Method store

src/openms/source/FORMAT/ConsensusXMLFile.cpp:39–79

  }

  void ConsensusXMLFile::store(const String& filename, const ConsensusMap& consensus_map)
  {
    if (!FileHandler::hasValidExtension(filename, FileTypes::CONSENSUSXML))
    {
      throw Exception::UnableToCreateFile(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename, "invalid file extension, expected '" + FileTypes::typeToName(FileTypes::CONSENSUSXML) + "'");
    }

    if (!consensus_map.isMapConsistent(&OpenMS_Log_warn))
    {
      // Currently it is possible that FeatureLinkerUnlabeledQT triggers this exception
      // throw Exception::MissingInformation(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "The ConsensusXML file contains invalid maps or references thereof. No data was written! Please fix the file or notify the maintainer of this tool if you did not provide a consensusXML file!");
      std::cerr << "The ConsensusXML file contains invalid maps or references thereof. Please fix the file or notify the maintainer of this tool if you did not provide a consensusXML file! Note that this warning will be a fatal error in the next version of OpenMS!" << std::endl;
    }

    if (Size invalid_unique_ids = consensus_map.applyMemberFunction(&UniqueIdInterface::hasInvalidUniqueId))
    {
      // TODO Take care *outside* that this does not happen.
      // We can detect this here but it is too late to fix the problem;
      // there is no straightforward action to be taken in all cases.
      // Note also that we are given a const reference.
      OPENMS_LOG_INFO << String("ConsensusXMLFile::store():  found ") + invalid_unique_ids + " invalid unique ids" << std::endl;
    }

    // This will throw if the unique ids are not unique,
    // so we never create bad files in this respect.
    try
    {
      consensus_map.updateUniqueIdToIndex();
    }
    catch (Exception::Postcondition& e)
    {
      OPENMS_LOG_FATAL_ERROR << e.getName() << ' ' << e.what() << std::endl;
      throw;
    }


    Internal::ConsensusXMLHandler handler(consensus_map, filename);
    handler.setOptions(options_);
    handler.setLogType(getLogType());
    save_(filename, &handler);
  }

  void ConsensusXMLFile::load(const String& filename, ConsensusMap& consensus_map)
  {