// print help info
int Help(int argc, char* argv[]) {
// check for 'bamtools help COMMAND' to print tool-specific help message
if (argc > 2) {
// determine desired sub-tool
AbstractTool* tool = CreateTool( argv[2] );
// if tool known, print its help screen
if ( tool ) return tool->Help();
}
// print general BamTools help message
cerr << endl;
cerr << "usage: bamtools [--help] COMMAND [ARGS]" << endl;
cerr << endl;
cerr << "Available bamtools commands:" << endl;
cerr << "\tconvert Converts between BAM and a number of other formats" << endl;
cerr << "\tcount Prints number of alignments in BAM file(s)" << endl;
cerr << "\tcoverage Prints coverage statistics from the input BAM file" << endl;
cerr << "\tfilter Filters BAM file(s) by user-specified criteria" << endl;
cerr << "\theader Prints BAM header information" << endl;
cerr << "\tindex Generates index for BAM file" << endl;
cerr << "\tmerge Merge multiple BAM files into single file" << endl;
cerr << "\trandom Select random alignments from existing BAM file(s), intended more as a testing tool." << endl;
cerr << "\tresolve Resolves paired-end reads (marking the IsProperPair flag as needed)" << endl;
cerr << "\trevert Removes duplicate marks and restores original base qualities" << endl;
cerr << "\tsort Sorts the BAM file according to some criteria" << endl;
cerr << "\tsplit Splits a BAM file on user-specified property, creating a new BAM output file for each value found" << endl;
cerr << "\tstats Prints some basic statistics from input BAM file(s)" << endl;
cerr << endl;
cerr << "See 'bamtools help COMMAND' for more information on a specific command." << endl;
cerr << endl;
return EXIT_SUCCESS;
}
void ToolsDockWidget::setScene(Scene * scene)
{
if (scene)
this->connect(scene, SIGNAL(destroyed()), this, SLOT(setScene()));
if (sender() && !scene && this->m_scene)
return;
m_scene = scene;
QWidget * w = d->toolArea->widget();
AbstractTool * tool = dynamic_cast<AbstractTool*>(w);
if (tool)
tool->setScene(m_scene);
}
/**
* Sets the MapDocument on which the registered tools will operate.
*/
void ToolManager::setMapDocument(MapDocument *mapDocument)
{
if (mMapDocument == mapDocument)
return;
mMapDocument = mapDocument;
const auto actions = mActionGroup->actions();
for (QAction *action : actions) {
AbstractTool *tool = action->data().value<AbstractTool*>();
tool->setMapDocument(mapDocument);
}
}
// toolkit entry point
int main(int argc, char* argv[]) {
// just 'bamtools'
if ( (argc == 1) ) return Help(argc, argv);
// 'bamtools help', 'bamtools --help', or 'bamtools -h'
if ( IsHelp(argv[1]) ) return Help(argc, argv);
// 'bamtools version', 'bamtools --version', or 'bamtools -v'
if ( IsVersion(argv[1]) ) return Version();
// determine desired sub-tool, run if found
AbstractTool* tool = CreateTool( argv[1] );
if ( tool ) return tool->Run(argc, argv);
// no tool matched, show help
return Help(argc, argv);
}
// toolkit entry point
int main(int argc, char* argv[]) {
// just 'bamtools'
if ( (argc == 1) ) return Help(argc, argv);
// 'bamtools help', 'bamtools --help', or 'bamtools -h'
if ( IsHelp(argv[1]) ) return Help(argc, argv);
// 'bamtools version', 'bamtools --version', or 'bamtools -v'
if ( IsVersion(argv[1]) ) return Version();
// determine desired sub-tool
AbstractTool* tool = CreateTool( argv[1] );
// if found, run tool... otherwise show help
if ( tool ) return tool->Run(argc, argv);
else return Help(argc, argv);
}
void ToolsManager::runTool()
{
QObject* sender = QObject::sender();
for (QMap<QAction*,Tool>::const_iterator it = this->m_Tools.begin() ; it != this->m_Tools.end() ; ++it)
{
if (it.key() == sender)
{
AbstractTool* tool = (*it)(this->parentWidget());
AbstractTool::RunState res = tool->run(this->mp_ToolsData->commands(), this->mp_ToolsData);
if (res == AbstractTool::Success)
this->mp_ToolsData->commands()->push();
else if (res == AbstractTool::Error)
{
QMessageBox error(QMessageBox::Warning, "Tool error", "Error occurred during the run of a tool.", QMessageBox::Ok);
error.setInformativeText("<nobr>Check the logger for more informations.</nobr>");
error.exec();
}
}
}
};
void ToolManager::retranslateTools()
{
// Allow the tools to adapt to the new language
const auto actions = mActionGroup->actions();
for (QAction *action : actions) {
AbstractTool *tool = action->data().value<AbstractTool*>();
tool->languageChanged();
// Update the text, shortcut and tooltip of the action
action->setText(tool->name());
action->setShortcut(tool->shortcut());
if (!tool->shortcut().isEmpty()) {
action->setToolTip(
QString(QLatin1String("%1 (%2)")).arg(tool->name(),
tool->shortcut().toString()));
} else {
action->setToolTip(tool->name());
}
}
}
