[Biococoa-dev] Annotation questions

Koen van der Drift kvddrift at earthlink.net
Sun May 29 18:08:54 EDT 2005

I just commited the code in cvs, so everyone can have a look what I am 
talking about :)

If the approach in readSwissProtFile seems good, I will update other 
read... methods as well.


- Koen.

On May 29, 2005, at 3:27 PM, Koen van der Drift wrote:

> Hi,
> Spent some time today on BCSequenceReader to include more annotations. 
> For the SwissProt format (and probably other formats as well), some 
> annotations are in multiple lines. So I modified the - (void) 
> addAnnotation:(NSString *)annotation forKey: (NSString *) key to test 
> for existing keys. In that case I am appending the annotation, instead 
> of replacing it.
> Right now, the code in readSwissProt now first creates an dummy 
> sequence, then iterates over all the lines to add th e annotations, 
> and then  needs to add the sequence to the BCSequence object. 
> Currently there is no 'setSequence' method, so I choose to create 
> another BCSequence object with the sequencestring, and then copy the 
> annotations from the dummy object to the real object. However, the 
> setAnnotations method was commented out. Are there any objections if I 
> uncomment that?
> Another approach could be to move the addAnnotation from 
> BCAbstractSequence to BCSequenceReader.
> Also, we need to think how to implement nested annotations. The 
> easiest would be to make a BCAnnotations object as the value for 
> another BCAnnotation.
> Let me know what you think,
> cheers,
> - Koen.
> _______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biococoa-dev

More information about the Biococoa-dev mailing list