Package org.biojava.bio.dist

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.

Interface Summary

Interface	Description
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

Class	Description
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.