mspire 0.6.26 → 0.7.2

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

@@ -1,12 +1,12 @@
 require 'spec_helper'
 
-require 'ms/mzml'
-require 'ms/mzml/index_list'
+require 'mspire/mzml'
+require 'mspire/mzml/index_list'
 
 describe 'non-indexed uncompressed peaks, mzML file' do
-  subject { TESTFILES + "/ms/mzml/openms.noidx_nocomp.12.mzML" }
+  subject { TESTFILES + "/mspire/mzml/openms.noidx_nocomp.12.mzML" }
 
-  describe 'MS::Mzml getting the IndexList' do
+  describe 'Mspire::Mzml getting the IndexList' do
     before do
       @io = File.open(subject)
     end
@@ -15,7 +15,7 @@ describe 'non-indexed uncompressed peaks, mzML file' do
     end
 
     it 'works for an un-indexed file' do
-      mzml = MS::Mzml.new(@io)
+      mzml = Mspire::Mzml.new(@io)
       index_list = mzml.index_list
       spectrum_idx = index_list[:spectrum]
       spectrum_idx.name.should == :spectrum
@@ -38,10 +38,10 @@ end
 
 
 describe 'indexed, compressed peaks, mzML file' do
-  subject { TESTFILES + "/ms/mzml/j24z.idx_comp.3.mzML"  }
+  subject { TESTFILES + "/mspire/mzml/j24z.idx_comp.3.mzML"  }
 
 
-  describe 'MS::Mzml getting the IndexList' do
+  describe 'Mspire::Mzml getting the IndexList' do
     before do
       @io = File.open(subject)
     end
@@ -65,21 +65,21 @@ describe 'indexed, compressed peaks, mzML file' do
     end
 
     it 'works for an indexed file' do
-      mzml = MS::Mzml.new(@io)
+      mzml = Mspire::Mzml.new(@io)
       index_list = mzml.index_list
       correct_index_list.call(index_list)
     end
 
     it 'can create the index manually, if requested' do
-      mzml = MS::Mzml.new(@io)
+      mzml = Mspire::Mzml.new(@io)
       index_list =  mzml.create_index_list
       correct_index_list.call(index_list)
     end
 
-    describe 'an MS::Mzxml::IndexList' do
+    describe 'an Mspire::Mzxml::IndexList' do
       before do
         @inner_io = File.open(subject)
-        mzml = MS::Mzml.new(@inner_io)
+        mzml = Mspire::Mzml.new(@inner_io)
         @index_list = mzml.index_list
       end
       after do
@@ -96,10 +96,10 @@ describe 'indexed, compressed peaks, mzML file' do
       end
     end
 
-    describe 'an MS::Mzxml::Index' do
+    describe 'an Mspire::Mzxml::Index' do
       before do
         @inner_io = File.open(subject)
-        mzml = MS::Mzml.new(@inner_io)
+        mzml = Mspire::Mzml.new(@inner_io)
         @spec_index = mzml.index_list[:spectrum]
       end
       after do

data/spec/{ms → mspire}/mzml/plms1_spec.rb

@@ -1,13 +1,13 @@
 require 'spec_helper'
 
-require 'ms/mzml'
-require 'ms/mzml/plms1'
+require 'mspire/mzml'
+require 'mspire/mzml/plms1'
 
 describe 'converting mzml to plms1' do
   describe 'converting no spectra mzml' do
     before do 
-      @mzml_file = File.open( TESTFILES + "/ms/mzml/openms.noidx_nocomp.12.mzML" )
-      @mzml = MS::Mzml.new(@mzml_file)
+      @mzml_file = File.open( TESTFILES + "/mspire/mzml/openms.noidx_nocomp.12.mzML" )
+      @mzml = Mspire::Mzml.new(@mzml_file)
     end
 
     after do
@@ -23,7 +23,7 @@ describe 'converting mzml to plms1' do
       plms1.scan_numbers.should == scan_nums
       plms1.spectra.each do |spec|
         spec.size.should == 2
-        spec.should be_a_kind_of(MS::SpectrumLike)
+        spec.should be_a_kind_of(Mspire::SpectrumLike)
         spec.mzs.should == []
         spec.intensities.should == []
       end
@@ -34,8 +34,8 @@ describe 'converting mzml to plms1' do
 
