mspire 0.6.7 → 0.6.9

data/obo/unit.obo

@@ -1,4 +1,3 @@
-
 format-version: 1.2
 date: 12:10:2011 11:21
 saved-by: George Gkoutos
@@ -2547,6 +2546,25 @@ is_a: UO:0000054 ! area density unit
 created_by: George Gkoutos
 creation_date: 2011-10-12T11:17:08Z
 
+[Term]
+id: UO:0000284
+name: count per nanomolar
+def: "A rate unit which is equal to one over one nanomolar." [UO:GVG]
+subset: unit_slim
+synonym: "nM^-1" EXACT []
+synonym: "1/nM" EXACT []
+is_a: UO:0000280 ! rate unit
+
+[Term]
+id: UO:0000285
+name: count per molar
+def: "A rate unit which is equal to one over one molar." [UO:GVG]
+subset: unit_slim
+synonym: "M^-1" EXACT []
+synonym: "1/M" EXACT []
+is_a: UO:0000280 ! rate unit
+
+
 [Term]
 id: UO:0000301
 name: microgram per liter
@@ -2561,3 +2579,7 @@ id: is_unit_of
 name: is_unit_of
 namespace: pato.ontology
 
+[Typedef]
+id: unit_of
+name: unit_of
+namespace: pato.ontology

data/spec/ms/cv/param_spec.rb

@@ -0,0 +1,33 @@
+require 'spec_helper'
+
+require 'ms/cv/param'
+require 'cv/param'
+
+describe MS::CV::Param do
+  describe 'object creation from class methods' do
+
+    it '::new allows full description' do
+      param1 = MS::CV::Param.new('MS', 'MS:1000052', 'suspension')
+      param1.value.should be_nil
+      # just nonsense: 32 ng suspensions
+      param2 = MS::CV::Param.new('MS', 'MS:1000052', 'suspension', 32, ::CV::Param.new('UO', 'UO:0000024', 'nanogram'))
+      param2.cv_ref.should == 'MS'
+      param2.value.should == 32
+      param2.unit.accession.should == 'UO:0000024'
+    end
+
+    it '::[] requires shortcut accession strings' do
+      param1 = MS::CV::Param['MS:1000052']
+      param1.cv_ref.should == 'MS'
+      param1.value.should be_nil
+
+      # just nonsense: 32 ng suspensions
+      param2 = MS::CV::Param['MS:1000052', 32, 'UO:0000024']
+      param2.cv_ref.should == 'MS'
+      param2.name.should == 'suspension'
+      param2.value.should == 32
+      param2.unit.accession.should == 'UO:0000024'
+    end
+
+  end
+end

data/spec/ms/mzml/cv_spec.rb

@@ -0,0 +1,17 @@
+require 'spec_helper'
+require 'builder'
+require 'ms/mzml/cv'
+
+describe MS::Mzml::CV do
+  
+  it 'can make CVList xml' do
+    cvs = [MS::Mzml::CV::MS, MS::Mzml::CV::UO, MS::Mzml::CV::IMS]
+    b = Builder::XmlMarkup.new(:indent => 2)
+    MS::Mzml::CV.list_xml(cvs, b)
+    xml = b.to_xml
+    [/cvList\s+count=/, /id="MS"/, /id="UO"/, /id="IMS"/, /URI="/].each do |regexp|
+      xml.should match(regexp)
+    end
+  end
+
+end

data/spec/ms/mzml/file_content_spec.rb

@@ -0,0 +1,25 @@
+require 'spec_helper'
+require 'builder'
+
+require 'ms/mzml/file_content'
+
+describe MS::Mzml::FileContent do 
+
+  it 'can be initialized with params' do
+    filecontent = MS::Mzml::FileContent.new(:params => ['MS:1000579', ['IMS:1000080', "{9D501BDC-5344-4916-B7E9-7E795B02C856}"]])
+
+    desc = filecontent.params
+    desc.size.should == 2
+    desc.all? {|par| par.class == MS::CV::Param }.should be_true
+    b = Builder::XmlMarkup.new
+    filecontent.to_xml(b)
+    xml = b.to_xml
+    [/<fileContent>/, /cvRef="MS"/, /name="universally/].each do |regexp|
+      xml.should match(regexp)
+    end
+  end
+
+
+end
+
+

