private double GetSelectedIonIntensity(int scanNumber)
{
double mz = -1;
_rawConnection.GetPrecursorMassForScanNum(scanNumber, 2, ref mz);
return(GetScan(GetPrecursor(scanNumber)).MassSpectrum.GetClosestPeak(mz).Intensity);
}
private static double GetPrecursorMz(IXRawfile5 rawFile, int scanNo, int msLevel)
{
double mz = 0;
rawFile.GetPrecursorMassForScanNum(scanNo, msLevel, ref mz);
return(mz);
}
public override double GetPrecursorMz(int spectrumNumber, int msnOrder = 2)
{
double mz = double.NaN;
_rawConnection.GetPrecursorMassForScanNum(spectrumNumber, msnOrder, ref mz);
return(mz);
}
public double GetPrecursorMass(int scanNum, int msOrder)
{
double pdPrecursorMass = 0.0;
rawConnect.GetPrecursorMassForScanNum(scanNum, msOrder, ref pdPrecursorMass);
return(pdPrecursorMass);
}
/// <summary>
/// Reads raw data. Puts spectra into a thread safe queue. Closes queue when done. Parses the rawfile-log into the statusLog object
/// </summary>
/// <param name="raw">Raw file</param>
/// <param name="rawScanQueue">Thread safe queue</param>
private void ReadRawFile(IXRawfile5 raw, BlockingCollection <RawScan> rawScanQueue)
{
int firstScanNumber = -1;
raw.GetFirstSpectrumNumber(ref firstScanNumber);
int lastScanNumber = -1;
raw.GetLastSpectrumNumber(ref lastScanNumber);
for (int scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++)
{
string scanFilter = null;
raw.GetFilterForScanNum(scanNumber, ref scanFilter);
//read scan header into key/value arrays
object keyRef = null;
object valueRef = null;
int indexRef = 0;
raw.GetTrailerExtraForScanNum(scanNumber, ref keyRef, ref valueRef, ref indexRef);
string[] trailerKeys = (string[])keyRef;
string[] trailerValues = (string[])valueRef;
//read tic and base peak mass using dummy variables
double tic = 0.0;
int int1 = 0;
int int2 = 0;
int int3 = 0;
double double1 = 0.0;
double double2 = 0.0;
double double3 = 0.0;
double basePeakMass = 0.0;
double double5 = 0.0;
double double6 = 0.0;
raw.GetScanHeaderInfoForScanNum(scanNumber, ref int1, ref double1, ref double2, ref double3, ref tic, ref basePeakMass, ref double5, ref int2, ref int3, ref double6);
//read data (mz,int,...) using dummy variables
object labels_obj = null;
object flags_obj = null;
raw.GetLabelData(ref labels_obj, ref flags_obj, ref scanNumber);
double[,] data = (double[, ])labels_obj;
//read precursorMz
double precursorMz = 0.0;
raw.GetPrecursorMassForScanNum(scanNumber, 2, ref precursorMz);
RawScan rawScan = new RawScan(scanNumber, scanFilter, tic, trailerKeys, trailerValues, data, precursorMz, basePeakMass);
rawScanQueue.Add(rawScan);
//read status log
double rtLog = 0.0;
object statuslogKeys = null;
object statuslogValues = null;
int statuslogN = 0;
raw.GetStatusLogForScanNum(scanNumber, ref rtLog, ref statuslogKeys, ref statuslogValues, ref statuslogN);
statusLog.Add(rtLog, (string[])statuslogKeys, (string[])statuslogValues);
}
rawScanQueue.CompleteAdding();
Log.Information("Read all spectra in base module");
}