org.forester.sdi
public abstract class SDI extends java.lang.Object
Constructor and Description |
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SDI(Phylogeny gene_tree,
Phylogeny species_tree)
Constructor which sets the gene tree and the species tree to be compared.
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Modifier and Type | Method and Description |
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int |
computeMappingCostL()
Computes the cost of mapping the gene tree gene_tree onto the species
tree species_tree.
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int |
getDuplicationsSum()
Returns the number of duplications.
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Phylogeny |
getGeneTree()
Returns the gene tree.
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Phylogeny |
getSpeciesTree()
Returns the species tree.
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java.lang.String |
toString() |
public SDI(Phylogeny gene_tree, Phylogeny species_tree)
Conditions:
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 nodespublic 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