Likelihood

Class StandardRoot

java.lang.Object

Likelihood.StandardRoot

All Implemented Interfaces:

Root

public class StandardRoot
extends java.lang.Object
implements Root

Root class for the standard root methods - e.g. root frequencies based on the stationary distribution or given by the model. Also used if the root distribution is given by the quasi-stationary distribution as this uses the same machinery.

Version:

2.0

Constructor Summary

Constructors

Constructor and Description
StandardRoot(double[] freq, java.util.Map<java.lang.String,java.lang.Integer> map) 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

StandardRoot

public StandardRoot(double[] freq,
            java.util.Map<java.lang.String,java.lang.Integer> map)

Default constructor

Parameters:

freq - The frequency of the various states

map - Map from state to position in the frequency array

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)

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