Did not realized I was incorrectly computing comparison time...Crap.

src/main/java/weka/finito/utils/shared.java

@@ -127,7 +127,7 @@ public static boolean compare(NodeInfo ld, int comparisonType,
  HashMap<String, BigIntegers> encrypted_features, alice Niu)
  throws ClassNotFoundException, HomomorphicException, IOException {
 
- long start_time = System.nanoTime();
+ boolean answer;
 
  BigIntegers encrypted_values = encrypted_features.get(ld.variable_name);
  BigInteger encrypted_client_value = null;
@@ -147,18 +147,19 @@ else if ((comparisonType == 3) || (comparisonType == 5)) {
  Niu.setDGKMode(true);
  }
  assert encrypted_client_value != null;
- long stop_time = System.nanoTime();
-
- double run_time = (double) (stop_time - start_time);
- run_time = run_time / 1000000;
- System.out.printf("Comparison took %f ms\n", run_time);
+ long start_time = System.nanoTime();
  if (((comparisonType == 1) && (ld.threshold == 0))
  || (comparisonType == 4) || (comparisonType == 5)) {
- return Niu.Protocol2(encrypted_thresh, encrypted_client_value);
+ answer = Niu.Protocol2(encrypted_thresh, encrypted_client_value);
  }
  else {
- return Niu.Protocol2(encrypted_client_value, encrypted_thresh);
+ answer = Niu.Protocol2(encrypted_client_value, encrypted_thresh);
  }
+ long stop_time = System.nanoTime();
+ double run_time = (double) (stop_time - start_time);
+ run_time = run_time / 1000000;
+ System.out.printf("Comparison took %f ms\n", run_time);
+ return answer;
  }
 
  public static void closeConnection(ObjectOutputStream oos,