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_SQLITE_ASSEMBLY_PACK_ALGORITHM_DBI_H_
23 #define _U2_SQLITE_ASSEMBLY_PACK_ALGORITHM_DBI_H_
24 
25 #include <U2Core/U2SqlHelpers.h>
26 
27 namespace U2 {
28 
29 class U2AssemblyPackStat;
30 class U2Region;
31 
32 class PackAlgorithmData {
33 public:
PackAlgorithmData()34     PackAlgorithmData()
35         : leftmostPos(0), effectiveLen(0) {
36     }
37 
38     U2DataId readId;
39     qint64 leftmostPos;
40     qint64 effectiveLen;
41 };
42 
43 class PackAlgorithmAdapter {
44 public:
45     virtual U2DbiIterator<PackAlgorithmData> *selectAllReads(U2OpStatus &os) = 0;
46     virtual void assignProw(const U2DataId &readId, qint64 prow, U2OpStatus &os) = 0;
~PackAlgorithmAdapter()47     virtual ~PackAlgorithmAdapter() {
48     }
49 };
50 
51 #define PACK_TAIL_SIZE 50000
52 
53 class PackAlgorithmContext {
54 public:
55     PackAlgorithmContext();
56 
57     int maxProw;
58     qint64 nReads;
59 
60     // used to assign prow for reads when TAIL_SIZE is not enough
61     qint64 peakEnd;
62     qint64 peakRow;
63     QVector<qint64> tails;
64 };
65 
66 class AssemblyPackAlgorithm {
67 public:
68     static void pack(PackAlgorithmAdapter &adapter, U2AssemblyPackStat &stat, U2OpStatus &os);
69     static int packRead(const U2Region &reg, PackAlgorithmContext &ctx, U2OpStatus &os);
70 };
71 
72 }  // namespace U2
73 
74 #endif
75