org.biojava.bio.dist

Class SimpleDistribution.Trainer

java.lang.Object

org.biojava.bio.dist.SimpleDistribution.Trainer

All Implemented Interfaces:

DistributionTrainer

Enclosing class:

SimpleDistribution

protected class SimpleDistribution.Trainer
extends Object
implements DistributionTrainer

A simple implementation of a trainer for this class.

Since:

1.0

Author:

Matthew Pocock

Constructor Summary

Constructors

Constructor and Description
SimpleDistribution.Trainer() Create a new trainer.

Method Summary

Methods

Modifier and Type	Method and Description
void	addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times) Registers that sym was counted in this state.
void	clearCounts(DistributionTrainerContext dtc) Clears all of the counts to zero.
double	getCount(DistributionTrainerContext dtc, AtomicSymbol sym) Get the current count for this state.
void	train(DistributionTrainerContext dtc, double weight) Trains the Distribution, given a null model.
protected void	trainImpl(DistributionTrainerContext dtc, double weight)

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleDistribution.Trainer

public SimpleDistribution.Trainer()

Create a new trainer.

Method Detail

addCount

public void addCount(DistributionTrainerContext dtc,
            AtomicSymbol sym,
            double times)
              throws IllegalSymbolException

Description copied from interface: DistributionTrainer

Registers that sym was counted in this state.

This method may be called multiple times with the same symbol. In this case, the times should be summed.

Specified by:

addCount in interface DistributionTrainer

Parameters:

dtc - the DistributionTrainerContext within which the count was added

sym - the Symbol seen

times - the number of times to add

Throws:

IllegalSymbolException - if sym is not recognised

getCount

public double getCount(DistributionTrainerContext dtc,
              AtomicSymbol sym)
                throws IllegalSymbolException

Description copied from interface: DistributionTrainer

Get the current count for this state.

This method may be called multiple times with the same symbol. Each time it should return the agregate of the counts added with addCount since the last invocation of clearCounts.

Specified by:

getCount in interface DistributionTrainer

Parameters:

dtc - the DistributionTrainerContext within which the count was added

sym - the Symbol seen

Returns:

the agregate of the counts

Throws:

IllegalSymbolException - if sym is not recognised

clearCounts

public void clearCounts(DistributionTrainerContext dtc)

Description copied from interface: DistributionTrainer

Clears all of the counts to zero.

Specified by:

clearCounts in interface DistributionTrainer

train

public void train(DistributionTrainerContext dtc,
         double weight)
           throws ChangeVetoException

Description copied from interface: DistributionTrainer

Trains the Distribution, given a null model.

This will use the information collected with multiple addCount calls, and the null model to generate the new weights.

This method should not modify the underlying counts.

Specified by:

train in interface DistributionTrainer

Parameters:

dtc - the context to use

weight - how many lots of the null model to add

Throws:

ChangeVetoException - if the distribution could not have its weights modified

trainImpl

protected void trainImpl(DistributionTrainerContext dtc,
             double weight)