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; }