data/spec/ms/mzml/file_description_spec.rb

@@ -0,0 +1,34 @@
+require 'spec_helper'
+require 'ms/mzml/file_description'
+require 'builder'
+
+describe 'creating mzml xml' do
+  describe 'making fileContent' do
+
+    end
+
+  describe 'making a SourceFile' do
+    it 'can be generated with params and a block' do
+      source_file = MS::Mzml::SourceFile.new("someFileID", "filename.mzML", "/home/jtprince/tmp", params: ['MS:1000584'])
+
+      params = source_file.params
+      params.size.should == 1
+      params.all? {|par| par.class == MS::CV::Param }.should be_true
+      b = Builder::XmlMarkup.new(:indent => 2)
+      source_file.to_xml(b)
+      xml = b.to_xml
+      [/<sourceFile/, /id="some/, /name="filen/, /location="\/home/, /cvRef="MS"/].each do |regexp|
+        xml.should match(regexp)
+      end
+    end
+
+  end
+
+  describe MS::Mzml::FileDescription do
+
+    it 'creates valid xml' do
+      #MS::Mzml::FileDescription
+
+    end
+  end
+end

data/spec/ms/mzml/referenceable_param_group_spec.rb

@@ -0,0 +1,33 @@
+require 'spec_helper'
+require 'builder'
+
+require 'ms/mzml/referenceable_param_group'
+
+describe MS::Mzml::ReferenceableParamGroup do
+
+  it 'is created with an id and params' do
+    # the id is required for these objects
+    # no compression
+    rfgroup1 = MS::Mzml::ReferenceableParamGroup.new("mzArray", params: ['MS:1000576', 'MS:1000514'])
+    rfgroup2 = MS::Mzml::ReferenceableParamGroup.new("intensityArray", params: ['MS:1000576', 'MS:1000515'])
+
+    b = Builder::XmlMarkup.new(:indent => 2)
+    z = MS::Mzml::ReferenceableParamGroup.list_xml([rfgroup1, rfgroup2], b)
+    xml = b.to_xml
+    [/referenceableParamGroupList.*count="2/, /cvParam.*cvRef/, /id="intensityArray"/].each do |regexp|
+      xml.should match(regexp)
+    end
+  end
+
+  it '#to_xml gives a ReferenceableParamGroupRef' do
+    rfgroup1 = MS::Mzml::ReferenceableParamGroup.new("mzArray", params: ['MS:1000576', 'MS:1000514'])
+    builder = Builder::XmlMarkup.new(:indent => 2)
+    rfgroup1.to_xml(builder)
+    xml = builder.to_xml
+    [/referenceableParamGroupRef/, /ref="mzArray"/].each do |regexp|
+      xml.should match(regexp)
+    end
+  end
+
+
+end

data/spec/ms/mzml_spec.rb

@@ -1,11 +1,11 @@
 require 'spec_helper'
+require 'builder'
 
 require 'ms/mzml'
 
-describe 'indexed, compressed peaks, mzML file' do
-
-  describe MS::Mzml do
+describe MS::Mzml do
 
+  describe 'reading an indexed, compressed peaks, mzML file' do
     describe 'reading a spectrum' do
 
       before do
@@ -42,9 +42,70 @@ describe 'indexed, compressed peaks, mzML file' do
           spec.mzs.size.should == mz_sizes.shift
         end
       end
+    end
+  end
+
+  describe 'writing mzml' do 
+
+    def sanitize_version(string)
+      string.gsub(/"mspire" version="([\.\d]+)"/, %Q{"mspire" version="X.X.X"})    
+    end
+
+    it 'reads MS1 spectra and retention times' do
+
+      spec_params = ['MS:1000127', ['MS:1000511', 1]]
+
+      spec1 = MS::Mzml::Spectrum.new('scan=1', params: spec_params) do |spec|
+        spec.data_arrays = [[1,2,3], [4,5,6]]
+        spec.scan_list = MS::Mzml::ScanList.new do |sl|
+          scan = MS::Mzml::Scan.new do |scan|
+            # retention time of 42 seconds
+            scan.describe! ['MS:1000016', 40.0, 'UO:0000010']
+          end
+          sl << scan
+        end
+      end
+      spec2 = MS::Mzml::Spectrum.new('scan=2', params: spec_params) do |spec| 
+        spec.data_arrays = [[1,2,3.5], [5,6,5]]
+        spec.scan_list = MS::Mzml::ScanList.new do |sl|
+          scan = MS::Mzml::Scan.new do |scan|
+            # retention time of 42 seconds
+            scan.describe! ['MS:1000016', 45.0, 'UO:0000010']
+          end
+          sl << scan
+        end
+      end
 
