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 _U2_SMITH_WATERMAN_RESULT_H_
23 #define _U2_SMITH_WATERMAN_RESULT_H_
24 
25 #include <U2Core/AnnotationData.h>
26 
27 namespace U2 {
28 
29 struct U2ALGORITHM_EXPORT SmithWatermanResult {
30     SharedAnnotationData toAnnotation(const QString &name) const;
31     bool operator<(const SmithWatermanResult &op1) const;
32 
33     U2Strand strand;
34     bool trans;
35     float score;
36     U2Region refSubseq;
37     bool isJoined;
38     U2Region refJoinedSubseq;
39 
40     U2Region ptrnSubseq;
41     QByteArray pairAlignment;
42 
43     static const char UP = 'u';
44     static const char LEFT = 'l';
45     static const char DIAG = 'd';
46 };
47 
48 class U2ALGORITHM_EXPORT SmithWatermanResultListener {
49 public:
50     virtual ~SmithWatermanResultListener();
51 
52     virtual void pushResult(const SmithWatermanResult &r);
53     virtual void pushResult(const QList<SmithWatermanResult> &r);
54     virtual QList<SmithWatermanResult> popResults();
55     virtual QList<SmithWatermanResult> getResults() const;
56 
57 private:
58     QList<SmithWatermanResult> result;
59 };
60 
61 }  // namespace U2
62 
63 #endif
64