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## 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 `Classifier`s that are based on `SequenceScore`s.
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling | Provides the classes for `AbstractScoreBasedClassifier`s that are based on `SamplingDifferentiableStatisticalModel`s and that sample parameters using the Metropolis-Hastings algorithm.
de.jstacs.classifiers.trainSMBased | Provides the classes for `Classifier`s that are based on `TrainableStatisticalModel`s
de.jstacs.data | Provides classes for the representation of data.
de.jstacs.data.sequences | Provides classes for representing sequences.
de.jstacs.data.sequences.annotation | Provides the facilities to annotate `Sequence`s 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 `SequenceScore`s, 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 `StatisticalModel`s, which can compute a proper (i.e., normalized) likelihood over the input space of sequences.
de.jstacs.sequenceScores.statisticalModels.differentiable | Provides all `DifferentiableStatisticalModel`s, which can compute the gradient with respect to their parameters for a given input `Sequence`.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels | Provides `DifferentiableStatisticalModel`s that are directed graphical models.
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous | Provides `DifferentiableStatisticalModel`s that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture | Provides `DifferentiableSequenceScore`s that are mixtures of other `DifferentiableSequenceScore`s.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif |
de.jstacs.sequenceScores.statisticalModels.trainable | Provides all `TrainableStatisticalModel`s, 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 `byte`s and can therefore be used for discrete `AlphabetContainer`s with alphabets that use only few symbols.
IntSequence This class is for sequences with the alphabet symbols encoded as `int`s and can therefore be used for discrete `AlphabetContainer`s with alphabets that use a huge number of symbols.
MappedDiscreteSequence This class allows to map a discrete `Sequence` to an new `Sequence` using some `DiscreteAlphabetMapping`s.
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 `shorts`s and can therefore be used for discrete `AlphabetContainer`s 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.

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