[Biococoa-dev] more ramblings

[Alexander Griekspoor]

> 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.

Yes, categories are nice for developers to quickly add features to 
classes, but we shouldn't use them in a framework in my opinion. It 
hopelessly scatters methods and often ends up in one big mess....
>
>
>>  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.

It's an idea about how to further organize and extend the sequence 
classes to a higher level. Especially with regards to annotations. The 
sequence class which we all know and love (haha) would be the core 
which contains the actual symbol sequence. Above that would be a 
wrapper that contains this sequence, but also the accompanying 
annotations, metadata and notes. Certainly when processing data you 
don't always need the annotations and this way you can keep things 
lightweight if needed. Above that you can envision the need for 
sequence groups or clusters, related sequences for instance 
(translations/conversions), alignments, genomes etc.
So, these is not a class hierarchy rather a wrapper hierarchy (if that 
exist). How we practically implement and name this is another issue 
(and probably long debate ;-), but  I think it's a nice working 
model...
Hope I did makes clearer, and not even more fussy.
Alex



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                     ** Alexander Griekspoor **
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               The Netherlands Cancer Institute
               Department of Tumorbiology (H4)
          Plesmanlaan 121, 1066 CX, Amsterdam
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                     E-mail: a.griekspoor at nki.nl
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