- 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);
assertEquals(PIDModel.computePID(s1, s2, params), 500d / 6);
assertEquals(PIDModel.computePID(s2, s1, params), 500d / 6);
params = new SimilarityParams(false, true, true, false);
assertEquals(PIDModel.computePID(s1, s2, params), 80d);
assertEquals(PIDModel.computePID(s2, s1, params), 80d);
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
/*
* 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);
params = new SimilarityParams(true, false, true, false);
assertEquals(PIDModel.computePID(s1, s2, params), 100d / 3);
assertEquals(PIDModel.computePID(s2, s1, params), 100d / 3);