org.forester.sdi
Class ORcount

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

public class ORcount
extends java.lang.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, java.lang.String[] group_1, java.lang.String[] group_2)
void	countSuperOrthologousRelations(int bootstrap_threshold)
static void	main(java.lang.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,
                                       java.lang.String[] group_1,
                                       java.lang.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(java.lang.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)