +01408 \textcolor{comment}{/* GC.G..UG */} +01409 \{\{ DEF, -709, -739, -619, -739\},\{-1009,-1668,-1698,-1578,-1698\},\{ -409,-1068,-1098, -978,-1098\},\{ -969,- + 1628,-1658,-1538,-1658\},\{ -599,-1258,-1288,-1168,-1288\}\}, +01410 \textcolor{comment}{/* GC.U..UG */} +01411 \{\{ DEF, -499, -499, -499, -569\},\{ -859,-1308,-1308,-1308,-1378\},\{ -529, -978, -978, -978,-1048\},\{ -859,- + 1308,-1308,-1308,-1378\},\{ -409, -858, -858, -858, -928\}\} +01412 \}, +01413 \{ +01414 \textcolor{comment}{/* GC.@..AU */} +01415 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01416 \textcolor{comment}{/* GC.A..AU */} +01417 \{\{ DEF, -519, -879, -559, -879\},\{ -479, -948,-1308, -988,-1308\},\{ -309, -778,-1138, -818,-1138\},\{ -389, - + 858,-1218, -898,-1218\},\{ -379, -848,-1208, -888,-1208\}\}, +01418 \textcolor{comment}{/* GC.C..AU */} +01419 \{\{ DEF, -719, -309, -309, -389\},\{ -649,-1318, -908, -908, -988\},\{ -289, -958, -548, -548, -628\},\{ -739,- + 1408, -998, -998,-1078\},\{ -379,-1048, -638, -638, -718\}\}, +01420 \textcolor{comment}{/* GC.G..AU */} +01421 \{\{ DEF, -709, -739, -619, -739\},\{ -649,-1308,-1338,-1218,-1338\},\{ -289, -948, -978, -858, -978\},\{ -739,- + 1398,-1428,-1308,-1428\},\{ -379,-1038,-1068, -948,-1068\}\}, +01422 \textcolor{comment}{/* GC.U..AU */} +01423 \{\{ DEF, -499, -499, -499, -569\},\{ -649,-1098,-1098,-1098,-1168\},\{ -289, -738, -738, -738, -808\},\{ -739,- + 1188,-1188,-1188,-1258\},\{ -379, -828, -828, -828, -898\}\} +01424 \}, +01425 \{ +01426 \textcolor{comment}{/* GC.@..UA */} +01427 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01428 \textcolor{comment}{/* GC.A..UA */} +01429 \{\{ DEF, -519, -879, -559, -879\},\{ -449, -918,-1278, -958,-1278\},\{ -479, -948,-1308, -988,-1308\},\{ -429, - + 898,-1258, -938,-1258\},\{ -329, -798,-1158, -838,-1158\}\}, +01430 \textcolor{comment}{/* GC.C..UA */} +01431 \{\{ DEF, -719, -309, -309, -389\},\{ -679,-1348, -938, -938,-1018\},\{ -559,-1228, -818, -818, -898\},\{ -729,- + 1398, -988, -988,-1068\},\{ -189, -858, -448, -448, -528\}\}, +01432 \textcolor{comment}{/* GC.G..UA */} +01433 \{\{ DEF, -709, -739, -619, -739\},\{ -939,-1598,-1628,-1508,-1628\},\{ -249, -908, -938, -818, -938\},\{ -939,- + 1598,-1628,-1508,-1628\},\{ -329, -988,-1018, -898,-1018\}\}, +01434 \textcolor{comment}{/* GC.U..UA */} +01435 \{\{ DEF, -499, -499, -499, -569\},\{ -639,-1088,-1088,-1088,-1158\},\{ -229, -678, -678, -678, -748\},\{ -729,- + 1178,-1178,-1178,-1248\},\{ -190, -639, -639, -639, -709\}\} +01436 \}, +01437 \{ +01438 \textcolor{comment}{/* GC.@.. @ */} +01439 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01440 \textcolor{comment}{/* GC.A.. @ */} +01441 \{\{ -100, -569, -929, -609, -929\},\{ -100, -569, -929, -609, -929\},\{ -100, -569, -929, -609, -929\},\{ -100, - + 569, -929, -609, -929\},\{ -100, -569, -929, -609, -929\}\}, +01442 \textcolor{comment}{/* GC.C.. @ */} +01443 \{\{ -100, -769, -359, -359, -439\},\{ -100, -769, -359, -359, -439\},\{ -100, -769, -359, -359, -439\},\{ -100, - + 769, -359, -359, -439\},\{ -100, -769, -359, -359, -439\}\}, +01444 \textcolor{comment}{/* GC.G.. @ */} +01445 \{\{ -100, -759, -789, -669, -789\},\{ -100, -759, -789, -669, -789\},\{ -100, -759, -789, -669, -789\},\{ -100, - + 759, -789, -669, -789\},\{ -100, -759, -789, -669, -789\}\}, +01446 \textcolor{comment}{/* GC.U.. @ */} +01447 \{\{ -100, -549, -549, -549, -619\},\{ -100, -549, -549, -549, -619\},\{ -100, -549, -549, -549, -619\},\{ -100, - + 549, -549, -549, -619\},\{ -100, -549, -549, -549, -619\}\} +01448 \} +01449 \}, +01450 \{ \textcolor{comment}{/* noPair */} \{\{\{0\}\}\}, +01451 \{ +01452 \textcolor{comment}{/* GU.@..CG */} +01453 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01454 \textcolor{comment}{/* GU.A..CG */} +01455 \{\{ DEF, -429, -599, -599, -599\},\{-1079,-1458,-1628,-1628,-1628\},\{ -569, -948,-1118,-1118,-1118\},\{ -989,- + 1368,-1538,-1538,-1538\},\{ -859,-1238,-1408,-1408,-1408\}\}, +01456 \textcolor{comment}{/* GU.C..CG */} +01457 \{\{ DEF, -259, -239, -239, -239\},\{ -999,-1208,-1188,-1188,-1188\},\{ -499, -708, -688, -688, -688\},\{ -989,- + 1198,-1178,-1178,-1178\},\{ -789, -998, -978, -978, -978\}\}, +01458 \textcolor{comment}{/* GU.G..CG */} +01459 \{\{ DEF, -339, -689, -689, -689\},\{-1079,-1368,-1718,-1718,-1718\},\{ -569, -858,-1208,-1208,-1208\},\{ -989,- + 1278,-1628,-1628,-1628\},\{ -859,-1148,-1498,-1498,-1498\}\}, +01460 \textcolor{comment}{/* GU.U..CG */} +01461 \{\{ DEF, -329, -329, -329, -329\},\{-1079,-1358,-1358,-1358,-1358\},\{ -719, -998, -998, -998, -998\},\{ -989,- + 1268,-1268,-1268,-1268\},\{ -909,-1188,-1188,-1188,-1188\}\} +01462 \}, +01463 \{ +01464 \textcolor{comment}{/* GU.@..GC */} +01465 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01466 \textcolor{comment}{/* GU.A..GC */} +01467 \{\{ DEF, -429, -599, -599, -599\},\{ -569, -948,-1118,-1118,-1118\},\{ -769,-1148,-1318,-1318,-1318\},\{ -759,- + 1138,-1308,-1308,-1308\},\{ -549, -928,-1098,-1098,-1098\}\}, +01468 \textcolor{comment}{/* GU.C..GC */} +01469 \{\{ DEF, -259, -239, -239, -239\},\{ -929,-1138,-1118,-1118,-1118\},\{ -359, -568, -548, -548, -548\},\{ -789, - + 998, -978, -978, -978\},\{ -549, -758, -738, -738, -738\}\}, +01470 \textcolor{comment}{/* GU.G..GC */} +01471 \{\{ DEF, -339, -689, -689, -689\},\{ -609, -898,-1248,-1248,-1248\},\{ -359, -648, -998, -998, -998\},\{ -669, - + 958,-1308,-1308,-1308\},\{ -549, -838,-1188,-1188,-1188\}\}, +01472 \textcolor{comment}{/* GU.U..GC */} +01473 \{\{ DEF, -329, -329, -329, -329\},\{ -929,-1208,-1208,-1208,-1208\},\{ -439, -718, -718, -718, -718\},\{ -789,- + 1068,-1068,-1068,-1068\},\{ -619, -898, -898, -898, -898\}\} +01474 \}, +01475 \{ +01476 \textcolor{comment}{/* GU.@..GU */} +01477 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01478 \textcolor{comment}{/* GU.A..GU */} +01479 \{\{ DEF, -429, -599, -599, -599\},\{ -479, -858,-1028,-1028,-1028\},\{ -309, -688, -858, -858, -858\},\{ -389, - + 768, -938, -938, -938\},\{ -379, -758, -928, -928, -928\}\}, +01480 \textcolor{comment}{/* GU.C..GU */} +01481 \{\{ DEF, -259, -239, -239, -239\},\{ -649, -858, -838, -838, -838\},\{ -289, -498, -478, -478, -478\},\{ -739, - + 948, -928, -928, -928\},\{ -379, -588, -568, -568, -568\}\}, +01482 \textcolor{comment}{/* GU.G..GU */} +01483 \{\{ DEF, -339, -689, -689, -689\},\{ -649, -938,-1288,-1288,-1288\},\{ -289, -578, -928, -928, -928\},\{ -739,- + 1028,-1378,-1378,-1378\},\{ -379, -668,-1018,-1018,-1018\}\}, +01484 \textcolor{comment}{/* GU.U..GU */} +01485 \{\{ DEF, -329, -329, -329, -329\},\{ -649, -928, -928, -928, -928\},\{ -289, -568, -568, -568, -568\},\{ -739,- + 1018,-1018,-1018,-1018\},\{ -379, -658, -658, -658, -658\}\} +01486 \}, +01487 \{ +01488 \textcolor{comment}{/* GU.@..UG */} +01489 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01490 \textcolor{comment}{/* GU.A..UG */} +01491 \{\{ DEF, -429, -599, -599, -599\},\{ -769,-1148,-1318,-1318,-1318\},\{ -529, -908,-1078,-1078,-1078\},\{ -709,- + 1088,-1258,-1258,-1258\},\{ -599, -978,-1148,-1148,-1148\}\}, +01492 \textcolor{comment}{/* GU.C..UG */} +01493 \{\{ DEF, -259, -239, -239, -239\},\{ -839,-1048,-1028,-1028,-1028\},\{ -529, -738, -718, -718, -718\},\{ -859,- + 1068,-1048,-1048,-1048\},\{ -489, -698, -678, -678, -678\}\}, +01494 \textcolor{comment}{/* GU.G..UG */} +01495 \{\{ DEF, -339, -689, -689, -689\},\{-1009,-1298,-1648,-1648,-1648\},\{ -409, -698,-1048,-1048,-1048\},\{ -969,- + 1258,-1608,-1608,-1608\},\{ -599, -888,-1238,-1238,-1238\}\}, +01496 \textcolor{comment}{/* GU.U..UG */} +01497 \{\{ DEF, -329, -329, -329, -329\},\{ -859,-1138,-1138,-1138,-1138\},\{ -529, -808, -808, -808, -808\},\{ -859,- + 1138,-1138,-1138,-1138\},\{ -409, -688, -688, -688, -688\}\} +01498 \}, +01499 \{ +01500 \textcolor{comment}{/* GU.@..AU */} +01501 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01502 \textcolor{comment}{/* GU.A..AU */} +01503 \{\{ DEF, -429, -599, -599, -599\},\{ -479, -858,-1028,-1028,-1028\},\{ -309, -688, -858, -858, -858\},\{ -389, - + 768, -938, -938, -938\},\{ -379, -758, -928, -928, -928\}\}, +01504 \textcolor{comment}{/* GU.C..AU */} +01505 \{\{ DEF, -259, -239, -239, -239\},\{ -649, -858, -838, -838, -838\},\{ -289, -498, -478, -478, -478\},\{ -739, - + 948, -928, -928, -928\},\{ -379, -588, -568, -568, -568\}\}, +01506 \textcolor{comment}{/* GU.G..AU */} +01507 \{\{ DEF, -339, -689, -689, -689\},\{ -649, -938,-1288,-1288,-1288\},\{ -289, -578, -928, -928, -928\},\{ -739,- + 1028,-1378,-1378,-1378\},\{ -379, -668,-1018,-1018,-1018\}\}, +01508 \textcolor{comment}{/* GU.U..AU */} +01509 \{\{ DEF, -329, -329, -329, -329\},\{ -649, -928, -928, -928, -928\},\{ -289, -568, -568, -568, -568\},\{ -739,- + 1018,-1018,-1018,-1018\},\{ -379, -658, -658, -658, -658\}\} +01510 \}, +01511 \{ +01512 \textcolor{comment}{/* GU.@..UA */} +01513 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01514 \textcolor{comment}{/* GU.A..UA */} +01515 \{\{ DEF, -429, -599, -599, -599\},\{ -449, -828, -998, -998, -998\},\{ -479, -858,-1028,-1028,-1028\},\{ -429, - + 808, -978, -978, -978\},\{ -329, -708, -878, -878, -878\}\}, +01516 \textcolor{comment}{/* GU.C..UA */} +01517 \{\{ DEF, -259, -239, -239, -239\},\{ -679, -888, -868, -868, -868\},\{ -559, -768, -748, -748, -748\},\{ -729, - + 938, -918, -918, -918\},\{ -189, -398, -378, -378, -378\}\}, +01518 \textcolor{comment}{/* GU.G..UA */} +01519 \{\{ DEF, -339, -689, -689, -689\},\{ -939,-1228,-1578,-1578,-1578\},\{ -249, -538, -888, -888, -888\},\{ -939,- + 1228,-1578,-1578,-1578\},\{ -329, -618, -968, -968, -968\}\}, +01520 \textcolor{comment}{/* GU.U..UA */} +01521 \{\{ DEF, -329, -329, -329, -329\},\{ -639, -918, -918, -918, -918\},\{ -229, -508, -508, -508, -508\},\{ -729,- + 1008,-1008,-1008,-1008\},\{ -190, -469, -469, -469, -469\}\} +01522 \}, +01523 \{ +01524 \textcolor{comment}{/* GU.@.. @ */} +01525 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01526 \textcolor{comment}{/* GU.A.. @ */} +01527 \{\{ -100, -479, -649, -649, -649\},\{ -100, -479, -649, -649, -649\},\{ -100, -479, -649, -649, -649\},\{ -100, - + 479, -649, -649, -649\},\{ -100, -479, -649, -649, -649\}\}, +01528 \textcolor{comment}{/* GU.C.. @ */} +01529 \{\{ -100, -309, -289, -289, -289\},\{ -100, -309, -289, -289, -289\},\{ -100, -309, -289, -289, -289\},\{ -100, - + 309, -289, -289, -289\},\{ -100, -309, -289, -289, -289\}\}, +01530 \textcolor{comment}{/* GU.G.. @ */} +01531 \{\{ -100, -389, -739, -739, -739\},\{ -100, -389, -739, -739, -739\},\{ -100, -389, -739, -739, -739\},\{ -100, - + 389, -739, -739, -739\},\{ -100, -389, -739, -739, -739\}\}, +01532 \textcolor{comment}{/* GU.U.. @ */} +01533 \{\{ -100, -379, -379, -379, -379\},\{ -100, -379, -379, -379, -379\},\{ -100, -379, -379, -379, -379\},\{ -100, - + 379, -379, -379, -379\},\{ -100, -379, -379, -379, -379\}\} +01534 \} +01535 \}, +01536 \{ \textcolor{comment}{/* noPair */} \{\{\{0\}\}\}, +01537 \{ +01538 \textcolor{comment}{/* UG.@..CG */} +01539 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01540 \textcolor{comment}{/* UG.A..CG */} +01541 \{\{ DEF, -719, -789, -959, -809\},\{-1079,-1748,-1818,-1988,-1838\},\{ -569,-1238,-1308,-1478,-1328\},\{ -989,- + 1658,-1728,-1898,-1748\},\{ -859,-1528,-1598,-1768,-1618\}\}, +01542 \textcolor{comment}{/* UG.C..CG */} +01543 \{\{ DEF, -479, -479, -359, -479\},\{ -999,-1428,-1428,-1308,-1428\},\{ -499, -928, -928, -808, -928\},\{ -989,- + 1418,-1418,-1298,-1418\},\{ -789,-1218,-1218,-1098,-1218\}\}, +01544 \textcolor{comment}{/* UG.G..CG */} +01545 \{\{ DEF, -659, -809, -919, -809\},\{-1079,-1688,-1838,-1948,-1838\},\{ -569,-1178,-1328,-1438,-1328\},\{ -989,- + 1598,-1748,-1858,-1748\},\{ -859,-1468,-1618,-1728,-1618\}\}, +01546 \textcolor{comment}{/* UG.U..CG */} +01547 \{\{ DEF, -549, -439, -549, -359\},\{-1079,-1578,-1468,-1578,-1388\},\{ -719,-1218,-1108,-1218,-1028\},\{ -989,- + 1488,-1378,-1488,-1298\},\{ -909,-1408,-1298,-1408,-1218\}\} +01548 \}, +01549 \{ +01550 \textcolor{comment}{/* UG.@..GC */} +01551 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01552 \textcolor{comment}{/* UG.A..GC */} +01553 \{\{ DEF, -719, -789, -959, -809\},\{ -569,-1238,-1308,-1478,-1328\},\{ -769,-1438,-1508,-1678,-1528\},\{ -759,- + 1428,-1498,-1668,-1518\},\{ -549,-1218,-1288,-1458,-1308\}\}, +01554 \textcolor{comment}{/* UG.C..GC */} +01555 \{\{ DEF, -479, -479, -359, -479\},\{ -929,-1358,-1358,-1238,-1358\},\{ -359, -788, -788, -668, -788\},\{ -789,- + 1218,-1218,-1098,-1218\},\{ -549, -978, -978, -858, -978\}\}, +01556 \textcolor{comment}{/* UG.G..GC */} +01557 \{\{ DEF, -659, -809, -919, -809\},\{ -609,-1218,-1368,-1478,-1368\},\{ -359, -968,-1118,-1228,-1118\},\{ -669,- + 1278,-1428,-1538,-1428\},\{ -549,-1158,-1308,-1418,-1308\}\}, +01558 \textcolor{comment}{/* UG.U..GC */} +01559 \{\{ DEF, -549, -439, -549, -359\},\{ -929,-1428,-1318,-1428,-1238\},\{ -439, -938, -828, -938, -748\},\{ -789,- + 1288,-1178,-1288,-1098\},\{ -619,-1118,-1008,-1118, -928\}\} +01560 \}, +01561 \{ +01562 \textcolor{comment}{/* UG.@..GU */} +01563 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01564 \textcolor{comment}{/* UG.A..GU */} +01565 \{\{ DEF, -719, -789, -959, -809\},\{ -479,-1148,-1218,-1388,-1238\},\{ -309, -978,-1048,-1218,-1068\},\{ -389,- + 1058,-1128,-1298,-1148\},\{ -379,-1048,-1118,-1288,-1138\}\}, +01566 \textcolor{comment}{/* UG.C..GU */} +01567 \{\{ DEF, -479, -479, -359, -479\},\{ -649,-1078,-1078, -958,-1078\},\{ -289, -718, -718, -598, -718\},\{ -739,- + 1168,-1168,-1048,-1168\},\{ -379, -808, -808, -688, -808\}\}, +01568 \textcolor{comment}{/* UG.G..GU */} +01569 \{\{ DEF, -659, -809, -919, -809\},\{ -649,-1258,-1408,-1518,-1408\},\{ -289, -898,-1048,-1158,-1048\},\{ -739,- + 1348,-1498,-1608,-1498\},\{ -379, -988,-1138,-1248,-1138\}\}, +01570 \textcolor{comment}{/* UG.U..GU */} +01571 \{\{ DEF, -549, -439, -549, -359\},\{ -649,-1148,-1038,-1148, -958\},\{ -289, -788, -678, -788, -598\},\{ -739,- + 1238,-1128,-1238,-1048\},\{ -379, -878, -768, -878, -688\}\} +01572 \}, +01573 \{ +01574 \textcolor{comment}{/* UG.@..UG */} +01575 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01576 \textcolor{comment}{/* UG.A..UG */} +01577 \{\{ DEF, -719, -789, -959, -809\},\{ -769,-1438,-1508,-1678,-1528\},\{ -529,-1198,-1268,-1438,-1288\},\{ -709,- + 1378,-1448,-1618,-1468\},\{ -599,-1268,-1338,-1508,-1358\}\}, +01578 \textcolor{comment}{/* UG.C..UG */} +01579 \{\{ DEF, -479, -479, -359, -479\},\{ -839,-1268,-1268,-1148,-1268\},\{ -529, -958, -958, -838, -958\},\{ -859,- + 1288,-1288,-1168,-1288\},\{ -489, -918, -918, -798, -918\}\}, +01580 \textcolor{comment}{/* UG.G..UG */} +01581 \{\{ DEF, -659, -809, -919, -809\},\{-1009,-1618,-1768,-1878,-1768\},\{ -409,-1018,-1168,-1278,-1168\},\{ -969,- + 1578,-1728,-1838,-1728\},\{ -599,-1208,-1358,-1468,-1358\}\}, +01582 \textcolor{comment}{/* UG.U..UG */} +01583 \{\{ DEF, -549, -439, -549, -359\},\{ -859,-1358,-1248,-1358,-1168\},\{ -529,-1028, -918,-1028, -838\},\{ -859,- + 1358,-1248,-1358,-1168\},\{ -409, -908, -798, -908, -718\}\} +01584 \}, +01585 \{ +01586 \textcolor{comment}{/* UG.@..AU */} +01587 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01588 \textcolor{comment}{/* UG.A..AU */} +01589 \{\{ DEF, -719, -789, -959, -809\},\{ -479,-1148,-1218,-1388,-1238\},\{ -309, -978,-1048,-1218,-1068\},\{ -389,- + 1058,-1128,-1298,-1148\},\{ -379,-1048,-1118,-1288,-1138\}\}, +01590 \textcolor{comment}{/* UG.C..AU */} +01591 \{\{ DEF, -479, -479, -359, -479\},\{ -649,-1078,-1078, -958,-1078\},\{ -289, -718, -718, -598, -718\},\{ -739,- + 1168,-1168,-1048,-1168\},\{ -379, -808, -808, -688, -808\}\}, +01592 \textcolor{comment}{/* UG.G..AU */} +01593 \{\{ DEF, -659, -809, -919, -809\},\{ -649,-1258,-1408,-1518,-1408\},\{ -289, -898,-1048,-1158,-1048\},\{ -739,- + 1348,-1498,-1608,-1498\},\{ -379, -988,-1138,-1248,-1138\}\}, +01594 \textcolor{comment}{/* UG.U..AU */} +01595 \{\{ DEF, -549, -439, -549, -359\},\{ -649,-1148,-1038,-1148, -958\},\{ -289, -788, -678, -788, -598\},\{ -739,- + 1238,-1128,-1238,-1048\},\{ -379, -878, -768, -878, -688\}\} +01596 \}, +01597 \{ +01598 \textcolor{comment}{/* UG.@..UA */} +01599 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01600 \textcolor{comment}{/* UG.A..UA */} +01601 \{\{ DEF, -719, -789, -959, -809\},\{ -449,-1118,-1188,-1358,-1208\},\{ -479,-1148,-1218,-1388,-1238\},\{ -429,- + 1098,-1168,-1338,-1188\},\{ -329, -998,-1068,-1238,-1088\}\}, +01602 \textcolor{comment}{/* UG.C..UA */} +01603 \{\{ DEF, -479, -479, -359, -479\},\{ -679,-1108,-1108, -988,-1108\},\{ -559, -988, -988, -868, -988\},\{ -729,- + 1158,-1158,-1038,-1158\},\{ -189, -618, -618, -498, -618\}\}, +01604 \textcolor{comment}{/* UG.G..UA */} +01605 \{\{ DEF, -659, -809, -919, -809\},\{ -939,-1548,-1698,-1808,-1698\},\{ -249, -858,-1008,-1118,-1008\},\{ -939,- + 1548,-1698,-1808,-1698\},\{ -329, -938,-1088,-1198,-1088\}\}, +01606 \textcolor{comment}{/* UG.U..UA */} +01607 \{\{ DEF, -549, -439, -549, -359\},\{ -639,-1138,-1028,-1138, -948\},\{ -229, -728, -618, -728, -538\},\{ -729,- + 1228,-1118,-1228,-1038\},\{ -190, -689, -579, -689, -499\}\} +01608 \}, +01609 \{ +01610 \textcolor{comment}{/* UG.@.. @ */} +01611 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01612 \textcolor{comment}{/* UG.A.. @ */} +01613 \{\{ -100, -769, -839,-1009, -859\},\{ -100, -769, -839,-1009, -859\},\{ -100, -769, -839,-1009, -859\},\{ -100, - + 769, -839,-1009, -859\},\{ -100, -769, -839,-1009, -859\}\}, +01614 \textcolor{comment}{/* UG.C.. @ */} +01615 \{\{ -100, -529, -529, -409, -529\},\{ -100, -529, -529, -409, -529\},\{ -100, -529, -529, -409, -529\},\{ -100, - + 529, -529, -409, -529\},\{ -100, -529, -529, -409, -529\}\}, +01616 \textcolor{comment}{/* UG.G.. @ */} +01617 \{\{ -100, -709, -859, -969, -859\},\{ -100, -709, -859, -969, -859\},\{ -100, -709, -859, -969, -859\},\{ -100, - + 709, -859, -969, -859\},\{ -100, -709, -859, -969, -859\}\}, +01618 \textcolor{comment}{/* UG.U.. @ */} +01619 \{\{ -100, -599, -489, -599, -409\},\{ -100, -599, -489, -599, -409\},\{ -100, -599, -489, -599, -409\},\{ -100, - + 599, -489, -599, -409\},\{ -100, -599, -489, -599, -409\}\} +01620 \} +01621 \}, +01622 \{ \textcolor{comment}{/* noPair */} \{\{\{0\}\}\}, +01623 \{ +01624 \textcolor{comment}{/* AU.@..CG */} +01625 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01626 \textcolor{comment}{/* AU.A..CG */} +01627 \{\{ DEF, -429, -599, -599, -599\},\{-1079,-1458,-1628,-1628,-1628\},\{ -569, -948,-1118,-1118,-1118\},\{ -989,- + 1368,-1538,-1538,-1538\},\{ -859,-1238,-1408,-1408,-1408\}\}, +01628 \textcolor{comment}{/* AU.C..CG */} +01629 \{\{ DEF, -259, -239, -239, -239\},\{ -999,-1208,-1188,-1188,-1188\},\{ -499, -708, -688, -688, -688\},\{ -989,- + 1198,-1178,-1178,-1178\},\{ -789, -998, -978, -978, -978\}\}, +01630 \textcolor{comment}{/* AU.G..CG */} +01631 \{\{ DEF, -339, -689, -689, -689\},\{-1079,-1368,-1718,-1718,-1718\},\{ -569, -858,-1208,-1208,-1208\},\{ -989,- + 1278,-1628,-1628,-1628\},\{ -859,-1148,-1498,-1498,-1498\}\}, +01632 \textcolor{comment}{/* AU.U..CG */} +01633 \{\{ DEF, -329, -329, -329, -329\},\{-1079,-1358,-1358,-1358,-1358\},\{ -719, -998, -998, -998, -998\},\{ -989,- + 1268,-1268,-1268,-1268\},\{ -909,-1188,-1188,-1188,-1188\}\} +01634 \}, +01635 \{ +01636 \textcolor{comment}{/* AU.@..GC */} +01637 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01638 \textcolor{comment}{/* AU.A..GC */} +01639 \{\{ DEF, -429, -599, -599, -599\},\{ -569, -948,-1118,-1118,-1118\},\{ -769,-1148,-1318,-1318,-1318\},\{ -759,- + 1138,-1308,-1308,-1308\},\{ -549, -928,-1098,-1098,-1098\}\}, +01640 \textcolor{comment}{/* AU.C..GC */} +01641 \{\{ DEF, -259, -239, -239, -239\},\{ -929,-1138,-1118,-1118,-1118\},\{ -359, -568, -548, -548, -548\},\{ -789, - + 998, -978, -978, -978\},\{ -549, -758, -738, -738, -738\}\}, +01642 \textcolor{comment}{/* AU.G..GC */} +01643 \{\{ DEF, -339, -689, -689, -689\},\{ -609, -898,-1248,-1248,-1248\},\{ -359, -648, -998, -998, -998\},\{ -669, - + 958,-1308,-1308,-1308\},\{ -549, -838,-1188,-1188,-1188\}\}, +01644 \textcolor{comment}{/* AU.U..GC */} +01645 \{\{ DEF, -329, -329, -329, -329\},\{ -929,-1208,-1208,-1208,-1208\},\{ -439, -718, -718, -718, -718\},\{ -789,- + 1068,-1068,-1068,-1068\},\{ -619, -898, -898, -898, -898\}\} +01646 \}, +01647 \{ +01648 \textcolor{comment}{/* AU.@..GU */} +01649 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01650 \textcolor{comment}{/* AU.A..GU */} +01651 \{\{ DEF, -429, -599, -599, -599\},\{ -479, -858,-1028,-1028,-1028\},\{ -309, -688, -858, -858, -858\},\{ -389, - + 768, -938, -938, -938\},\{ -379, -758, -928, -928, -928\}\}, +01652 \textcolor{comment}{/* AU.C..GU */} +01653 \{\{ DEF, -259, -239, -239, -239\},\{ -649, -858, -838, -838, -838\},\{ -289, -498, -478, -478, -478\},\{ -739, - + 948, -928, -928, -928\},\{ -379, -588, -568, -568, -568\}\}, +01654 \textcolor{comment}{/* AU.G..GU */} +01655 \{\{ DEF, -339, -689, -689, -689\},\{ -649, -938,-1288,-1288,-1288\},\{ -289, -578, -928, -928, -928\},\{ -739,- + 1028,-1378,-1378,-1378\},\{ -379, -668,-1018,-1018,-1018\}\}, +01656 \textcolor{comment}{/* AU.U..GU */} +01657 \{\{ DEF, -329, -329, -329, -329\},\{ -649, -928, -928, -928, -928\},\{ -289, -568, -568, -568, -568\},\{ -739,- + 1018,-1018,-1018,-1018\},\{ -379, -658, -658, -658, -658\}\} +01658 \}, +01659 \{ +01660 \textcolor{comment}{/* AU.@..UG */} +01661 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01662 \textcolor{comment}{/* AU.A..UG */} +01663 \{\{ DEF, -429, -599, -599, -599\},\{ -769,-1148,-1318,-1318,-1318\},\{ -529, -908,-1078,-1078,-1078\},\{ -709,- + 1088,-1258,-1258,-1258\},\{ -599, -978,-1148,-1148,-1148\}\}, +01664 \textcolor{comment}{/* AU.C..UG */} +01665 \{\{ DEF, -259, -239, -239, -239\},\{ -839,-1048,-1028,-1028,-1028\},\{ -529, -738, -718, -718, -718\},\{ -859,- + 1068,-1048,-1048,-1048\},\{ -489, -698, -678, -678, -678\}\}, +01666 \textcolor{comment}{/* AU.G..UG */} +01667 \{\{ DEF, -339, -689, -689, -689\},\{-1009,-1298,-1648,-1648,-1648\},\{ -409, -698,-1048,-1048,-1048\},\{ -969,- + 1258,-1608,-1608,-1608\},\{ -599, -888,-1238,-1238,-1238\}\}, +01668 \textcolor{comment}{/* AU.U..UG */} +01669 \{\{ DEF, -329, -329, -329, -329\},\{ -859,-1138,-1138,-1138,-1138\},\{ -529, -808, -808, -808, -808\},\{ -859,- + 1138,-1138,-1138,-1138\},\{ -409, -688, -688, -688, -688\}\} +01670 \}, +01671 \{ +01672 \textcolor{comment}{/* AU.@..AU */} +01673 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01674 \textcolor{comment}{/* AU.A..AU */} +01675 \{\{ DEF, -429, -599, -599, -599\},\{ -479, -858,-1028,-1028,-1028\},\{ -309, -688, -858, -858, -858\},\{ -389, - + 768, -938, -938, -938\},\{ -379, -758, -928, -928, -928\}\}, +01676 \textcolor{comment}{/* AU.C..AU */} +01677 \{\{ DEF, -259, -239, -239, -239\},\{ -649, -858, -838, -838, -838\},\{ -289, -498, -478, -478, -478\},\{ -739, - + 948, -928, -928, -928\},\{ -379, -588, -568, -568, -568\}\}, +01678 \textcolor{comment}{/* AU.G..AU */} +01679 \{\{ DEF, -339, -689, -689, -689\},\{ -649, -938,-1288,-1288,-1288\},\{ -289, -578, -928, -928, -928\},\{ -739,- + 1028,-1378,-1378,-1378\},\{ -379, -668,-1018,-1018,-1018\}\}, +01680 \textcolor{comment}{/* AU.U..AU */} +01681 \{\{ DEF, -329, -329, -329, -329\},\{ -649, -928, -928, -928, -928\},\{ -289, -568, -568, -568, -568\},\{ -739,- + 1018,-1018,-1018,-1018\},\{ -379, -658, -658, -658, -658\}\} +01682 \}, +01683 \{ +01684 \textcolor{comment}{/* AU.@..UA */} +01685 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01686 \textcolor{comment}{/* AU.A..UA */} +01687 \{\{ DEF, -429, -599, -599, -599\},\{ -449, -828, -998, -998, -998\},\{ -479, -858,-1028,-1028,-1028\},\{ -429, - + 808, -978, -978, -978\},\{ -329, -708, -878, -878, -878\}\}, +01688 \textcolor{comment}{/* AU.C..UA */} +01689 \{\{ DEF, -259, -239, -239, -239\},\{ -679, -888, -868, -868, -868\},\{ -559, -768, -748, -748, -748\},\{ -729, - + 938, -918, -918, -918\},\{ -189, -398, -378, -378, -378\}\}, +01690 \textcolor{comment}{/* AU.G..UA */} +01691 \{\{ DEF, -339, -689, -689, -689\},\{ -939,-1228,-1578,-1578,-1578\},\{ -249, -538, -888, -888, -888\},\{ -939,- + 1228,-1578,-1578,-1578\},\{ -329, -618, -968, -968, -968\}\}, +01692 \textcolor{comment}{/* AU.U..UA */} +01693 \{\{ DEF, -329, -329, -329, -329\},\{ -639, -918, -918, -918, -918\},\{ -229, -508, -508, -508, -508\},\{ -729,- + 1008,-1008,-1008,-1008\},\{ -190, -469, -469, -469, -469\}\} +01694 \}, +01695 \{ +01696 \textcolor{comment}{/* AU.@.. @ */} +01697 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01698 \textcolor{comment}{/* AU.A.. @ */} +01699 \{\{ -100, -479, -649, -649, -649\},\{ -100, -479, -649, -649, -649\},\{ -100, -479, -649, -649, -649\},\{ -100, - + 479, -649, -649, -649\},\{ -100, -479, -649, -649, -649\}\}, +01700 \textcolor{comment}{/* AU.C.. @ */} +01701 \{\{ -100, -309, -289, -289, -289\},\{ -100, -309, -289, -289, -289\},\{ -100, -309, -289, -289, -289\},\{ -100, - + 309, -289, -289, -289\},\{ -100, -309, -289, -289, -289\}\}, +01702 \textcolor{comment}{/* AU.G.. @ */} +01703 \{\{ -100, -389, -739, -739, -739\},\{ -100, -389, -739, -739, -739\},\{ -100, -389, -739, -739, -739\},\{ -100, - + 389, -739, -739, -739\},\{ -100, -389, -739, -739, -739\}\}, +01704 \textcolor{comment}{/* AU.U.. @ */} +01705 \{\{ -100, -379, -379, -379, -379\},\{ -100, -379, -379, -379, -379\},\{ -100, -379, -379, -379, -379\},\{ -100, - + 379, -379, -379, -379\},\{ -100, -379, -379, -379, -379\}\} +01706 \} +01707 \}, +01708 \{ \textcolor{comment}{/* noPair */} \{\{\{0\}\}\}, +01709 \{ +01710 \textcolor{comment}{/* UA.@..CG */} +01711 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01712 \textcolor{comment}{/* UA.A..CG */} +01713 \{\{ DEF, -399, -629, -889, -589\},\{-1079,-1428,-1658,-1918,-1618\},\{ -569, -918,-1148,-1408,-1108\},\{ -989,- + 1338,-1568,-1828,-1528\},\{ -859,-1208,-1438,-1698,-1398\}\}, +01714 \textcolor{comment}{/* UA.C..CG */} +01715 \{\{ DEF, -429, -509, -199, -179\},\{ -999,-1378,-1458,-1148,-1128\},\{ -499, -878, -958, -648, -628\},\{ -989,- + 1368,-1448,-1138,-1118\},\{ -789,-1168,-1248, -938, -918\}\}, +01716 \textcolor{comment}{/* UA.G..CG */} +01717 \{\{ DEF, -379, -679, -889, -679\},\{-1079,-1408,-1708,-1918,-1708\},\{ -569, -898,-1198,-1408,-1198\},\{ -989,- + 1318,-1618,-1828,-1618\},\{ -859,-1188,-1488,-1698,-1488\}\}, +01718 \textcolor{comment}{/* UA.U..CG */} +01719 \{\{ DEF, -279, -139, -279, -140\},\{-1079,-1308,-1168,-1308,-1169\},\{ -719, -948, -808, -948, -809\},\{ -989,- + 1218,-1078,-1218,-1079\},\{ -909,-1138, -998,-1138, -999\}\} +01720 \}, +01721 \{ +01722 \textcolor{comment}{/* UA.@..GC */} +01723 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01724 \textcolor{comment}{/* UA.A..GC */} +01725 \{\{ DEF, -399, -629, -889, -589\},\{ -569, -918,-1148,-1408,-1108\},\{ -769,-1118,-1348,-1608,-1308\},\{ -759,- + 1108,-1338,-1598,-1298\},\{ -549, -898,-1128,-1388,-1088\}\}, +01726 \textcolor{comment}{/* UA.C..GC */} +01727 \{\{ DEF, -429, -509, -199, -179\},\{ -929,-1308,-1388,-1078,-1058\},\{ -359, -738, -818, -508, -488\},\{ -789,- + 1168,-1248, -938, -918\},\{ -549, -928,-1008, -698, -678\}\}, +01728 \textcolor{comment}{/* UA.G..GC */} +01729 \{\{ DEF, -379, -679, -889, -679\},\{ -609, -938,-1238,-1448,-1238\},\{ -359, -688, -988,-1198, -988\},\{ -669, - + 998,-1298,-1508,-1298\},\{ -549, -878,-1178,-1388,-1178\}\}, +01730 \textcolor{comment}{/* UA.U..GC */} +01731 \{\{ DEF, -279, -139, -279, -140\},\{ -929,-1158,-1018,-1158,-1019\},\{ -439, -668, -528, -668, -529\},\{ -789,- + 1018, -878,-1018, -879\},\{ -619, -848, -708, -848, -709\}\} +01732 \}, +01733 \{ +01734 \textcolor{comment}{/* UA.@..GU */} +01735 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01736 \textcolor{comment}{/* UA.A..GU */} +01737 \{\{ DEF, -399, -629, -889, -589\},\{ -479, -828,-1058,-1318,-1018\},\{ -309, -658, -888,-1148, -848\},\{ -389, - + 738, -968,-1228, -928\},\{ -379, -728, -958,-1218, -918\}\}, +01738 \textcolor{comment}{/* UA.C..GU */} +01739 \{\{ DEF, -429, -509, -199, -179\},\{ -649,-1028,-1108, -798, -778\},\{ -289, -668, -748, -438, -418\},\{ -739,- + 1118,-1198, -888, -868\},\{ -379, -758, -838, -528, -508\}\}, +01740 \textcolor{comment}{/* UA.G..GU */} +01741 \{\{ DEF, -379, -679, -889, -679\},\{ -649, -978,-1278,-1488,-1278\},\{ -289, -618, -918,-1128, -918\},\{ -739,- + 1068,-1368,-1578,-1368\},\{ -379, -708,-1008,-1218,-1008\}\}, +01742 \textcolor{comment}{/* UA.U..GU */} +01743 \{\{ DEF, -279, -139, -279, -140\},\{ -649, -878, -738, -878, -739\},\{ -289, -518, -378, -518, -379\},\{ -739, - + 968, -828, -968, -829\},\{ -379, -608, -468, -608, -469\}\} +01744 \}, +01745 \{ +01746 \textcolor{comment}{/* UA.@..UG */} +01747 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01748 \textcolor{comment}{/* UA.A..UG */} +01749 \{\{ DEF, -399, -629, -889, -589\},\{ -769,-1118,-1348,-1608,-1308\},\{ -529, -878,-1108,-1368,-1068\},\{ -709,- + 1058,-1288,-1548,-1248\},\{ -599, -948,-1178,-1438,-1138\}\}, +01750 \textcolor{comment}{/* UA.C..UG */} +01751 \{\{ DEF, -429, -509, -199, -179\},\{ -839,-1218,-1298, -988, -968\},\{ -529, -908, -988, -678, -658\},\{ -859,- + 1238,-1318,-1008, -988\},\{ -489, -868, -948, -638, -618\}\}, +01752 \textcolor{comment}{/* UA.G..UG */} +01753 \{\{ DEF, -379, -679, -889, -679\},\{-1009,-1338,-1638,-1848,-1638\},\{ -409, -738,-1038,-1248,-1038\},\{ -969,- + 1298,-1598,-1808,-1598\},\{ -599, -928,-1228,-1438,-1228\}\}, +01754 \textcolor{comment}{/* UA.U..UG */} +01755 \{\{ DEF, -279, -139, -279, -140\},\{ -859,-1088, -948,-1088, -949\},\{ -529, -758, -618, -758, -619\},\{ -859,- + 1088, -948,-1088, -949\},\{ -409, -638, -498, -638, -499\}\} +01756 \}, +01757 \{ +01758 \textcolor{comment}{/* UA.@..AU */} +01759 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01760 \textcolor{comment}{/* UA.A..AU */} +01761 \{\{ DEF, -399, -629, -889, -589\},\{ -479, -828,-1058,-1318,-1018\},\{ -309, -658, -888,-1148, -848\},\{ -389, - + 738, -968,-1228, -928\},\{ -379, -728, -958,-1218, -918\}\}, +01762 \textcolor{comment}{/* UA.C..AU */} +01763 \{\{ DEF, -429, -509, -199, -179\},\{ -649,-1028,-1108, -798, -778\},\{ -289, -668, -748, -438, -418\},\{ -739,- + 1118,-1198, -888, -868\},\{ -379, -758, -838, -528, -508\}\}, +01764 \textcolor{comment}{/* UA.G..AU */} +01765 \{\{ DEF, -379, -679, -889, -679\},\{ -649, -978,-1278,-1488,-1278\},\{ -289, -618, -918,-1128, -918\},\{ -739,- + 1068,-1368,-1578,-1368\},\{ -379, -708,-1008,-1218,-1008\}\}, +01766 \textcolor{comment}{/* UA.U..AU */} +01767 \{\{ DEF, -279, -139, -279, -140\},\{ -649, -878, -738, -878, -739\},\{ -289, -518, -378, -518, -379\},\{ -739, - + 968, -828, -968, -829\},\{ -379, -608, -468, -608, -469\}\} +01768 \}, +01769 \{ +01770 \textcolor{comment}{/* UA.@..UA */} +01771 \{\{ 0, 0, 0, 0, 0\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01772 \textcolor{comment}{/* UA.A..UA */} +01773 \{\{ DEF, -399, -629, -889, -589\},\{ -449, -798,-1028,-1288, -988\},\{ -479, -828,-1058,-1318,-1018\},\{ -429, - + 778,-1008,-1268, -968\},\{ -329, -678, -908,-1168, -868\}\}, +01774 \textcolor{comment}{/* UA.C..UA */} +01775 \{\{ DEF, -429, -509, -199, -179\},\{ -679,-1058,-1138, -828, -808\},\{ -559, -938,-1018, -708, -688\},\{ -729,- + 1108,-1188, -878, -858\},\{ -189, -568, -648, -338, -318\}\}, +01776 \textcolor{comment}{/* UA.G..UA */} +01777 \{\{ DEF, -379, -679, -889, -679\},\{ -939,-1268,-1568,-1778,-1568\},\{ -249, -578, -878,-1088, -878\},\{ -939,- + 1268,-1568,-1778,-1568\},\{ -329, -658, -958,-1168, -958\}\}, +01778 \textcolor{comment}{/* UA.U..UA */} +01779 \{\{ DEF, -279, -139, -279, -140\},\{ -639, -868, -728, -868, -729\},\{ -229, -458, -318, -458, -319\},\{ -729, - + 958, -818, -958, -819\},\{ -190, -419, -279, -419, -280\}\} +01780 \}, +01781 \{ +01782 \textcolor{comment}{/* UA.@.. @ */} +01783 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\},\{ DEF, + DEF, DEF, DEF, DEF\},\{ DEF, DEF, DEF, DEF, DEF\}\}, +01784 \textcolor{comment}{/* UA.A.. @ */} +01785 \{\{ -100, -449, -679, -939, -639\},\{ -100, -449, -679, -939, -639\},\{ -100, -449, -679, -939, -639\},\{ -100, - + 449, -679, -939, -639\},\{ -100, -449, -679, -939, -639\}\}, +01786 \textcolor{comment}{/* UA.C.. @ */} +01787 \{\{ -100, -479, -559, -249, -229\},\{ -100, -479, -559, -249, -229\},\{ -100, -479, -559, -249, -229\},\{ -100, - + 479, -559, -249, -229\},\{ -100, -479, -559, -249, -229\}\}, +01788 \textcolor{comment}{/* UA.G.. @ */} +01789 \{\{ -100, -429, -729, -939, -729\},\{ -100, -429, -729, -939, -729\},\{ -100, -429, -729, -939, -729\},\{ -100, - + 429, -729, -939, -729\},\{ -100, -429, -729, -939, -729\}\}, +01790 \textcolor{comment}{/* UA.U.. @ */} +01791 \{\{ -100, -329, -189, -329, -190\},\{ -100, -329, -189, -329, -190\},\{ -100, -329, -189, -329, -190\},\{ -100, - + 329, -189, -329, -190\},\{ -100, -329, -189, -329, -190\}\} +01792 \} +01793 \}, +01794 \{ \textcolor{comment}{/* noPair */} \{\{\{0\}\}\}, +01795 \{ +01796 \textcolor{comment}{/* @.@..CG */} +01797 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -100, -100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\},\{ -100, - + 100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\}\}, +01798 \textcolor{comment}{/* @.A..CG */} +01799 \{\{ DEF, DEF, DEF, DEF, DEF\},\{-1079,-1079,-1079,-1079,-1079\},\{ -569, -569, -569, -569, -569\},\{ -989, - + 989, -989, -989, -989\},\{ -859, -859, -859, -859, -859\}\}, +01800 \textcolor{comment}{/* @.C..CG */} +01801 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -999, -999, -999, -999, -999\},\{ -499, -499, -499, -499, -499\},\{ -989, - + 989, -989, -989, -989\},\{ -789, -789, -789, -789, -789\}\}, +01802 \textcolor{comment}{/* @.G..CG */} +01803 \{\{ DEF, DEF, DEF, DEF, DEF\},\{-1079,-1079,-1079,-1079,-1079\},\{ -569, -569, -569, -569, -569\},\{ -989, - + 989, -989, -989, -989\},\{ -859, -859, -859, -859, -859\}\}, +01804 \textcolor{comment}{/* @.U..CG */} +01805 \{\{ DEF, DEF, DEF, DEF, DEF\},\{-1079,-1079,-1079,-1079,-1079\},\{ -719, -719, -719, -719, -719\},\{ -989, - + 989, -989, -989, -989\},\{ -909, -909, -909, -909, -909\}\} +01806 \}, +01807 \{ +01808 \textcolor{comment}{/* @.@..GC */} +01809 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -100, -100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\},\{ -100, - + 100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\}\}, +01810 \textcolor{comment}{/* @.A..GC */} +01811 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -569, -569, -569, -569, -569\},\{ -769, -769, -769, -769, -769\},\{ -759, - + 759, -759, -759, -759\},\{ -549, -549, -549, -549, -549\}\}, +01812 \textcolor{comment}{/* @.C..GC */} +01813 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -929, -929, -929, -929, -929\},\{ -359, -359, -359, -359, -359\},\{ -789, - + 789, -789, -789, -789\},\{ -549, -549, -549, -549, -549\}\}, +01814 \textcolor{comment}{/* @.G..GC */} +01815 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -609, -609, -609, -609, -609\},\{ -359, -359, -359, -359, -359\},\{ -669, - + 669, -669, -669, -669\},\{ -549, -549, -549, -549, -549\}\}, +01816 \textcolor{comment}{/* @.U..GC */} +01817 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -929, -929, -929, -929, -929\},\{ -439, -439, -439, -439, -439\},\{ -789, - + 789, -789, -789, -789\},\{ -619, -619, -619, -619, -619\}\} +01818 \}, +01819 \{ +01820 \textcolor{comment}{/* @.@..GU */} +01821 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -100, -100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\},\{ -100, - + 100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\}\}, +01822 \textcolor{comment}{/* @.A..GU */} +01823 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -479, -479, -479, -479, -479\},\{ -309, -309, -309, -309, -309\},\{ -389, - + 389, -389, -389, -389\},\{ -379, -379, -379, -379, -379\}\}, +01824 \textcolor{comment}{/* @.C..GU */} +01825 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -649, -649, -649, -649, -649\},\{ -289, -289, -289, -289, -289\},\{ -739, - + 739, -739, -739, -739\},\{ -379, -379, -379, -379, -379\}\}, +01826 \textcolor{comment}{/* @.G..GU */} +01827 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -649, -649, -649, -649, -649\},\{ -289, -289, -289, -289, -289\},\{ -739, - + 739, -739, -739, -739\},\{ -379, -379, -379, -379, -379\}\}, +01828 \textcolor{comment}{/* @.U..GU */} +01829 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -649, -649, -649, -649, -649\},\{ -289, -289, -289, -289, -289\},\{ -739, - + 739, -739, -739, -739\},\{ -379, -379, -379, -379, -379\}\} +01830 \}, +01831 \{ +01832 \textcolor{comment}{/* @.@..UG */} +01833 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -100, -100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\},\{ -100, - + 100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\}\}, +01834 \textcolor{comment}{/* @.A..UG */} +01835 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -769, -769, -769, -769, -769\},\{ -529, -529, -529, -529, -529\},\{ -709, - + 709, -709, -709, -709\},\{ -599, -599, -599, -599, -599\}\}, +01836 \textcolor{comment}{/* @.C..UG */} +01837 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -839, -839, -839, -839, -839\},\{ -529, -529, -529, -529, -529\},\{ -859, - + 859, -859, -859, -859\},\{ -489, -489, -489, -489, -489\}\}, +01838 \textcolor{comment}{/* @.G..UG */} +01839 \{\{ DEF, DEF, DEF, DEF, DEF\},\{-1009,-1009,-1009,-1009,-1009\},\{ -409, -409, -409, -409, -409\},\{ -969, - + 969, -969, -969, -969\},\{ -599, -599, -599, -599, -599\}\}, +01840 \textcolor{comment}{/* @.U..UG */} +01841 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -859, -859, -859, -859, -859\},\{ -529, -529, -529, -529, -529\},\{ -859, - + 859, -859, -859, -859\},\{ -409, -409, -409, -409, -409\}\} +01842 \}, +01843 \{ +01844 \textcolor{comment}{/* @.@..AU */} +01845 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -100, -100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\},\{ -100, - + 100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\}\}, +01846 \textcolor{comment}{/* @.A..AU */} +01847 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -479, -479, -479, -479, -479\},\{ -309, -309, -309, -309, -309\},\{ -389, - + 389, -389, -389, -389\},\{ -379, -379, -379, -379, -379\}\}, +01848 \textcolor{comment}{/* @.C..AU */} +01849 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -649, -649, -649, -649, -649\},\{ -289, -289, -289, -289, -289\},\{ -739, - + 739, -739, -739, -739\},\{ -379, -379, -379, -379, -379\}\}, +01850 \textcolor{comment}{/* @.G..AU */} +01851 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -649, -649, -649, -649, -649\},\{ -289, -289, -289, -289, -289\},\{ -739, - + 739, -739, -739, -739\},\{ -379, -379, -379, -379, -379\}\}, +01852 \textcolor{comment}{/* @.U..AU */} +01853 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -649, -649, -649, -649, -649\},\{ -289, -289, -289, -289, -289\},\{ -739, - + 739, -739, -739, -739\},\{ -379, -379, -379, -379, -379\}\} +01854 \}, +01855 \{ +01856 \textcolor{comment}{/* @.@..UA */} +01857 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -100, -100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\},\{ -100, - + 100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\}\}, +01858 \textcolor{comment}{/* @.A..UA */} +01859 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -449, -449, -449, -449, -449\},\{ -479, -479, -479, -479, -479\},\{ -429, - + 429, -429, -429, -429\},\{ -329, -329, -329, -329, -329\}\}, +01860 \textcolor{comment}{/* @.C..UA */} +01861 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -679, -679, -679, -679, -679\},\{ -559, -559, -559, -559, -559\},\{ -729, - + 729, -729, -729, -729\},\{ -189, -189, -189, -189, -189\}\}, +01862 \textcolor{comment}{/* @.G..UA */} +01863 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -939, -939, -939, -939, -939\},\{ -249, -249, -249, -249, -249\},\{ -939, - + 939, -939, -939, -939\},\{ -329, -329, -329, -329, -329\}\}, +01864 \textcolor{comment}{/* @.U..UA */} +01865 \{\{ DEF, DEF, DEF, DEF, DEF\},\{ -639, -639, -639, -639, -639\},\{ -229, -229, -229, -229, -229\},\{ -729, - + 729, -729, -729, -729\},\{ -190, -190, -190, -190, -190\}\} +01866 \}, +01867 \{ +01868 \textcolor{comment}{/* @.@.. @ */} +01869 \{\{ -100, -100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\},\{ -100, - + 100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\}\}, +01870 \textcolor{comment}{/* @.A.. @ */} +01871 \{\{ -100, -100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\},\{ -100, - + 100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\}\}, +01872 \textcolor{comment}{/* @.C.. @ */} +01873 \{\{ -100, -100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\},\{ -100, - + 100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\}\}, +01874 \textcolor{comment}{/* @.G.. @ */} +01875 \{\{ -100, -100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\},\{ -100, - + 100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\}\}, +01876 \textcolor{comment}{/* @.U.. @ */} +01877 \{\{ -100, -100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\},\{ -100, - + 100, -100, -100, -100\},\{ -100, -100, -100, -100, -100\}\} +01878 \} +01879 \} +01880 \}; +01881 +01882 PRIVATE \textcolor{keywordtype}{int} int22\_37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5][5] = \{ +01883 \textcolor{comment}{/* noPair */} \{\{\{\{\{0\}\}\}\}\}, +01884 \{ \textcolor{comment}{/* noPair */} \{\{\{\{0\}\}\}\}, +01885 \textcolor{comment}{/* CG....CG */} +01886 \{\{ +01887 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01888 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01889 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01890 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01891 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +01892 \}, +01893 \{ +01894 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01895 \{\{ 340, 340, 340, 340, 340\},\{ 340, 130, 160, 30, 200\},\{ 340, 120, 150, 20, 200\},\{ 340, 30, 60, -70, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +01896 \{\{ 340, 340, 340, 340, 340\},\{ 340, 160, 200, 60, 200\},\{ 340, 210, 180, 150, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 190, 170, 130, 200\}\}, +01897 \{\{ 340, 340, 340, 340, 340\},\{ 340, 30, 60, -70, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 100, 140, 0, 200 + \},\{ 340, -40, -110, -60, 200\}\}, +01898 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 190, 170, 130, 200\},\{ 340, 110, 40, 90, 200 + \},\{ 340, 140, 80, 130, 200\}\} +01899 \}, +01900 \{ +01901 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01902 \{\{ 340, 340, 340, 340, 340\},\{ 340, 120, 210, 200, 190\},\{ 340, 110, 140, 200, 120\},\{ 340, 20, 150, 200, 130 + \},\{ 340, 200, 200, 200, 200\}\}, +01903 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 180, 200, 170\},\{ 340, 140, 170, 200, 150\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 120, 150, 200, 140\}\}, +01904 \{\{ 340, 340, 340, 340, 340\},\{ 340, 20, 150, 200, 130\},\{ 340, 200, 200, 200, 200\},\{ 340, 90, 180, 200, 170 + \},\{ 340, -150, -20, 200, -40\}\}, +01905 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 120, 150, 200, 140\},\{ 340, 0, 130, 200, 110 + \},\{ 340, 30, 60, 200, 50\}\} +01906 \}, +01907 \{ +01908 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01909 \{\{ 340, 340, 340, 340, 340\},\{ 340, 30, 200, 100, 110\},\{ 340, 20, 200, 90, 0\},\{ 340, -70, 200, 0, 90 + \},\{ 340, 200, 200, 200, 200\}\}, +01910 \{\{ 340, 340, 340, 340, 340\},\{ 340, 60, 200, 140, 40\},\{ 340, 150, 200, 180, 130\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 130, 200, 170, 110\}\}, +01911 \{\{ 340, 340, 340, 340, 340\},\{ 340, -70, 200, 0, 90\},\{ 340, 200, 200, 200, 200\},\{ 340, 0, 200, 80, 90 + \},\{ 340, -60, 200, -70, -260\}\}, +01912 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 130, 200, 170, 110\},\{ 340, 90, 200, 90, - + 110\},\{ 340, 130, 200, 120, 110\}\} +01913 \}, +01914 \{ +01915 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01916 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 190, -40, 140\},\{ 340, 200, 120, -150, 30\},\{ 340, 200, 130, -60, + 130\},\{ 340, 200, 200, 200, 200\}\}, +01917 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 170, -110, 80\},\{ 340, 200, 150, -20, 60\},\{ 340, 200, 200, 200, + 200\},\{ 340, 200, 140, -40, 50\}\}, +01918 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 130, -60, 130\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 170, -70, 120 + \},\{ 340, 200, -40, -420, -50\}\}, +01919 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 140, -40, 50\},\{ 340, 200, 110, -260, + 110\},\{ 340, 200, 50, -50, -40\}\} +01920 \} +01921 \}, +01922 \textcolor{comment}{/* CG....GC */} +01923 \{\{ +01924 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01925 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01926 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01927 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01928 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +01929 \}, +01930 \{ +01931 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01932 \{\{ 340, 340, 340, 340, 340\},\{ 340, 50, 60, 0, 200\},\{ 340, 110, 150, -70, 200\},\{ 340, -30, 10, -160, + 200\},\{ 340, 200, 200, 200, 200\}\}, +01933 \{\{ 340, 340, 340, 340, 340\},\{ 340, 110, 110, -100, 200\},\{ 340, 170, 150, -60, 200\},\{ 340, 200, 200, 200, + 200\},\{ 340, 70, 50, 20, 200\}\}, +01934 \{\{ 340, 340, 340, 340, 340\},\{ 340, 40, 50, -70, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 100, 140, 0, 200 + \},\{ 340, 10, -70, -80, 200\}\}, +01935 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 180, 150, 120, 200\},\{ 340, -50, -60, -60, 200 + \},\{ 340, 150, 0, 90, 200\}\} +01936 \}, +01937 \{ +01938 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01939 \{\{ 340, 340, 340, 340, 340\},\{ 340, 130, 220, 200, 200\},\{ 340, 100, 130, 200, 120\},\{ 340, -70, 70, 200, 40 + \},\{ 340, 200, 200, 200, 200\}\}, +01940 \{\{ 340, 340, 340, 340, 340\},\{ 340, 100, 190, 200, 110\},\{ 340, 100, 130, 200, 120\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 0, 30, 200, 170\}\}, +01941 \{\{ 340, 340, 340, 340, 340\},\{ 340, 70, 70, 200, 100\},\{ 340, 200, 200, 200, 200\},\{ 340, 90, 180, 200, 170 + \},\{ 340, -190, -30, 200, -70\}\}, +01942 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 110, 140, 200, 120\},\{ 340, -150, -20, 200, - + 30\},\{ 340, -20, -10, 200, 20\}\} +01943 \}, +01944 \{ +01945 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01946 \{\{ 340, 340, 340, 340, 340\},\{ 340, -20, 200, 110, 90\},\{ 340, -40, 200, 90, 0\},\{ 340, -170, 200, -90, + 30\},\{ 340, 200, 200, 200, 200\}\}, +01947 \{\{ 340, 340, 340, 340, 340\},\{ 340, 70, 200, 80, -10\},\{ 340, 110, 200, 150, 100\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 20, 200, 50, 0\}\}, +01948 \{\{ 340, 340, 340, 340, 340\},\{ 340, -50, 200, -20, 60\},\{ 340, 200, 200, 200, 200\},\{ 340, 0, 200, 80, 90 + \},\{ 340, -90, 200, -100, -300\}\}, +01949 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 120, 200, 150, 100\},\{ 340, -130, 200, -60, - + 240\},\{ 340, 90, 200, 110, 60\}\} +01950 \}, +01951 \{ +01952 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01953 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, -10, 140\},\{ 340, 200, 120, -160, 30\},\{ 340, 200, 40, -160, + 50\},\{ 340, 200, 200, 200, 200\}\}, +01954 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 110, -160, 30\},\{ 340, 200, 120, -60, 30\},\{ 340, 200, 200, 200, + 200\},\{ 340, 200, 20, -160, 10\}\}, +01955 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 50, -60, 140\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 170, -70, 120 + \},\{ 340, 200, -70, -440, -100\}\}, +01956 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 120, -50, 30\},\{ 340, 200, -10, -410, + 10\},\{ 340, 200, 40, -100, 60\}\} +01957 \} +01958 \}, +01959 \textcolor{comment}{/* CG....GU */} +01960 \{\{ +01961 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01962 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01963 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01964 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01965 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +01966 \}, +01967 \{ +01968 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01969 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 240, 100, 200\},\{ 340, 180, 210, 80, 200\},\{ 340, 80, 110, -20, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +01970 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 220, 90, 200\},\{ 340, 230, 210, 170, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 230, 210, 170, 200\}\}, +01971 \{\{ 340, 340, 340, 340, 340\},\{ 340, 80, 110, -20, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 130, 170, 30, 200 + \},\{ 340, 60, 0, 40, 200\}\}, +01972 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 230, 210, 170, 200\},\{ 340, 160, 90, 140, 200 + \},\{ 340, 190, 130, 180, 200\}\} +01973 \}, +01974 \{ +01975 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01976 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 280, 200, 270\},\{ 340, 170, 200, 200, 180\},\{ 340, 70, 200, 200, 180 + \},\{ 340, 200, 200, 200, 200\}\}, +01977 \{\{ 340, 340, 340, 340, 340\},\{ 340, 180, 210, 200, 190\},\{ 340, 160, 190, 200, 180\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 160, 190, 200, 180\}\}, +01978 \{\{ 340, 340, 340, 340, 340\},\{ 340, 70, 200, 200, 180\},\{ 340, 200, 200, 200, 200\},\{ 340, 120, 210, 200, 200 + \},\{ 340, -50, 80, 200, 70\}\}, +01979 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 160, 190, 200, 180\},\{ 340, 50, 180, 200, 160 + \},\{ 340, 80, 110, 200, 100\}\} +01980 \}, +01981 \{ +01982 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01983 \{\{ 340, 340, 340, 340, 340\},\{ 340, 100, 200, 180, 180\},\{ 340, 80, 200, 150, 60\},\{ 340, -20, 200, 50, 140 + \},\{ 340, 200, 200, 200, 200\}\}, +01984 \{\{ 340, 340, 340, 340, 340\},\{ 340, 90, 200, 160, 70\},\{ 340, 170, 200, 210, 150\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 170, 200, 210, 150\}\}, +01985 \{\{ 340, 340, 340, 340, 340\},\{ 340, -20, 200, 50, 140\},\{ 340, 200, 200, 200, 200\},\{ 340, 30, 200, 110, 110 + \},\{ 340, 40, 200, 40, -160\}\}, +01986 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 170, 200, 210, 150\},\{ 340, 140, 200, 130, -60 + \},\{ 340, 180, 200, 170, 160\}\} +01987 \}, +01988 \{ +01989 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01990 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 270, 30, 220\},\{ 340, 200, 180, -90, 90\},\{ 340, 200, 180, -10, 180 + \},\{ 340, 200, 200, 200, 200\}\}, +01991 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 190, -80, 100\},\{ 340, 200, 180, 0, 90\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 180, 0, 90\}\}, +01992 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 180, -10, 180\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 200, -40, 150 + \},\{ 340, 200, 70, -310, 60\}\}, +01993 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 180, 0, 90\},\{ 340, 200, 160, -210, + 160\},\{ 340, 200, 100, 0, 10\}\} +01994 \} +01995 \}, +01996 \textcolor{comment}{/* CG....UG */} +01997 \{\{ +01998 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +01999 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02000 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02001 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02002 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02003 \}, +02004 \{ +02005 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02006 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 240, 100, 200\},\{ 340, 160, 190, 60, 200\},\{ 340, 100, 130, 0, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02007 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 240, 100, 200\},\{ 340, 260, 240, 200, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 260, 240, 200, 200\}\}, +02008 \{\{ 340, 340, 340, 340, 340\},\{ 340, 100, 130, 0, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 140, 170, 40, 200 + \},\{ 340, 20, -40, 0, 200\}\}, +02009 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 230, 210, 170, 200\},\{ 340, 150, 80, 130, 200 + \},\{ 340, 220, 150, 200, 200\}\} +02010 \}, +02011 \{ +02012 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02013 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 280, 200, 270\},\{ 340, 150, 180, 200, 160\},\{ 340, 90, 220, 200, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02014 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 220, 200, 210\},\{ 340, 190, 220, 200, 210\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 190, 220, 200, 210\}\}, +02015 \{\{ 340, 340, 340, 340, 340\},\{ 340, 90, 220, 200, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 130, 220, 200, 200 + \},\{ 340, -90, 40, 200, 30\}\}, +02016 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 160, 190, 200, 180\},\{ 340, 40, 170, 200, 150 + \},\{ 340, 110, 140, 200, 120\}\} +02017 \}, +02018 \{ +02019 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02020 \{\{ 340, 340, 340, 340, 340\},\{ 340, 100, 200, 180, 180\},\{ 340, 60, 200, 130, 40\},\{ 340, 0, 200, 70, 160 + \},\{ 340, 200, 200, 200, 200\}\}, +02021 \{\{ 340, 340, 340, 340, 340\},\{ 340, 100, 200, 180, 80\},\{ 340, 200, 200, 240, 180\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 200, 240, 180\}\}, +02022 \{\{ 340, 340, 340, 340, 340\},\{ 340, 0, 200, 70, 160\},\{ 340, 200, 200, 200, 200\},\{ 340, 40, 200, 110, 120 + \},\{ 340, 0, 200, 0, -200\}\}, +02023 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 170, 200, 210, 150\},\{ 340, 130, 200, 120, -70 + \},\{ 340, 200, 200, 190, 180\}\} +02024 \}, +02025 \{ +02026 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02027 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 270, 30, 220\},\{ 340, 200, 160, -110, 70\},\{ 340, 200, 200, 10, + 190\},\{ 340, 200, 200, 200, 200\}\}, +02028 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 210, -70, 120\},\{ 340, 200, 210, 30, 120\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 210, 30, 120\}\}, +02029 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 10, 190\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 200, -30, 150 + \},\{ 340, 200, 30, -350, 20\}\}, +02030 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 180, 0, 90\},\{ 340, 200, 150, -220, + 150\},\{ 340, 200, 120, 30, 30\}\} +02031 \} +02032 \}, +02033 \textcolor{comment}{/* CG....AU */} +02034 \{\{ +02035 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02036 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02037 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02038 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02039 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02040 \}, +02041 \{ +02042 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02043 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 240, 100, 200\},\{ 340, 180, 210, 80, 200\},\{ 340, 80, 110, -20, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02044 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 220, 90, 200\},\{ 340, 230, 210, 170, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 230, 210, 170, 200\}\}, +02045 \{\{ 340, 340, 340, 340, 340\},\{ 340, 80, 110, -20, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 130, 170, 30, 200 + \},\{ 340, 60, 0, 40, 200\}\}, +02046 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 230, 210, 170, 200\},\{ 340, 160, 90, 140, 200 + \},\{ 340, 190, 130, 180, 200\}\} +02047 \}, +02048 \{ +02049 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02050 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 280, 200, 270\},\{ 340, 170, 200, 200, 180\},\{ 340, 70, 200, 200, 180 + \},\{ 340, 200, 200, 200, 200\}\}, +02051 \{\{ 340, 340, 340, 340, 340\},\{ 340, 180, 210, 200, 190\},\{ 340, 160, 190, 200, 180\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 160, 190, 200, 180\}\}, +02052 \{\{ 340, 340, 340, 340, 340\},\{ 340, 70, 200, 200, 180\},\{ 340, 200, 200, 200, 200\},\{ 340, 120, 210, 200, 200 + \},\{ 340, -50, 80, 200, 70\}\}, +02053 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 160, 190, 200, 180\},\{ 340, 50, 180, 200, 160 + \},\{ 340, 80, 110, 200, 100\}\} +02054 \}, +02055 \{ +02056 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02057 \{\{ 340, 340, 340, 340, 340\},\{ 340, 100, 200, 180, 180\},\{ 340, 80, 200, 150, 60\},\{ 340, -20, 200, 50, 140 + \},\{ 340, 200, 200, 200, 200\}\}, +02058 \{\{ 340, 340, 340, 340, 340\},\{ 340, 90, 200, 160, 70\},\{ 340, 170, 200, 210, 150\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 170, 200, 210, 150\}\}, +02059 \{\{ 340, 340, 340, 340, 340\},\{ 340, -20, 200, 50, 140\},\{ 340, 200, 200, 200, 200\},\{ 340, 30, 200, 110, 110 + \},\{ 340, 40, 200, 40, -160\}\}, +02060 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 170, 200, 210, 150\},\{ 340, 140, 200, 130, -60 + \},\{ 340, 180, 200, 170, 160\}\} +02061 \}, +02062 \{ +02063 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02064 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 270, 30, 220\},\{ 340, 200, 180, -90, 90\},\{ 340, 200, 180, -10, 180 + \},\{ 340, 200, 200, 200, 200\}\}, +02065 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 190, -80, 100\},\{ 340, 200, 180, 0, 90\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 180, 0, 90\}\}, +02066 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 180, -10, 180\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 200, -40, 150 + \},\{ 340, 200, 70, -310, 60\}\}, +02067 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 180, 0, 90\},\{ 340, 200, 160, -210, + 160\},\{ 340, 200, 100, 0, 10\}\} +02068 \} +02069 \}, +02070 \textcolor{comment}{/* CG....UA */} +02071 \{\{ +02072 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02073 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02074 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02075 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02076 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02077 \}, +02078 \{ +02079 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02080 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 240, 100, 200\},\{ 340, 160, 190, 60, 200\},\{ 340, 100, 130, 0, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02081 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 240, 100, 200\},\{ 340, 260, 240, 200, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 260, 240, 200, 200\}\}, +02082 \{\{ 340, 340, 340, 340, 340\},\{ 340, 100, 130, 0, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 140, 170, 40, 200 + \},\{ 340, 20, -40, 0, 200\}\}, +02083 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 230, 210, 170, 200\},\{ 340, 150, 80, 130, 200 + \},\{ 340, 220, 150, 200, 200\}\} +02084 \}, +02085 \{ +02086 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02087 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 280, 200, 270\},\{ 340, 150, 180, 200, 160\},\{ 340, 90, 220, 200, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02088 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 220, 200, 210\},\{ 340, 190, 220, 200, 210\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 190, 220, 200, 210\}\}, +02089 \{\{ 340, 340, 340, 340, 340\},\{ 340, 90, 220, 200, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 130, 220, 200, 200 + \},\{ 340, -90, 40, 200, 30\}\}, +02090 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 160, 190, 200, 180\},\{ 340, 40, 170, 200, 150 + \},\{ 340, 110, 140, 200, 120\}\} +02091 \}, +02092 \{ +02093 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02094 \{\{ 340, 340, 340, 340, 340\},\{ 340, 100, 200, 180, 180\},\{ 340, 60, 200, 130, 40\},\{ 340, 0, 200, 70, 160 + \},\{ 340, 200, 200, 200, 200\}\}, +02095 \{\{ 340, 340, 340, 340, 340\},\{ 340, 100, 200, 180, 80\},\{ 340, 200, 200, 240, 180\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 200, 240, 180\}\}, +02096 \{\{ 340, 340, 340, 340, 340\},\{ 340, 0, 200, 70, 160\},\{ 340, 200, 200, 200, 200\},\{ 340, 40, 200, 110, 120 + \},\{ 340, 0, 200, 0, -200\}\}, +02097 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 170, 200, 210, 150\},\{ 340, 130, 200, 120, -70 + \},\{ 340, 200, 200, 190, 180\}\} +02098 \}, +02099 \{ +02100 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02101 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 270, 30, 220\},\{ 340, 200, 160, -110, 70\},\{ 340, 200, 200, 10, + 190\},\{ 340, 200, 200, 200, 200\}\}, +02102 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 210, -70, 120\},\{ 340, 200, 210, 30, 120\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 210, 30, 120\}\}, +02103 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 10, 190\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 200, -30, 150 + \},\{ 340, 200, 30, -350, 20\}\}, +02104 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 180, 0, 90\},\{ 340, 200, 150, -220, + 150\},\{ 340, 200, 120, 30, 30\}\} +02105 \} +02106 \}, +02107 \textcolor{comment}{/* CG....?? */} +02108 \{\{ +02109 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02110 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02111 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02112 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02113 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02114 \}, +02115 \{ +02116 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02117 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02118 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02119 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02120 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02121 \}, +02122 \{ +02123 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02124 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02125 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02126 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02127 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02128 \}, +02129 \{ +02130 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02131 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02132 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02133 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02134 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02135 \}, +02136 \{ +02137 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02138 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02139 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02140 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02141 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02142 \} +02143 \} +02144 \}, +02145 \{ \textcolor{comment}{/* noPair */} \{\{\{\{0\}\}\}\}, +02146 \textcolor{comment}{/* GC....CG */} +02147 \{\{ +02148 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02149 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02150 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02151 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02152 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02153 \}, +02154 \{ +02155 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02156 \{\{ 340, 340, 340, 340, 340\},\{ 340, 50, 110, 40, 200\},\{ 340, 130, 100, 70, 200\},\{ 340, -20, 70, -50, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02157 \{\{ 340, 340, 340, 340, 340\},\{ 340, 60, 110, 50, 200\},\{ 340, 220, 190, 70, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 110, 50, 200\}\}, +02158 \{\{ 340, 340, 340, 340, 340\},\{ 340, 0, -100, -70, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 110, 80, -20, + 200\},\{ 340, -10, -160, -60, 200\}\}, +02159 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 110, 100, 200\},\{ 340, 90, -10, 60, 200 + \},\{ 340, 140, 30, 140, 200\}\} +02160 \}, +02161 \{ +02162 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02163 \{\{ 340, 340, 340, 340, 340\},\{ 340, 110, 170, 200, 180\},\{ 340, 100, 100, 200, 110\},\{ 340, -40, 110, 200, 120 + \},\{ 340, 200, 200, 200, 200\}\}, +02164 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 150, 200, 150\},\{ 340, 130, 130, 200, 140\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 120, 120, 200, 120\}\}, +02165 \{\{ 340, 340, 340, 340, 340\},\{ 340, -70, -60, 200, 120\},\{ 340, 200, 200, 200, 200\},\{ 340, 90, 150, 200, 150 + \},\{ 340, -160, -60, 200, -50\}\}, +02166 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 120, 120, 200, 120\},\{ 340, 0, 100, 200, 100 + \},\{ 340, 30, 30, 200, 30\}\} +02167 \}, +02168 \{ +02169 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02170 \{\{ 340, 340, 340, 340, 340\},\{ 340, -30, 200, 100, -50\},\{ 340, -70, 200, 90, -150\},\{ 340, -170, 200, 0, - + 130\},\{ 340, 200, 200, 200, 200\}\}, +02171 \{\{ 340, 340, 340, 340, 340\},\{ 340, 10, 200, 140, -60\},\{ 340, 70, 200, 180, -20\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 40, 200, 170, -10\}\}, +02172 \{\{ 340, 340, 340, 340, 340\},\{ 340, -160, 200, 0, -60\},\{ 340, 200, 200, 200, 200\},\{ 340, -90, 200, 80, - + 60\},\{ 340, -160, 200, -70, -410\}\}, +02173 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 40, 200, 170, -30\},\{ 340, 30, 200, 90, - + 240\},\{ 340, 50, 200, 120, 10\}\} +02174 \}, +02175 \{ +02176 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02177 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 70, 10, 150\},\{ 340, 200, 0, -190, -20\},\{ 340, 200, 20, -90, + 90\},\{ 340, 200, 200, 200, 200\}\}, +02178 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 50, -70, 0\},\{ 340, 200, 30, -30, -10\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 20, -70, 40\}\}, +02179 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 20, -80, 90\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 50, -100, + 110\},\{ 340, 200, -160, -440, -100\}\}, +02180 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 170, -70, 20\},\{ 340, 200, 0, -300, + 60\},\{ 340, 200, 10, -100, 60\}\} +02181 \} +02182 \}, +02183 \textcolor{comment}{/* GC....GC */} +02184 \{\{ +02185 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02186 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02187 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02188 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02189 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02190 \}, +02191 \{ +02192 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02193 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 120, 10, 200\},\{ 340, 120, 90, -10, 200\},\{ 340, -50, -80, -190, + 200\},\{ 340, 200, 200, 200, 200\}\}, +02194 \{\{ 340, 340, 340, 340, 340\},\{ 340, 120, 90, -20, 200\},\{ 340, 180, 90, 90, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 80, 0, -10, 200\}\}, +02195 \{\{ 340, 340, 340, 340, 340\},\{ 340, 10, -20, -130, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 110, 80, -20, + 200\},\{ 340, -70, -200, -130, 200\}\}, +02196 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 190, 100, 90, 200\},\{ 340, -30, -160, -90, + 200\},\{ 340, 150, 20, 90, 200\}\} +02197 \}, +02198 \{ +02199 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02200 \{\{ 340, 340, 340, 340, 340\},\{ 340, 120, 180, 200, 190\},\{ 340, 100, 100, 200, 100\},\{ 340, -80, 20, 200, 30 + \},\{ 340, 200, 200, 200, 200\}\}, +02201 \{\{ 340, 340, 340, 340, 340\},\{ 340, 90, 90, 200, 100\},\{ 340, 100, 100, 200, 100\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 0, 0, 200, 0\}\}, +02202 \{\{ 340, 340, 340, 340, 340\},\{ 340, -10, 90, 200, 90\},\{ 340, 200, 200, 200, 200\},\{ 340, 90, 150, 200, 150 + \},\{ 340, -190, -90, 200, -90\}\}, +02203 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 100, 100, 200, 110\},\{ 340, -150, -50, 200, - + 50\},\{ 340, 20, 20, 200, 30\}\} +02204 \}, +02205 \{ +02206 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02207 \{\{ 340, 340, 340, 340, 340\},\{ 340, -50, 200, 110, -30\},\{ 340, -80, 200, 90, -150\},\{ 340, -260, 200, -90, - + 150\},\{ 340, 200, 200, 200, 200\}\}, +02208 \{\{ 340, 340, 340, 340, 340\},\{ 340, -80, 200, 80, -160\},\{ 340, 20, 200, 150, -50\},\{ 340, 200, 200, 200, + 200\},\{ 340, -80, 200, 50, -150\}\}, +02209 \{\{ 340, 340, 340, 340, 340\},\{ 340, -190, 200, -20, -90\},\{ 340, 200, 200, 200, 200\},\{ 340, -90, 200, 80, - + 60\},\{ 340, -190, 200, -100, -450\}\}, +02210 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 30, 200, 150, -50\},\{ 340, -150, 200, -60, - + 410\},\{ 340, 30, 200, 110, -50\}\} +02211 \}, +02212 \{ +02213 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02214 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 80, -70, 150\},\{ 340, 200, 0, -190, 20\},\{ 340, 200, -80, -190, + 30\},\{ 340, 200, 200, 200, 200\}\}, +02215 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 0, -200, 20\},\{ 340, 200, 0, -90, 20\},\{ 340, 200, 200, 200, + 200\},\{ 340, 200, -100, -190, -70\}\}, +02216 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, -10, -130, 90\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 50, -100, + 110\},\{ 340, 200, -190, -490, -90\}\}, +02217 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 0, -90, 30\},\{ 340, 200, -150, -450, - + 50\},\{ 340, 200, -70, -90, -50\}\} +02218 \} +02219 \}, +02220 \textcolor{comment}{/* GC....GU */} +02221 \{\{ +02222 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02223 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02224 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02225 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02226 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02227 \}, +02228 \{ +02229 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02230 \{\{ 340, 340, 340, 340, 340\},\{ 340, 210, 180, 70, 200\},\{ 340, 190, 160, 50, 200\},\{ 340, 90, 60, -50, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02231 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 170, 60, 200\},\{ 340, 240, 150, 140, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 240, 150, 140, 200\}\}, +02232 \{\{ 340, 340, 340, 340, 340\},\{ 340, 90, 60, -50, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 140, 110, 0, 200 + \},\{ 340, 70, -60, 10, 200\}\}, +02233 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 240, 150, 140, 200\},\{ 340, 170, 40, 110, 200 + \},\{ 340, 200, 70, 150, 200\}\} +02234 \}, +02235 \{ +02236 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02237 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 250, 200, 250\},\{ 340, 160, 160, 200, 170\},\{ 340, 60, 160, 200, 170 + \},\{ 340, 200, 200, 200, 200\}\}, +02238 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 170, 200, 180\},\{ 340, 160, 160, 200, 160\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 160, 160, 200, 160\}\}, +02239 \{\{ 340, 340, 340, 340, 340\},\{ 340, 60, 160, 200, 170\},\{ 340, 200, 200, 200, 200\},\{ 340, 120, 180, 200, 180 + \},\{ 340, -50, 50, 200, 50\}\}, +02240 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 160, 160, 200, 160\},\{ 340, 40, 140, 200, 150 + \},\{ 340, 80, 80, 200, 80\}\} +02241 \}, +02242 \{ +02243 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02244 \{\{ 340, 340, 340, 340, 340\},\{ 340, 10, 200, 180, 40\},\{ 340, -10, 200, 150, -90\},\{ 340, -110, 200, 50, - + 10\},\{ 340, 200, 200, 200, 200\}\}, +02245 \{\{ 340, 340, 340, 340, 340\},\{ 340, 0, 200, 160, -80\},\{ 340, 80, 200, 210, 10\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 80, 200, 210, 10\}\}, +02246 \{\{ 340, 340, 340, 340, 340\},\{ 340, -110, 200, 50, -10\},\{ 340, 200, 200, 200, 200\},\{ 340, -60, 200, 110, - + 30\},\{ 340, -50, 200, 40, -310\}\}, +02247 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 80, 200, 210, 10\},\{ 340, 50, 200, 130, - + 210\},\{ 340, 80, 200, 170, 10\}\} +02248 \}, +02249 \{ +02250 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02251 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 150, 0, 210\},\{ 340, 200, 60, -130, 90\},\{ 340, 200, 70, -50, + 170\},\{ 340, 200, 200, 200, 200\}\}, +02252 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 70, -120, 100\},\{ 340, 200, 60, -30, 80\},\{ 340, 200, 200, 200, + 200\},\{ 340, 200, 60, -30, 80\}\}, +02253 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 70, -50, 170\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 80, -70, 140 + \},\{ 340, 200, -50, -350, 50\}\}, +02254 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 60, -30, 80\},\{ 340, 200, 50, -250, + 150\},\{ 340, 200, -20, -30, 0\}\} +02255 \} +02256 \}, +02257 \textcolor{comment}{/* GC....UG */} +02258 \{\{ +02259 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02260 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02261 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02262 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02263 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02264 \}, +02265 \{ +02266 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02267 \{\{ 340, 340, 340, 340, 340\},\{ 340, 210, 180, 70, 200\},\{ 340, 170, 140, 30, 200\},\{ 340, 110, 80, -30, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02268 \{\{ 340, 340, 340, 340, 340\},\{ 340, 210, 180, 70, 200\},\{ 340, 270, 180, 170, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 270, 180, 170, 200\}\}, +02269 \{\{ 340, 340, 340, 340, 340\},\{ 340, 110, 80, -30, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 150, 120, 10, 200 + \},\{ 340, 30, -100, -30, 200\}\}, +02270 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 240, 150, 140, 200\},\{ 340, 160, 30, 100, 200 + \},\{ 340, 230, 100, 170, 200\}\} +02271 \}, +02272 \{ +02273 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02274 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 250, 200, 250\},\{ 340, 140, 140, 200, 150\},\{ 340, 80, 180, 200, 190 + \},\{ 340, 200, 200, 200, 200\}\}, +02275 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 190, 200, 190\},\{ 340, 190, 190, 200, 190\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 190, 190, 200, 190\}\}, +02276 \{\{ 340, 340, 340, 340, 340\},\{ 340, 80, 180, 200, 190\},\{ 340, 200, 200, 200, 200\},\{ 340, 120, 180, 200, 190 + \},\{ 340, -90, 10, 200, 10\}\}, +02277 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 160, 160, 200, 160\},\{ 340, 30, 130, 200, 140 + \},\{ 340, 100, 100, 200, 110\}\} +02278 \}, +02279 \{ +02280 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02281 \{\{ 340, 340, 340, 340, 340\},\{ 340, 10, 200, 180, 40\},\{ 340, -30, 200, 130, -110\},\{ 340, -90, 200, 70, + 10\},\{ 340, 200, 200, 200, 200\}\}, +02282 \{\{ 340, 340, 340, 340, 340\},\{ 340, 10, 200, 180, -60\},\{ 340, 110, 200, 240, 40\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 110, 200, 240, 40\}\}, +02283 \{\{ 340, 340, 340, 340, 340\},\{ 340, -90, 200, 70, 10\},\{ 340, 200, 200, 200, 200\},\{ 340, -50, 200, 110, -30 + \},\{ 340, -90, 200, 0, -350\}\}, +02284 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 80, 200, 210, 10\},\{ 340, 40, 200, 120, - + 220\},\{ 340, 110, 200, 190, 30\}\} +02285 \}, +02286 \{ +02287 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02288 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 150, 0, 210\},\{ 340, 200, 40, -150, 70\},\{ 340, 200, 90, -30, + 190\},\{ 340, 200, 200, 200, 200\}\}, +02289 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 90, -100, 110\},\{ 340, 200, 90, 0, 110\},\{ 340, 200, 200, 200, + 200\},\{ 340, 200, 90, 0, 110\}\}, +02290 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 90, -30, 190\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 80, -70, 150 + \},\{ 340, 200, -90, -390, 10\}\}, +02291 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 60, -30, 80\},\{ 340, 200, 40, -260, + 140\},\{ 340, 200, 0, -10, 30\}\} +02292 \} +02293 \}, +02294 \textcolor{comment}{/* GC....AU */} +02295 \{\{ +02296 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02297 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02298 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02299 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02300 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02301 \}, +02302 \{ +02303 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02304 \{\{ 340, 340, 340, 340, 340\},\{ 340, 210, 180, 70, 200\},\{ 340, 190, 160, 50, 200\},\{ 340, 90, 60, -50, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02305 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 170, 60, 200\},\{ 340, 240, 150, 140, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 240, 150, 140, 200\}\}, +02306 \{\{ 340, 340, 340, 340, 340\},\{ 340, 90, 60, -50, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 140, 110, 0, 200 + \},\{ 340, 70, -60, 10, 200\}\}, +02307 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 240, 150, 140, 200\},\{ 340, 170, 40, 110, 200 + \},\{ 340, 200, 70, 150, 200\}\} +02308 \}, +02309 \{ +02310 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02311 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 250, 200, 250\},\{ 340, 160, 160, 200, 170\},\{ 340, 60, 160, 200, 170 + \},\{ 340, 200, 200, 200, 200\}\}, +02312 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 170, 200, 180\},\{ 340, 160, 160, 200, 160\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 160, 160, 200, 160\}\}, +02313 \{\{ 340, 340, 340, 340, 340\},\{ 340, 60, 160, 200, 170\},\{ 340, 200, 200, 200, 200\},\{ 340, 120, 180, 200, 180 + \},\{ 340, -50, 50, 200, 50\}\}, +02314 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 160, 160, 200, 160\},\{ 340, 40, 140, 200, 150 + \},\{ 340, 80, 80, 200, 80\}\} +02315 \}, +02316 \{ +02317 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02318 \{\{ 340, 340, 340, 340, 340\},\{ 340, 10, 200, 180, 40\},\{ 340, -10, 200, 150, -90\},\{ 340, -110, 200, 50, - + 10\},\{ 340, 200, 200, 200, 200\}\}, +02319 \{\{ 340, 340, 340, 340, 340\},\{ 340, 0, 200, 160, -80\},\{ 340, 80, 200, 210, 10\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 80, 200, 210, 10\}\}, +02320 \{\{ 340, 340, 340, 340, 340\},\{ 340, -110, 200, 50, -10\},\{ 340, 200, 200, 200, 200\},\{ 340, -60, 200, 110, - + 30\},\{ 340, -50, 200, 40, -310\}\}, +02321 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 80, 200, 210, 10\},\{ 340, 50, 200, 130, - + 210\},\{ 340, 80, 200, 170, 10\}\} +02322 \}, +02323 \{ +02324 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02325 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 150, 0, 210\},\{ 340, 200, 60, -130, 90\},\{ 340, 200, 70, -50, + 170\},\{ 340, 200, 200, 200, 200\}\}, +02326 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 70, -120, 100\},\{ 340, 200, 60, -30, 80\},\{ 340, 200, 200, 200, + 200\},\{ 340, 200, 60, -30, 80\}\}, +02327 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 70, -50, 170\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 80, -70, 140 + \},\{ 340, 200, -50, -350, 50\}\}, +02328 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 60, -30, 80\},\{ 340, 200, 50, -250, + 150\},\{ 340, 200, -20, -30, 0\}\} +02329 \} +02330 \}, +02331 \textcolor{comment}{/* GC....UA */} +02332 \{\{ +02333 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02334 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02335 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02336 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02337 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02338 \}, +02339 \{ +02340 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02341 \{\{ 340, 340, 340, 340, 340\},\{ 340, 210, 180, 70, 200\},\{ 340, 170, 140, 30, 200\},\{ 340, 110, 80, -30, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02342 \{\{ 340, 340, 340, 340, 340\},\{ 340, 210, 180, 70, 200\},\{ 340, 270, 180, 170, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 270, 180, 170, 200\}\}, +02343 \{\{ 340, 340, 340, 340, 340\},\{ 340, 110, 80, -30, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 150, 120, 10, 200 + \},\{ 340, 30, -100, -30, 200\}\}, +02344 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 240, 150, 140, 200\},\{ 340, 160, 30, 100, 200 + \},\{ 340, 230, 100, 170, 200\}\} +02345 \}, +02346 \{ +02347 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02348 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 250, 200, 250\},\{ 340, 140, 140, 200, 150\},\{ 340, 80, 180, 200, 190 + \},\{ 340, 200, 200, 200, 200\}\}, +02349 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 190, 200, 190\},\{ 340, 190, 190, 200, 190\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 190, 190, 200, 190\}\}, +02350 \{\{ 340, 340, 340, 340, 340\},\{ 340, 80, 180, 200, 190\},\{ 340, 200, 200, 200, 200\},\{ 340, 120, 180, 200, 190 + \},\{ 340, -90, 10, 200, 10\}\}, +02351 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 160, 160, 200, 160\},\{ 340, 30, 130, 200, 140 + \},\{ 340, 100, 100, 200, 110\}\} +02352 \}, +02353 \{ +02354 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02355 \{\{ 340, 340, 340, 340, 340\},\{ 340, 10, 200, 180, 40\},\{ 340, -30, 200, 130, -110\},\{ 340, -90, 200, 70, + 10\},\{ 340, 200, 200, 200, 200\}\}, +02356 \{\{ 340, 340, 340, 340, 340\},\{ 340, 10, 200, 180, -60\},\{ 340, 110, 200, 240, 40\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 110, 200, 240, 40\}\}, +02357 \{\{ 340, 340, 340, 340, 340\},\{ 340, -90, 200, 70, 10\},\{ 340, 200, 200, 200, 200\},\{ 340, -50, 200, 110, -30 + \},\{ 340, -90, 200, 0, -350\}\}, +02358 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 80, 200, 210, 10\},\{ 340, 40, 200, 120, - + 220\},\{ 340, 110, 200, 190, 30\}\} +02359 \}, +02360 \{ +02361 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02362 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 150, 0, 210\},\{ 340, 200, 40, -150, 70\},\{ 340, 200, 90, -30, + 190\},\{ 340, 200, 200, 200, 200\}\}, +02363 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 90, -100, 110\},\{ 340, 200, 90, 0, 110\},\{ 340, 200, 200, 200, + 200\},\{ 340, 200, 90, 0, 110\}\}, +02364 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 90, -30, 190\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 80, -70, 150 + \},\{ 340, 200, -90, -390, 10\}\}, +02365 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 60, -30, 80\},\{ 340, 200, 40, -260, + 140\},\{ 340, 200, 0, -10, 30\}\} +02366 \} +02367 \}, +02368 \textcolor{comment}{/* GC....?? */} +02369 \{\{ +02370 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02371 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02372 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02373 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02374 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02375 \}, +02376 \{ +02377 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02378 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02379 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02380 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02381 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02382 \}, +02383 \{ +02384 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02385 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02386 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02387 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02388 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02389 \}, +02390 \{ +02391 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02392 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02393 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02394 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02395 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02396 \}, +02397 \{ +02398 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02399 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02400 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02401 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02402 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02403 \} +02404 \} +02405 \}, +02406 \{ \textcolor{comment}{/* noPair */} \{\{\{\{0\}\}\}\}, +02407 \textcolor{comment}{/* GU....CG */} +02408 \{\{ +02409 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02410 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02411 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02412 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02413 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02414 \}, +02415 \{ +02416 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02417 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 190, 80, 200\},\{ 340, 190, 180, 70, 200\},\{ 340, 100, 90, -20, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02418 \{\{ 340, 340, 340, 340, 340\},\{ 340, 240, 220, 110, 200\},\{ 340, 280, 210, 200, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 270, 190, 180, 200\}\}, +02419 \{\{ 340, 340, 340, 340, 340\},\{ 340, 100, 90, -20, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 180, 160, 50, 200 + \},\{ 340, 30, -80, -10, 200\}\}, +02420 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 270, 190, 180, 200\},\{ 340, 180, 70, 140, 200 + \},\{ 340, 220, 100, 180, 200\}\} +02421 \}, +02422 \{ +02423 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02424 \{\{ 340, 340, 340, 340, 340\},\{ 340, 180, 230, 200, 230\},\{ 340, 170, 160, 200, 160\},\{ 340, 80, 170, 200, 170 + \},\{ 340, 200, 200, 200, 200\}\}, +02425 \{\{ 340, 340, 340, 340, 340\},\{ 340, 210, 210, 200, 210\},\{ 340, 200, 190, 200, 190\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 180, 180, 200, 180\}\}, +02426 \{\{ 340, 340, 340, 340, 340\},\{ 340, 80, 170, 200, 170\},\{ 340, 200, 200, 200, 200\},\{ 340, 150, 210, 200, 210 + \},\{ 340, -90, 0, 200, 0\}\}, +02427 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 180, 180, 200, 180\},\{ 340, 60, 150, 200, 150 + \},\{ 340, 90, 90, 200, 90\}\} +02428 \}, +02429 \{ +02430 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02431 \{\{ 340, 340, 340, 340, 340\},\{ 340, 80, 200, 130, 160\},\{ 340, 70, 200, 120, 50\},\{ 340, -20, 200, 30, 140 + \},\{ 340, 200, 200, 200, 200\}\}, +02432 \{\{ 340, 340, 340, 340, 340\},\{ 340, 110, 200, 170, 90\},\{ 340, 200, 200, 210, 180\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 180, 200, 200, 160\}\}, +02433 \{\{ 340, 340, 340, 340, 340\},\{ 340, -20, 200, 30, 140\},\{ 340, 200, 200, 200, 200\},\{ 340, 50, 200, 110, 130 + \},\{ 340, -10, 200, -40, -210\}\}, +02434 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 180, 200, 200, 160\},\{ 340, 140, 200, 110, -60 + \},\{ 340, 180, 200, 150, 160\}\} +02435 \}, +02436 \{ +02437 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02438 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 230, 60, 190\},\{ 340, 200, 160, -50, 80\},\{ 340, 200, 170, 40, 180 + \},\{ 340, 200, 200, 200, 200\}\}, +02439 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 210, 0, 130\},\{ 340, 200, 190, 80, 110\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 180, 70, 100\}\}, +02440 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 170, 40, 180\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 210, 40, 170 + \},\{ 340, 200, 0, -310, 0\}\}, +02441 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 180, 70, 100\},\{ 340, 200, 150, -160, + 160\},\{ 340, 200, 90, 60, 10\}\} +02442 \} +02443 \}, +02444 \textcolor{comment}{/* GU....GC */} +02445 \{\{ +02446 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02447 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02448 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02449 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02450 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02451 \}, +02452 \{ +02453 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02454 \{\{ 340, 340, 340, 340, 340\},\{ 340, 210, 200, 90, 200\},\{ 340, 190, 170, 60, 200\},\{ 340, 10, 0, -110, + 200\},\{ 340, 200, 200, 200, 200\}\}, +02455 \{\{ 340, 340, 340, 340, 340\},\{ 340, 180, 170, 60, 200\},\{ 340, 250, 170, 160, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 150, 70, 70, 200\}\}, +02456 \{\{ 340, 340, 340, 340, 340\},\{ 340, 70, 60, -50, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 180, 160, 50, 200 + \},\{ 340, 0, -120, -50, 200\}\}, +02457 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 250, 180, 170, 200\},\{ 340, 40, -80, -10, 200 + \},\{ 340, 210, 100, 170, 200\}\} +02458 \}, +02459 \{ +02460 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02461 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 240, 200, 240\},\{ 340, 160, 160, 200, 160\},\{ 340, -10, 80, 200, 80 + \},\{ 340, 200, 200, 200, 200\}\}, +02462 \{\{ 340, 340, 340, 340, 340\},\{ 340, 160, 150, 200, 150\},\{ 340, 160, 160, 200, 160\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 60, 60, 200, 60\}\}, +02463 \{\{ 340, 340, 340, 340, 340\},\{ 340, 50, 140, 200, 140\},\{ 340, 200, 200, 200, 200\},\{ 340, 150, 210, 200, 210 + \},\{ 340, -130, -30, 200, -30\}\}, +02464 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 170, 160, 200, 160\},\{ 340, -90, 10, 200, 10 + \},\{ 340, 90, 80, 200, 80\}\} +02465 \}, +02466 \{ +02467 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02468 \{\{ 340, 340, 340, 340, 340\},\{ 340, 90, 200, 140, 170\},\{ 340, 60, 200, 120, 40\},\{ 340, -110, 200, -60, + 50\},\{ 340, 200, 200, 200, 200\}\}, +02469 \{\{ 340, 340, 340, 340, 340\},\{ 340, 60, 200, 110, 40\},\{ 340, 160, 200, 180, 140\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 70, 200, 80, 50\}\}, +02470 \{\{ 340, 340, 340, 340, 340\},\{ 340, -50, 200, 0, 110\},\{ 340, 200, 200, 200, 200\},\{ 340, 50, 200, 110, 130 + \},\{ 340, -50, 200, -70, -250\}\}, +02471 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 170, 200, 180, 150\},\{ 340, -10, 200, -30, - + 210\},\{ 340, 170, 200, 140, 150\}\} +02472 \}, +02473 \{ +02474 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02475 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 240, 70, 200\},\{ 340, 200, 160, -50, 80\},\{ 340, 200, 80, -50, 80 + \},\{ 340, 200, 200, 200, 200\}\}, +02476 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 150, -60, 70\},\{ 340, 200, 160, 50, 80\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 60, -50, -20\}\}, +02477 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 140, 10, 150\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 210, 40, 170 + \},\{ 340, 200, -30, -350, -30\}\}, +02478 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 160, 50, 80\},\{ 340, 200, 10, -310, + 10\},\{ 340, 200, 80, 50, 0\}\} +02479 \} +02480 \}, +02481 \textcolor{comment}{/* GU....GU */} +02482 \{\{ +02483 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02484 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02485 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02486 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02487 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02488 \}, +02489 \{ +02490 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02491 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 260, 150, 200\},\{ 340, 250, 240, 130, 200\},\{ 340, 150, 140, 30, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02492 \{\{ 340, 340, 340, 340, 340\},\{ 340, 260, 250, 140, 200\},\{ 340, 310, 230, 220, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 310, 230, 220, 200\}\}, +02493 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 140, 30, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 210, 190, 80, 200 + \},\{ 340, 130, 20, 90, 200\}\}, +02494 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 310, 230, 220, 200\},\{ 340, 230, 120, 190, 200 + \},\{ 340, 270, 150, 220, 200\}\} +02495 \}, +02496 \{ +02497 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02498 \{\{ 340, 340, 340, 340, 340\},\{ 340, 250, 310, 200, 310\},\{ 340, 230, 220, 200, 220\},\{ 340, 130, 220, 200, 220 + \},\{ 340, 200, 200, 200, 200\}\}, +02499 \{\{ 340, 340, 340, 340, 340\},\{ 340, 240, 230, 200, 230\},\{ 340, 220, 220, 200, 220\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 220, 220, 200, 220\}\}, +02500 \{\{ 340, 340, 340, 340, 340\},\{ 340, 130, 220, 200, 220\},\{ 340, 200, 200, 200, 200\},\{ 340, 180, 240, 200, 240 + \},\{ 340, 10, 100, 200, 100\}\}, +02501 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 220, 220, 200, 220\},\{ 340, 110, 200, 200, 200 + \},\{ 340, 140, 140, 200, 140\}\} +02502 \}, +02503 \{ +02504 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02505 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 200, 210, 230\},\{ 340, 130, 200, 180, 110\},\{ 340, 30, 200, 80, 190 + \},\{ 340, 200, 200, 200, 200\}\}, +02506 \{\{ 340, 340, 340, 340, 340\},\{ 340, 140, 200, 190, 120\},\{ 340, 220, 200, 240, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 220, 200, 240, 200\}\}, +02507 \{\{ 340, 340, 340, 340, 340\},\{ 340, 30, 200, 80, 190\},\{ 340, 200, 200, 200, 200\},\{ 340, 80, 200, 140, 160 + \},\{ 340, 90, 200, 70, -110\}\}, +02508 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 220, 200, 240, 200\},\{ 340, 190, 200, 160, -10 + \},\{ 340, 220, 200, 200, 200\}\} +02509 \}, +02510 \{ +02511 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02512 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 310, 130, 270\},\{ 340, 200, 220, 10, 140\},\{ 340, 200, 220, 90, 220 + \},\{ 340, 200, 200, 200, 200\}\}, +02513 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 230, 20, 150\},\{ 340, 200, 220, 100, 140\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 220, 100, 140\}\}, +02514 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 220, 90, 220\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 240, 70, 200 + \},\{ 340, 200, 100, -210, 110\}\}, +02515 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 220, 100, 140\},\{ 340, 200, 200, -110, + 200\},\{ 340, 200, 140, 110, 60\}\} +02516 \} +02517 \}, +02518 \textcolor{comment}{/* GU....UG */} +02519 \{\{ +02520 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02521 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02522 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02523 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02524 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02525 \}, +02526 \{ +02527 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02528 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 260, 150, 200\},\{ 340, 230, 220, 110, 200\},\{ 340, 170, 160, 50, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02529 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 260, 150, 200\},\{ 340, 340, 260, 250, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 340, 260, 250, 200\}\}, +02530 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 160, 50, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 210, 200, 90, 200 + \},\{ 340, 100, -20, 50, 200\}\}, +02531 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 310, 230, 220, 200\},\{ 340, 220, 110, 180, 200 + \},\{ 340, 290, 180, 250, 200\}\} +02532 \}, +02533 \{ +02534 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02535 \{\{ 340, 340, 340, 340, 340\},\{ 340, 250, 310, 200, 310\},\{ 340, 210, 200, 200, 200\},\{ 340, 150, 240, 200, 240 + \},\{ 340, 200, 200, 200, 200\}\}, +02536 \{\{ 340, 340, 340, 340, 340\},\{ 340, 250, 250, 200, 250\},\{ 340, 250, 250, 200, 250\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 250, 250, 200, 250\}\}, +02537 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 240, 200, 240\},\{ 340, 200, 200, 200, 200\},\{ 340, 190, 240, 200, 240 + \},\{ 340, -30, 70, 200, 70\}\}, +02538 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 220, 220, 200, 220\},\{ 340, 100, 190, 200, 190 + \},\{ 340, 170, 160, 200, 160\}\} +02539 \}, +02540 \{ +02541 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02542 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 200, 210, 230\},\{ 340, 110, 200, 160, 90\},\{ 340, 50, 200, 100, 210 + \},\{ 340, 200, 200, 200, 200\}\}, +02543 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 200, 210, 130\},\{ 340, 250, 200, 270, 230\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 250, 200, 270, 230\}\}, +02544 \{\{ 340, 340, 340, 340, 340\},\{ 340, 50, 200, 100, 210\},\{ 340, 200, 200, 200, 200\},\{ 340, 90, 200, 140, 170 + \},\{ 340, 50, 200, 30, -150\}\}, +02545 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 220, 200, 240, 200\},\{ 340, 180, 200, 150, -20 + \},\{ 340, 250, 200, 220, 230\}\} +02546 \}, +02547 \{ +02548 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02549 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 310, 130, 270\},\{ 340, 200, 200, -10, 120\},\{ 340, 200, 240, 110, 240 + \},\{ 340, 200, 200, 200, 200\}\}, +02550 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 250, 30, 170\},\{ 340, 200, 250, 130, 170\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 250, 130, 170\}\}, +02551 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 240, 110, 240\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 240, 70, 200 + \},\{ 340, 200, 70, -250, 70\}\}, +02552 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 220, 100, 140\},\{ 340, 200, 190, -120, + 190\},\{ 340, 200, 160, 130, 80\}\} +02553 \} +02554 \}, +02555 \textcolor{comment}{/* GU....AU */} +02556 \{\{ +02557 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02558 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02559 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02560 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02561 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02562 \}, +02563 \{ +02564 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02565 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 260, 150, 200\},\{ 340, 250, 240, 130, 200\},\{ 340, 150, 140, 30, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02566 \{\{ 340, 340, 340, 340, 340\},\{ 340, 260, 250, 140, 200\},\{ 340, 310, 230, 220, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 310, 230, 220, 200\}\}, +02567 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 140, 30, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 210, 190, 80, 200 + \},\{ 340, 130, 20, 90, 200\}\}, +02568 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 310, 230, 220, 200\},\{ 340, 230, 120, 190, 200 + \},\{ 340, 270, 150, 220, 200\}\} +02569 \}, +02570 \{ +02571 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02572 \{\{ 340, 340, 340, 340, 340\},\{ 340, 250, 310, 200, 310\},\{ 340, 230, 220, 200, 220\},\{ 340, 130, 220, 200, 220 + \},\{ 340, 200, 200, 200, 200\}\}, +02573 \{\{ 340, 340, 340, 340, 340\},\{ 340, 240, 230, 200, 230\},\{ 340, 220, 220, 200, 220\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 220, 220, 200, 220\}\}, +02574 \{\{ 340, 340, 340, 340, 340\},\{ 340, 130, 220, 200, 220\},\{ 340, 200, 200, 200, 200\},\{ 340, 180, 240, 200, 240 + \},\{ 340, 10, 100, 200, 100\}\}, +02575 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 220, 220, 200, 220\},\{ 340, 110, 200, 200, 200 + \},\{ 340, 140, 140, 200, 140\}\} +02576 \}, +02577 \{ +02578 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02579 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 200, 210, 230\},\{ 340, 130, 200, 180, 110\},\{ 340, 30, 200, 80, 190 + \},\{ 340, 200, 200, 200, 200\}\}, +02580 \{\{ 340, 340, 340, 340, 340\},\{ 340, 140, 200, 190, 120\},\{ 340, 220, 200, 240, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 220, 200, 240, 200\}\}, +02581 \{\{ 340, 340, 340, 340, 340\},\{ 340, 30, 200, 80, 190\},\{ 340, 200, 200, 200, 200\},\{ 340, 80, 200, 140, 160 + \},\{ 340, 90, 200, 70, -110\}\}, +02582 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 220, 200, 240, 200\},\{ 340, 190, 200, 160, -10 + \},\{ 340, 220, 200, 200, 200\}\} +02583 \}, +02584 \{ +02585 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02586 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 310, 130, 270\},\{ 340, 200, 220, 10, 140\},\{ 340, 200, 220, 90, 220 + \},\{ 340, 200, 200, 200, 200\}\}, +02587 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 230, 20, 150\},\{ 340, 200, 220, 100, 140\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 220, 100, 140\}\}, +02588 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 220, 90, 220\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 240, 70, 200 + \},\{ 340, 200, 100, -210, 110\}\}, +02589 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 220, 100, 140\},\{ 340, 200, 200, -110, + 200\},\{ 340, 200, 140, 110, 60\}\} +02590 \} +02591 \}, +02592 \textcolor{comment}{/* GU....UA */} +02593 \{\{ +02594 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02595 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02596 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02597 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02598 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02599 \}, +02600 \{ +02601 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02602 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 260, 150, 200\},\{ 340, 230, 220, 110, 200\},\{ 340, 170, 160, 50, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02603 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 260, 150, 200\},\{ 340, 340, 260, 250, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 340, 260, 250, 200\}\}, +02604 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 160, 50, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 210, 200, 90, 200 + \},\{ 340, 100, -20, 50, 200\}\}, +02605 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 310, 230, 220, 200\},\{ 340, 220, 110, 180, 200 + \},\{ 340, 290, 180, 250, 200\}\} +02606 \}, +02607 \{ +02608 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02609 \{\{ 340, 340, 340, 340, 340\},\{ 340, 250, 310, 200, 310\},\{ 340, 210, 200, 200, 200\},\{ 340, 150, 240, 200, 240 + \},\{ 340, 200, 200, 200, 200\}\}, +02610 \{\{ 340, 340, 340, 340, 340\},\{ 340, 250, 250, 200, 250\},\{ 340, 250, 250, 200, 250\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 250, 250, 200, 250\}\}, +02611 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 240, 200, 240\},\{ 340, 200, 200, 200, 200\},\{ 340, 190, 240, 200, 240 + \},\{ 340, -30, 70, 200, 70\}\}, +02612 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 220, 220, 200, 220\},\{ 340, 100, 190, 200, 190 + \},\{ 340, 170, 160, 200, 160\}\} +02613 \}, +02614 \{ +02615 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02616 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 200, 210, 230\},\{ 340, 110, 200, 160, 90\},\{ 340, 50, 200, 100, 210 + \},\{ 340, 200, 200, 200, 200\}\}, +02617 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 200, 210, 130\},\{ 340, 250, 200, 270, 230\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 250, 200, 270, 230\}\}, +02618 \{\{ 340, 340, 340, 340, 340\},\{ 340, 50, 200, 100, 210\},\{ 340, 200, 200, 200, 200\},\{ 340, 90, 200, 140, 170 + \},\{ 340, 50, 200, 30, -150\}\}, +02619 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 220, 200, 240, 200\},\{ 340, 180, 200, 150, -20 + \},\{ 340, 250, 200, 220, 230\}\} +02620 \}, +02621 \{ +02622 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02623 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 310, 130, 270\},\{ 340, 200, 200, -10, 120\},\{ 340, 200, 240, 110, 240 + \},\{ 340, 200, 200, 200, 200\}\}, +02624 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 250, 30, 170\},\{ 340, 200, 250, 130, 170\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 250, 130, 170\}\}, +02625 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 240, 110, 240\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 240, 70, 200 + \},\{ 340, 200, 70, -250, 70\}\}, +02626 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 220, 100, 140\},\{ 340, 200, 190, -120, + 190\},\{ 340, 200, 160, 130, 80\}\} +02627 \} +02628 \}, +02629 \textcolor{comment}{/* GU....?? */} +02630 \{\{ +02631 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02632 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02633 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02634 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02635 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02636 \}, +02637 \{ +02638 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02639 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02640 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02641 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02642 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02643 \}, +02644 \{ +02645 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02646 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02647 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02648 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02649 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02650 \}, +02651 \{ +02652 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02653 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02654 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02655 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02656 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02657 \}, +02658 \{ +02659 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02660 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02661 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02662 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02663 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02664 \} +02665 \} +02666 \}, +02667 \{ \textcolor{comment}{/* noPair */} \{\{\{\{0\}\}\}\}, +02668 \textcolor{comment}{/* UG....CG */} +02669 \{\{ +02670 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02671 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02672 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02673 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02674 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02675 \}, +02676 \{ +02677 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02678 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 100, 200\},\{ 340, 190, 190, 90, 200\},\{ 340, 100, 100, 0, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02679 \{\{ 340, 340, 340, 340, 340\},\{ 340, 240, 240, 130, 200\},\{ 340, 280, 220, 220, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 270, 210, 200, 200\}\}, +02680 \{\{ 340, 340, 340, 340, 340\},\{ 340, 100, 100, 0, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 180, 180, 70, 200 + \},\{ 340, 30, -70, 10, 200\}\}, +02681 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 270, 210, 200, 200\},\{ 340, 180, 80, 160, 200 + \},\{ 340, 220, 120, 190, 200\}\} +02682 \}, +02683 \{ +02684 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02685 \{\{ 340, 340, 340, 340, 340\},\{ 340, 160, 260, 200, 230\},\{ 340, 150, 190, 200, 160\},\{ 340, 60, 200, 200, 170 + \},\{ 340, 200, 200, 200, 200\}\}, +02686 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 240, 200, 210\},\{ 340, 180, 220, 200, 190\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 160, 210, 200, 180\}\}, +02687 \{\{ 340, 340, 340, 340, 340\},\{ 340, 60, 200, 200, 170\},\{ 340, 200, 200, 200, 200\},\{ 340, 130, 240, 200, 210 + \},\{ 340, -110, 30, 200, 0\}\}, +02688 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 160, 210, 200, 180\},\{ 340, 40, 180, 200, 150 + \},\{ 340, 70, 120, 200, 90\}\} +02689 \}, +02690 \{ +02691 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02692 \{\{ 340, 340, 340, 340, 340\},\{ 340, 100, 200, 140, 150\},\{ 340, 90, 200, 130, 40\},\{ 340, 0, 200, 40, 130 + \},\{ 340, 200, 200, 200, 200\}\}, +02693 \{\{ 340, 340, 340, 340, 340\},\{ 340, 130, 200, 170, 80\},\{ 340, 220, 200, 220, 170\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 200, 200, 150\}\}, +02694 \{\{ 340, 340, 340, 340, 340\},\{ 340, 0, 200, 40, 130\},\{ 340, 200, 200, 200, 200\},\{ 340, 70, 200, 110, 120 + \},\{ 340, 10, 200, -30, -220\}\}, +02695 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 200, 200, 150\},\{ 340, 160, 200, 120, -70 + \},\{ 340, 190, 200, 150, 150\}\} +02696 \}, +02697 \{ +02698 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02699 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 260, 20, 220\},\{ 340, 200, 190, -90, 110\},\{ 340, 200, 200, 0, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02700 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 240, -40, 150\},\{ 340, 200, 220, 40, 140\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 210, 30, 120\}\}, +02701 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 0, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 240, 0, 190 + \},\{ 340, 200, 30, -350, 30\}\}, +02702 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 210, 30, 120\},\{ 340, 200, 180, -200, + 180\},\{ 340, 200, 120, 20, 30\}\} +02703 \} +02704 \}, +02705 \textcolor{comment}{/* UG....GC */} +02706 \{\{ +02707 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02708 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02709 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02710 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02711 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02712 \}, +02713 \{ +02714 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02715 \{\{ 340, 340, 340, 340, 340\},\{ 340, 210, 210, 110, 200\},\{ 340, 190, 190, 80, 200\},\{ 340, 10, 10, -90, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02716 \{\{ 340, 340, 340, 340, 340\},\{ 340, 180, 180, 80, 200\},\{ 340, 250, 190, 180, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 150, 90, 90, 200\}\}, +02717 \{\{ 340, 340, 340, 340, 340\},\{ 340, 70, 70, -30, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 180, 180, 70, 200 + \},\{ 340, 0, -100, -30, 200\}\}, +02718 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 250, 190, 190, 200\},\{ 340, 40, -60, 10, 200 + \},\{ 340, 210, 110, 190, 200\}\} +02719 \}, +02720 \{ +02721 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02722 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 270, 200, 240\},\{ 340, 140, 190, 200, 160\},\{ 340, -30, 110, 200, 80 + \},\{ 340, 200, 200, 200, 200\}\}, +02723 \{\{ 340, 340, 340, 340, 340\},\{ 340, 140, 180, 200, 150\},\{ 340, 140, 190, 200, 160\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 40, 90, 200, 60\}\}, +02724 \{\{ 340, 340, 340, 340, 340\},\{ 340, 30, 170, 200, 140\},\{ 340, 200, 200, 200, 200\},\{ 340, 130, 240, 200, 210 + \},\{ 340, -150, 0, 200, -30\}\}, +02725 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 150, 190, 200, 160\},\{ 340, -110, 40, 200, + 10\},\{ 340, 70, 110, 200, 80\}\} +02726 \}, +02727 \{ +02728 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02729 \{\{ 340, 340, 340, 340, 340\},\{ 340, 110, 200, 150, 160\},\{ 340, 80, 200, 120, 30\},\{ 340, -90, 200, -50, 40 + \},\{ 340, 200, 200, 200, 200\}\}, +02730 \{\{ 340, 340, 340, 340, 340\},\{ 340, 80, 200, 120, 30\},\{ 340, 180, 200, 180, 130\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 90, 200, 80, 40\}\}, +02731 \{\{ 340, 340, 340, 340, 340\},\{ 340, -30, 200, 10, 100\},\{ 340, 200, 200, 200, 200\},\{ 340, 70, 200, 110, 120 + \},\{ 340, -30, 200, -70, -260\}\}, +02732 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 190, 200, 190, 140\},\{ 340, 10, 200, -30, - + 220\},\{ 340, 190, 200, 150, 140\}\} +02733 \}, +02734 \{ +02735 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02736 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 270, 30, 230\},\{ 340, 200, 190, -90, 100\},\{ 340, 200, 110, -90, 110 + \},\{ 340, 200, 200, 200, 200\}\}, +02737 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 180, -100, 100\},\{ 340, 200, 190, 10, 100\},\{ 340, 200, 200, 200, + 200\},\{ 340, 200, 90, -90, 0\}\}, +02738 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 170, -30, 170\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 240, 0, 190 + \},\{ 340, 200, 0, -390, -10\}\}, +02739 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 190, 10, 110\},\{ 340, 200, 40, -350, + 30\},\{ 340, 200, 110, 10, 30\}\} +02740 \} +02741 \}, +02742 \textcolor{comment}{/* UG....GU */} +02743 \{\{ +02744 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02745 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02746 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02747 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02748 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02749 \}, +02750 \{ +02751 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02752 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 280, 170, 200\},\{ 340, 250, 250, 150, 200\},\{ 340, 150, 150, 50, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02753 \{\{ 340, 340, 340, 340, 340\},\{ 340, 260, 260, 160, 200\},\{ 340, 310, 250, 240, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 310, 250, 240, 200\}\}, +02754 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 150, 50, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 210, 210, 100, 200 + \},\{ 340, 130, 30, 110, 200\}\}, +02755 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 310, 250, 240, 200\},\{ 340, 230, 130, 210, 200 + \},\{ 340, 270, 170, 240, 200\}\} +02756 \}, +02757 \{ +02758 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02759 \{\{ 340, 340, 340, 340, 340\},\{ 340, 230, 340, 200, 310\},\{ 340, 210, 250, 200, 220\},\{ 340, 110, 250, 200, 220 + \},\{ 340, 200, 200, 200, 200\}\}, +02760 \{\{ 340, 340, 340, 340, 340\},\{ 340, 220, 260, 200, 230\},\{ 340, 200, 250, 200, 220\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 250, 200, 220\}\}, +02761 \{\{ 340, 340, 340, 340, 340\},\{ 340, 110, 250, 200, 220\},\{ 340, 200, 200, 200, 200\},\{ 340, 160, 270, 200, 240 + \},\{ 340, -10, 130, 200, 100\}\}, +02762 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 250, 200, 220\},\{ 340, 90, 230, 200, 200 + \},\{ 340, 120, 170, 200, 140\}\} +02763 \}, +02764 \{ +02765 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02766 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 200, 210, 220\},\{ 340, 150, 200, 190, 100\},\{ 340, 50, 200, 90, 180 + \},\{ 340, 200, 200, 200, 200\}\}, +02767 \{\{ 340, 340, 340, 340, 340\},\{ 340, 160, 200, 200, 110\},\{ 340, 240, 200, 240, 190\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 240, 200, 240, 190\}\}, +02768 \{\{ 340, 340, 340, 340, 340\},\{ 340, 50, 200, 90, 180\},\{ 340, 200, 200, 200, 200\},\{ 340, 100, 200, 140, 150 + \},\{ 340, 110, 200, 70, -120\}\}, +02769 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 240, 200, 240, 190\},\{ 340, 210, 200, 170, -20 + \},\{ 340, 240, 200, 200, 190\}\} +02770 \}, +02771 \{ +02772 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02773 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 340, 100, 290\},\{ 340, 200, 250, -30, 170\},\{ 340, 200, 250, 50, 250 + \},\{ 340, 200, 200, 200, 200\}\}, +02774 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 260, -20, 180\},\{ 340, 200, 250, 70, 160\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 250, 70, 160\}\}, +02775 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 250, 50, 250\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 270, 30, 220 + \},\{ 340, 200, 130, -250, 130\}\}, +02776 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 250, 70, 160\},\{ 340, 200, 230, -150, + 230\},\{ 340, 200, 170, 70, 80\}\} +02777 \} +02778 \}, +02779 \textcolor{comment}{/* UG....UG */} +02780 \{\{ +02781 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02782 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02783 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02784 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02785 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02786 \}, +02787 \{ +02788 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02789 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 280, 170, 200\},\{ 340, 230, 230, 130, 200\},\{ 340, 170, 170, 70, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02790 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 280, 170, 200\},\{ 340, 340, 280, 270, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 340, 280, 270, 200\}\}, +02791 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 170, 70, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 210, 210, 110, 200 + \},\{ 340, 100, 0, 70, 200\}\}, +02792 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 310, 250, 240, 200\},\{ 340, 220, 120, 200, 200 + \},\{ 340, 290, 190, 270, 200\}\} +02793 \}, +02794 \{ +02795 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02796 \{\{ 340, 340, 340, 340, 340\},\{ 340, 230, 340, 200, 310\},\{ 340, 190, 230, 200, 200\},\{ 340, 130, 270, 200, 240 + \},\{ 340, 200, 200, 200, 200\}\}, +02797 \{\{ 340, 340, 340, 340, 340\},\{ 340, 230, 280, 200, 250\},\{ 340, 230, 280, 200, 250\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 230, 280, 200, 250\}\}, +02798 \{\{ 340, 340, 340, 340, 340\},\{ 340, 130, 270, 200, 240\},\{ 340, 200, 200, 200, 200\},\{ 340, 170, 270, 200, 240 + \},\{ 340, -50, 100, 200, 70\}\}, +02799 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 250, 200, 220\},\{ 340, 80, 220, 200, 190 + \},\{ 340, 150, 190, 200, 160\}\} +02800 \}, +02801 \{ +02802 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02803 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 200, 210, 220\},\{ 340, 130, 200, 170, 80\},\{ 340, 70, 200, 110, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02804 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 200, 210, 120\},\{ 340, 270, 200, 270, 220\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 270, 200, 270, 220\}\}, +02805 \{\{ 340, 340, 340, 340, 340\},\{ 340, 70, 200, 110, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 110, 200, 150, 160 + \},\{ 340, 70, 200, 30, -160\}\}, +02806 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 240, 200, 240, 190\},\{ 340, 200, 200, 160, -30 + \},\{ 340, 270, 200, 230, 220\}\} +02807 \}, +02808 \{ +02809 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02810 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 340, 100, 290\},\{ 340, 200, 230, -50, 150\},\{ 340, 200, 270, 70, 270 + \},\{ 340, 200, 200, 200, 200\}\}, +02811 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 280, 0, 190\},\{ 340, 200, 280, 100, 190\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 280, 100, 190\}\}, +02812 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 270, 70, 270\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 270, 30, 230 + \},\{ 340, 200, 100, -290, 90\}\}, +02813 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 250, 70, 160\},\{ 340, 200, 220, -160, + 220\},\{ 340, 200, 190, 90, 110\}\} +02814 \} +02815 \}, +02816 \textcolor{comment}{/* UG....AU */} +02817 \{\{ +02818 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02819 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02820 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02821 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02822 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02823 \}, +02824 \{ +02825 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02826 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 280, 170, 200\},\{ 340, 250, 250, 150, 200\},\{ 340, 150, 150, 50, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02827 \{\{ 340, 340, 340, 340, 340\},\{ 340, 260, 260, 160, 200\},\{ 340, 310, 250, 240, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 310, 250, 240, 200\}\}, +02828 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 150, 50, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 210, 210, 100, 200 + \},\{ 340, 130, 30, 110, 200\}\}, +02829 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 310, 250, 240, 200\},\{ 340, 230, 130, 210, 200 + \},\{ 340, 270, 170, 240, 200\}\} +02830 \}, +02831 \{ +02832 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02833 \{\{ 340, 340, 340, 340, 340\},\{ 340, 230, 340, 200, 310\},\{ 340, 210, 250, 200, 220\},\{ 340, 110, 250, 200, 220 + \},\{ 340, 200, 200, 200, 200\}\}, +02834 \{\{ 340, 340, 340, 340, 340\},\{ 340, 220, 260, 200, 230\},\{ 340, 200, 250, 200, 220\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 250, 200, 220\}\}, +02835 \{\{ 340, 340, 340, 340, 340\},\{ 340, 110, 250, 200, 220\},\{ 340, 200, 200, 200, 200\},\{ 340, 160, 270, 200, 240 + \},\{ 340, -10, 130, 200, 100\}\}, +02836 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 250, 200, 220\},\{ 340, 90, 230, 200, 200 + \},\{ 340, 120, 170, 200, 140\}\} +02837 \}, +02838 \{ +02839 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02840 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 200, 210, 220\},\{ 340, 150, 200, 190, 100\},\{ 340, 50, 200, 90, 180 + \},\{ 340, 200, 200, 200, 200\}\}, +02841 \{\{ 340, 340, 340, 340, 340\},\{ 340, 160, 200, 200, 110\},\{ 340, 240, 200, 240, 190\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 240, 200, 240, 190\}\}, +02842 \{\{ 340, 340, 340, 340, 340\},\{ 340, 50, 200, 90, 180\},\{ 340, 200, 200, 200, 200\},\{ 340, 100, 200, 140, 150 + \},\{ 340, 110, 200, 70, -120\}\}, +02843 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 240, 200, 240, 190\},\{ 340, 210, 200, 170, -20 + \},\{ 340, 240, 200, 200, 190\}\} +02844 \}, +02845 \{ +02846 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02847 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 340, 100, 290\},\{ 340, 200, 250, -30, 170\},\{ 340, 200, 250, 50, 250 + \},\{ 340, 200, 200, 200, 200\}\}, +02848 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 260, -20, 180\},\{ 340, 200, 250, 70, 160\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 250, 70, 160\}\}, +02849 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 250, 50, 250\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 270, 30, 220 + \},\{ 340, 200, 130, -250, 130\}\}, +02850 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 250, 70, 160\},\{ 340, 200, 230, -150, + 230\},\{ 340, 200, 170, 70, 80\}\} +02851 \} +02852 \}, +02853 \textcolor{comment}{/* UG....UA */} +02854 \{\{ +02855 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02856 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02857 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02858 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02859 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02860 \}, +02861 \{ +02862 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02863 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 280, 170, 200\},\{ 340, 230, 230, 130, 200\},\{ 340, 170, 170, 70, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02864 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 280, 170, 200\},\{ 340, 340, 280, 270, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 340, 280, 270, 200\}\}, +02865 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 170, 70, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 210, 210, 110, 200 + \},\{ 340, 100, 0, 70, 200\}\}, +02866 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 310, 250, 240, 200\},\{ 340, 220, 120, 200, 200 + \},\{ 340, 290, 190, 270, 200\}\} +02867 \}, +02868 \{ +02869 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02870 \{\{ 340, 340, 340, 340, 340\},\{ 340, 230, 340, 200, 310\},\{ 340, 190, 230, 200, 200\},\{ 340, 130, 270, 200, 240 + \},\{ 340, 200, 200, 200, 200\}\}, +02871 \{\{ 340, 340, 340, 340, 340\},\{ 340, 230, 280, 200, 250\},\{ 340, 230, 280, 200, 250\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 230, 280, 200, 250\}\}, +02872 \{\{ 340, 340, 340, 340, 340\},\{ 340, 130, 270, 200, 240\},\{ 340, 200, 200, 200, 200\},\{ 340, 170, 270, 200, 240 + \},\{ 340, -50, 100, 200, 70\}\}, +02873 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 250, 200, 220\},\{ 340, 80, 220, 200, 190 + \},\{ 340, 150, 190, 200, 160\}\} +02874 \}, +02875 \{ +02876 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02877 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 200, 210, 220\},\{ 340, 130, 200, 170, 80\},\{ 340, 70, 200, 110, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02878 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 200, 210, 120\},\{ 340, 270, 200, 270, 220\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 270, 200, 270, 220\}\}, +02879 \{\{ 340, 340, 340, 340, 340\},\{ 340, 70, 200, 110, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 110, 200, 150, 160 + \},\{ 340, 70, 200, 30, -160\}\}, +02880 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 240, 200, 240, 190\},\{ 340, 200, 200, 160, -30 + \},\{ 340, 270, 200, 230, 220\}\} +02881 \}, +02882 \{ +02883 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02884 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 340, 100, 290\},\{ 340, 200, 230, -50, 150\},\{ 340, 200, 270, 70, 270 + \},\{ 340, 200, 200, 200, 200\}\}, +02885 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 280, 0, 190\},\{ 340, 200, 280, 100, 190\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 280, 100, 190\}\}, +02886 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 270, 70, 270\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 270, 30, 230 + \},\{ 340, 200, 100, -290, 90\}\}, +02887 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 250, 70, 160\},\{ 340, 200, 220, -160, + 220\},\{ 340, 200, 190, 90, 110\}\} +02888 \} +02889 \}, +02890 \textcolor{comment}{/* UG....?? */} +02891 \{\{ +02892 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02893 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02894 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02895 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02896 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02897 \}, +02898 \{ +02899 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02900 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02901 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02902 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02903 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02904 \}, +02905 \{ +02906 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02907 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02908 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02909 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02910 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02911 \}, +02912 \{ +02913 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02914 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02915 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02916 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02917 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02918 \}, +02919 \{ +02920 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02921 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02922 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02923 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02924 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02925 \} +02926 \} +02927 \}, +02928 \{ \textcolor{comment}{/* noPair */} \{\{\{\{0\}\}\}\}, +02929 \textcolor{comment}{/* AU....CG */} +02930 \{\{ +02931 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02932 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02933 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02934 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02935 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02936 \}, +02937 \{ +02938 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02939 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 190, 80, 200\},\{ 340, 190, 180, 70, 200\},\{ 340, 100, 90, -20, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +02940 \{\{ 340, 340, 340, 340, 340\},\{ 340, 240, 220, 110, 200\},\{ 340, 280, 210, 200, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 270, 190, 180, 200\}\}, +02941 \{\{ 340, 340, 340, 340, 340\},\{ 340, 100, 90, -20, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 180, 160, 50, 200 + \},\{ 340, 30, -80, -10, 200\}\}, +02942 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 270, 190, 180, 200\},\{ 340, 180, 70, 140, 200 + \},\{ 340, 220, 100, 180, 200\}\} +02943 \}, +02944 \{ +02945 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02946 \{\{ 340, 340, 340, 340, 340\},\{ 340, 180, 230, 200, 230\},\{ 340, 170, 160, 200, 160\},\{ 340, 80, 170, 200, 170 + \},\{ 340, 200, 200, 200, 200\}\}, +02947 \{\{ 340, 340, 340, 340, 340\},\{ 340, 210, 210, 200, 210\},\{ 340, 200, 190, 200, 190\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 180, 180, 200, 180\}\}, +02948 \{\{ 340, 340, 340, 340, 340\},\{ 340, 80, 170, 200, 170\},\{ 340, 200, 200, 200, 200\},\{ 340, 150, 210, 200, 210 + \},\{ 340, -90, 0, 200, 0\}\}, +02949 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 180, 180, 200, 180\},\{ 340, 60, 150, 200, 150 + \},\{ 340, 90, 90, 200, 90\}\} +02950 \}, +02951 \{ +02952 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02953 \{\{ 340, 340, 340, 340, 340\},\{ 340, 80, 200, 130, 160\},\{ 340, 70, 200, 120, 50\},\{ 340, -20, 200, 30, 140 + \},\{ 340, 200, 200, 200, 200\}\}, +02954 \{\{ 340, 340, 340, 340, 340\},\{ 340, 110, 200, 170, 90\},\{ 340, 200, 200, 210, 180\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 180, 200, 200, 160\}\}, +02955 \{\{ 340, 340, 340, 340, 340\},\{ 340, -20, 200, 30, 140\},\{ 340, 200, 200, 200, 200\},\{ 340, 50, 200, 110, 130 + \},\{ 340, -10, 200, -40, -210\}\}, +02956 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 180, 200, 200, 160\},\{ 340, 140, 200, 110, -60 + \},\{ 340, 180, 200, 150, 160\}\} +02957 \}, +02958 \{ +02959 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02960 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 230, 60, 190\},\{ 340, 200, 160, -50, 80\},\{ 340, 200, 170, 40, 180 + \},\{ 340, 200, 200, 200, 200\}\}, +02961 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 210, 0, 130\},\{ 340, 200, 190, 80, 110\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 180, 70, 100\}\}, +02962 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 170, 40, 180\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 210, 40, 170 + \},\{ 340, 200, 0, -310, 0\}\}, +02963 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 180, 70, 100\},\{ 340, 200, 150, -160, + 160\},\{ 340, 200, 90, 60, 10\}\} +02964 \} +02965 \}, +02966 \textcolor{comment}{/* AU....GC */} +02967 \{\{ +02968 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02969 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02970 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02971 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02972 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +02973 \}, +02974 \{ +02975 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02976 \{\{ 340, 340, 340, 340, 340\},\{ 340, 210, 200, 90, 200\},\{ 340, 190, 170, 60, 200\},\{ 340, 10, 0, -110, + 200\},\{ 340, 200, 200, 200, 200\}\}, +02977 \{\{ 340, 340, 340, 340, 340\},\{ 340, 180, 170, 60, 200\},\{ 340, 250, 170, 160, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 150, 70, 70, 200\}\}, +02978 \{\{ 340, 340, 340, 340, 340\},\{ 340, 70, 60, -50, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 180, 160, 50, 200 + \},\{ 340, 0, -120, -50, 200\}\}, +02979 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 250, 180, 170, 200\},\{ 340, 40, -80, -10, 200 + \},\{ 340, 210, 100, 170, 200\}\} +02980 \}, +02981 \{ +02982 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02983 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 240, 200, 240\},\{ 340, 160, 160, 200, 160\},\{ 340, -10, 80, 200, 80 + \},\{ 340, 200, 200, 200, 200\}\}, +02984 \{\{ 340, 340, 340, 340, 340\},\{ 340, 160, 150, 200, 150\},\{ 340, 160, 160, 200, 160\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 60, 60, 200, 60\}\}, +02985 \{\{ 340, 340, 340, 340, 340\},\{ 340, 50, 140, 200, 140\},\{ 340, 200, 200, 200, 200\},\{ 340, 150, 210, 200, 210 + \},\{ 340, -130, -30, 200, -30\}\}, +02986 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 170, 160, 200, 160\},\{ 340, -90, 10, 200, 10 + \},\{ 340, 90, 80, 200, 80\}\} +02987 \}, +02988 \{ +02989 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02990 \{\{ 340, 340, 340, 340, 340\},\{ 340, 90, 200, 140, 170\},\{ 340, 60, 200, 120, 40\},\{ 340, -110, 200, -60, + 50\},\{ 340, 200, 200, 200, 200\}\}, +02991 \{\{ 340, 340, 340, 340, 340\},\{ 340, 60, 200, 110, 40\},\{ 340, 160, 200, 180, 140\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 70, 200, 80, 50\}\}, +02992 \{\{ 340, 340, 340, 340, 340\},\{ 340, -50, 200, 0, 110\},\{ 340, 200, 200, 200, 200\},\{ 340, 50, 200, 110, 130 + \},\{ 340, -50, 200, -70, -250\}\}, +02993 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 170, 200, 180, 150\},\{ 340, -10, 200, -30, - + 210\},\{ 340, 170, 200, 140, 150\}\} +02994 \}, +02995 \{ +02996 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +02997 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 240, 70, 200\},\{ 340, 200, 160, -50, 80\},\{ 340, 200, 80, -50, 80 + \},\{ 340, 200, 200, 200, 200\}\}, +02998 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 150, -60, 70\},\{ 340, 200, 160, 50, 80\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 60, -50, -20\}\}, +02999 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 140, 10, 150\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 210, 40, 170 + \},\{ 340, 200, -30, -350, -30\}\}, +03000 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 160, 50, 80\},\{ 340, 200, 10, -310, + 10\},\{ 340, 200, 80, 50, 0\}\} +03001 \} +03002 \}, +03003 \textcolor{comment}{/* AU....GU */} +03004 \{\{ +03005 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03006 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03007 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03008 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03009 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03010 \}, +03011 \{ +03012 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03013 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 260, 150, 200\},\{ 340, 250, 240, 130, 200\},\{ 340, 150, 140, 30, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +03014 \{\{ 340, 340, 340, 340, 340\},\{ 340, 260, 250, 140, 200\},\{ 340, 310, 230, 220, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 310, 230, 220, 200\}\}, +03015 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 140, 30, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 210, 190, 80, 200 + \},\{ 340, 130, 20, 90, 200\}\}, +03016 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 310, 230, 220, 200\},\{ 340, 230, 120, 190, 200 + \},\{ 340, 270, 150, 220, 200\}\} +03017 \}, +03018 \{ +03019 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03020 \{\{ 340, 340, 340, 340, 340\},\{ 340, 250, 310, 200, 310\},\{ 340, 230, 220, 200, 220\},\{ 340, 130, 220, 200, 220 + \},\{ 340, 200, 200, 200, 200\}\}, +03021 \{\{ 340, 340, 340, 340, 340\},\{ 340, 240, 230, 200, 230\},\{ 340, 220, 220, 200, 220\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 220, 220, 200, 220\}\}, +03022 \{\{ 340, 340, 340, 340, 340\},\{ 340, 130, 220, 200, 220\},\{ 340, 200, 200, 200, 200\},\{ 340, 180, 240, 200, 240 + \},\{ 340, 10, 100, 200, 100\}\}, +03023 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 220, 220, 200, 220\},\{ 340, 110, 200, 200, 200 + \},\{ 340, 140, 140, 200, 140\}\} +03024 \}, +03025 \{ +03026 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03027 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 200, 210, 230\},\{ 340, 130, 200, 180, 110\},\{ 340, 30, 200, 80, 190 + \},\{ 340, 200, 200, 200, 200\}\}, +03028 \{\{ 340, 340, 340, 340, 340\},\{ 340, 140, 200, 190, 120\},\{ 340, 220, 200, 240, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 220, 200, 240, 200\}\}, +03029 \{\{ 340, 340, 340, 340, 340\},\{ 340, 30, 200, 80, 190\},\{ 340, 200, 200, 200, 200\},\{ 340, 80, 200, 140, 160 + \},\{ 340, 90, 200, 70, -110\}\}, +03030 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 220, 200, 240, 200\},\{ 340, 190, 200, 160, -10 + \},\{ 340, 220, 200, 200, 200\}\} +03031 \}, +03032 \{ +03033 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03034 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 310, 130, 270\},\{ 340, 200, 220, 10, 140\},\{ 340, 200, 220, 90, 220 + \},\{ 340, 200, 200, 200, 200\}\}, +03035 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 230, 20, 150\},\{ 340, 200, 220, 100, 140\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 220, 100, 140\}\}, +03036 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 220, 90, 220\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 240, 70, 200 + \},\{ 340, 200, 100, -210, 110\}\}, +03037 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 220, 100, 140\},\{ 340, 200, 200, -110, + 200\},\{ 340, 200, 140, 110, 60\}\} +03038 \} +03039 \}, +03040 \textcolor{comment}{/* AU....UG */} +03041 \{\{ +03042 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03043 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03044 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03045 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03046 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03047 \}, +03048 \{ +03049 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03050 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 260, 150, 200\},\{ 340, 230, 220, 110, 200\},\{ 340, 170, 160, 50, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +03051 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 260, 150, 200\},\{ 340, 340, 260, 250, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 340, 260, 250, 200\}\}, +03052 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 160, 50, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 210, 200, 90, 200 + \},\{ 340, 100, -20, 50, 200\}\}, +03053 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 310, 230, 220, 200\},\{ 340, 220, 110, 180, 200 + \},\{ 340, 290, 180, 250, 200\}\} +03054 \}, +03055 \{ +03056 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03057 \{\{ 340, 340, 340, 340, 340\},\{ 340, 250, 310, 200, 310\},\{ 340, 210, 200, 200, 200\},\{ 340, 150, 240, 200, 240 + \},\{ 340, 200, 200, 200, 200\}\}, +03058 \{\{ 340, 340, 340, 340, 340\},\{ 340, 250, 250, 200, 250\},\{ 340, 250, 250, 200, 250\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 250, 250, 200, 250\}\}, +03059 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 240, 200, 240\},\{ 340, 200, 200, 200, 200\},\{ 340, 190, 240, 200, 240 + \},\{ 340, -30, 70, 200, 70\}\}, +03060 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 220, 220, 200, 220\},\{ 340, 100, 190, 200, 190 + \},\{ 340, 170, 160, 200, 160\}\} +03061 \}, +03062 \{ +03063 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03064 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 200, 210, 230\},\{ 340, 110, 200, 160, 90\},\{ 340, 50, 200, 100, 210 + \},\{ 340, 200, 200, 200, 200\}\}, +03065 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 200, 210, 130\},\{ 340, 250, 200, 270, 230\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 250, 200, 270, 230\}\}, +03066 \{\{ 340, 340, 340, 340, 340\},\{ 340, 50, 200, 100, 210\},\{ 340, 200, 200, 200, 200\},\{ 340, 90, 200, 140, 170 + \},\{ 340, 50, 200, 30, -150\}\}, +03067 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 220, 200, 240, 200\},\{ 340, 180, 200, 150, -20 + \},\{ 340, 250, 200, 220, 230\}\} +03068 \}, +03069 \{ +03070 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03071 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 310, 130, 270\},\{ 340, 200, 200, -10, 120\},\{ 340, 200, 240, 110, 240 + \},\{ 340, 200, 200, 200, 200\}\}, +03072 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 250, 30, 170\},\{ 340, 200, 250, 130, 170\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 250, 130, 170\}\}, +03073 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 240, 110, 240\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 240, 70, 200 + \},\{ 340, 200, 70, -250, 70\}\}, +03074 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 220, 100, 140\},\{ 340, 200, 190, -120, + 190\},\{ 340, 200, 160, 130, 80\}\} +03075 \} +03076 \}, +03077 \textcolor{comment}{/* AU....AU */} +03078 \{\{ +03079 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03080 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03081 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03082 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03083 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03084 \}, +03085 \{ +03086 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03087 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 260, 150, 200\},\{ 340, 250, 240, 130, 200\},\{ 340, 150, 140, 30, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +03088 \{\{ 340, 340, 340, 340, 340\},\{ 340, 260, 250, 140, 200\},\{ 340, 310, 230, 220, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 310, 230, 220, 200\}\}, +03089 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 140, 30, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 210, 190, 80, 200 + \},\{ 340, 130, 20, 90, 200\}\}, +03090 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 310, 230, 220, 200\},\{ 340, 230, 120, 190, 200 + \},\{ 340, 270, 150, 220, 200\}\} +03091 \}, +03092 \{ +03093 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03094 \{\{ 340, 340, 340, 340, 340\},\{ 340, 250, 310, 200, 310\},\{ 340, 230, 220, 200, 220\},\{ 340, 130, 220, 200, 220 + \},\{ 340, 200, 200, 200, 200\}\}, +03095 \{\{ 340, 340, 340, 340, 340\},\{ 340, 240, 230, 200, 230\},\{ 340, 220, 220, 200, 220\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 220, 220, 200, 220\}\}, +03096 \{\{ 340, 340, 340, 340, 340\},\{ 340, 130, 220, 200, 220\},\{ 340, 200, 200, 200, 200\},\{ 340, 180, 240, 200, 240 + \},\{ 340, 10, 100, 200, 100\}\}, +03097 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 220, 220, 200, 220\},\{ 340, 110, 200, 200, 200 + \},\{ 340, 140, 140, 200, 140\}\} +03098 \}, +03099 \{ +03100 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03101 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 200, 210, 230\},\{ 340, 130, 200, 180, 110\},\{ 340, 30, 200, 80, 190 + \},\{ 340, 200, 200, 200, 200\}\}, +03102 \{\{ 340, 340, 340, 340, 340\},\{ 340, 140, 200, 190, 120\},\{ 340, 220, 200, 240, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 220, 200, 240, 200\}\}, +03103 \{\{ 340, 340, 340, 340, 340\},\{ 340, 30, 200, 80, 190\},\{ 340, 200, 200, 200, 200\},\{ 340, 80, 200, 140, 160 + \},\{ 340, 90, 200, 70, -110\}\}, +03104 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 220, 200, 240, 200\},\{ 340, 190, 200, 160, -10 + \},\{ 340, 220, 200, 200, 200\}\} +03105 \}, +03106 \{ +03107 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03108 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 310, 130, 270\},\{ 340, 200, 220, 10, 140\},\{ 340, 200, 220, 90, 220 + \},\{ 340, 200, 200, 200, 200\}\}, +03109 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 230, 20, 150\},\{ 340, 200, 220, 100, 140\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 220, 100, 140\}\}, +03110 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 220, 90, 220\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 240, 70, 200 + \},\{ 340, 200, 100, -210, 110\}\}, +03111 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 220, 100, 140\},\{ 340, 200, 200, -110, + 200\},\{ 340, 200, 140, 110, 60\}\} +03112 \} +03113 \}, +03114 \textcolor{comment}{/* AU....UA */} +03115 \{\{ +03116 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03117 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03118 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03119 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03120 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03121 \}, +03122 \{ +03123 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03124 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 260, 150, 200\},\{ 340, 230, 220, 110, 200\},\{ 340, 170, 160, 50, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +03125 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 260, 150, 200\},\{ 340, 340, 260, 250, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 340, 260, 250, 200\}\}, +03126 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 160, 50, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 210, 200, 90, 200 + \},\{ 340, 100, -20, 50, 200\}\}, +03127 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 310, 230, 220, 200\},\{ 340, 220, 110, 180, 200 + \},\{ 340, 290, 180, 250, 200\}\} +03128 \}, +03129 \{ +03130 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03131 \{\{ 340, 340, 340, 340, 340\},\{ 340, 250, 310, 200, 310\},\{ 340, 210, 200, 200, 200\},\{ 340, 150, 240, 200, 240 + \},\{ 340, 200, 200, 200, 200\}\}, +03132 \{\{ 340, 340, 340, 340, 340\},\{ 340, 250, 250, 200, 250\},\{ 340, 250, 250, 200, 250\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 250, 250, 200, 250\}\}, +03133 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 240, 200, 240\},\{ 340, 200, 200, 200, 200\},\{ 340, 190, 240, 200, 240 + \},\{ 340, -30, 70, 200, 70\}\}, +03134 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 220, 220, 200, 220\},\{ 340, 100, 190, 200, 190 + \},\{ 340, 170, 160, 200, 160\}\} +03135 \}, +03136 \{ +03137 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03138 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 200, 210, 230\},\{ 340, 110, 200, 160, 90\},\{ 340, 50, 200, 100, 210 + \},\{ 340, 200, 200, 200, 200\}\}, +03139 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 200, 210, 130\},\{ 340, 250, 200, 270, 230\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 250, 200, 270, 230\}\}, +03140 \{\{ 340, 340, 340, 340, 340\},\{ 340, 50, 200, 100, 210\},\{ 340, 200, 200, 200, 200\},\{ 340, 90, 200, 140, 170 + \},\{ 340, 50, 200, 30, -150\}\}, +03141 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 220, 200, 240, 200\},\{ 340, 180, 200, 150, -20 + \},\{ 340, 250, 200, 220, 230\}\} +03142 \}, +03143 \{ +03144 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03145 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 310, 130, 270\},\{ 340, 200, 200, -10, 120\},\{ 340, 200, 240, 110, 240 + \},\{ 340, 200, 200, 200, 200\}\}, +03146 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 250, 30, 170\},\{ 340, 200, 250, 130, 170\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 250, 130, 170\}\}, +03147 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 240, 110, 240\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 240, 70, 200 + \},\{ 340, 200, 70, -250, 70\}\}, +03148 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 220, 100, 140\},\{ 340, 200, 190, -120, + 190\},\{ 340, 200, 160, 130, 80\}\} +03149 \} +03150 \}, +03151 \textcolor{comment}{/* AU....?? */} +03152 \{\{ +03153 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03154 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03155 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03156 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03157 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03158 \}, +03159 \{ +03160 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03161 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03162 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03163 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03164 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03165 \}, +03166 \{ +03167 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03168 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03169 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03170 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03171 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03172 \}, +03173 \{ +03174 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03175 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03176 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03177 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03178 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03179 \}, +03180 \{ +03181 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03182 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03183 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03184 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03185 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03186 \} +03187 \} +03188 \}, +03189 \{ \textcolor{comment}{/* noPair */} \{\{\{\{0\}\}\}\}, +03190 \textcolor{comment}{/* UA....CG */} +03191 \{\{ +03192 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03193 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03194 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03195 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03196 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03197 \}, +03198 \{ +03199 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03200 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 100, 200\},\{ 340, 190, 190, 90, 200\},\{ 340, 100, 100, 0, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +03201 \{\{ 340, 340, 340, 340, 340\},\{ 340, 240, 240, 130, 200\},\{ 340, 280, 220, 220, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 270, 210, 200, 200\}\}, +03202 \{\{ 340, 340, 340, 340, 340\},\{ 340, 100, 100, 0, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 180, 180, 70, 200 + \},\{ 340, 30, -70, 10, 200\}\}, +03203 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 270, 210, 200, 200\},\{ 340, 180, 80, 160, 200 + \},\{ 340, 220, 120, 190, 200\}\} +03204 \}, +03205 \{ +03206 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03207 \{\{ 340, 340, 340, 340, 340\},\{ 340, 160, 260, 200, 230\},\{ 340, 150, 190, 200, 160\},\{ 340, 60, 200, 200, 170 + \},\{ 340, 200, 200, 200, 200\}\}, +03208 \{\{ 340, 340, 340, 340, 340\},\{ 340, 190, 240, 200, 210\},\{ 340, 180, 220, 200, 190\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 160, 210, 200, 180\}\}, +03209 \{\{ 340, 340, 340, 340, 340\},\{ 340, 60, 200, 200, 170\},\{ 340, 200, 200, 200, 200\},\{ 340, 130, 240, 200, 210 + \},\{ 340, -110, 30, 200, 0\}\}, +03210 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 160, 210, 200, 180\},\{ 340, 40, 180, 200, 150 + \},\{ 340, 70, 120, 200, 90\}\} +03211 \}, +03212 \{ +03213 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03214 \{\{ 340, 340, 340, 340, 340\},\{ 340, 100, 200, 140, 150\},\{ 340, 90, 200, 130, 40\},\{ 340, 0, 200, 40, 130 + \},\{ 340, 200, 200, 200, 200\}\}, +03215 \{\{ 340, 340, 340, 340, 340\},\{ 340, 130, 200, 170, 80\},\{ 340, 220, 200, 220, 170\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 200, 200, 150\}\}, +03216 \{\{ 340, 340, 340, 340, 340\},\{ 340, 0, 200, 40, 130\},\{ 340, 200, 200, 200, 200\},\{ 340, 70, 200, 110, 120 + \},\{ 340, 10, 200, -30, -220\}\}, +03217 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 200, 200, 150\},\{ 340, 160, 200, 120, -70 + \},\{ 340, 190, 200, 150, 150\}\} +03218 \}, +03219 \{ +03220 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03221 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 260, 20, 220\},\{ 340, 200, 190, -90, 110\},\{ 340, 200, 200, 0, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +03222 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 240, -40, 150\},\{ 340, 200, 220, 40, 140\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 210, 30, 120\}\}, +03223 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 0, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 240, 0, 190 + \},\{ 340, 200, 30, -350, 30\}\}, +03224 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 210, 30, 120\},\{ 340, 200, 180, -200, + 180\},\{ 340, 200, 120, 20, 30\}\} +03225 \} +03226 \}, +03227 \textcolor{comment}{/* UA....GC */} +03228 \{\{ +03229 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03230 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03231 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03232 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03233 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03234 \}, +03235 \{ +03236 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03237 \{\{ 340, 340, 340, 340, 340\},\{ 340, 210, 210, 110, 200\},\{ 340, 190, 190, 80, 200\},\{ 340, 10, 10, -90, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +03238 \{\{ 340, 340, 340, 340, 340\},\{ 340, 180, 180, 80, 200\},\{ 340, 250, 190, 180, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 150, 90, 90, 200\}\}, +03239 \{\{ 340, 340, 340, 340, 340\},\{ 340, 70, 70, -30, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 180, 180, 70, 200 + \},\{ 340, 0, -100, -30, 200\}\}, +03240 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 250, 190, 190, 200\},\{ 340, 40, -60, 10, 200 + \},\{ 340, 210, 110, 190, 200\}\} +03241 \}, +03242 \{ +03243 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03244 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 270, 200, 240\},\{ 340, 140, 190, 200, 160\},\{ 340, -30, 110, 200, 80 + \},\{ 340, 200, 200, 200, 200\}\}, +03245 \{\{ 340, 340, 340, 340, 340\},\{ 340, 140, 180, 200, 150\},\{ 340, 140, 190, 200, 160\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 40, 90, 200, 60\}\}, +03246 \{\{ 340, 340, 340, 340, 340\},\{ 340, 30, 170, 200, 140\},\{ 340, 200, 200, 200, 200\},\{ 340, 130, 240, 200, 210 + \},\{ 340, -150, 0, 200, -30\}\}, +03247 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 150, 190, 200, 160\},\{ 340, -110, 40, 200, + 10\},\{ 340, 70, 110, 200, 80\}\} +03248 \}, +03249 \{ +03250 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03251 \{\{ 340, 340, 340, 340, 340\},\{ 340, 110, 200, 150, 160\},\{ 340, 80, 200, 120, 30\},\{ 340, -90, 200, -50, 40 + \},\{ 340, 200, 200, 200, 200\}\}, +03252 \{\{ 340, 340, 340, 340, 340\},\{ 340, 80, 200, 120, 30\},\{ 340, 180, 200, 180, 130\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 90, 200, 80, 40\}\}, +03253 \{\{ 340, 340, 340, 340, 340\},\{ 340, -30, 200, 10, 100\},\{ 340, 200, 200, 200, 200\},\{ 340, 70, 200, 110, 120 + \},\{ 340, -30, 200, -70, -260\}\}, +03254 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 190, 200, 190, 140\},\{ 340, 10, 200, -30, - + 220\},\{ 340, 190, 200, 150, 140\}\} +03255 \}, +03256 \{ +03257 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03258 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 270, 30, 230\},\{ 340, 200, 190, -90, 100\},\{ 340, 200, 110, -90, 110 + \},\{ 340, 200, 200, 200, 200\}\}, +03259 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 180, -100, 100\},\{ 340, 200, 190, 10, 100\},\{ 340, 200, 200, 200, + 200\},\{ 340, 200, 90, -90, 0\}\}, +03260 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 170, -30, 170\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 240, 0, 190 + \},\{ 340, 200, 0, -390, -10\}\}, +03261 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 190, 10, 110\},\{ 340, 200, 40, -350, + 30\},\{ 340, 200, 110, 10, 30\}\} +03262 \} +03263 \}, +03264 \textcolor{comment}{/* UA....GU */} +03265 \{\{ +03266 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03267 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03268 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03269 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03270 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03271 \}, +03272 \{ +03273 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03274 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 280, 170, 200\},\{ 340, 250, 250, 150, 200\},\{ 340, 150, 150, 50, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +03275 \{\{ 340, 340, 340, 340, 340\},\{ 340, 260, 260, 160, 200\},\{ 340, 310, 250, 240, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 310, 250, 240, 200\}\}, +03276 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 150, 50, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 210, 210, 100, 200 + \},\{ 340, 130, 30, 110, 200\}\}, +03277 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 310, 250, 240, 200\},\{ 340, 230, 130, 210, 200 + \},\{ 340, 270, 170, 240, 200\}\} +03278 \}, +03279 \{ +03280 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03281 \{\{ 340, 340, 340, 340, 340\},\{ 340, 230, 340, 200, 310\},\{ 340, 210, 250, 200, 220\},\{ 340, 110, 250, 200, 220 + \},\{ 340, 200, 200, 200, 200\}\}, +03282 \{\{ 340, 340, 340, 340, 340\},\{ 340, 220, 260, 200, 230\},\{ 340, 200, 250, 200, 220\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 250, 200, 220\}\}, +03283 \{\{ 340, 340, 340, 340, 340\},\{ 340, 110, 250, 200, 220\},\{ 340, 200, 200, 200, 200\},\{ 340, 160, 270, 200, 240 + \},\{ 340, -10, 130, 200, 100\}\}, +03284 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 250, 200, 220\},\{ 340, 90, 230, 200, 200 + \},\{ 340, 120, 170, 200, 140\}\} +03285 \}, +03286 \{ +03287 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03288 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 200, 210, 220\},\{ 340, 150, 200, 190, 100\},\{ 340, 50, 200, 90, 180 + \},\{ 340, 200, 200, 200, 200\}\}, +03289 \{\{ 340, 340, 340, 340, 340\},\{ 340, 160, 200, 200, 110\},\{ 340, 240, 200, 240, 190\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 240, 200, 240, 190\}\}, +03290 \{\{ 340, 340, 340, 340, 340\},\{ 340, 50, 200, 90, 180\},\{ 340, 200, 200, 200, 200\},\{ 340, 100, 200, 140, 150 + \},\{ 340, 110, 200, 70, -120\}\}, +03291 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 240, 200, 240, 190\},\{ 340, 210, 200, 170, -20 + \},\{ 340, 240, 200, 200, 190\}\} +03292 \}, +03293 \{ +03294 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03295 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 340, 100, 290\},\{ 340, 200, 250, -30, 170\},\{ 340, 200, 250, 50, 250 + \},\{ 340, 200, 200, 200, 200\}\}, +03296 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 260, -20, 180\},\{ 340, 200, 250, 70, 160\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 250, 70, 160\}\}, +03297 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 250, 50, 250\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 270, 30, 220 + \},\{ 340, 200, 130, -250, 130\}\}, +03298 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 250, 70, 160\},\{ 340, 200, 230, -150, + 230\},\{ 340, 200, 170, 70, 80\}\} +03299 \} +03300 \}, +03301 \textcolor{comment}{/* UA....UG */} +03302 \{\{ +03303 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03304 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03305 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03306 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03307 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03308 \}, +03309 \{ +03310 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03311 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 280, 170, 200\},\{ 340, 230, 230, 130, 200\},\{ 340, 170, 170, 70, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +03312 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 280, 170, 200\},\{ 340, 340, 280, 270, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 340, 280, 270, 200\}\}, +03313 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 170, 70, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 210, 210, 110, 200 + \},\{ 340, 100, 0, 70, 200\}\}, +03314 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 310, 250, 240, 200\},\{ 340, 220, 120, 200, 200 + \},\{ 340, 290, 190, 270, 200\}\} +03315 \}, +03316 \{ +03317 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03318 \{\{ 340, 340, 340, 340, 340\},\{ 340, 230, 340, 200, 310\},\{ 340, 190, 230, 200, 200\},\{ 340, 130, 270, 200, 240 + \},\{ 340, 200, 200, 200, 200\}\}, +03319 \{\{ 340, 340, 340, 340, 340\},\{ 340, 230, 280, 200, 250\},\{ 340, 230, 280, 200, 250\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 230, 280, 200, 250\}\}, +03320 \{\{ 340, 340, 340, 340, 340\},\{ 340, 130, 270, 200, 240\},\{ 340, 200, 200, 200, 200\},\{ 340, 170, 270, 200, 240 + \},\{ 340, -50, 100, 200, 70\}\}, +03321 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 250, 200, 220\},\{ 340, 80, 220, 200, 190 + \},\{ 340, 150, 190, 200, 160\}\} +03322 \}, +03323 \{ +03324 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03325 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 200, 210, 220\},\{ 340, 130, 200, 170, 80\},\{ 340, 70, 200, 110, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +03326 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 200, 210, 120\},\{ 340, 270, 200, 270, 220\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 270, 200, 270, 220\}\}, +03327 \{\{ 340, 340, 340, 340, 340\},\{ 340, 70, 200, 110, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 110, 200, 150, 160 + \},\{ 340, 70, 200, 30, -160\}\}, +03328 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 240, 200, 240, 190\},\{ 340, 200, 200, 160, -30 + \},\{ 340, 270, 200, 230, 220\}\} +03329 \}, +03330 \{ +03331 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03332 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 340, 100, 290\},\{ 340, 200, 230, -50, 150\},\{ 340, 200, 270, 70, 270 + \},\{ 340, 200, 200, 200, 200\}\}, +03333 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 280, 0, 190\},\{ 340, 200, 280, 100, 190\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 280, 100, 190\}\}, +03334 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 270, 70, 270\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 270, 30, 230 + \},\{ 340, 200, 100, -290, 90\}\}, +03335 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 250, 70, 160\},\{ 340, 200, 220, -160, + 220\},\{ 340, 200, 190, 90, 110\}\} +03336 \} +03337 \}, +03338 \textcolor{comment}{/* UA....AU */} +03339 \{\{ +03340 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03341 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03342 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03343 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03344 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03345 \}, +03346 \{ +03347 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03348 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 280, 170, 200\},\{ 340, 250, 250, 150, 200\},\{ 340, 150, 150, 50, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +03349 \{\{ 340, 340, 340, 340, 340\},\{ 340, 260, 260, 160, 200\},\{ 340, 310, 250, 240, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 310, 250, 240, 200\}\}, +03350 \{\{ 340, 340, 340, 340, 340\},\{ 340, 150, 150, 50, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 210, 210, 100, 200 + \},\{ 340, 130, 30, 110, 200\}\}, +03351 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 310, 250, 240, 200\},\{ 340, 230, 130, 210, 200 + \},\{ 340, 270, 170, 240, 200\}\} +03352 \}, +03353 \{ +03354 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03355 \{\{ 340, 340, 340, 340, 340\},\{ 340, 230, 340, 200, 310\},\{ 340, 210, 250, 200, 220\},\{ 340, 110, 250, 200, 220 + \},\{ 340, 200, 200, 200, 200\}\}, +03356 \{\{ 340, 340, 340, 340, 340\},\{ 340, 220, 260, 200, 230\},\{ 340, 200, 250, 200, 220\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 250, 200, 220\}\}, +03357 \{\{ 340, 340, 340, 340, 340\},\{ 340, 110, 250, 200, 220\},\{ 340, 200, 200, 200, 200\},\{ 340, 160, 270, 200, 240 + \},\{ 340, -10, 130, 200, 100\}\}, +03358 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 250, 200, 220\},\{ 340, 90, 230, 200, 200 + \},\{ 340, 120, 170, 200, 140\}\} +03359 \}, +03360 \{ +03361 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03362 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 200, 210, 220\},\{ 340, 150, 200, 190, 100\},\{ 340, 50, 200, 90, 180 + \},\{ 340, 200, 200, 200, 200\}\}, +03363 \{\{ 340, 340, 340, 340, 340\},\{ 340, 160, 200, 200, 110\},\{ 340, 240, 200, 240, 190\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 240, 200, 240, 190\}\}, +03364 \{\{ 340, 340, 340, 340, 340\},\{ 340, 50, 200, 90, 180\},\{ 340, 200, 200, 200, 200\},\{ 340, 100, 200, 140, 150 + \},\{ 340, 110, 200, 70, -120\}\}, +03365 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 240, 200, 240, 190\},\{ 340, 210, 200, 170, -20 + \},\{ 340, 240, 200, 200, 190\}\} +03366 \}, +03367 \{ +03368 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03369 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 340, 100, 290\},\{ 340, 200, 250, -30, 170\},\{ 340, 200, 250, 50, 250 + \},\{ 340, 200, 200, 200, 200\}\}, +03370 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 260, -20, 180\},\{ 340, 200, 250, 70, 160\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 250, 70, 160\}\}, +03371 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 250, 50, 250\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 270, 30, 220 + \},\{ 340, 200, 130, -250, 130\}\}, +03372 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 250, 70, 160\},\{ 340, 200, 230, -150, + 230\},\{ 340, 200, 170, 70, 80\}\} +03373 \} +03374 \}, +03375 \textcolor{comment}{/* UA....UA */} +03376 \{\{ +03377 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03378 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03379 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03380 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03381 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03382 \}, +03383 \{ +03384 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03385 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 280, 170, 200\},\{ 340, 230, 230, 130, 200\},\{ 340, 170, 170, 70, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +03386 \{\{ 340, 340, 340, 340, 340\},\{ 340, 280, 280, 170, 200\},\{ 340, 340, 280, 270, 200\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 340, 280, 270, 200\}\}, +03387 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 170, 70, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 210, 210, 110, 200 + \},\{ 340, 100, 0, 70, 200\}\}, +03388 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 310, 250, 240, 200\},\{ 340, 220, 120, 200, 200 + \},\{ 340, 290, 190, 270, 200\}\} +03389 \}, +03390 \{ +03391 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03392 \{\{ 340, 340, 340, 340, 340\},\{ 340, 230, 340, 200, 310\},\{ 340, 190, 230, 200, 200\},\{ 340, 130, 270, 200, 240 + \},\{ 340, 200, 200, 200, 200\}\}, +03393 \{\{ 340, 340, 340, 340, 340\},\{ 340, 230, 280, 200, 250\},\{ 340, 230, 280, 200, 250\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 230, 280, 200, 250\}\}, +03394 \{\{ 340, 340, 340, 340, 340\},\{ 340, 130, 270, 200, 240\},\{ 340, 200, 200, 200, 200\},\{ 340, 170, 270, 200, 240 + \},\{ 340, -50, 100, 200, 70\}\}, +03395 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 250, 200, 220\},\{ 340, 80, 220, 200, 190 + \},\{ 340, 150, 190, 200, 160\}\} +03396 \}, +03397 \{ +03398 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03399 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 200, 210, 220\},\{ 340, 130, 200, 170, 80\},\{ 340, 70, 200, 110, 200 + \},\{ 340, 200, 200, 200, 200\}\}, +03400 \{\{ 340, 340, 340, 340, 340\},\{ 340, 170, 200, 210, 120\},\{ 340, 270, 200, 270, 220\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 270, 200, 270, 220\}\}, +03401 \{\{ 340, 340, 340, 340, 340\},\{ 340, 70, 200, 110, 200\},\{ 340, 200, 200, 200, 200\},\{ 340, 110, 200, 150, 160 + \},\{ 340, 70, 200, 30, -160\}\}, +03402 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 240, 200, 240, 190\},\{ 340, 200, 200, 160, -30 + \},\{ 340, 270, 200, 230, 220\}\} +03403 \}, +03404 \{ +03405 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03406 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 340, 100, 290\},\{ 340, 200, 230, -50, 150\},\{ 340, 200, 270, 70, 270 + \},\{ 340, 200, 200, 200, 200\}\}, +03407 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 280, 0, 190\},\{ 340, 200, 280, 100, 190\},\{ 340, 200, 200, 200, 200 + \},\{ 340, 200, 280, 100, 190\}\}, +03408 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 270, 70, 270\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 270, 30, 230 + \},\{ 340, 200, 100, -290, 90\}\}, +03409 \{\{ 340, 340, 340, 340, 340\},\{ 340, 200, 200, 200, 200\},\{ 340, 200, 250, 70, 160\},\{ 340, 200, 220, -160, + 220\},\{ 340, 200, 190, 90, 110\}\} +03410 \} +03411 \}, +03412 \textcolor{comment}{/* UA....?? */} +03413 \{\{ +03414 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03415 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03416 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03417 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03418 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03419 \}, +03420 \{ +03421 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03422 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03423 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03424 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03425 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03426 \}, +03427 \{ +03428 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03429 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03430 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03431 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03432 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03433 \}, +03434 \{ +03435 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03436 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03437 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03438 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03439 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03440 \}, +03441 \{ +03442 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03443 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03444 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03445 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03446 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03447 \} +03448 \} +03449 \}, +03450 \{ \textcolor{comment}{/* noPair */} \{\{\{\{0\}\}\}\}, +03451 \textcolor{comment}{/* ??....CG */} +03452 \{\{ +03453 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03454 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03455 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03456 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03457 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03458 \}, +03459 \{ +03460 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03461 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03462 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03463 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03464 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03465 \}, +03466 \{ +03467 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03468 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03469 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03470 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03471 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03472 \}, +03473 \{ +03474 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03475 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03476 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03477 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03478 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03479 \}, +03480 \{ +03481 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03482 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03483 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03484 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03485 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03486 \} +03487 \}, +03488 \textcolor{comment}{/* ??....GC */} +03489 \{\{ +03490 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03491 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03492 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03493 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03494 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03495 \}, +03496 \{ +03497 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03498 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03499 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03500 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03501 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03502 \}, +03503 \{ +03504 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03505 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03506 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03507 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03508 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03509 \}, +03510 \{ +03511 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03512 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03513 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03514 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03515 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03516 \}, +03517 \{ +03518 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03519 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03520 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03521 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03522 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03523 \} +03524 \}, +03525 \textcolor{comment}{/* ??....GU */} +03526 \{\{ +03527 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03528 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03529 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03530 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03531 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03532 \}, +03533 \{ +03534 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03535 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03536 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03537 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03538 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03539 \}, +03540 \{ +03541 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03542 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03543 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03544 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03545 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03546 \}, +03547 \{ +03548 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03549 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03550 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03551 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03552 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03553 \}, +03554 \{ +03555 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03556 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03557 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03558 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03559 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03560 \} +03561 \}, +03562 \textcolor{comment}{/* ??....UG */} +03563 \{\{ +03564 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03565 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03566 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03567 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03568 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03569 \}, +03570 \{ +03571 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03572 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03573 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03574 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03575 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03576 \}, +03577 \{ +03578 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03579 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03580 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03581 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03582 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03583 \}, +03584 \{ +03585 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03586 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03587 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03588 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03589 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03590 \}, +03591 \{ +03592 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03593 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03594 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03595 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03596 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03597 \} +03598 \}, +03599 \textcolor{comment}{/* ??....AU */} +03600 \{\{ +03601 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03602 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03603 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03604 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03605 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03606 \}, +03607 \{ +03608 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03609 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03610 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03611 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03612 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03613 \}, +03614 \{ +03615 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03616 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03617 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03618 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03619 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03620 \}, +03621 \{ +03622 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03623 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03624 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03625 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03626 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03627 \}, +03628 \{ +03629 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03630 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03631 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03632 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03633 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03634 \} +03635 \}, +03636 \textcolor{comment}{/* ??....UA */} +03637 \{\{ +03638 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03639 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03640 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03641 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03642 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03643 \}, +03644 \{ +03645 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03646 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03647 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03648 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03649 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03650 \}, +03651 \{ +03652 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03653 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03654 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03655 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03656 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03657 \}, +03658 \{ +03659 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03660 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03661 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03662 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03663 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03664 \}, +03665 \{ +03666 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03667 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03668 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03669 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03670 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03671 \} +03672 \}, +03673 \textcolor{comment}{/* ??....?? */} +03674 \{\{ +03675 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03676 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03677 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03678 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03679 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03680 \}, +03681 \{ +03682 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03683 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03684 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03685 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03686 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03687 \}, +03688 \{ +03689 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03690 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03691 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03692 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03693 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03694 \}, +03695 \{ +03696 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03697 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03698 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03699 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03700 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03701 \}, +03702 \{ +03703 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03704 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03705 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03706 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\}, +03707 \{\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340\},\{ 340, 340, 340, 340, 340 + \},\{ 340, 340, 340, 340, 340\}\} +03708 \} +03709 \} +03710 \} +03711 \}; +03712 +03713 PRIVATE \textcolor{keywordtype}{int} int22\_H\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5][5] = +03714 \{ \textcolor{comment}{/* noPair */} \{\{\{\{\{0\}\}\}\}\}, +03715 \{ \textcolor{comment}{/* noPair */} \{\{\{\{0\}\}\}\}, +03716 \textcolor{comment}{/* CG.