require 'test/unit'
require 'spec_id/aa_freqs'


class FastaTest < Test::Unit::TestCase

  def initialize(arg)
    super(arg)
    @tfiles = File.dirname(__FILE__) + '/tfiles/'
    @sf = @tfiles + "small.fasta"
  end

  def test_basic
    obj = SpecID::AAFreqs.new(@sf)
    expect = {:I=>0.0628918621937819, :S=>0.0539719475147049, :D=>0.0526145691939758, :Z=>0.0, :L=>0.102772929998061, :T=>0.0491888048607071, :E=>0.0609527503070261, :O=>0.0, :C=>0.0157714433456144, :K=>0.0471850559110594, :U=>0.0, :Q=>0.0382651412319824, :W=>0.0137030573330748, :A=>0.101997285243359, :M=>0.0294745006786892, :J=>0.0, :G=>0.0811195139292871, :Y=>0.0254670027793937, :X=>0.0, :F=>0.0418201796910348, :R=>0.0546829552065154, :V=>0.0702604873634542, :H=>0.0213302307543145, :B=>0.0, :N=>0.03471010277293, :P=>0.0418201796910348}
    aaf =  obj.aafreqs
    expect.each do |k,v|
      assert(aaf.key?(k))
      assert_in_delta(v, aaf[k], 0.00000001, "freqs match up")
    end
    sum = 0.0
    aaf.values.each do |v|
      sum += v
    end
    assert_in_delta(1.0, sum, 0.0000000000001, "all freqs add to 1")
  end

  def test_probability_of_length_table
    # p SpecID::AAFreqs.probability_of_length_table(0.01, 4)
    assert_equal_arrs_in_delta([0.0, 0.01, 0.0199, 0.029701, 0.0394039900000001],  SpecID::AAFreqs.probability_of_length_table(0.01, 4), 0.000000001)
    
    assert_equal_arrs_in_delta([0.0, 0.2, 0.36, 0.488, 0.5904], SpecID::AAFreqs.probability_of_length_table(0.2, 4), 0.000000001)
  end
  
  def test_actual_and_expected_number
    fobj = Fasta.new.read_file(@sf)
    obj = SpecID::AAFreqs.new
    obj.aafreqs = obj.calculate_frequencies(fobj)

    peptide_aaseqs = fobj.prots.map do |prot|
      prot.aaseq[0..12]
    end
    assert_equal(50, peptide_aaseqs.size, 'sanity check')
    (ac,ex) = obj.actual_and_expected_number(peptide_aaseqs, :C, 1)
    assert_equal(9, ac)
    assert_in_delta( 9.33530631238985, ex, 0.0000000001)
  end

  private
  def assert_equal_arrs_in_delta(expect, actual, delta)
    expect.each_with_index do |v,i|
      assert_in_delta(v, actual[i], delta)
    end
  end


end