pal.eval

Class SimpleUnconstrainedLikelihoodModel.LeafImpl

java.lang.Object

pal.eval.SimpleUnconstrainedLikelihoodModel.LeafImpl

All Implemented Interfaces:

UnconstrainedLikelihoodModel.Leaf

Enclosing class:

SimpleUnconstrainedLikelihoodModel

public static final class SimpleUnconstrainedLikelihoodModel.LeafImpl
extends java.lang.Object
implements UnconstrainedLikelihoodModel.Leaf

Constructor Summary

Constructors

Constructor and Description
SimpleUnconstrainedLikelihoodModel.LeafImpl(LHCalculator.Leaf base, SubstitutionModel model)

Method Summary

Methods

Modifier and Type	Method and Description
UnconstrainedLikelihoodModel.Leaf	getCopy() Create a new Leaf calculator that has exactly the same properties as this one (but is different such that it may be used independently)
ConditionalProbabilityStore	getExtendedConditionalProbabilities(double distance)
ConditionalProbabilityStore	getFlatConditionalProbabilities()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SimpleUnconstrainedLikelihoodModel.LeafImpl

public SimpleUnconstrainedLikelihoodModel.LeafImpl(LHCalculator.Leaf base,
                                           SubstitutionModel model)

Method Detail

getFlatConditionalProbabilities

public ConditionalProbabilityStore getFlatConditionalProbabilities()

Specified by:

getFlatConditionalProbabilities in interface UnconstrainedLikelihoodModel.Leaf

getExtendedConditionalProbabilities

public ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance)

Specified by:

getExtendedConditionalProbabilities in interface UnconstrainedLikelihoodModel.Leaf

getCopy

public UnconstrainedLikelihoodModel.Leaf getCopy()

Description copied from interface: UnconstrainedLikelihoodModel.Leaf

Create a new Leaf calculator that has exactly the same properties as this one (but is different such that it may be used independently)

Specified by:

getCopy in interface UnconstrainedLikelihoodModel.Leaf

Returns:

a copy of this leaf calculator