mspire 0.6.26 → 0.7.2

data/lib/{ms → mspire}/mass/aa.rb

@@ -1,6 +1,6 @@
-require 'ms/mass'
+require 'mspire/mass'
 
-module MS
+module Mspire
   module Mass
     module AA
       # amino_acids keys as strings, average masses
@@ -69,11 +69,11 @@ module MS
       AVG_SYM = Hash[AVG_STRING.map {|aa,mass| [aa.to_sym, mass] } ]
 
       # Monoisotopic amino acid masses keyed as symbols and also strings (all
-      # upper case).  Also includes MS::Mass::MONO for things like protons ('h+')
-      MONO = MONO_SYM.merge(MONO_STRING).merge(MS::Mass::MONO)
+      # upper case).  Also includes Mspire::Mass::MONO for things like protons ('h+')
+      MONO = MONO_SYM.merge(MONO_STRING).merge(Mspire::Mass::MONO)
       # Average amino acid masses keyed as symbols and also strings (all
-      # uppder case).  Also includes MS::Mass::AVG for things like protons ('h+')
-      AVG = AVG_SYM.merge(AVG_STRING).merge(MS::Mass::AVG)
+      # uppder case).  Also includes Mspire::Mass::AVG for things like protons ('h+')
+      AVG = AVG_SYM.merge(AVG_STRING).merge(Mspire::Mass::AVG)
     end
   end
 end

data/lib/{ms → mspire}/molecular_formula.rb

@@ -1,8 +1,8 @@
-require 'ms/isotope'
-require 'ms/isotope/aa'
-require 'ms/mass'
+require 'mspire/isotope'
+require 'mspire/isotope/aa'
+require 'mspire/mass'
 
-module MS
+module Mspire
   class MolecularFormula < Hash
 
     # integer desribing the charge state
@@ -25,7 +25,7 @@ module MS
 
     def self.from_aaseq(aaseq)
       hash = aaseq.each_char.inject({}) do |hash,aa| 
-        hash.merge(MS::Isotope::AA::ATOM_COUNTS[aa]) {|h,o,n| (o ? o : 0) +n }
+        hash.merge(Mspire::Isotope::AA::ATOM_COUNTS[aa]) {|h,o,n| (o ? o : 0) +n }
       end
       hash[:h] += 2
       hash[:o] += 1
@@ -34,8 +34,8 @@ module MS
 
     # gives the monoisotopic mass adjusted by the current charge
     def mass
-      mss = inject(0.0) {|sum,(el,cnt)| sum + (MS::Mass::MONO[el]*cnt) }
-      mss - (MS::Mass::ELECTRON * charge)
+      mss = inject(0.0) {|sum,(el,cnt)| sum + (Mspire::Mass::MONO[el]*cnt) }
+      mss - (Mspire::Mass::ELECTRON * charge)
     end
 
   end

data/lib/{ms → mspire}/mzml.rb

@@ -3,28 +3,28 @@ require 'builder'
 require 'nokogiri'
 require 'io/bookmark'
 require 'zlib'
-require 'ms/mzml/index_list'
-require 'ms/mzml/spectrum'
-require 'ms/mzml/file_description'
-require 'ms/mzml/software'
-require 'ms/mzml/scan_list'
-require 'ms/mzml/selected_ion'
-require 'ms/mzml/scan'
-require 'ms/mzml/scan_settings'
-require 'ms/mzml/processing_method'
-require 'ms/mzml/run'
-require 'ms/mzml/spectrum_list'
-require 'ms/mzml/chromatogram_list'
-require 'ms/mzml/instrument_configuration'
-require 'ms/mzml/data_processing'
-require 'ms/mzml/referenceable_param_group'
-require 'ms/mzml/cv'
-require 'ms/mzml/sample'
-
-module MS
+require 'mspire/mzml/index_list'
+require 'mspire/mzml/spectrum'
+require 'mspire/mzml/file_description'
+require 'mspire/mzml/software'
+require 'mspire/mzml/scan_list'
+require 'mspire/mzml/selected_ion'
+require 'mspire/mzml/scan'
+require 'mspire/mzml/scan_settings'
+require 'mspire/mzml/processing_method'
+require 'mspire/mzml/run'
+require 'mspire/mzml/spectrum_list'
+require 'mspire/mzml/chromatogram_list'
+require 'mspire/mzml/instrument_configuration'
+require 'mspire/mzml/data_processing'
+require 'mspire/mzml/referenceable_param_group'
+require 'mspire/mzml/cv'
+require 'mspire/mzml/sample'
+
+module Mspire
   # Reading an mzxml file:
   #
-  #     MS::Mzml.open("somefile.mzML") do |mzml|
+  #     Mspire::Mzml.open("somefile.mzML") do |mzml|
   #       mzml.each do |spectrum|
   #         scan = spectrum.scan
   #         spectrum.mzs                  # array of m/zs
@@ -42,10 +42,10 @@ module MS
   #
   # Writing an mzml file from scratch:
   #
-  #     spec1 = MS::Mzml::Spectrum.new('scan=1', params: ['MS:1000127', ['MS:1000511', 1]]) do |spec|
+  #     spec1 = Mspire::Mzml::Spectrum.new('scan=1', params: ['MS:1000127', ['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 40 seconds
   #           scan.describe! ['MS:1000016', 40.0, 'UO:0000010']
   #         end
@@ -53,21 +53,21 @@ module MS
   #       end
   #     end
   #
-  #     mzml = MS::Mzml.new do |mzml|
+  #     mzml = Mspire::Mzml.new do |mzml|
   #       mzml.id = 'the_little_example'
-  #       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)
   #         run.spectrum_list = spectrum_list
   #       end
@@ -101,31 +101,31 @@ module MS
     # SUBELEMENTS
     ###############################################
 
