forester v1.4

forester.tools
Class SDIoe

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

public class SDIoe
extends SDI

Version:
1.010 -- last modified: 11/07/00
Author:
Christian M. Zmasek

Constructor Summary
SDIoe(Tree gene_tree, Tree species_tree)
          Constructor.
 
Method Summary
 int computeMappingCost()
          Computes the cost of mapping the gene tree gene_tree onto the species tree species_tree.
 int infer(boolean strip_species_tree)
          Infers for each Node of gene_tree whether it represents a speciation or duplication event.
 
Methods inherited from class forester.tools.SDI
main, stripTree
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SDIoe

public SDIoe(Tree gene_tree,
             Tree species_tree)
      throws java.lang.Exception
Constructor. Tree species_tree is a species Tree to which the gene Tree gene_tree will be compared to. Both Trees must be completely binary and rooted. The actual inference is accomplished with method "infer()".
Parameters:
gene_tree - reference to a rooted binary gene Tree to which assign duplication vs. speciation
species_tree - reference to a rooted binary species Tree which might be stripped in the process
Method Detail

infer

public int infer(boolean strip_species_tree)
          throws java.lang.Exception
Infers for each Node of gene_tree whether it represents a speciation or duplication event. The most parsimonious sequence of speciation and duplication events is assumed. The species tree MUST NOT contain species not found in the gene tree. If it does, set strip_species_tree to true. Uses a algorithm described by Oliver Eulenstein.
Overrides:
infer in class SDI
Parameters:
strip_species_tree - set to true if species are present in the species tree which are not in the gene tree
Returns:
number of duplications which have been assigned in the gene Tree

computeMappingCost

public int computeMappingCost()
Computes the cost of mapping the gene tree gene_tree onto the species tree species_tree. Before this method can be called, the mapping has to be calculated with method "infer()". Reference. Zhang, L. (1997) On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies. Journal of Computational Biology 4 177-187. (Last modified: 11/07/00)
Overrides:
computeMappingCost in class SDI
Returns:
the mapping cost "L"

forester v1.4