Uses of Class
org.forester.phylogeny.data.Taxonomy
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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 -
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Uses of Taxonomy in org.forester.analysis
Methods in org.forester.analysis with parameters of type Taxonomy Modifier and Type Method Description static UniProtTaxonomy
TaxonomyDataManager. obtainUniProtTaxonomy(Taxonomy tax, java.lang.Object query, org.forester.analysis.TaxonomyDataManager.QUERY_TYPE qt)
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Uses of Taxonomy in org.forester.archaeopteryx
Methods in org.forester.archaeopteryx that return types with arguments of type Taxonomy Modifier and Type Method Description static java.util.Set<Taxonomy>
AptxUtil. obtainAllDistinctTaxonomies(PhylogenyNode node)
static java.util.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 Description Taxonomy
TaxonomyParser. parse(XmlElement element)
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Uses of Taxonomy in org.forester.phylogeny
Methods in org.forester.phylogeny that return Taxonomy Modifier and Type Method 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 Description static java.util.Map<Taxonomy,java.lang.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 Description static boolean
PhylogenyMethods. isTaxonomyHasIdentifierOfGivenProvider(Taxonomy tax, java.lang.String[] providers)
Method parameters in org.forester.phylogeny with type arguments of type Taxonomy Modifier and Type Method Description static void
PhylogenyMethods. deleteExternalNodesPositiveSelectionT(java.util.List<Taxonomy> species_to_keep, Phylogeny phy)
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Uses of Taxonomy in org.forester.phylogeny.data
Methods in org.forester.phylogeny.data that return Taxonomy Modifier and Type Method 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 Description java.util.List<Taxonomy>
NodeData. getTaxonomies()
Methods in org.forester.phylogeny.data with parameters of type Taxonomy Modifier and Type Method 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 Description static java.lang.String[]
WabiTools. obtainLineage(Taxonomy tax)
static java.lang.String
WabiTools. obtainRank(Taxonomy tax)
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