private async void PlotSelected(object sender, SelectionChangedEventArgs e)
{
ObservableCollection <InSilicoPep> peptides = new ObservableCollection <InSilicoPep>();
Dictionary <string, ObservableCollection <InSilicoPep> > peptidesByProtease = new Dictionary <string, ObservableCollection <InSilicoPep> >();
Dictionary <string, Dictionary <Protein, (double, double)> > sequenceCoverageByProtease = new Dictionary <string, Dictionary <Protein, (double, double)> >();
var selectedPlot = HistogramComboBox.SelectedItem;
var objectName = selectedPlot.ToString().Split(':');
var plotName = objectName[1];
//var comboBox = HistogramComboBox as ComboBox;
//var plotName = comboBox.SelectedItem as string;
foreach (var db in DBSelected)
{
var PeptidesForAllProteases = PeptideByFile[db];
sequenceCoverageByProtease = CalculateProteinSequenceCoverage(PeptidesForAllProteases);
foreach (var protease in PeptidesForAllProteases)
{
ObservableCollection <InSilicoPep> proteasePeptides = new ObservableCollection <InSilicoPep>();
if (peptidesByProtease.ContainsKey(protease.Key))
{
foreach (var protein in protease.Value)
{
foreach (var peptide in protein.Value)
{
proteasePeptides.Add(peptide);
peptides.Add(peptide);
}
}
peptidesByProtease[protease.Key] = proteasePeptides;
}
else
{
foreach (var protein in protease.Value)
{
foreach (var peptide in protein.Value)
{
proteasePeptides.Add(peptide);
peptides.Add(peptide);
}
}
peptidesByProtease.Add(protease.Key, proteasePeptides);
}
}
}
PlotModelStat plot = await Task.Run(() => new PlotModelStat(plotName, peptides, peptidesByProtease, sequenceCoverageByProtease));
plotViewStat.DataContext = plot;
}
private async void PlotSelected(object sender, SelectionChangedEventArgs e)
{
var listview = sender as ListView;
var plotName = listview.SelectedItem as string;
// get psms from selected source files
ObservableCollection <InSilicoPeptide> peptides = new ObservableCollection <InSilicoPeptide>();
Dictionary <string, ObservableCollection <InSilicoPeptide> > peptidesByProtease = new Dictionary <string, ObservableCollection <InSilicoPeptide> >();
//MM code for this section
//need to update to get information from our task results to populate peptides
//foreach (string fileName in selectSourceFileListBox.SelectedItems)
//{
// psmsBSF.Add(fileName, psmsBySourceFile[fileName]);
// foreach (PsmFromTsv psm in psmsBySourceFile[fileName])
// {
// psms.Add(psm);
// }
//}
PlotModelStat plot = await Task.Run(() => new PlotModelStat(plotName, peptides, peptidesByProtease));
plotViewStat.DataContext = plot;
}
//if database selection is changed, refresh what is shown in the plot if that is not changed, similar code to PlotSelected(), but isnt triggered by user
private async void RefreshPlot()
{
HistogramDataTable.Clear();
Dictionary <string, Dictionary <Protein, List <InSilicoPep> > > databasePeptides = new Dictionary <string, Dictionary <Protein, List <InSilicoPep> > >();
if (dataGridProteinDBs.SelectedItems == null)
{
DBSelected.Add(listOfProteinDbs.First());
}
if (DBSelected.Count() > 1)
{
MessageBox.Show("Note: More than one protein database has been selected. Unique peptides are defined as being unique to a single protein in all selected databases.");
}
else
{
MessageBox.Show("Note: One protein database has been selected. Unique peptides are defined as being unique to a single protein in this database.");
}
List <InSilicoPep> allPeptides = new List <InSilicoPep>();
foreach (var db in DBSelected)
{
var pep = PeptideByFile[db];
foreach (var entry in pep)
{
foreach (var protein in entry.Value)
{
allPeptides.AddRange(protein.Value);
}
}
}
Dictionary <string, List <InSilicoPep> > peptidesToProteins = new Dictionary <string, List <InSilicoPep> >();
if (UserParams.TreatModifiedPeptidesAsDifferent)
{
peptidesToProteins = allPeptides.GroupBy(p => p.FullSequence).ToDictionary(group => group.Key, group => group.ToList());
}
else
{
peptidesToProteins = allPeptides.GroupBy(p => p.BaseSequence).ToDictionary(group => group.Key, group => group.ToList());
}
var unique = peptidesToProteins.Where(p => p.Value.Select(p => p.Protein).Distinct().Count() == 1).ToDictionary(group => group.Key, group => group.Value);
