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_MSA_UTIL_TASKS 23 #define _U2_MSA_UTIL_TASKS 24 25 #include <U2Core/MultipleSequenceAlignmentObject.h> 26 #include <U2Core/Task.h> 27 #include <U2Core/global.h> 28 29 namespace U2 { 30 31 class DNATranslation; 32 33 /** 34 Performs in-place translation of multiple sequence alignment object 35 */ 36 37 class U2ALGORITHM_EXPORT TranslateMsa2AminoTask : public Task { 38 Q_OBJECT 39 public: 40 TranslateMsa2AminoTask(MultipleSequenceAlignmentObject *obj); 41 TranslateMsa2AminoTask(MultipleSequenceAlignmentObject *obj, const QString &trId); getTaskResult()42 const MultipleSequenceAlignment &getTaskResult() { 43 return resultMA; 44 } 45 void run(); 46 ReportResult report(); 47 48 private: 49 MultipleSequenceAlignment resultMA; 50 MultipleSequenceAlignmentObject *maObj; 51 DNATranslation *translation; 52 }; 53 54 /** 55 Wrapper for multiple alignment task 56 */ 57 58 class U2ALGORITHM_EXPORT AlignGObjectTask : public Task { 59 Q_OBJECT 60 public: AlignGObjectTask(const QString & taskName,TaskFlags f,MultipleSequenceAlignmentObject * maobj)61 AlignGObjectTask(const QString &taskName, TaskFlags f, MultipleSequenceAlignmentObject *maobj) 62 : Task(taskName, f), obj(maobj) { 63 } setMAObject(MultipleSequenceAlignmentObject * maobj)64 virtual void setMAObject(MultipleSequenceAlignmentObject *maobj) { 65 obj = maobj; 66 } getMAObject()67 MultipleSequenceAlignmentObject *getMAObject() { 68 return obj; 69 } 70 71 protected: 72 QPointer<MultipleSequenceAlignmentObject> obj; 73 }; 74 75 /** 76 Multi task converts alignment object to amino representation if possible. 77 This allows to: 78 1) speed up alignment 79 2) avoid errors of inserting gaps within codon boundaries 80 */ 81 82 class U2ALGORITHM_EXPORT AlignInAminoFormTask : public Task { 83 Q_OBJECT 84 Q_DISABLE_COPY(AlignInAminoFormTask) 85 public: 86 AlignInAminoFormTask(MultipleSequenceAlignmentObject *obj, AlignGObjectTask *alignTask, const QString &traslId); 87 ~AlignInAminoFormTask(); 88 89 virtual void prepare(); 90 virtual void run(); 91 virtual ReportResult report(); 92 93 protected: 94 AlignGObjectTask *alignTask; 95 MultipleSequenceAlignmentObject *maObj, *clonedObj; 96 QString traslId; 97 Document *tmpDoc; 98 QMap<qint64, QList<U2MsaGap>> rowsGapModel; 99 QMap<qint64, QList<U2MsaGap>> emptyGapModel; 100 }; 101 102 } // namespace U2 103 104 #endif // _U2_MSA_UTIL_TASKS 105