# # test/unit/bio/util/restriction_enzyme/test_double_stranded.rb - Unit test for Bio::RestrictionEnzyme::DoubleStranded # # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) # License:: The Ruby License # # $Id:$ # # loading helper routine for testing bioruby require 'pathname' load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'bioruby_test_helper.rb')).cleanpath.to_s # libraries needed for the tests require 'test/unit' require 'bio/util/restriction_enzyme/double_stranded' require 'bio/sequence' module Bio; module TestRestrictionEnzyme #:nodoc: class TestDoubleStranded < Test::Unit::TestCase #:nodoc: def setup @t = Bio::RestrictionEnzyme::DoubleStranded @cl = Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation @s = String @obj_1 = @t.new(@s.new('gata'), [1,2]) @obj_2 = @t.new('gata', [1,2]) @obj_3 = @t.new('garraxt', [1,2]) @obj_4 = @t.new('nnnnnnngarraxtnn', [1,2]) @obj_5 = @t.new('garraxt', @cl.new(3,2), @cl.new(-2,-1), @cl.new(9,11)) @obj_6 = @t.new('garraxt', @cl.new(3,2)) @obj_7 = @t.new('garraxt', @cl.new(3,2), @cl.new(9,11)) # @obj_8 = @t.new('garraxt', 3..2, 9..11) @obj_9 = @t.new('garraxt', [3,2], [9,11]) @obj_10 = @t.new('garraxt', [3,2], [9,11]) @obj_11 = @t.new('n^ngar^raxtnn^n') @obj_12 = @t.new('nnnn^ngar^raxtnn^nnnn') @obj_13 = @t.new(Bio::RestrictionEnzyme.rebase['EcoRII']) @obj_14 = @t.new('EcoRII') @obj_15 = @t.new('ecorii') end def test_primary assert_equal('nngarraxtnnn', @obj_5.primary) end def test_primary_with_cut_symbols assert_equal('n^ngar^raxtnn^n', @obj_5.primary.with_cut_symbols) assert_equal('gar^raxt', @obj_6.primary.with_cut_symbols) assert_equal('gar^raxtnn^n', @obj_7.primary.with_cut_symbols) # assert_equal('gar^raxtnn^n', @obj_8.primary.with_cut_symbols) assert_equal('gar^raxtnn^n', @obj_9.primary.with_cut_symbols) assert_equal('gar^raxtnn^n', @obj_10.primary.with_cut_symbols) assert_equal('n^ngar^raxtnn^n', @obj_11.primary.with_cut_symbols) assert_equal('n^ngar^raxtnn^n', @obj_12.primary.with_cut_symbols) assert_equal('n^ccwgg', @obj_13.primary.with_cut_symbols) assert_equal('n^ccwgg', @obj_14.primary.with_cut_symbols) assert_equal('n^ccwgg', @obj_15.primary.with_cut_symbols) end def test_complement_with_cut_symbols assert_equal('n^ct^yytxannnn^n', @obj_5.complement.with_cut_symbols) assert_equal('ct^yytxa', @obj_6.complement.with_cut_symbols) assert_equal('ct^yytxannnn^n', @obj_7.complement.with_cut_symbols) # assert_equal('ct^yytxannnn^n', @obj_8.complement.with_cut_symbols) assert_equal('ct^yytxannnn^n', @obj_9.complement.with_cut_symbols) assert_equal('ct^yytxannnn^n', @obj_10.complement.with_cut_symbols) assert_equal('n^nnctyy^txan^n', @obj_11.complement.with_cut_symbols) assert_equal('n^nnctyy^txan^n', @obj_12.complement.with_cut_symbols) assert_equal('ggwcc^n', @obj_13.complement.with_cut_symbols) assert_equal('ggwcc^n', @obj_14.complement.with_cut_symbols) assert_equal('ggwcc^n', @obj_15.complement.with_cut_symbols) end def test_complement assert_equal('nctyytxannnnn', @obj_5.complement) end def test_cut_locations assert_equal([[4, 3], [0, 1], [10, 12]], @obj_5.cut_locations) end def test_cut_locations_in_enzyme_notation assert_equal([[3, 2], [-2, -1], [9, 11]], @obj_5.cut_locations_in_enzyme_notation) end def test_argument_error assert_raise(ArgumentError) { @t.new('garraxt', [3,2,9,11]) } assert_raise(ArgumentError) { @t.new(Bio::RestrictionEnzyme.rebase['ecorii'] )} assert_raise(ArgumentError) { @t.new(Bio::RestrictionEnzyme.rebase['EzzRII']) } end # NOTE def test_to_re end end end; end