public void DisplaySpectrumMatch(PlotView plotView, Canvas canvas, PsmFromTsv psm, ParentChildScanPlotsView parentChildScanPlotsView, out List <string> errors)
{
errors = null;
// clear old parent/child scans
parentChildScanPlotsView.Plots.Clear();
CurrentlyDisplayedPlots.Clear();
// get the scan
if (!MsDataFiles.TryGetValue(psm.FileNameWithoutExtension, out DynamicDataConnection spectraFile))
{
errors = new List <string>();
errors.Add("The spectra file could not be found for this PSM: " + psm.FileNameWithoutExtension);
return;
}
MsDataScan scan = spectraFile.GetOneBasedScanFromDynamicConnection(psm.Ms2ScanNumber);
LibrarySpectrum librarySpectrum = null;
// plot the annotated spectrum match
PeptideSpectrumMatchPlot plot;
if (psm.BetaPeptideBaseSequence == null)
{
// get the library spectrum if relevant
if (SpectralLibrary != null)
{
SpectralLibrary.TryGetSpectrum(psm.FullSequence, psm.PrecursorCharge, out var librarySpectrum1);
librarySpectrum = librarySpectrum1;
}
plot = new PeptideSpectrumMatchPlot(plotView, canvas, psm, scan, psm.MatchedIons, librarySpectrum: librarySpectrum);
}
else
{
plot = new CrosslinkSpectrumMatchPlot(plotView, canvas, psm, scan);
}
CurrentlyDisplayedPlots.Add(plot);
// plot parent/child scans
if (psm.ChildScanMatchedIons != null)
{
// draw parent scan
string parentAnnotation = "Scan: " + scan.OneBasedScanNumber
+ " Dissociation Type: " + scan.DissociationType
+ " MsOrder: " + scan.MsnOrder
+ " Selected Mz: " + scan.SelectedIonMZ.Value.ToString("0.##")
+ " Retention Time: " + scan.RetentionTime.ToString("0.##");
var parentPlotView = new PlotView(); // placeholder
var parentCanvas = new Canvas();
var item = new ParentChildScanPlotTemplate()
{
Plot = new PeptideSpectrumMatchPlot(parentPlotView, parentCanvas, psm, scan, psm.MatchedIons),
SpectrumLabel = parentAnnotation,
TheCanvas = parentCanvas
};
parentChildScanPlotsView.Plots.Add(item);
// remove model from placeholder (the model can only be referenced by 1 plotview at a time)
parentPlotView.Model = null;
// draw child scans
HashSet <int> scansDrawn = new HashSet <int>();
var allChildScanMatchedIons = psm.ChildScanMatchedIons;
if (psm.BetaPeptideChildScanMatchedIons != null)
{
allChildScanMatchedIons = allChildScanMatchedIons.Concat(psm.BetaPeptideChildScanMatchedIons)
.GroupBy(p => p.Key)
.ToDictionary(p => p.Key, q => q.SelectMany(p => p.Value).ToList());
}
foreach (var childScanMatchedIons in allChildScanMatchedIons)
{
int childScanNumber = childScanMatchedIons.Key;
if (scansDrawn.Contains(childScanNumber))
{
continue;
}
scansDrawn.Add(childScanNumber);
List <MatchedFragmentIon> matchedIons = childScanMatchedIons.Value;
MsDataScan childScan = spectraFile.GetOneBasedScanFromDynamicConnection(childScanNumber);
string childAnnotation = "Scan: " + childScan.OneBasedScanNumber
+ " Dissociation Type: " + childScan.DissociationType
+ " MsOrder: " + childScan.MsnOrder
+ " Selected Mz: " + childScan.SelectedIonMZ.Value.ToString("0.##")
+ " RetentionTime: " + childScan.RetentionTime.ToString("0.##");
Canvas childCanvas = new Canvas();
PlotView childPlotView = new PlotView(); // placeholder
// make the plot
var childPlot = new PeptideSpectrumMatchPlot(childPlotView, childCanvas, psm, childScan, matchedIons, annotateProperties: false);
childPlot.Model.Title = null;
childPlot.Model.Subtitle = null;
item = new ParentChildScanPlotTemplate()
{
Plot = childPlot, SpectrumLabel = childAnnotation, TheCanvas = childCanvas
};
// remove model from placeholder (the model can only be referenced by 1 plotview at a time)
childPlotView.Model = null;
parentChildScanPlotsView.Plots.Add(item);
CurrentlyDisplayedPlots.Add(childPlot);
}
}
}
public void ExportToPdf(PlotView plotView, Canvas canvas, List <PsmFromTsv> spectrumMatches, ParentChildScanPlotsView parentChildScanPlotsView, string directory, out List <string> errors)
{
errors = new List <string>();
if (!Directory.Exists(directory))
{
Directory.CreateDirectory(directory);
}
foreach (var psm in spectrumMatches)
{
DisplaySpectrumMatch(plotView, canvas, psm, parentChildScanPlotsView, out var displayErrors);
if (displayErrors != null)
{
errors.AddRange(displayErrors);
}
string sequence = illegalInFileName.Replace(psm.FullSequence, string.Empty);
if (sequence.Length > 30)
{
sequence = sequence.Substring(0, 30);
}
foreach (var plot in CurrentlyDisplayedPlots)
{
string filePath = Path.Combine(directory, plot.Scan.OneBasedScanNumber + "_" + sequence + ".pdf");
int i = 2;
while (File.Exists(filePath))
{
filePath = Path.Combine(directory, plot.Scan.OneBasedScanNumber + "_" + sequence + "_" + i + ".pdf");
i++;
}
plot.ExportToPdf(filePath, plotView.ActualWidth, plotView.ActualHeight);
}
}
DisplaySpectrumMatch(plotView, canvas, spectrumMatches.First(), parentChildScanPlotsView, out var moreDisplayErrors);
}
