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

Constructors
Constructor	Description
`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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`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()`
`java.util.Set<Node>`	`getNodes(int degree)`
`Node[]`	`getNodes(Edge edge)`	Returns an array of 2 nodes which are the nodes at either end of the edge.
`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

Class RootedFromUnrooted

Nested Class Summary

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

RootedFromUnrooted

RootedFromUnrooted

Method Detail

getChildren

hasHeights

getHeight

hasLengths

getLength

getParent

getRootNode

conceptuallyUnrooted

getExternalNodes

getInternalNodes

getTaxa

getTaxon

isExternal

getNode

renameTaxa

getEdges

getNodes

getAdjacencies

getEdgeLength

getEdge

getNodes

getEdges

getExternalEdges

getInternalEdges

getNodes

isRoot

setAttribute

getAttribute

removeAttribute

getAttributeNames

getAttributeMap