Uses of Class
org.forester.phylogeny.data.Taxonomy

Packages that use Taxonomy

Package	Description
org.forester.analysis
org.forester.archaeopteryx
org.forester.io.parsers.phyloxml.data
org.forester.phylogeny
org.forester.phylogeny.data
org.forester.ws.wabi

Uses of Taxonomy in org.forester.analysis

Methods in org.forester.analysis with parameters of type Taxonomy

Modifier and Type	Method and Description
static 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 Taxonomy

Modifier and Type	Method and Description
static Set<Taxonomy>	AptxUtil.obtainAllDistinctTaxonomies(PhylogenyNode node)
static Set<Taxonomy>	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

Modifier and Type	Method and Description
Taxonomy	TaxonomyParser.parse(XmlElement element)

Uses of Taxonomy in org.forester.phylogeny

Methods in org.forester.phylogeny that return Taxonomy

Modifier and Type	Method and Description
static 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 Taxonomy

Modifier and Type	Method and Description
static Map<Taxonomy,Integer>	PhylogenyMethods.obtainDistinctTaxonomyCounts(PhylogenyNode node) Returns a map of distinct taxonomies of all external nodes of node.

Methods in org.forester.phylogeny with parameters of type Taxonomy

Modifier and Type	Method and Description
static boolean	PhylogenyMethods.isTaxonomyHasIdentifierOfGivenProvider(Taxonomy tax, String[] providers)

Method parameters in org.forester.phylogeny with type arguments of type Taxonomy

Modifier and Type	Method and Description
static 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 Taxonomy

Modifier and Type	Method and Description
Taxonomy	NodeData.getTaxonomy() Convenience method -- always returns the first Taxonomy.
Taxonomy	NodeData.getTaxonomy(int index)

Methods in org.forester.phylogeny.data that return types with arguments of type Taxonomy

Modifier and Type	Method and Description
List<Taxonomy>	NodeData.getTaxonomies()

Methods in org.forester.phylogeny.data with parameters of type Taxonomy

Modifier and Type	Method and Description
void	NodeData.addTaxonomy(Taxonomy taxonomy)
int	Taxonomy.compareTo(Taxonomy o)
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 Taxonomy

Modifier and Type	Method and Description
static String[]	WabiTools.obtainLineage(Taxonomy tax)
static String	WabiTools.obtainRank(Taxonomy tax)