org.forester.sdi
Class SDI

java.lang.Object
  extended by org.forester.sdi.SDI
Direct Known Subclasses:
GSDI, SDIse, TaxonomyAssigner

public abstract class SDI
extends Object


Constructor Summary
SDI(Phylogeny gene_tree, Phylogeny species_tree)
          Constructor which sets the gene tree and the species tree to be compared.
 
Method Summary
 int computeMappingCostL()
          Computes the cost of mapping the gene tree gene_tree onto the species tree species_tree.
 int getDuplicationsSum()
          Returns the number of duplications.
 Phylogeny getGeneTree()
          Returns the gene tree.
 Phylogeny getSpeciesTree()
          Returns the species tree.
 String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

SDI

public SDI(Phylogeny gene_tree,
           Phylogeny species_tree)
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. Infers for each PhylogenyNode of gene_tree whether it represents a speciation or duplication event by calculating and interpreting the mapping function M. The most parsimonious sequence of speciation and duplication events is assumed. The mapping cost L can be calculated with method "computeMappingCost()".

Conditions:

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
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 String toString()
Overrides:
toString in class Object