JAL-3205 faster calculation with symmetric score matrix

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

diff --git a/test/jalview/analysis/scoremodels/PIDModelTest.java b/test/jalview/analysis/scoremodels/PIDModelTest.java
index 212f825..e8ffd2f 100644 (file)
--- a/test/jalview/analysis/scoremodels/PIDModelTest.java
+++ b/test/jalview/analysis/scoremodels/PIDModelTest.java
@@ -44,6 +44,8 @@ public class PIDModelTest
     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
@@ -54,6 +56,7 @@ public class PIDModelTest
     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
@@ -64,6 +67,7 @@ public class PIDModelTest
     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
@@ -74,6 +78,7 @@ public class PIDModelTest
     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
@@ -84,6 +89,7 @@ public class PIDModelTest
     newScore = PIDModel.computePID(s1, s2, params);
     oldScore = Comparison.PID(s1, s2);
     assertEquals(newScore, oldScore, DELTA);
+    assertEquals(newScore, PIDModel.computePID(s2, s1, params));
   }
 
   /**
@@ -102,6 +108,7 @@ public class PIDModelTest
      */
     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
@@ -109,6 +116,7 @@ public class PIDModelTest
      */
     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
@@ -117,6 +125,7 @@ public class PIDModelTest
      */
     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
@@ -125,6 +134,7 @@ public class PIDModelTest
      */
     params = new SimilarityParams(false, false, true, true);
     assertEquals(PIDModel.computePID(s1, s2, params), 25d);
+    assertEquals(PIDModel.computePID(s2, s1, params), 25d);
   }
 
   /**
@@ -144,6 +154,7 @@ public class PIDModelTest
      */
     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
@@ -151,6 +162,7 @@ public class PIDModelTest
      */
     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
@@ -159,6 +171,7 @@ public class PIDModelTest
      */
     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
@@ -167,6 +180,7 @@ public class PIDModelTest
      */
     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