Uses of Class
pal.misc.Identifier
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Packages that use Identifier 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. -
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Uses of Identifier in pal.alignment
Methods in pal.alignment that return Identifier Modifier and Type Method Description Identifier
AbstractAlignment. getIdentifier(int i)
Identifier
SimpleCharacterAlignment. getIdentifier(int i)
Methods in pal.alignment with parameters of type Identifier Modifier and Type Method Description void
AbstractAlignment. setIdentifier(int i, Identifier ident)
void
SimpleCharacterAlignment. setIdentifier(int i, Identifier ident)
Constructors in pal.alignment with parameters of type Identifier Constructor Description MultiLocusAnnotatedAlignment(Identifier[] ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
SimpleAlignment(Identifier[] ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
SimpleAlignment(Identifier[] ids, java.lang.String[] sequences, 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 Modifier and Type Method Description Identifier
DistanceMatrix. getIdentifier(int i)
Methods in pal.distance with parameters of type Identifier Modifier and Type Method Description void
DistanceMatrix. setIdentifier(int i, Identifier ident)
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Uses of Identifier in pal.gui
Methods in pal.gui with parameters of type Identifier Modifier and Type Method Description void
LayoutTracker. addMapping(Identifier id, java.awt.Rectangle bounds)
void
NameColouriser. addMapping(Identifier id, java.awt.Color colour)
java.awt.Rectangle
LayoutTracker. getBounds(Identifier id)
LabelDisplayer
NameColouriser. getDisplay(Identifier id, LabelDisplayer defaultDisplay)
Constructors in pal.gui with parameters of type Identifier Constructor Description NameColouriser(Identifier name, java.awt.Color colour)
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Uses of Identifier in pal.misc
Fields in pal.misc declared as Identifier Modifier and Type Field Description static Identifier
Identifier. ANONYMOUS
Methods in pal.misc that return Identifier Modifier and Type Method Description Identifier
IdGroup. getIdentifier(int i)
Returns the ith identifier.Identifier
SimpleIdGroup. getIdentifier(int i)
Returns the ith identifier.Identifier
TimeOrderCharacterData. getIdentifier(int i)
static Identifier[]
Identifier. getIdentifiers(java.lang.String[] names)
Translates an an array of strings into an array of identifiersstatic Identifier[]
Identifier. getIdentifiers(IdGroup idGroup)
Translates an IdGroup into an array of identifiersIdentifier
LabelMapping. getLabelIdentifier(Identifier id)
Identifier[]
TimeOrderCharacterData. getSubgroupMembers(int subgroupNumber)
Methods in pal.misc with parameters of type Identifier Modifier and Type Method 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 stringsstatic java.lang.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 Identifier Constructor Description SimpleIdGroup(Identifier[] id)
Constructor taking an array of identifiers. -
Uses of Identifier in pal.tree
Methods in pal.tree that return Identifier Modifier and Type Method Description Identifier
Node. getIdentifier()
Returns the identifier for this node.Identifier
ParameterizedTree.ParameterizedTreeBase. getIdentifier(int i)
Identifier
SimpleNode. getIdentifier()
Returns the identifier for this node.Identifier
SimpleTree. getIdentifier(int i)
Identifier
Tree.TreeBase. getIdentifier(int i)
Methods in pal.tree with parameters of type Identifier Modifier and Type Method Description static Node
NodeFactory. createNode(Identifier id)
create a node, with a specified identifierstatic Node
NodeFactory. createNode(Identifier id, double height)
create a node, with a specified identifierstatic Node
NodeFactory. createNodeBranchLength(double branchLength, Identifier id)
create a node, with a specified identifierstatic 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
ParameterizedTree.ParameterizedTreeBase. setIdentifier(int i, Identifier id)
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)
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Uses of Identifier in pal.xml
Methods in pal.xml with parameters of type Identifier Modifier and Type Method Description static org.w3c.dom.Element
ElementFactory. createSequenceElement(Identifier id, java.lang.String sequence, org.w3c.dom.Document document)
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