X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModelsTest.java;h=5e44d3ddadf2278bb83f85f4c1a0c8bff76f773e;hb=2fd148deccb2e939e3ca8780650e813c8a6b4611;hp=03c4b840dbd52c9aaabdeef8e59c5e7b0a5498fd;hpb=6129931bfa23eec90e6556a4d0412ef34aff5759;p=jalview.git

diff --git a/test/jalview/analysis/scoremodels/ScoreModelsTest.java b/test/jalview/analysis/scoremodels/ScoreModelsTest.java
index 03c4b84..5e44d3d 100644
--- a/test/jalview/analysis/scoremodels/ScoreModelsTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreModelsTest.java
@@ -4,6 +4,7 @@ import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.analysis.PairwiseScoreModelI;
 import jalview.api.analysis.ScoreModelI;
 
 import java.util.Iterator;
@@ -16,7 +17,7 @@ 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()
@@ -24,31 +25,81 @@ public class ScoreModelsTest
     assertTrue(models.hasNext());
 
     /*
-     * models are served in alphabetical order of name
-     * it so happens the 3 ScoreMatrix models precede the two
-     * others
+     * models are served in order of addition
      */
     ScoreModelI sm = models.next();
-    assertTrue(sm instanceof ScoreMatrix);
+    assertTrue(sm instanceof SimilarityScoreModel);
+    assertTrue(sm instanceof PairwiseScoreModelI);
+    assertFalse(sm instanceof DistanceScoreModel);
     assertEquals(sm.getName(), "BLOSUM62");
-    assertEquals(((ScoreMatrix) sm).getPairwiseScore('I', 'R'), -3f);
+    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('I', 'R'), -3f);
 
     sm = models.next();
-    assertTrue(sm instanceof ScoreMatrix);
-    assertEquals(sm.getName(), "DNA");
-    assertEquals(((ScoreMatrix) sm).getPairwiseScore('c', 'x'), 1f);
+    assertTrue(sm instanceof SimilarityScoreModel);
+    assertTrue(sm instanceof PairwiseScoreModelI);
+    assertFalse(sm instanceof DistanceScoreModel);
+    assertEquals(sm.getName(), "PAM250");
+    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), -4f);
 
     sm = models.next();
-    assertTrue(sm instanceof ScoreMatrix);
-    assertEquals(sm.getName(), "PAM250");
-    assertEquals(((ScoreMatrix) sm).getPairwiseScore('R', 'C'), -4f);
+    assertTrue(sm instanceof SimilarityScoreModel);
+    assertTrue(sm instanceof PairwiseScoreModelI);
+    assertFalse(sm instanceof DistanceScoreModel);
+    assertEquals(sm.getName(), "DNA");
+    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('c', 'x'), 1f);
 
     sm = models.next();
-    assertFalse(sm instanceof ScoreMatrix);
+    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 ScoreMatrix);
+    assertFalse(sm instanceof SimilarityScoreModel);
+    assertFalse(sm instanceof PairwiseScoreModelI);
+    assertTrue(sm instanceof DistanceScoreModel);
     assertEquals(sm.getName(), "Sequence Feature Similarity");
   }
+
+  /**
+   * 'Test' that prints out score matrices in tab-delimited format. This test is
+   * intentionally not assigned to any group so would not be run as part of a
+   * suite. It makes no assertions and is just provided as a utility method for
+   * printing out matrices. Relocated here from ScoreMatrixPrinter.
+   */
+  @Test(groups = "none")
+  public void printAllMatrices_tabDelimited()
+  {
+    printAllMatrices(false);
+  }
+
+  /**
+   * 'Test' that prints out score matrices in html format. This test is
+   * intentionally not assigned to any group so would not be run as part of a
+   * suite. It makes no assertions and is just provided as a utility method for
+   * printing out matrices. Relocated here from ScoreMatrixPrinter.
+   */
+  @Test(groups = "none")
+  public void printAllMatrices_asHtml()
+  {
+    printAllMatrices(true);
+  }
+
+  /**
+   * Print all registered ScoreMatrix as plain or html tables
+   * 
+   * @param asHtml
+   */
+  protected void printAllMatrices(boolean asHtml)
+  {
+    for (ScoreModelI sm : ScoreModels.getInstance().getModels())
+    {
+      if (sm instanceof ScoreMatrix)
+      {
+        System.out.println(((ScoreMatrix) sm).outputMatrix(asHtml));
+      }
+    }
+  }
 }