[Biococoa-dev] BCSequence class cluster

[Koen van der Drift]

Hi John,

Happy new year, and good to see you're still alive :)


> A class cluster is a potentially good thing, in that it would hide 
> some of
> the complexity of the implementation from users.  It doesn't 
> necessarily
> make Koen happier, since we may well have all the current classes used
> internally.

If they are all hidden inside a class cluster, it looks like a good 
compromise to me.


> As far as I can tell, though, nothing short of me getting
> around to implementing BCSequenceNucleotide would solve Koen's biggest
> gripe, the duplication of three methods in the DNA and RNA subclasses.

Actually the code in BCSequenceDNA and BCSequenceRNA has been cleaned 
up a lot by putting many methods in BCTools, so is not an issue for me 
anymore :) So I am not sure at this point what would be the benefit of 
adding an additional BCSequenceNucleotide class.


> I don't think that we have an analogous situation here, though I'm not
> positive about that.  Given that, I think we should proceed with 
> caution,


Those are also my thoughts a class cluster. It looks a very nice idea, 
but it's still unclear to me if our situation is a good example for the 
introduction of class clusters.


- Koen.