Uses of Class
Likelihood.SiteLikelihood

Packages that use SiteLikelihood

Package	Description
Likelihood	Provides classes for calculating the likelihood of a tree given a model and an alignment.

Uses of SiteLikelihood in Likelihood

Methods in Likelihood that return SiteLikelihood

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)
SiteLikelihood	Calculator.SiteCalculator.call()
SiteLikelihood	StandardLikelihood.getMissingLikelihood(Site s) Gets the likelihood result for a given missing site
SiteLikelihood	Calculator.SiteCalculator.getResult() Gets the computed result
SiteLikelihood	StandardLikelihood.getSiteLikelihood(Site s) Gets the likelihood result for a given site

Methods in Likelihood that return types with arguments of type SiteLikelihood

Modifier and Type	Method and Description
protected java.util.Map<Site,SiteLikelihood>	Calculator.siteCalculate(Parameters p) Calculates the likelihood for each site

Method parameters in Likelihood with type arguments of type SiteLikelihood

Modifier and Type	Method and Description
abstract R	Calculator.combineSites(java.util.Map<Site,SiteLikelihood> sites, Parameters p) Combines the likelihood from each site into a alignment likelihood
StandardLikelihood	StandardCalculator.combineSites(java.util.Map<Site,SiteLikelihood> sites, Parameters p)