Ancestors

Class AncestralJoint

java.lang.Object

Ancestors.AncestralJoint

Direct Known Subclasses:

AncestralJointBB, AncestralJointDP

public abstract class AncestralJoint
extends java.lang.Object

Abstract class that the two different ways of doing ancestral reconstruction extend. By using the static method in tis class users can avoid worrying about whether their model has a single rate category.

Version:

2.0

Constructor Summary

Constructors

Constructor and Description
AncestralJoint()

Method Summary

Methods

Modifier and Type	Method and Description
abstract Alignment	calculate(Parameters params) Calculates the reconstruction
static AncestralJoint	newInstance(java.util.Map<java.lang.String,Model> m, Alignment a, java.util.Map<java.lang.String,Tree> t) Returns an object of this class that can be used for joint reconstruction.
static AncestralJoint	newInstance(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t) Returns an object of this class that can be used for joint reconstruction.
static AncestralJoint	newInstance(Model m, Alignment a, java.util.Map<java.lang.String,Tree> t) Returns an object of this class that can be used for joint reconstruction.
static AncestralJoint	newInstance(Model m, Alignment a, Tree t) Returns an object of this class that can be used for joint reconstruction.

Methods inherited from class java.lang.Object

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

Constructor Detail

AncestralJoint

public AncestralJoint()

Method Detail

calculate

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

Calculates the reconstruction

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

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

newInstance

public static AncestralJoint newInstance(Model m,
                         Alignment a,
                         Tree t)

Returns an object of this class that can be used for joint reconstruction. If the model has a single rate category it returns an object that will do reconstruction using the dynamic programming method of Pupko 2000, else an object that will use the branch and bound method of Pupko 2002.

Parameters:

a - The alignment

m - The model

t - The tree

Returns:

An object that can be used for reconstruction

newInstance

public static AncestralJoint newInstance(java.util.Map<java.lang.String,Model> m,
                         Alignment a,
                         Tree t)
                                  throws AlignmentException

Returns an object of this class that can be used for joint reconstruction. Sites can belong to different classes and so use different models. If all models have a single rate category it returns an object that will do reconstruction using the dynamic programming method of Pupko 2000, else an object that will use the branch and bound method of Pupoko 2002.

Parameters:

a - The alignment

m - Map from site class to model

t - The tree

Returns:

An object that can be used for reconstruction

Throws:

AlignmentException - Thrown if a model isn't given for each site class in the alignment

newInstance

public static AncestralJoint newInstance(Model m,
                         Alignment a,
                         java.util.Map<java.lang.String,Tree> t)
                                  throws AlignmentException

Returns an object of this class that can be used for joint reconstruction. If the model has a single rate category it returns an object that will do reconstruction using the dynamic programming method of Pupko 2000, else an object that will use the branch and bound method of Pupko 2002.

Parameters:

a - The alignment

m - The model

t - Map from site class to tree

Returns:

An object that can be used for reconstruction

Throws:

AlignmentException - Thrown if a tree isn't given for each site class in the alignment

newInstance

public static AncestralJoint newInstance(java.util.Map<java.lang.String,Model> m,
                         Alignment a,
                         java.util.Map<java.lang.String,Tree> t)
                                  throws AlignmentException

Returns an object of this class that can be used for joint reconstruction. Sites can belong to different classes and so use different models. If all models have a single rate category it returns an object that will do reconstruction using the dynamic programming method of Pupko 2000, else an object that will use the branch and bound method of Pupoko 2002.

Parameters:

a - The alignment

m - Map from site class to model

t - Map from site class to tree

Returns:

An object that can be used for reconstruction

Throws:

AlignmentException - Thrown if a model or tree isn't given for each site class in the alignment