mspire 0.9.2 → 0.10.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: cacdee4487f5e6a98d31c9649cb02390bce1dd9d
-  data.tar.gz: 64ae39986bc3bb20dcbcff972ef8162bdd36609b
+  metadata.gz: 10f9f35036ad4f2a25b69644aa4157281bc18ccb
+  data.tar.gz: 3d5001ce1de7d3d5da82c5de7b3440c93d34abbb
 SHA512:
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-  data.tar.gz: fae953898b991b9f0cb6917fc8eaf4ff2e8557c6f73f82b750abe22b68f5f435de300c36c0b7835751b7a48ac22e40d59d340e4f4d6898478615fe6cbf66e892
+  metadata.gz: aa2b1352be5a165feeca924d1690fde4e43d980df05aee0dc9a30768644a6a7e6cac645171d93ff83cebddd340660c13fec17d6e27e9e8e31a134d35bfe1fed4
+  data.tar.gz: 8e6cc4877db87cbb408c53966570277ebb14eccbf308c8a7e9eadbe793c430e7f25cabd8be492d4f7cef93d0860955265cb48af3a4127fa86a7de5e7b83e99d2

data/lib/mspire/cv/paramable.rb

@@ -1,5 +1,4 @@
 require 'cv/param'
-require 'mspire/user_param'
 require 'mspire/cv/param'
 require 'nokogiri'
 require 'andand'
@@ -9,12 +8,9 @@ module Mspire
     module Paramable
 
       attr_accessor :cv_params
-      attr_accessor :user_params
-      attr_accessor :ref_param_groups
 
-      def params
-        cv_params + ref_param_groups.flat_map(&:params) + user_params 
-      end
+      alias_method :cv_params, :params
+      alias_method :cv_params=, :params=
 
       def each_param(&block)
         return enum_for __method__ unless block
@@ -30,17 +26,6 @@ module Mspire
           user_params.size > 0
       end
 
-      def each_accessionable_param(&block)
-        return enum_for __method__ unless block
-        cv_params.each(&block)
-        ref_param_groups.flat_map(&:params).each(&block)
-        nil
-      end
-
-      def accessionable_params
-        cv_params + ref_param_groups.flat_map(&:params)
-      end
-
       # yields each current param.  If the return value is not false or nil,
       # it is deleted (i.e., any true value and it is deleted).  Then adds the
       # given parameter or makes a new one by accession number.
@@ -51,8 +36,6 @@ module Mspire
       # returns self
       def reject!(&block)
         cv_params.reject!(&block)
-        ref_param_groups.each {|group| group.reject!(&block) }
-        user_params.reject!(&block)
         self
       end
 
@@ -60,14 +43,6 @@ module Mspire
         reject!(&block).describe_many!(describe_many_arg)
       end
 
-      #def params_by_name
-      #  params.index_by &:name
-      #end
-
-      #def params_by_accession
-      #  accessionable_params.index_by &:accession
-      #end
-      
       # returns the value if the param exists by that name.  Returns true if
       # the param exists but has no value. returns false if no param
       def fetch(name)
@@ -98,8 +73,6 @@ module Mspire
 
       def initialize
         @cv_params = []
-        @user_params = []
-        @ref_param_groups = []
       end
       alias_method :params_init, :initialize
 
