BufferedWriter seedWriter =
new BufferedWriter(new FileWriter(graphOutputFile + ".seed_vertices"));
RyanAlphabet alpha = new RyanAlphabet();
// we would like to avoid 0 as the index
alpha.lookupIndex("", true);
Iterator<String> vIter = _vertices.keySet().iterator();
while (vIter.hasNext()) {
String vName = vIter.next();
int vIdx = alpha.lookupIndex(vName, true);