Probability distributions over Alphabets.


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 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.