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## Uses of Class
de.jstacs.scoringFunctions.homogeneous.HomogeneousScoringFunction

Packages that use HomogeneousScoringFunction
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.motifSearch |

Uses of HomogeneousScoringFunction in de.jstacs.scoringFunctions.homogeneous

Subclasses of HomogeneousScoringFunction in de.jstacs.scoringFunctions.homogeneous
`class` | `HMM0ScoringFunction` This scoring function implements a homogeneous Markov model of order zero (hMM(0)) for a fixed sequence length.
`class` | `HMMScoringFunction` This scoring function implements a homogeneous Markov model of arbitrary order for any sequence length.
`class` | `UniformHomogeneousScoringFunction` This scoring function does nothing.

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

Constructors in de.jstacs.scoringFunctions.mix.motifSearch with parameters of type HomogeneousScoringFunction
`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`.

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