ExitCodes main_(int, const char**) override
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
String in = getStringOption_("in");
String out = getStringOption_("out");
IndexedMzMLFileLoader loader;
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
OnDiscPeakMap exp;
loader.load(in, exp);
// We could write out this warning in the constructor if no spectra have come our way ...
/*
if (ms_exp_raw.empty() && ms_exp_raw.getChromatograms().size() == 0)
{
LOG_WARN << "The given file does not contain any conventional peak data, but might"
" contain chromatograms. This tool currently cannot handle them, sorry.";
return INCOMPATIBLE_INPUT_DATA;
}
*/
// We could check with the first spectrum that we process whether it fulfills the requirements
// check for peak type (profile data required)
/*
if (!ms_exp_raw.empty() && PeakTypeEstimator().estimateType(ms_exp_raw[0].begin(), ms_exp_raw[0].end()) == SpectrumSettings::CENTROID)
{
writeLog_("Warning: OpenMS peak type estimation indicates that this is not profile data!");
}
*/
// We can check each spectrum and throw an error if it is not sorted
// check if spectra are sorted
/*
for (Size i = 0; i < ms_exp_raw.size(); ++i)
{
if (!ms_exp_raw[i].isSorted())
{
writeLog_("Error: Not all spectra are sorted according to peak m/z positions. Use FileFilter to sort the input!");
return INCOMPATIBLE_INPUT_DATA;
}
}
*/
// We can check each chromatogram and throw an error if it is not sorted
//check if chromatograms are sorted
/*
for (Size i = 0; i < ms_exp_raw.getChromatograms().size(); ++i)
{
if (!ms_exp_raw.getChromatogram(i).isSorted())
{
writeLog_("Error: Not all chromatograms are sorted according to peak m/z positions. Use FileFilter to sort the input!");
return INCOMPATIBLE_INPUT_DATA;
}
}
*/
//-------------------------------------------------------------
// pick
//-------------------------------------------------------------
PeakMap ms_exp_peaks;
///////////////////////////////////
// Create PeakPickerHiRes and hand it to the PPHiResMzMLConsumer
///////////////////////////////////
Param pepi_param = getParam_().copy("algorithm:", true);
writeDebug_("Parameters passed to LowMemPeakPickerHiRes", pepi_param, 3);
PeakPickerHiRes pp;
pp.setLogType(log_type_);
pp.setParameters(pepi_param);
pp.pickExperiment(exp, ms_exp_peaks);
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(ms_exp_peaks, getProcessingInfo_(DataProcessing::PEAK_PICKING));
MzMLFile mz_data_file;
mz_data_file.setLogType(log_type_);
mz_data_file.store(out, ms_exp_peaks);
return EXECUTION_OK;
}
ExitCodes main_(int, const char **) override
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
in = getStringOption_("in");
out = getStringOption_("out");
String process_option = getStringOption_("processOption");
Param pepi_param = getParam_().copy("algorithm:", true);
writeDebug_("Parameters passed to PeakPickerHiRes", pepi_param, 3);
PeakPickerHiRes pp;
pp.setLogType(log_type_);
pp.setParameters(pepi_param);
if (process_option == "lowmemory")
{
return doLowMemAlgorithm(pp);
}
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
MzMLFile mz_data_file;
mz_data_file.setLogType(log_type_);
PeakMap ms_exp_raw;
mz_data_file.load(in, ms_exp_raw);
if (ms_exp_raw.empty() && ms_exp_raw.getChromatograms().size() == 0)
{
LOG_WARN << "The given file does not contain any conventional peak data, but might"
" contain chromatograms. This tool currently cannot handle them, sorry.";
return INCOMPATIBLE_INPUT_DATA;
}
//check if spectra are sorted
for (Size i = 0; i < ms_exp_raw.size(); ++i)
{
if (!ms_exp_raw[i].isSorted())
{
writeLog_("Error: Not all spectra are sorted according to peak m/z positions. Use FileFilter to sort the input!");
return INCOMPATIBLE_INPUT_DATA;
}
}
//check if chromatograms are sorted
for (Size i = 0; i < ms_exp_raw.getChromatograms().size(); ++i)
{
if (!ms_exp_raw.getChromatogram(i).isSorted())
{
writeLog_("Error: Not all chromatograms are sorted according to peak m/z positions. Use FileFilter to sort the input!");
return INCOMPATIBLE_INPUT_DATA;
}
}
//-------------------------------------------------------------
// pick
//-------------------------------------------------------------
PeakMap ms_exp_peaks;
bool check_spectrum_type = !getFlag_("force");
pp.pickExperiment(ms_exp_raw, ms_exp_peaks, check_spectrum_type);
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(ms_exp_peaks, getProcessingInfo_(DataProcessing::PEAK_PICKING));
mz_data_file.store(out, ms_exp_peaks);
return EXECUTION_OK;
}