import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertTrue;
-import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.DistanceModelI;
import java.util.Iterator;
@Test
public void testConstructor()
{
- Iterator<ScoreModelI> models = ScoreModels.getInstance().getModels()
+ Iterator<DistanceModelI> models = ScoreModels.getInstance().getModels()
.iterator();
assertTrue(models.hasNext());
/*
* models are served in order of addition
*/
- ScoreModelI sm = models.next();
- assertTrue(sm instanceof ScoreMatrix);
+ DistanceModelI sm = models.next();
+ assertTrue(sm instanceof PairwiseDistanceModel);
assertEquals(sm.getName(), "BLOSUM62");
- assertEquals(((ScoreMatrix) sm).getPairwiseScore('I', 'R'), -3f);
+ assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
+ .getPairwiseScore('I', 'R'), -3f);
sm = models.next();
- assertTrue(sm instanceof ScoreMatrix);
+ assertTrue(sm instanceof PairwiseDistanceModel);
assertEquals(sm.getName(), "PAM250");
- assertEquals(((ScoreMatrix) sm).getPairwiseScore('R', 'C'), -4f);
+ assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
+ .getPairwiseScore('R', 'C'), -4f);
sm = models.next();
- assertTrue(sm instanceof ScoreMatrix);
+ assertTrue(sm instanceof PairwiseDistanceModel);
assertEquals(sm.getName(), "Identity (SeqSpace)");
- assertEquals(((ScoreMatrix) sm).getPairwiseScore('R', 'C'), 0f);
- assertEquals(((ScoreMatrix) sm).getPairwiseScore('R', 'r'), 1f);
+ assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
+ .getPairwiseScore('R', 'C'), 0f);
+ assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
+ .getPairwiseScore('R', 'r'), 1f);
sm = models.next();
- assertTrue(sm instanceof ScoreMatrix);
+ assertTrue(sm instanceof PairwiseDistanceModel);
assertEquals(sm.getName(), "DNA");
- assertEquals(((ScoreMatrix) sm).getPairwiseScore('c', 'x'), 1f);
+ assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
+ .getPairwiseScore('c', 'x'), 1f);
sm = models.next();
- assertFalse(sm instanceof ScoreMatrix);
+ assertFalse(sm instanceof PairwiseDistanceModel);
assertEquals(sm.getName(), "Sequence Feature Similarity");
sm = models.next();
- assertFalse(sm instanceof ScoreMatrix);
+ assertFalse(sm instanceof PairwiseDistanceModel);
assertEquals(sm.getName(), "PID");
}
}