[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
array)
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....
Cheers,
Alex
*********************************************************
** 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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