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Packages that use WrongAlphabetException | |
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de.jstacs.classifier.assessment | This package allows to assess classifiers. |
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.alphabets | Provides classes for the representation of discrete and continuous alphabets, including a DNAAlphabet for the most common case of DNA-sequences |
de.jstacs.data.bioJava | Provides an adapter between the representation of data in BioJava and the representation used in Jstacs. |
de.jstacs.data.sequences | Provides classes for representing sequences. |
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.shared | |
de.jstacs.models.mixture | This package is the super package for any mixture model. |
de.jstacs.models.utils |
Uses of WrongAlphabetException in de.jstacs.classifier.assessment |
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Methods in de.jstacs.classifier.assessment that throw WrongAlphabetException | |
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ListResult |
ClassifierAssessment.assess(MeasureParameters mp,
ClassifierAssessmentAssessParameterSet assessPS,
ProgressUpdater pU,
Sample... s)
Assesses the contained classifiers. |
ListResult |
ClassifierAssessment.assess(MeasureParameters mp,
ClassifierAssessmentAssessParameterSet assessPS,
ProgressUpdater pU,
Sample[][]... s)
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ListResult |
ClassifierAssessment.assess(MeasureParameters mp,
ClassifierAssessmentAssessParameterSet assessPS,
Sample... s)
Assesses the contained classifiers. |
protected void |
ClassifierAssessment.prepareAssessment(Sample... s)
Prepares an assessment. |
Constructors in de.jstacs.classifier.assessment that throw WrongAlphabetException | |
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ClassifierAssessment(AbstractClassifier... aCs)
Creates a new ClassifierAssessment from a set of AbstractClassifier s. |
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ClassifierAssessment(AbstractClassifier[] aCs,
boolean buildClassifiersByCrossProduct,
Model[]... aMs)
This constructor allows to assess a collection of given AbstractClassifier s and those constructed
using the given AbstractModel s. |
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ClassifierAssessment(AbstractClassifier[] aCs,
Model[][] aMs,
boolean buildClassifiersByCrossProduct,
boolean checkAlphabetConsistencyAndLength)
Creates a new ClassifierAssessment from an array of AbstractClassifier s and a two-dimensional array
of Model s, which are combined to additional classifiers. |
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ClassifierAssessment(boolean buildClassifiersByCrossProduct,
Model[]... aMs)
Creates a new ClassifierAssessment from a set of Model s. |
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KFoldCrossValidation(AbstractClassifier... aCs)
Creates a new KFoldCrossValidation from a set of AbstractClassifier s. |
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KFoldCrossValidation(AbstractClassifier[] aCs,
boolean buildClassifiersByCrossProduct,
Model[]... aMs)
This constructor allows to assess a collection of given AbstractClassifier s and those constructed
using the given AbstractModel s by a KFoldCrossValidation . |
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KFoldCrossValidation(AbstractClassifier[] aCs,
Model[][] aMs,
boolean buildClassifiersByCrossProduct,
boolean checkAlphabetConsistencyAndLength)
Creates a new KFoldCrossValidation from an array of AbstractClassifier s and a two-dimensional array
of Model s, which are combined to additional classifiers. |
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KFoldCrossValidation(boolean buildClassifiersByCrossProduct,
Model[]... aMs)
Creates a new KFoldCrossValidation from a set of Model s. |
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RepeatedHoldOutExperiment(AbstractClassifier... aCs)
Creates a new RepeatedHoldOutExperiment from a set of AbstractClassifier s. |
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RepeatedHoldOutExperiment(AbstractClassifier[] aCs,
boolean buildClassifiersByCrossProduct,
Model[]... aMs)
This constructor allows to assess a collection of given AbstractClassifier s and those constructed
using the given AbstractModel s by a RepeatedHoldOutExperiment . |
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RepeatedHoldOutExperiment(AbstractClassifier[] aCs,
Model[][] aMs,
boolean buildClassifiersByCrossProduct,
boolean checkAlphabetConsistencyAndLength)
Creates a new RepeatedHoldOutExperiment from an array of AbstractClassifier s and a two-dimensional array
of Model s, which are combined to additional classifiers. |
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RepeatedHoldOutExperiment(boolean buildClassifiersByCrossProduct,
Model[]... aMs)
Creates a new RepeatedHoldOutExperiment from a set of Model s. |
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RepeatedSubSamplingExperiment(AbstractClassifier... aCs)
Creates a new RepeatedSubSamplingExperiment from a set of AbstractClassifier s. |
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RepeatedSubSamplingExperiment(AbstractClassifier[] aCs,
boolean buildClassifiersByCrossProduct,
Model[]... aMs)
This constructor allows to assess a collection of given AbstractClassifier s and those constructed
using the given AbstractModel s by a RepeatedSubSamplingExperiment . |
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RepeatedSubSamplingExperiment(AbstractClassifier[] aCs,
Model[][] aMs,
boolean buildClassifiersByCrossProduct,
boolean checkAlphabetConsistencyAndLength)
Creates a new RepeatedSubSamplingExperiment from an array of AbstractClassifier s and a two-dimensional array
