public PeakList <T> Process(PeakList <T> t)
{
if (!t.Any(m => m.Charge > 0))
{
return(t);
}
Parallel.ForEach(t, m =>
{
if (m.Charge > 1)
{
m.Mz = m.Mz * m.Charge - Atom.H.MonoMass * (m.Charge - 1);
m.Charge = 1;
}
});
var peaks = (from p in t
where p.Charge == 1
orderby p.Intensity
select p).ToList();
var deleted = new HashSet <T>();
while (peaks.Count > 0)
{
var mz = peaks[0].Mz;
var mzTolerance = PrecursorUtils.ppm2mz(mz, ppmTolerance);
var minMz = mz - mzTolerance;
var maxMz = mz + mzTolerance;
var curPeaks = (from p in peaks
where p.Mz >= minMz && p.Mz <= maxMz
select p).ToList();
if (curPeaks.Count > 1)
{
var nIntensity = curPeaks.Sum(m => m.Intensity);
var nMz = curPeaks.Sum(m => m.Mz * m.Intensity) / nIntensity;
peaks[0].Mz = nMz;
peaks[0].Intensity = nIntensity;
curPeaks.Remove(peaks[0]);
deleted.UnionWith(curPeaks);
}
peaks.RemoveAll(m => curPeaks.Contains(m));
}
t.RemoveAll(m => deleted.Contains(m));
t.SortByMz();
return(t);
}
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);
}
public bool IsBy2Matched()
{
return(ExperimentalPeakList.Any(m => m.Matched && (m.PeakType == IonType.B2 || m.PeakType == IonType.Y2)));
}
