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_UTIL_H_
23 #define _U2_SMITH_WATERMAN_UTIL_H_
24 
25 #include "SmithWatermanResult.h"
26 
27 namespace U2 {
28 
29 class SMatrix;
30 
31 class U2ALGORITHM_EXPORT SmithWatermanUtil {
32 public:
33     static float calcScoreItSelf(const SMatrix &m,
34                                  const char *pattern,
35                                  int patternLen);
36 
37     static int calcWindowLen(bool transl,
38                              int sequenceLen,
39                              int patternLen,
40                              float scoreItSelf,
41                              float thresholdScore,
42                              float scoreGapOpen,
43                              float scoreGapExtd);
44 
45     static float calcScoreThreshold(float percent,
46                                     float scoreItSelf);
47 
48     static int calcOverlapSize(bool transl,
49                                int windowLen,
50                                float scoreItSelf,
51                                float scoreGapOpen,
52                                float scoreGapExtd);
53 
54     static bool removeIdenticalResults(QList<SmithWatermanResult> *lst);
55 };
56 
57 }  // namespace U2
58 
59 #endif
60