Modifier and Type | Method and Description |
---|---|
Taxon |
ConsensusSequence.getTaxon() |
Modifier and Type | Method and Description |
---|---|
java.util.List<Taxon> |
ResampledAlignment.getTaxa() |
java.util.List<Taxon> |
Pattern.getTaxa() |
java.util.List<Taxon> |
BasicAlignment.getTaxa() |
java.util.List<Taxon> |
Patterns.getTaxa() |
Modifier and Type | Method and Description |
---|---|
Sequence |
ResampledAlignment.getSequence(Taxon taxon) |
Sequence |
BasicAlignment.getSequence(Taxon taxon) |
Constructor and 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.
|
Modifier and Type | Method and Description |
---|---|
java.util.Set<Taxon> |
Character.getTaxa()
get a Set
|
java.util.Set<Taxon> |
ContinuousCharacter.getTaxa() |
java.util.Set<Taxon> |
DiscreteCharacter.getTaxa() |
Modifier and Type | Method and Description |
---|---|
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) |
java.lang.Object |
Character.getValue(Taxon taxon)
get a value for a taxon containing the character
|
java.lang.Object |
ContinuousCharacter.getValue(Taxon taxon) |
java.lang.Object |
DiscreteCharacter.getValue(Taxon taxon) |
Modifier and Type | Method and Description |
---|---|
void |
ContinuousCharacter.addTaxa(java.util.Set<Taxon> taxa)
set the taxa for this character with a previously constructed Set
|
Constructor and Description |
---|
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
|
Modifier and Type | Method and Description |
---|---|
java.util.List<Taxon> |
DistanceMatrix.getTaxa() |
java.util.List<Taxon> |
BasicDistanceMatrix.getTaxa() |
Modifier and Type | Method and Description |
---|---|
double |
DistanceMatrix.getDistance(Taxon taxonRow,
Taxon taxonColumn)
Gets the distance between 2 taxa
|
double |
BasicDistanceMatrix.getDistance(Taxon taxonRow,
Taxon taxonColumn)
Gets the distance between 2 taxa
|
Modifier and Type | Method and Description |
---|---|
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).
|
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).
|
Constructor and Description |
---|
BasicDistanceMatrix(java.util.Collection<Taxon> taxa,
double[][] distances) |
Modifier and Type | Method and Description |
---|---|
java.util.List<Taxon> |
NexusImporter.parseTaxaBlock()
Parse the next 'TAXA' block encountered in the input.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
Taxon |
CodonSequence.getTaxon() |
Taxon |
FilteredSequence.getTaxon() |
Taxon |
Sequence.getTaxon() |
Taxon |
CanonicalSequence.getTaxon() |
Taxon |
BasicSequence.getTaxon() |
Modifier and Type | Method and Description |
---|---|
Sequence |
Sequences.getSequence(Taxon taxon) |
Constructor and 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 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
|
CodonSequence(Taxon taxon,
State[] states)
Creates a sequence with a name corresponding to the taxon name
|
Modifier and Type | Method and Description |
---|---|
static Taxon |
Taxon.getTaxon(java.lang.String name)
A static method that returns a Taxon object with the given name.
|
Modifier and Type | Method and Description |
---|---|
static java.util.Set<Taxon> |
Taxon.getAllTaxa() |
Modifier and Type | Method and Description |
---|---|
boolean |
Taxon.equals(Taxon t) |
Constructor and Description |
---|
MissingTaxonException(Taxon taxon) |
Constructor and Description |
---|
CladeHeightMetric(java.util.List<Taxon> taxa) |
RobinsonsFouldMetric(java.util.List<Taxon> taxa) |
Modifier and Type | Method and Description |
---|---|
Taxon |
RootedSubtree.getTaxon(Node node) |
Taxon |
SimpleRootedTree.getTaxon(Node node) |
Taxon |
Tree.getTaxon(Node node) |
Taxon |
RootedFromUnrooted.getTaxon(Node node) |
Taxon |
CompactRootedTree.getTaxon(Node node) |
Taxon |
FilteredRootedTree.getTaxon(Node node) |
Taxon |
MutableRootedTree.getTaxon(Node node) |
Taxon |
SimpleTree.getTaxon(Node node) |
Modifier and Type | Method and Description |
---|---|
java.util.Set<Taxon> |
CladeSystem.getClade(int index) |
java.util.Set<Taxon> |
RootedSubtree.getTaxa() |
java.util.Set<Taxon> |
SimpleRootedTree.getTaxa() |
java.util.Set<Taxon> |
Tree.getTaxa() |
java.util.Set<Taxon> |
RootedFromUnrooted.getTaxa() |
java.util.Set<Taxon> |
CompactRootedTree.getTaxa() |
java.util.Set<Taxon> |
FilteredRootedTree.getTaxa() |
java.util.List<Taxon> |
SplitSystem.getTaxa()
get taxon list
|
java.util.Set<Taxon> |
MutableRootedTree.getTaxa() |
java.util.Set<Taxon> |
SimpleTree.getTaxa() |
Modifier and Type | Method and Description |
---|---|
static ConsensusTreeBuilder |
TreeBuilderFactory.buildUnRooted(Tree[] trees,
Taxon outGroup,
double supportThreshold,
TreeBuilderFactory.ConsensusMethod method) |
Node |
SimpleRootedTree.createExternalNode(Taxon taxon)
Creates a new external node with the given taxon.
|
Node |
MutableRootedTree.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 |
RootedSubtree.getNode(Taxon taxon) |
Node |
SimpleRootedTree.getNode(Taxon taxon) |
Node |
Tree.getNode(Taxon taxon) |
Node |
RootedFromUnrooted.getNode(Taxon taxon) |
Node |
CompactRootedTree.getNode(Taxon taxon) |
Node |
FilteredRootedTree.getNode(Taxon taxon) |
Node |
MutableRootedTree.getNode(Taxon taxon) |
Node |
SimpleTree.getNode(Taxon taxon) |
void |
RootedSubtree.renameTaxa(Taxon from,
Taxon to) |
void |
SimpleRootedTree.renameTaxa(Taxon from,
Taxon to) |
void |
Tree.renameTaxa(Taxon from,
Taxon to) |
void |
RootedFromUnrooted.renameTaxa(Taxon from,
Taxon to) |
void |
CompactRootedTree.renameTaxa(Taxon from,
Taxon to) |
void |
FilteredRootedTree.renameTaxa(Taxon from,
Taxon to) |
void |
MutableRootedTree.renameTaxa(Taxon from,
Taxon to) |
void |
SimpleTree.renameTaxa(Taxon from,
Taxon to) |
Modifier and Type | Method and Description |
---|---|
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 and Description |
---|
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) |
Constructor and Description |
---|
TreeSimulator(java.util.Collection<Taxon> taxa,
java.lang.String heightAttributeName)
A constructor for a given collection of taxa.
|
http://code.google.com/p/jebl2/