Package org.biojava.bio.dp

Class SimpleHMMTrainer

java.lang.Object

org.biojava.bio.dp.SimpleHMMTrainer

All Implemented Interfaces:

HMMTrainer

public class SimpleHMMTrainer
extends Object
implements HMMTrainer

Constructor Summary

Constructors

Constructor	Description
SimpleHMMTrainer(MarkovModel model)

Method Summary

Modifier and Type	Method	Description
void	completeCycle()	indicate that a cycle of training is completed and the emission/transition matrices should be updated.
void	recordEmittedSymbol(State state, Symbol symbol, double weight)	record that the specified symbol was emitted from the specified state.
void	recordTransition(State source, State dest, double weight)	record that a transition was observed between the specified states.
void	startCycle()	called to put the trainer into an initial state for a new round of training.

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleHMMTrainer

public SimpleHMMTrainer(MarkovModel model)
                 throws IllegalSymbolException

Throws:

IllegalSymbolException

Method Detail

startCycle

public void startCycle()

Description copied from interface: HMMTrainer

called to put the trainer into an initial state for a new round of training.

Specified by:

startCycle in interface HMMTrainer

recordEmittedSymbol

public void recordEmittedSymbol(State state,
                                Symbol symbol,
                                double weight)
                         throws IllegalSymbolException

Description copied from interface: HMMTrainer

record that the specified symbol was emitted from the specified state.

Specified by:

recordEmittedSymbol in interface HMMTrainer

Throws:

IllegalSymbolException

recordTransition

public void recordTransition(State source,
                             State dest,
                             double weight)
                      throws IllegalArgumentException

Description copied from interface: HMMTrainer

record that a transition was observed between the specified states.

Specified by:

recordTransition in interface HMMTrainer

Throws:

IllegalArgumentException

completeCycle

public void completeCycle()
                   throws BioException

Description copied from interface: HMMTrainer

indicate that a cycle of training is completed and the emission/transition matrices should be updated.

Specified by:

completeCycle in interface HMMTrainer

Throws:

BioException