Uses of Class
Trees.TreeException

Packages that use TreeException

Package	Description
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.
Trees	Provides classes to define a tree.

Uses of TreeException in Ancestors

Methods in Ancestors that throw TreeException

Modifier and Type	Method and Description
abstract Alignment	AncestralJoint.calculate(Parameters params) Calculates the reconstruction
Alignment	AncestralJointBB.calculate(Parameters p)
Alignment	AncestralJointDP.calculate(Parameters params)
AncestralMarginal.Result	AncestralMarginal.calculate(Parameters params) Calculates the reconstruction

Uses of TreeException in Likelihood

Methods in Likelihood that throw TreeException

Modifier and Type	Method and Description
R	Calculator.calculate(Parameters p) Abstract method for actually calculating the likelihood
abstract R	Calculator.combineSites(java.util.Map<Site,SiteLikelihood> sites, Parameters p) Combines the likelihood from each site into a alignment likelihood
Range	ConfidenceInterval.getCI(Parameter param, double conf) Calculates the confidence interval for a single parameter
protected java.util.Map<Site,SiteLikelihood>	Calculator.siteCalculate(Parameters p) Calculates the likelihood for each site

Constructors in Likelihood that throw TreeException

Constructor and Description
Probabilities(Model m, Tree t, Parameters p) Constructor
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, java.util.Map<java.lang.String,Tree> t) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, java.util.Map<java.lang.String,Tree> t, Alignment unobserved) Creates a class to calculate the likelihood for a given set of models, an alignment, a tree and unobserved data.
StandardCalculator(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.
StandardCalculator(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, and a tree.
StandardCalculator(Model m, Alignment a, java.util.Map<java.lang.String,Tree> t) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(Model m, Alignment a, java.util.Map<java.lang.String,Tree> t, Alignment unobserved) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(Model m, Alignment a, Tree t) Creates an object to calculate the likelihood for a given model, alignment and tree.
StandardCalculator(Model m, Alignment a, Tree t, Alignment unobserved) Creates a class to calculate the likelihood for a given model, alignment, tree and missing data

Uses of TreeException in Simulations

Constructors in Simulations that throw TreeException

Constructor and Description
Simulate(java.util.Map<java.lang.String,Model> m, java.util.Map<java.lang.String,Tree> t, Parameters p) Creates an object to simulate data for a given set of models and trees, parameters and unobserved states.
Simulate(java.util.Map<java.lang.String,Model> m, java.util.Map<java.lang.String,Tree> t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given set of models and trees, parameters and unobserved states.
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 states.
Simulate(Model m, java.util.Map<java.lang.String,Tree> t, Parameters p) Creates an object to simulate data for a given model, set of trees, parameters and unobserved states.
Simulate(Model m, java.util.Map<java.lang.String,Tree> t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given model, set of trees, parameters and unobserved states.
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.

Uses of TreeException in Trees

Methods in Trees that throw TreeException

Modifier and Type	Method and Description
double	Tree.branchScore(Tree t) Calculates the branch score distance between this tree and another tree
static Tree	Tree.fromNewickString(java.lang.String newick) Creates a tree from a newick string
Branch	Tree.getBranchByChild(java.lang.String child) Gets the branch which has the given node as the child node
java.util.Set<Branch>	Tree.getBranchesByParent(java.lang.String parent) Gets the set of branches which have the passed node as a parent
double	Branch.getLength() Get the length of the branch
double	Tree.getLength() Gets the length of the tree
Parameters	Tree.getParameters() Returns a Parameters object containing a parameter for each branch length.
java.lang.String	Tree.getParent(java.lang.String child) Gets the parent node of the given node
java.util.Set<Split>	Tree.getSplits() Gets the splits that represent the tree
Tree	Tree.midPointRoot(java.lang.String newRootName) Mid point roots the tree and returns a new tree
java.lang.String	Tree.MRCA(java.util.List<java.lang.String> leaves) Returns the most recent common ancestor of a set of leaves.
void	TreeFigure.printSVG(java.io.File f, boolean showLengths) Prints the tree to the given file
static Tree	Tree.randomTree(java.util.List<java.lang.String> taxa, boolean rooted) Creates a random rooted or unrooted tree from a list of taxa
int	Tree.RF(Tree t) Calculates the RF distance between this tree and another tree
Tree	Tree.scaledTo(double length) Returns a new tree where the lengths are scales so the total length is different
double	Tree.weightedRF(Tree t) Calculates the weighted (by branch length) RF distance between this tree and another tree

Constructors in Trees that throw TreeException

Constructor and Description
Tree(java.util.List<Branch> branches) Creates a tree from a list of branches
TreeFigure(Tree t) Constructor