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 "SnpEffSupport.h"
23
24 #include <U2Core/AppContext.h>
25 #include <U2Core/AppResources.h>
26 #include <U2Core/AppSettings.h>
27 #include <U2Core/DataPathRegistry.h>
28 #include <U2Core/ScriptingToolRegistry.h>
29 #include <U2Core/Settings.h>
30 #include <U2Core/U2OpStatusUtils.h>
31 #include <U2Core/U2SafePoints.h>
32
33 #include <U2Formats/ConvertFileTask.h>
34
35 #include "SnpEffDatabaseListModel.h"
36 #include "SnpEffDatabaseListTask.h"
37 #include "java/JavaSupport.h"
38
39 namespace U2 {
40
41 SnpEffDatabaseListModel *SnpEffSupport::databaseModel = new SnpEffDatabaseListModel();
42 const QString SnpEffSupport::ET_SNPEFF = "SnpEff";
43 const QString SnpEffSupport::ET_SNPEFF_ID = "USUPP_SNPEFF";
44
SnpEffSupport()45 SnpEffSupport::SnpEffSupport()
46 : ExternalTool(SnpEffSupport::ET_SNPEFF_ID, "snpeff", SnpEffSupport::ET_SNPEFF) {
47 if (AppContext::getMainWindow() != nullptr) {
48 icon = QIcon(":external_tool_support/images/cmdline.png");
49 grayIcon = QIcon(":external_tool_support/images/cmdline_gray.png");
50 warnIcon = QIcon(":external_tool_support/images/cmdline_warn.png");
51 }
52
53 executableFileName = "snpEff.jar";
54
55 validMessage = "Usage: snpEff \\[command\\] \\[options\\] \\[files\\]";
56 description = tr("<i>SnpEff</i>: Genetic variant annotation and effect prediction toolbox.");
57
58 versionRegExp = QRegExp("version SnpEff (\\d+.\\d+[a-zA-Z]?)");
59 validationArguments << "-h";
60 toolKitName = "SnpEff";
61
62 toolRunnerProgram = JavaSupport::ET_JAVA_ID;
63 dependencies << JavaSupport::ET_JAVA_ID;
64
65 connect(this, SIGNAL(si_toolValidationStatusChanged(bool)), SLOT(sl_validationStatusChanged(bool)));
66 }
67
getToolRunnerAdditionalOptions() const68 QStringList SnpEffSupport::getToolRunnerAdditionalOptions() const {
69 QStringList result;
70 AppResourcePool *s = AppContext::getAppSettings()->getAppResourcePool();
71 CHECK(s != nullptr, result);
72 //java VM can't allocate whole free memory, Xmx size should be lesser than free memory
73 int memSize = s->getMaxMemorySizeInMB();
74 #if (defined(Q_OS_WIN) || defined(Q_OS_LINUX))
75 ExternalToolRegistry *etRegistry = AppContext::getExternalToolRegistry();
76 JavaSupport *java = qobject_cast<JavaSupport *>(etRegistry->getById(JavaSupport::ET_JAVA_ID));
77 CHECK(java != nullptr, result);
78 if (java->getArchitecture() == JavaSupport::x32) {
79 memSize = memSize > 1212 ? 1212 : memSize;
80 }
81 #endif // windows or linux
82 result << "-Xmx" + QString::number(memSize > 150 ? memSize - 150 : memSize) + "M";
83 return result;
84 }
85
sl_validationStatusChanged(bool isValid)86 void SnpEffSupport::sl_validationStatusChanged(bool isValid) {
87 if (isValid) {
88 SnpEffDatabaseListTask *task = new SnpEffDatabaseListTask();
89 connect(task, SIGNAL(si_stateChanged()), SLOT(sl_databaseListIsReady()));
90 AppContext::getTaskScheduler()->registerTopLevelTask(task);
91 }
92 }
93
sl_databaseListIsReady()94 void SnpEffSupport::sl_databaseListIsReady() {
95 SnpEffDatabaseListTask *task = dynamic_cast<SnpEffDatabaseListTask *>(sender());
96 SAFE_POINT(task != nullptr, "SnpEffDatabaseListTask is NULL: wrong sender", );
97 if (task->isCanceled() || task->hasError() || !task->isFinished()) {
98 return;
99 }
100 QString dbListFilePath = task->getDbListFilePath();
101 SAFE_POINT(!dbListFilePath.isEmpty(), tr("Failed to get SnpEff database list"), );
102
103 SnpEffSupport::databaseModel->getData(dbListFilePath);
104 }
105
106 } // namespace U2
107
