Uses of Class
de.jstacs.utils.Pair

Packages that use Pair

de.jstacs.data	Provides classes for the representation of data. The base classes to represent data are Alphabet and AlphabetContainer for representing alphabets, Sequence and its sub-classes to represent continuous and discrete sequences, and DataSet to represent data sets comprising a set of sequences.
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.
de.jstacs.utils	This package contains a bundle of useful classes and interfaces like ...

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.
Pair<DataSet[],double[][]>	DataSet.partition(double[] sequenceWeights, DataSet.PartitionMethod method, int k) This method partitions the elements, i.e.
Pair<DataSet,double[]>	DataSet.resize(double[] weights, int subsequenceLength)
Pair<DataSet,double[]>	DataSet.subSampling(double number, double[] weights)
static Pair<DataSet,double[]>	DataSet.union(DataSet[] s, double[][] weights, boolean[] in) This method unites all DataSets of the array s regarding the array in and sets the element length in the united DataSet to subsequenceLength.

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.
Pair<double[][],double[]>	SignificantMotifOccurrencesFinder.getPWMAndPosDist(int motif, DataSet data, double[] weights, double[] mean, int addLeft, int addRight) Returns the Position weight matrix (PWM) of the binding sites of motif motif in the data set data of the MotifDiscoverer of this SignificantMotifOccurrencesFinder together with standard deviation of binding site positions computed using the provided mean values for each sequence.
Pair<double[][][],int[][]>	SignificantMotifOccurrencesFinder.getPWMAndPositions(int motif, DataSet data, double[] weights, int addLeft, int addRight) Returns the Position weight matrix (PWM) of the binding sites of motif motif in the data set data of the MotifDiscoverer of this SignificantMotifOccurrencesFinder together with the positions of the binding sites within the sequences of data and the corresponding p-values.

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 data set 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)

Uses of Pair in de.jstacs.utils

Methods in de.jstacs.utils that return Pair

protected static Pair<BufferedImage,Graphics2D>

SeqLogoPlotter.getBufferedImageAndGraphics(int height, double[][] ps) Creates a new BufferedImage with given height and width chosen automatically according to the number of rows of ps, and returns this BufferedImage and its Graphics2D object.