jebl.evolution.trees
Class FilteredRootedTree

java.lang.Object
  extended by jebl.evolution.trees.FilteredRootedTree
All Implemented Interfaces:
Graph, RootedTree, Tree, Attributable
Direct Known Subclasses:
SortedRootedTree, TransformedRootedTree

public abstract class FilteredRootedTree
extends Object
implements RootedTree

Author:
Andrew Rambaut, Alexei Drummond

Nested Class Summary
 
Nested classes/interfaces inherited from interface jebl.evolution.graphs.Graph
Graph.NoEdgeException, Graph.Utils
 
Field Summary
protected  RootedTree source
           
 
Constructor Summary
FilteredRootedTree(RootedTree source)
           
 
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.
 RootedTree getSource()
           
 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
 

Field Detail

source

protected final RootedTree source
Constructor Detail

FilteredRootedTree

public FilteredRootedTree(RootedTree source)
Method Detail

getSource

public RootedTree getSource()

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

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.

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.

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.

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.

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.

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.

getEdges

public Set<Edge> getEdges()
Specified by:
getEdges in interface Graph
Returns:
the set of all edges in this graph.

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

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 Set<Node> getNodes()
Specified by:
getNodes in interface Graph
Returns:
the set of all nodes 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.

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(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