## 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.