Class SDI


  • public class SDI
    extends java.lang.Object
    • Constructor Summary

      Constructors 
      Constructor Description
      SDI​(Phylogeny gene_tree, Phylogeny species_tree)
      Constructor which sets the gene tree and the species tree to be compared.
    • Constructor Detail

      • 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:
        #infer(boolean), computeMappingCostL()
    • Method Detail

      • 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 java.lang.String toString()
        Overrides:
        toString in class java.lang.Object