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Packages that use HomogeneousScoringFunction | |
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de.jstacs.scoringFunctions.homogeneous | Provides ScoringFunction s 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 |
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Subclasses of HomogeneousScoringFunction in de.jstacs.scoringFunctions.homogeneous | |
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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 |
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Constructors in de.jstacs.scoringFunctions.mix.motifSearch with parameters of type HomogeneousScoringFunction | |
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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 . |
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HiddenMotifsMixture(boolean type,
int length,
int starts,
boolean plugIn,
HomogeneousScoringFunction bg,
NormalizableScoringFunction[] motif,
DurationScoringFunction[] posPrior,
double sign,
boolean plugInBg)
This constructor creates an instance of HiddenMotifsMixture that allows to have one site of the specified motifs in a Sequence . |
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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 . |
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HiddenMotifsMixture(boolean type,
int length,
int starts,
boolean plugIn,
HomogeneousScoringFunction bg,
NormalizableScoringFunction motif,
DurationScoringFunction posPrior,
double sign,
boolean plugInBg)
This constructor creates an instance of HiddenMotifsMixture that is either an OOPS or a ZOOPS model depending on the chosen type . |
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