[Biococoa-dev] Subclassing BCSequence really needed?

Koen van der Drift kvddrift at earthlink.net
Sun Oct 24 17:26:18 EDT 2004

On Oct 23, 2004, at 5:59 PM, Alexander Griekspoor wrote:

> I think we should think a bit of how to setup annotations and 
> features, that's what these things should be in. Once that is in 
> place, one can add as many start and stop positions as he/she wants. 
> We can than get rid of these here.

Good idea, that will also allow us to start working on the BCSequenceIO 

Already a few things come to mind:

1. Should we have just one BCSequenceReader class, which takes care of 
all various file formats, or should we subclass for each format? I'm 
not sure yet what the best solution is.

2. Some formats can contain multiple seqeuences (eg fasta). Should we 
return an NSArray of BCSequences only in those cases, or to be more 
consistent for all formats? I suggest the latter.

3. Do we need an additional class that holds the BCSequence plus all 
other info, or should everything go into the BCSequence class?

shoot away :D

- Koen.

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