//Visualizing ProteinIdentification object
void MetaDataBrowser::visualize_(ProteinIdentification & meta, QTreeWidgetItem * parent)
{
ProteinIdentificationVisualizer * visualizer = new ProteinIdentificationVisualizer(isEditable(), this, this);
QStringList labels;
int id = ws_->addWidget(visualizer);
labels << QString("ProteinIdentification %1").arg(meta.getSearchEngine().c_str()) << QString::number(id);
visualizer->load(meta, id);
QTreeWidgetItem * item;
if (parent == nullptr)
{
item = new QTreeWidgetItem(treeview_, labels);
}
else
{
item = new QTreeWidgetItem(parent, labels);
}
//check for proteinhits objects
meta.assignRanks();
for (Size i = 0; i < meta.getHits().size(); ++i)
{
visualize_(const_cast<ProteinHit &>(meta.getHits()[i]), item);
}
visualize_(dynamic_cast<MetaInfoInterface &>(meta), item);
connectVisualizer_(visualizer);
}
//Visualizing DataProcessing object
void MetaDataBrowser::visualize_(DataProcessingPtr & meta, QTreeWidgetItem * parent)
{
DataProcessingVisualizer * visualizer = new DataProcessingVisualizer(isEditable(), this);
visualizer->load(*meta);
QStringList labels;
labels << "DataProcessing" << QString::number(ws_->addWidget(visualizer));
QTreeWidgetItem * item;
if (parent == nullptr)
{
item = new QTreeWidgetItem(treeview_, labels);
}
else
{
item = new QTreeWidgetItem(parent, labels);
}
//Software object
visualize_(meta->getSoftware(), item);
visualize_(dynamic_cast<MetaInfoInterface &>(*meta), item);
connectVisualizer_(visualizer);
}
//Visualizing Instrument object
void MetaDataBrowser::visualize_(Instrument & meta, QTreeWidgetItem * parent)
{
InstrumentVisualizer * visualizer = new InstrumentVisualizer(isEditable(), this);
visualizer->load(meta);
QStringList labels;
labels << "Instrument" << QString::number(ws_->addWidget(visualizer));
QTreeWidgetItem * item;
if (parent == nullptr)
{
item = new QTreeWidgetItem(treeview_, labels);
}
else
{
item = new QTreeWidgetItem(parent, labels);
}
//IonSources
visualizeAll_(meta.getIonSources(), item);
//MassAnalyzers
visualizeAll_(meta.getMassAnalyzers(), item);
//IonDectector
visualizeAll_(meta.getIonDetectors(), item);
//Software
visualize_(meta.getSoftware(), item);
visualize_(dynamic_cast<MetaInfoInterface &>(meta), item);
connectVisualizer_(visualizer);
}
//Visualizing ProteinHit object
void MetaDataBrowser::visualize_(ProteinHit & meta, QTreeWidgetItem * parent)
{
ProteinHitVisualizer * visualizer = new ProteinHitVisualizer(isEditable(), this);
visualizer->load(meta);
String name = String("Prot ") + meta.getAccession() + " (" + meta.getScore() + ')';
QString qs_name(name.c_str());
QStringList labels;
labels << qs_name << QString::number(ws_->addWidget(visualizer)) << QString::number(meta.getScore());
QTreeWidgetItem * item;
if (parent == nullptr)
{
item = new QTreeWidgetItem(treeview_, labels);
}
else
{
item = new QTreeWidgetItem(parent, labels);
}
visualize_(dynamic_cast<MetaInfoInterface &>(meta), item);
connectVisualizer_(visualizer);
}
//Visualizing MetaInfoDescription object
void MetaDataBrowser::visualize_(MetaInfoDescription & meta, QTreeWidgetItem * parent)
{
MetaInfoDescriptionVisualizer * visualizer = new MetaInfoDescriptionVisualizer(isEditable(), this);
visualizer->load(meta);
QStringList labels;
String name = String("MetaInfoDescription ") + meta.getName();
labels << name.c_str() << QString::number(ws_->addWidget(visualizer));
QTreeWidgetItem * item;
if (parent == nullptr)
{
item = new QTreeWidgetItem(treeview_, labels);
}
else
{
item = new QTreeWidgetItem(parent, labels);
