Likelihood

Class SiteLikelihood

java.lang.Object

Likelihood.SiteLikelihood

All Implemented Interfaces:

java.io.Serializable

public class SiteLikelihood
extends java.lang.Object
implements java.io.Serializable

Stored the result of a likelihood calculation for a single site

Version:

2.0

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SiteLikelihood.LikelihoodException Exception related to a likelihood calculation
static class	SiteLikelihood.NodeLikelihood Stores the results of a likelihood calculation for a single node in a tree.
static class	SiteLikelihood.RateLikelihood Stores the result of the likelihood calculations for a single site and a single rate class.

Constructor Summary

Constructors

Constructor and Description
SiteLikelihood(java.util.Map<RateCategory,SiteLikelihood.RateLikelihood> rateLikelihoods, Probabilities P) Default constructor

Method Summary

Methods

Modifier and Type	Method and Description
Real	getLikelihood() Get the likelihood
RateCategory	getMostProbableRateCategory() Gets the most probable rate category
Real	getRateCategoryProbability(RateCategory rc) Gets the probability of being in a rate category
SiteLikelihood.RateLikelihood	getRateLikelihood(RateCategory rate) Get the likelihood for a single rate class
static void	keepNodeLikelihoods(boolean keep) Sets whether to store the node likelihoods after they've been used.
static void	optKeepNL(boolean keep) Similar to keepNodeLikelihoods(boolean) but if set to false overrides the setting set by that function.
static void	realType(RealFactory.RealType type) Sets the real type to be used during calculations, either SmallDouble or StandardDouble.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

SiteLikelihood

public SiteLikelihood(java.util.Map<RateCategory,SiteLikelihood.RateLikelihood> rateLikelihoods,
              Probabilities P)

Default constructor

Parameters:

rateLikelihoods - The likelihood of the individual rates at that site

P - A Probabilities object from which the frequency of each rate will be fetched

Method Detail

getLikelihood

public Real getLikelihood()

Get the likelihood

Returns:

The likelihood

getRateLikelihood

public SiteLikelihood.RateLikelihood getRateLikelihood(RateCategory rate)
                                                throws SiteLikelihood.LikelihoodException

Get the likelihood for a single rate class

Parameters:

rate - Rate class to get the likelihood for

Returns:

The likelihood results for a given rate

Throws:

SiteLikelihood.LikelihoodException - Thrown if no likelihood has been calculated for the given rate

getRateCategoryProbability

public Real getRateCategoryProbability(RateCategory rc)

Gets the probability of being in a rate category

Parameters:

rc - The rate category

Returns:

The probability of being in that rate category

getMostProbableRateCategory

public RateCategory getMostProbableRateCategory()

Gets the most probable rate category

Returns:

The most probable rate category

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

keepNodeLikelihoods

public static void keepNodeLikelihoods(boolean keep)

Sets whether to store the node likelihoods after they've been used. Setting this to false can save significant amounts of memory

Parameters:

keep - Whether to keep the node likelihoods

optKeepNL

public static void optKeepNL(boolean keep)

Similar to keepNodeLikelihoods(boolean) but if set to false overrides the setting set by that function. Intended to only be used by optimizers so that the node likelihoods calculated while optimizing aren't kept. I.e. should be set to false before optimizing and back to true for the final calculation.

Parameters:

keep - Whether to keep the ndoe likelihoods

realType

public static void realType(RealFactory.RealType type)

Sets the real type to be used during calculations, either SmallDouble or StandardDouble.

Parameters:

type - The double type to use

See Also:

AncestralJointDP.realType(Maths.RealFactory.RealType)