RubyGems - ms-ident - Versions diffs - 0.0.2 - Mend

ms-ident 0.0.2

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Files changed (30) hide show

data/.document +5 -0
data/Gemfile +31 -0
data/Gemfile.lock +32 -0
data/LICENSE +61 -0
data/README.rdoc +97 -0
data/Rakefile +54 -0
data/VERSION +1 -0
data/lib/merge.rb +7 -0
data/lib/ms/ident/pepxml/modifications/sequest.rb +237 -0
data/lib/ms/ident/pepxml/modifications.rb +94 -0
data/lib/ms/ident/pepxml/msms_pipeline_analysis.rb +70 -0
data/lib/ms/ident/pepxml/msms_run_summary.rb +81 -0
data/lib/ms/ident/pepxml/parameters.rb +14 -0
data/lib/ms/ident/pepxml/pep_summary.rb +104 -0
data/lib/ms/ident/pepxml/prot_summary.rb +484 -0
data/lib/ms/ident/pepxml/sample_enzyme.rb +166 -0
data/lib/ms/ident/pepxml/search_database.rb +42 -0
data/lib/ms/ident/pepxml/search_hit/modification_info.rb +82 -0
data/lib/ms/ident/pepxml/search_hit.rb +141 -0
data/lib/ms/ident/pepxml/search_result.rb +28 -0
data/lib/ms/ident/pepxml/search_summary.rb +88 -0
data/lib/ms/ident/pepxml/spectrum_query.rb +83 -0
data/lib/ms/ident/pepxml.rb +61 -0
data/lib/ms/ident.rb +11 -0
data/schema/pepXML_v115.xsd +1458 -0
data/schema/pepXML_v19.xsd +1337 -0
data/spec/ms/ident/pepxml/sample_enzyme_spec.rb +181 -0
data/spec/ms/ident/pepxml_spec.rb +436 -0
data/spec/spec_helper.rb +40 -0
metadata +194 -0

metadata ADDED Viewed

@@ -0,0 +1,194 @@
+--- !ruby/object:Gem::Specification
+name: ms-ident
+version: !ruby/object:Gem::Version
+  prerelease: false
+  segments:
+  - 0
+  - 0
+  - 2
+  version: 0.0.2
+platform: ruby
+authors:
+- John T. Prince
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2011-02-26 00:00:00 -07:00
+default_executable:
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: nokogiri
+  requirement: &id001 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        segments:
+        - 0
+        version: "0"
+  type: :runtime
+  prerelease: false
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency
+  name: ms-core
+  requirement: &id002 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
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+      - !ruby/object:Gem::Version
+        segments:
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+        - 0
+        - 12
+        version: 0.0.12
+  type: :runtime
+  prerelease: false
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency
+  name: andand
+  requirement: &id003 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        segments:
+        - 0
+        version: "0"
+  type: :runtime
+  prerelease: false
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency
+  name: spec-more
+  requirement: &id004 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        segments:
+        - 0
+        - 0
+        - 4
+        version: 0.0.4
+  type: :development
+  prerelease: false
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &id005 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        segments:
+        - 1
+        - 0
+        - 0
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *id005
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &id006 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        segments:
+        - 1
+        - 5
+        - 2
+        version: 1.5.2
+  type: :development
+  prerelease: false
+  version_requirements: *id006
+- !ruby/object:Gem::Dependency
+  name: rcov
+  requirement: &id007 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        segments:
+        - 0
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id007
+description: mspire library for working with mzIdentML and pepxml
+email: jtprince@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE
+- README.rdoc
+files:
+- .document
+- Gemfile
+- Gemfile.lock
+- LICENSE
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/merge.rb
+- lib/ms/ident.rb
+- lib/ms/ident/pepxml.rb
+- lib/ms/ident/pepxml/modifications.rb
+- lib/ms/ident/pepxml/modifications/sequest.rb
+- lib/ms/ident/pepxml/msms_pipeline_analysis.rb
+- lib/ms/ident/pepxml/msms_run_summary.rb
+- lib/ms/ident/pepxml/parameters.rb
+- lib/ms/ident/pepxml/pep_summary.rb
+- lib/ms/ident/pepxml/prot_summary.rb
+- lib/ms/ident/pepxml/sample_enzyme.rb
+- lib/ms/ident/pepxml/search_database.rb
+- lib/ms/ident/pepxml/search_hit.rb
+- lib/ms/ident/pepxml/search_hit/modification_info.rb
+- lib/ms/ident/pepxml/search_result.rb
+- lib/ms/ident/pepxml/search_summary.rb
+- lib/ms/ident/pepxml/spectrum_query.rb
+- schema/pepXML_v115.xsd
+- schema/pepXML_v19.xsd
+- spec/ms/ident/pepxml/sample_enzyme_spec.rb
+- spec/ms/ident/pepxml_spec.rb
+- spec/spec_helper.rb
+has_rdoc: true
+homepage: http://github.com/jtprince/ms-ident
+licenses:
+- MIT
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      hash: 642659304812034666
+      segments:
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+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ">="
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+      segments:
+      - 0
+      version: "0"
+requirements: []
+rubyforge_project: mspire
+rubygems_version: 1.3.7
+signing_key:
+specification_version: 3
+summary: mspire library for working with mzIdentML and pepxml
+test_files:
+- spec/ms/ident/pepxml/sample_enzyme_spec.rb
+- spec/ms/ident/pepxml_spec.rb
+- spec/spec_helper.rb