@@..CG */} +03717 \{ \{ \{ \{ 0, 0, 0, 0, 0\}, +03718 \{ DEF, DEF, DEF, DEF, DEF\}, +03719 \{ DEF, DEF, DEF, DEF, DEF\}, +03720 \{ DEF, DEF, DEF, DEF, DEF\}, +03721 \{ DEF, DEF, DEF, DEF, DEF\}\}, +03722 \textcolor{comment}{/* CG.@A..CG */} +03723 \{ \{ 0, 0, 0, 0, 0\}, +03724 \{-1029,-1029,-1029,-1029,-1029\}, +03725 \{ -519, -519, -519, -519, -519\}, +03726 \{ -939, -939, -939, -939, -939\}, +03727 \{ -809, -809, -809, -809, -809\}\}, +03728 \textcolor{comment}{/* CG.@C..CG */} +03729 \{ \{ 0, 0, 0, 0, 0\}, +03730 \{ -949, -949, -949, -949, -949\}, +03731 \{ -449, -449, -449, -449, -449\}, +03732 \{ -939, -939, -939, -939, -939\}, +03733 \{ -739, -739, -739, -739, -739\}\}, +03734 \textcolor{comment}{/* CG.@G..CG */} +03735 \{ \{ 0, 0, 0, 0, 0\}, +03736 \{-1029,-1029,-1029,-1029,-1029\}, +03737 \{ -519, -519, -519, -519, -519\}, +03738 \{ -939, -939, -939, -939, -939\}, +03739 \{ -809, -809, -809, -809, -809\}\}, +03740 \textcolor{comment}{/* CG.@U..CG */} +03741 \{ \{ 0, 0, 0, 0, 0\}, +03742 \{-1029,-1029,-1029,-1029,-1029\}, +03743 \{ -669, -669, -669, -669, -669\}, +03744 \{ -939, -939, -939, -939, -939\}, +03745 \{ -859, -859, -859, -859, -859\}\}\}, +03746 \textcolor{comment}{/* CG.A@..CG */} +03747 \{\{\{ DEF,-1029, -949,-1029,-1029\}, +03748 \{ -100,-1079, -999,-1079,-1079\}, +03749 \{ -100,-1079, -999,-1079,-1079\}, +03750 \{ -100,-1079, -999,-1079,-1079\}, +03751 \{ -100,-1079, -999,-1079,-1079\}\}, +03752 \textcolor{comment}{/* CG.AA..CG */} +03753 \{\{ DEF,-1029, -949,-1029,-1029\}, +03754 \{-1079,-2058,-1978,-2058,-2058\}, +03755 \{ -569,-1548,-1468,-1548,-1548\}, +03756 \{ -989,-1968,-1888,-1968,-1968\}, +03757 \{ -859,-1838,-1758,-1838,-1838\}\}, +03758 \textcolor{comment}{/* CG.AC..CG */} +03759 \{\{ DEF,-1029, -949,-1029,-1029\}, +03760 \{ -999,-1978,-1898,-1978,-1978\}, +03761 \{ -499,-1478,-1398,-1478,-1478\}, +03762 \{ -989,-1968,-1888,-1968,-1968\}, +03763 \{ -789,-1768,-1688,-1768,-1768\}\}, +03764 \textcolor{comment}{/* CG.AG..CG */} +03765 \{\{ DEF,-1029, -949,-1029,-1029\}, +03766 \{-1079,-2058,-1978,-2058,-2058\}, +03767 \{ -569,-1548,-1468,-1548,-1548\}, +03768 \{ -989,-1968,-1888,-1968,-1968\}, +03769 \{ -859,-1838,-1758,-1838,-1838\}\}, +03770 \textcolor{comment}{/* CG.AU..CG */} +03771 \{\{ DEF,-1029, -949,-1029,-1029\}, +03772 \{-1079,-2058,-1978,-2058,-2058\}, +03773 \{ -719,-1698,-1618,-1698,-1698\}, +03774 \{ -989,-1968,-1888,-1968,-1968\}, +03775 \{ -909,-1888,-1808,-1888,-1888\}\}\}, +03776 \textcolor{comment}{/* CG.C@..CG */} +03777 \{\{\{ DEF, -519, -449, -519, -669\}, +03778 \{ -100, -569, -499, -569, -719\}, +03779 \{ -100, -569, -499, -569, -719\}, +03780 \{ -100, -569, -499, -569, -719\}, +03781 \{ -100, -569, -499, -569, -719\}\}, +03782 \textcolor{comment}{/* CG.CA..CG */} +03783 \{\{ DEF, -519, -449, -519, -669\}, +03784 \{-1079,-1548,-1478,-1548,-1698\}, +03785 \{ -569,-1038, -968,-1038,-1188\}, +03786 \{ -989,-1458,-1388,-1458,-1608\}, +03787 \{ -859,-1328,-1258,-1328,-1478\}\}, +03788 \textcolor{comment}{/* CG.CC..CG */} +03789 \{\{ DEF, -519, -449, -519, -669\}, +03790 \{ -999,-1468,-1398,-1468,-1618\}, +03791 \{ -499, -968, -898, -968,-1118\}, +03792 \{ -989,-1458,-1388,-1458,-1608\}, +03793 \{ -789,-1258,-1188,-1258,-1408\}\}, +03794 \textcolor{comment}{/* CG.CG..CG */} +03795 \{\{ DEF, -519, -449, -519, -669\}, +03796 \{-1079,-1548,-1478,-1548,-1698\}, +03797 \{ -569,-1038, -968,-1038,-1188\}, +03798 \{ -989,-1458,-1388,-1458,-1608\}, +03799 \{ -859,-1328,-1258,-1328,-1478\}\}, +03800 \textcolor{comment}{/* CG.CU..CG */} +03801 \{\{ DEF, -519, -449, -519, -669\}, +03802 \{-1079,-1548,-1478,-1548,-1698\}, +03803 \{ -719,-1188,-1118,-1188,-1338\}, +03804 \{ -989,-1458,-1388,-1458,-1608\}, +03805 \{ -909,-1378,-1308,-1378,-1528\}\}\}, +03806 \textcolor{comment}{/* CG.G@..CG */} +03807 \{\{\{ DEF, -939, -939, -939, -939\}, +03808 \{ -100, -989, -989, -989, -989\}, +03809 \{ -100, -989, -989, -989, -989\}, +03810 \{ -100, -989, -989, -989, -989\}, +03811 \{ -100, -989, -989, -989, -989\}\}, +03812 \textcolor{comment}{/* CG.GA..CG */} +03813 \{\{ DEF, -939, -939, -939, -939\}, +03814 \{-1079,-1968,-1968,-1968,-1968\}, +03815 \{ -569,-1458,-1458,-1458,-1458\}, +03816 \{ -989,-1878,-1878,-1878,-1878\}, +03817 \{ -859,-1748,-1748,-1748,-1748\}\}, +03818 \textcolor{comment}{/* CG.GC..CG */} +03819 \{\{ DEF, -939, -939, -939, -939\}, +03820 \{ -999,-1888,-1888,-1888,-1888\}, +03821 \{ -499,-1388,-1388,-1388,-1388\}, +03822 \{ -989,-1878,-1878,-1878,-1878\}, +03823 \{ -789,-1678,-1678,-1678,-1678\}\}, +03824 \textcolor{comment}{/* CG.GG..CG */} +03825 \{\{ DEF, -939, -939, -939, -939\}, +03826 \{-1079,-1968,-1968,-1968,-1968\}, +03827 \{ -569,-1458,-1458,-1458,-1458\}, +03828 \{ -989,-1878,-1878,-1878,-1878\}, +03829 \{ -859,-1748,-1748,-1748,-1748\}\}, +03830 \textcolor{comment}{/* CG.GU..CG */} +03831 \{\{ DEF, -939, -939, -939, -939\}, +03832 \{-1079,-1968,-1968,-1968,-1968\}, +03833 \{ -719,-1608,-1608,-1608,-1608\}, +03834 \{ -989,-1878,-1878,-1878,-1878\}, +03835 \{ -909,-1798,-1798,-1798,-1798\}\}\}, +03836 \textcolor{comment}{/* CG.U@..CG */} +03837 \{\{\{ DEF, -809, -739, -809, -859\}, +03838 \{ -100, -859, -789, -859, -909\}, +03839 \{ -100, -859, -789, -859, -909\}, +03840 \{ -100, -859, -789, -859, -909\}, +03841 \{ -100, -859, -789, -859, -909\}\}, +03842 \textcolor{comment}{/* CG.UA..CG */} +03843 \{\{ DEF, -809, -739, -809, -859\}, +03844 \{-1079,-1838,-1768,-1838,-1888\}, +03845 \{ -569,-1328,-1258,-1328,-1378\}, +03846 \{ -989,-1748,-1678,-1748,-1798\}, +03847 \{ -859,-1618,-1548,-1618,-1668\}\}, +03848 \textcolor{comment}{/* CG.UC..CG */} +03849 \{\{ DEF, -809, -739, -809, -859\}, +03850 \{ -999,-1758,-1688,-1758,-1808\}, +03851 \{ -499,-1258,-1188,-1258,-1308\}, +03852 \{ -989,-1748,-1678,-1748,-1798\}, +03853 \{ -789,-1548,-1478,-1548,-1598\}\}, +03854 \textcolor{comment}{/* CG.UG..CG */} +03855 \{\{ DEF, -809, -739, -809, -859\}, +03856 \{-1079,-1838,-1768,-1838,-1888\}, +03857 \{ -569,-1328,-1258,-1328,-1378\}, +03858 \{ -989,-1748,-1678,-1748,-1798\}, +03859 \{ -859,-1618,-1548,-1618,-1668\}\}, +03860 \textcolor{comment}{/* CG.UU..CG */} +03861 \{\{ DEF, -809, -739, -809, -859\}, +03862 \{-1079,-1838,-1768,-1838,-1888\}, +03863 \{ -719,-1478,-1408,-1478,-1528\}, +03864 \{ -989,-1748,-1678,-1748,-1798\}, +03865 \{ -909,-1668,-1598,-1668,-1718\}\}\}\}, +03866 \textcolor{comment}{/* CG.@@..GC */} +03867 \{\{\{\{ 0, 0, 0, 0, 0\}, +03868 \{ DEF, DEF, DEF, DEF, DEF\}, +03869 \{ DEF, DEF, DEF, DEF, DEF\}, +03870 \{ DEF, DEF, DEF, DEF, DEF\}, +03871 \{ DEF, DEF, DEF, DEF, DEF\}\}, +03872 \textcolor{comment}{/* CG.@A..GC */} +03873 \{\{ 0, 0, 0, 0, 0\}, +03874 \{ -519, -519, -519, -519, -519\}, +03875 \{ -719, -719, -719, -719, -719\}, +03876 \{ -709, -709, -709, -709, -709\}, +03877 \{ -499, -499, -499, -499, -499\}\}, +03878 \textcolor{comment}{/* CG.@C..GC */} +03879 \{\{ 0, 0, 0, 0, 0\}, +03880 \{ -879, -879, -879, -879, -879\}, +03881 \{ -309, -309, -309, -309, -309\}, +03882 \{ -739, -739, -739, -739, -739\}, +03883 \{ -499, -499, -499, -499, -499\}\}, +03884 \textcolor{comment}{/* CG.@G..GC */} +03885 \{\{ 0, 0, 0, 0, 0\}, +03886 \{ -559, -559, -559, -559, -559\}, +03887 \{ -309, -309, -309, -309, -309\}, +03888 \{ -619, -619, -619, -619, -619\}, +03889 \{ -499, -499, -499, -499, -499\}\}, +03890 \textcolor{comment}{/* CG.@U..GC */} +03891 \{\{ 0, 0, 0, 0, 0\}, +03892 \{ -879, -879, -879, -879, -879\}, +03893 \{ -389, -389, -389, -389, -389\}, +03894 \{ -739, -739, -739, -739, -739\}, +03895 \{ -569, -569, -569, -569, -569\}\}\}, +03896 \textcolor{comment}{/* CG.A@..GC */} +03897 \{\{\{ DEF,-1029, -949,-1029,-1029\}, +03898 \{ -100,-1079, -999,-1079,-1079\}, +03899 \{ -100,-1079, -999,-1079,-1079\}, +03900 \{ -100,-1079, -999,-1079,-1079\}, +03901 \{ -100,-1079, -999,-1079,-1079\}\}, +03902 \textcolor{comment}{/* CG.AA..GC */} +03903 \{\{ DEF,-1029, -949,-1029,-1029\}, +03904 \{ -569,-1548,-1468,-1548,-1548\}, +03905 \{ -769,-1748,-1668,-1748,-1748\}, +03906 \{ -759,-1738,-1658,-1738,-1738\}, +03907 \{ -549,-1528,-1448,-1528,-1528\}\}, +03908 \textcolor{comment}{/* CG.AC..GC */} +03909 \{\{ DEF,-1029, -949,-1029,-1029\}, +03910 \{ -929,-1908,-1828,-1908,-1908\}, +03911 \{ -359,-1338,-1258,-1338,-1338\}, +03912 \{ -789,-1768,-1688,-1768,-1768\}, +03913 \{ -549,-1528,-1448,-1528,-1528\}\}, +03914 \textcolor{comment}{/* CG.AG..GC */} +03915 \{\{ DEF,-1029, -949,-1029,-1029\}, +03916 \{ -609,-1588,-1508,-1588,-1588\}, +03917 \{ -359,-1338,-1258,-1338,-1338\}, +03918 \{ -669,-1648,-1568,-1648,-1648\}, +03919 \{ -549,-1528,-1448,-1528,-1528\}\}, +03920 \textcolor{comment}{/* CG.AU..GC */} +03921 \{\{ DEF,-1029, -949,-1029,-1029\}, +03922 \{ -929,-1908,-1828,-1908,-1908\}, +03923 \{ -439,-1418,-1338,-1418,-1418\}, +03924 \{ -789,-1768,-1688,-1768,-1768\}, +03925 \{ -619,-1598,-1518,-1598,-1598\}\}\}, +03926 \textcolor{comment}{/* CG.C@..GC */} +03927 \{\{\{ DEF, -519, -449, -519, -669\}, +03928 \{ -100, -569, -499, -569, -719\}, +03929 \{ -100, -569, -499, -569, -719\}, +03930 \{ -100, -569, -499, -569, -719\}, +03931 \{ -100, -569, -499, -569, -719\}\}, +03932 \textcolor{comment}{/* CG.CA..GC */} +03933 \{\{ DEF, -519, -449, -519, -669\}, +03934 \{ -569,-1038, -968,-1038,-1188\}, +03935 \{ -769,-1238,-1168,-1238,-1388\}, +03936 \{ -759,-1228,-1158,-1228,-1378\}, +03937 \{ -549,-1018, -948,-1018,-1168\}\}, +03938 \textcolor{comment}{/* CG.CC..GC */} +03939 \{\{ DEF, -519, -449, -519, -669\}, +03940 \{ -929,-1398,-1328,-1398,-1548\}, +03941 \{ -359, -828, -758, -828, -978\}, +03942 \{ -789,-1258,-1188,-1258,-1408\}, +03943 \{ -549,-1018, -948,-1018,-1168\}\}, +03944 \textcolor{comment}{/* CG.CG..GC */} +03945 \{\{ DEF, -519, -449, -519, -669\}, +03946 \{ -609,-1078,-1008,-1078,-1228\}, +03947 \{ -359, -828, -758, -828, -978\}, +03948 \{ -669,-1138,-1068,-1138,-1288\}, +03949 \{ -549,-1018, -948,-1018,-1168\}\}, +03950 \textcolor{comment}{/* CG.CU..GC */} +03951 \{\{ DEF, -519, -449, -519, -669\}, +03952 \{ -929,-1398,-1328,-1398,-1548\}, +03953 \{ -439, -908, -838, -908,-1058\}, +03954 \{ -789,-1258,-1188,-1258,-1408\}, +03955 \{ -619,-1088,-1018,-1088,-1238\}\}\}, +03956 \textcolor{comment}{/* CG.G@..GC */} +03957 \{\{\{ DEF, -939, -939, -939, -939\}, +03958 \{ -100, -989, -989, -989, -989\}, +03959 \{ -100, -989, -989, -989, -989\}, +03960 \{ -100, -989, -989, -989, -989\}, +03961 \{ -100, -989, -989, -989, -989\}\}, +03962 \textcolor{comment}{/* CG.GA..GC */} +03963 \{\{ DEF, -939, -939, -939, -939\}, +03964 \{ -569,-1458,-1458,-1458,-1458\}, +03965 \{ -769,-1658,-1658,-1658,-1658\}, +03966 \{ -759,-1648,-1648,-1648,-1648\}, +03967 \{ -549,-1438,-1438,-1438,-1438\}\}, +03968 \textcolor{comment}{/* CG.GC..GC */} +03969 \{\{ DEF, -939, -939, -939, -939\}, +03970 \{ -929,-1818,-1818,-1818,-1818\}, +03971 \{ -359,-1248,-1248,-1248,-1248\}, +03972 \{ -789,-1678,-1678,-1678,-1678\}, +03973 \{ -549,-1438,-1438,-1438,-1438\}\}, +03974 \textcolor{comment}{/* CG.GG..GC */} +03975 \{\{ DEF, -939, -939, -939, -939\}, +03976 \{ -609,-1498,-1498,-1498,-1498\}, +03977 \{ -359,-1248,-1248,-1248,-1248\}, +03978 \{ -669,-1558,-1558,-1558,-1558\}, +03979 \{ -549,-1438,-1438,-1438,-1438\}\}, +03980 \textcolor{comment}{/* CG.GU..GC */} +03981 \{\{ DEF, -939, -939, -939, -939\}, +03982 \{ -929,-1818,-1818,-1818,-1818\}, +03983 \{ -439,-1328,-1328,-1328,-1328\}, +03984 \{ -789,-1678,-1678,-1678,-3080\}, +03985 \{ -619,-1508,-1508,-1508,-1508\}\}\}, +03986 \textcolor{comment}{/* CG.U@..GC */} +03987 \{\{\{ DEF, -809, -739, -809, -859\}, +03988 \{ -100, -859, -789, -859, -909\}, +03989 \{ -100, -859, -789, -859, -909\}, +03990 \{ -100, -859, -789, -859, -909\}, +03991 \{ -100, -859, -789, -859, -909\}\}, +03992 \textcolor{comment}{/* CG.UA..GC */} +03993 \{\{ DEF, -809, -739, -809, -859\}, +03994 \{ -569,-1328,-1258,-1328,-1378\}, +03995 \{ -769,-1528,-1458,-1528,-1578\}, +03996 \{ -759,-1518,-1448,-1518,-1568\}, +03997 \{ -549,-1308,-1238,-1308,-1358\}\}, +03998 \textcolor{comment}{/* CG.UC..GC */} +03999 \{\{ DEF, -809, -739, -809, -859\}, +04000 \{ -929,-1688,-1618,-1688,-1738\}, +04001 \{ -359,-1118,-1048,-1118,-1168\}, +04002 \{ -789,-1548,-1478,-1548,-1598\}, +04003 \{ -549,-1308,-1238,-1308,-1358\}\}, +04004 \textcolor{comment}{/* CG.UG..GC */} +04005 \{\{ DEF, -809, -739, -809, -859\}, +04006 \{ -609,-1368,-1298,-1368,-1418\}, +04007 \{ -359,-1118,-1048,-1118,-1168\}, +04008 \{ -669,-1428,-1358,-1428,-1478\}, +04009 \{ -549,-1308,-1238,-1308,-1358\}\}, +04010 \textcolor{comment}{/* CG.UU..GC */} +04011 \{\{ DEF, -809, -739, -809, -859\}, +04012 \{ -929,-1688,-1618,-1688,-1738\}, +04013 \{ -439,-1198,-1128,-1198,-1248\}, +04014 \{ -789,-1548,-1478,-1548,-1598\}, +04015 \{ -619,-1378,-1308,-1378,-1428\}\}\}\}, +04016 \textcolor{comment}{/* CG.@@..GU */} +04017 \{\{\{\{ 0, 0, 0, 0, 0\}, +04018 \{ DEF, DEF, DEF, DEF, DEF\}, +04019 \{ DEF, DEF, DEF, DEF, DEF\}, +04020 \{ DEF, DEF, DEF, DEF, DEF\}, +04021 \{ DEF, DEF, DEF, DEF, DEF\}\}, +04022 \textcolor{comment}{/* CG.@A..GU */} +04023 \{\{ 0, 0, 0, 0, 0\}, +04024 \{ -429, -429, -429, -429, -429\}, +04025 \{ -259, -259, -259, -259, -259\}, +04026 \{ -339, -339, -339, -339, -339\}, +04027 \{ -329, -329, -329, -329, -329\}\}, +04028 \textcolor{comment}{/* CG.@C..GU */} +04029 \{\{ 0, 0, 0, 0, 0\}, +04030 \{ -599, -599, -599, -599, -599\}, +04031 \{ -239, -239, -239, -239, -239\}, +04032 \{ -689, -689, -689, -689, -689\}, +04033 \{ -329, -329, -329, -329, -329\}\}, +04034 \textcolor{comment}{/* CG.@G..GU */} +04035 \{\{ 0, 0, 0, 0, 0\}, +04036 \{ -599, -599, -599, -599, -599\}, +04037 \{ -239, -239, -239, -239, -239\}, +04038 \{ -689, -689, -689, -689, -689\}, +04039 \{ -329, -329, -329, -329, -329\}\}, +04040 \textcolor{comment}{/* CG.@U..GU */} +04041 \{\{ 0, 0, 0, 0, 0\}, +04042 \{ -599, -599, -599, -599, -599\}, +04043 \{ -239, -239, -239, -239, -239\}, +04044 \{ -689, -689, -689, -689, -689\}, +04045 \{ -329, -329, -329, -329, -329\}\}\}, +04046 \textcolor{comment}{/* CG.A@..GU */} +04047 \{\{\{ DEF,-1029, -949,-1029,-1029\}, +04048 \{ -100,-1079, -999,-1079,-1079\}, +04049 \{ -100,-1079, -999,-1079,-1079\}, +04050 \{ -100,-1079, -999,-1079,-1079\}, +04051 \{ -100,-1079, -999,-1079,-1079\}\}, +04052 \textcolor{comment}{/* CG.AA..GU */} +04053 \{\{ DEF,-1029, -949,-1029,-1029\}, +04054 \{ -479,-1458,-1378,-1458,-1458\}, +04055 \{ -309,-1288,-1208,-1288,-1288\}, +04056 \{ -389,-1368,-1288,-1368,-1368\}, +04057 \{ -379,-1358,-1278,-1358,-1358\}\}, +04058 \textcolor{comment}{/* CG.AC..GU */} +04059 \{\{ DEF,-1029, -949,-1029,-1029\}, +04060 \{ -649,-1628,-1548,-1628,-1628\}, +04061 \{ -289,-1268,-1188,-1268,-1268\}, +04062 \{ -739,-1718,-1638,-1718,-1718\}, +04063 \{ -379,-1358,-1278,-1358,-1358\}\}, +04064 \textcolor{comment}{/* CG.AG..GU */} +04065 \{\{ DEF,-1029, -949,-1029,-1029\}, +04066 \{ -649,-1628,-1548,-1628,-1628\}, +04067 \{ -289,-1268,-1188,-1268,-1268\}, +04068 \{ -739,-1718,-1638,-1718,-1718\}, +04069 \{ -379,-1358,-1278,-1358,-1358\}\}, +04070 \textcolor{comment}{/* CG.AU..GU */} +04071 \{\{ DEF,-1029, -949,-1029,-1029\}, +04072 \{ -649,-1628,-1548,-1628,-1628\}, +04073 \{ -289,-1268,-1188,-1268,-1268\}, +04074 \{ -739,-1718,-1638,-1718,-1718\}, +04075 \{ -379,-1358,-1278,-1358,-1358\}\}\}, +04076 \textcolor{comment}{/* CG.C@..GU */} +04077 \{\{\{ DEF, -519, -449, -519, -669\}, +04078 \{ -100, -569, -499, -569, -719\}, +04079 \{ -100, -569, -499, -569, -719\}, +04080 \{ -100, -569, -499, -569, -719\}, +04081 \{ -100, -569, -499, -569, -719\}\}, +04082 \textcolor{comment}{/* CG.CA..GU */} +04083 \{\{ DEF, -519, -449, -519, -669\}, +04084 \{ -479, -948, -878, -948,-1098\}, +04085 \{ -309, -778, -708, -778, -928\}, +04086 \{ -389, -858, -788, -858,-1008\}, +04087 \{ -379, -848, -778, -848, -998\}\}, +04088 \textcolor{comment}{/* CG.CC..GU */} +04089 \{\{ DEF, -519, -449, -519, -669\}, +04090 \{ -649,-1118,-1048,-1118,-1268\}, +04091 \{ -289, -758, -688, -758, -908\}, +04092 \{ -739,-1208,-1138,-1208,-1358\}, +04093 \{ -379, -848, -778, -848, -998\}\}, +04094 \textcolor{comment}{/* CG.CG..GU */} +04095 \{\{ DEF, -519, -449, -519, -669\}, +04096 \{ -649,-1118,-1048,-1118,-1268\}, +04097 \{ -289, -758, -688, -758, -908\}, +04098 \{ -739,-1208,-1138,-1208,-1358\}, +04099 \{ -379, -848, -778, -848, -998\}\}, +04100 \textcolor{comment}{/* CG.CU..GU */} +04101 \{\{ DEF, -519, -449, -519, -669\}, +04102 \{ -649,-1118,-1048,-1118,-1268\}, +04103 \{ -289, -758, -688, -758, -908\}, +04104 \{ -739,-1208,-1138,-1208,-1358\}, +04105 \{ -379, -848, -778, -848, -998\}\}\}, +04106 \textcolor{comment}{/* CG.G@..GU */} +04107 \{\{\{ DEF, -939, -939, -939, -939\}, +04108 \{ -100, -989, -989, -989, -989\}, +04109 \{ -100, -989, -989, -989, -989\}, +04110 \{ -100, -989, -989, -989, -989\}, +04111 \{ -100, -989, -989, -989, -989\}\}, +04112 \textcolor{comment}{/* CG.GA..GU */} +04113 \{\{ DEF, -939, -939, -939, -939\}, +04114 \{ -479,-1368,-1368,-1368,-1368\}, +04115 \{ -309,-1198,-1198,-1198,-1198\}, +04116 \{ -389,-1278,-1278,-1278,-1278\}, +04117 \{ -379,-1268,-1268,-1268,-1268\}\}, +04118 \textcolor{comment}{/* CG.GC..GU */} +04119 \{\{ DEF, -939, -939, -939, -939\}, +04120 \{ -649,-1538,-1538,-1538,-1538\}, +04121 \{ -289,-1178,-1178,-1178,-1178\}, +04122 \{ -739,-1628,-1628,-1628,-1628\}, +04123 \{ -379,-1268,-1268,-1268,-1268\}\}, +04124 \textcolor{comment}{/* CG.GG..GU */} +04125 \{\{ DEF, -939, -939, -939, -939\}, +04126 \{ -649,-1538,-1538,-1538,-1538\}, +04127 \{ -289,-1178,-1178,-1178,-1178\}, +04128 \{ -739,-1628,-1628,-1628,-1628\}, +04129 \{ -379,-1268,-1268,-1268,-1268\}\}, +04130 \textcolor{comment}{/* CG.GU..GU */} +04131 \{\{ DEF, -939, -939, -939, -939\}, +04132 \{ -649,-1538,-1538,-1538,-1538\}, +04133 \{ -289,-1178,-1178,-1178,-1178\}, +04134 \{ -739,-1628,-1628,-1628,-1628\}, +04135 \{ -379,-1268,-1268,-1268,-1268\}\}\}, +04136 \textcolor{comment}{/* CG.U@..GU */} +04137 \{\{\{ DEF, -809, -739, -809, -859\}, +04138 \{ -100, -859, -789, -859, -909\}, +04139 \{ -100, -859, -789, -859, -909\}, +04140 \{ -100, -859, -789, -859, -909\}, +04141 \{ -100, -859, -789, -859, -909\}\}, +04142 \textcolor{comment}{/* CG.UA..GU */} +04143 \{\{ DEF, -809, -739, -809, -859\}, +04144 \{ -479,-1238,-1168,-1238,-1288\}, +04145 \{ -309,-1068, -998,-1068,-1118\}, +04146 \{ -389,-1148,-1078,-1148,-1198\}, +04147 \{ -379,-1138,-1068,-1138,-1188\}\}, +04148 \textcolor{comment}{/* CG.UC..GU */} +04149 \{\{ DEF, -809, -739, -809, -859\}, +04150 \{ -649,-1408,-1338,-1408,-1458\}, +04151 \{ -289,-1048, -978,-1048,-1098\}, +04152 \{ -739,-1498,-1428,-1498,-1548\}, +04153 \{ -379,-1138,-1068,-1138,-1188\}\}, +04154 \textcolor{comment}{/* CG.UG..GU */} +04155 \{\{ DEF, -809, -739, -809, -859\}, +04156 \{ -649,-1408,-1338,-1408,-1458\}, +04157 \{ -289,-1048, -978,-1048,-1098\}, +04158 \{ -739,-1498,-1428,-1498,-1548\}, +04159 \{ -379,-1138,-1068,-1138,-1188\}\}, +04160 \textcolor{comment}{/* CG.UU..GU */} +04161 \{\{ DEF, -809, -739, -809, -859\}, +04162 \{ -649,-1408,-1338,-1408,-1458\}, +04163 \{ -289,-1048, -978,-1048,-1098\}, +04164 \{ -739,-1498,-1428,-1498,-1548\}, +04165 \{ -379,-1138,-1068,-1138,-1188\}\}\}\}, +04166 \textcolor{comment}{/* CG.@@..UG */} +04167 \{\{\{\{ 0, 0, 0, 0, 0\}, +04168 \{ DEF, DEF, DEF, DEF, DEF\}, +04169 \{ DEF, DEF, DEF, DEF, DEF\}, +04170 \{ DEF, DEF, DEF, DEF, DEF\}, +04171 \{ DEF, DEF, DEF, DEF, DEF\}\}, +04172 \textcolor{comment}{/* CG.@A..UG */} +04173 \{\{ 0, 0, 0, 0, 0\}, +04174 \{ -719, -719, -719, -719, -719\}, +04175 \{ -479, -479, -479, -479, -479\}, +04176 \{ -659, -659, -659, -659, -659\}, +04177 \{ -549, -549, -549, -549, -549\}\}, +04178 \textcolor{comment}{/* CG.@C..UG */} +04179 \{\{ 0, 0, 0, 0, 0\}, +04180 \{ -789, -789, -789, -789, -789\}, +04181 \{ -479, -479, -479, -479, -479\}, +04182 \{ -809, -809, -809, -809, -809\}, +04183 \{ -439, -439, -439, -439, -439\}\}, +04184 \textcolor{comment}{/* CG.@G..UG */} +04185 \{\{ 0, 0, 0, 0, 0\}, +04186 \{ -959, -959, -959, -959, -959\}, +04187 \{ -359, -359, -359, -359, -359\}, +04188 \{ -919, -919, -919, -919, -919\}, +04189 \{ -549, -549, -549, -549, -549\}\}, +04190 \textcolor{comment}{/* CG.@U..UG */} +04191 \{\{ 0, 0, 0, 0, 0\}, +04192 \{ -809, -809, -809, -809, -809\}, +04193 \{ -479, -479, -479, -479, -479\}, +04194 \{ -809, -809, -809, -809, -809\}, +04195 \{ -359, -359, -359, -359, -359\}\}\}, +04196 \textcolor{comment}{/* CG.A@..UG */} +04197 \{\{\{ DEF,-1029, -949,-1029,-1029\}, +04198 \{ -100,-1079, -999,-1079,-1079\}, +04199 \{ -100,-1079, -999,-1079,-1079\}, +04200 \{ -100,-1079, -999,-1079,-1079\}, +04201 \{ -100,-1079, -999,-1079,-1079\}\}, +04202 \textcolor{comment}{/* CG.AA..UG */} +04203 \{\{ DEF,-1029, -949,-1029,-1029\}, +04204 \{ -769,-1748,-1668,-1748,-1748\}, +04205 \{ -529,-1508,-1428,-1508,-1508\}, +04206 \{ -709,-1688,-1608,-1688,-1688\}, +04207 \{ -599,-1578,-1498,-1578,-1578\}\}, +04208 \textcolor{comment}{/* CG.AC..UG */} +04209 \{\{ DEF,-1029, -949,-1029,-1029\}, +04210 \{ -839,-1818,-1738,-1818,-1818\}, +04211 \{ -529,-1508,-1428,-1508,-1508\}, +04212 \{ -859,-1838,-1758,-1838,-1838\}, +04213 \{ -489,-1468,-1388,-1468,-1468\}\}, +04214 \textcolor{comment}{/* CG.AG..UG */} +04215 \{\{ DEF,-1029, -949,-1029,-1029\}, +04216 \{-1009,-1988,-1908,-1988,-1988\}, +04217 \{ -409,-1388,-1308,-1388,-1388\}, +04218 \{ -969,-1948,-1868,-1948,-1948\}, +04219 \{ -599,-1578,-1498,-1578,-1578\}\}, +04220 \textcolor{comment}{/* CG.AU..UG */} +04221 \{\{ DEF,-1029, -949,-1029,-1029\}, +04222 \{ -859,-1838,-1758,-1838,-1838\}, +04223 \{ -529,-1508,-1428,-1508,-1508\}, +04224 \{ -859,-1838,-1758,-1838,-1838\}, +04225 \{ -409,-1388,-1308,-1388,-1388\}\}\}, +04226 \textcolor{comment}{/* CG.C@..UG */} +04227 \{\{\{ DEF, -519, -449, -519, -669\}, +04228 \{ -100, -569, -499, -569, -719\}, +04229 \{ -100, -569, -499, -569, -719\}, +04230 \{ -100, -569, -499, -569, -719\}, +04231 \{ -100, -569, -499, -569, -719\}\}, +04232 \textcolor{comment}{/* CG.CA..UG */} +04233 \{\{ DEF, -519, -449, -519, -669\}, +04234 \{ -769,-1238,-1168,-1238,-1388\}, +04235 \{ -529, -998, -928, -998,-1148\}, +04236 \{ -709,-1178,-1108,-1178,-1328\}, +04237 \{ -599,-1068, -998,-1068,-1218\}\}, +04238 \textcolor{comment}{/* CG.CC..UG */} +04239 \{\{ DEF, -519, -449, -519, -669\}, +04240 \{ -839,-1308,-1238,-1308,-1458\}, +04241 \{ -529, -998, -928, -998,-1148\}, +04242 \{ -859,-1328,-1258,-1328,-1478\}, +04243 \{ -489, -958, -888, -958,-1108\}\}, +04244 \textcolor{comment}{/* CG.CG..UG */} +04245 \{\{ DEF, -519, -449, -519, -669\}, +04246 \{-1009,-1478,-1408,-1478,-1628\}, +04247 \{ -409, -878, -808, -878,-1028\}, +04248 \{ -969,-1438,-1368,-1438,-1588\}, +04249 \{ -599,-1068, -998,-1068,-1218\}\}, +04250 \textcolor{comment}{/* CG.CU..UG */} +04251 \{\{ DEF, -519, -449, -519, -669\}, +04252 \{ -859,-1328,-1258,-1328,-1478\}, +04253 \{ -529, -998, -928, -998,-1148\}, +04254 \{ -859,-1328,-1258,-1328,-1478\}, +04255 \{ -409, -878, -808, -878,-1028\}\}\}, +04256 \textcolor{comment}{/* CG.G@..UG */} +04257 \{\{\{ DEF, -939, -939, -939, -939\}, +04258 \{ -100, -989, -989, -989, -989\}, +04259 \{ -100, -989, -989, -989, -989\}, +04260 \{ -100, -989, -989, -989, -989\}, +04261 \{ -100, -989, -989, -989, -989\}\}, +04262 \textcolor{comment}{/* CG.GA..UG */} +04263 \{\{ DEF, -939, -939, -939, -939\}, +04264 \{ -769,-1658,-1658,-1658,-1658\}, +04265 \{ -529,-1418,-1418,-1418,-1418\}, +04266 \{ -709,-1598,-1598,-1598,-1598\}, +04267 \{ -599,-1488,-1488,-1488,-1488\}\}, +04268 \textcolor{comment}{/* CG.GC..UG */} +04269 \{\{ DEF, -939, -939, -939, -939\}, +04270 \{ -839,-1728,-1728,-1728,-1728\}, +04271 \{ -529,-1418,-1418,-1418,-1418\}, +04272 \{ -859,-1748,-1748,-1748,-1748\}, +04273 \{ -489,-1378,-1378,-1378,-1378\}\}, +04274 \textcolor{comment}{/* CG.GG..UG */} +04275 \{\{ DEF, -939, -939, -939, -939\}, +04276 \{-1009,-1898,-1898,-1898,-1898\}, +04277 \{ -409,-1298,-1298,-1298,-1298\}, +04278 \{ -969,-1858,-1858,-1858,-1858\}, +04279 \{ -599,-1488,-1488,-1488,-1488\}\}, +04280 \textcolor{comment}{/* CG.GU..UG */} +04281 \{\{ DEF, -939, -939, -939, -939\}, +04282 \{ -859,-1748,-1748,-1748,-1748\}, +04283 \{ -529,-1418,-1418,-1418,-1418\}, +04284 \{ -859,-1748,-1748,-1748,-1748\}, +04285 \{ -409,-1298,-1298,-1298,-1298\}\}\}, +04286 \textcolor{comment}{/* CG.U@..UG */} +04287 \{\{\{ DEF, -809, -739, -809, -859\}, +04288 \{ -100, -859, -789, -859, -909\}, +04289 \{ -100, -859, -789, -859, -909\}, +04290 \{ -100, -859, -789, -859, -909\}, +04291 \{ -100, -859, -789, -859, -909\}\}, +04292 \textcolor{comment}{/* CG.UA..UG */} +04293 \{\{ DEF, -809, -739, -809, -859\}, +04294 \{ -769,-1528,-1458,-1528,-1578\}, +04295 \{ -529,-1288,-1218,-1288,-1338\}, +04296 \{ -709,-1468,-1398,-1468,-1518\}, +04297 \{ -599,-1358,-1288,-1358,-1408\}\}, +04298 \textcolor{comment}{/* CG.UC..UG */} +04299 \{\{ DEF, -809, -739, -809, -859\}, +04300 \{ -839,-1598,-1528,-1598,-1648\}, +04301 \{ -529,-1288,-1218,-1288,-1338\}, +04302 \{ -859,-1618,-1548,-1618,-1668\}, +04303 \{ -489,-1248,-1178,-1248,-1298\}\}, +04304 \textcolor{comment}{/* CG.UG..UG */} +04305 \{\{ DEF, -809, -739, -809, -859\}, +04306 \{-1009,-1768,-1698,-1768,-1818\}, +04307 \{ -409,-1168,-1098,-1168,-1218\}, +04308 \{ -969,-1728,-1658,-1728,-1778\}, +04309 \{ -599,-1358,-1288,-1358,-1408\}\}, +04310 \textcolor{comment}{/* CG.UU..UG */} +04311 \{\{ DEF, -809, -739, -809, -859\}, +04312 \{ -859,-1618,-1548,-1618,-1668\}, +04313 \{ -529,-1288,-1218,-1288,-1338\}, +04314 \{ -859,-1618,-1548,-1618,-1668\}, +04315 \{ -409,-1168,-1098,-1168,-1218\}\}\}\}, +04316 \textcolor{comment}{/* CG.@@..AU */} +04317 \{\{\{\{ 0, 0, 0, 0, 0\}, +04318 \{ DEF, DEF, DEF, DEF, DEF\}, +04319 \{ DEF, DEF, DEF, DEF, DEF\}, +04320 \{ DEF, DEF, DEF, DEF, DEF\}, +04321 \{ DEF, DEF, DEF, DEF, DEF\}\}, +04322 \textcolor{comment}{/* CG.@A..AU */} +04323 \{\{ 0, 0, 0, 0, 0\}, +04324 \{ -429, -429, -429, -429, -429\}, +04325 \{ -259, -259, -259, -259, -259\}, +04326 \{ -339, -339, -339, -339, -339\}, +04327 \{ -329, -329, -329, -329, -329\}\}, +04328 \textcolor{comment}{/* CG.@C..AU */} +04329 \{\{ 0, 0, 0, 0, 0\}, +04330 \{ -599, -599, -599, -599, -599\}, +04331 \{ -239, -239, -239, -239, -239\}, +04332 \{ -689, -689, -689, -689, -689\}, +04333 \{ -329, -329, -329, -329, -329\}\}, +04334 \textcolor{comment}{/* CG.@G..AU */} +04335 \{\{ 0, 0, 0, 0, 0\}, +04336 \{ -599, -599, -599, -599, -599\}, +04337 \{ -239, -239, -239, -239, -239\}, +04338 \{ -689, -689, -689, -689, -689\}, +04339 \{ -329, -329, -329, -329, -329\}\}, +04340 \textcolor{comment}{/* CG.@U..AU */} +04341 \{\{ 0, 0, 0, 0, 0\}, +04342 \{ -599, -599, -599, -599, -599\}, +04343 \{ -239, -239, -239, -239, -239\}, +04344 \{ -689, -689, -689, -689, -689\}, +04345 \{ -329, -329, -329, -329, -329\}\}\}, +04346 \textcolor{comment}{/* CG.A@..AU */} +04347 \{\{\{ DEF,-1029, -949,-1029,-1029\}, +04348 \{ -100,-1079, -999,-1079,-1079\}, +04349 \{ -100,-1079, -999,-1079,-1079\}, +04350 \{ -100,-1079, -999,-1079,-1079\}, +04351 \{ -100,-1079, -999,-1079,-1079\}\}, +04352 \textcolor{comment}{/* CG.AA..AU */} +04353 \{\{ DEF,-1029, -949,-1029,-1029\}, +04354 \{ -479,-1458,-1378,-1458,-1458\}, +04355 \{ -309,-1288,-1208,-1288,-1288\}, +04356 \{ -389,-1368,-1288,-1368,-1368\}, +04357 \{ -379,-1358,-1278,-1358,-1358\}\}, +04358 \textcolor{comment}{/* CG.AC..AU */} +04359 \{\{ DEF,-1029, -949,-1029,-1029\}, +04360 \{ -649,-1628,-1548,-1628,-1628\}, +04361 \{ -289,-1268,-1188,-1268,-1268\}, +04362 \{ -739,-1718,-1638,-1718,-1718\}, +04363 \{ -379,-1358,-1278,-1358,-1358\}\}, +04364 \textcolor{comment}{/* CG.AG..AU */} +04365 \{\{ DEF,-1029, -949,-1029,-1029\}, +04366 \{ -649,-1628,-1548,-1628,-1628\}, +04367 \{ -289,-1268,-1188,-1268,-1268\}, +04368 \{ -739,-1718,-1638,-1718,-1718\}, +04369 \{ -379,-1358,-1278,-1358,-1358\}\}, +04370 \textcolor{comment}{/* CG.AU..AU */} +04371 \{\{ DEF,-1029, -949,-1029,-1029\}, +04372 \{ -649,-1628,-1548,-1628,-1628\}, +04373 \{ -289,-1268,-1188,-1268,-1268\}, +04374 \{ -739,-1718,-1638,-1718,-1718\}, +04375 \{ -379,-1358,-1278,-1358,-1358\}\}\}, +04376 \textcolor{comment}{/* CG.C@..AU */} +04377 \{\{\{ DEF, -519, -449, -519, -669\}, +04378 \{ -100, -569, -499, -569, -719\}, +04379 \{ -100, -569, -499, -569, -719\}, +04380 \{ -100, -569, -499, -569, -719\}, +04381 \{ -100, -569, -499, -569, -719\}\}, +04382 \textcolor{comment}{/* CG.CA..AU */} +04383 \{\{ DEF, -519, -449, -519, -669\}, +04384 \{ -479, -948, -878, -948,-1098\}, +04385 \{ -309, -778, -708, -778, -928\}, +04386 \{ -389, -858, -788, -858,-1008\}, +04387 \{ -379, -848, -778, -848, -998\}\}, +04388 \textcolor{comment}{/* CG.CC..AU */} +04389 \{\{ DEF, -519, -449, -519, -669\}, +04390 \{ -649,-1118,-1048,-1118,-1268\}, +04391 \{ -289, -758, -688, -758, -908\}, +04392 \{ -739,-1208,-1138,-1208,-1358\}, +04393 \{ -379, -848, -778, -848, -998\}\}, +04394 \textcolor{comment}{/* CG.CG..AU */} +04395 \{\{ DEF, -519, -449, -519, -669\}, +04396 \{ -649,-1118,-1048,-1118,-1268\}, +04397 \{ -289, -758, -688, -758, -908\}, +04398 \{ -739,-1208,-1138,-1208,-1358\}, +04399 \{ -379, -848, -778, -848, -998\}\}, +04400 \textcolor{comment}{/* CG.CU..AU */} +04401 \{\{ DEF, -519, -449, -519, -669\}, +04402 \{ -649,-1118,-1048,-1118,-1268\}, +04403 \{ -289, -758, -688, -758, -908\}, +04404 \{ -739,-1208,-1138,-1208,-1358\}, +04405 \{ -379, -848, -778, -848, -998\}\}\}, +04406 \textcolor{comment}{/* CG.G@..AU */} +04407 \{\{\{ DEF, -939, -939, -939, -939\}, +04408 \{ -100, -989, -989, -989, -989\}, +04409 \{ -100, -989, -989, -989, -989\}, +04410 \{ -100, -989, -989, -989, -989\}, +04411 \{ -100, -989, -989, -989, -989\}\}, +04412 \textcolor{comment}{/* CG.GA..AU */} +04413 \{\{ DEF, -939, -939, -939, -939\}, +04414 \{ -479,-1368,-1368,-1368,-1368\}, +04415 \{ -309,-1198,-1198,-1198,-1198\}, +04416 \{ -389,-1278,-1278,-1278,-1278\}, +04417 \{ -379,-1268,-1268,-1268,-1268\}\}, +04418 \textcolor{comment}{/* CG.GC..AU */} +04419 \{\{ DEF, -939, -939, -939, -939\}, +04420 \{ -649,-1538,-1538,-1538,-1538\}, +04421 \{ -289,-1178,-1178,-1178,-1178\}, +04422 \{ -739,-1628,-1628,-1628,-1628\}, +04423 \{ -379,-1268,-1268,-1268,-1268\}\}, +04424 \textcolor{comment}{/* CG.GG..AU */} +04425 \{\{ DEF, -939, -939, -939, -939\}, +04426 \{ -649,-1538,-1538,-1538,-1538\}, +04427 \{ -289,-1178,-1178,-1178,-1178\}, +04428 \{ -739,-1628,-1628,-1628,-1628\}, +04429 \{ -379,-1268,-1268,-1268,-1268\}\}, +04430 \textcolor{comment}{/* CG.GU..AU */} +04431 \{\{ DEF, -939, -939, -939, -939\}, +04432 \{ -649,-1538,-1538,-1538,-1538\}, +04433 \{ -289,-1178,-1178,-1178,-1178\}, +04434 \{ -739,-1628,-1628,-1628,-1628\}, +04435 \{ -379,-1268,-1268,-1268,-1268\}\}\}, +04436 \textcolor{comment}{/* CG.U@..AU */} +04437 \{\{\{ DEF, -809, -739, -809, -859\}, +04438 \{ -100, -859, -789, -859, -909\}, +04439 \{ -100, -859, -789, -859, -909\}, +04440 \{ -100, -859, -789, -859, -909\}, +04441 \{ -100, -859, -789, -859, -909\}\}, +04442 \textcolor{comment}{/* CG.UA..AU */} +04443 \{\{ DEF, -809, -739, -809, -859\}, +04444 \{ -479,-1238,-1168,-1238,-1288\}, +04445 \{ -309,-1068, -998,-1068,-1118\}, +04446 \{ -389,-1148,-1078,-1148,-1198\}, +04447 \{ -379,-1138,-1068,-1138,-1188\}\}, +04448 \textcolor{comment}{/* CG.UC..AU */} +04449 \{\{ DEF, -809, -739, -809, -859\}, +04450 \{ -649,-1408,-1338,-1408,-1458\}, +04451 \{ -289,-1048, -978,-1048,-1098\}, +04452 \{ -739,-1498,-1428,-1498,-1548\}, +04453 \{ -379,-1138,-1068,-1138,-1188\}\}, +04454 \textcolor{comment}{/* CG.UG..AU */} +04455 \{\{ DEF, -809, -739, -809, -859\}, +04456 \{ -649,-1408,-1338,-1408,-1458\}, +04457 \{ -289,-1048, -978,-1048,-1098\}, +04458 \{ -739,-1498,-1428,-1498,-1548\}, +04459 \{ -379,-1138,-1068,-1138,-1188\}\}, +04460 \textcolor{comment}{/* CG.UU..AU */} +04461 \{\{ DEF, -809, -739, -809, -859\}, +04462 \{ -649,-1408,-1338,-1408,-1458\}, +04463 \{ -289,-1048, -978,-1048,-1098\}, +04464 \{ -739,-1498,-1428,-1498,-1548\}, +04465 \{ -379,-1138,-1068,-1138,-1188\}\}\}\}, +04466 \textcolor{comment}{/* CG.@@..UA */} +04467 \{\{\{\{ 0, 0, 0, 0, 0\}, +04468 \{ DEF, DEF, DEF, DEF, DEF\}, +04469 \{ DEF, DEF, DEF, DEF, DEF\}, +04470 \{ DEF, DEF, DEF, DEF, DEF\}, +04471 \{ DEF, DEF, DEF, DEF, DEF\}\}, +04472 \textcolor{comment}{/* CG.@A..UA */} +04473 \{\{ 0, 0, 0, 0, 0\}, +04474 \{ -399, -399, -399, -399, -399\}, +04475 \{ -429, -429, -429, -429, -429\}, +04476 \{ -379, -379, -379, -379, -379\}, +04477 \{ -279, -279, -279, -279, -279\}\}, +04478 \textcolor{comment}{/* CG.@C..UA */} +04479 \{\{ 0, 0, 0, 0, 0\}, +04480 \{ -629, -629, -629, -629, -629\}, +04481 \{ -509, -509, -509, -509, -509\}, +04482 \{ -679, -679, -679, -679, -679\}, +04483 \{ -139, -139, -139, -139, -139\}\}, +04484 \textcolor{comment}{/* CG.@G..UA */} +04485 \{\{ 0, 0, 0, 0, 0\}, +04486 \{ -889, -889, -889, -889, -889\}, +04487 \{ -199, -199, -199, -199, -199\}, +04488 \{ -889, -889, -889, -889, -889\}, +04489 \{ -279, -279, -279, -279, -279\}\}, +04490 \textcolor{comment}{/* CG.@U..UA */} +04491 \{\{ 0, 0, 0, 0, 0\}, +04492 \{ -589, -589, -589, -589, -589\}, +04493 \{ -179, -179, -179, -179, -179\}, +04494 \{ -679, -679, -679, -679, -679\}, +04495 \{ -140, -140, -140, -140, -140\}\}\}, +04496 \textcolor{comment}{/* CG.A@..UA */} +04497 \{\{\{ DEF,-1029, -949,-1029,-1029\}, +04498 \{ -100,-1079, -999,-1079,-1079\}, +04499 \{ -100,-1079, -999,-1079,-1079\}, +04500 \{ -100,-1079, -999,-1079,-1079\}, +04501 \{ -100,-1079, -999,-1079,-1079\}\}, +04502 \textcolor{comment}{/* CG.AA..UA */} +04503 \{\{ DEF,-1029, -949,-1029,-1029\}, +04504 \{ -449,-1428,-1348,-1428,-1428\}, +04505 \{ -479,-1458,-1378,-1458,-1458\}, +04506 \{ -429,-1408,-1328,-1408,-1408\}, +04507 \{ -329,-1308,-1228,-1308,-1308\}\}, +04508 \textcolor{comment}{/* CG.AC..UA */} +04509 \{\{ DEF,-1029, -949,-1029,-1029\}, +04510 \{ -679,-1658,-1578,-1658,-1658\}, +04511 \{ -559,-1538,-1458,-1538,-1538\}, +04512 \{ -729,-1708,-1628,-1708,-1708\}, +04513 \{ -189,-1168,-1088,-1168,-1168\}\}, +04514 \textcolor{comment}{/* CG.AG..UA */} +04515 \{\{ DEF,-1029, -949,-1029,-1029\}, +04516 \{ -939,-1918,-1838,-1918,-1918\}, +04517 \{ -249,-1228,-1148,-1228,-1228\}, +04518 \{ -939,-1918,-1838,-1918,-1918\}, +04519 \{ -329,-1308,-1228,-1308,-1308\}\}, +04520 \textcolor{comment}{/* CG.AU..UA */} +04521 \{\{ DEF,-1029, -949,-1029,-1029\}, +04522 \{ -639,-1618,-1538,-1618,-1618\}, +04523 \{ -229,-1208,-1128,-1208,-1208\}, +04524 \{ -729,-1708,-1628,-1708,-1708\}, +04525 \{ -190,-1169,-1089,-1169,-1169\}\}\}, +04526 \textcolor{comment}{/* CG.C@..UA */} +04527 \{\{\{ DEF, -519, -449, -519, -669\}, +04528 \{ -100, -569, -499, -569, -719\}, +04529 \{ -100, -569, -499, -569, -719\}, +04530 \{ -100, -569, -499, -569, -719\}, +04531 \{ -100, -569, -499, -569, -719\}\}, +04532 \textcolor{comment}{/* CG.CA..UA */} +04533 \{\{ DEF, -519, -449, -519, -669\}, +04534 \{ -449, -918, -848, -918,-1068\}, +04535 \{ -479, -948, -878, -948,-1098\}, +04536 \{ -429, -898, -828, -898,-1048\}, +04537 \{ -329, -798, -728, -798, -948\}\}, +04538 \textcolor{comment}{/* CG.CC..UA */} +04539 \{\{ DEF, -519, -449, -519, -669\}, +04540 \{ -679,-1148,-1078,-1148,-1298\}, +04541 \{ -559,-1028, -958,-1028,-1178\}, +04542 \{ -729,-1198,-1128,-1198,-1348\}, +04543 \{ -189, -658, -588, -658, -808\}\}, +04544 \textcolor{comment}{/* CG.CG..UA */} +04545 \{\{ DEF, -519, -449, -519, -669\}, +04546 \{ -939,-1408,-1338,-1408,-1558\}, +04547 \{ -249, -718, -648, -718, -868\}, +04548 \{ -939,-1408,-1338,-1408,-1558\}, +04549 \{ -329, -798, -728, -798, -948\}\}, +04550 \textcolor{comment}{/* CG.CU..UA */} +04551 \{\{ DEF, -519, -449, -519, -669\}, +04552 \{ -639,-1108,-1038,-1108,-1258\}, +04553 \{ -229, -698, -628, -698, -848\}, +04554 \{ -729,-1198,-1128,-1198,-1348\}, +04555 \{ -190, -659, -589, -659, -809\}\}\}, +04556 \textcolor{comment}{/* CG.G@..UA */} +04557 \{\{\{ DEF, -939, -939, -939, -939\}, +04558 \{ -100, -989, -989, -989, -989\}, +04559 \{ -100, -989, -989, -989, -989\}, +04560 \{ -100, -989, -989, -989, -989\}, +04561 \{ -100, -989, -989, -989, -989\}\}, +04562 \textcolor{comment}{/* CG.GA..UA */} +04563 \{\{ DEF, -939, -939, -939, -939\}, +04564 \{ -449,-1338,-1338,-1338,-1338\}, +04565 \{ -479,-1368,-1368,-1368,-1368\}, +04566 \{ -429,-1318,-1318,-1318,-1318\}, +04567 \{ -329,-1218,-1218,-1218,-1218\}\}, +04568 \textcolor{comment}{/* CG.GC..UA */} +04569 \{\{ DEF, -939, -939, -939, -939\}, +04570 \{ -679,-1568,-1568,-1568,-1568\}, +04571 \{ -559,-1448,-1448,-1448,-1448\}, +04572 \{ -729,-1618,-1618,-1618,-1618\}, +04573 \{ -189,-1078,-1078,-1078,-1078\}\}, +04574 \textcolor{comment}{/* CG.GG..UA */} +04575 \{\{ DEF, -939, -939, -939, -939\}, +04576 \{ -939,-1828,-1828,-1828,-1828\}, +04577 \{ -249,-1138,-1138,-1138,-1138\}, +04578 \{ -939,-1828,-1828,-1828,-1828\}, +04579 \{ -329,-1218,-1218,-1218,-1218\}\}, +04580 \textcolor{comment}{/* CG.GU..UA */} +04581 \{\{ DEF, -939, -939, -939, -939\}, +04582 \{ -639,-1528,-1528,-1528,-1528\}, +04583 \{ -229,-1118,-1118,-1118,-1118\}, +04584 \{ -729,-1618,-1618,-1618,-1618\}, +04585 \{ -190,-1079,-1079,-1079,-1079\}\}\}, +04586 \textcolor{comment}{/* CG.U@..UA */} +04587 \{\{\{ DEF, -809, -739, -809, -859\}, +04588 \{ -100, -859, -789, -859, -909\}, +04589 \{ -100, -859, -789, -859, -909\}, +04590 \{ -100, -859, -789, -859, -909\}, +04591 \{ -100, -859, -789, -859, -909\}\}, +04592 \textcolor{comment}{/* CG.UA..UA */} +04593 \{\{ DEF, -809, -739, -809, -859\}, +04594 \{ -449,-1208,-1138,-1208,-1258\}, +04595 \{ -479,-1238,-1168,-1238,-1288\}, +04596 \{ -429,-1188,-1118,-1188,-1238\}, +04597 \{ -329,-1088,-1018,-1088,-1138\}\}, +04598 \textcolor{comment}{/* CG.UC..UA */} +04599 \{\{ DEF, -809, -739, -809, -859\}, +04600 \{ -679,-1438,-1368,-1438,-1488\}, +04601 \{ -559,-1318,-1248,-1318,-1368\}, +04602 \{ -729,-1488,-1418,-1488,-1538\}, +04603 \{ -189, -948, -878, -948, -998\}\}, +04604 \textcolor{comment}{/* CG.UG..UA */} +04605 \{\{ DEF, -809, -739, -809, -859\}, +04606 \{ -939,-1698,-1628,-1698,-1748\}, +04607 \{ -249,-1008, -938,-1008,-1058\}, +04608 \{ -939,-1698,-1628,-1698,-1748\}, +04609 \{ -329,-1088,-1018,-1088,-1138\}\}, +04610 \textcolor{comment}{/* CG.UU..UA */} +04611 \{\{ DEF, -809, -739, -809, -859\}, +04612 \{ -639,-1398,-1328,-1398,-1448\}, +04613 \{ -229, -988, -918, -988,-1038\}, +04614 \{ -729,-1488,-1418,-1488,-1538\}, +04615 \{ -190, -949, -879, -949, -999\}\}\}\}, +04616 \textcolor{comment}{/* CG.@@.. @ */} +04617 \{\{\{\{ DEF, DEF, DEF, DEF, DEF\}, +04618 \{ DEF, DEF, DEF, DEF, DEF\}, +04619 \{ DEF, DEF, DEF, DEF, DEF\}, +04620 \{ DEF, DEF, DEF, DEF, DEF\}, +04621 \{ DEF, DEF, DEF, DEF, DEF\}\}, +04622 \textcolor{comment}{/* CG.@A.. @ */} +04623 \{\{ DEF, DEF, DEF, DEF, DEF\}, +04624 \{ DEF, DEF, DEF, DEF, DEF\}, +04625 \{ DEF, DEF, DEF, DEF, DEF\}, +04626 \{ DEF, DEF, DEF, DEF, DEF\}, +04627 \{ DEF, DEF, DEF, DEF, DEF\}\}, +04628 \textcolor{comment}{/* CG.@C.. @ */} +04629 \{\{ DEF, DEF, DEF, DEF, DEF\}, +04630 \{ DEF, DEF, DEF, DEF, DEF\}, +04631 \{ DEF, DEF, DEF, DEF, DEF\}, +04632 \{ DEF, DEF, DEF, DEF, DEF\}, +04633 \{ DEF, DEF, DEF, DEF, DEF\}\}, +04634 \textcolor{comment}{/* CG.@G.. @ */} +04635 \{\{ DEF, DEF, DEF, DEF, DEF\}, +04636 \{ DEF, DEF, DEF, DEF, DEF\}, +04637 \{ DEF, DEF, DEF, DEF, DEF\}, +04638 \{ DEF, DEF, DEF, DEF, DEF\}, +04639 \{ DEF, DEF, DEF, DEF, DEF\}\}, +04640 \textcolor{comment}{/* CG.@U.. @ */} +04641 \{\{ DEF, DEF, DEF, DEF, DEF\}, +04642 \{ DEF, DEF, DEF, DEF, DEF\}, +04643 \{ DEF, DEF, DEF, DEF, DEF\}, +04644 \{ DEF, DEF, DEF, DEF, DEF\}, +04645 \{ DEF, DEF, DEF, DEF, DEF\}\}\}, +04646 \textcolor{comment}{/* CG.A@.. @ */} +04647 \{\{\{ -100,-1079, -999,-1079,-1079\}, +04648 \{ -100,-1079, -999,-1079,-1079\}, +04649 \{ -100,-1079, -999,-1079,-1079\}, +04650 \{ -100,-1079, -999,-1079,-1079\}, +04651 \{ -100,-1079, -999,-1079,-1079\}\}, +04652 \textcolor{comment}{/* CG.AA.. @ */} +04653 \{\{ -100,-1079, -999,-1079,-1079\}, +04654 \{ -100,-1079, -999,-1079,-1079\}, +04655 \{ -100,-1079, -999,-1079,-1079\}, +04656 \{ -100,-1079, -999,-1079,-1079\}, +04657 \{ -100,-1079, -999,-1079,-1079\}\}, +04658 \textcolor{comment}{/* CG.AC.. @ */} +04659 \{\{ -100,-1079, -999,-1079,-1079\}, +04660 \{ -100,-1079, -999,-1079,-1079\}, +04661 \{ -100,-1079, -999,-1079,-1079\}, +04662 \{ -100,-1079, -999,-1079,-1079\}, +04663 \{ -100,-1079, -999,-1079,-1079\}\}, +04664 \textcolor{comment}{/* CG.AG.. @ */} +04665 \{\{ -100,-1079, -999,-1079,-1079\}, +04666 \{ -100,-1079, -999,-1079,-1079\}, +04667 \{ -100,-1079, -999,-1079,-1079\}, +04668 \{ -100,-1079, -999,-1079,-1079\}, +04669 \{ -100,-1079, -999,-1079,-1079\}\}, +04670 \textcolor{comment}{/* CG.AU.. @ */} +04671 \{\{ -100,-1079, -999,-1079,-1079\}, +04672 \{ -100,-1079, -999,-1079,-1079\}, +04673 \{ -100,-1079, -999,-1079,-1079\}, +04674 \{ -100,-1079, -999,-1079,-1079\}, +04675 \{ -100,-1079, -999,-1079,-1079\}\}\}, +04676 \textcolor{comment}{/* CG.C@.. @ */} +04677 \{\{\{ -100, -569, -499, -569, -719\}, +04678 \{ -100, -569, -499, -569, -719\}, +04679 \{ -100, -569, -499, -569, -719\}, +04680 \{ -100, -569, -499, -569, -719\}, +04681 \{ -100, -569, -499, -569, -719\}\}, +04682 \textcolor{comment}{/* CG.CA.. @ */} +04683 \{\{ -100, -569, -499, -569, -719\}, +04684 \{ -100, -569, -499, -569, -719\}, +04685 \{ -100, -569, -499, -569, -719\}, +04686 \{ -100, -569, -499, -569, -719\}, +04687 \{ -100, -569, -499, -569, -719\}\}, +04688 \textcolor{comment}{/* CG.CC.. @ */} +04689 \{\{ -100, -569, -499, -569, -719\}, +04690 \{ -100, -569, -499, -569, -719\}, +04691 \{ -100, -569, -499, -569, -719\}, +04692 \{ -100, -569, -499, -569, -719\}, +04693 \{ -100, -569, -499, -569, -719\}\}, +04694 \textcolor{comment}{/* CG.CG.. @ */} +04695 \{\{ -100, -569, -499, -569, -719\}, +04696 \{ -100, -569, -499, -569, -719\}, +04697 \{ -100, -569, -499, -569, -719\}, +04698 \{ -100, -569, -499, -569, -719\}, +04699 \{ -100, -569, -499, -569, -719\}\}, +04700 \textcolor{comment}{/* CG.CU.. @ */} +04701 \{\{ -100, -569, -499, -569, -719\}, +04702 \{ -100, -569, -499, -569, -719\}, +04703 \{ -100, -569, -499, -569, -719\}, +04704 \{ -100, -569, -499, -569, -719\}, +04705 \{ -100, -569, -499, -569, -719\}\}\}, +04706 \textcolor{comment}{/* CG.G@.. @ */} +04707 \{\{\{ -100, -989, -989, -989, -989\}, +04708 \{ -100, -989, -989, -989, -989\}, +04709 \{ -100, -989, -989, -989, -989\}, +04710 \{ -100, -989, -989, -989, -989\}, +04711 \{ -100, -989, -989, -989, -989\}\}, +04712 \textcolor{comment}{/* CG.GA.. @ */} +04713 \{\{ -100, -989, -989, -989, -989\}, +04714 \{ -100, -989, -989, -989, -989\}, +04715 \{ -100, -989, -989, -989, -989\}, +04716 \{ -100, -989, -989, -989, -989\}, +04717 \{ -100, -989, -989, -989, -989\}\}, +04718 \textcolor{comment}{/* CG.GC.. @ */} +04719 \{\{ -100, -989, -989, -989, -989\}, +04720 \{ -100, -989, -989, -989, -989\}, +04721 \{ -100, -989, -989, -989, -989\}, +04722 \{ -100, -989, -989, -989, -989\}, +04723 \{ -100, -989, -989, -989, -989\}\}, +04724 \textcolor{comment}{/* CG.GG.. @ */} +04725 \{\{ -100, -989, -989, -989, -989\}, +04726 \{ -100, -989, -989, -989, -989\}, +04727 \{ -100, -989, -989, -989, -989\}, +04728 \{ -100, -989, -989, -989, -989\}, +04729 \{ -100, -989, -989, -989, -989\}\}, +04730 \textcolor{comment}{/* CG.GU.. @ */} +04731 \{\{ -100, -989, -989, -989, -989\}, +04732 \{ -100, -989, -989, -989, -989\}, +04733 \{ -100, -989, -989, -989, -989\}, +04734 \{ -100, -989, -989, -989, -989\}, +04735 \{ -100, -989, -989, -989, -989\}\}\}, +04736 \textcolor{comment}{/* CG.U@.. @ */} +04737 \{\{\{ -100, -859, -789, -859, -909\}, +04738 \{ -100, -859, -789, -859, -909\}, +04739 \{ -100, -859, -789, -859, -909\}, +04740 \{ -100, -859, -789, -859, -909\}, +04741 \{ -100, -859, -789, -859, -909\}\}, +04742 \textcolor{comment}{/* CG.UA.. @ */} +04743 \{\{ -100, -859, -789, -859, -909\}, +04744 \{ -100, -859, -789, -859, -909\}, +04745 \{ -100, -859, -789, -859, -909\}, +04746 \{ -100, -859, -789, -859, -909\}, +04747 \{ -100, -859, -789, -859, -909\}\}, +04748 \textcolor{comment}{/* CG.UC.. @ */} +04749 \{\{ -100, -859, -789, -859, -909\}, +04750 \{ -100, -859, -789, -859, -909\}, +04751 \{ -100, -859, -789, -859, -909\}, +04752 \{ -100, -859, -789, -859, -909\}, +04753 \{ -100, -859, -789, -859, -909\}\}, +04754 \textcolor{comment}{/* CG.UG.. @ */} +04755 \{\{ -100, -859, -789, -859, -909\}, +04756 \{ -100, -859, -789, -859, -909\}, +04757 \{ -100, -859, -789, -859, -909\}, +04758 \{ -100, -859, -789, -859, -909\}, +04759 \{ -100, -859, -789, -859, -909\}\}, +04760 \textcolor{comment}{/* CG.UU.. @ */} +04761 \{\{ -100, -859, -789, -859, -909\}, +04762 \{ -100, -859, -789, -859, -909\}, +04763 \{ -100, -859, -789, -859, -909\}, +04764 \{ -100, -859, -789, -859, -909\}, +04765 \{ -100, -859, -789, -859, -909\}\}\}\}\}, +04766 \{ \textcolor{comment}{/* noPair */} \{\{\{\{0\}\}\}\}, +04767 \textcolor{comment}{/* GC.@@..CG */} +04768 \{\{\{\{ 0, 0, 0, 0, 0\}, +04769 \{ DEF, DEF, DEF, DEF, DEF\}, +04770 \{ DEF, DEF, DEF, DEF, DEF\}, +04771 \{ DEF, DEF, DEF, DEF, DEF\}, +04772 \{ DEF, DEF, DEF, DEF, DEF\}\}, +04773 \textcolor{comment}{/* GC.@A..CG */} +04774 \{\{ 0, 0, 0, 0, 0\}, +04775 \{-1029,-1029,-1029,-1029,-1029\}, +04776 \{ -519, -519, -519, -519, -519\}, +04777 \{ -939, -939, -939, -939, -939\}, +04778 \{ -809, -809, -809, -809, -809\}\}, +04779 \textcolor{comment}{/* GC.@C..CG */} +04780 \{\{ 0, 0, 0, 0, 0\}, +04781 \{ -949, -949, -949, -949, -949\}, +04782 \{ -449, -449, -449, -449, -449\}, +04783 \{ -939, -939, -939, -939, -939\}, +04784 \{ -739, -739, -739, -739, -739\}\}, +04785 \textcolor{comment}{/* GC.@G..CG */} +04786 \{\{ 0, 0, 0, 0, 0\}, +04787 \{-1029,-1029,-1029,-1029,-1029\}, +04788 \{ -519, -519, -519, -519, -519\}, +04789 \{ -939, -939, -939, -939, -939\}, +04790 \{ -809, -809, -809, -809, -809\}\}, +04791 \textcolor{comment}{/* GC.@U..CG */} +04792 \{\{ 0, 0, 0, 0, 0\}, +04793 \{-1029,-1029,-1029,-1029,-1029\}, +04794 \{ -669, -669, -669, -669, -669\}, +04795 \{ -939, -939, -939, -939, -939\}, +04796 \{ -859, -859, -859, -859, -859\}\}\}, +04797 \textcolor{comment}{/* GC.A@..CG */} +04798 \{\{\{ DEF, -519, -879, -559, -879\}, +04799 \{ -100, -569, -929, -609, -929\}, +04800 \{ -100, -569, -929, -609, -929\}, +04801 \{ -100, -569, -929, -609, -929\}, +04802 \{ -100, -569, -929, -609, -929\}\}, +04803 \textcolor{comment}{/* GC.AA..CG */} +04804 \{\{ DEF, -519, -879, -559, -879\}, +04805 \{-1079,-1548,-1908,-1588,-1908\}, +04806 \{ -569,-1038,-1398,-1078,-1398\}, +04807 \{ -989,-1458,-1818,-1498,-1818\}, +04808 \{ -859,-1328,-1688,-1368,-1688\}\}, +04809 \textcolor{comment}{/* GC.AC..CG */} +04810 \{\{ DEF, -519, -879, -559, -879\}, +04811 \{ -999,-1468,-1828,-1508,-1828\}, +04812 \{ -499, -968,-1328,-1008,-1328\}, +04813 \{ -989,-1458,-1818,-1498,-1818\}, +04814 \{ -789,-1258,-1618,-1298,-1618\}\}, +04815 \textcolor{comment}{/* GC.AG..CG */} +04816 \{\{ DEF, -519, -879, -559, -879\}, +04817 \{-1079,-1548,-1908,-1588,-1908\}, +04818 \{ -569,-1038,-1398,-1078,-1398\}, +04819 \{ -989,-1458,-1818,-1498,-1818\}, +04820 \{ -859,-1328,-1688,-1368,-1688\}\}, +04821 \textcolor{comment}{/* GC.AU..CG */} +04822 \{\{ DEF, -519, -879, -559, -879\}, +04823 \{-1079,-1548,-1908,-1588,-1908\}, +04824 \{ -719,-1188,-1548,-1228,-1548\}, +04825 \{ -989,-1458,-1818,-1498,-1818\}, +04826 \{ -909,-1378,-1738,-1418,-1738\}\}\}, +04827 \textcolor{comment}{/* GC.C@..CG */} +04828 \{\{\{ DEF, -719, -309, -309, -389\}, +04829 \{ -100, -769, -359, -359, -439\}, +04830 \{ -100, -769, -359, -359, -439\}, +04831 \{ -100, -769, -359, -359, -439\}, +04832 \{ -100, -769, -359, -359, -439\}\}, +04833 \textcolor{comment}{/* GC.CA..CG */} +04834 \{\{ DEF, -719, -309, -309, -389\}, +04835 \{-1079,-1748,-1338,-1338,-1418\}, +04836 \{ -569,-1238, -828, -828, -908\}, +04837 \{ -989,-1658,-1248,-1248,-1328\}, +04838 \{ -859,-1528,-1118,-1118,-1198\}\}, +04839 \textcolor{comment}{/* GC.CC..CG */} +04840 \{\{ DEF, -719, -309, -309, -389\}, +04841 \{ -999,-1668,-1258,-1258,-1338\}, +04842 \{ -499,-1168, -758, -758, -838\}, +04843 \{ -989,-1658,-1248,-1248,-1328\}, +04844 \{ -789,-1458,-1048,-1048,-1128\}\}, +04845 \textcolor{comment}{/* GC.CG..CG */} +04846 \{\{ DEF, -719, -309, -309, -389\}, +04847 \{-1079,-1748,-1338,-1338,-1418\}, +04848 \{ -569,-1238, -828, -828, -908\}, +04849 \{ -989,-1658,-1248,-1248,-1328\}, +04850 \{ -859,-1528,-1118,-1118,-1198\}\}, +04851 \textcolor{comment}{/* GC.CU..CG */} +04852 \{\{ DEF, -719, -309, -309, -389\}, +04853 \{-1079,-1748,-1338,-1338,-1418\}, +04854 \{ -719,-1388, -978, -978,-1058\}, +04855 \{ -989,-1658,-1248,-1248,-1328\}, +04856 \{ -909,-1578,-1168,-1168,-1248\}\}\}, +04857 \textcolor{comment}{/* GC.G@..CG */} +04858 \{\{\{ DEF, -709, -739, -619, -739\}, +04859 \{ -100, -759, -789, -669, -789\}, +04860 \{ -100, -759, -789, -669, -789\}, +04861 \{ -100, -759, -789, -669, -789\}, +04862 \{ -100, -759, -789, -669, -789\}\}, +04863 \textcolor{comment}{/* GC.GA..CG */} +04864 \{\{ DEF, -709, -739, -619, -739\}, +04865 \{-1079,-1738,-1768,-1648,-1768\}, +04866 \{ -569,-1228,-1258,-1138,-1258\}, +04867 \{ -989,-1648,-1678,-1558,-1678\}, +04868 \{ -859,-1518,-1548,-1428,-1548\}\}, +04869 \textcolor{comment}{/* GC.GC..CG */} +04870 \{\{ DEF, -709, -739, -619, -739\}, +04871 \{ -999,-1658,-1688,-1568,-1688\}, +04872 \{ -499,-1158,-1188,-1068,-1188\}, +04873 \{ -989,-1648,-1678,-1558,-1678\}, +04874 \{ -789,-1448,-1478,-1358,-1478\}\}, +04875 \textcolor{comment}{/* GC.GG..CG */} +04876 \{\{ DEF, -709, -739, -619, -739\}, +04877 \{-1079,-1738,-1768,-1648,-1768\}, +04878 \{ -569,-1228,-1258,-1138,-1258\}, +04879 \{ -989,-1648,-1678,-1558,-1678\}, +04880 \{ -859,-1518,-1548,-1428,-1548\}\}, +04881 \textcolor{comment}{/* GC.GU..CG */} +04882 \{\{ DEF, -709, -739, -619, -739\}, +04883 \{-1079,-1738,-1768,-1648,-1768\}, +04884 \{ -719,-1378,-1408,-1288,-1408\}, +04885 \{ -989,-1648,-1678,-1558,-3080\}, +04886 \{ -909,-1568,-1598,-1478,-1598\}\}\}, +04887 \textcolor{comment}{/* GC.U@..CG */} +04888 \{\{\{ DEF, -499, -499, -499, -569\}, +04889 \{ -100, -549, -549, -549, -619\}, +04890 \{ -100, -549, -549, -549, -619\}, +04891 \{ -100, -549, -549, -549, -619\}, +04892 \{ -100, -549, -549, -549, -619\}\}, +04893 \textcolor{comment}{/* GC.UA..CG */} +04894 \{\{ DEF, -499, -499, -499, -569\}, +04895 \{-1079,-1528,-1528,-1528,-1598\}, +04896 \{ -569,-1018,-1018,-1018,-1088\}, +04897 \{ -989,-1438,-1438,-1438,-1508\}, +04898 \{ -859,-1308,-1308,-1308,-1378\}\}, +04899 \textcolor{comment}{/* GC.UC..CG */} +04900 \{\{ DEF, -499, -499, -499, -569\}, +04901 \{ -999,-1448,-1448,-1448,-1518\}, +04902 \{ -499, -948, -948, -948,-1018\}, +04903 \{ -989,-1438,-1438,-1438,-1508\}, +04904 \{ -789,-1238,-1238,-1238,-1308\}\}, +04905 \textcolor{comment}{/* GC.UG..CG */} +04906 \{\{ DEF, -499, -499, -499, -569\}, +04907 \{-1079,-1528,-1528,-1528,-1598\}, +04908 \{ -569,-1018,-1018,-1018,-1088\}, +04909 \{ -989,-1438,-1438,-1438,-1508\}, +04910 \{ -859,-1308,-1308,-1308,-1378\}\}, +04911 \textcolor{comment}{/* GC.UU..CG */} +04912 \{\{ DEF, -499, -499, -499, -569\}, +04913 \{-1079,-1528,-1528,-1528,-1598\}, +04914 \{ -719,-1168,-1168,-1168,-1238\}, +04915 \{ -989,-1438,-1438,-1438,-1508\}, +04916 \{ -909,-1358,-1358,-1358,-1428\}\}\}\}, +04917 \textcolor{comment}{/* GC.@@..GC */} +04918 \{\{\{\{ 0, 0, 0, 0, 0\}, +04919 \{ DEF, DEF, DEF, DEF, DEF\}, +04920 \{ DEF, DEF, DEF, DEF, DEF\}, +04921 \{ DEF, DEF, DEF, DEF, DEF\}, +04922 \{ DEF, DEF, DEF, DEF, DEF\}\}, +04923 \textcolor{comment}{/* GC.@A..GC */} +04924 \{\{ 0, 0, 0, 0, 0\}, +04925 \{ -519, -519, -519, -519, -519\}, +04926 \{ -719, -719, -719, -719, -719\}, +04927 \{ -709, -709, -709, -709, -709\}, +04928 \{ -499, -499, -499, -499, -499\}\}, +04929 \textcolor{comment}{/* GC.@C..GC */} +04930 \{\{ 0, 0, 0, 0, 0\}, +04931 \{ -879, -879, -879, -879, -879\}, +04932 \{ -309, -309, -309, -309, -309\}, +04933 \{ -739, -739, -739, -739, -739\}, +04934 \{ -499, -499, -499, -499, -499\}\}, +04935 \textcolor{comment}{/* GC.@G..GC */} +04936 \{\{ 0, 0, 0, 0, 0\}, +04937 \{ -559, -559, -559, -559, -559\}, +04938 \{ -309, -309, -309, -309, -309\}, +04939 \{ -619, -619, -619, -619, -619\}, +04940 \{ -499, -499, -499, -499, -499\}\}, +04941 \textcolor{comment}{/* GC.@U..GC */} +04942 \{\{ 0, 0, 0, 0, 0\}, +04943 \{ -879, -879, -879, -879, -879\}, +04944 \{ -389, -389, -389, -389, -389\}, +04945 \{ -739, -739, -739, -739, -739\}, +04946 \{ -569, -569, -569, -569, -569\}\}\}, +04947 \textcolor{comment}{/* GC.A@..GC */} +04948 \{\{\{ DEF, -519, -879, -559, -879\}, +04949 \{ -100, -569, -929, -609, -929\}, +04950 \{ -100, -569, -929, -609, -929\}, +04951 \{ -100, -569, -929, -609, -929\}, +04952 \{ -100, -569, -929, -609, -929\}\}, +04953 \textcolor{comment}{/* GC.AA..GC */} +04954 \{\{ DEF, -519, -879, -559, -879\}, +04955 \{ -569,-1038,-1398,-1078,-1398\}, +04956 \{ -769,-1238,-1598,-1278,-1598\}, +04957 \{ -759,-1228,-1588,-1268,-1588\}, +04958 \{ -549,-1018,-1378,-1058,-1378\}\}, +04959 \textcolor{comment}{/* GC.AC..GC */} +04960 \{\{ DEF, -519, -879, -559, -879\}, +04961 \{ -929,-1398,-1758,-1438,-1758\}, +04962 \{ -359, -828,-1188, -868,-1188\}, +04963 \{ -789,-1258,-1618,-1298,-1618\}, +04964 \{ -549,-1018,-1378,-1058,-1378\}\}, +04965 \textcolor{comment}{/* GC.AG..GC */} +04966 \{\{ DEF, -519, -879, -559, -879\}, +04967 \{ -609,-1078,-1438,-1118,-1438\}, +04968 \{ -359, -828,-1188, -868,-1188\}, +04969 \{ -669,-1138,-1498,-1178,-1498\}, +04970 \{ -549,-1018,-1378,-1058,-1378\}\}, +04971 \textcolor{comment}{/* GC.AU..GC */} +04972 \{\{ DEF, -519, -879, -559, -879\}, +04973 \{ -929,-1398,-1758,-1438,-1758\}, +04974 \{ -439, -908,-1268, -948,-1268\}, +04975 \{ -789,-1258,-1618,-1298,-1618\}, +04976 \{ -619,-1088,-1448,-1128,-1448\}\}\}, +04977 \textcolor{comment}{/* GC.C@..GC */} +04978 \{\{\{ DEF, -719, -309, -309, -389\}, +04979 \{ -100, -769, -359, -359, -439\}, +04980 \{ -100, -769, -359, -359, -439\}, +04981 \{ -100, -769, -359, -359, -439\}, +04982 \{ -100, -769, -359, -359, -439\}\}, +04983 \textcolor{comment}{/* GC.CA..GC */} +04984 \{\{ DEF, -719, -309, -309, -389\}, +04985 \{ -569,-1238, -828, -828, -908\}, +04986 \{ -769,-1438,-1028,-1028,-1108\}, +04987 \{ -759,-1428,-1018,-1018,-1098\}, +04988 \{ -549,-1218, -808, -808, -888\}\}, +04989 \textcolor{comment}{/* GC.CC..GC */} +04990 \{\{ DEF, -719, -309, -309, -389\}, +04991 \{ -929,-1598,-1188,-1188,-1268\}, +04992 \{ -359,-1028, -618, -618, -698\}, +04993 \{ -789,-1458,-1048,-1048,-1128\}, +04994 \{ -549,-1218, -808, -808, -888\}\}, +04995 \textcolor{comment}{/* GC.CG..GC */} +04996 \{\{ DEF, -719, -309, -309, -389\}, +04997 \{ -609,-1278, -868, -868, -948\}, +04998 \{ -359,-1028, -618, -618, -698\}, +04999 \{ -669,-1338, -928, -928,-1008\}, +05000 \{ -549,-1218, -808, -808, -888\}\}, +05001 \textcolor{comment}{/* GC.CU..GC */} +05002 \{\{ DEF, -719, -309, -309, -389\}, +05003 \{ -929,-1598,-1188,-1188,-1268\}, +05004 \{ -439,-1108, -698, -698, -778\}, +05005 \{ -789,-1458,-1048,-1048,-1128\}, +05006 \{ -619,-1288, -878, -878, -958\}\}\}, +05007 \textcolor{comment}{/* GC.G@..GC */} +05008 \{\{\{ DEF, -709, -739, -619, -739\}, +05009 \{ -100, -759, -789, -669, -789\}, +05010 \{ -100, -759, -789, -669, -789\}, +05011 \{ -100, -759, -789, -669, -789\}, +05012 \{ -100, -759, -789, -669, -789\}\}, +05013 \textcolor{comment}{/* GC.GA..GC */} +05014 \{\{ DEF, -709, -739, -619, -739\}, +05015 \{ -569,-1228,-1258,-1138,-1258\}, +05016 \{ -769,-1428,-1458,-1338,-1458\}, +05017 \{ -759,-1418,-1448,-1328,-1448\}, +05018 \{ -549,-1208,-1238,-1118,-1238\}\}, +05019 \textcolor{comment}{/* GC.GC..GC */} +05020 \{\{ DEF, -709, -739, -619, -739\}, +05021 \{ -929,-1588,-1618,-1498,-1618\}, +05022 \{ -359,-1018,-1048, -928,-1048\}, +05023 \{ -789,-1448,-1478,-1358,-1478\}, +05024 \{ -549,-1208,-1238,-1118,-1238\}\}, +05025 \textcolor{comment}{/* GC.GG..GC */} +05026 \{\{ DEF, -709, -739, -619, -739\}, +05027 \{ -609,-1268,-1298,-1178,-1298\}, +05028 \{ -359,-1018,-1048, -928,-1048\}, +05029 \{ -669,-1328,-1358,-1238,-1358\}, +05030 \{ -549,-1208,-1238,-1118,-1238\}\}, +05031 \textcolor{comment}{/* GC.GU..GC */} +05032 \{\{ DEF, -709, -739, -619, -739\}, +05033 \{ -929,-1588,-1618,-1498,-1618\}, +05034 \{ -439,-1098,-1128,-1008,-1128\}, +05035 \{ -789,-1448,-1478,-1358,-3080\}, +05036 \{ -619,-1278,-1308,-1188,-1308\}\}\}, +05037 \textcolor{comment}{/* GC.U@..GC */} +05038 \{\{\{ DEF, -499, -499, -499, -569\}, +05039 \{ -100, -549, -549, -549, -619\}, +05040 \{ -100, -549, -549, -549, -619\}, +05041 \{ -100, -549, -549, -549, -619\}, +05042 \{ -100, -549, -549, -549, -619\}\}, +05043 \textcolor{comment}{/* GC.UA..GC */} +05044 \{\{ DEF, -499, -499, -499, -569\}, +05045 \{ -569,-1018,-1018,-1018,-1088\}, +05046 \{ -769,-1218,-1218,-1218,-1288\}, +05047 \{ -759,-1208,-1208,-1208,-1278\}, +05048 \{ -549, -998, -998, -998,-1068\}\}, +05049 \textcolor{comment}{/* GC.UC..GC */} +05050 \{\{ DEF, -499, -499, -499, -569\}, +05051 \{ -929,-1378,-1378,-1378,-1448\}, +05052 \{ -359, -808, -808, -808, -878\}, +05053 \{ -789,-1238,-1238,-1238,-1308\}, +05054 \{ -549, -998, -998, -998,-1068\}\}, +05055 \textcolor{comment}{/* GC.UG..GC */} +05056 \{\{ DEF, -499, -499, -499, -569\}, +05057 \{ -609,-1058,-1058,-1058,-1128\}, +05058 \{ -359, -808, -808, -808, -878\}, +05059 \{ -669,-1118,-1118,-1118,-1188\}, +05060 \{ -549, -998, -998, -998,-1068\}\}, +05061 \textcolor{comment}{/* GC.UU..GC */} +05062 \{\{ DEF, -499, -499, -499, -569\}, +05063 \{ -929,-1378,-1378,-1378,-1448\}, +05064 \{ -439, -888, -888, -888, -958\}, +05065 \{ -789,-1238,-1238,-1238,-1308\}, +05066 \{ -619,-1068,-1068,-1068,-1138\}\}\}\}, +05067 \textcolor{comment}{/* GC.@@..GU */} +05068 \{\{\{\{ 0, 0, 0, 0, 0\}, +05069 \{ DEF, DEF, DEF, DEF, DEF\}, +05070 \{ DEF, DEF, DEF, DEF, DEF\}, +05071 \{ DEF, DEF, DEF, DEF, DEF\}, +05072 \{ DEF, DEF, DEF, DEF, DEF\}\}, +05073 \textcolor{comment}{/* GC.@A..GU */} +05074 \{\{ 0, 0, 0, 0, 0\}, +05075 \{ -429, -429, -429, -429, -429\}, +05076 \{ -259, -259, -259, -259, -259\}, +05077 \{ -339, -339, -339, -339, -339\}, +05078 \{ -329, -329, -329, -329, -329\}\}, +05079 \textcolor{comment}{/* GC.@C..GU */} +05080 \{\{ 0, 0, 0, 0, 0\}, +05081 \{ -599, -599, -599, -599, -599\}, +05082 \{ -239, -239, -239, -239, -239\}, +05083 \{ -689, -689, -689, -689, -689\}, +05084 \{ -329, -329, -329, -329, -329\}\}, +05085 \textcolor{comment}{/* GC.@G..GU */} +05086 \{\{ 0, 0, 0, 0, 0\}, +05087 \{ -599, -599, -599, -599, -599\}, +05088 \{ -239, -239, -239, -239, -239\}, +05089 \{ -689, -689, -689, -689, -689\}, +05090 \{ -329, -329, -329, -329, -329\}\}, +05091 \textcolor{comment}{/* GC.@U..GU */} +05092 \{\{ 0, 0, 0, 0, 0\}, +05093 \{ -599, -599, -599, -599, -599\}, +05094 \{ -239, -239, -239, -239, -239\}, +05095 \{ -689, -689, -689, -689, -689\}, +05096 \{ -329, -329, -329, -329, -329\}\}\}, +05097 \textcolor{comment}{/* GC.A@..GU */} +05098 \{\{\{ DEF, -519, -879, -559, -879\}, +05099 \{ -100, -569, -929, -609, -929\}, +05100 \{ -100, -569, -929, -609, -929\}, +05101 \{ -100, -569, -929, -609, -929\}, +05102 \{ -100, -569, -929, -609, -929\}\}, +05103 \textcolor{comment}{/* GC.AA..GU */} +05104 \{\{ DEF, -519, -879, -559, -879\}, +05105 \{ -479, -948,-1308, -988,-1308\}, +05106 \{ -309, -778,-1138, -818,-1138\}, +05107 \{ -389, -858,-1218, -898,-1218\}, +05108 \{ -379, -848,-1208, -888,-1208\}\}, +05109 \textcolor{comment}{/* GC.AC..GU */} +05110 \{\{ DEF, -519, -879, -559, -879\}, +05111 \{ -649,-1118,-1478,-1158,-1478\}, +05112 \{ -289, -758,-1118, -798,-1118\}, +05113 \{ -739,-1208,-1568,-1248,-1568\}, +05114 \{ -379, -848,-1208, -888,-1208\}\}, +05115 \textcolor{comment}{/* GC.AG..GU */} +05116 \{\{ DEF, -519, -879, -559, -879\}, +05117 \{ -649,-1118,-1478,-1158,-1478\}, +05118 \{ -289, -758,-1118, -798,-1118\}, +05119 \{ -739,-1208,-1568,-1248,-1568\}, +05120 \{ -379, -848,-1208, -888,-1208\}\}, +05121 \textcolor{comment}{/* GC.AU..GU */} +05122 \{\{ DEF, -519, -879, -559, -879\}, +05123 \{ -649,-1118,-1478,-1158,-1478\}, +05124 \{ -289, -758,-1118, -798,-1118\}, +05125 \{ -739,-1208,-1568,-1248,-1568\}, +05126 \{ -379, -848,-1208, -888,-1208\}\}\}, +05127 \textcolor{comment}{/* GC.C@..GU */} +05128 \{\{\{ DEF, -719, -309, -309, -389\}, +05129 \{ -100, -769, -359, -359, -439\}, +05130 \{ -100, -769, -359, -359, -439\}, +05131 \{ -100, -769, -359, -359, -439\}, +05132 \{ -100, -769, -359, -359, -439\}\}, +05133 \textcolor{comment}{/* GC.CA..GU */} +05134 \{\{ DEF, -719, -309, -309, -389\}, +05135 \{ -479,-1148, -738, -738, -818\}, +05136 \{ -309, -978, -568, -568, -648\}, +05137 \{ -389,-1058, -648, -648, -728\}, +05138 \{ -379,-1048, -638, -638, -718\}\}, +05139 \textcolor{comment}{/* GC.CC..GU */} +05140 \{\{ DEF, -719, -309, -309, -389\}, +05141 \{ -649,-1318, -908, -908, -988\}, +05142 \{ -289, -958, -548, -548, -628\}, +05143 \{ -739,-1408, -998, -998,-1078\}, +05144 \{ -379,-1048, -638, -638, -718\}\}, +05145 \textcolor{comment}{/* GC.CG..GU */} +05146 \{\{ DEF, -719, -309, -309, -389\}, +05147 \{ -649,-1318, -908, -908, -988\}, +05148 \{ -289, -958, -548, -548, -628\}, +05149 \{ -739,-1408, -998, -998,-1078\}, +05150 \{ -379,-1048, -638, -638, -718\}\}, +05151 \textcolor{comment}{/* GC.CU..GU */} +05152 \{\{ DEF, -719, -309, -309, -389\}, +05153 \{ -649,-1318, -908, -908, -988\}, +05154 \{ -289, -958, -548, -548, -628\}, +05155 \{ -739,-1408, -998, -998,-1078\}, +05156 \{ -379,-1048, -638, -638, -718\}\}\}, +05157 \textcolor{comment}{/* GC.G@..GU */} +05158 \{\{\{ DEF, -709, -739, -619, -739\}, +05159 \{ -100, -759, -789, -669, -789\}, +05160 \{ -100, -759, -789, -669, -789\}, +05161 \{ -100, -759, -789, -669, -789\}, +05162 \{ -100, -759, -789, -669, -789\}\}, +05163 \textcolor{comment}{/* GC.GA..GU */} +05164 \{\{ DEF, -709, -739, -619, -739\}, +05165 \{ -479,-1138,-1168,-1048,-1168\}, +05166 \{ -309, -968, -998, -878, -998\}, +05167 \{ -389,-1048,-1078, -958,-1078\}, +05168 \{ -379,-1038,-1068, -948,-1068\}\}, +05169 \textcolor{comment}{/* GC.GC..GU */} +05170 \{\{ DEF, -709, -739, -619, -739\}, +05171 \{ -649,-1308,-1338,-1218,-1338\}, +05172 \{ -289, -948, -978, -858, -978\}, +05173 \{ -739,-1398,-1428,-1308,-1428\}, +05174 \{ -379,-1038,-1068, -948,-1068\}\}, +05175 \textcolor{comment}{/* GC.GG..GU */} +05176 \{\{ DEF, -709, -739, -619, -739\}, +05177 \{ -649,-1308,-1338,-1218,-1338\}, +05178 \{ -289, -948, -978, -858, -978\}, +05179 \{ -739,-1398,-1428,-1308,-1428\}, +05180 \{ -379,-1038,-1068, -948,-1068\}\}, +05181 \textcolor{comment}{/* GC.GU..GU */} +05182 \{\{ DEF, -709, -739, -619, -739\}, +05183 \{ -649,-1308,-1338,-1218,-1338\}, +05184 \{ -289, -948, -978, -858, -978\}, +05185 \{ -739,-1398,-1428,-1308,-1428\}, +05186 \{ -379,-1038,-1068, -948,-1068\}\}\}, +05187 \textcolor{comment}{/* GC.U@..GU */} +05188 \{\{\{ DEF, -499, -499, -499, -569\}, +05189 \{ -100, -549, -549, -549, -619\}, +05190 \{ -100, -549, -549, -549, -619\}, +05191 \{ -100, -549, -549, -549, -619\}, +05192 \{ -100, -549, -549, -549, -619\}\}, +05193 \textcolor{comment}{/* GC.UA..GU */} +05194 \{\{ DEF, -499, -499, -499, -569\}, +05195 \{ -479, -928, -928, -928, -998\}, +05196 \{ -309, -758, -758, -758, -828\}, +05197 \{ -389, -838, -838, -838, -908\}, +05198 \{ -379, -828, -828, -828, -898\}\}, +05199 \textcolor{comment}{/* GC.UC..GU */} +05200 \{\{ DEF, -499, -499, -499, -569\}, +05201 \{ -649,-1098,-1098,-1098,-1168\}, +05202 \{ -289, -738, -738, -738, -808\}, +05203 \{ -739,-1188,-1188,-1188,-1258\}, +05204 \{ -379, -828, -828, -828, -898\}\}, +05205 \textcolor{comment}{/* GC.UG..GU */} +05206 \{\{ DEF, -499, -499, -499, -569\}, +05207 \{ -649,-1098,-1098,-1098,-1168\}, +05208 \{ -289, -738, -738, -738, -808\}, +05209 \{ -739,-1188,-1188,-1188,-1258\}, +05210 \{ -379, -828, -828, -828, -898\}\}, +05211 \textcolor{comment}{/* GC.UU..GU */} +05212 \{\{ DEF, -499, -499, -499, -569\}, +05213 \{ -649,-1098,-1098,-1098,-1168\}, +05214 \{ -289, -738, -738, -738, -808\}, +05215 \{ -739,-1188,-1188,-1188,-1258\}, +05216 \{ -379, -828, -828, -828, -898\}\}\}\}, +05217 \textcolor{comment}{/* GC.@@..UG */} +05218 \{\{\{\{ 0, 0, 0, 0, 0\}, +05219 \{ DEF, DEF, DEF, DEF, DEF\}, +05220 \{ DEF, DEF, DEF, DEF, DEF\}, +05221 \{ DEF, DEF, DEF, DEF, DEF\}, +05222 \{ DEF, DEF, DEF, DEF, DEF\}\}, +05223 \textcolor{comment}{/* GC.@A..UG */} +05224 \{\{ 0, 0, 0, 0, 0\}, +05225 \{ -719, -719, -719, -719, -719\}, +05226 \{ -479, -479, -479, -479, -479\}, +05227 \{ -659, -659, -659, -659, -659\}, +05228 \{ -549, -549, -549, -549, -549\}\}, +05229 \textcolor{comment}{/* GC.@C..UG */} +05230 \{\{ 0, 0, 0, 0, 0\}, +05231 \{ -789, -789, -789, -789, -789\}, +05232 \{ -479, -479, -479, -479, -479\}, +05233 \{ -809, -809, -809, -809, -809\}, +05234 \{ -439, -439, -439, -439, -439\}\}, +05235 \textcolor{comment}{/* GC.@G..UG */} +05236 \{\{ 0, 0, 0, 0, 0\}, +05237 \{ -959, -959, -959, -959, -959\}, +05238 \{ -359, -359, -359, -359, -359\}, +05239 \{ -919, -919, -919, -919, -919\}, +05240 \{ -549, -549, -549, -549, -549\}\}, +05241 \textcolor{comment}{/* GC.@U..UG */} +05242 \{\{ 0, 0, 0, 0, 0\}, +05243 \{ -809, -809, -809, -809, -809\}, +05244 \{ -479, -479, -479, -479, -479\}, +05245 \{ -809, -809, -809, -809, -809\}, +05246 \{ -359, -359, -359, -359, -359\}\}\}, +05247 \textcolor{comment}{/* GC.A@..UG */} +05248 \{\{\{ DEF, -519, -879, -559, -879\}, +05249 \{ -100, -569, -929, -609, -929\}, +05250 \{ -100, -569, -929, -609, -929\}, +05251 \{ -100, -569, -929, -609, -929\}, +05252 \{ -100, -569, -929, -609, -929\}\}, +05253 \textcolor{comment}{/* GC.AA..UG */} +05254 \{\{ DEF, -519, -879, -559, -879\}, +05255 \{ -769,-1238,-1598,-1278,-1598\}, +05256 \{ -529, -998,-1358,-1038,-1358\}, +05257 \{ -709,-1178,-1538,-1218,-1538\}, +05258 \{ -599,-1068,-1428,-1108,-1428\}\}, +05259 \textcolor{comment}{/* GC.AC..UG */} +05260 \{\{ DEF, -519, -879, -559, -879\}, +05261 \{ -839,-1308,-1668,-1348,-1668\}, +05262 \{ -529, -998,-1358,-1038,-1358\}, +05263 \{ -859,-1328,-1688,-1368,-1688\}, +05264 \{ -489, -958,-1318, -998,-1318\}\}, +05265 \textcolor{comment}{/* GC.AG..UG */} +05266 \{\{ DEF, -519, -879, -559, -879\}, +05267 \{-1009,-1478,-1838,-1518,-1838\}, +05268 \{ -409, -878,-1238, -918,-1238\}, +05269 \{ -969,-1438,-1798,-1478,-1798\}, +05270 \{ -599,-1068,-1428,-1108,-1428\}\}, +05271 \textcolor{comment}{/* GC.AU..UG */} +05272 \{\{ DEF, -519, -879, -559, -879\}, +05273 \{ -859,-1328,-1688,-1368,-1688\}, +05274 \{ -529, -998,-1358,-1038,-1358\}, +05275 \{ -859,-1328,-1688,-1368,-1688\}, +05276 \{ -409, -878,-1238, -918,-1238\}\}\}, +05277 \textcolor{comment}{/* GC.C@..UG */} +05278 \{\{\{ DEF, -719, -309, -309, -389\}, +05279 \{ -100, -769, -359, -359, -439\}, +05280 \{ -100, -769, -359, -359, -439\}, +05281 \{ -100, -769, -359, -359, -439\}, +05282 \{ -100, -769, -359, -359, -439\}\}, +05283 \textcolor{comment}{/* GC.CA..UG */} +05284 \{\{ DEF, -719, -309, -309, -389\}, +05285 \{ -769,-1438,-1028,-1028,-1108\}, +05286 \{ -529,-1198, -788, -788, -868\}, +05287 \{ -709,-1378, -968, -968,-1048\}, +05288 \{ -599,-1268, -858, -858, -938\}\}, +05289 \textcolor{comment}{/* GC.CC..UG */} +05290 \{\{ DEF, -719, -309, -309, -389\}, +05291 \{ -839,-1508,-1098,-1098,-1178\}, +05292 \{ -529,-1198, -788, -788, -868\}, +05293 \{ -859,-1528,-1118,-1118,-1198\}, +05294 \{ -489,-1158, -748, -748, -828\}\}, +05295 \textcolor{comment}{/* GC.CG..UG */} +05296 \{\{ DEF, -719, -309, -309, -389\}, +05297 \{-1009,-1678,-1268,-1268,-1348\}, +05298 \{ -409,-1078, -668, -668, -748\}, +05299 \{ -969,-1638,-1228,-1228,-1308\}, +05300 \{ -599,-1268, -858, -858, -938\}\}, +05301 \textcolor{comment}{/* GC.CU..UG */} +05302 \{\{ DEF, -719, -309, -309, -389\}, +05303 \{ -859,-1528,-1118,-1118,-1198\}, +05304 \{ -529,-1198, -788, -788, -868\}, +05305 \{ -859,-1528,-1118,-1118,-1198\}, +05306 \{ -409,-1078, -668, -668, -748\}\}\}, +05307 \textcolor{comment}{/* GC.G@..UG */} +05308 \{\{\{ DEF, -709, -739, -619, -739\}, +05309 \{ -100, -759, -789, -669, -789\}, +05310 \{ -100, -759, -789, -669, -789\}, +05311 \{ -100, -759, -789, -669, -789\}, +05312 \{ -100, -759, -789, -669, -789\}\}, +05313 \textcolor{comment}{/* GC.GA..UG */} +05314 \{\{ DEF, -709, -739, -619, -739\}, +05315 \{ -769,-1428,-1458,-1338,-1458\}, +05316 \{ -529,-1188,-1218,-1098,-1218\}, +05317 \{ -709,-1368,-1398,-1278,-1398\}, +05318 \{ -599,-1258,-1288,-1168,-1288\}\}, +05319 \textcolor{comment}{/* GC.GC..UG */} +05320 \{\{ DEF, -709, -739, -619, -739\}, +05321 \{ -839,-1498,-1528,-1408,-1528\}, +05322 \{ -529,-1188,-1218,-1098,-1218\}, +05323 \{ -859,-1518,-1548,-1428,-1548\}, +05324 \{ -489,-1148,-1178,-1058,-1178\}\}, +05325 \textcolor{comment}{/* GC.GG..UG */} +05326 \{\{ DEF, -709, -739, -619, -739\}, +05327 \{-1009,-1668,-1698,-1578,-1698\}, +05328 \{ -409,-1068,-1098, -978,-1098\}, +05329 \{ -969,-1628,-1658,-1538,-1658\}, +05330 \{ -599,-1258,-1288,-1168,-1288\}\}, +05331 \textcolor{comment}{/* GC.GU..UG */} +05332 \{\{ DEF, -709, -739, -619, -739\}, +05333 \{ -859,-1518,-1548,-1428,-1548\}, +05334 \{ -529,-1188,-1218,-1098,-1218\}, +05335 \{ -859,-1518,-1548,-1428,-1548\}, +05336 \{ -409,-1068,-1098, -978,-1098\}\}\}, +05337 \textcolor{comment}{/* GC.U@..UG */} +05338 \{\{\{ DEF, -499, -499, -499, -569\}, +05339 \{ -100, -549, -549, -549, -619\}, +05340 \{ -100, -549, -549, -549, -619\}, +05341 \{ -100, -549, -549, -549, -619\}, +05342 \{ -100, -549, -549, -549, -619\}\}, +05343 \textcolor{comment}{/* GC.UA..UG */} +05344 \{\{ DEF, -499, -499, -499, -569\}, +05345 \{ -769,-1218,-1218,-1218,-1288\}, +05346 \{ -529, -978, -978, -978,-1048\}, +05347 \{ -709,-1158,-1158,-1158,-1228\}, +05348 \{ -599,-1048,-1048,-1048,-1118\}\}, +05349 \textcolor{comment}{/* GC.UC..UG */} +05350 \{\{ DEF, -499, -499, -499, -569\}, +05351 \{ -839,-1288,-1288,-1288,-1358\}, +05352 \{ -529, -978, -978, -978,-1048\}, +05353 \{ -859,-1308,-1308,-1308,-1378\}, +05354 \{ -489, -938, -938, -938,-1008\}\}, +05355 \textcolor{comment}{/* GC.UG..UG */} +05356 \{\{ DEF, -499, -499, -499, -569\}, +05357 \{-1009,-1458,-1458,-1458,-1528\}, +05358 \{ -409, -858, -858, -858, -928\}, +05359 \{ -969,-1418,-1418,-1418,-1488\}, +05360 \{ -599,-1048,-1048,-1048,-1118\}\}, +05361 \textcolor{comment}{/* GC.UU..UG */} +05362 \{\{ DEF, -499, -499, -499, -569\}, +05363 \{ -859,-1308,-1308,-1308,-1378\}, +05364 \{ -529, -978, -978, -978,-1048\}, +05365 \{ -859,-1308,-1308,-1308,-1378\}, +05366 \{ -409, -858, -858, -858, -928\}\}\}\}, +05367 \textcolor{comment}{/* GC.@@..AU */} +05368 \{\{\{\{ 0, 0, 0, 0, 0\}, +05369 \{ DEF, DEF, DEF, DEF, DEF\}, +05370 \{ DEF, DEF, DEF, DEF, DEF\}, +05371 \{ DEF, DEF, DEF, DEF, DEF\}, +05372 \{ DEF, DEF, DEF, DEF, DEF\}\}, +05373 \textcolor{comment}{/* GC.@A..AU */} +05374 \{\{ 0, 0, 0, 0, 0\}, +05375 \{ -429, -429, -429, -429, -429\}, +05376 \{ -259, -259, -259, -259, -259\}, +05377 \{ -339, -339, -339, -339, -339\}, +05378 \{ -329, -329, -329, -329, -329\}\}, +05379 \textcolor{comment}{/* GC.@C..AU */} +05380 \{\{ 0, 0, 0, 0, 0\}, +05381 \{ -599, -599, -599, -599, -599\}, +05382 \{ -239, -239, -239, -239, -239\}, +05383 \{ -689, -689, -689, -689, -689\}, +05384 \{ -329, -329, -329, -329, -329\}\}, +05385 \textcolor{comment}{/* GC.@G..AU */} +05386 \{\{ 0, 0, 0, 0, 0\}, +05387 \{ -599, -599, -599, -599, -599\}, +05388 \{ -239, -239, -239, -239, -239\}, +05389 \{ -689, -689, -689, -689, -689\}, +05390 \{ -329, -329, -329, -329, -329\}\}, +05391 \textcolor{comment}{/* GC.@U..AU */} +05392 \{\{ 0, 0, 0, 0, 0\}, +05393 \{ -599, -599, -599, -599, -599\}, +05394 \{ -239, -239, -239, -239, -239\}, +05395 \{ -689, -689, -689, -689, -689\}, +05396 \{ -329, -329, -329, -329, -329\}\}\}, +05397 \textcolor{comment}{/* GC.A@..AU */} +05398 \{\{\{ DEF, -519, -879, -559, -879\}, +05399 \{ -100, -569, -929, -609, -929\}, +05400 \{ -100, -569, -929, -609, -929\}, +05401 \{ -100, -569, -929, -609, -929\}, +05402 \{ -100, -569, -929, -609, -929\}\}, +05403 \textcolor{comment}{/* GC.AA..AU */} +05404 \{\{ DEF, -519, -879, -559, -879\}, +05405 \{ -479, -948,-1308, -988,-1308\}, +05406 \{ -309, -778,-1138, -818,-1138\}, +05407 \{ -389, -858,-1218, -898,-1218\}, +05408 \{ -379, -848,-1208, -888,-1208\}\}, +05409 \textcolor{comment}{/* GC.AC..AU */} +05410 \{\{ DEF, -519, -879, -559, -879\}, +05411 \{ -649,-1118,-1478,-1158,-1478\}, +05412 \{ -289, -758,-1118, -798,-1118\}, +05413 \{ -739,-1208,-1568,-1248,-1568\}, +05414 \{ -379, -848,-1208, -888,-1208\}\}, +05415 \textcolor{comment}{/* GC.AG..AU */} +05416 \{\{ DEF, -519, -879, -559, -879\}, +05417 \{ -649,-1118,-1478,-1158,-1478\}, +05418 \{ -289, -758,-1118, -798,-1118\}, +05419 \{ -739,-1208,-1568,-1248,-1568\}, +05420 \{ -379, -848,-1208, -888,-1208\}\}, +05421 \textcolor{comment}{/* GC.AU..AU */} +05422 \{\{ DEF, -519, -879, -559, -879\}, +05423 \{ -649,-1118,-1478,-1158,-1478\}, +05424 \{ -289, -758,-1118, -798,-1118\}, +05425 \{ -739,-1208,-1568,-1248,-1568\}, +05426 \{ -379, -848,-1208, -888,-1208\}\}\}, +05427 \textcolor{comment}{/* GC.C@..AU */} +05428 \{\{\{ DEF, -719, -309, -309, -389\}, +05429 \{ -100, -769, -359, -359, -439\}, +05430 \{ -100, -769, -359, -359, -439\}, +05431 \{ -100, -769, -359, -359, -439\}, +05432 \{ -100, -769, -359, -359, -439\}\}, +05433 \textcolor{comment}{/* GC.CA..AU */} +05434 \{\{ DEF, -719, -309, -309, -389\}, +05435 \{ -479,-1148, -738, -738, -818\}, +05436 \{ -309, -978, -568, -568, -648\}, +05437 \{ -389,-1058, -648, -648, -728\}, +05438 \{ -379,-1048, -638, -638, -718\}\}, +05439 \textcolor{comment}{/* GC.CC..AU */} +05440 \{\{ DEF, -719, -309, -309, -389\}, +05441 \{ -649,-1318, -908, -908, -988\}, +05442 \{ -289, -958, -548, -548, -628\}, +05443 \{ -739,-1408, -998, -998,-1078\}, +05444 \{ -379,-1048, -638, -638, -718\}\}, +05445 \textcolor{comment}{/* GC.CG..AU */} +05446 \{\{ DEF, -719, -309, -309, -389\}, +05447 \{ -649,-1318, -908, -908, -988\}, +05448 \{ -289, -958, -548, -548, -628\}, +05449 \{ -739,-1408, -998, -998,-1078\}, +05450 \{ -379,-1048, -638, -638, -718\}\}, +05451 \textcolor{comment}{/* GC.CU..AU */} +05452 \{\{ DEF, -719, -309, -309, -389\}, +05453 \{ -649,-1318, -908, -908, -988\}, +05454 \{ -289, -958, -548, -548, -628\}, +05455 \{ -739,-1408, -998, -998,-1078\}, +05456 \{ -379,-1048, -638, -638, -718\}\}\}, +05457 \textcolor{comment}{/* GC.G@..AU */} +05458 \{\{\{ DEF, -709, -739, -619, -739\}, +05459 \{ -100, -759, -789, -669, -789\}, +05460 \{ -100, -759, -789, -669, -789\}, +05461 \{ -100, -759, -789, -669, -789\}, +05462 \{ -100, -759, -789, -669, -789\}\}, +05463 \textcolor{comment}{/* GC.GA..AU */} +05464 \{\{ DEF, -709, -739, -619, -739\}, +05465 \{ -479,-1138,-1168,-1048,-1168\}, +05466 \{ -309, -968, -998, -878, -998\}, +05467 \{ -389,-1048,-1078, -958,-1078\}, +05468 \{ -379,-1038,-1068, -948,-1068\}\}, +05469 \textcolor{comment}{/* GC.GC..AU */} +05470 \{\{ DEF, -709, -739, -619, -739\}, +05471 \{ -649,-1308,-1338,-1218,-1338\}, +05472 \{ -289, -948, -978, -858, -978\}, +05473 \{ -739,-1398,-1428,-1308,-1428\}, +05474 \{ -379,-1038,-1068, -948,-1068\}\}, +05475 \textcolor{comment}{/* GC.GG..AU */} +05476 \{\{ DEF, -709, -739, -619, -739\}, +05477 \{ -649,-1308,-1338,-1218,-1338\}, +05478 \{ -289, -948, -978, -858, -978\}, +05479 \{ -739,-1398,-1428,-1308,-1428\}, +05480 \{ -379,-1038,-1068, -948,-1068\}\}, +05481 \textcolor{comment}{/* GC.GU..AU */} +05482 \{\{ DEF, -709, -739, -619, -739\}, +05483 \{ -649,-1308,-1338,-1218,-1338\}, +05484 \{ -289, -948, -978, -858, -978\}, +05485 \{ -739,-1398,-1428,-1308,-1428\}, +05486 \{ -379,-1038,-1068, -948,-1068\}\}\}, +05487 \textcolor{comment}{/* GC.U@..AU */} +05488 \{\{\{ DEF, -499, -499, -499, -569\}, +05489 \{ -100, -549, -549, -549, -619\}, +05490 \{ -100, -549, -549, -549, -619\}, +05491 \{ -100, -549, -549, -549, -619\}, +05492 \{ -100, -549, -549, -549, -619\}\}, +05493 \textcolor{comment}{/* GC.UA..AU */} +05494 \{\{ DEF, -499, -499, -499, -569\}, +05495 \{ -479, -928, -928, -928, -998\}, +05496 \{ -309, -758, -758, -758, -828\}, +05497 \{ -389, -838, -838, -838, -908\}, +05498 \{ -379, -828, -828, -828, -898\}\}, +05499 \textcolor{comment}{/* GC.UC..AU */} +05500 \{\{ DEF, -499, -499, -499, -569\}, +05501 \{ -649,-1098,-1098,-1098,-1168\}, +05502 \{ -289, -738, -738, -738, -808\}, +05503 \{ -739,-1188,-1188,-1188,-1258\}, +05504 \{ -379, -828, -828, -828, -898\}\}, +05505 \textcolor{comment}{/* GC.UG..AU */} +05506 \{\{ DEF, -499, -499, -499, -569\}, +05507 \{ -649,-1098,-1098,-1098,-1168\}, +05508 \{ -289, -738, -738, -738, -808\}, +05509 \{ -739,-1188,-1188,-1188,-1258\}, +05510 \{ -379, -828, -828, -828, -898\}\}, +05511 \textcolor{comment}{/* GC.UU..AU */} +05512 \{\{ DEF, -499, -499, -499, -569\}, +05513 \{ -649,-1098,-1098,-1098,-1168\}, +05514 \{ -289, -738, -738, -738, -808\}, +05515 \{ -739,-1188,-1188,-1188,-1258\}, +05516 \{ -379, -828, -828, -828, -898\}\}\}\}, +05517 \textcolor{comment}{/* GC.@@..UA */} +05518 \{\{\{\{ 0, 0, 0, 0, 0\}, +05519 \{ DEF, DEF, DEF, DEF, DEF\}, +05520 \{ DEF, DEF, DEF, DEF, DEF\}, +05521 \{ DEF, DEF, DEF, DEF, DEF\}, +05522 \{ DEF, DEF, DEF, DEF, DEF\}\}, +05523 \textcolor{comment}{/* GC.@A..UA */} +05524 \{\{ 0, 0, 0, 0, 0\}, +05525 \{ -399, -399, -399, -399, -399\}, +05526 \{ -429, -429, -429, -429, -429\}, +05527 \{ -379, -379, -379, -379, -379\}, +05528 \{ -279, -279, -279, -279, -279\}\}, +05529 \textcolor{comment}{/* GC.@C..UA */} +05530 \{\{ 0, 0, 0, 0, 0\}, +05531 \{ -629, -629, -629, -629, -629\}, +05532 \{ -509, -509, -509, -509, -509\}, +05533 \{ -679, -679, -679, -679, -679\}, +05534 \{ -139, -139, -139, -139, -139\}\}, +05535 \textcolor{comment}{/* GC.@G..UA */} +05536 \{\{ 0, 0, 0, 0, 0\}, +05537 \{ -889, -889, -889, -889, -889\}, +05538 \{ -199, -199, -199, -199, -199\}, +05539 \{ -889, -889, -889, -889, -889\}, +05540 \{ -279, -279, -279, -279, -279\}\}, +05541 \textcolor{comment}{/* GC.@U..UA */} +05542 \{\{ 0, 0, 0, 0, 0\}, +05543 \{ -589, -589, -589, -589, -589\}, +05544 \{ -179, -179, -179, -179, -179\}, +05545 \{ -679, -679, -679, -679, -679\}, +05546 \{ -140, -140, -140, -140, -140\}\}\}, +05547 \textcolor{comment}{/* GC.A@..UA */} +05548 \{\{\{ DEF, -519, -879, -559, -879\}, +05549 \{ -100, -569, -929, -609, -929\}, +05550 \{ -100, -569, -929, -609, -929\}, +05551 \{ -100, -569, -929, -609, -929\}, +05552 \{ -100, -569, -929, -609, -929\}\}, +05553 \textcolor{comment}{/* GC.AA..UA */} +05554 \{\{ DEF, -519, -879, -559, -879\}, +05555 \{ -449, -918,-1278, -958,-1278\}, +05556 \{ -479, -948,-1308, -988,-1308\}, +05557 \{ -429, -898,-1258, -938,-1258\}, +05558 \{ -329, -798,-1158, -838,-1158\}\}, +05559 \textcolor{comment}{/* GC.AC..UA */} +05560 \{\{ DEF, -519, -879, -559, -879\}, +05561 \{ -679,-1148,-1508,-1188,-1508\}, +05562 \{ -559,-1028,-1388,-1068,-1388\}, +05563 \{ -729,-1198,-1558,-1238,-1558\}, +05564 \{ -189, -658,-1018, -698,-1018\}\}, +05565 \textcolor{comment}{/* GC.AG..UA */} +05566 \{\{ DEF, -519, -879, -559, -879\}, +05567 \{ -939,-1408,-1768,-1448,-1768\}, +05568 \{ -249, -718,-1078, -758,-1078\}, +05569 \{ -939,-1408,-1768,-1448,-1768\}, +05570 \{ -329, -798,-1158, -838,-1158\}\}, +05571 \textcolor{comment}{/* GC.AU..UA */} +05572 \{\{ DEF, -519, -879, -559, -879\}, +05573 \{ -639,-1108,-1468,-1148,-1468\}, +05574 \{ -229, -698,-1058, -738,-1058\}, +05575 \{ -729,-1198,-1558,-1238,-1558\}, +05576 \{ -190, -659,-1019, -699,-1019\}\}\}, +05577 \textcolor{comment}{/* GC.C@..UA */} +05578 \{\{\{ DEF, -719, -309, -309, -389\}, +05579 \{ -100, -769, -359, -359, -439\}, +05580 \{ -100, -769, -359, -359, -439\}, +05581 \{ -100, -769, -359, -359, -439\}, +05582 \{ -100, -769, -359, -359, -439\}\}, +05583 \textcolor{comment}{/* GC.CA..UA */} +05584 \{\{ DEF, -719, -309, -309, -389\}, +05585 \{ -449,-1118, -708, -708, -788\}, +05586 \{ -479,-1148, -738, -738, -818\}, +05587 \{ -429,-1098, -688, -688, -768\}, +05588 \{ -329, -998, -588, -588, -668\}\}, +05589 \textcolor{comment}{/* GC.CC..UA */} +05590 \{\{ DEF, -719, -309, -309, -389\}, +05591 \{ -679,-1348, -938, -938,-1018\}, +05592 \{ -559,-1228, -818, -818, -898\}, +05593 \{ -729,-1398, -988, -988,-1068\}, +05594 \{ -189, -858, -448, -448, -528\}\}, +05595 \textcolor{comment}{/* GC.CG..UA */} +05596 \{\{ DEF, -719, -309, -309, -389\}, +05597 \{ -939,-1608,-1198,-1198,-1278\}, +05598 \{ -249, -918, -508, -508, -588\}, +05599 \{ -939,-1608,-1198,-1198,-1278\}, +05600 \{ -329, -998, -588, -588, -668\}\}, +05601 \textcolor{comment}{/* GC.CU..UA */} +05602 \{\{ DEF, -719, -309, -309, -389\}, +05603 \{ -639,-1308, -898, -898, -978\}, +05604 \{ -229, -898, -488, -488, -568\}, +05605 \{ -729,-1398, -988, -988,-1068\}, +05606 \{ -190, -859, -449, -449, -529\}\}\}, +05607 \textcolor{comment}{/* GC.G@..UA */} +05608 \{\{\{ DEF, -709, -739, -619, -739\}, +05609 \{ -100, -759, -789, -669, -789\}, +05610 \{ -100, -759, -789, -669, -789\}, +05611 \{ -100, -759, -789, -669, -789\}, +05612 \{ -100, -759, -789, -669, -789\}\}, +05613 \textcolor{comment}{/* GC.GA..UA */} +05614 \{\{ DEF, -709, -739, -619, -739\}, +05615 \{ -449,-1108,-1138,-1018,-1138\}, +05616 \{ -479,-1138,-1168,-1048,-1168\}, +05617 \{ -429,-1088,-1118, -998,-1118\}, +05618 \{ -329, -988,-1018, -898,-1018\}\}, +05619 \textcolor{comment}{/* GC.GC..UA */} +05620 \{\{ DEF, -709, -739, -619, -739\}, +05621 \{ -679,-1338,-1368,-1248,-1368\}, +05622 \{ -559,-1218,-1248,-1128,-1248\}, +05623 \{ -729,-1388,-1418,-1298,-1418\}, +05624 \{ -189, -848, -878, -758, -878\}\}, +05625 \textcolor{comment}{/* GC.GG..UA */} +05626 \{\{ DEF, -709, -739, -619, -739\}, +05627 \{ -939,-1598,-1628,-1508,-1628\}, +05628 \{ -249, -908, -938, -818, -938\}, +05629 \{ -939,-1598,-1628,-1508,-1628\}, +05630 \{ -329, -988,-1018, -898,-1018\}\}, +05631 \textcolor{comment}{/* GC.GU..UA */} +05632 \{\{ DEF, -709, -739, -619, -739\}, +05633 \{ -639,-1298,-1328,-1208,-1328\}, +05634 \{ -229, -888, -918, -798, -918\}, +05635 \{ -729,-1388,-1418,-1298,-1418\}, +05636 \{ -190, -849, -879, -759, -879\}\}\}, +05637 \textcolor{comment}{/* GC.U@..UA */} +05638 \{\{\{ DEF, -499, -499, -499, -569\}, +05639 \{ -100, -549, -549, -549, -619\}, +05640 \{ -100, -549, -549, -549, -619\}, +05641 \{ -100, -549, -549, -549, -619\}, +05642 \{ -100, -549, -549, -549, -619\}\}, +05643 \textcolor{comment}{/* GC.UA..UA */} +05644 \{\{ DEF, -499, -499, -499, -569\}, +05645 \{ -449, -898, -898, -898, -968\}, +05646 \{ -479, -928, -928, -928, -998\}, +05647 \{ -429, -878, -878, -878, -948\}, +05648 \{ -329, -778, -778, -778, -848\}\}, +05649 \textcolor{comment}{/* GC.UC..UA */} +05650 \{\{ DEF, -499, -499, -499, -569\}, +05651 \{ -679,-1128,-1128,-1128,-1198\}, +05652 \{ -559,-1008,-1008,-1008,-1078\}, +05653 \{ -729,-1178,-1178,-1178,-1248\}, +05654 \{ -189, -638, -638, -638, -708\}\}, +05655 \textcolor{comment}{/* GC.UG..UA */} +05656 \{\{ DEF, -499, -499, -499, -569\}, +05657 \{ -939,-1388,-1388,-1388,-1458\}, +05658 \{ -249, -698, -698, -698, -768\}, +05659 \{ -939,-1388,-1388,-1388,-1458\}, +05660 \{ -329, -778, -778, -778, -848\}\}, +05661 \textcolor{comment}{/* GC.UU..UA */} +05662 \{\{ DEF, -499, -499, -499, -569\}, +05663 \{ -639,-1088,-1088,-1088,-1158\}, +05664 \{ -229, -678, -678, -678, -748\}, +05665 \{ -729,-1178,-1178,-1178,-1248\}, +05666 \{ -190, -639, -639, -639, -709\}\}\}\}, +05667 \textcolor{comment}{/* GC.@@.. @ */} +05668 \{\{\{\{ DEF, DEF, DEF, DEF, DEF\}, +05669 \{ DEF, DEF, DEF, DEF, DEF\}, +05670 \{ DEF, DEF, DEF, DEF, DEF\}, +05671 \{ DEF, DEF, DEF, DEF, DEF\}, +05672 \{ DEF, DEF, DEF, DEF, DEF\}\}, +05673 \textcolor{comment}{/* GC.@A.. @ */} +05674 \{\{ DEF, DEF, DEF, DEF, DEF\}, +05675 \{ DEF, DEF, DEF, DEF, DEF\}, +05676 \{ DEF, DEF, DEF, DEF, DEF\}, +05677 \{ DEF, DEF, DEF, DEF, DEF\}, +05678 \{ DEF, DEF, DEF, DEF, DEF\}\}, +05679 \textcolor{comment}{/* GC.@C.. @ */} +05680 \{\{ DEF, DEF, DEF, DEF, DEF\}, +05681 \{ DEF, DEF, DEF, DEF, DEF\}, +05682 \{ DEF, DEF, DEF, DEF, DEF\}, +05683 \{ DEF, DEF, DEF, DEF, DEF\}, +05684 \{ DEF, DEF, DEF, DEF, DEF\}\}, +05685 \textcolor{comment}{/* GC.@G.. @ */} +05686 \{\{ DEF, DEF, DEF, DEF, DEF\}, +05687 \{ DEF, DEF, DEF, DEF, DEF\}, +05688 \{ DEF, DEF, DEF, DEF, DEF\}, +05689 \{ DEF, DEF, DEF, DEF, DEF\}, +05690 \{ DEF, DEF, DEF, DEF, DEF\}\}, +05691 \textcolor{comment}{/* GC.@U.. @ */} +05692 \{\{ DEF, DEF, DEF, DEF, DEF\}, +05693 \{ DEF, DEF, DEF, DEF, DEF\}, +05694 \{ DEF, DEF, DEF, DEF, DEF\}, +05695 \{ DEF, DEF, DEF, DEF, DEF\}, +05696 \{ DEF, DEF, DEF, DEF, DEF\}\}\}, +05697 \textcolor{comment}{/* GC.A@.. @ */} +05698 \{\{\{ -100, -569, -929, -609, -929\}, +05699 \{ -100, -569, -929, -609, -929\}, +05700 \{ -100, -569, -929, -609, -929\}, +05701 \{ -100, -569, -929, -609, -929\}, +05702 \{ -100, -569, -929, -609, -929\}\}, +05703 \textcolor{comment}{/* GC.AA.. @ */} +05704 \{\{ -100, -569, -929, -609, -929\}, +05705 \{ -100, -569, -929, -609, -929\}, +05706 \{ -100, -569, -929, -609, -929\}, +05707 \{ -100, -569, -929, -609, -929\}, +05708 \{ -100, -569, -929, -609, -929\}\}, +05709 \textcolor{comment}{/* GC.AC.. @ */} +05710 \{\{ -100, -569, -929, -609, -929\}, +05711 \{ -100, -569, -929, -609, -929\}, +05712 \{ -100, -569, -929, -609, -929\}, +05713 \{ -100, -569, -929, -609, -929\}, +05714 \{ -100, -569, -929, -609, -929\}\}, +05715 \textcolor{comment}{/* GC.AG.. @ */} +05716 \{\{ -100, -569, -929, -609, -929\}, +05717 \{ -100, -569, -929, -609, -929\}, +05718 \{ -100, -569, -929, -609, -929\}, +05719 \{ -100, -569, -929, -609, -929\}, +05720 \{ -100, -569, -929, -609, -929\}\}, +05721 \textcolor{comment}{/* GC.AU.. @ */} +05722 \{\{ -100, -569, -929, -609, -929\}, +05723 \{ -100, -569, -929, -609, -929\}, +05724 \{ -100, -569, -929, -609, -929\}, +05725 \{ -100, -569, -929, -609, -929\}, +05726 \{ -100, -569, -929, -609, -929\}\}\}, +05727 \textcolor{comment}{/* GC.C@.. @ */} +05728 \{\{\{ -100, -769, -359, -359, -439\}, +05729 \{ -100, -769, -359, -359, -439\}, +05730 \{ -100, -769, -359, -359, -439\}, +05731 \{ -100, -769, -359, -359, -439\}, +05732 \{ -100, -769, -359, -359, -439\}\}, +05733 \textcolor{comment}{/* GC.CA.. @ */} +05734 \{\{ -100, -769, -359, -359, -439\}, +05735 \{ -100, -769, -359, -359, -439\}, +05736 \{ -100, -769, -359, -359, -439\}, +05737 \{ -100, -769, -359, -359, -439\}, +05738 \{ -100, -769, -359, -359, -439\}\}, +05739 \textcolor{comment}{/* GC.CC.. @ */} +05740 \{\{ -100, -769, -359, -359, -439\}, +05741 \{ -100, -769, -359, -359, -439\}, +05742 \{ -100, -769, -359, -359, -439\}, +05743 \{ -100, -769, -359, -359, -439\}, +05744 \{ -100, -769, -359, -359, -439\}\}, +05745 \textcolor{comment}{/* GC.CG.. @ */} +05746 \{\{ -100, -769, -359, -359, -439\}, +05747 \{ -100, -769, -359, -359, -439\}, +05748 \{ -100, -769, -359, -359, -439\}, +05749 \{ -100, -769, -359, -359, -439\}, +05750 \{ -100, -769, -359, -359, -439\}\}, +05751 \textcolor{comment}{/* GC.CU.. @ */} +05752 \{\{ -100, -769, -359, -359, -439\}, +05753 \{ -100, -769, -359, -359, -439\}, +05754 \{ -100, -769, -359, -359, -439\}, +05755 \{ -100, -769, -359, -359, -439\}, +05756 \{ -100, -769, -359, -359, -439\}\}\}, +05757 \textcolor{comment}{/* GC.G@.. @ */} +05758 \{\{\{ -100, -759, -789, -669, -789\}, +05759 \{ -100, -759, -789, -669, -789\}, +05760 \{ -100, -759, -789, -669, -789\}, +05761 \{ -100, -759, -789, -669, -789\}, +05762 \{ -100, -759, -789, -669, -789\}\}, +05763 \textcolor{comment}{/* GC.GA.. @ */} +05764 \{\{ -100, -759, -789, -669, -789\}, +05765 \{ -100, -759, -789, -669, -789\}, +05766 \{ -100, -759, -789, -669, -789\}, +05767 \{ -100, -759, -789, -669, -789\}, +05768 \{ -100, -759, -789, -669, -789\}\}, +05769 \textcolor{comment}{/* GC.GC.. @ */} +05770 \{\{ -100, -759, -789, -669, -789\}, +05771 \{ -100, -759, -789, -669, -789\}, +05772 \{ -100, -759, -789, -669, -789\}, +05773 \{ -100, -759, -789, -669, -789\}, +05774 \{ -100, -759, -789, -669, -789\}\}, +05775 \textcolor{comment}{/* GC.GG.. @ */} +05776 \{\{ -100, -759, -789, -669, -789\}, +05777 \{ -100, -759, -789, -669, -789\}, +05778 \{ -100, -759, -789, -669, -789\}, +05779 \{ -100, -759, -789, -669, -789\}, +05780 \{ -100, -759, -789, -669, -789\}\}, +05781 \textcolor{comment}{/* GC.GU.. @ */} +05782 \{\{ -100, -759, -789, -669, -789\}, +05783 \{ -100, -759, -789, -669, -789\}, +05784 \{ -100, -759, -789, -669, -789\}, +05785 \{ -100, -759, -789, -669, -789\}, +05786 \{ -100, -759, -789, -669, -789\}\}\}, +05787 \textcolor{comment}{/* GC.U@.. @ */} +05788 \{\{\{ -100, -549, -549, -549, -619\}, +05789 \{ -100, -549, -549, -549, -619\}, +05790 \{ -100, -549, -549, -549, -619\}, +05791 \{ -100, -549, -549, -549, -619\}, +05792 \{ -100, -549, -549, -549, -619\}\}, +05793 \textcolor{comment}{/* GC.UA.. @ */} +05794 \{\{ -100, -549, -549, -549, -619\}, +05795 \{ -100, -549, -549, -549, -619\}, +05796 \{ -100, -549, -549, -549, -619\}, +05797 \{ -100, -549, -549, -549, -619\}, +05798 \{ -100, -549, -549, -549, -619\}\}, +05799 \textcolor{comment}{/* GC.UC.. @ */} +05800 \{\{ -100, -549, -549, -549, -619\}, +05801 \{ -100, -549, -549, -549, -619\}, +05802 \{ -100, -549, -549, -549, -619\}, +05803 \{ -100, -549, -549, -549, -619\}, +05804 \{ -100, -549, -549, -549, -619\}\}, +05805 \textcolor{comment}{/* GC.UG.. @ */} +05806 \{\{ -100, -549, -549, -549, -619\}, +05807 \{ -100, -549, -549, -549, -619\}, +05808 \{ -100, -549, -549, -549, -619\}, +05809 \{ -100, -549, -549, -549, -619\}, +05810 \{ -100, -549, -549, -549, -619\}\}, +05811 \textcolor{comment}{/* GC.UU.. @ */} +05812 \{\{ -100, -549, -549, -549, -619\}, +05813 \{ -100, -549, -549, -549, -619\}, +05814 \{ -100, -549, -549, -549, -619\}, +05815 \{ -100, -549, -549, -549, -619\}, +05816 \{ -100, -549, -549, -549, -619\}\}\}\}\}, +05817 \{ \textcolor{comment}{/* noPair */} \{\{\{\{0\}\}\}\}, +05818 \textcolor{comment}{/* GU.@@..CG */} +05819 \{\{\{\{ 0, 0, 0, 0, 0\}, +05820 \{ DEF, DEF, DEF, DEF, DEF\}, +05821 \{ DEF, DEF, DEF, DEF, DEF\}, +05822 \{ DEF, DEF, DEF, DEF, DEF\}, +05823 \{ DEF, DEF, DEF, DEF, DEF\}\}, +05824 \textcolor{comment}{/* GU.@A..CG */} +05825 \{\{ 0, 0, 0, 0, 0\}, +05826 \{-1029,-1029,-1029,-1029,-1029\}, +05827 \{ -519, -519, -519, -519, -519\}, +05828 \{ -939, -939, -939, -939, -939\}, +05829 \{ -809, -809, -809, -809, -809\}\}, +05830 \textcolor{comment}{/* GU.@C..CG */} +05831 \{\{ 0, 0, 0, 0, 0\}, +05832 \{ -949, -949, -949, -949, -949\}, +05833 \{ -449, -449, -449, -449, -449\}, +05834 \{ -939, -939, -939, -939, -939\}, +05835 \{ -739, -739, -739, -739, -739\}\}, +05836 \textcolor{comment}{/* GU.@G..CG */} +05837 \{\{ 0, 0, 0, 0, 0\}, +05838 \{-1029,-1029,-1029,-1029,-1029\}, +05839 \{ -519, -519, -519, -519, -519\}, +05840 \{ -939, -939, -939, -939, -939\}, +05841 \{ -809, -809, -809, -809, -809\}\}, +05842 \textcolor{comment}{/* GU.@U..CG */} +05843 \{\{ 0, 0, 0, 0, 0\}, +05844 \{-1029,-1029,-1029,-1029,-1029\}, +05845 \{ -669, -669, -669, -669, -669\}, +05846 \{ -939, -939, -939, -939, -939\}, +05847 \{ -859, -859, -859, -859, -859\}\}\}, +05848 \textcolor{comment}{/* GU.A@..CG */} +05849 \{\{\{ DEF, -429, -599, -599, -599\}, +05850 \{ -100, -479, -649, -649, -649\}, +05851 \{ -100, -479, -649, -649, -649\}, +05852 \{ -100, -479, -649, -649, -649\}, +05853 \{ -100, -479, -649, -649, -649\}\}, +05854 \textcolor{comment}{/* GU.AA..CG */} +05855 \{\{ DEF, -429, -599, -599, -599\}, +05856 \{-1079,-1458,-1628,-1628,-1628\}, +05857 \{ -569, -948,-1118,-1118,-1118\}, +05858 \{ -989,-1368,-1538,-1538,-1538\}, +05859 \{ -859,-1238,-1408,-1408,-1408\}\}, +05860 \textcolor{comment}{/* GU.AC..CG */} +05861 \{\{ DEF, -429, -599, -599, -599\}, +05862 \{ -999,-1378,-1548,-1548,-1548\}, +05863 \{ -499, -878,-1048,-1048,-1048\}, +05864 \{ -989,-1368,-1538,-1538,-1538\}, +05865 \{ -789,-1168,-1338,-1338,-1338\}\}, +05866 \textcolor{comment}{/* GU.AG..CG */} +05867 \{\{ DEF, -429, -599, -599, -599\}, +05868 \{-1079,-1458,-1628,-1628,-1628\}, +05869 \{ -569, -948,-1118,-1118,-1118\}, +05870 \{ -989,-1368,-1538,-1538,-1538\}, +05871 \{ -859,-1238,-1408,-1408,-1408\}\}, +05872 \textcolor{comment}{/* GU.AU..CG */} +05873 \{\{ DEF, -429, -599, -599, -599\}, +05874 \{-1079,-1458,-1628,-1628,-1628\}, +05875 \{ -719,-1098,-1268,-1268,-1268\}, +05876 \{ -989,-1368,-1538,-1538,-1538\}, +05877 \{ -909,-1288,-1458,-1458,-1458\}\}\}, +05878 \textcolor{comment}{/* GU.C@..CG */} +05879 \{\{\{ DEF, -259, -239, -239, -239\}, +05880 \{ -100, -309, -289, -289, -289\}, +05881 \{ -100, -309, -289, -289, -289\}, +05882 \{ -100, -309, -289, -289, -289\}, +05883 \{ -100, -309, -289, -289, -289\}\}, +05884 \textcolor{comment}{/* GU.CA..CG */} +05885 \{\{ DEF, -259, -239, -239, -239\}, +05886 \{-1079,-1288,-1268,-1268,-1268\}, +05887 \{ -569, -778, -758, -758, -758\}, +05888 \{ -989,-1198,-1178,-1178,-1178\}, +05889 \{ -859,-1068,-1048,-1048,-1048\}\}, +05890 \textcolor{comment}{/* GU.CC..CG */} +05891 \{\{ DEF, -259, -239, -239, -239\}, +05892 \{ -999,-1208,-1188,-1188,-1188\}, +05893 \{ -499, -708, -688, -688, -688\}, +05894 \{ -989,-1198,-1178,-1178,-1178\}, +05895 \{ -789, -998, -978, -978, -978\}\}, +05896 \textcolor{comment}{/* GU.CG..CG */} +05897 \{\{ DEF, -259, -239, -239, -239\}, +05898 \{-1079,-1288,-1268,-1268,-1268\}, +05899 \{ -569, -778, -758, -758, -758\}, +05900 \{ -989,-1198,-1178,-1178,-1178\}, +05901 \{ -859,-1068,-1048,-1048,-1048\}\}, +05902 \textcolor{comment}{/* GU.CU..CG */} +05903 \{\{ DEF, -259, -239, -239, -239\}, +05904 \{-1079,-1288,-1268,-1268,-1268\}, +05905 \{ -719, -928, -908, -908, -908\}, +05906 \{ -989,-1198,-1178,-1178,-1178\}, +05907 \{ -909,-1118,-1098,-1098,-1098\}\}\}, +05908 \textcolor{comment}{/* GU.G@..CG */} +05909 \{\{\{ DEF, -339, -689, -689, -689\}, +05910 \{ -100, -389, -739, -739, -739\}, +05911 \{ -100, -389, -739, -739, -739\}, +05912 \{ -100, -389, -739, -739, -739\}, +05913 \{ -100, -389, -739, -739, -739\}\}, +05914 \textcolor{comment}{/* GU.GA..CG */} +05915 \{\{ DEF, -339, -689, -689, -689\}, +05916 \{-1079,-1368,-1718,-1718,-1718\}, +05917 \{ -569, -858,-1208,-1208,-1208\}, +05918 \{ -989,-1278,-1628,-1628,-1628\}, +05919 \{ -859,-1148,-1498,-1498,-1498\}\}, +05920 \textcolor{comment}{/* GU.GC..CG */} +05921 \{\{ DEF, -339, -689, -689, -689\}, +05922 \{ -999,-1288,-1638,-1638,-1638\}, +05923 \{ -499, -788,-1138,-1138,-1138\}, +05924 \{ -989,-1278,-1628,-1628,-1628\}, +05925 \{ -789,-1078,-1428,-1428,-1428\}\}, +05926 \textcolor{comment}{/* GU.GG..CG */} +05927 \{\{ DEF, -339, -689, -689, -689\}, +05928 \{-1079,-1368,-1718,-1718,-1718\}, +05929 \{ -569, -858,-1208,-1208,-1208\}, +05930 \{ -989,-1278,-1628,-1628,-1628\}, +05931 \{ -859,-1148,-1498,-1498,-1498\}\}, +05932 \textcolor{comment}{/* GU.GU..CG */} +05933 \{\{ DEF, -339, -689, -689, -689\}, +05934 \{-1079,-1368,-1718,-1718,-1718\}, +05935 \{ -719,-1008,-1358,-1358,-1358\}, +05936 \{ -989,-1278,-1628,-1628,-1628\}, +05937 \{ -909,-1198,-1548,-1548,-1548\}\}\}, +05938 \textcolor{comment}{/* GU.U@..CG */} +05939 \{\{\{ DEF, -329, -329, -329, -329\}, +05940 \{ -100, -379, -379, -379, -379\}, +05941 \{ -100, -379, -379, -379, -379\}, +05942 \{ -100, -379, -379, -379, -379\}, +05943 \{ -100, -379, -379, -379, -379\}\}, +05944 \textcolor{comment}{/* GU.UA..CG */} +05945 \{\{ DEF, -329, -329, -329, -329\}, +05946 \{-1079,-1358,-1358,-1358,-1358\}, +05947 \{ -569, -848, -848, -848, -848\}, +05948 \{ -989,-1268,-1268,-1268,-1268\}, +05949 \{ -859,-1138,-1138,-1138,-1138\}\}, +05950 \textcolor{comment}{/* GU.UC..CG */} +05951 \{\{ DEF, -329, -329, -329, -329\}, +05952 \{ -999,-1278,-1278,-1278,-1278\}, +05953 \{ -499, -778, -778, -778, -778\}, +05954 \{ -989,-1268,-1268,-1268,-1268\}, +05955 \{ -789,-1068,-1068,-1068,-1068\}\}, +05956 \textcolor{comment}{/* GU.UG..CG */} +05957 \{\{ DEF, -329, -329, -329, -329\}, +05958 \{-1079,-1358,-1358,-1358,-1358\}, +05959 \{ -569, -848, -848, -848, -848\}, +05960 \{ -989,-1268,-1268,-1268,-1268\}, +05961 \{ -859,-1138,-1138,-1138,-1138\}\}, +05962 \textcolor{comment}{/* GU.UU..CG */} +05963 \{\{ DEF, -329, -329, -329, -329\}, +05964 \{-1079,-1358,-1358,-1358,-1358\}, +05965 \{ -719, -998, -998, -998, -998\}, +05966 \{ -989,-1268,-1268,-1268,-1268\}, +05967 \{ -909,-1188,-1188,-1188,-1188\}\}\}\}, +05968 \textcolor{comment}{/* GU.@@..GC */} +05969 \{\{\{\{ 0, 0, 0, 0, 0\}, +05970 \{ DEF, DEF, DEF, DEF, DEF\}, +05971 \{ DEF, DEF, DEF, DEF, DEF\}, +05972 \{ DEF, DEF, DEF, DEF, DEF\}, +05973 \{ DEF, DEF, DEF, DEF, DEF\}\}, +05974 \textcolor{comment}{/* GU.@A..GC */} +05975 \{\{ 0, 0, 0, 0, 0\}, +05976 \{ -519, -519, -519, -519, -519\}, +05977 \{ -719, -719, -719, -719, -719\}, +05978 \{ -709, -709, -709, -709, -709\}, +05979 \{ -499, -499, -499, -499, -499\}\}, +05980 \textcolor{comment}{/* GU.@C..GC */} +05981 \{\{ 0, 0, 0, 0, 0\}, +05982 \{ -879, -879, -879, -879, -879\}, +05983 \{ -309, -309, -309, -309, -309\}, +05984 \{ -739, -739, -739, -739, -739\}, +05985 \{ -499, -499, -499, -499, -499\}\}, +05986 \textcolor{comment}{/* GU.@G..GC */} +05987 \{\{ 0, 0, 0, 0, 0\}, +05988 \{ -559, -559, -559, -559, -559\}, +05989 \{ -309, -309, -309, -309, -309\}, +05990 \{ -619, -619, -619, -619, -619\}, +05991 \{ -499, -499, -499, -499, -499\}\}, +05992 \textcolor{comment}{/* GU.@U..GC */} +05993 \{\{ 0, 0, 0, 0, 0\}, +05994 \{ -879, -879, -879, -879, -879\}, +05995 \{ -389, -389, -389, -389, -389\}, +05996 \{ -739, -739, -739, -739, -739\}, +05997 \{ -569, -569, -569, -569, -569\}\}\}, +05998 \textcolor{comment}{/* GU.A@..GC */} +05999 \{\{\{ DEF, -429, -599, -599, -599\}, +06000 \{ -100, -479, -649, -649, -649\}, +06001 \{ -100, -479, -649, -649, -649\}, +06002 \{ -100, -479, -649, -649, -649\}, +06003 \{ -100, -479, -649, -649, -649\}\}, +06004 \textcolor{comment}{/* GU.AA..GC */} +06005 \{\{ DEF, -429, -599, -599, -599\}, +06006 \{ -569, -948,-1118,-1118,-1118\}, +06007 \{ -769,-1148,-1318,-1318,-1318\}, +06008 \{ -759,-1138,-1308,-1308,-1308\}, +06009 \{ -549, -928,-1098,-1098,-1098\}\}, +06010 \textcolor{comment}{/* GU.AC..GC */} +06011 \{\{ DEF, -429, -599, -599, -599\}, +06012 \{ -929,-1308,-1478,-1478,-1478\}, +06013 \{ -359, -738, -908, -908, -908\}, +06014 \{ -789,-1168,-1338,-1338,-1338\}, +06015 \{ -549, -928,-1098,-1098,-1098\}\}, +06016 \textcolor{comment}{/* GU.AG..GC */} +06017 \{\{ DEF, -429, -599, -599, -599\}, +06018 \{ -609, -988,-1158,-1158,-1158\}, +06019 \{ -359, -738, -908, -908, -908\}, +06020 \{ -669,-1048,-1218,-1218,-1218\}, +06021 \{ -549, -928,-1098,-1098,-1098\}\}, +06022 \textcolor{comment}{/* GU.AU..GC */} +06023 \{\{ DEF, -429, -599, -599, -599\}, +06024 \{ -929,-1308,-1478,-1478,-1478\}, +06025 \{ -439, -818, -988, -988, -988\}, +06026 \{ -789,-1168,-1338,-1338,-1338\}, +06027 \{ -619, -998,-1168,-1168,-1168\}\}\}, +06028 \textcolor{comment}{/* GU.C@..GC */} +06029 \{\{\{ DEF, -259, -239, -239, -239\}, +06030 \{ -100, -309, -289, -289, -289\}, +06031 \{ -100, -309, -289, -289, -289\}, +06032 \{ -100, -309, -289, -289, -289\}, +06033 \{ -100, -309, -289, -289, -289\}\}, +06034 \textcolor{comment}{/* GU.CA..GC */} +06035 \{\{ DEF, -259, -239, -239, -239\}, +06036 \{ -569, -778, -758, -758, -758\}, +06037 \{ -769, -978, -958, -958, -958\}, +06038 \{ -759, -968, -948, -948, -948\}, +06039 \{ -549, -758, -738, -738, -738\}\}, +06040 \textcolor{comment}{/* GU.CC..GC */} +06041 \{\{ DEF, -259, -239, -239, -239\}, +06042 \{ -929,-1138,-1118,-1118,-1118\}, +06043 \{ -359, -568, -548, -548, -548\}, +06044 \{ -789, -998, -978, -978, -978\}, +06045 \{ -549, -758, -738, -738, -738\}\}, +06046 \textcolor{comment}{/* GU.CG..GC */} +06047 \{\{ DEF, -259, -239, -239, -239\}, +06048 \{ -609, -818, -798, -798, -798\}, +06049 \{ -359, -568, -548, -548, -548\}, +06050 \{ -669, -878, -858, -858, -858\}, +06051 \{ -549, -758, -738, -738, -738\}\}, +06052 \textcolor{comment}{/* GU.CU..GC */} +06053 \{\{ DEF, -259, -239, -239, -239\}, +06054 \{ -929,-1138,-1118,-1118,-1118\}, +06055 \{ -439, -648, -628, -628, -628\}, +06056 \{ -789, -998, -978, -978, -978\}, +06057 \{ -619, -828, -808, -808, -808\}\}\}, +06058 \textcolor{comment}{/* GU.G@..GC */} +06059 \{\{\{ DEF, -339, -689, -689, -689\}, +06060 \{ -100, -389, -739, -739, -739\}, +06061 \{ -100, -389, -739, -739, -739\}, +06062 \{ -100, -389, -739, -739, -739\}, +06063 \{ -100, -389, -739, -739, -739\}\}, +06064 \textcolor{comment}{/* GU.GA..GC */} +06065 \{\{ DEF, -339, -689, -689, -689\}, +06066 \{ -569, -858,-1208,-1208,-1208\}, +06067 \{ -769,-1058,-1408,-1408,-1408\}, +06068 \{ -759,-1048,-1398,-1398,-1398\}, +06069 \{ -549, -838,-1188,-1188,-1188\}\}, +06070 \textcolor{comment}{/* GU.GC..GC */} +06071 \{\{ DEF, -339, -689, -689, -689\}, +06072 \{ -929,-1218,-1568,-1568,-1568\}, +06073 \{ -359, -648, -998, -998, -998\}, +06074 \{ -789,-1078,-1428,-1428,-1428\}, +06075 \{ -549, -838,-1188,-1188,-1188\}\}, +06076 \textcolor{comment}{/* GU.GG..GC */} +06077 \{\{ DEF, -339, -689, -689, -689\}, +06078 \{ -609, -898,-1248,-1248,-1248\}, +06079 \{ -359, -648, -998, -998, -998\}, +06080 \{ -669, -958,-1308,-1308,-1308\}, +06081 \{ -549, -838,-1188,-1188,-1188\}\}, +06082 \textcolor{comment}{/* GU.GU..GC */} +06083 \{\{ DEF, -339, -689, -689, -689\}, +06084 \{ -929,-1218,-1568,-1568,-1568\}, +06085 \{ -439, -728,-1078,-1078,-1078\}, +06086 \{ -789,-1078,-1428,-1428,-1428\}, +06087 \{ -619, -908,-1258,-1258,-1258\}\}\}, +06088 \textcolor{comment}{/* GU.U@..GC */} +06089 \{\{\{ DEF, -329, -329, -329, -329\}, +06090 \{ -100, -379, -379, -379, -379\}, +06091 \{ -100, -379, -379, -379, -379\}, +06092 \{ -100, -379, -379, -379, -379\}, +06093 \{ -100, -379, -379, -379, -379\}\}, +06094 \textcolor{comment}{/* GU.UA..GC */} +06095 \{\{ DEF, -329, -329, -329, -329\}, +06096 \{ -569, -848, -848, -848, -848\}, +06097 \{ -769,-1048,-1048,-1048,-1048\}, +06098 \{ -759,-1038,-1038,-1038,-1038\}, +06099 \{ -549, -828, -828, -828, -828\}\}, +06100 \textcolor{comment}{/* GU.UC..GC */} +06101 \{\{ DEF, -329, -329, -329, -329\}, +06102 \{ -929,-1208,-1208,-1208,-1208\}, +06103 \{ -359, -638, -638, -638, -638\}, +06104 \{ -789,-1068,-1068,-1068,-1068\}, +06105 \{ -549, -828, -828, -828, -828\}\}, +06106 \textcolor{comment}{/* GU.UG..GC */} +06107 \{\{ DEF, -329, -329, -329, -329\}, +06108 \{ -609, -888, -888, -888, -888\}, +06109 \{ -359, -638, -638, -638, -638\}, +06110 \{ -669, -948, -948, -948, -948\}, +06111 \{ -549, -828, -828, -828, -828\}\}, +06112 \textcolor{comment}{/* GU.UU..GC */} +06113 \{\{ DEF, -329, -329, -329, -329\}, +06114 \{ -929,-1208,-1208,-1208,-1208\}, +06115 \{ -439, -718, -718, -718, -718\}, +06116 \{ -789,-1068,-1068,-1068,-1068\}, +06117 \{ -619, -898, -898, -898, -898\}\}\}\}, +06118 \textcolor{comment}{/* GU.@@..GU */} +06119 \{\{\{\{ 0, 0, 0, 0, 0\}, +06120 \{ DEF, DEF, DEF, DEF, DEF\}, +06121 \{ DEF, DEF, DEF, DEF, DEF\}, +06122 \{ DEF, DEF, DEF, DEF, DEF\}, +06123 \{ DEF, DEF, DEF, DEF, DEF\}\}, +06124 \textcolor{comment}{/* GU.@A..GU */} +06125 \{\{ 0, 0, 0, 0, 0\}, +06126 \{ -429, -429, -429, -429, -429\}, +06127 \{ -259, -259, -259, -259, -259\}, +06128 \{ -339, -339, -339, -339, -339\}, +06129 \{ -329, -329, -329, -329, -329\}\}, +06130 \textcolor{comment}{/* GU.@C..GU */} +06131 \{\{ 0, 0, 0, 0, 0\}, +06132 \{ -599, -599, -599, -599, -599\}, +06133 \{ -239, -239, -239, -239, -239\}, +06134 \{ -689, -689, -689, -689, -689\}, +06135 \{ -329, -329, -329, -329, -329\}\}, +06136 \textcolor{comment}{/* GU.@G..GU */} +06137 \{\{ 0, 0, 0, 0, 0\}, +06138 \{ -599, -599, -599, -599, -599\}, +06139 \{ -239, -239, -239, -239, -239\}, +06140 \{ -689, -689, -689, -689, -689\}, +06141 \{ -329, -329, -329, -329, -329\}\}, +06142 \textcolor{comment}{/* GU.@U..GU */} +06143 \{\{ 0, 0, 0, 0, 0\}, +06144 \{ -599, -599, -599, -599, -599\}, +06145 \{ -239, -239, -239, -239, -239\}, +06146 \{ -689, -689, -689, -689, -689\}, +06147 \{ -329, -329, -329, -329, -329\}\}\}, +06148 \textcolor{comment}{/* GU.A@..GU */} +06149 \{\{\{ DEF, -429, -599, -599, -599\}, +06150 \{ -100, -479, -649, -649, -649\}, +06151 \{ -100, -479, -649, -649, -649\}, +06152 \{ -100, -479, -649, -649, -649\}, +06153 \{ -100, -479, -649, -649, -649\}\}, +06154 \textcolor{comment}{/* GU.AA..GU */} +06155 \{\{ DEF, -429, -599, -599, -599\}, +06156 \{ -479, -858,-1028,-1028,-1028\}, +06157 \{ -309, -688, -858, -858, -858\}, +06158 \{ -389, -768, -938, -938, -938\}, +06159 \{ -379, -758, -928, -928, -928\}\}, +06160 \textcolor{comment}{/* GU.AC..GU */} +06161 \{\{ DEF, -429, -599, -599, -599\}, +06162 \{ -649,-1028,-1198,-1198,-1198\}, +06163 \{ -289, -668, -838, -838, -838\}, +06164 \{ -739,-1118,-1288,-1288,-1288\}, +06165 \{ -379, -758, -928, -928, -928\}\}, +06166 \textcolor{comment}{/* GU.AG..GU */} +06167 \{\{ DEF, -429, -599, -599, -599\}, +06168 \{ -649,-1028,-1198,-1198,-1198\}, +06169 \{ -289, -668, -838, -838, -838\}, +06170 \{ -739,-1118,-1288,-1288,-1288\}, +06171 \{ -379, -758, -928, -928, -928\}\}, +06172 \textcolor{comment}{/* GU.AU..GU */} +06173 \{\{ DEF, -429, -599, -599, -599\}, +06174 \{ -649,-1028,-1198,-1198,-1198\}, +06175 \{ -289, -668, -838, -838, -838\}, +06176 \{ -739,-1118,-1288,-1288,-1288\}, +06177 \{ -379, -758, -928, -928, -928\}\}\}, +06178 \textcolor{comment}{/* GU.C@..GU */} +06179 \{\{\{ DEF, -259, -239, -239, -239\}, +06180 \{ -100, -309, -289, -289, -289\}, +06181 \{ -100, -309, -289, -289, -289\}, +06182 \{ -100, -309, -289, -289, -289\}, +06183 \{ -100, -309, -289, -289, -289\}\}, +06184 \textcolor{comment}{/* GU.CA..GU */} +06185 \{\{ DEF, -259, -239, -239, -239\}, +06186 \{ -479, -688, -668, -668, -668\}, +06187 \{ -309, -518, -498, -498, -498\}, +06188 \{ -389, -598, -578, -578, -578\}, +06189 \{ -379, -588, -568, -568, -568\}\}, +06190 \textcolor{comment}{/* GU.CC..GU */} +06191 \{\{ DEF, -259, -239, -239, -239\}, +06192 \{ -649, -858, -838, -838, -838\}, +06193 \{ -289, -498, -478, -478, -478\}, +06194 \{ -739, -948, -928, -928, -928\}, +06195 \{ -379, -588, -568, -568, -568\}\}, +06196 \textcolor{comment}{/* GU.CG..GU */} +06197 \{\{ DEF, -259, -239, -239, -239\}, +06198 \{ -649, -858, -838, -838, -838\}, +06199 \{ -289, -498, -478, -478, -478\}, +06200 \{ -739, -948, -928, -928, -928\}, +06201 \{ -379, -588, -568, -568, -568\}\}, +06202 \textcolor{comment}{/* GU.CU..GU */} +06203 \{\{ DEF, -259, -239, -239, -239\}, +06204 \{ -649, -858, -838, -838, -838\}, +06205 \{ -289, -498, -478, -478, -478\}, +06206 \{ -739, -948, -928, -928, -928\}, +06207 \{ -379, -588, -568, -568, -568\}\}\}, +06208 \textcolor{comment}{/* GU.G@..GU */} +06209 \{\{\{ DEF, -339, -689, -689, -689\}, +06210 \{ -100, -389, -739, -739, -739\}, +06211 \{ -100, -389, -739, -739, -739\}, +06212 \{ -100, -389, -739, -739, -739\}, +06213 \{ -100, -389, -739, -739, -739\}\}, +06214 \textcolor{comment}{/* GU.GA..GU */} +06215 \{\{ DEF, -339, -689, -689, -689\}, +06216 \{ -479, -768,-1118,-1118,-1118\}, +06217 \{ -309, -598, -948, -948, -948\}, +06218 \{ -389, -678,-1028,-1028,-1028\}, +06219 \{ -379, -668,-1018,-1018,-1018\}\}, +06220 \textcolor{comment}{/* GU.GC..GU */} +06221 \{\{ DEF, -339, -689, -689, -689\}, +06222 \{ -649, -938,-1288,-1288,-1288\}, +06223 \{ -289, -578, -928, -928, -928\}, +06224 \{ -739,-1028,-1378,-1378,-1378\}, +06225 \{ -379, -668,-1018,-1018,-1018\}\}, +06226 \textcolor{comment}{/* GU.GG..GU */} +06227 \{\{ DEF, -339, -689, -689, -689\}, +06228 \{ -649, -938,-1288,-1288,-1288\}, +06229 \{ -289, -578, -928, -928, -928\}, +06230 \{ -739,-1028,-1378,-1378,-1378\}, +06231 \{ -379, -668,-1018,-1018,-1018\}\}, +06232 \textcolor{comment}{/* GU.GU..GU */} +06233 \{\{ DEF, -339, -689, -689, -689\}, +06234 \{ -649, -938,-1288,-1288,-1288\}, +06235 \{ -289, -578, -928, -928, -928\}, +06236 \{ -739,-1028,-1378,-1378,-1378\}, +06237 \{ -379, -668,-1018,-1018,-1018\}\}\}, +06238 \textcolor{comment}{/* GU.U@..GU */} +06239 \{\{\{ DEF, -329, -329, -329, -329\}, +06240 \{ -100, -379, -379, -379, -379\}, +06241 \{ -100, -379, -379, -379, -379\}, +06242 \{ -100, -379, -379, -379, -379\}, +06243 \{ -100, -379, -379, -379, -379\}\}, +06244 \textcolor{comment}{/* GU.UA..GU */} +06245 \{\{ DEF, -329, -329, -329, -329\}, +06246 \{ -479, -758, -758, -758, -758\}, +06247 \{ -309, -588, -588, -588, -588\}, +06248 \{ -389, -668, -668, -668, -668\}, +06249 \{ -379, -658, -658, -658, -658\}\}, +06250 \textcolor{comment}{/* GU.UC..GU */} +06251 \{\{ DEF, -329, -329, -329, -329\}, +06252 \{ -649, -928, -928, -928, -928\}, +06253 \{ -289, -568, -568, -568, -568\}, +06254 \{ -739,-1018,-1018,-1018,-1018\}, +06255 \{ -379, -658, -658, -658, -658\}\}, +06256 \textcolor{comment}{/* GU.UG..GU */} +06257 \{\{ DEF, -329, -329, -329, -329\}, +06258 \{ -649, -928, -928, -928, -928\}, +06259 \{ -289, -568, -568, -568, -568\}, +06260 \{ -739,-1018,-1018,-1018,-1018\}, +06261 \{ -379, -658, -658, -658, -658\}\}, +06262 \textcolor{comment}{/* GU.UU..GU */} +06263 \{\{ DEF, -329, -329, -329, -329\}, +06264 \{ -649, -928, -928, -928, -928\}, +06265 \{ -289, -568, -568, -568, -568\}, +06266 \{ -739,-1018,-1018,-1018,-1018\}, +06267 \{ -379, -658, -658, -658, -658\}\}\}\}, +06268 \textcolor{comment}{/* GU.@@..UG */} +06269 \{\{\{\{ 0, 0, 0, 0, 0\}, +06270 \{ DEF, DEF, DEF, DEF, DEF\}, +06271 \{ DEF, DEF, DEF, DEF, DEF\}, +06272 \{ DEF, DEF, DEF, DEF, DEF\}, +06273 \{ DEF, DEF, DEF, DEF, DEF\}\}, +06274 \textcolor{comment}{/* GU.@A..UG */} +06275 \{\{ 0, 0, 0, 0, 0\}, +06276 \{ -719, -719, -719, -719, -719\}, +06277 \{ -479, -479, -479, -479, -479\}, +06278 \{ -659, -659, -659, -659, -659\}, +06279 \{ -549, -549, -549, -549, -549\}\}, +06280 \textcolor{comment}{/* GU.@C..UG */} +06281 \{\{ 0, 0, 0, 0, 0\}, +06282 \{ -789, -789, -789, -789, -789\}, +06283 \{ -479, -479, -479, -479, -479\}, +06284 \{ -809, -809, -809, -809, -809\}, +06285 \{ -439, -439, -439, -439, -439\}\}, +06286 \textcolor{comment}{/* GU.@G..UG */} +06287 \{\{ 0, 0, 0, 0, 0\}, +06288 \{ -959, -959, -959, -959, -959\}, +06289 \{ -359, -359, -359, -359, -359\}, +06290 \{ -919, -919, -919, -919, -919\}, +06291 \{ -549, -549, -549, -549, -549\}\}, +06292 \textcolor{comment}{/* GU.@U..UG */} +06293 \{\{ 0, 0, 0, 0, 0\}, +06294 \{ -809, -809, -809, -809, -809\}, +06295 \{ -479, -479, -479, -479, -479\}, +06296 \{ -809, -809, -809, -809, -809\}, +06297 \{ -359, -359, -359, -359, -359\}\}\}, +06298 \textcolor{comment}{/* GU.A@..UG */} +06299 \{\{\{ DEF, -429, -599, -599, -599\}, +06300 \{ -100, -479, -649, -649, -649\}, +06301 \{ -100, -479, -649, -649, -649\}, +06302 \{ -100, -479, -649, -649, -649\}, +06303 \{ -100, -479, -649, -649, -649\}\}, +06304 \textcolor{comment}{/* GU.AA..UG */} +06305 \{\{ DEF, -429, -599, -599, -599\}, +06306 \{ -769,-1148,-1318,-1318,-1318\}, +06307 \{ -529, -908,-1078,-1078,-1078\}, +06308 \{ -709,-1088,-1258,-1258,-1258\}, +06309 \{ -599, -978,-1148,-1148,-1148\}\}, +06310 \textcolor{comment}{/* GU.AC..UG */} +06311 \{\{ DEF, -429, -599, -599, -599\}, +06312 \{ -839,-1218,-1388,-1388,-1388\}, +06313 \{ -529, -908,-1078,-1078,-1078\}, +06314 \{ -859,-1238,-1408,-1408,-1408\}, +06315 \{ -489, -868,-1038,-1038,-1038\}\}, +06316 \textcolor{comment}{/* GU.AG..UG */} +06317 \{\{ DEF, -429, -599, -599, -599\}, +06318 \{-1009,-1388,-1558,-1558,-1558\}, +06319 \{ -409, -788, -958, -958, -958\}, +06320 \{ -969,-1348,-1518,-1518,-1518\}, +06321 \{ -599, -978,-1148,-1148,-1148\}\}, +06322 \textcolor{comment}{/* GU.AU..UG */} +06323 \{\{ DEF, -429, -599, -599, -599\}, +06324 \{ -859,-1238,-1408,-1408,-1408\}, +06325 \{ -529, -908,-1078,-1078,-1078\}, +06326 \{ -859,-1238,-1408,-1408,-1408\}, +06327 \{ -409, -788, -958, -958, -958\}\}\}, +06328 \textcolor{comment}{/* GU.C@..UG */} +06329 \{\{\{ DEF, -259, -239, -239, -239\}, +06330 \{ -100, -309, -289, -289, -289\}, +06331 \{ -100, -309, -289, -289, -289\}, +06332 \{ -100, -309, -289, -289, -289\}, +06333 \{ -100, -309, -289, -289, -289\}\}, +06334 \textcolor{comment}{/* GU.CA..UG */} +06335 \{\{ DEF, -259, -239, -239, -239\}, +06336 \{ -769, -978, -958, -958, -958\}, +06337 \{ -529, -738, -718, -718, -718\}, +06338 \{ -709, -918, -898, -898, -898\}, +06339 \{ -599, -808, -788, -788, -788\}\}, +06340 \textcolor{comment}{/* GU.CC..UG */} +06341 \{\{ DEF, -259, -239, -239, -239\}, +06342 \{ -839,-1048,-1028,-1028,-1028\}, +06343 \{ -529, -738, -718, -718, -718\}, +06344 \{ -859,-1068,-1048,-1048,-1048\}, +06345 \{ -489, -698, -678, -678, -678\}\}, +06346 \textcolor{comment}{/* GU.CG..UG */} +06347 \{\{ DEF, -259, -239, -239, -239\}, +06348 \{-1009,-1218,-1198,-1198,-1198\}, +06349 \{ -409, -618, -598, -598, -598\}, +06350 \{ -969,-1178,-1158,-1158,-1158\}, +06351 \{ -599, -808, -788, -788, -788\}\}, +06352 \textcolor{comment}{/* GU.CU..UG */} +06353 \{\{ DEF, -259, -239, -239, -239\}, +06354 \{ -859,-1068,-1048,-1048,-1048\}, +06355 \{ -529, -738, -718, -718, -718\}, +06356 \{ -859,-1068,-1048,-1048,-1048\}, +06357 \{ -409, -618, -598, -598, -598\}\}\}, +06358 \textcolor{comment}{/* GU.G@..UG */} +06359 \{\{\{ DEF, -339, -689, -689, -689\}, +06360 \{ -100, -389, -739, -739, -739\}, +06361 \{ -100, -389, -739, -739, -739\}, +06362 \{ -100, -389, -739, -739, -739\}, +06363 \{ -100, -389, -739, -739, -739\}\}, +06364 \textcolor{comment}{/* GU.GA..UG */} +06365 \{\{ DEF, -339, -689, -689, -689\}, +06366 \{ -769,-1058,-1408,-1408,-1408\}, +06367 \{ -529, -818,-1168,-1168,-1168\}, +06368 \{ -709, -998,-1348,-1348,-1348\}, +06369 \{ -599, -888,-1238,-1238,-1238\}\}, +06370 \textcolor{comment}{/* GU.GC..UG */} +06371 \{\{ DEF, -339, -689, -689, -689\}, +06372 \{ -839,-1128,-1478,-1478,-1478\}, +06373 \{ -529, -818,-1168,-1168,-1168\}, +06374 \{ -859,-1148,-1498,-1498,-1498\}, +06375 \{ -489, -778,-1128,-1128,-1128\}\}, +06376 \textcolor{comment}{/* GU.GG..UG */} +06377 \{\{ DEF, -339, -689, -689, -689\}, +06378 \{-1009,-1298,-1648,-1648,-1648\}, +06379 \{ -409, -698,-1048,-1048,-1048\}, +06380 \{ -969,-1258,-1608,-1608,-1608\}, +06381 \{ -599, -888,-1238,-1238,-1238\}\}, +06382 \textcolor{comment}{/* GU.GU..UG */} +06383 \{\{ DEF, -339, -689, -689, -689\}, +06384 \{ -859,-1148,-1498,-1498,-1498\}, +06385 \{ -529, -818,-1168,-1168,-1168\}, +06386 \{ -859,-1148,-1498,-1498,-1498\}, +06387 \{ -409, -698,-1048,-1048,-1048\}\}\}, +06388 \textcolor{comment}{/* GU.U@..UG */} +06389 \{\{\{ DEF, -329, -329, -329, -329\}, +06390 \{ -100, -379, -379, -379, -379\}, +06391 \{ -100, -379, -379, -379, -379\}, +06392 \{ -100, -379, -379, -379, -379\}, +06393 \{ -100, -379, -379, -379, -379\}\}, +06394 \textcolor{comment}{/* GU.UA..UG */} +06395 \{\{ DEF, -329, -329, -329, -329\}, +06396 \{ -769,-1048,-1048,-1048,-1048\}, +06397 \{ -529, -808, -808, -808, -808\}, +06398 \{ -709, -988, -988, -988, -988\}, +06399 \{ -599, -878, -878, -878, -878\}\}, +06400 \textcolor{comment}{/* GU.UC..UG */} +06401 \{\{ DEF, -329, -329, -329, -329\}, +06402 \{ -839,-1118,-1118,-1118,-1118\}, +06403 \{ -529, -808, -808, -808, -808\}, +06404 \{ -859,-1138,-1138,-1138,-1138\}, +06405 \{ -489, -768, -768, -768, -768\}\}, +06406 \textcolor{comment}{/* GU.UG..UG */} +06407 \{\{ DEF, -329, -329, -329, -329\}, +06408 \{-1009,-1288,-1288,-1288,-1288\}, +06409 \{ -409, -688, -688, -688, -688\}, +06410 \{ -969,-1248,-1248,-1248,-1248\}, +06411 \{ -599, -878, -878, -878, -878\}\}, +06412 \textcolor{comment}{/* GU.UU..UG */} +06413 \{\{ DEF, -329, -329, -329, -329\}, +06414 \{ -859,-1138,-1138,-1138,-1138\}, +06415 \{ -529, -808, -808, -808, -808\}, +06416 \{ -859,-1138,-1138,-1138,-1138\}, +06417 \{ -409, -688, -688, -688, -688\}\}\}\}, +06418 \textcolor{comment}{/* GU.@@..AU */} +06419 \{\{\{\{ 0, 0, 0, 0, 0\}, +06420 \{ DEF, DEF, DEF, DEF, DEF\}, +06421 \{ DEF, DEF, DEF, DEF, DEF\}, +06422 \{ DEF, DEF, DEF, DEF, DEF\}, +06423 \{ DEF, DEF, DEF, DEF, DEF\}\}, +06424 \textcolor{comment}{/* GU.@A..AU */} +06425 \{\{ 0, 0, 0, 0, 0\}, +06426 \{ -429, -429, -429, -429, -429\}, +06427 \{ -259, -259, -259, -259, -259\}, +06428 \{ -339, -339, -339, -339, -339\}, +06429 \{ -329, -329, -329, -329, -329\}\}, +06430 \textcolor{comment}{/* GU.@C..AU */} +06431 \{\{ 0, 0, 0, 0, 0\}, +06432 \{ -599, -599, -599, -599, -599\}, +06433 \{ -239, -239, -239, -239, -239\}, +06434 \{ -689, -689, -689, -689, -689\}, +06435 \{ -329, -329, -329, -329, -329\}\}, +06436 \textcolor{comment}{/* GU.@G..AU */} +06437 \{\{ 0, 0, 0, 0, 0\}, +06438 \{ -599, -599, -599, -599, -599\}, +06439 \{ -239, -239, -239, -239, -239\}, +06440 \{ -689, -689, -689, -689, -689\}, +06441 \{ -329, -329, -329, -329, -329\}\}, +06442 \textcolor{comment}{/* GU.@U..AU */} +06443 \{\{ 0, 0, 0, 0, 0\}, +06444 \{ -599, -599, -599, -599, -599\}, +06445 \{ -239, -239, -239, -239, -239\}, +06446 \{ -689, -689, -689, -689, -689\}, +06447 \{ -329, -329, -329, -329, -329\}\}\}, +06448 \textcolor{comment}{/* GU.A@..AU */} +06449 \{\{\{ DEF, -429, -599, -599, -599\}, +06450 \{ -100, -479, -649, -649, -649\}, +06451 \{ -100, -479, -649, -649, -649\}, +06452 \{ -100, -479, -649, -649, -649\}, +06453 \{ -100, -479, -649, -649, -649\}\}, +06454 \textcolor{comment}{/* GU.AA..AU */} +06455 \{\{ DEF, -429, -599, -599, -599\}, +06456 \{ -479, -858,-1028,-1028,-1028\}, +06457 \{ -309, -688, -858, -858, -858\}, +06458 \{ -389, -768, -938, -938, -938\}, +06459 \{ -379, -758, -928, -928, -928\}\}, +06460 \textcolor{comment}{/* GU.AC..AU */} +06461 \{\{ DEF, -429, -599, -599, -599\}, +06462 \{ -649,-1028,-1198,-1198,-1198\}, +06463 \{ -289, -668, -838, -838, -838\}, +06464 \{ -739,-1118,-1288,-1288,-1288\}, +06465 \{ -379, -758, -928, -928, -928\}\}, +06466 \textcolor{comment}{/* GU.AG..AU */} +06467 \{\{ DEF, -429, -599, -599, -599\}, +06468 \{ -649,-1028,-1198,-1198,-1198\}, +06469 \{ -289, -668, -838, -838, -838\}, +06470 \{ -739,-1118,-1288,-1288,-1288\}, +06471 \{ -379, -758, -928, -928, -928\}\}, +06472 \textcolor{comment}{/* GU.AU..AU */} +06473 \{\{ DEF, -429, -599, -599, -599\}, +06474 \{ -649,-1028,-1198,-1198,-1198\}, +06475 \{ -289, -668, -838, -838, -838\}, +06476 \{ -739,-1118,-1288,-1288,-1288\}, +06477 \{ -379, -758, -928, -928, -928\}\}\}, +06478 \textcolor{comment}{/* GU.C@..AU */} +06479 \{\{\{ DEF, -259, -239, -239, -239\}, +06480 \{ -100, -309, -289, -289, -289\}, +06481 \{ -100, -309, -289, -289, -289\}, +06482 \{ -100, -309, -289, -289, -289\}, +06483 \{ -100, -309, -289, -289, -289\}\}, +06484 \textcolor{comment}{/* GU.CA..AU */} +06485 \{\{ DEF, -259, -239, -239, -239\}, +06486 \{ -479, -688, -668, -668, -668\}, +06487 \{ -309, -518, -498, -498, -498\}, +06488 \{ -389, -598, -578, -578, -578\}, +06489 \{ -379, -588, -568, -568, -568\}\}, +06490 \textcolor{comment}{/* GU.CC..AU */} +06491 \{\{ DEF, -259, -239, -239, -239\}, +06492 \{ -649, -858, -838, -838, -838\}, +06493 \{ -289, -498, -478, -478, -478\}, +06494 \{ -739, -948, -928, -928, -928\}, +06495 \{ -379, -588, -568, -568, -568\}\}, +06496 \textcolor{comment}{/* GU.CG..AU */} +06497 \{\{ DEF, -259, -239, -239, -239\}, +06498 \{ -649, -858, -838, -838, -838\}, +06499 \{ -289, -498, -478, -478, -478\}, +06500 \{ -739, -948, -928, -928, -928\}, +06501 \{ -379, -588, -568, -568, -568\}\}, +06502 \textcolor{comment}{/* GU.CU..AU */} +06503 \{\{ DEF, -259, -239, -239, -239\}, +06504 \{ -649, -858, -838, -838, -838\}, +06505 \{ -289, -498, -478, -478, -478\}, +06506 \{ -739, -948, -928, -928, -928\}, +06507 \{ -379, -588, -568, -568, -568\}\}\}, +06508 \textcolor{comment}{/* GU.G@..AU */} +06509 \{\{\{ DEF, -339, -689, -689, -689\}, +06510 \{ -100, -389, -739, -739, -739\}, +06511 \{ -100, -389, -739, -739, -739\}, +06512 \{ -100, -389, -739, -739, -739\}, +06513 \{ -100, -389, -739, -739, -739\}\}, +06514 \textcolor{comment}{/* GU.GA..AU */} +06515 \{\{ DEF, -339, -689, -689, -689\}, +06516 \{ -479, -768,-1118,-1118,-1118\}, +06517 \{ -309, -598, -948, -948, -948\}, +06518 \{ -389, -678,-1028,-1028,-1028\}, +06519 \{ -379, -668,-1018,-1018,-1018\}\}, +06520 \textcolor{comment}{/* GU.GC..AU */} +06521 \{\{ DEF, -339, -689, -689, -689\}, +06522 \{ -649, -938,-1288,-1288,-1288\}, +06523 \{ -289, -578, -928, -928, -928\}, +06524 \{ -739,-1028,-1378,-1378,-1378\}, +06525 \{ -379, -668,-1018,-1018,-1018\}\}, +06526 \textcolor{comment}{/* GU.GG..AU */} +06527 \{\{ DEF, -339, -689, -689, -689\}, +06528 \{ -649, -938,-1288,-1288,-1288\}, +06529 \{ -289, -578, -928, -928, -928\}, +06530 \{ -739,-1028,-1378,-1378,-1378\}, +06531 \{ -379, -668,-1018,-1018,-1018\}\}, +06532 \textcolor{comment}{/* GU.GU..AU */} +06533 \{\{ DEF, -339, -689, -689, -689\}, +06534 \{ -649, -938,-1288,-1288,-1288\}, +06535 \{ -289, -578, -928, -928, -928\}, +06536 \{ -739,-1028,-1378,-1378,-1378\}, +06537 \{ -379, -668,-1018,-1018,-1018\}\}\}, +06538 \textcolor{comment}{/* GU.U@..AU */} +06539 \{\{\{ DEF, -329, -329, -329, -329\}, +06540 \{ -100, -379, -379, -379, -379\}, +06541 \{ -100, -379, -379, -379, -379\}, +06542 \{ -100, -379, -379, -379, -379\}, +06543 \{ -100, -379, -379, -379, -379\}\}, +06544 \textcolor{comment}{/* GU.UA..AU */} +06545 \{\{ DEF, -329, -329, -329, -329\}, +06546 \{ -479, -758, -758, -758, -758\}, +06547 \{ -309, -588, -588, -588, -588\}, +06548 \{ -389, -668, -668, -668, -668\}, +06549 \{ -379, -658, -658, -658, -658\}\}, +06550 \textcolor{comment}{/* GU.UC..AU */} +06551 \{\{ DEF, -329, -329, -329, -329\}, +06552 \{ -649, -928, -928, -928, -928\}, +06553 \{ -289, -568, -568, -568, -568\}, +06554 \{ -739,-1018,-1018,-1018,-1018\}, +06555 \{ -379, -658, -658, -658, -658\}\}, +06556 \textcolor{comment}{/* GU.UG..AU */} +06557 \{\{ DEF, -329, -329, -329, -329\}, +06558 \{ -649, -928, -928, -928, -928\}, +06559 \{ -289, -568, -568, -568, -568\}, +06560 \{ -739,-1018,-1018,-1018,-1018\}, +06561 \{ -379, -658, -658, -658, -658\}\}, +06562 \textcolor{comment}{/* GU.UU..AU */} +06563 \{\{ DEF, -329, -329, -329, -329\}, +06564 \{ -649, -928, -928, -928, -928\}, +06565 \{ -289, -568, -568, -568, -568\}, +06566 \{ -739,-1018,-1018,-1018,-1018\}, +06567 \{ -379, -658, -658, -658, -658\}\}\}\}, +06568 \textcolor{comment}{/* GU.@@..UA */} +06569 \{\{\{\{ 0, 0, 0, 0, 0\}, +06570 \{ DEF, DEF, DEF, DEF, DEF\}, +06571 \{ DEF, DEF, DEF, DEF, DEF\}, +06572 \{ DEF, DEF, DEF, DEF, DEF\}, +06573 \{ DEF, DEF, DEF, DEF, DEF\}\}, +06574 \textcolor{comment}{/* GU.@A..UA */} +06575 \{\{ 0, 0, 0, 0, 0\}, +06576 \{ -399, -399, -399, -399, -399\}, +06577 \{ -429, -429, -429, -429, -429\}, +06578 \{ -379, -379, -379, -379, -379\}, +06579 \{ -279, -279, -279, -279, -279\}\}, +06580 \textcolor{comment}{/* GU.@C..UA */} +06581 \{\{ 0, 0, 0, 0, 0\}, +06582 \{ -629, -629, -629, -629, -629\}, +06583 \{ -509, -509, -509, -509, -509\}, +06584 \{ -679, -679, -679, -679, -679\}, +06585 \{ -139, -139, -139, -139, -139\}\}, +06586 \textcolor{comment}{/* GU.@G..UA */} +06587 \{\{ 0, 0, 0, 0, 0\}, +06588 \{ -889, -889, -889, -889, -889\}, +06589 \{ -199, -199, -199, -199, -199\}, +06590 \{ -889, -889, -889, -889, -889\}, +06591 \{ -279, -279, -279, -279, -279\}\}, +06592 \textcolor{comment}{/* GU.@U..UA */} +06593 \{\{ 0, 0, 0, 0, 0\}, +06594 \{ -589, -589, -589, -589, -589\}, +06595 \{ -179, -179, -179, -179, -179\}, +06596 \{ -679, -679, -679, -679, -679\}, +06597 \{ -140, -140, -140, -140, -140\}\}\}, +06598 \textcolor{comment}{/* GU.A@..UA */} +06599 \{\{\{ DEF, -429, -599, -599, -599\}, +06600 \{ -100, -479, -649, -649, -649\}, +06601 \{ -100, -479, -649, -649, -649\}, +06602 \{ -100, -479, -649, -649, -649\}, +06603 \{ -100, -479, -649, -649, -649\}\}, +06604 \textcolor{comment}{/* GU.AA..UA */} +06605 \{\{ DEF, -429, -599, -599, -599\}, +06606 \{ -449, -828, -998, -998, -998\}, +06607 \{ -479, -858,-1028,-1028,-1028\}, +06608 \{ -429, -808, -978, -978, -978\}, +06609 \{ -329, -708, -878, -878, -878\}\}, +06610 \textcolor{comment}{/* GU.AC..UA */} +06611 \{\{ DEF, -429, -599, -599, -599\}, +06612 \{ -679,-1058,-1228,-1228,-1228\}, +06613 \{ -559, -938,-1108,-1108,-1108\}, +06614 \{ -729,-1108,-1278,-1278,-1278\}, +06615 \{ -189, -568, -738, -738, -738\}\}, +06616 \textcolor{comment}{/* GU.AG..UA */} +06617 \{\{ DEF, -429, -599, -599, -599\}, +06618 \{ -939,-1318,-1488,-1488,-1488\}, +06619 \{ -249, -628, -798, -798, -798\}, +06620 \{ -939,-1318,-1488,-1488,-1488\}, +06621 \{ -329, -708, -878, -878, -878\}\}, +06622 \textcolor{comment}{/* GU.AU..UA */} +06623 \{\{ DEF, -429, -599, -599, -599\}, +06624 \{ -639,-1018,-1188,-1188,-1188\}, +06625 \{ -229, -608, -778, -778, -778\}, +06626 \{ -729,-1108,-1278,-1278,-1278\}, +06627 \{ -190, -569, -739, -739, -739\}\}\}, +06628 \textcolor{comment}{/* GU.C@..UA */} +06629 \{\{\{ DEF, -259, -239, -239, -239\}, +06630 \{ -100, -309, -289, -289, -289\}, +06631 \{ -100, -309, -289, -289, -289\}, +06632 \{ -100, -309, -289, -289, -289\}, +06633 \{ -100, -309, -289, -289, -289\}\}, +06634 \textcolor{comment}{/* GU.CA..UA */} +06635 \{\{ DEF, -259, -239, -239, -239\}, +06636 \{ -449, -658, -638, -638, -638\}, +06637 \{ -479, -688, -668, -668, -668\}, +06638 \{ -429, -638, -618, -618, -618\}, +06639 \{ -329, -538, -518, -518, -518\}\}, +06640 \textcolor{comment}{/* GU.CC..UA */} +06641 \{\{ DEF, -259, -239, -239, -239\}, +06642 \{ -679, -888, -868, -868, -868\}, +06643 \{ -559, -768, -748, -748, -748\}, +06644 \{ -729, -938, -918, -918, -918\}, +06645 \{ -189, -398, -378, -378, -378\}\}, +06646 \textcolor{comment}{/* GU.CG..UA */} +06647 \{\{ DEF, -259, -239, -239, -239\}, +06648 \{ -939,-1148,-1128,-1128,-1128\}, +06649 \{ -249, -458, -438, -438, -438\}, +06650 \{ -939,-1148,-1128,-1128,-1128\}, +06651 \{ -329, -538, -518, -518, -518\}\}, +06652 \textcolor{comment}{/* GU.CU..UA */} +06653 \{\{ DEF, -259, -239, -239, -239\}, +06654 \{ -639, -848, -828, -828, -828\}, +06655 \{ -229, -438, -418, -418, -418\}, +06656 \{ -729, -938, -918, -918, -918\}, +06657 \{ -190, -399, -379, -379, -379\}\}\}, +06658 \textcolor{comment}{/* GU.G@..UA */} +06659 \{\{\{ DEF, -339, -689, -689, -689\}, +06660 \{ -100, -389, -739, -739, -739\}, +06661 \{ -100, -389, -739, -739, -739\}, +06662 \{ -100, -389, -739, -739, -739\}, +06663 \{ -100, -389, -739, -739, -739\}\}, +06664 \textcolor{comment}{/* GU.GA..UA */} +06665 \{\{ DEF, -339, -689, -689, -689\}, +06666 \{ -449, -738,-1088,-1088,-1088\}, +06667 \{ -479, -768,-1118,-1118,-1118\}, +06668 \{ -429, -718,-1068,-1068,-1068\}, +06669 \{ -329, -618, -968, -968, -968\}\}, +06670 \textcolor{comment}{/* GU.GC..UA */} +06671 \{\{ DEF, -339, -689, -689, -689\}, +06672 \{ -679, -968,-1318,-1318,-1318\}, +06673 \{ -559, -848,-1198,-1198,-1198\}, +06674 \{ -729,-1018,-1368,-1368,-1368\}, +06675 \{ -189, -478, -828, -828, -828\}\}, +06676 \textcolor{comment}{/* GU.GG..UA */} +06677 \{\{ DEF, -339, -689, -689, -689\}, +06678 \{ -939,-1228,-1578,-1578,-1578\}, +06679 \{ -249, -538, -888, -888, -888\}, +06680 \{ -939,-1228,-1578,-1578,-1578\}, +06681 \{ -329, -618, -968, -968, -968\}\}, +06682 \textcolor{comment}{/* GU.GU..UA */} +06683 \{\{ DEF, -339, -689, -689, -689\}, +06684 \{ -639, -928,-1278,-1278,-1278\}, +06685 \{ -229, -518, -868, -868, -868\}, +06686 \{ -729,-1018,-1368,-1368,-1368\}, +06687 \{ -190, -479, -829, -829, -829\}\}\}, +06688 \textcolor{comment}{/* GU.U@..UA */} +06689 \{\{\{ DEF, -329, -329, -329, -329\}, +06690 \{ -100, -379, -379, -379, -379\}, +06691 \{ -100, -379, -379, -379, -379\}, +06692 \{ -100, -379, -379, -379, -379\}, +06693 \{ -100, -379, -379, -379, -379\}\}, +06694 \textcolor{comment}{/* GU.UA..UA */} +06695 \{\{ DEF, -329, -329, -329, -329\}, +06696 \{ -449, -728, -728, -728, -728\}, +06697 \{ -479, -758, -758, -758, -758\}, +06698 \{ -429, -708, -708, -708, -708\}, +06699 \{ -329, -608, -608, -608, -608\}\}, +06700 \textcolor{comment}{/* GU.UC..UA */} +06701 \{\{ DEF, -329, -329, -329, -329\}, +06702 \{ -679, -958, -958, -958, -958\}, +06703 \{ -559, -838, -838, -838, -838\}, +06704 \{ -729,-1008,-1008,-1008,-1008\}, +06705 \{ -189, -468, -468, -468, -468\}\}, +06706 \textcolor{comment}{/* GU.UG..UA */} +06707 \{\{ DEF, -329, -329, -329, -329\}, +06708 \{ -939,-1218,-1218,-1218,-1218\}, +06709 \{ -249, -528, -528, -528, -528\}, +06710 \{ -939,-1218,-1218,-1218,-1218\}, +06711 \{ -329, -608, -608, -608, -608\}\}, +06712 \textcolor{comment}{/* GU.UU..UA */} +06713 \{\{ DEF, -329, -329, -329, -329\}, +06714 \{ -639, -918, -918, -918, -918\}, +06715 \{ -229, -508, -508, -508, -508\}, +06716 \{ -729,-1008,-1008,-1008,-1008\}, +06717 \{ -190, -469, -469, -469, -469\}\}\}\}, +06718 \textcolor{comment}{/* GU.@@.. @ */} +06719 \{\{\{\{ DEF, DEF, DEF, DEF, DEF\}, +06720 \{ DEF, DEF, DEF, DEF, DEF\}, +06721 \{ DEF, DEF, DEF, DEF, DEF\}, +06722 \{ DEF, DEF, DEF, DEF, DEF\}, +06723 \{ DEF, DEF, DEF, DEF, DEF\}\}, +06724 \textcolor{comment}{/* GU.@A.. @ */} +06725 \{\{ DEF, DEF, DEF, DEF, DEF\}, +06726 \{ DEF, DEF, DEF, DEF, DEF\}, +06727 \{ DEF, DEF, DEF, DEF, DEF\}, +06728 \{ DEF, DEF, DEF, DEF, DEF\}, +06729 \{ DEF, DEF, DEF, DEF, DEF\}\}, +06730 \textcolor{comment}{/* GU.@C.. @ */} +06731 \{\{ DEF, DEF, DEF, DEF, DEF\}, +06732 \{ DEF, DEF, DEF, DEF, DEF\}, +06733 \{ DEF, DEF, DEF, DEF, DEF\}, +06734 \{ DEF, DEF, DEF, DEF, DEF\}, +06735 \{ DEF, DEF, DEF, DEF, DEF\}\}, +06736 \textcolor{comment}{/* GU.@G.. @ */} +06737 \{\{ DEF, DEF, DEF, DEF, DEF\}, +06738 \{ DEF, DEF, DEF, DEF, DEF\}, +06739 \{ DEF, DEF, DEF, DEF, DEF\}, +06740 \{ DEF, DEF, DEF, DEF, DEF\}, +06741 \{ DEF, DEF, DEF, DEF, DEF\}\}, +06742 \textcolor{comment}{/* GU.@U.. @ */} +06743 \{\{ DEF, DEF, DEF, DEF, DEF\}, +06744 \{ DEF, DEF, DEF, DEF, DEF\}, +06745 \{ DEF, DEF, DEF, DEF, DEF\}, +06746 \{ DEF, DEF, DEF, DEF, DEF\}, +06747 \{ DEF, DEF, DEF, DEF, DEF\}\}\}, +06748 \textcolor{comment}{/* GU.A@.. @ */} +06749 \{\{\{ -100, -479, -649, -649, -649\}, +06750 \{ -100, -479, -649, -649, -649\}, +06751 \{ -100, -479, -649, -649, -649\}, +06752 \{ -100, -479, -649, -649, -649\}, +06753 \{ -100, -479, -649, -649, -649\}\}, +06754 \textcolor{comment}{/* GU.AA.. @ */} +06755 \{\{ -100, -479, -649, -649, -649\}, +06756 \{ -100, -479, -649, -649, -649\}, +06757 \{ -100, -479, -649, -649, -649\}, +06758 \{ -100, -479, -649, -649, -649\}, +06759 \{ -100, -479, -649, -649, -649\}\}, +06760 \textcolor{comment}{/* GU.AC.. @ */} +06761 \{\{ -100, -479, -649, -649, -649\}, +06762 \{ -100, -479, -649, -649, -649\}, +06763 \{ -100, -479, -649, -649, -649\}, +06764 \{ -100, -479, -649, -649, -649\}, +06765 \{ -100, -479, -649, -649, -649\}\}, +06766 \textcolor{comment}{/* GU.AG.. @ */} +06767 \{\{ -100, -479, -649, -649, -649\}, +06768 \{ -100, -479, -649, -649, -649\}, +06769 \{ -100, -479, -649, -649, -649\}, +06770 \{ -100, -479, -649, -649, -649\}, +06771 \{ -100, -479, -649, -649, -649\}\}, +06772 \textcolor{comment}{/* GU.AU.. @ */} +06773 \{\{ -100, -479, -649, -649, -649\}, +06774 \{ -100, -479, -649, -649, -649\}, +06775 \{ -100, -479, -649, -649, -649\}, +06776 \{ -100, -479, -649, -649, -649\}, +06777 \{ -100, -479, -649, -649, -649\}\}\}, +06778 \textcolor{comment}{/* GU.C@.. @ */} +06779 \{\{\{ -100, -309, -289, -289, -289\}, +06780 \{ -100, -309, -289, -289, -289\}, +06781 \{ -100, -309, -289, -289, -289\}, +06782 \{ -100, -309, -289, -289, -289\}, +06783 \{ -100, -309, -289, -289, -289\}\}, +06784 \textcolor{comment}{/* GU.CA.. @ */} +06785 \{\{ -100, -309, -289, -289, -289\}, +06786 \{ -100, -309, -289, -289, -289\}, +06787 \{ -100, -309, -289, -289, -289\}, +06788 \{ -100, -309, -289, -289, -289\}, +06789 \{ -100, -309, -289, -289, -289\}\}, +06790 \textcolor{comment}{/* GU.CC.. @ */} +06791 \{\{ -100, -309, -289, -289, -289\}, +06792 \{ -100, -309, -289, -289, -289\}, +06793 \{ -100, -309, -289, -289, -289\}, +06794 \{ -100, -309, -289, -289, -289\}, +06795 \{ -100, -309, -289, -289, -289\}\}, +06796 \textcolor{comment}{/* GU.CG.. @ */} +06797 \{\{ -100, -309, -289, -289, -289\}, +06798 \{ -100, -309, -289, -289, -289\}, +06799 \{ -100, -309, -289, -289, -289\}, +06800 \{ -100, -309, -289, -289, -289\}, +06801 \{ -100, -309, -289, -289, -289\}\}, +06802 \textcolor{comment}{/* GU.CU.. @ */} +06803 \{\{ -100, -309, -289, -289, -289\}, +06804 \{ -100, -309, -289, -289, -289\}, +06805 \{ -100, -309, -289, -289, -289\}, +06806 \{ -100, -309, -289, -289, -289\}, +06807 \{ -100, -309, -289, -289, -289\}\}\}, +06808 \textcolor{comment}{/* GU.G@.. @ */} +06809 \{\{\{ -100, -389, -739, -739, -739\}, +06810 \{ -100, -389, -739, -739, -739\}, +06811 \{ -100, -389, -739, -739, -739\}, +06812 \{ -100, -389, -739, -739, -739\}, +06813 \{ -100, -389, -739, -739, -739\}\}, +06814 \textcolor{comment}{/* GU.GA.. @ */} +06815 \{\{ -100, -389, -739, -739, -739\}, +06816 \{ -100, -389, -739, -739, -739\}, +06817 \{ -100, -389, -739, -739, -739\}, +06818 \{ -100, -389, -739, -739, -739\}, +06819 \{ -100, -389, -739, -739, -739\}\}, +06820 \textcolor{comment}{/* GU.GC.. @ */} +06821 \{\{ -100, -389, -739, -739, -739\}, +06822 \{ -100, -389, -739, -739, -739\}, +06823 \{ -100, -389, -739, -739, -739\}, +06824 \{ -100, -389, -739, -739, -739\}, +06825 \{ -100, -389, -739, -739, -739\}\}, +06826 \textcolor{comment}{/* GU.GG.. @ */} +06827 \{\{ -100, -389, -739, -739, -739\}, +06828 \{ -100, -389, -739, -739, -739\}, +06829 \{ -100, -389, -739, -739, -739\}, +06830 \{ -100, -389, -739, -739, -739\}, +06831 \{ -100, -389, -739, -739, -739\}\}, +06832 \textcolor{comment}{/* GU.GU.. @ */} +06833 \{\{ -100, -389, -739, -739, -739\}, +06834 \{ -100, -389, -739, -739, -739\}, +06835 \{ -100, -389, -739, -739, -739\}, +06836 \{ -100, -389, -739, -739, -739\}, +06837 \{ -100, -389, -739, -739, -739\}\}\}, +06838 \textcolor{comment}{/* GU.U@.. @ */} +06839 \{\{\{ -100, -379, -379, -379, -379\}, +06840 \{ -100, -379, -379, -379, -379\}, +06841 \{ -100, -379, -379, -379, -379\}, +06842 \{ -100, -379, -379, -379, -379\}, +06843 \{ -100, -379, -379, -379, -379\}\}, +06844 \textcolor{comment}{/* GU.UA.. @ */} +06845 \{\{ -100, -379, -379, -379, -379\}, +06846 \{ -100, -379, -379, -379, -379\}, +06847 \{ -100, -379, -379, -379, -379\}, +06848 \{ -100, -379, -379, -379, -379\}, +06849 \{ -100, -379, -379, -379, -379\}\}, +06850 \textcolor{comment}{/* GU.UC.. @ */} +06851 \{\{ -100, -379, -379, -379, -379\}, +06852 \{ -100, -379, -379, -379, -379\}, +06853 \{ -100, -379, -379, -379, -379\}, +06854 \{ -100, -379, -379, -379, -379\}, +06855 \{ -100, -379, -379, -379, -379\}\}, +06856 \textcolor{comment}{/* GU.UG.. @ */} +06857 \{\{ -100, -379, -379, -379, -379\}, +06858 \{ -100, -379, -379, -379, -379\}, +06859 \{ -100, -379, -379, -379, -379\}, +06860 \{ -100, -379, -379, -379, -379\}, +06861 \{ -100, -379, -379, -379, -379\}\}, +06862 \textcolor{comment}{/* GU.UU.. @ */} +06863 \{\{ -100, -379, -379, -379, -379\}, +06864 \{ -100, -379, -379, -379, -379\}, +06865 \{ -100, -379, -379, -379, -379\}, +06866 \{ -100, -379, -379, -379, -379\}, +06867 \{ -100, -379, -379, -379, -379\}\}\}\}\}, +06868 \{ \textcolor{comment}{/* noPair */} \{\{\{\{0\}\}\}\}, +06869 \textcolor{comment}{/* UG.@@..CG */} +06870 \{\{\{\{ 0, 0, 0, 0, 0\}, +06871 \{ DEF, DEF, DEF, DEF, DEF\}, +06872 \{ DEF, DEF, DEF, DEF, DEF\}, +06873 \{ DEF, DEF, DEF, DEF, DEF\}, +06874 \{ DEF, DEF, DEF, DEF, DEF\}\}, +06875 \textcolor{comment}{/* UG.@A..CG */} +06876 \{\{ 0, 0, 0, 0, 0\}, +06877 \{-1029,-1029,-1029,-1029,-1029\}, +06878 \{ -519, -519, -519, -519, -519\}, +06879 \{ -939, -939, -939, -939, -939\}, +06880 \{ -809, -809, -809, -809, -809\}\}, +06881 \textcolor{comment}{/* UG.@C..CG */} +06882 \{\{ 0, 0, 0, 0, 0\}, +06883 \{ -949, -949, -949, -949, -949\}, +06884 \{ -449, -449, -449, -449, -449\}, +06885 \{ -939, -939, -939, -939, -939\}, +06886 \{ -739, -739, -739, -739, -739\}\}, +06887 \textcolor{comment}{/* UG.@G..CG */} +06888 \{\{ 0, 0, 0, 0, 0\}, +06889 \{-1029,-1029,-1029,-1029,-1029\}, +06890 \{ -519, -519, -519, -519, -519\}, +06891 \{ -939, -939, -939, -939, -939\}, +06892 \{ -809, -809, -809, -809, -809\}\}, +06893 \textcolor{comment}{/* UG.@U..CG */} +06894 \{\{ 0, 0, 0, 0, 0\}, +06895 \{-1029,-1029,-1029,-1029,-1029\}, +06896 \{ -669, -669, -669, -669, -669\}, +06897 \{ -939, -939, -939, -939, -939\}, +06898 \{ -859, -859, -859, -859, -859\}\}\}, +06899 \textcolor{comment}{/* UG.A@..CG */} +06900 \{\{\{ DEF, -719, -789, -959, -809\}, +06901 \{ -100, -769, -839,-1009, -859\}, +06902 \{ -100, -769, -839,-1009, -859\}, +06903 \{ -100, -769, -839,-1009, -859\}, +06904 \{ -100, -769, -839,-1009, -859\}\}, +06905 \textcolor{comment}{/* UG.AA..CG */} +06906 \{\{ DEF, -719, -789, -959, -809\}, +06907 \{-1079,-1748,-1818,-1988,-1838\}, +06908 \{ -569,-1238,-1308,-1478,-1328\}, +06909 \{ -989,-1658,-1728,-1898,-1748\}, +06910 \{ -859,-1528,-1598,-1768,-1618\}\}, +06911 \textcolor{comment}{/* UG.AC..CG */} +06912 \{\{ DEF, -719, -789, -959, -809\}, +06913 \{ -999,-1668,-1738,-1908,-1758\}, +06914 \{ -499,-1168,-1238,-1408,-1258\}, +06915 \{ -989,-1658,-1728,-1898,-1748\}, +06916 \{ -789,-1458,-1528,-1698,-1548\}\}, +06917 \textcolor{comment}{/* UG.AG..CG */} +06918 \{\{ DEF, -719, -789, -959, -809\}, +06919 \{-1079,-1748,-1818,-1988,-1838\}, +06920 \{ -569,-1238,-1308,-1478,-1328\}, +06921 \{ -989,-1658,-1728,-1898,-1748\}, +06922 \{ -859,-1528,-1598,-1768,-1618\}\}, +06923 \textcolor{comment}{/* UG.AU..CG */} +06924 \{\{ DEF, -719, -789, -959, -809\}, +06925 \{-1079,-1748,-1818,-1988,-1838\}, +06926 \{ -719,-1388,-1458,-1628,-1478\}, +06927 \{ -989,-1658,-1728,-1898,-1748\}, +06928 \{ -909,-1578,-1648,-1818,-1668\}\}\}, +06929 \textcolor{comment}{/* UG.C@..CG */} +06930 \{\{\{ DEF, -479, -479, -359, -479\}, +06931 \{ -100, -529, -529, -409, -529\}, +06932 \{ -100, -529, -529, -409, -529\}, +06933 \{ -100, -529, -529, -409, -529\}, +06934 \{ -100, -529, -529, -409, -529\}\}, +06935 \textcolor{comment}{/* UG.CA..CG */} +06936 \{\{ DEF, -479, -479, -359, -479\}, +06937 \{-1079,-1508,-1508,-1388,-1508\}, +06938 \{ -569, -998, -998, -878, -998\}, +06939 \{ -989,-1418,-1418,-1298,-1418\}, +06940 \{ -859,-1288,-1288,-1168,-1288\}\}, +06941 \textcolor{comment}{/* UG.CC..CG */} +06942 \{\{ DEF, -479, -479, -359, -479\}, +06943 \{ -999,-1428,-1428,-1308,-1428\}, +06944 \{ -499, -928, -928, -808, -928\}, +06945 \{ -989,-1418,-1418,-1298,-1418\}, +06946 \{ -789,-1218,-1218,-1098,-1218\}\}, +06947 \textcolor{comment}{/* UG.CG..CG */} +06948 \{\{ DEF, -479, -479, -359, -479\}, +06949 \{-1079,-1508,-1508,-1388,-1508\}, +06950 \{ -569, -998, -998, -878, -998\}, +06951 \{ -989,-1418,-1418,-1298,-1418\}, +06952 \{ -859,-1288,-1288,-1168,-1288\}\}, +06953 \textcolor{comment}{/* UG.CU..CG */} +06954 \{\{ DEF, -479, -479, -359, -479\}, +06955 \{-1079,-1508,-1508,-1388,-1508\}, +06956 \{ -719,-1148,-1148,-1028,-1148\}, +06957 \{ -989,-1418,-1418,-1298,-1418\}, +06958 \{ -909,-1338,-1338,-1218,-1338\}\}\}, +06959 \textcolor{comment}{/* UG.G@..CG */} +06960 \{\{\{ DEF, -659, -809, -919, -809\}, +06961 \{ -100, -709, -859, -969, -859\}, +06962 \{ -100, -709, -859, -969, -859\}, +06963 \{ -100, -709, -859, -969, -859\}, +06964 \{ -100, -709, -859, -969, -859\}\}, +06965 \textcolor{comment}{/* UG.GA..CG */} +06966 \{\{ DEF, -659, -809, -919, -809\}, +06967 \{-1079,-1688,-1838,-1948,-1838\}, +06968 \{ -569,-1178,-1328,-1438,-1328\}, +06969 \{ -989,-1598,-1748,-1858,-1748\}, +06970 \{ -859,-1468,-1618,-1728,-1618\}\}, +06971 \textcolor{comment}{/* UG.GC..CG */} +06972 \{\{ DEF, -659, -809, -919, -809\}, +06973 \{ -999,-1608,-1758,-1868,-1758\}, +06974 \{ -499,-1108,-1258,-1368,-1258\}, +06975 \{ -989,-1598,-1748,-1858,-1748\}, +06976 \{ -789,-1398,-1548,-1658,-1548\}\}, +06977 \textcolor{comment}{/* UG.GG..CG */} +06978 \{\{ DEF, -659, -809, -919, -809\}, +06979 \{-1079,-1688,-1838,-1948,-1838\}, +06980 \{ -569,-1178,-1328,-1438,-1328\}, +06981 \{ -989,-1598,-1748,-1858,-1748\}, +06982 \{ -859,-1468,-1618,-1728,-1618\}\}, +06983 \textcolor{comment}{/* UG.GU..CG */} +06984 \{\{ DEF, -659, -809, -919, -809\}, +06985 \{-1079,-1688,-1838,-1948,-1838\}, +06986 \{ -719,-1328,-1478,-1588,-1478\}, +06987 \{ -989,-1598,-1748,-1858,-1748\}, +06988 \{ -909,-1518,-1668,-1778,-1668\}\}\}, +06989 \textcolor{comment}{/* UG.U@..CG */} +06990 \{\{\{ DEF, -549, -439, -549, -359\}, +06991 \{ -100, -599, -489, -599, -409\}, +06992 \{ -100, -599, -489, -599, -409\}, +06993 \{ -100, -599, -489, -599, -409\}, +06994 \{ -100, -599, -489, -599, -409\}\}, +06995 \textcolor{comment}{/* UG.UA..CG */} +06996 \{\{ DEF, -549, -439, -549, -359\}, +06997 \{-1079,-1578,-1468,-1578,-1388\}, +06998 \{ -569,-1068, -958,-1068, -878\}, +06999 \{ -989,-1488,-1378,-1488,-1298\}, +07000 \{ -859,-1358,-1248,-1358,-1168\}\}, +07001 \textcolor{comment}{/* UG.UC..CG */} +07002 \{\{ DEF, -549, -439, -549, -359\}, +07003 \{ -999,-1498,-1388,-1498,-1308\}, +07004 \{ -499, -998, -888, -998, -808\}, +07005 \{ -989,-1488,-1378,-1488,-1298\}, +07006 \{ -789,-1288,-1178,-1288,-1098\}\}, +07007 \textcolor{comment}{/* UG.UG..CG */} +07008 \{\{ DEF, -549, -439, -549, -359\}, +07009 \{-1079,-1578,-1468,-1578,-1388\}, +07010 \{ -569,-1068, -958,-1068, -878\}, +07011 \{ -989,-1488,-1378,-1488,-1298\}, +07012 \{ -859,-1358,-1248,-1358,-1168\}\}, +07013 \textcolor{comment}{/* UG.UU..CG */} +07014 \{\{ DEF, -549, -439, -549, -359\}, +07015 \{-1079,-1578,-1468,-1578,-1388\}, +07016 \{ -719,-1218,-1108,-1218,-1028\}, +07017 \{ -989,-1488,-1378,-1488,-1298\}, +07018 \{ -909,-1408,-1298,-1408,-1218\}\}\}\}, +07019 \textcolor{comment}{/* UG.