X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FPIDModelTest.java;h=e8ffd2f691eca7ce389c34dbe5884e4da054a965;hb=d90895bf6eed41ff1b2d413306afae3cac458756;hp=d968e0e7a2bab641cdc2e2bcd75bba42cfb69c50;hpb=332b50975c0463993efaf16723b3bdb4080d16c5;p=jalview.git

diff --git a/test/jalview/analysis/scoremodels/PIDModelTest.java b/test/jalview/analysis/scoremodels/PIDModelTest.java
index d968e0e..e8ffd2f 100644
--- 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
@@ -167,5 +180,11 @@ 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
+     * as it don't make sense
+     */
   }
 }