Merge branch 'develop' into bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail...

[jalview.git] / src / jalview / datamodel / GroupSet.java

diff --git a/src/jalview/datamodel/GroupSet.java b/src/jalview/datamodel/GroupSet.java
index db38e7b..95d0127 100644 (file)
--- a/src/jalview/datamodel/GroupSet.java
+++ b/src/jalview/datamodel/GroupSet.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.datamodel;
 
 import java.awt.Color;
@@ -149,8 +169,9 @@ public class GroupSet implements GroupSetI
   {
     return makeGroups(matrix, autoCut, 0, autoCut);
   }
-  public static GroupSet makeGroups(ContactMatrixI matrix, boolean auto, float thresh,
-          boolean abs)
+
+  public static GroupSet makeGroups(ContactMatrixI matrix, boolean auto,
+          float thresh, boolean abs)
   {
     AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null,
             matrix, true);
@@ -197,7 +218,7 @@ public class GroupSet implements GroupSetI
         nodegroups.add(clusterer.getTopNode());
       }
     }
-    
+
     List<BitSet> groups = new ArrayList<>();
     for (BinaryNode root : nodegroups)
     {