Uses of Class
Constraints.SiteConstraints

Packages that use SiteConstraints
Alignments Provides class for dealing with "alignments" and the sites in an alignment. 
Constraints Provides classes to constrain the state of internal nodes. 
Likelihood Provides classes for calculating the likelihood of a tree given a model and an alignment. 
 

Uses of SiteConstraints in Alignments
 

Methods in Alignments with parameters of type SiteConstraints
 ArrayMap<java.lang.String,Likelihood.NodeLikelihood> Site.getInitialNodeLikelihoods(Tree t, ArrayMap<java.lang.String,java.lang.Integer> map, SiteConstraints scon)
          Gdets initial node likelihoods based on the site, tree and any constraints.
 

Uses of SiteConstraints in Constraints
 

Methods in Constraints that return SiteConstraints
 SiteConstraints SiteConstraints.clone()
           
 SiteConstraints Constrainer.getConstraints(Tree t, Site s)
          Gets the consraints on an the external nodes of a site given the tree and the state of the leafs.
 SiteConstraints NoConstraints.getConstraints(Tree t, Site s)
           
 

Uses of SiteConstraints in Likelihood
 

Constructors in Likelihood with parameters of type SiteConstraints
Calculator.SiteCalculator(Site s, Tree t, SiteConstraints con, Probabilities tp)
          Constructor mainly for backwards compitability although also still used by some of the ancestral calculations.