public SilacMatchEvidence(int silacId, int rawFileIndex, SilacCluster silacCluster,
int charge, double intensity0, double intensity1,
double intensity2, double calibRT, MascotPeptide peptide)
:
base(silacId, rawFileIndex, silacCluster, charge, intensity0,
intensity1, intensity2, calibRT)
{
massErrPpm = (silacCluster.Mass - peptide.Mass) / peptide.Mass * 1e6;
}
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();
}
public static void CollectSequences(Identifications identifications, double peptidePep,
HashSet <string> sequences)
{
int n = identifications.Count;
for (int i = 0; i < n; i++)
{
MascotPeptide p = identifications.GetPeptidesAt(i)[0];
if ((p.Pep <= peptidePep) || (double.IsNaN(p.Pep) && double.IsNaN(peptidePep)))
{
sequences.Add(p.Sequence);
}
}
}
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();
}
public static double FindReverseHitThresholdValue(Identifications identifications, double totalPeptideFDR,
string reverseStr, IProteinSet proteinSet)
{
int n = identifications.Count;
if (n == 0)
{
return(1);
}
double[] peps = new double[n];
bool[] correct = new bool[n];
for (int i = 0; i < n; i++)
{
MascotPeptide p = identifications.GetPeptidesAt(i)[0];
peps[i] = p.Pep;
correct[i] = !p.HasOnlyReverseHits(reverseStr, proteinSet);
}
int[] o = ArrayUtil.Order(peps);
double forwardCount = 0;
List <double> validPeps = new List <double>();
for (int i = 0; i < n; i++)
{
int index = o[i];
if (correct[index])
{
forwardCount++;
}
double reverseCount = (i + 1) - forwardCount;
if (reverseCount / forwardCount <= totalPeptideFDR)
{
validPeps.Add(peps[index]);
}
}
if (validPeps.Count > 0)
{
return(ArrayUtil.Max(validPeps.ToArray()));
}
return(0);
}