Uses of Class
de.jstacs.WrongAlphabetException

Packages that use WrongAlphabetException

de.jstacs.classifier.assessment	This package allows to assess classifiers.
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.homogeneous
de.jstacs.models.discrete.inhomogeneous	This package contains various inhomogeneous models.
de.jstacs.models.discrete.inhomogeneous.shared
de.jstacs.models.hmm	The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.models.hmm.models	The package provides different implementations of hidden Markov models based on AbstractHMM
de.jstacs.models.mixture	This package is the super package for any mixture model.
de.jstacs.models.mixture.motif
de.jstacs.motifDiscovery	This package provides the framework including the interface for any de novo motif discoverer
de.jstacs.scoringFunctions	Provides ScoringFunctions that can be used in a ScoreClassifier.
de.jstacs.scoringFunctions.mix	Provides ScoringFunctions that are mixtures of other ScoringFunctions.
de.jstacs.scoringFunctions.mix.motifSearch

Uses of WrongAlphabetException in de.jstacs.classifier.assessment

Methods in de.jstacs.classifier.assessment that throw WrongAlphabetException

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) Assesses the contained classifiers.
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

ClassifierAssessment(AbstractClassifier... aCs)
Creates a new ClassifierAssessment from a set of AbstractClassifiers.

ClassifierAssessment(AbstractClassifier[] aCs, boolean buildClassifiersByCrossProduct, Model[]... aMs)
This constructor allows to assess a collection of given AbstractClassifiers and, in addition, classifiers that will be constructed using the given AbstractModels.

ClassifierAssessment(AbstractClassifier[] aCs, Model[][] aMs, boolean buildClassifiersByCrossProduct, boolean checkAlphabetConsistencyAndLength)
Creates a new ClassifierAssessment from an array of AbstractClassifiers and a two-dimensional array of Model s, which are combined to additional classifiers.

ClassifierAssessment(boolean buildClassifiersByCrossProduct, Model[]... aMs)
Creates a new ClassifierAssessment from a set of Models.

KFoldCrossValidation(AbstractClassifier... aCs)
Creates a new KFoldCrossValidation from a set of AbstractClassifiers.

KFoldCrossValidation(AbstractClassifier[] aCs, boolean buildClassifiersByCrossProduct, Model[]... aMs)
This constructor allows to assess a collection of given AbstractClassifiers and those constructed using the given AbstractModels by a KFoldCrossValidation .

KFoldCrossValidation(AbstractClassifier[] aCs, Model[][] aMs, boolean buildClassifiersByCrossProduct, boolean checkAlphabetConsistencyAndLength)
Creates a new KFoldCrossValidation from an array of AbstractClassifiers and a two-dimensional array of Model s, which are combined to additional classifiers.

KFoldCrossValidation(boolean buildClassifiersByCrossProduct, Model[]... aMs)
Creates a new KFoldCrossValidation from a set of Models.

RepeatedHoldOutExperiment(AbstractClassifier... aCs)
Creates a new RepeatedHoldOutExperiment from a set of AbstractClassifiers.

RepeatedHoldOutExperiment(AbstractClassifier[] aCs, boolean buildClassifiersByCrossProduct, Model[]... aMs)
This constructor allows to assess a collection of given AbstractClassifiers and those constructed using the given AbstractModels by a RepeatedHoldOutExperiment.

RepeatedHoldOutExperiment(AbstractClassifier[] aCs, Model[][] aMs, boolean buildClassifiersByCrossProduct, boolean checkAlphabetConsistencyAndLength)
Creates a new RepeatedHoldOutExperiment from an array of AbstractClassifiers and a two-dimensional array of Model s, which are combined to additional classifiers.

RepeatedHoldOutExperiment(boolean buildClassifiersByCrossProduct, Model[]... aMs)
Creates a new RepeatedHoldOutExperiment from a set of Models.

RepeatedSubSamplingExperiment(AbstractClassifier... aCs)
Creates a new RepeatedSubSamplingExperiment from a set of AbstractClassifiers.

RepeatedSubSamplingExperiment(AbstractClassifier[] aCs, boolean buildClassifiersByCrossProduct, Model[]... aMs)
This constructor allows to assess a collection of given AbstractClassifiers and those constructed using the given AbstractModels by a RepeatedSubSamplingExperiment.

RepeatedSubSamplingExperiment(AbstractClassifier[] aCs, Model[][] aMs, boolean buildClassifiersByCrossProduct, boolean checkAlphabetConsistencyAndLength)
Creates a new RepeatedSubSamplingExperiment from an array of AbstractClassifiers and a two-dimensional array of Model s, which are combined to additional classifiers.

RepeatedSubSamplingExperiment(boolean buildClassifiersByCrossProduct, Model[]... aMs)
Creates a new RepeatedSubSamplingExperiment from a set of Models.

