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
|
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 |
RIOdirectory
public RIOdirectory()
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 formatoutdir - a directory where to write resultssuffix_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 utilizedsort - order and sort prioritythreshhold_orthologs - the minimal number of observations for a
a sequence to be reported as orthologous in listthreshhold_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 formatargs[ - 2 ] a directory where to write resultsargs[ - 3 ] a suffix for the multiple gene
trees files to read (e.g. .mlt), is
case sensitiveargs[ - 4 ] a suffix for the pairwise distance matrix
files to read (e.g. .dst), is
case sensitiveargs[ - 5 ] (int) order and sort priorityargs[ - 6 ] (double) the minimal number of observations for a
a sequence to be reported as orthologous in listargs[ - 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)