verifyPAEmatrix(seq, aa, 0, 0, 4);
// test clustering
- paematrix.setGroupSet(GroupSet.makeGroups(paematrix, 0.1f, false));
+ paematrix.setGroupSet(GroupSet.makeGroups(paematrix, false,0.1f, false));
// remap - test the MappableContactMatrix.liftOver method
SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");