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 UniProtTaxonomyTaxonomyDataManager.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 TaxonomyPhylogenyMethods.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 booleanPhylogenyMethods.isTaxonomyHasIdentifierOfGivenProvider(Taxonomy tax, String[] providers) Method parameters in org.forester.phylogeny with type arguments of type TaxonomyModifier and TypeMethodDescriptionstatic voidPhylogenyMethods.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 TypeMethodDescriptionvoidNodeData.addTaxonomy(Taxonomy taxonomy) intvoidNodeData.setTaxonomy(int index, Taxonomy taxonomy) voidNodeData.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 StringWabiTools.obtainRank(Taxonomy tax)