Uses of Interface
pal.misc.IdGroup
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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). -
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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 alignmentclass
ConcatenatedAlignment
concatenates a list of alignments to one single alignment, increasing the number of sitesclass
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 patternsclass
StrippedAlignment
takes an alignment and repeatedly removes sitesclass
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 identifiersprotected IdGroup
SimpleCharacterAlignment. idGroup
sequence identifiersMethods 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 IdGroupMultiLocusAnnotatedAlignment(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 IdGroupSimpleAnnotatedAlignment(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 SimpleCharacterAlignmentSimpleCharacterAlignment(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 matrixclass
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 IdGroupMethods 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 IdGroupDistanceMatrix(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 groupMethods 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 IdGroupIdGroup
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 identifiersIdGroup
LabelMapping. getMapped(IdGroup original)
static java.lang.String[]
Identifier. getNames(IdGroup ids)
Translates an IdGroup into an array of stringsstatic java.lang.String[]
Identifier. getNames(IdGroup ids, int toIgnore)
Translates an IDgroup into an array of strings, with optional removal of particular identifierstatic java.lang.String[]
Identifier. getNames(IdGroup ids, int[] toIgnore)
Translates an IDgroup into an array of strings, with optional removal of particular identifierTimeOrderCharacterData
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 implementationsConstructors 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 interfaceinterface
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 treesclass
SimpleTree
data structure for a binary/non-binary rooted/unrooted treesclass
SimulatedAlignment
generates an artificial data setstatic 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 ClusterTreeMethods in pal.tree that return IdGroup Modifier and Type Method Description IdGroup
CladeSystem. getIdGroup()
get idGroupIdGroup
SplitSystem. getIdGroup()
get idGroupstatic IdGroup
TreeUtils. getLeafIdGroup(Tree tree)
get list of the identifiers of the external nodesMethods 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 nodestatic 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 identifiersstatic void
SplitUtils. getSplit(IdGroup idGroup, Node internalNode, boolean[] split)
get split for branch associated with internal nodestatic 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 lengthsTreeDistanceMatrix(Tree t, IdGroup idGroup, boolean countEdges, double epsilon)
compute induced distance matrix
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