void PeakPickerSH::pickExperiment(const MSExperiment<> & input, MSExperiment<> & output)
{
// make sure that output is clear
output.clear(true);
// copy experimental settings
static_cast<ExperimentalSettings &>(output) = input;
// resize output with respect to input
output.resize(input.size());
std::cout << "Before loop, input size = " << input.size() << std::endl;
Size progress = 0;
for (Size scan_idx = 0; scan_idx != input.size(); ++scan_idx)
{
output[scan_idx].clear(true);
output[scan_idx].SpectrumSettings::operator=(input[scan_idx]);
output[scan_idx].MetaInfoInterface::operator=(input[scan_idx]);
output[scan_idx].setRT(input[scan_idx].getRT());
output[scan_idx].setMSLevel(input[scan_idx].getMSLevel());
output[scan_idx].setName(input[scan_idx].getName());
output[scan_idx].setType(SpectrumSettings::PEAKS);
if (input[scan_idx].getMSLevel() != 1)
{
// When not considering MS2 data (MS2 fragment mass tracing=0), Lukas leaves out
// the entire scan (instead of just copying it to the output as seen in
// another plugin).
// pick(input[scan_idx], output[scan_idx], 4.0);
}
else
{
// TODO: Read value 4.0 from parameters # PeakPickerSH.cpp
pick(input[scan_idx], output[scan_idx], 5.0);
}
setProgress(++progress);
}
std::cout << "After loop" << std::endl;
endProgress();
}
