public PeptideForTreeView(string displayName, ProteinForTreeView parent)
{
Children = new ObservableCollection <PsmForTreeView>();
Parent = parent;
DisplayName = displayName;
Expanded = false;
}
// 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));
}
// create a new instance of a protein group
private ProteinForTreeView CreateNewProtein(string accession, string sequence, string name, Dictionary <string, PeptideForTreeView> unique = null, Dictionary <string, PeptideForTreeView> shared = null)
{
proteinGroups.Add(accession, sequence);
var ptv = new ProteinForTreeView(name, accession, unique, shared, new Dictionary <string, PeptideForTreeView>());
proteinGroupsForTreeView.Add(accession, ptv);
proteinTree.Add(ptv);
return(ptv);
}
private void OnSelectionChanged()
{
// can select protein or peptide only at a time (not both)
if (proteinTreeView.SelectedItem == null)
{
return;
}
// draw the selected PSM
propertyView.Clear();
// differentiate item click protein VS psm
var selection = proteinTreeView.SelectedItem.GetType().Name;
PsmForTreeView psmToDisplay = null;
switch (selection)
{
case "ProteinForTreeView":
{
ProteinForTreeView selectedItem = (ProteinForTreeView)proteinTreeView.SelectedItem;
itemsControlSampleViewModel.Data.Clear();
if (proteinGroups[selectedItem.Accession] != null)
{
DrawSequenceCoverageMap(selectedItem);
ChangeMapScrollViewVisibility();
}
}
break;
case "PeptideForTreeView":
{
// find psm with best score
PeptideForTreeView selectedItem = (PeptideForTreeView)proteinTreeView.SelectedItem;
psmToDisplay = selectedItem.Children.OrderByDescending(psm => psm.Psm.Score).First();
goto case "display";
}
case "PsmForTreeView":
{
psmToDisplay = (PsmForTreeView)proteinTreeView.SelectedItem;
goto case "display";
}
case "display":
{
mapViewer.Visibility = Visibility.Collapsed;
legend.Visibility = Visibility.Collapsed;
displayPsm(psmToDisplay);
}
break;
}
}
private void DrawPdfCoverageMap(ProteinForTreeView protein, Grid mapGrid, string path)
{
// draw coverage map
mapGrid.Width = 1000;
DrawSequenceCoverageMap(protein);
string pathToCoverageMap = Path.Combine(Path.GetDirectoryName(path), "map.png");
CustomPdfWriter.RenderImage((int)mapGrid.Width, (int)mapGrid.Height, pathToCoverageMap, map);
// draw legend
SequenceCoverageMap.drawLegend(legend, proteaseByColor, proteases, legendGrid);
string pathToLegend = Path.Combine(Path.GetDirectoryName(path), "legend.png");
CustomPdfWriter.RenderImage((int)(legend.Width), 50, pathToLegend, legend);
CustomPdfWriter.WriteToPdfMetaDraw(mapGrid.Width, mapGrid.Height, pathToCoverageMap, pathToLegend, path);
}
// search through psm list based on user input
private ProteinForTreeView searchPsm(ProteinForTreeView prot, PeptideForTreeView peptide, string txt)
{
// create copy of peptide
var pep = new PeptideForTreeView(peptide.DisplayName, peptide.Parent);
foreach (var psm in peptide.Children)
{
if (psm.ScanNo.ToString().StartsWith(txt))
{
pep.Expanded = true;
pep.Children.Add(psm);
}
}
if (pep.Children.Count() > 0)
{
prot.Children.Add(pep);
}
return(prot);
}
// redraw display based on first selection
private void RestoreDefault(object defaultSelection)
{
mapGrid.Width = 485;
var selection = defaultSelection.GetType().Name;
switch (selection)
{
case "ProteinForTreeView":
{
ProteinForTreeView protein = (ProteinForTreeView)defaultSelection;
