[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.)
>      |
>  Sequence

Sorry, but I have no idea what you mean by the scheme above.

- Koen.

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