Method main_

src/topp/MSFraggerAdapter.cpp:387–914

  }

  ExitCodes main_(int, const char**) override
  {
    if (getStringOption_(TOPPMSFraggerAdapter::license) != "yes" && !getFlag_("test"))
    {
      _fatalError("MSFragger may only be used upon acceptance of license terms.");
    }

    File::TempDir working_directory(debug_level_ >= 2);
    try
    {
      // java executable
      this->java_exe = this->getStringOption_(TOPPMSFraggerAdapter::java_executable);

      if (!JavaInfo::canRun(this->java_exe, true))
      {
        _fatalError("Java executable cannot be run!");
      }

      // executable
      this->exe = this->getStringOption_(TOPPMSFraggerAdapter::executable);

      if (this->exe.empty())
      {
        // looks for MSFRAGGER_PATH in the environment
        QString qmsfragger_path = QProcessEnvironment::systemEnvironment().value("MSFRAGGER_PATH");
        if (qmsfragger_path.isEmpty())
        {
          _fatalError("No executable for MSFragger could be found!");
        }
        this->exe = qmsfragger_path;
      }

      // input, output, database name
      const String database = this->getStringOption_(TOPPMSFraggerAdapter::database);
      input_file = (this->getStringOption_(TOPPMSFraggerAdapter::in)).toQString();
      output_file = this->getStringOption_(TOPPMSFraggerAdapter::out);
      optional_output_file = this->getStringOption_(TOPPMSFraggerAdapter::opt_out);

      // tolerance
      const double arg_precursor_mass_tolerance_lower(this->getDoubleOption_(TOPPMSFraggerAdapter::precursor_mass_tolerance_lower));
      const double arg_precursor_mass_tolerance_upper(this->getDoubleOption_(TOPPMSFraggerAdapter::precursor_mass_tolerance_upper));
      const String & arg_precursor_mass_unit = this->getStringOption_(TOPPMSFraggerAdapter::precursor_mass_unit);
      const double arg_precursor_true_tolerance(this->getDoubleOption_(TOPPMSFraggerAdapter::precursor_true_tolerance));
      const String & arg_precursor_true_unit = this->getStringOption_(TOPPMSFraggerAdapter::precursor_true_unit);
      const double arg_fragment_mass_tolerance(this->getDoubleOption_(TOPPMSFraggerAdapter::fragment_mass_tolerance));
      const String & arg_fragment_mass_unit = this->getStringOption_(TOPPMSFraggerAdapter::fragment_mass_unit);
      const String & arg_isotope_error = this->getStringOption_(TOPPMSFraggerAdapter::isotope_error);

      // digest
      const String & arg_search_enzyme_name = this->getStringOption_(TOPPMSFraggerAdapter::search_enzyme_name);
      const String & arg_search_enzyme_cutafter = this->getStringOption_(TOPPMSFraggerAdapter::search_enzyme_cutafter);
      const String & arg_search_enzyme_nocutbefore = this->getStringOption_(TOPPMSFraggerAdapter::search_enzyme_nocutbefore);

      std::map< String,int > num_enzyme_termini;
      num_enzyme_termini["non-enzymatic"] = 0;
      num_enzyme_termini["semi"] = 1;
      num_enzyme_termini["fully"] = 2;
      const int arg_num_enzyme_termini = num_enzyme_termini[this->getStringOption_(TOPPMSFraggerAdapter::num_enzyme_termini)];