Package org.forester.sdi
Class SDI
- java.lang.Object
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- org.forester.sdi.SDI
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public class SDI extends java.lang.Object
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Method Summary
All Methods Instance Methods Concrete Methods 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()
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Constructor Detail
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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 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 nodes- Throws:
SDIException
- See Also:
#infer(boolean)
,computeMappingCostL()
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Method Detail
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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"
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getDuplicationsSum
public int getDuplicationsSum()
Returns the number of duplications.- Returns:
- number of duplications
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getGeneTree
public Phylogeny getGeneTree()
Returns the gene tree.- Returns:
- gene tree
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getSpeciesTree
public Phylogeny getSpeciesTree()
Returns the species tree.- Returns:
- species tree
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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