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();
}
public static void AnnotateModifications(PsmFromTsv spectrumMatch, Canvas sequenceDrawingCanvas, string fullSequence, int yLoc, double?spacer = null, int xShift = 12)
{
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) * (spacer ?? MetaDrawSettings.AnnotatedSequenceTextSpacing) - xShift;
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);
}
}
}
// add psm to corresponding peptide
private void AddPsmToTreeView(ProteinForTreeView protein, PsmFromTsv psm)
{
PeptideForTreeView peptide = null;
if (protein.AllPeptides.ContainsKey(psm.BaseSeq)) // retrieve corresponding peptide
{
peptide = protein.AllPeptides[psm.BaseSeq];
}
else // psm doesnt match any peptide, create new peptide
{
peptide = new PeptideForTreeView(psm.BaseSeq, protein);
protein.Children.Add(peptide);
protein.AllPeptides.Add(psm.BaseSeq, peptide);
}
int i = 0;
while (i < peptide.Children.Count) // O(N)
{
// add to sorted collection
if (psm.Ms2ScanNumber < peptide.Children[i].ScanNo)
{
peptide.Children.Insert(i, new PsmForTreeView(psm.Ms2ScanNumber, psm, peptide));
return;
}
++i;
}
peptide.Children.Add(new PsmForTreeView(psm.Ms2ScanNumber, psm, peptide));
}
public static void TestParenthesesRemovalForSilac()
{
string baseSequence = "ASDF(+8.01)ASDF";
string cleanedSequence = PsmFromTsv.RemoveParentheses(baseSequence);
Assert.IsTrue(cleanedSequence.Equals("ASDFASDF"));
}
private void OnSelectionChanged()
{
if (dataGridScanNums.SelectedItem == null)
{
return;
}
// draw the selected PSM
propertyView.Clear();
PsmFromTsv row = (PsmFromTsv)dataGridScanNums.SelectedItem;
System.Reflection.PropertyInfo[] temp = row.GetType().GetProperties();
for (int i = 0; i < temp.Length; i++)
{
if (temp[i].Name == nameof(row.MatchedIons))
{
propertyView.Rows.Add(temp[i].Name, string.Join(", ", row.MatchedIons.Select(p => p.Annotation)));
}
else
{
propertyView.Rows.Add(temp[i].Name, temp[i].GetValue(row, null));
}
}
dataGridProperties.Items.Refresh();
itemsControlSampleViewModel.Data.Clear();
DrawPsm(row.Ms2ScanNumber, row.FullSequence);
}
private PlotModel DrawPdf(MsDataScan msDataScan, PropertyInfo[] properties, PsmFromTsv psm, bool redraw)
{
if (redraw)
{
this.Model = Draw(msDataScan, psm);
}
var y = Model.DefaultYAxis.ActualMaximum - Model.DefaultYAxis.ActualMaximum * 0.03;
var x = Model.DefaultXAxis.ActualMaximum - Model.DefaultXAxis.ActualMaximum * 0.01;
var diff = (y - (Model.DefaultYAxis.ActualMaximum * 0.1)) / properties.Length;
// properties to include
string[] propertiesToWrite =
{
"Filename",
"PrecursorCharge",
"PrecursorMass",
"PeptideMonoMass",
"MassDiffDa",
"MassDiffPpm",
"Score",
"DeltaScore",
"ProteinAccession",
"ProteinName",
"GeneName",
"DecoyContamTarget",
"QValue",
"QValueNotch"
};
var propertiesList = properties.Where(p => propertiesToWrite.Contains(p.Name)).OrderBy(p => Array.IndexOf(propertiesToWrite, p.Name)).ToList();
var displayedProperties = propertiesList.Where(p => p.GetValue(psm) != null); // only display non-null properties
foreach (PropertyInfo property in displayedProperties)
{
// trim property values > 50 characters
var val = "" + property.GetValue(psm);
if (val.Length > 50)
{
val = val.Substring(0, 50) + "...";
}
var propertyAnnotation = new TextAnnotation
{
Text = property.Name + ": " + val,
TextPosition = new DataPoint(x, y),
FontSize = 9,
StrokeThickness = 0,
TextHorizontalAlignment = HorizontalAlignment.Right
};
y -= diff;
Model.Annotations.Add(propertyAnnotation);
}
return(Model);
}
private void DrawPdfAnnotatedBaseSequence(PsmFromTsv psm, Canvas canvas, string path)
{
if (psm.CrossType == null)
{
DrawAnnotatedBaseSequence(psm);
}
string pathToBaseSeq = Path.Combine(Path.GetDirectoryName(path), "annotation.png");
CustomPdfWriter.RenderImage((int)canvas.Width, 600, pathToBaseSeq, canvas);
}
/// <summary>
/// Event triggers when a different cell is selected in the PSM data grid
/// </summary>
private void dataGridScanNums_SelectedCellsChanged(object sender, SelectedCellsChangedEventArgs e)
{
