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## Uses of Class
de.jstacs.data.AlphabetContainer

Packages that use AlphabetContainer
de.jstacs.classifier | This package provides the framework for any classifier.
de.jstacs.classifier.modelBased | Provides the classes for `Classifier`s that are based on `Model`s
de.jstacs.classifier.scoringFunctionBased | Provides the classes for `Classifier`s that are based on `ScoringFunction`s.
de.jstacs.classifier.scoringFunctionBased.cll | Provides the implementation of the log conditional likelihood as an `OptimizableFunction` and a classifier that uses log conditional likelihood or supervised posterior to learn the parameters of a set of `ScoringFunctions`
de.jstacs.data | Provides classes for the representation of data.
de.jstacs.data.sequences | Provides classes for representing sequences.
de.jstacs.io | Provides classes for reading data from and writing to a file and storing a number of datatypes, including all primitives, arrays of primitives, and `Storable`s to an XML-representation
de.jstacs.models | Provides the interface `Model` and its abstract implementation `AbstractModel`, which is the super class of all other models.
de.jstacs.models.discrete |
de.jstacs.models.discrete.homogeneous.parameters |
de.jstacs.models.discrete.inhomogeneous | This package contains various inhomogeneous models.
de.jstacs.models.discrete.inhomogeneous.parameters |
de.jstacs.models.mixture | This package is the super package for any mixture model.
de.jstacs.models.mixture.gibbssampling | This package contains many classes that can be used while a Gibbs sampling.
de.jstacs.models.utils |
de.jstacs.parameters | This package provides classes for parameters that establish a general convention for the description of parameters as defined in the `Parameter`-interface.
de.jstacs.scoringFunctions | Provides `ScoringFunction`s that can be used in a `ScoreClassifier`.
de.jstacs.scoringFunctions.directedGraphicalModels | Provides `ScoringFunction`s that are equivalent to directed graphical models.
de.jstacs.scoringFunctions.homogeneous | Provides `ScoringFunction`s that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence

Uses of AlphabetContainer in de.jstacs.classifier

Methods in de.jstacs.classifier that return AlphabetContainer
`AlphabetContainer` | `AbstractClassifier.getAlphabetContainer()` This method returns the container of alphabets that is used in the classifier.

Methods in de.jstacs.classifier with parameters of type AlphabetContainer
`boolean` | `AbstractClassifier.setNewAlphabetContainerInstance(AlphabetContainer abc)` This method tries to set a new instance of an `AlphabetContainer` for the current model.

Constructors in de.jstacs.classifier with parameters of type AlphabetContainer
`AbstractClassifier(AlphabetContainer abc)` The constructor for a homogeneous classifier.
`AbstractClassifier(AlphabetContainer abc, int length)` The constructor for an inhomogeneous classifier.
`AbstractScoreBasedClassifier(AlphabetContainer abc, int classes)` The constructor for a homogeneous classifier.
`AbstractScoreBasedClassifier(AlphabetContainer abc, int classes, double classWeight)` The constructor for a homogeneous classifier.
`AbstractScoreBasedClassifier(AlphabetContainer abc, int length, int classes)` The constructor for an inhomogeneous classifier.
`AbstractScoreBasedClassifier(AlphabetContainer abc, int length, int classes, double classWeight)` The constructor for an inhomogeneous classifier.

Uses of AlphabetContainer in de.jstacs.classifier.modelBased

Methods in de.jstacs.classifier.modelBased with parameters of type AlphabetContainer
`boolean` | `ModelBasedClassifier.setNewAlphabetContainerInstance(AlphabetContainer abc)`

Uses of AlphabetContainer in de.jstacs.classifier.scoringFunctionBased

Constructors in de.jstacs.classifier.scoringFunctionBased with parameters of type AlphabetContainer
`ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass, AlphabetContainer alphabet, int length, byte algo, double eps, double lineps, double startD, boolean free, OptimizableFunction.KindOfParameter kind)` The constructor for a simple, instantiated parameter set.

Uses of AlphabetContainer in de.jstacs.classifier.scoringFunctionBased.cll

Constructors in de.jstacs.classifier.scoringFunctionBased.cll with parameters of type AlphabetContainer
`CLLClassifierParameterSet(AlphabetContainer alphabet, int length, byte algo, double eps, double lineps, double startD, boolean free, OptimizableFunction.KindOfParameter kind, boolean norm)` The default constructor.
`CLLClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass, AlphabetContainer alphabet, int length, byte algo, double eps, double lineps, double startD, boolean free, OptimizableFunction.KindOfParameter kind, boolean norm)` The default constructor.

