Uses of Interface
Constraints.Constrainer

Packages that use Constrainer
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 Constrainer in Ancestors
 

Constructors in Ancestors with parameters of type Constrainer
AncestralMarginal(Model m, Alignment a, Tree t, Constrainer con)
          Creates an object to calculate an ancestral reconstruction for a given model, alignment, tree and a constrainter
 

Constructor parameters in Ancestors with type arguments of type Constrainer
AncestralMarginal(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t, java.util.Map<java.lang.String,Constrainer> con)
          Creates an object to calculate an ancestral reconstruction for a given set of models, an alignment, a tree and s et of constrainers.
 

Uses of Constrainer in Constraints
 

Classes in Constraints that implement Constrainer
 class NoConstraints
          Simple implementation of Constrainer that imposes no constraints
 

Uses of Constrainer in Likelihood
 

Constructors in Likelihood with parameters of type Constrainer
Calculator(Model m, Alignment a, Tree t, Alignment unobserved, Constrainer con)
          Creates a class to calculate the likelihood for a given model, alignment, tree, unobserved data and constraints
Calculator(Model m, Alignment a, Tree t, Constrainer con)
          Creates a class to calculate the likelihood for a given model, alignment, tree and constraints
 

Constructor parameters in Likelihood with type arguments of type Constrainer
Calculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t, Alignment unobserved, java.util.Map<java.lang.String,Constrainer> con)
          Creates a class to calculate the likelihood for a given set of models, an alignment, a tree, unobserved data and a set of constraints.
Calculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t, java.util.Map<java.lang.String,Constrainer> con)
          Creates a class to calculate the likelihood for a given set of models, an alignment, a tree and a set of constraints.
 

Uses of Constrainer in Simulations
 

Constructors in Simulations with parameters of type Constrainer
HypothesisTest(Model nullModel, Model altModel, Constrainer nullConstrainer, Constrainer altConstrainer, Optimizer o, int reps)
          Constructor for use when one or both of the null hypothesis and alternative hypothesis have constraints.
Simulate(Model m, Tree t, Parameters p, Alignment unobserved, Constrainer con)
          Creates an object to simulate data for a given model, tree, parameters, unobserved states and constraints.
 

Constructor parameters in Simulations with type arguments of type Constrainer
Simulate(java.util.Map<java.lang.String,Model> m, Tree t, Parameters p, Alignment unobserved, java.util.Map<java.lang.String,Constrainer> con)
          Creates an object to simulate data for a given set of models, a tree, parameters, unobserved states and constrainers.