public void CombineLikeMZPeaks(List <MZPeak> peaks, double value)
{
if (peaks.Count > 0)
{
double currentMZ = peaks[0].MZ;
double totalIntensity = peaks[0].Intensity;
List <MZPeak> combinedPeaks = new List <MZPeak>();
for (int i = 1; i < peaks.Count; i++)
{
MZPeak currentPeak = peaks[i];
if (Math.Round(currentPeak.MZ) == Math.Round(currentMZ))
{
totalIntensity += currentPeak.Intensity;
}
else
{
MZPeak newPeak = new MZPeak(Math.Round(currentMZ), totalIntensity);
combinedPeaks.Add(newPeak);
currentMZ = Math.Round(currentPeak.MZ);
totalIntensity = currentPeak.Intensity;
}
}
MZPeak peak = new MZPeak(currentMZ, totalIntensity);
combinedPeaks.Add(peak);
peaks.Clear();
peaks.AddRange(combinedPeaks);
NormalizePeaksOnlyIntensities(peaks, value);
}
}
public RTPeak(MZPeak peak, double RT)
{
this._Intensity = peak.Intensity;
this._MZ = peak.MZ;
this._RT = RT;
this._peak = peak;
}
public double GetPrecusorMz(int spectrumNumber, double searchMZ, int msnOrder = 2)
{
int parentScanNumber = GetParentSpectrumNumber(spectrumNumber);
var ms1Scan = GetSpectrum(parentScanNumber);
MZPeak peak = ms1Scan.GetClosestPeak(MassRange.FromDa(searchMZ, 50));
if (peak != null)
{
return(peak.MZ);
}
return(double.NaN);
}
public Feature(MZPeak firstPeak, double RT, double HCDEnergy = 0)
{
this.allRTPeaks = new List <RTPeak>();
this.smoothRTPeaks = new List <RTPeak>();
this.minRT = RT;
this.maxRT = RT;
RTPeak newRTPeak = new RTPeak(firstPeak, RT);
this.allRTPeaks.Add(newRTPeak);
this.maxPeak = newRTPeak;
this.totalMZTimesIntensity += (firstPeak.Intensity * firstPeak.MZ);
this.totalIntensity += (firstPeak.Intensity);
this.averageMZ = firstPeak.MZ;
newRTPeak.HCDEnergy = HCDEnergy;
}
public void AddPeak(MZPeak peak, double RT, double HCDEnergy = 0)
{
RTPeak newRTPeak = new RTPeak(peak, RT);
this.allRTPeaks.Add(newRTPeak);
if (peak.Intensity > maxPeak.Intensity)
{
apexTime = RT;
maxPeak = newRTPeak;
}
this.maxRT = RT;
this.totalMZTimesIntensity += (peak.Intensity * peak.MZ);
this.totalIntensity += (peak.Intensity);
this.averageMZ = (this.totalMZTimesIntensity / this.totalIntensity);
newRTPeak.HCDEnergy = HCDEnergy;
}
public List <MZPeak> GetPeaksFromNearestSpectrum(FeatureGroup group, ThermoRawFile rawFile)
{
int scanNum = rawFile.GetSpectrumNumber(group.ApexTime);
List <MZPeak> returnPeaks = new List <MZPeak>();
ThermoSpectrum spectrum = rawFile.GetLabeledSpectrum(scanNum);
HashSet <double> peakMZs = new HashSet <double>();
foreach (Feature feature in group.allFeatures)
{
MZPeak outPeak = spectrum.GetClosestPeak(MassRange.FromPPM(feature.AverageMZ, 10));
if (outPeak != null)
{
if (!peakMZs.Contains(outPeak.Intensity))
{
returnPeaks.Add(new MZPeak(feature.AverageMZ, outPeak.Intensity));
peakMZs.Add(outPeak.Intensity);
}
}
}
returnPeaks = returnPeaks.OrderBy(x => x.MZ).ToList();
return(returnPeaks);
}
private void MatchPeaks(List <Feature> features, MZPeak[] currentPeaks, double ppmTolerance, double rt, bool allowMultipleFeatureMatches = false)
{
if (features == null || currentPeaks == null)
{
return;
}
int fCount = features.Count;
if (fCount == 0)
{
features.AddRange(currentPeaks.Select(p => new Feature(p, rt)));
return;
}
int cCount = currentPeaks.Length;
if (cCount == 0)
{
return;
}
int c = 0;
int f = 0;
Feature feature = features[f];
double featureMZ = feature.AverageMZ;
MZPeak cPeak = currentPeaks[c];
ppmTolerance /= 2e6;
double tolerance = cPeak.MZ * ppmTolerance;
double lowmz = cPeak.MZ - tolerance;
List <Feature> featuresToAdd = new List <Feature>(cCount);
while (true)
{
if (featureMZ < lowmz)
{
if (++f == fCount) // Feature mz is to small, go to the next one
{
break; // no more features, so just break out now
}
feature = features[f];
featureMZ = feature.AverageMZ;
continue; // keep the current peak, so continue the loop right away
}
if (featureMZ < cPeak.MZ + tolerance)
{
feature.AddPeak(cPeak, rt); // Peak matches feature, add it to the feature
if (!allowMultipleFeatureMatches)
{
if (++f == fCount) // Feature mz is to small, go to the next one
{
break; // no more features, so just break out now
}
feature = features[f];
featureMZ = feature.AverageMZ;
}
}
else
{
// Peak didn't match any features, so save this peak to start a new feature
featuresToAdd.Add(new Feature(cPeak, rt));
}
if (++c == cCount)
{
break; // no more current peaks, so just break out now
}
cPeak = currentPeaks[c];
tolerance = cPeak.MZ * ppmTolerance;
lowmz = cPeak.MZ - tolerance;
}
// Append unmatched peaks as new features
features.AddRange(featuresToAdd);
// Add left over peaks as new features
while (c < cCount)
{
features.Add(new Feature(currentPeaks[c++], rt));
}
}
