jebl.evolution.trees
Interface Tree

All Superinterfaces:

Attributable, Graph

All Known Subinterfaces:

RootedTree

All Known Implementing Classes:

CompactRootedTree, FilteredRootedTree, MutableRootedTree, RootedFromUnrooted, SimpleRootedTree, SimpleTree, SortedRootedTree, TransformedRootedTree

public interface Tree
extends Graph

An unrooted tree.

Author:

rambaut, Alexei Drummond

Nested Class Summary

Nested classes/interfaces inherited from interface jebl.evolution.graphs.Graph

Graph.NoEdgeException, Graph.Utils

Method Summary

Set<Edge>	getExternalEdges()
Set<Node>	getExternalNodes()
Set<Edge>	getInternalEdges()
Set<Node>	getInternalNodes()
Node	getNode(Taxon taxon)
Set<Taxon>	getTaxa()
Taxon	getTaxon(Node node)
boolean	isExternal(Node node)

Methods inherited from interface jebl.evolution.graphs.Graph

getAdjacencies, getEdge, getEdgeLength, getEdges, getEdges, getNodes, getNodes, getNodes

Methods inherited from interface jebl.util.Attributable

getAttribute, getAttributeMap, getAttributeNames, removeAttribute, setAttribute

Method Detail

getExternalNodes

Set<Node> getExternalNodes()

Returns:

a set of all nodes that have degree 1. These nodes are often refered to as 'tips'.

getInternalNodes

Set<Node> getInternalNodes()

Returns:

a set of all nodes that have degree 2 or more. These nodes are often refered to as internal nodes.

getExternalEdges

Set<Edge> getExternalEdges()

Returns:

a set of all edges that have a degree 1 node.

getInternalEdges

Set<Edge> getInternalEdges()

Returns:

a set of all edges for which both nodes have degree 2 or more.

getTaxa

Set<Taxon> getTaxa()

Returns:

the set of taxa associated with the external nodes of this tree. The size of this set should be the same as the size of the external nodes set.

getTaxon

Taxon getTaxon(Node node)

Parameters:

node - the node whose associated taxon is being requested.

Returns:

the taxon object associated with the given node, or null if the node is an internal node.

isExternal

boolean isExternal(Node node)

Parameters:

node - the node

Returns:

true if the node is of degree 1.

getNode

Node getNode(Taxon taxon)

Parameters:

taxon - the taxon

Returns:

the external node associated with the given taxon, or null if the taxon is not a member of the taxa set associated with this tree.