Uses of Class
Likelihood.SiteLikelihood.NodeLikelihood

Packages that use SiteLikelihood.NodeLikelihood

Package	Description
Alignments	Provides class for dealing with "alignments" and the sites in an alignment.
Ancestors	Provides classed to calculate ancestral reconstruction.
Likelihood	Provides classes for calculating the likelihood of a tree given a model and an alignment.

Uses of SiteLikelihood.NodeLikelihood in Alignments

Methods in Alignments that return types with arguments of type SiteLikelihood.NodeLikelihood

Modifier and Type	Method and Description
java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood>	Site.getInitialNodeLikelihoods(Tree t, java.util.Map<java.lang.String,java.lang.Integer> map) Gets initial node likelihoods based on the site and tree.

Uses of SiteLikelihood.NodeLikelihood in Ancestors

Methods in Ancestors that return types with arguments of type SiteLikelihood.NodeLikelihood

Modifier and Type	Method and Description
java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood>	Assignment.getInitialNodeLikelihoods(Tree t, Site s, java.util.Map<java.lang.String,java.lang.Integer> map) Creates initial node likelihoods using this assignment.

Uses of SiteLikelihood.NodeLikelihood in Likelihood

Fields in Likelihood with type parameters of type SiteLikelihood.NodeLikelihood

Modifier and Type	Field and Description
protected java.util.HashMap<Site,java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood>>	Calculator.snl The site node likelihoods.

Methods in Likelihood that return SiteLikelihood.NodeLikelihood

Modifier and Type	Method and Description
SiteLikelihood.NodeLikelihood	SiteLikelihood.NodeLikelihood.clone()
SiteLikelihood.NodeLikelihood	SiteLikelihood.RateLikelihood.getNodeLikelihood(java.lang.String node) Returns the likelihood results for a given node on the tree

Methods in Likelihood with parameters of type SiteLikelihood.NodeLikelihood

Modifier and Type	Method and Description
Real	FitzJohnRoot.calculate(SiteLikelihood.NodeLikelihood root)
Real	Root.calculate(SiteLikelihood.NodeLikelihood root) Calculate the total likelihood from the root node likelihood
Real	StandardRoot.calculate(SiteLikelihood.NodeLikelihood root)

Method parameters in Likelihood with type arguments of type SiteLikelihood.NodeLikelihood

Modifier and Type	Method and Description
abstract SiteLikelihood	Calculator.calculateSite(Site s, Tree t, Parameters p, Probabilities tp, java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood> nl) Calculate the likelihood for a single site.
SiteLikelihood	StandardCalculator.calculateSite(Site s, Tree t, Parameters p, Probabilities tp, java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood> nl)

Constructor parameters in Likelihood with type arguments of type SiteLikelihood.NodeLikelihood

Constructor and Description
Calculator.SiteCalculator(Site s, Tree t, Parameters p, Probabilities tp, java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood> nl) Standard constructor
Calculator(java.util.Map<java.lang.String,Model> m, java.util.Map<java.lang.String,Tree> t, java.util.HashMap<Site,java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood>> snl) Default constructor.
SiteLikelihood.RateLikelihood(Real l, java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood> nodeLikelihoods) Default constructor