@@..GC */} +07020 \{\{\{\{ 0, 0, 0, 0, 0\}, +07021 \{ DEF, DEF, DEF, DEF, DEF\}, +07022 \{ DEF, DEF, DEF, DEF, DEF\}, +07023 \{ DEF, DEF, DEF, DEF, DEF\}, +07024 \{ DEF, DEF, DEF, DEF, DEF\}\}, +07025 \textcolor{comment}{/* UG.@A..GC */} +07026 \{\{ 0, 0, 0, 0, 0\}, +07027 \{ -519, -519, -519, -519, -519\}, +07028 \{ -719, -719, -719, -719, -719\}, +07029 \{ -709, -709, -709, -709, -709\}, +07030 \{ -499, -499, -499, -499, -499\}\}, +07031 \textcolor{comment}{/* UG.@C..GC */} +07032 \{\{ 0, 0, 0, 0, 0\}, +07033 \{ -879, -879, -879, -879, -879\}, +07034 \{ -309, -309, -309, -309, -309\}, +07035 \{ -739, -739, -739, -739, -739\}, +07036 \{ -499, -499, -499, -499, -499\}\}, +07037 \textcolor{comment}{/* UG.@G..GC */} +07038 \{\{ 0, 0, 0, 0, 0\}, +07039 \{ -559, -559, -559, -559, -559\}, +07040 \{ -309, -309, -309, -309, -309\}, +07041 \{ -619, -619, -619, -619, -619\}, +07042 \{ -499, -499, -499, -499, -499\}\}, +07043 \textcolor{comment}{/* UG.@U..GC */} +07044 \{\{ 0, 0, 0, 0, 0\}, +07045 \{ -879, -879, -879, -879, -879\}, +07046 \{ -389, -389, -389, -389, -389\}, +07047 \{ -739, -739, -739, -739, -739\}, +07048 \{ -569, -569, -569, -569, -569\}\}\}, +07049 \textcolor{comment}{/* UG.A@..GC */} +07050 \{\{\{ DEF, -719, -789, -959, -809\}, +07051 \{ -100, -769, -839,-1009, -859\}, +07052 \{ -100, -769, -839,-1009, -859\}, +07053 \{ -100, -769, -839,-1009, -859\}, +07054 \{ -100, -769, -839,-1009, -859\}\}, +07055 \textcolor{comment}{/* UG.AA..GC */} +07056 \{\{ DEF, -719, -789, -959, -809\}, +07057 \{ -569,-1238,-1308,-1478,-1328\}, +07058 \{ -769,-1438,-1508,-1678,-1528\}, +07059 \{ -759,-1428,-1498,-1668,-1518\}, +07060 \{ -549,-1218,-1288,-1458,-1308\}\}, +07061 \textcolor{comment}{/* UG.AC..GC */} +07062 \{\{ DEF, -719, -789, -959, -809\}, +07063 \{ -929,-1598,-1668,-1838,-1688\}, +07064 \{ -359,-1028,-1098,-1268,-1118\}, +07065 \{ -789,-1458,-1528,-1698,-1548\}, +07066 \{ -549,-1218,-1288,-1458,-1308\}\}, +07067 \textcolor{comment}{/* UG.AG..GC */} +07068 \{\{ DEF, -719, -789, -959, -809\}, +07069 \{ -609,-1278,-1348,-1518,-1368\}, +07070 \{ -359,-1028,-1098,-1268,-1118\}, +07071 \{ -669,-1338,-1408,-1578,-1428\}, +07072 \{ -549,-1218,-1288,-1458,-1308\}\}, +07073 \textcolor{comment}{/* UG.AU..GC */} +07074 \{\{ DEF, -719, -789, -959, -809\}, +07075 \{ -929,-1598,-1668,-1838,-1688\}, +07076 \{ -439,-1108,-1178,-1348,-1198\}, +07077 \{ -789,-1458,-1528,-1698,-1548\}, +07078 \{ -619,-1288,-1358,-1528,-1378\}\}\}, +07079 \textcolor{comment}{/* UG.C@..GC */} +07080 \{\{\{ DEF, -479, -479, -359, -479\}, +07081 \{ -100, -529, -529, -409, -529\}, +07082 \{ -100, -529, -529, -409, -529\}, +07083 \{ -100, -529, -529, -409, -529\}, +07084 \{ -100, -529, -529, -409, -529\}\}, +07085 \textcolor{comment}{/* UG.CA..GC */} +07086 \{\{ DEF, -479, -479, -359, -479\}, +07087 \{ -569, -998, -998, -878, -998\}, +07088 \{ -769,-1198,-1198,-1078,-1198\}, +07089 \{ -759,-1188,-1188,-1068,-1188\}, +07090 \{ -549, -978, -978, -858, -978\}\}, +07091 \textcolor{comment}{/* UG.CC..GC */} +07092 \{\{ DEF, -479, -479, -359, -479\}, +07093 \{ -929,-1358,-1358,-1238,-1358\}, +07094 \{ -359, -788, -788, -668, -788\}, +07095 \{ -789,-1218,-1218,-1098,-1218\}, +07096 \{ -549, -978, -978, -858, -978\}\}, +07097 \textcolor{comment}{/* UG.CG..GC */} +07098 \{\{ DEF, -479, -479, -359, -479\}, +07099 \{ -609,-1038,-1038, -918,-1038\}, +07100 \{ -359, -788, -788, -668, -788\}, +07101 \{ -669,-1098,-1098, -978,-1098\}, +07102 \{ -549, -978, -978, -858, -978\}\}, +07103 \textcolor{comment}{/* UG.CU..GC */} +07104 \{\{ DEF, -479, -479, -359, -479\}, +07105 \{ -929,-1358,-1358,-1238,-1358\}, +07106 \{ -439, -868, -868, -748, -868\}, +07107 \{ -789,-1218,-1218,-1098,-1218\}, +07108 \{ -619,-1048,-1048, -928,-1048\}\}\}, +07109 \textcolor{comment}{/* UG.G@..GC */} +07110 \{\{\{ DEF, -659, -809, -919, -809\}, +07111 \{ -100, -709, -859, -969, -859\}, +07112 \{ -100, -709, -859, -969, -859\}, +07113 \{ -100, -709, -859, -969, -859\}, +07114 \{ -100, -709, -859, -969, -859\}\}, +07115 \textcolor{comment}{/* UG.GA..GC */} +07116 \{\{ DEF, -659, -809, -919, -809\}, +07117 \{ -569,-1178,-1328,-1438,-1328\}, +07118 \{ -769,-1378,-1528,-1638,-1528\}, +07119 \{ -759,-1368,-1518,-1628,-1518\}, +07120 \{ -549,-1158,-1308,-1418,-1308\}\}, +07121 \textcolor{comment}{/* UG.GC..GC */} +07122 \{\{ DEF, -659, -809, -919, -809\}, +07123 \{ -929,-1538,-1688,-1798,-1688\}, +07124 \{ -359, -968,-1118,-1228,-1118\}, +07125 \{ -789,-1398,-1548,-1658,-1548\}, +07126 \{ -549,-1158,-1308,-1418,-1308\}\}, +07127 \textcolor{comment}{/* UG.GG..GC */} +07128 \{\{ DEF, -659, -809, -919, -809\}, +07129 \{ -609,-1218,-1368,-1478,-1368\}, +07130 \{ -359, -968,-1118,-1228,-1118\}, +07131 \{ -669,-1278,-1428,-1538,-1428\}, +07132 \{ -549,-1158,-1308,-1418,-1308\}\}, +07133 \textcolor{comment}{/* UG.GU..GC */} +07134 \{\{ DEF, -659, -809, -919, -809\}, +07135 \{ -929,-1538,-1688,-1798,-1688\}, +07136 \{ -439,-1048,-1198,-1308,-1198\}, +07137 \{ -789,-1398,-1548,-1658,-1548\}, +07138 \{ -619,-1228,-1378,-1488,-1378\}\}\}, +07139 \textcolor{comment}{/* UG.U@..GC */} +07140 \{\{\{ DEF, -549, -439, -549, -359\}, +07141 \{ -100, -599, -489, -599, -409\}, +07142 \{ -100, -599, -489, -599, -409\}, +07143 \{ -100, -599, -489, -599, -409\}, +07144 \{ -100, -599, -489, -599, -409\}\}, +07145 \textcolor{comment}{/* UG.UA..GC */} +07146 \{\{ DEF, -549, -439, -549, -359\}, +07147 \{ -569,-1068, -958,-1068, -878\}, +07148 \{ -769,-1268,-1158,-1268,-1078\}, +07149 \{ -759,-1258,-1148,-1258,-1068\}, +07150 \{ -549,-1048, -938,-1048, -858\}\}, +07151 \textcolor{comment}{/* UG.UC..GC */} +07152 \{\{ DEF, -549, -439, -549, -359\}, +07153 \{ -929,-1428,-1318,-1428,-1238\}, +07154 \{ -359, -858, -748, -858, -668\}, +07155 \{ -789,-1288,-1178,-1288,-1098\}, +07156 \{ -549,-1048, -938,-1048, -858\}\}, +07157 \textcolor{comment}{/* UG.UG..GC */} +07158 \{\{ DEF, -549, -439, -549, -359\}, +07159 \{ -609,-1108, -998,-1108, -918\}, +07160 \{ -359, -858, -748, -858, -668\}, +07161 \{ -669,-1168,-1058,-1168, -978\}, +07162 \{ -549,-1048, -938,-1048, -858\}\}, +07163 \textcolor{comment}{/* UG.UU..GC */} +07164 \{\{ DEF, -549, -439, -549, -359\}, +07165 \{ -929,-1428,-1318,-1428,-1238\}, +07166 \{ -439, -938, -828, -938, -748\}, +07167 \{ -789,-1288,-1178,-1288,-1098\}, +07168 \{ -619,-1118,-1008,-1118, -928\}\}\}\}, +07169 \textcolor{comment}{/* UG.@@..GU */} +07170 \{\{\{\{ 0, 0, 0, 0, 0\}, +07171 \{ DEF, DEF, DEF, DEF, DEF\}, +07172 \{ DEF, DEF, DEF, DEF, DEF\}, +07173 \{ DEF, DEF, DEF, DEF, DEF\}, +07174 \{ DEF, DEF, DEF, DEF, DEF\}\}, +07175 \textcolor{comment}{/* UG.@A..GU */} +07176 \{\{ 0, 0, 0, 0, 0\}, +07177 \{ -429, -429, -429, -429, -429\}, +07178 \{ -259, -259, -259, -259, -259\}, +07179 \{ -339, -339, -339, -339, -339\}, +07180 \{ -329, -329, -329, -329, -329\}\}, +07181 \textcolor{comment}{/* UG.@C..GU */} +07182 \{\{ 0, 0, 0, 0, 0\}, +07183 \{ -599, -599, -599, -599, -599\}, +07184 \{ -239, -239, -239, -239, -239\}, +07185 \{ -689, -689, -689, -689, -689\}, +07186 \{ -329, -329, -329, -329, -329\}\}, +07187 \textcolor{comment}{/* UG.@G..GU */} +07188 \{\{ 0, 0, 0, 0, 0\}, +07189 \{ -599, -599, -599, -599, -599\}, +07190 \{ -239, -239, -239, -239, -239\}, +07191 \{ -689, -689, -689, -689, -689\}, +07192 \{ -329, -329, -329, -329, -329\}\}, +07193 \textcolor{comment}{/* UG.@U..GU */} +07194 \{\{ 0, 0, 0, 0, 0\}, +07195 \{ -599, -599, -599, -599, -599\}, +07196 \{ -239, -239, -239, -239, -239\}, +07197 \{ -689, -689, -689, -689, -689\}, +07198 \{ -329, -329, -329, -329, -329\}\}\}, +07199 \textcolor{comment}{/* UG.A@..GU */} +07200 \{\{\{ DEF, -719, -789, -959, -809\}, +07201 \{ -100, -769, -839,-1009, -859\}, +07202 \{ -100, -769, -839,-1009, -859\}, +07203 \{ -100, -769, -839,-1009, -859\}, +07204 \{ -100, -769, -839,-1009, -859\}\}, +07205 \textcolor{comment}{/* UG.AA..GU */} +07206 \{\{ DEF, -719, -789, -959, -809\}, +07207 \{ -479,-1148,-1218,-1388,-1238\}, +07208 \{ -309, -978,-1048,-1218,-1068\}, +07209 \{ -389,-1058,-1128,-1298,-1148\}, +07210 \{ -379,-1048,-1118,-1288,-1138\}\}, +07211 \textcolor{comment}{/* UG.AC..GU */} +07212 \{\{ DEF, -719, -789, -959, -809\}, +07213 \{ -649,-1318,-1388,-1558,-1408\}, +07214 \{ -289, -958,-1028,-1198,-1048\}, +07215 \{ -739,-1408,-1478,-1648,-1498\}, +07216 \{ -379,-1048,-1118,-1288,-1138\}\}, +07217 \textcolor{comment}{/* UG.AG..GU */} +07218 \{\{ DEF, -719, -789, -959, -809\}, +07219 \{ -649,-1318,-1388,-1558,-1408\}, +07220 \{ -289, -958,-1028,-1198,-1048\}, +07221 \{ -739,-1408,-1478,-1648,-1498\}, +07222 \{ -379,-1048,-1118,-1288,-1138\}\}, +07223 \textcolor{comment}{/* UG.AU..GU */} +07224 \{\{ DEF, -719, -789, -959, -809\}, +07225 \{ -649,-1318,-1388,-1558,-1408\}, +07226 \{ -289, -958,-1028,-1198,-1048\}, +07227 \{ -739,-1408,-1478,-1648,-1498\}, +07228 \{ -379,-1048,-1118,-1288,-1138\}\}\}, +07229 \textcolor{comment}{/* UG.C@..GU */} +07230 \{\{\{ DEF, -479, -479, -359, -479\}, +07231 \{ -100, -529, -529, -409, -529\}, +07232 \{ -100, -529, -529, -409, -529\}, +07233 \{ -100, -529, -529, -409, -529\}, +07234 \{ -100, -529, -529, -409, -529\}\}, +07235 \textcolor{comment}{/* UG.CA..GU */} +07236 \{\{ DEF, -479, -479, -359, -479\}, +07237 \{ -479, -908, -908, -788, -908\}, +07238 \{ -309, -738, -738, -618, -738\}, +07239 \{ -389, -818, -818, -698, -818\}, +07240 \{ -379, -808, -808, -688, -808\}\}, +07241 \textcolor{comment}{/* UG.CC..GU */} +07242 \{\{ DEF, -479, -479, -359, -479\}, +07243 \{ -649,-1078,-1078, -958,-1078\}, +07244 \{ -289, -718, -718, -598, -718\}, +07245 \{ -739,-1168,-1168,-1048,-1168\}, +07246 \{ -379, -808, -808, -688, -808\}\}, +07247 \textcolor{comment}{/* UG.CG..GU */} +07248 \{\{ DEF, -479, -479, -359, -479\}, +07249 \{ -649,-1078,-1078, -958,-1078\}, +07250 \{ -289, -718, -718, -598, -718\}, +07251 \{ -739,-1168,-1168,-1048,-1168\}, +07252 \{ -379, -808, -808, -688, -808\}\}, +07253 \textcolor{comment}{/* UG.CU..GU */} +07254 \{\{ DEF, -479, -479, -359, -479\}, +07255 \{ -649,-1078,-1078, -958,-1078\}, +07256 \{ -289, -718, -718, -598, -718\}, +07257 \{ -739,-1168,-1168,-1048,-1168\}, +07258 \{ -379, -808, -808, -688, -808\}\}\}, +07259 \textcolor{comment}{/* UG.G@..GU */} +07260 \{\{\{ DEF, -659, -809, -919, -809\}, +07261 \{ -100, -709, -859, -969, -859\}, +07262 \{ -100, -709, -859, -969, -859\}, +07263 \{ -100, -709, -859, -969, -859\}, +07264 \{ -100, -709, -859, -969, -859\}\}, +07265 \textcolor{comment}{/* UG.GA..GU */} +07266 \{\{ DEF, -659, -809, -919, -809\}, +07267 \{ -479,-1088,-1238,-1348,-1238\}, +07268 \{ -309, -918,-1068,-1178,-1068\}, +07269 \{ -389, -998,-1148,-1258,-1148\}, +07270 \{ -379, -988,-1138,-1248,-1138\}\}, +07271 \textcolor{comment}{/* UG.GC..GU */} +07272 \{\{ DEF, -659, -809, -919, -809\}, +07273 \{ -649,-1258,-1408,-1518,-1408\}, +07274 \{ -289, -898,-1048,-1158,-1048\}, +07275 \{ -739,-1348,-1498,-1608,-1498\}, +07276 \{ -379, -988,-1138,-1248,-1138\}\}, +07277 \textcolor{comment}{/* UG.GG..GU */} +07278 \{\{ DEF, -659, -809, -919, -809\}, +07279 \{ -649,-1258,-1408,-1518,-1408\}, +07280 \{ -289, -898,-1048,-1158,-1048\}, +07281 \{ -739,-1348,-1498,-1608,-1498\}, +07282 \{ -379, -988,-1138,-1248,-1138\}\}, +07283 \textcolor{comment}{/* UG.GU..GU */} +07284 \{\{ DEF, -659, -809, -919, -809\}, +07285 \{ -649,-1258,-1408,-1518,-1408\}, +07286 \{ -289, -898,-1048,-1158,-1048\}, +07287 \{ -739,-1348,-1498,-1608,-1498\}, +07288 \{ -379, -988,-1138,-1248,-1138\}\}\}, +07289 \textcolor{comment}{/* UG.U@..GU */} +07290 \{\{\{ DEF, -549, -439, -549, -359\}, +07291 \{ -100, -599, -489, -599, -409\}, +07292 \{ -100, -599, -489, -599, -409\}, +07293 \{ -100, -599, -489, -599, -409\}, +07294 \{ -100, -599, -489, -599, -409\}\}, +07295 \textcolor{comment}{/* UG.UA..GU */} +07296 \{\{ DEF, -549, -439, -549, -359\}, +07297 \{ -479, -978, -868, -978, -788\}, +07298 \{ -309, -808, -698, -808, -618\}, +07299 \{ -389, -888, -778, -888, -698\}, +07300 \{ -379, -878, -768, -878, -688\}\}, +07301 \textcolor{comment}{/* UG.UC..GU */} +07302 \{\{ DEF, -549, -439, -549, -359\}, +07303 \{ -649,-1148,-1038,-1148, -958\}, +07304 \{ -289, -788, -678, -788, -598\}, +07305 \{ -739,-1238,-1128,-1238,-1048\}, +07306 \{ -379, -878, -768, -878, -688\}\}, +07307 \textcolor{comment}{/* UG.UG..GU */} +07308 \{\{ DEF, -549, -439, -549, -359\}, +07309 \{ -649,-1148,-1038,-1148, -958\}, +07310 \{ -289, -788, -678, -788, -598\}, +07311 \{ -739,-1238,-1128,-1238,-1048\}, +07312 \{ -379, -878, -768, -878, -688\}\}, +07313 \textcolor{comment}{/* UG.UU..GU */} +07314 \{\{ DEF, -549, -439, -549, -359\}, +07315 \{ -649,-1148,-1038,-1148, -958\}, +07316 \{ -289, -788, -678, -788, -598\}, +07317 \{ -739,-1238,-1128,-1238,-1048\}, +07318 \{ -379, -878, -768, -878, -688\}\}\}\}, +07319 \textcolor{comment}{/* UG.@@..UG */} +07320 \{\{\{\{ 0, 0, 0, 0, 0\}, +07321 \{ DEF, DEF, DEF, DEF, DEF\}, +07322 \{ DEF, DEF, DEF, DEF, DEF\}, +07323 \{ DEF, DEF, DEF, DEF, DEF\}, +07324 \{ DEF, DEF, DEF, DEF, DEF\}\}, +07325 \textcolor{comment}{/* UG.@A..UG */} +07326 \{\{ 0, 0, 0, 0, 0\}, +07327 \{ -719, -719, -719, -719, -719\}, +07328 \{ -479, -479, -479, -479, -479\}, +07329 \{ -659, -659, -659, -659, -659\}, +07330 \{ -549, -549, -549, -549, -549\}\}, +07331 \textcolor{comment}{/* UG.@C..UG */} +07332 \{\{ 0, 0, 0, 0, 0\}, +07333 \{ -789, -789, -789, -789, -789\}, +07334 \{ -479, -479, -479, -479, -479\}, +07335 \{ -809, -809, -809, -809, -809\}, +07336 \{ -439, -439, -439, -439, -439\}\}, +07337 \textcolor{comment}{/* UG.@G..UG */} +07338 \{\{ 0, 0, 0, 0, 0\}, +07339 \{ -959, -959, -959, -959, -959\}, +07340 \{ -359, -359, -359, -359, -359\}, +07341 \{ -919, -919, -919, -919, -919\}, +07342 \{ -549, -549, -549, -549, -549\}\}, +07343 \textcolor{comment}{/* UG.@U..UG */} +07344 \{\{ 0, 0, 0, 0, 0\}, +07345 \{ -809, -809, -809, -809, -809\}, +07346 \{ -479, -479, -479, -479, -479\}, +07347 \{ -809, -809, -809, -809, -809\}, +07348 \{ -359, -359, -359, -359, -359\}\}\}, +07349 \textcolor{comment}{/* UG.A@..UG */} +07350 \{\{\{ DEF, -719, -789, -959, -809\}, +07351 \{ -100, -769, -839,-1009, -859\}, +07352 \{ -100, -769, -839,-1009, -859\}, +07353 \{ -100, -769, -839,-1009, -859\}, +07354 \{ -100, -769, -839,-1009, -859\}\}, +07355 \textcolor{comment}{/* UG.AA..UG */} +07356 \{\{ DEF, -719, -789, -959, -809\}, +07357 \{ -769,-1438,-1508,-1678,-1528\}, +07358 \{ -529,-1198,-1268,-1438,-1288\}, +07359 \{ -709,-1378,-1448,-1618,-1468\}, +07360 \{ -599,-1268,-1338,-1508,-1358\}\}, +07361 \textcolor{comment}{/* UG.AC..UG */} +07362 \{\{ DEF, -719, -789, -959, -809\}, +07363 \{ -839,-1508,-1578,-1748,-1598\}, +07364 \{ -529,-1198,-1268,-1438,-1288\}, +07365 \{ -859,-1528,-1598,-1768,-1618\}, +07366 \{ -489,-1158,-1228,-1398,-1248\}\}, +07367 \textcolor{comment}{/* UG.AG..UG */} +07368 \{\{ DEF, -719, -789, -959, -809\}, +07369 \{-1009,-1678,-1748,-1918,-1768\}, +07370 \{ -409,-1078,-1148,-1318,-1168\}, +07371 \{ -969,-1638,-1708,-1878,-1728\}, +07372 \{ -599,-1268,-1338,-1508,-1358\}\}, +07373 \textcolor{comment}{/* UG.AU..UG */} +07374 \{\{ DEF, -719, -789, -959, -809\}, +07375 \{ -859,-1528,-1598,-1768,-1618\}, +07376 \{ -529,-1198,-1268,-1438,-1288\}, +07377 \{ -859,-1528,-1598,-1768,-1618\}, +07378 \{ -409,-1078,-1148,-1318,-1168\}\}\}, +07379 \textcolor{comment}{/* UG.C@..UG */} +07380 \{\{\{ DEF, -479, -479, -359, -479\}, +07381 \{ -100, -529, -529, -409, -529\}, +07382 \{ -100, -529, -529, -409, -529\}, +07383 \{ -100, -529, -529, -409, -529\}, +07384 \{ -100, -529, -529, -409, -529\}\}, +07385 \textcolor{comment}{/* UG.CA..UG */} +07386 \{\{ DEF, -479, -479, -359, -479\}, +07387 \{ -769,-1198,-1198,-1078,-1198\}, +07388 \{ -529, -958, -958, -838, -958\}, +07389 \{ -709,-1138,-1138,-1018,-1138\}, +07390 \{ -599,-1028,-1028, -908,-1028\}\}, +07391 \textcolor{comment}{/* UG.CC..UG */} +07392 \{\{ DEF, -479, -479, -359, -479\}, +07393 \{ -839,-1268,-1268,-1148,-1268\}, +07394 \{ -529, -958, -958, -838, -958\}, +07395 \{ -859,-1288,-1288,-1168,-1288\}, +07396 \{ -489, -918, -918, -798, -918\}\}, +07397 \textcolor{comment}{/* UG.CG..UG */} +07398 \{\{ DEF, -479, -479, -359, -479\}, +07399 \{-1009,-1438,-1438,-1318,-1438\}, +07400 \{ -409, -838, -838, -718, -838\}, +07401 \{ -969,-1398,-1398,-1278,-1398\}, +07402 \{ -599,-1028,-1028, -908,-1028\}\}, +07403 \textcolor{comment}{/* UG.CU..UG */} +07404 \{\{ DEF, -479, -479, -359, -479\}, +07405 \{ -859,-1288,-1288,-1168,-1288\}, +07406 \{ -529, -958, -958, -838, -958\}, +07407 \{ -859,-1288,-1288,-1168,-1288\}, +07408 \{ -409, -838, -838, -718, -838\}\}\}, +07409 \textcolor{comment}{/* UG.G@..UG */} +07410 \{\{\{ DEF, -659, -809, -919, -809\}, +07411 \{ -100, -709, -859, -969, -859\}, +07412 \{ -100, -709, -859, -969, -859\}, +07413 \{ -100, -709, -859, -969, -859\}, +07414 \{ -100, -709, -859, -969, -859\}\}, +07415 \textcolor{comment}{/* UG.GA..UG */} +07416 \{\{ DEF, -659, -809, -919, -809\}, +07417 \{ -769,-1378,-1528,-1638,-1528\}, +07418 \{ -529,-1138,-1288,-1398,-1288\}, +07419 \{ -709,-1318,-1468,-1578,-1468\}, +07420 \{ -599,-1208,-1358,-1468,-1358\}\}, +07421 \textcolor{comment}{/* UG.GC..UG */} +07422 \{\{ DEF, -659, -809, -919, -809\}, +07423 \{ -839,-1448,-1598,-1708,-1598\}, +07424 \{ -529,-1138,-1288,-1398,-1288\}, +07425 \{ -859,-1468,-1618,-1728,-1618\}, +07426 \{ -489,-1098,-1248,-1358,-1248\}\}, +07427 \textcolor{comment}{/* UG.GG..UG */} +07428 \{\{ DEF, -659, -809, -919, -809\}, +07429 \{-1009,-1618,-1768,-1878,-1768\}, +07430 \{ -409,-1018,-1168,-1278,-1168\}, +07431 \{ -969,-1578,-1728,-1838,-1728\}, +07432 \{ -599,-1208,-1358,-1468,-1358\}\}, +07433 \textcolor{comment}{/* UG.GU..UG */} +07434 \{\{ DEF, -659, -809, -919, -809\}, +07435 \{ -859,-1468,-1618,-1728,-1618\}, +07436 \{ -529,-1138,-1288,-1398,-1288\}, +07437 \{ -859,-1468,-1618,-1728,-1618\}, +07438 \{ -409,-1018,-1168,-1278,-1168\}\}\}, +07439 \textcolor{comment}{/* UG.U@..UG */} +07440 \{\{\{ DEF, -549, -439, -549, -359\}, +07441 \{ -100, -599, -489, -599, -409\}, +07442 \{ -100, -599, -489, -599, -409\}, +07443 \{ -100, -599, -489, -599, -409\}, +07444 \{ -100, -599, -489, -599, -409\}\}, +07445 \textcolor{comment}{/* UG.UA..UG */} +07446 \{\{ DEF, -549, -439, -549, -359\}, +07447 \{ -769,-1268,-1158,-1268,-1078\}, +07448 \{ -529,-1028, -918,-1028, -838\}, +07449 \{ -709,-1208,-1098,-1208,-1018\}, +07450 \{ -599,-1098, -988,-1098, -908\}\}, +07451 \textcolor{comment}{/* UG.UC..UG */} +07452 \{\{ DEF, -549, -439, -549, -359\}, +07453 \{ -839,-1338,-1228,-1338,-1148\}, +07454 \{ -529,-1028, -918,-1028, -838\}, +07455 \{ -859,-1358,-1248,-1358,-1168\}, +07456 \{ -489, -988, -878, -988, -798\}\}, +07457 \textcolor{comment}{/* UG.UG..UG */} +07458 \{\{ DEF, -549, -439, -549, -359\}, +07459 \{-1009,-1508,-1398,-1508,-1318\}, +07460 \{ -409, -908, -798, -908, -718\}, +07461 \{ -969,-1468,-1358,-1468,-1278\}, +07462 \{ -599,-1098, -988,-1098, -908\}\}, +07463 \textcolor{comment}{/* UG.UU..UG */} +07464 \{\{ DEF, -549, -439, -549, -359\}, +07465 \{ -859,-1358,-1248,-1358,-1168\}, +07466 \{ -529,-1028, -918,-1028, -838\}, +07467 \{ -859,-1358,-1248,-1358,-1168\}, +07468 \{ -409, -908, -798, -908, -718\}\}\}\}, +07469 \textcolor{comment}{/* UG.@@..AU */} +07470 \{\{\{\{ 0, 0, 0, 0, 0\}, +07471 \{ DEF, DEF, DEF, DEF, DEF\}, +07472 \{ DEF, DEF, DEF, DEF, DEF\}, +07473 \{ DEF, DEF, DEF, DEF, DEF\}, +07474 \{ DEF, DEF, DEF, DEF, DEF\}\}, +07475 \textcolor{comment}{/* UG.@A..AU */} +07476 \{\{ 0, 0, 0, 0, 0\}, +07477 \{ -429, -429, -429, -429, -429\}, +07478 \{ -259, -259, -259, -259, -259\}, +07479 \{ -339, -339, -339, -339, -339\}, +07480 \{ -329, -329, -329, -329, -329\}\}, +07481 \textcolor{comment}{/* UG.@C..AU */} +07482 \{\{ 0, 0, 0, 0, 0\}, +07483 \{ -599, -599, -599, -599, -599\}, +07484 \{ -239, -239, -239, -239, -239\}, +07485 \{ -689, -689, -689, -689, -689\}, +07486 \{ -329, -329, -329, -329, -329\}\}, +07487 \textcolor{comment}{/* UG.@G..AU */} +07488 \{\{ 0, 0, 0, 0, 0\}, +07489 \{ -599, -599, -599, -599, -599\}, +07490 \{ -239, -239, -239, -239, -239\}, +07491 \{ -689, -689, -689, -689, -689\}, +07492 \{ -329, -329, -329, -329, -329\}\}, +07493 \textcolor{comment}{/* UG.@U..AU */} +07494 \{\{ 0, 0, 0, 0, 0\}, +07495 \{ -599, -599, -599, -599, -599\}, +07496 \{ -239, -239, -239, -239, -239\}, +07497 \{ -689, -689, -689, -689, -689\}, +07498 \{ -329, -329, -329, -329, -329\}\}\}, +07499 \textcolor{comment}{/* UG.A@..AU */} +07500 \{\{\{ DEF, -719, -789, -959, -809\}, +07501 \{ -100, -769, -839,-1009, -859\}, +07502 \{ -100, -769, -839,-1009, -859\}, +07503 \{ -100, -769, -839,-1009, -859\}, +07504 \{ -100, -769, -839,-1009, -859\}\}, +07505 \textcolor{comment}{/* UG.AA..AU */} +07506 \{\{ DEF, -719, -789, -959, -809\}, +07507 \{ -479,-1148,-1218,-1388,-1238\}, +07508 \{ -309, -978,-1048,-1218,-1068\}, +07509 \{ -389,-1058,-1128,-1298,-1148\}, +07510 \{ -379,-1048,-1118,-1288,-1138\}\}, +07511 \textcolor{comment}{/* UG.AC..AU */} +07512 \{\{ DEF, -719, -789, -959, -809\}, +07513 \{ -649,-1318,-1388,-1558,-1408\}, +07514 \{ -289, -958,-1028,-1198,-1048\}, +07515 \{ -739,-1408,-1478,-1648,-1498\}, +07516 \{ -379,-1048,-1118,-1288,-1138\}\}, +07517 \textcolor{comment}{/* UG.AG..AU */} +07518 \{\{ DEF, -719, -789, -959, -809\}, +07519 \{ -649,-1318,-1388,-1558,-1408\}, +07520 \{ -289, -958,-1028,-1198,-1048\}, +07521 \{ -739,-1408,-1478,-1648,-1498\}, +07522 \{ -379,-1048,-1118,-1288,-1138\}\}, +07523 \textcolor{comment}{/* UG.AU..AU */} +07524 \{\{ DEF, -719, -789, -959, -809\}, +07525 \{ -649,-1318,-1388,-1558,-1408\}, +07526 \{ -289, -958,-1028,-1198,-1048\}, +07527 \{ -739,-1408,-1478,-1648,-1498\}, +07528 \{ -379,-1048,-1118,-1288,-1138\}\}\}, +07529 \textcolor{comment}{/* UG.C@..AU */} +07530 \{\{\{ DEF, -479, -479, -359, -479\}, +07531 \{ -100, -529, -529, -409, -529\}, +07532 \{ -100, -529, -529, -409, -529\}, +07533 \{ -100, -529, -529, -409, -529\}, +07534 \{ -100, -529, -529, -409, -529\}\}, +07535 \textcolor{comment}{/* UG.CA..AU */} +07536 \{\{ DEF, -479, -479, -359, -479\}, +07537 \{ -479, -908, -908, -788, -908\}, +07538 \{ -309, -738, -738, -618, -738\}, +07539 \{ -389, -818, -818, -698, -818\}, +07540 \{ -379, -808, -808, -688, -808\}\}, +07541 \textcolor{comment}{/* UG.CC..AU */} +07542 \{\{ DEF, -479, -479, -359, -479\}, +07543 \{ -649,-1078,-1078, -958,-1078\}, +07544 \{ -289, -718, -718, -598, -718\}, +07545 \{ -739,-1168,-1168,-1048,-1168\}, +07546 \{ -379, -808, -808, -688, -808\}\}, +07547 \textcolor{comment}{/* UG.CG..AU */} +07548 \{\{ DEF, -479, -479, -359, -479\}, +07549 \{ -649,-1078,-1078, -958,-1078\}, +07550 \{ -289, -718, -718, -598, -718\}, +07551 \{ -739,-1168,-1168,-1048,-1168\}, +07552 \{ -379, -808, -808, -688, -808\}\}, +07553 \textcolor{comment}{/* UG.CU..AU */} +07554 \{\{ DEF, -479, -479, -359, -479\}, +07555 \{ -649,-1078,-1078, -958,-1078\}, +07556 \{ -289, -718, -718, -598, -718\}, +07557 \{ -739,-1168,-1168,-1048,-1168\}, +07558 \{ -379, -808, -808, -688, -808\}\}\}, +07559 \textcolor{comment}{/* UG.G@..AU */} +07560 \{\{\{ DEF, -659, -809, -919, -809\}, +07561 \{ -100, -709, -859, -969, -859\}, +07562 \{ -100, -709, -859, -969, -859\}, +07563 \{ -100, -709, -859, -969, -859\}, +07564 \{ -100, -709, -859, -969, -859\}\}, +07565 \textcolor{comment}{/* UG.GA..AU */} +07566 \{\{ DEF, -659, -809, -919, -809\}, +07567 \{ -479,-1088,-1238,-1348,-1238\}, +07568 \{ -309, -918,-1068,-1178,-1068\}, +07569 \{ -389, -998,-1148,-1258,-1148\}, +07570 \{ -379, -988,-1138,-1248,-1138\}\}, +07571 \textcolor{comment}{/* UG.GC..AU */} +07572 \{\{ DEF, -659, -809, -919, -809\}, +07573 \{ -649,-1258,-1408,-1518,-1408\}, +07574 \{ -289, -898,-1048,-1158,-1048\}, +07575 \{ -739,-1348,-1498,-1608,-1498\}, +07576 \{ -379, -988,-1138,-1248,-1138\}\}, +07577 \textcolor{comment}{/* UG.GG..AU */} +07578 \{\{ DEF, -659, -809, -919, -809\}, +07579 \{ -649,-1258,-1408,-1518,-1408\}, +07580 \{ -289, -898,-1048,-1158,-1048\}, +07581 \{ -739,-1348,-1498,-1608,-1498\}, +07582 \{ -379, -988,-1138,-1248,-1138\}\}, +07583 \textcolor{comment}{/* UG.GU..AU */} +07584 \{\{ DEF, -659, -809, -919, -809\}, +07585 \{ -649,-1258,-1408,-1518,-1408\}, +07586 \{ -289, -898,-1048,-1158,-1048\}, +07587 \{ -739,-1348,-1498,-1608,-1498\}, +07588 \{ -379, -988,-1138,-1248,-1138\}\}\}, +07589 \textcolor{comment}{/* UG.U@..AU */} +07590 \{\{\{ DEF, -549, -439, -549, -359\}, +07591 \{ -100, -599, -489, -599, -409\}, +07592 \{ -100, -599, -489, -599, -409\}, +07593 \{ -100, -599, -489, -599, -409\}, +07594 \{ -100, -599, -489, -599, -409\}\}, +07595 \textcolor{comment}{/* UG.UA..AU */} +07596 \{\{ DEF, -549, -439, -549, -359\}, +07597 \{ -479, -978, -868, -978, -788\}, +07598 \{ -309, -808, -698, -808, -618\}, +07599 \{ -389, -888, -778, -888, -698\}, +07600 \{ -379, -878, -768, -878, -688\}\}, +07601 \textcolor{comment}{/* UG.UC..AU */} +07602 \{\{ DEF, -549, -439, -549, -359\}, +07603 \{ -649,-1148,-1038,-1148, -958\}, +07604 \{ -289, -788, -678, -788, -598\}, +07605 \{ -739,-1238,-1128,-1238,-1048\}, +07606 \{ -379, -878, -768, -878, -688\}\}, +07607 \textcolor{comment}{/* UG.UG..AU */} +07608 \{\{ DEF, -549, -439, -549, -359\}, +07609 \{ -649,-1148,-1038,-1148, -958\}, +07610 \{ -289, -788, -678, -788, -598\}, +07611 \{ -739,-1238,-1128,-1238,-1048\}, +07612 \{ -379, -878, -768, -878, -688\}\}, +07613 \textcolor{comment}{/* UG.UU..AU */} +07614 \{\{ DEF, -549, -439, -549, -359\}, +07615 \{ -649,-1148,-1038,-1148, -958\}, +07616 \{ -289, -788, -678, -788, -598\}, +07617 \{ -739,-1238,-1128,-1238,-1048\}, +07618 \{ -379, -878, -768, -878, -688\}\}\}\}, +07619 \textcolor{comment}{/* UG.@@..UA */} +07620 \{\{\{\{ 0, 0, 0, 0, 0\}, +07621 \{ DEF, DEF, DEF, DEF, DEF\}, +07622 \{ DEF, DEF, DEF, DEF, DEF\}, +07623 \{ DEF, DEF, DEF, DEF, DEF\}, +07624 \{ DEF, DEF, DEF, DEF, DEF\}\}, +07625 \textcolor{comment}{/* UG.@A..UA */} +07626 \{\{ 0, 0, 0, 0, 0\}, +07627 \{ -399, -399, -399, -399, -399\}, +07628 \{ -429, -429, -429, -429, -429\}, +07629 \{ -379, -379, -379, -379, -379\}, +07630 \{ -279, -279, -279, -279, -279\}\}, +07631 \textcolor{comment}{/* UG.@C..UA */} +07632 \{\{ 0, 0, 0, 0, 0\}, +07633 \{ -629, -629, -629, -629, -629\}, +07634 \{ -509, -509, -509, -509, -509\}, +07635 \{ -679, -679, -679, -679, -679\}, +07636 \{ -139, -139, -139, -139, -139\}\}, +07637 \textcolor{comment}{/* UG.@G..UA */} +07638 \{\{ 0, 0, 0, 0, 0\}, +07639 \{ -889, -889, -889, -889, -889\}, +07640 \{ -199, -199, -199, -199, -199\}, +07641 \{ -889, -889, -889, -889, -889\}, +07642 \{ -279, -279, -279, -279, -279\}\}, +07643 \textcolor{comment}{/* UG.@U..UA */} +07644 \{\{ 0, 0, 0, 0, 0\}, +07645 \{ -589, -589, -589, -589, -589\}, +07646 \{ -179, -179, -179, -179, -179\}, +07647 \{ -679, -679, -679, -679, -679\}, +07648 \{ -140, -140, -140, -140, -140\}\}\}, +07649 \textcolor{comment}{/* UG.A@..UA */} +07650 \{\{\{ DEF, -719, -789, -959, -809\}, +07651 \{ -100, -769, -839,-1009, -859\}, +07652 \{ -100, -769, -839,-1009, -859\}, +07653 \{ -100, -769, -839,-1009, -859\}, +07654 \{ -100, -769, -839,-1009, -859\}\}, +07655 \textcolor{comment}{/* UG.AA..UA */} +07656 \{\{ DEF, -719, -789, -959, -809\}, +07657 \{ -449,-1118,-1188,-1358,-1208\}, +07658 \{ -479,-1148,-1218,-1388,-1238\}, +07659 \{ -429,-1098,-1168,-1338,-1188\}, +07660 \{ -329, -998,-1068,-1238,-1088\}\}, +07661 \textcolor{comment}{/* UG.AC..UA */} +07662 \{\{ DEF, -719, -789, -959, -809\}, +07663 \{ -679,-1348,-1418,-1588,-1438\}, +07664 \{ -559,-1228,-1298,-1468,-1318\}, +07665 \{ -729,-1398,-1468,-1638,-1488\}, +07666 \{ -189, -858, -928,-1098, -948\}\}, +07667 \textcolor{comment}{/* UG.AG..UA */} +07668 \{\{ DEF, -719, -789, -959, -809\}, +07669 \{ -939,-1608,-1678,-1848,-1698\}, +07670 \{ -249, -918, -988,-1158,-1008\}, +07671 \{ -939,-1608,-1678,-1848,-1698\}, +07672 \{ -329, -998,-1068,-1238,-1088\}\}, +07673 \textcolor{comment}{/* UG.AU..UA */} +07674 \{\{ DEF, -719, -789, -959, -809\}, +07675 \{ -639,-1308,-1378,-1548,-1398\}, +07676 \{ -229, -898, -968,-1138, -988\}, +07677 \{ -729,-1398,-1468,-1638,-1488\}, +07678 \{ -190, -859, -929,-1099, -949\}\}\}, +07679 \textcolor{comment}{/* UG.C@..UA */} +07680 \{\{\{ DEF, -479, -479, -359, -479\}, +07681 \{ -100, -529, -529, -409, -529\}, +07682 \{ -100, -529, -529, -409, -529\}, +07683 \{ -100, -529, -529, -409, -529\}, +07684 \{ -100, -529, -529, -409, -529\}\}, +07685 \textcolor{comment}{/* UG.CA..UA */} +07686 \{\{ DEF, -479, -479, -359, -479\}, +07687 \{ -449, -878, -878, -758, -878\}, +07688 \{ -479, -908, -908, -788, -908\}, +07689 \{ -429, -858, -858, -738, -858\}, +07690 \{ -329, -758, -758, -638, -758\}\}, +07691 \textcolor{comment}{/* UG.CC..UA */} +07692 \{\{ DEF, -479, -479, -359, -479\}, +07693 \{ -679,-1108,-1108, -988,-1108\}, +07694 \{ -559, -988, -988, -868, -988\}, +07695 \{ -729,-1158,-1158,-1038,-1158\}, +07696 \{ -189, -618, -618, -498, -618\}\}, +07697 \textcolor{comment}{/* UG.CG..UA */} +07698 \{\{ DEF, -479, -479, -359, -479\}, +07699 \{ -939,-1368,-1368,-1248,-1368\}, +07700 \{ -249, -678, -678, -558, -678\}, +07701 \{ -939,-1368,-1368,-1248,-1368\}, +07702 \{ -329, -758, -758, -638, -758\}\}, +07703 \textcolor{comment}{/* UG.CU..UA */} +07704 \{\{ DEF, -479, -479, -359, -479\}, +07705 \{ -639,-1068,-1068, -948,-1068\}, +07706 \{ -229, -658, -658, -538, -658\}, +07707 \{ -729,-1158,-1158,-1038,-1158\}, +07708 \{ -190, -619, -619, -499, -619\}\}\}, +07709 \textcolor{comment}{/* UG.G@..UA */} +07710 \{\{\{ DEF, -659, -809, -919, -809\}, +07711 \{ -100, -709, -859, -969, -859\}, +07712 \{ -100, -709, -859, -969, -859\}, +07713 \{ -100, -709, -859, -969, -859\}, +07714 \{ -100, -709, -859, -969, -859\}\}, +07715 \textcolor{comment}{/* UG.GA..UA */} +07716 \{\{ DEF, -659, -809, -919, -809\}, +07717 \{ -449,-1058,-1208,-1318,-1208\}, +07718 \{ -479,-1088,-1238,-1348,-1238\}, +07719 \{ -429,-1038,-1188,-1298,-1188\}, +07720 \{ -329, -938,-1088,-1198,-1088\}\}, +07721 \textcolor{comment}{/* UG.GC..UA */} +07722 \{\{ DEF, -659, -809, -919, -809\}, +07723 \{ -679,-1288,-1438,-1548,-1438\}, +07724 \{ -559,-1168,-1318,-1428,-1318\}, +07725 \{ -729,-1338,-1488,-1598,-1488\}, +07726 \{ -189, -798, -948,-1058, -948\}\}, +07727 \textcolor{comment}{/* UG.GG..UA */} +07728 \{\{ DEF, -659, -809, -919, -809\}, +07729 \{ -939,-1548,-1698,-1808,-1698\}, +07730 \{ -249, -858,-1008,-1118,-1008\}, +07731 \{ -939,-1548,-1698,-1808,-1698\}, +07732 \{ -329, -938,-1088,-1198,-1088\}\}, +07733 \textcolor{comment}{/* UG.GU..UA */} +07734 \{\{ DEF, -659, -809, -919, -809\}, +07735 \{ -639,-1248,-1398,-1508,-1398\}, +07736 \{ -229, -838, -988,-1098, -988\}, +07737 \{ -729,-1338,-1488,-1598,-1488\}, +07738 \{ -190, -799, -949,-1059, -949\}\}\}, +07739 \textcolor{comment}{/* UG.U@..UA */} +07740 \{\{\{ DEF, -549, -439, -549, -359\}, +07741 \{ -100, -599, -489, -599, -409\}, +07742 \{ -100, -599, -489, -599, -409\}, +07743 \{ -100, -599, -489, -599, -409\}, +07744 \{ -100, -599, -489, -599, -409\}\}, +07745 \textcolor{comment}{/* UG.UA..UA */} +07746 \{\{ DEF, -549, -439, -549, -359\}, +07747 \{ -449, -948, -838, -948, -758\}, +07748 \{ -479, -978, -868, -978, -788\}, +07749 \{ -429, -928, -818, -928, -738\}, +07750 \{ -329, -828, -718, -828, -638\}\}, +07751 \textcolor{comment}{/* UG.UC..UA */} +07752 \{\{ DEF, -549, -439, -549, -359\}, +07753 \{ -679,-1178,-1068,-1178, -988\}, +07754 \{ -559,-1058, -948,-1058, -868\}, +07755 \{ -729,-1228,-1118,-1228,-1038\}, +07756 \{ -189, -688, -578, -688, -498\}\}, +07757 \textcolor{comment}{/* UG.UG..UA */} +07758 \{\{ DEF, -549, -439, -549, -359\}, +07759 \{ -939,-1438,-1328,-1438,-1248\}, +07760 \{ -249, -748, -638, -748, -558\}, +07761 \{ -939,-1438,-1328,-1438,-1248\}, +07762 \{ -329, -828, -718, -828, -638\}\}, +07763 \textcolor{comment}{/* UG.UU..UA */} +07764 \{\{ DEF, -549, -439, -549, -359\}, +07765 \{ -639,-1138,-1028,-1138, -948\}, +07766 \{ -229, -728, -618, -728, -538\}, +07767 \{ -729,-1228,-1118,-1228,-1038\}, +07768 \{ -190, -689, -579, -689, -499\}\}\}\}, +07769 \textcolor{comment}{/* UG.@@.. @ */} +07770 \{\{\{\{ DEF, DEF, DEF, DEF, DEF\}, +07771 \{ DEF, DEF, DEF, DEF, DEF\}, +07772 \{ DEF, DEF, DEF, DEF, DEF\}, +07773 \{ DEF, DEF, DEF, DEF, DEF\}, +07774 \{ DEF, DEF, DEF, DEF, DEF\}\}, +07775 \textcolor{comment}{/* UG.@A.. @ */} +07776 \{\{ DEF, DEF, DEF, DEF, DEF\}, +07777 \{ DEF, DEF, DEF, DEF, DEF\}, +07778 \{ DEF, DEF, DEF, DEF, DEF\}, +07779 \{ DEF, DEF, DEF, DEF, DEF\}, +07780 \{ DEF, DEF, DEF, DEF, DEF\}\}, +07781 \textcolor{comment}{/* UG.@C.. @ */} +07782 \{\{ DEF, DEF, DEF, DEF, DEF\}, +07783 \{ DEF, DEF, DEF, DEF, DEF\}, +07784 \{ DEF, DEF, DEF, DEF, DEF\}, +07785 \{ DEF, DEF, DEF, DEF, DEF\}, +07786 \{ DEF, DEF, DEF, DEF, DEF\}\}, +07787 \textcolor{comment}{/* UG.@G.. @ */} +07788 \{\{ DEF, DEF, DEF, DEF, DEF\}, +07789 \{ DEF, DEF, DEF, DEF, DEF\}, +07790 \{ DEF, DEF, DEF, DEF, DEF\}, +07791 \{ DEF, DEF, DEF, DEF, DEF\}, +07792 \{ DEF, DEF, DEF, DEF, DEF\}\}, +07793 \textcolor{comment}{/* UG.@U.. @ */} +07794 \{\{ DEF, DEF, DEF, DEF, DEF\}, +07795 \{ DEF, DEF, DEF, DEF, DEF\}, +07796 \{ DEF, DEF, DEF, DEF, DEF\}, +07797 \{ DEF, DEF, DEF, DEF, DEF\}, +07798 \{ DEF, DEF, DEF, DEF, DEF\}\}\}, +07799 \textcolor{comment}{/* UG.A@.. @ */} +07800 \{\{\{ -100, -769, -839,-1009, -859\}, +07801 \{ -100, -769, -839,-1009, -859\}, +07802 \{ -100, -769, -839,-1009, -859\}, +07803 \{ -100, -769, -839,-1009, -859\}, +07804 \{ -100, -769, -839,-1009, -859\}\}, +07805 \textcolor{comment}{/* UG.AA.. @ */} +07806 \{\{ -100, -769, -839,-1009, -859\}, +07807 \{ -100, -769, -839,-1009, -859\}, +07808 \{ -100, -769, -839,-1009, -859\}, +07809 \{ -100, -769, -839,-1009, -859\}, +07810 \{ -100, -769, -839,-1009, -859\}\}, +07811 \textcolor{comment}{/* UG.AC.. @ */} +07812 \{\{ -100, -769, -839,-1009, -859\}, +07813 \{ -100, -769, -839,-1009, -859\}, +07814 \{ -100, -769, -839,-1009, -859\}, +07815 \{ -100, -769, -839,-1009, -859\}, +07816 \{ -100, -769, -839,-1009, -859\}\}, +07817 \textcolor{comment}{/* UG.AG.. @ */} +07818 \{\{ -100, -769, -839,-1009, -859\}, +07819 \{ -100, -769, -839,-1009, -859\}, +07820 \{ -100, -769, -839,-1009, -859\}, +07821 \{ -100, -769, -839,-1009, -859\}, +07822 \{ -100, -769, -839,-1009, -859\}\}, +07823 \textcolor{comment}{/* UG.AU.. @ */} +07824 \{\{ -100, -769, -839,-1009, -859\}, +07825 \{ -100, -769, -839,-1009, -859\}, +07826 \{ -100, -769, -839,-1009, -859\}, +07827 \{ -100, -769, -839,-1009, -859\}, +07828 \{ -100, -769, -839,-1009, -859\}\}\}, +07829 \textcolor{comment}{/* UG.C@.. @ */} +07830 \{\{\{ -100, -529, -529, -409, -529\}, +07831 \{ -100, -529, -529, -409, -529\}, +07832 \{ -100, -529, -529, -409, -529\}, +07833 \{ -100, -529, -529, -409, -529\}, +07834 \{ -100, -529, -529, -409, -529\}\}, +07835 \textcolor{comment}{/* UG.CA.. @ */} +07836 \{\{ -100, -529, -529, -409, -529\}, +07837 \{ -100, -529, -529, -409, -529\}, +07838 \{ -100, -529, -529, -409, -529\}, +07839 \{ -100, -529, -529, -409, -529\}, +07840 \{ -100, -529, -529, -409, -529\}\}, +07841 \textcolor{comment}{/* UG.CC.. @ */} +07842 \{\{ -100, -529, -529, -409, -529\}, +07843 \{ -100, -529, -529, -409, -529\}, +07844 \{ -100, -529, -529, -409, -529\}, +07845 \{ -100, -529, -529, -409, -529\}, +07846 \{ -100, -529, -529, -409, -529\}\}, +07847 \textcolor{comment}{/* UG.CG.. @ */} +07848 \{\{ -100, -529, -529, -409, -529\}, +07849 \{ -100, -529, -529, -409, -529\}, +07850 \{ -100, -529, -529, -409, -529\}, +07851 \{ -100, -529, -529, -409, -529\}, +07852 \{ -100, -529, -529, -409, -529\}\}, +07853 \textcolor{comment}{/* UG.CU.. @ */} +07854 \{\{ -100, -529, -529, -409, -529\}, +07855 \{ -100, -529, -529, -409, -529\}, +07856 \{ -100, -529, -529, -409, -529\}, +07857 \{ -100, -529, -529, -409, -529\}, +07858 \{ -100, -529, -529, -409, -529\}\}\}, +07859 \textcolor{comment}{/* UG.G@.. @ */} +07860 \{\{\{ -100, -709, -859, -969, -859\}, +07861 \{ -100, -709, -859, -969, -859\}, +07862 \{ -100, -709, -859, -969, -859\}, +07863 \{ -100, -709, -859, -969, -859\}, +07864 \{ -100, -709, -859, -969, -859\}\}, +07865 \textcolor{comment}{/* UG.GA.. @ */} +07866 \{\{ -100, -709, -859, -969, -859\}, +07867 \{ -100, -709, -859, -969, -859\}, +07868 \{ -100, -709, -859, -969, -859\}, +07869 \{ -100, -709, -859, -969, -859\}, +07870 \{ -100, -709, -859, -969, -859\}\}, +07871 \textcolor{comment}{/* UG.GC.. @ */} +07872 \{\{ -100, -709, -859, -969, -859\}, +07873 \{ -100, -709, -859, -969, -859\}, +07874 \{ -100, -709, -859, -969, -859\}, +07875 \{ -100, -709, -859, -969, -859\}, +07876 \{ -100, -709, -859, -969, -859\}\}, +07877 \textcolor{comment}{/* UG.GG.. @ */} +07878 \{\{ -100, -709, -859, -969, -859\}, +07879 \{ -100, -709, -859, -969, -859\}, +07880 \{ -100, -709, -859, -969, -859\}, +07881 \{ -100, -709, -859, -969, -859\}, +07882 \{ -100, -709, -859, -969, -859\}\}, +07883 \textcolor{comment}{/* UG.GU.. @ */} +07884 \{\{ -100, -709, -859, -969, -859\}, +07885 \{ -100, -709, -859, -969, -859\}, +07886 \{ -100, -709, -859, -969, -859\}, +07887 \{ -100, -709, -859, -969, -859\}, +07888 \{ -100, -709, -859, -969, -859\}\}\}, +07889 \textcolor{comment}{/* UG.U@.. @ */} +07890 \{\{\{ -100, -599, -489, -599, -409\}, +07891 \{ -100, -599, -489, -599, -409\}, +07892 \{ -100, -599, -489, -599, -409\}, +07893 \{ -100, -599, -489, -599, -409\}, +07894 \{ -100, -599, -489, -599, -409\}\}, +07895 \textcolor{comment}{/* UG.UA.. @ */} +07896 \{\{ -100, -599, -489, -599, -409\}, +07897 \{ -100, -599, -489, -599, -409\}, +07898 \{ -100, -599, -489, -599, -409\}, +07899 \{ -100, -599, -489, -599, -409\}, +07900 \{ -100, -599, -489, -599, -409\}\}, +07901 \textcolor{comment}{/* UG.UC.. @ */} +07902 \{\{ -100, -599, -489, -599, -409\}, +07903 \{ -100, -599, -489, -599, -409\}, +07904 \{ -100, -599, -489, -599, -409\}, +07905 \{ -100, -599, -489, -599, -409\}, +07906 \{ -100, -599, -489, -599, -409\}\}, +07907 \textcolor{comment}{/* UG.UG.. @ */} +07908 \{\{ -100, -599, -489, -599, -409\}, +07909 \{ -100, -599, -489, -599, -409\}, +07910 \{ -100, -599, -489, -599, -409\}, +07911 \{ -100, -599, -489, -599, -409\}, +07912 \{ -100, -599, -489, -599, -409\}\}, +07913 \textcolor{comment}{/* UG.UU.. @ */} +07914 \{\{ -100, -599, -489, -599, -409\}, +07915 \{ -100, -599, -489, -599, -409\}, +07916 \{ -100, -599, -489, -599, -409\}, +07917 \{ -100, -599, -489, -599, -409\}, +07918 \{ -100, -599, -489, -599, -409\}\}\}\}\}, +07919 \{ \textcolor{comment}{/* noPair */} \{\{\{\{0\}\}\}\}, +07920 \textcolor{comment}{/* AU.@@..CG */} +07921 \{\{\{\{ 0, 0, 0, 0, 0\}, +07922 \{ DEF, DEF, DEF, DEF, DEF\}, +07923 \{ DEF, DEF, DEF, DEF, DEF\}, +07924 \{ DEF, DEF, DEF, DEF, DEF\}, +07925 \{ DEF, DEF, DEF, DEF, DEF\}\}, +07926 \textcolor{comment}{/* AU.@A..CG */} +07927 \{\{ 0, 0, 0, 0, 0\}, +07928 \{-1029,-1029,-1029,-1029,-1029\}, +07929 \{ -519, -519, -519, -519, -519\}, +07930 \{ -939, -939, -939, -939, -939\}, +07931 \{ -809, -809, -809, -809, -809\}\}, +07932 \textcolor{comment}{/* AU.@C..CG */} +07933 \{\{ 0, 0, 0, 0, 0\}, +07934 \{ -949, -949, -949, -949, -949\}, +07935 \{ -449, -449, -449, -449, -449\}, +07936 \{ -939, -939, -939, -939, -939\}, +07937 \{ -739, -739, -739, -739, -739\}\}, +07938 \textcolor{comment}{/* AU.@G..CG */} +07939 \{\{ 0, 0, 0, 0, 0\}, +07940 \{-1029,-1029,-1029,-1029,-1029\}, +07941 \{ -519, -519, -519, -519, -519\}, +07942 \{ -939, -939, -939, -939, -939\}, +07943 \{ -809, -809, -809, -809, -809\}\}, +07944 \textcolor{comment}{/* AU.@U..CG */} +07945 \{\{ 0, 0, 0, 0, 0\}, +07946 \{-1029,-1029,-1029,-1029,-1029\}, +07947 \{ -669, -669, -669, -669, -669\}, +07948 \{ -939, -939, -939, -939, -939\}, +07949 \{ -859, -859, -859, -859, -859\}\}\}, +07950 \textcolor{comment}{/* AU.A@..CG */} +07951 \{\{\{ DEF, -429, -599, -599, -599\}, +07952 \{ -100, -479, -649, -649, -649\}, +07953 \{ -100, -479, -649, -649, -649\}, +07954 \{ -100, -479, -649, -649, -649\}, +07955 \{ -100, -479, -649, -649, -649\}\}, +07956 \textcolor{comment}{/* AU.AA..CG */} +07957 \{\{ DEF, -429, -599, -599, -599\}, +07958 \{-1079,-1458,-1628,-1628,-1628\}, +07959 \{ -569, -948,-1118,-1118,-1118\}, +07960 \{ -989,-1368,-1538,-1538,-1538\}, +07961 \{ -859,-1238,-1408,-1408,-1408\}\}, +07962 \textcolor{comment}{/* AU.AC..CG */} +07963 \{\{ DEF, -429, -599, -599, -599\}, +07964 \{ -999,-1378,-1548,-1548,-1548\}, +07965 \{ -499, -878,-1048,-1048,-1048\}, +07966 \{ -989,-1368,-1538,-1538,-1538\}, +07967 \{ -789,-1168,-1338,-1338,-1338\}\}, +07968 \textcolor{comment}{/* AU.AG..CG */} +07969 \{\{ DEF, -429, -599, -599, -599\}, +07970 \{-1079,-1458,-1628,-1628,-1628\}, +07971 \{ -569, -948,-1118,-1118,-1118\}, +07972 \{ -989,-1368,-1538,-1538,-1538\}, +07973 \{ -859,-1238,-1408,-1408,-1408\}\}, +07974 \textcolor{comment}{/* AU.AU..CG */} +07975 \{\{ DEF, -429, -599, -599, -599\}, +07976 \{-1079,-1458,-1628,-1628,-1628\}, +07977 \{ -719,-1098,-1268,-1268,-1268\}, +07978 \{ -989,-1368,-1538,-1538,-1538\}, +07979 \{ -909,-1288,-1458,-1458,-1458\}\}\}, +07980 \textcolor{comment}{/* AU.C@..CG */} +07981 \{\{\{ DEF, -259, -239, -239, -239\}, +07982 \{ -100, -309, -289, -289, -289\}, +07983 \{ -100, -309, -289, -289, -289\}, +07984 \{ -100, -309, -289, -289, -289\}, +07985 \{ -100, -309, -289, -289, -289\}\}, +07986 \textcolor{comment}{/* AU.CA..CG */} +07987 \{\{ DEF, -259, -239, -239, -239\}, +07988 \{-1079,-1288,-1268,-1268,-1268\}, +07989 \{ -569, -778, -758, -758, -758\}, +07990 \{ -989,-1198,-1178,-1178,-1178\}, +07991 \{ -859,-1068,-1048,-1048,-1048\}\}, +07992 \textcolor{comment}{/* AU.CC..CG */} +07993 \{\{ DEF, -259, -239, -239, -239\}, +07994 \{ -999,-1208,-1188,-1188,-1188\}, +07995 \{ -499, -708, -688, -688, -688\}, +07996 \{ -989,-1198,-1178,-1178,-1178\}, +07997 \{ -789, -998, -978, -978, -978\}\}, +07998 \textcolor{comment}{/* AU.CG..CG */} +07999 \{\{ DEF, -259, -239, -239, -239\}, +08000 \{-1079,-1288,-1268,-1268,-1268\}, +08001 \{ -569, -778, -758, -758, -758\}, +08002 \{ -989,-1198,-1178,-1178,-1178\}, +08003 \{ -859,-1068,-1048,-1048,-1048\}\}, +08004 \textcolor{comment}{/* AU.CU..CG */} +08005 \{\{ DEF, -259, -239, -239, -239\}, +08006 \{-1079,-1288,-1268,-1268,-1268\}, +08007 \{ -719, -928, -908, -908, -908\}, +08008 \{ -989,-1198,-1178,-1178,-1178\}, +08009 \{ -909,-1118,-1098,-1098,-1098\}\}\}, +08010 \textcolor{comment}{/* AU.G@..CG */} +08011 \{\{\{ DEF, -339, -689, -689, -689\}, +08012 \{ -100, -389, -739, -739, -739\}, +08013 \{ -100, -389, -739, -739, -739\}, +08014 \{ -100, -389, -739, -739, -739\}, +08015 \{ -100, -389, -739, -739, -739\}\}, +08016 \textcolor{comment}{/* AU.GA..CG */} +08017 \{\{ DEF, -339, -689, -689, -689\}, +08018 \{-1079,-1368,-1718,-1718,-1718\}, +08019 \{ -569, -858,-1208,-1208,-1208\}, +08020 \{ -989,-1278,-1628,-1628,-1628\}, +08021 \{ -859,-1148,-1498,-1498,-1498\}\}, +08022 \textcolor{comment}{/* AU.GC..CG */} +08023 \{\{ DEF, -339, -689, -689, -689\}, +08024 \{ -999,-1288,-1638,-1638,-1638\}, +08025 \{ -499, -788,-1138,-1138,-1138\}, +08026 \{ -989,-1278,-1628,-1628,-1628\}, +08027 \{ -789,-1078,-1428,-1428,-1428\}\}, +08028 \textcolor{comment}{/* AU.GG..CG */} +08029 \{\{ DEF, -339, -689, -689, -689\}, +08030 \{-1079,-1368,-1718,-1718,-1718\}, +08031 \{ -569, -858,-1208,-1208,-1208\}, +08032 \{ -989,-1278,-1628,-1628,-1628\}, +08033 \{ -859,-1148,-1498,-1498,-1498\}\}, +08034 \textcolor{comment}{/* AU.GU..CG */} +08035 \{\{ DEF, -339, -689, -689, -689\}, +08036 \{-1079,-1368,-1718,-1718,-1718\}, +08037 \{ -719,-1008,-1358,-1358,-1358\}, +08038 \{ -989,-1278,-1628,-1628,-1628\}, +08039 \{ -909,-1198,-1548,-1548,-1548\}\}\}, +08040 \textcolor{comment}{/* AU.U@..CG */} +08041 \{\{\{ DEF, -329, -329, -329, -329\}, +08042 \{ -100, -379, -379, -379, -379\}, +08043 \{ -100, -379, -379, -379, -379\}, +08044 \{ -100, -379, -379, -379, -379\}, +08045 \{ -100, -379, -379, -379, -379\}\}, +08046 \textcolor{comment}{/* AU.UA..CG */} +08047 \{\{ DEF, -329, -329, -329, -329\}, +08048 \{-1079,-1358,-1358,-1358,-1358\}, +08049 \{ -569, -848, -848, -848, -848\}, +08050 \{ -989,-1268,-1268,-1268,-1268\}, +08051 \{ -859,-1138,-1138,-1138,-1138\}\}, +08052 \textcolor{comment}{/* AU.UC..CG */} +08053 \{\{ DEF, -329, -329, -329, -329\}, +08054 \{ -999,-1278,-1278,-1278,-1278\}, +08055 \{ -499, -778, -778, -778, -778\}, +08056 \{ -989,-1268,-1268,-1268,-1268\}, +08057 \{ -789,-1068,-1068,-1068,-1068\}\}, +08058 \textcolor{comment}{/* AU.UG..CG */} +08059 \{\{ DEF, -329, -329, -329, -329\}, +08060 \{-1079,-1358,-1358,-1358,-1358\}, +08061 \{ -569, -848, -848, -848, -848\}, +08062 \{ -989,-1268,-1268,-1268,-1268\}, +08063 \{ -859,-1138,-1138,-1138,-1138\}\}, +08064 \textcolor{comment}{/* AU.UU..CG */} +08065 \{\{ DEF, -329, -329, -329, -329\}, +08066 \{-1079,-1358,-1358,-1358,-1358\}, +08067 \{ -719, -998, -998, -998, -998\}, +08068 \{ -989,-1268,-1268,-1268,-1268\}, +08069 \{ -909,-1188,-1188,-1188,-1188\}\}\}\}, +08070 \textcolor{comment}{/* AU.@@..GC */} +08071 \{\{\{\{ 0, 0, 0, 0, 0\}, +08072 \{ DEF, DEF, DEF, DEF, DEF\}, +08073 \{ DEF, DEF, DEF, DEF, DEF\}, +08074 \{ DEF, DEF, DEF, DEF, DEF\}, +08075 \{ DEF, DEF, DEF, DEF, DEF\}\}, +08076 \textcolor{comment}{/* AU.@A..GC */} +08077 \{\{ 0, 0, 0, 0, 0\}, +08078 \{ -519, -519, -519, -519, -519\}, +08079 \{ -719, -719, -719, -719, -719\}, +08080 \{ -709, -709, -709, -709, -709\}, +08081 \{ -499, -499, -499, -499, -499\}\}, +08082 \textcolor{comment}{/* AU.@C..GC */} +08083 \{\{ 0, 0, 0, 0, 0\}, +08084 \{ -879, -879, -879, -879, -879\}, +08085 \{ -309, -309, -309, -309, -309\}, +08086 \{ -739, -739, -739, -739, -739\}, +08087 \{ -499, -499, -499, -499, -499\}\}, +08088 \textcolor{comment}{/* AU.@G..GC */} +08089 \{\{ 0, 0, 0, 0, 0\}, +08090 \{ -559, -559, -559, -559, -559\}, +08091 \{ -309, -309, -309, -309, -309\}, +08092 \{ -619, -619, -619, -619, -619\}, +08093 \{ -499, -499, -499, -499, -499\}\}, +08094 \textcolor{comment}{/* AU.@U..GC */} +08095 \{\{ 0, 0, 0, 0, 0\}, +08096 \{ -879, -879, -879, -879, -879\}, +08097 \{ -389, -389, -389, -389, -389\}, +08098 \{ -739, -739, -739, -739, -739\}, +08099 \{ -569, -569, -569, -569, -569\}\}\}, +08100 \textcolor{comment}{/* AU.A@..GC */} +08101 \{\{\{ DEF, -429, -599, -599, -599\}, +08102 \{ -100, -479, -649, -649, -649\}, +08103 \{ -100, -479, -649, -649, -649\}, +08104 \{ -100, -479, -649, -649, -649\}, +08105 \{ -100, -479, -649, -649, -649\}\}, +08106 \textcolor{comment}{/* AU.AA..GC */} +08107 \{\{ DEF, -429, -599, -599, -599\}, +08108 \{ -569, -948,-1118,-1118,-1118\}, +08109 \{ -769,-1148,-1318,-1318,-1318\}, +08110 \{ -759,-1138,-1308,-1308,-1308\}, +08111 \{ -549, -928,-1098,-1098,-1098\}\}, +08112 \textcolor{comment}{/* AU.AC..GC */} +08113 \{\{ DEF, -429, -599, -599, -599\}, +08114 \{ -929,-1308,-1478,-1478,-1478\}, +08115 \{ -359, -738, -908, -908, -908\}, +08116 \{ -789,-1168,-1338,-1338,-1338\}, +08117 \{ -549, -928,-1098,-1098,-1098\}\}, +08118 \textcolor{comment}{/* AU.AG..GC */} +08119 \{\{ DEF, -429, -599, -599, -599\}, +08120 \{ -609, -988,-1158,-1158,-1158\}, +08121 \{ -359, -738, -908, -908, -908\}, +08122 \{ -669,-1048,-1218,-1218,-1218\}, +08123 \{ -549, -928,-1098,-1098,-1098\}\}, +08124 \textcolor{comment}{/* AU.AU..GC */} +08125 \{\{ DEF, -429, -599, -599, -599\}, +08126 \{ -929,-1308,-1478,-1478,-1478\}, +08127 \{ -439, -818, -988, -988, -988\}, +08128 \{ -789,-1168,-1338,-1338,-1338\}, +08129 \{ -619, -998,-1168,-1168,-1168\}\}\}, +08130 \textcolor{comment}{/* AU.C@..GC */} +08131 \{\{\{ DEF, -259, -239, -239, -239\}, +08132 \{ -100, -309, -289, -289, -289\}, +08133 \{ -100, -309, -289, -289, -289\}, +08134 \{ -100, -309, -289, -289, -289\}, +08135 \{ -100, -309, -289, -289, -289\}\}, +08136 \textcolor{comment}{/* AU.CA..GC */} +08137 \{\{ DEF, -259, -239, -239, -239\}, +08138 \{ -569, -778, -758, -758, -758\}, +08139 \{ -769, -978, -958, -958, -958\}, +08140 \{ -759, -968, -948, -948, -948\}, +08141 \{ -549, -758, -738, -738, -738\}\}, +08142 \textcolor{comment}{/* AU.CC..GC */} +08143 \{\{ DEF, -259, -239, -239, -239\}, +08144 \{ -929,-1138,-1118,-1118,-1118\}, +08145 \{ -359, -568, -548, -548, -548\}, +08146 \{ -789, -998, -978, -978, -978\}, +08147 \{ -549, -758, -738, -738, -738\}\}, +08148 \textcolor{comment}{/* AU.CG..GC */} +08149 \{\{ DEF, -259, -239, -239, -239\}, +08150 \{ -609, -818, -798, -798, -798\}, +08151 \{ -359, -568, -548, -548, -548\}, +08152 \{ -669, -878, -858, -858, -858\}, +08153 \{ -549, -758, -738, -738, -738\}\}, +08154 \textcolor{comment}{/* AU.CU..GC */} +08155 \{\{ DEF, -259, -239, -239, -239\}, +08156 \{ -929,-1138,-1118,-1118,-1118\}, +08157 \{ -439, -648, -628, -628, -628\}, +08158 \{ -789, -998, -978, -978, -978\}, +08159 \{ -619, -828, -808, -808, -808\}\}\}, +08160 \textcolor{comment}{/* AU.G@..GC */} +08161 \{\{\{ DEF, -339, -689, -689, -689\}, +08162 \{ -100, -389, -739, -739, -739\}, +08163 \{ -100, -389, -739, -739, -739\}, +08164 \{ -100, -389, -739, -739, -739\}, +08165 \{ -100, -389, -739, -739, -739\}\}, +08166 \textcolor{comment}{/* AU.GA..GC */} +08167 \{\{ DEF, -339, -689, -689, -689\}, +08168 \{ -569, -858,-1208,-1208,-1208\}, +08169 \{ -769,-1058,-1408,-1408,-1408\}, +08170 \{ -759,-1048,-1398,-1398,-1398\}, +08171 \{ -549, -838,-1188,-1188,-1188\}\}, +08172 \textcolor{comment}{/* AU.GC..GC */} +08173 \{\{ DEF, -339, -689, -689, -689\}, +08174 \{ -929,-1218,-1568,-1568,-1568\}, +08175 \{ -359, -648, -998, -998, -998\}, +08176 \{ -789,-1078,-1428,-1428,-1428\}, +08177 \{ -549, -838,-1188,-1188,-1188\}\}, +08178 \textcolor{comment}{/* AU.GG..GC */} +08179 \{\{ DEF, -339, -689, -689, -689\}, +08180 \{ -609, -898,-1248,-1248,-1248\}, +08181 \{ -359, -648, -998, -998, -998\}, +08182 \{ -669, -958,-1308,-1308,-1308\}, +08183 \{ -549, -838,-1188,-1188,-1188\}\}, +08184 \textcolor{comment}{/* AU.GU..GC */} +08185 \{\{ DEF, -339, -689, -689, -689\}, +08186 \{ -929,-1218,-1568,-1568,-1568\}, +08187 \{ -439, -728,-1078,-1078,-1078\}, +08188 \{ -789,-1078,-1428,-1428,-1428\}, +08189 \{ -619, -908,-1258,-1258,-1258\}\}\}, +08190 \textcolor{comment}{/* AU.U@..GC */} +08191 \{\{\{ DEF, -329, -329, -329, -329\}, +08192 \{ -100, -379, -379, -379, -379\}, +08193 \{ -100, -379, -379, -379, -379\}, +08194 \{ -100, -379, -379, -379, -379\}, +08195 \{ -100, -379, -379, -379, -379\}\}, +08196 \textcolor{comment}{/* AU.UA..GC */} +08197 \{\{ DEF, -329, -329, -329, -329\}, +08198 \{ -569, -848, -848, -848, -848\}, +08199 \{ -769,-1048,-1048,-1048,-1048\}, +08200 \{ -759,-1038,-1038,-1038,-1038\}, +08201 \{ -549, -828, -828, -828, -828\}\}, +08202 \textcolor{comment}{/* AU.UC..GC */} +08203 \{\{ DEF, -329, -329, -329, -329\}, +08204 \{ -929,-1208,-1208,-1208,-1208\}, +08205 \{ -359, -638, -638, -638, -638\}, +08206 \{ -789,-1068,-1068,-1068,-1068\}, +08207 \{ -549, -828, -828, -828, -828\}\}, +08208 \textcolor{comment}{/* AU.UG..GC */} +08209 \{\{ DEF, -329, -329, -329, -329\}, +08210 \{ -609, -888, -888, -888, -888\}, +08211 \{ -359, -638, -638, -638, -638\}, +08212 \{ -669, -948, -948, -948, -948\}, +08213 \{ -549, -828, -828, -828, -828\}\}, +08214 \textcolor{comment}{/* AU.UU..GC */} +08215 \{\{ DEF, -329, -329, -329, -329\}, +08216 \{ -929,-1208,-1208,-1208,-1208\}, +08217 \{ -439, -718, -718, -718, -718\}, +08218 \{ -789,-1068,-1068,-1068,-1068\}, +08219 \{ -619, -898, -898, -898, -898\}\}\}\}, +08220 \textcolor{comment}{/* AU.@@..GU */} +08221 \{\{\{\{ 0, 0, 0, 0, 0\}, +08222 \{ DEF, DEF, DEF, DEF, DEF\}, +08223 \{ DEF, DEF, DEF, DEF, DEF\}, +08224 \{ DEF, DEF, DEF, DEF, DEF\}, +08225 \{ DEF, DEF, DEF, DEF, DEF\}\}, +08226 \textcolor{comment}{/* AU.@A..GU */} +08227 \{\{ 0, 0, 0, 0, 0\}, +08228 \{ -429, -429, -429, -429, -429\}, +08229 \{ -259, -259, -259, -259, -259\}, +08230 \{ -339, -339, -339, -339, -339\}, +08231 \{ -329, -329, -329, -329, -329\}\}, +08232 \textcolor{comment}{/* AU.@C..GU */} +08233 \{\{ 0, 0, 0, 0, 0\}, +08234 \{ -599, -599, -599, -599, -599\}, +08235 \{ -239, -239, -239, -239, -239\}, +08236 \{ -689, -689, -689, -689, -689\}, +08237 \{ -329, -329, -329, -329, -329\}\}, +08238 \textcolor{comment}{/* AU.@G..GU */} +08239 \{\{ 0, 0, 0, 0, 0\}, +08240 \{ -599, -599, -599, -599, -599\}, +08241 \{ -239, -239, -239, -239, -239\}, +08242 \{ -689, -689, -689, -689, -689\}, +08243 \{ -329, -329, -329, -329, -329\}\}, +08244 \textcolor{comment}{/* AU.@U..GU */} +08245 \{\{ 0, 0, 0, 0, 0\}, +08246 \{ -599, -599, -599, -599, -599\}, +08247 \{ -239, -239, -239, -239, -239\}, +08248 \{ -689, -689, -689, -689, -689\}, +08249 \{ -329, -329, -329, -329, -329\}\}\}, +08250 \textcolor{comment}{/* AU.A@..GU */} +08251 \{\{\{ DEF, -429, -599, -599, -599\}, +08252 \{ -100, -479, -649, -649, -649\}, +08253 \{ -100, -479, -649, -649, -649\}, +08254 \{ -100, -479, -649, -649, -649\}, +08255 \{ -100, -479, -649, -649, -649\}\}, +08256 \textcolor{comment}{/* AU.AA..GU */} +08257 \{\{ DEF, -429, -599, -599, -599\}, +08258 \{ -479, -858,-1028,-1028,-1028\}, +08259 \{ -309, -688, -858, -858, -858\}, +08260 \{ -389, -768, -938, -938, -938\}, +08261 \{ -379, -758, -928, -928, -928\}\}, +08262 \textcolor{comment}{/* AU.AC..GU */} +08263 \{\{ DEF, -429, -599, -599, -599\}, +08264 \{ -649,-1028,-1198,-1198,-1198\}, +08265 \{ -289, -668, -838, -838, -838\}, +08266 \{ -739,-1118,-1288,-1288,-1288\}, +08267 \{ -379, -758, -928, -928, -928\}\}, +08268 \textcolor{comment}{/* AU.AG..GU */} +08269 \{\{ DEF, -429, -599, -599, -599\}, +08270 \{ -649,-1028,-1198,-1198,-1198\}, +08271 \{ -289, -668, -838, -838, -838\}, +08272 \{ -739,-1118,-1288,-1288,-1288\}, +08273 \{ -379, -758, -928, -928, -928\}\}, +08274 \textcolor{comment}{/* AU.AU..GU */} +08275 \{\{ DEF, -429, -599, -599, -599\}, +08276 \{ -649,-1028,-1198,-1198,-1198\}, +08277 \{ -289, -668, -838, -838, -838\}, +08278 \{ -739,-1118,-1288,-1288,-1288\}, +08279 \{ -379, -758, -928, -928, -928\}\}\}, +08280 \textcolor{comment}{/* AU.C@..GU */} +08281 \{\{\{ DEF, -259, -239, -239, -239\}, +08282 \{ -100, -309, -289, -289, -289\}, +08283 \{ -100, -309, -289, -289, -289\}, +08284 \{ -100, -309, -289, -289, -289\}, +08285 \{ -100, -309, -289, -289, -289\}\}, +08286 \textcolor{comment}{/* AU.CA..GU */} +08287 \{\{ DEF, -259, -239, -239, -239\}, +08288 \{ -479, -688, -668, -668, -668\}, +08289 \{ -309, -518, -498, -498, -498\}, +08290 \{ -389, -598, -578, -578, -578\}, +08291 \{ -379, -588, -568, -568, -568\}\}, +08292 \textcolor{comment}{/* AU.CC..GU */} +08293 \{\{ DEF, -259, -239, -239, -239\}, +08294 \{ -649, -858, -838, -838, -838\}, +08295 \{ -289, -498, -478, -478, -478\}, +08296 \{ -739, -948, -928, -928, -928\}, +08297 \{ -379, -588, -568, -568, -568\}\}, +08298 \textcolor{comment}{/* AU.CG..GU */} +08299 \{\{ DEF, -259, -239, -239, -239\}, +08300 \{ -649, -858, -838, -838, -838\}, +08301 \{ -289, -498, -478, -478, -478\}, +08302 \{ -739, -948, -928, -928, -928\}, +08303 \{ -379, -588, -568, -568, -568\}\}, +08304 \textcolor{comment}{/* AU.CU..GU */} +08305 \{\{ DEF, -259, -239, -239, -239\}, +08306 \{ -649, -858, -838, -838, -838\}, +08307 \{ -289, -498, -478, -478, -478\}, +08308 \{ -739, -948, -928, -928, -928\}, +08309 \{ -379, -588, -568, -568, -568\}\}\}, +08310 \textcolor{comment}{/* AU.G@..GU */} +08311 \{\{\{ DEF, -339, -689, -689, -689\}, +08312 \{ -100, -389, -739, -739, -739\}, +08313 \{ -100, -389, -739, -739, -739\}, +08314 \{ -100, -389, -739, -739, -739\}, +08315 \{ -100, -389, -739, -739, -739\}\}, +08316 \textcolor{comment}{/* AU.GA..GU */} +08317 \{\{ DEF, -339, -689, -689, -689\}, +08318 \{ -479, -768,-1118,-1118,-1118\}, +08319 \{ -309, -598, -948, -948, -948\}, +08320 \{ -389, -678,-1028,-1028,-1028\}, +08321 \{ -379, -668,-1018,-1018,-1018\}\}, +08322 \textcolor{comment}{/* AU.GC..GU */} +08323 \{\{ DEF, -339, -689, -689, -689\}, +08324 \{ -649, -938,-1288,-1288,-1288\}, +08325 \{ -289, -578, -928, -928, -928\}, +08326 \{ -739,-1028,-1378,-1378,-1378\}, +08327 \{ -379, -668,-1018,-1018,-1018\}\}, +08328 \textcolor{comment}{/* AU.GG..GU */} +08329 \{\{ DEF, -339, -689, -689, -689\}, +08330 \{ -649, -938,-1288,-1288,-1288\}, +08331 \{ -289, -578, -928, -928, -928\}, +08332 \{ -739,-1028,-1378,-1378,-1378\}, +08333 \{ -379, -668,-1018,-1018,-1018\}\}, +08334 \textcolor{comment}{/* AU.GU..GU */} +08335 \{\{ DEF, -339, -689, -689, -689\}, +08336 \{ -649, -938,-1288,-1288,-1288\}, +08337 \{ -289, -578, -928, -928, -928\}, +08338 \{ -739,-1028,-1378,-1378,-1378\}, +08339 \{ -379, -668,-1018,-1018,-1018\}\}\}, +08340 \textcolor{comment}{/* AU.U@..GU */} +08341 \{\{\{ DEF, -329, -329, -329, -329\}, +08342 \{ -100, -379, -379, -379, -379\}, +08343 \{ -100, -379, -379, -379, -379\}, +08344 \{ -100, -379, -379, -379, -379\}, +08345 \{ -100, -379, -379, -379, -379\}\}, +08346 \textcolor{comment}{/* AU.UA..GU */} +08347 \{\{ DEF, -329, -329, -329, -329\}, +08348 \{ -479, -758, -758, -758, -758\}, +08349 \{ -309, -588, -588, -588, -588\}, +08350 \{ -389, -668, -668, -668, -668\}, +08351 \{ -379, -658, -658, -658, -658\}\}, +08352 \textcolor{comment}{/* AU.UC..GU */} +08353 \{\{ DEF, -329, -329, -329, -329\}, +08354 \{ -649, -928, -928, -928, -928\}, +08355 \{ -289, -568, -568, -568, -568\}, +08356 \{ -739,-1018,-1018,-1018,-1018\}, +08357 \{ -379, -658, -658, -658, -658\}\}, +08358 \textcolor{comment}{/* AU.UG..GU */} +08359 \{\{ DEF, -329, -329, -329, -329\}, +08360 \{ -649, -928, -928, -928, -928\}, +08361 \{ -289, -568, -568, -568, -568\}, +08362 \{ -739,-1018,-1018,-1018,-1018\}, +08363 \{ -379, -658, -658, -658, -658\}\}, +08364 \textcolor{comment}{/* AU.UU..GU */} +08365 \{\{ DEF, -329, -329, -329, -329\}, +08366 \{ -649, -928, -928, -928, -928\}, +08367 \{ -289, -568, -568, -568, -568\}, +08368 \{ -739,-1018,-1018,-1018,-1018\}, +08369 \{ -379, -658, -658, -658, -658\}\}\}\}, +08370 \textcolor{comment}{/* AU.@@..UG */} +08371 \{\{\{\{ 0, 0, 0, 0, 0\}, +08372 \{ DEF, DEF, DEF, DEF, DEF\}, +08373 \{ DEF, DEF, DEF, DEF, DEF\}, +08374 \{ DEF, DEF, DEF, DEF, DEF\}, +08375 \{ DEF, DEF, DEF, DEF, DEF\}\}, +08376 \textcolor{comment}{/* AU.@A..UG */} +08377 \{\{ 0, 0, 0, 0, 0\}, +08378 \{ -719, -719, -719, -719, -719\}, +08379 \{ -479, -479, -479, -479, -479\}, +08380 \{ -659, -659, -659, -659, -659\}, +08381 \{ -549, -549, -549, -549, -549\}\}, +08382 \textcolor{comment}{/* AU.@C..UG */} +08383 \{\{ 0, 0, 0, 0, 0\}, +08384 \{ -789, -789, -789, -789, -789\}, +08385 \{ -479, -479, -479, -479, -479\}, +08386 \{ -809, -809, -809, -809, -809\}, +08387 \{ -439, -439, -439, -439, -439\}\}, +08388 \textcolor{comment}{/* AU.@G..UG */} +08389 \{\{ 0, 0, 0, 0, 0\}, +08390 \{ -959, -959, -959, -959, -959\}, +08391 \{ -359, -359, -359, -359, -359\}, +08392 \{ -919, -919, -919, -919, -919\}, +08393 \{ -549, -549, -549, -549, -549\}\}, +08394 \textcolor{comment}{/* AU.@U..UG */} +08395 \{\{ 0, 0, 0, 0, 0\}, +08396 \{ -809, -809, -809, -809, -809\}, +08397 \{ -479, -479, -479, -479, -479\}, +08398 \{ -809, -809, -809, -809, -809\}, +08399 \{ -359, -359, -359, -359, -359\}\}\}, +08400 \textcolor{comment}{/* AU.A@..UG */} +08401 \{\{\{ DEF, -429, -599, -599, -599\}, +08402 \{ -100, -479, -649, -649, -649\}, +08403 \{ -100, -479, -649, -649, -649\}, +08404 \{ -100, -479, -649, -649, -649\}, +08405 \{ -100, -479, -649, -649, -649\}\}, +08406 \textcolor{comment}{/* AU.AA..UG */} +08407 \{\{ DEF, -429, -599, -599, -599\}, +08408 \{ -769,-1148,-1318,-1318,-1318\}, +08409 \{ -529, -908,-1078,-1078,-1078\}, +08410 \{ -709,-1088,-1258,-1258,-1258\}, +08411 \{ -599, -978,-1148,-1148,-1148\}\}, +08412 \textcolor{comment}{/* AU.AC..UG */} +08413 \{\{ DEF, -429, -599, -599, -599\}, +08414 \{ -839,-1218,-1388,-1388,-1388\}, +08415 \{ -529, -908,-1078,-1078,-1078\}, +08416 \{ -859,-1238,-1408,-1408,-1408\}, +08417 \{ -489, -868,-1038,-1038,-1038\}\}, +08418 \textcolor{comment}{/* AU.AG..UG */} +08419 \{\{ DEF, -429, -599, -599, -599\}, +08420 \{-1009,-1388,-1558,-1558,-1558\}, +08421 \{ -409, -788, -958, -958, -958\}, +08422 \{ -969,-1348,-1518,-1518,-1518\}, +08423 \{ -599, -978,-1148,-1148,-1148\}\}, +08424 \textcolor{comment}{/* AU.AU..UG */} +08425 \{\{ DEF, -429, -599, -599, -599\}, +08426 \{ -859,-1238,-1408,-1408,-1408\}, +08427 \{ -529, -908,-1078,-1078,-1078\}, +08428 \{ -859,-1238,-1408,-1408,-1408\}, +08429 \{ -409, -788, -958, -958, -958\}\}\}, +08430 \textcolor{comment}{/* AU.C@..UG */} +08431 \{\{\{ DEF, -259, -239, -239, -239\}, +08432 \{ -100, -309, -289, -289, -289\}, +08433 \{ -100, -309, -289, -289, -289\}, +08434 \{ -100, -309, -289, -289, -289\}, +08435 \{ -100, -309, -289, -289, -289\}\}, +08436 \textcolor{comment}{/* AU.CA..UG */} +08437 \{\{ DEF, -259, -239, -239, -239\}, +08438 \{ -769, -978, -958, -958, -958\}, +08439 \{ -529, -738, -718, -718, -718\}, +08440 \{ -709, -918, -898, -898, -898\}, +08441 \{ -599, -808, -788, -788, -788\}\}, +08442 \textcolor{comment}{/* AU.CC..UG */} +08443 \{\{ DEF, -259, -239, -239, -239\}, +08444 \{ -839,-1048,-1028,-1028,-1028\}, +08445 \{ -529, -738, -718, -718, -718\}, +08446 \{ -859,-1068,-1048,-1048,-1048\}, +08447 \{ -489, -698, -678, -678, -678\}\}, +08448 \textcolor{comment}{/* AU.CG..UG */} +08449 \{\{ DEF, -259, -239, -239, -239\}, +08450 \{-1009,-1218,-1198,-1198,-1198\}, +08451 \{ -409, -618, -598, -598, -598\}, +08452 \{ -969,-1178,-1158,-1158,-1158\}, +08453 \{ -599, -808, -788, -788, -788\}\}, +08454 \textcolor{comment}{/* AU.CU..UG */} +08455 \{\{ DEF, -259, -239, -239, -239\}, +08456 \{ -859,-1068,-1048,-1048,-1048\}, +08457 \{ -529, -738, -718, -718, -718\}, +08458 \{ -859,-1068,-1048,-1048,-1048\}, +08459 \{ -409, -618, -598, -598, -598\}\}\}, +08460 \textcolor{comment}{/* AU.G@..UG */} +08461 \{\{\{ DEF, -339, -689, -689, -689\}, +08462 \{ -100, -389, -739, -739, -739\}, +08463 \{ -100, -389, -739, -739, -739\}, +08464 \{ -100, -389, -739, -739, -739\}, +08465 \{ -100, -389, -739, -739, -739\}\}, +08466 \textcolor{comment}{/* AU.GA..UG */} +08467 \{\{ DEF, -339, -689, -689, -689\}, +08468 \{ -769,-1058,-1408,-1408,-1408\}, +08469 \{ -529, -818,-1168,-1168,-1168\}, +08470 \{ -709, -998,-1348,-1348,-1348\}, +08471 \{ -599, -888,-1238,-1238,-1238\}\}, +08472 \textcolor{comment}{/* AU.GC..UG */} +08473 \{\{ DEF, -339, -689, -689, -689\}, +08474 \{ -839,-1128,-1478,-1478,-1478\}, +08475 \{ -529, -818,-1168,-1168,-1168\}, +08476 \{ -859,-1148,-1498,-1498,-1498\}, +08477 \{ -489, -778,-1128,-1128,-1128\}\}, +08478 \textcolor{comment}{/* AU.GG..UG */} +08479 \{\{ DEF, -339, -689, -689, -689\}, +08480 \{-1009,-1298,-1648,-1648,-1648\}, +08481 \{ -409, -698,-1048,-1048,-1048\}, +08482 \{ -969,-1258,-1608,-1608,-1608\}, +08483 \{ -599, -888,-1238,-1238,-1238\}\}, +08484 \textcolor{comment}{/* AU.GU..UG */} +08485 \{\{ DEF, -339, -689, -689, -689\}, +08486 \{ -859,-1148,-1498,-1498,-1498\}, +08487 \{ -529, -818,-1168,-1168,-1168\}, +08488 \{ -859,-1148,-1498,-1498,-1498\}, +08489 \{ -409, -698,-1048,-1048,-1048\}\}\}, +08490 \textcolor{comment}{/* AU.U@..UG */} +08491 \{\{\{ DEF, -329, -329, -329, -329\}, +08492 \{ -100, -379, -379, -379, -379\}, +08493 \{ -100, -379, -379, -379, -379\}, +08494 \{ -100, -379, -379, -379, -379\}, +08495 \{ -100, -379, -379, -379, -379\}\}, +08496 \textcolor{comment}{/* AU.UA..UG */} +08497 \{\{ DEF, -329, -329, -329, -329\}, +08498 \{ -769,-1048,-1048,-1048,-1048\}, +08499 \{ -529, -808, -808, -808, -808\}, +08500 \{ -709, -988, -988, -988, -988\}, +08501 \{ -599, -878, -878, -878, -878\}\}, +08502 \textcolor{comment}{/* AU.UC..UG */} +08503 \{\{ DEF, -329, -329, -329, -329\}, +08504 \{ -839,-1118,-1118,-1118,-1118\}, +08505 \{ -529, -808, -808, -808, -808\}, +08506 \{ -859,-1138,-1138,-1138,-1138\}, +08507 \{ -489, -768, -768, -768, -768\}\}, +08508 \textcolor{comment}{/* AU.UG..UG */} +08509 \{\{ DEF, -329, -329, -329, -329\}, +08510 \{-1009,-1288,-1288,-1288,-1288\}, +08511 \{ -409, -688, -688, -688, -688\}, +08512 \{ -969,-1248,-1248,-1248,-1248\}, +08513 \{ -599, -878, -878, -878, -878\}\}, +08514 \textcolor{comment}{/* AU.UU..UG */} +08515 \{\{ DEF, -329, -329, -329, -329\}, +08516 \{ -859,-1138,-1138,-1138,-1138\}, +08517 \{ -529, -808, -808, -808, -808\}, +08518 \{ -859,-1138,-1138,-1138,-1138\}, +08519 \{ -409, -688, -688, -688, -688\}\}\}\}, +08520 \textcolor{comment}{/* AU.@@..AU */} +08521 \{\{\{\{ 0, 0, 0, 0, 0\}, +08522 \{ DEF, DEF, DEF, DEF, DEF\}, +08523 \{ DEF, DEF, DEF, DEF, DEF\}, +08524 \{ DEF, DEF, DEF, DEF, DEF\}, +08525 \{ DEF, DEF, DEF, DEF, DEF\}\}, +08526 \textcolor{comment}{/* AU.@A..AU */} +08527 \{\{ 0, 0, 0, 0, 0\}, +08528 \{ -429, -429, -429, -429, -429\}, +08529 \{ -259, -259, -259, -259, -259\}, +08530 \{ -339, -339, -339, -339, -339\}, +08531 \{ -329, -329, -329, -329, -329\}\}, +08532 \textcolor{comment}{/* AU.@C..AU */} +08533 \{\{ 0, 0, 0, 0, 0\}, +08534 \{ -599, -599, -599, -599, -599\}, +08535 \{ -239, -239, -239, -239, -239\}, +08536 \{ -689, -689, -689, -689, -689\}, +08537 \{ -329, -329, -329, -329, -329\}\}, +08538 \textcolor{comment}{/* AU.@G..AU */} +08539 \{\{ 0, 0, 0, 0, 0\}, +08540 \{ -599, -599, -599, -599, -599\}, +08541 \{ -239, -239, -239, -239, -239\}, +08542 \{ -689, -689, -689, -689, -689\}, +08543 \{ -329, -329, -329, -329, -329\}\}, +08544 \textcolor{comment}{/* AU.@U..AU */} +08545 \{\{ 0, 0, 0, 0, 0\}, +08546 \{ -599, -599, -599, -599, -599\}, +08547 \{ -239, -239, -239, -239, -239\}, +08548 \{ -689, -689, -689, -689, -689\}, +08549 \{ -329, -329, -329, -329, -329\}\}\}, +08550 \textcolor{comment}{/* AU.A@..AU */} +08551 \{\{\{ DEF, -429, -599, -599, -599\}, +08552 \{ -100, -479, -649, -649, -649\}, +08553 \{ -100, -479, -649, -649, -649\}, +08554 \{ -100, -479, -649, -649, -649\}, +08555 \{ -100, -479, -649, -649, -649\}\}, +08556 \textcolor{comment}{/* AU.AA..AU */} +08557 \{\{ DEF, -429, -599, -599, -599\}, +08558 \{ -479, -858,-1028,-1028,-1028\}, +08559 \{ -309, -688, -858, -858, -858\}, +08560 \{ -389, -768, -938, -938, -938\}, +08561 \{ -379, -758, -928, -928, -928\}\}, +08562 \textcolor{comment}{/* AU.AC..AU */} +08563 \{\{ DEF, -429, -599, -599, -599\}, +08564 \{ -649,-1028,-1198,-1198,-1198\}, +08565 \{ -289, -668, -838, -838, -838\}, +08566 \{ -739,-1118,-1288,-1288,-1288\}, +08567 \{ -379, -758, -928, -928, -928\}\}, +08568 \textcolor{comment}{/* AU.AG..AU */} +08569 \{\{ DEF, -429, -599, -599, -599\}, +08570 \{ -649,-1028,-1198,-1198,-1198\}, +08571 \{ -289, -668, -838, -838, -838\}, +08572 \{ -739,-1118,-1288,-1288,-1288\}, +08573 \{ -379, -758, -928, -928, -928\}\}, +08574 \textcolor{comment}{/* AU.AU..AU */} +08575 \{\{ DEF, -429, -599, -599, -599\}, +08576 \{ -649,-1028,-1198,-1198,-1198\}, +08577 \{ -289, -668, -838, -838, -838\}, +08578 \{ -739,-1118,-1288,-1288,-1288\}, +08579 \{ -379, -758, -928, -928, -928\}\}\}, +08580 \textcolor{comment}{/* AU.C@..AU */} +08581 \{\{\{ DEF, -259, -239, -239, -239\}, +08582 \{ -100, -309, -289, -289, -289\}, +08583 \{ -100, -309, -289, -289, -289\}, +08584 \{ -100, -309, -289, -289, -289\}, +08585 \{ -100, -309, -289, -289, -289\}\}, +08586 \textcolor{comment}{/* AU.CA..AU */} +08587 \{\{ DEF, -259, -239, -239, -239\}, +08588 \{ -479, -688, -668, -668, -668\}, +08589 \{ -309, -518, -498, -498, -498\}, +08590 \{ -389, -598, -578, -578, -578\}, +08591 \{ -379, -588, -568, -568, -568\}\}, +08592 \textcolor{comment}{/* AU.CC..AU */} +08593 \{\{ DEF, -259, -239, -239, -239\}, +08594 \{ -649, -858, -838, -838, -838\}, +08595 \{ -289, -498, -478, -478, -478\}, +08596 \{ -739, -948, -928, -928, -928\}, +08597 \{ -379, -588, -568, -568, -568\}\}, +08598 \textcolor{comment}{/* AU.CG..AU */} +08599 \{\{ DEF, -259, -239, -239, -239\}, +08600 \{ -649, -858, -838, -838, -838\}, +08601 \{ -289, -498, -478, -478, -478\}, +08602 \{ -739, -948, -928, -928, -928\}, +08603 \{ -379, -588, -568, -568, -568\}\}, +08604 \textcolor{comment}{/* AU.CU..AU */} +08605 \{\{ DEF, -259, -239, -239, -239\}, +08606 \{ -649, -858, -838, -838, -838\}, +08607 \{ -289, -498, -478, -478, -478\}, +08608 \{ -739, -948, -928, -928, -928\}, +08609 \{ -379, -588, -568, -568, -568\}\}\}, +08610 \textcolor{comment}{/* AU.G@..AU */} +08611 \{\{\{ DEF, -339, -689, -689, -689\}, +08612 \{ -100, -389, -739, -739, -739\}, +08613 \{ -100, -389, -739, -739, -739\}, +08614 \{ -100, -389, -739, -739, -739\}, +08615 \{ -100, -389, -739, -739, -739\}\}, +08616 \textcolor{comment}{/* AU.GA..AU */} +08617 \{\{ DEF, -339, -689, -689, -689\}, +08618 \{ -479, -768,-1118,-1118,-1118\}, +08619 \{ -309, -598, -948, -948, -948\}, +08620 \{ -389, -678,-1028,-1028,-1028\}, +08621 \{ -379, -668,-1018,-1018,-1018\}\}, +08622 \textcolor{comment}{/* AU.GC..AU */} +08623 \{\{ DEF, -339, -689, -689, -689\}, +08624 \{ -649, -938,-1288,-1288,-1288\}, +08625 \{ -289, -578, -928, -928, -928\}, +08626 \{ -739,-1028,-1378,-1378,-1378\}, +08627 \{ -379, -668,-1018,-1018,-1018\}\}, +08628 \textcolor{comment}{/* AU.GG..AU */} +08629 \{\{ DEF, -339, -689, -689, -689\}, +08630 \{ -649, -938,-1288,-1288,-1288\}, +08631 \{ -289, -578, -928, -928, -928\}, +08632 \{ -739,-1028,-1378,-1378,-1378\}, +08633 \{ -379, -668,-1018,-1018,-1018\}\}, +08634 \textcolor{comment}{/* AU.GU..AU */} +08635 \{\{ DEF, -339, -689, -689, -689\}, +08636 \{ -649, -938,-1288,-1288,-1288\}, +08637 \{ -289, -578, -928, -928, -928\}, +08638 \{ -739,-1028,-1378,-1378,-1378\}, +08639 \{ -379, -668,-1018,-1018,-1018\}\}\}, +08640 \textcolor{comment}{/* AU.U@..AU */} +08641 \{\{\{ DEF, -329, -329, -329, -329\}, +08642 \{ -100, -379, -379, -379, -379\}, +08643 \{ -100, -379, -379, -379, -379\}, +08644 \{ -100, -379, -379, -379, -379\}, +08645 \{ -100, -379, -379, -379, -379\}\}, +08646 \textcolor{comment}{/* AU.UA..AU */} +08647 \{\{ DEF, -329, -329, -329, -329\}, +08648 \{ -479, -758, -758, -758, -758\}, +08649 \{ -309, -588, -588, -588, -588\}, +08650 \{ -389, -668, -668, -668, -668\}, +08651 \{ -379, -658, -658, -658, -658\}\}, +08652 \textcolor{comment}{/* AU.UC..AU */} +08653 \{\{ DEF, -329, -329, -329, -329\}, +08654 \{ -649, -928, -928, -928, -928\}, +08655 \{ -289, -568, -568, -568, -568\}, +08656 \{ -739,-1018,-1018,-1018,-1018\}, +08657 \{ -379, -658, -658, -658, -658\}\}, +08658 \textcolor{comment}{/* AU.UG..AU */} +08659 \{\{ DEF, -329, -329, -329, -329\}, +08660 \{ -649, -928, -928, -928, -928\}, +08661 \{ -289, -568, -568, -568, -568\}, +08662 \{ -739,-1018,-1018,-1018,-1018\}, +08663 \{ -379, -658, -658, -658, -658\}\}, +08664 \textcolor{comment}{/* AU.UU..AU */} +08665 \{\{ DEF, -329, -329, -329, -329\}, +08666 \{ -649, -928, -928, -928, -928\}, +08667 \{ -289, -568, -568, -568, -568\}, +08668 \{ -739,-1018,-1018,-1018,-1018\}, +08669 \{ -379, -658, -658, -658, -658\}\}\}\}, +08670 \textcolor{comment}{/* AU.@@..UA */} +08671 \{\{\{\{ 0, 0, 0, 0, 0\}, +08672 \{ DEF, DEF, DEF, DEF, DEF\}, +08673 \{ DEF, DEF, DEF, DEF, DEF\}, +08674 \{ DEF, DEF, DEF, DEF, DEF\}, +08675 \{ DEF, DEF, DEF, DEF, DEF\}\}, +08676 \textcolor{comment}{/* AU.@A..UA */} +08677 \{\{ 0, 0, 0, 0, 0\}, +08678 \{ -399, -399, -399, -399, -399\}, +08679 \{ -429, -429, -429, -429, -429\}, +08680 \{ -379, -379, -379, -379, -379\}, +08681 \{ -279, -279, -279, -279, -279\}\}, +08682 \textcolor{comment}{/* AU.@C..UA */} +08683 \{\{ 0, 0, 0, 0, 0\}, +08684 \{ -629, -629, -629, -629, -629\}, +08685 \{ -509, -509, -509, -509, -509\}, +08686 \{ -679, -679, -679, -679, -679\}, +08687 \{ -139, -139, -139, -139, -139\}\}, +08688 \textcolor{comment}{/* AU.@G..UA */} +08689 \{\{ 0, 0, 0, 0, 0\}, +08690 \{ -889, -889, -889, -889, -889\}, +08691 \{ -199, -199, -199, -199, -199\}, +08692 \{ -889, -889, -889, -889, -889\}, +08693 \{ -279, -279, -279, -279, -279\}\}, +08694 \textcolor{comment}{/* AU.@U..UA */} +08695 \{\{ 0, 0, 0, 0, 0\}, +08696 \{ -589, -589, -589, -589, -589\}, +08697 \{ -179, -179, -179, -179, -179\}, +08698 \{ -679, -679, -679, -679, -679\}, +08699 \{ -140, -140, -140, -140, -140\}\}\}, +08700 \textcolor{comment}{/* AU.A@..UA */} +08701 \{\{\{ DEF, -429, -599, -599, -599\}, +08702 \{ -100, -479, -649, -649, -649\}, +08703 \{ -100, -479, -649, -649, -649\}, +08704 \{ -100, -479, -649, -649, -649\}, +08705 \{ -100, -479, -649, -649, -649\}\}, +08706 \textcolor{comment}{/* AU.AA..UA */} +08707 \{\{ DEF, -429, -599, -599, -599\}, +08708 \{ -449, -828, -998, -998, -998\}, +08709 \{ -479, -858,-1028,-1028,-1028\}, +08710 \{ -429, -808, -978, -978, -978\}, +08711 \{ -329, -708, -878, -878, -878\}\}, +08712 \textcolor{comment}{/* AU.AC..UA */} +08713 \{\{ DEF, -429, -599, -599, -599\}, +08714 \{ -679,-1058,-1228,-1228,-1228\}, +08715 \{ -559, -938,-1108,-1108,-1108\}, +08716 \{ -729,-1108,-1278,-1278,-1278\}, +08717 \{ -189, -568, -738, -738, -738\}\}, +08718 \textcolor{comment}{/* AU.AG..UA */} +08719 \{\{ DEF, -429, -599, -599, -599\}, +08720 \{ -939,-1318,-1488,-1488,-1488\}, +08721 \{ -249, -628, -798, -798, -798\}, +08722 \{ -939,-1318,-1488,-1488,-1488\}, +08723 \{ -329, -708, -878, -878, -878\}\}, +08724 \textcolor{comment}{/* AU.AU..UA */} +08725 \{\{ DEF, -429, -599, -599, -599\}, +08726 \{ -639,-1018,-1188,-1188,-1188\}, +08727 \{ -229, -608, -778, -778, -778\}, +08728 \{ -729,-1108,-1278,-1278,-1278\}, +08729 \{ -190, -569, -739, -739, -739\}\}\}, +08730 \textcolor{comment}{/* AU.C@..UA */} +08731 \{\{\{ DEF, -259, -239, -239, -239\}, +08732 \{ -100, -309, -289, -289, -289\}, +08733 \{ -100, -309, -289, -289, -289\}, +08734 \{ -100, -309, -289, -289, -289\}, +08735 \{ -100, -309, -289, -289, -289\}\}, +08736 \textcolor{comment}{/* AU.CA..UA */} +08737 \{\{ DEF, -259, -239, -239, -239\}, +08738 \{ -449, -658, -638, -638, -638\}, +08739 \{ -479, -688, -668, -668, -668\}, +08740 \{ -429, -638, -618, -618, -618\}, +08741 \{ -329, -538, -518, -518, -518\}\}, +08742 \textcolor{comment}{/* AU.CC..UA */} +08743 \{\{ DEF, -259, -239, -239, -239\}, +08744 \{ -679, -888, -868, -868, -868\}, +08745 \{ -559, -768, -748, -748, -748\}, +08746 \{ -729, -938, -918, -918, -918\}, +08747 \{ -189, -398, -378, -378, -378\}\}, +08748 \textcolor{comment}{/* AU.CG..UA */} +08749 \{\{ DEF, -259, -239, -239, -239\}, +08750 \{ -939,-1148,-1128,-1128,-1128\}, +08751 \{ -249, -458, -438, -438, -438\}, +08752 \{ -939,-1148,-1128,-1128,-1128\}, +08753 \{ -329, -538, -518, -518, -518\}\}, +08754 \textcolor{comment}{/* AU.CU..UA */} +08755 \{\{ DEF, -259, -239, -239, -239\}, +08756 \{ -639, -848, -828, -828, -828\}, +08757 \{ -229, -438, -418, -418, -418\}, +08758 \{ -729, -938, -918, -918, -918\}, +08759 \{ -190, -399, -379, -379, -379\}\}\}, +08760 \textcolor{comment}{/* AU.G@..UA */} +08761 \{\{\{ DEF, -339, -689, -689, -689\}, +08762 \{ -100, -389, -739, -739, -739\}, +08763 \{ -100, -389, -739, -739, -739\}, +08764 \{ -100, -389, -739, -739, -739\}, +08765 \{ -100, -389, -739, -739, -739\}\}, +08766 \textcolor{comment}{/* AU.GA..UA */} +08767 \{\{ DEF, -339, -689, -689, -689\}, +08768 \{ -449, -738,-1088,-1088,-1088\}, +08769 \{ -479, -768,-1118,-1118,-1118\}, +08770 \{ -429, -718,-1068,-1068,-1068\}, +08771 \{ -329, -618, -968, -968, -968\}\}, +08772 \textcolor{comment}{/* AU.GC..UA */} +08773 \{\{ DEF, -339, -689, -689, -689\}, +08774 \{ -679, -968,-1318,-1318,-1318\}, +08775 \{ -559, -848,-1198,-1198,-1198\}, +08776 \{ -729,-1018,-1368,-1368,-1368\}, +08777 \{ -189, -478, -828, -828, -828\}\}, +08778 \textcolor{comment}{/* AU.GG..UA */} +08779 \{\{ DEF, -339, -689, -689, -689\}, +08780 \{ -939,-1228,-1578,-1578,-1578\}, +08781 \{ -249, -538, -888, -888, -888\}, +08782 \{ -939,-1228,-1578,-1578,-1578\}, +08783 \{ -329, -618, -968, -968, -968\}\}, +08784 \textcolor{comment}{/* AU.GU..UA */} +08785 \{\{ DEF, -339, -689, -689, -689\}, +08786 \{ -639, -928,-1278,-1278,-1278\}, +08787 \{ -229, -518, -868, -868, -868\}, +08788 \{ -729,-1018,-1368,-1368,-1368\}, +08789 \{ -190, -479, -829, -829, -829\}\}\}, +08790 \textcolor{comment}{/* AU.U@..UA */} +08791 \{\{\{ DEF, -329, -329, -329, -329\}, +08792 \{ -100, -379, -379, -379, -379\}, +08793 \{ -100, -379, -379, -379, -379\}, +08794 \{ -100, -379, -379, -379, -379\}, +08795 \{ -100, -379, -379, -379, -379\}\}, +08796 \textcolor{comment}{/* AU.UA..UA */} +08797 \{\{ DEF, -329, -329, -329, -329\}, +08798 \{ -449, -728, -728, -728, -728\}, +08799 \{ -479, -758, -758, -758, -758\}, +08800 \{ -429, -708, -708, -708, -708\}, +08801 \{ -329, -608, -608, -608, -608\}\}, +08802 \textcolor{comment}{/* AU.UC..UA */} +08803 \{\{ DEF, -329, -329, -329, -329\}, +08804 \{ -679, -958, -958, -958, -958\}, +08805 \{ -559, -838, -838, -838, -838\}, +08806 \{ -729,-1008,-1008,-1008,-1008\}, +08807 \{ -189, -468, -468, -468, -468\}\}, +08808 \textcolor{comment}{/* AU.UG..UA */} +08809 \{\{ DEF, -329, -329, -329, -329\}, +08810 \{ -939,-1218,-1218,-1218,-1218\}, +08811 \{ -249, -528, -528, -528, -528\}, +08812 \{ -939,-1218,-1218,-1218,-1218\}, +08813 \{ -329, -608, -608, -608, -608\}\}, +08814 \textcolor{comment}{/* AU.UU..UA */} +08815 \{\{ DEF, -329, -329, -329, -329\}, +08816 \{ -639, -918, -918, -918, -918\}, +08817 \{ -229, -508, -508, -508, -508\}, +08818 \{ -729,-1008,-1008,-1008,-1008\}, +08819 \{ -190, -469, -469, -469, -469\}\}\}\}, +08820 \textcolor{comment}{/* AU.@@.. @ */} +08821 \{\{\{\{ DEF, DEF, DEF, DEF, DEF\}, +08822 \{ DEF, DEF, DEF, DEF, DEF\}, +08823 \{ DEF, DEF, DEF, DEF, DEF\}, +08824 \{ DEF, DEF, DEF, DEF, DEF\}, +08825 \{ DEF, DEF, DEF, DEF, DEF\}\}, +08826 \textcolor{comment}{/* AU.@A.. @ */} +08827 \{\{ DEF, DEF, DEF, DEF, DEF\}, +08828 \{ DEF, DEF, DEF, DEF, DEF\}, +08829 \{ DEF, DEF, DEF, DEF, DEF\}, +08830 \{ DEF, DEF, DEF, DEF, DEF\}, +08831 \{ DEF, DEF, DEF, DEF, DEF\}\}, +08832 \textcolor{comment}{/* AU.@C.. @ */} +08833 \{\{ DEF, DEF, DEF, DEF, DEF\}, +08834 \{ DEF, DEF, DEF, DEF, DEF\}, +08835 \{ DEF, DEF, DEF, DEF, DEF\}, +08836 \{ DEF, DEF, DEF, DEF, DEF\}, +08837 \{ DEF, DEF, DEF, DEF, DEF\}\}, +08838 \textcolor{comment}{/* AU.@G.. @ */} +08839 \{\{ DEF, DEF, DEF, DEF, DEF\}, +08840 \{ DEF, DEF, DEF, DEF, DEF\}, +08841 \{ DEF, DEF, DEF, DEF, DEF\}, +08842 \{ DEF, DEF, DEF, DEF, DEF\}, +08843 \{ DEF, DEF, DEF, DEF, DEF\}\}, +08844 \textcolor{comment}{/* AU.@U.. @ */} +08845 \{\{ DEF, DEF, DEF, DEF, DEF\}, +08846 \{ DEF, DEF, DEF, DEF, DEF\}, +08847 \{ DEF, DEF, DEF, DEF, DEF\}, +08848 \{ DEF, DEF, DEF, DEF, DEF\}, +08849 \{ DEF, DEF, DEF, DEF, DEF\}\}\}, +08850 \textcolor{comment}{/* AU.A@.. @ */} +08851 \{\{\{ -100, -479, -649, -649, -649\}, +08852 \{ -100, -479, -649, -649, -649\}, +08853 \{ -100, -479, -649, -649, -649\}, +08854 \{ -100, -479, -649, -649, -649\}, +08855 \{ -100, -479, -649, -649, -649\}\}, +08856 \textcolor{comment}{/* AU.AA.. @ */} +08857 \{\{ -100, -479, -649, -649, -649\}, +08858 \{ -100, -479, -649, -649, -649\}, +08859 \{ -100, -479, -649, -649, -649\}, +08860 \{ -100, -479, -649, -649, -649\}, +08861 \{ -100, -479, -649, -649, -649\}\}, +08862 \textcolor{comment}{/* AU.AC.. @ */} +08863 \{\{ -100, -479, -649, -649, -649\}, +08864 \{ -100, -479, -649, -649, -649\}, +08865 \{ -100, -479, -649, -649, -649\}, +08866 \{ -100, -479, -649, -649, -649\}, +08867 \{ -100, -479, -649, -649, -649\}\}, +08868 \textcolor{comment}{/* AU.AG.. @ */} +08869 \{\{ -100, -479, -649, -649, -649\}, +08870 \{ -100, -479, -649, -649, -649\}, +08871 \{ -100, -479, -649, -649, -649\}, +08872 \{ -100, -479, -649, -649, -649\}, +08873 \{ -100, -479, -649, -649, -649\}\}, +08874 \textcolor{comment}{/* AU.AU.. @ */} +08875 \{\{ -100, -479, -649, -649, -649\}, +08876 \{ -100, -479, -649, -649, -649\}, +08877 \{ -100, -479, -649, -649, -649\}, +08878 \{ -100, -479, -649, -649, -649\}, +08879 \{ -100, -479, -649, -649, -649\}\}\}, +08880 \textcolor{comment}{/* AU.C@.. @ */} +08881 \{\{\{ -100, -309, -289, -289, -289\}, +08882 \{ -100, -309, -289, -289, -289\}, +08883 \{ -100, -309, -289, -289, -289\}, +08884 \{ -100, -309, -289, -289, -289\}, +08885 \{ -100, -309, -289, -289, -289\}\}, +08886 \textcolor{comment}{/* AU.CA.. @ */} +08887 \{\{ -100, -309, -289, -289, -289\}, +08888 \{ -100, -309, -289, -289, -289\}, +08889 \{ -100, -309, -289, -289, -289\}, +08890 \{ -100, -309, -289, -289, -289\}, +08891 \{ -100, -309, -289, -289, -289\}\}, +08892 \textcolor{comment}{/* AU.CC.. @ */} +08893 \{\{ -100, -309, -289, -289, -289\}, +08894 \{ -100, -309, -289, -289, -289\}, +08895 \{ -100, -309, -289, -289, -289\}, +08896 \{ -100, -309, -289, -289, -289\}, +08897 \{ -100, -309, -289, -289, -289\}\}, +08898 \textcolor{comment}{/* AU.CG.. @ */} +08899 \{\{ -100, -309, -289, -289, -289\}, +08900 \{ -100, -309, -289, -289, -289\}, +08901 \{ -100, -309, -289, -289, -289\}, +08902 \{ -100, -309, -289, -289, -289\}, +08903 \{ -100, -309, -289, -289, -289\}\}, +08904 \textcolor{comment}{/* AU.CU.. @ */} +08905 \{\{ -100, -309, -289, -289, -289\}, +08906 \{ -100, -309, -289, -289, -289\}, +08907 \{ -100, -309, -289, -289, -289\}, +08908 \{ -100, -309, -289, -289, -289\}, +08909 \{ -100, -309, -289, -289, -289\}\}\}, +08910 \textcolor{comment}{/* AU.G@.. @ */} +08911 \{\{\{ -100, -389, -739, -739, -739\}, +08912 \{ -100, -389, -739, -739, -739\}, +08913 \{ -100, -389, -739, -739, -739\}, +08914 \{ -100, -389, -739, -739, -739\}, +08915 \{ -100, -389, -739, -739, -739\}\}, +08916 \textcolor{comment}{/* AU.GA.. @ */} +08917 \{\{ -100, -389, -739, -739, -739\}, +08918 \{ -100, -389, -739, -739, -739\}, +08919 \{ -100, -389, -739, -739, -739\}, +08920 \{ -100, -389, -739, -739, -739\}, +08921 \{ -100, -389, -739, -739, -739\}\}, +08922 \textcolor{comment}{/* AU.GC.. @ */} +08923 \{\{ -100, -389, -739, -739, -739\}, +08924 \{ -100, -389, -739, -739, -739\}, +08925 \{ -100, -389, -739, -739, -739\}, +08926 \{ -100, -389, -739, -739, -739\}, +08927 \{ -100, -389, -739, -739, -739\}\}, +08928 \textcolor{comment}{/* AU.GG.. @ */} +08929 \{\{ -100, -389, -739, -739, -739\}, +08930 \{ -100, -389, -739, -739, -739\}, +08931 \{ -100, -389, -739, -739, -739\}, +08932 \{ -100, -389, -739, -739, -739\}, +08933 \{ -100, -389, -739, -739, -739\}\}, +08934 \textcolor{comment}{/* AU.GU.. @ */} +08935 \{\{ -100, -389, -739, -739, -739\}, +08936 \{ -100, -389, -739, -739, -739\}, +08937 \{ -100, -389, -739, -739, -739\}, +08938 \{ -100, -389, -739, -739, -739\}, +08939 \{ -100, -389, -739, -739, -739\}\}\}, +08940 \textcolor{comment}{/* AU.U@.. @ */} +08941 \{\{\{ -100, -379, -379, -379, -379\}, +08942 \{ -100, -379, -379, -379, -379\}, +08943 \{ -100, -379, -379, -379, -379\}, +08944 \{ -100, -379, -379, -379, -379\}, +08945 \{ -100, -379, -379, -379, -379\}\}, +08946 \textcolor{comment}{/* AU.UA.. @ */} +08947 \{\{ -100, -379, -379, -379, -379\}, +08948 \{ -100, -379, -379, -379, -379\}, +08949 \{ -100, -379, -379, -379, -379\}, +08950 \{ -100, -379, -379, -379, -379\}, +08951 \{ -100, -379, -379, -379, -379\}\}, +08952 \textcolor{comment}{/* AU.UC.. @ */} +08953 \{\{ -100, -379, -379, -379, -379\}, +08954 \{ -100, -379, -379, -379, -379\}, +08955 \{ -100, -379, -379, -379, -379\}, +08956 \{ -100, -379, -379, -379, -379\}, +08957 \{ -100, -379, -379, -379, -379\}\}, +08958 \textcolor{comment}{/* AU.UG.. @ */} +08959 \{\{ -100, -379, -379, -379, -379\}, +08960 \{ -100, -379, -379, -379, -379\}, +08961 \{ -100, -379, -379, -379, -379\}, +08962 \{ -100, -379, -379, -379, -379\}, +08963 \{ -100, -379, -379, -379, -379\}\}, +08964 \textcolor{comment}{/* AU.UU.. @ */} +08965 \{\{ -100, -379, -379, -379, -379\}, +08966 \{ -100, -379, -379, -379, -379\}, +08967 \{ -100, -379, -379, -379, -379\}, +08968 \{ -100, -379, -379, -379, -379\}, +08969 \{ -100, -379, -379, -379, -379\}\}\}\}\}, +08970 \{ \textcolor{comment}{/* noPair */} \{\{\{\{0\}\}\}\}, +08971 \textcolor{comment}{/* UA.@@..CG */} +08972 \{\{\{\{ 0, 0, 0, 0, 0\}, +08973 \{ DEF, DEF, DEF, DEF, DEF\}, +08974 \{ DEF, DEF, DEF, DEF, DEF\}, +08975 \{ DEF, DEF, DEF, DEF, DEF\}, +08976 \{ DEF, DEF, DEF, DEF, DEF\}\}, +08977 \textcolor{comment}{/* UA.@A..CG */} +08978 \{\{ 0, 0, 0, 0, 0\}, +08979 \{-1029,-1029,-1029,-1029,-1029\}, +08980 \{ -519, -519, -519, -519, -519\}, +08981 \{ -939, -939, -939, -939, -939\}, +08982 \{ -809, -809, -809, -809, -809\}\}, +08983 \textcolor{comment}{/* UA.@C..CG */} +08984 \{\{ 0, 0, 0, 0, 0\}, +08985 \{ -949, -949, -949, -949, -949\}, +08986 \{ -449, -449, -449, -449, -449\}, +08987 \{ -939, -939, -939, -939, -939\}, +08988 \{ -739, -739, -739, -739, -739\}\}, +08989 \textcolor{comment}{/* UA.@G..CG */} +08990 \{\{ 0, 0, 0, 0, 0\}, +08991 \{-1029,-1029,-1029,-1029,-1029\}, +08992 \{ -519, -519, -519, -519, -519\}, +08993 \{ -939, -939, -939, -939, -939\}, +08994 \{ -809, -809, -809, -809, -809\}\}, +08995 \textcolor{comment}{/* UA.@U..CG */} +08996 \{\{ 0, 0, 0, 0, 0\}, +08997 \{-1029,-1029,-1029,-1029,-1029\}, +08998 \{ -669, -669, -669, -669, -669\}, +08999 \{ -939, -939, -939, -939, -939\}, +09000 \{ -859, -859, -859, -859, -859\}\}\}, +09001 \textcolor{comment}{/* UA.A@..CG */} +09002 \{\{\{ DEF, -399, -629, -889, -589\}, +09003 \{ -100, -449, -679, -939, -639\}, +09004 \{ -100, -449, -679, -939, -639\}, +09005 \{ -100, -449, -679, -939, -639\}, +09006 \{ -100, -449, -679, -939, -639\}\}, +09007 \textcolor{comment}{/* UA.AA..CG */} +09008 \{\{ DEF, -399, -629, -889, -589\}, +09009 \{-1079,-1428,-1658,-1918,-1618\}, +09010 \{ -569, -918,-1148,-1408,-1108\}, +09011 \{ -989,-1338,-1568,-1828,-1528\}, +09012 \{ -859,-1208,-1438,-1698,-1398\}\}, +09013 \textcolor{comment}{/* UA.AC..CG */} +09014 \{\{ DEF, -399, -629, -889, -589\}, +09015 \{ -999,-1348,-1578,-1838,-1538\}, +09016 \{ -499, -848,-1078,-1338,-1038\}, +09017 \{ -989,-1338,-1568,-1828,-1528\}, +09018 \{ -789,-1138,-1368,-1628,-1328\}\}, +09019 \textcolor{comment}{/* UA.AG..CG */} +09020 \{\{ DEF, -399, -629, -889, -589\}, +09021 \{-1079,-1428,-1658,-1918,-1618\}, +09022 \{ -569, -918,-1148,-1408,-1108\}, +09023 \{ -989,-1338,-1568,-1828,-1528\}, +09024 \{ -859,-1208,-1438,-1698,-1398\}\}, +09025 \textcolor{comment}{/* UA.AU..CG */} +09026 \{\{ DEF, -399, -629, -889, -589\}, +09027 \{-1079,-1428,-1658,-1918,-1618\}, +09028 \{ -719,-1068,-1298,-1558,-1258\}, +09029 \{ -989,-1338,-1568,-1828,-1528\}, +09030 \{ -909,-1258,-1488,-1748,-1448\}\}\}, +09031 \textcolor{comment}{/* UA.C@..CG */} +09032 \{\{\{ DEF, -429, -509, -199, -179\}, +09033 \{ -100, -479, -559, -249, -229\}, +09034 \{ -100, -479, -559, -249, -229\}, +09035 \{ -100, -479, -559, -249, -229\}, +09036 \{ -100, -479, -559, -249, -229\}\}, +09037 \textcolor{comment}{/* UA.CA..CG */} +09038 \{\{ DEF, -429, -509, -199, -179\}, +09039 \{-1079,-1458,-1538,-1228,-1208\}, +09040 \{ -569, -948,-1028, -718, -698\}, +09041 \{ -989,-1368,-1448,-1138,-1118\}, +09042 \{ -859,-1238,-1318,-1008, -988\}\}, +09043 \textcolor{comment}{/* UA.CC..CG */} +09044 \{\{ DEF, -429, -509, -199, -179\}, +09045 \{ -999,-1378,-1458,-1148,-1128\}, +09046 \{ -499, -878, -958, -648, -628\}, +09047 \{ -989,-1368,-1448,-1138,-1118\}, +09048 \{ -789,-1168,-1248, -938, -918\}\}, +09049 \textcolor{comment}{/* UA.CG..CG */} +09050 \{\{ DEF, -429, -509, -199, -179\}, +09051 \{-1079,-1458,-1538,-1228,-1208\}, +09052 \{ -569, -948,-1028, -718, -698\}, +09053 \{ -989,-1368,-1448,-1138,-1118\}, +09054 \{ -859,-1238,-1318,-1008, -988\}\}, +09055 \textcolor{comment}{/* UA.CU..CG */} +09056 \{\{ DEF, -429, -509, -199, -179\}, +09057 \{-1079,-1458,-1538,-1228,-1208\}, +09058 \{ -719,-1098,-1178, -868, -848\}, +09059 \{ -989,-1368,-1448,-1138,-1118\}, +09060 \{ -909,-1288,-1368,-1058,-1038\}\}\}, +09061 \textcolor{comment}{/* UA.G@..CG */} +09062 \{\{\{ DEF, -379, -679, -889, -679\}, +09063 \{ -100, -429, -729, -939, -729\}, +09064 \{ -100, -429, -729, -939, -729\}, +09065 \{ -100, -429, -729, -939, -729\}, +09066 \{ -100, -429, -729, -939, -729\}\}, +09067 \textcolor{comment}{/* UA.GA..CG */} +09068 \{\{ DEF, -379, -679, -889, -679\}, +09069 \{-1079,-1408,-1708,-1918,-1708\}, +09070 \{ -569, -898,-1198,-1408,-1198\}, +09071 \{ -989,-1318,-1618,-1828,-1618\}, +09072 \{ -859,-1188,-1488,-1698,-1488\}\}, +09073 \textcolor{comment}{/* UA.GC..CG */} +09074 \{\{ DEF, -379, -679, -889, -679\}, +09075 \{ -999,-1328,-1628,-1838,-1628\}, +09076 \{ -499, -828,-1128,-1338,-1128\}, +09077 \{ -989,-1318,-1618,-1828,-1618\}, +09078 \{ -789,-1118,-1418,-1628,-1418\}\}, +09079 \textcolor{comment}{/* UA.GG..CG */} +09080 \{\{ DEF, -379, -679, -889, -679\}, +09081 \{-1079,-1408,-1708,-1918,-1708\}, +09082 \{ -569, -898,-1198,-1408,-1198\}, +09083 \{ -989,-1318,-1618,-1828,-1618\}, +09084 \{ -859,-1188,-1488,-1698,-1488\}\}, +09085 \textcolor{comment}{/* UA.GU..CG */} +09086 \{\{ DEF, -379, -679, -889, -679\}, +09087 \{-1079,-1408,-1708,-1918,-1708\}, +09088 \{ -719,-1048,-1348,-1558,-1348\}, +09089 \{ -989,-1318,-1618,-1828,-1618\}, +09090 \{ -909,-1238,-1538,-1748,-1538\}\}\}, +09091 \textcolor{comment}{/* UA.U@..CG */} +09092 \{\{\{ DEF, -279, -139, -279, -140\}, +09093 \{ -100, -329, -189, -329, -190\}, +09094 \{ -100, -329, -189, -329, -190\}, +09095 \{ -100, -329, -189, -329, -190\}, +09096 \{ -100, -329, -189, -329, -190\}\}, +09097 \textcolor{comment}{/* UA.UA..CG */} +09098 \{\{ DEF, -279, -139, -279, -140\}, +09099 \{-1079,-1308,-1168,-1308,-1169\}, +09100 \{ -569, -798, -658, -798, -659\}, +09101 \{ -989,-1218,-1078,-1218,-1079\}, +09102 \{ -859,-1088, -948,-1088, -949\}\}, +09103 \textcolor{comment}{/* UA.UC..CG */} +09104 \{\{ DEF, -279, -139, -279, -140\}, +09105 \{ -999,-1228,-1088,-1228,-1089\}, +09106 \{ -499, -728, -588, -728, -589\}, +09107 \{ -989,-1218,-1078,-1218,-1079\}, +09108 \{ -789,-1018, -878,-1018, -879\}\}, +09109 \textcolor{comment}{/* UA.UG..CG */} +09110 \{\{ DEF, -279, -139, -279, -140\}, +09111 \{-1079,-1308,-1168,-1308,-1169\}, +09112 \{ -569, -798, -658, -798, -659\}, +09113 \{ -989,-1218,-1078,-1218,-1079\}, +09114 \{ -859,-1088, -948,-1088, -949\}\}, +09115 \textcolor{comment}{/* UA.UU..CG */} +09116 \{\{ DEF, -279, -139, -279, -140\}, +09117 \{-1079,-1308,-1168,-1308,-1169\}, +09118 \{ -719, -948, -808, -948, -809\}, +09119 \{ -989,-1218,-1078,-1218,-1079\}, +09120 \{ -909,-1138, -998,-1138, -999\}\}\}\}, +09121 \textcolor{comment}{/* UA.@@..GC */} +09122 \{\{\{\{ 0, 0, 0, 0, 0\}, +09123 \{ DEF, DEF, DEF, DEF, DEF\}, +09124 \{ DEF, DEF, DEF, DEF, DEF\}, +09125 \{ DEF, DEF, DEF, DEF, DEF\}, +09126 \{ DEF, DEF, DEF, DEF, DEF\}\}, +09127 \textcolor{comment}{/* UA.@A..GC */} +09128 \{\{ 0, 0, 0, 0, 0\}, +09129 \{ -519, -519, -519, -519, -519\}, +09130 \{ -719, -719, -719, -719, -719\}, +09131 \{ -709, -709, -709, -709, -709\}, +09132 \{ -499, -499, -499, -499, -499\}\}, +09133 \textcolor{comment}{/* UA.@C..GC */} +09134 \{\{ 0, 0, 0, 0, 0\}, +09135 \{ -879, -879, -879, -879, -879\}, +09136 \{ -309, -309, -309, -309, -309\}, +09137 \{ -739, -739, -739, -739, -739\}, +09138 \{ -499, -499, -499, -499, -499\}\}, +09139 \textcolor{comment}{/* UA.@G..GC */} +09140 \{\{ 0, 0, 0, 0, 0\}, +09141 \{ -559, -559, -559, -559, -559\}, +09142 \{ -309, -309, -309, -309, -309\}, +09143 \{ -619, -619, -619, -619, -619\}, +09144 \{ -499, -499, -499, -499, -499\}\}, +09145 \textcolor{comment}{/* UA.@U..GC */} +09146 \{\{ 0, 0, 0, 0, 0\}, +09147 \{ -879, -879, -879, -879, -879\}, +09148 \{ -389, -389, -389, -389, -389\}, +09149 \{ -739, -739, -739, -739, -739\}, +09150 \{ -569, -569, -569, -569, -569\}\}\}, +09151 \textcolor{comment}{/* UA.A@..GC */} +09152 \{\{\{ DEF, -399, -629, -889, -589\}, +09153 \{ -100, -449, -679, -939, -639\}, +09154 \{ -100, -449, -679, -939, -639\}, +09155 \{ -100, -449, -679, -939, -639\}, +09156 \{ -100, -449, -679, -939, -639\}\}, +09157 \textcolor{comment}{/* UA.AA..GC */} +09158 \{\{ DEF, -399, -629, -889, -589\}, +09159 \{ -569, -918,-1148,-1408,-1108\}, +09160 \{ -769,-1118,-1348,-1608,-1308\}, +09161 \{ -759,-1108,-1338,-1598,-1298\}, +09162 \{ -549, -898,-1128,-1388,-1088\}\}, +09163 \textcolor{comment}{/* UA.AC..GC */} +09164 \{\{ DEF, -399, -629, -889, -589\}, +09165 \{ -929,-1278,-1508,-1768,-1468\}, +09166 \{ -359, -708, -938,-1198, -898\}, +09167 \{ -789,-1138,-1368,-1628,-1328\}, +09168 \{ -549, -898,-1128,-1388,-1088\}\}, +09169 \textcolor{comment}{/* UA.AG..GC */} +09170 \{\{ DEF, -399, -629, -889, -589\}, +09171 \{ -609, -958,-1188,-1448,-1148\}, +09172 \{ -359, -708, -938,-1198, -898\}, +09173 \{ -669,-1018,-1248,-1508,-1208\}, +09174 \{ -549, -898,-1128,-1388,-1088\}\}, +09175 \textcolor{comment}{/* UA.AU..GC */} +09176 \{\{ DEF, -399, -629, -889, -589\}, +09177 \{ -929,-1278,-1508,-1768,-1468\}, +09178 \{ -439, -788,-1018,-1278, -978\}, +09179 \{ -789,-1138,-1368,-1628,-1328\}, +09180 \{ -619, -968,-1198,-1458,-1158\}\}\}, +09181 \textcolor{comment}{/* UA.C@..GC */} +09182 \{\{\{ DEF, -429, -509, -199, -179\}, +09183 \{ -100, -479, -559, -249, -229\}, +09184 \{ -100, -479, -559, -249, -229\}, +09185 \{ -100, -479, -559, -249, -229\}, +09186 \{ -100, -479, -559, -249, -229\}\}, +09187 \textcolor{comment}{/* UA.CA..GC */} +09188 \{\{ DEF, -429, -509, -199, -179\}, +09189 \{ -569, -948,-1028, -718, -698\}, +09190 \{ -769,-1148,-1228, -918, -898\}, +09191 \{ -759,-1138,-1218, -908, -888\}, +09192 \{ -549, -928,-1008, -698, -678\}\}, +09193 \textcolor{comment}{/* UA.CC..GC */} +09194 \{\{ DEF, -429, -509, -199, -179\}, +09195 \{ -929,-1308,-1388,-1078,-1058\}, +09196 \{ -359, -738, -818, -508, -488\}, +09197 \{ -789,-1168,-1248, -938, -918\}, +09198 \{ -549, -928,-1008, -698, -678\}\}, +09199 \textcolor{comment}{/* UA.CG..GC */} +09200 \{\{ DEF, -429, -509, -199, -179\}, +09201 \{ -609, -988,-1068, -758, -738\}, +09202 \{ -359, -738, -818, -508, -488\}, +09203 \{ -669,-1048,-1128, -818, -798\}, +09204 \{ -549, -928,-1008, -698, -678\}\}, +09205 \textcolor{comment}{/* UA.CU..GC */} +09206 \{\{ DEF, -429, -509, -199, -179\}, +09207 \{ -929,-1308,-1388,-1078,-1058\}, +09208 \{ -439, -818, -898, -588, -568\}, +09209 \{ -789,-1168,-1248, -938, -918\}, +09210 \{ -619, -998,-1078, -768, -748\}\}\}, +09211 \textcolor{comment}{/* UA.G@..GC */} +09212 \{\{\{ DEF, -379, -679, -889, -679\}, +09213 \{ -100, -429, -729, -939, -729\}, +09214 \{ -100, -429, -729, -939, -729\}, +09215 \{ -100, -429, -729, -939, -729\}, +09216 \{ -100, -429, -729, -939, -729\}\}, +09217 \textcolor{comment}{/* UA.GA..GC */} +09218 \{\{ DEF, -379, -679, -889, -679\}, +09219 \{ -569, -898,-1198,-1408,-1198\}, +09220 \{ -769,-1098,-1398,-1608,-1398\}, +09221 \{ -759,-1088,-1388,-1598,-1388\}, +09222 \{ -549, -878,-1178,-1388,-1178\}\}, +09223 \textcolor{comment}{/* UA.GC..GC */} +09224 \{\{ DEF, -379, -679, -889, -679\}, +09225 \{ -929,-1258,-1558,-1768,-1558\}, +09226 \{ -359, -688, -988,-1198, -988\}, +09227 \{ -789,-1118,-1418,-1628,-1418\}, +09228 \{ -549, -878,-1178,-1388,-1178\}\}, +09229 \textcolor{comment}{/* UA.GG..GC */} +09230 \{\{ DEF, -379, -679, -889, -679\}, +09231 \{ -609, -938,-1238,-1448,-1238\}, +09232 \{ -359, -688, -988,-1198, -988\}, +09233 \{ -669, -998,-1298,-1508,-1298\}, +09234 \{ -549, -878,-1178,-1388,-1178\}\}, +09235 \textcolor{comment}{/* UA.GU..GC */} +09236 \{\{ DEF, -379, -679, -889, -679\}, +09237 \{ -929,-1258,-1558,-1768,-1558\}, +09238 \{ -439, -768,-1068,-1278,-1068\}, +09239 \{ -789,-1118,-1418,-1628,-1418\}, +09240 \{ -619, -948,-1248,-1458,-1248\}\}\}, +09241 \textcolor{comment}{/* UA.U@..GC */} +09242 \{\{\{ DEF, -279, -139, -279, -140\}, +09243 \{ -100, -329, -189, -329, -190\}, +09244 \{ -100, -329, -189, -329, -190\}, +09245 \{ -100, -329, -189, -329, -190\}, +09246 \{ -100, -329, -189, -329, -190\}\}, +09247 \textcolor{comment}{/* UA.UA..GC */} +09248 \{\{ DEF, -279, -139, -279, -140\}, +09249 \{ -569, -798, -658, -798, -659\}, +09250 \{ -769, -998, -858, -998, -859\}, +09251 \{ -759, -988, -848, -988, -849\}, +09252 \{ -549, -778, -638, -778, -639\}\}, +09253 \textcolor{comment}{/* UA.UC..GC */} +09254 \{\{ DEF, -279, -139, -279, -140\}, +09255 \{ -929,-1158,-1018,-1158,-1019\}, +09256 \{ -359, -588, -448, -588, -449\}, +09257 \{ -789,-1018, -878,-1018, -879\}, +09258 \{ -549, -778, -638, -778, -639\}\}, +09259 \textcolor{comment}{/* UA.UG..GC */} +09260 \{\{ DEF, -279, -139, -279, -140\}, +09261 \{ -609, -838, -698, -838, -699\}, +09262 \{ -359, -588, -448, -588, -449\}, +09263 \{ -669, -898, -758, -898, -759\}, +09264 \{ -549, -778, -638, -778, -639\}\}, +09265 \textcolor{comment}{/* UA.UU..GC */} +09266 \{\{ DEF, -279, -139, -279, -140\}, +09267 \{ -929,-1158,-1018,-1158,-1019\}, +09268 \{ -439, -668, -528, -668, -529\}, +09269 \{ -789,-1018, -878,-1018, -879\}, +09270 \{ -619, -848, -708, -848, -709\}\}\}\}, +09271 \textcolor{comment}{/* UA.@@..GU */} +09272 \{\{\{\{ 0, 0, 0, 0, 0\}, +09273 \{ DEF, DEF, DEF, DEF, DEF\}, +09274 \{ DEF, DEF, DEF, DEF, DEF\}, +09275 \{ DEF, DEF, DEF, DEF, DEF\}, +09276 \{ DEF, DEF, DEF, DEF, DEF\}\}, +09277 \textcolor{comment}{/* UA.@A..GU */} +09278 \{\{ 0, 0, 0, 0, 0\}, +09279 \{ -429, -429, -429, -429, -429\}, +09280 \{ -259, -259, -259, -259, -259\}, +09281 \{ -339, -339, -339, -339, -339\}, +09282 \{ -329, -329, -329, -329, -329\}\}, +09283 \textcolor{comment}{/* UA.@C..GU */} +09284 \{\{ 0, 0, 0, 0, 0\}, +09285 \{ -599, -599, -599, -599, -599\}, +09286 \{ -239, -239, -239, -239, -239\}, +09287 \{ -689, -689, -689, -689, -689\}, +09288 \{ -329, -329, -329, -329, -329\}\}, +09289 \textcolor{comment}{/* UA.@G..GU */} +09290 \{\{ 0, 0, 0, 0, 0\}, +09291 \{ -599, -599, -599, -599, -599\}, +09292 \{ -239, -239, -239, -239, -239\}, +09293 \{ -689, -689, -689, -689, -689\}, +09294 \{ -329, -329, -329, -329, -329\}\}, +09295 \textcolor{comment}{/* UA.@U..GU */} +09296 \{\{ 0, 0, 0, 0, 0\}, +09297 \{ -599, -599, -599, -599, -599\}, +09298 \{ -239, -239, -239, -239, -239\}, +09299 \{ -689, -689, -689, -689, -689\}, +09300 \{ -329, -329, -329, -329, -329\}\}\}, +09301 \textcolor{comment}{/* UA.A@..GU */} +09302 \{\{\{ DEF, -399, -629, -889, -589\}, +09303 \{ -100, -449, -679, -939, -639\}, +09304 \{ -100, -449, -679, -939, -639\}, +09305 \{ -100, -449, -679, -939, -639\}, +09306 \{ -100, -449, -679, -939, -639\}\}, +09307 \textcolor{comment}{/* UA.AA..GU */} +09308 \{\{ DEF, -399, -629, -889, -589\}, +09309 \{ -479, -828,-1058,-1318,-1018\}, +09310 \{ -309, -658, -888,-1148, -848\}, +09311 \{ -389, -738, -968,-1228, -928\}, +09312 \{ -379, -728, -958,-1218, -918\}\}, +09313 \textcolor{comment}{/* UA.AC..GU */} +09314 \{\{ DEF, -399, -629, -889, -589\}, +09315 \{ -649, -998,-1228,-1488,-1188\}, +09316 \{ -289, -638, -868,-1128, -828\}, +09317 \{ -739,-1088,-1318,-1578,-1278\}, +09318 \{ -379, -728, -958,-1218, -918\}\}, +09319 \textcolor{comment}{/* UA.AG..GU */} +09320 \{\{ DEF, -399, -629, -889, -589\}, +09321 \{ -649, -998,-1228,-1488,-1188\}, +09322 \{ -289, -638, -868,-1128, -828\}, +09323 \{ -739,-1088,-1318,-1578,-1278\}, +09324 \{ -379, -728, -958,-1218, -918\}\}, +09325 \textcolor{comment}{/* UA.AU..GU */} +09326 \{\{ DEF, -399, -629, -889, -589\}, +09327 \{ -649, -998,-1228,-1488,-1188\}, +09328 \{ -289, -638, -868,-1128, -828\}, +09329 \{ -739,-1088,-1318,-1578,-1278\}, +09330 \{ -379, -728, -958,-1218, -918\}\}\}, +09331 \textcolor{comment}{/* UA.C@..GU */} +09332 \{\{\{ DEF, -429, -509, -199, -179\}, +09333 \{ -100, -479, -559, -249, -229\}, +09334 \{ -100, -479, -559, -249, -229\}, +09335 \{ -100, -479, -559, -249, -229\}, +09336 \{ -100, -479, -559, -249, -229\}\}, +09337 \textcolor{comment}{/* UA.CA..GU */} +09338 \{\{ DEF, -429, -509, -199, -179\}, +09339 \{ -479, -858, -938, -628, -608\}, +09340 \{ -309, -688, -768, -458, -438\}, +09341 \{ -389, -768, -848, -538, -518\}, +09342 \{ -379, -758, -838, -528, -508\}\}, +09343 \textcolor{comment}{/* UA.CC..GU */} +09344 \{\{ DEF, -429, -509, -199, -179\}, +09345 \{ -649,-1028,-1108, -798, -778\}, +09346 \{ -289, -668, -748, -438, -418\}, +09347 \{ -739,-1118,-1198, -888, -868\}, +09348 \{ -379, -758, -838, -528, -508\}\}, +09349 \textcolor{comment}{/* UA.CG..GU */} +09350 \{\{ DEF, -429, -509, -199, -179\}, +09351 \{ -649,-1028,-1108, -798, -778\}, +09352 \{ -289, -668, -748, -438, -418\}, +09353 \{ -739,-1118,-1198, -888, -868\}, +09354 \{ -379, -758, -838, -528, -508\}\}, +09355 \textcolor{comment}{/* UA.CU..GU */} +09356 \{\{ DEF, -429, -509, -199, -179\}, +09357 \{ -649,-1028,-1108, -798, -778\}, +09358 \{ -289, -668, -748, -438, -418\}, +09359 \{ -739,-1118,-1198, -888, -868\}, +09360 \{ -379, -758, -838, -528, -508\}\}\}, +09361 \textcolor{comment}{/* UA.G@..GU */} +09362 \{\{\{ DEF, -379, -679, -889, -679\}, +09363 \{ -100, -429, -729, -939, -729\}, +09364 \{ -100, -429, -729, -939, -729\}, +09365 \{ -100, -429, -729, -939, -729\}, +09366 \{ -100, -429, -729, -939, -729\}\}, +09367 \textcolor{comment}{/* UA.GA..GU */} +09368 \{\{ DEF, -379, -679, -889, -679\}, +09369 \{ -479, -808,-1108,-1318,-1108\}, +09370 \{ -309, -638, -938,-1148, -938\}, +09371 \{ -389, -718,-1018,-1228,-1018\}, +09372 \{ -379, -708,-1008,-1218,-1008\}\}, +09373 \textcolor{comment}{/* UA.GC..GU */} +09374 \{\{ DEF, -379, -679, -889, -679\}, +09375 \{ -649, -978,-1278,-1488,-1278\}, +09376 \{ -289, -618, -918,-1128, -918\}, +09377 \{ -739,-1068,-1368,-1578,-1368\}, +09378 \{ -379, -708,-1008,-1218,-1008\}\}, +09379 \textcolor{comment}{/* UA.GG..GU */} +09380 \{\{ DEF, -379, -679, -889, -679\}, +09381 \{ -649, -978,-1278,-1488,-1278\}, +09382 \{ -289, -618, -918,-1128, -918\}, +09383 \{ -739,-1068,-1368,-1578,-1368\}, +09384 \{ -379, -708,-1008,-1218,-1008\}\}, +09385 \textcolor{comment}{/* UA.GU..GU */} +09386 \{\{ DEF, -379, -679, -889, -679\}, +09387 \{ -649, -978,-1278,-1488,-1278\}, +09388 \{ -289, -618, -918,-1128, -918\}, +09389 \{ -739,-1068,-1368,-1578,-1368\}, +09390 \{ -379, -708,-1008,-1218,-1008\}\}\}, +09391 \textcolor{comment}{/* UA.U@..GU */} +09392 \{\{\{ DEF, -279, -139, -279, -140\}, +09393 \{ -100, -329, -189, -329, -190\}, +09394 \{ -100, -329, -189, -329, -190\}, +09395 \{ -100, -329, -189, -329, -190\}, +09396 \{ -100, -329, -189, -329, -190\}\}, +09397 \textcolor{comment}{/* UA.UA..GU */} +09398 \{\{ DEF, -279, -139, -279, -140\}, +09399 \{ -479, -708, -568, -708, -569\}, +09400 \{ -309, -538, -398, -538, -399\}, +09401 \{ -389, -618, -478, -618, -479\}, +09402 \{ -379, -608, -468, -608, -469\}\}, +09403 \textcolor{comment}{/* UA.UC..GU */} +09404 \{\{ DEF, -279, -139, -279, -140\}, +09405 \{ -649, -878, -738, -878, -739\}, +09406 \{ -289, -518, -378, -518, -379\}, +09407 \{ -739, -968, -828, -968, -829\}, +09408 \{ -379, -608, -468, -608, -469\}\}, +09409 \textcolor{comment}{/* UA.UG..GU */} +09410 \{\{ DEF, -279, -139, -279, -140\}, +09411 \{ -649, -878, -738, -878, -739\}, +09412 \{ -289, -518, -378, -518, -379\}, +09413 \{ -739, -968, -828, -968, -829\}, +09414 \{ -379, -608, -468, -608, -469\}\}, +09415 \textcolor{comment}{/* UA.UU..GU */} +09416 \{\{ DEF, -279, -139, -279, -140\}, +09417 \{ -649, -878, -738, -878, -739\}, +09418 \{ -289, -518, -378, -518, -379\}, +09419 \{ -739, -968, -828, -968, -829\}, +09420 \{ -379, -608, -468, -608, -469\}\}\}\}, +09421 \textcolor{comment}{/* UA.@@..UG */} +09422 \{\{\{\{ 0, 0, 0, 0, 0\}, +09423 \{ DEF, DEF, DEF, DEF, DEF\}, +09424 \{ DEF, DEF, DEF, DEF, DEF\}, +09425 \{ DEF, DEF, DEF, DEF, DEF\}, +09426 \{ DEF, DEF, DEF, DEF, DEF\}\}, +09427 \textcolor{comment}{/* UA.@A..UG */} +09428 \{\{ 0, 0, 0, 0, 0\}, +09429 \{ -719, -719, -719, -719, -719\}, +09430 \{ -479, -479, -479, -479, -479\}, +09431 \{ -659, -659, -659, -659, -659\}, +09432 \{ -549, -549, -549, -549, -549\}\}, +09433 \textcolor{comment}{/* UA.@C..UG */} +09434 \{\{ 0, 0, 0, 0, 0\}, +09435 \{ -789, -789, -789, -789, -789\}, +09436 \{ -479, -479, -479, -479, -479\}, +09437 \{ -809, -809, -809, -809, -809\}, +09438 \{ -439, -439, -439, -439, -439\}\}, +09439 \textcolor{comment}{/* UA.@G..UG */} +09440 \{\{ 0, 0, 0, 0, 0\}, +09441 \{ -959, -959, -959, -959, -959\}, +09442 \{ -359, -359, -359, -359, -359\}, +09443 \{ -919, -919, -919, -919, -919\}, +09444 \{ -549, -549, -549, -549, -549\}\}, +09445 \textcolor{comment}{/* UA.@U..UG */} +09446 \{\{ 0, 0, 0, 0, 0\}, +09447 \{ -809, -809, -809, -809, -809\}, +09448 \{ -479, -479, -479, -479, -479\}, +09449 \{ -809, -809, -809, -809, -809\}, +09450 \{ -359, -359, -359, -359, -359\}\}\}, +09451 \textcolor{comment}{/* UA.A@..UG */} +09452 \{\{\{ DEF, -399, -629, -889, -589\}, +09453 \{ -100, -449, -679, -939, -639\}, +09454 \{ -100, -449, -679, -939, -639\}, +09455 \{ -100, -449, -679, -939, -639\}, +09456 \{ -100, -449, -679, -939, -639\}\}, +09457 \textcolor{comment}{/* UA.AA..UG */} +09458 \{\{ DEF, -399, -629, -889, -589\}, +09459 \{ -769,-1118,-1348,-1608,-1308\}, +09460 \{ -529, -878,-1108,-1368,-1068\}, +09461 \{ -709,-1058,-1288,-1548,-1248\}, +09462 \{ -599, -948,-1178,-1438,-1138\}\}, +09463 \textcolor{comment}{/* UA.AC..UG */} +09464 \{\{ DEF, -399, -629, -889, -589\}, +09465 \{ -839,-1188,-1418,-1678,-1378\}, +09466 \{ -529, -878,-1108,-1368,-1068\}, +09467 \{ -859,-1208,-1438,-1698,-1398\}, +09468 \{ -489, -838,-1068,-1328,-1028\}\}, +09469 \textcolor{comment}{/* UA.AG..UG */} +09470 \{\{ DEF, -399, -629, -889, -589\}, +09471 \{-1009,-1358,-1588,-1848,-1548\}, +09472 \{ -409, -758, -988,-1248, -948\}, +09473 \{ -969,-1318,-1548,-1808,-1508\}, +09474 \{ -599, -948,-1178,-1438,-1138\}\}, +09475 \textcolor{comment}{/* UA.AU..UG */} +09476 \{\{ DEF, -399, -629, -889, -589\}, +09477 \{ -859,-1208,-1438,-1698,-1398\}, +09478 \{ -529, -878,-1108,-1368,-1068\}, +09479 \{ -859,-1208,-1438,-1698,-1398\}, +09480 \{ -409, -758, -988,-1248, -948\}\}\}, +09481 \textcolor{comment}{/* UA.C@..UG */} +09482 \{\{\{ DEF, -429, -509, -199, -179\}, +09483 \{ -100, -479, -559, -249, -229\}, +09484 \{ -100, -479, -559, -249, -229\}, +09485 \{ -100, -479, -559, -249, -229\}, +09486 \{ -100, -479, -559, -249, -229\}\}, +09487 \textcolor{comment}{/* UA.CA..UG */} +09488 \{\{ DEF, -429, -509, -199, -179\}, +09489 \{ -769,-1148,-1228, -918, -898\}, +09490 \{ -529, -908, -988, -678, -658\}, +09491 \{ -709,-1088,-1168, -858, -838\}, +09492 \{ -599, -978,-1058, -748, -728\}\}, +09493 \textcolor{comment}{/* UA.CC..UG */} +09494 \{\{ DEF, -429, -509, -199, -179\}, +09495 \{ -839,-1218,-1298, -988, -968\}, +09496 \{ -529, -908, -988, -678, -658\}, +09497 \{ -859,-1238,-1318,-1008, -988\}, +09498 \{ -489, -868, -948, -638, -618\}\}, +09499 \textcolor{comment}{/* UA.CG..UG */} +09500 \{\{ DEF, -429, -509, -199, -179\}, +09501 \{-1009,-1388,-1468,-1158,-1138\}, +09502 \{ -409, -788, -868, -558, -538\}, +09503 \{ -969,-1348,-1428,-1118,-1098\}, +09504 \{ -599, -978,-1058, -748, -728\}\}, +09505 \textcolor{comment}{/* UA.CU..UG */} +09506 \{\{ DEF, -429, -509, -199, -179\}, +09507 \{ -859,-1238,-1318,-1008, -988\}, +09508 \{ -529, -908, -988, -678, -658\}, +09509 \{ -859,-1238,-1318,-1008, -988\}, +09510 \{ -409, -788, -868, -558, -538\}\}\}, +09511 \textcolor{comment}{/* UA.G@..UG */} +09512 \{\{\{ DEF, -379, -679, -889, -679\}, +09513 \{ -100, -429, -729, -939, -729\}, +09514 \{ -100, -429, -729, -939, -729\}, +09515 \{ -100, -429, -729, -939, -729\}, +09516 \{ -100, -429, -729, -939, -729\}\}, +09517 \textcolor{comment}{/* UA.GA..UG */} +09518 \{\{ DEF, -379, -679, -889, -679\}, +09519 \{ -769,-1098,-1398,-1608,-1398\}, +09520 \{ -529, -858,-1158,-1368,-1158\}, +09521 \{ -709,-1038,-1338,-1548,-1338\}, +09522 \{ -599, -928,-1228,-1438,-1228\}\}, +09523 \textcolor{comment}{/* UA.GC..UG */} +09524 \{\{ DEF, -379, -679, -889, -679\}, +09525 \{ -839,-1168,-1468,-1678,-1468\}, +09526 \{ -529, -858,-1158,-1368,-1158\}, +09527 \{ -859,-1188,-1488,-1698,-1488\}, +09528 \{ -489, -818,-1118,-1328,-1118\}\}, +09529 \textcolor{comment}{/* UA.GG..UG */} +09530 \{\{ DEF, -379, -679, -889, -679\}, +09531 \{-1009,-1338,-1638,-1848,-1638\}, +09532 \{ -409, -738,-1038,-1248,-1038\}, +09533 \{ -969,-1298,-1598,-1808,-1598\}, +09534 \{ -599, -928,-1228,-1438,-1228\}\}, +09535 \textcolor{comment}{/* UA.GU..UG */} +09536 \{\{ DEF, -379, -679, -889, -679\}, +09537 \{ -859,-1188,-1488,-1698,-1488\}, +09538 \{ -529, -858,-1158,-1368,-1158\}, +09539 \{ -859,-1188,-1488,-1698,-1488\}, +09540 \{ -409, -738,-1038,-1248,-1038\}\}\}, +09541 \textcolor{comment}{/* UA.U@..UG */} +09542 \{\{\{ DEF, -279, -139, -279, -140\}, +09543 \{ -100, -329, -189, -329, -190\}, +09544 \{ -100, -329, -189, -329, -190\}, +09545 \{ -100, -329, -189, -329, -190\}, +09546 \{ -100, -329, -189, -329, -190\}\}, +09547 \textcolor{comment}{/* UA.UA..UG */} +09548 \{\{ DEF, -279, -139, -279, -140\}, +09549 \{ -769, -998, -858, -998, -859\}, +09550 \{ -529, -758, -618, -758, -619\}, +09551 \{ -709, -938, -798, -938, -799\}, +09552 \{ -599, -828, -688, -828, -689\}\}, +09553 \textcolor{comment}{/* UA.UC..UG */} +09554 \{\{ DEF, -279, -139, -279, -140\}, +09555 \{ -839,-1068, -928,-1068, -929\}, +09556 \{ -529, -758, -618, -758, -619\}, +09557 \{ -859,-1088, -948,-1088, -949\}, +09558 \{ -489, -718, -578, -718, -579\}\}, +09559 \textcolor{comment}{/* UA.UG..UG */} +09560 \{\{ DEF, -279, -139, -279, -140\}, +09561 \{-1009,-1238,-1098,-1238,-1099\}, +09562 \{ -409, -638, -498, -638, -499\}, +09563 \{ -969,-1198,-1058,-1198,-1059\}, +09564 \{ -599, -828, -688, -828, -689\}\}, +09565 \textcolor{comment}{/* UA.UU..UG */} +09566 \{\{ DEF, -279, -139, -279, -140\}, +09567 \{ -859,-1088, -948,-1088, -949\}, +09568 \{ -529, -758, -618, -758, -619\}, +09569 \{ -859,-1088, -948,-1088, -949\}, +09570 \{ -409, -638, -498, -638, -499\}\}\}\}, +09571 \textcolor{comment}{/* UA.@@..AU */} +09572 \{\{\{\{ 0, 0, 0, 0, 0\}, +09573 \{ DEF, DEF, DEF, DEF, DEF\}, +09574 \{ DEF, DEF, DEF, DEF, DEF\}, +09575 \{ DEF, DEF, DEF, DEF, DEF\}, +09576 \{ DEF, DEF, DEF, DEF, DEF\}\}, +09577 \textcolor{comment}{/* UA.@A..AU */} +09578 \{\{ 0, 0, 0, 0, 0\}, +09579 \{ -429, -429, -429, -429, -429\}, +09580 \{ -259, -259, -259, -259, -259\}, +09581 \{ -339, -339, -339, -339, -339\}, +09582 \{ -329, -329, -329, -329, -329\}\}, +09583 \textcolor{comment}{/* UA.@C..AU */} +09584 \{\{ 0, 0, 0, 0, 0\}, +09585 \{ -599, -599, -599, -599, -599\}, +09586 \{ -239, -239, -239, -239, -239\}, +09587 \{ -689, -689, -689, -689, -689\}, +09588 \{ -329, -329, -329, -329, -329\}\}, +09589 \textcolor{comment}{/* UA.@G..AU */} +09590 \{\{ 0, 0, 0, 0, 0\}, +09591 \{ -599, -599, -599, -599, -599\}, +09592 \{ -239, -239, -239, -239, -239\}, +09593 \{ -689, -689, -689, -689, -689\}, +09594 \{ -329, -329, -329, -329, -329\}\}, +09595 \textcolor{comment}{/* UA.@U..AU */} +09596 \{\{ 0, 0, 0, 0, 0\}, +09597 \{ -599, -599, -599, -599, -599\}, +09598 \{ -239, -239, -239, -239, -239\}, +09599 \{ -689, -689, -689, -689, -689\}, +09600 \{ -329, -329, -329, -329, -329\}\}\}, +09601 \textcolor{comment}{/* UA.A@..AU */} +09602 \{\{\{ DEF, -399, -629, -889, -589\}, +09603 \{ -100, -449, -679, -939, -639\}, +09604 \{ -100, -449, -679, -939, -639\}, +09605 \{ -100, -449, -679, -939, -639\}, +09606 \{ -100, -449, -679, -939, -639\}\}, +09607 \textcolor{comment}{/* UA.AA..AU */} +09608 \{\{ DEF, -399, -629, -889, -589\}, +09609 \{ -479, -828,-1058,-1318,-1018\}, +09610 \{ -309, -658, -888,-1148, -848\}, +09611 \{ -389, -738, -968,-1228, -928\}, +09612 \{ -379, -728, -958,-1218, -918\}\}, +09613 \textcolor{comment}{/* UA.AC..AU */} +09614 \{\{ DEF, -399, -629, -889, -589\}, +09615 \{ -649, -998,-1228,-1488,-1188\}, +09616 \{ -289, -638, -868,-1128, -828\}, +09617 \{ -739,-1088,-1318,-1578,-1278\}, +09618 \{ -379, -728, -958,-1218, -918\}\}, +09619 \textcolor{comment}{/* UA.AG..AU */} +09620 \{\{ DEF, -399, -629, -889, -589\}, +09621 \{ -649, -998,-1228,-1488,-1188\}, +09622 \{ -289, -638, -868,-1128, -828\}, +09623 \{ -739,-1088,-1318,-1578,-1278\}, +09624 \{ -379, -728, -958,-1218, -918\}\}, +09625 \textcolor{comment}{/* UA.AU..AU */} +09626 \{\{ DEF, -399, -629, -889, -589\}, +09627 \{ -649, -998,-1228,-1488,-1188\}, +09628 \{ -289, -638, -868,-1128, -828\}, +09629 \{ -739,-1088,-1318,-1578,-1278\}, +09630 \{ -379, -728, -958,-1218, -918\}\}\}, +09631 \textcolor{comment}{/* UA.C@..AU */} +09632 \{\{\{ DEF, -429, -509, -199, -179\}, +09633 \{ -100, -479, -559, -249, -229\}, +09634 \{ -100, -479, -559, -249, -229\}, +09635 \{ -100, -479, -559, -249, -229\}, +09636 \{ -100, -479, -559, -249, -229\}\}, +09637 \textcolor{comment}{/* UA.CA..AU */} +09638 \{\{ DEF, -429, -509, -199, -179\}, +09639 \{ -479, -858, -938, -628, -608\}, +09640 \{ -309, -688, -768, -458, -438\}, +09641 \{ -389, -768, -848, -538, -518\}, +09642 \{ -379, -758, -838, -528, -508\}\}, +09643 \textcolor{comment}{/* UA.CC..AU */} +09644 \{\{ DEF, -429, -509, -199, -179\}, +09645 \{ -649,-1028,-1108, -798, -778\}, +09646 \{ -289, -668, -748, -438, -418\}, +09647 \{ -739,-1118,-1198, -888, -868\}, +09648 \{ -379, -758, -838, -528, -508\}\}, +09649 \textcolor{comment}{/* UA.CG..AU */} +09650 \{\{ DEF, -429, -509, -199, -179\}, +09651 \{ -649,-1028,-1108, -798, -778\}, +09652 \{ -289, -668, -748, -438, -418\}, +09653 \{ -739,-1118,-1198, -888, -868\}, +09654 \{ -379, -758, -838, -528, -508\}\}, +09655 \textcolor{comment}{/* UA.CU..AU */} +09656 \{\{ DEF, -429, -509, -199, -179\}, +09657 \{ -649,-1028,-1108, -798, -778\}, +09658 \{ -289, -668, -748, -438, -418\}, +09659 \{ -739,-1118,-1198, -888, -868\}, +09660 \{ -379, -758, -838, -528, -508\}\}\}, +09661 \textcolor{comment}{/* UA.G@..AU */} +09662 \{\{\{ DEF, -379, -679, -889, -679\}, +09663 \{ -100, -429, -729, -939, -729\}, +09664 \{ -100, -429, -729, -939, -729\}, +09665 \{ -100, -429, -729, -939, -729\}, +09666 \{ -100, -429, -729, -939, -729\}\}, +09667 \textcolor{comment}{/* UA.GA..AU */} +09668 \{\{ DEF, -379, -679, -889, -679\}, +09669 \{ -479, -808,-1108,-1318,-1108\}, +09670 \{ -309, -638, -938,-1148, -938\}, +09671 \{ -389, -718,-1018,-1228,-1018\}, +09672 \{ -379, -708,-1008,-1218,-1008\}\}, +09673 \textcolor{comment}{/* UA.GC..AU */} +09674 \{\{ DEF, -379, -679, -889, -679\}, +09675 \{ -649, -978,-1278,-1488,-1278\}, +09676 \{ -289, -618, -918,-1128, -918\}, +09677 \{ -739,-1068,-1368,-1578,-1368\}, +09678 \{ -379, -708,-1008,-1218,-1008\}\}, +09679 \textcolor{comment}{/* UA.GG..AU */} +09680 \{\{ DEF, -379, -679, -889, -679\}, +09681 \{ -649, -978,-1278,-1488,-1278\}, +09682 \{ -289, -618, -918,-1128, -918\}, +09683 \{ -739,-1068,-1368,-1578,-1368\}, +09684 \{ -379, -708,-1008,-1218,-1008\}\}, +09685 \textcolor{comment}{/* UA.GU..AU */} +09686 \{\{ DEF, -379, -679, -889, -679\}, +09687 \{ -649, -978,-1278,-1488,-1278\}, +09688 \{ -289, -618, -918,-1128, -918\}, +09689 \{ -739,-1068,-1368,-1578,-1368\}, +09690 \{ -379, -708,-1008,-1218,-1008\}\}\}, +09691 \textcolor{comment}{/* UA.U@..AU */} +09692 \{\{\{ DEF, -279, -139, -279, -140\}, +09693 \{ -100, -329, -189, -329, -190\}, +09694 \{ -100, -329, -189, -329, -190\}, +09695 \{ -100, -329, -189, -329, -190\}, +09696 \{ -100, -329, -189, -329, -190\}\}, +09697 \textcolor{comment}{/* UA.UA..AU */} +09698 \{\{ DEF, -279, -139, -279, -140\}, +09699 \{ -479, -708, -568, -708, -569\}, +09700 \{ -309, -538, -398, -538, -399\}, +09701 \{ -389, -618, -478, -618, -479\}, +09702 \{ -379, -608, -468, -608, -469\}\}, +09703 \textcolor{comment}{/* UA.UC..AU */} +09704 \{\{ DEF, -279, -139, -279, -140\}, +09705 \{ -649, -878, -738, -878, -739\}, +09706 \{ -289, -518, -378, -518, -379\}, +09707 \{ -739, -968, -828, -968, -829\}, +09708 \{ -379, -608, -468, -608, -469\}\}, +09709 \textcolor{comment}{/* UA.UG..AU */} +09710 \{\{ DEF, -279, -139, -279, -140\}, +09711 \{ -649, -878, -738, -878, -739\}, +09712 \{ -289, -518, -378, -518, -379\}, +09713 \{ -739, -968, -828, -968, -829\}, +09714 \{ -379, -608, -468, -608, -469\}\}, +09715 \textcolor{comment}{/* UA.UU..AU */} +09716 \{\{ DEF, -279, -139, -279, -140\}, +09717 \{ -649, -878, -738, -878, -739\}, +09718 \{ -289, -518, -378, -518, -379\}, +09719 \{ -739, -968, -828, -968, -829\}, +09720 \{ -379, -608, -468, -608, -469\}\}\}\}, +09721 \textcolor{comment}{/* UA.@@..UA */} +09722 \{\{\{\{ 0, 0, 0, 0, 0\}, +09723 \{ DEF, DEF, DEF, DEF, DEF\}, +09724 \{ DEF, DEF, DEF, DEF, DEF\}, +09725 \{ DEF, DEF, DEF, DEF, DEF\}, +09726 \{ DEF, DEF, DEF, DEF, DEF\}\}, +09727 \textcolor{comment}{/* UA.@A..UA */} +09728 \{\{ 0, 0, 0, 0, 0\}, +09729 \{ -399, -399, -399, -399, -399\}, +09730 \{ -429, -429, -429, -429, -429\}, +09731 \{ -379, -379, -379, -379, -379\}, +09732 \{ -279, -279, -279, -279, -279\}\}, +09733 \textcolor{comment}{/* UA.@C..UA */} +09734 \{\{ 0, 0, 0, 0, 0\}, +09735 \{ -629, -629, -629, -629, -629\}, +09736 \{ -509, -509, -509, -509, -509\}, +09737 \{ -679, -679, -679, -679, -679\}, +09738 \{ -139, -139, -139, -139, -139\}\}, +09739 \textcolor{comment}{/* UA.@G..UA */} +09740 \{\{ 0, 0, 0, 0, 0\}, +09741 \{ -889, -889, -889, -889, -889\}, +09742 \{ -199, -199, -199, -199, -199\}, +09743 \{ -889, -889, -889, -889, -889\}, +09744 \{ -279, -279, -279, -279, -279\}\}, +09745 \textcolor{comment}{/* UA.@U..UA */} +09746 \{\{ 0, 0, 0, 0, 0\}, +09747 \{ -589, -589, -589, -589, -589\}, +09748 \{ -179, -179, -179, -179, -179\}, +09749 \{ -679, -679, -679, -679, -679\}, +09750 \{ -140, -140, -140, -140, -140\}\}\}, +09751 \textcolor{comment}{/* UA.A@..UA */} +09752 \{\{\{ DEF, -399, -629, -889, -589\}, +09753 \{ -100, -449, -679, -939, -639\}, +09754 \{ -100, -449, -679, -939, -639\}, +09755 \{ -100, -449, -679, -939, -639\}, +09756 \{ -100, -449, -679, -939, -639\}\}, +09757 \textcolor{comment}{/* UA.AA..UA */} +09758 \{\{ DEF, -399, -629, -889, -589\}, +09759 \{ -449, -798,-1028,-1288, -988\}, +09760 \{ -479, -828,-1058,-1318,-1018\}, +09761 \{ -429, -778,-1008,-1268, -968\}, +09762 \{ -329, -678, -908,-1168, -868\}\}, +09763 \textcolor{comment}{/* UA.AC..UA */} +09764 \{\{ DEF, -399, -629, -889, -589\}, +09765 \{ -679,-1028,-1258,-1518,-1218\}, +09766 \{ -559, -908,-1138,-1398,-1098\}, +09767 \{ -729,-1078,-1308,-1568,-1268\}, +09768 \{ -189, -538, -768,-1028, -728\}\}, +09769 \textcolor{comment}{/* UA.AG..UA */} +09770 \{\{ DEF, -399, -629, -889, -589\}, +09771 \{ -939,-1288,-1518,-1778,-1478\}, +09772 \{ -249, -598, -828,-1088, -788\}, +09773 \{ -939,-1288,-1518,-1778,-1478\}, +09774 \{ -329, -678, -908,-1168, -868\}\}, +09775 \textcolor{comment}{/* UA.AU..UA */} +09776 \{\{ DEF, -399, -629, -889, -589\}, +09777 \{ -639, -988,-1218,-1478,-1178\}, +09778 \{ -229, -578, -808,-1068, -768\}, +09779 \{ -729,-1078,-1308,-1568,-1268\}, +09780 \{ -190, -539, -769,-1029, -729\}\}\}, +09781 \textcolor{comment}{/* UA.C@..UA */} +09782 \{\{\{ DEF, -429, -509, -199, -179\}, +09783 \{ -100, -479, -559, -249, -229\}, +09784 \{ -100, -479, -559, -249, -229\}, +09785 \{ -100, -479, -559, -249, -229\}, +09786 \{ -100, -479, -559, -249, -229\}\}, +09787 \textcolor{comment}{/* UA.CA..UA */} +09788 \{\{ DEF, -429, -509, -199, -179\}, +09789 \{ -449, -828, -908, -598, -578\}, +09790 \{ -479, -858, -938, -628, -608\}, +09791 \{ -429, -808, -888, -578, -558\}, +09792 \{ -329, -708, -788, -478, -458\}\}, +09793 \textcolor{comment}{/* UA.CC..UA */} +09794 \{\{ DEF, -429, -509, -199, -179\}, +09795 \{ -679,-1058,-1138, -828, -808\}, +09796 \{ -559, -938,-1018, -708, -688\}, +09797 \{ -729,-1108,-1188, -878, -858\}, +09798 \{ -189, -568, -648, -338, -318\}\}, +09799 \textcolor{comment}{/* UA.CG..UA */} +09800 \{\{ DEF, -429, -509, -199, -179\}, +09801 \{ -939,-1318,-1398,-1088,-1068\}, +09802 \{ -249, -628, -708, -398, -378\}, +09803 \{ -939,-1318,-1398,-1088,-1068\}, +09804 \{ -329, -708, -788, -478, -458\}\}, +09805 \textcolor{comment}{/* UA.CU..UA */} +09806 \{\{ DEF, -429, -509, -199, -179\}, +09807 \{ -639,-1018,-1098, -788, -768\}, +09808 \{ -229, -608, -688, -378, -358\}, +09809 \{ -729,-1108,-1188, -878, -858\}, +09810 \{ -190, -569, -649, -339, -319\}\}\}, +09811 \textcolor{comment}{/* UA.G@..UA */} +09812 \{\{\{ DEF, -379, -679, -889, -679\}, +09813 \{ -100, -429, -729, -939, -729\}, +09814 \{ -100, -429, -729, -939, -729\}, +09815 \{ -100, -429, -729, -939, -729\}, +09816 \{ -100, -429, -729, -939, -729\}\}, +09817 \textcolor{comment}{/* UA.GA..UA */} +09818 \{\{ DEF, -379, -679, -889, -679\}, +09819 \{ -449, -778,-1078,-1288,-1078\}, +09820 \{ -479, -808,-1108,-1318,-1108\}, +09821 \{ -429, -758,-1058,-1268,-1058\}, +09822 \{ -329, -658, -958,-1168, -958\}\}, +09823 \textcolor{comment}{/* UA.GC..UA */} +09824 \{\{ DEF, -379, -679, -889, -679\}, +09825 \{ -679,-1008,-1308,-1518,-1308\}, +09826 \{ -559, -888,-1188,-1398,-1188\}, +09827 \{ -729,-1058,-1358,-1568,-1358\}, +09828 \{ -189, -518, -818,-1028, -818\}\}, +09829 \textcolor{comment}{/* UA.GG..UA */} +09830 \{\{ DEF, -379, -679, -889, -679\}, +09831 \{ -939,-1268,-1568,-1778,-1568\}, +09832 \{ -249, -578, -878,-1088, -878\}, +09833 \{ -939,-1268,-1568,-1778,-1568\}, +09834 \{ -329, -658, -958,-1168, -958\}\}, +09835 \textcolor{comment}{/* UA.GU..UA */} +09836 \{\{ DEF, -379, -679, -889, -679\}, +09837 \{ -639, -968,-1268,-1478,-1268\}, +09838 \{ -229, -558, -858,-1068, -858\}, +09839 \{ -729,-1058,-1358,-1568,-1358\}, +09840 \{ -190, -519, -819,-1029, -819\}\}\}, +09841 \textcolor{comment}{/* UA.U@..UA */} +09842 \{\{\{ DEF, -279, -139, -279, -140\}, +09843 \{ -100, -329, -189, -329, -190\}, +09844 \{ -100, -329, -189, -329, -190\}, +09845 \{ -100, -329, -189, -329, -190\}, +09846 \{ -100, -329, -189, -329, -190\}\}, +09847 \textcolor{comment}{/* UA.UA..UA */} +09848 \{\{ DEF, -279, -139, -279, -140\}, +09849 \{ -449, -678, -538, -678, -539\}, +09850 \{ -479, -708, -568, -708, -569\}, +09851 \{ -429, -658, -518, -658, -519\}, +09852 \{ -329, -558, -418, -558, -419\}\}, +09853 \textcolor{comment}{/* UA.UC..UA */} +09854 \{\{ DEF, -279, -139, -279, -140\}, +09855 \{ -679, -908, -768, -908, -769\}, +09856 \{ -559, -788, -648, -788, -649\}, +09857 \{ -729, -958, -818, -958, -819\}, +09858 \{ -189, -418, -278, -418, -279\}\}, +09859 \textcolor{comment}{/* UA.UG..UA */} +09860 \{\{ DEF, -279, -139, -279, -140\}, +09861 \{ -939,-1168,-1028,-1168,-1029\}, +09862 \{ -249, -478, -338, -478, -339\}, +09863 \{ -939,-1168,-1028,-1168,-1029\}, +09864 \{ -329, -558, -418, -558, -419\}\}, +09865 \textcolor{comment}{/* UA.UU..UA */} +09866 \{\{ DEF, -279, -139, -279, -140\}, +09867 \{ -639, -868, -728, -868, -729\}, +09868 \{ -229, -458, -318, -458, -319\}, +09869 \{ -729, -958, -818, -958, -819\}, +09870 \{ -190, -419, -279, -419, -280\}\}\}\}, +09871 \textcolor{comment}{/* UA.@@.. @ */} +09872 \{\{\{\{ DEF, DEF, DEF, DEF, DEF\}, +09873 \{ DEF, DEF, DEF, DEF, DEF\}, +09874 \{ DEF, DEF, DEF, DEF, DEF\}, +09875 \{ DEF, DEF, DEF, DEF, DEF\}, +09876 \{ DEF, DEF, DEF, DEF, DEF\}\}, +09877 \textcolor{comment}{/* UA.@A.. @ */} +09878 \{\{ DEF, DEF, DEF, DEF, DEF\}, +09879 \{ DEF, DEF, DEF, DEF, DEF\}, +09880 \{ DEF, DEF, DEF, DEF, DEF\}, +09881 \{ DEF, DEF, DEF, DEF, DEF\}, +09882 \{ DEF, DEF, DEF, DEF, DEF\}\}, +09883 \textcolor{comment}{/* UA.@C.. @ */} +09884 \{\{ DEF, DEF, DEF, DEF, DEF\}, +09885 \{ DEF, DEF, DEF, DEF, DEF\}, +09886 \{ DEF, DEF, DEF, DEF, DEF\}, +09887 \{ DEF, DEF, DEF, DEF, DEF\}, +09888 \{ DEF, DEF, DEF, DEF, DEF\}\}, +09889 \textcolor{comment}{/* UA.@G.. @ */} +09890 \{\{ DEF, DEF, DEF, DEF, DEF\}, +09891 \{ DEF, DEF, DEF, DEF, DEF\}, +09892 \{ DEF, DEF, DEF, DEF, DEF\}, +09893 \{ DEF, DEF, DEF, DEF, DEF\}, +09894 \{ DEF, DEF, DEF, DEF, DEF\}\}, +09895 \textcolor{comment}{/* UA.@U.. @ */} +09896 \{\{ DEF, DEF, DEF, DEF, DEF\}, +09897 \{ DEF, DEF, DEF, DEF, DEF\}, +09898 \{ DEF, DEF, DEF, DEF, DEF\}, +09899 \{ DEF, DEF, DEF, DEF, DEF\}, +09900 \{ DEF, DEF, DEF, DEF, DEF\}\}\}, +09901 \textcolor{comment}{/* UA.A@.. @ */} +09902 \{\{\{ -100, -449, -679, -939, -639\}, +09903 \{ -100, -449, -679, -939, -639\}, +09904 \{ -100, -449, -679, -939, -639\}, +09905 \{ -100, -449, -679, -939, -639\}, +09906 \{ -100, -449, -679, -939, -639\}\}, +09907 \textcolor{comment}{/* UA.AA.. @ */} +09908 \{\{ -100, -449, -679, -939, -639\}, +09909 \{ -100, -449, -679, -939, -639\}, +09910 \{ -100, -449, -679, -939, -639\}, +09911 \{ -100, -449, -679, -939, -639\}, +09912 \{ -100, -449, -679, -939, -639\}\}, +09913 \textcolor{comment}{/* UA.AC.. @ */} +09914 \{\{ -100, -449, -679, -939, -639\}, +09915 \{ -100, -449, -679, -939, -639\}, +09916 \{ -100, -449, -679, -939, -639\}, +09917 \{ -100, -449, -679, -939, -639\}, +09918 \{ -100, -449, -679, -939, -639\}\}, +09919 \textcolor{comment}{/* UA.AG.. @ */} +09920 \{\{ -100, -449, -679, -939, -639\}, +09921 \{ -100, -449, -679, -939, -639\}, +09922 \{ -100, -449, -679, -939, -639\}, +09923 \{ -100, -449, -679, -939, -639\}, +09924 \{ -100, -449, -679, -939, -639\}\}, +09925 \textcolor{comment}{/* UA.AU.. @ */} +09926 \{\{ -100, -449, -679, -939, -639\}, +09927 \{ -100, -449, -679, -939, -639\}, +09928 \{ -100, -449, -679, -939, -639\}, +09929 \{ -100, -449, -679, -939, -639\}, +09930 \{ -100, -449, -679, -939, -639\}\}\}, +09931 \textcolor{comment}{/* UA.C@.. @ */} +09932 \{\{\{ -100, -479, -559, -249, -229\}, +09933 \{ -100, -479, -559, -249, -229\}, +09934 \{ -100, -479, -559, -249, -229\}, +09935 \{ -100, -479, -559, -249, -229\}, +09936 \{ -100, -479, -559, -249, -229\}\}, +09937 \textcolor{comment}{/* UA.CA.. @ */} +09938 \{\{ -100, -479, -559, -249, -229\}, +09939 \{ -100, -479, -559, -249, -229\}, +09940 \{ -100, -479, -559, -249, -229\}, +09941 \{ -100, -479, -559, -249, -229\}, +09942 \{ -100, -479, -559, -249, -229\}\}, +09943 \textcolor{comment}{/* UA.CC.. @ */} +09944 \{\{ -100, -479, -559, -249, -229\}, +09945 \{ -100, -479, -559, -249, -229\}, +09946 \{ -100, -479, -559, -249, -229\}, +09947 \{ -100, -479, -559, -249, -229\}, +09948 \{ -100, -479, -559, -249, -229\}\}, +09949 \textcolor{comment}{/* UA.CG.. @ */} +09950 \{\{ -100, -479, -559, -249, -229\}, +09951 \{ -100, -479, -559, -249, -229\}, +09952 \{ -100, -479, -559, -249, -229\}, +09953 \{ -100, -479, -559, -249, -229\}, +09954 \{ -100, -479, -559, -249, -229\}\}, +09955 \textcolor{comment}{/* UA.CU.. @ */} +09956 \{\{ -100, -479, -559, -249, -229\}, +09957 \{ -100, -479, -559, -249, -229\}, +09958 \{ -100, -479, -559, -249, -229\}, +09959 \{ -100, -479, -559, -249, -229\}, +09960 \{ -100, -479, -559, -249, -229\}\}\}, +09961 \textcolor{comment}{/* UA.G@.. @ */} +09962 \{\{\{ -100, -429, -729, -939, -729\}, +09963 \{ -100, -429, -729, -939, -729\}, +09964 \{ -100, -429, -729, -939, -729\}, +09965 \{ -100, -429, -729, -939, -729\}, +09966 \{ -100, -429, -729, -939, -729\}\}, +09967 \textcolor{comment}{/* UA.GA.. @ */} +09968 \{\{ -100, -429, -729, -939, -729\}, +09969 \{ -100, -429, -729, -939, -729\}, +09970 \{ -100, -429, -729, -939, -729\}, +09971 \{ -100, -429, -729, -939, -729\}, +09972 \{ -100, -429, -729, -939, -729\}\}, +09973 \textcolor{comment}{/* UA.GC.. @ */} +09974 \{\{ -100, -429, -729, -939, -729\}, +09975 \{ -100, -429, -729, -939, -729\}, +09976 \{ -100, -429, -729, -939, -729\}, +09977 \{ -100, -429, -729, -939, -729\}, +09978 \{ -100, -429, -729, -939, -729\}\}, +09979 \textcolor{comment}{/* UA.GG.. @ */} +09980 \{\{ -100, -429, -729, -939, -729\}, +09981 \{ -100, -429, -729, -939, -729\}, +09982 \{ -100, -429, -729, -939, -729\}, +09983 \{ -100, -429, -729, -939, -729\}, +09984 \{ -100, -429, -729, -939, -729\}\}, +09985 \textcolor{comment}{/* UA.GU.. @ */} +09986 \{\{ -100, -429, -729, -939, -729\}, +09987 \{ -100, -429, -729, -939, -729\}, +09988 \{ -100, -429, -729, -939, -729\}, +09989 \{ -100, -429, -729, -939, -729\}, +09990 \{ -100, -429, -729, -939, -729\}\}\}, +09991 \textcolor{comment}{/* UA.U@.. @ */} +09992 \{\{\{ -100, -329, -189, -329, -190\}, +09993 \{ -100, -329, -189, -329, -190\}, +09994 \{ -100, -329, -189, -329, -190\}, +09995 \{ -100, -329, -189, -329, -190\}, +09996 \{ -100, -329, -189, -329, -190\}\}, +09997 \textcolor{comment}{/* UA.UA.. @ */} +09998 \{\{ -100, -329, -189, -329, -190\}, +09999 \{ -100, -329, -189, -329, -190\}, +10000 \{ -100, -329, -189, -329, -190\}, +10001 \{ -100, -329, -189, -329, -190\}, +10002 \{ -100, -329, -189, -329, -190\}\}, +10003 \textcolor{comment}{/* UA.UC.. @ */} +10004 \{\{ -100, -329, -189, -329, -190\}, +10005 \{ -100, -329, -189, -329, -190\}, +10006 \{ -100, -329, -189, -329, -190\}, +10007 \{ -100, -329, -189, -329, -190\}, +10008 \{ -100, -329, -189, -329, -190\}\}, +10009 \textcolor{comment}{/* UA.UG.. @ */} +10010 \{\{ -100, -329, -189, -329, -190\}, +10011 \{ -100, -329, -189, -329, -190\}, +10012 \{ -100, -329, -189, -329, -190\}, +10013 \{ -100, -329, -189, -329, -190\}, +10014 \{ -100, -329, -189, -329, -190\}\}, +10015 \textcolor{comment}{/* UA.UU.. @ */} +10016 \{\{ -100, -329, -189, -329, -190\}, +10017 \{ -100, -329, -189, -329, -190\}, +10018 \{ -100, -329, -189, -329, -190\}, +10019 \{ -100, -329, -189, -329, -190\}, +10020 \{ -100, -329, -189, -329, -190\}\}\}\}\}, +10021 \{ \textcolor{comment}{/* noPair */} \{\{\{\{0\}\}\}\}, +10022 \textcolor{comment}{/* @.@@..CG */} +10023 \{\{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10024 \{ -100, -100, -100, -100, -100\}, +10025 \{ -100, -100, -100, -100, -100\}, +10026 \{ -100, -100, -100, -100, -100\}, +10027 \{ -100, -100, -100, -100, -100\}\}, +10028 \textcolor{comment}{/* @.@A..CG */} +10029 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10030 \{-1079,-1079,-1079,-1079,-1079\}, +10031 \{ -569, -569, -569, -569, -569\}, +10032 \{ -989, -989, -989, -989, -989\}, +10033 \{ -859, -859, -859, -859, -859\}\}, +10034 \textcolor{comment}{/* @.@C..CG */} +10035 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10036 \{ -999, -999, -999, -999, -999\}, +10037 \{ -499, -499, -499, -499, -499\}, +10038 \{ -989, -989, -989, -989, -989\}, +10039 \{ -789, -789, -789, -789, -789\}\}, +10040 \textcolor{comment}{/* @.@G..CG */} +10041 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10042 \{-1079,-1079,-1079,-1079,-1079\}, +10043 \{ -569, -569, -569, -569, -569\}, +10044 \{ -989, -989, -989, -989, -989\}, +10045 \{ -859, -859, -859, -859, -859\}\}, +10046 \textcolor{comment}{/* @.@U..CG */} +10047 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10048 \{-1079,-1079,-1079,-1079,-1079\}, +10049 \{ -719, -719, -719, -719, -719\}, +10050 \{ -989, -989, -989, -989, -989\}, +10051 \{ -909, -909, -909, -909, -909\}\}\}, +10052 \textcolor{comment}{/* @.A@..CG */} +10053 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10054 \{ -100, -100, -100, -100, -100\}, +10055 \{ -100, -100, -100, -100, -100\}, +10056 \{ -100, -100, -100, -100, -100\}, +10057 \{ -100, -100, -100, -100, -100\}\}, +10058 \textcolor{comment}{/* @.AA..CG */} +10059 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10060 \{-1079,-1079,-1079,-1079,-1079\}, +10061 \{ -569, -569, -569, -569, -569\}, +10062 \{ -989, -989, -989, -989, -989\}, +10063 \{ -859, -859, -859, -859, -859\}\}, +10064 \textcolor{comment}{/* @.AC..CG */} +10065 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10066 \{ -999, -999, -999, -999, -999\}, +10067 \{ -499, -499, -499, -499, -499\}, +10068 \{ -989, -989, -989, -989, -989\}, +10069 \{ -789, -789, -789, -789, -789\}\}, +10070 \textcolor{comment}{/* @.AG..CG */} +10071 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10072 \{-1079,-1079,-1079,-1079,-1079\}, +10073 \{ -569, -569, -569, -569, -569\}, +10074 \{ -989, -989, -989, -989, -989\}, +10075 \{ -859, -859, -859, -859, -859\}\}, +10076 \textcolor{comment}{/* @.AU..CG */} +10077 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10078 \{-1079,-1079,-1079,-1079,-1079\}, +10079 \{ -719, -719, -719, -719, -719\}, +10080 \{ -989, -989, -989, -989, -989\}, +10081 \{ -909, -909, -909, -909, -909\}\}\}, +10082 \textcolor{comment}{/* @.C@..CG */} +10083 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10084 \{ -100, -100, -100, -100, -100\}, +10085 \{ -100, -100, -100, -100, -100\}, +10086 \{ -100, -100, -100, -100, -100\}, +10087 \{ -100, -100, -100, -100, -100\}\}, +10088 \textcolor{comment}{/* @.CA..CG */} +10089 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10090 \{-1079,-1079,-1079,-1079,-1079\}, +10091 \{ -569, -569, -569, -569, -569\}, +10092 \{ -989, -989, -989, -989, -989\}, +10093 \{ -859, -859, -859, -859, -859\}\}, +10094 \textcolor{comment}{/* @.CC..CG */} +10095 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10096 \{ -999, -999, -999, -999, -999\}, +10097 \{ -499, -499, -499, -499, -499\}, +10098 \{ -989, -989, -989, -989, -989\}, +10099 \{ -789, -789, -789, -789, -789\}\}, +10100 \textcolor{comment}{/* @.CG..CG */} +10101 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10102 \{-1079,-1079,-1079,-1079,-1079\}, +10103 \{ -569, -569, -569, -569, -569\}, +10104 \{ -989, -989, -989, -989, -989\}, +10105 \{ -859, -859, -859, -859, -859\}\}, +10106 \textcolor{comment}{/* @.CU..CG */} +10107 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10108 \{-1079,-1079,-1079,-1079,-1079\}, +10109 \{ -719, -719, -719, -719, -719\}, +10110 \{ -989, -989, -989, -989, -989\}, +10111 \{ -909, -909, -909, -909, -909\}\}\}, +10112 \textcolor{comment}{/* @.G@..CG */} +10113 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10114 \{ -100, -100, -100, -100, -100\}, +10115 \{ -100, -100, -100, -100, -100\}, +10116 \{ -100, -100, -100, -100, -100\}, +10117 \{ -100, -100, -100, -100, -100\}\}, +10118 \textcolor{comment}{/* @.GA..CG */} +10119 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10120 \{-1079,-1079,-1079,-1079,-1079\}, +10121 \{ -569, -569, -569, -569, -569\}, +10122 \{ -989, -989, -989, -989, -989\}, +10123 \{ -859, -859, -859, -859, -859\}\}, +10124 \textcolor{comment}{/* @.GC..CG */} +10125 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10126 \{ -999, -999, -999, -999, -999\}, +10127 \{ -499, -499, -499, -499, -499\}, +10128 \{ -989, -989, -989, -989, -989\}, +10129 \{ -789, -789, -789, -789, -789\}\}, +10130 \textcolor{comment}{/* @.GG..CG */} +10131 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10132 \{-1079,-1079,-1079,-1079,-1079\}, +10133 \{ -569, -569, -569, -569, -569\}, +10134 \{ -989, -989, -989, -989, -989\}, +10135 \{ -859, -859, -859, -859, -859\}\}, +10136 \textcolor{comment}{/* @.GU..CG */} +10137 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10138 \{-1079,-1079,-1079,-1079,-1079\}, +10139 \{ -719, -719, -719, -719, -719\}, +10140 \{ -989, -989, -989, -989, -989\}, +10141 \{ -909, -909, -909, -909, -909\}\}\}, +10142 \textcolor{comment}{/* @.U@..CG */} +10143 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10144 \{ -100, -100, -100, -100, -100\}, +10145 \{ -100, -100, -100, -100, -100\}, +10146 \{ -100, -100, -100, -100, -100\}, +10147 \{ -100, -100, -100, -100, -100\}\}, +10148 \textcolor{comment}{/* @.UA..CG */} +10149 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10150 \{-1079,-1079,-1079,-1079,-1079\}, +10151 \{ -569, -569, -569, -569, -569\}, +10152 \{ -989, -989, -989, -989, -989\}, +10153 \{ -859, -859, -859, -859, -859\}\}, +10154 \textcolor{comment}{/* @.UC..CG */} +10155 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10156 \{ -999, -999, -999, -999, -999\}, +10157 \{ -499, -499, -499, -499, -499\}, +10158 \{ -989, -989, -989, -989, -989\}, +10159 \{ -789, -789, -789, -789, -789\}\}, +10160 \textcolor{comment}{/* @.UG..CG */} +10161 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10162 \{-1079,-1079,-1079,-1079,-1079\}, +10163 \{ -569, -569, -569, -569, -569\}, +10164 \{ -989, -989, -989, -989, -989\}, +10165 \{ -859, -859, -859, -859, -859\}\}, +10166 \textcolor{comment}{/* @.UU..CG */} +10167 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10168 \{-1079,-1079,-1079,-1079,-1079\}, +10169 \{ -719, -719, -719, -719, -719\}, +10170 \{ -989, -989, -989, -989, -989\}, +10171 \{ -909, -909, -909, -909, -909\}\}\}\}, +10172 \textcolor{comment}{/* @.@@..GC */} +10173 \{\{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10174 \{ -100, -100, -100, -100, -100\}, +10175 \{ -100, -100, -100, -100, -100\}, +10176 \{ -100, -100, -100, -100, -100\}, +10177 \{ -100, -100, -100, -100, -100\}\}, +10178 \textcolor{comment}{/* @.@A..GC */} +10179 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10180 \{ -569, -569, -569, -569, -569\}, +10181 \{ -769, -769, -769, -769, -769\}, +10182 \{ -759, -759, -759, -759, -759\}, +10183 \{ -549, -549, -549, -549, -549\}\}, +10184 \textcolor{comment}{/* @.@C..GC */} +10185 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10186 \{ -929, -929, -929, -929, -929\}, +10187 \{ -359, -359, -359, -359, -359\}, +10188 \{ -789, -789, -789, -789, -789\}, +10189 \{ -549, -549, -549, -549, -549\}\}, +10190 \textcolor{comment}{/* @.@G..GC */} +10191 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10192 \{ -609, -609, -609, -609, -609\}, +10193 \{ -359, -359, -359, -359, -359\}, +10194 \{ -669, -669, -669, -669, -669\}, +10195 \{ -549, -549, -549, -549, -549\}\}, +10196 \textcolor{comment}{/* @.@U..GC */} +10197 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10198 \{ -929, -929, -929, -929, -929\}, +10199 \{ -439, -439, -439, -439, -439\}, +10200 \{ -789, -789, -789, -789, -789\}, +10201 \{ -619, -619, -619, -619, -619\}\}\}, +10202 \textcolor{comment}{/* @.A@..GC */} +10203 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10204 \{ -100, -100, -100, -100, -100\}, +10205 \{ -100, -100, -100, -100, -100\}, +10206 \{ -100, -100, -100, -100, -100\}, +10207 \{ -100, -100, -100, -100, -100\}\}, +10208 \textcolor{comment}{/* @.AA..GC */} +10209 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10210 \{ -569, -569, -569, -569, -569\}, +10211 \{ -769, -769, -769, -769, -769\}, +10212 \{ -759, -759, -759, -759, -759\}, +10213 \{ -549, -549, -549, -549, -549\}\}, +10214 \textcolor{comment}{/* @.AC..GC */} +10215 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10216 \{ -929, -929, -929, -929, -929\}, +10217 \{ -359, -359, -359, -359, -359\}, +10218 \{ -789, -789, -789, -789, -789\}, +10219 \{ -549, -549, -549, -549, -549\}\}, +10220 \textcolor{comment}{/* @.AG..GC */} +10221 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10222 \{ -609, -609, -609, -609, -609\}, +10223 \{ -359, -359, -359, -359, -359\}, +10224 \{ -669, -669, -669, -669, -669\}, +10225 \{ -549, -549, -549, -549, -549\}\}, +10226 \textcolor{comment}{/* @.AU..GC */} +10227 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10228 \{ -929, -929, -929, -929, -929\}, +10229 \{ -439, -439, -439, -439, -439\}, +10230 \{ -789, -789, -789, -789, -789\}, +10231 \{ -619, -619, -619, -619, -619\}\}\}, +10232 \textcolor{comment}{/* @.C@..GC */} +10233 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10234 \{ -100, -100, -100, -100, -100\}, +10235 \{ -100, -100, -100, -100, -100\}, +10236 \{ -100, -100, -100, -100, -100\}, +10237 \{ -100, -100, -100, -100, -100\}\}, +10238 \textcolor{comment}{/* @.CA..GC */} +10239 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10240 \{ -569, -569, -569, -569, -569\}, +10241 \{ -769, -769, -769, -769, -769\}, +10242 \{ -759, -759, -759, -759, -759\}, +10243 \{ -549, -549, -549, -549, -549\}\}, +10244 \textcolor{comment}{/* @.CC..GC */} +10245 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10246 \{ -929, -929, -929, -929, -929\}, +10247 \{ -359, -359, -359, -359, -359\}, +10248 \{ -789, -789, -789, -789, -789\}, +10249 \{ -549, -549, -549, -549, -549\}\}, +10250 \textcolor{comment}{/* @.CG..GC */} +10251 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10252 \{ -609, -609, -609, -609, -609\}, +10253 \{ -359, -359, -359, -359, -359\}, +10254 \{ -669, -669, -669, -669, -669\}, +10255 \{ -549, -549, -549, -549, -549\}\}, +10256 \textcolor{comment}{/* @.CU..GC */} +10257 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10258 \{ -929, -929, -929, -929, -929\}, +10259 \{ -439, -439, -439, -439, -439\}, +10260 \{ -789, -789, -789, -789, -789\}, +10261 \{ -619, -619, -619, -619, -619\}\}\}, +10262 \textcolor{comment}{/* @.G@..GC */} +10263 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10264 \{ -100, -100, -100, -100, -100\}, +10265 \{ -100, -100, -100, -100, -100\}, +10266 \{ -100, -100, -100, -100, -100\}, +10267 \{ -100, -100, -100, -100, -100\}\}, +10268 \textcolor{comment}{/* @.GA..GC */} +10269 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10270 \{ -569, -569, -569, -569, -569\}, +10271 \{ -769, -769, -769, -769, -769\}, +10272 \{ -759, -759, -759, -759, -759\}, +10273 \{ -549, -549, -549, -549, -549\}\}, +10274 \textcolor{comment}{/* @.GC..GC */} +10275 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10276 \{ -929, -929, -929, -929, -929\}, +10277 \{ -359, -359, -359, -359, -359\}, +10278 \{ -789, -789, -789, -789, -789\}, +10279 \{ -549, -549, -549, -549, -549\}\}, +10280 \textcolor{comment}{/* @.GG..GC */} +10281 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10282 \{ -609, -609, -609, -609, -609\}, +10283 \{ -359, -359, -359, -359, -359\}, +10284 \{ -669, -669, -669, -669, -669\}, +10285 \{ -549, -549, -549, -549, -549\}\}, +10286 \textcolor{comment}{/* @.GU..GC */} +10287 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10288 \{ -929, -929, -929, -929, -929\}, +10289 \{ -439, -439, -439, -439, -439\}, +10290 \{ -789, -789, -789, -789, -789\}, +10291 \{ -619, -619, -619, -619, -619\}\}\}, +10292 \textcolor{comment}{/* @.U@..GC */} +10293 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10294 \{ -100, -100, -100, -100, -100\}, +10295 \{ -100, -100, -100, -100, -100\}, +10296 \{ -100, -100, -100, -100, -100\}, +10297 \{ -100, -100, -100, -100, -100\}\}, +10298 \textcolor{comment}{/* @.UA..GC */} +10299 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10300 \{ -569, -569, -569, -569, -569\}, +10301 \{ -769, -769, -769, -769, -769\}, +10302 \{ -759, -759, -759, -759, -759\}, +10303 \{ -549, -549, -549, -549, -549\}\}, +10304 \textcolor{comment}{/* @.UC..GC */} +10305 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10306 \{ -929, -929, -929, -929, -929\}, +10307 \{ -359, -359, -359, -359, -359\}, +10308 \{ -789, -789, -789, -789, -789\}, +10309 \{ -549, -549, -549, -549, -549\}\}, +10310 \textcolor{comment}{/* @.UG..GC */} +10311 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10312 \{ -609, -609, -609, -609, -609\}, +10313 \{ -359, -359, -359, -359, -359\}, +10314 \{ -669, -669, -669, -669, -669\}, +10315 \{ -549, -549, -549, -549, -549\}\}, +10316 \textcolor{comment}{/* @.UU..GC */} +10317 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10318 \{ -929, -929, -929, -929, -929\}, +10319 \{ -439, -439, -439, -439, -439\}, +10320 \{ -789, -789, -789, -789, -789\}, +10321 \{ -619, -619, -619, -619, -619\}\}\}\}, +10322 \textcolor{comment}{/* @.@@..GU */} +10323 \{\{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10324 \{ -100, -100, -100, -100, -100\}, +10325 \{ -100, -100, -100, -100, -100\}, +10326 \{ -100, -100, -100, -100, -100\}, +10327 \{ -100, -100, -100, -100, -100\}\}, +10328 \textcolor{comment}{/* @.@A..GU */} +10329 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10330 \{ -479, -479, -479, -479, -479\}, +10331 \{ -309, -309, -309, -309, -309\}, +10332 \{ -389, -389, -389, -389, -389\}, +10333 \{ -379, -379, -379, -379, -379\}\}, +10334 \textcolor{comment}{/* @.@C..GU */} +10335 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10336 \{ -649, -649, -649, -649, -649\}, +10337 \{ -289, -289, -289, -289, -289\}, +10338 \{ -739, -739, -739, -739, -739\}, +10339 \{ -379, -379, -379, -379, -379\}\}, +10340 \textcolor{comment}{/* @.@G..GU */} +10341 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10342 \{ -649, -649, -649, -649, -649\}, +10343 \{ -289, -289, -289, -289, -289\}, +10344 \{ -739, -739, -739, -739, -739\}, +10345 \{ -379, -379, -379, -379, -379\}\}, +10346 \textcolor{comment}{/* @.@U..GU */} +10347 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10348 \{ -649, -649, -649, -649, -649\}, +10349 \{ -289, -289, -289, -289, -289\}, +10350 \{ -739, -739, -739, -739, -739\}, +10351 \{ -379, -379, -379, -379, -379\}\}\}, +10352 \textcolor{comment}{/* @.A@..GU */} +10353 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10354 \{ -100, -100, -100, -100, -100\}, +10355 \{ -100, -100, -100, -100, -100\}, +10356 \{ -100, -100, -100, -100, -100\}, +10357 \{ -100, -100, -100, -100, -100\}\}, +10358 \textcolor{comment}{/* @.AA..GU */} +10359 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10360 \{ -479, -479, -479, -479, -479\}, +10361 \{ -309, -309, -309, -309, -309\}, +10362 \{ -389, -389, -389, -389, -389\}, +10363 \{ -379, -379, -379, -379, -379\}\}, +10364 \textcolor{comment}{/* @.AC..GU */} +10365 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10366 \{ -649, -649, -649, -649, -649\}, +10367 \{ -289, -289, -289, -289, -289\}, +10368 \{ -739, -739, -739, -739, -739\}, +10369 \{ -379, -379, -379, -379, -379\}\}, +10370 \textcolor{comment}{/* @.AG..GU */} +10371 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10372 \{ -649, -649, -649, -649, -649\}, +10373 \{ -289, -289, -289, -289, -289\}, +10374 \{ -739, -739, -739, -739, -739\}, +10375 \{ -379, -379, -379, -379, -379\}\}, +10376 \textcolor{comment}{/* @.AU..GU */} +10377 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10378 \{ -649, -649, -649, -649, -649\}, +10379 \{ -289, -289, -289, -289, -289\}, +10380 \{ -739, -739, -739, -739, -739\}, +10381 \{ -379, -379, -379, -379, -379\}\}\}, +10382 \textcolor{comment}{/* @.C@..GU */} +10383 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10384 \{ -100, -100, -100, -100, -100\}, +10385 \{ -100, -100, -100, -100, -100\}, +10386 \{ -100, -100, -100, -100, -100\}, +10387 \{ -100, -100, -100, -100, -100\}\}, +10388 \textcolor{comment}{/* @.CA..GU */} +10389 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10390 \{ -479, -479, -479, -479, -479\}, +10391 \{ -309, -309, -309, -309, -309\}, +10392 \{ -389, -389, -389, -389, -389\}, +10393 \{ -379, -379, -379, -379, -379\}\}, +10394 \textcolor{comment}{/* @.CC..GU */} +10395 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10396 \{ -649, -649, -649, -649, -649\}, +10397 \{ -289, -289, -289, -289, -289\}, +10398 \{ -739, -739, -739, -739, -739\}, +10399 \{ -379, -379, -379, -379, -379\}\}, +10400 \textcolor{comment}{/* @.CG..GU */} +10401 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10402 \{ -649, -649, -649, -649, -649\}, +10403 \{ -289, -289, -289, -289, -289\}, +10404 \{ -739, -739, -739, -739, -739\}, +10405 \{ -379, -379, -379, -379, -379\}\}, +10406 \textcolor{comment}{/* @.CU..GU */} +10407 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10408 \{ -649, -649, -649, -649, -649\}, +10409 \{ -289, -289, -289, -289, -289\}, +10410 \{ -739, -739, -739, -739, -739\}, +10411 \{ -379, -379, -379, -379, -379\}\}\}, +10412 \textcolor{comment}{/* @.G@..GU */} +10413 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10414 \{ -100, -100, -100, -100, -100\}, +10415 \{ -100, -100, -100, -100, -100\}, +10416 \{ -100, -100, -100, -100, -100\}, +10417 \{ -100, -100, -100, -100, -100\}\}, +10418 \textcolor{comment}{/* @.GA..GU */} +10419 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10420 \{ -479, -479, -479, -479, -479\}, +10421 \{ -309, -309, -309, -309, -309\}, +10422 \{ -389, -389, -389, -389, -389\}, +10423 \{ -379, -379, -379, -379, -379\}\}, +10424 \textcolor{comment}{/* @.GC..GU */} +10425 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10426 \{ -649, -649, -649, -649, -649\}, +10427 \{ -289, -289, -289, -289, -289\}, +10428 \{ -739, -739, -739, -739, -739\}, +10429 \{ -379, -379, -379, -379, -379\}\}, +10430 \textcolor{comment}{/* @.GG..GU */} +10431 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10432 \{ -649, -649, -649, -649, -649\}, +10433 \{ -289, -289, -289, -289, -289\}, +10434 \{ -739, -739, -739, -739, -739\}, +10435 \{ -379, -379, -379, -379, -379\}\}, +10436 \textcolor{comment}{/* @.GU..GU */} +10437 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10438 \{ -649, -649, -649, -649, -649\}, +10439 \{ -289, -289, -289, -289, -289\}, +10440 \{ -739, -739, -739, -739, -739\}, +10441 \{ -379, -379, -379, -379, -379\}\}\}, +10442 \textcolor{comment}{/* @.U@..GU */} +10443 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10444 \{ -100, -100, -100, -100, -100\}, +10445 \{ -100, -100, -100, -100, -100\}, +10446 \{ -100, -100, -100, -100, -100\}, +10447 \{ -100, -100, -100, -100, -100\}\}, +10448 \textcolor{comment}{/* @.UA..GU */} +10449 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10450 \{ -479, -479, -479, -479, -479\}, +10451 \{ -309, -309, -309, -309, -309\}, +10452 \{ -389, -389, -389, -389, -389\}, +10453 \{ -379, -379, -379, -379, -379\}\}, +10454 \textcolor{comment}{/* @.UC..GU */} +10455 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10456 \{ -649, -649, -649, -649, -649\}, +10457 \{ -289, -289, -289, -289, -289\}, +10458 \{ -739, -739, -739, -739, -739\}, +10459 \{ -379, -379, -379, -379, -379\}\}, +10460 \textcolor{comment}{/* @.UG..GU */} +10461 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10462 \{ -649, -649, -649, -649, -649\}, +10463 \{ -289, -289, -289, -289, -289\}, +10464 \{ -739, -739, -739, -739, -739\}, +10465 \{ -379, -379, -379, -379, -379\}\}, +10466 \textcolor{comment}{/* @.UU..GU */} +10467 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10468 \{ -649, -649, -649, -649, -649\}, +10469 \{ -289, -289, -289, -289, -289\}, +10470 \{ -739, -739, -739, -739, -739\}, +10471 \{ -379, -379, -379, -379, -379\}\}\}\}, +10472 \textcolor{comment}{/* @.@@..UG */} +10473 \{\{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10474 \{ -100, -100, -100, -100, -100\}, +10475 \{ -100, -100, -100, -100, -100\}, +10476 \{ -100, -100, -100, -100, -100\}, +10477 \{ -100, -100, -100, -100, -100\}\}, +10478 \textcolor{comment}{/* @.@A..UG */} +10479 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10480 \{ -769, -769, -769, -769, -769\}, +10481 \{ -529, -529, -529, -529, -529\}, +10482 \{ -709, -709, -709, -709, -709\}, +10483 \{ -599, -599, -599, -599, -599\}\}, +10484 \textcolor{comment}{/* @.@C..UG */} +10485 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10486 \{ -839, -839, -839, -839, -839\}, +10487 \{ -529, -529, -529, -529, -529\}, +10488 \{ -859, -859, -859, -859, -859\}, +10489 \{ -489, -489, -489, -489, -489\}\}, +10490 \textcolor{comment}{/* @.@G..UG */} +10491 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10492 \{-1009,-1009,-1009,-1009,-1009\}, +10493 \{ -409, -409, -409, -409, -409\}, +10494 \{ -969, -969, -969, -969, -969\}, +10495 \{ -599, -599, -599, -599, -599\}\}, +10496 \textcolor{comment}{/* @.@U..UG */} +10497 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10498 \{ -859, -859, -859, -859, -859\}, +10499 \{ -529, -529, -529, -529, -529\}, +10500 \{ -859, -859, -859, -859, -859\}, +10501 \{ -409, -409, -409, -409, -409\}\}\}, +10502 \textcolor{comment}{/* @.A@..UG */} +10503 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10504 \{ -100, -100, -100, -100, -100\}, +10505 \{ -100, -100, -100, -100, -100\}, +10506 \{ -100, -100, -100, -100, -100\}, +10507 \{ -100, -100, -100, -100, -100\}\}, +10508 \textcolor{comment}{/* @.AA..UG */} +10509 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10510 \{ -769, -769, -769, -769, -769\}, +10511 \{ -529, -529, -529, -529, -529\}, +10512 \{ -709, -709, -709, -709, -709\}, +10513 \{ -599, -599, -599, -599, -599\}\}, +10514 \textcolor{comment}{/* @.AC..UG */} +10515 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10516 \{ -839, -839, -839, -839, -839\}, +10517 \{ -529, -529, -529, -529, -529\}, +10518 \{ -859, -859, -859, -859, -859\}, +10519 \{ -489, -489, -489, -489, -489\}\}, +10520 \textcolor{comment}{/* @.AG..UG */} +10521 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10522 \{-1009,-1009,-1009,-1009,-1009\}, +10523 \{ -409, -409, -409, -409, -409\}, +10524 \{ -969, -969, -969, -969, -969\}, +10525 \{ -599, -599, -599, -599, -599\}\}, +10526 \textcolor{comment}{/* @.AU..UG */} +10527 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10528 \{ -859, -859, -859, -859, -859\}, +10529 \{ -529, -529, -529, -529, -529\}, +10530 \{ -859, -859, -859, -859, -859\}, +10531 \{ -409, -409, -409, -409, -409\}\}\}, +10532 \textcolor{comment}{/* @.C@..UG */} +10533 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10534 \{ -100, -100, -100, -100, -100\}, +10535 \{ -100, -100, -100, -100, -100\}, +10536 \{ -100, -100, -100, -100, -100\}, +10537 \{ -100, -100, -100, -100, -100\}\}, +10538 \textcolor{comment}{/* @.CA..UG */} +10539 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10540 \{ -769, -769, -769, -769, -769\}, +10541 \{ -529, -529, -529, -529, -529\}, +10542 \{ -709, -709, -709, -709, -709\}, +10543 \{ -599, -599, -599, -599, -599\}\}, +10544 \textcolor{comment}{/* @.CC..UG */} +10545 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10546 \{ -839, -839, -839, -839, -839\}, +10547 \{ -529, -529, -529, -529, -529\}, +10548 \{ -859, -859, -859, -859, -859\}, +10549 \{ -489, -489, -489, -489, -489\}\}, +10550 \textcolor{comment}{/* @.CG..UG */} +10551 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10552 \{-1009,-1009,-1009,-1009,-1009\}, +10553 \{ -409, -409, -409, -409, -409\}, +10554 \{ -969, -969, -969, -969, -969\}, +10555 \{ -599, -599, -599, -599, -599\}\}, +10556 \textcolor{comment}{/* @.CU..UG */} +10557 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10558 \{ -859, -859, -859, -859, -859\}, +10559 \{ -529, -529, -529, -529, -529\}, +10560 \{ -859, -859, -859, -859, -859\}, +10561 \{ -409, -409, -409, -409, -409\}\}\}, +10562 \textcolor{comment}{/* @.G@..UG */} +10563 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10564 \{ -100, -100, -100, -100, -100\}, +10565 \{ -100, -100, -100, -100, -100\}, +10566 \{ -100, -100, -100, -100, -100\}, +10567 \{ -100, -100, -100, -100, -100\}\}, +10568 \textcolor{comment}{/* @.GA..UG */} +10569 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10570 \{ -769, -769, -769, -769, -769\}, +10571 \{ -529, -529, -529, -529, -529\}, +10572 \{ -709, -709, -709, -709, -709\}, +10573 \{ -599, -599, -599, -599, -599\}\}, +10574 \textcolor{comment}{/* @.GC..UG */} +10575 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10576 \{ -839, -839, -839, -839, -839\}, +10577 \{ -529, -529, -529, -529, -529\}, +10578 \{ -859, -859, -859, -859, -859\}, +10579 \{ -489, -489, -489, -489, -489\}\}, +10580 \textcolor{comment}{/* @.GG..UG */} +10581 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10582 \{-1009,-1009,-1009,-1009,-1009\}, +10583 \{ -409, -409, -409, -409, -409\}, +10584 \{ -969, -969, -969, -969, -969\}, +10585 \{ -599, -599, -599, -599, -599\}\}, +10586 \textcolor{comment}{/* @.GU..UG */} +10587 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10588 \{ -859, -859, -859, -859, -859\}, +10589 \{ -529, -529, -529, -529, -529\}, +10590 \{ -859, -859, -859, -859, -859\}, +10591 \{ -409, -409, -409, -409, -409\}\}\}, +10592 \textcolor{comment}{/* @.U@..UG */} +10593 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10594 \{ -100, -100, -100, -100, -100\}, +10595 \{ -100, -100, -100, -100, -100\}, +10596 \{ -100, -100, -100, -100, -100\}, +10597 \{ -100, -100, -100, -100, -100\}\}, +10598 \textcolor{comment}{/* @.UA..UG */} +10599 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10600 \{ -769, -769, -769, -769, -769\}, +10601 \{ -529, -529, -529, -529, -529\}, +10602 \{ -709, -709, -709, -709, -709\}, +10603 \{ -599, -599, -599, -599, -599\}\}, +10604 \textcolor{comment}{/* @.UC..UG */} +10605 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10606 \{ -839, -839, -839, -839, -839\}, +10607 \{ -529, -529, -529, -529, -529\}, +10608 \{ -859, -859, -859, -859, -859\}, +10609 \{ -489, -489, -489, -489, -489\}\}, +10610 \textcolor{comment}{/* @.UG..UG */} +10611 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10612 \{-1009,-1009,-1009,-1009,-1009\}, +10613 \{ -409, -409, -409, -409, -409\}, +10614 \{ -969, -969, -969, -969, -969\}, +10615 \{ -599, -599, -599, -599, -599\}\}, +10616 \textcolor{comment}{/* @.UU..UG */} +10617 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10618 \{ -859, -859, -859, -859, -859\}, +10619 \{ -529, -529, -529, -529, -529\}, +10620 \{ -859, -859, -859, -859, -859\}, +10621 \{ -409, -409, -409, -409, -409\}\}\}\}, +10622 \textcolor{comment}{/* @.@@..AU */} +10623 \{\{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10624 \{ -100, -100, -100, -100, -100\}, +10625 \{ -100, -100, -100, -100, -100\}, +10626 \{ -100, -100, -100, -100, -100\}, +10627 \{ -100, -100, -100, -100, -100\}\}, +10628 \textcolor{comment}{/* @.@A..AU */} +10629 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10630 \{ -479, -479, -479, -479, -479\}, +10631 \{ -309, -309, -309, -309, -309\}, +10632 \{ -389, -389, -389, -389, -389\}, +10633 \{ -379, -379, -379, -379, -379\}\}, +10634 \textcolor{comment}{/* @.@C..AU */} +10635 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10636 \{ -649, -649, -649, -649, -649\}, +10637 \{ -289, -289, -289, -289, -289\}, +10638 \{ -739, -739, -739, -739, -739\}, +10639 \{ -379, -379, -379, -379, -379\}\}, +10640 \textcolor{comment}{/* @.@G..AU */} +10641 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10642 \{ -649, -649, -649, -649, -649\}, +10643 \{ -289, -289, -289, -289, -289\}, +10644 \{ -739, -739, -739, -739, -739\}, +10645 \{ -379, -379, -379, -379, -379\}\}, +10646 \textcolor{comment}{/* @.@U..AU */} +10647 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10648 \{ -649, -649, -649, -649, -649\}, +10649 \{ -289, -289, -289, -289, -289\}, +10650 \{ -739, -739, -739, -739, -739\}, +10651 \{ -379, -379, -379, -379, -379\}\}\}, +10652 \textcolor{comment}{/* @.A@..AU */} +10653 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10654 \{ -100, -100, -100, -100, -100\}, +10655 \{ -100, -100, -100, -100, -100\}, +10656 \{ -100, -100, -100, -100, -100\}, +10657 \{ -100, -100, -100, -100, -100\}\}, +10658 \textcolor{comment}{/* @.AA..AU */} +10659 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10660 \{ -479, -479, -479, -479, -479\}, +10661 \{ -309, -309, -309, -309, -309\}, +10662 \{ -389, -389, -389, -389, -389\}, +10663 \{ -379, -379, -379, -379, -379\}\}, +10664 \textcolor{comment}{/* @.AC..AU */} +10665 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10666 \{ -649, -649, -649, -649, -649\}, +10667 \{ -289, -289, -289, -289, -289\}, +10668 \{ -739, -739, -739, -739, -739\}, +10669 \{ -379, -379, -379, -379, -379\}\}, +10670 \textcolor{comment}{/* @.AG..AU */} +10671 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10672 \{ -649, -649, -649, -649, -649\}, +10673 \{ -289, -289, -289, -289, -289\}, +10674 \{ -739, -739, -739, -739, -739\}, +10675 \{ -379, -379, -379, -379, -379\}\}, +10676 \textcolor{comment}{/* @.AU..AU */} +10677 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10678 \{ -649, -649, -649, -649, -649\}, +10679 \{ -289, -289, -289, -289, -289\}, +10680 \{ -739, -739, -739, -739, -739\}, +10681 \{ -379, -379, -379, -379, -379\}\}\}, +10682 \textcolor{comment}{/* @.C@..AU */} +10683 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10684 \{ -100, -100, -100, -100, -100\}, +10685 \{ -100, -100, -100, -100, -100\}, +10686 \{ -100, -100, -100, -100, -100\}, +10687 \{ -100, -100, -100, -100, -100\}\}, +10688 \textcolor{comment}{/* @.CA..AU */} +10689 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10690 \{ -479, -479, -479, -479, -479\}, +10691 \{ -309, -309, -309, -309, -309\}, +10692 \{ -389, -389, -389, -389, -389\}, +10693 \{ -379, -379, -379, -379, -379\}\}, +10694 \textcolor{comment}{/* @.CC..AU */} +10695 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10696 \{ -649, -649, -649, -649, -649\}, +10697 \{ -289, -289, -289, -289, -289\}, +10698 \{ -739, -739, -739, -739, -739\}, +10699 \{ -379, -379, -379, -379, -379\}\}, +10700 \textcolor{comment}{/* @.CG..AU */} +10701 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10702 \{ -649, -649, -649, -649, -649\}, +10703 \{ -289, -289, -289, -289, -289\}, +10704 \{ -739, -739, -739, -739, -739\}, +10705 \{ -379, -379, -379, -379, -379\}\}, +10706 \textcolor{comment}{/* @.CU..AU */} +10707 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10708 \{ -649, -649, -649, -649, -649\}, +10709 \{ -289, -289, -289, -289, -289\}, +10710 \{ -739, -739, -739, -739, -739\}, +10711 \{ -379, -379, -379, -379, -379\}\}\}, +10712 \textcolor{comment}{/* @.G@..AU */} +10713 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10714 \{ -100, -100, -100, -100, -100\}, +10715 \{ -100, -100, -100, -100, -100\}, +10716 \{ -100, -100, -100, -100, -100\}, +10717 \{ -100, -100, -100, -100, -100\}\}, +10718 \textcolor{comment}{/* @.GA..AU */} +10719 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10720 \{ -479, -479, -479, -479, -479\}, +10721 \{ -309, -309, -309, -309, -309\}, +10722 \{ -389, -389, -389, -389, -389\}, +10723 \{ -379, -379, -379, -379, -379\}\}, +10724 \textcolor{comment}{/* @.GC..AU */} +10725 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10726 \{ -649, -649, -649, -649, -649\}, +10727 \{ -289, -289, -289, -289, -289\}, +10728 \{ -739, -739, -739, -739, -739\}, +10729 \{ -379, -379, -379, -379, -379\}\}, +10730 \textcolor{comment}{/* @.GG..AU */} +10731 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10732 \{ -649, -649, -649, -649, -649\}, +10733 \{ -289, -289, -289, -289, -289\}, +10734 \{ -739, -739, -739, -739, -739\}, +10735 \{ -379, -379, -379, -379, -379\}\}, +10736 \textcolor{comment}{/* @.GU..AU */} +10737 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10738 \{ -649, -649, -649, -649, -649\}, +10739 \{ -289, -289, -289, -289, -289\}, +10740 \{ -739, -739, -739, -739, -739\}, +10741 \{ -379, -379, -379, -379, -379\}\}\}, +10742 \textcolor{comment}{/* @.U@..AU */} +10743 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10744 \{ -100, -100, -100, -100, -100\}, +10745 \{ -100, -100, -100, -100, -100\}, +10746 \{ -100, -100, -100, -100, -100\}, +10747 \{ -100, -100, -100, -100, -100\}\}, +10748 \textcolor{comment}{/* @.UA..AU */} +10749 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10750 \{ -479, -479, -479, -479, -479\}, +10751 \{ -309, -309, -309, -309, -309\}, +10752 \{ -389, -389, -389, -389, -389\}, +10753 \{ -379, -379, -379, -379, 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-100, -100, -100, -100\}\}, +10778 \textcolor{comment}{/* @.