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 CountAn encapsulation of a count over the Symbols within an alphabet. DistributionAn encapsulation of a probability distribution over the Symbols within an alphabet. DistributionFactoryA thing that can make Distributions. DistributionTrainerAn object that can be used to train a distribution up. DistributionTrainerContextA context within a group of DistributionTrainers can be trained together. OrderNDistributionProvides an N'th order distribution.
Class Summary Class Description AbstractDistributionAn abstract implementation of Distribution. AbstractOrderNDistributionSimple base class for OrderNDistributions. Distribution.NullModelForwarder Deprecated.use
new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY)instead
DistributionFactory.DefaultDistributionFactoryThe default DistributionFactory implementation. DistributionToolsA class to hold static methods for calculations and manipulations using Distributions. GapDistributionThis distribution emits gap symbols. IgnoreCountsTrainerA distribution trainer that just ignores all counts. IndexedCountAn encapsulation of a count over the Symbols within a FiniteAlphabet using an AlphabetIndex object. OrderNDistributionFactoryDefault factory for Order-N distributions. PairDistributionClass for pairing up two independant distributions. SimpleDistributionA simple implementation of a distribution, which works with any finite alphabet. SimpleDistributionTrainer Deprecated.Distribution impls should be providing custom trainers. SimpleDistributionTrainerContextA no-frills implementation of DistributionTrainerContext. TranslatedDistributionA translated view of some underlying distribution. UniformDistributionAn implementation of an uniform distribution UntrainableDistributionA distribution which does not interact with the training framework. XMLDistributionReaderA SAX parser that reads an XML representation of a Distribution from a file and recreates it as a Distribution Object. XMLDistributionWriterWrites an OrderNDistribution or simple Distribution to an XML file.