of Model s, which are combined to additional classifiers. |
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RepeatedSubSamplingExperiment(boolean buildClassifiersByCrossProduct,
Model[]... aMs)
Creates a new RepeatedSubSamplingExperiment from a set of Model s. |
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Sampled_RepeatedHoldOutExperiment(AbstractClassifier... aCs)
Creates a new Sampled_RepeatedHoldOutExperiment from a set of AbstractClassifier s. |
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Sampled_RepeatedHoldOutExperiment(AbstractClassifier[] aCs,
boolean buildClassifiersByCrossProduct,
Model[]... aMs)
This constructor allows to assess a collection of given AbstractClassifier s and those constructed
using the given AbstractModel s by a Sampled_RepeatedHoldOutExperiment . |
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Sampled_RepeatedHoldOutExperiment(AbstractClassifier[] aCs,
Model[][] aMs,
boolean buildClassifiersByCrossProduct,
boolean checkAlphabetConsistencyAndLength)
Creates a new Sampled_RepeatedHoldOutExperiment from an array of AbstractClassifier s and a two-dimensional array
of Model s, which are combined to additional classifiers. |
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Sampled_RepeatedHoldOutExperiment(boolean buildClassifiersByCrossProduct,
Model[]... aMs)
Creates a new Sampled_RepeatedHoldOutExperiment from a set of Model s. |
Uses of WrongAlphabetException in de.jstacs.classifier.scoringFunctionBased.cll |
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Constructors in de.jstacs.classifier.scoringFunctionBased.cll that throw WrongAlphabetException | |
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NormConditionalLogLikelihood(ScoringFunction[] score,
Sample[] data,
double[][] weights,
boolean norm,
boolean freeParams)
The constructor creates an instance of the log conditional likelihood. |
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NormConditionalLogLikelihood(ScoringFunction[] score,
Sample[] data,
double[][] weights,
LogPrior prior,
boolean norm,
boolean freeParams)
The constructor creates an instance using the given prior. |
Uses of WrongAlphabetException in de.jstacs.data |
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Methods in de.jstacs.data that throw WrongAlphabetException | |
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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. |
double |
AlphabetContainer.getCode(int pos,
String sym)
Returns the encoded symbol sym for position pos . |
Constructors in de.jstacs.data that throw WrongAlphabetException | |
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Sample.WeightedSampleFactory(Sample.WeightedSampleFactory.SortOperation sort,
Sample... data)
This constructor creates a Sample.WeightedSampleFactory on the given Sample (s). |
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Sample.WeightedSampleFactory(Sample.WeightedSampleFactory.SortOperation sort,
Sample[] data,
double[][] weights,
int length)
This constructor creates a Sample.WeightedSampleFactory on the given array of Sample s and weights . |
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Sample.WeightedSampleFactory(Sample.WeightedSampleFactory.SortOperation sort,
Sample data,
double[] weights)
This constructor creates a Sample.WeightedSampleFactory on the given Sample and weights . |
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Sample.WeightedSampleFactory(Sample.WeightedSampleFactory.SortOperation sort,
Sample data,
double[] weights,
int length)
This constructor creates a Sample.WeightedSampleFactory on the given Sample and weights . |
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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 . |
Uses of WrongAlphabetException in de.jstacs.data.alphabets |
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Methods in de.jstacs.data.alphabets that throw WrongAlphabetException | |
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int |
DiscreteAlphabet.getCode(String symbol)
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Uses of WrongAlphabetException in de.jstacs.data.bioJava |
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Methods in de.jstacs.data.bioJava that throw WrongAlphabetException | |
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static SequenceIterator |
BioJavaAdapter.sampleToSequenceIterator(Sample sample,
boolean flat)
Creates a SequenceIterator from sample preserving
as much annotation as possible. |
Uses of WrongAlphabetException in de.jstacs.data.sequences |
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Constructors in de.jstacs.data.sequences that throw WrongAlphabetException | |
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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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PermutedSequence(Sequence seq)
This constructor creates an instance by shuffling the symbols. |
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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 WrongAlphabetException in de.jstacs.models |
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Methods in de.jstacs.models that throw WrongAlphabetException | |
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double |
UniformModel.getProbFor(Sequence sequence,
int startpos,
int endpos)
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Constructors in de.jstacs.models that throw WrongAlphabetException | |
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CompositeModel(AlphabetContainer alphabets,
int[] assignment,
Model... models)
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Uses of WrongAlphabetException in de.jstacs.models.discrete |
