code: @Override
  	public AbstractSequence<AminoAcidCompound> getSequence(String sequence, long index) throws CompoundNotFoundException, IOException {
  		SequenceFileProxyLoader<AminoAcidCompound> sequenceFileProxyLoader =
  				new SequenceFileProxyLoader<AminoAcidCompound>(
  						file,
  						sequenceParser,
  						index,
  						sequence.length(),
  						compoundSet
  						);
  		return new ProteinSequence(sequenceFileProxyLoader, compoundSet);
  	}
docs: Even though we are passing in the sequence we really only care about the length of the sequence and the offset
  index in the fasta file.
  @param sequence
  @param index
  @return
  @throws CompoundNotFoundException
  @throws IOException