Method CMMzTabStream

src/openms/source/FORMAT/MzTab.cpp:2566–2885

  MzTab::CMMzTabStream::CMMzTabStream(
    const ConsensusMap& consensus_map,
    const String& filename,
    const bool first_run_inference_only,
    const bool export_unidentified_features,
    const bool export_unassigned_ids,
    const bool export_subfeatures,
    const bool export_empty_pep_ids,
    const bool export_all_psms,
    const String& title) 
  :
    consensus_map_(consensus_map),
    filename_(filename), 
    export_unidentified_features_(export_unidentified_features),
    export_subfeatures_(export_subfeatures),
    export_empty_pep_ids_(export_empty_pep_ids),
    export_all_psms_(export_all_psms)
  {
    // fill ID datastructure without copying
    const vector<ProteinIdentification>& prot_id = consensus_map.getProteinIdentifications();
    prot_ids_.reserve(prot_id.size());
    for (const auto & i : prot_id)
    {
      prot_ids_.push_back(&i);
    }
 
    // extract mapped IDs
    for (Size i = 0; i < consensus_map.size(); ++i)
    {
      const ConsensusFeature& c = consensus_map[i];
      const vector<PeptideIdentification>& p = c.getPeptideIdentifications();
      peptide_ids_.reserve(peptide_ids_.size() + p.size());
      for (const PeptideIdentification& pi : p) { peptide_ids_.push_back(&pi); }
    }

    // also export PSMs of unassigned peptide identifications
    if (export_unassigned_ids)
    {
      const vector<PeptideIdentification>& up = consensus_map.getUnassignedPeptideIdentifications();
      peptide_ids_.reserve(peptide_ids_.size() + up.size());
      for (const PeptideIdentification& pi : up) { peptide_ids_.push_back(&pi); }
    }

    ////////////////////////////////////////////////
    // create some lookup structures and precalculate some values
    idrunid_2_idrunindex_ = MzTab::mapIDRunIdentifier2IDRunIndex_(prot_ids_);

    bool has_inference_data = !prot_ids_.empty() && prot_ids_[0]->hasInferenceData();

    first_run_inference_ = has_inference_data && first_run_inference_only;
    if (first_run_inference_)
    {
      OPENMS_LOG_INFO << "MzTab: Inference data provided. Considering first run only for inference data." << std::endl;
    }

    map<String, size_t> msfilename_2_msrunindex;
    map<size_t, String> msrunindex_2_msfilename;
    MzTab::mapBetweenMSFileNameAndMSRunIndex_(prot_ids_, first_run_inference_, msfilename_2_msrunindex, msrunindex_2_msfilename);