forester.tools
Class SDI
java.lang.Object
|
+--forester.tools.SDI
- Direct Known Subclasses:
- SDIoe, SDIse
- public abstract class SDI
- extends java.lang.Object
- Version:
- 1.002 -- last modified: 10/12/00
- Author:
- Christian M. Zmasek
Constructor Summary |
SDI(Tree gene_tree,
Tree species_tree)
Constructor. |
Method Summary |
abstract int |
infer(boolean strip_species_tree)
Abstract method. |
static void |
main(java.lang.String[] args)
A "main method" for SDI (Speciation versus Duplication Inference). |
static int |
stripTree(Tree reference,
Tree to_be_stripped)
Removes from Tree to_be_stripped all external Nodes which
are assocaited with a species not found in Tree reference. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SDI
public SDI(Tree gene_tree,
Tree species_tree)
throws java.lang.Exception
- Constructor.
Tree species_tree is a species Tree to which the gene Tree
gene_tree will be compared to.
Both Trees must be completely binary and rooted.
The actual inference is accomplished with method infer().
- Parameters:
gene_tree
- reference to a rooted binary gene Tree to which assign
duplication vs. speciationspecies_tree
- reference to a rooted binary species Tree which might
be stripped in the process
infer
public abstract int infer(boolean strip_species_tree)
throws java.lang.Exception
- Abstract method.
Should infer for each Node of gene_tree whether it
represents a speciation or duplication event. The most parsimonious
sequence of speciation and duplication events should be assumed.
- Parameters:
strip_species_tree
- set to true to remove from the species tree
species not found in the gene tree- Returns:
- number of duplications which have been assigned in the gene Tree
stripTree
public static int stripTree(Tree reference,
Tree to_be_stripped)
- Removes from Tree to_be_stripped all external Nodes which
are assocaited with a species not found in Tree reference.
- Parameters:
reference
- to_be_stripped
- - Returns:
- number of external nodes removed
main
public static void main(java.lang.String[] args)
- A "main method" for SDI (Speciation versus Duplication Inference).
- Parameters:
[args[
- 0 ] = -e to use Eulenstein's algorithm]args[
- 0 or 1 ] species-tree file nameargs[
- 1 or 2 ] gene-tree file name