forester v1.2

forester.tools
Class SDI

java.lang.Object
  |
  +--forester.tools.SDI

public class SDI
extends java.lang.Object

Version:
0.94 -- last modified: 07/09/00
Author:
Christian M. Zmasek

Constructor Summary
SDI()
           
 
Method Summary
static int assign(Tree gene_tree, Tree species_tree)
          Determines for each Node of a gene Tree (gene_tree) whether it represents a speciation or duplication event.
static int stripTree(Tree reference, Tree to_be_stripped)
          Removes from Tree to_be_stripped all external Nodes which are assocaited with a species not found in Tree reference.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SDI

public SDI()
Method Detail

assign

public static int assign(Tree gene_tree,
                         Tree species_tree)
                  throws java.lang.Exception
Determines for each Node of a gene Tree (gene_tree) whether it represents a speciation or duplication event. The most parsimonious sequence of speciation and duplication events is assumed. Tree species_tree is a species Tree to which the gene Tree is compared to. Both Trees must be completely binary and rooted.
Parameters:
gene_tree - a gene Tree
species_tree - a species Tree
Returns:
number of duplications which have been assigned in the gene Tree

stripTree

public static int stripTree(Tree reference,
                            Tree to_be_stripped)
Removes from Tree to_be_stripped all external Nodes which are assocaited with a species not found in Tree reference.
Returns:
number of external nodes removed

forester v1.2