From c6879258ff9ea86c41bd2ce734b8f095fa96a89a Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 24 Feb 2017 15:23:14 +0000 Subject: [PATCH] JAL-2403 PIDModel added (wip) --- src/jalview/analysis/scoremodels/ScoreModels.java | 4 ++-- test/jalview/analysis/scoremodels/ScoreModelsTest.java | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java index 011d8ba..41b99e2 100644 --- a/src/jalview/analysis/scoremodels/ScoreModels.java +++ b/src/jalview/analysis/scoremodels/ScoreModels.java @@ -49,9 +49,9 @@ public class ScoreModels models = new LinkedHashMap(); BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm"); PAM250 = loadScoreMatrix("scoreModel/pam250.scm"); - loadScoreMatrix("scoreModel/seqspace.scm"); + // loadScoreMatrix("scoreModel/seqspace.scm"); // drop seqspace.scm for IdentityScoreModel once JAL-2379 merged in? - // registerScoreModel(new IdentityScoreModel()); + registerScoreModel(new PIDModel()); DNA = loadScoreMatrix("scoreModel/dna.scm"); registerScoreModel(new FeatureDistanceModel()); registerScoreModel(new PIDDistanceModel()); diff --git a/test/jalview/analysis/scoremodels/ScoreModelsTest.java b/test/jalview/analysis/scoremodels/ScoreModelsTest.java index c4c3edb..d70516c 100644 --- a/test/jalview/analysis/scoremodels/ScoreModelsTest.java +++ b/test/jalview/analysis/scoremodels/ScoreModelsTest.java @@ -47,7 +47,7 @@ public class ScoreModelsTest assertTrue(sm instanceof SimilarityScoreModelI); assertTrue(sm instanceof PairwiseScoreModelI); assertFalse(sm instanceof DistanceScoreModelI); - assertEquals(sm.getName(), "Identity (SeqSpace)"); + assertEquals(sm.getName(), "% Identity (PID)"); assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), 0f); assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'r'), 1f); -- 1.7.10.2