search_biomodel 0.1.2 → 1.0.0

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/Manifest.txt

@@ -0,0 +1,283 @@
+.autotest
+.gemtest
+CHANGELOG.ja.rdoc
+CHANGELOG.rdoc
+Manifest.txt
+README.ja.rdoc
+README.rdoc
+Rakefile
+bin/nokogiri
+ext/nokogiri/depend
+ext/nokogiri/extconf.rb
+ext/nokogiri/html_document.c
+ext/nokogiri/html_document.h
+ext/nokogiri/html_element_description.c
+ext/nokogiri/html_element_description.h
+ext/nokogiri/html_entity_lookup.c
+ext/nokogiri/html_entity_lookup.h
+ext/nokogiri/html_sax_parser_context.c
+ext/nokogiri/html_sax_parser_context.h
+ext/nokogiri/nokogiri.c
+ext/nokogiri/nokogiri.h
+ext/nokogiri/xml_attr.c
+ext/nokogiri/xml_attr.h
+ext/nokogiri/xml_attribute_decl.c
+ext/nokogiri/xml_attribute_decl.h
+ext/nokogiri/xml_cdata.c
+ext/nokogiri/xml_cdata.h
+ext/nokogiri/xml_comment.c
+ext/nokogiri/xml_comment.h
+ext/nokogiri/xml_document.c
+ext/nokogiri/xml_document.h
+ext/nokogiri/xml_document_fragment.c
+ext/nokogiri/xml_document_fragment.h
+ext/nokogiri/xml_dtd.c
+ext/nokogiri/xml_dtd.h
+ext/nokogiri/xml_element_content.c
+ext/nokogiri/xml_element_content.h
+ext/nokogiri/xml_element_decl.c
+ext/nokogiri/xml_element_decl.h
+ext/nokogiri/xml_encoding_handler.c
+ext/nokogiri/xml_encoding_handler.h
+ext/nokogiri/xml_entity_decl.c
+ext/nokogiri/xml_entity_decl.h
+ext/nokogiri/xml_entity_reference.c
+ext/nokogiri/xml_entity_reference.h
+ext/nokogiri/xml_io.c
+ext/nokogiri/xml_io.h
+ext/nokogiri/xml_libxml2_hacks.c
+ext/nokogiri/xml_libxml2_hacks.h
+ext/nokogiri/xml_namespace.c
+ext/nokogiri/xml_namespace.h
+ext/nokogiri/xml_node.c
+ext/nokogiri/xml_node.h
+ext/nokogiri/xml_node_set.c
+ext/nokogiri/xml_node_set.h
+ext/nokogiri/xml_processing_instruction.c
+ext/nokogiri/xml_processing_instruction.h
+ext/nokogiri/xml_reader.c
+ext/nokogiri/xml_reader.h
+ext/nokogiri/xml_relax_ng.c
+ext/nokogiri/xml_relax_ng.h
+ext/nokogiri/xml_sax_parser.c
+ext/nokogiri/xml_sax_parser.h
+ext/nokogiri/xml_sax_parser_context.c
+ext/nokogiri/xml_sax_parser_context.h
+ext/nokogiri/xml_sax_push_parser.c
+ext/nokogiri/xml_sax_push_parser.h
+ext/nokogiri/xml_schema.c
+ext/nokogiri/xml_schema.h
+ext/nokogiri/xml_syntax_error.c
+ext/nokogiri/xml_syntax_error.h
+ext/nokogiri/xml_text.c
+ext/nokogiri/xml_text.h
+ext/nokogiri/xml_xpath_context.c
+ext/nokogiri/xml_xpath_context.h
+ext/nokogiri/xslt_stylesheet.c
+ext/nokogiri/xslt_stylesheet.h
+lib/nokogiri.rb
+lib/nokogiri/css.rb
+lib/nokogiri/css/node.rb
+lib/nokogiri/css/parser.rb
+lib/nokogiri/css/parser.y
+lib/nokogiri/css/parser_extras.rb
+lib/nokogiri/css/syntax_error.rb
+lib/nokogiri/css/tokenizer.rb
