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Packages that use AlphabetContainer | |
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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.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 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 |
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Methods in de.jstacs.classifier that return AlphabetContainer | |
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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 | |
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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 | |
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AbstractClassifier(AlphabetContainer abc)
The constructor for a homogeneous classifier. |
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AbstractClassifier(AlphabetContainer abc,
int length)
The constructor for an inhomogeneous classifier. |
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AbstractScoreBasedClassifier(AlphabetContainer abc,
int classes)
The constructor for a homogeneous classifier. |
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AbstractScoreBasedClassifier(AlphabetContainer abc,
int classes,
double classWeight)
The constructor for a homogeneous classifier. |
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AbstractScoreBasedClassifier(AlphabetContainer abc,
int length,
int classes)
The constructor for an inhomogeneous classifier. |
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AbstractScoreBasedClassifier(AlphabetContainer abc,
int length,
int classes,
double classWeight)
The constructor for an inhomogeneous classifier. |
Uses of AlphabetContainer in de.jstacs.classifier.modelBased |
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Methods in de.jstacs.classifier.modelBased with parameters of type AlphabetContainer | |
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boolean |
ModelBasedClassifier.setNewAlphabetContainerInstance(AlphabetContainer abc)
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Uses of AlphabetContainer in de.jstacs.classifier.scoringFunctionBased |
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Constructors in de.jstacs.classifier.scoringFunctionBased with parameters of type AlphabetContainer | |
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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 |
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Constructors in de.jstacs.classifier.scoringFunctionBased.cll with parameters of type AlphabetContainer | |
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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 |
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Fields in de.jstacs.data declared as AlphabetContainer | |
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protected AlphabetContainer |
Sequence.alphabetCon
the underlying alphabets |
Methods in de.jstacs.data that return AlphabetContainer | |
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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 | |
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boolean |
AlphabetContainer.checkConsistency(AlphabetContainer abc)
Checks whether to alphabets are consistent. |
int |
AlphabetContainer.compareTo(AlphabetContainer abc)
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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 | |
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AlphabetContainer(AlphabetContainer[] cons,
int[] lengths)
This constructor creates an new sparse AlphabetContainer based on given AlphabetContainers. |
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DiscreteSequenceEnumerator(AlphabetContainer con,
int length,
boolean sparse)
The constructor. |
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Sample(AlphabetContainer abc,
StringExtractor se)
Creates a Sample from a StringExctractor using the given AlphabetContainer. |
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Sample(AlphabetContainer abc,
StringExtractor se,
int subsequenceLength)
Creates a Sample from a StringExctractor using the given AlphabetContainer and all overlapping windows of subsequenceLength . |
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Sample(AlphabetContainer abc,
StringExtractor se,
String delim)
Creates a Sample from a StringExctractor using the given AlphabetContainer and delimiter. |
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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 . |
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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. |
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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. |
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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 |
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Constructors in de.jstacs.data.sequences with parameters of type AlphabetContainer | |
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ArbitrarySequence(AlphabetContainer alphabetContainer,
double[] content)
This constructor is designed for the emitSample( int n ) of AbstractModel . |
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ArbitrarySequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new sequence from a string representation using the delimiter delim . |
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ArbitrarySequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new sequence from a SymbolExctractor. |
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ArbitrarySequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new sequence from a string representation using the default delimiter. |
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ByteSequence(AlphabetContainer alphabetContainer,
byte[] content)
This constructor is designed for the emitSample( int n ) of AbstractModel . |
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ByteSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new sequence from a string representation using the delimiter delim . |
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ByteSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new sequence from a SymbolExctractor. |
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ByteSequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new sequence from a string representation using the default delimiter. |
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DiscreteSequence(AlphabetContainer container,
SequenceAnnotation[] annotation)
This constructor creates an instance with the AlphabetContainer and the annotation, but without the content. |
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IntSequence(AlphabetContainer alphabetContainer,
int[] content)
This constructor is designed for Model.emitSample(int, int...) . |
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IntSequence(AlphabetContainer alphabetContainer,
int[] content,
int start,
int length)
This constructor creates an instance from a part of the content. |
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IntSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new sequence from a string representation using the delimiter delim . |
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IntSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new sequence from a SymbolExctractor. |
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IntSequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new sequence from a string representation using the default delimiter. |
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RecursiveSequence(AlphabetContainer alphabet,
Sequence seq)
This constructor creates a recursive sequence using the annotation of the given sequence. |
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RecursiveSequence(AlphabetContainer alphabet,
SequenceAnnotation[] annotation,
Sequence seq)
This constructor creates a recursive sequence. |
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ShortSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new sequence from a string representation using the delimiter delim . |
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ShortSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new sequence from a SymbolExctractor. |
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ShortSequence(AlphabetContainer alphabetContainer,
short[] content)
This constructor is designed for the emitSample( int n ) of AbstractModel . |
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ShortSequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new sequence from a string representation using the default delimiter. |
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SparseSequence(AlphabetContainer alphCon,
String seq)
This constructor creates an instance from a String. |
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SparseSequence(AlphabetContainer alphCon,
