jebl.evolution.graphs
Interface Graph

All Superinterfaces:

Attributable

All Known Subinterfaces:

RootedTree, Tree

All Known Implementing Classes:

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

public interface Graph
extends Attributable

Author:

Andrew Rambaut, Alexei Drummond

Nested Class Summary

static class	Graph.NoEdgeException This class is thrown by getEdgeLength(node1, node2) if node1 and node2 are not directly connected by an edge.
static class	Graph.Utils

Method Summary

List<Node>	getAdjacencies(Node node) Returns a list of nodes connected to this node by an edge
Edge	getEdge(Node node1, Node node2) Returns the Edge that connects these two nodes
double	getEdgeLength(Node node1, Node node2) Returns the length of the edge that connects these two nodes
Set<Edge>	getEdges()
List<Edge>	getEdges(Node node) Returns a list of edges connected to this node
Set<Node>	getNodes()
Node[]	getNodes(Edge edge) Returns an array of 2 nodes which are the nodes at either end of the edge.
Set<Node>	getNodes(int degree)

Methods inherited from interface jebl.util.Attributable

getAttribute, getAttributeMap, getAttributeNames, removeAttribute, setAttribute

Method Detail

getEdges

List<Edge> getEdges(Node node)

Returns a list of edges connected to this node

Parameters:

node -

Returns:

the set of nodes that are attached by edges to the given node.

getAdjacencies

List<Node> getAdjacencies(Node node)

Returns a list of nodes connected to this node by an edge

Parameters:

node -

Returns:

the set of nodes that are attached by edges to the given node.

getEdge

Edge getEdge(Node node1,
             Node node2)
             throws Graph.NoEdgeException

Returns the Edge that connects these two nodes

Parameters:

node1 -

node2 -

Returns:

the edge object.

Throws:

Graph.NoEdgeException - if the nodes are not directly connected by an edge.

getEdgeLength

double getEdgeLength(Node node1,
                     Node node2)
                     throws Graph.NoEdgeException

Returns the length of the edge that connects these two nodes

Parameters:

node1 -

node2 -

Returns:

the edge length.

Throws:

Graph.NoEdgeException - if the nodes are not directly connected by an edge.

getNodes

Node[] getNodes(Edge edge)

Returns an array of 2 nodes which are the nodes at either end of the edge.

Parameters:

edge -

Returns:

an array of 2 edges

getNodes

Set<Node> getNodes()

Returns:

the set of all nodes in this graph.

getEdges

Set<Edge> getEdges()

Returns:

the set of all edges in this graph.

getNodes

Set<Node> getNodes(int degree)

Parameters:

degree - the number of edges connected to a node

Returns:

a set containing all nodes in this graph of the given degree.