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;
}
}
// 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);
}
// 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;
}
}
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));
}
}
