/**
@brief Applies the peak-picking algorithm to a map (MSExperiment). This
method picks peaks for each scan in the map consecutively. The resulting
picked peaks are written to the output map.
Currently we have to give up const-correctness but we know that everything on disc is constant
*/
void PeakPickerHiRes::pickExperiment(/* const */ OnDiscMSExperiment& input, PeakMap& output, const bool check_spectrum_type) const
{
// make sure that output is clear
output.clear(true);
// copy experimental settings
static_cast<ExperimentalSettings &>(output) = *input.getExperimentalSettings();
Size progress = 0;
startProgress(0, input.size() + input.getNrChromatograms(), "picking peaks");
// resize output with respect to input
output.resize(input.size());
if (input.getNrSpectra() > 0)
{
for (Size scan_idx = 0; scan_idx != input.size(); ++scan_idx)
{
if (ms_levels_.empty()) //auto mode
{
MSSpectrum s = input[scan_idx];
s.sortByPosition();
// determine type of spectral data (profile or centroided)
SpectrumSettings::SpectrumType spectrumType = s.getType();
if (spectrumType == SpectrumSettings::CENTROID)
{
output[scan_idx] = input[scan_idx];
}
else
{
pick(s, output[scan_idx]);
}
}
else if (!ListUtils::contains(ms_levels_, input[scan_idx].getMSLevel())) // manual mode
{
output[scan_idx] = input[scan_idx];
}
else
{
MSSpectrum s = input[scan_idx];
s.sortByPosition();
// determine type of spectral data (profile or centroided)
SpectrumSettings::SpectrumType spectrum_type = s.getType();
if (spectrum_type == SpectrumSettings::CENTROID && check_spectrum_type)
{
throw OpenMS::Exception::IllegalArgument(__FILE__, __LINE__, __FUNCTION__, "Error: Centroided data provided but profile spectra expected.");
}
pick(s, output[scan_idx]);
}
setProgress(++progress);
}
}
for (Size i = 0; i < input.getNrChromatograms(); ++i)
{
MSChromatogram chromatogram;
pick(input.getChromatogram(i), chromatogram);
output.addChromatogram(chromatogram);
setProgress(++progress);
}
endProgress();
return;
}
/**
* @brief Applies the peak-picking algorithm to a map (MSExperiment). This
* method picks peaks for each scan in the map consecutively. The resulting
* picked peaks are written to the output map.
*
* @param input input map in profile mode
* @param output output map with picked peaks
* @param boundaries_spec boundaries of the picked peaks in spectra
* @param boundaries_chrom boundaries of the picked peaks in chromatograms
* @param check_spectrum_type if set, checks spectrum type and throws an exception if a centroided spectrum is passed
*/
void PeakPickerHiRes::pickExperiment(const PeakMap& input, PeakMap& output,
std::vector<std::vector<PeakBoundary> >& boundaries_spec,
std::vector<std::vector<PeakBoundary> >& boundaries_chrom,
const bool check_spectrum_type) const
{
// 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());
Size progress = 0;
startProgress(0, input.size() + input.getChromatograms().size(), "picking peaks");
if (input.getNrSpectra() > 0)
{
for (Size scan_idx = 0; scan_idx != input.size(); ++scan_idx)
{
if (ms_levels_.empty()) // auto mode
{
SpectrumSettings::SpectrumType spectrum_type = input[scan_idx].getType();
if (spectrum_type == SpectrumSettings::CENTROID)
{
output[scan_idx] = input[scan_idx];
}
else
{
std::vector<PeakBoundary> boundaries_s; // peak boundaries of a single spectrum
pick(input[scan_idx], output[scan_idx], boundaries_s);
boundaries_spec.push_back(boundaries_s);
}
}
else if (!ListUtils::contains(ms_levels_, input[scan_idx].getMSLevel())) // manual mode
{
output[scan_idx] = input[scan_idx];
}
else
{
std::vector<PeakBoundary> boundaries_s; // peak boundaries of a single spectrum
// determine type of spectral data (profile or centroided)
SpectrumSettings::SpectrumType spectrum_type = input[scan_idx].getType();
if (spectrum_type == SpectrumSettings::CENTROID && check_spectrum_type)
{
throw OpenMS::Exception::IllegalArgument(__FILE__, __LINE__, __FUNCTION__, "Error: Centroided data provided but profile spectra expected.");
}
pick(input[scan_idx], output[scan_idx], boundaries_s);
boundaries_spec.push_back(boundaries_s);
}
setProgress(++progress);
}
}
for (Size i = 0; i < input.getChromatograms().size(); ++i)
{
MSChromatogram chromatogram;
std::vector<PeakBoundary> boundaries_c; // peak boundaries of a single chromatogram
pick(input.getChromatograms()[i], chromatogram, boundaries_c);
output.addChromatogram(chromatogram);
boundaries_chrom.push_back(boundaries_c);
setProgress(++progress);
}
endProgress();
return;
}