jebl.evolution.trees
Class TransformedRootedTree

java.lang.Object
  jebl.evolution.trees.FilteredRootedTree
      jebl.evolution.trees.TransformedRootedTree

All Implemented Interfaces:

Graph, RootedTree, Tree, Attributable

public class TransformedRootedTree
extends FilteredRootedTree

This RootedTree class wraps another RootedTree and transforms the branch lengths and node heights using various functions. Currently implemented are equal lengths (all branch lengths are 1.0) and cladogram (the height of a node is proportional to the number of external nodes). Note that all these functions are recalculated on the fly for every call to getHeight and getLength and it may be desirable to precalculate them.

Author:

Andrew Rambaut

Nested Class Summary

static class

TransformedRootedTree.Transform

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

Graph.NoEdgeException, Graph.Utils

Field Summary

Fields inherited from class jebl.evolution.trees.FilteredRootedTree

source

Constructor Summary

TransformedRootedTree(RootedTree source, TransformedRootedTree.Transform transform)

Method Summary

double	getHeight(Node node)
double	getLength(Node node)
boolean	hasHeights()
boolean	hasLengths()

Methods inherited from class jebl.evolution.trees.FilteredRootedTree

conceptuallyUnrooted, getAdjacencies, getAttribute, getAttributeMap, getAttributeNames, getChildren, getEdge, getEdgeLength, getEdges, getEdges, getExternalEdges, getExternalNodes, getInternalEdges, getInternalNodes, getNode, getNodes, getNodes, getNodes, getParent, getRootNode, getSource, getTaxa, getTaxon, isExternal, isRoot, removeAttribute, setAttribute

Methods inherited from class java.lang.Object

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

Constructor Detail

TransformedRootedTree

public TransformedRootedTree(RootedTree source,
                             TransformedRootedTree.Transform transform)

Method Detail

hasHeights

public boolean hasHeights()

Specified by:

hasHeights in interface RootedTree

Overrides:

hasHeights in class FilteredRootedTree

Returns:

Whether this tree has node heights available

getHeight

public double getHeight(Node node)

Specified by:

getHeight in interface RootedTree

Overrides:

getHeight in class FilteredRootedTree

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

Overrides:

hasLengths in class FilteredRootedTree

Returns:

Whether this tree has branch lengths available

getLength

public double getLength(Node node)

Specified by:

getLength in interface RootedTree

Overrides:

getLength in class FilteredRootedTree

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).