mspire 0.10.2 → 0.10.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 833962e9730b48a8d4c88558f237c7b780655187
+  metadata.gz: 1d16ef25df8a77a1eade1a626b95f7bf0f74e9c3
+  data.tar.gz: d0711a02fdf295ea0cd168a47ef256dafe3f6fa1
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+  data.tar.gz: 5ca19c3e84c71cfe4b99d9f409f0d78a97eb6f7c61e3f20d51c57114c9403e37c1353be92843cc9ea6d802548f72c94d2559e6504fafdfe4fe1b9a008cb5ad76

data/.gitignore

@@ -4,3 +4,4 @@ doc/output/*
 .*.swp
 playing_around_with
 coverage
+/.bundle

data/lib/mspire/isotope/distribution.rb

@@ -17,11 +17,19 @@ end
 module Mspire
   class MolecularFormula < Hash
 
-    # takes any element composition (see any_to_num_elements).
+    # Returns isotopic distribution beginning with the lightest possible peak.
+    # (for most molecules this will also be the monoisotopic peak)
     #
-    # returns isotopic distribution beginning with monoisotopic peak.  It cuts
-    # off when no more peaks contribute more than percent_cutoff to the total
-    # distribution.  After that, normalization is performed.
+    # Two cutoff protocols may be specified, percent_cutoff or
+    # peak_cutoff.  Normalization is performed *after* cutoff.
+    #
+    #     percent_cutoff: cuts off when no more peaks contribute more than percent_cutoff 
+    #                         to the total distribution.  
+    #     peak_cutoff:    cuts off after that many peaks.
+    #
+    # prefer_lowest_index controls the behavior if both percent_cutoff and
+    # peak_cutoff are specified.  If true, then the lowest index found between
+    # the two methods will be used, otherwise the highest index.
     #
     # all values will be fractional.  normalize may be one of:
     #
@@ -29,22 +37,24 @@ module Mspire
     #     :max     normalize to the highest peak intensity
     #     :first   normalize to the intensity of the first peak 
     #             (this is typically the monoisotopic peak)
-    def isotope_distribution(normalize=Mspire::Isotope::Distribution::NORMALIZE, percent_cutoff=nil, isotope_table=Mspire::Isotope::BY_ELEMENT)
-      mono_dist = raw_isotope_distribution(isotope_table)
+    def isotope_distribution(normalize: Mspire::Isotope::Distribution::NORMALIZE, peak_cutoff: nil, percent_cutoff: nil, prefer_lowest_index: true, isotope_table: Mspire::Isotope::BY_ELEMENT)
+      mono_dist = raw_isotope_distribution(isotope_table: isotope_table)
 
-      if percent_cutoff
-        total_signal = mono_dist.reduce(:+)
-        cutoff_index = (mono_dist.size-1).downto(0).find do |i|
-          (mono_dist[i] / total_signal) >= (percent_cutoff/100.0)
-        end
-        # deletes these elements
-        if cutoff_index
-          mono_dist.slice!((cutoff_index+1)..-1)
-        else
-          # no peaks pass that percent cutoff threshold!
-          mono_dist = []
-        end
-      end
+      cutoff_index = [ 
+        if percent_cutoff
+          total_signal = mono_dist.reduce(:+)
+          cutoff_index_less1 = (mono_dist.size-1).downto(0).find do |i|
+            # finds the index
+            (mono_dist[i] / total_signal) >= (percent_cutoff/100.0)
+          end
+          cutoff_index = cutoff_index_less1 ? (cutoff_index_less1 + 1) : 0
+        end,
+        peak_cutoff
+      ].compact.send( prefer_lowest_index ? :min : :max ) || mono_dist.size
+
+      # mono_dist.size will result in nothing sliced off (i.e., for no cutoff)
+
+      mono_dist.slice!(cutoff_index..-1)
 
       # normalization
       norm_by =
@@ -83,7 +93,7 @@ module Mspire
 
     # returns relative ratios from low nominal mass to high nominal mass.
     # These are *not* normalized at all.
-    def raw_isotope_distribution(isotope_table=Mspire::Isotope::BY_ELEMENT)
+    def raw_isotope_distribution(isotope_table: Mspire::Isotope::BY_ELEMENT)
       low_nominal = 0
       high_nominal = 0
       self.each do |el,cnt|
@@ -112,14 +122,14 @@ module Mspire
           obj.is_a?(Mspire::MolecularFormula) ? obj : Mspire::MolecularFormula.from_any(obj)
         end
 
