X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModelsTest.java;h=c5c8673865b7563543dbfdf60abbafb26a50906f;hb=fcb39fa3bc47777bf4e0eb209f765dd254dc3cb9;hp=2ebbe5c72562fa9c12ccab400b2c169783459811;hpb=69b6e688c0a87bffc1fc7ae970fa0f8cd2976007;p=jalview.git

diff --git a/test/jalview/analysis/scoremodels/ScoreModelsTest.java b/test/jalview/analysis/scoremodels/ScoreModelsTest.java
index 2ebbe5c..c5c8673 100644
--- a/test/jalview/analysis/scoremodels/ScoreModelsTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreModelsTest.java
@@ -4,7 +4,7 @@ import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertTrue;
 
-import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.DistanceModelI;
 
 import java.util.Iterator;
 
@@ -19,40 +19,45 @@ public class ScoreModelsTest
   @Test
   public void testConstructor()
   {
-    Iterator<ScoreModelI> models = ScoreModels.getInstance().getModels()
+    Iterator<DistanceModelI> models = ScoreModels.getInstance().getModels()
             .iterator();
     assertTrue(models.hasNext());
 
     /*
      * models are served in order of addition
      */
-    ScoreModelI sm = models.next();
-    assertTrue(sm instanceof ScoreMatrix);
+    DistanceModelI sm = models.next();
+    assertTrue(sm instanceof PairwiseDistanceModel);
     assertEquals(sm.getName(), "BLOSUM62");
-    assertEquals(((ScoreMatrix) sm).getPairwiseScore('I', 'R'), -3f);
+    assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
+            .getPairwiseScore('I', 'R'), -3f);
 
     sm = models.next();
-    assertTrue(sm instanceof ScoreMatrix);
+    assertTrue(sm instanceof PairwiseDistanceModel);
     assertEquals(sm.getName(), "PAM250");
-    assertEquals(((ScoreMatrix) sm).getPairwiseScore('R', 'C'), -4f);
+    assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
+            .getPairwiseScore('R', 'C'), -4f);
 
     sm = models.next();
-    assertTrue(sm instanceof ScoreMatrix);
+    assertTrue(sm instanceof PairwiseDistanceModel);
     assertEquals(sm.getName(), "Identity (SeqSpace)");
-    assertEquals(((ScoreMatrix) sm).getPairwiseScore('R', 'C'), 0f);
-    assertEquals(((ScoreMatrix) sm).getPairwiseScore('R', 'r'), 1f);
+    assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
+            .getPairwiseScore('R', 'C'), 0f);
+    assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
+            .getPairwiseScore('R', 'r'), 1f);
 
     sm = models.next();
-    assertTrue(sm instanceof ScoreMatrix);
+    assertTrue(sm instanceof PairwiseDistanceModel);
     assertEquals(sm.getName(), "DNA");
-    assertEquals(((ScoreMatrix) sm).getPairwiseScore('c', 'x'), 1f);
+    assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
+            .getPairwiseScore('c', 'x'), 1f);
 
     sm = models.next();
-    assertFalse(sm instanceof ScoreMatrix);
+    assertFalse(sm instanceof PairwiseDistanceModel);
     assertEquals(sm.getName(), "Sequence Feature Similarity");
 
     sm = models.next();
-    assertFalse(sm instanceof ScoreMatrix);
+    assertFalse(sm instanceof PairwiseDistanceModel);
     assertEquals(sm.getName(), "PID");
   }
 }