private void resetFilesButton_Click(object sender, RoutedEventArgs e)
{
// clear spectra file path
if ((sender as Button).Name.Equals(resetSpectraFileButton.Name))
{
spectraFilePath = null;
spectraFileNameLabel.Text = "None Selected";
spectraFileNameLabel.ToolTip = null;
resetSpectraFileButton.IsEnabled = false;
}
// clear psm file path, psm data, and stat plot
else
{
tsvResultsFilePath = null;
psmFileNameLabel.Text = "None Selected";
psmFileNameLabel.ToolTip = null;
psmFileNameLabelStat.Text = "None Selected";
psmFileNameLabelStat.ToolTip = null;
resetPsmFileButton.IsEnabled = false;
resetPsmFileButtonStat.IsEnabled = false;
allPsms.Clear();
filteredListOfPsms.Clear();
psmsBySourceFile.Clear();
sourceFilesList.Clear();
plotViewStat.DataContext = null;
}
// clear main plot, base sequence, and properties table
mainViewModel.Model = null;
BaseDraw.clearCanvas(canvas);
propertyView.Clear();
MsDataFile = null;
}
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 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);
}
}
private void DrawAnnotatedBaseSequence(MetaDrawPsm psm)
{
double spacing = 22;
BaseDraw.clearCanvas(canvas);
// draw base sequence
for (int r = 0; r < psm.BaseSequence.Length; r++)
{
BaseDraw.txtDrawing(canvas, new Point(r * spacing + 10, 10), psm.BaseSequence[r].ToString(), Brushes.Black);
}
// draw b ions
foreach (var bIon in psm.FragmentIons.Where(p => p.ProductType == ProductType.B))
{
int residue = bIon.IonNumber;
BaseDraw.botSplittingDrawing(canvas, new Point(residue * spacing + 8, 50), Colors.Blue, bIon.ProductType.ToString().ToLower() + bIon.IonNumber);
}
// draw c ions
foreach (var cIon in psm.FragmentIons.Where(p => p.ProductType == ProductType.C))
{
int residue = psm.BaseSequence.Length - cIon.IonNumber;
BaseDraw.botSplittingDrawing(canvas, new Point(residue * spacing + 8, 50), Colors.Gold, cIon.ProductType.ToString().ToLower() + cIon.IonNumber);
}
// draw y ions
foreach (var yIon in psm.FragmentIons.Where(p => p.ProductType == ProductType.Y))
{
int residue = psm.BaseSequence.Length - yIon.IonNumber;
BaseDraw.topSplittingDrawing(canvas, new Point(residue * spacing + 8, 0), Colors.Purple, yIon.ProductType.ToString().ToLower() + yIon.IonNumber);
}
// draw zdot ions
foreach (var zDotIon in psm.FragmentIons.Where(p => p.ProductType == ProductType.Zdot))
{
int residue = zDotIon.IonNumber;
BaseDraw.topSplittingDrawing(canvas, new Point(residue * spacing + 8, 0), Colors.Orange, zDotIon.ProductType.ToString().ToLower() + zDotIon.IonNumber);
}
// draw modifications
int aa = 0;
bool currentlyReadingMod = false;
for (int c = 0; c < psm.FullSequence.Length; c++)
{
switch (psm.FullSequence[c])
{
case '[':
currentlyReadingMod = true;
BaseDraw.circledTxtDraw(canvas, new Point(aa * spacing - 17, 12), Brushes.Yellow);
break;
case ']':
currentlyReadingMod = false;
break;
default:
if (!currentlyReadingMod)
{
aa++;
}
break;
}
}
}
private void DrawSequenceCoverageMap(ProteinForTreeView protein) //string accession, Dictionary<string, PeptideForTreeView> uniquePeptides, Dictionary<string, PeptideForTreeView> sharedPeptides)
{
string protease = "trypsin"; // only works for single protease for now
string seqCoverage = proteinGroups[protein.Accession];
mapViewer.Visibility = Visibility.Visible;
BaseDraw.clearCanvas(map);
mainViewModel.Model = null; // clear plot
BaseDraw.clearCanvas(canvas);
double spacing = 22;
int height = 10;
int totalHeight = 0;
int accumIndex = 0;
foreach (string seq in seqCoverage.Split('|'))
{
var splitSeq = Split(seq, spacing);
var allPeptides = new List <string>(protein.AllPeptides.Keys);
foreach (var line in splitSeq)
{
List <int> indices = new List <int>();
// draw sequence
for (int r = 0; r < line.Length; r++)
{
SequenceCoverageMap.txtDrawing(map, new Point(r * spacing + 10, height), line[r].ToString().ToUpper(), Brushes.Black);
}
// highlight partial peptide sequences (broken off into multiple lines)
if (partialPeptideMatches.Count > 0)
{
var temp = new Dictionary <string, int>(partialPeptideMatches);
partialPeptideMatches.Clear();
foreach (var peptide in temp)
{
if (MatchPeptideSequence(peptide.Key, line, 0, peptide.Value, accumIndex - peptide.Value == seq.IndexOf(peptide.Key)))
{
int start = 0;
int end = Math.Min(start + peptide.Key.Length - peptide.Value - 1, line.Length - 1);
SequenceCoverageMap.Highlight(start, end, map, indices, height, proteaseByColor[protease], protein.UniquePeptides.Keys.Any(u => u.Contains(peptide.Key))); // draw line for peptide sequence
}
}
}
// highlight full peptide sequences
for (int i = 0; i < line.Length; ++i)
{
var temp = new List <string>(allPeptides);
foreach (string peptide in temp)
{
if (MatchPeptideSequence(peptide, line, i, 0, accumIndex + i == seq.IndexOf(peptide)))
{
int start = i;
int end = Math.Min(start + peptide.Length - 1, line.Length - 1);
SequenceCoverageMap.Highlight(start, end, map, indices, height, proteaseByColor[protease], protein.UniquePeptides.Keys.Any(u => u.Contains(peptide)));
allPeptides.Remove(peptide);
}
}
}
height += 50;
accumIndex += line.Length;
}
totalHeight += splitSeq.Count() * 50;
height += 50;
}
mapGrid.Height = totalHeight + 50 * seqCoverage.Split('|').Count();
SequenceCoverageMap.drawLegend(legend, proteaseByColor, proteases, legendGrid);
}