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Methods in de.jstacs.models.discrete that throw WrongAlphabetException | |
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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. |
Uses of WrongAlphabetException in de.jstacs.models.discrete.inhomogeneous |
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Methods in de.jstacs.models.discrete.inhomogeneous that throw WrongAlphabetException | |
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SymmetricTensor |
StructureLearner.getTensor(Sample data,
double[] weights,
byte order,
StructureLearner.LearningType method)
This method can be used to compute a tensor that can be used to determine the optimal structure. |
Uses of WrongAlphabetException in de.jstacs.models.discrete.inhomogeneous.shared |
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Constructors in de.jstacs.models.discrete.inhomogeneous.shared that throw WrongAlphabetException | |
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SharedStructureMixture(FSDAGModel[] m,
StructureLearner.ModelType model,
byte order,
int starts,
boolean estimateComponentProbs,
double[] weights,
double alpha,
double epsilon)
This constructor is used from the other main constructors. |
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SharedStructureMixture(FSDAGModel[] m,
StructureLearner.ModelType model,
byte order,
int starts,
double[] weights,
double alpha,
double epsilon)
This main constructor creates an instance with fixed component weights. |
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SharedStructureMixture(FSDAGModel[] m,
StructureLearner.ModelType model,
byte order,
int starts,
double alpha,
double epsilon)
This main constructor creates an instance which estimates the component probabilities. |
Uses of WrongAlphabetException in de.jstacs.models.mixture |
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Constructors in de.jstacs.models.mixture that throw WrongAlphabetException | |
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AbstractMixtureModel(int length,
Model[] models,
boolean[] optimizeModel,
int dimension,
int starts,
boolean estimateComponentProbs,
double[] componentHyperParams,
double[] weights,
AbstractMixtureModel.Algorithm algorithm,
double alpha,
double eps,
AbstractMixtureModel.Parameterization parametrization,
int initialIteration,
int stationaryIteration,
BurnInTest burnInTest)
Creates a new AbstractMixtureModel. |
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MixtureModel(int length,
Model[] models,
double[] weights,
int starts,
double alpha,
double eps,
AbstractMixtureModel.Parameterization parametrization)
Creates an instance using EM and fixed component probabilities. |
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MixtureModel(int length,
Model[] models,
double[] weights,
int starts,
int initialIteration,
int stationaryIteration,
BurnInTest burnInTest)
Creates an instance using Gibbs Sampling and fixed component probabilities. |
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MixtureModel(int length,
Model[] models,
int starts,
boolean estimateComponentProbs,
double[] componentHyperParams,
double[] weights,
AbstractMixtureModel.Algorithm algorithm,
double alpha,
double eps,
AbstractMixtureModel.Parameterization parametrization,
int initialIteration,
int stationaryIteration,
BurnInTest burnInTest)
Creates a new MixtureModel. |
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MixtureModel(int length,
Model[] models,
int starts,
double[] componentHyperParams,
double alpha,
double eps,
AbstractMixtureModel.Parameterization parametrization)
Creates an instance using EM and estimating the component probabilities. |
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MixtureModel(int length,
Model[] models,
int starts,
double[] componentHyperParams,
int initialIteration,
int stationaryIteration,
BurnInTest burnInTest)
Creates an instance using Gibbs Sampling and sampling the component probabilities. |
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StrandModel(Model model,
int starts,
boolean estimateComponentProbs,
double[] componentHyperParams,
double forwardStrandProb,
AbstractMixtureModel.Algorithm algorithm,
double alpha,
double eps,
AbstractMixtureModel.Parameterization parametrization,
int initialIteration,
int stationaryIteration,
BurnInTest burnInTest)
Creates a new StrandModel. |
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StrandModel(Model model,
int starts,
double[] componentHyperParams,
double alpha,
double eps,
AbstractMixtureModel.Parameterization parametrization)
Creates an instance using EM and estimating the component probabilities. |
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StrandModel(Model model,
int starts,
double[] componentHyperParams,
int initialIteration,
int stationaryIteration,
BurnInTest burnInTest)
Creates an instance using Gibbs Sampling and sampling the component probabilities. |
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StrandModel(Model model,
int starts,
double forwardStrandProb,
double alpha,
double eps,
AbstractMixtureModel.Parameterization parametrization)
Creates an instance using EM and fixed component probabilities. |
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StrandModel(Model model,
int starts,
double forwardStrandProb,
int initialIteration,
int stationaryIteration,
BurnInTest burnInTest)
Creates an instance using Gibbs Sampling and fixed component probabilities. |
Uses of WrongAlphabetException in de.jstacs.models.utils |
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Methods in de.jstacs.models.utils that throw WrongAlphabetException | |
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Sequence |
ModelTester.SeqIterator.getSequence()
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