Uses of Interface pal.misc.IdGroup

Packages that use IdGroup
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.coalescent	Classes to model population genetic processes using the coalescent.
pal.distance	Classes for reading and generating distance matrices, including computation of pairwise distances for sequence data (maximum-likelihood and observed distances).
pal.misc	Classes that don't fit elsewhere ;^)
pal.supgma
pal.tree	Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).

Uses of IdGroup in pal.alignment

Subinterfaces of IdGroup in pal.alignment
Modifier and Type	Interface	Description
`interface`	`Alignment`	interface for any alignment data.
`interface`	`AnnotationAlignment`	The AnnotationAlignment interface is designed to provide annotation for an alignment.
`interface`	`CharacterAlignment`	This interface is designed to hold quantitative character states.

Classes in pal.alignment that implement IdGroup
Modifier and Type	Class	Description
`class`	`AbstractAlignment`	abstract base class for any alignment data.
`static class`	`AlignmentReaders.PhylipClustalAlignment`
`static class`	`AlignmentReaders.UnalignedAlignment`
`class`	`BootstrappedAlignment`	generates bootstrapped alignments from a raw alignment
`class`	`ConcatenatedAlignment`	concatenates a list of alignments to one single alignment, increasing the number of sites
`class`	`ConcatenatedAnnotatedAlignment`	This is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences.
`class`	`GapBalancedAlignment`	Creates a "Gap-Balanced" alignment.
`class`	`IndelAlignment`	This class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms.
`class`	`IndelAnnotatedAlignment`	an extension of the IndelAlignment that includes annotation.
`class`	`JumbledAlignment`	generates jumbled alignments (randomizing input order of sequences)
`class`	`MultiLocusAnnotatedAlignment`	MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.
`class`	`ReadAlignment`	reads aligned sequence data from plain text files.
`class`	`ReadAlignmentOld`	reads aligned sequence data from plain text files.
`class`	`SimpleAlignment`	An alignment class that can be efficiently constructed from an array of strings.
`class`	`SimpleAnnotatedAlignment`	This is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment.
`class`	`SimpleCharacterAlignment`	This provides a basic implementation of CharacterAlignment.
`class`	`SitePattern`	takes an Alignment and determines its site patterns
`class`	`StrippedAlignment`	takes an alignment and repeatedly removes sites
`class`	`StrippedAnnotatedAlignment`	This is the stripped implementation of the Annotation interface, which is designed to provide stripped and annotated alignments.

Fields in pal.alignment declared as IdGroup
Modifier and Type	Field	Description
`protected IdGroup`	AbstractAlignment.`idGroup`	sequence identifiers
`protected IdGroup`	SimpleCharacterAlignment.`idGroup`	sequence identifiers

Methods in pal.alignment with parameters of type IdGroup
Modifier and Type	Method	Description
`protected void`	MultiLocusAnnotatedAlignment.`init(IdGroup group, java.lang.String[] sequences)`

Constructors in pal.alignment with parameters of type IdGroup
Constructor	Description
`DataTranslator(int[][] stateData, MolecularDataType dt, IdGroup ids)`
`MultiLocusAnnotatedAlignment(AnnotationAlignment a, IdGroup newGroup)`	This constructor will subset the alignment based on the taxa in IdGroup
`MultiLocusAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, java.lang.String gaps, DataType dt)`
`MultiLocusAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, DataType dt)`
`SimpleAlignment(IdGroup group, char[][] cSequences, java.lang.String gaps, DataType dt)`
`SimpleAlignment(IdGroup group, char[][] cSequences, DataType dt)`
`SimpleAlignment(IdGroup ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)`
`SimpleAlignment(IdGroup ids, java.lang.String[] sequences, DataType dt)`
`SimpleAlignment(IdGroup group, DataType dt, int[][] sSequences)`
`SimpleAnnotatedAlignment(AnnotationAlignment a, IdGroup newGroup)`	This constructor will subset the alignment based on the taxa in IdGroup
`SimpleAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, java.lang.String gaps, DataType dt)`	This constructor creates a basic SimpleAnnotatedAlignment.
`SimpleAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, DataType dt)`	This constructor creates a basic SimpleAnnotatedAlignment.
`SimpleCharacterAlignment(IdGroup group, double[][] traitValues, java.lang.String[] traitNames)`	Constructor for SimpleCharacterAlignment.
`SimpleCharacterAlignment(IdGroup group, double[][] traitValues, java.lang.String[] traitNames, java.lang.String[] environNames)`	Constructor for SimpleCharacterAlignment
`SimpleCharacterAlignment(IdGroup group, double[] traitValue, java.lang.String traitName)`	Constructor for SimpleCharacterAlignment when there is only a single trait.
`SitePattern(DataType dataType, int numSites, int numSeqs, IdGroup idGroup, int numPatterns, int[] alias, int[] weight, byte[][] pattern)`	construct SitePattern from scratch

Uses of IdGroup in pal.coalescent

Classes in pal.coalescent that implement IdGroup
Modifier and Type	Class	Description
`class`	`DemographicClockTree`	Provides parameter interface to a clock-like genealogy which is assumed to have some demographic pattern of theta (diversity) as well as branch parameters (the minimal node height differences at each internal node).

