Method main_

src/topp/LuciphorAdapter.cpp:450–656

  }
  
  ExitCodes main_(int, const char**) override
  {
    String java_executable = getStringOption_("java_executable");
    if (!getFlag_("force"))
    {
      if (!JavaInfo::canRun(java_executable))
      {
        writeLogError_("Fatal error: Java is needed to run LuciPHOr2!");
        return EXTERNAL_PROGRAM_ERROR;
      }
    }
    else
    {
      writeLogWarn_("The installation of Java was not checked.");
    }

    //tmp_dir
    File::TempDir tmp_dir(debug_level_ >= 2);

    // create a temporary config file for LuciPHOr2 parameters
    String conf_file = tmp_dir.getPath() + "luciphor2_input_template.txt";
    
    String id = getStringOption_("id");
    String in = getStringOption_("in");
    String out = getStringOption_("out");
    double rt_tolerance = getDoubleOption_("rt_tolerance");
    
    FileHandler fh;
    FileTypes::Type in_type = fh.getType(id);

    vector<PeptideIdentification> pep_ids;
    vector<ProteinIdentification> prot_ids;

    PeakMap exp;
    MzMLFile file;
    file.setLogType(log_type_);
    PeakFileOptions options;
    options.clearMSLevels();
    options.addMSLevel(2);

    file.load(in, exp);
    exp.sortSpectra(true);

    // convert idXML input to pepXML if necessary
    if (in_type == FileTypes::IDXML)
    {
      IdXMLFile().load(id, prot_ids, pep_ids);
      if (!pep_ids.empty())
      {
        IDFilter::keepNBestHits(pep_ids, 1); // LuciPHOR2 only calculates the best hit
      }
      else
      {
        OPENMS_LOG_WARN << "No PeptideIdentifications found in the IdXMLFile. Please check your previous steps.\n";
      }
      // create a temporary pepXML file for LuciPHOR2 input
      String id_file_name = FileHandler::swapExtension(File::basename(id), FileTypes::PEPXML);
      id = tmp_dir.getPath() + id_file_name;