+lib/nokogiri/css/tokenizer.rex
+lib/nokogiri/css/xpath_visitor.rb
+lib/nokogiri/decorators/slop.rb
+lib/nokogiri/ffi/encoding_handler.rb
+lib/nokogiri/ffi/html/document.rb
+lib/nokogiri/ffi/html/element_description.rb
+lib/nokogiri/ffi/html/entity_lookup.rb
+lib/nokogiri/ffi/html/sax/parser_context.rb
+lib/nokogiri/ffi/io_callbacks.rb
+lib/nokogiri/ffi/libxml.rb
+lib/nokogiri/ffi/structs/common_node.rb
+lib/nokogiri/ffi/structs/html_elem_desc.rb
+lib/nokogiri/ffi/structs/html_entity_desc.rb
+lib/nokogiri/ffi/structs/xml_alloc.rb
+lib/nokogiri/ffi/structs/xml_attr.rb
+lib/nokogiri/ffi/structs/xml_attribute.rb
+lib/nokogiri/ffi/structs/xml_buffer.rb
+lib/nokogiri/ffi/structs/xml_char_encoding_handler.rb
+lib/nokogiri/ffi/structs/xml_document.rb
+lib/nokogiri/ffi/structs/xml_dtd.rb
+lib/nokogiri/ffi/structs/xml_element.rb
+lib/nokogiri/ffi/structs/xml_element_content.rb
+lib/nokogiri/ffi/structs/xml_entity.rb
+lib/nokogiri/ffi/structs/xml_enumeration.rb
+lib/nokogiri/ffi/structs/xml_node.rb
+lib/nokogiri/ffi/structs/xml_node_set.rb
+lib/nokogiri/ffi/structs/xml_notation.rb
+lib/nokogiri/ffi/structs/xml_ns.rb
+lib/nokogiri/ffi/structs/xml_parser_context.rb
+lib/nokogiri/ffi/structs/xml_parser_input.rb
+lib/nokogiri/ffi/structs/xml_relax_ng.rb
+lib/nokogiri/ffi/structs/xml_sax_handler.rb
+lib/nokogiri/ffi/structs/xml_sax_push_parser_context.rb
+lib/nokogiri/ffi/structs/xml_schema.rb
+lib/nokogiri/ffi/structs/xml_syntax_error.rb
+lib/nokogiri/ffi/structs/xml_text_reader.rb
+lib/nokogiri/ffi/structs/xml_xpath_context.rb
+lib/nokogiri/ffi/structs/xml_xpath_object.rb
+lib/nokogiri/ffi/structs/xml_xpath_parser_context.rb
+lib/nokogiri/ffi/structs/xslt_stylesheet.rb
+lib/nokogiri/ffi/weak_bucket.rb
+lib/nokogiri/ffi/xml/attr.rb
+lib/nokogiri/ffi/xml/attribute_decl.rb
+lib/nokogiri/ffi/xml/cdata.rb
+lib/nokogiri/ffi/xml/comment.rb
+lib/nokogiri/ffi/xml/document.rb
+lib/nokogiri/ffi/xml/document_fragment.rb
+lib/nokogiri/ffi/xml/dtd.rb
+lib/nokogiri/ffi/xml/element_content.rb
+lib/nokogiri/ffi/xml/element_decl.rb
+lib/nokogiri/ffi/xml/entity_decl.rb
+lib/nokogiri/ffi/xml/entity_reference.rb
+lib/nokogiri/ffi/xml/namespace.rb
+lib/nokogiri/ffi/xml/node.rb
+lib/nokogiri/ffi/xml/node_set.rb
+lib/nokogiri/ffi/xml/processing_instruction.rb
+lib/nokogiri/ffi/xml/reader.rb
+lib/nokogiri/ffi/xml/relax_ng.rb
+lib/nokogiri/ffi/xml/sax/parser.rb
+lib/nokogiri/ffi/xml/sax/parser_context.rb
+lib/nokogiri/ffi/xml/sax/push_parser.rb
+lib/nokogiri/ffi/xml/schema.rb
+lib/nokogiri/ffi/xml/syntax_error.rb
+lib/nokogiri/ffi/xml/text.rb
+lib/nokogiri/ffi/xml/xpath.rb
+lib/nokogiri/ffi/xml/xpath_context.rb