}
//check for DataProcessing
visualizeAll_(meta.getDataProcessing(), item);
visualize_(dynamic_cast<MetaInfoInterface &>(meta), item);
connectVisualizer_(visualizer);
}
//Visualizing InstrumentSettings object
void MetaDataBrowser::visualize_(InstrumentSettings & meta, QTreeWidgetItem * parent)
{
InstrumentSettingsVisualizer * visualizer = new InstrumentSettingsVisualizer(isEditable(), this);
visualizer->load(meta);
QStringList labels;
labels << "InstrumentSettings" << QString::number(ws_->addWidget(visualizer));
QTreeWidgetItem * item;
if (parent == nullptr)
{
item = new QTreeWidgetItem(treeview_, labels);
}
else
{
item = new QTreeWidgetItem(parent, labels);
}
//ScanWindows
visualizeAll_(meta.getScanWindows(), item);
visualize_(dynamic_cast<MetaInfoInterface &>(meta), item);
connectVisualizer_(visualizer);
}
//Visualizing AcquisitionInfo object
void MetaDataBrowser::visualize_(AcquisitionInfo & meta, QTreeWidgetItem * parent)
{
AcquisitionInfoVisualizer * visualizer = new AcquisitionInfoVisualizer(isEditable(), this);
visualizer->load(meta);
QStringList labels;
labels << "Acquisition Info" << QString::number(ws_->addWidget(visualizer));
QTreeWidgetItem * item;
if (parent == nullptr)
{
item = new QTreeWidgetItem(treeview_, labels);
}
else
{
item = new QTreeWidgetItem(parent, labels);
}
//Get Aquisition objects
visualizeAll_(meta, item);
visualize_(dynamic_cast<MetaInfoInterface &>(meta), item);
connectVisualizer_(visualizer);
}
void OpenniVisualizer::visualizerThread()
{
#ifdef USE_PCL_VIEWER
if (visualizeCloud_) {
// prepare visualizer named "viewer"
viewer_ = boost::shared_ptr<pcl::visualization::PCLVisualizer>(
new pcl::visualization::PCLVisualizer ("3D Viewer"));
viewer_->initCameraParameters ();
viewer_->setBackgroundColor (255, 255, 255);
viewer_->addCoordinateSystem (1.0);
viewer_->setSize(1000,1000);
while (!viewer_->wasStopped ()) {
viewer_->spinOnce (10);
char key = cv::waitKey(10);
// Get lock on the boolean update and check if cloud was updated
boost::mutex::scoped_lock updateLock(updateModelMutex);
if (update_) {
visualize_(key);
update_ = false;
}
}
} else {
while (42) {
char key = cv::waitKey(10);
// Get lock on the boolean update and check if cloud was updated
boost::mutex::scoped_lock updateLock(updateModelMutex);
if (update_) {
visualize_(key);
update_ = false;
}
}
}
#else
while (42)
{
char key = cv::waitKey(10);
// Get lock on the boolean update and check if cloud was updated
boost::mutex::scoped_lock updateLock(updateModelMutex);
if (update_)
{
visualize_(key);
update_ = false;
}
}
#endif
}
//Visualizing sample object
void MetaDataBrowser::visualize_(Sample & meta, QTreeWidgetItem * parent)
{
SampleVisualizer * visualizer = new SampleVisualizer(isEditable(), this);
visualizer->load(meta);
QStringList labels;
labels << (String("Sample ") + meta.getName()).c_str() << QString::number(ws_->addWidget(visualizer));
QTreeWidgetItem * item;
if (parent == nullptr)
{
item = new QTreeWidgetItem(treeview_, labels);
}
else
{
item = new QTreeWidgetItem(parent, labels);
}
//check for treatments
if (meta.countTreatments() != 0)
{
for (Int i = 0; i < meta.countTreatments(); ++i)
{
if (meta.getTreatment(i).getType() == "Digestion")
{
visualize_((const_cast<Digestion &>(dynamic_cast<const Digestion &>(meta.getTreatment(i)))), item);
}
else if (meta.getTreatment(i).getType() == "Modification")
{
//Cast SampleTreatment reference to a const modification reference
visualize_((const_cast<Modification &>(dynamic_cast<const Modification &>(meta.getTreatment(i)))), item);
