code: private void setAllMapping(List<Map<IAtom, IAtom>> mappings) {
          try {
              int counter = 0;
              for (Map<IAtom, IAtom> solution : mappings) {
                  Map<Integer, Integer> atomMappings = new TreeMap<Integer, Integer>();
                  for (Map.Entry<IAtom, IAtom> map : solution.entrySet()) {
                      IAtom sourceAtom = map.getKey();
                      IAtom targetAtom = map.getValue();
                      atomMappings.put(source.indexOf(sourceAtom), target.indexOf(targetAtom));
                  }
                  allMCS.add(counter++, atomMappings);
              }
          } catch (Exception I) {
              I.getCause();
          }
      }
docs: {@inheritDoc}
  
  Set the mappings