Package | Description |
---|---|
pal.alignment |
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
|
pal.distance |
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
|
pal.gui |
GUI components for some special objects (e.g., trees).
|
pal.misc |
Classes that don't fit elsewhere ;^)
|
pal.tree |
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
|
pal.xml |
Utility classes for converting PAL objects to and from XML documents.
|
Modifier and Type | Method and Description |
---|---|
Identifier |
SimpleCharacterAlignment.getIdentifier(int i) |
Identifier |
AbstractAlignment.getIdentifier(int i) |
Modifier and Type | Method and Description |
---|---|
void |
SimpleCharacterAlignment.setIdentifier(int i,
Identifier ident) |
void |
AbstractAlignment.setIdentifier(int i,
Identifier ident) |
Constructor and Description |
---|
MultiLocusAnnotatedAlignment(Identifier[] ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt) |
SimpleAlignment(Identifier[] ids,
java.lang.String[] sequences,
DataType dt) |
SimpleAlignment(Identifier[] ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt) |
SimpleAlignment(Identifier id,
java.lang.String sequence,
DataType dataType)
Constructor taking single identifier and sequence.
|
SimpleAnnotatedAlignment(Identifier[] ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt)
This constructor creates a basic SimpleAnnotatedAlignment.
|
SimpleCharacterAlignment(Identifier[] ids,
double[][] traitValues,
java.lang.String[] traitNames)
Constructor for SimpleCharacterAlignment.
|
Modifier and Type | Method and Description |
---|---|
Identifier |
DistanceMatrix.getIdentifier(int i) |
Modifier and Type | Method and Description |
---|---|
void |
DistanceMatrix.setIdentifier(int i,
Identifier ident) |
Modifier and Type | Method and Description |
---|---|
void |
NameColouriser.addMapping(Identifier id,
java.awt.Color colour) |
void |
LayoutTracker.addMapping(Identifier id,
java.awt.Rectangle bounds) |
java.awt.Rectangle |
LayoutTracker.getBounds(Identifier id) |
LabelDisplayer |
NameColouriser.getDisplay(Identifier id,
LabelDisplayer defaultDisplay) |
Constructor and Description |
---|
NameColouriser(Identifier name,
java.awt.Color colour) |
Modifier and Type | Field and Description |
---|---|
static Identifier |
Identifier.ANONYMOUS |
Modifier and Type | Method and Description |
---|---|
Identifier |
IdGroup.getIdentifier(int i)
Returns the ith identifier.
|
Identifier |
TimeOrderCharacterData.getIdentifier(int i) |
Identifier |
SimpleIdGroup.getIdentifier(int i)
Returns the ith identifier.
|
static Identifier[] |
Identifier.getIdentifiers(IdGroup idGroup)
Translates an IdGroup into an array of identifiers
|
static Identifier[] |
Identifier.getIdentifiers(java.lang.String[] names)
Translates an an array of strings into an array of identifiers
|
Identifier |
LabelMapping.getLabelIdentifier(Identifier id) |
Identifier[] |
TimeOrderCharacterData.getSubgroupMembers(int subgroupNumber) |
Modifier and Type | Method and Description |
---|---|
void |
LabelMapping.addMapping(Identifier id,
java.lang.String label) |
java.lang.String |
LabelMapping.getLabel(Identifier id) |
java.lang.String |
LabelMapping.getLabel(Identifier id,
java.lang.String defaultLabel) |
Identifier |
LabelMapping.getLabelIdentifier(Identifier id) |
static java.lang.String[] |
Identifier.getNames(Identifier[] ids)
Translates an array of identifiers into an array of strings
|
static java.lang.String[] |
Identifier.getNames(Identifier[] ids,
int toIgnore)
Translates an array of identifiers into an array of strings, with optional removal of particular identifier
|
int |
TimeOrderCharacterData.getTimeOrdinal(Identifier taxonName) |
void |
IdGroup.setIdentifier(int i,
Identifier id)
Sets the ith identifier.
|
void |
TimeOrderCharacterData.setIdentifier(int i,
Identifier ident) |
void |
SimpleIdGroup.setIdentifier(int i,
Identifier id)
Sets the ith identifier.
|
Constructor and Description |
---|
SimpleIdGroup(Identifier[] id)
Constructor taking an array of identifiers.
|
Modifier and Type | Method and Description |
---|---|
Identifier |
Node.getIdentifier()
Returns the identifier for this node.
|
Identifier |
SimpleNode.getIdentifier()
Returns the identifier for this node.
|
Identifier |
ParameterizedTree.ParameterizedTreeBase.getIdentifier(int i) |
Identifier |
Tree.TreeBase.getIdentifier(int i) |
Identifier |
SimpleTree.getIdentifier(int i) |
Modifier and Type | Method and Description |
---|---|
static Node |
NodeFactory.createNode(Identifier id)
create a node, with a specified identifier
|
static Node |
NodeFactory.createNode(Identifier id,
double height)
create a node, with a specified identifier
|
static Node |
NodeFactory.createNodeBranchLength(double branchLength,
Identifier id)
create a node, with a specified identifier
|
static Node |
NodeUtils.findByIdentifier(Node node,
Identifier identifier)
Returns the first node in this tree that has the
required identifier.
|
static Node[] |
NodeUtils.findByIdentifier(Node node,
Identifier[] identifiers)
Returns the first nodes in this tree that has the
required identifiers.
|
void |
Node.setIdentifier(Identifier id)
Set identifier for this node.
|
void |
SimpleNode.setIdentifier(Identifier id)
Set identifier for this node.
|
void |
ParameterizedTree.ParameterizedTreeBase.setIdentifier(int i,
Identifier id) |
void |
Tree.TreeBase.setIdentifier(int i,
Identifier id) |
void |
SimpleTree.setIdentifier(int i,
Identifier id) |
Modifier and Type | Method and Description |
---|---|
static org.w3c.dom.Element |
ElementFactory.createSequenceElement(Identifier id,
java.lang.String sequence,
org.w3c.dom.Document document) |