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## A

AbsoluteValueCondition - Class in de.jstacs.algorithms.optimization.termination
  Deprecated. use of the absolute value condition is not recommended and it may be removed in future releases
AbsoluteValueCondition(double) - Constructor for class de.jstacs.algorithms.optimization.termination.AbsoluteValueCondition
  Deprecated. This constructor creates an instance that stops an minimization when the value of the function is below the given `threshold`
  Be careful!
AbstractBurnInTest - Class in de.jstacs.models.mixture.gibbssampling
  This abstract class implements some of the methods of `BurnInTest` to alleviate the implementation of efficient and new burn-in tests.
AbstractBurnInTest(int) - Constructor for class de.jstacs.models.mixture.gibbssampling.AbstractBurnInTest
  This is the main constructor that creates a burn-in test for a specified number of Gibbs sampling starts.
AbstractBurnInTest(StringBuffer) - Constructor for class de.jstacs.models.mixture.gibbssampling.AbstractBurnInTest
  This is the constructor for the `Storable` interface.
AbstractClassifier - Class in de.jstacs.classifier
  The super class for any classifier.
AbstractClassifier(AlphabetContainer) - Constructor for class de.jstacs.classifier.AbstractClassifier
  The constructor for a homogeneous classifier.
AbstractClassifier(AlphabetContainer, int) - Constructor for class de.jstacs.classifier.AbstractClassifier
  The constructor for an inhomogeneous classifier.
AbstractClassifier(StringBuffer) - Constructor for class de.jstacs.classifier.AbstractClassifier
  The standard constructor for the interface `Storable`.
AbstractMixtureModel - Class in de.jstacs.models.mixture
  This is the abstract class for all kinds of mixture models.
AbstractMixtureModel(int, Model[], boolean[], int, int, boolean, double[], double[], AbstractMixtureModel.Algorithm, double, double, AbstractMixtureModel.Parameterization, int, int, BurnInTest) - Constructor for class de.jstacs.models.mixture.AbstractMixtureModel
  Creates a new `AbstractMixtureModel`.
AbstractMixtureModel(StringBuffer) - Constructor for class de.jstacs.models.mixture.AbstractMixtureModel
  The standard constructor for the interface `Storable`.
AbstractMixtureModel.Algorithm - Enum in de.jstacs.models.mixture
  This `enum` defines the different types of algorithms that can be used in an `AbstractMixtureModel`.
AbstractMixtureModel.Parameterization - Enum in de.jstacs.models.mixture
  This `enum` defines the different types of parameterization for a probability that can be used in an `AbstractMixtureModel`.
AbstractMixtureScoringFunction - Class in de.jstacs.scoringFunctions.mix
  This main abstract class for any mixture scoring function (e.g.
AbstractMixtureScoringFunction(int, int, int, boolean, boolean, NormalizableScoringFunction...) - Constructor for class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
  This constructor creates a new `AbstractMixtureScoringFunction`.
AbstractMixtureScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
  This is the constructor for the interface `Storable`.
AbstractModel - Class in de.jstacs.models
  Abstract class for a model for pattern recognition.
AbstractModel(AlphabetContainer, int) - Constructor for class de.jstacs.models.AbstractModel
  Constructor that sets the length of the model to `length` and the `AlphabetContainer` to `alphabets`.
AbstractModel(StringBuffer) - Constructor for class de.jstacs.models.AbstractModel
  The standard constructor for the interface `Storable`.
AbstractMultiThreadedOptimizableFunction - Class in de.jstacs.classifier.scoringFunctionBased
  This class enables the user to exploit all CPUs of an computer by using threads.
AbstractMultiThreadedOptimizableFunction(int, Sample[], double[][], boolean, boolean) - Constructor for class de.jstacs.classifier.scoringFunctionBased.AbstractMultiThreadedOptimizableFunction
  The constructor for an multi-threaded instance.
AbstractNormalizableScoringFunction - Class in de.jstacs.scoringFunctions
  This class is the main part of any `ScoreClassifier`.
AbstractNormalizableScoringFunction(AlphabetContainer, int) - Constructor for class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
  The main constructor.
AbstractNormalizableScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
  This is the constructor for `Storable`.
