mspire 0.6.26 → 0.7.2

data/spec/{ms → mspire}/ident/pepxml/sample_enzyme_spec.rb

@@ -1,9 +1,9 @@
 
 require 'spec_helper'
-require 'ms/ident/pepxml/sample_enzyme'
+require 'mspire/ident/pepxml/sample_enzyme'
 require 'nokogiri'
 
-describe 'creating an MS::Ident::Pepxml::SampleEnzyme' do
+describe 'creating an Mspire::Ident::Pepxml::SampleEnzyme' do
   before do
     @hash = {
       :name => 'trypsin',
@@ -13,23 +13,23 @@ describe 'creating an MS::Ident::Pepxml::SampleEnzyme' do
     }
   end
   it 'can be set by a known enzyme name' do
-    se = MS::Ident::Pepxml::SampleEnzyme.new('trypsin')
+    se = Mspire::Ident::Pepxml::SampleEnzyme.new('trypsin')
     @hash.each do |k,v|
       se.send(k).should == v
     end
   end
 
   it 'can be set manually with a hash' do
-    se = MS::Ident::Pepxml::SampleEnzyme.new(@hash)
+    se = Mspire::Ident::Pepxml::SampleEnzyme.new(@hash)
     @hash.each do |k,v|
       se.send(k).should == v
     end
   end
 end
 
-describe 'an MS::Ident::Pepxml::SampleEnzyme' do
+describe 'an Mspire::Ident::Pepxml::SampleEnzyme' do
   before do
-    @sample_enzyme = MS::Ident::Pepxml::SampleEnzyme.new(:name=>'trypsin',:cut=>'KR',:no_cut=>'P',:sense=>'C')
+    @sample_enzyme = Mspire::Ident::Pepxml::SampleEnzyme.new(:name=>'trypsin',:cut=>'KR',:no_cut=>'P',:sense=>'C')
   end
   it 'generates a valid xml fragment' do
     string = @sample_enzyme.to_xml
@@ -48,15 +48,15 @@ describe 'an MS::Ident::Pepxml::SampleEnzyme' do
   end
 end
 
-describe 'an MS::Ident::Pepxml::SampleEnzyme making enzyme digestion calculations' do
+describe 'an Mspire::Ident::Pepxml::SampleEnzyme making enzyme digestion calculations' do
   before do
-    @full_KRP = MS::Ident::Pepxml::SampleEnzyme.new(
+    @full_KRP = Mspire::Ident::Pepxml::SampleEnzyme.new(
       :name => 'trypsin',
       :cut => 'KR',
       :no_cut => 'P',
       :sense => 'C',
     )
-    @just_KR = MS::Ident::Pepxml::SampleEnzyme.new(
+    @just_KR = Mspire::Ident::Pepxml::SampleEnzyme.new(
       :name => 'trypsin',
       :cut => 'KR',
       :no_cut => '',
@@ -138,7 +138,7 @@ end
 =begin
 require 'set'
 
-describe 'MS::Ident::Pepxml::SampleEnzyme digesting sequences' do
+describe 'Mspire::Ident::Pepxml::SampleEnzyme digesting sequences' do
   it 'can digest with no missed cleavages' do
     st = "CRGATKKTAGRPMEK"
     SampleEnzyme.tryptic(st).should == %w(CR GATK K TAGRPMEK)

data/spec/{ms → mspire}/ident/pepxml/search_hit/modification_info_spec.rb

@@ -1,12 +1,12 @@
 require 'spec_helper'
 
-require 'ms/ident/pepxml/search_hit/modification_info'
+require 'mspire/ident/pepxml/search_hit/modification_info'
 
