A B C D E F G H I K L M N O P Q R S T U V W X

B

backward(ParameterTree[], int[][]) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree

Starts the computation of the backward-part of the normalization constant starting from this ParameterTree.

BayesianNetworkModel - Class in de.jstacs.models.discrete.inhomogeneous

The class implements a Bayesian network of fixed order.

BayesianNetworkModel(BayesianNetworkModelParameterSet) - Constructor for class de.jstacs.models.discrete.inhomogeneous.BayesianNetworkModel

The default constructor.

BayesianNetworkModel(StringBuffer) - Constructor for class de.jstacs.models.discrete.inhomogeneous.BayesianNetworkModel

The constructor for a model in xml format.

BayesianNetworkModelParameterSet - Class in de.jstacs.models.discrete.inhomogeneous.parameters

The ParameterSet for the class BayesianNetworkModel.

BayesianNetworkModelParameterSet(StringBuffer) - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.BayesianNetworkModelParameterSet

The constructor for the Storable interface.

BayesianNetworkModelParameterSet() - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.BayesianNetworkModelParameterSet

The simple constructor for an empty parameter set of a BayesianNetworkModel.

BayesianNetworkModelParameterSet(AlphabetContainer, int, double, String, StructureLearner.ModelType, byte, StructureLearner.LearningType) - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.BayesianNetworkModelParameterSet

This is the constructor of a filled parameter set for a BayesianNetworkModel.

BayesianNetworkScoringFunction - Class in de.jstacs.scoringFunctions.directedGraphicalModels

This class implements a scoring function that is a moral directed graphical model, i.e. a moral Bayesian network.

BayesianNetworkScoringFunction(AlphabetContainer, int, double, boolean, Measure) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction

Creates a new BayesianNetworkScoringFunction that has neither been initialized nor trained.

BayesianNetworkScoringFunction(BayesianNetworkScoringFunctionParameterSet) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction

Creates a new BayesianNetworkScoringFunction that has neither been initialized nor trained from a BayesianNetworkScoringFunctionParameterSet.

BayesianNetworkScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction

Re-creates a BayesianNetworkScoringFunction from its XML-representation, as saved by the BayesianNetworkScoringFunction.toXML()} method.

BayesianNetworkScoringFunctionParameterSet - Class in de.jstacs.scoringFunctions.directedGraphicalModels

Class for the parameters of a BayesianNetworkScoringFunction.

BayesianNetworkScoringFunctionParameterSet(AlphabetContainer, int, double, boolean, Measure) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunctionParameterSet

Creates a new BayesianNetworkScoringFunctionParameterSet with pre-defined parameter values.

BayesianNetworkScoringFunctionParameterSet() - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunctionParameterSet

Creates a new BayesianNetworkScoringFunctionParameterSet with empty parameter values.

BayesianNetworkScoringFunctionParameterSet(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunctionParameterSet

Creates a new BayesianNetworkScoringFunctionParameterSet from its XML-representation as defined by the Storable interface.

bgMaxMarkovOrder - Variable in class de.jstacs.models.mixture.motif.HiddenMotifMixture

The order of the background model.

BioJavaAdapter - Class in de.jstacs.data.bioJava

This class provides static methods to convert BioJava datatypes ( SequenceIterator, Sequence) to Samples and vice versa.

BioJavaAdapter() - Constructor for class de.jstacs.data.bioJava.BioJavaAdapter

BooleanArrayWithTags(boolean[]) - Static method in class de.jstacs.io.XMLParser

Encodes a boolean array.

brentsMethod(OneDimensionalFunction, double, double, double, double, double) - Static method in class de.jstacs.algorithms.optimization.Optimizer

Approximates a minimum (not necessary the global) in the interval [lower,upper].

brentsMethod(OneDimensionalFunction, double, double, double, double) - Static method in class de.jstacs.algorithms.optimization.Optimizer

Approximates a minimum (not necessary the global) in the interval [lower,upper].

