+/*
+ * 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;
return;
}
- refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(
- dbLocation, true);
+ refFile = ReferenceSequenceFileFactory
+ .getReferenceSequenceFile(dbLocation, true);
if (refFile == null || refFile.getSequenceDictionary() == null)
{
// refFile = initSequenceDictionaryFor(dbLocation);
}
-
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 ----
*
* broadinstitute/picard/commit/270580d3e28123496576f0b91b3433179bb5d876
*/
-
/*
* The MIT License
*
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()))
{