bio-nexml 0.0.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/Gemfile +15 -0
- data/Gemfile.lock +24 -0
- data/LICENSE.txt +20 -0
- data/README.rdoc +47 -0
- data/Rakefile +55 -0
- data/TODO.txt +6 -0
- data/VERSION +1 -0
- data/bio-nexml.gemspec +126 -0
- data/extconf.rb +2 -0
- data/lib/bio-nexml.rb +0 -0
- data/lib/bio.rb +321 -0
- data/lib/bio/db/nexml.rb +109 -0
- data/lib/bio/db/nexml/mapper.rb +113 -0
- data/lib/bio/db/nexml/mapper/framework.rb +157 -0
- data/lib/bio/db/nexml/mapper/inflection.rb +99 -0
- data/lib/bio/db/nexml/mapper/repository.rb +59 -0
- data/lib/bio/db/nexml/matrix.rb +1046 -0
- data/lib/bio/db/nexml/parser.rb +622 -0
- data/lib/bio/db/nexml/schema/README.txt +21 -0
- data/lib/bio/db/nexml/schema/abstract.xsd +159 -0
- data/lib/bio/db/nexml/schema/characters/README.txt +1 -0
- data/lib/bio/db/nexml/schema/characters/abstractcharacters.xsd +361 -0
- data/lib/bio/db/nexml/schema/characters/characters.xsd +22 -0
- data/lib/bio/db/nexml/schema/characters/continuous.xsd +190 -0
- data/lib/bio/db/nexml/schema/characters/dna.xsd +282 -0
- data/lib/bio/db/nexml/schema/characters/protein.xsd +280 -0
- data/lib/bio/db/nexml/schema/characters/restriction.xsd +239 -0
- data/lib/bio/db/nexml/schema/characters/rna.xsd +283 -0
- data/lib/bio/db/nexml/schema/characters/standard.xsd +261 -0
- data/lib/bio/db/nexml/schema/external/sawsdl.xsd +21 -0
- data/lib/bio/db/nexml/schema/external/xhtml-datatypes-1.xsd +177 -0
- data/lib/bio/db/nexml/schema/external/xlink.xsd +75 -0
- data/lib/bio/db/nexml/schema/external/xml.xsd +145 -0
- data/lib/bio/db/nexml/schema/meta/README.txt +2 -0
- data/lib/bio/db/nexml/schema/meta/annotations.xsd +100 -0
- data/lib/bio/db/nexml/schema/meta/meta.xsd +294 -0
- data/lib/bio/db/nexml/schema/nexml.xsd +104 -0
- data/lib/bio/db/nexml/schema/taxa/README.txt +2 -0
- data/lib/bio/db/nexml/schema/taxa/taxa.xsd +39 -0
- data/lib/bio/db/nexml/schema/trees/README.txt +2 -0
- data/lib/bio/db/nexml/schema/trees/abstracttrees.xsd +135 -0
- data/lib/bio/db/nexml/schema/trees/network.xsd +113 -0
- data/lib/bio/db/nexml/schema/trees/tree.xsd +149 -0
- data/lib/bio/db/nexml/schema/trees/trees.xsd +36 -0
- data/lib/bio/db/nexml/taxa.rb +147 -0
- data/lib/bio/db/nexml/trees.rb +663 -0
- data/lib/bio/db/nexml/writer.rb +265 -0
- data/test/data/nexml/test.xml +69 -0
- data/test/test_bio-nexml.rb +17 -0
- data/test/unit/bio/db/nexml/tc_factory.rb +119 -0
- data/test/unit/bio/db/nexml/tc_mapper.rb +78 -0
- data/test/unit/bio/db/nexml/tc_matrix.rb +551 -0
- data/test/unit/bio/db/nexml/tc_parser.rb +21 -0
- data/test/unit/bio/db/nexml/tc_taxa.rb +118 -0
- data/test/unit/bio/db/nexml/tc_trees.rb +370 -0
- data/test/unit/bio/db/nexml/tc_writer.rb +633 -0
- metadata +253 -0
metadata
ADDED
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--- !ruby/object:Gem::Specification
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name: bio-nexml
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version: !ruby/object:Gem::Version
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version: 0.0.1
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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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default_executable:
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dependencies:
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name: bio
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version: 1.1.4
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type: :runtime
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name: libxml-ruby
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version: 1.1.4
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type: :development
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version_requirements: *id008
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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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extensions: []
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extra_rdoc_files:
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- LICENSE.txt
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- README.rdoc
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files:
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- Gemfile
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- Gemfile.lock
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- LICENSE.txt
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- README.rdoc
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- Rakefile
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- TODO.txt
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- VERSION
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- bio-nexml.gemspec
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- extconf.rb
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- lib/bio-nexml.rb
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- lib/bio.rb
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- lib/bio/db/nexml.rb
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- lib/bio/db/nexml/mapper.rb
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- lib/bio/db/nexml/mapper/framework.rb
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- lib/bio/db/nexml/mapper/inflection.rb
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- lib/bio/db/nexml/mapper/repository.rb
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- lib/bio/db/nexml/matrix.rb
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- lib/bio/db/nexml/parser.rb
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- lib/bio/db/nexml/schema/README.txt
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- lib/bio/db/nexml/schema/abstract.xsd
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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
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- lib/bio/db/nexml/schema/characters/rna.xsd
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- 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
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- 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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require_paths:
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- lib
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required_ruby_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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hash: 3
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segments:
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- 0
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version: "0"
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required_rubygems_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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hash: 3
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segments:
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- 0
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version: "0"
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requirements: []
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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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- 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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