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 static List <MZPeak> ConvertPeakListString(string peakList)
{
List <MZPeak> returnList = new List <MZPeak>();
string[] parts = peakList.Split(';');
foreach (var part in parts)
{
if (!string.IsNullOrEmpty(part))
{
string[] subparts = part.Split(',');
double mz = double.Parse(subparts[0]);
double intensity = double.Parse(subparts[1]);
var newPeak = new MZPeak(mz, intensity);
returnList.Add(newPeak);
}
}
return(returnList);
}
