Uses of Class
Parameters.Parameter

Packages that use Parameter
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
 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
 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, boolean matrix)
          Creates a new bounded paramater that is estimated and is optionally in a rate matrix
static Parameter Parameter.newEstimatedParameter(java.lang.String name)
          Creates a new (unbounded) paramater that is estimated.
static Parameter Parameter.newEstimatedParameter(java.lang.String name, boolean matrix)
          Creates a new unbounded parameter that is estimated and is optionally in a rate matrix.
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, boolean matrix)
          Creates a new positive parameter that is estimated and is optionally in a rate matrix.
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
 java.util.Iterator<Parameter> Parameters.iterator()
           
 

Methods in Parameters with parameters of type Parameter
 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
Parameters(java.util.ArrayList<Parameter> params)
          Creates a set of parameters containing the given parameters