} catch (IOException e) {
e.printStackTrace();
}
for (int t = 0; t < tree.getNodeNum(); t++) {
int deg = tree.outDeg(t);
RNANodeLabel tLabel = (RNANodeLabel) tree.getLabel(t);
for (int d = 0; d < deg; d++) {
int v = tree.getNeighbor(t, d);
RNANodeLabel vLabel = (RNANodeLabel) tree.getLabel(v);
if ((tLabel.getType() == RNANodeLabel.BASE_PAIR && vLabel