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Packages that use Identifier | |
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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. |
Uses of Identifier in pal.alignment |
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Methods in pal.alignment that return Identifier | |
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Identifier |
SimpleCharacterAlignment.getIdentifier(int i)
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Identifier |
AbstractAlignment.getIdentifier(int i)
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Methods in pal.alignment with parameters of type Identifier | |
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void |
SimpleCharacterAlignment.setIdentifier(int i,
Identifier ident)
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void |
AbstractAlignment.setIdentifier(int i,
Identifier ident)
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Constructors in pal.alignment with parameters of type Identifier | |
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MultiLocusAnnotatedAlignment(Identifier[] ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt)
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SimpleAlignment(Identifier[] ids,
java.lang.String[] sequences,
DataType dt)
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SimpleAlignment(Identifier[] ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt)
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SimpleAlignment(Identifier id,
java.lang.String sequence,
DataType dataType)
Constructor taking single identifier and sequence. |
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SimpleAnnotatedAlignment(Identifier[] ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt)
This constructor creates a basic SimpleAnnotatedAlignment. |
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SimpleCharacterAlignment(Identifier[] ids,
double[][] traitValues,
java.lang.String[] traitNames)
Constructor for SimpleCharacterAlignment. |
Uses of Identifier in pal.distance |
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Methods in pal.distance that return Identifier | |
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Identifier |
DistanceMatrix.getIdentifier(int i)
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Methods in pal.distance with parameters of type Identifier | |
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void |
DistanceMatrix.setIdentifier(int i,
Identifier ident)
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Uses of Identifier in pal.gui |
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Methods in pal.gui with parameters of type Identifier | |
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void |
NameColouriser.addMapping(Identifier id,
java.awt.Color colour)
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void |
LayoutTracker.addMapping(Identifier id,
java.awt.Rectangle bounds)
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java.awt.Rectangle |
LayoutTracker.getBounds(Identifier id)
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LabelDisplayer |
NameColouriser.getDisplay(Identifier id,
LabelDisplayer defaultDisplay)
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Constructors in pal.gui with parameters of type Identifier | |
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NameColouriser(Identifier name,
java.awt.Color colour)
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Uses of Identifier in pal.misc |
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Fields in pal.misc declared as Identifier | |
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static Identifier |
Identifier.ANONYMOUS
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Methods in pal.misc that return Identifier | |
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Identifier |
TimeOrderCharacterData.getIdentifier(int i)
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Identifier |
SimpleIdGroup.getIdentifier(int i)
Returns the ith identifier. |
Identifier |
IdGroup.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)
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Methods in pal.misc with parameters of type Identifier | |
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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)
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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 |
TimeOrderCharacterData.setIdentifier(int i,
Identifier ident)
|
void |
SimpleIdGroup.setIdentifier(int i,
Identifier id)
Sets the ith identifier. |
void |
IdGroup.setIdentifier(int i,
Identifier id)
Sets the ith identifier. |
Constructors in pal.misc with parameters of type Identifier | |
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SimpleIdGroup(Identifier[] id)
Constructor taking an array of identifiers. |
Uses of Identifier in pal.tree |
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Methods in pal.tree that return Identifier | |
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Identifier |
SimpleNode.getIdentifier()
Returns the identifier for this node. |
Identifier |
Node.getIdentifier()
Returns the identifier for this node. |
Identifier |
ParameterizedTree.ParameterizedTreeBase.getIdentifier(int i)
|
Identifier |
Tree.TreeBase.getIdentifier(int i)
|
Identifier |
SimpleTree.getIdentifier(int i)
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Methods in pal.tree with parameters of type Identifier | |
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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 |
SimpleNode.setIdentifier(Identifier id)
Set identifier for this node. |
void |
Node.setIdentifier(Identifier id)
Set identifier for this node. |
void |
ParameterizedTree.ParameterizedTreeBase.setIdentifier(int i,
Identifier id)
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void |
Tree.TreeBase.setIdentifier(int i,
Identifier id)
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void |
SimpleTree.setIdentifier(int i,
Identifier id)
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Uses of Identifier in pal.xml |
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Methods in pal.xml with parameters of type Identifier | |
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static org.w3c.dom.Element |
ElementFactory.createSequenceElement(Identifier id,
java.lang.String sequence,
org.w3c.dom.Document document)
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