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W

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

The weight of the edge.

WeightedDataSetFactory(DataSet.WeightedDataSetFactory.SortOperation, DataSet...) - Constructor for class de.jstacs.data.DataSet.WeightedDataSetFactory

Creates a new DataSet.WeightedDataSetFactory on the given DataSet(s) with DataSet.WeightedDataSetFactory.SortOperation sort.

WeightedDataSetFactory(DataSet.WeightedDataSetFactory.SortOperation, DataSet, double[]) - Constructor for class de.jstacs.data.DataSet.WeightedDataSetFactory

Creates a new DataSet.WeightedDataSetFactory on the given DataSet and an array of weights with DataSet.WeightedDataSetFactory.SortOperation sort.

WeightedDataSetFactory(DataSet.WeightedDataSetFactory.SortOperation, DataSet, double[], int) - Constructor for class de.jstacs.data.DataSet.WeightedDataSetFactory

Creates a new DataSet.WeightedDataSetFactory on the given DataSet and an array of weights with a given length and DataSet.WeightedDataSetFactory.SortOperation sort.

WeightedDataSetFactory(DataSet.WeightedDataSetFactory.SortOperation, DataSet[], double[][], int) - Constructor for class de.jstacs.data.DataSet.WeightedDataSetFactory

Creates a new DataSet.WeightedDataSetFactory on the given array of DataSets and an array of weights with a given length and DataSet.WeightedDataSetFactory.SortOperation sort.

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

Returns the element in the sorted variant of array (considered in descending order) that yields percent of the cumulative value of array elements.

weights - Variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.AbstractOptimizableFunction

The weights for the data.

weights - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM

The probabilities for each component.

wiki() - Method in class de.jstacs.tools.ui.cli.CLI

Creates the HTML code for wiki entries for the supplied tools.

worker - Variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.AbstractMultiThreadedOptimizableFunction

The worker threads for computing value and gradient of this AbstractMultiThreadedOptimizableFunction

write(Writer, CharSequence) - Static method in class de.jstacs.io.FileManager

This method saves a StringBuffer to a given Writer.

write(int) - Method in class de.jstacs.utils.RegExFilterOutputStream

write(Object) - Method in class de.jstacs.utils.SafeOutputStream

Writes an Object using Object.toString().

write(int) - Method in class de.jstacs.utils.SafeOutputStream

writeFile(File, CharSequence) - Static method in class de.jstacs.io.FileManager

This method saves a StringBuffer to a given File.

writeFile(String, CharSequence) - Static method in class de.jstacs.io.FileManager

This method saves a StringBuffer to a File with user-specified file name.

writeln() - Method in class de.jstacs.utils.SafeOutputStream

Writes a line break.

writeln(Object) - Method in class de.jstacs.utils.SafeOutputStream

Writes an Object and a line break.

writeOutput(DataSetResult, File) - Method in class de.jstacs.results.savers.DataSetResultSaver

writeOutput(DataSetResult, StringBuffer) - Method in class de.jstacs.results.savers.DataSetResultSaver

writeOutput(ListResult, File) - Method in class de.jstacs.results.savers.ListResultSaver

writeOutput(ListResult, StringBuffer) - Method in class de.jstacs.results.savers.ListResultSaver

writeOutput(PlotGeneratorResult, File) - Method in class de.jstacs.results.savers.PlotGeneratorResultSaver

writeOutput(PlotGeneratorResult, StringBuffer) - Method in class de.jstacs.results.savers.PlotGeneratorResultSaver

Deprecated.

writeOutput(T, File) - Method in interface de.jstacs.results.savers.ResultSaver

Writes the output (i.e., the result contents) to the supplied file.

writeOutput(T, StringBuffer) - Method in interface de.jstacs.results.savers.ResultSaver

Appends the output (i.e., the result contents) to the supplied StringBuffer

writeOutput(ResultSetResult, File) - Method in class de.jstacs.results.savers.ResultSetResultSaver

writeOutput(ResultSetResult, StringBuffer) - Method in class de.jstacs.results.savers.ResultSetResultSaver

writeOutput(StorableResult, File) - Method in class de.jstacs.results.savers.StorableResultSaver

writeOutput(StorableResult, StringBuffer) - Method in class de.jstacs.results.savers.StorableResultSaver

writeOutput(TextResult, File) - Method in class de.jstacs.results.savers.TextResultSaver

writeOutput(TextResult, StringBuffer) - Method in class de.jstacs.results.savers.TextResultSaver

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

Writes all output files of one program execution.

writeOutputStream(OutputStream, CharSequence) - Static method in class de.jstacs.io.FileManager

This method saves a StringBuffer to a given OutputStream.

writer - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.FSDAGModelForGibbsSampling

The writer for the paramsFile in a sampling.

writer - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission

The writer for the paramsFile in a sampling.

writer - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.HigherOrderTransition

The writer for the paramsFile in a sampling.

writeTensorToFile(String, OutputStream) - Method in class de.jstacs.algorithms.graphs.tensor.Tensor

This method writes a Tensor in the exchange format in a specified file.

WrongAlphabetException - Exception in de.jstacs.data

A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

WrongAlphabetException() - Constructor for exception de.jstacs.data.WrongAlphabetException

Creates a new WrongAlphabetException with standard error message ("The data of the selected file does not match the entered alphabet.").

WrongAlphabetException(String) - Constructor for exception de.jstacs.data.WrongAlphabetException

Creates a new WrongAlphabetException with given error message.

WrongLengthException - Exception in de.jstacs.data

A WrongLengthException is thrown if a given (sub)sequence length is not correct.

WrongLengthException(int) - Constructor for exception de.jstacs.data.WrongLengthException

Simple Constructor.

WrongLengthException(String) - Constructor for exception de.jstacs.data.WrongLengthException

Creates a new WrongLengthException with your own message.

WrongParameterTypeException(String) - Constructor for exception de.jstacs.io.ParameterSetParser.WrongParameterTypeException

Creates a new instance of a ParameterSetParser.WrongParameterTypeException with a given error message.

WrongSequenceTypeException - Exception in de.jstacs.data.sequences

This Exception indicates that the type of the sequence ( ByteSequence, ShortSequence, ...) is not suitable for a given AlphabetContainer.

WrongSequenceTypeException() - Constructor for exception de.jstacs.data.sequences.WrongSequenceTypeException

This constructor creates a new WrongSequenceTypeException with default error message ("The sequence type is not suitable for this AlphabetContainer.").

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