//Properly handles removing a protein and updating FDR's, peptide lists, scan lists
public void RemoveProtein(List <MyProtein> proteins)
{
//For each of this protein's peptide lets see if this peptide still maps to some other protein, or else we should remove it.
foreach (MyProtein p in proteins)
{
MyProteins.MyProteinList.Remove(p);
List <string> remainingProteins = MyProteins.MyProteinList.Select(a => a.Locus).ToList();
List <PeptideResult> peptidesToRemove = new List <PeptideResult>();
foreach (PeptideResult pr in p.PeptideResults)
{
if (pr.MyMapableProteins.Intersect(remainingProteins).ToList().Count == 0)
{
peptidesToRemove.Add(pr);
}
}
foreach (PeptideResult pr in peptidesToRemove)
{
PeptideResult pr2 = MyProteins.MyPeptideList.Find(a => a.PeptideSequence.Equals(pr.CleanedPeptideSequence));
bool removed = MyProteins.MyPeptideList.Remove(pr2);
}
}
MyProteins.RebuildScansFromProteins();
MyFDRResult = FDRStatistics.GenerateFDRStatistics(MyProteins, MyParameters);
NotifyPropertyChanged("MyProteinList");
}
private void RebuildPeptideListFromUpdatedProteinList()
{
Console.WriteLine(" Building peptide list from protein list");
List <string> cleanedSequences = AllCleanedPeptideSequences;
//Patch pointed out by tiago balbuena to deal with peptides of same sequence but different flanking aa.
Dictionary <string, List <PeptideResult> >
seqCounter = (from prot in MyProteinList.AsParallel()
from pep in prot.PeptideResults
where cleanedSequences.Contains(pep.CleanedPeptideSequence)
group pep by pep.CleanedPeptideSequence into g
select new { Sequence = g.Key, Peptides = g }).ToDictionary(a => a.Sequence, a => a.Peptides.ToList());
foreach (KeyValuePair <string, List <PeptideResult> > kvp in seqCounter)
{
if (kvp.Value.Count > 1)
{
List <string> dSequences = (from pr in kvp.Value
select pr.PeptideSequence).Distinct().ToList();
if (dSequences.Count > 1)
{
//Lets create a new peptide result
List <SQTScan> allScans = new List <SQTScan>();
foreach (PeptideResult pr in kvp.Value)
{
allScans.AddRange(pr.MyScans);
}
allScans = allScans.Distinct().ToList();
PeptideResult surrogate = new PeptideResult(kvp.Key, allScans);
kvp.Value.Clear();
kvp.Value.Add(surrogate);
}
}
}
MyPeptideList = new List <PeptideResult>(seqCounter.Keys.Count);
foreach (KeyValuePair <string, List <PeptideResult> > kvp in seqCounter)
{
MyPeptideList.Add(kvp.Value[0]);
}
//RebuildScansFromProteins();
Console.WriteLine(" Done building peptide list");
}