void tst_QQuickAccessible::cleanup()
{
const EventList list = QTestAccessibility::events();
if (!list.isEmpty()) {
qWarning("%d accessibility event(s) were not handled in testfunction '%s':", list.count(),
QString(QTest::currentTestFunction()).toLatin1().constData());
for (int i = 0; i < list.count(); ++i)
qWarning(" %d: Object: %p Event: '%s' Child: %d", i + 1, list.at(i)->object(),
qAccessibleEventString(list.at(i)->type()), list.at(i)->child());
}
QTestAccessibility::clearEvents();
}
void EventsWindow::eventContextMenu(const QPoint &pos)
{
EventsView *view = qobject_cast<EventsView*>(sender());
if (!view)
return;
EventList selectedEvents = view->selectedEvents();
EventList selectedMediaEvents = selectedEvents.filter(MediaEventFilter());
EventList selectedCameraEvents = selectedEvents.filter(CameraEventFilter());
QMenu menu(view);
QAction *aPlay = menu.addAction(tr("Play video"));
aPlay->setEnabled(selectedMediaEvents.size() == 1);
menu.setDefaultAction(aPlay);
QAction *aPlayWindow = menu.addAction(tr("Play in a new window"));
aPlayWindow->setEnabled(selectedMediaEvents.size() == 1);
menu.addSeparator();
QAction *aSave = menu.addAction(tr("Save video"));
aSave->setEnabled(!selectedMediaEvents.isEmpty());
menu.addSeparator();
QAction *aSelectOnly = menu.addAction(tr("Show only this camera"));
aSelectOnly->setEnabled(!selectedCameraEvents.isEmpty());
QAction *aSelectElse = menu.addAction(tr("Exclude this camera"));
aSelectElse->setEnabled(!selectedCameraEvents.isEmpty());
QAction *act = menu.exec(view->mapToGlobal(pos));
if (!act)
return;
else if (act == aPlay)
showEvent(view->currentIndex());
else if (act == aPlayWindow)
{
ModelEventsCursor *modelEventsCursor = new ModelEventsCursor();
modelEventsCursor->setModel(view->model());
modelEventsCursor->setCameraFilter(selectedMediaEvents.at(0).locationCamera());
modelEventsCursor->setIndex(view->currentIndex().row());
EventViewWindow::open(selectedMediaEvents.at(0), modelEventsCursor);
}
else if (act == aSave)
{
if (selectedMediaEvents.size() == 1)
bcApp->eventDownloadManager()->startEventDownload(selectedMediaEvents.at(0));
else
bcApp->eventDownloadManager()->startMultipleEventDownloads(selectedMediaEvents);
}
else if (act == aSelectOnly || act == aSelectElse)
{
EventSourcesModel *sModel = qobject_cast<EventSourcesModel*>(m_sourcesView->model());
Q_ASSERT(sModel);
if (!sModel)
return;
QSet<DVRCamera *> cameras = selectedCameraEvents.cameras();
QModelIndex sIdx = sModel->indexOfCamera(*cameras.begin());
if (act == aSelectOnly)
{
m_sourcesView->checkOnlyIndex(sIdx); // uncheck all, some kind of temporary hack
foreach (DVRCamera *camera, cameras)
sModel->setData(sModel->indexOfCamera(camera), Qt::Checked, Qt::CheckStateRole);
}
else
{
foreach (DVRCamera *camera, cameras)
sModel->setData(sModel->indexOfCamera(camera), Qt::Unchecked, Qt::CheckStateRole);
}
}
}
int runFishhook(int argc, char** argv) {
parseFishOptions(argc, argv);
if (opt::verbose) {
std::cerr << "FishHook Params: " << std::endl
<< "\tWidth: " << SeqLib::AddCommas(opt::width) << std::endl
<< "\tEvents: " << opt::events << std::endl
<< "\tCoverage Mask: " << opt::coverage << std::endl
<< "\tSlop: " << SeqLib::AddCommas(opt::slop) << std::endl
<< "\tInterval Tracks: " << std::endl;
for (auto& i : opt::interval_files)
std::cerr << "\t-- " << i << std::endl;
std::cerr << "\tScored Tracks: " << std::endl;
for (auto& i : opt::scored_files)
std::cerr << "\t-- " << i << std::endl;
std::cerr << "\tSequence Features: " << std::endl;
for (auto& i : opt::seq_features)
