public MassSpectrum GetMassSpectrum(object idOrIndex)
{
int index = -1;
if (idOrIndex is int)
{
index = (int)idOrIndex;
}
else if (idOrIndex is string)
{
SpectrumList sl = source.MSDataFile.run.spectrumList;
int findIndex = sl.find(idOrIndex as string);
if (findIndex != sl.size())
{
index = findIndex;
}
}
return(GetMassSpectrum(index, source.MSDataFile.run.spectrumList));
}
public ParseSpectraFile(string mzmlPath, HashSet <int> scanNumSet, string ext)
{
int currentScanNum = -1;
try
{
MSDataFile msd = new MSDataFile(mzmlPath);
SpectrumList spectrumList = msd.run.spectrumList;
for (int i = 0; i < spectrumList.size(); ++i)
{
Spectrum spectrum = spectrumList.spectrum(i, true);
if (int.Parse(spectrum.cvParams[0].value) == 2)
{
Match match = scanNumPattern.Match(spectrum.id);
currentScanNum = int.Parse(match.Groups[1].Value);
if (scanNumSet.Contains(currentScanNum))
{
MZIntensityPairList mzIntensityPairs = new MZIntensityPairList();
spectrum.getMZIntensityPairs(ref mzIntensityPairs);
Dictionary <float, int> originalPeakList = new Dictionary <float, int>(mzIntensityPairs.Count);
foreach (MZIntensityPair mzIntensity in mzIntensityPairs)
{
originalPeakList[(float)mzIntensity.mz] = (int)mzIntensity.intensity;
}
spectraMap[currentScanNum] = originalPeakList;
}
}
}
}
catch (Exception ex)
{
MessageBox.Show(ex.Message + ": " + currentScanNum, "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
Application.Exit();
}
}
private static bool HasDriftTimeSpectraInList(SpectrumList spectrumList)
{
if (spectrumList == null || spectrumList.size() == 0)
return false;
// Assume that if any spectra have drift times, all do
using (var spectrum = spectrumList.spectrum(0, false))
{
return GetDriftTimeMsec(spectrum).HasValue;
}
}
private static bool HasSrmSpectraInList(SpectrumList spectrumList)
{
if (spectrumList == null || spectrumList.size() == 0)
return false;
// If the first spectrum is not SRM, the others will not be either
using (var spectrum = spectrumList.spectrum(0, false))
{
return IsSrmSpectrum(spectrum);
}
}
