private List<List<XYPoint>> GetMSMSDataArraysFromMSScans(List<int> scanList, double mzlower, double mzupper)
{
List<List<XYPoint>> msValuesList = new List<List<XYPoint>>(500);
SpectrumList spectrumList = run.spectrumList;
int timePoints = spectrumList.size();
List<List<XYPoint>> msmsValuesList = new List<List<XYPoint>>(500);
List<int> tempScanList = new List<int>();
if (scanList == null)
{
for (int i = 0; i < timePoints; i++)
{
tempScanList.Add(i);
}
}
else
{
tempScanList = scanList;
}
for (int i = 0; i < tempScanList.Count; i++)
{
pwiz.CLI.msdata.Spectrum spectrum = spectrumList.spectrum(tempScanList[i], true);
string level = (string)spectrum.cvParam(CVID.MS_ms_level).value;
bool foundSelectedIon = false;
if (level == "2")
{
PrecursorList precursorlist = spectrum.precursors;
foreach (Precursor pc in precursorlist)
{
foreach (SelectedIon si in pc.selectedIons)
{
double selectedIonMZ = (double)si.cvParam(CVID.MS_selected_ion_m_z).value;
if (selectedIonMZ >= mzlower && selectedIonMZ <= mzupper)
{
foundSelectedIon = true;
}
}
}
}
if (foundSelectedIon)
{
BinaryDataArray mzArray = spectrum.getMZArray();
BinaryDataArray intensityArray = spectrum.getIntensityArray();
BinaryData mzData = mzArray.data;
BinaryData intensityData = intensityArray.data;
List<XYPoint> msmsValues = new List<XYPoint>(1000);
for (int j = 0; j < mzData.Count; j++)
{
XYPoint pair = new XYPoint(mzData[j], intensityData[j]);
pair.NumberOfDuplicates = 0;
msmsValues.Add(pair);
}
msmsValuesList.Add(msmsValues);
}
}
return msmsValuesList;
}
private static void ApplyThreshold(XYPoint point)
{
point.XValue = Math.Truncate(point.XValue * 1000000) / 1000000;
}