[Biococoa-dev] SequenceIO

Koen van der Drift kvddrift at earthlink.net
Fri Jul 1 06:21:21 EDT 2005

On Jul 1, 2005, at 4:42 AM, Peter Schols wrote:

>> Therefore I propose that BCSequenceReader simply returns an array of 
>> objects. We can either store BCSequence objects in the array or 
>> create some kind of wrapper for each sequence, eg a new SequenceIO 
>> class. Annotations and features are now handled in the BCSequence 
>> class, so can be added in the IO code.
> I agree. Using an NSArray of sequences is better given that we now 
> deal with BCSequences. However, it would still be better if the IO 
> methods could return an NSSequenceSet or something. This class would 
> of course mainly consist of an NSArray containing sequences, but it 
> could also add support for annotations that apply to more than one 
> BCSequence (in phylogeny, you often have annotations that apply to a 
> group of sequences).

I think that Alex and John also were talking about something similar 
for alignments. So that could be a good addition.

- Koen.

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