Package org.forester.sdi

Class SDI

java.lang.Object
org.forester.sdi.SDI
public class SDI extends Object

  • Constructor Details

    • SDI

      public SDI(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:

  • Method Details

    • computeMappingCostL

      public int computeMappingCostL()
      Computes the cost of mapping the gene tree gene_tree onto the species tree species_tree. Before this method can be called, the mapping has to be calculated with method "infer(boolean)".

      Reference. Zhang, L. (1997) On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies. Journal of Computational Biology 4 177-187.

      Returns:
      the mapping cost "L"

    • getDuplicationsSum

      public int getDuplicationsSum()
      Returns the number of duplications.
      Returns:
      number of duplications

    • getGeneTree

      public Phylogeny getGeneTree()
      Returns the gene tree.
      Returns:
      gene tree

    • getSpeciesTree

      public Phylogeny getSpeciesTree()
      Returns the species tree.
      Returns:
      species tree

    • toString

      public String toString()
      Overrides:
      toString in class Object