org.forester.sdi

Class SDIse

java.lang.Object

org.forester.sdi.SDI

org.forester.sdi.SDIse

public class SDIse
extends SDI

Nested Class Summary

Nested classes/interfaces inherited from class org.forester.sdi.SDI

SDI.TaxonomyComparisonBase

Constructor Summary

Constructors

Constructor and Description
SDIse(Phylogeny gene_tree, Phylogeny species_tree) Constructor which sets the gene tree and the species tree to be compared.

Method Summary

Methods inherited from class org.forester.sdi.SDI

computeMappingCostL, getDuplicationsSum, getGeneTree, getSpeciesTree, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

SDIse

public SDIse(Phylogeny gene_tree,
     Phylogeny species_tree)
      throws SDIException

Constructor which sets the gene tree and the species tree to be compared. species_tree is the species tree to which the gene tree gene_tree will be compared to - with method "infer(boolean)". Both Trees must be completely binary and rooted. The actual inference is accomplished with method "infer(boolean)". The mapping cost L can then be calculated with method "computeMappingCost()".

(Last modified: 01/11/01)

Parameters:

gene_tree - reference to a rooted binary gene Phylogeny to which assign duplication vs speciation, must have species names in the species name fields for all external nodes

species_tree - reference to a rooted binary species Phylogeny which might get stripped in the process, must have species names in the species name fields for all external nodes

Throws:

SDIException

See Also:

#infer(boolean), SDI.computeMappingCostL()