forester v1.3

forester.tools
Class SDIdirectory

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

public class SDIdirectory
extends java.lang.Object

Version:
1.002 -- last modified: 10/26/00
Author:
Christian M. Zmasek

Constructor Summary
SDIdirectory()
           
 
Method Summary
static void infer(java.io.File indir, java.io.File species_tree_file, java.io.File outdir, java.io.File outfile, java.lang.String suffix, boolean write_trees, boolean use_eulenstein)
          Purpose.
static void main(java.lang.String[] args)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SDIdirectory

public SDIdirectory()
Method Detail

infer

public static void infer(java.io.File indir,
                         java.io.File species_tree_file,
                         java.io.File outdir,
                         java.io.File outfile,
                         java.lang.String suffix,
                         boolean write_trees,
                         boolean use_eulenstein)
                  throws java.lang.Exception
Purpose. Runs method infer of class SDIunrooted on all trees in directory indir. One resulting tree for each (out of possibly many) is stored in outdir and a summary outfile is created.
Parameters:
indir - a directory containing trees in NHX format
species_tree_file - a species tree file
outdir - a directory where to write trees
outfile - a file name for the summary file
suffix - a suffix for the trees to read (e.g. nhx), is case sensitive
write_trees - set to true to write out one tree with minmal duplications each
use_eulenstein - set to true to use Eulenstein's algorithm, otherwise our algorithm is used is used

main

public static void main(java.lang.String[] args)

forester v1.3