Method mergeIds_

src/topp/IDMerger.cpp:332–472

  }

  void mergeIds_(StringList file_names,
                 bool annotate_file_origin,
                 const String& add_to,
                 vector<ProteinIdentification>& proteins,
                 vector<PeptideIdentification>& peptides)
  {
    map<String, ProteinIdentification> proteins_by_id;
    vector<vector<PeptideIdentification> > peptides_by_file;
    StringList add_to_ids; // IDs from the "add_to" file (if any)

    if (!add_to.empty())
    { // make 'add_to' filename the first in the list
      file_names.erase(remove(file_names.begin(), file_names.end(), add_to), file_names.end());
      file_names.insert(file_names.begin(), add_to);
    }

    peptides_by_file.resize(file_names.size());
    for (Size i = 0; i < file_names.size(); ++i)
    {
      const String& file_name = file_names[i];
      vector<ProteinIdentification> additional_proteins;
      IdXMLFile().load(file_name, additional_proteins, peptides_by_file[i]);

      if (annotate_file_origin) // set MetaValue "file_origin" if flag is set
      {
        annotateFileOrigin_(additional_proteins, peptides_by_file[i],
                            file_name);
      }

      for (const ProteinIdentification& prot : additional_proteins)
      {
        const String& id = prot.getIdentifier();
        proteins_by_id[id] = prot;
        if (i == 0) { add_to_ids.push_back(id); }
      }
    }

    if (add_to.empty()) // copy proteins from map into vector for writing
    {
      // append peptides in same vector
      for (vector<PeptideIdentification> & peps : peptides_by_file)
      {
        peptides.insert(peptides.end(), peps.begin(), peps.end());
      }
      // only append the runs (no merging of proteins)
      for (auto map_it = proteins_by_id.begin(); map_it != proteins_by_id.end(); ++map_it)
      {
        proteins.push_back(map_it->second);
      }
    }
    else // add only new IDs to an existing file
    {
      // copy over data from reference file ("add_to"):
      map<String, ProteinIdentification> selected_proteins;
      for (auto ids_it = add_to_ids.begin();
            ids_it != add_to_ids.end(); ++ids_it)
      {
        selected_proteins[*ids_it] = proteins_by_id[*ids_it];