pal.tree
Class Local

java.lang.Object
  pal.tree.Local

public class Local

extends java.lang.Object

Implements LOCAL (Larget and Simon, 1999) and stochastic NNI moves for unrooted trees.

Constructor Summary

Local()

Method Summary

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.

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)