[Biococoa-dev] Annotation

Charles PARNOT charles.parnot at stanford.edu
Mon Feb 21 01:42:32 EST 2005

At 9:46 PM -0500 2/20/05, Koen van der Drift wrote:
>On Feb 20, 2005, at 2:05 PM, Charles PARNOT wrote:
>>It is because you have not #import-ed the BCSequenceProtein header, so the compiler does not know it is a subclass of BCAbstractSequence.
>Thanks - I added some more code and fixes. If everyone agress this is the right approach for the annotations, I will start adding more code.
>- Koen.

I do think the NSMutableDictionary is very appropriate for annotations. Regarding the current implementation, it looks good to me. My only comment is I don't think we need a 'setAnnotations:' method. This is a bit dangerous, particularly with a mutable dictionary as argument. Instead, methods 'removeAnnotationWithKey:', 'removeAllAnnotations' and 'addAnnotationsFromDictionary:' will do the job.

BTW, I corrected some of the code because I needed the compiled framework for the testing unit thing and there was a compiler error.

Let me know, guys, if and when you want me to incorporate the tests in the cvs?

Also, Koen, I have one question about the symbolSet: it seems that all instances of one sequence type use the same symbol set. Is that right? Do you think it is going to stay like this, or are there special cases where we will want to change that? If this is true, we could leverage that knowledge to simplify the init methods of the sequence classes. Let me know, I can explain better what I mean.


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Charles Parnot
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