Uses of Class
Trees.Branch

Packages that use Branch

Package	Description
Likelihood	Provides classes for calculating the likelihood of a tree given a model and an alignment.
Trees	Provides classes to define a tree.

Uses of Branch in Likelihood

Methods in Likelihood with parameters of type Branch

Modifier and Type	Method and Description
SquareMatrix	Probabilities.RateProbabilities.getP(Branch b) Gets the probability matrix for a single branch
double	Probabilities.RateProbabilities.getP(Branch b, java.lang.String startState, java.lang.String endState) Gets the probability of a single transition on a single branch

Uses of Branch in Trees

Methods in Trees that return Branch

Modifier and Type	Method and Description
Branch	Tree.getBranchByChild(java.lang.String child) Gets the branch which has the given node as the child node

Methods in Trees that return types with arguments of type Branch

Modifier and Type	Method and Description
java.util.List<Branch>	Tree.getBranches() Gets a list of branches.
java.util.Set<Branch>	Tree.getBranchesByParent(java.lang.String parent) Gets the set of branches which have the passed node as a parent
java.util.List<Branch>	Tree.getBranchesReversed() Gets the branches in the reverse order to that returned by Tree.getBranches().
java.util.Iterator<Branch>	Tree.iterator()

Methods in Trees with parameters of type Branch

Modifier and Type	Method and Description
boolean	Tree.isExternal(Branch b) Tests whether the given branch is an external branch (i.e.

Method parameters in Trees with type arguments of type Branch

Modifier and Type	Method and Description
void	TreeFigure.setBranchColors(java.util.Map<Branch,java.lang.String> colors) Sets the colour of branches.

Constructor parameters in Trees with type arguments of type Branch

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