@A..UA */} +10779 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10780 \{ -449, -449, -449, -449, -449\}, +10781 \{ -479, -479, -479, -479, -479\}, +10782 \{ -429, -429, -429, -429, -429\}, +10783 \{ -329, -329, -329, -329, -329\}\}, +10784 \textcolor{comment}{/* @.@C..UA */} +10785 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10786 \{ -679, -679, -679, -679, -679\}, +10787 \{ -559, -559, -559, -559, -559\}, +10788 \{ -729, -729, -729, -729, -729\}, +10789 \{ -189, -189, -189, -189, -189\}\}, +10790 \textcolor{comment}{/* @.@G..UA */} +10791 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10792 \{ -939, -939, -939, -939, -939\}, +10793 \{ -249, -249, -249, -249, -249\}, +10794 \{ -939, -939, -939, -939, -939\}, +10795 \{ -329, -329, -329, -329, -329\}\}, +10796 \textcolor{comment}{/* @.@U..UA */} +10797 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10798 \{ -639, -639, -639, -639, -639\}, +10799 \{ -229, -229, -229, -229, -229\}, +10800 \{ -729, -729, -729, -729, -729\}, +10801 \{ -190, -190, -190, -190, -190\}\}\}, +10802 \textcolor{comment}{/* @.A@..UA */} +10803 \{\{\{ DEF, DEF, DEF, DEF, DEF\}, +10804 \{ -100, -100, -100, -100, -100\}, +10805 \{ -100, -100, -100, -100, -100\}, +10806 \{ -100, -100, -100, -100, -100\}, +10807 \{ -100, -100, -100, -100, -100\}\}, +10808 \textcolor{comment}{/* @.AA..UA */} +10809 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10810 \{ -449, -449, -449, -449, -449\}, +10811 \{ -479, -479, -479, -479, -479\}, +10812 \{ -429, -429, -429, -429, -429\}, +10813 \{ -329, -329, -329, -329, -329\}\}, +10814 \textcolor{comment}{/* @.AC..UA */} +10815 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10816 \{ -679, -679, -679, -679, -679\}, +10817 \{ -559, -559, -559, -559, -559\}, +10818 \{ -729, -729, -729, -729, -729\}, +10819 \{ -189, -189, -189, -189, -189\}\}, +10820 \textcolor{comment}{/* @.AG..UA */} +10821 \{\{ DEF, DEF, DEF, DEF, DEF\}, +10822 \{ -939, -939, -939, -939, -939\}, +10823 \{ -249, -249, -249, -249, -249\}, +10824 \{ -939, -939, -939, -939, 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+10989 \{\{ -100, -100, -100, -100, -100\}, +10990 \{ -100, -100, -100, -100, -100\}, +10991 \{ -100, -100, -100, -100, -100\}, +10992 \{ -100, -100, -100, -100, -100\}, +10993 \{ -100, -100, -100, -100, -100\}\}, +10994 \textcolor{comment}{/* @.CC.. @ */} +10995 \{\{ -100, -100, -100, -100, -100\}, +10996 \{ -100, -100, -100, -100, -100\}, +10997 \{ -100, -100, -100, -100, -100\}, +10998 \{ -100, -100, -100, -100, -100\}, +10999 \{ -100, -100, -100, -100, -100\}\}, +11000 \textcolor{comment}{/* @.CG.. @ */} +11001 \{\{ -100, -100, -100, -100, -100\}, +11002 \{ -100, -100, -100, -100, -100\}, +11003 \{ -100, -100, -100, -100, -100\}, +11004 \{ -100, -100, -100, -100, -100\}, +11005 \{ -100, -100, -100, -100, -100\}\}, +11006 \textcolor{comment}{/* @.CU.. @ */} +11007 \{\{ -100, -100, -100, -100, -100\}, +11008 \{ -100, -100, -100, -100, -100\}, +11009 \{ -100, -100, -100, -100, -100\}, +11010 \{ -100, -100, -100, -100, -100\}, +11011 \{ -100, -100, -100, -100, -100\}\}\}, +11012 \textcolor{comment}{/* @.G@.. @ */} +11013 \{\{\{ -100, -100, -100, -100, -100\}, +11014 \{ -100, -100, -100, -100, -100\}, +11015 \{ -100, -100, -100, -100, -100\}, +11016 \{ -100, -100, -100, -100, -100\}, +11017 \{ -100, -100, -100, -100, -100\}\}, +11018 \textcolor{comment}{/* @.GA.. @ */} +11019 \{\{ -100, -100, -100, -100, -100\}, +11020 \{ -100, -100, -100, -100, -100\}, +11021 \{ -100, -100, -100, -100, -100\}, +11022 \{ -100, -100, -100, -100, -100\}, +11023 \{ -100, -100, -100, -100, -100\}\}, +11024 \textcolor{comment}{/* @.GC.. @ */} +11025 \{\{ -100, -100, -100, -100, -100\}, +11026 \{ -100, -100, -100, -100, -100\}, +11027 \{ -100, -100, -100, -100, -100\}, +11028 \{ -100, -100, -100, -100, -100\}, +11029 \{ -100, -100, -100, -100, -100\}\}, +11030 \textcolor{comment}{/* @.GG.. @ */} +11031 \{\{ -100, -100, -100, -100, -100\}, +11032 \{ -100, -100, -100, -100, -100\}, +11033 \{ -100, -100, -100, -100, -100\}, +11034 \{ -100, -100, -100, -100, -100\}, +11035 \{ -100, -100, 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-100, -100\}, +11059 \{ -100, -100, -100, -100, -100\}\}, +11060 \textcolor{comment}{/* @.UG.. @ */} +11061 \{\{ -100, -100, -100, -100, -100\}, +11062 \{ -100, -100, -100, -100, -100\}, +11063 \{ -100, -100, -100, -100, -100\}, +11064 \{ -100, -100, -100, -100, -100\}, +11065 \{ -100, -100, -100, -100, -100\}\}, +11066 \textcolor{comment}{/* @.UU.. @ */} +11067 \{\{ -100, -100, -100, -100, -100\}, +11068 \{ -100, -100, -100, -100, -100\}, +11069 \{ -100, -100, -100, -100, -100\}, +11070 \{ -100, -100, -100, -100, -100\}, +11071 \{ -100, -100, -100, -100, -100\}\}\}\}\}\}; +11072 +11073 +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/2Dfold_8h.tex b/binaries/src/ViennaRNA/doc/latex/2Dfold_8h.tex new file mode 100644 index 0000000..0d3e519 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/2Dfold_8h.tex @@ -0,0 +1,22 @@ +\hypertarget{2Dfold_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dfold.h File Reference} +\label{2Dfold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dfold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dfold.\-h}} +} +Include dependency graph for 2\-Dfold.h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{2Dfold_8h__incl} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +\hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} $\ast$ \hyperlink{group__kl__neighborhood__mfe_gac9284f132cf0eaa0a2f43590eda05488}{get\-\_\-\-Two\-Dfold\-\_\-variables} (const char $\ast$seq, const char $\ast$structure1, const char $\ast$structure2, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ}) +\begin{DoxyCompactList}\small\item\em Get a structure of type \hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} prefilled with current global settings. \end{DoxyCompactList}\item +void \hyperlink{group__kl__neighborhood__mfe_ga05bf4f31d216b1b160fd2d3d68e9b487}{destroy\-\_\-\-Two\-Dfold\-\_\-variables} (\hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} $\ast$our\-\_\-variables) +\begin{DoxyCompactList}\small\item\em Destroy a \hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} datastructure without memory loss. \end{DoxyCompactList}\item +\hyperlink{structTwoDfold__solution}{Two\-Dfold\-\_\-solution} $\ast$ \hyperlink{group__kl__neighborhood__mfe_ga47da790166020558d27323aef489703e}{Two\-Dfold\-List} (\hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} $\ast$vars, int distance1, int distance2) +\begin{DoxyCompactList}\small\item\em Compute M\-F\-E's and representative for distance partitioning. \end{DoxyCompactList}\item +char $\ast$ \hyperlink{group__kl__neighborhood__mfe_gaf4dc05bf8fc1ea53acd7aeb798ba80c2}{Two\-Dfold\-\_\-backtrack\-\_\-f5} (unsigned int j, int k, int l, \hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} $\ast$vars) +\begin{DoxyCompactList}\small\item\em Backtrack a minimum free energy structure from a 5' section of specified length. \end{DoxyCompactList}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/2Dfold_8h__incl.md5 b/binaries/src/ViennaRNA/doc/latex/2Dfold_8h__incl.md5 new file mode 100644 index 0000000..07424da --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/2Dfold_8h__incl.md5 @@ -0,0 +1 @@ +7b0fc68d1e87c6af5d6c4d5cc8e2c9e8 \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/2Dfold_8h__incl.pdf b/binaries/src/ViennaRNA/doc/latex/2Dfold_8h__incl.pdf new file mode 100644 index 0000000000000000000000000000000000000000..b0883e123c8073d6aad20b677e727f3af2eed5fa GIT binary patch literal 7976 zcmb7pbzGEN7p{aNt%Q`oAR!@4(V>J49nv5TLo>h(jf!+ggVF*LN_R^)A|>4&QUU@Z z3U>zeeCIpoyT9MP^D^_Y*Is+Cy=wpQJglk@VccLIJ_6RtouV@WC;$X-Fts5N6$Jnl z;Rs7-D*!KAq(%S$0Dv%SJ7+i&{kAi4hChUxIhexecF6kwvR 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+\label{2Dfold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dfold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dfold.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{comment}{/*} +00002 \textcolor{comment}{ minimum free energy} +00003 \textcolor{comment}{ RNA secondary structure with} +00004 \textcolor{comment}{ basepair distance d to reference structure prediction} +00005 \textcolor{comment}{} +00006 \textcolor{comment}{*/} +00007 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_TWO\_D\_FOLD\_H\_\_} +00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_TWO\_D\_FOLD\_H\_\_} +00009 \textcolor{preprocessor}{} +00032 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"} +00033 +00034 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_} +00035 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func \_\_attribute\_\_ ((deprecated))} +00036 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else} +00037 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func} +00038 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif} +00039 \textcolor{preprocessor}{} +00057 \hyperlink{structTwoDfold__vars}{TwoDfold\_vars} *\hyperlink{group__kl__neighborhood__mfe_gac9284f132cf0eaa0a2f43590eda05488}{get\_TwoDfold\_variables}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *seq, +00058 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure1, +00059 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure2, +00060 \textcolor{keywordtype}{int} circ); +00061 +00071 \textcolor{keywordtype}{void} \hyperlink{group__kl__neighborhood__mfe_ga05bf4f31d216b1b160fd2d3d68e9b487}{destroy\_TwoDfold\_variables}(\hyperlink{structTwoDfold__vars}{TwoDfold\_vars} * + our\_variables); +00072 +00076 DEPRECATED(\hyperlink{structTwoDfold__solution}{TwoDfold\_solution} **TwoDfold(\hyperlink{structTwoDfold__vars}{TwoDfold\_vars} *our\_variables, +00077 \textcolor{keywordtype}{int} distance1, +00078 \textcolor{keywordtype}{int} distance2)); +00079 +00104 \hyperlink{structTwoDfold__solution}{TwoDfold\_solution} *\hyperlink{group__kl__neighborhood__mfe_ga47da790166020558d27323aef489703e}{TwoDfoldList}(\hyperlink{structTwoDfold__vars}{TwoDfold\_vars} *vars, +00105 \textcolor{keywordtype}{int} distance1, +00106 \textcolor{keywordtype}{int} distance2); +00107 +00126 \textcolor{keywordtype}{char} *\hyperlink{group__kl__neighborhood__mfe_gaf4dc05bf8fc1ea53acd7aeb798ba80c2}{TwoDfold\_backtrack\_f5}(\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} j, +00127 \textcolor{keywordtype}{int} k, +00128 \textcolor{keywordtype}{int} l, +00129 \hyperlink{structTwoDfold__vars}{TwoDfold\_vars} *vars); +00130 +00134 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/2Dpfold_8h.tex b/binaries/src/ViennaRNA/doc/latex/2Dpfold_8h.tex new file mode 100644 index 0000000..af9d609 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/2Dpfold_8h.tex @@ -0,0 +1,26 @@ +\hypertarget{2Dpfold_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dpfold.h File Reference} +\label{2Dpfold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dpfold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dpfold.\-h}} +} +Include dependency graph for 2\-Dpfold.h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{2Dpfold_8h__incl} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$ \hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\-\_\-\-Two\-Dpfold\-\_\-variables} (const char $\ast$seq, const char $\ast$structure1, char $\ast$structure2, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ}) +\begin{DoxyCompactList}\small\item\em Get a datastructure containing all necessary attributes and global folding switches. \end{DoxyCompactList}\item +\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$ \hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E} (\hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} $\ast$mfe\-\_\-vars) +\begin{DoxyCompactList}\small\item\em Get the datastructure containing all necessary attributes and global folding switches from a pre-\/filled mfe-\/datastructure. \end{DoxyCompactList}\item +void \hyperlink{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{destroy\-\_\-\-Two\-Dpfold\-\_\-variables} (\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$vars) +\begin{DoxyCompactList}\small\item\em Free all memory occupied by a \hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} datastructure. \end{DoxyCompactList}\item +\hyperlink{structTwoDpfold__solution}{Two\-Dpfold\-\_\-solution} $\ast$ \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List} (\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$vars, int max\-Distance1, int max\-Distance2) +\begin{DoxyCompactList}\small\item\em Compute the partition function for all distance classes. \end{DoxyCompactList}\item +char $\ast$ \hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{Two\-Dpfold\-\_\-pbacktrack} (\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$vars, int d1, int d2) +\begin{DoxyCompactList}\small\item\em Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability. \end{DoxyCompactList}\item +char $\ast$ \hyperlink{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}{Two\-Dpfold\-\_\-pbacktrack5} (\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$vars, int d1, int d2, unsigned int length) +\begin{DoxyCompactList}\small\item\em Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability. \end{DoxyCompactList}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/2Dpfold_8h__incl.md5 b/binaries/src/ViennaRNA/doc/latex/2Dpfold_8h__incl.md5 new file mode 100644 index 0000000..1623b14 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/2Dpfold_8h__incl.md5 @@ -0,0 +1 @@ +142b9f81ff232b7ca3841a54b1273644 \ No newline at end of file diff --git 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/dev/null +++ b/binaries/src/ViennaRNA/doc/latex/2Dpfold_8h_source.tex @@ -0,0 +1,61 @@ +\hypertarget{2Dpfold_8h}{\section{2\-Dpfold.h} +\label{2Dpfold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dpfold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dpfold.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{comment}{/*} +00002 \textcolor{comment}{ minimum free energy} +00003 \textcolor{comment}{ RNA secondary structure with} +00004 \textcolor{comment}{ basepair distance d to reference structure prediction} +00005 \textcolor{comment}{} +00006 \textcolor{comment}{*/} +00007 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_TWO\_D\_PF\_FOLD\_H\_\_} +00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_TWO\_D\_PF\_FOLD\_H\_\_} +00009 \textcolor{preprocessor}{} +00010 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"} +00011 +00012 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_} +00013 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func \_\_attribute\_\_ ((deprecated))} +00014 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else} +00015 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func} +00016 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif} +00017 \textcolor{preprocessor}{} +00042 \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *\hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\_TwoDpfold\_variables}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *seq, +00043 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure1, +00044 \textcolor{keywordtype}{char} *structure2, +00045 \textcolor{keywordtype}{int} circ); +00046 +00059 \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *\hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get\_TwoDpfold\_variables\_from\_MFE}( + \hyperlink{structTwoDfold__vars}{TwoDfold\_vars} *mfe\_vars); +00060 +00071 \textcolor{keywordtype}{void} \hyperlink{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{destroy\_TwoDpfold\_variables}( + \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *vars); +00072 +00094 \hyperlink{structTwoDpfold__solution}{TwoDpfold\_solution} *\hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{TwoDpfoldList}( + \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *vars, +00095 \textcolor{keywordtype}{int} maxDistance1, +00096 \textcolor{keywordtype}{int} maxDistance2); +00097 \textcolor{comment}{/* End of group kl\_neighborhood\_pf */} +00099 +00123 \textcolor{keywordtype}{char} *\hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{TwoDpfold\_pbacktrack}(\hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *vars, +00124 \textcolor{keywordtype}{int} d1, +00125 \textcolor{keywordtype}{int} d2); +00126 +00146 \textcolor{keywordtype}{char} *\hyperlink{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}{TwoDpfold\_pbacktrack5}( \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *vars, +00147 \textcolor{keywordtype}{int} d1, +00148 \textcolor{keywordtype}{int} d2, +00149 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length); +00150 \textcolor{comment}{/* End of group kl\_neighborhood\_stochbt */} +00152 +00158 DEPRECATED(FLT\_OR\_DBL **TwoDpfold(\hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *our\_variables, +00159 \textcolor{keywordtype}{int} maxDistance1, +00160 \textcolor{keywordtype}{int} maxDistance2)); +00161 +00167 DEPRECATED(FLT\_OR\_DBL **TwoDpfold\_circ( +00168 \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *our\_variables, +00169 \textcolor{keywordtype}{int} maxDistance1, +00170 \textcolor{keywordtype}{int} maxDistance2)); +00171 +00172 +00173 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/LPfold_8h.tex b/binaries/src/ViennaRNA/doc/latex/LPfold_8h.tex new file mode 100644 index 0000000..740a045 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/LPfold_8h.tex @@ -0,0 +1,46 @@ +\hypertarget{LPfold_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-L\-Pfold.h File Reference} +\label{LPfold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-L\-Pfold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-L\-Pfold.\-h}} +} + + +Function declarations of partition function variants of the Lfold algorithm. + + +Include dependency graph for L\-Pfold.\-h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{LPfold_8h__incl} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +void \hyperlink{group__local__pf__fold_ga5a019014d37fe6105131dfc2fc447880}{update\-\_\-pf\-\_\-params\-L\-P} (int length) +\item +\hyperlink{structplist}{plist} $\ast$ \hyperlink{group__local__pf__fold_gaa1ecd401617ebc748a0220026543c777}{pfl\-\_\-fold} (char $\ast$sequence, int win\-Size, int pair\-Size, float cutoffb, double $\ast$$\ast$p\-U, struct \hyperlink{structplist}{plist} $\ast$$\ast$dpp2, F\-I\-L\-E $\ast$p\-Ufp, F\-I\-L\-E $\ast$spup) +\begin{DoxyCompactList}\small\item\em Compute partition functions for locally stable secondary structures. \end{DoxyCompactList}\item +\hypertarget{group__local__pf__fold_gab354507e8028f3e1c52ef96bb1eb9df8}{\hyperlink{structplist}{plist} $\ast$ \hyperlink{group__local__pf__fold_gab354507e8028f3e1c52ef96bb1eb9df8}{pfl\-\_\-fold\-\_\-par} (char $\ast$sequence, int win\-Size, int pair\-Size, float cutoffb, double $\ast$$\ast$p\-U, struct \hyperlink{structplist}{plist} $\ast$$\ast$dpp2, F\-I\-L\-E $\ast$p\-Ufp, F\-I\-L\-E $\ast$spup, \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters)}\label{group__local__pf__fold_gab354507e8028f3e1c52ef96bb1eb9df8} + +\begin{DoxyCompactList}\small\item\em Compute partition functions for locally stable secondary structures. \end{DoxyCompactList}\item +void \hyperlink{group__local__pf__fold_ga0bcb751860bbf34e3dfee8c2fbdb3ef3}{putoutp\-U\-\_\-prob} (double $\ast$$\ast$p\-U, int length, int ulength, F\-I\-L\-E $\ast$fp, int energies) +\begin{DoxyCompactList}\small\item\em Writes the unpaired probabilities (p\-U) or opening energies into a file. \end{DoxyCompactList}\item +void \hyperlink{group__local__pf__fold_ga9acb00ee10e96b1ca4ea394cd8bcec75}{putoutp\-U\-\_\-prob\-\_\-bin} (double $\ast$$\ast$p\-U, int length, int ulength, F\-I\-L\-E $\ast$fp, int energies) +\begin{DoxyCompactList}\small\item\em Writes the unpaired probabilities (p\-U) or opening energies into a binary file. \end{DoxyCompactList}\item +void \hyperlink{LPfold_8h_ae85bf55053e9fb295208be322e0fa07a}{init\-\_\-pf\-\_\-fold\-L\-P} (int length) +\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Function declarations of partition function variants of the Lfold algorithm. + +\subsection{Function Documentation} +\hypertarget{LPfold_8h_ae85bf55053e9fb295208be322e0fa07a}{\index{L\-Pfold.\-h@{L\-Pfold.\-h}!init\-\_\-pf\-\_\-fold\-L\-P@{init\-\_\-pf\-\_\-fold\-L\-P}} +\index{init\-\_\-pf\-\_\-fold\-L\-P@{init\-\_\-pf\-\_\-fold\-L\-P}!LPfold.h@{L\-Pfold.\-h}} +\subsubsection[{init\-\_\-pf\-\_\-fold\-L\-P}]{\setlength{\rightskip}{0pt plus 5cm}void init\-\_\-pf\-\_\-fold\-L\-P ( +\begin{DoxyParamCaption} +\item[{int}]{length} +\end{DoxyParamCaption} +)}}\label{LPfold_8h_ae85bf55053e9fb295208be322e0fa07a} +Dunno if this function was ever used by external programs linking to R\-N\-Alib, but it was declared P\-U\-B\-L\-I\-C before. 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zN_5sg?4+gsH3k?&;>zFcU^0k**}-IFh&8gm+rgnQqC5VHA&4>jJBEOenEVe+ipZTm zF#;Y*On&_FZfAt?MU#9*+Eff(U5N}J`TSP~YT@jOktVU=m{%SIB%W~WT?7;=LnkDp Irl(H#Kfs$gEC2ui literal 0 HcmV?d00001 diff --git a/binaries/src/ViennaRNA/doc/latex/MEA_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/MEA_8h_source.tex new file mode 100644 index 0000000..7669db1 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/MEA_8h_source.tex @@ -0,0 +1,22 @@ +\hypertarget{MEA_8h}{\section{M\-E\-A.\-h} +\label{MEA_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-M\-E\-A.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-M\-E\-A.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_MEA\_H\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_MEA\_H\_\_} +00003 \textcolor{preprocessor}{} +00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"} +00005 +00022 \textcolor{keywordtype}{float} \hyperlink{MEA_8h_a396ec6144c6a74fcbab4cea6b42d76c3}{MEA}(\hyperlink{structplist}{plist} *p, +00023 \textcolor{keywordtype}{char} *structure, +00024 \textcolor{keywordtype}{double} gamma); +00025 +00026 \textcolor{keywordtype}{float} MEA\_seq(\hyperlink{structplist}{plist} *p, +00027 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence, +00028 \textcolor{keywordtype}{char} *structure, +00029 \textcolor{keywordtype}{double} gamma, +00030 \hyperlink{structpf__paramT}{pf\_paramT} *pf); +00031 +00032 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/Makefile b/binaries/src/ViennaRNA/doc/latex/Makefile new file mode 100644 index 0000000..9a6d99d --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/Makefile @@ -0,0 +1,21 @@ +all: refman.pdf + +pdf: refman.pdf + +refman.pdf: clean refman.tex + pdflatex refman + /usr/bin/makeindex refman.idx + bibtex refman + pdflatex refman + pdflatex refman + latex_count=5 ; \ + while egrep -s 'Rerun (LaTeX|to get cross-references right)' refman.log && [ $$latex_count -gt 0 ] ;\ + do \ + echo "Rerunning latex...." ;\ + pdflatex refman ;\ + latex_count=`expr $$latex_count - 1` ;\ + done + + +clean: + rm -f *.ps *.dvi *.aux *.toc *.idx *.ind *.ilg *.log *.out *.brf *.blg *.bbl refman.pdf diff --git a/binaries/src/ViennaRNA/doc/latex/PKplex_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/PKplex_8h_source.tex new file mode 100644 index 0000000..bdc4615 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/PKplex_8h_source.tex @@ -0,0 +1,28 @@ +\hypertarget{PKplex_8h}{\section{P\-Kplex.\-h} +\label{PKplex_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-P\-Kplex.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-P\-Kplex.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef PKPLEX\_H} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define PKPLEX\_H} +00003 \textcolor{preprocessor}{} +00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"} +00005 +00006 \textcolor{keyword}{extern} \hyperlink{structdupVar}{dupVar} *PlexHits; +00007 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} PlexHitsArrayLength; +00008 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} NumberOfHits; +00009 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} verbose; +00010 +00011 +00015 \hyperlink{structdupVar}{dupVar} **PKLduplexfold\_XS( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1, +00016 \textcolor{keywordtype}{int} **access\_s1, +00017 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshold, +00018 \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length, +00019 \textcolor{keyword}{const} \textcolor{keywordtype}{int} delta); +00020 +00021 \textcolor{keywordtype}{int} arraySize(\hyperlink{structduplexT}{duplexT} **array); +00022 +00023 \textcolor{keywordtype}{void} freeDuplexT(\hyperlink{structduplexT}{duplexT} **array); +00024 +00025 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/PS__dot_8h.tex b/binaries/src/ViennaRNA/doc/latex/PS__dot_8h.tex new file mode 100644 index 0000000..346d814 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/PS__dot_8h.tex @@ -0,0 +1,276 @@ +\hypertarget{PS__dot_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-P\-S\-\_\-dot.h File Reference} +\label{PS__dot_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-P\-S\-\_\-dot.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-P\-S\-\_\-dot.\-h}} +} + + +Various functions for plotting R\-N\-A secondary structures, dot-\/plots and other visualizations. + + +Include dependency graph for P\-S\-\_\-dot.\-h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{PS__dot_8h__incl} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +int \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{P\-S\-\_\-rna\-\_\-plot} (char $\ast$string, char $\ast$structure, char $\ast$file) +\begin{DoxyCompactList}\small\item\em Produce a secondary structure graph in Post\-Script and write it to 'filename'. \end{DoxyCompactList}\item +int \hyperlink{PS__dot_8h_a47856b2504b566588785597b6ebb8271}{P\-S\-\_\-rna\-\_\-plot\-\_\-a} (char $\ast$string, char $\ast$structure, char $\ast$file, char $\ast$pre, char $\ast$post) +\begin{DoxyCompactList}\small\item\em Produce a secondary structure graph in Post\-Script including additional annotation macros and write it to 'filename'. \end{DoxyCompactList}\item +int \hyperlink{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329}{gml\-R\-N\-A} (char $\ast$string, char $\ast$structure, char $\ast$ssfile, char option) +\begin{DoxyCompactList}\small\item\em Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file. \end{DoxyCompactList}\item +int \hyperlink{PS__dot_8h_add368528755f9a830727b680243541df}{ssv\-\_\-rna\-\_\-plot} (char $\ast$string, char $\ast$structure, char $\ast$ssfile) +\begin{DoxyCompactList}\small\item\em Produce a secondary structure graph in S\-Struct\-View format. \end{DoxyCompactList}\item +int \hyperlink{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{svg\-\_\-rna\-\_\-plot} (char $\ast$string, char $\ast$structure, char $\ast$ssfile) +\begin{DoxyCompactList}\small\item\em Produce a secondary structure plot in S\-V\-G format and write it to a file. \end{DoxyCompactList}\item +int \hyperlink{PS__dot_8h_a2f6d5953e6a323df898896b8d6614483}{xrna\-\_\-plot} (char $\ast$string, char $\ast$structure, char $\ast$ssfile) +\begin{DoxyCompactList}\small\item\em Produce a secondary structure plot for further editing in X\-R\-N\-A. \end{DoxyCompactList}\item +int \hyperlink{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}{P\-S\-\_\-dot\-\_\-plot\-\_\-list} (char $\ast$seq, char $\ast$filename, \hyperlink{structplist}{plist} $\ast$pl, \hyperlink{structplist}{plist} $\ast$mf, char $\ast$comment) +\begin{DoxyCompactList}\small\item\em Produce a postscript dot-\/plot from two pair lists. \end{DoxyCompactList}\item +int \hyperlink{PS__dot_8h_aab48d4dac655d688abe921389ac2847c}{ali\-P\-S\-\_\-color\-\_\-aln} (const char $\ast$structure, const char $\ast$filename, const char $\ast$seqs\mbox{[}$\,$\mbox{]}, const char $\ast$names\mbox{[}$\,$\mbox{]}) +\item +int \hyperlink{PS__dot_8h_a689a97a7e3b8a2df14728b8204d9d57b}{P\-S\-\_\-dot\-\_\-plot} (char $\ast$string, char $\ast$file) +\begin{DoxyCompactList}\small\item\em Produce postscript dot-\/plot. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Various functions for plotting R\-N\-A secondary structures, dot-\/plots and other visualizations. + +\subsection{Function Documentation} +\hypertarget{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!P\-S\-\_\-rna\-\_\-plot@{P\-S\-\_\-rna\-\_\-plot}} +\index{P\-S\-\_\-rna\-\_\-plot@{P\-S\-\_\-rna\-\_\-plot}!PS_dot.h@{P\-S\-\_\-dot.\-h}} +\subsubsection[{P\-S\-\_\-rna\-\_\-plot}]{\setlength{\rightskip}{0pt plus 5cm}int P\-S\-\_\-rna\-\_\-plot ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{string, } +\item[{char $\ast$}]{structure, } +\item[{char $\ast$}]{file} +\end{DoxyParamCaption} +)}}\label{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9} + + +Produce a secondary structure graph in Post\-Script and write it to 'filename'. + +Note that this function has changed from previous versions and now expects the structure to be plotted in dot-\/bracket notation as an argument. It does not make use of the global \hyperlink{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}{base\-\_\-pair} array anymore. + + +\begin{DoxyParams}{Parameters} +{\em string} & The R\-N\-A sequence \\ +\hline +{\em structure} & The secondary structure in dot-\/bracket notation \\ +\hline +{\em file} & The filename of the postscript output \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +1 on success, 0 otherwise +\end{DoxyReturn} +\hypertarget{PS__dot_8h_a47856b2504b566588785597b6ebb8271}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!P\-S\-\_\-rna\-\_\-plot\-\_\-a@{P\-S\-\_\-rna\-\_\-plot\-\_\-a}} +\index{P\-S\-\_\-rna\-\_\-plot\-\_\-a@{P\-S\-\_\-rna\-\_\-plot\-\_\-a}!PS_dot.h@{P\-S\-\_\-dot.\-h}} +\subsubsection[{P\-S\-\_\-rna\-\_\-plot\-\_\-a}]{\setlength{\rightskip}{0pt plus 5cm}int P\-S\-\_\-rna\-\_\-plot\-\_\-a ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{string, } +\item[{char $\ast$}]{structure, } +\item[{char $\ast$}]{file, } +\item[{char $\ast$}]{pre, } +\item[{char $\ast$}]{post} +\end{DoxyParamCaption} +)}}\label{PS__dot_8h_a47856b2504b566588785597b6ebb8271} + + +Produce a secondary structure graph in Post\-Script including additional annotation macros and write it to 'filename'. + +Same as \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{P\-S\-\_\-rna\-\_\-plot()} but adds extra Post\-Script macros for various annotations (see generated P\-S code). The 'pre' and 'post' variables contain Post\-Script code that is verbatim copied in the resulting P\-S file just before and after the structure plot. If both arguments ('pre' and 'post') are N\-U\-L\-L, no additional macros will be printed into the Post\-Script. + + +\begin{DoxyParams}{Parameters} +{\em string} & The R\-N\-A sequence \\ +\hline +{\em structure} & The secondary structure in dot-\/bracket notation \\ +\hline +{\em file} & The filename of the postscript output \\ +\hline +{\em pre} & Post\-Script code to appear before the secondary structure plot \\ +\hline +{\em post} & Post\-Script code to appear after the secondary structure plot \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +1 on success, 0 otherwise +\end{DoxyReturn} +\hypertarget{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!gml\-R\-N\-A@{gml\-R\-N\-A}} +\index{gml\-R\-N\-A@{gml\-R\-N\-A}!PS_dot.h@{P\-S\-\_\-dot.\-h}} +\subsubsection[{gml\-R\-N\-A}]{\setlength{\rightskip}{0pt plus 5cm}int gml\-R\-N\-A ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{string, } +\item[{char $\ast$}]{structure, } +\item[{char $\ast$}]{ssfile, } +\item[{char}]{option} +\end{DoxyParamCaption} +)}}\label{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329} + + +Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file. + +If 'option' is an uppercase letter the R\-N\-A sequence is used to label nodes, if 'option' equals {\itshape 'X'} or {\itshape 'x'} the resulting file will coordinates for an initial layout of the graph. + + +\begin{DoxyParams}{Parameters} +{\em string} & The R\-N\-A sequence \\ +\hline +{\em structure} & The secondary structure in dot-\/bracket notation \\ +\hline +{\em ssfile} & The filename of the gml output \\ +\hline +{\em option} & The option flag \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +1 on success, 0 otherwise +\end{DoxyReturn} +\hypertarget{PS__dot_8h_add368528755f9a830727b680243541df}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!ssv\-\_\-rna\-\_\-plot@{ssv\-\_\-rna\-\_\-plot}} +\index{ssv\-\_\-rna\-\_\-plot@{ssv\-\_\-rna\-\_\-plot}!PS_dot.h@{P\-S\-\_\-dot.\-h}} +\subsubsection[{ssv\-\_\-rna\-\_\-plot}]{\setlength{\rightskip}{0pt plus 5cm}int ssv\-\_\-rna\-\_\-plot ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{string, } +\item[{char $\ast$}]{structure, } +\item[{char $\ast$}]{ssfile} +\end{DoxyParamCaption} +)}}\label{PS__dot_8h_add368528755f9a830727b680243541df} + + +Produce a secondary structure graph in S\-Struct\-View format. + +Write coord file for S\-Struct\-View + + +\begin{DoxyParams}{Parameters} +{\em string} & The R\-N\-A sequence \\ +\hline +{\em structure} & The secondary structure in dot-\/bracket notation \\ +\hline +{\em ssfile} & The filename of the ssv output \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +1 on success, 0 otherwise +\end{DoxyReturn} +\hypertarget{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!svg\-\_\-rna\-\_\-plot@{svg\-\_\-rna\-\_\-plot}} +\index{svg\-\_\-rna\-\_\-plot@{svg\-\_\-rna\-\_\-plot}!PS_dot.h@{P\-S\-\_\-dot.\-h}} +\subsubsection[{svg\-\_\-rna\-\_\-plot}]{\setlength{\rightskip}{0pt plus 5cm}int svg\-\_\-rna\-\_\-plot ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{string, } +\item[{char $\ast$}]{structure, } +\item[{char $\ast$}]{ssfile} +\end{DoxyParamCaption} +)}}\label{PS__dot_8h_ae7853539b5df98f294b4af434e979304} + + +Produce a secondary structure plot in S\-V\-G format and write it to a file. + + +\begin{DoxyParams}{Parameters} +{\em string} & The R\-N\-A sequence \\ +\hline +{\em structure} & The secondary structure in dot-\/bracket notation \\ +\hline +{\em ssfile} & The filename of the svg output \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +1 on success, 0 otherwise +\end{DoxyReturn} +\hypertarget{PS__dot_8h_a2f6d5953e6a323df898896b8d6614483}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!xrna\-\_\-plot@{xrna\-\_\-plot}} +\index{xrna\-\_\-plot@{xrna\-\_\-plot}!PS_dot.h@{P\-S\-\_\-dot.\-h}} +\subsubsection[{xrna\-\_\-plot}]{\setlength{\rightskip}{0pt plus 5cm}int xrna\-\_\-plot ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{string, } +\item[{char $\ast$}]{structure, } +\item[{char $\ast$}]{ssfile} +\end{DoxyParamCaption} +)}}\label{PS__dot_8h_a2f6d5953e6a323df898896b8d6614483} + + +Produce a secondary structure plot for further editing in X\-R\-N\-A. + + +\begin{DoxyParams}{Parameters} +{\em string} & The R\-N\-A sequence \\ +\hline +{\em structure} & The secondary structure in dot-\/bracket notation \\ +\hline +{\em ssfile} & The filename of the xrna output \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +1 on success, 0 otherwise +\end{DoxyReturn} +\hypertarget{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!P\-S\-\_\-dot\-\_\-plot\-\_\-list@{P\-S\-\_\-dot\-\_\-plot\-\_\-list}} +\index{P\-S\-\_\-dot\-\_\-plot\-\_\-list@{P\-S\-\_\-dot\-\_\-plot\-\_\-list}!PS_dot.h@{P\-S\-\_\-dot.\-h}} +\subsubsection[{P\-S\-\_\-dot\-\_\-plot\-\_\-list}]{\setlength{\rightskip}{0pt plus 5cm}int P\-S\-\_\-dot\-\_\-plot\-\_\-list ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{seq, } +\item[{char $\ast$}]{filename, } +\item[{{\bf plist} $\ast$}]{pl, } +\item[{{\bf plist} $\ast$}]{mf, } +\item[{char $\ast$}]{comment} +\end{DoxyParamCaption} +)}}\label{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12} + + +Produce a postscript dot-\/plot from two pair lists. + +This function reads two plist structures (e.\-g. base pair probabilities and a secondary structure) as produced by \hyperlink{group__pf__fold_ga03e15e831a31b1154855ab47edbdb019}{assign\-\_\-plist\-\_\-from\-\_\-pr()} and \hyperlink{fold_8h_adaa59b81664e2e36cb9932e891558fae}{assign\-\_\-plist\-\_\-from\-\_\-db()} and produces a postscript \char`\"{}dot plot\char`\"{} that is written to 'filename'.\par + Using base pair probabilities in the first and mfe structure in the second plist, the resulting \char`\"{}dot plot\char`\"{} represents each base pairing probability by a square of corresponding area in a upper triangle matrix. The lower part of the matrix contains the minimum free energy structure. + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__pf__fold_ga03e15e831a31b1154855ab47edbdb019}{assign\-\_\-plist\-\_\-from\-\_\-pr()}, \hyperlink{fold_8h_adaa59b81664e2e36cb9932e891558fae}{assign\-\_\-plist\-\_\-from\-\_\-db()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em seq} & The R\-N\-A sequence \\ +\hline +{\em filename} & A filename for the postscript output \\ +\hline +{\em pl} & The base pair probability pairlist \\ +\hline +{\em mf} & The mfe secondary structure pairlist \\ +\hline +{\em comment} & A comment \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +1 if postscript was successfully written, 0 otherwise +\end{DoxyReturn} +\hypertarget{PS__dot_8h_aab48d4dac655d688abe921389ac2847c}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!ali\-P\-S\-\_\-color\-\_\-aln@{ali\-P\-S\-\_\-color\-\_\-aln}} +\index{ali\-P\-S\-\_\-color\-\_\-aln@{ali\-P\-S\-\_\-color\-\_\-aln}!PS_dot.h@{P\-S\-\_\-dot.\-h}} +\subsubsection[{ali\-P\-S\-\_\-color\-\_\-aln}]{\setlength{\rightskip}{0pt plus 5cm}int ali\-P\-S\-\_\-color\-\_\-aln ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{structure, } +\item[{const char $\ast$}]{filename, } +\item[{const char $\ast$}]{seqs\mbox{[}$\,$\mbox{]}, } +\item[{const char $\ast$}]{names\mbox{[}$\,$\mbox{]}} +\end{DoxyParamCaption} +)}}\label{PS__dot_8h_aab48d4dac655d688abe921389ac2847c} +P\-S\-\_\-color\-\_\-aln for duplexes \hypertarget{PS__dot_8h_a689a97a7e3b8a2df14728b8204d9d57b}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!P\-S\-\_\-dot\-\_\-plot@{P\-S\-\_\-dot\-\_\-plot}} +\index{P\-S\-\_\-dot\-\_\-plot@{P\-S\-\_\-dot\-\_\-plot}!PS_dot.h@{P\-S\-\_\-dot.\-h}} +\subsubsection[{P\-S\-\_\-dot\-\_\-plot}]{\setlength{\rightskip}{0pt plus 5cm}int P\-S\-\_\-dot\-\_\-plot ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{string, } +\item[{char $\ast$}]{file} +\end{DoxyParamCaption} +)}}\label{PS__dot_8h_a689a97a7e3b8a2df14728b8204d9d57b} + + +Produce postscript dot-\/plot. + +Wrapper to P\-S\-\_\-dot\-\_\-plot\-\_\-list + +Reads base pair probabilities produced by \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} from the global array \hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr} and the pair list \hyperlink{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}{base\-\_\-pair} produced by \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()} and produces a postscript \char`\"{}dot plot\char`\"{} that is written to 'filename'. The \char`\"{}dot plot\char`\"{} represents each base pairing probability by a square of corresponding area in a upper triangle matrix. The lower part of the matrix contains the minimum free energy \begin{DoxyNote}{Note} +D\-O N\-O\-T U\-S\-E T\-H\-I\-S F\-U\-N\-C\-T\-I\-O\-N A\-N\-Y\-M\-O\-R\-E S\-I\-N\-C\-E I\-T I\-S N\-O\-T T\-H\-R\-E\-A\-D\-S\-A\-F\-E +\end{DoxyNote} +\begin{DoxyRefDesc}{Deprecated} +\item[\hyperlink{deprecated__deprecated000019}{Deprecated}]This function is deprecated and will be removed soon! 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zKQ$e}Kg-2Gvr-n0NepM(iwL;T=T}+hKZCqc2pb|yE`f=Fe_t4{2@44WYyiJ7s4y6# zJN5!N{l)}=AdCGpa{nN|HK3ZLI1{tu>St197G7~)Bnb> zG4)@V2xhnc!a)C;4+_Di&_BmQq2NC-cN83x`lyQ{ybjVAfwdL3Zlvw(jEMlO&41>f fvXc$Q(|?zw+}z HIT [incl. root] */} +00034 +00042 \textcolor{keywordtype}{char} *\hyperlink{RNAstruct_8h_a9c80d92391f2833549a8b6dac92233f0}{b2C}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure); \textcolor{comment}{/* Full -> Coarse [incl. root] */} +00043 +00052 \textcolor{keywordtype}{char} *\hyperlink{RNAstruct_8h_a5cd2feb367feeacad0c03cb7ddba5f10}{b2Shapiro}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure); \textcolor{comment}{/* Full -> weighted Shapiro [i.r.] */} +00053 +00060 \textcolor{keywordtype}{char} *\hyperlink{RNAstruct_8h_a880d33066dd95441e5fbb73c57ed1c3e}{add\_root}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure); \textcolor{comment}{/* \{Tree\} -> (\{Tree\}R) */} +00061 +00069 \textcolor{keywordtype}{char} *\hyperlink{RNAstruct_8h_abe3d815b420dc4553bfb23511198b4c6}{expand\_Shapiro}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *coarse); +00070 +00071 \textcolor{comment}{/* add S for stacks to coarse struct */} +00079 \textcolor{keywordtype}{char} *\hyperlink{RNAstruct_8h_a78d73cd54a068ef2812812771cdddc6f}{expand\_Full}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure); \textcolor{comment}{/* Full -> FFull */} +00080 +00088 \textcolor{keywordtype}{char} *\hyperlink{RNAstruct_8h_a260c4b622093b76a883bf96628280de1}{unexpand\_Full}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *ffull); \textcolor{comment}{/* FFull -> Full */} +00089 +00096 \textcolor{keywordtype}{char} *\hyperlink{RNAstruct_8h_a09a80253ac7b6bae606871ba7c6e5136}{unweight}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *wcoarse); \textcolor{comment}{/* remove weights from coarse struct */} +00097 +00107 \textcolor{keywordtype}{void} \hyperlink{RNAstruct_8h_a1054c4477d53b31d79d4cb132100e87a}{unexpand\_aligned\_F}(\textcolor{keywordtype}{char} *align[2]); +00108 +00119 \textcolor{keywordtype}{void} \hyperlink{RNAstruct_8h_a3c79042e6bf6f01706bf30ec9e69e8ac}{parse\_structure}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure); \textcolor{comment}{/* make structure statistics */} +00120 +00125 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{RNAstruct_8h_a3f31e0e48125601bfa57b52f8b038e8e}{loop\_size}[STRUC]; \textcolor{comment}{/* loop sizes of a structure */} +00126 +00130 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{RNAstruct_8h_a8218c0d581a3fba2a1a56a196abe19a5}{helix\_size}[STRUC]; \textcolor{comment}{/* helix sizes of a structure */} +00131 +00135 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{RNAstruct_8h_aef14e2f8ab3f61e8e659ba6b9003b08a}{loop\_degree}[STRUC]; \textcolor{comment}{/* loop degrees of a structure */} +00136 +00140 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{RNAstruct_8h_a439fcb9f8d4f9f4d2227fde5fbfecb30}{loops}; \textcolor{comment}{/* n of loops and stacks */} +00141 +00145 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{RNAstruct_8h_add2f952597e02d66e1116a9d11d252d6}{unpaired}; +00146 +00150 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{RNAstruct_8h_a6341cbb704924824e0236c1dce791032}{pairs}; \textcolor{comment}{/* n of unpaired digits and pairs */} +00151 +00152 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/ali__plex_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/ali__plex_8h_source.tex new file mode 100644 index 0000000..1a5aa3e --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/ali__plex_8h_source.tex @@ -0,0 +1,40 @@ +\hypertarget{ali__plex_8h}{\section{ali\-\_\-plex.\-h} +\label{ali__plex_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/ali\-\_\-plex.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/ali\-\_\-plex.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_ALI\_PLEX\_H\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_ALI\_PLEX\_H\_\_} +00003 \textcolor{preprocessor}{} +00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"} +00008 \hyperlink{structduplexT}{duplexT}** aliLduplexfold( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1[], +00009 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2[], +00010 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshold, +00011 \textcolor{keyword}{const} \textcolor{keywordtype}{int} extension\_cost, +00012 \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length, +00013 \textcolor{keyword}{const} \textcolor{keywordtype}{int} delta, +00014 \textcolor{keyword}{const} \textcolor{keywordtype}{int} fast, +00015 \textcolor{keyword}{const} \textcolor{keywordtype}{int} il\_a, +00016 \textcolor{keyword}{const} \textcolor{keywordtype}{int} il\_b, +00017 \textcolor{keyword}{const} \textcolor{keywordtype}{int} b\_a, +00018 \textcolor{keyword}{const} \textcolor{keywordtype}{int} b\_b); +00022 \hyperlink{structduplexT}{duplexT}** aliLduplexfold\_XS(\textcolor{keyword}{const} \textcolor{keywordtype}{char}* s1[], +00023 \textcolor{keyword}{const} \textcolor{keywordtype}{char}* s2[], +00024 \textcolor{keyword}{const} \textcolor{keywordtype}{int} **access\_s1, +00025 \textcolor{keyword}{const} \textcolor{keywordtype}{int} **access\_s2, +00026 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshold, +00027 \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length, +00028 \textcolor{keyword}{const} \textcolor{keywordtype}{int} delta, +00029 \textcolor{keyword}{const} \textcolor{keywordtype}{int} fast, +00030 \textcolor{keyword}{const} \textcolor{keywordtype}{int} il\_a, +00031 \textcolor{keyword}{const} \textcolor{keywordtype}{int} il\_b, +00032 \textcolor{keyword}{const} \textcolor{keywordtype}{int} b\_a, +00033 \textcolor{keyword}{const} \textcolor{keywordtype}{int} b\_b); +00034 +00035 \textcolor{comment}{/*} +00036 \textcolor{comment}{extern duplexT aliduplexfold(const char *s1[], const char *s2[], const int extension\_cost);} +00037 \textcolor{comment}{extern duplexT aliduplexfold\_XS(const char *s1[], const char *s2[],const int **access\_s1, } +00038 \textcolor{comment}{const int **access\_s2, const int i\_pos, const int j\_pos, const int threshold);} +00039 \textcolor{comment}{*/} +00040 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/alifold_8h.tex b/binaries/src/ViennaRNA/doc/latex/alifold_8h.tex new file mode 100644 index 0000000..298de2f --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/alifold_8h.tex @@ -0,0 +1,79 @@ +\hypertarget{alifold_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/alifold.h File Reference} +\label{alifold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/alifold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/alifold.\-h}} +} + + +compute various properties (consensus M\-F\-E structures, partition function, Boltzmann distributed stochastic samples, ...) for R\-N\-A sequence alignments + + +Include dependency graph for alifold.\-h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{alifold_8h__incl} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +void \hyperlink{alifold_8h_ac484c6bd429bafbd353b91044508d8e9}{update\-\_\-alifold\-\_\-params} (void) +\begin{DoxyCompactList}\small\item\em Update the energy parameters for alifold function. \end{DoxyCompactList}\item +float \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold} (const char $\ast$$\ast$strings, char $\ast$structure) +\begin{DoxyCompactList}\small\item\em Compute M\-F\-E and according consensus structure of an alignment of sequences. \end{DoxyCompactList}\item +float \hyperlink{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{circalifold} (const char $\ast$$\ast$strings, char $\ast$structure) +\begin{DoxyCompactList}\small\item\em Compute M\-F\-E and according structure of an alignment of sequences assuming the sequences are circular instead of linear. \end{DoxyCompactList}\item +\hypertarget{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{void \hyperlink{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{free\-\_\-alifold\-\_\-arrays} (void)}\label{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e} + +\begin{DoxyCompactList}\small\item\em Free the memory occupied by M\-F\-E alifold functions. \end{DoxyCompactList}\item +int \hyperlink{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f}{get\-\_\-mpi} (char $\ast$Alseq\mbox{[}$\,$\mbox{]}, int n\-\_\-seq, int length, int $\ast$mini) +\begin{DoxyCompactList}\small\item\em Get the mean pairwise identity in steps from ?to?(ident) \end{DoxyCompactList}\item +\hypertarget{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}{float $\ast$$\ast$ \hyperlink{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}{readribosum} (char $\ast$name)}\label{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc} + +\begin{DoxyCompactList}\small\item\em Read a ribosum or other user-\/defined scoring matrix. \end{DoxyCompactList}\item +float \hyperlink{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}{energy\-\_\-of\-\_\-alistruct} (const char $\ast$$\ast$sequences, const char $\ast$structure, int n\-\_\-seq, float $\ast$energy) +\begin{DoxyCompactList}\small\item\em Calculate the free energy of a consensus structure given a set of aligned sequences. \end{DoxyCompactList}\item +void \hyperlink{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786}{encode\-\_\-ali\-\_\-sequence} (const char $\ast$sequence, short $\ast$S, short $\ast$s5, short $\ast$s3, char $\ast$ss, unsigned short $\ast$as, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ}) +\begin{DoxyCompactList}\small\item\em Get arrays with encoded sequence of the alignment. \end{DoxyCompactList}\item +void \hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc\-\_\-sequence\-\_\-arrays} (const char $\ast$$\ast$sequences, short $\ast$$\ast$$\ast$S, short $\ast$$\ast$$\ast$S5, short $\ast$$\ast$$\ast$S3, unsigned short $\ast$$\ast$$\ast$a2s, char $\ast$$\ast$$\ast$Ss, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ}) +\begin{DoxyCompactList}\small\item\em Allocate memory for sequence array used to deal with aligned sequences. \end{DoxyCompactList}\item +void \hyperlink{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{free\-\_\-sequence\-\_\-arrays} (unsigned int n\-\_\-seq, short $\ast$$\ast$$\ast$S, short $\ast$$\ast$$\ast$S5, short $\ast$$\ast$$\ast$S3, unsigned short $\ast$$\ast$$\ast$a2s, char $\ast$$\ast$$\ast$Ss) +\begin{DoxyCompactList}\small\item\em Free the memory of the sequence arrays used to deal with aligned sequences. \end{DoxyCompactList}\item +float \hyperlink{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{alipf\-\_\-fold\-\_\-par} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl, \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters, int calculate\-\_\-bppm, int is\-\_\-constrained, int is\-\_\-circular) +\item +float \hyperlink{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{alipf\-\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl) +\begin{DoxyCompactList}\small\item\em The partition function version of \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold()} works in analogy to \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()}. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of \hyperlink{structpair__info}{pair\-\_\-info} structs. The list is terminated by the first entry with pi.\-i = 0. \end{DoxyCompactList}\item +float \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf\-\_\-circ\-\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl) +\item +double $\ast$ \hyperlink{group__consensus__pf__fold_gadaaf83394216413505e48d913dbc1b4e}{export\-\_\-ali\-\_\-bppm} (void) +\begin{DoxyCompactList}\small\item\em Get a pointer to the base pair probability array. \end{DoxyCompactList}\item +char $\ast$ \hyperlink{group__consensus__stochbt_ga0df40248788f0fb17ebdc59d74116d1c}{alipbacktrack} (double $\ast$prob) +\begin{DoxyCompactList}\small\item\em Sample a consensus secondary structure from the Boltzmann ensemble according its probability\par +. \end{DoxyCompactList}\item +int \hyperlink{group__consensus__fold_ga0cc49457fd79eeb04d4a7f97c868b09b}{get\-\_\-alipf\-\_\-arrays} (short $\ast$$\ast$$\ast$S\-\_\-p, short $\ast$$\ast$$\ast$S5\-\_\-p, short $\ast$$\ast$$\ast$S3\-\_\-p, unsigned short $\ast$$\ast$$\ast$a2s\-\_\-p, char $\ast$$\ast$$\ast$Ss\-\_\-p, double $\ast$$\ast$qb\-\_\-p, double $\ast$$\ast$qm\-\_\-p, double $\ast$$\ast$q1k\-\_\-p, double $\ast$$\ast$qln\-\_\-p, short $\ast$$\ast$pscore) +\begin{DoxyCompactList}\small\item\em Get pointers to (almost) all relavant arrays used in alifold's partition function computation. \end{DoxyCompactList}\end{DoxyCompactItemize} +\subsection*{Variables} +\begin{DoxyCompactItemize} +\item +double \hyperlink{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{cv\-\_\-fact} +\begin{DoxyCompactList}\small\item\em This variable controls the weight of the covariance term in the energy function of alignment folding algorithms. \end{DoxyCompactList}\item +double \hyperlink{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{nc\-\_\-fact} +\begin{DoxyCompactList}\small\item\em This variable controls the magnitude of the penalty for non-\/compatible sequences in the covariance term of alignment folding algorithms. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +compute various properties (consensus M\-F\-E structures, partition function, Boltzmann distributed stochastic samples, ...) for R\-N\-A sequence alignments + +\subsection{Function Documentation} +\hypertarget{alifold_8h_ac484c6bd429bafbd353b91044508d8e9}{\index{alifold.\-h@{alifold.\-h}!update\-\_\-alifold\-\_\-params@{update\-\_\-alifold\-\_\-params}} +\index{update\-\_\-alifold\-\_\-params@{update\-\_\-alifold\-\_\-params}!alifold.h@{alifold.\-h}} +\subsubsection[{update\-\_\-alifold\-\_\-params}]{\setlength{\rightskip}{0pt plus 5cm}void update\-\_\-alifold\-\_\-params ( +\begin{DoxyParamCaption} +\item[{void}]{} +\end{DoxyParamCaption} +)}}\label{alifold_8h_ac484c6bd429bafbd353b91044508d8e9} + + +Update the energy parameters for alifold function. + +Call this to recalculate the pair matrix and energy parameters 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Qx(Fzoq!Ej18|%>jAECAf8UO$Q literal 0 HcmV?d00001 diff --git a/binaries/src/ViennaRNA/doc/latex/cofold_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/cofold_8h_source.tex new file mode 100644 index 0000000..4b49e78 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/cofold_8h_source.tex @@ -0,0 +1,62 @@ +\hypertarget{cofold_8h}{\section{cofold.\-h} +\label{cofold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/cofold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/cofold.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_COFOLD\_H\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_COFOLD\_H\_\_} +00003 \textcolor{preprocessor}{} +00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"} +00005 +00006 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_} +00007 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func \_\_attribute\_\_ ((deprecated))} +00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else} +00009 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func} +00010 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif} +00011 \textcolor{preprocessor}{} +00065 \textcolor{keywordtype}{float} \hyperlink{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}{cofold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence, +00066 \textcolor{keywordtype}{char} *structure); +00067 +00072 \textcolor{keywordtype}{float} \hyperlink{group__mfe__cofold_gafe430060533f14b11fc611f60b3f1f6f}{cofold\_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}, +00073 \textcolor{keywordtype}{char} *structure, +00074 \hyperlink{structparamT}{paramT} *parameters, +00075 \textcolor{keywordtype}{int} is\_constrained); +00076 +00080 \textcolor{keywordtype}{void} \hyperlink{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}{free\_co\_arrays}(\textcolor{keywordtype}{void}); +00081 +00085 \textcolor{keywordtype}{void} \hyperlink{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}{update\_cofold\_params}(\textcolor{keywordtype}{void}); +00086 +00087 \textcolor{keywordtype}{void} update\_cofold\_params\_par(\hyperlink{structparamT}{paramT} *parameters); +00088 +00089 +00105 \textcolor{keywordtype}{void} \hyperlink{group__mfe__cofold_ga5f5bf4df35d0554f6ace9579f8744c48}{export\_cofold\_arrays\_gq}( \textcolor{keywordtype}{int} **f5\_p, +00106 \textcolor{keywordtype}{int} **c\_p, +00107 \textcolor{keywordtype}{int} **fML\_p, +00108 \textcolor{keywordtype}{int} **fM1\_p, +00109 \textcolor{keywordtype}{int} **fc\_p, +00110 \textcolor{keywordtype}{int} **ggg\_p, +00111 \textcolor{keywordtype}{int} **indx\_p, +00112 \textcolor{keywordtype}{char} **ptype\_p); +00113 +00128 \textcolor{keywordtype}{void} \hyperlink{group__mfe__cofold_ga5cb6b59983f1f74ccc00b9b9c4e84482}{export\_cofold\_arrays}(\textcolor{keywordtype}{int} **f5\_p, +00129 \textcolor{keywordtype}{int} **c\_p, +00130 \textcolor{keywordtype}{int} **fML\_p, +00131 \textcolor{keywordtype}{int} **fM1\_p, +00132 \textcolor{keywordtype}{int} **fc\_p, +00133 \textcolor{keywordtype}{int} **indx\_p, +00134 \textcolor{keywordtype}{char} **ptype\_p); +00135 +00136 +00153 \hyperlink{structSOLUTION}{SOLUTION} *\hyperlink{group__subopt__zuker_ga0d5104e3ecf119d8eabd40aa5fe47f90}{zukersubopt}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}); +00154 +00161 \hyperlink{structSOLUTION}{SOLUTION} *\hyperlink{group__subopt__zuker_ga6d98a9450d1affadf144ac79f543da8c}{zukersubopt\_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}, +00162 \hyperlink{structparamT}{paramT} *parameters); +00163 +00172 \textcolor{keywordtype}{void} \hyperlink{cofold_8h_a4958b517c613e4d2afd5bce6c1060a79}{get\_monomere\_mfes}( \textcolor{keywordtype}{float} *e1, +00173 \textcolor{keywordtype}{float} *e2); +00174 +00175 +00180 DEPRECATED(\textcolor{keywordtype}{void} \hyperlink{cofold_8h_afee0c32208aa2ac97338b6e3fbad7fa5}{initialize\_cofold}(\textcolor{keywordtype}{int} length)); +00181 +00182 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/convert__epars_8h.tex b/binaries/src/ViennaRNA/doc/latex/convert__epars_8h.tex new file mode 100644 index 0000000..61430bf --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/convert__epars_8h.tex @@ -0,0 +1,64 @@ +\hypertarget{convert__epars_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/convert\-\_\-epars.h File Reference} +\label{convert__epars_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/convert\-\_\-epars.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/convert\-\_\-epars.\-h}} +} + + +Functions and definitions for energy parameter file format conversion. + + +\subsection*{Macros} +\begin{DoxyCompactItemize} +\item +\#define \hyperlink{group__energy__parameters__convert_ga8dc6aee5a806c49b71557152f9616bc4}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-A\-L\-L}~1\-U +\item +\#define \hyperlink{group__energy__parameters__convert_gaf66fe2cb11dfcfd32d791049c254a8a4}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-H\-P}~2\-U +\item +\#define \hyperlink{group__energy__parameters__convert_gad23522d63f8d4c50d5a5deee9bee3ef2}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-T\-A\-C\-K}~4\-U +\item +\#define \hyperlink{group__energy__parameters__convert_gaa892c7b4957459090f3e08da298cc347}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-H\-P}~8\-U +\item +\#define \hyperlink{group__energy__parameters__convert_ga4ff223fb1f9c62cd92d9ab811ad03d55}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T}~16\-U +\item +\#define \hyperlink{group__energy__parameters__convert_gaf5d3743219f83c6348155cd81e755bbb}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-1\-N}~32\-U +\item +\#define \hyperlink{group__energy__parameters__convert_ga78382ec622ba99e0ac2262317bdd7316}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-23}~64\-U +\item +\#define \hyperlink{group__energy__parameters__convert_gae67af9f1cdf7baf2865481282a5d1034}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-M\-U\-L\-T\-I}~128\-U +\item +\#define \hyperlink{group__energy__parameters__convert_gaf14ead7ef1fdbe725ade653750fc51e3}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-E\-X\-T}~256\-U +\item +\#define \hyperlink{group__energy__parameters__convert_ga036ffd996d8c8a9acf631760dd1da24b}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E5}~512\-U +\item +\#define \hyperlink{group__energy__parameters__convert_ga34a8a5479ef885834ef32f3fb43d79bc}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E3}~1024\-U +\item +\#define \hyperlink{group__energy__parameters__convert_ga079aafefd5f8ab57ee5120099a34bd25}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-11}~2048\-U +\item +\#define \hyperlink{group__energy__parameters__convert_gacf770881d9034431ebe741642342a1f9}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-21}~4096\-U +\item +\#define \hyperlink{group__energy__parameters__convert_gaa307671e2631cdacad9cbe4c6583b05f}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-22}~8192\-U +\item +\#define \hyperlink{group__energy__parameters__convert_ga7092fe0be4de6f02cc0bf08e81af726a}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-B\-U\-L\-G\-E}~16384\-U +\item +\#define \hyperlink{group__energy__parameters__convert_gac5c2289fdf8ff1b980976d1613ff943a}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T}~32768\-U +\item +\#define \hyperlink{group__energy__parameters__convert_gaf2c8755d64eff3852aa45df9ac80a4fe}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-L}~65536\-U +\item +\#define \hyperlink{group__energy__parameters__convert_ga46d5b1535ae86060b6317565b7c6b40b}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-I\-S\-C}~131072\-U +\item +\#define \hyperlink{group__energy__parameters__convert_gaa1ff48a79642d69579d1766561ec6db6}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-P\-E\-C\-I\-A\-L\-\_\-\-H\-P}~262144\-U +\item +\#define \hyperlink{group__energy__parameters__convert_ga0d4e8a836bb4864ab5129c085dbf592d}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-V\-A\-N\-I\-L\-L\-A}~524288\-U +\item +\#define \hyperlink{group__energy__parameters__convert_ga2eb0462f16939ddacdaf751a88d675ce}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-N\-I\-N\-I\-O}~1048576\-U +\item +\#define \hyperlink{group__energy__parameters__convert_gac86976e9c2a55b3a6481ea60044f6098}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-U\-M\-P}~2097152\-U +\end{DoxyCompactItemize} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +void \hyperlink{group__energy__parameters__convert_gafbe538bc4eb2cf2a33326e1010005f8a}{convert\-\_\-parameter\-\_\-file} (const char $\ast$iname, const char $\ast$oname, unsigned int options) +\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Functions and definitions for energy parameter file format conversion. \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/convert__epars_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/convert__epars_8h_source.tex new file mode 100644 index 0000000..2e9fc80 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/convert__epars_8h_source.tex @@ -0,0 +1,58 @@ +\hypertarget{convert__epars_8h}{\section{convert\-\_\-epars.\-h} +\label{convert__epars_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/convert\-\_\-epars.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/convert\-\_\-epars.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_CONVERT\_EPARS\_H\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_CONVERT\_EPARS\_H\_\_} +00003 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00018}{}\hyperlink{group__energy__parameters__convert_ga8dc6aee5a806c49b71557152f9616bc4}{00018} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_ALL 1U} +00019 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00020}{}\hyperlink{group__energy__parameters__convert_gaf66fe2cb11dfcfd32d791049c254a8a4}{00020} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_HP 2U} +00021 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00022}{}\hyperlink{group__energy__parameters__convert_gad23522d63f8d4c50d5a5deee9bee3ef2}{00022} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_STACK 4U} +00023 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00024}{}\hyperlink{group__energy__parameters__convert_gaa892c7b4957459090f3e08da298cc347}{00024} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_MM\_HP 8U} +00025 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00026}{}\hyperlink{group__energy__parameters__convert_ga4ff223fb1f9c62cd92d9ab811ad03d55}{00026} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_MM\_INT 16U} +00027 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00028}{}\hyperlink{group__energy__parameters__convert_gaf5d3743219f83c6348155cd81e755bbb}{00028} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_MM\_INT\_1N 32U} +00029 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00030}{}\hyperlink{group__energy__parameters__convert_ga78382ec622ba99e0ac2262317bdd7316}{00030} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_MM\_INT\_23 64U} +00031 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00032}{}\hyperlink{group__energy__parameters__convert_gae67af9f1cdf7baf2865481282a5d1034}{00032} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_MM\_MULTI 128U} +00033 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00034}{}\hyperlink{group__energy__parameters__convert_gaf14ead7ef1fdbe725ade653750fc51e3}{00034} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_MM\_EXT 256U} +00035 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00036}{}\hyperlink{group__energy__parameters__convert_ga036ffd996d8c8a9acf631760dd1da24b}{00036} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_DANGLE5 512U} +00037 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00038}{}\hyperlink{group__energy__parameters__convert_ga34a8a5479ef885834ef32f3fb43d79bc}{00038} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_DANGLE3 1024U} +00039 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00040}{}\hyperlink{group__energy__parameters__convert_ga079aafefd5f8ab57ee5120099a34bd25}{00040} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_INT\_11 2048U} +00041 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00042}{}\hyperlink{group__energy__parameters__convert_gacf770881d9034431ebe741642342a1f9}{00042} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_INT\_21 4096U} +00043 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00044}{}\hyperlink{group__energy__parameters__convert_gaa307671e2631cdacad9cbe4c6583b05f}{00044} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_INT\_22 8192U} +00045 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00046}{}\hyperlink{group__energy__parameters__convert_ga7092fe0be4de6f02cc0bf08e81af726a}{00046} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_BULGE 16384U} +00047 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00048}{}\hyperlink{group__energy__parameters__convert_gac5c2289fdf8ff1b980976d1613ff943a}{00048} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_INT 32768U} +00049 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00050}{}\hyperlink{group__energy__parameters__convert_gaf2c8755d64eff3852aa45df9ac80a4fe}{00050} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_ML 65536U} +00051 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00052}{}\hyperlink{group__energy__parameters__convert_ga46d5b1535ae86060b6317565b7c6b40b}{00052} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_MISC 131072U} +00053 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00054}{}\hyperlink{group__energy__parameters__convert_gaa1ff48a79642d69579d1766561ec6db6}{00054} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_SPECIAL\_HP 262144U} +00055 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00056}{}\hyperlink{group__energy__parameters__convert_ga0d4e8a836bb4864ab5129c085dbf592d}{00056} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_VANILLA 524288U} +00057 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00058}{}\hyperlink{group__energy__parameters__convert_ga2eb0462f16939ddacdaf751a88d675ce}{00058} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_NINIO 1048576U} +00059 \textcolor{preprocessor}{} +\hypertarget{convert__epars_8h_source_l00060}{}\hyperlink{group__energy__parameters__convert_gac86976e9c2a55b3a6481ea60044f6098}{00060} \textcolor{preprocessor}{#define VRNA\_CONVERT\_OUTPUT\_DUMP 2097152U} +00061 \textcolor{preprocessor}{} +00084 \textcolor{keywordtype}{void} \hyperlink{group__energy__parameters__convert_gafbe538bc4eb2cf2a33326e1010005f8a}{convert\_parameter\_file}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *iname, +00085 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *oname, +00086 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} options); +00087 +00091 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/data__structures_8h.tex b/binaries/src/ViennaRNA/doc/latex/data__structures_8h.tex new file mode 100644 index 0000000..e664757 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/data__structures_8h.tex @@ -0,0 +1,102 @@ +\hypertarget{data__structures_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/data\-\_\-structures.h File Reference} +\label{data__structures_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/data\-\_\-structures.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/data\-\_\-structures.\-h}} +} + + +All datastructures and typedefs shared among the Vienna R\-N\-A Package can be found here. + + +Include dependency graph for data\-\_\-structures.\-h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{data__structures_8h__incl} +\end{center} +\end{figure} +This graph shows which files directly or indirectly include this file\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=350pt]{data__structures_8h__dep__incl} +\end{center} +\end{figure} +\subsection*{Data Structures} +\begin{DoxyCompactItemize} +\item +struct \hyperlink{structplist}{plist} +\begin{DoxyCompactList}\small\item\em this datastructure is used as input parameter in functions of \hyperlink{PS__dot_8h}{P\-S\-\_\-dot.\-h} and others \end{DoxyCompactList}\item +struct \hyperlink{structcpair}{cpair} +\begin{DoxyCompactList}\small\item\em this datastructure is used as input parameter in functions of P\-S\-\_\-dot.\-c \end{DoxyCompactList}\item +struct \hyperlink{structCOORDINATE}{C\-O\-O\-R\-D\-I\-N\-A\-T\-E} +\begin{DoxyCompactList}\small\item\em this is a workarround for the S\-W\-I\-G Perl Wrapper R\-N\-A plot function that returns an array of type \hyperlink{structCOORDINATE}{C\-O\-O\-R\-D\-I\-N\-A\-T\-E} \end{DoxyCompactList}\item +struct \hyperlink{structsect}{sect} +\begin{DoxyCompactList}\small\item\em Stack of partial structures for backtracking. \end{DoxyCompactList}\item +struct \hyperlink{structbondT}{bond\-T} +\begin{DoxyCompactList}\small\item\em Base pair. \end{DoxyCompactList}\item +struct \hyperlink{structbondTEn}{bond\-T\-En} +\begin{DoxyCompactList}\small\item\em Base pair with associated energy. \end{DoxyCompactList}\item +struct \hyperlink{structmodel__detailsT}{model\-\_\-details\-T} +\begin{DoxyCompactList}\small\item\em The data structure that contains the complete model details used throughout the calculations. \end{DoxyCompactList}\item +struct \hyperlink{structparamT}{param\-T} +\begin{DoxyCompactList}\small\item\em The datastructure that contains temperature scaled energy parameters. \end{DoxyCompactList}\item +struct \hyperlink{structpf__paramT}{pf\-\_\-param\-T} +\begin{DoxyCompactList}\small\item\em The datastructure that contains temperature scaled Boltzmann weights of the energy parameters. \end{DoxyCompactList}\item +struct \hyperlink{structPAIR}{P\-A\-I\-R} +\begin{DoxyCompactList}\small\item\em Base pair data structure used in subopt.\-c. \end{DoxyCompactList}\item +struct \hyperlink{structINTERVAL}{I\-N\-T\-E\-R\-V\-A\-L} +\begin{DoxyCompactList}\small\item\em Sequence interval stack element used in subopt.\-c. \end{DoxyCompactList}\item +struct \hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N} +\begin{DoxyCompactList}\small\item\em Solution element from subopt.\-c. \end{DoxyCompactList}\item +struct \hyperlink{structcofoldF}{cofold\-F} +\item +struct \hyperlink{structConcEnt}{Conc\-Ent} +\item +struct \hyperlink{structpairpro}{pairpro} +\item +struct \hyperlink{structpair__info}{pair\-\_\-info} +\begin{DoxyCompactList}\small\item\em A base pair info structure. \end{DoxyCompactList}\item +struct \hyperlink{structmove__t}{move\-\_\-t} +\item +struct \hyperlink{structintermediate__t}{intermediate\-\_\-t} +\item +struct \hyperlink{structpath__t}{path\-\_\-t} +\item +struct \hyperlink{structpu__contrib}{pu\-\_\-contrib} +\begin{DoxyCompactList}\small\item\em contributions to p\-\_\-u \end{DoxyCompactList}\item +struct \hyperlink{structinteract}{interact} +\item +struct \hyperlink{structpu__out}{pu\-\_\-out} +\begin{DoxyCompactList}\small\item\em Collection of all free\-\_\-energy of beeing unpaired values for output. \end{DoxyCompactList}\item +struct \hyperlink{structconstrain}{constrain} +\begin{DoxyCompactList}\small\item\em constraints for cofolding \end{DoxyCompactList}\item +struct \hyperlink{structduplexT}{duplex\-T} +\item +struct \hyperlink{structfolden}{folden} +\item +struct \hyperlink{structsnoopT}{snoop\-T} +\item +struct \hyperlink{structdupVar}{dup\-Var} +\item +struct \hyperlink{structTwoDfold__solution}{Two\-Dfold\-\_\-solution} +\begin{DoxyCompactList}\small\item\em Solution element returned from Two\-Dfold\-List. \end{DoxyCompactList}\item +struct \hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} +\begin{DoxyCompactList}\small\item\em Variables compound for 2\-Dfold M\-F\-E folding. \end{DoxyCompactList}\item +struct \hyperlink{structTwoDpfold__solution}{Two\-Dpfold\-\_\-solution} +\begin{DoxyCompactList}\small\item\em Solution element returned from Two\-Dpfold\-List. \end{DoxyCompactList}\item +struct \hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} +\begin{DoxyCompactList}\small\item\em Variables compound for 2\-Dfold partition function folding. \end{DoxyCompactList}\end{DoxyCompactItemize} +\subsection*{Macros} +\begin{DoxyCompactItemize} +\item +\hypertarget{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{\#define \hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{M\-A\-X\-A\-L\-P\-H\-A}~20}\label{data__structures_8h_a05a5ffe718aa431d97419a12fb082379} + +\begin{DoxyCompactList}\small\item\em Maximal length of alphabet. \end{DoxyCompactList}\item +\hypertarget{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}{\#define \hyperlink{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}{M\-A\-X\-D\-O\-S}~1000}\label{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89} + +\begin{DoxyCompactList}\small\item\em Maximum density of states discretization for subopt. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +All datastructures and typedefs shared among the Vienna R\-N\-A Package can be found here. \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/data__structures_8h__dep__incl.md5 b/binaries/src/ViennaRNA/doc/latex/data__structures_8h__dep__incl.md5 new file mode 100644 index 0000000..899a712 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/data__structures_8h__dep__incl.md5 @@ -0,0 +1 @@ +35557042722c97039374fbd41f90bb8d \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/data__structures_8h__dep__incl.pdf 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\_\_VIENNA\_RNA\_PACKAGE\_DATA\_STRUCTURES\_H\_\_} +00003 \textcolor{preprocessor}{} +00004 \textcolor{preprocessor}{#include "\hyperlink{energy__const_8h}{energy\_const.h}"} +00010 \textcolor{comment}{/* to use floats instead of doubles in pf\_fold() comment next line */} +00011 \textcolor{preprocessor}{#define LARGE\_PF} +00012 \textcolor{preprocessor}{}\textcolor{preprocessor}{#ifdef LARGE\_PF} +00013 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define FLT\_OR\_DBL double} +00014 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else} +00015 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define FLT\_OR\_DBL float} +00016 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif} +00017 \textcolor{preprocessor}{} +00018 \textcolor{preprocessor}{#ifndef NBASES} +00019 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define NBASES 8} +00020 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif} +00021 \textcolor{preprocessor}{} +00022 \textcolor{preprocessor}{#ifndef MAXALPHA} +00023 \textcolor{preprocessor}{} +\hypertarget{data__structures_8h_source_l00026}{}\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{00026} \textcolor{preprocessor}{#define MAXALPHA 20} +00027 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif} +00028 \textcolor{preprocessor}{} +\hypertarget{data__structures_8h_source_l00032}{}\hyperlink{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}{00032} \textcolor{preprocessor}{#define MAXDOS 1000} +00033 \textcolor{preprocessor}{} +00034 \textcolor{preprocessor}{#define VRNA\_GQUAD\_MAX\_STACK\_SIZE 7} +00035 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define VRNA\_GQUAD\_MIN\_STACK\_SIZE 2} +00036 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define VRNA\_GQUAD\_MAX\_LINKER\_LENGTH 15} +00037 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define VRNA\_GQUAD\_MIN\_LINKER\_LENGTH 1} +00038 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define VRNA\_GQUAD\_MIN\_BOX\_SIZE ((4*VRNA\_GQUAD\_MIN\_STACK\_SIZE)+(3*VRNA\_GQUAD\_MIN\_LINKER\_LENGTH))} +00039 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define VRNA\_GQUAD\_MAX\_BOX\_SIZE ((4*VRNA\_GQUAD\_MAX\_STACK\_SIZE)+(3*VRNA\_GQUAD\_MAX\_LINKER\_LENGTH))} +00040 \textcolor{preprocessor}{} +00041 +00042 \textcolor{comment}{/*} +00043 \textcolor{comment}{* ############################################################} +00044 \textcolor{comment}{* Here are the type definitions of various datastructures} +00045 \textcolor{comment}{* shared among the Vienna RNA Package} +00046 \textcolor{comment}{* ############################################################} +00047 \textcolor{comment}{*/} +00048 +\hypertarget{data__structures_8h_source_l00052}{}\hyperlink{structplist}{00052} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structplist}{plist} \{ +00053 \textcolor{keywordtype}{int} i; +00054 \textcolor{keywordtype}{int} j; +00055 \textcolor{keywordtype}{float} p; +00056 \textcolor{keywordtype}{int} type; +00057 \} \hyperlink{structplist}{plist}; +00058 +\hypertarget{data__structures_8h_source_l00062}{}\hyperlink{structcpair}{00062} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structcpair}{cpair} \{ +00063 \textcolor{keywordtype}{int} i,j,mfe; +00064 \textcolor{keywordtype}{float} p, hue, sat; +00065 \} \hyperlink{structcpair}{cpair}; +00066 +\hypertarget{data__structures_8h_source_l00071}{}\hyperlink{structCOORDINATE}{00071} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{ +00072 \textcolor{keywordtype}{float} X; \textcolor{comment}{/* X coords */} +00073 \textcolor{keywordtype}{float} Y; \textcolor{comment}{/* Y coords */} +00074 \} \hyperlink{structCOORDINATE}{COORDINATE}; +00075 +\hypertarget{data__structures_8h_source_l00079}{}\hyperlink{structsect}{00079} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structsect}{sect} \{ +00080 \textcolor{keywordtype}{int} i; +00081 \textcolor{keywordtype}{int} j; +00082 \textcolor{keywordtype}{int} ml; +00083 \} \hyperlink{structsect}{sect}; +00084 +\hypertarget{data__structures_8h_source_l00088}{}\hyperlink{structbondT}{00088} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structbondT}{bondT} \{ +00089 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} i; +00090 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} j; +00091 \} \hyperlink{structbondT}{bondT}; +00092 +\hypertarget{data__structures_8h_source_l00096}{}\hyperlink{structbondTEn}{00096} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structbondTEn}{bondTEn} \{ +00097 \textcolor{keywordtype}{int} i; +00098 \textcolor{keywordtype}{int} j; +00099 \textcolor{keywordtype}{int} energy; +00100 \} \hyperlink{structbondTEn}{bondTEn}; +00101 +\hypertarget{data__structures_8h_source_l00106}{}\hyperlink{structmodel__detailsT}{00106} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{ +\hypertarget{data__structures_8h_source_l00107}{}\hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{00107} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}; +\hypertarget{data__structures_8h_source_l00113}{}\hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{00113} \textcolor{keywordtype}{int} \hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{special\_hp}; +\hypertarget{data__structures_8h_source_l00114}{}\hyperlink{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{00114} \textcolor{keywordtype}{int} \hyperlink{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{noLP}; +\hypertarget{data__structures_8h_source_l00115}{}\hyperlink{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{00115} \textcolor{keywordtype}{int} \hyperlink{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{noGU}; +\hypertarget{data__structures_8h_source_l00116}{}\hyperlink{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}{00116} \textcolor{keywordtype}{int} \hyperlink{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}{noGUclosure}; +\hypertarget{data__structures_8h_source_l00117}{}\hyperlink{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}{00117} \textcolor{keywordtype}{int} \hyperlink{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}{logML}; +\hypertarget{data__structures_8h_source_l00118}{}\hyperlink{structmodel__detailsT_a55f083dad18c216505805a8062e63074}{00118} \textcolor{keywordtype}{int} \hyperlink{structmodel__detailsT_a55f083dad18c216505805a8062e63074}{circ}; +\hypertarget{data__structures_8h_source_l00119}{}\hyperlink{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}{00119} \textcolor{keywordtype}{int} \hyperlink{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}{gquad}; +00120 \} \hyperlink{structmodel__detailsT}{model\_detailsT}; +00121 +\hypertarget{data__structures_8h_source_l00125}{}\hyperlink{structparamT}{00125} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{ +00126 \textcolor{keywordtype}{int} id; +00127 \textcolor{keywordtype}{int} stack[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1]; +00128 \textcolor{keywordtype}{int} hairpin[31]; +00129 \textcolor{keywordtype}{int} bulge[\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1]; +00130 \textcolor{keywordtype}{int} internal\_loop[\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1]; +00131 \textcolor{keywordtype}{int} mismatchExt[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00132 \textcolor{keywordtype}{int} mismatchI[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00133 \textcolor{keywordtype}{int} mismatch1nI[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00134 \textcolor{keywordtype}{int} mismatch23I[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00135 \textcolor{keywordtype}{int} mismatchH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00136 \textcolor{keywordtype}{int} mismatchM[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00137 \textcolor{keywordtype}{int} dangle5[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5]; +00138 \textcolor{keywordtype}{int} dangle3[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5]; +00139 \textcolor{keywordtype}{int} int11[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00140 \textcolor{keywordtype}{int} int21[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5]; +00141 \textcolor{keywordtype}{int} int22[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5][5]; +00142 \textcolor{keywordtype}{int} ninio[5]; +00143 \textcolor{keywordtype}{double} lxc; +00144 \textcolor{keywordtype}{int} MLbase; +00145 \textcolor{keywordtype}{int} MLintern[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1]; +00146 \textcolor{keywordtype}{int} MLclosing; +00147 \textcolor{keywordtype}{int} TerminalAU; +00148 \textcolor{keywordtype}{int} DuplexInit; +00149 \textcolor{keywordtype}{int} Tetraloop\_E[200]; +00150 \textcolor{keywordtype}{char} Tetraloops[1401]; +00151 \textcolor{keywordtype}{int} Triloop\_E[40]; +00152 \textcolor{keywordtype}{char} Triloops[241]; +00153 \textcolor{keywordtype}{int} Hexaloop\_E[40]; +00154 \textcolor{keywordtype}{char} Hexaloops[1801]; +00155 \textcolor{keywordtype}{int} TripleC; +00156 \textcolor{keywordtype}{int} MultipleCA; +00157 \textcolor{keywordtype}{int} MultipleCB; +00158 \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_a25f2bdcdf56e813d288845484a13d704}{gquad} [VRNA\_GQUAD\_MAX\_STACK\_SIZE + 1] +00159 [3*VRNA\_GQUAD\_MAX\_LINKER\_LENGTH + 1]; +00160 +\hypertarget{data__structures_8h_source_l00161}{}\hyperlink{structparamT_a8ed207b95868d1085bd9c197fbc6924f}{00161} \textcolor{keywordtype}{double} \hyperlink{structparamT_a8ed207b95868d1085bd9c197fbc6924f}{temperature}; +\hypertarget{data__structures_8h_source_l00163}{}\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{00163} \hyperlink{structmodel__detailsT}{model\_detailsT} \hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model\_details}; +00165 \} \hyperlink{structparamT}{paramT}; +00166 +\hypertarget{data__structures_8h_source_l00170}{}\hyperlink{structpf__paramT}{00170} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{ +00171 \textcolor{keywordtype}{int} id; +00172 \textcolor{keywordtype}{double} expstack[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1]; +00173 \textcolor{keywordtype}{double} exphairpin[31]; +00174 \textcolor{keywordtype}{double} expbulge[\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1]; +00175 \textcolor{keywordtype}{double} expinternal[\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1]; +00176 \textcolor{keywordtype}{double} expmismatchExt[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00177 \textcolor{keywordtype}{double} expmismatchI[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00178 \textcolor{keywordtype}{double} expmismatch23I[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00179 \textcolor{keywordtype}{double} expmismatch1nI[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00180 \textcolor{keywordtype}{double} expmismatchH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00181 \textcolor{keywordtype}{double} expmismatchM[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00182 \textcolor{keywordtype}{double} expdangle5[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5]; +00183 \textcolor{keywordtype}{double} expdangle3[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5]; +00184 \textcolor{keywordtype}{double} expint11[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00185 \textcolor{keywordtype}{double} expint21[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5]; +00186 \textcolor{keywordtype}{double} expint22[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5][5]; +00187 \textcolor{keywordtype}{double} expninio[5][\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}+1]; +00188 \textcolor{keywordtype}{double} lxc; +00189 \textcolor{keywordtype}{double} expMLbase; +00190 \textcolor{keywordtype}{double} expMLintern[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1]; +00191 \textcolor{keywordtype}{double} expMLclosing; +00192 \textcolor{keywordtype}{double} expTermAU; +00193 \textcolor{keywordtype}{double} expDuplexInit; +00194 \textcolor{keywordtype}{double} exptetra[40]; +00195 \textcolor{keywordtype}{double} exptri[40]; +00196 \textcolor{keywordtype}{double} exphex[40]; +00197 \textcolor{keywordtype}{char} Tetraloops[1401]; +00198 \textcolor{keywordtype}{double} expTriloop[40]; +00199 \textcolor{keywordtype}{char} Triloops[241]; +00200 \textcolor{keywordtype}{char} Hexaloops[1801]; +00201 \textcolor{keywordtype}{double} expTripleC; +00202 \textcolor{keywordtype}{double} expMultipleCA; +00203 \textcolor{keywordtype}{double} expMultipleCB; +00204 \textcolor{keywordtype}{double} expgquad[VRNA\_GQUAD\_MAX\_STACK\_SIZE + 1] +00205 [3*VRNA\_GQUAD\_MAX\_LINKER\_LENGTH + 1]; +00206 +00207 \textcolor{keywordtype}{double} kT; +\hypertarget{data__structures_8h_source_l00208}{}\hyperlink{structpf__paramT_aef40322e7ca1adbd9b438aeda0352e8f}{00208} \textcolor{keywordtype}{double} \hyperlink{structpf__paramT_aef40322e7ca1adbd9b438aeda0352e8f}{pf\_scale}; +\hypertarget{data__structures_8h_source_l00210}{}\hyperlink{structpf__paramT_aa0e11e9f1f6e212640baf40d7195a014}{00210} \textcolor{keywordtype}{double} \hyperlink{structpf__paramT_aa0e11e9f1f6e212640baf40d7195a014}{temperature}; +\hypertarget{data__structures_8h_source_l00211}{}\hyperlink{structpf__paramT_a3d2af9040acfa08295efb50f0219149d}{00211} \textcolor{keywordtype}{double} alpha; +\hypertarget{data__structures_8h_source_l00218}{}\hyperlink{structpf__paramT_a43ec875779c5e7c8bf5fa7e837ec6d09}{00218} \hyperlink{structmodel__detailsT}{model\_detailsT} \hyperlink{structpf__paramT_a43ec875779c5e7c8bf5fa7e837ec6d09}{model\_details}; +00220 \} \hyperlink{structpf__paramT}{pf\_paramT}; +00221 +00222 +00223 +00224 \textcolor{comment}{/*} +00225 \textcolor{comment}{* ############################################################} +00226 \textcolor{comment}{* SUBOPT data structures} +00227 \textcolor{comment}{* ############################################################} +00228 \textcolor{comment}{*/} +00229 +00230 +\hypertarget{data__structures_8h_source_l00234}{}\hyperlink{structPAIR}{00234} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{ +00235 \textcolor{keywordtype}{int} i; +00236 \textcolor{keywordtype}{int} j; +00237 \} \hyperlink{structPAIR}{PAIR}; +00238 +\hypertarget{data__structures_8h_source_l00242}{}\hyperlink{structINTERVAL}{00242} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{ +00243 \textcolor{keywordtype}{int} i; +00244 \textcolor{keywordtype}{int} j; +00245 \textcolor{keywordtype}{int} array\_flag; +00246 \} \hyperlink{structINTERVAL}{INTERVAL}; +00247 +\hypertarget{data__structures_8h_source_l00251}{}\hyperlink{structSOLUTION}{00251} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{ +\hypertarget{data__structures_8h_source_l00252}{}\hyperlink{structSOLUTION_a4fe8e9027171f2dc4031587d7fab6b87}{00252} \textcolor{keywordtype}{float} \hyperlink{structSOLUTION_a4fe8e9027171f2dc4031587d7fab6b87}{energy}; +\hypertarget{data__structures_8h_source_l00253}{}\hyperlink{structSOLUTION_a89ae453dfad0509468c39a62c303a63b}{00253} \textcolor{keywordtype}{char} *\hyperlink{structSOLUTION_a89ae453dfad0509468c39a62c303a63b}{structure}; +00254 \} \hyperlink{structSOLUTION}{SOLUTION}; +00255 +00256 \textcolor{comment}{/*} +00257 \textcolor{comment}{* ############################################################} +00258 \textcolor{comment}{* COFOLD data structures} +00259 \textcolor{comment}{* ############################################################} +00260 \textcolor{comment}{*/} +00261 +\hypertarget{data__structures_8h_source_l00265}{}\hyperlink{structcofoldF}{00265} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structcofoldF}{cofoldF} \{ +00266 \textcolor{comment}{/* free energies for: */} +\hypertarget{data__structures_8h_source_l00267}{}\hyperlink{structcofoldF_af6c496438321eb8bb907a21de1915c23}{00267} \textcolor{keywordtype}{double} \hyperlink{structcofoldF_af6c496438321eb8bb907a21de1915c23}{F0AB}; +\hypertarget{data__structures_8h_source_l00268}{}\hyperlink{structcofoldF_a2ae1245ff4a93cd11f882f490f777cb7}{00268} \textcolor{keywordtype}{double} \hyperlink{structcofoldF_a2ae1245ff4a93cd11f882f490f777cb7}{FAB}; +\hypertarget{data__structures_8h_source_l00269}{}\hyperlink{structcofoldF_a4899a4f9b42e416baf46c5fe10751c45}{00269} \textcolor{keywordtype}{double} \hyperlink{structcofoldF_a4899a4f9b42e416baf46c5fe10751c45}{FcAB}; +\hypertarget{data__structures_8h_source_l00270}{}\hyperlink{structcofoldF_a460f3ba205c205e6f5ec27cc2e2eb2b2}{00270} \textcolor{keywordtype}{double} \hyperlink{structcofoldF_a460f3ba205c205e6f5ec27cc2e2eb2b2}{FA}; +\hypertarget{data__structures_8h_source_l00271}{}\hyperlink{structcofoldF_ad3e5466724f3987be9d6f388b8ee5129}{00271} \textcolor{keywordtype}{double} \hyperlink{structcofoldF_ad3e5466724f3987be9d6f388b8ee5129}{FB}; +00272 \} \hyperlink{structcofoldF}{cofoldF}; +00273 +\hypertarget{data__structures_8h_source_l00277}{}\hyperlink{structConcEnt}{00277} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structConcEnt}{ConcEnt} \{ +\hypertarget{data__structures_8h_source_l00278}{}\hyperlink{structConcEnt_adcf4d93c7efeaa4e6c4154b64d367681}{00278} \textcolor{keywordtype}{double} \hyperlink{structConcEnt_adcf4d93c7efeaa4e6c4154b64d367681}{A0}; +\hypertarget{data__structures_8h_source_l00279}{}\hyperlink{structConcEnt_add4c33b94b34e847fbf5838b04cce346}{00279} \textcolor{keywordtype}{double} \hyperlink{structConcEnt_add4c33b94b34e847fbf5838b04cce346}{B0}; +\hypertarget{data__structures_8h_source_l00280}{}\hyperlink{structConcEnt_ac59c07a31d844e7b05bcdc05c4413b19}{00280} \textcolor{keywordtype}{double} \hyperlink{structConcEnt_ac59c07a31d844e7b05bcdc05c4413b19}{ABc}; +00281 \textcolor{keywordtype}{double} AAc; +00282 \textcolor{keywordtype}{double} BBc; +00283 \textcolor{keywordtype}{double} Ac; +00284 \textcolor{keywordtype}{double} Bc; +00285 \} \hyperlink{structConcEnt}{ConcEnt}; +00286 +\hypertarget{data__structures_8h_source_l00290}{}\hyperlink{structpairpro}{00290} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structpairpro}{pairpro}\{ +00291 \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *AB; +00292 \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *AA; +00293 \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *A; +00294 \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *B; +00295 \textcolor{keyword}{struct }\hyperlink{structplist}{plist} *BB; +00296 \}\hyperlink{structpairpro}{pairpro}; +00297 +\hypertarget{data__structures_8h_source_l00308}{}\hyperlink{structpair__info}{00308} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{ +\hypertarget{data__structures_8h_source_l00309}{}\hyperlink{structpair__info_a7905e17da6a6cc48230ee6205628ed7f}{00309} \textcolor{keywordtype}{unsigned} \hyperlink{structpair__info_a7905e17da6a6cc48230ee6205628ed7f}{i}; +\hypertarget{data__structures_8h_source_l00310}{}\hyperlink{structpair__info_a35665817b5792703ff4325e1bcbe5e21}{00310} \textcolor{keywordtype}{unsigned} \hyperlink{structpair__info_a35665817b5792703ff4325e1bcbe5e21}{j}; +\hypertarget{data__structures_8h_source_l00311}{}\hyperlink{structpair__info_af0895ea40ec0c23bfe8aa2c3babf0e80}{00311} \textcolor{keywordtype}{float} \hyperlink{structpair__info_af0895ea40ec0c23bfe8aa2c3babf0e80}{p}; +\hypertarget{data__structures_8h_source_l00312}{}\hyperlink{structpair__info_ab3aa7a54e6976f46e69c6ffcddd0e782}{00312} \textcolor{keywordtype}{float} \hyperlink{structpair__info_ab3aa7a54e6976f46e69c6ffcddd0e782}{ent}; +\hypertarget{data__structures_8h_source_l00313}{}\hyperlink{structpair__info_a23fc316453d179474bed7f6ed2489723}{00313} \textcolor{keywordtype}{short} bp[8]; +\hypertarget{data__structures_8h_source_l00314}{}\hyperlink{structpair__info_a4da3d6c9042500c16c4b06e0bbc48190}{00314} \textcolor{keywordtype}{char} \hyperlink{structpair__info_a4da3d6c9042500c16c4b06e0bbc48190}{comp}; +00315 \} \hyperlink{structpair__info}{pair\_info}; +00316 +00317 +00318 \textcolor{comment}{/*} +00319 \textcolor{comment}{* ############################################################} +00320 \textcolor{comment}{* FINDPATH data structures} +00321 \textcolor{comment}{* ############################################################} +00322 \textcolor{comment}{*/} +00323 +\hypertarget{data__structures_8h_source_l00327}{}\hyperlink{structmove__t}{00327} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }move \{ +00328 \textcolor{keywordtype}{int} i; \textcolor{comment}{/* i,j>0 insert; i,j<0 delete */} +00329 \textcolor{keywordtype}{int} j; +00330 \textcolor{keywordtype}{int} when; \textcolor{comment}{/* 0 if still available, else resulting distance from start */} +00331 \textcolor{keywordtype}{int} E; +00332 \} \hyperlink{structmove__t}{move\_t}; +00333 +\hypertarget{data__structures_8h_source_l00337}{}\hyperlink{structintermediate__t}{00337} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }intermediate \{ +\hypertarget{data__structures_8h_source_l00338}{}\hyperlink{structintermediate__t_a9a2b6258aa1af06ea3504631de8dadba}{00338} \textcolor{keywordtype}{short} *\hyperlink{structintermediate__t_a9a2b6258aa1af06ea3504631de8dadba}{pt}; +\hypertarget{data__structures_8h_source_l00339}{}\hyperlink{structintermediate__t_ac44e091915da58927978d54ef59234c7}{00339} \textcolor{keywordtype}{int} \hyperlink{structintermediate__t_ac44e091915da58927978d54ef59234c7}{Sen}; +\hypertarget{data__structures_8h_source_l00340}{}\hyperlink{structintermediate__t_af84d640df33aea99e959b2e4f61a7367}{00340} \textcolor{keywordtype}{int} \hyperlink{structintermediate__t_af84d640df33aea99e959b2e4f61a7367}{curr\_en}; +\hypertarget{data__structures_8h_source_l00341}{}\hyperlink{structintermediate__t_a94e947f18273bbfe3dd544085b025a7b}{00341} \hyperlink{structmove__t}{move\_t} *\hyperlink{structintermediate__t_a94e947f18273bbfe3dd544085b025a7b}{moves}; +00342 \} \hyperlink{structintermediate__t}{intermediate\_t}; +00343 +\hypertarget{data__structures_8h_source_l00347}{}\hyperlink{structpath__t}{00347} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }path \{ +00348 \textcolor{keywordtype}{double} en; +00349 \textcolor{keywordtype}{char} *s; +00350 \} \hyperlink{structpath__t}{path\_t}; +00351 +00352 \textcolor{comment}{/*} +00353 \textcolor{comment}{* ############################################################} +00354 \textcolor{comment}{* RNAup data structures} +00355 \textcolor{comment}{* ############################################################} +00356 \textcolor{comment}{*/} +00357 +\hypertarget{data__structures_8h_source_l00361}{}\hyperlink{structpu__contrib}{00361} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structpu__contrib}{pu\_contrib} \{ +\hypertarget{data__structures_8h_source_l00362}{}\hyperlink{structpu__contrib_ac9034ac9a84ed0647587659d6e9be1e8}{00362} \textcolor{keywordtype}{double} **\hyperlink{structpu__contrib_ac9034ac9a84ed0647587659d6e9be1e8}{H}; +\hypertarget{data__structures_8h_source_l00363}{}\hyperlink{structpu__contrib_a8ca0da20536780589fb3e3472ca0581f}{00363} \textcolor{keywordtype}{double} **\hyperlink{structpu__contrib_a8ca0da20536780589fb3e3472ca0581f}{I}; +\hypertarget{data__structures_8h_source_l00364}{}\hyperlink{structpu__contrib_a1222ebf74f426bbcd843dcc325da207b}{00364} \textcolor{keywordtype}{double} **\hyperlink{structpu__contrib_a1222ebf74f426bbcd843dcc325da207b}{M}; +\hypertarget{data__structures_8h_source_l00365}{}\hyperlink{structpu__contrib_accb192ba6b4b91a1cb2f8080934fd428}{00365} \textcolor{keywordtype}{double} **\hyperlink{structpu__contrib_accb192ba6b4b91a1cb2f8080934fd428}{E}; +\hypertarget{data__structures_8h_source_l00366}{}\hyperlink{structpu__contrib_a33d5ada6e861db0c81aa3d5b2989262e}{00366} \textcolor{keywordtype}{int} \hyperlink{structpu__contrib_a33d5ada6e861db0c81aa3d5b2989262e}{length}; +\hypertarget{data__structures_8h_source_l00367}{}\hyperlink{structpu__contrib_a403c1c7f20beeeffba7632fac0cfcbff}{00367} \textcolor{keywordtype}{int} \hyperlink{structpu__contrib_a403c1c7f20beeeffba7632fac0cfcbff}{w}; +00368 \} \hyperlink{structpu__contrib}{pu\_contrib}; +00369 +\hypertarget{data__structures_8h_source_l00373}{}\hyperlink{structinteract}{00373} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structinteract}{interact} \{ +\hypertarget{data__structures_8h_source_l00374}{}\hyperlink{structinteract_a1fc8b3860c083f164daa9712690a3a56}{00374} \textcolor{keywordtype}{double} *\hyperlink{structinteract_a1fc8b3860c083f164daa9712690a3a56}{Pi}; +\hypertarget{data__structures_8h_source_l00375}{}\hyperlink{structinteract_a54f8183542fff4c32ab7ace49a16c02c}{00375} \textcolor{keywordtype}{double} *\hyperlink{structinteract_a54f8183542fff4c32ab7ace49a16c02c}{Gi}; +\hypertarget{data__structures_8h_source_l00376}{}\hyperlink{structinteract_ad58303190f9e085c3ab59890cbf61223}{00376} \textcolor{keywordtype}{double} \hyperlink{structinteract_ad58303190f9e085c3ab59890cbf61223}{Gikjl}; +\hypertarget{data__structures_8h_source_l00378}{}\hyperlink{structinteract_a41793812abae560805414761fec398fe}{00378} \textcolor{keywordtype}{double} \hyperlink{structinteract_a41793812abae560805414761fec398fe}{Gikjl\_wo}; +\hypertarget{data__structures_8h_source_l00379}{}\hyperlink{structinteract_ab6d031a21388be8763b75ea74c937f17}{00379} \textcolor{keywordtype}{int} \hyperlink{structinteract_ab6d031a21388be8763b75ea74c937f17}{i}; +\hypertarget{data__structures_8h_source_l00380}{}\hyperlink{structinteract_a61e457fbf943d57364be6ddf1b4e7b8a}{00380} \textcolor{keywordtype}{int} \hyperlink{structinteract_a61e457fbf943d57364be6ddf1b4e7b8a}{k}; +\hypertarget{data__structures_8h_source_l00381}{}\hyperlink{structinteract_a7555cb6363d1479341eb72b9c087aa34}{00381} \textcolor{keywordtype}{int} \hyperlink{structinteract_a7555cb6363d1479341eb72b9c087aa34}{j}; +\hypertarget{data__structures_8h_source_l00382}{}\hyperlink{structinteract_a030ab45056342e12cb3955e4defd3904}{00382} \textcolor{keywordtype}{int} \hyperlink{structinteract_a030ab45056342e12cb3955e4defd3904}{l}; +\hypertarget{data__structures_8h_source_l00383}{}\hyperlink{structinteract_ac9fcb5dca54ec5faa76e02b6488b9524}{00383} \textcolor{keywordtype}{int} \hyperlink{structinteract_ac9fcb5dca54ec5faa76e02b6488b9524}{length}; +00384 \} \hyperlink{structinteract}{interact}; +00385 +\hypertarget{data__structures_8h_source_l00389}{}\hyperlink{structpu__out}{00389} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structpu__out}{pu\_out} \{ +\hypertarget{data__structures_8h_source_l00390}{}\hyperlink{structpu__out_a314b8f43c3ee0bf6060afbeced5dbe6c}{00390} \textcolor{keywordtype}{int} \hyperlink{structpu__out_a314b8f43c3ee0bf6060afbeced5dbe6c}{len}; +\hypertarget{data__structures_8h_source_l00391}{}\hyperlink{structpu__out_a7697bc7a46cd1b8e37e337e708cb6023}{00391} \textcolor{keywordtype}{int} \hyperlink{structpu__out_a7697bc7a46cd1b8e37e337e708cb6023}{u\_vals}; +\hypertarget{data__structures_8h_source_l00392}{}\hyperlink{structpu__out_a638b0de1837cfd441871d005d3ab2938}{00392} \textcolor{keywordtype}{int} \hyperlink{structpu__out_a638b0de1837cfd441871d005d3ab2938}{contribs}; +\hypertarget{data__structures_8h_source_l00393}{}\hyperlink{structpu__out_ac9e9e30b16e7d04c770460b8487fb09d}{00393} \textcolor{keywordtype}{char} **\hyperlink{structpu__out_ac9e9e30b16e7d04c770460b8487fb09d}{header}; +\hypertarget{data__structures_8h_source_l00394}{}\hyperlink{structpu__out_a366edbc4170d5c177908e178ff340828}{00394} \textcolor{keywordtype}{double} **\hyperlink{structpu__out_a366edbc4170d5c177908e178ff340828}{u\_values}; +00395 \} \hyperlink{structpu__out}{pu\_out}; +00396 +\hypertarget{data__structures_8h_source_l00400}{}\hyperlink{structconstrain}{00400} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structconstrain}{constrain}\{ +00401 \textcolor{keywordtype}{int} *indx; +00402 \textcolor{keywordtype}{char} *ptype; +00403 \} \hyperlink{structconstrain}{constrain}; +00404 +00405 \textcolor{comment}{/*} +00406 \textcolor{comment}{* ############################################################} +00407 \textcolor{comment}{* RNAduplex data structures} +00408 \textcolor{comment}{* ############################################################} +00409 \textcolor{comment}{*/} +00410 +\hypertarget{data__structures_8h_source_l00414}{}\hyperlink{structduplexT}{00414} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{ +00415 \textcolor{keywordtype}{int} i; +00416 \textcolor{keywordtype}{int} j; +00417 \textcolor{keywordtype}{int} end; +00418 \textcolor{keywordtype}{char} *structure; +00419 \textcolor{keywordtype}{double} energy; +00420 \textcolor{keywordtype}{double} energy\_backtrack; +00421 \textcolor{keywordtype}{double} opening\_backtrack\_x; +00422 \textcolor{keywordtype}{double} opening\_backtrack\_y; +00423 \textcolor{keywordtype}{int} offset; +00424 \textcolor{keywordtype}{double} dG1; +00425 \textcolor{keywordtype}{double} dG2; +00426 \textcolor{keywordtype}{double} ddG; +00427 \textcolor{keywordtype}{int} tb; +00428 \textcolor{keywordtype}{int} te; +00429 \textcolor{keywordtype}{int} qb; +00430 \textcolor{keywordtype}{int} qe; +00431 \} \hyperlink{structduplexT}{duplexT}; +00432 +00433 \textcolor{comment}{/*} +00434 \textcolor{comment}{* ############################################################} +00435 \textcolor{comment}{* RNAsnoop data structures} +00436 \textcolor{comment}{* ############################################################} +00437 \textcolor{comment}{*/} +00438 +\hypertarget{data__structures_8h_source_l00442}{}\hyperlink{structfolden}{00442} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }node \{ +00443 \textcolor{keywordtype}{int} k; +00444 \textcolor{keywordtype}{int} energy; +00445 \textcolor{keyword}{struct }node *next; +00446 \} \hyperlink{structfolden}{folden}; +00447 +\hypertarget{data__structures_8h_source_l00451}{}\hyperlink{structsnoopT}{00451} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{ +00452 \textcolor{keywordtype}{int} i; +00453 \textcolor{keywordtype}{int} j; +00454 \textcolor{keywordtype}{int} u; +00455 \textcolor{keywordtype}{char} *structure; +00456 \textcolor{keywordtype}{float} energy; +00457 \textcolor{keywordtype}{float} Duplex\_El; +00458 \textcolor{keywordtype}{float} Duplex\_Er; +00459 \textcolor{keywordtype}{float} Loop\_E; +00460 \textcolor{keywordtype}{float} Loop\_D; +00461 \textcolor{keywordtype}{float} pscd; +00462 \textcolor{keywordtype}{float} psct; +00463 \textcolor{keywordtype}{float} pscg; +00464 \textcolor{keywordtype}{float} Duplex\_Ol; +00465 \textcolor{keywordtype}{float} Duplex\_Or; +00466 \textcolor{keywordtype}{float} Duplex\_Ot; +00467 \textcolor{keywordtype}{float} fullStemEnergy; +00468 \} \hyperlink{structsnoopT}{snoopT}; +00469 +00470 +00471 +00472 +00473 +00474 +00475 +00476 \textcolor{comment}{/*} +00477 \textcolor{comment}{* ############################################################} +00478 \textcolor{comment}{* PKplex data structures} +00479 \textcolor{comment}{* ############################################################} +00480 \textcolor{comment}{*/} +00481 +\hypertarget{data__structures_8h_source_l00485}{}\hyperlink{structdupVar}{00485} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structdupVar}{dupVar}\{ +00486 \textcolor{keywordtype}{int} i; +00487 \textcolor{keywordtype}{int} j; +00488 \textcolor{keywordtype}{int} end; +00489 \textcolor{keywordtype}{char} *pk\_helix; +00490 \textcolor{keywordtype}{char} *structure; +00491 \textcolor{keywordtype}{double} energy; +00492 \textcolor{keywordtype}{int} offset; +00493 \textcolor{keywordtype}{double} dG1; +00494 \textcolor{keywordtype}{double} dG2; +00495 \textcolor{keywordtype}{double} ddG; +00496 \textcolor{keywordtype}{int} tb; +00497 \textcolor{keywordtype}{int} te; +00498 \textcolor{keywordtype}{int} qb; +00499 \textcolor{keywordtype}{int} qe; +00500 \textcolor{keywordtype}{int} inactive; +00501 \textcolor{keywordtype}{int} processed; +00502 \} \hyperlink{structdupVar}{dupVar}; +00503 +00504 +00505 +00506 \textcolor{comment}{/*} +00507 \textcolor{comment}{* ############################################################} +00508 \textcolor{comment}{* 2Dfold data structures} +00509 \textcolor{comment}{* ############################################################} +00510 \textcolor{comment}{*/} +00511 +\hypertarget{data__structures_8h_source_l00526}{}\hyperlink{structTwoDfold__solution}{00526} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{ +\hypertarget{data__structures_8h_source_l00527}{}\hyperlink{structTwoDfold__solution_a298767110e07490d361bf7da920fd153}{00527} \textcolor{keywordtype}{int} \hyperlink{structTwoDfold__solution_a298767110e07490d361bf7da920fd153}{k}; +\hypertarget{data__structures_8h_source_l00528}{}\hyperlink{structTwoDfold__solution_a64fb28259cf925c3bba7b8d14592363a}{00528} \textcolor{keywordtype}{int} \hyperlink{structTwoDfold__solution_a64fb28259cf925c3bba7b8d14592363a}{l}; +\hypertarget{data__structures_8h_source_l00529}{}\hyperlink{structTwoDfold__solution_a3f65891d0c931f88440150bb32bcf753}{00529} \textcolor{keywordtype}{float} \hyperlink{structTwoDfold__solution_a3f65891d0c931f88440150bb32bcf753}{en}; +\hypertarget{data__structures_8h_source_l00530}{}\hyperlink{structTwoDfold__solution_ac87e00bbdb13e0b6ef45c4f65608b416}{00530} \textcolor{keywordtype}{char} *\hyperlink{structTwoDfold__solution_ac87e00bbdb13e0b6ef45c4f65608b416}{s}; +00531 \} \hyperlink{structTwoDfold__solution}{TwoDfold\_solution}; +00532 +\hypertarget{data__structures_8h_source_l00538}{}\hyperlink{structTwoDfold__vars}{00538} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{ +\hypertarget{data__structures_8h_source_l00539}{}\hyperlink{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26}{00539} \hyperlink{structparamT}{paramT} *\hyperlink{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26}{P}; +\hypertarget{data__structures_8h_source_l00540}{}\hyperlink{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64}{00540} \textcolor{keywordtype}{int} \hyperlink{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64}{do\_backtrack}; +\hypertarget{data__structures_8h_source_l00541}{}\hyperlink{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208}{00541} \textcolor{keywordtype}{char} *\hyperlink{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208}{ptype}; +\hypertarget{data__structures_8h_source_l00542}{}\hyperlink{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56}{00542} \textcolor{keywordtype}{char} *\hyperlink{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56}{sequence}; +\hypertarget{data__structures_8h_source_l00543}{}\hyperlink{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc}{00543} \textcolor{keywordtype}{short} *S, *\hyperlink{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc}{S1}; +\hypertarget{data__structures_8h_source_l00544}{}\hyperlink{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb}{00544} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} \hyperlink{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb}{maxD1}; +\hypertarget{data__structures_8h_source_l00545}{}\hyperlink{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4}{00545} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} \hyperlink{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4}{maxD2}; +\hypertarget{data__structures_8h_source_l00548}{}\hyperlink{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5}{00548} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5}{mm1}; +\hypertarget{data__structures_8h_source_l00549}{}\hyperlink{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c}{00549} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c}{mm2}; +\hypertarget{data__structures_8h_source_l00551}{}\hyperlink{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7}{00551} \textcolor{keywordtype}{int} *\hyperlink{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7}{my\_iindx}; +00553 \textcolor{keywordtype}{double} \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}; +00554 +\hypertarget{data__structures_8h_source_l00555}{}\hyperlink{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18}{00555} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18}{referenceBPs1}; +\hypertarget{data__structures_8h_source_l00556}{}\hyperlink{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f}{00556} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f}{referenceBPs2}; +\hypertarget{data__structures_8h_source_l00557}{}\hyperlink{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0}{00557} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0}{bpdist}; +00559 \textcolor{keywordtype}{short} *reference\_pt1; +00560 \textcolor{keywordtype}{short} *reference\_pt2; +00561 \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ}; +00562 \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}; +00563 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} seq\_length; +00564 +00565 \textcolor{keywordtype}{int} ***E\_F5; +00566 \textcolor{keywordtype}{int} ***E\_F3; +00567 \textcolor{keywordtype}{int} ***E\_C; +00568 \textcolor{keywordtype}{int} ***E\_M; +00569 \textcolor{keywordtype}{int} ***E\_M1; +00570 \textcolor{keywordtype}{int} ***E\_M2; +00571 +00572 \textcolor{keywordtype}{int} **E\_Fc; +00573 \textcolor{keywordtype}{int} **E\_FcH; +00574 \textcolor{keywordtype}{int} **E\_FcI; +00575 \textcolor{keywordtype}{int} **E\_FcM; +00576 +00577 \textcolor{keywordtype}{int} **l\_min\_values; +00578 \textcolor{keywordtype}{int} **l\_max\_values; +00579 \textcolor{keywordtype}{int} *k\_min\_values; +00580 \textcolor{keywordtype}{int} *k\_max\_values; +00581 +00582 \textcolor{keywordtype}{int} **l\_min\_values\_m; +00583 \textcolor{keywordtype}{int} **l\_max\_values\_m; +00584 \textcolor{keywordtype}{int} *k\_min\_values\_m; +00585 \textcolor{keywordtype}{int} *k\_max\_values\_m; +00586 +00587 \textcolor{keywordtype}{int} **l\_min\_values\_m1; +00588 \textcolor{keywordtype}{int} **l\_max\_values\_m1; +00589 \textcolor{keywordtype}{int} *k\_min\_values\_m1; +00590 \textcolor{keywordtype}{int} *k\_max\_values\_m1; +00591 +00592 \textcolor{keywordtype}{int} **l\_min\_values\_f; +00593 \textcolor{keywordtype}{int} **l\_max\_values\_f; +00594 \textcolor{keywordtype}{int} *k\_min\_values\_f; +00595 \textcolor{keywordtype}{int} *k\_max\_values\_f; +00596 +00597 \textcolor{keywordtype}{int} **l\_min\_values\_f3; +00598 \textcolor{keywordtype}{int} **l\_max\_values\_f3; +00599 \textcolor{keywordtype}{int} *k\_min\_values\_f3; +00600 \textcolor{keywordtype}{int} *k\_max\_values\_f3; +00601 +00602 \textcolor{keywordtype}{int} **l\_min\_values\_m2; +00603 \textcolor{keywordtype}{int} **l\_max\_values\_m2; +00604 \textcolor{keywordtype}{int} *k\_min\_values\_m2; +00605 \textcolor{keywordtype}{int} *k\_max\_values\_m2; +00606 +00607 \textcolor{keywordtype}{int} *l\_min\_values\_fc; +00608 \textcolor{keywordtype}{int} *l\_max\_values\_fc; +00609 \textcolor{keywordtype}{int} k\_min\_values\_fc; +00610 \textcolor{keywordtype}{int} k\_max\_values\_fc; +00611 +00612 \textcolor{keywordtype}{int} *l\_min\_values\_fcH; +00613 \textcolor{keywordtype}{int} *l\_max\_values\_fcH; +00614 \textcolor{keywordtype}{int} k\_min\_values\_fcH; +00615 \textcolor{keywordtype}{int} k\_max\_values\_fcH; +00616 +00617 \textcolor{keywordtype}{int} *l\_min\_values\_fcI; +00618 \textcolor{keywordtype}{int} *l\_max\_values\_fcI; +00619 \textcolor{keywordtype}{int} k\_min\_values\_fcI; +00620 \textcolor{keywordtype}{int} k\_max\_values\_fcI; +00621 +00622 \textcolor{keywordtype}{int} *l\_min\_values\_fcM; +00623 \textcolor{keywordtype}{int} *l\_max\_values\_fcM; +00624 \textcolor{keywordtype}{int} k\_min\_values\_fcM; +00625 \textcolor{keywordtype}{int} k\_max\_values\_fcM; +00626 +00627 \textcolor{comment}{/* auxilary arrays for remaining set of coarse graining (k,l) > (k\_max, l\_max) */} +00628 \textcolor{keywordtype}{int} *E\_F5\_rem; +00629 \textcolor{keywordtype}{int} *E\_F3\_rem; +00630 \textcolor{keywordtype}{int} *E\_C\_rem; +00631 \textcolor{keywordtype}{int} *E\_M\_rem; +00632 \textcolor{keywordtype}{int} *E\_M1\_rem; +00633 \textcolor{keywordtype}{int} *E\_M2\_rem; +00634 +00635 \textcolor{keywordtype}{int} E\_Fc\_rem; +00636 \textcolor{keywordtype}{int} E\_FcH\_rem; +00637 \textcolor{keywordtype}{int} E\_FcI\_rem; +00638 \textcolor{keywordtype}{int} E\_FcM\_rem; +00639 +00640 \textcolor{preprocessor}{#ifdef COUNT\_STATES} +00641 \textcolor{preprocessor}{} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long} ***N\_F5; +00642 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long} ***N\_C; +00643 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long} ***N\_M; +00644 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long} ***N\_M1; +00645 \textcolor{preprocessor}{#endif} +00646 \textcolor{preprocessor}{}\} \hyperlink{structTwoDfold__vars}{TwoDfold\_vars}; +00647 +\hypertarget{data__structures_8h_source_l00660}{}\hyperlink{structTwoDpfold__solution}{00660} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{ +\hypertarget{data__structures_8h_source_l00661}{}\hyperlink{structTwoDpfold__solution_a40ad24e311b193866111623dd1331567}{00661} \textcolor{keywordtype}{int} \hyperlink{structTwoDpfold__solution_a40ad24e311b193866111623dd1331567}{k}; +\hypertarget{data__structures_8h_source_l00662}{}\hyperlink{structTwoDpfold__solution_aeaad6adc35413c76a2e2f18d96a6508c}{00662} \textcolor{keywordtype}{int} \hyperlink{structTwoDpfold__solution_aeaad6adc35413c76a2e2f18d96a6508c}{l}; +\hypertarget{data__structures_8h_source_l00663}{}\hyperlink{structTwoDpfold__solution_af0bf3071502b4a4fa81eeb6dfacef94c}{00663} FLT\_OR\_DBL \hyperlink{structTwoDpfold__solution_af0bf3071502b4a4fa81eeb6dfacef94c}{q}; +00664 \} \hyperlink{structTwoDpfold__solution}{TwoDpfold\_solution}; +00665 +\hypertarget{data__structures_8h_source_l00672}{}\hyperlink{structTwoDpfold__vars}{00672} \textcolor{keyword}{typedef} \textcolor{keyword}{struct}\{ +00673 +00674 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} alloc; +\hypertarget{data__structures_8h_source_l00675}{}\hyperlink{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}{00675} \textcolor{keywordtype}{char} *\hyperlink{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}{ptype}; +\hypertarget{data__structures_8h_source_l00676}{}\hyperlink{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}{00676} \textcolor{keywordtype}{char} *\hyperlink{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}{sequence}; +\hypertarget{data__structures_8h_source_l00677}{}\hyperlink{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}{00677} \textcolor{keywordtype}{short} *S, *\hyperlink{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}{S1}; +\hypertarget{data__structures_8h_source_l00678}{}\hyperlink{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}{00678} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} \hyperlink{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}{maxD1}; +\hypertarget{data__structures_8h_source_l00679}{}\hyperlink{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}{00679} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} \hyperlink{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}{maxD2}; +00681 \textcolor{keywordtype}{double} \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}; \textcolor{comment}{/* temperature in last call to scale\_pf\_params */} +00682 \textcolor{keywordtype}{double} init\_temp; \textcolor{comment}{/* temperature in last call to scale\_pf\_params */} +00683 FLT\_OR\_DBL *scale; +00684 FLT\_OR\_DBL \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\_scale}; +00685 \hyperlink{structpf__paramT}{pf\_paramT} *pf\_params; \textcolor{comment}{/* holds all [unscaled] pf parameters */} +00686 +\hypertarget{data__structures_8h_source_l00687}{}\hyperlink{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}{00687} \textcolor{keywordtype}{int} *\hyperlink{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}{my\_iindx}; +\hypertarget{data__structures_8h_source_l00688}{}\hyperlink{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}{00688} \textcolor{keywordtype}{int} *\hyperlink{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}{jindx}; +00690 \textcolor{keywordtype}{short} *reference\_pt1; +00691 \textcolor{keywordtype}{short} *reference\_pt2; +00692 +\hypertarget{data__structures_8h_source_l00693}{}\hyperlink{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}{00693} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}{referenceBPs1}; +\hypertarget{data__structures_8h_source_l00694}{}\hyperlink{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}{00694} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}{referenceBPs2}; +\hypertarget{data__structures_8h_source_l00695}{}\hyperlink{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}{00695} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}{bpdist}; +\hypertarget{data__structures_8h_source_l00697}{}\hyperlink{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}{00697} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}{mm1}; +\hypertarget{data__structures_8h_source_l00698}{}\hyperlink{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}{00698} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *\hyperlink{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}{mm2}; +00700 \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ}; +00701 \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}; +00702 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} seq\_length; +00703 +00704 FLT\_OR\_DBL ***Q; +00705 FLT\_OR\_DBL ***Q\_B; +00706 FLT\_OR\_DBL ***Q\_M; +00707 FLT\_OR\_DBL ***Q\_M1; +00708 FLT\_OR\_DBL ***Q\_M2; +00709 +00710 FLT\_OR\_DBL **Q\_c; +00711 FLT\_OR\_DBL **Q\_cH; +00712 FLT\_OR\_DBL **Q\_cI; +00713 FLT\_OR\_DBL **Q\_cM; +00714 +00715 \textcolor{keywordtype}{int} **l\_min\_values; +00716 \textcolor{keywordtype}{int} **l\_max\_values; +00717 \textcolor{keywordtype}{int} *k\_min\_values; +00718 \textcolor{keywordtype}{int} *k\_max\_values; +00719 +00720 \textcolor{keywordtype}{int} **l\_min\_values\_b; +00721 \textcolor{keywordtype}{int} **l\_max\_values\_b; +00722 \textcolor{keywordtype}{int} *k\_min\_values\_b; +00723 \textcolor{keywordtype}{int} *k\_max\_values\_b; +00724 +00725 \textcolor{keywordtype}{int} **l\_min\_values\_m; +00726 \textcolor{keywordtype}{int} **l\_max\_values\_m; +00727 \textcolor{keywordtype}{int} *k\_min\_values\_m; +00728 \textcolor{keywordtype}{int} *k\_max\_values\_m; +00729 +00730 \textcolor{keywordtype}{int} **l\_min\_values\_m1; +00731 \textcolor{keywordtype}{int} **l\_max\_values\_m1; +00732 \textcolor{keywordtype}{int} *k\_min\_values\_m1; +00733 \textcolor{keywordtype}{int} *k\_max\_values\_m1; +00734 +00735 \textcolor{keywordtype}{int} **l\_min\_values\_m2; +00736 \textcolor{keywordtype}{int} **l\_max\_values\_m2; +00737 \textcolor{keywordtype}{int} *k\_min\_values\_m2; +00738 \textcolor{keywordtype}{int} *k\_max\_values\_m2; +00739 +00740 \textcolor{keywordtype}{int} *l\_min\_values\_qc; +00741 \textcolor{keywordtype}{int} *l\_max\_values\_qc; +00742 \textcolor{keywordtype}{int} k\_min\_values\_qc; +00743 \textcolor{keywordtype}{int} k\_max\_values\_qc; +00744 +00745 \textcolor{keywordtype}{int} *l\_min\_values\_qcH; +00746 \textcolor{keywordtype}{int} *l\_max\_values\_qcH; +00747 \textcolor{keywordtype}{int} k\_min\_values\_qcH; +00748 \textcolor{keywordtype}{int} k\_max\_values\_qcH; +00749 +00750 \textcolor{keywordtype}{int} *l\_min\_values\_qcI; +00751 \textcolor{keywordtype}{int} *l\_max\_values\_qcI; +00752 \textcolor{keywordtype}{int} k\_min\_values\_qcI; +00753 \textcolor{keywordtype}{int} k\_max\_values\_qcI; +00754 +00755 \textcolor{keywordtype}{int} *l\_min\_values\_qcM; +00756 \textcolor{keywordtype}{int} *l\_max\_values\_qcM; +00757 \textcolor{keywordtype}{int} k\_min\_values\_qcM; +00758 \textcolor{keywordtype}{int} k\_max\_values\_qcM; +00759 +00760 \textcolor{comment}{/* auxilary arrays for remaining set of coarse graining (k,l) > (k\_max, l\_max) */} +00761 FLT\_OR\_DBL *Q\_rem; +00762 FLT\_OR\_DBL *Q\_B\_rem; +00763 FLT\_OR\_DBL *Q\_M\_rem; +00764 FLT\_OR\_DBL *Q\_M1\_rem; +00765 FLT\_OR\_DBL *Q\_M2\_rem; +00766 +00767 FLT\_OR\_DBL Q\_c\_rem; +00768 FLT\_OR\_DBL Q\_cH\_rem; +00769 FLT\_OR\_DBL Q\_cI\_rem; +00770 FLT\_OR\_DBL Q\_cM\_rem; +00771 +00772 \} \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars}; +00773 +00774 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/deprecated.tex b/binaries/src/ViennaRNA/doc/latex/deprecated.tex new file mode 100644 index 0000000..146077a --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/deprecated.tex @@ -0,0 +1,60 @@ + +\begin{DoxyRefList} +\item[\label{deprecated__deprecated000008}% +\hypertarget{deprecated__deprecated000008}{}% +Global \hyperlink{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}{base\-\_\-pair} ]Do not use this variable anymore! +\item[\label{deprecated__deprecated000012}% +\hypertarget{deprecated__deprecated000012}{}% +Global \hyperlink{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{centroid} (int length, double $\ast$dist)]This function is deprecated and should not be used anymore as it is not threadsafe! +\item[\label{deprecated__deprecated000007}% +\hypertarget{deprecated__deprecated000007}{}% +Global \hyperlink{fold_8h_a657222e2758c46bf13b416ef3032e417}{energy\-\_\-of\-\_\-circ\-\_\-struct} (const char $\ast$string, const char $\ast$structure)]This function is deprecated and should not be used in future programs Use \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure()} instead! +\item[\label{deprecated__deprecated000005}% +\hypertarget{deprecated__deprecated000005}{}% +Global \hyperlink{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{energy\-\_\-of\-\_\-struct} (const char $\ast$string, const char $\ast$structure)]This function is deprecated and should not be used in future programs! Use \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure()} instead! +\item[\label{deprecated__deprecated000006}% +\hypertarget{deprecated__deprecated000006}{}% +Global \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy\-\_\-of\-\_\-struct\-\_\-pt} (const char $\ast$string, short $\ast$ptable, short $\ast$s, short $\ast$s1)]This function is deprecated and should not be used in future programs! Use \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\-\_\-of\-\_\-structure\-\_\-pt()} instead! +\item[\label{deprecated__deprecated000015}% +\hypertarget{deprecated__deprecated000015}{}% +Global \hyperlink{part__func_8h_a7b6ab474cc80accc48010ccfcc59f96b}{exp\-Hairpin\-Energy} (int u, int type, short si1, short sj1, const char $\ast$string)]Use \hyperlink{loop__energies_8h_a0e128184bb097dc2da33706f33b555a6}{exp\-\_\-\-E\-\_\-\-Hairpin()} from \hyperlink{loop__energies_8h}{loop\-\_\-energies.\-h} instead +\item[\label{deprecated__deprecated000014}% +\hypertarget{deprecated__deprecated000014}{}% +Global \hyperlink{part__func_8h_a68ba6f3a48e08ca131ab54621ce3a2d7}{exp\-Loop\-Energy} (int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)]Use \hyperlink{loop__energies_8h_aa5e98e524e2a41e290b942b09544bc9e}{exp\-\_\-\-E\-\_\-\-Int\-Loop()} from \hyperlink{loop__energies_8h}{loop\-\_\-energies.\-h} instead +\item[\label{deprecated__deprecated000016}% +\hypertarget{deprecated__deprecated000016}{}% +Global \hyperlink{part__func__co_8h_a334de3c96e2186abfbdc0eaea6d08b14}{get\-\_\-plist} (struct plist $\ast$pl, int length, double cut\-\_\-off)]\{ This function is deprecated and will be removed soon!\} use \hyperlink{group__pf__fold_ga03e15e831a31b1154855ab47edbdb019}{assign\-\_\-plist\-\_\-from\-\_\-pr()} instead! +\item[\label{deprecated__deprecated000003}% +\hypertarget{deprecated__deprecated000003}{}% +Global \hyperlink{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}{Hairpin\-E} (int size, int type, int si1, int sj1, const char $\ast$string)]\{This function is deprecated and will be removed soon. Use \hyperlink{loop__energies_8h_aa362183cf6db89a10cdb0f5c4bd180c6}{E\-\_\-\-Hairpin()} instead!\} +\item[\label{deprecated__deprecated000010}% +\hypertarget{deprecated__deprecated000010}{}% +Global \hyperlink{fold__vars_8h_a92089ae3a51b5d75a14ce9cc29cc8317}{iindx} ]Do not use this variable anymore! +\item[\label{deprecated__deprecated000017}% +\hypertarget{deprecated__deprecated000017}{}% +Global \hyperlink{part__func__co_8h_aa12dda9dd6179cdd22bcce87c0682c07}{init\-\_\-co\-\_\-pf\-\_\-fold} (int length)]\{ This function is deprecated and will be removed soon!\} +\item[\label{deprecated__deprecated000011}% +\hypertarget{deprecated__deprecated000011}{}% +Global \hyperlink{part__func_8h_a15176e23eceeff8c7d14eabcfec8a2af}{init\-\_\-pf\-\_\-fold} (int length)]This function is obsolete and will be removed soon! +\item[\label{deprecated__deprecated000001}% +\hypertarget{deprecated__deprecated000001}{}% +Global \hyperlink{cofold_8h_afee0c32208aa2ac97338b6e3fbad7fa5}{initialize\-\_\-cofold} (int length)]\{This function is obsolete and will be removed soon!\} +\item[\label{deprecated__deprecated000004}% +\hypertarget{deprecated__deprecated000004}{}% +Global \hyperlink{fold_8h_ac3f0a28d9cb609d388b155445073fd20}{initialize\-\_\-fold} (int length)]\{This function is deprecated and will be removed soon!\} +\item[\label{deprecated__deprecated000002}% +\hypertarget{deprecated__deprecated000002}{}% +Global \hyperlink{fold_8h_a2163034a25c6115d894b199e97e03f6c}{Loop\-Energy} (int n1, int n2, int type, int type\-\_\-2, int si1, int sj1, int sp1, int sq1)]\{This function is deprecated and will be removed soon. Use \hyperlink{loop__energies_8h_a3e5ad89f451254b1fe366d77aa8ff7bd}{E\-\_\-\-Int\-Loop()} instead!\} +\item[\label{deprecated__deprecated000018}% +\hypertarget{deprecated__deprecated000018}{}% +Global \hyperlink{profiledist_8h_a904c7eaf4a2413567c00ac4891749d18}{Make\-\_\-bp\-\_\-profile} (int length)]This function is deprecated and will be removed soon! See \hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\-\_\-bp\-\_\-profile\-\_\-bppm()} for a replacement +\item[\label{deprecated__deprecated000013}% +\hypertarget{deprecated__deprecated000013}{}% +Global \hyperlink{part__func_8h_ae9556ba7ded44fe2321b6f67c3fc02a3}{mean\-\_\-bp\-\_\-dist} (int length)]This function is not threadsafe and should not be used anymore. Use \hyperlink{group__pf__fold_ga79cbc375af65f11609feb6b055269e7d}{mean\-\_\-bp\-\_\-distance()} instead! +\item[\label{deprecated__deprecated000009}% +\hypertarget{deprecated__deprecated000009}{}% +Global \hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr} ]Do not use this variable anymore! +\item[\label{deprecated__deprecated000019}% +\hypertarget{deprecated__deprecated000019}{}% +Global \hyperlink{PS__dot_8h_a689a97a7e3b8a2df14728b8204d9d57b}{P\-S\-\_\-dot\-\_\-plot} (char $\ast$string, char $\ast$file)]This function is deprecated and will be removed soon! Use \hyperlink{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}{P\-S\-\_\-dot\-\_\-plot\-\_\-list()} instead! +\end{DoxyRefList} \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/dir_97aefd0d527b934f1d99a682da8fe6a9.tex b/binaries/src/ViennaRNA/doc/latex/dir_97aefd0d527b934f1d99a682da8fe6a9.tex new file mode 100644 index 0000000..c808dca --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/dir_97aefd0d527b934f1d99a682da8fe6a9.tex @@ -0,0 +1,32 @@ +\hypertarget{dir_97aefd0d527b934f1d99a682da8fe6a9}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib Directory Reference} +\label{dir_97aefd0d527b934f1d99a682da8fe6a9}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib Directory Reference@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib Directory Reference}} +} +Directory dependency graph for lib\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=134pt]{dir_97aefd0d527b934f1d99a682da8fe6a9_dep} +\end{center} +\end{figure} +\subsection*{Files} +\begin{DoxyCompactItemize} +\item +file \hyperlink{1_88_84__epars_8h}{1.\-8.\-4\-\_\-epars.\-h} +\begin{DoxyCompactList}\small\item\em Free energy parameters for parameter file conversion. \end{DoxyCompactList}\item +file \hyperlink{1_88_84__intloops_8h}{1.\-8.\-4\-\_\-intloops.\-h} +\begin{DoxyCompactList}\small\item\em Free energy parameters for interior loop contributions needed by the parameter file conversion functions. \end{DoxyCompactList}\item +file {\bfseries intl11.\-h} +\item +file {\bfseries intl11d\-H.\-h} +\item +file {\bfseries intl21.\-h} +\item +file {\bfseries intl21d\-H.\-h} +\item +file {\bfseries intl22.\-h} +\item +file {\bfseries intl22d\-H.\-h} +\item +file {\bfseries list.\-h} +\end{DoxyCompactItemize} diff --git 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include this file\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=350pt]{dist__vars_8h__dep__incl} +\end{center} +\end{figure} +\subsection*{Data Structures} +\begin{DoxyCompactItemize} +\item +struct \hyperlink{structPostorder__list}{Postorder\-\_\-list} +\item +struct \hyperlink{structTree}{Tree} +\item +struct \hyperlink{structswString}{sw\-String} +\end{DoxyCompactItemize} +\subsection*{Variables} +\begin{DoxyCompactItemize} +\item +int \hyperlink{dist__vars_8h_aa03194c513af6b860e7b33e370b82bdb}{edit\-\_\-backtrack} +\begin{DoxyCompactList}\small\item\em Produce an alignment of the two structures being compared by tracing the editing path giving the minimum distance. \end{DoxyCompactList}\item +\hypertarget{dist__vars_8h_ac1605fe3448ad0a0b809c4fb8f6a854a}{char $\ast$ \hyperlink{dist__vars_8h_ac1605fe3448ad0a0b809c4fb8f6a854a}{aligned\-\_\-line} \mbox{[}4\mbox{]}}\label{dist__vars_8h_ac1605fe3448ad0a0b809c4fb8f6a854a} + +\begin{DoxyCompactList}\small\item\em Contains the two aligned structures after a call to one of the distance functions with \hyperlink{dist__vars_8h_aa03194c513af6b860e7b33e370b82bdb}{edit\-\_\-backtrack} set to 1. \end{DoxyCompactList}\item +int \hyperlink{dist__vars_8h_ab65d8ff14c6937612212526a60f59b3c}{cost\-\_\-matrix} +\begin{DoxyCompactList}\small\item\em Specify the cost matrix to be used for distance calculations. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Global variables for Distance-\/\-Package. + +\subsection{Variable Documentation} +\hypertarget{dist__vars_8h_aa03194c513af6b860e7b33e370b82bdb}{\index{dist\-\_\-vars.\-h@{dist\-\_\-vars.\-h}!edit\-\_\-backtrack@{edit\-\_\-backtrack}} +\index{edit\-\_\-backtrack@{edit\-\_\-backtrack}!dist_vars.h@{dist\-\_\-vars.\-h}} +\subsubsection[{edit\-\_\-backtrack}]{\setlength{\rightskip}{0pt plus 5cm}int edit\-\_\-backtrack}}\label{dist__vars_8h_aa03194c513af6b860e7b33e370b82bdb} + + +Produce an alignment of the two structures being compared by tracing the editing path giving the minimum distance. + +set to 1 if you want backtracking \hypertarget{dist__vars_8h_ab65d8ff14c6937612212526a60f59b3c}{\index{dist\-\_\-vars.\-h@{dist\-\_\-vars.\-h}!cost\-\_\-matrix@{cost\-\_\-matrix}} +\index{cost\-\_\-matrix@{cost\-\_\-matrix}!dist_vars.h@{dist\-\_\-vars.\-h}} +\subsubsection[{cost\-\_\-matrix}]{\setlength{\rightskip}{0pt plus 5cm}int cost\-\_\-matrix}}\label{dist__vars_8h_ab65d8ff14c6937612212526a60f59b3c} + + +Specify the cost matrix to be used for distance calculations. + +if 0, use the default cost matrix (upper matrix in example), otherwise use Shapiro's costs (lower matrix). \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/dist__vars_8h__dep__incl.md5 b/binaries/src/ViennaRNA/doc/latex/dist__vars_8h__dep__incl.md5 new file mode 100644 index 0000000..359e150 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/dist__vars_8h__dep__incl.md5 @@ 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+\label{dist__vars_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/dist\-\_\-vars.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/dist\-\_\-vars.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_DIST\_VARS\_H\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_DIST\_VARS\_H\_\_} +00003 \textcolor{preprocessor}{} +00015 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{dist__vars_8h_aa03194c513af6b860e7b33e370b82bdb}{edit\_backtrack}; +00016 +00021 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} *\hyperlink{dist__vars_8h_ac1605fe3448ad0a0b809c4fb8f6a854a}{aligned\_line}[4]; +00022 +00029 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{dist__vars_8h_ab65d8ff14c6937612212526a60f59b3c}{cost\_matrix}; +00030 +00031 \textcolor{comment}{/* Global type defs for Distance-Package */} +00032 +\hypertarget{dist__vars_8h_source_l00033}{}\hyperlink{structPostorder__list}{00033} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{ +00034 \textcolor{keywordtype}{int} type; +00035 \textcolor{keywordtype}{int} weight; +00036 \textcolor{keywordtype}{int} father; +00037 \textcolor{keywordtype}{int} sons; +00038 \textcolor{keywordtype}{int} leftmostleaf; +00039 \} \hyperlink{structPostorder__list}{Postorder\_list}; +00040 +\hypertarget{dist__vars_8h_source_l00041}{}\hyperlink{structTree}{00041} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{ +00042 \hyperlink{structPostorder__list}{Postorder\_list} *postorder\_list; +00043 \textcolor{keywordtype}{int} *keyroots; +00044 \} \hyperlink{structTree}{Tree}; +00045 +\hypertarget{dist__vars_8h_source_l00046}{}\hyperlink{structswString}{00046} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\{ +00047 \textcolor{keywordtype}{int} type; +00048 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\textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"} +00005 +00012 \hyperlink{structduplexT}{duplexT} duplexfold( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1, +00013 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2); +00014 +00015 \hyperlink{structduplexT}{duplexT} *duplex\_subopt( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1, +00016 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2, +00017 \textcolor{keywordtype}{int} delta, +00018 \textcolor{keywordtype}{int} w); +00019 +00020 \hyperlink{structduplexT}{duplexT} aliduplexfold(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1[], +00021 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2[]); +00022 +00023 \hyperlink{structduplexT}{duplexT} *aliduplex\_subopt(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1[], +00024 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2[], +00025 \textcolor{keywordtype}{int} delta, +00026 \textcolor{keywordtype}{int} w); +00027 +00028 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/edit__cost_8h.tex b/binaries/src/ViennaRNA/doc/latex/edit__cost_8h.tex new file mode 100644 index 0000000..1e354cc --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/edit__cost_8h.tex @@ -0,0 +1,12 @@ +\hypertarget{edit__cost_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/edit\-\_\-cost.h File Reference} +\label{edit__cost_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/edit\-\_\-cost.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/edit\-\_\-cost.\-h}} +} + + +global variables for Edit Costs included by treedist.\-c and stringdist.\-c + + + + +\subsection{Detailed Description} +global variables for Edit Costs included by treedist.\-c and stringdist.\-c \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/edit__cost_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/edit__cost_8h_source.tex new file mode 100644 index 0000000..f4abf3e --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/edit__cost_8h_source.tex @@ -0,0 +1,55 @@ +\hypertarget{edit__cost_8h}{\section{edit\-\_\-cost.\-h} +\label{edit__cost_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/edit\-\_\-cost.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/edit\-\_\-cost.\-h}} +} + +\begin{DoxyCode} +00001 +00006 \textcolor{preprocessor}{#define PRIVATE static} +00007 \textcolor{preprocessor}{} +00008 PRIVATE \textcolor{keywordtype}{char} sep = \textcolor{charliteral}{':'}; +00009 PRIVATE \textcolor{keywordtype}{char} *coding = \textcolor{stringliteral}{"Null:U:P:H:B:I:M:S:E:R"}; +00010 +00011 \textcolor{preprocessor}{#define INF 10000 }\textcolor{comment}{/* infinity */}\textcolor{preprocessor}{} +00012 \textcolor{preprocessor}{} +00013 \textcolor{keyword}{typedef} \textcolor{keywordtype}{int} CostMatrix[10][10]; +00014 +00015 PRIVATE CostMatrix *EditCost; \textcolor{comment}{/* will point to UsualCost or ShapiroCost */} +00016 +00017 PRIVATE CostMatrix UsualCost = +00018 \{ +00019 +00020 \textcolor{comment}{/* Null, U, P, H, B, I, M, S, E, R */} +00021 +00022 \{ 0, 1, 2, 2, 2, 2, 2, 1, 1, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}\}, \textcolor{comment}{/* Null replaced */} +00023 \{ 1, 0, 1, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* U replaced */} +00024 \{ 2, 1, 0, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* P replaced */} +00025 \{ 2, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 0, 2, 2, 2, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* H replaced */} +00026 \{ 2, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 2, 0, 1, 2, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* B replaced */} +00027 \{ 2, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 2, 1, 0, 2, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* I replaced */} +00028 \{ 2, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 2, 2, 2, 0, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* M replaced */} +00029 \{ 1, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 0, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* S replaced */} +00030 \{ 1, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 0, INF\}, \textcolor{comment}{/* E replaced */} +00031 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 0\}, \textcolor{comment}{/* R replaced */} +00032 +00033 \}; +00034 +00035 +00036 PRIVATE CostMatrix ShapiroCost = +00037 \{ +00038 +00039 \textcolor{comment}{/* Null, U, P, H, B, I, M, S, E, R */} +00040 +00041 \{ 0, 1, 2, 100, 5, 5, 75, 5, 5, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}\}, \textcolor{comment}{/* Null replaced */} +00042 \{ 1, 0, 1, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* U replaced */} +00043 \{ 2, 1, 0, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* P replaced */} +00044 \{ 100, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 0, 8, 8, 8, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* H replaced */} +00045 \{ 5, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 8, 0, 3, 8, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* B replaced */} +00046 \{ 5, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 8, 3, 0, 8, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* I replaced */} +00047 \{ 75, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 8, 8, 8, 0, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* M replaced */} +00048 \{ 5, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 0, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* S replaced */} +00049 \{ 5, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 0, INF\}, \textcolor{comment}{/* E replaced */} +00050 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 0\}, \textcolor{comment}{/* R replaced */} +00051 +00052 \}; +00053 +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/energy__const_8h.tex b/binaries/src/ViennaRNA/doc/latex/energy__const_8h.tex new file mode 100644 index 0000000..68d9c6d --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/energy__const_8h.tex @@ -0,0 +1,69 @@ +\hypertarget{energy__const_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/energy\-\_\-const.h File Reference} +\label{energy__const_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/energy\-\_\-const.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/energy\-\_\-const.\-h}} +} +Include dependency graph for energy\-\_\-const.\-h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{energy__const_8h__incl} +\end{center} +\end{figure} +This graph shows which files directly or indirectly include this file\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=350pt]{energy__const_8h__dep__incl} +\end{center} +\end{figure} +\subsection*{Macros} +\begin{DoxyCompactItemize} +\item +\#define \hyperlink{energy__const_8h_ab1e4a8d82f24ed5db01dde5f25269cf1}{G\-A\-S\-C\-O\-N\-S\-T}~1.\-98717 /$\ast$ in \mbox{[}cal/K\mbox{]} $\ast$/ +\item +\#define \hyperlink{energy__const_8h_a307c72605e3713972b4f4fb2d53ea20e}{K0}~273.\-15 +\item +\#define \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{I\-N\-F}~10000000 /$\ast$ (I\-N\-T\-\_\-\-M\-A\-X/10) $\ast$/ +\item +\#define \hyperlink{energy__const_8h_a5064c29ab2d1e20c2304b3c67562774d}{F\-O\-R\-B\-I\-D\-D\-E\-N}~9999 +\item +\#define \hyperlink{energy__const_8h_a96a9822fa134450197dd454b1478a193}{B\-O\-N\-U\-S}~10000 +\item +\#define \hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{N\-B\-P\-A\-I\-R\-S}~7 +\item +\#define \hyperlink{energy__const_8h_ae646250fd59311356c7e5722a81c3a96}{T\-U\-R\-N}~3 +\item +\#define \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{M\-A\-X\-L\-O\-O\-P}~30 +\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +energy constants + +\subsection{Macro Definition Documentation} +\hypertarget{energy__const_8h_ab1e4a8d82f24ed5db01dde5f25269cf1}{\index{energy\-\_\-const.\-h@{energy\-\_\-const.\-h}!G\-A\-S\-C\-O\-N\-S\-T@{G\-A\-S\-C\-O\-N\-S\-T}} +\index{G\-A\-S\-C\-O\-N\-S\-T@{G\-A\-S\-C\-O\-N\-S\-T}!energy_const.h@{energy\-\_\-const.\-h}} +\subsubsection[{G\-A\-S\-C\-O\-N\-S\-T}]{\setlength{\rightskip}{0pt plus 5cm}\#define G\-A\-S\-C\-O\-N\-S\-T~1.\-98717 /$\ast$ in \mbox{[}cal/K\mbox{]} $\ast$/}}\label{energy__const_8h_ab1e4a8d82f24ed5db01dde5f25269cf1} +The gas constant \hypertarget{energy__const_8h_a307c72605e3713972b4f4fb2d53ea20e}{\index{energy\-\_\-const.\-h@{energy\-\_\-const.\-h}!K0@{K0}} +\index{K0@{K0}!energy_const.h@{energy\-\_\-const.\-h}} +\subsubsection[{K0}]{\setlength{\rightskip}{0pt plus 5cm}\#define K0~273.\-15}}\label{energy__const_8h_a307c72605e3713972b4f4fb2d53ea20e} +0 deg Celsius in Kelvin \hypertarget{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{\index{energy\-\_\-const.\-h@{energy\-\_\-const.\-h}!I\-N\-F@{I\-N\-F}} +\index{I\-N\-F@{I\-N\-F}!energy_const.h@{energy\-\_\-const.\-h}} +\subsubsection[{I\-N\-F}]{\setlength{\rightskip}{0pt plus 5cm}\#define I\-N\-F~10000000 /$\ast$ (I\-N\-T\-\_\-\-M\-A\-X/10) $\ast$/}}\label{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6} +Infinity as used in minimization routines \hypertarget{energy__const_8h_a5064c29ab2d1e20c2304b3c67562774d}{\index{energy\-\_\-const.\-h@{energy\-\_\-const.\-h}!F\-O\-R\-B\-I\-D\-D\-E\-N@{F\-O\-R\-B\-I\-D\-D\-E\-N}} +\index{F\-O\-R\-B\-I\-D\-D\-E\-N@{F\-O\-R\-B\-I\-D\-D\-E\-N}!energy_const.h@{energy\-\_\-const.\-h}} +\subsubsection[{F\-O\-R\-B\-I\-D\-D\-E\-N}]{\setlength{\rightskip}{0pt plus 5cm}\#define F\-O\-R\-B\-I\-D\-D\-E\-N~9999}}\label{energy__const_8h_a5064c29ab2d1e20c2304b3c67562774d} +forbidden \hypertarget{energy__const_8h_a96a9822fa134450197dd454b1478a193}{\index{energy\-\_\-const.\-h@{energy\-\_\-const.\-h}!B\-O\-N\-U\-S@{B\-O\-N\-U\-S}} +\index{B\-O\-N\-U\-S@{B\-O\-N\-U\-S}!energy_const.h@{energy\-\_\-const.\-h}} +\subsubsection[{B\-O\-N\-U\-S}]{\setlength{\rightskip}{0pt plus 5cm}\#define B\-O\-N\-U\-S~10000}}\label{energy__const_8h_a96a9822fa134450197dd454b1478a193} +bonus contribution \hypertarget{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{\index{energy\-\_\-const.\-h@{energy\-\_\-const.\-h}!N\-B\-P\-A\-I\-R\-S@{N\-B\-P\-A\-I\-R\-S}} +\index{N\-B\-P\-A\-I\-R\-S@{N\-B\-P\-A\-I\-R\-S}!energy_const.h@{energy\-\_\-const.\-h}} +\subsubsection[{N\-B\-P\-A\-I\-R\-S}]{\setlength{\rightskip}{0pt plus 5cm}\#define N\-B\-P\-A\-I\-R\-S~7}}\label{energy__const_8h_a5e75221c779d618eab81e096f37e32ce} +The number of distinguishable base pairs \hypertarget{energy__const_8h_ae646250fd59311356c7e5722a81c3a96}{\index{energy\-\_\-const.\-h@{energy\-\_\-const.\-h}!T\-U\-R\-N@{T\-U\-R\-N}} +\index{T\-U\-R\-N@{T\-U\-R\-N}!energy_const.h@{energy\-\_\-const.\-h}} +\subsubsection[{T\-U\-R\-N}]{\setlength{\rightskip}{0pt plus 5cm}\#define T\-U\-R\-N~3}}\label{energy__const_8h_ae646250fd59311356c7e5722a81c3a96} +The minimum loop length \hypertarget{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{\index{energy\-\_\-const.\-h@{energy\-\_\-const.\-h}!M\-A\-X\-L\-O\-O\-P@{M\-A\-X\-L\-O\-O\-P}} +\index{M\-A\-X\-L\-O\-O\-P@{M\-A\-X\-L\-O\-O\-P}!energy_const.h@{energy\-\_\-const.\-h}} +\subsubsection[{M\-A\-X\-L\-O\-O\-P}]{\setlength{\rightskip}{0pt plus 5cm}\#define M\-A\-X\-L\-O\-O\-P~30}}\label{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988} +The maximum loop length \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/energy__const_8h__dep__incl.md5 b/binaries/src/ViennaRNA/doc/latex/energy__const_8h__dep__incl.md5 new file mode 100644 index 0000000..dd6dfdb --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/energy__const_8h__dep__incl.md5 @@ -0,0 +1 @@ +59a6047517f9b2d4442026bfd43acb55 \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/energy__const_8h__dep__incl.pdf b/binaries/src/ViennaRNA/doc/latex/energy__const_8h__dep__incl.pdf new file 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+\label{energy__const_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/energy\-\_\-const.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/energy\-\_\-const.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_ENERGY\_CONST\_H\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_ENERGY\_CONST\_H\_\_} +00003 \textcolor{preprocessor}{} +00004 \textcolor{preprocessor}{#include } +00005 +\hypertarget{energy__const_8h_source_l00012}{}\hyperlink{energy__const_8h_ab1e4a8d82f24ed5db01dde5f25269cf1}{00012} \textcolor{preprocessor}{#define GASCONST 1.98717 }\textcolor{comment}{/* in [cal/K] */}\textcolor{preprocessor}{} +00013 \textcolor{preprocessor}{} +\hypertarget{energy__const_8h_source_l00014}{}\hyperlink{energy__const_8h_a307c72605e3713972b4f4fb2d53ea20e}{00014} \textcolor{preprocessor}{#define K0 273.15} +00015 \textcolor{preprocessor}{} +\hypertarget{energy__const_8h_source_l00016}{}\hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{00016} \textcolor{preprocessor}{#define INF 10000000 }\textcolor{comment}{/* (INT\_MAX/10) */}\textcolor{preprocessor}{} +00017 \textcolor{preprocessor}{} +00018 \textcolor{preprocessor}{#define EMAX (INF/10)} +00019 \textcolor{preprocessor}{} +\hypertarget{energy__const_8h_source_l00020}{}\hyperlink{energy__const_8h_a5064c29ab2d1e20c2304b3c67562774d}{00020} \textcolor{preprocessor}{#define FORBIDDEN 9999} +00021 \textcolor{preprocessor}{} +\hypertarget{energy__const_8h_source_l00022}{}\hyperlink{energy__const_8h_a96a9822fa134450197dd454b1478a193}{00022} \textcolor{preprocessor}{#define BONUS 10000} +00023 \textcolor{preprocessor}{} +\hypertarget{energy__const_8h_source_l00024}{}\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{00024} \textcolor{preprocessor}{#define NBPAIRS 7} +00025 \textcolor{preprocessor}{} +\hypertarget{energy__const_8h_source_l00026}{}\hyperlink{energy__const_8h_ae646250fd59311356c7e5722a81c3a96}{00026} \textcolor{preprocessor}{#define TURN 3} +00027 \textcolor{preprocessor}{} +\hypertarget{energy__const_8h_source_l00028}{}\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{00028} \textcolor{preprocessor}{#define MAXLOOP 30} +00029 \textcolor{preprocessor}{} +00030 \textcolor{preprocessor}{#define VRNA\_GQUAD\_MISMATCH\_PENALTY 300 }\textcolor{comment}{/* penalty for incompatible nucleotides in an alignment that + destruct a gquad layer */}\textcolor{preprocessor}{} +00031 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define VRNA\_GQUAD\_MISMATCH\_NUM\_ALI 1 }\textcolor{comment}{/* maximum number of mismatching sequences in the alignment + when gquad should be formed */}\textcolor{preprocessor}{} +00032 \textcolor{preprocessor}{} +00033 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/energy__par_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/energy__par_8h_source.tex new file mode 100644 index 0000000..1175d19 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/energy__par_8h_source.tex @@ -0,0 +1,106 @@ +\hypertarget{energy__par_8h}{\section{energy\-\_\-par.\-h} +\label{energy__par_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/energy\-\_\-par.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/energy\-\_\-par.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{comment}{/*} +00002 \textcolor{comment}{ prototypes for energy\_par.c} +00003 \textcolor{comment}{*/} +00004 +00005 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_ENERGY\_PAR\_H\_\_} +00006 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_ENERGY\_PAR\_H\_\_} +00007 \textcolor{preprocessor}{} +00008 \textcolor{preprocessor}{#include "\hyperlink{energy__const_8h}{energy\_const.h}"} +00009 +00010 \textcolor{preprocessor}{#define PUBLIC} +00011 \textcolor{preprocessor}{} +00012 +00013 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} lxc37; \textcolor{comment}{/* parameter for logarithmic loop} +00014 \textcolor{comment}{ energy extrapolation */} +00015 +00016 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} stack37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1]; +00017 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} stackdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1]; \textcolor{comment}{/* stack enthalpies */} +00018 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} entropies[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1]; \textcolor{comment}{/* not used anymore */} +00019 +00020 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} hairpin37[31]; +00021 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} hairpindH[31]; +00022 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} bulge37[31]; +00023 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} bulgedH[31]; +00024 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} internal\_loop37[31]; +00025 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} internal\_loopdH[31]; +00026 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} internal2\_energy; +00027 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} old\_mismatch\_37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00028 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchI37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; \textcolor{comment}{/* interior loop mismatches */} +00029 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchIdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; \textcolor{comment}{/* interior loop mismatches */} +00030 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatch1nI37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; \textcolor{comment}{/* interior loop mismatches */} +00031 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatch23I37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; \textcolor{comment}{/* interior loop mismatches */} +00032 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatch1nIdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; \textcolor{comment}{/* interior loop mismatches */} +00033 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatch23IdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; \textcolor{comment}{/* interior loop mismatches */} +00034 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchH37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; \textcolor{comment}{/* same for hairpins */} +00035 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchM37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; \textcolor{comment}{/* same for multiloops */} +00036 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchHdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; \textcolor{comment}{/* same for hairpins */} +00037 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchMdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; \textcolor{comment}{/* same for multiloops */} +00038 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchExt37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00039 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} mismatchExtdH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00040 +00041 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} dangle5\_37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5]; \textcolor{comment}{/* 5' dangle exterior of pair */} +00042 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} dangle3\_37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5]; \textcolor{comment}{/* 3' dangle */} +00043 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} dangle3\_dH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5]; \textcolor{comment}{/* corresponding enthalpies */} +00044 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} dangle5\_dH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5]; +00045 +00046 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} int11\_37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; \textcolor{comment}{/* 1x1 interior loops */} +00047 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} int11\_dH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5]; +00048 +00049 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} int21\_37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5]; \textcolor{comment}{/* 2x1 interior loops */} +00050 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} int21\_dH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5]; +00051 +00052 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} int22\_37[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5][5]; \textcolor{comment}{/* 2x2 interior loops */} +00053 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} int22\_dH[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5][5][5]; +00054 +00055 \textcolor{comment}{/* constants for linearly destabilizing contributions for multi-loops} +00056 \textcolor{comment}{ F = ML\_closing + ML\_intern*(k-1) + ML\_BASE*u */} +00057 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_BASE37; +00058 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_BASEdH; +00059 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_closing37; +00060 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_closingdH; +00061 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_intern37; +00062 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ML\_interndH; +00063 +00064 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} TripleC37; +00065 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} TripleCdH; +00066 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} MultipleCA37; +00067 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} MultipleCAdH; +00068 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} MultipleCB37; +00069 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} MultipleCBdH; +00070 +00071 \textcolor{comment}{/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */} +00072 \textcolor{comment}{/* ninio\_energy = min\{max\_ninio, |n1-n2|*F\_ninio[min\{4.0, n1, n2\}] \} */} +00073 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} MAX\_NINIO; \textcolor{comment}{/* maximum correction */} +00074 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} ninio37; +00075 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} niniodH; +00076 \textcolor{comment}{/* penalty for helices terminated by AU (actually not GC) */} +00077 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} TerminalAU37; +00078 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} TerminalAUdH; +00079 \textcolor{comment}{/* penalty for forming bi-molecular duplex */} +00080 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} DuplexInit37; +00081 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} DuplexInitdH; +00082 \textcolor{comment}{/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */} +00083 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} Tetraloops[]; \textcolor{comment}{/* string containing the special tetraloops */} +00084 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} Tetraloop37[]; \textcolor{comment}{/* Bonus energy for special tetraloops */} +00085 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} TetraloopdH[]; +00086 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} Triloops[]; \textcolor{comment}{/* string containing the special triloops */} +00087 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} Triloop37[]; \textcolor{comment}{/* Bonus energy for special Triloops */} +00088 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} TriloopdH[]; \textcolor{comment}{/* Bonus energy for special Triloops */} +00089 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} Hexaloops[]; \textcolor{comment}{/* string containing the special triloops */} +00090 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} Hexaloop37[]; \textcolor{comment}{/* Bonus energy for special Triloops */} +00091 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} HexaloopdH[]; \textcolor{comment}{/* Bonus energy for special Triloops */} +00092 +00093 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} GQuadAlpha37; +00094 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} GQuadAlphadH; +00095 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} GQuadBeta37; +00096 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} GQuadBetadH; +00097 +00098 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} Tmeasure; \textcolor{comment}{/* temperature of param measurements */} +00099 +00100 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/files.tex b/binaries/src/ViennaRNA/doc/latex/files.tex new file mode 100644 index 0000000..5b16e50 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/files.tex @@ -0,0 +1,59 @@ +\section{File List} +Here is a list of all documented files with brief descriptions\-:\begin{DoxyCompactList} +\item\contentsline{section}{{\bfseries mainpage.\-h} }{\pageref{mainpage_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{2Dfold_8h}{2\-Dfold.\-h} }{\pageref{2Dfold_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{2Dpfold_8h}{2\-Dpfold.\-h} }{\pageref{2Dpfold_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries ali\-\_\-plex.\-h} }{\pageref{ali__plex_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{alifold_8h}{alifold.