org.biojava.bio.dist

Class SimpleDistribution

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.dist.AbstractDistribution

org.biojava.bio.dist.SimpleDistribution

All Implemented Interfaces:

Serializable, Distribution, Changeable

Direct Known Subclasses:

UntrainableDistribution

public class SimpleDistribution
extends AbstractDistribution
implements Serializable

A simple implementation of a distribution, which works with any finite alphabet.

Since:

1.0

Author:

Matthew Pocock, Thomas Down, Mark Schreiber

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	SimpleDistribution.Trainer A simple implementation of a trainer for this class.

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
SimpleDistribution(Distribution dist) make an instance of SimpleDistribution with weights identical to the specified Distribution.
SimpleDistribution(FiniteAlphabet alphabet) make an instance of SimpleDistribution for the specified Alphabet.

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.
double	getWeightImpl(AtomicSymbol s) Override this method to implement getting the weight for an atomic symbol.
protected double[]	getWeights() Get the underlying array that stores the weights.
protected boolean	hasWeights() Indicate whether the weights array has been allocated yet.
void	registerWithTrainer(DistributionTrainerContext dtc) Register an SimpleDistribution.Trainer instance as the trainer for this distribution.
protected void	setNullModelImpl(Distribution nullModel) Implement this to set the null model.
protected void	setWeightImpl(AtomicSymbol s, double w) 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

SimpleDistribution

public SimpleDistribution(FiniteAlphabet alphabet)

make an instance of SimpleDistribution for the specified Alphabet.

SimpleDistribution

public SimpleDistribution(Distribution dist)

make an instance of SimpleDistribution with weights identical to the specified Distribution.

Parameters:

dist - Distribution to copy the weights from.

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,
                                ChangeVetoException

Description copied from class: AbstractDistribution

Implement this to set the null model.

You should not inform any change listeners in this method. All of that work has been done for you.

Specified by:

setNullModelImpl in class AbstractDistribution

Parameters:

nullModel - the new null model Distribution

Throws:

IllegalAlphabetException - if the null model is for the wrong alphabet

ChangeVetoException - if your implementation wishes to block this opperation

hasWeights

protected boolean hasWeights()

Indicate whether the weights array has been allocated yet.

Returns:

true if the weights are allocated

getWeights

protected double[] getWeights()

Get the underlying array that stores the weights.

Modifying this will modify the state of the distribution.

Returns:

the weights array

getWeightImpl

public 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 s,
                             double w)
                      throws IllegalSymbolException,
                             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:

s - the AtomicSymbol to update for

w - the new weight for that symbol

Throws:

IllegalSymbolException - if the symbol is not known

ChangeVetoException - if the change is to be prevented

registerWithTrainer

public void registerWithTrainer(DistributionTrainerContext dtc)

Register an SimpleDistribution.Trainer instance as the trainer for this distribution.

Specified by:

registerWithTrainer in interface Distribution

Overrides:

registerWithTrainer in class AbstractDistribution

Parameters:

dtc - the context to register with