//public ConcurrentDictionary<string, List<Protein>> DicOfProteins = new ConcurrentDictionary<string, List<Protein>>();
private void ComputePSMs(Query query, Peptide modified_peptide)
{
PeptideSpectrumMatch psm = new PeptideSpectrumMatch(query, modified_peptide, options);
if (psm.MatchingProducts > options.fragments.Count)
{
//DicOfProteins.GetOrAdd(psm.Peptide.BaseSequence, new List<Protein>()).Add(psm.Peptide.Parent);
// if (!DicOfProteins.ContainsKey(psm.Peptide.BaseSequence))
// DicOfProteins.AddOrUpdate(psm.Peptide.BaseSequence, new List<Protein>());
// DicOfProteins[psm.Peptide.BaseSequence].Add(psm.Peptide.Parent);
//List<PeptideSpectrumMatch> psmsOfQuery = query.psms;
if (query.psms.Count < options.NbPSMToKeep)
{
query.psms.Add(psm);
}
else if (query.psms[options.NbPSMToKeep - 1].ProbabilityScore() < psm.ProbabilityScore())
{
for (int i = 0; i < query.psms.Count; i++)
{
if (query.psms[i].ProbabilityScore() <= psm.ProbabilityScore())
{
query.psms.Insert(i, psm);
break;
}
}
if (query.psms.Count > options.NbPSMToKeep)
{
query.psms.RemoveAt(options.NbPSMToKeep - 1);
}
}//*/
//TODO check optimal number of PSM to store
/*
* //TODO Reactivate this to save on memory space
* if (psmsOfPrecursor.Count == 0 || psmsOfPrecursor[0].MaxQuantScore() == psm.MaxQuantScore())
* psmsOfPrecursor.Add(psm);
* else
* if (psm.MaxQuantScore() > psmsOfPrecursor[0].MaxQuantScore())
* {
* psmsOfPrecursor.Clear();
* psmsOfPrecursor.Add(psm);
* }
* //*/
}
}
public bool KeepPSM(PeptideSpectrumMatch psm)
{
return(psm.MatchingIntensity >= minIntensityScore &&
psm.MatchingIntensityFraction >= minIntensityFractionScore &&
psm.ProductScore >= minProductScore &&
psm.PrecursorScore >= minPrecursorScore &&
psm.MatchingProductsFraction >= minMatchingProductFractionScore &&
psm.MatchingProducts >= minMatchingProductScore &&
psm.ProteinScore >= minProteinScore &&
psm.PeptideScore >= minPeptideScore &&
psm.FragmentScore >= minFragmentScore &&
psm.ProbabilityScore() >= minProbabilityScore);
}
public double OptimizedBestPsmScore(Peptide peptide = null, bool checkMods = false)
{
PeptideSpectrumMatch psm = OptimizedBestPsm(peptide, checkMods);
if (psm != null)
{
return(psm.ProbabilityScore());
}
else
{
return(0);
}
}
public static int DescendingOptimizedScoreComparison(PeptideSpectrumMatch left, PeptideSpectrumMatch right)
{
int comparison = -(left.ProbabilityScore().CompareTo(right.ProbabilityScore()));
if (comparison != 0)
{
return(comparison);
}
else
{
return(left.Target.CompareTo(right.Target));
}
}
public IEnumerable <PeptideSpectrumMatch> OptimizedBestPsms()
{
if (psms.Count > 0)
{
PeptideSpectrumMatch bestpsm = OptimizedBestPsm();
double score = bestpsm.ProbabilityScore();
for (int i = 0; i < psms.Count; i++)
{
if (psms[i].ProbabilityScore() >= score)
{
yield return(psms[i]);
}
}
}
}