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.treemetrics   
jebl.evolution.trees   
jebl.evolution.treesimulation   
 

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

Methods in jebl.evolution.alignments with parameters of type Taxon
 Sequence ResampledAlignment.getSequence(Taxon taxon)
           
 Sequence BasicAlignment.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
 java.util.Set<Taxon> DiscreteCharacter.getTaxa()
           
 java.util.Set<Taxon> ContinuousCharacter.getTaxa()
           
 java.util.Set<Taxon> Character.getTaxa()
          get a Set of all the taxa for this character
 

Methods in jebl.evolution.characters with parameters of type Taxon
 void DiscreteCharacter.addTaxon(Taxon taxon)
           
 void ContinuousCharacter.addTaxon(Taxon taxon)
           
 void Character.addTaxon(Taxon taxon)
          add a taxon with this character
 double ContinuousCharacter.getSE(Taxon taxon)
           
 java.lang.Object DiscreteCharacter.getValue(Taxon taxon)
           
 java.lang.Object ContinuousCharacter.getValue(Taxon taxon)
           
 java.lang.Object Character.getValue(Taxon taxon)
          get a value for a taxon containing the character
 

Method parameters in jebl.evolution.characters with type arguments of type Taxon
 void ContinuousCharacter.addTaxa(java.util.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(java.lang.String name, java.lang.String desc, java.util.Set<Taxon> taxa)
          Constructs a basic ContinuousCharacter object with taxa added
DiscreteCharacter(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
 java.util.List<Taxon> BasicDistanceMatrix.getTaxa()
           
 java.util.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(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
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
 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
 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
 Taxon CanonicalSequence.getTaxon()
           
 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, 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 name
CanonicalSequence(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 name
 

Uses of Taxon in jebl.evolution.taxa
 

Methods in jebl.evolution.taxa that return Taxon
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
static java.util.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.treemetrics
 

Constructor parameters in jebl.evolution.treemetrics with type arguments of type Taxon
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
 Taxon RootedFromUnrooted.getTaxon(Node node)
           
 Taxon MutableRootedTree.getTaxon(Node node)
           
 Taxon CompactRootedTree.getTaxon(Node node)
           
 Taxon SimpleRootedTree.getTaxon(Node node)
           
 Taxon Tree.getTaxon(Node node)
           
 Taxon FilteredRootedTree.getTaxon(Node node)
           
 Taxon SimpleTree.getTaxon(Node node)
           
 Taxon RootedSubtree.getTaxon(Node node)
           
 

Methods in jebl.evolution.trees that return types with arguments of type Taxon
 java.util.Set<Taxon> CladeSystem.getClade(int index)
           
 java.util.List<Taxon> SplitSystem.getTaxa()
          get taxon list
 java.util.Set<Taxon> RootedFromUnrooted.getTaxa()
           
 java.util.Set<Taxon> MutableRootedTree.getTaxa()
           
 java.util.Set<Taxon> CompactRootedTree.getTaxa()
           
 java.util.Set<Taxon> SimpleRootedTree.getTaxa()
           
 java.util.Set<Taxon> Tree.getTaxa()
           
 java.util.Set<Taxon> FilteredRootedTree.getTaxa()
           
 java.util.Set<Taxon> SimpleTree.getTaxa()
           
 java.util.Set<Taxon> RootedSubtree.getTaxa()
           
 

Methods in jebl.evolution.trees with parameters of type Taxon
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 RootedFromUnrooted.getNode(Taxon taxon)
           
 Node MutableRootedTree.getNode(Taxon taxon)
           
 Node CompactRootedTree.getNode(Taxon taxon)
           
 Node SimpleRootedTree.getNode(Taxon taxon)
           
 Node Tree.getNode(Taxon taxon)
           
 Node FilteredRootedTree.getNode(Taxon taxon)
           
 Node SimpleTree.getNode(Taxon taxon)
           
 Node RootedSubtree.getNode(Taxon taxon)
           
 void RootedFromUnrooted.renameTaxa(Taxon from, Taxon to)
           
 void MutableRootedTree.renameTaxa(Taxon from, Taxon to)
           
 void CompactRootedTree.renameTaxa(Taxon from, Taxon to)
           
 void SimpleRootedTree.renameTaxa(Taxon from, Taxon to)
           
 void Tree.renameTaxa(Taxon from, Taxon to)
           
 void FilteredRootedTree.renameTaxa(Taxon from, Taxon to)
           
 void SimpleTree.renameTaxa(Taxon from, Taxon to)
           
 void RootedSubtree.renameTaxa(Taxon from, Taxon to)
           
 

Method parameters in jebl.evolution.trees with type arguments of type Taxon
static void SplitUtils.getSplit(java.util.List<Taxon> taxa, Tree tree, Edge edge, boolean[] split)
          get split for branch associated with internal node
static 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
RootedSubtree(RootedTree tree, java.util.Set<Taxon> includedTaxa)
          Make a copy of the given rooted tree
SplitSystem(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
TreeSimulator(java.util.Collection<Taxon> taxa, java.lang.String heightAttributeName)
          A constructor for a given collection of taxa.
 



http://code.google.com/p/jebl2/