Method main_

src/topp/OpenPepXL.cpp:148–269

  }

  ExitCodes main_(int, const char**) override
  {
    ProgressLogger progresslogger;
    progresslogger.setLogType(log_type_);

    const string in_mzml(getStringOption_("in"));
    const string in_fasta(getStringOption_("database"));
    const string in_decoy_fasta(getStringOption_("decoy_database"));
    const string in_consensus(getStringOption_("consensus"));
    const string out_idXML(getStringOption_("out_idXML"));
    const string out_xquest = getStringOption_("out_xquestxml");
    const string out_xquest_specxml = getStringOption_("out_xquest_specxml");
    const string out_mzIdentML = getStringOption_("out_mzIdentML");

    OPENMS_LOG_INFO << "Analyzing file: " << endl;
    OPENMS_LOG_INFO << in_mzml << endl;

    // load MS2 map
    PeakMap unprocessed_spectra;
    MzMLFile f;
    f.setLogType(log_type_);

    PeakFileOptions options;
    options.clearMSLevels();
    options.addMSLevel(1);
    options.addMSLevel(2);
    f.getOptions() = options;
    f.load(in_mzml, unprocessed_spectra);

    // load linked features
    ConsensusMap cfeatures;
    ConsensusXMLFile cf;
    cf.load(in_consensus, cfeatures);

    // load fasta database
    progresslogger.startProgress(0, 1, "Load database from FASTA file...");
    FASTAFile fastaFile;
    vector<FASTAFile::FASTAEntry> fasta_db;
    fastaFile.load(in_fasta, fasta_db);

    if (!in_decoy_fasta.empty())
    {
      vector<FASTAFile::FASTAEntry> fasta_decoys;
      fastaFile.load(in_decoy_fasta, fasta_decoys);
      fasta_db.reserve(fasta_db.size() + fasta_decoys.size());
      fasta_db.insert(fasta_db.end(), fasta_decoys.begin(), fasta_decoys.end());
    }
    progresslogger.endProgress();

    // initialize solution vectors
    vector<ProteinIdentification> protein_ids(1);
    vector<PeptideIdentification> peptide_ids;

    // these are mainly necessary for writing out xQuest type spectrum files
    OPXLDataStructs::PreprocessedPairSpectra preprocessed_pair_spectra(0);
    vector< pair<Size, Size> > spectrum_pairs;
    vector< vector< OPXLDataStructs::CrossLinkSpectrumMatch > > all_top_csms;
    PeakMap spectra;