Likelihood

Class Calculator<R extends Likelihood>

java.lang.Object

Likelihood.Calculator<R>

Type Parameters:

R - The return type from the calculation

All Implemented Interfaces:

Optimizable<R>

Direct Known Subclasses:

StandardCalculator

public abstract class Calculator<R extends Likelihood>
extends java.lang.Object
implements Optimizable<R>

Abstract class for calculating a likelihood. Likelihood calculators should extend this class as then this class will deal with multi-threading.

Version:

2.0

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Calculator.CalculatorException Exception thrown when there is a problem with the calculation
class	Calculator.SiteCalculator Calculates the likelihood of a single site.

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.Map<java.lang.String,Model>	m The model to do the calculation on.
protected java.util.HashMap<Site,java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood>>	snl The site node likelihoods.
protected java.util.Map<java.lang.String,Tree>	t The tree to do the calculation on.

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	Calculator(java.util.Map<java.lang.String,Model> m, java.util.Map<java.lang.String,Tree> t, java.util.HashMap<Site,java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood>> snl) Default constructor.

Method Summary

Methods

Modifier and Type	Method and Description
R	calculate(Parameters p) Abstract method for actually calculating the likelihood
abstract 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.
abstract R	combineSites(java.util.Map<Site,SiteLikelihood> sites, Parameters p) Combines the likelihood from each site into a alignment likelihood
abstract int	getAlignmentLength() Get the length of the alignment the calculator is using
static void	setNoThreads(int number) Set the number of threads to be used during the calculations
void	setThread(boolean thread) Set whether threaded calculations should be performed
protected java.util.Map<Site,SiteLikelihood>	siteCalculate(Parameters p) Calculates the likelihood for each site

Methods inherited from class java.lang.Object

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

Field Detail

snl

protected java.util.HashMap<Site,java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood>> snl

The site node likelihoods. That is the initial likelihood values for each state at each node for each site. Will usually be 1.0 if that state at that node of that site is possible, else 0.0. Should be used by implementing classes.

t

protected java.util.Map<java.lang.String,Tree> t

The tree to do the calculation on. Should be used by implementing classes.

m

protected java.util.Map<java.lang.String,Model> m

The model to do the calculation on. Should be used by implementing classes.

Constructor Detail

Calculator

protected Calculator(java.util.Map<java.lang.String,Model> m,
          java.util.Map<java.lang.String,Tree> t,
          java.util.HashMap<Site,java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood>> snl)

Default constructor. The Site-Node-Likelihoods (snl) are passed here as it is much quicker to clone them for each calculation than re-create them

Parameters:

m - The model

t - The tree

snl - The site node likelihoods. That is the initial likelihood values for each state at each node for each site. Will usually be 1.0 if that state at that node of that site is possible, else 0.0.

Method Detail

calculate

public R calculate(Parameters p)
                               throws TreeException,
                                      RateCategory.RateException,
                                      Model.ModelException,
                                      Parameters.ParameterException,
                                      Calculator.CalculatorException

Abstract method for actually calculating the likelihood

Specified by:

calculate in interface Optimizable<R extends Likelihood>

Parameters:

p - The parameters to be used in the calculation

Returns:

A Likelihood object which contains the likelihood as well as likelihoods for each site.

Throws:

TreeException - Thrown if there is a problem with the Tree (e.g. if there is a branch with no length given in parameters)

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)

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

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

combineSites

public abstract R combineSites(java.util.Map<Site,SiteLikelihood> sites,
             Parameters p)
                                           throws Calculator.CalculatorException,
                                                  TreeException,
                                                  Parameters.ParameterException,
                                                  RateCategory.RateException,
                                                  Model.ModelException

Combines the likelihood from each site into a alignment likelihood

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:

TreeException - Thrown if there is a problem with the Tree (e.g. if there is a branch with no length given in parameters)

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)

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

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

calculateSite

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

Calculate the likelihood for a single site.

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

Throws:

Parameters.ParameterException - Thrown if there is a problem with a passed parameter

siteCalculate

protected java.util.Map<Site,SiteLikelihood> siteCalculate(Parameters p)
                                                    throws TreeException,
                                                           RateCategory.RateException,
                                                           Model.ModelException,
                                                           Parameters.ParameterException,
                                                           Calculator.CalculatorException

Calculates the likelihood for each site

Parameters:

p - The parameters to be used in the calculation

Returns:

A Map from site to result

Throws:

TreeException - Thrown if there is a problem with the Tree (e.g. if there is a branch with no length given in parameters)

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)

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

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

setThread

public void setThread(boolean thread)

Set whether threaded calculations should be performed

Parameters:

thread - Whether to perform threaded calculations

getAlignmentLength

public abstract int getAlignmentLength()

Get the length of the alignment the calculator is using

Returns:

The length of the alignment

setNoThreads

public static void setNoThreads(int number)

Set the number of threads to be used during the calculations

Parameters:

number - Number of threads