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 _SMITHWATERMANALGORITHM_H
23 #define _SMITHWATERMANALGORITHM_H
24 
25 #include <QByteArray>
26 #include <QVector>
27 
28 #include <U2Algorithm/SmithWatermanSettings.h>
29 
30 #include <U2Core/SMatrix.h>
31 
32 #include "PairAlignSequences.h"
33 
34 namespace U2 {
35 
36 class SmithWatermanAlgorithm {
37 public:
38     SmithWatermanAlgorithm();
~SmithWatermanAlgorithm()39     virtual ~SmithWatermanAlgorithm() {
40     }
41 
42     virtual void launch(const SMatrix &m, const QByteArray &_patternSeq, const QByteArray &_searchSeq, int _gapOpen, int _gapExtension, int _minScore, SmithWatermanSettings::SWResultView _resultView);
43 
44     QList<PairAlignSequences> getResults();
45     static void sortByScore(QList<PairAlignSequences> &pairAlignmentStrings);
46     static quint64 estimateNeededRamAmount(const qint32 gapOpen, const qint32 gapExtension, const quint32 minScore, const quint32 maxScore, const QByteArray &patternSeq, const QByteArray &searchSeq, const SmithWatermanSettings::SWResultView resultView);
47     static const char STOP;
48     static const char UP;
49     static const char LEFT;
50     static const char DIAG;
51 
52 protected:
53     bool calculateMatrixLength();
54     bool isValidParams();
55     void setValues(const SMatrix &_substitutionMatrix,
56                    const QByteArray &_patternSeq,
57                    const QByteArray &_searchSeq,
58                    int _gapOpen,
59                    int _gapExtension,
60                    int _minScore,
61                    SmithWatermanSettings::SWResultView _resultView);
62 
63     QList<PairAlignSequences> pairAlignmentStrings;
64 
65     SMatrix substitutionMatrix;
66 
67     QByteArray patternSeq;
68     QByteArray searchSeq;
69 
70     int gapOpen;
71     int gapExtension;
72     int minScore;
73     int matrixLength;
74     SmithWatermanSettings::SWResultView resultView;
75 
76     QVector<QVector<char>> directionMatrix;
77 
78     struct KeyOfPairAlignSeq {
KeyOfPairAlignSeqKeyOfPairAlignSeq79         KeyOfPairAlignSeq(int _score, U2Region const &_intervalSeq1) {
80             setValues(_score, _intervalSeq1);
81         }
82 
KeyOfPairAlignSeqKeyOfPairAlignSeq83         KeyOfPairAlignSeq() {
84             score = 0;
85 
86             intervalSeq1.startPos = 0;
87             intervalSeq1.length = 0;
88         };
89 
exchangeKeyOfPairAlignSeq90         static void exchange(PairAlignSequences &a, PairAlignSequences &b) {
91             PairAlignSequences bufKey;
92 
93             bufKey = a;
94             a = b;
95             b = bufKey;
96         }
97 
setValuesKeyOfPairAlignSeq98         void setValues(int _score, U2Region const &_intervalSeq1) {
99             score = _score;
100             intervalSeq1 = _intervalSeq1;
101         }
102 
103         int score;
104         U2Region intervalSeq1;
105     };
106 
107 private:
108     QVector<QVector<int>> matrix;
109     QVector<int> EMatrix;
110     QVector<int> FMatrix;
111 
112     void calculateMatrixForMultipleAlignmentResult();
113     void calculateMatrixForAnnotationsResult();
114 };
115 
116 }  // namespace U2
117 
118 #endif
119