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_CONVERT_ACE_TO_SQLITE_TASK_H_
23 #define _U2_CONVERT_ACE_TO_SQLITE_TASK_H_
24 
25 #include <U2Core/GUrl.h>
26 #include <U2Core/Task.h>
27 #include <U2Core/U2Assembly.h>
28 #include <U2Core/U2AssemblyDbi.h>
29 #include <U2Core/U2OpStatusUtils.h>
30 
31 #include "ace/AceImportUtils.h"
32 
33 namespace U2 {
34 
35 class ConvertAceToSqliteTask : public Task {
36     Q_OBJECT
37 public:
38     ConvertAceToSqliteTask(const GUrl &sourceUrl, const U2DbiRef &dstDbiRef);
39 
40     virtual void run();
41     virtual ReportResult report();
42 
43     GUrl getDestinationUrl() const;
44     QMap<U2Sequence, U2Assembly> getImportedObjects() const;
45 
46 private:
47     qint64 importAssemblies(IOAdapter &ioAdapter);
48     qint64 packReads();
49     void updateAttributeDbi();
50 
51     const GUrl sourceUrl;
52 
53     U2DbiRef dstDbiRef;
54     U2Dbi *dbi;
55 
56     bool databaseWasCreated;
57     int countImportedAssembly;
58     QMap<int, Assembly::Sequence> referencesData;
59     QMap<int, U2Assembly> assemblies;
60     QMap<int, U2AssemblyReadsImportInfo> importInfos;
61     QMap<int, U2Sequence> importedReferences;
62 };
63 
64 }  // namespace U2
65 
66 #endif  // _U2_CONVERT_ACE_TO_SQLITE_TASK_H_
67