X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fhtsjdk%2FHtsContigDb.java;h=37ce625bbc95119702cfcee32605b92cb562d242;hb=0a4a46233a09da979e8e2936ee994f80f66e4ed2;hp=f3b5098cb7c4fd88610124fb110a714eded7fe9a;hpb=ad251609d6d0d12aaa6d466b91d719dabf269d7b;p=jalview.git

diff --git a/src/jalview/ext/htsjdk/HtsContigDb.java b/src/jalview/ext/htsjdk/HtsContigDb.java
index f3b5098..37ce625 100644
--- 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;
@@ -50,8 +70,8 @@ public class HtsContigDb
       return;
     }
 
-    refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(
-            dbLocation, true);
+    refFile = ReferenceSequenceFileFactory
+            .getReferenceSequenceFile(dbLocation, true);
     if (refFile == null || refFile.getSequenceDictionary() == null)
     {
       // refFile = initSequenceDictionaryFor(dbLocation);
@@ -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
    * 
@@ -122,7 +144,8 @@ public class HtsContigDb
     ReferenceSequence refSeq;
     List<SAMSequenceRecord> ret = new ArrayList<SAMSequenceRecord>();
     Set<String> sequenceNames = new HashSet<String>();
-    for (int numSequences = 0; (refSeq = refSeqFile.nextSequence()) != null; ++numSequences)
+    for (int numSequences = 0; (refSeq = refSeqFile
+            .nextSequence()) != null; ++numSequences)
     {
       if (sequenceNames.contains(refSeq.getName()))
       {