Uses of Package
org.biojava.bio.dist

Packages that use org.biojava.bio.dist

Package	Description
org.biojava.bio.dist	Probability distributions over Alphabets.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.gui	Graphical interfaces for biojava objects.
org.biojava.bio.molbio	The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
org.biojava.bio.program.fastq	FASTQ and variants sequence format I/O.
org.biojava.bio.program.hmmer	Tools for working with profile Hidden Markov Models from the HMMer package.
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.
org.biojavax.ga.functions	GA functions A genetic algorithm requires a number of functions.
org.biojavax.ga.util	Utility functions and helper classes

Classes in org.biojava.bio.dist used by org.biojava.bio.dist

Class and Description
AbstractDistribution An abstract implementation of Distribution.
Count An encapsulation of a count over the Symbols within an alphabet.
Distribution An encapsulation of a probability distribution over the Symbols within an alphabet.
DistributionFactory A thing that can make Distributions.
DistributionTrainer An object that can be used to train a distribution up.
DistributionTrainerContext A context within a group of DistributionTrainers can be trained together.
IgnoreCountsTrainer A distribution trainer that just ignores all counts.
OrderNDistribution Provides an N'th order distribution.
SimpleDistribution A simple implementation of a distribution, which works with any finite alphabet.

Classes in org.biojava.bio.dist used by org.biojava.bio.dp

Class and Description
Distribution An encapsulation of a probability distribution over the Symbols within an alphabet.
DistributionFactory A thing that can make Distributions.
DistributionTrainerContext A context within a group of DistributionTrainers can be trained together.
SimpleDistributionTrainerContext A no-frills implementation of DistributionTrainerContext.

Classes in org.biojava.bio.dist used by org.biojava.bio.gui

Class and Description
Distribution An encapsulation of a probability distribution over the Symbols within an alphabet.

Classes in org.biojava.bio.dist used by org.biojava.bio.molbio

Class and Description
Distribution An encapsulation of a probability distribution over the Symbols within an alphabet.

Classes in org.biojava.bio.dist used by org.biojava.bio.program.fastq

Class and Description
Distribution An encapsulation of a probability distribution over the Symbols within an alphabet.

Classes in org.biojava.bio.dist used by org.biojava.bio.program.hmmer

Class and Description
Distribution An encapsulation of a probability distribution over the Symbols within an alphabet.
DistributionFactory A thing that can make Distributions.

Classes in org.biojava.bio.dist used by org.biojava.bio.program.phred

Class and Description
Distribution An encapsulation of a probability distribution over the Symbols within an alphabet.

Classes in org.biojava.bio.dist used by org.biojava.bio.seq

Class and Description
Distribution An encapsulation of a probability distribution over the Symbols within an alphabet.

Classes in org.biojava.bio.dist used by org.biojava.bio.symbol

Class and Description
Distribution An encapsulation of a probability distribution over the Symbols within an alphabet.

Classes in org.biojava.bio.dist used by org.biojavax.ga.functions

Class and Description
OrderNDistribution Provides an N'th order distribution.

Classes in org.biojava.bio.dist used by org.biojavax.ga.util

Class and Description
OrderNDistribution Provides an N'th order distribution.