Uses of Package
org.biojava.bio.dp

Packages that use org.biojava.bio.dp

Package	Description
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

Class	Description
ModelTrainer	Encapsulates the training of an entire model.

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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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.