# All Classes and Interfaces

Class
Description
AbstractRateMatrix
abstract base class for all rate matrices
AbstractRootedTree
Align
AlignCommand
A command line interface for the algorithms in jebl.evolution.align.
Aligner
As of 2006-12-06, this interface is not used anywhere in JEBL, and it doesn't have any implementing classes.
Alignment
AlignmentExporter
AlignmentImporter
AlignmentTreeBuilderFactory
AlignmentTreeBuilderFactory.Result
AminoAcidModel
base class of rate matrices for amino acids
AminoAcids
Uninstantiable utility class with only static methods.
AminoAcidScores
AminoAcidState
Attributable
Interface for associating attributeNames with an object.
Attributable.Utils
AttributableHelper
AttributedCladeSystem
Stores a set of unique clades for a tree
BartonSternberg
BaseEdge
Common implementation of Attributable interface used by Nodes.
BaseNode
Common implementation of Attributable interface used by Nodes.
BasicAlignment
A basic implementation of the Alignment interface.
BasicDistanceMatrix
BasicProgressListener
A basic `ProgressListener` implementation that allows the caller to set the canceled status.
BasicSequence
A default implementation of the Sequence interface.
BilleraMetric
Billera tree distance - sum of change in branch lengths required to transform one tree to the second Note that this interface is not optimal for a large set where all pairs are required.
Binomial
Binomial coefficients
Blosum45
Blosum50
Blosum55
Blosum60
Blosum62
Blosum65
Blosum70
Blosum75
Blosum80
Blosum85
Blosum90
BootstrappedAlignment
Date: 15/01/2006 Time: 10:13:50
ByteBuilder
Similar to a StringBuilder, but its internal buffer is a byte[] with one entry for each character, so it can only correctly append single-byte characters.
CalculateSplitRates
Created by IntelliJ IDEA.
Cancelable
Checks whether some operation has been cancelled; This will typically be used as a callback because it can only query whether a task has been cancelled, rather than cancel it (there is no cancel() method).
CannotBuildDistanceMatrixException
CanonicalSequence
A default implementation of the Sequence interface that converts sequence characters to States such that calling getString() will always return uppercase residues with nucleotide U residues converted to T
CataclysmicDemographic
This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).
Character
CharacterType
CladeHeightMetric
For each clade_j in treeB, find the MRCA_j of the taxa in clade_j in treeA.
CladeSystem
Stores a set of unique clades for a tree
ClusteringTreeBuilder<T>
An abstract base class for clustering algorithms from pairwise distances
Coalescent
A likelihood function for the coalescent.
CoalescentIntervalGenerator
This is a class that draws coalescent intervals under the given demographic function.
Codons
CodonSequence
A codon implementation of the Sequence interface.
CodonState
As of 2007-07-30, instances of this class are only constructed for non-ambigous nucleotide triplets - see `Codons`.
CompactRootedTree
A memory efficient rooted tree.
CompositeProgressListener
A `ProgressListener` that is suitable for a task that consists of several subtasks.
ConsensusSequence
ConsensusTreeBuilder<T>
A `TreeBuilder` that builds a consensus tree for a set of trees on identical leaf sets.
ConsensusTreeBuilder.Method
Supported consensus methods.
ConstantPopulation
This class models coalescent intervals for a constant population (parameter: N0=present-day population size).
ConstExponential
This class models exponential growth from an initial population size.
ConstLogistic
This class models logistic growth from an initial population size.
ContinuousCharacter
DemographicFunction
This interface provides methods that describe a demographic function.
DemographicFunction.Utils
DiscreteCharacter
DistanceMatrix
DistanceMatrixImporter
DistanceMatrixImporter.Triangle
Edge
Represents a node in a graph or tree.
EmpiricalDemographicFunction
Expansion
This class models exponential growth from an initial ancestral population size.
ExponentialGrowth
This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).
ExponentialLogistic
This class models logistic growth from an initial exponential phase.
F84DistanceMatrix
FastaExporter
Class for exporting a fasta file format.
FastaImporter
Class for importing Fasta sequential file format.
