public PeptideSpectrumMatchPlot(OxyPlot.Wpf.PlotView plotView, Canvas sequenceDrawingCanvas, PsmFromTsv psm, MsDataScan scan,
List <MatchedFragmentIon> matchedFragmentIons, bool annotateProperties = true, LibrarySpectrum librarySpectrum = null) : base(plotView)
{
Model.Title = string.Empty;
Model.Subtitle = string.Empty;
SpectrumMatch = psm;
Scan = scan;
SequenceDrawingCanvas = sequenceDrawingCanvas;
SequenceDrawingCanvas.Height = 60;
sequenceDrawingCanvas.Width = 600;
ClearCanvas(SequenceDrawingCanvas);
DrawSpectrum();
AnnotateBaseSequence(psm.BaseSeq, psm.FullSequence, 10, matchedFragmentIons);
AnnotateMatchedIons(isBetaPeptide: false, matchedFragmentIons);
if (annotateProperties)
{
AnnotateProperties();
}
ZoomAxes(matchedFragmentIons);
if (librarySpectrum != null)
{
AnnotateLibraryIons(isBetaPeptide: false, librarySpectrum.MatchedFragmentIons);
}
RefreshChart();
}
protected void AnnotateModifications(string fullSequence, int yLoc)
{
var peptide = new PeptideWithSetModifications(fullSequence, GlobalVariables.AllModsKnownDictionary);
// read glycans if applicable
List <Tuple <int, string, double> > localGlycans = null;
if (SpectrumMatch.GlycanLocalizationLevel != null)
{
localGlycans = PsmFromTsv.ReadLocalizedGlycan(SpectrumMatch.LocalizedGlycan);
}
// annotate mods
foreach (var mod in peptide.AllModsOneIsNterminus)
{
double xLocation = (mod.Key - 1) * MetaDrawSettings.AnnotatedSequenceTextSpacing - 12;
double yLocation = yLoc + 2;
if (mod.Value.ModificationType == "O-Glycosylation")
{
if (localGlycans.Where(p => p.Item1 + 1 == mod.Key).Count() > 0)
{
DrawCircle(SequenceDrawingCanvas, new Point(xLocation, yLocation), MetaDrawSettings.ModificationAnnotationColor);
}
else
{
DrawCircle(SequenceDrawingCanvas, new Point(xLocation, yLocation), Brushes.Gray);
}
}
else
{
DrawCircle(SequenceDrawingCanvas, new Point(xLocation, yLocation), MetaDrawSettings.ModificationAnnotationColor);
}
}
}
public static bool FilterAcceptsPsm(PsmFromTsv psm)
{
if (psm.QValue <= QValueFilter &&
(psm.QValueNotch == null || psm.QValueNotch <= QValueFilter) &&
(psm.DecoyContamTarget == "T" || (psm.DecoyContamTarget == "D" && ShowDecoys) || (psm.DecoyContamTarget == "C" && ShowContaminants)) &&
(psm.GlycanLocalizationLevel == null || psm.GlycanLocalizationLevel >= LocalizationLevelStart && psm.GlycanLocalizationLevel <= LocalizationLevelEnd))
{
return(true);
}
return(false);
}
public void FilterPsmsByString(string searchString)
{
if (searchString == "")
{
PeptideSpectralMatchesView.Filter = null;
}
else
{
PeptideSpectralMatchesView.Filter = obj =>
{
PsmFromTsv psm = obj as PsmFromTsv;
return((psm.Ms2ScanNumber.ToString()).StartsWith(searchString) || psm.FullSequence.ToUpper().Contains(searchString.ToUpper()));
};
}
}
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);
}
}
}