private bool IsVisibleIon(MatchedFragmentIon mfi)
{
// Show precursor ions when they are supposed to be shown, regardless of charge
// N.B. for fragments, we look at abs value of charge. CONSIDER(bspratt): for small mol libs we may want finer per-adduct control
return(mfi.Ordinal > 0 && ShowTypes.Contains(mfi.IonType) &&
(mfi.IonType == IonType.precursor || ShowCharges.Contains(Math.Abs(mfi.Charge.AdductCharge))));
}
private string GetLabel(MatchedFragmentIon mfi, int rank, bool showMz)
{
var label = new StringBuilder(string.IsNullOrEmpty(mfi.FragmentName) ? mfi.IonType.GetLocalizedString() : mfi.FragmentName);
if (string.IsNullOrEmpty(mfi.FragmentName) && !Transition.IsPrecursor(mfi.IonType))
{
label.Append(mfi.Ordinal.ToString(LocalizationHelper.CurrentCulture));
}
if (mfi.Losses != null)
{
label.Append(@" -");
label.Append(Math.Round(mfi.Losses.Mass, 1));
}
var chargeIndicator = mfi.Charge.Equals(Adduct.SINGLY_PROTONATED) ? string.Empty : Transition.GetChargeIndicator(mfi.Charge);
label.Append(chargeIndicator);
if (showMz)
{
label.Append(string.Format(@" = {0:F01}", mfi.PredictedMz));
}
if (rank > 0 && ShowRanks)
{
label.Append(TextUtil.SEPARATOR_SPACE).Append(string.Format(@"({0})", string.Format(Resources.AbstractSpectrumGraphItem_GetLabel_rank__0__, rank)));
}
return(label.ToString());
}
private void AnnotatePeak(PlotModel model, LineSeries[] allIons, MsDataScan msDataScan, MatchedFragmentIon matchedIon, double[] spectrumIntensities, PsmFromTsv psmToDraw,
bool annotateCharge, bool annotateMz, bool annotateBold, int annotateFontSize, bool isBetaPeptide)
{
OxyColor ionColor;
if (psmToDraw.VariantCrossingIons.Contains(matchedIon))
{
ionColor = variantCrossColor;
}
else if (productTypeDrawColors.ContainsKey(matchedIon.NeutralTheoreticalProduct.ProductType))
{
ionColor = productTypeDrawColors[matchedIon.NeutralTheoreticalProduct.ProductType];
}
else
{
ionColor = OxyColors.Turquoise;
}
int i = msDataScan.MassSpectrum.GetClosestPeakIndex(matchedIon.NeutralTheoreticalProduct.NeutralMass.ToMz(matchedIon.Charge));
// peak line
allIons[i] = new LineSeries();
allIons[i].Color = ionColor;
allIons[i].StrokeThickness = STROKE_THICKNESS_ANNOTATED;
allIons[i].Points.Add(new DataPoint(matchedIon.Mz, 0));
allIons[i].Points.Add(new DataPoint(matchedIon.Mz, spectrumIntensities[i]));
// peak annotation
string prefix = "";
if (psmToDraw.BetaPeptideBaseSequence != null)
{
if (isBetaPeptide)
{
//prefix = "β";
prefix = "B-";
}
else
{
//prefix = "α";
prefix = "A-";
}
}
string productType = matchedIon.NeutralTheoreticalProduct.ProductType.ToString().ToLower();//.Replace("star", "*").Replace("degree", "°").Replace("dot", "");
string productNumber = matchedIon.NeutralTheoreticalProduct.FragmentNumber.ToString();
string peakAnnotationText = prefix + productType + productNumber;
if (matchedIon.NeutralTheoreticalProduct.NeutralLoss != 0)
{
peakAnnotationText += "-" + matchedIon.NeutralTheoreticalProduct.NeutralLoss.ToString("F2");
}
if (annotateCharge)
{
peakAnnotationText += "+" + matchedIon.Charge;
}
if (annotateMz)
{
peakAnnotationText += " (" + matchedIon.Mz.ToString("F3") + ")";
}
var peakAnnotation = new TextAnnotation();
peakAnnotation.Font = "Arial";
peakAnnotation.FontSize = annotateFontSize;
peakAnnotation.FontWeight = annotateBold ? FontWeights.Bold : 2.0;
peakAnnotation.TextColor = ionColor;
peakAnnotation.StrokeThickness = 0;
peakAnnotation.Text = peakAnnotationText;
peakAnnotation.TextPosition = new DataPoint(allIons[i].Points[1].X, allIons[i].Points[1].Y);
