public void ProcessParsedData(bool considerOnlyUnique)
{
//If we wish to eliminate decoy proteins
if (MyParameters.EliminateDecoys)
{
foreach (ResultEntry re in MyResultPackages)
{
re.MyResultPackage.MyProteins.RemoveDecoyProteins(MyParameters.DecoyTag);
}
}
List <string> globalPeptideList = (from re in MyResultPackages
from p in re.MyResultPackage.AllPeptideSequences
select p).Distinct().ToList();
foreach (string p in globalPeptideList)
{
List <List <string> > mappableProteins = (from re in MyResultPackages.AsParallel()
from pepR in re.MyResultPackage.MyProteins.MyPeptideList
where pepR.CleanedPeptideSequence == p
select pepR.MyMapableProteins).ToList();
List <string> uniqueList = new List <string>(mappableProteins.Count);
foreach (List <string> list in mappableProteins)
{
uniqueList.AddRange(list);
}
uniqueList = uniqueList.Distinct().ToList();
GlobalPeptideResult gpp = new GlobalPeptideResult();
gpp.Sequence = p;
gpp.MappableProteins = uniqueList;
globalPeptideIndex.Add(gpp);
}
if (MyParameters.PeptideParserOnlyUniquePeptides)
{
globalPeptideIndex.RemoveAll(a => a.MappableProteins.Count > 1);
}
}
/// <summary>
/// This eliminates decoys and builds the index
/// </summary>
public void ProcessParsedData()
{
//Generate a SEPro Fusion---------------------
ResultPackage seprofusion = FusionSEPro(MyResultPackages.Select(a => a.MyResultPackage).ToList());
///-------------------------------------------
//If we wish to eliminate decoy proteins
if (MyParameters.EliminateDecoys)
{
seprofusion.MyProteins.RemoveDecoyProteins(MyParameters.DecoyTag);
}
//we do this in two steps... first we build the index, then, we build the sparse matrix rows
List <MyProtein> myProteins = seprofusion.MyProteins.MyProteinList;
if (UseMaxParsimony)
{
myProteins = seprofusion.MaxParsimonyList();
}
List <TMPProt> result = (from prot in myProteins
select new TMPProt(prot.Locus, prot.Description, prot.ContainsUniquePeptide)).ToList();
//If we only want proteins of unique peptides
if (MyParameters.MyProteinType == ProteinOutputType.SpecCountsOfUniquePeptides)
{
result = (from r in result
where r.UniquePeptides > 0
select r).ToList();
}
theIndex = new List <ProteinIndexStruct>(result.Count());
for (int i = 0; i < result.Count; i++)
{
ProteinIndexStruct p = new ProteinIndexStruct();
p.Locus = result[i].Locus;
p.Description = result[i].Description;
p.Index = i;
if (!theIndex.Exists(a => a.Locus.Equals(result[i].Locus)))
{
theIndex.Add(p);
}
else
{
throw new Exception("Problems generating SEPro fusion file");
}
}
//int counter = 0;
//foreach (TMPProt r in result)
//{
// counter++;
// ProteinIndexStruct p = new ProteinIndexStruct();
// p.Locus = r.Locus;
// p.Description = r.Description;
// p.Index = counter;
// if (!theIndex.Exists(a => a.Locus.Equals(r.Locus)))
// {
// theIndex.Add(p);
// }
// else
// {
// counter--;
// }
//}
}
