Uses of Interface
org.biojava.bio.dist.DistributionFactory

Packages that use DistributionFactory

Package	Description
org.biojava.bio.dist	Probability distributions over Alphabets.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.program.hmmer	Tools for working with profile Hidden Markov Models from the HMMer package.

Uses of DistributionFactory in org.biojava.bio.dist

Classes in org.biojava.bio.dist that implement DistributionFactory

Modifier and Type	Class and Description
static class	DistributionFactory.DefaultDistributionFactory The default DistributionFactory implementation.
class	OrderNDistributionFactory Default factory for Order-N distributions.

Fields in org.biojava.bio.dist declared as DistributionFactory

Modifier and Type	Field and Description
static DistributionFactory	OrderNDistributionFactory.DEFAULT Factory which used DistributionFactory.DEFAULT to create conditioned distributions.
static DistributionFactory	DistributionFactory.DEFAULT The default DistributionFactory object.

Constructors in org.biojava.bio.dist with parameters of type DistributionFactory

Constructor and Description
OrderNDistributionFactory(DistributionFactory df) Construct a new OrderNDistributionFactory with a specified factory for conditioned distributions.
TranslatedDistribution(ReversibleTranslationTable table, Distribution other, DistributionFactory distFact) Create a new TranslatedDistribution.

Uses of DistributionFactory in org.biojava.bio.dp

Constructors in org.biojava.bio.dp with parameters of type DistributionFactory

Constructor and Description
ProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory) Deprecated.
ProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name) Create a new ProfileHMM.
SimpleWeightMatrix(Alphabet alpha, int columns, DistributionFactory dFact)

Uses of DistributionFactory in org.biojava.bio.program.hmmer

Constructors in org.biojava.bio.program.hmmer with parameters of type DistributionFactory

Constructor and Description
HmmerProfileHMM(Alphabet alpha, int columns, DistributionFactory matchFactory, DistributionFactory insertFactory, String name)