+/*
+ * 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.io.gff;
import jalview.datamodel.AlignedCodonFrame;
*/
if ("-".equals(strand))
{
- System.err
- .println("Skipping mapping from reverse complement as not yet supported");
+ System.err.println(
+ "Skipping mapping from reverse complement as not yet supported");
return null;
}
* @return
*/
@SuppressWarnings("unused")
- protected String findTargetId(String target, Map<String, List<String>> set)
+ protected String findTargetId(String target,
+ Map<String, List<String>> set)
{
return target;
}
* @throws IOException
*/
protected SequenceFeature processProteinMatch(
- Map<String, List<String>> set, SequenceI seq,
- String[] gffColumns, AlignmentI align, List<SequenceI> newseqs,
+ Map<String, List<String>> set, SequenceI seq, String[] gffColumns,
+ AlignmentI align, List<SequenceI> newseqs,
boolean relaxedIdMatching)
{
// This is currently tailored to InterProScan GFF output:
* renamed with its qualified accession id; renaming has to wait until
* all sequence reference resolution is complete
*/
- String accessionId = StringUtils.listToDelimitedString(
- set.get(NAME), ",");
+ String accessionId = StringUtils
+ .listToDelimitedString(set.get(NAME), ",");
if (accessionId.length() > 0)
{
String database = sf.getType(); // TODO InterProScan only??