Uses of Class
de.jstacs.data.sequences.WrongSequenceTypeException

Packages that use WrongSequenceTypeException

Package	Description
de.jstacs.clustering.distances
de.jstacs.data	Provides classes for the representation of data. The base classes to represent data are Alphabet and AlphabetContainer for representing alphabets, Sequence and its sub-classes to represent continuous and discrete sequences, and DataSet to represent data sets comprising a set of sequences.
de.jstacs.data.sequences	Provides classes for representing sequences. The implementations of sequences currently include DiscreteSequences prepared for alphabets of different sizes, and ArbitrarySequences that may contain continuous values as well. As sub-package provides the facilities to annotate Sequences.
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous

Uses of WrongSequenceTypeException in de.jstacs.clustering.distances

Methods in de.jstacs.clustering.distances that throw WrongSequenceTypeException

Modifier and Type	Method and Description
static CyclicSequenceAdaptor[]	RandomSequenceScoreDistance.createSequences(DiscreteAlphabet alphabet, int n) Creates a new random sequence of the given length and alphabet.

Constructors in de.jstacs.clustering.distances that throw WrongSequenceTypeException

Constructor and Description
RandomSequenceScoreDistance(DiscreteAlphabet alphabet, int n, boolean exp) Creates a distance using a random sequence of length .
SequenceScoreDistance(DiscreteAlphabet alphabet, int n, boolean exp) Creates a new distance.

Uses of WrongSequenceTypeException in de.jstacs.data

Methods in de.jstacs.data that throw WrongSequenceTypeException

Modifier and Type	Method and Description
static CyclicSequenceAdaptor[]	DeBruijnSequenceGenerator.generate(DiscreteAlphabet alphabet, int n) Generates a De Bruijn sequence of length , where A denotes the alphabet.
static CyclicSequenceAdaptor[]	DeBruijnGraphSequenceGenerator.generate(DiscreteAlphabet alphabet, int n) Generates a De Bruijn sequence of length , where A denotes the alphabet.
static CyclicSequenceAdaptor	DeBruijnSequenceGenerator.generate(DiscreteAlphabet alphabet, int n, int alphabetShift) Generates a De Bruijn sequence using the supplied alphabet and the given alphabet shift, i.e., for a cyclic shift of the symbols of the alphabet.
static DataSet	DinucleotideProperty.getDataSetForProperty(DataSet original, DinucleotideProperty... properties) Creates a new DataSet by converting each Sequence in original to the DinucleotidePropertys properties and setting these as ReferenceSequenceAnnotation of each original sequence.
static DataSet	DinucleotideProperty.getDataSetForProperty(DataSet original, DinucleotideProperty.Smoothing smoothing, boolean addToAnnotation, DinucleotideProperty... properties) Creates a new DataSet by converting each Sequence in original to the DinucleotidePropertys properties and adding or setting these as ReferenceSequenceAnnotation of each original sequence.
static DataSet	DinucleotideProperty.getDataSetForProperty(DataSet original, DinucleotideProperty.Smoothing smoothing, boolean originalAsAnnotation, DinucleotideProperty property) Creates a new DataSet by converting each Sequence in original to the DinucleotideProperty property using the DinucleotideProperty.Smoothing smoothing.
static DataSet	DinucleotideProperty.getDataSetForProperty(DataSet original, DinucleotideProperty property) Creates a new DataSet by converting each Sequence in original to the DinucleotideProperty property.
double[]	DinucleotideProperty.getProperty(Sequence original) Computes this dinucleotide property for all overlapping twomers in original and returns the result as a double array of length original.getLength()-1
double[]	DinucleotideProperty.getProperty(Sequence original, DinucleotideProperty.Smoothing smoothing) Computes this dinucleotide property for all overlapping twomers in original, smoothes the result using smoothing, and returns the smoothed property as a double array.
ArbitrarySequence	DinucleotideProperty.getPropertyAsSequence(Sequence original) Computes this dinucleotide property for all overlapping dimers in original and returns the result as a Sequence of length original.getLength()-1
ArbitrarySequence	DinucleotideProperty.getPropertyAsSequence(Sequence original, DinucleotideProperty.Smoothing smoothing) Computes this dinucleotide property for all overlapping dimers in original, smoothes the result using smoothing, and returns the smoothed property as a Sequence.

Uses of WrongSequenceTypeException in de.jstacs.data.sequences

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

Modifier and Type	Method and Description
static DataSet	SparseSequence.getDataSet(AlphabetContainer con, AbstractStringExtractor... se) This method allows to create a DataSet containing SparseSequences.
static DataSet	ArbitraryFloatSequence.getDataSet(AlphabetContainer con, AbstractStringExtractor... se) This method allows to create a DataSet containing ArbitraryFloatSequences.
static DataSet	SparseSequence.getDataSet(AlphabetContainer con, String filename) This method allows to create a DataSet containing SparseSequences using a file name.
static DataSet	ArbitraryFloatSequence.getDataSet(AlphabetContainer con, String filename) This method allows to create a DataSet containing ArbitraryFloatSequences using a file name.
static DataSet	SparseSequence.getDataSet(AlphabetContainer con, String filename, SequenceAnnotationParser parser) This method allows to create a DataSet containing SparseSequences using a file name.
static DataSet	ArbitraryFloatSequence.getDataSet(AlphabetContainer con, String filename, SequenceAnnotationParser parser) This method allows to create a DataSet containing ArbitraryFloatSequences using a file name.

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

Constructor and Description
ArbitraryFloatSequence(AlphabetContainer alphabetContainer, float[] content) Creates a new ArbitraryFloatSequence from an array of float-encoded alphabet symbols.
ArbitraryFloatSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim) Creates a new ArbitraryFloatSequence from a String representation using the delimiter delim.
ArbitraryFloatSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor) Creates a new ArbitraryFloatSequence from a SymbolExtractor.
ArbitraryFloatSequence(AlphabetContainer alphabetContainer, String sequence) Creates a new ArbitraryFloatSequence from a String representation using the default delimiter.
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.
ShortSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim) Creates a new ShortSequence from a String representation using the delimiter delim.
ShortSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor) Creates a new ShortSequence from a SymbolExtractor.
ShortSequence(AlphabetContainer alphabetContainer, short[] content) Creates a new ShortSequence from an array of short- encoded alphabet symbols.
ShortSequence(AlphabetContainer alphabetContainer, String sequence) Creates a new ShortSequence from a String representation using the default delimiter.
SparseSequence(AlphabetContainer alphCon, String seq) Creates a new SparseSequence from a String representation.
SparseSequence(AlphabetContainer alphCon, SymbolExtractor se) Creates a new SparseSequence from a SymbolExtractor.

Uses of WrongSequenceTypeException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous that throw WrongSequenceTypeException

Modifier and Type	Method and Description
DataSet	HomogeneousTrainSM.emitDataSet(int no, int... length) Creates a DataSet of a given number of Sequences from a trained homogeneous model.
protected abstract Sequence	HomogeneousTrainSM.getRandomSequence(Random r, int length) This method creates a random Sequence from a trained homogeneous model.
protected Sequence	HomogeneousMM.getRandomSequence(Random r, int length)