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

T

target - Variable in class de.jstacs.algorithms.graphs.Edge

The target node.

template - Variable in class de.jstacs.parameters.ExpandableParameterSet

The template for each ParameterSet

tensor - Variable in class de.jstacs.algorithms.graphs.tensor.AsymmetricTensor

The internal tensor.

Tensor - Class in de.jstacs.algorithms.graphs.tensor

This is the super class for any tensor.

Tensor(int, byte) - Constructor for class de.jstacs.algorithms.graphs.tensor.Tensor

Creates a new Tensor for n nodes and order k.

TerminationException - Exception in de.jstacs.algorithms.optimization

This class is for an exception thrown if something with a termination was not correct.

TerminationException() - Constructor for exception de.jstacs.algorithms.optimization.TerminationException

Creates a new TerminationException with standard message ("The termination mode was incorrect, please check your choice.

test(Sample...) - Method in class de.jstacs.classifier.AbstractClassifier

This method computes the confusion matrix for a given array of test data.

test(Sample...) - Method in class de.jstacs.classifier.AbstractScoreBasedClassifier

test(MeasureParameters, boolean, Sample...) - Method in class de.jstacs.classifier.assessment.ClassifierAssessment

Uses the given test samples to call the evaluate( ... ) -methods of the local AbstractClassifiers.

Time - Class in de.jstacs.utils

This interface is the framework for stopping the time of anything.

Time() - Constructor for class de.jstacs.utils.Time

Creates a new time object and starts the clock.

TimeLimitedProgressUpdater - Class in de.jstacs.utils

This class is an extension of DefaultProgressUpdater.

TimeLimitedProgressUpdater(Time, int, int, int, int) - Constructor for class de.jstacs.utils.TimeLimitedProgressUpdater

Creates a new TimeLimitedProgressUpdater.

toArray() - Method in class de.jstacs.utils.DoubleList

This method returns a double array containing all elements of the list.

toArray() - Method in class de.jstacs.utils.IntList

This method returns an int array containing all elements of the list.

toDirectedGraphvizFormat(int[][]) - Static method in class de.jstacs.algorithms.graphs.DAG

This method returns a String representation of the structure that can be used in Graphviz to create an image.

toDiscrete(int, double) - Method in class de.jstacs.data.AlphabetContainer

Returns the discrete value for val at a position pos.

toDiscrete(int, double) - Method in class de.jstacs.data.Sequence

This method converts a continuous value in a discrete one.

toDouble3DArray() - Method in class de.jstacs.algorithms.graphs.tensor.Tensor

toGraphvizFormat(int[][], String) - Static method in class de.jstacs.algorithms.graphs.DAG

This method returns a String representation of the structure that can be used in Graphviz to create an image.

toParents(int[], byte) - Static method in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.Measure

Creates a new parent structure as defined by Measure.getParents(Sample, Sample, double[], double[], int) from an order and a topological ordering of positions.

TopSort - Class in de.jstacs.algorithms.graphs

Class for a topological sort.

TopSort() - Constructor for class de.jstacs.algorithms.graphs.TopSort

toString() - Method in class de.jstacs.algorithms.Alignment.StringAlignment

toString() - Method in class de.jstacs.algorithms.graphs.Edge

toString() - Method in class de.jstacs.algorithms.optimization.QuadraticFunction

toString() - Method in class de.jstacs.classifier.AbstractScoreBasedClassifier.DoubleTableResult

toString() - Method in class de.jstacs.data.Alphabet

toString() - Method in class de.jstacs.data.AlphabetContainer

toString() - Method in class de.jstacs.data.alphabets.ContinuousAlphabet

toString() - Method in class de.jstacs.data.alphabets.DiscreteAlphabet

toString() - Method in class de.jstacs.data.Sample

toString() - Method in class de.jstacs.data.Sample.WeightedSampleFactory

toString() - Method in class de.jstacs.data.Sequence

Returns a String representation of the sequence (normally the sequence in its original alphabet)

toString(int) - Method in class de.jstacs.data.Sequence

Returns a string representation of the sequence (normally the sequence in its original alphabet) with default delimiter as separator.

