public PeakList <Peak> Process(PeakList <Peak> t)
{
if (t.Count == 0)
{
return(t);
}
t.SortByMz();
List <Peak> final = new List <Peak>();
List <Peak> kept = new List <Peak>();
double minMz = 0;
double lastMz = t.Last().Mz;
int index = 0;
while (index < t.Count)
{
var maxMz = minMz + 100;
kept.Clear();
while (index < t.Count)
{
if (t[index].Mz > maxMz)
{
break;
}
kept.Add(t[index]);
index++;
}
if (kept.Count > count)
{
kept.Sort((m1, m2) => m2.Intensity.CompareTo(m1.Intensity));
kept.RemoveRange(count, kept.Count - count);
}
final.AddRange(kept);
minMz += 100;
}
t.Clear();
t.AddRange(final);
return(t);
}
public List <PeakList <T> > GetEnvelopes(double ppmTolerance)
{
var tmp = new PeakList <T>(this);
var result = new List <PeakList <T> >();
while (tmp.Count > 0)
{
double mzTolerance = 2 * PrecursorUtils.ppm2mz(tmp[0].Mz, ppmTolerance);
PeakList <T> envelope = tmp.FindEnvelope(tmp[0], mzTolerance, true);
result.Add(envelope);
foreach (T peak in envelope)
{
//Remove all peaks around current peak
PeakList <T> findPeaks = tmp.FindPeak(peak.Mz, peak.Charge, mzTolerance);
foreach (T findPeak in findPeaks)
{
tmp.Remove(findPeak);
}
}
}
result.Sort(new PeakListMzAscendingComparer <T>());
int current = 0;
while (current < result.Count - 1)
{
PeakList <T> currentPkl = result[current];
if (currentPkl[0].Charge > 0)
{
double expectMz = currentPkl[currentPkl.Count - 1].Mz + ChargeDeconvolution.C_GAP / currentPkl[0].Charge;
double mzTolerance = 4 * PrecursorUtils.ppm2mz(currentPkl[0].Mz, ppmTolerance);
int next = current + 1;
while (next < result.Count)
{
double gap = result[next][0].Mz - expectMz;
if (gap >= 2.0)
{
break;
}
if (Math.Abs(gap) > mzTolerance)
{
next++;
continue;
}
if (result[next][0].Charge != currentPkl[0].Charge)
{
next++;
continue;
}
currentPkl.AddRange(result[next]);
result.RemoveAt(next);
}
}
current++;
}
return(result);
}
