[Biococoa-dev] more ramblings

Koen van der Drift kvddrift at earthlink.net
Sun Nov 21 07:19:45 EST 2004

On Nov 19, 2004, at 5:41 AM, Alexander Griekspoor wrote:

> It's an idea about how to further organize and extend the sequence 
> classes to a higher level. Especially with regards to annotations. The 
> sequence class which we all know and love (haha) would be the core 
> which contains the actual symbol sequence. Above that would be a 
> wrapper that contains this sequence, but also the accompanying 
> annotations, metadata and notes. Certainly when processing data you 
> don't always need the annotations and this way you can keep things 
> lightweight if needed. Above that you can envision the need for 
> sequence groups or clusters, related sequences for instance 
> (translations/conversions), alignments, genomes etc.
> So, these is not a class hierarchy rather a wrapper hierarchy (if that 
> exist). How we practically implement and name this is another issue 
> (and probably long debate ;-), but  I think it's a nice working 
> model...
> Hope I did makes clearer, and not even more fussy.

Thanks - that indeed sounds like a good plan. I was working a bit on 
readClustalFile and it would indeed make a lot of sense to keep the 
files together, including the line that indicates the alignment. Also 
so far readFile ignores all information but the sequence. Right now, 
readFile returns an NSArray with sequences from the same file, but that 
should be not too difficult change, maybe to an NSDictionary? Or are 
you guys talking about a complete wrapper class?


- Koen.

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