Package org.biojava.bio.dist
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.
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ClassDescriptionAn abstract implementation of Distribution.Simple base class for OrderNDistributions.An encapsulation of a count over the Symbols within an alphabet.An encapsulation of a probability distribution over the Symbols within an alphabet.Deprecated.A thing that can make Distributions.The default DistributionFactory implementation.A class to hold static methods for calculations and manipulations using Distributions.An object that can be used to train a distribution up.A context within a group of DistributionTrainers can be trained together.This distribution emits gap symbols.A distribution trainer that just ignores all counts.An encapsulation of a count over the Symbols within a FiniteAlphabet using an AlphabetIndex object.Provides an N'th order distribution.Default factory for Order-N distributions.Class for pairing up two independant distributions.A simple implementation of a distribution, which works with any finite alphabet.Deprecated.Distribution impls should be providing custom trainers.A no-frills implementation of DistributionTrainerContext.A translated view of some underlying distribution.An implementation of an uniform distributionA distribution which does not interact with the training framework.A SAX parser that reads an XML representation of a Distribution from a file and recreates it as a Distribution Object.Writes an OrderNDistribution or simple Distribution to an XML file.
new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY)
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