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 CalcFdr(string[] rawFiles, string decoyPrefix, MascotQueryType type, IProteinSet proteinSet, bool debug,
IIdentificationProvider ip)
{
List <bool> correct = new List <bool>();
List <double> scores = new List <double>();
List <double> seqLen = new List <double>();
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++)
{
bool c = ident.IsHighestScoringCorrect(j, decoyPrefix, proteinSet);
double s = ident.GetHighestAltScore(j);
double l = Math.Log(ident.GetBestSequence(j).Length);
if (!double.IsNaN(s) && !double.IsInfinity(s))
{
correct.Add(c);
scores.Add(s);
seqLen.Add(l);
}
}
ip.Dispose();
if (correct.Count > 10000000)
{
break;
}
}
if (correct.Count == 0)
{
return;
}
bool write = debug && (type == MascotQueryType.Silac);
BayesianInversion2D bi = new BayesianInversion2D(scores.ToArray(), seqLen.ToArray(), correct.ToArray(), write);
if (write)
{
Write(rawFiles, bi);
}
for (int i = 0; i < rawFiles.Length; i++)
{
SetPep(ip.GetIdentifications(rawFiles[i], type), bi);
ip.Dispose();
}
}
private static void Write(string[] rawFiles, BayesianInversion2D bi)
{
string combinedFolder = rawFiles[0].Substring(0, rawFiles[0].LastIndexOf("\\")) + "\\combined";
for (int len = 6; len <= 80; len++)
{
double loglen = Math.Log(len);
string filename = "scoreDist" + len + ".txt";
StreamWriter writer = new StreamWriter(combinedFolder + "\\" + filename);
for (double score = 0; score < 600; score += 0.5)
{
double pep = bi.GetValue(score, loglen);
double forw = bi.GetForwardHist(score, loglen);
double reve = bi.GetReverseHist(score, loglen);
writer.WriteLine(score + "\t" + pep + "\t" + forw + "\t" + reve);
}
writer.Close();
}
}