org.biojava.bio.dp
Class BaumWelchSampler

java.lang.Object
  |
  +--org.biojava.bio.dp.AbstractTrainer
        |
        +--org.biojava.bio.dp.BaumWelchSampler

All Implemented Interfaces:

java.io.Serializable, TrainingAlgorithm

public class BaumWelchSampler

extends AbstractTrainer

implements java.io.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

See Also:

Serialized Form

Constructor Summary

BaumWelchSampler(DP dp)

Method Summary

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

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

IllegalSymbolException

IllegalTransitionException

IllegalAlphabetException