require 'spec_helper'

require 'mspire/isotope/distribution'

describe 'Mspire::Isotope::Distribution class methods' do
  before do 
    @first = [1.0, 0.08919230588715311, 0.017894161377222138, 0.0013573997600723345, 0.0001398330738144181]
  end
  # can also be used on a real MolecularFormula object
  subject { 'C102H120O15' }

  describe 'normalizing isotope distributions' do

    it 'defaults to normalizing by total signal with no cutoff' do
      dist = Mspire::Isotope::Distribution.calculate( subject )
      dist.size.should == 253
      dist[0,5].should == [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 )
      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)
      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).should == []
      Mspire::Isotope::Distribution.calculate(subject, :max, 20).should == [0.8906942209481861, 1.0, 0.5834999040187656]
      Mspire::Isotope::Distribution.calculate(subject, :max, 5).should == [0.8906942209481861, 1.0, 0.5834999040187656, 0.23496817670469172]
      Mspire::Isotope::Distribution.calculate(subject, :max, 0.0001).size.should == 11
    end
  end

  describe 'calculating an isotope distribution spectrum' do

    it 'gives neutral masses if no charge' do
      spec = Mspire::Isotope::Distribution.spectrum( subject )
      [: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]
    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 )
      [: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
  end
end