Class Utils


  • public final class Utils
    extends java.lang.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 Detail

      • toNewick

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

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

        public static java.lang.String toUniqueNewickByAttribute​(RootedTree tree,
                                                                 java.lang.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 java.lang.String asText​(Tree tree)
      • asText

        public static java.lang.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 java.util.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 java.util.Comparator<Node> createNodeDensityComparator​(RootedTree tree)
      • createNodeDensityMinNodeHeightComparator

        public static java.util.Comparator<Node> createNodeDensityMinNodeHeightComparator​(RootedTree tree)
      • assertAllTreesHaveTheSameTaxa

        public static void assertAllTreesHaveTheSameTaxa​(java.util.List<? extends Tree> trees)
                                                  throws java.lang.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:
        java.lang.IllegalArgumentException - if not all of the trees have the same taxa
        java.lang.NullPointerException - if trees is null
      • DEBUGsubTreeRep

        public static java.lang.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)