Uses of Class
Alignments.Site

Packages that use Site

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.
Simulations	Provides a class to create simulated data.

Uses of Site in Alignments

Subclasses of Site in Alignments

Modifier and Type	Class and Description
class	UniqueSite Used to represent a unique site in an alignment.

Methods in Alignments that return Site

Modifier and Type	Method and Description
Site	Alignment.getSite(int s) Returns the site at a given position in the alignment
Site	Site.limitToTaxa(java.util.Collection<java.lang.String> limit) Returns a new Site which is the same as this one except it is limited to certain taxa
Site	Site.recode(java.util.Map<java.lang.String,java.lang.String> recode) Recodes the site and returns it
Site	Site.recode(java.util.Map<java.lang.String,java.lang.String> recode, Ambiguous ambig) Recodes the alignment and returns it and also allows the definition of new ambiguous states

Methods in Alignments that return types with arguments of type Site

Modifier and Type	Method and Description
java.util.Iterator<Site>	Alignment.iterator()

Constructors in Alignments with parameters of type Site

Constructor and Description
Site(Site s) Creates a copy of a site
UniqueSite(Site s, int c) Default constructor

Constructor parameters in Alignments with type arguments of type Site

Constructor and Description
Alignment(java.util.List<Site> data) Creates an alignment

Uses of Site in Ancestors

Methods in Ancestors that return Site

Modifier and Type	Method and Description
Site	AncestralMarginal.SiteResult.getSite() Returns the reconstructed site

Methods in Ancestors with parameters of type Site

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.
AncestralMarginal.SiteResult	AncestralMarginal.Result.getSiteResult(Site s) Gets the site results for a given site

Uses of Site in Likelihood

Fields in Likelihood with type parameters of type Site

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 types with arguments of type Site

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

Methods in Likelihood with parameters of type Site

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	StandardLikelihood.getMissingLikelihood(Site s) Gets the likelihood result for a given missing site
SiteLikelihood	StandardLikelihood.getSiteLikelihood(Site s) Gets the likelihood result for a given site

Method parameters in Likelihood with type arguments of type Site

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)

Constructors in Likelihood with parameters of type Site

Constructor and Description
Calculator.SiteCalculator(Site s, Tree t, Parameters p, Probabilities tp, java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood> nl) Standard constructor

Constructor parameters in Likelihood with type arguments of type Site

Constructor and Description
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.

Uses of Site in Simulations

Methods in Simulations that return Site

Modifier and Type	Method and Description
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(boolean internal, java.util.Map<java.lang.String,java.lang.String> recode, java.lang.String siteClass) Gets a simulated site.
Site	Simulate.getSite(boolean internal, java.lang.String siteClass) 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.
Site	Simulate.getSite(java.util.Map<java.lang.String,java.lang.String> recode, java.lang.String siteClass) Gets a simulated site without returning the state of the internal nodes.
Site	Simulate.getSite(java.lang.String siteClass) Gets a simulated site without returning the state of the internal nodes