bio-nexml 0.0.1

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Files changed (57) hide show
  1. data/Gemfile +15 -0
  2. data/Gemfile.lock +24 -0
  3. data/LICENSE.txt +20 -0
  4. data/README.rdoc +47 -0
  5. data/Rakefile +55 -0
  6. data/TODO.txt +6 -0
  7. data/VERSION +1 -0
  8. data/bio-nexml.gemspec +126 -0
  9. data/extconf.rb +2 -0
  10. data/lib/bio-nexml.rb +0 -0
  11. data/lib/bio.rb +321 -0
  12. data/lib/bio/db/nexml.rb +109 -0
  13. data/lib/bio/db/nexml/mapper.rb +113 -0
  14. data/lib/bio/db/nexml/mapper/framework.rb +157 -0
  15. data/lib/bio/db/nexml/mapper/inflection.rb +99 -0
  16. data/lib/bio/db/nexml/mapper/repository.rb +59 -0
  17. data/lib/bio/db/nexml/matrix.rb +1046 -0
  18. data/lib/bio/db/nexml/parser.rb +622 -0
  19. data/lib/bio/db/nexml/schema/README.txt +21 -0
  20. data/lib/bio/db/nexml/schema/abstract.xsd +159 -0
  21. data/lib/bio/db/nexml/schema/characters/README.txt +1 -0
  22. data/lib/bio/db/nexml/schema/characters/abstractcharacters.xsd +361 -0
  23. data/lib/bio/db/nexml/schema/characters/characters.xsd +22 -0
  24. data/lib/bio/db/nexml/schema/characters/continuous.xsd +190 -0
  25. data/lib/bio/db/nexml/schema/characters/dna.xsd +282 -0
  26. data/lib/bio/db/nexml/schema/characters/protein.xsd +280 -0
  27. data/lib/bio/db/nexml/schema/characters/restriction.xsd +239 -0
  28. data/lib/bio/db/nexml/schema/characters/rna.xsd +283 -0
  29. data/lib/bio/db/nexml/schema/characters/standard.xsd +261 -0
  30. data/lib/bio/db/nexml/schema/external/sawsdl.xsd +21 -0
  31. data/lib/bio/db/nexml/schema/external/xhtml-datatypes-1.xsd +177 -0
  32. data/lib/bio/db/nexml/schema/external/xlink.xsd +75 -0
  33. data/lib/bio/db/nexml/schema/external/xml.xsd +145 -0
  34. data/lib/bio/db/nexml/schema/meta/README.txt +2 -0
  35. data/lib/bio/db/nexml/schema/meta/annotations.xsd +100 -0
  36. data/lib/bio/db/nexml/schema/meta/meta.xsd +294 -0
  37. data/lib/bio/db/nexml/schema/nexml.xsd +104 -0
  38. data/lib/bio/db/nexml/schema/taxa/README.txt +2 -0
  39. data/lib/bio/db/nexml/schema/taxa/taxa.xsd +39 -0
  40. data/lib/bio/db/nexml/schema/trees/README.txt +2 -0
  41. data/lib/bio/db/nexml/schema/trees/abstracttrees.xsd +135 -0
  42. data/lib/bio/db/nexml/schema/trees/network.xsd +113 -0
  43. data/lib/bio/db/nexml/schema/trees/tree.xsd +149 -0
  44. data/lib/bio/db/nexml/schema/trees/trees.xsd +36 -0
  45. data/lib/bio/db/nexml/taxa.rb +147 -0
  46. data/lib/bio/db/nexml/trees.rb +663 -0
  47. data/lib/bio/db/nexml/writer.rb +265 -0
  48. data/test/data/nexml/test.xml +69 -0
  49. data/test/test_bio-nexml.rb +17 -0
  50. data/test/unit/bio/db/nexml/tc_factory.rb +119 -0
  51. data/test/unit/bio/db/nexml/tc_mapper.rb +78 -0
  52. data/test/unit/bio/db/nexml/tc_matrix.rb +551 -0
  53. data/test/unit/bio/db/nexml/tc_parser.rb +21 -0
  54. data/test/unit/bio/db/nexml/tc_taxa.rb +118 -0
  55. data/test/unit/bio/db/nexml/tc_trees.rb +370 -0
  56. data/test/unit/bio/db/nexml/tc_writer.rb +633 -0
  57. metadata +253 -0
metadata ADDED
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+ platform: ruby
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+ authors:
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+ - rvosa
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+ date: 2011-03-01 00:00:00 +01:00
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+ type: :development
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+ description: This plugin reads, writes and generates NeXML
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+ email: rutgeraldo@gmail.com
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+ executables: []
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+
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+ extensions: []
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+ extra_rdoc_files:
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+ - LICENSE.txt
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+ - README.rdoc
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+ - Gemfile
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+ - TODO.txt
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+ - bio-nexml.gemspec
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+ - lib/bio/db/nexml/mapper.rb
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+ - lib/bio/db/nexml/matrix.rb
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+ - lib/bio/db/nexml/schema/characters/README.txt
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+ - lib/bio/db/nexml/schema/characters/abstractcharacters.xsd
