Package org.biojava.bio.dp

Class BaumWelchSampler

java.lang.Object

org.biojava.bio.dp.AbstractTrainer

org.biojava.bio.dp.BaumWelchSampler

All Implemented Interfaces:

Serializable, TrainingAlgorithm

public class BaumWelchSampler
extends AbstractTrainer
implements Serializable

Train a hidden markov model using a sampling algorithm.

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

Since:

1.0

Author:

Matthew Pocock, Richard Holland

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
BaumWelchSampler(DP dp)

Method Summary

Modifier and Type	Method	Description
protected double	singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
protected double	singleSequenceIteration(ModelTrainer trainer, SymbolList symList, ScoreType scoreType)

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

BaumWelchSampler

public BaumWelchSampler(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

singleSequenceIteration

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

Throws:

IllegalSymbolException

IllegalTransitionException

IllegalAlphabetException