[Biococoa-dev] Annotation

[Alexander Griekspoor]

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...
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?
- 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

On 22-feb-05, at 10:01, Alexander Griekspoor wrote:

>> One thing is actually still unclear to me. Do we need a BCFeatureSet 
>> (or BCFeatures)? Alex, could you lay out in more details what you are 
>> thinking about, what goes in the different class and what goes in 
>> BCSequence? Either here on the mailing list or commit some code on 
>> the cvs...
> Damn, your right, I should keep my mouth shut and implement the stuff 
> instead of talking all the time... I'm ashamed...
>
>
> *********************************************************
>                     ** Alexander Griekspoor **
> *********************************************************
>               The Netherlands Cancer Institute
>               Department of Tumorbiology (H4)
>          Plesmanlaan 121, 1066 CX, Amsterdam
>                     Tel:  + 31 20 - 512 2023
>                     Fax:  + 31 20 - 512 2029
>                     AIM: mekentosj at mac.com
>                     E-mail: a.griekspoor at nki.nl
>                 Web: http://www.mekentosj.com
>
> Windows is a 32-bit patch to a 16-bit shell for an 8-bit
> operating system, written for a 4-bit processor by a 2-
> bit company without 1 bit of sense.
>
> *********************************************************
>
> _______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biococoa-dev
>
>
*********************************************************
                     ** Alexander Griekspoor **
*********************************************************
               The Netherlands Cancer Institute
               Department of Tumorbiology (H4)
          Plesmanlaan 121, 1066 CX, Amsterdam
                     Tel:  + 31 20 - 512 2023
                     Fax:  + 31 20 - 512 2029
                     AIM: mekentosj at mac.com
                     E-mail: a.griekspoor at nki.nl
                 Web: http://www.mekentosj.com

Windows is a 32-bit patch to a 16-bit shell for an 8-bit
operating system, written for a 4-bit processor by a 2-
bit company without 1 bit of sense.

*********************************************************