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