org.biojava.bio.dp
Class SimpleHMMTrainer

java.lang.Object
  extended by org.biojava.bio.dp.SimpleHMMTrainer
All Implemented Interfaces:
HMMTrainer

public class SimpleHMMTrainer
extends java.lang.Object
implements HMMTrainer


Constructor Summary
SimpleHMMTrainer(MarkovModel model)
           
 
Method Summary
 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 java.lang.IllegalArgumentException
Description copied from interface: HMMTrainer
record that a transition was observed between the specified states.

Specified by:
recordTransition in interface HMMTrainer
Throws:
java.lang.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