Package pal.tree

Class Local

  • public class Local
extends java.lang.Object
    Implements LOCAL (Larget and Simon, 1999) and stochastic NNI moves for unrooted trees.
    Version:
    $Id: Local.java,v 1.1 2002/01/08 02:09:53 alexi Exp $
    Author:
    Alexei Drummond

    • Constructor Summary

      Constructors 
      Constructor Description
      Local()  

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static void displayLabel​(java.io.PrintWriter out, java.lang.String label, int width, boolean center)
      print label with a prespecified length (label will be shortened or spaces will introduced, if necessary)
      static Tree local​(Tree tree)  
      static Tree local​(Tree tree, double scaleFactor)
      This method does a local interchange on the given tree: Note the original tree is modified.
      static void main​(java.lang.String[] args)  
      static void print4TaxonTree​(Tree tree, java.io.PrintWriter out)  
      static Tree stochasticNNI​(Tree tree)  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • Local

        public Local()

    • Method Detail

      • local

        public static Tree local​(Tree tree)

      • local

        public static Tree local​(Tree tree,
                         double scaleFactor)
        This method does a local interchange on the given tree: Note the original tree is modified. If this behaviour is inappropriate then pass new SimpleTree(tree) to this method. 
         Actual          Logical
     2                 1            4
    /|\                 \          /
   / | \                 \        /
  /  |  \                 \      /       
 1   A   3                 2----3
        / \               /      \
       /   \             /        \
      /     \           /          \
     B       4         A            B
        A random internal edge (2,3) is selected and extended in both directions to create a back bone (1,2,3,4). One of the two internal nodes (2,3) is moved to a new random position on backbone and the backbone is scale in size.
        Parameters:
        scale - determines whether or not the backbone is scaled
        Returns:
        a perturbation of given tree.

      • stochasticNNI

        public static Tree stochasticNNI​(Tree tree)

      • print4TaxonTree

        public static void print4TaxonTree​(Tree tree,
                                   java.io.PrintWriter out)

      • displayLabel

        public static void displayLabel​(java.io.PrintWriter out,
                                java.lang.String label,
                                int width,
                                boolean center)
        print label with a prespecified length (label will be shortened or spaces will introduced, if necessary)
        Parameters:
        out - output stream
        label - label to be printed
        width - desired length

      • main

        public static final void main​(java.lang.String[] args)