peakAnnotation.TextHorizontalAlignment = HorizontalAlignment.Center;
model.Annotations.Add(peakAnnotation);
model.Series.Add(allIons[i]);
}
//draw the sequence coverage map: write out the sequence, overlay modifications, and display matched fragments
public void DrawSequenceCoverageMap(PsmFromTsv psm, Canvas sequenceText, Canvas map)
{
map.Children.Clear();
sequenceText.Children.Clear();
int spacing = 20;
const int textHeight = 140;
const int heightIncrement = 5;
const int xShift = 10;
int peptideLength = psm.BaseSeq.Length;
//intensity arrays for each ion type
double[] nIntensityArray = new double[peptideLength - 1];
double[] cIntensityArray = new double[peptideLength - 1];
double[] internalIntensityArray = new double[peptideLength - 1];
//colors for annotation
Color nColor = Colors.Blue;
Color cColor = Colors.Red;
Color internalColor = Colors.Purple;
//draw sequence text
for (int r = 0; r < psm.BaseSeq.Length; r++)
{
TextDrawing(sequenceText, new Point(r * spacing + xShift, textHeight - 30), (r + 1).ToString(), Brushes.Black, 8);
TextDrawing(sequenceText, new Point(r * spacing + xShift, textHeight - 15), (psm.BaseSeq.Length - r).ToString(), Brushes.Black, 8);
TextDrawing(sequenceText, new Point(r * spacing + xShift, textHeight), psm.BaseSeq[r].ToString(), Brushes.Black, 16);
}
//create circles for mods, if needed and able
if (!psm.FullSequence.Contains("|")) //can't draw mods if not localized/identified
{
PeptideSpectrumMatchPlot.AnnotateModifications(psm, sequenceText, psm.FullSequence, textHeight - 4, spacing, xShift + 5);
}
//draw lines for each matched fragment
List <bool[]> index = new List <bool[]>();
//N-terminal
List <MatchedFragmentIon> nTermFragments = psm.MatchedIons.Where(x => x.NeutralTheoreticalProduct.Terminus == FragmentationTerminus.N).ToList();
//C-terminal in reverse order
List <MatchedFragmentIon> cTermFragments = psm.MatchedIons.Where(x => x.NeutralTheoreticalProduct.Terminus == FragmentationTerminus.C).OrderByDescending(x => x.NeutralTheoreticalProduct.FragmentNumber).ToList();
//add internal fragments
List <MatchedFragmentIon> internalFragments = psm.MatchedIons.Where(x => x.NeutralTheoreticalProduct.SecondaryProductType != null).OrderBy(x => x.NeutralTheoreticalProduct.FragmentNumber).ToList();
//indexes to navigate terminal ions
int n = 0;
int c = 0;
int heightForThisFragment = 70; //location to draw a fragment
//line up terminal fragments so that complementary ions are paired on the same line
while (n < nTermFragments.Count && c < cTermFragments.Count)
{
MatchedFragmentIon nProduct = nTermFragments[n];
MatchedFragmentIon cProduct = cTermFragments[c];
int expectedComplementary = peptideLength - nProduct.NeutralTheoreticalProduct.FragmentNumber;
//if complementary pair
if (cProduct.NeutralTheoreticalProduct.FragmentNumber == expectedComplementary)
{
//plot sequences
DrawHorizontalLine(0, nProduct.NeutralTheoreticalProduct.FragmentNumber, map, heightForThisFragment, nColor, spacing);
DrawHorizontalLine(peptideLength - cProduct.NeutralTheoreticalProduct.FragmentNumber, peptideLength, map, heightForThisFragment, cColor, spacing);
//record intensities
nIntensityArray[nProduct.NeutralTheoreticalProduct.FragmentNumber - 1] += nProduct.Intensity;
cIntensityArray[peptideLength - cProduct.NeutralTheoreticalProduct.FragmentNumber - 1] += cProduct.Intensity;
//increment indexes
n++;
c++;
}
//if n-terminal ion is present without complementary
else if (cProduct.NeutralTheoreticalProduct.FragmentNumber < expectedComplementary)
{
DrawHorizontalLine(0, nProduct.NeutralTheoreticalProduct.FragmentNumber, map, heightForThisFragment, nColor, spacing);
