Uses of Package
de.jstacs.data.sequences

Packages that use de.jstacs.data.sequences

de.jstacs.algorithms.alignment	Provides classes for alignments.
de.jstacs.algorithms.alignment.cost	Provides classes for cost functions used in alignments.
de.jstacs.classifiers	This package provides the framework for any classifier.
de.jstacs.classifiers.differentiableSequenceScoreBased	Provides the classes for Classifiers that are based on SequenceScores. It includes a sub-package for discriminative objective functions, namely conditional likelihood and supervised posterior, and a separate sub-package for the parameter priors, that can be used for the supervised posterior.
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling	Provides the classes for AbstractScoreBasedClassifiers that are based on SamplingDifferentiableStatisticalModels and that sample parameters using the Metropolis-Hastings algorithm.
de.jstacs.classifiers.trainSMBased	Provides the classes for Classifiers that are based on TrainableStatisticalModels.
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.data.sequences	Provides classes for representing sequences. The implementations of sequences currently include DiscreteSequences prepared for alphabets of different sizes, and ArbitrarySequences that may contain continuous values as well. As sub-package provides the facilities to annotate Sequences.
de.jstacs.data.sequences.annotation	Provides the facilities to annotate Sequences using a number of pre-defined annotation types, or additional implementations of the SequenceAnnotation class.
de.jstacs.motifDiscovery	This package provides the framework including the interface for any de novo motif discoverer.
de.jstacs.sequenceScores	Provides all SequenceScores, which can be used to score a Sequence, typically using some model assumptions.
de.jstacs.sequenceScores.differentiable
de.jstacs.sequenceScores.differentiable.logistic
de.jstacs.sequenceScores.statisticalModels	Provides all StatisticalModels, which can compute a proper (i.e., normalized) likelihood over the input space of sequences. StatisticalModels can be further differentiated into TrainableStatisticalModels, which can be learned from a single input DataSet, and DifferentiableStatisticalModels, which define a proper likelihood but can also compute gradients like DifferentiableSequenceScores.
de.jstacs.sequenceScores.statisticalModels.differentiable	Provides all DifferentiableStatisticalModels, which can compute the gradient with respect to their parameters for a given input Sequence.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels	Provides DifferentiableStatisticalModels that are directed graphical models.
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous	Provides DifferentiableStatisticalModels that are homogeneous, i.e.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture	Provides DifferentiableSequenceScores that are mixtures of other DifferentiableSequenceScores.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif
de.jstacs.sequenceScores.statisticalModels.trainable	Provides all TrainableStatisticalModels, which can be learned from a single DataSet.
de.jstacs.sequenceScores.statisticalModels.trainable.discrete
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous	This package contains various inhomogeneous models.
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.sequenceScores.statisticalModels.trainable.hmm.states	The package provides all interfaces and classes for states used in hidden Markov models.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions	The package provides all interfaces and classes for transitions used in hidden Markov models.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements
de.jstacs.sequenceScores.statisticalModels.trainable.mixture	This package is the super package for any mixture model.
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif
de.jstacs.utils	This package contains a bundle of useful classes and interfaces like ...

Classes in de.jstacs.data.sequences used by de.jstacs.algorithms.alignment

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.algorithms.alignment.cost

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.classifiers

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.classifiers.differentiableSequenceScoreBased

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.classifiers.differentiableSequenceScoreBased.sampling

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.classifiers.trainSMBased

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.data

Sequence
This is the main class for all sequences.

WrongSequenceTypeException
This Exception indicates that the type of the sequence ( ByteSequence, ShortSequence, ...) is not suitable for a given AlphabetContainer.

Classes in de.jstacs.data.sequences used by de.jstacs.data.sequences

ArbitraryFloatSequence
This class is for any continuous or hybrid sequence.

ArbitrarySequence
This class is for any continuous or hybrid sequence.

ByteSequence
This class is for sequences with the alphabet symbols encoded as bytes and can therefore be used for discrete AlphabetContainers with alphabets that use only few symbols.

IntSequence
This class is for sequences with the alphabet symbols encoded as ints and can therefore be used for discrete AlphabetContainers with alphabets that use a huge number of symbols.

MappedDiscreteSequence
This class allows to map a discrete Sequence to an new Sequence using some DiscreteAlphabetMappings.

MultiDimensionalArbitrarySequence
This class is for multidimensional arbitrary sequences.

MultiDimensionalDiscreteSequence
This class is for multidimensional discrete sequences that can be used, for instance, for phylogenetic footprinting.

MultiDimensionalSequence
This class is for multidimensional sequences that can be used, for instance, for phylogenetic footprinting.

PermutedSequence
This class is for permuted sequences.

Sequence
This is the main class for all sequences.

Sequence.RecursiveSequence
This is the main class for subsequences, composite sequences, ...

ShortSequence
This class is for sequences with the alphabet symbols encoded as shortss and can therefore be used for discrete AlphabetContainers with alphabets that use many different symbols.

SimpleDiscreteSequence
This is the main class for any discrete sequence.

SparseSequence
This class is an implementation for sequences on one alphabet with length 4.

WrongSequenceTypeException
This Exception indicates that the type of the sequence ( ByteSequence, ShortSequence, ...) is not suitable for a given AlphabetContainer.

Classes in de.jstacs.data.sequences used by de.jstacs.data.sequences.annotation

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.motifDiscovery

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.differentiable

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.differentiable.logistic

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.differentiable

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.differentiable.mixture

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous

Sequence
This is the main class for all sequences.

WrongSequenceTypeException
This Exception indicates that the type of the sequence ( ByteSequence, ShortSequence, ...) is not suitable for a given AlphabetContainer.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.mixture

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif

Sequence
This is the main class for all sequences.

Classes in de.jstacs.data.sequences used by de.jstacs.utils

Sequence
This is the main class for all sequences.