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

Packages that use Pair
de.jstacs.data | Provides classes for the representation of data.
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer
de.jstacs.sequenceScores.statisticalModels.trainable.hmm | The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models | The package provides different implementations of hidden Markov models based on `AbstractHMM`

Uses of Pair in de.jstacs.data

Methods in de.jstacs.data that return Pair
`Pair<DataSet[],double[][]>` | `DataSet.partition(double[] sequenceWeights, DataSet.PartitionMethod method, double... percentage)` This method partitions the elements, i.e. the `Sequence`s, of the `DataSet` and the corresponding weights in distinct parts where each part holds the corresponding percentage given in the array `percentage`.
`Pair<DataSet[],double[][]>` | `DataSet.partition(double[] sequenceWeights, int k, DataSet.PartitionMethod method)` This method partitions the elements, i.e. the `Sequence`s, of the `DataSet` and the corresponding weights in `k` distinct parts.

Uses of Pair in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery that return Pair
`static Pair<Sequence,BitSet[]>[]` | `KMereStatistic.getKmereSequenceStatistic(boolean bothStrands, int maxMismatch, HashSet<Sequence> filter, DataSet... data)` This method enables the user to get a statistic for a set of `k`-mers.

Uses of Pair in de.jstacs.sequenceScores.statisticalModels.trainable.hmm

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm that return Pair
`abstract Pair<IntList,Double>` | `AbstractHMM.getViterbiPathFor(int startPos, int endPos, Sequence seq)`
`Pair<IntList,Double>` | `AbstractHMM.getViterbiPathFor(Sequence seq)`
`Pair<IntList,Double>[]` | `AbstractHMM.getViterbiPathsFor(DataSet data)` This method returns the viterbi paths and scores for all sequences of the sample `data`.
`static Pair<double[][],double[]>` | `HMMFactory.propagateESS(double ess, ArrayList<HMMFactory.PseudoTransitionElement> list)` Propagates the `ess` for an HMM with absorbing states.

Uses of Pair in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models that return Pair
`Pair<IntList,Double>` | `SamplingHigherOrderHMM.getViterbiPath(int startPos, int endPos, Sequence seq, SamplingHigherOrderHMM.ViterbiComputation compute)` This method returns a viterbi path that is the optimum for the choosen ViterbiComputation method
`Pair<IntList,Double>` | `SamplingHigherOrderHMM.getViterbiPathFor(int startPos, int endPos, Sequence seq)`
`Pair<IntList,Double>` | `HigherOrderHMM.getViterbiPathFor(int startPos, int endPos, Sequence seq)`

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