public MetaDraw()
{
UsefulProteomicsDatabases.Loaders.LoadElements();
InitializeComponent();
itemsControlSampleViewModel = new ItemsControlSampleViewModel();
DataContext = itemsControlSampleViewModel;
mainViewModel = new PsmAnnotationViewModel();
plotView.DataContext = mainViewModel;
allPsms = new ObservableCollection<PsmFromTsv>();
filteredListOfPsms = new ObservableCollection<PsmFromTsv>();
propertyView = new DataTable();
propertyView.Columns.Add("Name", typeof(string));
propertyView.Columns.Add("Value", typeof(string));
peptideSpectralMatchesView = CollectionViewSource.GetDefaultView(filteredListOfPsms);
dataGridScanNums.DataContext = peptideSpectralMatchesView;
dataGridProperties.DataContext = propertyView.DefaultView;
Title = "MetaDraw: version " + GlobalVariables.MetaMorpheusVersion;
spectraFileManager = new MyFileManager(true);
SetUpDictionaries();
modificationAnnotationColor = Brushes.Yellow;
metaDrawGraphicalSettings = new MetaDrawGraphicalSettings();
metaDrawFilterSettings = new MetaDrawFilterSettings();
base.Closing += this.OnClosing;
ParentChildScanView.Visibility = Visibility.Collapsed;
ParentScanView.Visibility = Visibility.Collapsed;
plotTypes = new ObservableCollection<string>();
SetUpPlots();
//plotsListBox.ItemsSource = plotTypes;
}
public void AddNewRow(PsmAnnotationViewModel psmAnnotationViewModel, string annotation)
{
Data.Add(new ItemsControlSampleData()
{
PsmAnnotationViewModel = psmAnnotationViewModel, SpectrumLabel = annotation
});
}
public MetaDraw()
{
InitializeComponent();
mainViewModel = new PsmAnnotationViewModel();
plotView.DataContext = mainViewModel;
peptideSpectralMatches = new ObservableCollection <MetaDrawPsm>();
propertyView = new DataTable();
propertyView.Columns.Add("Name", typeof(string));
propertyView.Columns.Add("Value", typeof(string));
peptideSpectralMatchesView = CollectionViewSource.GetDefaultView(peptideSpectralMatches);
dataGridScanNums.DataContext = peptideSpectralMatchesView;
dataGridProperties.DataContext = propertyView.DefaultView;
Title = "MetaDraw: version " + GlobalVariables.MetaMorpheusVersion;
spectraFileManager = new MyFileManager(true);
}
public MetaDraw()
{
UsefulProteomicsDatabases.Loaders.LoadElements();
InitializeComponent();
itemsControlSampleViewModel = new ItemsControlSampleViewModel();
DataContext = itemsControlSampleViewModel;
mainViewModel = new PsmAnnotationViewModel();
plotView.DataContext = mainViewModel;
allPsms = new ObservableCollection <PsmFromTsv>();
filteredListOfPsms = new ObservableCollection <PsmFromTsv>();
proteinTree = new ObservableCollection <ProteinForTreeView>();
filteredTree = new ObservableCollection <ProteinForTreeView>();
propertyView = new DataTable();
propertyView.Columns.Add("Name", typeof(string));
propertyView.Columns.Add("Value", typeof(string));
psmsWithMatch = new List <PsmFromTsv>();
proteinTreeView.DataContext = proteinTree;
dataGridProperties.DataContext = propertyView.DefaultView;
Title = "MetaDraw: version " + GlobalVariables.MetaMorpheusVersion;
spectraFileManager = new MyFileManager(true);
SetUpDictionaries();
variantCrossColor = Colors.Green;
modificationAnnotationColor = Brushes.Orange;
metaDrawGraphicalSettings = new MetaDrawGraphicalSettings();
metaDrawFilterSettings = new MetaDrawFilterSettings();
SearchModifications.Timer.Tick += new EventHandler(searchBox_TextChangedHandler);
base.Closing += this.OnClosing;
ParentChildScanView.Visibility = Visibility.Collapsed;
ParentScanView.Visibility = Visibility.Collapsed;
mapViewer.Visibility = Visibility.Collapsed;
legend.Visibility = Visibility.Collapsed;
plotTypes = new ObservableCollection <string>();
proteases = new string[1] {
"trypsin"
};
SetUpPlots();
//plotsListBox.ItemsSource = plotTypes;
ChangeMapScrollViewSize();
}