-describe 'MS::Ident::Pepxml::SearchHit::ModificationInfo' do
+describe 'Mspire::Ident::Pepxml::SearchHit::ModificationInfo' do
 
   before do
     modaaobjs = [[3, 150.3], [6, 345.2]].map do |ar| 
-      MS::Ident::Pepxml::SearchHit::ModificationInfo::ModAminoacidMass.new(*ar)
+      Mspire::Ident::Pepxml::SearchHit::ModificationInfo::ModAminoacidMass.new(*ar)
     end
     hash = {
       :mod_nterm_mass => 520.2,
@@ -14,7 +14,7 @@ describe 'MS::Ident::Pepxml::SearchHit::ModificationInfo' do
       :mod_aminoacid_masses => modaaobjs,
     }
     #answ = "<modification_info mod_nterm_mass=\"520.2\" modified_peptide=\"MOD*IFI^E&amp;D\">\n\t<mod_aminoacid_mass position=\"3\" mass=\"150.3\"/>\n\t<mod_aminoacid_mass position=\"6\" mass=\"345.2\"/>\n</modification_info>\n"
-    @obj = MS::Ident::Pepxml::SearchHit::ModificationInfo.new(hash)
+    @obj = Mspire::Ident::Pepxml::SearchHit::ModificationInfo.new(hash)
   end
 
   it 'can produce valid pepxml xml' do

data/spec/{ms → mspire}/ident/pepxml_spec.rb

@@ -1,20 +1,20 @@
 require 'spec_helper'
 
-require 'ms/mass'
-require 'ms/mass/aa'
-require 'ms/ident/pepxml'
-require 'ms/ident/pepxml/modifications'
-require 'ms/ident/pepxml/spectrum_query'
-require 'ms/ident/pepxml/search_result'
-require 'ms/ident/pepxml/search_hit'
-require 'ms/ident/pepxml/search_hit/modification_info'
+require 'mspire/mass'
+require 'mspire/mass/aa'
+require 'mspire/ident/pepxml'
+require 'mspire/ident/pepxml/modifications'
+require 'mspire/ident/pepxml/spectrum_query'
+require 'mspire/ident/pepxml/search_result'
+require 'mspire/ident/pepxml/search_hit'
+require 'mspire/ident/pepxml/search_hit/modification_info'
 
-describe "creating an MS::Ident::Pepxml" do
+describe "creating an Mspire::Ident::Pepxml" do
 
   it "can be creating in a nested fashion reflecting internal structure" do
     tags_that_should_be_present = %w(msms_pipeline_analysis msms_run_summary sample_enzyme search_summary spectrum_query search_result search_hit modification_info mod_aminoacid_mass search_score)
 
