require 'spec_helper'
require 'ms/ident/pepxml/sample_enzyme'
require 'nokogiri'

describe 'creating an MS::Ident::Pepxml::SampleEnzyme' do
  before do
    @hash = {
      :name => 'trypsin',
      :cut => 'KR',
      :no_cut => 'P',
      :sense => 'C',
    }
  end
  it 'can be set by a known enzyme name' do
    se = MS::Ident::Pepxml::SampleEnzyme.new('trypsin')
    @hash.each do |k,v|
      se.send(k).should == v
    end
  end

  it 'can be set manually with a hash' do
    se = MS::Ident::Pepxml::SampleEnzyme.new(@hash)
    @hash.each do |k,v|
      se.send(k).should == v
    end
  end
end

describe 'an MS::Ident::Pepxml::SampleEnzyme' do
  before do
    @sample_enzyme = MS::Ident::Pepxml::SampleEnzyme.new(:name=>'trypsin',:cut=>'KR',:no_cut=>'P',:sense=>'C')
  end
  it 'generates a valid xml fragment' do
    string = @sample_enzyme.to_xml
    string.is_a?(String).should == true
    string.should match(/<sample_enzyme name="trypsin"/)
    string.should match(/<specificity/) 
    %w(cut="KR" no_cut="P" sense="C").each {|re| string.should match(/#{re}/) }
    !string.include?('version').should == true
  end
  it 'adds to an xml builder object' do
    builder = Nokogiri::XML::Builder.new
    after = @sample_enzyme.to_xml(builder)
    after.is_a?(Nokogiri::XML::Builder).should == true
    after.should == builder
    after.to_xml.is_a?(String).should == true
  end
end

describe 'an MS::Ident::Pepxml::SampleEnzyme making enzyme digestion calculations' do
  before do
    @full_KRP = MS::Ident::Pepxml::SampleEnzyme.new(
      :name => 'trypsin',
      :cut => 'KR',
      :no_cut => 'P',
      :sense => 'C',
    )
    @just_KR = MS::Ident::Pepxml::SampleEnzyme.new(
      :name => 'trypsin',
      :cut => 'KR',
      :no_cut => '',
      :sense => 'C',
    )
  end

  it 'calculates the number of tolerant termini' do
    exp = [{
      # full KR/P
      %w(K EPTIDR E) => 2,
      %w(K PEPTIDR E) => 1,
      %w(F EEPTIDR E) => 1,
      %w(F PEPTIDW R) => 0,
    },
    {
      # just KR
      %w(K EPTIDR E) => 2,
      %w(K PEPTIDR E) => 2,
      %w(F EEPTIDR E) => 1,
      %w(F PEPTIDW R) => 0,
    }
    ]
    sample_enzyme_ar = [@full_KRP, @just_KR]
    sample_enzyme_ar.zip(exp) do |sample_enzyme,hash|
      hash.each do |seq, val|
        sample_enzyme.num_tol_term(*seq).should == val
      end
    end
  end

  it 'calculates number of missed cleavages' do
    exp = [{
      "EPTIDR" => 0,
      "PEPTIDR" => 0,
      "EEPTIDR" => 0,
      "PEPTIDW" => 0,
      "PERPTIDW" => 0,
      "PEPKPTIDW" => 0,
      "PEPKTIDW" => 1,
      "RTTIDR" => 1,
      "RTTIKK" => 2,
      "PKEPRTIDW" => 2,
      "PKEPRTIDKP" => 2,
      "PKEPRAALKPEERPTIDKW" => 3,
    },
    {
      "EPTIDR" => 0,
      "PEPTIDR" => 0,
      "EEPTIDR" => 0,
      "PEPTIDW" => 0,
      "PERPTIDW" => 1,
      "PEPKPTIDW" => 1,
      "PEPKTIDW" => 1,
      "RTTIDR" => 1,
      "RTTIKK" => 2,
      "PKEPRTIDW" => 2,
      "PKEPRTIDKP" => 3,
      "PKEPRAALKPEERPTIDKW" => 5,
    }
    ]

    sample_enzyme_ar = [@full_KRP, @just_KR]
    sample_enzyme_ar.zip(exp) do |sample_enzyme, hash|
      hash.each do |aaseq, val|
        sample_enzyme.num_missed_cleavages(aaseq).should == val
      end
    end
  end
end

#xdescribe 'read in from an xml node' do
#  # placeholder until written
#end

### DOES this kind of functionality belong in this kind of container????
### SHOULD it be with ms-enzyme or ms-in_silico  ???????

=begin
require 'set'

describe 'MS::Ident::Pepxml::SampleEnzyme digesting sequences' do
  it 'can digest with no missed cleavages' do
    st = "CRGATKKTAGRPMEK"
    SampleEnzyme.tryptic(st).should == %w(CR GATK K TAGRPMEK)
    st = "CATRP"
    SampleEnzyme.tryptic(st).should == %w(CATRP)
    st = "RCATRP"
    SampleEnzyme.tryptic(st).should == %w(R CATRP)
    st = ""
    SampleEnzyme.tryptic(st).should == []
    st = "R"
    SampleEnzyme.tryptic(st).should == %w(R)
  end

  it 'can digest with missed cleavages' do
    st = "CRGATKKTAGRPMEKLLLERTKY"
    zero = %w(CR GATK K TAGRPMEK LLLER TK Y)
    SampleEnzyme.tryptic(st,0).to_set.should == zero.to_set
    one = %w(CRGATK GATKK KTAGRPMEK TAGRPMEKLLLER LLLERTK TKY)
    SampleEnzyme.tryptic(st,1).to_set.should == (zero+one).to_set
    two = %w(CRGATKK GATKKTAGRPMEK KTAGRPMEKLLLER TAGRPMEKLLLERTK LLLERTKY)
    all = zero + one + two
    SampleEnzyme.tryptic(st,2).to_set.should == all.to_set
  end

  it 'contains duplicates IF there are duplicate tryptic sequences' do
    st = "AAAAKCCCCKDDDDKCCCCK"
    peps = SampleEnzyme.new('trypsin').digest(st, 2)
    peps.select {|aaseq| aaseq == 'CCCCK'}.size.should == 2
  end
  
end

describe SampleEnzyme, 'making enzyme calculations on sequences and aaseqs' do


end
=end