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));
}
}
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 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));
}
}
