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Packages that use IntList | |
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de.jstacs.scoringFunctions | Provides ScoringFunction s that can be used in a ScoreClassifier . |
de.jstacs.scoringFunctions.directedGraphicalModels | Provides ScoringFunction s that are equivalent to directed graphical models. |
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 | Provides ScoringFunction s that are mixtures of other ScoringFunction s. |
de.jstacs.scoringFunctions.mix.motifSearch |
Uses of IntList in de.jstacs.scoringFunctions |
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Methods in de.jstacs.scoringFunctions with parameters of type IntList | |
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abstract double |
VariableLengthScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
int length,
IntList indices,
DoubleList dList)
This method computes the logarithm of the score and the partial derivations for a given subsequence. |
double |
VariableLengthScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList dList)
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double |
UniformScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList dList)
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double |
ScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
Returns the logarithmic score for a Sequence beginning at
position start in the Sequence and fills lists with
the indices and the partial derivations. |
double |
NormalizedScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
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double |
MRFScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
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double |
IndependentProductScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
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double |
ScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
IntList indices,
DoubleList partialDer)
Returns the logarithmic score for a Sequence seq and
fills lists with the indices and the partial derivations. |
double |
AbstractNormalizableScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
IntList indices,
DoubleList partialDer)
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Uses of IntList in de.jstacs.scoringFunctions.directedGraphicalModels |
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Methods in de.jstacs.scoringFunctions.directedGraphicalModels with parameters of type IntList | |
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double |
BayesianNetworkScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
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Uses of IntList in de.jstacs.scoringFunctions.homogeneous |
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Methods in de.jstacs.scoringFunctions.homogeneous with parameters of type IntList | |
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double |
UniformHomogeneousScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
int length,
IntList indices,
DoubleList dList)
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double |
HMMScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
int length,
IntList indices,
DoubleList dList)
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double |
HMM0ScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
int length,
IntList indices,
DoubleList dList)
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Uses of IntList in de.jstacs.scoringFunctions.mix |
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Fields in de.jstacs.scoringFunctions.mix declared as IntList | |
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protected IntList[] |
AbstractMixtureScoringFunction.iList
This array contains some IntList s that are used while computing
the partial derivation. |
Methods in de.jstacs.scoringFunctions.mix with parameters of type IntList | |
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double |
StrandScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
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double |
MixtureScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
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Uses of IntList in de.jstacs.scoringFunctions.mix.motifSearch |
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Methods in de.jstacs.scoringFunctions.mix.motifSearch with parameters of type IntList | |
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protected double |
UniformDurationScoringFunction.getLogScoreAndPartialDerivation(IntList indices,
DoubleList partialDer,
int... values)
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double |
SkewNormalLikeScoringFunction.getLogScoreAndPartialDerivation(IntList indices,
DoubleList partialDer,
int... values)
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protected abstract double |
PositionScoringFunction.getLogScoreAndPartialDerivation(IntList indices,
DoubleList partialDer,
int... values)
This method enables the user to get the log-score and the partial derivations without using a sequence object. |
double |
PositionScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
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double |
HiddenMotifsMixture.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
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double |
PositionScoringFunction.getLogScoreAndPartialDerivationForInternal(IntList indices,
DoubleList partialDer)
This method enables the user to get the log-score and the partial derivations without using a sequence object by using the internal iterator. |
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