Uses of Class
jebl.evolution.taxa.Taxon
Packages that use Taxon
Package
Description
-
Uses of Taxon in jebl.evolution.alignments
Methods in jebl.evolution.alignments that return TaxonMethods in jebl.evolution.alignments that return types with arguments of type TaxonModifier and TypeMethodDescriptionBasicAlignment.getTaxa()
Pattern.getTaxa()
Patterns.getTaxa()
ResampledAlignment.getTaxa()
Methods in jebl.evolution.alignments with parameters of type TaxonModifier and TypeMethodDescriptionBasicAlignment.getSequence
(Taxon taxon) ResampledAlignment.getSequence
(Taxon taxon) Constructors in jebl.evolution.alignments with parameters of type TaxonModifierConstructorDescriptionConsensusSequence
(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 TaxonModifier and TypeMethodDescriptionCharacter.getTaxa()
get a Setof all the taxa for this character ContinuousCharacter.getTaxa()
DiscreteCharacter.getTaxa()
Methods in jebl.evolution.characters with parameters of type TaxonModifier and TypeMethodDescriptionvoid
add a taxon with this charactervoid
void
double
get a value for a taxon containing the characterMethod parameters in jebl.evolution.characters with type arguments of type TaxonModifier and TypeMethodDescriptionvoid
set the taxa for this character with a previously constructed SetConstructor parameters in jebl.evolution.characters with type arguments of type TaxonModifierConstructorDescriptionContinuousCharacter
(String name, String desc, Set<Taxon> taxa) Constructs a basic ContinuousCharacter object with taxa addedDiscreteCharacter
(String name, String desc, int numOfStates, 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 TaxonMethods in jebl.evolution.distances with parameters of type TaxonModifier and TypeMethodDescriptiondouble
BasicDistanceMatrix.getDistance
(Taxon taxonRow, Taxon taxonColumn) Gets the distance between 2 taxadouble
DistanceMatrix.getDistance
(Taxon taxonRow, Taxon taxonColumn) Gets the distance between 2 taxaMethod parameters in jebl.evolution.distances with type arguments of type TaxonModifier and TypeMethodDescriptionBasicDistanceMatrix.getSubmatrix
(Collection<Taxon> taxonSubset) Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).DistanceMatrix.getSubmatrix
(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 -
Uses of Taxon in jebl.evolution.io
Methods in jebl.evolution.io that return types with arguments of type TaxonModifier and TypeMethodDescriptionNexusImporter.parseTaxaBlock()
Parse the next 'TAXA' block encountered in the input.Method parameters in jebl.evolution.io with type arguments of type TaxonModifier and TypeMethodDescriptionNexusImporter.parseCharactersBlock
(List<Taxon> taxonList) Parse the next 'CHARACTERS' block encountered in the input.NexusImporter.parseDataBlock
(List<Taxon> taxonList) Parse the next 'DATA' block encountered in the input.NexusImporter.parseDistancesBlock
(List<Taxon> taxonList) Parse the next 'DISTANCES' block encountered in the input.NexusImporter.parseTreesBlock
(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 TaxonModifier and TypeMethodDescriptionBasicSequence.getTaxon()
CanonicalSequence.getTaxon()
CodonSequence.getTaxon()
FilteredSequence.getTaxon()
Sequence.getTaxon()
Methods in jebl.evolution.sequences with parameters of type TaxonConstructors in jebl.evolution.sequences with parameters of type TaxonModifierConstructorDescriptionBasicSequence
(SequenceType sequenceType, Taxon taxon, 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, 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 TaxonModifier and TypeMethodDescriptionstatic Taxon
A static method that returns a Taxon object with the given name.Methods in jebl.evolution.taxa that return types with arguments of type TaxonMethods in jebl.evolution.taxa with parameters of type TaxonConstructors in jebl.evolution.taxa with parameters of type Taxon -
Uses of Taxon in jebl.evolution.treemetrics
Constructor parameters in jebl.evolution.treemetrics with type arguments of type TaxonModifierConstructorDescriptionCladeHeightMetric
(List<Taxon> taxa) RobinsonsFouldMetric
(List<Taxon> taxa) -
Uses of Taxon in jebl.evolution.trees
Methods in jebl.evolution.trees that return TaxonModifier and TypeMethodDescriptionMethods in jebl.evolution.trees that return types with arguments of type TaxonModifier and TypeMethodDescriptionCladeSystem.getClade
(int index) CompactRootedTree.getTaxa()
FilteredRootedTree.getTaxa()
MutableRootedTree.getTaxa()
RootedFromUnrooted.getTaxa()
RootedSubtree.getTaxa()
SimpleRootedTree.getTaxa()
SimpleTree.getTaxa()
SplitSystem.getTaxa()
get taxon listTree.getTaxa()
Methods in jebl.evolution.trees with parameters of type TaxonModifier and TypeMethodDescriptionstatic ConsensusTreeBuilder
TreeBuilderFactory.buildUnRooted
(Tree[] trees, Taxon outGroup, double supportThreshold, TreeBuilderFactory.ConsensusMethod method) MutableRootedTree.createExternalNode
(Taxon taxon) Creates a new external node with the given taxon.SimpleRootedTree.createExternalNode
(Taxon taxon) Creates a new external node with the given taxon.SimpleTree.createExternalNode
(Taxon taxon) Creates a new external node with the given taxon.void
CompactRootedTree.renameTaxa
(Taxon from, Taxon to) void
FilteredRootedTree.renameTaxa
(Taxon from, Taxon to) void
MutableRootedTree.renameTaxa
(Taxon from, Taxon to) void
RootedFromUnrooted.renameTaxa
(Taxon from, Taxon to) void
RootedSubtree.renameTaxa
(Taxon from, Taxon to) void
SimpleRootedTree.renameTaxa
(Taxon from, Taxon to) void
SimpleTree.renameTaxa
(Taxon from, Taxon to) void
Tree.renameTaxa
(Taxon from, Taxon to) Method parameters in jebl.evolution.trees with type arguments of type TaxonModifier and TypeMethodDescriptionstatic void
get split for branch associated with internal nodestatic SplitSystem
creates a split system from a tree (using a pre-specified order of sequences)RootedTreeUtils.getTipsForTaxa
(RootedTree tree, 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 TaxonModifierConstructorDescriptionRootedSubtree
(RootedTree tree, Set<Taxon> includedTaxa) Make a copy of the given rooted treeSplitSystem
(Collection<Taxon> taxa, int size) TreeBiPartitionInfo
(RootedTree t, List<Taxon> taxa) -
Uses of Taxon in jebl.evolution.treesimulation
Constructor parameters in jebl.evolution.treesimulation with type arguments of type TaxonModifierConstructorDescriptionTreeSimulator
(Collection<Taxon> taxa, String heightAttributeName) A constructor for a given collection of taxa.