Merge remote-tracking branch 'origin/tasks/JAL-3035_remove_dasobert_dependency' into...

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

diff --git a/test/jalview/analysis/scoremodels/ScoreModelsTest.java b/test/jalview/analysis/scoremodels/ScoreModelsTest.java
index f63843d..5e44d3d 100644 (file)
--- a/test/jalview/analysis/scoremodels/ScoreModelsTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreModelsTest.java
@@ -4,7 +4,8 @@ import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertTrue;
 
-import jalview.api.analysis.DistanceModelI;
+import jalview.api.analysis.PairwiseScoreModelI;
+import jalview.api.analysis.ScoreModelI;
 
 import java.util.Iterator;
 
@@ -16,49 +17,50 @@ public class ScoreModelsTest
    * Verify that the singleton constructor successfully loads Jalview's built-in
    * score models
    */
-  @Test
+  @Test(groups = "Functional")
   public void testConstructor()
   {
-    Iterator<DistanceModelI> models = ScoreModels.getInstance().getModels()
+    Iterator<ScoreModelI> models = ScoreModels.getInstance().getModels()
             .iterator();
     assertTrue(models.hasNext());
 
     /*
      * models are served in order of addition
      */
-    DistanceModelI sm = models.next();
-    assertTrue(sm instanceof PairwiseDistanceModel);
+    ScoreModelI sm = models.next();
+    assertTrue(sm instanceof SimilarityScoreModel);
+    assertTrue(sm instanceof PairwiseScoreModelI);
+    assertFalse(sm instanceof DistanceScoreModel);
     assertEquals(sm.getName(), "BLOSUM62");
-    assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
-            .getPairwiseScore('I', 'R'), -3f);
+    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('I', 'R'), -3f);
 
     sm = models.next();
-    assertTrue(sm instanceof PairwiseDistanceModel);
+    assertTrue(sm instanceof SimilarityScoreModel);
+    assertTrue(sm instanceof PairwiseScoreModelI);
+    assertFalse(sm instanceof DistanceScoreModel);
     assertEquals(sm.getName(), "PAM250");
-    assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
-            .getPairwiseScore('R', 'C'), -4f);
+    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), -4f);
 
     sm = models.next();
-    assertTrue(sm instanceof PairwiseDistanceModel);
-    assertEquals(sm.getName(), "Identity (SeqSpace)");
-    assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
-            .getPairwiseScore('R', 'C'), 0f);
-    assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
-            .getPairwiseScore('R', 'r'), 1f);
-
-    sm = models.next();
-    assertTrue(sm instanceof PairwiseDistanceModel);
+    assertTrue(sm instanceof SimilarityScoreModel);
+    assertTrue(sm instanceof PairwiseScoreModelI);
+    assertFalse(sm instanceof DistanceScoreModel);
     assertEquals(sm.getName(), "DNA");
-    assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
-            .getPairwiseScore('c', 'x'), 1f);
+    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('c', 'x'), 1f);
 
     sm = models.next();
-    assertFalse(sm instanceof PairwiseDistanceModel);
-    assertEquals(sm.getName(), "Sequence Feature Similarity");
+    assertTrue(sm instanceof SimilarityScoreModel);
+    assertTrue(sm instanceof PairwiseScoreModelI);
+    assertFalse(sm instanceof DistanceScoreModel);
+    assertEquals(sm.getName(), "PID");
+    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), 0f);
+    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'r'), 1f);
 
     sm = models.next();
-    assertFalse(sm instanceof PairwiseDistanceModel);
-    assertEquals(sm.getName(), "PID");
+    assertFalse(sm instanceof SimilarityScoreModel);
+    assertFalse(sm instanceof PairwiseScoreModelI);
+    assertTrue(sm instanceof DistanceScoreModel);
+    assertEquals(sm.getName(), "Sequence Feature Similarity");
   }
 
   /**
@@ -67,7 +69,7 @@ public class ScoreModelsTest
    * suite. It makes no assertions and is just provided as a utility method for
    * printing out matrices. Relocated here from ScoreMatrixPrinter.
    */
-  @Test
+  @Test(groups = "none")
   public void printAllMatrices_tabDelimited()
   {
     printAllMatrices(false);
@@ -79,7 +81,7 @@ public class ScoreModelsTest
    * suite. It makes no assertions and is just provided as a utility method for
    * printing out matrices. Relocated here from ScoreMatrixPrinter.
    */
-  @Test
+  @Test(groups = "none")
   public void printAllMatrices_asHtml()
   {
     printAllMatrices(true);
@@ -92,18 +94,11 @@ public class ScoreModelsTest
    */
   protected void printAllMatrices(boolean asHtml)
   {
-    for (DistanceModelI dm : ScoreModels.getInstance().getModels())
+    for (ScoreModelI sm : ScoreModels.getInstance().getModels())
     {
-      if (dm instanceof PairwiseDistanceModel)
+      if (sm instanceof ScoreMatrix)
       {
-        PairwiseScoreModelI psm = ((PairwiseDistanceModel) dm)
-                .getScoreModel();
-        if (psm instanceof ScoreMatrix)
-        {
-          ScoreMatrix sm = (ScoreMatrix) psm;
-          System.out.println("ScoreMatrix " + sm.getName());
-          System.out.println(sm.outputMatrix(asHtml));
-        }
+        System.out.println(((ScoreMatrix) sm).outputMatrix(asHtml));
       }
     }
   }