int main(int argc, const char** argv)
{
if (argc < 2) return 1;
// the path to the data should be given on the command line
String tutorial_data_path(argv[1]);
IndexedMzMLFileLoader imzml;
// load data from an indexed MzML file
OnDiscMSExperiment<> map;
imzml.load(tutorial_data_path + "/data/Tutorial_FileIO_indexed.mzML", map);
// Get the first spectrum in memory, do some constant (non-changing) data processing
MSSpectrum<> s = map.getSpectrum(0);
std::cout << "There are " << map.getNrSpectra() << " spectra in the input file." << std::endl;
std::cout << "The first spectrum has " << s.size() << " peaks." << std::endl;
// store the (unmodified) data in a different file
imzml.store("Tutorial_FileIO_output.mzML", map);
return 0;
} //end of main
TEST_EQUAL(tmp2.getExperimentalSettings()->getInstrument().getModel(), tmp.getExperimentalSettings()->getInstrument().getModel() )
TEST_EQUAL(tmp2.getExperimentalSettings()->getInstrument().getMassAnalyzers().size(), tmp.getExperimentalSettings()->getInstrument().getMassAnalyzers().size() )
TEST_EQUAL(tmp2.size(),tmp.size());
}
END_SECTION
START_SECTION((OnDiscMSExperiment(const String& filename)))
{
OnDiscMSExperiment<> tmp(OPENMS_GET_TEST_DATA_PATH("IndexedmzMLFile_1.mzML"));
TEST_EQUAL(tmp.size(), 2);
}
END_SECTION
START_SECTION((bool operator== (const OnDiscMSExperiment& rhs) const))
{
OnDiscMSExperiment<> tmp(OPENMS_GET_TEST_DATA_PATH("IndexedmzMLFile_1.mzML"));
OnDiscMSExperiment<> same(OPENMS_GET_TEST_DATA_PATH("IndexedmzMLFile_1.mzML"));
OnDiscMSExperiment<> failed(OPENMS_GET_TEST_DATA_PATH("MzMLFile_1.mzML"));
TEST_EQUAL(tmp==same, true);
TEST_EQUAL((*tmp.getExperimentalSettings())==(*same.getExperimentalSettings()), true);
TEST_EQUAL(tmp==failed, false);
}
END_SECTION
START_SECTION((bool operator!= (const OnDiscMSExperiment& rhs) const))
{
OnDiscMSExperiment<> tmp(OPENMS_GET_TEST_DATA_PATH("IndexedmzMLFile_1.mzML"));
OnDiscMSExperiment<> same(OPENMS_GET_TEST_DATA_PATH("IndexedmzMLFile_1.mzML"));
OnDiscMSExperiment<> failed(OPENMS_GET_TEST_DATA_PATH("MzMLFile_1.mzML"));
/**
@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;
}
