org.biojava.bio.dist

Class UniformDistribution

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.dist.AbstractDistribution

org.biojava.bio.dist.UniformDistribution

All Implemented Interfaces:

Serializable, Distribution, Changeable

public class UniformDistribution
extends AbstractDistribution
implements Serializable

An implementation of an uniform distribution

Since:

1.0

Author:

Matthew Pocock, Mark Schreiber, Thomas Down

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.dist.Distribution

Distribution.NullModelForwarder

Field Summary

Fields inherited from class org.biojava.bio.dist.AbstractDistribution

nullModelForwarder

Fields inherited from interface org.biojava.bio.dist.Distribution

NULL_MODEL, WEIGHTS

Constructor Summary

Constructors

Constructor and Description
UniformDistribution(FiniteAlphabet alphabet) Create a new UniformDistribution.

Method Summary

Modifier and Type	Method and Description
Alphabet	getAlphabet() The alphabet from which this spectrum emits symbols.
Distribution	getNullModel() Retrieve the null model Distribution that this Distribution recognizes.
protected double	getWeightImpl(AtomicSymbol s) Override this method to implement getting the weight for an atomic symbol.
void	registerWithTrainer(DistributionTrainerContext dtc) Register an IgnoreCountsTrainer instance as the trainer for this distribution.
protected void	setNullModelImpl(Distribution nullModel) Assign a background distribution.
protected void	setWeightImpl(AtomicSymbol sym, double weight) Implement this to actually set the weight.

Methods inherited from class org.biojava.bio.dist.AbstractDistribution

equals, getChangeSupport, getWeight, hashCode, sampleSymbol, setNullModel, setWeight

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

UniformDistribution

public UniformDistribution(FiniteAlphabet alphabet)

Create a new UniformDistribution.

Parameters:

alphabet - the finite alphabet to be over

Method Detail

getAlphabet

public Alphabet getAlphabet()

Description copied from interface: Distribution

The alphabet from which this spectrum emits symbols.

Specified by:

getAlphabet in interface Distribution

Returns:

the Alphabet associated with this spectrum

getNullModel

public Distribution getNullModel()

Description copied from interface: Distribution

Retrieve the null model Distribution that this Distribution recognizes.

Specified by:

getNullModel in interface Distribution

Returns:

the apropriate null model

setNullModelImpl

protected void setNullModelImpl(Distribution nullModel)
                         throws IllegalAlphabetException

Assign a background distribution.

Specified by:

setNullModelImpl in class AbstractDistribution

Parameters:

nullModel - the background distribution to assign

Throws:

IllegalAlphabetException - if nullModel is over an incompattible alphabet

getWeightImpl

protected double getWeightImpl(AtomicSymbol s)
                        throws IllegalSymbolException

Description copied from class: AbstractDistribution

Override this method to implement getting the weight for an atomic symbol. You should just do what is necessary to fetch state. All the work with exceptions and listeners will have been handled for you.

Specified by:

getWeightImpl in class AbstractDistribution

Parameters:

s - the AtomicSymbol to get the weight for

Returns:

the weight

Throws:

IllegalSymbolException - if sym is not known

setWeightImpl

protected void setWeightImpl(AtomicSymbol sym,
                             double weight)
                      throws ChangeVetoException

Description copied from class: AbstractDistribution

Implement this to actually set the weight.

Do not inform any listeners. This has already been done for you. Just update state.

Specified by:

setWeightImpl in class AbstractDistribution

Parameters:

sym - the AtomicSymbol to update for

weight - the new weight for that symbol

Throws:

ChangeVetoException - if the change is to be prevented

registerWithTrainer

public void registerWithTrainer(DistributionTrainerContext dtc)

Description copied from class: AbstractDistribution

Register an IgnoreCountsTrainer instance as the trainer for this distribution. Override this if you wish to implement a trainable distribution.

Specified by:

registerWithTrainer in interface Distribution

Overrides:

registerWithTrainer in class AbstractDistribution

Parameters:

dtc - the context to register with