Uses of AlphabetContainer in de.jstacs.data

Fields in de.jstacs.data declared as AlphabetContainer
`protected AlphabetContainer` | `Sequence.alphabetCon` the underlying alphabets

Methods in de.jstacs.data that return AlphabetContainer
`AlphabetContainer` | `Sequence.getAlphabetContainer()` Return the alphabets used in this sequence.
`AlphabetContainer` | `Sample.getAlphabetContainer()` Returns the `AlphabetContainer` of this `Sample`.
`AlphabetContainer` | `AlphabetContainer.getCompositeContainer(int[] start, int[] length)` This method returns a container of alphabets e.g. for composite motifs/sequences.
`static AlphabetContainer` | `AlphabetContainer.getSimplifiedAlphabetContainer(Alphabet[] abc, int[] assignment)` This method creates a new `AlphabetContainer` that uses as less as possible alphabets to describe the container.
`AlphabetContainer` | `AlphabetContainer.getSubContainer(int start, int length)` This method returns a subcontainer for the positions starting at `start` and with length `length`.
`static AlphabetContainer` | `AlphabetContainer.insertAlphabet(AlphabetContainer aC, Alphabet a, boolean[] useNewAlphabet)` This method may be used to construct a new `AlphabetContainer` by incorporating additional alphabets into an existing `AlphabetContainer`.

Methods in de.jstacs.data with parameters of type AlphabetContainer
`boolean` | `AlphabetContainer.checkConsistency(AlphabetContainer abc)` Checks whether two alphabets are consistent.
`int` | `AlphabetContainer.compareTo(AlphabetContainer abc)`
`static Sequence` | `Sequence.create(AlphabetContainer con, SequenceAnnotation[] annotation, String sequence, String delim)` Creates a sequence from a string based on the given AlphabetContainer using the given delimiter.
`static Sequence` | `Sequence.create(AlphabetContainer con, String sequence)` Creates a sequence from a string based on the given AlphabetContainer using the standard delimiter for this AlphabetContainer.
`static Sequence` | `Sequence.create(AlphabetContainer con, String sequence, String delim)` Creates a sequence from a string based on the given AlphabetContainer using the given delimiter.
`Sequence` | `Sequence.getCompositeSequence(AlphabetContainer abc, int[] starts, int[] lengths)` This constructor should be used if one wants to create a sample of composite sequences.
`Sequence` | `Sequence.getSubSequence(AlphabetContainer abc, int start)` This method should be used if one wants to create a sample of subsequences of defined length.
`Sequence` | `Sequence.getSubSequence(AlphabetContainer abc, int start, int length)` This method should be used if one wants to create a sample of subsequences of defined length.
`static AlphabetContainer` | `AlphabetContainer.insertAlphabet(AlphabetContainer aC, Alphabet a, boolean[] useNewAlphabet)` This method may be used to construct a new `AlphabetContainer` by incorporating additional alphabets into an existing `AlphabetContainer`.

Constructors in de.jstacs.data with parameters of type AlphabetContainer
`AlphabetContainer(AlphabetContainer[] cons, int[] lengths)` This constructor creates an new sparse `AlphabetContainer` based on given `AlphabetContainer`s.
`DiscreteSequenceEnumerator(AlphabetContainer con, int length, boolean sparse)` The constructor.
`Sample(AlphabetContainer abc, AbstractStringExtractor se)` Creates a `Sample` from a `StringExtractor` using the given `AlphabetContainer`.
`Sample(AlphabetContainer abc, AbstractStringExtractor se, int subsequenceLength)` Creates a `Sample` from a `StringExtractor` using the given `AlphabetContainer` and all overlapping windows of `subsequenceLength`.
`Sample(AlphabetContainer abc, AbstractStringExtractor se, String delim)` Creates a `Sample` from a `StringExtractor` using the given `AlphabetContainer` and delimiter.
`Sample(AlphabetContainer abc, AbstractStringExtractor se, String delim, int subsequenceLength)` Creates a `Sample` from a `StringExtractor` using the given `AlphabetContainer`, the given delimiter and all overlapping windows of `subsequenceLength`.
`Sequence.CompositeSequence(AlphabetContainer abc, Sequence seq, int[] starts, int[] lengths)` This constructor should be used if one wants to create a sample of composite sequences.
`Sequence.SubSequence(AlphabetContainer abc, Sequence seq, int start, int length)` This constructor should be used if one wants to create a sample of subsequences of defined length.
`Sequence(AlphabetContainer container, SequenceAnnotation[] annotation)` This constructor creates an instance with the AlphabetContainer and the annotation, but without the content.

