Uses of Class
jebl.evolution.taxa.Taxon

Packages that use Taxon

jebl.evolution.alignments
jebl.evolution.characters
jebl.evolution.distances
jebl.evolution.io
jebl.evolution.sequences
jebl.evolution.taxa
jebl.evolution.trees
jebl.gui.trees.treeviewer
jebl.gui.trees.treeviewer.decorators

Uses of Taxon in jebl.evolution.alignments

Methods in jebl.evolution.alignments that return Taxon

Taxon

ConsensusSequence.getTaxon()

Methods in jebl.evolution.alignments that return types with arguments of type Taxon

List<Taxon>	BasicAlignment.getTaxa()
List<Taxon>	Pattern.getTaxa()
List<Taxon>	Patterns.getTaxa()
List<Taxon>	ResampledAlignment.getTaxa()

Methods in jebl.evolution.alignments with parameters of type Taxon

Sequence	BasicAlignment.getSequence(Taxon taxon)
Sequence	ResampledAlignment.getSequence(Taxon taxon)

Constructors in jebl.evolution.alignments with parameters of type Taxon

ConsensusSequence(Taxon taxon, Alignment source)
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

Set<Taxon>	Character.getTaxa() get a Set of all the taxa for this character
Set<Taxon>	ContinuousCharacter.getTaxa()
Set<Taxon>	DiscreteCharacter.getTaxa()

Methods in jebl.evolution.characters with parameters of type Taxon

void	Character.addTaxon(Taxon taxon) add a taxon with this character
void	ContinuousCharacter.addTaxon(Taxon taxon)
void	DiscreteCharacter.addTaxon(Taxon taxon)
double	ContinuousCharacter.getSE(Taxon taxon)
Object	Character.getValue(Taxon taxon) get a value for a taxon containing the character
Object	ContinuousCharacter.getValue(Taxon taxon)
Object	DiscreteCharacter.getValue(Taxon taxon)

Method parameters in jebl.evolution.characters with type arguments of type Taxon

void	ContinuousCharacter.addTaxa(Set<Taxon> taxa) set the taxa for this character with a previously constructed Set

Constructor parameters in jebl.evolution.characters with type arguments of type Taxon

ContinuousCharacter(String name, String desc, Set<Taxon> taxa)
Constructs a basic ContinuousCharacter object with taxa added

DiscreteCharacter(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 Taxon

List<Taxon>	BasicDistanceMatrix.getTaxa()
List<Taxon>	DistanceMatrix.getTaxa()

Methods in jebl.evolution.distances with parameters of type Taxon

double	BasicDistanceMatrix.getDistance(Taxon taxonRow, Taxon taxonColumn) Gets the distance between 2 taxa
double	DistanceMatrix.getDistance(Taxon taxonRow, Taxon taxonColumn) Gets the distance between 2 taxa

Method parameters in jebl.evolution.distances with type arguments of type Taxon

DistanceMatrix	BasicDistanceMatrix.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	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

BasicDistanceMatrix(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

List<Taxon>

NexusImporter.parseTaxaBlock() Parses a 'TAXA' block.

Method parameters in jebl.evolution.io with type arguments of type Taxon

List<Sequence>	NexusImporter.parseCharactersBlock(List<Taxon> taxonList) Parses a 'CHARACTERS' block.
List<Sequence>	NexusImporter.parseDataBlock(List<Taxon> taxonList) Parses a 'DATA' block.
DistanceMatrix	NexusImporter.parseDistancesBlock(List<Taxon> taxonList)
List<Tree>	NexusImporter.parseTreesBlock(List<Taxon> taxonList) Parses a 'TREES' block.

