mspire 0.6.6 → 0.6.7

data/VERSION

@@ -1 +1 @@
-0.6.6
+0.6.7

data/lib/cv/description.rb

@@ -11,6 +11,7 @@ module CV
       push CV::Param.new(*args)
     end
 
+    # for now, assumes xml is a Nokogiri::XML::Builder object
     def to_xml(xml)
       each {|param| param.to_xml(xml) }
     end

data/lib/cv/param.rb

@@ -9,6 +9,7 @@ module CV
       (@cv_ref, @accession, @name, @value) = [cv_ref, accession, name, value]
     end
 
+    # for now, assumes this is a Nokogiri::XML::Builder object
     def to_xml(xml, name=:cvParam)
       hash_to_send = {:cvRef => @cvref, :accession => @accession, :name => @name}
       hash_to_send[:value] = @value if @value

data/lib/ms/cv/description.rb

@@ -0,0 +1,44 @@
+require 'ms/cv/param'
+
+module MS
+  module CV
+    # An MS::Description is a convenient way to specify several mass spec related
+    # cvParam objects at once. 
+    #
+    # examples of usage:
+    #
+    #     Description.new( <CV::Param> )
+    #     Description['MS:1000004', ['MS:1000004'], ['IMS:1000042', 23], param_obj, args]
+    #     Description.new do
+    #       param MS:1000004
+    #       param MS:1000042, 23
+    #     end
+    class Description < Array
+
+      # ensures that each argument is an argument that can be handled by
+      # CV::Param. Returns the Description object it creates
+      def self.[](*args)
+        list = self.new
+        args.each do |arg| 
+          arg.is_a?(Array) ? list.param(*arg) : list.param(arg) 
+        end
+        list
+      end
+
+      # takes a list of valid CV::Param objects, or they can be set in the block
+      # using param
+      def initialize(*args, &block)
+        args.each {|arg| param(arg) }
+        instance_eval &block if block
+      end
+
+      # if the first object is a MS::CV::Param it is just pushed onto the list,
+      # otherwise the arguments are sent in to initialize a fresh MS::CV::Param,
+      # and this object is pushed onto the list.
+      def param(*args)
+        push args.first.is_a?(::CV::Param) ? args.first : MS::CV::Param.new(*args)
+      end
+    end
+
+  end
+end

data/lib/ms/cv/param.rb

@@ -0,0 +1,39 @@
+
+require 'ms/cv'
+
+module MS
+  module CV
+
+    # a mass spec related CVParam.  It initializes with a variety of obo
+    # accession numbers or objects to make writing CV's as easy as possible.
+    class Param < ::CV::Param
+
+      # takes a variety of arguments (acc = accession):
+      #
+      #     acc#
+      #     acc#, value
+      #     acc#, unit_acc# or CV::Param object
+      #     acc#, value, unit_acc# or CV::Param object
+      #     cvref, acc#, name
+      #     cvref, acc#, name, value
+      #     cvref, acc#, name, unit_acc# or CV::Param object
+      #     cvref, acc#, name, value, unit_acc# or CV::Param object
+      def initialize(*args)
+        @unit = 
+          if args.size > 1 && ((args.last.is_a?(::CV::Param) || args.last =~ /[A-Za-z]+:\d+/))
+            unit_arg = args.pop
+            unit_arg.is_a?(::CV::Param) ? unit_arg : self.class.new(unit_arg)
+          end
+        (@cv_ref, @accession, @name, @value) = 
+          case args.size
+          when 1..2  # accession number (maybe with value)
+            (obo_type, accnum) = args.first.split(':')
+            [obo_type, args.first, MS::CV::Obo[obo_type][args.first], args[1]]
+          when 3..4  # they have fully specified the object
+            args
+          end
+      end
+    end
+  end
+
+end

data/lib/ms/cv.rb

@@ -0,0 +1,16 @@
+
+require 'cv'
+require 'obo/ms'
+require 'obo/ims'
+require 'obo/unit'
+
+module MS
+  module CV
+    Obo = {
+      'MS' => Obo::MS.id_to_name,
+      'IMS' => Obo::IMS.id_to_name,
+      'UO' => Obo::Unit.id_to_name,
+    }
+  end
+end
+

data/lib/ms/mass.rb

@@ -1,4 +1,3 @@
-
 module MS
   module Mass
 
@@ -39,6 +38,7 @@ module MS
       'h2o' => 18.0105647,
       'oh' => 17.002739665,
       'e' => 0.0005486,
+      'se' => 79.9165196
     }
     AVG_STR = {
       'h+' => 1.007276, # using Mascot_H_plus mass (is this right for AVG??)

