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

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[], double[][]) - Method in class de.jstacs.classifiers.assessment.ClassifierAssessment

Uses the given test data sets to call the evaluate( ...

TextResult - Class in de.jstacs.results

Class for a result that is basically a text file (or its contents).

TextResult(String, String, FileParameter.FileRepresentation, String, String, String, boolean) - Constructor for class de.jstacs.results.TextResult

Creates a new TextResult with given name, comment, content, mime type, and additional info.

TextResult(StringBuffer) - Constructor for class de.jstacs.results.TextResult

Creates a TextResult from its XML representation.

TextResultSaver - Class in de.jstacs.results.savers

ResultSaver for a TextResult.

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.

TimeConditionParameterSet() - Constructor for class de.jstacs.algorithms.optimization.termination.TimeCondition.TimeConditionParameterSet

This constructor creates an empty parameter set.

TimeConditionParameterSet(StringBuffer) - Constructor for class de.jstacs.algorithms.optimization.termination.TimeCondition.TimeConditionParameterSet

The standard constructor for the interface Storable.

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 AnnotatedEntitys 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(double[]) - Method in class de.jstacs.utils.DoubleList

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

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

This method returns a double array containing all elements of the list between start and end (exclusive).

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, boolean) - Method in class de.jstacs.parameters.AbstractSelectionParameter

toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean) - Method in class de.jstacs.parameters.ExpandableParameterSet

toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean) - Method in class de.jstacs.parameters.FileParameter

toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean) - 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, boolean) - Method in class de.jstacs.parameters.ParameterSet

toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean) - Method in class de.jstacs.parameters.ParameterSetContainer

toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean) - Method in class de.jstacs.parameters.RangeParameter

toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean) - Method in class de.jstacs.parameters.SimpleParameter

toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean[]) - Method in class de.jstacs.parameters.SimpleParameterSet

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, boolean) - Method in class de.jstacs.parameters.validation.NumberValidator

toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean) - Method in class de.jstacs.parameters.validation.RegExpValidator

toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean) - Method in class de.jstacs.tools.DataColumnParameter

toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean) - Method in class de.jstacs.tools.ui.galaxy.MultilineSimpleParameter

toGalaxyConfig(boolean) - Method in class de.jstacs.tools.ui.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.

toHtml(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BayesianNetworkDiffSM

Returns an HTML representation of this BayesianNetworkDiffSM.

toHtml(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree

Returns an HTML representation of this tree.

tokenize() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser.NewickParser

This method construct a PhyloTree from the given input stream

toNewick() - Method in class de.jstacs.clustering.hierachical.ClusterTree

Returns a string representation of this cluster tree in newick format.

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

ToolBox.TiedRanks - Enum in de.jstacs.utils

Handling of tied ranks in ToolBox.rank(double[], TiedRanks).

ToolResult - Class in de.jstacs.tools

Class for the results of a JstacsTool.

ToolResult(String, String, ResultSet, ResultSet, ParameterSet, String, Date) - Constructor for class de.jstacs.tools.ToolResult

Creates a new ToolResult with most arguments identical to those of a ListResult.

ToolResult(StringBuffer) - Constructor for class de.jstacs.tools.ToolResult

The standard constructor for the interface Storable.

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.classifiers.differentiableSequenceScoreBased.sampling.SamplingScoreBasedClassifier

toString() - Method in class de.jstacs.classifiers.trainSMBased.TrainSMBasedClassifier

toString() - Method in class de.jstacs.clustering.hierachical.ClusterTree

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

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.AbstractDifferentiableSequenceScore

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.differentiable.IndependentProductDiffSS

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.differentiable.logistic.LogisticDiffSS

toString() - Method in class de.jstacs.sequenceScores.differentiable.logistic.ProductConstraint

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.differentiable.MultiDimensionalSequenceWrapperDiffSS

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.differentiable.UniformDiffSS

toString(NumberFormat) - Method in interface de.jstacs.sequenceScores.SequenceScore

This method returns a String representation of the instance.

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.CyclicMarkovModelDiffSM

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BayesianNetworkDiffSM

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree

Returns a string representation of this tree using the provided NumberFormat.

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.HomogeneousMM0DiffSM

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.HomogeneousMMDiffSM

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.UniformHomogeneousDiffSM

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.localMixture.LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.MappingDiffSM

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.MarkovRandomFieldDiffSM

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.MixtureDiffSM

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.DurationDiffSM

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.ExtendedZOOPSDiffSM

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.StrandDiffSM

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.NormalizedDiffSM

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.differentiable.UniformDiffSM

toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.CompositeTrainSM

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.DifferentiableStatisticalModelWrapperTrainSM

toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.Constraint

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DiscreteGraphicalTrainSM

toString(NumberFormat) - 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(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.DAGTrainSM

toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.InhCondProb

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.MEM

This method returns some String using a given NumberFormat.

