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.