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

Methods

Modifier and Type	Method and Description
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

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

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

void clearCounts()

Clears all of the counts to zero.