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 and any constraints on that tree.
|
Modifier and Type | Method and Description |
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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
|
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
|
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() |
Modifier and Type | Method and Description |
---|---|
boolean |
Tree.isExternal(Branch b)
Tests whether the given branch is an external branch (i.e.
|
Constructor and Description |
---|
Tree(java.util.List<Branch> branches)
Creates a tree from a list of branches
|