public PeakList <T> Process(PeakList <T> t)
{
for (int i = t.Count - 1; i >= 0; i--)
{
if (t[i].Intensity < this.minIonIntensity)
{
t.RemoveAt(i);
}
}
if (0 == t.Count)
{
return(null);
}
else
{
return(t);
}
}
public void TestFindEnvelope()
{
var peaks = new PeakList <Peak>();
peaks.Add(new Peak(301, 1, 1));
peaks.Add(new Peak(302, 2, 1));
peaks.Add(new Peak(303, 1, 1));
peaks.Add(new Peak(304, 2, 1));
var env = this.FindEnvelope(peaks, peaks[0], 0.1);
Assert.AreEqual(3, env.Count);
Assert.IsTrue(!env.Contains(peaks[3]));
peaks.RemoveAt(0);
env = this.FindEnvelope(peaks, peaks[0], 0.1);
Assert.AreEqual(2, env.Count);
Assert.IsTrue(!env.Contains(peaks[2]));
}
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);
}
}
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);
}
