mspire 0.6.26 → 0.7.2

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

@@ -1,6 +1,6 @@
-require 'ms/mzml/list'
+require 'mspire/mzml/list'
 
-module MS
+module Mspire
   class Mzml
     class DataProcessing
 
@@ -21,7 +21,7 @@ module MS
         builder
       end
 
-      extend(MS::Mzml::List)
+      extend(Mspire::Mzml::List)
     end
   end
 end

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

@@ -1,6 +1,6 @@
-require 'ms/cv/paramable'
+require 'mspire/cv/paramable'
 
-module MS
+module Mspire
   class Mzml
     # This summarizes the different types of spectra that can be expected in
     # the file. This is expected to aid processing software in skipping files
@@ -8,7 +8,7 @@ module MS
     # describe the nativeID format used in the file by referring to an
     # appropriate CV term.
     class FileContent
-      include MS::CV::Paramable
+      include Mspire::CV::Paramable
 
       def to_xml(builder, &block)
         builder.fileContent do |fc_n|

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

@@ -1,8 +1,8 @@
-require 'ms/mzml/file_content'
-require 'ms/mzml/source_file'
-require 'ms/mzml/contact'
+require 'mspire/mzml/file_content'
+require 'mspire/mzml/source_file'
+require 'mspire/mzml/contact'
 
-module MS
+module Mspire
   class Mzml
     class FileDescription
 

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

@@ -1,4 +1,4 @@
-module MS
+module Mspire
   class Mzml
     # A simple array of indices but #[] has been overloaded to find an index
     # by name
@@ -12,7 +12,7 @@ module MS
 
       # @param [Object] an Integer (index number) or a Symbol (:spectrum or
       #   :chromatogram)
-      # @return [MS::Mzml::Index] an index object
+      # @return [Mspire::Mzml::Index] an index object
       def [](int_or_symbol)
         if int_or_symbol.is_a?(Integer)
           old_bracket_slice(int_or_symbol)

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

@@ -1,11 +1,11 @@
-require 'ms/cv/paramable'
-require 'ms/mzml/component'
-require 'ms/mzml/list'
+require 'mspire/cv/paramable'
+require 'mspire/mzml/component'
+require 'mspire/mzml/list'
 
-module MS
+module Mspire
   class Mzml
     class InstrumentConfiguration
-      include MS::CV::Paramable
+      include Mspire::CV::Paramable
 
       # (required) the id that this guy can be referenced from
       attr_accessor :id
@@ -25,13 +25,13 @@ module MS
       def to_xml(builder)
         builder.instrumentConfiguration(id: @id) do |inst_conf_n|
           super(builder)
-          MS::Mzml::Component.list_xml(components, inst_conf_n)
+          Mspire::Mzml::Component.list_xml(components, inst_conf_n)
           inst_conf_n.softwareRef(ref: @software.id) if @software
         end
         builder
       end
 
-      self.extend(MS::Mzml::List)
+      self.extend(Mspire::Mzml::List)
     end
   end
 end

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

@@ -1,6 +1,6 @@
-require 'ms/cv/paramable'
+require 'mspire/cv/paramable'
 
-module MS
+module Mspire
   class Mzml
 
     # MUST supply a *child* term of MS:1000792 (isolation window attribute) one or more times
@@ -15,7 +15,7 @@ module MS
     #     e.g.: MS:1000828 (isolation window lower offset)
     #     e.g.: MS:1000829 (isolation window upper offset)
     class IsolationWindow
-      include MS::CV::Paramable
+      include Mspire::CV::Paramable
     end
   end
 end

data/lib/{ms → mspire}/mzml/list.rb

@@ -1,5 +1,5 @@
 
-module MS
+module Mspire
   class Mzml
     # Methods for simple List objects (scanList, instrumentConfigurationList,
     # etc.)

data/lib/{ms → mspire}/mzml/plms1.rb

@@ -1,7 +1,7 @@
 
-require 'ms/plms1'
+require 'mspire/plms1'
 