toString(int, int) - Method in class de.jstacs.data.Sequence

Returns a string representation of the sequence (normally the sequence in its original alphabet) with default delimiter as separator.

toString(String, int, int) - Method in class de.jstacs.data.Sequence

Returns a string representation of the sequence (normally the sequence in its original alphabet) with delim as separator.

toString() - Method in class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation

toString() - Method in class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotationWithLength

toString() - Method in class de.jstacs.data.sequences.annotation.SequenceAnnotation

toString() - Method in enum de.jstacs.data.sequences.annotation.SinglePositionSequenceAnnotation.Type

toString() - Method in class de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength

toString() - Method in class de.jstacs.models.CompositeModel

toString() - Method in class de.jstacs.models.discrete.Constraint

toString() - Method in class de.jstacs.models.discrete.DiscreteGraphicalModel

toString() - Method in class de.jstacs.models.discrete.homogeneous.HomogeneousMM

toString() - Method in class de.jstacs.models.discrete.homogeneous.HomogeneousModel.HomCondProb

toString() - Method in class de.jstacs.models.discrete.inhomogeneous.DAGModel

toString() - Method in class de.jstacs.models.discrete.inhomogeneous.InhCondProb

toString() - Method in class de.jstacs.models.discrete.inhomogeneous.MEMConstraint

toString() - Method in class de.jstacs.models.mixture.MixtureModel

toString() - Method in class de.jstacs.models.mixture.motif.HiddenMotifMixture

toString() - Method in class de.jstacs.models.mixture.StrandModel

toString() - Method in interface de.jstacs.models.Model

Should give a simple representation (text) of the model as String.

toString() - Method in class de.jstacs.models.UniformModel

Returns the String "".

toString() - Method in class de.jstacs.results.ImageResult

toString() - Method in class de.jstacs.results.ListResult

toString() - Method in class de.jstacs.results.NumericalResult

toString() - Method in class de.jstacs.results.ResultSet

toString() - Method in class de.jstacs.results.SimpleResult

toString() - Method in class de.jstacs.results.StorableResult

toString() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction

toString() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree

toString() - Method in class de.jstacs.scoringFunctions.homogeneous.HMM0ScoringFunction

toString() - Method in class de.jstacs.scoringFunctions.homogeneous.HMMScoringFunction

toString() - Method in class de.jstacs.scoringFunctions.homogeneous.UniformHomogeneousScoringFunction

toString() - Method in class de.jstacs.scoringFunctions.IndependentProductScoringFunction

toString() - Method in class de.jstacs.scoringFunctions.mix.MixtureScoringFunction

toString() - Method in class de.jstacs.scoringFunctions.UniformScoringFunction

toString() - Method in class de.jstacs.utils.ComparableElement

toString() - Method in class de.jstacs.utils.TimeLimitedProgressUpdater

toStringArray(ParameterTree[]) - Static method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree

Creates a String array from the XML-representation of all ParameterTrees in trees as returned by the corresponding ParameterTree.toXML() methods.

toUndirectedGraphvizFormat(int[][]) - Static method in class de.jstacs.algorithms.graphs.DAG

This method returns a String representation of the structure that can be used in Graphviz to create an image.

toWeightedGraphvizFormat(int[][], String, Tensor) - Static method in class de.jstacs.algorithms.graphs.DAG

This method returns a String representation of the weighted structure that can be used in Graphviz to create an image.

toXML() - Method in class de.jstacs.classifier.AbstractClassifier

toXML() - Method in class de.jstacs.classifier.AbstractScoreBasedClassifier.DoubleTableResult

toXML() - Method in class de.jstacs.classifier.ConfusionMatrix

toXML() - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.DoesNothingLogPrior

Deprecated.

toXML() - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.LogPrior

Encodes the prior as an XML representation.