Uses of AlphabetContainer in de.jstacs.data.sequences

Constructors in de.jstacs.data.sequences with parameters of type AlphabetContainer
`ArbitrarySequence(AlphabetContainer alphabetContainer, double[] content)` This constructor is designed for the method `AbstractModel.emitSample(int, int...)`.
`ArbitrarySequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)` Creates a new sequence from a string representation using the delimiter `delim`.
`ArbitrarySequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)` Creates a new sequence from a `SymbolExtractor`.
`ArbitrarySequence(AlphabetContainer alphabetContainer, String sequence)` Creates a new sequence from a string representation using the default delimiter.
`ByteSequence(AlphabetContainer alphabetContainer, byte[] content)` This constructor is designed for the method `AbstractModel.emitSample(int, int...)`.
`ByteSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)` Creates a new sequence from a string representation using the delimiter `delim`.
`ByteSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)` Creates a new sequence from a `SymbolExtractor`.
`ByteSequence(AlphabetContainer alphabetContainer, String sequence)` Creates a new sequence from a string representation using the default delimiter.
`DiscreteSequence(AlphabetContainer container, SequenceAnnotation[] annotation)` This constructor creates an instance with the `AlphabetContainer` and the annotation, but without the content.
`IntSequence(AlphabetContainer alphabetContainer, int[] content)` This constructor is designed for `Model.emitSample(int, int...)`.
`IntSequence(AlphabetContainer alphabetContainer, int[] content, int start, int length)` This constructor creates an instance from a part of the content.
`IntSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)` Creates a new sequence from a string representation using the delimiter `delim`.
`IntSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)` Creates a new sequence from a `SymbolExtractor`.
`IntSequence(AlphabetContainer alphabetContainer, String sequence)` Creates a new sequence from a string representation using the default delimiter.
`RecursiveSequence(AlphabetContainer alphabet, Sequence seq)` This constructor creates a recursive sequence using the annotation of the given sequence.
`RecursiveSequence(AlphabetContainer alphabet, SequenceAnnotation[] annotation, Sequence seq)` This constructor creates a recursive sequence.
`ShortSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)` Creates a new sequence from a string representation using the delimiter `delim`.
`ShortSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)` Creates a new sequence from a `SymbolExtractor`.
`ShortSequence(AlphabetContainer alphabetContainer, short[] content)` This constructor is designed for the method `AbstractModel.emitSample(int, int...)`.
`ShortSequence(AlphabetContainer alphabetContainer, String sequence)` Creates a new sequence from a string representation using the default delimiter.
`SparseSequence(AlphabetContainer alphCon, String seq)` This constructor creates an instance from a `String`.
`SparseSequence(AlphabetContainer alphCon, SymbolExtractor se)` This constructor creates an instance from a `SymbolExtractor`.

Uses of AlphabetContainer in de.jstacs.io

Methods in de.jstacs.io with parameters of type AlphabetContainer
`static int` | `SymbolExtractor.filter(String inFile, char ignore, AlphabetContainer con, int minLength, String outFile)` This method allows the user to filter a file using a given alphabet container and a minimal sequence length.

Uses of AlphabetContainer in de.jstacs.models

Fields in de.jstacs.models declared as AlphabetContainer
`protected AlphabetContainer` | `AbstractModel.alphabets` The underlying alphabets

Methods in de.jstacs.models that return AlphabetContainer
`AlphabetContainer` | `Model.getAlphabetContainer()` Returns the container of alphabets that were used when constructing the model.
`AlphabetContainer` | `AbstractModel.getAlphabetContainer()`

Methods in de.jstacs.models with parameters of type AlphabetContainer
`protected void` | `CompositeModel.set(AlphabetContainer abc)`
`protected void` | `AbstractModel.set(AlphabetContainer abc)` This method should only be invoked by the method `setNewAlphabetContainerInstance( AlphabetContainer )` and not be made public.
`boolean` | `Model.setNewAlphabetContainerInstance(AlphabetContainer abc)` This method tries to set a new instance of an AlphabetContainer for the current model.
`boolean` | `AbstractModel.setNewAlphabetContainerInstance(AlphabetContainer abc)`

