public static void SetPep(Identifications identifications, BayesianInversion2D bi)
{
int n = identifications.Count;
for (int i = 0; i < n; i++)
{
MascotPeptide p = identifications.GetPeptidesAt(i)[0];
p.Pep = bi.GetValue(p.AltScore, Math.Log(p.Sequence.Length));
}
identifications.Write();
}
private static void LimitPep(string[] rawFiles, MascotQueryType type, IIdentificationProvider ip)
{
for (int i = 0; i < rawFiles.Length; i++)
{
Identifications ident = ip.GetIdentifications(rawFiles[i], type);
int n = ident.Count;
for (int j = 0; j < n; j++)
{
MascotPeptide p = ident.GetPeptidesAt(j)[0];
p.Pep = Math.Min(p.Pep, 1);
}
ident.Write();
ip.Dispose();
}
}
public static void ApplyReverseHitThreshold(Identifications identifications, double pepThreshold)
{
int n = identifications.Count;
List <int> o = new List <int>();
for (int i = 0; i < n; i++)
{
MascotPeptide p = identifications.GetPeptidesAt(i)[0];
if (p.Pep <= pepThreshold)
{
o.Add(i);
}
}
identifications.Extract(o.ToArray());
identifications.Write();
}
public static void FilterBySequence(Identifications identifications, HashSet <string> sequences)
{
int n = identifications.Count;
List <int> oo = new List <int>();
for (int i = 0; i < n; i++)
{
MascotPeptide p = identifications.GetPeptidesAt(i)[0];
if (sequences.Contains(p.Sequence))
{
oo.Add(i);
}
}
identifications.Extract(oo.ToArray());
identifications.Write();
}