internal static void AddMatchedIonsData(Dictionary <string, string> s, List <MatchedFragmentIon> matchedIons)
{
bool nullPsm = matchedIons == null;
StringBuilder seriesStringBuilder = new StringBuilder();
StringBuilder mzStringBuilder = new StringBuilder();
StringBuilder fragmentDaErrorStringBuilder = new StringBuilder();
StringBuilder fragmentPpmErrorStringBuilder = new StringBuilder();
StringBuilder fragmentIntensityStringBuilder = new StringBuilder();
List <StringBuilder> stringBuilders = new List <StringBuilder> {
seriesStringBuilder, mzStringBuilder, fragmentDaErrorStringBuilder, fragmentPpmErrorStringBuilder, fragmentIntensityStringBuilder
};
if (!nullPsm)
{
// using ", " instead of "," improves human readability
const string delimiter = ", ";
var matchedIonsGroupedByProductType = matchedIons.GroupBy(x => new { x.NeutralTheoreticalProduct.ProductType, x.NeutralTheoreticalProduct.SecondaryProductType }).ToList();
foreach (var productType in matchedIonsGroupedByProductType)
{
var products = productType.OrderBy(p => p.NeutralTheoreticalProduct.FragmentNumber)
.ToList();
stringBuilders.ForEach(p => p.Append("["));
for (int i = 0; i < products.Count; i++)
{
MatchedFragmentIon ion = products[i];
string ionLabel;
double massError = ion.Mz.ToMass(ion.Charge) - ion.NeutralTheoreticalProduct.NeutralMass;
double ppmMassError = massError / ion.NeutralTheoreticalProduct.NeutralMass * 1e6;
ionLabel = ion.Annotation;
// append ion label
seriesStringBuilder.Append(ionLabel);
// append experimental m/z
mzStringBuilder.Append(ionLabel + ":" + ion.Mz.ToString("F5"));
// append absolute mass error
fragmentDaErrorStringBuilder.Append(ionLabel + ":" + massError.ToString("F5"));
// append ppm mass error
fragmentPpmErrorStringBuilder.Append(ionLabel + ":" + ppmMassError.ToString("F2"));
// append fragment ion intensity
fragmentIntensityStringBuilder.Append(ionLabel + ":" + ion.Intensity.ToString("F0"));
// append delimiter ", "
if (i < products.Count - 1)
{
stringBuilders.ForEach(p => p.Append(delimiter));
}
}
// append product type delimiter
stringBuilders.ForEach(p => p.Append("];"));
}
}
// save ion series strings to output dictionary
s[PsmTsvHeader.MatchedIonSeries] = nullPsm ? " " : seriesStringBuilder.ToString().TrimEnd(';');
s[PsmTsvHeader.MatchedIonMzRatios] = nullPsm ? " " : mzStringBuilder.ToString().TrimEnd(';');
s[PsmTsvHeader.MatchedIonMassDiffDa] = nullPsm ? " " : fragmentDaErrorStringBuilder.ToString().TrimEnd(';');
s[PsmTsvHeader.MatchedIonMassDiffPpm] = nullPsm ? " " : fragmentPpmErrorStringBuilder.ToString().TrimEnd(';');
s[PsmTsvHeader.MatchedIonIntensities] = nullPsm ? " " : fragmentIntensityStringBuilder.ToString().TrimEnd(';');
// number of matched ions
s[PsmTsvHeader.MatchedIonCounts] = nullPsm ? " " : matchedIons.Count.ToString();
}
protected void AnnotatePeak(MatchedFragmentIon matchedIon, bool isBetaPeptide, bool useLiteralPassedValues = false)
{
OxyColor ionColor;
if (SpectrumMatch.VariantCrossingIons.Contains(matchedIon))
{
ionColor = MetaDrawSettings.VariantCrossColor;
}
else
{
if (isBetaPeptide)
{
ionColor = MetaDrawSettings.BetaProductTypeToColor[matchedIon.NeutralTheoreticalProduct.ProductType];
}
else
{
ionColor = MetaDrawSettings.ProductTypeToColor[matchedIon.NeutralTheoreticalProduct.ProductType];
}
}
int i = Scan.MassSpectrum.GetClosestPeakIndex(matchedIon.NeutralTheoreticalProduct.NeutralMass.ToMz(matchedIon.Charge));
double mz = Scan.MassSpectrum.XArray[i];
double intensity = Scan.MassSpectrum.YArray[i];
if (useLiteralPassedValues)
{
mz = matchedIon.Mz;
intensity = matchedIon.Intensity;
}
// peak annotation
string prefix = "";
if (SpectrumMatch.BetaPeptideBaseSequence != null)
{
if (isBetaPeptide)
{
//prefix = "β";
prefix = "B-";
}
else
{
//prefix = "α";
prefix = "A-";
}
}
string productType = matchedIon.NeutralTheoreticalProduct.ProductType.ToString()
//.Replace("star", "*", StringComparison.OrdinalIgnoreCase)
//.Replace("degree", "°", StringComparison.OrdinalIgnoreCase)
//.Replace("dot", "·", StringComparison.OrdinalIgnoreCase)
;
string productNumber = matchedIon.NeutralTheoreticalProduct.FragmentNumber.ToString();
string peakAnnotationText = prefix + productType + productNumber;
if (matchedIon.NeutralTheoreticalProduct.NeutralLoss != 0)
{
peakAnnotationText += "-" + matchedIon.NeutralTheoreticalProduct.NeutralLoss.ToString("F2");
}
if (MetaDrawSettings.AnnotateCharges)
{
peakAnnotationText += "+" + matchedIon.Charge;
}
if (MetaDrawSettings.AnnotateMzValues)
{
peakAnnotationText += " (" + matchedIon.Mz.ToString("F3") + ")";
}
var peakAnnotation = new TextAnnotation();
peakAnnotation.Font = "Arial";
peakAnnotation.FontSize = MetaDrawSettings.AnnotatedFontSize;
peakAnnotation.FontWeight = MetaDrawSettings.AnnotationBold ? OxyPlot.FontWeights.Bold : 2.0;
peakAnnotation.TextColor = ionColor;
peakAnnotation.StrokeThickness = 0;
peakAnnotation.Text = peakAnnotationText;
peakAnnotation.TextPosition = new DataPoint(mz, intensity);
peakAnnotation.TextVerticalAlignment = intensity < 0 ? OxyPlot.VerticalAlignment.Top : OxyPlot.VerticalAlignment.Bottom;
peakAnnotation.TextHorizontalAlignment = OxyPlot.HorizontalAlignment.Center;
if (!MetaDrawSettings.DisplayIonAnnotations)
{
peakAnnotation.Text = string.Empty;
}
DrawPeak(mz, intensity, MetaDrawSettings.StrokeThicknessAnnotated, ionColor, peakAnnotation);
}
