Ancestors

Class AncestralJointBB

java.lang.Object

Ancestors.AncestralJoint

Ancestors.AncestralJointBB

public class AncestralJointBB
extends AncestralJoint

Class to perform joint ancestral reconstrion using the method of Pupko 2002 slightly modified

Version:

2.0

Method Summary

Methods

Modifier and Type	Method and Description
Alignment	calculate(Parameters p) Calculates the reconstruction

Methods inherited from class Ancestors.AncestralJoint

newInstance, newInstance, newInstance, newInstance

Methods inherited from class java.lang.Object

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

Method Detail

calculate

public Alignment calculate(Parameters p)
                    throws RateCategory.RateException,
                           Model.ModelException,
                           AncestralException,
                           TreeException,
                           Parameters.ParameterException,
                           AlignmentException,
                           SiteLikelihood.LikelihoodException

Description copied from class: AncestralJoint

Calculates the reconstruction

Specified by:

calculate in class AncestralJoint

Parameters:

p - The parameters to be used in the reconstruction

Returns:

An alignment based on the original alignment but augmented with the reconstruction

Throws:

RateCategory.RateException - Thrown if there is an issue with a rate category in the model (e.g. a badly formatted rate).

Model.ModelException - Thrown if there is a problem with the model (e.g. the rate categories differ in their states)

AncestralException - Thrown if there is ambiguous data as these methods can't currently deal with it

TreeException - Thrown if there is a problem with the tree.

Parameters.ParameterException - Thrown if there is a problem with the parameters (e.g. a required parameter is not present)

AlignmentException - Thrown if there is a problem with the alignment

SiteLikelihood.LikelihoodException - Thrown if there is a problem initialise likelihoods