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
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 |
SDIdirectory
public SDIdirectory()
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 formatspecies_tree_file
- a species tree file in NHX formatoutdir
- a directory where to write treesoutfile
- a file name for the summary filesuffix
- a suffix for the trees to read (e.g. nhx), is
case sensitivewrite_trees
- set to true to write out one tree with minmal
duplications or L eachminimize_mapping_cost
- set to true to root by minimizing the mapping
cost L, otherwis rooting is accomplished by
minimizing the sum of duplicationsminimize_height
- set to true to root by minimizing the
tree height of the trees with minimal
duplications or minimal mapping costuse_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 treesargs[
- 2 or 3 ] speciestree fileargs[
- 3 or 4 ] output directoryargs[
- 4 or 5 ] output file name