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 Models
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.classifier.scoringFunctionBased.sampling	Provides the classes for AbstractScoreBasedClassifiers that are based on SamplingScoringFunctions and that sample parameters using the Metropolis-Hastings algorithm.
de.jstacs.data	Provides classes for the representation of data.
de.jstacs.data.sequences	Provides classes for representing sequences.
de.jstacs.data.sequences.annotation	Provides the facilities to annotate Sequences using a number of pre-defined annotation types, or additional implementations of the SequenceAnnotation class
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.hmm	The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.models.hmm.states.emissions
de.jstacs.models.hmm.states.emissions.continuous
de.jstacs.models.hmm.states.emissions.discrete
de.jstacs.models.mixture	This package is the super package for any mixture model.
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.classifier.scoringFunctionBased.sampling

Constructors in de.jstacs.classifier.scoringFunctionBased.sampling with parameters of type AlphabetContainer

SamplingGenDisMixClassifierParameterSet(AlphabetContainer alphabet, int length, int numStarts, int testSamplings, int stationarySamplings, String outfilePrefix, int threads)
Create a new SamplingGenDisMixClassifierParameterSet with a grouped sampling scheme, sampling all parameters (and not only the free ones), and adaption of the variance.

SamplingGenDisMixClassifierParameterSet(AlphabetContainer alphabet, int length, int numStarts, SamplingScoreBasedClassifier.SamplingScheme scheme, int testSamplings, int stationarySamplings, boolean freeParameters, boolean adaptVariance, String outfilePrefix, int threads)
Create a new SamplingGenDisMixClassifierParameterSet.

SamplingGenDisMixClassifierParameterSet(Class<? extends SamplingScoreBasedClassifier> instanceClass, AlphabetContainer alphabet, int length, int numStarts, SamplingScoreBasedClassifier.SamplingScheme scheme, int testSamplings, int stationarySamplings, boolean freeParameters, boolean adaptVariance, String outfilePrefix, int threads)
Create a new SamplingGenDisMixClassifierParameterSet.

SamplingScoreBasedClassifierParameterSet(Class<? extends SamplingScoreBasedClassifier> instanceClass, AlphabetContainer alphabet, int length, int numStarts, int testSamplings, int stationarySamplings, String outfilePrefix)
Create a new SamplingScoreBasedClassifierParameterSet with a grouped sampling scheme, sampling all parameters (and not only the free ones), and adaption of the variance.

SamplingScoreBasedClassifierParameterSet(Class<? extends SamplingScoreBasedClassifier> instanceClass, AlphabetContainer alphabet, int length, int numStarts, SamplingScoreBasedClassifier.SamplingScheme scheme, int testSamplings, int stationarySamplings, boolean freeParameters, boolean adaptVariance, String outfilePrefix)
Create a new SamplingScoreBasedClassifierParameterSet.

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.
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 from a String based on the given AlphabetContainer using the given delimiter delim and some annotation for the Sequence.
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 delim.
Sequence<T>	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<T> seq, int[] starts, int[] lengths)
This constructor should be used if one wants to create a Sample of Sequence.CompositeSequences.

Sequence.RecursiveSequence(AlphabetContainer alphabet, Sequence<T> seq)
Creates a new Sequence.RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet using the annotation of the given Sequence.

Sequence.RecursiveSequence(AlphabetContainer alphabet, SequenceAnnotation[] annotation, Sequence<T> seq)
Creates a new Sequence.RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet and the annotation annotation.

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 with the given AlphabetContainer and the given annotation, but without the content.

Uses of AlphabetContainer in de.jstacs.data.sequences

Fields in de.jstacs.data.sequences declared as AlphabetContainer

protected AlphabetContainer

MappedDiscreteSequence.originalAlphabetContainer The original AlphabetContainer.

Methods in de.jstacs.data.sequences that return AlphabetContainer

static AlphabetContainer

MappedDiscreteSequence.getNewAlphabetContainer(AlphabetContainer original, DiscreteAlphabetMapping... transformation) This method allows to create a new AlphabetContainer given an old AlphabetContainer and some DiscreteAlphabetMappings.

Methods in de.jstacs.data.sequences with parameters of type AlphabetContainer

static AlphabetContainer	MappedDiscreteSequence.getNewAlphabetContainer(AlphabetContainer original, DiscreteAlphabetMapping... transformation) This method allows to create a new AlphabetContainer given an old AlphabetContainer and some DiscreteAlphabetMappings.
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.

