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## Uses of Class
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.HomogeneousDiffSM

Packages that use HomogeneousDiffSM
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.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.motif |

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

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable with parameters of type HomogeneousDiffSM
`static ExtendedZOOPSDiffSM` | `DifferentiableStatisticalModelFactory.createZOOPS(int length, DifferentiableStatisticalModel motif, HomogeneousDiffSM bg)` This method allows to create a "zero or one occurrence per sequence" (ZOOPS) model that allows to discover binding sites in a `DataSet`.

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

Subclasses of HomogeneousDiffSM in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous
`class` | `HomogeneousMM0DiffSM` This scoring function implements a homogeneous Markov model of order zero (hMM(0)) for a fixed sequence length.
`class` | `HomogeneousMMDiffSM` This scoring function implements a homogeneous Markov model of arbitrary order for any sequence length.
`class` | `UniformHomogeneousDiffSM` This scoring function does nothing.

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

Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif with parameters of type HomogeneousDiffSM
`ExtendedZOOPSDiffSM(boolean type, int length, int starts, boolean plugIn, HomogeneousDiffSM bg, DifferentiableStatisticalModel[] motif, DurationDiffSM[] posPrior, boolean plugInBg)` This constructor creates an instance of `ExtendedZOOPSDiffSM` that allows to have one site of the specified motifs in a `Sequence`.
`ExtendedZOOPSDiffSM(boolean type, int length, int starts, boolean plugIn, HomogeneousDiffSM bg, DifferentiableStatisticalModel motif, DurationDiffSM posPrior, boolean plugInBg)` This constructor creates an instance of `ExtendedZOOPSDiffSM` that is either an OOPS or a ZOOPS model depending on the chosen `type`.

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