Likelihood

Class StandardCalculator

java.lang.Object

Likelihood.Calculator<StandardLikelihood>

Likelihood.StandardCalculator

All Implemented Interfaces:

Optimizable<StandardLikelihood>

public class StandardCalculator
extends Calculator<StandardLikelihood>

Calculates the likelihood for different parameter values. Successive calls to an instance of this class are used to maximise the parameters values for one case. Uses the pruning technique of Felenstein 1981 and can account for unobserved states using Felsenstein 1992.

Version:

2.0

Nested Class Summary

Nested classes/interfaces inherited from class Likelihood.Calculator

Calculator.CalculatorException, Calculator.SiteCalculator

Field Summary

Fields inherited from class Likelihood.Calculator

m, snl, t

Constructor Summary

Constructors

Constructor and Description
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, java.util.Map<java.lang.String,Tree> t) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, java.util.Map<java.lang.String,Tree> t, Alignment unobserved) Creates a class to calculate the likelihood for a given set of models, an alignment, a tree and unobserved data.
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t, Alignment unobserved) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(Model m, Alignment a, java.util.Map<java.lang.String,Tree> t) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(Model m, Alignment a, java.util.Map<java.lang.String,Tree> t, Alignment unobserved) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(Model m, Alignment a, Tree t) Creates an object to calculate the likelihood for a given model, alignment and tree.
StandardCalculator(Model m, Alignment a, Tree t, Alignment unobserved) Creates a class to calculate the likelihood for a given model, alignment, tree and missing data

Method Summary

Methods

Modifier and Type	Method and Description
SiteLikelihood	calculateSite(Site s, Tree t, Parameters p, Probabilities tp, java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood> nl) Calculate the likelihood for a single site.
StandardLikelihood	combineSites(java.util.Map<Site,SiteLikelihood> sites, Parameters p) Combines the likelihood from each site into a alignment likelihood
int	getAlignmentLength() Get the length of the alignment the calculator is using

Methods inherited from class Likelihood.Calculator

calculate, setNoThreads, setThread, siteCalculate

Methods inherited from class java.lang.Object

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

Constructor Detail

StandardCalculator

public StandardCalculator(Model m,
                  Alignment a,
                  Tree t)
                   throws TreeException,
                          SiteLikelihood.LikelihoodException,
                          AlignmentException

Creates an object to calculate the likelihood for a given model, alignment and tree. Has no unobserved data

Parameters:

m - The model

a - The alignment

t - The tree

Throws:

TreeException - If there is a problem with the tree

SiteLikelihood.LikelihoodException - Thrown if a node is initialised to every state having zero probability (most probably due to the state at the node not being in the model).

AlignmentException - Thrown if the tree and site have incompatible taxa

StandardCalculator

public StandardCalculator(Model m,
                  Alignment a,
                  Tree t,
                  Alignment unobserved)
                   throws TreeException,
                          SiteLikelihood.LikelihoodException,
                          AlignmentException

Creates a class to calculate the likelihood for a given model, alignment, tree and missing data

Parameters:

m - The model

a - The alignment

t - The tree

unobserved - Unobserved data given as another alignment

Throws:

TreeException - If there is a problem with the tree

SiteLikelihood.LikelihoodException - Thrown if a node is initialised to every state having zero probability (most probably due to the state at the node not being in the model).

AlignmentException - Thrown if the tree and site have incompatible taxa

StandardCalculator

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

Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree. There should be one model and tree 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 isn't given for each site class in the alignment

TreeException - If there is a problem with the tree

SiteLikelihood.LikelihoodException - Thrown if a node is initialised to every state having zero probability (most probably due to the state at the node not being in the model).

StandardCalculator

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

Creates a class to calculate the likelihood 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

TreeException - If there is a problem with the tree

SiteLikelihood.LikelihoodException - Thrown if a node is initialised to every state having zero probability (most probably due to the state at the node not being in the model).

StandardCalculator

public StandardCalculator(java.util.Map<java.lang.String,Model> m,
                  Alignment a,
                  Tree t,
                  Alignment unobserved)
                   throws AlignmentException,
                          TreeException,
                          SiteLikelihood.LikelihoodException

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

Parameters:

m - The model

a - The alignment

t - Map from site class to tree

unobserved - Unobserved data given as another alignment

Throws:

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

TreeException - If there is a problem with the tree

SiteLikelihood.LikelihoodException - Thrown if a node is initialised to every state having zero probability (most probably due to the state at the node not being in the model).

StandardCalculator

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

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

Parameters:

m - The model

a - The alignment

t - Map from site class to tree

Throws:

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

TreeException - If there is a problem with the tree

SiteLikelihood.LikelihoodException - Thrown if a node is initialised to every state having zero probability (most probably due to the state at the node not being in the model).

StandardCalculator

public StandardCalculator(Model m,
                  Alignment a,
                  java.util.Map<java.lang.String,Tree> t,
                  Alignment unobserved)
                   throws AlignmentException,
                          TreeException,
                          SiteLikelihood.LikelihoodException

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

Parameters:

m - The model

a - The alignment

t - Map from site class to tree

unobserved - Unobserved data given as another alignment

Throws:

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

TreeException - If there is a problem with the tree

SiteLikelihood.LikelihoodException - Thrown if a node is initialised to every state having zero probability (most probably due to the state at the node not being in the model).

StandardCalculator

public StandardCalculator(java.util.Map<java.lang.String,Model> m,
                  Alignment a,
                  java.util.Map<java.lang.String,Tree> t,
                  Alignment unobserved)
                   throws AlignmentException,
                          TreeException,
                          SiteLikelihood.LikelihoodException

Creates a class to calculate the likelihood for a given set of models, an alignment, a tree and unobserved data. 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

unobserved - Unobserved data given as another alignment

Throws:

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

TreeException - If there is a problem with the tree

SiteLikelihood.LikelihoodException - Thrown if a node is initialised to every state having zero probability (most probably due to the state at the node not being in the model).

Method Detail

combineSites

public StandardLikelihood combineSites(java.util.Map<Site,SiteLikelihood> sites,
                              Parameters p)
                                throws Calculator.CalculatorException

Description copied from class: Calculator

Combines the likelihood from each site into a alignment likelihood

Specified by:

combineSites in class Calculator<StandardLikelihood>

Parameters:

sites - A map from sites to the likelihood of those sites.

p - The parameters to use in the calculation

Returns:

The likelihood of the alignment

Throws:

Calculator.CalculatorException - If an unexpected (i.e. positive or NaN) log likelihood is calculated

calculateSite

public SiteLikelihood calculateSite(Site s,
                           Tree t,
                           Parameters p,
                           Probabilities tp,
                           java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood> nl)

Description copied from class: Calculator

Calculate the likelihood for a single site.

Specified by:

calculateSite in class Calculator<StandardLikelihood>

Parameters:

s - The site to calculate the likelihood for

t - The tree to use in calculating the likelihood

p - The parameters to use in calculating the likelihood

tp - Pre-calculated transition probabilities to be used in the calculation (passed in as they don't need to be calculated separately for each site). See Probabilities for more information

nl - The starting node-likelihoods are passed here as it is much quicker to clone them for each calculation than re-create them

Returns:

An instance of SiteLikelihood given the likelihood and any other information

getAlignmentLength

public int getAlignmentLength()

Description copied from class: Calculator

Get the length of the alignment the calculator is using

Specified by:

getAlignmentLength in class Calculator<StandardLikelihood>

Returns:

The length of the alignment