Ancestors

Class AncestralJointDP

java.lang.Object

Ancestors.AncestralJoint

Ancestors.AncestralJointDP

public class AncestralJointDP
extends AncestralJoint

Class to perform joint ancestral reconstruction using the method of Pupko 2000

Version:

2.0

Method Summary

Methods

Modifier and Type	Method and Description
Alignment	calculate(Parameters params) Calculates the reconstruction
static void	realType(RealFactory.RealType type) Sets the real type to be used during calculations, either SmallDouble or StandardDouble

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 params)
                    throws RateCategory.RateException,
                           Model.ModelException,
                           AncestralException,
                           TreeException,
                           Parameters.ParameterException,
                           AlignmentException

Description copied from class: AncestralJoint

Calculates the reconstruction

Specified by:

calculate in class AncestralJoint

Parameters:

params - 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

realType

public static void realType(RealFactory.RealType type)

Sets the real type to be used during calculations, either SmallDouble or StandardDouble

Parameters:

type - The double type to use

See Also:

SiteLikelihood.realType(Maths.RealFactory.RealType)