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_KRAKEN_CLASSIFY_WORKER_H_
23 #define _U2_KRAKEN_CLASSIFY_WORKER_H_
24 
25 #include <U2Lang/LocalDomain.h>
26 
27 #include "../ngs_reads_classification/src/TaxonomySupport.h"
28 #include "KrakenClassifyTask.h"
29 
30 namespace U2 {
31 namespace LocalWorkflow {
32 
33 class KrakenClassifyWorker : public BaseWorker {
34     Q_OBJECT
35 public:
36     KrakenClassifyWorker(Actor *actor);
37 
38     void init();
39     Task *tick();
40     void cleanup();
41 
42 private slots:
43     void sl_taskFinished(Task *task);
44 
45 private:
46     bool isReadyToRun() const;
47     bool dataFinished() const;
48 
49     KrakenClassifyTaskSettings getSettings(U2OpStatus &os);
50     IntegralBus *input;
51     IntegralBus *output;
52 
53     bool pairedReadsInput;
54 
55     static const QString KRAKEN_DIR;
56 };
57 
58 }  // namespace LocalWorkflow
59 }  // namespace U2
60 
61 #endif  // _U2_KRAKEN_CLASSIFY_WORKER_H_
62