public final class SimpleTree extends java.lang.Object implements Tree
Graph.NoEdgeException, Graph.Utils
Constructor and Description |
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SimpleTree()
Tree (to be constructed by subsequent calls).
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SimpleTree(Tree tree)
Duplicate a tree.
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Modifier and Type | Method and Description |
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void |
addEdge(Node node1,
Node node2,
double length)
Add a new edge between two existing (non adjacent yet) nodes.
|
Node |
createExternalNode(Taxon taxon)
Creates a new external node with the given taxon.
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Node |
createInternalNode(java.util.List<Node> adjacencies)
Once a SimpleTree has been created, the node stucture can be created by
calling createExternalNode and createInternalNode.
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java.util.List<Node> |
getAdjacencies(Node node)
Returns a list of nodes connected to this node by an edge
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java.lang.Object |
getAttribute(java.lang.String name) |
java.util.Map<java.lang.String,java.lang.Object> |
getAttributeMap()
Gets the entire attribute map.
|
java.util.Set<java.lang.String> |
getAttributeNames() |
Edge |
getEdge(Node node1,
Node node2)
Returns the Edge that connects these two nodes
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double |
getEdgeLength(Node node1,
Node node2)
Returns the length of the edge that connects these two nodes
|
java.util.Set<Edge> |
getEdges() |
java.util.List<Edge> |
getEdges(Node node)
Returns a list of edges connected to this node
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java.util.Set<Edge> |
getExternalEdges()
The set of external edges.
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java.util.Set<Node> |
getExternalNodes() |
java.util.Set<Edge> |
getInternalEdges()
The set of internal edges.
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java.util.Set<Node> |
getInternalNodes() |
Node |
getNode(Taxon taxon) |
java.util.Set<Node> |
getNodes() |
Node[] |
getNodes(Edge edge)
Returns an array of 2 nodes which are the nodes at either end of the edge.
|
java.util.Set<Node> |
getNodes(int degree) |
java.util.Set<Taxon> |
getTaxa() |
Taxon |
getTaxon(Node node) |
boolean |
isExternal(Edge edge) |
boolean |
isExternal(Node node) |
void |
removeAttribute(java.lang.String name) |
void |
renameTaxa(Taxon from,
Taxon to) |
void |
setAttribute(java.lang.String name,
java.lang.Object value)
Sets an named attribute for this object.
|
void |
setEdgeLength(Edge edge,
double length)
Change length of an existing edge.
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void |
setEdgeLength(Node node1,
Node node2,
double length)
Set edge distance between two adjacent nodes.
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public SimpleTree()
public SimpleTree(Tree tree)
tree
- public Node createExternalNode(Taxon taxon)
taxon
- the taxon associated with this nodepublic Node createInternalNode(java.util.List<Node> adjacencies)
adjacencies
- the child nodes of this nodepublic void setEdgeLength(Node node1, Node node2, double length)
node1
- node2
- length
- public void setEdgeLength(Edge edge, double length)
edge
- length
- public void addEdge(Node node1, Node node2, double length)
node1
- node2
- length
- public java.util.List<Edge> getEdges(Node node)
public java.util.List<Node> getAdjacencies(Node node)
Graph
getAdjacencies
in interface Graph
node
- public Edge getEdge(Node node1, Node node2) throws Graph.NoEdgeException
getEdge
in interface Graph
node1
- node2
- Graph.NoEdgeException
- if the nodes are not directly connected by an edge.public java.util.Set<Node> getExternalNodes()
getExternalNodes
in interface Tree
public java.util.Set<Node> getInternalNodes()
getInternalNodes
in interface Tree
public java.util.Set<Taxon> getTaxa()
public boolean isExternal(Node node)
isExternal
in interface Tree
node
- the nodepublic boolean isExternal(Edge edge)
edge
- the edgepublic void renameTaxa(Taxon from, Taxon to)
renameTaxa
in interface Tree
public double getEdgeLength(Node node1, Node node2) throws Graph.NoEdgeException
Graph
getEdgeLength
in interface Graph
node1
- node2
- NoEdgeException
- if the nodes are not directly connected by an edge.Graph.NoEdgeException
public Node[] getNodes(Edge edge)
public java.util.Set<Node> getNodes()
public java.util.Set<Edge> getEdges()
public java.util.Set<Node> getNodes(int degree)
public java.util.Set<Edge> getExternalEdges()
getExternalEdges
in interface Tree
public java.util.Set<Edge> getInternalEdges()
getInternalEdges
in interface Tree
public void setAttribute(java.lang.String name, java.lang.Object value)
Attributable
setAttribute
in interface Attributable
name
- the name of the attribute.value
- the new value of the attribute.public java.lang.Object getAttribute(java.lang.String name)
getAttribute
in interface Attributable
name
- the name of the attribute of interest, or null if the attribute doesn't exist.public void removeAttribute(java.lang.String name)
removeAttribute
in interface Attributable
name
- name of attribute to removepublic java.util.Set<java.lang.String> getAttributeNames()
getAttributeNames
in interface Attributable
public java.util.Map<java.lang.String,java.lang.Object> getAttributeMap()
Attributable
getAttributeMap
in interface Attributable
http://code.google.com/p/jebl2/