std::cerr << "\t-- " << i << std::endl;
}
// read in the covariate tracks
SeqHashMap<std::string, Fractions> intervals;
// read a header for info
SeqLib::BamReader rdr;
if (!rdr.Open(opt::bam)) {
std::cerr << "Error: Could not read BAM supplied by -b: " << opt::bam << std::endl;
exit(EXIT_FAILURE);
}
hdr = rdr.Header();
// read in the reference genome
SeqLib::RefGenome ref;
if (!ref.LoadIndex(opt::refgenome)) {
if (opt::seq_features.size()) {
std::cerr << "Error: Could not read referene genome supplied by -G: " << opt::refgenome << std::endl;
exit(EXIT_FAILURE);
}
}
// read in the events
if (opt::verbose) std::cerr << "...reading events " << opt::events << std::endl;
EventList events;
if (!events.readFromBed(opt::events, hdr)) {
std::cerr << "Error: Could not read events BED: " << opt::events << std::endl;
exit(EXIT_FAILURE);
}
if (opt::verbose) std::cerr << "...read in " << SeqLib::AddCommas(events.size()) << " events" << std::endl;
events.CreateTreeMap();
// create the tiled regions
FishHookTiles fish(opt::width, opt::slop, hdr.GetHeaderSequenceVector());
if (opt::verbose)
std::cerr << "...constructed " << SeqLib::AddCommas(fish.size()) << " fishhook intervals" << std::endl;
fish.CreateTreeMap();
// read the coverage mask
SeqLib::GRC cov;
if (!opt::coverage.empty()) {
if (opt::verbose) std::cerr << "...reading coverage mask " << opt::coverage << std::endl;
cov.ReadBED(opt::coverage, hdr);
if (opt::verbose) std::cerr << "...read in " << SeqLib::AddCommas(cov.size()) << " covered regions " << std::endl;
if (!cov.size()) {
std::cerr << "Non-empty coverage track read with 0 regions. Check that is non-empty BED" << std::endl;
exit(EXIT_FAILURE);
}
if (opt::verbose) std::cerr << "...creating interval tree map on covered regions and overlapping with tiles" << std::endl;
cov.CreateTreeMap();
// find covered amount per tile
std::vector<int32_t> q, s;
SeqLib::GRC ovlp;
// fish is subject
if (fish.size() > cov.size()) // do in most efficient order
ovlp = cov.FindOverlaps(fish, q, s, false);
else
ovlp = fish.FindOverlaps(cov, s, q, false);
if (opt::verbose) std::cerr << "..." << SeqLib::AddCommas(ovlp.size()) << " regions are covered" << std::endl;
// set the amount covered by each
for (size_t i = 0; i < ovlp.size(); ++i) {
fish[s[i]].covered += (double)ovlp[i].Width() / fish[s[i]].Width();
}
// mask the events
q.clear(); s.clear(); ovlp.clear();
// events is subject
if (events.size() > cov.size()) // do in most efficient order
ovlp = cov.FindOverlaps(events, q, s, false);
else
ovlp = events.FindOverlaps(cov, s, q, false);
EventList newe;
// set the amount covered by each
for (size_t i = 0; i < ovlp.size(); ++i) {
newe.add(Event(ovlp[i], events.at(s[i]).id));
}
events = newe;
events.CreateTreeMap();
if (opt::verbose) std::cerr << "...kept " << SeqLib::AddCommas(events.size()) << " events after mask" << std::endl;
} else {
for (auto& i : fish)
i.covered = 1; // the entire thing is covered if no mask provided
}
// read in the interval tracks
for (auto& i : opt::interval_files)
read_track(i, intervals, cov, false);
for (auto& i : opt::scored_files)
read_track(i, intervals, cov, true);
// count events per tile (also de-dupes on patient per bin)
fish.CountEvents(events);
// overlap the covariates with the tiles
for (auto& i : intervals) {
fish.AddIntervalCovariate(i.first, i.second);
}
// make the matrix
FishModel fm;
fm.AddTiles(fish);
fm.SetNumThreads(opt::num_threads);
fm.EstimateOLS();
fm.CooksDistance(fm.GetOLS());
// write the covariates
fish.PrintBEDHeader(std::cout);
fish.PrintBED(std::cout, hdr);
return 0;
}