[Biococoa-dev] BCSequenceCluster

[Koen van der Drift]

On Oct 5, 2005, at 7:51 PM, Charles Parnot wrote:

> I think that returning the array of offset to the user is like  
> giving the user the Bible not as a string, but as a list of  
> positions of all the letters of the alphabet!!
>
> The offset array should remain private, I think. We should return  
> sequences with gaps (either generate them using the offsetArray, or  
> use gaps symbols from the start).
>

Making the offsetArray private sounds like a good idea. I also like  
the use of the gap symbol.  However, what I am starting to sense now  
is that we are actually making a BCAlignment class in disguise and I  
am not sure if we should do that in this case. It's not clear to me  
from Peter's original request if that's what he meant. What type of  
alignment is used for instance for phylogenetic sequence clusters, I  
assume that's what he is talking about?

- Koen.