Sampled_RepeatedHoldOutExperiment(AbstractClassifier... aCs)
Creates a new Sampled_RepeatedHoldOutExperiment from a set of AbstractClassifiers.

Sampled_RepeatedHoldOutExperiment(AbstractClassifier[] aCs, boolean buildClassifiersByCrossProduct, Model[]... aMs)
This constructor allows to assess a collection of given AbstractClassifiers and those constructed using the given AbstractModels by a Sampled_RepeatedHoldOutExperiment.

Sampled_RepeatedHoldOutExperiment(AbstractClassifier[] aCs, Model[][] aMs, boolean buildClassifiersByCrossProduct, boolean checkAlphabetConsistencyAndLength)
Creates a new Sampled_RepeatedHoldOutExperiment from an array of AbstractClassifiers and a two-dimensional array of Model s, which are combined to additional classifiers.

Sampled_RepeatedHoldOutExperiment(boolean buildClassifiersByCrossProduct, Model[]... aMs)
Creates a new Sampled_RepeatedHoldOutExperiment from a set of Models.

Uses of WrongAlphabetException in de.jstacs.data

Methods in de.jstacs.data that throw WrongAlphabetException

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.
static Sample	Sample.diff(Sample data, Sample... samples) This method computes the difference between the Sample data and the Samples samples.
double	AlphabetContainer.getCode(int pos, String sym) Returns the encoded symbol for sym of the Alphabet of position pos of this AlphabetContainer.
int	Sequence.getHammingDistance(Sequence seq) This method returns the Hamming distance between the current Sequence and seq.
Sequence	DinucleotideProperty.getPropertyAsSequence(Sequence original) Computes this dinucleotide property for all overlapping twomers in original and returns the result as a Sequence of length original.getLength()-1
boolean	Sequence.matches(int maxHammingDistance, Sequence shortSequence) This method allows to answer the question whether there is a similar pattern find a match with a given maximal number of mismatches.

Constructors in de.jstacs.data that throw WrongAlphabetException

DNASample(String fName)
Creates a new sample of DNA sequence from a FASTA file with file name fName.

DNASample(String fName, char ignore)
Creates a new sample of DNA sequence from a file with file name fName.

DNASample(String fName, char ignore, SequenceAnnotationParser parser)
Creates a new sample of DNA sequence from a file with file name fName using the given parser.

Sample.WeightedSampleFactory(Sample.WeightedSampleFactory.SortOperation sort, Sample... data)
Creates a new Sample.WeightedSampleFactory on the given Sample(s) with Sample.WeightedSampleFactory.SortOperation sort.

Sample.WeightedSampleFactory(Sample.WeightedSampleFactory.SortOperation sort, Sample[] data, double[][] weights, int length)
Creates a new Sample.WeightedSampleFactory on the given array of Samples and an array of weights with a given length and Sample.WeightedSampleFactory.SortOperation sort.

Sample.WeightedSampleFactory(Sample.WeightedSampleFactory.SortOperation sort, Sample data, double[] weights)
Creates a new Sample.WeightedSampleFactory on the given Sample and an array of weights with Sample.WeightedSampleFactory.SortOperation sort.

Sample.WeightedSampleFactory(Sample.WeightedSampleFactory.SortOperation sort, Sample data, double[] weights, int length)
Creates a new Sample.WeightedSampleFactory on the given Sample and an array of weights with a given length and Sample.WeightedSampleFactory.SortOperation sort.

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.

Sample(String annotation, Sequence... seqs)
Creates a new Sample from an array of Sequences and a given annotation.

Uses of WrongAlphabetException in de.jstacs.data.alphabets

Methods in de.jstacs.data.alphabets that throw WrongAlphabetException

int	DiscreteAlphabet.getCode(String symbol) Returns the code of a given symbol.

Uses of WrongAlphabetException in de.jstacs.data.bioJava

Methods in de.jstacs.data.bioJava that throw WrongAlphabetException

static SequenceIterator

BioJavaAdapter.sampleToSequenceIterator(Sample sample, boolean flat) Creates a SequenceIterator from the Sample sample preserving as much annotation as possible.

Uses of WrongAlphabetException in de.jstacs.data.sequences

Methods in de.jstacs.data.sequences that throw WrongAlphabetException

static Sample

SparseSequence.getSample(AlphabetContainer con, AbstractStringExtractor... se) This method allows to create a Sample containing SparseSequences.

Constructors in de.jstacs.data.sequences that throw WrongAlphabetException

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.

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.

MappedDiscreteSequence(SimpleDiscreteSequence original, DiscreteAlphabetMapping... transformation)
This method allows to create a MappedDiscreteSequence from a given Sequence and some given DiscreteAlphabetMappings.

