[BioRuby-cvs] bioruby/test/unit/bio/util/restriction_enzyme test_analysis.rb, 1.4, 1.5 test_double_stranded.rb, 1.3, 1.4

[Trevor Wennblom]

Update of /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme
In directory dev.open-bio.org:/tmp/cvs-serv3107/restriction_enzyme

Modified Files:
	test_analysis.rb test_double_stranded.rb 
Log Message:


Index: test_double_stranded.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** test_double_stranded.rb	1 Jan 2007 02:16:05 -0000	1.3
--- test_double_stranded.rb	2 Jan 2007 06:18:07 -0000	1.4
***************
*** 35,39 ****
      @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])
  
--- 35,39 ----
      @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])
  
***************
*** 57,61 ****
      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)
  
--- 57,61 ----
      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)
  
***************
*** 75,79 ****
      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)
  
--- 75,79 ----
      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)
  

Index: test_analysis.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_analysis.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** test_analysis.rb	31 Dec 2006 18:46:14 -0000	1.4
--- test_analysis.rb	2 Jan 2007 06:18:07 -0000	1.5
***************
*** 31,34 ****
--- 31,36 ----
      @obj_4 = @t.cut('atgcatgcatgc', e1)
  
+     @obj_4bd = @t.cut('atgcatgcatgccccc', e1, 'cc^c')
+ 
      e2 = @enz.new('atgcatgc', [3,5])
      @obj_5 = @t.cut('atgcatgcatgc', e2)
***************
*** 39,42 ****
--- 41,47 ----
  
      @obj_7 = @t.cut('gaccaggaaaaagaccaggaaagcctggaaaagttaac', 'EcoRII')
+     @obj_7b = @t.cut('gaccaggaaaaagaccaggaaagcctggaaaagttaaccc', 'EcoRII', 'HincII', 'cc^c')
+     @obj_7bd = @t.cut_without_permutations('gaccaggaaaaagaccaggaaagcctggaaaagttaaccc', 'EcoRII', 'HincII', 'cc^c')
+     
      @obj_8 = @t.cut('gaccaggaaaaagaccaggaaagcctggaaaagttaac', 'EcoRII', 'HincII')
  
***************
*** 76,83 ****
--- 81,105 ----
      assert_equal(["ag", "agt", "cag"], @obj_3.primary)
      assert_equal(["atg", "atgcatg", "catg", "catgc"], @obj_4.primary)
+ =begin
+     A T G^C A T G C
+     
+     A T G C A T G C A T G C
+     
+     A T G^C A T G^C A T G C
+     
+     A T G C A T G^C A T G C
+ =end
+     
+     
+     e1 = @enz.new('atgcatgc', [3,3])
+     @obj_4 = @t.cut('atgcatgcatgc', e1)
+     
      assert_equal(["atg", "atgcatg", "catgc", "catgcatgc"], @obj_5.primary)
      assert_equal(["a", "ag", "g", "ga"], @obj_6.primary)
      assert_equal(["ccaggaaaaaga", "ccaggaaag", "cctggaaaagttaac", "ga"], @obj_7.primary)
      assert_equal(["aac", "ccaggaaaaaga", "ccaggaaag", "cctggaaaagtt", "ga"], @obj_8.primary)
+         
+     assert_equal(["atg", "atgcatg", "c", "catg", "catgcc", "catgccc", "cc", "cc"], @obj_4bd.primary)
+     assert_equal(["gg", "gg", "ggg", "gtac", "gtacg", "gtacgg", "tac", "tacgtac"], @obj_4bd.complement)
    end