code: @Override
  	public AbstractSequence<AminoAcidCompound> getSequence(
  			List<AminoAcidCompound> list) {
  		AbstractSequence<AminoAcidCompound> seq =super.getSequence(list);
  		Collection<Object> strCase = new ArrayList<Object>(seq.getLength());
  		for(int i=0;i<seq.getLength();i++) {
  			strCase.add(true);
  		}
  		seq.setUserCollection(strCase);
  		return seq;
  	}
docs: Assumes all compounds were uppercase
  @see org.biojava.nbio.core.sequence.io.ProteinSequenceCreator#getSequence(java.util.List)