bioruby-phyloxml 1.0.0

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Files changed (29) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +9 -0
  3. data/BSDL +22 -0
  4. data/COPYING +57 -0
  5. data/COPYING.ja +51 -0
  6. data/GPL +340 -0
  7. data/Gemfile +4 -0
  8. data/LEGAL +36 -0
  9. data/LGPL +504 -0
  10. data/README.md +214 -0
  11. data/Rakefile +20 -0
  12. data/bioruby-phyloxml.gemspec +36 -0
  13. data/doc/Tutorial.rd +152 -0
  14. data/lib/bio-phyloxml.rb +27 -0
  15. data/lib/bio-phyloxml/compat/cleanup.rb +13 -0
  16. data/lib/bio-phyloxml/compat/stub_phyloxml_elements.rb +1 -0
  17. data/lib/bio-phyloxml/compat/stub_phyloxml_parser.rb +1 -0
  18. data/lib/bio-phyloxml/compat/stub_phyloxml_writer.rb +1 -0
  19. data/lib/bio-phyloxml/phyloxml.xsd +582 -0
  20. data/lib/bio-phyloxml/phyloxml_elements.rb +1186 -0
  21. data/lib/bio-phyloxml/phyloxml_parser.rb +1001 -0
  22. data/lib/bio-phyloxml/phyloxml_writer.rb +227 -0
  23. data/lib/bio-phyloxml/version.rb +7 -0
  24. data/lib/bio/db/phyloxml/phyloxml_elements.rb +4 -0
  25. data/lib/bio/db/phyloxml/phyloxml_parser.rb +4 -0
  26. data/lib/bio/db/phyloxml/phyloxml_writer.rb +4 -0
  27. data/lib/bioruby-phyloxml.rb +10 -0
  28. data/sample/test_phyloxml_big.rb +205 -0
  29. metadata +156 -0
metadata ADDED
@@ -0,0 +1,156 @@
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+ --- !ruby/object:Gem::Specification
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+ name: bioruby-phyloxml
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+ version: !ruby/object:Gem::Version
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+ version: 1.0.0
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+ platform: ruby
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+ authors:
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+ - Diana Jaunzeikare
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+ - Clayton Wheeler
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+ - BioRuby project
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+ autorequire:
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+ bindir: exe
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+ cert_chain: []
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+ date: 2016-06-15 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: bio
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 1.5.0
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 1.5.0
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+ - !ruby/object:Gem::Dependency
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+ name: libxml-ruby
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '2.8'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '2.8'
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+ - !ruby/object:Gem::Dependency
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+ name: bundler
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
47
+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '1.10'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '1.10'
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+ - !ruby/object:Gem::Dependency
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+ name: rake
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '10.0'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '10.0'
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+ - !ruby/object:Gem::Dependency
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+ name: rdoc
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
75
+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '4'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '4'
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+ description: Provides PhyloXML support for BioRuby. This bioruby-phyloxml gem replaces
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+ old unmaintained bio-phyloxml gem.
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+ email:
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+ - staff@bioruby.org
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+ executables: []
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+ extensions: []
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+ extra_rdoc_files:
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+ - README.md
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+ - COPYING
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+ - COPYING.ja
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+ - BSDL
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+ - LGPL
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+ - GPL
98
+ - doc/Tutorial.rd
99
+ files:
100
+ - ".gitignore"
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+ - BSDL
102
+ - COPYING
103
+ - COPYING.ja
104
+ - GPL
105
+ - Gemfile
106
+ - LEGAL
107
+ - LGPL
108
+ - README.md
109
+ - Rakefile
110
+ - bioruby-phyloxml.gemspec
111
+ - doc/Tutorial.rd
112
+ - lib/bio-phyloxml.rb
113
+ - lib/bio-phyloxml/compat/cleanup.rb
114
+ - lib/bio-phyloxml/compat/stub_phyloxml_elements.rb
115
+ - lib/bio-phyloxml/compat/stub_phyloxml_parser.rb
116
+ - lib/bio-phyloxml/compat/stub_phyloxml_writer.rb
117
+ - lib/bio-phyloxml/phyloxml.xsd
118
+ - lib/bio-phyloxml/phyloxml_elements.rb
119
+ - lib/bio-phyloxml/phyloxml_parser.rb
120
+ - lib/bio-phyloxml/phyloxml_writer.rb
121
+ - lib/bio-phyloxml/version.rb
122
+ - lib/bio/db/phyloxml/phyloxml_elements.rb
123
+ - lib/bio/db/phyloxml/phyloxml_parser.rb
124
+ - lib/bio/db/phyloxml/phyloxml_writer.rb
125
+ - lib/bioruby-phyloxml.rb
126
+ - sample/test_phyloxml_big.rb
127
+ homepage: http://github.com/bioruby/bioruby-phyloxml
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+ licenses:
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+ - Ruby
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+ metadata: {}
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+ post_install_message:
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+ rdoc_options:
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+ - "--main"
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+ - README.md
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+ - "--title"
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+ - Bio::PhyloXML API documentation
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+ - "--line-numbers"
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+ require_paths:
139
+ - lib
140
+ required_ruby_version: !ruby/object:Gem::Requirement
141
+ requirements:
142
+ - - ">="
143
+ - !ruby/object:Gem::Version
144
+ version: '0'
145
+ required_rubygems_version: !ruby/object:Gem::Requirement
146
+ requirements:
147
+ - - ">="
148
+ - !ruby/object:Gem::Version
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+ version: '0'
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+ requirements: []
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+ rubyforge_project:
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+ rubygems_version: 2.4.5.1
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+ signing_key:
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+ specification_version: 4
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+ summary: PhyloXML plugin for BioRuby
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+ test_files: []