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## Uses of Class
de.jstacs.scoringFunctions.mix.motifSearch.DurationScoringFunction

Packages that use DurationScoringFunction
de.jstacs.scoringFunctions.directedGraphicalModels | Provides `ScoringFunction`s that are equivalent to directed graphical models.
de.jstacs.scoringFunctions.mix.motifSearch |

Uses of DurationScoringFunction in de.jstacs.scoringFunctions.directedGraphicalModels

Constructors in de.jstacs.scoringFunctions.directedGraphicalModels with parameters of type DurationScoringFunction
`MutableMarkovModelScoringFunction(AlphabetContainer alphabet, int length, double ess, boolean plugInParameters, InhomogeneousMarkov structureMeasure, DurationScoringFunction lengthPenalty)` This constructor creates an instance with an prior for the modeled length.
`MutableMarkovModelScoringFunction(AlphabetContainer alphabet, int length, double ess, boolean plugInParameters, int order, DurationScoringFunction lengthPenalty)` This constructor creates an instance with an prior for the modeled length.

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

Subclasses of DurationScoringFunction in de.jstacs.scoringFunctions.mix.motifSearch
`class` | `MixtureDuration` This class implements a mixture of `DurationScoringFunction`s.
`class` | `SkewNormalLikeScoringFunction` This class implements a skew normal like discrete truncated distribution.
`class` | `UniformDurationScoringFunction` This scoring function implements a uniform distribution for positions.

Constructors in de.jstacs.scoringFunctions.mix.motifSearch with parameters of type DurationScoringFunction
`HiddenMotifsMixture(boolean type, int length, int starts, boolean plugIn, HomogeneousScoringFunction bg, NormalizableScoringFunction[] motif, DurationScoringFunction[] posPrior, boolean plugInBg)` This constructor creates an instance of `HiddenMotifsMixture` that allows to have one site of the specified motifs in a `Sequence`.
`HiddenMotifsMixture(boolean type, int length, int starts, boolean plugIn, HomogeneousScoringFunction bg, NormalizableScoringFunction[] motif, DurationScoringFunction[] posPrior, double sign, boolean plugInBg)` This constructor creates an instance of `HiddenMotifsMixture` that allows to have one site of the specified motifs in a `Sequence`.
`HiddenMotifsMixture(boolean type, int length, int starts, boolean plugIn, HomogeneousScoringFunction bg, NormalizableScoringFunction motif, DurationScoringFunction posPrior, boolean plugInBg)` This constructor creates an instance of `HiddenMotifsMixture` that is either an OOPS or a ZOOPS model depending on the chosen `type`.
`HiddenMotifsMixture(boolean type, int length, int starts, boolean plugIn, HomogeneousScoringFunction bg, NormalizableScoringFunction motif, DurationScoringFunction posPrior, double sign, boolean plugInBg)` This constructor creates an instance of `HiddenMotifsMixture` that is either an OOPS or a ZOOPS model depending on the chosen `type`.
`MixtureDuration(int starts, DurationScoringFunction... function)` The main constructor of a `MixtureDuration`.

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