if (dataGridScanNums.SelectedItem == null)
{
return;
}
PsmFromTsv psm = (PsmFromTsv)dataGridScanNums.SelectedItem;
// draw the annotated spectrum
MetaDrawLogic.DisplaySpectrumMatch(plotView, canvas, psm, itemsControlSampleViewModel, out var errors);
//draw the sequence coverage if not crosslinked
if (psm.ChildScanMatchedIons == null)
{
MetaDrawLogic.DrawSequenceCoverageMap(psm, sequenceText, map); //TODO: figure out how to show coverage on crosslinked peptides
ParentChildScanView.Visibility = Visibility.Collapsed;
SequenceCoverageAnnotationView.Visibility = Visibility.Visible;
}
else
{
ParentChildScanView.Visibility = Visibility.Visible;
SequenceCoverageAnnotationView.Visibility = Visibility.Collapsed;
}
mapViewer.Width = map.Width;
if (errors != null && errors.Any())
{
MessageBox.Show(errors.First());
return;
}
// display PSM properties
propertyView.Clear();
System.Reflection.PropertyInfo[] temp = psm.GetType().GetProperties();
for (int i = 0; i < temp.Length; i++)
{
if (temp[i].Name == nameof(psm.MatchedIons))
{
propertyView.Rows.Add(temp[i].Name, string.Join(", ", psm.MatchedIons.Select(p => p.Annotation)));
}
else if (temp[i].Name == nameof(psm.VariantCrossingIons))
{
propertyView.Rows.Add(temp[i].Name, string.Join(", ", psm.VariantCrossingIons.Select(p => p.Annotation)));
}
else
{
propertyView.Rows.Add(temp[i].Name, temp[i].GetValue(psm, null));
}
}
}
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);
}
private void PDFButton_Click(object sender, RoutedEventArgs e)
{
PsmFromTsv tempPsm = null;
if (dataGridScanNums.SelectedCells.Count == 0)
{
MessageBox.Show("Please select at least one scan to export");
}
else
{
int numberOfScansToExport = dataGridScanNums.SelectedItems.Count;
foreach (object selectedItem in dataGridScanNums.SelectedItems)
{
PsmFromTsv psm = (PsmFromTsv)selectedItem;
if (tempPsm == null)
{
tempPsm = psm;
}
MsDataScan msDataScanToDraw = MsDataFile.GetOneBasedScan(psm.Ms2ScanNumber);
string myString = illegalInFileName.Replace(psm.FullSequence, "");
if (myString.Length > 30)
{
myString = myString.Substring(0, 30);
}
string filePath = Path.Combine(Path.GetDirectoryName(tsvResultsFilePath), "MetaDrawExport", psm.Ms2ScanNumber + "_" + myString + ".pdf");
string dir = Path.GetDirectoryName(filePath);
if (!Directory.Exists(dir))
{
Directory.CreateDirectory(dir);
}
DrawPdfAnnotatedBaseSequence(psm, canvas, filePath); // captures the annotation for the pdf
mainViewModel.DrawPeptideSpectralMatchPdf(msDataScanToDraw, psm, filePath, numberOfScansToExport > 1);
}
dataGridScanNums.SelectedItem = dataGridScanNums.SelectedItem;
DrawPsm(tempPsm.Ms2ScanNumber, tempPsm.FullSequence);
MessageBox.Show(string.Format("{0} PDFs exported", numberOfScansToExport));
}
}
/// <summary>
/// Event triggers when a different cell is selected in the PSM data grid
/// </summary>
private void dataGridScanNums_SelectedCellsChanged(object sender, SelectedCellsChangedEventArgs e)
{
if (dataGridScanNums.SelectedItem == null)
{
return;
}
PsmFromTsv psm = (PsmFromTsv)dataGridScanNums.SelectedItem;
// draw the PSM
MetaDrawLogic.DisplaySpectrumMatch(plotView, canvas, psm, itemsControlSampleViewModel, out var errors);
if (psm.ChildScanMatchedIons != null)
{
ParentChildScanView.Visibility = Visibility.Visible;
ParentScanView.Visibility = Visibility.Visible;
}
else
{
ParentChildScanView.Visibility = Visibility.Collapsed;
ParentScanView.Visibility = Visibility.Collapsed;
}
if (errors != null && errors.Any())
{
MessageBox.Show(errors.First());
return;
}
// display PSM properties
propertyView.Clear();
System.Reflection.PropertyInfo[] temp = psm.GetType().GetProperties();
for (int i = 0; i < temp.Length; i++)
{
if (temp[i].Name == nameof(psm.MatchedIons))
{
propertyView.Rows.Add(temp[i].Name, string.Join(", ", psm.MatchedIons.Select(p => p.Annotation)));
}
else if (temp[i].Name == nameof(psm.VariantCrossingIons))
{
propertyView.Rows.Add(temp[i].Name, string.Join(", ", psm.VariantCrossingIons.Select(p => p.Annotation)));
}
else
{
propertyView.Rows.Add(temp[i].Name, temp[i].GetValue(psm, null));
