public double GetPep(IIdentifiedPeptideList peptides, string[] sequences, int minPeptides, int minUniquePeptides,
PeptideScoring peptideScoring, int nsilac)
{
if (peptideSequences.Length < minPeptides)
{
return(1.1);
}
double result = 1;
int uniqueCount = 0;
for (int i = 0; i < peptideSequences.Length; i++)
{
int index = Array.BinarySearch(sequences, peptideSequences[i]);
if (peptides.IsUniqueGroup(index))
{
uniqueCount++;
}
result *= peptides.GetPep(index, peptideScoring, nsilac);
}
if (uniqueCount < minUniquePeptides)
{
return(1.1);
}
return(result);
}
public static int[] ExtractProteinGroups(TmpIdentifiedProteinGroup[] tmpProteinGroups, IIdentifiedPeptideList peptides,
double proteinFDR, PeptideScoring peptideScoring, int nsilac, int minPeptides,
int minUniquePeptides, string reversePrefix)
{
double[] peps = new double[tmpProteinGroups.Length];
string[] sequences = AllPeptideSequences(peptides);
for (int i = 0; i < tmpProteinGroups.Length; i++)
{
peps[i] = tmpProteinGroups[i].GetPep(peptides, sequences, minPeptides, minUniquePeptides, peptideScoring, nsilac);
}
int[] o = ArrayUtil.Order(peps);
int revCount = 0;
List <double> goodThresholdValues = new List <double>();
for (int i = 0; i < tmpProteinGroups.Length; i++)
{
if (tmpProteinGroups[o[i]].HasReverseProteins(reversePrefix))
{
revCount++;
}
double forwCount = i + 1.0 - revCount;
if (revCount / forwCount <= proteinFDR && peps[o[i]] < 1.01)
{
goodThresholdValues.Add(peps[o[i]]);
}
}
double thresholdValue = ArrayUtil.Max(goodThresholdValues.ToArray());
revCount = 0;
List <int> oo = new List <int>();
for (int i = 0; i < tmpProteinGroups.Length; i++)
{
if (tmpProteinGroups[o[i]].HasReverseProteins(reversePrefix))
{
revCount++;
}
double forwCount = i + 1.0 - revCount;
if (revCount / forwCount <= proteinFDR || peps[o[i]] < thresholdValue)
{
oo.Add(o[i]);
}
}
string[] dummy1 = new string[oo.Count];
for (int i = 0; i < oo.Count; i++)
{
dummy1[i] = tmpProteinGroups[oo[i]].ProteinIds[0];
}
int[] ooo = ArrayUtil.Order(dummy1);
o = ArrayUtil.SubArray(oo, ooo);
return(o);
}
