org.forester.sdi
Class GSDI
java.lang.Object
org.forester.sdi.SDI
org.forester.sdi.GSDI
public class GSDI
- extends SDI
Constructor Summary |
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. |
GSDI
public 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.
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()".
- Parameters:
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.- See Also:
#infer(boolean)
,
SDI.computeMappingCostL()
getSpeciationOrDuplicationEventsSum
public int getSpeciationOrDuplicationEventsSum()
getSpeciationsSum
public int getSpeciationsSum()
toString
public String toString()
- Overrides:
toString
in class SDI