org.forester.sdi
Class ORcount

java.lang.Object
  extended by org.forester.sdi.ORcount

public class ORcount
extends Object


Constructor Summary
ORcount(Phylogeny[] trees)
          Default contructor which
 
Method Summary
 void countSharedAncestralClades(Phylogeny[] trees, int bootstrap_threshold)
           
 void countSharedAncestralClades(Phylogeny tree, int bootstrap_threshold, String[] group_1, String[] group_2)
           
 void countSuperOrthologousRelations(int bootstrap_threshold)
           
static void main(String[] args)
          Main method for this class.
 void reset()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ORcount

public ORcount(Phylogeny[] trees)
Default contructor which

Method Detail

countSharedAncestralClades

public void countSharedAncestralClades(Phylogeny tree,
                                       int bootstrap_threshold,
                                       String[] group_1,
                                       String[] group_2)

countSharedAncestralClades

public void countSharedAncestralClades(Phylogeny[] trees,
                                       int bootstrap_threshold)

countSuperOrthologousRelations

public void countSuperOrthologousRelations(int bootstrap_threshold)

reset

public void reset()

main

public static void main(String[] args)
Main method for this class.

(Last modified: 11/26/03)

Parameters:
args[1or2] - gene tree file name (in NHX format with species names in species name fields and sequence names in sequence name fields; unless -n option is used)