org.biojava.bio.dp
Class BaumWelchSampler

java.lang.Object
  extended by org.biojava.bio.dp.AbstractTrainer
      extended by 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
BaumWelchSampler(DP dp)
           
 
Method Summary
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