@@ -128,28 +101,17 @@ module Mspire
         self
       end
 
-      # takes a node with children that are cvParam, userParam or
-      # referenceableParamGroupRef and a hash containing
-      # referenceableParamGroup objects indexed by id.  The only time ref_hash
-      # should be left nil is for the referenceableParamGroup itself.
-      #
-      # All param elements are required to appear before other elements, so
-      # the code walks through each child node to see if it is a paramable
-      # element.  The first child node that is not paramable is returned (or
-      # nil if none)
-      #
+      # takes a node with children that are cvParam objects 
       # returns the next child node after the paramable elements or nil if none
       def describe_from_xml!(xml_node, ref_hash=nil)
+        # TODO: this was merely cleaned up from Paramable and should be
+        # re-factored
         return nil unless (child_n = xml_node.child) 
         loop do
           array = 
             case child_n.name
-            when 'referenceableParamGroupRef'
-              @ref_param_groups << ref_hash[child_n[:ref]]
             when 'cvParam'
               @cv_params << Mspire::CV::Param[ child_n[:accession], child_n[:value] ]
-            when 'userParam'
-              @user_params << Mspire::UserParam.new(child_n[:name], child_n[:value], child_n[:type])
             else # assumes that the above precede any following children as per the spec
               break 
             end
@@ -161,8 +123,7 @@ module Mspire
         child_n
       end
 
-      # Expects arguments describing a single CV::Param, Mspire::UserParam, or
-      # Mspire::Mzml::ReferenceableParamGroup
+      # Expects arguments describing a single CV::Param
       #
       #     obj.describe! 'MS:1000130'  # a positive scan
       #     obj.describe! CV::Param['MS:1000130']  # same behavior
@@ -176,24 +137,16 @@ module Mspire
         case (arg=args.first)
         when String
           @cv_params << Mspire::CV::Param[ *args ]
-        when Mspire::Mzml::ReferenceableParamGroup
-          @ref_param_groups << arg
         else
-          if arg.is_a?(Mspire::UserParam)
-            @user_params << arg
-          else
-            @cv_params << arg
-          end
+          @cv_params << arg
         end
         self
       end
 
       # iterates over @params and calls .to_xml on each object.
       def to_xml(xml)
-        [:ref_param_groups, :cv_params, :user_params].each do |kind|
-          self.send(kind).each do |obj|
-            obj.to_xml(xml)
-          end
+        self.cv_params.each do |obj|
+          obj.to_xml(xml)
         end
         xml
       end

data/lib/mspire/mzid/modification.rb

@@ -0,0 +1,29 @@
+require 'mspire/cv/paramable'
+
+module Mspire
+  module Mzid
+    class Modification
+      include Mspire::CV::Paramable
+      # optional avg mass
+      attr_accessor :avg_mass_delta
+
+      # From IdentML spec: "Location of the modification within the peptide -
+      # position in peptide sequence, counted from the N-terminus residue,
+      # starting at position 1.  Specific modifications to the N-terminus
+      # should be given the location 0. Modification to the C-terminus should
+      # be given as peptide length + 1. If the modification location is
+      # unknown e.g. for PMF data, this attribute should be omitted."
+      attr_accessor :location
+
+      attr_accessor :monoisotopic_mass_delta
+
+      # Array of residues. Specification of the residue (amino acid) on which
+      # the modification occurs. If multiple values are given, it is assumed
+      # that the exact residue modified is unknown i.e. the modification is to
+      # ONE of the residues listed. Multiple residues would usually only be
+      # specified for PMF data.
+      attr_accessor :residues
+
+    end
+  end
+end

data/lib/mspire/mzid/search_modification.rb

@@ -0,0 +1,29 @@
+require 'mspire/cv/paramable'
+
+module Mspire
+  module Identml
+
+    # a parameter for a spectral search.  An idealized modification.  See
+    # Modification for describing a modification on an actual peptide.
+    class SearchModification
+      include Mspire::CV::Paramable
+
+      # boolean
+      attr_accessor :fixed_mod
+
+      # mass delta in daltons
+      attr_accessor :mass_delta
+
+      # A *Set* of characters. From mzIdentml: "The residue(s) searched with the
+      # specified modification. For N or C terminal modifications that can occur
+      # on any residue, the . character should be used to specify any, otherwise
+      # the list of amino acids should be provided."
+      attr_accessor :residues
+
+      # A single SpecificityRules object
+      attr_accessor :specificity_rules
+
+    end
+
+  end
+end

