Models
Class DuplicationModelFactory

java.lang.Object
  extended by Models.DuplicationModelFactory

public class DuplicationModelFactory
extends java.lang.Object

A factory for easing the creation of some simple gene-family models

Version:
1.0

Method Summary
static Model BDI_Gamma(Parameters p, int num, int numCats)
          Creates a simple BDI model with gamma-distributed rate across sites
static Model BDI(Parameters p, int num)
          Creates a simple BDI model
static Model Parsimony_Gamma(Parameters p, int num, int numCats)
          Creates a simple parsimony-style model with gamma-distributed rate across sites
static Model Parsimony(Parameters p, int num)
          Creates a simple parsimony-style model
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Method Detail

Parsimony

public static Model Parsimony(Parameters p,
                              int num)
Creates a simple parsimony-style model

Parameters:
p - Parameters structure to add the model parameters to (none in this case but for consistency this is left here)
num - The maximum family size
Returns:
The model

Parsimony_Gamma

public static Model Parsimony_Gamma(Parameters p,
                                    int num,
                                    int numCats)
Creates a simple parsimony-style model with gamma-distributed rate across sites

Parameters:
p - Parameters structure to add the model parameters to
num - The maximum family size
numCats - The number of gamma categories to use
Returns:
The model

BDI

public static Model BDI(Parameters p,
                        int num)
Creates a simple BDI model

Parameters:
p - Parameters structure to add the model parameters to
num - The maximum family size
Returns:
The model

BDI_Gamma

public static Model BDI_Gamma(Parameters p,
                              int num,
                              int numCats)
Creates a simple BDI model with gamma-distributed rate across sites

Parameters:
p - Parameters structure to add the model parameters to
num - The maximum family size
numCats - The number of gamma categories to use
Returns:
The model