+      mzml = MS::Mzml.new do |mzml|
+        mzml.id = 'the_little_one'
+        mzml.cvs = MS::Mzml::CV::DEFAULT_CVS
+        mzml.file_description = MS::Mzml::FileDescription.new  do |fd|
+          fd.file_content = MS::Mzml::FileContent.new
+          fd.source_files << MS::Mzml::SourceFile.new
+        end
+        default_instrument_config = MS::Mzml::InstrumentConfiguration.new("IC",[], params: ['MS:1000031'])
+        mzml.instrument_configurations << default_instrument_config
+        software = MS::Mzml::Software.new
+        mzml.software_list << software
+        default_data_processing = MS::Mzml::DataProcessing.new("did_nothing")
+        mzml.data_processing_list << default_data_processing
+        mzml.run = MS::Mzml::Run.new("little_run", default_instrument_config) do |run|
+          spectrum_list = MS::Mzml::SpectrumList.new(default_data_processing)
+          spectrum_list.push(spec1, spec2)
+          run.spectrum_list = spectrum_list
+        end
+      end
+
+      check = TESTFILES + '/ms/mzml/mspire_simulated.noidx.check.mzML'
+      tmpfile = TESTFILES + '/ms/mzml/mspire_simulated.TMP.mzML'
+      mzml.to_xml(tmpfile)
+      xml = sanitize_version(IO.read(tmpfile))
+      xml.should be_a(String)
+      sanitize_version(mzml.to_xml).should == xml
+      xml.should == sanitize_version(IO.read(check))
+      xml.should match(/<mzML/)
+      File.unlink(tmpfile)
     end
   end
 end
 
-

data/spec/ms/user_param_spec.rb

@@ -0,0 +1,51 @@
+require 'spec_helper'
+
+require 'ms/user_param'
+require 'ms/cv/param'
+
+describe MS::UserParam do
+
+  describe 'initializing with various args' do
+
+    it 'can be initialized with the name' do
+      arg = 'special_user_param'
+      param = MS::UserParam.new arg
+      param.name.should == arg
+      param.unit.should be_nil
+    end
+
+    it' can be initialized with an included UO accession' do
+      arg = 'special_user_param'
+      param = MS::UserParam.new arg, 'UO:0000108'
+      param.name.should == arg
+      param.unit.should_not be_nil
+      param.unit.accession.should == 'UO:0000108'
+    end
+
+    it' can be initialized with an included CV::Param (unit)' do
+      arg = 'special_user_param'
+      param = MS::UserParam.new arg, MS::CV::Param['UO:0000108']
+      param.name.should == arg
+      param.unit.should_not be_nil
+      param.unit.accession.should == 'UO:0000108'
+    end
+
+    it 'can be initialized with a name and value (and type)' do
+      args = %w(some_user_param 88 xsd:float)
+      param = MS::UserParam.new *args
+      param.name.should == args[0]
+      param.value.should == args[1]
+      param.type.should == args[2]
+      param.unit.should be_nil
+
+      args = %w(some_user_param 88 xsd:float UO:0000108)
+      param = MS::UserParam.new *args
+      param.name.should == args[0]
+      param.value.should == args[1]
+      param.type.should == args[2]
+      param.unit.accession.should == 'UO:0000108'
+    end
+
+  end
+
+end

data/spec/mspire_spec.rb

@@ -0,0 +1,9 @@
+require 'spec_helper'
+
+require 'mspire'
+
+describe Mspire do
+  it 'has a VERSION constant derived from upper level VERSION file' do
+    Mspire::VERSION.should match(/^\d+\.\d+\.\d+(\.\d+)?$/)
+  end
+end

