Uses of Class
Utils.ArrayMap

Packages that use ArrayMap
Alignments Provides class for dealing with "alignments" and the sites in an alignment. 
Likelihood Provides classes for calculating the likelihood of a tree given a model and an alignment. 
Models Provides classes for defing a phylogenetic model. 
 

Uses of ArrayMap in Alignments
 

Methods in Alignments that return ArrayMap
 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.
 

Methods in Alignments with parameters of type ArrayMap
 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 ArrayMap in Likelihood
 

Methods in Likelihood that return ArrayMap
 ArrayMap<java.lang.String,java.lang.Integer> Probabilities.getArrayMap()
          Gets an ArrayMap linking states to position in an array
 

Constructors in Likelihood with parameters of type ArrayMap
Calculator.SiteCalculator(Tree t, Probabilities tp, ArrayMap<java.lang.String,Likelihood.NodeLikelihood> nl)
          Standard constructor
Likelihood.NodeLikelihood(ArrayMap<java.lang.String,java.lang.Integer> states, java.util.Set<java.lang.String> allowedStates)
          Default constructor
 

Uses of ArrayMap in Models
 

Methods in Models that return ArrayMap
 ArrayMap<java.lang.String,java.lang.Integer> Model.getArrayMap()
          Gets a map from the rate name to its index in the rate matrix Called this as Model.getMap() is kept for comptability
 ArrayMap<java.lang.String,java.lang.Integer> RateCategory.getArrayMap()
          Gets the map that maps state to position in matrix Called this as RateCategory.getMap() is kept for comptability