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_SNPEFF_VARIATIONS_TO_ANNOTATIONS_TASK_H_ 23 #define _U2_CONVERT_SNPEFF_VARIATIONS_TO_ANNOTATIONS_TASK_H_ 24 25 #include <QMap> 26 27 #include <U2Core/AnnotationData.h> 28 #include <U2Core/Task.h> 29 30 namespace U2 { 31 32 class AnnotationTableObject; 33 class CreateAnnotationsTask; 34 class Document; 35 class LoadDocumentTask; 36 class SaveDocumentTask; 37 class VariantTrackObject; 38 39 class ConvertSnpeffVariationsToAnnotationsTask : public Task { 40 Q_OBJECT 41 public: 42 ConvertSnpeffVariationsToAnnotationsTask(const QList<VariantTrackObject *> &variantTrackObjects); 43 44 const QMap<QString, QList<SharedAnnotationData>> &getAnnotationsData() const; 45 46 private: 47 void run(); 48 49 const QList<VariantTrackObject *> variantTrackObjects; 50 QMap<QString, QList<SharedAnnotationData>> annotationTablesData; 51 52 static const QString CHROM_QUALIFIER_NAME; 53 static const QString LOCATION_QUALIFIER_NAME; 54 static const QString REFERENCE_QUALIFIER_NAME; 55 static const QString ALTERNATE_QUALIFIER_NAME; 56 static const QString ALLELE_QUALIFIER_NAME; 57 static const QString ID_QUALIFIER_NAME; 58 }; 59 60 class U2FORMATS_EXPORT LoadConvertAndSaveSnpeffVariationsToAnnotationsTask : public Task { 61 Q_OBJECT 62 public: 63 LoadConvertAndSaveSnpeffVariationsToAnnotationsTask(const QString &variationsUrl, const U2DbiRef &dstDbiRef, const QString &dstUrl, const QString &formatId); 64 ~LoadConvertAndSaveSnpeffVariationsToAnnotationsTask(); 65 66 const QString &getResultUrl() const; 67 68 private: 69 void prepare(); 70 QList<Task *> onSubTaskFinished(Task *subTask); 71 72 Document *prepareDocument(); 73 void prepareSaveTask(); 74 75 const QString variationsUrl; 76 const U2DbiRef dstDbiRef; 77 const QString dstUrl; 78 const QString formatId; 79 80 LoadDocumentTask *loadTask; 81 ConvertSnpeffVariationsToAnnotationsTask *convertTask; 82 QList<Task *> createAnnotationsTasks; 83 SaveDocumentTask *saveTask; 84 85 Document *loadedVariationsDocument; 86 Document *annotationsDocument; 87 QList<AnnotationTableObject *> annotationTableObjects; 88 }; 89 90 } // namespace U2 91 92 #endif // _U2_CONVERT_SNPEFF_VARIATIONS_TO_ANNOTATIONS_TASK_H_ 93