FORESTER 1.6

forester.tools
Class RIOdirectory

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

public class RIOdirectory
extends java.lang.Object

Version:
1.000 -- last modified: 12/11/00
Author:
Christian M. Zmasek

Constructor Summary
RIOdirectory()
           
 
Method Summary
static void inferAllOrthologs(java.io.File indir, java.io.File species_tree_file, java.io.File outdir, java.lang.String suffix_multi, java.lang.String suffix_dist, int sort, double threshhold_orthologs, double threshhold_super_orthologs)
          Counts all orthologs for all multiple gene trees files 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

RIOdirectory

public RIOdirectory()
Method Detail

inferAllOrthologs

public static void inferAllOrthologs(java.io.File indir,
                                     java.io.File species_tree_file,
                                     java.io.File outdir,
                                     java.lang.String suffix_multi,
                                     java.lang.String suffix_dist,
                                     int sort,
                                     double threshhold_orthologs,
                                     double threshhold_super_orthologs)
                              throws java.lang.Exception
Counts all orthologs for all multiple gene trees files in directory indir. (Last modified: 12/11/00)
Parameters:
indir - a directory containing multiple gene trees files (=result of bootstrap analysis)
species_tree_file - a species tree file in NHX format
outdir - a directory where to write results
suffix_multi - a suffix for the multiple gene trees files to read (e.g. mlt)
suffix_dist - a suffix for the pairwise distance matrix files to read (e.g. dst), if sort <= 2, suffix_dist can be null or empty, since in this cases pairwise distances or not utilized
sort - order and sort priority
threshhold_orthologs - the minimal number of observations for a a sequence to be reported as orthologous in list
threshhold_super_orthologs - the minimal number of observations for a a sequence to be reported as super orthologous in list -- the relation between "threshhold_orthologs" and "threshhold_super_orthologs" is AND
See Also:
RIO.inferredOrthologsToString(String,int,double,double)

main

public static void main(java.lang.String[] args)
Main method for this class. (Last modified: 12/11/00)
Parameters:
args[ - 0 ] a directory containing multiple gene trees files (=result of bootstrap analysis)
args[ - 1 ] a species tree file in NHX format
args[ - 2 ] a directory where to write results
args[ - 3 ] a suffix for the multiple gene trees files to read (e.g. .mlt), is case sensitive
args[ - 4 ] a suffix for the pairwise distance matrix files to read (e.g. .dst), is case sensitive
args[ - 5 ] (int) order and sort priority
args[ - 6 ] (double) the minimal number of observations for a a sequence to be reported as orthologous in list
args[ - 7 ] (double) the minimal number of observations for a a sequence to be reported as super orthologous in list -- the relation between "threshhold orthologs" and "threshhold super orthologs" is AND
See Also:
RIO.inferredOrthologsToString(String,int,double,double)

FORESTER 1.6