PeakType fillPeak(double rt, double mz, double it)
{
PeakType p;
p.setIntensity((OpenMS::Peak2D::IntensityType)it);
p.setMZ(mz);
p.setRT((rt));
return p;
}
MSSpectrum<FeatureFinderAlgorithmIsotopeWavelet::PeakType>* FeatureFinderAlgorithmIsotopeWavelet::createHRData(const UInt i)
{
MSSpectrum<PeakType> spec((*this->map_)[i]);
const MSSpectrum<PeakType>& specr((*this->map_)[i]);
for (UInt j = 0; j < spec.size() - 1; ++j)
{
spec[j].setMZ(-1 * (specr[j + 1].getMZ() - specr[j].getMZ()));
spec[j].setIntensity((specr[j].getIntensity() + specr[j + 1].getIntensity()));
}
spec[spec.size() - 1].setMZ(-1); spec[spec.size() - 1].setIntensity(-1);
ConstRefVector<MSSpectrum<PeakType> > c_sorted_spec(spec.begin(), spec.end());
//Sort in ascending order according to the intensities present in the transform
c_sorted_spec.sortByPosition();
#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET
std::ofstream ofilex("spacings.trans");
for (UInt j = 0; j < spec.size() - 1; ++j)
{
ofilex << ::std::setprecision(12) << std::fixed << spec[j].getMZ() << "\t" << spec[j].getIntensity() << std::endl;
}
ofilex.close();
#endif
UInt pos = 0;
while (c_sorted_spec[pos].getIntensity() <= 0)
{
if (++pos >= c_sorted_spec.size())
{
std::cout << "Detected empty scan or a scan that cannot be interpolated with zeros in HR mode. " << std::endl;
std::cout << "Please check scan # " << i << " of your data set." << std::endl;
exit(-1);
}
}
double bound = -1 * c_sorted_spec[pos].getMZ();
if (bound > (1. / max_charge_) / 2.)
{
//that might be case for simulated spectra,
//which might show a very artificial spacing
bound = (1. / max_charge_) / 2. / 4.;
}
MSSpectrum<PeakType>* new_spec = new MSSpectrum<PeakType>;
new_spec->reserve(200000);
new_spec->setRT(((*this->map_)[i]).getRT());
PeakType p; p.setMZ(specr[0].getMZ()); p.setIntensity(specr[0].getIntensity());
new_spec->push_back(p);
UInt count;
for (UInt j = 0; j < spec.size() - 1; ++j)
{
count = 0;
while (-spec[j].getMZ() - count * bound > bound)
{
++count;
p.setMZ(specr[j].getMZ() + count * bound); p.setIntensity(0);
new_spec->push_back(p);
}
p.setMZ(specr[j + 1].getMZ()); p.setIntensity(specr[j + 1].getIntensity());
new_spec->push_back(p);
}
#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET
std::ofstream ofiley("new_spec.trans");
for (UInt j = 0; j < new_spec->size(); ++j)
{
ofiley << ::std::setprecision(12) << std::fixed << (*new_spec)[j].getMZ() << "\t" << (*new_spec)[j].getIntensity() << std::endl;
}
ofiley.close();
#endif
return new_spec;
}
void fillIntensity(PeakType& peak) const
{
peak.setIntensity(getIntensity(peak.getPosition()));
}
