Package jebl.evolution.trees
Class RootedFromUnrooted
- java.lang.Object
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- jebl.evolution.trees.AbstractRootedTree
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- jebl.evolution.trees.RootedFromUnrooted
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- All Implemented Interfaces:
Graph
,RootedTree
,Tree
,Attributable
public class RootedFromUnrooted extends AbstractRootedTree
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
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Nested Class Summary
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Nested classes/interfaces inherited from interface jebl.evolution.graphs.Graph
Graph.NoEdgeException, Graph.Utils
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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.
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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 edgejava.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 nodesdouble
getEdgeLength(Node node1, Node node2)
Returns the length of the edge that connects these two nodesjava.util.Set<Edge>
getEdges()
java.util.List<Edge>
getEdges(Node node)
Returns a list of edges connected to this nodejava.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
isHeightsKnown()
boolean
isLengthsKnown()
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 jebl.evolution.trees.AbstractRootedTree
getExternalNodeCount, getExternalNodes
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Method Detail
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getChildren
public java.util.List<Node> getChildren(Node node)
- 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).
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hasHeights
public boolean hasHeights()
- Returns:
- Whether this tree has node heights available
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getHeight
public double getHeight(Node node)
- 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.
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hasLengths
public boolean hasLengths()
- Returns:
- Whether this tree has branch lengths available
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getLength
public double getLength(Node node)
- 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).
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isHeightsKnown
public boolean isHeightsKnown()
- Returns:
- Whether the node heights are known or need to be recalculated from the lengths
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isLengthsKnown
public boolean isLengthsKnown()
- Returns:
- Whether the branch lengths are known or need to be recalculated from the heights
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getParent
public Node getParent(Node node)
- 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.
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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.- Returns:
- the root of the tree.
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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.- Returns:
- true if tree(s) are to be viewed as unrooted
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getExternalNodes
public java.util.Set<Node> getExternalNodes()
- Returns:
- a set of all nodes that have degree 1. These nodes are often refered to as 'tips'.
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getInternalNodes
public java.util.Set<Node> getInternalNodes()
- Returns:
- a set of all nodes that have degree 2 or more. These nodes are often refered to as internal nodes.
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getTaxa
public java.util.Set<Taxon> getTaxa()
- 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.
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getTaxon
public Taxon getTaxon(Node node)
- 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.
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isExternal
public boolean isExternal(Node node)
- Parameters:
node
- the node- Returns:
- true if the node is of degree 1.
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getNode
public Node getNode(Taxon taxon)
- 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.
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getEdges
public java.util.List<Edge> getEdges(Node node)
Returns a list of edges connected to this node- Parameters:
node
-- Returns:
- the set of nodes that are attached by edges to the given node.
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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.- Returns:
- an array of 2 edges
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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- Returns:
- the set of nodes that are attached by edges to the given node.
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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- Returns:
- the edge length.
- Throws:
Graph.NoEdgeException
- if the nodes are not directly connected by an edge.
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getEdge
public Edge getEdge(Node node1, Node node2) throws Graph.NoEdgeException
Description copied from interface:Graph
Returns the Edge that connects these two nodes- Returns:
- the edge object.
- Throws:
Graph.NoEdgeException
- if the nodes are not directly connected by an edge.
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getNodes
public java.util.Set<Node> getNodes()
- Returns:
- the set of all nodes in this graph.
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getEdges
public java.util.Set<Edge> getEdges()
- Returns:
- the set of all edges in this graph.
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getExternalEdges
public java.util.Set<Edge> getExternalEdges()
The set of external edges.- Returns:
- the set of external edges.
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getInternalEdges
public java.util.Set<Edge> getInternalEdges()
The set of internal edges.- Returns:
- the set of internal edges.
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getNodes
public java.util.Set<Node> getNodes(int degree)
- Parameters:
degree
- the number of edges connected to a node- Returns:
- a set containing all nodes in this graph of the given degree.
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isRoot
public boolean isRoot(Node node)
- Parameters:
node
- the node- Returns:
- true if the node is the root of this tree.
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setAttribute
public void setAttribute(java.lang.String name, java.lang.Object value)
Description copied from interface:Attributable
Sets an named attribute for this object.- Parameters:
name
- the name of the attribute.value
- the new value of the attribute.
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getAttribute
public java.lang.Object getAttribute(java.lang.String name)
- 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.
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removeAttribute
public void removeAttribute(java.lang.String name)
- Parameters:
name
- name of attribute to remove
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getAttributeNames
public java.util.Set<java.lang.String> getAttributeNames()
- Returns:
- an array of the attributeNames that this object has.
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getAttributeMap
public java.util.Map<java.lang.String,java.lang.Object> getAttributeMap()
Description copied from interface:Attributable
Gets the entire attribute map.- Returns:
- an unmodifiable map
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