AbstractOptimizableFunction - Class in de.jstacs.classifier.scoringFunctionBased
  This class extends `OptimizableFunction` and implements some common methods.
AbstractOptimizableFunction(Sample[], double[][], boolean, boolean) - Constructor for class de.jstacs.classifier.scoringFunctionBased.AbstractOptimizableFunction
  The constructor creates an instance using the given weighted data.
AbstractScoreBasedClassifier - Class in de.jstacs.classifier
  This class is the main class for all score based classifiers.
AbstractScoreBasedClassifier(AlphabetContainer, int) - Constructor for class de.jstacs.classifier.AbstractScoreBasedClassifier
  The constructor for a homogeneous classifier.
AbstractScoreBasedClassifier(AlphabetContainer, int, double) - Constructor for class de.jstacs.classifier.AbstractScoreBasedClassifier
  The constructor for a homogeneous classifier.
AbstractScoreBasedClassifier(AlphabetContainer, int, int) - Constructor for class de.jstacs.classifier.AbstractScoreBasedClassifier
  The constructor for an inhomogeneous classifier.
AbstractScoreBasedClassifier(AlphabetContainer, int, int, double) - Constructor for class de.jstacs.classifier.AbstractScoreBasedClassifier
  The constructor for an inhomogeneous classifier.
AbstractScoreBasedClassifier(StringBuffer) - Constructor for class de.jstacs.classifier.AbstractScoreBasedClassifier
  The standard constructor for the interface `Storable`.
AbstractScoreBasedClassifier.DoubleTableResult - Class in de.jstacs.classifier
  This class is for `Result`s given as a table of `double` s.
AbstractScoreBasedClassifier.DoubleTableResult(String, String, AbstractList<double[]>) - Constructor for class de.jstacs.classifier.AbstractScoreBasedClassifier.DoubleTableResult
  This is the default constructor that creates an instance based on the results given in `list`
AbstractScoreBasedClassifier.DoubleTableResult(StringBuffer) - Constructor for class de.jstacs.classifier.AbstractScoreBasedClassifier.DoubleTableResult
  The standard constructor for the interface `Storable` .
AbstractStringExtractor - Class in de.jstacs.io
  This class implements the reader that extracts strings.
AbstractStringExtractor(char) - Constructor for class de.jstacs.io.AbstractStringExtractor
  Creates a new `AbstractStringExtractor` with the specified character as start of each comment line.
AbstractVariableLengthScoringFunction - Class in de.jstacs.scoringFunctions
  This abstract class implements some methods declared in `NormalizableScoringFunction` based on the declaration of methods in `VariableLengthScoringFunction`.
AbstractVariableLengthScoringFunction(AlphabetContainer) - Constructor for class de.jstacs.scoringFunctions.AbstractVariableLengthScoringFunction
  This is the main constructor that creates an instance of a `VariableLengthScoringFunction` that models sequences of arbitrary length.
AbstractVariableLengthScoringFunction(AlphabetContainer, int) - Constructor for class de.jstacs.scoringFunctions.AbstractVariableLengthScoringFunction
  This is the main constructor that creates an instance of a `VariableLengthScoringFunction` that models sequences of a given length.
AbstractVariableLengthScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.AbstractVariableLengthScoringFunction
  This is the constructor for the interface `Storable`.
accept(File) - Method in class de.jstacs.io.CombinedFileFilter
accept(File) - Method in class de.jstacs.io.DateFileFilter
accept(File) - Method in class de.jstacs.io.RegExFilenameFilter
accept(File, String) - Method in class de.jstacs.io.RegExFilenameFilter
actionPerformed(ActionEvent) - Method in class de.jstacs.utils.GUIProgressUpdater
add(int, int) - Method in class de.jstacs.classifier.ConfusionMatrix
  This method updates the confusion matrix.
add(int, double) - Method in class de.jstacs.models.discrete.Constraint
  Adds the given `weight` to the count with index `index`.
add(Sequence, int, double) - Method in class de.jstacs.models.discrete.Constraint
  This method determines the specific constraint that is fulfilled by the `Sequence` `seq` and adds the `weight` to the specific counter.
add(int, Parameter) - Method in class de.jstacs.parameters.ParameterSet.ParameterList
add(Parameter) - Method in class de.jstacs.parameters.ParameterSet.ParameterList
add(double) - Method in class de.jstacs.utils.DoubleList
  Adds the element `val` at the end of the list.
