org.biojava.bio.dp
Class AbstractTrainer

java.lang.Object
  |
  +--org.biojava.bio.dp.AbstractTrainer
Direct Known Subclasses:
BaumWelchSampler, BaumWelchTrainer

public abstract class AbstractTrainer
extends java.lang.Object
implements TrainingAlgorithm


Constructor Summary
protected AbstractTrainer()
           
  AbstractTrainer(DP dp)
           
 
Method Summary
 double getCurrentScore()
           
 int getCycle()
           
 DP getDP()
           
 double getLastScore()
           
protected abstract  double singleSequenceIteration(ModelTrainer trainer, SymbolList resList)
           
 void train(SequenceDB db, Distribution nullModel, double nullWeight, 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 Detail

AbstractTrainer

public AbstractTrainer(DP dp)

AbstractTrainer

protected AbstractTrainer()
Method Detail

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 resList)
                                           throws IllegalSymbolException,
                                                  IllegalTransitionException,
                                                  IllegalAlphabetException

train

public void train(SequenceDB db,
                  Distribution nullModel,
                  double nullWeight,
                  StoppingCriteria stopper)
           throws IllegalSymbolException,
                  BioException
Trains the sequences in db until stopper says to finnish.
Specified by:
train in interface TrainingAlgorithm