pal.eval
Class SimpleLeafCalculator

java.lang.Object
  pal.eval.SimpleLeafCalculator

All Implemented Interfaces:

LHCalculator.Leaf

public class SimpleLeafCalculator

extends java.lang.Object

implements LHCalculator.Leaf

Constructor Summary

SimpleLeafCalculator(int[] patternStateMatchup, int numberOfPatterns, int numberOfStates, int numberOfCategories, LHCalculator.Generator parent)

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()

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleLeafCalculator

public SimpleLeafCalculator(int[] patternStateMatchup,
                            int numberOfPatterns,
                            int numberOfStates,
                            int numberOfCategories,
                            LHCalculator.Generator parent)

Method Detail

getCopy

public LHCalculator.Leaf getCopy()

Description copied from interface: LHCalculator.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 LHCalculator.Leaf

Returns:

a copy of this leaf calculator

getFlatConditionalProbabilities

public ConditionalProbabilityStore getFlatConditionalProbabilities()

Specified by:

getFlatConditionalProbabilities in interface LHCalculator.Leaf

getExtendedConditionalProbabilities

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

Specified by:

getExtendedConditionalProbabilities in interface LHCalculator.Leaf