test/unit/bio/sequence/test_na.rb in bio-1.0.0 vs test/unit/bio/sequence/test_na.rb in bio-1.1.0

@@ -1,13 +1,13 @@
 #
 # = test/unit/bio/sequence/test_na.rb - Unit test for Bio::Sequencce::NA
 #
 # Copyright::   Copyright (C) 2006 
 #               Mitsuteru C. Nakao <[e-mail]>
-# Lisence::     Ruby's
+# License::     The Ruby License
 #
-# $Id: test_na.rb,v 1.1 2006/02/08 07:08:22 nakao Exp $
+# $Id: test_na.rb,v 1.5 2007/04/05 23:35:44 trevor Exp $
 #
 
 require 'pathname'
 libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
 $:.unshift(libpath) unless $:.include?(libpath)
@@ -96,10 +96,36 @@
       assert_equal(40, @obj.gc_percent)
       @obj[0, 1] = 'g'
       assert_equal(45, @obj.gc_percent)
     end
 
+    def test_gc_content
+      assert_in_delta(0.4, @obj.gc_content, Float::EPSILON)
+      @obj[0, 1] = 'g'
+      assert_in_delta(0.45, @obj.gc_content, Float::EPSILON)
+    end
+
+    def test_at_content
+      assert_in_delta(0.6, @obj.at_content, Float::EPSILON)
+      @obj[0, 1] = 'g'
+      assert_in_delta(0.55, @obj.at_content, Float::EPSILON)
+    end
+
+    def test_gc_skew
+      assert_in_delta(0.0, @obj.gc_skew, Float::EPSILON)
+      @obj[0, 1] = 'g'
+      assert_in_delta(1.0/9.0, @obj.gc_skew, Float::EPSILON)
+      @obj.gsub!(/a/, 'c')
+      assert_in_delta(-3.0/8.0, @obj.gc_skew, Float::EPSILON)
+    end
+
+    def test_at_skew
+      assert_in_delta(1.0/3.0, @obj.at_skew, Float::EPSILON)
+      @obj[0, 1] = 'g'
+      assert_in_delta(3.0/11.0, @obj.at_skew, Float::EPSILON)
+    end
+
     def test_iliegal_bases
       @obj[0, 1] = 'n'
       @obj[1, 1] = 'y'
       assert_equal(['n', 'y'], @obj.illegal_bases)
     end
@@ -113,10 +139,10 @@
       @obj[1,1] = 'n'
       @obj[2,1] = 'r'
       @obj[3,1] = 's'
       @obj[4,1] = 'y'
       @obj[5,1] = 'w'
-      assert_equal(/a[atgc][ag][gc][tc][at]gcatgcatgcaaaa/, @obj.to_re)
+      assert_equal(/a[atgcyrwskmbdhvn][agr][gcw][tcy][atw]gcatgcatgcaaaa/, @obj.to_re)
     end
 
     def test_names
       ary = ["Adenine", "Thymine", "Guanine"]
       assert_equal(ary , @obj.splice("1..3").names)