var shared = peptidesToProteins.Where(p => p.Value.Select(p => p.Protein).Distinct().Count() > 1).ToDictionary(group => group.Key, group => group.Value);
foreach (var db in DBSelected)
{
var pep = PeptideByFile[db];
foreach (var entry in pep)
{
if (databasePeptides.ContainsKey(entry.Key))
{
foreach (var prot in pep[entry.Key])
{
if (databasePeptides[entry.Key].ContainsKey(prot.Key))
{
List <InSilicoPep> proteinSpecificPeptides = new List <InSilicoPep>();
foreach (var peptide in prot.Value)
{
if (UserParams.TreatModifiedPeptidesAsDifferent)
{
if (unique.ContainsKey(peptide.FullSequence))
{
peptide.Unique = true;
proteinSpecificPeptides.Add(peptide);
}
else
{
peptide.Unique = false;
proteinSpecificPeptides.Add(peptide);
}
}
else
{
if (unique.ContainsKey(peptide.BaseSequence))
{
peptide.Unique = true;
proteinSpecificPeptides.Add(peptide);
}
else
{
peptide.Unique = false;
proteinSpecificPeptides.Add(peptide);
}
}
}
databasePeptides[entry.Key][prot.Key].AddRange(proteinSpecificPeptides);
}
else
{
List <InSilicoPep> proteinSpecificPeptides = new List <InSilicoPep>();
foreach (var peptide in prot.Value)
{
if (UserParams.TreatModifiedPeptidesAsDifferent)
{
if (unique.ContainsKey(peptide.FullSequence))
{
peptide.Unique = true;
proteinSpecificPeptides.Add(peptide);
}
else
{
peptide.Unique = false;
proteinSpecificPeptides.Add(peptide);
}
}
else
{
if (unique.ContainsKey(peptide.BaseSequence))
{
peptide.Unique = true;
proteinSpecificPeptides.Add(peptide);
}
else
{
peptide.Unique = false;
proteinSpecificPeptides.Add(peptide);
}
}
}
databasePeptides[entry.Key].Add(prot.Key, proteinSpecificPeptides);
}
}
}
else
{
Dictionary <Protein, List <InSilicoPep> > proteinDic = new Dictionary <Protein, List <InSilicoPep> >();
foreach (var prot in entry.Value)
{
List <InSilicoPep> proteinSpecificPeptides = new List <InSilicoPep>();
foreach (var peptide in prot.Value)
{
if (UserParams.TreatModifiedPeptidesAsDifferent)
{
if (unique.ContainsKey(peptide.FullSequence))
{
peptide.Unique = true;
proteinSpecificPeptides.Add(peptide);
}
else
{
peptide.Unique = false;
proteinSpecificPeptides.Add(peptide);
}
}
else
{
if (unique.ContainsKey(peptide.BaseSequence))
{
peptide.Unique = true;
proteinSpecificPeptides.Add(peptide);
}
else
{
peptide.Unique = false;
proteinSpecificPeptides.Add(peptide);
}
}
}
proteinDic.Add(prot.Key, proteinSpecificPeptides);
}
databasePeptides.Add(entry.Key, proteinDic);
}
}
}
ObservableCollection <InSilicoPep> peptides = new ObservableCollection <InSilicoPep>();
Dictionary <string, ObservableCollection <InSilicoPep> > peptidesByProtease = new Dictionary <string, ObservableCollection <InSilicoPep> >();
Dictionary <string, Dictionary <Protein, (double, double)> > sequenceCoverageByProtease = new Dictionary <string, Dictionary <Protein, (double, double)> >();
var selectedPlot = HistogramComboBox.SelectedItem;
var objectName = selectedPlot.ToString().Split(':');
var plotName = objectName[1];
sequenceCoverageByProtease = CalculateProteinSequenceCoverage(databasePeptides);
foreach (var protease in databasePeptides)
{
ObservableCollection <InSilicoPep> proteasePeptides = new ObservableCollection <InSilicoPep>();
if (peptidesByProtease.ContainsKey(protease.Key))
{
foreach (var protein in protease.Value)
{
foreach (var peptide in protein.Value)
{
proteasePeptides.Add(peptide);
peptides.Add(peptide);
}
}
peptidesByProtease[protease.Key] = proteasePeptides;
}
else
{
foreach (var protein in protease.Value)
{
foreach (var peptide in protein.Value)
{
proteasePeptides.Add(peptide);
peptides.Add(peptide);
}
}
peptidesByProtease.Add(protease.Key, proteasePeptides);
}
}
ProgressBar progressBar = new ProgressBar();
progressBar.Orientation = Orientation.Horizontal;
progressBar.Width = 200;
progressBar.Height = 30;
progressBar.IsIndeterminate = true;
HistogramLoading.Items.Add(progressBar);
//make the plot
PlotModelStat plot = await Task.Run(() => new PlotModelStat(plotName, peptides, peptidesByProtease, sequenceCoverageByProtease));
progressBar.IsIndeterminate = false;
//send the plot to GUI
plotViewStat.DataContext = plot;
//send the data table with plot info to GUI for export if desired
HistogramDataTable = plot.DataTable;
HistogramLoading.Items.Clear();
}
