Uses of Package
org.biojava.bio.dp

Packages that use org.biojava.bio.dp

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

Classes in org.biojava.bio.dp used by org.biojava.bio.dist

ModelTrainer
Encapsulates the training of an entire model.

Classes in org.biojava.bio.dp used by org.biojava.bio.dp

AbstractTrainer
An abstract implementation of TrainingAlgorithm that provides a framework for plugging in per-cycle code for parameter optimization.

BackPointer
A backpointer.

DotState
A Dot state.

DP
Objects that can perform dymamic programming operations upon sequences with HMMs.

DPFactory
The interface for objects that can generate a DP object for a MarkovModel.

DPMatrix

EmissionState
A state in a markov process that has an emission spectrum.

HMMTrainer
interface implemented by objects that train HMMs.

IllegalTransitionException
This exception indicates that there is no transition between two states.

MagicalState
Start/end state for HMMs.

MarkovModel
A markov model.

ModelInState
A state that contains an entire sub-model.

ModelTrainer
Encapsulates the training of an entire model.

ScoreType
This class computes the score that is used to be used in a DP optimisation.

SimpleEmissionState

SimpleMarkovModel

State
A state in a markov process.

StatePath
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.

StoppingCriteria
A callback that is invoked during the training of an HMM.

Trainable
Flags an object as being able to register itself with a model trainer.

TrainingAlgorithm

TransitionTrainer
An object that can be used to train the transitions within a MarkovModel.

WeightMatrix
A log odds weight matrix.

Classes in org.biojava.bio.dp used by org.biojava.bio.dp.onehead

DP
Objects that can perform dymamic programming operations upon sequences with HMMs.

DPMatrix

IllegalTransitionException
This exception indicates that there is no transition between two states.

MarkovModel
A markov model.

ScoreType
This class computes the score that is used to be used in a DP optimisation.

State
A state in a markov process.

StatePath
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.

Classes in org.biojava.bio.dp used by org.biojava.bio.dp.twohead

BackPointer
A backpointer.

DP
Objects that can perform dymamic programming operations upon sequences with HMMs.

DPMatrix

IllegalTransitionException
This exception indicates that there is no transition between two states.

MarkovModel
A markov model.

ScoreType
This class computes the score that is used to be used in a DP optimisation.

State
A state in a markov process.

StatePath
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.

Classes in org.biojava.bio.dp used by org.biojava.bio.program.hmmer

EmissionState
A state in a markov process that has an emission spectrum.

IllegalTransitionException
This exception indicates that there is no transition between two states.

MarkovModel
A markov model.

ModelInState
A state that contains an entire sub-model.

ProfileHMM

SimpleEmissionState

SimpleMarkovModel

State
A state in a markov process.

Trainable
Flags an object as being able to register itself with a model trainer.