Uses of Taxon in jebl.evolution.sequences

Methods in jebl.evolution.sequences that return Taxon

Taxon	BasicSequence.getTaxon()
Taxon	FilteredSequence.getTaxon()
Taxon	Sequence.getTaxon()

Methods in jebl.evolution.sequences with parameters of type Taxon

Sequence

Sequences.getSequence(Taxon taxon)

Constructors in jebl.evolution.sequences with parameters of type Taxon

BasicSequence(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 name

Uses of Taxon in jebl.evolution.taxa

Methods in jebl.evolution.taxa that return Taxon

static Taxon

Taxon.getTaxon(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

static Set<Taxon>

Taxon.getAllTaxa()

Methods in jebl.evolution.taxa with parameters of type Taxon

boolean

Taxon.equals(Taxon t)

Constructors in jebl.evolution.taxa with parameters of type Taxon

MissingTaxonException(Taxon taxon)

Uses of Taxon in jebl.evolution.trees

Fields in jebl.evolution.trees with type parameters of type Taxon

protected List<Taxon>

ConsensusTreeBuilder.taxons List of common taxa in all trees

Methods in jebl.evolution.trees that return Taxon

Taxon	CompactRootedTree.getTaxon(Node node)
Taxon	FilteredRootedTree.getTaxon(Node node)
Taxon	MutableRootedTree.getTaxon(Node node)
Taxon	RootedFromUnrooted.getTaxon(Node node)
Taxon	SimpleRootedTree.getTaxon(Node node)
Taxon	SimpleTree.getTaxon(Node node)
Taxon	Tree.getTaxon(Node node)

Methods in jebl.evolution.trees that return types with arguments of type Taxon

Set<Taxon>	CladeSystem.getClade(int index)
Set<Taxon>	CompactRootedTree.getTaxa()
Set<Taxon>	FilteredRootedTree.getTaxa()
Set<Taxon>	MutableRootedTree.getTaxa()
Set<Taxon>	RootedFromUnrooted.getTaxa()
Set<Taxon>	SimpleRootedTree.getTaxa()
Set<Taxon>	SimpleTree.getTaxa()
List<Taxon>	SplitSystem.getTaxa() get taxon list
Set<Taxon>	Tree.getTaxa()

Methods in jebl.evolution.trees with parameters of type Taxon

static ConsensusTreeBuilder	TreeBuilderFactory.buildUnRooted(Tree[] trees, Taxon outGroup, double supportThreshold, TreeBuilderFactory.ConsensusMethod method)
protected abstract Node	ClusteringTreeBuilder.createExternalNode(Taxon taxon)
Node	MutableRootedTree.createExternalNode(Taxon taxon) Creates a new external node with the given taxon.
protected Node	NeighborJoiningTreeBuilder.createExternalNode(Taxon taxon)
Node	SimpleRootedTree.createExternalNode(Taxon taxon) Creates a new external node with the given taxon.
Node	SimpleTree.createExternalNode(Taxon taxon) Creates a new external node with the given taxon.
Node	CompactRootedTree.getNode(Taxon taxon)
Node	FilteredRootedTree.getNode(Taxon taxon)
Node	MutableRootedTree.getNode(Taxon taxon)
Node	RootedFromUnrooted.getNode(Taxon taxon)
Node	SimpleRootedTree.getNode(Taxon taxon)
Node	SimpleTree.getNode(Taxon taxon)
Node	Tree.getNode(Taxon taxon)

Method parameters in jebl.evolution.trees with type arguments of type Taxon

static void	SplitUtils.getSplit(List<Taxon> taxa, Tree tree, Edge edge, boolean[] split) get split for branch associated with internal node
static SplitSystem	SplitUtils.getSplits(List<Taxon> taxa, Tree tree) creates a split system from a tree (using a pre-specified order of sequences)
static Set<Node>	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 Taxon

SplitSystem(Collection<Taxon> taxa, int size)

TreeSimulator(IntervalGenerator intervalGenerator, Collection<Taxon> taxa, String heightAttributeName)
A constructor for a given collection of taxa.

Uses of Taxon in jebl.gui.trees.treeviewer

Methods in jebl.gui.trees.treeviewer that return types with arguments of type Taxon

Set<Taxon>

TreePane.getSelectedTaxa()

Methods in jebl.gui.trees.treeviewer with parameters of type Taxon

void	TreePane.addSelectedTaxon(Taxon selectedTaxon)
void	TreePane.setSelectedTaxon(Taxon selectedTaxon)

Uses of Taxon in jebl.gui.trees.treeviewer.decorators

Methods in jebl.gui.trees.treeviewer.decorators with parameters of type Taxon

Font	TaxonDecorator.getTaxonFont(Taxon taxon, Font font)
Paint	TaxonDecorator.getTaxonPaint(Taxon taxon)