Package | Description |
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de.jstacs.sequenceScores.statisticalModels.trainable.hmm |
The package provides all interfaces and classes for a hidden Markov model (HMM).
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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.
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de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements |
Modifier and Type | Method and Description |
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protected void |
AbstractHMM.initTransition(BasicHigherOrderTransition.AbstractTransitionElement... te)
This method creates the internal transition.
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Constructor and Description |
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HigherOrderHMM(HMMTrainingParameterSet trainingParameterSet,
String[] name,
Emission[] emission,
BasicHigherOrderTransition.AbstractTransitionElement... te)
This is a convenience constructor.
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HigherOrderHMM(HMMTrainingParameterSet trainingParameterSet,
String[] name,
int[] emissionIdx,
boolean[] forward,
Emission[] emission,
BasicHigherOrderTransition.AbstractTransitionElement... te)
This is the main constructor.
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Modifier and Type | Field and Description |
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protected BasicHigherOrderTransition.AbstractTransitionElement[] |
BasicHigherOrderTransition.transitions
The internally used
BasicHigherOrderTransition.AbstractTransitionElement s. |
Modifier and Type | Method and Description |
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BasicHigherOrderTransition.AbstractTransitionElement |
BasicHigherOrderTransition.AbstractTransitionElement.clone() |
Modifier and Type | Method and Description |
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void |
BasicHigherOrderTransition.AbstractTransitionElement.joinStatistics(BasicHigherOrderTransition.AbstractTransitionElement... te)
This method joins the statistics of different instances and sets this joined statistic as statistic of each instance.
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void |
BasicHigherOrderTransition.AbstractTransitionElement.setParameters(BasicHigherOrderTransition.AbstractTransitionElement t)
Set values of parameters of the instance to the value of the parameters of the given instance.
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Constructor and Description |
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BasicHigherOrderTransition(boolean[] isSilent,
BasicHigherOrderTransition.AbstractTransitionElement... transitions)
The main constructor.
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Modifier and Type | Class and Description |
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class |
BasicPluginTransitionElement
Basic transition element without random initialization of parameters.
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class |
BasicTransitionElement
This class implements the probability distribution for a given context, i.e.
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class |
DistanceBasedScaledTransitionElement
Distance-based scaled transition element for an HMM with distance-scaled transition matrices (DSHMM).
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class |
ReferenceBasedTransitionElement
This class implements transition elements that utilize a reference sequence to determine the transition probability.
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class |
ScaledTransitionElement
Scaled transition element for an HMM with scaled transition matrices (SHMM).
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class |
TransitionElement
This class implements an transition element implements method used
for training via sampling or gradient based optimization approach.
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