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 #include "ExportSequencesTask.h"
23
24 #include <QFile>
25 #include <QScopedPointer>
26
27 #include <U2Core/AppContext.h>
28 #include <U2Core/DNAAlphabet.h>
29 #include <U2Core/DNASequenceObject.h>
30 #include <U2Core/DocumentSelection.h>
31 #include <U2Core/GUrlUtils.h>
32 #include <U2Core/IOAdapterUtils.h>
33 #include <U2Core/MSAUtils.h>
34 #include <U2Core/MultiTask.h>
35 #include <U2Core/ProjectModel.h>
36 #include <U2Core/SaveDocumentTask.h>
37 #include <U2Core/U2ObjectDbi.h>
38 #include <U2Core/U2SequenceUtils.h>
39
40 #include <U2Formats/DocumentFormatUtils.h>
41
42 #include <U2Gui/ObjectViewModel.h>
43
44 namespace U2 {
45
ExportSequencesTask(const MultipleSequenceAlignment & msa,const QSet<qint64> & rowIds,bool trimGaps,bool addToProjectFlag,const QString & dirUrl,const DocumentFormatId & format,const QString & extension,const QString & customFileName)46 ExportSequencesTask::ExportSequencesTask(const MultipleSequenceAlignment &msa, const QSet<qint64> &rowIds, bool trimGaps, bool addToProjectFlag, const QString &dirUrl, const DocumentFormatId &format, const QString &extension, const QString &customFileName)
47 : Task(tr("Export selected sequences from alignment"), TaskFlags_NR_FOSE_COSC),
48 addToProjectFlag(addToProjectFlag),
49 dirUrl(dirUrl),
50 format(format),
51 extension(extension),
52 customFileName(customFileName) {
53 sequences = MSAUtils::convertMsaToSequenceList(msa, stateInfo, trimGaps, rowIds);
54 }
55
prepare()56 void ExportSequencesTask::prepare() {
57 QList<Task *> tasks;
58 QSet<QString> existingFilenames;
59 for (const DNASequence &sequence : qAsConst(sequences)) {
60 QString filename = GUrlUtils::fixFileName(customFileName.isEmpty() ? sequence.getName() : customFileName);
61 QString filePath = GUrlUtils::prepareFileLocation(dirUrl + "/" + filename + "." + extension, stateInfo);
62 CHECK_OP(stateInfo, );
63
64 filePath = GUrlUtils::rollFileName(filePath, "_", existingFilenames);
65 existingFilenames.insert(filePath);
66 GUrl url(filePath);
67 IOAdapterFactory *iof = AppContext::getIOAdapterRegistry()->getIOAdapterFactoryById(IOAdapterUtils::url2io(url));
68 DocumentFormat *df = AppContext::getDocumentFormatRegistry()->getFormatById(format);
69 SAFE_POINT(df != nullptr, "Cant get DocuemtFormat by given DocumentFormatId", );
70
71 QScopedPointer<Document> doc(df->createNewLoadedDocument(iof, filePath, stateInfo));
72 CHECK_OP(stateInfo, );
73
74 QVariantMap hints;
75 hints.insert(DocumentFormat::DBI_FOLDER_HINT, U2ObjectDbi::ROOT_FOLDER);
76 U2EntityRef ref = U2SequenceUtils::import(stateInfo, doc->getDbiRef(), U2ObjectDbi::ROOT_FOLDER, sequence, sequence.alphabet->getId());
77 CHECK_OP(stateInfo, );
78
79 auto sequenceObject = new U2SequenceObject(sequence.getName(), ref);
80 doc->addObject(sequenceObject);
81
82 Document *takenDoc = doc.take();
83 auto saveTask = new SaveDocumentTask(takenDoc, takenDoc->getIOAdapterFactory(), takenDoc->getURL());
84 saveTask->addFlag(addToProjectFlag ? SaveDoc_OpenAfter : SaveDoc_DestroyAfter);
85 addSubTask(saveTask);
86 }
87 }
88
89 } // namespace U2
90