}
else if (meta.getTreatment(i).getType() == "Tagging")
{
visualize_((const_cast<Tagging &>(dynamic_cast<const Tagging &>(meta.getTreatment(i)))), item);
}
}
}
//subsamples
visualizeAll_(meta.getSubsamples(), item);
visualize_(dynamic_cast<MetaInfoInterface &>(meta), item);
connectVisualizer_(visualizer);
}
//Visualizing SpectrumSettings object
void MetaDataBrowser::visualize_(SpectrumSettings & meta, QTreeWidgetItem * parent)
{
SpectrumSettingsVisualizer * visualizer = new SpectrumSettingsVisualizer(isEditable(), this);
visualizer->load(meta);
QStringList labels;
labels << "SpectrumSettings" << QString::number(ws_->addWidget(visualizer));
QTreeWidgetItem * item;
if (parent == nullptr)
{
item = new QTreeWidgetItem(treeview_, labels);
}
else
{
item = new QTreeWidgetItem(parent, labels);
}
//check for InstrumentSettings
visualize_(meta.getInstrumentSettings(), item);
//check for DataProcessing
visualizeAll_(meta.getDataProcessing(), item);
//check for Precursors
for (Size i = 0; i < meta.getPrecursors().size(); ++i)
{
visualize_(meta.getPrecursors()[i], item);
}
//check for Products
for (Size i = 0; i < meta.getProducts().size(); ++i)
{
visualize_(meta.getProducts()[i], item);
}
//check for AcquisitionInfo
visualize_(meta.getAcquisitionInfo(), item);
//check for PeptideIdentification
visualizeAll_(meta.getPeptideIdentifications(), item);
connectVisualizer_(visualizer);
}
//Visualizing ExperimentalSettings object
void MetaDataBrowser::visualize_(ExperimentalSettings & meta, QTreeWidgetItem * parent)
{
ExperimentalSettingsVisualizer * visualizer = new ExperimentalSettingsVisualizer(isEditable(), this);
visualizer->load(meta);
QStringList labels;
labels << "ExperimentalSettings" << QString::number(ws_->addWidget(visualizer));
QTreeWidgetItem * item;
if (parent == nullptr)
{
item = new QTreeWidgetItem(treeview_, labels);
}
else
{
item = new QTreeWidgetItem(parent, labels);
}
visualize_(dynamic_cast<DocumentIdentifier &>(meta), item);
//check for Sample
visualize_(meta.getSample(), item);
//check for ProteinIdentification
visualizeAll_(meta.getProteinIdentifications(), item);
//check for Instrument
visualize_(meta.getInstrument(), item);
//check for SourceFiles
visualizeAll_(meta.getSourceFiles(), item);
//check for ContactPersons
visualizeAll_(meta.getContacts(), item);
//check for HPLC
visualize_(meta.getHPLC(), item);
visualize_(dynamic_cast<MetaInfoInterface &>(meta), item);
connectVisualizer_(visualizer);
}
//Visualizing SourceFile object
void MetaDataBrowser::visualize_(SourceFile & meta, QTreeWidgetItem * parent)
{
SourceFileVisualizer * visualizer = new SourceFileVisualizer(isEditable(), this);
visualizer->load(meta);
QStringList labels;
labels << "SourceFile" << QString::number(ws_->addWidget(visualizer));
QTreeWidgetItem * item;
if (parent == nullptr)
{
item = new QTreeWidgetItem(treeview_, labels);
}
else
{
item = new QTreeWidgetItem(parent, labels);
}
visualize_(dynamic_cast<MetaInfoInterface &>(meta), item);
connectVisualizer_(visualizer);
}
//Visualizing HPLC object
void MetaDataBrowser::visualize_(HPLC & meta, QTreeWidgetItem * parent)
{
HPLCVisualizer * visualizer = new HPLCVisualizer(isEditable(), this);
visualizer->load(meta);
QStringList labels;
labels << "HPLC" << QString::number(ws_->addWidget(visualizer));
QTreeWidgetItem * item;
if (parent == nullptr)
{
item = new QTreeWidgetItem(treeview_, labels);
}
else
{
item = new QTreeWidgetItem(parent, labels);
}
visualize_(meta.getGradient(), item);
connectVisualizer_(visualizer);
}
