[Biococoa-dev] Annotation questions
biococoa at bioworxx.com
Sun May 29 16:04:56 EDT 2005
nice to hear something going on.
> 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.
The Annotation and Feature stuff has to be designed very carefully.
Btw i need it as well in my ProteinStructure classes. I think using
dictionaries and dictionaries in dictionaries are a solution, but
very difficult to understand for the user of the framework. On the
other hand it's very flexible and could be easily saved as a .plist.
So we should consider where we will need it in the future. I think
features are even more difficult to realize, because they could have
the same key and have a special order.
Finaly i would suggest to discuss at least for 2 - 3 weeks, what we
want to do with features and annotations and of course where they
appear in "real life". We should take the time, because this is a
very fundamental structure. I would also suggest to look at the
implementations of BioJava and the others. Btw. is there a BioJava
user in our group, to tell about pros and cons of their
implementation. Ok so far from me .....
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