TransformedRootedTree (JEBL2 lib API)

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 and cache them.

Version:

$Id: TransformedRootedTree.java 545 2006-11-28 00:08:34Z twobeers $

Author:

Andrew Rambaut

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class TransformedRootedTree.Transform
- Nested classes/interfaces inherited from interface jebl.evolution.graphs.Graph
  Graph.NoEdgeException, Graph.Utils

Nested Classes
Modifier and Type	Class	Description
`static class`	`TransformedRootedTree.Transform`

Constructor Summary

Constructors
Constructor Description

TransformedRootedTree(RootedTree source, TransformedRootedTree.Transform transform)

Constructors
Constructor	Description
`TransformedRootedTree(RootedTree source, TransformedRootedTree.Transform transform)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`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, renameTaxa, setAttribute

Methods inherited from class java.lang.Object
equals, 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).

Class TransformedRootedTree

Nested Class Summary

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

Constructor Summary

Method Summary

Methods inherited from class jebl.evolution.trees.FilteredRootedTree

Methods inherited from class java.lang.Object

Constructor Detail

TransformedRootedTree

Method Detail

hasHeights

getHeight

hasLengths

getLength