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;
* 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()
* 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);
+ assertTrue(sm instanceof SimilarityScoreModel);
+ assertTrue(sm instanceof PairwiseScoreModelI);
+ assertFalse(sm instanceof DistanceScoreModel);
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 SimilarityScoreModel);
+ assertTrue(sm instanceof PairwiseScoreModelI);
+ assertFalse(sm instanceof DistanceScoreModel);
+ assertEquals(sm.getName(), "DNA");
+ assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('c', 'x'), 1f);
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(), "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");
+ }
- sm = models.next();
- assertFalse(sm instanceof ScoreMatrix);
- 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(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));
+ }
+ }
}
}