   describe 'converting normal mzml' do
     before do 
-      @mzml_file = File.open( TESTFILES + "/ms/mzml/j24z.idx_comp.3.mzML" )
-      @mzml = MS::Mzml.new(@mzml_file)
+      @mzml_file = File.open( TESTFILES + "/mspire/mzml/j24z.idx_comp.3.mzML" )
+      @mzml = Mspire::Mzml.new(@mzml_file)
     end
 
     after do
@@ -51,7 +51,7 @@ describe 'converting mzml to plms1' do
       plms1.scan_numbers.should == [1, 2, 3] 
       sizes = [20168, 315, 634]
       plms1.spectra.zip(sizes).each do |spec,exp_size|
-        spec.should be_a_kind_of(MS::SpectrumLike)
+        spec.should be_a_kind_of(Mspire::SpectrumLike)
         spec.size.should == 2
         spec.mzs.size.should == exp_size
         spec.intensities.size.should == exp_size

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

@@ -1,18 +1,18 @@
 require 'spec_helper'
 require 'builder'
 
-require 'ms/mzml/referenceable_param_group'
+require 'mspire/mzml/referenceable_param_group'
 
-describe MS::Mzml::ReferenceableParamGroup do
+describe Mspire::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'])
+    rfgroup1 = Mspire::Mzml::ReferenceableParamGroup.new("mzArray", params: ['MS:1000576', 'MS:1000514'])
+    rfgroup2 = Mspire::Mzml::ReferenceableParamGroup.new("intensityArray", params: ['MS:1000576', 'MS:1000515'])
 
     b = Builder::XmlMarkup.new(:indent => 2)
-    z = MS::Mzml::ReferenceableParamGroup.list_xml([rfgroup1, rfgroup2], b)
+    z = Mspire::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)
@@ -20,7 +20,7 @@ describe MS::Mzml::ReferenceableParamGroup do
   end
 
   it '#to_xml gives a ReferenceableParamGroupRef' do
-    rfgroup1 = MS::Mzml::ReferenceableParamGroup.new("mzArray", params: ['MS:1000576', 'MS:1000514'])
+    rfgroup1 = Mspire::Mzml::ReferenceableParamGroup.new("mzArray", params: ['MS:1000576', 'MS:1000514'])
     builder = Builder::XmlMarkup.new(:indent => 2)
     rfgroup1.to_xml(builder)
     xml = builder.to_xml

data/spec/{ms → mspire}/mzml_spec.rb

@@ -1,17 +1,17 @@
 require 'spec_helper'
 require 'builder'
 
-require 'ms/mzml'
+require 'mspire/mzml'
 
-describe MS::Mzml do
+describe Mspire::Mzml do
 
   describe 'reading an indexed, compressed peaks, mzML file' do
     describe 'reading a spectrum' do
 
       before do
-        @file = TESTFILES + "/ms/mzml/j24z.idx_comp.3.mzML"
+        @file = TESTFILES + "/mspire/mzml/j24z.idx_comp.3.mzML"
         @io = File.open(@file)
-        @mzml = MS::Mzml.new(@io)
+        @mzml = Mspire::Mzml.new(@io)
       end
       after do
         @io.close
@@ -22,7 +22,7 @@ describe MS::Mzml do
         spectrum1 = @mzml[1] # can get with brackets
         spectrum.ms_level.should == 2
         spectrum.should == spectrum1
-        spectrum.should be_a(MS::Mzml::Spectrum)
+        spectrum.should be_a(Mspire::Mzml::Spectrum)
         spectrum.should respond_to(:mzs)
         spectrum.should respond_to(:intensities)
         spectrum.mzs.size.should == 315
@@ -35,13 +35,13 @@ describe MS::Mzml do
         spectrum1 = @mzml["controllerType=0 controllerNumber=1 scan=2"]
         spectrum.ms_level.should == 2
         spectrum.should == spectrum1
-        spectrum.should be_a(MS::Mzml::Spectrum)
+        spectrum.should be_a(Mspire::Mzml::Spectrum)
       end
 
       it 'each spectrum knows its retention_time' do
         spec = @mzml[1]
         rt = @mzml[1].retention_time
-        rt.should == 33.035128333333333
+        rt.should == 1982.1077
       end
 
