jebl.evolution.trees

Class MutableRootedTree

java.lang.Object

jebl.evolution.trees.MutableRootedTree

All Implemented Interfaces:

Graph, RootedTree, Tree, Attributable

public class MutableRootedTree
extends java.lang.Object
implements RootedTree

A simple rooted tree providing some ability to manipulate the tree. - Root an unrooted tree using an outgroup. - Remove internal node: all children of node are adopted by it's parent. - Split/Refine node by creating two new children and distributing the children to new nodes. - Re-root a rooted tree given an outgroup.

Version:

$Id: MutableRootedTree.java 935 2008-07-22 16:52:04Z 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
MutableRootedTree(RootedTree tree) Construct a rooted tree from an immutable rooted tree.
MutableRootedTree(Tree tree, Node outGroup) Construct a rooted tree from unrooted.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	conceptuallyUnrooted() Due to current implementation limitations, trees store "branch" information in nodes.
Node	createExternalNode(Taxon taxon) Creates a new external node with the given taxon.
jebl.evolution.trees.MutableRootedTree.MutableRootedNode	createInternalNode(java.util.List<? extends Node> children) Once a SimpleRootedTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.
Node	detachChildren(Node node, java.util.List<java.lang.Integer> split)
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)
Edge	getParentEdge(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	refineNode(Node node, int[] leftSet)
void	removeAttribute(java.lang.String name)
void	removeInternalNode(Node node) Remove internal node.
void	renameTaxa(Taxon from, Taxon to)
void	reRootWithOutgroup(Node outGroup, java.util.Set<java.lang.String> attributeNames) Re-root tree using an outgroup.
void	setAttribute(java.lang.String name, java.lang.Object value) Sets an named attribute for this object.
void	setConceptuallyUnrooted(boolean intent)
void	setHeight(Node node, double height)
void	setLength(Node node, double length)

Methods inherited from class java.lang.Object

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

Constructor Detail

MutableRootedTree

public MutableRootedTree(Tree tree,
                 Node outGroup)

Construct a rooted tree from unrooted.

Parameters:

tree - Unrooted tree to root

outGroup - Node in tree assumed to be the outgroup

MutableRootedTree

public MutableRootedTree(RootedTree tree)

Construct a rooted tree from an immutable rooted tree.

Parameters:

tree - Rooted tree to copy

Method Detail

removeInternalNode

public void removeInternalNode(Node node)

Remove internal node. Move all children to their grandparent.

Parameters:

node - to be removed

refineNode

public void refineNode(Node node,
              int[] leftSet)

Parameters:

node - Node to refine

leftSet - indices of children in the left new subtree.

reRootWithOutgroup

public void reRootWithOutgroup(Node outGroup,
                      java.util.Set<java.lang.String> attributeNames)

Re-root tree using an outgroup.

Parameters:

outGroup -

attributeNames - Move those attributes (if they exist in node) to their previous parent. The idea is to preserve "branch" attributes which we now store in the child since only "node" properties are supported.

detachChildren

public Node detachChildren(Node node,
                  java.util.List<java.lang.Integer> split)

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 jebl.evolution.trees.MutableRootedTree.MutableRootedNode createInternalNode(java.util.List<? extends Node> children)

Once a SimpleRootedTree 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 a parent of these nodes. The last node created using createInternalNode is automatically the root so when all the nodes are created, the tree is complete.

Parameters:

children - the child nodes of this nodes

Returns:

the created node reference

setHeight

public void setHeight(Node node,
             double height)

Parameters:

node - the node whose height is being set

height - the height

setLength

public void setLength(Node node,
             double length)

Parameters:

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

length - the length

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 list 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.

getParentEdge

public Edge getParentEdge(Node node)

getRootNode

public Node getRootNode()

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.

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.

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)

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

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.

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:

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. 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.

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.

setConceptuallyUnrooted

public void setConceptuallyUnrooted(boolean intent)

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

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