toXML() - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.SeparateLogPrior

toXML() - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.SimpleGaussianSumLogPrior

toXML() - Method in class de.jstacs.data.AlphabetContainer

toXML() - Method in class de.jstacs.data.AlphabetContainerParameterSet.AlphabetArrayParameterSet

toXML() - Method in class de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet

toXML() - Method in class de.jstacs.data.AlphabetContainerParameterSet

toXML() - Method in class de.jstacs.data.alphabets.ContinuousAlphabet

toXML() - Method in class de.jstacs.data.alphabets.DiscreteAlphabet

toXML() - Method in class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation

toXML() - Method in class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotationWithLength

toXML() - Method in class de.jstacs.data.sequences.annotation.SequenceAnnotation

toXML() - Method in class de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength

toXML() - Method in class de.jstacs.models.CompositeModel

toXML() - Method in class de.jstacs.models.discrete.Constraint

toXML() - Method in class de.jstacs.models.discrete.DiscreteGraphicalModel

toXML() - Method in class de.jstacs.models.discrete.inhomogeneous.shared.SharedStructureMixture

toXML() - Method in class de.jstacs.models.mixture.AbstractMixtureModel

toXML() - Method in class de.jstacs.models.mixture.gibbssampling.AbstractBurnInTest

toXML() - Method in class de.jstacs.models.mixture.gibbssampling.SimpleBurnInTest

toXML() - Method in class de.jstacs.models.mixture.motif.positionprior.PositionPrior

toXML() - Method in class de.jstacs.models.UniformModel

toXML() - Method in class de.jstacs.parameters.ArrayParameterSet

toXML() - Method in class de.jstacs.parameters.CollectionParameter

toXML() - Method in class de.jstacs.parameters.ExpandableParameterSet

toXML() - Method in class de.jstacs.parameters.FileParameter.FileRepresentation

toXML() - Method in class de.jstacs.parameters.FileParameter

toXML() - Method in class de.jstacs.parameters.InstanceParameterSet

toXML() - Method in class de.jstacs.parameters.MultiSelectionCollectionParameter

toXML() - Method in class de.jstacs.parameters.Parameter

toXML() - Method in class de.jstacs.parameters.ParameterSet

toXML() - Method in class de.jstacs.parameters.ParameterSetContainer

toXML() - Method in class de.jstacs.parameters.RangeParameter

toXML() - Method in class de.jstacs.parameters.SequenceScoringParameterSet

toXML() - Method in class de.jstacs.parameters.SimpleParameter

toXML() - Method in class de.jstacs.parameters.validation.ConstraintValidator

toXML() - Method in class de.jstacs.parameters.validation.NumberValidator

toXML() - Method in class de.jstacs.parameters.validation.ReferenceConstraint

toXML() - Method in class de.jstacs.parameters.validation.SimpleReferenceConstraint

toXML() - Method in class de.jstacs.parameters.validation.SimpleStaticConstraint

toXML() - Method in class de.jstacs.parameters.validation.StorableValidator

toXML() - Method in class de.jstacs.results.CategoricalResult

toXML() - Method in class de.jstacs.results.ImageResult

toXML() - Method in class de.jstacs.results.ListResult

toXML() - Method in class de.jstacs.results.MeanResultSet

toXML() - Method in class de.jstacs.results.NumericalResult

toXML() - Method in class de.jstacs.results.ResultSet

toXML() - Method in class de.jstacs.results.SampleResult

toXML() - Method in class de.jstacs.results.SimpleResult

toXML() - Method in class de.jstacs.results.StorableResult

toXML() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction

toXML() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter

toXML() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree

Works as defined in Storable.

