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java.lang.Objectorg.forester.sdi.SDI
public abstract class SDI
Constructor Summary | |
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SDI(Phylogeny gene_tree,
Phylogeny species_tree)
Constructor which sets the gene tree and the species tree to be compared. |
Method Summary | |
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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()
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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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 nodesMethod Detail |
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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 String toString()
toString
in class Object
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