org.biojava.bio.dp
Class AbstractTrainer

java.lang.Object
  org.biojava.bio.dp.AbstractTrainer

All Implemented Interfaces:

TrainingAlgorithm

Direct Known Subclasses:

BaumWelchSampler, BaumWelchTrainer

public abstract class AbstractTrainer
extends Object
implements TrainingAlgorithm

An abstract implementation of TrainingAlgorithm that provides a framework for plugging in per-cycle code for parameter optimization.

Author:

Matthew Pocock, Thomas Down

Constructor Summary

protected	AbstractTrainer()
	AbstractTrainer(DP dp)

Method Summary

double	getCurrentScore()
int	getCycle()
DP	getDP()
double	getLastScore()
protected abstract double	singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
void	train(SequenceDB db, double nullModelWeight, StoppingCriteria stopper) Trains the sequences in db until stopper says to finnish.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AbstractTrainer

public AbstractTrainer(DP dp)

AbstractTrainer

protected AbstractTrainer()

Method Detail

getLastScore

public double getLastScore()

Specified by:

getLastScore in interface TrainingAlgorithm

getCurrentScore

public double getCurrentScore()

Specified by:

getCurrentScore in interface TrainingAlgorithm

getCycle

public int getCycle()

Specified by:

getCycle in interface TrainingAlgorithm

getDP

public DP getDP()

Specified by:

getDP in interface TrainingAlgorithm

singleSequenceIteration

protected abstract double singleSequenceIteration(ModelTrainer trainer,
                                                  SymbolList symList)
                                           throws IllegalSymbolException,
                                                  IllegalTransitionException,
                                                  IllegalAlphabetException

Throws:

IllegalSymbolException

IllegalTransitionException

IllegalAlphabetException

train

public void train(SequenceDB db,
                  double nullModelWeight,
                  StoppingCriteria stopper)
           throws IllegalSymbolException,
                  BioException

Trains the sequences in db until stopper says to finnish.

Specified by:

train in interface TrainingAlgorithm

Throws:

IllegalSymbolException

BioException