// 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));
}
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 LoadProteinGroups(string filename)
{
try
{
proteinGroups.Clear();
proteinGroupsForTreeView = new Dictionary <string, ProteinForTreeView>();
int lineCount = 0;
foreach (string line in File.ReadLines(filename))
{
++lineCount;
if (lineCount == 1)
{
continue;
}
var spl = line.Split('\t');
string accession = spl[0];
string name = spl[3];
string sequence = spl[11];
var uniquePeptides = spl[6].Trim().Length > 0 ? spl[6].Split('|') : new string[0];
var sharedPeptides = spl[7].Trim().Length > 0 ? spl[7].Split('|') : new string[0];
var ptv = CreateNewProtein(accession, sequence, name, new Dictionary <string, PeptideForTreeView>(), new Dictionary <string, PeptideForTreeView>());
// store unique peptides
foreach (string pep in uniquePeptides)
{
var pepTV = new PeptideForTreeView(pep, ptv);
ptv.Children.Add(pepTV);
ptv.UniquePeptides.Add(pep, pepTV);
ptv.AllPeptides.Add(pep, pepTV);
}
// store shared peptides
foreach (string pep in sharedPeptides)
{
var pepTV = new PeptideForTreeView(pep, ptv);
ptv.Children.Add(pepTV);
ptv.SharedPeptides.Add(pep, pepTV);
ptv.AllPeptides.Add(pep, pepTV);
}
}
}
catch (Exception e)
{
MessageBox.Show("Could not open protein groups file:\n" + e.Message);
}
}
// 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);
}
public PsmForTreeView(int scan, PsmFromTsv psm, PeptideForTreeView parent)
{
Parent = parent;
Psm = psm;
ScanNo = scan;
}
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));
}
}
