Method writeModParam_

src/openms/source/FORMAT/HANDLERS/MzIdentMLHandler.cpp:1008–1054

    }

    void MzIdentMLHandler::writeModParam_(String& s, const std::vector<String>& mod_names, bool fixed, UInt indent) const
    {
      String cv_ns = unimod_.name();
      for (std::vector<String>::const_iterator it = mod_names.begin(); it != mod_names.end(); ++it)
      {
        std::set<const ResidueModification*> mods;
        ModificationsDB::getInstance()->searchModifications(mods, *it);
        if (!mods.empty())
        {
          // @TODO: if multiple mods match, we write all of them?
          for (std::set<const ResidueModification*>::const_iterator mt = mods.begin(); mt != mods.end(); ++mt)
          {
            char origin = (*mt)->getOrigin();
            if (origin == 'X') origin = '.'; // terminal without res. spec.

            s += String(indent + 1, '\t') + "<SearchModification fixedMod=\"" + (fixed ? "true" : "false") + "\" massDelta=\"" + String((*mt)->getDiffMonoMass()) + "\" residues=\"" + origin + "\">\n";

            // @TODO: handle protein C-term/N-term
            ResidueModification::TermSpecificity spec = (*mt)->getTermSpecificity();
            if ((spec == ResidueModification::C_TERM) || (spec == ResidueModification::N_TERM))
            {
              const String& cv_name = "modification specificity peptide " + (*mt)->getTermSpecificityName();
              s += String(indent + 2, '\t') + "<SpecificityRules>\n";
              s += String(indent + 3, '\t') + cv_.getTermByName(cv_name).toXMLString(cv_ns) + "\n";
              s += String(indent + 2, '\t') + "</SpecificityRules>\n";
            }

            String ac = (*mt)->getUniModAccession();
            if (ac.hasPrefix("UniMod:")) ac = "UNIMOD:" + ac.suffix(':');
            if (!ac.empty())
            {
              s += String(indent + 2, '\t') + unimod_.getTerm(ac).toXMLString(cv_ns) + "\n";
            }
            else
            {
              s += String(indent + 2, '\t') + "<cvParam cvRef=\"MS\" accession=\"MS:1001460\" name=\"unknown modification\"/>\n";
            }
            s += String(indent + 1, '\t') + "</SearchModification>\n";
          }
        }
        else
        {
          String message = String("Registered ") + (fixed ? "fixed" : "variable") + " modification '" + *it + "' is unknown and will be ignored.";
          throw Exception::ElementNotFound(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, message);
        }
      }
    }

    void MzIdentMLHandler::writeFragmentAnnotations_(String& s, const std::vector<PeptideHit::PeakAnnotation>& annotations, UInt indent, bool is_ppxl) const
    {