nIntensityArray[nProduct.NeutralTheoreticalProduct.FragmentNumber - 1] += nProduct.Intensity;
n++;
}
//if c-terminal ion is present without complementary
else
{
DrawHorizontalLine(peptideLength - cProduct.NeutralTheoreticalProduct.FragmentNumber, peptideLength, map, heightForThisFragment, cColor, spacing);
cIntensityArray[peptideLength - cProduct.NeutralTheoreticalProduct.FragmentNumber - 1] += cProduct.Intensity;
c++;
}
heightForThisFragment += heightIncrement;
}
//wrap up leftover fragments without complementary pairs
for (; n < nTermFragments.Count; n++)
{
MatchedFragmentIon nProduct = nTermFragments[n];
DrawHorizontalLine(0, nProduct.NeutralTheoreticalProduct.FragmentNumber, map, heightForThisFragment, nColor, spacing);
nIntensityArray[nProduct.NeutralTheoreticalProduct.FragmentNumber - 1] += nProduct.Intensity;
heightForThisFragment += heightIncrement;
}
for (; c < cTermFragments.Count; c++)
{
MatchedFragmentIon cProduct = cTermFragments[c];
DrawHorizontalLine(peptideLength - cProduct.NeutralTheoreticalProduct.FragmentNumber, peptideLength, map, heightForThisFragment, cColor, spacing);
cIntensityArray[peptideLength - cProduct.NeutralTheoreticalProduct.FragmentNumber - 1] += cProduct.Intensity;
heightForThisFragment += heightIncrement;
}
//internal fragments
foreach (MatchedFragmentIon fragment in internalFragments)
{
DrawHorizontalLine(fragment.NeutralTheoreticalProduct.FragmentNumber, fragment.NeutralTheoreticalProduct.SecondaryFragmentNumber, map, heightForThisFragment, internalColor, spacing);
internalIntensityArray[fragment.NeutralTheoreticalProduct.FragmentNumber - 1] += fragment.Intensity;
internalIntensityArray[fragment.NeutralTheoreticalProduct.SecondaryFragmentNumber - 1] += fragment.Intensity;
heightForThisFragment += heightIncrement;
}
map.Height = heightForThisFragment + 100;
map.Width = spacing * psm.BaseSeq.Length + 100;
sequenceText.Width = spacing * psm.BaseSeq.Length + 100;
////PLOT INTENSITY HISTOGRAM////
double[] intensityArray = new double[peptideLength - 1];
for (int i = 0; i < intensityArray.Length; i++)
{
intensityArray[i] = nIntensityArray[i] + cIntensityArray[i] + internalIntensityArray[i];
}
double maxIntensity = intensityArray.Max();
//foreach cleavage site
for (int i = 0; i < intensityArray.Length; i++)
{
//if anything
if (intensityArray[i] > 0)
{
int x = (i + 1) * spacing + 7;
//n-terminal
int nY = 100 - (int)Math.Round(nIntensityArray[i] * 100 / maxIntensity, 0);
if (nY != 100)
{
DrawVerticalLine(104, nY + 4, sequenceText, (i + 1) * spacing + 5, nColor);
}
//c-terminal
int cY = nY - (int)Math.Round(cIntensityArray[i] * 100 / maxIntensity, 0);
if (nY != cY)
{
DrawVerticalLine(nY + 2, cY + 2, sequenceText, (i + 1) * spacing + 5, cColor);
}
//internal
int iY = cY - (int)Math.Round(internalIntensityArray[i] * 100 / maxIntensity, 0);
if (cY != iY)
{
DrawVerticalLine(cY, iY, sequenceText, (i + 1) * spacing + 5, internalColor);
}
}
}
}
protected void AnnotatePeak(MatchedFragmentIon matchedIon, bool isBetaPeptide, bool useLiteralPassedValues = false)
{
OxyColor ionColor;
if (SpectrumMatch.VariantCrossingIons.Contains(matchedIon))
{
ionColor = MetaDrawSettings.VariantCrossColor;
}
else if (matchedIon.NeutralTheoreticalProduct.SecondaryProductType != null) //if internal fragment
{
ionColor = OxyColors.Purple;
}
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 peakAnnotationText = prefix + matchedIon.NeutralTheoreticalProduct.Annotation;
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);
}
