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