[Biococoa-dev] Sequence Structure

Charles Parnot charles.parnot at gmail.com
Sun Jul 10 20:35:47 EDT 2005

On Jul 10, 2005, at 4:53 PM, Koen van der Drift wrote:

> On Jul 10, 2005, at 7:42 PM, Philipp Seibel wrote:
>> I suggest to use one single class to represent a sequence ->  
>> BCSequence. (BCAbstractSequence and others are really not  
>> present :-)).
>> But it seems everybody except from me likes the oversized ( just  
>> my opinion ;-) ) inheritance model.
> I am not in favor of them too, just check the archives for some  
> nice discussions :)

Phil, I am also more in favor of a single public class, but not for  
the same reason: for a simpler interface. However, I would not mind  
some subclasses hidden behind a class cluster design (I don't know if  
people knew about that idea? ;-)... which means I am OK with the  
inheritance model.

In any case, there will and there is already a strong request for  
typed sequences, mostly for compile-time checking. And also, there is  
a strong willingness to choose between the two structures: either one- 
class-do-it-all or a tree of typed classes. Up until now, we had both  
structures in parallel, which was a way of not choosing. The  
consensus is now to choose, as everybody seem confused by the current  
design... well, except me ;-)

And if we are going to choose, we should listen to those people  
asking for typed classes. And I can already see the first FAQ if we  
did not have typed sequence:
"Q1: Where is the DNA sequence class?
A: Eu... There ain't any.
Q2: WTF?"

So the bottom line is: let's go with the typed classes :-)


Help science move fast forward:

Charles Parnot
charles.parnot at gmail.com

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