RNASpecificTree tree = new RNASpecificTree();
tree.buildFromViennaFormat(
"CGACAGGAAACUGACAAACCCUUUCAUCUUAA".toCharArray(),
"...((((...))...(((...)))..))....".toCharArray());
tree.groupByStructure();
try {
tree.toDotFile("/home/milon/tmp/1.dot", true);
} catch (IOException e) {
e.printStackTrace();
}