Method main_

src/topp/FileMerger.cpp:150–489

  }

  ExitCodes main_(int, const char**) override
  {

    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------
    // file list
    StringList file_list = getStringList_("in");

    // file type
    FileHandler file_handler;
    FileTypes::Type force_type;
    if (!getStringOption_("in_type").empty())
    {
      force_type = FileTypes::nameToType(getStringOption_("in_type"));
    }
    else
    {
      force_type = file_handler.getType(file_list[0]);
    }

    // output file names and types
    String out_file = getStringOption_("out");
   
    // append method
    bool append_rows = false;
    bool append_cols = false;
    String append_method = getStringOption_("append_method");
    append_method == "append_rows" ? append_rows = true : append_cols = true; 
   
    bool annotate_file_origin =  getFlag_("annotate_file_origin");
    rt_gap_ = getDoubleOption_("rt_concat:gap");
    vector<String> trafo_out = getStringList_("rt_concat:trafo_out");
    if (trafo_out.empty())
    {
      // resize now so we don't have to worry about indexing out of bounds:
      trafo_out.resize(file_list.size());
    }
    else if (trafo_out.size() != file_list.size())
    {
      writeLogError_("Error: Number of transformation output files must equal the number of input files (parameters 'rt_concat:trafo_out'/'in')!");
      return ILLEGAL_PARAMETERS;
    }

    //-------------------------------------------------------------
    // calculations
    //-------------------------------------------------------------

    if (force_type == FileTypes::FEATUREXML)
    {
      FeatureMap out;
      FeatureXMLFile fh;
      for (Size i = 0; i < file_list.size(); ++i)
      {
        FeatureMap map;
        fh.load(file_list[i], map);

        if (annotate_file_origin)