test/unit/bio/test_alignment.rb in bio-0.7.1 vs test/unit/bio/test_alignment.rb in bio-1.0.0

@@ -16,11 +16,11 @@
 #
 #  You should have received a copy of the GNU Lesser General Public
 #  License along with this library; if not, write to the Free Software
 #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
 #
-#  $Id: test_alignment.rb,v 1.6 2005/12/02 13:01:49 ngoto Exp $
+#  $Id: test_alignment.rb,v 1.7 2006/01/24 14:11:34 ngoto Exp $
 #
 
 require 'pathname'
 libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
 $:.unshift(libpath) unless $:.include?(libpath)
@@ -517,15 +517,23 @@
       assert_equal(Alignment::SequenceArray[ '', 't', 'tgc', 'tg', nil ],
                    a.alignment_slice(1, 3))
     end
 
     def test_alignment_subseq
-      a = A[ Sequence.new('a'), Sequence.new('at'), Sequence.new('atgca'),
-        Sequence.new('atg'), Sequence.new('') ]
-      assert_equal(Alignment::SequenceArray[ Sequence.new(''),
-                     Sequence.new('t'), Sequence.new('tgc'),
-                     Sequence.new('tg'), nil ],
-                   a.alignment_subseq(2,4))
+      a = A[
+        Sequence::NA.new('a'),
+        Sequence::NA.new('at'),
+        Sequence::NA.new('atgca'),
+        Sequence::NA.new('atg'),
+        Sequence::NA.new('')
+      ]
+      assert_equal(Alignment::SequenceArray[
+                     Sequence::NA.new(''),
+                     Sequence::NA.new('t'),
+                     Sequence::NA.new('tgc'),
+                     Sequence::NA.new('tg'),
+                     nil
+                   ], a.alignment_subseq(2,4))
     end
 
     def test_alignment_concat
       a = A[ 'aaa',  'c', 'gg', 't' ]
       a.alignment_concat(A[ 'ttt', 'gg', 'aa', 'cc', 'aa' ])