Likelihood

Class FitzJohnRoot

java.lang.Object

Likelihood.FitzJohnRoot

All Implemented Interfaces:

Root

public class FitzJohnRoot
extends java.lang.Object
implements Root

Root class for the FitzJohn et al 2009 method

Version:

2.0

Constructor Summary

Constructors

Constructor and Description
FitzJohnRoot(java.util.Set<java.lang.String> states) Default constructor

Method Summary

Methods

Modifier and Type	Method and Description
Real	calculate(SiteLikelihood.NodeLikelihood root) Calculate the total likelihood from the root node likelihood
double	getFreq(java.lang.String state) Get the frequency of the given state at the root

Methods inherited from class java.lang.Object

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

Constructor Detail

FitzJohnRoot

public FitzJohnRoot(java.util.Set<java.lang.String> states)

Default constructor

Parameters:

states - The possible states of the model

Method Detail

calculate

public Real calculate(SiteLikelihood.NodeLikelihood root)

Description copied from interface: Root

Calculate the total likelihood from the root node likelihood

Specified by:

calculate in interface Root

Parameters:

root - The root node likelihood

Returns:

The total likelihood

getFreq

public double getFreq(java.lang.String state)
               throws RateCategory.RateException

Description copied from interface: Root

Get the frequency of the given state at the root

Specified by:

getFreq in interface Root

Parameters:

state - The state to get the frequency of

Returns:

The frequency

Throws:

RateCategory.RateException - If the frequency is not independent of the root likelihoods (as in the case of FitzJohn et al 2009).