account for gapped columns when mapping RNAalifold results to Jalview alignment

It looks like when RNAalifold is given an alignment which includes columns where everything is a gap - e.g.:
>a
ACG--TU
>b
ACU--TG
>c
TCU-TTA

RNAAliFold will return output that contains 6 columns, rather than 7, since it strips out the 4th column, where no residues are found.

The attached file demonstrates this.