SVG export: insert space to materialize hidden columns + other details

Hi Vincent.

It looks like you have a reference sequence set, but then have hidden the reference sequence - is that correct ? Not having a reference sequence set would remove the letters from the alignment ruler, but then the ruler would count column numbers.

Jalview currently can’t do exactly what you ask for re materialise hidden columns, not showing the residue letter along side reference sequence numbering in the ruler and showing the position numbers on the left and right extent of the ruler - but it is fairly easy to implement them (though enhanced hidden column visibility will need some rigorous testing, since it means adjusting the MSA layout grid).

However, in the situation you’ve shown, we usually recommend using wrap mode if you want to have sequence numbers at the left and right hand side. You could perhaps try to enable that to see if it suits your needs ? In wrap mode Jalview can show sequence numbers at the left and right of each sequence.

Jim