Method checkPeptideIdentification_

src/topp/FileFilter.cpp:163–268

  }

  static bool checkPeptideIdentification_(BaseFeature& feature,
                                          const bool remove_annotated_features,
                                          const bool remove_unannotated_features,
                                          const StringList& sequences,
                                          const String& sequence_comparison_method,
                                          const StringList& accessions,
                                          const bool keep_best_score_id,
                                          const bool remove_clashes)
  {
    //flag: remove_annotated_features and non-empty peptideIdentifications
    if (remove_annotated_features && !feature.getPeptideIdentifications().empty())
    {
      return false;
    }
    //flag: remove_unannotated_features and no peptideIdentifications
    if (remove_unannotated_features && feature.getPeptideIdentifications().empty())
    {
      return false;
    }
    //flag: remove_clashes
    if (remove_clashes && !feature.getPeptideIdentifications().empty())
    {
      String temp = feature.getPeptideIdentifications().begin()->getHits().begin()->getSequence().toString();
      //loop over all peptideIdentifications
      for (const PeptideIdentification& pep : feature.getPeptideIdentifications())
      {
        //loop over all peptideHits
        for (const PeptideHit& pep_hit : pep.getHits())
        {
          if (pep_hit.getSequence().toString() != temp)
          {
            return false;
          }
        }
      }
    }
    //flag: keep_best_score_id
    if (keep_best_score_id && !feature.getPeptideIdentifications().empty())
    {
      PeptideIdentification temp = feature.getPeptideIdentifications().front();
      //loop over all peptideIdentifications
      for (const PeptideIdentification& pep : feature.getPeptideIdentifications())
      {
        //loop over all peptideHits
        for (const PeptideHit& pep_hit : pep.getHits())
        {
          if ((pep.isHigherScoreBetter() && pep_hit.getScore() > temp.getHits().front().getScore()) ||
              (!pep.isHigherScoreBetter() && pep_hit.getScore() < temp.getHits().front().getScore()))
          {
            temp = pep;
          }
        }
      }
      feature.setPeptideIdentifications(vector<PeptideIdentification>(1, temp));
      // not filtering sequences or accessions
      if (sequences.empty() && accessions.empty())
      {
        return true;