[Biococoa-dev] Base test

[Alexander Griekspoor]

>>  If we go for a strict separation between model (data), controller, 
>> and view (which I strongly am in favour of),
>
> Me too! BioCocoa should focus on the model and maybe the controller 
> part, I think.
Yep, perhaps we can in the future add some appkit stuff like views / 
sequence pickers etc, but that is a long way down the road.

>
>>  we should move all these kind of methods outside of our data classes 
>> (which the sequence clearly is). That way we don't have to update 
>> these methods everytime we edit the sequence.
>
> I disagree, the sequence takes care of it's own internal bookkeeping. 
> But it doesn't have to be recalculated with each edit, only when 
> another class want that info.

Well, I guess we are hitting the grey borderline here. I strongly 
suggest not to add things like translation and stuff in the sequence 
classes, this simply requires to much logic (like managing/choosing 
translation dictionaries etc). On the other hand you might be right 
that a simple method like the occurrence of certain amino acids might 
go in the sequence classes themselves, although even that I would 
rather see in the utils class. Just keep the sequences data containers. 
If we prevent the addition of these 'type specific' methods in the 
sequence classes themselves we can keep them as similar as possible an 
put as much as possible in the superclass. Of course it would be nice 
if the util objects would show a consistent setup as well.
I think we should compare the sequence class to the nsstring class. 
Things like representations, editing, subranges, comparison methods and 
stuff go in the string class, things like translations to different 
languages, spell checking, etc goes in separate controllers.
In the end this probably will have to be decided on a method per method 
basis....

Alex

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                       ** Alexander Griekspoor **
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                 The Netherlands Cancer Institute
                 Department of Tumorbiology (H4)
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                     E-mail: a.griekspoor at nki.nl
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