[Biococoa-dev] BCSequenceCluster

[Koen van der Drift]

On Oct 8, 2005, at 12:20 AM, Charles Parnot wrote:

> The conceptual differences are quite small, and I think to make the  
> framework really taste like Cocoa, it has to have a simple  
> interface. In fact, this is really the essence of what I was  
> wondering about. How many classes do we need for all these related  
> concepts? Is one enough?
>
> Regarding the implementation, I would tend to prefer using gaps,  
> because we already have the BCSymbol, we can easily generate  
> sequences without them (good suggestion, Peter), and it is easy to  
> use for display, comparisons,... On the other hand, using offsets  
> renders some task like "get the symbols at position 827 of all the  
> sequences" a bit hard (basically trading off simplicity and speed  
> for data compression). But in the end, I would be happy with any  
> implementation, as long as it works, particularly because I am  
> probably not going to be doing much of it!!
>
> so, just one class??

Let's at least start with one class. We could then either subclass  
them, or write categories for them to extend the various  
functionalities.

One thing that occurred to me, are we concerned about the order of  
the sequences? Otherwise we could use a set instead of an array, and  
create a BCSequenceSet class (I also like that name :)  It also fits  
nice in the framework: BCSymbol <-> BCSymbolSet, and BCSequence <->  
BCSequenceSet.

cheers,

- Koen.