Package jebl.evolution.trees
Class RootedFromUnrooted
java.lang.Object
jebl.evolution.trees.AbstractRootedTree
jebl.evolution.trees.RootedFromUnrooted
- All Implemented Interfaces:
Graph
,RootedTree
,Tree
,Attributable
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
Nested classes/interfaces inherited from interface jebl.evolution.graphs.Graph
Graph.NoEdgeException, Graph.Utils
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Constructor Summary
ConstructorsConstructorDescriptionRootedFromUnrooted
(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
Modifier and TypeMethodDescriptionboolean
Due to current implementation limitations, trees store "branch" information in nodes.getAdjacencies
(Node node) Returns a list of nodes connected to this node by an edgegetAttribute
(String name) Gets the entire attribute map.getChildren
(Node node) Returns the Edge that connects these two nodesdouble
getEdgeLength
(Node node1, Node node2) Returns the length of the edge that connects these two nodesgetEdges()
Returns a list of edges connected to this nodeThe set of external edges.double
The set of internal edges.double
getNodes()
getNodes
(int degree) Node[]
Returns an array of 2 nodes which are the nodes at either end of the edge.The root of the tree has the largest node height of all nodes in the tree.getTaxa()
boolean
boolean
boolean
isExternal
(Node node) boolean
boolean
boolean
void
removeAttribute
(String name) void
renameTaxa
(Taxon from, Taxon to) void
setAttribute
(String name, Object value) Sets an named attribute for this object.Methods inherited from class jebl.evolution.trees.AbstractRootedTree
getExternalNodeCount, getExternalNodes
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Constructor Details
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RootedFromUnrooted
Root tree at some internal node.- Parameters:
source
- tree to rootroot
- internal node to root atintentUnrooted
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RootedFromUnrooted
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.
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Method Details
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getChildren
- 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
- 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
- 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
- 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
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
- Returns:
- a set of all nodes that have degree 1. These nodes are often refered to as 'tips'.
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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
- 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
- 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
- Parameters:
node
- the node- Returns:
- true if the node is of degree 1.
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getNode
- 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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renameTaxa
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getEdges
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
Description copied from interface:Graph
Returns an array of 2 nodes which are the nodes at either end of the edge.- Parameters:
edge
-- Returns:
- an array of 2 edges
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getAdjacencies
Description copied from interface:Graph
Returns a list of nodes connected to this node by an edge- Parameters:
node
-- Returns:
- the set of nodes that are attached by edges to the given node.
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getEdgeLength
Description copied from interface:Graph
Returns the length of the edge that connects these two nodes- Parameters:
node1
-node2
-- Returns:
- the edge length.
- Throws:
Graph.NoEdgeException
- if the nodes are not directly connected by an edge.
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getEdge
Description copied from interface:Graph
Returns the Edge that connects these two nodes- Parameters:
node1
-node2
-- Returns:
- the edge object.
- Throws:
Graph.NoEdgeException
- if the nodes are not directly connected by an edge.
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getNodes
- Returns:
- the set of all nodes in this graph.
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getEdges
- Returns:
- the set of all edges in this graph.
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getExternalEdges
The set of external edges.- Returns:
- the set of external edges.
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getInternalEdges
The set of internal edges.- Returns:
- the set of internal edges.
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getNodes
- 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
- Parameters:
node
- the node- Returns:
- true if the node is the root of this tree.
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setAttribute
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
- 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
- Parameters:
name
- name of attribute to remove
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getAttributeNames
- Returns:
- an array of the attributeNames that this object has.
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getAttributeMap
Description copied from interface:Attributable
Gets the entire attribute map.- Returns:
- an unmodifiable map
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