\-h} \\*Compute various properties (consensus M\-F\-E structures, partition function, Boltzmann distributed stochastic samples, ...) for R\-N\-A sequence alignments }{\pageref{alifold_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries aln\-\_\-util.\-h} }{\pageref{aln__util_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{cofold_8h}{cofold.\-h} \\*M\-F\-E version of cofolding routines }{\pageref{cofold_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{convert__epars_8h}{convert\-\_\-epars.\-h} \\*Functions and definitions for energy parameter file format conversion }{\pageref{convert__epars_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h} \\*All datastructures and typedefs shared among the Vienna R\-N\-A Package can be found here }{\pageref{data__structures_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{dist__vars_8h}{dist\-\_\-vars.\-h} \\*Global variables for Distance-\/\-Package }{\pageref{dist__vars_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{duplex_8h}{duplex.\-h} \\*Duplex folding function declarations.. }{\pageref{duplex_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{edit__cost_8h}{edit\-\_\-cost.\-h} \\*Global variables for Edit Costs included by treedist.\-c and stringdist.\-c }{\pageref{edit__cost_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{energy__const_8h}{energy\-\_\-const.\-h} }{\pageref{energy__const_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries energy\-\_\-par.\-h} }{\pageref{energy__par_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{findpath_8h}{findpath.\-h} \\*Compute direct refolding paths between two secondary structures }{\pageref{findpath_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{fold_8h}{fold.\-h} \\*M\-F\-E calculations and energy evaluations for single R\-N\-A sequences }{\pageref{fold_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{fold__vars_8h}{fold\-\_\-vars.\-h} \\*Here all all declarations of the global variables used throughout R\-N\-Alib }{\pageref{fold__vars_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{gquad_8h}{gquad.\-h} \\*Various functions related to G-\/quadruplex computations }{\pageref{gquad_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{inverse_8h}{inverse.\-h} \\*Inverse folding routines }{\pageref{inverse_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{Lfold_8h}{Lfold.\-h} \\*Predicting local M\-F\-E structures of large sequences }{\pageref{Lfold_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{loop__energies_8h}{loop\-\_\-energies.\-h} \\*Energy evaluation for M\-F\-E and partition function calculations }{\pageref{loop__energies_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{LPfold_8h}{L\-Pfold.\-h} \\*Function declarations of partition function variants of the Lfold algorithm }{\pageref{LPfold_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{MEA_8h}{M\-E\-A.\-h} \\*Computes a M\-E\-A (maximum expected accuracy) structure }{\pageref{MEA_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{mm_8h}{mm.\-h} \\*Several Maximum Matching implementations }{\pageref{mm_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries move\-\_\-set.\-h} }{\pageref{move__set_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{naview_8h}{naview.\-h} }{\pageref{naview_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries pair\-\_\-mat.\-h} }{\pageref{pair__mat_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{params_8h}{params.\-h} }{\pageref{params_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{part__func_8h}{part\-\_\-func.\-h} \\*Partition function of single R\-N\-A sequences }{\pageref{part__func_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{part__func__co_8h}{part\-\_\-func\-\_\-co.\-h} \\*Partition function for two R\-N\-A sequences }{\pageref{part__func__co_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{part__func__up_8h}{part\-\_\-func\-\_\-up.\-h} \\*Partition Function Cofolding as stepwise process }{\pageref{part__func__up_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries P\-Kplex.\-h} }{\pageref{PKplex_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries plex.\-h} }{\pageref{plex_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{plot__layouts_8h}{plot\-\_\-layouts.\-h} \\*Secondary structure plot layout algorithms }{\pageref{plot__layouts_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries Profile\-Aln.\-h} }{\pageref{ProfileAln_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{profiledist_8h}{profiledist.\-h} }{\pageref{profiledist_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{PS__dot_8h}{P\-S\-\_\-dot.\-h} \\*Various functions for plotting R\-N\-A secondary structures, dot-\/plots and other visualizations }{\pageref{PS__dot_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{read__epars_8h}{read\-\_\-epars.\-h} }{\pageref{read__epars_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries ribo.\-h} }{\pageref{ribo_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{RNAstruct_8h}{R\-N\-Astruct.\-h} \\*Parsing and Coarse Graining of Structures }{\pageref{RNAstruct_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries snofold.\-h} }{\pageref{snofold_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries snoop.\-h} }{\pageref{snoop_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{stringdist_8h}{stringdist.\-h} \\*Functions for String Alignment }{\pageref{stringdist_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{subopt_8h}{subopt.\-h} \\*R\-N\-Asubopt and density of states declarations }{\pageref{subopt_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/{\bfseries svm\-\_\-utils.\-h} }{\pageref{svm__utils_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{treedist_8h}{treedist.\-h} \\*Functions for \hyperlink{structTree}{Tree} Edit Distances }{\pageref{treedist_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{utils_8h}{utils.\-h} \\*Various utility-\/ and helper-\/functions used throughout the Vienna R\-N\-A package }{\pageref{utils_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/\hyperlink{1_88_84__epars_8h}{1.\-8.\-4\-\_\-epars.\-h} \\*Free energy parameters for parameter file conversion }{\pageref{1_88_84__epars_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/\hyperlink{1_88_84__intloops_8h}{1.\-8.\-4\-\_\-intloops.\-h} \\*Free energy parameters for interior loop contributions needed by the parameter file conversion functions }{\pageref{1_88_84__intloops_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/{\bfseries intl11.\-h} }{\pageref{intl11_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/{\bfseries intl11d\-H.\-h} }{\pageref{intl11dH_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/{\bfseries intl21.\-h} }{\pageref{intl21_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/{\bfseries intl21d\-H.\-h} }{\pageref{intl21dH_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/{\bfseries intl22.\-h} }{\pageref{intl22_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/{\bfseries intl22d\-H.\-h} }{\pageref{intl22dH_8h}}{} +\item\contentsline{section}{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/{\bfseries list.\-h} }{\pageref{list_8h}}{} +\end{DoxyCompactList} diff --git a/binaries/src/ViennaRNA/doc/latex/findpath_8h.tex b/binaries/src/ViennaRNA/doc/latex/findpath_8h.tex new file mode 100644 index 0000000..094bf87 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/findpath_8h.tex @@ -0,0 +1,103 @@ +\hypertarget{findpath_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/findpath.h File Reference} +\label{findpath_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/findpath.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/findpath.\-h}} +} + + +Compute direct refolding paths between two secondary structures. + + +Include dependency graph for findpath.\-h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{findpath_8h__incl} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +int \hyperlink{findpath_8h_ad0e14268e309af773ecd1fce6244ee50}{find\-\_\-saddle} (const char $\ast$seq, const char $\ast$struc1, const char $\ast$struc2, int max) +\begin{DoxyCompactList}\small\item\em Find energy of a saddle point between 2 structures (serch only direct path) \end{DoxyCompactList}\item +\hyperlink{structpath__t}{path\-\_\-t} $\ast$ \hyperlink{findpath_8h_a0ff35d65c892a3403af937c00a867ef9}{get\-\_\-path} (const char $\ast$seq, const char $\ast$s1, const char $\ast$s2, int maxkeep) +\begin{DoxyCompactList}\small\item\em Find refolding path between 2 structures (serch only direct path) \end{DoxyCompactList}\item +void \hyperlink{findpath_8h_a326e6d1640bbfd035e3869f5f4c188f7}{free\-\_\-path} (\hyperlink{structpath__t}{path\-\_\-t} $\ast$path) +\begin{DoxyCompactList}\small\item\em Free memory allocated by \hyperlink{findpath_8h_a0ff35d65c892a3403af937c00a867ef9}{get\-\_\-path()} function. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Compute direct refolding paths between two secondary structures. + +\subsection{Function Documentation} +\hypertarget{findpath_8h_ad0e14268e309af773ecd1fce6244ee50}{\index{findpath.\-h@{findpath.\-h}!find\-\_\-saddle@{find\-\_\-saddle}} +\index{find\-\_\-saddle@{find\-\_\-saddle}!findpath.h@{findpath.\-h}} +\subsubsection[{find\-\_\-saddle}]{\setlength{\rightskip}{0pt plus 5cm}int find\-\_\-saddle ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{seq, } +\item[{const char $\ast$}]{struc1, } +\item[{const char $\ast$}]{struc2, } +\item[{int}]{max} +\end{DoxyParamCaption} +)}}\label{findpath_8h_ad0e14268e309af773ecd1fce6244ee50} + + +Find energy of a saddle point between 2 structures (serch only direct path) + + +\begin{DoxyParams}{Parameters} +{\em seq} & R\-N\-A sequence \\ +\hline +{\em struc1} & A pointer to the character array where the first secondary structure in dot-\/bracket notation will be written to \\ +\hline +{\em struc2} & A pointer to the character array where the second secondary structure in dot-\/bracket notation will be written to \\ +\hline +{\em max} & integer how many strutures are being kept during the search \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +the saddle energy in 10cal/mol +\end{DoxyReturn} +\hypertarget{findpath_8h_a0ff35d65c892a3403af937c00a867ef9}{\index{findpath.\-h@{findpath.\-h}!get\-\_\-path@{get\-\_\-path}} +\index{get\-\_\-path@{get\-\_\-path}!findpath.h@{findpath.\-h}} +\subsubsection[{get\-\_\-path}]{\setlength{\rightskip}{0pt plus 5cm}{\bf path\-\_\-t}$\ast$ get\-\_\-path ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{seq, } +\item[{const char $\ast$}]{s1, } +\item[{const char $\ast$}]{s2, } +\item[{int}]{maxkeep} +\end{DoxyParamCaption} +)}}\label{findpath_8h_a0ff35d65c892a3403af937c00a867ef9} + + +Find refolding path between 2 structures (serch only direct path) + + +\begin{DoxyParams}{Parameters} +{\em seq} & R\-N\-A sequence \\ +\hline +{\em s1} & A pointer to the character array where the first secondary structure in dot-\/bracket notation will be written to \\ +\hline +{\em s2} & A pointer to the character array where the second secondary structure in dot-\/bracket notation will be written to \\ +\hline +{\em maxkeep} & integer how many strutures are being kept during the search \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +direct refolding path between two structures +\end{DoxyReturn} +\hypertarget{findpath_8h_a326e6d1640bbfd035e3869f5f4c188f7}{\index{findpath.\-h@{findpath.\-h}!free\-\_\-path@{free\-\_\-path}} +\index{free\-\_\-path@{free\-\_\-path}!findpath.h@{findpath.\-h}} +\subsubsection[{free\-\_\-path}]{\setlength{\rightskip}{0pt plus 5cm}void free\-\_\-path ( +\begin{DoxyParamCaption} +\item[{{\bf path\-\_\-t} $\ast$}]{path} +\end{DoxyParamCaption} +)}}\label{findpath_8h_a326e6d1640bbfd035e3869f5f4c188f7} + + +Free memory allocated by \hyperlink{findpath_8h_a0ff35d65c892a3403af937c00a867ef9}{get\-\_\-path()} function. + + +\begin{DoxyParams}{Parameters} +{\em path} & pointer to memory to be freed \\ +\hline +\end{DoxyParams} diff --git a/binaries/src/ViennaRNA/doc/latex/findpath_8h__incl.md5 b/binaries/src/ViennaRNA/doc/latex/findpath_8h__incl.md5 new file mode 100644 index 0000000..764cf93 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/findpath_8h__incl.md5 @@ -0,0 +1 @@ +5e0c02e0bb973f0f4dfc9817315b67d3 \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/findpath_8h__incl.pdf b/binaries/src/ViennaRNA/doc/latex/findpath_8h__incl.pdf new file mode 100644 index 0000000000000000000000000000000000000000..c1d17a628a2a11918e06a16250ba8ca18dff6aa6 GIT binary patch literal 10106 zcmd6NbzIZm_df_Cjda6EL24s58l+oFkY=#aIYyU&(v6~|g3>7=-AE%LC@r9(v?8K_ 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\textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_FIND\_PATH\_H\_\_} +00003 \textcolor{preprocessor}{} +00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"} +00005 +00023 \textcolor{keywordtype}{int} \hyperlink{findpath_8h_ad0e14268e309af773ecd1fce6244ee50}{find\_saddle}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *seq, +00024 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *struc1, +00025 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *struc2, +00026 \textcolor{keywordtype}{int} max); +00027 +00028 +00041 \hyperlink{structpath__t}{path\_t}* \hyperlink{findpath_8h_a0ff35d65c892a3403af937c00a867ef9}{get\_path}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *seq, +00042 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1, +00043 \textcolor{keyword}{const} \textcolor{keywordtype}{char}* s2, +00044 \textcolor{keywordtype}{int} maxkeep); +00045 +00051 \textcolor{keywordtype}{void} \hyperlink{findpath_8h_a326e6d1640bbfd035e3869f5f4c188f7}{free\_path}(\hyperlink{structpath__t}{path\_t} *path); +00052 +00053 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/fold_8h.tex b/binaries/src/ViennaRNA/doc/latex/fold_8h.tex new file mode 100644 index 0000000..0f1ae02 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/fold_8h.tex @@ -0,0 +1,383 @@ +\hypertarget{fold_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold.h File Reference} +\label{fold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold.\-h}} +} + + +M\-F\-E calculations and energy evaluations for single R\-N\-A sequences. + + +Include dependency graph for fold.\-h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{fold_8h__incl} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +float \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par} (const char $\ast$sequence, char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int is\-\_\-constrained, int is\-\_\-circular) +\begin{DoxyCompactList}\small\item\em Compute minimum free energy and an appropriate secondary structure of an R\-N\-A sequence. \end{DoxyCompactList}\item +float \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold} (const char $\ast$sequence, char $\ast$structure) +\begin{DoxyCompactList}\small\item\em Compute minimum free energy and an appropriate secondary structure of an R\-N\-A sequence. \end{DoxyCompactList}\item +float \hyperlink{group__mfe__fold_ga4ac63ab3e8d9a80ced28b8052d94e423}{circfold} (const char $\ast$sequence, char $\ast$structure) +\begin{DoxyCompactList}\small\item\em Compute minimum free energy and an appropriate secondary structure of a circular R\-N\-A sequence. \end{DoxyCompactList}\item +float \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure} (const char $\ast$string, const char $\ast$structure, int verbosity\-\_\-level) +\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A using global model detail settings. \end{DoxyCompactList}\item +float \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par} (const char $\ast$string, const char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int verbosity\-\_\-level) +\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \end{DoxyCompactList}\item +float \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure} (const char $\ast$string, const char $\ast$structure, int verbosity\-\_\-level) +\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded circular R\-N\-A. \end{DoxyCompactList}\item +float \hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par} (const char $\ast$string, const char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int verbosity\-\_\-level) +\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded circular R\-N\-A. \end{DoxyCompactList}\item +int \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\-\_\-of\-\_\-structure\-\_\-pt} (const char $\ast$string, short $\ast$ptable, short $\ast$s, short $\ast$s1, int verbosity\-\_\-level) +\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \end{DoxyCompactList}\item +int \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par} (const char $\ast$string, short $\ast$ptable, short $\ast$s, short $\ast$s1, \hyperlink{structparamT}{param\-T} $\ast$parameters, int verbosity\-\_\-level) +\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \end{DoxyCompactList}\item +\hypertarget{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}{void \hyperlink{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}{free\-\_\-arrays} (void)}\label{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7} + +\begin{DoxyCompactList}\small\item\em Free arrays for mfe folding. \end{DoxyCompactList}\item +void \hyperlink{fold_8h_a87b7869bd1d8dc79c60775c74e009e9b}{parenthesis\-\_\-structure} (char $\ast$structure, \hyperlink{structbondT}{bond\-T} $\ast$bp, int length) +\begin{DoxyCompactList}\small\item\em Create a dot-\/backet/parenthesis structure from backtracking stack. \end{DoxyCompactList}\item +void \hyperlink{fold_8h_a325f3835c68f34fe833b2b7a5828857f}{parenthesis\-\_\-zuker} (char $\ast$structure, \hyperlink{structbondT}{bond\-T} $\ast$bp, int length) +\begin{DoxyCompactList}\small\item\em Create a dot-\/backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.\-c. \end{DoxyCompactList}\item +\hypertarget{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3}{void \hyperlink{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3}{update\-\_\-fold\-\_\-params} (void)}\label{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3} + +\begin{DoxyCompactList}\small\item\em Recalculate energy parameters. \end{DoxyCompactList}\item +float \hyperlink{fold_8h_a539ecaed89730f7644c202f304d7529b}{energy\-\_\-of\-\_\-move} (const char $\ast$string, const char $\ast$structure, int m1, int m2) +\begin{DoxyCompactList}\small\item\em Calculate energy of a move (closing or opening of a base pair) \end{DoxyCompactList}\item +int \hyperlink{fold_8h_a49e0ee561be69faf0568213546f6a53f}{energy\-\_\-of\-\_\-move\-\_\-pt} (short $\ast$pt, short $\ast$s, short $\ast$s1, int m1, int m2) +\begin{DoxyCompactList}\small\item\em Calculate energy of a move (closing or opening of a base pair) \end{DoxyCompactList}\item +int \hyperlink{fold_8h_a507d4fd93f4b398d793ba2402731388d}{loop\-\_\-energy} (short $\ast$ptable, short $\ast$s, short $\ast$s1, int i) +\begin{DoxyCompactList}\small\item\em Calculate energy of a loop. \end{DoxyCompactList}\item +void \hyperlink{fold_8h_adaa59b81664e2e36cb9932e891558fae}{assign\-\_\-plist\-\_\-from\-\_\-db} (\hyperlink{structplist}{plist} $\ast$$\ast$pl, const char $\ast$struc, float \hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr}) +\begin{DoxyCompactList}\small\item\em Create a plist from a dot-\/bracket string. \end{DoxyCompactList}\item +int \hyperlink{fold_8h_a2163034a25c6115d894b199e97e03f6c}{Loop\-Energy} (int n1, int n2, int type, int type\-\_\-2, int si1, int sj1, int sp1, int sq1) +\item +int \hyperlink{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}{Hairpin\-E} (int size, int type, int si1, int sj1, const char $\ast$string) +\item +void \hyperlink{fold_8h_ac3f0a28d9cb609d388b155445073fd20}{initialize\-\_\-fold} (int length) +\item +float \hyperlink{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{energy\-\_\-of\-\_\-struct} (const char $\ast$string, const char $\ast$structure) +\item +int \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy\-\_\-of\-\_\-struct\-\_\-pt} (const char $\ast$string, short $\ast$ptable, short $\ast$s, short $\ast$s1) +\item +float \hyperlink{fold_8h_a657222e2758c46bf13b416ef3032e417}{energy\-\_\-of\-\_\-circ\-\_\-struct} (const char $\ast$string, const char $\ast$structure) +\end{DoxyCompactItemize} +\subsection*{Variables} +\begin{DoxyCompactItemize} +\item +\hypertarget{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}{int \hyperlink{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}{log\-M\-L}}\label{fold_8h_a80c3c5fd35e7479704cc91d2d0367743} + +\begin{DoxyCompactList}\small\item\em if nonzero use logarithmic M\-L energy in energy\-\_\-of\-\_\-struct \end{DoxyCompactList}\item +\hypertarget{fold_8h_a6c5655c8b272e3e6cab74dd0f540294f}{int \hyperlink{fold_8h_a6c5655c8b272e3e6cab74dd0f540294f}{uniq\-\_\-\-M\-L}}\label{fold_8h_a6c5655c8b272e3e6cab74dd0f540294f} + +\begin{DoxyCompactList}\small\item\em do M\-L decomposition uniquely (for subopt) \end{DoxyCompactList}\item +\hypertarget{fold_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{int \hyperlink{fold_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\-\_\-point}}\label{fold_8h_ab9b2c3a37a5516614c06d0ab54b97cda} + +\begin{DoxyCompactList}\small\item\em set to first pos of second seq for cofolding \end{DoxyCompactList}\item +\hypertarget{group__eval_ga567530678f6260a1a649a5beca5da4c5}{int \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\-\_\-debug}}\label{group__eval_ga567530678f6260a1a649a5beca5da4c5} + +\begin{DoxyCompactList}\small\item\em verbose info from energy\-\_\-of\-\_\-struct \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +M\-F\-E calculations and energy evaluations for single R\-N\-A sequences. This file includes (almost) all function declarations within the R\-N\-Alib that are related to M\-F\-E folding... + +\subsection{Function Documentation} +\hypertarget{fold_8h_a87b7869bd1d8dc79c60775c74e009e9b}{\index{fold.\-h@{fold.\-h}!parenthesis\-\_\-structure@{parenthesis\-\_\-structure}} +\index{parenthesis\-\_\-structure@{parenthesis\-\_\-structure}!fold.h@{fold.\-h}} +\subsubsection[{parenthesis\-\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}void parenthesis\-\_\-structure ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{structure, } +\item[{{\bf bond\-T} $\ast$}]{bp, } +\item[{int}]{length} +\end{DoxyParamCaption} +)}}\label{fold_8h_a87b7869bd1d8dc79c60775c74e009e9b} + + +Create a dot-\/backet/parenthesis structure from backtracking stack. + +\begin{DoxyNote}{Note} +This function is threadsafe +\end{DoxyNote} +\hypertarget{fold_8h_a325f3835c68f34fe833b2b7a5828857f}{\index{fold.\-h@{fold.\-h}!parenthesis\-\_\-zuker@{parenthesis\-\_\-zuker}} +\index{parenthesis\-\_\-zuker@{parenthesis\-\_\-zuker}!fold.h@{fold.\-h}} +\subsubsection[{parenthesis\-\_\-zuker}]{\setlength{\rightskip}{0pt plus 5cm}void parenthesis\-\_\-zuker ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{structure, } +\item[{{\bf bond\-T} $\ast$}]{bp, } +\item[{int}]{length} +\end{DoxyParamCaption} +)}}\label{fold_8h_a325f3835c68f34fe833b2b7a5828857f} + + +Create a dot-\/backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.\-c. + +\begin{DoxyNote}{Note} +This function is threadsafe +\end{DoxyNote} +\hypertarget{fold_8h_a539ecaed89730f7644c202f304d7529b}{\index{fold.\-h@{fold.\-h}!energy\-\_\-of\-\_\-move@{energy\-\_\-of\-\_\-move}} +\index{energy\-\_\-of\-\_\-move@{energy\-\_\-of\-\_\-move}!fold.h@{fold.\-h}} +\subsubsection[{energy\-\_\-of\-\_\-move}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-move ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{string, } +\item[{const char $\ast$}]{structure, } +\item[{int}]{m1, } +\item[{int}]{m2} +\end{DoxyParamCaption} +)}}\label{fold_8h_a539ecaed89730f7644c202f304d7529b} + + +Calculate energy of a move (closing or opening of a base pair) + +If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening). + +\begin{DoxySeeAlso}{See Also} +\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table()}, \hyperlink{fold_8h_a539ecaed89730f7644c202f304d7529b}{energy\-\_\-of\-\_\-move()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em string} & R\-N\-A sequence \\ +\hline +{\em structure} & secondary structure in dot-\/bracket notation \\ +\hline +{\em m1} & first coordinate of base pair \\ +\hline +{\em m2} & second coordinate of base pair \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +energy change of the move in kcal/mol +\end{DoxyReturn} +\hypertarget{fold_8h_a49e0ee561be69faf0568213546f6a53f}{\index{fold.\-h@{fold.\-h}!energy\-\_\-of\-\_\-move\-\_\-pt@{energy\-\_\-of\-\_\-move\-\_\-pt}} +\index{energy\-\_\-of\-\_\-move\-\_\-pt@{energy\-\_\-of\-\_\-move\-\_\-pt}!fold.h@{fold.\-h}} +\subsubsection[{energy\-\_\-of\-\_\-move\-\_\-pt}]{\setlength{\rightskip}{0pt plus 5cm}int energy\-\_\-of\-\_\-move\-\_\-pt ( +\begin{DoxyParamCaption} +\item[{short $\ast$}]{pt, } +\item[{short $\ast$}]{s, } +\item[{short $\ast$}]{s1, } +\item[{int}]{m1, } +\item[{int}]{m2} +\end{DoxyParamCaption} +)}}\label{fold_8h_a49e0ee561be69faf0568213546f6a53f} + + +Calculate energy of a move (closing or opening of a base pair) + +If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening). + +\begin{DoxySeeAlso}{See Also} +\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table()}, \hyperlink{fold_8h_a539ecaed89730f7644c202f304d7529b}{energy\-\_\-of\-\_\-move()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em pt} & the pair table of the secondary structure \\ +\hline +{\em s} & encoded R\-N\-A sequence \\ +\hline +{\em s1} & encoded R\-N\-A sequence \\ +\hline +{\em m1} & first coordinate of base pair \\ +\hline +{\em m2} & second coordinate of base pair \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +energy change of the move in 10cal/mol +\end{DoxyReturn} +\hypertarget{fold_8h_a507d4fd93f4b398d793ba2402731388d}{\index{fold.\-h@{fold.\-h}!loop\-\_\-energy@{loop\-\_\-energy}} +\index{loop\-\_\-energy@{loop\-\_\-energy}!fold.h@{fold.\-h}} +\subsubsection[{loop\-\_\-energy}]{\setlength{\rightskip}{0pt plus 5cm}int loop\-\_\-energy ( +\begin{DoxyParamCaption} +\item[{short $\ast$}]{ptable, } +\item[{short $\ast$}]{s, } +\item[{short $\ast$}]{s1, } +\item[{int}]{i} +\end{DoxyParamCaption} +)}}\label{fold_8h_a507d4fd93f4b398d793ba2402731388d} + + +Calculate energy of a loop. + + +\begin{DoxyParams}{Parameters} +{\em ptable} & the pair table of the secondary structure \\ +\hline +{\em s} & encoded R\-N\-A sequence \\ +\hline +{\em s1} & encoded R\-N\-A sequence \\ +\hline +{\em i} & position of covering base pair \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +free energy of the loop in 10cal/mol +\end{DoxyReturn} +\hypertarget{fold_8h_adaa59b81664e2e36cb9932e891558fae}{\index{fold.\-h@{fold.\-h}!assign\-\_\-plist\-\_\-from\-\_\-db@{assign\-\_\-plist\-\_\-from\-\_\-db}} +\index{assign\-\_\-plist\-\_\-from\-\_\-db@{assign\-\_\-plist\-\_\-from\-\_\-db}!fold.h@{fold.\-h}} +\subsubsection[{assign\-\_\-plist\-\_\-from\-\_\-db}]{\setlength{\rightskip}{0pt plus 5cm}void assign\-\_\-plist\-\_\-from\-\_\-db ( +\begin{DoxyParamCaption} +\item[{{\bf plist} $\ast$$\ast$}]{pl, } +\item[{const char $\ast$}]{struc, } +\item[{float}]{pr} +\end{DoxyParamCaption} +)}}\label{fold_8h_adaa59b81664e2e36cb9932e891558fae} + + +Create a plist from a dot-\/bracket string. + +The dot-\/bracket string is parsed and for each base pair an entry in the plist is created. The probability of each pair in the list is set by a function parameter. + +The end of the plist is marked by sequence positions i as well as j equal to 0. This condition should be used to stop looping over its entries + +This function is threadsafe + + +\begin{DoxyParams}{Parameters} +{\em pl} & A pointer to the plist that is to be created \\ +\hline +{\em struc} & The secondary structure in dot-\/bracket notation \\ +\hline +{\em pr} & The probability for each base pair \\ +\hline +\end{DoxyParams} +\hypertarget{fold_8h_a2163034a25c6115d894b199e97e03f6c}{\index{fold.\-h@{fold.\-h}!Loop\-Energy@{Loop\-Energy}} +\index{Loop\-Energy@{Loop\-Energy}!fold.h@{fold.\-h}} +\subsubsection[{Loop\-Energy}]{\setlength{\rightskip}{0pt plus 5cm}int Loop\-Energy ( +\begin{DoxyParamCaption} +\item[{int}]{n1, } +\item[{int}]{n2, } +\item[{int}]{type, } +\item[{int}]{type\-\_\-2, } +\item[{int}]{si1, } +\item[{int}]{sj1, } +\item[{int}]{sp1, } +\item[{int}]{sq1} +\end{DoxyParamCaption} +)}}\label{fold_8h_a2163034a25c6115d894b199e97e03f6c} +\begin{DoxyRefDesc}{Deprecated} +\item[\hyperlink{deprecated__deprecated000002}{Deprecated}]\{This function is deprecated and will be removed soon. Use \hyperlink{loop__energies_8h_a3e5ad89f451254b1fe366d77aa8ff7bd}{E\-\_\-\-Int\-Loop()} instead!\} \end{DoxyRefDesc} +\hypertarget{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}{\index{fold.\-h@{fold.\-h}!Hairpin\-E@{Hairpin\-E}} +\index{Hairpin\-E@{Hairpin\-E}!fold.h@{fold.\-h}} +\subsubsection[{Hairpin\-E}]{\setlength{\rightskip}{0pt plus 5cm}int Hairpin\-E ( +\begin{DoxyParamCaption} +\item[{int}]{size, } +\item[{int}]{type, } +\item[{int}]{si1, } +\item[{int}]{sj1, } +\item[{const char $\ast$}]{string} +\end{DoxyParamCaption} +)}}\label{fold_8h_ab327ce11972f5ac069d52c8dedfdb700} +\begin{DoxyRefDesc}{Deprecated} +\item[\hyperlink{deprecated__deprecated000003}{Deprecated}]\{This function is deprecated and will be removed soon. Use \hyperlink{loop__energies_8h_aa362183cf6db89a10cdb0f5c4bd180c6}{E\-\_\-\-Hairpin()} instead!\} \end{DoxyRefDesc} +\hypertarget{fold_8h_ac3f0a28d9cb609d388b155445073fd20}{\index{fold.\-h@{fold.\-h}!initialize\-\_\-fold@{initialize\-\_\-fold}} +\index{initialize\-\_\-fold@{initialize\-\_\-fold}!fold.h@{fold.\-h}} +\subsubsection[{initialize\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}void initialize\-\_\-fold ( +\begin{DoxyParamCaption} +\item[{int}]{length} +\end{DoxyParamCaption} +)}}\label{fold_8h_ac3f0a28d9cb609d388b155445073fd20} +Allocate arrays for folding\par + \begin{DoxyRefDesc}{Deprecated} +\item[\hyperlink{deprecated__deprecated000004}{Deprecated}]\{This function is deprecated and will be removed soon!\}\end{DoxyRefDesc} +\hypertarget{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{\index{fold.\-h@{fold.\-h}!energy\-\_\-of\-\_\-struct@{energy\-\_\-of\-\_\-struct}} +\index{energy\-\_\-of\-\_\-struct@{energy\-\_\-of\-\_\-struct}!fold.h@{fold.\-h}} +\subsubsection[{energy\-\_\-of\-\_\-struct}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-struct ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{string, } +\item[{const char $\ast$}]{structure} +\end{DoxyParamCaption} +)}}\label{fold_8h_ac2b37fea2145c94d925a3f33378ef87b} +Calculate the free energy of an already folded R\-N\-A + +\begin{DoxyNote}{Note} +This function is not entirely threadsafe! Depending on the state of the global variable \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\-\_\-debug} it prints energy information to stdout or not...\par + +\end{DoxyNote} +\begin{DoxyRefDesc}{Deprecated} +\item[\hyperlink{deprecated__deprecated000005}{Deprecated}]This function is deprecated and should not be used in future programs! Use \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure()} instead!\end{DoxyRefDesc} + + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure}, \hyperlink{fold_8h_a657222e2758c46bf13b416ef3032e417}{energy\-\_\-of\-\_\-circ\-\_\-struct()}, \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy\-\_\-of\-\_\-struct\-\_\-pt()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em string} & R\-N\-A sequence \\ +\hline +{\em structure} & secondary structure in dot-\/bracket notation \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +the free energy of the input structure given the input sequence in kcal/mol +\end{DoxyReturn} +\hypertarget{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{\index{fold.\-h@{fold.\-h}!energy\-\_\-of\-\_\-struct\-\_\-pt@{energy\-\_\-of\-\_\-struct\-\_\-pt}} +\index{energy\-\_\-of\-\_\-struct\-\_\-pt@{energy\-\_\-of\-\_\-struct\-\_\-pt}!fold.h@{fold.\-h}} +\subsubsection[{energy\-\_\-of\-\_\-struct\-\_\-pt}]{\setlength{\rightskip}{0pt plus 5cm}int energy\-\_\-of\-\_\-struct\-\_\-pt ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{string, } +\item[{short $\ast$}]{ptable, } +\item[{short $\ast$}]{s, } +\item[{short $\ast$}]{s1} +\end{DoxyParamCaption} +)}}\label{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c} +Calculate the free energy of an already folded R\-N\-A + +\begin{DoxyNote}{Note} +This function is not entirely threadsafe! Depending on the state of the global variable \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\-\_\-debug} it prints energy information to stdout or not...\par + +\end{DoxyNote} +\begin{DoxyRefDesc}{Deprecated} +\item[\hyperlink{deprecated__deprecated000006}{Deprecated}]This function is deprecated and should not be used in future programs! Use \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\-\_\-of\-\_\-structure\-\_\-pt()} instead!\end{DoxyRefDesc} + + +\begin{DoxySeeAlso}{See Also} +\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table()}, \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em string} & R\-N\-A sequence \\ +\hline +{\em ptable} & the pair table of the secondary structure \\ +\hline +{\em s} & encoded R\-N\-A sequence \\ +\hline +{\em s1} & encoded R\-N\-A sequence \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +the free energy of the input structure given the input sequence in 10kcal/mol +\end{DoxyReturn} +\hypertarget{fold_8h_a657222e2758c46bf13b416ef3032e417}{\index{fold.\-h@{fold.\-h}!energy\-\_\-of\-\_\-circ\-\_\-struct@{energy\-\_\-of\-\_\-circ\-\_\-struct}} +\index{energy\-\_\-of\-\_\-circ\-\_\-struct@{energy\-\_\-of\-\_\-circ\-\_\-struct}!fold.h@{fold.\-h}} +\subsubsection[{energy\-\_\-of\-\_\-circ\-\_\-struct}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-circ\-\_\-struct ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{string, } +\item[{const char $\ast$}]{structure} +\end{DoxyParamCaption} +)}}\label{fold_8h_a657222e2758c46bf13b416ef3032e417} +Calculate the free energy of an already folded circular R\-N\-A + +\begin{DoxyNote}{Note} +This function is not entirely threadsafe! Depending on the state of the global variable \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\-\_\-debug} it prints energy information to stdout or not...\par + +\end{DoxyNote} +\begin{DoxyRefDesc}{Deprecated} +\item[\hyperlink{deprecated__deprecated000007}{Deprecated}]This function is deprecated and should not be used in future programs Use \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure()} instead!\end{DoxyRefDesc} + + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure()}, \hyperlink{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{energy\-\_\-of\-\_\-struct()}, \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy\-\_\-of\-\_\-struct\-\_\-pt()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em string} & R\-N\-A sequence \\ +\hline +{\em structure} & secondary structure in dot-\/bracket notation \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +the free energy of the input structure given the input sequence in kcal/mol +\end{DoxyReturn} diff --git a/binaries/src/ViennaRNA/doc/latex/fold_8h__incl.md5 b/binaries/src/ViennaRNA/doc/latex/fold_8h__incl.md5 new file mode 100644 index 0000000..34fef63 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/fold_8h__incl.md5 @@ -0,0 +1 @@ +ba444e7f7f1559b1c5c5aa0b41a7debe \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/fold_8h__incl.pdf b/binaries/src/ViennaRNA/doc/latex/fold_8h__incl.pdf new file mode 100644 index 0000000000000000000000000000000000000000..308f073350f23a2228bc33239d6038cde98cd3b6 GIT binary patch literal 7730 zcmb7}cRbbqALwn_8I|os$##}=i0l^#UdM)EBA43lEv=bfBA8B|+8pbY z)~`CQN&7H7xNZea?KnVVx>rl~UCM^6mXfJ+?uMn6&4Zjkzd#zBK=>6(3K~k2k8jcB zFQmfl9o!$_bVR%84VWkeYWi7++&y0v=%GYZUQ0-|K};+xpB=N?vB<{ei{YkK8_*M% z5fWRiuNP|>u;9!)4rg)qqJTF)**6B$?TXZbA$@9)ei;EQSU6q;QiKq|v 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+00005 +00006 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_} +00007 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func \_\_attribute\_\_ ((deprecated))} +00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else} +00009 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func} +00010 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif} +00011 \textcolor{preprocessor}{} +00061 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}{logML}; +00062 +00064 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold_8h_a6c5655c8b272e3e6cab74dd0f540294f}{uniq\_ML}; +00065 +00067 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\_point}; +00068 +00073 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\_debug}; +00074 +00075 +00119 \textcolor{keywordtype}{float} \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence, +00120 \textcolor{keywordtype}{char} *structure, +00121 \hyperlink{structparamT}{paramT} *parameters, +00122 \textcolor{keywordtype}{int} is\_constrained, +00123 \textcolor{keywordtype}{int} is\_circular); +00124 +00143 \textcolor{keywordtype}{float} \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence, +00144 \textcolor{keywordtype}{char} *structure); +00145 +00164 \textcolor{keywordtype}{float} \hyperlink{group__mfe__fold_ga4ac63ab3e8d9a80ced28b8052d94e423}{circfold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence, +00165 \textcolor{keywordtype}{char} *structure); +00166 +00167 +00195 \textcolor{keywordtype}{float} \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\_of\_structure}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}, +00196 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure, +00197 \textcolor{keywordtype}{int} verbosity\_level); +00198 +00214 \textcolor{keywordtype}{float} \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\_of\_struct\_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}, +00215 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure, +00216 \hyperlink{structparamT}{paramT} *parameters, +00217 \textcolor{keywordtype}{int} verbosity\_level); +00218 +00237 \textcolor{keywordtype}{float} \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\_of\_circ\_structure}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}, +00238 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure, +00239 \textcolor{keywordtype}{int} verbosity\_level); +00240 +00256 \textcolor{keywordtype}{float} \hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\_of\_circ\_struct\_par}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}, +00257 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure, +00258 \hyperlink{structparamT}{paramT} *parameters, +00259 \textcolor{keywordtype}{int} verbosity\_level); +00260 +00261 +00262 \textcolor{keywordtype}{float} energy\_of\_gquad\_structure(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}, +00263 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure, +00264 \textcolor{keywordtype}{int} verbosity\_level); +00265 +00286 \textcolor{keywordtype}{int} \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\_of\_structure\_pt}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}, +00287 \textcolor{keywordtype}{short} *ptable, +00288 \textcolor{keywordtype}{short} *s, +00289 \textcolor{keywordtype}{short} *s1, +00290 \textcolor{keywordtype}{int} verbosity\_level); +00291 +00309 \textcolor{keywordtype}{int} \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\_of\_struct\_pt\_par}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}, +00310 \textcolor{keywordtype}{short} *ptable, +00311 \textcolor{keywordtype}{short} *s, +00312 \textcolor{keywordtype}{short} *s1, +00313 \hyperlink{structparamT}{paramT} *parameters, +00314 \textcolor{keywordtype}{int} verbosity\_level); +00315 +00322 \textcolor{keywordtype}{void} \hyperlink{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}{free\_arrays}(\textcolor{keywordtype}{void}); +00323 +00324 +00330 \textcolor{keywordtype}{void} \hyperlink{fold_8h_a87b7869bd1d8dc79c60775c74e009e9b}{parenthesis\_structure}(\textcolor{keywordtype}{char} *structure, +00331 \hyperlink{structbondT}{bondT} *bp, +00332 \textcolor{keywordtype}{int} length); +00333 +00340 \textcolor{keywordtype}{void} \hyperlink{fold_8h_a325f3835c68f34fe833b2b7a5828857f}{parenthesis\_zuker}( \textcolor{keywordtype}{char} *structure, +00341 \hyperlink{structbondT}{bondT} *bp, +00342 \textcolor{keywordtype}{int} length); +00343 +00344 \textcolor{keywordtype}{void} letter\_structure(\textcolor{keywordtype}{char} *structure, +00345 \hyperlink{structbondT}{bondT} *bp, +00346 \textcolor{keywordtype}{int} length); +00347 +00348 +00354 \textcolor{keywordtype}{void} \hyperlink{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3}{update\_fold\_params}(\textcolor{keywordtype}{void}); +00355 +00361 \textcolor{keywordtype}{void} update\_fold\_params\_par(\hyperlink{structparamT}{paramT} *parameters); +00362 +00368 \textcolor{keywordtype}{char} *backtrack\_fold\_from\_pair(\textcolor{keywordtype}{char} *sequence, +00369 \textcolor{keywordtype}{int} i, +00370 \textcolor{keywordtype}{int} j); +00371 +00385 \textcolor{keywordtype}{float} \hyperlink{fold_8h_a539ecaed89730f7644c202f304d7529b}{energy\_of\_move}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}, +00386 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure, +00387 \textcolor{keywordtype}{int} m1, +00388 \textcolor{keywordtype}{int} m2); +00389 +00390 +00406 \textcolor{keywordtype}{int} \hyperlink{fold_8h_a49e0ee561be69faf0568213546f6a53f}{energy\_of\_move\_pt}(\textcolor{keywordtype}{short} *pt, +00407 \textcolor{keywordtype}{short} *s, +00408 \textcolor{keywordtype}{short} *s1, +00409 \textcolor{keywordtype}{int} m1, +00410 \textcolor{keywordtype}{int} m2); +00411 +00421 \textcolor{keywordtype}{int} \hyperlink{fold_8h_a507d4fd93f4b398d793ba2402731388d}{loop\_energy}(\textcolor{keywordtype}{short} *ptable, +00422 \textcolor{keywordtype}{short} *s, +00423 \textcolor{keywordtype}{short} *s1, +00424 \textcolor{keywordtype}{int} i); +00425 +00431 \textcolor{keywordtype}{void} export\_fold\_arrays(\textcolor{keywordtype}{int} **f5\_p, +00432 \textcolor{keywordtype}{int} **c\_p, +00433 \textcolor{keywordtype}{int} **fML\_p, +00434 \textcolor{keywordtype}{int} **fM1\_p, +00435 \textcolor{keywordtype}{int} **indx\_p, +00436 \textcolor{keywordtype}{char} **ptype\_p); +00437 +00443 \textcolor{keywordtype}{void} export\_fold\_arrays\_par(\textcolor{keywordtype}{int} **f5\_p, +00444 \textcolor{keywordtype}{int} **c\_p, +00445 \textcolor{keywordtype}{int} **fML\_p, +00446 \textcolor{keywordtype}{int} **fM1\_p, +00447 \textcolor{keywordtype}{int} **indx\_p, +00448 \textcolor{keywordtype}{char} **ptype\_p, +00449 \hyperlink{structparamT}{paramT} **P\_p); +00450 +00456 \textcolor{keywordtype}{void} export\_circfold\_arrays(\textcolor{keywordtype}{int} *Fc\_p, +00457 \textcolor{keywordtype}{int} *FcH\_p, +00458 \textcolor{keywordtype}{int} *FcI\_p, +00459 \textcolor{keywordtype}{int} *FcM\_p, +00460 \textcolor{keywordtype}{int} **fM2\_p, +00461 \textcolor{keywordtype}{int} **f5\_p, +00462 \textcolor{keywordtype}{int} **c\_p, +00463 \textcolor{keywordtype}{int} **fML\_p, +00464 \textcolor{keywordtype}{int} **fM1\_p, +00465 \textcolor{keywordtype}{int} **indx\_p, +00466 \textcolor{keywordtype}{char} **ptype\_p); +00467 +00473 \textcolor{keywordtype}{void} export\_circfold\_arrays\_par(\textcolor{keywordtype}{int} *Fc\_p, +00474 \textcolor{keywordtype}{int} *FcH\_p, +00475 \textcolor{keywordtype}{int} *FcI\_p, +00476 \textcolor{keywordtype}{int} *FcM\_p, +00477 \textcolor{keywordtype}{int} **fM2\_p, +00478 \textcolor{keywordtype}{int} **f5\_p, +00479 \textcolor{keywordtype}{int} **c\_p, +00480 \textcolor{keywordtype}{int} **fML\_p, +00481 \textcolor{keywordtype}{int} **fM1\_p, +00482 \textcolor{keywordtype}{int} **indx\_p, +00483 \textcolor{keywordtype}{char} **ptype\_p, +00484 \hyperlink{structparamT}{paramT} **P\_p); +00485 +00486 +00504 \textcolor{keywordtype}{void} \hyperlink{fold_8h_adaa59b81664e2e36cb9932e891558fae}{assign\_plist\_from\_db}(\hyperlink{structplist}{plist} **pl, +00505 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *struc, +00506 \textcolor{keywordtype}{float} pr); +00507 +00508 \textcolor{comment}{/* finally moved the loop energy function declarations to this header... */} +00509 \textcolor{comment}{/* BUT: The functions only exist for backward compatibility reasons! */} +00510 \textcolor{comment}{/* You better include "loop\_energies.h" and call the functions: */} +00511 \textcolor{comment}{/* E\_Hairpin() and E\_IntLoop() which are (almost) threadsafe as they get */} +00512 \textcolor{comment}{/* a pointer to the energy parameter datastructure as additional argument */} +00513 +00518 DEPRECATED(\textcolor{keywordtype}{int} \hyperlink{fold_8h_a2163034a25c6115d894b199e97e03f6c}{LoopEnergy}(\textcolor{keywordtype}{int} n1, +00519 \textcolor{keywordtype}{int} n2, +00520 \textcolor{keywordtype}{int} type, +00521 \textcolor{keywordtype}{int} type\_2, +00522 \textcolor{keywordtype}{int} si1, +00523 \textcolor{keywordtype}{int} sj1, +00524 \textcolor{keywordtype}{int} sp1, +00525 \textcolor{keywordtype}{int} sq1)); +00526 +00531 DEPRECATED(\textcolor{keywordtype}{int} \hyperlink{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}{HairpinE}(\textcolor{keywordtype}{int} size, +00532 \textcolor{keywordtype}{int} type, +00533 \textcolor{keywordtype}{int} si1, +00534 \textcolor{keywordtype}{int} sj1, +00535 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string})); +00536 +00542 DEPRECATED(\textcolor{keywordtype}{void} \hyperlink{fold_8h_ac3f0a28d9cb609d388b155445073fd20}{initialize\_fold}(\textcolor{keywordtype}{int} length)); +00543 +00558 DEPRECATED(\textcolor{keywordtype}{float} \hyperlink{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{energy\_of\_struct}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}, +00559 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure)); +00560 +00577 DEPRECATED(\textcolor{keywordtype}{int} \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy\_of\_struct\_pt}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}, +00578 \textcolor{keywordtype}{short} *ptable, +00579 \textcolor{keywordtype}{short} *s, +00580 \textcolor{keywordtype}{short} *s1)); +00581 +00596 DEPRECATED(\textcolor{keywordtype}{float} \hyperlink{fold_8h_a657222e2758c46bf13b416ef3032e417}{energy\_of\_circ\_struct}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}, +00597 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure)); +00598 +00599 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/fold__vars_8h.tex b/binaries/src/ViennaRNA/doc/latex/fold__vars_8h.tex new file mode 100644 index 0000000..b81518e --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/fold__vars_8h.tex @@ -0,0 +1,233 @@ +\hypertarget{fold__vars_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold\-\_\-vars.h File Reference} +\label{fold__vars_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold\-\_\-vars.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold\-\_\-vars.\-h}} +} + + +Here all all declarations of the global variables used throughout R\-N\-Alib. + + +Include dependency graph for fold\-\_\-vars.\-h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{fold__vars_8h__incl} +\end{center} +\end{figure} +This graph shows which files directly or indirectly include this file\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=350pt]{fold__vars_8h__dep__incl} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +void \hyperlink{fold__vars_8h_a4c3257186a796182462f18a5480ac8b3}{set\-\_\-model\-\_\-details} (\hyperlink{structmodel__detailsT}{model\-\_\-details\-T} $\ast$md) +\begin{DoxyCompactList}\small\item\em Set default model details. \end{DoxyCompactList}\end{DoxyCompactItemize} +\subsection*{Variables} +\begin{DoxyCompactItemize} +\item +\hypertarget{fold__vars_8h_a0afc287c2464866d94858c39175154af}{int \hyperlink{fold__vars_8h_a0afc287c2464866d94858c39175154af}{fold\-\_\-constrained}}\label{fold__vars_8h_a0afc287c2464866d94858c39175154af} + +\begin{DoxyCompactList}\small\item\em Global switch to activate/deactivate folding with structure constraints. \end{DoxyCompactList}\item +int \hyperlink{fold__vars_8h_a097eccaabd6ae8b4fef83cccff85bb5d}{no\-Lonely\-Pairs} +\begin{DoxyCompactList}\small\item\em Global switch to avoid/allow helices of length 1. \end{DoxyCompactList}\item +int \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles} +\begin{DoxyCompactList}\small\item\em Switch the energy model for dangling end contributions (0, 1, 2, 3) \end{DoxyCompactList}\item +\hypertarget{fold__vars_8h_abf380d09e4f1ab94fc6af57cf0ad5d32}{int \hyperlink{fold__vars_8h_abf380d09e4f1ab94fc6af57cf0ad5d32}{no\-G\-U}}\label{fold__vars_8h_abf380d09e4f1ab94fc6af57cf0ad5d32} + +\begin{DoxyCompactList}\small\item\em Global switch to forbid/allow G\-U base pairs at all. \end{DoxyCompactList}\item +\hypertarget{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259}{int \hyperlink{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259}{no\-\_\-closing\-G\-U}}\label{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259} + +\begin{DoxyCompactList}\small\item\em G\-U allowed only inside stacks if set to 1. \end{DoxyCompactList}\item +int \hyperlink{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}{tetra\-\_\-loop} +\begin{DoxyCompactList}\small\item\em Include special stabilizing energies for some tri-\/, tetra-\/ and hexa-\/loops;. \end{DoxyCompactList}\item +int \hyperlink{fold__vars_8h_afb1ef1166da85092ae8a325e02dcae71}{energy\-\_\-set} +\begin{DoxyCompactList}\small\item\em 0 = B\-P; 1=any mit G\-C; 2=any mit A\-U-\/parameter \end{DoxyCompactList}\item +\hypertarget{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ}}\label{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111} + +\begin{DoxyCompactList}\small\item\em backward compatibility variable.. this does not effect anything \end{DoxyCompactList}\item +\hypertarget{fold__vars_8h_af2763d55a74663a5e60652b8880baa5b}{int \hyperlink{fold__vars_8h_af2763d55a74663a5e60652b8880baa5b}{csv}}\label{fold__vars_8h_af2763d55a74663a5e60652b8880baa5b} + +\begin{DoxyCompactList}\small\item\em generate comma seperated output \end{DoxyCompactList}\item +int \hyperlink{fold__vars_8h_ac408868ba00671cbc7d1d535105af045}{old\-Ali\-En} +\item +int \hyperlink{fold__vars_8h_a0656afca1d2853f9ee6591172f5638de}{ribo} +\item +char $\ast$ \hyperlink{fold__vars_8h_a5dbaa0cca2c8c82048a0f0e38e164944}{Ribosum\-File} +\item +char $\ast$ \hyperlink{fold__vars_8h_a2695d91cc535d09c2eae5c3884e2ec64}{nonstandards} +\begin{DoxyCompactList}\small\item\em contains allowed non standard base pairs \end{DoxyCompactList}\item +double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature} +\begin{DoxyCompactList}\small\item\em Rescale energy parameters to a temperature in deg\-C. \end{DoxyCompactList}\item +int \hyperlink{fold__vars_8h_af349001ad3b4d008d0051d935b1b6261}{james\-\_\-rule} +\item +int \hyperlink{fold__vars_8h_a80c3c5fd35e7479704cc91d2d0367743}{log\-M\-L} +\item +int \hyperlink{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\-\_\-point} +\begin{DoxyCompactList}\small\item\em Marks the position (starting from 1) of the first nucleotide of the second molecule within the concatenated sequence. \end{DoxyCompactList}\item +\hyperlink{structbondT}{bond\-T} $\ast$ \hyperlink{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}{base\-\_\-pair} +\begin{DoxyCompactList}\small\item\em Contains a list of base pairs after a call to \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()}. \end{DoxyCompactList}\item +double $\ast$ \hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr} +\begin{DoxyCompactList}\small\item\em A pointer to the base pair probability matrix. \end{DoxyCompactList}\item +int $\ast$ \hyperlink{fold__vars_8h_a92089ae3a51b5d75a14ce9cc29cc8317}{iindx} +\begin{DoxyCompactList}\small\item\em index array to move through pr. \end{DoxyCompactList}\item +double \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\-\_\-scale} +\begin{DoxyCompactList}\small\item\em A scaling factor used by \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} to avoid overflows. \end{DoxyCompactList}\item +int \hyperlink{fold__vars_8h_ad512b5dd4dbec60faccfe137bb474489}{do\-\_\-backtrack} +\begin{DoxyCompactList}\small\item\em do backtracking, i.\-e. compute secondary structures or base pair probabilities \end{DoxyCompactList}\item +char \hyperlink{fold__vars_8h_a83bdb43472a259c71e69fa9f70f420c3}{backtrack\-\_\-type} +\begin{DoxyCompactList}\small\item\em A backtrack array marker for \hyperlink{group__inverse__fold_ga7af026de55d4babad879f2c92559cbbc}{inverse\-\_\-fold()} \end{DoxyCompactList}\item +\hypertarget{fold__vars_8h_a25f2bdcdf56e813d288845484a13d704}{int \hyperlink{fold__vars_8h_a25f2bdcdf56e813d288845484a13d704}{gquad}}\label{fold__vars_8h_a25f2bdcdf56e813d288845484a13d704} + +\begin{DoxyCompactList}\small\item\em Allow G-\/quadruplex formation. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Here all all declarations of the global variables used throughout R\-N\-Alib. + +\subsection{Function Documentation} +\hypertarget{fold__vars_8h_a4c3257186a796182462f18a5480ac8b3}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!set\-\_\-model\-\_\-details@{set\-\_\-model\-\_\-details}} +\index{set\-\_\-model\-\_\-details@{set\-\_\-model\-\_\-details}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{set\-\_\-model\-\_\-details}]{\setlength{\rightskip}{0pt plus 5cm}void set\-\_\-model\-\_\-details ( +\begin{DoxyParamCaption} +\item[{{\bf model\-\_\-details\-T} $\ast$}]{md} +\end{DoxyParamCaption} +)}}\label{fold__vars_8h_a4c3257186a796182462f18a5480ac8b3} + + +Set default model details. + +Use this function if you wish to initialize a \hyperlink{structmodel__detailsT}{model\-\_\-details\-T} data structure with its default values, i.\-e. the global model settings + +\begin{DoxySeeAlso}{See Also} + +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em md} & A pointer to the data structure that shall be initialized \\ +\hline +\end{DoxyParams} + + +\subsection{Variable Documentation} +\hypertarget{fold__vars_8h_a097eccaabd6ae8b4fef83cccff85bb5d}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!no\-Lonely\-Pairs@{no\-Lonely\-Pairs}} +\index{no\-Lonely\-Pairs@{no\-Lonely\-Pairs}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{no\-Lonely\-Pairs}]{\setlength{\rightskip}{0pt plus 5cm}int no\-Lonely\-Pairs}}\label{fold__vars_8h_a097eccaabd6ae8b4fef83cccff85bb5d} + + +Global switch to avoid/allow helices of length 1. + +Disallow all pairs which can only occur as lonely pairs (i.\-e. as helix of length 1). This avoids lonely base pairs in the predicted structures in most cases. \hypertarget{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!dangles@{dangles}} +\index{dangles@{dangles}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{dangles}]{\setlength{\rightskip}{0pt plus 5cm}int dangles}}\label{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74} + + +Switch the energy model for dangling end contributions (0, 1, 2, 3) + +If set to 0 no stabilizing energies are assigned to bases adjacent to helices in free ends and multiloops (so called dangling ends). Normally (dangles = 1) dangling end energies are assigned only to unpaired bases and a base cannot participate simultaneously in two dangling ends. In the partition function algorithm \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} these checks are neglected. If \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles} is set to 2, all folding routines will follow this convention. This treatment of dangling ends gives more favorable energies to helices directly adjacent to one another, which can be beneficial since such helices often do engage in stabilizing interactions through co-\/axial stacking.\par + If dangles = 3 co-\/axial stacking is explicitly included for adjacent helices in mutli-\/loops. The option affects only mfe folding and energy evaluation (\hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()} and \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure()}), as well as suboptimal folding (\hyperlink{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{subopt()}) via re-\/evaluation of energies. Co-\/axial stacking with one intervening mismatch is not considered so far. + +Default is 2 in most algorithms, partition function algorithms can only handle 0 and 2 \hypertarget{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!tetra\-\_\-loop@{tetra\-\_\-loop}} +\index{tetra\-\_\-loop@{tetra\-\_\-loop}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{tetra\-\_\-loop}]{\setlength{\rightskip}{0pt plus 5cm}int tetra\-\_\-loop}}\label{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e} + + +Include special stabilizing energies for some tri-\/, tetra-\/ and hexa-\/loops;. + +default is 1. \hypertarget{fold__vars_8h_afb1ef1166da85092ae8a325e02dcae71}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!energy\-\_\-set@{energy\-\_\-set}} +\index{energy\-\_\-set@{energy\-\_\-set}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{energy\-\_\-set}]{\setlength{\rightskip}{0pt plus 5cm}int energy\-\_\-set}}\label{fold__vars_8h_afb1ef1166da85092ae8a325e02dcae71} + + +0 = B\-P; 1=any mit G\-C; 2=any mit A\-U-\/parameter + +If set to 1 or 2\-: fold sequences from an artificial alphabet A\-B\-C\-D..., where A pairs B, C pairs D, etc. using either G\-C (1) or A\-U parameters (2); default is 0, you probably don't want to change it. \hypertarget{fold__vars_8h_ac408868ba00671cbc7d1d535105af045}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!old\-Ali\-En@{old\-Ali\-En}} +\index{old\-Ali\-En@{old\-Ali\-En}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{old\-Ali\-En}]{\setlength{\rightskip}{0pt plus 5cm}int old\-Ali\-En}}\label{fold__vars_8h_ac408868ba00671cbc7d1d535105af045} +use old alifold energies (with gaps) \hypertarget{fold__vars_8h_a0656afca1d2853f9ee6591172f5638de}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!ribo@{ribo}} +\index{ribo@{ribo}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{ribo}]{\setlength{\rightskip}{0pt plus 5cm}int ribo}}\label{fold__vars_8h_a0656afca1d2853f9ee6591172f5638de} +use ribosum matrices \hypertarget{fold__vars_8h_a5dbaa0cca2c8c82048a0f0e38e164944}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!Ribosum\-File@{Ribosum\-File}} +\index{Ribosum\-File@{Ribosum\-File}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{Ribosum\-File}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ Ribosum\-File}}\label{fold__vars_8h_a5dbaa0cca2c8c82048a0f0e38e164944} +warning this variable will vanish in the future ribosums will be compiled in instead \hypertarget{fold__vars_8h_a2695d91cc535d09c2eae5c3884e2ec64}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!nonstandards@{nonstandards}} +\index{nonstandards@{nonstandards}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{nonstandards}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ nonstandards}}\label{fold__vars_8h_a2695d91cc535d09c2eae5c3884e2ec64} + + +contains allowed non standard base pairs + +Lists additional base pairs that will be allowed to form in addition to G\-C, C\-G, A\-U, U\-A, G\-U and U\-G. Nonstandard base pairs are given a stacking energy of 0. \hypertarget{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!temperature@{temperature}} +\index{temperature@{temperature}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{temperature}]{\setlength{\rightskip}{0pt plus 5cm}double temperature}}\label{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead} + + +Rescale energy parameters to a temperature in deg\-C. + +Default is 37\-C. You have to call the update\-\_\-...\-\_\-params() functions after changing this parameter. \hypertarget{fold__vars_8h_af349001ad3b4d008d0051d935b1b6261}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!james\-\_\-rule@{james\-\_\-rule}} +\index{james\-\_\-rule@{james\-\_\-rule}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{james\-\_\-rule}]{\setlength{\rightskip}{0pt plus 5cm}int james\-\_\-rule}}\label{fold__vars_8h_af349001ad3b4d008d0051d935b1b6261} +interior loops of size 2 get energy 0.\-8\-Kcal and no mismatches, default 1 \hypertarget{fold__vars_8h_a80c3c5fd35e7479704cc91d2d0367743}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!log\-M\-L@{log\-M\-L}} +\index{log\-M\-L@{log\-M\-L}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{log\-M\-L}]{\setlength{\rightskip}{0pt plus 5cm}int log\-M\-L}}\label{fold__vars_8h_a80c3c5fd35e7479704cc91d2d0367743} +use logarithmic multiloop energy function \hypertarget{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!cut\-\_\-point@{cut\-\_\-point}} +\index{cut\-\_\-point@{cut\-\_\-point}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{cut\-\_\-point}]{\setlength{\rightskip}{0pt plus 5cm}int cut\-\_\-point}}\label{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda} + + +Marks the position (starting from 1) of the first nucleotide of the second molecule within the concatenated sequence. + +To evaluate the energy of a duplex structure (a structure formed by two strands), concatenate the to sequences and set it to the first base of the second strand in the concatenated sequence. The default value of -\/1 stands for single molecule folding. The cut\-\_\-point variable is also used by \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{P\-S\-\_\-rna\-\_\-plot()} and \hyperlink{PS__dot_8h_a689a97a7e3b8a2df14728b8204d9d57b}{P\-S\-\_\-dot\-\_\-plot()} to mark the chain break in postscript plots. \hypertarget{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!base\-\_\-pair@{base\-\_\-pair}} +\index{base\-\_\-pair@{base\-\_\-pair}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{base\-\_\-pair}]{\setlength{\rightskip}{0pt plus 5cm}{\bf bond\-T}$\ast$ base\-\_\-pair}}\label{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc} + + +Contains a list of base pairs after a call to \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()}. + +base\-\_\-pair\mbox{[}0\mbox{]}.i contains the total number of pairs. \begin{DoxyRefDesc}{Deprecated} +\item[\hyperlink{deprecated__deprecated000008}{Deprecated}]Do not use this variable anymore! \end{DoxyRefDesc} +\hypertarget{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!pr@{pr}} +\index{pr@{pr}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{pr}]{\setlength{\rightskip}{0pt plus 5cm}double$\ast$ pr}}\label{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52} + + +A pointer to the base pair probability matrix. + +\begin{DoxyRefDesc}{Deprecated} +\item[\hyperlink{deprecated__deprecated000009}{Deprecated}]Do not use this variable anymore! \end{DoxyRefDesc} +\hypertarget{fold__vars_8h_a92089ae3a51b5d75a14ce9cc29cc8317}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!iindx@{iindx}} +\index{iindx@{iindx}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{iindx}]{\setlength{\rightskip}{0pt plus 5cm}int$\ast$ iindx}}\label{fold__vars_8h_a92089ae3a51b5d75a14ce9cc29cc8317} + + +index array to move through pr. + +The probability for base i and j to form a pair is in pr\mbox{[}iindx\mbox{[}i\mbox{]}-\/j\mbox{]}. \begin{DoxyRefDesc}{Deprecated} +\item[\hyperlink{deprecated__deprecated000010}{Deprecated}]Do not use this variable anymore! \end{DoxyRefDesc} +\hypertarget{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!pf\-\_\-scale@{pf\-\_\-scale}} +\index{pf\-\_\-scale@{pf\-\_\-scale}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{pf\-\_\-scale}]{\setlength{\rightskip}{0pt plus 5cm}double pf\-\_\-scale}}\label{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd} + + +A scaling factor used by \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} to avoid overflows. + +Should be set to approximately $exp{((-F/kT)/length)}$, where $F$ is an estimate for the ensemble free energy, for example the minimum free energy. You must call \hyperlink{group__pf__fold_ga384e927890f9c034ff09fa66da102d28}{update\-\_\-pf\-\_\-params()} after changing this parameter.\par + If pf\-\_\-scale is -\/1 (the default) , an estimate will be provided automatically when computing partition functions, e.\-g. \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} The automatic estimate is usually insufficient for sequences more than a few hundred bases long. \hypertarget{fold__vars_8h_ad512b5dd4dbec60faccfe137bb474489}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!do\-\_\-backtrack@{do\-\_\-backtrack}} +\index{do\-\_\-backtrack@{do\-\_\-backtrack}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{do\-\_\-backtrack}]{\setlength{\rightskip}{0pt plus 5cm}int do\-\_\-backtrack}}\label{fold__vars_8h_ad512b5dd4dbec60faccfe137bb474489} + + +do backtracking, i.\-e. compute secondary structures or base pair probabilities + +If 0, do not calculate pair probabilities in \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()}; this is about twice as fast. Default is 1. \hypertarget{fold__vars_8h_a83bdb43472a259c71e69fa9f70f420c3}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!backtrack\-\_\-type@{backtrack\-\_\-type}} +\index{backtrack\-\_\-type@{backtrack\-\_\-type}!fold_vars.h@{fold\-\_\-vars.\-h}} +\subsubsection[{backtrack\-\_\-type}]{\setlength{\rightskip}{0pt plus 5cm}char backtrack\-\_\-type}}\label{fold__vars_8h_a83bdb43472a259c71e69fa9f70f420c3} + + +A backtrack array marker for \hyperlink{group__inverse__fold_ga7af026de55d4babad879f2c92559cbbc}{inverse\-\_\-fold()} + +If set to 'C'\-: force (1,N) to be paired, 'M' fold as if the sequence were inside a multi-\/loop. 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HcmV?d00001 diff --git a/binaries/src/ViennaRNA/doc/latex/fold__vars_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/fold__vars_8h_source.tex new file mode 100644 index 0000000..00ad574 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/fold__vars_8h_source.tex @@ -0,0 +1,67 @@ +\hypertarget{fold__vars_8h}{\section{fold\-\_\-vars.\-h} +\label{fold__vars_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold\-\_\-vars.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold\-\_\-vars.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_FOLD\_VARS\_H\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_FOLD\_VARS\_H\_\_} +00003 \textcolor{preprocessor}{} +00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"} +00005 +00012 \textcolor{preprocessor}{#define PUBLIC} +00013 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define PRIVATE static} +00014 \textcolor{preprocessor}{} +00018 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_a0afc287c2464866d94858c39175154af}{fold\_constrained}; +00019 +00027 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_a097eccaabd6ae8b4fef83cccff85bb5d}{noLonelyPairs}; +00028 +00050 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}; +00051 +00055 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_abf380d09e4f1ab94fc6af57cf0ad5d32}{noGU}; +00056 +00060 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259}{no\_closingGU}; +00061 +00067 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}{tetra\_loop}; +00068 +00076 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_afb1ef1166da85092ae8a325e02dcae71}{energy\_set}; +00077 +00081 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ}; +00082 +00086 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_af2763d55a74663a5e60652b8880baa5b}{csv}; +00087 +00091 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_ac408868ba00671cbc7d1d535105af045}{oldAliEn}; +00095 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_a0656afca1d2853f9ee6591172f5638de}{ribo}; +00096 +00101 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} *\hyperlink{fold__vars_8h_a5dbaa0cca2c8c82048a0f0e38e164944}{RibosumFile}; +00102 +00110 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} *\hyperlink{fold__vars_8h_a2695d91cc535d09c2eae5c3884e2ec64}{nonstandards}; +00111 +00118 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}; +00119 +00124 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_af349001ad3b4d008d0051d935b1b6261}{james\_rule}; +00125 +00129 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}{logML}; +00130 +00142 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\_point}; +00143 +00150 \textcolor{keyword}{extern} \hyperlink{structbondT}{bondT} *\hyperlink{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}{base\_pair}; +00151 +00157 \textcolor{keyword}{extern} FLT\_OR\_DBL *\hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr}; +00158 +00165 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} *\hyperlink{fold__vars_8h_a92089ae3a51b5d75a14ce9cc29cc8317}{iindx}; +00166 +00178 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\_scale}; +00179 +00186 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_ad512b5dd4dbec60faccfe137bb474489}{do\_backtrack}; +00187 +00195 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} \hyperlink{fold__vars_8h_a83bdb43472a259c71e69fa9f70f420c3}{backtrack\_type}; +00196 +00200 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{fold__vars_8h_a25f2bdcdf56e813d288845484a13d704}{gquad}; +00201 +00202 +00203 \textcolor{keywordtype}{char} * option\_string(\textcolor{keywordtype}{void}); +00204 +00215 \textcolor{keywordtype}{void} \hyperlink{fold__vars_8h_a4c3257186a796182462f18a5480ac8b3}{set\_model\_details}(\hyperlink{structmodel__detailsT}{model\_detailsT} *md); +00216 +00217 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/gquad_8h.tex b/binaries/src/ViennaRNA/doc/latex/gquad_8h.tex new file mode 100644 index 0000000..f1b3475 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/gquad_8h.tex @@ -0,0 +1,155 @@ +\hypertarget{gquad_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/gquad.h File Reference} +\label{gquad_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/gquad.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/gquad.\-h}} +} + + +Various functions related to G-\/quadruplex computations. + + +Include dependency graph for gquad.\-h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{gquad_8h__incl} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +int $\ast$ \hyperlink{gquad_8h_a8b0784c14fa1208d0aebbebdc1318b7a}{get\-\_\-gquad\-\_\-matrix} (short $\ast$S, \hyperlink{structparamT}{param\-T} $\ast$P) +\begin{DoxyCompactList}\small\item\em Get a triangular matrix prefilled with minimum free energy contributions of G-\/quadruplexes. \end{DoxyCompactList}\item +int \hyperlink{gquad_8h_ae41763215b9c64d2a7b67f0df8a28078}{parse\-\_\-gquad} (const char $\ast$struc, int $\ast$L, int l\mbox{[}3\mbox{]}) +\item +P\-R\-I\-V\-A\-T\-E int \hyperlink{gquad_8h_a54475a8eb898fa1e8af8ab5f5375f3be}{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop} (int c, int i, int j, int type, short $\ast$S, int $\ast$ggg, int $\ast$index, int $\ast$p, int $\ast$q, \hyperlink{structparamT}{param\-T} $\ast$P) +\item +P\-R\-I\-V\-A\-T\-E int \hyperlink{gquad_8h_a118ec7289f1936bd810be7fe50b98212}{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop\-\_\-\-L} (int c, int i, int j, int type, short $\ast$S, int $\ast$$\ast$ggg, int maxdist, int $\ast$p, int $\ast$q, \hyperlink{structparamT}{param\-T} $\ast$P) +\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Various functions related to G-\/quadruplex computations. + +\subsection{Function Documentation} +\hypertarget{gquad_8h_a8b0784c14fa1208d0aebbebdc1318b7a}{\index{gquad.\-h@{gquad.\-h}!get\-\_\-gquad\-\_\-matrix@{get\-\_\-gquad\-\_\-matrix}} +\index{get\-\_\-gquad\-\_\-matrix@{get\-\_\-gquad\-\_\-matrix}!gquad.h@{gquad.\-h}} +\subsubsection[{get\-\_\-gquad\-\_\-matrix}]{\setlength{\rightskip}{0pt plus 5cm}int$\ast$ get\-\_\-gquad\-\_\-matrix ( +\begin{DoxyParamCaption} +\item[{short $\ast$}]{S, } +\item[{{\bf param\-T} $\ast$}]{P} +\end{DoxyParamCaption} +)}}\label{gquad_8h_a8b0784c14fa1208d0aebbebdc1318b7a} + + +Get a triangular matrix prefilled with minimum free energy contributions of G-\/quadruplexes. + +At each position ij in the matrix, the minimum free energy of any G-\/quadruplex delimited by i and j is stored. If no G-\/quadruplex formation is possible, the matrix element is set to I\-N\-F. Access the elements in the matrix via matrix\mbox{[}indx\mbox{[}j\mbox{]}+i\mbox{]}. To get the integer array indx see get\-\_\-jindx(). + +\begin{DoxySeeAlso}{See Also} +get\-\_\-jindx(), encode\-\_\-sequence() +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em S} & The encoded sequence \\ +\hline +{\em P} & A pointer to the data structure containing the precomputed energy contributions \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +A pointer to the G-\/quadruplex contribution matrix +\end{DoxyReturn} +\hypertarget{gquad_8h_ae41763215b9c64d2a7b67f0df8a28078}{\index{gquad.\-h@{gquad.\-h}!parse\-\_\-gquad@{parse\-\_\-gquad}} +\index{parse\-\_\-gquad@{parse\-\_\-gquad}!gquad.h@{gquad.\-h}} +\subsubsection[{parse\-\_\-gquad}]{\setlength{\rightskip}{0pt plus 5cm}int parse\-\_\-gquad ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{struc, } +\item[{int $\ast$}]{L, } +\item[{int}]{l\mbox{[}3\mbox{]}} +\end{DoxyParamCaption} +)}}\label{gquad_8h_ae41763215b9c64d2a7b67f0df8a28078} +given a dot-\/bracket structure (possibly) containing gquads encoded by '+' signs, find first gquad, return end position or 0 if none found Upon return L and l\mbox{[}\mbox{]} contain the number of stacked layers, as well as the lengths of the linker regions. To parse a string with many gquads, call parse\-\_\-gquad repeatedly e.\-g. end1 = parse\-\_\-gquad(struc, \&\-L, l); ... ; end2 = parse\-\_\-gquad(struc+end1, \&L, l); end2+=end1; ... ; end3 = parse\-\_\-gquad(struc+end2, \&L, l); end3+=end2; ... ; \hypertarget{gquad_8h_a54475a8eb898fa1e8af8ab5f5375f3be}{\index{gquad.\-h@{gquad.\-h}!backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop@{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop}} +\index{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop@{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop}!gquad.h@{gquad.\-h}} +\subsubsection[{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop}]{\setlength{\rightskip}{0pt plus 5cm}P\-R\-I\-V\-A\-T\-E int backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop ( +\begin{DoxyParamCaption} +\item[{int}]{c, } +\item[{int}]{i, } +\item[{int}]{j, } +\item[{int}]{type, } +\item[{short $\ast$}]{S, } +\item[{int $\ast$}]{ggg, } +\item[{int $\ast$}]{index, } +\item[{int $\ast$}]{p, } +\item[{int $\ast$}]{q, } +\item[{{\bf param\-T} $\ast$}]{P} +\end{DoxyParamCaption} +)}}\label{gquad_8h_a54475a8eb898fa1e8af8ab5f5375f3be} +backtrack an interior loop like enclosed g-\/quadruplex with closing pair (i,j) + + +\begin{DoxyParams}{Parameters} +{\em c} & The total contribution the loop should resemble \\ +\hline +{\em i} & position i of enclosing pair \\ +\hline +{\em j} & position j of enclosing pair \\ +\hline +{\em type} & base pair type of enclosing pair (must be reverse type) \\ +\hline +{\em S} & integer encoded sequence \\ +\hline +{\em ggg} & triangular matrix containing g-\/quadruplex contributions \\ +\hline +{\em index} & the index for accessing the triangular matrix \\ +\hline +{\em p} & here the 5' position of the gquad is stored \\ +\hline +{\em q} & here the 3' position of the gquad is stored \\ +\hline +{\em P} & the datastructure containing the precalculated contibutions\\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +1 on success, 0 if no gquad found +\end{DoxyReturn} +\hypertarget{gquad_8h_a118ec7289f1936bd810be7fe50b98212}{\index{gquad.\-h@{gquad.\-h}!backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop\-\_\-\-L@{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop\-\_\-\-L}} +\index{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop\-\_\-\-L@{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop\-\_\-\-L}!gquad.h@{gquad.\-h}} +\subsubsection[{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop\-\_\-\-L}]{\setlength{\rightskip}{0pt plus 5cm}P\-R\-I\-V\-A\-T\-E int backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop\-\_\-\-L ( +\begin{DoxyParamCaption} +\item[{int}]{c, } +\item[{int}]{i, } +\item[{int}]{j, } +\item[{int}]{type, } +\item[{short $\ast$}]{S, } +\item[{int $\ast$$\ast$}]{ggg, } +\item[{int}]{maxdist, } +\item[{int $\ast$}]{p, } +\item[{int $\ast$}]{q, } +\item[{{\bf param\-T} $\ast$}]{P} +\end{DoxyParamCaption} +)}}\label{gquad_8h_a118ec7289f1936bd810be7fe50b98212} +backtrack an interior loop like enclosed g-\/quadruplex with closing pair (i,j) with underlying Lfold matrix + + +\begin{DoxyParams}{Parameters} +{\em c} & The total contribution the loop should resemble \\ +\hline +{\em i} & position i of enclosing pair \\ +\hline +{\em j} & position j of enclosing pair \\ +\hline +{\em type} & base pair type of enclosing pair (must be reverse type) \\ +\hline +{\em S} & integer encoded sequence \\ +\hline +{\em ggg} & triangular matrix containing g-\/quadruplex contributions \\ +\hline +{\em p} & here the 5' position of the gquad is stored \\ +\hline +{\em q} & here the 3' position of the gquad is stored \\ +\hline +{\em P} & the datastructure containing the precalculated contibutions\\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +1 on success, 0 if no gquad found +\end{DoxyReturn} diff --git a/binaries/src/ViennaRNA/doc/latex/gquad_8h__incl.md5 b/binaries/src/ViennaRNA/doc/latex/gquad_8h__incl.md5 new file mode 100644 index 0000000..f07d791 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/gquad_8h__incl.md5 @@ -0,0 +1 @@ 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\textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_GQUAD\_H\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_GQUAD\_H\_\_} +00003 \textcolor{preprocessor}{} +00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"} +00005 +00006 \textcolor{preprocessor}{#ifndef INLINE} +00007 \textcolor{preprocessor}{}\textcolor{preprocessor}{#ifdef \_\_GNUC\_\_} +00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{# define INLINE inline} +00009 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else} +00010 \textcolor{preprocessor}{}\textcolor{preprocessor}{# define INLINE} +00011 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif} +00012 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif} +00013 \textcolor{preprocessor}{} +00020 \textcolor{keywordtype}{int} E\_gquad(\textcolor{keywordtype}{int} L, +00021 \textcolor{keywordtype}{int} l[3], +00022 \hyperlink{structparamT}{paramT} *P); +00023 +00024 FLT\_OR\_DBL exp\_E\_gquad( \textcolor{keywordtype}{int} L, +00025 \textcolor{keywordtype}{int} l[3], +00026 \hyperlink{structpf__paramT}{pf\_paramT} *pf); +00027 +00028 \textcolor{keywordtype}{int} E\_gquad\_ali(\textcolor{keywordtype}{int} i, +00029 \textcolor{keywordtype}{int} L, +00030 \textcolor{keywordtype}{int} l[3], +00031 \textcolor{keyword}{const} \textcolor{keywordtype}{short} **S, +00032 \textcolor{keywordtype}{int} n\_seq, +00033 \hyperlink{structparamT}{paramT} *P); +00034 +00035 +00036 \textcolor{keywordtype}{void} E\_gquad\_ali\_en( \textcolor{keywordtype}{int} i, +00037 \textcolor{keywordtype}{int} L, +00038 \textcolor{keywordtype}{int} l[3], +00039 \textcolor{keyword}{const} \textcolor{keywordtype}{short} **S, +00040 \textcolor{keywordtype}{int} n\_seq, +00041 \textcolor{keywordtype}{int} en[2], +00042 \hyperlink{structparamT}{paramT} *P); +00043 +00060 \textcolor{keywordtype}{int} *\hyperlink{gquad_8h_a8b0784c14fa1208d0aebbebdc1318b7a}{get\_gquad\_matrix}(\textcolor{keywordtype}{short} *S, \hyperlink{structparamT}{paramT} *P); +00061 +00062 \textcolor{keywordtype}{int} *get\_gquad\_ali\_matrix(\textcolor{keywordtype}{short} *S\_cons, +00063 \textcolor{keywordtype}{short} **S, +00064 \textcolor{keywordtype}{int} n\_seq, +00065 \hyperlink{structparamT}{paramT} *P); +00066 +00067 FLT\_OR\_DBL *get\_gquad\_pf\_matrix( \textcolor{keywordtype}{short} *S, +00068 FLT\_OR\_DBL *scale, +00069 \hyperlink{structpf__paramT}{pf\_paramT} *pf); +00070 +00071 \textcolor{keywordtype}{int} **get\_gquad\_L\_matrix( \textcolor{keywordtype}{short} *S, +00072 \textcolor{keywordtype}{int} start, +00073 \textcolor{keywordtype}{int} maxdist, +00074 \textcolor{keywordtype}{int} **g, +00075 \hyperlink{structparamT}{paramT} *P); +00076 +00077 \textcolor{keywordtype}{void} get\_gquad\_pattern\_mfe(\textcolor{keywordtype}{short} *S, +00078 \textcolor{keywordtype}{int} i, +00079 \textcolor{keywordtype}{int} j, +00080 \hyperlink{structparamT}{paramT} *P, +00081 \textcolor{keywordtype}{int} *L, +00082 \textcolor{keywordtype}{int} l[3]); +00083 +00084 \textcolor{keywordtype}{void} get\_gquad\_pattern\_pf( \textcolor{keywordtype}{short} *S, +00085 \textcolor{keywordtype}{int} i, +00086 \textcolor{keywordtype}{int} j, +00087 \hyperlink{structpf__paramT}{pf\_paramT} *pf, +00088 \textcolor{keywordtype}{int} *L, +00089 \textcolor{keywordtype}{int} l[3]); +00090 +00091 \hyperlink{structplist}{plist} *get\_plist\_gquad\_from\_pr( \textcolor{keywordtype}{short} *S, +00092 \textcolor{keywordtype}{int} gi, +00093 \textcolor{keywordtype}{int} gj, +00094 FLT\_OR\_DBL *G, +00095 FLT\_OR\_DBL *probs, +00096 FLT\_OR\_DBL *scale, +00097 \hyperlink{structpf__paramT}{pf\_paramT} *pf); +00098 \hyperlink{structplist}{plist} *get\_plist\_gquad\_from\_pr\_max(\textcolor{keywordtype}{short} *S, +00099 \textcolor{keywordtype}{int} gi, +00100 \textcolor{keywordtype}{int} gj, +00101 FLT\_OR\_DBL *G, +00102 FLT\_OR\_DBL *probs, +00103 FLT\_OR\_DBL *scale, +00104 \textcolor{keywordtype}{int} *L, +00105 \textcolor{keywordtype}{int} l[3], +00106 \hyperlink{structpf__paramT}{pf\_paramT} *pf); +00107 +00108 \hyperlink{structplist}{plist} *get\_plist\_gquad\_from\_db( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure, +00109 \textcolor{keywordtype}{float} pr); +00110 +00121 \textcolor{keywordtype}{int} \hyperlink{gquad_8h_ae41763215b9c64d2a7b67f0df8a28078}{parse\_gquad}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *struc, \textcolor{keywordtype}{int} *L, \textcolor{keywordtype}{int} l[3]); +00122 +00123 +00124 +\hypertarget{gquad_8h_source_l00142}{}\hyperlink{gquad_8h_a54475a8eb898fa1e8af8ab5f5375f3be}{00142} INLINE PRIVATE \textcolor{keywordtype}{int} \hyperlink{gquad_8h_a54475a8eb898fa1e8af8ab5f5375f3be}{backtrack\_GQuad\_IntLoop}(\textcolor{keywordtype}{int} c, +00143 \textcolor{keywordtype}{int} i, +00144 \textcolor{keywordtype}{int} j, +00145 \textcolor{keywordtype}{int} type, +00146 \textcolor{keywordtype}{short} *S, +00147 \textcolor{keywordtype}{int} *ggg, +00148 \textcolor{keywordtype}{int} *index, +00149 \textcolor{keywordtype}{int} *p, +00150 \textcolor{keywordtype}{int} *q, +00151 \hyperlink{structparamT}{paramT} *P)\{ +00152 +00153 \textcolor{keywordtype}{int} energy, \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}, k, l, maxl, minl, c0, l1; +00154 \textcolor{keywordtype}{short} si, sj; +00155 +00156 dangles = P->\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model\_details}.\hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{dangles}; +00157 si = S[i + 1]; +00158 sj = S[j - 1]; +00159 energy = 0; +00160 +00161 \textcolor{keywordflow}{if}(dangles == 2) +00162 energy += P->mismatchI[type][si][sj]; +00163 +00164 \textcolor{keywordflow}{if}(type > 2) +00165 energy += P->TerminalAU; +00166 +00167 k = i + 1; +00168 \textcolor{keywordflow}{if}(S[k] == 3)\{ +00169 \textcolor{keywordflow}{if}(k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{ +00170 minl = j - i + k - \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP} - 2; +00171 c0 = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1; +00172 minl = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minl); +00173 c0 = j - 3; +00174 maxl = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1; +00175 maxl = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxl); +00176 \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{ +00177 \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue}; +00178 \textcolor{keywordflow}{if}(c == energy + ggg[index[l] + k] + P->internal\_loop[j - l - 1])\{ +00179 *p = k; *q = l; +00180 \textcolor{keywordflow}{return} 1; +00181 \} +00182 \} +00183 \} +00184 \} +00185 +00186 \textcolor{keywordflow}{for}(k = i + 2; +00187 k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; +00188 k++)\{ +00189 l1 = k - i - 1; +00190 \textcolor{keywordflow}{if}(l1>\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}) \textcolor{keywordflow}{break}; +00191 \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue}; +00192 minl = j - i + k - \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP} - 2; +00193 c0 = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1; +00194 minl = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minl); +00195 c0 = j - 1; +00196 maxl = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1; +00197 maxl = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxl); +00198 \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{ +00199 \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue}; +00200 \textcolor{keywordflow}{if}(c == energy + ggg[index[l] + k] + P->internal\_loop[l1 + j - l - 1])\{ +00201 *p = k; *q = l; +00202 \textcolor{keywordflow}{return} 1; +00203 \} +00204 \} +00205 \} +00206 +00207 l = j - 1; +00208 \textcolor{keywordflow}{if}(S[l] == 3) +00209 \textcolor{keywordflow}{for}(k = i + 4; +00210 k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; +00211 k++)\{ +00212 l1 = k - i - 1; +00213 \textcolor{keywordflow}{if}(l1>\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}) \textcolor{keywordflow}{break}; +00214 \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue}; +00215 \textcolor{keywordflow}{if}(c == energy + ggg[index[l] + k] + P->internal\_loop[l1])\{ +00216 *p = k; *q = l; +00217 \textcolor{keywordflow}{return} 1; +00218 \} +00219 \} +00220 +00221 \textcolor{keywordflow}{return} 0; +00222 \} +00223 +\hypertarget{gquad_8h_source_l00240}{}\hyperlink{gquad_8h_a118ec7289f1936bd810be7fe50b98212}{00240} INLINE PRIVATE \textcolor{keywordtype}{int} \hyperlink{gquad_8h_a118ec7289f1936bd810be7fe50b98212}{backtrack\_GQuad\_IntLoop\_L}(\textcolor{keywordtype}{int} c, +00241 \textcolor{keywordtype}{int} i, +00242 \textcolor{keywordtype}{int} j, +00243 \textcolor{keywordtype}{int} type, +00244 \textcolor{keywordtype}{short} *S, +00245 \textcolor{keywordtype}{int} **ggg, +00246 \textcolor{keywordtype}{int} maxdist, +00247 \textcolor{keywordtype}{int} *p, +00248 \textcolor{keywordtype}{int} *q, +00249 \hyperlink{structparamT}{paramT} *P)\{ +00250 +00251 \textcolor{keywordtype}{int} energy, \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}, k, l, maxl, minl, c0, l1; +00252 \textcolor{keywordtype}{short} si, sj; +00253 +00254 dangles = P->\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model\_details}.\hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{dangles}; +00255 si = S[i + 1]; +00256 sj = S[j - 1]; +00257 energy = 0; +00258 +00259 \textcolor{keywordflow}{if}(dangles == 2) +00260 energy += P->mismatchI[type][si][sj]; +00261 +00262 \textcolor{keywordflow}{if}(type > 2) +00263 energy += P->TerminalAU; +00264 +00265 k = i + 1; +00266 \textcolor{keywordflow}{if}(S[k] == 3)\{ +00267 \textcolor{keywordflow}{if}(k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{ +00268 minl = j - i + k - \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP} - 2; +00269 c0 = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1; +00270 minl = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minl); +00271 c0 = j - 3; +00272 maxl = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1; +00273 maxl = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxl); +00274 \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{ +00275 \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue}; +00276 \textcolor{keywordflow}{if}(c == energy + ggg[k][l - k] + P->internal\_loop[j - l - 1])\{ +00277 *p = k; *q = l; +00278 \textcolor{keywordflow}{return} 1; +00279 \} +00280 \} +00281 \} +00282 \} +00283 +00284 \textcolor{keywordflow}{for}(k = i + 2; +00285 k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; +00286 k++)\{ +00287 l1 = k - i - 1; +00288 \textcolor{keywordflow}{if}(l1>\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}) \textcolor{keywordflow}{break}; +00289 \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue}; +00290 minl = j - i + k - \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP} - 2; +00291 c0 = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1; +00292 minl = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minl); +00293 c0 = j - 1; +00294 maxl = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1; +00295 maxl = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxl); +00296 \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{ +00297 \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue}; +00298 \textcolor{keywordflow}{if}(c == energy + ggg[k][l - k] + P->internal\_loop[l1 + j - l - 1])\{ +00299 *p = k; *q = l; +00300 \textcolor{keywordflow}{return} 1; +00301 \} +00302 \} +00303 \} +00304 +00305 l = j - 1; +00306 \textcolor{keywordflow}{if}(S[l] == 3) +00307 \textcolor{keywordflow}{for}(k = i + 4; +00308 k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; +00309 k++)\{ +00310 l1 = k - i - 1; +00311 \textcolor{keywordflow}{if}(l1>\hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}) \textcolor{keywordflow}{break}; +00312 \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue}; +00313 \textcolor{keywordflow}{if}(c == energy + ggg[k][l - k] + P->internal\_loop[l1])\{ +00314 *p = k; *q = l; +00315 \textcolor{keywordflow}{return} 1; +00316 \} +00317 \} +00318 +00319 \textcolor{keywordflow}{return} 0; +00320 \} +00321 +00322 INLINE PRIVATE +00323 \textcolor{keywordtype}{int} +00324 E\_GQuad\_IntLoop(\textcolor{keywordtype}{int} i, +00325 \textcolor{keywordtype}{int} j, +00326 \textcolor{keywordtype}{int} type, +00327 \textcolor{keywordtype}{short} *S, +00328 \textcolor{keywordtype}{int} *ggg, +00329 \textcolor{keywordtype}{int} *index, +00330 \hyperlink{structparamT}{paramT} *P)\{ +00331 +00332 \textcolor{keywordtype}{int} energy, ge, en1, en2, \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}, p, q, l1, minq, maxq; +00333 \textcolor{keywordtype}{int} c0, c1, c2, c3, up, d53, d5, d3; +00334 \textcolor{keywordtype}{short} si, sj; +00335 +00336 dangles = P->\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model\_details}.\hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{dangles}; +00337 si = S[i + 1]; +00338 sj = S[j - 1]; +00339 energy = 0; +00340 +00341 \textcolor{keywordflow}{if}(dangles == 2) +00342 energy += P->mismatchI[type][si][sj]; +00343 +00344 \textcolor{keywordflow}{if}(type > 2) +00345 energy += P->TerminalAU; +00346 +00347 ge = \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}; +00348 +00349 p = i + 1; +00350 \textcolor{keywordflow}{if}(S[p] == 3)\{ +00351 \textcolor{keywordflow}{if}(p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{ +00352 minq = j - i + p - \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP} - 2; +00353 c0 = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1; +00354 minq = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq); +00355 c0 = j - 3; +00356 maxq = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1; +00357 maxq = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq); +00358 \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{ +00359 \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue}; +00360 c0 = energy + ggg[index[q] + p] + P->internal\_loop[j - q - 1]; +00361 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0); +00362 \} +00363 \} +00364 \} +00365 +00366 \textcolor{keywordflow}{for}(p = i + 2; +00367 p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; +00368 p++)\{ +00369 l1 = p - i - 1; +00370 \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break}; +00371 \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue}; +00372 minq = j - i + p - MAXLOOP - 2; +00373 c0 = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1; +00374 minq = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq); +00375 c0 = j - 1; +00376 maxq = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1; +00377 maxq = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq); +00378 \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{ +00379 \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue}; +00380 c0 = energy + ggg[index[q] + p] + P->internal\_loop[l1 + j - q - 1]; +00381 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0); +00382 \} +00383 \} +00384 +00385 q = j - 1; +00386 \textcolor{keywordflow}{if}(S[q] == 3) +00387 \textcolor{keywordflow}{for}(p = i + 4; +00388 p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; +00389 p++)\{ +00390 l1 = p - i - 1; +00391 \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break}; +00392 \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue}; +00393 c0 = energy + ggg[index[q] + p] + P->internal\_loop[l1]; +00394 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0); +00395 \} +00396 +00397 \textcolor{preprocessor}{#if 0} +00398 \textcolor{preprocessor}{} \textcolor{comment}{/* here comes the additional stuff for the odd dangle models */} +00399 \textcolor{keywordflow}{if}(dangles % 1)\{ +00400 en1 = energy + P->dangle5[type][si]; +00401 en2 = energy + P->dangle5[type][sj]; +00402 en3 = energy + P->mismatchI[type][si][sj]; +00403 +00404 \textcolor{comment}{/* first case with 5' dangle (i.e. j-1) onto enclosing pair */} +00405 p = i + 1; +00406 \textcolor{keywordflow}{if}(S[p] == 3)\{ +00407 \textcolor{keywordflow}{if}(p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{ +00408 minq = j - i + p - MAXLOOP - 2; +00409 c0 = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1; +00410 minq = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq); +00411 c0 = j - 4; +00412 maxq = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1; +00413 maxq = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq); +00414 \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{ +00415 \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue}; +00416 c0 = en1 + ggg[index[q] + p] + P->internal\_loop[j - q - 1]; +00417 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0); +00418 \} +00419 \} +00420 \} +00421 +00422 \textcolor{keywordflow}{for}(p = i + 2; p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; p++)\{ +00423 l1 = p - i - 1; +00424 \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break}; +00425 \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue}; +00426 minq = j - i + p - MAXLOOP - 2; +00427 c0 = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1; +00428 minq = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq); +00429 c0 = j - 2; +00430 maxq = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1; +00431 maxq = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq); +00432 \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{ +00433 \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue}; +00434 c0 = en1 + ggg[index[q] + p] + P->internal\_loop[l1 + j - q - 1]; +00435 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0); +00436 \} +00437 \} +00438 +00439 q = j - 2; +00440 \textcolor{keywordflow}{if}(S[q] == 3) +00441 \textcolor{keywordflow}{for}(p = i + 4; p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; p++)\{ +00442 l1 = p - i - 1; +00443 \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break}; +00444 \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue}; +00445 c0 = en1 + ggg[index[q] + p] + P->internal\_loop[l1 + 1]; +00446 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0); +00447 \} +00448 +00449 \textcolor{comment}{/* second case with 3' dangle (i.e. i+1) onto enclosing pair */} +00450 +00451 \} +00452 \textcolor{preprocessor}{#endif} +00453 \textcolor{preprocessor}{} \textcolor{keywordflow}{return} ge; +00454 \} +00455 +00456 INLINE PRIVATE +00457 \textcolor{keywordtype}{int} +00458 E\_GQuad\_IntLoop\_L(\textcolor{keywordtype}{int} i, +00459 \textcolor{keywordtype}{int} j, +00460 \textcolor{keywordtype}{int} type, +00461 \textcolor{keywordtype}{short} *S, +00462 \textcolor{keywordtype}{int} **ggg, +00463 \textcolor{keywordtype}{int} maxdist, +00464 \hyperlink{structparamT}{paramT} *P)\{ +00465 +00466 \textcolor{keywordtype}{int} energy, ge, en1, en2, dangles, p, q, l1, minq, maxq; +00467 \textcolor{keywordtype}{int} c0, c1, c2, c3, up, d53, d5, d3; +00468 \textcolor{keywordtype}{short} si, sj; +00469 +00470 dangles = P->\hyperlink{structparamT_aeb912822ef912705bc202b14f9d71ad9}{model\_details}.\hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{dangles}; +00471 si = S[i + 1]; +00472 sj = S[j - 1]; +00473 energy = 0; +00474 +00475 \textcolor{keywordflow}{if}(dangles == 2) +00476 energy += P->mismatchI[type][si][sj]; +00477 +00478 \textcolor{keywordflow}{if}(type > 2) +00479 energy += P->TerminalAU; +00480 +00481 ge = \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}; +00482 +00483 p = i + 1; +00484 \textcolor{keywordflow}{if}(S[p] == 3)\{ +00485 \textcolor{keywordflow}{if}(p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{ +00486 minq = j - i + p - MAXLOOP - 2; +00487 c0 = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1; +00488 minq = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq); +00489 c0 = j - 3; +00490 maxq = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1; +00491 maxq = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq); +00492 \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{ +00493 \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue}; +00494 c0 = energy + ggg[p][q-p] + P->internal\_loop[j - q - 1]; +00495 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0); +00496 \} +00497 \} +00498 \} +00499 +00500 \textcolor{keywordflow}{for}(p = i + 2; +00501 p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; +00502 p++)\{ +00503 l1 = p - i - 1; +00504 \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break}; +00505 \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue}; +00506 minq = j - i + p - MAXLOOP - 2; +00507 c0 = p + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1; +00508 minq = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(c0, minq); +00509 c0 = j - 1; +00510 maxq = p + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1; +00511 maxq = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(c0, maxq); +00512 \textcolor{keywordflow}{for}(q = minq; q < maxq; q++)\{ +00513 \textcolor{keywordflow}{if}(S[q] != 3) \textcolor{keywordflow}{continue}; +00514 c0 = energy + ggg[p][q - p] + P->internal\_loop[l1 + j - q - 1]; +00515 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0); +00516 \} +00517 \} +00518 +00519 q = j - 1; +00520 \textcolor{keywordflow}{if}(S[q] == 3) +00521 \textcolor{keywordflow}{for}(p = i + 4; +00522 p < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; +00523 p++)\{ +00524 l1 = p - i - 1; +00525 \textcolor{keywordflow}{if}(l1>MAXLOOP) \textcolor{keywordflow}{break}; +00526 \textcolor{keywordflow}{if}(S[p] != 3) \textcolor{keywordflow}{continue}; +00527 c0 = energy + ggg[p][q - p] + P->internal\_loop[l1]; +00528 ge = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(ge, c0); +00529 \} +00530 +00531 \textcolor{keywordflow}{return} ge; +00532 \} +00533 +00534 INLINE PRIVATE +00535 FLT\_OR\_DBL +00536 exp\_E\_GQuad\_IntLoop(\textcolor{keywordtype}{int} i, +00537 \textcolor{keywordtype}{int} j, +00538 \textcolor{keywordtype}{int} type, +00539 \textcolor{keywordtype}{short} *S, +00540 FLT\_OR\_DBL *G, +00541 \textcolor{keywordtype}{int} *index, +00542 \hyperlink{structpf__paramT}{pf\_paramT} *pf)\{ +00543 +00544 \textcolor{keywordtype}{int} k, l, minl, maxl, u, r; +00545 FLT\_OR\_DBL q, qe, *expintern; +00546 \textcolor{keywordtype}{short} si, sj; +00547 +00548 q = 0; +00549 si = S[i + 1]; +00550 sj = S[j - 1]; +00551 qe = pf->expmismatchI[type][si][sj]; +00552 expintern = pf->expinternal; +00553 +00554 \textcolor{keywordflow}{if}(type > 2) +00555 qe *= pf->expTermAU; +00556 +00557 k = i + 1; +00558 \textcolor{keywordflow}{if}(S[k] == 3)\{ +00559 \textcolor{keywordflow}{if}(k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE)\{ +00560 minl = j - i + k - MAXLOOP - 2; +00561 u = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1; +00562 minl = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(u, minl); +00563 u = j - 3; +00564 maxl = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1; +00565 maxl = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(u, maxl); +00566 \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{ +00567 \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue}; +00568 q += qe * G[index[k]-l] * expintern[j - l - 1]; +00569 \} +00570 \} +00571 \} +00572 +00573 +00574 \textcolor{keywordflow}{for}(k = i + 2; +00575 k <= j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; +00576 k++)\{ +00577 u = k - i - 1; +00578 \textcolor{keywordflow}{if}(u > MAXLOOP) \textcolor{keywordflow}{break}; +00579 \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue}; +00580 minl = j - i + k - MAXLOOP - 2; +00581 r = k + VRNA\_GQUAD\_MIN\_BOX\_SIZE - 1; +00582 minl = \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{MAX2}(r, minl); +00583 maxl = k + VRNA\_GQUAD\_MAX\_BOX\_SIZE + 1; +00584 r = j - 1; +00585 maxl = \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{MIN2}(r, maxl); +00586 \textcolor{keywordflow}{for}(l = minl; l < maxl; l++)\{ +00587 \textcolor{keywordflow}{if}(S[l] != 3) \textcolor{keywordflow}{continue}; +00588 q += qe * G[index[k]-l] * expintern[u + j - l - 1]; +00589 \} +00590 \} +00591 +00592 l = j - 1; +00593 \textcolor{keywordflow}{if}(S[l] == 3) +00594 \textcolor{keywordflow}{for}(k = i + 4; k < j - VRNA\_GQUAD\_MIN\_BOX\_SIZE; k++)\{ +00595 u = k - i - 1; +00596 \textcolor{keywordflow}{if}(u>MAXLOOP) \textcolor{keywordflow}{break}; +00597 \textcolor{keywordflow}{if}(S[k] != 3) \textcolor{keywordflow}{continue}; +00598 q += qe * G[index[k]-l] * expintern[u]; +00599 \} +00600 +00601 \textcolor{keywordflow}{return} q; +00602 \} +00603 +00604 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/group__centroid__fold.aux b/binaries/src/ViennaRNA/doc/latex/group__centroid__fold.aux new file mode 100644 index 0000000..232436a --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/group__centroid__fold.aux @@ -0,0 +1,49 @@ +\relax +\gdef \LT@xi {\LT@entry + {1}{55.42702pt}\LT@entry + {1}{77.78368pt}\LT@entry + {1}{321.34094pt}} +\@writefile{toc}{\contentsline {section}{\numberline {9.5}Compute the centroid structure}{33}{section.9.5}} 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{\em dist} & A pointer to the distance variable where the centroid distance will be written to \\ +\hline +\mbox{\tt in} & {\em pl} & A pair list containing base pair probability information about the ensemble \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The centroid structure of the ensemble in dot-\/bracket notation +\end{DoxyReturn} +\hypertarget{group__centroid__fold_gacdabece4aa1e20c9eaa97acb4c4dcc38}{\index{Compute the centroid structure@{Compute the centroid structure}!get\-\_\-centroid\-\_\-struct\-\_\-pr@{get\-\_\-centroid\-\_\-struct\-\_\-pr}} +\index{get\-\_\-centroid\-\_\-struct\-\_\-pr@{get\-\_\-centroid\-\_\-struct\-\_\-pr}!Compute the centroid structure@{Compute the centroid structure}} +\subsubsection[{get\-\_\-centroid\-\_\-struct\-\_\-pr}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ get\-\_\-centroid\-\_\-struct\-\_\-pr ( +\begin{DoxyParamCaption} +\item[{int}]{length, } +\item[{double $\ast$}]{dist, } +\item[{double $\ast$}]{pr} +\end{DoxyParamCaption} +)}}\label{group__centroid__fold_gacdabece4aa1e20c9eaa97acb4c4dcc38} + + +Get the centroid structure of the ensemble. + +This function is a threadsafe replacement for \hyperlink{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{centroid()} with a probability array input + +The centroid is the structure with the minimal average distance to all other structures \par + $ = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij} $ \par + Thus, the centroid is simply the structure containing all pairs with $p_ij>0.5$ The distance of the centroid to the ensemble is written to the memory adressed by {\itshape dist}. + + +\begin{DoxyParams}[1]{Parameters} +\mbox{\tt in} & {\em length} & The length of the sequence \\ +\hline +\mbox{\tt out} & {\em dist} & A pointer to the distance variable where the centroid distance will be written to \\ +\hline +\mbox{\tt in} & {\em pr} & A upper triangular matrix containing base pair probabilities (access via iindx \hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\-\_\-iindx()} ) \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The centroid structure of the ensemble in dot-\/bracket notation +\end{DoxyReturn} diff --git a/binaries/src/ViennaRNA/doc/latex/group__class__fold.aux b/binaries/src/ViennaRNA/doc/latex/group__class__fold.aux new file mode 100644 index 0000000..9238067 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/group__class__fold.aux @@ -0,0 +1,36 @@ +\relax +\@writefile{toc}{\contentsline {section}{\numberline {9.27}Classified Dynamic Programming}{79}{section.9.27}} +\newlabel{group__class__fold}{{9.27}{79}{Classified Dynamic Programming\relax }{section.9.27}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {9.27.1}Detailed Description}{79}{subsection.9.27.1}} +\@setckpt{group__class__fold}{ +\setcounter{page}{80} +\setcounter{equation}{0} +\setcounter{enumi}{0} +\setcounter{enumii}{0} +\setcounter{enumiii}{0} +\setcounter{enumiv}{0} 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+\end{figure} +\subsection*{Modules} +\begin{DoxyCompactItemize} +\item +\hyperlink{group__kl__neighborhood}{Distance based partitioning of the Secondary Structure Space} +\begin{DoxyCompactList}\small\item\em Compute Thermodynamic properties for a Distance Class Partitioning of the Secondary Structure Space. \end{DoxyCompactList}\item +\hyperlink{group__dos}{Compute the Density of States} +\end{DoxyCompactItemize} + + +\subsection{Detailed Description} diff --git a/binaries/src/ViennaRNA/doc/latex/group__cofold.aux b/binaries/src/ViennaRNA/doc/latex/group__cofold.aux new file mode 100644 index 0000000..202d8ff --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/group__cofold.aux @@ -0,0 +1,36 @@ +\relax +\@writefile{toc}{\contentsline {section}{\numberline {9.10}Calculate Secondary Structures of two R\discretionary {-}{}{}N\discretionary {-}{}{}As upon Dimerization}{41}{section.9.10}} +\newlabel{group__cofold}{{9.10}{41}{Calculate Secondary Structures of two R\-N\-As upon Dimerization\relax }{section.9.10}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {9.10.1}Detailed Description}{41}{subsection.9.10.1}} +\@setckpt{group__cofold}{ +\setcounter{page}{42} +\setcounter{equation}{0} +\setcounter{enumi}{0} +\setcounter{enumii}{0} +\setcounter{enumiii}{0} +\setcounter{enumiv}{0} +\setcounter{footnote}{0} +\setcounter{mpfootnote}{0} +\setcounter{part}{0} +\setcounter{chapter}{9} +\setcounter{section}{10} +\setcounter{subsection}{1} +\setcounter{subsubsection}{0} +\setcounter{paragraph}{0} +\setcounter{subparagraph}{0} +\setcounter{figure}{0} +\setcounter{table}{17} +\setcounter{NAT@ctr}{0} +\setcounter{float@type}{8} +\setcounter{lstnumber}{1} +\setcounter{Item}{0} +\setcounter{Hfootnote}{0} +\setcounter{bookmark@seq@number}{61} +\setcounter{lofdepth}{1} +\setcounter{lotdepth}{1} +\setcounter{LT@tables}{17} +\setcounter{LT@chunks}{1} +\setcounter{PWSTtable}{0} +\setcounter{lstlisting}{0} +\setcounter{section@level}{2} +} diff --git 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R\-N\-As upon Dimerization} +\label{group__cofold}\index{Calculate Secondary Structures of two R\-N\-As upon Dimerization@{Calculate Secondary Structures of two R\-N\-As upon Dimerization}} +} + + +Predict structures formed by two molecules upon hybridization. + + +Collaboration diagram for Calculate Secondary Structures of two R\-N\-As upon Dimerization\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=350pt]{group__cofold} +\end{center} +\end{figure} +\subsection*{Modules} +\begin{DoxyCompactItemize} +\item +\hyperlink{group__mfe__cofold}{M\-F\-E Structures of two hybridized Sequences} +\item +\hyperlink{group__pf__cofold}{Partition Function for two hybridized Sequences} +\begin{DoxyCompactList}\small\item\em Partition Function Cofolding. \end{DoxyCompactList}\item +\hyperlink{group__up__cofold}{Partition Function for two hybridized Sequences as a stepwise Process} +\begin{DoxyCompactList}\small\item\em Partition Function Cofolding as a stepwise process. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Predict structures formed by two molecules upon hybridization. The function of an R\-N\-A molecule often depends on its interaction with other R\-N\-As. The following routines therefore allow to predict structures formed by two R\-N\-A molecules upon hybridization.\par + One approach to co-\/folding two R\-N\-As consists of concatenating the two sequences and keeping track of the concatenation point in all energy evaluations. Correspondingly, many of the \hyperlink{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}{cofold()} and \hyperlink{group__pf__cofold_gaa86a5f998789ed71813d23d7307a791b}{co\-\_\-pf\-\_\-fold()} routines below take one sequence string as argument and use the the global variable \hyperlink{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\-\_\-point} to mark the concatenation point. Note that while the {\itshape R\-N\-Acofold} program uses the '\&' character to mark the chain break in its input, you should not use an '\&' when using the library routines (set \hyperlink{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\-\_\-point} instead).\par + In a second approach to co-\/folding two R\-N\-As, cofolding is seen as a stepwise process. In the first step the probability of an unpaired region is calculated and in a second step this probability of an unpaired region is multiplied with the probability of an interaction between the two R\-N\-As. This approach is implemented for the interaction between a long target sequence and a short ligand R\-N\-A. Function \hyperlink{group__up__cofold_ga5b4ee40e190d2f633cd01cf0d2fe93cf}{pf\-\_\-unstru()} calculates the partition function over all unpaired regions in the input sequence. 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Predicting Consensus Structures from Alignment(s)\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=350pt]{group__consensus__fold} +\end{center} +\end{figure} +\subsection*{Modules} +\begin{DoxyCompactItemize} +\item +\hyperlink{group__consensus__mfe__fold}{M\-F\-E Consensus Structures for Sequence Alignment(s)} +\item +\hyperlink{group__consensus__pf__fold}{Partition Function and Base Pair Probabilities for Sequence Alignment(s)} +\item +\hyperlink{group__consensus__stochbt}{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)} +\item +\hyperlink{group__local__consensus__fold}{Local M\-F\-E consensus structures for Sequence Alignments} +\end{DoxyCompactItemize} +\subsection*{Files} +\begin{DoxyCompactItemize} +\item +file \hyperlink{alifold_8h}{alifold.\-h} +\begin{DoxyCompactList}\small\item\em compute various properties (consensus M\-F\-E structures, partition function, Boltzmann distributed stochastic samples, ...) for R\-N\-A sequence alignments \end{DoxyCompactList}\end{DoxyCompactItemize} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +int \hyperlink{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f}{get\-\_\-mpi} (char $\ast$Alseq\mbox{[}$\,$\mbox{]}, int n\-\_\-seq, int length, int $\ast$mini) +\begin{DoxyCompactList}\small\item\em Get the mean pairwise identity in steps from ?to?(ident) \end{DoxyCompactList}\item +\hypertarget{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}{float $\ast$$\ast$ \hyperlink{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}{readribosum} (char $\ast$name)}\label{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc} + +\begin{DoxyCompactList}\small\item\em Read a ribosum or other user-\/defined scoring matrix. \end{DoxyCompactList}\item +float \hyperlink{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}{energy\-\_\-of\-\_\-alistruct} (const char $\ast$$\ast$sequences, const char $\ast$structure, int n\-\_\-seq, float $\ast$energy) +\begin{DoxyCompactList}\small\item\em Calculate the free energy of a consensus structure given a set of aligned sequences. \end{DoxyCompactList}\item +void \hyperlink{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786}{encode\-\_\-ali\-\_\-sequence} (const char $\ast$sequence, short $\ast$S, short $\ast$s5, short $\ast$s3, char $\ast$ss, unsigned short $\ast$as, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ}) +\begin{DoxyCompactList}\small\item\em Get arrays with encoded sequence of the alignment. \end{DoxyCompactList}\item +void \hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc\-\_\-sequence\-\_\-arrays} (const char $\ast$$\ast$sequences, short $\ast$$\ast$$\ast$S, short $\ast$$\ast$$\ast$S5, short $\ast$$\ast$$\ast$S3, unsigned short $\ast$$\ast$$\ast$a2s, char $\ast$$\ast$$\ast$Ss, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ}) +\begin{DoxyCompactList}\small\item\em Allocate memory for sequence array used to deal with aligned sequences. \end{DoxyCompactList}\item +void \hyperlink{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{free\-\_\-sequence\-\_\-arrays} (unsigned int n\-\_\-seq, short $\ast$$\ast$$\ast$S, short $\ast$$\ast$$\ast$S5, short $\ast$$\ast$$\ast$S3, unsigned short $\ast$$\ast$$\ast$a2s, char $\ast$$\ast$$\ast$Ss) +\begin{DoxyCompactList}\small\item\em Free the memory of the sequence arrays used to deal with aligned sequences. \end{DoxyCompactList}\item +int \hyperlink{group__consensus__fold_ga0cc49457fd79eeb04d4a7f97c868b09b}{get\-\_\-alipf\-\_\-arrays} (short $\ast$$\ast$$\ast$S\-\_\-p, short $\ast$$\ast$$\ast$S5\-\_\-p, short $\ast$$\ast$$\ast$S3\-\_\-p, unsigned short $\ast$$\ast$$\ast$a2s\-\_\-p, char $\ast$$\ast$$\ast$Ss\-\_\-p, double $\ast$$\ast$qb\-\_\-p, double $\ast$$\ast$qm\-\_\-p, double $\ast$$\ast$q1k\-\_\-p, double $\ast$$\ast$qln\-\_\-p, short $\ast$$\ast$pscore) +\begin{DoxyCompactList}\small\item\em Get pointers to (almost) all relavant arrays used in alifold's partition function computation. \end{DoxyCompactList}\end{DoxyCompactItemize} +\subsection*{Variables} +\begin{DoxyCompactItemize} +\item +double \hyperlink{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{cv\-\_\-fact} +\begin{DoxyCompactList}\small\item\em This variable controls the weight of the covariance term in the energy function of alignment folding algorithms. \end{DoxyCompactList}\item +double \hyperlink{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{nc\-\_\-fact} +\begin{DoxyCompactList}\small\item\em This variable controls the magnitude of the penalty for non-\/compatible sequences in the covariance term of alignment folding algorithms. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +compute various properties (consensus M\-F\-E structures, partition function, Boltzmann distributed stochastic samples, ...) for R\-N\-A sequence alignments Consensus structures can be predicted by a modified version of the \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()} algorithm that takes a set of aligned sequences instead of a single sequence. The energy function consists of the mean energy averaged over the sequences, plus a covariance term that favors pairs with consistent and compensatory mutations and penalizes pairs that cannot be formed by all structures. For details see\cite{hofacker:2002} and \cite{bernhart:2008}. + +\subsection{Function Documentation} +\hypertarget{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!get\-\_\-mpi@{get\-\_\-mpi}} +\index{get\-\_\-mpi@{get\-\_\-mpi}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}} +\subsubsection[{get\-\_\-mpi}]{\setlength{\rightskip}{0pt plus 5cm}int get\-\_\-mpi ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{Alseq\mbox{[}$\,$\mbox{]}, } +\item[{int}]{n\-\_\-seq, } +\item[{int}]{length, } +\item[{int $\ast$}]{mini} +\end{DoxyParamCaption} +)}}\label{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f} + + +Get the mean pairwise identity in steps from ?to?(ident) + + +\begin{DoxyParams}{Parameters} +{\em Alseq} & \\ +\hline +{\em n\-\_\-seq} & The number of sequences in the alignment \\ +\hline +{\em length} & The length of the alignment \\ +\hline +{\em mini} & \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The mean pairwise identity +\end{DoxyReturn} +\hypertarget{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!energy\-\_\-of\-\_\-alistruct@{energy\-\_\-of\-\_\-alistruct}} +\index{energy\-\_\-of\-\_\-alistruct@{energy\-\_\-of\-\_\-alistruct}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}} +\subsubsection[{energy\-\_\-of\-\_\-alistruct}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-alistruct ( +\begin{DoxyParamCaption} +\item[{const char $\ast$$\ast$}]{sequences, } +\item[{const char $\ast$}]{structure, } +\item[{int}]{n\-\_\-seq, } +\item[{float $\ast$}]{energy} +\end{DoxyParamCaption} +)}}\label{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081} + + +Calculate the free energy of a consensus structure given a set of aligned sequences. + + +\begin{DoxyParams}{Parameters} +{\em sequences} & The N\-U\-L\-L terminated array of sequences \\ +\hline +{\em structure} & The consensus structure \\ +\hline +{\em n\-\_\-seq} & The number of sequences in the alignment \\ +\hline +{\em energy} & A pointer to an array of at least two floats that will hold the free energies (energy\mbox{[}0\mbox{]} will contain the free energy, energy\mbox{[}1\mbox{]} will be filled with the covariance energy term) \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +free energy in kcal/mol +\end{DoxyReturn} +\hypertarget{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!encode\-\_\-ali\-\_\-sequence@{encode\-\_\-ali\-\_\-sequence}} +\index{encode\-\_\-ali\-\_\-sequence@{encode\-\_\-ali\-\_\-sequence}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}} +\subsubsection[{encode\-\_\-ali\-\_\-sequence}]{\setlength{\rightskip}{0pt plus 5cm}void encode\-\_\-ali\-\_\-sequence ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{sequence, } +\item[{short $\ast$}]{S, } +\item[{short $\ast$}]{s5, } +\item[{short $\ast$}]{s3, } +\item[{char $\ast$}]{ss, } +\item[{unsigned short $\ast$}]{as, } +\item[{int}]{circ} +\end{DoxyParamCaption} +)}}\label{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786} + + +Get arrays with encoded sequence of the alignment. + +this function assumes that in S, S5, s3, ss and as enough space is already allocated (size must be at least sequence length+2) + + +\begin{DoxyParams}{Parameters} +{\em sequence} & The gapped sequence from the alignment \\ +\hline +{\em S} & pointer to an array that holds encoded sequence \\ +\hline +{\em s5} & pointer to an array that holds the next base 5' of alignment position i \\ +\hline +{\em s3} & pointer to an array that holds the next base 3' of alignment position i \\ +\hline +{\em ss} & \\ +\hline +{\em as} & \\ +\hline +{\em circ} & assume the molecules to be circular instead of linear (circ=0) \\ +\hline +\end{DoxyParams} +\hypertarget{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!alloc\-\_\-sequence\-\_\-arrays@{alloc\-\_\-sequence\-\_\-arrays}} +\index{alloc\-\_\-sequence\-\_\-arrays@{alloc\-\_\-sequence\-\_\-arrays}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}} +\subsubsection[{alloc\-\_\-sequence\-\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}void alloc\-\_\-sequence\-\_\-arrays ( +\begin{DoxyParamCaption} +\item[{const char $\ast$$\ast$}]{sequences, } +\item[{short $\ast$$\ast$$\ast$}]{S, } +\item[{short $\ast$$\ast$$\ast$}]{S5, } +\item[{short $\ast$$\ast$$\ast$}]{S3, } +\item[{unsigned short $\ast$$\ast$$\ast$}]{a2s, } +\item[{char $\ast$$\ast$$\ast$}]{Ss, } +\item[{int}]{circ} +\end{DoxyParamCaption} +)}}\label{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa} + + +Allocate memory for sequence array used to deal with aligned sequences. + +Note that these arrays will also be initialized according to the sequence alignment given + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{free\-\_\-sequence\-\_\-arrays()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em sequences} & The aligned sequences \\ +\hline +{\em S} & A pointer to the array of encoded sequences \\ +\hline +{\em S5} & A pointer to the array that contains the next 5' nucleotide of a sequence position \\ +\hline +{\em S3} & A pointer to the array that contains the next 3' nucleotide of a sequence position \\ +\hline +{\em a2s} & A pointer to the array that contains the alignment to sequence position mapping \\ +\hline +{\em Ss} & A pointer to the array that contains the ungapped sequence \\ +\hline +{\em circ} & assume the molecules to be circular instead of linear (circ=0) \\ +\hline +\end{DoxyParams} +\hypertarget{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!free\-\_\-sequence\-\_\-arrays@{free\-\_\-sequence\-\_\-arrays}} +\index{free\-\_\-sequence\-\_\-arrays@{free\-\_\-sequence\-\_\-arrays}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}} +\subsubsection[{free\-\_\-sequence\-\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}void free\-\_\-sequence\-\_\-arrays ( +\begin{DoxyParamCaption} +\item[{unsigned int}]{n\-\_\-seq, } +\item[{short $\ast$$\ast$$\ast$}]{S, } +\item[{short $\ast$$\ast$$\ast$}]{S5, } +\item[{short $\ast$$\ast$$\ast$}]{S3, } +\item[{unsigned short $\ast$$\ast$$\ast$}]{a2s, } +\item[{char $\ast$$\ast$$\ast$}]{Ss} +\end{DoxyParamCaption} +)}}\label{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38} + + +Free the memory of the sequence arrays used to deal with aligned sequences. + +This function frees the memory previously allocated with \hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc\-\_\-sequence\-\_\-arrays()} + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc\-\_\-sequence\-\_\-arrays()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em n\-\_\-seq} & The number of aligned sequences \\ +\hline +{\em S} & A pointer to the array of encoded sequences \\ +\hline +{\em S5} & A pointer to the array that contains the next 5' nucleotide of a sequence position \\ +\hline +{\em S3} & A pointer to the array that contains the next 3' nucleotide of a sequence position \\ +\hline +{\em a2s} & A pointer to the array that contains the alignment to sequence position mapping \\ +\hline +{\em Ss} & A pointer to the array that contains the ungapped sequence \\ +\hline +\end{DoxyParams} +\hypertarget{group__consensus__fold_ga0cc49457fd79eeb04d4a7f97c868b09b}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!get\-\_\-alipf\-\_\-arrays@{get\-\_\-alipf\-\_\-arrays}} +\index{get\-\_\-alipf\-\_\-arrays@{get\-\_\-alipf\-\_\-arrays}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}} +\subsubsection[{get\-\_\-alipf\-\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}int get\-\_\-alipf\-\_\-arrays ( +\begin{DoxyParamCaption} +\item[{short $\ast$$\ast$$\ast$}]{S\-\_\-p, } +\item[{short $\ast$$\ast$$\ast$}]{S5\-\_\-p, } +\item[{short $\ast$$\ast$$\ast$}]{S3\-\_\-p, } +\item[{unsigned short $\ast$$\ast$$\ast$}]{a2s\-\_\-p, } +\item[{char $\ast$$\ast$$\ast$}]{Ss\-\_\-p, } +\item[{double $\ast$$\ast$}]{qb\-\_\-p, } +\item[{double $\ast$$\ast$}]{qm\-\_\-p, } +\item[{double $\ast$$\ast$}]{q1k\-\_\-p, } +\item[{double $\ast$$\ast$}]{qln\-\_\-p, } +\item[{short $\ast$$\ast$}]{pscore} +\end{DoxyParamCaption} +)}}\label{group__consensus__fold_ga0cc49457fd79eeb04d4a7f97c868b09b} + + +Get pointers to (almost) all relavant arrays used in alifold's partition function computation. + +\begin{DoxyNote}{Note} +To obtain meaningful pointers, call alipf\-\_\-fold first! +\end{DoxyNote} +\begin{DoxySeeAlso}{See Also} +pf\-\_\-alifold(), \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf\-\_\-circ\-\_\-fold()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em S\-\_\-p} & A pointer to the 'S' array (integer representation of nucleotides) \\ +\hline +{\em S5\-\_\-p} & A pointer to the 'S5' array \\ +\hline +{\em S3\-\_\-p} & A pointer to the 'S3' array \\ +\hline +{\em a2s\-\_\-p} & A pointer to the pair type matrix \\ +\hline +{\em Ss\-\_\-p} & A pointer to the 'Ss' array \\ +\hline +{\em qb\-\_\-p} & A pointer to the Q$^{\mbox{B}}$ matrix \\ +\hline +{\em qm\-\_\-p} & A pointer to the Q$^{\mbox{M}}$ matrix \\ +\hline +{\em q1k\-\_\-p} & A pointer to the 5' slice of the Q matrix ( $q1k(k) = Q(1, k)$) \\ +\hline +{\em qln\-\_\-p} & A pointer to the 3' slice of the Q matrix ( $qln(l) = Q(l, n)$) \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +Non Zero if everything went fine, 0 otherwise +\end{DoxyReturn} + + +\subsection{Variable Documentation} +\hypertarget{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!cv\-\_\-fact@{cv\-\_\-fact}} +\index{cv\-\_\-fact@{cv\-\_\-fact}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}} +\subsubsection[{cv\-\_\-fact}]{\setlength{\rightskip}{0pt plus 5cm}double cv\-\_\-fact}}\label{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c} + + +This variable controls the weight of the covariance term in the energy function of alignment folding algorithms. + +Default is 1. \hypertarget{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!nc\-\_\-fact@{nc\-\_\-fact}} +\index{nc\-\_\-fact@{nc\-\_\-fact}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}} +\subsubsection[{nc\-\_\-fact}]{\setlength{\rightskip}{0pt plus 5cm}double nc\-\_\-fact}}\label{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61} + + +This variable controls the magnitude of the penalty for non-\/compatible sequences in the covariance term of alignment folding algorithms. + +Default is 1. \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/group__consensus__mfe__fold.aux b/binaries/src/ViennaRNA/doc/latex/group__consensus__mfe__fold.aux new file mode 100644 index 0000000..aaa41be --- /dev/null +++ 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Consensus Structures for Sequence Alignment(s)\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=350pt]{group__consensus__mfe__fold} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +float \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold} (const char $\ast$$\ast$strings, char $\ast$structure) +\begin{DoxyCompactList}\small\item\em Compute M\-F\-E and according consensus structure of an alignment of sequences. \end{DoxyCompactList}\item +float \hyperlink{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{circalifold} (const char $\ast$$\ast$strings, char $\ast$structure) +\begin{DoxyCompactList}\small\item\em Compute M\-F\-E and according structure of an alignment of sequences assuming the sequences are circular instead of linear. \end{DoxyCompactList}\item +\hypertarget{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{void \hyperlink{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{free\-\_\-alifold\-\_\-arrays} (void)}\label{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e} + +\begin{DoxyCompactList}\small\item\em Free the memory occupied by M\-F\-E alifold functions. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} + + +\subsection{Function Documentation} +\hypertarget{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{\index{M\-F\-E Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}!alifold@{alifold}} +\index{alifold@{alifold}!MFE Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}} +\subsubsection[{alifold}]{\setlength{\rightskip}{0pt plus 5cm}float alifold ( +\begin{DoxyParamCaption} +\item[{const char $\ast$$\ast$}]{strings, } +\item[{char $\ast$}]{structure} +\end{DoxyParamCaption} +)}}\label{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1} + + +Compute M\-F\-E and according consensus structure of an alignment of sequences. + +This function predicts the consensus structure for the aligned 'sequences' and returns the minimum free energy; the mfe structure in bracket notation is returned in 'structure'. + +Sufficient space must be allocated for 'structure' before calling \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold()}. + + +\begin{DoxyParams}{Parameters} +{\em strings} & A pointer to a N\-U\-L\-L terminated array of character arrays \\ +\hline +{\em structure} & A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the M\-F\-E) \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The free energy score in kcal/mol +\end{DoxyReturn} +\hypertarget{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{\index{M\-F\-E Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}!circalifold@{circalifold}} +\index{circalifold@{circalifold}!MFE Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}} +\subsubsection[{circalifold}]{\setlength{\rightskip}{0pt plus 5cm}float circalifold ( +\begin{DoxyParamCaption} +\item[{const char $\ast$$\ast$}]{strings, } +\item[{char $\ast$}]{structure} +\end{DoxyParamCaption} +)}}\label{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96} + + +Compute M\-F\-E and according structure of an alignment of sequences assuming the sequences are circular instead of linear. + + +\begin{DoxyParams}{Parameters} +{\em strings} & A pointer to a N\-U\-L\-L terminated array of character arrays \\ +\hline +{\em structure} & A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the M\-F\-E) \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The free energy score in kcal/mol +\end{DoxyReturn} diff --git a/binaries/src/ViennaRNA/doc/latex/group__consensus__pf__fold.aux b/binaries/src/ViennaRNA/doc/latex/group__consensus__pf__fold.aux new file mode 100644 index 0000000..61eacdc --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/group__consensus__pf__fold.aux @@ -0,0 +1,54 @@ +\relax +\gdef \LT@xxxvii {\LT@entry + {1}{78.18367pt}\LT@entry + {1}{380.5249pt}} +\@writefile{toc}{\contentsline {section}{\numberline {9.16}Partition Function and Base Pair Probabilities for Sequence Alignment(s)}{56}{section.9.16}} +\newlabel{group__consensus__pf__fold}{{9.16}{56}{Partition Function and Base Pair Probabilities for Sequence Alignment(s)\relax }{section.9.16}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {9.16.1}Detailed Description}{56}{subsection.9.16.1}} 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--- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/group__dos.tex @@ -0,0 +1,37 @@ +\hypertarget{group__dos}{\section{Compute the Density of States} +\label{group__dos}\index{Compute the Density of States@{Compute the Density of States}} +} +Collaboration diagram for Compute the Density of States\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=320pt]{group__dos} +\end{center} +\end{figure} +\subsection*{Variables} +\begin{DoxyCompactItemize} +\item +int \hyperlink{group__dos_ga937634a76b46a22530a74906f1957a9e}{density\-\_\-of\-\_\-states} \mbox{[}\hyperlink{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}{M\-A\-X\-D\-O\-S}+1\mbox{]} +\begin{DoxyCompactList}\small\item\em The Density of States. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} + + +\subsection{Variable Documentation} +\hypertarget{group__dos_ga937634a76b46a22530a74906f1957a9e}{\index{Compute the Density of States@{Compute the Density of States}!density\-\_\-of\-\_\-states@{density\-\_\-of\-\_\-states}} +\index{density\-\_\-of\-\_\-states@{density\-\_\-of\-\_\-states}!Compute the Density of States@{Compute the Density of States}} +\subsubsection[{density\-\_\-of\-\_\-states}]{\setlength{\rightskip}{0pt plus 5cm}int density\-\_\-of\-\_\-states\mbox{[}{\bf M\-A\-X\-D\-O\-S}+1\mbox{]}}}\label{group__dos_ga937634a76b46a22530a74906f1957a9e} + + +The Density of States. + +This array contains the density of states for an R\-N\-A sequences after a call to \hyperlink{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}{subopt\-\_\-par()}, \hyperlink{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{subopt()} or \hyperlink{group__subopt__wuchty_ga8634516e4740e0b6c9a46d2bae940340}{subopt\-\_\-circ()}. + +\begin{DoxyPrecond}{Precondition} +Call one of the functions \hyperlink{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}{subopt\-\_\-par()}, \hyperlink{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{subopt()} or \hyperlink{group__subopt__wuchty_ga8634516e4740e0b6c9a46d2bae940340}{subopt\-\_\-circ()} prior accessing the contents of this array +\end{DoxyPrecond} +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}{subopt\-\_\-par()}, \hyperlink{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{subopt()}, \hyperlink{group__subopt__wuchty_ga8634516e4740e0b6c9a46d2bae940340}{subopt\-\_\-circ()} +\end{DoxySeeAlso} diff --git a/binaries/src/ViennaRNA/doc/latex/group__energy__parameters.aux b/binaries/src/ViennaRNA/doc/latex/group__energy__parameters.aux new file mode 100644 index 0000000..528a7a3 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/group__energy__parameters.aux @@ -0,0 +1,58 @@ +\relax +\@writefile{toc}{\contentsline {section}{\numberline {9.22}Change and Precalculate Energy Parameter Sets and Boltzmann Factors}{64}{section.9.22}} 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b/binaries/src/ViennaRNA/doc/latex/group__energy__parameters.tex new file mode 100644 index 0000000..c3ea7ee --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/group__energy__parameters.tex @@ -0,0 +1,161 @@ +\hypertarget{group__energy__parameters}{\section{Change and Precalculate Energy Parameter Sets and Boltzmann Factors} +\label{group__energy__parameters}\index{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}} +} + + +All relevant functions to retrieve and copy precalculated energy parameter sets as well as reading/writing the energy parameter set from/to file(s). + + +Collaboration diagram for Change and Precalculate Energy Parameter Sets and Boltzmann Factors\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=350pt]{group__energy__parameters} +\end{center} +\end{figure} +\subsection*{Modules} +\begin{DoxyCompactItemize} +\item +\hyperlink{group__energy__parameters__rw}{Reading/\-Writing energy parameter sets from/to File} +\begin{DoxyCompactList}\small\item\em Read and Write energy parameter sets from and to text files. \end{DoxyCompactList}\end{DoxyCompactItemize} +\subsection*{Files} +\begin{DoxyCompactItemize} +\item +file \hyperlink{params_8h}{params.\-h} +\end{DoxyCompactItemize} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +\hyperlink{structparamT}{param\-T} $\ast$ \hyperlink{group__energy__parameters_ga527ef619cd8210b84d5d53be1e0e29b6}{scale\-\_\-parameters} (void) +\begin{DoxyCompactList}\small\item\em Get precomputed energy contributions for all the known loop types. \end{DoxyCompactList}\item +\hyperlink{structparamT}{param\-T} $\ast$ \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters} (double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, \hyperlink{structmodel__detailsT}{model\-\_\-details\-T} md) +\begin{DoxyCompactList}\small\item\em Get precomputed energy contributions for all the known loop types. \end{DoxyCompactList}\item +\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba}{get\-\_\-scaled\-\_\-pf\-\_\-parameters} (void) +\item +\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_ga6fc2f3eef5a3024d44963ac59a42e39d}{get\-\_\-boltzmann\-\_\-factors} (double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, double beta\-Scale, \hyperlink{structmodel__detailsT}{model\-\_\-details\-T} md, double \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\-\_\-scale}) +\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent thermodynamic temperature. \end{DoxyCompactList}\item +\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_gacba212326a051734797e65987260fdd0}{get\-\_\-boltzmann\-\_\-factor\-\_\-copy} (\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters) +\begin{DoxyCompactList}\small\item\em Get a copy of already precomputed Boltzmann factors. \end{DoxyCompactList}\item +\hypertarget{group__energy__parameters_gaa6a4297a2b91d6f7ae47dd61ca1862a0}{\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_gaa6a4297a2b91d6f7ae47dd61ca1862a0}{get\-\_\-scaled\-\_\-alipf\-\_\-parameters} (unsigned int n\-\_\-seq)}\label{group__energy__parameters_gaa6a4297a2b91d6f7ae47dd61ca1862a0} + +\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) \end{DoxyCompactList}\item +\hypertarget{group__energy__parameters_gaaa049a8c9f1c2ed4398cb1b5a3d65a66}{P\-U\-B\-L\-I\-C \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_gaaa049a8c9f1c2ed4398cb1b5a3d65a66}{get\-\_\-boltzmann\-\_\-factors\-\_\-ali} (unsigned int n\-\_\-seq, double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, double beta\-Scale, \hyperlink{structmodel__detailsT}{model\-\_\-details\-T} md, double \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\-\_\-scale})}\label{group__energy__parameters_gaaa049a8c9f1c2ed4398cb1b5a3d65a66} + +\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) with independent thermodynamic temperature. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +All relevant functions to retrieve and copy precalculated energy parameter sets as well as reading/writing the energy parameter set from/to file(s). This module covers all relevant functions for precalculation of the energy parameters necessary for the folding routines provided by R\-N\-Alib. Furthermore, the energy parameter set in the R\-N\-Alib can be easily exchanged by a user-\/defined one. It is also possible to write the current energy parameter set into a text file. + +\subsection{Function Documentation} +\hypertarget{group__energy__parameters_ga527ef619cd8210b84d5d53be1e0e29b6}{\index{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}!scale\-\_\-parameters@{scale\-\_\-parameters}} +\index{scale\-\_\-parameters@{scale\-\_\-parameters}!Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}} +\subsubsection[{scale\-\_\-parameters}]{\setlength{\rightskip}{0pt plus 5cm}{\bf param\-T}$\ast$ scale\-\_\-parameters ( +\begin{DoxyParamCaption} +\item[{void}]{} +\end{DoxyParamCaption} +)}}\label{group__energy__parameters_ga527ef619cd8210b84d5d53be1e0e29b6} + + +Get precomputed energy contributions for all the known loop types. + +\begin{DoxyNote}{Note} +Open\-M\-P\-: This function relies on several global model settings variables and thus is not to be considered threadsafe. See \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters()} for a completely threadsafe implementation. +\end{DoxyNote} +\begin{DoxyReturn}{Returns} +A set of precomputed energy contributions +\end{DoxyReturn} +\hypertarget{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{\index{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}!get\-\_\-scaled\-\_\-parameters@{get\-\_\-scaled\-\_\-parameters}} +\index{get\-\_\-scaled\-\_\-parameters@{get\-\_\-scaled\-\_\-parameters}!Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}} +\subsubsection[{get\-\_\-scaled\-\_\-parameters}]{\setlength{\rightskip}{0pt plus 5cm}{\bf param\-T}$\ast$ get\-\_\-scaled\-\_\-parameters ( +\begin{DoxyParamCaption} +\item[{double}]{temperature, } +\item[{{\bf model\-\_\-details\-T}}]{md} +\end{DoxyParamCaption} +)}}\label{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72} + + +Get precomputed energy contributions for all the known loop types. + +Call this function to retrieve precomputed energy contributions, i.\-e. scaled according to the temperature passed. Furthermore, this function assumes a data structure that contains the model details as well, such that subsequent folding recursions are able to retrieve the correct model settings + +\begin{DoxySeeAlso}{See Also} +\hyperlink{structmodel__detailsT}{model\-\_\-details\-T}, \hyperlink{fold__vars_8h_a4c3257186a796182462f18a5480ac8b3}{set\-\_\-model\-\_\-details()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em temperature} & The temperature in degrees Celcius \\ +\hline +{\em md} & The model details \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +precomputed energy contributions and model settings +\end{DoxyReturn} +\hypertarget{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba}{\index{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}!get\-\_\-scaled\-\_\-pf\-\_\-parameters@{get\-\_\-scaled\-\_\-pf\-\_\-parameters}} +\index{get\-\_\-scaled\-\_\-pf\-\_\-parameters@{get\-\_\-scaled\-\_\-pf\-\_\-parameters}!Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}} +\subsubsection[{get\-\_\-scaled\-\_\-pf\-\_\-parameters}]{\setlength{\rightskip}{0pt plus 5cm}{\bf pf\-\_\-param\-T}$\ast$ get\-\_\-scaled\-\_\-pf\-\_\-parameters ( +\begin{DoxyParamCaption} +\item[{void}]{} +\end{DoxyParamCaption} +)}}\label{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba} +get a datastructure of type \hyperlink{structpf__paramT}{pf\-\_\-param\-T} which contains the Boltzmann weights of several energy parameters scaled according to the current temperature \begin{DoxyReturn}{Returns} +The datastructure containing Boltzmann weights for use in partition function calculations +\end{DoxyReturn} +\hypertarget{group__energy__parameters_ga6fc2f3eef5a3024d44963ac59a42e39d}{\index{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}!get\-\_\-boltzmann\-\_\-factors@{get\-\_\-boltzmann\-\_\-factors}} +\index{get\-\_\-boltzmann\-\_\-factors@{get\-\_\-boltzmann\-\_\-factors}!Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}} +\subsubsection[{get\-\_\-boltzmann\-\_\-factors}]{\setlength{\rightskip}{0pt plus 5cm}{\bf pf\-\_\-param\-T}$\ast$ get\-\_\-boltzmann\-\_\-factors ( +\begin{DoxyParamCaption} +\item[{double}]{temperature, } +\item[{double}]{beta\-Scale, } +\item[{{\bf model\-\_\-details\-T}}]{md, } +\item[{double}]{pf\-\_\-scale} +\end{DoxyParamCaption} +)}}\label{group__energy__parameters_ga6fc2f3eef5a3024d44963ac59a42e39d} + + +Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent thermodynamic temperature. + +This function returns a data structure that contains all necessary precalculated Boltzmann factors for each loop type contribution.\par + In contrast to \hyperlink{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba}{get\-\_\-scaled\-\_\-pf\-\_\-parameters()}, this function enables setting of independent temperatures for both, the individual energy contributions as well as the thermodynamic temperature used in $ exp(-\Delta G / kT) $ + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba}{get\-\_\-scaled\-\_\-pf\-\_\-parameters()}, \hyperlink{group__energy__parameters_gacba212326a051734797e65987260fdd0}{get\-\_\-boltzmann\-\_\-factor\-\_\-copy()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em temperature} & The temperature in degrees Celcius used for (re-\/)scaling the energy contributions \\ +\hline +{\em beta\-Scale} & A scaling value that is used as a multiplication factor for the absolute temperature of the system \\ +\hline +{\em md} & The model details to be used \\ +\hline +{\em pf\-\_\-scale} & The scaling factor for the Boltzmann factors \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +A set of precomputed Boltzmann factors +\end{DoxyReturn} +\hypertarget{group__energy__parameters_gacba212326a051734797e65987260fdd0}{\index{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}!get\-\_\-boltzmann\-\_\-factor\-\_\-copy@{get\-\_\-boltzmann\-\_\-factor\-\_\-copy}} +\index{get\-\_\-boltzmann\-\_\-factor\-\_\-copy@{get\-\_\-boltzmann\-\_\-factor\-\_\-copy}!Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}} +\subsubsection[{get\-\_\-boltzmann\-\_\-factor\-\_\-copy}]{\setlength{\rightskip}{0pt plus 5cm}{\bf pf\-\_\-param\-T}$\ast$ get\-\_\-boltzmann\-\_\-factor\-\_\-copy ( +\begin{DoxyParamCaption} +\item[{{\bf pf\-\_\-param\-T} $\ast$}]{parameters} +\end{DoxyParamCaption} +)}}\label{group__energy__parameters_gacba212326a051734797e65987260fdd0} + + +Get a copy of already precomputed Boltzmann factors. + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__energy__parameters_ga6fc2f3eef5a3024d44963ac59a42e39d}{get\-\_\-boltzmann\-\_\-factors()}, \hyperlink{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba}{get\-\_\-scaled\-\_\-pf\-\_\-parameters()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em parameters} & The input data structure that shall be copied \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +A copy of the provided Boltzmann factor dataset +\end{DoxyReturn} diff --git a/binaries/src/ViennaRNA/doc/latex/group__energy__parameters__convert.aux b/binaries/src/ViennaRNA/doc/latex/group__energy__parameters__convert.aux new file mode 100644 index 0000000..fb41c6a --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/group__energy__parameters__convert.aux @@ -0,0 +1,87 @@ +\relax +\@writefile{toc}{\contentsline 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+\begin{center} +\leavevmode +\includegraphics[width=350pt]{group__energy__parameters__rw} +\end{center} +\end{figure} +\subsection*{Modules} +\begin{DoxyCompactItemize} +\item +\hyperlink{group__energy__parameters__convert}{Converting energy parameter files} +\begin{DoxyCompactList}\small\item\em Convert energy parameter files into the latest format. \end{DoxyCompactList}\end{DoxyCompactItemize} +\subsection*{Files} +\begin{DoxyCompactItemize} +\item +file \hyperlink{read__epars_8h}{read\-\_\-epars.\-h} +\end{DoxyCompactItemize} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +void \hyperlink{group__energy__parameters__rw_ga165a142a3c68fb6655c69ef4ab7cd749}{read\-\_\-parameter\-\_\-file} (const char fname\mbox{[}$\,$\mbox{]}) +\begin{DoxyCompactList}\small\item\em Read energy parameters from a file. \end{DoxyCompactList}\item +void \hyperlink{group__energy__parameters__rw_ga8a43459be386a7489feeab68dc2c6c76}{write\-\_\-parameter\-\_\-file} (const char fname\mbox{[}$\,$\mbox{]}) +\begin{DoxyCompactList}\small\item\em Write energy parameters to a file. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Read and Write energy parameter sets from and to text files. A default set of parameters, identical to the one described in \cite{mathews:2004} and\cite{turner:2010}, is compiled into the library. + +\subsection{Function Documentation} +\hypertarget{group__energy__parameters__rw_ga165a142a3c68fb6655c69ef4ab7cd749}{\index{Reading/\-Writing energy parameter sets from/to File@{Reading/\-Writing energy parameter sets from/to File}!read\-\_\-parameter\-\_\-file@{read\-\_\-parameter\-\_\-file}} +\index{read\-\_\-parameter\-\_\-file@{read\-\_\-parameter\-\_\-file}!Reading/Writing energy parameter sets from/to File@{Reading/\-Writing energy parameter sets from/to File}} +\subsubsection[{read\-\_\-parameter\-\_\-file}]{\setlength{\rightskip}{0pt plus 5cm}void read\-\_\-parameter\-\_\-file ( +\begin{DoxyParamCaption} +\item[{const char}]{fname\mbox{[}$\,$\mbox{]}} +\end{DoxyParamCaption} +)}}\label{group__energy__parameters__rw_ga165a142a3c68fb6655c69ef4ab7cd749} + + +Read energy parameters from a file. + + +\begin{DoxyParams}{Parameters} +{\em fname} & The path to the file containing the energy parameters \\ +\hline +\end{DoxyParams} +\hypertarget{group__energy__parameters__rw_ga8a43459be386a7489feeab68dc2c6c76}{\index{Reading/\-Writing energy parameter sets from/to File@{Reading/\-Writing energy parameter sets from/to File}!write\-\_\-parameter\-\_\-file@{write\-\_\-parameter\-\_\-file}} +\index{write\-\_\-parameter\-\_\-file@{write\-\_\-parameter\-\_\-file}!Reading/Writing energy parameter sets from/to File@{Reading/\-Writing energy parameter sets from/to File}} +\subsubsection[{write\-\_\-parameter\-\_\-file}]{\setlength{\rightskip}{0pt plus 5cm}void write\-\_\-parameter\-\_\-file ( +\begin{DoxyParamCaption} +\item[{const char}]{fname\mbox{[}$\,$\mbox{]}} +\end{DoxyParamCaption} +)}}\label{group__energy__parameters__rw_ga8a43459be386a7489feeab68dc2c6c76} + + +Write energy parameters to a file. + + +\begin{DoxyParams}{Parameters} +{\em fname} & A filename (path) for the file where the current energy parameters will be written to \\ 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evaluation} +\label{group__eval}\index{Energy evaluation@{Energy evaluation}} +} + + +This module contains all functions and variables related to energy evaluation of sequence/structure pairs. + + +Collaboration diagram for Energy evaluation\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=336pt]{group__eval} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +float \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure} (const char $\ast$string, const char $\ast$structure, int verbosity\-\_\-level) +\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A using global model detail settings. \end{DoxyCompactList}\item +float \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par} (const char $\ast$string, const char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int verbosity\-\_\-level) +\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \end{DoxyCompactList}\item +float \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure} (const char $\ast$string, const char $\ast$structure, int verbosity\-\_\-level) +\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded circular R\-N\-A. \end{DoxyCompactList}\item +float \hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par} (const char $\ast$string, const char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int verbosity\-\_\-level) +\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded circular R\-N\-A. \end{DoxyCompactList}\item +int \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\-\_\-of\-\_\-structure\-\_\-pt} (const char $\ast$string, short $\ast$ptable, short $\ast$s, short $\ast$s1, int verbosity\-\_\-level) +\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \end{DoxyCompactList}\item +int \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par} (const char $\ast$string, short $\ast$ptable, short $\ast$s, short $\ast$s1, \hyperlink{structparamT}{param\-T} $\ast$parameters, int verbosity\-\_\-level) +\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \end{DoxyCompactList}\end{DoxyCompactItemize} +\subsection*{Variables} +\begin{DoxyCompactItemize} +\item +\hypertarget{group__eval_ga567530678f6260a1a649a5beca5da4c5}{int \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\-\_\-debug}}\label{group__eval_ga567530678f6260a1a649a5beca5da4c5} + +\begin{DoxyCompactList}\small\item\em verbose info from energy\-\_\-of\-\_\-struct \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +This module contains all functions and variables related to energy evaluation of sequence/structure pairs. + +\subsection{Function Documentation} +\hypertarget{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-structure@{energy\-\_\-of\-\_\-structure}} +\index{energy\-\_\-of\-\_\-structure@{energy\-\_\-of\-\_\-structure}!Energy evaluation@{Energy evaluation}} +\subsubsection[{energy\-\_\-of\-\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-structure ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{string, } +\item[{const char $\ast$}]{structure, } +\item[{int}]{verbosity\-\_\-level} +\end{DoxyParamCaption} +)}}\label{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf} + + +Calculate the free energy of an already folded R\-N\-A using global model detail settings. + +If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout + +\begin{DoxyNote}{Note} +Open\-M\-P\-: This function relies on several global model settings variables and thus is not to be considered threadsafe. See \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()} for a completely threadsafe implementation. +\end{DoxyNote} +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()}, \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em string} & R\-N\-A sequence \\ +\hline +{\em structure} & secondary structure in dot-\/bracket notation \\ +\hline +{\em verbosity\-\_\-level} & a flag to turn verbose output on/off \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +the free energy of the input structure given the input sequence in kcal/mol +\end{DoxyReturn} +\hypertarget{group__eval_gab5169ea4f72f250e43811463a33f4e40}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-struct\-\_\-par@{energy\-\_\-of\-\_\-struct\-\_\-par}} +\index{energy\-\_\-of\-\_\-struct\-\_\-par@{energy\-\_\-of\-\_\-struct\-\_\-par}!Energy evaluation@{Energy evaluation}} +\subsubsection[{energy\-\_\-of\-\_\-struct\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-struct\-\_\-par ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{string, } +\item[{const char $\ast$}]{structure, } +\item[{{\bf param\-T} $\ast$}]{parameters, } +\item[{int}]{verbosity\-\_\-level} +\end{DoxyParamCaption} +)}}\label{group__eval_gab5169ea4f72f250e43811463a33f4e40} + + +Calculate the free energy of an already folded R\-N\-A. + +If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure()}, \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\-\_\-of\-\_\-structure\-\_\-pt()}, \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em string} & R\-N\-A sequence in uppercase letters \\ +\hline +{\em structure} & Secondary structure in dot-\/bracket notation \\ +\hline +{\em parameters} & A data structure containing the prescaled energy contributions and the model details. \\ +\hline +{\em verbosity\-\_\-level} & A flag to turn verbose output on/off \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The free energy of the input structure given the input sequence in kcal/mol +\end{DoxyReturn} +\hypertarget{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-circ\-\_\-structure@{energy\-\_\-of\-\_\-circ\-\_\-structure}} +\index{energy\-\_\-of\-\_\-circ\-\_\-structure@{energy\-\_\-of\-\_\-circ\-\_\-structure}!Energy evaluation@{Energy evaluation}} +\subsubsection[{energy\-\_\-of\-\_\-circ\-\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-circ\-\_\-structure ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{string, } +\item[{const char $\ast$}]{structure, } +\item[{int}]{verbosity\-\_\-level} +\end{DoxyParamCaption} +)}}\label{group__eval_gaeb14f3664aec67fc03268ac75253f0f8} + + +Calculate the free energy of an already folded circular R\-N\-A. + +\begin{DoxyNote}{Note} +Open\-M\-P\-: This function relies on several global model settings variables and thus is not to be considered threadsafe. See \hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par()} for a completely threadsafe implementation. +\end{DoxyNote} +If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par()}, \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em string} & R\-N\-A sequence \\ +\hline +{\em structure} & Secondary structure in dot-\/bracket notation \\ +\hline +{\em verbosity\-\_\-level} & A flag to turn verbose output on/off \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The free energy of the input structure given the input sequence in kcal/mol +\end{DoxyReturn} +\hypertarget{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par@{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par}} +\index{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par@{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par}!Energy evaluation@{Energy evaluation}} +\subsubsection[{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{string, } +\item[{const char $\ast$}]{structure, } +\item[{{\bf param\-T} $\ast$}]{parameters, } +\item[{int}]{verbosity\-\_\-level} +\end{DoxyParamCaption} +)}}\label{group__eval_ga75dc765ee4a1177832bc817c94cf88e5} + + +Calculate the free energy of an already folded circular R\-N\-A. + +If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()}, \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em string} & R\-N\-A sequence \\ +\hline +{\em structure} & Secondary structure in dot-\/bracket notation \\ +\hline +{\em parameters} & A data structure containing the prescaled energy contributions and the model details. \\ +\hline +{\em verbosity\-\_\-level} & A flag to turn verbose output on/off \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The free energy of the input structure given the input sequence in kcal/mol +\end{DoxyReturn} +\hypertarget{group__eval_ga8831445966b761417e713360791299d8}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-structure\-\_\-pt@{energy\-\_\-of\-\_\-structure\-\_\-pt}} +\index{energy\-\_\-of\-\_\-structure\-\_\-pt@{energy\-\_\-of\-\_\-structure\-\_\-pt}!Energy evaluation@{Energy evaluation}} +\subsubsection[{energy\-\_\-of\-\_\-structure\-\_\-pt}]{\setlength{\rightskip}{0pt plus 5cm}int energy\-\_\-of\-\_\-structure\-\_\-pt ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{string, } +\item[{short $\ast$}]{ptable, } +\item[{short $\ast$}]{s, } +\item[{short $\ast$}]{s1, } +\item[{int}]{verbosity\-\_\-level} +\end{DoxyParamCaption} +)}}\label{group__eval_ga8831445966b761417e713360791299d8} + + +Calculate the free energy of an already folded R\-N\-A. + +If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout + +\begin{DoxyNote}{Note} +Open\-M\-P\-: This function relies on several global model settings variables and thus is not to be considered threadsafe. See \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par()} for a completely threadsafe implementation. +\end{DoxyNote} +\begin{DoxySeeAlso}{See Also} +\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table()}, \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em string} & R\-N\-A sequence \\ +\hline +{\em ptable} & the pair table of the secondary structure \\ +\hline +{\em s} & encoded R\-N\-A sequence \\ +\hline +{\em s1} & encoded R\-N\-A sequence \\ +\hline +{\em verbosity\-\_\-level} & a flag to turn verbose output on/off \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +the free energy of the input structure given the input sequence in 10kcal/mol +\end{DoxyReturn} +\hypertarget{group__eval_gada4701dd7519b29da75ceac147601f4e}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par@{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par}} +\index{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par@{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par}!Energy evaluation@{Energy evaluation}} +\subsubsection[{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}int energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{string, } +\item[{short $\ast$}]{ptable, } +\item[{short $\ast$}]{s, } +\item[{short $\ast$}]{s1, } +\item[{{\bf param\-T} $\ast$}]{parameters, } +\item[{int}]{verbosity\-\_\-level} +\end{DoxyParamCaption} +)}}\label{group__eval_gada4701dd7519b29da75ceac147601f4e} + + +Calculate the free energy of an already folded R\-N\-A. + +If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout + +\begin{DoxySeeAlso}{See Also} +\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table()}, \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()}, \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em string} & R\-N\-A sequence in uppercase letters \\ +\hline +{\em ptable} & The pair table of the secondary structure \\ +\hline +{\em s} & Encoded R\-N\-A sequence \\ +\hline +{\em s1} & Encoded R\-N\-A sequence \\ +\hline +{\em parameters} & A data structure containing the prescaled energy contributions and the model details. \\ +\hline +{\em verbosity\-\_\-level} & A flag to turn verbose output on/off \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The free energy of the input structure given the input sequence in 10kcal/mol +\end{DoxyReturn} diff --git a/binaries/src/ViennaRNA/doc/latex/group__folding__routines.md5 b/binaries/src/ViennaRNA/doc/latex/group__folding__routines.md5 new file mode 100644 index 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qu(qQk3UC_#vweu!_khzCdHPf1f`U1tP9rTM0t6AVvB_&F5dIIieowCe literal 0 HcmV?d00001 diff --git a/binaries/src/ViennaRNA/doc/latex/group__inverse__fold.tex b/binaries/src/ViennaRNA/doc/latex/group__inverse__fold.tex new file mode 100644 index 0000000..7d00358 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/group__inverse__fold.tex @@ -0,0 +1,102 @@ +\hypertarget{group__inverse__fold}{\section{Searching Sequences for Predefined Structures} +\label{group__inverse__fold}\index{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}} +} +Collaboration diagram for Searching Sequences for Predefined Structures\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=350pt]{group__inverse__fold} +\end{center} +\end{figure} +\subsection*{Files} +\begin{DoxyCompactItemize} +\item +file \hyperlink{inverse_8h}{inverse.