data/lib/mspire/mzml/activation.rb

@@ -1,4 +1,4 @@
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 
 module Mspire
   class Mzml
@@ -27,7 +27,7 @@ module Mspire
     #     e.g.: MS:1000433 (low-energy collision-induced dissociation)
     #     et al.
     class Activation
-      include Mspire::CV::Paramable
+      include Mspire::Paramable
 
       def to_xml(builder)
         builder.activation {|xml| super(xml) }

data/lib/mspire/mzml/component.rb

@@ -1,11 +1,11 @@
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 require 'mspire/mzml/list'
 
 module Mspire
   class Mzml
     # order is not an intrinsic property of this object, so it 
     module Component
-      include Mspire::CV::Paramable
+      include Mspire::Paramable
       # using custom list_xml, so no extend Mspire::Mzml::List
 
       def initialize

data/lib/mspire/mzml/contact.rb

@@ -1,4 +1,4 @@
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 
 module Mspire
   class Mzml
@@ -11,7 +11,7 @@ module Mspire
         email: 'MS:1000589'
       }
 
-      include Mspire::CV::Paramable
+      include Mspire::Paramable
 
       def to_xml(builder)
         builder.contact do |fc_n|

data/lib/mspire/mzml/data_array.rb

@@ -1,6 +1,6 @@
 require 'base64'
 require 'zlib'
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 
 module Mspire
   class Mzml
@@ -16,7 +16,7 @@ end
 # will be written with the same precision as it was read in with.
 class Mspire::Mzml::DataArray < Array 
   alias_method :array_init, :initialize
-  include Mspire::CV::Paramable
+  include Mspire::Paramable
 
   DEFAULT_DTYPE_ACC = 'MS:1000523' # float64
   DEFAULT_COMPRESSION_ACC = 'MS:1000574'

data/lib/mspire/mzml/data_array_container_like.rb

@@ -1,10 +1,10 @@
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 require 'mspire/mzml/data_array'
 
 module Mspire
   class Mzml
     module DataArrayContainerLike
-      include Mspire::CV::Paramable
+      include Mspire::Paramable
 
       ###########################################
       # ATTRIBUTES

data/lib/mspire/mzml/file_content.rb

@@ -1,4 +1,4 @@
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 
 module Mspire
   class Mzml
@@ -8,7 +8,7 @@ module Mspire
     # describe the nativeID format used in the file by referring to an
     # appropriate CV term.
     class FileContent
-      include Mspire::CV::Paramable
+      include Mspire::Paramable
 
       def to_xml(builder, &block)
         builder.fileContent do |fc_n|

data/lib/mspire/mzml/instrument_configuration.rb

@@ -1,11 +1,11 @@
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 require 'mspire/mzml/component'
 require 'mspire/mzml/list'
 
 module Mspire
   class Mzml
     class InstrumentConfiguration
-      include Mspire::CV::Paramable
+      include Mspire::Paramable
       extend Mspire::Mzml::List
 
       # (required) the id that this guy can be referenced from

data/lib/mspire/mzml/isolation_window.rb

@@ -1,4 +1,4 @@
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 
 module Mspire
   class Mzml
@@ -15,7 +15,7 @@ module Mspire
     #     e.g.: MS:1000828 (isolation window lower offset)
     #     e.g.: MS:1000829 (isolation window upper offset)
     class IsolationWindow
-      include Mspire::CV::Paramable
+      include Mspire::Paramable
 
       def to_xml(builder)
         builder.isolationWindow {|xml| super(xml) }

data/lib/mspire/mzml/processing_method.rb

@@ -1,4 +1,4 @@
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 
 module Mspire
   class Mzml
@@ -22,7 +22,7 @@ module Mspire
     #     e.g.: MS:1000745 (retention time alignment)
     #     e.g.: MS:1000746 (high intensity data point removal)
     class ProcessingMethod
-      include Mspire::CV::Paramable
+      include Mspire::Paramable
 
