//Code for the generation of the digestion results summary that is displayed in TreeView
private void GenerateResultsSummary()
{
if (PeptideByFile.Count > 1) // if there is more than one database then we need to do all database summary
{
ProteaseSummaryForTreeView allDatabases = new ProteaseSummaryForTreeView("Cumulative Database Results:");
//get all the peptides from all the databases together
Dictionary <string, List <InSilicoPep> > allDatabasePeptidesByProtease = new Dictionary <string, List <InSilicoPep> >();
foreach (var database in PeptideByFile)
{
foreach (var protease in database.Value)
{
if (allDatabasePeptidesByProtease.ContainsKey(protease.Key))
{
foreach (var protein in protease.Value)
{
allDatabasePeptidesByProtease[protease.Key].AddRange(protein.Value);
}
}
else
{
allDatabasePeptidesByProtease.Add(protease.Key, protease.Value.SelectMany(p => p.Value).ToList());
}
}
}
foreach (var protease in allDatabasePeptidesByProtease)
{
Dictionary <string, List <InSilicoPep> > peptidesToProteins = new Dictionary <string, List <InSilicoPep> >();
if (UserParams.TreatModifiedPeptidesAsDifferent)
{
peptidesToProteins = protease.Value.GroupBy(p => p.FullSequence).ToDictionary(group => group.Key, group => group.ToList());
}
else
{
peptidesToProteins = protease.Value.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).ToList();
var shared = peptidesToProteins.Where(p => p.Value.Select(p => p.Protein).Distinct().Count() > 1).ToList();
var sharedPeptidesInOneDb = shared.Where(p => p.Value.Select(p => p.Database).Distinct().Count() == 1);
List <InSilicoPep> peptidesInOneDb = new List <InSilicoPep>();
foreach (var pep in unique)
{
peptidesInOneDb.AddRange(pep.Value);
}
foreach (var pep in sharedPeptidesInOneDb)
{
peptidesInOneDb.AddRange(pep.Value);
}
string prot = protease.Key;
DigestionSummaryForTreeView thisDigestion = new DigestionSummaryForTreeView(prot + " Results:");
List <InSilicoPep> allPeptides = peptidesToProteins.SelectMany(p => p.Value).ToList();
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Peptides: " + allPeptides.Count));
thisDigestion.Summary.Add(new SummaryForTreeView(" Number of Distinct Peptide Sequences: " + peptidesToProteins.Count()));
var peptidesForSingleDatabase = peptidesInOneDb.GroupBy(p => p.Database).ToDictionary(group => group.Key, group => group.ToList());
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Unique Peptide Sequences: " + unique.Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Shared Peptide Sequences: " + shared.Count()));
foreach (var db in peptidesForSingleDatabase)
{
if (UserParams.TreatModifiedPeptidesAsDifferent)
{
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Peptide Sequences Found Only in " + db.Key + ": " + db.Value.Select(p => p.FullSequence).Distinct().Count()));
}
else
{
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Peptide Sequences Found Only in " + db.Key + ": " + db.Value.Select(p => p.BaseSequence).Distinct().Count()));
}
}
allDatabases.Summary.Add(thisDigestion);
}
//put the results summary in the GUI for users to view
SummaryForTreeViewObservableCollection.Add(allDatabases);
//Now do a similar results summary for each individual database on its own
foreach (var database in PeptideByFile)
{
ProteaseSummaryForTreeView thisProtease = new ProteaseSummaryForTreeView(database.Key + " Results:");
foreach (var protease in database.Value)
{
string prot = protease.Key;
DigestionSummaryForTreeView thisDigestion = new DigestionSummaryForTreeView(prot + " Results:");
var allPeptides = protease.Value.SelectMany(p => p.Value);
if (UserParams.TreatModifiedPeptidesAsDifferent)
{
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Peptides: " + allPeptides.Count()));
thisDigestion.Summary.Add(new SummaryForTreeView(" Number of Distinct Peptide Sequences: " + allPeptides.Select(p => p.FullSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Unique Peptides: " + allPeptides.Where(pep => pep.Unique == true).Select(p => p.FullSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Shared Peptides: " + allPeptides.Where(pep => pep.Unique == false).Select(p => p.FullSequence).Distinct().Count()));
}
else
{
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Peptides: " + allPeptides.Count()));
