require File.expand_path( File.dirname(__FILE__) + '/../../spec_helper' )

require 'spec_id/proph/pep_summary'

ToCheck = {
  :spectrum_query => {:first => {:spectrum => "020.42.42.3", :start_scan=>42, :end_scan=>42, :precursor_neutral_mass=>1015.77285654469, :assumed_charge=>3, :index=>1 },
    :last => {:spectrum=>"020.344.344.3", :start_scan=>344, :end_scan=>344, :precursor_neutral_mass=>1447.6040333025, :assumed_charge=>3, :index=>18 },
},

:search_hit => {:first => {:hit_rank=>1, :peptide=>"GTGVSVTR", :peptide_prev_aa=>"R", :peptide_next_aa=>"S", :protein=>"gi|49176370|ref|YP_026228.1|", :num_tot_proteins=>1, :num_matched_ions=>10, :tot_num_ions=>70, :calc_neutral_pep_mass=>1015.79382542, :massdiff=>-0.0209688753124055, :num_tol_term=>2, :num_missed_cleavages=>0, :is_rejected=>0, :xcorr=>1.06543827056885, :deltacn => 0.192325830459595, :deltacnstar=>0, :spscore=>77.8397979736328, :sprank=>3, :probability=>0.07881571, :fval=>0.1592, :ntt=>2, :nmc=> 0, :massd=>-0.021}, 
  :last => { :hit_rank=>1, :peptide=>"VAALRVPGGASLTR", :peptide_prev_aa=>"R", :peptide_next_aa=>"K", :protein=>"gi|16129819|ref|NP_416380.1|", :num_tot_proteins=>1, :num_matched_ions=>16, :tot_num_ions=>78, :calc_neutral_pep_mass=>1447.58289842, :massdiff=> 0.0211348825000641, :num_tol_term=>2, :num_missed_cleavages=>1, :is_rejected=>0, :xcorr=>1.3090912103653, :deltacn => 0.259967535734177, :deltacnstar => 0, :spscore => 118.513412475586, :sprank => 4, :probability=>0.27738378, :fval=>1.3810, :ntt=>2, :nmc=>1, :massd=>0.021 },
}
}


describe Proph::PepSummary, "reading a .xml file" do
  before(:each) do
    file = Tfiles + '/opd1_2runs_2mods/interact-opd1_mods__small.xml'
    @obj = Proph::PepSummary.new(file)
  end

  it 'should raise an error if not a peptide prophet file' do
    lambda { Proph::PepSummary.new(Tfiles + '/opd1/000.tpp_2.9.2.first10.xml')}.should raise_error(ArgumentError)
  end

  it 'has spectrum queries' do
    @obj.spectrum_queries.size.should == 18

    [:first, :last].each do |mth|
      ToCheck[:spectrum_query][mth].each do |k,v|
        @obj.spectrum_queries.send(mth).send(k).should == v
      end
      ToCheck[:search_hit][mth].each do |k,v|
        @obj.spectrum_queries.send(mth).search_results.first.search_hits.first.send(k).should == v
      end
    end
  end

  it 'has pephits (which are descended from SearchHit)' do
    @obj.peps.size.should == 18
    [:hit_rank, :probability, :fval, :ntt, :nmc, :massd].each do |guy|
      @obj.peps.first.should respond_to(guy)
    end

    [:first, :last].each do |mth|
      ToCheck[:search_hit][mth].each do |k,v|
        @obj.peps.send(mth).send(k).should == v
      end
    end

  end

end

####################################################
# OTHER TESTS NOT IMPLEMENTED (do we need these??)
####################################################

=begin

require 'test/unit'
require 'spec_id'
require 'ms/scan'

class ProphTest < Test::Unit::TestCase

  def initialize(arg)
    super(arg)
    @tfiles = File.dirname(__FILE__) + '/tfiles/'
    @pepproph_xml = @tfiles + 'pepproph_small.xml'
  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 = MS::Scan.new(1,1, t1)
    p2 = MS::Scan.new(2,1, t2)
    p3 = MS::Scan.new(3,1, t3)
    s1 = MS::Scan.new(1,2,0.10, 300.2, i1, p1)
    s2 = MS::Scan.new(2,2,0.20, 301.1, i2, p2)
    s3 = MS::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

=end