X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModelsTest.java;h=d70516c19bd398fb49be9d77ededdb6598e01ca1;hb=8717834368bd00d8adfa47ee099288acd34363ef;hp=2ebbe5c72562fa9c12ccab400b2c169783459811;hpb=3b42127c52b4e7c7fa3b11948db8b5cc9a8a3721;p=jalview.git

diff --git a/test/jalview/analysis/scoremodels/ScoreModelsTest.java b/test/jalview/analysis/scoremodels/ScoreModelsTest.java
index 2ebbe5c..d70516c 100644
--- a/test/jalview/analysis/scoremodels/ScoreModelsTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreModelsTest.java
@@ -4,7 +4,10 @@ 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;
 
@@ -27,32 +30,84 @@ public class ScoreModelsTest
      * models are served in order of addition
      */
     ScoreModelI sm = models.next();
-    assertTrue(sm instanceof ScoreMatrix);
+    assertTrue(sm instanceof SimilarityScoreModelI);
+    assertTrue(sm instanceof PairwiseScoreModelI);
+    assertFalse(sm instanceof DistanceScoreModelI);
     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);
+    assertTrue(sm instanceof SimilarityScoreModelI);
+    assertTrue(sm instanceof PairwiseScoreModelI);
+    assertFalse(sm instanceof DistanceScoreModelI);
     assertEquals(sm.getName(), "PAM250");
-    assertEquals(((ScoreMatrix) sm).getPairwiseScore('R', 'C'), -4f);
+    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), -4f);
 
     sm = models.next();
-    assertTrue(sm instanceof ScoreMatrix);
-    assertEquals(sm.getName(), "Identity (SeqSpace)");
-    assertEquals(((ScoreMatrix) sm).getPairwiseScore('R', 'C'), 0f);
-    assertEquals(((ScoreMatrix) sm).getPairwiseScore('R', 'r'), 1f);
+    assertTrue(sm instanceof SimilarityScoreModelI);
+    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 ScoreMatrix);
+    assertTrue(sm instanceof SimilarityScoreModelI);
+    assertTrue(sm instanceof PairwiseScoreModelI);
+    assertFalse(sm instanceof DistanceScoreModelI);
     assertEquals(sm.getName(), "DNA");
-    assertEquals(((ScoreMatrix) sm).getPairwiseScore('c', 'x'), 1f);
+    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('c', 'x'), 1f);
 
     sm = models.next();
-    assertFalse(sm instanceof ScoreMatrix);
+    assertFalse(sm instanceof SimilarityScoreModelI);
+    assertFalse(sm instanceof PairwiseScoreModelI);
+    assertTrue(sm instanceof DistanceScoreModelI);
     assertEquals(sm.getName(), "Sequence Feature Similarity");
 
     sm = models.next();
-    assertFalse(sm instanceof ScoreMatrix);
+    assertFalse(sm instanceof SimilarityScoreModelI);
+    assertFalse(sm instanceof PairwiseScoreModelI);
+    assertTrue(sm instanceof DistanceScoreModelI);
     assertEquals(sm.getName(), "PID");
   }
+
+  /**
+   * '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
+  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
+  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));
+      }
+    }
+  }
 }