PermutedSequence(Sequence<T> seq)
Creates a new PermutedSequence by shuffling the symbols of a given Sequence.

PermutedSequence(Sequence<T> seq, int[] permutation)
Creates a new PermutedSequence for a given permutation

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 WrongAlphabetException in de.jstacs.models

Methods in de.jstacs.models that throw WrongAlphabetException

double

UniformModel.getProbFor(Sequence sequence, int startpos, int endpos)

Constructors in de.jstacs.models that throw WrongAlphabetException

CompositeModel(AlphabetContainer alphabets, int[] assignment, Model... models)
Creates a new CompositeModel.

Uses of WrongAlphabetException in de.jstacs.models.discrete

Methods in de.jstacs.models.discrete that throw WrongAlphabetException

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.

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

Methods in de.jstacs.models.discrete.homogeneous that throw WrongAlphabetException

Sample	HomogeneousModel.emitSample(int no, int... length) Creates a Sample of a given number of Sequences from a trained homogeneous model.
protected abstract Sequence	HomogeneousModel.getRandomSequence(Random r, int length) This method creates a random Sequence from a trained homogeneous model.
protected Sequence	HomogeneousMM.getRandomSequence(Random r, int length)

Uses of WrongAlphabetException in de.jstacs.models.discrete.inhomogeneous

Methods in de.jstacs.models.discrete.inhomogeneous that throw WrongAlphabetException

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

Constructors in de.jstacs.models.discrete.inhomogeneous.shared that throw WrongAlphabetException

SharedStructureMixture(FSDAGModel[] m, StructureLearner.ModelType model, byte order, int starts, boolean estimateComponentProbs, double[] weights, double alpha, TerminationCondition tc)
Creates a new SharedStructureMixture instance with all relevant values.

SharedStructureMixture(FSDAGModel[] m, StructureLearner.ModelType model, byte order, int starts, double[] weights, double alpha, TerminationCondition tc)
Creates a new SharedStructureMixture instance with fixed component weights.

SharedStructureMixture(FSDAGModel[] m, StructureLearner.ModelType model, byte order, int starts, double alpha, TerminationCondition tc)
Creates a new SharedStructureMixture instance which estimates the component probabilities/weights.

Uses of WrongAlphabetException in de.jstacs.models.hmm

Constructors in de.jstacs.models.hmm that throw WrongAlphabetException

AbstractHMM(HMMTrainingParameterSet trainingParameterSet, String[] name, int[] emissionIdx, boolean[] forward, Emission[] emission)
This is the main constructor for an HMM.

Uses of WrongAlphabetException in de.jstacs.models.hmm.models

Constructors in de.jstacs.models.hmm.models that throw WrongAlphabetException

SamplingPhyloHMM(SamplingHMMTrainingParameterSet trainingParameterSet, String[] name, int[] emissionIdx, boolean[] forward, PhyloDiscreteEmission[] emission, TransitionElement... te)
This is the main constructor for a hidden markov model with phylogenetic emission(s) This model can be trained using a metropolis hastings algorithm

Uses of WrongAlphabetException in de.jstacs.models.mixture

Constructors in de.jstacs.models.mixture that throw WrongAlphabetException

AbstractMixtureModel(int length, Model[] models, boolean[] optimizeModel, int dimension, int starts, boolean estimateComponentProbs, double[] componentHyperParams, double[] weights, AbstractMixtureModel.Algorithm algorithm, double alpha, TerminationCondition tc, AbstractMixtureModel.Parameterization parametrization, int initialIteration, int stationaryIteration, BurnInTest burnInTest)
Creates a new AbstractMixtureModel.

MixtureModel(int length, Model[] models, double[] weights, int starts, double alpha, TerminationCondition tc, AbstractMixtureModel.Parameterization parametrization)
Creates an instance using EM and fixed component probabilities.

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.

MixtureModel(int length, Model[] models, int starts, boolean estimateComponentProbs, double[] componentHyperParams, double[] weights, AbstractMixtureModel.Algorithm algorithm, double alpha, TerminationCondition tc, AbstractMixtureModel.Parameterization parametrization, int initialIteration, int stationaryIteration, BurnInTest burnInTest)
Creates a new MixtureModel.

MixtureModel(int length, Model[] models, int starts, double[] componentHyperParams, double alpha, TerminationCondition tc, AbstractMixtureModel.Parameterization parametrization)
Creates an instance using EM and estimating the component probabilities.

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.

StrandModel(Model model, int starts, boolean estimateComponentProbs, double[] componentHyperParams, double forwardStrandProb, AbstractMixtureModel.Algorithm algorithm, double alpha, TerminationCondition tc, AbstractMixtureModel.Parameterization parametrization, int initialIteration, int stationaryIteration, BurnInTest burnInTest)
Creates a new StrandModel.

