DNAModelFactory (GeLL)

java.lang.Object
- Models.DNAModelFactory

```
public class DNAModelFactory
extends java.lang.Object
```
A factory for easing the creation of many standard DNA models

Version:

2.0

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class DNAModelFactory.DNAModel
Represents the various types of DNA models

Nested Classes
Modifier and Type	Class and Description
`static class`	`DNAModelFactory.DNAModel` Represents the various types of DNA models

Constructor Summary

Constructors
Constructor and Description
`DNAModelFactory(DNAModelFactory.DNAModel model)` Constructor so that calls to `getModel()` and `getParameters()` return the appropiate model or the appropiate parameters.
`DNAModelFactory(DNAModelFactory.DNAModel model, int numCats)` Constructor so that calls to `getModel()` and `getParameters()` return the appropriate model or the appropriate parameters.

Method Summary

Methods
Modifier and Type	Method and Description
`static Model`	`Felsenstein81_Gamma(int numCats)` Creates an instance of a JFelsenstein 81 model with gamma-distributed rate across sites
`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()` Creates an instance of a Felsenstein 81 model
`static Model`	`Felsenstein81(Parameters p)` Creates an instance of a Felsenstein 81 model
`Model`	`getModel()` Returns a new instance of the relevant model
`Parameters`	`getParameters()` Gets the parameters for the relevant model
`static Model`	`GTR_Gamma(int numCats)` Creates an instance of a General Time Reversible model with gamma-distributed rate across sites
`static Model`	`GTR_Gamma(Parameters p, int numCats)` Creates an instance of a General Time Reversible model with gamma-distributed rate across sites
`static Model`	`GTR()` Creates an instance of a General Time Reversible model
`static Model`	`GTR(Parameters p)` Creates an instance of a General Time Reversible model
`static Model`	`HKY_Gamma(int numCats)` Creates an instance of a HKY model with gamma-distributed rate across sites
`static Model`	`HKY_Gamma(Parameters p, int numCats)` Creates an instance of a HKY model with gamma-distributed rate across sites
`static Model`	`HKY()` Creates an instance of a HKY model
`static Model`	`HKY(Parameters p)` Creates an instance of a HKY model
`static Model`	`JukesCantor_Gamma(int numCats)` Creates an instance of a Jukes-Cantor model with gamma-distributed rate across sites
`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()` Creates an instance of a Jukes-Cantor model
`static Model`	`JukesCantor(Parameters p)` Creates an instance of a Jukes-Cantor model
`static Model`	`Kimura_Gamma(int numCats)` Creates an instance of a Kimura 2-parameter model with gamma-distributed rate across sites
`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()` Creates an instance of a Kimura 2-paramter model
`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

- Constructor Detail
  - DNAModelFactory
```
public DNAModelFactory(DNAModelFactory.DNAModel model)
```
    Constructor so that calls to getModel() and getParameters() return the appropiate model or the appropiate parameters.
    
    Parameters:
    model - The model
  - DNAModelFactory
```
public DNAModelFactory(DNAModelFactory.DNAModel model,
               int numCats)
                throws Model.ModelException
```
    Constructor so that calls to getModel() and getParameters() return the appropriate model or the appropriate parameters.
    
    Parameters:
    model - The model
    numCats - The number of categories for the model
    
    Throws:
    
    Model.ModelException
- 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
```
public static Model JukesCantor()
```
    Creates an instance of a Jukes-Cantor model
    
    Returns:
    The model
  - JukesCantor_Gamma
```
public static Model JukesCantor_Gamma(Parameters p,
                      int numCats)
                               throws Parameters.ParameterException
```
    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
    
    Throws:
    
    Parameters.ParameterException - Thrown if the name of one of the parameters to be added by this method is already in use.
  - JukesCantor_Gamma
```
public static Model JukesCantor_Gamma(int numCats)
```
    Creates an instance of a Jukes-Cantor model with gamma-distributed rate across sites
    
    Parameters:
    numCats - The number of gamma categories to use
    
    Returns:
    The model
  - Kimura
```
public static Model Kimura(Parameters p)
                    throws Parameters.ParameterException
```
    Creates an instance of a Kimura 2-paramter model
    
