public PrositMS2Spectrum(SrmSettings settings, PrositIntensityModel.PeptidePrecursorNCE peptidePrecursorNCE,
int precursorIndex, PrositIntensityModel.PrositIntensityOutput prositIntensityOutput, IsotopeLabelType labelTypeOverride = null)
{
PeptidePrecursorNCE = peptidePrecursorNCE;
Settings = settings;
var precursor = peptidePrecursorNCE.NodeGroup;
var peptide = peptidePrecursorNCE.NodePep;
var calc = settings.GetFragmentCalc(IsotopeLabelType.light, peptide.ExplicitMods);
var ionTable = calc.GetFragmentIonMasses(peptide.Target); // TODO: get mods and pass them as explicit mods above?
var ions = ionTable.GetLength(1);
var mis = new List <SpectrumPeaksInfo.MI>(ions * PrositConstants.IONS_PER_RESIDUE);
for (int i = 0; i < ions; ++i)
{
var intensities = prositIntensityOutput.OutputRows[precursorIndex].Intensities[i].Intensities
.Select(ReLu).ToArray();
var yMIs = CalcMIs(ionTable[IonType.y, ions - i - 1], intensities, 0);
var bMIs = CalcMIs(ionTable[IonType.b, i], intensities, PrositConstants.IONS_PER_RESIDUE / 2);
mis.AddRange(yMIs);
mis.AddRange(bMIs);
}
var maxIntensity = mis.Max(mi => mi.Intensity);
// Max Norm
for (int i = 0; i < mis.Count; ++i)
{
mis[i] = new SpectrumPeaksInfo.MI {
Mz = mis[i].Mz, Intensity = mis[i].Intensity / maxIntensity
}
}
;
SpectrumPeaks = new SpectrumPeaksInfo(mis.ToArray());
}
public PrositMS2Spectra(SrmSettings settings, IList <PrositIntensityModel.PeptidePrecursorNCE> peptidePrecursorPairs, PrositIntensityModel.PrositIntensityOutput prositIntensityOutput)
{
Spectra = new PrositMS2Spectrum[peptidePrecursorPairs.Count];
for (int i = 0; i < peptidePrecursorPairs.Count; ++i)
{
Spectra[i] = new PrositMS2Spectrum(settings, peptidePrecursorPairs[i], i, prositIntensityOutput);
}
}
