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_CUFFLINKS_SUPPORT_TASK_H_ 23 #define _U2_CUFFLINKS_SUPPORT_TASK_H_ 24 25 #include <U2Core/AnnotationData.h> 26 #include <U2Core/DocumentModel.h> 27 #include <U2Core/ExternalToolRunTask.h> 28 #include <U2Core/Task.h> 29 30 #include <U2Formats/ConvertAssemblyToSamTask.h> 31 32 #include "CufflinksSettings.h" 33 #include "CufflinksSupport.h" 34 35 namespace U2 { 36 37 class AnnotationTableObject; 38 class LoadDocumentTask; 39 40 enum CufflinksOutputFormat { 41 CufflinksOutputFpkm, 42 CufflinksOutputGtf 43 }; 44 45 class CufflinksSupportTask : public ExternalToolSupportTask { 46 Q_OBJECT 47 public: 48 CufflinksSupportTask(const CufflinksSettings &settings); 49 ~CufflinksSupportTask(); 50 51 void prepare(); 52 QList<Task *> onSubTaskFinished(Task *subTask); 53 ReportResult report(); 54 55 QList<AnnotationTableObject *> getIsoformAnnotationTables() const; 56 const QStringList &getOutputFiles() const; 57 58 private: 59 static DocumentFormatId getFormatId(CufflinksOutputFormat format); 60 void initLoadIsoformAnnotationsTask(const QString &fileName, CufflinksOutputFormat format); 61 62 CufflinksSettings settings; 63 64 QPointer<Document> tmpDoc; 65 QString workingDirectory; 66 QString url; 67 68 ConvertAssemblyToSamTask *convertAssToSamTask; 69 ExternalToolRunTask *cufflinksExtToolTask; 70 LoadDocumentTask *loadIsoformAnnotationsTask; 71 72 QList<AnnotationTableObject *> isoformLevelAnnotationTables; 73 QStringList outputFiles; 74 75 static const QString outSubDirBaseName; 76 77 private: 78 QString initTmpDir(); 79 ExternalToolRunTask *runCufflinks(); 80 }; 81 82 } // namespace U2 83 84 #endif // _U2_CUFFLINKS_SUPPORT_TASK_H_ 85