[Biococoa-dev] Annotation
Koen van der Drift
kvddrift at earthlink.net
Tue Feb 22 19:58:25 EST 2005
On Feb 22, 2005, at 1:32 PM, Alexander Griekspoor wrote:
>
>>> - 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...
>>
>> 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?
> Yes, guess so, but those are relative positions, so 0 in that case is
> the base itself.
>> 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!
>
> Yep, I would like to have it 0 based as well.... The ranges the
> findSubsequence methods use are also 0-based right? Guess, that's
> settled then... Correct me if I'm wrong but I believe BioJava's
> sequences are 1-based, but Koen might know better.
>
Ha, I missed this in all the messages from today, and already replied
on Alex's original question in a separate email. Yes, I think BioJava
uses a 1-based sequence. But I don't think Java have nice build-in
array's, so they had to write them theirselves. As I said, internally
we can use the 0-based code. However, imagine a find sequence dialog
window. That should accept and return values that are 1-based. Should
that be the responsibility of the developer, or should it be
BioCocoa's? I would say the latter, but if we decide on going 0-based
all the way, then we have to document that very well.
>> Of course, the BCSequenceView would have to display the correct
>> numbers, Alex ;-)
> Yeah yeah, LOL I got the message ;-)
> I'll let you know when the BCAnnotation class is in the CVS, ready to
> burn it down, haha
>
I can add something too, including symbols numbers. I probably have to
add a view + nib and maybe a controller. Any ideas how we are going to
organize the code within BCAppKit?
- Koen.
ps - great work everyone - it's good to see all the new code being
added!!!
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