public class sdi_dir
extends java.lang.Object
Constructor and Description |
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sdi_dir() |
Modifier and Type | Method and Description |
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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_sum_of_dup,
boolean minimize_height)
Runs method "infer" of class SDIunrooted on all gene trees in directory
indir.
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static void |
main(java.lang.String[] args)
Main method for this class.
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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_sum_of_dup, boolean minimize_height) throws java.io.IOException, SDIException
Trees are rooted by minimizing either the sum of duplications, the mapping cost L, or the tree height (or combinations thereof). 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.
If both minimize_sum_of_dup and minimize_mapping_cost are true, trees are rooted by minimizing by minimizing the mapping cost L.
If minimize_sum_of_dup, minimize_mapping_cost, and minimize_height are false trees are assumed to be alreadty rooted.
(Last modified: 02/02/01)
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 Lminimize_sum_of_dup
- set to true to root by minimizing the sum of duplicationsminimize_height
- set to true to root by minimizing the tree height -- if
minimize_mapping_cost is set to true or minimize_sum_of_dup is
set to true, then out of the resulting trees with minimal
mapping cost or minimal number of duplications the tree with
the minimal height is chosenSDIException
java.io.IOException
SDIR#infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
public static void main(java.lang.String[] args)
(Last modified: 04/26/10)
[args[0]
- -l to root by minimizing mapping cost L][args[0]
- -d to root by minimizing sum of duplications][args[0]
- -w to write out trees into outdir][args[0]
- -h to root by minimizing tree height][args[0]
- -n input trees are in New Hampshire format instead of NHX --
or gene tree is in NHX, but species information in gene tree
is only present in the form of SWISS-PROT sequence names]args[0or1]
- trees directory nameargs[1or2]
- suffix for gene treesargs[2or3]
- speciestree file nameargs[3or4]
- output directory nameargs[4or5]
- output file name