#
# test/unit/bio/util/restriction_enzyme/test_single_strand.rb - Unit test for Bio::RestrictionEnzyme::SingleStrand
#
# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
# License::   The Ruby License
#
#  $Id:$
#

require 'pathname'
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)

require 'test/unit'
require 'bio/util/restriction_enzyme/single_strand'

module Bio; module TestRestrictionEnzyme #:nodoc:

class TestSingleStrand < Test::Unit::TestCase #:nodoc:

  def setup
    @t = Bio::RestrictionEnzyme::SingleStrand
    @cl = Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
    @s = Bio::Sequence::NA

    @obj_1 = @t.new(@s.new('gata'), @cl.new(-2,1,3))
    @obj_2 = @t.new('gata', -2, 1, 3)
    @obj_3 = @t.new('garraxt', [-2, 1, 7])
    @obj_4 = @t.new('nnnnnnngarraxtnn', [-2, 1, 7])

    @obj_5 = @t.new('ga^rr^axt')
    @obj_6 = @t.new('^ga^rr^axt')
    @obj_7 = @t.new('n^ngar^raxtnn^n')
  end

  def test_pattern_palindromic?
    assert_equal(true, @t.new('atgcat', 1).palindromic?)
    assert_equal(false, @t.new('atgcgta', 1).palindromic?)

    assert_equal(false, @obj_1.palindromic?)
    assert_equal(false, @obj_2.palindromic?)
    assert_equal(false, @obj_3.palindromic?)
    assert_equal(false, @obj_4.palindromic?)
  end

  def test_stripped
    assert_equal('gata', @obj_1.stripped)
    assert_equal('gata', @obj_2.stripped)
    assert_equal('garraxt', @obj_3.stripped)
    assert_equal('garraxt', @obj_4.stripped)
  end

  def test_pattern
    assert_equal('nngata', @obj_1.pattern)
    assert_equal('nngata', @obj_2.pattern)
    assert_equal('nngarraxtn', @obj_3.pattern)
    assert_equal('nngarraxtn', @obj_4.pattern)

    assert_equal('nngata', @obj_1)
    assert_equal('nngata', @obj_2)
    assert_equal('nngarraxtn', @obj_3)
    assert_equal('nngarraxtn', @obj_4)
  end

  def test_with_cut_symbols
    assert_equal('n^ng^at^a', @obj_1.with_cut_symbols)
    assert_equal('n^ng^at^a', @obj_2.with_cut_symbols)
    assert_equal('n^ng^arraxt^n', @obj_3.with_cut_symbols)
    assert_equal('n^ng^arraxt^n', @obj_4.with_cut_symbols)
  end

  def test_with_spaces
    assert_equal('n^n g^a t^a', @obj_1.with_spaces)
    assert_equal('n^n g^a t^a', @obj_2.with_spaces)
    assert_equal('n^n g^a r r a x t^n', @obj_3.with_spaces)
    assert_equal('n^n g^a r r a x t^n', @obj_4.with_spaces)
  end

  def test_cut_locations_in_enzyme_notation
    assert_equal([-2,1,3], @obj_1.cut_locations_in_enzyme_notation)
    assert_equal([-2,1,3], @obj_2.cut_locations_in_enzyme_notation)
    assert_equal([-2,1,7], @obj_3.cut_locations_in_enzyme_notation)
    assert_equal([-2,1,7], @obj_4.cut_locations_in_enzyme_notation)

    assert_equal([2,4], @obj_5.cut_locations_in_enzyme_notation)
    assert_equal([-1,2,4], @obj_6.cut_locations_in_enzyme_notation)
    assert_equal([-2,3,9], @obj_7.cut_locations_in_enzyme_notation)
  end

  def test_cut_locations
    assert_equal([0,2,4], @obj_1.cut_locations)
    assert_equal([0,2,4], @obj_2.cut_locations)
    assert_equal([0,2,8], @obj_3.cut_locations)
    assert_equal([0,2,8], @obj_4.cut_locations)

    assert_equal([1,3], @obj_5.cut_locations)
    assert_equal([0,2,4], @obj_6.cut_locations)
    assert_equal([0,4,10], @obj_7.cut_locations)
  end

  def test_orientation
    assert_equal([5,3], @obj_1.orientation)
    assert_equal([5,3], @obj_2.orientation)
    assert_equal([5,3], @obj_3.orientation)
    assert_equal([5,3], @obj_4.orientation)
  end

  def test_creation_with_no_cuts
    @obj_8 = @t.new('garraxt')
    assert_equal([5,3], @obj_8.orientation)
    assert_equal([], @obj_8.cut_locations)
    assert_equal([], @obj_8.cut_locations_in_enzyme_notation)
    assert_equal('garraxt', @obj_8.pattern)
  end

  # NOTE
  def test_to_re
  end

  def test_argument_error
    assert_raise(ArgumentError) { @t.new('a', [0,1,2]) }
    assert_raise(ArgumentError) { @t.new('a', 0,1,2,0) }

    assert_raise(ArgumentError) { @t.new('a', [nil,1,2]) }
    assert_raise(ArgumentError) { @t.new('a', nil,1,2,nil) }

    assert_raise(ArgumentError) { @t.new('a', [1,1,2]) }
    assert_raise(ArgumentError) { @t.new('a', 1,1,2,2) }

    assert_raise(ArgumentError) { @t.new(1, [1,2,3]) }
    assert_raise(ArgumentError) { @t.new('gaat^aca', [1,2,3]) }
    assert_raise(ArgumentError) { @t.new('gaat^^aca') }
    assert_raise(ArgumentError) { @t.new('z', [1,2,3]) }

    assert_raise(ArgumentError) { @t.new('g', [0,1,2]) }
    assert_raise(ArgumentError) { @t.new('g', 0,1,2,0) }
    assert_raise(ArgumentError) { @t.new('g', [0,1,1,2]) }
    assert_raise(ArgumentError) { @t.new('g', 0,1,1,2,2) }
    assert_raise(ArgumentError) { @t.new(1,2,3) }
    assert_raise(ArgumentError) { @t.new(1,2,'g') }
  end


end

end; end