Some database interfaces do not provide access to the annotations stored in the low-level databases
As discussed in bob#235 (closed), there are some databases that do not take care of the annotations stored in the low-level databases. New
BioDatabase interfaces (and new
BioFile interfaces) need to be provided.
I think, having a generic
BioFile derivative (maybe called
BioFileFromLowLevel or alike) that keeps track of the low-level
File object (which is required to query the annotations) would be easier than writing specialized
XXXBioFile's for each case. Also, a generic
BioDatabaseWithAnnotations can be created, from which the
XXXBioDatabase's can be derived, so that the implementation needs to be done only once.
The question is A) if we want to have these intermediate level
BioDatabaseWithAnnotations implementations and B) where we should put them? Is there any need for such intermediate level classes in other packages than