[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.
On May 29, 2005, at 3:27 PM, Koen van der Drift wrote:
> 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,
> - Koen.
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
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