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+ - lib/bio/db/nexml/schema/characters/characters.xsd
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+ - lib/bio/db/nexml/schema/characters/continuous.xsd
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+ - lib/bio/db/nexml/schema/characters/dna.xsd
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+ - lib/bio/db/nexml/schema/characters/protein.xsd
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+ - lib/bio/db/nexml/schema/characters/restriction.xsd
182
+ - lib/bio/db/nexml/schema/characters/rna.xsd
183
+ - lib/bio/db/nexml/schema/characters/standard.xsd
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+ - lib/bio/db/nexml/schema/external/sawsdl.xsd
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+ - lib/bio/db/nexml/schema/external/xhtml-datatypes-1.xsd
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+ - lib/bio/db/nexml/schema/external/xlink.xsd
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+ - lib/bio/db/nexml/schema/external/xml.xsd
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+ - lib/bio/db/nexml/schema/meta/README.txt
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+ - lib/bio/db/nexml/schema/meta/annotations.xsd
190
+ - lib/bio/db/nexml/schema/meta/meta.xsd
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+ - lib/bio/db/nexml/schema/nexml.xsd
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+ - lib/bio/db/nexml/schema/taxa/README.txt
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+ - lib/bio/db/nexml/schema/taxa/taxa.xsd
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+ - lib/bio/db/nexml/schema/trees/README.txt
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+ - lib/bio/db/nexml/schema/trees/abstracttrees.xsd
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+ - lib/bio/db/nexml/schema/trees/network.xsd
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+ - lib/bio/db/nexml/schema/trees/tree.xsd
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+ - lib/bio/db/nexml/schema/trees/trees.xsd
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+ - lib/bio/db/nexml/taxa.rb
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+ - lib/bio/db/nexml/trees.rb
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+ - lib/bio/db/nexml/writer.rb
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+ - test/data/nexml/test.xml
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+ - test/test_bio-nexml.rb
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+ - test/unit/bio/db/nexml/tc_factory.rb
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+ - test/unit/bio/db/nexml/tc_mapper.rb
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+ - test/unit/bio/db/nexml/tc_matrix.rb
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+ - test/unit/bio/db/nexml/tc_parser.rb
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+ - test/unit/bio/db/nexml/tc_taxa.rb
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+ - test/unit/bio/db/nexml/tc_trees.rb
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+ - test/unit/bio/db/nexml/tc_writer.rb
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+ has_rdoc: true
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+ homepage: http://github.com/rvosa/bioruby-nexml
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+ licenses:
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+ - MIT
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+ post_install_message:
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+ rdoc_options: []
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+
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+ require_paths:
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+ - lib
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+ rubyforge_project:
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+ rubygems_version: 1.4.2
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+ signing_key:
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+ specification_version: 3
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+ summary: BioRuby plugin for reading and writing NeXML (http://nexml.org)
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+ test_files:
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+ - test/test_bio-nexml.rb
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+ - test/unit/bio/db/nexml/tc_factory.rb
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+ - test/unit/bio/db/nexml/tc_mapper.rb
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