public static double CalcPtmScore(double ms2Tol, string ms2TolUnit, int topx, string sequence, Modification[] fixedModifications,
Modification[] variableModifications, int[] modCount, double[] specMasses, float[] specIntensities, double mz,
int charge, out bool incomplete, out PeptideModificationState outMods, out int counts,
out double delta, out MsmsPeakAnnotation[] description, out float[] intensities,
out float[] massDiffs, out Dictionary <ushort, double[]> modProb,
out Dictionary <ushort, double[]> modScoreDiffs, bool alternative)
{
if (!AminoAcid.ValidSequence(sequence))
{
incomplete = true;
outMods = null;
counts = 0;
delta = 0;
description = null;
intensities = null;
massDiffs = null;
modProb = null;
modScoreDiffs = null;
return(0);
}
Peptide p = new Peptide(sequence);
p.ApplyFixedModifications(fixedModifications);
PeptideModificationState[] mpeps = p.ApplyVariableModificationsFixedNumbers(variableModifications, modCount, out incomplete);
counts = mpeps.Length;
double maxScore = -double.MaxValue;
double maxScore2 = -double.MaxValue;
PeptideModificationState bestPep = null;
description = null;
intensities = null;
massDiffs = null;
double sumScore = 0;
modProb = new Dictionary <ushort, double[]>();
Dictionary <ushort, double[, ]> scoreDiffs = new Dictionary <ushort, double[, ]>();
ushort[] w = mpeps[0].GetModifications();
HashSet <ushort> um = new HashSet <ushort>();
foreach (ushort x in w)
{
if (x != ushort.MaxValue && !um.Contains(x))
{
um.Add(x);
}
}
ushort[] uniqueMods = um.ToArray();
foreach (ushort m in uniqueMods)
{
if (!modProb.ContainsKey(m))
{
modProb.Add(m, new double[w.Length]);
scoreDiffs.Add(m, new double[2, w.Length]);
}
}
foreach (PeptideModificationState mpep in mpeps)
{
MsmsPeakAnnotation[] desc;
float[] intens;
float[] dm;
double score = Score(specMasses, specIntensities, p, ms2Tol, ms2TolUnit, mz, charge,
out desc, out intens, out dm, topx, mpep);
ushort[] mm = mpep.GetModifications();
double x = Math.Exp((score - 100) * NumUtil.log10 / 10.0);
for (int i = 0; i < mm.Length; i++)
{
if (mm[i] != ushort.MaxValue)
{
modProb[mm[i]][i] += x;
}
foreach (ushort mod in uniqueMods)
{
if (mm[i] == mod)
{
if (score > scoreDiffs[mod][0, i])
{
scoreDiffs[mod][0, i] = score;
}
}
else
{
if (score > scoreDiffs[mod][1, i])
{
scoreDiffs[mod][1, i] = score;
}
}
}
}
sumScore += x;
if (score > maxScore)
{
maxScore2 = maxScore;
maxScore = score;
bestPep = mpep;
description = desc;
intensities = intens;
massDiffs = dm;
}
else if (score > maxScore2)
{
maxScore2 = score;
}
}
modScoreDiffs = new Dictionary <ushort, double[]>();
foreach (ushort mod in uniqueMods)
{
Modification modi = Tables.modificationList[mod];
modScoreDiffs.Add(mod, new double[w.Length]);
for (int i = 0; i < sequence.Length; i++)
{
char aa = sequence[i];
if (modi.HasAA(aa))
{
modScoreDiffs[mod][i] = scoreDiffs[mod][0, i] - scoreDiffs[mod][1, i];
}
else
{
modScoreDiffs[mod][i] = double.NaN;
}
}
}
foreach (double[] y in modProb.Values)
{
for (int i = 0; i < y.Length; i++)
{
y[i] /= sumScore;
}
}
if (maxScore2 == -double.MaxValue)
{
delta = maxScore;
}
else
{
delta = maxScore - maxScore2;
}
outMods = bestPep;
return(maxScore);
}
