Merge branch 'releases/Release_2_10_Branch' into develop

[jalview.git] / src / jalview / ext / htsjdk / HtsContigDb.java

diff --git a/src/jalview/ext/htsjdk/HtsContigDb.java b/src/jalview/ext/htsjdk/HtsContigDb.java
index f3b5098..4357abd 100644 (file)
--- a/src/jalview/ext/htsjdk/HtsContigDb.java
+++ b/src/jalview/ext/htsjdk/HtsContigDb.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.ext.htsjdk;
 
 import htsjdk.samtools.SAMSequenceDictionary;
@@ -59,18 +79,21 @@ public class HtsContigDb
 
   }
 
-
   SAMSequenceDictionary rrefDict = null;
-  private ReferenceSequenceFile initSequenceDictionaryFor(File dbLocation2) throws Exception
+
+  private ReferenceSequenceFile initSequenceDictionaryFor(File dbLocation2)
+          throws Exception
   {
     rrefDict = getDictionary(dbLocation2, true);
     if (rrefDict != null)
     {
-      ReferenceSequenceFile rrefFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(dbLocation2, true);
+      ReferenceSequenceFile rrefFile = ReferenceSequenceFileFactory
+              .getReferenceSequenceFile(dbLocation2, true);
       return rrefFile;
     }
     return null;
   }
+
   /**
    * code below hacked out from picard ----
    * 
@@ -79,7 +102,6 @@ public class HtsContigDb
    * broadinstitute/picard/commit/270580d3e28123496576f0b91b3433179bb5d876
    */
 
-
   /*
    * The MIT License
    *