From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 24 Feb 2017 15:23:14 +0000 (+0000)
Subject: JAL-2403 PIDModel added (wip)
X-Git-Tag: Release_2_10_2~3^2~105^2~2^2~86
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c6879258ff9ea86c41bd2ce734b8f095fa96a89a;p=jalview.git

JAL-2403 PIDModel added (wip)
---

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<String, ScoreModelI>();
     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);