Method main_

src/topp/ProteinResolver.cpp:487–671

  }

  ExitCodes main_(int, const char**) override
  {
    //-------------------------------------------------------------
    // parsing parameters
    //-------------------------------------------------------------
    String fastafile_name = getStringOption_("fasta");
    StringList input_list = getStringList_("in");
    String input_path = getStringOption_("in_path");

    String design = getStringOption_("design");
    String output_pep_table = getStringOption_("peptide_table");
    String ouput_prot_groups = getStringOption_("protein_groups");
    String output_prot_table = getStringOption_("protein_table");
    String output_stats = getStringOption_("additional_info");

    //-------------------------------------------------------------
    // check input parameters
    //-------------------------------------------------------------
    if (input_list.empty() && input_path.empty())
    {
      throw Exception::InvalidParameter(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
                                        "All input options are empty.");
    }

    //-------------------------------------------------------------
    // check output parameters
    //-------------------------------------------------------------
    if (output_pep_table.empty() && ouput_prot_groups.empty() && output_prot_table.empty())
    {
      throw Exception::InvalidParameter(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
                                        "All output options are empty.");
    }

    //-------------------------------------------------------------
    // read fasta file
    //-------------------------------------------------------------
    FASTAFile file;
    std::vector<FASTAFile::FASTAEntry> protein_data;
    file.load(fastafile_name, protein_data);

    //-------------------------------------------------------------
    // set up protein resolver ( parameters )
    //-------------------------------------------------------------
    ProteinResolver resolver;
    resolver_params_ = resolver.getParameters();
    Logger::LogStream nirvana; // avoid parameter update messages
    resolver_params_.update(getParam_(), false, nirvana);
    resolver.setParameters(resolver_params_);
    resolver.setProteinData(protein_data);

    //-------------------------------------------------------------
    // initialize rest
    //-------------------------------------------------------------
    IdXMLFile idXML_file;
    ConsensusXMLFile consensusXML_file;
    ConsensusMap consensus;
    vector<ProteinIdentification> protein_identifications;
    vector<PeptideIdentification> peptide_identifications;