| Package | Description |
|---|---|
| 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.clustering.distances | |
| 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.io |
Provides classes for reading data from and writing to a file and storing a number of datatypes, including all primitives, arrays of primitives, and
Storables to an XML-representation. |
| 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.localMixture | |
| 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 ...
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| CyclicSequenceAdaptor
This class is an adapter for sequence to mimic cyclic sequences.
|
| WrongSequenceTypeException
This
Exception indicates that the type of the sequence (
ByteSequence, ShortSequence, ...) is not suitable for a given
AlphabetContainer. |
| Class and Description |
|---|
| ArbitrarySequence
This class is for any continuous or hybrid sequence.
|
| CyclicSequenceAdaptor
This class is an adapter for sequence to mimic cyclic sequences.
|
| 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. |
| Class and Description |
|---|
| 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. |
| CyclicSequenceAdaptor
This class is an adapter for sequence to mimic cyclic sequences.
|
| 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. |
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| 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. |
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|
| Class and Description |
|---|
| Sequence
This is the main class for all sequences.
|