void OpenSwathDataAccessHelper::convertToOpenMSChromatogram(OpenMS::MSChromatogram<> & chromatogram, const OpenSwath::ChromatogramPtr cptr)
{
OpenSwath::BinaryDataArrayPtr rt_arr = cptr->getTimeArray();
OpenSwath::BinaryDataArrayPtr int_arr = cptr->getIntensityArray();
chromatogram.reserve(rt_arr->data.size());
for (Size i = 0; i < rt_arr->data.size(); i++)
{
ChromatogramPeak p;
p.setRT(rt_arr->data[i]);
p.setIntensity(int_arr->data[i]);
chromatogram.push_back(p);
}
}
void PeakPickerHiRes::pick(const MSChromatogram& input, MSChromatogram& output, std::vector<PeakBoundary>& boundaries) const
{
// copy meta data of the input chromatogram
output.clear(true);
output.ChromatogramSettings::operator=(input);
output.MetaInfoInterface::operator=(input);
output.setName(input.getName());
MSSpectrum input_spectrum;
MSSpectrum output_spectrum;
for (MSChromatogram::const_iterator it = input.begin(); it != input.end(); ++it)
{
Peak1D p;
p.setMZ(it->getRT());
p.setIntensity(it->getIntensity());
input_spectrum.push_back(p);
}
pick(input_spectrum, output_spectrum, boundaries, false); // no spacing checks!
for (MSSpectrum::const_iterator it = output_spectrum.begin(); it != output_spectrum.end(); ++it)
{
ChromatogramPeak p;
p.setRT(it->getMZ());
p.setIntensity(it->getIntensity());
output.push_back(p);
}
// copy float data arrays (for FWHM)
output.getFloatDataArrays().resize(output_spectrum.getFloatDataArrays().size());
for (Size i = 0; i < output_spectrum.getFloatDataArrays().size(); ++i)
{
output.getFloatDataArrays()[i].insert(output.getFloatDataArrays()[i].begin(), output_spectrum.getFloatDataArrays()[i].begin(), output_spectrum.getFloatDataArrays()[i].end());
output.getFloatDataArrays()[i].setName(output_spectrum.getFloatDataArrays()[i].getName());
}
}
