ExitCodes main_(int, const char **)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
//input/output files
String in(getStringOption_("in"));
String out(getStringOption_("out"));
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
MSExperiment<> exp;
MzMLFile f;
f.setLogType(log_type_);
f.load(in, exp);
//-------------------------------------------------------------
// if meta data arrays are present, remove them and warn
//-------------------------------------------------------------
if (exp.clearMetaDataArrays())
{
writeLog_("Warning: Spectrum meta data arrays cannot be sorted. They are deleted.");
}
//-------------------------------------------------------------
// filter
//-------------------------------------------------------------
Param filter_param = getParam_().copy("algorithm:", true);
writeDebug_("Used filter parameters", filter_param, 3);
BernNorm filter;
filter.setParameters(filter_param);
filter.filterPeakMap(exp);
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(exp, getProcessingInfo_(DataProcessing::FILTERING));
f.store(out, exp);
return EXECUTION_OK;
}
ExitCodes main_(int, const char **)
{
//----------------------------------------------------------------
// load data
//----------------------------------------------------------------
String in = getStringOption_("in");
String out = getStringOption_("out");
MSExperiment<> exp;
MzMLFile f;
f.setLogType(log_type_);
f.load(in, exp);
DoubleReal sampling_rate = getDoubleOption_("sampling_rate");
LinearResampler lin_resampler;
Param resampler_param;
resampler_param.setValue("spacing", sampling_rate);
lin_resampler.setParameters(resampler_param);
// resample every scan
for (Size i = 0; i < exp.size(); ++i)
{
lin_resampler.raster(exp[i]);
}
//clear meta data because they are no longer meaningful
exp.clearMetaDataArrays();
//annotate output with data processing info
addDataProcessing_(exp,
getProcessingInfo_(DataProcessing::DATA_PROCESSING));
//store output
f.store(out, exp);
return EXECUTION_OK;
}