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_RF_SARRAYWK_ALG_H_
23 #define _U2_RF_SARRAYWK_ALG_H_
24 
25 #include <QVector>
26 
27 #include <U2Algorithm/SArrayBasedFindTask.h>
28 #include <U2Algorithm/SArrayIndex.h>
29 
30 #include "RFBase.h"
31 
32 namespace U2 {
33 
34 class SArrayIndex;
35 class RFSArrayWKSubtask;
36 class RFRollingArray;
37 
38 class RFSArrayWKAlgorithm : public RFAlgorithmBase {
39     Q_OBJECT
40     friend class RFSArrayWKSubtask;
41 
42 public:
43     RFSArrayWKAlgorithm(RFResultsListener *rl, const char *seqX, int sizeX, const char *seqY, int sizeY, DNAAlphabetType seqType, int w, int k);
44 
~RFSArrayWKAlgorithm()45     ~RFSArrayWKAlgorithm() {
46         cleanup();
47     }
48 
49     void prepare();
50     QList<Task *> onSubTaskFinished(Task *subTask);
51 
52     void cleanup();
53 
54 private:
55     void addResult(int a, int s, int l, int c);
56     void calculate(RFSArrayWKSubtask *t);
57 
58 public:
59     QVector<int> diagOffsets;  // holds start position for the last checked window
60     int ARRAY_SIZE;
61     int SEARCH_SIZE;
62 
63     const char *arraySeq;
64     const char *searchSeq;
65     bool arrayIsX;
66 
67     quint32 q;
68 
69     CreateSArrayIndexTask *indexTask;
70     int nThreads;
71 };
72 
73 class RFSArrayWKSubtask : public Task, public SArrayIndex::SAISearchContext {
74     Q_OBJECT
75     friend class RFSArrayWKAlgorithm;
76 
77 public:
78     RFSArrayWKSubtask(RFSArrayWKAlgorithm *owner, int _tid);
~RFSArrayWKSubtask()79     virtual ~RFSArrayWKSubtask() {
80     }
81     void run();
82 
83     RFSArrayWKAlgorithm *owner;
84 
85     const int tid;
86 };
87 
88 }  // namespace U2
89 
90 #endif
91