Constructors in de.jstacs.models with parameters of type AlphabetContainer
`AbstractModel(AlphabetContainer alphabets, int length)` Constructor that sets the length of the model to `length` and the AlphabetContainer to `alphabets`.
`CompositeModel(AlphabetContainer alphabets, int[] assignment, Model... models)`
`UniformModel(AlphabetContainer alphabet)`

Uses of AlphabetContainer in de.jstacs.models.discrete

Methods in de.jstacs.models.discrete with parameters of type AlphabetContainer
`static double` | `ConstraintManager.countInhomogeneous(AlphabetContainer alphabets, int length, Sample data, double[] weights, boolean reset, Constraint... constr)` Fills the (inhomogeneous) `constr` with the weighted absolute frequency of the sample `data` and computes the frequencies will not be computed.

Constructors in de.jstacs.models.discrete with parameters of type AlphabetContainer
`DGMParameterSet(Class<? extends DiscreteGraphicalModel> instanceClass, AlphabetContainer alphabet, double ess, String description)` The constructor for models, that can handle variable lengths.
`DGMParameterSet(Class<? extends DiscreteGraphicalModel> instanceClass, AlphabetContainer alphabet, int length, double ess, String description)` The constructor for models that can handle only sequences of fixed length.

Uses of AlphabetContainer in de.jstacs.models.discrete.homogeneous.parameters

Constructors in de.jstacs.models.discrete.homogeneous.parameters with parameters of type AlphabetContainer
`HomMMParameterSet(AlphabetContainer alphabet, double ess, String description, byte order)` The constructor that sets already the ALphabetContainer, ESS, description and order.
`HomogeneousModelParameterSet(Class<? extends HomogeneousModel> instanceClass, AlphabetContainer alphabet, double ess, String description, byte order)` The constructor for models, that can handle variable lengths.

Uses of AlphabetContainer in de.jstacs.models.discrete.inhomogeneous

Methods in de.jstacs.models.discrete.inhomogeneous that return AlphabetContainer
`AlphabetContainer` | `StructureLearner.getAlphabetContainer()` This method returns the AlphabetContainer of the StructureLearner.

Constructors in de.jstacs.models.discrete.inhomogeneous with parameters of type AlphabetContainer
`StructureLearner(AlphabetContainer con, int length)` Creates a StructureLearner with ess = 0.
`StructureLearner(AlphabetContainer con, int length, double ess)` Creates a StructureLearner

Uses of AlphabetContainer in de.jstacs.models.discrete.inhomogeneous.parameters

Constructors in de.jstacs.models.discrete.inhomogeneous.parameters with parameters of type AlphabetContainer
`BayesianNetworkModelParameterSet(AlphabetContainer alphabet, int length, double ess, String description, StructureLearner.ModelType model, byte order, StructureLearner.LearningType method)` This is the constructor of a filled parameter set for a BayesianNetworkModel.
`FSDAGMParameterSet(AlphabetContainer alphabet, int length, double ess, String description, String graph)` This is the constructor that creates a filled parameter set.
`FSDAGMParameterSet(Class<? extends FSDAGModel> clazz, AlphabetContainer alphabet, int length, double ess, String description, String graph)` This is the constructor that creates a filled parameter set.
`IDGMParameterSet(Class<? extends InhomogeneousDGM> instanceClass, AlphabetContainer alphabet, int length, double ess, String description)` This constructor creates a parameter set instance for the specified class.

Uses of AlphabetContainer in de.jstacs.models.mixture

Methods in de.jstacs.models.mixture with parameters of type AlphabetContainer
`protected void` | `AbstractMixtureModel.set(AlphabetContainer abc)`

Uses of AlphabetContainer in de.jstacs.models.mixture.gibbssampling

Constructors in de.jstacs.models.mixture.gibbssampling with parameters of type AlphabetContainer
`FSDAGModelForGibbsSamplingParameterSet(AlphabetContainer alphabet, int length, double ess, String description, String graph)` This is the constructor that creates a filled parameter set.

