int CMSPeak::Read(const CMSSpectrum& Spectrum,
const CMSSearchSettings& Settings)
{
try {
SetTolerance(Settings.GetMsmstol());
SetPrecursorTol(Settings.GetPeptol());
// note that there are two scales -- input scale and computational scale
// Precursormz = MSSCALE * (Spectrum.GetPrecursormz()/(double)MSSCALE);
// for now, we assume one scale
Precursormz = Spectrum.GetPrecursormz();
const CMSSpectrum::TMz& Mz = Spectrum.GetMz();
const CMSSpectrum::TAbundance& Abundance = Spectrum.GetAbundance();
SetPeakLists()[eMSPeakListOriginal]->CreateLists(Mz.size());
int i;
for (i = 0; i < SetPeakLists()[eMSPeakListOriginal]->GetNum(); i++) {
// for now, we assume one scale
SetPeakLists()[eMSPeakListOriginal]->GetMZI()[i].SetMZ() = Mz[i];
SetPeakLists()[eMSPeakListOriginal]->GetMZI()[i].SetIntensity() = Abundance[i];
}
SetPeakLists()[eMSPeakListOriginal]->Sort(eMSPeakListSortMZ);
}
catch (NCBI_NS_STD::exception& e) {
ERR_POST(Info << "Exception in CMSPeak::Read: " << e.what());
throw;
}
return 0;
}
// Initialization Funciton
void LINEAR_SOLVER::Initialize(const T& tolerance_input, const int& max_iteration_input, MULTITHREADING* multithreading_input)
{
multithreading = multithreading_input;
max_iteration = max_iteration_input;
SetTolerance(tolerance_input);
}
