AbstractTrainer (biojava-legacy 1.9.7 API)

java.lang.Object

org.biojava.bio.dp.AbstractTrainer

All Implemented Interfaces:: TrainingAlgorithm

Direct Known Subclasses:: BaumWelchSampler, BaumWelchTrainer

public abstract class AbstractTrainer extends Object implements TrainingAlgorithm

An abstract implementation of TrainingAlgorithm that provides a framework for plugging in per-cycle code for parameter optimization.

Author:: Matthew Pocock, Thomas Down

Constructor Summary

Constructors

Modifier

Constructor

Description

protected

AbstractTrainer()

AbstractTrainer(DP dp)
Method Summary

Modifier and Type

Method

Description

double

getCurrentScore()

int

getCycle()

DP

getDP()

double

getLastScore()

protected abstract double

singleSequenceIteration(ModelTrainer trainer, SymbolList symList)

void

train(SequenceDB db, double nullModelWeight, StoppingCriteria stopper)

Trains the sequences in db until stopper says to finnish.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- AbstractTrainer
  
  public AbstractTrainer(DP dp)
- AbstractTrainer
  
  protected AbstractTrainer()
Method Details
- getLastScore
  
  public double getLastScore()
  
  Specified by:
  
  getLastScore in interface TrainingAlgorithm
- getCurrentScore
  
  public double getCurrentScore()
  
  Specified by:
  
  getCurrentScore in interface TrainingAlgorithm
- getCycle
  
  public int getCycle()
  
  Specified by:
  
  getCycle in interface TrainingAlgorithm
- getDP
  
  public DP getDP()
  
  Specified by:
  
  getDP in interface TrainingAlgorithm
- singleSequenceIteration
  
  protected abstract double singleSequenceIteration(ModelTrainer trainer, SymbolList symList) throws IllegalSymbolException, IllegalTransitionException, IllegalAlphabetException
  
  Throws:
  
  IllegalSymbolException
  
  IllegalTransitionException
  
  IllegalAlphabetException
- train
  
  public void train(SequenceDB db, double nullModelWeight, StoppingCriteria stopper) throws IllegalSymbolException, BioException
  
  Trains the sequences in db until stopper says to finnish.
  
  Specified by:
  
  train in interface TrainingAlgorithm
  
  Throws:
  
  IllegalSymbolException
  
  BioException