[BioRuby] Bioruby HTML output

[Pjotr Prins]

Dear Toshiaki,

On Wed, Jan 20, 2010 at 01:21:54AM +0900, Toshiaki Katayama wrote:
> > 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.
> 
> I'm not sure about HTML but FASTA and RDF, for example, are tightly
> related to the original database format/contents. So, I proposed
> to have methods to generate formatted string in each database class.
> 
> There can be many ways to design OO class trees and to find the best
> way to represent/abstract things is always a difficult task.

I wrote a nice alignment HTML output generator. Which also displays PAML
output. Currently it is in bio/output/html/htmlalignment.rb and the
class is named Bio::Html::Alignment. 

For the current Bioruby, where do you want to put that? I don't feel
it should be cluttering alignment.rb. Naohisa has suggested
bio/alignment/output/html/alignment.rb instead. I feel uncomfortable
with this. But it is kinda consistent with above, tightly relating it
to the alignment object.

What do you think of the class name?

The code is in my color-alignment branch, see

  http://github.com/pjotrp/bioruby/tree/color-alignment

Is anyone else interested in this type of discussion? We can take it
off-list.

Pj.