jebl.evolution.trees
Class RootedFromUnrooted

java.lang.Object
  jebl.evolution.trees.RootedFromUnrooted

All Implemented Interfaces:

Graph, RootedTree, Tree, Attributable

public class RootedFromUnrooted
extends java.lang.Object
implements RootedTree

Root an unrooted tree. This class works as a wrapper over any tree to root it. There are two constructors, one which roots the tree at any internal node, the other roots the tree between any two internal nodes. Be aware that rooting between nodes where one of them has less than 3 adjacencies may be problematic when converting back from the Newick format.

Version:

$Id: RootedFromUnrooted.java 936 2008-08-06 14:12:07Z rambaut $

Author:

Joseph Heled

Nested Class Summary

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

Graph.NoEdgeException, Graph.Utils

Constructor Summary

RootedFromUnrooted(Tree source, Node root, boolean intentUnrooted)
Root tree at some internal node.

RootedFromUnrooted(Tree source, Node left, Node right, double fromLeft)
Root source by creating a new internal node whose children are (the adjacent) left and right.

Method Summary

boolean	conceptuallyUnrooted() Due to current implementation limitations, trees store "branch" information in nodes.
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()
java.util.List<Node>	getChildren(Node node)
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()
double	getHeight(Node node)
java.util.Set<Edge>	getInternalEdges() The set of internal edges.
java.util.Set<Node>	getInternalNodes()
double	getLength(Node node)
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)
Node	getParent(Node node)
Node	getRootNode() The root of the tree has the largest node height of all nodes in the tree.
java.util.Set<Taxon>	getTaxa()
Taxon	getTaxon(Node node)
boolean	hasHeights()
boolean	hasLengths()
boolean	isExternal(Node node)
boolean	isRoot(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.

Methods inherited from class java.lang.Object

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

Constructor Detail

RootedFromUnrooted

public RootedFromUnrooted(Tree source,
                          Node root,
                          boolean intentUnrooted)

Root tree at some internal node.

Parameters:

source - tree to root

root - internal node to root at

intentUnrooted -

RootedFromUnrooted

public RootedFromUnrooted(Tree source,
                          Node left,
                          Node right,
                          double fromLeft)

Root source by creating a new internal node whose children are (the adjacent) left and right.

Parameters:

source -

left -

right -

fromLeft - branch from new root to left node.

Method Detail

getChildren

public java.util.List<Node> getChildren(Node node)

Specified by:

getChildren in interface RootedTree

Parameters:

node - the node whose children are being requested.

Returns:

the list of nodes that are the children of the given node. The set may be empty for a terminal node (a tip).

hasHeights

public boolean hasHeights()

Specified by:

hasHeights in interface RootedTree

Returns:

Whether this tree has node heights available

getHeight

public double getHeight(Node node)

Specified by:

getHeight in interface RootedTree

Parameters:

node - the node whose height is being requested.

Returns:

the height of the given node. The height will be less than the parent's height and greater than it children's heights.

hasLengths

public boolean hasLengths()

Specified by:

hasLengths in interface RootedTree

Returns:

Whether this tree has branch lengths available

getLength

public double getLength(Node node)

Specified by:

getLength in interface RootedTree

Parameters:

node - the node whose branch length (to its parent) is being requested.

Returns:

the length of the branch to the parent node (0.0 if the node is the root).

getParent

public Node getParent(Node node)

Specified by:

getParent in interface RootedTree

Parameters:

node - the node whose parent is requested

Returns:

the parent node of the given node, or null if the node is the root node.

getRootNode

public Node getRootNode()

Description copied from interface: RootedTree

The root of the tree has the largest node height of all nodes in the tree.

Specified by:

getRootNode in interface RootedTree

Returns:

the root of the tree.

conceptuallyUnrooted

public boolean conceptuallyUnrooted()

Description copied from interface: RootedTree

Due to current implementation limitations, trees store "branch" information in nodes. So, internally rooted trees are genetrated when un-rooted would be more natural. This should be removed. If this is a rooted tree then it is rooted. This can really only confuse things. Trees are unrooted, RootedTrees are rooted. This is not an implementation limitation. It may be that a RootedTree has an arbitrary root but it is still rooted. With a rooted tree, it is convenient to store branch information at the node (i.e., for the branch above the node) because there is no "branch" object. Andrew. This function will probably become deprecated once the "development" tree viewer becomes in sync with the main tree viewer branch and some method of handling this concept has been introduced. Until then, this method remains.

Specified by:

conceptuallyUnrooted in interface RootedTree

Returns:

true if tree(s) are to be viewed as unrooted

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.

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

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.

getNodes

public Node[] getNodes(Edge edge)

Description copied from interface: Graph

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

Specified by:

getNodes in interface Graph

Returns:

an array of 2 edges

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

Returns:

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

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

Returns:

the edge length.

Throws:

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

getEdge

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

Description copied from interface: Graph

Returns the Edge that connects these two nodes

Specified by:

getEdge in interface Graph

Returns:

the edge object.

Throws:

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

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.

getExternalEdges

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

The set of external edges.

Specified by:

getExternalEdges in interface Tree

Returns:

the set of external edges.

getInternalEdges

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

The set of internal edges.

Specified by:

getInternalEdges in interface Tree

Returns:

the set of internal edges.

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.

isRoot

public boolean isRoot(Node node)

Specified by:

isRoot in interface RootedTree

Parameters:

node - the node

Returns:

true if the node is the root of this tree.

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