add(double, int, int) - Method in class de.jstacs.utils.DoubleList
  Adds the element `val` from `fromIndex` to `toIndex` (exclusive).
add(int) - Method in class de.jstacs.utils.IntList
  Adds the element `val` at the end of the list.
addAll(Sequence, double, int, int) - Method in class de.jstacs.models.discrete.homogeneous.HomogeneousModel.HomCondProb
  Adds the given `weight` to the counts corresponding to the `Sequence` `seq` from `start` to the end of the `Sequence`.
addAll(Collection<? extends Parameter>) - Method in class de.jstacs.parameters.ParameterSet.ParameterList
addAll(int, Collection<? extends Parameter>) - Method in class de.jstacs.parameters.ParameterSet.ParameterList
addConstraint(Constraint) - Method in class de.jstacs.parameters.validation.ConstraintValidator
  Adds an additional `Constraint` to the list of `Constraint`s.
addCount(double) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter
  Adds `count2` to the counts of this parameter.
addCount(Sequence, int, double) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree
  Adds `count` to the parameter as returned by `ParameterTree.getParameterFor(Sequence, int)`.
addGradientFor(double[], double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.CompositeLogPrior
addGradientFor(double[], double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.DoesNothingLogPrior
addGradientFor(double[], double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.LogPrior
  Adds the gradient of the log-prior using the current parameters to a given vector.
addGradientFor(double[], double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.SeparateGaussianLogPrior
addGradientFor(double[], double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.SeparateLaplaceLogPrior
addGradientFor(double[], double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.SimpleGaussianSumLogPrior
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.CMMScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.homogeneous.HMM0ScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.homogeneous.HMMScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.homogeneous.UniformHomogeneousScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.IndependentProductScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.MixtureDuration
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.SkewNormalLikeScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.UniformDurationScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.MRFScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in interface de.jstacs.scoringFunctions.NormalizableScoringFunction
  This method computes the gradient of `NormalizableScoringFunction.getLogPriorTerm()` for each parameter of this model.
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.NormalizedScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.UniformScoringFunction
addParameterToSet() - Method in class de.jstacs.parameters.ExpandableParameterSet
  Adds a new `ParameterSetContainer` containing a clone of the `ParameterSet`-template to the set of `Parameter`s.
addResults(MeanResultSet, MeanResultSet) - Static method in class de.jstacs.results.MeanResultSet
  Adds two `MeanResultSet`s together.
addResults(NumericalResultSet...) - Method in class de.jstacs.results.MeanResultSet
  Adds `NumericalResultSet`s to this `MeanResultSet`.
addTags(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Frames the `StringBuffer` `source` with equal tags "< `tag`>" and "<`/tag` >".
addTagsAndAttributes(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Frames the `StringBuffer` `source` with "< `tag attributes`>" and "<`/tag` >".
addTermToClassParameter(int, double) - Method in class de.jstacs.classifier.scoringFunctionBased.SFBasedOptimizableFunction
  This method adds the `term` to the class parameter of the class with index `classIndex`.
addToAnnotation(String) - Method in class de.jstacs.data.sequences.annotation.NullSequenceAnnotationParser
addToAnnotation(String) - Method in interface de.jstacs.data.sequences.annotation.SequenceAnnotationParser
  This method adds the `unparsed` `String` in some way to the `SequenceAnnotation`.
addToAnnotation(String) - Method in class de.jstacs.data.sequences.annotation.SimpleSequenceAnnotationParser
addToAnnotation(String) - Method in class de.jstacs.data.sequences.annotation.SplitSequenceAnnotationParser
adjust(int[], double[]) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.DurationScoringFunction
  This method adjust the parameter based on the given statistic.
adjust(int[], double[]) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.MixtureDuration
adjust(int[], double[]) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.SkewNormalLikeScoringFunction
adjust(int[], double[]) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.UniformDurationScoringFunction
adjustHiddenParameters(int, Sample[], double[][]) - Method in interface de.jstacs.motifDiscovery.MutableMotifDiscoverer
  Adjusts all hidden parameters including duration and mixture parameters according to the current values of the remaining parameters.
