1 /**
2  * UGENE - Integrated Bioinformatics Tools.
3  * Copyright (C) 2008-2021 UniPro <ugene@unipro.ru>
4  * http://ugene.net
5  *
6  * This program is free software; you can redistribute it and/or
7  * modify it under the terms of the GNU General Public License
8  * as published by the Free Software Foundation; either version 2
9  * of the License, or (at your option) any later version.
10  *
11  * This program is distributed in the hope that it will be useful,
12  * but WITHOUT ANY WARRANTY; without even the implied warranty of
13  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14  * GNU General Public License for more details.
15  *
16  * You should have received a copy of the GNU General Public License
17  * along with this program; if not, write to the Free Software
18  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
19  * MA 02110-1301, USA.
20  */
21 
22 #ifndef PAIRALIGNMENTSTRINGS_H
23 #define PAIRALIGNMENTSTRINGS_H
24 
25 #include <U2Core/U2Region.h>
26 
27 namespace U2 {
28 
29 class PairAlignSequences {
30 public:
31     PairAlignSequences();
32     void setValues(int _score, const U2Region &_refSubseqInterval, const U2Region &_ptrnSubseqInterval, QByteArray _pairAlignment);
33 
34     U2Region refSubseqInterval;
35     U2Region ptrnSubseqInterval;
36     int score;
37     QByteArray pairAlignment;
38 
39     bool isAminoTranslated;
40     bool isDNAComplemented;
41 
42     static const char UP = 'u';
43     static const char LEFT = 'l';
44     static const char DIAG = 'd';
45 };
46 
47 }  // namespace U2
48 
49 #endif
50