private void OnSelectionChanged()
{
if (dataGridScanNums.SelectedItem == null)
{
return;
}
// draw the selected PSM
propertyView.Clear();
PsmFromTsv row = (PsmFromTsv)dataGridScanNums.SelectedItem;
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);
}
/// <summary>
/// Event triggers when a different cell is selected in the PSM data grid
/// </summary>
private void dataGridScanNums_SelectedCellsChanged(object sender, SelectedCellsChangedEventArgs e)
{
if (dataGridScanNums.SelectedItem == null)
{
return;
}
PsmFromTsv psm = (PsmFromTsv)dataGridScanNums.SelectedItem;
// draw the annotated spectrum
MetaDrawLogic.DisplaySpectrumMatch(plotView, canvas, psm, itemsControlSampleViewModel, out var errors);
//draw the sequence coverage if not crosslinked
if (psm.ChildScanMatchedIons == null)
{
MetaDrawLogic.DrawSequenceCoverageMap(psm, sequenceText, map); //TODO: figure out how to show coverage on crosslinked peptides
ParentChildScanView.Visibility = Visibility.Collapsed;
SequenceCoverageAnnotationView.Visibility = Visibility.Visible;
}
else
{
ParentChildScanView.Visibility = Visibility.Visible;
SequenceCoverageAnnotationView.Visibility = Visibility.Collapsed;
}
mapViewer.Width = map.Width;
if (errors != null && errors.Any())
{
MessageBox.Show(errors.First());
return;
}
// display PSM properties
propertyView.Clear();
System.Reflection.PropertyInfo[] temp = psm.GetType().GetProperties();
for (int i = 0; i < temp.Length; i++)
{
if (temp[i].Name == nameof(psm.MatchedIons))
{
propertyView.Rows.Add(temp[i].Name, string.Join(", ", psm.MatchedIons.Select(p => p.Annotation)));
}
else if (temp[i].Name == nameof(psm.VariantCrossingIons))
{
propertyView.Rows.Add(temp[i].Name, string.Join(", ", psm.VariantCrossingIons.Select(p => p.Annotation)));
}
else
{
propertyView.Rows.Add(temp[i].Name, temp[i].GetValue(psm, null));
}
}
}
/// <summary>
/// Event triggers when a different cell is selected in the PSM data grid
/// </summary>
private void dataGridScanNums_SelectedCellsChanged(object sender, SelectedCellsChangedEventArgs e)
{
if (dataGridScanNums.SelectedItem == null)
{
return;
}
PsmFromTsv psm = (PsmFromTsv)dataGridScanNums.SelectedItem;
// draw the PSM
MetaDrawLogic.DisplaySpectrumMatch(plotView, canvas, psm, itemsControlSampleViewModel, out var errors);
if (psm.ChildScanMatchedIons != null)
{
ParentChildScanView.Visibility = Visibility.Visible;
ParentScanView.Visibility = Visibility.Visible;
}
else
{
ParentChildScanView.Visibility = Visibility.Collapsed;
ParentScanView.Visibility = Visibility.Collapsed;
}
if (errors != null && errors.Any())
{
MessageBox.Show(errors.First());
return;
}
// display PSM properties
propertyView.Clear();
System.Reflection.PropertyInfo[] temp = psm.GetType().GetProperties();
for (int i = 0; i < temp.Length; i++)
{
if (temp[i].Name == nameof(psm.MatchedIons))
{
propertyView.Rows.Add(temp[i].Name, string.Join(", ", psm.MatchedIons.Select(p => p.Annotation)));
}
else if (temp[i].Name == nameof(psm.VariantCrossingIons))
{
propertyView.Rows.Add(temp[i].Name, string.Join(", ", psm.VariantCrossingIons.Select(p => p.Annotation)));
}
else
{
propertyView.Rows.Add(temp[i].Name, temp[i].GetValue(psm, null));
}
}
}
// 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);
}
public void DrawPeptideSpectralMatchPdf(MsDataScan msDataScan, PsmFromTsv psm, string fileName, bool redraw)
{
var properties = psm.GetType().GetProperties();
var pdfModel = DrawPdf(msDataScan, properties, psm, redraw);
string tempPath = Path.Combine(Path.GetDirectoryName(fileName), "sequence.pdf");
string baseSeqTempPath = Path.Combine(Path.GetDirectoryName(fileName), "annotation.png");
// exports plot to pdf
using (var stream = File.Create(tempPath))
{
PdfExporter pdf = new PdfExporter {
Width = 800, Height = 500
};
pdf.Export(pdfModel, stream);
}
// adds base seq annotation to pdf
using (Stream inputPdfStream = new FileStream(tempPath, FileMode.Open, FileAccess.Read, FileShare.Read))
using (Stream inputImageStream = new FileStream(baseSeqTempPath, FileMode.Open, FileAccess.Read, FileShare.Read))
using (Stream outputPdfStream = new FileStream(fileName, FileMode.Create, FileAccess.Write, FileShare.None))
{
var reader = new PdfReader(inputPdfStream);
var stamper = new PdfStamper(reader, outputPdfStream);
var pdfContentByte = stamper.GetOverContent(1);
var image = iTextSharp.text.Image.GetInstance(inputImageStream);
image.ScaleAbsoluteHeight(500);
image.ScaleAbsoluteWidth(500);
image.SetAbsolutePosition(95, 190);
pdfContentByte.AddImage(image);
stamper.Close();
}
File.Delete(tempPath);
File.Delete(baseSeqTempPath);
}
