pal.eval
Interface UnconstrainedLikelihoodModel.Leaf

All Known Implementing Classes:
SimpleUnconstrainedLikelihoodModel.LeafImpl
Enclosing interface:
UnconstrainedLikelihoodModel

public static interface UnconstrainedLikelihoodModel.Leaf

A LHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch. Allows for quick implementations as well as implementations that cope correctly with ambiguous characters


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()
           
 

Method Detail

getFlatConditionalProbabilities

ConditionalProbabilityStore getFlatConditionalProbabilities()

getExtendedConditionalProbabilities

ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance)

getCopy

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)

Returns:
a copy of this leaf calculator