-    # (required) an array of MS::Mzml::CV objects
+    # (required) an array of Mspire::Mzml::CV objects
     attr_accessor :cvs
 
-    # (required) an MS::Mzml::FileDescription
+    # (required) an Mspire::Mzml::FileDescription
     attr_accessor :file_description
 
     # (optional) an array of CV::ReferenceableParamGroup objects
     attr_accessor :referenceable_param_groups
 
-    # (optional) an array of MS::Mzml::Sample objects
+    # (optional) an array of Mspire::Mzml::Sample objects
     attr_accessor :samples
 
-    # (required) an array of MS::Mzml::Software objects 
+    # (required) an array of Mspire::Mzml::Software objects 
     attr_accessor :software_list
 
-    # (optional) an array of MS::Mzml::ScanSettings objects
+    # (optional) an array of Mspire::Mzml::ScanSettings objects
     attr_accessor :scan_settings_list
 
-    # (required) an array of MS::Mzml::InstrumentConfiguration objects
+    # (required) an array of Mspire::Mzml::InstrumentConfiguration objects
     attr_accessor :instrument_configurations
 
-    # (required) an array of MS::Mzml::DataProcessing objects
+    # (required) an array of Mspire::Mzml::DataProcessing objects
     attr_accessor :data_processing_list
 
-    # (required) an MS::Mzml::Run object
+    # (required) an Mspire::Mzml::Run object
     attr_accessor :run
 
     module Parser
@@ -219,11 +219,11 @@ module MS
     end
 
     # @param [Object] arg an index number (Integer) or id string (String)
-    # @return [MS::Spectrum] a spectrum object
+    # @return [Mspire::Spectrum] a spectrum object
     def spectrum(arg)
       start_byte = index_list[0].start_byte(arg)
       spec_n = spectrum_node_from_start_byte(start_byte)
-      MS::Mzml::Spectrum.from_xml(spec_n)
+      Mspire::Mzml::Spectrum.from_xml(spec_n)
     end
 
     # returns the number of spectra
@@ -234,7 +234,7 @@ module MS
     alias_method :'[]', :spectrum
 
     # @param [Integer] scan_num the scan number 
-    # @return [MS::Spectrum] a spectrum object, or nil if not found
+    # @return [Mspire::Spectrum] a spectrum object, or nil if not found
     # @raise [ScanNumbersNotUnique] if scan numbers are not unique
     # @raise [ScanNumbersNotFound] if spectra exist but scan numbers were not
     #   found
@@ -245,10 +245,10 @@ module MS
       spectrum(@scan_to_index[scan_num])
     end
 
-    # @return [MS::Mzml::IndexList] or nil if there is no indexList in the
+    # @return [Mspire::Mzml::IndexList] or nil if there is no indexList in the
     # mzML
     def read_index_list
-      if offset=MS::Mzml::Index.index_offset(@io)
+      if offset=Mspire::Mzml::Index.index_offset(@io)
         @io.seek(offset)
         xml = Nokogiri::XML.parse(@io.read, nil, @encoding, Parser::NOBLANKS)
         index_list = xml.root
@@ -269,7 +269,7 @@ module MS
       end
     end
     # Reads through and captures start bytes
-    # @return [MS::Mzml::IndexList] 
+    # @return [Mspire::Mzml::IndexList] 
     def create_index_list
       indices_hash = @io.bookmark(true) do |inner_io|   # sets to beginning of file
         indices = {:spectrum => {}, :chromatogram => {}}
@@ -316,21 +316,21 @@ module MS
 
