Package org.biojava.bio.dist

Class SimpleDistributionTrainer

java.lang.Object

org.biojava.bio.dist.SimpleDistributionTrainer

All Implemented Interfaces:

Serializable, DistributionTrainer

public final class SimpleDistributionTrainer
extends Object
implements DistributionTrainer, Serializable

Deprecated.

Distribution impls should be providing custom trainers.

A simple implemenation of a distribution trainer.

This requires the distribuiton being trained to have a working setWeight method that doesn't throw an UnsupportedOperationExcepiton.

Author:

Matthew Pocock

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
SimpleDistributionTrainer(Distribution dis)	Deprecated.

Method Summary

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

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleDistributionTrainer

public SimpleDistributionTrainer(Distribution dis)
                          throws IllegalAlphabetException

Deprecated.

Throws:

IllegalAlphabetException

Method Detail

addCount

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

Deprecated.

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

count - the number of times to add

Throws:

IllegalSymbolException - if sym is not recognised

getCount

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

Deprecated.

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

train

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

Deprecated.

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

clearCounts

public void clearCounts(DistributionTrainerContext dtc)

Deprecated.

Description copied from interface: DistributionTrainer

Clears all of the counts to zero.

Specified by:

clearCounts in interface DistributionTrainer