Method main_

src/topp/IDMerger.cpp:184–330

  }

  ExitCodes main_(int, const char**) override
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------
    StringList file_names = getStringList_("in");
    String out = getStringOption_("out");
    String add_to = getStringOption_("add_to");
    bool annotate_file_origin = getStringOption_("annotate_file_origin") == "true" ? true : false;

    if (file_names.empty())
    {
      // this also allows exactly 1 file, because it might be useful for
      // a TOPPAS pipeline containing an IDMerger, to run only with one file
      writeLogError_("No input filename given. Aborting!");
      printUsage_();
      return ILLEGAL_PARAMETERS;
    }

    bool pepxml_protxml = getFlag_("pepxml_protxml");
    if (pepxml_protxml && (file_names.size() != 2))
    {
      writeLogError_("Exactly two input filenames expected for option 'pepxml_protxml'. Aborting!");
      printUsage_();
      return ILLEGAL_PARAMETERS;
    }
    if (pepxml_protxml && !add_to.empty())
    {
      // currently not allowed to keep the code simpler and because it doesn't
      // seem useful, but should be possible in principle:
      writeLogError_("The options 'add_to' and 'pepxml_protxml' cannot be used together. Aborting!");
      printUsage_();
      return ILLEGAL_PARAMETERS;
    }

    bool merge_proteins_add_PSMs = getFlag_("merge_proteins_add_PSMs");
    if (merge_proteins_add_PSMs && (pepxml_protxml || !add_to.empty()))
    {
      // currently not allowed to keep the code simpler and because it doesn't
      // seem useful, but should be possible in principle:
      writeLogError_("The options 'merge_proteins_add_PSMs', 'add_to' and 'pepxml_protxml' cannot be used together. Aborting!");
      printUsage_();
      return ILLEGAL_PARAMETERS;
    }

    // check file types:
    FileTypes::Type type;
    String out_type = getStringOption_("out_type");
    if (!out_type.empty())
    {
      type = FileTypes::nameToType(out_type);
    }
    else
    {
      type = FileHandler::getTypeByFileName(out);
    }
    for (const String& file_name : file_names)
    {