/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-public class CigarCigar
- extends CigarSimple
+public class CigarCigar extends CigarSimple
{
SeqCigar refCigar;
+
/**
* Apply CIGAR operations to the result of another cigar
- * @param cigar Cigar
+ *
+ * @param cigar
+ * Cigar
*/
CigarCigar(SeqCigar cigar)
{
}
/**
- *
+ *
* @return String formed by applying CIGAR operations to the reference object
- * @param GapChar char
+ * @param GapChar
+ * char
* @todo Implement this jalview.datamodel.Cigar method
*/
public String getSequenceString(char GapChar)
String refString = refCigar.getSequenceString(GapChar);
if (refString != null)
{
- return (length == 0) ? "" :
- (String) getSequenceAndDeletions(refString, GapChar)[0];
+ return (length == 0) ? "" : (String) getSequenceAndDeletions(
+ refString, GapChar)[0];
}
else
{