[BioRuby-cvs] bioruby/test/unit/bio/util/restriction_enzyme test_analysis.rb, 1.11, 1.12

[Trevor Wennblom]

Update of /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme
In directory dev.open-bio.org:/tmp/cvs-serv5059/test/unit/bio/util/restriction_enzyme

Modified Files:
	test_analysis.rb 
Log Message:
Added view_ranges parameter to indicate preservation of cut location data in results.


Index: test_analysis.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_analysis.rb,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** test_analysis.rb	23 Apr 2007 19:42:55 -0000	1.11
--- test_analysis.rb	13 May 2007 04:08:02 -0000	1.12
***************
*** 69,72 ****
--- 69,74 ----
      @obj_99 = @t.cut_without_permutations('', 'EcoRII', 'HincII')
  
+     @obj_vr1 = @t.cut('gaccaggaaaaagaccaggaaagcctggaaaagttaac', 'EcoRII', {:view_ranges => true})
+     @obj_vr2 = @t.cut('cagagag', {:view_ranges => true}, 'ag^ag')
    end
  
***************
*** 167,170 ****
--- 169,243 ----
      assert_equal(["a", "gtctctcggtcc"], Bio::Sequence::NA.new('cagagagccaggt').cut_with_enzymes('EcoRII').complement )  
    end
+   
+   def test_view_ranges
+     assert_equal(["ccaggaaaaaga", "ccaggaaag", "cctggaaaagttaac", "ga"], @obj_vr1.primary)
+     assert_equal(["ctggtcc", "tttcggacc", "ttttcaattg", "tttttctggtcc"], @obj_vr1.complement)
+ 
+     a0 = @obj_vr1[0]
+     assert_equal('ga     ', a0.primary)
+     assert_equal('ctggtcc', a0.complement)
+     assert_equal(0, a0.p_left)
+     assert_equal(1, a0.p_right)
+     assert_equal(0, a0.c_left)
+     assert_equal(6, a0.c_right)
+     
+     a1 = @obj_vr1[1]
+     assert_equal('ccaggaaaaaga     ', a1.primary)
+     assert_equal('     tttttctggtcc', a1.complement)
+     assert_equal(2,  a1.p_left)
+     assert_equal(13, a1.p_right)
+     assert_equal(7,  a1.c_left)
+     assert_equal(18, a1.c_right)     
+ 
+     a2 = @obj_vr1[2]
+     assert_equal('ccaggaaag     ', a2.primary)
+     assert_equal('     tttcggacc', a2.complement)
+     assert_equal(14, a2.p_left)
+     assert_equal(22, a2.p_right)
+     assert_equal(19, a2.c_left)
+     assert_equal(27, a2.c_right)
+ 
+     a3 = @obj_vr1[3]
+     assert_equal('cctggaaaagttaac', a3.primary)
+     assert_equal('     ttttcaattg', a3.complement)
+     assert_equal(23, a3.p_left)
+     assert_equal(37, a3.p_right)
+     assert_equal(28, a3.c_left)
+     assert_equal(37, a3.c_right)
+     
+     a4 = @obj_vr1[4]
+     assert_equal(nil, a4)
+     
+     assert_equal(["ag", "ag", "cag"], @obj_vr2.primary)
+     assert_equal(["gtc", "tc", "tc"], @obj_vr2.complement)
+ 
+     a0 = @obj_vr2[0]
+     assert_equal('cag', a0.primary)
+     assert_equal('gtc', a0.complement)
+     assert_equal(0, a0.p_left)
+     assert_equal(2, a0.p_right)
+     assert_equal(0, a0.c_left)
+     assert_equal(2, a0.c_right)
+     
+     a1 = @obj_vr2[1]
+     assert_equal('ag', a1.primary)
+     assert_equal('tc', a1.complement)
+     assert_equal(3, a1.p_left)
+     assert_equal(4, a1.p_right)
+     assert_equal(3, a1.c_left)
+     assert_equal(4, a1.c_right)
+     
+     a2 = @obj_vr2[2]
+     assert_equal('ag', a2.primary)
+     assert_equal('tc', a2.complement)
+     assert_equal(5, a2.p_left)
+     assert_equal(6, a2.p_right)
+     assert_equal(5, a2.c_left)
+     assert_equal(6, a2.c_right)
+     
+     a3 = @obj_vr2[3]
+     assert_equal(nil, a3)
+   end
+   
  
  end