| Package | Description |
|---|---|
| de.jstacs |
This package is the root package for the most and important packages.
|
| de.jstacs.algorithms.alignment |
Provides classes for alignments.
|
| de.jstacs.algorithms.alignment.cost |
Provides classes for cost functions used in alignments.
|
| de.jstacs.algorithms.optimization.termination |
Provides classes for termination conditions that can be used in algorithms.
|
| de.jstacs.classifiers |
This package provides the framework for any classifier.
|
| de.jstacs.classifiers.assessment |
This package allows to assess classifiers.
It contains the class ClassifierAssessment that
is used as a super-class of all implemented methodologies of
an assessment to assess classifiers. |
| 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.gendismix |
Provides an implementation of a classifier that allows to train the parameters of a set of
DifferentiableStatisticalModels by
a unified generative-discriminative learning principle. |
| de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior |
Provides a general definition of a parameter log-prior and a number of implementations of Laplace and Gaussian priors.
|
| de.jstacs.classifiers.differentiableSequenceScoreBased.msp |
Provides an implementation of a classifier that allows to train the parameters of a set of
DifferentiableStatisticalModels either
by maximum supervised posterior (MSP) or by maximum conditional likelihood (MCL). |
| 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.performanceMeasures |
This package provides the implementations of performance measures that can be used to assess any classifier.
|
| de.jstacs.classifiers.trainSMBased |
Provides the classes for
Classifiers that are based on TrainableStatisticalModels. |
| de.jstacs.clustering.hierachical | |
| 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.alphabets |
Provides classes for the representation of discrete and continuous alphabets, including a
DNAAlphabet for the most common case of DNA-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.motifDiscovery.history | |
| de.jstacs.parameters |
This package provides classes for parameters that establish a general convention for the description of parameters
as defined in the
Parameter-interface. |
| de.jstacs.parameters.validation |
Provides classes for the validation of
Parameter values. |
| de.jstacs.results |
This package provides classes for results and sets of results.
|
| de.jstacs.sampling |
This package contains many classes that can be used while a sampling.
|
| 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.directedGraphicalModels.structureLearning.measures |
Provides the facilities to learn the structure of a
BayesianNetworkDiffSM. |
| de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures |
Provides the facilities to learn the structure of a
BayesianNetworkDiffSM as
a Bayesian tree using a number of measures to define a rating of structures. |
| de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures |
Provides the facilities to learn the structure of a
BayesianNetworkDiffSM as
a permuted Markov model using a number of measures to define a rating of structures. |
| 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.homogeneous.parameters | |
| de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous |
This package contains various inhomogeneous models.
|
| de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters | |
| de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared | |
| 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.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.training |
The package provides all classes used to determine the training algorithm of a hidden Markov model.
|
| 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.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior | |
| de.jstacs.sequenceScores.statisticalModels.trainable.phylo | |
| de.jstacs.tools | |
| de.jstacs.tools.ui.galaxy | |
| de.jstacs.utils |
This package contains a bundle of useful classes and interfaces like ...
|
| Class and Description |
|---|
| AnnotatedEntity
Superclass for all Jstacs entities that have a name, a comment, and a data type as annotations.
|
| DataType |
| InstantiableFromParameterSet
Interface for all classes that can be instantiated from a
InstanceParameterSet. |
| Singleton
This interface states that the implementing class has only one immutable instance.
|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| InstantiableFromParameterSet
Interface for all classes that can be instantiated from a
InstanceParameterSet. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| AnnotatedEntity
Superclass for all Jstacs entities that have a name, a comment, and a data type as annotations.
|
| NotTrainedException
A
NotTrainedException is thrown if the user tries to use an untrained
model. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| NotTrainedException
A
NotTrainedException is thrown if the user tries to use an untrained
model. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| NotTrainedException
A
NotTrainedException is thrown if the user tries to use an untrained
model. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| InstantiableFromParameterSet
Interface for all classes that can be instantiated from a
InstanceParameterSet. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| InstantiableFromParameterSet
Interface for all classes that can be instantiated from a
InstanceParameterSet. |
| Singleton
This interface states that the implementing class has only one immutable instance.
|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| InstantiableFromParameterSet
Interface for all classes that can be instantiated from a
InstanceParameterSet. |
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| AnnotatedEntity
Superclass for all Jstacs entities that have a name, a comment, and a data type as annotations.
|
| AnnotatedEntityList
Class for a list of
AnnotatedEntitys where
elements can be accessed either by index or by the name
of the AnnotatedEntity. |
| DataType |
| InstantiableFromParameterSet
Interface for all classes that can be instantiated from a
InstanceParameterSet. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| AnnotatedEntity
Superclass for all Jstacs entities that have a name, a comment, and a data type as annotations.
|
| AnnotatedEntityList
Class for a list of
AnnotatedEntitys where
elements can be accessed either by index or by the name
of the AnnotatedEntity. |
| DataType |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| InstantiableFromParameterSet
Interface for all classes that can be instantiated from a
InstanceParameterSet. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| NotTrainedException
A
NotTrainedException is thrown if the user tries to use an untrained
model. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| NotTrainedException
A
NotTrainedException is thrown if the user tries to use an untrained
model. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| InstantiableFromParameterSet
Interface for all classes that can be instantiated from a
InstanceParameterSet. |
| NotTrainedException
A
NotTrainedException is thrown if the user tries to use an untrained
model. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| InstantiableFromParameterSet
Interface for all classes that can be instantiated from a
InstanceParameterSet. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| InstantiableFromParameterSet
Interface for all classes that can be instantiated from a
InstanceParameterSet. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| InstantiableFromParameterSet
Interface for all classes that can be instantiated from a
InstanceParameterSet. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| NotTrainedException
A
NotTrainedException is thrown if the user tries to use an untrained
model. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| InstantiableFromParameterSet
Interface for all classes that can be instantiated from a
InstanceParameterSet. |
| NotTrainedException
A
NotTrainedException is thrown if the user tries to use an untrained
model. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| InstantiableFromParameterSet
Interface for all classes that can be instantiated from a
InstanceParameterSet. |
| NotTrainedException
A
NotTrainedException is thrown if the user tries to use an untrained
model. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| InstantiableFromParameterSet
Interface for all classes that can be instantiated from a
InstanceParameterSet. |
| NotTrainedException
A
NotTrainedException is thrown if the user tries to use an untrained
model. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| NotTrainedException
A
NotTrainedException is thrown if the user tries to use an untrained
model. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| NotTrainedException
A
NotTrainedException is thrown if the user tries to use an untrained
model. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| AnnotatedEntity
Superclass for all Jstacs entities that have a name, a comment, and a data type as annotations.
|
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| AnnotatedEntity
Superclass for all Jstacs entities that have a name, a comment, and a data type as annotations.
|
| DataType |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|
| Class and Description |
|---|
| InstantiableFromParameterSet
Interface for all classes that can be instantiated from a
InstanceParameterSet. |
| NotTrainedException
A
NotTrainedException is thrown if the user tries to use an untrained
model. |
| Storable
This is the root interface for all immutable objects that must be stored in
e.g.
|