ModelTest

Class EmpiricalAdapter

java.lang.Object

ModelTest.EmpiricalAdapter

All Implemented Interfaces:

Adapter

public class EmpiricalAdapter
extends java.lang.Object
implements Adapter

The empirical adapter. See Whelan et al 2015 for more

Version:

2.0

Constructor Summary

Constructors

Constructor and Description
EmpiricalAdapter(java.util.Map<java.lang.String,java.lang.String> mapping) Creates an instance
EmpiricalAdapter(java.util.Map<java.lang.String,java.lang.String> mapping, java.util.Set<java.lang.String> ignore) Creates an instance including a set of states to ignore in the calculation (such as the gap state)

Method Summary

Methods

Modifier and Type	Method and Description
double	likelihood(Alignment distinct) Return the likelihood of the adapter given the distinct alignment
int	numberParameters() Return the number of parameters associated with the adapter

Methods inherited from class java.lang.Object

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

Constructor Detail

EmpiricalAdapter

public EmpiricalAdapter(java.util.Map<java.lang.String,java.lang.String> mapping)

Creates an instance

Parameters:

mapping - Map from compound state to distinct state

EmpiricalAdapter

public EmpiricalAdapter(java.util.Map<java.lang.String,java.lang.String> mapping,
                java.util.Set<java.lang.String> ignore)

Creates an instance including a set of states to ignore in the calculation (such as the gap state)

Parameters:

mapping - Map from compound state to distinct state

ignore - States to ignore

Method Detail

likelihood

public double likelihood(Alignment distinct)

Description copied from interface: Adapter

Return the likelihood of the adapter given the distinct alignment

Specified by:

likelihood in interface Adapter

Parameters:

distinct - The distinct alignment

Returns:

The likelihood of the adapter

numberParameters

public int numberParameters()

Description copied from interface: Adapter

Return the number of parameters associated with the adapter

Specified by:

numberParameters in interface Adapter

Returns:

The number of parameters