MappedDiscreteSequence(AlphabetContainer originalAlphabetContainer, SequenceAnnotation[] seqAn, DiscreteAlphabetMapping... transformation)
This method allows to create an empty MappedDiscreteSequence.

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.

SimpleDiscreteSequence(AlphabetContainer container, SequenceAnnotation[] annotation)
This constructor creates a new SimpleDiscreteSequence with the AlphabetContainer container and the annotation annotation but without the content.

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.data.sequences.annotation

Constructors in de.jstacs.data.sequences.annotation with parameters of type AlphabetContainer

ReferenceSequenceAnnotationParser(String key, AlphabetContainer alphabet, String keyValueDelimiter, String annotationDelimiter)
Creates a new ReferenceSequenceAnnotationParser with user-specified delimiters.

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

static BayesianNetworkModel	ModelFactory.createBayesianNetworkModel(AlphabetContainer con, int length, double ess, byte order) This method returns a Bayesian network model (BN) with user-specified order.
static HomogeneousMM	ModelFactory.createHomogeneousMarkovModel(AlphabetContainer con, double ess, byte order) This method returns a homogeneous Markov model with user-specified order.
static BayesianNetworkModel	ModelFactory.createInhomogeneousMarkovModel(AlphabetContainer con, int length, double ess, byte order) This method returns a inhomogeneous Markov model (IMM) with user-specified order.
static BayesianNetworkModel	ModelFactory.createPermutedMarkovModel(AlphabetContainer con, int length, double ess, byte order) This method returns a permuted Markov model (PMM) with user-specified order.
static FSDAGModel	ModelFactory.createPWM(AlphabetContainer con, int length, double ess) This method returns a position weight matrix (PWM).
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.

FSDAGModelForGibbsSamplingParameterSet(AlphabetContainer alphabet, int length, double ess, String description, String graph)
This is the constructor that creates a filled parameter set.

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.hmm

Fields in de.jstacs.models.hmm declared as AlphabetContainer

protected AlphabetContainer

AbstractHMM.con The AlphabetContainer of the HMM.

Methods in de.jstacs.models.hmm that return AlphabetContainer

AlphabetContainer

AbstractHMM.getAlphabetContainer()

Methods in de.jstacs.models.hmm with parameters of type AlphabetContainer

static AbstractHMM	HMMFactory.createProfileHMM(MaxHMMTrainingParameterSet trainingParameterSet, double[][] initFromTo, boolean likelihood, int order, int numLayers, AlphabetContainer con, double ess, boolean conditionalMain, boolean closeCircle, double[][] conditionInitProbs) Creates a new profile HMM for a given architecture and number of layers.
static AbstractHMM	HMMFactory.createProfileHMM(MaxHMMTrainingParameterSet trainingParameterSet, HMMFactory.HMMType type, boolean likelihood, int order, int numLayers, AlphabetContainer con, double ess, boolean conditionalMain, boolean closeCircle, double[][] conditionInitProbs) Creates a new profile HMM for a given architecture and number of layers.
static AbstractHMM	HMMFactory.createSunflowerHMM(HMMTrainingParameterSet pars, AlphabetContainer con, double ess, int expectedSequenceLength, boolean startCentral, int... motifLength) This method creates a first order sunflower HMM.
static AbstractHMM	HMMFactory.createSunflowerHMM(HMMTrainingParameterSet pars, AlphabetContainer con, double ess, int expectedSequenceLength, boolean startCentral, PhyloTree[] t, double[] motifProb, int[] motifLength) This method creates a first order sunflower HMM allowing phylogenetic emissions.
boolean	AbstractHMM.setNewAlphabetContainerInstance(AlphabetContainer abc)

Uses of AlphabetContainer in de.jstacs.models.hmm.states.emissions

Methods in de.jstacs.models.hmm.states.emissions that return AlphabetContainer

AlphabetContainer	SilentEmission.getAlphabetContainer()
AlphabetContainer	MixtureEmission.getAlphabetContainer()
AlphabetContainer	Emission.getAlphabetContainer() This method returns the AlphabetContainer of this emission.

