Package | Description |
---|---|
de.jstacs.sequenceScores.statisticalModels.trainable.hmm |
The package provides all interfaces and classes for a hidden Markov model (HMM).
|
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models |
The package provides different implementations of hidden Markov models based on
AbstractHMM . |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions |
The package provides all interfaces and classes for transitions used in hidden Markov models.
|
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements |
Modifier and Type | Method and Description |
---|---|
static TransitionElement[] |
HMMFactory.createTransition(double[][] hyperParams,
ArrayList<HMMFactory.PseudoTransitionElement> list)
Creates the real
TransitionElement s that can be used to create the HMM. |
Modifier and Type | Method and Description |
---|---|
TransitionElement[] |
HigherOrderHMM.getTransisionElements()
Returns the transition elements of the internal
Transition . |
Constructor and Description |
---|
DifferentiableHigherOrderHMM(MaxHMMTrainingParameterSet trainingParameterSet,
String[] name,
int[] emissionIdx,
boolean[] forward,
DifferentiableEmission[] emission,
boolean likelihood,
double ess,
TransitionElement... te)
This is the main constructor.
|
SamplingHigherOrderHMM(SamplingHMMTrainingParameterSet trainingParameterSet,
String[] name,
int[] emissionIdx,
boolean[] forward,
SamplingEmission[] emission,
TransitionElement... te)
This is the main constructor.
|
SamplingPhyloHMM(SamplingHMMTrainingParameterSet trainingParameterSet,
String[] name,
int[] emissionIdx,
boolean[] forward,
PhyloDiscreteEmission[] emission,
TransitionElement... te)
This is the main constructor for a hidden markov model with phylogenetic emission(s)
This model can be trained using a metropolis hastings algorithm
|
Modifier and Type | Method and Description |
---|---|
TransitionElement[] |
HigherOrderTransition.getTransisionElements()
Returns a clone of the internal transition elements.
|
Constructor and Description |
---|
HigherOrderTransition(boolean[] isSilent,
TransitionElement... transitions)
The main constructor.
|
Modifier and Type | Method and Description |
---|---|
TransitionElement |
TransitionElement.clone() |