Package jebl.evolution.graphs
Interface Graph
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- All Superinterfaces:
Attributable
- All Known Subinterfaces:
RootedTree
,Tree
- All Known Implementing Classes:
AbstractRootedTree
,CompactRootedTree
,FilteredRootedTree
,MutableRootedTree
,ReRootedTree
,RootedFromUnrooted
,RootedSubtree
,SimpleRootedTree
,SimpleTree
,SortedRootedTree
,TransformedRootedTree
public interface Graph extends Attributable
- Version:
- $Id: Graph.java 849 2007-12-06 00:10:14Z twobeers $
- Author:
- Andrew Rambaut, Alexei Drummond
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Nested Class Summary
Nested Classes Modifier and Type Interface Description 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
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.util.List<Node>
getAdjacencies(Node node)
Returns a list of nodes connected to this node by an edgeEdge
getEdge(Node node1, Node node2)
Returns the Edge that connects these two nodesdouble
getEdgeLength(Node node1, Node node2)
Returns the length of the edge that connects these two nodesjava.util.Set<Edge>
getEdges()
java.util.List<Edge>
getEdges(Node node)
Returns a list of edges connected to this nodejava.util.Set<Node>
getNodes()
java.util.Set<Node>
getNodes(int degree)
Node[]
getNodes(Edge edge)
Returns an array of 2 nodes which are the nodes at either end of the edge.-
Methods inherited from interface jebl.util.Attributable
getAttribute, getAttributeMap, getAttributeNames, removeAttribute, setAttribute
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Method Detail
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getEdges
java.util.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.
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getAdjacencies
java.util.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.
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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.
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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.
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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
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getNodes
java.util.Set<Node> getNodes()
- Returns:
- the set of all nodes in this graph.
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getEdges
java.util.Set<Edge> getEdges()
- Returns:
- the set of all edges in this graph.
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getNodes
java.util.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.
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