public void ReducePsms(IEqualityComparer <Peptide> comparer)
{
Dictionary <Peptide, Peptide> peptides = new Dictionary <Peptide, Peptide>(comparer);
foreach (PSM psm in PeptideSpectralMatches)
{
Peptide peptide = new Peptide(psm);
Peptide realPeptide;
if (peptides.TryGetValue(peptide, out realPeptide))
{
realPeptide.AddPsm(psm);
}
else
{
peptides.Add(peptide, peptide);
}
}
Peptides = peptides.Values.ToList();
}
public int CompareTo(Peptide other)
{
return(BestMatch.CompareTo(other.BestMatch));
}
private void ReducePsms(IList <InputFile> csvFiles, UniquePeptideType uniquePeptideType, bool isBatched = false)
{
string msg = "Converting PSMs into unique peptides based ";
IEqualityComparer <Peptide> comparer;
switch (uniquePeptideType)
{
default:
msg += "on sequence only";
comparer = new SequenceComparer();
break;
case UniquePeptideType.Mass:
msg += "on mass";
comparer = new MassComparer();
break;
case UniquePeptideType.SequenceAndModifications:
msg += "on sequence and positional modifications";
comparer = new SequenceModComparer();
break;
case UniquePeptideType.SequenceAndModLocations:
msg += "on sequence and modification locations";
comparer = new SequenceAndModPositionComparer();
break;
case UniquePeptideType.SequenceAndMass:
msg += "on sequence and mass";
comparer = new SequenceMassComparer();
break;
case UniquePeptideType.Nothing:
msg += "on nothing (no reduction)";
comparer = new IdentityComparer <Peptide>();
break;
}
Log(msg);
foreach (InputFile csvFile in csvFiles)
{
csvFile.ReducePsms(comparer);
Log(string.Format("{0:N0} unique peptides remain from {1:N0} PSMs from {2}", csvFile.Peptides.Count, csvFile.PeptideSpectralMatches.Count, csvFile.Name));
}
if (!isBatched)
{
return;
}
Dictionary <Peptide, Peptide> peptideDictionary = new Dictionary <Peptide, Peptide>(comparer);
foreach (Peptide peptide in csvFiles.SelectMany(csvFile => csvFile.Peptides))
{
Peptide realPeptide;
if (peptideDictionary.TryGetValue(peptide, out realPeptide))
{
foreach (PSM psm in peptide.PSMs)
{
realPeptide.AddPsm(psm);
}
}
else
{
Peptide newPeptide = new Peptide(peptide);
peptideDictionary.Add(newPeptide, newPeptide);
}
}
_allPeptides = peptideDictionary.Values.ToList();
Log(string.Format("{0:N0} unique peptides from all files [Batched]", _allPeptides.Count));
}