Add a colourer for secondary-structure (and accessibility)

[tonyelewis]

It would often be useful to colour by secondary structure. Now that thid code is able to do its own secondary structure calculations, this can be more consistently applied. Some work may be required to work out how to handle if/when to do the necessary secondary-structure calculations.

Also, this would require a change to the options, which currently just offer --gradient-colour-alignment.

Along the same lines, it may be useful to be able to colour by accessibility.

The idea of a secondary-structure coloured alignment (--aln-to-html-file) relates to the 2DSEC issues in #29.