2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.datamodel;
20 public class CigarCigar extends CigarSimple
25 * Apply CIGAR operations to the result of another cigar
30 CigarCigar(SeqCigar cigar)
38 * @return String formed by applying CIGAR operations to the reference object
41 * @todo Implement this jalview.datamodel.Cigar method
43 public String getSequenceString(char GapChar)
49 String refString = refCigar.getSequenceString(GapChar);
50 if (refString != null)
52 return (length == 0) ? "" : (String) getSequenceAndDeletions(
53 refString, GapChar)[0];