X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FPIDModelTest.java;h=e8ffd2f691eca7ce389c34dbe5884e4da054a965;hb=df81a9e1abd4d4424d6d24b37d93f17bffd3649c;hp=24b44a3c7fe6652f7237bf5e343b4970a1a03035;hpb=5346ea15df13baf5b342e467b70358c2212fd1ef;p=jalview.git

diff --git a/test/jalview/analysis/scoremodels/PIDModelTest.java b/test/jalview/analysis/scoremodels/PIDModelTest.java
index 24b44a3..e8ffd2f 100644
--- a/test/jalview/analysis/scoremodels/PIDModelTest.java
+++ b/test/jalview/analysis/scoremodels/PIDModelTest.java
@@ -2,6 +2,7 @@ package jalview.analysis.scoremodels;
 
 import static org.testng.Assert.assertEquals;
 
+import jalview.api.analysis.SimilarityParamsI;
 import jalview.util.Comparison;
 
 import org.testng.annotations.Test;
@@ -31,53 +32,159 @@ public class PIDModelTest
   @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";
-    double newScore = new PIDModel().computePID(s1, s2,
-            SimilarityParams.Jalview);
+
+    new PIDModel();
+    double newScore = PIDModel.computePID(s1, s2, params);
     double oldScore = Comparison.PID(s1, s2);
     assertEquals(newScore, oldScore, DELTA);
+    // and verify PIDModel calculation is symmetric
+    assertEquals(newScore, PIDModel.computePID(s2, s1, params));
 
     /*
      * same length, with gaps
      */
     s1 = "-RFNQDWSGI";
     s2 = "ARKNQ-QSGI";
-    newScore = new PIDModel().computePID(s1, s2,
-            SimilarityParams.Jalview);
+    new PIDModel();
+    newScore = PIDModel.computePID(s1, s2, params);
     oldScore = Comparison.PID(s1, s2);
     assertEquals(newScore, oldScore, DELTA);
+    assertEquals(newScore, PIDModel.computePID(s2, s1, params));
 
     /*
      * s2 longer than s1, with gaps
      */
     s1 = "ARK-";
     s2 = "-RFNQ";
-    newScore = new PIDModel().computePID(s1, s2,
-            SimilarityParams.Jalview);
+    new PIDModel();
+    newScore = PIDModel.computePID(s1, s2, params);
     oldScore = Comparison.PID(s1, s2);
     assertEquals(newScore, oldScore, DELTA);
+    assertEquals(newScore, PIDModel.computePID(s2, s1, params));
 
     /*
      * s1 longer than s2, with gaps
      */
     s1 = "-RFNQ";
     s2 = "ARK-";
-    newScore = new PIDModel().computePID(s1, s2,
-            SimilarityParams.Jalview);
+    new PIDModel();
+    newScore = PIDModel.computePID(s1, s2, params);
     oldScore = Comparison.PID(s1, s2);
     assertEquals(newScore, oldScore, DELTA);
+    assertEquals(newScore, PIDModel.computePID(s2, s1, params));
 
     /*
      * same but now also with gapped columns
      */
     s1 = "-R-F-NQ";
     s2 = "AR-K--";
-    newScore = new PIDModel().computePID(s1, s2, SimilarityParams.Jalview);
+    new PIDModel();
+    newScore = PIDModel.computePID(s1, s2, params);
     oldScore = Comparison.PID(s1, s2);
     assertEquals(newScore, oldScore, DELTA);
+    assertEquals(newScore, PIDModel.computePID(s2, s1, params));
+  }
+
+  /**
+   * 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);
+    assertEquals(PIDModel.computePID(s2, s1, 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);
+    assertEquals(PIDModel.computePID(s2, s1, 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);
+    assertEquals(PIDModel.computePID(s2, s1, 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);
+    assertEquals(PIDModel.computePID(s2, s1, 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);
+    assertEquals(PIDModel.computePID(s2, s1, 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);
+    assertEquals(PIDModel.computePID(s2, s1, 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);
+    assertEquals(PIDModel.computePID(s2, s1, 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);
+    assertEquals(PIDModel.computePID(s2, s1, params), 20d);
+
+    /*
+     * no tests for matchGaps=true, includeGaps=false
+     * as it don't make sense
+     */
   }
 }