adjustHiddenParameters(int, Sample[], double[][]) - Method in class de.jstacs.scoringFunctions.IndependentProductScoringFunction
adjustHiddenParameters(int, Sample[], double[][]) - Method in class de.jstacs.scoringFunctions.mix.MixtureScoringFunction
  Adjusts all hidden parameters including duration and mixture parameters according to the current values of the remaining parameters.
adjustHiddenParameters(int, Sample[], double[][]) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.HiddenMotifsMixture
algorithm - Variable in class de.jstacs.models.mixture.AbstractMixtureModel
  The type of algorithm.
algorithmHasBeenRun - Variable in class de.jstacs.models.mixture.AbstractMixtureModel
  A switch which indicates that the algorithm for determining the parameters has been run.
algorithmHasBeenRun() - Method in class de.jstacs.models.mixture.AbstractMixtureModel
  This method indicates whether the parameters of the model has been determined by the internal algorithm.
Alignment - Class in de.jstacs.algorithms
  Class for gapped global alignments using the extended Needleman-Wunsch algorithm.
Alignment(Sequence, Sequence, Alignment.Costs) - Constructor for class de.jstacs.algorithms.Alignment
  Creates a new `Alignment.StringAlignment` instance that aligns the sequences `s1` and `s2` using the costs defined in `costs`.
Alignment.Costs - Interface in de.jstacs.algorithms
  The general interface for the costs of an alignment.
Alignment.Costs.Direction - Enum in de.jstacs.algorithms
  The direction of the predecessor in the DP (dynamic programming)-matrix.
Alignment.SimpleCosts - Class in de.jstacs.algorithms
  Class for simple costs with costs `mismatch` for a mismatch, costs `start` to start a new gap, costs `elong` to elongate a gap by one position and costs of `0` for a match.
Alignment.SimpleCosts(double, double, double) - Constructor for class de.jstacs.algorithms.Alignment.SimpleCosts
  Creates a new instance of simple costs with costs `mismatch` for a mismatch, costs `start` to start a new gap, costs `elong` to elongate a gap by one position and costs of `0` for a match.
Alignment.StringAlignment - Class in de.jstacs.algorithms
  Class for the representation of an alignment of two `String`s.
Alignment.StringAlignment(String, String, double) - Constructor for class de.jstacs.algorithms.Alignment.StringAlignment
  Creates the instance for the two (extended) `String`s and the edit-costs.
Alphabet - Class in de.jstacs.data
  Class for a set of symbols, i.e. an `Alphabet`.
Alphabet() - Constructor for class de.jstacs.data.Alphabet
alphabet - Variable in class de.jstacs.parameters.SequenceScoringParameterSet
  The alphabet the model works on
Alphabet.AlphabetParameterSet - Class in de.jstacs.data
  The super class for the `InstanceParameterSet` of any `Alphabet`.
Alphabet.AlphabetParameterSet(Class<? extends Alphabet>) - Constructor for class de.jstacs.data.Alphabet.AlphabetParameterSet
  Creates a new `Alphabet.AlphabetParameterSet` from the class that can be instantiated using this `Alphabet.AlphabetParameterSet`.
Alphabet.AlphabetParameterSet(StringBuffer) - Constructor for class de.jstacs.data.Alphabet.AlphabetParameterSet
  The standard constructor for the interface `Storable` .
alphabetCon - Variable in class de.jstacs.data.Sequence
  The underlying alphabets.
AlphabetContainer - Class in de.jstacs.data
  The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
AlphabetContainer(Alphabet) - Constructor for class de.jstacs.data.AlphabetContainer
  Creates a new simple `AlphabetContainer`.
AlphabetContainer(Alphabet[]) - Constructor for class de.jstacs.data.AlphabetContainer
  Creates a new `AlphabetContainer` with different `Alphabet`s for each position.
AlphabetContainer(AlphabetContainer[], int[]) - Constructor for class de.jstacs.data.AlphabetContainer
  Creates an new sparse `AlphabetContainer` based on given `AlphabetContainer`s.
AlphabetContainer(Alphabet[], int[]) - Constructor for class de.jstacs.data.AlphabetContainer
  Creates a new `AlphabetContainer` that uses different `Alphabet`s.
