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

Packages that use HomogeneousScoringFunction

de.jstacs.scoringFunctions.homogeneous	Provides ScoringFunctions 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, boolean plugInBg)
This constructor creates an instance of HiddenMotifsMixture that is either an OOPS or a ZOOPS model depending on the chosen type.