Method applyBasic

src/openms/source/ANALYSIS/ID/FalseDiscoveryRate.cpp:996–1070

  }

  void FalseDiscoveryRate::applyBasic(ConsensusMap & cmap, bool include_unassigned_peptides)
  {
    bool q_value = !param_.getValue("no_qvalues").toBool();
    const string& score_type = q_value ? "q-value" : "FDR";
    bool all_hits = param_.getValue("use_all_hits").toBool();

    bool treat_runs_separately = param_.getValue("treat_runs_separately").toBool();
    bool split_charge_variants = param_.getValue("split_charge_variants").toBool();

    //TODO this assumes all used search engine scores have the same score orientation
    // include the determination of orientation in the getScores methods instead
    bool higher_score_better = false;
    for (const auto& cf : cmap)
    {
      const auto& pep_ids = cf.getPeptideIdentifications();
      if (!pep_ids.empty())
      {
        higher_score_better = pep_ids[0].isHigherScoreBetter();
        break;
      }
    }
    if (cmap.empty())
    {
      for (const auto& id : cmap.getUnassignedPeptideIdentifications())
      {
        higher_score_better = id.isHigherScoreBetter();
        break;
      }
    }

    bool add_decoy_peptides = param_.getValue("add_decoy_peptides").toBool();
    ScoreToTgtDecLabelPairs scores_labels;

    //Warning: this assumes that there are no dangling identifier references in the PeptideIDs
    // because this disables checking
    if (cmap.getProteinIdentifications().size() == 1)
    {
      treat_runs_separately = false;
    }

    if (treat_runs_separately)
    {
      for (const auto& protID : cmap.getProteinIdentifications())
      {
        if (split_charge_variants)
        {
          pair<int, int> chargeRange = protID.getSearchParameters().getChargeRange();
          for (int c = chargeRange.first; c <= chargeRange.second; ++c)
          {
            if (c == 0) continue;
            IDScoreGetterSetter::getPeptideScoresFromMap_(scores_labels, cmap, include_unassigned_peptides,
             [&protID](const PeptideIdentification& id){return protID.getIdentifier() == id.getIdentifier();}, all_hits,
             [&c](const PeptideHit& hit){return c == hit.getCharge();});
            map<double, double> scores_to_fdr;
            calculateFDRBasic_(scores_to_fdr, scores_labels, q_value, higher_score_better);
            IDScoreGetterSetter::setPeptideScoresForMap_(scores_to_fdr, cmap, include_unassigned_peptides, score_type, higher_score_better, add_decoy_peptides, c, protID.getIdentifier());
          }
        }