org.forester.sdi
Class GSDI

java.lang.Object
  extended by org.forester.sdi.SDI
      extended by org.forester.sdi.GSDI

public class GSDI
extends SDI


Constructor Summary
GSDI(Phylogeny gene_tree, Phylogeny species_tree, boolean most_parsimonious_duplication_model)
          Constructor which sets the gene tree and the species tree to be compared.
 
Method Summary
 int getSpeciationOrDuplicationEventsSum()
           
 int getSpeciationsSum()
           
 String toString()
           
 
Methods inherited from class org.forester.sdi.SDI
computeMappingCostL, getDuplicationsSum, getGeneTree, getSpeciesTree
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

GSDI

public GSDI(Phylogeny gene_tree,
            Phylogeny species_tree,
            boolean most_parsimonious_duplication_model)
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()".

Parameters:
gene_tree - reference to a rooted gene tree 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 tree which might get stripped in the process, must have species names in the species name fields for all external nodes
most_parsimonious_duplication_model - set to true to assign nodes as speciations which would otherwise be assiged as unknown because of polytomies in the species tree.
See Also:
#infer(boolean), SDI.computeMappingCostL()
Method Detail

getSpeciationOrDuplicationEventsSum

public int getSpeciationOrDuplicationEventsSum()

getSpeciationsSum

public int getSpeciationsSum()

toString

public String toString()
Overrides:
toString in class SDI