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## Uses of Class
de.jstacs.motifDiscovery.MotifDiscoverer.KindOfProfile

Packages that use MotifDiscoverer.KindOfProfile
de.jstacs.models.mixture.motif |
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer
de.jstacs.scoringFunctions | Provides `ScoringFunction`s that can be used in a `ScoreClassifier`.
de.jstacs.scoringFunctions.mix | Provides `ScoringFunction`s that are mixtures of other `ScoringFunction`s.
de.jstacs.scoringFunctions.mix.motifSearch |

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

Methods in de.jstacs.models.mixture.motif with parameters of type MotifDiscoverer.KindOfProfile
`double[]` | `SingleHiddenMotifMixture.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile kind)`

Uses of MotifDiscoverer.KindOfProfile in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery that return MotifDiscoverer.KindOfProfile
`static MotifDiscoverer.KindOfProfile` | `MotifDiscoverer.KindOfProfile.valueOf(String name)` Returns the enum constant of this type with the specified name.
`static MotifDiscoverer.KindOfProfile[]` | `MotifDiscoverer.KindOfProfile.values()` Returns an array containing the constants of this enum type, in the order they are declared.

Methods in de.jstacs.motifDiscovery with parameters of type MotifDiscoverer.KindOfProfile
`double[]` | `MotifDiscoverer.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile kind)` Returns the profile of the scores for component `component` and motif `motif` at all possible start positions of the motif in the sequence `sequence` beginning at `startpos`.
`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 that have a higher score than `threshold`.

Uses of MotifDiscoverer.KindOfProfile in de.jstacs.scoringFunctions

Methods in de.jstacs.scoringFunctions with parameters of type MotifDiscoverer.KindOfProfile
`double[]` | `IndependentProductScoringFunction.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile dist)`

Uses of MotifDiscoverer.KindOfProfile in de.jstacs.scoringFunctions.mix

Methods in de.jstacs.scoringFunctions.mix with parameters of type MotifDiscoverer.KindOfProfile
`double[]` | `MixtureScoringFunction.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile kind)`

Uses of MotifDiscoverer.KindOfProfile in de.jstacs.scoringFunctions.mix.motifSearch

Methods in de.jstacs.scoringFunctions.mix.motifSearch with parameters of type MotifDiscoverer.KindOfProfile
`double[]` | `HiddenMotifsMixture.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile dist)`

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