code: private static Collection<Set<Node>> prepareNodeSets(Set<BioPAXElement> elements, Graph graph)
  	{
  		Collection<Set<Node>> sets = new HashSet<Set<Node>>();
  
  		Map<BioPAXElement, Set<PhysicalEntity>> map = getRelatedPhysicalEntityMap(elements);
  
  		for (Set<PhysicalEntity> pes : map.values())
  		{
  			Set<Node> set = graph.getWrapperSet(pes);
  
  			if (!set.isEmpty()) sets.add(set);
  		}
  		
  		// Add interactions in the seed as single node set
  
  		Set<Node> inters = getSeedInteractions(elements, graph);
  		for (Node node : inters)
  		{
  			sets.add(Collections.singleton(node));
  		}
  
  		return sets;
  	}
docs: Gets the related wrappers of the given elements in individual sets. An object can be related
  to more than one wrapper and they will appear in the same set. This method created a set for
  each parameter element that has a related wrapper.
  @param elements Elements to get the related wrappers
  @param graph Owner graph
  @return Related wrappers in individual sets