[Biojava-dev] DP memory leak

[Lachlan James Coin]

Hi,

I came across a bit of a memory leak while using the dp code.  The 
problem is that AlphabetManager keeps a reference to every alphabet 
created, including StateAlphabetcreated when using the dp package.  I 
had extended the EmissionState class in such a way that the instances 
were of a non-trivial size.  I am also creating (one after the other) a 
lot of different state alphabets.  The result was that I ran out of 
memory farily quickly.

One possible fix I thought of was to add "deregisterAlphabet(name)" 
method to AlphabetManager, and to call this from the finalize mehod of 
SimpleMarkovModel, so that when the garbage collector thinks it can 
clear the markov model the statealphabet is removed from the 
AlphabetManager registry and can then also be garbage collected.   Also, 
it would be necessary to make alphabetToIndex a WeakHashMap.

Any other suggestions?  Can I make these changes?

Thanks,

Lachlan