org.biojava.bio.dp
Class BaumWelchTrainer

java.lang.Object
  extended by org.biojava.bio.dp.AbstractTrainer
      extended by org.biojava.bio.dp.BaumWelchTrainer
All Implemented Interfaces:
java.io.Serializable, TrainingAlgorithm

public class BaumWelchTrainer
extends AbstractTrainer
implements java.io.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
BaumWelchTrainer(DP dp)
           
 
Method Summary
 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)