Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
CigarCigar | 23 | 8 | 5 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
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 | |
10 | * of the License, or (at your option) any later version. | |
11 | * | |
12 | * Jalview is distributed in the hope that it will be useful, but | |
13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
15 | * PURPOSE. See the GNU General Public License for more details. | |
16 | * | |
17 | * You should have received a copy of the GNU General Public License | |
18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
20 | */ | |
21 | package jalview.datamodel; | |
22 | ||
23 | public class CigarCigar extends CigarSimple | |
24 | { | |
25 | SeqCigar refCigar; | |
26 | ||
27 | /** | |
28 | * Apply CIGAR operations to the result of another cigar | |
29 | * | |
30 | * @param cigar | |
31 | * Cigar | |
32 | */ | |
33 | 0 | CigarCigar(SeqCigar cigar) |
34 | { | |
35 | 0 | super(); |
36 | 0 | refCigar = cigar; |
37 | } | |
38 | ||
39 | /** | |
40 | * | |
41 | * @return String formed by applying CIGAR operations to the reference object | |
42 | * @param GapChar | |
43 | * char | |
44 | * @todo Implement this jalview.datamodel.Cigar method | |
45 | */ | |
46 | 0 | public String getSequenceString(char GapChar) |
47 | { | |
48 | 0 | if (length == 0) |
49 | { | |
50 | 0 | return ""; |
51 | } | |
52 | 0 | String refString = refCigar.getSequenceString(GapChar); |
53 | 0 | if (refString != null) |
54 | { | |
55 | 0 | return (length == 0) ? "" |
56 | : (String) getSequenceAndDeletions(refString, GapChar)[0]; | |
57 | } | |
58 | else | |
59 | { | |
60 | 0 | return null; |
61 | } | |
62 | } | |
63 | ||
64 | } |