Likelihood

Class SiteLikelihood.NodeLikelihood

java.lang.Object

Likelihood.SiteLikelihood.NodeLikelihood

All Implemented Interfaces:

java.io.Serializable

Enclosing class:

SiteLikelihood

public static class SiteLikelihood.NodeLikelihood
extends java.lang.Object
implements java.io.Serializable

Stores the results of a likelihood calculation for a single node in a tree. That is the partial likelihoods for each possible state.

Version:

2.0

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
SiteLikelihood.NodeLikelihood(java.util.Map<java.lang.String,java.lang.Integer> states) Constructor where all sates are allowed at a node
SiteLikelihood.NodeLikelihood(java.util.Map<java.lang.String,java.lang.Integer> states, java.util.Set<java.lang.String> allowedStates) Constructor where only some states are allowed at a node
SiteLikelihood.NodeLikelihood(java.util.Map<java.lang.String,java.lang.Integer> states, java.lang.String allowedState) Constructor where only a single state is allowed at a node

Method Summary

Methods

Modifier and Type	Method and Description
SiteLikelihood.NodeLikelihood	clone()
Real	getLikelihood(int i) Returns the partial likelihood for the state at position i.
Real	getLikelihood(java.lang.String state) Returns the partial likelihood for a given state
Real[]	getLikelihoods() Returns the partial likelihood for each state as an array.
void	multiply(java.lang.String state, double by) This is a fudge to stop to allow this code to be reused in some of the ancestor classes.
void	multiply(java.lang.String state, Real by) This is a fudge to stop to allow this code to be reused in some of the ancestor classes.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

SiteLikelihood.NodeLikelihood

public SiteLikelihood.NodeLikelihood(java.util.Map<java.lang.String,java.lang.Integer> states)
                              throws SiteLikelihood.LikelihoodException

Constructor where all sates are allowed at a node

Parameters:

states - Map from a state to it's position in the array

Throws:

SiteLikelihood.LikelihoodException - Thrown if a node is initalised to every state having zero probability (most probably due to the state at the node not being in the model).

SiteLikelihood.NodeLikelihood

public SiteLikelihood.NodeLikelihood(java.util.Map<java.lang.String,java.lang.Integer> states,
                             java.util.Set<java.lang.String> allowedStates)
                              throws SiteLikelihood.LikelihoodException

Constructor where only some states are allowed at a node

Parameters:

states - Map from a state to it's position in the array

allowedStates - The allowed states at this state

Throws:

SiteLikelihood.LikelihoodException - Thrown if a node is initalised to every state having zero probability (most probably due to the state at the node not being in the model).

SiteLikelihood.NodeLikelihood

public SiteLikelihood.NodeLikelihood(java.util.Map<java.lang.String,java.lang.Integer> states,
                             java.lang.String allowedState)
                              throws SiteLikelihood.LikelihoodException

Constructor where only a single state is allowed at a node

Parameters:

states - Map from a state to it's position in the array

allowedState - The allowed state at this state

Throws:

SiteLikelihood.LikelihoodException - Thrown if a node is initalised to every state having zero probability (most probably due to the state at the node not being in the model).

Method Detail

clone

public SiteLikelihood.NodeLikelihood clone()

Overrides:

clone in class java.lang.Object

multiply

public void multiply(java.lang.String state,
            Real by)

This is a fudge to stop to allow this code to be reused in some of the ancestor classes. Should be no reason to use.

Parameters:

state - The state probility to multiply

by - How much to mutliply the probabilty by

multiply

public void multiply(java.lang.String state,
            double by)

This is a fudge to stop to allow this code to be reused in some of the ancestor classes. Should be no reason to use.

Parameters:

state - The state probility to multiply

by - How much to mutliply the probabilty by

getLikelihood

public Real getLikelihood(java.lang.String state)
                   throws SiteLikelihood.LikelihoodException

Returns the partial likelihood for a given state

Parameters:

state - The state to return the partial likelihood for

Returns:

The partial likelihood for the given state

Throws:

SiteLikelihood.LikelihoodException - Thrown if no likelihood has been calculated for the given state

getLikelihood

public Real getLikelihood(int i)

Returns the partial likelihood for the state at position i. Mainly intended to be used internally

Parameters:

i - The position

Returns:

The likelihood for the state associated with that position (as defined by the map passed to the constructor)

getLikelihoods

public Real[] getLikelihoods()

Returns the partial likelihood for each state as an array. Mainly intended to be used internally

Returns:

The likelihood for each state. Position is associated with state based on the map passed to the constructor.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object