Uses of IdGroup in pal.distance

Classes in pal.distance that implement IdGroup
Modifier and Type	Class	Description
`class`	`AlignmentDistanceMatrix`	compute distance matrix (observed and ML) from alignment (SitePattern)
`class`	`DistanceMatrix`	storage for pairwise distance matrices.
`class`	`JukesCantorDistanceMatrix`	compute jukes-cantor corrected distance matrix
`class`	`ReadDistanceMatrix`	reads pairwise distance matrices in PHYLIP format (full matrix)

Methods in pal.distance that return IdGroup
Modifier and Type	Method	Description
`IdGroup`	DistanceMatrix.`getIdGroup()`	Deprecated. distance matrix now implements IdGroup

Methods in pal.distance with parameters of type IdGroup
Modifier and Type	Method	Description
`protected void`	DistanceMatrix.`setIdGroup(IdGroup base)`

Constructors in pal.distance with parameters of type IdGroup
Constructor	Description
`DistanceMatrix(double[][] distance, IdGroup idGroup)`	constructor taking distances array and IdGroup
`DistanceMatrix(DistanceMatrix dm, IdGroup subset)`	constructor that takes a distance matrix and clones the distances, of a the identifiers in idGroup.

Uses of IdGroup in pal.misc

Classes in pal.misc that implement IdGroup
Modifier and Type	Class	Description
`class`	`SimpleIdGroup`	Default implementation of IdGroup interface.
`class`	`TimeOrderCharacterData`	Character data that expresses an order through time.

Fields in pal.misc declared as IdGroup
Modifier and Type	Field	Description
`protected IdGroup`	TimeOrderCharacterData.`taxa`	the identifier group

Methods in pal.misc that return IdGroup
Modifier and Type	Method	Description
`static IdGroup`	IdGenerator.`createIdGroup(int size)`	generates a group of unique identifiers numbered from zero.
`IdGroup`	TimeOrderCharacterData.`getIdGroup()`	Deprecated. TimeOrderCharacterData now implements IdGroup
`IdGroup`	LabelMapping.`getMapped(IdGroup original)`

Methods in pal.misc with parameters of type IdGroup
Modifier and Type	Method	Description
`static Identifier[]`	Identifier.`getIdentifiers(IdGroup idGroup)`	Translates an IdGroup into an array of identifiers
`IdGroup`	LabelMapping.`getMapped(IdGroup original)`
`static java.lang.String[]`	Identifier.`getNames(IdGroup ids)`	Translates an IdGroup into an array of strings
`static java.lang.String[]`	Identifier.`getNames(IdGroup ids, int toIgnore)`	Translates an IDgroup into an array of strings, with optional removal of particular identifier
`static java.lang.String[]`	Identifier.`getNames(IdGroup ids, int[] toIgnore)`	Translates an IDgroup into an array of strings, with optional removal of particular identifier
`TimeOrderCharacterData`	TimeOrderCharacterData.`getReordered(IdGroup base)`	Creates a new TimeOrderCharacterData object with the same properites as this one but the identifier positions match that of base (ie whichIdNumber(Name) returns the same as for base)
`static boolean`	IdGroup.Utils.`isContainedWithin(IdGroup sub, IdGroup full)`
`static boolean`	IdGroup.Utils.`isEqualIgnoringOrder(IdGroup id1, IdGroup id2)`
`void`	TimeOrderCharacterData.`setOrdinals(TimeOrderCharacterData tocd, IdGroup standard, boolean doTimes)`	Set time ordinals from another TimeOrderCharacterData.
`TimeOrderCharacterData`	TimeOrderCharacterData.`subset(IdGroup staxa)`	Extracts a subset of a TimeOrderCharacterData.
`static int`	IdGroup.Utils.`whichIdNumber(IdGroup group, java.lang.String s)`	A convenience implementation of whichIdNumber that can be used by IdGroup implementations

Constructors in pal.misc with parameters of type IdGroup
Constructor	Description
`SimpleIdGroup(IdGroup a)`	Impersonating Constructor.
`SimpleIdGroup(IdGroup a, int toIgnore)`	Impersonating Constructor.
`SimpleIdGroup(IdGroup a, IdGroup b)`	Constructor taking two separate id groups and merging them.
`TimeOrderCharacterData(IdGroup taxa, int units)`	Constructor taking only IdGroup.
`TimeOrderCharacterData(IdGroup taxa, int units, boolean contemp)`	Constructor taking only IdGroup.

