Class AbstractDistribution
- All Implemented Interfaces:
Distribution
,Changeable
- Direct Known Subclasses:
AbstractOrderNDistribution
,SimpleDistribution
,UniformDistribution
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
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.dist.Distribution
Distribution.NullModelForwarder
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected ChangeForwarder
Forwarder for modifications to the null model.Fields inherited from interface org.biojava.bio.dist.Distribution
NULL_MODEL, WEIGHTS
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionboolean
protected ChangeSupport
Called to retrieve the ChangeSupport for this object.final double
Retrieve the weight for this distribution.protected abstract double
Override this method to implement getting the weight for an atomic symbol.int
hashCode()
void
Register an IgnoreCountsTrainer instance as the trainer for this distribution.Sample a symbol from this state's probability distribution.final 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.final void
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
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Field Details
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nullModelForwarder
Forwarder for modifications to the null model.
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Constructor Details
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AbstractDistribution
public AbstractDistribution()
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Method Details
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getChangeSupport
Description copied from class:AbstractChangeable
Called to retrieve the ChangeSupport for this object.Your implementation of this method should have the following structure:
It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register invalid input: '&' unregister the forwarder in the code that does the ChangeEvent handling in setter methods.ChangeSupport cs = super.getChangeSupport(ct); if(someForwarder == null invalid input: '&'invalid input: '&' ct.isMatching(SomeInterface.SomeChangeType)) { someForwarder = new ChangeForwarder(... this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange); } return cs;
- Overrides:
getChangeSupport
in classAbstractChangeable
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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 forweight
- the new weight for that symbol- Throws:
IllegalSymbolException
- if the symbol is not knownChangeVetoException
- if the change is to be prevented
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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 interfaceDistribution
- Parameters:
sym
- the Symbol to set the weight forweight
- it's new weight- Throws:
IllegalSymbolException
- if sym is not knownChangeVetoException
- if the update was prevented
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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 alphabetChangeVetoException
- if your implementation wishes to block this opperation
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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 interfaceDistribution
- Parameters:
nullModel
- the new null model Distribution- Throws:
IllegalAlphabetException
- if the null model has the wrong alphabetChangeVetoException
- if this Distirbution doesn't support setting the null model, or if one of its listeners objects
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getWeight
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 interfaceDistribution
- 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
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getWeightImpl
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
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sampleSymbol
Description copied from interface:Distribution
Sample a symbol from this state's probability distribution.- Specified by:
sampleSymbol
in interfaceDistribution
- Returns:
- the symbol sampled
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registerWithTrainer
Register an IgnoreCountsTrainer instance as the trainer for this distribution. Override this if you wish to implement a trainable distribution.- Specified by:
registerWithTrainer
in interfaceDistribution
- Parameters:
dtc
- the context to register with
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hashCode
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equals
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