/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
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;
+ }
}
}