forester v1.4

forester.tools
Class SDIdirectory

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

public class SDIdirectory
extends java.lang.Object

Version:
1.020 -- last modified: 11/11/00
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 minimize_mapping_cost, boolean minimize_height, boolean use_eulenstein)
          Runs method "infer" of class SDIunrooted on all gene trees in directory indir.
static void main(java.lang.String[] args)
          Main method for this class.
 
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 minimize_mapping_cost,
                         boolean minimize_height,
                         boolean use_eulenstein)
                  throws java.lang.Exception
Runs method "infer" of class SDIunrooted on all gene trees in directory indir. Trees are rooted by either minimizing the sum of duplications for each tree, or by minimizing the mapping cost L. One resulting tree for each (out of possibly many) is stored in outdir and a summary outfile is created. The distributions of the tree sizes (name of outfile + _Ddist) and the distributions of the sum of duplications per tree (name of outfile + _Sdist) are written out as well. (Last modified: 11/11/00)
Parameters:
indir - a directory containing gene trees in NHX format
species_tree_file - a species tree file in NHX format
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 or L each
minimize_mapping_cost - set to true to root by minimizing the mapping cost L, otherwis rooting is accomplished by minimizing the sum of duplications
minimize_height - set to true to root by minimizing the tree height of the trees with minimal duplications or minimal mapping cost
use_eulenstein - set to true to use Eulenstein's algorithm, otherwise Eddy's algorithm is used for the duplication inference

main

public static void main(java.lang.String[] args)
Main method for this class. (Last modified: 11/11/00)
Parameters:
[args[ - 0 ] = -e to use Eulenstein's algorithm instead of Eddy's]
[args[ - 0 ] = -l to minimize mapping cost L instead of duplications]
[args[ - 0 ] = -w to write out trees into outdir]
[args[ - 0 ] = -h to minimize height of trees with minimal duplications or minimal mapping cost]
args[ - 0 or 1 ] trees directory (e.g. Pfamtrees)
args[ - 1 or 2 ] suffix for gene trees
args[ - 2 or 3 ] speciestree file
args[ - 3 or 4 ] output directory
args[ - 4 or 5 ] output file name

forester v1.4