data/spec/testfiles/ms/mzml/mspire_simulated.noidx.check.mzML

@@ -0,0 +1,81 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" version="1.1.0" id="the_little_one">
+  <cvList count="3">
+    <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" version="3.18.0"/>
+    <cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" version="16:02:2012"/>
+    <cv id="IMS" fullName="Imaging MS Ontology" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" version="0.9.1"/>
+  </cvList>
+  <fileDescription>
+    <fileContent>
+    </fileContent>
+    <sourceFileList count="1">
+      <sourceFile id="sourcefile1" name="mspire-simulated" location="file://">
+      </sourceFile>
+    </sourceFileList>
+  </fileDescription>
+  <softwareList count="1">
+    <software id="mspire" version="0.6.7">
+    </software>
+  </softwareList>
+  <instrumentConfigurationList count="1">
+    <instrumentConfiguration id="IC">
+      <cvParam cvRef="MS" accession="MS:1000031" name="instrument model"/>
+      <componentList count="0">
+      </componentList>
+    </instrumentConfiguration>
+  </instrumentConfigurationList>
+  <dataProcessingList count="1">
+    <dataProcessing id="did_nothing">
+    </dataProcessing>
+  </dataProcessingList>
+  <run id="little_run" defaultInstrumentConfigurationRef="IC">
+    <spectrumList count="2" defaultDataProcessingRef="did_nothing">
+      <spectrum id="scan=1" index="0" defaultArrayLength="3">
+        <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
+        <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
+        <scanList count="1">
+          <scan>
+            <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="40.0" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
+          </scan>
+        </scanList>
+        <binaryDataArrayList count="2">
+          <binaryDataArray encodedLength="28">
+            <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float"/>
+            <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression"/>
+            <cvParam cvRef="MS" accession="MS:1000514" name="m/z array"/>
+            <binary>eJxjYACBD/YMEOAAoTgcABe3Abg=</binary>
+          </binaryDataArray>
+          <binaryDataArray encodedLength="28">
+            <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float"/>
+            <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression"/>
+            <cvParam cvRef="MS" accession="MS:1000515" name="intensity array"/>
+            <binary>eJxjYAABAQcwxSACpSUcAAjwAP0=</binary>
+          </binaryDataArray>
+        </binaryDataArrayList>
+      </spectrum>
+      <spectrum id="scan=2" index="1" defaultArrayLength="3">
+        <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
+        <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
+        <scanList count="1">
+          <scan>
+            <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="45.0" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
+          </scan>
+        </scanList>
+        <binaryDataArrayList count="2">
+          <binaryDataArray encodedLength="28">
+            <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float"/>
+            <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression"/>
+            <cvParam cvRef="MS" accession="MS:1000514" name="m/z array"/>
+            <binary>eJxjYACBD/YMEOAAoXgcABe/Abw=</binary>
+          </binaryDataArray>
+          <binaryDataArray encodedLength="28">
+            <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float"/>
+            <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression"/>
+            <cvParam cvRef="MS" accession="MS:1000515" name="intensity array"/>
+            <binary>eJxjYAABEQcwxSABpUUcAAlYAQE=</binary>
+          </binaryDataArray>
+        </binaryDataArrayList>
+      </spectrum>
+    </spectrumList>
+  </run>
+</mzML>