AlphabetContainer(AlphabetContainerParameterSet) - Constructor for class de.jstacs.data.AlphabetContainer
  Creates a new `AlphabetContainer` from an `AlphabetContainerParameterSet` that contains all necessary parameters.
AlphabetContainer(StringBuffer) - Constructor for class de.jstacs.data.AlphabetContainer
  The standard constructor for the interface `Storable`.
AlphabetContainer.AlphabetContainerType - Enum in de.jstacs.data
  This `enum` defines types of `AlphabetContainer`s.
AlphabetContainerParameterSet - Class in de.jstacs.data
  Class for the `AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet` of an `AlphabetContainer`.
AlphabetContainerParameterSet(AlphabetContainer.AlphabetContainerType, boolean) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet
  Creates a new `AlphabetContainerParameterSet` of an `AlphabetContainer` with `AlphabetContainer.AlphabetContainerType` `type`.
AlphabetContainerParameterSet(StringBuffer) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet
  The standard constructor for the interface `Storable`.
AlphabetContainerParameterSet(Alphabet) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet
  Creates a new `AlphabetContainerParameterSet` of a simple `AlphabetContainer` from a single `Alphabet`.
AlphabetContainerParameterSet(Alphabet[]) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet
  Creates a new `AlphabetContainerParameterSet` from an array of `Alphabet`s.
AlphabetContainerParameterSet(Alphabet[], int[]) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet
  Creates a new `AlphabetContainerParameterSet` from an array of `Alphabet`s and an array of `int`s defining the `Alphabet` index `i` in `alphabets` that is used for position `i`.
AlphabetContainerParameterSet.AlphabetArrayParameterSet - Class in de.jstacs.data
  Class for the parameters of an array of `Alphabet`s of defined length.
AlphabetContainerParameterSet.AlphabetArrayParameterSet(AlphabetContainer.AlphabetContainerType) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet.AlphabetArrayParameterSet
  Creates a new `AlphabetContainerParameterSet.AlphabetArrayParameterSet` from the information about the `type` of the `Alphabet`s, e.g. if the array shall contain only the parameters for discrete `Alphabet` s.
AlphabetContainerParameterSet.AlphabetArrayParameterSet(StringBuffer) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet.AlphabetArrayParameterSet
  The standard constructor for the interface `Storable` .
AlphabetContainerParameterSet.AlphabetArrayParameterSet(Alphabet[], AlphabetContainer.AlphabetContainerType) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet.AlphabetArrayParameterSet
  Creates a new `AlphabetContainerParameterSet.AlphabetArrayParameterSet` from an array of `Alphabet`s and the information about the `type` of the `Alphabet`s.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet - Class in de.jstacs.data
  Class for the parameter set of an array of `Alphabet`s where each `Alphabet` may be used for one or more sections of positions.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(AlphabetContainer.AlphabetContainerType) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
  Creates a new `AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet` for a set of discrete or continuous `Alphabet`s.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(Alphabet[], int[]) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
  Creates a new `AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet` from an array of `Alphabet`s and an array of indexes that define the index of the `Alphabet` in `alphabets` belonging to that position in `indexes`.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(StringBuffer) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
  The standard constructor for the interface `Storable` .
alphabets - Variable in class de.jstacs.models.AbstractModel
  The underlying alphabets
alphabets - Variable in class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
  The `AlphabetContainer` of this `NormalizableScoringFunction` .
alternativeModel - Variable in class de.jstacs.models.mixture.AbstractMixtureModel
  The alternative models for the EM.
annotate(boolean, SequenceAnnotation...) - Method in class de.jstacs.data.Sequence
  This method allows to append annotation to a `Sequence.CompositeSequence`.
annotateMotif(Sample, int) - Method in class de.jstacs.motifDiscovery.SignificantMotifOccurrencesFinder
  This method annotates a `Sample`.
annotateMotif(int, Sample, int) - Method in class de.jstacs.motifDiscovery.SignificantMotifOccurrencesFinder
  This method annotates a `Sample` starting in each sequence at `startPos`.
annotateMotif(Sample, int, int) - Method in class de.jstacs.motifDiscovery.SignificantMotifOccurrencesFinder
  This method annotates a `Sample`.