       it 'goes through spectrum with #each or #each_spectrum' do
@@ -62,13 +62,13 @@ describe MS::Mzml do
 
       it 'iterates with foreach' do
         mz_sizes = [20168, 315, 634]
-        iter = MS::Mzml.foreach(@file)
+        iter = Mspire::Mzml.foreach(@file)
         3.times { iter.next.mzs.size.should == mz_sizes.shift }
         lambda {iter.next}.should raise_error
       end
 
       it 'can gracefully determine the m/z with highest peak in select scans' do
-        highest_mzs = MS::Mzml.foreach(@file).select {|v| v.ms_level > 1 }.map do |spec|
+        highest_mzs = Mspire::Mzml.foreach(@file).select {|v| v.ms_level > 1 }.map do |spec|
           spec.points.sort_by(&:last).first.first
         end
         highest_mzs.map(&:round).should == [453, 866]
@@ -84,10 +84,10 @@ describe MS::Mzml do
 
     it 'writes MS1 and MS2 spectra' do
       # params: profile and ms_level 1
-      spec1 = MS::Mzml::Spectrum.new('scan=1', params: ['MS:1000128', ['MS:1000511', 1]]) do |spec|
+      spec1 = Mspire::Mzml::Spectrum.new('scan=1', params: ['MS:1000128', ['MS:1000511', 1]]) 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|
+        spec.scan_list = Mspire::Mzml::ScanList.new do |sl|
+          scan = Mspire::Mzml::Scan.new do |scan|
             # retention time of 42 seconds
             scan.describe! ['MS:1000016', 40.0, 'UO:0000010']
           end
@@ -98,17 +98,17 @@ describe MS::Mzml do
       # centroid,  ms_level 2, MSn spectrum, 
       spec_params = ['MS:1000127', ['MS:1000511', 2], "MS:1000580"]
 
-      spec2 = MS::Mzml::Spectrum.new('scan=2', params: spec_params) do |spec| 
+      spec2 = Mspire::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|
+        spec.scan_list = Mspire::Mzml::ScanList.new do |sl|
+          scan = Mspire::Mzml::Scan.new do |scan|
             # retention time of 42 seconds
             scan.describe! ['MS:1000016', 45.0, 'UO:0000010']
           end
           sl << scan
         end
-        precursor = MS::Mzml::Precursor.new( spec1 )
-        si = MS::Mzml::SelectedIon.new
+        precursor = Mspire::Mzml::Precursor.new( spec1 )
+        si = Mspire::Mzml::SelectedIon.new
         # the selected ion m/z:
         si.describe! ["MS:1000744", 2.0]
         # the selected ion charge state
@@ -119,31 +119,31 @@ describe MS::Mzml do
         spec.precursors = [precursor]
       end
 
-      mzml = MS::Mzml.new do |mzml|
+      mzml = Mspire::Mzml.new do |mzml|
         mzml.id = 'ms1_and_ms2'
-        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
+        mzml.cvs = Mspire::Mzml::CV::DEFAULT_CVS
+        mzml.file_description = Mspire::Mzml::FileDescription.new  do |fd|
+          fd.file_content = Mspire::Mzml::FileContent.new
+          fd.source_files << Mspire::Mzml::SourceFile.new
         end
-        default_instrument_config = MS::Mzml::InstrumentConfiguration.new("IC",[], params: ['MS:1000031'])
+        default_instrument_config = Mspire::Mzml::InstrumentConfiguration.new("IC",[], params: ['MS:1000031'])
         mzml.instrument_configurations << default_instrument_config
-        software = MS::Mzml::Software.new
+        software = Mspire::Mzml::Software.new
         mzml.software_list << software
-        default_data_processing = MS::Mzml::DataProcessing.new("did_nothing")
+        default_data_processing = Mspire::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)
+        mzml.run = Mspire::Mzml::Run.new("little_run", default_instrument_config) do |run|
+          spectrum_list = Mspire::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.MSn.TMP.mzML'
+      #check = TESTFILES + '/mspire/mzml/mspire_simulated.noidx.check.mzML'
+      tmpfile = TESTFILES + '/mspire/mzml/mspire_simulated.MSn.TMP.mzML'
       mzml.to_xml(tmpfile)
       as_string = mzml.to_xml
-      check_string = IO.read(TESTFILES + '/ms/mzml/mspire_simulated.MSn.check.mzML')
+      check_string = IO.read(TESTFILES + '/mspire/mzml/mspire_simulated.MSn.check.mzML')
 