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.6.7
+  version: 0.6.9
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-02-16 00:00:00.000000000 Z
+date: 2012-02-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: &8166300 !ruby/object:Gem::Requirement
+  requirement: &15540200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,10 +22,10 @@ dependencies:
         version: '1.5'
   type: :runtime
   prerelease: false
-  version_requirements: *8166300
+  version_requirements: *15540200
 - !ruby/object:Gem::Dependency
   name: bsearch
-  requirement: &8165640 !ruby/object:Gem::Requirement
+  requirement: &15538300 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: 1.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *8165640
+  version_requirements: *15538300
 - !ruby/object:Gem::Dependency
   name: andand
-  requirement: &8164920 !ruby/object:Gem::Requirement
+  requirement: &15535660 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: 1.3.1
   type: :runtime
   prerelease: false
-  version_requirements: *8164920
+  version_requirements: *15535660
 - !ruby/object:Gem::Dependency
   name: obo
-  requirement: &8163980 !ruby/object:Gem::Requirement
+  requirement: &15553840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: 0.1.0
   type: :runtime
   prerelease: false
-  version_requirements: *8163980
+  version_requirements: *15553840
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &8162940 !ruby/object:Gem::Requirement
+  requirement: &15552520 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: '2.6'
   type: :development
   prerelease: false
-  version_requirements: *8162940
+  version_requirements: *15552520
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &8162280 !ruby/object:Gem::Requirement
+  requirement: &15551260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: *8162280
+  version_requirements: *15551260
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &8161500 !ruby/object:Gem::Requirement
+  requirement: &15550400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,7 +88,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *8161500
+  version_requirements: *15550400
 description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
   merging of ms-* gems
 email: jtprince@gmail.com
@@ -105,14 +105,14 @@ files:
 - lib/bin.rb
 - lib/core_ext/array/in_groups.rb
 - lib/cv.rb
-- lib/cv/description.rb
 - lib/cv/param.rb
+- lib/cv/referenceable_param_group_ref.rb
 - lib/io/bookmark.rb
 - lib/merge.rb
 - lib/ms.rb
 - lib/ms/cv.rb
-- lib/ms/cv/description.rb
 - lib/ms/cv/param.rb
+- lib/ms/cv/paramable.rb
 - lib/ms/digester.rb
 - lib/ms/fasta.rb
 - lib/ms/ident.rb
@@ -140,8 +140,36 @@ files:
 - lib/ms/mass.rb
 - lib/ms/mass/aa.rb
 - lib/ms/mzml.rb
+- lib/ms/mzml/activation.rb
+- lib/ms/mzml/chromatogram.rb
+- lib/ms/mzml/chromatogram_list.rb
+- lib/ms/mzml/component.rb
+- lib/ms/mzml/contact.rb
+- lib/ms/mzml/cv.rb
+- lib/ms/mzml/data_array.rb
+- lib/ms/mzml/data_array_container_like.rb
+- lib/ms/mzml/data_processing.rb
+- lib/ms/mzml/file_content.rb
+- lib/ms/mzml/file_description.rb
 - lib/ms/mzml/index_list.rb
+- lib/ms/mzml/instrument_configuration.rb
+- lib/ms/mzml/isolation_window.rb
+- lib/ms/mzml/list.rb
 - lib/ms/mzml/plms1.rb
+- lib/ms/mzml/precursor.rb
+- lib/ms/mzml/processing_method.rb
+- lib/ms/mzml/product.rb
+- lib/ms/mzml/referenceable_param_group.rb
+- lib/ms/mzml/run.rb
+- lib/ms/mzml/sample.rb
+- lib/ms/mzml/scan.rb
+- lib/ms/mzml/scan_list.rb
+- lib/ms/mzml/scan_settings.rb
+- lib/ms/mzml/selected_ion.rb
+- lib/ms/mzml/software.rb
+- lib/ms/mzml/source_file.rb
+- lib/ms/mzml/spectrum.rb
+- lib/ms/mzml/spectrum_list.rb
 - lib/ms/obo.rb
 - lib/ms/peak.rb
 - lib/ms/peak/point.rb
@@ -150,7 +178,9 @@ files:
 - lib/ms/quant/qspec/protein_group_comparison.rb
 - lib/ms/spectrum.rb
 - lib/ms/spectrum/centroid.rb
-- lib/msplat.rb
+- lib/ms/spectrum_like.rb
+- lib/ms/user_param.rb
+- lib/mspire.rb
 - lib/obo/ims.rb
 - lib/obo/ms.rb
 - lib/obo/ontology.rb
@@ -161,7 +191,7 @@ files:
 - obo/ms.obo
 - obo/unit.obo
 - spec/bin_spec.rb
-- spec/ms/cv/description_spec.rb
+- spec/ms/cv/param_spec.rb
 - spec/ms/digester_spec.rb
 - spec/ms/fasta_spec.rb
 - spec/ms/ident/peptide/db_spec.rb
@@ -171,19 +201,25 @@ files:
 - spec/ms/ident/protein_group_spec.rb
 - spec/ms/isotope/aa_spec.rb
 - spec/ms/mass_spec.rb
+- spec/ms/mzml/cv_spec.rb
+- spec/ms/mzml/file_content_spec.rb
+- spec/ms/mzml/file_description_spec.rb
 - spec/ms/mzml/index_list_spec.rb
 - spec/ms/mzml/plms1_spec.rb
+- spec/ms/mzml/referenceable_param_group_spec.rb
 - spec/ms/mzml_spec.rb
 - spec/ms/peak_spec.rb
 - spec/ms/plms1_spec.rb
 - spec/ms/quant/qspec_spec.rb
 - spec/ms/spectrum_spec.rb
-- spec/msplat_spec.rb
+- spec/ms/user_param_spec.rb
+- spec/mspire_spec.rb
 - spec/obo_spec.rb
 - spec/spec_helper.rb
 - spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.fasta
 - spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml
 - spec/testfiles/ms/mzml/j24z.idx_comp.3.mzML
+- spec/testfiles/ms/mzml/mspire_simulated.noidx.check.mzML
 - spec/testfiles/ms/mzml/openms.noidx_nocomp.12.mzML
 - spec/testfiles/ms/quant/kill_extra_tabs.rb
 - spec/testfiles/ms/quant/max_quant_output.provenance.txt

data/lib/cv/description.rb

@@ -1,19 +0,0 @@
-
-module CV
-  class Description < Array
-    def initialize(*args, &block)
-      super(args)
-      self.instance_eval &block
-    end
-
-    # pushes a CV::Param object onto the description array
-    def param(*args)
-      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
-  end
-end