ExitCodes main_(int, const char **)
{
String in = getStringOption_("in");
String out = getStringOption_("out");
String tr_file = getStringOption_("tr");
bool force = getFlag_("force");
boost::shared_ptr<PeakMap > exp ( new PeakMap );
MzMLFile mzmlfile;
mzmlfile.setLogType(log_type_);
mzmlfile.load(in, *exp);
TargetedExpType transition_exp;
TraMLFile().load(tr_file, transition_exp);
FeatureMap output;
OpenSwath::SpectrumAccessPtr input = SimpleOpenMSSpectraFactory::getSpectrumAccessOpenMSPtr(exp);
run_(input, output, transition_exp, force);
output.ensureUniqueId();
StringList ms_runs;
exp->getPrimaryMSRunPath(ms_runs);
output.setPrimaryMSRunPath(ms_runs);
FeatureXMLFile().store(out, output);
return EXECUTION_OK;
}
ExitCodes main_(int, const char **)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
String in = getStringOption_("in");
String out = getStringOption_("out");
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
MzMLFile mzMLFile;
mzMLFile.setLogType(log_type_);
MSExperiment<Peak1D> input;
mzMLFile.getOptions().addMSLevel(1);
mzMLFile.load(in, input);
if (input.empty())
{
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 < input.size(); ++i)
{
if (!input[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;
}
}
//-------------------------------------------------------------
// pick
//-------------------------------------------------------------
FeatureMap<> output;
FeatureFinder ff;
Param param = getParam_().copy("algorithm:", true);
FFSH ffsh;
ffsh.setParameters(param);
ffsh.setData(input, output, ff);
ffsh.run();
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(output, getProcessingInfo_(DataProcessing::PEAK_PICKING));
addDataProcessing_(output, getProcessingInfo_(DataProcessing::QUANTITATION));
output.ensureUniqueId();
for (Size i = 0; i < output.size(); i++)
{
output[i].ensureUniqueId();
}
FeatureXMLFile().store(out, output);
return EXECUTION_OK;
}
