public class SDI
extends java.lang.Object
Constructor | Description |
---|---|
SDI(Phylogeny gene_tree,
Phylogeny species_tree) |
Constructor which sets the gene tree and the species tree to be compared.
|
Modifier and Type | Method | Description |
---|---|---|
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.
|
java.lang.String |
toString() |
public SDI(Phylogeny gene_tree, Phylogeny species_tree) throws SDIException
(Last modified: 01/11/01)
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 nodesspecies_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 nodesSDIException
#infer(boolean)
,
computeMappingCostL()
public int computeMappingCostL()
Reference. Zhang, L. (1997) On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies. Journal of Computational Biology 4 177-187.
public int getDuplicationsSum()
public Phylogeny getGeneTree()
public Phylogeny getSpeciesTree()
public java.lang.String toString()
toString
in class java.lang.Object