[Biococoa-dev] more ramblings
Koen van der Drift
kvddrift at earthlink.net
Thu Nov 18 18:37:06 EST 2004
Some short comments here - too busy to read all the recent postings.
> Yeah, the more I look at BioJava’s actual code, the less excited I
> become about using their progress as a model. Have you ever tried to
> trace through their process for translation? I never got to the point
> where I could see anything actually related to an amino acid. It
> calls through so many methods before it attempts to do anything that
> it must take about a half an hour to accomplish anything
I like their interface, however the implementation is a twisty little
maze of passages.
> BioJava rant aside – I’m comfortable with the idea mentioned
> somewhere in Alex’s message of shifting the actual code for some of
> the sequence manipulation/calculation into wrapper classes, but
> providing call throughs to the methods in the sequence classes.
> Another alternative would be to have these methods attached as
> categories on BCSequences. With either of these, you would get Koen’s
> code separation and I’d be happy about the more direct connection of
> methods to data.
I think we all agree on this approach then. I wouldn't use categories,
though, we can leave it in BCSequence. So we put the sequence
manipulations in wrapper classes and provide appropriate convenience
methods in BCSequence or one of its subclasses.
> Anyway, to stir up more controversy around here, I had always
> envisioned something along the following structure:
> Sequence bundle
> (groups related sequences)
> Sequence wrapper
> (holds features, notes, etc.)
Sorry, but I have no idea what you mean by the scheme above.
More information about the Biococoa-dev