+/*
+ * 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
+ * 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.
+ *
+ * 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
+ */
package jalview.datamodel;
public class CigarCigar
extends CigarSimple
{
SeqCigar refCigar;
- /**
- * Apply CIGAR operations to the result of another cigar
- * @param cigar Cigar
- */
- CigarCigar(SeqCigar cigar) {
- super();
- refCigar = cigar;
- }
+ /**
+ * Apply CIGAR operations to the result of another cigar
+ * @param cigar Cigar
+ */
+ CigarCigar(SeqCigar cigar)
+ {
+ super();
+ refCigar = cigar;
+ }
+
/**
*
* @return String formed by applying CIGAR operations to the reference object
*/
public String getSequenceString(char GapChar)
{
- if (length==0)
+ if (length == 0)
+ {
return "";
+ }
String refString = refCigar.getSequenceString(GapChar);
- if (refString!=null) {
- return (length==0) ? "" : (String) getSequenceAndDeletions(refString, GapChar)[0];
- } else
+ if (refString != null)
+ {
+ return (length == 0) ? "" :
+ (String) getSequenceAndDeletions(refString, GapChar)[0];
+ }
+ else
+ {
return null;
+ }
}
}