thisDigestion.Summary.Add(new SummaryForTreeView(" Number of Distinct Peptide Sequences: " + allPeptides.Select(p => p.BaseSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Unique Peptides: " + allPeptides.Where(pep => pep.Unique == true).Select(p => p.BaseSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Shared Peptides: " + allPeptides.Where(pep => pep.Unique == false).Select(p => p.BaseSequence).Distinct().Count()));
}
thisProtease.Summary.Add(thisDigestion);
}
//Put the database specific results summary in the GUI
SummaryForTreeViewObservableCollection.Add(thisProtease);
}
}
else // if there is only one database then is results and all database results are the same thing
{
foreach (var database in PeptideByFile)
{
ProteaseSummaryForTreeView thisProtease = new ProteaseSummaryForTreeView(database.Key + " Results:");
foreach (var protease in database.Value)
{
string prot = protease.Key;
DigestionSummaryForTreeView thisDigestion = new DigestionSummaryForTreeView(prot + " Results:");
var allPeptides = protease.Value.SelectMany(p => p.Value);
if (UserParams.TreatModifiedPeptidesAsDifferent)
{
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Peptides: " + allPeptides.Count()));
thisDigestion.Summary.Add(new SummaryForTreeView(" Number of Distinct Peptide Sequences: " + allPeptides.Select(p => p.FullSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Unique Peptides: " + allPeptides.Where(pep => pep.Unique == true).Select(p => p.FullSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Shared Peptides: " + allPeptides.Where(pep => pep.Unique == false).Select(p => p.FullSequence).Distinct().Count()));
}
else
{
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Peptides: " + allPeptides.Count()));
thisDigestion.Summary.Add(new SummaryForTreeView(" Number of Distinct Peptide Sequences: " + allPeptides.Select(p => p.BaseSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Unique Peptides: " + allPeptides.Where(pep => pep.Unique == true).Select(p => p.BaseSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Shared Peptides: " + allPeptides.Where(pep => pep.Unique == false).Select(p => p.BaseSequence).Distinct().Count()));
}
thisProtease.Summary.Add(thisDigestion);
}
SummaryForTreeViewObservableCollection.Add(thisProtease);
}
}
//Results are provided to the user at this point
ProteaseSummaryTreeView.DataContext = SummaryForTreeViewObservableCollection;
}
private void GenerateResultsSummary()
{
if (PeptideByFile.Count > 1) // if there is more than one database then we need to do all database summary
{
ProteaseSummaryForTreeView allDatabases = new ProteaseSummaryForTreeView("Cumulative Database Results:");
Dictionary <string, List <InSilicoPep> > allDatabasePeptidesByProtease = new Dictionary <string, List <InSilicoPep> >();
foreach (var database in PeptideByFile)
{
foreach (var protease in database.Value)
{
if (allDatabasePeptidesByProtease.ContainsKey(protease.Key))
{
foreach (var protein in protease.Value)
{
allDatabasePeptidesByProtease[protease.Key].AddRange(protein.Value);
}
}
else
{
allDatabasePeptidesByProtease.Add(protease.Key, protease.Value.SelectMany(p => p.Value).ToList());
}
}
}
if (UserParams.TreatModifiedPeptidesAsDifferent)
{
foreach (var protease in allDatabasePeptidesByProtease)
{
string prot = protease.Key;
DigestionSummaryForTreeView thisDigestion = new DigestionSummaryForTreeView(prot + " Results:");
var peptidesToProteins = protease.Value.GroupBy(p => p.FullSequence).ToDictionary(group => group.Key, group => group.ToList());
List <InSilicoPep> allPeptides = peptidesToProteins.SelectMany(p => p.Value).ToList();
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Peptides: " + allPeptides.Count));
thisDigestion.Summary.Add(new SummaryForTreeView(" Number of Distinct Peptide Sequences: " + allPeptides.Select(p => p.FullSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Unique Peptides: " + peptidesToProteins.Where(p => p.Value.Select(p => p.Protein).Distinct().Count() == 1).Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Shared Peptides: " + peptidesToProteins.Where(p => p.Value.Select(p => p.Protein).Distinct().Count() > 1).Count()));
allDatabases.Summary.Add(thisDigestion);
}
}
else
{
foreach (var protease in allDatabasePeptidesByProtease)
{
string prot = protease.Key;
DigestionSummaryForTreeView thisDigestion = new DigestionSummaryForTreeView(prot + " Results:");
