org.biojava.bio.dp

Class BaumWelchTrainer

java.lang.Object

org.biojava.bio.dp.AbstractTrainer

org.biojava.bio.dp.BaumWelchTrainer

All Implemented Interfaces:

Serializable, TrainingAlgorithm

public class BaumWelchTrainer
extends AbstractTrainer
implements Serializable

Train a hidden markov model using maximum likelihood.

Note: this class currently only works for one-head models.

Since:

1.0

Author:

Matthew Pocock, Thomas Down, Todd Riley

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
BaumWelchTrainer(DP dp)

Method Summary

Modifier and Type	Method and Description
double	mathExp(double arg)
protected double	singleSequenceIteration(ModelTrainer trainer, SymbolList symList)

Methods inherited from class org.biojava.bio.dp.AbstractTrainer

getCurrentScore, getCycle, getDP, getLastScore, train

Methods inherited from class java.lang.Object

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

Constructor Detail

BaumWelchTrainer

public BaumWelchTrainer(DP dp)

Method Detail

singleSequenceIteration

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

Specified by:

singleSequenceIteration in class AbstractTrainer

Throws:

IllegalSymbolException

IllegalTransitionException

IllegalAlphabetException

mathExp

public double mathExp(double arg)