}
}
}
// filter psms based on settings and group psms by protein
private void FilterPsm(PsmFromTsv psm)
{
if (psm.QValue <= metaDrawFilterSettings.QValueFilter && (psm.QValueNotch < metaDrawFilterSettings.QValueFilter || psm.QValueNotch == null) &&
(psm.DecoyContamTarget == "T" || (psm.DecoyContamTarget == "D" && metaDrawFilterSettings.ShowDecoys) || (psm.DecoyContamTarget == "C" && metaDrawFilterSettings.ShowContaminants)))
{
filteredListOfPsms.Add(psm);
// group psms by protein
foreach (var protein in proteinGroupsForTreeView.Where(x => psm.ProteinAccession.Contains(x.Key) || x.Key.Contains(psm.ProteinAccession)).Select(x => x.Value))
{
AddPsmToTreeView(protein, psm);
psmsWithMatch.Add(psm);
}
}
}
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()));
};
}
}
private void TextBox_TextChanged(object sender, TextChangedEventArgs e)
{
string txt = (sender as TextBox).Text;
if (txt == "")
{
peptideSpectralMatchesView.Filter = null;
}
else
{
peptideSpectralMatchesView.Filter = obj =>
{
PsmFromTsv psm = obj as PsmFromTsv;
return ((psm.Ms2ScanNumber.ToString()).StartsWith(txt) || psm.FullSequence.ToUpper().Contains(txt.ToUpper()));
};
}
}
// displays psm spectrum annotation
private void displayPsm(PsmForTreeView selection)
{
PsmFromTsv row = selection.Psm;
System.Reflection.PropertyInfo[] temp = row.GetType().GetProperties();
for (int i = 0; i < temp.Length; i++)
{
if (temp[i].Name == nameof(row.MatchedIons))
{
propertyView.Rows.Add(temp[i].Name, string.Join(", ", row.MatchedIons.Select(p => p.Annotation)));
}
else
{
propertyView.Rows.Add(temp[i].Name, temp[i].GetValue(row, null));
}
}
dataGridProperties.Items.Refresh();
itemsControlSampleViewModel.Data.Clear();
DrawPsm(row.Ms2ScanNumber, row.FullSequence);
}
private void DrawPdfAnnotatedBaseSequence(PsmFromTsv psm, Canvas canvas, string path)
{
if (psm.CrossType == null)
{
DrawAnnotatedBaseSequence(psm);
}
canvas.Measure(new Size((int)canvas.Width, 600));
canvas.Arrange(new Rect(new Size((int)canvas.Width, 600)));
RenderTargetBitmap renderBitmap = new RenderTargetBitmap((int)(canvas.Width), 600, 96, 96, PixelFormats.Pbgra32);
renderBitmap.Render(canvas);
PngBitmapEncoder encoder = new PngBitmapEncoder();
encoder.Frames.Add(BitmapFrame.Create(renderBitmap));
string tempPath = Path.Combine(Path.GetDirectoryName(tsvResultsFilePath), "MetaDrawExport", "annotation.png");
using (FileStream file = File.Create(tempPath))
{
encoder.Save(file);
}
}
public void DrawPeptideSpectralMatchPdf(MsDataScan msDataScan, PsmFromTsv psm, string fileName, bool redraw)
{
var properties = psm.GetType().GetProperties();
var pdfModel = DrawPdf(msDataScan, properties, psm, redraw);
string tempPath = Path.Combine(Path.GetDirectoryName(fileName), "sequence.pdf");
string baseSeqTempPath = Path.Combine(Path.GetDirectoryName(fileName), "annotation.png");
// exports plot to pdf
using (var stream = File.Create(tempPath))
{
PdfExporter pdf = new PdfExporter {
Width = 800, Height = 500
};
pdf.Export(pdfModel, stream);
}
// adds base seq annotation to pdf
using (Stream inputPdfStream = new FileStream(tempPath, FileMode.Open, FileAccess.Read, FileShare.Read))
using (Stream inputImageStream = new FileStream(baseSeqTempPath, FileMode.Open, FileAccess.Read, FileShare.Read))
using (Stream outputPdfStream = new FileStream(fileName, FileMode.Create, FileAccess.Write, FileShare.None))
{
var reader = new PdfReader(inputPdfStream);
var stamper = new PdfStamper(reader, outputPdfStream);
var pdfContentByte = stamper.GetOverContent(1);
var image = iTextSharp.text.Image.GetInstance(inputImageStream);
image.ScaleAbsoluteHeight(500);
image.ScaleAbsoluteWidth(500);
image.SetAbsolutePosition(95, 190);
pdfContentByte.AddImage(image);
stamper.Close();
}
File.Delete(tempPath);
File.Delete(baseSeqTempPath);
}
public CrosslinkSpectrumMatchPlot(OxyPlot.Wpf.PlotView plotView, Canvas sequenceDrawingCanvas, PsmFromTsv csm, MsDataScan scan)
: base(plotView, sequenceDrawingCanvas, csm, scan, csm.MatchedIons)
{
SequenceDrawingCanvas.Height = 150;
