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