A B C D E F G H I J K L M N O P Q R S T U V W

O

Optimizable<R extends Likelihood> - Interface in Optimizers

Interface for classes that represent optimisable likelihood functions.

Optimizer - Interface in Optimizers

Interface for different likelihood optimisers

Optimizer.OptimizerException - Exception in Optimizers

Exception for when there is a problem with an optimiser.

Optimizer.OptimizerException(String) - Constructor for exception Optimizers.Optimizer.OptimizerException

Default constructor

Optimizers - package Optimizers

Provides classes for optimising a likelihood.

optKeepNL(boolean) - Static method in class Likelihood.SiteLikelihood

Similar to SiteLikelihood.keepNodeLikelihoods(boolean) but if set to false overrides the setting set by that function.

OutputException - Exception in Exceptions

Exception for problems writing an output file

OutputException(String, String, Throwable) - Constructor for exception Exceptions.OutputException

Default constructor

A B C D E F G H I J K L M N O P Q R S T U V W