pal.eval
Interface LHCalculator.Leaf

All Known Implementing Classes:
SimpleLeafCalculator
Enclosing interface:
LHCalculator

public static interface LHCalculator.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
 LHCalculator.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, SubstitutionModel model, boolean modelChanged)
           
 ConditionalProbabilityStore getFlatConditionalProbabilities()
           
 

Method Detail

getFlatConditionalProbabilities

ConditionalProbabilityStore getFlatConditionalProbabilities()

getExtendedConditionalProbabilities

ConditionalProbabilityStore getExtendedConditionalProbabilities(double distance,
                                                                SubstitutionModel model,
                                                                boolean modelChanged)

getCopy

LHCalculator.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