/// <summary>
/// Builds and assigns the spectral trees for each detected chromatogram peak
/// </summary>
/// <remarks>
/// For each detected peak, spectral trees are generated from the MS1 scans including all matching data dependent scans eluting in that retention time range.
/// Matching means that the precursor mass of the MS2 scan must match the mass used to create the chromatogram trace within the given mass tolerance. Finally all
/// spectral tree with matching data dependent scans are assigned to the detected peak.
/// </remarks>
private void BuildSpectralTrees(IEnumerable <SpectrumDescriptor> spectrumDescriptors, IEnumerable <DetectedPeakDetails> peakDetails)
{
SendAndLogTemporaryMessage("Building spectral trees...");
var timer = Stopwatch.StartNew();
DetectedPeakDetailsHelper.AssignSpectrumTreesToPeakDetails(spectrumDescriptors.OfType <ISpectrumDescriptor>(), peakDetails);
timer.Stop();
SendAndLogMessage("Building spectral trees takes {0:F2} s.", timer.Elapsed.TotalSeconds);
}
/// <summary>
/// Assigns to each detected chromatogram peak the nearest MS1 spectrum and all related data dependent spectra and persists the spectra afterwards.
/// </summary>
/// <param name="spectrumDescriptors">The spectrum descriptors group by file identifier.</param>
/// <param name="compoundIon2IsotopePeaksDictionary">The detected peaks for each compound ion as dictionary.</param>
private void AssignAndPersistMassSpectra(IEnumerable <SpectrumDescriptor> spectrumDescriptors, IEnumerable <KeyValuePair <UnknownFeatureIonInstanceItem, List <ChromatogramPeakItem> > > compoundIon2IsotopePeaksDictionary)
{
var time = Stopwatch.StartNew();
SendAndLogTemporaryMessage("Assigning MS1 spectra...");
var defaultCharge = 1;
if (spectrumDescriptors.First().ScanEvent.Polarity == PolarityType.Negative)
{
defaultCharge = -1;
}
var orderedSpectrumDescriptors = spectrumDescriptors
.OrderBy(o => o.Header.RetentionTimeCenter)
.ToList();
if (orderedSpectrumDescriptors.Any(a => a.ScanEvent.MSOrder == MSOrderType.MS1) == false)
{
SendAndLogErrorMessage("Exception, MS1 spectra not available (check spectrum selector node).");
return;
}
// Create peak details for each detected peak using the charge of the related compound ion
var detectedPeakDetails = compoundIon2IsotopePeaksDictionary.SelectMany(
sm => sm.Value.Select(
s => new DetectedPeakDetails(s)
{
Charge = sm.Key.Charge == 0 ? defaultCharge : sm.Key.Charge
}))
.ToList();
DetectedPeakDetailsHelper.AssignMassSpectraToPeakApexes(orderedSpectrumDescriptors, detectedPeakDetails);
SendAndLogMessage("Assigning MS1 spectra to chromatogram peak apexes finished after {0}", StringHelper.GetDisplayString(time.Elapsed));
time.Restart();
BuildSpectralTrees(orderedSpectrumDescriptors, detectedPeakDetails);
SendAndLogTemporaryMessage("Persisting assigned spectra...");
// get spectrum ids of distinct spectra
var distinctSpectrumIds = detectedPeakDetails.SelectMany(s => s.AssignedSpectrumDescriptors)
.Select(s => s.Header.SpectrumID)
.Distinct()
.ToList();
// Divide spectrum ids into parts to reduce the memory foot print. Therefore it is necessary to interrupt the spectra reading,
// because otherwise a database locked exception will be thrown when storing the spectra
foreach (var spectrumIdsPartition in distinctSpectrumIds
.Partition(ServerConfiguration.ProcessingPacketSize))
{
// Retrieve mass spectra and create MassSpectrumItem's
var distinctSpectra =
ProcessingServices.SpectrumProcessingService.ReadSpectraFromCache(spectrumIdsPartition.ToList())
.Select(
s => new MassSpectrumItem
{
ID = s.Header.SpectrumID,
FileID = s.Header.FileID,
Spectrum = s
})
.ToList();
// Persist mass spectra
PersistMassSpectra(distinctSpectra);
}
// Persists peak <-> mass spectrum connections
var peaksToMassSpectrumConnectionList = new List <EntityConnectionItemList <ChromatogramPeakItem, MassSpectrumItem> >(detectedPeakDetails.Count);
// Get connections between spectrum and chromatographic peak
foreach (var item in detectedPeakDetails
.Where(w => w.AssignedSpectrumDescriptors.Any()))
{
var connection = new EntityConnectionItemList <ChromatogramPeakItem, MassSpectrumItem>(item.Peak);
peaksToMassSpectrumConnectionList.Add(connection);
foreach (var spectrumDescriptor in item.AssignedSpectrumDescriptors)
{
connection.AddConnection(new MassSpectrumItem
{
ID = spectrumDescriptor.Header.SpectrumID,
FileID = spectrumDescriptor.Header.FileID,
// Omit mass spectrum here to reduce the memory footprint (only the IDs are required to persist the connections)
});
}
}
// Persists peak <-> mass spectrum connections
EntityDataService.ConnectItems(peaksToMassSpectrumConnectionList);
SendAndLogMessage("Persisting spectra finished after {0}", StringHelper.GetDisplayString(time.Elapsed));
m_currentStep += 1;
ReportTotalProgress((double)m_currentStep / m_numSteps);
time.Stop();
}