-        def calculate(molecular_formula_like, normalize=NORMALIZE, percent_cutoff=nil, isotope_table=Mspire::Isotope::BY_ELEMENT)
+        def calculate(molecular_formula_like, *args)
           mf = to_mf(molecular_formula_like)
-          mf.isotope_distribution(normalize, percent_cutoff, isotope_table)
+          mf.isotope_distribution(*args)
         end
 
-        def spectrum(molecular_formula_like, normalize=NORMALIZE, percent_cutoff=nil, isotope_table=Mspire::Isotope::BY_ELEMENT)
+        def spectrum(molecular_formula_like, *args)
           mf = to_mf(molecular_formula_like)
-          mf.isotope_distribution_spectrum(normalize, percent_cutoff, isotope_table)
+          mf.isotope_distribution_spectrum(*args)
         end
       end
     end

data/lib/mspire/version.rb

@@ -1,3 +1,3 @@
 module Mspire
-  VERSION = "0.10.2"
+  VERSION = "0.10.3"
 end

data/spec/mspire/isotope/distribution_spec.rb

@@ -4,6 +4,12 @@ require 'mspire/isotope/distribution'
 
 describe 'Mspire::Isotope::Distribution class methods' do
 
+  def similar_distributions(a_dist, b_dist)
+    b_dist.zip(a_dist) do |b,a| 
+      expect(a).to be_within(1e-9).of b
+    end
+  end
+
   before(:all) do
     @nist = Mspire::Isotope::NIST::BY_ELEMENT
     @norm = Mspire::Isotope::Distribution::NORMALIZE
@@ -19,47 +25,57 @@ describe 'Mspire::Isotope::Distribution class methods' do
 
   describe 'normalizing isotope distributions' do
 
+
     it 'defaults to normalizing by total signal with no cutoff' do
-      dist = Mspire::Isotope::Distribution.calculate( subject, @norm, @pcut, @nist )
-      dist.size.should == 253
-      dist[0,5].should == [0.31740518639058685, 0.35635707398291416, 0.20793431846543858, 0.08373257192958428, 0.026084566135229446]
+      dist = Mspire::Isotope::Distribution.calculate( subject, normalize: @norm, percent_cutoff: @pcut, isotope_table: @nist )
+      expect(dist.size).to eq(253)
+      similar_distributions dist[0,5], [0.31740518639058685, 0.35635707398291416, 0.20793431846543858, 0.08373257192958428, 0.026084566135229446]
     end
 
     it 'can normalize by first peak' do
-      dist = Mspire::Isotope::Distribution.calculate( subject, :first, @pcut, @nist )
+      dist = Mspire::Isotope::Distribution.calculate( subject, normalize: :first, percent_cutoff: @pcut, isotope_table: @nist )
       dist.size.should == 253
       dist[0].should == 1.0
       dist[1].should_not == 1.0
     end
 
     it 'can normalize by the max peak' do
-      dist = Mspire::Isotope::Distribution.calculate( subject, :max, @pcut, @nist )
+      dist = Mspire::Isotope::Distribution.calculate( subject, normalize: :max, percent_cutoff: @pcut, isotope_table: @nist )
       dist.size.should == 253
       dist[0].should_not == 1.0
       dist[1].should == 1.0
     end
 
