Method common_main_

src/topp/FeatureLinkerBase.cpp:66–351

  }

  ExitCodes common_main_(FeatureGroupingAlgorithm * algorithm,
                         bool labeled = false)
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------
    StringList ins;
    if (labeled)
    {
      ins.push_back(getStringOption_("in"));
    }
    else
    {
      ins = getStringList_("in");
    }
    String out = getStringOption_("out");
    
    //-------------------------------------------------------------
    // check for valid input
    //-------------------------------------------------------------
    // check if all input files have the correct type
    FileTypes::Type file_type = FileHandler::getType(ins[0]);
    for (Size i = 0; i < ins.size(); ++i)
    {
      if (FileHandler::getType(ins[i]) != file_type)
      {
        writeLogError_("Error: All input files must be of the same type!");
        return ILLEGAL_PARAMETERS;
      }
    }

    //-------------------------------------------------------------
    // set up algorithm
    //-------------------------------------------------------------
    Param algorithm_param = getParam_().copy("algorithm:", true);
    writeDebug_("Used algorithm parameters", algorithm_param, 3);
    algorithm->setParameters(algorithm_param);

    //-------------------------------------------------------------
    // perform grouping
    //-------------------------------------------------------------
    // load input
    ConsensusMap out_map;
    StringList ms_run_locations;

    String design_file;

    // TODO: support design in labeled feature linker
    if (!labeled)
    {
      design_file = getStringOption_("design");
    }

    if (file_type == FileTypes::CONSENSUSXML && !design_file.empty())
    {
      writeLogError_("Error: Using fractionated design with consensusXML als input is not supported!");
      return ILLEGAL_PARAMETERS;
    }