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## Uses of Class
de.jstacs.utils.DoubleList

Packages that use DoubleList
de.jstacs.classifiers.differentiableSequenceScoreBased | Provides the classes for `Classifier`s that are based on `SequenceScore`s.
de.jstacs.sampling | This package contains many classes that can be used while a sampling.
de.jstacs.sequenceScores.differentiable |
de.jstacs.sequenceScores.differentiable.logistic |
de.jstacs.sequenceScores.statisticalModels.differentiable | Provides all `DifferentiableStatisticalModel`s, which can compute the gradient with respect to their parameters for a given input `Sequence`.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels | Provides `DifferentiableStatisticalModel`s that are directed graphical models.
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous | Provides `DifferentiableStatisticalModel`s that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture | Provides `DifferentiableSequenceScore`s that are mixtures of other `DifferentiableSequenceScore`s.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif |
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 |
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 |
de.jstacs.utils | This package contains a bundle of useful classes and interfaces like ...

Uses of DoubleList in de.jstacs.classifiers.differentiableSequenceScoreBased

Fields in de.jstacs.classifiers.differentiableSequenceScoreBased declared as DoubleList
`protected DoubleList[][]` | `DiffSSBasedOptimizableFunction.dList` These `DoubleList`s are used during the parallel computation of the gradient.

Uses of DoubleList in de.jstacs.sampling

Fields in de.jstacs.sampling declared as DoubleList
`protected DoubleList[]` | `AbstractBurnInTest.values` This array contains all values that will be set via `BurnInTest.setValue(double)`.

Uses of DoubleList in de.jstacs.sequenceScores.differentiable

Methods in de.jstacs.sequenceScores.differentiable with parameters of type DoubleList
`double` | `DifferentiableSequenceScore.getLogScoreAndPartialDerivation(Sequence seq, int start, int end, IntList indices, DoubleList partialDer)` Returns the logarithmic score for a `Sequence` beginning at position `start` in the `Sequence` and fills lists with the indices and the partial derivations.
`double` | `AbstractDifferentiableSequenceScore.getLogScoreAndPartialDerivation(Sequence seq, int startpos, int endpos, IntList indices, DoubleList partialDer)`
`double` | `UniformDiffSS.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList dList)`
`double` | `IndependentProductDiffSS.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `DifferentiableSequenceScore.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)` Returns the logarithmic score for a `Sequence` beginning at position `start` in the `Sequence` and fills lists with the indices and the partial derivations.
`double` | `DifferentiableSequenceScore.getLogScoreAndPartialDerivation(Sequence seq, IntList indices, DoubleList partialDer)` Returns the logarithmic score for a `Sequence` `seq` and fills lists with the indices and the partial derivations.
`double` | `AbstractDifferentiableSequenceScore.getLogScoreAndPartialDerivation(Sequence seq, IntList indices, DoubleList partialDer)`

Uses of DoubleList in de.jstacs.sequenceScores.differentiable.logistic

Methods in de.jstacs.sequenceScores.differentiable.logistic with parameters of type DoubleList
`double` | `LogisticDiffSS.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.differentiable

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable with parameters of type DoubleList
`double` | `VariableLengthDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int startpos, int endpos, IntList indices, DoubleList partialDer)`
`double` | `CyclicMarkovModelDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, int end, IntList indices, DoubleList dList)`
`abstract double` | `AbstractVariableLengthDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int startpos, int endpos, IntList indices, DoubleList partialDer)`
`double` | `UniformDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList dList)`
`double` | `NormalizedDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `MultiDimensionalSequenceWrapperDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `MarkovRandomFieldDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `MappingDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `AbstractVariableLengthDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList dList)`

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels with parameters of type DoubleList
`double` | `BayesianNetworkDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous with parameters of type DoubleList
`double` | `UniformHomogeneousDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, int end, IntList indices, DoubleList dList)`
`double` | `HomogeneousMMDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, int end, IntList indices, DoubleList dList)`
`double` | `HomogeneousMM0DiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, int end, IntList indices, DoubleList dList)`

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture

Fields in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture declared as DoubleList
`protected DoubleList[]` | `AbstractMixtureDiffSM.dList` This array contains some `DoubleList`s that are used while computing the partial derivation.

