[Biococoa-dev] more ramblings

Alexander Griekspoor mek at mekentosj.com
Thu Dec 2 02:02:01 EST 2004

> Why not describe a class structure on the list first, this way we can 
> all discuss about it. Once it's in CVS it will be more difficult 
> (albeit not
> impossible) to change stuff.
> What I mean is a scheme such as:
> BCSequenceBundle
>       |
>       -> has-a  NSArray of BCSequenceWrapper
> BCSequenceWrapper
>       |
>       -> has-a BCSequence, BCFeatures, etc
> BCFeatures
>       |
>       -> has-a dictionary of features (d'oh)
> etc
> This is just an example, not the way I think it should be, because I 
> have no idea how it should be :)
The basic setup is something we all agree on I think, it would be nice 
indeed if all classes had the same BCSequence prefix, although not easy 
;-) I like BCSequenceBundle, but I'm not sure if wrapper is 
appropriate. I know we consider it a wrapper object, but I would like 
to keep it closer to sequences, I thought of BCAnnotatedSequence, but 
it would loose the common prefix. Still, better than BCSequenceWrapper. 
Anyway, the (semi-)native englishmen on this list can jump in here ;-). 
Wait, would it be an idea to make it:

BCAnnotatedSequenceBundle - a bundle of BCAnnotatedSequences (in an 

BCAnnotatedSequence - contains a dictionary of BCFeatures (so no 
BCFeatures object, because that has no advantage over a dictionary), a 
BCSequence, a dictionary of BCAnnotation

BCFeature - a feature
BCAnnotation - a non-feature annotation (notes, authors, links, etc etc)
These two resemble BioPerls setup

>> Anyway, personally, I feel that throwing errors at compile time 
>> rather than
>> while a program is running is the better option
> Actually, I think that is a good point. But we have to be aware of the 
> fact that a developer can have all compiler warnings turned off.
Then it's a stupid developer IMHO....

                     ** Alexander Griekspoor **
              The Netherlands Cancer Institute
              Department of Tumorbiology (H4)
         Plesmanlaan 121, 1066 CX, Amsterdam
                    Tel:  + 31 20 - 512 2023
                    Fax:  + 31 20 - 512 2029
                    AIM: mekentosj at mac.com
                    E-mail: a.griekspoor at nki.nl
                Web: http://www.mekentosj.com

       Microsoft is not the answer,
       Microsoft is the question,
       NO is the answer


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