var peptidesToProteins = protease.Value.GroupBy(p => p.BaseSequence).ToDictionary(group => group.Key, group => group.ToList());
List <InSilicoPep> allPeptides = peptidesToProteins.SelectMany(p => p.Value).ToList();
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Peptides: " + allPeptides.Count));
thisDigestion.Summary.Add(new SummaryForTreeView(" Number of Distinct Peptide Sequences: " + allPeptides.Select(p => p.BaseSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Unique Peptides: " + peptidesToProteins.Where(p => p.Value.Select(p => p.Protein).Distinct().Count() == 1).Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Shared Peptides: " + peptidesToProteins.Where(p => p.Value.Select(p => p.Protein).Distinct().Count() > 1).Count()));
allDatabases.Summary.Add(thisDigestion);
}
}
SummaryForTreeViewObservableCollection.Add(allDatabases);
foreach (var database in PeptideByFile)
{
ProteaseSummaryForTreeView thisProtease = new ProteaseSummaryForTreeView(database.Key + " Results:");
foreach (var protease in database.Value)
{
string prot = protease.Key;
DigestionSummaryForTreeView thisDigestion = new DigestionSummaryForTreeView(prot + " Results:");
var allPeptides = protease.Value.SelectMany(p => p.Value);
if (UserParams.TreatModifiedPeptidesAsDifferent)
{
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Peptides: " + allPeptides.Count()));
thisDigestion.Summary.Add(new SummaryForTreeView(" Number of Distinct Peptide Sequences: " + allPeptides.Select(p => p.FullSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Unique Peptides: " + allPeptides.Where(pep => pep.Unique == true).Select(p => p.FullSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Shared Peptides: " + allPeptides.Where(pep => pep.Unique == false).Select(p => p.FullSequence).Distinct().Count()));
}
else
{
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Peptides: " + allPeptides.Count()));
thisDigestion.Summary.Add(new SummaryForTreeView(" Number of Distinct Peptide Sequences: " + allPeptides.Select(p => p.BaseSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Unique Peptides: " + allPeptides.Where(pep => pep.Unique == true).Select(p => p.BaseSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Shared Peptides: " + allPeptides.Where(pep => pep.Unique == false).Select(p => p.BaseSequence).Distinct().Count()));
}
thisProtease.Summary.Add(thisDigestion);
}
SummaryForTreeViewObservableCollection.Add(thisProtease);
}
}
else // if there is only one database then is results and all database results are the same thing
{
foreach (var database in PeptideByFile)
{
ProteaseSummaryForTreeView thisProtease = new ProteaseSummaryForTreeView(database.Key + " Results:");
foreach (var protease in database.Value)
{
string prot = protease.Key;
DigestionSummaryForTreeView thisDigestion = new DigestionSummaryForTreeView(prot + " Results:");
var allPeptides = protease.Value.SelectMany(p => p.Value);
if (UserParams.TreatModifiedPeptidesAsDifferent)
{
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Peptides: " + allPeptides.Count()));
thisDigestion.Summary.Add(new SummaryForTreeView(" Number of Distinct Peptide Sequences: " + allPeptides.Select(p => p.FullSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Unique Peptides: " + allPeptides.Where(pep => pep.Unique == true).Select(p => p.FullSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Shared Peptides: " + allPeptides.Where(pep => pep.Unique == false).Select(p => p.FullSequence).Distinct().Count()));
}
else
{
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Peptides: " + allPeptides.Count()));
thisDigestion.Summary.Add(new SummaryForTreeView(" Number of Distinct Peptide Sequences: " + allPeptides.Select(p => p.BaseSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Unique Peptides: " + allPeptides.Where(pep => pep.Unique == true).Select(p => p.BaseSequence).Distinct().Count()));
thisDigestion.Summary.Add(new SummaryForTreeView("Number of Shared Peptides: " + allPeptides.Where(pep => pep.Unique == false).Select(p => p.BaseSequence).Distinct().Count()));
}
thisProtease.Summary.Add(thisDigestion);
}
SummaryForTreeViewObservableCollection.Add(thisProtease);
}
}
ProteaseSummaryTreeView.DataContext = SummaryForTreeViewObservableCollection;
}