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## T

target - Variable in class de.jstacs.algorithms.graphs.Edge
  The target node.
template - Variable in class de.jstacs.classifier.scoringFunctionBased.ScoreClassifier
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`.
TerminationCondition - Interface in de.jstacs.algorithms.optimization.termination
  This interface declares a method that can be used to decide whether another iteration in an optimization should be done or not.
TerminationException - Exception in de.jstacs.algorithms.optimization
  This class is for an `Exception` that is thrown if something with a termination was not correct.
TerminationException() - Constructor for exception de.jstacs.algorithms.optimization.TerminationException
  Creates a new `TerminationException` with standard error 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 `AbstractClassifier`s.
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.
TimeCondition - Class in de.jstacs.algorithms.optimization.termination
  This class implements a `TerminationCondition` that stops the optimization if the elapsed time in seconds is greater than a given value.
TimeCondition(double) - Constructor for class de.jstacs.algorithms.optimization.termination.TimeCondition
  This constructor creates an instance that does not allow any further iteration after `s` seconds
TimeCondition(TimeCondition.TimeConditionParameterSet) - Constructor for class de.jstacs.algorithms.optimization.termination.TimeCondition
  This is the main constructor creating an instance from a given parameter set.
TimeCondition(StringBuffer) - Constructor for class de.jstacs.algorithms.optimization.termination.TimeCondition
  The standard constructor for the interface `Storable`.
TimeCondition.TimeConditionParameterSet - Class in de.jstacs.algorithms.optimization.termination
  This class implements the parameter set for a `TimeCondition`.
TimeCondition.TimeConditionParameterSet() - Constructor for class de.jstacs.algorithms.optimization.termination.TimeCondition.TimeConditionParameterSet
  This constructor creates an empty parameter set.
TimeCondition.TimeConditionParameterSet(StringBuffer) - Constructor for class de.jstacs.algorithms.optimization.termination.TimeCondition.TimeConditionParameterSet
  The standard constructor for the interface `Storable`.
TimeCondition.TimeConditionParameterSet(double) - Constructor for class de.jstacs.algorithms.optimization.termination.TimeCondition.TimeConditionParameterSet
  This constructor creates a filled instance of a parameters set.
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 directed `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` of the `Alphabet` of position `pos` in the `AlphabetContainer`.
toDiscrete(int, double) - Method in class de.jstacs.data.Sequence
  This method converts a continuous value at position `pos` of the `Sequence.RecursiveSequence` into a discrete one.
toDouble3DArray() - Method in class de.jstacs.algorithms.graphs.tensor.Tensor
  Creates a three-dimensional `double` array representation of the `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.
ToolBox - Class in de.jstacs.utils
  This class is a collection of methods which might be useful for the programmer.
ToolBox() - Constructor for class de.jstacs.utils.ToolBox
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.classifier.ScoreBasedPerformanceMeasureDefinitions.ThresholdMeasurePair
toString() - Method in class de.jstacs.classifier.scoringFunctionBased.gendismix.GenDisMixClassifier
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.DinucleotideProperty.MeanSmoothing
toString() - Method in class de.jstacs.data.DinucleotideProperty.MedianSmoothing
toString() - Method in class de.jstacs.data.DinucleotideProperty.NoSmoothing
toString() - Method in class de.jstacs.data.DinucleotideProperty.Smoothing
  Returns a `String` representation of this smoothing method.
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.RecursiveSequence` (normally the `Sequence.RecursiveSequence` in its original `Alphabet`).
toString(int) - Method in class de.jstacs.data.Sequence
  Returns a `String` representation of the `Sequence.RecursiveSequence` (normally the `Sequence.RecursiveSequence` in its original `Alphabet`) beginning at position `start` with a default delimiter as separator.
toString(int, int) - Method in class de.jstacs.data.Sequence
  Returns a `String` representation of the `Sequence.RecursiveSequence` (normally the `Sequence.RecursiveSequence` in its original `Alphabet`) between `start` and `end` with a default delimiter as separator.
toString(String, int, int) - Method in class de.jstacs.data.Sequence
  Returns a `String` representation of the `Sequence.RecursiveSequence` (normally the `Sequence.RecursiveSequence` in its original alphabet) between `start` and `end` 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.ReferenceSequenceAnnotation
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.io.CombinedFileFilter
toString() - Method in class de.jstacs.io.DateFileFilter
toString() - Method in class de.jstacs.io.RegExFilenameFilter
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.NormalizableScoringFunctionModel
toString() - Method in class de.jstacs.models.UniformModel
  Returns the String "".
