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:

Changeable, Distribution, java.io.Serializable

Direct Known Subclasses:

UntrainableDistribution

public class SimpleDistribution

extends AbstractDistribution

implements java.io.Serializable

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

Author:

Matthew Pocock, Thomas Down, Mark Schreiber

See Also:

Serialized Form

Nested Class Summary

protected class

SimpleDistribution.Trainer

Nested classes inherited from class org.biojava.bio.dist.Distribution

Distribution.NullModelForwarder

Field Summary

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

nullModelForwarder, symbolIndices

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

NULL_MODEL, WEIGHTS

Constructor Summary

SimpleDistribution(FiniteAlphabet alphabet)

Method Summary

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)
protected double[]	getWeights()
protected boolean	hasWeights()
void	registerWithTrainer(DistributionTrainerContext dtc) Register a simple trainer for this distribution.
protected void	setNullModelImpl(Distribution nullModel)
protected void	setWeightImpl(AtomicSymbol s, double w)

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

getChangeSupport, getWeight, sampleSymbol, setNullModel, setWeight

Methods inherited from class org.biojava.utils.AbstractChangeable

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, 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)

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

Specified by:

setNullModelImpl in class AbstractDistribution

IllegalAlphabetException

ChangeVetoException

hasWeights

protected boolean hasWeights()

getWeights

protected double[] getWeights()

getWeightImpl

public double getWeightImpl(AtomicSymbol s)
                     throws IllegalSymbolException

Specified by:

getWeightImpl in class AbstractDistribution

IllegalSymbolException

setWeightImpl

protected void setWeightImpl(AtomicSymbol s,
                             double w)
                      throws IllegalSymbolException,
                             ChangeVetoException

Specified by:

setWeightImpl in class AbstractDistribution

IllegalSymbolException

ChangeVetoException

registerWithTrainer

public void registerWithTrainer(DistributionTrainerContext dtc)

Register a simple trainer for this distribution.

Specified by:

registerWithTrainer in interface Distribution

Overrides:

registerWithTrainer in class AbstractDistribution

Parameters:

dtc - the DistributionTrainerContext with witch to register a trainer