Uses of IdGroup in pal.supgma

Classes in pal.supgma that implement IdGroup
Modifier and Type	Class	Description
`class`	`SUPGMADistanceMatrix`	Corrects distances in a distance matrix such that all tips appear contemporaneous, given a time/date and rate information for the taxa.
`class`	`SUPGMATree`	constructs an SUPGMA tree from pairwise distances.

Uses of IdGroup in pal.tree

Subinterfaces of IdGroup in pal.tree
Modifier and Type	Interface	Description
`interface`	`ParameterizedTree`	abstract base class for a tree with an Parameterized interface
`interface`	`Tree`	Interface for a phylogenetic or genealogical tree.

Classes in pal.tree that implement IdGroup
Modifier and Type	Class	Description
`class`	`ClockTree`	provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)
`class`	`ClusterTree`
`class`	`LogParameterizedTree`	This class logarithmically transforms tree parameters.
`class`	`MutationRateModelTree`	Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).
`class`	`NeighborJoiningTree`	constructs a neighbor-joining tree from pairwise distances Saitou, N., and Nei, M., (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees.
`static class`	`ParameterizedTree.ParameterizedTreeBase`	For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)
`class`	`ReadTree`	constructs a tree reading in a New Hampshire treefile, taking care for internal labels and branch lengths and binary/nonbinary and rooted/unrooted trees
`class`	`SimpleTree`	data structure for a binary/non-binary rooted/unrooted trees
`class`	`SimulatedAlignment`	generates an artificial data set
`static class`	`Tree.TreeBase`
`class`	`TreeDistanceMatrix`	computes distance matrix induced by a tree (needs only O(n^2) time, following algorithm DistanceInTree by D.Bryant and P.
`class`	`UnconstrainedTree`	provides parameter interface to an unconstrained tree (parameters are all available branch lengths)
`class`	`UPGMATree`	Deprecated. Use ClusterTree

Methods in pal.tree that return IdGroup
Modifier and Type	Method	Description
`IdGroup`	CladeSystem.`getIdGroup()`	get idGroup
`IdGroup`	SplitSystem.`getIdGroup()`	get idGroup
`static IdGroup`	TreeUtils.`getLeafIdGroup(Tree tree)`	get list of the identifiers of the external nodes

Methods in pal.tree with parameters of type IdGroup
Modifier and Type	Method	Description
`static void`	CladeSystem.`getClade(IdGroup idGroup, Node internalNode, boolean[] clade)`	get clade for internal node
`static CladeSystem`	CladeSystem.`getClades(IdGroup idGroup, Tree tree)`	creates a clade system from a tree (using a pre-specified order of sequences)
`static Tree`	TreeUtils.`getNumberRelabelledTree(Tree baseTree, IdGroup ids)`	Create a new tree such that the labels are redifined from a base tree in such a manner: For each leaf label If the base label is not a number the new label is just the original label If the base label is a number the new label appropriately index label from a set identifiers
`static void`	SplitUtils.`getSplit(IdGroup idGroup, Node internalNode, boolean[] split)`	get split for branch associated with internal node
`static SplitSystem`	SplitUtils.`getSplits(IdGroup idGroup, Tree tree)`	creates a split system from a tree (using a pre-specified order of sequences)
`static int[]`	TreeUtils.`mapExternalIdentifiers(IdGroup idGroup, Tree tree)`	map external identifiers in the tree to a set of given identifiers (which can be larger than the set of external identifiers but must contain all of them) NOTE: for efficiency it is assumed that the node lists of the tree are correctly maintained.

Constructors in pal.tree with parameters of type IdGroup
Constructor	Description
`CladeSystem(IdGroup idGroup, int size)`
`SplitSystem(IdGroup idGroup, int size)`
`TreeDistanceMatrix(Tree t, IdGroup idGroup)`	compute induced distance matrix using actual branch lengths
`TreeDistanceMatrix(Tree t, IdGroup idGroup, boolean countEdges, double epsilon)`	compute induced distance matrix