DrawSequenceCoverageMap(protein);
}
break;
case "PsmForTreeView":
{
PsmForTreeView psm = (PsmForTreeView)defaultSelection;
DrawPsm(psm.Psm.Ms2ScanNumber, psm.Psm.FullSequence);
}
break;
}
}
// search through peptide list based on user input
private void searchPeptide(ProteinForTreeView protein, string txt)
{
// create copy of protein
var prot = new ProteinForTreeView(protein.DisplayName, protein.Accession, protein.UniquePeptides, protein.SharedPeptides, protein.AllPeptides);
foreach (var peptide in protein.Children)
{
if (peptide.DisplayName.ToUpper().Contains(txt.ToUpper()))
{
prot.Children.Add(peptide);
}
else
{
prot = searchPsm(prot, peptide, txt);
}
}
if (prot.Children.Count() > 0)
{
prot.Expanded = true;
filteredTree.Add(prot);
}
}
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);
}
private void PDFButton_Click(object sender, RoutedEventArgs e)
{
object temp = null;
var selections = new List <object>();
// select best scoring psm for any peptide selections
foreach (object selectedItem in proteinTreeView.SelectedItems)
{
if (selectedItem.GetType().Name.Equals("PeptideForTreeView"))
{
PeptideForTreeView peptide = (PeptideForTreeView)selectedItem;
PsmForTreeView bestScoringPsm = peptide.Children.OrderByDescending(psm => psm.Psm.Score).First();
selections.Add(bestScoringPsm);
continue;
}
selections.Add(selectedItem);
}
if (proteinTreeView.SelectedItems.Count == 0)
{
MessageBox.Show("Please select at least one scan or coverage map to export");
}
else
{
int numberOfScansToExport = selections.Distinct().Count();
foreach (object selectedItem in selections.Distinct())
{
if (temp == null)
{
temp = selectedItem;
}
var selection = selectedItem.GetType().Name;
switch (selection)
{
case "ProteinForTreeView":
{
ProteinForTreeView protein = (ProteinForTreeView)selectedItem;
string myString = illegalInFileName.Replace(protein.DisplayName, "");
myString = myString.Length > 30 ? myString.Substring(0, 30) : myString;
string filePath = Path.Combine(Path.GetDirectoryName(psmFilePath), "MetaDrawExport", myString.Trim(), myString + ".pdf");
string dir = Path.GetDirectoryName(filePath);
if (!Directory.Exists(dir))
{
Directory.CreateDirectory(dir);
}
DrawPdfCoverageMap(protein, mapGrid, filePath);
}
break;
case "PsmForTreeView":
{
PsmForTreeView psm = (PsmForTreeView)selectedItem;
var proteinFolder = illegalInFileName.Replace(psm.Parent.Parent.DisplayName, "");
proteinFolder = proteinFolder.Length > 30 ? proteinFolder.Substring(0, 30) : proteinFolder;
string peptideFolder = illegalInFileName.Replace(psm.Parent.DisplayName, "");
peptideFolder = peptideFolder.Length > 30 ? peptideFolder.Substring(0, 30) : peptideFolder;
string filePath = Path.Combine(Path.GetDirectoryName(psmFilePath), "MetaDrawExport", proteinFolder.Trim(), peptideFolder.Trim(), psm.ScanNo + ".pdf");
string dir = Path.GetDirectoryName(filePath);
MsDataScan msDataScanToDraw = MsDataFile.GetOneBasedScan(psm.ScanNo);
if (!Directory.Exists(dir))
{
Directory.CreateDirectory(dir);
}
DrawPdfAnnotatedBaseSequence(psm.Psm, canvas, filePath); // captures the annotation for the pdf
mainViewModel.DrawPeptideSpectralMatchPdf(msDataScanToDraw, psm.Psm, filePath, numberOfScansToExport > 1);
}
break;
}
}
RestoreDefault(temp);
MessageBox.Show(string.Format("{0} PDFs exported", numberOfScansToExport));
}
}