{
String s1 = "FR-K-S";
String s2 = "FS--L";
-
+
/*
* match gap-gap and gap-char
* shorter sequence treated as if with trailing gaps
* PID = 5/6 = 83.333...%
*/
- SimilarityParamsI params = new SimilarityParams(true, true, true, false);
+ SimilarityParamsI params = new SimilarityParams(true, true, true,
+ false);
assertEquals(PIDModel.computePID(s1, s2, params), 500d / 6);
assertEquals(PIDModel.computePID(s2, s1, params), 500d / 6);
-
+
/*
* match gap-char but not gap-gap
* PID = 4/5 = 80%
params = new SimilarityParams(false, true, true, false);
assertEquals(PIDModel.computePID(s1, s2, params), 80d);
assertEquals(PIDModel.computePID(s2, s1, params), 80d);
-
+
/*
* include gaps but don't match them
* include gap-gap, counted as identity
params = new SimilarityParams(true, false, true, false);
assertEquals(PIDModel.computePID(s1, s2, params), 100d / 3);
assertEquals(PIDModel.computePID(s2, s1, params), 100d / 3);
-
+
/*
* include gaps but don't match them
* exclude gap-gap