// annotate beta peptide base sequence
AnnotateBaseSequence(csm.BetaPeptideBaseSequence, csm.BetaPeptideFullSequence, 100, csm.BetaPeptideMatchedIons);
// annotate beta peptide matched ions
AnnotateMatchedIons(isBetaPeptide: true, csm.BetaPeptideMatchedIons);
// annotate crosslinker
int alphaSite = int.Parse(Regex.Match(SpectrumMatch.FullSequence, @"\d+").Value);
int betaSite = int.Parse(Regex.Match(SpectrumMatch.BetaPeptideFullSequence, @"\d+").Value);
AnnotateCrosslinker(SequenceDrawingCanvas,
new Point(alphaSite * MetaDrawSettings.AnnotatedSequenceTextSpacing, 50),
new Point(betaSite * MetaDrawSettings.AnnotatedSequenceTextSpacing, 90),
Colors.Black);
ZoomAxes(csm.MatchedIons.Concat(csm.BetaPeptideMatchedIons), yZoom: 1.5);
RefreshChart();
}
public PsmForTreeView(int scan, PsmFromTsv psm, PeptideForTreeView parent)
{
Parent = parent;
Psm = psm;
ScanNo = scan;
}
private void PDFButton_Click(object sender, RoutedEventArgs e)
{
PsmFromTsv tempPsm = null;
if (dataGridScanNums.SelectedCells.Count == 0)
{
MessageBox.Show("Please select at least one scan to export");
}
else
{
int numberOfScansToExport = dataGridScanNums.SelectedItems.Count;
foreach (object selectedItem in dataGridScanNums.SelectedItems)
{
PsmFromTsv psm = (PsmFromTsv)selectedItem;
if (tempPsm == null)
{
tempPsm = psm;
}
MsDataScan msDataScanToDraw = MsDataFile.GetOneBasedScan(psm.Ms2ScanNumber);
string myString = illegalInFileName.Replace(psm.FullSequence, "");
if (myString.Length > 30)
{
myString = myString.Substring(0, 30);
}
string filePath = Path.Combine(Path.GetDirectoryName(tsvResultsFilePath), "MetaDrawExport", psm.Ms2ScanNumber + "_" + myString + ".pdf");
string dir = Path.GetDirectoryName(filePath);
if (!Directory.Exists(dir))
{
Directory.CreateDirectory(dir);
}
DrawPdfAnnotatedBaseSequence(psm, canvas, filePath); // captures the annotation for the pdf
mainViewModel.DrawPeptideSpectralMatchPdf(msDataScanToDraw, psm, filePath, numberOfScansToExport > 1);
// if this spectrum has child scans, draw them in the "advanced" tab
if ((psm.ChildScanMatchedIons != null && psm.ChildScanMatchedIons.Count > 0) ||
(psm.BetaPeptideChildScanMatchedIons != null && psm.BetaPeptideChildScanMatchedIons.Count > 0))
{
// draw child scans
HashSet <int> scansDrawn = new HashSet <int>();
var allChildScanMatchedIons = psm.ChildScanMatchedIons;
if (psm.BetaPeptideChildScanMatchedIons != null)
{
allChildScanMatchedIons = allChildScanMatchedIons.Concat(psm.BetaPeptideChildScanMatchedIons).ToDictionary(p => p.Key, q => q.Value);
}
foreach (var childScanMatchedIons in allChildScanMatchedIons)
{
int scanNumber = childScanMatchedIons.Key;
if (scansDrawn.Contains(scanNumber))
{
continue;
}
scansDrawn.Add(scanNumber);
List <MatchedFragmentIon> matchedIons = childScanMatchedIons.Value;
var childPsmModel = new PsmAnnotationViewModel();
MsDataScan childScan = MsDataFile.GetOneBasedScan(scanNumber);
childPsmModel.DrawPeptideSpectralMatch(childScan, psm, metaDrawGraphicalSettings.ShowMzValues,
metaDrawGraphicalSettings.ShowAnnotationCharges, metaDrawGraphicalSettings.AnnotatedFontSize, metaDrawGraphicalSettings.BoldText);
string childfilePath = Path.Combine(Path.GetDirectoryName(tsvResultsFilePath), "MetaDrawExport", childScan.OneBasedScanNumber + "_" + myString + ".pdf");
DrawPdfAnnotatedBaseSequence(psm, canvas, childfilePath); // captures the annotation for the pdf
childPsmModel.DrawPeptideSpectralMatchPdf(childScan, psm, childfilePath, false);
}
}
}
dataGridScanNums.SelectedItem = dataGridScanNums.SelectedItem;
itemsControlSampleViewModel.Data.Clear();
DrawPsm(tempPsm.Ms2ScanNumber, tempPsm.FullSequence);
MessageBox.Show(string.Format("{0} PDFs exported", numberOfScansToExport));
}
}
private void DrawAnnotatedBaseSequence(Canvas canvas, PsmFromTsv psm, bool ToAnnotateChildScan = false)
{
double spacing = 22;
BaseDraw.clearCanvas(canvas);
// don't draw ambiguous sequences
if (psm.FullSequence.Contains("|"))
{
return;
}
// draw base sequence
for (int r = 0; r < psm.BaseSeq.Length; r++)
{
