org.biojava.bio.dist
Class AbstractOrderNDistribution

java.lang.Object
  |
  +--org.biojava.utils.AbstractChangeable
        |
        +--org.biojava.bio.dist.AbstractDistribution
              |
              +--org.biojava.bio.dist.AbstractOrderNDistribution

All Implemented Interfaces:

Changeable, Distribution, OrderNDistribution, java.io.Serializable

public abstract class AbstractOrderNDistribution

extends AbstractDistribution

implements OrderNDistribution

Simple base class for OrderNDistributions

Author:

Samiul Hasan, Matthew Pocock, Thomas Down

See Also:

Serialized Form

Nested Class Summary

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

Distribution.NullModelForwarder

Field Summary

protected org.biojava.bio.dist.AbstractOrderNDistribution.WeigthForwarder

weightForwarder

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

protected

AbstractOrderNDistribution(Alphabet alpha) Construct a new NthOrderDistribution.

Method Summary

Alphabet	getAlphabet() The alphabet from which this spectrum emits symbols.
protected ChangeSupport	getChangeSupport(ChangeType ct) Called to retrieve the ChangeSupport for this object
Alphabet	getConditionedAlphabet() Get the conditioned alphabet.
Alphabet	getConditioningAlphabet() Get the conditioning alphabet of this distribution.
Distribution	getNullModel() Retrieve the null model Distribution that this Distribution recognizes.
protected double	getWeightImpl(AtomicSymbol sym) Get a weight from one of the sub-distributions, conditioned on the first part of the symbol.
void	registerWithTrainer(DistributionTrainerContext dtc) Register this distribution with a training context.
void	setNullModelImpl(Distribution nullModel)
void	setWeightImpl(AtomicSymbol sym, double w) Set a weight in one of the conditioned distributions.

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

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.bio.dist.OrderNDistribution

conditionedDistributions, getDistribution, setDistribution

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

getWeight, sampleSymbol, setNullModel, setWeight

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

weightForwarder

protected transient org.biojava.bio.dist.AbstractOrderNDistribution.WeigthForwarder weightForwarder

Constructor Detail

AbstractOrderNDistribution

protected AbstractOrderNDistribution(Alphabet alpha)
                              throws IllegalAlphabetException

Construct a new NthOrderDistribution.

Method Detail

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType ct)

Description copied from class: AbstractChangeable

Called to retrieve the ChangeSupport for this object

Overrides:

getChangeSupport in class AbstractDistribution

getConditioningAlphabet

public Alphabet getConditioningAlphabet()

Get the conditioning alphabet of this distribution. If the `overall' alphabet is a cross-product of two alphabets, this will be the first of those alphabets. If it is a cross-product of more than two alphabets, the conditioning alphabet is the cross-product of all but the last alphabet.

Specified by:

getConditioningAlphabet in interface OrderNDistribution

getConditionedAlphabet

public Alphabet getConditionedAlphabet()

Get the conditioned alphabet. This is the last alphabet in the distribution's overall cross-product. It will be the alphabet of all the sub-distributions contained within this OrderNDistribution.

Specified by:

getConditionedAlphabet in interface OrderNDistribution

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

getWeightImpl

protected double getWeightImpl(AtomicSymbol sym)
                        throws IllegalSymbolException

Get a weight from one of the sub-distributions, conditioned on the first part of the symbol.

Specified by:

getWeightImpl in class AbstractDistribution

IllegalSymbolException

setWeightImpl

public void setWeightImpl(AtomicSymbol sym,
                          double w)
                   throws IllegalSymbolException,
                          ChangeVetoException

Set a weight in one of the conditioned distributions. It is the callers responsibility to ensure that all the conditioned distributions have total weights which sum to 1.0.

Specified by:

setWeightImpl in class AbstractDistribution

IllegalSymbolException

ChangeVetoException

setNullModelImpl

public void setNullModelImpl(Distribution nullModel)

Specified by:

setNullModelImpl in class AbstractDistribution

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

registerWithTrainer

public void registerWithTrainer(DistributionTrainerContext dtc)

Description copied from interface: Distribution

Register this distribution with a training context.

This should be invoked from within dtc.addDistribution(). This method is responsible for constructing a suitable DistributionTrainer instance and registering it by calling dtc.registerDistributionTrainer(this, trainer). If the distribution is a view onto another distribution, it can force the other to be registered by calling dtc.addDistribution(other), and can then get on with registering it's own trainer.

Specified by:

registerWithTrainer in interface Distribution

Overrides:

registerWithTrainer in class AbstractDistribution

Parameters:

dtc - the DistributionTrainerContext with witch to register a trainer