StrandModel(Model model, int starts, double[] componentHyperParams, double alpha, TerminationCondition tc, AbstractMixtureModel.Parameterization parametrization)
Creates an instance using EM and estimating the component probabilities.

StrandModel(Model model, int starts, double[] componentHyperParams, int initialIteration, int stationaryIteration, BurnInTest burnInTest)
Creates an instance using Gibbs Sampling and sampling the component probabilities.

StrandModel(Model model, int starts, double forwardStrandProb, double alpha, TerminationCondition tc, AbstractMixtureModel.Parameterization parametrization)
Creates an instance using EM and fixed component probabilities.

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.mixture.motif

Constructors in de.jstacs.models.mixture.motif that throw WrongAlphabetException

HiddenMotifMixture(Model[] models, boolean[] optimzeArray, int components, int starts, boolean estimateComponentProbs, double[] componentHyperParams, double[] weights, PositionPrior posPrior, AbstractMixtureModel.Algorithm algorithm, double alpha, TerminationCondition tc, AbstractMixtureModel.Parameterization parametrization, int initialIteration, int stationaryIteration, BurnInTest burnInTest)
Creates a new HiddenMotifMixture.

SingleHiddenMotifMixture(Model motif, Model bg, boolean trainOnlyMotifModel, int starts, double[] componentHyperParams, double[] weights, PositionPrior posPrior, AbstractMixtureModel.Algorithm algorithm, double alpha, TerminationCondition tc, AbstractMixtureModel.Parameterization parametrization, int initialIteration, int stationaryIteration, BurnInTest burnInTest)
Creates a new SingleHiddenMotifMixture.

SingleHiddenMotifMixture(Model motif, Model bg, boolean trainOnlyMotifModel, int starts, double[] componentHyperParams, PositionPrior posPrior, double alpha, TerminationCondition tc, AbstractMixtureModel.Parameterization parametrization)
Creates a new SingleHiddenMotifMixture using EM and estimating the probability for finding a motif.

SingleHiddenMotifMixture(Model motif, Model bg, boolean trainOnlyMotifModel, int starts, double motifProb, PositionPrior posPrior, double alpha, TerminationCondition tc, AbstractMixtureModel.Parameterization parametrization)
Creates a new SingleHiddenMotifMixture using EM and fixed probability for finding a motif.

Uses of WrongAlphabetException in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery that throw WrongAlphabetException

static Pair<Sequence,BitSet[]>[]	KMereStatistic.getKmereSequenceStatistic(boolean bothStrands, int maxMismatch, HashSet<Sequence> filter, Sample... data) This method enables the user to get a statistic for a set of k-mers.
static Hashtable<Sequence,BitSet[]>	KMereStatistic.getKmereSequenceStatistic(int k, boolean bothStrands, int addIndex, Sample... data) This method enables the user to get a statistic over all k-mers in the sequences.
static Hashtable<Sequence,BitSet[]>	KMereStatistic.merge(Hashtable<Sequence,BitSet[]> statistic, int maximalMissmatch, boolean bothStrands) This method allows to merge the statistics of k-mers by allowing mismatches.

Uses of WrongAlphabetException in de.jstacs.scoringFunctions

Constructors in de.jstacs.scoringFunctions that throw WrongAlphabetException

IndependentProductScoringFunction(double ess, boolean plugIn, NormalizableScoringFunction... functions)
This constructor creates an instance of an IndependentProductScoringFunction from a given series of independent NormalizableScoringFunctions.

IndependentProductScoringFunction(double ess, boolean plugIn, NormalizableScoringFunction[] functions, int[] length)
This constructor creates an instance of an IndependentProductScoringFunction from given series of independent NormalizableScoringFunctions and lengths.

IndependentProductScoringFunction(double ess, boolean plugIn, NormalizableScoringFunction[] functions, int[] index, int[] length, boolean[] reverse)
This is the main constructor.

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

Uses of WrongAlphabetException in de.jstacs.scoringFunctions.mix

Constructors in de.jstacs.scoringFunctions.mix that throw WrongAlphabetException

StrandScoringFunction(NormalizableScoringFunction function, double forwardPartOfESS, int starts, boolean plugIn, StrandScoringFunction.InitMethod initMethod)
This constructor creates a StrandScoringFunction that optimizes the usage of each strand.

StrandScoringFunction(NormalizableScoringFunction function, int starts, boolean plugIn, StrandScoringFunction.InitMethod initMethod, double forward)
This constructor creates a StrandScoringFunction that has a fixed frequency for the strand usage.

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

Constructors in de.jstacs.scoringFunctions.mix.motifSearch that throw WrongAlphabetException

MixtureDuration(int starts, DurationScoringFunction... function)
The main constructor of a MixtureDuration.