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Packages that use IdGroup | |
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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 |
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Subinterfaces of IdGroup in pal.alignment | |
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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 | |
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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 | |
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protected IdGroup |
SimpleCharacterAlignment.idGroup
sequence identifiers |
protected IdGroup |
AbstractAlignment.idGroup
sequence identifiers |
Methods in pal.alignment with parameters of type IdGroup | |
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protected void |
MultiLocusAnnotatedAlignment.init(IdGroup group,
java.lang.String[] sequences)
|
Constructors in pal.alignment with parameters of type IdGroup | |
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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)
|
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SimpleAlignment(IdGroup group,
char[][] cSequences,
java.lang.String gaps,
DataType dt)
|
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SimpleAlignment(IdGroup group,
DataType dt,
int[][] sSequences)
|
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SimpleAlignment(IdGroup ids,
java.lang.String[] sequences,
DataType dt)
|
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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 |
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Classes in pal.coalescent that implement IdGroup | |
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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 |
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Classes in pal.distance that implement IdGroup | |
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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 | |
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IdGroup |
DistanceMatrix.getIdGroup()
Deprecated. distance matrix now implements IdGroup |
Methods in pal.distance with parameters of type IdGroup | |
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protected void |
DistanceMatrix.setIdGroup(IdGroup base)
|
Constructors in pal.distance with parameters of type IdGroup | |
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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 |
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Classes in pal.misc that implement IdGroup | |
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class |
SimpleIdGroup
Default implementation of IdGroup interface. |
class |
TimeOrderCharacterData
Character data that expresses an order through time. |
Fields in pal.misc declared as IdGroup | |
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protected IdGroup |
TimeOrderCharacterData.taxa
the identifier group |
Methods in pal.misc that return IdGroup | |
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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 | |
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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 | |
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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 |
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Classes in pal.supgma that implement IdGroup | |
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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 |
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Subinterfaces of IdGroup in pal.tree | |
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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 | |
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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 | |
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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 | |
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CladeSystem(IdGroup idGroup,
int size)
|
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SplitSystem(IdGroup idGroup,
int size)
|
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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 |
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