Uses of Class
Likelihood.SiteLikelihood.LikelihoodException

Packages that use SiteLikelihood.LikelihoodException

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.LikelihoodException in Alignments

Methods in Alignments that throw SiteLikelihood.LikelihoodException

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.LikelihoodException in Ancestors

Methods in Ancestors that throw SiteLikelihood.LikelihoodException

Modifier and Type	Method and Description
abstract Alignment	AncestralJoint.calculate(Parameters params) Calculates the reconstruction
Alignment	AncestralJointBB.calculate(Parameters p)
AncestralMarginal.Result	AncestralMarginal.calculate(Parameters params) Calculates the reconstruction
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.LikelihoodException in Likelihood

Methods in Likelihood that throw SiteLikelihood.LikelihoodException

Modifier and Type	Method and Description
Real	SiteLikelihood.NodeLikelihood.getLikelihood(java.lang.String state) Returns the partial likelihood for a given state
SiteLikelihood	StandardLikelihood.getMissingLikelihood(Site s) Gets the likelihood result for a given missing site
SiteLikelihood.NodeLikelihood	SiteLikelihood.RateLikelihood.getNodeLikelihood(java.lang.String node) Returns the likelihood results for a given node on the tree
SiteLikelihood.RateLikelihood	SiteLikelihood.getRateLikelihood(RateCategory rate) Get the likelihood for a single rate class
SiteLikelihood	StandardLikelihood.getSiteLikelihood(Site s) Gets the likelihood result for a given site

Constructors in Likelihood that throw SiteLikelihood.LikelihoodException

Constructor and Description
SiteLikelihood.NodeLikelihood(java.util.Map<java.lang.String,java.lang.Integer> states) Constructor where all sates are allowed at a node
SiteLikelihood.NodeLikelihood(java.util.Map<java.lang.String,java.lang.Integer> states, java.util.Set<java.lang.String> allowedStates) Constructor where only some states are allowed at a node
SiteLikelihood.NodeLikelihood(java.util.Map<java.lang.String,java.lang.Integer> states, java.lang.String allowedState) Constructor where only a single state is allowed at a node
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, java.util.Map<java.lang.String,Tree> t) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, java.util.Map<java.lang.String,Tree> t, Alignment unobserved) Creates a class to calculate the likelihood for a given set of models, an alignment, a tree and unobserved data.
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t, Alignment unobserved) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(Model m, Alignment a, java.util.Map<java.lang.String,Tree> t) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(Model m, Alignment a, java.util.Map<java.lang.String,Tree> t, Alignment unobserved) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(Model m, Alignment a, Tree t) Creates an object to calculate the likelihood for a given model, alignment and tree.
StandardCalculator(Model m, Alignment a, Tree t, Alignment unobserved) Creates a class to calculate the likelihood for a given model, alignment, tree and missing data