/**
* Filters spectrum by number of highest abundance ions and by base peak percentage
* @param s spectrum
* @param topIons number of top ions to retain
* @param basePeakPercentage percentage of base peak above which to retain
* @return filtered spectrum
*/
protected ISpectrum filterSpectrum(ISpectrum s, int topIons, double basePeakPercentage)
{
List <Ion> ions = s.GetIons();
// Find base peak intensity
double basePeakIntensity = 0.0;
foreach (Ion ion in ions)
{
if (ion.Intensity > basePeakIntensity)
{
basePeakIntensity = ion.Intensity;
}
}
// Filter by base peak percentage if needed
if (basePeakPercentage >= 0)
{
List <Ion> filteredIons = new List <Ion>();
foreach (Ion ion in ions)
{
if (ion.Intensity + EPSILON >= basePeakPercentage * basePeakIntensity)
{
filteredIons.Add(new Ion(ion.MZ, ion.Intensity));
}
}
ions = filteredIons;
}
// Filter by top ions if necessary
if (topIons > 0 && ions.Count > topIons)
{
ions = ions.OrderByDescending(i => i.Intensity).ThenBy(m => m.MZ).ToList();
ions = ions.GetRange(0, topIons);
}
return(new MSSpectrum(ions));
}
/**
* Filters spectrum by number of highest abundance ions and by base peak percentage
* @param s spectrum
* @param topIons number of top ions to retain
* @param basePeakPercentage percentage of base peak above which to retain
* @return filtered spectrum
*/
protected ISpectrum filterSpectrum(ISpectrum s, int topIons, double basePeakPercentage)
{
List<Ion> ions = s.GetIons();
// Find base peak intensity
double basePeakIntensity = 0.0;
foreach (Ion ion in ions)
{
if (ion.Intensity > basePeakIntensity)
basePeakIntensity = ion.Intensity;
}
// Filter by base peak percentage if needed
if (basePeakPercentage >= 0)
{
List<Ion> filteredIons = new List<Ion>();
foreach (Ion ion in ions)
{
if (ion.Intensity + EPSILON >= basePeakPercentage * basePeakIntensity)
filteredIons.Add(new Ion(ion.MZ, ion.Intensity));
}
ions = filteredIons;
}
// Filter by top ions if necessary
if (topIons > 0 && ions.Count > topIons)
{
ions = ions.OrderByDescending(i => i.Intensity).ThenBy(m => m.MZ).ToList();
ions = ions.GetRange(0, topIons);
}
return new MSSpectrum(ions);
}