require 'test/unit'
require 'spec_id'
require 'spec/scan'



class ProphTest < Test::Unit::TestCase

  def initialize(arg)
    super(arg)
    @tfiles = File.dirname(__FILE__) + '/tfiles/'
    @pepproph_xml = @tfiles + 'pepproph_small.xml'
  end

  def test_parse_protxml_file
    file = @tfiles + 'opd1/000_020_3prots-prot.xml'
    #obj = Proph::ProtSummary.new
    obj = Proph::ProtSummary.new(file)
    assert_equal(3, obj.prot_groups.size)
    assert_equal("1.00", obj.prot_groups.first.probability)
    assert_equal("0.98", obj.prot_groups[2].probability)
    assert_equal_xml_atts_to_obj('protein_name="gi|16132019|ref|NP_418618.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="13.0" unique_stripped_peptides="FRDGLK+AIQFAQDVGIRVIQLAGYDVYYQEANNETRR" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="0.41"', obj.prot_groups[1].prots.first) 
  end

  def assert_equal_xml_atts_to_obj(string, obj, msg=nil)
    parts = string.split(/\s+/)
    parts.each do |part|
      pi = part.split('=')
      value = pi[1].sub(/^"/,'').sub(/"$/,'')
      if pi[0] == "probability"
        value = value.to_f
      end
      assert_equal(value, obj.send(pi[0].to_sym))
    end
  end


  def Xtest_filter_by_min_pep_prob
    obj = Proph::Pep::Parser.new
    new_file = "tfiles/tmp.xml"
    assert_match(/peptideprophet_result probability="0.[0-5]/, IO.read(@pepproph_xml))
    obj.filter_by_min_pep_prob(@pepproph_xml, new_file, 0.50)
    assert_no_match(/peptideprophet_result probability="0.[0-5]/, IO.read(new_file))
    assert_match(/<peptideprophet_result[^>]*probability="0.[6-9][^>]*>/, IO.read(new_file))
    File.unlink new_file
  end

  def Xtest_uniq_by_seqcharge
    cls = Proph::Pep
    p1 = cls.new({ :charge => '2', :sequence => 'PEPTIDE' })
    p2 = cls.new({ :charge => '3', :sequence => 'PEPTIDE' })
    p3 = cls.new({ :charge => '2', :sequence => 'PEPTIDE' })
    p4 = cls.new({ :charge => '2', :sequence => 'APEPTIDE' })
    p5 = cls.new({ :charge => '2', :sequence => 'APEPTIDE' })
    un_peps = cls.uniq_by_seqcharge([p1,p2,p3,p4,p5])
    ## WHY ISn't that working? below!
    ##assert_equal([p1,p2,p4].to_set, un_peps.to_set)
    assert(equal_sets([p1,p2,p4], un_peps))
  end

  def Xequal_sets(arr1, arr2)
    c1 = arr1.dup
    c2 = arr2.dup
    arr1.each do |c|
      arr2.each do |d|
        if c == d
          c1.delete c
          c2.delete d
        end
      end
    end
    if (c1.size == c2.size) && (c1.size == 0)
      true
    else
      false
    end
  end

  def Xtest_arithmetic_avg_scan_by_parent_time
    i1 = 100015.0
    i2 = 30000.0
    i3 = 100.0
    t1 = 0.13
    t2 = 0.23
    t3 = 0.33
    p1 = Spec::Scan.new(1,1, t1)
    p2 = Spec::Scan.new(2,1, t2)
    p3 = Spec::Scan.new(3,1, t3)
    s1 = Spec::Scan.new(1,2,0.10, 300.2, i1, p1)
    s2 = Spec::Scan.new(2,2,0.20, 301.1, i2, p2)
    s3 = Spec::Scan.new(3,2,0.30, 302.0, i3, p3)
    scan = Proph::Pep.new({:scans => [s1,s2,s3]}).arithmetic_avg_scan_by_parent_time
    tot_inten = i1 + i2 + i3
    tm = ( t1 * (i1/tot_inten) + t2 * (i2/tot_inten) + t3 * (i3/tot_inten) )
    {:ms_level => 2, :prec_inten => 130115.0/3, :num => nil, :prec_mz => 301.1.to_f, :time => tm }.each do |k,v|
      if k == :prec_mz  # not sure why this is bugging out, but..
        assert_equal(v.to_s, scan.send(k).to_s)
      else
        assert_equal(v, scan.send(k))
      end
    end

  end


end