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:

Serializable, Distribution, OrderNDistribution, Changeable

public abstract class AbstractOrderNDistribution
extends AbstractDistribution
implements OrderNDistribution, Serializable

Simple base class for OrderNDistributions.

Since:

1.2

Author:

Samiul Hasan, Matthew Pocock, 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

Modifier and Type	Field and Description
protected ChangeForwarder	weightForwarder The listener that will forward events from the underlying distributions to listeners for this distribution.

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

Modifier	Constructor and Description
protected	AbstractOrderNDistribution(Alphabet alpha) Construct a new NthOrderDistribution.

Method Summary

Methods

Modifier and Type	Method and Description
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 an IgnoreCountsTrainer instance as the trainer for this distribution.
void	setNullModelImpl(Distribution nullModel) Implement this to set the null model.
void	setWeightImpl(AtomicSymbol sym, double w) Set a weight in one of the conditioned distributions.

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

equals, 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.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 ChangeForwarder weightForwarder

The listener that will forward events from the underlying distributions to listeners for this distribution.

Constructor Detail

AbstractOrderNDistribution

protected AbstractOrderNDistribution(Alphabet alpha)
                              throws IllegalAlphabetException

Construct a new NthOrderDistribution.

Parameters:

alpha - the Alpahbet this is over

Throws:

IllegalAlphabetException

Method Detail

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType ct)

Description copied from class: AbstractChangeable

Called to retrieve the ChangeSupport for this object.

Your implementation of this method should have the following structure:

 ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
 

It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.

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

Returns:

the conditioning Alphabet

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

Returns:

the conditioned Alphabet

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

Parameters:

sym - the symbol to look up

Returns:

the weight

Throws:

IllegalSymbolException - if sym is not recognised

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

Parameters:

sym - the symbol to set the weight for

w - the new weight

Throws:

IllegalSymbolException - if the symbol is not known

ChangeVetoException - if the change is to be prevented

setNullModelImpl

public void setNullModelImpl(Distribution nullModel)

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

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 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