       xml.mzML(mzml_atts) do |mzml_n|
         # the 'if' statements capture whether or not the list is required or not
-        raise "#{self.class}#cvs must have > 0 MS::Mzml::CV objects" unless @cvs.size > 0 
-        MS::Mzml::CV.list_xml(@cvs, mzml_n)
+        raise "#{self.class}#cvs must have > 0 Mspire::Mzml::CV objects" unless @cvs.size > 0 
+        Mspire::Mzml::CV.list_xml(@cvs, mzml_n)
         @file_description.to_xml(mzml_n)
         if @referenceable_param_groups
-          MS::Mzml::ReferenceableParamGroup.list_xml(@referenceable_param_groups, mzml_n)
+          Mspire::Mzml::ReferenceableParamGroup.list_xml(@referenceable_param_groups, mzml_n)
         end
         if @samples
-          MS::Mzml::Sample.list_xml(@samples, mzml_n)
+          Mspire::Mzml::Sample.list_xml(@samples, mzml_n)
         end
-        MS::Mzml::Software.list_xml(@software_list, mzml_n)
+        Mspire::Mzml::Software.list_xml(@software_list, mzml_n)
         if @scan_settings_list && @scan_settings_list.size > 0
-          MS::Mzml::ScanSettings.list_xml(@scan_settings_list, mzml_n)
+          Mspire::Mzml::ScanSettings.list_xml(@scan_settings_list, mzml_n)
         end
-        icl = MS::Mzml::InstrumentConfiguration.list_xml(@instrument_configurations, mzml_n)
-        MS::Mzml::DataProcessing.list_xml(@data_processing_list, mzml_n)
+        icl = Mspire::Mzml::InstrumentConfiguration.list_xml(@instrument_configurations, mzml_n)
+        Mspire::Mzml::DataProcessing.list_xml(@data_processing_list, mzml_n)
         @run.to_xml(mzml_n)
       end
       

data/lib/{ms → mspire}/mzml/activation.rb

@@ -1,6 +1,6 @@
-require 'ms/cv/paramable'
+require 'mspire/cv/paramable'
 
-module MS
+module Mspire
   class Mzml
 
     # MAY supply a *child* term of MS:1000510 (precursor activation attribute) one or more times
@@ -27,7 +27,7 @@ module MS
     #     e.g.: MS:1000433 (low-energy collision-induced dissociation)
     #     et al.
     class Activation
-      include MS::CV::Paramable
+      include Mspire::CV::Paramable
     end
   end
 end

data/lib/{ms → mspire}/mzml/chromatogram.rb

@@ -1,9 +1,9 @@
-require 'ms/mzml/data_array_container_like'
+require 'mspire/mzml/data_array_container_like'
 
-module MS
+module Mspire
   class Mzml
     class Chromatogram
-      include MS::Mzml::DataArrayContainerLike
+      include Mspire::Mzml::DataArrayContainerLike
 
       # (optional) precursor isolations to the chromatogram currently being
       # described

data/lib/{ms → mspire}/mzml/chromatogram_list.rb

@@ -1,6 +1,6 @@
 
 
-module MS
+module Mspire
   class Mzml
     class ChromatogramList < Array
 

data/lib/{ms → mspire}/mzml/component.rb

@@ -1,10 +1,10 @@
-require 'ms/cv/paramable'
-require 'ms/mzml/list'
+require 'mspire/cv/paramable'
+require 'mspire/mzml/list'
 
-module MS
+module Mspire
   class Mzml
     module Component
-      include MS::CV::Paramable
+      include Mspire::CV::Paramable
 
       attr_accessor :order
 
@@ -15,7 +15,7 @@ module MS
         builder
       end
 
-      extend(MS::Mzml::List)
+      extend(Mspire::Mzml::List)
     end
   end
 end

data/lib/{ms → mspire}/mzml/contact.rb

@@ -1,6 +1,6 @@
-require 'ms/cv/paramable'
+require 'mspire/cv/paramable'
 
-module MS
+module Mspire
   class Mzml
     class Contact
 
@@ -11,7 +11,7 @@ module MS
         email: 'MS:1000589'
       }
 
-      include MS::CV::Paramable
+      include Mspire::CV::Paramable
 
       def to_xml(builder)
         builder.contact do |fc_n|

data/lib/{ms → mspire}/mzml/cv.rb

@@ -1,5 +1,5 @@
 
-module MS
+module Mspire
   class Mzml
     class CV
 

data/lib/{ms → mspire}/mzml/data_array.rb

@@ -1,12 +1,12 @@
 require 'base64'
 require 'zlib'
-require 'ms/cv/paramable'
+require 'mspire/cv/paramable'
 
