code: @Override
  	protected void postProcessCompoundLists(
  			List<List<AminoAcidCompound>> compoundLists) {
  		for (List<AminoAcidCompound> compounds : compoundLists) {
  			if (trimStops) {
  				trimStop(compounds);
  			}
  		}
  	}
docs: Performs the trimming of stop codons and the conversion of a valid start
  amino acid to M