Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[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 03c4b84..0a3af64 100644 (file)
--- a/test/jalview/analysis/scoremodels/ScoreModelsTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreModelsTest.java
@@ -1,9 +1,30 @@
+/*
+ * 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.PairwiseScoreModelI;
 import jalview.api.analysis.ScoreModelI;
 
 import java.util.Iterator;
@@ -16,7 +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()
@@ -24,31 +45,83 @@ 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));
+      }
+    }
+  }
 }