Method preprocessingSirius

src/openms/source/ANALYSIS/ID/SiriusAdapterAlgorithm.cpp:436–487

    }

    void SiriusAdapterAlgorithm::preprocessingSirius(const String& featureinfo,
                                                     const MSExperiment& spectra,
                                                     FeatureMapping::FeatureMappingInfo& fm_info,
                                                     FeatureMapping::FeatureToMs2Indices& feature_mapping) const
    {
      // if fileparameter is given and should be not empty
      if (!featureinfo.empty())
      {
        if (File::exists(featureinfo) && !File::empty(featureinfo))
        {
          // read featureXML          
          FeatureMap feature_map;
          FileHandler().loadFeatures(featureinfo, feature_map);

          UInt num_masstrace_filter = getFilterByNumMassTraces();
          double precursor_mz_tol = getPrecursorMzTolerance();
          double precursor_rt_tol = getPrecursorRtTolerance();

          if (num_masstrace_filter != 1 && !isFeatureOnly())
          {
            num_masstrace_filter = 1;
            OPENMS_LOG_WARN << "Parameter: filter_by_num_masstraces, was set to 1 to retain the adduct information for all MS2 spectra, if available. Masstrace filtering only makes sense in combination with feature_only." << std::endl;
          }

          // filter feature by number of masstraces
          auto map_it = remove_if(feature_map.begin(), feature_map.end(),
                                  [&num_masstrace_filter](const Feature &feat) -> bool
                                  {
                                    unsigned int n_masstraces = feat.getMetaValue(Constants::UserParam::NUM_OF_MASSTRACES);
                                    return n_masstraces < num_masstrace_filter;
                                  });
          feature_map.erase(map_it, feature_map.end());
  
          fm_info.feature_maps.push_back(feature_map);
          fm_info.kd_tree.addMaps(fm_info.feature_maps); // KDTree references into feature_map
  
          // mapping of MS2 spectra to features
          feature_mapping = FeatureMapping::assignMS2IndexToFeature(spectra,
                                                                    fm_info,
                                                                    precursor_mz_tol,
                                                                    precursor_rt_tol,
                                                                    precursorMzToleranceUnitIsPPM());
        }
        else
        {
          throw OpenMS::Exception::FileEmpty(__FILE__,
                                             __LINE__,
                                             __FUNCTION__,
                                             "Error: FeatureXML was empty, please provide a valid file.");
        }
      }
    }   

    void SiriusAdapterAlgorithm::logFeatureSpectraNumber(const String& featureinfo,
                                                         const FeatureMapping::FeatureToMs2Indices& feature_mapping,