public static float[] IntegrateTranslatedPeak(Peak peak, double delta, SpectrumCache spectrumCache,
IRawFile rawFile, bool subtractBackground,
int backgroundSubtractionQuantile)
{
int[] scanIndices = peak.GetScanIndices();
float[] intensities = peak.GetOriginalIntensities();
int q = ArrayUtil.MaxInd(intensities);
float maxInt = intensities[q];
int maxScanIndex = scanIndices[q];
float[] result = new float[scanIndices.Length];
for (int i = 0; i < scanIndices.Length; i++)
{
int scanIndex = scanIndices[i];
if (intensities[i] < maxInt * 0.01)
{
continue;
}
if (scanIndex > maxScanIndex + 20 || scanIndex < maxScanIndex - 20)
{
continue;
}
Spectrum spectrum;
if (!spectrumCache.ContainsScanIndex(scanIndex))
{
spectrum = rawFile.GetMS1Spectrum(scanIndex, subtractBackground, backgroundSubtractionQuantile);
spectrumCache.Add(scanIndex, spectrum);
}
else
{
spectrum = spectrumCache[scanIndex];
}
double minMass = peak.GetMinMass(i) + delta;
double maxMass = peak.GetMaxMass(i) + delta;
int minInd = spectrum.GetCeilIndex(minMass);
int maxInd = spectrum.GetFloorIndex(maxMass);
if (minInd == -1 || maxInd == -1)
{
result[i] = 0;
}
else
{
float[] intensityProfile = new float[maxInd - minInd + 1];
for (int ind = minInd; ind <= maxInd; ind++)
{
intensityProfile[ind - minInd] = spectrum.GetIntensity(ind);
}
result[i] = IntegrateProfile(intensityProfile, T01PeakDetection.maxIntensity);
}
}
return(result);
}