SymbolExtractor se)
This constructor creates an instance from a SymbolExtractor. |
Uses of AlphabetContainer in de.jstacs.io |
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Methods in de.jstacs.io with parameters of type AlphabetContainer | |
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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 |
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Fields in de.jstacs.models declared as AlphabetContainer | |
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protected AlphabetContainer |
AbstractModel.alphabets
The underlying alphabets |
Methods in de.jstacs.models that return AlphabetContainer | |
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AlphabetContainer |
Model.getAlphabetContainer()
Returns the container of alphabets that were used when constructing the model. |
AlphabetContainer |
AbstractModel.getAlphabetContainer()
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Methods in de.jstacs.models with parameters of type AlphabetContainer | |
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protected void |
CompositeModel.set(AlphabetContainer abc)
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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)
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Constructors in de.jstacs.models with parameters of type AlphabetContainer | |
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AbstractModel(AlphabetContainer alphabets,
int length)
Constructor that sets the length of the model to length and the AlphabetContainer to
alphabets . |
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CompositeModel(AlphabetContainer alphabets,
int[] assignment,
Model... models)
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UniformModel(AlphabetContainer alphabet)
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Uses of AlphabetContainer in de.jstacs.models.discrete |
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Methods in de.jstacs.models.discrete with parameters of type AlphabetContainer | |
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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 | |
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DGMParameterSet(Class<? extends DiscreteGraphicalModel> instanceClass,
AlphabetContainer alphabet,
double ess,
String description)
The constructor for models, that can handle variable lengths. |
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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 |
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Methods in de.jstacs.models.discrete.inhomogeneous that return AlphabetContainer | |
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AlphabetContainer |
StructureLearner.getAlphabetContainer()
This method returns the AlphabetContainer of the StructureLearner. |
Constructors in de.jstacs.models.discrete.inhomogeneous with parameters of type AlphabetContainer | |
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StructureLearner(AlphabetContainer con,
int length)
Creates a StructureLearner with ess = 0. |
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StructureLearner(AlphabetContainer con,
int length,
double ess)
Creates a StructureLearner |
Uses of AlphabetContainer in de.jstacs.models.discrete.inhomogeneous.parameters |
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Constructors in de.jstacs.models.discrete.inhomogeneous.parameters with parameters of type AlphabetContainer | |
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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. |
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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. |
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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 |
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Methods in de.jstacs.models.mixture with parameters of type AlphabetContainer | |
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protected void |
AbstractMixtureModel.set(AlphabetContainer abc)
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Uses of AlphabetContainer in de.jstacs.models.utils |
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Constructors in de.jstacs.models.utils with parameters of type AlphabetContainer | |
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ModelTester.SeqIterator(AlphabetContainer abc,
int length)
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Uses of AlphabetContainer in de.jstacs.parameters |
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Methods in de.jstacs.parameters that return AlphabetContainer | |
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AlphabetContainer |
InstanceParameterSet.getAlphabet()
Returns the alphabet |
Constructors in de.jstacs.parameters with parameters of type AlphabetContainer | |
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InstanceParameterSet(Class instanceClass,
AlphabetContainer alphabet)
Constructs a InstanceParameterSet for an object that can handle sequences of variable length and with the alphabet. |
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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 |
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Fields in de.jstacs.scoringFunctions declared as AlphabetContainer | |
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protected AlphabetContainer |
AbstractNormalizableScoringFunction.alphabets
The AlphabetContainer of this NormalizableScoringFunction |
Methods in de.jstacs.scoringFunctions that return AlphabetContainer | |
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AlphabetContainer |
ScoringFunction.getAlphabetContainer()
Returns the AlphabetContainer for this ScoringFunction . |
AlphabetContainer |
AbstractNormalizableScoringFunction.getAlphabetContainer()
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Constructors in de.jstacs.scoringFunctions with parameters of type AlphabetContainer | |
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AbstractNormalizableScoringFunction(AlphabetContainer alphabets,
int length)
The main constructor. |
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MRFScoringFunction(AlphabetContainer alphabets,
int length,
double ess,
String constr)
This is the main constructor. |
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MRFScoringFunction(AlphabetContainer alphabets,
int length,
String constr)
This constructor creates an instance with ess 0. |
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UniformScoringFunction(AlphabetContainer alphabets,
int length,
double ess)
The main constructor. |
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VariableLengthScoringFunction(AlphabetContainer alphabets)
This is the main constructor that creates an instance that models sequence s of arbitrary length. |
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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 |
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Methods in de.jstacs.scoringFunctions.directedGraphicalModels with parameters of type AlphabetContainer | |
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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 | |
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BayesianNetworkScoringFunction(AlphabetContainer alphabet,
int length,
double ess,
boolean plugInParameters,
Measure structureMeasure)
Creates a new BayesianNetworkScoringFunction that has neither been initialized nor trained. |
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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 . |
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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 |
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Constructors in de.jstacs.scoringFunctions.homogeneous with parameters of type AlphabetContainer | |
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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. |
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HMMScoringFunction(AlphabetContainer alphabets,
int order,
double classEss,
double[] sumOfHyperParams,
boolean plugIn,
boolean optimize,
int starts)
This is the main constructor. |
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HomogeneousScoringFunction(AlphabetContainer alphabets)
This is the main constructor that creates an instance that models sequence s of arbitrary length. |
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HomogeneousScoringFunction(AlphabetContainer alphabets,
int length)
This is the main constructor that creates an instance that models sequence s of a given length. |
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UniformHomogeneousScoringFunction(AlphabetContainer alphabets,
double ess)
This is the main constructor that creates an instance that models each sequence uniformly. |
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