Uses of Interface
pal.misc.IdGroup
Packages that use IdGroup
Package
Description
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
Classes to model population genetic processes using the coalescent.
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
Classes that don't fit elsewhere ;^)
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.alignmentModifier and TypeInterfaceDescriptioninterface
interface for any alignment data.interface
The AnnotationAlignment interface is designed to provide annotation for an alignment.interface
This interface is designed to hold quantitative character states.Classes in pal.alignment that implement IdGroupModifier and TypeClassDescriptionclass
abstract base class for any alignment data.static class
static class
class
generates bootstrapped alignments from a raw alignmentclass
concatenates a list of alignments to one single alignment, increasing the number of sitesclass
This is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences.class
Creates a "Gap-Balanced" alignment.class
This class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms.class
an extension of the IndelAlignment that includes annotation.class
generates jumbled alignments (randomizing input order of sequences)class
MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.class
reads aligned sequence data from plain text files.class
reads aligned sequence data from plain text files.class
An alignment class that can be efficiently constructed from an array of strings.class
This is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment.class
This provides a basic implementation of CharacterAlignment.class
takes an Alignment and determines its site patternsclass
takes an alignment and repeatedly removes sitesclass
This is the stripped implementation of the Annotation interface, which is designed to provide stripped and annotated alignments.Fields in pal.alignment declared as IdGroupModifier and TypeFieldDescriptionprotected IdGroup
AbstractAlignment.idGroup
sequence identifiersprotected IdGroup
SimpleCharacterAlignment.idGroup
sequence identifiersMethods in pal.alignment with parameters of type IdGroupModifier and TypeMethodDescriptionprotected void
Constructors in pal.alignment with parameters of type IdGroupModifierConstructorDescriptionDataTranslator
(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, String[] sequences, String gaps, DataType dt) MultiLocusAnnotatedAlignment
(IdGroup group, String[] sequences, DataType dt) SimpleAlignment
(IdGroup group, char[][] cSequences, String gaps, DataType dt) SimpleAlignment
(IdGroup group, char[][] cSequences, DataType dt) SimpleAlignment
(IdGroup ids, String[] sequences, String gaps, DataType dt) SimpleAlignment
(IdGroup ids, 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, String[] sequences, String gaps, DataType dt) This constructor creates a basic SimpleAnnotatedAlignment.SimpleAnnotatedAlignment
(IdGroup group, String[] sequences, DataType dt) This constructor creates a basic SimpleAnnotatedAlignment.SimpleCharacterAlignment
(IdGroup group, double[][] traitValues, String[] traitNames) Constructor for SimpleCharacterAlignment.SimpleCharacterAlignment
(IdGroup group, double[][] traitValues, String[] traitNames, String[] environNames) Constructor for SimpleCharacterAlignmentSimpleCharacterAlignment
(IdGroup group, double[] traitValue, 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 IdGroupModifier and TypeClassDescriptionclass
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 IdGroupModifier and TypeClassDescriptionclass
compute distance matrix (observed and ML) from alignment (SitePattern)class
storage for pairwise distance matrices.class
compute jukes-cantor corrected distance matrixclass
reads pairwise distance matrices in PHYLIP format (full matrix)Methods in pal.distance that return IdGroupModifier and TypeMethodDescriptionDistanceMatrix.getIdGroup()
Deprecated.distance matrix now implements IdGroupMethods in pal.distance with parameters of type IdGroupConstructors in pal.distance with parameters of type IdGroupModifierConstructorDescriptionDistanceMatrix
(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
Modifier and TypeClassDescriptionclass
Default implementation of IdGroup interface.class
Character data that expresses an order through time.Modifier and TypeFieldDescriptionprotected IdGroup
TimeOrderCharacterData.taxa
the identifier groupModifier and TypeMethodDescriptionstatic IdGroup
IdGenerator.createIdGroup
(int size) generates a group of unique identifiers numbered from zero.TimeOrderCharacterData.getIdGroup()
Deprecated.TimeOrderCharacterData now implements IdGroupModifier and TypeMethodDescriptionstatic final Identifier[]
Identifier.getIdentifiers
(IdGroup idGroup) Translates an IdGroup into an array of identifiersstatic final String[]
Translates an IdGroup into an array of stringsstatic final String[]
Translates an IDgroup into an array of strings, with optional removal of particular identifierstatic final String[]
Translates an IDgroup into an array of strings, with optional removal of particular identifierTimeOrderCharacterData.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 final boolean
IdGroup.Utils.isContainedWithin
(IdGroup sub, IdGroup full) static final boolean
IdGroup.Utils.isEqualIgnoringOrder
(IdGroup id1, IdGroup id2) void
TimeOrderCharacterData.setOrdinals
(TimeOrderCharacterData tocd, IdGroup standard, boolean doTimes) Set time ordinals from another TimeOrderCharacterData.Extracts a subset of a TimeOrderCharacterData.static final int
IdGroup.Utils.whichIdNumber
(IdGroup group, String s) A convenience implementation of whichIdNumber that can be used by IdGroup implementationsModifierConstructorDescriptionImpersonating 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 IdGroupModifier and TypeClassDescriptionclass
Corrects distances in a distance matrix such that all tips appear contemporaneous, given a time/date and rate information for the taxa.class
constructs an SUPGMA tree from pairwise distances. -
Uses of IdGroup in pal.tree
Modifier and TypeInterfaceDescriptioninterface
abstract base class for a tree with an Parameterized interfaceinterface
Interface for a phylogenetic or genealogical tree.Modifier and TypeClassDescriptionclass
provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)class
class
This class logarithmically transforms tree parameters.class
Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).class
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
For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)class
constructs a tree reading in a New Hampshire treefile, taking care for internal labels and branch lengths and binary/nonbinary and rooted/unrooted treesclass
data structure for a binary/non-binary rooted/unrooted treesclass
generates an artificial data setstatic class
class
computes distance matrix induced by a tree (needs only O(n^2) time, following algorithm DistanceInTree by D.Bryant and P.class
provides parameter interface to an unconstrained tree (parameters are all available branch lengths)class
Deprecated.Use ClusterTreeModifier and TypeMethodDescriptionCladeSystem.getIdGroup()
get idGroupSplitSystem.getIdGroup()
get idGroupstatic final IdGroup
TreeUtils.getLeafIdGroup
(Tree tree) get list of the identifiers of the external nodesModifier and TypeMethodDescriptionstatic void
get clade for internal nodestatic CladeSystem
creates a clade system from a tree (using a pre-specified order of sequences)static final 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
get split for branch associated with internal nodestatic SplitSystem
creates a split system from a tree (using a pre-specified order of sequences)static final 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.ModifierConstructorDescriptionCladeSystem
(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