annotateMotif(int, Sample, int, int, boolean) - Method in class de.jstacs.motifDiscovery.SignificantMotifOccurrencesFinder
  This method annotates a `Sample` starting in each sequence at `startPos`.
annotation - Variable in class de.jstacs.data.Sequence
  The annotation of the `Sequence.CompositeSequence`.
annotation - Variable in class de.jstacs.io.AbstractStringExtractor
  The annotation of the source.
annotationParser - Variable in class de.jstacs.io.SparseStringExtractor
  A parser for the sequence annotation.
appendAdditionalInfo(StringBuffer) - Method in class de.jstacs.models.discrete.Constraint
  This method appends additional information that is not stored in the base class to the `StringBuffer`.
appendAdditionalInfo(StringBuffer) - Method in class de.jstacs.models.discrete.homogeneous.HomogeneousModel.HomCondProb
appendAdditionalInfo(StringBuffer) - Method in class de.jstacs.models.discrete.inhomogeneous.InhCondProb
appendAdditionalInfo(StringBuffer) - Method in class de.jstacs.models.discrete.inhomogeneous.InhConstraint
appendAdditionalInfo(StringBuffer) - Method in class de.jstacs.models.discrete.inhomogeneous.MEMConstraint
appendBoolean2ArrayWithTags(StringBuffer, boolean[][], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional `boolean` array with equal tags to the `StringBuffer` `source`.
appendBoolean2ArrayWithTagsAndAttributes(StringBuffer, boolean[][], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional `boolean` array with the tags to the `StringBuffer` `source`.
appendBooleanArrayWithTags(StringBuffer, boolean[], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded `boolean` array with equal tags to the `StringBuffer` `source`.
appendBooleanArrayWithTagsAndAttributes(StringBuffer, boolean[], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded `boolean` array with the tags to the `StringBuffer` `source`.
appendBooleanWithTags(StringBuffer, boolean, String) - Static method in class de.jstacs.io.XMLParser
  Appends a `boolean` value with equal tags to the `StringBuffer` `source` in the following way: "< `tag`>`b`<`/tag`>".
appendBooleanWithTagsAndAttributes(StringBuffer, boolean, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends a `boolean` value with the tags to the `StringBuffer` `source` in the following way: "< `tag attributes`>`b`<`/tag` >".
appendByte2ArrayWithTags(StringBuffer, byte[][], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional `byte` array with equal tags to the `StringBuffer` `source`.
appendByte2ArrayWithTagsAndAttributes(StringBuffer, byte[][], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional `byte` array with the tags to the `StringBuffer` `source`.
appendByteArrayWithTags(StringBuffer, byte[], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded `byte` array with equal tags to the `StringBuffer` `source`.
appendByteArrayWithTagsAndAttributes(StringBuffer, byte[], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded `byte` array with the tags to the `StringBuffer` `source`.
appendByteWithTags(StringBuffer, byte, String) - Static method in class de.jstacs.io.XMLParser
  Appends a `byte` value with equal tags to the `StringBuffer` `source` in the following way: "< `tag`>`b`<`/tag`>".
appendByteWithTagsAndAttributes(StringBuffer, byte, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends a `byte` value with the tags to the `StringBuffer` `source` in the following way: "< `tag attributes`>`b`<`/tag` >".
appendCollection(StringBuffer) - Method in class de.jstacs.parameters.CollectionParameter
  Appends the internal `ParameterSet` in its XML representation ( `ParameterSet.toXML()`) to the `StringBuffer` `buf`.
appendCollection(StringBuffer) - Method in class de.jstacs.parameters.EnumParameter
appendDouble2ArrayWithTags(StringBuffer, double[][], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional `double` array with equal tags to the `StringBuffer` `source`.
appendDouble2ArrayWithTagsAndAttributes(StringBuffer, double[][], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional `double` array with the tags to the `StringBuffer` `source`.
appendDoubleArrayWithTags(StringBuffer, double[], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded `double` array with equal tags to the `StringBuffer` `source`.
appendDoubleArrayWithTagsAndAttributes(StringBuffer, double[], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded `double` array with the tags to the `StringBuffer` `source`.
appendDoubleWithTags(StringBuffer, double, String) - Static method in class de.jstacs.io.XMLParser
  Appends a `double` value with equal tags to the `StringBuffer` `source` in the following way: "< `tag`>`d`<`/tag`>".
