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 Taxon
ConsensusSequence. 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 Sequence
BasicAlignment. getSequence(Taxon taxon)
Sequence
ResampledAlignment. 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 void
Character. addTaxon(Taxon taxon)
add a taxon with this charactervoid
ContinuousCharacter. addTaxon(Taxon taxon)
void
DiscreteCharacter. addTaxon(Taxon taxon)
double
ContinuousCharacter. getSE(Taxon taxon)
java.lang.Object
Character. getValue(Taxon taxon)
get a value for a taxon containing the characterjava.lang.Object
ContinuousCharacter. getValue(Taxon taxon)
java.lang.Object
DiscreteCharacter. getValue(Taxon taxon)
Method parameters in jebl.evolution.characters with type arguments of type Taxon Modifier and Type Method Description void
ContinuousCharacter. 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 double
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 Taxon Modifier and Type Method Description DistanceMatrix
BasicDistanceMatrix. 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).DistanceMatrix
DistanceMatrix. 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)
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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.DistanceMatrix
NexusImporter. 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 Taxon
BasicSequence. getTaxon()
Taxon
CanonicalSequence. getTaxon()
Taxon
CodonSequence. getTaxon()
Taxon
FilteredSequence. getTaxon()
Taxon
Sequence. getTaxon()
Methods in jebl.evolution.sequences with parameters of type Taxon Modifier and Type Method Description Sequence
Sequences. 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 Taxon
Taxon. 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 boolean
Taxon. equals(Taxon t)
Constructors in jebl.evolution.taxa with parameters of type Taxon Constructor Description MissingTaxonException(Taxon taxon)
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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)
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Uses of Taxon in jebl.evolution.trees
Methods in jebl.evolution.trees that return Taxon Modifier and Type Method Description Taxon
CompactRootedTree. getTaxon(Node node)
Taxon
FilteredRootedTree. getTaxon(Node node)
Taxon
MutableRootedTree. getTaxon(Node node)
Taxon
RootedFromUnrooted. getTaxon(Node node)
Taxon
RootedSubtree. 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 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 ConsensusTreeBuilder
TreeBuilderFactory. buildUnRooted(Tree[] trees, Taxon outGroup, double supportThreshold, TreeBuilderFactory.ConsensusMethod method)
Node
MutableRootedTree. createExternalNode(Taxon taxon)
Creates a new external node with the given 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
RootedSubtree. getNode(Taxon taxon)
Node
SimpleRootedTree. getNode(Taxon taxon)
Node
SimpleTree. getNode(Taxon taxon)
Node
Tree. getNode(Taxon 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 Taxon Modifier and Type Method Description static void
SplitUtils. getSplit(java.util.List<Taxon> taxa, Tree tree, Edge edge, boolean[] split)
get split for branch associated with internal nodestatic SplitSystem
SplitUtils. 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)
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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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