mspire 0.6.7 → 0.6.9

data/lib/ms/cv/description.rb

@@ -1,44 +0,0 @@
-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/msplat.rb

@@ -1,2 +0,0 @@
-
-require 'ms/mass/aa' # requires ms/mass

data/spec/ms/cv/description_spec.rb

@@ -1,60 +0,0 @@
-require 'spec_helper'
-require 'ms/cv/description'
-require 'cv'
-
-describe 'appending CV params objects to an MS::CV::Description' do
-  describe 'intelligently appending params with #param' do
-    before do
-      @cv = MS::CV::Description.new
-    end
-    it 'sends detailed descriptions to CV::Param.new' do
-      arglist = [
-        ['IMS', 'IMS:1000052', 'position z', 22],
-        ['IMS', 'IMS:1000030', 'continuous'],
-        ['IMS', 'IMS:1000052', 'position z', 22, 'UO:0000008'],
-        ['IMS', 'IMS:1000030', 'continuous', 'UO:0000008'],
-        ['IMS', 'IMS:1000052', 'position z', 22, MS::CV::Param.new('UO:0000008')],
-        ['IMS', 'IMS:1000030', 'continuous', MS::CV::Param.new('UO:0000008')],
-      ]
-      arglist.each do |args|
-        @cv.param *args
-      end
-      @cv.size.should == arglist.size
-      arglist.each_with_index do |args, i|
-        @cv[i].should == MS::CV::Param.new(*args)
-      end
-    end
-    it 'deciphers short accession descriptions' do
-      @cv.param 'MS:1000004'  # sample mass
-      @cv.param 'IMS:1000042', 23 # max count of pixels x
-      {cv_ref: 'MS', accession: 'MS:1000004', name: 'sample mass', value: nil}.each do |key,val|
-        @cv[0].send(key).should == val
-      end
-      {cv_ref: 'IMS', accession: 'IMS:1000042', name: 'max count of pixels x', value: 23}.each do |key,val|
-        @cv[1].send(key).should == val
-      end
-    end
-    describe 'appending on initialization' do
-      it 'can be done with a block' do
-        cvlist = MS::CV::Description.new do
-          param 'MS:1000004'  # sample mass
-          param 'IMS:1000042', 23 # max count of pixels of y
-        end
-        cvlist.size.should == 2
-      end
-    end
-
-    it 'can be done with brackets' do
-      args = ['IMS', 'IMS:1000052', 'position z', 22]
-      param_obj = CV::Param.new(*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|
-        param.accession.should_not be_nil
-        param.name.should_not be_nil
-        param.cv_ref.should_not be_nil
-      end
-    end
-  end
-end

data/spec/msplat_spec.rb

@@ -1,24 +0,0 @@
-require 'spec_helper'
-
-require 'msplat'
-
-class String
-  def const
-    self.split('::').inject(Kernel) {|scope, const_name| scope.const_get(const_name)}
-  end
-end
-
-describe "msplat" do
-  it "requires major classes/modules" do
-    %w(
-      MS::Mass
-      MS::Mass::AA
-    ).each do |str|
-      expect { str.const }.to be_true
-    end
-    # for sanity's sake
-    %w(MS::DoesntExit).each do |str|
-      expect { str.const }.to raise_error(NameError)
-    end
-  end
-end