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.gendismix Provides an implementation of a classifier that allows to train the parameters of a set of NormalizableScoringFunctions by a unified generative-discriminative learning principle 
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.homogeneous   
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.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 
de.jstacs.scoringFunctions.mix.motifSearch   
 

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 classifier.
 

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.gendismix
 

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

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, i.e. the AlphabetContainer, used in this Sequence.CompositeSequence.
 AlphabetContainer Sample.getAlphabetContainer()
          Returns the AlphabetContainer of this Sample.
 AlphabetContainer AlphabetContainer.getCompositeContainer(int[] start, int[] length)
          Returns an AlphabetContainer 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)
          Returns a sub-container with the Alphabets 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 if this AlphabetContainer is consistent consistent with another AlphabetContainer.
 int AlphabetContainer.compareTo(AlphabetContainer abc)
           
static Sequence Sequence.create(AlphabetContainer con, SequenceAnnotation[] annotation, String sequence, String delim)
          Creates a Sequence.CompositeSequence from a String based on the given AlphabetContainer using the given delimiter delim and some annotation for the Sequence.CompositeSequence.
static Sequence Sequence.create(AlphabetContainer con, String sequence)
          Creates a Sequence.CompositeSequence 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.CompositeSequence from a String based on the given AlphabetContainer using the given delimiter delim.
 Sequence Sequence.getCompositeSequence(AlphabetContainer abc, int[] starts, int[] lengths)
          This method should be used if one wants to create a Sample of Sequence.CompositeSequences.
 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)
          Creates an new sparse AlphabetContainer based on given AlphabetContainers.
DiscreteSequenceEnumerator(AlphabetContainer con, int length, boolean sparse)
          Creates a new DiscreteSequenceEnumerator from a given AlphabetContainer and a length.
Sample(AlphabetContainer abc, AbstractStringExtractor se)
          Creates a new Sample from a StringExtractor using the given AlphabetContainer.
Sample(AlphabetContainer abc, AbstractStringExtractor se, int subsequenceLength)
          Creates a new Sample from a StringExtractor using the given AlphabetContainer and all overlapping windows of length subsequenceLength.
Sample(AlphabetContainer abc, AbstractStringExtractor se, String delim)
          Creates a new Sample from a StringExtractor using the given AlphabetContainer and a delimiter delim.
Sample(AlphabetContainer abc, AbstractStringExtractor se, String delim, int subsequenceLength)
          Creates a new Sample from a StringExtractor using the given AlphabetContainer, the given delimiter delim and all overlapping windows of length subsequenceLength.
Sequence.CompositeSequence(AlphabetContainer abc, Sequence seq, int[] starts, int[] lengths)
          This constructor should be used if one wants to create a Sample of Sequence.CompositeSequences.
Sequence.SubSequence(AlphabetContainer abc, Sequence seq, int start, int length)
          This constructor should be used if one wants to create a Sample of Sequence.SubSequences of defined length.
Sequence(AlphabetContainer container, SequenceAnnotation[] annotation)
          Creates a new Sequence.CompositeSequence with the given AlphabetContainer and the given annotation, but without the content.
 

Uses of AlphabetContainer in de.jstacs.data.sequences
 

Methods in de.jstacs.data.sequences with parameters of type AlphabetContainer
static Sample SparseSequence.getSample(AlphabetContainer con, AbstractStringExtractor... se)
          This method allows to create a Sample containing SparseSequences.
 

