public double Area(IResult glycan)
{
// search xic
double mz = glycan.GetMZ();
int scan = glycan.GetScan();
int charge = glycan.GetCharge();
// get neighbors
List <ISpectrum> neighbors = new List <ISpectrum>();
int nextScan = scan;
while (nextScan > spectrumReader.GetFirstScan())
{
if (spectrumReader.GetMSnOrder(nextScan) == 1)
{
ISpectrum spectrum = spectrumReader.GetSpectrum(nextScan);
int index = BinarySearch.Search(spectrum.GetPeaks(), mz, tol, by);
if (index < 0)
{
break;
}
neighbors.Add(spectrum);
}
nextScan--;
}
nextScan = scan + 1;
while (nextScan <= spectrumReader.GetLastScan())
{
if (spectrumReader.GetMSnOrder(nextScan) == 1)
{
ISpectrum spectrum = spectrumReader.GetSpectrum(nextScan);
int index = BinarySearch.Search(spectrum.GetPeaks(), mz, tol, by);
if (index < 0)
{
break;
}
neighbors.Add(spectrum);
}
nextScan++;
}
// each neighbor get top 3 peaks
List <double> topArea = new List <double>();
List <int> delta = new List <int>()
{
-2, -1, 0, 1, 2
};
foreach (ISpectrum spetrum in neighbors)
{
List <IPeak> top = new List <IPeak>();
foreach (int j in delta)
{
int index = BinarySearch.BestSearch(spetrum.GetPeaks(), mz + 1.0 / charge * j, tol, by);
if (index < 0)
{
continue;
}
top.Add(spetrum.GetPeaks()[index]);
}
topArea.Add(top.OrderByDescending(p => p.GetIntensity()).
Take(3).Select(p => p.GetIntensity()).Sum());
}
return(topArea.OrderByDescending(a => a).Take(3).Sum());
}
