forester.tools
Class SDIunrooted
java.lang.Object
|
+--forester.tools.SDIunrooted
- public class SDIunrooted
- extends java.lang.Object
- Version:
- 1.010 -- last modified: 10/18/00
- Author:
- Christian M. Zmasek
Method Summary |
int |
getCount()
Returns the number of differently rooted trees with minimal number
of duplications, as determined by method infer. |
int |
getMinimalDuplications()
Returns the minimal number of duplications, as determined
by method infer. |
long |
getTimeSumSDI()
Returns the sum of times (in ms) needed to run method infer of class SDI. |
Tree[] |
infer(Tree gene_tree,
Tree species_tree,
boolean return_trees,
int max_trees_to_return,
boolean use_eulenstein)
Infers gene duplications on a unrooted gene Tree. |
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 |
SDIunrooted
public SDIunrooted()
- Default constructor.
getCount
public int getCount()
- Returns the number of differently rooted trees with minimal number
of duplications, as determined by method infer.
- Returns:
- number of trees with minimal number of duplications
getMinimalDuplications
public int getMinimalDuplications()
- Returns the minimal number of duplications, as determined
by method infer.
- Returns:
- number of duplications
getTimeSumSDI
public long getTimeSumSDI()
- Returns the sum of times (in ms) needed to run method infer of class SDI.
Final variable TIME needs to be set to true.
- Returns:
- sum of times (in ms) needed to run method infer of class SDI
infer
public Tree[] infer(Tree gene_tree,
Tree species_tree,
boolean return_trees,
int max_trees_to_return,
boolean use_eulenstein)
throws java.lang.Exception
- Infers gene duplications on a unrooted gene Tree.
If return_trees is set to true, it returns an array of differently
rooted Trees which have the minimal number of duplications. The
maximal number of returned trees is set with max_trees_to_return.
If use_eulenstein is set to true, Eulenstein's algorithm is used,
otherwise our algorithm is used.
Tree species is a species Tree to which the gene Tree gene
is compared to.
Conditions: Both Trees must be completely binary.
The species Tree must be rooted.
Species found in gene Tree must be a subset of those
found in species Tree.
Both Trees must have species names in the species name
field of their Nodes.
(See "TreeHelper.cleanSpeciesNamesInExtNodes" and
and "TreeHelper.extractSpeciesNameFromSPseqName".)
- Parameters:
gene_tree
- a unrooted binary (except deepest node) gene Treespecies_tree
- a rooted binary species Treereturn_trees
- set to true to return Array of Trees, otherwise
null is returnedmax_trees_to_return
- maximal number of Trees to return
(=maximal size of returned Array)
must be no lower than 1use_eulenstein
- set to true to use Eulenstein's algorithm- Returns:
- array of rooted Trees which have the minimal number
of duplications, if return_trees is set to true, null otherwise
main
public static void main(java.lang.String[] args)
- Main method for this class.
- Parameters:
[args[
- 0 ] = -e to use Eulenstein's algorithm]args[
- 0 or 1 ] species-tree file nameargs[
- 1 or 2 ] gene-tree file name