       [IO.read(tmpfile), as_string].each do |st|
         sanitize_version(check_string).should == sanitize_version(st)

data/spec/{ms → mspire}/peak_spec.rb

@@ -1,9 +1,9 @@
 require 'spec_helper'
 
-require 'ms/peak'
-require 'ms/peak/point'
+require 'mspire/peak'
+require 'mspire/peak/point'
 
-describe MS::Peak do
+describe Mspire::Peak do
 
   describe '#split' do
 
@@ -25,11 +25,11 @@ describe MS::Peak do
         mz += diff
       end
       @xs.map! {|mz| mz.round(2) }
-      @points = @xs.zip(@intensities).map {|pair| MS::Peak::Point.new(pair) }
+      @points = @xs.zip(@intensities).map {|pair| Mspire::Peak::Point.new(pair) }
     end
 
     it 'splits on zeros by default' do
-      peak = MS::Peak.new(@points) # <- maybe more like a collection of peaks, but Peak is flexible
+      peak = Mspire::Peak.new(@points) # <- maybe more like a collection of peaks, but Peak is flexible
       peaks = peak.split
       peaks.size.should == 4
       peaks.should == [
@@ -46,17 +46,17 @@ describe MS::Peak do
 
     # which it should since zeros are the ultimate local min!
     it 'always cleans up surrounding zeros and does not split non-multipeaks' do
-      peak = MS::Peak.new(@points[0,7])  # simple
+      peak = Mspire::Peak.new(@points[0,7])  # simple
       [:share, :greedy_y].each do |multipeak_split_method|
         peaks = peak.split(multipeak_split_method)
-        peaks.first.should be_an_instance_of(MS::Peak)
+        peaks.first.should be_an_instance_of(Mspire::Peak)
         peaks.first.to_a.should == [[50.01, 3], [50.02, 8], [50.03, 9], [50.04, 7], [50.05, 2]]
       end
     end
 
     it 'does #split(:share) and shares the peak proportional to adjacent peaks' do
       data = [[50.07, 0], [50.08, 3], [50.09, 8], [50.1, 2], [50.11, 9], [50.12, 7], [50.13, 1], [50.14, 3], [50.15, 0]]
-      multipeak1 = MS::Peak.new( data )
+      multipeak1 = Mspire::Peak.new( data )
 
       answer = [
         [[50.08, 3], [50.09, 8], [50.1, (2*8.0/17)]], 
@@ -80,8 +80,8 @@ describe MS::Peak do
 
       # test a tie -> goes left!
       points = @points[7,9]
-      points[2] = MS::Peak::Point.new([points[2][0], 9])
-      multipeak2 = MS::Peak.new( points )
+      points[2] = Mspire::Peak::Point.new([points[2][0], 9])
+      multipeak2 = Mspire::Peak.new( points )
       multipeak2.split(:greedy_y).should == answer
 
     end

data/spec/{ms → mspire}/plms1_spec.rb

@@ -1,7 +1,7 @@
 require 'spec_helper'
 
-require 'ms/plms1'
-require 'ms/spectrum'
+require 'mspire/plms1'
+require 'mspire/spectrum'
 
 describe 'plms1 - Prince Lab MS 1 specification' do
   before do
@@ -9,15 +9,15 @@ describe 'plms1 - Prince Lab MS 1 specification' do
     times = [0.55, 0.9]
     scan_numbers = [1,2]
     spectra = [
-      MS::Spectrum.new([[300.0, 301.5, 303.1], [10, 20, 35.5]]),
-      MS::Spectrum.new([[300.5, 302, 303.6], [11, 21, 36.5]])
+      Mspire::Spectrum.new([[300.0, 301.5, 303.1], [10, 20, 35.5]]),
+      Mspire::Spectrum.new([[300.5, 302, 303.6], [11, 21, 36.5]])
     ]
-    @plms1_obj = MS::Plms1.new(scan_numbers, times, spectra)
+    @plms1_obj = Mspire::Plms1.new(scan_numbers, times, spectra)
     @outfile = @keyfile.sub(/\.key$/, ".tmp")
   end
 
