Merge branch 'features/JAL-2393customMatrices' into develop

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

diff --git a/test/jalview/analysis/scoremodels/ScoreModelsTest.java b/test/jalview/analysis/scoremodels/ScoreModelsTest.java
new file mode 100644 (file)
index 0000000..ffcd1a8
--- /dev/null
+++ b/test/jalview/analysis/scoremodels/ScoreModelsTest.java
@@ -0,0 +1,105 @@
+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;
+
+import org.testng.annotations.Test;
+
+public class ScoreModelsTest
+{
+  /**
+   * Verify that the singleton constructor successfully loads Jalview's built-in
+   * score models
+   */
+  @Test(groups = "Functional")
+  public void testConstructor()
+  {
+    Iterator<ScoreModelI> models = ScoreModels.getInstance().getModels()
+            .iterator();
+    assertTrue(models.hasNext());
+
+    /*
+     * models are served in order of addition
+     */
+    ScoreModelI sm = models.next();
+    assertTrue(sm instanceof SimilarityScoreModel);
+    assertTrue(sm instanceof PairwiseScoreModelI);
+    assertFalse(sm instanceof DistanceScoreModel);
+    assertEquals(sm.getName(), "BLOSUM62");
+    assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('I', 'R'), -3f);
+
+    sm = models.next();
+    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 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();
+    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 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));
+      }
+    }
+  }
+}