code: public static void setLowercaseToNull( ProteinSequence seq,
  			Object[] out) {
  		// should have been set by seq creator
  		Collection<Object> userCollection = seq.getUserCollection();
  		if(userCollection == null)
  			throw new IllegalArgumentException("Sequence doesn't contain valid case info");
  		if(userCollection.size() != out.length)
  			throw new IllegalArgumentException("Sequence length doesn't math output array length");
  
  		int pos = 0;
  		for(Object isAligned : userCollection) {
  			assert(isAligned instanceof Boolean);
  			if(!(Boolean)isAligned) {
  				out[pos] = null;
  			}
  			pos++;
  		}
  	}
docs: Takes a {@link ProteinSequence} which was created by a
  {@link CasePreservingProteinSequenceCreator}. Uses the case info
  stored in the user collection to modify the output array.
  
  <p>Sets elements of the output array which correspond to lowercase letters
  to null.
  
  @param seq Input sequence with case stored as the user collection
  @param out