public XYData GenerateChromatogram(Run run, double targetMz, double elutionTimeCenter = 0.5, Globals.ElutionTimeUnit elutionTimeUnit = Globals.ElutionTimeUnit.NormalizedElutionTime)
{
var targetMzList = new List <double> {
targetMz
};
return(GenerateChromatogram(run, targetMzList, elutionTimeCenter, elutionTimeUnit));
}
public XYData GenerateChromatogram(Run run, IsotopicProfile theorProfile, double elutionTimeCenter = 0.5, Globals.ElutionTimeUnit elutionTimeUnit = Globals.ElutionTimeUnit.NormalizedElutionTime)
{
if (ChromatogramGeneratorMode == Globals.ChromatogramGeneratorMode.MZ_BASED)
{
throw new NotSupportedException("Don't use this method for MZ_BASED chromatogram generation. Use a different overload");
}
var targetMZList = GetTargetMzList(theorProfile);
return(GenerateChromatogram(run, targetMZList, elutionTimeCenter, elutionTimeUnit));
}
public XYData GenerateChromatogram(Run run, List <double> targetMzList, double elutionTimeCenter = 0.5, Globals.ElutionTimeUnit elutionTimeUnit = Globals.ElutionTimeUnit.NormalizedElutionTime)
{
var lowerScan = run.MinLCScan;
var upperScan = run.MaxLCScan;
if (elutionTimeUnit == Globals.ElutionTimeUnit.NormalizedElutionTime)
{
float minNetVal;
float maxNetVal;
if (run.NETIsAligned)
{
minNetVal = (float)(elutionTimeCenter - ChromWindowWidthForAlignedData);
maxNetVal = (float)(elutionTimeCenter + ChromWindowWidthForAlignedData);
}
else
{
minNetVal = (float)(elutionTimeCenter - ChromWindowWidthForNonAlignedData);
maxNetVal = (float)(elutionTimeCenter + ChromWindowWidthForNonAlignedData);
}
if (minNetVal < 0)
{
minNetVal = 0;
}
if (maxNetVal > 1)
{
maxNetVal = 1;
}
lowerScan = (int)Math.Floor(run.NetAlignmentInfo.GetScanForNet(minNetVal));
if (lowerScan == -1)
{
lowerScan = run.MinLCScan;
}
upperScan = (int)Math.Ceiling(run.NetAlignmentInfo.GetScanForNet(maxNetVal));
if (upperScan == -1)
{
upperScan = run.MaxLCScan;
}
}
else if (elutionTimeUnit == Globals.ElutionTimeUnit.ScanNum)
{
if (run.NETIsAligned)
{
lowerScan = (int)(elutionTimeCenter - ChromWindowWidthForAlignedData);
upperScan = (int)(elutionTimeCenter + ChromWindowWidthForAlignedData);
}
else
{
lowerScan = (int)(elutionTimeCenter - ChromWindowWidthForNonAlignedData);
upperScan = (int)(elutionTimeCenter + ChromWindowWidthForNonAlignedData);
}
}
if (lowerScan == -1)
{
lowerScan = run.MinLCScan;
}
if (upperScan == -1)
{
upperScan = run.MaxLCScan;
}
var midScan = (int)((lowerScan + (double)upperScan) / 2);
if (run.MassIsAligned)
{
for (var i = 0; i < targetMzList.Count; i++)
{
targetMzList[i] = getAlignedMZValue(targetMzList[i], run, midScan);
}
}
var chromValues = _chromGen.GenerateChromatogram(run.ResultCollection.MSPeakResultList, lowerScan, upperScan, targetMzList, Tolerance, ToleranceUnit);
chromValues = FilterOutDataBasedOnMsMsLevel(run, chromValues, 1, false);
return(chromValues);
}