Package jebl.evolution.trees
Class SimpleTree
- java.lang.Object
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- jebl.evolution.trees.SimpleTree
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- All Implemented Interfaces:
Graph
,Tree
,Attributable
public final class SimpleTree extends java.lang.Object implements Tree
A basic implementation on an unrooted tree.- Version:
- $Id: SimpleTree.java 956 2008-11-30 01:18:20Z rambaut $
- Author:
- Joseph Heled
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Nested Class Summary
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Nested classes/interfaces inherited from interface jebl.evolution.graphs.Graph
Graph.NoEdgeException, Graph.Utils
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Constructor Summary
Constructors Constructor Description SimpleTree()
Tree (to be constructed by subsequent calls).SimpleTree(Tree tree)
Duplicate a tree.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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.Node
createInternalNode(java.util.List<Node> adjacencies)
Once a SimpleTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.java.util.List<Node>
getAdjacencies(Node node)
Returns a list of nodes connected to this node by an edgejava.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 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<Edge>
getExternalEdges()
The set of external edges.java.util.Set<Node>
getExternalNodes()
java.util.Set<Edge>
getInternalEdges()
The set of internal edges.java.util.Set<Node>
getInternalNodes()
Node
getNode(Taxon taxon)
java.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.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.void
setEdgeLength(Node node1, Node node2, double length)
Set edge distance between two adjacent nodes.
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Constructor Detail
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SimpleTree
public SimpleTree()
Tree (to be constructed by subsequent calls).
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SimpleTree
public SimpleTree(Tree tree)
Duplicate a tree.- Parameters:
tree
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Method Detail
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createExternalNode
public Node createExternalNode(Taxon taxon)
Creates a new external node with the given taxon. See createInternalNode for a description of how to use these methods.- Parameters:
taxon
- the taxon associated with this node- Returns:
- the created node reference
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createInternalNode
public Node createInternalNode(java.util.List<Node> adjacencies)
Once a SimpleTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode. First of all createExternalNode is called giving Taxon objects for the external nodes. Then these are put into sets and passed to createInternalNode to create new internal nodes. It is the caller responsibility to insure no cycles are created.- Parameters:
adjacencies
- the child nodes of this node- Returns:
- the created node.
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setEdgeLength
public void setEdgeLength(Node node1, Node node2, double length)
Set edge distance between two adjacent nodes.- Parameters:
node1
-node2
-length
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setEdgeLength
public void setEdgeLength(Edge edge, double length)
Change length of an existing edge.- Parameters:
edge
-length
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addEdge
public void addEdge(Node node1, Node node2, double length)
Add a new edge between two existing (non adjacent yet) nodes.- Parameters:
node1
-node2
-length
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getEdges
public java.util.List<Edge> getEdges(Node node)
Returns a list of edges connected to this node
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getAdjacencies
public java.util.List<Node> getAdjacencies(Node node)
Description copied from interface:Graph
Returns a list of nodes connected to this node by an edge- Specified by:
getAdjacencies
in interfaceGraph
- Parameters:
node
-- Returns:
- the set of nodes that are attached by edges to the given node.
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getEdge
public Edge getEdge(Node node1, Node node2) throws Graph.NoEdgeException
Returns the Edge that connects these two nodes- Specified by:
getEdge
in interfaceGraph
- Parameters:
node1
-node2
-- Returns:
- the edge object.
- Throws:
Graph.NoEdgeException
- if the nodes are not directly connected by an edge.
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getExternalNodes
public java.util.Set<Node> getExternalNodes()
- Specified by:
getExternalNodes
in interfaceTree
- Returns:
- a set of all nodes that have degree 1. These nodes are often refered to as 'tips'.
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getInternalNodes
public java.util.Set<Node> getInternalNodes()
- Specified by:
getInternalNodes
in interfaceTree
- Returns:
- a set of all nodes that have degree 2 or more. These nodes are often refered to as internal nodes.
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getTaxa
public java.util.Set<Taxon> getTaxa()
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isExternal
public boolean isExternal(Node node)
- Specified by:
isExternal
in interfaceTree
- Parameters:
node
- the node- Returns:
- true if the node is of degree 1.
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isExternal
public boolean isExternal(Edge edge)
- Parameters:
edge
- the edge- Returns:
- true if the edge has a node of degree 1.
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renameTaxa
public void renameTaxa(Taxon from, Taxon to)
- Specified by:
renameTaxa
in interfaceTree
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getEdgeLength
public double getEdgeLength(Node node1, Node node2) throws Graph.NoEdgeException
Description copied from interface:Graph
Returns the length of the edge that connects these two nodes- Specified by:
getEdgeLength
in interfaceGraph
- Parameters:
node1
-node2
-- Returns:
- the length of the edge connecting node1 and node2.
- Throws:
Graph.NoEdgeException
- if the nodes are not directly connected by an edge.
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getNodes
public Node[] getNodes(Edge edge)
Returns an array of 2 nodes which are the nodes at either end of the edge.
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getNodes
public java.util.Set<Node> getNodes()
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getEdges
public java.util.Set<Edge> getEdges()
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getNodes
public java.util.Set<Node> getNodes(int degree)
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getExternalEdges
public java.util.Set<Edge> getExternalEdges()
The set of external edges. This is a pretty inefficient implementation because a new set is constructed each time this is called.- Specified by:
getExternalEdges
in interfaceTree
- Returns:
- the set of external edges.
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getInternalEdges
public java.util.Set<Edge> getInternalEdges()
The set of internal edges. This is a pretty inefficient implementation because a new set is constructed each time this is called.- Specified by:
getInternalEdges
in interfaceTree
- Returns:
- the set of internal edges.
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setAttribute
public void setAttribute(java.lang.String name, java.lang.Object value)
Description copied from interface:Attributable
Sets an named attribute for this object.- Specified by:
setAttribute
in interfaceAttributable
- Parameters:
name
- the name of the attribute.value
- the new value of the attribute.
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getAttribute
public java.lang.Object getAttribute(java.lang.String name)
- Specified by:
getAttribute
in interfaceAttributable
- Parameters:
name
- the name of the attribute of interest, or null if the attribute doesn't exist.- Returns:
- an object representing the named attributed for this object.
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removeAttribute
public void removeAttribute(java.lang.String name)
- Specified by:
removeAttribute
in interfaceAttributable
- Parameters:
name
- name of attribute to remove
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getAttributeNames
public java.util.Set<java.lang.String> getAttributeNames()
- Specified by:
getAttributeNames
in interfaceAttributable
- Returns:
- an array of the attributeNames that this object has.
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getAttributeMap
public java.util.Map<java.lang.String,java.lang.Object> getAttributeMap()
Description copied from interface:Attributable
Gets the entire attribute map.- Specified by:
getAttributeMap
in interfaceAttributable
- Returns:
- an unmodifiable map
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