org.forester.sdi
public class GSDI extends SDI
Constructor and Description |
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GSDI(Phylogeny gene_tree,
Phylogeny species_tree,
boolean most_parsimonious_duplication_model)
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 |
getSpeciationOrDuplicationEventsSum() |
int |
getSpeciationsSum() |
java.lang.String |
toString() |
computeMappingCostL, getDuplicationsSum, getGeneTree, getSpeciesTree
public GSDI(Phylogeny gene_tree, Phylogeny species_tree, boolean most_parsimonious_duplication_model)
gene_tree
- reference to a rooted gene tree 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 tree which might get
stripped in the process, must have species names in the
species name fields for all external nodesmost_parsimonious_duplication_model
- set to true to assign nodes as speciations which would
otherwise be assiged as unknown because of polytomies in the
species tree.#infer(boolean)
,
SDI.computeMappingCostL()