/// <summary>
/// This function ranks peaks based on the increasing order of intenstiy.
/// </summary>
/// <param name="peaks">Peaks in spectrum</param>
/// <returns>Ranked peaks</returns>
public static Set <Peak> rankPeaks(List <Peak> peaks)
{
Stack <Peak> rankedPeaks = new Stack <Peak>();
IntensityComparer intensitySorter = new IntensityComparer(SortOrder.ASCENDING);
peaks.Sort(intensitySorter);
int peakCount = 1;
foreach (var peak in peaks)
{
Peak newPeak = new Peak(peak);
newPeak.rankOrIntensity = peakCount;
if (rankedPeaks.Count > 0)
{
Peak lastPeak = rankedPeaks.Peek();
if (lastPeak.rankOrIntensity == newPeak.rankOrIntensity)
{
newPeak.rankOrIntensity = lastPeak.rankOrIntensity;
}
}
rankedPeaks.Push(newPeak);
++peakCount;
}
Set <Peak> retPeaks = new Set <Peak>();
foreach (var peak in rankedPeaks)
{
retPeaks.Add(peak);
}
return(retPeaks);
}
/// <summary>
/// This function takes top N intense peaks to meet the target TIC.
/// </summary>
/// <param name="peaks">Peaks in the spectrum</param>
/// <param name="percentTIC">Percentage of total ion current to be retained</param>
/// <returns></returns>
public static List <Peak> filterByPercentTIC(List <Peak> peaks, double percentTIC)
{
// Compute the total ion current in the spectrum
double totalTIC = 0.0;
foreach (var peak in peaks)
{
totalTIC += peak.rankOrIntensity;
}
// Sort the peaks by descending order of intensity and take as many peaks as
// possible to meet the target TIC.
IntensityComparer intensitySorter = new IntensityComparer(SortOrder.DESCENDING);
peaks.Sort(intensitySorter);
List <Peak> finalList = new List <Peak>();
double TICSoFar = 0.0;
foreach (var peak in peaks)
{
TICSoFar += peak.rankOrIntensity;
if ((TICSoFar / totalTIC) >= percentTIC)
{
break;
}
finalList.Add(peak);
}
MassComparer mzComparer = new MassComparer(SortOrder.ASCENDING);
finalList.Sort(mzComparer);
return(finalList);
}
// End comparators for Peak
/// <summary>
/// This function takes top N intense peaks from each spectrum
/// </summary>
/// <param name="peaks">Spectrum peaks</param>
/// <param name="numPeaks">Number of peaks to be retained</param>
/// <returns></returns>
public static List <Peak> filterByPeakCount(List <Peak> peaks, int numPeaks)
{
// Sort the peaks by decreasing order of intensity and take numPeaks
IntensityComparer intensitySorter = new IntensityComparer(SortOrder.DESCENDING);
peaks.Sort(intensitySorter);
List <Peak> finalList = new List <Peak>();
foreach (var peak in peaks)
{
if (numPeaks == 0)
{
break;
}
--numPeaks;
finalList.Add(peak);
}
MassComparer mzComparer = new MassComparer(SortOrder.ASCENDING);
finalList.Sort(mzComparer);
return(finalList);
}