BaseDraw.txtDrawing(canvas, new Point(r * spacing + 10, 10), psm.BaseSeq[r].ToString(), Brushes.Black);
}
var matchIons = psm.MatchedIons;
if (ToAnnotateChildScan)
{
matchIons = new List <MatchedFragmentIon>();
foreach (var x in psm.ChildScanMatchedIons)
{
matchIons.AddRange(x.Value);
}
}
// draw the fragment ion annotations on the base sequence
foreach (var ion in matchIons)
{
int residue = ion.NeutralTheoreticalProduct.AminoAcidPosition;
string annotation = ion.NeutralTheoreticalProduct.ProductType + "" + ion.NeutralTheoreticalProduct.FragmentNumber;
Color color = psm.VariantCrossingIons.Contains(ion) ? variantCrossColor : productTypeToColor[ion.NeutralTheoreticalProduct.ProductType];
if (ion.NeutralTheoreticalProduct.NeutralLoss != 0)
{
annotation += "-" + ion.NeutralTheoreticalProduct.NeutralLoss;
}
if (ion.NeutralTheoreticalProduct.Terminus == FragmentationTerminus.C)
{
BaseDraw.topSplittingDrawing(canvas, new Point(residue * spacing + 8,
productTypeToYOffset[ion.NeutralTheoreticalProduct.ProductType]), color, annotation);
}
else if (ion.NeutralTheoreticalProduct.Terminus == FragmentationTerminus.N)
{
BaseDraw.botSplittingDrawing(canvas, new Point(residue * spacing + 8,
productTypeToYOffset[ion.NeutralTheoreticalProduct.ProductType]), color, annotation);
}
// don't draw diagnostic ions, precursor ions, etc
}
// draw modifications
var peptide = new PeptideWithSetModifications(psm.FullSequence, GlobalVariables.AllModsKnownDictionary);
if (psm.GlycanLocalizationLevel != null)
{
var localGlycans = PsmFromTsv.ReadLocalizedGlycan(psm.LocalizedGlycan);
foreach (var mod in peptide.AllModsOneIsNterminus)
{
if (mod.Value.ModificationType == "O-Glycosylation")
{
if (localGlycans.Where(p => p.Item1 + 1 == mod.Key).Count() > 0)
{
BaseDraw.circledTxtDraw(canvas, new Point((mod.Key - 1) * spacing - 17, 12), modificationAnnotationColor);
}
else
{
BaseDraw.circledTxtDraw(canvas, new Point((mod.Key - 1) * spacing - 17, 12), Brushes.Gray);
}
}
}
}
else
{
foreach (var mod in peptide.AllModsOneIsNterminus)
{
BaseDraw.circledTxtDraw(canvas, new Point((mod.Key - 1) * spacing - 17, 12), modificationAnnotationColor);
}
}
if (psm.BetaPeptideBaseSequence != null)
{
for (int r = 0; r < psm.BetaPeptideBaseSequence.Length; r++)
{
BaseDraw.txtDrawing(canvas, new Point(r * spacing + 10, 100), psm.BetaPeptideBaseSequence[r].ToString(), Brushes.Black);
}
foreach (var ion in psm.BetaPeptideMatchedIons)
{
int residue = ion.NeutralTheoreticalProduct.AminoAcidPosition;
string annotation = ion.NeutralTheoreticalProduct.ProductType + "" + ion.NeutralTheoreticalProduct.FragmentNumber;
if (ion.NeutralTheoreticalProduct.NeutralLoss != 0)
{
annotation += "-" + ion.NeutralTheoreticalProduct.NeutralLoss;
}
if (ion.NeutralTheoreticalProduct.Terminus == FragmentationTerminus.C)
{
BaseDraw.topSplittingDrawing(canvas, new Point(residue * spacing + 8,
productTypeToYOffset[ion.NeutralTheoreticalProduct.ProductType] + 90), productTypeToColor[ion.NeutralTheoreticalProduct.ProductType], annotation);
}
else if (ion.NeutralTheoreticalProduct.Terminus == FragmentationTerminus.N)
{
BaseDraw.botSplittingDrawing(canvas, new Point(residue * spacing + 8,
productTypeToYOffset[ion.NeutralTheoreticalProduct.ProductType] + 90), productTypeToColor[ion.NeutralTheoreticalProduct.ProductType], annotation);
}
// don't draw diagnostic ions, precursor ions, etc
}
var betaPeptide = new PeptideWithSetModifications(psm.BetaPeptideFullSequence, GlobalVariables.AllModsKnownDictionary);
foreach (var mod in betaPeptide.AllModsOneIsNterminus)
{
BaseDraw.circledTxtDraw(canvas, new Point((mod.Key - 1) * spacing - 17, 12 + 90), modificationAnnotationColor);
}
int alphaSite = Int32.Parse(Regex.Match(psm.FullSequence, @"\d+").Value);
int betaSite = Int32.Parse(Regex.Match(psm.BetaPeptideFullSequence, @"\d+").Value);
BaseDraw.DrawCrosslinker(canvas, new Point(alphaSite * spacing, 50), new Point(betaSite * spacing, 90), Colors.Black);
}
}
private void DrawPsm(int oneBasedScanNumber, string fullSequence = null, string fileName = null)
