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## Uses of Interface
de.jstacs.motifDiscovery.MotifDiscoverer

Packages that use MotifDiscoverer
de.jstacs.models.mixture.motif |
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer

Uses of MotifDiscoverer in de.jstacs.models.mixture.motif

Classes in de.jstacs.models.mixture.motif that implement MotifDiscoverer
`class` | `HiddenMotifMixture` This is the main class that every generative motif discoverer should implement.
`class` | `SingleHiddenMotifMixture` This class enables the user to search for a single motif in a sequence.

Uses of MotifDiscoverer in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery with parameters of type MotifDiscoverer
`static ImageResult` | `MotifDiscovererToolBox.plot(MotifDiscoverer motifDisc, int component, int motif, Sequence sequence, int startpos, REnvironment r, int width, int height, MotifDiscoverer.KindOfProfile kind)` This method creates a simple plot of the profile of scores for a sequence and a start position.
`static ImageResult` | `MotifDiscovererToolBox.plotAndAnnotate(MotifDiscoverer motifDisc, int component, int motif, Sequence sequence, int startpos, REnvironment r, int width, int height, double yMin, double yMax, double threshold, MotifDiscoverer.KindOfProfile kind)` This method creates a plot of the profile of scores for a sequence and a start position and annotates bindings sites in the plot.

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