public List <CompoundData> ReadSpectraData(List <CompoundData> combinedTransitions)
{
var scanTimes = new Dictionary <int, double>();
using (var rawReader = new XRawFileIO(DatasetPath))
{
var numScans = rawReader.GetNumScans();
if (numScans <= 0)
{
// dataset has no MS data. Return.
return(null);
}
for (var i = 1; i <= numScans; i++)
{
var err = rawReader.GetRetentionTime(i, out double time);
scanTimes.Add(i, time);
// Filter string parsing for speed: "+ c NSI SRM ms2 [precursor/parent m/z] [[list of product m/z ranges]]
}
// Map transition start/stop times to scans
var scansAndTargets = new Dictionary <int, List <CompoundData> >();
foreach (var scan in scanTimes)
{
var matches = combinedTransitions
.Where(x => x.StartTimeMinutes <= scan.Value && scan.Value <= x.StopTimeMinutes).ToList();
if (matches.Count > 0)
{
scansAndTargets.Add(scan.Key, matches);
}
}
rawReader.ScanInfoCacheMaxSize = 2;
// read spectra data for each transition from the file, in an optimized fashion
foreach (var scan in scansAndTargets)
{
rawReader.GetScanInfo(scan.Key, out clsScanInfo scanInfo);
var preMz = scanInfo.ParentIonMZ;
rawReader.GetScanData(scan.Key, out var mzs, out var intensities);
foreach (var compound in scan.Value.Where(x => Math.Abs(x.PrecursorMz - preMz) < 0.01))
{
foreach (var massRange in scanInfo.MRMInfo.MRMMassList)
{
var match = compound.Transitions.FirstOrDefault(x => massRange.StartMass <= x.ProductMz && x.ProductMz <= massRange.EndMass);
if (match == null)
{
continue;
}
for (var j = 0; j < mzs.Length; j++)
{
var mz = mzs[j];
var intensity = intensities[j];
if (massRange.StartMass <= mz && mz <= massRange.EndMass)
{
match.IntensitySum += intensity;
match.Intensities.Add(new TransitionData.DataPoint(scan.Key, scanTimes[scan.Key], intensity));
if (intensity > match.MaxIntensity)
{
match.MaxIntensity = intensity;
match.MaxIntensityTime = scanTimes[scan.Key];
}
}
}
}
}
}
}
return(combinedTransitions.ToList());
}
