jebl.evolution.trees

Class SimpleTree

java.lang.Object

jebl.evolution.trees.SimpleTree

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

Nested Class Summary

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

Graph.NoEdgeException, Graph.Utils

Constructor Summary

Constructors

Constructor and Description
SimpleTree() Tree (to be constructed by subsequent calls).
SimpleTree(Tree tree) Duplicate a tree.

Method Summary

Methods

Modifier and Type	Method and 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 edge
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
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
java.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()
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.
void	setEdgeLength(Node node1, Node node2, double length) Set edge distance between two adjacent nodes.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SimpleTree

public SimpleTree()

Tree (to be constructed by subsequent calls).

SimpleTree

public SimpleTree(Tree tree)

Duplicate a tree.

Parameters:

tree -

Method Detail

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

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.

setEdgeLength

public void setEdgeLength(Node node1,
                 Node node2,
                 double length)

Set edge distance between two adjacent nodes.

Parameters:

node1 -

node2 -

length -

setEdgeLength

public void setEdgeLength(Edge edge,
                 double length)

Change length of an existing edge.

Parameters:

edge -

length -

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 -

getEdges

public java.util.List<Edge> getEdges(Node node)

Returns a list of edges connected to this node

Specified by:

getEdges in interface Graph

Parameters:

node -

Returns:

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

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 interface Graph

Parameters:

node -

Returns:

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

getEdge

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

Returns the Edge that connects these two nodes

Specified by:

getEdge in interface Graph

Parameters:

node1 -

node2 -

Returns:

the edge object.

Throws:

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

getExternalNodes

public java.util.Set<Node> getExternalNodes()

Specified by:

getExternalNodes in interface Tree

Returns:

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

getInternalNodes

public java.util.Set<Node> getInternalNodes()

Specified by:

getInternalNodes in interface Tree

Returns:

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

getTaxa

public java.util.Set<Taxon> getTaxa()

Specified by:

getTaxa in interface Tree

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

public Taxon getTaxon(Node node)

Specified by:

getTaxon in interface Tree

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

public boolean isExternal(Node node)

Specified by:

isExternal in interface Tree

Parameters:

node - the node

Returns:

true if the node is of degree 1.

isExternal

public boolean isExternal(Edge edge)

Parameters:

edge - the edge

Returns:

true if the edge has a node of degree 1.

getNode

public Node getNode(Taxon taxon)

Specified by:

getNode in interface Tree

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.

renameTaxa

public void renameTaxa(Taxon from,
              Taxon to)

Specified by:

renameTaxa in interface Tree

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 interface Graph

Parameters:

node1 -

node2 -

Returns:

the length of the edge connecting node1 and node2.

Throws:

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

Graph.NoEdgeException

getNodes

public Node[] getNodes(Edge edge)

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

Specified by:

getNodes in interface Graph

Parameters:

edge -

Returns:

an array of 2 edges

getNodes

public java.util.Set<Node> getNodes()

Specified by:

getNodes in interface Graph

Returns:

the set of all nodes in this graph.

getEdges

public java.util.Set<Edge> getEdges()

Specified by:

getEdges in interface Graph

Returns:

the set of all edges in this graph.

getNodes

public java.util.Set<Node> getNodes(int degree)

Specified by:

getNodes in interface Graph

Parameters:

degree - the number of edges connected to a node

Returns:

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

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 interface Tree

Returns:

the set of external edges.

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 interface Tree

Returns:

the set of internal edges.

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 interface Attributable

Parameters:

name - the name of the attribute.

value - the new value of the attribute.

getAttribute

public java.lang.Object getAttribute(java.lang.String name)

Specified by:

getAttribute in interface Attributable

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.

removeAttribute

public void removeAttribute(java.lang.String name)

Specified by:

removeAttribute in interface Attributable

Parameters:

name - name of attribute to remove

getAttributeNames

public java.util.Set<java.lang.String> getAttributeNames()

Specified by:

getAttributeNames in interface Attributable

Returns:

an array of the attributeNames that this object has.

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 interface Attributable

Returns:

an unmodifiable map