Models

Class RYModelFactory

java.lang.Object

Models.RYModelFactory

public class RYModelFactory
extends java.lang.Object

A factory for easing the creation of the standard RY model

Version:

2.0

Constructor Summary

Constructors

Constructor and Description
RYModelFactory()

Method Summary

Methods

Modifier and Type	Method and Description
static Model	RY_Gamma(int numCats) Creates an instance of a RY model with gamma-distributed rate across sites
static Model	RY_Gamma(Parameters p, int numCats) Creates an instance of a RY model with gamma-distributed rate across sites
static Model	RY() Creates an instance of a RY model
static Model	RY(Parameters p) Creates an instance of a RY model

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RYModelFactory

public RYModelFactory()

Method Detail

RY

public static Model RY(Parameters p)
                throws Parameters.ParameterException

Creates an instance of a RY model

Parameters:

p - Parameters structure to add the model parameters to (none in this case but for consistency this is left here)

Returns:

The model

Throws:

Parameters.ParameterException - Thrown if the name of one of the parameters to be added by this method is already in use.

RY

public static Model RY()

Creates an instance of a RY model

Returns:

The model

RY_Gamma

public static Model RY_Gamma(Parameters p,
             int numCats)
                      throws Parameters.ParameterException

Creates an instance of a RY model with gamma-distributed rate across sites

Parameters:

p - Parameters structure to add the model parameters to

numCats - The number of gamma categories to use

Returns:

The model

Throws:

Parameters.ParameterException - Thrown if the name of one of the parameters to be added by this method is already in use.

RY_Gamma

public static Model RY_Gamma(int numCats)

Creates an instance of a RY model with gamma-distributed rate across sites

Parameters:

numCats - The number of gamma categories to use

Returns:

The model