JAL-2515 Id panel in applet updated for NPE on urlProvider

[jalview.git] / test / jalview / analysis / scoremodels / FeatureDistanceModelTest.java

diff --git a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
index 02e64b6..0577fae 100644 (file)
--- a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
@@ -264,11 +264,9 @@ public class FeatureDistanceModelTest
     assertEquals(distances.getValue(0, 0), 0d);
     assertEquals(distances.getValue(1, 1), 0d);
 
-    // these left to fail pending resolution of
-    // JAL-2424 (computing score as 5/6, should be 5/5)
-    // see also PCATest.testComputeSimilarity_featureDistances()
-    assertEquals(distances.getValue(0, 1), 1f, "JAL-2424!");
-    assertEquals(distances.getValue(1, 0), 1f);
+    assertEquals(distances.getValue(0, 1), 1d,
+            "expected identical pairs. (check normalisation for similarity score)");
+    assertEquals(distances.getValue(1, 0), 1d);
   }
 
   /**
@@ -293,23 +291,21 @@ public class FeatureDistanceModelTest
     /*
      * include gaps
      * score = 3 + 3 + 0 + 2 + 3 + 2 = 13/6
-    // FIXME out by 1 error in cpwidth JAL-2424 - dividing by 7
      */
     SimilarityParamsI params = new SimilarityParams(true, true, true, true);
     MatrixI distances = sm.findDistances(view, params);
     assertEquals(distances.getValue(0, 0), 0d);
     assertEquals(distances.getValue(1, 1), 0d);
-    assertEquals(distances.getValue(0, 1), 13d / 7); // should be 13d/6
-    assertEquals(distances.getValue(1, 0), 13d / 7);
+    assertEquals(distances.getValue(0, 1), 13d / 6); // should be 13d/6
+    assertEquals(distances.getValue(1, 0), 13d / 6);
   
     /*
      * exclude gaps
      * score = 3 + 3 + 0 + 0 + 0 + 0 = 6/6
-    // FIXME out by 1 error in cpwidth JAL-2424 - dividing by 7
      */
     params = new SimilarityParams(true, true, false, true);
     distances = sm.findDistances(view, params);
-    assertEquals(distances.getValue(0, 1), 6d / 7);// should be 6d/6
+    assertEquals(distances.getValue(0, 1), 6d / 6);// should be 6d/6
   }
 
   /**