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_BAM_DBI_PLUGIN_H_ 23 #define _U2_BAM_DBI_PLUGIN_H_ 24 25 #include <time.h> 26 27 #include <U2Core/DocumentImport.h> 28 #include <U2Core/DocumentProviderTask.h> 29 #include <U2Core/Log.h> 30 #include <U2Core/PluginModel.h> 31 #include <U2Core/U2Dbi.h> 32 33 #include "PrepareToImportTask.h" 34 35 namespace U2 { 36 37 class CloneObjectTask; 38 class LoadDocumentTask; 39 40 namespace BAM { 41 42 class BAMDbiPlugin : public Plugin { 43 Q_OBJECT 44 public: 45 BAMDbiPlugin(); 46 }; 47 48 class BAMImporter : public DocumentImporter { 49 Q_OBJECT 50 public: 51 BAMImporter(); 52 53 virtual FormatCheckResult checkRawData(const QByteArray &rawData, const GUrl &url); 54 55 virtual DocumentProviderTask *createImportTask(const FormatDetectionResult &res, bool showGui, const QVariantMap &hints); 56 }; 57 58 class LoadInfoTask; 59 class ConvertToSQLiteTask; 60 61 class BAMImporterTask : public DocumentProviderTask { 62 Q_OBJECT 63 public: 64 BAMImporterTask(const GUrl &url, bool useGui, const QVariantMap &hints); 65 66 void prepare(); 67 QList<Task *> onSubTaskFinished(Task *subTask); 68 ReportResult report(); 69 70 private: 71 void initPrepareToImportTask(); 72 void initLoadBamInfoTask(); 73 void initConvertToSqliteTask(); 74 void initCloneObjectTasks(); 75 void initLoadDocumentTask(); 76 77 LoadInfoTask *loadInfoTask; 78 LoadInfoTask *loadBamInfoTask; 79 PrepareToImportTask *prepareToImportTask; 80 ConvertToSQLiteTask *convertTask; 81 QList<Task *> cloneTasks; 82 LoadDocumentTask *loadDocTask; 83 84 bool isSqliteDbTransit; 85 bool useGui; 86 bool sam; 87 88 QVariantMap hints; 89 U2DbiRef hintedDbiRef; 90 U2DbiRef localDbiRef; 91 time_t startTime; 92 }; 93 94 } // namespace BAM 95 } // namespace U2 96 97 #endif // _U2_BAM_DBI_PLUGIN_H_ 98