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

Packages that use DoubleList
de.jstacs.models.mixture.gibbssampling | This package contains many classes that can be used while a Gibbs sampling.
de.jstacs.scoringFunctions | Provides `ScoringFunction`s that can be used in a `ScoreClassifier`.
de.jstacs.scoringFunctions.directedGraphicalModels | Provides `ScoringFunction`s that are equivalent to directed graphical models.
de.jstacs.scoringFunctions.homogeneous | Provides `ScoringFunction`s that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.scoringFunctions.mix | Provides `ScoringFunction`s that are mixtures of other `ScoringFunction`s.
de.jstacs.scoringFunctions.mix.motifSearch |

Uses of DoubleList in de.jstacs.models.mixture.gibbssampling

Fields in de.jstacs.models.mixture.gibbssampling 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.scoringFunctions

Methods in de.jstacs.scoringFunctions with parameters of type DoubleList
`abstract double` | `VariableLengthScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList)` This method computes the logarithm of the score and the partial derivations for a given subsequence.
`double` | `VariableLengthScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList dList)`
`double` | `UniformScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList dList)`
`double` | `ScoringFunction.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` | `NormalizedScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `MRFScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `IndependentProductScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `ScoringFunction.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` | `AbstractNormalizableScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, IntList indices, DoubleList partialDer)`

Uses of DoubleList in de.jstacs.scoringFunctions.directedGraphicalModels

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

Uses of DoubleList in de.jstacs.scoringFunctions.homogeneous

Methods in de.jstacs.scoringFunctions.homogeneous with parameters of type DoubleList
`double` | `UniformHomogeneousScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList)`
`double` | `HMMScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList)`
`double` | `HMM0ScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList)`

Uses of DoubleList in de.jstacs.scoringFunctions.mix

Fields in de.jstacs.scoringFunctions.mix declared as DoubleList
`protected DoubleList[]` | `AbstractMixtureScoringFunction.dList` This array contains some `DoubleList`s that are used while computing the partial derivation.

Methods in de.jstacs.scoringFunctions.mix with parameters of type DoubleList
`double` | `StrandScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `MixtureScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`

Uses of DoubleList in de.jstacs.scoringFunctions.mix.motifSearch

Methods in de.jstacs.scoringFunctions.mix.motifSearch with parameters of type DoubleList
`protected double` | `UniformDurationScoringFunction.getLogScoreAndPartialDerivation(IntList indices, DoubleList partialDer, int... values)`
`double` | `SkewNormalLikeScoringFunction.getLogScoreAndPartialDerivation(IntList indices, DoubleList partialDer, int... values)`
`protected abstract double` | `PositionScoringFunction.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` | `PositionScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `HiddenMotifsMixture.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `PositionScoringFunction.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.

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