| Constructor | Description |
|---|---|
GSDIR(Phylogeny gene_tree,
Phylogeny species_tree,
boolean strip_gene_tree,
boolean strip_species_tree,
boolean transfer_taxonomy) |
| Modifier and Type | Method | Description |
|---|---|---|
BasicDescriptiveStatistics |
getDuplicationsSumStats() |
|
static java.util.List<java.lang.Integer> |
getIndexesOfShortestTree(java.util.List<Phylogeny> assigned_trees) |
|
java.util.Set<PhylogenyNode> |
getMappedExternalSpeciesTreeNodes() |
|
int |
getMinDuplicationsSum() |
|
Phylogeny |
getMinDuplicationsSumGeneTree() |
|
java.util.SortedSet<java.lang.String> |
getReMappedScientificNamesFromGeneTree() |
|
int |
getSpeciationsSum() |
|
java.util.List<PhylogenyNode> |
getStrippedExternalGeneTreeNodes() |
|
java.util.List<PhylogenyNode> |
getStrippedSpeciesTreeNodes() |
|
SDIutil.TaxonomyComparisonBase |
getTaxCompBase() |
public GSDIR(Phylogeny gene_tree, Phylogeny species_tree, boolean strip_gene_tree, boolean strip_species_tree, boolean transfer_taxonomy) throws SDIException
SDIExceptionpublic BasicDescriptiveStatistics getDuplicationsSumStats()
public java.util.Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes()
getMappedExternalSpeciesTreeNodes in interface GSDIIpublic int getMinDuplicationsSum()
public Phylogeny getMinDuplicationsSumGeneTree()
public final java.util.SortedSet<java.lang.String> getReMappedScientificNamesFromGeneTree()
getReMappedScientificNamesFromGeneTree in interface GSDIIpublic int getSpeciationsSum()
getSpeciationsSum in interface GSDIIpublic java.util.List<PhylogenyNode> getStrippedExternalGeneTreeNodes()
getStrippedExternalGeneTreeNodes in interface GSDIIpublic java.util.List<PhylogenyNode> getStrippedSpeciesTreeNodes()
getStrippedSpeciesTreeNodes in interface GSDIIpublic SDIutil.TaxonomyComparisonBase getTaxCompBase()
getTaxCompBase in interface GSDIIpublic static final java.util.List<java.lang.Integer> getIndexesOfShortestTree(java.util.List<Phylogeny> assigned_trees)