Uses of Interface
Optimizers.Optimizable

Packages that use Optimizable

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

Uses of Optimizable in Likelihood

Classes in Likelihood that implement Optimizable

Modifier and Type	Class and Description
class	Calculator<R extends Likelihood> Abstract class for calculating a likelihood.
class	StandardCalculator Calculates the likelihood for different parameter values.

Uses of Optimizable in Optimizers

Methods in Optimizers with parameters of type Optimizable

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.