Method main_

src/topp/CometAdapter.cpp:583–735

  }

  ExitCodes main_(int, const char**) override
  {
    //-------------------------------------------------------------
    // parsing parameters
    //-------------------------------------------------------------

    // do this early, to see if comet is installed
    String comet_executable = getStringOption_("comet_executable");
    File::TempDir tmp_dir(debug_level_ >= 2);

    writeDebug_("Comet is writing the default parameter file...", 1);
    
    TOPPBase::ExitCodes exit_code = runExternalProcess_(comet_executable.toQString(), QStringList() << "-p", tmp_dir.getPath().toQString());
    if (exit_code != EXECUTION_OK)
    {
      return EXTERNAL_PROGRAM_ERROR;
    }
    // the first line of 'comet.params.new' contains a string like: "# comet_version 2017.01 rev. 1"
    String comet_version; 
    {
      std::ifstream ifs(tmp_dir.getPath() + "/comet.params.new");
      getline(ifs, comet_version);
    }
    writeDebug_("Comet Version extracted is: '" + comet_version + "\n", 2);

    //-------------------------------------------------------------
    // reading input
    //-------------------------------------------------------------


    int ms_level = getIntOption_("ms_level");
    String inputfile_name = getRawfileName(ms_level);
    String out = getStringOption_("out");
    String db_name = getDBFilename();

    // tmp_dir
    String tmp_pepxml = tmp_dir.getPath() + "result.pep.xml";
    String tmp_pin = tmp_dir.getPath() + "result.pin";
    String default_params = getStringOption_("default_params_file");
    String tmp_file;

    // default params given or to be written
    if (default_params.empty())
    {
        tmp_file = tmp_dir.getPath() + "param.txt";
        ofstream os(tmp_file.c_str());
        auto ret = createParamFile_(os, comet_version);
        os.close();
        if (ret != EXECUTION_OK)
        {
          return ret;
        }
    }
    else
    {
        tmp_file = default_params;
    }