jebl.evolution.trees
Class CompactRootedTree

java.lang.Object
  jebl.evolution.trees.CompactRootedTree

All Implemented Interfaces:

Graph, RootedTree, Tree, Attributable

public class CompactRootedTree
extends Object
implements RootedTree

A memory efficient rooted tree. - Uses a compact representation for the tree structure based primarily on indices instead of pointers and objects - Minimize penalty for unused features. Trees not using attributes or edges do not require additional per node/edge memory. Limitations: - Maximun of 2^16 nodes and 2^15 external nodes. This should not be a problem with the current sizes of phlogenetic trees we currently handle. - Some of the accessors are slower, typically the ones getting all nodes, all edges, all internal nodes etc. Traversing the tree and handling attributes speed should be fine (compared to SimpkeRootedTree)

Author:

Joseph Heled

Nested Class Summary

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

Graph.NoEdgeException, Graph.Utils

Constructor Summary

CompactRootedTree(RootedTree t)
Do all the hard work.

Method Summary

boolean	conceptuallyUnrooted() Due to current implementation limitations, trees store "branch" information in nodes.
List<Node>	getAdjacencies(Node node) Returns a list of nodes connected to this node by an edge
Object	getAttribute(String name)
Map<String,Object>	getAttributeMap() Gets the entire attribute map.
Set<String>	getAttributeNames()
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
Set<Edge>	getEdges()
List<Edge>	getEdges(Node node) Returns a list of edges connected to this node
Set<Edge>	getExternalEdges()
Set<Node>	getExternalNodes()
double	getHeight(Node node)
Set<Edge>	getInternalEdges()
Set<Node>	getInternalNodes()
double	getLength(Node node)
Node	getNode(Taxon taxon)
Set<Node>	getNodes()
Node[]	getNodes(Edge edge) Returns an array of 2 nodes which are the nodes at either end of the edge.
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.
Set<Taxon>	getTaxa()
Taxon	getTaxon(Node node)
boolean	hasHeights()
boolean	hasLengths()
boolean	isExternal(Node node)
boolean	isRoot(Node node)
void	removeAttribute(String name)
void	setAttribute(String name, Object value) Sets an named attribute for this object.

Methods inherited from class java.lang.Object

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

Methods inherited from interface jebl.util.Attributable

getAttribute, getAttributeMap, getAttributeNames, removeAttribute, setAttribute

Constructor Detail

CompactRootedTree

public CompactRootedTree(RootedTree t)

Do all the hard work.

Parameters:

t -

Method Detail

getChildren

public 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.

Specified by:

conceptuallyUnrooted in interface RootedTree

Returns:

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

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 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 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.

getExternalEdges

public Set<Edge> getExternalEdges()

Specified by:

getExternalEdges in interface Tree

Returns:

a set of all edges that have a degree 1 node.

getInternalEdges

public Set<Edge> getInternalEdges()

Specified by:

getInternalEdges in interface Tree

Returns:

a set of all edges for which both nodes have degree 2 or more.

getTaxa

public 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.

getEdges

public List<Edge> getEdges(Node node)

Description copied from interface: Graph

Returns a list of edges connected to this node

Specified by:

getEdges in interface Graph

Returns:

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

getAdjacencies

public 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.

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.

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.

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

getNodes

public Set<Node> getNodes()

Specified by:

getNodes in interface Graph

Returns:

the set of all nodes in this graph.

getEdges

public Set<Edge> getEdges()

Specified by:

getEdges in interface Graph

Returns:

the set of all edges in this graph.

getNodes

public 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.

setAttribute

public void setAttribute(String name,
                         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 Object getAttribute(String name)

Specified by:

getAttribute in interface Attributable

Parameters:

name - the name of the attribute of interest.

Returns:

an object representing the named attributed for this object.

removeAttribute

public void removeAttribute(String name)

Specified by:

removeAttribute in interface Attributable

Parameters:

name - name of attribute to remove

getAttributeNames

public Set<String> getAttributeNames()

Specified by:

getAttributeNames in interface Attributable

Returns:

an array of the attributeNames that this object has.

getAttributeMap

public Map<String,Object> getAttributeMap()

Description copied from interface: Attributable

Gets the entire attribute map.

Specified by:

getAttributeMap in interface Attributable

Returns:

an unmodifiable map