Uses of Class
jebl.evolution.taxa.Taxon
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Uses of Taxon in jebl.evolution.alignments
Methods in jebl.evolution.alignments that return Taxon Modifier and Type Method Description TaxonConsensusSequence. getTaxon()Methods in jebl.evolution.alignments that return types with arguments of type Taxon Modifier and Type Method Description java.util.List<Taxon>BasicAlignment. getTaxa()java.util.List<Taxon>Pattern. getTaxa()java.util.List<Taxon>Patterns. getTaxa()java.util.List<Taxon>ResampledAlignment. getTaxa()Methods in jebl.evolution.alignments with parameters of type Taxon Modifier and Type Method Description SequenceBasicAlignment. getSequence(Taxon taxon)SequenceResampledAlignment. getSequence(Taxon taxon)Constructors in jebl.evolution.alignments with parameters of type Taxon Constructor Description ConsensusSequence(Taxon taxon, Alignment source)Creates a FilteredSequence wrapper to the given source sequence.ConsensusSequence(Taxon taxon, Alignment source, boolean includeAmbiguities)Creates a FilteredSequence wrapper to the given source sequence. -
Uses of Taxon in jebl.evolution.characters
Methods in jebl.evolution.characters that return types with arguments of type Taxon Modifier and Type Method Description java.util.Set<Taxon>Character. getTaxa()get a Setof all the taxa for this character java.util.Set<Taxon>ContinuousCharacter. getTaxa()java.util.Set<Taxon>DiscreteCharacter. getTaxa()Methods in jebl.evolution.characters with parameters of type Taxon Modifier and Type Method Description voidCharacter. addTaxon(Taxon taxon)add a taxon with this charactervoidContinuousCharacter. addTaxon(Taxon taxon)voidDiscreteCharacter. addTaxon(Taxon taxon)doubleContinuousCharacter. getSE(Taxon taxon)java.lang.ObjectCharacter. getValue(Taxon taxon)get a value for a taxon containing the characterjava.lang.ObjectContinuousCharacter. getValue(Taxon taxon)java.lang.ObjectDiscreteCharacter. getValue(Taxon taxon)Method parameters in jebl.evolution.characters with type arguments of type Taxon Modifier and Type Method Description voidContinuousCharacter. addTaxa(java.util.Set<Taxon> taxa)set the taxa for this character with a previously constructed SetConstructor parameters in jebl.evolution.characters with type arguments of type Taxon Constructor Description ContinuousCharacter(java.lang.String name, java.lang.String desc, java.util.Set<Taxon> taxa)Constructs a basic ContinuousCharacter object with taxa addedDiscreteCharacter(java.lang.String name, java.lang.String desc, int numOfStates, java.util.Set<Taxon> taxa)Constructs a basic DiscreteCharacter object with taxa -
Uses of Taxon in jebl.evolution.distances
Methods in jebl.evolution.distances that return types with arguments of type Taxon Modifier and Type Method Description java.util.List<Taxon>BasicDistanceMatrix. getTaxa()java.util.List<Taxon>DistanceMatrix. getTaxa()Methods in jebl.evolution.distances with parameters of type Taxon Modifier and Type Method Description doubleBasicDistanceMatrix. getDistance(Taxon taxonRow, Taxon taxonColumn)Gets the distance between 2 taxadoubleDistanceMatrix. getDistance(Taxon taxonRow, Taxon taxonColumn)Gets the distance between 2 taxaMethod parameters in jebl.evolution.distances with type arguments of type Taxon Modifier and Type Method Description DistanceMatrixBasicDistanceMatrix. getSubmatrix(java.util.Collection<Taxon> taxonSubset)Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).DistanceMatrixDistanceMatrix. getSubmatrix(java.util.Collection<Taxon> taxa)Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).Constructor parameters in jebl.evolution.distances with type arguments of type Taxon Constructor Description BasicDistanceMatrix(java.util.Collection<Taxon> taxa, double[][] distances) -
Uses of Taxon in jebl.evolution.io
Methods in jebl.evolution.io that return types with arguments of type Taxon Modifier and Type Method Description java.util.List<Taxon>NexusImporter. parseTaxaBlock()Parse the next 'TAXA' block encountered in the input.Method parameters in jebl.evolution.io with type arguments of type Taxon Modifier and Type Method Description java.util.List<Sequence>NexusImporter. parseCharactersBlock(java.util.List<Taxon> taxonList)Parse the next 'CHARACTERS' block encountered in the input.java.util.List<Sequence>NexusImporter. parseDataBlock(java.util.List<Taxon> taxonList)Parse the next 'DATA' block encountered in the input.DistanceMatrixNexusImporter. parseDistancesBlock(java.util.List<Taxon> taxonList)Parse the next 'DISTANCES' block encountered in the input.java.util.List<Tree>NexusImporter. parseTreesBlock(java.util.List<Taxon> taxonList)Parse the next 'TREES' block encountered in the input. -
Uses of Taxon in jebl.evolution.sequences
