Method parseParameters_

src/topp/LuciphorAdapter.cpp:174–220

  }
 
  ExitCodes parseParameters_(map<String, vector<String> >& config_map, const String& id, const String& in,
    const String& out, const vector<String>& target_mods, String selection_method)
  {
    FileHandler fh;
    
    config_map["SPECTRUM_PATH"].push_back(File::path(File::absolutePath(in)));
    config_map["SPECTRUM_SUFFIX"].push_back(FileTypes::typeToName(fh.getTypeByFileName(in)));
    config_map["INPUT_DATA"].push_back(id);
    
    String type = FileTypes::typeToName(fh.getTypeByFileName(id));
    config_map["INPUT_TYPE"].push_back(0);
    
    config_map["ALGORITHM"].push_back(ListUtils::getIndex<String>(fragment_methods_, getStringOption_("fragment_method")));
    config_map["MS2_TOL"].push_back(getDoubleOption_("fragment_mass_tolerance"));
    config_map["MS2_TOL_UNITS"].push_back(ListUtils::getIndex<String>(fragment_error_units_, getStringOption_("fragment_error_units")));
    config_map["MIN_MZ"].push_back(getDoubleOption_("min_mz"));
    config_map["OUTPUT_FILE"].push_back(out);
    config_map["DECOY_MASS"].push_back(getDoubleOption_("decoy_mass"));
    config_map["MAX_CHARGE_STATE"].push_back(getIntOption_("max_charge_state"));
    config_map["MAX_PEP_LEN"].push_back(getIntOption_("max_peptide_length"));
    config_map["MAX_NUM_PERM"].push_back(getIntOption_("max_num_perm"));
    config_map["SELECTION_METHOD"].push_back(ListUtils::getIndex<String>(score_selection_method_, selection_method));    
    config_map["MODELING_SCORE_THRESHOLD"].push_back(getDoubleOption_("modeling_score_threshold"));
    config_map["SCORING_THRESHOLD"].push_back(getDoubleOption_("scoring_threshold"));
    config_map["MIN_NUM_PSMS_MODEL"].push_back(getIntOption_("min_num_psms_model"));
    config_map["NUM_THREADS"].push_back(getIntOption_("num_threads"));
    config_map["RUN_MODE"].push_back(getStringOption_("run_mode"));
    
    for (vector<String>::const_iterator it = target_mods.begin(); it != target_mods.end(); ++it)
    {
      config_map["TARGET_MOD"].push_back(makeModString_(*it));
    }
    
    vector<String> neutral_losses = getStringList_("neutral_losses");
    for (vector<String>::const_iterator it = neutral_losses.begin(); it != neutral_losses.end(); ++it)
    {
      config_map["NL"].push_back(*it);
    }
    
    vector<String> dcy_neutral_losses = getStringList_("decoy_neutral_losses");
    for (vector<String>::const_iterator it = dcy_neutral_losses.begin(); it != dcy_neutral_losses.end(); ++it)
    {
      config_map["DECOY_NL"].push_back(*it);
    }
    
    return EXECUTION_OK;
  }
  
  void writeConfigurationFile_(const String& out_path, map<String, vector<String> >& config_map)
  {