require 'helper'

class TestSequence < Test::Unit::TestCase
  context Scaffolder::Region::Sequence do

    context "attributes" do
      should_have_method_attribute Scaffolder::Region::Sequence
      should_have_attribute Scaffolder::Region::Sequence, :source, :inserts
    end

    context "insert attribute method" do

      setup do
        @sequence = Scaffolder::Region::Sequence.new
        @hash = {'open' => 2, 'close' => 3}
        @insert = Scaffolder::Region::Insert.new
        @insert.open  @hash['open']
        @insert.close @hash['close']
      end

      should "return empty array as default value" do
        assert_equal(@sequence.inserts,Array.new)
      end

      should "allow array of inserts to be set as value" do
        @sequence.inserts [@insert]
        assert_equal(@sequence.inserts,[@insert])
      end

      should "process insert data hash into an array of inserts" do
        @sequence.inserts [@hash]
        insert = @sequence.inserts.first
        assert_instance_of(Scaffolder::Region::Insert,insert)
        assert_equal(@hash['close'],insert.close)
        assert_equal(@hash['open'],insert.open)
      end

      should "process mixed insert data into an array of inserts" do
        @sequence.inserts [@hash,@insert]
        @sequence.inserts.each do |insert|
          assert_instance_of(Scaffolder::Region::Insert,insert)
          assert_equal(@hash['close'],insert.close)
          assert_equal(@hash['open'],insert.open)
        end
      end

    end

    context "with inserts added" do

      setup do
        @sequence = Scaffolder::Region::Sequence.new
        @sequence.raw_sequence 'ATGCCAGATAACTGACTAGCATG'

        @insert = Scaffolder::Region::Insert.new
        @insert.raw_sequence 'GGTAGTA'
        @insert.open  5
        @insert.close 10
      end

      should "raise when the insert open is after the sequence stop" do
        @insert.open 24
        @insert.close 25
        @sequence.inserts [@insert]
        assert_raise(Scaffolder::Errors::CoordinateError){ @sequence.sequence }
      end

      should "raise when the insert close is before the sequence start" do
        @insert.open -5
        @insert.close 0
        @sequence.inserts [@insert]
        assert_raise(Scaffolder::Errors::CoordinateError){ @sequence.sequence }
      end

      should "raise when the insert open is greater than the insert close" do
        @insert.open 11
        @sequence.inserts [@insert]
        assert_raise(Scaffolder::Errors::CoordinateError){ @sequence.sequence }
      end

      should "update the sequence with a simple insert" do
        @sequence.inserts [@insert]
        assert_equal(@sequence.sequence,'ATGCGGTAGTAACTGACTAGCATG')
      end

      should "update the sequence stop position after adding a simple insert" do
        @sequence.inserts [@insert]
        assert_equal(@sequence.stop,24)
      end

      should "update sequence with inserts in reverse order" do
        insert_two = @insert.clone
        insert_two.open 12
        insert_two.close 15
        @sequence.inserts [@insert,insert_two]
        assert_equal(@sequence.sequence,"ATGCGGTAGTAAGGTAGTACTAGCATG")
      end
    end

  end
end