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## Uses of Class
de.jstacs.utils.IntList

Packages that use IntList
de.jstacs.classifier.scoringFunctionBased | Provides the classes for `Classifier`s that are based on `ScoringFunction`s.
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.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.classifier.scoringFunctionBased

Fields in de.jstacs.classifier.scoringFunctionBased declared as IntList
`protected IntList[][]` | `SFBasedOptimizableFunction.iList` These `IntList`s are used during the parallel computation of the gradient.

Uses of IntList in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery that return IntList
`IntList` | `SignificantMotifOccurrencesFinder.getStartPositions(int startPos, Sample data, int motifIndex, int addMax)` This method returns a list of start positions of binding sites.

Uses of IntList in de.jstacs.scoringFunctions

Methods in de.jstacs.scoringFunctions with parameters of type IntList
`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` | `CMMScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList)`
`double` | `UniformScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList dList)`
`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)`
`double` | `MRFScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `IndependentProductScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `AbstractVariableLengthScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList dList)`
`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)`

Uses of IntList in de.jstacs.scoringFunctions.directedGraphicalModels

Methods in de.jstacs.scoringFunctions.directedGraphicalModels with parameters of type IntList
`double` | `BayesianNetworkScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`

Uses of IntList in de.jstacs.scoringFunctions.homogeneous

Methods in de.jstacs.scoringFunctions.homogeneous with parameters of type IntList
`double` | `UniformHomogeneousScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList)`
`double` | `HMMScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList)`
`double` | `HMM0ScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList)`

Uses of IntList in de.jstacs.scoringFunctions.mix

Fields in de.jstacs.scoringFunctions.mix declared as IntList
`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
`double` | `VariableLengthMixtureScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList partialDer)`
`double` | `StrandScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `MixtureScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`

Uses of IntList in de.jstacs.scoringFunctions.mix.motifSearch

Methods in de.jstacs.scoringFunctions.mix.motifSearch with parameters of type IntList
`double` | `UniformDurationScoringFunction.getLogScoreAndPartialDerivation(IntList indices, DoubleList partialDer, int... values)`
`double` | `SkewNormalLikeScoringFunction.getLogScoreAndPartialDerivation(IntList indices, DoubleList partialDer, int... values)`
`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` | `MixtureDuration.getLogScoreAndPartialDerivation(IntList indices, DoubleList partialDer, int... values)`
`double` | `PositionScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `HiddenMotifsMixture.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`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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