Method main_

src/topp/MultiplexResolver.cpp:563–618

  }

  ExitCodes main_(int, const char**) override
  {
    /**
     * handle parameters
     */
    getParameters_in_out_();
    getParameters_labels_();
    getParameters_algorithm_();

    /**
     * load consensus map
     */
    ConsensusXMLFile file;
    ConsensusMap map_in;
    file.load(in_, map_in);

    /**
     * load (optional) blacklist
     */
    MzMLFile file_blacklist;
    if (!(in_blacklist_.empty()))
    {
      file_blacklist.load(in_blacklist_, exp_blacklist_);
    }

    /**
     * generate patterns
     */
    MultiplexDeltaMassesGenerator generator = MultiplexDeltaMassesGenerator(labels_, missed_cleavages_, label_mass_shift_);
    #ifdef DEBUG
    generator.printSamplesLabelsList(std::cout);
    generator.printDeltaMassesList(std::cout);
    #endif
        
    /**
     * construct the new consensus map
     */
    ConsensusMap map_out = map_in;
    ConsensusMap map_conflicts = map_in;
    map_out.resize(0);
    map_conflicts.resize(0);
    constructNewConsensusMap_(map_in, map_out, map_conflicts, generator);
         
    /**
     * store consensus maps
     */
    ConsensusXMLFile file_out;
    ConsensusXMLFile file_out_conflicts;
    file_out.store(out_, map_out);
    if (!out_conflicts_.empty())
    {
      file_out_conflicts.store(out_conflicts_, map_conflicts);
    }
   
    return EXECUTION_OK;
  }

};