Package | Description |
---|---|
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
Classifier s that are based on SequenceScore s.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
DifferentiableStatisticalModel s by
a unified generative-discriminative learning principle. |
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.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
Storable s 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
DifferentiableStatisticalModel s 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.tools | |
de.jstacs.tools.ui.galaxy | |
de.jstacs.utils |
This package contains a bundle of useful classes and interfaces like ...
|
Class and Description |
---|
InstanceParameterSet
Container class for a set of
Parameter s that can be used to
instantiate another class. |
Class and Description |
---|
GalaxyConvertible |
InstanceParameterSet
Container class for a set of
Parameter s 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
Parameter s. |
SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.
|
Class and Description |
---|
GalaxyConvertible |
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
Parameter s. |
SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.
|
SimpleParameterSet
Class for a
ParameterSet that is constructed from an array of Parameter s. |
Class and Description |
---|
GalaxyConvertible |
InstanceParameterSet
Container class for a set of
Parameter s that can be used to
instantiate another class. |
ParameterSet
(Container) class for a set of
Parameter s. |
SequenceScoringParameterSet
Abstract class for a
ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet . |
Class and Description |
---|
GalaxyConvertible |
InstanceParameterSet
Container class for a set of
Parameter s that can be used to
instantiate another class. |
ParameterSet
(Container) class for a set of
Parameter s. |
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.
|
Class and Description |
---|
GalaxyConvertible |
InstanceParameterSet
Container class for a set of
Parameter s that can be used to
instantiate another class. |
ParameterSet
(Container) class for a set of
Parameter s. |
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.
|
Class and Description |
---|
ExpandableParameterSet
A class for a
ParameterSet that can be expanded by additional
Parameter s at runtime. |
GalaxyConvertible |
ParameterSet
(Container) class for a set of
Parameter s. |
SelectionParameter
Class for a collection parameter, i.e.
|
SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.
|
Class and Description |
---|
ArrayParameterSet
Class for a
ParameterSet that consists of a length-Parameter
that defines the length of the array and an array of
ParameterSetContainer s of this length. |
ExpandableParameterSet
A class for a
ParameterSet that can be expanded by additional
Parameter s at runtime. |
GalaxyConvertible |
InstanceParameterSet
Container class for a set of
Parameter s that can be used to
instantiate another class. |
ParameterSet
(Container) class for a set of
Parameter s. |
Class and Description |
---|
GalaxyConvertible |
InstanceParameterSet
Container class for a set of
Parameter s 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
Parameter s. |
Class and Description |
---|
InstanceParameterSet
Container class for a set of
Parameter s 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
Parameter s. |
Class and Description |
---|
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
Parameter s at runtime. |
FileParameter
Class for a
Parameter that represents a local file. |
FileParameter.FileRepresentation
Class that represents a file.
|
GalaxyConvertible |
InstanceParameterSet
Container class for a set of
Parameter s 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
Parameter s. |
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
Parameter s 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
SimpleParameter s 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 |
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 |
SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.
|
SimpleParameterSet
Class for a
ParameterSet that is constructed from an array of Parameter s. |
Class and Description |
---|
GalaxyConvertible |
Class and Description |
---|
FileParameter
Class for a
Parameter that represents a local file. |
FileParameter.FileRepresentation
Class that represents a file.
|
SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.
|
Class and Description |
---|
GalaxyConvertible |
InstanceParameterSet
Container class for a set of
Parameter s that can be used to
instantiate another class. |
ParameterSet
(Container) class for a set of
Parameter s. |
SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.
|
Class and Description |
---|
GalaxyConvertible |
InstanceParameterSet
Container class for a set of
Parameter s that can be used to
instantiate another class. |
ParameterSet
(Container) class for a set of
Parameter s. |
SequenceScoringParameterSet
Abstract class for a
ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet . |
Class and Description |
---|
GalaxyConvertible |
InstanceParameterSet
Container class for a set of
Parameter s that can be used to
instantiate another class. |
ParameterSet
(Container) class for a set of
Parameter s. |
SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.
|
Class and Description |
---|
GalaxyConvertible |
InstanceParameterSet
Container class for a set of
Parameter s 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
Parameter s. |
SimpleParameter.DatatypeNotValidException |
Class and Description |
---|
GalaxyConvertible |
InstanceParameterSet
Container class for a set of
Parameter s 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
Parameter s. |
SimpleParameter.DatatypeNotValidException |
Class and Description |
---|
GalaxyConvertible |
InstanceParameterSet
Container class for a set of
Parameter s that can be used to
instantiate another class. |
ParameterSet
(Container) class for a set of
Parameter s. |
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.
|
Class and Description |
---|
GalaxyConvertible |
InstanceParameterSet
Container class for a set of
Parameter s that can be used to
instantiate another class. |
ParameterSet
(Container) class for a set of
Parameter s. |
SequenceScoringParameterSet
Abstract class for a
ParameterSet containing all parameters necessary
to construct an Object that implements
InstantiableFromParameterSet . |
Class and Description |
---|
GalaxyConvertible |
InstanceParameterSet
Container class for a set of
Parameter s that can be used to
instantiate another class. |
ParameterSet
(Container) class for a set of
Parameter s. |
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.
|
Class and Description |
---|
GalaxyConvertible |
ParameterSet
(Container) class for a set of
Parameter s. |
SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.
|
Class and Description |
---|
FileParameter
Class for a
Parameter that represents a local file. |
GalaxyConvertible |
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
Parameter s. |
Rangeable
Interface for
Parameter s that potentially can be varied over a
certain interval or a list of values. |
SimpleParameter
Class for a "simple" parameter.
|
SimpleParameter.DatatypeNotValidException |
SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.
|
Class and Description |
---|
GalaxyConvertible |
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
Parameter s. |
Rangeable
Interface for
Parameter s that potentially can be varied over a
certain interval or a list of values. |
SimpleParameter
Class for a "simple" parameter.
|
SimpleParameter.DatatypeNotValidException |
SimpleParameter.IllegalValueException
This exception is thrown if a parameter is not valid.
|
Class and Description |
---|
InstanceParameterSet
Container class for a set of
Parameter s that can be used to
instantiate another class. |
ParameterSet
(Container) class for a set of
Parameter s. |
SelectionParameter
Class for a collection parameter, i.e.
|