       attr_accessor :software
 

data/lib/mspire/mzml/referenceable_param_group.rb

@@ -1,4 +1,4 @@
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 
 module Mspire
   class Mzml
@@ -8,7 +8,7 @@ module Mspire
     # object itself (and not a reference).  Merely callying #to_xml will
     # result in a referenceableParamGroupRef being created.
     class ReferenceableParamGroup
-      include Mspire::CV::Paramable
+      include Mspire::Paramable
 
       attr_accessor :id
 

data/lib/mspire/mzml/run.rb

@@ -1,4 +1,4 @@
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 require 'mspire/mzml/io_index'
 require 'mspire/mzml/spectrum_list'
 require 'mspire/mzml/chromatogram_list'
@@ -6,7 +6,7 @@ require 'mspire/mzml/chromatogram_list'
 module Mspire
   class Mzml
     class Run
-      include Mspire::CV::Paramable
+      include Mspire::Paramable
 
       # required
       attr_accessor :default_instrument_configuration

data/lib/mspire/mzml/sample.rb

@@ -1,10 +1,10 @@
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 require 'mspire/mzml/list'
 
 module Mspire
   class Mzml
     class Sample
-      include Mspire::CV::Paramable
+      include Mspire::Paramable
       extend Mspire::Mzml::List
 
       # A unique identifier across the samples with which to reference this sample description.

data/lib/mspire/mzml/scan.rb

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

data/lib/mspire/mzml/scan_list.rb

@@ -1,4 +1,4 @@
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 require 'mspire/mzml/scan'
 
 module Mspire
@@ -11,7 +11,7 @@ module Mspire
     #     e.g.: MS:1000575 (mean of spectra)
     #     e.g.: MS:1000795 (no combination)
     class ScanList < Array
-      include Mspire::CV::Paramable
+      include Mspire::Paramable
 
       def initialize
         params_init

data/lib/mspire/mzml/scan_settings.rb

@@ -1,10 +1,10 @@
 require 'mspire/mzml/list'
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 
 module Mspire
   class Mzml
     class ScanSettings
-      include Mspire::CV::Paramable
+      include Mspire::Paramable
       extend Mspire::Mzml::List
 
       attr_accessor :id

data/lib/mspire/mzml/scan_window.rb

@@ -1,4 +1,4 @@
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 
 module Mspire
   class Mzml
@@ -7,7 +7,7 @@ module Mspire
     #     accession="MS:1000501" name="scan window lower limit" value="400"
     #     accession="MS:1000500" name="scan window upper limit" value="1800"
     class ScanWindow
-      include Mspire::CV::Paramable
+      include Mspire::Paramable
       extend Mspire::Mzml::List
 
       def to_xml(builder)

data/lib/mspire/mzml/selected_ion.rb

@@ -1,5 +1,5 @@
 require 'mspire/mzml/list'
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 
 module Mspire
   class Mzml
@@ -10,7 +10,7 @@ module Mspire
     #     e.g.: MS:1000633 (possible charge state)
     #     e.g.: MS:1000744 (selected ion m/z)
     class SelectedIon
-      include Mspire::CV::Paramable
+      include Mspire::Paramable
       extend Mspire::Mzml::List
 
       def to_xml(builder)

data/lib/mspire/mzml/software.rb

@@ -1,11 +1,11 @@
 require 'mspire'
 require 'mspire/mzml/list'
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 
 module Mspire
   class Mzml
     class Software
-      include Mspire::CV::Paramable
+      include Mspire::Paramable
       extend Mspire::Mzml::List
 
       attr_accessor :id, :version

data/lib/mspire/mzml/source_file.rb

@@ -1,11 +1,11 @@
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 require 'mspire/mzml/list'
 require 'pathname'
 
 module Mspire
   class Mzml
     class SourceFile
-      include Mspire::CV::Paramable
+      include Mspire::Paramable
       extend Mspire::Mzml::List
 
