void SpectrumSettings::unify(const SpectrumSettings & rhs)
{
// append metavalues (overwrite when already present)
std::vector<UInt> keys;
rhs.getKeys(keys);
for (Size i = 0; i < keys.size(); ++i)
setMetaValue(keys[i], rhs.getMetaValue(keys[i]));
if (type_ != rhs.type_)
type_ = UNKNOWN; // only keep if both are equal
//native_id_ == rhs.native_id_ // keep
comment_ += rhs.comment_; // append
//instrument_settings_ == rhs.instrument_settings_ // keep
//acquisition_info_ == rhs.acquisition_info_
//source_file_ == rhs.source_file_ &&
precursors_.insert(precursors_.end(), rhs.precursors_.begin(), rhs.precursors_.end());
products_.insert(products_.end(), rhs.products_.begin(), rhs.products_.end());
identification_.insert(identification_.end(), rhs.identification_.begin(), rhs.identification_.end());
data_processing_.insert(data_processing_.end(), rhs.data_processing_.begin(), rhs.data_processing_.end());
}
//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);
}
void ChromatogramExtractor::return_chromatogram(std::vector< OpenSwath::ChromatogramPtr > & chromatograms,
std::vector< ChromatogramExtractor::ExtractionCoordinates > & coordinates,
OpenMS::TargetedExperiment & transition_exp_used, SpectrumSettings settings,
std::vector<OpenMS::MSChromatogram<> > & output_chromatograms, bool ms1) const
{
typedef std::map<String, const ReactionMonitoringTransition* > TransitionMapType;
TransitionMapType trans_map;
for (Size i = 0; i < transition_exp_used.getTransitions().size(); i++)
{
trans_map[transition_exp_used.getTransitions()[i].getNativeID()] = &transition_exp_used.getTransitions()[i];
}
for (Size i = 0; i < chromatograms.size(); i++)
{
const OpenSwath::ChromatogramPtr & chromptr = chromatograms[i];
const ChromatogramExtractor::ExtractionCoordinates & coord = coordinates[i];
TargetedExperiment::Peptide pep;
OpenMS::ReactionMonitoringTransition transition;
OpenMS::MSChromatogram<> chrom;
// copy data
OpenSwathDataAccessHelper::convertToOpenMSChromatogram(chrom, chromptr);
chrom.setNativeID(coord.id);
// Create precursor and set
// 1) the target m/z
// 2) the isolation window (upper/lower)
// 3) the peptide sequence
Precursor prec;
if (ms1)
{
pep = transition_exp_used.getPeptideByRef(coord.id);
prec.setMZ(coord.mz);
chrom.setChromatogramType(ChromatogramSettings::BASEPEAK_CHROMATOGRAM);
}
else
{
transition = (*trans_map[coord.id]);
pep = transition_exp_used.getPeptideByRef(transition.getPeptideRef());
prec.setMZ(transition.getPrecursorMZ());
if (settings.getPrecursors().size() > 0)
{
prec.setIsolationWindowLowerOffset(settings.getPrecursors()[0].getIsolationWindowLowerOffset());
prec.setIsolationWindowUpperOffset(settings.getPrecursors()[0].getIsolationWindowUpperOffset());
}
// Create product and set its m/z
Product prod;
prod.setMZ(transition.getProductMZ());
chrom.setProduct(prod);
chrom.setChromatogramType(ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM);
}
prec.setMetaValue("peptide_sequence", pep.sequence);
chrom.setPrecursor(prec);
// Set the rest of the meta-data
chrom.setInstrumentSettings(settings.getInstrumentSettings());
chrom.setAcquisitionInfo(settings.getAcquisitionInfo());
chrom.setSourceFile(settings.getSourceFile());
for (Size i = 0; i < settings.getDataProcessing().size(); ++i)
{
DataProcessing dp = settings.getDataProcessing()[i];
dp.setMetaValue("performed_on_spectra", "true");
chrom.getDataProcessing().push_back(dp);
}
output_chromatograms.push_back(chrom);
}
}