Constructors in de.jstacs.data.sequences with parameters of type AlphabetContainer
ArbitrarySequence(AlphabetContainer alphabetContainer, double[] content)
          Creates a new ArbitrarySequence from an array of double-encoded alphabet symbols.
ArbitrarySequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)
          Creates a new ArbitrarySequence from a String representation using the delimiter delim.
ArbitrarySequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)
          Creates a new ArbitrarySequence from a SymbolExtractor.
ArbitrarySequence(AlphabetContainer alphabetContainer, String sequence)
          Creates a new ArbitrarySequence from a String representation using the default delimiter.
ByteSequence(AlphabetContainer alphabetContainer, byte[] content)
          Creates a new ByteSequence from an array of byte- encoded alphabet symbols.
ByteSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)
          Creates a new ByteSequence from a String representation using the delimiter delim.
ByteSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)
          Creates a new ByteSequence from a SymbolExtractor.
ByteSequence(AlphabetContainer alphabetContainer, String sequence)
          Creates a new ByteSequence from a String representation using the default delimiter.
DiscreteSequence(AlphabetContainer container, SequenceAnnotation[] annotation)
          This constructor creates a new DiscreteSequence with the AlphabetContainer container and the annotation annotation but without the content.
IntSequence(AlphabetContainer alphabetContainer, int... content)
          Creates a new IntSequence from an array of int- encoded alphabet symbols.
IntSequence(AlphabetContainer alphabetContainer, int[] content, int start, int length)
          Creates a new IntSequence from a part of the array of int- encoded alphabet symbols.
IntSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)
          Creates a new IntSequence from a String representation using the delimiter delim.
IntSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)
          Creates a new IntSequence from a SymbolExtractor.
IntSequence(AlphabetContainer alphabetContainer, String sequence)
          Creates a new IntSequence from a String representation using the default delimiter.
RecursiveSequence(AlphabetContainer alphabet, Sequence seq)
          Creates a new RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet using the annotation of the given Sequence.
RecursiveSequence(AlphabetContainer alphabet, SequenceAnnotation[] annotation, Sequence seq)
          Creates a new RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet and the annotation annotation.
ShortSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)
          Creates a new ShortSequence from a String representation using the delimiter delim.
ShortSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)
          Creates a new ShortSequence from a SymbolExtractor.
ShortSequence(AlphabetContainer alphabetContainer, short[] content)
          Creates a new ShortSequence from an array of short- encoded alphabet symbols.
ShortSequence(AlphabetContainer alphabetContainer, String sequence)
          Creates a new ShortSequence from a String representation using the default delimiter.
SparseSequence(AlphabetContainer alphCon, String seq)
          Creates a new SparseSequence from a String representation.
SparseSequence(AlphabetContainer alphCon, SymbolExtractor se)
          Creates a new SparseSequence 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 the content of a File using a given AlphabetContainer 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 AbstractModel.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)
          Creates a new CompositeModel.
UniformModel(AlphabetContainer alphabet)
          Creates a new UniformModel using a given AlphabetContainer.
 

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) Constraint constr with the weighted absolute frequencies of the Sample data.
abstract  String Constraint.getDescription(AlphabetContainer con, int i)
          Returns the decoded symbol for the encoded symbol i.
 String Constraint.getFreqInfo(AlphabetContainer con)
          Returns an information about the stored frequencies.
 

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 given by length.
 

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

Methods in de.jstacs.models.discrete.homogeneous with parameters of type AlphabetContainer
 String HomogeneousModel.HomCondProb.getDescription(AlphabetContainer con, int i)
           
 

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)
          Creates a new HomMMParameterSet with AlphabetContainer, ess (equivalent sample size), description and order of the homogeneous Markov model.
HomogeneousModelParameterSet(Class<? extends HomogeneousModel> instanceClass, AlphabetContainer alphabet, double ess, String description, byte order)
          Creates a new HomogeneousModelParameterSet with AlphabetContainer, ess (equivalent sample size), description and order of the homogeneous Markov model.
 

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.
 

Methods in de.jstacs.models.discrete.inhomogeneous with parameters of type AlphabetContainer
 String InhConstraint.getDescription(AlphabetContainer con, int i)
           
 String InhCondProb.getDescription(AlphabetContainer con, int i)
           
 

Constructors in de.jstacs.models.discrete.inhomogeneous with parameters of type AlphabetContainer
StructureLearner(AlphabetContainer con, int length)
          Creates a StructureLearner with equivalent sample size (ess) = 0.
StructureLearner(AlphabetContainer con, int length, double ess)
          Creates a new StructureLearner for a given AlphabetContainer, a given length and a given equivalent sample size (ess).
 

