JAL-4090 JAL-1551 source license

[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..24ddad4 100644 (file)
--- a/test/jalview/analysis/scoremodels/PIDModelTest.java
+++ b/test/jalview/analysis/scoremodels/PIDModelTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.analysis.scoremodels;
 
 import static org.testng.Assert.assertEquals;
@@ -44,6 +64,8 @@ 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 +76,7 @@ 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 +87,7 @@ 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 +98,7 @@ 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 +109,7 @@ 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 +128,7 @@ 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 +136,7 @@ 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 +145,7 @@ 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 +154,7 @@ public class PIDModelTest
      */
     params = new SimilarityParams(false, false, true, true);
     assertEquals(PIDModel.computePID(s1, s2, params), 25d);
+    assertEquals(PIDModel.computePID(s2, s1, params), 25d);
   }
 
   /**
@@ -136,22 +166,25 @@ public class PIDModelTest
   {
     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);
+    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
@@ -159,7 +192,8 @@ 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
      * exclude gap-gap
@@ -167,6 +201,7 @@ 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