Uses of Class
Parameters.Parameter

Packages that use Parameter

Package	Description
Likelihood	Provides classes for calculating the likelihood of a tree given a model and an alignment.
Parameters	Provides classes for defining parameters used in the various calculations.

Uses of Parameter in Likelihood

Methods in Likelihood with parameters of type Parameter

Modifier and Type	Method and Description
Range	ConfidenceInterval.getCI(Parameter param, double conf) Calculates the confidence interval for a single parameter

Uses of Parameter in Parameters

Methods in Parameters that return Parameter

Modifier and Type	Method and Description
Parameter	Parameter.clone()
Parameter	Parameters.getParam(java.lang.String name) Gets the parameter with the given name
static Parameter	Parameter.newEstimatedBoundedParameter(java.lang.String name, double lbound, double ubound) Creates a new bounded parameter that is estimated.
static Parameter	Parameter.newEstimatedBoundedParameter(java.lang.String name, double lbound, double ubound, double start) Creates a new bounded parameter that is estimated.
static Parameter	Parameter.newEstimatedParameter(java.lang.String name) Creates a new (unbounded) parameter that is estimated.
static Parameter	Parameter.newEstimatedParameter(java.lang.String name, double start) Creates a new (unbounded) parameter that is estimated.
static Parameter	Parameter.newEstimatedPositiveParameter(java.lang.String name) Creates a new parameter that has to be positive and is estimated.
static Parameter	Parameter.newEstimatedPositiveParameter(java.lang.String name, double start) Creates a new parameter that has to be positive and is estimated.
static Parameter	Parameter.newFixedParameter(java.lang.String name, double value) Creates a new fixed parameter (i.e.

Methods in Parameters that return types with arguments of type Parameter

Modifier and Type	Method and Description
java.util.Iterator<Parameter>	Parameters.iterator()

Methods in Parameters with parameters of type Parameter

Modifier and Type	Method and Description
void	Parameters.addParameter(Parameter p) Add a parameter
void	Parameters.setValue(Parameter p, double v) Sets the value of a parameter

Constructor parameters in Parameters with type arguments of type Parameter

Constructor and Description
Parameters(java.util.List<Parameter> params) Creates a set of parameters containing the given parameters