Method main_

src/topp/TargetedFileConverter.cpp:87–171

  }

  ExitCodes main_(int, const char**) override
  {
    FileHandler fh;

    //input file type
    String in = getStringOption_("in");
    FileTypes::Type in_type = FileTypes::nameToType(getStringOption_("in_type"));

    if (in_type == FileTypes::UNKNOWN)
    {
      in_type = fh.getType(in);
      writeDebug_(String("Input file type: ") + FileTypes::typeToName(in_type), 2);
    }

    if (in_type == FileTypes::UNKNOWN)
    {
      writeLogError_("Error: Could not determine input file type!");
      return PARSE_ERROR;
    }

    //output file names and types
    String out = getStringOption_("out");
    FileTypes::Type out_type = FileTypes::nameToType(getStringOption_("out_type"));

    if (out_type == FileTypes::UNKNOWN)
    {
      out_type = fh.getTypeByFileName(out);
    }

    if (out_type == FileTypes::UNKNOWN)
    {
      writeLogError_("Error: Could not determine output file type!");
      return PARSE_ERROR;
    }

    bool legacy_traml_id = getFlag_("legacy_traml_id");

    //--------------------------------------------------------------------------- 
    // Start Conversion
    //--------------------------------------------------------------------------- 
    TargetedExperiment targeted_exp;
    if (in_type == FileTypes::TSV || in_type == FileTypes::MRM)
    {
      Param reader_parameters = getParam_().copy("algorithm:", true);
      TransitionTSVFile tsv_reader;
      tsv_reader.setLogType(log_type_);
      tsv_reader.setParameters(reader_parameters);
      tsv_reader.convertTSVToTargetedExperiment(in.c_str(), in_type, targeted_exp);
      tsv_reader.validateTargetedExperiment(targeted_exp);
    }
    else if (in_type == FileTypes::PQP)
    {
      TransitionPQPFile pqp_reader;
      Param reader_parameters = getParam_().copy("algorithm:", true);
      pqp_reader.setLogType(log_type_);
      pqp_reader.setParameters(reader_parameters);
      pqp_reader.convertPQPToTargetedExperiment(in.c_str(), targeted_exp, legacy_traml_id);
      pqp_reader.validateTargetedExperiment(targeted_exp);