public double GetScore(Sequence sequence, int charge, int scan, LcMsRun lcmsRun)
{
var mass = sequence.Composition.Mass + Composition.H2O.Mass;
var spectrum = lcmsRun.GetSpectrum(scan);
var ionTypes = _rankScore.GetIonTypes(charge, mass);
var filteredSpectrum = SpectrumFilter.FilterIonPeaks(sequence, spectrum, ionTypes, _tolerance);
var match = new SpectrumMatch(sequence, filteredSpectrum, charge);
var score = 0.0;
var rankedPeaks = new RankedPeaks(filteredSpectrum);
foreach (var ionType in ionTypes)
{
var ions = match.GetCleavageIons(ionType);
foreach (var ion in ions)
{
var rank = rankedPeaks.RankIon(ion, _tolerance);
score += _rankScore.GetScore(ionType, rank, charge, mass);
}
}
return score;
}
/// <summary>
/// Add single Peptide-Spectrum match to RankTable.
/// </summary>
/// <param name="match"></param>
public void AddMatch(SpectrumMatch match)
{
var ranks = new RankedPeaks(match.Spectrum);
for (int i = 0; i < ranks.Peaks.Length; i++)
{
var index = i;
if (index >= MaxRanks) index = MaxRanks - 1;
_rankTotals[index]++;
_rankTotals[MaxRanks]++;
}
foreach (var ionType in IonTypes)
{
var ions = match.GetCleavageIons(ionType);
foreach (var ion in ions)
{
var rank = ranks.RankIon(ion, _tolerance);
var rankIndex = GetRankIndex(rank);
_rankTable[ionType][rankIndex]++;
}
}
}