private void PlotSpeciesIsotopeXics(AnnotatedSpecies species, MsDataScan scan, int?charge = null)
{
double rtWindowHalfWidth = 2.5;
MsDataScan startScan = null;
for (int i = scan.OneBasedScanNumber; i >= 1; i--)
{
var theScan = CurrentlySelectedSpectraFile.Value.GetOneBasedScanFromDynamicConnection(i);
if (theScan.RetentionTime < scan.RetentionTime - rtWindowHalfWidth)
{
break;
}
startScan = theScan;
}
List <MsDataScan> scans = new List <MsDataScan>();
for (int i = startScan.OneBasedScanNumber; i < 1000000; i++)
{
var theScan = CurrentlySelectedSpectraFile.Value.GetOneBasedScanFromDynamicConnection(i);
if (theScan.RetentionTime > scan.RetentionTime + rtWindowHalfWidth)
{
break;
}
if (theScan.MsnOrder == 1)
{
scans.Add(theScan);
}
}
int z = species.DeconvolutionFeature.Charges[species.DeconvolutionFeature.Charges.Count / 2];
for (int i = 0; i < 10; i++)
{
List <Datum> xicData = new List <Datum>();
double isotopeMass = species.DeconvolutionFeature.MonoisotopicMass + i * Constants.C13MinusC12;
Tolerance t = new PpmTolerance(5);
foreach (var item in scans)
{
int index = item.MassSpectrum.GetClosestPeakIndex(isotopeMass.ToMz(z));
if (t.Within(item.MassSpectrum.XArray[index], isotopeMass.ToMz(z)))
{
xicData.Add(new Datum(item.RetentionTime, item.MassSpectrum.YArray[index]));
}
else
{
xicData.Add(new Datum(item.RetentionTime, 0));
}
}
if (i == 0)
{
XicPlot = new LinePlot(topPlotView, xicData);
}
else
{
XicPlot.AddLinePlot(xicData);
}
}
}
private void PlotSpeciesInSpectrum(AnnotatedSpecies species, MsDataScan scan, int?charge = null)
{
// add non-annotated peaks
List <Datum> spectrumData = new List <Datum>();
for (int i = 0; i < scan.MassSpectrum.XArray.Length; i++)
{
spectrumData.Add(new Datum(scan.MassSpectrum.XArray[i], scan.MassSpectrum.YArray[i]));
}
SpectrumPlot = new SpectrumPlot(bottomPlotView, spectrumData);
// add annotated peaks
List <Datum> annotatedData = new List <Datum>();
List <int> chargesToPlot = new List <int>();
if (species.DeconvolutionFeature != null)
{
double mass = species.DeconvolutionFeature.MonoisotopicMass;
if (charge == null)
{
chargesToPlot.AddRange(species.DeconvolutionFeature.Charges);
}
else
{
chargesToPlot.Add(charge.Value);
}
foreach (var z in chargesToPlot)
{
Tolerance t = new PpmTolerance(5);
bool peakHasBeenObserved = false;
for (int i = 0; i < 20; i++)
{
double isotopeMass = (mass + i * Constants.C13MinusC12).ToMz(z);
int index = scan.MassSpectrum.GetClosestPeakIndex(isotopeMass);
double expMz = scan.MassSpectrum.XArray[index];
if (t.Within(expMz.ToMass(z), isotopeMass.ToMass(z)))
{
annotatedData.Add(new Datum(scan.MassSpectrum.XArray[index], scan.MassSpectrum.YArray[index]));
peakHasBeenObserved = true;
}
//else if (peakHasBeenObserved)
//{
// break;
//}
}
}
}
else if (species.Identification != null)
{
//TODO
}
SpectrumPlot.AddSpectrumPlot(annotatedData, OxyPlot.OxyColors.Blue, 2.0);
ZoomAxes(annotatedData, SpectrumPlot);
}