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)