code: public List<Subunit> getAlignedSubunits1() {
  
  		List<Subunit> aligned = new ArrayList<Subunit>(subunitMap.size());
  
  		for (Integer key : subunitMap.keySet())
  			aligned.add(subunits1.get(key));
  
  		return aligned;
  	}
docs: Return the aligned subunits of the first Subunit group, in the alignment
  order.
  
  @return a List of Subunits in the alignment order