|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
Packages that use Branch | |
---|---|
Likelihood | Provides classes for calculating the likelihood of a tree given a model and an alignment. |
Trees | Provides classes to define a tree and any constraints on that tree. |
Uses of Branch in Likelihood |
---|
Methods in Likelihood with parameters of type Branch | |
---|---|
double |
Probabilities.getP(RateCategory r,
Branch b,
java.lang.String startState,
java.lang.String endState)
Gets a specific probability for a change from one state to another along a specific branch under a specific RateClass |
Uses of Branch in Trees |
---|
Methods in Trees that return Branch | |
---|---|
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 | |
---|---|
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 | |
---|---|
boolean |
Tree.isExternal(Branch b)
Tests whether the given branch is an external branch (i.e. |
Constructor parameters in Trees with type arguments of type Branch | |
---|---|
Tree(java.util.List<Branch> branches)
Creates a tree from a list of branches |
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |