[BioRuby] Bioruby HTML output

[Tomoaki NISHIYAMA]

Hi,
Pjotr Prins wrote:
 > On second thought, escaping is less obvious than I thought. I can
 > escape all generated HTML, but that leaves no way to customize the
 > output. Say I want to include an href in a sequence descriptor - which
 > is a fairly typical requirement - that would be disabled.

I agree this. Having a link to original sequence on the name
is usually good idea.

 > I am going to add a 'master' switch for escaping of HTML. The default
 > will be with escaping.

How do you think to test if the object responds to to_html
and then call to_html else pass to escapeHTML.
The object may internally plain text and htmlized text or
plain text plus link information or just the plain text
but cares how is output as html inline element.

If properly imlemented, it can generate a link from "gi|112233|..."
within a text and cache for the converted result.

The object can also simply pass the user supplied html.

I think it is a predictable use that user supplied sequence be aligned
with sequences obtained from databases. Isn't it better to be able to
regard user supplied text as a simple text but the sequence from 
databases having proper link?  This may not be simple with a master switch.