       # (required) An identifier for this file.

data/lib/mspire/paramable.rb

@@ -0,0 +1,201 @@
+require 'cv/param'
+require 'mspire/user_param'
+require 'mspire/cv/param'
+require 'nokogiri'
+require 'andand'
+
+module Mspire
+  module Paramable
+
+    attr_accessor :cv_params
+    attr_accessor :user_params
+    attr_accessor :ref_param_groups
+
+    def params
+      cv_params + ref_param_groups.flat_map(&:params) + user_params 
+    end
+
+    def each_param(&block)
+      return enum_for __method__ unless block
+      cv_params.each(&block)
+      ref_param_groups.flat_map(&:params).each(&block)
+      user_params.each(&block)
+      nil
+    end
+
+    def params?
+      cv_params.size > 0 || 
+        ref_param_groups.any? {|group| group.params.size > 0 } || 
+        user_params.size > 0
+    end
+
+    def each_accessionable_param(&block)
+      return enum_for __method__ unless block
+      cv_params.each(&block)
+      ref_param_groups.flat_map(&:params).each(&block)
+      nil
+    end
+
+    def accessionable_params
+      cv_params + ref_param_groups.flat_map(&:params)
+    end
+
+    # yields each current param.  If the return value is not false or nil,
+    # it is deleted (i.e., any true value and it is deleted).  Then adds the
+    # given parameter or makes a new one by accession number.
+    def replace!(*describe_args, &block)
+      reject!(&block).describe!(*describe_args)
+    end
+
+    # returns self
+    def reject!(&block)
+      cv_params.reject!(&block)
+      ref_param_groups.each {|group| group.reject!(&block) }
+      user_params.reject!(&block)
+      self
+    end
+
+    def replace_many!(describe_many_arg, &block)
+      reject!(&block).describe_many!(describe_many_arg)
+    end
+
+    #def params_by_name
+    #  params.index_by &:name
+    #end
+
+    #def params_by_accession
+    #  accessionable_params.index_by &:accession
+    #end
+
+    # returns the value if the param exists by that name.  Returns true if
+    # the param exists but has no value. returns false if no param
+    def fetch(name)
+      param = each_param.find {|param| param.name == name}
+      if param
+        param.value || true
+      else
+        false
+      end
+    end
+
+    # returns the value if the param exists with that accession.  Returns
+    # true if the param exists but has no value. returns false if no param
+    # with that accession.
+    def fetch_by_accession(acc)
+      param = accessionable_params.find {|v| v.accession == acc }
+      if param
+        param.value || true
+      else
+        false
+      end
+    end
+    alias_method :fetch_by_acc, :fetch_by_accession
+
+    def param?(name)
+      params.any? {|param| param.name == name }
+    end
+
+    def initialize
+      @cv_params = []
+      @user_params = []
+      @ref_param_groups = []
+    end
+    alias_method :params_init, :initialize
+
+    def param_by_accession(acc)
+      each_accessionable_param.find {|v| v.accession == acc }
+    end
+    alias_method :param_by_acc, :param_by_accession
+
+    # takes an array of values, each of which is fed into describe!
+    # returns self.
+    def describe_many!(array)
+      array.each do |arg|
+        if arg.is_a?(Array)
+          describe!(*arg)
+        else
+          describe!(arg)
+        end
+      end
+      self
+    end
+
+    # reads the paramable nodes and returns self.  Use this if your element
+    # does not have anything besides paramable elements.
+    def describe_self_from_xml!(xml_node, ref_hash=nil)
+      describe_from_xml!(xml_node, ref_hash)
+      self
+    end
+
+    # takes a node with children that are cvParam, userParam or
+    # referenceableParamGroupRef and a hash containing
+    # referenceableParamGroup objects indexed by id.  The only time ref_hash
+    # should be left nil is for the referenceableParamGroup itself.
+    #
+    # All param elements are required to appear before other elements, so
+    # the code walks through each child node to see if it is a paramable
+    # element.  The first child node that is not paramable is returned (or
+    # nil if none)
+    #
+    # returns the next child node after the paramable elements or nil if none
+    def describe_from_xml!(xml_node, ref_hash=nil)
+      return nil unless (child_n = xml_node.child) 
+      loop do
+        array = 
+          case child_n.name
+          when 'referenceableParamGroupRef'
+            @ref_param_groups << ref_hash[child_n[:ref]]
+          when 'cvParam'
+            @cv_params << Mspire::CV::Param[ child_n[:accession], child_n[:value] ]
+          when 'userParam'
+            @user_params << Mspire::UserParam.new(child_n[:name], child_n[:value], child_n[:type])
+          else # assumes that the above precede any following children as per the spec
+            break 
+          end
+        if (unit_acc = child_n[:unitAccession])
+          array.last.unit = ::CV::Param.new(child_n[:unitCvRef], unit_acc, child_n[:unitName])
+        end
+        break unless child_n = child_n.next
+      end
+      child_n
+    end
+
+    # Expects arguments describing a single CV::Param, Mspire::UserParam, or
+    # Mspire::Mzml::ReferenceableParamGroup
+    #
+    #     obj.describe! 'MS:1000130'  # a positive scan
+    #     obj.describe! CV::Param['MS:1000130']  # same behavior
+    #
+    #     # base peak intensity, units=number of counts
+    #     obj.describe! "MS:1000505", 1524.5865478515625, 'MS:1000131'
+    #
+    # returns self
+    def describe!(*args)
+      return self if args.first.nil?
+      case (arg=args.first)
+      when String
+        @cv_params << Mspire::CV::Param[ *args ]
+      when Mspire::Mzml::ReferenceableParamGroup
+        @ref_param_groups << arg
+      else
+        if arg.is_a?(Mspire::UserParam)
+          @user_params << arg
+        else
+          @cv_params << arg
+        end
+      end
+      self
+    end
+
+    # iterates over @params and calls .to_xml on each object.
+    def to_xml(xml)
+      [:ref_param_groups, :cv_params, :user_params].each do |kind|
+        self.send(kind).each do |obj|
+          obj.to_xml(xml)
+        end
+      end
+      xml
+    end
+
+  end
+end