\-h} +\begin{DoxyCompactList}\small\item\em Inverse folding routines. \end{DoxyCompactList}\end{DoxyCompactItemize} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +float \hyperlink{group__inverse__fold_ga7af026de55d4babad879f2c92559cbbc}{inverse\-\_\-fold} (char $\ast$start, const char $\ast$target) +\begin{DoxyCompactList}\small\item\em Find sequences with predefined structure. \end{DoxyCompactList}\item +float \hyperlink{group__inverse__fold_gaeef52ecbf2a2450ad585a344f9826806}{inverse\-\_\-pf\-\_\-fold} (char $\ast$start, const char $\ast$target) +\begin{DoxyCompactList}\small\item\em Find sequence that maximizes probability of a predefined structure. \end{DoxyCompactList}\end{DoxyCompactItemize} +\subsection*{Variables} +\begin{DoxyCompactItemize} +\item +\hypertarget{group__inverse__fold_ga8f791e7740a5a28b9f6fafb4e60301d9}{char $\ast$ \hyperlink{group__inverse__fold_ga8f791e7740a5a28b9f6fafb4e60301d9}{symbolset}}\label{group__inverse__fold_ga8f791e7740a5a28b9f6fafb4e60301d9} + +\begin{DoxyCompactList}\small\item\em This global variable points to the allowed bases, initially \char`\"{}\-A\-U\-G\-C\char`\"{}. It can be used to design sequences from reduced alphabets. \end{DoxyCompactList}\item +float \hyperlink{group__inverse__fold_ga7f17d3b169af048d32bb185039a9c09c}{final\-\_\-cost} +\item +int \hyperlink{group__inverse__fold_ga7ec4ba51f86e1717a1e174264e4a75ce}{give\-\_\-up} +\item +int \hyperlink{group__inverse__fold_gafcfc65fba01b9cca5946726ed9057a63}{inv\-\_\-verbose} +\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +We provide two functions that search for sequences with a given structure, thereby inverting the folding routines. + +\subsection{Function Documentation} +\hypertarget{group__inverse__fold_ga7af026de55d4babad879f2c92559cbbc}{\index{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}!inverse\-\_\-fold@{inverse\-\_\-fold}} +\index{inverse\-\_\-fold@{inverse\-\_\-fold}!Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}} +\subsubsection[{inverse\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float inverse\-\_\-fold ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{start, } +\item[{const char $\ast$}]{target} +\end{DoxyParamCaption} +)}}\label{group__inverse__fold_ga7af026de55d4babad879f2c92559cbbc} + + +Find sequences with predefined structure. + +This function searches for a sequence with minimum free energy structure provided in the parameter 'target', starting with sequence 'start'. It returns 0 if the search was successful, otherwise a structure distance in terms of the energy difference between the search result and the actual target 'target' is returned. The found sequence is returned in 'start'. If \hyperlink{group__inverse__fold_ga7ec4ba51f86e1717a1e174264e4a75ce}{give\-\_\-up} is set to 1, the function will return as soon as it is clear that the search will be unsuccessful, this speeds up the algorithm if you are only interested in exact solutions. + + +\begin{DoxyParams}{Parameters} +{\em start} & The start sequence \\ +\hline +{\em target} & The target secondary structure in dot-\/bracket notation \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The distance to the target in case a search was unsuccessful, 0 otherwise +\end{DoxyReturn} +\hypertarget{group__inverse__fold_gaeef52ecbf2a2450ad585a344f9826806}{\index{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}!inverse\-\_\-pf\-\_\-fold@{inverse\-\_\-pf\-\_\-fold}} +\index{inverse\-\_\-pf\-\_\-fold@{inverse\-\_\-pf\-\_\-fold}!Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}} +\subsubsection[{inverse\-\_\-pf\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float inverse\-\_\-pf\-\_\-fold ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{start, } +\item[{const char $\ast$}]{target} +\end{DoxyParamCaption} +)}}\label{group__inverse__fold_gaeef52ecbf2a2450ad585a344f9826806} + + +Find sequence that maximizes probability of a predefined structure. + +This function searches for a sequence with maximum probability to fold into the provided structure 'target' using the partition function algorithm. It returns $-kT \cdot \log(p)$ where $p$ is the frequency of 'target' in the ensemble of possible structures. This is usually much slower than \hyperlink{group__inverse__fold_ga7af026de55d4babad879f2c92559cbbc}{inverse\-\_\-fold()}. + + +\begin{DoxyParams}{Parameters} +{\em start} & The start sequence \\ +\hline +{\em target} & The target secondary structure in dot-\/bracket notation \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The distance to the target in case a search was unsuccessful, 0 otherwise +\end{DoxyReturn} + + +\subsection{Variable Documentation} +\hypertarget{group__inverse__fold_ga7f17d3b169af048d32bb185039a9c09c}{\index{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}!final\-\_\-cost@{final\-\_\-cost}} +\index{final\-\_\-cost@{final\-\_\-cost}!Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}} +\subsubsection[{final\-\_\-cost}]{\setlength{\rightskip}{0pt plus 5cm}float final\-\_\-cost}}\label{group__inverse__fold_ga7f17d3b169af048d32bb185039a9c09c} +when to stop \hyperlink{group__inverse__fold_gaeef52ecbf2a2450ad585a344f9826806}{inverse\-\_\-pf\-\_\-fold()} \hypertarget{group__inverse__fold_ga7ec4ba51f86e1717a1e174264e4a75ce}{\index{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}!give\-\_\-up@{give\-\_\-up}} +\index{give\-\_\-up@{give\-\_\-up}!Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}} +\subsubsection[{give\-\_\-up}]{\setlength{\rightskip}{0pt plus 5cm}int give\-\_\-up}}\label{group__inverse__fold_ga7ec4ba51f86e1717a1e174264e4a75ce} +default 0\-: try to minimize structure distance even if no exact solution can be found \hypertarget{group__inverse__fold_gafcfc65fba01b9cca5946726ed9057a63}{\index{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}!inv\-\_\-verbose@{inv\-\_\-verbose}} +\index{inv\-\_\-verbose@{inv\-\_\-verbose}!Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}} +\subsubsection[{inv\-\_\-verbose}]{\setlength{\rightskip}{0pt plus 5cm}int inv\-\_\-verbose}}\label{group__inverse__fold_gafcfc65fba01b9cca5946726ed9057a63} +print out substructure on which \hyperlink{group__inverse__fold_ga7af026de55d4babad879f2c92559cbbc}{inverse\-\_\-fold()} fails \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/group__kl__neighborhood.aux b/binaries/src/ViennaRNA/doc/latex/group__kl__neighborhood.aux new file mode 100644 index 0000000..536c77d --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/group__kl__neighborhood.aux @@ -0,0 +1,38 @@ +\relax +\citation{lorenz:2009} +\@writefile{toc}{\contentsline {section}{\numberline {9.28}Distance based partitioning of the Secondary Structure Space}{80}{section.9.28}} +\newlabel{group__kl__neighborhood}{{9.28}{80}{Distance based partitioning of the Secondary Structure Space\relax }{section.9.28}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {9.28.1}Detailed 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Partitioning}} +} + + +Compute the minimum free energy (M\-F\-E) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures. + + +Collaboration diagram for Calculating M\-F\-E representatives of a Distance Based Partitioning\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=350pt]{group__kl__neighborhood__mfe} +\end{center} +\end{figure} +\subsection*{Files} +\begin{DoxyCompactItemize} +\item +file \hyperlink{2Dfold_8h}{2\-Dfold.\-h} +\end{DoxyCompactItemize} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +\hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} $\ast$ \hyperlink{group__kl__neighborhood__mfe_gac9284f132cf0eaa0a2f43590eda05488}{get\-\_\-\-Two\-Dfold\-\_\-variables} (const char $\ast$seq, const char $\ast$structure1, const char $\ast$structure2, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ}) +\begin{DoxyCompactList}\small\item\em Get a structure of type \hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} prefilled with current global settings. \end{DoxyCompactList}\item +void \hyperlink{group__kl__neighborhood__mfe_ga05bf4f31d216b1b160fd2d3d68e9b487}{destroy\-\_\-\-Two\-Dfold\-\_\-variables} (\hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} $\ast$our\-\_\-variables) +\begin{DoxyCompactList}\small\item\em Destroy a \hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} datastructure without memory loss. \end{DoxyCompactList}\item +\hyperlink{structTwoDfold__solution}{Two\-Dfold\-\_\-solution} $\ast$ \hyperlink{group__kl__neighborhood__mfe_ga47da790166020558d27323aef489703e}{Two\-Dfold\-List} (\hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} $\ast$vars, int distance1, int distance2) +\begin{DoxyCompactList}\small\item\em Compute M\-F\-E's and representative for distance partitioning. \end{DoxyCompactList}\item +char $\ast$ \hyperlink{group__kl__neighborhood__mfe_gaf4dc05bf8fc1ea53acd7aeb798ba80c2}{Two\-Dfold\-\_\-backtrack\-\_\-f5} (unsigned int j, int k, int l, \hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} $\ast$vars) +\begin{DoxyCompactList}\small\item\em Backtrack a minimum free energy structure from a 5' section of specified length. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Compute the minimum free energy (M\-F\-E) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures. + +\subsection{Function Documentation} +\hypertarget{group__kl__neighborhood__mfe_gac9284f132cf0eaa0a2f43590eda05488}{\index{Calculating M\-F\-E representatives of a Distance Based Partitioning@{Calculating M\-F\-E representatives of a Distance Based Partitioning}!get\-\_\-\-Two\-Dfold\-\_\-variables@{get\-\_\-\-Two\-Dfold\-\_\-variables}} +\index{get\-\_\-\-Two\-Dfold\-\_\-variables@{get\-\_\-\-Two\-Dfold\-\_\-variables}!Calculating MFE representatives of a Distance Based Partitioning@{Calculating M\-F\-E representatives of a Distance Based Partitioning}} +\subsubsection[{get\-\_\-\-Two\-Dfold\-\_\-variables}]{\setlength{\rightskip}{0pt plus 5cm}{\bf Two\-Dfold\-\_\-vars}$\ast$ get\-\_\-\-Two\-Dfold\-\_\-variables ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{seq, } +\item[{const char $\ast$}]{structure1, } +\item[{const char $\ast$}]{structure2, } +\item[{int}]{circ} +\end{DoxyParamCaption} +)}}\label{group__kl__neighborhood__mfe_gac9284f132cf0eaa0a2f43590eda05488} + + +Get a structure of type \hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} prefilled with current global settings. + +This function returns a datastructure of type \hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars}. The data fields inside the \hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} are prefilled by global settings and all memory allocations necessary to start a computation are already done for the convenience of the user + +\begin{DoxyNote}{Note} +Make sure that the reference structures are compatible with the sequence according to Watson-\/\-Crick-\/ and Wobble-\/base pairing +\end{DoxyNote} +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__kl__neighborhood__mfe_ga05bf4f31d216b1b160fd2d3d68e9b487}{destroy\-\_\-\-Two\-Dfold\-\_\-variables()}, Two\-Dfold(), Two\-Dfold\-\_\-circ +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em seq} & The R\-N\-A sequence \\ +\hline +{\em structure1} & The first reference structure in dot-\/bracket notation \\ +\hline +{\em structure2} & The second reference structure in dot-\/bracket notation \\ +\hline +{\em circ} & A switch to indicate the assumption to fold a circular instead of linear R\-N\-A (0=O\-F\-F, 1=O\-N) \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +A datastructure prefilled with folding options and allocated memory +\end{DoxyReturn} +\hypertarget{group__kl__neighborhood__mfe_ga05bf4f31d216b1b160fd2d3d68e9b487}{\index{Calculating M\-F\-E representatives of a Distance Based Partitioning@{Calculating M\-F\-E representatives of a Distance Based Partitioning}!destroy\-\_\-\-Two\-Dfold\-\_\-variables@{destroy\-\_\-\-Two\-Dfold\-\_\-variables}} +\index{destroy\-\_\-\-Two\-Dfold\-\_\-variables@{destroy\-\_\-\-Two\-Dfold\-\_\-variables}!Calculating MFE representatives of a Distance Based Partitioning@{Calculating M\-F\-E representatives of a Distance Based Partitioning}} +\subsubsection[{destroy\-\_\-\-Two\-Dfold\-\_\-variables}]{\setlength{\rightskip}{0pt plus 5cm}void destroy\-\_\-\-Two\-Dfold\-\_\-variables ( +\begin{DoxyParamCaption} +\item[{{\bf Two\-Dfold\-\_\-vars} $\ast$}]{our\-\_\-variables} +\end{DoxyParamCaption} +)}}\label{group__kl__neighborhood__mfe_ga05bf4f31d216b1b160fd2d3d68e9b487} + + +Destroy a \hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} datastructure without memory loss. + +This function free's all allocated memory that depends on the datastructure given. + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__kl__neighborhood__mfe_gac9284f132cf0eaa0a2f43590eda05488}{get\-\_\-\-Two\-Dfold\-\_\-variables()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em our\-\_\-variables} & A pointer to the datastructure to be destroyed \\ +\hline +\end{DoxyParams} +\hypertarget{group__kl__neighborhood__mfe_ga47da790166020558d27323aef489703e}{\index{Calculating M\-F\-E representatives of a Distance Based Partitioning@{Calculating M\-F\-E representatives of a Distance Based Partitioning}!Two\-Dfold\-List@{Two\-Dfold\-List}} +\index{Two\-Dfold\-List@{Two\-Dfold\-List}!Calculating MFE representatives of a Distance Based Partitioning@{Calculating M\-F\-E representatives of a Distance Based Partitioning}} +\subsubsection[{Two\-Dfold\-List}]{\setlength{\rightskip}{0pt plus 5cm}{\bf Two\-Dfold\-\_\-solution}$\ast$ Two\-Dfold\-List ( +\begin{DoxyParamCaption} +\item[{{\bf Two\-Dfold\-\_\-vars} $\ast$}]{vars, } +\item[{int}]{distance1, } +\item[{int}]{distance2} +\end{DoxyParamCaption} +)}}\label{group__kl__neighborhood__mfe_ga47da790166020558d27323aef489703e} + + +Compute M\-F\-E's and representative for distance partitioning. + +This function computes the minimum free energies and a representative secondary structure for each distance class according to the two references specified in the datastructure 'vars'. The maximum basepair distance to each of both references may be set by the arguments 'distance1' and 'distance2', respectively. If both distance arguments are set to '-\/1', no restriction is assumed and the calculation is performed for each distance class possible. + +The returned list contains an entry for each distance class. If a maximum basepair distance to either of the references was passed, an entry with k=l=-\/1 will be appended in the list, denoting the class where all structures exceeding the maximum will be thrown into. The end of the list is denoted by an attribute value of \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{I\-N\-F} in the k-\/attribute of the list entry. + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__kl__neighborhood__mfe_gac9284f132cf0eaa0a2f43590eda05488}{get\-\_\-\-Two\-Dfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__mfe_ga05bf4f31d216b1b160fd2d3d68e9b487}{destroy\-\_\-\-Two\-Dfold\-\_\-variables()}, \hyperlink{structTwoDfold__solution}{Two\-Dfold\-\_\-solution} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em vars} & the datastructure containing all predefined folding attributes \\ +\hline +{\em distance1} & maximum distance to reference1 (-\/1 means no restriction) \\ +\hline +{\em distance2} & maximum distance to reference2 (-\/1 means no restriction) \\ +\hline +\end{DoxyParams} +\hypertarget{group__kl__neighborhood__mfe_gaf4dc05bf8fc1ea53acd7aeb798ba80c2}{\index{Calculating M\-F\-E representatives of a Distance Based Partitioning@{Calculating M\-F\-E representatives of a Distance Based Partitioning}!Two\-Dfold\-\_\-backtrack\-\_\-f5@{Two\-Dfold\-\_\-backtrack\-\_\-f5}} +\index{Two\-Dfold\-\_\-backtrack\-\_\-f5@{Two\-Dfold\-\_\-backtrack\-\_\-f5}!Calculating MFE representatives of a Distance Based Partitioning@{Calculating M\-F\-E representatives of a Distance Based Partitioning}} +\subsubsection[{Two\-Dfold\-\_\-backtrack\-\_\-f5}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ Two\-Dfold\-\_\-backtrack\-\_\-f5 ( +\begin{DoxyParamCaption} +\item[{unsigned int}]{j, } +\item[{int}]{k, } +\item[{int}]{l, } +\item[{{\bf Two\-Dfold\-\_\-vars} $\ast$}]{vars} +\end{DoxyParamCaption} +)}}\label{group__kl__neighborhood__mfe_gaf4dc05bf8fc1ea53acd7aeb798ba80c2} + + +Backtrack a minimum free energy structure from a 5' section of specified length. + +This function allows to backtrack a secondary structure beginning at the 5' end, a specified length and residing in a specific distance class. If the argument 'k' gets a value of -\/1, the structure that is backtracked is assumed to reside in the distance class where all structures exceeding the maximum basepair distance specified in \hyperlink{group__kl__neighborhood__mfe_ga47da790166020558d27323aef489703e}{Two\-Dfold\-List()} belong to. \begin{DoxyNote}{Note} +The argument 'vars' must contain precalculated energy values in the energy matrices, i.\-e. a call to \hyperlink{group__kl__neighborhood__mfe_ga47da790166020558d27323aef489703e}{Two\-Dfold\-List()} preceding this function is mandatory! +\end{DoxyNote} +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__kl__neighborhood__mfe_ga47da790166020558d27323aef489703e}{Two\-Dfold\-List()}, \hyperlink{group__kl__neighborhood__mfe_gac9284f132cf0eaa0a2f43590eda05488}{get\-\_\-\-Two\-Dfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__mfe_ga05bf4f31d216b1b160fd2d3d68e9b487}{destroy\-\_\-\-Two\-Dfold\-\_\-variables()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em j} & The length in nucleotides beginning from the 5' end \\ +\hline +{\em k} & distance to reference1 (may be -\/1) \\ +\hline +{\em l} & distance to reference2 \\ +\hline +{\em vars} & the datastructure containing all predefined folding attributes \\ +\hline +\end{DoxyParams} diff --git a/binaries/src/ViennaRNA/doc/latex/group__kl__neighborhood__pf.aux b/binaries/src/ViennaRNA/doc/latex/group__kl__neighborhood__pf.aux new file mode 100644 index 0000000..f7d9767 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/group__kl__neighborhood__pf.aux @@ -0,0 +1,57 @@ +\relax +\@writefile{toc}{\contentsline {section}{\numberline {9.30}Calculate Partition Functions of a Distance Based Partitioning}{84}{section.9.30}} +\newlabel{group__kl__neighborhood__pf}{{9.30}{84}{Calculate Partition Functions of a Distance Based Partitioning\relax }{section.9.30}{}} +\@writefile{toc}{\contentsline {subsection}{\numberline {9.30.1}Detailed Description}{84}{subsection.9.30.1}} 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a/binaries/src/ViennaRNA/doc/latex/group__kl__neighborhood__pf.tex b/binaries/src/ViennaRNA/doc/latex/group__kl__neighborhood__pf.tex new file mode 100644 index 0000000..ac9e371 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/group__kl__neighborhood__pf.tex @@ -0,0 +1,143 @@ +\hypertarget{group__kl__neighborhood__pf}{\section{Calculate Partition Functions of a Distance Based Partitioning} +\label{group__kl__neighborhood__pf}\index{Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}} +} + + +Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures. + + +Collaboration diagram for Calculate Partition Functions of a Distance Based Partitioning\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=350pt]{group__kl__neighborhood__pf} +\end{center} +\end{figure} +\subsection*{Files} +\begin{DoxyCompactItemize} +\item +file \hyperlink{2Dpfold_8h}{2\-Dpfold.\-h} +\end{DoxyCompactItemize} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$ \hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\-\_\-\-Two\-Dpfold\-\_\-variables} (const char $\ast$seq, const char $\ast$structure1, char $\ast$structure2, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ}) +\begin{DoxyCompactList}\small\item\em Get a datastructure containing all necessary attributes and global folding switches. \end{DoxyCompactList}\item +\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$ \hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E} (\hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} $\ast$mfe\-\_\-vars) +\begin{DoxyCompactList}\small\item\em Get the datastructure containing all necessary attributes and global folding switches from a pre-\/filled mfe-\/datastructure. \end{DoxyCompactList}\item +void \hyperlink{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{destroy\-\_\-\-Two\-Dpfold\-\_\-variables} (\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$vars) +\begin{DoxyCompactList}\small\item\em Free all memory occupied by a \hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} datastructure. \end{DoxyCompactList}\item +\hyperlink{structTwoDpfold__solution}{Two\-Dpfold\-\_\-solution} $\ast$ \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List} (\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$vars, int max\-Distance1, int max\-Distance2) +\begin{DoxyCompactList}\small\item\em Compute the partition function for all distance classes. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures. + +\subsection{Function Documentation} +\hypertarget{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{\index{Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}!get\-\_\-\-Two\-Dpfold\-\_\-variables@{get\-\_\-\-Two\-Dpfold\-\_\-variables}} +\index{get\-\_\-\-Two\-Dpfold\-\_\-variables@{get\-\_\-\-Two\-Dpfold\-\_\-variables}!Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}} +\subsubsection[{get\-\_\-\-Two\-Dpfold\-\_\-variables}]{\setlength{\rightskip}{0pt plus 5cm}{\bf Two\-Dpfold\-\_\-vars}$\ast$ get\-\_\-\-Two\-Dpfold\-\_\-variables ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{seq, } +\item[{const char $\ast$}]{structure1, } +\item[{char $\ast$}]{structure2, } +\item[{int}]{circ} +\end{DoxyParamCaption} +)}}\label{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64} + + +Get a datastructure containing all necessary attributes and global folding switches. + +This function prepares all necessary attributes and matrices etc which are needed for a call of Two\-Dpfold\-List. A snapshot of all current global model switches (dangles, temperature and so on) is done and stored in the returned datastructure. Additionally, all matrices that will hold the partition function values are prepared. + + +\begin{DoxyParams}{Parameters} +{\em seq} & the R\-N\-A sequence in uppercase format with letters from the alphabet \{A\-U\-C\-G\} \\ +\hline +{\em structure1} & the first reference structure in dot-\/bracket notation \\ +\hline +{\em structure2} & the second reference structure in dot-\/bracket notation \\ +\hline +{\em circ} & a switch indicating if the sequence is linear (0) or circular (1) \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +the datastructure containing all necessary partition function attributes +\end{DoxyReturn} +\hypertarget{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{\index{Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}!get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E@{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E}} +\index{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E@{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E}!Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}} +\subsubsection[{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E}]{\setlength{\rightskip}{0pt plus 5cm}{\bf Two\-Dpfold\-\_\-vars}$\ast$ get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E ( +\begin{DoxyParamCaption} +\item[{{\bf Two\-Dfold\-\_\-vars} $\ast$}]{mfe\-\_\-vars} +\end{DoxyParamCaption} +)}}\label{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216} + + +Get the datastructure containing all necessary attributes and global folding switches from a pre-\/filled mfe-\/datastructure. + +This function actually does the same as get\-\_\-\-Two\-Dpfold\-\_\-variables but takes its switches and settings from a pre-\/filled M\-F\-E equivalent datastructure + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__kl__neighborhood__mfe_gac9284f132cf0eaa0a2f43590eda05488}{get\-\_\-\-Two\-Dfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\-\_\-\-Two\-Dpfold\-\_\-variables()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em mfe\-\_\-vars} & the pre-\/filled mfe datastructure \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +the datastructure containing all necessary partition function attributes +\end{DoxyReturn} +\hypertarget{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{\index{Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}!destroy\-\_\-\-Two\-Dpfold\-\_\-variables@{destroy\-\_\-\-Two\-Dpfold\-\_\-variables}} +\index{destroy\-\_\-\-Two\-Dpfold\-\_\-variables@{destroy\-\_\-\-Two\-Dpfold\-\_\-variables}!Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}} +\subsubsection[{destroy\-\_\-\-Two\-Dpfold\-\_\-variables}]{\setlength{\rightskip}{0pt plus 5cm}void destroy\-\_\-\-Two\-Dpfold\-\_\-variables ( +\begin{DoxyParamCaption} +\item[{{\bf Two\-Dpfold\-\_\-vars} $\ast$}]{vars} +\end{DoxyParamCaption} +)}}\label{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15} + + +Free all memory occupied by a \hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} datastructure. + +This function free's all memory occupied by a datastructure obtained from from \hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\-\_\-\-Two\-Dpfold\-\_\-variables()} or \hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E()} + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\-\_\-\-Two\-Dpfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em vars} & the datastructure to be free'd \\ +\hline +\end{DoxyParams} +\hypertarget{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{\index{Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}!Two\-Dpfold\-List@{Two\-Dpfold\-List}} +\index{Two\-Dpfold\-List@{Two\-Dpfold\-List}!Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}} +\subsubsection[{Two\-Dpfold\-List}]{\setlength{\rightskip}{0pt plus 5cm}{\bf Two\-Dpfold\-\_\-solution}$\ast$ Two\-Dpfold\-List ( +\begin{DoxyParamCaption} +\item[{{\bf Two\-Dpfold\-\_\-vars} $\ast$}]{vars, } +\item[{int}]{max\-Distance1, } +\item[{int}]{max\-Distance2} +\end{DoxyParamCaption} +)}}\label{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb} + + +Compute the partition function for all distance classes. + +This function computes the partition functions for all distance classes according the two reference structures specified in the datastructure 'vars'. Similar to \hyperlink{group__kl__neighborhood__mfe_ga47da790166020558d27323aef489703e}{Two\-Dfold\-List()} the arguments max\-Distance1 and max\-Distance2 specify the maximum distance to both reference structures. A value of '-\/1' in either of them makes the appropriate distance restrictionless, i.\-e. all basepair distancies to the reference are taken into account during computation. In case there is a restriction, the returned solution contains an entry where the attribute k=l=-\/1 contains the partition function for all structures exceeding the restriction. A values of \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{I\-N\-F} in the attribute 'k' of the returned list denotes the end of the list + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\-\_\-\-Two\-Dpfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{destroy\-\_\-\-Two\-Dpfold\-\_\-variables()}, \hyperlink{structTwoDpfold__solution}{Two\-Dpfold\-\_\-solution} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em vars} & the datastructure containing all necessary folding attributes and matrices \\ +\hline +{\em max\-Distance1} & the maximum basepair distance to reference1 (may be -\/1) \\ +\hline +{\em max\-Distance2} & the maximum basepair distance to reference2 (may be -\/1) \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +a list of partition funtions for the appropriate distance classes +\end{DoxyReturn} diff --git 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new file mode 100644 index 0000000..52effd9 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/group__local__consensus__fold.tex @@ -0,0 +1,43 @@ +\hypertarget{group__local__consensus__fold}{\section{Local M\-F\-E consensus structures for Sequence Alignments} +\label{group__local__consensus__fold}\index{Local M\-F\-E consensus structures for Sequence Alignments@{Local M\-F\-E consensus structures for Sequence Alignments}} +} +Collaboration diagram for Local M\-F\-E consensus structures for Sequence Alignments\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=350pt]{group__local__consensus__fold} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +float \hyperlink{group__local__consensus__fold_ga20a173a3cdb83f5d1778e36c1a6b1f2b}{ali\-Lfold} (const char $\ast$$\ast$strings, char $\ast$structure, int maxdist) +\end{DoxyCompactItemize} + + +\subsection{Detailed Description} + + +\subsection{Function Documentation} +\hypertarget{group__local__consensus__fold_ga20a173a3cdb83f5d1778e36c1a6b1f2b}{\index{Local M\-F\-E consensus structures for Sequence Alignments@{Local M\-F\-E consensus structures for Sequence Alignments}!ali\-Lfold@{ali\-Lfold}} +\index{ali\-Lfold@{ali\-Lfold}!Local MFE consensus structures for Sequence Alignments@{Local M\-F\-E consensus structures for Sequence Alignments}} +\subsubsection[{ali\-Lfold}]{\setlength{\rightskip}{0pt plus 5cm}float ali\-Lfold ( +\begin{DoxyParamCaption} +\item[{const char $\ast$$\ast$}]{strings, } +\item[{char $\ast$}]{structure, } +\item[{int}]{maxdist} +\end{DoxyParamCaption} +)}}\label{group__local__consensus__fold_ga20a173a3cdb83f5d1778e36c1a6b1f2b} + +\begin{DoxyParams}{Parameters} +{\em strings} & \\ +\hline +{\em structure} & \\ +\hline +{\em maxdist} & \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} + +\end{DoxyReturn} diff --git a/binaries/src/ViennaRNA/doc/latex/group__local__fold.aux 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Note that in contrast to \hyperlink{group__local__mfe__fold_ga16e5a70e60835bb969eaecbe6482f1be}{Lfold()}, bases outside of the window do not influence the structure at all. Only probabilities higher than 'cutoffb' are kept. + +If 'p\-U' is supplied (i.\-e is not the N\-U\-L\-L pointer), \hyperlink{group__local__pf__fold_gaa1ecd401617ebc748a0220026543c777}{pfl\-\_\-fold()} will also compute the mean probability that regions of length 'u' and smaller are unpaired. The parameter 'u' is supplied in 'pup\mbox{[}0\mbox{]}\mbox{[}0\mbox{]}'. On return the 'pup' array will contain these probabilities, with the entry on 'pup\mbox{[}x\mbox{]}\mbox{[}y\mbox{]}' containing the mean probability that x and the y-\/1 preceding bases are unpaired. The 'p\-U' array needs to be large enough to hold n+1 float$\ast$ entries, where n is the sequence length. + +If an array dpp2 is supplied, the probability of base pair (i,j) given that there already exists a base pair (i+1,j-\/1) is also computed and saved in this array. If p\-Ufp is given (i.\-e. not N\-U\-L\-L), p\-U is not saved but put out imediately. If spup is given (i.\-e. is not N\-U\-L\-L), the pair probabilities in pl are not saved but put out imediately. + + +\begin{DoxyParams}{Parameters} +{\em sequence} & R\-N\-A sequence \\ +\hline +{\em win\-Size} & size of the window \\ +\hline +{\em pair\-Size} & maximum size of base pair \\ +\hline +{\em cutoffb} & cutoffb for base pairs \\ +\hline +{\em p\-U} & array holding all unpaired probabilities \\ +\hline +{\em dpp2} & array of dependent pair probabilities \\ +\hline +{\em p\-Ufp} & file pointer for p\-U \\ +\hline +{\em spup} & file pointer for pair probabilities \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +list of pair probabilities +\end{DoxyReturn} +\hypertarget{group__local__pf__fold_ga0bcb751860bbf34e3dfee8c2fbdb3ef3}{\index{Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}!putoutp\-U\-\_\-prob@{putoutp\-U\-\_\-prob}} +\index{putoutp\-U\-\_\-prob@{putoutp\-U\-\_\-prob}!Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}} +\subsubsection[{putoutp\-U\-\_\-prob}]{\setlength{\rightskip}{0pt plus 5cm}void putoutp\-U\-\_\-prob ( +\begin{DoxyParamCaption} +\item[{double $\ast$$\ast$}]{p\-U, } +\item[{int}]{length, } +\item[{int}]{ulength, } +\item[{F\-I\-L\-E $\ast$}]{fp, } +\item[{int}]{energies} +\end{DoxyParamCaption} +)}}\label{group__local__pf__fold_ga0bcb751860bbf34e3dfee8c2fbdb3ef3} + + +Writes the unpaired probabilities (p\-U) or opening energies into a file. + +Can write either the unpaired probabilities (accessibilities) p\-U or the opening energies -\/log(p\-U)k\-T into a file + + +\begin{DoxyParams}{Parameters} +{\em p\-U} & pair probabilities \\ +\hline +{\em length} & length of R\-N\-A sequence \\ +\hline +{\em ulength} & maximum length of unpaired stretch \\ +\hline +{\em fp} & file pointer of destination file \\ +\hline +{\em energies} & switch to put out as opening energies \\ +\hline +\end{DoxyParams} +\hypertarget{group__local__pf__fold_ga9acb00ee10e96b1ca4ea394cd8bcec75}{\index{Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}!putoutp\-U\-\_\-prob\-\_\-bin@{putoutp\-U\-\_\-prob\-\_\-bin}} +\index{putoutp\-U\-\_\-prob\-\_\-bin@{putoutp\-U\-\_\-prob\-\_\-bin}!Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}} +\subsubsection[{putoutp\-U\-\_\-prob\-\_\-bin}]{\setlength{\rightskip}{0pt plus 5cm}void putoutp\-U\-\_\-prob\-\_\-bin ( +\begin{DoxyParamCaption} +\item[{double $\ast$$\ast$}]{p\-U, } +\item[{int}]{length, } +\item[{int}]{ulength, } +\item[{F\-I\-L\-E $\ast$}]{fp, } +\item[{int}]{energies} +\end{DoxyParamCaption} +)}}\label{group__local__pf__fold_ga9acb00ee10e96b1ca4ea394cd8bcec75} + + +Writes the unpaired probabilities (p\-U) or opening energies into a binary file. + +Can write either the unpaired probabilities (accessibilities) p\-U or the opening energies -\/log(p\-U)k\-T into a file + + +\begin{DoxyParams}{Parameters} +{\em p\-U} & pair probabilities \\ +\hline +{\em length} & length of R\-N\-A sequence \\ +\hline +{\em ulength} & maximum length of unpaired stretch \\ +\hline +{\em fp} & file pointer of destination file \\ +\hline +{\em energies} & switch to put out as opening energies \\ +\hline +\end{DoxyParams} diff --git a/binaries/src/ViennaRNA/doc/latex/group__mea__fold.aux b/binaries/src/ViennaRNA/doc/latex/group__mea__fold.aux new file mode 100644 index 0000000..ed4b446 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/group__mea__fold.aux @@ -0,0 +1,35 @@ +\relax +\@writefile{toc}{\contentsline {section}{\numberline {9.4}Compute the structure with maximum expected accuracy (M\discretionary {-}{}{}E\discretionary {-}{}{}A)}{32}{section.9.4}} +\newlabel{group__mea__fold}{{9.4}{32}{Compute the structure with maximum expected accuracy (M\-E\-A)\relax }{section.9.4}{}} 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--- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/group__mfe__fold.tex @@ -0,0 +1,165 @@ +\hypertarget{group__mfe__fold}{\section{Calculating Minimum Free Energy (M\-F\-E) Structures} +\label{group__mfe__fold}\index{Calculating Minimum Free Energy (\-M\-F\-E) Structures@{Calculating Minimum Free Energy (\-M\-F\-E) Structures}} +} + + +This module contains all functions and variables related to the calculation of global minimum free energy structures for single sequences. + + +Collaboration diagram for Calculating Minimum Free Energy (M\-F\-E) Structures\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=350pt]{group__mfe__fold} +\end{center} +\end{figure} +\subsection*{Modules} +\begin{DoxyCompactItemize} +\item +\hyperlink{group__mfe__cofold}{M\-F\-E Structures of two hybridized Sequences} +\item +\hyperlink{group__consensus__mfe__fold}{M\-F\-E Consensus Structures for Sequence Alignment(s)} +\item +\hyperlink{group__local__mfe__fold}{Local M\-F\-E structure Prediction and Z-\/scores} +\item +\hyperlink{group__kl__neighborhood__mfe}{Calculating M\-F\-E representatives of a Distance Based Partitioning} +\begin{DoxyCompactList}\small\item\em Compute the minimum free energy (M\-F\-E) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures. \end{DoxyCompactList}\end{DoxyCompactItemize} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +float \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par} (const char $\ast$sequence, char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int is\-\_\-constrained, int is\-\_\-circular) +\begin{DoxyCompactList}\small\item\em Compute minimum free energy and an appropriate secondary structure of an R\-N\-A sequence. \end{DoxyCompactList}\item +float \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold} (const char $\ast$sequence, char $\ast$structure) +\begin{DoxyCompactList}\small\item\em Compute minimum free energy and an appropriate secondary structure of an R\-N\-A sequence. \end{DoxyCompactList}\item +float \hyperlink{group__mfe__fold_ga4ac63ab3e8d9a80ced28b8052d94e423}{circfold} (const char $\ast$sequence, char $\ast$structure) +\begin{DoxyCompactList}\small\item\em Compute minimum free energy and an appropriate secondary structure of a circular R\-N\-A sequence. \end{DoxyCompactList}\item +\hypertarget{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}{void \hyperlink{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}{free\-\_\-arrays} (void)}\label{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7} + +\begin{DoxyCompactList}\small\item\em Free arrays for mfe folding. \end{DoxyCompactList}\item +\hypertarget{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3}{void \hyperlink{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3}{update\-\_\-fold\-\_\-params} (void)}\label{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3} + +\begin{DoxyCompactList}\small\item\em Recalculate energy parameters. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +This module contains all functions and variables related to the calculation of global minimum free energy structures for single sequences. This section covers all functions and variables related to the calculation of minimum free energy (M\-F\-E) structures. + +The library provides a fast dynamic programming minimum free energy folding algorithm as described by Zuker \& Stiegler (1981). + +The library provides a fast dynamic programming minimum free energy folding algorithm as described in\cite{zuker:1981}. All relevant parts that directly implement the \char`\"{}\-Zuker \& Stiegler\char`\"{} algorithm for single sequences are described in this section. + +Folding of circular R\-N\-A sequences is handled as a post-\/processing step of the forward recursions. See\cite{hofacker:2006} for further details. + +Nevertheless, the R\-N\-Alib also provides interfaces for the prediction of consensus M\-F\-E structures of sequence alignments, M\-F\-E structure for two hybridized sequences, local optimal structures and many more. For those more specialized variants of M\-F\-E folding routines, please consult the appropriate subsections (Modules) as listed above. + +\subsection{Function Documentation} +\hypertarget{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{\index{Calculating Minimum Free Energy (\-M\-F\-E) Structures@{Calculating Minimum Free Energy (\-M\-F\-E) Structures}!fold\-\_\-par@{fold\-\_\-par}} +\index{fold\-\_\-par@{fold\-\_\-par}!Calculating Minimum Free Energy (MFE) Structures@{Calculating Minimum Free Energy (\-M\-F\-E) Structures}} +\subsubsection[{fold\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float fold\-\_\-par ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{sequence, } +\item[{char $\ast$}]{structure, } +\item[{{\bf param\-T} $\ast$}]{parameters, } +\item[{int}]{is\-\_\-constrained, } +\item[{int}]{is\-\_\-circular} +\end{DoxyParamCaption} +)}}\label{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e} + + +Compute minimum free energy and an appropriate secondary structure of an R\-N\-A sequence. + +The first parameter given, the R\-N\-A sequence, must be {\itshape uppercase} and should only contain an alphabet $\Sigma$ that is understood by the R\-N\-Alib\par + (e.\-g. $ \Sigma = \{A,U,C,G\} $)\par + + +The second parameter, {\itshape structure}, must always point to an allocated block of memory with a size of at least $\mathrm{strlen}(\mathrm{sequence})+1$ + +If the third parameter is N\-U\-L\-L, global model detail settings are assumed for the folding recursions. Otherwise, the provided parameters are used. + +The fourth parameter indicates whether a secondary structure constraint in enhanced dot-\/bracket notation is passed through the structure parameter or not. If so, the characters \char`\"{} $|$ x $<$ $>$ \char`\"{} are recognized to mark bases that are paired, unpaired, paired upstream, or downstream, respectively. Matching brackets \char`\"{} ( ) \char`\"{} denote base pairs, dots \char`\"{}.\char`\"{} are used for unconstrained bases. + +To indicate that the R\-N\-A sequence is circular and thus has to be post-\/processed, set the last parameter to non-\/zero + +After a successful call of \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par()}, a backtracked secondary structure (in dot-\/bracket notation) that exhibits the minimum of free energy will be written to the memory {\itshape structure} is pointing to. The function returns the minimum of free energy for any fold of the sequence given. + +\begin{DoxyNote}{Note} +Open\-M\-P\-: Passing N\-U\-L\-L to the 'parameters' argument involves access to several global model detail variables and thus is not to be considered threadsafe +\end{DoxyNote} +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()}, \hyperlink{group__mfe__fold_ga4ac63ab3e8d9a80ced28b8052d94e423}{circfold()}, \hyperlink{structmodel__detailsT}{model\-\_\-details\-T}, set\-\_\-energy\-\_\-model(), \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em sequence} & R\-N\-A sequence \\ +\hline +{\em structure} & A pointer to the character array where the secondary structure in dot-\/bracket notation will be written to \\ +\hline +{\em parameters} & A data structure containing the prescaled energy contributions and the model details. (N\-U\-L\-L may be passed, see Open\-M\-P notes above) \\ +\hline +{\em is\-\_\-constrained} & Switch to indicate that a structure contraint is passed via the structure argument (0==off) \\ +\hline +{\em is\-\_\-circular} & Switch to (de-\/)activate postprocessing steps in case R\-N\-A sequence is circular (0==off)\\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +the minimum free energy (M\-F\-E) in kcal/mol +\end{DoxyReturn} +\hypertarget{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{\index{Calculating Minimum Free Energy (\-M\-F\-E) Structures@{Calculating Minimum Free Energy (\-M\-F\-E) Structures}!fold@{fold}} +\index{fold@{fold}!Calculating Minimum Free Energy (MFE) Structures@{Calculating Minimum Free Energy (\-M\-F\-E) Structures}} +\subsubsection[{fold}]{\setlength{\rightskip}{0pt plus 5cm}float fold ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{sequence, } +\item[{char $\ast$}]{structure} +\end{DoxyParamCaption} +)}}\label{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b} + + +Compute minimum free energy and an appropriate secondary structure of an R\-N\-A sequence. + +This function essentially does the same thing as \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par()}. However, it takes its model details, i.\-e. \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}, \hyperlink{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}{tetra\-\_\-loop}, \hyperlink{fold__vars_8h_abf380d09e4f1ab94fc6af57cf0ad5d32}{no\-G\-U}, \hyperlink{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259}{no\-\_\-closing\-G\-U}, \hyperlink{fold__vars_8h_a0afc287c2464866d94858c39175154af}{fold\-\_\-constrained}, \hyperlink{fold__vars_8h_a097eccaabd6ae8b4fef83cccff85bb5d}{no\-Lonely\-Pairs} from the current global settings within the library + +Use \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par()} for a completely threadsafe variant + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par()}, \hyperlink{group__mfe__fold_ga4ac63ab3e8d9a80ced28b8052d94e423}{circfold()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em sequence} & R\-N\-A sequence \\ +\hline +{\em structure} & A pointer to the character array where the secondary structure in dot-\/bracket notation will be written to \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +the minimum free energy (M\-F\-E) in kcal/mol +\end{DoxyReturn} +\hypertarget{group__mfe__fold_ga4ac63ab3e8d9a80ced28b8052d94e423}{\index{Calculating Minimum Free Energy (\-M\-F\-E) Structures@{Calculating Minimum Free Energy (\-M\-F\-E) Structures}!circfold@{circfold}} +\index{circfold@{circfold}!Calculating Minimum Free Energy (MFE) Structures@{Calculating Minimum Free Energy (\-M\-F\-E) Structures}} +\subsubsection[{circfold}]{\setlength{\rightskip}{0pt plus 5cm}float circfold ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{sequence, } +\item[{char $\ast$}]{structure} +\end{DoxyParamCaption} +)}}\label{group__mfe__fold_ga4ac63ab3e8d9a80ced28b8052d94e423} + + +Compute minimum free energy and an appropriate secondary structure of a circular R\-N\-A sequence. + +This function essentially does the same thing as \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par()}. However, it takes its model details, i.\-e. \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}, \hyperlink{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}{tetra\-\_\-loop}, \hyperlink{fold__vars_8h_abf380d09e4f1ab94fc6af57cf0ad5d32}{no\-G\-U}, \hyperlink{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259}{no\-\_\-closing\-G\-U}, \hyperlink{fold__vars_8h_a0afc287c2464866d94858c39175154af}{fold\-\_\-constrained}, \hyperlink{fold__vars_8h_a097eccaabd6ae8b4fef83cccff85bb5d}{no\-Lonely\-Pairs} from the current global settings within the library + +Use \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par()} for a completely threadsafe variant + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par()}, \hyperlink{group__mfe__fold_ga4ac63ab3e8d9a80ced28b8052d94e423}{circfold()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em sequence} & R\-N\-A sequence \\ +\hline +{\em structure} & A pointer to the character array where the secondary structure in dot-\/bracket notation will be written to \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +the minimum free energy (M\-F\-E) in kcal/mol +\end{DoxyReturn} diff --git a/binaries/src/ViennaRNA/doc/latex/group__parse.aux b/binaries/src/ViennaRNA/doc/latex/group__parse.aux new file mode 100644 index 0000000..7d24919 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/group__parse.aux @@ -0,0 +1,35 @@ +\relax +\@writefile{toc}{\contentsline {section}{\numberline {9.33}Parsing and Comparing -\/ Functions to Manipulate Structures}{90}{section.9.33}} +\newlabel{group__parse}{{9.33}{90}{Parsing and Comparing -\/ Functions to Manipulate Structures\relax }{section.9.33}{}} +\@setckpt{group__parse}{ +\setcounter{page}{91} +\setcounter{equation}{0} +\setcounter{enumi}{0} +\setcounter{enumii}{0} +\setcounter{enumiii}{0} 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Manipulate Structures} +\label{group__parse}\index{Parsing and Comparing -\/ Functions to Manipulate Structures@{Parsing and Comparing -\/ Functions to Manipulate Structures}} +} diff --git a/binaries/src/ViennaRNA/doc/latex/group__pf__cofold.aux b/binaries/src/ViennaRNA/doc/latex/group__pf__cofold.aux new file mode 100644 index 0000000..cb22d1e --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/group__pf__cofold.aux @@ -0,0 +1,74 @@ +\relax +\@writefile{toc}{\contentsline {section}{\numberline {9.12}Partition Function for two hybridized Sequences}{44}{section.9.12}} +\newlabel{group__pf__cofold}{{9.12}{44}{Partition Function for two hybridized Sequences\relax }{section.9.12}{}} +\newlabel{group__pf__cofold_gade3ce34ae8214811374b1d28a40dc247}{{9.12}{44}{Functions\relax }{section*.26}{}} +\citation{bernhart:2006} +\gdef \LT@xxi {\LT@entry + {1}{78.18367pt}\LT@entry + {1}{380.5249pt}} +\gdef \LT@xxii {\LT@entry + {1}{78.18367pt}\LT@entry + {1}{380.5249pt}} 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b/binaries/src/ViennaRNA/doc/latex/group__pf__cofold.tex @@ -0,0 +1,262 @@ +\hypertarget{group__pf__cofold}{\section{Partition Function for two hybridized Sequences} +\label{group__pf__cofold}\index{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}} +} + + +Partition Function Cofolding. + + +Collaboration diagram for Partition Function for two hybridized Sequences\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=350pt]{group__pf__cofold} +\end{center} +\end{figure} +\subsection*{Files} +\begin{DoxyCompactItemize} +\item +file \hyperlink{part__func__co_8h}{part\-\_\-func\-\_\-co.\-h} +\begin{DoxyCompactList}\small\item\em Partition function for two R\-N\-A sequences. \end{DoxyCompactList}\end{DoxyCompactItemize} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +\hyperlink{structcofoldF}{cofold\-F} \hyperlink{group__pf__cofold_gaa86a5f998789ed71813d23d7307a791b}{co\-\_\-pf\-\_\-fold} (char $\ast$sequence, char $\ast$structure) +\begin{DoxyCompactList}\small\item\em Calculate partition function and base pair probabilities. \end{DoxyCompactList}\item +\hyperlink{structcofoldF}{cofold\-F} \hyperlink{group__pf__cofold_gabd873b450832ab5f21101fc5ab354d21}{co\-\_\-pf\-\_\-fold\-\_\-par} (char $\ast$sequence, char $\ast$structure, \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters, int calculate\-\_\-bppm, int is\-\_\-constrained) +\begin{DoxyCompactList}\small\item\em Calculate partition function and base pair probabilities. \end{DoxyCompactList}\item +double $\ast$ \hyperlink{group__pf__cofold_ga11f0252c1d2c4697253ff4b5bd392d3c}{export\-\_\-co\-\_\-bppm} (void) +\begin{DoxyCompactList}\small\item\em Get a pointer to the base pair probability array. \end{DoxyCompactList}\item +\hypertarget{group__pf__cofold_gade3ce34ae8214811374b1d28a40dc247}{void \hyperlink{group__pf__cofold_gade3ce34ae8214811374b1d28a40dc247}{free\-\_\-co\-\_\-pf\-\_\-arrays} (void)}\label{group__pf__cofold_gade3ce34ae8214811374b1d28a40dc247} + +\begin{DoxyCompactList}\small\item\em Free the memory occupied by \hyperlink{group__pf__cofold_gaa86a5f998789ed71813d23d7307a791b}{co\-\_\-pf\-\_\-fold()} \end{DoxyCompactList}\item +void \hyperlink{group__pf__cofold_ga6e0f36c1f9b7d9dd4bfbad914c1119e5}{update\-\_\-co\-\_\-pf\-\_\-params} (int length) +\begin{DoxyCompactList}\small\item\em Recalculate energy parameters. \end{DoxyCompactList}\item +void \hyperlink{group__pf__cofold_ga117d880df45bef444d5e2785ffa40a53}{update\-\_\-co\-\_\-pf\-\_\-params\-\_\-par} (int length, \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters) +\begin{DoxyCompactList}\small\item\em Recalculate energy parameters. \end{DoxyCompactList}\item +void \hyperlink{group__pf__cofold_ga15ae04ac5ab84e876dcf0093120cb617}{compute\-\_\-probabilities} (double F\-A\-B, double F\-E\-A, double F\-E\-B, struct \hyperlink{structplist}{plist} $\ast$pr\-A\-B, struct \hyperlink{structplist}{plist} $\ast$pr\-A, struct \hyperlink{structplist}{plist} $\ast$pr\-B, int Alength) +\begin{DoxyCompactList}\small\item\em Compute Boltzmann probabilities of dimerization without homodimers. \end{DoxyCompactList}\item +\hyperlink{structConcEnt}{Conc\-Ent} $\ast$ \hyperlink{group__pf__cofold_ga5545cb936ac4ff93c7d699d46e72e8c7}{get\-\_\-concentrations} (double F\-E\-A\-B, double F\-E\-A\-A, double F\-E\-B\-B, double F\-E\-A, double F\-E\-B, double $\ast$startconc) +\begin{DoxyCompactList}\small\item\em Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers. \end{DoxyCompactList}\end{DoxyCompactItemize} +\subsection*{Variables} +\begin{DoxyCompactItemize} +\item +\hypertarget{group__pf__cofold_gaff27888c4088cc1f60fd59cbd589474c}{int \hyperlink{group__pf__cofold_gaff27888c4088cc1f60fd59cbd589474c}{mirnatog}}\label{group__pf__cofold_gaff27888c4088cc1f60fd59cbd589474c} + +\begin{DoxyCompactList}\small\item\em Toggles no intrabp in 2nd mol. \end{DoxyCompactList}\item +\hypertarget{group__pf__cofold_gac2d1851a710a8561390861155ca988fe}{double \hyperlink{group__pf__cofold_gac2d1851a710a8561390861155ca988fe}{F\-\_\-monomer} \mbox{[}2\mbox{]}}\label{group__pf__cofold_gac2d1851a710a8561390861155ca988fe} + +\begin{DoxyCompactList}\small\item\em Free energies of the two monomers. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Partition Function Cofolding. To simplify the implementation the partition function computation is done internally in a null model that does not include the duplex initiation energy, i.\-e. the entropic penalty for producing a dimer from two monomers). The resulting free energies and pair probabilities are initially relative to that null model. In a second step the free energies can be corrected to include the dimerization penalty, and the pair probabilities can be divided into the conditional pair probabilities given that a re dimer is formed or not formed. See\cite{bernhart:2006} for further details. + +\subsection{Function Documentation} +\hypertarget{group__pf__cofold_gaa86a5f998789ed71813d23d7307a791b}{\index{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!co\-\_\-pf\-\_\-fold@{co\-\_\-pf\-\_\-fold}} +\index{co\-\_\-pf\-\_\-fold@{co\-\_\-pf\-\_\-fold}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}} +\subsubsection[{co\-\_\-pf\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}{\bf cofold\-F} co\-\_\-pf\-\_\-fold ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{sequence, } +\item[{char $\ast$}]{structure} +\end{DoxyParamCaption} +)}}\label{group__pf__cofold_gaa86a5f998789ed71813d23d7307a791b} + + +Calculate partition function and base pair probabilities. + +This is the cofold partition function folding. The second molecule starts at the \hyperlink{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\-\_\-point} nucleotide. + +\begin{DoxyNote}{Note} +Open\-M\-P\-: Since this function relies on the global parameters \hyperlink{fold__vars_8h_ad512b5dd4dbec60faccfe137bb474489}{do\-\_\-backtrack}, \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}, \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature} and \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\-\_\-scale} it is not threadsafe according to concurrent changes in these variables! Use \hyperlink{group__pf__cofold_gabd873b450832ab5f21101fc5ab354d21}{co\-\_\-pf\-\_\-fold\-\_\-par()} instead to circumvent this issue. +\end{DoxyNote} +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__pf__cofold_gabd873b450832ab5f21101fc5ab354d21}{co\-\_\-pf\-\_\-fold\-\_\-par()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em sequence} & Concatenated R\-N\-A sequences \\ +\hline +{\em structure} & Will hold the structure or constraints \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +\hyperlink{structcofoldF}{cofold\-F} structure containing a set of energies needed for concentration computations. +\end{DoxyReturn} +\hypertarget{group__pf__cofold_gabd873b450832ab5f21101fc5ab354d21}{\index{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!co\-\_\-pf\-\_\-fold\-\_\-par@{co\-\_\-pf\-\_\-fold\-\_\-par}} +\index{co\-\_\-pf\-\_\-fold\-\_\-par@{co\-\_\-pf\-\_\-fold\-\_\-par}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}} +\subsubsection[{co\-\_\-pf\-\_\-fold\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}{\bf cofold\-F} co\-\_\-pf\-\_\-fold\-\_\-par ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{sequence, } +\item[{char $\ast$}]{structure, } +\item[{{\bf pf\-\_\-param\-T} $\ast$}]{parameters, } +\item[{int}]{calculate\-\_\-bppm, } +\item[{int}]{is\-\_\-constrained} +\end{DoxyParamCaption} +)}}\label{group__pf__cofold_gabd873b450832ab5f21101fc5ab354d21} + + +Calculate partition function and base pair probabilities. + +This is the cofold partition function folding. The second molecule starts at the \hyperlink{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\-\_\-point} nucleotide. + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__energy__parameters_ga6fc2f3eef5a3024d44963ac59a42e39d}{get\-\_\-boltzmann\-\_\-factors()}, \hyperlink{group__pf__cofold_gaa86a5f998789ed71813d23d7307a791b}{co\-\_\-pf\-\_\-fold()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em sequence} & Concatenated R\-N\-A sequences \\ +\hline +{\em structure} & Pointer to the structure constraint \\ +\hline +{\em parameters} & Data structure containing the precalculated Boltzmann factors \\ +\hline +{\em calculate\-\_\-bppm} & Switch to turn Base pair probability calculations on/off (0==off) \\ +\hline +{\em is\-\_\-constrained} & Switch to indicate that a structure contraint is passed via the structure argument (0==off) \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +\hyperlink{structcofoldF}{cofold\-F} structure containing a set of energies needed for concentration computations. +\end{DoxyReturn} +\hypertarget{group__pf__cofold_ga11f0252c1d2c4697253ff4b5bd392d3c}{\index{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!export\-\_\-co\-\_\-bppm@{export\-\_\-co\-\_\-bppm}} +\index{export\-\_\-co\-\_\-bppm@{export\-\_\-co\-\_\-bppm}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}} +\subsubsection[{export\-\_\-co\-\_\-bppm}]{\setlength{\rightskip}{0pt plus 5cm}double$\ast$ export\-\_\-co\-\_\-bppm ( +\begin{DoxyParamCaption} +\item[{void}]{} +\end{DoxyParamCaption} +)}}\label{group__pf__cofold_ga11f0252c1d2c4697253ff4b5bd392d3c} + + +Get a pointer to the base pair probability array. + +Accessing the base pair probabilities for a pair (i,j) is achieved by \begin{DoxyVerb}FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; \end{DoxyVerb} + + +\begin{DoxySeeAlso}{See Also} +\hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\-\_\-iindx()} +\end{DoxySeeAlso} +\begin{DoxyReturn}{Returns} +A pointer to the base pair probability array +\end{DoxyReturn} +\hypertarget{group__pf__cofold_ga6e0f36c1f9b7d9dd4bfbad914c1119e5}{\index{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!update\-\_\-co\-\_\-pf\-\_\-params@{update\-\_\-co\-\_\-pf\-\_\-params}} +\index{update\-\_\-co\-\_\-pf\-\_\-params@{update\-\_\-co\-\_\-pf\-\_\-params}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}} +\subsubsection[{update\-\_\-co\-\_\-pf\-\_\-params}]{\setlength{\rightskip}{0pt plus 5cm}void update\-\_\-co\-\_\-pf\-\_\-params ( +\begin{DoxyParamCaption} +\item[{int}]{length} +\end{DoxyParamCaption} +)}}\label{group__pf__cofold_ga6e0f36c1f9b7d9dd4bfbad914c1119e5} + + +Recalculate energy parameters. + +This function recalculates all energy parameters given the current model settings. + +\begin{DoxyNote}{Note} +This function relies on the global variables \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\-\_\-scale}, \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles} and \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}. Thus it might not be threadsafe in certain situations. Use \hyperlink{group__pf__cofold_ga117d880df45bef444d5e2785ffa40a53}{update\-\_\-co\-\_\-pf\-\_\-params\-\_\-par()} instead. +\end{DoxyNote} +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__energy__parameters_ga6fc2f3eef5a3024d44963ac59a42e39d}{get\-\_\-boltzmann\-\_\-factors()}, \hyperlink{group__pf__cofold_ga117d880df45bef444d5e2785ffa40a53}{update\-\_\-co\-\_\-pf\-\_\-params\-\_\-par()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em length} & Length of the current R\-N\-A sequence \\ +\hline +\end{DoxyParams} +\hypertarget{group__pf__cofold_ga117d880df45bef444d5e2785ffa40a53}{\index{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!update\-\_\-co\-\_\-pf\-\_\-params\-\_\-par@{update\-\_\-co\-\_\-pf\-\_\-params\-\_\-par}} +\index{update\-\_\-co\-\_\-pf\-\_\-params\-\_\-par@{update\-\_\-co\-\_\-pf\-\_\-params\-\_\-par}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}} +\subsubsection[{update\-\_\-co\-\_\-pf\-\_\-params\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}void update\-\_\-co\-\_\-pf\-\_\-params\-\_\-par ( +\begin{DoxyParamCaption} +\item[{int}]{length, } +\item[{{\bf pf\-\_\-param\-T} $\ast$}]{parameters} +\end{DoxyParamCaption} +)}}\label{group__pf__cofold_ga117d880df45bef444d5e2785ffa40a53} + + +Recalculate energy parameters. + +This function recalculates all energy parameters given the current model settings. It's second argument can either be N\-U\-L\-L or a data structure containing the precomputed Boltzmann factors. In the first scenario, the necessary data structure will be created automatically according to the current global model settings, i.\-e. this mode might not be threadsafe. However, if the provided data structure is not N\-U\-L\-L, threadsafety for the model parameters \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}, \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\-\_\-scale} and \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature} is regained, since their values are taken from this data structure during subsequent calculations. + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__energy__parameters_ga6fc2f3eef5a3024d44963ac59a42e39d}{get\-\_\-boltzmann\-\_\-factors()}, \hyperlink{group__pf__cofold_ga6e0f36c1f9b7d9dd4bfbad914c1119e5}{update\-\_\-co\-\_\-pf\-\_\-params()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em length} & Length of the current R\-N\-A sequence \\ +\hline +{\em parameters} & data structure containing the precomputed Boltzmann factors \\ +\hline +\end{DoxyParams} +\hypertarget{group__pf__cofold_ga15ae04ac5ab84e876dcf0093120cb617}{\index{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!compute\-\_\-probabilities@{compute\-\_\-probabilities}} +\index{compute\-\_\-probabilities@{compute\-\_\-probabilities}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}} +\subsubsection[{compute\-\_\-probabilities}]{\setlength{\rightskip}{0pt plus 5cm}void compute\-\_\-probabilities ( +\begin{DoxyParamCaption} +\item[{double}]{F\-A\-B, } +\item[{double}]{F\-E\-A, } +\item[{double}]{F\-E\-B, } +\item[{struct {\bf plist} $\ast$}]{pr\-A\-B, } +\item[{struct {\bf plist} $\ast$}]{pr\-A, } +\item[{struct {\bf plist} $\ast$}]{pr\-B, } +\item[{int}]{Alength} +\end{DoxyParamCaption} +)}}\label{group__pf__cofold_ga15ae04ac5ab84e876dcf0093120cb617} + + +Compute Boltzmann probabilities of dimerization without homodimers. + +Given the pair probabilities and free energies (in the null model) for a dimer A\-B and the two constituent monomers A and B, compute the conditional pair probabilities given that a dimer A\-B actually forms. Null model pair probabilities are given as a list as produced by \hyperlink{group__pf__fold_ga03e15e831a31b1154855ab47edbdb019}{assign\-\_\-plist\-\_\-from\-\_\-pr()}, the dimer probabilities 'pr\-A\-B' are modified in place. + + +\begin{DoxyParams}{Parameters} +{\em F\-A\-B} & free energy of dimer A\-B \\ +\hline +{\em F\-E\-A} & free energy of monomer A \\ +\hline +{\em F\-E\-B} & free energy of monomer B \\ +\hline +{\em pr\-A\-B} & pair probabilities for dimer \\ +\hline +{\em pr\-A} & pair probabilities monomer \\ +\hline +{\em pr\-B} & pair probabilities monomer \\ +\hline +{\em Alength} & Length of molecule A \\ +\hline +\end{DoxyParams} +\hypertarget{group__pf__cofold_ga5545cb936ac4ff93c7d699d46e72e8c7}{\index{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!get\-\_\-concentrations@{get\-\_\-concentrations}} +\index{get\-\_\-concentrations@{get\-\_\-concentrations}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}} +\subsubsection[{get\-\_\-concentrations}]{\setlength{\rightskip}{0pt plus 5cm}{\bf Conc\-Ent}$\ast$ get\-\_\-concentrations ( +\begin{DoxyParamCaption} +\item[{double}]{F\-E\-A\-B, } +\item[{double}]{F\-E\-A\-A, } +\item[{double}]{F\-E\-B\-B, } +\item[{double}]{F\-E\-A, } +\item[{double}]{F\-E\-B, } +\item[{double $\ast$}]{startconc} +\end{DoxyParamCaption} +)}}\label{group__pf__cofold_ga5545cb936ac4ff93c7d699d46e72e8c7} + + +Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers. + +This function takes an array 'startconc' of input concentrations with alternating entries for the initial concentrations of molecules A and B (terminated by two zeroes), then computes the resulting equilibrium concentrations from the free energies for the dimers. Dimer free energies should be the dimer-\/only free energies, i.\-e. the Fc\-A\-B entries from the \hyperlink{structcofoldF}{cofold\-F} struct. + + +\begin{DoxyParams}{Parameters} +{\em F\-E\-A\-B} & Free energy of A\-B dimer (Fc\-A\-B entry) \\ +\hline +{\em F\-E\-A\-A} & Free energy of A\-A dimer (Fc\-A\-B entry) \\ +\hline +{\em F\-E\-B\-B} & Free energy of B\-B dimer (Fc\-A\-B entry) \\ +\hline +{\em F\-E\-A} & Free energy of monomer A \\ +\hline +{\em F\-E\-B} & Free energy of monomer B \\ +\hline +{\em startconc} & List of start concentrations \mbox{[}a0\mbox{]},\mbox{[}b0\mbox{]},\mbox{[}a1\mbox{]},\mbox{[}b1\mbox{]},...,\mbox{[}an\mbox{]}\mbox{[}bn\mbox{]},\mbox{[}0\mbox{]},\mbox{[}0\mbox{]} \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +\hyperlink{structConcEnt}{Conc\-Ent} array containing the equilibrium energies and start concentrations +\end{DoxyReturn} diff --git a/binaries/src/ViennaRNA/doc/latex/group__pf__fold.aux 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+00514 \(\backslash\)endhtmlonly +00515 +00516 \(\backslash\)section utils\_dot Producing (colored) dot plots for base pair probabilities +00517 +00518 \(\backslash\)verbatim +00519 \textcolor{keywordtype}{int} PS\_color\_dot\_plot ( \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}, +00520 \hyperlink{structcpair}{cpair} *pi, +00521 \textcolor{keywordtype}{char} *filename) +00522 \(\backslash\)endverbatim +00523 \(\backslash\)copybrief PS\_color\_dot\_plot() +00524 +00525 \(\backslash\)verbatim +00526 \textcolor{keywordtype}{int} PS\_color\_dot\_plot\_turn (\textcolor{keywordtype}{char} *seq, +00527 \hyperlink{structcpair}{cpair} *pi, +00528 \textcolor{keywordtype}{char} *filename, +00529 \textcolor{keywordtype}{int} winSize) +00530 \(\backslash\)endverbatim +00531 \(\backslash\)copybrief PS\_color\_dot\_plot\_turn() +00532 +00533 \(\backslash\)verbatim +00534 \textcolor{keywordtype}{int} \hyperlink{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}{PS\_dot\_plot\_list} (\textcolor{keywordtype}{char} *seq, +00535 \textcolor{keywordtype}{char} *filename, +00536 \hyperlink{structplist}{plist} *pl, +00537 \hyperlink{structplist}{plist} *mf, +00538 \textcolor{keywordtype}{char} *comment) +00539 \(\backslash\)endverbatim +00540 \(\backslash\)copybrief \hyperlink{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}{PS\_dot\_plot\_list}() +00541 +00542 \(\backslash\)verbatim +00543 \textcolor{keywordtype}{int} PS\_dot\_plot\_turn (\textcolor{keywordtype}{char} *seq, +00544 struct \hyperlink{structplist}{plist} *pl, +00545 \textcolor{keywordtype}{char} *filename, +00546 \textcolor{keywordtype}{int} winSize) +00547 \(\backslash\)endverbatim +00548 \(\backslash\)copybrief PS\_dot\_plot\_turn() +00549 +00550 \(\backslash\)see PS\_dot.h for more detailed descriptions. +00551 +00552 \(\backslash\)section utils\_aln Producing (colored) alignments +00553 +00554 \(\backslash\)verbatim +00555 \textcolor{keywordtype}{int} PS\_color\_aln ( +00556 const \textcolor{keywordtype}{char} *structure, +00557 const \textcolor{keywordtype}{char} *filename, +00558 const \textcolor{keywordtype}{char} *seqs[], +00559 const \textcolor{keywordtype}{char} *names[]) +00560 \(\backslash\)endverbatim +00561 \(\backslash\)copybrief PS\_color\_aln() +00562 +00563 \(\backslash\)htmlonly +00564
+00565 Table of Contents} +00566 \textcolor{preprocessor}{}
+00567 \(\backslash\)endhtmlonly +00568 +00569 \(\backslash\)section utils\_seq RNA sequence related utilities +00570 +00571 Several functions provide useful applications to RNA sequences +00572 +00573 \(\backslash\)verbatim +00574 \textcolor{keywordtype}{char} *\hyperlink{utils_8h_a1b95eac365a021572e1c37e5993a89be}{random\_string} (\textcolor{keywordtype}{int} l, +00575 \textcolor{keyword}{const} \textcolor{keywordtype}{char} symbols[]) +00576 \(\backslash\)endverbatim +00577 \(\backslash\)copybrief \hyperlink{utils_8h_a1b95eac365a021572e1c37e5993a89be}{random\_string}() +00578 +00579 \(\backslash\)verbatim +00580 \textcolor{keywordtype}{int} \hyperlink{utils_8h_ad9dc7bfc9aa664dc6698f17ce07fc7e7}{hamming} ( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1, +00581 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2) +00582 \(\backslash\)endverbatim +00583 \(\backslash\)copybrief \hyperlink{utils_8h_ad9dc7bfc9aa664dc6698f17ce07fc7e7}{hamming}() +00584 +00585 \(\backslash\)verbatim +00586 \textcolor{keywordtype}{void} \hyperlink{utils_8h_ad3f18dd83f958f18b2f26ecb99305208}{str\_DNA2RNA}(\textcolor{keywordtype}{char} *sequence); +00587 \(\backslash\)endverbatim +00588 \(\backslash\)copybrief \hyperlink{utils_8h_ad3f18dd83f958f18b2f26ecb99305208}{str\_DNA2RNA}() +00589 +00590 \(\backslash\)verbatim +00591 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a17b796b806f96b70382077fb5bc519bb}{str\_uppercase}(\textcolor{keywordtype}{char} *sequence); +00592 \(\backslash\)endverbatim +00593 \(\backslash\)copybrief \hyperlink{utils_8h_a17b796b806f96b70382077fb5bc519bb}{str\_uppercase}() +00594 +00595 \(\backslash\)htmlonly +00596
+00597 Table of Contents +00598
+00599 \(\backslash\)endhtmlonly +00600 +00601 \(\backslash\)section utils\_struc RNA secondary structure related utilities +00602 +00603 \(\backslash\)verbatim +00604 \textcolor{keywordtype}{char} *\hyperlink{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{pack\_structure} (\textcolor{keyword}{const} \textcolor{keywordtype}{char} *struc) +00605 \(\backslash\)endverbatim +00606 \(\backslash\)copybrief \hyperlink{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{pack\_structure}() +00607 +00608 \(\backslash\)verbatim +00609 \textcolor{keywordtype}{char} *\hyperlink{utils_8h_a071c6921efe1eb974f115ee6fefa3c39}{unpack\_structure} (\textcolor{keyword}{const} \textcolor{keywordtype}{char} *packed) +00610 \(\backslash\)endverbatim +00611 \(\backslash\)copybrief \hyperlink{utils_8h_a071c6921efe1eb974f115ee6fefa3c39}{unpack\_structure}() +00612 +00613 \(\backslash\)verbatim +00614 \textcolor{keywordtype}{short} *\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\_pair\_table} (\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure) +00615 \(\backslash\)endverbatim +00616 \(\backslash\)copybrief \hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\_pair\_table}() +00617 +00618 \(\backslash\)verbatim +00619 \textcolor{keywordtype}{short} *\hyperlink{utils_8h_afeaa6d68eef3a99d0a7aa08aa91c6601}{copy\_pair\_table} (\textcolor{keyword}{const} \textcolor{keywordtype}{short} *pt) +00620 \(\backslash\)endverbatim +00621 \(\backslash\)copybrief \hyperlink{utils_8h_afeaa6d68eef3a99d0a7aa08aa91c6601}{copy\_pair\_table}() +00622 +00623 \(\backslash\)htmlonly +00624
+00625 Table of Contents +00626
+00627 \(\backslash\)endhtmlonly +00628 +00629 \(\backslash\)section utils\_misc Miscellaneous Utilities +00630 +00631 \(\backslash\)verbatim +00632 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a6bf778117d31b7fd90db435323f4ef74}{print\_tty\_input\_seq} (\textcolor{keywordtype}{void}) +00633 \(\backslash\)endverbatim +00634 \(\backslash\)copybrief \hyperlink{utils_8h_a6bf778117d31b7fd90db435323f4ef74}{print\_tty\_input\_seq}() +00635 +00636 \(\backslash\)verbatim +00637 \textcolor{keywordtype}{void} \hyperlink{utils_8h_ae8ae8a34962b9959be3f6c40f0a80ac1}{print\_tty\_constraint\_full} (\textcolor{keywordtype}{void}) +00638 \(\backslash\)endverbatim +00639 \(\backslash\)copybrief \hyperlink{utils_8h_ae8ae8a34962b9959be3f6c40f0a80ac1}{print\_tty\_constraint\_full}() +00640 +00641 \(\backslash\)verbatim +00642 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a4d167deb70bb51723e44374dc981deb2}{print\_tty\_constraint} (\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} option) +00643 \(\backslash\)endverbatim +00644 \(\backslash\)copybrief \hyperlink{utils_8h_a4d167deb70bb51723e44374dc981deb2}{print\_tty\_constraint}() +00645 +00646 \(\backslash\)verbatim +00647 \textcolor{keywordtype}{int} *\hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\_iindx} (\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length) +00648 \(\backslash\)endverbatim +00649 \(\backslash\)copybrief \hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\_iindx}() +00650 +00651 \(\backslash\)verbatim +00652 \textcolor{keywordtype}{int} *\hyperlink{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f}{get\_indx} (\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length) +00653 \(\backslash\)endverbatim +00654 \(\backslash\)copybrief \hyperlink{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f}{get\_indx}() +00655 +00656 \(\backslash\)verbatim +00657 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a36c3a6c3218b041f992052767bc74549}{constrain\_ptypes} ( +00658 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *constraint, +00659 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length, +00660 \textcolor{keywordtype}{char} *ptype, +00661 \textcolor{keywordtype}{int} *BP, +00662 \textcolor{keywordtype}{int} min\_loop\_size, +00663 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} idx\_type) +00664 \(\backslash\)endverbatim +00665 \(\backslash\)copybrief \hyperlink{utils_8h_a36c3a6c3218b041f992052767bc74549}{constrain\_ptypes}() +00666 +00667 \(\backslash\)verbatim +00668 \textcolor{keywordtype}{char} *\hyperlink{utils_8h_abe51806d14cff0789a8c1df7dbc45b71}{get\_line}(FILE *fp); +00669 \(\backslash\)endverbatim +00670 \(\backslash\)copybrief \hyperlink{utils_8h_abe51806d14cff0789a8c1df7dbc45b71}{get\_line}() +00671 +00672 \(\backslash\)verbatim +00673 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\_record}( +00674 \textcolor{keywordtype}{char} **header, +00675 \textcolor{keywordtype}{char} **sequence, +00676 \textcolor{keywordtype}{char} ***rest, +00677 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} options); +00678 \(\backslash\)endverbatim +00679 \(\backslash\)copybrief \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\_record}() +00680 +00681 \(\backslash\)verbatim +00682 \textcolor{keywordtype}{char} *\hyperlink{utils_8h_a7afeb906cb36e9d77379eabc6907ac46}{time\_stamp} (\textcolor{keywordtype}{void}) +00683 \(\backslash\)endverbatim +00684 \(\backslash\)copybrief \hyperlink{utils_8h_a7afeb906cb36e9d77379eabc6907ac46}{time\_stamp}() +00685 +00686 \(\backslash\)verbatim +00687 \textcolor{keywordtype}{void} \hyperlink{utils_8h_af2355fa8746f2f30fbe71db65dea3d51}{warn\_user} (\textcolor{keyword}{const} \textcolor{keywordtype}{char} message[]) +00688 \(\backslash\)endverbatim +00689 \(\backslash\)copybrief \hyperlink{utils_8h_af2355fa8746f2f30fbe71db65dea3d51}{warn\_user}() +00690 +00691 \(\backslash\)verbatim +00692 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{nrerror} (\textcolor{keyword}{const} \textcolor{keywordtype}{char} message[]) +00693 \(\backslash\)endverbatim +00694 \(\backslash\)copybrief \hyperlink{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{nrerror}() +00695 +00696 \(\backslash\)verbatim +00697 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a8aaa6d9be6f803f496d9b97375c371f3}{init\_rand} (\textcolor{keywordtype}{void}) +00698 \(\backslash\)endverbatim +00699 \(\backslash\)copybrief \hyperlink{utils_8h_a8aaa6d9be6f803f496d9b97375c371f3}{init\_rand}() +00700 +00701 \(\backslash\)verbatim +00702 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} \hyperlink{utils_8h_af9a866c8417afda7368bbac939ab3c47}{xsubi}[3]; +00703 \(\backslash\)endverbatim +00704 \(\backslash\)copybrief xsubi +00705 +00706 \(\backslash\)verbatim +00707 \textcolor{keywordtype}{double} \hyperlink{utils_8h_aaa328491c84996e445d027fde9800f2e}{urn} (\textcolor{keywordtype}{void}) +00708 \(\backslash\)endverbatim +00709 \(\backslash\)copybrief \hyperlink{utils_8h_aaa328491c84996e445d027fde9800f2e}{urn}() +00710 +00711 \(\backslash\)verbatim +00712 \textcolor{keywordtype}{int} \hyperlink{utils_8h_a68ff0849d44f62fe491800378a5ffcb4}{int\_urn} (\textcolor{keywordtype}{int} from, \textcolor{keywordtype}{int} to) +00713 \(\backslash\)endverbatim +00714 \(\backslash\)copybrief \hyperlink{utils_8h_a68ff0849d44f62fe491800378a5ffcb4}{int\_urn}() +00715 +00716 \(\backslash\)verbatim +00717 \textcolor{keywordtype}{void} *\hyperlink{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{space} (\textcolor{keywordtype}{unsigned} size) +00718 \(\backslash\)endverbatim +00719 \(\backslash\)copybrief \hyperlink{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{space}() +00720 +00721 \(\backslash\)verbatim +00722 \textcolor{keywordtype}{void} *\hyperlink{utils_8h_a9037ada838835b1b9db41581a021b0c8}{xrealloc} ( \textcolor{keywordtype}{void} *p, +00723 \textcolor{keywordtype}{unsigned} size) +00724 \(\backslash\)endverbatim +00725 \(\backslash\)copybrief \hyperlink{utils_8h_a9037ada838835b1b9db41581a021b0c8}{xrealloc}() +00726 +00727 \(\backslash\)see utils.h \textcolor{keywordflow}{for} a complete overview and detailed description of the utility functions +00728 +00729 \(\backslash\)htmlonly +00730
+00731 Table of Contents +00732
+00733 \(\backslash\)endhtmlonly +00734 +00735 \(\backslash\)ref mp\_example \textcolor{stringliteral}{"Next Page: Examples"} +00736 +00737 \(\backslash\)page mp\_example Example - A Small Example Program +00738 +00739 The following program exercises most commonly used functions of the library. +00740 The program folds two sequences \textcolor{keyword}{using} both the mfe and partition \textcolor{keyword}{function} +00741 algorithms and calculates the tree edit and profile distance of the +00742 resulting structures and base pairing probabilities. +00743 +00744 \(\backslash\)code\{.c\} +00745 \textcolor{preprocessor}{#include } +00746 \textcolor{preprocessor}{#include } +00747 \textcolor{preprocessor}{#include } +00748 \textcolor{preprocessor}{#include } +00749 \textcolor{preprocessor}{#include "\hyperlink{utils_8h}{utils.h}"} +00750 \textcolor{preprocessor}{#include "\hyperlink{fold__vars_8h}{fold\_vars.h}"} +00751 \textcolor{preprocessor}{#include "\hyperlink{fold_8h}{fold.h}"} +00752 \textcolor{preprocessor}{#include "\hyperlink{part__func_8h}{part\_func.h}"} +00753 \textcolor{preprocessor}{#include "\hyperlink{inverse_8h}{inverse.h}"} +00754 \textcolor{preprocessor}{#include "\hyperlink{RNAstruct_8h}{RNAstruct.h}"} +00755 \textcolor{preprocessor}{#include "\hyperlink{treedist_8h}{treedist.h}"} +00756 \textcolor{preprocessor}{#include "\hyperlink{stringdist_8h}{stringdist.h}"} +00757 \textcolor{preprocessor}{#include "\hyperlink{profiledist_8h}{profiledist.h}"} +00758 +00759 \textcolor{keywordtype}{void} main() +00760 \{ +00761 \textcolor{keywordtype}{char} *seq1=\textcolor{stringliteral}{"CGCAGGGAUACCCGCG"}, *seq2=\textcolor{stringliteral}{"GCGCCCAUAGGGACGC"}, +00762 *struct1,* struct2,* xstruc; +00763 \textcolor{keywordtype}{float} e1, e2, tree\_dist, string\_dist, profile\_dist, kT; +00764 \hyperlink{structTree}{Tree} *T1, *T2; +00765 \hyperlink{structswString}{swString} *S1, *S2; +00766 \textcolor{keywordtype}{float} *pf1, *pf2; +00767 FLT\_OR\_DBL *bppm; +00768 \textcolor{comment}{/* fold at 30C instead of the default 37C */} +00769 \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature} = 30.; \textcolor{comment}{/* must be set *before* initializing */} +00770 +00771 \textcolor{comment}{/* allocate memory for structure and fold */} +00772 struct1 = (\textcolor{keywordtype}{char}* ) \hyperlink{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{space}(\textcolor{keyword}{sizeof}(\textcolor{keywordtype}{char})*(strlen(seq1)+1)); +00773 e1 = \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold}(seq1, struct1); +00774 +00775 struct2 = (\textcolor{keywordtype}{char}* ) \hyperlink{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{space}(\textcolor{keyword}{sizeof}(\textcolor{keywordtype}{char})*(strlen(seq2)+1)); +00776 e2 = \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold}(seq2, struct2); +00777 +00778 \hyperlink{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}{free\_arrays}(); \textcolor{comment}{/* free arrays used in fold() */} +00779 +00780 \textcolor{comment}{/* produce tree and string representations for comparison */} +00781 xstruc = \hyperlink{RNAstruct_8h_a78d73cd54a068ef2812812771cdddc6f}{expand\_Full}(struct1); +00782 T1 = \hyperlink{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}{make\_tree}(xstruc); +00783 S1 = \hyperlink{stringdist_8h_a3125991b3a403b3f89230474deb3f22e}{Make\_swString}(xstruc); +00784 free(xstruc); +00785 +00786 xstruc = \hyperlink{RNAstruct_8h_a78d73cd54a068ef2812812771cdddc6f}{expand\_Full}(struct2); +00787 T2 = \hyperlink{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}{make\_tree}(xstruc); +00788 S2 = \hyperlink{stringdist_8h_a3125991b3a403b3f89230474deb3f22e}{Make\_swString}(xstruc); +00789 free(xstruc); +00790 +00791 \textcolor{comment}{/* calculate tree edit distance and aligned structures with gaps */} +00792 \hyperlink{dist__vars_8h_aa03194c513af6b860e7b33e370b82bdb}{edit\_backtrack} = 1; +00793 tree\_dist = \hyperlink{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{tree\_edit\_distance}(T1, T2); +00794 \hyperlink{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}{free\_tree}(T1); \hyperlink{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}{free\_tree}(T2); +00795 \hyperlink{RNAstruct_8h_a1054c4477d53b31d79d4cb132100e87a}{unexpand\_aligned\_F}(aligned\_line); +00796 printf(\textcolor{stringliteral}{"%s\(\backslash\)n%s %3.2f\(\backslash\)n"}, aligned\_line[0], aligned\_line[1], tree\_dist); +00797 +00798 \textcolor{comment}{/* same thing using string edit (alignment) distance */} +00799 string\_dist = \hyperlink{stringdist_8h_a89e3c335ef17780576d7c0e713830db9}{string\_edit\_distance}(S1, S2); +00800 free(S1); free(S2); +00801 printf(\textcolor{stringliteral}{"%s mfe=%5.2f\(\backslash\)n%s mfe=%5.2f dist=%3.2f\(\backslash\)n"}, +00802 aligned\_line[0], e1, aligned\_line[1], e2, string\_dist); +00803 +00804 \textcolor{comment}{/* for longer sequences one should also set a scaling factor for} +00805 \textcolor{comment}{ partition function folding, e.g: */} +00806 kT = (\hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}+273.15)*1.98717/1000.; \textcolor{comment}{/* kT in kcal/mol */} +00807 \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\_scale} = exp(-e1/kT/strlen(seq1)); +00808 +00809 \textcolor{comment}{/* calculate partition function and base pair probabilities */} +00810 e1 = \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\_fold}(seq1, struct1); +00811 \textcolor{comment}{/* get the base pair probability matrix for the previous run of pf\_fold() */} +00812 bppm = \hyperlink{group__pf__fold_ga6d463707d5f64bdc4d21515b7dd9b115}{export\_bppm}(); +00813 pf1 = \hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\_bp\_profile\_bppm}(bppm, strlen(seq1)); +00814 +00815 e2 = \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\_fold}(seq2, struct2); +00816 \textcolor{comment}{/* get the base pair probability matrix for the previous run of pf\_fold() */} +00817 bppm = \hyperlink{group__pf__fold_ga6d463707d5f64bdc4d21515b7dd9b115}{export\_bppm}(); +00818 pf2 = \hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\_bp\_profile\_bppm}(bppm, strlen(seq2)); +00819 +00820 \hyperlink{group__pf__fold_gae73db3f49a94f0f72e067ecd12681dbd}{free\_pf\_arrays}(); \textcolor{comment}{/* free space allocated for pf\_fold() */} +00821 +00822 profile\_dist = \hyperlink{profiledist_8h_abe75e90e00a1e5dd8862944ed53dad5d}{profile\_edit\_distance}(pf1, pf2); +00823 printf(\textcolor{stringliteral}{"%s free energy=%5.2f\(\backslash\)n%s free energy=%5.2f dist=%3.2f\(\backslash\)n"}, +00824 aligned\_line[0], e1, aligned\_line[1], e2, profile\_dist); +00825 +00826 \hyperlink{profiledist_8h_a9b0b84a5a45761bf42d7c835dcdb3b85}{free\_profile}(pf1); \hyperlink{profiledist_8h_a9b0b84a5a45761bf42d7c835dcdb3b85}{free\_profile}(pf2); +00827 \} +00828 \(\backslash\)endcode +00829 +00830 In a typical Unix environment you would compile \textcolor{keyword}{this} program \textcolor{keyword}{using}: +00831 \(\backslash\)verbatim +00832 cc $\{OPENMP\_CFLAGS\} -c example.c -I$\{hpath\} +00833 \(\backslash\)endverbatim +00834 and link using +00835 \(\backslash\)verbatim +00836 cc $\{OPENMP\_CFLAGS\} -o example -L$\{lpath\} -lRNA -lm +00837 \(\backslash\)endverbatim +00838 where \(\backslash\)e $\{hpath\} and \(\backslash\)e $\{lpath\} point to the location of the header +00839 files and library, respectively. +00840 \(\backslash\)note As \textcolor{keywordflow}{default}, the RNAlib is compiled with build-in \(\backslash\)e OpenMP multithreading +00841 support. Thus, when linking your own \textcolor{keywordtype}{object} files to the library you have to pass +00842 the compiler specific \(\backslash\)e $\{OPENMP\_CFLAGS\} (e.g. \textcolor{stringliteral}{'-fopenmp'} for \(\backslash\)b gcc) even \textcolor{keywordflow}{if} your code does not +00843 use openmp specific code. However, in that \textcolor{keywordflow}{case} the \(\backslash\)e OpenMP flags may be ommited when compiling +00844 example.c +00845 +00846 +00847 **/ +00848 +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/mm_8h.tex b/binaries/src/ViennaRNA/doc/latex/mm_8h.tex new file mode 100644 index 0000000..46b0f6b --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/mm_8h.tex @@ -0,0 +1,12 @@ +\hypertarget{mm_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/mm.h File Reference} +\label{mm_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/mm.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/mm.\-h}} +} + + +Several Maximum Matching implementations. + + + + +\subsection{Detailed Description} +Several Maximum Matching implementations. This file contains the declarations for several maximum matching implementations \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/mm_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/mm_8h_source.tex new file mode 100644 index 0000000..9ae388c --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/mm_8h_source.tex @@ -0,0 +1,19 @@ +\hypertarget{mm_8h}{\section{mm.\-h} +\label{mm_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/mm.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/mm.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_MM\_H\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_MM\_H\_\_} +00003 \textcolor{preprocessor}{} +00012 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} maximumMatching(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}); +00013 +00014 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *maximumMatchingConstraint(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}, +00015 \textcolor{keywordtype}{short} *ptable); +00016 +00017 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *maximumMatching2Constraint( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}, +00018 \textcolor{keywordtype}{short} *ptable, +00019 \textcolor{keywordtype}{short} *ptable2); +00020 +00021 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/modules.tex b/binaries/src/ViennaRNA/doc/latex/modules.tex new file mode 100644 index 0000000..61f26bb --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/modules.tex @@ -0,0 +1,72 @@ +\section{Modules} +Here is a list of all modules\-:\begin{DoxyCompactList} +\item \contentsline{section}{R\-N\-A Secondary Structure Folding}{\pageref{group__folding__routines}}{} +\begin{DoxyCompactList} +\item \contentsline{section}{Calculating Minimum Free Energy (M\-F\-E) Structures}{\pageref{group__mfe__fold}}{} +\begin{DoxyCompactList} +\item \contentsline{section}{M\-F\-E Structures of two hybridized Sequences}{\pageref{group__mfe__cofold}}{} +\item \contentsline{section}{M\-F\-E Consensus Structures for Sequence Alignment(s)}{\pageref{group__consensus__mfe__fold}}{} +\item \contentsline{section}{Local M\-F\-E structure Prediction and Z-\/scores}{\pageref{group__local__mfe__fold}}{} +\item \contentsline{section}{Calculating M\-F\-E representatives of a Distance Based Partitioning}{\pageref{group__kl__neighborhood__mfe}}{} +\end{DoxyCompactList} +\item \contentsline{section}{Calculating Partition Functions and Pair Probabilities}{\pageref{group__pf__fold}}{} +\begin{DoxyCompactList} +\item \contentsline{section}{Compute the structure with maximum expected accuracy (M\-E\-A)}{\pageref{group__mea__fold}}{} +\item \contentsline{section}{Compute the centroid structure}{\pageref{group__centroid__fold}}{} +\item \contentsline{section}{Partition Function for two hybridized Sequences}{\pageref{group__pf__cofold}}{} +\item \contentsline{section}{Partition Function for two hybridized Sequences as a stepwise Process}{\pageref{group__up__cofold}}{} +\item \contentsline{section}{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}{\pageref{group__consensus__pf__fold}}{} +\item \contentsline{section}{Partition functions for locally stable secondary structures}{\pageref{group__local__pf__fold}}{} +\item \contentsline{section}{Calculate Partition Functions of a Distance Based Partitioning}{\pageref{group__kl__neighborhood__pf}}{} +\end{DoxyCompactList} +\item \contentsline{section}{Enumerating Suboptimal Structures}{\pageref{group__subopt__fold}}{} +\begin{DoxyCompactList} +\item \contentsline{section}{Suboptimal structures according to Zuker et al. 1989}{\pageref{group__subopt__zuker}}{} +\item \contentsline{section}{Suboptimal structures within an energy band arround the M\-F\-E}{\pageref{group__subopt__wuchty}}{} +\item \contentsline{section}{Stochastic backtracking in the Ensemble}{\pageref{group__subopt__stochbt}}{} +\begin{DoxyCompactList} +\item \contentsline{section}{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}{\pageref{group__consensus__stochbt}}{} +\item \contentsline{section}{Stochastic Backtracking of Structures from Distance Based Partitioning}{\pageref{group__kl__neighborhood__stochbt}}{} +\end{DoxyCompactList} +\end{DoxyCompactList} +\item \contentsline{section}{Calculate Secondary Structures of two R\-N\-As upon Dimerization}{\pageref{group__cofold}}{} +\begin{DoxyCompactList} +\item \contentsline{section}{M\-F\-E Structures of two hybridized Sequences}{\pageref{group__mfe__cofold}}{} +\item \contentsline{section}{Partition Function for two hybridized Sequences}{\pageref{group__pf__cofold}}{} +\item \contentsline{section}{Partition Function for two hybridized Sequences as a stepwise Process}{\pageref{group__up__cofold}}{} +\end{DoxyCompactList} +\item \contentsline{section}{Predicting Consensus Structures from Alignment(s)}{\pageref{group__consensus__fold}}{} +\begin{DoxyCompactList} +\item \contentsline{section}{M\-F\-E Consensus Structures for Sequence Alignment(s)}{\pageref{group__consensus__mfe__fold}}{} +\item \contentsline{section}{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}{\pageref{group__consensus__pf__fold}}{} +\item \contentsline{section}{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}{\pageref{group__consensus__stochbt}}{} +\item \contentsline{section}{Local M\-F\-E consensus structures for Sequence Alignments}{\pageref{group__local__consensus__fold}}{} +\end{DoxyCompactList} +\item \contentsline{section}{Predicting Locally stable structures of large sequences}{\pageref{group__local__fold}}{} +\begin{DoxyCompactList} +\item \contentsline{section}{Local M\-F\-E structure Prediction and Z-\/scores}{\pageref{group__local__mfe__fold}}{} +\item \contentsline{section}{Partition functions for locally stable secondary structures}{\pageref{group__local__pf__fold}}{} +\item \contentsline{section}{Local M\-F\-E consensus structures for Sequence Alignments}{\pageref{group__local__consensus__fold}}{} +\end{DoxyCompactList} +\item \contentsline{section}{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}{\pageref{group__energy__parameters}}{} +\begin{DoxyCompactList} +\item \contentsline{section}{Reading/\-Writing energy parameter sets from/to File}{\pageref{group__energy__parameters__rw}}{} +\begin{DoxyCompactList} +\item \contentsline{section}{Converting energy parameter files}{\pageref{group__energy__parameters__convert}}{} +\end{DoxyCompactList} +\end{DoxyCompactList} +\item \contentsline{section}{Energy evaluation}{\pageref{group__eval}}{} +\item \contentsline{section}{Searching Sequences for Predefined Structures}{\pageref{group__inverse__fold}}{} +\item \contentsline{section}{Classified Dynamic Programming}{\pageref{group__class__fold}}{} +\begin{DoxyCompactList} +\item \contentsline{section}{Distance based partitioning of the Secondary Structure Space}{\pageref{group__kl__neighborhood}}{} +\begin{DoxyCompactList} +\item \contentsline{section}{Calculating M\-F\-E representatives of a Distance Based Partitioning}{\pageref{group__kl__neighborhood__mfe}}{} +\item \contentsline{section}{Calculate Partition Functions of a Distance Based Partitioning}{\pageref{group__kl__neighborhood__pf}}{} +\item \contentsline{section}{Stochastic Backtracking of Structures from Distance Based Partitioning}{\pageref{group__kl__neighborhood__stochbt}}{} +\end{DoxyCompactList} +\item \contentsline{section}{Compute the Density of States}{\pageref{group__dos}}{} +\end{DoxyCompactList} +\end{DoxyCompactList} +\item \contentsline{section}{Parsing and Comparing -\/ Functions to Manipulate Structures}{\pageref{group__parse}}{} +\end{DoxyCompactList} diff --git a/binaries/src/ViennaRNA/doc/latex/move__set_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/move__set_8h_source.tex new file mode 100644 index 0000000..c749e6d --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/move__set_8h_source.tex @@ -0,0 +1,71 @@ +\hypertarget{move__set_8h}{\section{move\-\_\-set.\-h} +\label{move__set_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/move\-\_\-set.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/move\-\_\-set.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_MOVE\_SET\_H} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_MOVE\_SET\_H} +00003 \textcolor{preprocessor}{} +00004 \textcolor{comment}{/* used data structure*/} +\hypertarget{move__set_8h_source_l00005}{}\hyperlink{structstruct__en}{00005} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\_struct\_en\{ +00006 \textcolor{keywordtype}{int} energy; \textcolor{comment}{/* energy in 10kcal/mol*/} +00007 \textcolor{keywordtype}{short} *structure; \textcolor{comment}{/* structure in energy\_of\_move format*/} +00008 \} \hyperlink{structstruct__en}{struct\_en}; +00009 +00010 \textcolor{comment}{/* prints structure*/} +00011 \textcolor{keywordtype}{void} print\_stren(FILE *out, \hyperlink{structstruct__en}{struct\_en} *str); +00012 \textcolor{keywordtype}{void} print\_str(FILE *out, \textcolor{keywordtype}{short} *str); +00013 +00014 \textcolor{comment}{/* copying functions*/} +00015 \textcolor{keywordtype}{void} copy\_arr(\textcolor{keywordtype}{short} *dest, \textcolor{keywordtype}{short} *src); \textcolor{comment}{/*just copy*/} +00016 \textcolor{keywordtype}{short} *allocopy(\textcolor{keywordtype}{short} *src); \textcolor{comment}{/*copy and make space*/} +00017 +00018 \textcolor{comment}{/* walking methods (verbose\_lvl 0-2, shifts = use shift moves? noLP = no lone pairs? (not compatible with + shifts))} +00019 \textcolor{comment}{ input: seq - sequence} +00020 \textcolor{comment}{ ptable - structure encoded with make\_pair\_table() from pair\_mat.h} +00021 \textcolor{comment}{ s, s1 - sequence encoded with encode\_sequence from pair\_mat.h} +00022 \textcolor{comment}{ methods: deepest - lowest energy structure is used} +00023 \textcolor{comment}{ first - first found lower energy structure is used} +00024 \textcolor{comment}{ rand - random lower energy structure is used} +00025 \textcolor{comment}{ returns local minima structure in ptable and its energy in 10kcal/mol as output */} +00026 +00027 \textcolor{keywordtype}{int} move\_deepest( \textcolor{keywordtype}{char} *seq, +00028 \textcolor{keywordtype}{short} *ptable, +00029 \textcolor{keywordtype}{short} *s, +00030 \textcolor{keywordtype}{short} *s1, +00031 \textcolor{keywordtype}{int} verbosity\_level, +00032 \textcolor{keywordtype}{int} shifts, +00033 \textcolor{keywordtype}{int} noLP); +00034 \textcolor{keywordtype}{int} move\_first( \textcolor{keywordtype}{char} *seq, +00035 \textcolor{keywordtype}{short} *ptable, +00036 \textcolor{keywordtype}{short} *s, +00037 \textcolor{keywordtype}{short} *s1, +00038 \textcolor{keywordtype}{int} verbosity\_level, +00039 \textcolor{keywordtype}{int} shifts, +00040 \textcolor{keywordtype}{int} noLP); +00041 \textcolor{keywordtype}{int} move\_rand( \textcolor{keywordtype}{char} *seq, +00042 \textcolor{keywordtype}{short} *ptable, +00043 \textcolor{keywordtype}{short} *s, +00044 \textcolor{keywordtype}{short} *s1, +00045 \textcolor{keywordtype}{int} verbosity\_level); +00046 +00047 +00048 \textcolor{comment}{/* browse\_neighbours and do funct function on each of them (used mainly for user specified flooding)} +00049 \textcolor{comment}{ input: seq - sequence} +00050 \textcolor{comment}{ ptable - structure encoded with make\_pair\_table() from pair\_mat.h} +00051 \textcolor{comment}{ s, s1 - sequence encoded with encode\_sequence from pair\_mat.h} +00052 \textcolor{comment}{ funct - function (moved structure, current structure (or altered by funct)) to do with every + structure in neigbourhood} +00053 \textcolor{comment}{ returns energy of the structure funct sets as second argument*/} +00054 \textcolor{keywordtype}{int} browse\_neighs( \textcolor{keywordtype}{char} *seq, +00055 \textcolor{keywordtype}{short} *ptable, +00056 \textcolor{keywordtype}{short} *s, +00057 \textcolor{keywordtype}{short} *s1, +00058 \textcolor{keywordtype}{int} verbosity\_level, +00059 \textcolor{keywordtype}{int} shifts, +00060 \textcolor{keywordtype}{int} noLP, +00061 \textcolor{keywordtype}{int} (*funct) (\hyperlink{structstruct__en}{struct\_en}*, \hyperlink{structstruct__en}{struct\_en}*)); +00062 +00063 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/mp_example.tex b/binaries/src/ViennaRNA/doc/latex/mp_example.tex new file mode 100644 index 0000000..b82d3a7 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/mp_example.tex @@ -0,0 +1,97 @@ +The following program exercises most commonly used functions of the library. The program folds two sequences using both the mfe and partition function algorithms and calculates the tree edit and profile distance of the resulting structures and base pairing probabilities. + + +\begin{DoxyCode} +\textcolor{preprocessor}{#include } +\textcolor{preprocessor}{#include } +\textcolor{preprocessor}{#include } +\textcolor{preprocessor}{#include } +\textcolor{preprocessor}{#include "\hyperlink{utils_8h}{utils.h}"} +\textcolor{preprocessor}{#include "\hyperlink{fold__vars_8h}{fold\_vars.h}"} +\textcolor{preprocessor}{#include "\hyperlink{fold_8h}{fold.h}"} +\textcolor{preprocessor}{#include "\hyperlink{part__func_8h}{part\_func.h}"} +\textcolor{preprocessor}{#include "\hyperlink{inverse_8h}{inverse.h}"} +\textcolor{preprocessor}{#include "\hyperlink{RNAstruct_8h}{RNAstruct.h}"} +\textcolor{preprocessor}{#include "\hyperlink{treedist_8h}{treedist.h}"} +\textcolor{preprocessor}{#include "\hyperlink{stringdist_8h}{stringdist.h}"} +\textcolor{preprocessor}{#include "\hyperlink{profiledist_8h}{profiledist.h}"} + +\textcolor{keywordtype}{void} main() +\{ + \textcolor{keywordtype}{char} *seq1=\textcolor{stringliteral}{"CGCAGGGAUACCCGCG"}, *seq2=\textcolor{stringliteral}{"GCGCCCAUAGGGACGC"}, + *struct1,* struct2,* xstruc; + \textcolor{keywordtype}{float} e1, e2, tree\_dist, string\_dist, profile\_dist, kT; + \hyperlink{structTree}{Tree} *T1, *T2; + \hyperlink{structswString}{swString} *S1, *S2; + \textcolor{keywordtype}{float} *pf1, *pf2; + FLT\_OR\_DBL *bppm; + \textcolor{comment}{/* fold at 30C instead of the default 37C */} + \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature} = 30.; \textcolor{comment}{/* must be set *before* initializing */} + + \textcolor{comment}{/* allocate memory for structure and fold */} + struct1 = (\textcolor{keywordtype}{char}* ) \hyperlink{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{space}(\textcolor{keyword}{sizeof}(\textcolor{keywordtype}{char})*(strlen(seq1)+1)); + e1 = \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold}(seq1, struct1); + + struct2 = (\textcolor{keywordtype}{char}* ) \hyperlink{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{space}(\textcolor{keyword}{sizeof}(\textcolor{keywordtype}{char})*(strlen(seq2)+1)); + e2 = \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold}(seq2, struct2); + + \hyperlink{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}{free\_arrays}(); \textcolor{comment}{/* free arrays used in fold() */} + + \textcolor{comment}{/* produce tree and string representations for comparison */} + xstruc = \hyperlink{RNAstruct_8h_a78d73cd54a068ef2812812771cdddc6f}{expand\_Full}(struct1); + T1 = \hyperlink{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}{make\_tree}(xstruc); + S1 = \hyperlink{stringdist_8h_a3125991b3a403b3f89230474deb3f22e}{Make\_swString}(xstruc); + free(xstruc); + + xstruc = \hyperlink{RNAstruct_8h_a78d73cd54a068ef2812812771cdddc6f}{expand\_Full}(struct2); + T2 = \hyperlink{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}{make\_tree}(xstruc); + S2 = \hyperlink{stringdist_8h_a3125991b3a403b3f89230474deb3f22e}{Make\_swString}(xstruc); + free(xstruc); + + \textcolor{comment}{/* calculate tree edit distance and aligned structures with gaps */} + \hyperlink{dist__vars_8h_aa03194c513af6b860e7b33e370b82bdb}{edit\_backtrack} = 1; + tree\_dist = \hyperlink{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{tree\_edit\_distance}(T1, T2); + \hyperlink{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}{free\_tree}(T1); \hyperlink{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}{free\_tree}(T2); + \hyperlink{RNAstruct_8h_a1054c4477d53b31d79d4cb132100e87a}{unexpand\_aligned\_F}(aligned\_line); + printf(\textcolor{stringliteral}{"%s\(\backslash\)n%s %3.2f\(\backslash\)n"}, aligned\_line[0], aligned\_line[1], tree\_dist); + + \textcolor{comment}{/* same thing using string edit (alignment) distance */} + string\_dist = \hyperlink{stringdist_8h_a89e3c335ef17780576d7c0e713830db9}{string\_edit\_distance}(S1, S2); + free(S1); free(S2); + printf(\textcolor{stringliteral}{"%s mfe=%5.2f\(\backslash\)n%s mfe=%5.2f dist=%3.2f\(\backslash\)n"}, + aligned\_line[0], e1, aligned\_line[1], e2, string\_dist); + + \textcolor{comment}{/* for longer sequences one should also set a scaling factor for} +\textcolor{comment}{ partition function folding, e.g: */} + kT = (\hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}+273.15)*1.98717/1000.; \textcolor{comment}{/* kT in kcal/mol */} + \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\_scale} = exp(-e1/kT/strlen(seq1)); + + \textcolor{comment}{/* calculate partition function and base pair probabilities */} + e1 = \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\_fold}(seq1, struct1); + \textcolor{comment}{/* get the base pair probability matrix for the previous run of pf\_fold() */} + bppm = \hyperlink{group__pf__fold_ga6d463707d5f64bdc4d21515b7dd9b115}{export\_bppm}(); + pf1 = \hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\_bp\_profile\_bppm}(bppm, strlen(seq1)); + + e2 = \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\_fold}(seq2, struct2); + \textcolor{comment}{/* get the base pair probability matrix for the previous run of pf\_fold() */} + bppm = \hyperlink{group__pf__fold_ga6d463707d5f64bdc4d21515b7dd9b115}{export\_bppm}(); + pf2 = \hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\_bp\_profile\_bppm}(bppm, strlen(seq2)); + + \hyperlink{group__pf__fold_gae73db3f49a94f0f72e067ecd12681dbd}{free\_pf\_arrays}(); \textcolor{comment}{/* free space allocated for pf\_fold() */} + + profile\_dist = \hyperlink{profiledist_8h_abe75e90e00a1e5dd8862944ed53dad5d}{profile\_edit\_distance}(pf1, pf2); + printf(\textcolor{stringliteral}{"%s free energy=%5.2f\(\backslash\)n%s free energy=%5.2f dist=%3.2f\(\backslash\)n"}, + aligned\_line[0], e1, aligned\_line[1], e2, profile\_dist); + + \hyperlink{profiledist_8h_a9b0b84a5a45761bf42d7c835dcdb3b85}{free\_profile}(pf1); \hyperlink{profiledist_8h_a9b0b84a5a45761bf42d7c835dcdb3b85}{free\_profile}(pf2); +\} +\end{DoxyCode} + + +In a typical Unix environment you would compile this program using\-: \begin{DoxyVerb}cc ${OPENMP_CFLAGS} -c example.c -I${hpath} +\end{DoxyVerb} + and link using \begin{DoxyVerb}cc ${OPENMP_CFLAGS} -o example -L${lpath} -lRNA -lm +\end{DoxyVerb} + where {\itshape \$\{hpath\}} and {\itshape \$\{lpath\}} point to the location of the header files and library, respectively. \begin{DoxyNote}{Note} +As default, the R\-N\-Alib is compiled with build-\/in {\itshape Open\-M\-P} multithreading support. Thus, when linking your own object files to the library you have to pass the compiler specific {\itshape \$\{O\-P\-E\-N\-M\-P\-\_\-\-C\-F\-L\-A\-G\-S\}} (e.\-g. '-\/fopenmp' for {\bfseries gcc}) even if your code does not use openmp specific code. However, in that case the {\itshape Open\-M\-P} flags may be ommited when compiling example.\-c +\end{DoxyNote} diff --git a/binaries/src/ViennaRNA/doc/latex/mp_parse.tex b/binaries/src/ViennaRNA/doc/latex/mp_parse.tex new file mode 100644 index 0000000..0e1d9ba --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/mp_parse.tex @@ -0,0 +1,40 @@ +\subsection*{Representations of Secondary Structures} + +The standard representation of a secondary structure is the {\itshape bracket notation}, where matching brackets symbolize base pairs and unpaired bases are shown as dots. Alternatively, one may use two types of node labels, 'P' for paired and 'U' for unpaired; a dot is then replaced by '(U)', and each closed bracket is assigned an additional identifier 'P'. We call this the expanded notation. In\cite{fontana:1993b} a condensed representation of the secondary structure is proposed, the so-\/called homeomorphically irreducible tree (H\-I\-T) representation. Here a stack is represented as a single pair of matching brackets labeled 'P' and weighted by the number of base pairs. Correspondingly, a contiguous strain of unpaired bases is shown as one pair of matching brackets labeled 'U' and weighted by its length. Generally any string consisting of matching brackets and identifiers is equivalent to a plane tree with as many different types of nodes as there are identifiers. + +Bruce Shapiro proposed a coarse grained representation\cite{shapiro:1988}, which, does not retain the full information of the secondary structure. He represents the different structure elements by single matching brackets and labels them as 'H' (hairpin loop), 'I' (interior loop), 'B' (bulge), 'M' (multi-\/loop), and 'S' (stack). We extend his alphabet by an extra letter for external elements 'E'. Again these identifiers may be followed by a weight corresponding to the number of unpaired bases or base pairs in the structure element. All tree representations (except for the dot-\/bracket form) can be encapsulated into a virtual root (labeled 'R'), see the example below. + +The following example illustrates the different linear tree representations used by the package. All lines show the same secondary structure. + +\begin{DoxyVerb}a) .((((..(((...)))..((..)))).)). + (U)(((((U)(U)((((U)(U)(U)P)P)P)(U)(U)(((U)(U)P)P)P)P)(U)P)P)(U) +b) (U)(((U2)((U3)P3)(U2)((U2)P2)P2)(U)P2)(U) +c) (((H)(H)M)B) + ((((((H)S)((H)S)M)S)B)S) + (((((((H)S)((H)S)M)S)B)S)E) +d) ((((((((H3)S3)((H2)S2)M4)S2)B1)S2)E2)R) +\end{DoxyVerb} + + +Above\-: \hyperlink{structTree}{Tree} representations of secondary structures. a) Full structure\-: the first line shows the more convenient condensed notation which is used by our programs; the second line shows the rather clumsy expanded notation for completeness, b) H\-I\-T structure, c) different versions of coarse grained structures\-: the second line is exactly Shapiro's representation, the first line is obtained by neglecting the stems. Since each loop is closed by a unique stem, these two lines are equivalent. The third line is an extension taking into account also the external digits. d) weighted coarse structure, this time including the virtual root. + +For the output of aligned structures from string editing, different representations are needed, where we put the label on both sides. The above examples for tree representations would then look like\-: + +\begin{DoxyVerb}a) (UU)(P(P(P(P(UU)(UU)(P(P(P(UU)(UU)(UU)P)P)P)(UU)(UU)(P(P(UU)(U... +b) (UU)(P2(P2(U2U2)(P2(U3U3)P3)(U2U2)(P2(U2U2)P2)P2)(UU)P2)(UU) +c) (B(M(HH)(HH)M)B) + (S(B(S(M(S(HH)S)(S(HH)S)M)S)B)S) + (E(S(B(S(M(S(HH)S)(S(HH)S)M)S)B)S)E) +d) (R(E2(S2(B1(S2(M4(S3(H3)S3)((H2)S2)M4)S2)B1)S2)E2)R) +\end{DoxyVerb} + + +Aligned structures additionally contain the gap character '\-\_\-'. + +\subsection*{Parsing and Coarse Graining of Structures} + +Several functions are provided for parsing structures and converting to different representations. + +\begin{DoxyVerb}char *expand_Full(const char *structure) +\end{DoxyVerb} + Convert the full structure from bracket notation to the expanded notation including root. \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/mp_utils.tex b/binaries/src/ViennaRNA/doc/latex/mp_utils.tex new file mode 100644 index 0000000..91cb941 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/mp_utils.tex @@ -0,0 +1,18 @@ +\label{mp_utils_toc}% +\hypertarget{mp_utils_toc}{}% + \subsubsection*{Table of Contents} + + + + + +\begin{DoxyItemize} +\item \hyperlink{mp_utils_utils_ss}{Producing secondary structure graphs} \item \hyperlink{mp_utils_utils_dot}{Producing (colored) dot plots for base pair probabilities} \item \hyperlink{mp_utils_utils_aln}{Producing (colored) alignments} \item \hyperlink{mp_utils_utils_seq}{R\-N\-A sequence related utilities} \item \hyperlink{mp_utils_utils_struc}{R\-N\-A secondary structure related utilities} \item \hyperlink{mp_utils_utils_misc}{Miscellaneous Utilities}\end{DoxyItemize} + + +\hypertarget{mp_utils_utils_ss}{}\section{Producing secondary structure graphs}\label{mp_utils_utils_ss} +\begin{DoxyVerb}int PS_rna_plot ( char *string, + char *structure, + char *file) +\end{DoxyVerb} + Produce a secondary structure graph in Post\-Script and write it to 'filename'. \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/naview_8h.tex b/binaries/src/ViennaRNA/doc/latex/naview_8h.tex new file mode 100644 index 0000000..d6563b6 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/naview_8h.tex @@ -0,0 +1,11 @@ +\hypertarget{naview_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/naview.h File Reference} +\label{naview_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/naview.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/naview.\-h}} +} +This graph shows which files directly or indirectly include this file\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{naview_8h__dep__incl} +\end{center} +\end{figure} diff --git a/binaries/src/ViennaRNA/doc/latex/naview_8h__dep__incl.md5 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+\label{naview_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/naview.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/naview.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_NAVIEW\_H\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_NAVIEW\_H\_\_} +00003 \textcolor{preprocessor}{} +00012 \textcolor{keywordtype}{int} naview\_xy\_coordinates(\textcolor{keywordtype}{short} *pair\_table, +00013 \textcolor{keywordtype}{float} *X, +00014 \textcolor{keywordtype}{float} *Y); +00015 +00016 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/pair__mat_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/pair__mat_8h_source.tex new file mode 100644 index 0000000..c970d82 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/pair__mat_8h_source.tex @@ -0,0 +1,154 @@ +\hypertarget{pair__mat_8h}{\section{pair\-\_\-mat.\-h} +\label{pair__mat_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/pair\-\_\-mat.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/pair\-\_\-mat.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#include } +00002 \textcolor{preprocessor}{#include "\hyperlink{utils_8h}{utils.h}"} +00003 \textcolor{preprocessor}{#include "\hyperlink{fold__vars_8h}{fold\_vars.h}"} +00004 +00005 \textcolor{preprocessor}{#define NBASES 8} +00006 \textcolor{preprocessor}{}\textcolor{comment}{/*@notnull@*/} +00007 +00008 \textcolor{keyword}{static} \textcolor{keyword}{const} \textcolor{keywordtype}{char} Law\_and\_Order[] = \textcolor{stringliteral}{"\_ACGUTXKI"}; +00009 \textcolor{keyword}{static} \textcolor{keywordtype}{int} BP\_pair[NBASES][NBASES]= +00010 \textcolor{comment}{/* \_ A C G U X K I */} +00011 \{\{ 0, 0, 0, 0, 0, 0, 0, 0\}, +00012 \{ 0, 0, 0, 0, 5, 0, 0, 5\}, +00013 \{ 0, 0, 0, 1, 0, 0, 0, 0\}, +00014 \{ 0, 0, 2, 0, 3, 0, 0, 0\}, +00015 \{ 0, 6, 0, 4, 0, 0, 0, 6\}, +00016 \{ 0, 0, 0, 0, 0, 0, 2, 0\}, +00017 \{ 0, 0, 0, 0, 0, 1, 0, 0\}, +00018 \{ 0, 6, 0, 0, 5, 0, 0, 0\}\}; +00019 +00020 \textcolor{preprocessor}{#define MAXALPHA 20 }\textcolor{comment}{/* maximal length of alphabet */}\textcolor{preprocessor}{} +00021 \textcolor{preprocessor}{} +00022 \textcolor{keyword}{static} \textcolor{keywordtype}{short} alias[\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}+1]; +00023 \textcolor{keyword}{static} \textcolor{keywordtype}{int} pair[\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}+1][\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}+1]; +00024 \textcolor{comment}{/* rtype[pair[i][j]]:=pair[j][i] */} +00025 \textcolor{keyword}{static} \textcolor{keywordtype}{int} rtype[8] = \{0, 2, 1, 4, 3, 6, 5, 7\}; +00026 +00027 \textcolor{preprocessor}{#ifdef \_OPENMP} +00028 \textcolor{preprocessor}{}\textcolor{preprocessor}{#pragma omp threadprivate(Law\_and\_Order, BP\_pair, alias, pair, rtype)} +00029 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif} +00030 \textcolor{preprocessor}{} +00031 \textcolor{comment}{/* for backward compatibility */} +00032 \textcolor{preprocessor}{#define ENCODE(c) encode\_char(c)} +00033 \textcolor{preprocessor}{} +00034 \textcolor{keyword}{static} \textcolor{keywordtype}{int} encode\_char(\textcolor{keywordtype}{char} c) \{ +00035 \textcolor{comment}{/* return numerical representation of base used e.g. in pair[][] */} +00036 \textcolor{keywordtype}{int} code; +00037 \textcolor{keywordflow}{if} (energy\_set>0) code = (int) (c-\textcolor{charliteral}{'A'})+1; +00038 \textcolor{keywordflow}{else} \{ +00039 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *pos; +00040 pos = strchr(Law\_and\_Order, c); +00041 \textcolor{keywordflow}{if} (pos==NULL) code=0; +00042 \textcolor{keywordflow}{else} code = (int) (pos-Law\_and\_Order); +00043 \textcolor{keywordflow}{if} (code>5) code = 0; +00044 \textcolor{keywordflow}{if} (code>4) code--; \textcolor{comment}{/* make T and U equivalent */} +00045 \} +00046 \textcolor{keywordflow}{return} code; +00047 \} +00048 +00049 \textcolor{comment}{/*@+boolint +charint@*/} +00050 \textcolor{comment}{/*@null@*/} +00051 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} *\hyperlink{fold__vars_8h_a2695d91cc535d09c2eae5c3884e2ec64}{nonstandards}; +00052 \textcolor{keyword}{extern} \textcolor{keywordtype}{void} \hyperlink{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{nrerror}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} message[]); +00053 \textcolor{keyword}{static} \textcolor{keywordtype}{void} make\_pair\_matrix(\textcolor{keywordtype}{void}) +00054 \{ +00055 \textcolor{keywordtype}{int} i,j; +00056 +00057 \textcolor{keywordflow}{if} (energy\_set==0) \{ +00058 \textcolor{keywordflow}{for} (i=0; i<5; i++) alias[i] = (\textcolor{keywordtype}{short}) i; +00059 alias[5] = 3; \textcolor{comment}{/* X <-> G */} +00060 alias[6] = 2; \textcolor{comment}{/* K <-> C */} +00061 alias[7] = 0; \textcolor{comment}{/* I <-> default base '@' */} +00062 \textcolor{keywordflow}{for} (i=0; i G */} +00084 alias[i++] = 2; \textcolor{comment}{/* B <-> C */} +00085 \} +00086 \textcolor{keywordflow}{for} (i=1; i<\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; i++) \{ +00087 pair[i][i+1] = 2; \textcolor{comment}{/* AB <-> GC */} +00088 i++; +00089 pair[i][i-1] = 1; \textcolor{comment}{/* BA <-> CG */} +00090 \} +00091 \} +00092 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (energy\_set==2) \{ +00093 \textcolor{keywordflow}{for} (i=1; i<\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA};) \{ +00094 alias[i++] = 1; \textcolor{comment}{/* A <-> A*/} +00095 alias[i++] = 4; \textcolor{comment}{/* B <-> U */} +00096 \} +00097 \textcolor{keywordflow}{for} (i=1; i<\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; i++) \{ +00098 pair[i][i+1] = 5; \textcolor{comment}{/* AB <-> AU */} +00099 i++; +00100 pair[i][i-1] = 6; \textcolor{comment}{/* BA <-> UA */} +00101 \} +00102 \} +00103 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (energy\_set==3) \{ +00104 \textcolor{keywordflow}{for} (i=1; i G */} +00106 alias[i++] = 2; \textcolor{comment}{/* B <-> C */} +00107 alias[i++] = 1; \textcolor{comment}{/* C <-> A */} +00108 alias[i++] = 4; \textcolor{comment}{/* D <-> U */} +00109 \} +00110 \textcolor{keywordflow}{for} (i=1; i GC */} +00112 i++; +00113 pair[i][i-1] = 1; \textcolor{comment}{/* BA <-> CG */} +00114 i++; +00115 pair[i][i+1] = 5; \textcolor{comment}{/* CD <-> AU */} +00116 i++; +00117 pair[i][i-1] = 6; \textcolor{comment}{/* DC <-> UA */} +00118 \} +00119 \} +00120 \textcolor{keywordflow}{else} \hyperlink{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{nrerror}(\textcolor{stringliteral}{"What energy\_set are YOU using??"}); +00121 \textcolor{keywordflow}{for} (i=0; i<=\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; i++) \{ +00122 \textcolor{keywordflow}{for} (j=0; j<=\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; j++) +00123 rtype[pair[i][j]] = pair[j][i]; +00124 \} +00125 \} +00126 \} +00127 +00128 \textcolor{keyword}{static} \textcolor{keywordtype}{short} *encode\_sequence(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence, \textcolor{keywordtype}{short} how)\{ +00129 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} i,l = (\textcolor{keywordtype}{unsigned} int)strlen(sequence); +00130 \textcolor{keywordtype}{short} *S = (\textcolor{keywordtype}{short} *) \hyperlink{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{space}(\textcolor{keyword}{sizeof}(\textcolor{keywordtype}{short})*(l+2)); +00131 +00132 \textcolor{keywordflow}{switch}(how)\{ +00133 \textcolor{comment}{/* standard encoding as always used for S */} +00134 \textcolor{keywordflow}{case} 0: \textcolor{keywordflow}{for}(i=1; i<=l; i++) \textcolor{comment}{/* make numerical encoding of sequence */} +00135 S[i]= (\textcolor{keywordtype}{short}) encode\_char(toupper(sequence[i-1])); +00136 S[l+1] = S[1]; +00137 S[0] = (short) l; +00138 \textcolor{keywordflow}{break}; +00139 \textcolor{comment}{/* encoding for mismatches of nostandard bases (normally used for S1) */} +00140 \textcolor{keywordflow}{case} 1: \textcolor{keywordflow}{for}(i=1; i<=l; i++) +00141 S[i] = alias[(\textcolor{keywordtype}{short}) encode\_char(toupper(sequence[i-1]))]; +00142 S[l+1] = S[1]; +00143 S[0] = S[l]; +00144 \textcolor{keywordflow}{break}; +00145 \} +00146 +00147 \textcolor{keywordflow}{return} S; +00148 \} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/params_8h.tex b/binaries/src/ViennaRNA/doc/latex/params_8h.tex new file mode 100644 index 0000000..cb38616 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/params_8h.tex @@ -0,0 +1,38 @@ +\hypertarget{params_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/params.h File Reference} +\label{params_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/params.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/params.\-h}} +} +Include dependency graph for params.\-h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{params_8h__incl} +\end{center} +\end{figure} +This graph shows which files directly or indirectly include this file\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{params_8h__dep__incl} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +\hyperlink{structparamT}{param\-T} $\ast$ \hyperlink{group__energy__parameters_ga527ef619cd8210b84d5d53be1e0e29b6}{scale\-\_\-parameters} (void) +\begin{DoxyCompactList}\small\item\em Get precomputed energy contributions for all the known loop types. \end{DoxyCompactList}\item +\hyperlink{structparamT}{param\-T} $\ast$ \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters} (double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, \hyperlink{structmodel__detailsT}{model\-\_\-details\-T} md) +\begin{DoxyCompactList}\small\item\em Get precomputed energy contributions for all the known loop types. \end{DoxyCompactList}\item +\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba}{get\-\_\-scaled\-\_\-pf\-\_\-parameters} (void) +\item +\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_ga6fc2f3eef5a3024d44963ac59a42e39d}{get\-\_\-boltzmann\-\_\-factors} (double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, double beta\-Scale, \hyperlink{structmodel__detailsT}{model\-\_\-details\-T} md, double \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\-\_\-scale}) +\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent thermodynamic temperature. \end{DoxyCompactList}\item +\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_gacba212326a051734797e65987260fdd0}{get\-\_\-boltzmann\-\_\-factor\-\_\-copy} (\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters) +\begin{DoxyCompactList}\small\item\em Get a copy of already precomputed Boltzmann factors. \end{DoxyCompactList}\item +\hypertarget{group__energy__parameters_gaa6a4297a2b91d6f7ae47dd61ca1862a0}{\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_gaa6a4297a2b91d6f7ae47dd61ca1862a0}{get\-\_\-scaled\-\_\-alipf\-\_\-parameters} (unsigned int n\-\_\-seq)}\label{group__energy__parameters_gaa6a4297a2b91d6f7ae47dd61ca1862a0} + +\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) \end{DoxyCompactList}\item +\hypertarget{group__energy__parameters_gaaa049a8c9f1c2ed4398cb1b5a3d65a66}{P\-U\-B\-L\-I\-C \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_gaaa049a8c9f1c2ed4398cb1b5a3d65a66}{get\-\_\-boltzmann\-\_\-factors\-\_\-ali} (unsigned int n\-\_\-seq, double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, double beta\-Scale, \hyperlink{structmodel__detailsT}{model\-\_\-details\-T} md, double \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\-\_\-scale})}\label{group__energy__parameters_gaaa049a8c9f1c2ed4398cb1b5a3d65a66} + +\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) with independent thermodynamic temperature. \end{DoxyCompactList}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/params_8h__dep__incl.md5 b/binaries/src/ViennaRNA/doc/latex/params_8h__dep__incl.md5 new file mode 100644 index 0000000..a47dfde --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/params_8h__dep__incl.md5 @@ -0,0 +1 @@ +61af4ec8b4b0441946fdca501adfd82e \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/params_8h__dep__incl.pdf b/binaries/src/ViennaRNA/doc/latex/params_8h__dep__incl.pdf new file mode 100644 index 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\textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_PART\_FUNC\_H\_\_} +00003 \textcolor{preprocessor}{} +00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"} +00005 +00006 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_} +00007 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func \_\_attribute\_\_ ((deprecated))} +00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else} +00009 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func} +00010 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif} +00011 \textcolor{preprocessor}{} +00012 +00041 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{group__subopt__stochbt_gacd79b1a570e6ad9be24cb11fe8cae30a}{st\_back}; +00042 +00043 \textcolor{comment}{/*} +00044 \textcolor{comment}{#################################################} +00045 \textcolor{comment}{# PARTITION FUNCTION COMPUTATION #} +00046 \textcolor{comment}{#################################################} +00047 \textcolor{comment}{*/} +00048 +00087 \textcolor{keywordtype}{float} \hyperlink{group__pf__fold_ga1839c61275760944b3a007c41d5c0823}{pf\_fold\_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence, +00088 \textcolor{keywordtype}{char} *structure, +00089 \hyperlink{structpf__paramT}{pf\_paramT} *parameters, +00090 \textcolor{keywordtype}{int} calculate\_bppm, +00091 \textcolor{keywordtype}{int} is\_constrained, +00092 \textcolor{keywordtype}{int} is\_circular); +00093 +00133 \textcolor{keywordtype}{float} \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\_fold}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence, +00134 \textcolor{keywordtype}{char} *structure); +00135 +00161 \textcolor{keywordtype}{float} \hyperlink{group__pf__fold_ga819ce5fca8984004ac81c4a3b04cb735}{pf\_circ\_fold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence, +00162 \textcolor{keywordtype}{char} *structure); +00163 +00173 \textcolor{keywordtype}{char} *\hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack}(\textcolor{keywordtype}{char} *sequence); +00174 +00186 \textcolor{keywordtype}{char} *\hyperlink{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{pbacktrack\_circ}(\textcolor{keywordtype}{char} *sequence); +00187 +00203 \textcolor{keywordtype}{void} \hyperlink{group__pf__fold_gae73db3f49a94f0f72e067ecd12681dbd}{free\_pf\_arrays}(\textcolor{keywordtype}{void}); +00204 +00214 \textcolor{keywordtype}{void} \hyperlink{group__pf__fold_ga384e927890f9c034ff09fa66da102d28}{update\_pf\_params}(\textcolor{keywordtype}{int} length); +00215 +00222 \textcolor{keywordtype}{void} \hyperlink{group__pf__fold_ga0733527a94de3b79eee3c3c03c99c1bc}{update\_pf\_params\_par}(\textcolor{keywordtype}{int} length, \hyperlink{structpf__paramT}{pf\_paramT} *parameters); +00223 +00240 FLT\_OR\_DBL *\hyperlink{group__pf__fold_ga6d463707d5f64bdc4d21515b7dd9b115}{export\_bppm}(\textcolor{keywordtype}{void}); +00241 +00242 \textcolor{comment}{/*} +00243 \textcolor{comment}{#################################################} +00244 \textcolor{comment}{# OTHER PARTITION FUNCTION RELATED DECLARATIONS #} +00245 \textcolor{comment}{#################################################} +00246 \textcolor{comment}{*/} +00247 +00265 \textcolor{keywordtype}{void} \hyperlink{group__pf__fold_ga03e15e831a31b1154855ab47edbdb019}{assign\_plist\_from\_pr}( \hyperlink{structplist}{plist} **pl, +00266 FLT\_OR\_DBL *probs, +00267 \textcolor{keywordtype}{int} length, +00268 \textcolor{keywordtype}{double} cutoff); +00269 +00270 \textcolor{comment}{/* this doesn't work if free\_pf\_arrays() is called before */} +00271 \textcolor{keywordtype}{void} assign\_plist\_gquad\_from\_pr(\hyperlink{structplist}{plist} **pl, +00272 \textcolor{keywordtype}{int} length, +00273 \textcolor{keywordtype}{double} cut\_off); +00274 +00275 \textcolor{keywordtype}{char} *get\_centroid\_struct\_gquad\_pr(\textcolor{keywordtype}{int} length, +00276 \textcolor{keywordtype}{double} *dist); +00277 +00293 \textcolor{keywordtype}{int} \hyperlink{group__pf__fold_ga18607e79e106cad827f482eedd2f632e}{get\_pf\_arrays}(\textcolor{keywordtype}{short} **S\_p, +00294 \textcolor{keywordtype}{short} **S1\_p, +00295 \textcolor{keywordtype}{char} **ptype\_p, +00296 FLT\_OR\_DBL **qb\_p, +00297 FLT\_OR\_DBL **qm\_p, +00298 FLT\_OR\_DBL **q1k\_p, +00299 FLT\_OR\_DBL **qln\_p); +00300 +00304 \textcolor{keywordtype}{double} \hyperlink{part__func_8h_a189e2a1ec6cc32c53ea72f7543b0441e}{get\_subseq\_F}(\textcolor{keywordtype}{int} i, \textcolor{keywordtype}{int} j); +00305 +00322 \textcolor{keywordtype}{char} *\hyperlink{group__centroid__fold_ga9aba0ba1433a6d259331e0fe9fc4a9a6}{get\_centroid\_struct\_pl}(\textcolor{keywordtype}{int} length, +00323 \textcolor{keywordtype}{double} *dist, +00324 \hyperlink{structplist}{plist} *pl); +00325 +00342 \textcolor{keywordtype}{char} *\hyperlink{group__centroid__fold_gacdabece4aa1e20c9eaa97acb4c4dcc38}{get\_centroid\_struct\_pr}(\textcolor{keywordtype}{int} length, +00343 \textcolor{keywordtype}{double} *dist, +00344 FLT\_OR\_DBL *pr); +00345 +00358 \textcolor{keywordtype}{double} \hyperlink{group__pf__fold_ga79cbc375af65f11609feb6b055269e7d}{mean\_bp\_distance}(\textcolor{keywordtype}{int} length); +00359 +00377 \textcolor{keywordtype}{double} \hyperlink{group__pf__fold_ga72d84525f0afd3a9d60d830a2f501fa5}{mean\_bp\_distance\_pr}(\textcolor{keywordtype}{int} length, +00378 FLT\_OR\_DBL *pr); +00379 +00383 \textcolor{keywordtype}{void} \hyperlink{part__func_8h_a1f562d463c14d4703d9656056200eb38}{bppm\_to\_structure}(\textcolor{keywordtype}{char} *structure, +00384 FLT\_OR\_DBL *pr, +00385 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length); +00386 +00387 \hyperlink{structplist}{plist} *stackProb(\textcolor{keywordtype}{double} cutoff); +00388 +00392 \textcolor{keywordtype}{char} \hyperlink{part__func_8h_a49962ad6242b8c628de6ca16bb831c1d}{bppm\_symbol}(\textcolor{keyword}{const} \textcolor{keywordtype}{float} *x); +00393 +00394 +00395 \textcolor{comment}{/*} +00396 \textcolor{comment}{#################################################} +00397 \textcolor{comment}{# DEPRECATED FUNCTIONS #} +00398 \textcolor{comment}{#################################################} +00399 \textcolor{comment}{*/} +00400 +00406 DEPRECATED(\textcolor{keywordtype}{void} \hyperlink{part__func_8h_a15176e23eceeff8c7d14eabcfec8a2af}{init\_pf\_fold}(\textcolor{keywordtype}{int} length)); +00407 +00412 DEPRECATED(\textcolor{keywordtype}{char} *\hyperlink{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{centroid}(\textcolor{keywordtype}{int} length, +00413 \textcolor{keywordtype}{double} *dist)); \textcolor{comment}{/* mean pair distance of ensemble */} +00414 +00420 DEPRECATED(\textcolor{keywordtype}{double} \hyperlink{part__func_8h_ae9556ba7ded44fe2321b6f67c3fc02a3}{mean\_bp\_dist}(\textcolor{keywordtype}{int} length)); +00421 +00425 DEPRECATED(\textcolor{keywordtype}{double} \hyperlink{part__func_8h_a68ba6f3a48e08ca131ab54621ce3a2d7}{expLoopEnergy}(\textcolor{keywordtype}{int} u1, +00426 \textcolor{keywordtype}{int} u2, +00427 \textcolor{keywordtype}{int} type, +00428 \textcolor{keywordtype}{int} type2, +00429 \textcolor{keywordtype}{short} si1, +00430 \textcolor{keywordtype}{short} sj1, +00431 \textcolor{keywordtype}{short} sp1, +00432 \textcolor{keywordtype}{short} sq1)); +00433 +00437 DEPRECATED(\textcolor{keywordtype}{double} \hyperlink{part__func_8h_a7b6ab474cc80accc48010ccfcc59f96b}{expHairpinEnergy}( \textcolor{keywordtype}{int} u, +00438 \textcolor{keywordtype}{int} type, +00439 \textcolor{keywordtype}{short} si1, +00440 \textcolor{keywordtype}{short} sj1, +00441 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string})); +00442 +00443 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/part__func__co_8h.tex b/binaries/src/ViennaRNA/doc/latex/part__func__co_8h.tex new file mode 100644 index 0000000..9eb9d92 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/part__func__co_8h.tex @@ -0,0 +1,81 @@ +\hypertarget{part__func__co_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func\-\_\-co.h File Reference} +\label{part__func__co_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func\-\_\-co.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func\-\_\-co.\-h}} +} + + +Partition function for two R\-N\-A sequences. + + +Include dependency graph for part\-\_\-func\-\_\-co.\-h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{part__func__co_8h__incl} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +\hyperlink{structcofoldF}{cofold\-F} \hyperlink{group__pf__cofold_gaa86a5f998789ed71813d23d7307a791b}{co\-\_\-pf\-\_\-fold} (char $\ast$sequence, char $\ast$structure) +\begin{DoxyCompactList}\small\item\em Calculate partition function and base pair probabilities. \end{DoxyCompactList}\item +\hyperlink{structcofoldF}{cofold\-F} \hyperlink{group__pf__cofold_gabd873b450832ab5f21101fc5ab354d21}{co\-\_\-pf\-\_\-fold\-\_\-par} (char $\ast$sequence, char $\ast$structure, \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters, int calculate\-\_\-bppm, int is\-\_\-constrained) +\begin{DoxyCompactList}\small\item\em Calculate partition function and base pair probabilities. \end{DoxyCompactList}\item +double $\ast$ \hyperlink{group__pf__cofold_ga11f0252c1d2c4697253ff4b5bd392d3c}{export\-\_\-co\-\_\-bppm} (void) +\begin{DoxyCompactList}\small\item\em Get a pointer to the base pair probability array. \end{DoxyCompactList}\item +\hypertarget{group__pf__cofold_gade3ce34ae8214811374b1d28a40dc247}{void \hyperlink{group__pf__cofold_gade3ce34ae8214811374b1d28a40dc247}{free\-\_\-co\-\_\-pf\-\_\-arrays} (void)}\label{group__pf__cofold_gade3ce34ae8214811374b1d28a40dc247} + +\begin{DoxyCompactList}\small\item\em Free the memory occupied by \hyperlink{group__pf__cofold_gaa86a5f998789ed71813d23d7307a791b}{co\-\_\-pf\-\_\-fold()} \end{DoxyCompactList}\item +void \hyperlink{group__pf__cofold_ga6e0f36c1f9b7d9dd4bfbad914c1119e5}{update\-\_\-co\-\_\-pf\-\_\-params} (int length) +\begin{DoxyCompactList}\small\item\em Recalculate energy parameters. \end{DoxyCompactList}\item +void \hyperlink{group__pf__cofold_ga117d880df45bef444d5e2785ffa40a53}{update\-\_\-co\-\_\-pf\-\_\-params\-\_\-par} (int length, \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters) +\begin{DoxyCompactList}\small\item\em Recalculate energy parameters. \end{DoxyCompactList}\item +void \hyperlink{group__pf__cofold_ga15ae04ac5ab84e876dcf0093120cb617}{compute\-\_\-probabilities} (double F\-A\-B, double F\-E\-A, double F\-E\-B, struct \hyperlink{structplist}{plist} $\ast$pr\-A\-B, struct \hyperlink{structplist}{plist} $\ast$pr\-A, struct \hyperlink{structplist}{plist} $\ast$pr\-B, int Alength) +\begin{DoxyCompactList}\small\item\em Compute Boltzmann probabilities of dimerization without homodimers. \end{DoxyCompactList}\item +\hyperlink{structConcEnt}{Conc\-Ent} $\ast$ \hyperlink{group__pf__cofold_ga5545cb936ac4ff93c7d699d46e72e8c7}{get\-\_\-concentrations} (double F\-E\-A\-B, double F\-E\-A\-A, double F\-E\-B\-B, double F\-E\-A, double F\-E\-B, double $\ast$startconc) +\begin{DoxyCompactList}\small\item\em Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers. \end{DoxyCompactList}\item +\hyperlink{structplist}{plist} $\ast$ \hyperlink{part__func__co_8h_a334de3c96e2186abfbdc0eaea6d08b14}{get\-\_\-plist} (struct \hyperlink{structplist}{plist} $\ast$pl, int length, double cut\-\_\-off) +\item +void \hyperlink{part__func__co_8h_aa12dda9dd6179cdd22bcce87c0682c07}{init\-\_\-co\-\_\-pf\-\_\-fold} (int length) +\end{DoxyCompactItemize} +\subsection*{Variables} +\begin{DoxyCompactItemize} +\item +\hypertarget{group__pf__cofold_gaff27888c4088cc1f60fd59cbd589474c}{int \hyperlink{group__pf__cofold_gaff27888c4088cc1f60fd59cbd589474c}{mirnatog}}\label{group__pf__cofold_gaff27888c4088cc1f60fd59cbd589474c} + +\begin{DoxyCompactList}\small\item\em Toggles no intrabp in 2nd mol. \end{DoxyCompactList}\item +\hypertarget{group__pf__cofold_gac2d1851a710a8561390861155ca988fe}{double \hyperlink{group__pf__cofold_gac2d1851a710a8561390861155ca988fe}{F\-\_\-monomer} \mbox{[}2\mbox{]}}\label{group__pf__cofold_gac2d1851a710a8561390861155ca988fe} + +\begin{DoxyCompactList}\small\item\em Free energies of the two monomers. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Partition function for two R\-N\-A sequences. As for folding one R\-N\-A molecule, this computes the partition function of all possible structures and the base pair probabilities. Uses the same global \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\-\_\-scale} variable to avoid overflows. + +To simplify the implementation the partition function computation is done internally in a null model that does not include the duplex initiation energy, i.\-e. the entropic penalty for producing a dimer from two monomers). The resulting free energies and pair probabilities are initially relative to that null model. In a second step the free energies can be corrected to include the dimerization penalty, and the pair probabilities can be divided into the conditional pair probabilities given that a re dimer is formed or not formed. + +After computing the partition functions of all possible dimeres one can compute the probabilities of base pairs, the concentrations out of start concentrations and sofar and soaway. + +Dimer formation is inherently concentration dependent. Given the free energies of the monomers A and B and dimers A\-B, A\-A, and B\-B one can compute the equilibrium concentrations, given input concentrations of A and B, see e.\-g. Dimitrov \& Zuker (2004) + +\subsection{Function Documentation} +\hypertarget{part__func__co_8h_a334de3c96e2186abfbdc0eaea6d08b14}{\index{part\-\_\-func\-\_\-co.\-h@{part\-\_\-func\-\_\-co.\-h}!get\-\_\-plist@{get\-\_\-plist}} +\index{get\-\_\-plist@{get\-\_\-plist}!part_func_co.h@{part\-\_\-func\-\_\-co.\-h}} +\subsubsection[{get\-\_\-plist}]{\setlength{\rightskip}{0pt plus 5cm}{\bf plist}$\ast$ get\-\_\-plist ( +\begin{DoxyParamCaption} +\item[{struct {\bf plist} $\ast$}]{pl, } +\item[{int}]{length, } +\item[{double}]{cut\-\_\-off} +\end{DoxyParamCaption} +)}}\label{part__func__co_8h_a334de3c96e2186abfbdc0eaea6d08b14} +D\-O N\-O\-T U\-S\-E T\-H\-I\-S F\-U\-N\-C\-T\-I\-O\-N A\-N\-Y\-M\-O\-R\-E \begin{DoxyRefDesc}{Deprecated} +\item[\hyperlink{deprecated__deprecated000016}{Deprecated}]\{ This function is deprecated and will be removed soon!\} use \hyperlink{group__pf__fold_ga03e15e831a31b1154855ab47edbdb019}{assign\-\_\-plist\-\_\-from\-\_\-pr()} instead! \end{DoxyRefDesc} +\hypertarget{part__func__co_8h_aa12dda9dd6179cdd22bcce87c0682c07}{\index{part\-\_\-func\-\_\-co.\-h@{part\-\_\-func\-\_\-co.\-h}!init\-\_\-co\-\_\-pf\-\_\-fold@{init\-\_\-co\-\_\-pf\-\_\-fold}} +\index{init\-\_\-co\-\_\-pf\-\_\-fold@{init\-\_\-co\-\_\-pf\-\_\-fold}!part_func_co.h@{part\-\_\-func\-\_\-co.\-h}} +\subsubsection[{init\-\_\-co\-\_\-pf\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}void init\-\_\-co\-\_\-pf\-\_\-fold ( +\begin{DoxyParamCaption} +\item[{int}]{length} +\end{DoxyParamCaption} +)}}\label{part__func__co_8h_aa12dda9dd6179cdd22bcce87c0682c07} +D\-O N\-O\-T U\-S\-E T\-H\-I\-S F\-U\-N\-C\-T\-I\-O\-N A\-N\-Y\-M\-O\-R\-E \begin{DoxyRefDesc}{Deprecated} +\item[\hyperlink{deprecated__deprecated000017}{Deprecated}]\{ This function is deprecated and will be removed soon!\} \end{DoxyRefDesc} diff --git a/binaries/src/ViennaRNA/doc/latex/part__func__co_8h__incl.md5 b/binaries/src/ViennaRNA/doc/latex/part__func__co_8h__incl.md5 new file mode 100644 index 0000000..30b9bbe --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/part__func__co_8h__incl.md5 @@ -0,0 +1 @@ +52b80c13a02d5fbe583c38e745d45d07 \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/part__func__co_8h__incl.pdf b/binaries/src/ViennaRNA/doc/latex/part__func__co_8h__incl.pdf new file mode 100644 index 0000000000000000000000000000000000000000..3e36f6f2a39f936e7796d25080c95a9f12fa414c GIT binary patch literal 7745 zcmb7p1z3}7*uS8Hl!$~hLqh2dHb$o)NJ*DSjKRpkHjofRkPZPADMbkp>5}g5kZu7< zL0UrKzoDMvIp@2s|M$J`*t_TV+|T>m`CMGTo8#^+MLrNegqWjvE$4_>2mk~iEo_M; 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+00056 +00060 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} \hyperlink{group__pf__cofold_gac2d1851a710a8561390861155ca988fe}{F\_monomer}[2]; +00061 +00080 \hyperlink{structcofoldF}{cofoldF} \hyperlink{group__pf__cofold_gaa86a5f998789ed71813d23d7307a791b}{co\_pf\_fold}( \textcolor{keywordtype}{char} *sequence, +00081 \textcolor{keywordtype}{char} *structure); +00082 +00100 \hyperlink{structcofoldF}{cofoldF} \hyperlink{group__pf__cofold_gabd873b450832ab5f21101fc5ab354d21}{co\_pf\_fold\_par}( \textcolor{keywordtype}{char} *sequence, +00101 \textcolor{keywordtype}{char} *structure, +00102 \hyperlink{structpf__paramT}{pf\_paramT} *parameters, +00103 \textcolor{keywordtype}{int} calculate\_bppm, +00104 \textcolor{keywordtype}{int} is\_constrained); +00105 +00115 FLT\_OR\_DBL *\hyperlink{group__pf__cofold_ga11f0252c1d2c4697253ff4b5bd392d3c}{export\_co\_bppm}(\textcolor{keywordtype}{void}); +00116 +00120 \textcolor{keywordtype}{void} \hyperlink{group__pf__cofold_gade3ce34ae8214811374b1d28a40dc247}{free\_co\_pf\_arrays}(\textcolor{keywordtype}{void}); +00121 +00136 \textcolor{keywordtype}{void} \hyperlink{group__pf__cofold_ga6e0f36c1f9b7d9dd4bfbad914c1119e5}{update\_co\_pf\_params}(\textcolor{keywordtype}{int} length); +00137 +00157 \textcolor{keywordtype}{void} \hyperlink{group__pf__cofold_ga117d880df45bef444d5e2785ffa40a53}{update\_co\_pf\_params\_par}(\textcolor{keywordtype}{int} length, +00158 \hyperlink{structpf__paramT}{pf\_paramT} *parameters); +00159 +00177 \textcolor{keywordtype}{void} \hyperlink{group__pf__cofold_ga15ae04ac5ab84e876dcf0093120cb617}{compute\_probabilities}(\textcolor{keywordtype}{double} FAB, +00178 \textcolor{keywordtype}{double} FEA, +00179 \textcolor{keywordtype}{double} FEB, +00180 \textcolor{keyword}{struct} \hyperlink{structplist}{plist} *prAB, +00181 \textcolor{keyword}{struct} \hyperlink{structplist}{plist} *prA, +00182 \textcolor{keyword}{struct} \hyperlink{structplist}{plist} *prB, +00183 \textcolor{keywordtype}{int} Alength); +00184 +00203 \hyperlink{structConcEnt}{ConcEnt} *\hyperlink{group__pf__cofold_ga5545cb936ac4ff93c7d699d46e72e8c7}{get\_concentrations}(\textcolor{keywordtype}{double} FEAB, +00204 \textcolor{keywordtype}{double} FEAA, +00205 \textcolor{keywordtype}{double} FEBB, +00206 \textcolor{keywordtype}{double} FEA, +00207 \textcolor{keywordtype}{double} FEB, +00208 \textcolor{keywordtype}{double} *startconc); +00209 +00210 +00215 \textcolor{comment}{/*} +00216 \textcolor{comment}{#################################################} +00217 \textcolor{comment}{# DEPRECATED FUNCTIONS #} +00218 \textcolor{comment}{#################################################} +00219 \textcolor{comment}{*/} +00220 +00226 DEPRECATED(\hyperlink{structplist}{plist} *\hyperlink{part__func__co_8h_a334de3c96e2186abfbdc0eaea6d08b14}{get\_plist}( \textcolor{keyword}{struct} \hyperlink{structplist}{plist} *pl, +00227 \textcolor{keywordtype}{int} length, +00228 \textcolor{keywordtype}{double} cut\_off)); +00233 DEPRECATED(\textcolor{keywordtype}{void} \hyperlink{part__func__co_8h_aa12dda9dd6179cdd22bcce87c0682c07}{init\_co\_pf\_fold}(\textcolor{keywordtype}{int} length)); +00234 +00235 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/part__func__up_8h.tex b/binaries/src/ViennaRNA/doc/latex/part__func__up_8h.tex new file mode 100644 index 0000000..bedb3ae --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/part__func__up_8h.tex @@ -0,0 +1,33 @@ +\hypertarget{part__func__up_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func\-\_\-up.h File Reference} +\label{part__func__up_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func\-\_\-up.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func\-\_\-up.\-h}} +} + + +Partition Function Cofolding as stepwise process. + + +Include dependency graph for part\-\_\-func\-\_\-up.\-h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{part__func__up_8h__incl} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +\hyperlink{structpu__contrib}{pu\-\_\-contrib} $\ast$ \hyperlink{group__up__cofold_ga5b4ee40e190d2f633cd01cf0d2fe93cf}{pf\-\_\-unstru} (char $\ast$sequence, int max\-\_\-w) +\begin{DoxyCompactList}\small\item\em Calculate the partition function over all unpaired regions of a maximal length. \end{DoxyCompactList}\item +\hyperlink{structinteract}{interact} $\ast$ \hyperlink{group__up__cofold_ga1aa0aa02bc3a724f87360c03097afd00}{pf\-\_\-interact} (const char $\ast$s1, const char $\ast$s2, \hyperlink{structpu__contrib}{pu\-\_\-contrib} $\ast$p\-\_\-c, \hyperlink{structpu__contrib}{pu\-\_\-contrib} $\ast$p\-\_\-c2, int max\-\_\-w, char $\ast$cstruc, int incr3, int incr5) +\begin{DoxyCompactList}\small\item\em Calculates the probability of a local interaction between two sequences. \end{DoxyCompactList}\item +\hypertarget{group__up__cofold_gadde308fd5f696dc271b1532aa96fd12f}{void \hyperlink{group__up__cofold_gadde308fd5f696dc271b1532aa96fd12f}{free\-\_\-interact} (\hyperlink{structinteract}{interact} $\ast$pin)}\label{group__up__cofold_gadde308fd5f696dc271b1532aa96fd12f} + +\begin{DoxyCompactList}\small\item\em Frees the output of function \hyperlink{group__up__cofold_ga1aa0aa02bc3a724f87360c03097afd00}{pf\-\_\-interact()}. \end{DoxyCompactList}\item +\hypertarget{group__up__cofold_gac20bd61824981d45ce0dc9934aa56df8}{void \hyperlink{group__up__cofold_gac20bd61824981d45ce0dc9934aa56df8}{free\-\_\-pu\-\_\-contrib\-\_\-struct} (\hyperlink{structpu__contrib}{pu\-\_\-contrib} $\ast$pu)}\label{group__up__cofold_gac20bd61824981d45ce0dc9934aa56df8} + +\begin{DoxyCompactList}\small\item\em Frees the output of function \hyperlink{group__up__cofold_ga5b4ee40e190d2f633cd01cf0d2fe93cf}{pf\-\_\-unstru()}. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Partition Function Cofolding as stepwise process. In this approach to cofolding the interaction between two R\-N\-A molecules is seen as a stepwise process. In a first step, the target molecule has to adopt a structure in which a binding site is accessible. In a second step, the ligand molecule will hybridize with a region accessible to an interaction. Consequently the algorithm is designed as a two step process\-: The first step is the calculation of the probability that a region within the target is unpaired, or equivalently, the calculation of the free energy needed to expose a region. 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+\hypertarget{plot__layouts_8h}{\section{plot\-\_\-layouts.\-h} +\label{plot__layouts_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/plot\-\_\-layouts.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/plot\-\_\-layouts.\-h}} +} + +\begin{DoxyCode} +00001 +00009 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_PLOT\_LAYOUTS\_H\_\_} +00010 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_PLOT\_LAYOUTS\_H\_\_} +00011 \textcolor{preprocessor}{} +00012 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"} +00013 \textcolor{preprocessor}{#include "\hyperlink{naview_8h}{naview.h}"} +00014 +00015 \textcolor{preprocessor}{#ifndef PI} +00016 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define PI 3.141592654} +00017 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif} +00018 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define PIHALF PI/2.} +00019 \textcolor{preprocessor}{} +00020 +\hypertarget{plot__layouts_8h_source_l00029}{}\hyperlink{plot__layouts_8h_ae6d17b9f0a53cf5205a9181e0f8422e9}{00029} \textcolor{preprocessor}{#define VRNA\_PLOT\_TYPE\_SIMPLE 0} +00030 \textcolor{preprocessor}{} +\hypertarget{plot__layouts_8h_source_l00039}{}\hyperlink{plot__layouts_8h_a94d4c863ecac2f220f76658afb92f964}{00039} \textcolor{preprocessor}{#define VRNA\_PLOT\_TYPE\_NAVIEW 1} +00040 \textcolor{preprocessor}{} +\hypertarget{plot__layouts_8h_source_l00049}{}\hyperlink{plot__layouts_8h_a8c9eac631348da92136c8363ecdd9fb9}{00049} \textcolor{preprocessor}{#define VRNA\_PLOT\_TYPE\_CIRCULAR 2} +00050 \textcolor{preprocessor}{} +00051 +00064 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{plot__layouts_8h_a5964c4581431b098b80027d6e14dcdd4}{rna\_plot\_type}; +00065 +00077 \textcolor{keywordtype}{int} \hyperlink{plot__layouts_8h_af4b9173e7d3fd361c3c85e6def194123}{simple\_xy\_coordinates}(\textcolor{keywordtype}{short} *pair\_table, +00078 \textcolor{keywordtype}{float} *X, +00079 \textcolor{keywordtype}{float} *Y); +00080 +00101 \textcolor{keywordtype}{int} \hyperlink{plot__layouts_8h_ac4ea13d35308f09940178d2b05a248c2}{simple\_circplot\_coordinates}(\textcolor{keywordtype}{short} *pair\_table, +00102 \textcolor{keywordtype}{float} *x, +00103 \textcolor{keywordtype}{float} *y); +00104 +00105 +00106 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/profiledist_8h.tex b/binaries/src/ViennaRNA/doc/latex/profiledist_8h.tex new file mode 100644 index 0000000..d5e377b --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/profiledist_8h.tex @@ -0,0 +1,92 @@ +\hypertarget{profiledist_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/profiledist.h File Reference} +\label{profiledist_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/profiledist.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/profiledist.\-h}} +} +Include dependency graph for profiledist.\-h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{profiledist_8h__incl} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +float \hyperlink{profiledist_8h_abe75e90e00a1e5dd8862944ed53dad5d}{profile\-\_\-edit\-\_\-distance} (const float $\ast$T1, const float $\ast$T2) +\begin{DoxyCompactList}\small\item\em Align the 2 probability profiles T1, T2\par +. \end{DoxyCompactList}\item +float $\ast$ \hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\-\_\-bp\-\_\-profile\-\_\-bppm} (double $\ast$bppm, int length) +\begin{DoxyCompactList}\small\item\em condense pair probability matrix into a vector containing probabilities for unpaired, upstream paired and downstream paired. \end{DoxyCompactList}\item +\hypertarget{profiledist_8h_a8e0b4fe3698b3502945116ecc0ba6160}{void \hyperlink{profiledist_8h_a8e0b4fe3698b3502945116ecc0ba6160}{print\-\_\-bppm} (const float $\ast$T)}\label{profiledist_8h_a8e0b4fe3698b3502945116ecc0ba6160} + +\begin{DoxyCompactList}\small\item\em print string representation of probability profile \end{DoxyCompactList}\item +void \hyperlink{profiledist_8h_a9b0b84a5a45761bf42d7c835dcdb3b85}{free\-\_\-profile} (float $\ast$T) +\begin{DoxyCompactList}\small\item\em free space allocated in Make\-\_\-bp\-\_\-profile \end{DoxyCompactList}\item +float $\ast$ \hyperlink{profiledist_8h_a904c7eaf4a2413567c00ac4891749d18}{Make\-\_\-bp\-\_\-profile} (int length) +\end{DoxyCompactItemize} + + +\subsection{Function Documentation} +\hypertarget{profiledist_8h_abe75e90e00a1e5dd8862944ed53dad5d}{\index{profiledist.\-h@{profiledist.\-h}!profile\-\_\-edit\-\_\-distance@{profile\-\_\-edit\-\_\-distance}} +\index{profile\-\_\-edit\-\_\-distance@{profile\-\_\-edit\-\_\-distance}!profiledist.h@{profiledist.\-h}} +\subsubsection[{profile\-\_\-edit\-\_\-distance}]{\setlength{\rightskip}{0pt plus 5cm}float profile\-\_\-edit\-\_\-distance ( +\begin{DoxyParamCaption} +\item[{const float $\ast$}]{T1, } +\item[{const float $\ast$}]{T2} +\end{DoxyParamCaption} +)}}\label{profiledist_8h_abe75e90e00a1e5dd8862944ed53dad5d} + + +Align the 2 probability profiles T1, T2\par +. + +This is like a Needleman-\/\-Wunsch alignment, we should really use affine gap-\/costs ala Gotoh \hypertarget{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{\index{profiledist.\-h@{profiledist.\-h}!Make\-\_\-bp\-\_\-profile\-\_\-bppm@{Make\-\_\-bp\-\_\-profile\-\_\-bppm}} +\index{Make\-\_\-bp\-\_\-profile\-\_\-bppm@{Make\-\_\-bp\-\_\-profile\-\_\-bppm}!profiledist.h@{profiledist.\-h}} +\subsubsection[{Make\-\_\-bp\-\_\-profile\-\_\-bppm}]{\setlength{\rightskip}{0pt plus 5cm}float$\ast$ Make\-\_\-bp\-\_\-profile\-\_\-bppm ( +\begin{DoxyParamCaption} +\item[{double $\ast$}]{bppm, } +\item[{int}]{length} +\end{DoxyParamCaption} +)}}\label{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc} + + +condense pair probability matrix into a vector containing probabilities for unpaired, upstream paired and downstream paired. + +This resulting probability profile is used as input for profile\-\_\-edit\-\_\-distance + + +\begin{DoxyParams}{Parameters} +{\em bppm} & A pointer to the base pair probability matrix \\ +\hline +{\em length} & The length of the sequence \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The bp profile +\end{DoxyReturn} +\hypertarget{profiledist_8h_a9b0b84a5a45761bf42d7c835dcdb3b85}{\index{profiledist.\-h@{profiledist.\-h}!free\-\_\-profile@{free\-\_\-profile}} +\index{free\-\_\-profile@{free\-\_\-profile}!profiledist.h@{profiledist.\-h}} +\subsubsection[{free\-\_\-profile}]{\setlength{\rightskip}{0pt plus 5cm}void free\-\_\-profile ( +\begin{DoxyParamCaption} +\item[{float $\ast$}]{T} +\end{DoxyParamCaption} +)}}\label{profiledist_8h_a9b0b84a5a45761bf42d7c835dcdb3b85} + + +free space allocated in Make\-\_\-bp\-\_\-profile + +Backward compatibility only. You can just use plain free() \hypertarget{profiledist_8h_a904c7eaf4a2413567c00ac4891749d18}{\index{profiledist.\-h@{profiledist.\-h}!Make\-\_\-bp\-\_\-profile@{Make\-\_\-bp\-\_\-profile}} +\index{Make\-\_\-bp\-\_\-profile@{Make\-\_\-bp\-\_\-profile}!profiledist.h@{profiledist.\-h}} +\subsubsection[{Make\-\_\-bp\-\_\-profile}]{\setlength{\rightskip}{0pt plus 5cm}float$\ast$ Make\-\_\-bp\-\_\-profile ( +\begin{DoxyParamCaption} +\item[{int}]{length} +\end{DoxyParamCaption} +)}}\label{profiledist_8h_a904c7eaf4a2413567c00ac4891749d18} +\begin{DoxyNote}{Note} +This function is N\-O\-T threadsafe +\end{DoxyNote} +\begin{DoxySeeAlso}{See Also} +\hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\-\_\-bp\-\_\-profile\-\_\-bppm()} +\end{DoxySeeAlso} +\begin{DoxyRefDesc}{Deprecated} +\item[\hyperlink{deprecated__deprecated000018}{Deprecated}]This function is deprecated and will be removed soon! See \hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\-\_\-bp\-\_\-profile\-\_\-bppm()} for a replacement\end{DoxyRefDesc} diff --git a/binaries/src/ViennaRNA/doc/latex/profiledist_8h__incl.md5 b/binaries/src/ViennaRNA/doc/latex/profiledist_8h__incl.md5 new file mode 100644 index 0000000..242b422 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/profiledist_8h__incl.md5 @@ -0,0 +1 @@ +c8ba9c258244933692a24638752e9345 \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/profiledist_8h__incl.pdf b/binaries/src/ViennaRNA/doc/latex/profiledist_8h__incl.pdf new file mode 100644 index 0000000000000000000000000000000000000000..85eb5fa22a92ef18d06ab368655cf6ca3bacc4a0 GIT binary patch literal 10110 zcmd6Nc|4Tg+dnDUW#1WVWScR}*vY;{mdI|Hu``UZhfrkSimXK`JB937v&#}?-zu_4 zQV7os=~Lf6-{13k{`<`^Gv_+jIrp`kbME*3K8O3Nl8PWmNQ{WPa;;>a2n+xMkk*bw z($WB7ErhEb+8!W^5$O>D003bX2WK<_h52@dp%F?58zdY-Br8kgfkq)V#RfA- zDiBFvzvWynnX1!_LVO^|Q6j?(y z=9UYhHeDSOZ 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+\label{profiledist_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/profiledist.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/profiledist.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_PROFILEDIST\_H\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_PROFILEDIST\_H\_\_} +00003 \textcolor{preprocessor}{} +00004 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_} +00005 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func \_\_attribute\_\_ ((deprecated))} +00006 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else} +00007 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func} +00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif} +00009 \textcolor{preprocessor}{} +00010 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"} +00011 +00020 \textcolor{keywordtype}{float} \hyperlink{profiledist_8h_abe75e90e00a1e5dd8862944ed53dad5d}{profile\_edit\_distance}(\textcolor{keyword}{const} \textcolor{keywordtype}{float} *T1, +00021 \textcolor{keyword}{const} \textcolor{keywordtype}{float} *T2); +00022 +00033 \textcolor{keywordtype}{float} *\hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\_bp\_profile\_bppm}(FLT\_OR\_DBL *bppm, +00034 \textcolor{keywordtype}{int} length); +00035 +00039 \textcolor{keywordtype}{void} \hyperlink{profiledist_8h_a8e0b4fe3698b3502945116ecc0ba6160}{print\_bppm}(\textcolor{keyword}{const} \textcolor{keywordtype}{float} *T); +00040 +00046 \textcolor{keywordtype}{void} \hyperlink{profiledist_8h_a9b0b84a5a45761bf42d7c835dcdb3b85}{free\_profile}(\textcolor{keywordtype}{float} *T); +00047 +00056 DEPRECATED(\textcolor{keywordtype}{float} *\hyperlink{profiledist_8h_a904c7eaf4a2413567c00ac4891749d18}{Make\_bp\_profile}(\textcolor{keywordtype}{int} length)); +00057 +00058 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/read__epars_8h.tex b/binaries/src/ViennaRNA/doc/latex/read__epars_8h.tex new file mode 100644 index 0000000..2f6287b --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/read__epars_8h.tex @@ -0,0 +1,10 @@ +\hypertarget{read__epars_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/read\-\_\-epars.h File Reference} +\label{read__epars_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/read\-\_\-epars.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/read\-\_\-epars.\-h}} +} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +void \hyperlink{group__energy__parameters__rw_ga165a142a3c68fb6655c69ef4ab7cd749}{read\-\_\-parameter\-\_\-file} (const char fname\mbox{[}$\,$\mbox{]}) +\begin{DoxyCompactList}\small\item\em Read energy parameters from a file. \end{DoxyCompactList}\item +void \hyperlink{group__energy__parameters__rw_ga8a43459be386a7489feeab68dc2c6c76}{write\-\_\-parameter\-\_\-file} (const char fname\mbox{[}$\,$\mbox{]}) +\begin{DoxyCompactList}\small\item\em Write energy parameters to a file. \end{DoxyCompactList}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/read__epars_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/read__epars_8h_source.tex new file mode 100644 index 0000000..bc4cb7a --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/read__epars_8h_source.tex @@ -0,0 +1,25 @@ +\hypertarget{read__epars_8h}{\section{read\-\_\-epars.\-h} +\label{read__epars_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/read\-\_\-epars.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/read\-\_\-epars.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_READ\_EPARS\_H\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_READ\_EPARS\_H\_\_} +00003 \textcolor{preprocessor}{} +00020 \textcolor{keyword}{enum} parset \{ +00021 UNKNOWN= -1, QUIT, +00022 S, S\_H, HP, HP\_H, B, B\_H, IL, IL\_H, MMH, MMH\_H, MMI, MMI\_H, +00023 MMI1N, MMI1N\_H, MMI23, MMI23\_H, MMM, MMM\_H, MME, MME\_H, D5, D5\_H, D3, D3\_H, +00024 INT11, INT11\_H, INT21, INT21\_H, INT22, INT22\_H, ML, TL, +00025 TRI, HEX, NIN, MISC\}; +00026 +00032 \textcolor{keywordtype}{void} 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@@ -0,0 +1,86 @@ +\begin{thebibliography}{10} + +\bibitem{bernhart:2008} +S.H. Bernhart, I.L. Hofacker, S.~Will, A.R. Gruber, and P.F. Stadler. +\newblock {RNAalifold}: Improved consensus structure prediction for {RNA} + alignments. +\newblock {\em BMC bioinformatics}, 9(1):474, 2008. + +\bibitem{bernhart:2006} +S.H. Bernhart, H.~Tafer, U.~M{\"u}ckstein, C.~Flamm, P.F. Stadler, and I.L. + Hofacker. +\newblock Partition function and base pairing probabilities of {RNA} + heterodimers. +\newblock {\em Algorithms for Molecular Biology}, 1(1):3, 2006. + +\bibitem{fontana:1993b} +W.~Fontana, P.F. Stadler, E.G. Bornberg-Bauer, T.~Griesmacher, I.L. Hofacker, + M.~Tacker, P.~Tarazona, E.D. Weinberger, and P.~Schuster. +\newblock {RNA} folding and combinatory landscapes. +\newblock {\em Physical review E}, 47(3):2083, 1993. + +\bibitem{hofacker:2002} +I.L. Hofacker, M.~Fekete, and P.F. Stadler. +\newblock Secondary structure prediction for aligned {RNA} sequences. +\newblock {\em Journal of molecular biology}, 319(5):1059--1066, 2002. + +\bibitem{hofacker:1994} +I.L. Hofacker, W.~Fontana, P.F. Stadler, L.S. Bonhoeffer, M.~Tacker, and + P.~Schuster. +\newblock Fast folding and comparison of {RNA} secondary structures. +\newblock {\em Monatshefte f{\"u}r Chemie/Chemical Monthly}, 125(2):167--188, + 1994. + +\bibitem{hofacker:2006} +I.L. Hofacker and P.F. Stadler. +\newblock Memory efficient folding algorithms for circular {RNA} secondary + structures. +\newblock {\em Bioinformatics}, 22(10):1172--1176, 2006. + +\bibitem{lorenz:2011} +Ronny Lorenz, Stephan~H. Bernhart, Christian H{\"o}ner~zu Siederdissen, Hakim + Tafer, Christoph Flamm, Peter~F. Stadler, and Ivo~L. Hofacker. +\newblock {ViennaRNA} package 2.0. +\newblock {\em Algorithms for Molecular Biology}, 6(1):26, 2011. + +\bibitem{lorenz:2009} +Ronny Lorenz, Christoph Flamm, and Ivo~L. Hofacker. +\newblock 2d projections of {RNA} folding landscapes. +\newblock In Ivo Grosse, Steffen Neumann, Stefan Posch, Falk Schreiber, and + Peter~F. Stadler, editors, {\em German Conference on Bioinformatics 2009}, + volume 157 of {\em Lecture Notes in Informatics}, pages 11--20, Bonn, + September 2009. Gesellschaft f.\ Informatik. + +\bibitem{mathews:2004} +D.H. Mathews, M.D. Disney, J.L. Childs, S.J. Schroeder, M.~Zuker, and D.H. + Turner. +\newblock Incorporating chemical modification constraints into a dynamic + programming algorithm for prediction of {RNA} secondary structure. +\newblock {\em Proceedings of the National Academy of Sciences of the United + States of America}, 101(19):7287, 2004. + +\bibitem{mccaskill:1990} +J.S. McCaskill. +\newblock The equilibrium partition function and base pair binding + probabilities for {RNA} secondary structure. +\newblock {\em Biopolymers}, 29(6-7):1105--1119, 1990. + +\bibitem{shapiro:1988} +B.A. Shapiro. +\newblock An algorithm for comparing multiple {RNA} secondary structures. +\newblock {\em Computer applications in the biosciences: CABIOS}, + 4(3):387--393, 1988. + +\bibitem{turner:2010} +D.H. Turner and D.H. Mathews. +\newblock {NNDB}: The nearest neighbor parameter database for predicting + stability of nucleic acid secondary structure. +\newblock {\em Nucleic Acids Research}, 38(suppl 1):D280--D282, 2010. + +\bibitem{zuker:1981} +M.