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## 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 `Sequence`s, of the `Sample` in two distinct parts.
`static Sample` | `Sample.union(Sample[] s, boolean[] in, int subsequenceLength)` This method unites all `Sample`s 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 `Sample`s 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 `Sample`s 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 `SimpleDiscreteSequence`s.

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)`

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