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 "TBlastXPlusSupportTask.h"
23
24 #include <QDomDocument>
25 #include <QFileInfo>
26
27 #include <U2Core/AppContext.h>
28 #include <U2Core/AppResources.h>
29 #include <U2Core/AppSettings.h>
30 #include <U2Core/CreateAnnotationTask.h>
31 #include <U2Core/DocumentModel.h>
32 #include <U2Core/ExternalToolRegistry.h>
33 #include <U2Core/Log.h>
34 #include <U2Core/ProjectModel.h>
35 #include <U2Core/UserApplicationsSettings.h>
36
37 #include "BlastPlusSupport.h"
38
39 namespace U2 {
40
createBlastPlusTask()41 ExternalToolRunTask *TBlastXPlusSupportTask::createBlastPlusTask() {
42 QStringList arguments;
43
44 arguments << "-db" << settings.databaseNameAndPath;
45 arguments << "-evalue" << QString::number(settings.expectValue);
46 if (settings.wordSize <= 0) {
47 arguments << "-word_size"
48 << "3";
49 } else {
50 arguments << "-word_size" << QString::number(settings.wordSize);
51 }
52
53 if (settings.directStrand == TriState_Yes) {
54 arguments << "-strand"
55 << "plus";
56 } else if (settings.directStrand == TriState_No) {
57 arguments << "-strand"
58 << "minus";
59 }
60
61 if (settings.isNucleotideSeq && (!settings.isDefautScores)) {
62 assert(false);
63 coreLog.error(tr("Unexpected settings combination"));
64 } else {
65 if (!settings.isDefaultMatrix) {
66 arguments << "-matrix" << settings.matrix;
67 }
68 }
69 if (settings.numberOfHits != 0) {
70 arguments << "-culling_limit" << QString::number(settings.numberOfHits); //???
71 }
72 arguments << "-query" << url;
73
74 if (settings.xDropoffUnGA != 7) {
75 arguments << "-xdrop_ungap" << QString::number(settings.xDropoffUnGA);
76 }
77 if (!settings.isDefaultThreshold) {
78 arguments << "-threshold" << QString::number(settings.threshold);
79 }
80 if (settings.windowSize != 40) {
81 arguments << "-window_size" << QString::number(settings.windowSize);
82 }
83 arguments << "-num_threads" << QString::number(settings.numberOfProcessors);
84 arguments << "-outfmt" << QString::number(settings.outputType); //"5";//Set output file format to xml
85 if (settings.outputOriginalFile.isEmpty()) {
86 arguments << "-out" << url + ".xml";
87 settings.outputOriginalFile = url + ".xml";
88 } else {
89 arguments << "-out" << settings.outputOriginalFile;
90 }
91
92 algoLog.trace("TBlastX+ arguments: " + arguments.join(" "));
93 QString workingDirectory = QFileInfo(url).absolutePath();
94
95 ExternalToolRunTask *runTask = new ExternalToolRunTask(BlastPlusSupport::ET_TBLASTX_ID, arguments, new ExternalToolLogParser(), workingDirectory);
96 setListenerForTask(runTask);
97 return runTask;
98 }
99
100 } // namespace U2
101