code: private void addAmbiguousEquivalents(String one, String two, String either) {
  		Set<AminoAcidCompound> equivalents;
  		AminoAcidCompound cOne, cTwo, cEither;
  
  		equivalents = new HashSet<AminoAcidCompound>();
  		equivalents.add(cOne = aminoAcidCompoundCache.get(one));
  		equivalents.add(cTwo = aminoAcidCompoundCache.get(two));
  		equivalents.add(cEither = aminoAcidCompoundCache.get(either));
  		equivalentsCache.put(cEither, equivalents);
  
  		equivalents = new HashSet<AminoAcidCompound>();
  		equivalents.add(cOne);
  		equivalents.add(cEither);
  		equivalentsCache.put(cOne, equivalents);
  
  		equivalents = new HashSet<AminoAcidCompound>();
  		equivalents.add(cTwo);
  		equivalents.add(cEither);
  		equivalentsCache.put(cTwo, equivalents);
  	}
docs: helper method to initialize the equivalent sets for 2 amino acid compounds and their ambiguity compound