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 BayesianNetworkModelParameterSet for a BayesianNetworkModel.
FSDAGMParameterSet(AlphabetContainer alphabet, int length, double ess, String description, String graph)
          This constructor creates an FSDAGMParameterSet instance.
FSDAGMParameterSet(Class<? extends FSDAGModel> clazz, AlphabetContainer alphabet, int length, double ess, String description, String graph)
          This constructor creates an FSDAGMParameterSet instance for the specified class.
IDGMParameterSet(Class<? extends InhomogeneousDGM> instanceClass, AlphabetContainer alphabet, int length, double ess, String description)
          This constructor creates an IDGMParameterSet 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.parameters
 

Methods in de.jstacs.parameters that return AlphabetContainer
 AlphabetContainer SequenceScoringParameterSet.getAlphabetContainer()
          Returns the AlphabetContainer of the current instance.
 

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

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.
AbstractVariableLengthScoringFunction(AlphabetContainer alphabets)
          This is the main constructor that creates an instance of a VariableLengthScoringFunction that models sequences of arbitrary length.
AbstractVariableLengthScoringFunction(AlphabetContainer alphabets, int length)
          This is the main constructor that creates an instance of a VariableLengthScoringFunction that models sequences of a given length.
CMMScoringFunction(AlphabetContainer alphabets, int order, int period, double classEss, double[] sumOfHyperParams, boolean plugIn, boolean optimize, int starts, int initFrame)
          The main constructor.
MRFScoringFunction(AlphabetContainer alphabets, int length, double ess, String constr)
          This is the main constructor that creates an instance of a MRFScoringFunction.
MRFScoringFunction(AlphabetContainer alphabets, int length, String constr)
          This constructor creates an instance of a MRFScoringFunction with equivalent sample size (ess) 0.
UniformScoringFunction(AlphabetContainer alphabets, int length, double ess)
          This is the main constructor that creates an instance of a UniformScoringFunction that models each sequence uniformly.
 

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)
          Recreates 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.
BayesianNetworkScoringFunctionParameterSet(AlphabetContainer alphabet, int length, double ess, boolean plugInParameters, Measure structureMeasure)
          Creates a new BayesianNetworkScoringFunctionParameterSet with pre-defined parameter values.
MutableMarkovModelScoringFunction(AlphabetContainer alphabet, int length, double ess, boolean plugInParameters, InhomogeneousMarkov structureMeasure)
          This constructor creates an instance without any prior for the modeled length.
MutableMarkovModelScoringFunction(AlphabetContainer alphabet, int length, double ess, boolean plugInParameters, InhomogeneousMarkov structureMeasure, DurationScoringFunction lengthPenalty)
          This constructor creates an instance with an prior for the modeled length.
MutableMarkovModelScoringFunction(AlphabetContainer alphabet, int length, double ess, boolean plugInParameters, int order, DurationScoringFunction lengthPenalty)
          This constructor creates an instance with an prior for the modeled length.
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)
          Recreates 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 that creates an instance of a homogeneous Markov model of arbitrary order.
HomogeneousScoringFunction(AlphabetContainer alphabets)
          This is the main constructor that creates an instance of a HomogeneousScoringFunction that models sequences of arbitrary length.
HomogeneousScoringFunction(AlphabetContainer alphabets, int length)
          This is the main constructor that creates an instance of a HomogeneousScoringFunction that models sequences of a given length.
UniformHomogeneousScoringFunction(AlphabetContainer alphabets, double ess)
          This is the main constructor that creates an instance of a UniformHomogeneousScoringFunction that models each sequence uniformly.
 

Uses of AlphabetContainer in de.jstacs.scoringFunctions.mix.motifSearch
 

Constructors in de.jstacs.scoringFunctions.mix.motifSearch with parameters of type AlphabetContainer
PositionScoringFunction(AlphabetContainer con, int length)
          This constructor allows create instance with more than one dimension.