ms-core 0.0.5 → 0.0.6

data/History

@@ -1,3 +1,8 @@
+== version 0.0.6
+
+* added cv_param (CvParam) object
+* added spectrum documentation
+
 == version 0.0.3
 
 * switched specs to spec/more

data/VERSION

@@ -1 +1 @@
-0.0.5
+0.0.6

data/lib/cv_param.rb

@@ -0,0 +1,16 @@
+
+# Controlled vocabulary
+class CvParam
+  attr_accessor :cv_ref, :accession, :name, :value
+
+  def initialize(cv_ref, accession, name, value=nil)
+   (@cv_ref, @accession, @name, @value) = [cv_ref, accession, name, value]
+  end
+
+  def to_xml(xml, name=:cvParam)
+    hash_to_send = {:cvRef => @cvref, :accession => @accession, :name => @name}
+    hash_to_send[:value] = @value if @value
+    xml.send(name, hash_to_send)
+  end
+end
+

data/lib/ms/spectrum.rb

@@ -36,6 +36,7 @@ module Ms
       [@data[0], @data[1]]
     end
 
+    # retrieve an m/z and intensity doublet at that index
     def [](array_index)
       [mzs[array_index], intensities[array_index]]
     end

data/spec/ms/calc_spec.rb

@@ -1,4 +1,4 @@
-require File.dirname(__FILE__) + "/../spec_helper.rb"
+require "spec_helper.rb"
 require 'ms/calc'
 
 describe 'Ms::Calc - calculating ppm tolerances' do

data/spec/ms/data_spec.rb

@@ -1,4 +1,4 @@
-require File.dirname(__FILE__) + "/../spec_helper.rb"
+require "spec_helper.rb"
 require 'ms/data'
 
 describe "Data.new" do

data/spec/ms/support/binary_search_spec.rb

@@ -1,4 +1,4 @@
-require File.dirname(__FILE__) + "/../../spec_helper.rb"
+require "spec_helper.rb"
 require 'ms/support/binary_search'
 
 describe 'binary searching' do

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 0
-  - 5
-  version: 0.0.5
+  - 6
+  version: 0.0.6
 platform: ruby
 authors: 
 - Simon Chiang
@@ -15,13 +15,14 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-08-04 00:00:00 -06:00
+date: 2011-02-09 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: molecules
   prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -36,6 +37,7 @@ dependencies:
   name: spec-more
   prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -53,12 +55,12 @@ extensions: []
 extra_rdoc_files: 
 - README.rdoc
 files: 
-- .gitignore
 - History
 - MIT-LICENSE
 - README.rdoc
 - Rakefile
 - VERSION
+- lib/cv_param.rb
 - lib/ms.rb
 - lib/ms/calc.rb
 - lib/ms/data.rb
@@ -84,11 +86,12 @@ homepage: http://github.com/jtprince/ms-core/rdoc
 licenses: []
 
 post_install_message: 
-rdoc_options: 
-- --charset=UTF-8
+rdoc_options: []
+
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
@@ -96,6 +99,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       - 0
       version: "0"
 required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
@@ -105,12 +109,12 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.3.6
+rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
 summary: basic, shared functionality for mspire libraries
 test_files: 
-- spec/ms/support/binary_search_spec.rb
 - spec/ms/calc_spec.rb
 - spec/ms/data_spec.rb
+- spec/ms/support/binary_search_spec.rb
 - spec/spec_helper.rb

data/.gitignore

@@ -1,9 +0,0 @@
-.DS_Store
-pkg/
-rdoc/
-backup/
-config/
-data/
-doc/
-*.swp
-*.gemspec