[Biococoa-dev] Annotation questions

Koen van der Drift kvddrift at earthlink.net
Sun May 29 15:27:31 EDT 2005


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 

Let me know what you think,


- Koen.

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