Likelihood
Class Likelihood

java.lang.Object
  extended by Likelihood.Likelihood
All Implemented Interfaces:
java.io.Serializable

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

Stores the results of a likelihood calculation. As well as the overall likelihood it stores the likelihood of each site and also of each missing site.

Version:
1.2
See Also:
Serialized Form

Nested Class Summary
static class Likelihood.LikelihoodException
          Exception related to a likelihood calculation
static class Likelihood.NodeLikelihood
          Stores the results of a likelihood claculation for a single node in a tree.
static class Likelihood.RateLikelihood
          Stores the result of the likelihood calculations for a single site and a single rate class.
static class Likelihood.SiteLikelihood
          Stored the result of a likelihood calculation for a single site
 
Method Summary
 double getLikelihood()
          Gets the total likelihood
 Likelihood.SiteLikelihood getMissingLikelihood(Site s)
          Gets the likelihood result for a given missing site
 Parameters getParameters()
          Gets the parameters used to calculate this likelihood
 Likelihood.SiteLikelihood getSiteLikelihood(Site s)
          Gets the likelihood result for a given site
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Method Detail

getLikelihood

public double getLikelihood()
Gets the total likelihood

Returns:
The total likelihood

getSiteLikelihood

public Likelihood.SiteLikelihood getSiteLikelihood(Site s)
                                            throws Likelihood.LikelihoodException
Gets the likelihood result for a given site

Parameters:
s - The site to return the likelihood results for
Returns:
The likelihood results for the given site
Throws:
Likelihood.LikelihoodException - Thrown if no likelihood has been calculated for the given site

getMissingLikelihood

public Likelihood.SiteLikelihood getMissingLikelihood(Site s)
                                               throws Likelihood.LikelihoodException
Gets the likelihood result for a given missing site

Parameters:
s - The missing site to return the likelihood results for
Returns:
The likelihood results for the given missing site
Throws:
Likelihood.LikelihoodException - Thrown if no likelihood has been calculated for the given site

getParameters

public Parameters getParameters()
Gets the parameters used to calculate this likelihood

Returns:
The parameters

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object