-    pepxml = MS::Ident::Pepxml.new do |msms_pipeline_analysis|
+    pepxml = Mspire::Ident::Pepxml.new do |msms_pipeline_analysis|
       msms_pipeline_analysis.merge!(:summary_xml => "020.xml") do |msms_run_summary|
         # prep the sample enzyme and search_summary
         msms_run_summary.merge!(
@@ -38,17 +38,17 @@ describe "creating an MS::Ident::Pepxml" do
               :max_num_internal_cleavages => 2,
               :min_number_termini => 2
             )
-            modifications << MS::Ident::Pepxml::AminoacidModification.new(
-              :aminoacid => 'M', :massdiff => 15.9994, :mass => MS::Mass::AA::MONO['M']+15.9994,
+            modifications << Mspire::Ident::Pepxml::AminoacidModification.new(
+              :aminoacid => 'M', :massdiff => 15.9994, :mass => Mspire::Mass::AA::MONO['M']+15.9994,
               :variable => 'Y', :symbol => '*')
               # invented, for example, a protein terminating mod
-            modifications << MS::Ident::Pepxml::TerminalModification.new( 
-              :terminus => 'c', :massdiff => 23.3333, :mass => MS::Mass::MONO['oh'] + 23.3333, 
+            modifications << Mspire::Ident::Pepxml::TerminalModification.new( 
+              :terminus => 'c', :massdiff => 23.3333, :mass => Mspire::Mass::MONO['oh'] + 23.3333, 
               :variable => 'Y', :symbol => '[', :protein_terminus => 'c', 
               :description => 'leave protein_terminus off if not protein mod'
             )
-            modifications << MS::Ident::Pepxml::TerminalModification.new( 
-              :terminus => 'c', :massdiff => 25.42322, :mass => MS::Mass::MONO['h+'] + 25.42322, 
+            modifications << Mspire::Ident::Pepxml::TerminalModification.new( 
+              :terminus => 'c', :massdiff => 25.42322, :mass => Mspire::Mass::MONO['h+'] + 25.42322, 
               :variable => 'N', :symbol => ']', :description => 'example: c term mod'
             )
             parameters.merge!( 
@@ -57,18 +57,18 @@ describe "creating an MS::Ident::Pepxml" do
                               :enzyme_info => 'Trypsin(KR/P) 1 1 KR P', # etc.... 
                              )
           end
-          spectrum_query1 = MS::Ident::Pepxml::SpectrumQuery.new(
+          spectrum_query1 = Mspire::Ident::Pepxml::SpectrumQuery.new(
             :spectrum  => '020.3.3.1', :start_scan => 3, :end_scan => 3, 
             :precursor_neutral_mass => 1120.93743421875, :assumed_charge => 1
           ) do |search_results|
-            search_result1 = MS::Ident::Pepxml::SearchResult.new do |search_hits|
+            search_result1 = Mspire::Ident::Pepxml::SearchResult.new do |search_hits|
               modpositions = [[1, 243.1559], [6, 167.0581], [7,181.085]].map do |pair|  
-                MS::Ident::Pepxml::SearchHit::ModificationInfo::ModAminoacidMass.new(*pair)
+                Mspire::Ident::Pepxml::SearchHit::ModificationInfo::ModAminoacidMass.new(*pair)
               end
               # order(modified_peptide, mod_aminoacid_masses, :mod_nterm_mass, :mod_cterm_mass)
               # or can be set by hash
-              mod_info = MS::Ident::Pepxml::SearchHit::ModificationInfo.new('Y#RLGGS#T#K', modpositions)
-              search_hit1 = MS::Ident::Pepxml::SearchHit.new( 
+              mod_info = Mspire::Ident::Pepxml::SearchHit::ModificationInfo.new('Y#RLGGS#T#K', modpositions)
+              search_hit1 = Mspire::Ident::Pepxml::SearchHit.new( 
                 :hit_rank=>1, :peptide=>'YRLGGSTK', :peptide_prev_aa => "R", :peptide_next_aa => "K",
                 :protein => "gi|16130113|ref|NP_416680.1|", :num_tot_proteins => 1, :num_matched_ions => 5,
                 :tot_num_ions => 35, :calc_neutral_pep_mass => 1120.93163442, :massdiff => 0.00579979875010395,
@@ -141,7 +141,7 @@ end
 
 
 =begin
-describe "MS::Ident::Pepxml created from small bioworks.xml" do
+describe "Mspire::Ident::Pepxml created from small bioworks.xml" do
 
   spec_large do
     before(:all) do

data/spec/{ms → mspire}/ident/protein_group_spec.rb

@@ -1,6 +1,6 @@
 require 'spec_helper'
 
-require 'ms/ident/protein_group'
+require 'mspire/ident/protein_group'
 
 PeptideHit = Struct.new(:aaseq, :charge, :proteins) do
   def inspect # easier to read output
@@ -36,21 +36,21 @@ describe 'creating minimal protein groups from peptide hits' do
   it 'is a greedy algorithm' do
     @prot_hits.each {|prthit| @prot_hits_hash[prthit.id].each {|pep| pep.proteins << prthit } }
     # big_guy has all the peptides, so it takes them all
-    protein_groups = MS::Ident::ProteinGroup.peptide_hits_to_protein_groups(@pep_hits)
+    protein_groups = Mspire::Ident::ProteinGroup.peptide_hits_to_protein_groups(@pep_hits)
     protein_groups.first.size.should == 1# the group
     protein_groups.first.first.id.should == 'big_guy'
   end
 
   it 'removes proteins accounted for only as little pieces of larger proteins' do
     @prot_hits[1..-1].each {|prthit| @prot_hits_hash[prthit.id].each {|pep| pep.proteins << prthit } }
-    protein_groups = MS::Ident::ProteinGroup.peptide_hits_to_protein_groups(@pep_hits)
+    protein_groups = Mspire::Ident::ProteinGroup.peptide_hits_to_protein_groups(@pep_hits)
     # no subsumed_by_medium
     protein_groups.any? {|prot_group| prot_group.any? {|v| v.id == 'subsumed_by_medium' }}.should == false
   end
 
