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_BOWTIE2_SUPPORT_WORKER_ 23 #define _U2_BOWTIE2_SUPPORT_WORKER_ 24 25 #include "utils/BaseShortReadsAlignerWorker.h" 26 27 namespace U2 { 28 29 class DnaAssemblyToRefTaskSettings; 30 class U2OpStatus; 31 32 namespace LocalWorkflow { 33 34 class Bowtie2Worker : public BaseShortReadsAlignerWorker { 35 Q_OBJECT 36 public: 37 Bowtie2Worker(Actor *p); 38 39 protected: 40 QVariantMap getCustomParameters() const; 41 QString getDefaultFileName() const; 42 QString getBaseSubdir() const; 43 void setGenomeIndex(DnaAssemblyToRefTaskSettings &settings); 44 }; // Bowtie2Worker 45 46 class Bowtie2WorkerFactory : public BaseShortReadsAlignerWorkerFactory { 47 public: 48 static const QString ACTOR_ID; 49 Bowtie2WorkerFactory()50 Bowtie2WorkerFactory() 51 : BaseShortReadsAlignerWorkerFactory(ACTOR_ID) { 52 } 53 static void init(); 54 virtual Worker *createWorker(Actor *a); 55 }; // Bowtie2WorkerFactory 56 57 } // namespace LocalWorkflow 58 } // namespace U2 59 60 #endif // _U2_BOWTIE2_SUPPORT_WORKER_ 61