X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fext%2Fhtsjdk%2FHtsContigDb.java;h=37ce625bbc95119702cfcee32605b92cb562d242;hb=b9cc00124dff0ad97f8b154f16d14ef530d03120;hp=667e5678753a1ebb736e6446757a6d8f70c54d8c;hpb=853624fb32058cccc544ae7d13af6ad4b0800b6c;p=jalview.git
diff --git a/src/jalview/ext/htsjdk/HtsContigDb.java b/src/jalview/ext/htsjdk/HtsContigDb.java
index 667e567..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 .
+ * 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);
@@ -124,7 +144,8 @@ public class HtsContigDb
ReferenceSequence refSeq;
List ret = new ArrayList();
Set sequenceNames = new HashSet();
- for (int numSequences = 0; (refSeq = refSeqFile.nextSequence()) != null; ++numSequences)
+ for (int numSequences = 0; (refSeq = refSeqFile
+ .nextSequence()) != null; ++numSequences)
{
if (sequenceNames.contains(refSeq.getName()))
{