Package org.biojava.bio.dist

Class AbstractDistribution

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.dist.AbstractDistribution

All Implemented Interfaces:

Distribution, Changeable

Direct Known Subclasses:

AbstractOrderNDistribution, SimpleDistribution, UniformDistribution

public abstract class AbstractDistribution
extends AbstractChangeable
implements Distribution

An abstract implementation of Distribution.

You will need to override getWeight() for a simple implementation. You may also wish to override the other methods if the default implementation is not suitable.

The registerWithTrainer method registers an IgnoreCountsTrainer. To make an AbstractDistribution subclass trainable, this method must be overridden.

Since:

1.0

Author:

Matthew Pocock, Thomas Down, Mark Schreiber (serialization support), Greg Cox

Nested Class Summary

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

Distribution.NullModelForwarder

Field Summary

Fields

Modifier and Type	Field	Description
protected ChangeForwarder	nullModelForwarder	Forwarder for modifications to the null model.

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

NULL_MODEL, WEIGHTS

Constructor Summary

Constructors

Constructor	Description
AbstractDistribution()

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)
protected ChangeSupport	getChangeSupport(ChangeType ct)	Called to retrieve the ChangeSupport for this object.
double	getWeight(Symbol sym)	Retrieve the weight for this distribution.
protected abstract double	getWeightImpl(AtomicSymbol sym)	Override this method to implement getting the weight for an atomic symbol.
int	hashCode()
void	registerWithTrainer(DistributionTrainerContext dtc)	Register an IgnoreCountsTrainer instance as the trainer for this distribution.
Symbol	sampleSymbol()	Sample a symbol from this state's probability distribution.
void	setNullModel(Distribution nullModel)	Set the null model Distribution that this Distribution recognizes.
protected abstract void	setNullModelImpl(Distribution nullModel)	Implement this to set the null model.
void	setWeight(Symbol sym, double weight)	Set the weight of a given symbol in this distribution.
protected abstract void	setWeightImpl(AtomicSymbol sym, double weight)	Implement this to actually set the weight.

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

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

getAlphabet, getNullModel

Field Detail

nullModelForwarder

protected transient ChangeForwarder nullModelForwarder

Forwarder for modifications to the null model.

Constructor Detail

AbstractDistribution

public AbstractDistribution()

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 AbstractChangeable

setWeightImpl

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

Implement this to actually set the weight.

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

Parameters:

sym - the AtomicSymbol to update for

weight - the new weight for that symbol

Throws:

IllegalSymbolException - if the symbol is not known

ChangeVetoException - if the change is to be prevented

setWeight

public final void setWeight(Symbol sym,
                            double weight)
                     throws IllegalSymbolException,
                            ChangeVetoException

Set the weight of a given symbol in this distribution.

This implementation informs all listeners of the change, and then calls setWeightImpl to make the actual change. Sub-classes should over-ride setWeightImpl to implement the actual storage of the weights.

Specified by:

setWeight in interface Distribution

Parameters:

sym - the Symbol to set the weight for

weight - it's new weight

Throws:

IllegalSymbolException - if sym is not known

ChangeVetoException - if the update was prevented

setNullModelImpl

protected abstract void setNullModelImpl(Distribution nullModel)
                                  throws IllegalAlphabetException,
                                         ChangeVetoException

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.

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

setNullModel

public final void setNullModel(Distribution nullModel)
                        throws IllegalAlphabetException,
                               ChangeVetoException

Description copied from interface: Distribution

Set the null model Distribution that this Distribution recognizes.

Specified by:

setNullModel in interface Distribution

Parameters:

nullModel - the new null model Distribution

Throws:

IllegalAlphabetException - if the null model has the wrong alphabet

ChangeVetoException - if this Distirbution doesn't support setting the null model, or if one of its listeners objects

getWeight

public final double getWeight(Symbol sym)
                       throws IllegalSymbolException

Retrieve the weight for this distribution.

Performs the standard munge to handle ambiguity symbols. The actual weights for each atomic symbol should be calculated by the getWeightImpl functions.

Specified by:

getWeight in interface Distribution

Parameters:

sym - the Symbol to find the probability of

Returns:

the probability that one of the symbols matching amb was emitted

Throws:

IllegalSymbolException - if for any reason the symbols within amb are not recognized by this state

getWeightImpl

protected abstract double getWeightImpl(AtomicSymbol sym)
                                 throws IllegalSymbolException

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.

Parameters:

sym - the AtomicSymbol to get the weight for

Returns:

the weight

Throws:

IllegalSymbolException - if sym is not known

sampleSymbol

public Symbol sampleSymbol()

Description copied from interface: Distribution

Sample a symbol from this state's probability distribution.

Specified by:

sampleSymbol in interface Distribution

Returns:

the symbol sampled

registerWithTrainer

public void registerWithTrainer(DistributionTrainerContext dtc)

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

Parameters:

dtc - the context to register with

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object