public PeakList <T> Process(PeakList <T> t)
{
List <PeakList <T> > envelopes = t.GetEnvelopes(this.ppmTolerance);
((List <T>)t).Clear();
foreach (var envelope in envelopes)
{
t.Add(envelope[0]);
}
t.Sort((m1, m2) => m1.Mz.CompareTo(m2.Mz));
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 XCorrelationSpectrumScore(PeakList <U> experimentalPkl)
{
var tmp = new PeakList <U>(experimentalPkl);
tmp.Sort((m1, m2) => m1.Mz.CompareTo(m2.Mz));
//A 10-u window around the precursor ion is removed
double minPrecursor = tmp.PrecursorMZ - 10.0;
double maxPrecursor = tmp.PrecursorMZ + 10.0;
for (int i = tmp.Count - 1; i >= 0; i--)
{
if (tmp[i].Mz > maxPrecursor)
{
continue;
}
if (tmp[i].Mz < minPrecursor)
{
break;
}
tmp.RemoveAt(i);
}
//The spectrum is then divided into 10 equal sections and the ion abundances in each section are normalized to 50.0;
double maxMz = (int)Math.Round(tmp[tmp.Count - 1].Mz + 2.0);
double stepMz = (maxMz) / 10.0;
var peakBin = new List <PeakList <U> >();
for (int i = 0; i < 10; i++)
{
peakBin.Add(new PeakList <U>());
}
foreach (U p in tmp)
{
var index = (int)(p.Mz / stepMz);
peakBin[index].Add(p);
}
foreach (var peaks in peakBin)
{
if (peaks.Count > 0)
{
double maxIntensity = peaks.FindMaxIntensityPeak().Intensity;
foreach (U p in peaks)
{
p.Intensity = p.Intensity * 50 / maxIntensity;
}
}
}
//convert to discrte signals
this._maxIndex = GetMinPowerOfTwo(maxMz);
this._experimentalIntensities = new double[this._maxIndex];
for (int i = 0; i < this._maxIndex; i++)
{
this._experimentalIntensities[i] = 0.0;
}
foreach (U p in tmp)
{
var index = (int)Math.Round(p.Mz);
AssignIntensity(this._experimentalIntensities, index, (int)p.Intensity);
}
}
