Package | Description |
---|---|
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.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.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.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.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.bioJava |
Provides an adapter between the representation of data in BioJava and the representation used in Jstacs.
|
de.jstacs.data.sequences |
Provides classes for representing sequences.
The implementations of sequences currently include DiscreteSequence s prepared for alphabets of different sizes, and ArbitrarySequence s that may
contain continuous values as well.As sub-package provides the facilities to annotate Sequence s. |
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.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.motifDiscovery |
This package provides the framework including the interface for any de novo motif discoverer.
|
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.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
SequenceScore s, 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
StatisticalModel s, which can compute a proper (i.e., normalized) likelihood over the input space of sequences.StatisticalModel s can be further differentiated into TrainableStatisticalModel s,
which can be learned from a single input DataSet , and DifferentiableStatisticalModel s,
which define a proper likelihood but can also compute gradients like DifferentiableSequenceScore s. |
de.jstacs.sequenceScores.statisticalModels.differentiable |
Provides all
DifferentiableStatisticalModel s, which can compute the gradient with
respect to their parameters for a given input Sequence . |
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.differentiable.homogeneous |
Provides
DifferentiableStatisticalModel s that are homogeneous, i.e. |
de.jstacs.sequenceScores.statisticalModels.differentiable.localMixture | |
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture |
Provides
DifferentiableSequenceScore s that are mixtures of other DifferentiableSequenceScore s. |
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif | |
de.jstacs.sequenceScores.statisticalModels.trainable |
Provides all
TrainableStatisticalModel s, 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 |
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.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 |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
Class and Description |
---|
DataSet
This is the class for any data set of
Sequence s. |
DataSet.PartitionMethod
This
enum defines different partition methods for a
DataSet . |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
Class and Description |
---|
AlphabetContainer |
AlphabetContainer.AlphabetContainerType
This
enum defines types of AlphabetContainer s. |
DataSet
This is the class for any data set of
Sequence s. |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
Class and Description |
---|
DataSet
This is the class for any data set of
Sequence s. |
Class and Description |
---|
DataSet
This is the class for any data set of
Sequence s. |
Class and Description |
---|
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
Class and Description |
---|
AlphabetContainer |
AlphabetContainer.AbstractAlphabetContainerParameterSet
This class is the super class of any
InstanceParameterSet for AlphabetContainer . |
AlphabetContainer.AlphabetContainerType
This
enum defines types of AlphabetContainer s. |
AlphabetContainerParameterSet
Class for the
ParameterSet of an AlphabetContainer . |
AlphabetContainerParameterSet.AlphabetArrayParameterSet
Class for the parameters of an array of
Alphabet s of defined
length. |
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet |
DataSet
This is the class for any data set of
Sequence s. |
DataSet.PartitionMethod
This
enum defines different partition methods for a
DataSet . |
DataSet.WeightedDataSetFactory.SortOperation
This
enum defines the different types of sort operations
that can be performed while creating a DataSet.WeightedDataSetFactory . |
DinucleotideProperty
This
enum defines physicochemical, conformational, and letter-based dinucleotide properties of nucleotide sequences. |
DinucleotideProperty.HowCreated
This enum defines the origins of nucleotide properties
|
DinucleotideProperty.Smoothing
Abstract class for methods that smooth a series of real values.
|
DinucleotideProperty.Type
This enum defines the types of dinucleotide properties.
|
EmptyDataSetException |
RecyclableSequenceEnumerator
This interface extends
Enumeration of Sequence s by declaring an additional method that allows to reuse the Enumeration. |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
WrongLengthException
A
WrongLengthException is thrown if a given (sub)sequence length is
not correct. |
Class and Description |
---|
AlphabetContainer |
AlphabetContainer.AbstractAlphabetContainerParameterSet
This class is the super class of any
InstanceParameterSet for AlphabetContainer . |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
EmptyDataSetException |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
WrongLengthException
A
WrongLengthException is thrown if a given (sub)sequence length is
not correct. |
Class and Description |
---|
AlphabetContainer |
Class and Description |
---|
AlphabetContainer |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
Class and Description |
---|
DataSet
This is the class for any data set of
Sequence s. |
DataSet.WeightedDataSetFactory |
DataSet.WeightedDataSetFactory.SortOperation
This
enum defines the different types of sort operations
that can be performed while creating a DataSet.WeightedDataSetFactory . |
RecyclableSequenceEnumerator
This interface extends
Enumeration of Sequence s by declaring an additional method that allows to reuse the Enumeration. |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
WrongLengthException
A
WrongLengthException is thrown if a given (sub)sequence length is
not correct. |
Class and Description |
---|
AlphabetContainer |
AlphabetContainer.AlphabetContainerType
This
enum defines types of AlphabetContainer s. |
Class and Description |
---|
DataSet
This is the class for any data set of
Sequence s. |
Class and Description |
---|
DataSet
This is the class for any data set of
Sequence s. |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
WrongLengthException
A
WrongLengthException is thrown if a given (sub)sequence length is
not correct. |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
Class and Description |
---|
DataSet
This is the class for any data set of
Sequence s. |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
Class and Description |
---|
DataSet
This is the class for any data set of
Sequence s. |
Class and Description |
---|
DataSet
This is the class for any data set of
Sequence s. |
Class and Description |
---|
DataSet
This is the class for any data set of
Sequence s. |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
Class and Description |
---|
DataSet
This is the class for any data set of
Sequence s. |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
WrongLengthException
A
WrongLengthException is thrown if a given (sub)sequence length is
not correct. |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
EmptyDataSetException |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
Class and Description |
---|
AlphabetContainer |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
Class and Description |
---|
AlphabetContainer |
Class and Description |
---|
DataSet
This is the class for any data set of
Sequence s. |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
Class and Description |
---|
DataSet
This is the class for any data set of
Sequence s. |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
WrongLengthException
A
WrongLengthException is thrown if a given (sub)sequence length is
not correct. |
Class and Description |
---|
WrongLengthException
A
WrongLengthException is thrown if a given (sub)sequence length is
not correct. |
Class and Description |
---|
AlphabetContainer |
Class and Description |
---|
AlphabetContainer |
Class and Description |
---|
AlphabetContainer |
Class and Description |
---|
DataSet
This is the class for any data set of
Sequence s. |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
Class and Description |
---|
DataSet
This is the class for any data set of
Sequence s. |
WrongAlphabetException
A
WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer
does not support some data. |
Class and Description |
---|
AlphabetContainer |
DataSet
This is the class for any data set of
Sequence s. |