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| Packages that use de.jstacs.parameters | |
|---|---|
| de.jstacs | This package is the root package for the most and important packages. |
| de.jstacs.algorithms.optimization.termination | Provides classes for termination conditions that can be used in algorithms. |
| 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.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.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.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.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.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.trainable.discrete | |
| de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters | |
| de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters | |
| 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.utils | This package contains a bundle of useful classes and interfaces like ... |
| de.jstacs.utils.galaxy | |
| Classes in de.jstacs.parameters used by de.jstacs | |
|---|---|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| Classes in de.jstacs.parameters used by de.jstacs.algorithms.optimization.termination | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| SimpleParameter.DatatypeNotValidException
Class for an Exception that can be thrown if the provided
int-value that represents a data type is not one of the
values defined in DataType. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.classifiers.assessment | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| SimpleParameterSet
Class for a ParameterSet that is constructed from an array of Parameters. |
|
| Classes in de.jstacs.parameters used by de.jstacs.classifiers.differentiableSequenceScoreBased | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet. |
|
| Classes in de.jstacs.parameters used by de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.classifiers.differentiableSequenceScoreBased.sampling | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.classifiers.performanceMeasures | |
|---|---|
| ExpandableParameterSet
A class for a ParameterSet that can be expanded by additional
Parameters at runtime. |
|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| SelectionParameter
Class for a collection parameter, i.e. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.data | |
|---|---|
| ArrayParameterSet
Class for a ParameterSet that consists of a length-Parameter
that defines the length of the array and an array of
ParameterSetContainers of this length. |
|
| ExpandableParameterSet
A class for a ParameterSet that can be expanded by additional
Parameters at runtime. |
|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| Classes in de.jstacs.parameters used by de.jstacs.data.alphabets | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| Classes in de.jstacs.parameters used by de.jstacs.io | |
|---|---|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| Parameter
Abstract class for a parameter that shall be used as the parameter of some method, constructor, etc. |
|
| ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| Classes in de.jstacs.parameters used by de.jstacs.parameters | |
|---|---|
| AbstractSelectionParameter
Class for a collection parameter, i.e. |
|
| AbstractSelectionParameter.InconsistentCollectionException
This exception is thrown if the AbstractSelectionParameter is
inconsistent for some reason. |
|
| EnumParameter
This class implements a SelectionParameter based on an Enum. |
|
| ExpandableParameterSet
A class for a ParameterSet that can be expanded by additional
Parameters at runtime. |
|
| FileParameter
Class for a Parameter that represents a local file. |
|
| FileParameter.FileRepresentation
Class that represents a file. |
|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| MultiSelectionParameter
Class for a Parameter that provides a collection of possible values. |
|
| Parameter
Abstract class for a parameter that shall be used as the parameter of some method, constructor, etc. |
|
| ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| ParameterSet.ParameterList
Class for a AnnotatedEntityList that automatically sets
the Parameter.parent field to the enclosing ParameterSet. |
|
| ParameterSetContainer
Class for a ParameterSetContainer that contains a
ParameterSet as value. |
|
| Rangeable
Interface for Parameters that potentially can be varied over a
certain interval or a list of values. |
|
| RangeIterator
Interface for a Parameter or ParameterSet that can have
multiple values at the same time. |
|
| RangeParameter
Class for a parameter wrapper that allows SimpleParameters to be set
to a set of values.These values may be given either as a list of values separated by spaces, as a range between a first and a last value with a given number of steps between these values, or a single value. |
|
| RangeParameter.RangeType
The possible types of defining ranges for a RangeParameter. |
|
| RangeParameter.Scale
This enum defines possible scales, if RangeParameter.RangeType is
RangeParameter.RangeType.RANGE. |
|
| SelectionParameter
Class for a collection parameter, i.e. |
|
| SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet. |
|
| SimpleParameter
Class for a "simple" parameter. |
|
| SimpleParameter.DatatypeNotValidException
Class for an Exception that can be thrown if the provided
int-value that represents a data type is not one of the
values defined in DataType. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| SimpleParameterSet
Class for a ParameterSet that is constructed from an array of Parameters. |
|
| Classes in de.jstacs.parameters used by de.jstacs.parameters.validation | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| Classes in de.jstacs.parameters used by de.jstacs.results | |
|---|---|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.sampling | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet. |
|
| Classes in de.jstacs.parameters used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| SimpleParameter.DatatypeNotValidException
Class for an Exception that can be thrown if the provided
int-value that represents a data type is not one of the
values defined in DataType. |
|
| Classes in de.jstacs.parameters used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| SimpleParameter.DatatypeNotValidException
Class for an Exception that can be thrown if the provided
int-value that represents a data type is not one of the
values defined in DataType. |
|
| Classes in de.jstacs.parameters used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet. |
|
| Classes in de.jstacs.parameters used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| SequenceScoringParameterSet
Abstract class for a ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
| Classes in de.jstacs.parameters used by de.jstacs.utils | |
|---|---|
| InstanceParameterSet
Container class for a set of Parameters that can be used to
instantiate another class. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| SelectionParameter
Class for a collection parameter, i.e. |
|
| Classes in de.jstacs.parameters used by de.jstacs.utils.galaxy | |
|---|---|
| GalaxyConvertible
Interface for Parameters that can be converted to and extracted from
Galaxy representations. |
|
| Parameter
Abstract class for a parameter that shall be used as the parameter of some method, constructor, etc. |
|
| ParameterException
Class for an exception that is thrown if some error occurs while setting a parameter's value or constructing a parameter. |
|
| ParameterSet
(Container) class for a set of Parameters. |
|
| Rangeable
Interface for Parameters that potentially can be varied over a
certain interval or a list of values. |
|
| SimpleParameter
Class for a "simple" parameter. |
|
| SimpleParameter.DatatypeNotValidException
Class for an Exception that can be thrown if the provided
int-value that represents a data type is not one of the
values defined in DataType. |
|
| SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid. |
|
|
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