Uses of Class
Likelihood.Likelihood

Packages that use Likelihood

Package	Description
Likelihood	Provides classes for calculating the likelihood of a tree given a model and an alignment.
ModelTest
Optimizers	Provides classes for optimising a likelihood.

Uses of Likelihood in Likelihood

Classes in Likelihood with type parameters of type Likelihood

Modifier and Type	Class and Description
class	Calculator<R extends Likelihood> Abstract class for calculating a likelihood.

Subclasses of Likelihood in Likelihood

Modifier and Type	Class and Description
class	StandardLikelihood Stores the results of a likelihood calculation.

Uses of Likelihood in ModelTest

Methods in ModelTest that return types with arguments of type Likelihood

Modifier and Type	Method and Description
Calculator<Likelihood>	TestInstance.getCalculator() Get the calculator associated with this instance
java.util.Map<TestInstance,Likelihood>	AIC.getLikelihoods() Returns the likelihood for each instance
java.util.Map<TestInstance,Likelihood>	BIC.getLikelihoods() Returns the likelihood for each instance

Constructor parameters in ModelTest with type arguments of type Likelihood

Constructor and Description
TestInstance(Calculator<Likelihood> c, Parameters p) Creates an instance
TestInstance(Calculator<Likelihood> c, Parameters p, Adapter adapter, Alignment distinct) Creates a named instance.
TestInstance(Calculator<Likelihood> c, Parameters p, java.lang.String name) Creates a named instance.
TestInstance(Calculator<Likelihood> c, Parameters p, java.lang.String name, Adapter adapter, Alignment distinct) Creates a named instance.

Uses of Likelihood in Optimizers

Classes in Optimizers with type parameters of type Likelihood

Modifier and Type	Interface and Description
interface	Optimizable<R extends Likelihood> Interface for classes that represent optimisable likelihood functions.

Methods in Optimizers with type parameters of type Likelihood

Modifier and Type	Method and Description
<R extends Likelihood> R	ConjugateGradient.maximise(Optimizable<R> c, Parameters p)
<R extends Likelihood> R	GoldenSection.maximise(Optimizable<R> l, Parameters params)
<R extends Likelihood> R	NelderMead.maximise(Optimizable<R> l, Parameters params)
<R extends Likelihood> R	Optimizer.maximise(Optimizable<R> l, Parameters p) Maximises the likelihood, logging to screen.
<R extends Likelihood> R	ConjugateGradient.maximise(Optimizable<R> c, Parameters p, java.io.File log)
<R extends Likelihood> R	GoldenSection.maximise(Optimizable<R> l, Parameters params, java.io.File log)
<R extends Likelihood> R	NelderMead.maximise(Optimizable<R> l, Parameters params, java.io.File log)
<R extends Likelihood> R	Optimizer.maximise(Optimizable<R> l, Parameters params, java.io.File log) Maximises the likelihood, logging to a file.
<R extends Likelihood> R	ConjugateGradient.restart(Optimizable<R> l, java.io.File checkPoint)
<R extends Likelihood> R	GoldenSection.restart(Optimizable<R> l, java.io.File checkPoint)
<R extends Likelihood> R	NelderMead.restart(Optimizable<R> l, java.io.File checkPoint)
<R extends Likelihood> R	Optimizer.restart(Optimizable<R> l, java.io.File checkPoint) Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File), logging to the screen.
<R extends Likelihood> R	ConjugateGradient.restart(Optimizable<R> l, java.io.File checkPoint, java.io.File log)
<R extends Likelihood> R	GoldenSection.restart(Optimizable<R> l, java.io.File checkPoint, java.io.File log)
<R extends Likelihood> R	NelderMead.restart(Optimizable<R> l, java.io.File checkPoint, java.io.File log)
<R extends Likelihood> R	Optimizer.restart(Optimizable<R> l, java.io.File checkPoint, java.io.File log) Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File), logging to a file.