/// <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();
}
/// <summary>
/// Creates and persists XIC traces for all compound ion items.
/// </summary>
private void RebuildAndPersistCompoundIonTraces(
int fileID,
IEnumerable <SpectrumDescriptor> spectrumDescriptors,
Dictionary <UnknownFeatureIonInstanceItem, List <ChromatogramPeakItem> > ionInstanceToPeaksMap)
{
SendAndLogTemporaryMessage("Re-creating XIC traces...");
var time = Stopwatch.StartNew();
// init XICPattern builder
var xicPatternBuilder = new Func <List <ChromatogramPeakItem>, XICPattern>(
peaks =>
{
var masks = peaks.Select(
peak => new XICMask(
peak.IsotopeNumber,
peak.Mass,
MassTolerance.Value)
).ToList();
return(new XICPattern(masks));
});
// make XIC patterns
var xicPatterns = ionInstanceToPeaksMap.ToDictionary(item => item.Key, item => xicPatternBuilder(item.Value));
// init XIC tracer
var tracer = new XICTraceGenerator <UnknownFeatureIonInstanceItem>(xicPatterns);
// get sprectrum IDs
var spectrumIds = spectrumDescriptors
.Where(s => s.ScanEvent.MSOrder == MSOrderType.MS1)
.OrderBy(o => o.Header.RetentionTimeRange.LowerLimit)
.Select(s => s.Header.SpectrumID)
.ToList();
// add spectrum to tracer
foreach (var spectrum in ProcessingServices.SpectrumProcessingService.ReadSpectraFromCache(spectrumIds))
{
tracer.AddSpectrum(spectrum);
}
// make trace items
var ionInstanceToTraceMap = new Dictionary <UnknownFeatureIonInstanceItem, XicTraceItem>();
foreach (var item in ionInstanceToPeaksMap)
{
// get trace
var trace = tracer.GetXICTrace(item.Key, useFullRange: true, useFullRaster: false);
// make XicTraceItem
ionInstanceToTraceMap.Add(
item.Key,
new XicTraceItem
{
ID = EntityDataService.NextId <XicTraceItem>(),
FileID = fileID,
Trace = new TraceData(trace),
});
}
// make raster
var rasterItem = MakeRetentionTimeRasterItem(tracer, fileID);
// persist traces
EntityDataService.InsertItems(ionInstanceToTraceMap.Values);
EntityDataService.ConnectItems(ionInstanceToTraceMap.Select(s => Tuple.Create(s.Key, s.Value)));
// persist raster
EntityDataService.InsertItems(new[] { rasterItem });
EntityDataService.ConnectItems(ionInstanceToTraceMap.Select(s => Tuple.Create(s.Value, rasterItem)));
time.Stop();
SendAndLogVerboseMessage("Re-creating and persisting {0} XIC traces took {1:F2} s.", ionInstanceToTraceMap.Values.Count, time.Elapsed.TotalSeconds);
m_currentStep += 4;
ReportTotalProgress((double)m_currentStep / m_numSteps);
}
