Uses of Class
de.jstacs.data.WrongLengthException

Packages that use WrongLengthException

de.jstacs.data	Provides classes for the representation of data.
de.jstacs.data.sequences	Provides classes for representing sequences.
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.hmm.states	The package provides all interfaces and classes for states used in hidden Markov models.
de.jstacs.motifDiscovery	This package provides the framework including the interface for any de novo motif discoverer
de.jstacs.scoringFunctions.mix.motifSearch

Uses of WrongLengthException in de.jstacs.data

Methods in de.jstacs.data that throw WrongLengthException

int	Sample.getNumberOfElementsWithLength(int len) Returns the number of overlapping elements that can be extracted.
double	Sample.getNumberOfElementsWithLength(int len, double[] weights) Returns the weighted number of overlapping elements that can be extracted.
Sample[]	Sample.partition(double p, Sample.PartitionMethod method, int subsequenceLength) This method partitions the elements, i.e. the Sequences, of the Sample in two distinct parts.
static Sample	Sample.union(Sample[] s, boolean[] in, int subsequenceLength) This method unites all Samples of the array s regarding the array in and sets the element length in the united Sample to subsequenceLength.
static Sample	Sample.union(Sample[] s, int subsequenceLength) This method unites all Samples of the array s and sets the element length in the united sample to subsequenceLength.

Constructors in de.jstacs.data that throw WrongLengthException

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(Sample s, int subsequenceLength)
Creates a new Sample from a given Sample and a given length subsequenceLength.

Uses of WrongLengthException in de.jstacs.data.sequences

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

MultiDimensionalDiscreteSequence(SequenceAnnotation[] seqAnnotations, SimpleDiscreteSequence... sequence)
This constructor creates an MultiDimensionalDiscreteSequence from a set of individual SimpleDiscreteSequences.

Uses of WrongLengthException in de.jstacs.models.hmm

Methods in de.jstacs.models.hmm that throw WrongLengthException

double

State.getLogScoreFor(int startPos, int endPos, Sequence seq) This method returns the logarithm of the score for a given sequence with given start and end position.

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

Methods in de.jstacs.models.hmm.models that throw WrongLengthException

protected void

HigherOrderHMM.fillFwdMatrix(int startPos, int endPos, Sequence seq)

Uses of WrongLengthException in de.jstacs.models.hmm.states

Methods in de.jstacs.models.hmm.states that throw WrongLengthException

double	SimpleDifferentiableState.getLogScoreAndPartialDerivation(int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq)
double	DifferentiableState.getLogScoreAndPartialDerivation(int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq) This method allows to compute the logarithm of the score and the gradient for the given subsequences.
double	SimpleState.getLogScoreFor(int startPos, int endPos, Sequence seq)

Uses of WrongLengthException in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery that throw WrongLengthException

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 WrongLengthException in de.jstacs.scoringFunctions.mix.motifSearch

Methods in de.jstacs.scoringFunctions.mix.motifSearch that throw WrongLengthException

double[]

HiddenMotifsMixture.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile dist)