};
TIntArrayList[] alignment = new TIntArrayList[3];
UnorderedMatcherFactory matcherFactory = new UnorderedMatcherFactory();
HSA hsa = new HSA(w, matcherFactory);
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) + "), ");
}
System.out.println("\nCost s-t: " + hsa.computeHSA(s, t, alignment));
for (int i = 0; i < alignment[0].size(); ++i) {
System.out.print("(" + alignment[0].get(i) + ","
+ alignment[1].get(i) + "), ");
}
System.out.println("\nCost t-t: " + hsa.computeHSA(t, t, alignment));
for (int i = 0; i < alignment[0].size(); ++i) {
System.out.print("(" + alignment[0].get(i) + ","
+ alignment[1].get(i) + "), ");
}
System.out.println("\nCost s-s: " + hsa.computeHSA(s, s, alignment));
for (int i = 0; i < alignment[0].size(); ++i) {
System.out.print("(" + alignment[0].get(i) + ","
+ alignment[1].get(i) + "), ");
}
long start = System.currentTimeMillis();
int iters = 10000;
for (int i = 0; i < iters; ++i) {
hsa.computeHSA(t, s);
}
System.out.println("\nTime of " + iters + " iterations for t-s: "
+ (System.currentTimeMillis() - start));
start = System.currentTimeMillis();
for (int i = 0; i < iters; ++i) {
hsa.computeHSA(s, t);
}
System.out.println("\nTime of " + iters + " iterations for s-t: "
+ (System.currentTimeMillis() - start));
start = System.currentTimeMillis();
for (int i = 0; i < iters; ++i) {
hsa.computeHSA(t, t);
}
System.out.println("\nTime of " + iters + " iterations for t-t: "
+ (System.currentTimeMillis() - start));
start = System.currentTimeMillis();
for (int i = 0; i < iters; ++i) {
hsa.computeHSA(s, s);
}
System.out.println("\nTime of " + iters + " iterations for s-s: "
+ (System.currentTimeMillis() - start));
String flowType;