TIntArrayList[] alignment = new TIntArrayList[3];
UnorderedMatcherFactory matcherFactory = new UnorderedMatcherFactory();
HSA hsa = new HSA(w, matcherFactory,false);
System.out.println("Cost t-s: " + hsa.computeHSA(t, s, alignment));
for (int i = 0; i < alignment[0].size(); ++i) {
System.out.print("(" + alignment[0].get(i) + ","
+ alignment[1].get(i) + "), ");
}