Merge branch 'features/JAL-4071_visibleFeaturesCounter' into features/JAL-3417_sdppre...

[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 e8ffd2f..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;
@@ -146,16 +166,17 @@ 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%
@@ -163,7 +184,7 @@ 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
      * include gap-gap, counted as identity
@@ -172,7 +193,7 @@ 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
      * exclude gap-gap