public PeptideSpectrumMatch OptimizedBestPsm(Peptide peptide = null, bool checkMods = false)
{
if (psms.Count > 0)
{
if (peptide == null)
{
double bestScore = psms[0].ProbabilityScore();
int bestProteinIndex = 0;
double tmpScore;
for (int i = 1; i < psms.Count; i++)
{
tmpScore = psms[i].ProbabilityScore();
if (tmpScore > bestScore || (tmpScore == bestScore && psms[i].Target))//.ProteinScore >= proteinScore))
{
bestProteinIndex = i;
bestScore = tmpScore;
}
}
return(psms[bestProteinIndex]);
}
else
{
double bestScore = 0;
int bestProteinIndex = 0;
double proteinScore = 0;
for (int i = 0; i < psms.Count; i++)
{
if (peptide.IsSamePeptide(psms[i].Peptide, checkMods) && (psms[i].ProbabilityScore() > bestScore || (psms[i].ProbabilityScore() == bestScore && psms[i].Target)))//.ProteinScore > proteinScore)))
{
bestProteinIndex = i;
bestScore = psms[i].ProbabilityScore();
proteinScore = psms[i].ProteinScore;
}
}
if (bestScore > 0)
{
return(psms[bestProteinIndex]);
}
}
}
return(null);
}
public double ProbabilityScore(Peptide peptide = null, bool checkMods = false)
{/*
* double score = 0;
* foreach(PeptideSpectrumMatch psm in psms)
* if(
* foreach (PeptideSpectrumMatch psm in OptimizedBestPsms(peptide))
* score += (1 - score) * psm.OptimizedScore();
* return score;
* //*/
if (peptide != null)
{
double score = 0;
foreach (PeptideSpectrumMatch psm in psms)
{
if (peptide.IsSamePeptide(psm.Peptide, checkMods))
{
score += psm.ProbabilityScore();
}
}
return(score);
}
else
{
return(OptimizedBestPsmScore(peptide, checkMods));//TODO Reactivate Optimized Precursor Score
}
//PeptideSpectrumMatch psmLeft = OptimizedBestPsm(peptide, checkMods);
//if (psmLeft != null)
// return psmLeft.OptimizedScore();
/* (dIntensity * psmLeft.MatchingIntensityFraction +
* dProduct * psmLeft.ProductScore +
* dPrecursor * psmLeft.PrecursorScore +
* dMatching * psmLeft.MatchingProductsFraction +
* dProtein * psmLeft.ProteinScore +
* dScore * psmLeft.MaxQuantScore() +
* (Isotopes.Count > 0 ? dIsotope : 0) +
* (Track.Invented ? dInvented : 0) +
* dPeptideScore * psmLeft.PeptideScore);//*/
//else
// return 0;//*/
}