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;
* 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 SimilarityScoreModelI);
+ assertTrue(sm instanceof SimilarityScoreModel);
assertTrue(sm instanceof PairwiseScoreModelI);
- assertFalse(sm instanceof DistanceScoreModelI);
+ assertFalse(sm instanceof DistanceScoreModel);
assertEquals(sm.getName(), "BLOSUM62");
assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('I', 'R'), -3f);
sm = models.next();
- assertTrue(sm instanceof SimilarityScoreModelI);
+ assertTrue(sm instanceof SimilarityScoreModel);
assertTrue(sm instanceof PairwiseScoreModelI);
- assertFalse(sm instanceof DistanceScoreModelI);
+ assertFalse(sm instanceof DistanceScoreModel);
assertEquals(sm.getName(), "PAM250");
assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), -4f);
sm = models.next();
- assertTrue(sm instanceof SimilarityScoreModelI);
+ assertTrue(sm instanceof SimilarityScoreModel);
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 SimilarityScoreModelI);
- assertTrue(sm instanceof PairwiseScoreModelI);
- assertFalse(sm instanceof DistanceScoreModelI);
+ assertFalse(sm instanceof DistanceScoreModel);
assertEquals(sm.getName(), "DNA");
assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('c', 'x'), 1f);
sm = models.next();
- assertFalse(sm instanceof SimilarityScoreModelI);
- assertFalse(sm instanceof PairwiseScoreModelI);
- assertTrue(sm instanceof DistanceScoreModelI);
- assertEquals(sm.getName(), "Sequence Feature Similarity");
+ 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 SimilarityScoreModelI);
+ assertFalse(sm instanceof SimilarityScoreModel);
assertFalse(sm instanceof PairwiseScoreModelI);
- assertTrue(sm instanceof DistanceScoreModelI);
- assertEquals(sm.getName(), "PID");
+ assertTrue(sm instanceof DistanceScoreModel);
+ assertEquals(sm.getName(), "Sequence Feature Similarity");
}
/**
* suite. It makes no assertions and is just provided as a utility method for
* printing out matrices. Relocated here from ScoreMatrixPrinter.
*/
- @Test
+ @Test(groups = "none")
public void printAllMatrices_tabDelimited()
{
printAllMatrices(false);
* suite. It makes no assertions and is just provided as a utility method for
* printing out matrices. Relocated here from ScoreMatrixPrinter.
*/
- @Test
+ @Test(groups = "none")
public void printAllMatrices_asHtml()
{
printAllMatrices(true);