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