   it 'allows alternate sorting algorithms for greediness' do
     @prot_hits.each {|prthit| @prot_hits_hash[prthit.id].each {|pep| pep.proteins << prthit } }
-    prot_groups = MS::Ident::ProteinGroup.peptide_hits_to_protein_groups(@pep_hits) do |prot_and_peptide_hits|
+    prot_groups = Mspire::Ident::ProteinGroup.peptide_hits_to_protein_groups(@pep_hits) do |prot_and_peptide_hits|
       # deliberate using a counterintuitive sorting method to give little guys
       # a chance
       -prot_and_peptide_hits.last.size

data/spec/{ms → mspire}/isotope/aa_spec.rb

@@ -1,6 +1,6 @@
 require 'spec_helper'
 
-require 'ms/isotope/aa'
+require 'mspire/isotope/aa'
 
 describe 'accessing an amino acid atom count' do
   before do
@@ -8,12 +8,12 @@ describe 'accessing an amino acid atom count' do
   end
 
   it 'residue can be accessed with a symbol' do
-    hash = MS::Isotope::AA::ATOM_COUNTS[:A]
+    hash = Mspire::Isotope::AA::ATOM_COUNTS[:A]
     [:c, :h, :o, :n, :s].each {|key| hash[key].should == @alanine[key] }
   end
     
   it 'residue can be accessed with a string' do
-    hash = MS::Isotope::AA::ATOM_COUNTS['A']
+    hash = Mspire::Isotope::AA::ATOM_COUNTS['A']
     [:c, :h, :o, :n, :s].each {|key| hash[key].should == @alanine[key] }
   end
 

data/spec/{ms → mspire}/isotope/distribution_spec.rb

@@ -1,19 +1,19 @@
 require 'spec_helper'
 
-require 'ms/isotope/distribution'
+require 'mspire/isotope/distribution'
 
-describe 'MS::Isotope::Distribution class methods' do
+describe 'Mspire::Isotope::Distribution class methods' do
   before do 
     @data = [1.0, 0.08919230588715289, 0.017894161377222082, 0.0013573997600723623, 0.0001398330738144092]
   end
 
   it 'can calculate isotope distributions' do
-    MS::Isotope::Distribution.calculate('C8O7', :max).should == @data
+    Mspire::Isotope::Distribution.calculate('C8O7', :max).should == @data
   end
 
   # no m/z values, just mass values
   it 'can calculate isotope distribution spectrum' do
-    spec = MS::Isotope::Distribution.spectrum('C8O7', :max)
+    spec = Mspire::Isotope::Distribution.spectrum('C8O7', :max)
     spec.mzs.should == [207.96440233692, 208.97306725252, 209.98173216812, 210.99039708372, 211.99906199932002]
     spec.intensities.should == [1.0, 0.08919230588715289, 0.017894161377222082, 0.0013573997600723623, 0.0001398330738144092]
   end

data/spec/{ms → mspire}/isotope_spec.rb

@@ -1,12 +1,12 @@
 require 'spec_helper'
 
-require 'ms/isotope'
+require 'mspire/isotope'
 
-describe 'MS::Isotope constants' do
-  it 'has all the common isotopes: MS::Isotope::ISOTOPES' do
+describe 'Mspire::Isotope constants' do
+  it 'has all the common isotopes: Mspire::Isotope::ISOTOPES' do
     # frozen
-    MS::Isotope::ISOTOPES.size.should == 288
-    hydrogen_isotopes = MS::Isotope::ISOTOPES.select {|iso| iso.element == :h }
+    Mspire::Isotope::ISOTOPES.size.should == 288
+    hydrogen_isotopes = Mspire::Isotope::ISOTOPES.select {|iso| iso.element == :h }
     hydrogen_isotopes.size.should == 2
 
