Likelihood

Interface Root

All Known Implementing Classes:

FitzJohnRoot, StandardRoot

public interface Root

Provides information on what to do once the root of the tree is reached. Can be used to calculate the total likelihood from the root node likelihoods or provide the frequencies of the various states at the root

Version:

2.0

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

Method Detail

calculate

Real calculate(SiteLikelihood.NodeLikelihood root)

Calculate the total likelihood from the root node likelihood

Parameters:

root - The root node likelihood

Returns:

The total likelihood

getFreq

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

Get the frequency of the given state at the 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).