bio-nexml 1.0.0 → 1.1.0
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- data/.gitignore +3 -0
- data/.travis.yml +10 -0
- data/Gemfile +11 -0
- data/README.mkd +459 -0
- data/Rakefile +36 -0
- data/TODO.txt +6 -0
- data/VERSION +1 -0
- data/bio-nexml.gemspec +27 -0
- data/lib/bio/db/nexml.rb +6 -19
- data/lib/bio/db/nexml/mapper/framework.rb +6 -9
- data/test/data/nexml/test.xml +69 -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 +61 -73
- data/README.rdoc +0 -53
metadata
CHANGED
@@ -1,79 +1,72 @@
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-
--- !ruby/object:Gem::Specification
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1
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+
--- !ruby/object:Gem::Specification
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2
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name: bio-nexml
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-
version: !ruby/object:Gem::Version
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version: !ruby/object:Gem::Version
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version: 1.1.0
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prerelease:
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segments:
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- 1
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- 0
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- 0
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version: 1.0.0
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platform: ruby
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authors:
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7
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authors:
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8
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- Rutger Vos
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9
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- Anurag Priyam
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autorequire:
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bindir: bin
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cert_chain: []
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- !ruby/object:Gem::Dependency
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date: 2012-05-09 00:00:00.000000000Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio
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requirement: &id001 !ruby/object:Gem::Requirement
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requirement: &78329210 !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: 5
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segments:
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- 1
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- 4
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- 1
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: 1.4.1
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type: :runtime
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version_requirements: *id001
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- !ruby/object:Gem::Dependency
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name: libxml-ruby
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prerelease: false
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-
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version_requirements: *78329210
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- !ruby/object:Gem::Dependency
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name: libxml-ruby
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requirement: &78370740 !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: 27
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segments:
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requirements:
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- - =
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- !ruby/object:Gem::Version
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version: 1.1.4
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type: :runtime
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-
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prerelease: false
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version_requirements: *78370740
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description: This plugin reads, writes and generates NeXML
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email:
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email:
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- rutgeraldo@gmail.com
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- anurag08priyam@gmail.com
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executables: []
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extensions: []
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-
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extra_rdoc_files: []
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-
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-
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files:
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- .gitignore
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- .travis.yml
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- Gemfile
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- LICENSE.txt
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- README.mkd
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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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- lib/bio-nexml.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/mapper.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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69
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- lib/bio/db/nexml/schema/characters/protein.xsd
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-
- lib/bio/db/nexml/schema/characters/README.txt
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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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@@ -81,58 +74,53 @@ files:
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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/meta/README.txt
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- lib/bio/db/nexml/schema/nexml.xsd
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-
- lib/bio/db/nexml/schema/README.txt
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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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85
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- lib/bio/db/nexml/schema/trees/network.xsd
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-
- lib/bio/db/nexml/schema/trees/README.txt
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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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90
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- lib/bio/db/nexml/writer.rb
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-
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- lib/bio-nexml.rb
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- LICENSE.txt
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-
- README.rdoc
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91
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- test/data/nexml/test.xml
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92
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- test/test_bio-nexml.rb
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-
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105
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-
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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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homepage: https://github.com/nexml/bio-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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require_paths:
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- lib
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required_ruby_version: !ruby/object:Gem::Requirement
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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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-
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-
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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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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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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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segments:
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- 0
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version: "0"
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requirements:
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- - ! '>='
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version: '0'
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requirements: []
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rubyforge_project:
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rubygems_version: 1.8.
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rubygems_version: 1.8.10
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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_files:
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- test/test_bio-nexml.rb
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data/README.rdoc
DELETED
@@ -1,53 +0,0 @@
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= bio-nexml
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NeXML is a file format for phylogenetic data. It is inspired by the modular
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architecture of the commonly-used NEXUS file format (hence the name) in that
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a NeXML instance document can contain:
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* sets of Operational Taxonomic Units (OTUs), i.e. the tips in phylogenetic
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trees, and that which comparative observations are made on. Often these are
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species ("taxa").
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* sets of phylogenetic trees (or reticulate trees, i.e. networks)
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* sets of comparative data, i.e. molecular sequences, morphological categorical
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data, continuous data, and other types.
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The elements in a NeXML document can be annotated using RDFa
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(http://en.wikipedia.org/wiki/RDFa), which means that every object that can
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be parsed out of a NeXML document must be an object that, in turn, can be
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annotated with predicates (and their namespaces) and other objects (with,
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perhaps, their own namespaces). The advantage over previous file formats is
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that we can retain all metadata for all objects within one file, regardless
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where the metadata come from.
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NeXML can be transformed to RDF using an XSL stylesheet. As such, NeXML forms
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an intermediate format between traditional flat file formats (with predictable
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structure but no semantics) and RDF (with loose structure, but lots of
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semantics) that is both easy to work with, yet ready for the Semantic Web.
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To learn more, visit http://www.nexml.org
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== Getting Started
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https://www.nescent.org/wg_phyloinformatics/NeXML_and_RDF_API_for_BioRuby
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It is not complete, but definitely enough to get started.
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== Contributing to bio-nexml
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* Check out the latest master to make sure the feature hasn't been implemented
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or the bug hasn't been fixed yet
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* Check out the issue tracker to make sure someone already hasn't requested it
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and/or contributed it
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* Fork the project
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* Start a feature/bugfix branch
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* Commit and push until you are happy with your contribution
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* Make sure to add tests for it. This is important so I don't break it in a
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future version unintentionally.
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* Please try not to mess with the Rakefile, version, or history. If you want to
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have your own version, or is otherwise necessary, that is fine, but please
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isolate to its own commit so I can cherry-pick around it.
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== Copyright
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Copyright (c) 2011 rvosa. See LICENSE.txt for
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further details.
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