Method buildGraphWithRunInfo_

src/openms/source/ANALYSIS/ID/IDBoostGraph.cpp:286–348

  }

  void IDBoostGraph::buildGraphWithRunInfo_(ProteinIdentification& proteins,
                                           ConsensusMap& cmap,
                                           Size use_top_psms,
                                           bool use_unassigned_ids,
                                           const ExperimentalDesign& ed)
  {
    unordered_map<unsigned, unsigned> indexToPrefractionationGroup;

    {
      // TODO check that the files in the ProteinID run are all in the Exp. Design
      //StringList files;
      //proteins.getPrimaryMSRunPath(files); // files merged in the protein identification run to be inferred
      const ConsensusMap::ColumnHeaders& colHeaders = cmap.getColumnHeaders(); // all possible files and labels in the experiment
      //TODO use exp. design to merge fractions
      map<pair<String, unsigned>, unsigned> fileLabelToPrefractionationGroup = ed.getPathLabelToPrefractionationMapping(false);
      nrPrefractionationGroups_ = fileLabelToPrefractionationGroup.size();
      indexToPrefractionationGroup = convertMap_(fileLabelToPrefractionationGroup, colHeaders, cmap.getExperimentType()); // convert to index in the peptide ids
    }

    //TODO is this vertex_map really necessary. I think PSMs are always unique in our datastructures and could be
    // added without lookup.
    // And for the proteins we could add the vertex ID to the accession_map here and use that for lookup
    unordered_map<IDPointer, vertex_t, boost::hash<IDPointer>> vertex_map{};
    unordered_map<std::string, ProteinHit*> accession_map{};

    for (auto& prot : proteins.getHits())
    {
      accession_map[prot.getAccession()] = &prot;
    }

    ProgressLogger pl;
    Size roughNrIds = cmap.size();
    if (use_unassigned_ids) roughNrIds += cmap.getUnassignedPeptideIdentifications().size();
    pl.setLogType(ProgressLogger::CMD);
    pl.startProgress(0, roughNrIds, "Building graph with run information...");
    const String& protRun = proteins.getIdentifier();
    for (auto& feat : cmap)
    {
      for (auto& spectrum : feat.getPeptideIdentifications())
      {
        if (spectrum.getIdentifier() == protRun)
        {
          addPeptideAndAssociatedProteinsWithRunInfo_(spectrum, indexToPrefractionationGroup,
                                                      vertex_map, accession_map, use_top_psms);
        }
      }
      pl.nextProgress();
    }

    if (use_unassigned_ids)
    {
      for (auto& id : cmap.getUnassignedPeptideIdentifications())
      {
        if (id.getIdentifier() == protRun)
        {
          addPeptideAndAssociatedProteinsWithRunInfo_(id, indexToPrefractionationGroup,
                                                      vertex_map, accession_map, use_top_psms);
        }