SimpleHMMTrainer (biojava-legacy 1.9.7 API)

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 Details
- SimpleHMMTrainer
  
  public SimpleHMMTrainer(MarkovModel model) throws IllegalSymbolException
  
  Throws:
  
  IllegalSymbolException
Method Details
- 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