Ancestors

Class AncestralMarginal

java.lang.Object

Ancestors.AncestralMarginal

public class AncestralMarginal
extends java.lang.Object

Class to perform marginal reconstruction of internal nodes. Uses the principles of Yang, Kurma and Nei 1995.

Version:

2.0

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	AncestralMarginal.Result Class to store the results of a marginal ancestral reconstruction
class	AncestralMarginal.SiteResult Class to store the results of a marginal ancestral reconstruction for a single site

Constructor Summary

Constructors

Constructor and Description
AncestralMarginal(java.util.Map<java.lang.String,Model> m, Alignment a, java.util.Map<java.lang.String,Tree> t) Creates an object to calculate an ancestral reconstruction for a given set of models, an alignment and a tree.
AncestralMarginal(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t) Creates an object to calculate an ancestral reconstruction for a given set of models, an alignment and a tree.
AncestralMarginal(Model m, Alignment a, java.util.Map<java.lang.String,Tree> t) Creates an object to calculate an ancestral reconstruction for a given model, alignment and tree
AncestralMarginal(Model m, Alignment a, Tree t) Creates an object to calculate an ancestral reconstruction for a given model, alignment and tree

Method Summary

Methods

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

Methods inherited from class java.lang.Object

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

Constructor Detail

AncestralMarginal

public AncestralMarginal(Model m,
                 Alignment a,
                 Tree t)

Creates an object to calculate an ancestral reconstruction for a given model, alignment and tree

Parameters:

m - The model

a - The alignment

t - The tree

AncestralMarginal

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

Creates an object to calculate an ancestral reconstruction for a given model, alignment and tree

Parameters:

m - The model

a - The alignment

t - Map from site class to tree

Throws:

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

AncestralMarginal

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

Creates an object to calculate an ancestral reconstruction for a given set of models, an alignment and a tree. There should be one model per site class in the alignment

Parameters:

m - Map from site class to model

a - The alignment

t - The tree

Throws:

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

AncestralMarginal

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

Creates an object to calculate an ancestral reconstruction for a given set of models, an alignment and a tree. There should be one model per site class in the alignment

Parameters:

m - Map from site class to model

a - The alignment

t - Map from site class to tree

Throws:

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

Method Detail

calculate

public AncestralMarginal.Result calculate(Parameters params)
                                   throws RateCategory.RateException,
                                          Model.ModelException,
                                          TreeException,
                                          Parameters.ParameterException,
                                          AlignmentException,
                                          SiteLikelihood.LikelihoodException

Calculates the reconstruction

Parameters:

params - The parameters to be used in the reconstruction

Returns:

An object containing the reconstruction and the probability of each state at each node for each site

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)

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

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

AlignmentException - Thrown if there is a problem with the alignment

SiteLikelihood.LikelihoodException - Thrown if there is a problem with calculating likelihoods

newInstance

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

Returns an object of this class that can be used for marginal reconstruction. Included for consistency with AncestralJoint which requires a static method as there is two different classes that are used based on the situation.

Parameters:

a - The alignment

m - The model

t - The tree

Returns:

An object that can be used for reconstruction

newInstance

public static AncestralMarginal 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 marginal reconstruction. Sites can belong to different classes and so use different models. Included for consistency with AncestralJoint which requires a static method as there is two different classes that are used based on the situation.

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