Package pal.tree

Class TreeDistanceMatrix

  • All Implemented Interfaces:
    java.io.Serializable, IdGroup

    public class TreeDistanceMatrix
    extends DistanceMatrix
    computes distance matrix induced by a tree (needs only O(n^2) time, following algorithm DistanceInTree by D.Bryant and P. Wadell. 1998. MBE 15:1346-1359)
    Version:
    $Id: TreeDistanceMatrix.java,v 1.9 2002/12/05 04:27:28 matt Exp $
    Author:
    Korbinian Strimmer, Alexei Drummond
    See Also:
    Serialized Form
    • Constructor Detail

      • TreeDistanceMatrix

        public TreeDistanceMatrix​(Tree t,
                                  IdGroup idGroup,
                                  boolean countEdges,
                                  double epsilon)
        compute induced distance matrix
        Parameters:
        idGroup - sequence order for the matrix
        t - tree
        countEdges - boolean variable deciding whether the actual branch lengths are used in computing the distance or whether simply all edges larger or equal a certain threshold length are counted (each with weight 1.0)
        epsilon - minimum branch length for a which an edge is counted
      • TreeDistanceMatrix

        public TreeDistanceMatrix​(Tree t,
                                  IdGroup idGroup)
        compute induced distance matrix using actual branch lengths
        Parameters:
        idGroup - sequence order for the matrix
        t - tree
      • TreeDistanceMatrix

        public TreeDistanceMatrix​(Tree t,
                                  boolean countEdges,
                                  double epsilon)
        compute induced distance matrix (using tree-induced order of sequences)
        Parameters:
        t - tree
        countEdges - boolean variable deciding whether the actual branch lengths are used in computing the distance or whether simply all edges larger or equal a certain threshold length are counted (each with weight 1.0)
        epsilon - minimum branch length for a which an edge is counted
      • TreeDistanceMatrix

        public TreeDistanceMatrix​(Tree t)
        compute induced distance matrix using actual branch lengths (using tree-induced order of sequences)
        Parameters:
        t - tree
    • Method Detail

      • recompute

        public void recompute​(Tree t)