FilteredRootedTree
FilteredSequence
FitchParsimony
Class for reconstructing characters using Fitch parsimony.
FixedBitSet
A bit-set of fixed size.
GammaFunction
gamma function
GaplessSequence
GeneticCode
A set of standard genetic codes.
Graph
Graph.NoEdgeException
This class is thrown by getEdgeLength(node1, node2) if node1 and node2 are not directly connected by an edge.
Graph.Utils
Hamming
HashPair<T>
A pair suitable for use in a HashMap.
HKYDistanceMatrix
Compute HKY corrected distance matrix
IllegalCharacterPolicy
What to do when an imported document contains illegal characters
ImmediateSequenceImporter
A sequence importer sending the sequences back one by one, which makes it possible to import larger documents if handled wisely on the other side.
ImmediateSequenceImporter.Callback
ImportException
ImportException.BadFormatException
ImportException.DuplicateFieldException
ImportException.DuplicateTaxaException
ImportException.MissingFieldException
ImportException.ShortSequenceException
ImportException.TooFewTaxaException
ImportException.UnknownTaxonException
ImportException.UnparsableDataException
ImportHelper
A helper class for phylogenetic file format importers
IntervalGenerator
IntervalList
An interface for a set of coalescent intevals.
IntervalList.IntervalType
IntervalList.Utils
Intervals
A concrete class for a set of coalescent intevals.
JackknifedAlignment
Date: 17/01/2006 Time: 08:18:32
JukesCantor
Jukes Cantor assumes equal substitution frequencies and equal nucleotide equilibrium frequencies.
JukesCantorDistanceMatrix
Compute jukes-cantor corrected distance matrix for a set of aligned sequences.
LogisticGrowth
This class models logistic growth.
MachineAccuracy
determines machine accuracy
MatrixCalc
MatrixCalcException
MatrixCalcException.NotSquareMatrixException
MatrixCalcException.PositiveDefiniteException
MatrixExponential
compute matrix exponential and, subsequently, transition probabilities for a given rate matrix
MaximalSegmentPair
MaybeBoolean
A tri-state boolean value that can also be "Maybe" besides True and False.
MEGAExporter
* Export to MEGA.
MinimiserMonitor
interface for a classes that wish to monitor the progress of a Minimiser
MinimiserMonitor.Utils
MissingTaxonException
ModelBasedDistanceMatrix
MostProbableTopology
Given a set of trees determine the most probable trees, i.e.
MultipleAligner
MultivariateFunction
interface for a function of several variables
MultivariateMinimum
abstract base class for minimisation of a multivariate function
MultivariateMinimum.Factory
A factory interface for MultivariateMinimums (because they aren't statefree)
MutableRootedTree
A simple rooted tree providing some ability to manipulate the tree.
NeedlemanWunsch
NeedlemanWunschAffine
NeedlemanWunschLinearSpace
NeedlemanWunschLinearSpaceAffine
NeighborJoiningTreeBuilder
Constructs an unrooted tree by neighbor-joining using pairwise distances.
NewickExporter
NewickImporter
NexusExporter
Export sequences and trees to Nexus format.
NexusImporter
Class for importing NEXUS file format.
NexusImporter.MissingBlockException
Thrown when a block is missing that is required for importing a particular type of data from the nexus input.
NexusImporter.NexusBlock
Represents the block types used in the nexus format
Node
Represents a node in a graph or tree.
NonOverlapMultipleLocalAffine
Performs recursive local alignments.
Nucleotides
Uninstantiable utility class with only static methods.
NucleotideScores
NucleotideState
NumberFormatter
An interface for a numerical column in a log.
NumericalDerivative
approximates numerically the first and second derivatives of a function of a single variable and approximates gradient and diagonal of Hessian for multivariate functions
OldNeedlemanWunschAffine
OrderEnumerator
A means for describing odering information, and Utilities for creating such Orderings
OrderEnumerator.OEFactory
OrderEnumerator.Utils
OrthogonalHints
Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum) hints about the function that may alow it to optimise better.
