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## T

target - Variable in class de.jstacs.algorithms.graphs.Edge
  The target node.
template - Variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.ScoreClassifier
  The default history
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 can be used in any iterative algorithm for determining the end of the algorithm.
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(NumericalPerformanceMeasureParameterSet, boolean, DataSet...) - Method in class de.jstacs.classifiers.assessment.ClassifierAssessment
  Uses the given test samples to call the `evaluate( ... )` -methods of the local `AbstractClassifier`s.
threads - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.AbstractHMM
  The number of threads that is internally used.
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(E[]) - Method in class de.jstacs.AnnotatedEntityList
  Returns the `AnnotatedEntity`s in this list as an array.
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.sequences.Sequence
  This method converts a continuous value at position `pos` of the `Sequence` into a discrete one.
toDouble3DArray() - Method in class de.jstacs.algorithms.graphs.tensor.Tensor
  Creates a three-dimensional `double` array representation of the `Tensor`.
toGalaxy(String, String, int, StringBuffer, StringBuffer) - Method in class de.jstacs.parameters.AbstractSelectionParameter
toGalaxy(String, String, int, StringBuffer, StringBuffer) - Method in class de.jstacs.parameters.ExpandableParameterSet
toGalaxy(String, String, int, StringBuffer, StringBuffer) - Method in class de.jstacs.parameters.FileParameter
toGalaxy(String, String, int, StringBuffer, StringBuffer) - Method in interface de.jstacs.parameters.GalaxyConvertible
  Creates an Galaxy XML-representation of the parameters and appends it to `descBuffer` and variable configuration and appends it to `configBuffer`.
toGalaxy(String, String, int, StringBuffer, StringBuffer) - Method in class de.jstacs.parameters.ParameterSet
toGalaxy(String, String, int, StringBuffer, StringBuffer) - Method in class de.jstacs.parameters.ParameterSetContainer
toGalaxy(String, String, int, StringBuffer, StringBuffer) - Method in class de.jstacs.parameters.RangeParameter
toGalaxy(String, String, int, StringBuffer, StringBuffer) - Method in class de.jstacs.parameters.SimpleParameter
toGalaxy(String, String, int, StringBuffer, StringBuffer) - Method in class de.jstacs.parameters.validation.NumberValidator
toGalaxyConfig() - Method in class de.jstacs.utils.galaxy.GalaxyAdaptor
  Creates the contents of a Galaxy configuration file from all the information provided to this `GalaxyAdaptor`.
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.
tokenize() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser.NewickParser
  This method construct a `PhyloTree` from the given input stream
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.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.Measure
  Creates a new parent structure as defined by `Measure.getParents(DataSet, DataSet, 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(int, int, List<String>) - Method in class de.jstacs.algorithms.alignment.StringAlignment
  This method returns a String representation of the alignment with a given chunk size.
toString() - Method in class de.jstacs.algorithms.graphs.Edge
toString() - Method in class de.jstacs.algorithms.optimization.QuadraticFunction
toString() - Method in class de.jstacs.classifiers.AbstractScoreBasedClassifier.DoubleTableResult
toString() - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.GenDisMixClassifier
toString() - Method in class de.jstacs.data.AlphabetContainer
toString() - Method in class de.jstacs.data.alphabets.Alphabet
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.DataSet
toString() - Method in class de.jstacs.data.DataSet.WeightedDataSetFactory
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.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.data.sequences.Sequence
  Returns a `String` representation of the `Sequence` (normally the `Sequence` in its original `Alphabet`).
toString(int) - Method in class de.jstacs.data.sequences.Sequence
  Returns a `String` representation of the `Sequence` (normally the `Sequence` in its original `Alphabet`) beginning at position `start` with a default delimiter as separator.
toString(int, int) - Method in class de.jstacs.data.sequences.Sequence
  Returns a `String` representation of the `Sequence` (normally the `Sequence` in its original `Alphabet`) between `start` and `end` with a default delimiter as separator.
toString(String, int, int) - Method in class de.jstacs.data.sequences.Sequence
  Returns a `String` representation of the `Sequence` (normally the `Sequence` in its original alphabet) between `start` and `end` with `delim` as separator.
