Method main_

src/topp/MSGFPlusAdapter.cpp:414–796

  }

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

    String in = getRawfileName();
    String out = getStringOption_("out");
    String mzid_out = getStringOption_("mzid_out");
    if (mzid_out.empty() && out.empty())
    {
      writeLogError_("Error:  no output file given (parameter 'out' or 'mzid_out')");
      return ILLEGAL_PARAMETERS;
    }

    String java_executable = getStringOption_("java_executable");
    String db_name = getDBFilename();

    vector<String> fixed_mods = getStringList_("fixed_modifications");
    vector<String> variable_mods = getStringList_("variable_modifications");
    bool no_mods = fixed_mods.empty() && variable_mods.empty();
    Int max_mods = getIntOption_("max_mods");
    if ((max_mods == 0) && !no_mods)
    {
      writeLogWarn_("Warning: Modifications are defined ('fixed_modifications'/'variable_modifications'), but the number of allowed modifications is zero ('max_mods'). Is that intended?");
    }

    if (!getFlag_("force"))
    {
      if (!JavaInfo::canRun(java_executable))
      {
        writeLogError_("Fatal error: Java is needed to run MS-GF+!");
        return EXTERNAL_PROGRAM_ERROR;
      }
    }
    else
    {
      writeLogWarn_("The installation of Java was not checked.");
    }

    // create temporary directory (and modifications file, if necessary):
    File::TempDir tmp_dir(debug_level_ >= 2);
    String mzid_temp, mod_file;
    // always create a temporary mzid file first, even if mzid output is requested via "mzid_out"
    // (reason: TOPPAS may pass a filename with wrong extension to "mzid_out", which would cause an error in MzIDToTSVConverter below,
    // so we make sure that we have a properly named mzid file for the converter; see https://github.com/OpenMS/OpenMS/issues/1251)
    mzid_temp = tmp_dir.getPath() + "msgfplus_output.mzid";
    if (!no_mods)
    {
      mod_file = tmp_dir.getPath() + "msgfplus_mods.txt";
      writeModificationsFile_(mod_file, fixed_mods, variable_mods, max_mods);
    }

    // parameters also used by OpenMS (see idXML creation below):
    String enzyme = getStringOption_("enzyme");
    double precursor_mass_tol = getDoubleOption_("precursor_mass_tolerance");
    String precursor_error_units = getStringOption_("precursor_error_units");
    Int min_precursor_charge = getIntOption_("min_precursor_charge");