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.MEManager

toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.MEMConstraint

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.AbstractHMM

toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.HMMFactory.PseudoTransitionElement

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.GaussianEmission

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.MultivariateGaussianEmission

toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.PluginGaussianEmission

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.DiscreteEmission

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.ReferenceSequenceDiscreteEmission

toString(NumberFormat) - Method in interface de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.Emission

This method returns a String representation of the instance.

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.MixtureEmission

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.SilentEmission

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.UniformEmission

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SimpleState

toString(NumberFormat) - Method in interface de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.State

This method returns a String representation of the instance.

toString() - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement

toString(String[], NumberFormat) - 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[], NumberFormat) - 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

Returns a string representation of the transition probabilities.

toString(String[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.ScaledTransitionElement

Returns a string representation of the transition probabilities.

toString(String[], NumberFormat) - 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(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.MixtureTrainSM

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.HiddenMotifMixture

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.StrandTrainSM

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.PFMWrapperTrainSM

toString() - Method in interface de.jstacs.sequenceScores.statisticalModels.trainable.TrainableStatisticalModel

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

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.UniformTrainSM

Returns the String "".

toString(NumberFormat) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.VariableLengthWrapperTrainSM

toString() - Method in class de.jstacs.tools.ui.galaxy.GalaxyAdaptor.Protocol

Returns the current version of the protocol as String.

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

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

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

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

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

toString(double[], NumberFormat) - Static method in class de.jstacs.utils.ToolBox

This methods returns a String representation of a double array using the specified NumberFormat.

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.alignment.cost.AffineCosts

toXML() - Method in class de.jstacs.algorithms.alignment.cost.MatrixCosts

toXML() - Method in class de.jstacs.algorithms.alignment.cost.SimpleCosts

toXML() - Method in class de.jstacs.algorithms.alignment.PairwiseStringAlignment

toXML() - Method in class de.jstacs.algorithms.alignment.StringAlignment

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.clustering.hierachical.ClusterTree

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.RegExpValidator

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.MultiDimensionalSequenceWrapperDiffSS

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.localMixture.LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder

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.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.MEM

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.MultivariateGaussianEmission

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.PFMWrapperTrainSM

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

toXML() - Method in class de.jstacs.utils.SeqLogoPlotter.SeqLogoPlotGenerator

train(DataSet...) - Method in class de.jstacs.classifiers.AbstractClassifier

Trains the AbstractClassifier object given the data as DataSets.
This method should work non-incrementally.

train(DataSet[], double[][]) - Method in class de.jstacs.classifiers.AbstractClassifier

This method trains a classifier over an array of weighted DataSet s.

train(DataSet[], double[][]) - Method in class de.jstacs.classifiers.assessment.ClassifierAssessment

Trains the local classifiers using the given training data sets.

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 DataSets.

train(DataSet[], double[][]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.HomogeneousTrainSM

Trains the homogeneous model using an array of weighted DataSets.

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.FSMEManager

train(SequenceIterator, byte, TerminationCondition, SafeOutputStream) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.MEM

This method approximates the distribution either analytically or numerically.

train(MEMConstraint[], int[][], SequenceIterator, byte, TerminationCondition, OutputStream, int[]) - Static method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.MEMTools

This method approximates the distribution either analytically or numerically.

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, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.PFMWrapperTrainSM

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.

trainFactors(DataSet, double[]) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.MEManager

This method trains the internal MEM array, i.e., it optimizes the parameters of the underlying MEMConstraints.

trainingParameter - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.AbstractHMM

The ParameterSet containing all Parameters for the training of the HMM.

TrainSMBasedClassifier - Class in de.jstacs.classifiers.trainSMBased

Classifier that works on TrainableStatisticalModels 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 TrainableStatisticalModels 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 TrainableStatisticalModels.

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 DiscreteAlphabetMappings 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.AbstractTransitionElements.

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.

TreeElement(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree.TreeElement

Constructor for the Storable interface.

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.

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 - Variable in class de.jstacs.algorithms.alignment.Alignment

The type of the alignment

TYPE - Static variable in class de.jstacs.data.sequences.annotation.ReferenceSequenceAnnotation

The type of a ReferenceSequenceAnnotation.

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