appendDoubleWithTagsAndAttributes(StringBuffer, double, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends a `double` value with the tags to the `StringBuffer` `source` in the following way: "< `tag attributes`>`d`<`/tag` >".
appendEnumWithTags(StringBuffer, Enum<T>, String) - Static method in class de.jstacs.io.XMLParser
  Appends an `Enum` object with equal tags to the `StringBuffer` `source`.
appendEnumWithTagsAndAttributes(StringBuffer, Enum<T>, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an `Enum` object with the tags to the `StringBuffer` `source`.
appendInt2ArrayWithTags(StringBuffer, int[][], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional `int` array with equal tags to the `StringBuffer` `source`.
appendInt2ArrayWithTagsAndAttributes(StringBuffer, int[][], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional `int` array with the tags to the `StringBuffer` `source`.
appendIntArrayWithTags(StringBuffer, int[], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded `int` array with equal tags to the `StringBuffer` `source`.
appendIntArrayWithTagsAndAttributes(StringBuffer, int[], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded `int` array with the tags to the `StringBuffer` `source`.
appendIntWithTags(StringBuffer, int, String) - Static method in class de.jstacs.io.XMLParser
  Appends an `int` value with equal tags to the `StringBuffer` `source` in the following way: "< `tag`>`i`<`/tag`>"
appendIntWithTagsAndAttributes(StringBuffer, int, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an `int` value with the tags to the `StringBuffer` `source` in the following way: "< `tag attributes`>`i`<`/tag` >".
appendLongWithTags(StringBuffer, long, String) - Static method in class de.jstacs.io.XMLParser
  Appends a `long` value with equal tags to the `StringBuffer` `source` in the following way: "< `tag`>`i`<`/tag`>".
appendLongWithTagsAndAttributes(StringBuffer, long, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends a `long` value with the tags to the `StringBuffer` `source` in the following way: "< `tag attributes`>`i`<`/tag` >".
appendMainInfo(StringBuffer) - Method in class de.jstacs.results.Result
  This method can be used in the method `Storable.toXML()` to append the main information (name, comment, datatype).
appendStorable2ArrayWithTags(StringBuffer, Storable[][], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional `Storable` array with equal tags to the `StringBuffer` `source`.
appendStorable2ArrayWithTagsAndAttributes(StringBuffer, Storable[][], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional `Storable` array with the tags to the `StringBuffer` `source`.
appendStorable3ArrayWithTags(StringBuffer, Storable[][][], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded three dimensional `Storable` array with equal tags to the `StringBuffer` `source`.
appendStorable3ArrayWithTagsAndAttributes(StringBuffer, Storable[][][], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded three dimensional `Storable` array with the tags to the `StringBuffer` `source`.
appendStorableArrayWithTags(StringBuffer, Storable[], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded `Storable` array with equal tags to the `StringBuffer` `source`.
appendStorableArrayWithTagsAndAttributes(StringBuffer, Storable[], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded `Storable` array with the tags to the `StringBuffer` `source`.
appendStorableWithTags(StringBuffer, Storable, String) - Static method in class de.jstacs.io.XMLParser
  Appends a `Storable` object or "null" with equal tags to the `StringBuffer` `source`.
appendStorableWithTagsAndAttributes(StringBuffer, Storable, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends a `Storable` object or "null" with the tags to the `StringBuffer` `source`.
appendString2ArrayWithTags(StringBuffer, String[][], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional `String` array with equal tags to the `StringBuffer` `source`.
appendString2ArrayWithTagsAndAttributes(StringBuffer, String[][], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional `String` array with the tags to the `StringBuffer` `source`.
appendStringArrayWithTags(StringBuffer, String[], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded `String` array with equal tags to the `StringBuffer` `source`.
appendStringArrayWithTagsAndAttributes(StringBuffer, String[], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded `String` array with the tags to the `StringBuffer` `source`.
appendStringWithTags(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends a `String` with equal tags to the `StringBuffer` `source` in the following way: "<`tag`> `s`<`/tag` >".
appendStringWithTagsAndAttributes(StringBuffer, String, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends a `String` with the tags to the `StringBuffer` `source` in the following way: "< `tag attributes`>`s`<`/tag` >".