     it 'can cutoff based on percent of total signal' do
-      Mspire::Isotope::Distribution.calculate(subject, :max, 100, @nist).should == []
-      Mspire::Isotope::Distribution.calculate(subject, :max, 20, @nist).should == [0.8906942209481861, 1.0, 0.5834999040187656]
-      Mspire::Isotope::Distribution.calculate(subject, :max, 5, @nist).should == [0.8906942209481861, 1.0, 0.5834999040187656, 0.23496817670469172]
-      Mspire::Isotope::Distribution.calculate(subject, :max, 0.0001, @nist).size.should == 11
+      Mspire::Isotope::Distribution.calculate(subject, normalize: :max, percent_cutoff: 100, isotope_table: @nist).should == []
+      similar_distributions Mspire::Isotope::Distribution.calculate(subject, normalize: :max, percent_cutoff: 20, isotope_table: @nist), [0.8906942209481861, 1.0, 0.5834999040187656]
+      similar_distributions Mspire::Isotope::Distribution.calculate(subject, normalize: :max, percent_cutoff: 5, isotope_table: @nist), [0.8906942209481861, 1.0, 0.5834999040187656, 0.23496817670469172]
+      Mspire::Isotope::Distribution.calculate(subject, normalize: :max, percent_cutoff: 0.0001, isotope_table: @nist).size.should == 11
     end
+
+    it 'can cutoff based on a given number of peaks' do
+      Mspire::Isotope::Distribution.calculate(subject, normalize: :max, peak_cutoff: 0, isotope_table: @nist).should == []
+      similar_distributions Mspire::Isotope::Distribution.calculate(subject, normalize: :total, peak_cutoff: 4, isotope_table: @nist), [0.3287710818944283, 0.3691177894299527, 0.2153801947039964, 0.08673093397162249]
+      expect(Mspire::Isotope::Distribution.calculate(subject, normalize: :max, peak_cutoff: 1, isotope_table: @nist)).to eql([1.0])
+    end
+
+    xspecify 'prefers the lowest of cutoffs'  ## need to test
+
   end
 
   describe 'calculating an isotope distribution spectrum' do
 
     it 'gives neutral masses if no charge' do
-      spec = Mspire::Isotope::Distribution.spectrum( subject, @norm, @pcut, @nist )
+      spec = Mspire::Isotope::Distribution.spectrum( subject, normalize: @norm, percent_cutoff: @pcut, isotope_table: @nist )
       [:mzs, :intensities].each {|att| spec.send(att).size.should == 253 }
       spec.mzs[0,5].should == [1584.8627231418, 1585.8713880574, 1586.8800529730001, 1587.8887178886002, 1588.8973828042003]
-      spec.intensities[0,5].should == [0.31740518639058685, 0.35635707398291416, 0.20793431846543858, 0.08373257192958428, 0.026084566135229446]
+      similar_distributions spec.intensities[0,5], [0.31740518639058685, 0.35635707398291416, 0.20793431846543858, 0.08373257192958428, 0.026084566135229446]
     end
 
     it 'gives proper m/z values if the molecule is charged' do
       charged_molecule = Mspire::MolecularFormula.from_any( subject )
       charged_molecule.charge = -3
-      spec = Mspire::Isotope::Distribution.spectrum( charged_molecule, @norm, @pcut, @nist )
+      spec = Mspire::Isotope::Distribution.spectrum( charged_molecule, normalize: @norm, percent_cutoff: @pcut, isotope_table: @nist )
       [:mzs, :intensities].each {|att| spec.send(att).size.should == 253 }
       spec.mzs[0,5].should == [-528.2881229806, -528.6243446191334, -528.9605662576668, -529.2967878962, -529.6330095347334]
     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.10.2
+  version: 0.10.3
 platform: ruby
 authors:
 - John T. Prince
@@ -9,202 +9,202 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-10-02 00:00:00.000000000 Z
+date: 2014-01-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 1.5.9
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 1.5.9
 - !ruby/object:Gem::Dependency
   name: bsearch
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.5.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.5.0
 - !ruby/object:Gem::Dependency
   name: andand
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.3.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.3.3
 - !ruby/object:Gem::Dependency
   name: obo
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.1.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.1.3
 - !ruby/object:Gem::Dependency
   name: builder
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 3.2.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 3.2.0
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 1.4.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 1.4.3
 - !ruby/object:Gem::Dependency
   name: trollop
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 2.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 2.0.0
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.3'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 2.13.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 2.13.0
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.12'
 - !ruby/object:Gem::Dependency
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: coveralls
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: fftw3
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.3'
 description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
@@ -216,8 +216,8 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
-- .gitignore
-- .travis.yml
+- ".gitignore"
+- ".travis.yml"
 - Gemfile
 - LICENSE
 - README.md
@@ -450,17 +450,17 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.3
+rubygems_version: 2.2.0
 signing_key: 
 specification_version: 4
 summary: mass spectrometry proteomics, lipidomics, and tools