[BioSQL-l] adding non-positional features via bioperl to a biosql database

[James Procter]

Hilmar Lapp wrote:
> 
> On Feb 10, 2009, at 6:25 PM, James Procter wrote:
> 
>> I tried adding annotation directly to the sequence object, but
>> couldn't work out
>> where they appeared in Biojava.
> 
> I think this is where the bug is more likely, in that this is something
> that I think we will all agree that it should work but apparently doesn't.

Yes. I would have used that method if it appeared to work with the
existing biojava codebase for retrieving annotation from BioSQL and
serving it over DAS.

I have to check here, but I think that the other reason I didn't use the
annotation object (in the current bioperl 1.6 state) was that it does
not support all the attributes needed for this - and that was probably
why it was not used in the biojava implementation, either. I'll verify
this and post again later.

Jim.

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J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
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