[BioRuby] Bioruby HTML output

[Pjotr Prins]

Hi all,

OK, I'll adapt the output generator to escape symbols. And I think
you are right it belongs in the generator. There are three scenario's
really:

1. Output that never contains symbols (sequence)
2. Output that can contain symbols, but should be escaped
(descriptions, id's)
3. Output that can contain HTML

In my case I have all three. 

I think with a sequence we can assume the content is a legal string.
Escaping is overkill and (if needed) points to a bigger problem. I
think we should not clutter the code with (1) - or degrade performance
by default.

Case (2) yes!

case (3), like a title or some text to plug in, we should escape by
default, but add a parameter :html_escape == false for the cases the user
wants to plug in HTML.

OK?

Pj.