Uses of AlphabetContainer in de.jstacs.models.utils

Constructors in de.jstacs.models.utils with parameters of type AlphabetContainer
`ModelTester.SeqIterator(AlphabetContainer abc, int length)`

Uses of AlphabetContainer in de.jstacs.parameters

Methods in de.jstacs.parameters that return AlphabetContainer
`AlphabetContainer` | `SequenceScoringParameterSet.getAlphabet()` Returns the alphabet

Constructors in de.jstacs.parameters with parameters of type AlphabetContainer
`SequenceScoringParameterSet(Class instanceClass, AlphabetContainer alphabet)` Constructs a `InstanceParameterSet` for an object that can handle sequences of variable length and with the alphabet.
`SequenceScoringParameterSet(Class instanceClass, AlphabetContainer alphabet, int length, boolean variableLength)` Constructs a `InstanceParameterSet` from the alphabet and the length.

Uses of AlphabetContainer in de.jstacs.scoringFunctions

Fields in de.jstacs.scoringFunctions declared as AlphabetContainer
`protected AlphabetContainer` | `AbstractNormalizableScoringFunction.alphabets` The AlphabetContainer of this `NormalizableScoringFunction`

Methods in de.jstacs.scoringFunctions that return AlphabetContainer
`AlphabetContainer` | `ScoringFunction.getAlphabetContainer()` Returns the `AlphabetContainer` for this `ScoringFunction`.
`AlphabetContainer` | `AbstractNormalizableScoringFunction.getAlphabetContainer()`

Constructors in de.jstacs.scoringFunctions with parameters of type AlphabetContainer
`AbstractNormalizableScoringFunction(AlphabetContainer alphabets, int length)` The main constructor.
`MRFScoringFunction(AlphabetContainer alphabets, int length, double ess, String constr)` This is the main constructor.
`MRFScoringFunction(AlphabetContainer alphabets, int length, String constr)` This constructor creates an instance with ess 0.
`UniformScoringFunction(AlphabetContainer alphabets, int length, double ess)` The main constructor.
`VariableLengthScoringFunction(AlphabetContainer alphabets)` This is the main constructor that creates an instance that models sequence s of arbitrary length.
`VariableLengthScoringFunction(AlphabetContainer alphabets, int length)` This is the main constructor that creates an instance that models sequence s of a given length.

Uses of AlphabetContainer in de.jstacs.scoringFunctions.directedGraphicalModels

Methods in de.jstacs.scoringFunctions.directedGraphicalModels with parameters of type AlphabetContainer
`static ParameterTree[]` | `ParameterTree.fromStringArray(String[] strs, AlphabetContainer alphabet)` Re-creates an array of `ParameterTree`s from their XML-representation as given in `strs`.

Constructors in de.jstacs.scoringFunctions.directedGraphicalModels with parameters of type AlphabetContainer
`BayesianNetworkScoringFunction(AlphabetContainer alphabet, int length, double ess, boolean plugInParameters, Measure structureMeasure)` Creates a new BayesianNetworkScoringFunction that has neither been initialized nor trained.
`BayesianNetworkScoringFunctionParameterSet(AlphabetContainer alphabet, int length, double ess, boolean plugInParameters, Measure structureMeasure)` Creates a new `BayesianNetworkScoringFunctionParameterSet` with pre-defined parameter values.
`ParameterTree(int pos, int[] contextPoss, AlphabetContainer alphabet, int firstParent, int[] firstChildren)` Creates a new `ParameterTree` for the parameters at position `pos` using the parent positions in `contextPoss`.
`ParameterTree(StringBuffer source, AlphabetContainer alphabet)` Re-creates a `ParameterTree` from its XML-representation as returned by `ParameterTree.toXML()`.

Uses of AlphabetContainer in de.jstacs.scoringFunctions.homogeneous

Constructors in de.jstacs.scoringFunctions.homogeneous with parameters of type AlphabetContainer
`HMM0ScoringFunction(AlphabetContainer alphabets, int length, double ess, boolean plugIn, boolean optimize)` The main constructor that creates an instance of a homogeneous Markov model of order 0.
`HMMScoringFunction(AlphabetContainer alphabets, int order, double classEss, double[] sumOfHyperParams, boolean plugIn, boolean optimize, int starts)` This is the main constructor.
`HomogeneousScoringFunction(AlphabetContainer alphabets)` This is the main constructor that creates an instance that models sequence s of arbitrary length.
`HomogeneousScoringFunction(AlphabetContainer alphabets, int length)` This is the main constructor that creates an instance that models sequence s of a given length.
`UniformHomogeneousScoringFunction(AlphabetContainer alphabets, double ess)` This is the main constructor that creates an instance that models each sequence uniformly.

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