public void GetRatioBasedOnTopPeaks(IsotopicProfile iso1, IsotopicProfile iso2,
IsotopicProfile theorIso1, IsotopicProfile theorIso2, double backgroundIntensity, int numPeaks,
out double ratio, out double ratioContribForIso1, out double ratioContribForIso2)
{
//Find top n peaks of the theor profile. Reference them by their peak index so that they can be looked up in the experimental.
//List<int> sortedTheorIso1Indexes = getIndexValsOfTopPeaks(theorIso1);
//List<int> sortedTheorIso2Indexes = getIndexValsOfTopPeaks(theorIso2);
IList <Peak> topTheorIso1Peaks = GetTopPeaks(theorIso1, numPeaks);
IList <Peak> topTheorIso2Peaks = GetTopPeaks(theorIso2, numPeaks);
//get the top n peaks of the experimental profile, based on peaks of the theor profile
//adjust intensity (subtract background intensity)
var topIso1Peaks = GetTopPeaksBasedOnTheor(iso1, topTheorIso1Peaks, MSToleranceInPPM);
var topIso2Peaks = GetTopPeaksBasedOnTheor(iso2, topTheorIso2Peaks, MSToleranceInPPM);
//Since the number of top experimental iso peaks may be less than the number of top theor iso peaks,
//we have to filter and ensure that they have the same peak numbers, so that the correction factor
// (applied below) is properly applied. HOWEVER, this may induce some differences between runs
var filteredTopTheorIso1Peaks = GetTopPeaksBasedOnTheor(theorIso1, topIso1Peaks, MSToleranceInPPM);
var filteredTopTheorIso2Peaks = GetTopPeaksBasedOnTheor(theorIso2, topIso2Peaks, MSToleranceInPPM);
var summedTopIso1PeakIntensities = PeakUtilities.GetSumOfIntensities(topIso1Peaks, backgroundIntensity);
var summedTopIso2PeakIntensities = PeakUtilities.GetSumOfIntensities(topIso2Peaks, backgroundIntensity);
//Console.WriteLine(backgroundIntensity);
//need to find out the contribution of the top n peaks to the overall isotopic envelope. Base this on the theor profile
double summedTheorIso1Intensities = filteredTopTheorIso1Peaks.Sum(p => (p.Height));
double summedTheorIso2Intensities = filteredTopTheorIso2Peaks.Sum(p => (p.Height));
var fractionTheor1 = summedTheorIso1Intensities / theorIso1.Peaklist.Sum(p => p.Height);
var fractionTheor2 = summedTheorIso2Intensities / theorIso2.Peaklist.Sum(p => p.Height);
//use the above ratio to correct the intensities based on how much the top n peaks contribute to the profile.
var correctedIso1SummedIntensity = summedTopIso1PeakIntensities / fractionTheor1;
var correctedIso2SummedIntensity = summedTopIso2PeakIntensities / fractionTheor2;
var summedAllIsos1PeakIntensities = iso1.Peaklist.Sum(p => (p.Height - backgroundIntensity));
var summedAllIsos2PeakIntensities = iso2.Peaklist.Sum(p => (p.Height - backgroundIntensity));
switch (RatioType)
{
case RatioType.ISO1_OVER_ISO2:
ratio = correctedIso1SummedIntensity / correctedIso2SummedIntensity;
break;
case RatioType.ISO2_OVER_ISO1:
ratio = correctedIso2SummedIntensity / correctedIso1SummedIntensity;
break;
default:
ratio = correctedIso1SummedIntensity / correctedIso2SummedIntensity;
break;
}
ratioContribForIso1 = summedTopIso1PeakIntensities / summedAllIsos1PeakIntensities * 1 / fractionTheor1; //we expect a value of '1'
ratioContribForIso2 = summedTopIso2PeakIntensities / summedAllIsos2PeakIntensities * 1 / fractionTheor2;
}