Thanks for the reply, Richard - you've cleared up the situation immensely. Richard Holland wrote: > > (d) why are Terms using the == equality test instead of equals(). > (d) for speed, and on the assumption that nobody would want to have two > copies of the exact same ontology in memory at any one time. this is what I thought - and I understand both sides. However, there is always a potential bone of contention here. Is there some kind of mechanism to normalise (or register) an ontology/term instance against the set of known ontology instances ? This might prove useful in situations where ontologies have been imported ad-hoc from alternative sources (such as a web service, where a clone of the object structure is received by the server which will have their own object references).
> (b) how can you get a singleton ontology instance loaded from BioSQL > (b) Use the getObject() method on the RichObjectFactory after already > having called the connectToBioSQL() method. Ah - this is what I missed - in the documentation or otherwise :) However - this isn't going to work perfectly in my situation. I am expecting to need thread safe access (as far as is possible) to several biosql backed rich sequence databases - and potentially, each instance may work in a different namespace. I'm sure you can see how this requirement conflicts with the use of a default ontology singleton for term import in equivalence methods. > (a) getProperty()/getProperties() is deprecated but hasn't been marked Its good to know this - as it happens, I ended up using the getNoteSet and implementing an equals() based term equivalence mechanism for my specific sitation. > I hope this helps. it does ! thanks again, Jim. -- ------------------------------------------------------------------- J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
