Package pal.tree

Class RootedTreeUtils

  • public class RootedTreeUtils
extends java.lang.Object
    This class contains utility methods. These include:
    1. gathering information about subtrees from a set of trees
    2. comparing subtrees and clades.
    All these methods assume rooted trees!
    Version:
    $Id: RootedTreeUtils.java,v 1.3 2003/06/11 05:26:46 matt Exp $
    Author:
    Alexei Drummond

    • Constructor Detail

      • RootedTreeUtils

        public RootedTreeUtils()

    • Method Detail

      • containsSubtree

        public static boolean containsSubtree​(Node root,
                                      Node node)
        Parameters:
        root - the root of the tree in which search for a subtree
        node - the subtree to search for.
        Returns:
        true if the first node contains a subtree identical to the second node or is identical to the second node.

      • containsClade

        public static boolean containsClade​(Node root,
                                    Node clade)
        Parameters:
        root - the root of the tree in which search for a subtree
        taxa - the hashtable of taxa.
        Returns:
        true if the given tree contains a clade holding all the taxa in the given subtree.

      • getSubtree

        public static Node getSubtree​(Node root,
                              Node node)
        Returns:
        a subtree within the first node with the same labelled topology as the second node or null if it doesn't exist.

      • getClade

        public static Node getClade​(Node root,
                            Node clade)
        Returns:
        a subtree within the first node with the same labels as the second node or null if it doesn't exist.

      • equal

        public static boolean equal​(Node node1,
                            Node node2)
        Returns:
        true if the trees have the same tip-labelled structure. Child order is not important.

      • sameTaxa

        public static boolean sameTaxa​(Node node1,
                               Node node2)
        Returns:
        true if the trees have the same tip labels. topology unimportant.

      • collectTaxa

        public static int collectTaxa​(Node root,
                              java.util.Hashtable table)
        Collects all of the names of the taxa in the tree into a hashtable.
        Parameters:
        root - the root node of the tree.
        taxa - a hashtable to hold the taxa names, may already hold some taxa names.
        Returns:
        the number of new taxa added to the hashtable from this tree.

      • containsNovelTaxa

        public static boolean containsNovelTaxa​(Node root,
                                        java.util.Hashtable taxa)
        Parameters:
        root - the root node of the tree.
        taxa - a hashtable holding taxa names.
        Returns:
        true if the given tree contains taxa not already in the given hashtable.

      • subtreeCount

        public static int subtreeCount​(Node subtree,
                               java.util.Vector trees)
        Parameters:
        subtree - the subtree being searched for.
        trees - a vector of trees to search for the subtree in.
        Returns:
        the number of times the subtree was found in the given list of trees. If a subtree occurs more than once in a tree (for some bizarre reason) it is counted only once.

      • getMeanSubtreeHeight

        public static double getMeanSubtreeHeight​(Node subtree,
                                          java.util.Vector trees)
        Parameters:
        subtree - the subtree being searched for.
        trees - a vector of trees to search for the subtree in.
        Returns:
        the mean height of the given subtree in the given list of trees. If a subtree occurs more than once in a tree (for some bizarre reason) results are undefined.

      • getMeanCladeHeight

        public static double getMeanCladeHeight​(Node clade,
                                        java.util.Vector trees)
        Parameters:
        clade - a node containing the clade being searched for.
        trees - a vector of trees to search for the clade in.
        Returns:
        the mean height of the given clade in the given list of trees. If a clade occurs more than once in a tree (for some bizarre reason) results are undefined.

      • cladeCount

        public static int cladeCount​(Node subtree,
                             java.util.Vector trees)
        Parameters:
        subtree - a subtree containing the taxaset being searched for.
        trees - a vector of trees to search for the clade in.
        Returns:
        the number of times the clade was found in the given list of trees. If a clade occurs more than once in a tree (for some bizarre reason) it is counted only once.

      • collectProportions

        public static void collectProportions​(Tree tree,
                                      java.util.Vector trees)