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(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.SelectionParameter
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.sequenceScores.differentiable.IndependentProductDiffSS
toString() - Method in class de.jstacs.sequenceScores.differentiable.logistic.LogisticDiffSS
toString() - Method in class de.jstacs.sequenceScores.differentiable.UniformDiffSS
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.CyclicMarkovModelDiffSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BayesianNetworkDiffSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.HomogeneousMM0DiffSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.HomogeneousMMDiffSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.UniformHomogeneousDiffSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.MappingDiffSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.MarkovRandomFieldDiffSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.MixtureDiffSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.DurationDiffSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.ExtendedZOOPSDiffSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.StrandDiffSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.MultiDimensionalSequenceWrapperDiffSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.NormalizedDiffSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.UniformDiffSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.CompositeTrainSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.DifferentiableStatisticalModelWrapperTrainSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.Constraint
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DiscreteGraphicalTrainSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.HomogeneousMM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.HomogeneousTrainSM.HomCondProb
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.DAGTrainSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.InhCondProb
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.MEMConstraint
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.AbstractHMM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.HMMFactory.PseudoTransitionElement
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.GaussianEmission
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.PluginGaussianEmission
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.DiscreteEmission
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.ReferenceSequenceDiscreteEmission
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.SilentEmission
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SimpleState
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement
toString(String[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement
  This method returns a `String` representation of the transition element using the given names of the states.
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition
toString(String[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition
toString(String[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.DistanceBasedScaledTransitionElement
toString(String[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.ScaledTransitionElement
toString(String[]) - Method in interface de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.Transition
  This method returns a `String` representation of the `Transition` using the given names of the states.
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.MixtureTrainSM
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.HiddenMotifMixture
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.StrandTrainSM
toString() - Method in interface de.jstacs.sequenceScores.statisticalModels.trainable.TrainableStatisticalModel
  Should give a simple representation (text) of the model as `String`.
toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.UniformTrainSM
  Returns the String "".
toString() - Method in class de.jstacs.utils.ComparableElement
toString() - Method in class de.jstacs.utils.DoubleList
toString() - Method in class de.jstacs.utils.galaxy.GalaxyAdaptor.Protocol
  Returns the current version of the protocol as `String`.
toString() - Method in class de.jstacs.utils.IntList
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.AnnotatedEntity
toXML() - Method in class de.jstacs.classifiers.AbstractClassifier
toXML() - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.CompositeLogPrior
toXML() - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.DoesNothingLogPrior
  Deprecated.
toXML() - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.LogPrior
  Encodes the prior as an XML representation.
toXML() - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.SeparateLogPrior
toXML() - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.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.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.ExpandableParameterSet
toXML() - Method in class de.jstacs.parameters.FileParameter.FileRepresentation
toXML() - Method in class de.jstacs.parameters.InstanceParameterSet
toXML() - Method in class de.jstacs.parameters.ParameterSet
toXML() - Method in class de.jstacs.parameters.SequenceScoringParameterSet
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.SimpleStaticConstraint
toXML() - Method in class de.jstacs.parameters.validation.StorableValidator
toXML() - Method in class de.jstacs.results.MeanResultSet
toXML() - Method in class de.jstacs.results.ResultSet
toXML() - Method in class de.jstacs.sampling.AbstractBurnInTest
toXML() - Method in class de.jstacs.sampling.SimpleBurnInTest
  Deprecated.
toXML() - Method in class de.jstacs.sequenceScores.differentiable.IndependentProductDiffSS
toXML() - Method in class de.jstacs.sequenceScores.differentiable.logistic.LogisticDiffSS
toXML() - Method in class de.jstacs.sequenceScores.differentiable.logistic.ProductConstraint
toXML() - Method in class de.jstacs.sequenceScores.differentiable.UniformDiffSS
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.CyclicMarkovModelDiffSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BayesianNetworkDiffSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree
  Works as defined in `Storable`.
