public CentroidStreamData(CentroidStream centroidStream)
{
if (centroidStream.Length > 0)
{
Masses = centroidStream.Masses;
Intensities = centroidStream.Intensities;
Resolutions = centroidStream.Resolutions;
Noises = centroidStream.Noises;
Baselines = centroidStream.Baselines;
SignalToNoise = new double[Intensities.Length];
for (int i = 0; i < SignalToNoise.Length; i++)
{
SignalToNoise[i] = Intensities[i] / Noises[i];
}
}
else
{
Masses = new double[0];
Intensities = new double[0];
Resolutions = new double[0];
Noises = new double[0];
Baselines = new double[0];
SignalToNoise = new double[0];
}
}
private static PScan GetPScan(ScanStatistics scanStats, CentroidStream centroidStream, int msOrder,
string fileName, double?precursorMz = null, int?precursorCharge = null)
{
var scan = new PScan
{
FileName = fileName,
BasePeakMass = scanStats.BasePeakMass,
ScanType = scanStats.ScanType,
BasePeakIntensity = scanStats.BasePeakIntensity,
PacketType = scanStats.PacketType,
ScanNumber = scanStats.ScanNumber,
RetentionTime = scanStats.StartTime,
Masses = centroidStream.Masses.ToArray(),
Intensities = centroidStream.Intensities.ToArray(),
LowMass = scanStats.LowMass,
HighMass = scanStats.HighMass,
TIC = scanStats.TIC,
FileId = fileName + ".raw",
PrecursorMz = precursorMz,
PrecursorCharge = precursorCharge,
MsOrder = msOrder
};
return(scan);
}
private static void WritePScans(string fileName,
IRawDataPlus raw,
List <PScan> scans)
{
var enumerator = raw.GetFilteredScanEnumerator(" ");
foreach (var scanNumber in enumerator) // note in my tests serial is faster than Parallel.Foreach() (this involves disk access, so it makes sense)
{
//trailer iinformation is extracted via index
var trailers = raw.GetTrailerExtraValues(scanNumber);
var trailerLabels = raw.GetTrailerExtraInformation(scanNumber);
object chargeState = 0;
for (int i = 0; i < trailerLabels.Labels.Length; i++)
{
if (trailerLabels.Labels[i] == "Charge State:")
{
chargeState = raw.GetTrailerExtraValue(scanNumber, i);
break;
}
}
var scanFilter = raw.GetFilterForScanNumber(scanNumber);
var scanStats = raw.GetScanStatsForScanNumber(scanNumber);
CentroidStream centroidStream = new CentroidStream();
//check for FT mass analyzer data
if (scanFilter.MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
centroidStream = raw.GetCentroidStream(scanNumber, false);
}
//check for IT mass analyzer data
if (scanFilter.MassAnalyzer == MassAnalyzerType.MassAnalyzerITMS)
{
var scanData = raw.GetSimplifiedScan(scanNumber);
centroidStream.Masses = scanData.Masses;
centroidStream.Intensities = scanData.Intensities;
}
var msOrder = raw.GetScanEventForScanNumber(scanNumber).MSOrder;
if (msOrder == MSOrderType.Ms)
{
var pscan = GetPScan(scanStats, centroidStream, 1, fileName, Convert.ToInt32(chargeState));
scans.Add(pscan);
}
if (msOrder == MSOrderType.Ms2)
{
var precursorMz = raw.GetScanEventForScanNumber(scanNumber).GetReaction(0).PrecursorMass;
var pscan = GetPScan(scanStats, centroidStream, 2, fileName, precursorMz, Convert.ToInt32(chargeState));
scans.Add(pscan);
}
var t = raw.GetTrailerExtraValues(scanNumber);
}
WriteScans(scans, fileName);
}
public Spectrum(CentroidStream centroidStream)
{
Ions = new List <Ion>();
for (int i = 0; i < centroidStream.Length; i++)
{
Ions.Add(new Ion(centroidStream.Masses[i], centroidStream.Intensities[i]));
}
MaximumMass = (from x in Ions select x.Mass).Max();
MinimumMass = (from x in Ions select x.Mass).Min();
SummedIntensity = (from x in Ions select x.Intensity).Sum();
MaximumIntensity = (from x in Ions select x.Intensity).Max();
}
