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 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)); } } } }