[Biojava-dev] DP memory leak

[mark.schreiber at group.novartis.com]

Hi -

Does this Alphabet unloading do anything to PhredAlphabet that is created 
and registered by the PhredTools class or does it only deal with DP 
generated Alphas?

General question: Is there any reason why the DP generated Alpha needs to 
be registered with the AlphabetManager? Presumably not registering would 
prevent memory leaks?

Also, there is currently no way to deregister an Alphabet from 
AlphabetManager. Adding that functionality may be useful (even if not 
needed for this case). Might be good to allow exception throwing if people 
try to unload something that shouldn't be. For BioJava2 it might be good 
to allow change veto exceptions or similar to the register and deregister 
methods. The current registerAlphabet method simply overwrites the 
previous object associated with that name.

- Mark


Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
1 Science Park Road
#04-14 The Capricorn
Singapore 117528

phone +65 6722 2973
fax  +65 6722 2910