X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModelsTest.java;h=0a3af64477fdb2616d0ece971da7c236d7c7ea1f;hb=e9a1c2c372f4bbf6cf658de3dba73ef326b20c20;hp=d70516c19bd398fb49be9d77ededdb6598e01ca1;hpb=c6879258ff9ea86c41bd2ce734b8f095fa96a89a;p=jalview.git

diff --git a/test/jalview/analysis/scoremodels/ScoreModelsTest.java b/test/jalview/analysis/scoremodels/ScoreModelsTest.java
index d70516c..0a3af64 100644
--- a/test/jalview/analysis/scoremodels/ScoreModelsTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreModelsTest.java
@@ -1,13 +1,31 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.analysis.scoremodels;
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertTrue;
 
-import jalview.api.analysis.DistanceScoreModelI;
 import jalview.api.analysis.PairwiseScoreModelI;
 import jalview.api.analysis.ScoreModelI;
-import jalview.api.analysis.SimilarityScoreModelI;
 
 import java.util.Iterator;
 
@@ -19,7 +37,7 @@ public class ScoreModelsTest
    * Verify that the singleton constructor successfully loads Jalview's built-in
    * score models
    */
-  @Test
+  @Test(groups = "Functional")
   public void testConstructor()
   {
     Iterator<ScoreModelI> models = ScoreModels.getInstance().getModels()
@@ -30,45 +48,41 @@ public class ScoreModelsTest
      * models are served in order of addition
      */
     ScoreModelI sm = models.next();
-    assertTrue(sm instanceof SimilarityScoreModelI);
+    assertTrue(sm instanceof SimilarityScoreModel);
     assertTrue(sm instanceof PairwiseScoreModelI);
-    assertFalse(sm instanceof DistanceScoreModelI);
+    assertFalse(sm instanceof DistanceScoreModel);
     assertEquals(sm.getName(), "BLOSUM62");
-    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('I', 'R'), -3f);
+    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('I', 'R'),
+            -3f);
 
     sm = models.next();
-    assertTrue(sm instanceof SimilarityScoreModelI);
+    assertTrue(sm instanceof SimilarityScoreModel);
     assertTrue(sm instanceof PairwiseScoreModelI);
-    assertFalse(sm instanceof DistanceScoreModelI);
+    assertFalse(sm instanceof DistanceScoreModel);
     assertEquals(sm.getName(), "PAM250");
-    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), -4f);
+    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'),
+            -4f);
 
     sm = models.next();
-    assertTrue(sm instanceof SimilarityScoreModelI);
+    assertTrue(sm instanceof SimilarityScoreModel);
     assertTrue(sm instanceof PairwiseScoreModelI);
-    assertFalse(sm instanceof DistanceScoreModelI);
-    assertEquals(sm.getName(), "% Identity (PID)");
-    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), 0f);
-    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'r'), 1f);
-
-    sm = models.next();
-    assertTrue(sm instanceof SimilarityScoreModelI);
-    assertTrue(sm instanceof PairwiseScoreModelI);
-    assertFalse(sm instanceof DistanceScoreModelI);
+    assertFalse(sm instanceof DistanceScoreModel);
     assertEquals(sm.getName(), "DNA");
     assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('c', 'x'), 1f);
 
     sm = models.next();
-    assertFalse(sm instanceof SimilarityScoreModelI);
-    assertFalse(sm instanceof PairwiseScoreModelI);
-    assertTrue(sm instanceof DistanceScoreModelI);
-    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 SimilarityScoreModelI);
+    assertFalse(sm instanceof SimilarityScoreModel);
     assertFalse(sm instanceof PairwiseScoreModelI);
-    assertTrue(sm instanceof DistanceScoreModelI);
-    assertEquals(sm.getName(), "PID");
+    assertTrue(sm instanceof DistanceScoreModel);
+    assertEquals(sm.getName(), "Sequence Feature Similarity");
   }
 
   /**
@@ -77,7 +91,7 @@ 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);
@@ -89,7 +103,7 @@ 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);