data/spec/ms/{cvlist_spec.rb → cv/description_spec.rb}

@@ -1,11 +1,11 @@
 require 'spec_helper'
-require 'ms/cvlist'
+require 'ms/cv/description'
 require 'cv'
 
-describe 'appending CV params objects to an MS::CVList' do
+describe 'appending CV params objects to an MS::CV::Description' do
   describe 'intelligently appending params with #param' do
     before do
-      @cv = MS::CVList.new
+      @cv = MS::CV::Description.new
     end
     it 'sends detailed descriptions to CV::Param.new' do
       arglist = [
@@ -36,7 +36,7 @@ describe 'appending CV params objects to an MS::CVList' do
     end
     describe 'appending on initialization' do
       it 'can be done with a block' do
-        cvlist = MS::CVList.new do
+        cvlist = MS::CV::Description.new do
           param 'MS:1000004'  # sample mass
           param 'IMS:1000042', 23 # max count of pixels of y
         end
@@ -47,7 +47,7 @@ describe 'appending CV params objects to an MS::CVList' do
     it 'can be done with brackets' do
       args = ['IMS', 'IMS:1000052', 'position z', 22]
       param_obj = CV::Param.new(*args)
-      cvlist = MS::CVList['MS:1000004', ['MS:1000004'], ['IMS:1000042', 23], param_obj, args]
+      cvlist = MS::CV::Description['MS:1000004', ['MS:1000004'], ['IMS:1000042', 23], param_obj, args]
       cvlist.size.should == 5
       cvlist[0].should == cvlist[1]
       cvlist.each do |param|

metadata

@@ -1,105 +1,103 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: mspire
-version: !ruby/object:Gem::Version 
+version: !ruby/object:Gem::Version
+  version: 0.6.7
   prerelease: 
-  version: 0.6.6
 platform: ruby
-authors: 
+authors:
 - John T. Prince
 - Simon Chiang
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-02-13 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2012-02-16 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: nokogiri
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  requirement: &8166300 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        version: "1.5"
+      - !ruby/object:Gem::Version
+        version: '1.5'
   type: :runtime
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: bsearch
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: *8166300
+- !ruby/object:Gem::Dependency
+  name: bsearch
+  requirement: &8165640 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 1.5.0
   type: :runtime
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: andand
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  version_requirements: *8165640
+- !ruby/object:Gem::Dependency
+  name: andand
+  requirement: &8164920 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 1.3.1
   type: :runtime
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  name: obo
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  version_requirements: *8164920
+- !ruby/object:Gem::Dependency
+  name: obo
+  requirement: &8163980 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 0.1.0
   type: :runtime
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
-  name: rspec
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  version_requirements: *8163980
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: &8162940 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        version: "2.6"
+      - !ruby/object:Gem::Version
+        version: '2.6'
   type: :development
-  version_requirements: *id005
-- !ruby/object:Gem::Dependency 
-  name: jeweler
   prerelease: false
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  version_requirements: *8162940
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &8162280 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
+      - !ruby/object:Gem::Version
         version: 1.5.2
   type: :development
-  version_requirements: *id006
-- !ruby/object:Gem::Dependency 
-  name: rcov
   prerelease: false
-  requirement: &id007 !ruby/object:Gem::Requirement 
+  version_requirements: *8162280
+- !ruby/object:Gem::Dependency
+  name: rcov
+  requirement: &8161500 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-  version_requirements: *id007
-description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire, merging of ms-* gems
+  prerelease: false
+  version_requirements: *8161500
+description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
+  merging of ms-* gems
 email: jtprince@gmail.com
 executables: []
-
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE
 - README.rdoc
-files: 
+files:
 - LICENSE
 - README.rdoc
 - Rakefile
@@ -112,7 +110,9 @@ files:
 - lib/io/bookmark.rb
 - lib/merge.rb
 - lib/ms.rb
-- lib/ms/cvlist.rb
+- lib/ms/cv.rb
+- lib/ms/cv/description.rb
+- lib/ms/cv/param.rb
 - lib/ms/digester.rb
 - lib/ms/fasta.rb
 - lib/ms/ident.rb
@@ -161,7 +161,7 @@ files:
 - obo/ms.obo
 - obo/unit.obo
 - spec/bin_spec.rb
-- spec/ms/cvlist_spec.rb
+- spec/ms/cv/description_spec.rb
 - spec/ms/digester_spec.rb
 - spec/ms/fasta_spec.rb
 - spec/ms/ident/peptide/db_spec.rb
@@ -206,31 +206,28 @@ files:
 - spec/testfiles/ms/quant/unlog_transform.rb
 - spec/testfiles/plms1/output.key
 homepage: http://github.com/princelab/mspire
-licenses: 
+licenses:
 - MIT
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.8.10
+rubygems_version: 1.8.15
 signing_key: 
 specification_version: 3
 summary: mass spectrometry proteomics, lipidomics, and tools
 test_files: []
-