-module MS
+module Mspire
   class Mzml
     class DataArray < Array
       alias_method :array_initialize, :initialize
-      include MS::CV::Paramable
+      include Mspire::CV::Paramable
 
       DEFAULT_DTYPE = :float64
       DEFAULT_COMPRESSION = true
@@ -25,16 +25,16 @@ module MS
         array_initialize(*args)
       end
 
-      # returns a new MS::Mzml::DataArray object (an array)
+      # returns a new Mspire::Mzml::DataArray object (an array)
       #
       #     args:
       #       base64, set-like               # where set-like responds to include?
       #       base64, type=:float64, compression=true
       #
       #     examples:
-      #     MS::Mzml::Spectrum.unpack_binary('eJxjYACBD/YMEOAAoTgcABe3Abg=', ['MS:1000574', MS:1000523']).
-      #     MS::Mzml::Spectrum.unpack_binary("ADBA/=", :float32, true)
-      #     MS::Mzml::Spectrum.unpack_binary("ADBA/=") # uses float64 and compression
+      #     Mspire::Mzml::Spectrum.unpack_binary('eJxjYACBD/YMEOAAoTgcABe3Abg=', ['MS:1000574', MS:1000523']).
+      #     Mspire::Mzml::Spectrum.unpack_binary("ADBA/=", :float32, true)
+      #     Mspire::Mzml::Spectrum.unpack_binary("ADBA/=") # uses float64 and compression
       def self.from_binary(base64, *args)
         if args.first.respond_to?(:include?)
           accessions = args.first
@@ -119,11 +119,11 @@ module MS
         builder.binaryDataArray(encodedLength: encoded_length) do |bda_n|
           @params.each {|param| param.to_xml(bda_n) } if @params
           unless @external
-            MS::CV::Param[ DTYPE_TO_ACC[dtype] ].to_xml(bda_n)
-            MS::CV::Param[ compression ? 'MS:1000574' : 'MS:1000576' ].to_xml(bda_n)
+            Mspire::CV::Param[ DTYPE_TO_ACC[dtype] ].to_xml(bda_n)
+            Mspire::CV::Param[ compression ? 'MS:1000574' : 'MS:1000576' ].to_xml(bda_n)
             if @type
               accession = ( (@type == :mz) ? 'MS:1000514' : 'MS:1000515' )
-              MS::CV::Param[accession].to_xml(bda_n)
+              Mspire::CV::Param[accession].to_xml(bda_n)
               bda_n.binary(base64)
             end
           end
@@ -135,10 +135,10 @@ module MS
         builder.binaryDataArrayList(count: arrays.size) do |bdal_n|
           arrays.zip([:mz, :intensity]) do |data_ar, typ|
             ar = 
-              if data_ar.is_a?(MS::Mzml::DataArray)
+              if data_ar.is_a?(Mspire::Mzml::DataArray)
                 data_ar
               else
-                real_data_array = MS::Mzml::DataArray.new(data_ar)
+                real_data_array = Mspire::Mzml::DataArray.new(data_ar)
                 real_data_array.type = typ
                 real_data_array
               end

data/lib/{ms → mspire}/mzml/data_array_container_like.rb

@@ -1,10 +1,10 @@
-require 'ms/cv/paramable'
-require 'ms/mzml/data_array'
+require 'mspire/cv/paramable'
+require 'mspire/mzml/data_array'
 
-module MS
+module Mspire
   class Mzml
     module DataArrayContainerLike
-      include MS::CV::Paramable
+      include Mspire::CV::Paramable
 
       ###########################################
       # ATTRIBUTES
@@ -16,14 +16,14 @@ module MS
       # (required [at xml write time]) the index in the spectrum list
       attr_accessor :index
 
-      # (optional) an MS::Mzml::DataProcessing object
+      # (optional) an Mspire::Mzml::DataProcessing object
       attr_accessor :data_processing
 
       ###########################################
       # SUBELEMENTS
       ###########################################
 
-      # (optional) an array of MS::Mzml::DataArray
+      # (optional) an array of Mspire::Mzml::DataArray
       attr_accessor :data_arrays
 
       def initialize(id, opts={params: []})
@@ -55,7 +55,7 @@ module MS
         builder.spectrum(atts) do |sp_n|
           super(sp_n) # params
           block.call(sp_n) if block
-          MS::Mzml::DataArray.list_xml(@data_arrays, sp_n) if @data_arrays
+          Mspire::Mzml::DataArray.list_xml(@data_arrays, sp_n) if @data_arrays
         end
         builder
       end