ms-ident 0.0.17 → 0.0.18

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 0
-  - 17
-  version: 0.0.17
+  - 18
+  version: 0.0.18
 platform: ruby
 authors: 
 - John T. Prince
@@ -14,11 +14,12 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-03-08 00:00:00 -07:00
+date: 2011-03-28 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: nokogiri
+  prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -28,10 +29,10 @@ dependencies:
         - 0
         version: "0"
   type: :runtime
-  prerelease: false
   version_requirements: *id001
 - !ruby/object:Gem::Dependency 
   name: ms-core
+  prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -43,10 +44,10 @@ dependencies:
         - 12
         version: 0.0.12
   type: :runtime
-  prerelease: false
   version_requirements: *id002
 - !ruby/object:Gem::Dependency 
-  name: andand
+  name: ms-in_silico
+  prerelease: false
   requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -56,10 +57,10 @@ dependencies:
         - 0
         version: "0"
   type: :runtime
-  prerelease: false
   version_requirements: *id003
 - !ruby/object:Gem::Dependency 
-  name: spec-more
+  name: andand
+  prerelease: false
   requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -67,45 +68,26 @@ dependencies:
       - !ruby/object:Gem::Version 
         segments: 
         - 0
-        - 0
-        - 4
-        version: 0.0.4
-  type: :development
-  prerelease: false
+        version: "0"
+  type: :runtime
   version_requirements: *id004
 - !ruby/object:Gem::Dependency 
-  name: bundler
+  name: spec-more
+  prerelease: false
   requirement: &id005 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version 
         segments: 
-        - 1
         - 0
-        - 0
-        version: 1.0.0
+        version: "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 
+  requirement: &id006 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -114,8 +96,7 @@ dependencies:
         - 0
         version: "0"
   type: :development
-  prerelease: false
-  version_requirements: *id007
+  version_requirements: *id006
 description: mspire library for working with mzIdentML and pepxml
 email: jtprince@gmail.com
 executables: []
@@ -127,8 +108,6 @@ extra_rdoc_files:
 - README.rdoc
 files: 
 - .document
-- Gemfile
-- Gemfile.lock
 - LICENSE
 - README.rdoc
 - Rakefile
@@ -136,6 +115,7 @@ files:
 - lib/merge.rb
 - lib/ms/ident.rb
 - lib/ms/ident/peptide.rb
+- lib/ms/ident/peptide/db.rb
 - lib/ms/ident/pepxml.rb
 - lib/ms/ident/pepxml/modifications.rb
 - lib/ms/ident/pepxml/msms_pipeline_analysis.rb
@@ -154,10 +134,14 @@ files:
 - lib/ms/ident/search.rb
 - schema/pepXML_v115.xsd
 - schema/pepXML_v19.xsd
+- spec/ms/ident/peptide/db_spec.rb
 - spec/ms/ident/pepxml/sample_enzyme_spec.rb
 - spec/ms/ident/pepxml/search_hit/modification_info_spec.rb
 - spec/ms/ident/pepxml_spec.rb
+- spec/ms/ident/protein_spec.rb
 - spec/spec_helper.rb
+- spec/tfiles/ms/ident/peptide/db/uni_11_sp_tr.fasta
+- spec/tfiles/ms/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml
 has_rdoc: true
 homepage: http://github.com/jtprince/ms-ident
 licenses: 
@@ -172,7 +156,6 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: -1969914373934932629
       segments: 
       - 0
       version: "0"
@@ -192,7 +175,9 @@ signing_key:
 specification_version: 3
 summary: mspire library for working with mzIdentML and pepxml
 test_files: 
+- spec/ms/ident/peptide/db_spec.rb
 - spec/ms/ident/pepxml/sample_enzyme_spec.rb
 - spec/ms/ident/pepxml/search_hit/modification_info_spec.rb
 - spec/ms/ident/pepxml_spec.rb
+- spec/ms/ident/protein_spec.rb
 - spec/spec_helper.rb

data/Gemfile

@@ -1,31 +0,0 @@
-source "http://rubygems.org"
-# Add dependencies required to use your gem here.
-# Example:
-#   gem "activesupport", ">= 2.3.5"
-gem 'nokogiri'
-gem 'ms-core', ">= 0.0.12"
-gem 'andand'
-
-dev_gems = {
-    "spec-more" => ">= 0.0.4",
-    "bundler" => "~> 1.0.0",
-    "jeweler" => "~> 1.5.2",
-    "rcov" => ">= 0",
-}
-
-# Add dependencies to develop your gem here.
-# Include everything needed to run rake, tests, features, etc.
-group :development do
-  dev_gems.each do |name,version_string|
-    gem name, version_string
-  end
-end
-
-# Add dependencies to develop your gem here.
-# Include everything needed to run rake, tests, features, etc.
-group :development_large do
-  dev_gems.each do |name,version_string|
-    gem name, version_string
-  end
-  gem "ms-testdata", ">= 0.1.1"
-end

data/Gemfile.lock

@@ -1,32 +0,0 @@
-GEM
-  remote: http://rubygems.org/
-  specs:
-    andand (1.3.1)
-    bacon (1.1.0)
-    bio (1.4.1)
-    git (1.2.5)
-    jeweler (1.5.2)
-      bundler (~> 1.0.0)
-      git (>= 1.2.5)
-      rake
-    ms-core (0.0.12)
-      bio (>= 1.4.1)
-    ms-testdata (0.1.1)
-    nokogiri (1.4.4)
-    rake (0.8.7)
-    rcov (0.9.9)
-    spec-more (0.0.4)
-      bacon
-
-PLATFORMS
-  ruby
-
-DEPENDENCIES
-  andand
-  bundler (~> 1.0.0)
-  jeweler (~> 1.5.2)
-  ms-core (>= 0.0.12)
-  ms-testdata (>= 0.1.1)
-  nokogiri
-  rcov
-  spec-more (>= 0.0.4)