org.biojava.bio.dist

Class GapDistribution

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.dist.GapDistribution

All Implemented Interfaces:

Serializable, Distribution, Changeable

public class GapDistribution
extends Unchangeable
implements Distribution, Serializable

This distribution emits gap symbols.

It is a useful thing to have around for pair-wise alignment, as you can build a PairDistribution that emits gaps in one sequence and Symbols in the other. The GapDistriution will always emit with a probability of 1, as every symbol has a matches alphabet that contains the empty set. Or is this so?

Since:

1.0

Author:

Matthew Pocock

See Also:

Serialized Form

Nested Class Summary

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

Distribution.NullModelForwarder

Field Summary

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

NULL_MODEL, WEIGHTS

Constructor Summary

Constructors

Constructor and Description
GapDistribution(Alphabet alpha) Get a GapDistribution for an alphabet.

Method Summary

Methods

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	getWeight(Symbol sym) Return the probability that Symbol s is emitted by this spectrum.
void	registerWithTrainer(DistributionTrainerContext dtc) Register this distribution with a training context.
Symbol	sampleSymbol() Sample a symbol from this state's probability distribution.
void	setNullModel(Distribution nullModel) Set the null model Distribution that this Distribution recognizes.
void	setWeight(Symbol s, double w) Set the probability or odds that Symbol s is emitted by this state.

Methods inherited from class org.biojava.utils.Unchangeable

addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder

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

GapDistribution

public GapDistribution(Alphabet alpha)

Get a GapDistribution for an alphabet.

Parameters:

alpha - the Alphabet that this distribution is over

Method Detail

getWeight

public double getWeight(Symbol sym)
                 throws IllegalSymbolException

Description copied from interface: Distribution

Return the probability that Symbol s is emitted by this spectrum.

If the symbol is ambiguou, then it is the sum of the probability that each one of the matching symbols was emitted.

Specified by:

getWeight in interface Distribution

Parameters:

sym - the Symbol emitted

Returns:

the probability of emitting that symbol

Throws:

IllegalSymbolException - if s is not from this state's alphabet

setWeight

public void setWeight(Symbol s,
             double w)
               throws IllegalSymbolException,
                      UnsupportedOperationException

Description copied from interface: Distribution

Set the probability or odds that Symbol s is emitted by this state.

Specified by:

setWeight in interface Distribution

Parameters:

s - the Symbol emitted

w - the probability of emitting that symbol

Throws:

IllegalSymbolException - if s is not from this state's alphabet, or if it is an ambiguity symbol and the implementation can't handle this case

UnsupportedOperationException

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

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

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

setNullModel

public 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

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

Parameters:

dtc - the DistributionTrainerContext with witch to register a trainer