OrthogonalHints.Utils
OrthogonalLineFunction
converts a multivariate function into a univariate function by keeping all but one argument constant
OrthogonalSearch
minimization of a real-valued function of several variables without using derivatives, using the simple strategy of optimizing variables one by one.
Output
OverlapAlign
PairwiseAligner
PairwiseAligner.Result
Pam100
Pam110
Pam120
Pam130
Pam140
Pam150
Pam160
Pam170
Pam180
Pam190
Pam200
Pam210
Pam220
Pam230
Pam240
Pam250
ParsimonyCriterion
Pattern
An interface representing a list of states for a list of taxa (e.g.
Patterns
An interface representing a set of site patterns.
PHYLIPExporter
Export alignment to Phylip format.
PhylipSequentialImporter
Class for importing PHYLIP sequential file format
ProfileCharacter
ProgressListener
ProgressListener.Wrapper
A decorator progress listener which delegates all method calls to an internal progress listener.
Random
Random number generation.
RateMatrix
abstract base class for all rate matrices
ReRootedTree
A rooted tree concrete class that wraps another tree and provides a differently rooted view of that tree.
ResampledAlignment
Date: 17/01/2006 Time: 08:08:44
RobinsonsFouldMetric
RootedFromUnrooted
Root an unrooted tree.
RootedSubtree
A simple, immutable rooted tree implementation that is a subtree of an existing tree subtending a specified set of taxa..
RootedTree
A tree with a root (node with maximum height).
RootedTreeMetric
RootedTreeUtils
Static utility functions for rooted trees.
ScoreMatrix
Scores
Base class for all score matrices in the package.
ScoresFactory
Sequence
A biomolecular sequence.
SequenceAlignmentsDistanceMatrix
Builds a distance matrix by performing a series of pairwise alignments between the specified sequences (unlike the methods in jebl.evolution.distances, which extract the pairwise distances from a multiple sequence alignment).
SequenceExporter
SequenceImporter
Interface for importers that do sequences
Sequences
A set of sequence objects.
SequenceShuffler
Shuffles a sequence and aligns it again multiple times to give mean and variance of alignments on random sequences.
SequenceStateException
SequenceTester
SequenceType
Interface for sequences data types.
SequenceType.Utils
SimpleListener
SimpleRootedTree
A simple, and initially immutable rooted tree implementation.
SimpleTree
A basic implementation on an unrooted tree.
SmithWaterman
SmithWatermanLinearSpace
SmithWatermanLinearSpaceAffine
SortedRootedTree
SortedRootedTree.BranchOrdering
SplitSystem
data structure for a set of splits
SplitUtils
utilities for split systems
State
StateClassification
StateClassification.Default
SubstScoreMatrix
SystemOut
TabDelimitedImporter
TamuraNeiDistanceMatrix
Date: 22/01/2006 Time: 17:28:59
Taxon
TaxonomicLevel
Traceback
TracebackPlotter
TransformedRootedTree
This RootedTree class wraps another RootedTree and transforms the branch lengths and node heights using various functions.
TransformedRootedTree.Transform
TranslatedSequence
Tree
A rooted or unrooted tree.
TreeBiPartitionInfo
Work in progress
TreeBiPartitionInfo.DistanceNorm
TreeBuilder<T>
TreeBuilderFactory
A meeting point for tree building from sequence data.
TreeBuilderFactory.ConsensusMethod
Supported consensus methods.
TreeBuilderFactory.DistanceModel
Supported pairwise distance methods
TreeBuilderFactory.Method
Supported methods for tree building
TreeChangeEvent
Represents a change to a tree.
TreeChangeListener
A listener for notifying about changes to a tree or to the selected nodes in a tree.
TreeExporter
TreeImporter
Interface for importers that do trees
TreeSelectionChangeEvent
Represents a change to the selected nodes in a tree.
TreeSimulator
This class provides the framework for (backwards-through-time) tree simulation.
UnivariateFunction
interface for a function of one variable
UnivariateMinimum
minimization of a real-valued function of one variable without using derivatives.
Utils
A collection of utility functions for graphs.
Utils
Utils
A collection of utility functions for trees.
Utils
Provides some miscellaneous methods.
WAG
WAG model of amino acid evolution (S.