+lib/nokogiri/ffi/xslt/stylesheet.rb
+lib/nokogiri/html.rb
+lib/nokogiri/html/builder.rb
+lib/nokogiri/html/document.rb
+lib/nokogiri/html/document_fragment.rb
+lib/nokogiri/html/element_description.rb
+lib/nokogiri/html/entity_lookup.rb
+lib/nokogiri/html/sax/parser.rb
+lib/nokogiri/html/sax/parser_context.rb
+lib/nokogiri/syntax_error.rb
+lib/nokogiri/version.rb
+lib/nokogiri/version_warning.rb
+lib/nokogiri/xml.rb
+lib/nokogiri/xml/attr.rb
+lib/nokogiri/xml/attribute_decl.rb
+lib/nokogiri/xml/builder.rb
+lib/nokogiri/xml/cdata.rb
+lib/nokogiri/xml/character_data.rb
+lib/nokogiri/xml/document.rb
+lib/nokogiri/xml/document_fragment.rb
+lib/nokogiri/xml/dtd.rb
+lib/nokogiri/xml/element_content.rb
+lib/nokogiri/xml/element_decl.rb
+lib/nokogiri/xml/entity_decl.rb
+lib/nokogiri/xml/namespace.rb
+lib/nokogiri/xml/node.rb
+lib/nokogiri/xml/node/save_options.rb
+lib/nokogiri/xml/node_set.rb
+lib/nokogiri/xml/notation.rb
+lib/nokogiri/xml/parse_options.rb
+lib/nokogiri/xml/pp.rb
+lib/nokogiri/xml/pp/character_data.rb
+lib/nokogiri/xml/pp/node.rb
+lib/nokogiri/xml/processing_instruction.rb
+lib/nokogiri/xml/reader.rb
+lib/nokogiri/xml/relax_ng.rb
+lib/nokogiri/xml/sax.rb
+lib/nokogiri/xml/sax/document.rb
+lib/nokogiri/xml/sax/parser.rb
+lib/nokogiri/xml/sax/parser_context.rb
+lib/nokogiri/xml/sax/push_parser.rb
+lib/nokogiri/xml/schema.rb
+lib/nokogiri/xml/syntax_error.rb
+lib/nokogiri/xml/text.rb
+lib/nokogiri/xml/xpath.rb
+lib/nokogiri/xml/xpath/syntax_error.rb
+lib/nokogiri/xml/xpath_context.rb
+lib/nokogiri/xslt.rb
+lib/nokogiri/xslt/stylesheet.rb
+lib/xsd/xmlparser/nokogiri.rb
+tasks/cross_compile.rb
+tasks/test.rb
+test/css/test_nthiness.rb
+test/css/test_parser.rb
+test/css/test_tokenizer.rb
+test/css/test_xpath_visitor.rb
+test/decorators/test_slop.rb
+test/ffi/test_document.rb
+test/files/2ch.html
+test/files/address_book.rlx
+test/files/address_book.xml
+test/files/bar/bar.xsd
+test/files/dont_hurt_em_why.xml
+test/files/encoding.html
+test/files/encoding.xhtml
+test/files/exslt.xml
+test/files/exslt.xslt
+test/files/foo/foo.xsd
+test/files/po.xml
+test/files/po.xsd
+test/files/shift_jis.html
+test/files/shift_jis.xml
+test/files/snuggles.xml
+test/files/staff.dtd
+test/files/staff.xml
+test/files/staff.xslt
+test/files/tlm.html
+test/files/valid_bar.xml
+test/helper.rb
+test/html/sax/test_parser.rb
+test/html/sax/test_parser_context.rb
+test/html/test_builder.rb
+test/html/test_document.rb
+test/html/test_document_encoding.rb
+test/html/test_document_fragment.rb
+test/html/test_element_description.rb
+test/html/test_named_characters.rb
+test/html/test_node.rb
+test/html/test_node_encoding.rb
