## Package org.biojava.bio.dist

Probability distributions over Alphabets.

See:
Description

Interface Summary
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.
OrderNDistribution: Provides an N'th order distribution.

Class Summary
AbstractDistribution: An abstract implementation of Distribution.
AbstractOrderNDistribution: Simple base class for OrderNDistributions.
Distribution.NullModelForwarder: Deprecated. use `new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY)` instead
DistributionFactory.DefaultDistributionFactory: The default DistributionFactory implementation.
DistributionTools: A class to hold static methods for calculations and manipulations using Distributions.
GapDistribution: This distribution emits gap symbols.
IgnoreCountsTrainer: A distribution trainer that just ignores all counts.
IndexedCount: An encapsulation of a count over the Symbols within a FiniteAlphabet using an AlphabetIndex object.
OrderNDistributionFactory: Default factory for Order-N distributions.
PairDistribution: Class for pairing up two independant distributions.
SimpleDistribution: A simple implementation of a distribution, which works with any finite alphabet.
SimpleDistributionTrainer: Deprecated. Distribution impls should be providing custom trainers.
SimpleDistributionTrainerContext: A no-frills implementation of DistributionTrainerContext.
TranslatedDistribution: A translated view of some underlying distribution.
UniformDistribution: An implementation of an uniform distribution
UntrainableDistribution: A distribution which does not interact with the training framework.
XMLDistributionReader: A SAX parser that reads an XML representation of a Distribution from a file and recreates it as a Distribution Object.
XMLDistributionWriter: Writes an OrderNDistribution or simple Distribution to an XML file.

## Package org.biojava.bio.dist Description

Probability distributions over Alphabets. Distributions are useful in many aspects of bioinformatics, especially when performing statistical methods. They are used to encapsulate emission spectra in weight matrices and Hidden Markov Models.