Class Utils

java.lang.Object
jebl.evolution.trees.Utils

public final class Utils extends Object
A collection of utility functions for trees.
Version:
$Id: Utils.java 979 2009-02-24 11:15:18Z rambaut $
Author:
rambaut, Alexei Drummond
  • Method Details

    • toNewick

      public static String toNewick(RootedTree tree)
      Parameters:
      tree -
      Returns:
      the rooted tree as a newick format string
    • toUniqueNewick

      public static String toUniqueNewick(RootedTree tree)
      Constructs a unique newick representation of a tree
      Parameters:
      tree -
    • toUniqueNewickByAttribute

      public static String toUniqueNewickByAttribute(RootedTree tree, String attribute)
      Constructs a unique newick representation of a tree print only an attribute
      Parameters:
      tree -
    • safeNodeHeight

      public static double safeNodeHeight(RootedTree tree, Node node)
    • maxLevels

      public static int maxLevels(RootedTree tree)
    • asText

      public static String asText(Tree tree)
    • asText

      public static String[] asText(Tree tree, int widthGuide)
    • rootTheTree

      public static RootedTree rootTheTree(Tree tree)
      Return a rooted tree from any tree.

      If tree already rooted, return it. Otherwise if there is a "natuarl root" (i.e. a node of degree 2) use it as root. Otherwise use an internal node close to the center of the tree as a root.

      Parameters:
      tree - to root
      Returns:
      rooted representation
    • rootTreeAtCenter

      public static RootedTree rootTreeAtCenter(Tree tree)
      Root any tree by locating the "center" of tree and adding a new root node at that point

      for any point on the tree x let D(x) = Max{distance between x and t : for all tips t} The "center" c is the point with the smallest distance, i.e. D(c) = min{ D(x) : x in tree }

      Parameters:
      tree - to root
      Returns:
      rooted tree
    • getPathLength

      public static double getPathLength(Tree tree, Node node1, Node node2)
      Parameters:
      tree - the tree
      node1 -
      node2 -
      Returns:
      the path length between the two nodes
    • isBinary

      public static boolean isBinary(RootedTree rootedTree)
      Parameters:
      rootedTree - the rooted tree
      Returns:
      true if all internal nodes in the given tree are of degree 3, except the root which must have a degree of 2.
    • isUltrametric

      public static boolean isUltrametric(RootedTree rootedTree)
      Parameters:
      rootedTree - the rooted tree
      Returns:
      true if all the external nodes in the tree have a height of 0.0
    • getExternalNodeCount

      public static int getExternalNodeCount(RootedTree tree, Node node)
      Return the number of external nodes under this node.
      Parameters:
      tree -
      node -
      Returns:
      the number of external nodes under this node.
    • getNodes

      public static List<Node> getNodes(RootedTree tree, Node node)
      All nodes in subtree - parents before children (pre - order).
      Parameters:
      tree -
      node -
      Returns:
      nodes in pre-order
    • rightNb

      public static Node rightNb(RootedTree tree, Node tipNode)
      Right Neighbour of a tip (taxon).

      When tree is laid with children in given order, this would be the taxon to the right.

      Parameters:
      tree -
      tipNode -
      Returns:
      Right Neighbour. null if node is the rightmost in tree or not a tip.
    • leftNb

      public static Node leftNb(RootedTree tree, Node node)
      Left Neighbour of a tip (taxon).

      When tree is laid with children in given order, this would be the taxon to the left.

      Parameters:
      tree -
      node -
      Returns:
      Left Neighbour. null if node is the leftmost in tree or not a tip.
    • getMinNodeHeight

      public static double getMinNodeHeight(RootedTree tree, Node node)
      Parameters:
      tree -
      node -
      Returns:
      the minimum node height
    • createNodeDensityComparator

      public static Comparator<Node> createNodeDensityComparator(RootedTree tree)
    • createNodeDensityMinNodeHeightComparator

      public static Comparator<Node> createNodeDensityMinNodeHeightComparator(RootedTree tree)
    • assertAllTreesHaveTheSameTaxa

      public static void assertAllTreesHaveTheSameTaxa(List<? extends Tree> trees) throws IllegalArgumentException
      Checks whether all of the trees passed in have the same taxa sets (ignoring order of taxa), and throws an IllegalArgumentException if this is not the case. If no tree or only one tree is passed in, immediately returns without throwing an exception.
      Parameters:
      trees - Zero or more trees
      Throws:
      IllegalArgumentException - if not all of the trees have the same taxa
      NullPointerException - if trees is null
    • DEBUGsubTreeRep

      public static String DEBUGsubTreeRep(RootedTree tree, Node node)
    • copyTree

      public static RootedTree copyTree(RootedTree treeToCopy)
      This method creates an unattached copy of the given rooted tree such that changes to the copied tree do not affect the original tree.
      Parameters:
      treeToCopy - the tree to copy
      Returns:
      an equivalent tree to treeToCopy (NB this may not be of the same RootedTree subclass as treeToCopy)