forester v1.4

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 v1.4