    Parameters:
    p - Parameters structure to add the model parameters to
    
    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.
  - Kimura
```
public static Model Kimura()
```
    Creates an instance of a Kimura 2-paramter model
    
    Returns:
    The model
  - Kimura_Gamma
```
public static Model Kimura_Gamma(Parameters p,
                 int numCats)
                          throws Parameters.ParameterException
```
    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
    
    Throws:
    
    Parameters.ParameterException - Thrown if the name of one of the parameters to be added by this method is already in use.
  - Kimura_Gamma
```
public static Model Kimura_Gamma(int numCats)
```
    Creates an instance of a Kimura 2-parameter model with gamma-distributed rate across sites
    
    Parameters:
    numCats - The number of gamma categories to use
    
    Returns:
    The model
  - Felsenstein81
```
public static Model Felsenstein81(Parameters p)
                           throws Parameters.ParameterException
```
    Creates an instance of a Felsenstein 81 model
    
    Parameters:
    p - Parameters structure to add the model parameters to
    
    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.
  - Felsenstein81
```
public static Model Felsenstein81()
```
    Creates an instance of a Felsenstein 81 model
    
    Returns:
    The model
  - Felsenstein81_Gamma
```
public static Model Felsenstein81_Gamma(Parameters p,
                        int numCats)
                                 throws Parameters.ParameterException
```
    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
    
    Throws:
    
    Parameters.ParameterException - Thrown if the name of one of the parameters to be added by this method is already in use.
  - Felsenstein81_Gamma
```
public static Model Felsenstein81_Gamma(int numCats)
```
    Creates an instance of a JFelsenstein 81 model with gamma-distributed rate across sites
    
    Parameters:
    numCats - The number of gamma categories to use
    
    Returns:
    The model
  - HKY
```
public static Model HKY(Parameters p)
                 throws Parameters.ParameterException
```
    Creates an instance of a HKY model
    
    Parameters:
    p - Parameters structure to add the model parameters to
    
    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.
  - HKY
```
public static Model HKY()
```
    Creates an instance of a HKY model
    
    Returns:
    The model
  - HKY_Gamma
```
public static Model HKY_Gamma(Parameters p,
              int numCats)
                       throws Parameters.ParameterException
```
    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
    
    Throws:
    
    Parameters.ParameterException - Thrown if the name of one of the parameters to be added by this method is already in use.
  - HKY_Gamma
```
public static Model HKY_Gamma(int numCats)
```
    Creates an instance of a HKY model with gamma-distributed rate across sites
    
    Parameters:
    numCats - The number of gamma categories to use
    
    Returns:
    The model
  - GTR
```
public static Model GTR(Parameters p)
                 throws Parameters.ParameterException
```
    Creates an instance of a General Time Reversible model
    
    Parameters:
    p - Parameters structure to add the model parameters to
    
    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.
  - GTR
```
public static Model GTR()
```
    Creates an instance of a General Time Reversible model
    
    Returns:
    The model
  - GTR_Gamma
```
public static Model GTR_Gamma(Parameters p,
              int numCats)
                       throws Parameters.ParameterException
```
    Creates an instance of a General Time Reversible 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.
  - GTR_Gamma
```
public static Model GTR_Gamma(int numCats)
```
    Creates an instance of a General Time Reversible model with gamma-distributed rate across sites
    
    Parameters:
    numCats - The number of gamma categories to use
    
    Returns:
    The model
  - getModel
```
public Model getModel()
```
    Returns a new instance of the relevant model
    
    Returns:
    The new model
  - getParameters
```
public Parameters getParameters()
```
    Gets the parameters for the relevant model
    
    Returns:
    The parameters

Class DNAModelFactory

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

DNAModelFactory

DNAModelFactory

Method Detail

JukesCantor

JukesCantor

JukesCantor_Gamma

JukesCantor_Gamma

Kimura

Kimura

Kimura_Gamma

Kimura_Gamma

Felsenstein81

Felsenstein81

Felsenstein81_Gamma

Felsenstein81_Gamma

HKY

HKY

HKY_Gamma

HKY_Gamma

GTR

GTR

GTR_Gamma

GTR_Gamma

getModel

getParameters