Uses of AlphabetContainer in de.jstacs.models.hmm.states.emissions.continuous

Methods in de.jstacs.models.hmm.states.emissions.continuous that return AlphabetContainer

AlphabetContainer

GaussianEmission.getAlphabetContainer()

Constructors in de.jstacs.models.hmm.states.emissions.continuous with parameters of type AlphabetContainer

GaussianEmission(AlphabetContainer con)
Creates a GaussianEmission which can be used for maximum likelihood.

GaussianEmission(AlphabetContainer con, double ess, double priorMu, double priorAlpha, double priorBeta, boolean transformed)
Creates a GaussianEmission with normal-gamma prior by directly defining the hyper-parameters of the prior.

GaussianEmission(double ess, AlphabetContainer con, double priorMu, double expectedPrecision, double sdPrecision, boolean transformed)
Creates a GaussianEmission with normal-gamma prior by defining the expected precision and the expected standard deviation of the precision, i.e. via the expectation and variance of the gamma part of the normal-gamma prior.

Uses of AlphabetContainer in de.jstacs.models.hmm.states.emissions.discrete

Fields in de.jstacs.models.hmm.states.emissions.discrete declared as AlphabetContainer

protected AlphabetContainer

AbstractConditionalDiscreteEmission.con The alphabet of the emissions

Methods in de.jstacs.models.hmm.states.emissions.discrete that return AlphabetContainer

AlphabetContainer

AbstractConditionalDiscreteEmission.getAlphabetContainer()

Constructors in de.jstacs.models.hmm.states.emissions.discrete with parameters of type AlphabetContainer

AbstractConditionalDiscreteEmission(AlphabetContainer con, double[][] hyperParams)
This is a simple constructor for a AbstractConditionalDiscreteEmission defining the individual hyper parameters.

AbstractConditionalDiscreteEmission(AlphabetContainer con, double[][] hyperParams, double[][] initHyperParams)
This constructor creates a AbstractConditionalDiscreteEmission defining the individual hyper parameters for the prior used during training and initialization.

AbstractConditionalDiscreteEmission(AlphabetContainer con, int numberOfConditions, double ess)
This is a simple constructor for a AbstractConditionalDiscreteEmission based on the equivalent sample size.

DiscreteEmission(AlphabetContainer con, double ess)
This is a simple constructor for a DiscreteEmission based on the equivalent sample size.

DiscreteEmission(AlphabetContainer con, double[] hyperParams)
This is a simple constructor for a DiscreteEmission defining the individual hyper parameters.

PhyloDiscreteEmission(AlphabetContainer con, double[] hyperParams, PhyloTree t)
This is a simple constructor for a DiscreteEmission defining the individual hyper parameters.

PhyloDiscreteEmission(AlphabetContainer con, double ess, PhyloTree t)
This is a simple constructor for a PhyloDiscreteEmission based on the equivalent sample size.

ReferenceSequenceDiscreteEmission(AlphabetContainer con, AlphabetContainer refCon, int refIdx, double ess)
This is a simple constructor for a ReferenceSequenceDiscreteEmission based on the equivalent sample size.

ReferenceSequenceDiscreteEmission(AlphabetContainer con, AlphabetContainer refCon, int refIdx, double[][] hyperParams)
This constructor creates a ReferenceSequenceDiscreteEmission defining the individual hyper parameters.

ReferenceSequenceDiscreteEmission(AlphabetContainer con, AlphabetContainer refCon, int refIdx, double[][] hyperParams, double[][] initHyperParams)
This constructor creates a ReferenceSequenceDiscreteEmission defining the individual hyper parameters.

ReferenceSequenceDiscreteEmission(AlphabetContainer con, AlphabetContainer refCon, int refIdx, double ess, double[][] initHyperParams)
This is a simple constructor for a ReferenceSequenceDiscreteEmission based on the equivalent sample size.

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.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, double[] frameHyper, double[][][] hyper, boolean plugIn, boolean optimize, int starts, int initFrame)
This constructor allows to create an instance with specific hyper-parameters for all conditional distributions.

CMMScoringFunction(AlphabetContainer alphabets, int order, int period, double classEss, double[] sumOfHyperParams, boolean plugIn, boolean optimize, int starts, int initFrame)
The main constructor.

MappingScoringFunction(AlphabetContainer originalAlphabetContainer, NormalizableScoringFunction nsf, DiscreteAlphabetMapping... mapping)
The main constructor creating a MappingScoringFunction.

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

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.

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.

HMMScoringFunction(AlphabetContainer alphabets, int order, double classEss, int length)
This is a convenience constructor for creating 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.