protected void WritePeak(StreamWriter writer, PeakList <T> pl)
{
PeakList <T> pkl;
//Mascot Generic Format 要求每个spectrum不能超过10000个离子。
if (pl.Count > 10000)
{
pkl = new PeakList <T>(pl);
pkl.SortByIntensity();
pkl.RemoveRange(10000, pkl.Count - 10000);
pkl.SortByMz();
}
else
{
pkl = pl;
}
//if (pkl.Any(m => m.Charge > 0))
//{
// foreach (T peak in pkl)
// {
// writer.WriteLine(MyConvert.Format("{0:0.#####} {1:0.0} {2}", peak.Mz, peak.Intensity, peak.Charge));
// }
//}
//else
//{
foreach (T peak in pkl)
{
writer.WriteLine(MyConvert.Format("{0:0.#####} {1:0.0###}", peak.Mz, peak.Intensity));
}
//}
writer.WriteLine(MascotGenericFormatConstants.END_PEAK_LIST_TAG);
writer.WriteLine();
}
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 void AddPeaks(int minMz, int maxMz, int scan, PeakList <Peak> pkl)
{
this.MinMz = minMz;
this.MaxMz = maxMz;
List <Peak> peaks = new List <Peak>();
for (int i = 0; i <= maxMz; i++)
{
peaks.Add(new Peak(0.0, 0.0));
}
pkl.SortByMz();
foreach (var p in pkl)
{
var mz = (int)Math.Round(p.Mz);
if (mz < minMz)
{
continue;
}
if (mz > maxMz)
{
break;
}
peaks[mz] = p;
}
for (int i = minMz; i <= maxMz; i++)
{
string peak = i.ToString();
this[peak, scan] = new PeakItem(scan, peaks[i].Mz, peaks[i].Intensity);
}
}
public PeakList <T> Process(PeakList <T> t)
{
t.SortByMz();
//删除固定区间。
var index = 0;
while (index < t.Count)
{
var peak = t[index];
if (peak.Mz > options.MaxFixIonMz)
{
break;
}
double mass;
if (peak.Charge > 1)
{
mass = PrecursorUtils.MzToMH(peak.Mz, peak.Charge, true);
if (mass > options.MaxFixIonMz)
{
index++;
continue;
}
}
else
{
mass = peak.Mz;
}
bool bRemoved = false;
for (int i = 0; i < options.FixIonRanges.Count; i++)
{
var ion = options.FixIonRanges[i];
if (mass < ion.First)
{
break;
}
if (mass > ion.Second)
{
continue;
}
bRemoved = true;
t.RemoveAt(index);
break;
}
if (!bRemoved)
{
index++;
}
}
var precursorMass = PrecursorUtils.MzToMH(t.PrecursorMZ, t.PrecursorCharge, true);
if (options.RemoveHighRange)
{
var maxPeak = precursorMass - options.Protease.GetHighBYFreeWindow() - options.MzTolerance;
if (options.RemovePrecusor)
{
t.RemoveAll(peak =>
{
double mass = PrecursorUtils.MzToMH(peak.Mz, peak.Charge, true);
return(mass >= maxPeak);
});
}
else
{
var precursorLess = precursorMass - options.MzTolerance;
var precursorLarge = precursorMass + options.MzTolerance;
t.RemoveAll(peak =>
{
double mass = PrecursorUtils.MzToMH(peak.Mz, peak.Charge, true);
return((mass >= maxPeak && mass <= precursorLess) || mass > precursorLarge);
});
}
}
if (options.RemovePrecursorMinusLabel)
{
var ionmass = precursorMass - options.LabelMass;
var minIonMass = ionmass - options.MzTolerance;
var maxIonMass = ionmass + options.MzTolerance;
t.RemoveAll(peak =>
{
double mass = PrecursorUtils.MzToMH(peak.Mz, peak.Charge, true);
return(mass >= minIonMass && mass <= maxIonMass);
});
}
return(t);
}