+test/test_convert_xpath.rb
+test/test_css_cache.rb
+test/test_encoding_handler.rb
+test/test_memory_leak.rb
+test/test_nokogiri.rb
+test/test_reader.rb
+test/test_soap4r_sax.rb
+test/test_xslt_transforms.rb
+test/xml/node/test_save_options.rb
+test/xml/node/test_subclass.rb
+test/xml/sax/test_parser.rb
+test/xml/sax/test_parser_context.rb
+test/xml/sax/test_push_parser.rb
+test/xml/test_attr.rb
+test/xml/test_attribute_decl.rb
+test/xml/test_builder.rb
+test/xml/test_cdata.rb
+test/xml/test_comment.rb
+test/xml/test_document.rb
+test/xml/test_document_encoding.rb
+test/xml/test_document_fragment.rb
+test/xml/test_dtd.rb
+test/xml/test_dtd_encoding.rb
+test/xml/test_element_content.rb
+test/xml/test_element_decl.rb
+test/xml/test_entity_decl.rb
+test/xml/test_entity_reference.rb
+test/xml/test_namespace.rb
+test/xml/test_node.rb
+test/xml/test_node_attributes.rb
+test/xml/test_node_encoding.rb
+test/xml/test_node_reparenting.rb
+test/xml/test_node_set.rb
+test/xml/test_parse_options.rb
+test/xml/test_processing_instruction.rb
+test/xml/test_reader_encoding.rb
+test/xml/test_relax_ng.rb
+test/xml/test_schema.rb
+test/xml/test_syntax_error.rb
+test/xml/test_text.rb
+test/xml/test_unparented_node.rb
+test/xml/test_xpath.rb
+test/xslt/test_custom_functions.rb

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/README.ja.rdoc

@@ -0,0 +1,102 @@
+= Nokogiri (鋸)
+
+* http://nokogiri.org/
+* http://github.com/tenderlove/nokogiri/wikis
+* http://github.com/tenderlove/nokogiri/tree/master
+* http://groups.google.com/group/nokogiri-list
+* http://github.com/tenderlove/nokogiri/issues
+
+== DESCRIPTION:
+
+Nokogiri はHTMLとXMLとSAXとXSLTとReaderのパーサーです。とりわけ重要な特徴は、
+ドキュメントをXPathやCSS3セレクター経由で探索する機能を持つことです。
+
+XMLは暴力に似ている - XMLが君の問題を解決しないとしたら、君はXMLを十分に
+使いこなしていない事になる。
+
+== FEATURES:
+
+* XPath による探索
+* CSS3 のセレクターによる探索
+* XML/HTMLのビルダー
+
+XML/HTMLの高速な解析と探索検索、ならびにCSS3セレクタとXPathをサポートしています。
+
+== SUPPORT:
+
+日本語でNokogiriの
+{メーリングリスト}[http://groups.google.com/group/nokogiri-list]
+
+  * http://groups.google.com/group/nokogiri-list
+
+{バグ報告}[http://github.com/tenderlove/nokogiri/issues]
+
+  * http://github.com/tenderlove/nokogiri/issues
+
+IRCのチャンネルはfreenodeの #nokogiri です。
+
+== SYNOPSIS:
+
+  require 'nokogiri'
+  require 'open-uri'
+  
+  doc = Nokogiri::HTML(open('http://www.google.com/search?q=tenderlove'))
+  
+  ####
+  # Search for nodes by css
+  doc.css('h3.r a.l').each do |link|
+    puts link.content
+  end
+  
+  ####
+  # Search for nodes by xpath
+  doc.xpath('//h3/a[@class="l"]').each do |link|
+    puts link.content
+  end
+  
+  ####
+  # Or mix and match.
