private void ProcessSrmSpectrum(double time,
string modifiedSequence,
Color peptideColor,
double precursorMz,
int filterIndex,
double[] mzs,
double[] intensities,
double ionMobilityValue,
double ionMobilityExtractionWidth,
ChromDataCollectorSet chromMap)
{
float[] intensityFloats = new float[intensities.Length];
for (int i = 0; i < intensities.Length; i++)
intensityFloats[i] = (float) intensities[i];
var productFilters = mzs.Select(mz => new SpectrumProductFilter(mz, 0)).ToArray();
var spectrum = new ExtractedSpectrum(modifiedSequence, peptideColor, precursorMz, ionMobilityValue, ionMobilityExtractionWidth,
ChromExtractor.summed, filterIndex, productFilters, intensityFloats, null);
chromMap.ProcessExtractedSpectrum((float)time, _collectors, -1, spectrum, null);
}
/// <summary>
/// Process a list of spectra - typically of length one,
/// but possibly a set of drift bins all with same retention time,
/// or a set of Agilent ramped-CE Mse scans to be averaged
/// </summary>
private void ProcessSpectrumList(MsDataSpectrum[] spectra,
ChromDataCollectorSet chromMap,
double rt,
SpectrumFilter filter,
string scanId)
{
lock (_blockWriter)
{
foreach (var spectrum in filter.Extract(rt, spectra))
{
if (_loader.IsCanceled)
throw new LoadCanceledException(Status);
chromMap.ProcessExtractedSpectrum((float) rt, _collectors, GetScanIdIndex(scanId), spectrum, AddChromCollector);
}
}
}
private void ExtractChromatogramsLocked()
{
// First read all of the spectra, building chromatogram time, intensity lists
var fragmentTimeSharing = _spectra.HasSrmSpectra ? TimeSharing.single : TimeSharing.grouped;
var chromMap = new ChromDataCollectorSet(ChromSource.fragment, fragmentTimeSharing, _allChromData, _blockWriter);
var ms1TimeSharing = _filter.IsSharedTime ? TimeSharing.shared : TimeSharing.grouped;
var chromMapMs1 = new ChromDataCollectorSet(ChromSource.ms1, ms1TimeSharing, _allChromData, _blockWriter);
var chromMapSim = new ChromDataCollectorSet(ChromSource.sim, TimeSharing.grouped, _allChromData, _blockWriter);
var chromMaps = new[] {chromMap, chromMapSim, chromMapMs1};
var dictPrecursorMzToIndex = new Dictionary<double, int>(); // For SRM processing
var peptideFinder = _spectra.HasSrmSpectra ? new PeptideFinder(_document) : null;
while (_spectra.NextSpectrum())
{
if (_isDisposing)
{
CompleteChromatograms(chromMaps);
return;
}
UpdatePercentComplete();
if (_spectra.HasSrmSpectra)
{
var dataSpectrum = _spectra.CurrentSpectrum;
double precursorMz = dataSpectrum.Precursors[0].PrecursorMz ?? 0;
int filterIndex;
if (!dictPrecursorMzToIndex.TryGetValue(precursorMz, out filterIndex))
{
filterIndex = dictPrecursorMzToIndex.Count;
dictPrecursorMzToIndex.Add(precursorMz, filterIndex);
}
// Process the one SRM spectrum
var peptideNode = peptideFinder != null ? peptideFinder.FindPeptide(precursorMz) : null;
ProcessSrmSpectrum(
dataSpectrum.RetentionTime.Value,
peptideNode != null ? peptideNode.ModifiedSequence : string.Empty,
peptideNode != null ? peptideNode.Color : PeptideDocNode.UNKNOWN_COLOR,
precursorMz,
filterIndex,
dataSpectrum.Mzs,
dataSpectrum.Intensities,
0, 0, // ion mobility unknown
chromMap);
}
else if (_filter.EnabledMsMs || _filter.EnabledMs)
{
var dataSpectrum = _spectra.CurrentSpectrum;
var spectra = _spectra.CurrentSpectra;
float rt = _spectra.CurrentTime;
if (_allChromData != null)
_allChromData.CurrentTime = rt;
if (_filter.IsMsSpectrum(dataSpectrum))
{
var chromMapMs = _filter.IsSimSpectrum(dataSpectrum) ? chromMapSim : chromMapMs1;
string scanId = dataSpectrum.Id;
// Process all SRM spectra that can be generated by filtering this full-scan MS1
if (chromMapMs.IsSharedTime)
{
chromMapMs.AddSharedTime(rt, (short) GetScanIdIndex(scanId));
}
lock (_blockWriter)
{
foreach (var spectrum in _filter.SrmSpectraFromMs1Scan(rt, dataSpectrum.Precursors, spectra))
{
chromMapMs.ProcessExtractedSpectrum(rt, _collectors, GetScanIdIndex(scanId), spectrum, AddChromCollector);
}
}
}
if (_filter.IsMsMsSpectrum(dataSpectrum))
{
// Process all SRM spectra that can be generated by filtering this full-scan MS/MS
if (_demultiplexer == null)
{
ProcessSpectrumList(spectra, chromMap, rt, _filter, dataSpectrum.Id);
}
else
{
int i = _spectra.CurrentIndex;
foreach (var deconvSpectrum in _demultiplexer.GetDeconvolvedSpectra(i, dataSpectrum))
{
ProcessSpectrumList(new[] {deconvSpectrum}, chromMap, rt, _filter, dataSpectrum.Id);
}
}
}
// Complete any chromatograms with filter pairs with a maximum time earlier
// than the current retention time.
