--- /dev/null
+package jalview.analysis.scoremodels;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.util.Comparison;
+
+import org.testng.annotations.Test;
+
+public class PIDModelTest
+{
+ private static final double DELTA = 0.00001D;
+
+ @Test(groups = "Functional")
+ public void testGetPairwiseScore()
+ {
+ PIDModel sm = new PIDModel();
+ assertEquals(sm.getPairwiseScore('A', 'A'), 1f);
+ assertEquals(sm.getPairwiseScore('A', 'a'), 1f);
+ assertEquals(sm.getPairwiseScore('a', 'A'), 1f);
+ assertEquals(sm.getPairwiseScore('A', 'B'), 0f);
+ assertEquals(sm.getPairwiseScore('A', ' '), 0f);
+ assertEquals(sm.getPairwiseScore(' ', ' '), 0f);
+ assertEquals(sm.getPairwiseScore('.', '.'), 0f);
+ assertEquals(sm.getPairwiseScore('-', '-'), 0f);
+ }
+
+ /**
+ * Regression test to verify that a (suitably configured) PIDModel computes
+ * the same percentage identities as the Comparison.PID method
+ */
+ @Test(groups = "Functional")
+ public void testComputePID_matchesComparisonPID()
+ {
+ /*
+ * same length, no gaps
+ */
+ String s1 = "ARFNQDWSGI";
+ String s2 = "ARKNQDQSGI";
+ double newScore = new PIDModel().computePID(s1, s2,
+ SimilarityParams.Jalview);
+ double oldScore = Comparison.PID(s1, s2);
+ assertEquals(newScore, oldScore, DELTA);
+
+ /*
+ * same length, with gaps
+ */
+ s1 = "-RFNQDWSGI";
+ s2 = "ARKNQ-QSGI";
+ newScore = new PIDModel().computePID(s1, s2,
+ SimilarityParams.Jalview);
+ oldScore = Comparison.PID(s1, s2);
+ assertEquals(newScore, oldScore, DELTA);
+
+ /*
+ * s2 longer than s1, with gaps
+ */
+ s1 = "ARK-";
+ s2 = "-RFNQ";
+ newScore = new PIDModel().computePID(s1, s2,
+ SimilarityParams.Jalview);
+ oldScore = Comparison.PID(s1, s2);
+ assertEquals(newScore, oldScore, DELTA);
+
+ /*
+ * s1 longer than s2, with gaps
+ */
+ s1 = "-RFNQ";
+ s2 = "ARK-";
+ newScore = new PIDModel().computePID(s1, s2,
+ SimilarityParams.Jalview);
+ oldScore = Comparison.PID(s1, s2);
+ assertEquals(newScore, oldScore, DELTA);
+
+ /*
+ * same but now also with gapped columns
+ */
+ s1 = "-R-F-NQ";
+ s2 = "AR-K--";
+ newScore = new PIDModel().computePID(s1, s2, SimilarityParams.Jalview);
+ oldScore = Comparison.PID(s1, s2);
+ assertEquals(newScore, oldScore, DELTA);
+ }
+}