Models

Class DuplicationModelFactory

java.lang.Object

Models.DuplicationModelFactory

public class DuplicationModelFactory
extends java.lang.Object

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

Version:

2.0

Method Summary

Methods

Modifier and Type	Method and Description
static Model	BD_NoZero_Gamma(Parameters p, int num, int numCats) Creates a Birth Death model with no zero state and gamma distributed rates-across sites.
static Model	BD_NoZero_Gamma(Parameters p, int num, int numCats, boolean fixed) Creates a Birth Death model with no zero state and gamma distributed rates-across sites.
static Model	BD_NoZero(Parameters p, int num) Creates a Birth Death model with no zero state.
static Model	BD_NoZero(Parameters p, int num, boolean fixed) Creates a Birth Death model with no zero state.
static Model	BDI_Gamma(Parameters p, int num, int numCats) Creates a simple BDI model with gamma-distributed rate across sites.
static Model	BDI_Gamma(Parameters p, int num, int numCats, boolean fixed) 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	BDI(Parameters p, int num, boolean fixed) Creates a simple BDI model
static Model	BDIE_Gamma(Parameters p, int num, int numCats) Creates a simple BDI model with gamma-distributed rate across sites.
static Model	BDIE_Gamma(Parameters p, int num, int numCats, boolean fixed) Creates a simple BDIE model with gamma-distributed rate across sites
static Model	BDIE(Parameters p, int num, boolean fixed) Creates a simple BDIE 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_Gamma(Parameters p, int num, int numCats, boolean fixed) 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
static Model	Parsimony(Parameters p, int num, boolean fixed) 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)
                       throws Parameters.ParameterException

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). Assumes branch lengths are to be estimated.

num - The maximum family size

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.

Parsimony

public static Model Parsimony(Parameters p,
              int num,
              boolean fixed)
                       throws Parameters.ParameterException

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

fixed - Whether fixed branch lengths are being used (and so whether or not one parameter should have a fixed value)

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.

Parsimony_Gamma

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

Creates a simple parsimony-style model with gamma-distributed rate across sites. Assumes branch lengths are to be estimated.

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

Throws:

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

Parsimony_Gamma

public static Model Parsimony_Gamma(Parameters p,
                    int num,
                    int numCats,
                    boolean fixed)
                             throws Parameters.ParameterException

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

fixed - Whether fixed branch lengths are being used (and so whether or not one parameter should have a fixed value)

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.

BDI

public static Model BDI(Parameters p,
        int num)
                 throws Parameters.ParameterException

Creates a simple BDI model. Assumes branch lengths are estimated.

Parameters:

p - Parameters structure to add the model parameters to

num - The maximum family size

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.

BDI

public static Model BDI(Parameters p,
        int num,
        boolean fixed)
                 throws Parameters.ParameterException

Creates a simple BDI model

Parameters:

p - Parameters structure to add the model parameters to

num - The maximum family size

fixed - Whether fixed branch lengths are being used (and so whether or not one parameter should have a fixed value)

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.

BDI_Gamma

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

Creates a simple BDI model with gamma-distributed rate across sites. Assumes branch lengths are estimated

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

Throws:

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

BDI_Gamma

public static Model BDI_Gamma(Parameters p,
              int num,
              int numCats,
              boolean fixed)
                       throws Parameters.ParameterException

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

fixed - Whether fixed branch lengths are being used (and so whether or not one parameter should have a fixed value)

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.

BD_NoZero

public static Model BD_NoZero(Parameters p,
              int num)
                       throws Parameters.ParameterException

Creates a Birth Death model with no zero state. Assumes branch lengths are estimated

Parameters:

p - Parameters structure to add the model parameters to

num - The maximum family size

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.

BD_NoZero

public static Model BD_NoZero(Parameters p,
              int num,
              boolean fixed)
                       throws Parameters.ParameterException

Creates a Birth Death model with no zero state.

Parameters:

p - Parameters structure to add the model parameters to

num - The maximum family size

fixed - Whether fixed branch lengths are being used (and so whether or not one parameter should have a fixed value)

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.

BD_NoZero_Gamma

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

Creates a Birth Death model with no zero state and gamma distributed rates-across sites. Assumes branch lengths are estimated

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

Throws:

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

BD_NoZero_Gamma

public static Model BD_NoZero_Gamma(Parameters p,
                    int num,
                    int numCats,
                    boolean fixed)
                             throws Parameters.ParameterException

Creates a Birth Death model with no zero state and gamma distributed rates-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

fixed - Whether fixed branch lengths are being used (and so whether or not one parameter should have a fixed value)

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.

BDIE

public static Model BDIE(Parameters p,
         int num,
         boolean fixed)
                  throws Parameters.ParameterException

Creates a simple BDIE model

Parameters:

p - Parameters structure to add the model parameters to

num - The maximum family size

fixed - Whether fixed branch lengths are being used (and so whether or not one parameter should have a fixed value)

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.

BDIE_Gamma

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

Creates a simple BDI model with gamma-distributed rate across sites. Assumes branch lengths are estimated

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

Throws:

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

BDIE_Gamma

public static Model BDIE_Gamma(Parameters p,
               int num,
               int numCats,
               boolean fixed)
                        throws Parameters.ParameterException

Creates a simple BDIE 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

fixed - Whether fixed branch lengths are being used (and so whether or not one parameter should have a fixed value)

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.