   it 'has a detailed specification' do
-    specification = MS::Plms1::SPECIFICATION
+    specification = Mspire::Plms1::SPECIFICATION
     specification.should be_an_instance_of String
     (specification.size > 50).should == true
   end
@@ -30,7 +30,7 @@ describe 'plms1 - Prince Lab MS 1 specification' do
   end
 
   it 'reads a plms1 file' do
-    obj = MS::Plms1.new.read(@keyfile)
+    obj = Mspire::Plms1.new.read(@keyfile)
     [:scan_numbers, :times, :spectra].each do |val|
       obj.send(val).should == @plms1_obj.send(val)
     end

data/spec/{ms → mspire}/quant/qspec_spec.rb

@@ -1,11 +1,11 @@
 require 'spec_helper'
 
-require 'ms/quant/qspec'
+require 'mspire/quant/qspec'
 require 'csv'
 
 describe 'running qspec' do 
   before do
-    #@file = TESTFILES + '/ms/quant/max_quant_output.txt'
+    #@file = TESTFILES + '/mspire/quant/max_quant_output.txt'
     #rows = IO.readlines(@file).map {|line| line.chomp.split("\t") }
     #p rows.map(&:size)
     #abort 'here'

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

@@ -1,11 +1,11 @@
 require 'spec_helper'
 
-require 'ms/spectrum'
+require 'mspire/spectrum'
 
-describe MS::Spectrum do
+describe Mspire::Spectrum do
 
   describe 'useful utilities' do
-    subject { MS::Spectrum.new [ [10.1, 10.5, 10.7, 11.5], [1, 2, 3, 4] ] }
+    subject { Mspire::Spectrum.new [ [10.1, 10.5, 10.7, 11.5], [1, 2, 3, 4] ] }
     it 'finds the nearest m/z or index' do
 
       queries = {
@@ -38,7 +38,7 @@ describe MS::Spectrum do
     end
 
     it 'can sort itself by m/z' do
-      spec = MS::Spectrum.new [[10.5, 10.1, 11.5, 10.7], [2, 1, 4, 3]]
+      spec = Mspire::Spectrum.new [[10.5, 10.1, 11.5, 10.7], [2, 1, 4, 3]]
       spec.sort!
       spec.mzs.should == subject.mzs
       spec.intensities.should == subject.intensities
@@ -51,13 +51,13 @@ describe MS::Spectrum do
         [ [10.11, 10.49, 10.71, 11.48], [5, 6, 7, 8] ],
         [ [10.09, 10.51, 10.72, 11.51], [9, 10, 11, 12] 
       ]
-      data.map {|datum| MS::Spectrum.new( datum ) }
+      data.map {|datum| Mspire::Spectrum.new( datum ) }
     end
     it 'merges, giving exact weighted average m/z values for each cluster' do
-      (spec1, data) = MS::Spectrum.merge(subject, :bin_width => 0.08, :bin_unit => :amu, :return_data => true)
-      spec2 = MS::Spectrum.merge(subject, :bin_width => 0.08, :bin_unit => :amu)
+      (spec1, data) = Mspire::Spectrum.merge(subject, :bin_width => 0.08, :bin_unit => :amu, :return_data => true)
+      spec2 = Mspire::Spectrum.merge(subject, :bin_width => 0.08, :bin_unit => :amu)
       spec1.should == spec2
-      spec1.should == MS::Spectrum.new([[10.097333333333331, 10.502222222222223, 10.713809523809525, 11.498333333333333], [5.0, 6.0, 7.0, 8.0]])
+      spec1.should == Mspire::Spectrum.new([[10.097333333333331, 10.502222222222223, 10.713809523809525, 11.498333333333333], [5.0, 6.0, 7.0, 8.0]])
       data.should == [[[10.1, 1], [10.11, 5], [10.09, 9]], [[10.5, 2], [10.49, 6], [10.51, 10]], [[10.7, 3], [10.71, 7], [10.72, 11]], [[11.5, 4], [11.48, 8], [11.51, 12]]] 
     end
   end