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 DrawPsm(int oneBasedScanNumber, string fullSequence = null, string fileName = null)
{
MsDataScan msDataScanToDraw = MsDataFile.GetOneBasedScan(oneBasedScanNumber);
IEnumerable <PsmFromTsv> scanPsms = filteredListOfPsms.Where(p => p.Ms2ScanNumber == oneBasedScanNumber);
if (fullSequence != null)
{
scanPsms = scanPsms.Where(p => p.FullSequence == fullSequence);
}
PsmFromTsv psmToDraw = scanPsms.FirstOrDefault();
// if this spectrum has child scans, draw them in the "advanced" tab
if ((psmToDraw.ChildScanMatchedIons != null && psmToDraw.ChildScanMatchedIons.Count > 0) ||
(psmToDraw.BetaPeptideChildScanMatchedIons != null && psmToDraw.BetaPeptideChildScanMatchedIons.Count > 0))
{
ParentChildScanView.Visibility = Visibility.Visible;
ParentScanView.Visibility = Visibility.Visible;
// draw parent scans
var parentPsmModel = new PsmAnnotationViewModel();
MsDataScan parentScan = MsDataFile.GetOneBasedScan(psmToDraw.Ms2ScanNumber);
parentPsmModel.DrawPeptideSpectralMatch(parentScan, psmToDraw, metaDrawGraphicalSettings.ShowMzValues,
metaDrawGraphicalSettings.ShowAnnotationCharges, metaDrawGraphicalSettings.AnnotatedFontSize, metaDrawGraphicalSettings.BoldText);
string parentAnnotation = "Scan: " + parentScan.OneBasedScanNumber.ToString()
+ " Dissociation Type: " + parentScan.DissociationType.ToString()
+ " MsOrder: " + parentScan.MsnOrder.ToString()
+ " Selected Mz: " + parentScan.SelectedIonMZ.Value.ToString("0.##")
+ " Retention Time: " + parentScan.RetentionTime.ToString("0.##");
itemsControlSampleViewModel.AddNewRow(parentPsmModel, parentAnnotation, null);
// draw child scans
HashSet <int> scansDrawn = new HashSet <int>();
var allChildScanMatchedIons = psmToDraw.ChildScanMatchedIons;
if (psmToDraw.BetaPeptideChildScanMatchedIons != null)
{
allChildScanMatchedIons = allChildScanMatchedIons.Concat(psmToDraw.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, psmToDraw, metaDrawGraphicalSettings.ShowMzValues,
metaDrawGraphicalSettings.ShowAnnotationCharges, metaDrawGraphicalSettings.AnnotatedFontSize, metaDrawGraphicalSettings.BoldText);
string childAnnotation = "Scan: " + scanNumber.ToString()
+ " Dissociation Type: " + childScan.DissociationType.ToString()
+ " MsOrder: " + childScan.MsnOrder.ToString()
+ " Selected Mz: " + childScan.SelectedIonMZ.Value.ToString("0.##")
+ " RetentionTime: " + childScan.RetentionTime.ToString("0.##");
Canvas aCanvas = new Canvas {
Height = 60
};
DrawAnnotatedBaseSequence(aCanvas, psmToDraw, true);
itemsControlSampleViewModel.AddNewRow(childPsmModel, childAnnotation, aCanvas);
}
}
else
{
ParentChildScanView.Visibility = Visibility.Collapsed;
ParentScanView.Visibility = Visibility.Collapsed;
}
// if this is a crosslink spectrum match, there are two base sequence annotations to draw
// this makes the canvas taller to fit both of these peptide sequences
if (psmToDraw.BetaPeptideBaseSequence != null)
{
int height = 150;
canvas.Height = height;
PsmAnnotationGrid.RowDefinitions[1].Height = new GridLength(height);
}
else
{
int height = 60;
canvas.Height = height;
PsmAnnotationGrid.RowDefinitions[1].Height = new GridLength(height);
}
// draw annotated spectrum
mainViewModel.DrawPeptideSpectralMatch(msDataScanToDraw, psmToDraw, metaDrawGraphicalSettings.ShowMzValues,
metaDrawGraphicalSettings.ShowAnnotationCharges, metaDrawGraphicalSettings.AnnotatedFontSize, metaDrawGraphicalSettings.BoldText);
// draw annotated base sequence
DrawAnnotatedBaseSequence(canvas, psmToDraw);
}
public void AddNewRow(PsmAnnotationViewModel psmAnnotationViewModel, string annotation, Canvas canvas)
{
Data.Add(new ItemsControlSampleData {
PsmAnnotationViewModel = psmAnnotationViewModel, SpectrumLabel = annotation, TheCanvas = canvas
});
}