data/lib/mspire/version.rb

@@ -1,3 +1,3 @@
 module Mspire
-  VERSION = "0.9.2"
+  VERSION = "0.10.0"
 end

data/spec/mspire/cv/paramable_spec.rb

@@ -1,15 +1,15 @@
 require 'spec_helper'
 
-require 'mspire/cv/paramable'
+require 'mspire/paramable'
 require 'mspire/cv/param'
 require 'mspire/user_param'
 require 'mspire/mzml/referenceable_param_group'
 
 class ParamableObject
-  include Mspire::CV::Paramable
+  include Mspire::Paramable
 end
 
-describe 'Mspire::CV::Paramable' do
+describe 'Mspire::Paramable' do
 
   subject do
     paramable = ParamableObject.new.describe_many!(['MS:1000007', ['MS:1000511', 2]])

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.9.2
+  version: 0.10.0
 platform: ruby
 authors:
 - John T. Prince
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-28 00:00:00.000000000 Z
+date: 2013-09-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
@@ -281,6 +281,8 @@ files:
 - lib/mspire/mass/subatomic.rb
 - lib/mspire/mass/util.rb
 - lib/mspire/molecular_formula.rb
+- lib/mspire/mzid/modification.rb
+- lib/mspire/mzid/search_modification.rb
 - lib/mspire/mzml.rb
 - lib/mspire/mzml/activation.rb
 - lib/mspire/mzml/chromatogram.rb
@@ -319,6 +321,7 @@ files:
 - lib/mspire/mzml/spectrum.rb
 - lib/mspire/mzml/spectrum_list.rb
 - lib/mspire/obo.rb
+- lib/mspire/paramable.rb
 - lib/mspire/peak.rb
 - lib/mspire/peaklist.rb
 - lib/mspire/plms1.rb