~Zuker and P.~Stiegler. +\newblock Optimal computer folding of large {RNA} sequences using + thermodynamics and auxiliary information. +\newblock {\em Nucleic acids research}, 9(1):133--148, 1981. + +\end{thebibliography} diff --git a/binaries/src/ViennaRNA/doc/latex/refman.blg b/binaries/src/ViennaRNA/doc/latex/refman.blg new file mode 100644 index 0000000..a081bf0 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/refman.blg @@ -0,0 +1,78 @@ +This is BibTeX, Version 0.99d (TeX Live 2012/Debian) +Capacity: max_strings=35307, hash_size=35307, hash_prime=30011 +The top-level auxiliary file: refman.aux +A level-1 auxiliary file: group__mfe__fold.aux +A level-1 auxiliary file: group__pf__fold.aux +A level-1 auxiliary file: group__mea__fold.aux +A level-1 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Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{29} +\indexentry{Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}!export\discretionary {-}{}{}\_\discretionary {-}{}{}bppm@{export\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}|hyperpage}{29} +\indexentry{export\discretionary {-}{}{}\_\discretionary {-}{}{}bppm@{export\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}!Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{29} +\indexentry{Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}!assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}pr@{assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary 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{-}{}{}arrays@{get\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}!Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{30} +\indexentry{Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}!mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance@{mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance}|hyperpage}{30} +\indexentry{mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance@{mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance}!Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{30} +\indexentry{Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}!mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance\discretionary {-}{}{}\_\discretionary {-}{}{}pr@{mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance\discretionary {-}{}{}\_\discretionary {-}{}{}pr}|hyperpage}{31} +\indexentry{mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance\discretionary {-}{}{}\_\discretionary {-}{}{}pr@{mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance\discretionary {-}{}{}\_\discretionary {-}{}{}pr}!Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{31} +\indexentry{Compute the structure with maximum expected accuracy (\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}A)@{Compute the structure with maximum expected accuracy (\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}A)}|hyperpage}{32} +\indexentry{Compute the centroid structure@{Compute the centroid structure}|hyperpage}{33} +\indexentry{Compute the centroid structure@{Compute the centroid structure}!get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pl@{get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pl}|hyperpage}{33} +\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pl@{get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pl}!Compute the centroid structure@{Compute the centroid structure}|hyperpage}{33} +\indexentry{Compute the centroid structure@{Compute the centroid structure}!get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pr@{get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pr}|hyperpage}{33} +\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pr@{get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pr}!Compute the centroid structure@{Compute the centroid structure}|hyperpage}{33} +\indexentry{Enumerating Suboptimal Structures@{Enumerating Suboptimal Structures}|hyperpage}{35} +\indexentry{Suboptimal structures according to Zuker et al. 1989@{Suboptimal structures according to Zuker et al. 1989}|hyperpage}{36} +\indexentry{Suboptimal structures according to Zuker et al. 1989@{Suboptimal structures according to Zuker et al. 1989}!zukersubopt@{zukersubopt}|hyperpage}{36} +\indexentry{zukersubopt@{zukersubopt}!Suboptimal structures according to Zuker et al. 1989@{Suboptimal structures according to Zuker et al. 1989}|hyperpage}{36} +\indexentry{Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E@{Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E}|hyperpage}{37} +\indexentry{Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E@{Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E}!subopt@{subopt}|hyperpage}{37} +\indexentry{subopt@{subopt}!Suboptimal structures within an energy band arround the MFE@{Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E}|hyperpage}{37} +\indexentry{Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E@{Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E}!subopt\discretionary {-}{}{}\_\discretionary {-}{}{}circ@{subopt\discretionary {-}{}{}\_\discretionary {-}{}{}circ}|hyperpage}{38} +\indexentry{subopt\discretionary {-}{}{}\_\discretionary {-}{}{}circ@{subopt\discretionary {-}{}{}\_\discretionary {-}{}{}circ}!Suboptimal structures within an energy band arround the MFE@{Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E}|hyperpage}{38} +\indexentry{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}|hyperpage}{39} +\indexentry{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}!pbacktrack@{pbacktrack}|hyperpage}{39} +\indexentry{pbacktrack@{pbacktrack}!Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}|hyperpage}{39} +\indexentry{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}!pbacktrack\discretionary {-}{}{}\_\discretionary {-}{}{}circ@{pbacktrack\discretionary {-}{}{}\_\discretionary {-}{}{}circ}|hyperpage}{40} +\indexentry{pbacktrack\discretionary {-}{}{}\_\discretionary {-}{}{}circ@{pbacktrack\discretionary {-}{}{}\_\discretionary {-}{}{}circ}!Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}|hyperpage}{40} +\indexentry{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}!st\discretionary {-}{}{}\_\discretionary {-}{}{}back@{st\discretionary {-}{}{}\_\discretionary {-}{}{}back}|hyperpage}{40} +\indexentry{st\discretionary {-}{}{}\_\discretionary {-}{}{}back@{st\discretionary {-}{}{}\_\discretionary {-}{}{}back}!Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}|hyperpage}{40} +\indexentry{Calculate Secondary Structures of two R\discretionary {-}{}{}N\discretionary {-}{}{}As upon Dimerization@{Calculate Secondary Structures of two R\discretionary {-}{}{}N\discretionary {-}{}{}As upon Dimerization}|hyperpage}{41} +\indexentry{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}|hyperpage}{42} +\indexentry{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}!cofold@{cofold}|hyperpage}{42} +\indexentry{cofold@{cofold}!MFE Structures of two hybridized Sequences@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}|hyperpage}{42} +\indexentry{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}!export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays\discretionary {-}{}{}\_\discretionary {-}{}{}gq@{export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays\discretionary {-}{}{}\_\discretionary {-}{}{}gq}|hyperpage}{43} +\indexentry{export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays\discretionary {-}{}{}\_\discretionary {-}{}{}gq@{export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays\discretionary {-}{}{}\_\discretionary {-}{}{}gq}!MFE Structures of two hybridized Sequences@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}|hyperpage}{43} +\indexentry{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}!export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays@{export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}|hyperpage}{43} +\indexentry{export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays@{export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}!MFE Structures of two hybridized Sequences@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}|hyperpage}{43} +\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{44} +\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}|hyperpage}{45} +\indexentry{co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{45} +\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par@{co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}|hyperpage}{45} +\indexentry{co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par@{co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{45} +\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!export\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}bppm@{export\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}|hyperpage}{46} +\indexentry{export\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}bppm@{export\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{46} +\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params@{update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params}|hyperpage}{46} +\indexentry{update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params@{update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{46} +\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}\_\discretionary {-}{}{}par@{update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}\_\discretionary {-}{}{}par}|hyperpage}{46} +\indexentry{update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}\_\discretionary {-}{}{}par@{update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}\_\discretionary {-}{}{}par}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{46} +\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!compute\discretionary {-}{}{}\_\discretionary {-}{}{}probabilities@{compute\discretionary {-}{}{}\_\discretionary {-}{}{}probabilities}|hyperpage}{47} +\indexentry{compute\discretionary {-}{}{}\_\discretionary {-}{}{}probabilities@{compute\discretionary {-}{}{}\_\discretionary {-}{}{}probabilities}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{47} +\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!get\discretionary {-}{}{}\_\discretionary {-}{}{}concentrations@{get\discretionary {-}{}{}\_\discretionary {-}{}{}concentrations}|hyperpage}{47} +\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}concentrations@{get\discretionary {-}{}{}\_\discretionary {-}{}{}concentrations}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{47} +\indexentry{Partition Function for two hybridized Sequences as a stepwise Process@{Partition Function for two hybridized Sequences as a stepwise Process}|hyperpage}{48} +\indexentry{Partition Function for two hybridized Sequences as a stepwise Process@{Partition Function for two hybridized Sequences as a stepwise Process}!pf\discretionary {-}{}{}\_\discretionary {-}{}{}unstru@{pf\discretionary {-}{}{}\_\discretionary {-}{}{}unstru}|hyperpage}{48} +\indexentry{pf\discretionary {-}{}{}\_\discretionary {-}{}{}unstru@{pf\discretionary {-}{}{}\_\discretionary {-}{}{}unstru}!Partition Function for two hybridized Sequences as a stepwise Process@{Partition Function for two hybridized Sequences as a stepwise Process}|hyperpage}{48} +\indexentry{Partition Function for two hybridized Sequences as a stepwise Process@{Partition Function for two hybridized Sequences as a stepwise Process}!pf\discretionary {-}{}{}\_\discretionary {-}{}{}interact@{pf\discretionary {-}{}{}\_\discretionary {-}{}{}interact}|hyperpage}{49} +\indexentry{pf\discretionary {-}{}{}\_\discretionary {-}{}{}interact@{pf\discretionary {-}{}{}\_\discretionary {-}{}{}interact}!Partition Function for two hybridized Sequences as a stepwise Process@{Partition Function for two hybridized Sequences as a stepwise Process}|hyperpage}{49} +\indexentry{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}|hyperpage}{50} +\indexentry{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!get\discretionary {-}{}{}\_\discretionary {-}{}{}mpi@{get\discretionary {-}{}{}\_\discretionary {-}{}{}mpi}|hyperpage}{51} +\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}mpi@{get\discretionary {-}{}{}\_\discretionary {-}{}{}mpi}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}|hyperpage}{51} +\indexentry{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}alistruct@{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}alistruct}|hyperpage}{51} +\indexentry{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}alistruct@{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}alistruct}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}|hyperpage}{51} +\indexentry{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!encode\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}sequence@{encode\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}sequence}|hyperpage}{51} +\indexentry{encode\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}sequence@{encode\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}sequence}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}|hyperpage}{51} +\indexentry{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!alloc\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays@{alloc\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}|hyperpage}{52} +\indexentry{alloc\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays@{alloc\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}|hyperpage}{52} +\indexentry{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!free\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays@{free\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}|hyperpage}{52} +\indexentry{free\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays@{free\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}|hyperpage}{52} +\indexentry{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!get\discretionary {-}{}{}\_\discretionary {-}{}{}alipf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays@{get\discretionary {-}{}{}\_\discretionary {-}{}{}alipf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}|hyperpage}{53} +\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}alipf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays@{get\discretionary {-}{}{}\_\discretionary {-}{}{}alipf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}|hyperpage}{53} +\indexentry{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!cv\discretionary {-}{}{}\_\discretionary {-}{}{}fact@{cv\discretionary {-}{}{}\_\discretionary {-}{}{}fact}|hyperpage}{53} +\indexentry{cv\discretionary {-}{}{}\_\discretionary {-}{}{}fact@{cv\discretionary {-}{}{}\_\discretionary {-}{}{}fact}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}|hyperpage}{53} +\indexentry{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!nc\discretionary {-}{}{}\_\discretionary {-}{}{}fact@{nc\discretionary {-}{}{}\_\discretionary {-}{}{}fact}|hyperpage}{53} +\indexentry{nc\discretionary {-}{}{}\_\discretionary {-}{}{}fact@{nc\discretionary {-}{}{}\_\discretionary {-}{}{}fact}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}|hyperpage}{53} +\indexentry{M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)}|hyperpage}{54} +\indexentry{M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)}!alifold@{alifold}|hyperpage}{54} +\indexentry{alifold@{alifold}!MFE Consensus Structures for Sequence Alignment(s)@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)}|hyperpage}{54} +\indexentry{M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)}!circalifold@{circalifold}|hyperpage}{54} +\indexentry{circalifold@{circalifold}!MFE Consensus Structures for Sequence Alignment(s)@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)}|hyperpage}{54} +\indexentry{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}|hyperpage}{56} +\indexentry{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}!alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par@{alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}|hyperpage}{56} +\indexentry{alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par@{alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}!Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}|hyperpage}{56} +\indexentry{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}!alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}|hyperpage}{56} +\indexentry{alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}!Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}|hyperpage}{56} +\indexentry{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}!alipf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{alipf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold}|hyperpage}{57} +\indexentry{alipf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{alipf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold}!Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}|hyperpage}{57} +\indexentry{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}!export\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}bppm@{export\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}|hyperpage}{57} +\indexentry{export\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}bppm@{export\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}!Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}|hyperpage}{57} +\indexentry{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)@{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}|hyperpage}{58} +\indexentry{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)@{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}!alipbacktrack@{alipbacktrack}|hyperpage}{58} +\indexentry{alipbacktrack@{alipbacktrack}!Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)@{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}|hyperpage}{58} +\indexentry{Predicting Locally stable structures of large sequences@{Predicting Locally stable structures of large sequences}|hyperpage}{59} +\indexentry{Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores@{Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores}|hyperpage}{60} +\indexentry{Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores@{Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores}!Lfold@{Lfold}|hyperpage}{60} +\indexentry{Lfold@{Lfold}!Local MFE structure Prediction and Z-scores@{Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores}|hyperpage}{60} +\indexentry{Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores@{Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores}!Lfoldz@{Lfoldz}|hyperpage}{60} +\indexentry{Lfoldz@{Lfoldz}!Local MFE structure Prediction and Z-scores@{Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores}|hyperpage}{60} +\indexentry{Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}|hyperpage}{61} +\indexentry{Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}!update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}L\discretionary {-}{}{}P@{update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}L\discretionary {-}{}{}P}|hyperpage}{61} +\indexentry{update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}L\discretionary {-}{}{}P@{update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}L\discretionary {-}{}{}P}!Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}|hyperpage}{61} +\indexentry{Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}!pfl\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{pfl\discretionary {-}{}{}\_\discretionary {-}{}{}fold}|hyperpage}{61} +\indexentry{pfl\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{pfl\discretionary {-}{}{}\_\discretionary {-}{}{}fold}!Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}|hyperpage}{61} +\indexentry{Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}!putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob@{putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob}|hyperpage}{62} +\indexentry{putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob@{putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob}!Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}|hyperpage}{62} +\indexentry{Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}!putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob\discretionary {-}{}{}\_\discretionary {-}{}{}bin@{putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob\discretionary {-}{}{}\_\discretionary {-}{}{}bin}|hyperpage}{62} +\indexentry{putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob\discretionary {-}{}{}\_\discretionary {-}{}{}bin@{putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob\discretionary {-}{}{}\_\discretionary {-}{}{}bin}!Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}|hyperpage}{62} +\indexentry{Local M\discretionary {-}{}{}F\discretionary {-}{}{}E consensus structures for Sequence Alignments@{Local M\discretionary {-}{}{}F\discretionary {-}{}{}E consensus structures for Sequence Alignments}|hyperpage}{63} +\indexentry{Local M\discretionary {-}{}{}F\discretionary {-}{}{}E consensus structures for Sequence Alignments@{Local M\discretionary {-}{}{}F\discretionary {-}{}{}E consensus structures for Sequence Alignments}!ali\discretionary {-}{}{}Lfold@{ali\discretionary {-}{}{}Lfold}|hyperpage}{63} +\indexentry{ali\discretionary {-}{}{}Lfold@{ali\discretionary {-}{}{}Lfold}!Local MFE consensus structures for Sequence Alignments@{Local M\discretionary {-}{}{}F\discretionary {-}{}{}E consensus structures for Sequence Alignments}|hyperpage}{63} +\indexentry{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}|hyperpage}{64} +\indexentry{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}!scale\discretionary {-}{}{}\_\discretionary {-}{}{}parameters@{scale\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}|hyperpage}{65} +\indexentry{scale\discretionary {-}{}{}\_\discretionary {-}{}{}parameters@{scale\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}!Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}|hyperpage}{65} +\indexentry{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}!get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}parameters@{get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}|hyperpage}{65} +\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}parameters@{get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}!Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}|hyperpage}{65} +\indexentry{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}!get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}parameters@{get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}|hyperpage}{65} +\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}parameters@{get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}!Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}|hyperpage}{65} +\indexentry{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}!get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factors@{get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factors}|hyperpage}{65} +\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factors@{get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factors}!Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}|hyperpage}{65} +\indexentry{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}!get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factor\discretionary {-}{}{}\_\discretionary {-}{}{}copy@{get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factor\discretionary {-}{}{}\_\discretionary {-}{}{}copy}|hyperpage}{66} +\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factor\discretionary {-}{}{}\_\discretionary {-}{}{}copy@{get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factor\discretionary {-}{}{}\_\discretionary {-}{}{}copy}!Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}|hyperpage}{66} +\indexentry{Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File@{Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File}|hyperpage}{67} +\indexentry{Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File@{Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File}!read\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file@{read\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}|hyperpage}{67} +\indexentry{read\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file@{read\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}!Reading/Writing energy parameter sets from/to File@{Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File}|hyperpage}{67} +\indexentry{Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File@{Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File}!write\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file@{write\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}|hyperpage}{67} +\indexentry{write\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file@{write\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}!Reading/Writing energy parameter sets from/to File@{Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File}|hyperpage}{67} +\indexentry{Converting energy parameter files@{Converting energy parameter files}|hyperpage}{69} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}A\discretionary {-}{}{}L\discretionary {-}{}{}L@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}A\discretionary {-}{}{}L\discretionary {-}{}{}L}|hyperpage}{70} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}A\discretionary {-}{}{}L\discretionary {-}{}{}L@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}A\discretionary {-}{}{}L\discretionary {-}{}{}L}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{70} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P}|hyperpage}{70} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{70} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}A\discretionary {-}{}{}C\discretionary {-}{}{}K@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}A\discretionary {-}{}{}C\discretionary {-}{}{}K}|hyperpage}{70} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}A\discretionary {-}{}{}C\discretionary {-}{}{}K@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}A\discretionary {-}{}{}C\discretionary {-}{}{}K}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{70} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P}|hyperpage}{70} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{70} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary 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files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}1\discretionary {-}{}{}N@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary 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{-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}23@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary 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{-}{}{}T\discretionary {-}{}{}I@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}U\discretionary {-}{}{}L\discretionary {-}{}{}T\discretionary {-}{}{}I}|hyperpage}{70} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}U\discretionary {-}{}{}L\discretionary {-}{}{}T\discretionary {-}{}{}I@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}U\discretionary {-}{}{}L\discretionary {-}{}{}T\discretionary {-}{}{}I}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{70} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}X\discretionary {-}{}{}T@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}X\discretionary {-}{}{}T}|hyperpage}{70} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}X\discretionary {-}{}{}T@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}X\discretionary {-}{}{}T}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{70} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}L\discretionary {-}{}{}E5@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary 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+\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}L\discretionary {-}{}{}E3@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}L\discretionary {-}{}{}E3}|hyperpage}{70} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}L\discretionary {-}{}{}E3@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}L\discretionary {-}{}{}E3}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{70} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}11@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}11}|hyperpage}{70} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}11@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}11}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{70} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}21@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}21}|hyperpage}{70} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}21@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}21}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{70} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}22@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}22}|hyperpage}{71} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}22@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}22}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{71} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}U\discretionary {-}{}{}L\discretionary {-}{}{}G\discretionary {-}{}{}E@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}U\discretionary {-}{}{}L\discretionary {-}{}{}G\discretionary {-}{}{}E}|hyperpage}{71} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}U\discretionary {-}{}{}L\discretionary {-}{}{}G\discretionary {-}{}{}E@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}U\discretionary {-}{}{}L\discretionary {-}{}{}G\discretionary {-}{}{}E}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{71} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T}|hyperpage}{71} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{71} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}L@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}L}|hyperpage}{71} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}L@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}L}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{71} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}C@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}C}|hyperpage}{71} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}C@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}C}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{71} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}P\discretionary {-}{}{}E\discretionary {-}{}{}C\discretionary {-}{}{}I\discretionary {-}{}{}A\discretionary {-}{}{}L\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}P\discretionary {-}{}{}E\discretionary {-}{}{}C\discretionary {-}{}{}I\discretionary {-}{}{}A\discretionary {-}{}{}L\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P}|hyperpage}{71} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}P\discretionary {-}{}{}E\discretionary {-}{}{}C\discretionary {-}{}{}I\discretionary {-}{}{}A\discretionary {-}{}{}L\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}P\discretionary {-}{}{}E\discretionary {-}{}{}C\discretionary {-}{}{}I\discretionary {-}{}{}A\discretionary {-}{}{}L\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{71} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}V\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}L\discretionary {-}{}{}A@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}V\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}L\discretionary {-}{}{}A}|hyperpage}{71} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}V\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}L\discretionary {-}{}{}A@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}V\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}L\discretionary {-}{}{}A}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{71} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}O@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}O}|hyperpage}{71} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}O@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}O}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{71} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}U\discretionary {-}{}{}M\discretionary {-}{}{}P@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}U\discretionary {-}{}{}M\discretionary {-}{}{}P}|hyperpage}{71} +\indexentry{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}U\discretionary {-}{}{}M\discretionary {-}{}{}P@{V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}U\discretionary {-}{}{}M\discretionary {-}{}{}P}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{71} +\indexentry{Converting energy parameter files@{Converting energy parameter files}!convert\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file@{convert\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}|hyperpage}{71} +\indexentry{convert\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file@{convert\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}!Converting energy parameter files@{Converting energy parameter files}|hyperpage}{71} +\indexentry{Energy evaluation@{Energy evaluation}|hyperpage}{73} +\indexentry{Energy evaluation@{Energy evaluation}!energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure@{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure}|hyperpage}{73} +\indexentry{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure@{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure}!Energy evaluation@{Energy evaluation}|hyperpage}{73} +\indexentry{Energy evaluation@{Energy evaluation}!energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par@{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par}|hyperpage}{74} +\indexentry{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par@{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par}!Energy evaluation@{Energy evaluation}|hyperpage}{74} +\indexentry{Energy evaluation@{Energy evaluation}!energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}structure@{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}structure}|hyperpage}{74} +\indexentry{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}structure@{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}structure}!Energy evaluation@{Energy evaluation}|hyperpage}{74} +\indexentry{Energy evaluation@{Energy evaluation}!energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par@{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par}|hyperpage}{75} +\indexentry{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par@{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par}!Energy evaluation@{Energy evaluation}|hyperpage}{75} +\indexentry{Energy evaluation@{Energy evaluation}!energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure\discretionary {-}{}{}\_\discretionary {-}{}{}pt@{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure\discretionary {-}{}{}\_\discretionary {-}{}{}pt}|hyperpage}{75} +\indexentry{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure\discretionary {-}{}{}\_\discretionary {-}{}{}pt@{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure\discretionary {-}{}{}\_\discretionary {-}{}{}pt}!Energy evaluation@{Energy evaluation}|hyperpage}{75} +\indexentry{Energy evaluation@{Energy evaluation}!energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt\discretionary {-}{}{}\_\discretionary {-}{}{}par@{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt\discretionary {-}{}{}\_\discretionary {-}{}{}par}|hyperpage}{76} +\indexentry{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt\discretionary {-}{}{}\_\discretionary {-}{}{}par@{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt\discretionary {-}{}{}\_\discretionary {-}{}{}par}!Energy evaluation@{Energy evaluation}|hyperpage}{76} +\indexentry{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}|hyperpage}{77} +\indexentry{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}!inverse\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{inverse\discretionary {-}{}{}\_\discretionary {-}{}{}fold}|hyperpage}{77} +\indexentry{inverse\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{inverse\discretionary {-}{}{}\_\discretionary {-}{}{}fold}!Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}|hyperpage}{77} +\indexentry{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}!inverse\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{inverse\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}|hyperpage}{78} +\indexentry{inverse\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{inverse\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}!Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}|hyperpage}{78} +\indexentry{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}!final\discretionary {-}{}{}\_\discretionary {-}{}{}cost@{final\discretionary {-}{}{}\_\discretionary {-}{}{}cost}|hyperpage}{78} +\indexentry{final\discretionary {-}{}{}\_\discretionary {-}{}{}cost@{final\discretionary {-}{}{}\_\discretionary {-}{}{}cost}!Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}|hyperpage}{78} +\indexentry{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}!give\discretionary {-}{}{}\_\discretionary {-}{}{}up@{give\discretionary {-}{}{}\_\discretionary {-}{}{}up}|hyperpage}{78} +\indexentry{give\discretionary {-}{}{}\_\discretionary {-}{}{}up@{give\discretionary {-}{}{}\_\discretionary {-}{}{}up}!Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}|hyperpage}{78} +\indexentry{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}!inv\discretionary {-}{}{}\_\discretionary {-}{}{}verbose@{inv\discretionary {-}{}{}\_\discretionary {-}{}{}verbose}|hyperpage}{78} +\indexentry{inv\discretionary {-}{}{}\_\discretionary {-}{}{}verbose@{inv\discretionary {-}{}{}\_\discretionary {-}{}{}verbose}!Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}|hyperpage}{78} +\indexentry{Classified Dynamic Programming@{Classified Dynamic Programming}|hyperpage}{79} +\indexentry{Distance based partitioning of the Secondary Structure Space@{Distance based partitioning of the Secondary Structure Space}|hyperpage}{80} +\indexentry{Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning@{Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning}|hyperpage}{81} +\indexentry{Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning@{Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning}!get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables@{get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}|hyperpage}{81} +\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables@{get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}!Calculating MFE representatives of a Distance Based Partitioning@{Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning}|hyperpage}{81} +\indexentry{Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning@{Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning}!destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables@{destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}|hyperpage}{82} +\indexentry{destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables@{destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}!Calculating MFE representatives of a Distance Based Partitioning@{Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning}|hyperpage}{82} +\indexentry{Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning@{Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning}!Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}List@{Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}List}|hyperpage}{82} +\indexentry{Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}List@{Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}List}!Calculating MFE representatives of a Distance Based Partitioning@{Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning}|hyperpage}{82} +\indexentry{Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning@{Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning}!Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}f5@{Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}f5}|hyperpage}{83} +\indexentry{Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}f5@{Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}f5}!Calculating MFE representatives of a Distance Based Partitioning@{Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning}|hyperpage}{83} +\indexentry{Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}|hyperpage}{84} +\indexentry{Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}!get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables@{get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}|hyperpage}{84} +\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables@{get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}!Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}|hyperpage}{84} +\indexentry{Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}!get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E@{get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E}|hyperpage}{85} +\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E@{get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E}!Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}|hyperpage}{85} +\indexentry{Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}!destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables@{destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}|hyperpage}{85} +\indexentry{destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables@{destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}!Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}|hyperpage}{85} +\indexentry{Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}!Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}List@{Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}List}|hyperpage}{85} +\indexentry{Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}List@{Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}List}!Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}|hyperpage}{85} +\indexentry{Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}|hyperpage}{87} +\indexentry{Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}!Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack@{Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack}|hyperpage}{87} +\indexentry{Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack@{Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack}!Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}|hyperpage}{87} +\indexentry{Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}!Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack5@{Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack5}|hyperpage}{88} +\indexentry{Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack5@{Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack5}!Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}|hyperpage}{88} +\indexentry{Compute the Density of States@{Compute the Density of States}|hyperpage}{89} +\indexentry{Compute the Density of States@{Compute the Density of States}!density\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}states@{density\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}states}|hyperpage}{89} +\indexentry{density\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}states@{density\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}states}!Compute the Density of States@{Compute the Density of States}|hyperpage}{89} +\indexentry{Parsing and Comparing -\/ Functions to Manipulate Structures@{Parsing and Comparing -\/ Functions to Manipulate Structures}|hyperpage}{90} +\indexentry{bond\discretionary {-}{}{}T@{bond\discretionary {-}{}{}T}|hyperpage}{91} +\indexentry{bond\discretionary {-}{}{}T\discretionary {-}{}{}En@{bond\discretionary {-}{}{}T\discretionary {-}{}{}En}|hyperpage}{91} +\indexentry{cofold\discretionary {-}{}{}F@{cofold\discretionary {-}{}{}F}|hyperpage}{91} +\indexentry{Conc\discretionary {-}{}{}Ent@{Conc\discretionary {-}{}{}Ent}|hyperpage}{92} +\indexentry{constrain@{constrain}|hyperpage}{92} +\indexentry{C\discretionary {-}{}{}O\discretionary {-}{}{}O\discretionary {-}{}{}R\discretionary {-}{}{}D\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}T\discretionary {-}{}{}E@{C\discretionary {-}{}{}O\discretionary {-}{}{}O\discretionary {-}{}{}R\discretionary {-}{}{}D\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}T\discretionary {-}{}{}E}|hyperpage}{92} +\indexentry{cpair@{cpair}|hyperpage}{93} +\indexentry{duplex\discretionary {-}{}{}T@{duplex\discretionary {-}{}{}T}|hyperpage}{93} +\indexentry{dup\discretionary {-}{}{}Var@{dup\discretionary {-}{}{}Var}|hyperpage}{93} +\indexentry{folden@{folden}|hyperpage}{93} +\indexentry{interact@{interact}|hyperpage}{93} +\indexentry{intermediate\discretionary {-}{}{}\_\discretionary {-}{}{}t@{intermediate\discretionary {-}{}{}\_\discretionary {-}{}{}t}|hyperpage}{94} +\indexentry{I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}V\discretionary {-}{}{}A\discretionary {-}{}{}L@{I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}V\discretionary {-}{}{}A\discretionary {-}{}{}L}|hyperpage}{94} +\indexentry{L\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}T@{L\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}T}|hyperpage}{95} +\indexentry{L\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}U\discretionary {-}{}{}C\discretionary {-}{}{}K\discretionary {-}{}{}E\discretionary {-}{}{}T@{L\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}U\discretionary {-}{}{}C\discretionary {-}{}{}K\discretionary {-}{}{}E\discretionary {-}{}{}T}|hyperpage}{95} +\indexentry{model\discretionary {-}{}{}\_\discretionary {-}{}{}details\discretionary {-}{}{}T@{model\discretionary {-}{}{}\_\discretionary {-}{}{}details\discretionary {-}{}{}T}|hyperpage}{96} +\indexentry{model\discretionary {-}{}{}\_\discretionary {-}{}{}details\discretionary {-}{}{}T@{model\discretionary {-}{}{}\_\discretionary {-}{}{}details\discretionary {-}{}{}T}!dangles@{dangles}|hyperpage}{96} +\indexentry{dangles@{dangles}!model_detailsT@{model\discretionary {-}{}{}\_\discretionary {-}{}{}details\discretionary {-}{}{}T}|hyperpage}{96} +\indexentry{move\discretionary {-}{}{}\_\discretionary {-}{}{}t@{move\discretionary {-}{}{}\_\discretionary {-}{}{}t}|hyperpage}{96} +\indexentry{P\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}R@{P\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}R}|hyperpage}{97} +\indexentry{pair\discretionary {-}{}{}\_\discretionary {-}{}{}info@{pair\discretionary {-}{}{}\_\discretionary {-}{}{}info}|hyperpage}{97} +\indexentry{pairpro@{pairpro}|hyperpage}{98} +\indexentry{param\discretionary {-}{}{}T@{param\discretionary {-}{}{}T}|hyperpage}{98} +\indexentry{path\discretionary {-}{}{}\_\discretionary {-}{}{}t@{path\discretionary {-}{}{}\_\discretionary {-}{}{}t}|hyperpage}{99} +\indexentry{pf\discretionary {-}{}{}\_\discretionary {-}{}{}param\discretionary {-}{}{}T@{pf\discretionary {-}{}{}\_\discretionary {-}{}{}param\discretionary {-}{}{}T}|hyperpage}{99} +\indexentry{pf\discretionary {-}{}{}\_\discretionary {-}{}{}param\discretionary {-}{}{}T@{pf\discretionary {-}{}{}\_\discretionary {-}{}{}param\discretionary {-}{}{}T}!alpha@{alpha}|hyperpage}{100} +\indexentry{alpha@{alpha}!pf_paramT@{pf\discretionary {-}{}{}\_\discretionary {-}{}{}param\discretionary {-}{}{}T}|hyperpage}{100} +\indexentry{plist@{plist}|hyperpage}{100} +\indexentry{Postorder\discretionary {-}{}{}\_\discretionary {-}{}{}list@{Postorder\discretionary {-}{}{}\_\discretionary {-}{}{}list}|hyperpage}{100} +\indexentry{pu\discretionary {-}{}{}\_\discretionary {-}{}{}contrib@{pu\discretionary {-}{}{}\_\discretionary {-}{}{}contrib}|hyperpage}{100} +\indexentry{pu\discretionary {-}{}{}\_\discretionary {-}{}{}out@{pu\discretionary {-}{}{}\_\discretionary {-}{}{}out}|hyperpage}{101} +\indexentry{sect@{sect}|hyperpage}{101} +\indexentry{snoop\discretionary {-}{}{}T@{snoop\discretionary {-}{}{}T}|hyperpage}{102} +\indexentry{S\discretionary {-}{}{}O\discretionary {-}{}{}L\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}I\discretionary {-}{}{}O\discretionary {-}{}{}N@{S\discretionary {-}{}{}O\discretionary {-}{}{}L\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}I\discretionary {-}{}{}O\discretionary {-}{}{}N}|hyperpage}{102} +\indexentry{struct\discretionary {-}{}{}\_\discretionary {-}{}{}en@{struct\discretionary {-}{}{}\_\discretionary {-}{}{}en}|hyperpage}{102} +\indexentry{svm\discretionary {-}{}{}\_\discretionary {-}{}{}model@{svm\discretionary {-}{}{}\_\discretionary {-}{}{}model}|hyperpage}{102} +\indexentry{sw\discretionary {-}{}{}String@{sw\discretionary {-}{}{}String}|hyperpage}{102} +\indexentry{Tree@{Tree}|hyperpage}{103} +\indexentry{Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}solution@{Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}solution}|hyperpage}{103} +\indexentry{Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}vars@{Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}vars}|hyperpage}{104} +\indexentry{Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}solution@{Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}solution}|hyperpage}{105} +\indexentry{Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}vars@{Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}vars}|hyperpage}{106} +\indexentry{/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/2\discretionary {-}{}{}Dfold.\discretionary {-}{}{}h@{/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/2\discretionary {-}{}{}Dfold.\discretionary {-}{}{}h}|hyperpage}{109} +\indexentry{/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/2\discretionary {-}{}{}Dpfold.\discretionary {-}{}{}h@{/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/2\discretionary {-}{}{}Dpfold.\discretionary {-}{}{}h}|hyperpage}{110} +\indexentry{/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/alifold.\discretionary {-}{}{}h@{/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/alifold.\discretionary {-}{}{}h}|hyperpage}{111} +\indexentry{alifold.\discretionary {-}{}{}h@{alifold.\discretionary {-}{}{}h}!update\discretionary {-}{}{}\_\discretionary {-}{}{}alifold\discretionary {-}{}{}\_\discretionary {-}{}{}params@{update\discretionary {-}{}{}\_\discretionary {-}{}{}alifold\discretionary {-}{}{}\_\discretionary {-}{}{}params}|hyperpage}{112} +\indexentry{update\discretionary {-}{}{}\_\discretionary {-}{}{}alifold\discretionary {-}{}{}\_\discretionary {-}{}{}params@{update\discretionary {-}{}{}\_\discretionary {-}{}{}alifold\discretionary {-}{}{}\_\discretionary {-}{}{}params}!alifold.h@{alifold.\discretionary {-}{}{}h}|hyperpage}{112} +\indexentry{/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/cofold.\discretionary {-}{}{}h@{/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/cofold.\discretionary {-}{}{}h}|hyperpage}{113} +\indexentry{cofold.\discretionary {-}{}{}h@{cofold.\discretionary {-}{}{}h}!get\discretionary {-}{}{}\_\discretionary {-}{}{}monomere\discretionary {-}{}{}\_\discretionary {-}{}{}mfes@{get\discretionary {-}{}{}\_\discretionary {-}{}{}monomere\discretionary {-}{}{}\_\discretionary {-}{}{}mfes}|hyperpage}{114} +\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}monomere\discretionary {-}{}{}\_\discretionary {-}{}{}mfes@{get\discretionary {-}{}{}\_\discretionary {-}{}{}monomere\discretionary {-}{}{}\_\discretionary {-}{}{}mfes}!cofold.h@{cofold.\discretionary {-}{}{}h}|hyperpage}{114} +\indexentry{cofold.\discretionary {-}{}{}h@{cofold.\discretionary {-}{}{}h}!initialize\discretionary {-}{}{}\_\discretionary {-}{}{}cofold@{initialize\discretionary {-}{}{}\_\discretionary {-}{}{}cofold}|hyperpage}{114} +\indexentry{initialize\discretionary {-}{}{}\_\discretionary {-}{}{}cofold@{initialize\discretionary {-}{}{}\_\discretionary {-}{}{}cofold}!cofold.h@{cofold.\discretionary {-}{}{}h}|hyperpage}{114} +\indexentry{/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/convert\discretionary {-}{}{}\_\discretionary {-}{}{}epars.\discretionary {-}{}{}h@{/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/convert\discretionary {-}{}{}\_\discretionary {-}{}{}epars.\discretionary {-}{}{}h}|hyperpage}{114} +\indexentry{/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/data\discretionary {-}{}{}\_\discretionary {-}{}{}structures.\discretionary {-}{}{}h@{/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary 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+\indexentry{utils.\discretionary {-}{}{}h@{utils.\discretionary {-}{}{}h}!xsubi@{xsubi}|hyperpage}{182} +\indexentry{xsubi@{xsubi}!utils.h@{utils.\discretionary {-}{}{}h}|hyperpage}{182} +\indexentry{/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/lib/1.\discretionary {-}{}{}8.\discretionary {-}{}{}4\discretionary {-}{}{}\_\discretionary {-}{}{}epars.\discretionary {-}{}{}h@{/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/lib/1.\discretionary {-}{}{}8.\discretionary {-}{}{}4\discretionary {-}{}{}\_\discretionary {-}{}{}epars.\discretionary {-}{}{}h}|hyperpage}{182} +\indexentry{/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/lib/1.\discretionary {-}{}{}8.\discretionary {-}{}{}4\discretionary {-}{}{}\_\discretionary {-}{}{}intloops.\discretionary {-}{}{}h@{/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/lib/1.\discretionary {-}{}{}8.\discretionary {-}{}{}4\discretionary {-}{}{}\_\discretionary {-}{}{}intloops.\discretionary {-}{}{}h}|hyperpage}{182} diff --git a/binaries/src/ViennaRNA/doc/latex/refman.ilg b/binaries/src/ViennaRNA/doc/latex/refman.ilg new file mode 100644 index 0000000..6474a8f --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/refman.ilg @@ -0,0 +1,160 @@ +This is makeindex, version 2.15 [TeX Live 2012] (kpathsea + Thai support). +Scanning input file refman.idx.... +!! Input index error (file = refman.idx, line = 149): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 150): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 151): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 152): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 153): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 154): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 155): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 156): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 157): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 158): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 159): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 160): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 161): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 162): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 163): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 164): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 165): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 166): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 167): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 168): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 169): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 170): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 171): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 172): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 173): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 174): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 175): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 176): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 177): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 178): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 179): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 180): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 181): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 182): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 183): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 184): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 185): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 186): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 187): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 188): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 189): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 190): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 191): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 192): + -- First argument too long (max 1024). + +!! Input index error (file = refman.idx, line = 448): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 449): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 450): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 451): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 452): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 453): + -- First argument too long (max 1024). + +!! Input index error (file = refman.idx, line = 530): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 531): + -- First argument too long (max 1024). + +!! Input index error (file = refman.idx, line = 534): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 535): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 536): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 537): + -- First argument too long (max 1024). + +!! Input index error (file = refman.idx, line = 542): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 543): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 544): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 545): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 546): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 547): + -- First argument too long (max 1024). + +!! Input index error (file = refman.idx, line = 550): + -- First argument too long (max 1024). + +!! Input index error (file = refman.idx, line = 556): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 557): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 558): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 559): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 560): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 561): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 562): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 563): + -- First argument too long (max 1024). + +!! Input index error (file = refman.idx, line = 568): + -- First argument too long (max 1024). +!! Input index error (file = refman.idx, line = 569): + -- First argument too long (max 1024). +done (572 entries accepted, 73 rejected). +Sorting entries.......done (5600 comparisons). +Generating output file refman.ind....done (1321 lines written, 0 warnings). +Output written in refman.ind. +Transcript written in refman.ilg. diff --git a/binaries/src/ViennaRNA/doc/latex/refman.ind b/binaries/src/ViennaRNA/doc/latex/refman.ind new file mode 100644 index 0000000..7ba087a --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/refman.ind @@ -0,0 +1,1321 @@ +\begin{theindex} + + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/2\discretionary {-}{}{}Dfold.\discretionary {-}{}{}h}, + \hyperpage{109} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/2\discretionary {-}{}{}Dpfold.\discretionary {-}{}{}h}, + \hyperpage{110} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}L\discretionary {-}{}{}Pfold.\discretionary {-}{}{}h}, + \hyperpage{141} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}Lfold.\discretionary {-}{}{}h}, + \hyperpage{135} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}A.\discretionary {-}{}{}h}, + \hyperpage{142} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h}, + \hyperpage{157} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h}, + \hyperpage{161} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/alifold.\discretionary {-}{}{}h}, + \hyperpage{111} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/cofold.\discretionary {-}{}{}h}, + \hyperpage{113} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/convert\discretionary {-}{}{}\_\discretionary {-}{}{}epars.\discretionary {-}{}{}h}, + \hyperpage{114} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/data\discretionary {-}{}{}\_\discretionary {-}{}{}structures.\discretionary {-}{}{}h}, + \hyperpage{115} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/dist\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{117} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/duplex.\discretionary {-}{}{}h}, + \hyperpage{118} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/edit\discretionary {-}{}{}\_\discretionary {-}{}{}cost.\discretionary {-}{}{}h}, + \hyperpage{119} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h}, + \hyperpage{119} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/findpath.\discretionary {-}{}{}h}, + \hyperpage{120} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/fold.\discretionary {-}{}{}h}, + \hyperpage{122} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{128} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/gquad.\discretionary {-}{}{}h}, + \hyperpage{133} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/inverse.\discretionary {-}{}{}h}, + \hyperpage{135} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h}, + \hyperpage{136} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/mm.\discretionary {-}{}{}h}, + \hyperpage{144} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/naview.\discretionary {-}{}{}h}, + \hyperpage{144} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/params.\discretionary {-}{}{}h}, + \hyperpage{145} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h}, + \hyperpage{146} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/part\discretionary {-}{}{}\_\discretionary {-}{}{}func\discretionary {-}{}{}\_\discretionary {-}{}{}co.\discretionary {-}{}{}h}, + \hyperpage{148} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/part\discretionary {-}{}{}\_\discretionary {-}{}{}func\discretionary {-}{}{}\_\discretionary {-}{}{}up.\discretionary {-}{}{}h}, + \hyperpage{150} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/plot\discretionary {-}{}{}\_\discretionary {-}{}{}layouts.\discretionary {-}{}{}h}, + \hyperpage{152} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/profiledist.\discretionary {-}{}{}h}, + \hyperpage{155} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/read\discretionary {-}{}{}\_\discretionary {-}{}{}epars.\discretionary {-}{}{}h}, + \hyperpage{160} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/stringdist.\discretionary {-}{}{}h}, + \hyperpage{164} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/subopt.\discretionary {-}{}{}h}, + \hyperpage{166} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/treedist.\discretionary {-}{}{}h}, + \hyperpage{167} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/utils.\discretionary {-}{}{}h}, + \hyperpage{168} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/lib/1.\discretionary {-}{}{}8.\discretionary {-}{}{}4\discretionary {-}{}{}\_\discretionary {-}{}{}epars.\discretionary {-}{}{}h}, + \hyperpage{182} + \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/lib/1.\discretionary {-}{}{}8.\discretionary {-}{}{}4\discretionary {-}{}{}\_\discretionary {-}{}{}intloops.\discretionary {-}{}{}h}, + \hyperpage{182} + + \indexspace + + \item {add\discretionary {-}{}{}\_\discretionary {-}{}{}root} + \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h}, + \hyperpage{163} + \item {ali\discretionary {-}{}{}Lfold} + \subitem {Local M\discretionary {-}{}{}F\discretionary {-}{}{}E consensus structures for Sequence Alignments}, + \hyperpage{63} + \item {ali\discretionary {-}{}{}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}color\discretionary {-}{}{}\_\discretionary {-}{}{}aln} + \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h}, + \hyperpage{160} + \item {alifold} + \subitem {M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)}, + \hyperpage{54} + \item {alifold.\discretionary {-}{}{}h} + \subitem {update\discretionary {-}{}{}\_\discretionary {-}{}{}alifold\discretionary {-}{}{}\_\discretionary {-}{}{}params}, + \hyperpage{112} + \item {alimake\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179} + \item {alipbacktrack} + \subitem {Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}, + \hyperpage{58} + \item {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold} + \subitem {Partition Function and Base Pair Probabilities for Sequence Alignment(s)}, + \hyperpage{57} + \item {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold} + \subitem {Partition Function and Base Pair Probabilities for Sequence Alignment(s)}, + \hyperpage{56} + \item {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par} + \subitem {Partition Function and Base Pair Probabilities for Sequence Alignment(s)}, + \hyperpage{56} + \item {alloc\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays} + \subitem {Predicting Consensus Structures from Alignment(s)}, + \hyperpage{52} + \item {alpha} + \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}param\discretionary {-}{}{}T}, + \hyperpage{100} + \item {assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}db} + \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{126} + \item {assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}pr} + \subitem {Calculating Partition Functions and Pair Probabilities}, + \hyperpage{29} + + \indexspace + + \item {b2\discretionary {-}{}{}C} + \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h}, + \hyperpage{162} + \item {b2\discretionary {-}{}{}H\discretionary {-}{}{}I\discretionary {-}{}{}T} + \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h}, + \hyperpage{162} + \item {b2\discretionary {-}{}{}Shapiro} + \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h}, + \hyperpage{162} + \item {B\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}U\discretionary {-}{}{}S} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h}, + \hyperpage{120} + \item {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G\discretionary {-}{}{}Quad\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop} + \subitem {gquad.\discretionary {-}{}{}h}, \hyperpage{134} + \item {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G\discretionary {-}{}{}Quad\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L} + \subitem {gquad.\discretionary {-}{}{}h}, \hyperpage{134} + \item {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}type} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{132} + \item {base\discretionary {-}{}{}\_\discretionary {-}{}{}pair} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{132} + \item {bond\discretionary {-}{}{}T}, \hyperpage{91} + \item {bond\discretionary {-}{}{}T\discretionary {-}{}{}En}, + \hyperpage{91} + + \indexspace + + \item {C\discretionary {-}{}{}O\discretionary {-}{}{}O\discretionary {-}{}{}R\discretionary {-}{}{}D\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}T\discretionary {-}{}{}E}, + \hyperpage{92} + \item {Calculate Partition Functions of a Distance Based Partitioning}, + \hyperpage{84} + \subitem {destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}, + \hyperpage{85} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}, + \hyperpage{84} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E}, + \hyperpage{85} + \subitem {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}List}, + \hyperpage{85} + \item {Calculate Secondary Structures of two R\discretionary {-}{}{}N\discretionary {-}{}{}As upon Dimerization}, + \hyperpage{41} + \item {Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning}, + \hyperpage{81} + \subitem {destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}, + \hyperpage{82} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}, + \hyperpage{81} + \subitem {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}f5}, + \hyperpage{83} + \subitem {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}List}, + \hyperpage{82} + \item {Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures}, + \hyperpage{22} + \subitem {circfold}, \hyperpage{24} + \subitem {fold}, \hyperpage{23} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}, + \hyperpage{23} + \item {Calculating Partition Functions and Pair Probabilities}, + \hyperpage{25} + \subitem {assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}pr}, + \hyperpage{29} + \subitem {export\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}, + \hyperpage{29} + \subitem {free\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}, + \hyperpage{29} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}, + \hyperpage{30} + \subitem {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance}, + \hyperpage{30} + \subitem {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance\discretionary {-}{}{}\_\discretionary {-}{}{}pr}, + \hyperpage{31} + \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold}, + \hyperpage{28} + \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}, + \hyperpage{27} + \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}, + \hyperpage{26} + \subitem {update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params}, + \hyperpage{29} + \item {centroid} + \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h}, + \hyperpage{148} + \item {Change and Precalculate Energy Parameter Sets and Boltzmann Factors}, + \hyperpage{64} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factor\discretionary {-}{}{}\_\discretionary {-}{}{}copy}, + \hyperpage{66} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factors}, + \hyperpage{65} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}, + \hyperpage{65} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}, + \hyperpage{65} + \subitem {scale\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}, + \hyperpage{65} + \item {circalifold} + \subitem {M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)}, + \hyperpage{54} + \item {circfold} + \subitem {Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures}, + \hyperpage{24} + \item {Classified Dynamic Programming}, \hyperpage{79} + \item {co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold} + \subitem {Partition Function for two hybridized Sequences}, + \hyperpage{45} + \item {co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par} + \subitem {Partition Function for two hybridized Sequences}, + \hyperpage{45} + \item {cofold} + \subitem {M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}, + \hyperpage{42} + \item {cofold.\discretionary {-}{}{}h} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}monomere\discretionary {-}{}{}\_\discretionary {-}{}{}mfes}, + \hyperpage{114} + \subitem {initialize\discretionary {-}{}{}\_\discretionary {-}{}{}cofold}, + \hyperpage{114} + \item {cofold\discretionary {-}{}{}F}, \hyperpage{91} + \item {Compute the centroid structure}, \hyperpage{33} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pl}, + \hyperpage{33} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pr}, + \hyperpage{33} + \item {Compute the Density of States}, \hyperpage{89} + \subitem {density\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}states}, + \hyperpage{89} + \item {Compute the structure with maximum expected accuracy (\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}A)}, + \hyperpage{32} + \item {compute\discretionary {-}{}{}\_\discretionary {-}{}{}probabilities} + \subitem {Partition Function for two hybridized Sequences}, + \hyperpage{47} + \item {Conc\discretionary {-}{}{}Ent}, \hyperpage{92} + \item {constrain}, \hyperpage{92} + \item {constrain\discretionary {-}{}{}\_\discretionary {-}{}{}ptypes} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{181} + \item {convert\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file} + \subitem {Converting energy parameter files}, \hyperpage{71} + \item {Converting energy parameter files}, \hyperpage{69} + \subitem {convert\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}, + \hyperpage{71} + \item {copy\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179} + \item {cost\discretionary {-}{}{}\_\discretionary {-}{}{}matrix} + \subitem {dist\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{118} + \item {cpair}, \hyperpage{93} + \item {cut\discretionary {-}{}{}\_\discretionary {-}{}{}point} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{132} + \item {cv\discretionary {-}{}{}\_\discretionary {-}{}{}fact} + \subitem {Predicting Consensus Structures from Alignment(s)}, + \hyperpage{53} + + \indexspace + + \item {dangles} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{130} + \subitem {model\discretionary {-}{}{}\_\discretionary {-}{}{}details\discretionary {-}{}{}T}, + \hyperpage{96} + \item {density\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}states} + \subitem {Compute the Density of States}, \hyperpage{89} + \item {destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables} + \subitem {Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning}, + \hyperpage{82} + \item {destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables} + \subitem {Calculate Partition Functions of a Distance Based Partitioning}, + \hyperpage{85} + \item {dist\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h} + \subitem {cost\discretionary {-}{}{}\_\discretionary {-}{}{}matrix}, + \hyperpage{118} + \subitem {edit\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack}, + \hyperpage{118} + \item {Distance based partitioning of the Secondary Structure Space}, + \hyperpage{80} + \item {do\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{132} + \item {dup\discretionary {-}{}{}Var}, \hyperpage{93} + \item {duplex\discretionary {-}{}{}T}, \hyperpage{93} + + \indexspace + + \item {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Hairpin} + \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h}, + \hyperpage{138} + \item {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop} + \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h}, + \hyperpage{137} + \item {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Stem} + \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h}, + \hyperpage{138} + \item {edit\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack} + \subitem {dist\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{118} + \item {encode\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}sequence} + \subitem {Predicting Consensus Structures from Alignment(s)}, + \hyperpage{51} + \item {Energy evaluation}, \hyperpage{73} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par}, + \hyperpage{75} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}structure}, + \hyperpage{74} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par}, + \hyperpage{74} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt\discretionary {-}{}{}\_\discretionary {-}{}{}par}, + \hyperpage{76} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure}, + \hyperpage{73} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure\discretionary {-}{}{}\_\discretionary {-}{}{}pt}, + \hyperpage{75} + \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h} + \subitem {B\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}U\discretionary {-}{}{}S}, + \hyperpage{120} + \subitem {F\discretionary {-}{}{}O\discretionary {-}{}{}R\discretionary {-}{}{}B\discretionary {-}{}{}I\discretionary {-}{}{}D\discretionary {-}{}{}D\discretionary {-}{}{}E\discretionary {-}{}{}N}, + \hyperpage{120} + \subitem {G\discretionary {-}{}{}A\discretionary {-}{}{}S\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T}, + \hyperpage{120} + \subitem {I\discretionary {-}{}{}N\discretionary {-}{}{}F}, + \hyperpage{120} + \subitem {K0}, \hyperpage{120} + \subitem {M\discretionary {-}{}{}A\discretionary {-}{}{}X\discretionary {-}{}{}L\discretionary {-}{}{}O\discretionary {-}{}{}O\discretionary {-}{}{}P}, + \hyperpage{120} + \subitem {N\discretionary {-}{}{}B\discretionary {-}{}{}P\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}R\discretionary {-}{}{}S}, + \hyperpage{120} + \subitem {T\discretionary {-}{}{}U\discretionary {-}{}{}R\discretionary {-}{}{}N}, + \hyperpage{120} + \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}alistruct} + \subitem {Predicting Consensus Structures from Alignment(s)}, + \hyperpage{51} + \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct} + \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{127} + \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par} + \subitem {Energy evaluation}, \hyperpage{75} + \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}structure} + \subitem {Energy evaluation}, \hyperpage{74} + \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}move} + \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{125} + \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}move\discretionary {-}{}{}\_\discretionary {-}{}{}pt} + \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{125} + \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct} + \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{126} + \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par} + \subitem {Energy evaluation}, \hyperpage{74} + \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt} + \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{127} + \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt\discretionary {-}{}{}\_\discretionary {-}{}{}par} + \subitem {Energy evaluation}, \hyperpage{76} + \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure} + \subitem {Energy evaluation}, \hyperpage{73} + \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure\discretionary {-}{}{}\_\discretionary {-}{}{}pt} + \subitem {Energy evaluation}, \hyperpage{75} + \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}set} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{131} + \item {Enumerating Suboptimal Structures}, \hyperpage{35} + \item {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Hairpin} + \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h}, + \hyperpage{140} + \item {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop} + \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h}, + \hyperpage{140} + \item {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Stem} + \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h}, + \hyperpage{139} + \item {exp\discretionary {-}{}{}Hairpin\discretionary {-}{}{}Energy} + \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h}, + \hyperpage{148} + \item {exp\discretionary {-}{}{}Loop\discretionary {-}{}{}Energy} + \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h}, + \hyperpage{148} + \item {expand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Full} + \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h}, + \hyperpage{163} + \item {expand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Shapiro} + \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h}, + \hyperpage{163} + \item {export\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}bppm} + \subitem {Partition Function and Base Pair Probabilities for Sequence Alignment(s)}, + \hyperpage{57} + \item {export\discretionary {-}{}{}\_\discretionary {-}{}{}bppm} + \subitem {Calculating Partition Functions and Pair Probabilities}, + \hyperpage{29} + \item {export\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}bppm} + \subitem {Partition Function for two hybridized Sequences}, + \hyperpage{46} + \item {export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays} + \subitem {M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}, + \hyperpage{43} + \item {export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays\discretionary {-}{}{}\_\discretionary {-}{}{}gq} + \subitem {M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}, + \hyperpage{43} + + \indexspace + + \item {F\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}D\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}T\discretionary {-}{}{}H} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{174} + \item {F\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}A\discretionary {-}{}{}X\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}T\discretionary {-}{}{}H} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{174} + \item {F\discretionary {-}{}{}O\discretionary {-}{}{}R\discretionary {-}{}{}B\discretionary {-}{}{}I\discretionary {-}{}{}D\discretionary {-}{}{}D\discretionary {-}{}{}E\discretionary {-}{}{}N} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h}, + \hyperpage{120} + \item {final\discretionary {-}{}{}\_\discretionary {-}{}{}cost} + \subitem {Searching Sequences for Predefined Structures}, + \hyperpage{78} + \item {find\discretionary {-}{}{}\_\discretionary {-}{}{}saddle} + \subitem {findpath.\discretionary {-}{}{}h}, \hyperpage{121} + \item {findpath.\discretionary {-}{}{}h} + \subitem {find\discretionary {-}{}{}\_\discretionary {-}{}{}saddle}, + \hyperpage{121} + \subitem {free\discretionary {-}{}{}\_\discretionary {-}{}{}path}, + \hyperpage{122} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}path}, + \hyperpage{122} + \item {fold} + \subitem {Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures}, + \hyperpage{23} + \item {fold.\discretionary {-}{}{}h} + \subitem {assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}db}, + \hyperpage{126} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct}, + \hyperpage{127} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}move}, + \hyperpage{125} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}move\discretionary {-}{}{}\_\discretionary {-}{}{}pt}, + \hyperpage{125} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct}, + \hyperpage{126} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt}, + \hyperpage{127} + \subitem {Hairpin\discretionary {-}{}{}E}, \hyperpage{126} + \subitem {initialize\discretionary {-}{}{}\_\discretionary {-}{}{}fold}, + \hyperpage{126} + \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energy}, + \hyperpage{125} + \subitem {Loop\discretionary {-}{}{}Energy}, \hyperpage{126} + \subitem {parenthesis\discretionary {-}{}{}\_\discretionary {-}{}{}structure}, + \hyperpage{124} + \subitem {parenthesis\discretionary {-}{}{}\_\discretionary {-}{}{}zuker}, + \hyperpage{124} + \item {fold\discretionary {-}{}{}\_\discretionary {-}{}{}par} + \subitem {Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures}, + \hyperpage{23} + \item {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h} + \subitem {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}type}, + \hyperpage{132} + \subitem {base\discretionary {-}{}{}\_\discretionary {-}{}{}pair}, + \hyperpage{132} + \subitem {cut\discretionary {-}{}{}\_\discretionary {-}{}{}point}, + \hyperpage{132} + \subitem {dangles}, \hyperpage{130} + \subitem {do\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack}, + \hyperpage{132} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}set}, + \hyperpage{131} + \subitem {iindx}, \hyperpage{132} + \subitem {james\discretionary {-}{}{}\_\discretionary {-}{}{}rule}, + \hyperpage{131} + \subitem {log\discretionary {-}{}{}M\discretionary {-}{}{}L}, + \hyperpage{131} + \subitem {no\discretionary {-}{}{}Lonely\discretionary {-}{}{}Pairs}, + \hyperpage{130} + \subitem {nonstandards}, \hyperpage{131} + \subitem {old\discretionary {-}{}{}Ali\discretionary {-}{}{}En}, + \hyperpage{131} + \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}scale}, + \hyperpage{132} + \subitem {pr}, \hyperpage{132} + \subitem {ribo}, \hyperpage{131} + \subitem {Ribosum\discretionary {-}{}{}File}, \hyperpage{131} + \subitem {set\discretionary {-}{}{}\_\discretionary {-}{}{}model\discretionary {-}{}{}\_\discretionary {-}{}{}details}, + \hyperpage{130} + \subitem {temperature}, \hyperpage{131} + \subitem {tetra\discretionary {-}{}{}\_\discretionary {-}{}{}loop}, + \hyperpage{131} + \item {folden}, \hyperpage{93} + \item {free\discretionary {-}{}{}\_\discretionary {-}{}{}path} + \subitem {findpath.\discretionary {-}{}{}h}, \hyperpage{122} + \item {free\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays} + \subitem {Calculating Partition Functions and Pair Probabilities}, + \hyperpage{29} + \item {free\discretionary {-}{}{}\_\discretionary {-}{}{}profile} + \subitem {profiledist.\discretionary {-}{}{}h}, \hyperpage{156} + \item {free\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays} + \subitem {Predicting Consensus Structures from Alignment(s)}, + \hyperpage{52} + \item {free\discretionary {-}{}{}\_\discretionary {-}{}{}tree} + \subitem {treedist.\discretionary {-}{}{}h}, \hyperpage{168} + + \indexspace + + \item {G\discretionary {-}{}{}A\discretionary {-}{}{}S\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h}, + \hyperpage{120} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables} + \subitem {Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning}, + \hyperpage{81} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables} + \subitem {Calculate Partition Functions of a Distance Based Partitioning}, + \hyperpage{84} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E} + \subitem {Calculate Partition Functions of a Distance Based Partitioning}, + \hyperpage{85} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}alipf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays} + \subitem {Predicting Consensus Structures from Alignment(s)}, + \hyperpage{53} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factor\discretionary {-}{}{}\_\discretionary {-}{}{}copy} + \subitem {Change and Precalculate Energy Parameter Sets and Boltzmann Factors}, + \hyperpage{66} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factors} + \subitem {Change and Precalculate Energy Parameter Sets and Boltzmann Factors}, + \hyperpage{65} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pl} + \subitem {Compute the centroid structure}, \hyperpage{33} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pr} + \subitem {Compute the centroid structure}, \hyperpage{33} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}concentrations} + \subitem {Partition Function for two hybridized Sequences}, + \hyperpage{47} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}gquad\discretionary {-}{}{}\_\discretionary {-}{}{}matrix} + \subitem {gquad.\discretionary {-}{}{}h}, \hyperpage{134} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}iindx} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{180} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}indx} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{181} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}line} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{176} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}line} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{176} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}monomere\discretionary {-}{}{}\_\discretionary {-}{}{}mfes} + \subitem {cofold.\discretionary {-}{}{}h}, \hyperpage{114} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}mpi} + \subitem {Predicting Consensus Structures from Alignment(s)}, + \hyperpage{51} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}path} + \subitem {findpath.\discretionary {-}{}{}h}, \hyperpage{122} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays} + \subitem {Calculating Partition Functions and Pair Probabilities}, + \hyperpage{30} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}plist} + \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func\discretionary {-}{}{}\_\discretionary {-}{}{}co.\discretionary {-}{}{}h}, + \hyperpage{150} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}parameters} + \subitem {Change and Precalculate Energy Parameter Sets and Boltzmann Factors}, + \hyperpage{65} + \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}parameters} + \subitem {Change and Precalculate Energy Parameter Sets and Boltzmann Factors}, + \hyperpage{65} + \item {give\discretionary {-}{}{}\_\discretionary {-}{}{}up} + \subitem {Searching Sequences for Predefined Structures}, + \hyperpage{78} + \item {gml\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A} + \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h}, + \hyperpage{158} + \item {gquad.\discretionary {-}{}{}h} + \subitem {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G\discretionary {-}{}{}Quad\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop}, + \hyperpage{134} + \subitem {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G\discretionary {-}{}{}Quad\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L}, + \hyperpage{134} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}gquad\discretionary {-}{}{}\_\discretionary {-}{}{}matrix}, + \hyperpage{134} + \subitem {parse\discretionary {-}{}{}\_\discretionary {-}{}{}gquad}, + \hyperpage{134} + + \indexspace + + \item {Hairpin\discretionary {-}{}{}E} + \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{126} + \item {hamming} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{176} + \item {hamming\discretionary {-}{}{}\_\discretionary {-}{}{}bound} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{176} + + \indexspace + + \item {I\discretionary {-}{}{}N\discretionary {-}{}{}F} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h}, + \hyperpage{120} + \item {I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}V\discretionary {-}{}{}A\discretionary {-}{}{}L}, + \hyperpage{94} + \item {iindx} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{132} + \item {init\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold} + \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func\discretionary {-}{}{}\_\discretionary {-}{}{}co.\discretionary {-}{}{}h}, + \hyperpage{150} + \item {init\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold} + \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h}, + \hyperpage{148} + \item {init\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}L\discretionary {-}{}{}P} + \subitem {L\discretionary {-}{}{}Pfold.\discretionary {-}{}{}h}, + \hyperpage{142} + \item {initialize\discretionary {-}{}{}\_\discretionary {-}{}{}cofold} + \subitem {cofold.\discretionary {-}{}{}h}, \hyperpage{114} + \item {initialize\discretionary {-}{}{}\_\discretionary {-}{}{}fold} + \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{126} + \item {int\discretionary {-}{}{}\_\discretionary {-}{}{}urn} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{175} + \item {interact}, \hyperpage{93} + \item {intermediate\discretionary {-}{}{}\_\discretionary {-}{}{}t}, + \hyperpage{94} + \item {inv\discretionary {-}{}{}\_\discretionary {-}{}{}verbose} + \subitem {Searching Sequences for Predefined Structures}, + \hyperpage{78} + \item {inverse\discretionary {-}{}{}\_\discretionary {-}{}{}fold} + \subitem {Searching Sequences for Predefined Structures}, + \hyperpage{77} + \item {inverse\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold} + \subitem {Searching Sequences for Predefined Structures}, + \hyperpage{78} + + \indexspace + + \item {james\discretionary {-}{}{}\_\discretionary {-}{}{}rule} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{131} + + \indexspace + + \item {K0} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h}, + \hyperpage{120} + + \indexspace + + \item {L\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}T}, + \hyperpage{95} + \item {L\discretionary {-}{}{}Pfold.\discretionary {-}{}{}h} + \subitem {init\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}L\discretionary {-}{}{}P}, + \hyperpage{142} + \item {L\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}U\discretionary {-}{}{}C\discretionary {-}{}{}K\discretionary {-}{}{}E\discretionary {-}{}{}T}, + \hyperpage{95} + \item {Lfold} + \subitem {Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores}, + \hyperpage{60} + \item {Lfoldz} + \subitem {Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores}, + \hyperpage{60} + \item {Local M\discretionary {-}{}{}F\discretionary {-}{}{}E consensus structures for Sequence Alignments}, + \hyperpage{63} + \subitem {ali\discretionary {-}{}{}Lfold}, \hyperpage{63} + \item {Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores}, + \hyperpage{60} + \subitem {Lfold}, \hyperpage{60} + \subitem {Lfoldz}, \hyperpage{60} + \item {log\discretionary {-}{}{}M\discretionary {-}{}{}L} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{131} + \item {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h} + \subitem {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Hairpin}, + \hyperpage{138} + \subitem {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop}, + \hyperpage{137} + \subitem {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Stem}, + \hyperpage{138} + \subitem {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Hairpin}, + \hyperpage{140} + \subitem {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop}, + \hyperpage{140} + \subitem {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Stem}, + \hyperpage{139} + \item {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energy} + \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{125} + \item {Loop\discretionary {-}{}{}Energy} + \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{126} + + \indexspace + + \item {M\discretionary {-}{}{}A\discretionary {-}{}{}X2} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173} + \item {M\discretionary {-}{}{}A\discretionary {-}{}{}X3} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173} + \item {M\discretionary {-}{}{}A\discretionary {-}{}{}X\discretionary {-}{}{}L\discretionary {-}{}{}O\discretionary {-}{}{}O\discretionary {-}{}{}P} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h}, + \hyperpage{120} + \item {M\discretionary {-}{}{}E\discretionary {-}{}{}A} + \subitem {M\discretionary {-}{}{}E\discretionary {-}{}{}A.\discretionary {-}{}{}h}, + \hyperpage{143} + \item {M\discretionary {-}{}{}E\discretionary {-}{}{}A.\discretionary {-}{}{}h} + \subitem {M\discretionary {-}{}{}E\discretionary {-}{}{}A}, + \hyperpage{143} + \item {M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)}, + \hyperpage{54} + \subitem {alifold}, \hyperpage{54} + \subitem {circalifold}, \hyperpage{54} + \item {M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}, + \hyperpage{42} + \subitem {cofold}, \hyperpage{42} + \subitem {export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}, + \hyperpage{43} + \subitem {export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays\discretionary {-}{}{}\_\discretionary {-}{}{}gq}, + \hyperpage{43} + \item {M\discretionary {-}{}{}I\discretionary {-}{}{}N2} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173} + \item {M\discretionary {-}{}{}I\discretionary {-}{}{}N3} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173} + \item {Make\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}profile} + \subitem {profiledist.\discretionary {-}{}{}h}, \hyperpage{156} + \item {Make\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}profile\discretionary {-}{}{}\_\discretionary {-}{}{}bppm} + \subitem {profiledist.\discretionary {-}{}{}h}, \hyperpage{156} + \item {make\discretionary {-}{}{}\_\discretionary {-}{}{}loop\discretionary {-}{}{}\_\discretionary {-}{}{}index\discretionary {-}{}{}\_\discretionary {-}{}{}pt} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179} + \item {make\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{178} + \item {make\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table\discretionary {-}{}{}\_\discretionary {-}{}{}snoop} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179} + \item {Make\discretionary {-}{}{}\_\discretionary {-}{}{}sw\discretionary {-}{}{}String} + \subitem {stringdist.\discretionary {-}{}{}h}, \hyperpage{165} + \item {make\discretionary {-}{}{}\_\discretionary {-}{}{}tree} + \subitem {treedist.\discretionary {-}{}{}h}, \hyperpage{168} + \item {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}dist} + \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h}, + \hyperpage{148} + \item {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance} + \subitem {Calculating Partition Functions and Pair Probabilities}, + \hyperpage{30} + \item {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance\discretionary {-}{}{}\_\discretionary {-}{}{}pr} + \subitem {Calculating Partition Functions and Pair Probabilities}, + \hyperpage{31} + \item {model\discretionary {-}{}{}\_\discretionary {-}{}{}details\discretionary {-}{}{}T}, + \hyperpage{96} + \subitem {dangles}, \hyperpage{96} + \item {move\discretionary {-}{}{}\_\discretionary {-}{}{}t}, + \hyperpage{96} + + \indexspace + + \item {N\discretionary {-}{}{}B\discretionary {-}{}{}P\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}R\discretionary {-}{}{}S} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h}, + \hyperpage{120} + \item {nc\discretionary {-}{}{}\_\discretionary {-}{}{}fact} + \subitem {Predicting Consensus Structures from Alignment(s)}, + \hyperpage{53} + \item {no\discretionary {-}{}{}Lonely\discretionary {-}{}{}Pairs} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{130} + \item {nonstandards} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{131} + \item {nrerror} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{174} + + \indexspace + + \item {old\discretionary {-}{}{}Ali\discretionary {-}{}{}En} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{131} + + \indexspace + + \item {P\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}R}, + \hyperpage{97} + \item {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h} + \subitem {ali\discretionary {-}{}{}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}color\discretionary {-}{}{}\_\discretionary {-}{}{}aln}, + \hyperpage{160} + \subitem {gml\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A}, + \hyperpage{158} + \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot\discretionary {-}{}{}\_\discretionary {-}{}{}plot}, + \hyperpage{160} + \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}list}, + \hyperpage{159} + \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}, + \hyperpage{158} + \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}a}, + \hyperpage{158} + \subitem {ssv\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}, + \hyperpage{159} + \subitem {svg\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}, + \hyperpage{159} + \subitem {xrna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}, + \hyperpage{159} + \item {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot\discretionary {-}{}{}\_\discretionary {-}{}{}plot} + \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h}, + \hyperpage{160} + \item {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}list} + \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h}, + \hyperpage{159} + \item {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot} + \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h}, + \hyperpage{158} + \item {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}a} + \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h}, + \hyperpage{158} + \item {pack\discretionary {-}{}{}\_\discretionary {-}{}{}structure} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{178} + \item {pair\discretionary {-}{}{}\_\discretionary {-}{}{}info}, + \hyperpage{97} + \item {pairpro}, \hyperpage{98} + \item {param\discretionary {-}{}{}T}, \hyperpage{98} + \item {parenthesis\discretionary {-}{}{}\_\discretionary {-}{}{}structure} + \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{124} + \item {parenthesis\discretionary {-}{}{}\_\discretionary {-}{}{}zuker} + \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{124} + \item {parse\discretionary {-}{}{}\_\discretionary {-}{}{}gquad} + \subitem {gquad.\discretionary {-}{}{}h}, \hyperpage{134} + \item {parse\discretionary {-}{}{}\_\discretionary {-}{}{}structure} + \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h}, + \hyperpage{164} + \item {Parsing and Comparing -\/ Functions to Manipulate Structures}, + \hyperpage{90} + \item {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h} + \subitem {centroid}, \hyperpage{148} + \subitem {exp\discretionary {-}{}{}Hairpin\discretionary {-}{}{}Energy}, + \hyperpage{148} + \subitem {exp\discretionary {-}{}{}Loop\discretionary {-}{}{}Energy}, + \hyperpage{148} + \subitem {init\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}, + \hyperpage{148} + \subitem {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}dist}, + \hyperpage{148} + \item {part\discretionary {-}{}{}\_\discretionary {-}{}{}func\discretionary {-}{}{}\_\discretionary {-}{}{}co.\discretionary {-}{}{}h} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}plist}, + \hyperpage{150} + \subitem {init\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}, + \hyperpage{150} + \item {Partition Function and Base Pair Probabilities for Sequence Alignment(s)}, + \hyperpage{56} + \subitem {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold}, + \hyperpage{57} + \subitem {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}, + \hyperpage{56} + \subitem {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}, + \hyperpage{56} + \subitem {export\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}, + \hyperpage{57} + \item {Partition Function for two hybridized Sequences}, + \hyperpage{44} + \subitem {co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}, + \hyperpage{45} + \subitem {co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}, + \hyperpage{45} + \subitem {compute\discretionary {-}{}{}\_\discretionary {-}{}{}probabilities}, + \hyperpage{47} + \subitem {export\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}, + \hyperpage{46} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}concentrations}, + \hyperpage{47} + \subitem {update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params}, + \hyperpage{46} + \subitem {update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}\_\discretionary {-}{}{}par}, + \hyperpage{46} + \item {Partition Function for two hybridized Sequences as a stepwise Process}, + \hyperpage{48} + \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}interact}, + \hyperpage{49} + \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}unstru}, + \hyperpage{48} + \item {Partition functions for locally stable secondary structures}, + \hyperpage{61} + \subitem {pfl\discretionary {-}{}{}\_\discretionary {-}{}{}fold}, + \hyperpage{61} + \subitem {putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob}, + \hyperpage{62} + \subitem {putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob\discretionary {-}{}{}\_\discretionary {-}{}{}bin}, + \hyperpage{62} + \subitem {update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}L\discretionary {-}{}{}P}, + \hyperpage{61} + \item {path\discretionary {-}{}{}\_\discretionary {-}{}{}t}, + \hyperpage{99} + \item {pbacktrack} + \subitem {Stochastic backtracking in the Ensemble}, \hyperpage{39} + \item {pbacktrack\discretionary {-}{}{}\_\discretionary {-}{}{}circ} + \subitem {Stochastic backtracking in the Ensemble}, \hyperpage{40} + \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold} + \subitem {Calculating Partition Functions and Pair Probabilities}, + \hyperpage{28} + \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold} + \subitem {Calculating Partition Functions and Pair Probabilities}, + \hyperpage{27} + \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par} + \subitem {Calculating Partition Functions and Pair Probabilities}, + \hyperpage{26} + \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}interact} + \subitem {Partition Function for two hybridized Sequences as a stepwise Process}, + \hyperpage{49} + \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}param\discretionary {-}{}{}T}, + \hyperpage{99} + \subitem {alpha}, \hyperpage{100} + \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}scale} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{132} + \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}unstru} + \subitem {Partition Function for two hybridized Sequences as a stepwise Process}, + \hyperpage{48} + \item {pfl\discretionary {-}{}{}\_\discretionary {-}{}{}fold} + \subitem {Partition functions for locally stable secondary structures}, + \hyperpage{61} + \item {plist}, \hyperpage{100} + \item {plot\discretionary {-}{}{}\_\discretionary {-}{}{}layouts.\discretionary {-}{}{}h} + \subitem {rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}type}, + \hyperpage{155} + \subitem {simple\discretionary {-}{}{}\_\discretionary {-}{}{}circplot\discretionary {-}{}{}\_\discretionary {-}{}{}coordinates}, + \hyperpage{154} + \subitem {simple\discretionary {-}{}{}\_\discretionary {-}{}{}xy\discretionary {-}{}{}\_\discretionary {-}{}{}coordinates}, + \hyperpage{154} + \item {Postorder\discretionary {-}{}{}\_\discretionary {-}{}{}list}, + \hyperpage{100} + \item {pr} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{132} + \item {Predicting Consensus Structures from Alignment(s)}, + \hyperpage{50} + \subitem {alloc\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}, + \hyperpage{52} + \subitem {cv\discretionary {-}{}{}\_\discretionary {-}{}{}fact}, + \hyperpage{53} + \subitem {encode\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}sequence}, + \hyperpage{51} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}alistruct}, + \hyperpage{51} + \subitem {free\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}, + \hyperpage{52} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}alipf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}, + \hyperpage{53} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}mpi}, + \hyperpage{51} + \subitem {nc\discretionary {-}{}{}\_\discretionary {-}{}{}fact}, + \hyperpage{53} + \item {Predicting Locally stable structures of large sequences}, + \hyperpage{59} + \item {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}constraint} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{180} + \item {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}seq} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179} + \item {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}seq\discretionary {-}{}{}\_\discretionary {-}{}{}str} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179} + \item {profile\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance} + \subitem {profiledist.\discretionary {-}{}{}h}, \hyperpage{156} + \item {profiledist.\discretionary {-}{}{}h} + \subitem {free\discretionary {-}{}{}\_\discretionary {-}{}{}profile}, + \hyperpage{156} + \subitem {Make\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}profile}, + \hyperpage{156} + \subitem {Make\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}profile\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}, + \hyperpage{156} + \subitem {profile\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance}, + \hyperpage{156} + \item {pu\discretionary {-}{}{}\_\discretionary {-}{}{}contrib}, + \hyperpage{100} + \item {pu\discretionary {-}{}{}\_\discretionary {-}{}{}out}, + \hyperpage{101} + \item {putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob} + \subitem {Partition functions for locally stable secondary structures}, + \hyperpage{62} + \item {putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob\discretionary {-}{}{}\_\discretionary {-}{}{}bin} + \subitem {Partition functions for locally stable secondary structures}, + \hyperpage{62} + + \indexspace + + \item {R\discretionary {-}{}{}N\discretionary {-}{}{}A Secondary Structure Folding}, + \hyperpage{19} + \item {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h} + \subitem {add\discretionary {-}{}{}\_\discretionary {-}{}{}root}, + \hyperpage{163} + \subitem {b2\discretionary {-}{}{}C}, \hyperpage{162} + \subitem {b2\discretionary {-}{}{}H\discretionary {-}{}{}I\discretionary {-}{}{}T}, + \hyperpage{162} + \subitem {b2\discretionary {-}{}{}Shapiro}, \hyperpage{162} + \subitem {expand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Full}, + \hyperpage{163} + \subitem {expand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Shapiro}, + \hyperpage{163} + \subitem {parse\discretionary {-}{}{}\_\discretionary {-}{}{}structure}, + \hyperpage{164} + \subitem {unexpand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Full}, + \hyperpage{163} + \subitem {unexpand\discretionary {-}{}{}\_\discretionary {-}{}{}aligned\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}F}, + \hyperpage{164} + \subitem {unweight}, \hyperpage{163} + \item {random\discretionary {-}{}{}\_\discretionary {-}{}{}string} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{175} + \item {read\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file} + \subitem {Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File}, + \hyperpage{67} + \item {read\discretionary {-}{}{}\_\discretionary {-}{}{}record} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{177} + \item {Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File}, + \hyperpage{67} + \subitem {read\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}, + \hyperpage{67} + \subitem {write\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}, + \hyperpage{67} + \item {ribo} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{131} + \item {Ribosum\discretionary {-}{}{}File} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{131} + \item {rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}type} + \subitem {plot\discretionary {-}{}{}\_\discretionary {-}{}{}layouts.\discretionary {-}{}{}h}, + \hyperpage{155} + + \indexspace + + \item {S\discretionary {-}{}{}O\discretionary {-}{}{}L\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}I\discretionary {-}{}{}O\discretionary {-}{}{}N}, + \hyperpage{102} + \item {S\discretionary {-}{}{}T\discretionary {-}{}{}R} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173} + \item {scale\discretionary {-}{}{}\_\discretionary {-}{}{}parameters} + \subitem {Change and Precalculate Energy Parameter Sets and Boltzmann Factors}, + \hyperpage{65} + \item {Searching Sequences for Predefined Structures}, \hyperpage{77} + \subitem {final\discretionary {-}{}{}\_\discretionary {-}{}{}cost}, + \hyperpage{78} + \subitem {give\discretionary {-}{}{}\_\discretionary {-}{}{}up}, + \hyperpage{78} + \subitem {inv\discretionary {-}{}{}\_\discretionary {-}{}{}verbose}, + \hyperpage{78} + \subitem {inverse\discretionary {-}{}{}\_\discretionary {-}{}{}fold}, + \hyperpage{77} + \subitem {inverse\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}, + \hyperpage{78} + \item {sect}, \hyperpage{101} + \item {set\discretionary {-}{}{}\_\discretionary {-}{}{}model\discretionary {-}{}{}\_\discretionary {-}{}{}details} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{130} + \item {simple\discretionary {-}{}{}\_\discretionary {-}{}{}circplot\discretionary {-}{}{}\_\discretionary {-}{}{}coordinates} + \subitem {plot\discretionary {-}{}{}\_\discretionary {-}{}{}layouts.\discretionary {-}{}{}h}, + \hyperpage{154} + \item {simple\discretionary {-}{}{}\_\discretionary {-}{}{}xy\discretionary {-}{}{}\_\discretionary {-}{}{}coordinates} + \subitem {plot\discretionary {-}{}{}\_\discretionary {-}{}{}layouts.\discretionary {-}{}{}h}, + \hyperpage{154} + \item {snoop\discretionary {-}{}{}T}, \hyperpage{102} + \item {space} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{174} + \item {ssv\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot} + \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h}, + \hyperpage{159} + \item {st\discretionary {-}{}{}\_\discretionary {-}{}{}back} + \subitem {Stochastic backtracking in the Ensemble}, \hyperpage{40} + \item {Stochastic backtracking in the Ensemble}, \hyperpage{39} + \subitem {pbacktrack}, \hyperpage{39} + \subitem {pbacktrack\discretionary {-}{}{}\_\discretionary {-}{}{}circ}, + \hyperpage{40} + \subitem {st\discretionary {-}{}{}\_\discretionary {-}{}{}back}, + \hyperpage{40} + \item {Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}, + \hyperpage{58} + \subitem {alipbacktrack}, \hyperpage{58} + \item {Stochastic Backtracking of Structures from Distance Based Partitioning}, + \hyperpage{87} + \subitem {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack}, + \hyperpage{87} + \subitem {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack5}, + \hyperpage{88} + \item {str\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}N\discretionary {-}{}{}A2\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{180} + \item {str\discretionary {-}{}{}\_\discretionary {-}{}{}uppercase} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{180} + \item {string\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance} + \subitem {stringdist.\discretionary {-}{}{}h}, \hyperpage{165} + \item {stringdist.\discretionary {-}{}{}h} + \subitem {Make\discretionary {-}{}{}\_\discretionary {-}{}{}sw\discretionary {-}{}{}String}, + \hyperpage{165} + \subitem {string\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance}, + \hyperpage{165} + \item {struct\discretionary {-}{}{}\_\discretionary {-}{}{}en}, + \hyperpage{102} + \item {subopt} + \subitem {Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E}, + \hyperpage{37} + \item {subopt\discretionary {-}{}{}\_\discretionary {-}{}{}circ} + \subitem {Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E}, + \hyperpage{38} + \item {Suboptimal structures according to Zuker et al. 1989}, + \hyperpage{36} + \subitem {zukersubopt}, \hyperpage{36} + \item {Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E}, + \hyperpage{37} + \subitem {subopt}, \hyperpage{37} + \subitem {subopt\discretionary {-}{}{}\_\discretionary {-}{}{}circ}, + \hyperpage{38} + \item {svg\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot} + \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h}, + \hyperpage{159} + \item {svm\discretionary {-}{}{}\_\discretionary {-}{}{}model}, + \hyperpage{102} + \item {sw\discretionary {-}{}{}String}, \hyperpage{102} + + \indexspace + + \item {T\discretionary {-}{}{}U\discretionary {-}{}{}R\discretionary {-}{}{}N} + \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h}, + \hyperpage{120} + \item {temperature} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{131} + \item {tetra\discretionary {-}{}{}\_\discretionary {-}{}{}loop} + \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}, + \hyperpage{131} + \item {time\discretionary {-}{}{}\_\discretionary {-}{}{}stamp} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{175} + \item {Tree}, \hyperpage{103} + \item {tree\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance} + \subitem {treedist.\discretionary {-}{}{}h}, \hyperpage{168} + \item {treedist.\discretionary {-}{}{}h} + \subitem {free\discretionary {-}{}{}\_\discretionary {-}{}{}tree}, + \hyperpage{168} + \subitem {make\discretionary {-}{}{}\_\discretionary {-}{}{}tree}, + \hyperpage{168} + \subitem {tree\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance}, + \hyperpage{168} + \item {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}f5} + \subitem {Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning}, + \hyperpage{83} + \item {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}solution}, + \hyperpage{103} + \item {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}vars}, + \hyperpage{104} + \item {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}List} + \subitem {Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning}, + \hyperpage{82} + \item {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack} + \subitem {Stochastic Backtracking of Structures from Distance Based Partitioning}, + \hyperpage{87} + \item {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack5} + \subitem {Stochastic Backtracking of Structures from Distance Based Partitioning}, + \hyperpage{88} + \item {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}solution}, + \hyperpage{105} + \item {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}vars}, + \hyperpage{106} + \item {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}List} + \subitem {Calculate Partition Functions of a Distance Based Partitioning}, + \hyperpage{85} + + \indexspace + + \item {unexpand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Full} + \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h}, + \hyperpage{163} + \item {unexpand\discretionary {-}{}{}\_\discretionary {-}{}{}aligned\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}F} + \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h}, + \hyperpage{164} + \item {unpack\discretionary {-}{}{}\_\discretionary {-}{}{}structure} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{178} + \item {unweight} + \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h}, + \hyperpage{163} + \item {update\discretionary {-}{}{}\_\discretionary {-}{}{}alifold\discretionary {-}{}{}\_\discretionary {-}{}{}params} + \subitem {alifold.\discretionary {-}{}{}h}, \hyperpage{112} + \item {update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params} + \subitem {Partition Function for two hybridized Sequences}, + \hyperpage{46} + \item {update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}\_\discretionary {-}{}{}par} + \subitem {Partition Function for two hybridized Sequences}, + \hyperpage{46} + \item {update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params} + \subitem {Calculating Partition Functions and Pair Probabilities}, + \hyperpage{29} + \item {update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}L\discretionary {-}{}{}P} + \subitem {Partition functions for locally stable secondary structures}, + \hyperpage{61} + \item {urn} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{175} + \item {utils.\discretionary {-}{}{}h} + \subitem {alimake\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table}, + \hyperpage{179} + \subitem {constrain\discretionary {-}{}{}\_\discretionary {-}{}{}ptypes}, + \hyperpage{181} + \subitem {copy\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table}, + \hyperpage{179} + \subitem {F\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}D\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}T\discretionary {-}{}{}H}, + \hyperpage{174} + \subitem {F\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}A\discretionary {-}{}{}X\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}T\discretionary {-}{}{}H}, + \hyperpage{174} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}iindx}, + \hyperpage{180} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}indx}, + \hyperpage{181} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}line}, + \hyperpage{176} + \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}line}, + \hyperpage{176} + \subitem {hamming}, \hyperpage{176} + \subitem {hamming\discretionary {-}{}{}\_\discretionary {-}{}{}bound}, + \hyperpage{176} + \subitem {int\discretionary {-}{}{}\_\discretionary {-}{}{}urn}, + \hyperpage{175} + \subitem {M\discretionary {-}{}{}A\discretionary {-}{}{}X2}, + \hyperpage{173} + \subitem {M\discretionary {-}{}{}A\discretionary {-}{}{}X3}, + \hyperpage{173} + \subitem {M\discretionary {-}{}{}I\discretionary {-}{}{}N2}, + \hyperpage{173} + \subitem {M\discretionary {-}{}{}I\discretionary {-}{}{}N3}, + \hyperpage{173} + \subitem {make\discretionary {-}{}{}\_\discretionary {-}{}{}loop\discretionary {-}{}{}\_\discretionary {-}{}{}index\discretionary {-}{}{}\_\discretionary {-}{}{}pt}, + \hyperpage{179} + \subitem {make\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table}, + \hyperpage{178} + \subitem {make\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table\discretionary {-}{}{}\_\discretionary {-}{}{}snoop}, + \hyperpage{179} + \subitem {nrerror}, \hyperpage{174} + \subitem {pack\discretionary {-}{}{}\_\discretionary {-}{}{}structure}, + \hyperpage{178} + \subitem {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}constraint}, + \hyperpage{180} + \subitem {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}seq}, + \hyperpage{179} + \subitem {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}seq\discretionary {-}{}{}\_\discretionary {-}{}{}str}, + \hyperpage{179} + \subitem {random\discretionary {-}{}{}\_\discretionary {-}{}{}string}, + \hyperpage{175} + \subitem {read\discretionary {-}{}{}\_\discretionary {-}{}{}record}, + \hyperpage{177} + \subitem {S\discretionary {-}{}{}T\discretionary {-}{}{}R}, + \hyperpage{173} + \subitem {space}, \hyperpage{174} + \subitem {str\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}N\discretionary {-}{}{}A2\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A}, + \hyperpage{180} + \subitem {str\discretionary {-}{}{}\_\discretionary {-}{}{}uppercase}, + \hyperpage{180} + \subitem {time\discretionary {-}{}{}\_\discretionary {-}{}{}stamp}, + \hyperpage{175} + \subitem {unpack\discretionary {-}{}{}\_\discretionary {-}{}{}structure}, + \hyperpage{178} + \subitem {urn}, \hyperpage{175} + \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}A\discretionary {-}{}{}L\discretionary {-}{}{}L}, + \hyperpage{173} + \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}O\discretionary {-}{}{}T}, + \hyperpage{172} + \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G}, + \hyperpage{173} + \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}X}, + \hyperpage{172} + \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}T}, + \hyperpage{172} + \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}R\discretionary {-}{}{}O\discretionary {-}{}{}R}, + \hyperpage{171} + \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}C}, + \hyperpage{171} + \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}O\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}R\discretionary {-}{}{}E\discretionary {-}{}{}S\discretionary {-}{}{}T}, + \hyperpage{172} + \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}O\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}P\discretionary {-}{}{}A\discretionary {-}{}{}N}, + \hyperpage{172} + \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Q\discretionary {-}{}{}U\discretionary {-}{}{}I\discretionary {-}{}{}T}, + \hyperpage{171} + \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}E\discretionary {-}{}{}Q\discretionary {-}{}{}U\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}C\discretionary {-}{}{}E}, + \hyperpage{171} + \subitem {warn\discretionary {-}{}{}\_\discretionary {-}{}{}user}, + \hyperpage{175} + \subitem {X\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R}, + \hyperpage{173} + \subitem {xrealloc}, \hyperpage{174} + \subitem {xsubi}, \hyperpage{182} + + \indexspace + + \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}A\discretionary {-}{}{}L\discretionary {-}{}{}L} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173} + \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}O\discretionary {-}{}{}T} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172} + \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173} + \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}P\discretionary {-}{}{}I\discretionary {-}{}{}P\discretionary {-}{}{}E} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172} + \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}X} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172} + \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}T} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172} + \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}R\discretionary {-}{}{}O\discretionary {-}{}{}R} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{171} + \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}C} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{171} + \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}O\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}R\discretionary {-}{}{}E\discretionary {-}{}{}S\discretionary {-}{}{}T} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172} + \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}O\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}P\discretionary {-}{}{}A\discretionary {-}{}{}N} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172} + \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Q\discretionary {-}{}{}U\discretionary {-}{}{}I\discretionary {-}{}{}T} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{171} + \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}E\discretionary {-}{}{}Q\discretionary {-}{}{}U\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}C\discretionary {-}{}{}E} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{171} + + \indexspace + + \item {warn\discretionary {-}{}{}\_\discretionary {-}{}{}user} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{175} + \item {write\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file} + \subitem {Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File}, + \hyperpage{67} + + \indexspace + + \item {X\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173} + \item {xrealloc} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{174} + \item {xrna\discretionary {-}{}{}\_\discretionary {-}{}{}plot} + \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h}, + \hyperpage{159} + \item {xsubi} + \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{182} + + \indexspace + + \item {zukersubopt} + \subitem {Suboptimal structures according to Zuker et al. 1989}, + \hyperpage{36} + +\end{theindex} diff --git a/binaries/src/ViennaRNA/doc/latex/refman.log b/binaries/src/ViennaRNA/doc/latex/refman.log new file mode 100644 index 0000000..1177aaa --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/refman.log @@ -0,0 +1,4018 @@ +This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian) 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b/binaries/src/ViennaRNA/doc/latex/refman.tex new file mode 100644 index 0000000..792b091 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/refman.tex @@ -0,0 +1,205 @@ +\batchmode +\documentclass{book} +\usepackage[a4paper,top=2.5cm,bottom=2.5cm,left=2.5cm,right=2.5cm]{geometry} +\usepackage{makeidx} +\usepackage{natbib} +\usepackage{graphicx} +\usepackage{multicol} +\usepackage{float} +\usepackage{listings} +\usepackage{color} +\usepackage{ifthen} +\usepackage[table]{xcolor} +\usepackage{textcomp} +\usepackage{alltt} +\usepackage{ifpdf} +\ifpdf +\usepackage[pdftex, + pagebackref=true, + colorlinks=true, + linkcolor=blue, + unicode + ]{hyperref} +\else +\usepackage[ps2pdf, + pagebackref=true, + colorlinks=true, + linkcolor=blue, + unicode + ]{hyperref} +\usepackage{pspicture} +\fi +\usepackage[utf8]{inputenc} +\usepackage{mathptmx} +\usepackage[scaled=.90]{helvet} +\usepackage{courier} +\usepackage{sectsty} +\usepackage{amssymb} +\usepackage[titles]{tocloft} +\usepackage{doxygen} +\lstset{language=C++,inputencoding=utf8,basicstyle=\footnotesize,breaklines=true,breakatwhitespace=true,tabsize=2,numbers=left } +\makeindex +\setcounter{tocdepth}{3} +\renewcommand{\footrulewidth}{0.4pt} +\renewcommand{\familydefault}{\sfdefault} +\hfuzz=15pt +\setlength{\emergencystretch}{15pt} +\hbadness=750 +\tolerance=750 +\begin{document} +\hypersetup{pageanchor=false,citecolor=blue} +\begin{titlepage} +\vspace*{7cm} +\begin{center} +{\Large R\-N\-Alib-\/2.1.2 }\\ +\vspace*{1cm} +{\large Generated by Doxygen 1.8.3.1}\\ +\vspace*{0.5cm} +{\small Thu Sep 5 2013 11:51:49}\\ +\end{center} +\end{titlepage} +\clearemptydoublepage +\pagenumbering{roman} +\tableofcontents +\clearemptydoublepage +\pagenumbering{arabic} +\hypersetup{pageanchor=true,citecolor=blue} +\chapter{Vienna\-R\-N\-A Package core -\/ R\-N\-Alib} +\label{index}\hypertarget{index}{}\input{index} +\chapter{Parsing and Comparing -\/ Functions to Manipulate Structures} +\label{mp_parse} +\hypertarget{mp_parse}{} +\input{mp_parse} +\chapter{Utilities -\/ Odds and Ends} +\label{mp_utils} +\hypertarget{mp_utils}{} +\input{mp_utils} +\chapter{Example -\/ A Small Example Program} +\label{mp_example} +\hypertarget{mp_example}{} +\input{mp_example} +\chapter{Deprecated List} +\label{deprecated} +\hypertarget{deprecated}{} +\input{deprecated} +\chapter{Module Index} +\input{modules} +\chapter{Data Structure Index} +\input{annotated} +\chapter{File Index} +\input{files} +\chapter{Module Documentation} +\input{group__folding__routines} +\include{group__mfe__fold} +\include{group__pf__fold} +\include{group__mea__fold} +\include{group__centroid__fold} +\include{group__subopt__fold} +\include{group__subopt__zuker} +\include{group__subopt__wuchty} +\include{group__subopt__stochbt} +\include{group__cofold} +\include{group__mfe__cofold} +\include{group__pf__cofold} +\include{group__up__cofold} +\include{group__consensus__fold} +\include{group__consensus__mfe__fold} +\include{group__consensus__pf__fold} +\include{group__consensus__stochbt} +\include{group__local__fold} +\include{group__local__mfe__fold} +\include{group__local__pf__fold} +\include{group__local__consensus__fold} +\include{group__energy__parameters} +\include{group__energy__parameters__rw} +\include{group__energy__parameters__convert} +\include{group__eval} +\include{group__inverse__fold} +\include{group__class__fold} +\include{group__kl__neighborhood} +\include{group__kl__neighborhood__mfe} +\include{group__kl__neighborhood__pf} +\include{group__kl__neighborhood__stochbt} +\include{group__dos} +\include{group__parse} +\chapter{Data Structure Documentation} +\input{structbondT} +\input{structbondTEn} +\input{structcofoldF} +\input{structConcEnt} +\input{structconstrain} +\input{structCOORDINATE} +\input{structcpair} +\input{structduplexT} +\input{structdupVar} +\input{structfolden} +\input{structinteract} +\input{structintermediate__t} +\input{structINTERVAL} +\input{structLIST} +\input{structLST__BUCKET} +\input{structmodel__detailsT} +\input{structmove__t} +\input{structPAIR} +\input{structpair__info} +\input{structpairpro} +\input{structparamT} +\input{structpath__t} +\input{structpf__paramT} +\input{structplist} +\input{structPostorder__list} +\input{structpu__contrib} +\input{structpu__out} +\input{structsect} +\input{structsnoopT} +\input{structSOLUTION} +\input{structstruct__en} +\input{structsvm__model} +\input{structswString} +\input{structTree} +\input{structTwoDfold__solution} +\input{structTwoDfold__vars} +\input{structTwoDpfold__solution} +\input{structTwoDpfold__vars} +\chapter{File Documentation} +\input{2Dfold_8h} +\input{2Dpfold_8h} +\input{alifold_8h} +\input{cofold_8h} +\input{convert__epars_8h} +\input{data__structures_8h} +\input{dist__vars_8h} +\input{duplex_8h} +\input{edit__cost_8h} +\input{energy__const_8h} +\input{findpath_8h} +\input{fold_8h} +\input{fold__vars_8h} +\input{gquad_8h} +\input{inverse_8h} +\input{Lfold_8h} +\input{loop__energies_8h} +\input{LPfold_8h} +\input{MEA_8h} +\input{mm_8h} +\input{naview_8h} +\input{params_8h} +\input{part__func_8h} +\input{part__func__co_8h} +\input{part__func__up_8h} +\input{plot__layouts_8h} +\input{profiledist_8h} +\input{PS__dot_8h} +\input{read__epars_8h} +\input{RNAstruct_8h} +\input{stringdist_8h} +\input{subopt_8h} +\input{treedist_8h} +\input{utils_8h} +\input{1_88_84__epars_8h} +\input{1_88_84__intloops_8h} +\newpage \bibliographystyle{plain} +\bibliography{viennarna} +\addcontentsline{toc}{part}{Index} +\printindex +\end{document} diff --git a/binaries/src/ViennaRNA/doc/latex/refman.toc b/binaries/src/ViennaRNA/doc/latex/refman.toc new file mode 100644 index 0000000..945f189 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/refman.toc @@ -0,0 +1,530 @@ +\contentsline {chapter}{\numberline {1}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A Package core -\/ R\discretionary {-}{}{}N\discretionary {-}{}{}Alib}{1}{chapter.1} +\contentsline {section}{\numberline {1.1}Introduction}{1}{section.1.1} +\contentsline {chapter}{\numberline {2}Parsing and Comparing -\/ Functions to Manipulate Structures}{3}{chapter.2} +\contentsline {chapter}{\numberline {3}Utilities -\/ Odds and Ends}{5}{chapter.3} +\contentsline {section}{\numberline {3.1}Producing secondary structure graphs}{5}{section.3.1} +\contentsline {chapter}{\numberline {4}Example -\/ A Small Example Program}{7}{chapter.4} +\contentsline {chapter}{\numberline {5}Deprecated List}{9}{chapter.5} +\contentsline {chapter}{\numberline {6}Module Index}{11}{chapter.6} +\contentsline {section}{\numberline {6.1}Modules}{11}{section.6.1} +\contentsline {chapter}{\numberline {7}Data Structure Index}{13}{chapter.7} +\contentsline {section}{\numberline {7.1}Data Structures}{13}{section.7.1} +\contentsline {chapter}{\numberline {8}File Index}{15}{chapter.8} +\contentsline {section}{\numberline {8.1}File List}{15}{section.8.1} +\contentsline {chapter}{\numberline {9}Module Documentation}{19}{chapter.9} +\contentsline {section}{\numberline {9.1}R\discretionary {-}{}{}N\discretionary {-}{}{}A Secondary Structure Folding}{19}{section.9.1} +\contentsline {subsection}{\numberline {9.1.1}Detailed Description}{21}{subsection.9.1.1} +\contentsline {section}{\numberline {9.2}Calculating Minimum Free Energy (M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures}{22}{section.9.2} +\contentsline {subsection}{\numberline {9.2.1}Detailed Description}{22}{subsection.9.2.1} +\contentsline {subsection}{\numberline {9.2.2}Function Documentation}{23}{subsection.9.2.2} +\contentsline {subsubsection}{\numberline {9.2.2.1}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}{23}{subsubsection.9.2.2.1} +\contentsline {subsubsection}{\numberline {9.2.2.2}fold}{24}{subsubsection.9.2.2.2} +\contentsline {subsubsection}{\numberline {9.2.2.3}circfold}{24}{subsubsection.9.2.2.3} +\contentsline {section}{\numberline {9.3}Calculating Partition Functions and Pair Probabilities}{25}{section.9.3} +\contentsline {subsection}{\numberline {9.3.1}Detailed Description}{26}{subsection.9.3.1} +\contentsline {subsection}{\numberline {9.3.2}Function Documentation}{26}{subsection.9.3.2} +\contentsline {subsubsection}{\numberline {9.3.2.1}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}{26}{subsubsection.9.3.2.1} +\contentsline {subsubsection}{\numberline {9.3.2.2}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{27}{subsubsection.9.3.2.2} +\contentsline {subsubsection}{\numberline {9.3.2.3}pf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{28}{subsubsection.9.3.2.3} +\contentsline {subsubsection}{\numberline {9.3.2.4}free\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}{29}{subsubsection.9.3.2.4} +\contentsline {subsubsection}{\numberline {9.3.2.5}update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params}{29}{subsubsection.9.3.2.5} +\contentsline {subsubsection}{\numberline {9.3.2.6}export\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}{29}{subsubsection.9.3.2.6} +\contentsline {subsubsection}{\numberline {9.3.2.7}assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}pr}{30}{subsubsection.9.3.2.7} +\contentsline {subsubsection}{\numberline {9.3.2.8}get\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}{30}{subsubsection.9.3.2.8} +\contentsline {subsubsection}{\numberline {9.3.2.9}mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance}{30}{subsubsection.9.3.2.9} +\contentsline {subsubsection}{\numberline {9.3.2.10}mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance\discretionary {-}{}{}\_\discretionary {-}{}{}pr}{31}{subsubsection.9.3.2.10} +\contentsline {section}{\numberline {9.4}Compute the structure with maximum expected accuracy (M\discretionary {-}{}{}E\discretionary {-}{}{}A)}{32}{section.9.4} +\contentsline {section}{\numberline {9.5}Compute the centroid structure}{33}{section.9.5} +\contentsline {subsection}{\numberline {9.5.1}Detailed Description}{33}{subsection.9.5.1} +\contentsline {subsection}{\numberline {9.5.2}Function Documentation}{33}{subsection.9.5.2} +\contentsline {subsubsection}{\numberline {9.5.2.1}get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pl}{33}{subsubsection.9.5.2.1} +\contentsline {subsubsection}{\numberline {9.5.2.2}get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pr}{33}{subsubsection.9.5.2.2} +\contentsline {section}{\numberline {9.6}Enumerating Suboptimal Structures}{35}{section.9.6} +\contentsline {subsection}{\numberline {9.6.1}Detailed Description}{35}{subsection.9.6.1} +\contentsline {section}{\numberline {9.7}Suboptimal structures according to Zuker et al. 1989}{36}{section.9.7} +\contentsline {subsection}{\numberline {9.7.1}Detailed Description}{36}{subsection.9.7.1} +\contentsline {subsection}{\numberline {9.7.2}Function Documentation}{36}{subsection.9.7.2} +\contentsline {subsubsection}{\numberline {9.7.2.1}zukersubopt}{36}{subsubsection.9.7.2.1} +\contentsline {section}{\numberline {9.8}Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E}{37}{section.9.8} +\contentsline {subsection}{\numberline {9.8.1}Detailed Description}{37}{subsection.9.8.1} +\contentsline {subsection}{\numberline {9.8.2}Function Documentation}{37}{subsection.9.8.2} +\contentsline {subsubsection}{\numberline {9.8.2.1}subopt}{37}{subsubsection.9.8.2.1} +\contentsline {subsubsection}{\numberline {9.8.2.2}subopt\discretionary {-}{}{}\_\discretionary {-}{}{}circ}{38}{subsubsection.9.8.2.2} +\contentsline {section}{\numberline {9.9}Stochastic backtracking in the Ensemble}{39}{section.9.9} +\contentsline {subsection}{\numberline {9.9.1}Detailed Description}{39}{subsection.9.9.1} +\contentsline {subsection}{\numberline {9.9.2}Function Documentation}{39}{subsection.9.9.2} +\contentsline {subsubsection}{\numberline {9.9.2.1}pbacktrack}{39}{subsubsection.9.9.2.1} +\contentsline {subsubsection}{\numberline {9.9.2.2}pbacktrack\discretionary {-}{}{}\_\discretionary {-}{}{}circ}{40}{subsubsection.9.9.2.2} +\contentsline {subsection}{\numberline {9.9.3}Variable Documentation}{40}{subsection.9.9.3} +\contentsline {subsubsection}{\numberline {9.9.3.1}st\discretionary {-}{}{}\_\discretionary {-}{}{}back}{40}{subsubsection.9.9.3.1} +\contentsline {section}{\numberline {9.10}Calculate Secondary Structures of two R\discretionary {-}{}{}N\discretionary {-}{}{}As upon Dimerization}{41}{section.9.10} +\contentsline {subsection}{\numberline {9.10.1}Detailed Description}{41}{subsection.9.10.1} +\contentsline {section}{\numberline {9.11}M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}{42}{section.9.11} +\contentsline {subsection}{\numberline {9.11.1}Detailed Description}{42}{subsection.9.11.1} +\contentsline {subsection}{\numberline {9.11.2}Function Documentation}{42}{subsection.9.11.2} +\contentsline {subsubsection}{\numberline {9.11.2.1}cofold}{42}{subsubsection.9.11.2.1} +\contentsline {subsubsection}{\numberline {9.11.2.2}export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays\discretionary {-}{}{}\_\discretionary {-}{}{}gq}{43}{subsubsection.9.11.2.2} +\contentsline {subsubsection}{\numberline {9.11.2.3}export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}{43}{subsubsection.9.11.2.3} +\contentsline {section}{\numberline {9.12}Partition Function for two hybridized Sequences}{44}{section.9.12} +\contentsline {subsection}{\numberline {9.12.1}Detailed Description}{45}{subsection.9.12.1} +\contentsline {subsection}{\numberline {9.12.2}Function Documentation}{45}{subsection.9.12.2} +\contentsline {subsubsection}{\numberline {9.12.2.1}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{45}{subsubsection.9.12.2.1} +\contentsline {subsubsection}{\numberline {9.12.2.2}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}{45}{subsubsection.9.12.2.2} +\contentsline {subsubsection}{\numberline {9.12.2.3}export\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}{46}{subsubsection.9.12.2.3} 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{9.13.1}Detailed Description}{48}{subsection.9.13.1} +\contentsline {subsection}{\numberline {9.13.2}Function Documentation}{48}{subsection.9.13.2} +\contentsline {subsubsection}{\numberline {9.13.2.1}pf\discretionary {-}{}{}\_\discretionary {-}{}{}unstru}{48}{subsubsection.9.13.2.1} +\contentsline {subsubsection}{\numberline {9.13.2.2}pf\discretionary {-}{}{}\_\discretionary {-}{}{}interact}{49}{subsubsection.9.13.2.2} +\contentsline {section}{\numberline {9.14}Predicting Consensus Structures from Alignment(s)}{50}{section.9.14} +\contentsline {subsection}{\numberline {9.14.1}Detailed Description}{51}{subsection.9.14.1} +\contentsline {subsection}{\numberline {9.14.2}Function Documentation}{51}{subsection.9.14.2} +\contentsline {subsubsection}{\numberline {9.14.2.1}get\discretionary {-}{}{}\_\discretionary {-}{}{}mpi}{51}{subsubsection.9.14.2.1} +\contentsline {subsubsection}{\numberline {9.14.2.2}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary 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{9.14.3.1}cv\discretionary {-}{}{}\_\discretionary {-}{}{}fact}{53}{subsubsection.9.14.3.1} +\contentsline {subsubsection}{\numberline {9.14.3.2}nc\discretionary {-}{}{}\_\discretionary {-}{}{}fact}{53}{subsubsection.9.14.3.2} +\contentsline {section}{\numberline {9.15}M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)}{54}{section.9.15} +\contentsline {subsection}{\numberline {9.15.1}Detailed Description}{54}{subsection.9.15.1} +\contentsline {subsection}{\numberline {9.15.2}Function Documentation}{54}{subsection.9.15.2} +\contentsline {subsubsection}{\numberline {9.15.2.1}alifold}{54}{subsubsection.9.15.2.1} +\contentsline {subsubsection}{\numberline {9.15.2.2}circalifold}{54}{subsubsection.9.15.2.2} +\contentsline {section}{\numberline {9.16}Partition Function and Base Pair Probabilities for Sequence Alignment(s)}{56}{section.9.16} +\contentsline {subsection}{\numberline {9.16.1}Detailed Description}{56}{subsection.9.16.1} +\contentsline {subsection}{\numberline {9.16.2}Function Documentation}{56}{subsection.9.16.2} +\contentsline {subsubsection}{\numberline {9.16.2.1}alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}{56}{subsubsection.9.16.2.1} +\contentsline {subsubsection}{\numberline {9.16.2.2}alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{56}{subsubsection.9.16.2.2} +\contentsline {subsubsection}{\numberline {9.16.2.3}alipf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{57}{subsubsection.9.16.2.3} +\contentsline {subsubsection}{\numberline {9.16.2.4}export\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}{57}{subsubsection.9.16.2.4} +\contentsline {section}{\numberline {9.17}Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}{58}{section.9.17} +\contentsline {subsection}{\numberline {9.17.1}Detailed Description}{58}{subsection.9.17.1} +\contentsline {subsection}{\numberline {9.17.2}Function Documentation}{58}{subsection.9.17.2} +\contentsline {subsubsection}{\numberline {9.17.2.1}alipbacktrack}{58}{subsubsection.9.17.2.1} +\contentsline {section}{\numberline {9.18}Predicting Locally stable structures of large sequences}{59}{section.9.18} +\contentsline {subsection}{\numberline {9.18.1}Detailed Description}{59}{subsection.9.18.1} +\contentsline {section}{\numberline {9.19}Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores}{60}{section.9.19} +\contentsline {subsection}{\numberline {9.19.1}Detailed Description}{60}{subsection.9.19.1} +\contentsline {subsection}{\numberline {9.19.2}Function Documentation}{60}{subsection.9.19.2} +\contentsline {subsubsection}{\numberline {9.19.2.1}Lfold}{60}{subsubsection.9.19.2.1} +\contentsline {subsubsection}{\numberline {9.19.2.2}Lfoldz}{60}{subsubsection.9.19.2.2} +\contentsline {section}{\numberline {9.20}Partition functions for locally stable secondary structures}{61}{section.9.20} +\contentsline {subsection}{\numberline {9.20.1}Detailed Description}{61}{subsection.9.20.1} +\contentsline {subsection}{\numberline {9.20.2}Function Documentation}{61}{subsection.9.20.2} +\contentsline {subsubsection}{\numberline {9.20.2.1}update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}L\discretionary {-}{}{}P}{61}{subsubsection.9.20.2.1} +\contentsline {subsubsection}{\numberline {9.20.2.2}pfl\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{61}{subsubsection.9.20.2.2} +\contentsline {subsubsection}{\numberline {9.20.2.3}putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob}{62}{subsubsection.9.20.2.3} +\contentsline {subsubsection}{\numberline {9.20.2.4}putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob\discretionary {-}{}{}\_\discretionary {-}{}{}bin}{62}{subsubsection.9.20.2.4} +\contentsline {section}{\numberline {9.21}Local M\discretionary {-}{}{}F\discretionary {-}{}{}E consensus structures for Sequence Alignments}{63}{section.9.21} +\contentsline {subsection}{\numberline {9.21.1}Detailed Description}{63}{subsection.9.21.1} +\contentsline {subsection}{\numberline {9.21.2}Function Documentation}{63}{subsection.9.21.2} +\contentsline {subsubsection}{\numberline {9.21.2.1}ali\discretionary {-}{}{}Lfold}{63}{subsubsection.9.21.2.1} +\contentsline {section}{\numberline {9.22}Change and Precalculate Energy Parameter Sets and Boltzmann Factors}{64}{section.9.22} +\contentsline {subsection}{\numberline {9.22.1}Detailed Description}{64}{subsection.9.22.1} +\contentsline {subsection}{\numberline {9.22.2}Function Documentation}{65}{subsection.9.22.2} +\contentsline {subsubsection}{\numberline {9.22.2.1}scale\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}{65}{subsubsection.9.22.2.1} +\contentsline {subsubsection}{\numberline {9.22.2.2}get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}{65}{subsubsection.9.22.2.2} +\contentsline {subsubsection}{\numberline {9.22.2.3}get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}{65}{subsubsection.9.22.2.3} +\contentsline {subsubsection}{\numberline {9.22.2.4}get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factors}{65}{subsubsection.9.22.2.4} +\contentsline {subsubsection}{\numberline {9.22.2.5}get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factor\discretionary {-}{}{}\_\discretionary {-}{}{}copy}{66}{subsubsection.9.22.2.5} +\contentsline {section}{\numberline {9.23}Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File}{67}{section.9.23} +\contentsline {subsection}{\numberline {9.23.1}Detailed Description}{67}{subsection.9.23.1} +\contentsline {subsection}{\numberline {9.23.2}Function Documentation}{67}{subsection.9.23.2} +\contentsline {subsubsection}{\numberline {9.23.2.1}read\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}{67}{subsubsection.9.23.2.1} +\contentsline {subsubsection}{\numberline {9.23.2.2}write\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}{67}{subsubsection.9.23.2.2} +\contentsline {section}{\numberline {9.24}Converting energy parameter files}{69}{section.9.24} +\contentsline {subsection}{\numberline {9.24.1}Detailed Description}{69}{subsection.9.24.1} +\contentsline {subsection}{\numberline {9.24.2}Macro Definition Documentation}{70}{subsection.9.24.2} +\contentsline {subsubsection}{\numberline {9.24.2.1}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary 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{subsubsection}{\numberline {11.34.3.27}get\discretionary {-}{}{}\_\discretionary {-}{}{}indx}{181}{subsubsection.11.34.3.27} +\contentsline {subsubsection}{\numberline {11.34.3.28}constrain\discretionary {-}{}{}\_\discretionary {-}{}{}ptypes}{181}{subsubsection.11.34.3.28} +\contentsline {subsection}{\numberline {11.34.4}Variable Documentation}{182}{subsection.11.34.4} +\contentsline {subsubsection}{\numberline {11.34.4.1}xsubi}{182}{subsubsection.11.34.4.1} +\contentsline {section}{\numberline {11.35}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/lib/1.8.4\discretionary {-}{}{}\_\discretionary {-}{}{}epars.h File Reference}{182}{section.11.35} +\contentsline {subsection}{\numberline {11.35.1}Detailed Description}{182}{subsection.11.35.1} +\contentsline {section}{\numberline {11.36}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/lib/1.8.4\discretionary {-}{}{}\_\discretionary {-}{}{}intloops.h File Reference}{182}{section.11.36} +\contentsline {subsection}{\numberline {11.36.1}Detailed Description}{182}{subsection.11.36.1} +\contentsline {part}{Index}{183}{chapter*.131} diff --git a/binaries/src/ViennaRNA/doc/latex/ribo_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/ribo_8h_source.tex new file mode 100644 index 0000000..b237995 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/ribo_8h_source.tex @@ -0,0 +1,14 @@ +\hypertarget{ribo_8h}{\section{ribo.\-h} +\label{ribo_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/ribo.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/ribo.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_RIBOSUM\_H\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_RIBOSUM\_H\_\_} +00003 \textcolor{preprocessor}{} +00004 \textcolor{keywordtype}{float} **get\_ribosum(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **Alseq, +00005 \textcolor{keywordtype}{int} n\_seq, +00006 \textcolor{keywordtype}{int} length); +00007 +00008 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/snofold_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/snofold_8h_source.tex new file mode 100644 index 0000000..19c2572 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/snofold_8h_source.tex @@ -0,0 +1,57 @@ +\hypertarget{snofold_8h}{\section{snofold.\-h} +\label{snofold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/snofold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/snofold.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{comment}{/* function from fold.c */} +00002 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_SNOFOLD\_H\_\_} +00003 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_SNOFOLD\_H\_\_} +00004 \textcolor{preprocessor}{} +00005 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"} +00006 +00007 \textcolor{comment}{/* Normal fold */} +00008 +00012 \textcolor{keywordtype}{int} snofold( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence, +00013 \textcolor{keywordtype}{char} *structure, +00014 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_assym, +00015 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshold, +00016 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2, +00017 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2, +00018 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem, +00019 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem); +00024 \textcolor{keywordtype}{void} snofree\_arrays(\textcolor{keyword}{const} \textcolor{keywordtype}{int} length); \textcolor{comment}{/* free arrays for mfe folding */} +00025 \textcolor{keywordtype}{void} snoinitialize\_fold(\textcolor{keywordtype}{int} length); \textcolor{comment}{/* allocate arrays for folding */} +00026 \textcolor{keywordtype}{void} snoupdate\_fold\_params(\textcolor{keywordtype}{void}); \textcolor{comment}{/* recalculate parameters */} +00027 \textcolor{keywordtype}{int} snoloop\_energy(\textcolor{keywordtype}{short} *ptable, +00028 \textcolor{keywordtype}{short} *s, +00029 \textcolor{keywordtype}{short} *s1, +00030 \textcolor{keywordtype}{int} i); +00031 \textcolor{keywordtype}{void} snoexport\_fold\_arrays( \textcolor{keywordtype}{int} **indx\_p, +00032 \textcolor{keywordtype}{int} **mLoop\_p, +00033 \textcolor{keywordtype}{int} **cLoop, +00034 \hyperlink{structfolden}{folden} ***fold\_p, +00035 \hyperlink{structfolden}{folden} ***fold\_p\_XS); +00036 \textcolor{keywordtype}{char} * snobacktrack\_fold\_from\_pair( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence, +00037 \textcolor{keywordtype}{int} i, +00038 \textcolor{keywordtype}{int} j); +00039 \textcolor{comment}{/* alifold */} +00040 \textcolor{keywordtype}{float} alisnofold( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **strings, +00041 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_assym, +00042 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, +00043 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2, +00044 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2, +00045 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem, +00046 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem); +00047 \textcolor{keywordtype}{void} alisnofree\_arrays(\textcolor{keyword}{const} \textcolor{keywordtype}{int} length); +00048 \textcolor{keywordtype}{char} *alisnobacktrack\_fold\_from\_pair(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequence, +00049 \textcolor{keywordtype}{int} i, +00050 \textcolor{keywordtype}{int} j, +00051 \textcolor{keywordtype}{int} *cov); +00052 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} \hyperlink{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{cv\_fact} \textcolor{comment}{/* =1 */}; +00053 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} \hyperlink{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{nc\_fact} \textcolor{comment}{/* =1 */}; +00054 +00055 \textcolor{comment}{/* max number of mismatch >>>>>..(( )).>>>> */} +00056 \textcolor{preprocessor}{#define MISMATCH 3} +00057 \textcolor{preprocessor}{} +00058 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/snoop_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/snoop_8h_source.tex new file mode 100644 index 0000000..872efc5 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/snoop_8h_source.tex @@ -0,0 +1,240 @@ +\hypertarget{snoop_8h}{\section{snoop.\-h} +\label{snoop_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/snoop.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/snoop.