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture with parameters of type DoubleList
`double` | `VariableLengthMixtureDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, int end, IntList indices, DoubleList partialDer)`
`double` | `StrandDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `MixtureDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif with parameters of type DoubleList
`double` | `UniformDurationDiffSM.getLogScoreAndPartialDerivation(IntList indices, DoubleList partialDer, int... values)`
`double` | `SkewNormalLikeDurationDiffSM.getLogScoreAndPartialDerivation(IntList indices, DoubleList partialDer, int... values)`
`abstract double` | `PositionDiffSM.getLogScoreAndPartialDerivation(IntList indices, DoubleList partialDer, int... values)` This method enables the user to get the log-score and the partial derivations without using a sequence object.
`double` | `MixtureDurationDiffSM.getLogScoreAndPartialDerivation(IntList indices, DoubleList partialDer, int... values)`
`double` | `PositionDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `ExtendedZOOPSDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `PositionDiffSM.getLogScoreAndPartialDerivationForInternal(IntList indices, DoubleList partialDer)` This method enables the user to get the log-score and the partial derivations without using a sequence object by using the internal iterator.

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models

Fields in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models declared as DoubleList
`protected DoubleList[]` | `DifferentiableHigherOrderHMM.partDerState` Help array for the derivatives of the parameters of the states
`protected DoubleList[]` | `DifferentiableHigherOrderHMM.partDerTransition` Help array for the derivatives of the parameters of the transition

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models with parameters of type DoubleList
`double` | `DifferentiableHigherOrderHMM.getLogScoreAndPartialDerivation(Sequence seq, int startPos, int endPos, IntList indices, DoubleList partialDer)`
`double` | `DifferentiableHigherOrderHMM.getLogScoreAndPartialDerivation(Sequence seq, int startPos, IntList indices, DoubleList partialDer)`
`double` | `DifferentiableHigherOrderHMM.getLogScoreAndPartialDerivation(Sequence seq, IntList indices, DoubleList partialDer)`

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states with parameters of type DoubleList
`double` | `SimpleDifferentiableState.getLogScoreAndPartialDerivation(int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq)`
`double` | `DifferentiableState.getLogScoreAndPartialDerivation(int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq)` This method allows to compute the logarithm of the score and the gradient for the given subsequences.

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions with parameters of type DoubleList
`double` | `UniformEmission.getLogProbAndPartialDerivationFor(boolean forward, int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq)`
`double` | `SilentEmission.getLogProbAndPartialDerivationFor(boolean forward, int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq)`
`double` | `DifferentiableEmission.getLogProbAndPartialDerivationFor(boolean forward, int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq)` Returns the logarithmic score for a `Sequence` beginning at position `start` in the `Sequence` and fills lists with the indices and the partial derivations.

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous with parameters of type DoubleList
`double` | `GaussianEmission.getLogProbAndPartialDerivationFor(boolean forward, int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq)`

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete with parameters of type DoubleList
`double` | `PhyloDiscreteEmission.getLogProbAndPartialDerivationFor(boolean forward, int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq)`
`double` | `AbstractConditionalDiscreteEmission.getLogProbAndPartialDerivationFor(boolean forward, int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq)`

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions with parameters of type DoubleList
`double` | `HigherOrderTransition.getLogScoreAndPartialDerivation(int layer, int index, int childIdx, IntList indices, DoubleList partDer, Sequence sequence, int sequencePosition)`
`double` | `DifferentiableTransition.getLogScoreAndPartialDerivation(int layer, int index, int childIdx, IntList indices, DoubleList partDer, Sequence sequence, int sequencePosition)` This method allows to compute the logarithm of the score and the gradient for a specific transition.

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements with parameters of type DoubleList
`double` | `TransitionElement.getLogScoreAndPartialDerivation(int childIdx, IntList indices, DoubleList partialDer, Sequence sequence, int sequencePosition)` Returns the logarithmic score and fills lists with the indices and the partial derivations.

Uses of DoubleList in de.jstacs.utils

Methods in de.jstacs.utils that return DoubleList
`DoubleList` | `DoubleList.clone()`

Methods in de.jstacs.utils with parameters of type DoubleList
`void` | `DoubleList.addAll(DoubleList list2)` This method adds all elements of `DoubleList` `list2` to the current list.

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