public void GenerateiRTChromatogram(Run run)
{
foreach (IRTPeak irtpeak in run.IRTPeaks)
{
float TotalFWHM = 0;
float Totalpeaksym = 0;
int count = 0;
foreach (var transition in irtpeak.AssociatedTransitions)
{
starttimes = irtpeak.Spectrum.Where(x => Math.Abs(x.Mz - transition.ProductMz) < run.AnalysisSettings.MassTolerance && Math.Abs(x.RetentionTime - irtpeak.RetentionTime) < run.AnalysisSettings.RtTolerance).Select(x => (double)x.RetentionTime).ToArray();
intensities = irtpeak.Spectrum.Where(x => Math.Abs(x.Mz - transition.ProductMz) < run.AnalysisSettings.MassTolerance).Select(x => (double)x.Intensity).ToArray();
cPF = new CrawdadSharp.CrawdadPeakFinder();
cPF.SetChromatogram(starttimes, intensities);
crawPeaks = cPF.CalcPeaks();
foreach (CrawdadSharp.CrawdadPeak crawPeak in crawPeaks)
{
TotalFWHM += crawPeak.Fwhm;
if (crawPeak.Fvalue > 0)
{
Totalpeaksym += crawPeak.Fwfpct / (crawPeak.Fvalue * 2);
}
else
{
Totalpeaksym += crawPeak.Fwfpct;
}
count++;
}
}
irtpeak.FWHM = TotalFWHM / count; //average fwhm
irtpeak.Peaksym = Totalpeaksym / count; //Because we have ordered the possible peaks according to their intensities, this value corresponds to their intensity rank
}
}
public void GenerateChromatogram(Run run)
{
//Crawdad
foreach (BasePeak basepeak in run.BasePeaks)
{
//for each peak within the spectrum
for (int yyy = 0; yyy < basepeak.BpkRTs.Count(); yyy++)
{
//change these two arrays to be only the spectra surrounding that bpkrt:
intensities = basepeak.Spectrum.Where(x => Math.Abs(x.RetentionTime - basepeak.BpkRTs[yyy]) < run.AnalysisSettings.RtTolerance).Select(x => (double)x.Intensity).ToArray();
starttimes = basepeak.Spectrum.Where(x => Math.Abs(x.RetentionTime - basepeak.BpkRTs[yyy]) < run.AnalysisSettings.RtTolerance).Select(x => (double)x.RetentionTime).ToArray();
if (intensities.Count() > 1)
{
RTandInt inter = new RTandInt();
inter = Interpolate(starttimes, intensities);
starttimes = inter.starttimes;
intensities = inter.intensities;
}
cPF = new CrawdadSharp.CrawdadPeakFinder();
cPF.SetChromatogram(starttimes, intensities);
crawPeaks = cPF.CalcPeaks();
double totalFwhm = 0;
double totalPeakSym = 0;
double totalBaseWidth = 0;
foreach (CrawdadSharp.CrawdadPeak crawPeak in crawPeaks)
{
double peakTime = starttimes[crawPeak.TimeIndex];
double fwhm = crawPeak.Fwhm;
double fvalue = crawPeak.Fvalue;
if (fwhm == 0)
{
continue;
}
else if (fvalue != 0)
{
totalPeakSym += crawPeak.Fwfpct / (2 * crawPeak.Fvalue); //From USP31: General Chapters <621> Chromatography equation for calculating the tailing factor(Available at: http://www.uspbpep.com/usp31/v31261/usp31nf26s1_c621.asp). A high value means that the peak is highly asymmetrical.
}
totalFwhm += fwhm;
if (!float.IsNaN(crawPeak.FwBaseline))
{
totalBaseWidth += crawPeak.FwBaseline;
}
else
{
totalBaseWidth += crawPeak.Fwfpct;
}
}
if (crawPeaks.Count() > 0)
{
basepeak.FWHMs.Add(totalFwhm / crawPeaks.Count());
basepeak.Peaksyms.Add(totalPeakSym / crawPeaks.Count());
basepeak.FullWidthBaselines.Add(totalBaseWidth / crawPeaks.Count());
}
else
{
basepeak.FWHMs.Add(0);
basepeak.FullWidthBaselines.Add(0);
basepeak.Peaksyms.Add(0);
}
}
}
}