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree.TreeElement
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.MarkovModelDiffSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.Measure
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.HomogeneousMM0DiffSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.HomogeneousMMDiffSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.UniformHomogeneousDiffSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.MappingDiffSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.MarkovRandomFieldDiffSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.AbstractMixtureDiffSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.DurationDiffSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.MixtureDurationDiffSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.PositionDiffSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.SkewNormalLikeDurationDiffSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.MultiDimensionalSequenceWrapperDiffSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.NormalizedDiffSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.CompositeTrainSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.DifferentiableStatisticalModelWrapperTrainSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.Constraint
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DiscreteGraphicalTrainSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared.SharedStructureMixture
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.AbstractHMM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.GaussianEmission
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.PluginGaussianEmission
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.MixtureEmission
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.SilentEmission
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.UniformEmission
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior.PositionPrior
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.phylo.PhyloNode
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.phylo.PhyloTree
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.UniformTrainSM
toXML() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.VariableLengthWrapperTrainSM
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(DataSet...) - Method in class de.jstacs.classifiers.AbstractClassifier
  Trains the `AbstractClassifier` object given the data as `DataSet`s.
train(DataSet[], double[][]) - Method in class de.jstacs.classifiers.AbstractClassifier
  This method trains a classifier over an array of weighted `DataSet` s.
train(DataSet...) - Method in class de.jstacs.classifiers.assessment.ClassifierAssessment
  Trains the local classifiers using the given training samples.
train(DataSet[], double[][]) - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.sampling.SamplingScoreBasedClassifier
train(DataSet[], double[][]) - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.ScoreClassifier
train(DataSet[], double[][]) - Method in class de.jstacs.classifiers.MappingClassifier
train(DataSet[], double[][]) - Method in class de.jstacs.classifiers.trainSMBased.TrainSMBasedClassifier
train(DataSet) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel
train(DataSet, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.CompositeTrainSM
train(DataSet, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.DifferentiableStatisticalModelWrapperTrainSM
train(DataSet, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.HomogeneousMM
train(DataSet[], double[][]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.HomogeneousMM
train(DataSet[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.HomogeneousTrainSM
  Trains the homogeneous model on all given `DataSet`s.
train(DataSet[], double[][]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.HomogeneousTrainSM
  Trains the homogeneous model using an array of weighted `DataSet`s.
train(DataSet, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.BayesianNetworkTrainSM
train(DataSet, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.FSDAGModelForGibbsSampling
train(DataSet, double[], int[][]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.FSDAGModelForGibbsSampling
train(DataSet, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.FSDAGTrainSM
train(DataSet, double[], int[][]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.FSDAGTrainSM
  Computes the model with structure `graph`.
train(TrainableStatisticalModel[], int[][], double[][], DataSet...) - Static method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.FSDAGTrainSM
  Computes the models with structure `graph`.
train(DataSet[], double[][]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared.SharedStructureClassifier
train(DataSet) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.AbstractHMM
train(DataSet, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.DifferentiableHigherOrderHMM
train(DataSet, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.HigherOrderHMM
train(DataSet, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.SamplingHigherOrderHMM
train(DataSet, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM
train(DataSet, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.HiddenMotifMixture
train(DataSet) - Method in interface de.jstacs.sequenceScores.statisticalModels.trainable.TrainableStatisticalModel
  Trains the `TrainableStatisticalModel` object given the data as `DataSet`.
train(DataSet, double[]) - Method in interface de.jstacs.sequenceScores.statisticalModels.trainable.TrainableStatisticalModel
  Trains the `TrainableStatisticalModel` object given the data as `DataSet` using the specified weights.
train(DataSet, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.UniformTrainSM
  Deprecated.
train(DataSet, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.VariableLengthWrapperTrainSM
TrainableAndDifferentiableTransition - Interface in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions
  This interface unifies the interfaces `TrainableTransition` and `DifferentiableTransition`.
TrainableState - Interface in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states
  This class implements method that allows to fill a statistic, which is used to estimate the parameters of a state during, for instance, the Baum-Welch training.
