[Biococoa-dev] Re: Using annotations

Koen van der Drift kvddrift at earthlink.net
Thu Feb 24 06:52:32 EST 2005

On Feb 24, 2005, at 4:51 AM, Alexander Griekspoor wrote:

>> Now how do I add it to the dictionary of the sequence? I already used 
>> the key (organism) inside BCAnnotation, so should I use it again? If 
>> yes, why is the key/name repeated inside the annotation object? This 
>> is not a critisicm, because I really like the way it is set up now. I 
>> am just trying to understand how it works :-)
> No problem, and I can see why it sounds strange at first so criticism 
> is at place here, hope it has become more clear now why I choose for 
> this approach. About how to add an annotation? I still have to add 
> that code to the sequence class ;-)

Thanks for the explanation. I understnad now your plan, and it looks 
good to me. And most of the code in the sequence class is already in 
place (in BCAbstractSequence), so you just have to change it to make it 
work with BCAnnotaion.

> Something else, as I proposed to make BCFeature a subclass of 
> BCAnnotation, do we want a single mutable dictionary annotations in 
> the sequence class containing both, or one annotations and one 
> features dict? I think the first or not?

I would make two separate dictionaries. Maybe sometimes people are only 
interested in features, and maybe sometimes only in annotations. With 2 
dictionaries that would make it easier to find. Or if you want to sort 
the features from symbol 1234 to 2345, it's easier I think if you 
dont't have to differentiate between features and annotations.

Now, one question, in another mail the word 'attributes' was used. Is 
this yet something else than annotations and features?

- Koen.

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