+  doc.search('h3.r a.l', '//h3/a[@class="l"]').each do |link|
+    puts link.content
+  end
+
+
+== REQUIREMENTS:
+
+* ruby 1.8 or 1.9
+* libxml2
+* libxml2-dev
+* libxslt
+* libxslt-dev
+
+== INSTALL:
+
+* sudo gem install nokogiri
+
+== LICENSE:
+
+(The MIT License)
+
+Copyright (c) 2008 - 2010:
+
+* {Aaron Patterson}[http://tenderlovemaking.com]
+* {Mike Dalessio}[http://mike.daless.io]
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+'Software'), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/README.rdoc

@@ -0,0 +1,146 @@
+= Nokogiri
+
+* http://nokogiri.org
+* http://github.com/tenderlove/nokogiri/wikis
+* http://github.com/tenderlove/nokogiri/tree/master
+* http://groups.google.com/group/nokogiri-talk
+* http://github.com/tenderlove/nokogiri/issues
+
+== DESCRIPTION:
+
+Nokogiri (鋸) is an HTML, XML, SAX, and Reader parser.  Among Nokogiri's
+many features is the ability to search documents via XPath or CSS3 selectors.
+
+XML is like violence - if it doesn’t solve your problems, you are not using
+enough of it.
+
+== FEATURES:
+
+* XPath support for document searching
+* CSS3 selector support for document searching
+* XML/HTML builder
+
+Nokogiri parses and searches XML/HTML very quickly, and also has
+correctly implemented CSS3 selector support as well as XPath support.
+
+== SUPPORT:
+
+The Nokogiri {mailing list}[http://groups.google.com/group/nokogiri-talk]
+is available here:
+
+  * http://groups.google.com/group/nokogiri-talk
+
+The {bug tracker}[http://github.com/tenderlove/nokogiri/issues]
+is available here:
+
+  * http://github.com/tenderlove/nokogiri/issues
+
+The IRC channel is #nokogiri on freenode.
+
+== SYNOPSIS:
+
+  require 'nokogiri'
+  require 'open-uri'
+
+  # Get a Nokogiri::HTML:Document for the page we’re interested in...
+
+  doc = Nokogiri::HTML(open('http://www.google.com/search?q=tenderlove'))
+
+  # Do funky things with it using Nokogiri::XML::Node methods...
+
+  ####
+  # Search for nodes by css
+  doc.css('h3.r a.l').each do |link|
+    puts link.content
+  end
+
+  ####
+  # Search for nodes by xpath
+  doc.xpath('//h3/a[@class="l"]').each do |link|
+    puts link.content
+  end
+
+  ####
+  # Or mix and match.
+  doc.search('h3.r a.l', '//h3/a[@class="l"]').each do |link|
+    puts link.content
+  end
+
+
+== REQUIREMENTS:
+
+* ruby 1.8 or 1.9
+* libxml2
+* libxml2-dev
+* libxslt
+* libxslt-dev
+
+== ENCODING:
+
+Strings are always stored as UTF-8 internally.  Methods that return
+text values will always return UTF-8 encoded strings.  Methods that
+return XML (like to_xml, to_html and inner_html) will return a string
+encoded like the source document.
+
+*WARNING*
+
+Some documents declare one particular encoding, but use a different
+one. So, which encoding should the parser choose?
+
+Remember that data is just a stream of bytes. Only us humans add
+meaning to that stream. Any particular set of bytes could be valid
+characters in multiple encodings, so detecting encoding with 100%
+accuracy is not possible. libxml2 does its best, but it can't be right
+100% of the time.
+
+If you want Nokogiri to handle the document encoding properly, your
+best bet is to explicitly set the encoding.  Here is an example of
+explicitly setting the encoding to EUC-JP on the parser:
+
+    doc = Nokogiri.XML('<foo><bar /><foo>', nil, 'EUC-JP')
+
+== INSTALL:
+
+* sudo gem install nokogiri
+
+=== Binary packages
+
+Binary packages are available for:
+
+* SuSE[http://download.opensuse.org/repositories/devel:/languages:/ruby:/extensions/]
+* Fedora[http://s390.koji.fedoraproject.org/koji/packageinfo?packageID=6756]
+
+== DEVELOPMENT:
+
+Developing Nokogiri requires racc and rexical.
+
+* rake install:deps
+* rake test
+
+== LICENSE:
+
+(The MIT License)
+
+Copyright (c) 2008 - 2010:
+
+* {Aaron Patterson}[http://tenderlovemaking.com]
+* {Mike Dalessio}[http://mike.daless.io]
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+'Software'), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.