Method store

src/openms/source/FORMAT/IBSpectraFile.cpp:160–288

  }

  void IBSpectraFile::store(const String& filename, const ConsensusMap& cm)
  {
    // typdefs for shorter code
    typedef std::vector<ProteinHit>::iterator ProtHitIt;

    // general settings .. do we need to expose these?
    // ----------------------------------------------------------------------
    /// Allow also non-unique peptides to be exported
    bool allow_non_unique = true;
    /// Intensities below this value will be set to 0.0 to avoid numerical problems when quantifying
    double intensity_threshold = 0.00001;
    // ----------------------------------------------------------------------


    // guess experiment type
    boost::shared_ptr<IsobaricQuantitationMethod> quantMethod = guessExperimentType_(cm);

    // we need the protein identifications to reference the protein names
    ProteinIdentification protIdent;
    bool has_proteinIdentifications = false;
    if (!cm.getProteinIdentifications().empty())
    {
      protIdent = cm.getProteinIdentifications()[0];
      has_proteinIdentifications = true;
    }

    // start the file by adding the tsv header
    TextFile textFile;
    textFile.addLine(ListUtils::concatenate(constructHeader_(*quantMethod), "\t"));

    for (ConsensusMap::ConstIterator cm_iter = cm.begin();
         cm_iter != cm.end();
         ++cm_iter)
    {
      const ConsensusFeature& cFeature = *cm_iter;
      std::vector<IdCSV> entries;

      /// 1st we extract the identification information from the consensus feature
      if (cFeature.getPeptideIdentifications().empty() || !has_proteinIdentifications)
      {
        // we store unidentified hits anyway, because the iTRAQ quant is still helpful for normalization
        entries.emplace_back();
      }
      else
      {
        // protein name:
        const PeptideHit& peptide_hit = cFeature.getPeptideIdentifications()[0].getHits()[0];
        std::set<String> protein_accessions = peptide_hit.extractProteinAccessionsSet();
        if (protein_accessions.size() != 1)
        {
          if (!allow_non_unique) continue; // we only want unique peptides
        }

        for (std::set<String>::const_iterator prot_ac = protein_accessions.begin(); prot_ac != protein_accessions.end(); ++prot_ac)
        {
          IdCSV entry;
          entry.charge = cFeature.getPeptideIdentifications()[0].getHits()[0].getCharge();
          entry.peptide = cFeature.getPeptideIdentifications()[0].getHits()[0].getSequence().toUnmodifiedString();