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);
}
public void ProcessExtractedSpectrum(float time, SpectraChromDataProvider.Collectors chromatograms, int scanId, ExtractedSpectrum spectrum, Action<int, ChromCollector> addCollector)
{
double precursorMz = spectrum.PrecursorMz;
double? ionMobilityValue = spectrum.IonMobilityValue;
double ionMobilityExtractionWidth = spectrum.IonMobilityExtractionWidth;
string textId = spectrum.TextId;
ChromExtractor extractor = spectrum.Extractor;
int ionScanCount = spectrum.ProductFilters.Length;
ChromDataCollector collector;
var key = new PrecursorTextId(precursorMz, textId, extractor);
int index = spectrum.FilterIndex;
while (PrecursorCollectorMap.Count <= index)
PrecursorCollectorMap.Add(null);
if (PrecursorCollectorMap[index] != null)
collector = PrecursorCollectorMap[index].Item2;
else
{
collector = new ChromDataCollector(textId, precursorMz, ionMobilityValue, ionMobilityExtractionWidth, index, IsGroupedTime);
PrecursorCollectorMap[index] = new Tuple<PrecursorTextId, ChromDataCollector>(key, collector);
}
int ionCount = collector.ProductIntensityMap.Count;
if (ionCount == 0)
ionCount = ionScanCount;
// Add new time to the shared time list if not SRM, which doesn't share times, or
// the times are shared with the entire set, as in MS1
int lenTimes = collector.TimeCount;
if (IsGroupedTime)
{
// Shared scan ids and times do not belong to a group.
collector.AddScanId(scanId);
collector.AddGroupedTime(time);
lenTimes = collector.GroupedTimesCollector.Count;
}
// Add intensity values to ion scans
for (int j = 0; j < ionScanCount; j++)
{
var productFilter = spectrum.ProductFilters[j];
var chromIndex = chromatograms.ProductFilterIdToId(productFilter.FilterId);
ChromCollector chromCollector;
if (!collector.ProductIntensityMap.TryGetValue(productFilter, out chromCollector))
{
chromCollector = new ChromCollector(chromIndex, IsSingleTime, spectrum.MassErrors != null);
// If more than a single ion scan, add any zeros necessary
// to make this new chromatogram have an entry for each time.
if (ionScanCount > 1 && lenTimes > 1)
chromCollector.FillIntensities(chromIndex, lenTimes - 1, _blockWriter);
collector.ProductIntensityMap.Add(productFilter, chromCollector);
if (addCollector != null)
addCollector(productFilter.FilterId, chromCollector);
}
if (IsSingleTime)
chromCollector.AddTime(chromIndex, time, _blockWriter);
if (spectrum.MassErrors != null)
chromCollector.AddMassError(chromIndex, spectrum.MassErrors[j], _blockWriter);
chromCollector.AddIntensity(chromIndex, spectrum.Intensities[j], _blockWriter);
}
// Add data for chromatogram graph.
if (_allChromData != null && spectrum.PrecursorMz != 0) // Exclude TIC and BPC
_allChromData.Add(spectrum.TextId, spectrum.PeptideColor, spectrum.FilterIndex, time, spectrum.Intensities);
// If this was a multiple ion scan and not all ions had measurements,
// make sure missing ions have zero intensities in the chromatogram.
if (ionScanCount > 1 &&
(ionCount != ionScanCount || ionCount != collector.ProductIntensityMap.Count))
{
// Times should have gotten one longer
foreach (var item in collector.ProductIntensityMap)
{
var productFilter = item.Key;
var chromCollector = item.Value;
var chromIndex = chromatograms.ProductFilterIdToId(productFilter.FilterId);
if (chromCollector.Count < lenTimes)
chromCollector.AddIntensity(chromIndex, 0, _blockWriter);
}
}
}