-module MS
+module Mspire
   class Mzml
     # will use scan numbers if use_scan_nums is true, otherwise it will use index
     # numbers in place of scan nums
@@ -28,7 +28,7 @@ module MS
       end
       # plms1 only requires that the obect respond to :each, giving a spectrum
       # object, so an Mzml object will work.
-      MS::Plms1.new(scan_nums, retention_times, self)
+      Mspire::Plms1.new(scan_nums, retention_times, self)
     end
   end
 end

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

@@ -1,11 +1,11 @@
-require 'ms/mzml/list'
-require 'ms/mzml/selected_ion'
+require 'mspire/mzml/list'
+require 'mspire/mzml/selected_ion'
 
-module MS
+module Mspire
   class Mzml
     # The method of precursor ion selection and activation
     class Precursor
-      # (optional) the MS::Mzml::Spectrum object from which the precursor is
+      # (optional) the Mspire::Mzml::Spectrum object from which the precursor is
       # derived
       attr_accessor :spectrum
 
@@ -35,12 +35,12 @@ module MS
         end
         builder.precursor(atts) do |prec_n|
           @isolation_window.to_xml(prec_n) if @isolation_window
-          MS::Mzml::SelectedIon.list_xml(@selected_ions, prec_n) if @selected_ions
+          Mspire::Mzml::SelectedIon.list_xml(@selected_ions, prec_n) if @selected_ions
           @activation.to_xml(prec_n) if @activation
         end
       end
 
-      extend(MS::Mzml::List)
+      extend(Mspire::Mzml::List)
 
     end
   end

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

@@ -1,9 +1,9 @@
-require 'ms/cv/paramable'
+require 'mspire/cv/paramable'
 
-module MS
+module Mspire
   class Mzml
     class ProcessingMethod
-      include MS::CV::Paramable
+      include Mspire::CV::Paramable
 
       attr_accessor :order, :software
 

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

@@ -1,6 +1,6 @@
-require 'ms/mzml/list'
+require 'mspire/mzml/list'
 
-module MS
+module Mspire
   class Mzml
     class Product
       attr_accessor :isolation_window
@@ -15,7 +15,7 @@ module MS
         end
       end
 
-      extend(MS::Mzml::List)
+      extend(Mspire::Mzml::List)
     end
   end
 end

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

@@ -1,14 +1,14 @@
-require 'ms/cv/paramable'
+require 'mspire/cv/paramable'
 
-module MS
+module Mspire
   class Mzml
 
     # need to call to_xml_definition (or use
-    # MS::Mzml::ReferenceableParamGroupList.list_xml) to get the xml for the
+    # Mspire::Mzml::ReferenceableParamGroupList.list_xml) to get the xml for the
     # object itself (and not a reference).  Merely callying #to_xml will
     # result in a referenceableParamGroupRef being created.
     class ReferenceableParamGroup
-      include MS::CV::Paramable
+      include Mspire::CV::Paramable
 
       attr_accessor :id
 

data/lib/{ms → mspire}/mzml/run.rb

@@ -1,9 +1,9 @@
-require 'ms/cv/paramable'
+require 'mspire/cv/paramable'
 
-module MS
+module Mspire
   class Mzml
     class Run
-      include MS::CV::Paramable
+      include Mspire::CV::Paramable
 
       # required
       attr_accessor :default_instrument_configuration

data/lib/{ms → mspire}/mzml/sample.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
     class Sample
-      include MS::CV::Paramable
+      include Mspire::CV::Paramable
 
       attr_accessor :id, :name
 
@@ -21,7 +21,7 @@ module MS
         builder
       end
 
-      extend(MS::Mzml::List)
+      extend(Mspire::Mzml::List)
     end
   end
 end

data/lib/{ms → mspire}/mzml/scan.rb

@@ -1,11 +1,11 @@
-require 'ms/cv/paramable'
+require 'mspire/cv/paramable'
 
-module MS
+module Mspire
   class Mzml
     class Scan
-      include MS::CV::Paramable
+      include Mspire::CV::Paramable
 
-      # (optional) the MS::Mzml::Spectrum object from which the precursor is
+      # (optional) the Mspire::Mzml::Spectrum object from which the precursor is
       # derived.  (the sourceFileRef is derived from this spectrum object if
       # from_external_source_file == true)
       attr_accessor :spectrum

