Method inferFromPeptides

src/openms/source/CHEMISTRY/ModificationDefinitionsSet.cpp:337–382

@TODO: should this function handle "max_mods_per_peptide_" as well?

  // @TODO: should this function handle "max_mods_per_peptide_" as well?
  void ModificationDefinitionsSet::inferFromPeptides(const vector<PeptideIdentification>& peptides)
  {
    // amino acid (or terminus) -> set of modifications (incl. no mod. = 0):
    map<String, set<const ResidueModification*> > mod_map;

    for (const PeptideIdentification& pep : peptides)
    {
      for (const PeptideHit& hit : pep.getHits())
      {
        const AASequence& seq = hit.getSequence();
        mod_map["N-term"].insert(seq.getNTerminalModification());
        mod_map["C-term"].insert(seq.getCTerminalModification());
        for (AASequence::ConstIterator seq_it = seq.begin();
             seq_it != seq.end(); ++seq_it)
        {
          mod_map[seq_it->getOneLetterCode()].insert(seq_it->getModification());
        }
      }
    }

    fixed_mods_.clear();
    variable_mods_.clear();
    for (map<String, set<const ResidueModification*> >::const_iterator map_it =
           mod_map.begin(); map_it != mod_map.end(); ++map_it)
    {
      set<const ResidueModification*>::const_iterator set_it =
        map_it->second.begin();
      // if there's only one mod, it's probably a fixed one:
      if ((map_it->second.size() == 1) && (*set_it != 0))
      {
        ModificationDefinition mod_def(**set_it, true);
        fixed_mods_.insert(mod_def);
      }
      else // variable mod(s)
      {
        for (; set_it != map_it->second.end(); ++set_it)
        {
          if (*set_it != 0)
          {
            ModificationDefinition mod_def(**set_it, false);
            variable_mods_.insert(mod_def);
          }
        }
      }
    }
  }


} // namespace OpenMS