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 and cache them.
Version:
$Id: TransformedRootedTree.java 545 2006-11-28 00:08:34Z twobeers $
Author:
Andrew Rambaut
  • Constructor Details

  • Method Details

    • 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).