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

Packages that use WrongSequenceTypeException

de.jstacs.data	Provides classes for the representation of data.
de.jstacs.data.sequences	Provides classes for representing sequences.
de.jstacs.models.discrete.homogeneous

Uses of WrongSequenceTypeException in de.jstacs.data

Methods in de.jstacs.data that throw WrongSequenceTypeException

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.
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
Sequence	DinucleotideProperty.getPropertyAsSequence(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 Sequence.
static Sample	DinucleotideProperty.getSampleForProperty(Sample original, DinucleotideProperty... properties) Creates a new Sample by converting each Sequence in original to the DinucleotidePropertys properties and setting these as ReferenceSequenceAnnotation of each original sequence.
static Sample	DinucleotideProperty.getSampleForProperty(Sample original, DinucleotideProperty.Smoothing smoothing, boolean addToAnnotation, DinucleotideProperty... properties) Creates a new Sample by converting each Sequence in original to the DinucleotidePropertys properties and adding or setting these as ReferenceSequenceAnnotation of each original sequence.
static Sample	DinucleotideProperty.getSampleForProperty(Sample original, DinucleotideProperty.Smoothing smoothing, boolean originalAsAnnotation, DinucleotideProperty property) Creates a new Sample by converting each Sequence in original to the DinucleotideProperty property using the DinucleotideProperty.Smoothing smoothing.
static Sample	DinucleotideProperty.getSampleForProperty(Sample original, DinucleotideProperty property) Creates a new Sample by converting each Sequence in original to the DinucleotideProperty property.

Uses of WrongSequenceTypeException in de.jstacs.data.sequences

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

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 WrongSequenceTypeException

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.models.discrete.homogeneous

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

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)