BTExplainingAwayResidual - Class in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures

Structure learning Measure that computes a maximum spanning tree based on the explaining away residual and uses the resulting tree structure as structure of a Bayesian tree (special case of a Bayesian network) in a BayesianNetworkScoringFunction.

BTExplainingAwayResidual(double[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual

Creates a new explaining away residual Bayesian tree Measure.

BTExplainingAwayResidual(BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual

Creates a new BTExplainingAwayResidual from the corresponding InstanceParameterSet parameters/code>.

BTExplainingAwayResidual(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual

Re-creates a BTExplainingAwayResidual from is XML-representation as returned by BTExplainingAwayResidual.toXML().

BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet - Class in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures

Class for the parameters of a BTExplainingAwayResidual structure Measure.

BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet() - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet

Creates a new BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet with empty parameter values.

BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet(double[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet

Creates a new BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet with the parameter for the ess set to ess.

BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet

Creates a new BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet from its XML-representation as defined by the Storable interface.

BTMutualInformation - Class in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures

Structure learning Measure that computes a maximum spanning tree based on mutual information and uses the resulting tree structure as structure of a Bayesian tree (special case of a Bayesian network) in a BayesianNetworkScoringFunction.

BTMutualInformation(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation

Re-creates a BTMutualInformation from is XML-representation as returned by BTMutualInformation.toXML().

BTMutualInformation(BTMutualInformation.DataSource, double[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation

Creates a new mutual information Bayesian tree Measure.

BTMutualInformation(BTMutualInformation.BTMutualInformationParameterSet) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation

Creates a new BTMutualInformation from the corresponding InstanceParameterSet parameters/code>.

BTMutualInformation.BTMutualInformationParameterSet - Class in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures

Class for the parameters of a BTMutualInformation structure Measure.

BTMutualInformation.BTMutualInformationParameterSet() - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation.BTMutualInformationParameterSet

Creates a new BTMutualInformation.BTMutualInformationParameterSet with empty parameter values.

BTMutualInformation.BTMutualInformationParameterSet(BTMutualInformation.DataSource, double[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation.BTMutualInformationParameterSet

Creates a new BTMutualInformation.BTMutualInformationParameterSet with the parameter for the BTMutualInformation.DataSource set to clazz and the parameter for the ess set to ess.

BTMutualInformation.BTMutualInformationParameterSet(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation.BTMutualInformationParameterSet

Creates a new BTMutualInformation.BTMutualInformationParameterSet from its XML-representation as defined by the Storable interface.

BTMutualInformation.DataSource - Enum in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures

Enum defining the possible sources of data to compute the mutual information.

burnInTest - Variable in class de.jstacs.models.mixture.AbstractMixtureModel

The BurnInTest that is used to stop the sampling

BurnInTest - Class in de.jstacs.models.mixture.gibbssampling

This is the abstract super class for any test of the length of the burn-in phase.

BurnInTest() - Constructor for class de.jstacs.models.mixture.gibbssampling.BurnInTest

ByteArrayWithTags(byte[]) - Static method in class de.jstacs.io.XMLParser

Encodes a byte array.

ByteSequence - Class in de.jstacs.data.sequences

This class can be used for discrete AlphabetContainers with alphabets that use only few symbols.

ByteSequence(AlphabetContainer, byte[]) - Constructor for class de.jstacs.data.sequences.ByteSequence

This constructor is designed for the method AbstractModel.emitSample(int, int...).

ByteSequence(AlphabetContainer, String) - Constructor for class de.jstacs.data.sequences.ByteSequence

Creates a new sequence from a string representation using the default delimiter.

ByteSequence(AlphabetContainer, SequenceAnnotation[], String, String) - Constructor for class de.jstacs.data.sequences.ByteSequence

Creates a new sequence from a string representation using the delimiter delim.

ByteSequence(AlphabetContainer, SequenceAnnotation[], SymbolExtractor) - Constructor for class de.jstacs.data.sequences.ByteSequence

Creates a new sequence from a SymbolExtractor.