Merge branch 'features/JAL-2393customMatrices' into develop

[jalview.git] / test / jalview / analysis / scoremodels / PIDModelTest.java

diff --git a/test/jalview/analysis/scoremodels/PIDModelTest.java b/test/jalview/analysis/scoremodels/PIDModelTest.java
new file mode 100644 (file)
index 0000000..212f825
--- /dev/null
+++ b/test/jalview/analysis/scoremodels/PIDModelTest.java
@@ -0,0 +1,176 @@
+package jalview.analysis.scoremodels;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.api.analysis.SimilarityParamsI;
+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()
+  {
+    SimilarityParamsI params = new SimilarityParams(true, true, true, true);
+
+    /*
+     * same length, no gaps
+     */
+    String s1 = "ARFNQDWSGI";
+    String s2 = "ARKNQDQSGI";
+
+    new PIDModel();
+    double newScore = PIDModel.computePID(s1, s2, params);
+    double oldScore = Comparison.PID(s1, s2);
+    assertEquals(newScore, oldScore, DELTA);
+
+    /*
+     * same length, with gaps
+     */
+    s1 = "-RFNQDWSGI";
+    s2 = "ARKNQ-QSGI";
+    new PIDModel();
+    newScore = PIDModel.computePID(s1, s2, params);
+    oldScore = Comparison.PID(s1, s2);
+    assertEquals(newScore, oldScore, DELTA);
+
+    /*
+     * s2 longer than s1, with gaps
+     */
+    s1 = "ARK-";
+    s2 = "-RFNQ";
+    new PIDModel();
+    newScore = PIDModel.computePID(s1, s2, params);
+    oldScore = Comparison.PID(s1, s2);
+    assertEquals(newScore, oldScore, DELTA);
+
+    /*
+     * s1 longer than s2, with gaps
+     */
+    s1 = "-RFNQ";
+    s2 = "ARK-";
+    new PIDModel();
+    newScore = PIDModel.computePID(s1, s2, params);
+    oldScore = Comparison.PID(s1, s2);
+    assertEquals(newScore, oldScore, DELTA);
+
+    /*
+     * same but now also with gapped columns
+     */
+    s1 = "-R-F-NQ";
+    s2 = "AR-K--";
+    new PIDModel();
+    newScore = PIDModel.computePID(s1, s2, params);
+    oldScore = Comparison.PID(s1, s2);
+    assertEquals(newScore, oldScore, DELTA);
+  }
+
+  /**
+   * Tests for percentage identity variants where only the shorter length of two
+   * sequences is used
+   */
+  @Test(groups = "Functional")
+  public void testComputePID_matchShortestSequence()
+  {
+    String s1 = "FR-K-S";
+    String s2 = "FS--L";
+
+    /*
+     * match gap-gap and gap-char
+     * PID = 4/5 = 80%
+     */
+    SimilarityParamsI params = new SimilarityParams(true, true, true, true);
+    assertEquals(PIDModel.computePID(s1, s2, params), 80d);
+
+    /*
+     * match gap-char but not gap-gap
+     * PID = 3/4 = 75%
+     */
+    params = new SimilarityParams(false, true, true, true);
+    assertEquals(PIDModel.computePID(s1, s2, params), 75d);
+
+    /*
+     * include gaps but don't match them
+     * include gap-gap, counted as identity
+     * PID = 2/5 = 40%
+     */
+    params = new SimilarityParams(true, false, true, true);
+    assertEquals(PIDModel.computePID(s1, s2, params), 40d);
+
+    /*
+     * include gaps but don't match them
+     * exclude gap-gap
+     * PID = 1/4 = 25%
+     */
+    params = new SimilarityParams(false, false, true, true);
+    assertEquals(PIDModel.computePID(s1, s2, params), 25d);
+  }
+
+  /**
+   * Tests for percentage identity variants where the longer length of two
+   * sequences is used
+   */
+  @Test(groups = "Functional")
+  public void testComputePID_matchLongestSequence()
+  {
+    String s1 = "FR-K-S";
+    String s2 = "FS--L";
+  
+    /*
+     * match gap-gap and gap-char
+     * shorter sequence treated as if with trailing gaps
+     * PID = 5/6 = 83.333...%
+     */
+    SimilarityParamsI params = new SimilarityParams(true, true, true, false);
+    assertEquals(PIDModel.computePID(s1, s2, params), 500d / 6);
+  
+    /*
+     * match gap-char but not gap-gap
+     * PID = 4/5 = 80%
+     */
+    params = new SimilarityParams(false, true, true, false);
+    assertEquals(PIDModel.computePID(s1, s2, params), 80d);
+  
+    /*
+     * include gaps but don't match them
+     * include gap-gap, counted as identity
+     * PID = 2/6 = 33.333...%
+     */
+    params = new SimilarityParams(true, false, true, false);
+    assertEquals(PIDModel.computePID(s1, s2, params), 100d / 3);
+  
+    /*
+     * include gaps but don't match them
+     * exclude gap-gap
+     * PID = 1/5 = 25%
+     */
+    params = new SimilarityParams(false, false, true, false);
+    assertEquals(PIDModel.computePID(s1, s2, params), 20d);
+
+    /*
+     * no tests for matchGaps=true, includeGaps=false
+     * as it don't make sense
+     */
+  }
+}