sq.getLength(), sq.getLength());
assertEquals(vals[3][4], paevals[3][4]);
assertEquals(vals[4][3], paevals[4][3]);
- dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, 0.5f, false));
+ dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, false,0.5f, false));
Assert.assertNotSame(dummyMat.getNewick(), "");
AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
al.addAnnotation(paeCm);