//-----------------------------
//-----------------------------------------------------------------------------------------------------
public void RebuildProteinsFromScans()
{
//Find the proteins that have
MyProteinList.AsParallel().ForAll(a => a.Scans = a.Scans.Intersect(AllSQTScans).ToList());
MyProteinList.RemoveAll(a => a.Scans.Count == 0);
RebuildPeptideListFromUpdatedProteinList();
}
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");
}
