org.biojava.bio.dp
Interface TransitionTrainer


public interface TransitionTrainer

An object that can be used to train the transitions within a MarkovModel.

Author:
Matthew Pocock

Method Summary
 void addCount(State from, State to, double count)
          Add 'count' to the transition from->to.
 void clearCounts()
          Clears all of the counts to zero.
 void train(double nullModel, double weight)
          Trains the transition, given an expected probability, and a weight for that probability.
 

Method Detail

addCount

public void addCount(State from,
                     State to,
                     double count)
              throws IllegalSymbolException,
                     IllegalTransitionException
Add 'count' to the transition from->to.

This method may be called multiple times with the same from,to pair in which case, the times should be summed.

Parameters:
from - the source state
to - the destination state
count - the number of counts to add
Throws:
IllegalSymbolException
IllegalTransitionException

train

public void train(double nullModel,
                  double weight)
           throws IllegalSymbolException
Trains the transition, given an expected probability, and a weight for that probability.

This is equivalent to adding a count of nullModel * weight to each transition and then training with a weight of 0.

Parameters:
nullModel - the nullModel to use
weight - how many lots of the null model to add
Throws:
IllegalSymbolException

clearCounts

public void clearCounts()
Clears all of the counts to zero.