Ancestors

Class Assignment

java.lang.Object

Ancestors.Assignment

public class Assignment
extends java.lang.Object

Stores the ancestral reconstruction assignment for a single site

Version:

2.0

Constructor Summary

Constructors

Constructor and Description
Assignment() Standard constructor that creates an object with no assignments

Method Summary

Methods

Modifier and Type	Method and Description
void	addAssignment(java.lang.String n, java.lang.String c) Adds a assignment
Assignment	clone()
java.lang.String	getAssignment(java.lang.String n) Gets the assignment for a node
java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood>	getInitialNodeLikelihoods(Tree t, Site s, java.util.Map<java.lang.String,java.lang.Integer> map) Creates initial node likelihoods using this assignment.
boolean	nodeIsAssigned(java.lang.String n) Tests whether a node has an assignment

Methods inherited from class java.lang.Object

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

Constructor Detail

Assignment

public Assignment()

Standard constructor that creates an object with no assignments

Method Detail

addAssignment

public void addAssignment(java.lang.String n,
                 java.lang.String c)

Adds a assignment

Parameters:

n - The node

c - The state it is assigned

getAssignment

public java.lang.String getAssignment(java.lang.String n)

Gets the assignment for a node

Parameters:

n - The node to get the assignment for

Returns:

The state that node is assigned

nodeIsAssigned

public boolean nodeIsAssigned(java.lang.String n)

Tests whether a node has an assignment

Parameters:

n - The node

Returns:

Whether the node is assigned

clone

public Assignment clone()

Overrides:

clone in class java.lang.Object

getInitialNodeLikelihoods

public java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood> getInitialNodeLikelihoods(Tree t,
                                                                                      Site s,
                                                                                      java.util.Map<java.lang.String,java.lang.Integer> map)
                                                                                        throws SiteLikelihood.LikelihoodException

Creates initial node likelihoods using this assignment. Internal nodes with an assignment are set so only that state is allowed.

Parameters:

t - The tree to create the node likelihood for.

s - The site being reconstructed

map - A map from state to position in array

Returns:

An Map of NodeLikelihoods which can be used to initialise likelihood calculations

Throws:

SiteLikelihood.LikelihoodException - Thrown if all states are initialised to a zero likelihood