{
MsDataScan msDataScanToDraw = MsDataFile.GetOneBasedScan(oneBasedScanNumber);
IEnumerable <PsmFromTsv> scanPsms = filteredListOfPsms.Where(p => p.Ms2ScanNumber == oneBasedScanNumber);
if (fullSequence != null)
{
scanPsms = scanPsms.Where(p => p.FullSequence == fullSequence);
}
PsmFromTsv psmToDraw = scanPsms.FirstOrDefault();
// if this spectrum has child scans, draw them in the "advanced" tab
if ((psmToDraw.ChildScanMatchedIons != null && psmToDraw.ChildScanMatchedIons.Count > 0) ||
(psmToDraw.BetaPeptideChildScanMatchedIons != null && psmToDraw.BetaPeptideChildScanMatchedIons.Count > 0))
{
ParentChildScanView.Visibility = Visibility.Visible;
ParentScanView.Visibility = Visibility.Visible;
// draw parent scans
var parentPsmModel = new PsmAnnotationViewModel();
MsDataScan parentScan = MsDataFile.GetOneBasedScan(psmToDraw.Ms2ScanNumber);
parentPsmModel.DrawPeptideSpectralMatch(parentScan, psmToDraw, metaDrawGraphicalSettings.ShowMzValues,
metaDrawGraphicalSettings.ShowAnnotationCharges, metaDrawGraphicalSettings.AnnotatedFontSize, metaDrawGraphicalSettings.BoldText);
string parentAnnotation = "Scan: " + parentScan.OneBasedScanNumber.ToString()
+ " Dissociation Type: " + parentScan.DissociationType.ToString()
+ " MsOrder: " + parentScan.MsnOrder.ToString()
+ " Selected Mz: " + parentScan.SelectedIonMZ.Value.ToString("0.##")
+ " Retention Time: " + parentScan.RetentionTime.ToString("0.##");
itemsControlSampleViewModel.AddNewRow(parentPsmModel, parentAnnotation, null);
// draw child scans
HashSet <int> scansDrawn = new HashSet <int>();
var allChildScanMatchedIons = psmToDraw.ChildScanMatchedIons;
if (psmToDraw.BetaPeptideChildScanMatchedIons != null)
{
allChildScanMatchedIons = allChildScanMatchedIons.Concat(psmToDraw.BetaPeptideChildScanMatchedIons).ToDictionary(p => p.Key, q => q.Value);
}
foreach (var childScanMatchedIons in allChildScanMatchedIons)
{
int scanNumber = childScanMatchedIons.Key;
if (scansDrawn.Contains(scanNumber))
{
continue;
}
scansDrawn.Add(scanNumber);
List <MatchedFragmentIon> matchedIons = childScanMatchedIons.Value;
var childPsmModel = new PsmAnnotationViewModel();
MsDataScan childScan = MsDataFile.GetOneBasedScan(scanNumber);
childPsmModel.DrawPeptideSpectralMatch(childScan, psmToDraw, metaDrawGraphicalSettings.ShowMzValues,
metaDrawGraphicalSettings.ShowAnnotationCharges, metaDrawGraphicalSettings.AnnotatedFontSize, metaDrawGraphicalSettings.BoldText);
string childAnnotation = "Scan: " + scanNumber.ToString()
+ " Dissociation Type: " + childScan.DissociationType.ToString()
+ " MsOrder: " + childScan.MsnOrder.ToString()
+ " Selected Mz: " + childScan.SelectedIonMZ.Value.ToString("0.##")
+ " RetentionTime: " + childScan.RetentionTime.ToString("0.##");
Canvas aCanvas = new Canvas {
Height = 60
};
DrawAnnotatedBaseSequence(aCanvas, psmToDraw, true);
itemsControlSampleViewModel.AddNewRow(childPsmModel, childAnnotation, aCanvas);
}
}
else
{
ParentChildScanView.Visibility = Visibility.Collapsed;
ParentScanView.Visibility = Visibility.Collapsed;
}
// if this is a crosslink spectrum match, there are two base sequence annotations to draw
// this makes the canvas taller to fit both of these peptide sequences
if (psmToDraw.BetaPeptideBaseSequence != null)
{
int height = 150;
canvas.Height = height;
PsmAnnotationGrid.RowDefinitions[1].Height = new GridLength(height);
}
else
{
int height = 60;
canvas.Height = height;
PsmAnnotationGrid.RowDefinitions[1].Height = new GridLength(height);
}
// draw annotated spectrum
mainViewModel.DrawPeptideSpectralMatch(msDataScanToDraw, psmToDraw, metaDrawGraphicalSettings.ShowMzValues,
metaDrawGraphicalSettings.ShowAnnotationCharges, metaDrawGraphicalSettings.AnnotatedFontSize, metaDrawGraphicalSettings.BoldText);
// draw annotated base sequence
DrawAnnotatedBaseSequence(canvas, psmToDraw);
}
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 not crosslinked
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 //crosslinked
{
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);
