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 IdentifierAbstractAlignment. getIdentifier(int i)IdentifierSimpleCharacterAlignment. getIdentifier(int i)Methods in pal.alignment with parameters of type Identifier Modifier and Type Method Description voidAbstractAlignment. setIdentifier(int i, Identifier ident)voidSimpleCharacterAlignment. 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 IdentifierDistanceMatrix. getIdentifier(int i)Methods in pal.distance with parameters of type Identifier Modifier and Type Method Description voidDistanceMatrix. setIdentifier(int i, Identifier ident) -
Uses of Identifier in pal.gui
Methods in pal.gui with parameters of type Identifier Modifier and Type Method Description voidLayoutTracker. addMapping(Identifier id, java.awt.Rectangle bounds)voidNameColouriser. addMapping(Identifier id, java.awt.Color colour)java.awt.RectangleLayoutTracker. getBounds(Identifier id)LabelDisplayerNameColouriser. getDisplay(Identifier id, LabelDisplayer defaultDisplay)Constructors in pal.gui with parameters of type Identifier Constructor Description NameColouriser(Identifier name, java.awt.Color colour) -
Uses of Identifier in pal.misc
Fields in pal.misc declared as Identifier Modifier and Type Field Description static IdentifierIdentifier. ANONYMOUSMethods in pal.misc that return Identifier Modifier and Type Method Description IdentifierIdGroup. getIdentifier(int i)Returns the ith identifier.IdentifierSimpleIdGroup. getIdentifier(int i)Returns the ith identifier.IdentifierTimeOrderCharacterData. 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 identifiersIdentifierLabelMapping. getLabelIdentifier(Identifier id)Identifier[]TimeOrderCharacterData. getSubgroupMembers(int subgroupNumber)Methods in pal.misc with parameters of type Identifier Modifier and Type Method Description voidLabelMapping. addMapping(Identifier id, java.lang.String label)java.lang.StringLabelMapping. getLabel(Identifier id)java.lang.StringLabelMapping. getLabel(Identifier id, java.lang.String defaultLabel)IdentifierLabelMapping. 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 identifierintTimeOrderCharacterData. getTimeOrdinal(Identifier taxonName)voidIdGroup. setIdentifier(int i, Identifier id)Sets the ith identifier.voidSimpleIdGroup. setIdentifier(int i, Identifier id)Sets the ith identifier.voidTimeOrderCharacterData. 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 IdentifierNode. getIdentifier()Returns the identifier for this node.IdentifierParameterizedTree.ParameterizedTreeBase. getIdentifier(int i)IdentifierSimpleNode. getIdentifier()Returns the identifier for this node.IdentifierSimpleTree. getIdentifier(int i)IdentifierTree.TreeBase. getIdentifier(int i)Methods in pal.tree with parameters of type Identifier Modifier and Type Method Description static NodeNodeFactory. createNode(Identifier id)create a node, with a specified identifierstatic NodeNodeFactory. createNode(Identifier id, double height)create a node, with a specified identifierstatic NodeNodeFactory. createNodeBranchLength(double branchLength, Identifier id)create a node, with a specified identifierstatic NodeNodeUtils. 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.voidNode. setIdentifier(Identifier id)Set identifier for this node.voidParameterizedTree.ParameterizedTreeBase. setIdentifier(int i, Identifier id)voidSimpleNode. setIdentifier(Identifier id)Set identifier for this node.voidSimpleTree. setIdentifier(int i, Identifier id)voidTree.TreeBase. setIdentifier(int i, Identifier id) -
Uses of Identifier in pal.xml
Methods in pal.xml with parameters of type Identifier Modifier and Type Method Description static org.w3c.dom.ElementElementFactory. createSequenceElement(Identifier id, java.lang.String sequence, org.w3c.dom.Document document)
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