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

@@ -1,6 +1,6 @@
-require 'ms/cv/paramable'
+require 'mspire/cv/paramable'
 
-module MS
+module Mspire
   class Mzml
 
     # MUST supply a *child* term of MS:1000570 (spectra combination) only once
@@ -10,7 +10,7 @@ module MS
     #     e.g.: MS:1000575 (mean of spectra)
     #     e.g.: MS:1000795 (no combination)
     class ScanList < Array
-      include MS::CV::Paramable
+      include Mspire::CV::Paramable
 
       def initialize(opts={params: []}, &block)
         describe!(*opts[:params])

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

@@ -1,10 +1,10 @@
-require 'ms/mzml/list'
-require 'ms/cv/paramable'
+require 'mspire/mzml/list'
+require 'mspire/cv/paramable'
 
-module MS
+module Mspire
   class Mzml
     class ScanSettings
-      include MS::CV::Paramable
+      include Mspire::CV::Paramable
 
       attr_accessor :id
 
@@ -21,7 +21,7 @@ module MS
         builder
       end
 
-      extend(MS::Mzml::List)
+      extend(Mspire::Mzml::List)
 
     end
   end

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

@@ -1,8 +1,8 @@
-require 'ms/mzml/list'
-require 'ms/cv/paramable'
+require 'mspire/mzml/list'
+require 'mspire/cv/paramable'
 
 
-module MS
+module Mspire
   class Mzml
     # MUST supply a *child* term of MS:1000455 (ion selection attribute) one or more times
     #
@@ -11,8 +11,8 @@ module MS
     #     e.g.: MS:1000633 (possible charge state)
     #     e.g.: MS:1000744 (selected ion m/z)
     class SelectedIon
-      include MS::CV::Paramable
-      extend(MS::Mzml::List)
+      include Mspire::CV::Paramable
+      extend(Mspire::Mzml::List)
     end
   end
 end

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

@@ -1,11 +1,11 @@
 require 'mspire'
-require 'ms/mzml/list'
-require 'ms/cv/paramable'
+require 'mspire/mzml/list'
+require 'mspire/cv/paramable'
 
-module MS
+module Mspire
   class Mzml
     class Software
-      include MS::CV::Paramable
+      include Mspire::CV::Paramable
 
       attr_accessor :id, :version
 
@@ -22,7 +22,7 @@ module MS
         builder
       end
 
-      extend(MS::Mzml::List)
+      extend(Mspire::Mzml::List)
     end
   end
 end

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

@@ -1,11 +1,11 @@
-require 'ms/cv/paramable'
-require 'ms/mzml/list'
+require 'mspire/cv/paramable'
+require 'mspire/mzml/list'
 require 'pathname'
 
-module MS
+module Mspire
   class Mzml
     class SourceFile
-      include MS::CV::Paramable
+      include Mspire::CV::Paramable
 
       DEFAULT_SOURCEFILE_ID = 'sourcefile1'
 
@@ -44,7 +44,7 @@ module MS
         builder
       end
 
-      extend(MS::Mzml::List)
+      extend(Mspire::Mzml::List)
     end
   end
 end

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

@@ -1,11 +1,11 @@
-require 'ms/mzml/data_array_container_like'
-require 'ms/spectrum_like'
-require 'ms/mzml/data_array'
-require 'ms/mzml/scan_list'
-require 'ms/mzml/precursor'
-require 'ms/mzml/product'
-
-module MS
+require 'mspire/mzml/data_array_container_like'
+require 'mspire/spectrum_like'
+require 'mspire/mzml/data_array'
+require 'mspire/mzml/scan_list'
+require 'mspire/mzml/precursor'
+require 'mspire/mzml/product'
+
+module Mspire
   class Mzml
 
     #     MAY supply a *child* term of MS:1000465 (scan polarity) only once
@@ -39,10 +39,10 @@ module MS
     #       e.g.: MS:1000796 (spectrum title)
     #       et al.
     class Spectrum
-      include MS::SpectrumLike
-      include MS::Mzml::DataArrayContainerLike
+      include Mspire::SpectrumLike
+      include Mspire::Mzml::DataArrayContainerLike
 