}
}
}
//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);
}
}
}
}
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]);
}
// single peptides (not crosslink)
public void DrawPeptideSpectralMatch(MsDataScan msDataScan, PsmFromTsv psmToDraw,
bool annotateMz = false, bool annotateCharge = false, int annotateFontSize = 12, bool annotateBold = false)
{
// Set the Model property, the INotifyPropertyChanged event will make the WPF Plot control update its content
this.Model = Draw(msDataScan, psmToDraw, annotateMz, annotateCharge, annotateFontSize, annotateBold);
}
private PlotModel Draw(MsDataScan msDataScan, PsmFromTsv psmToDraw,
bool annotateMz = false, bool annotateCharge = false, int annotateFontSize = 12, bool annotateBold = false)
{
// x is m/z, y is intensity
var spectrumMzs = msDataScan.MassSpectrum.XArray;
var spectrumIntensities = msDataScan.MassSpectrum.YArray;
string subtitle = psmToDraw.FullSequence;
if (psmToDraw != null && psmToDraw.BetaPeptideBaseSequence != null)
{
subtitle = psmToDraw.FullSequence + "\n" + psmToDraw.BetaPeptideFullSequence;
}
PlotModel model = new PlotModel {
Title = "Spectrum Annotation of Scan #" + msDataScan.OneBasedScanNumber, DefaultFontSize = 15, Subtitle = subtitle
};
model.Axes.Add(new LinearAxis
{
Position = AxisPosition.Bottom,
Title = "m/z",
Minimum = msDataScan.ScanWindowRange.Minimum,
Maximum = msDataScan.ScanWindowRange.Maximum,
AbsoluteMinimum = 0,
AbsoluteMaximum = msDataScan.ScanWindowRange.Maximum * 2,
MajorStep = Math.Round(msDataScan.ScanWindowRange.Maximum / 2),
MinorStep = Math.Round(msDataScan.ScanWindowRange.Maximum / 4)
});
model.Axes.Add(new LinearAxis
{
Position = AxisPosition.Left,
Title = "Intensity",
Minimum = 0,
Maximum = spectrumIntensities.Max(),
AbsoluteMinimum = 0,
AbsoluteMaximum = spectrumIntensities.Max() * 2,
MajorStep = spectrumIntensities.Max(),
MinorStep = spectrumIntensities.Max() / 2,
StringFormat = "0e-0",
});
model.Axes[1].Zoom(0, spectrumIntensities.Max() * 1.1);
LineSeries[] allIons = new LineSeries[spectrumMzs.Length];
// draw the remaining unmatched peaks
for (int i = 0; i < spectrumMzs.Length; i++)
{
// peak has already been drawn (it is a matched peak)
if (allIons[i] != null)
{
continue;
}
allIons[i] = new LineSeries();
allIons[i].Color = OxyColors.DimGray;
allIons[i].StrokeThickness = STROKE_THICKNESS_UNANNOTATED;
allIons[i].Points.Add(new DataPoint(spectrumMzs[i], 0));
allIons[i].Points.Add(new DataPoint(spectrumMzs[i], spectrumIntensities[i]));
model.Series.Add(allIons[i]);
}
// draw the matched peaks; if the PSM is null, we're just drawing the peaks in the scan without annotation, so skip this part
if (psmToDraw != null)
{
List <MatchedFragmentIon> ionsToDraw = new List <MatchedFragmentIon>();
// check to see if we're drawing a child scan or a parent scan
if (psmToDraw.Ms2ScanNumber == msDataScan.OneBasedScanNumber)
{
// parent scan
ionsToDraw = psmToDraw.MatchedIons;
}
else if (msDataScan.OneBasedScanNumber != psmToDraw.Ms2ScanNumber &&
psmToDraw.ChildScanMatchedIons.Keys.Any(p => p == msDataScan.OneBasedScanNumber))
{
// child scan
var scan = psmToDraw.ChildScanMatchedIons.FirstOrDefault(p => p.Key == msDataScan.OneBasedScanNumber);
ionsToDraw = scan.Value;
}
// annotate peaks (typical PSM, or alpha peptide of CSM)
foreach (MatchedFragmentIon matchedIon in ionsToDraw)
{
AnnotatePeak(model, allIons, msDataScan, matchedIon, spectrumIntensities, psmToDraw, annotateCharge,
annotateMz, annotateBold, annotateFontSize, false);
}
// annotate peaks of beta peptide of CSM
if (psmToDraw.BetaPeptideBaseSequence != null)
{
ionsToDraw = new List <MatchedFragmentIon>();
// check to see if we're drawing a child scan or a parent scan
if (psmToDraw.Ms2ScanNumber == msDataScan.OneBasedScanNumber)
{
// parent scan
ionsToDraw = psmToDraw.BetaPeptideMatchedIons;
}
else if (msDataScan.OneBasedScanNumber != psmToDraw.Ms2ScanNumber &&
psmToDraw.BetaPeptideChildScanMatchedIons.Keys.Any(p => p == msDataScan.OneBasedScanNumber))
{
// child scan
