Uses of Class
pal.misc.Identifier

Packages that use Identifier
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
 

Methods in pal.alignment that return Identifier
 Identifier SimpleCharacterAlignment.getIdentifier(int i)
           
 Identifier AbstractAlignment.getIdentifier(int i)
           
 

Methods in pal.alignment with parameters of type Identifier
 void SimpleCharacterAlignment.setIdentifier(int i, Identifier ident)
           
 void AbstractAlignment.setIdentifier(int i, Identifier ident)
           
 

Constructors in pal.alignment with parameters of type Identifier
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.
 

Uses of Identifier in pal.distance
 

Methods in pal.distance that return Identifier
 Identifier DistanceMatrix.getIdentifier(int i)
           
 

Methods in pal.distance with parameters of type Identifier
 void DistanceMatrix.setIdentifier(int i, Identifier ident)
           
 

Uses of Identifier in pal.gui
 

Methods in pal.gui with parameters of type Identifier
 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)
           
 

Constructors in pal.gui with parameters of type Identifier
NameColouriser(Identifier name, java.awt.Color colour)
           
 

Uses of Identifier in pal.misc
 

Fields in pal.misc declared as Identifier
static Identifier Identifier.ANONYMOUS
           
 

Methods in pal.misc that return Identifier
 Identifier TimeOrderCharacterData.getIdentifier(int i)
           
 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)
           
 

Methods in pal.misc with parameters of type Identifier
 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 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
SimpleIdGroup(Identifier[] id)
          Constructor taking an array of identifiers.
 

Uses of Identifier in pal.tree
 

Methods in pal.tree that return Identifier
 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)
           
 

Methods in pal.tree with parameters of type Identifier
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)
           
 void Tree.TreeBase.setIdentifier(int i, Identifier id)
           
 void SimpleTree.setIdentifier(int i, Identifier id)
           
 

Uses of Identifier in pal.xml
 

Methods in pal.xml with parameters of type Identifier
static org.w3c.dom.Element ElementFactory.createSequenceElement(Identifier id, java.lang.String sequence, org.w3c.dom.Document document)