All Classes and Interfaces
Class
Description
abstract base class for all rate matrices
A command line interface for the algorithms in jebl.evolution.align.
As of 2006-12-06, this interface is not used anywhere in JEBL, and it doesn't have
any implementing classes.
base class of rate matrices for amino acids
Uninstantiable utility class with only static methods.
Interface for associating attributeNames with an object.
Stores a set of unique clades for a tree
Common implementation of Attributable interface used by Nodes.
Common implementation of Attributable interface used by Nodes.
A basic implementation of the Alignment interface.
A basic
ProgressListener implementation that allows the caller to set the canceled
status.A default implementation of the Sequence interface.
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 coefficients
Date: 15/01/2006
Time: 10:13:50
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.
Created by IntelliJ IDEA.
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).
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
This class models an exponentially growing (or shrinking) population
(Parameters: N0=present-day population size; r=growth rate).
For each clade_j in treeB, find the MRCA_j of the taxa in clade_j in treeA.
Stores a set of unique clades for a tree
An abstract base class for clustering algorithms from pairwise distances
A likelihood function for the coalescent.
This is a class that draws coalescent intervals under the given demographic function.
A codon implementation of the Sequence interface.
As of 2007-07-30, instances of this class are only constructed for non-ambigous
nucleotide triplets - see
Codons.A memory efficient rooted tree.
A
ProgressListener that is suitable for a task that consists of several subtasks.A
TreeBuilder that builds a consensus tree for a set of trees on identical leaf sets.Supported consensus methods.
This class models coalescent intervals for a constant population
(parameter: N0=present-day population size).
This class models exponential growth from an initial population size.
This class models logistic growth from an initial population size.
This interface provides methods that describe a demographic function.
Represents a node in a graph or tree.
This class models exponential growth from an initial ancestral population size.
This class models an exponentially growing (or shrinking) population
(Parameters: N0=present-day population size; r=growth rate).
This class models logistic growth from an initial exponential phase.
Class for exporting a fasta file format.
Class for importing Fasta sequential file format.
Class for reconstructing characters using Fitch parsimony.
A bit-set of fixed size.
gamma function
A set of standard genetic codes.
This class is thrown by getEdgeLength(node1, node2) if node1 and node2
are not directly connected by an edge.
A pair suitable for use in a HashMap.
Compute HKY corrected distance matrix
What to do when an imported document contains illegal characters
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.
A helper class for phylogenetic file format importers
An interface for a set of coalescent intevals.
A concrete class for a set of coalescent intevals.
Date: 17/01/2006
Time: 08:18:32
Jukes Cantor assumes equal substitution frequencies and equal nucleotide
equilibrium frequencies.
Compute jukes-cantor corrected distance matrix for a set of aligned sequences.
This class models logistic growth.
determines machine accuracy
compute matrix exponential and, subsequently, transition probabilities
for a given rate matrix
A tri-state boolean value that can also be "Maybe" besides True and False.
* Export to MEGA.
interface for a classes that wish to monitor the progress of a Minimiser
Given a set of trees determine the most probable trees, i.e.
interface for a function of several variables
abstract base class for minimisation of a multivariate function
A factory interface for MultivariateMinimums (because they aren't statefree)
A simple rooted tree providing some ability to manipulate the tree.
Constructs an unrooted tree by neighbor-joining using pairwise distances.
Export sequences and trees to Nexus format.
Class for importing NEXUS file format.
Thrown when a block is missing that is required for importing a particular type of data from the nexus input.
Represents the block types used in the nexus format
Represents a node in a graph or tree.
Performs recursive local alignments.
Uninstantiable utility class with only static methods.
An interface for a numerical column in a log.
approximates numerically the first and second derivatives of a
function of a single variable and approximates gradient and
diagonal of Hessian for multivariate functions
A means for describing odering information, and Utilities for creating such Orderings
Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum)
hints about the function that may alow it to optimise better.
converts a multivariate function into a univariate function
by keeping all but one argument constant
minimization of a real-valued function of
several variables without using derivatives, using the simple
strategy of optimizing variables one by one.
An interface representing a list of states for a list of taxa
(e.g.
An interface representing a set of site patterns.
Export alignment to Phylip format.
Class for importing PHYLIP sequential file format
A decorator progress listener which delegates all method calls to an internal progress listener.
Random number generation.
abstract base class for all rate matrices
Date: 17/01/2006
Time: 08:08:44
Root an unrooted tree.
A simple, immutable rooted tree implementation that is a subtree of an existing tree
subtending a specified set of taxa..
A tree with a root (node with maximum height).
Static utility functions for rooted trees.
Base class for all score matrices in the package.
A biomolecular sequence.
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).
Interface for importers that do sequences
A set of sequence objects.
Shuffles a sequence and aligns it again multiple times to give mean and variance of
alignments on random sequences.
Interface for sequences data types.
A simple, and initially immutable rooted tree implementation.
A basic implementation on an unrooted tree.
data structure for a set of splits
utilities for split systems
Date: 22/01/2006
Time: 17:28:59
This RootedTree class wraps another RootedTree and transforms
the branch lengths and node heights using various functions.
A rooted or unrooted tree.
Work in progress
A meeting point for tree building from sequence data.
Supported consensus methods.
Supported pairwise distance methods
Supported methods for tree building
Represents a change to a tree.
A listener for notifying about changes to a tree or to the selected nodes in a tree.
Interface for importers that do trees
Represents a change to the selected nodes in a tree.
This class provides the framework for (backwards-through-time) tree simulation.
interface for a function of one variable
minimization of a real-valued function of one variable
without using derivatives.
A collection of utility functions for graphs.
A collection of utility functions for trees.
Provides some miscellaneous methods.
WAG model of amino acid evolution (S.