var scan = psmToDraw.BetaPeptideChildScanMatchedIons.FirstOrDefault(p => p.Key == msDataScan.OneBasedScanNumber);
ionsToDraw = scan.Value;
}
foreach (MatchedFragmentIon matchedIon in ionsToDraw)
{
AnnotatePeak(model, allIons, msDataScan, matchedIon, spectrumIntensities, psmToDraw, annotateCharge,
annotateMz, annotateBold, annotateFontSize, true);
}
}
}
// Axes are created automatically if they are not defined
return(model);
}
private void DrawAnnotatedBaseSequence(PsmFromTsv psm)
{
double spacing = 22;
BaseDraw.clearCanvas(canvas);
// don't draw ambiguous sequences
if (psm.FullSequence.Contains("|"))
{
return;
}
// draw base sequence
for (int r = 0; r < psm.BaseSeq.Length; r++)
{
BaseDraw.txtDrawing(canvas, new Point(r * spacing + 10, 10), psm.BaseSeq[r].ToString(), Brushes.Black);
}
// draw the fragment ion annotations on the base sequence
foreach (var ion in psm.MatchedIons)
{
int residue = ion.NeutralTheoreticalProduct.TerminusFragment.AminoAcidPosition;
string annotation = ion.NeutralTheoreticalProduct.ProductType + "" + ion.NeutralTheoreticalProduct.TerminusFragment.FragmentNumber;
if (ion.NeutralTheoreticalProduct.NeutralLoss != 0)
{
annotation += "-" + ion.NeutralTheoreticalProduct.NeutralLoss;
}
if (ion.NeutralTheoreticalProduct.TerminusFragment.Terminus == FragmentationTerminus.C)
{
BaseDraw.topSplittingDrawing(canvas, new Point(residue * spacing + 8,
productTypeToYOffset[ion.NeutralTheoreticalProduct.ProductType]), productTypeToColor[ion.NeutralTheoreticalProduct.ProductType], annotation);
}
else if (ion.NeutralTheoreticalProduct.TerminusFragment.Terminus == FragmentationTerminus.N)
{
BaseDraw.botSplittingDrawing(canvas, new Point(residue * spacing + 8,
productTypeToYOffset[ion.NeutralTheoreticalProduct.ProductType]), productTypeToColor[ion.NeutralTheoreticalProduct.ProductType], annotation);
}
// don't draw diagnostic ions, precursor ions, etc
}
// draw modifications
var peptide = new PeptideWithSetModifications(psm.FullSequence, GlobalVariables.AllModsKnownDictionary);
foreach (var mod in peptide.AllModsOneIsNterminus)
{
BaseDraw.circledTxtDraw(canvas, new Point((mod.Key - 1) * spacing - 17, 12), modificationAnnotationColor);
}
if (psm.BetaPeptideBaseSequence != null)
{
for (int r = 0; r < psm.BetaPeptideBaseSequence.Length; r++)
{
BaseDraw.txtDrawing(canvas, new Point(r * spacing + 10, 100), psm.BetaPeptideBaseSequence[r].ToString(), Brushes.Black);
}
foreach (var ion in psm.BetaPeptideMatchedIons)
{
int residue = ion.NeutralTheoreticalProduct.TerminusFragment.AminoAcidPosition;
string annotation = ion.NeutralTheoreticalProduct.ProductType + "" + ion.NeutralTheoreticalProduct.TerminusFragment.FragmentNumber;
if (ion.NeutralTheoreticalProduct.NeutralLoss != 0)
{
annotation += "-" + ion.NeutralTheoreticalProduct.NeutralLoss;
}
if (ion.NeutralTheoreticalProduct.TerminusFragment.Terminus == FragmentationTerminus.C)
{
BaseDraw.topSplittingDrawing(canvas, new Point(residue * spacing + 8,
productTypeToYOffset[ion.NeutralTheoreticalProduct.ProductType] + 90), productTypeToColor[ion.NeutralTheoreticalProduct.ProductType], annotation);
}
else if (ion.NeutralTheoreticalProduct.TerminusFragment.Terminus == FragmentationTerminus.N)
{
BaseDraw.botSplittingDrawing(canvas, new Point(residue * spacing + 8,
productTypeToYOffset[ion.NeutralTheoreticalProduct.ProductType] + 90), productTypeToColor[ion.NeutralTheoreticalProduct.ProductType], annotation);
}
// don't draw diagnostic ions, precursor ions, etc
}
var betaPeptide = new PeptideWithSetModifications(psm.BetaPeptideFullSequence, GlobalVariables.AllModsKnownDictionary);
foreach (var mod in betaPeptide.AllModsOneIsNterminus)
{
BaseDraw.circledTxtDraw(canvas, new Point((mod.Key - 1) * spacing - 17, 12 + 90), modificationAnnotationColor);
}
int alphaSite = Int32.Parse(Regex.Match(psm.FullSequence, @"\d+").Value);
int betaSite = Int32.Parse(Regex.Match(psm.BetaPeptideFullSequence, @"\d+").Value);
BaseDraw.DrawCrosslinker(canvas, new Point(alphaSite * spacing, 50), new Point(betaSite * spacing, 90), Colors.Black);
}
}
