Uses of Package
org.biojava.bio.dp
Packages that use org.biojava.bio.dp
Package
Description
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Tools for working with profile Hidden Markov Models from the HMMer package.
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Classes in org.biojava.bio.dp used by org.biojava.bio.dist
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Classes in org.biojava.bio.dp used by org.biojava.bio.dpClassDescriptionAn abstract implementation of TrainingAlgorithm that provides a framework for plugging in per-cycle code for parameter optimization.A backpointer.A Dot state.Objects that can perform dymamic programming operations upon sequences with HMMs.The interface for objects that can generate a DP object for a MarkovModel.A state in a markov process that has an emission spectrum.interface implemented by objects that train HMMs.This exception indicates that there is no transition between two states.Start/end state for HMMs.A markov model.A state that contains an entire sub-model.Encapsulates the training of an entire model.This class computes the score that is used to be used in a DP optimisation.A state in a markov process.Extends the Alignment interface so that it is explicitly used to represent a state path through an HMM, and the associated emitted sequence and likelihoods.A callback that is invoked during the training of an HMM.Flags an object as being able to register itself with a model trainer.An object that can be used to train the transitions within a MarkovModel.A log odds weight matrix.
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Classes in org.biojava.bio.dp used by org.biojava.bio.dp.oneheadClassDescriptionObjects that can perform dymamic programming operations upon sequences with HMMs.This exception indicates that there is no transition between two states.A markov model.This class computes the score that is used to be used in a DP optimisation.A state in a markov process.Extends the Alignment interface so that it is explicitly used to represent a state path through an HMM, and the associated emitted sequence and likelihoods.
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Classes in org.biojava.bio.dp used by org.biojava.bio.dp.twoheadClassDescriptionA backpointer.Objects that can perform dymamic programming operations upon sequences with HMMs.This exception indicates that there is no transition between two states.A markov model.This class computes the score that is used to be used in a DP optimisation.A state in a markov process.Extends the Alignment interface so that it is explicitly used to represent a state path through an HMM, and the associated emitted sequence and likelihoods.
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Classes in org.biojava.bio.dp used by org.biojava.bio.program.hmmerClassDescriptionA state in a markov process that has an emission spectrum.This exception indicates that there is no transition between two states.A markov model.A state that contains an entire sub-model.A state in a markov process.Flags an object as being able to register itself with a model trainer.