private void DisplayTic()
{
if (CurrentlySelectedSpectraFile.Value == null)
{
return;
}
// display TIC over RT
List <Datum> tic = new List <Datum>();
List <Datum> identifiedTic = new List <Datum>();
HashSet <double> mzs = new HashSet <double>();
int scanNum = 1;
var scan = CurrentlySelectedSpectraFile.Value.GetOneBasedScanFromDynamicConnection(scanNum);
while (scan != null)
{
if (scan.MsnOrder == 1)
{
// calculate TIC
tic.Add(new Datum(scan.RetentionTime, scan.TotalIonCurrent));
// calculate TIC identified
double identifiedScanTic = 0;
if (ScanNumberToAnnotatedEnvelopes.TryGetValue(scan.OneBasedScanNumber, out var envs))
{
mzs.Clear();
foreach (var env in envs)
{
foreach (var peak in env.PeakMzs)
{
if (!mzs.Contains(peak))
{
mzs.Add(peak);
identifiedScanTic += scan.MassSpectrum.YArray[scan.MassSpectrum.GetClosestPeakIndex(peak)];
}
}
}
}
identifiedTic.Add(new Datum(scan.RetentionTime, identifiedScanTic));
}
scanNum++;
scan = CurrentlySelectedSpectraFile.Value.GetOneBasedScanFromDynamicConnection(scanNum);
}
TicPlot = new mzPlot.LinePlot(topPlotView, tic, OxyColors.Black, 1, seriesTitle: "TIC",
chartTitle: Path.GetFileName(CurrentlySelectedSpectraFile.Key), chartSubtitle: "");
if (LoadedAnnotatedSpecies.Any())
{
TicPlot.AddLinePlot(identifiedTic, OxyColors.Blue, 1, seriesTitle: "Identified TIC");
}
}
private void DisplayAnnotatedSpectrum(int scanNum)
{
if (CurrentlySelectedSpectraFile.Value == null)
{
return;
}
var scan = CurrentlySelectedSpectraFile.Value.GetOneBasedScanFromDynamicConnection(scanNum);
if (scan == null)
{
return;
}
CurrentScan = scan;
ClearTicChartAnnotations();
//List<MsDataScan> childScans = new List<MsDataScan>();
//for (int i = 1; i < 100; i++)
//{
// if (scanNum + i > SpectraFile.NumSpectra)
// {
// break;
// }
// var nextScan = SpectraFile.GetOneBasedScan(scanNum + i);
// if (nextScan.MsnOrder == CurrentScan.MsnOrder)
// {
// break;
// }
// childScans.Add(nextScan);
//}
List <Datum> spectrum = new List <Datum>();
for (int i = 0; i < scan.MassSpectrum.XArray.Length; i++)
{
spectrum.Add(new Datum(scan.MassSpectrum.XArray[i], scan.MassSpectrum.YArray[i]));
}
SpectrumPlot = new mzPlot.SpectrumPlot(bottomPlotView, spectrum, chartTitle: "",
chartSubtitle: "RT: " + scan.RetentionTime.ToString("F3") + "; Scan #" + scan.OneBasedScanNumber + "; MS" + scan.MsnOrder);
SpectrumPlot.Model.Axes.First(p => p.Position == AxisPosition.Left).AbsoluteMinimum = 0;
SpectrumPlot.Model.Axes.First(p => p.Position == AxisPosition.Bottom).AbsoluteMinimum = 0;
SpectrumPlot.Model.Axes.First(p => p.Position == AxisPosition.Bottom).AbsoluteMaximum = scan.MassSpectrum.Range.Maximum * 1.5;
//if (scan.MsnOrder == 1)
//{
var colors = SpectrumPlot.Model.DefaultColors.ToList();
int colorIndex = 0;
string fileNameNoExt = Path.GetFileNameWithoutExtension(CurrentlySelectedSpectraFile.Key);
if (LoadedAnnotatedSpecies != null)
{
foreach (var species in LoadedAnnotatedSpecies.Where(p => p.DeconvolutionFeature != null && p.DeconvolutionFeature.SpectraFileNameWithoutExtension == fileNameNoExt))
{
List <Datum> peakData = new List <Datum>();
foreach (var envelope in species.DeconvolutionFeature.AnnotatedEnvelopes.Where(p => p.OneBasedScanNumber == scan.OneBasedScanNumber))
{
foreach (double mz in envelope.PeakMzs)
{
int ind = scan.MassSpectrum.GetClosestPeakIndex(mz);
peakData.Add(new Datum(scan.MassSpectrum.XArray[ind], scan.MassSpectrum.YArray[ind]));
}
}
SpectrumPlot.AddSpectrumPlot(peakData, colors[colorIndex], 1.5);
colorIndex++;
if (colorIndex >= colors.Count)
{
colorIndex = 0;
}
}
}
//var annot = new LineAnnotation();
//annot.Color = OxyColors.Red;
//annot.StrokeThickness = 1.5;
//annot.X = scan.RetentionTime;
//annot.Type = LineAnnotationType.Vertical;
//annot.LineStyle = LineStyle.Solid;
//TicPlot.Model.Annotations.Add(annot);
//foreach (var childScan in childScans)
//{
// if (childScan.IsolationRange != null)
// {
// var isolationAnnotBegin = new LineAnnotation();
// isolationAnnotBegin.Color = OxyColors.Blue;
// isolationAnnotBegin.StrokeThickness = 1.5;
// isolationAnnotBegin.X = childScan.IsolationRange.Minimum;
// isolationAnnotBegin.Type = LineAnnotationType.Vertical;
// isolationAnnotBegin.LineStyle = LineStyle.Dash;
// isolationAnnotBegin.Text = "#" + childScan.OneBasedScanNumber;
// isolationAnnotBegin.Tag = new DataTag(TagType.ChildScan, isolationAnnotBegin.Text);
// SpectrumPlot.Model.Annotations.Add(isolationAnnotBegin);
// var isolationAnnotEnd = new LineAnnotation();
// isolationAnnotEnd.Color = OxyColors.Blue;
// isolationAnnotEnd.StrokeThickness = 1.5;
// isolationAnnotEnd.X = childScan.IsolationRange.Maximum;
// isolationAnnotEnd.Type = LineAnnotationType.Vertical;
// isolationAnnotEnd.LineStyle = LineStyle.Dash;
// isolationAnnotEnd.Tag = new DataTag(TagType.ChildScan, isolationAnnotBegin.Text);
// SpectrumPlot.Model.Annotations.Add(isolationAnnotEnd);
// }
//}
TicPlot.RefreshChart();
SpectrumPlot.RefreshChart();
}
