Uses of Class
de.jstacs.utils.Pair

Packages that use Pair

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

Uses of Pair in de.jstacs.data

Methods in de.jstacs.data that return Pair

Pair<Sample[],double[][]>	Sample.partition(double[] sequenceWeights, int k, Sample.PartitionMethod method) This method partitions the elements, i.e. the Sequences, of the Sample and the corresponding weights in k distinct parts.
Pair<Sample[],double[][]>	Sample.partition(double[] sequenceWeights, Sample.PartitionMethod method, double... percentage) This method partitions the elements, i.e. the Sequences, of the Sample and the corresponding weights in distinct parts where each part holds the corresponding percentage given in the array percentage.

Uses of Pair in de.jstacs.models.hmm

Methods in de.jstacs.models.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(Sample data) This method returns the viterbi paths and scores for all sequences of the sample data.

Uses of Pair in de.jstacs.models.hmm.models

Methods in de.jstacs.models.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)

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, Sample... data) This method enables the user to get a statistic for a set of k-mers.