[BioRuby] Bioruby HTML output

[Pjotr Prins]

On Tue, Jan 19, 2010 at 09:41:31PM +0900, Toshiaki Katayama wrote:
> All we need to do is to add these methods in every database class
> comprehensively.
> 
> I think this is simple enough and beautiful.
> I'll attach a primitive pseudo code in below.
> Comments are welcome.

I agree with Tomoaki it is too restrictive. What, indeed, if we want
to present the HTML in a different way?

The second comment is that I dislike the way the current files like
sequence.rb and alignment.rb are mushrooming in size. There is much
too much in there, which discourages people from diving in. I believe
code should be readable, and easy to understand/digest.

Sticking in output 'details', like HTML generation, does not help.

I really would like all HTML to be in one sub-tree. Also XML, RDF and
whatnot. When it is 'business' logic it should be in database. When it
is output transformations it is not 'business' logic any longer.

Don't you think the Sequence, or KEGG, object should not care about
HTML? Or RDF, or plotting? Those are separate functionalities. They
share common access patterns - which are part of the DB class.

Finally, why not use method names? What is the added value of 

  output(:html)

over 

  output_html

Pj.