Method main_

src/topp/SiriusAdapter.cpp:140–295

  }

  ExitCodes main_(int, const char **) override
  {
    //-------------------------------------------------------------
    // Parsing parameters
    //-------------------------------------------------------------
    String sirius_executable = getStringOption_("sirius_executable");
    String in = getStringOption_("in");
    String out_sirius = getStringOption_("out_sirius");
    String out_csifingerid = getStringOption_("out_fingerid");
    String featureinfo = getStringOption_("in_featureinfo");
    String out_ms = getStringOption_("out_ms");
    String out_ann_spectra = getStringOption_("out_annotated_spectra");
    String sirius_workspace_directory = getStringOption_("out_project_space");
    String sirius_user_email = getStringOption_("sirius_user_email");
    String sirius_user_password = getStringOption_("sirius_user_password");
    bool converter_mode = getFlag_("converter_mode");

    auto params = getParam_();
    if (debug_level_ > 3)
    {
      params.setValue("read_sirius_stdout", "true");
    }
    params.setValue("project:processors", params.getValue("threads"));
    algorithm.updateExistingParameter(params);

    writeDebug_("Parameters passed to SiriusAdapterAlgorithm", algorithm.getParameters(), 3);

    //-------------------------------------------------------------
    // Calculations
    //-------------------------------------------------------------
    MSExperiment spectra;
    MzMLFile f;
    f.setLogType(log_type_);
    f.load(in, spectra);

    // make temporary files
    SiriusAdapterAlgorithm::SiriusTemporaryFileSystemObjects sirius_tmp(debug_level_);

    // run masstrace filter and feature mapping
    FeatureMapping::FeatureMappingInfo fm_info;
    FeatureMapping::FeatureToMs2Indices feature_mapping; // reference to *basefeature in Feature Maps stored in fm_info using a KDTree
    algorithm.preprocessingSirius(featureinfo,
                                  spectra,
                                  fm_info,
                                  feature_mapping);

    // returns Log of feature and/or spectra number
    algorithm.logFeatureSpectraNumber(featureinfo, feature_mapping, spectra);

    // write msfile and store the compound information in CompoundInfo Object
    vector<SiriusMSFile::CompoundInfo> v_cmpinfo;
    SiriusMSFile::store(spectra,
                        sirius_tmp.getTmpMsFile(),
                        feature_mapping,
                        algorithm.isFeatureOnly(),
                        algorithm.getIsotopePatternIterations(),
                        algorithm.isNoMasstraceInfoIsotopePattern(),
                        v_cmpinfo);