[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
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,
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