Package org.biojava.bio.dist

Class SimpleDistributionTrainerContext

java.lang.Object

org.biojava.bio.dist.SimpleDistributionTrainerContext

All Implemented Interfaces:

Serializable, DistributionTrainerContext

Direct Known Subclasses:

SimpleModelTrainer

public class SimpleDistributionTrainerContext
extends Object
implements DistributionTrainerContext, Serializable

A no-frills implementation of DistributionTrainerContext.

Since:

1.0

Author:

Matthew Pocock

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
SimpleDistributionTrainerContext()	Create a new context with no initial distributions or trainers.

Method Summary

Modifier and Type	Method	Description
void	addCount(Distribution dist, Symbol sym, double times)	Registers that sym was counted in this state.
void	clearCounts()	Clears all of the counts to zero.
double	getCount(Distribution dist, Symbol sym)	Return the number of counts of a particular symbol which will be used to train the specified distribution.
double	getNullModelWeight()	Return the number of pseudocounts added to the distribution when training.
DistributionTrainer	getTrainer(Distribution dist)	Return the Distribution trainer object from the current context.
void	registerDistribution(Distribution dist)	Register a distribution object with this context.
void	registerTrainer(Distribution dist, DistributionTrainer trainer)	Register a Distribution and an associated DistributionTrainer object.
void	setNullModelWeight(double nullModelWeight)	Set the number of pseudocounts to add when training the distribution.
void	train()	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

SimpleDistributionTrainerContext

public SimpleDistributionTrainerContext()

Create a new context with no initial distributions or trainers.

Method Detail

getNullModelWeight

public double getNullModelWeight()

Description copied from interface: DistributionTrainerContext

Return the number of pseudocounts added to the distribution when training.

Specified by:

getNullModelWeight in interface DistributionTrainerContext

Returns:

the null model weight

setNullModelWeight

public void setNullModelWeight(double nullModelWeight)

Description copied from interface: DistributionTrainerContext

Set the number of pseudocounts to add when training the distribution. These counts are added in proportion to the null model of the distribution being trained.

Specified by:

setNullModelWeight in interface DistributionTrainerContext

Parameters:

nullModelWeight - the new null model weight

registerDistribution

public void registerDistribution(Distribution dist)

Description copied from interface: DistributionTrainerContext

Register a distribution object with this context.

This method is a request to the context to register dist. If dist is already registered then this method should do nothing. If it is not registered, then it should invoke dist.registerWithTrainer

Specified by:

registerDistribution in interface DistributionTrainerContext

Parameters:

dist - the Distribution to register

registerTrainer

public void registerTrainer(Distribution dist,
                            DistributionTrainer trainer)

Description copied from interface: DistributionTrainerContext

Register a Distribution and an associated DistributionTrainer object.

In the registerWithTrainer method of a Distribution, it should associate itself with a trainer using this method.

Specified by:

registerTrainer in interface DistributionTrainerContext

Parameters:

dist - the distribution to be registered.

trainer - the distribution's trainer object to be registered.

getTrainer

public DistributionTrainer getTrainer(Distribution dist)

Description copied from interface: DistributionTrainerContext

Return the Distribution trainer object from the current context.

Specified by:

getTrainer in interface DistributionTrainerContext

Parameters:

dist - the Distribution whose trainer is required

Returns:

the DistributionTrainer for the distribution

addCount

public void addCount(Distribution dist,
                     Symbol sym,
                     double times)
              throws IllegalSymbolException

Description copied from interface: DistributionTrainerContext

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 DistributionTrainerContext

Parameters:

dist - the Distribution that the symbol was associated with

sym - the Symbol seen

times - the number of times to add

Throws:

IllegalSymbolException - if sym is not recognised by dist

getCount

public double getCount(Distribution dist,
                       Symbol sym)
                throws IllegalSymbolException

Description copied from interface: DistributionTrainerContext

Return the number of counts of a particular symbol which will be used to train the specified distribution.

Specified by:

getCount in interface DistributionTrainerContext

Parameters:

dist - the Distribution to return counts for

sym - the symbol to get the count for

Returns:

the number of counts

Throws:

IllegalSymbolException - if the symbol is not accepted by the distribution

train

public void train()
           throws ChangeVetoException

Description copied from interface: DistributionTrainerContext

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.

Specified by:

train in interface DistributionTrainerContext

Throws:

ChangeVetoException - if any of the distributions can't be trained

clearCounts

public void clearCounts()

Description copied from interface: DistributionTrainerContext

Clears all of the counts to zero.

Specified by:

clearCounts in interface DistributionTrainerContext