+
+ @Test(groups = { "Functional" })
+ public void testGetContactMap()
+ {
+ // TODO
+ // 1. test adding/removing/manipulating contact maps with/without associated
+ // sequence(s) or groups
+ // 2. For sequence associated - ensure that inserting a gap in sequence
+ // results in the contact map being relocated accordingly
+ // 3. RENDERER QUESTION - should contact maps reflect gaps in the alignment
+ // ?
+
+ }
+ @Test(groups = {"Functional"})
+ public void testEquals()
+ {
+ SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+ SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+ SequenceI seq3 = new Sequence("seq2", "-PQR");
+ AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+ a.setDataset(null);
+ assertEquals(a.getDataset(),a.getDataset());
+ }