Uses of Class
Alignments.Site

Packages that use Site
Alignments Provides class for dealing with "alignments" and the sites in an alignment. 
Ancestors Provides classed to calculate ancestral reconstruction. 
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. 
Simulations Provides a class to create simulate data. 
 

Uses of Site in Alignments
 

Fields in Alignments with type parameters of type Site
protected  java.util.List<Site> Alignment.data
          The list of sites in the alignment
 

Methods in Alignments that return Site
 Site Alignment.getSite(int s)
          Returns the site at a given position in the alignment
 Site Site.recode(java.util.Map<java.lang.String,java.lang.String> recode)
          Recodes the site and returns it
 

Methods in Alignments that return types with arguments of type Site
 java.util.Set<Site> Alignment.getUniqueSites()
          Returns a list of unique sites in the aligment.
 java.util.Iterator<Site> Alignment.iterator()
           
 

Methods in Alignments with parameters of type Site
 int Alignment.getCount(Site s)
          Gets a count of hoften a site occurs in the alignment
 

Constructor parameters in Alignments with type arguments of type Site
Alignment(java.util.List<Site> data)
          Creates an alignment
 

Uses of Site in Ancestors
 

Methods in Ancestors that return Site
 Site AncestralMarginal.SiteResult.getSite()
          Returns the reconstructed site
 

Methods in Ancestors with parameters of type Site
 AncestralMarginal.SiteResult AncestralMarginal.Result.getSiteResult(Site s)
          Gets the site results for a given site
 

Uses of Site in Constraints
 

Methods in Constraints with parameters of type Site
 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)
           
 boolean SiteConstraints.meetsConstrains(Site s)
          Tests whether a given site (that should include data for internal nodes) meets the defined constraints
 

Uses of Site in Likelihood
 

Methods in Likelihood with parameters of type Site
 Likelihood.SiteLikelihood Likelihood.getMissingLikelihood(Site s)
          Gets the likelihood result for a given missing site
 Likelihood.SiteLikelihood Likelihood.getSiteLikelihood(Site s)
          Gets the likelihood result for a given site
 

Constructors in Likelihood with parameters of type Site
Calculator.SiteCalculator(Site s, Tree t, SiteConstraints con, Probabilities tp)
          Standard constructor
 

Uses of Site in Simulations
 

Methods in Simulations that return Site
 Site Simulate.getSite()
          Gets a simulated site without returning the state of the internal nodes
 Site Simulate.getSite(boolean internal)
          Gets a simulated site
 Site Simulate.getSite(boolean internal, java.util.Map<java.lang.String,java.lang.String> recode)
          Gets a simulated site.
 Site Simulate.getSite(java.util.Map<java.lang.String,java.lang.String> recode)
          Gets a simulated site without returning the state of the internal nodes.