public void Convert(TaskProgress progress)
{
// temporarily keep the previous MS1 and MS2 spectra for possible speeding up;
MassSpectrum lastMS1Spec = null;
int lastMS1ScanNum = -1;
MassSpectrum lastMS2Spec = null;
int lastMS2ScanNum = -1;
int spectrumProcessed = 0;
// get instrument method names;
int pnNumInstMethods = 0;
object pvarNames = null;
_rawReader.GetInstMethodNames(ref pnNumInstMethods, ref pvarNames);
// create instance for data preprocessing;
PrecursorPredictor pp = null;
if (expType == ExperimentType.DIA && predictPrecursors)
{
pp = new PrecursorPredictor(DEFAULT_DIA_ISO_WIN_SIZE, 1, 6, 0);
}
//Scan whole raw file to remember scan Number of MS1
if (correctPrecMz)
{
for (int scanNum = FirstScanNum; scanNum <= LastScanNum; scanNum++)
{
int MSOrder = 0;
_rawReader.GetNumberOfMSOrdersFromScanNum(scanNum, ref MSOrder);
// check the MS level;
if (MSOrder == 0)
{
MS1ScanNum.Add(scanNum);
}
}
}
for (int scanNum = FirstScanNum; scanNum <= LastScanNum; scanNum++)
{
MassSpectrum spec = GetSpectrumByScanNum(scanNum);
// Console.Write("^^^^^" + spec.Peaks.Count);
if (spec == null)
{
continue;
}
// get the mass analyzer type;
int pnMassAnalyzerType = 0;
_rawReader.GetMassAnalyzerTypeForScanNum(scanNum, ref pnMassAnalyzerType);
// get the precursors;
//if (spec.MsLevel > 1)
//{
// Object pvarPrecursorInfos = null;
// int pnArraySize = 0;
// _rawReader.GetPrecursorInfoFromScanNum(scanNum, ref pvarPrecursorInfos, ref pnArraySize);
//}
// if the spectrum has an empty peak list, abandon this spectrum;
if (spec.Peaks.Count > 0)
{
if (spec.MsLevel > 1)
{
if (spec.PrecursorScanNumber == 0)
{
if (spec.MsLevel == 2)
{
spec.PrecursorScanNumber = lastMS1Spec == null ? 0 : lastMS1ScanNum;
}
else if (spec.MsLevel == 3)
{
spec.PrecursorScanNumber = lastMS2Spec == null ? 0 : lastMS2ScanNum;
}
}
}
if (spec.MsLevel == 2)
{
if (expType == ExperimentType.DDA)
{
if (spec.PrecursorScanNumber == lastMS1ScanNum)
{
// double check the precursor m/z value in the MS1 scan;
ExtractPrecursorMz(spec, lastMS1Spec);
if (correctPrecMz)
{
spec = CalCorrectPrecursor(spec, lastMS1Spec);
}
}
else
{
// check whether the precursor scan number is available;
if (spec.PrecursorScanNumber > 0)
{
MassSpectrum precSpec = GetSpectrumByScanNum(spec.PrecursorScanNumber);
// double check the precursor m/z value in the MS1 scan;
ExtractPrecursorMz(spec, precSpec);
if (correctPrecMz)
{
spec = CalCorrectPrecursor(spec, lastMS1Spec);
}
}
}
}
else if (expType == ExperimentType.DIA && predictPrecursors)
{
if (spec.PrecursorScanNumber == lastMS1ScanNum)
{
pp.PredictPrecursors(ref spec, ref lastMS1Spec);
}
else
{
// check whether the precursor scan number is available;
if (spec.PrecursorScanNumber > 0)
{
MassSpectrum precSpec = GetSpectrumByScanNum(spec.PrecursorScanNumber);
pp.PredictPrecursors(ref spec, ref precSpec);
}
}
}
}
if (spec.MsLevel == 3)
{
if (expType == ExperimentType.DDA)
{
if (spec.PrecursorScanNumber == lastMS2ScanNum)
{
// double check the precursor m/z value in the MS2 scan;
ExtractPrecursorMz(spec, lastMS2Spec);
}
else
{
// check whether the precursor scan number is available;
if (spec.PrecursorScanNumber > 0)
{
// double check the precursor m/z value in the MS2 scan;
MassSpectrum precSpec = GetSpectrumByScanNum(spec.PrecursorScanNumber);
ExtractPrecursorMz(spec, precSpec);
}
}
}
else if (expType == ExperimentType.DIA && predictPrecursors)
{
if (spec.PrecursorScanNumber == lastMS1ScanNum)
{
pp.PredictPrecursors(ref spec, ref lastMS1Spec);
}
else
{
// check whether the precursor scan number is available;
if (spec.PrecursorScanNumber > 0)
{
MassSpectrum precSpec = GetSpectrumByScanNum(spec.PrecursorScanNumber);
pp.PredictPrecursors(ref spec, ref precSpec);
}
}
}
}
if (spec.MsLevel == 2 && exportChargeState)
{
if (expType == ExperimentType.DDA)
{
//Collection charge of MS2
if (chargeNum.ContainsKey(spec.Precursors[0].Item2))
{
chargeNum[spec.Precursors[0].Item2] += 1;
}
else
{
chargeNum.Add(spec.Precursors[0].Item2, 1);
}
}
}
// write into the output files;
WriteToOutFiles(spec);
}
if (spec.MsLevel == 1)
{
lastMS1ScanNum = spec.ScanNumber;
lastMS1Spec = spec;
}
else if (spec.MsLevel == 2)
{
lastMS2ScanNum = spec.ScanNumber;
lastMS2Spec = spec;
}
if (progress.Aborted)
{
break;
}
spectrumProcessed++;
progress.CurrentProgress = (int)((double)spectrumProcessed / (LastScanNum - FirstScanNum + 1) * 100);
if (progress.CurrentProgress > lastProgress)
{
try
{
int currentLineCursor = Console.CursorTop;
Console.SetCursorPosition(0, Console.CursorTop);
lastProgress = progress.CurrentProgress;
Console.WriteLine(" Reading RAW File: " + lastProgress + "%");
Console.SetCursorPosition(0, currentLineCursor);
}
catch (IOException ex)
{
if (progress.CurrentProgress - lastProgress >= 10 || progress.CurrentProgress == 100)
{
lastProgress = progress.CurrentProgress;
Console.WriteLine(" Reading RAW File: " + lastProgress + "%");
}
}
}
}
if (expType == ExperimentType.DDA && exportChargeState)
{
_chargeNumWriter = new StreamWriter(outFileWithoutExtentionName + "txt");
//export charge states to file
ExportChargeStatesToFile(chargeNum);
}
// complete mzXML file writing if mzXMLWriter is available;
if (_mzXMLWriter != null)
{
_mzXMLWriter.WriteIndex();
_mzXMLWriter.WriteEnd();
}
}