toXML() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual

toXML() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation

toXML() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.InhomogeneousMarkov

toXML() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMExplainingAwayResidual

toXML() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMMutualInformation

toXML() - Method in class de.jstacs.scoringFunctions.homogeneous.HMM0ScoringFunction

toXML() - Method in class de.jstacs.scoringFunctions.homogeneous.HMMScoringFunction

toXML() - Method in class de.jstacs.scoringFunctions.homogeneous.UniformHomogeneousScoringFunction

toXML() - Method in class de.jstacs.scoringFunctions.IndependentProductScoringFunction

toXML() - Method in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction

toXML() - Method in class de.jstacs.scoringFunctions.MRFScoringFunction

toXML() - Method in class de.jstacs.scoringFunctions.UniformScoringFunction

toXML() - Method in interface de.jstacs.Storable

This method returns an XML-representation of an instance of the implementing class.

toXML() - Method in class de.jstacs.utils.DoubleList

train(Sample...) - Method in class de.jstacs.classifier.AbstractClassifier

Trains the AbstractClassifier object given the data as Samples.

train(Sample[], double[][]) - Method in class de.jstacs.classifier.AbstractClassifier

This method trains a classifier over an array of weighted Samples.

train(Sample...) - Method in class de.jstacs.classifier.assessment.ClassifierAssessment

Trains the local classifiers using the given training samples.

train(Sample[], double[][]) - Method in class de.jstacs.classifier.MappingClassifier

train(Sample[], double[][]) - Method in class de.jstacs.classifier.modelBased.ModelBasedClassifier

train(Sample[], double[][]) - Method in class de.jstacs.classifier.scoringFunctionBased.ScoreClassifier

train(Sample) - Method in class de.jstacs.models.AbstractModel

train(Sample, double[]) - Method in class de.jstacs.models.CompositeModel

train(Sample, double[]) - Method in class de.jstacs.models.discrete.homogeneous.HomogeneousMM

train(Sample[], double[][]) - Method in class de.jstacs.models.discrete.homogeneous.HomogeneousMM

train(Sample[]) - Method in class de.jstacs.models.discrete.homogeneous.HomogeneousModel

Trains the model on all given samples.

train(Sample[], double[][]) - Method in class de.jstacs.models.discrete.homogeneous.HomogeneousModel

Trains the model using an array of weighted samples.

train(Sample, double[]) - Method in class de.jstacs.models.discrete.inhomogeneous.BayesianNetworkModel

train(Sample, double[]) - Method in class de.jstacs.models.discrete.inhomogeneous.FSDAGModel

train(Sample, double[], int[][]) - Method in class de.jstacs.models.discrete.inhomogeneous.FSDAGModel

Computes the model with structure graph

train(Model[], int[][], double[][], Sample...) - Static method in class de.jstacs.models.discrete.inhomogeneous.FSDAGModel

Computes the models with structure graph

train(Sample[], double[][]) - Method in class de.jstacs.models.discrete.inhomogeneous.shared.SharedStructureClassifier

train(Sample, double[]) - Method in class de.jstacs.models.mixture.AbstractMixtureModel

train(Sample, double[]) - Method in class de.jstacs.models.mixture.gibbssampling.FSDAGModelForGibbsSampling

train(Sample, double[], int[][]) - Method in class de.jstacs.models.mixture.gibbssampling.FSDAGModelForGibbsSampling

train(Sample, double[]) - Method in class de.jstacs.models.mixture.motif.HiddenMotifMixture

train(Sample) - Method in interface de.jstacs.models.Model

Trains the AbstractModel object given the data as Sample.

train(Sample, double[]) - Method in interface de.jstacs.models.Model

Trains the Model object given the data as Sample using the specified weights.

train(Sample, double[]) - Method in class de.jstacs.models.UniformModel

Deprecated.

trainBgModel(Sample, double[]) - Method in class de.jstacs.models.mixture.motif.HiddenMotifMixture

This method trains the bg-model.

trained - Variable in class de.jstacs.models.discrete.DiscreteGraphicalModel

Indicates whether the model is trained or not

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

A switch that enables to train only the motif model.

trees - Variable in class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction

The trees that represent the context of the random variable (i.e. configuration of parent random variables) of the parameters.

TRUE - Static variable in class de.jstacs.results.StorableResult

the model/classifier has been trained

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

This class is for visualizing two point dependency between sequence positions.

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