     { atomic_number: 1, element: :h, mass_number: 1, atomic_mass: 1.00782503207, relative_abundance: 0.999885, average_mass: 1.00794, mono: true }.each do |k,v|
@@ -15,17 +15,17 @@ describe 'MS::Isotope constants' do
     {atomic_number: 1, element: :h, mass_number: 2, atomic_mass: 2.0141017778, relative_abundance: 0.000115, average_mass: 1.00794, mono: false}.each do |k,v|
       hydrogen_isotopes.last.send(k).should == v
     end
-    u = MS::Isotope::ISOTOPES.last
+    u = Mspire::Isotope::ISOTOPES.last
     {atomic_number: 92, element: :u, mass_number: 238, atomic_mass: 238.0507882, relative_abundance: 0.992742, average_mass: 238.02891, mono: true}.each do |k,v|
       u.send(k).should == v
     end
   end
-  it 'has all common isotopes by element: MS::Isotope::BY_ELEMENT' do
-    [{atomic_number: 6, element: :c, mass_number: 12, atomic_mass: 12.0, relative_abundance: 0.9893, average_mass: 12.0107, mono: true}, {atomic_number: 6, element: :c, mass_number: 13, atomic_mass: 13.0033548378, relative_abundance: 0.0107, average_mass: 12.0107, mono: false}].zip(MS::Isotope::BY_ELEMENT[:c]) do |hash, iso|
+  it 'has all common isotopes by element: Mspire::Isotope::BY_ELEMENT' do
+    [{atomic_number: 6, element: :c, mass_number: 12, atomic_mass: 12.0, relative_abundance: 0.9893, average_mass: 12.0107, mono: true}, {atomic_number: 6, element: :c, mass_number: 13, atomic_mass: 13.0033548378, relative_abundance: 0.0107, average_mass: 12.0107, mono: false}].zip(Mspire::Isotope::BY_ELEMENT[:c]) do |hash, iso|
       hash.each do |k,v|
         iso.send(k).should == v
       end
     end
-    MS::Isotope::BY_ELEMENT[:h].size.should == 2
+    Mspire::Isotope::BY_ELEMENT[:h].size.should == 2
   end
 end

data/spec/{ms → mspire}/mass_spec.rb

@@ -1,8 +1,8 @@
 require 'spec_helper'
 
-require 'ms/mass'
+require 'mspire/mass'
 
-describe 'MS::Mass' do
+describe 'Mspire::Mass' do
   it 'can access elemental masses by string or symbol' do
     {
       'c' => 12.0,  # +
@@ -26,16 +26,16 @@ describe 'MS::Mass' do
       'e' => 0.0005486,
       'se' => 79.9165196
     }.each do |el, mass|
-      MS::Mass::MONO[el].should_not be_nil
-      MS::Mass::MONO[el].should == MS::Mass::MONO[el.to_sym]
-      MS::Mass::MONO[el].should be_within(0.00001).of(mass) 
+      Mspire::Mass::MONO[el].should_not be_nil
+      Mspire::Mass::MONO[el].should == Mspire::Mass::MONO[el.to_sym]
+      Mspire::Mass::MONO[el].should be_within(0.00001).of(mass) 
     end
 
 
     { h: 1.00794, he: 4.002602, ni: 58.6934 }.each do |el, mass|
-      MS::Mass::AVG[el].should_not be_nil
-      MS::Mass::AVG[el].should == MS::Mass::AVG[el.to_sym]
-      MS::Mass::AVG[el].should be_within(0.00001).of(mass) 
+      Mspire::Mass::AVG[el].should_not be_nil
+      Mspire::Mass::AVG[el].should == Mspire::Mass::AVG[el.to_sym]
+      Mspire::Mass::AVG[el].should be_within(0.00001).of(mass) 
     end
 
   end

data/spec/{ms → mspire}/molecular_formula_spec.rb

@@ -1,14 +1,14 @@
 require 'spec_helper'
 
-require 'ms/molecular_formula'
+require 'mspire/molecular_formula'
 
-describe MS::MolecularFormula do
+describe Mspire::MolecularFormula do
 
   it 'can be initialized with a String or Hash' do
     data = {h: 22, c: 12, n: 1, o: 3, s: 2}
-    mf = MS::MolecularFormula.new "H22BeC12N1O3S2Li2"
+    mf = Mspire::MolecularFormula.new "H22BeC12N1O3S2Li2"
     mf.should == {:h=>22, :be=>1, :c=>12, :n=>1, :o=>3, :s=>2, :li=>2}
-    mf = MS::MolecularFormula.new(data)
+    mf = Mspire::MolecularFormula.new(data)
     mf.should == data
   end
 

data/spec/{ms → mspire}/mzml/cv_spec.rb

@@ -1,13 +1,13 @@
 require 'spec_helper'
 require 'builder'
-require 'ms/mzml/cv'
+require 'mspire/mzml/cv'
 
