private O18QuanEnvelope GetCorrespondingEnvelope(IRawFile rawFile, double theoreticalMz, int charge, double mzTolerance, int scan)
{
PeakList <Peak> pkl = rawFile.GetPeakList(scan);
if (pkl.ScanTimes.Count == 0)
{
pkl.ScanTimes.Add(new ScanTime(scan, rawFile.ScanToRetentionTime(scan)));
}
PeakList <Peak> O16 = pkl.FindEnvelopeDirectly(theoreticalMz, charge, mzTolerance, 4, () => new Peak());
PeakList <Peak> O181 = pkl.FindEnvelopeDirectly(theoreticalMz + chargeGapMap1[charge], charge, mzTolerance, 2, () => new Peak());
for (int i = 2; i < 4; i++)
{
if (O16[i].Intensity < O181[i - 2].Intensity)
{
O16[i].Mz = O181[i - 2].Mz;
O16[i].Intensity = O181[i - 2].Intensity;
}
}
PeakList <Peak> O182 = pkl.FindEnvelopeDirectly(theoreticalMz + chargeGapMap2[charge], charge, mzTolerance, 2, () => new Peak());
O16.AddRange(O182);
return(new O18QuanEnvelope(O16));
}
private static void MergeTogether(double mzTolerance, PeakList <Peak> mergedEnvelopes, PeakList <Peak> envelope)
{
if (mergedEnvelopes.Count < envelope.Count)
{
PeakList <Peak> tmp = new PeakList <Peak>(mergedEnvelopes);
mergedEnvelopes.Clear();
mergedEnvelopes.AddRange(envelope);
mergedEnvelopes.AddToCurrentPeakListIntensity(tmp, mzTolerance);
}
else
{
mergedEnvelopes.AddToCurrentPeakListIntensity(envelope, mzTolerance);
}
}
public PeakList <T> Process(PeakList <T> t)
{
if (!t.Any(m => m.Charge > 0))
{
return(t);
}
List <T> kept = (from p in t
where p.Charge == 0
select p).ToList();
t.RemoveAll(m => m.Charge == 0);
while (t.Count > 0)
{
var curPeaks = FindEnvelope(t, t[0], PrecursorUtils.ppm2mz(t[0].Mz, this.ppmTolerance));
t.RemoveAll(m => curPeaks.Contains(m));
if (curPeaks.Count == 1 || curPeaks[0].Intensity >= curPeaks[1].Intensity)
{
kept.Add(curPeaks[0]);
continue;
}
var mass = curPeaks[0].Mz * curPeaks[0].Charge - Atom.H.MonoMass;
if (mass > 1800)
{
kept.Add(curPeaks[0]);
continue;
}
kept.Add(curPeaks[0]);
kept.Add(curPeaks[1]);
}
t.AddRange(kept);
t.Sort((m1, m2) => m1.Mz.CompareTo(m2.Mz));
return(t);
}
