[Biococoa-dev] Base test

[Peter Schols]

Hi Koen and others,

This seems like a very good architecture to me.
The naming scheme makes sense as well, so maybe - as Alexander is 
suggesting - we should try to agree on this one.
My only concern at this point is that a new object will be created for 
every base. This might lead to performance problems with huge datasets 
(e.g. entire genomes). On the other hand, the other Bio frameworks seem 
to use a similar implementation so if it works in Java, it should 
definitely work in Cocoa ;-)

peter

On 13 Aug 2004, at 00:50, Koen van der Drift wrote:

> John,
>
> Why do you have a separate class for each base? Idon;t think that's 
> how a singleton is supposed to work (although I don't have an example 
> ready now that shows you how it *should* work :-).  You could just 
> have a BCSequenceUnit (or whatever we decide to call it) class and 
> create a base by eg passing only a name.  All the info about each base 
> can be stored in an external plist file. The same BCSequenceUnit class 
> can be used to create other structural objects.  This way most code 
> for getting name, properties is written only once, instead repeated 
> for each type of sequence unit.
>
>
> So for instance:
>
> BCSequenceUnit
> |
> |
> ----------------BCBase
> |
> |
> ----------------BCAminoAcid
> |
> |
> ----------------BCFunctionalGroup
> |
> |
> ----------etc
>
>
> I also suggest that BCSequenceDNA should be a subclass of BCSequence, 
> just as BCBase /BCSequenceDNABase should be a subclass of 
> BCSequenceUnit:
>
> BCSequence
> |
> |
> ----------------BCSequenceDNA
> |
> |
> ----------------BCSequenceProtein
>
>
> - Koen.
>
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