Uses of Class
org.forester.phylogeny.data.Taxonomy
Packages that use Taxonomy
Package
Description
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Uses of Taxonomy in org.forester.analysis
Methods in org.forester.analysis with parameters of type TaxonomyModifier and TypeMethodDescriptionstatic final UniProtTaxonomy
TaxonomyDataManager.obtainUniProtTaxonomy
(Taxonomy tax, Object query, org.forester.analysis.TaxonomyDataManager.QUERY_TYPE qt) -
Uses of Taxonomy in org.forester.archaeopteryx
Methods in org.forester.archaeopteryx that return types with arguments of type TaxonomyModifier and TypeMethodDescriptionAptxUtil.obtainAllDistinctTaxonomies
(PhylogenyNode node) TreePanelUtil.obtainDistinctTaxonomies
(PhylogenyNode node) Returns the set of distinct taxonomies of all external nodes of node. -
Uses of Taxonomy in org.forester.io.parsers.phyloxml.data
Methods in org.forester.io.parsers.phyloxml.data that return Taxonomy -
Uses of Taxonomy in org.forester.phylogeny
Methods in org.forester.phylogeny that return TaxonomyModifier and TypeMethodDescriptionstatic Taxonomy
PhylogenyMethods.getExternalDescendantsTaxonomy
(PhylogenyNode node) Returns taxonomy t if all external descendants have the same taxonomy t, null otherwise.Methods in org.forester.phylogeny that return types with arguments of type TaxonomyModifier and TypeMethodDescriptionPhylogenyMethods.obtainDistinctTaxonomyCounts
(PhylogenyNode node) Returns a map of distinct taxonomies of all external nodes of node.Methods in org.forester.phylogeny with parameters of type TaxonomyModifier and TypeMethodDescriptionstatic boolean
PhylogenyMethods.isTaxonomyHasIdentifierOfGivenProvider
(Taxonomy tax, String[] providers) Method parameters in org.forester.phylogeny with type arguments of type TaxonomyModifier and TypeMethodDescriptionstatic void
PhylogenyMethods.deleteExternalNodesPositiveSelectionT
(List<Taxonomy> species_to_keep, Phylogeny phy) -
Uses of Taxonomy in org.forester.phylogeny.data
Methods in org.forester.phylogeny.data that return TaxonomyModifier and TypeMethodDescriptionNodeData.getTaxonomy()
Convenience method -- always returns the first Taxonomy.NodeData.getTaxonomy
(int index) Methods in org.forester.phylogeny.data that return types with arguments of type TaxonomyMethods in org.forester.phylogeny.data with parameters of type TaxonomyModifier and TypeMethodDescriptionvoid
NodeData.addTaxonomy
(Taxonomy taxonomy) int
void
NodeData.setTaxonomy
(int index, Taxonomy taxonomy) void
NodeData.setTaxonomy
(Taxonomy taxonomy) Convenience method -- always sets the first Taxonomy. -
Uses of Taxonomy in org.forester.ws.wabi
Methods in org.forester.ws.wabi with parameters of type TaxonomyModifier and TypeMethodDescriptionstatic String[]
WabiTools.obtainLineage
(Taxonomy tax) static String
WabiTools.obtainRank
(Taxonomy tax)