void applyTransformation_(const String& in, const String& out, const TransformationDescription& trafo, TFile& file, TMap& map) { file.load(in, map); bool store_original_rt = getFlag_("store_original_rt"); MapAlignmentTransformer::transformRetentionTimes(map, trafo, store_original_rt); addDataProcessing_(map, getProcessingInfo_(DataProcessing::ALIGNMENT)); file.store(out, map); }