Package | Description |
---|---|
de.jstacs.algorithms.alignment |
Provides classes for alignments.
|
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
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.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.classifiers.trainSMBased |
Provides the classes for
Classifier s that are based on TrainableStatisticalModel s. |
de.jstacs.classifiers.utils |
Provides some useful classes for working with classifiers.
|
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.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.results |
This package provides classes for results and sets of results.
|
de.jstacs.results.savers | |
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.statisticalModels.trainable |
Provides all
TrainableStatisticalModel s, which can
be learned from a single DataSet . |
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.discrete.inhomogeneous.shared | |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models |
The package provides different implementations of hidden Markov models based on
AbstractHMM . |
de.jstacs.sequenceScores.statisticalModels.trainable.mixture |
This package is the super package for any mixture 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 |
---|
Result
The abstract class for any result.
|
Class and Description |
---|
CategoricalResult
A class for categorical results (i.e.
|
ImageResult
A class for results that are images of the PNG format.
|
NumericalResultSet
Class for a set of numerical result values, which are all of the type
NumericalResult . |
Result
The abstract class for any result.
|
ResultSet |
Class and Description |
---|
ListResult |
MeanResultSet
Class that computes the mean and the standard error of a series of
NumericalResultSet s. |
MeanResultSet.AdditionImpossibleException
Class for the exception that is thrown if two
MeanResultSet s
should be added that do not match. |
MeanResultSet.InconsistentResultNumberException
Class for the exception that is thrown if a
NumericalResultSet is
added to the MeanResultSet that has a number of results which is
not equal to the number of results of the previously added results. |
Result
The abstract class for any result.
|
Class and Description |
---|
CategoricalResult
A class for categorical results (i.e.
|
NumericalResultSet
Class for a set of numerical result values, which are all of the type
NumericalResult . |
Class and Description |
---|
CategoricalResult
A class for categorical results (i.e.
|
NumericalResultSet
Class for a set of numerical result values, which are all of the type
NumericalResult . |
Class and Description |
---|
NumericalResultSet
Class for a set of numerical result values, which are all of the type
NumericalResult . |
ResultSet |
Class and Description |
---|
CategoricalResult
A class for categorical results (i.e.
|
NumericalResultSet
Class for a set of numerical result values, which are all of the type
NumericalResult . |
ResultSet |
Class and Description |
---|
ImageResult
A class for results that are images of the PNG format.
|
Class and Description |
---|
ImageResult
A class for results that are images of the PNG format.
|
Class and Description |
---|
Result
The abstract class for any result.
|
ResultSet |
Class and Description |
---|
ImageResult
A class for results that are images of the PNG format.
|
ListResult |
Class and Description |
---|
ListResult |
MeanResultSet
Class that computes the mean and the standard error of a series of
NumericalResultSet s. |
MeanResultSet.AdditionImpossibleException
Class for the exception that is thrown if two
MeanResultSet s
should be added that do not match. |
MeanResultSet.InconsistentResultNumberException
Class for the exception that is thrown if a
NumericalResultSet is
added to the MeanResultSet that has a number of results which is
not equal to the number of results of the previously added results. |
NumericalResult
Class for numerical
Result values. |
NumericalResultSet
Class for a set of numerical result values, which are all of the type
NumericalResult . |
PlotGeneratorResult.PlotGenerator
Interface for a class that may generate a plot using the specified
GraphicsAdaptor . |
Result
The abstract class for any result.
|
ResultSet |
SimpleResult |
Class and Description |
---|
DataSetResult |
ListResult |
PlotGeneratorResult
Class for a
Result that may be used to generate plots for different output formats using
GraphicsAdaptor sub-classes. |
Result
The abstract class for any result.
|
ResultSetResult |
StorableResult |
TextResult
Class for a result that is basically a text file (or its contents).
|
Class and Description |
---|
NumericalResultSet
Class for a set of numerical result values, which are all of the type
NumericalResult . |
ResultSet |
Class and Description |
---|
NumericalResultSet
Class for a set of numerical result values, which are all of the type
NumericalResult . |
ResultSet |
Class and Description |
---|
NumericalResultSet
Class for a set of numerical result values, which are all of the type
NumericalResult . |
ResultSet |
Class and Description |
---|
NumericalResultSet
Class for a set of numerical result values, which are all of the type
NumericalResult . |
Class and Description |
---|
NumericalResultSet
Class for a set of numerical result values, which are all of the type
NumericalResult . |
Class and Description |
---|
CategoricalResult
A class for categorical results (i.e.
|
Class and Description |
---|
NumericalResultSet
Class for a set of numerical result values, which are all of the type
NumericalResult . |
ResultSet |
Class and Description |
---|
NumericalResultSet
Class for a set of numerical result values, which are all of the type
NumericalResult . |
ResultSet |
Class and Description |
---|
ListResult |
Result
The abstract class for any result.
|
ResultSet |
ResultSetResult |
Class and Description |
---|
CategoricalResult
A class for categorical results (i.e.
|
ImageResult
A class for results that are images of the PNG format.
|
Result
The abstract class for any result.
|
ResultSet |
SimpleResult |
Class and Description |
---|
PlotGeneratorResult.PlotGenerator
Interface for a class that may generate a plot using the specified
GraphicsAdaptor . |