Uses of Interface
pal.misc.IdGroup

Packages that use IdGroup
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
 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
 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
protected  IdGroup SimpleCharacterAlignment.idGroup
          sequence identifiers
protected  IdGroup AbstractAlignment.idGroup
          sequence identifiers
 

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

Constructors in pal.alignment with parameters of type IdGroup
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, DataType dt)
           
MultiLocusAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
           
SimpleAlignment(IdGroup group, char[][] cSequences, DataType dt)
           
SimpleAlignment(IdGroup group, char[][] cSequences, java.lang.String gaps, DataType dt)
           
SimpleAlignment(IdGroup group, DataType dt, int[][] sSequences)
           
SimpleAlignment(IdGroup ids, java.lang.String[] sequences, DataType dt)
           
SimpleAlignment(IdGroup ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
           
SimpleAnnotatedAlignment(AnnotationAlignment a, IdGroup newGroup)
          This constructor will subset the alignment based on the taxa in IdGroup
SimpleAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, DataType dt)
          This constructor creates a basic SimpleAnnotatedAlignment.
SimpleAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, java.lang.String gaps, 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
 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
 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
 IdGroup DistanceMatrix.getIdGroup()
          Deprecated. distance matrix now implements IdGroup
 

Methods in pal.distance with parameters of type IdGroup
protected  void DistanceMatrix.setIdGroup(IdGroup base)
           
 

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

Uses of IdGroup in pal.misc
 

Classes in pal.misc that implement IdGroup
 class SimpleIdGroup
          Default implementation of IdGroup interface.
 class TimeOrderCharacterData
          Character data that expresses an order through time.
 

Fields in pal.misc declared as IdGroup
protected  IdGroup TimeOrderCharacterData.taxa
          the identifier group
 

Methods in pal.misc that return IdGroup
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
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
SimpleIdGroup(IdGroup a)
          Impersonating Constructor.
SimpleIdGroup(IdGroup a, IdGroup b)
          Constructor taking two separate id groups and merging them.
SimpleIdGroup(IdGroup a, int toIgnore)
          Impersonating Constructor.
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
 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
 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
 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
 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
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
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