pal.eval
Class SimpleUnconstrainedLikelihoodModel.LeafImpl

java.lang.Object
  extended by 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
SimpleUnconstrainedLikelihoodModel.LeafImpl(LHCalculator.Leaf base, SubstitutionModel model)
           
 
Method Summary
 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