[Biojava-dev] Problems with parameter change event notification in profile HMM

[hlr02 at doc.ic.ac.uk]

Hi,

I tested the change event notification for changes in profile HMM transition 
and emission probabilities, which should result in firing of a 
MarkovModel.PARAMETER change event. This doesn't always work:

1. Changing emission distributions by using setDistribution(distribution) 
results in no PARAMETER change events being fired at all, i.e.

for (Iterator i = profile.stateAlphabet().iterator(); i.hasNext(); ) {
  State s = (State) i.next();
  // this should generate parameter change events
  if (s instanceof EmissionState && ! (s instanceof MagicalState)) {
    EmissionState es = (EmissionState) s;
    // this doesn't generate change events
    es.setDistribution(
      new UniformDistribution((FiniteAlphabet)profile.emissionAlphabet())
    );
  } 
}

However, changing the emission distribution by stepping through the 
distribution and changing probabilities one by one using setWeight(symbol, 
weight) works fine and does result in change events.

2. Changing transition probabilities one by one in the transition alphabet 
returned by transitionFrom(state) doesn't result in any change events, i.e.

for (Iterator i = profile.stateAlphabet().iterator(); i.hasNext(); ) {
  
  State s = (State) i.next();
  double length = ( (FiniteAlphabet) profile.transitionsFrom(s)).size();
  FiniteAlphabet fromStates = profile.transitionsFrom(s);
  Distribution dist = profile.getWeights(s);
  // this doesn't result in change events
  for (Iterator j = fromStates.iterator(); j.hasNext(); ) {
    State t = (State) j.next();
    dist.setWeight(t, (1/length) );
  }
} 

However, changing the transition probability from a state in one go by using 
setWeights(state,distribution) does result in firing a PARAMETER change event.

I used two change listeners, a change forwarder and ChangeListener.LOG_TO_OUT 
to test the above.

Since the above may allow changes in the model without any change notification, 
this could create serious problems when for example a Change Listener in a GUI 
relies on change events to update its state.

Any ideas how to fix this?

Regards,

Henry