CompleteChromatograms(chromMaps, rt);
}
}
string log = _spectra.GetLog();
if (log != null) // in case perf logging is enabled
DebugLog.Info(log);
if (_spectra.HasSrmSpectra)
{
foreach (var map in chromMaps)
AddChromatograms(map);
}
else
{
CompleteChromatograms(chromMaps);
}
if (chromMap.Count == 0 && chromMapMs1.Count == 0 && chromMapSim.Count == 0)
throw new NoFullScanDataException(_filePath);
}
private void CompleteChromatograms(ChromDataCollectorSet[] chromMaps, double retentionTime = -1)
{
var finishedFilterPairs = _filter.RemoveFinishedFilterPairs(retentionTime);
foreach (var filterPair in finishedFilterPairs)
AddChromatogramsForFilterPair(chromMaps, filterPair);
// Update time for which chromatograms are available.
_collectors.AddComplete(retentionTime >= 0 ? (float)retentionTime : float.MaxValue);
}
private void AddChromatogramsForFilterPair(ChromDataCollectorSet[] chromMaps, SpectrumFilterPair filterPair)
{
// Fill the chromatograms that were actually extracted
foreach (var chromMap in chromMaps)
{
if (filterPair.Id >= chromMap.PrecursorCollectorMap.Count ||
chromMap.PrecursorCollectorMap[filterPair.Id] == null)
continue;
var pairPrecursor = chromMap.PrecursorCollectorMap[filterPair.Id];
chromMap.PrecursorCollectorMap[filterPair.Id] = null;
var collector = pairPrecursor.Item2;
var scanIdCollector = chromMap.ScanIdsCollector;
var timesCollector = chromMap.SharedTimesCollector;
if (chromMap.IsGroupedTime)
{
scanIdCollector = collector.ScansCollector;
timesCollector = collector.GroupedTimesCollector;
}
foreach (var pairProduct in collector.ProductIntensityMap)
{
var chromCollector = pairProduct.Value;
if (timesCollector != null)
{
chromCollector.SetScans(scanIdCollector);
chromCollector.SetTimes(timesCollector);
}
_collectors.AddCollector(pairProduct.Key.FilterId, chromCollector);
}
}
}
private void AddChromatograms(ChromDataCollectorSet chromMap)
{
var scanIdCollector = chromMap.ScanIdsCollector;
var timesCollector = chromMap.SharedTimesCollector;
foreach (var pairPrecursor in chromMap.PrecursorCollectorMap)
{
if (pairPrecursor == null)
continue;
var modSeq = pairPrecursor.Item1;
var collector = pairPrecursor.Item2;
if (chromMap.IsGroupedTime)
{
scanIdCollector = collector.ScansCollector;
timesCollector = collector.GroupedTimesCollector;
}
foreach (var pairProduct in collector.ProductIntensityMap)
{
var chromCollector = pairProduct.Value;
if (timesCollector != null)
{
chromCollector.SetScans(scanIdCollector);
chromCollector.SetTimes(timesCollector);
}
var key = new ChromKey(
collector.ModifiedSequence,
collector.PrecursorMz,
collector.IonMobilityValue,
collector.IonMobilityExtractionWidth,
pairProduct.Key.TargetMz,
0,
pairProduct.Key.FilterWidth,
chromMap.ChromSource,
modSeq.Extractor,
true,
true,
null,
null);
_collectors.AddSrmCollector(key, chromCollector);
}
}
}
