+ /**
+ * test the contact matrix nogroups property methods
+ */
+ @Test(groups= {"Functional"})
+ public void test_contactMatrixGroups()
+ {
+ AlignmentAnnotation aa = new AlignmentAnnotation("foo","foo desc",null);
+ assertTrue(aa.isShowGroupsForContactMatrix());
+ aa.setShowGroupsForContactMatrix(false);
+ assertFalse(aa.isShowGroupsForContactMatrix());
+ AlignmentAnnotation copy = new AlignmentAnnotation(aa);
+ assertFalse(copy.isShowGroupsForContactMatrix());
+ aa.setShowGroupsForContactMatrix(true);
+ assertTrue(aa.isShowGroupsForContactMatrix());
+ // copy should not be updated
+ assertFalse(copy.isShowGroupsForContactMatrix());
+
+
+ }