Uses of Class
Trees.Tree

Packages that use Tree
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. 
Trees Provides classes to define a tree and any constraints on that tree. 
 

Uses of Tree in Alignments
 

Methods in Alignments with parameters of type Tree
 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 Tree in Ancestors
 

Methods in Ancestors with parameters of type Tree
static AncestralJoint AncestralJoint.newInstance(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t)
          Returns an object of this class that can be used for joint reconstruction.
static AncestralJoint AncestralJoint.newInstance(Model m, Alignment a, Tree t)
          Returns an object of this class that can be used for joint reconstruction.
 

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

Uses of Tree in Constraints
 

Methods in Constraints with parameters of type Tree
 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 Tree in Likelihood
 

Constructors in Likelihood with parameters of type Tree
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.
Calculator.SiteCalculator(Tree t, Probabilities tp, ArrayMap<java.lang.String,Likelihood.NodeLikelihood> nl)
          Standard constructor
Calculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t)
          Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
Calculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t, Alignment unobserved)
          Creates a class to calculate the likelihood for a given set of models, an alignment, a tree, and unobserved data.
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.
Calculator(Model m, Alignment a, Tree t)
          Creates an object to calculate the likelihood for a given model, alignment, tree.
Calculator(Model m, Alignment a, Tree t, Alignment unobserved)
          Creates a class to calculate the likelihood for a given model, alignment, tree, missing data and constraints
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
Probabilities(Model m, Tree t, Parameters p)
          Constructor
 

Uses of Tree in Simulations
 

Methods in Simulations with parameters of type Tree
 double HypothesisTest.test(Tree t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams)
          Does a hpyothesis test on the given data and gives a p-value
 double HypothesisTest.test(Tree t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams, java.util.Map<java.lang.String,java.lang.String> recode)
          Does a hpyothesis test on the given data and gives a p-value
 

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

Uses of Tree in Trees
 

Methods in Trees that return Tree
static Tree Tree.fromFile(java.io.File f)
          Creates a tree from a file containing a Newick string
static Tree Tree.fromNewickString(java.lang.String newick)
          Creates a tree from a newick string
 Tree Tree.midPointRoot(java.lang.String newRootName)
          Mid point roots the tree and returns a new tree
 Tree Tree.scaledTo(double length)
          Returns a new tree where the lengths are scales so the total length is different
 

Constructors in Trees with parameters of type Tree
Tree(Tree old, Parameters p)
          Duplicates a tree topology while replacing branch lengths using the appropiate parameter
TreeFigure(Tree t)
          Constructor