Methods in jebl.evolution.sequences that return Taxon Modifier and Type Method Description TaxonBasicSequence. getTaxon()TaxonCanonicalSequence. getTaxon()TaxonCodonSequence. getTaxon()TaxonFilteredSequence. getTaxon()TaxonSequence. getTaxon()Methods in jebl.evolution.sequences with parameters of type Taxon Modifier and Type Method Description SequenceSequences. getSequence(Taxon taxon)Constructors in jebl.evolution.sequences with parameters of type Taxon Constructor Description BasicSequence(SequenceType sequenceType, Taxon taxon, java.lang.CharSequence sequenceString)Creates a sequence with a name corresponding to the taxon name.BasicSequence(SequenceType sequenceType, Taxon taxon, State[] states)Creates a sequence with a name corresponding to the taxon nameCanonicalSequence(SequenceType sequenceType, Taxon taxon, java.lang.CharSequence sequenceString)Creates a sequence with a name corresponding to the taxon name.CanonicalSequence(SequenceType sequenceType, Taxon taxon, State[] states)Creates a sequence with a name corresponding to the taxon nameCodonSequence(Taxon taxon, State[] states)Creates a sequence with a name corresponding to the taxon name -
Uses of Taxon in jebl.evolution.taxa
Methods in jebl.evolution.taxa that return Taxon Modifier and Type Method Description static TaxonTaxon. getTaxon(java.lang.String name)A static method that returns a Taxon object with the given name.Methods in jebl.evolution.taxa that return types with arguments of type Taxon Modifier and Type Method Description static java.util.Set<Taxon>Taxon. getAllTaxa()Methods in jebl.evolution.taxa with parameters of type Taxon Modifier and Type Method Description booleanTaxon. equals(Taxon t)Constructors in jebl.evolution.taxa with parameters of type Taxon Constructor Description MissingTaxonException(Taxon taxon) -
Uses of Taxon in jebl.evolution.treemetrics
Constructor parameters in jebl.evolution.treemetrics with type arguments of type Taxon Constructor Description CladeHeightMetric(java.util.List<Taxon> taxa)RobinsonsFouldMetric(java.util.List<Taxon> taxa) -
Uses of Taxon in jebl.evolution.trees
Methods in jebl.evolution.trees that return Taxon Modifier and Type Method Description TaxonCompactRootedTree. getTaxon(Node node)TaxonFilteredRootedTree. getTaxon(Node node)TaxonMutableRootedTree. getTaxon(Node node)TaxonRootedFromUnrooted. getTaxon(Node node)TaxonRootedSubtree. getTaxon(Node node)TaxonSimpleRootedTree. getTaxon(Node node)TaxonSimpleTree. getTaxon(Node node)TaxonTree. getTaxon(Node node)Methods in jebl.evolution.trees that return types with arguments of type Taxon Modifier and Type Method Description java.util.Set<Taxon>CladeSystem. getClade(int index)java.util.Set<Taxon>CompactRootedTree. getTaxa()java.util.Set<Taxon>FilteredRootedTree. getTaxa()java.util.Set<Taxon>MutableRootedTree. getTaxa()java.util.Set<Taxon>RootedFromUnrooted. getTaxa()java.util.Set<Taxon>RootedSubtree. getTaxa()java.util.Set<Taxon>SimpleRootedTree. getTaxa()java.util.Set<Taxon>SimpleTree. getTaxa()java.util.List<Taxon>SplitSystem. getTaxa()get taxon listjava.util.Set<Taxon>Tree. getTaxa()Methods in jebl.evolution.trees with parameters of type Taxon Modifier and Type Method Description static ConsensusTreeBuilderTreeBuilderFactory. buildUnRooted(Tree[] trees, Taxon outGroup, double supportThreshold, TreeBuilderFactory.ConsensusMethod method)NodeMutableRootedTree. createExternalNode(Taxon taxon)Creates a new external node with the given taxon.NodeSimpleRootedTree. createExternalNode(Taxon taxon)Creates a new external node with the given taxon.NodeSimpleTree. createExternalNode(Taxon taxon)Creates a new external node with the given taxon.NodeCompactRootedTree. getNode(Taxon taxon)NodeFilteredRootedTree. getNode(Taxon taxon)NodeMutableRootedTree. getNode(Taxon taxon)NodeRootedFromUnrooted. getNode(Taxon taxon)NodeRootedSubtree. getNode(Taxon taxon)NodeSimpleRootedTree. getNode(Taxon taxon)NodeSimpleTree. getNode(Taxon taxon)NodeTree. getNode(Taxon taxon)voidCompactRootedTree. renameTaxa(Taxon from, Taxon to)voidFilteredRootedTree. renameTaxa(Taxon from, Taxon to)voidMutableRootedTree. renameTaxa(Taxon from, Taxon to)voidRootedFromUnrooted. renameTaxa(Taxon from, Taxon to)voidRootedSubtree. renameTaxa(Taxon from, Taxon to)voidSimpleRootedTree. renameTaxa(Taxon from, Taxon to)voidSimpleTree. renameTaxa(Taxon from, Taxon to)voidTree. renameTaxa(Taxon from, Taxon to)Method parameters in jebl.evolution.trees with type arguments of type Taxon Modifier and Type Method Description static voidSplitUtils. getSplit(java.util.List<Taxon> taxa, Tree tree, Edge edge, boolean[] split)get split for branch associated with internal nodestatic SplitSystemSplitUtils. getSplits(java.util.List<Taxon> taxa, Tree tree)creates a split system from a tree (using a pre-specified order of sequences)static java.util.Set<Node>RootedTreeUtils. getTipsForTaxa(RootedTree tree, java.util.Collection<Taxon> taxa)Gets a set of external nodes that correspond to the given taxa.Constructor parameters in jebl.evolution.trees with type arguments of type Taxon Constructor Description RootedSubtree(RootedTree tree, java.util.Set<Taxon> includedTaxa)Make a copy of the given rooted treeSplitSystem(java.util.Collection<Taxon> taxa, int size)TreeBiPartitionInfo(RootedTree t, java.util.List<Taxon> taxa) -
Uses of Taxon in jebl.evolution.treesimulation
Constructor parameters in jebl.evolution.treesimulation with type arguments of type Taxon Constructor Description TreeSimulator(java.util.Collection<Taxon> taxa, java.lang.String heightAttributeName)A constructor for a given collection of taxa.
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