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_SNOOP\_H\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_SNOOP\_H\_\_} +00003 \textcolor{preprocessor}{} +00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"} +00009 \hyperlink{structsnoopT}{snoopT} snoopfold( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1, +00010 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2, +00011 \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty, +00012 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, +00013 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE, +00014 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE, +00015 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE, +00016 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD, +00017 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem, +00018 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem, +00019 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2, +00020 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2, +00021 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1, +00022 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1, +00023 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1, +00024 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2, +00025 \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy); +00026 +00032 \hyperlink{structsnoopT}{snoopT} *snoop\_subopt( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1, +00033 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2, +00034 \textcolor{keywordtype}{int} delta, +00035 \textcolor{keywordtype}{int} w, +00036 \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty, +00037 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, +00038 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE, +00039 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE, +00040 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE, +00041 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE, +00042 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE, +00043 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD, +00044 \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance, +00045 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem, +00046 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem, +00047 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2, +00048 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2, +00049 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1, +00050 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1, +00051 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1, +00052 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2, +00053 \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy); +00054 +00061 \textcolor{keywordtype}{void} Lsnoop\_subopt( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1, +00062 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2, +00063 \textcolor{keywordtype}{int} delta, +00064 \textcolor{keywordtype}{int} w, +00065 \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty, +00066 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, +00067 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE, +00068 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE, +00069 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE, +00070 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE, +00071 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE, +00072 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD, +00073 \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance, +00074 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem, +00075 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem, +00076 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2, +00077 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2, +00078 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1, +00079 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1, +00080 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1, +00081 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2, +00082 \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length, +00083 \textcolor{keyword}{const} \textcolor{keywordtype}{char}* name, +00084 \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy); +00085 +00092 \textcolor{keywordtype}{void} Lsnoop\_subopt\_list ( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1, +00093 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2, +00094 \textcolor{keywordtype}{int} delta, +00095 \textcolor{keywordtype}{int} w, +00096 \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty, +00097 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, +00098 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE, +00099 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE, +00100 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE, +00101 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE, +00102 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE, +00103 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD, +00104 \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance, +00105 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem, +00106 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem, +00107 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2, +00108 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2, +00109 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1, +00110 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1, +00111 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1, +00112 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2, +00113 \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length, +00114 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *name, +00115 \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy); +00116 +00122 \textcolor{keywordtype}{void} Lsnoop\_subopt\_list\_XS (\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1, +00123 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2, +00124 \textcolor{keyword}{const} \textcolor{keywordtype}{int} **access\_s1, +00125 \textcolor{keywordtype}{int} delta, +00126 \textcolor{keywordtype}{int} w, +00127 \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty, +00128 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, +00129 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE, +00130 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE, +00131 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE, +00132 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE, +00133 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE, +00134 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD, +00135 \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance, +00136 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem, +00137 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem, +00138 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2, +00139 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2, +00140 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1, +00141 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1, +00142 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1, +00143 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2, +00144 \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length, +00145 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *name, +00146 \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy); +00147 +00148 +00154 \textcolor{keywordtype}{void} snoop\_subopt\_XS (\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1, +00155 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2, +00156 \textcolor{keyword}{const} \textcolor{keywordtype}{int} **access\_s1, +00157 \textcolor{keywordtype}{int} delta, +00158 \textcolor{keywordtype}{int} w, +00159 \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty, +00160 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, +00161 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE, +00162 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE, +00163 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE, +00164 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE, +00165 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE, +00166 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD, +00167 \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance, +00168 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem, +00169 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem, +00170 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2, +00171 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2, +00172 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1, +00173 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1, +00174 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1, +00175 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2, +00176 \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length, +00177 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *name, +00178 \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy); +00179 +00184 \hyperlink{structsnoopT}{snoopT} *alisnoop\_subopt(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **s1, +00185 \textcolor{keyword}{const} \textcolor{keywordtype}{char} **s2, +00186 \textcolor{keywordtype}{int} delta, +00187 \textcolor{keywordtype}{int} w, +00188 \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty, +00189 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, +00190 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE, +00191 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE, +00192 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE, +00193 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE, +00194 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE, +00195 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD, +00196 \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance, +00197 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem, +00198 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem, +00199 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2, +00200 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2, +00201 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1, +00202 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1, +00203 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1, +00204 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2); +00205 +00212 \hyperlink{structsnoopT}{snoopT} *aliLsnoop\_subopt\_list ( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **s1, +00213 \textcolor{keyword}{const} \textcolor{keywordtype}{char} **s2, +00214 \textcolor{keywordtype}{int} delta, +00215 \textcolor{keywordtype}{int} w, +00216 \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty, +00217 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, +00218 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE, +00219 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE, +00220 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE, +00221 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshTE, +00222 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshSE, +00223 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD, +00224 \textcolor{keyword}{const} \textcolor{keywordtype}{int} distance, +00225 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem, +00226 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem, +00227 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2, +00228 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2, +00229 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1, +00230 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1, +00231 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1, +00232 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2, +00233 \textcolor{keyword}{const} \textcolor{keywordtype}{int} alignment\_length); +00239 \hyperlink{structsnoopT}{snoopT} alisnoopfold(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **s1, +00240 \textcolor{keyword}{const} \textcolor{keywordtype}{char} **s2, +00241 \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty, +00242 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, +00243 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE, +00244 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE, +00245 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE, +00246 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD, +00247 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem, +00248 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem, +00249 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2, +00250 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2, +00251 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1, +00252 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1, +00253 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1, +00254 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2); +00259 \hyperlink{structsnoopT}{snoopT} snoopfold\_XS(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1, +00260 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2, +00261 \textcolor{keyword}{const} \textcolor{keywordtype}{int} **access\_s1, +00262 \textcolor{keyword}{const} \textcolor{keywordtype}{int} pos, +00263 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_pos\_j, +00264 \textcolor{keyword}{const} \textcolor{keywordtype}{int} penalty, +00265 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, +00266 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshLE, +00267 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshRE, +00268 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshDE, +00269 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshD, +00270 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem, +00271 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem, +00272 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2, +00273 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2, +00274 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s1, +00275 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s1, +00276 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d1, +00277 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_d2, +00278 \textcolor{keyword}{const} \textcolor{keywordtype}{int} fullStemEnergy); +00279 +00280 +00281 +00282 +00283 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} snoop\_subopt\_sorted; +00284 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/stringdist_8h.tex b/binaries/src/ViennaRNA/doc/latex/stringdist_8h.tex new file mode 100644 index 0000000..a33fc78 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/stringdist_8h.tex @@ -0,0 +1,70 @@ +\hypertarget{stringdist_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/stringdist.h File Reference} +\label{stringdist_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/stringdist.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/stringdist.\-h}} +} + + +Functions for String Alignment. + + +Include dependency graph for stringdist.\-h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{stringdist_8h__incl} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +\hyperlink{structswString}{sw\-String} $\ast$ \hyperlink{stringdist_8h_a3125991b3a403b3f89230474deb3f22e}{Make\-\_\-sw\-String} (char $\ast$string) +\begin{DoxyCompactList}\small\item\em Convert a structure into a format suitable for \hyperlink{stringdist_8h_a89e3c335ef17780576d7c0e713830db9}{string\-\_\-edit\-\_\-distance()}. \end{DoxyCompactList}\item +float \hyperlink{stringdist_8h_a89e3c335ef17780576d7c0e713830db9}{string\-\_\-edit\-\_\-distance} (\hyperlink{structswString}{sw\-String} $\ast$T1, \hyperlink{structswString}{sw\-String} $\ast$T2) +\begin{DoxyCompactList}\small\item\em Calculate the string edit distance of T1 and T2. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Functions for String Alignment. + +\subsection{Function Documentation} +\hypertarget{stringdist_8h_a3125991b3a403b3f89230474deb3f22e}{\index{stringdist.\-h@{stringdist.\-h}!Make\-\_\-sw\-String@{Make\-\_\-sw\-String}} +\index{Make\-\_\-sw\-String@{Make\-\_\-sw\-String}!stringdist.h@{stringdist.\-h}} +\subsubsection[{Make\-\_\-sw\-String}]{\setlength{\rightskip}{0pt plus 5cm}{\bf sw\-String}$\ast$ Make\-\_\-sw\-String ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{string} +\end{DoxyParamCaption} +)}}\label{stringdist_8h_a3125991b3a403b3f89230474deb3f22e} + + +Convert a structure into a format suitable for \hyperlink{stringdist_8h_a89e3c335ef17780576d7c0e713830db9}{string\-\_\-edit\-\_\-distance()}. + + +\begin{DoxyParams}{Parameters} +{\em string} & \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} + +\end{DoxyReturn} +\hypertarget{stringdist_8h_a89e3c335ef17780576d7c0e713830db9}{\index{stringdist.\-h@{stringdist.\-h}!string\-\_\-edit\-\_\-distance@{string\-\_\-edit\-\_\-distance}} +\index{string\-\_\-edit\-\_\-distance@{string\-\_\-edit\-\_\-distance}!stringdist.h@{stringdist.\-h}} +\subsubsection[{string\-\_\-edit\-\_\-distance}]{\setlength{\rightskip}{0pt plus 5cm}float string\-\_\-edit\-\_\-distance ( +\begin{DoxyParamCaption} +\item[{{\bf sw\-String} $\ast$}]{T1, } +\item[{{\bf sw\-String} $\ast$}]{T2} +\end{DoxyParamCaption} +)}}\label{stringdist_8h_a89e3c335ef17780576d7c0e713830db9} + + +Calculate the string edit distance of T1 and T2. + + +\begin{DoxyParams}{Parameters} +{\em T1} & \\ +\hline +{\em T2} & \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} + +\end{DoxyReturn} diff --git a/binaries/src/ViennaRNA/doc/latex/stringdist_8h__incl.md5 b/binaries/src/ViennaRNA/doc/latex/stringdist_8h__incl.md5 new file mode 100644 index 0000000..85d3305 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/stringdist_8h__incl.md5 @@ -0,0 +1 @@ +6ec489e18b334b0e836d67591fb5d937 \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/stringdist_8h__incl.pdf b/binaries/src/ViennaRNA/doc/latex/stringdist_8h__incl.pdf new file mode 100644 index 0000000000000000000000000000000000000000..de831e4ca229f9ca898631ec6f53f6750519213c GIT binary patch literal 7354 zcmb7JcRZWj+pnrolrFSptfE$kBu3SUQEJbc6%nIGh}fH|+N-ENT6@)2t5mJ3^;l7A zucBIN6vdn9_&v|l-{;qh3u+%Y?aO}=A z3DZz&R(}ck!cu06&0TU$Al-gYLB`i9LA6U(>hC?XE_Fp5*vt_Ka9Y1$qix*FYN-;t zDb{u`jHkeW5>_(}%pGcc_pK`>JIVTL=6D9XMhS^B%r4Vx*mlkbEm{5gpsIxuQAL00 z>-C0CZtcSOtD=!I;e1Y`gN0jU2)<(VN~DKQLV|Y2g2Y(f;LR5vl4gZxSJ&h7V$$xG z*FLTE&Qf8AnyU?GFzv4G&ZmFJ-nipljj&VqR`a7&xzh;HTv;4;sbgO`e{hB(R^sRj 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+\label{stringdist_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/stringdist.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/stringdist.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_STRING\_DIST\_H\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_STRING\_DIST\_H\_\_} +00003 \textcolor{preprocessor}{} +00009 \textcolor{preprocessor}{#include "\hyperlink{dist__vars_8h}{dist\_vars.h}"} +00010 +00011 +00018 \hyperlink{structswString}{swString} *\hyperlink{stringdist_8h_a3125991b3a403b3f89230474deb3f22e}{Make\_swString}(\textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}); +00019 +00027 \textcolor{keywordtype}{float} \hyperlink{stringdist_8h_a89e3c335ef17780576d7c0e713830db9}{string\_edit\_distance}( \hyperlink{structswString}{swString} *T1, +00028 \hyperlink{structswString}{swString} *T2); +00029 +00030 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/structCOORDINATE.tex b/binaries/src/ViennaRNA/doc/latex/structCOORDINATE.tex new file mode 100644 index 0000000..9be95e3 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structCOORDINATE.tex @@ -0,0 +1,16 @@ +\hypertarget{structCOORDINATE}{\section{C\-O\-O\-R\-D\-I\-N\-A\-T\-E Struct Reference} +\label{structCOORDINATE}\index{C\-O\-O\-R\-D\-I\-N\-A\-T\-E@{C\-O\-O\-R\-D\-I\-N\-A\-T\-E}} +} + + +this is a workarround for the S\-W\-I\-G Perl Wrapper R\-N\-A plot function that returns an array of type \hyperlink{structCOORDINATE}{C\-O\-O\-R\-D\-I\-N\-A\-T\-E} + + + + +\subsection{Detailed Description} +this is a workarround for the S\-W\-I\-G Perl Wrapper R\-N\-A plot function that returns an array of type \hyperlink{structCOORDINATE}{C\-O\-O\-R\-D\-I\-N\-A\-T\-E} + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structConcEnt.tex b/binaries/src/ViennaRNA/doc/latex/structConcEnt.tex new file mode 100644 index 0000000..a0eb950 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structConcEnt.tex @@ -0,0 +1,20 @@ +\hypertarget{structConcEnt}{\section{Conc\-Ent Struct Reference} +\label{structConcEnt}\index{Conc\-Ent@{Conc\-Ent}} +} +\subsection*{Data Fields} +\begin{DoxyCompactItemize} +\item +\hypertarget{structConcEnt_adcf4d93c7efeaa4e6c4154b64d367681}{double \hyperlink{structConcEnt_adcf4d93c7efeaa4e6c4154b64d367681}{A0}}\label{structConcEnt_adcf4d93c7efeaa4e6c4154b64d367681} + +\begin{DoxyCompactList}\small\item\em start concentration A \end{DoxyCompactList}\item +\hypertarget{structConcEnt_add4c33b94b34e847fbf5838b04cce346}{double \hyperlink{structConcEnt_add4c33b94b34e847fbf5838b04cce346}{B0}}\label{structConcEnt_add4c33b94b34e847fbf5838b04cce346} + +\begin{DoxyCompactList}\small\item\em start concentration B \end{DoxyCompactList}\item +\hypertarget{structConcEnt_ac59c07a31d844e7b05bcdc05c4413b19}{double \hyperlink{structConcEnt_ac59c07a31d844e7b05bcdc05c4413b19}{A\-Bc}}\label{structConcEnt_ac59c07a31d844e7b05bcdc05c4413b19} + +\begin{DoxyCompactList}\small\item\em End concentration A\-B. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structINTERVAL.tex b/binaries/src/ViennaRNA/doc/latex/structINTERVAL.tex new file mode 100644 index 0000000..c481225 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structINTERVAL.tex @@ -0,0 +1,16 @@ +\hypertarget{structINTERVAL}{\section{I\-N\-T\-E\-R\-V\-A\-L Struct Reference} +\label{structINTERVAL}\index{I\-N\-T\-E\-R\-V\-A\-L@{I\-N\-T\-E\-R\-V\-A\-L}} +} + + +Sequence interval stack element used in subopt.\-c. + + + + +\subsection{Detailed Description} +Sequence interval stack element used in subopt.\-c. + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structLIST.tex b/binaries/src/ViennaRNA/doc/latex/structLIST.tex new file mode 100644 index 0000000..6d76cfd --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structLIST.tex @@ -0,0 +1,18 @@ +\hypertarget{structLIST}{\section{L\-I\-S\-T Struct Reference} +\label{structLIST}\index{L\-I\-S\-T@{L\-I\-S\-T}} +} + + +Collaboration diagram for L\-I\-S\-T\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=197pt]{structLIST__coll__graph} +\end{center} +\end{figure} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/list.\-h\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structLIST__coll__graph.md5 b/binaries/src/ViennaRNA/doc/latex/structLIST__coll__graph.md5 new file mode 100644 index 0000000..ef04b42 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structLIST__coll__graph.md5 @@ -0,0 +1 @@ +d26879f1cbf89a65eb95b12cdca8fcef \ No newline at end of file diff --git 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a/binaries/src/ViennaRNA/doc/latex/structPostorder__list.tex b/binaries/src/ViennaRNA/doc/latex/structPostorder__list.tex new file mode 100644 index 0000000..ee46eb1 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structPostorder__list.tex @@ -0,0 +1,8 @@ +\hypertarget{structPostorder__list}{\section{Postorder\-\_\-list Struct Reference} +\label{structPostorder__list}\index{Postorder\-\_\-list@{Postorder\-\_\-list}} +} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{dist__vars_8h}{dist\-\_\-vars.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structSOLUTION.tex b/binaries/src/ViennaRNA/doc/latex/structSOLUTION.tex new file mode 100644 index 0000000..6b3c9bd --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structSOLUTION.tex @@ -0,0 +1,25 @@ +\hypertarget{structSOLUTION}{\section{S\-O\-L\-U\-T\-I\-O\-N Struct Reference} +\label{structSOLUTION}\index{S\-O\-L\-U\-T\-I\-O\-N@{S\-O\-L\-U\-T\-I\-O\-N}} +} + + +Solution element from subopt.\-c. + + +\subsection*{Data Fields} +\begin{DoxyCompactItemize} +\item +\hypertarget{structSOLUTION_a4fe8e9027171f2dc4031587d7fab6b87}{float \hyperlink{structSOLUTION_a4fe8e9027171f2dc4031587d7fab6b87}{energy}}\label{structSOLUTION_a4fe8e9027171f2dc4031587d7fab6b87} + +\begin{DoxyCompactList}\small\item\em Free Energy of structure in kcal/mol. \end{DoxyCompactList}\item +\hypertarget{structSOLUTION_a89ae453dfad0509468c39a62c303a63b}{char $\ast$ \hyperlink{structSOLUTION_a89ae453dfad0509468c39a62c303a63b}{structure}}\label{structSOLUTION_a89ae453dfad0509468c39a62c303a63b} + +\begin{DoxyCompactList}\small\item\em Structure in dot-\/bracket notation. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Solution element from subopt.\-c. + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structTree.tex b/binaries/src/ViennaRNA/doc/latex/structTree.tex new file mode 100644 index 0000000..2ac3cfe --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structTree.tex @@ -0,0 +1,18 @@ +\hypertarget{structTree}{\section{Tree Struct Reference} +\label{structTree}\index{Tree@{Tree}} +} + + +Collaboration diagram for Tree\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=177pt]{structTree__coll__graph} +\end{center} +\end{figure} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item 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\hyperlink{structTwoDfold__solution_a298767110e07490d361bf7da920fd153}{k}}\label{structTwoDfold__solution_a298767110e07490d361bf7da920fd153} + +\begin{DoxyCompactList}\small\item\em Distance to first reference. \end{DoxyCompactList}\item +\hypertarget{structTwoDfold__solution_a64fb28259cf925c3bba7b8d14592363a}{int \hyperlink{structTwoDfold__solution_a64fb28259cf925c3bba7b8d14592363a}{l}}\label{structTwoDfold__solution_a64fb28259cf925c3bba7b8d14592363a} + +\begin{DoxyCompactList}\small\item\em Distance to second reference. \end{DoxyCompactList}\item +\hypertarget{structTwoDfold__solution_a3f65891d0c931f88440150bb32bcf753}{float \hyperlink{structTwoDfold__solution_a3f65891d0c931f88440150bb32bcf753}{en}}\label{structTwoDfold__solution_a3f65891d0c931f88440150bb32bcf753} + +\begin{DoxyCompactList}\small\item\em Free energy in kcal/mol. \end{DoxyCompactList}\item +\hypertarget{structTwoDfold__solution_ac87e00bbdb13e0b6ef45c4f65608b416}{char $\ast$ \hyperlink{structTwoDfold__solution_ac87e00bbdb13e0b6ef45c4f65608b416}{s}}\label{structTwoDfold__solution_ac87e00bbdb13e0b6ef45c4f65608b416} + +\begin{DoxyCompactList}\small\item\em M\-F\-E representative structure in dot-\/bracket notation. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Solution element returned from Two\-Dfold\-List. + +This element contains free energy and structure for the appropriate kappa (k), lambda (l) neighborhood The datastructure contains two integer attributes 'k' and 'l' as well as an attribute 'en' of type float representing the free energy in kcal/mol and an attribute 's' of type char$\ast$ containg the secondary structure representative, + +A value of \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{I\-N\-F} in k denotes the end of a list + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__kl__neighborhood__mfe_ga47da790166020558d27323aef489703e}{Two\-Dfold\-List()} +\end{DoxySeeAlso} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structTwoDfold__vars.tex b/binaries/src/ViennaRNA/doc/latex/structTwoDfold__vars.tex new file mode 100644 index 0000000..9816bc9 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structTwoDfold__vars.tex @@ -0,0 +1,73 @@ +\hypertarget{structTwoDfold__vars}{\section{Two\-Dfold\-\_\-vars Struct Reference} +\label{structTwoDfold__vars}\index{Two\-Dfold\-\_\-vars@{Two\-Dfold\-\_\-vars}} +} + + +Variables compound for 2\-Dfold M\-F\-E folding. + + + + +Collaboration diagram for Two\-Dfold\-\_\-vars\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=183pt]{structTwoDfold__vars__coll__graph} +\end{center} +\end{figure} +\subsection*{Data Fields} +\begin{DoxyCompactItemize} +\item +\hypertarget{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26}{\hyperlink{structparamT}{param\-T} $\ast$ \hyperlink{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26}{P}}\label{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26} + +\begin{DoxyCompactList}\small\item\em Precomputed energy parameters and model details. \end{DoxyCompactList}\item +\hypertarget{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64}{int \hyperlink{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64}{do\-\_\-backtrack}}\label{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64} + +\begin{DoxyCompactList}\small\item\em Flag whether to do backtracing of the structure(s) or not. \end{DoxyCompactList}\item +\hypertarget{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208}{char $\ast$ \hyperlink{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208}{ptype}}\label{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208} + +\begin{DoxyCompactList}\small\item\em Precomputed array of pair types. \end{DoxyCompactList}\item +\hypertarget{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56}{char $\ast$ \hyperlink{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56}{sequence}}\label{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56} + +\begin{DoxyCompactList}\small\item\em The input sequence. \end{DoxyCompactList}\item +\hypertarget{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc}{short $\ast$ \hyperlink{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc}{S1}}\label{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc} + +\begin{DoxyCompactList}\small\item\em The input sequences in numeric form. \end{DoxyCompactList}\item +\hypertarget{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb}{unsigned int \hyperlink{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb}{max\-D1}}\label{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb} + +\begin{DoxyCompactList}\small\item\em Maximum allowed base pair distance to first reference. \end{DoxyCompactList}\item +\hypertarget{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4}{unsigned int \hyperlink{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4}{max\-D2}}\label{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4} + +\begin{DoxyCompactList}\small\item\em Maximum allowed base pair distance to second reference. \end{DoxyCompactList}\item +\hypertarget{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5}{unsigned int $\ast$ \hyperlink{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5}{mm1}}\label{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5} + +\begin{DoxyCompactList}\small\item\em Maximum matching matrix, reference struct 1 disallowed. \end{DoxyCompactList}\item +\hypertarget{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c}{unsigned int $\ast$ \hyperlink{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c}{mm2}}\label{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c} + +\begin{DoxyCompactList}\small\item\em Maximum matching matrix, reference struct 2 disallowed. \end{DoxyCompactList}\item +\hypertarget{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7}{int $\ast$ \hyperlink{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7}{my\-\_\-iindx}}\label{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7} + +\begin{DoxyCompactList}\small\item\em Index for moving in quadratic distancy dimensions. \end{DoxyCompactList}\item +\hypertarget{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18}{unsigned int $\ast$ \hyperlink{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18}{reference\-B\-Ps1}}\label{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18} + +\begin{DoxyCompactList}\small\item\em Matrix containing number of basepairs of reference structure1 in interval \mbox{[}i,j\mbox{]}. \end{DoxyCompactList}\item +\hypertarget{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f}{unsigned int $\ast$ \hyperlink{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f}{reference\-B\-Ps2}}\label{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f} + +\begin{DoxyCompactList}\small\item\em Matrix containing number of basepairs of reference structure2 in interval \mbox{[}i,j\mbox{]}. \end{DoxyCompactList}\item +\hypertarget{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0}{unsigned int $\ast$ \hyperlink{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0}{bpdist}}\label{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0} + +\begin{DoxyCompactList}\small\item\em Matrix containing base pair distance of reference structure 1 and 2 on interval \mbox{[}i,j\mbox{]}. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Variables compound for 2\-Dfold M\-F\-E folding. + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__kl__neighborhood__mfe_gac9284f132cf0eaa0a2f43590eda05488}{get\-\_\-\-Two\-Dfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__mfe_ga05bf4f31d216b1b160fd2d3d68e9b487}{destroy\-\_\-\-Two\-Dfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__mfe_ga47da790166020558d27323aef489703e}{Two\-Dfold\-List()} +\end{DoxySeeAlso} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structTwoDfold__vars__coll__graph.md5 b/binaries/src/ViennaRNA/doc/latex/structTwoDfold__vars__coll__graph.md5 new file mode 100644 index 0000000..cde1738 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structTwoDfold__vars__coll__graph.md5 @@ -0,0 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+\label{structTwoDpfold__solution}\index{Two\-Dpfold\-\_\-solution@{Two\-Dpfold\-\_\-solution}} +} + + +Solution element returned from Two\-Dpfold\-List. + + +\subsection*{Data Fields} +\begin{DoxyCompactItemize} +\item +\hypertarget{structTwoDpfold__solution_a40ad24e311b193866111623dd1331567}{int \hyperlink{structTwoDpfold__solution_a40ad24e311b193866111623dd1331567}{k}}\label{structTwoDpfold__solution_a40ad24e311b193866111623dd1331567} + +\begin{DoxyCompactList}\small\item\em Distance to first reference. \end{DoxyCompactList}\item +\hypertarget{structTwoDpfold__solution_aeaad6adc35413c76a2e2f18d96a6508c}{int \hyperlink{structTwoDpfold__solution_aeaad6adc35413c76a2e2f18d96a6508c}{l}}\label{structTwoDpfold__solution_aeaad6adc35413c76a2e2f18d96a6508c} + +\begin{DoxyCompactList}\small\item\em Distance to second reference. \end{DoxyCompactList}\item +\hypertarget{structTwoDpfold__solution_af0bf3071502b4a4fa81eeb6dfacef94c}{double \hyperlink{structTwoDpfold__solution_af0bf3071502b4a4fa81eeb6dfacef94c}{q}}\label{structTwoDpfold__solution_af0bf3071502b4a4fa81eeb6dfacef94c} + +\begin{DoxyCompactList}\small\item\em partition function \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Solution element returned from Two\-Dpfold\-List. + +This element contains the partition function for the appropriate kappa (k), lambda (l) neighborhood The datastructure contains two integer attributes 'k' and 'l' as well as an attribute 'q' of type \#\-F\-L\-T\-\_\-\-O\-R\-\_\-\-D\-B\-L + +A value of \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{I\-N\-F} in k denotes the end of a list + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List()} +\end{DoxySeeAlso} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structTwoDpfold__vars.tex b/binaries/src/ViennaRNA/doc/latex/structTwoDpfold__vars.tex new file mode 100644 index 0000000..01e0bd7 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structTwoDpfold__vars.tex @@ -0,0 +1,70 @@ +\hypertarget{structTwoDpfold__vars}{\section{Two\-Dpfold\-\_\-vars Struct Reference} +\label{structTwoDpfold__vars}\index{Two\-Dpfold\-\_\-vars@{Two\-Dpfold\-\_\-vars}} +} + + +Variables compound for 2\-Dfold partition function folding. + + + + +Collaboration diagram for Two\-Dpfold\-\_\-vars\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=184pt]{structTwoDpfold__vars__coll__graph} +\end{center} +\end{figure} +\subsection*{Data Fields} +\begin{DoxyCompactItemize} +\item +\hypertarget{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}{char $\ast$ \hyperlink{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}{ptype}}\label{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07} + +\begin{DoxyCompactList}\small\item\em Precomputed array of pair types. \end{DoxyCompactList}\item +\hypertarget{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}{char $\ast$ \hyperlink{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}{sequence}}\label{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6} + +\begin{DoxyCompactList}\small\item\em The input sequence. \end{DoxyCompactList}\item +\hypertarget{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}{short $\ast$ \hyperlink{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}{S1}}\label{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac} + +\begin{DoxyCompactList}\small\item\em The input sequences in numeric form. \end{DoxyCompactList}\item +\hypertarget{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}{unsigned int \hyperlink{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}{max\-D1}}\label{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef} + +\begin{DoxyCompactList}\small\item\em Maximum allowed base pair distance to first reference. \end{DoxyCompactList}\item +\hypertarget{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}{unsigned int \hyperlink{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}{max\-D2}}\label{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834} + +\begin{DoxyCompactList}\small\item\em Maximum allowed base pair distance to second reference. \end{DoxyCompactList}\item +\hypertarget{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}{int $\ast$ \hyperlink{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}{my\-\_\-iindx}}\label{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e} + +\begin{DoxyCompactList}\small\item\em Index for moving in quadratic distancy dimensions. \end{DoxyCompactList}\item +\hypertarget{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}{int $\ast$ \hyperlink{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}{jindx}}\label{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384} + +\begin{DoxyCompactList}\small\item\em Index for moving in the triangular matrix qm1. \end{DoxyCompactList}\item +\hypertarget{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}{unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}{reference\-B\-Ps1}}\label{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a} + +\begin{DoxyCompactList}\small\item\em Matrix containing number of basepairs of reference structure1 in interval \mbox{[}i,j\mbox{]}. \end{DoxyCompactList}\item +\hypertarget{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}{unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}{reference\-B\-Ps2}}\label{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f} + +\begin{DoxyCompactList}\small\item\em Matrix containing number of basepairs of reference structure2 in interval \mbox{[}i,j\mbox{]}. \end{DoxyCompactList}\item +\hypertarget{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}{unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}{bpdist}}\label{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff} + +\begin{DoxyCompactList}\small\item\em Matrix containing base pair distance of reference structure 1 and 2 on interval \mbox{[}i,j\mbox{]}. \end{DoxyCompactList}\item +\hypertarget{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}{unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}{mm1}}\label{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d} + +\begin{DoxyCompactList}\small\item\em Maximum matching matrix, reference struct 1 disallowed. \end{DoxyCompactList}\item +\hypertarget{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}{unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}{mm2}}\label{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269} + +\begin{DoxyCompactList}\small\item\em Maximum matching matrix, reference struct 2 disallowed. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Variables compound for 2\-Dfold partition function folding. + +\begin{DoxySeeAlso}{See Also} +\hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\-\_\-\-Two\-Dpfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E()}, \hyperlink{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{destroy\-\_\-\-Two\-Dpfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List()} +\end{DoxySeeAlso} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structTwoDpfold__vars__coll__graph.md5 b/binaries/src/ViennaRNA/doc/latex/structTwoDpfold__vars__coll__graph.md5 new file mode 100644 index 0000000..785c0e0 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structTwoDpfold__vars__coll__graph.md5 @@ -0,0 +1 @@ +5c75856983243498944e57f34bc52c72 \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/structTwoDpfold__vars__coll__graph.pdf b/binaries/src/ViennaRNA/doc/latex/structTwoDpfold__vars__coll__graph.pdf new file mode 100644 index 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b/binaries/src/ViennaRNA/doc/latex/structbondT.tex new file mode 100644 index 0000000..27b5759 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structbondT.tex @@ -0,0 +1,16 @@ +\hypertarget{structbondT}{\section{bond\-T Struct Reference} +\label{structbondT}\index{bond\-T@{bond\-T}} +} + + +Base pair. + + + + +\subsection{Detailed Description} +Base pair. + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structbondTEn.tex b/binaries/src/ViennaRNA/doc/latex/structbondTEn.tex new file mode 100644 index 0000000..9cbbbb9 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structbondTEn.tex @@ -0,0 +1,16 @@ +\hypertarget{structbondTEn}{\section{bond\-T\-En Struct Reference} +\label{structbondTEn}\index{bond\-T\-En@{bond\-T\-En}} +} + + +Base pair with associated energy. + + + + +\subsection{Detailed Description} +Base pair with associated energy. + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structcofoldF.tex b/binaries/src/ViennaRNA/doc/latex/structcofoldF.tex new file mode 100644 index 0000000..bbf3451 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structcofoldF.tex @@ -0,0 +1,26 @@ +\hypertarget{structcofoldF}{\section{cofold\-F Struct Reference} +\label{structcofoldF}\index{cofold\-F@{cofold\-F}} +} +\subsection*{Data Fields} +\begin{DoxyCompactItemize} +\item +\hypertarget{structcofoldF_af6c496438321eb8bb907a21de1915c23}{double \hyperlink{structcofoldF_af6c496438321eb8bb907a21de1915c23}{F0\-A\-B}}\label{structcofoldF_af6c496438321eb8bb907a21de1915c23} + +\begin{DoxyCompactList}\small\item\em Null model without Duplex\-Init. \end{DoxyCompactList}\item +\hypertarget{structcofoldF_a2ae1245ff4a93cd11f882f490f777cb7}{double \hyperlink{structcofoldF_a2ae1245ff4a93cd11f882f490f777cb7}{F\-A\-B}}\label{structcofoldF_a2ae1245ff4a93cd11f882f490f777cb7} + +\begin{DoxyCompactList}\small\item\em all states with Duplex\-Init correction \end{DoxyCompactList}\item +\hypertarget{structcofoldF_a4899a4f9b42e416baf46c5fe10751c45}{double \hyperlink{structcofoldF_a4899a4f9b42e416baf46c5fe10751c45}{Fc\-A\-B}}\label{structcofoldF_a4899a4f9b42e416baf46c5fe10751c45} + +\begin{DoxyCompactList}\small\item\em true hybrid states only \end{DoxyCompactList}\item +\hypertarget{structcofoldF_a460f3ba205c205e6f5ec27cc2e2eb2b2}{double \hyperlink{structcofoldF_a460f3ba205c205e6f5ec27cc2e2eb2b2}{F\-A}}\label{structcofoldF_a460f3ba205c205e6f5ec27cc2e2eb2b2} + +\begin{DoxyCompactList}\small\item\em monomer A \end{DoxyCompactList}\item +\hypertarget{structcofoldF_ad3e5466724f3987be9d6f388b8ee5129}{double \hyperlink{structcofoldF_ad3e5466724f3987be9d6f388b8ee5129}{F\-B}}\label{structcofoldF_ad3e5466724f3987be9d6f388b8ee5129} + +\begin{DoxyCompactList}\small\item\em monomer B \end{DoxyCompactList}\end{DoxyCompactItemize} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structconstrain.tex b/binaries/src/ViennaRNA/doc/latex/structconstrain.tex new file mode 100644 index 0000000..034f77a --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structconstrain.tex @@ -0,0 +1,16 @@ +\hypertarget{structconstrain}{\section{constrain Struct Reference} +\label{structconstrain}\index{constrain@{constrain}} +} + + +constraints for cofolding + + + + +\subsection{Detailed Description} +constraints for cofolding + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structcpair.tex b/binaries/src/ViennaRNA/doc/latex/structcpair.tex new file mode 100644 index 0000000..a408ce7 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structcpair.tex @@ -0,0 +1,16 @@ +\hypertarget{structcpair}{\section{cpair Struct Reference} +\label{structcpair}\index{cpair@{cpair}} +} + + +this datastructure is used as input parameter in functions of P\-S\-\_\-dot.\-c + + + + +\subsection{Detailed Description} +this datastructure is used as input parameter in functions of P\-S\-\_\-dot.\-c + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structdupVar.tex b/binaries/src/ViennaRNA/doc/latex/structdupVar.tex new file mode 100644 index 0000000..95dfd6c --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structdupVar.tex @@ -0,0 +1,8 @@ +\hypertarget{structdupVar}{\section{dup\-Var Struct Reference} +\label{structdupVar}\index{dup\-Var@{dup\-Var}} +} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structduplexT.tex b/binaries/src/ViennaRNA/doc/latex/structduplexT.tex new file mode 100644 index 0000000..03b456c --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structduplexT.tex @@ -0,0 +1,8 @@ +\hypertarget{structduplexT}{\section{duplex\-T Struct Reference} +\label{structduplexT}\index{duplex\-T@{duplex\-T}} +} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structfolden.tex b/binaries/src/ViennaRNA/doc/latex/structfolden.tex new file mode 100644 index 0000000..0027d0c --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structfolden.tex @@ -0,0 +1,8 @@ +\hypertarget{structfolden}{\section{folden Struct Reference} +\label{structfolden}\index{folden@{folden}} +} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structinteract.tex b/binaries/src/ViennaRNA/doc/latex/structinteract.tex new file mode 100644 index 0000000..d8881f6 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structinteract.tex @@ -0,0 +1,38 @@ +\hypertarget{structinteract}{\section{interact Struct Reference} +\label{structinteract}\index{interact@{interact}} +} +\subsection*{Data Fields} +\begin{DoxyCompactItemize} +\item +\hypertarget{structinteract_a1fc8b3860c083f164daa9712690a3a56}{double $\ast$ \hyperlink{structinteract_a1fc8b3860c083f164daa9712690a3a56}{Pi}}\label{structinteract_a1fc8b3860c083f164daa9712690a3a56} + +\begin{DoxyCompactList}\small\item\em probabilities of interaction \end{DoxyCompactList}\item +\hypertarget{structinteract_a54f8183542fff4c32ab7ace49a16c02c}{double $\ast$ \hyperlink{structinteract_a54f8183542fff4c32ab7ace49a16c02c}{Gi}}\label{structinteract_a54f8183542fff4c32ab7ace49a16c02c} + +\begin{DoxyCompactList}\small\item\em free energies of interaction \end{DoxyCompactList}\item +\hypertarget{structinteract_ad58303190f9e085c3ab59890cbf61223}{double \hyperlink{structinteract_ad58303190f9e085c3ab59890cbf61223}{Gikjl}}\label{structinteract_ad58303190f9e085c3ab59890cbf61223} + +\begin{DoxyCompactList}\small\item\em full free energy for interaction between \mbox{[}k,i\mbox{]} k$<$i in longer seq and \mbox{[}j,l\mbox{]} j$<$l in shorter seq \end{DoxyCompactList}\item +\hypertarget{structinteract_a41793812abae560805414761fec398fe}{double \hyperlink{structinteract_a41793812abae560805414761fec398fe}{Gikjl\-\_\-wo}}\label{structinteract_a41793812abae560805414761fec398fe} + +\begin{DoxyCompactList}\small\item\em Gikjl without contributions for prob\-\_\-unpaired. \end{DoxyCompactList}\item +\hypertarget{structinteract_ab6d031a21388be8763b75ea74c937f17}{int \hyperlink{structinteract_ab6d031a21388be8763b75ea74c937f17}{i}}\label{structinteract_ab6d031a21388be8763b75ea74c937f17} + +\begin{DoxyCompactList}\small\item\em k$<$i in longer seq \end{DoxyCompactList}\item +\hypertarget{structinteract_a61e457fbf943d57364be6ddf1b4e7b8a}{int \hyperlink{structinteract_a61e457fbf943d57364be6ddf1b4e7b8a}{k}}\label{structinteract_a61e457fbf943d57364be6ddf1b4e7b8a} + +\begin{DoxyCompactList}\small\item\em k$<$i in longer seq \end{DoxyCompactList}\item +\hypertarget{structinteract_a7555cb6363d1479341eb72b9c087aa34}{int \hyperlink{structinteract_a7555cb6363d1479341eb72b9c087aa34}{j}}\label{structinteract_a7555cb6363d1479341eb72b9c087aa34} + +\begin{DoxyCompactList}\small\item\em j$<$l in shorter seq \end{DoxyCompactList}\item +\hypertarget{structinteract_a030ab45056342e12cb3955e4defd3904}{int \hyperlink{structinteract_a030ab45056342e12cb3955e4defd3904}{l}}\label{structinteract_a030ab45056342e12cb3955e4defd3904} + +\begin{DoxyCompactList}\small\item\em j$<$l in shorter seq \end{DoxyCompactList}\item +\hypertarget{structinteract_ac9fcb5dca54ec5faa76e02b6488b9524}{int \hyperlink{structinteract_ac9fcb5dca54ec5faa76e02b6488b9524}{length}}\label{structinteract_ac9fcb5dca54ec5faa76e02b6488b9524} + +\begin{DoxyCompactList}\small\item\em length of longer sequence \end{DoxyCompactList}\end{DoxyCompactItemize} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structintermediate__t.tex b/binaries/src/ViennaRNA/doc/latex/structintermediate__t.tex new file mode 100644 index 0000000..c981146 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structintermediate__t.tex @@ -0,0 +1,33 @@ +\hypertarget{structintermediate__t}{\section{intermediate\-\_\-t Struct Reference} +\label{structintermediate__t}\index{intermediate\-\_\-t@{intermediate\-\_\-t}} +} + + +Collaboration diagram for intermediate\-\_\-t\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=158pt]{structintermediate__t__coll__graph} +\end{center} +\end{figure} +\subsection*{Data Fields} +\begin{DoxyCompactItemize} +\item +\hypertarget{structintermediate__t_a9a2b6258aa1af06ea3504631de8dadba}{short $\ast$ \hyperlink{structintermediate__t_a9a2b6258aa1af06ea3504631de8dadba}{pt}}\label{structintermediate__t_a9a2b6258aa1af06ea3504631de8dadba} + +\begin{DoxyCompactList}\small\item\em pair table \end{DoxyCompactList}\item +\hypertarget{structintermediate__t_ac44e091915da58927978d54ef59234c7}{int \hyperlink{structintermediate__t_ac44e091915da58927978d54ef59234c7}{Sen}}\label{structintermediate__t_ac44e091915da58927978d54ef59234c7} + +\begin{DoxyCompactList}\small\item\em saddle energy so far \end{DoxyCompactList}\item +\hypertarget{structintermediate__t_af84d640df33aea99e959b2e4f61a7367}{int \hyperlink{structintermediate__t_af84d640df33aea99e959b2e4f61a7367}{curr\-\_\-en}}\label{structintermediate__t_af84d640df33aea99e959b2e4f61a7367} + +\begin{DoxyCompactList}\small\item\em current energy \end{DoxyCompactList}\item +\hypertarget{structintermediate__t_a94e947f18273bbfe3dd544085b025a7b}{\hyperlink{structmove__t}{move\-\_\-t} $\ast$ \hyperlink{structintermediate__t_a94e947f18273bbfe3dd544085b025a7b}{moves}}\label{structintermediate__t_a94e947f18273bbfe3dd544085b025a7b} + +\begin{DoxyCompactList}\small\item\em remaining moves to target \end{DoxyCompactList}\end{DoxyCompactItemize} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structintermediate__t__coll__graph.md5 b/binaries/src/ViennaRNA/doc/latex/structintermediate__t__coll__graph.md5 new file mode 100644 index 0000000..69176b5 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structintermediate__t__coll__graph.md5 @@ -0,0 +1 @@ +128749ca1e4638d5a755d06e486e4b6b \ No newline at end of file diff --git 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+\label{structmodel__detailsT}\index{model\-\_\-details\-T@{model\-\_\-details\-T}} +} + + +The data structure that contains the complete model details used throughout the calculations. + + +\subsection*{Data Fields} +\begin{DoxyCompactItemize} +\item +int \hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{dangles} +\begin{DoxyCompactList}\small\item\em Specifies the dangle model used in any energy evaluation (0,1,2 or 3) \end{DoxyCompactList}\item +\hypertarget{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{int \hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{special\-\_\-hp}}\label{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617} + +\begin{DoxyCompactList}\small\item\em Include special hairpin contributions for tri, tetra and hexaloops. \end{DoxyCompactList}\item +\hypertarget{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{int \hyperlink{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{no\-L\-P}}\label{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d} + +\begin{DoxyCompactList}\small\item\em Only consider canonical structures, i.\-e. no 'lonely' base pairs. \end{DoxyCompactList}\item +\hypertarget{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{int \hyperlink{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{no\-G\-U}}\label{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d} + +\begin{DoxyCompactList}\small\item\em Do not allow G\-U pairs. \end{DoxyCompactList}\item +\hypertarget{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}{int \hyperlink{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}{no\-G\-Uclosure}}\label{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9} + +\begin{DoxyCompactList}\small\item\em Do not allow loops to be closed by G\-U pair. \end{DoxyCompactList}\item +\hypertarget{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}{int \hyperlink{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}{log\-M\-L}}\label{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85} + +\begin{DoxyCompactList}\small\item\em Use logarithmic scaling for multi loops. \end{DoxyCompactList}\item +\hypertarget{structmodel__detailsT_a55f083dad18c216505805a8062e63074}{int \hyperlink{structmodel__detailsT_a55f083dad18c216505805a8062e63074}{circ}}\label{structmodel__detailsT_a55f083dad18c216505805a8062e63074} + +\begin{DoxyCompactList}\small\item\em Assume molecule to be circular. \end{DoxyCompactList}\item +\hypertarget{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}{int \hyperlink{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}{gquad}}\label{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea} + +\begin{DoxyCompactList}\small\item\em Include G-\/quadruplexes in structure prediction. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +The data structure that contains the complete model details used throughout the calculations. + +\subsection{Field Documentation} +\hypertarget{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{\index{model\-\_\-details\-T@{model\-\_\-details\-T}!dangles@{dangles}} +\index{dangles@{dangles}!model_detailsT@{model\-\_\-details\-T}} +\subsubsection[{dangles}]{\setlength{\rightskip}{0pt plus 5cm}int model\-\_\-details\-T\-::dangles}}\label{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b} + + +Specifies the dangle model used in any energy evaluation (0,1,2 or 3) + +\begin{DoxyNote}{Note} +Some function do not implement all dangle model but only a subset of (0,1,2,3). Read the documentaion of the particular recurrences or energy evaluation function for information about the provided dangle model. +\end{DoxyNote} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structmove__t.tex b/binaries/src/ViennaRNA/doc/latex/structmove__t.tex new file mode 100644 index 0000000..d84e8f5 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structmove__t.tex @@ -0,0 +1,8 @@ +\hypertarget{structmove__t}{\section{move\-\_\-t Struct Reference} +\label{structmove__t}\index{move\-\_\-t@{move\-\_\-t}} +} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structpair__info.tex b/binaries/src/ViennaRNA/doc/latex/structpair__info.tex new file mode 100644 index 0000000..651004e --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structpair__info.tex @@ -0,0 +1,48 @@ +\hypertarget{structpair__info}{\section{pair\-\_\-info Struct Reference} +\label{structpair__info}\index{pair\-\_\-info@{pair\-\_\-info}} +} + + +A base pair info structure. + + +\subsection*{Data Fields} +\begin{DoxyCompactItemize} +\item +\hypertarget{structpair__info_a7905e17da6a6cc48230ee6205628ed7f}{unsigned \hyperlink{structpair__info_a7905e17da6a6cc48230ee6205628ed7f}{i}}\label{structpair__info_a7905e17da6a6cc48230ee6205628ed7f} + +\begin{DoxyCompactList}\small\item\em nucleotide position i \end{DoxyCompactList}\item +\hypertarget{structpair__info_a35665817b5792703ff4325e1bcbe5e21}{unsigned \hyperlink{structpair__info_a35665817b5792703ff4325e1bcbe5e21}{j}}\label{structpair__info_a35665817b5792703ff4325e1bcbe5e21} + +\begin{DoxyCompactList}\small\item\em nucleotide position j \end{DoxyCompactList}\item +\hypertarget{structpair__info_af0895ea40ec0c23bfe8aa2c3babf0e80}{float \hyperlink{structpair__info_af0895ea40ec0c23bfe8aa2c3babf0e80}{p}}\label{structpair__info_af0895ea40ec0c23bfe8aa2c3babf0e80} + +\begin{DoxyCompactList}\small\item\em Probability. \end{DoxyCompactList}\item +\hypertarget{structpair__info_ab3aa7a54e6976f46e69c6ffcddd0e782}{float \hyperlink{structpair__info_ab3aa7a54e6976f46e69c6ffcddd0e782}{ent}}\label{structpair__info_ab3aa7a54e6976f46e69c6ffcddd0e782} + +\begin{DoxyCompactList}\small\item\em Pseudo entropy for $ p(i,j) = S_i + S_j - p_ij*ln(p_ij) $. \end{DoxyCompactList}\item +\hypertarget{structpair__info_a23fc316453d179474bed7f6ed2489723}{short \hyperlink{structpair__info_a23fc316453d179474bed7f6ed2489723}{bp} \mbox{[}8\mbox{]}}\label{structpair__info_a23fc316453d179474bed7f6ed2489723} + +\begin{DoxyCompactList}\small\item\em Frequencies of pair\-\_\-types. \end{DoxyCompactList}\item +\hypertarget{structpair__info_a4da3d6c9042500c16c4b06e0bbc48190}{char \hyperlink{structpair__info_a4da3d6c9042500c16c4b06e0bbc48190}{comp}}\label{structpair__info_a4da3d6c9042500c16c4b06e0bbc48190} + +\begin{DoxyCompactList}\small\item\em 1 iff pair is in mfe structure \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +A base pair info structure. + +For each base pair (i,j) with i,j in \mbox{[}0, n-\/1\mbox{]} the structure lists\-: +\begin{DoxyItemize} +\item its probability 'p' +\item an entropy-\/like measure for its well-\/definedness 'ent' +\item the frequency of each type of pair in 'bp\mbox{[}\mbox{]}' +\begin{DoxyItemize} +\item 'bp\mbox{[}0\mbox{]}' contains the number of non-\/compatible sequences +\item 'bp\mbox{[}1\mbox{]}' the number of C\-G pairs, etc. +\end{DoxyItemize} +\end{DoxyItemize} + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structpairpro.tex b/binaries/src/ViennaRNA/doc/latex/structpairpro.tex new file mode 100644 index 0000000..036c767 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structpairpro.tex @@ -0,0 +1,18 @@ +\hypertarget{structpairpro}{\section{pairpro Struct Reference} +\label{structpairpro}\index{pairpro@{pairpro}} +} + + +Collaboration diagram for pairpro\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=126pt]{structpairpro__coll__graph} +\end{center} +\end{figure} + + +The documentation for this struct was 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\hyperlink{PS__dot_8h}{P\-S\-\_\-dot.\-h} and others + + + + +\subsection{Detailed Description} +this datastructure is used as input parameter in functions of \hyperlink{PS__dot_8h}{P\-S\-\_\-dot.\-h} and others + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structpu__contrib.tex b/binaries/src/ViennaRNA/doc/latex/structpu__contrib.tex new file mode 100644 index 0000000..298ebca --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structpu__contrib.tex @@ -0,0 +1,37 @@ +\hypertarget{structpu__contrib}{\section{pu\-\_\-contrib Struct Reference} +\label{structpu__contrib}\index{pu\-\_\-contrib@{pu\-\_\-contrib}} +} + + +contributions to p\-\_\-u + + +\subsection*{Data Fields} +\begin{DoxyCompactItemize} +\item +\hypertarget{structpu__contrib_ac9034ac9a84ed0647587659d6e9be1e8}{double $\ast$$\ast$ \hyperlink{structpu__contrib_ac9034ac9a84ed0647587659d6e9be1e8}{H}}\label{structpu__contrib_ac9034ac9a84ed0647587659d6e9be1e8} + +\begin{DoxyCompactList}\small\item\em hairpin loops \end{DoxyCompactList}\item +\hypertarget{structpu__contrib_a8ca0da20536780589fb3e3472ca0581f}{double $\ast$$\ast$ \hyperlink{structpu__contrib_a8ca0da20536780589fb3e3472ca0581f}{I}}\label{structpu__contrib_a8ca0da20536780589fb3e3472ca0581f} + +\begin{DoxyCompactList}\small\item\em interior loops \end{DoxyCompactList}\item +\hypertarget{structpu__contrib_a1222ebf74f426bbcd843dcc325da207b}{double $\ast$$\ast$ \hyperlink{structpu__contrib_a1222ebf74f426bbcd843dcc325da207b}{M}}\label{structpu__contrib_a1222ebf74f426bbcd843dcc325da207b} + +\begin{DoxyCompactList}\small\item\em multi loops \end{DoxyCompactList}\item +\hypertarget{structpu__contrib_accb192ba6b4b91a1cb2f8080934fd428}{double $\ast$$\ast$ \hyperlink{structpu__contrib_accb192ba6b4b91a1cb2f8080934fd428}{E}}\label{structpu__contrib_accb192ba6b4b91a1cb2f8080934fd428} + +\begin{DoxyCompactList}\small\item\em exterior loop \end{DoxyCompactList}\item +\hypertarget{structpu__contrib_a33d5ada6e861db0c81aa3d5b2989262e}{int \hyperlink{structpu__contrib_a33d5ada6e861db0c81aa3d5b2989262e}{length}}\label{structpu__contrib_a33d5ada6e861db0c81aa3d5b2989262e} + +\begin{DoxyCompactList}\small\item\em length of the input sequence \end{DoxyCompactList}\item +\hypertarget{structpu__contrib_a403c1c7f20beeeffba7632fac0cfcbff}{int \hyperlink{structpu__contrib_a403c1c7f20beeeffba7632fac0cfcbff}{w}}\label{structpu__contrib_a403c1c7f20beeeffba7632fac0cfcbff} + +\begin{DoxyCompactList}\small\item\em longest unpaired region \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +contributions to p\-\_\-u + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structpu__out.tex b/binaries/src/ViennaRNA/doc/latex/structpu__out.tex new file mode 100644 index 0000000..7f59b83 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structpu__out.tex @@ -0,0 +1,34 @@ +\hypertarget{structpu__out}{\section{pu\-\_\-out Struct Reference} +\label{structpu__out}\index{pu\-\_\-out@{pu\-\_\-out}} +} + + +Collection of all free\-\_\-energy of beeing unpaired values for output. + + +\subsection*{Data Fields} +\begin{DoxyCompactItemize} +\item +\hypertarget{structpu__out_a314b8f43c3ee0bf6060afbeced5dbe6c}{int \hyperlink{structpu__out_a314b8f43c3ee0bf6060afbeced5dbe6c}{len}}\label{structpu__out_a314b8f43c3ee0bf6060afbeced5dbe6c} + +\begin{DoxyCompactList}\small\item\em sequence length \end{DoxyCompactList}\item +\hypertarget{structpu__out_a7697bc7a46cd1b8e37e337e708cb6023}{int \hyperlink{structpu__out_a7697bc7a46cd1b8e37e337e708cb6023}{u\-\_\-vals}}\label{structpu__out_a7697bc7a46cd1b8e37e337e708cb6023} + +\begin{DoxyCompactList}\small\item\em number of different -\/u values \end{DoxyCompactList}\item +\hypertarget{structpu__out_a638b0de1837cfd441871d005d3ab2938}{int \hyperlink{structpu__out_a638b0de1837cfd441871d005d3ab2938}{contribs}}\label{structpu__out_a638b0de1837cfd441871d005d3ab2938} + +\begin{DoxyCompactList}\small\item\em \mbox{[}-\/c \char`\"{}\-S\-H\-I\-M\-E\char`\"{}\mbox{]} \end{DoxyCompactList}\item +\hypertarget{structpu__out_ac9e9e30b16e7d04c770460b8487fb09d}{char $\ast$$\ast$ \hyperlink{structpu__out_ac9e9e30b16e7d04c770460b8487fb09d}{header}}\label{structpu__out_ac9e9e30b16e7d04c770460b8487fb09d} + +\begin{DoxyCompactList}\small\item\em header line \end{DoxyCompactList}\item +\hypertarget{structpu__out_a366edbc4170d5c177908e178ff340828}{double $\ast$$\ast$ \hyperlink{structpu__out_a366edbc4170d5c177908e178ff340828}{u\-\_\-values}}\label{structpu__out_a366edbc4170d5c177908e178ff340828} + +\begin{DoxyCompactList}\small\item\em (the -\/u values $\ast$ \mbox{[}-\/c \char`\"{}\-S\-H\-I\-M\-E\char`\"{}\mbox{]}) $\ast$ seq len \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Collection of all free\-\_\-energy of beeing unpaired values for output. + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structsect.tex b/binaries/src/ViennaRNA/doc/latex/structsect.tex new file mode 100644 index 0000000..40d499b --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structsect.tex @@ -0,0 +1,16 @@ +\hypertarget{structsect}{\section{sect Struct Reference} +\label{structsect}\index{sect@{sect}} +} + + +Stack of partial structures for backtracking. + + + + +\subsection{Detailed Description} +Stack of partial structures for backtracking. + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structsnoopT.tex b/binaries/src/ViennaRNA/doc/latex/structsnoopT.tex new file mode 100644 index 0000000..43f1872 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structsnoopT.tex @@ -0,0 +1,8 @@ +\hypertarget{structsnoopT}{\section{snoop\-T Struct Reference} +\label{structsnoopT}\index{snoop\-T@{snoop\-T}} +} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structstruct__en.tex b/binaries/src/ViennaRNA/doc/latex/structstruct__en.tex new file mode 100644 index 0000000..146fc68 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structstruct__en.tex @@ -0,0 +1,8 @@ +\hypertarget{structstruct__en}{\section{struct\-\_\-en Struct Reference} +\label{structstruct__en}\index{struct\-\_\-en@{struct\-\_\-en}} +} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/move\-\_\-set.\-h\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structsvm__model.tex b/binaries/src/ViennaRNA/doc/latex/structsvm__model.tex new file mode 100644 index 0000000..1ebb8c9 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structsvm__model.tex @@ -0,0 +1,8 @@ +\hypertarget{structsvm__model}{\section{svm\-\_\-model Struct Reference} +\label{structsvm__model}\index{svm\-\_\-model@{svm\-\_\-model}} +} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/svm\-\_\-utils.\-h\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/structswString.tex b/binaries/src/ViennaRNA/doc/latex/structswString.tex new file mode 100644 index 0000000..0b48841 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/structswString.tex @@ -0,0 +1,8 @@ +\hypertarget{structswString}{\section{sw\-String Struct Reference} +\label{structswString}\index{sw\-String@{sw\-String}} +} + + +The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize} +\item +/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{dist__vars_8h}{dist\-\_\-vars.\-h}\end{DoxyCompactItemize} diff --git a/binaries/src/ViennaRNA/doc/latex/subopt_8h.tex b/binaries/src/ViennaRNA/doc/latex/subopt_8h.tex new file mode 100644 index 0000000..1f54199 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/subopt_8h.tex @@ -0,0 +1,41 @@ +\hypertarget{subopt_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/subopt.h File Reference} +\label{subopt_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/subopt.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/subopt.\-h}} +} + + +R\-N\-Asubopt and density of states declarations. + + +Include dependency graph for subopt.\-h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{subopt_8h__incl} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +\hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N} $\ast$ \hyperlink{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{subopt} (char $\ast$seq, char $\ast$structure, int delta, F\-I\-L\-E $\ast$fp) +\begin{DoxyCompactList}\small\item\em Returns list of subopt structures or writes to fp. \end{DoxyCompactList}\item +\hypertarget{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}{\hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N} $\ast$ \hyperlink{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}{subopt\-\_\-par} (char $\ast$seq, char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int delta, int is\-\_\-constrained, int is\-\_\-circular, F\-I\-L\-E $\ast$fp)}\label{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d} + +\begin{DoxyCompactList}\small\item\em Returns list of subopt structures or writes to fp. \end{DoxyCompactList}\item +\hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N} $\ast$ \hyperlink{group__subopt__wuchty_ga8634516e4740e0b6c9a46d2bae940340}{subopt\-\_\-circ} (char $\ast$seq, char $\ast$sequence, int delta, F\-I\-L\-E $\ast$fp) +\begin{DoxyCompactList}\small\item\em Returns list of circular subopt structures or writes to fp. \end{DoxyCompactList}\end{DoxyCompactItemize} +\subsection*{Variables} +\begin{DoxyCompactItemize} +\item +\hypertarget{group__subopt__wuchty_ga873cf8ed69e0437f8efa8b1fec854a0e}{int \hyperlink{group__subopt__wuchty_ga873cf8ed69e0437f8efa8b1fec854a0e}{subopt\-\_\-sorted}}\label{group__subopt__wuchty_ga873cf8ed69e0437f8efa8b1fec854a0e} + +\begin{DoxyCompactList}\small\item\em Sort output by energy. \end{DoxyCompactList}\item +\hypertarget{group__subopt__wuchty_ga5e57d914bcb5feeecdf520e25313fcfe}{double \hyperlink{group__subopt__wuchty_ga5e57d914bcb5feeecdf520e25313fcfe}{print\-\_\-energy}}\label{group__subopt__wuchty_ga5e57d914bcb5feeecdf520e25313fcfe} + +\begin{DoxyCompactList}\small\item\em printing threshold for use with log\-M\-L \end{DoxyCompactList}\item +int \hyperlink{group__dos_ga937634a76b46a22530a74906f1957a9e}{density\-\_\-of\-\_\-states} \mbox{[}\hyperlink{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}{M\-A\-X\-D\-O\-S}+1\mbox{]} +\begin{DoxyCompactList}\small\item\em The Density of States. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +R\-N\-Asubopt and density of states declarations. \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/subopt_8h__incl.md5 b/binaries/src/ViennaRNA/doc/latex/subopt_8h__incl.md5 new file mode 100644 index 0000000..9c444d1 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/subopt_8h__incl.md5 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b/binaries/src/ViennaRNA/doc/latex/subopt_8h_source.tex new file mode 100644 index 0000000..dfe8906 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/subopt_8h_source.tex @@ -0,0 +1,41 @@ +\hypertarget{subopt_8h}{\section{subopt.\-h} +\label{subopt_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/subopt.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/subopt.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{comment}{/* subopt.h */} +00002 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_SUBOPT\_H\_\_} +00003 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_SUBOPT\_H\_\_} +00004 \textcolor{preprocessor}{} +00005 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"} +00006 +00007 \textcolor{preprocessor}{#define MAXDOS 1000} +00008 \textcolor{preprocessor}{} +00043 \hyperlink{structSOLUTION}{SOLUTION} *\hyperlink{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{subopt} (\textcolor{keywordtype}{char} *seq, +00044 \textcolor{keywordtype}{char} *structure, +00045 \textcolor{keywordtype}{int} delta, +00046 FILE *fp); +00047 +00053 \hyperlink{structSOLUTION}{SOLUTION} *\hyperlink{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}{subopt\_par}( \textcolor{keywordtype}{char} *seq, +00054 \textcolor{keywordtype}{char} *structure, +00055 \hyperlink{structparamT}{paramT} *parameters, +00056 \textcolor{keywordtype}{int} delta, +00057 \textcolor{keywordtype}{int} is\_constrained, +00058 \textcolor{keywordtype}{int} is\_circular, +00059 FILE *fp); +00060 +00075 \hyperlink{structSOLUTION}{SOLUTION} *\hyperlink{group__subopt__wuchty_ga8634516e4740e0b6c9a46d2bae940340}{subopt\_circ} ( \textcolor{keywordtype}{char} *seq, +00076 \textcolor{keywordtype}{char} *sequence, +00077 \textcolor{keywordtype}{int} delta, +00078 FILE *fp); +00079 +00086 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{group__subopt__wuchty_ga873cf8ed69e0437f8efa8b1fec854a0e}{subopt\_sorted}; +00087 +00088 +00095 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} \hyperlink{group__subopt__wuchty_ga5e57d914bcb5feeecdf520e25313fcfe}{print\_energy}; +00096 +00113 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \hyperlink{group__dos_ga937634a76b46a22530a74906f1957a9e}{density\_of\_states}[\hyperlink{data__structures_8h_a5ec740b80afb4906ba4311dbd8ddbd89}{MAXDOS}+1]; +00114 \textcolor{comment}{/* End of group dos */} +00116 +00117 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/svm__utils_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/svm__utils_8h_source.tex new file mode 100644 index 0000000..bda377e --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/svm__utils_8h_source.tex @@ -0,0 +1,52 @@ +\hypertarget{svm__utils_8h}{\section{svm\-\_\-utils.\-h} +\label{svm__utils_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/svm\-\_\-utils.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/svm\-\_\-utils.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_SUBOPT\_H\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_SUBOPT\_H\_\_} +00003 \textcolor{preprocessor}{} +\hypertarget{svm__utils_8h_source_l00004}{}\hyperlink{structsvm__model}{00004} \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\hyperlink{structsvm__model}{svm\_model}\{ +00005 \textcolor{keyword}{struct }svm\_parameter param; +00006 \textcolor{keywordtype}{int} nr\_class; +00007 \textcolor{keywordtype}{int} l; +00008 \textcolor{keyword}{struct }svm\_node **SV; +00009 \textcolor{keywordtype}{double} **sv\_coef; +00010 \textcolor{keywordtype}{double} *rho; +00011 \textcolor{keywordtype}{double} *probA; +00012 \textcolor{keywordtype}{double} *probB; +00013 \textcolor{keywordtype}{int} *label; +00014 \textcolor{keywordtype}{int} *nSV; +00015 \textcolor{keywordtype}{int} free\_sv; +00016 \} \hyperlink{structsvm__model}{svm\_model}; +00017 +00018 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} *avg\_model\_string; +00019 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} *sd\_model\_string; +00020 +00021 \textcolor{keywordtype}{float} get\_z(\textcolor{keywordtype}{char} *sequence, +00022 \textcolor{keywordtype}{double} energy); +00023 \textcolor{keywordtype}{double} avg\_regression (\textcolor{keywordtype}{int} N, +00024 \textcolor{keywordtype}{int} A, +00025 \textcolor{keywordtype}{int} C, +00026 \textcolor{keywordtype}{int} G, +00027 \textcolor{keywordtype}{int} T, +00028 \textcolor{keyword}{struct} \hyperlink{structsvm__model}{svm\_model} *avg\_model, +00029 \textcolor{keywordtype}{int} *info ); +00030 \textcolor{keywordtype}{double} sd\_regression (\textcolor{keywordtype}{int} N, +00031 \textcolor{keywordtype}{int} A, +00032 \textcolor{keywordtype}{int} C, +00033 \textcolor{keywordtype}{int} G, +00034 \textcolor{keywordtype}{int} T, +00035 \textcolor{keyword}{struct} \hyperlink{structsvm__model}{svm\_model} *sd\_model); +00036 \textcolor{keywordtype}{double} minimal\_sd (\textcolor{keywordtype}{int} N, +00037 \textcolor{keywordtype}{int} A, +00038 \textcolor{keywordtype}{int} C, +00039 \textcolor{keywordtype}{int} G, +00040 \textcolor{keywordtype}{int} T); +00041 \hyperlink{structsvm__model}{svm\_model} *svm\_load\_model\_string(\textcolor{keywordtype}{char} *modelString); +00042 \textcolor{keywordtype}{int} *get\_seq\_composition( \textcolor{keywordtype}{short} *S, +00043 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} start, +00044 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} stop); +00045 +00046 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/treedist_8h.tex b/binaries/src/ViennaRNA/doc/latex/treedist_8h.tex new file mode 100644 index 0000000..88b12bf --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/treedist_8h.tex @@ -0,0 +1,91 @@ +\hypertarget{treedist_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/treedist.h File Reference} +\label{treedist_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/treedist.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/treedist.\-h}} +} + + +Functions for \hyperlink{structTree}{Tree} Edit Distances. + + +Include dependency graph for treedist.\-h\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{treedist_8h__incl} +\end{center} +\end{figure} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +\hyperlink{structTree}{Tree} $\ast$ \hyperlink{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}{make\-\_\-tree} (char $\ast$struc) +\begin{DoxyCompactList}\small\item\em Constructs a \hyperlink{structTree}{Tree} ( essentially the postorder list ) of the structure 'struc', for use in \hyperlink{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{tree\-\_\-edit\-\_\-distance()}. \end{DoxyCompactList}\item +float \hyperlink{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{tree\-\_\-edit\-\_\-distance} (\hyperlink{structTree}{Tree} $\ast$T1, \hyperlink{structTree}{Tree} $\ast$T2) +\begin{DoxyCompactList}\small\item\em Calculates the edit distance of the two trees. \end{DoxyCompactList}\item +\hypertarget{treedist_8h_a21ad4de3ba4055aeef08b28c9ad48894}{void \hyperlink{treedist_8h_a21ad4de3ba4055aeef08b28c9ad48894}{print\-\_\-tree} (\hyperlink{structTree}{Tree} $\ast$t)}\label{treedist_8h_a21ad4de3ba4055aeef08b28c9ad48894} + +\begin{DoxyCompactList}\small\item\em Print a tree (mainly for debugging) \end{DoxyCompactList}\item +void \hyperlink{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}{free\-\_\-tree} (\hyperlink{structTree}{Tree} $\ast$t) +\begin{DoxyCompactList}\small\item\em Free the memory allocated for \hyperlink{structTree}{Tree} t. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Functions for \hyperlink{structTree}{Tree} Edit Distances. + +\subsection{Function Documentation} +\hypertarget{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}{\index{treedist.\-h@{treedist.\-h}!make\-\_\-tree@{make\-\_\-tree}} +\index{make\-\_\-tree@{make\-\_\-tree}!treedist.h@{treedist.\-h}} +\subsubsection[{make\-\_\-tree}]{\setlength{\rightskip}{0pt plus 5cm}{\bf Tree}$\ast$ make\-\_\-tree ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{struc} +\end{DoxyParamCaption} +)}}\label{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3} + + +Constructs a \hyperlink{structTree}{Tree} ( essentially the postorder list ) of the structure 'struc', for use in \hyperlink{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{tree\-\_\-edit\-\_\-distance()}. + + +\begin{DoxyParams}{Parameters} +{\em struc} & may be any rooted structure representation. \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} + +\end{DoxyReturn} +\hypertarget{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{\index{treedist.\-h@{treedist.\-h}!tree\-\_\-edit\-\_\-distance@{tree\-\_\-edit\-\_\-distance}} +\index{tree\-\_\-edit\-\_\-distance@{tree\-\_\-edit\-\_\-distance}!treedist.h@{treedist.\-h}} +\subsubsection[{tree\-\_\-edit\-\_\-distance}]{\setlength{\rightskip}{0pt plus 5cm}float tree\-\_\-edit\-\_\-distance ( +\begin{DoxyParamCaption} +\item[{{\bf Tree} $\ast$}]{T1, } +\item[{{\bf Tree} $\ast$}]{T2} +\end{DoxyParamCaption} +)}}\label{treedist_8h_a3b21f1925f7071f46d93431a835217bb} + + +Calculates the edit distance of the two trees. + + +\begin{DoxyParams}{Parameters} +{\em T1} & \\ +\hline +{\em T2} & \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} + +\end{DoxyReturn} +\hypertarget{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}{\index{treedist.\-h@{treedist.\-h}!free\-\_\-tree@{free\-\_\-tree}} +\index{free\-\_\-tree@{free\-\_\-tree}!treedist.h@{treedist.\-h}} +\subsubsection[{free\-\_\-tree}]{\setlength{\rightskip}{0pt plus 5cm}void free\-\_\-tree ( +\begin{DoxyParamCaption} +\item[{{\bf Tree} $\ast$}]{t} +\end{DoxyParamCaption} +)}}\label{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa} + + +Free the memory allocated for \hyperlink{structTree}{Tree} t. + + +\begin{DoxyParams}{Parameters} +{\em t} & \\ +\hline +\end{DoxyParams} diff --git a/binaries/src/ViennaRNA/doc/latex/treedist_8h__incl.md5 b/binaries/src/ViennaRNA/doc/latex/treedist_8h__incl.md5 new file mode 100644 index 0000000..fba8b4f --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/treedist_8h__incl.md5 @@ -0,0 +1 @@ +be5317cd4fdbebf2169f17e4b15c6e4e \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/treedist_8h__incl.pdf 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b/binaries/src/ViennaRNA/doc/latex/treedist_8h_source.tex new file mode 100644 index 0000000..828cdfb --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/treedist_8h_source.tex @@ -0,0 +1,21 @@ +\hypertarget{treedist_8h}{\section{treedist.\-h} +\label{treedist_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/treedist.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/treedist.\-h}} +} + +\begin{DoxyCode} +00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_TREE\_DIST\_H\_\_} +00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_TREE\_DIST\_H\_\_} +00003 \textcolor{preprocessor}{} +00009 \textcolor{preprocessor}{#include "\hyperlink{dist__vars_8h}{dist\_vars.h}"} +00010 +00018 \hyperlink{structTree}{Tree} *\hyperlink{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}{make\_tree}(\textcolor{keywordtype}{char} *struc); +00019 +00027 \textcolor{keywordtype}{float} \hyperlink{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{tree\_edit\_distance}( \hyperlink{structTree}{Tree} *T1, +00028 \hyperlink{structTree}{Tree} *T2); +00029 +00033 \textcolor{keywordtype}{void} \hyperlink{treedist_8h_a21ad4de3ba4055aeef08b28c9ad48894}{print\_tree}(\hyperlink{structTree}{Tree} *t); +00034 +00040 \textcolor{keywordtype}{void} \hyperlink{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}{free\_tree}(\hyperlink{structTree}{Tree} *t); +00041 +00042 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/utils_8h.tex b/binaries/src/ViennaRNA/doc/latex/utils_8h.tex new file mode 100644 index 0000000..e0c01e9 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/utils_8h.tex @@ -0,0 +1,924 @@ +\hypertarget{utils_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/utils.h File Reference} +\label{utils_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/utils.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/utils.\-h}} +} + + +Various utility-\/ and helper-\/functions used throughout the Vienna R\-N\-A package. + + +This graph shows which files directly or indirectly include this file\-: +\nopagebreak +\begin{figure}[H] +\begin{center} +\leavevmode +\includegraphics[width=250pt]{utils_8h__dep__incl} +\end{center} +\end{figure} +\subsection*{Macros} +\begin{DoxyCompactItemize} +\item +\#define \hyperlink{utils_8h_ad403c9ea58f1836689404c2931419c8c}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-E\-R\-R\-O\-R}~1\-U +\item +\#define \hyperlink{utils_8h_a72f3c6ca5c83d2b9baed2922d19c403d}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-Q\-U\-I\-T}~2\-U +\item +\#define \hyperlink{utils_8h_a8e3241b321c9c1a78a69e59e2e019a71}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-M\-I\-S\-C}~4\-U +\item +\#define \hyperlink{utils_8h_a2f0d8069e93d3ac54d9320d6bdb8e7e7}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-F\-A\-S\-T\-A\-\_\-\-H\-E\-A\-D\-E\-R}~8\-U +\item +\#define \hyperlink{utils_8h_a8566d6787972100e68b5a2a159b4cf45}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-S\-E\-Q\-U\-E\-N\-C\-E}~16\-U +\item +\#define \hyperlink{utils_8h_ac08a9df45b9721b97a47dbfe7a6e5f85}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T}~32\-U +\item +\#define \hyperlink{utils_8h_a086742158293217a46ae2f71bb296937}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-T\-R\-U\-N\-C\-A\-T\-I\-O\-N}~256\-U +\item +\#define \hyperlink{utils_8h_a7a2e8c50a0c7ce82e60da1016e1367fd}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-R\-E\-S\-T}~512\-U +\item +\#define \hyperlink{utils_8h_a0de536599b881c787b0943a2671da476}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-S\-P\-A\-N}~1024\-U +\item +\#define \hyperlink{utils_8h_ab4db885222b3b69608310d7c7e63e286}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\-S}~2048\-U +\item +\#define \hyperlink{utils_8h_a305474b93ccb79ae4c7754016a8ddd84}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E}~4096\-U +\item +\#define \hyperlink{utils_8h_a0f6311f11bed1842e3a527ab27b294c6}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S}~128\-U +\item +\#define \hyperlink{utils_8h_af2062e0eeefffd3ed639af460b3d4fab}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-M\-M\-E\-N\-T}~8192\-U +\item +\#define \hyperlink{utils_8h_a4e8d7120619b21df0309af425acbc9a2}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-P\-I\-P\-E}~1\-U +\item +\#define \hyperlink{utils_8h_a55e1d16fd693ae9ec8e987b0750da804}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-D\-O\-T}~2\-U +\item +\#define \hyperlink{utils_8h_a077c56550c915d4516d84a5ed8d051f4}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-X}~4\-U +\item +\#define \hyperlink{utils_8h_a0512d790f738742cbdcf3f7c87b46f48}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-N\-G\-\_\-\-B\-R\-A\-C\-K}~8\-U +\item +\#define \hyperlink{utils_8h_aa20bfca4bb2903c8548000a33d7bbb53}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-R\-N\-D\-\_\-\-B\-R\-A\-C\-K}~16\-U +\item +\#define \hyperlink{utils_8h_a7d725ef525b29891abef3f1ed42599a4}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E}~32\-U +\item +\#define \hyperlink{utils_8h_a08d12a9a846ea593b7171d277c9f033f}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-N\-O\-\_\-\-H\-E\-A\-D\-E\-R}~64\-U +\item +\#define \hyperlink{utils_8h_a0a697f77a6fbb10f34e16fa68ed9e655}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-L\-L}~128\-U +\item +\#define \hyperlink{utils_8h_a99dc6b23dc4080a76e2ed1a81c20e94d}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-G}~256\-U +\item +\#define \hyperlink{utils_8h_abec89c09874528c6cb73140a4c3d86d7}{V\-R\-N\-A\-\_\-\-O\-P\-T\-I\-O\-N\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E}~32\-U +\item +\#define \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{M\-I\-N2}(A, B)~((A) $<$ (B) ? (A) \-: (B)) +\item +\#define \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{M\-A\-X2}(A, B)~((A) $>$ (B) ? (A) \-: (B)) +\item +\#define \hyperlink{utils_8h_a721b8d5f3abef17f10293f1f7f8c958e}{M\-I\-N3}(A, B, C)~(\hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{M\-I\-N2}( (\hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{M\-I\-N2}((A),(B))) ,(C))) +\item +\#define \hyperlink{utils_8h_a8d577123d2e66d2b7d0bf9af6e172b93}{M\-A\-X3}(A, B, C)~(\hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{M\-A\-X2}( (\hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{M\-A\-X2}((A),(B))) ,(C))) +\item +\#define \hyperlink{utils_8h_a03943706e48069237cd57f2d35ca987e}{X\-S\-T\-R}(s)~\hyperlink{utils_8h_a6388870e639eee9c0a69446876f1f8cc}{S\-T\-R}(s) +\item +\#define \hyperlink{utils_8h_a6388870e639eee9c0a69446876f1f8cc}{S\-T\-R}(s)~\#s +\item +\#define \hyperlink{utils_8h_afb228174279df9486a5cb56ac0bc79a3}{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-M\-A\-X\-\_\-\-L\-E\-N\-G\-T\-H}~80 +\begin{DoxyCompactList}\small\item\em Maximum length of filenames that are generated by our programs. \end{DoxyCompactList}\item +\#define \hyperlink{utils_8h_a33c3b1826b8e2739f09f111ec719ded5}{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-I\-D\-\_\-\-L\-E\-N\-G\-T\-H}~42 +\begin{DoxyCompactList}\small\item\em Maximum length of id taken from fasta header for filename generation. \end{DoxyCompactList}\end{DoxyCompactItemize} +\subsection*{Functions} +\begin{DoxyCompactItemize} +\item +void $\ast$ \hyperlink{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{space} (unsigned size) +\begin{DoxyCompactList}\small\item\em Allocate space safely. \end{DoxyCompactList}\item +void $\ast$ \hyperlink{utils_8h_a9037ada838835b1b9db41581a021b0c8}{xrealloc} (void $\ast$p, unsigned size) +\begin{DoxyCompactList}\small\item\em Reallocate space safely. \end{DoxyCompactList}\item +void \hyperlink{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{nrerror} (const char message\mbox{[}$\,$\mbox{]}) +\begin{DoxyCompactList}\small\item\em Die with an error message. \end{DoxyCompactList}\item +void \hyperlink{utils_8h_af2355fa8746f2f30fbe71db65dea3d51}{warn\-\_\-user} (const char message\mbox{[}$\,$\mbox{]}) +\begin{DoxyCompactList}\small\item\em Print a warning message. \end{DoxyCompactList}\item +\hypertarget{utils_8h_a8aaa6d9be6f803f496d9b97375c371f3}{void \hyperlink{utils_8h_a8aaa6d9be6f803f496d9b97375c371f3}{init\-\_\-rand} (void)}\label{utils_8h_a8aaa6d9be6f803f496d9b97375c371f3} + +\begin{DoxyCompactList}\small\item\em Make random number seeds. \end{DoxyCompactList}\item +double \hyperlink{utils_8h_aaa328491c84996e445d027fde9800f2e}{urn} (void) +\begin{DoxyCompactList}\small\item\em get a random number from \mbox{[}0..1\mbox{]} \end{DoxyCompactList}\item +int \hyperlink{utils_8h_a68ff0849d44f62fe491800378a5ffcb4}{int\-\_\-urn} (int from, int to) +\begin{DoxyCompactList}\small\item\em Generates a pseudo random integer in a specified range. \end{DoxyCompactList}\item +char $\ast$ \hyperlink{utils_8h_a7afeb906cb36e9d77379eabc6907ac46}{time\-\_\-stamp} (void) +\begin{DoxyCompactList}\small\item\em Get a timestamp. \end{DoxyCompactList}\item +char $\ast$ \hyperlink{utils_8h_a1b95eac365a021572e1c37e5993a89be}{random\-\_\-string} (int l, const char symbols\mbox{[}$\,$\mbox{]}) +\begin{DoxyCompactList}\small\item\em Create a random string using characters from a specified symbol set. \end{DoxyCompactList}\item +int \hyperlink{utils_8h_ad9dc7bfc9aa664dc6698f17ce07fc7e7}{hamming} (const char $\ast$s1, const char $\ast$s2) +\begin{DoxyCompactList}\small\item\em Calculate hamming distance between two sequences. \end{DoxyCompactList}\item +int \hyperlink{utils_8h_a96d3c36717d624514055ce201cab1542}{hamming\-\_\-bound} (const char $\ast$s1, const char $\ast$s2, int n) +\begin{DoxyCompactList}\small\item\em Calculate hamming distance between two sequences up to a specified length. \end{DoxyCompactList}\item +char $\ast$ \hyperlink{utils_8h_abe51806d14cff0789a8c1df7dbc45b71}{get\-\_\-line} (F\-I\-L\-E $\ast$fp) +\begin{DoxyCompactList}\small\item\em Read a line of arbitrary length from a stream. \end{DoxyCompactList}\item +unsigned int \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line} (char $\ast$$\ast$string, unsigned int options) +\item +unsigned int \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\-\_\-record} (char $\ast$$\ast$header, char $\ast$$\ast$sequence, char $\ast$$\ast$$\ast$rest, unsigned int options) +\begin{DoxyCompactList}\small\item\em Get a data record from stdin. \end{DoxyCompactList}\item +char $\ast$ \hyperlink{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{pack\-\_\-structure} (const char $\ast$struc) +\begin{DoxyCompactList}\small\item\em Pack secondary secondary structure, 5\-:1 compression using base 3 encoding. \end{DoxyCompactList}\item +char $\ast$ \hyperlink{utils_8h_a071c6921efe1eb974f115ee6fefa3c39}{unpack\-\_\-structure} (const char $\ast$packed) +\begin{DoxyCompactList}\small\item\em Unpack secondary structure previously packed with \hyperlink{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{pack\-\_\-structure()} \end{DoxyCompactList}\item +short $\ast$ \hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table} (const char $\ast$structure) +\begin{DoxyCompactList}\small\item\em Create a pair table of a secondary structure. \end{DoxyCompactList}\item +short $\ast$ \hyperlink{utils_8h_afeaa6d68eef3a99d0a7aa08aa91c6601}{copy\-\_\-pair\-\_\-table} (const short $\ast$pt) +\begin{DoxyCompactList}\small\item\em Get an exact copy of a pair table. \end{DoxyCompactList}\item +short $\ast$ \hyperlink{utils_8h_a3c81b3967056c3888b8472b65fbb16f5}{alimake\-\_\-pair\-\_\-table} (const char $\ast$structure) +\item +short $\ast$ \hyperlink{utils_8h_a9aa3bf3b4346bb7fb88efc154dd07a79}{make\-\_\-pair\-\_\-table\-\_\-snoop} (const char $\ast$structure) +\item +int $\ast$ \hyperlink{utils_8h_a4358e89f64cc87a563b7ef3855f75bed}{make\-\_\-loop\-\_\-index\-\_\-pt} (short $\ast$pt) +\begin{DoxyCompactList}\small\item\em Compute the \char`\"{}base pair\char`\"{} distance between two secondary structures s1 and s2. \end{DoxyCompactList}\item +void \hyperlink{utils_8h_a6bf778117d31b7fd90db435323f4ef74}{print\-\_\-tty\-\_\-input\-\_\-seq} (void) +\begin{DoxyCompactList}\small\item\em Print a line to {\itshape stdout} that asks for an input sequence. \end{DoxyCompactList}\item +void \hyperlink{utils_8h_ae4ef89b662a3e9b5b5f0781d9757aba0}{print\-\_\-tty\-\_\-input\-\_\-seq\-\_\-str} (const char $\ast$s) +\begin{DoxyCompactList}\small\item\em Print a line with a user defined string and a ruler to stdout. \end{DoxyCompactList}\item +\hypertarget{utils_8h_ae8ae8a34962b9959be3f6c40f0a80ac1}{void \hyperlink{utils_8h_ae8ae8a34962b9959be3f6c40f0a80ac1}{print\-\_\-tty\-\_\-constraint\-\_\-full} (void)}\label{utils_8h_ae8ae8a34962b9959be3f6c40f0a80ac1} + +\begin{DoxyCompactList}\small\item\em Print structure constraint characters to stdout (full constraint support) \end{DoxyCompactList}\item +void \hyperlink{utils_8h_a4d167deb70bb51723e44374dc981deb2}{print\-\_\-tty\-\_\-constraint} (unsigned int option) +\begin{DoxyCompactList}\small\item\em Print structure constraint characters to stdout. (constraint support is specified by option parameter) \end{DoxyCompactList}\item +void \hyperlink{utils_8h_ad3f18dd83f958f18b2f26ecb99305208}{str\-\_\-\-D\-N\-A2\-R\-N\-A} (char $\ast$sequence) +\begin{DoxyCompactList}\small\item\em Convert a D\-N\-A input sequence to R\-N\-A alphabet. \end{DoxyCompactList}\item +void \hyperlink{utils_8h_a17b796b806f96b70382077fb5bc519bb}{str\-\_\-uppercase} (char $\ast$sequence) +\begin{DoxyCompactList}\small\item\em Convert an input sequence to uppercase. \end{DoxyCompactList}\item +int $\ast$ \hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\-\_\-iindx} (unsigned int length) +\begin{DoxyCompactList}\small\item\em Get an index mapper array (iindx) for accessing the energy matrices, e.\-g. in partition function related functions. \end{DoxyCompactList}\item +int $\ast$ \hyperlink{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f}{get\-\_\-indx} (unsigned int length) +\begin{DoxyCompactList}\small\item\em Get an index mapper array (indx) for accessing the energy matrices, e.\-g. in M\-F\-E related functions. \end{DoxyCompactList}\item +void \hyperlink{utils_8h_a36c3a6c3218b041f992052767bc74549}{constrain\-\_\-ptypes} (const char $\ast$constraint, unsigned int length, char $\ast$ptype, int $\ast$B\-P, int min\-\_\-loop\-\_\-size, unsigned int idx\-\_\-type) +\begin{DoxyCompactList}\small\item\em Insert constraining pair types according to constraint structure string. \end{DoxyCompactList}\end{DoxyCompactItemize} +\subsection*{Variables} +\begin{DoxyCompactItemize} +\item +unsigned short \hyperlink{utils_8h_af9a866c8417afda7368bbac939ab3c47}{xsubi} \mbox{[}3\mbox{]} +\begin{DoxyCompactList}\small\item\em Current 48 bit random number. \end{DoxyCompactList}\end{DoxyCompactItemize} + + +\subsection{Detailed Description} +Various utility-\/ and helper-\/functions used throughout the Vienna R\-N\-A package. + +\subsection{Macro Definition Documentation} +\hypertarget{utils_8h_ad403c9ea58f1836689404c2931419c8c}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-E\-R\-R\-O\-R@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-E\-R\-R\-O\-R}} +\index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-E\-R\-R\-O\-R@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-E\-R\-R\-O\-R}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-E\-R\-R\-O\-R}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-E\-R\-R\-O\-R~1\-U}}\label{utils_8h_ad403c9ea58f1836689404c2931419c8c} +Output flag of \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()}\-: \char`\"{}\-An E\-R\-R\-O\-R has occured, maybe E\-O\-F\char`\"{} \hypertarget{utils_8h_a72f3c6ca5c83d2b9baed2922d19c403d}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-Q\-U\-I\-T@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-Q\-U\-I\-T}} +\index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-Q\-U\-I\-T@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-Q\-U\-I\-T}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-Q\-U\-I\-T}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-Q\-U\-I\-T~2\-U}}\label{utils_8h_a72f3c6ca5c83d2b9baed2922d19c403d} +Output flag of \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()}\-: \char`\"{}the user requested quitting the program\char`\"{} \hypertarget{utils_8h_a8e3241b321c9c1a78a69e59e2e019a71}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-M\-I\-S\-C@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-M\-I\-S\-C}} +\index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-M\-I\-S\-C@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-M\-I\-S\-C}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-M\-I\-S\-C}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-M\-I\-S\-C~4\-U}}\label{utils_8h_a8e3241b321c9c1a78a69e59e2e019a71} +Output flag of \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()}\-: \char`\"{}something was read\char`\"{} \hypertarget{utils_8h_a2f0d8069e93d3ac54d9320d6bdb8e7e7}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-F\-A\-S\-T\-A\-\_\-\-H\-E\-A\-D\-E\-R@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-F\-A\-S\-T\-A\-\_\-\-H\-E\-A\-D\-E\-R}} +\index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-F\-A\-S\-T\-A\-\_\-\-H\-E\-A\-D\-E\-R@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-F\-A\-S\-T\-A\-\_\-\-H\-E\-A\-D\-E\-R}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-F\-A\-S\-T\-A\-\_\-\-H\-E\-A\-D\-E\-R}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-F\-A\-S\-T\-A\-\_\-\-H\-E\-A\-D\-E\-R~8\-U}}\label{utils_8h_a2f0d8069e93d3ac54d9320d6bdb8e7e7} +Input/\-Output flag of \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()}\-:\par + if used as input option this tells \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()} that the data to be read should comply with the F\-A\-S\-T\-A format + +the function will return this flag if a fasta header was read \hypertarget{utils_8h_a8566d6787972100e68b5a2a159b4cf45}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-S\-E\-Q\-U\-E\-N\-C\-E@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-S\-E\-Q\-U\-E\-N\-C\-E}} +\index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-S\-E\-Q\-U\-E\-N\-C\-E@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-S\-E\-Q\-U\-E\-N\-C\-E}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-S\-E\-Q\-U\-E\-N\-C\-E}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-S\-E\-Q\-U\-E\-N\-C\-E~16\-U}}\label{utils_8h_a8566d6787972100e68b5a2a159b4cf45} +Input flag for \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()}\-:\par + Tell \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()} that we assume to read a nucleotide sequence \hypertarget{utils_8h_ac08a9df45b9721b97a47dbfe7a6e5f85}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T}} +\index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T~32\-U}}\label{utils_8h_ac08a9df45b9721b97a47dbfe7a6e5f85} +Input flag for \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()}\-:\par + Tell \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()} that we assume to read a structure constraint \hypertarget{utils_8h_a086742158293217a46ae2f71bb296937}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-T\-R\-U\-N\-C\-A\-T\-I\-O\-N@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-T\-R\-U\-N\-C\-A\-T\-I\-O\-N}} +\index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-T\-R\-U\-N\-C\-A\-T\-I\-O\-N@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-T\-R\-U\-N\-C\-A\-T\-I\-O\-N}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-T\-R\-U\-N\-C\-A\-T\-I\-O\-N}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-T\-R\-U\-N\-C\-A\-T\-I\-O\-N~256\-U}}\label{utils_8h_a086742158293217a46ae2f71bb296937} +Input switch for \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()}\-: \char`\"{}do not trunkate the line by eliminating white spaces at end of line\char`\"{} \hypertarget{utils_8h_a7a2e8c50a0c7ce82e60da1016e1367fd}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-R\-E\-S\-T@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-R\-E\-S\-T}} +\index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-R\-E\-S\-T@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-R\-E\-S\-T}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-R\-E\-S\-T}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-R\-E\-S\-T~512\-U}}\label{utils_8h_a7a2e8c50a0c7ce82e60da1016e1367fd} +Input switch for \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\-\_\-record()}\-: \char`\"{}do fill rest array\char`\"{} \hypertarget{utils_8h_a0de536599b881c787b0943a2671da476}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-S\-P\-A\-N@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-S\-P\-A\-N}} +\index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-S\-P\-A\-N@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-S\-P\-A\-N}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-S\-P\-A\-N}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-S\-P\-A\-N~1024\-U}}\label{utils_8h_a0de536599b881c787b0943a2671da476} +Input switch for \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\-\_\-record()}\-: \char`\"{}never allow data to span more than one line\char`\"{} \hypertarget{utils_8h_ab4db885222b3b69608310d7c7e63e286}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\-S@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\-S}} +\index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\-S@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\-S}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\-S}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\-S~2048\-U}}\label{utils_8h_ab4db885222b3b69608310d7c7e63e286} +Input switch for \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\-\_\-record()}\-: \char`\"{}do not skip empty lines\char`\"{} \hypertarget{utils_8h_a305474b93ccb79ae4c7754016a8ddd84}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E}} +\index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E~4096\-U}}\label{utils_8h_a305474b93ccb79ae4c7754016a8ddd84} +Output flag for \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\-\_\-record()}\-: \char`\"{}read an empty line\char`\"{} \hypertarget{utils_8h_a0f6311f11bed1842e3a527ab27b294c6}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S}} +\index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S~128\-U}}\label{utils_8h_a0f6311f11bed1842e3a527ab27b294c6} +Input switch for \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()}\-: \char`\"{}do not skip comment lines\char`\"{} \hypertarget{utils_8h_af2062e0eeefffd3ed639af460b3d4fab}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-M\-M\-E\-N\-T@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-M\-M\-E\-N\-T}} +\index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-M\-M\-E\-N\-T@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-M\-M\-E\-N\-T}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-M\-M\-E\-N\-T}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-M\-M\-E\-N\-T~8192\-U}}\label{utils_8h_af2062e0eeefffd3ed639af460b3d4fab} +Output flag for \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\-\_\-record()}\-: \char`\"{}read a comment\char`\"{} \hypertarget{utils_8h_a4e8d7120619b21df0309af425acbc9a2}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-P\-I\-P\-E@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-P\-I\-P\-E}} +\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-P\-I\-P\-E@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-P\-I\-P\-E}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-P\-I\-P\-E}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-P\-I\-P\-E~1\-U}}\label{utils_8h_a4e8d7120619b21df0309af425acbc9a2} +pipe sign '$|$' switch for structure constraints (paired with another base) \hypertarget{utils_8h_a55e1d16fd693ae9ec8e987b0750da804}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-D\-O\-T@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-D\-O\-T}} +\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-D\-O\-T@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-D\-O\-T}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-D\-O\-T}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-D\-O\-T~2\-U}}\label{utils_8h_a55e1d16fd693ae9ec8e987b0750da804} +dot '.' switch for structure constraints (no constraint at all) \hypertarget{utils_8h_a077c56550c915d4516d84a5ed8d051f4}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-X@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-X}} +\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-X@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-X}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-X}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-X~4\-U}}\label{utils_8h_a077c56550c915d4516d84a5ed8d051f4} +'x' switch for structure constraint (base must not pair) \hypertarget{utils_8h_a0512d790f738742cbdcf3f7c87b46f48}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-N\-G\-\_\-\-B\-R\-A\-C\-K@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-N\-G\-\_\-\-B\-R\-A\-C\-K}} +\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-N\-G\-\_\-\-B\-R\-A\-C\-K@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-N\-G\-\_\-\-B\-R\-A\-C\-K}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-N\-G\-\_\-\-B\-R\-A\-C\-K}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-N\-G\-\_\-\-B\-R\-A\-C\-K~8\-U}}\label{utils_8h_a0512d790f738742cbdcf3f7c87b46f48} +angle brackets '$<$', '$>$' switch for structure constraint (paired downstream/upstream) \hypertarget{utils_8h_aa20bfca4bb2903c8548000a33d7bbb53}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-R\-N\-D\-\_\-\-B\-R\-A\-C\-K@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-R\-N\-D\-\_\-\-B\-R\-A\-C\-K}} +\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-R\-N\-D\-\_\-\-B\-R\-A\-C\-K@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-R\-N\-D\-\_\-\-B\-R\-A\-C\-K}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-R\-N\-D\-\_\-\-B\-R\-A\-C\-K}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-R\-N\-D\-\_\-\-B\-R\-A\-C\-K~16\-U}}\label{utils_8h_aa20bfca4bb2903c8548000a33d7bbb53} +round brackets '(',')' switch for structure constraint (base i pairs base j) \hypertarget{utils_8h_a7d725ef525b29891abef3f1ed42599a4}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E}} +\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E~32\-U}}\label{utils_8h_a7d725ef525b29891abef3f1ed42599a4} +constraint may span over several lines \hypertarget{utils_8h_a08d12a9a846ea593b7171d277c9f033f}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-N\-O\-\_\-\-H\-E\-A\-D\-E\-R@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-N\-O\-\_\-\-H\-E\-A\-D\-E\-R}} +\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-N\-O\-\_\-\-H\-E\-A\-D\-E\-R@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-N\-O\-\_\-\-H\-E\-A\-D\-E\-R}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-N\-O\-\_\-\-H\-E\-A\-D\-E\-R}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-N\-O\-\_\-\-H\-E\-A\-D\-E\-R~64\-U}}\label{utils_8h_a08d12a9a846ea593b7171d277c9f033f} +do not print the header information line \hypertarget{utils_8h_a0a697f77a6fbb10f34e16fa68ed9e655}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-L\-L@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-L\-L}} +\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-L\-L@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-L\-L}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-L\-L}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-L\-L~128\-U}}\label{utils_8h_a0a697f77a6fbb10f34e16fa68ed9e655} +placeholder for all constraining characters \hypertarget{utils_8h_a99dc6b23dc4080a76e2ed1a81c20e94d}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-G@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-G}} +\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-G@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-G}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-G}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-G~256\-U}}\label{utils_8h_a99dc6b23dc4080a76e2ed1a81c20e94d} +'+' switch for structure constraint (base is involved in a gquad) \hypertarget{utils_8h_abec89c09874528c6cb73140a4c3d86d7}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-O\-P\-T\-I\-O\-N\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E@{V\-R\-N\-A\-\_\-\-O\-P\-T\-I\-O\-N\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E}} +\index{V\-R\-N\-A\-\_\-\-O\-P\-T\-I\-O\-N\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E@{V\-R\-N\-A\-\_\-\-O\-P\-T\-I\-O\-N\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E}!utils.h@{utils.\-h}} +\subsubsection[{V\-R\-N\-A\-\_\-\-O\-P\-T\-I\-O\-N\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-O\-P\-T\-I\-O\-N\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E~32\-U}}\label{utils_8h_abec89c09874528c6cb73140a4c3d86d7} +Tell a function that an input is assumed to span several lines if used as input-\/option A function might also be returning this state telling that it has read data from multiple lines. + +\begin{DoxySeeAlso}{See Also} +extract\-\_\-record\-\_\-rest\-\_\-structure(), \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\-\_\-record()}, get\-Constraint() +\end{DoxySeeAlso} +\hypertarget{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{\index{utils.\-h@{utils.\-h}!M\-I\-N2@{M\-I\-N2}} +\index{M\-I\-N2@{M\-I\-N2}!utils.h@{utils.\-h}} +\subsubsection[{M\-I\-N2}]{\setlength{\rightskip}{0pt plus 5cm}\#define M\-I\-N2( +\begin{DoxyParamCaption} +\item[{}]{A, } +\item[{}]{B} +\end{DoxyParamCaption} +)~((A) $<$ (B) ? (A) \-: (B))}}\label{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d} +Get the minimum of two comparable values \hypertarget{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{\index{utils.\-h@{utils.\-h}!M\-A\-X2@{M\-A\-X2}} +\index{M\-A\-X2@{M\-A\-X2}!utils.h@{utils.\-h}} +\subsubsection[{M\-A\-X2}]{\setlength{\rightskip}{0pt plus 5cm}\#define M\-A\-X2( +\begin{DoxyParamCaption} +\item[{}]{A, } +\item[{}]{B} +\end{DoxyParamCaption} +)~((A) $>$ (B) ? (A) \-: (B))}}\label{utils_8h_a33297b3679c713b0c4d897cd0fe3b122} +Get the maximum of two comparable values \hypertarget{utils_8h_a721b8d5f3abef17f10293f1f7f8c958e}{\index{utils.\-h@{utils.\-h}!M\-I\-N3@{M\-I\-N3}} +\index{M\-I\-N3@{M\-I\-N3}!utils.h@{utils.\-h}} +\subsubsection[{M\-I\-N3}]{\setlength{\rightskip}{0pt plus 5cm}\#define M\-I\-N3( +\begin{DoxyParamCaption} +\item[{}]{A, } +\item[{}]{B, } +\item[{}]{C} +\end{DoxyParamCaption} +)~({\bf M\-I\-N2}( ({\bf M\-I\-N2}((A),(B))) ,(C)))}}\label{utils_8h_a721b8d5f3abef17f10293f1f7f8c958e} +Get the minimum of three comparable values \hypertarget{utils_8h_a8d577123d2e66d2b7d0bf9af6e172b93}{\index{utils.\-h@{utils.\-h}!M\-A\-X3@{M\-A\-X3}} +\index{M\-A\-X3@{M\-A\-X3}!utils.h@{utils.\-h}} +\subsubsection[{M\-A\-X3}]{\setlength{\rightskip}{0pt plus 5cm}\#define M\-A\-X3( +\begin{DoxyParamCaption} +\item[{}]{A, } +\item[{}]{B, } +\item[{}]{C} +\end{DoxyParamCaption} +)~({\bf M\-A\-X2}( ({\bf M\-A\-X2}((A),(B))) ,(C)))}}\label{utils_8h_a8d577123d2e66d2b7d0bf9af6e172b93} +Get the maximum of three comparable values \hypertarget{utils_8h_a03943706e48069237cd57f2d35ca987e}{\index{utils.\-h@{utils.\-h}!X\-S\-T\-R@{X\-S\-T\-R}} +\index{X\-S\-T\-R@{X\-S\-T\-R}!utils.h@{utils.\-h}} +\subsubsection[{X\-S\-T\-R}]{\setlength{\rightskip}{0pt plus 5cm}\#define X\-S\-T\-R( +\begin{DoxyParamCaption} +\item[{}]{s} +\end{DoxyParamCaption} +)~{\bf S\-T\-R}(s)}}\label{utils_8h_a03943706e48069237cd57f2d35ca987e} +Stringify a macro after expansion \hypertarget{utils_8h_a6388870e639eee9c0a69446876f1f8cc}{\index{utils.\-h@{utils.\-h}!S\-T\-R@{S\-T\-R}} +\index{S\-T\-R@{S\-T\-R}!utils.h@{utils.\-h}} +\subsubsection[{S\-T\-R}]{\setlength{\rightskip}{0pt plus 5cm}\#define S\-T\-R( +\begin{DoxyParamCaption} +\item[{}]{s} +\end{DoxyParamCaption} +)~\#s}}\label{utils_8h_a6388870e639eee9c0a69446876f1f8cc} +Stringify a macro argument \hypertarget{utils_8h_afb228174279df9486a5cb56ac0bc79a3}{\index{utils.\-h@{utils.\-h}!F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-M\-A\-X\-\_\-\-L\-E\-N\-G\-T\-H@{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-M\-A\-X\-\_\-\-L\-E\-N\-G\-T\-H}} +\index{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-M\-A\-X\-\_\-\-L\-E\-N\-G\-T\-H@{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-M\-A\-X\-\_\-\-L\-E\-N\-G\-T\-H}!utils.h@{utils.\-h}} +\subsubsection[{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-M\-A\-X\-\_\-\-L\-E\-N\-G\-T\-H}]{\setlength{\rightskip}{0pt plus 5cm}\#define F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-M\-A\-X\-\_\-\-L\-E\-N\-G\-T\-H~80}}\label{utils_8h_afb228174279df9486a5cb56ac0bc79a3} + + +Maximum length of filenames that are generated by our programs. + +This definition should be used throughout the complete Vienna\-R\-N\-A package wherever a static array holding filenames of output files is declared. \hypertarget{utils_8h_a33c3b1826b8e2739f09f111ec719ded5}{\index{utils.\-h@{utils.\-h}!F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-I\-D\-\_\-\-L\-E\-N\-G\-T\-H@{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-I\-D\-\_\-\-L\-E\-N\-G\-T\-H}} +\index{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-I\-D\-\_\-\-L\-E\-N\-G\-T\-H@{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-I\-D\-\_\-\-L\-E\-N\-G\-T\-H}!utils.h@{utils.\-h}} +\subsubsection[{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-I\-D\-\_\-\-L\-E\-N\-G\-T\-H}]{\setlength{\rightskip}{0pt plus 5cm}\#define F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-I\-D\-\_\-\-L\-E\-N\-G\-T\-H~42}}\label{utils_8h_a33c3b1826b8e2739f09f111ec719ded5} + + +Maximum length of id taken from fasta header for filename generation. + +this has to be smaller than F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-M\-A\-X\-\_\-\-L\-E\-N\-G\-T\-H since in most cases, some suffix will be appended to the I\-D + +\subsection{Function Documentation} +\hypertarget{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{\index{utils.\-h@{utils.\-h}!space@{space}} +\index{space@{space}!utils.h@{utils.\-h}} +\subsubsection[{space}]{\setlength{\rightskip}{0pt plus 5cm}void$\ast$ space ( +\begin{DoxyParamCaption} +\item[{unsigned}]{size} +\end{DoxyParamCaption} +)}}\label{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177} + + +Allocate space safely. + + +\begin{DoxyParams}{Parameters} +{\em size} & The size of the memory to be allocated in bytes \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +A pointer to the allocated memory +\end{DoxyReturn} +\hypertarget{utils_8h_a9037ada838835b1b9db41581a021b0c8}{\index{utils.\-h@{utils.\-h}!xrealloc@{xrealloc}} +\index{xrealloc@{xrealloc}!utils.h@{utils.\-h}} +\subsubsection[{xrealloc}]{\setlength{\rightskip}{0pt plus 5cm}void$\ast$ xrealloc ( +\begin{DoxyParamCaption} +\item[{void $\ast$}]{p, } +\item[{unsigned}]{size} +\end{DoxyParamCaption} +)}}\label{utils_8h_a9037ada838835b1b9db41581a021b0c8} + + +Reallocate space safely. + + +\begin{DoxyParams}{Parameters} +{\em p} & A pointer to the memory region to be reallocated \\ +\hline +{\em size} & The size of the memory to be allocated in bytes \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +A pointer to the newly allocated memory +\end{DoxyReturn} +\hypertarget{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{\index{utils.\-h@{utils.\-h}!nrerror@{nrerror}} +\index{nrerror@{nrerror}!utils.h@{utils.\-h}} +\subsubsection[{nrerror}]{\setlength{\rightskip}{0pt plus 5cm}void nrerror ( +\begin{DoxyParamCaption} +\item[{const char}]{message\mbox{[}$\,$\mbox{]}} +\end{DoxyParamCaption} +)}}\label{utils_8h_a127ce946e56b5a5773781cabe68e38c5} + + +Die with an error message. + +\begin{DoxySeeAlso}{See Also} +\hyperlink{utils_8h_af2355fa8746f2f30fbe71db65dea3d51}{warn\-\_\-user()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em message} & The error message to be printed before exiting with 'F\-A\-I\-L\-U\-R\-E' \\ +\hline +\end{DoxyParams} +\hypertarget{utils_8h_af2355fa8746f2f30fbe71db65dea3d51}{\index{utils.\-h@{utils.\-h}!warn\-\_\-user@{warn\-\_\-user}} +\index{warn\-\_\-user@{warn\-\_\-user}!utils.h@{utils.\-h}} +\subsubsection[{warn\-\_\-user}]{\setlength{\rightskip}{0pt plus 5cm}void warn\-\_\-user ( +\begin{DoxyParamCaption} +\item[{const char}]{message\mbox{[}$\,$\mbox{]}} +\end{DoxyParamCaption} +)}}\label{utils_8h_af2355fa8746f2f30fbe71db65dea3d51} + + +Print a warning message. + +Print a warning message to {\itshape stderr} + + +\begin{DoxyParams}{Parameters} +{\em message} & The warning message \\ +\hline +\end{DoxyParams} +\hypertarget{utils_8h_aaa328491c84996e445d027fde9800f2e}{\index{utils.\-h@{utils.\-h}!urn@{urn}} +\index{urn@{urn}!utils.h@{utils.\-h}} +\subsubsection[{urn}]{\setlength{\rightskip}{0pt plus 5cm}double urn ( +\begin{DoxyParamCaption} +\item[{void}]{} +\end{DoxyParamCaption} +)}}\label{utils_8h_aaa328491c84996e445d027fde9800f2e} + + +get a random number from \mbox{[}0..1\mbox{]} + +\begin{DoxyNote}{Note} +Usually implemented by calling {\itshape erand48()}. +\end{DoxyNote} +\begin{DoxyReturn}{Returns} +A random number in range \mbox{[}0..1\mbox{]} +\end{DoxyReturn} +\hypertarget{utils_8h_a68ff0849d44f62fe491800378a5ffcb4}{\index{utils.\-h@{utils.\-h}!int\-\_\-urn@{int\-\_\-urn}} +\index{int\-\_\-urn@{int\-\_\-urn}!utils.h@{utils.\-h}} +\subsubsection[{int\-\_\-urn}]{\setlength{\rightskip}{0pt plus 5cm}int int\-\_\-urn ( +\begin{DoxyParamCaption} +\item[{int}]{from, } +\item[{int}]{to} +\end{DoxyParamCaption} +)}}\label{utils_8h_a68ff0849d44f62fe491800378a5ffcb4} + + +Generates a pseudo random integer in a specified range. + + +\begin{DoxyParams}{Parameters} +{\em from} & The first number in range \\ +\hline +{\em to} & The last number in range \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +A pseudo random number in range \mbox{[}from, to\mbox{]} +\end{DoxyReturn} +\hypertarget{utils_8h_a7afeb906cb36e9d77379eabc6907ac46}{\index{utils.\-h@{utils.\-h}!time\-\_\-stamp@{time\-\_\-stamp}} +\index{time\-\_\-stamp@{time\-\_\-stamp}!utils.h@{utils.\-h}} +\subsubsection[{time\-\_\-stamp}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ time\-\_\-stamp ( +\begin{DoxyParamCaption} +\item[{void}]{} +\end{DoxyParamCaption} +)}}\label{utils_8h_a7afeb906cb36e9d77379eabc6907ac46} + + +Get a timestamp. + +Returns a string containing the current date in the format \begin{DoxyVerb}Fri Mar 19 21:10:57 1993\end{DoxyVerb} + + +\begin{DoxyReturn}{Returns} +A string containing the timestamp +\end{DoxyReturn} +\hypertarget{utils_8h_a1b95eac365a021572e1c37e5993a89be}{\index{utils.\-h@{utils.\-h}!random\-\_\-string@{random\-\_\-string}} +\index{random\-\_\-string@{random\-\_\-string}!utils.h@{utils.\-h}} +\subsubsection[{random\-\_\-string}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ random\-\_\-string ( +\begin{DoxyParamCaption} +\item[{int}]{l, } +\item[{const char}]{symbols\mbox{[}$\,$\mbox{]}} +\end{DoxyParamCaption} +)}}\label{utils_8h_a1b95eac365a021572e1c37e5993a89be} + + +Create a random string using characters from a specified symbol set. + + +\begin{DoxyParams}{Parameters} +{\em l} & The length of the sequence \\ +\hline +{\em symbols} & The symbol set \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +A random string of length 'l' containing characters from the symbolset +\end{DoxyReturn} +\hypertarget{utils_8h_ad9dc7bfc9aa664dc6698f17ce07fc7e7}{\index{utils.\-h@{utils.\-h}!hamming@{hamming}} +\index{hamming@{hamming}!utils.h@{utils.\-h}} +\subsubsection[{hamming}]{\setlength{\rightskip}{0pt plus 5cm}int hamming ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{s1, } +\item[{const char $\ast$}]{s2} +\end{DoxyParamCaption} +)}}\label{utils_8h_ad9dc7bfc9aa664dc6698f17ce07fc7e7} + + +Calculate hamming distance between two sequences. + +Calculate the number of positions in which +\begin{DoxyParams}{Parameters} +{\em s1} & The first sequence \\ +\hline +{\em s2} & The second sequence \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The hamming distance between s1 and s2 +\end{DoxyReturn} +\hypertarget{utils_8h_a96d3c36717d624514055ce201cab1542}{\index{utils.\-h@{utils.\-h}!hamming\-\_\-bound@{hamming\-\_\-bound}} +\index{hamming\-\_\-bound@{hamming\-\_\-bound}!utils.h@{utils.\-h}} +\subsubsection[{hamming\-\_\-bound}]{\setlength{\rightskip}{0pt plus 5cm}int hamming\-\_\-bound ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{s1, } +\item[{const char $\ast$}]{s2, } +\item[{int}]{n} +\end{DoxyParamCaption} +)}}\label{utils_8h_a96d3c36717d624514055ce201cab1542} + + +Calculate hamming distance between two sequences up to a specified length. + +This function is similar to \hyperlink{utils_8h_ad9dc7bfc9aa664dc6698f17ce07fc7e7}{hamming()} but instead of comparing both sequences up to their actual length only the first 'n' characters are taken into account +\begin{DoxyParams}{Parameters} +{\em s1} & The first sequence \\ +\hline +{\em s2} & The second sequence \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The hamming distance between s1 and s2 +\end{DoxyReturn} +\hypertarget{utils_8h_abe51806d14cff0789a8c1df7dbc45b71}{\index{utils.\-h@{utils.\-h}!get\-\_\-line@{get\-\_\-line}} +\index{get\-\_\-line@{get\-\_\-line}!utils.h@{utils.\-h}} +\subsubsection[{get\-\_\-line}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ get\-\_\-line ( +\begin{DoxyParamCaption} +\item[{F\-I\-L\-E $\ast$}]{fp} +\end{DoxyParamCaption} +)}}\label{utils_8h_abe51806d14cff0789a8c1df7dbc45b71} + + +Read a line of arbitrary length from a stream. + +Returns a pointer to the resulting string. The necessary memory is allocated and should be released using {\itshape free()} when the string is no longer needed. + + +\begin{DoxyParams}{Parameters} +{\em fp} & A file pointer to the stream where the function should read from \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +A pointer to the resulting string +\end{DoxyReturn} +\hypertarget{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{\index{utils.\-h@{utils.\-h}!get\-\_\-input\-\_\-line@{get\-\_\-input\-\_\-line}} +\index{get\-\_\-input\-\_\-line@{get\-\_\-input\-\_\-line}!utils.h@{utils.\-h}} +\subsubsection[{get\-\_\-input\-\_\-line}]{\setlength{\rightskip}{0pt plus 5cm}unsigned int get\-\_\-input\-\_\-line ( +\begin{DoxyParamCaption} +\item[{char $\ast$$\ast$}]{string, } +\item[{unsigned int}]{options} +\end{DoxyParamCaption} +)}}\label{utils_8h_a8ef1835eb83f542396f59f0b205965e5} +Retrieve a line from 'stdin' savely while skipping comment characters and other features This function returns the type of input it has read if recognized. An option argument allows to switch between different reading modes.\par + Currently available options are\-:\par + \#\-V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-P\-R\-I\-N\-T\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S, \hyperlink{utils_8h_a0f6311f11bed1842e3a527ab27b294c6}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S}, \#\-V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-E\-L\-I\-M\-\_\-\-W\-S\-\_\-\-S\-U\-F\-F\-I\-X + +pass a collection of options as one value like this\-: \begin{DoxyVerb}get_input_line(string, option_1 | option_2 | option_n) \end{DoxyVerb} + + +If the function recognizes the type of input, it will report it in the return value. It also reports if a user defined 'quit' command (@-\/sign on 'stdin') was given. Possible return values are\-:\par + \hyperlink{utils_8h_a2f0d8069e93d3ac54d9320d6bdb8e7e7}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-F\-A\-S\-T\-A\-\_\-\-H\-E\-A\-D\-E\-R}, \hyperlink{utils_8h_ad403c9ea58f1836689404c2931419c8c}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-E\-R\-R\-O\-R}, \hyperlink{utils_8h_a8e3241b321c9c1a78a69e59e2e019a71}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-M\-I\-S\-C}, \hyperlink{utils_8h_a72f3c6ca5c83d2b9baed2922d19c403d}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-Q\-U\-I\-T} + + +\begin{DoxyParams}{Parameters} +{\em string} & A pointer to the character array that contains the line read \\ +\hline +{\em options} & A collection of options for switching the functions behavior \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +A flag with information about what has been read +\end{DoxyReturn} +\hypertarget{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{\index{utils.\-h@{utils.\-h}!read\-\_\-record@{read\-\_\-record}} +\index{read\-\_\-record@{read\-\_\-record}!utils.h@{utils.\-h}} +\subsubsection[{read\-\_\-record}]{\setlength{\rightskip}{0pt plus 5cm}unsigned int read\-\_\-record ( +\begin{DoxyParamCaption} +\item[{char $\ast$$\ast$}]{header, } +\item[{char $\ast$$\ast$}]{sequence, } +\item[{char $\ast$$\ast$$\ast$}]{rest, } +\item[{unsigned int}]{options} +\end{DoxyParamCaption} +)}}\label{utils_8h_afd194a69af9d92b5b0412a7627ac1595} + + +Get a data record from stdin. + +\begin{DoxyVerb}This function may be used to obtain complete datasets from stdin. A dataset is always +defined to contain at least a sequence. If data on stdin starts with a fasta header, +i.e. a line like +\end{DoxyVerb} + \begin{DoxyVerb}>some header info \end{DoxyVerb} + then \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\-\_\-record()} will assume that the sequence that follows the header may span over several lines. To disable this behavior and to assign a single line to the argument 'sequence' one can pass V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-S\-P\-A\-N in the 'options' argument. If no fasta header is read in the beginning of a data block, a sequence must not span over multiple lines!\par + Unless the options \hyperlink{utils_8h_a0f6311f11bed1842e3a527ab27b294c6}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S} or \hyperlink{utils_8h_ab4db885222b3b69608310d7c7e63e286}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\-S} are passed, a sequence may be interrupted by lines starting with a comment character or empty lines.\par + A sequence is regarded as completely read if it was either assumed to not span over multiple lines, a secondary structure or structure constraint follows the sequence on the next line or a new header marks the beginning of a new sequence...\par + All lines following the sequence (this includes comments) and not initiating a new dataset are available through the line-\/array 'rest'. Here one can usually find the structure constraint or other information belonging to the current dataset. Filling of 'rest' may be prevented by passing \hyperlink{utils_8h_a7a2e8c50a0c7ce82e60da1016e1367fd}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-R\-E\-S\-T} to the options argument.\par + + +\begin{DoxyNote}{Note} +This function will exit any program with an error message if no sequence could be read! \begin{DoxyVerb}The main purpose of this function is to be able to easily parse blocks of data from stdin +in the header of a loop where all calculations for the appropriate data is done inside the +loop. The loop may be then left on certain return values, e.g.: +\end{DoxyVerb} + \begin{DoxyVerb}char *id, *seq, **rest; +int i; +while(!(read_record(&id, &seq, &rest, 0) & (VRNA_INPUT_ERROR | VRNA_INPUT_QUIT))){ + if(id) printf("%s\n", id); + printf("%s\n", seq); + if(rest) + for(i=0;rest[i];i++) + printf("%s\n", rest[i]); +} \end{DoxyVerb} + \begin{DoxyVerb}In the example above, the while loop will be terminated when read_record() returns either an +error or a user initiated quit request.\n +As long as data is read from stdin, the id is printed if it is available for the current block +of data. The sequence will be printed in any case and if some more lines belong to the current +block of data each line will be printed as well. +\end{DoxyVerb} + + +Do not forget to free the memory occupied by header, sequence and rest! +\end{DoxyNote} + +\begin{DoxyParams}{Parameters} +{\em header} & A pointer which will be set such that it points to the header of the record \\ +\hline +{\em sequence} & A pointer which will be set such that it points to the sequence of the record \\ +\hline +{\em rest} & A pointer which will be set such that it points to an array of lines which also belong to the record \\ +\hline +{\em options} & Some options which may be passed to alter the behavior of the function, use 0 for no options \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +A flag with information about what the function actually did read +\end{DoxyReturn} +\hypertarget{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{\index{utils.\-h@{utils.\-h}!pack\-\_\-structure@{pack\-\_\-structure}} +\index{pack\-\_\-structure@{pack\-\_\-structure}!utils.h@{utils.\-h}} +\subsubsection[{pack\-\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ pack\-\_\-structure ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{struc} +\end{DoxyParamCaption} +)}}\label{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced} + + +Pack secondary secondary structure, 5\-:1 compression using base 3 encoding. + +Returns a binary string encoding of the secondary structure using a 5\-:1 compression scheme. The string is N\-U\-L\-L terminated and can therefore be used with standard string functions such as strcmp(). Useful for programs that need to keep many structures in memory. + + +\begin{DoxyParams}{Parameters} +{\em struc} & The secondary structure in dot-\/bracket notation \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The binary encoded structure +\end{DoxyReturn} +\hypertarget{utils_8h_a071c6921efe1eb974f115ee6fefa3c39}{\index{utils.\-h@{utils.\-h}!unpack\-\_\-structure@{unpack\-\_\-structure}} +\index{unpack\-\_\-structure@{unpack\-\_\-structure}!utils.h@{utils.\-h}} +\subsubsection[{unpack\-\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ unpack\-\_\-structure ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{packed} +\end{DoxyParamCaption} +)}}\label{utils_8h_a071c6921efe1eb974f115ee6fefa3c39} + + +Unpack secondary structure previously packed with \hyperlink{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{pack\-\_\-structure()} + +Translate a compressed binary string produced by \hyperlink{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{pack\-\_\-structure()} back into the familiar dot-\/bracket notation. + + +\begin{DoxyParams}{Parameters} +{\em packed} & The binary encoded packed secondary structure \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The unpacked secondary structure in dot-\/bracket notation +\end{DoxyReturn} +\hypertarget{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{\index{utils.\-h@{utils.\-h}!make\-\_\-pair\-\_\-table@{make\-\_\-pair\-\_\-table}} +\index{make\-\_\-pair\-\_\-table@{make\-\_\-pair\-\_\-table}!utils.h@{utils.\-h}} +\subsubsection[{make\-\_\-pair\-\_\-table}]{\setlength{\rightskip}{0pt plus 5cm}short$\ast$ make\-\_\-pair\-\_\-table ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{structure} +\end{DoxyParamCaption} +)}}\label{utils_8h_a89c32307ee50a0026f4a3131fac0845a} + + +Create a pair table of a secondary structure. + +Returns a newly allocated table, such that table\mbox{[}i\mbox{]}=j if (i.\-j) pair or 0 if i is unpaired, table\mbox{[}0\mbox{]} contains the length of the structure. + + +\begin{DoxyParams}{Parameters} +{\em structure} & The secondary structure in dot-\/bracket notation \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +A pointer to the created pair\-\_\-table +\end{DoxyReturn} +\hypertarget{utils_8h_afeaa6d68eef3a99d0a7aa08aa91c6601}{\index{utils.\-h@{utils.\-h}!copy\-\_\-pair\-\_\-table@{copy\-\_\-pair\-\_\-table}} +\index{copy\-\_\-pair\-\_\-table@{copy\-\_\-pair\-\_\-table}!utils.h@{utils.\-h}} +\subsubsection[{copy\-\_\-pair\-\_\-table}]{\setlength{\rightskip}{0pt plus 5cm}short$\ast$ copy\-\_\-pair\-\_\-table ( +\begin{DoxyParamCaption} +\item[{const short $\ast$}]{pt} +\end{DoxyParamCaption} +)}}\label{utils_8h_afeaa6d68eef3a99d0a7aa08aa91c6601} + + +Get an exact copy of a pair table. + + +\begin{DoxyParams}{Parameters} +{\em pt} & The pair table to be copied \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +A pointer to the copy of 'pt' +\end{DoxyReturn} +\hypertarget{utils_8h_a3c81b3967056c3888b8472b65fbb16f5}{\index{utils.\-h@{utils.\-h}!alimake\-\_\-pair\-\_\-table@{alimake\-\_\-pair\-\_\-table}} +\index{alimake\-\_\-pair\-\_\-table@{alimake\-\_\-pair\-\_\-table}!utils.h@{utils.\-h}} +\subsubsection[{alimake\-\_\-pair\-\_\-table}]{\setlength{\rightskip}{0pt plus 5cm}short$\ast$ alimake\-\_\-pair\-\_\-table ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{structure} +\end{DoxyParamCaption} +)}}\label{utils_8h_a3c81b3967056c3888b8472b65fbb16f5} +$\ast$$\ast$$\ast$\-Pair table for snoop align \hypertarget{utils_8h_a9aa3bf3b4346bb7fb88efc154dd07a79}{\index{utils.\-h@{utils.\-h}!make\-\_\-pair\-\_\-table\-\_\-snoop@{make\-\_\-pair\-\_\-table\-\_\-snoop}} +\index{make\-\_\-pair\-\_\-table\-\_\-snoop@{make\-\_\-pair\-\_\-table\-\_\-snoop}!utils.h@{utils.\-h}} +\subsubsection[{make\-\_\-pair\-\_\-table\-\_\-snoop}]{\setlength{\rightskip}{0pt plus 5cm}short$\ast$ make\-\_\-pair\-\_\-table\-\_\-snoop ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{structure} +\end{DoxyParamCaption} +)}}\label{utils_8h_a9aa3bf3b4346bb7fb88efc154dd07a79} +returns a newly allocated table, such that\-: table\mbox{[}i\mbox{]}=j if (i.\-j) pair or 0 if i is unpaired, table\mbox{[}0\mbox{]} contains the length of the structure. The special pseudoknotted H/\-A\-C\-A-\/m\-R\-N\-A structure is taken into account. \hypertarget{utils_8h_a4358e89f64cc87a563b7ef3855f75bed}{\index{utils.\-h@{utils.\-h}!make\-\_\-loop\-\_\-index\-\_\-pt@{make\-\_\-loop\-\_\-index\-\_\-pt}} +\index{make\-\_\-loop\-\_\-index\-\_\-pt@{make\-\_\-loop\-\_\-index\-\_\-pt}!utils.h@{utils.\-h}} +\subsubsection[{make\-\_\-loop\-\_\-index\-\_\-pt}]{\setlength{\rightskip}{0pt plus 5cm}int$\ast$ make\-\_\-loop\-\_\-index\-\_\-pt ( +\begin{DoxyParamCaption} +\item[{short $\ast$}]{pt} +\end{DoxyParamCaption} +)}}\label{utils_8h_a4358e89f64cc87a563b7ef3855f75bed} + + +Compute the \char`\"{}base pair\char`\"{} distance between two secondary structures s1 and s2. + +The sequences should have the same length. dist = number of base pairs in one structure but not in the other same as edit distance with open-\/pair close-\/pair as move-\/set + + +\begin{DoxyParams}{Parameters} +{\em str1} & First structure in dot-\/bracket notation \\ +\hline +{\em str2} & Second structure in dot-\/bracket notation \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The base pair distance between str1 and str2 +\end{DoxyReturn} +\hypertarget{utils_8h_a6bf778117d31b7fd90db435323f4ef74}{\index{utils.\-h@{utils.\-h}!print\-\_\-tty\-\_\-input\-\_\-seq@{print\-\_\-tty\-\_\-input\-\_\-seq}} +\index{print\-\_\-tty\-\_\-input\-\_\-seq@{print\-\_\-tty\-\_\-input\-\_\-seq}!utils.h@{utils.\-h}} +\subsubsection[{print\-\_\-tty\-\_\-input\-\_\-seq}]{\setlength{\rightskip}{0pt plus 5cm}void print\-\_\-tty\-\_\-input\-\_\-seq ( +\begin{DoxyParamCaption} +\item[{void}]{} +\end{DoxyParamCaption} +)}}\label{utils_8h_a6bf778117d31b7fd90db435323f4ef74} + + +Print a line to {\itshape stdout} that asks for an input sequence. + +There will also be a ruler (scale line) printed that helps orientation of the sequence positions \hypertarget{utils_8h_ae4ef89b662a3e9b5b5f0781d9757aba0}{\index{utils.\-h@{utils.\-h}!print\-\_\-tty\-\_\-input\-\_\-seq\-\_\-str@{print\-\_\-tty\-\_\-input\-\_\-seq\-\_\-str}} +\index{print\-\_\-tty\-\_\-input\-\_\-seq\-\_\-str@{print\-\_\-tty\-\_\-input\-\_\-seq\-\_\-str}!utils.h@{utils.\-h}} +\subsubsection[{print\-\_\-tty\-\_\-input\-\_\-seq\-\_\-str}]{\setlength{\rightskip}{0pt plus 5cm}void print\-\_\-tty\-\_\-input\-\_\-seq\-\_\-str ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{s} +\end{DoxyParamCaption} +)}}\label{utils_8h_ae4ef89b662a3e9b5b5f0781d9757aba0} + + +Print a line with a user defined string and a ruler to stdout. + +(usually this is used to ask for user input) There will also be a ruler (scale line) printed that helps orientation of the sequence positions + + +\begin{DoxyParams}{Parameters} +{\em s} & A user defined string that will be printed to stdout \\ +\hline +\end{DoxyParams} +\hypertarget{utils_8h_a4d167deb70bb51723e44374dc981deb2}{\index{utils.\-h@{utils.\-h}!print\-\_\-tty\-\_\-constraint@{print\-\_\-tty\-\_\-constraint}} +\index{print\-\_\-tty\-\_\-constraint@{print\-\_\-tty\-\_\-constraint}!utils.h@{utils.\-h}} +\subsubsection[{print\-\_\-tty\-\_\-constraint}]{\setlength{\rightskip}{0pt plus 5cm}void print\-\_\-tty\-\_\-constraint ( +\begin{DoxyParamCaption} +\item[{unsigned int}]{option} +\end{DoxyParamCaption} +)}}\label{utils_8h_a4d167deb70bb51723e44374dc981deb2} + + +Print structure constraint characters to stdout. (constraint support is specified by option parameter) + +Currently available options are\-:\par + \hyperlink{utils_8h_a4e8d7120619b21df0309af425acbc9a2}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-P\-I\-P\-E} (paired with another base)\par + \hyperlink{utils_8h_a55e1d16fd693ae9ec8e987b0750da804}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-D\-O\-T} (no constraint at all)\par + \hyperlink{utils_8h_a077c56550c915d4516d84a5ed8d051f4}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-X} (base must not pair)\par + \hyperlink{utils_8h_a0512d790f738742cbdcf3f7c87b46f48}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-N\-G\-\_\-\-B\-R\-A\-C\-K} (paired downstream/upstream)\par + \hyperlink{utils_8h_aa20bfca4bb2903c8548000a33d7bbb53}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-R\-N\-D\-\_\-\-B\-R\-A\-C\-K} (base i pairs base j)\par + + +pass a collection of options as one value like this\-: \begin{DoxyVerb}print_tty_constraint(option_1 | option_2 | option_n) \end{DoxyVerb} + + + +\begin{DoxyParams}{Parameters} +{\em option} & Option switch that tells which constraint help will be printed \\ +\hline +\end{DoxyParams} +\hypertarget{utils_8h_ad3f18dd83f958f18b2f26ecb99305208}{\index{utils.\-h@{utils.\-h}!str\-\_\-\-D\-N\-A2\-R\-N\-A@{str\-\_\-\-D\-N\-A2\-R\-N\-A}} +\index{str\-\_\-\-D\-N\-A2\-R\-N\-A@{str\-\_\-\-D\-N\-A2\-R\-N\-A}!utils.h@{utils.\-h}} +\subsubsection[{str\-\_\-\-D\-N\-A2\-R\-N\-A}]{\setlength{\rightskip}{0pt plus 5cm}void str\-\_\-\-D\-N\-A2\-R\-N\-A ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{sequence} +\end{DoxyParamCaption} +)}}\label{utils_8h_ad3f18dd83f958f18b2f26ecb99305208} + + +Convert a D\-N\-A input sequence to R\-N\-A alphabet. + +This function substitudes {\itshape T} and {\itshape t} with {\itshape U} and {\itshape u}, respectively + + +\begin{DoxyParams}{Parameters} +{\em sequence} & The sequence to be converted \\ +\hline +\end{DoxyParams} +\hypertarget{utils_8h_a17b796b806f96b70382077fb5bc519bb}{\index{utils.\-h@{utils.\-h}!str\-\_\-uppercase@{str\-\_\-uppercase}} +\index{str\-\_\-uppercase@{str\-\_\-uppercase}!utils.h@{utils.\-h}} +\subsubsection[{str\-\_\-uppercase}]{\setlength{\rightskip}{0pt plus 5cm}void str\-\_\-uppercase ( +\begin{DoxyParamCaption} +\item[{char $\ast$}]{sequence} +\end{DoxyParamCaption} +)}}\label{utils_8h_a17b796b806f96b70382077fb5bc519bb} + + +Convert an input sequence to uppercase. + + +\begin{DoxyParams}{Parameters} +{\em sequence} & The sequence to be converted \\ +\hline +\end{DoxyParams} +\hypertarget{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{\index{utils.\-h@{utils.\-h}!get\-\_\-iindx@{get\-\_\-iindx}} +\index{get\-\_\-iindx@{get\-\_\-iindx}!utils.h@{utils.\-h}} +\subsubsection[{get\-\_\-iindx}]{\setlength{\rightskip}{0pt plus 5cm}int$\ast$ get\-\_\-iindx ( +\begin{DoxyParamCaption} +\item[{unsigned int}]{length} +\end{DoxyParamCaption} +)}}\label{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397} + + +Get an index mapper array (iindx) for accessing the energy matrices, e.\-g. in partition function related functions. + +Access of a position \char`\"{}(i,j)\char`\"{} is then accomplished by using\begin{DoxyVerb}(i,j) ~ iindx[i]-j \end{DoxyVerb} + This function is necessary as most of the two-\/dimensional energy matrices are actually one-\/dimensional arrays throughout the Vienna\-R\-N\-A\-Package + +Consult the implemented code to find out about the mapping formula ;) + +\begin{DoxySeeAlso}{See Also} +\hyperlink{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f}{get\-\_\-indx()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em length} & The length of the R\-N\-A sequence \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The mapper array +\end{DoxyReturn} +\hypertarget{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f}{\index{utils.\-h@{utils.\-h}!get\-\_\-indx@{get\-\_\-indx}} +\index{get\-\_\-indx@{get\-\_\-indx}!utils.h@{utils.\-h}} +\subsubsection[{get\-\_\-indx}]{\setlength{\rightskip}{0pt plus 5cm}int$\ast$ get\-\_\-indx ( +\begin{DoxyParamCaption} +\item[{unsigned int}]{length} +\end{DoxyParamCaption} +)}}\label{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f} + + +Get an index mapper array (indx) for accessing the energy matrices, e.\-g. in M\-F\-E related functions. + +Access of a position \char`\"{}(i,j)\char`\"{} is then accomplished by using\begin{DoxyVerb}(i,j) ~ indx[j]+i \end{DoxyVerb} + This function is necessary as most of the two-\/dimensional energy matrices are actually one-\/dimensional arrays throughout the Vienna\-R\-N\-A\-Package + +Consult the implemented code to find out about the mapping formula ;) + +\begin{DoxySeeAlso}{See Also} +\hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\-\_\-iindx()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em length} & The length of the R\-N\-A sequence \\ +\hline +\end{DoxyParams} +\begin{DoxyReturn}{Returns} +The mapper array +\end{DoxyReturn} +\hypertarget{utils_8h_a36c3a6c3218b041f992052767bc74549}{\index{utils.\-h@{utils.\-h}!constrain\-\_\-ptypes@{constrain\-\_\-ptypes}} +\index{constrain\-\_\-ptypes@{constrain\-\_\-ptypes}!utils.h@{utils.\-h}} +\subsubsection[{constrain\-\_\-ptypes}]{\setlength{\rightskip}{0pt plus 5cm}void constrain\-\_\-ptypes ( +\begin{DoxyParamCaption} +\item[{const char $\ast$}]{constraint, } +\item[{unsigned int}]{length, } +\item[{char $\ast$}]{ptype, } +\item[{int $\ast$}]{B\-P, } +\item[{int}]{min\-\_\-loop\-\_\-size, } +\item[{unsigned int}]{idx\-\_\-type} +\end{DoxyParamCaption} +)}}\label{utils_8h_a36c3a6c3218b041f992052767bc74549} + + +Insert constraining pair types according to constraint structure string. + +\begin{DoxySeeAlso}{See Also} +\hyperlink{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f}{get\-\_\-indx()}, \hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\-\_\-iindx()} +\end{DoxySeeAlso} + +\begin{DoxyParams}{Parameters} +{\em constraint} & The structure constraint string \\ +\hline +{\em length} & The actual length of the sequence (constraint may be shorter) \\ +\hline +{\em ptype} & A pointer to the basepair type array \\ +\hline +{\em min\-\_\-loop\-\_\-size} & The minimal loop size (usually \hyperlink{energy__const_8h_ae646250fd59311356c7e5722a81c3a96}{T\-U\-R\-N} ) \\ +\hline +{\em idx\-\_\-type} & Define the access type for base pair type array (0 = indx, 1 = iindx) \\ +\hline +\end{DoxyParams} + + +\subsection{Variable Documentation} +\hypertarget{utils_8h_af9a866c8417afda7368bbac939ab3c47}{\index{utils.\-h@{utils.\-h}!xsubi@{xsubi}} +\index{xsubi@{xsubi}!utils.h@{utils.\-h}} +\subsubsection[{xsubi}]{\setlength{\rightskip}{0pt plus 5cm}unsigned short xsubi\mbox{[}3\mbox{]}}}\label{utils_8h_af9a866c8417afda7368bbac939ab3c47} + + +Current 48 bit random number. + +This variable is used by \hyperlink{utils_8h_aaa328491c84996e445d027fde9800f2e}{urn()}. These should be set to some random number seeds before the first call to \hyperlink{utils_8h_aaa328491c84996e445d027fde9800f2e}{urn()}. + +\begin{DoxySeeAlso}{See Also} +\hyperlink{utils_8h_aaa328491c84996e445d027fde9800f2e}{urn()} +\end{DoxySeeAlso} diff --git a/binaries/src/ViennaRNA/doc/latex/utils_8h__dep__incl.md5 b/binaries/src/ViennaRNA/doc/latex/utils_8h__dep__incl.md5 new file mode 100644 index 0000000..71cf429 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/utils_8h__dep__incl.md5 @@ -0,0 +1 @@ +3b7e7180bd5c0bd6bfa01e6b08e1a9bc \ No newline at end of file diff --git a/binaries/src/ViennaRNA/doc/latex/utils_8h__dep__incl.pdf b/binaries/src/ViennaRNA/doc/latex/utils_8h__dep__incl.pdf new file mode 100644 index 0000000000000000000000000000000000000000..f76c498dc5376153a4c260401b5da73f0d215987 GIT binary patch literal 7358 zcmb7JbzGDE*A|gRumB}TcWrDVB}NF+AV|s>BP0gfXpk1^P(V^d>5>uzK@cfv2|-#K z0R;)^cSC)C&-3{EeBSrHZ?=2i>ptfj=Uj(BuEVLVs4OTd1SaRKS}Qpq2LVI?D9gL# z($WB7b)=IG))pX!gLKIO0D!QvodXt$#yuV2SfnBnfwDr9U%yU{!J?6HM{@*0=TkYoXz^ibazA!CLxeHMN;Cw z{~{<}Q0c5myOoNp1W_|Ib53lN;XU@wZh%X{bFPs3%U4xj^<((Qo8|$8kSmwja#lk3 z0{X96*_UMARl4C=6KbkC3;fLP)Zs+^jLg_qFyyX`+_J-&P8|%#Zp304Rm8wKhIR>o zkS;@8=4uOVj2-%R$W{B+${{|?O@vUFb|KPR`KHNA@*vaqfxL^A1HIaj{%htg$}cc> zJItRTuRpMU8e!K}%}qLT^Kp@^k9uwz`9`*Y)~tGnUj!(MRAz!Pz_mvg1qv5lpx!4ZP$Hb3F0-QkB~SSDB!+q7B8kxo{>5{vtV zrv#n{_$Q7DVh|wyJ$?lIi!i4YQS!j5=wWg607y&Y0o)}F7r_kx!Z3M&C_oqi$9>~S zgM0DwTUZ(8g#DYfwV;Tg2mt(>bT}j2->=0We=P{LyveU)>LM{HS2O~N0pLTX`?pg; 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(A) : (B))} +00139 \textcolor{preprocessor}{} +\hypertarget{utils_8h_source_l00142}{}\hyperlink{utils_8h_a721b8d5f3abef17f10293f1f7f8c958e}{00142} \textcolor{preprocessor}{#define MIN3(A, B, C) (MIN2( (MIN2((A),(B))) ,(C)))} +00143 \textcolor{preprocessor}{} +\hypertarget{utils_8h_source_l00146}{}\hyperlink{utils_8h_a8d577123d2e66d2b7d0bf9af6e172b93}{00146} \textcolor{preprocessor}{#define MAX3(A, B, C) (MAX2( (MAX2((A),(B))) ,(C)))} +00147 \textcolor{preprocessor}{} +00148 +\hypertarget{utils_8h_source_l00152}{}\hyperlink{utils_8h_a03943706e48069237cd57f2d35ca987e}{00152} \textcolor{preprocessor}{#define XSTR(s) STR(s)} +00153 \textcolor{preprocessor}{} +\hypertarget{utils_8h_source_l00156}{}\hyperlink{utils_8h_a6388870e639eee9c0a69446876f1f8cc}{00156} \textcolor{preprocessor}{#define STR(s) #s} +00157 \textcolor{preprocessor}{} +00158 \textcolor{preprocessor}{#ifndef FILENAME\_MAX\_LENGTH} +00159 \textcolor{preprocessor}{} +\hypertarget{utils_8h_source_l00165}{}\hyperlink{utils_8h_afb228174279df9486a5cb56ac0bc79a3}{00165} \textcolor{preprocessor}{#define FILENAME\_MAX\_LENGTH 80} +00166 \textcolor{preprocessor}{} +\hypertarget{utils_8h_source_l00172}{}\hyperlink{utils_8h_a33c3b1826b8e2739f09f111ec719ded5}{00172} \textcolor{preprocessor}{#define FILENAME\_ID\_LENGTH 42} +00173 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif} +00174 \textcolor{preprocessor}{} +00175 +00176 \textcolor{preprocessor}{#ifdef HAVE\_CONFIG\_H} +00177 \textcolor{preprocessor}{}\textcolor{preprocessor}{#include } +00178 \textcolor{preprocessor}{#ifndef HAVE\_STRDUP} +00179 \textcolor{preprocessor}{}\textcolor{keywordtype}{char} *strdup(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s); +00180 \textcolor{preprocessor}{#endif} +00181 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif} +00182 \textcolor{preprocessor}{}\textcolor{preprocessor}{#ifdef WITH\_DMALLOC} +00183 \textcolor{preprocessor}{}\textcolor{comment}{/* use dmalloc library to check for memory management bugs */} +00184 \textcolor{preprocessor}{#include "dmalloc.h"} +00185 \textcolor{preprocessor}{#define space(S) calloc(1,(S))} +00186 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else} +00187 \textcolor{preprocessor}{} +00194 \textcolor{comment}{/*@only@*/} \textcolor{comment}{/*@notnull@*/} +00195 \textcolor{keywordtype}{void} *\hyperlink{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{space}(\textcolor{keywordtype}{unsigned} size) \textcolor{comment}{/*@ensures MaxSet(result) == (size-1);@*/}; +00196 +00204 \textcolor{comment}{/*@only@*/} \textcolor{comment}{/*@notnull@*/} +00205 \textcolor{keywordtype}{void} *\hyperlink{utils_8h_a9037ada838835b1b9db41581a021b0c8}{xrealloc}(\textcolor{comment}{/*@null@*/} \textcolor{comment}{/*@only@*/} \textcolor{comment}{/*@out@*/} \textcolor{comment}{/*@returned@*/} \textcolor{keywordtype}{void} *p, +00206 \textcolor{keywordtype}{unsigned} size) \textcolor{comment}{/*@modifies *p @*/} \textcolor{comment}{/*@ensures MaxSet(result) == (size-1) @*/}; +00207 \textcolor{preprocessor}{#endif} +00208 \textcolor{preprocessor}{} +00215 \textcolor{comment}{/*@exits@*/} +00216 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{nrerror}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} message[]); +00217 +00225 \textcolor{keywordtype}{void} \hyperlink{utils_8h_af2355fa8746f2f30fbe71db65dea3d51}{warn\_user}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} message[]); +00226 +00230 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a8aaa6d9be6f803f496d9b97375c371f3}{init\_rand}(\textcolor{keywordtype}{void}); +00231 +00240 \textcolor{keyword}{extern} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} \hyperlink{utils_8h_af9a866c8417afda7368bbac939ab3c47}{xsubi}[3]; +00241 +00248 \textcolor{keywordtype}{double} \hyperlink{utils_8h_aaa328491c84996e445d027fde9800f2e}{urn}(\textcolor{keywordtype}{void}); +00249 +00257 \textcolor{keywordtype}{int} \hyperlink{utils_8h_a68ff0849d44f62fe491800378a5ffcb4}{int\_urn}(\textcolor{keywordtype}{int} from, \textcolor{keywordtype}{int} to); +00258 +00259 \textcolor{keywordtype}{void} filecopy(FILE *from, FILE *to); \textcolor{comment}{/* inefficient `cp' */} +00260 +00269 \textcolor{comment}{/*@observer@*/} +00270 \textcolor{keywordtype}{char} *\hyperlink{utils_8h_a7afeb906cb36e9d77379eabc6907ac46}{time\_stamp}(\textcolor{keywordtype}{void}); +00271 +00279 \textcolor{comment}{/*@only@*/} \textcolor{comment}{/*@notnull@*/} +00280 \textcolor{keywordtype}{char} *\hyperlink{utils_8h_a1b95eac365a021572e1c37e5993a89be}{random\_string}(\textcolor{keywordtype}{int} l, \textcolor{keyword}{const} \textcolor{keywordtype}{char} symbols[]); +00281 +00290 \textcolor{keywordtype}{int} \hyperlink{utils_8h_ad9dc7bfc9aa664dc6698f17ce07fc7e7}{hamming}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1, \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2); +00291 +00301 \textcolor{keywordtype}{int} \hyperlink{utils_8h_a96d3c36717d624514055ce201cab1542}{hamming\_bound}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1, \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2, \textcolor{keywordtype}{int} n); +00302 +00313 \textcolor{comment}{/*@only@*/} \textcolor{comment}{/*@null@*/} +00314 \textcolor{keywordtype}{char} *\hyperlink{utils_8h_abe51806d14cff0789a8c1df7dbc45b71}{get\_line}(FILE *fp); +00315 +00316 \textcolor{keywordtype}{int} skip\_comment\_lines(\textcolor{keywordtype}{char} **line); +00317 +00338 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\_input\_line}(\textcolor{keywordtype}{char} **\textcolor{keywordtype}{string}, +00339 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} options); +00340 +00341 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} get\_multi\_input\_line(\textcolor{keywordtype}{char} **\textcolor{keywordtype}{string}, +00342 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} options); +00343 +00396 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\_record}( \textcolor{keywordtype}{char} **header, +00397 \textcolor{keywordtype}{char} **sequence, +00398 \textcolor{keywordtype}{char} ***rest, +00399 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} options); +00400 +00401 +00402 \textcolor{comment}{/* \(\backslash\)brief Extract a dot-bracket structure string from (multiline)character array} +00403 \textcolor{comment}{ *} +00404 \textcolor{comment}{ * This function extracts a dot-bracket structure string from the 'rest' array as} +00405 \textcolor{comment}{ * returned by read\_record() and returns it. All occurences of comments within the} +00406 \textcolor{comment}{ * 'lines' array will be skipped as long as they do not break the structure string.} +00407 \textcolor{comment}{ * If no structure could be read, this function returns NULL.} +00408 \textcolor{comment}{ *} +00409 \textcolor{comment}{ * \(\backslash\)see read\_record()} +00410 \textcolor{comment}{ *} +00411 \textcolor{comment}{ * \(\backslash\)param lines The (multiline) character array to be parsed} +00412 \textcolor{comment}{ * \(\backslash\)param length The assumed length of the dot-bracket string (passing a value < 1 results in no length + limit)} +00413 \textcolor{comment}{ * \(\backslash\)param option Some options which may be passed to alter the behavior of the function, use 0 for no + options} +00414 \textcolor{comment}{ * \(\backslash\)return The dot-bracket string read from lines or NULL} +00415 \textcolor{comment}{ */} +00416 \textcolor{keywordtype}{char} *extract\_record\_rest\_structure(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **lines, +00417 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length, +00418 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} option); +00419 +00431 \textcolor{keywordtype}{char} *\hyperlink{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{pack\_structure}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *struc); +00432 +00442 \textcolor{keywordtype}{char} *\hyperlink{utils_8h_a071c6921efe1eb974f115ee6fefa3c39}{unpack\_structure}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *packed); +00443 +00453 \textcolor{keywordtype}{short} *\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\_pair\_table}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure); +00454 +00455 \textcolor{keywordtype}{short} *make\_pair\_table\_pk(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure); +00456 +00463 \textcolor{keywordtype}{short} *\hyperlink{utils_8h_afeaa6d68eef3a99d0a7aa08aa91c6601}{copy\_pair\_table}(\textcolor{keyword}{const} \textcolor{keywordtype}{short} *pt); +00464 +00470 \textcolor{keywordtype}{short} *\hyperlink{utils_8h_a3c81b3967056c3888b8472b65fbb16f5}{alimake\_pair\_table}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure); +00471 +00477 \textcolor{keywordtype}{short} *\hyperlink{utils_8h_a9aa3bf3b4346bb7fb88efc154dd07a79}{make\_pair\_table\_snoop}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure); +00478 +00491 \textcolor{keywordtype}{int} *\hyperlink{utils_8h_a4358e89f64cc87a563b7ef3855f75bed}{make\_loop\_index\_pt}(\textcolor{keywordtype}{short} *pt); +00492 +00493 +00494 \textcolor{keywordtype}{int} bp\_distance(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *str1, +00495 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *str2); +00496 +00502 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a6bf778117d31b7fd90db435323f4ef74}{print\_tty\_input\_seq}(\textcolor{keywordtype}{void}); +00503 +00512 \textcolor{keywordtype}{void} \hyperlink{utils_8h_ae4ef89b662a3e9b5b5f0781d9757aba0}{print\_tty\_input\_seq\_str}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *s); +00513 +00519 \textcolor{keywordtype}{void} \hyperlink{utils_8h_ae8ae8a34962b9959be3f6c40f0a80ac1}{print\_tty\_constraint\_full}(\textcolor{keywordtype}{void}); +00520 +00537 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a4d167deb70bb51723e44374dc981deb2}{print\_tty\_constraint}(\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} option); +00538 +00546 \textcolor{keywordtype}{void} \hyperlink{utils_8h_ad3f18dd83f958f18b2f26ecb99305208}{str\_DNA2RNA}(\textcolor{keywordtype}{char} *sequence); +00547 +00553 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a17b796b806f96b70382077fb5bc519bb}{str\_uppercase}(\textcolor{keywordtype}{char} *sequence); +00554 +00568 \textcolor{keywordtype}{int} *\hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\_iindx}(\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length); +00569 +00584 \textcolor{keywordtype}{int} *\hyperlink{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f}{get\_indx}(\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length); +00585 +00586 \textcolor{keywordtype}{void} getConstraint( \textcolor{keywordtype}{char} **cstruc, +00587 \textcolor{keyword}{const} \textcolor{keywordtype}{char} **lines, +00588 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} option); +00589 +00601 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a36c3a6c3218b041f992052767bc74549}{constrain\_ptypes}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *constraint, +00602 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length, +00603 \textcolor{keywordtype}{char} *ptype, +00604 \textcolor{keywordtype}{int} *BP, +00605 \textcolor{keywordtype}{int} min\_loop\_size, +00606 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} idx\_type); +00607 +00608 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *make\_referenceBP\_array(\textcolor{keywordtype}{short} *reference\_pt, +00609 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} turn); +00610 +00611 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} *compute\_BPdifferences( \textcolor{keywordtype}{short} *pt1, +00612 \textcolor{keywordtype}{short} *pt2, +00613 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} turn); +00614 +00615 \textcolor{preprocessor}{#endif} +\end{DoxyCode} diff --git a/binaries/src/ViennaRNA/doc/latex/viennarna.bib b/binaries/src/ViennaRNA/doc/latex/viennarna.bib new file mode 100644 index 0000000..0fac6b7 --- /dev/null +++ b/binaries/src/ViennaRNA/doc/latex/viennarna.bib @@ -0,0 +1,281 @@ +@article{zuker:1981, + title={Optimal computer folding of large {RNA} sequences using thermodynamics and auxiliary information}, + author={Zuker, M. and Stiegler, P.}, + journal={Nucleic acids research}, + volume={9}, + number={1}, + pages={133--148}, + year={1981}, + publisher={Oxford Univ Press} +} +@article{mccaskill:1990, + title={The equilibrium partition function and base pair binding probabilities for {RNA} secondary structure}, + author={McCaskill, J.S.}, + journal={Biopolymers}, + volume={29}, + number={6-7}, + pages={1105--1119}, + year={1990}, + publisher={Wiley Online Library} +} + +@article{mathews:2004, + title={Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of {RNA} secondary structure}, + author={Mathews, D.H. and Disney, M.D. and Childs, J.L. and Schroeder, S.J. and Zuker, M. and Turner, D.H.}, + journal={Proceedings of the National Academy of Sciences of the United States of America}, + volume={101}, + number={19}, + pages={7287}, + year={2004}, + publisher={National Acad Sciences} +} + +@article{mathews:1999, + title={Expanded sequence dependence of thermodynamic parameters improves prediction of {RNA} secondary structure}, + author={Mathews, D.H. and Sabina, J. and Zuker, M. and Turner, D.H. and others}, + journal={Journal of molecular biology}, + volume={288}, + number={5}, + pages={911--940}, + year={1999}, + publisher={Elsevier Science} +} + +@article{turner:2010 , + title={{NNDB}: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure}, + author={Turner, D.H. and Mathews, D.H.}, + journal={Nucleic Acids Research}, + volume={38}, + number={suppl 1}, + pages={D280--D282}, + year={2010}, + publisher={Oxford Univ Press} +} + +@article{turner:1988, + title={{RNA} structure prediction}, + author={Turner, D.H. and Sugimoto, N. and Freier, S.M.}, + journal={Annual review of biophysics and biophysical chemistry}, + volume={17}, + number={1}, + pages={167--192}, + year={1988}, + publisher={Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA} +} + +@article{jaeger:1989, + title={Improved predictions of secondary structures for {RNA}}, + author={Jaeger, J.A. and Turner, D.H. and Zuker, M.}, + journal={Proceedings of the National Academy of Sciences}, + volume={86}, + number={20}, + pages={7706}, + year={1989}, + publisher={National Acad Sciences} +} +@article{he:1991, + title={Nearest-neighbor parameters for {G-U} mismatches: {5'GU3'}/{3'UG5'} is destabilizing in the contexts {CGUG/GUGC}, {UGUA/AUGU}, and {AGUU/UUGA} but stabilizing in {GGUC/CUGG}}, + author={He, L. and Kierzek, R. and SantaLucia Jr, J. and Walter, A.E. and Turner, D.H.}, + journal={Biochemistry}, + volume={30}, + number={46}, + pages={11124--11132}, + year={1991}, + publisher={ACS Publications} +} +@article{peritz:1991, + title={Thermodynamic study of internal loops in oligoribonucleotides: symmetric loops are more stable than asymmetric loops}, + author={Peritz, A.E. and Kierzek, R. and Sugimoto, N. and Turner, D.H.}, + journal={Biochemistry}, + volume={30}, + number={26}, + pages={6428--6436}, + year={1991}, + publisher={ACS Publications} +} +@article{walter:1994, + title={Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of {RNA} folding}, + author={Walter, A.E. and Turner, D.H. and Kim, J. and Lyttle, M.H. and M{\"u}ller, P. and Mathews, D.H. and Zuker, M.}, + journal={Proceedings of the National Academy of Sciences}, + volume={91}, + number={20}, + pages={9218}, + year={1994}, + publisher={National Acad Sciences} +} +@article{bruccoleri:1988, + title={An improved algorithm for nucleic acid secondary structure display}, + author={Bruccoleri, R.E. and Heinrich, G.}, + journal={Computer applications in the biosciences: CABIOS}, + volume={4}, + number={1}, + pages={167--173}, + year={1988}, + publisher={Oxford Univ Press} +} +@article{hofacker:1994a, + title={The rules of the evolutionary game for {RNA}: {A} statistical characterization of the sequence to structure mapping in {RNA}}, + author={Hofacker, I.L. and Organisiert, C.F.}, + year={1994}, + publisher={Citeseer} +} +@book{adams:1979, + title = {{T}he {H}itchhikers {Guide} to the {G}alaxy}, + author = {Douglas Adams}, + year = {1979}, +} + +@article{dimitrov:2004, + title={Prediction of hybridization and melting for double-stranded nucleic acids}, + author={Dimitrov, R.A. and Zuker, M.}, + journal={Biophysical Journal}, + volume={87}, + number={1}, + pages={215--226}, + year={2004}, + publisher={Elsevier} +} + +@article{hofacker:1994, + title={Fast folding and comparison of {RNA} secondary structures}, + author={Hofacker, I.L. and Fontana, W. and Stadler, P.F. and Bonhoeffer, L.S. and Tacker, M. and Schuster, P.}, + journal={Monatshefte f{\"u}r Chemie/Chemical Monthly}, + volume={125}, + number={2}, + pages={167--188}, + year={1994}, + publisher={Springer} +} + +@article{hofacker:2002, + title={Secondary structure prediction for aligned {RNA} sequences}, + author={Hofacker, I.L. and Fekete, M. and Stadler, P.F.}, + journal={Journal of molecular biology}, + volume={319}, + number={5}, + pages={1059--1066}, + year={2002}, + publisher={Elsevier} +} +@article{hofacker:2006, + title={Memory efficient folding algorithms for circular {RNA} secondary structures}, + author={Hofacker, I.L. and Stadler, P.F.}, + journal={Bioinformatics}, + volume={22}, + number={10}, + pages={1172--1176}, + year={2006}, + publisher={Oxford Univ Press} +} +@article{bernhart:2008, + title={{RNAalifold}: Improved consensus structure prediction for {RNA} alignments}, + author={Bernhart, S.H. and Hofacker, I.L. and Will, S. and Gruber, A.R. and Stadler, P.F.}, + journal={BMC bioinformatics}, + volume={9}, + number={1}, + pages={474}, + year={2008}, + publisher={BioMed Central Ltd} +} +@article{bernhart:2006, + title={Partition function and base pairing probabilities of {RNA} heterodimers}, + author={Bernhart, S.H. and Tafer, H. and M{\"u}ckstein, U. and Flamm, C. and Stadler, P.F. and Hofacker, I.L.}, + journal={Algorithms for Molecular Biology}, + volume={1}, + number={1}, + pages={3}, + year={2006}, + publisher={BioMed Central Ltd} +} +@article{fontana:1993a, + title={Statistics of {RNA} secondary structures}, + author={Fontana, W. and Konings, D.A.M. and Stadler, P.F. and Schuster, P.}, + journal={Biopolymers}, + volume={33}, + number={9}, + pages={1389--1404}, + year={1993}, + publisher={Wiley Online Library} +} +@article{fontana:1993b, + title={{RNA} folding and combinatory landscapes}, + author={Fontana, W. and Stadler, P.F. and Bornberg-Bauer, E.G. and Griesmacher, T. and Hofacker, I.L. and Tacker, M. and Tarazona, P. and Weinberger, E.D. and Schuster, P.}, + journal={Physical review E}, + volume={47}, + number={3}, + pages={2083}, + year={1993}, + publisher={APS} +} +@article{shapiro:1990, + title={Comparing multiple {RNA} secondary structures using tree comparisons}, + author={Shapiro, B.A. and Zhang, K.}, + journal={Computer applications in the biosciences: CABIOS}, + volume={6}, + number={4}, + pages={309--318}, + year={1990}, + publisher={Oxford Univ Press} +} +@article{shapiro:1988, + title={An algorithm for comparing multiple {RNA} secondary structures}, + author={Shapiro, B.A.}, + journal={Computer applications in the biosciences: CABIOS}, + volume={4}, + number={3}, + pages={387--393}, + year={1988}, + publisher={Oxford Univ Press} +} + +@article{lorenz:2012, + title = {{RNA} Folding Algorithms with {G-Quadruplexes}}, + author = {Lorenz, Ronny and Bernhart, Stephan H. and Externbrink, Fabian and Qin, Jing and H{\"{o}}ner zu Siederdissen, Christian and Amman, Fabian and Hofacker, Ivo L. and Stadler, Peter F.}, + year = {2012}, + note = {submitted}, + abstract = {G-quadruplexes are abundant locally stable structural elements in nucleic acids. The combinatorial theory of RNA structures and the dynamic programming algorithms for RNA secondary structure prediction are extended here to incorporate G-quadruplexes. Using a simple but plausible energy model for quadruplexes, we find that the overwhelming majority of putative quadruplex-forming sequences in the human genome are likely to fold into canonical secondary structures instead.} +} + +@article{lorenz:2011, + title={{ViennaRNA} Package 2.0}, + author={Lorenz, Ronny and Bernhart, Stephan H. and H{\"o}ner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L.}, + journal={Algorithms for Molecular Biology}, + volume={6}, + number={1}, + pages={26}, + year={2011}, + publisher={BioMed Central Ltd}, + doi={10.1186/1748-7188-6-26}, + abstract={BACKGROUND: Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely used as a basis to explain experimental findings. Based on carefully measured thermodynamic parameters exact dynamic programming algorithms can be used to compute ground states, base pairing probabilities, as well as thermodynamic properties.\\ + RESULTS: The ViennaRNA Package has been a widely used compilation of RNA secondary structure related computer programs for nearly two decades. Major changes in the structure of the standard energy model, the Turner 2004 parameters, the pervasive use of multi-core CPUs, and an increasing number of algorithmic variants prompted a major technical overhaul of both the underlying RNAlib and the interactive user programs. New features include an expanded repertoire of tools to assess RNA-RNA interactions and restricted ensembles of structures, additional output information such as centroid structures and maximum expected accuracy structures derived from base pairing probabilities, or z-scores for locally stable secondary structures, and support for input in fasta format. Updates were implemented without compromising the computational efficiency of the core algorithms and ensuring compatibility with earlier versions.\\ + CONCLUSIONS: The ViennaRNA Package 2.0, supporting concurrent computations via OpenMP, can be downloaded from www.tbi.univie.ac.at/RNA } +} + +@InProceedings{lorenz:2009, + editor = {Grosse, Ivo and Neumann, Steffen and Posch, Stefan + and Schreiber, Falk and Stadler, Peter F.}, + author = {Lorenz, Ronny and Flamm, Christoph and Hofacker, Ivo L.}, + title = {2D Projections of {RNA} folding Landscapes}, + booktitle = {German Conference on Bioinformatics 2009}, + volume = {157}, + month = {September}, + year = {2009}, + pages = {11--20}, + isbn = {978-3-88579-251-2}, + publisher = {Gesellschaft f.\ Informatik}, + address = {Bonn}, + series = {Lecture Notes in Informatics}, + abstract = {The analysis of RNA folding landscapes yields insights into the kinetic folding +behavior not available from classical structure prediction methods. This is especially +important for multi-stable RNAs whose function is related to structural changes, +as in the case of riboswitches. However, exact methods such as barrier tree analysis +scale exponentially with sequence length. Here we present an algorithm that computes +a projection of the energy landscape into two dimensions, namely the distances +to two reference structures. This yields an abstraction of the high-dimensional energy +landscape that can be conveniently visualized, and can serve as the basis for estimating +energy barriers and refolding pathways. With an asymptotic time complexity of O(n^7) +the algorithm is computationally demanding. However, by exploiting the sparsity of +the dynamic programming matrices and parallelization for multi-core processors, our +implementation is practical for sequences of up to 400 nt, which includes most RNAs +of biological interest.} +} -- 1.7.10.2