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java.lang.Object | +--forester.tools.SDIdirectory
Allows to infer duplications - speciations on all (rooted or unrooted) gene trees in a directory by using method "infer" of class SDIunrooted.
The output of this is a (re)rooted tree with speciation - duplication assigned (in NHX format) for each tree (in "gene tree directory" with suffix "suffix for gene trees"), as well as a summary list ("outputfile name").
The summary list contains the following. The number in brackets indicates how many external nodes of the gene tree had to be removed since the associated species was not found in the species tree. "en" indicates the number of external nodes in the resulting (analyzed and returned) gene tree. "d" are the number of duplications, "L=" the mapping cost, "h=" the height, "d=" the minimal difference in tree heights (of the two subtrees at the root; this number is 0.0 for a midpoint rooted tree) of the resulting, analyzed and rooted gene tree(s).
The output file ending with "_Sdist" is a file which lists the distribution of trees sizes, "_Ddist" lists the distribution of the sums of duplications (up to a certain maximal size, set with final variables MAX_EXT_NODE_DIST and MAX_DUP_DIST).
SDIunrooted
Constructor Summary | |
SDIdirectory()
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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_sum_of_dup,
boolean minimize_height,
boolean input_trees_in_nh)
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 |
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Constructor Detail |
public SDIdirectory()
Method Detail |
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, boolean input_trees_in_nh) throws java.lang.Exception
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 choseninput_trees_in_nh
- set to true if
input trees are in New Hampshire format instead
of NHX;
or
gene trees are in NHX, but species
information in gene trees is only present in the
form of SWISS-PROT sequence namesSDIunrooted#infer(Tree,Tree,boolean,boolean,boolean,boolean,int,boolean)
public static void main(java.lang.String[] args)
(Last modified: 01/13/01)
[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
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FORESTER 1.92 | |||||||
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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |