Models
Class DNAModelFactory

java.lang.Object
  extended by Models.DNAModelFactory

public class DNAModelFactory
extends java.lang.Object

A factory for easing the creation of many standard DNA models

Version:
1.0

Method Summary
static Model Felsenstein81_Gamma(Parameters p, int numCats)
          Creates an instance of a JFelsenstein 81 model with gamma-distributed rate across sites
static Model Felsenstein81(Parameters p)
          Creates an instance of a Felsenstein 81 model
static Model GTR_Gamma(Parameters p, int numCats)
          Creates an instance of a General Time Reversable model with gamma-distributed rate across sites
static Model GTR(Parameters p)
          Creates an instance of a General Time Reversable model
static Model HKY_Gamma(Parameters p, int numCats)
          Creates an instance of a HKY model with gamma-distributed rate across sites
static Model HKY(Parameters p)
          Creates an instance of a HKY model
static Model JukesCantor_Gamma(Parameters p, int numCats)
          Creates an instance of a Jukes-Cantor model with gamma-distributed rate across sites
static Model JukesCantor(Parameters p)
          Creates an instance of a Jukes-Cantor model
static Model Kimura_Gamma(Parameters p, int numCats)
          Creates an instance of a Kimura 2-parameter model with gamma-distributed rate across sites
static Model Kimura(Parameters p)
          Creates an instance of a Kimura 2-paramter model
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Method Detail

JukesCantor

public static Model JukesCantor(Parameters p)
Creates an instance of a Jukes-Cantor 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

JukesCantor_Gamma

public static Model JukesCantor_Gamma(Parameters p,
                                      int numCats)
Creates an instance of a Jukes-Cantor 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

Kimura

public static Model Kimura(Parameters p)
Creates an instance of a Kimura 2-paramter model

Parameters:
p - Parameters structure to add the model parameters to
Returns:
The model

Kimura_Gamma

public static Model Kimura_Gamma(Parameters p,
                                 int numCats)
Creates an instance of a Kimura 2-parameter 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

Felsenstein81

public static Model Felsenstein81(Parameters p)
Creates an instance of a Felsenstein 81 model

Parameters:
p - Parameters structure to add the model parameters to
Returns:
The model

Felsenstein81_Gamma

public static Model Felsenstein81_Gamma(Parameters p,
                                        int numCats)
Creates an instance of a JFelsenstein 81 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

HKY

public static Model HKY(Parameters p)
Creates an instance of a HKY model

Parameters:
p - Parameters structure to add the model parameters to
Returns:
The model

HKY_Gamma

public static Model HKY_Gamma(Parameters p,
                              int numCats)
Creates an instance of a HKY 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

GTR

public static Model GTR(Parameters p)
Creates an instance of a General Time Reversable model

Parameters:
p - Parameters structure to add the model parameters to
Returns:
The model

GTR_Gamma

public static Model GTR_Gamma(Parameters p,
                              int numCats)
Creates an instance of a General Time Reversable 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