Package | Description |
---|---|
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.states |
The package provides all interfaces and classes for states used in hidden Markov models.
|
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions | |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous | |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete |
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.
|
Constructor and Description |
---|
SimpleDifferentiableState(DifferentiableEmission e,
String name,
boolean forward)
This is the constructor of a
SimpleState . |
Modifier and Type | Class and Description |
---|---|
class |
SilentEmission
This class implements a silent emission which is used to create silent states.
|
class |
UniformEmission
This class implements a simple uniform emission.
|
Modifier and Type | Class and Description |
---|---|
class |
GaussianEmission
Emission for continuous values following a Gaussian distribution.
|
class |
PluginGaussianEmission
Basic Gaussian emission distribution without random initialization of parameters.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractConditionalDiscreteEmission
The abstract super class of discrete emissions.
|
class |
DiscreteEmission
This class implements a simple discrete emission without any condition.
|
class |
PhyloDiscreteEmission
Phylogenetic discrete emission
This class uses a phylogenetic tree to describe multidimensional data
It implements Felsensteins model for nucleotide substitution (F81)
|
class |
ReferenceSequenceDiscreteEmission
This class implements a discrete emission that depends on some
ReferenceSequenceAnnotation
at a certain reference position. |