-describe MS::Mzml::CV do
+describe Mspire::Mzml::CV do
   
   it 'can make CVList xml' do
-    cvs = [MS::Mzml::CV::MS, MS::Mzml::CV::UO, MS::Mzml::CV::IMS]
+    cvs = [Mspire::Mzml::CV::MS, Mspire::Mzml::CV::UO, Mspire::Mzml::CV::IMS]
     b = Builder::XmlMarkup.new(:indent => 2)
-    MS::Mzml::CV.list_xml(cvs, b)
+    Mspire::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)

data/spec/{ms → mspire}/mzml/data_array_spec.rb

@@ -1,26 +1,26 @@
 require 'spec_helper'
 
-require 'ms/mzml/data_array'
+require 'mspire/mzml/data_array'
 
-describe MS::Mzml::DataArray do
+describe Mspire::Mzml::DataArray do
 
   it 'can be created from base64 binary data' do
-    d_ar = MS::Mzml::DataArray.from_binary('eJxjYACBD/YMEOAAoTgcABe3Abg=', :float64, zlib=true)
+    d_ar = Mspire::Mzml::DataArray.from_binary('eJxjYACBD/YMEOAAoTgcABe3Abg=', :float64, zlib=true)
     d_ar.is_a?(Array)
     d_ar.should == [1.0, 2.0, 3.0]
-    d_ar = MS::Mzml::DataArray.from_binary('eJxjYACBD/YMEOAAoTgcABe3Abg=', ['MS:1000523', 'MS:1000574'])
+    d_ar = Mspire::Mzml::DataArray.from_binary('eJxjYACBD/YMEOAAoTgcABe3Abg=', ['MS:1000523', 'MS:1000574'])
     d_ar.is_a?(Array)
     d_ar.should == [1.0, 2.0, 3.0]
   end
 
   it "can be initialized like any ol' array" do
     data = [1,2,3]
-    d_ar = MS::Mzml::DataArray.new( data )
+    d_ar = Mspire::Mzml::DataArray.new( data )
     d_ar.should == data
   end
 
-  describe 'an instantiated MS::Mzml::DataArray' do
-    subject { MS::Mzml::DataArray.new [1,2,3] }
+  describe 'an instantiated Mspire::Mzml::DataArray' do
+    subject { Mspire::Mzml::DataArray.new [1,2,3] }
 
     it "can have a 'type'" do
       subject.type = :mz

data/spec/{ms → mspire}/mzml/file_content_spec.rb

@@ -1,16 +1,16 @@
 require 'spec_helper'
 require 'builder'
 
-require 'ms/mzml/file_content'
+require 'mspire/mzml/file_content'
 
-describe MS::Mzml::FileContent do 
+describe Mspire::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}"]])
+    filecontent = Mspire::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
+    desc.all? {|par| par.class == Mspire::CV::Param }.should be_true
     b = Builder::XmlMarkup.new
     filecontent.to_xml(b)
     xml = b.to_xml

data/spec/{ms → mspire}/mzml/file_description_spec.rb

@@ -1,5 +1,5 @@
 require 'spec_helper'
-require 'ms/mzml/file_description'
+require 'mspire/mzml/file_description'
 require 'builder'
 
 describe 'creating mzml xml' do
@@ -9,11 +9,11 @@ describe 'creating mzml xml' do
 
   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'])
+      source_file = Mspire::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
+      params.all? {|par| par.class == Mspire::CV::Param }.should be_true
       b = Builder::XmlMarkup.new(:indent => 2)
       source_file.to_xml(b)
       xml = b.to_xml
@@ -24,7 +24,7 @@ describe 'creating mzml xml' do
 
   end
 
-  describe MS::Mzml::FileDescription do
+  describe Mspire::Mzml::FileDescription do
 
     it 'creates valid xml' do
       #MS::Mzml::FileDescription