| 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.
|
| Class and Description |
|---|
| ModelTrainer
Encapsulates the training of an entire model.
|
| Class and 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.
|
| Class and 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.
|
| Class and 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.
|
| Class and 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.
|
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