data/lib/ms/cvlist.rb

@@ -1,76 +0,0 @@
-
-require 'cv'
-require 'obo/ms'
-require 'obo/ims'
-require 'obo/unit'
-
-module MS
-  module CV
-    Obo = {
-      'MS' => Obo::MS.id_to_name,
-      'IMS' => Obo::IMS.id_to_name,
-      'UO' => Obo::Unit.id_to_name,
-    }
-
-    class Param < ::CV::Param
-      # takes a variety of arguments (acc = accession):
-      #
-      #     acc#
-      #     acc#, value
-      #     acc#, unit_acc# or CV::Param object
-      #     acc#, value, unit_acc# or CV::Param object
-      #     cvref, acc#, name
-      #     cvref, acc#, name, value
-      #     cvref, acc#, name, unit_acc# or CV::Param object
-      #     cvref, acc#, name, value, unit_acc# or CV::Param object
-      def initialize(*args)
-        @unit = 
-          if args.size > 1 && ((args.last.is_a?(::CV::Param) || args.last =~ /[A-Za-z]+:\d+/))
-            unit_arg = args.pop
-            unit_arg.is_a?(::CV::Param) ? unit_arg : self.class.new(unit_arg)
-          end
-        (@cv_ref, @accession, @name, @value) = 
-          case args.size
-          when 1..2  # accession number (maybe with value)
-            (obo_type, accnum) = args.first.split(':')
-            [obo_type, args.first, MS::CV::Obo[obo_type][args.first], args[1]]
-          when 3..4  # they have fully specified the object
-            args
-          end
-      end
-    end
-  end
-
-  #     CVList.new( <CV::Param> )
-  #     CVList['MS:1000004', ['MS:1000004'], ['IMS:1000042', 23], param_obj, args]
-  #     CVList.new do
-  #       param MS:1000004
-  #       param MS:1000042, 23
-  #     end
-  class CVList < Array
-
-    # ensures that each argument is an argument that can be handled by
-    # CV::Param. Returns the CVList object it creates
-    def self.[](*args)
-      list = self.new
-      args.each do |arg| 
-        arg.is_a?(Array) ? list.param(*arg) : list.param(arg) 
-      end
-      list
-    end
-
-    # takes a list of valid CV::Param objects, or they can be set in the block
-    # using param
-    def initialize(*args, &block)
-      args.each {|arg| param(arg) }
-      instance_eval &block if block
-    end
-
-    # if the first object is a MS::CV::Param it is just pushed onto the list,
-    # otherwise the arguments are sent in to initialize a fresh MS::CV::Param,
-    # and this object is pushed onto the list.
-    def param(*args)
-      push args.first.is_a?(::CV::Param) ? args.first : MS::CV::Param.new(*args)
-    end
-  end
-end