public override PeakList <Peak> GetPeakList(int scan, double minMz, double maxMz)
{
PeakList <Peak> result = GetPeakList(scan);
result.RemoveAll(m => m.Mz < minMz);
result.RemoveAll(m => m.Mz > maxMz);
return(result);
}
public override PeakList <Peak> GetPeakList(int scan, double minMz, double maxMz)
{
long position = positions[scan].Position;
sr.SetCharpos(position);
PeakList <Peak> result = iter.Next();
result.RemoveAll(m => { return(m.Mz < minMz || m.Mz > maxMz); });
return(result);
}
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 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.PrecursorCharge > 0)
{
var mzWindow = massTolerance / t.PrecursorCharge;
foreach (var offset in offsets)
{
var mz = t.PrecursorMZ + offset / t.PrecursorCharge;
var minMz = mz - mzWindow;
var maxMz = mz + mzWindow;
t.RemoveAll(m => m.Mz >= minMz && m.Mz <= maxMz);
}
}
return(t);
}
public PeakList <T> Process(PeakList <T> t)
{
if (t.PrecursorCharge > 0)
{
var precursorMass = PrecursorUtils.MzToMH(t.PrecursorMZ, t.PrecursorCharge, true);
t.RemoveAll(m =>
{
double mass;
if (m.Charge > 1)
{
mass = PrecursorUtils.MzToMH(m.Mz, m.Charge, true);
}
else
{
mass = m.Mz;
}
return(mass > precursorMass);
});
}
return(t);
}
public PeakList <T> Process(PeakList <T> t)
{
if (t.PrecursorCharge > 0)
{
var isobaricList = new List <T>();
var mzPrecursor = PrecursorUtils.ppm2mz(t.PrecursorMZ, options.PPMTolerance);
var precursurIons = FindPeakConsideringCharge(t, t.PrecursorMZ, t.PrecursorCharge, mzPrecursor);
//First of all, we need to find precursor
if (precursurIons.Count > 0)
{
precursurIons.ForEach(m => { t.Remove(m); });
isobaricList.Add(new T()
{
Mz = t.PrecursorMZ,
Charge = t.PrecursorCharge,
Intensity = mzPrecursor
});
if (options.RemoveChargeMinus1Precursor && t.PrecursorCharge > 1)
{
//Get charge-1 precursor
var p1mz = PrecursorUtils.MHToMz(PrecursorUtils.MzToMH(t.PrecursorMZ, t.PrecursorCharge, true), t.PrecursorCharge - 1, true);
var p1Window = PrecursorUtils.ppm2mz(p1mz, options.PPMTolerance);
var p1Ions = FindPeakConsideringCharge(t, p1mz, t.PrecursorCharge - 1, p1Window);
if (p1Ions.Count > 0)
{
p1Ions.ForEach(m => { t.Remove(m); });
isobaricList.Add(new T()
{
Mz = p1mz,
Charge = t.PrecursorCharge - 1,
Intensity = p1Window
});
}
}
if (options.RemoveIsotopicIons)
{
foreach (var ion in isobaricList)
{
RemoveIsotopicIons(t, ion);
}
}
}
foreach (var offset in offsets)
{
var mz = t.PrecursorMZ + offset / t.PrecursorCharge;
var mzWindow = PrecursorUtils.ppm2mz(mz, options.PPMTolerance);
var minMz = mz - mzWindow;
var maxMz = mz + mzWindow;
t.RemoveAll(m =>
{
if (m.Charge == t.PrecursorCharge || m.Charge == 0)
{
return(m.Mz >= minMz && m.Mz <= maxMz);
}
else
{
return(false);
}
});
}
if (options.RemoveIonLargerThanPrecursor)
{
var pmass = PrecursorUtils.MzToMH(t.PrecursorMZ, t.PrecursorCharge, true);
t.RemoveAll(m =>
{
var mass = m.Charge > 0 ? PrecursorUtils.MzToMH(m.Mz, m.Charge, true) : m.Mz;
return(mass >= pmass);
});
}
}
return(t);
}
public PeakList <T> Process(PeakList <T> t)
{
t.RemoveAll(m => m.Mz >= minMass && m.Mz <= maxMass);
return(t);
}
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);
}