-      # (optional) an MS::Mzml::SourceFile object
+      # (optional) an Mspire::Mzml::SourceFile object
       attr_accessor :source_file
 
       # (optional) The identifier for the spot from which this spectrum was derived, if a
@@ -64,13 +64,14 @@ module MS
       # currently being described, ordered.
       attr_accessor :products
 
+      # retention time in seconds
       attr_accessor :retention_time
       # when properly implemented, this will access the first scan and the
       # 'scan start time' cv element.
 
       # takes a Nokogiri node and sets relevant properties
       def self.from_xml(xml)
-        spec = MS::Mzml::Spectrum.new(xml[:id])
+        spec = Mspire::Mzml::Spectrum.new(xml[:id])
 
         params = {}
         xml.xpath("./cvParam").each do |cvparam|
@@ -84,27 +85,39 @@ module MS
         # this is a quick hack to get retention time, implement fully as shown
         # below!
         cv_param = xml.xpath("./scanList/scan/cvParam[@accession='MS:1000016']").first
-        retention_time = cv_param && cv_param['value'].to_f
+        if cv_param
+          retention_time = cv_param['value'].to_f
+          units = cv_param['unitAccession']
+          multiplier = 
+            case units
+            when 'UO:0000010' ; 1  # second
+            when 'UO:0000031' ; 60 # minute
+            when 'UO:0000032' ; 3600 # hour
+            when 'UO:0000028' ; 0.001 # millisecond
+            else raise 'unsupported units'
+            end
+          retention_time *= multiplier
+        end
 
         # this is roughly how the scan list stuff should be implemented:
 =begin
-        sl_obj = MS::Mzml::ScanList.new
+        sl_obj = Mspire::Mzml::ScanList.new
 
         # TODO: need to slot in all the other info in reasonable ways
         # TODO: need to make sure we deal with referencable params
         scan_list = xml.xpath('.scanList/scan').each do |scan_n|
-          sl_obj << MS::Mzml::Scan.from_xml(scan_n)
+          sl_obj << Mspire::Mzml::Scan.from_xml(scan_n)
         end
 =end
 
         data_arrays = xml.xpath('./binaryDataArrayList/binaryDataArray').map do |binary_data_array_n|
           accessions = binary_data_array_n.xpath('./cvParam').map {|node| node['accession'] }
           base64 = binary_data_array_n.xpath('./binary').text
-          MS::Mzml::DataArray.from_binary(base64, accessions)
+          Mspire::Mzml::DataArray.from_binary(base64, accessions)
         end
         # if there is no spectrum, we will still return a spectrum object, it
         # just has no mzs or intensities
-        data_arrays = [MS::Mzml::DataArray.new, MS::Mzml::DataArray.new] if data_arrays.size == 0
+        data_arrays = [Mspire::Mzml::DataArray.new, Mspire::Mzml::DataArray.new] if data_arrays.size == 0
         spec.data_arrays = data_arrays
         spec.retention_time = retention_time
         spec
@@ -114,7 +127,7 @@ module MS
       #
       # This would generate a spectrum of ms_level=2 :
       #
-      #     MS::Mzml::Spectrum.new(0, "scan=1", 'MS:1000511')
+      #     Mspire::Mzml::Spectrum.new(0, "scan=1", 'MS:1000511')
       #
       def initialize(id, opts={params: []}, &block)
         @id = id
@@ -130,8 +143,8 @@ module MS
         atts[:spotID] = @spot_id if @spot_id
         super(builder, atts) do |node|
           @scan_list.list_xml( node ) if @scan_list
-          MS::Mzml::Precursor.list_xml(@precursors, node) if @precursors
-          MS::Mzml::Product.list_xml(@products, node) if @products
+          Mspire::Mzml::Precursor.list_xml(@precursors, node) if @precursors
+          Mspire::Mzml::Product.list_xml(@products, node) if @products
         end
       end