[Biococoa-dev] Annotation

[Charles PARNOT]

At 12:00 +0100 2/22/05, Alexander Griekspoor wrote:
>Having said that, I'll add a basic BCAnnotation class tonight (based on my Enzyme example), and modify the sequence class to represent the addition. The BCFeature class will be its subclass and contain an NSRange property and some position related methods (similar to the once in the sequence class). Many questions on the implementation will come along I guess. I'll have a look at the methods Charles (or John?) was proposing with the plists and predefined keys...

That was John

>I have two questions already though:
>- if we request subsequences, do we add a boolean argument to include the annotations? It would mean that we have to include ALL position independent annotations, and all the ones that are within the range requested?

I think we can include that later, but yes, we would have to do that to be consistent. We may even need to add a new annotation to the subsequence to keep track of the history of that sequence, using one of these 'segment' tag you cited in your initial Annotation email.


>- do we use 1 or 0 based ranges? For the first 10 bases, do I create a range {0,10} or {1,10}. I think it would be nicest to use NSRanges, we can compensate in the accessors if necessary I guess...
>
>Cheers,
>Alex

The issue of 0 vs 1 is  a problem with cDNAs and the transcription or translation starting point, or is it a more widely used convention? One problem with the +1 convention is the absence of 0, IIRC. The positions goes -2, -1, +1, +2, right?
Anyway, that's a tough question. IMO, we should use a 0 based range to stick to the Cocoa conventions. In the Cocoa NSRange convention, the first character of a string is anyway not at position 0 or 1, but in between the two!
Of course,  the BCSequenceView would have to display the correct numbers, Alex ;-)

charles

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Charles Parnot
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