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