+/*
+ * 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.
+ *
+ * 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.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
- */
- 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
- * @param GapChar char
+ * @param GapChar
+ * char
* @todo Implement this jalview.datamodel.Cigar method
*/
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;
+ }
}
}