+
+ // test to see if consensus sequence maps to alignment correctly
+ // see HMMAlignmentTest.sto for corresponding alignment file
+ SequenceI seq2 = alignmentHmm.getConsensusSequence();
+ assertEquals(seq2.getCharAt(0), '-');
+ assertEquals(seq2.getCharAt(7), '-');
+ assertEquals(seq2.getCharAt(8), 's');
+