ArbitrarySequence - Class in de.jstacs.data.sequences
  This class is for any continuous or hybrid sequence.
ArbitrarySequence(AlphabetContainer, double[]) - Constructor for class de.jstacs.data.sequences.ArbitrarySequence
  Creates a new `ArbitrarySequence` from an array of `double`-encoded alphabet symbols.
ArbitrarySequence(AlphabetContainer, String) - Constructor for class de.jstacs.data.sequences.ArbitrarySequence
  Creates a new `ArbitrarySequence` from a `String` representation using the default delimiter.
ArbitrarySequence(AlphabetContainer, SequenceAnnotation[], String, String) - Constructor for class de.jstacs.data.sequences.ArbitrarySequence
  Creates a new `ArbitrarySequence` from a `String` representation using the delimiter `delim`.
ArbitrarySequence(AlphabetContainer, SequenceAnnotation[], SymbolExtractor) - Constructor for class de.jstacs.data.sequences.ArbitrarySequence
  Creates a new `ArbitrarySequence` from a `SymbolExtractor`.
ArrayHandler - Class in de.jstacs.io
  This class handles arrays with elements of generic type and enables the user to cast and clone arrays easily.
ArrayHandler() - Constructor for class de.jstacs.io.ArrayHandler
ArrayParameterSet - Class in de.jstacs.parameters
  Class for a `ParameterSet` that consists of a length-`Parameter` that defines the length of the array and an array of `ParameterSetContainer`s of this length.
ArrayParameterSet(ParameterSet, String, String, String, String, NumberValidator<Integer>) - Constructor for class de.jstacs.parameters.ArrayParameterSet
  Creates a new `ArrayParameterSet` from a `Class` that can be instantiated using this `ArrayParameterSet` and templates for the `ParameterSet` in each element of the array, the name and the comment that are displayed for the `ParameterSetContainer`s enclosing the `ParameterSet`s.
ArrayParameterSet(ParameterSet, String, String) - Constructor for class de.jstacs.parameters.ArrayParameterSet
  Creates a new `ArrayParameterSet` from a `Class` that can be instantiated using this `ArrayParameterSet` and templates for the `ParameterSet` in each element of the array, the name and the comment that are displayed for the `ParameterSetContainer`s enclosing the `ParameterSet`s.
ArrayParameterSet(StringBuffer) - Constructor for class de.jstacs.parameters.ArrayParameterSet
  The standard constructor for the interface `Storable`.
assess(MeasureParameters, ClassifierAssessmentAssessParameterSet, Sample...) - Method in class de.jstacs.classifier.assessment.ClassifierAssessment
  Assesses the contained classifiers.
assess(MeasureParameters, ClassifierAssessmentAssessParameterSet, ProgressUpdater, Sample...) - Method in class de.jstacs.classifier.assessment.ClassifierAssessment
  Assesses the contained classifiers.
assess(MeasureParameters, ClassifierAssessmentAssessParameterSet, ProgressUpdater, Sample[][]...) - Method in class de.jstacs.classifier.assessment.ClassifierAssessment
  Assesses the contained classifiers.
assess(Sample, Sample, int) - Static method in class de.jstacs.motifDiscovery.MotifDiscoveryAssessment
  This method computes the nucleotide and site measures.
assessWithPredefinedSplits(MeasureParameters, ClassifierAssessmentAssessParameterSet, ProgressUpdater, Sample[]...) - Method in class de.jstacs.classifier.assessment.KFoldCrossValidation
  This method implements a k-fold crossvalidation on previously split data.
AsymmetricTensor - Class in de.jstacs.algorithms.graphs.tensor
  This class can be used for `Tensor`s which are not symmetric, as opposed to the symmetry defined in `SymmetricTensor`.
AsymmetricTensor(int, byte) - Constructor for class de.jstacs.algorithms.graphs.tensor.AsymmetricTensor
  This constructor creates an empty asymmetric tensor with given dimension.
AsymmetricTensor(double[][][], int, byte) - Constructor for class de.jstacs.algorithms.graphs.tensor.AsymmetricTensor
  This constructor creates and checks a filled asymmetric tensor with given dimension.

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