toString() - Method in class de.jstacs.parameters.CollectionParameter
toString(Comparator<Map.Entry<String, ComparableElement<Parameter, Integer>>>) - Method in class de.jstacs.parameters.ParameterSetTagger
  This method allows to get a String representation where the tagged parameters are sorted in some specific way.
toString() - Method in class de.jstacs.parameters.ParameterSetTagger
toString() - Method in class de.jstacs.parameters.SimpleParameter
toString() - Method in class de.jstacs.parameters.validation.NumberValidator
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.CMMScoringFunction
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.mix.motifSearch.DurationScoringFunction
toString() - Method in class de.jstacs.scoringFunctions.mix.motifSearch.HiddenMotifsMixture
toString() - Method in class de.jstacs.scoringFunctions.mix.StrandScoringFunction
toString() - Method in class de.jstacs.scoringFunctions.MRFScoringFunction
toString() - Method in class de.jstacs.scoringFunctions.NormalizedScoringFunction
toString() - Method in class de.jstacs.scoringFunctions.UniformScoringFunction
toString() - Method in class de.jstacs.utils.ComparableElement
toString() - Method in class de.jstacs.utils.TimeLimitedProgressUpdater
toUndirectedGraphvizFormat(int[][]) - Static method in class de.jstacs.algorithms.graphs.DAG
  This method returns an undirected `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.algorithms.optimization.termination.AbstractTerminationCondition
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.CompositeLogPrior
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.alphabets.DiscreteAlphabetMapping
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.ReferenceSequenceAnnotation
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
  Deprecated.
toXML() - Method in class de.jstacs.models.mixture.motif.positionprior.PositionPrior
toXML() - Method in class de.jstacs.models.NormalizableScoringFunctionModel
toXML() - Method in class de.jstacs.models.UniformModel
toXML() - Method in class de.jstacs.models.VariableLengthWrapperModel
toXML() - Method in class de.jstacs.motifDiscovery.history.CappedHistory
toXML() - Method in class de.jstacs.motifDiscovery.history.NoRevertHistory
toXML() - Method in class de.jstacs.motifDiscovery.history.RestrictedRepeatHistory
toXML() - Method in class de.jstacs.motifDiscovery.history.SimpleHistory
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.CMMScoringFunction
toXML() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
toXML() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.MutableMarkovModelScoringFunction
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.ParameterTree.TreeElement
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.mix.motifSearch.DurationScoringFunction
toXML() - Method in class de.jstacs.scoringFunctions.mix.motifSearch.MixtureDuration
toXML() - Method in class de.jstacs.scoringFunctions.mix.motifSearch.PositionScoringFunction
toXML() - Method in class de.jstacs.scoringFunctions.mix.motifSearch.SkewNormalLikeScoringFunction
toXML() - Method in class de.jstacs.scoringFunctions.MRFScoringFunction
toXML() - Method in class de.jstacs.scoringFunctions.NormalizedScoringFunction
toXML() - Method in class de.jstacs.scoringFunctions.UniformScoringFunction
toXML() - Method in interface de.jstacs.Storable
  This method returns an XML representation as `StringBuffer` 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 `Sample`s.
train(Sample[], double[][]) - Method in class de.jstacs.classifier.AbstractClassifier
  This method trains a classifier over an array of weighted `Sample` s.
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 homogeneous model on all given `Sample`s.
train(Sample[], double[][]) - Method in class de.jstacs.models.discrete.homogeneous.HomogeneousModel
  Trains the homogeneous model using an array of weighted `Sample`s.
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 `Model` 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.NormalizableScoringFunctionModel
train(Sample, double[]) - Method in class de.jstacs.models.UniformModel
  Deprecated.
train(Sample, double[]) - Method in class de.jstacs.models.VariableLengthWrapperModel
trainBgModel(Sample, double[]) - Method in class de.jstacs.models.mixture.motif.HiddenMotifMixture
  This method trains the background model.
trainBgModel(Sample, double[]) - Method in class de.jstacs.models.mixture.motif.SingleHiddenMotifMixture
trained - Variable in class de.jstacs.models.discrete.DiscreteGraphicalModel
  Indicates whether the model is trained or not.
transformation - Variable in class de.jstacs.data.sequences.MappedDiscreteSequence
  The `DiscreteAlphabetMapping`s used for mapping the original `Sequence`.
trees - Variable in class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
  The trees that represent the context of the random variable (i.e.
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
TYPE - Static variable in class de.jstacs.data.sequences.annotation.ReferenceSequenceAnnotation
  The type of a `ReferenceSequenceAnnotation`.

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