code: @Override
  	public AbstractSequence<AminoAcidCompound> getSequence(String sequence,
  			long index) throws CompoundNotFoundException {
  		AbstractSequence<AminoAcidCompound> seq = super.getSequence(sequence.toUpperCase(Locale.ENGLISH), index);
  		seq.setUserCollection(getStringCase(sequence));
  		return seq;
  	}
docs: /* (non-Javadoc)
  @see org.biojava.nbio.core.sequence.io.ProteinSequenceCreator#getSequence(java.lang.String, long)