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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.dist.AbstractDistribution
org.biojava.bio.dist.UniformDistribution
public class UniformDistribution
An implementation of an uniform distribution
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojava.bio.dist.Distribution |
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Distribution.NullModelForwarder |
Field Summary |
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Fields inherited from class org.biojava.bio.dist.AbstractDistribution |
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nullModelForwarder |
Fields inherited from interface org.biojava.bio.dist.Distribution |
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NULL_MODEL, WEIGHTS |
Constructor Summary | |
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UniformDistribution(FiniteAlphabet alphabet)
Create a new UniformDistribution. |
Method Summary | |
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Alphabet |
getAlphabet()
The alphabet from which this spectrum emits symbols. |
Distribution |
getNullModel()
Retrieve the null model Distribution that this Distribution recognizes. |
protected double |
getWeightImpl(AtomicSymbol s)
Override this method to implement getting the weight for an atomic symbol. |
void |
registerWithTrainer(DistributionTrainerContext dtc)
Register an IgnoreCountsTrainer instance as the trainer for this distribution. |
protected void |
setNullModelImpl(Distribution nullModel)
Assign a background distribution. |
protected void |
setWeightImpl(AtomicSymbol sym,
double weight)
Implement this to actually set the weight. |
Methods inherited from class org.biojava.bio.dist.AbstractDistribution |
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equals, getChangeSupport, getWeight, hashCode, sampleSymbol, setNullModel, setWeight |
Methods inherited from class org.biojava.utils.AbstractChangeable |
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addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Constructor Detail |
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public UniformDistribution(FiniteAlphabet alphabet)
alphabet
- the finite alphabet to be overMethod Detail |
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public Alphabet getAlphabet()
Distribution
getAlphabet
in interface Distribution
public Distribution getNullModel()
Distribution
getNullModel
in interface Distribution
protected void setNullModelImpl(Distribution nullModel) throws IllegalAlphabetException
setNullModelImpl
in class AbstractDistribution
nullModel
- the background distribution to assign
IllegalAlphabetException
- if nullModel is over an incompattible
alphabetprotected double getWeightImpl(AtomicSymbol s) throws IllegalSymbolException
AbstractDistribution
getWeightImpl
in class AbstractDistribution
s
- the AtomicSymbol to get the weight for
IllegalSymbolException
- if sym is not knownprotected void setWeightImpl(AtomicSymbol sym, double weight) throws ChangeVetoException
AbstractDistribution
Do not inform any listeners. This has already been done for you. Just update state.
setWeightImpl
in class AbstractDistribution
sym
- the AtomicSymbol to update forweight
- the new weight for that symbol
ChangeVetoException
- if the change is to be preventedpublic void registerWithTrainer(DistributionTrainerContext dtc)
AbstractDistribution
registerWithTrainer
in interface Distribution
registerWithTrainer
in class AbstractDistribution
dtc
- the context to register with
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