code: protected void trimStop(List<AminoAcidCompound> sequence) {
  		AminoAcidCompound stop = sequence.get(sequence.size() - 1);
  		boolean isStop = false;
  		if (aminoAcidToCodon.containsKey(stop)) {
  			for (Codon c : aminoAcidToCodon.get(stop)) {
  				if (c.isStop()) {
  					isStop = true;
  					break;
  				}
  			}
  		}
  
  		if (isStop) {
  			sequence.remove(sequence.size() - 1);
  		}
  	}
docs: Imperfect code. Checks the last amino acid to see if a codon could have
  translated a stop for it. Left in for the moment