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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.dist.AbstractDistribution
org.biojava.bio.dist.AbstractOrderNDistribution
Simple base class for OrderNDistributions
Nested Class Summary |
Nested classes inherited from class org.biojava.bio.dist.Distribution |
Distribution.NullModelForwarder |
Field Summary | |
protected org.biojava.bio.dist.AbstractOrderNDistribution.WeigthForwarder |
weightForwarder
|
Fields inherited from class org.biojava.bio.dist.AbstractDistribution |
nullModelForwarder, symbolIndices |
Fields inherited from interface org.biojava.bio.dist.Distribution |
NULL_MODEL, WEIGHTS |
Constructor Summary | |
protected |
AbstractOrderNDistribution(Alphabet alpha)
Construct a new NthOrderDistribution. |
Method Summary | |
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 this distribution with a training context. |
void |
setNullModelImpl(Distribution nullModel)
|
void |
setWeightImpl(AtomicSymbol sym,
double w)
Set a weight in one of the conditioned distributions. |
Methods inherited from class org.biojava.bio.dist.AbstractDistribution |
getWeight, sampleSymbol, setNullModel, setWeight |
Methods inherited from class org.biojava.utils.AbstractChangeable |
addChangeListener, addChangeListener, generateChangeSupport, hasListeners, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, 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 |
protected transient org.biojava.bio.dist.AbstractOrderNDistribution.WeigthForwarder weightForwarder
Constructor Detail |
protected AbstractOrderNDistribution(Alphabet alpha) throws IllegalAlphabetException
Method Detail |
protected ChangeSupport getChangeSupport(ChangeType ct)
AbstractChangeable
getChangeSupport
in class AbstractDistribution
public Alphabet getConditioningAlphabet()
getConditioningAlphabet
in interface OrderNDistribution
public Alphabet getConditionedAlphabet()
getConditionedAlphabet
in interface OrderNDistribution
public Alphabet getAlphabet()
Distribution
getAlphabet
in interface Distribution
protected double getWeightImpl(AtomicSymbol sym) throws IllegalSymbolException
getWeightImpl
in class AbstractDistribution
IllegalSymbolException
public void setWeightImpl(AtomicSymbol sym, double w) throws IllegalSymbolException, ChangeVetoException
setWeightImpl
in class AbstractDistribution
IllegalSymbolException
ChangeVetoException
public void setNullModelImpl(Distribution nullModel)
setNullModelImpl
in class AbstractDistribution
public Distribution getNullModel()
Distribution
getNullModel
in interface Distribution
public void registerWithTrainer(DistributionTrainerContext dtc)
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.
registerWithTrainer
in interface Distribution
registerWithTrainer
in class AbstractDistribution
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