TrainableStatisticalModel - Interface in de.jstacs.sequenceScores.statisticalModels.trainable
  This interface defines all methods for a probabilistic model.
TrainableStatisticalModelFactory - Class in de.jstacs.sequenceScores.statisticalModels.trainable
  This class allows to easily create some frequently used models.
TrainableStatisticalModelFactory() - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.TrainableStatisticalModelFactory
TrainableTransition - Interface in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions
  This class declares methods that allow for estimating the parameters from a sufficient statistic, as for instance done in the (modified) Baum-Welch algorithm, viterbi training, or Gibbs sampling.
trainBgModel(DataSet, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.HiddenMotifMixture
  This method trains the background model.
trainBgModel(DataSet, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.ZOOPSTrainSM
trained - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DiscreteGraphicalTrainSM
  Indicates whether the model is trained or not.
trainingParameter - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.AbstractHMM
  The `ParameterSet` containing all `Parameter`s for the training of the HMM.
TrainSMBasedClassifier - Class in de.jstacs.classifiers.trainSMBased
  Classifier that works on `TrainableStatisticalModel`s for each of the different classes.
TrainSMBasedClassifier(boolean, TrainableStatisticalModel...) - Constructor for class de.jstacs.classifiers.trainSMBased.TrainSMBasedClassifier
  This constructor creates a new instance with the given `TrainableStatisticalModel`s and clones these if necessary.
TrainSMBasedClassifier(TrainableStatisticalModel...) - Constructor for class de.jstacs.classifiers.trainSMBased.TrainSMBasedClassifier
  The default constructor that creates a new instance with the given `TrainableStatisticalModel`s.
TrainSMBasedClassifier(StringBuffer) - Constructor for class de.jstacs.classifiers.trainSMBased.TrainSMBasedClassifier
  The standard constructor for the interface `Storable`.
transformation - Variable in class de.jstacs.data.sequences.MappedDiscreteSequence
  The `DiscreteAlphabetMapping`s used for mapping the original `Sequence`.
transition - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.AbstractHMM
  The transitions between all (hidden) states of the HMM.
Transition - Interface in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions
  This interface declares the methods of the transition used in a hidden Markov model.
TransitionElement - Class in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements
  This class implements an transition element implements method used for training via sampling or gradient based optimization approach.
TransitionElement(int[], int[], double[]) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.TransitionElement
  This is the main constructor creating a new instance with given context, descendant states, and hyper parameters.
TransitionElement(int[], int[], double[], double[]) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.TransitionElement
  This is the main constructor creating a new instance with given context, descendant states, and hyper parameters.
TransitionElement(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.TransitionElement
  The standard constructor for the interface `Storable`.
transitions - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition
  The internally used `BasicHigherOrderTransition.AbstractTransitionElement`s.
TransitionWithSufficientStatistic - Interface in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions
  This interface defines method for reseting and filling an internal sufficient statistic.
transpose(double[][]) - Static method in class de.jstacs.utils.ToolBox
  Transpose a `double` matrix.
trees - Variable in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BayesianNetworkDiffSM
  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.
TwoClassAbstractPerformanceMeasure - Class in de.jstacs.classifiers.performanceMeasures
  This class is the abstract super class of any performance measure that can only be computed for binary classifiers.
TwoClassAbstractPerformanceMeasure() - Constructor for class de.jstacs.classifiers.performanceMeasures.TwoClassAbstractPerformanceMeasure
  Constructs a new `TwoClassAbstractPerformanceMeasure` with empty parameter values.
TwoClassAbstractPerformanceMeasure(StringBuffer) - Constructor for class de.jstacs.classifiers.performanceMeasures.TwoClassAbstractPerformanceMeasure
  The standard constructor for the interface `Storable`.
TwoPointEvaluater - Class in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous
  This class is for visualizing two point dependency between sequence positions.
TwoPointEvaluater() - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.TwoPointEvaluater
TYPE - Static variable in class de.jstacs.data.sequences.annotation.ReferenceSequenceAnnotation
  The type of a `ReferenceSequenceAnnotation`.

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