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 Classifiers that are based on Model
de.jstacs.classifier.scoringFunctionBased Provides the classes for Classifiers that are based on ScoringFunctions. 
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 Storables 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.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.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 ScoringFunctions that can be used in a ScoreClassifier
de.jstacs.scoringFunctions.directedGraphicalModels Provides ScoringFunctions that are equivalent to directed graphical models. 
de.jstacs.scoringFunctions.homogeneous Provides ScoringFunctions 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 return 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 AlphabetConatiner 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(AlphabetContainer alphabet, int length, byte algo, double eps, double lineps, double startD, boolean free, boolean plugIn)
          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, boolean plugIn, 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 used 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 exsisting AlphabetContainer.
 

Methods in de.jstacs.data with parameters of type AlphabetContainer
 boolean AlphabetContainer.checkConsistency(AlphabetContainer abc)
          Checks whether to 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 exsisting 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 AlphabetContainers.
DiscreteSequenceEnumerator(AlphabetContainer con, int length, boolean sparse)
          The constructor.
Sample(AlphabetContainer abc, StringExtractor se)
          Creates a Sample from a StringExctractor using the given AlphabetContainer.
Sample(AlphabetContainer abc, StringExtractor se, int subsequenceLength)
          Creates a Sample from a StringExctractor using the given AlphabetContainer and all overlapping windows of subsequenceLength.
Sample(AlphabetContainer abc, StringExtractor se, String delim)
          Creates a Sample from a StringExctractor using the given AlphabetContainer and delimiter.
Sample(AlphabetContainer abc, StringExtractor se, String delim, int subsequenceLength)
          Creates a Sample from a StringExctractor 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 emitSample( int n ) of AbstractModel.
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 SymbolExctractor.
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 emitSample( int n ) of AbstractModel.
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 SymbolExctractor.
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 SymbolExctractor.
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 SymbolExctractor.
ShortSequence(AlphabetContainer alphabetContainer, short[] content)
          This constructor is designed for the emitSample( int n ) of AbstractModel.
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.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(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.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 InstanceParameterSet.getAlphabet()
          Returns the alphabet
 

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