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).
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Uses of IdGroup in pal.alignment
Subinterfaces of IdGroup in pal.alignmentModifier and TypeInterfaceDescriptioninterfaceinterface for any alignment data.interfaceThe AnnotationAlignment interface is designed to provide annotation for an alignment.interfaceThis interface is designed to hold quantitative character states.Classes in pal.alignment that implement IdGroupModifier and TypeClassDescriptionclassabstract base class for any alignment data.static classstatic classclassgenerates bootstrapped alignments from a raw alignmentclassconcatenates a list of alignments to one single alignment, increasing the number of sitesclassThis is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences.classCreates a "Gap-Balanced" alignment.classThis class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms.classan extension of the IndelAlignment that includes annotation.classgenerates jumbled alignments (randomizing input order of sequences)classMultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.classreads aligned sequence data from plain text files.classreads aligned sequence data from plain text files.classAn alignment class that can be efficiently constructed from an array of strings.classThis is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment.classThis provides a basic implementation of CharacterAlignment.classtakes an Alignment and determines its site patternsclasstakes an alignment and repeatedly removes sitesclassThis 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 IdGroupAbstractAlignment.idGroupsequence identifiersprotected IdGroupSimpleCharacterAlignment.idGroupsequence identifiersMethods in pal.alignment with parameters of type IdGroupModifier and TypeMethodDescriptionprotected voidConstructors 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 TypeClassDescriptionclassProvides 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 TypeClassDescriptionclasscompute distance matrix (observed and ML) from alignment (SitePattern)classstorage for pairwise distance matrices.classcompute jukes-cantor corrected distance matrixclassreads 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 TypeClassDescriptionclassDefault implementation of IdGroup interface.classCharacter data that expresses an order through time.Modifier and TypeFieldDescriptionprotected IdGroupTimeOrderCharacterData.taxathe identifier groupModifier and TypeMethodDescriptionstatic IdGroupIdGenerator.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 booleanIdGroup.Utils.isContainedWithin(IdGroup sub, IdGroup full) static final booleanIdGroup.Utils.isEqualIgnoringOrder(IdGroup id1, IdGroup id2) voidTimeOrderCharacterData.setOrdinals(TimeOrderCharacterData tocd, IdGroup standard, boolean doTimes) Set time ordinals from another TimeOrderCharacterData.Extracts a subset of a TimeOrderCharacterData.static final intIdGroup.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 TypeClassDescriptionclassCorrects distances in a distance matrix such that all tips appear contemporaneous, given a time/date and rate information for the taxa.classconstructs an SUPGMA tree from pairwise distances. -
Uses of IdGroup in pal.tree
Modifier and TypeInterfaceDescriptioninterfaceabstract base class for a tree with an Parameterized interfaceinterfaceInterface for a phylogenetic or genealogical tree.Modifier and TypeClassDescriptionclassprovides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)classclassThis class logarithmically transforms tree parameters.classProvides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).classconstructs 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 classFor parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)classconstructs a tree reading in a New Hampshire treefile, taking care for internal labels and branch lengths and binary/nonbinary and rooted/unrooted treesclassdata structure for a binary/non-binary rooted/unrooted treesclassgenerates an artificial data setstatic classclasscomputes distance matrix induced by a tree (needs only O(n^2) time, following algorithm DistanceInTree by D.Bryant and P.classprovides parameter interface to an unconstrained tree (parameters are all available branch lengths)classDeprecated.Use ClusterTreeModifier and TypeMethodDescriptionCladeSystem.getIdGroup()get idGroupSplitSystem.getIdGroup()get idGroupstatic final IdGroupTreeUtils.getLeafIdGroup(Tree tree) get list of the identifiers of the external nodesModifier and TypeMethodDescriptionstatic voidget clade for internal nodestatic CladeSystemcreates a clade system from a tree (using a pre-specified order of sequences)static final TreeTreeUtils.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 voidget split for branch associated with internal nodestatic SplitSystemcreates 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