A B C D E F G H I J 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.
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 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.
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
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.CompositeSequence 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.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.CompositeSequence (normally the Sequence.CompositeSequence in its original Alphabet).
toString(int) - Method in class de.jstacs.data.Sequence
Returns a String representation of the Sequence.CompositeSequence (normally the Sequence.CompositeSequence 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.CompositeSequence (normally the Sequence.CompositeSequence 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.CompositeSequence (normally the Sequence.CompositeSequence 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.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
 
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 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.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.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.NormalizableScoringFunctionModel
 
toXML() - Method in class de.jstacs.models.UniformModel
 
toXML() - Method in class de.jstacs.models.VariableLengthWrapperModel
 
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.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 Samples.
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 Samples.
train(Sample[], double[][]) - Method in class de.jstacs.models.discrete.homogeneous.HomogeneousModel
Trains the homogeneous 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 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.
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
 

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