Uses of Class
de.jstacs.data.WrongLengthException

Packages that use WrongLengthException

Package	Description
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.motifDiscovery	This package provides the framework including the interface for any de novo motif discoverer.
de.jstacs.sequenceScores.differentiable
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models	The package provides different implementations of hidden Markov models based on AbstractHMM.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states	The package provides all interfaces and classes for states used in hidden Markov models.

Uses of WrongLengthException in de.jstacs.data

Methods in de.jstacs.data that throw WrongLengthException

Modifier and Type	Method and Description
int	DataSet.getNumberOfElementsWithLength(int len) Returns the number of overlapping elements that can be extracted.
double	DataSet.getNumberOfElementsWithLength(int len, double[] weights) Returns the weighted number of overlapping elements that can be extracted.
Pair<DataSet,double[]>	DataSet.resize(double[] weights, int subsequenceLength) Returns modified version of this data set with adjusted subsequence length.
static Pair<DataSet,double[]>	DataSet.union(DataSet[] s, double[][] weights, boolean[] in) This method unites all DataSets of the array s regarding the array in and sets the element length in the united DataSet to subsequenceLength.

Constructors in de.jstacs.data that throw WrongLengthException

Constructor and Description
DataSet.WeightedDataSetFactory(DataSet.WeightedDataSetFactory.SortOperation sort, DataSet... data) Creates a new DataSet.WeightedDataSetFactory on the given DataSet(s) with DataSet.WeightedDataSetFactory.SortOperation sort.
DataSet.WeightedDataSetFactory(DataSet.WeightedDataSetFactory.SortOperation sort, DataSet[] data, double[][] weights, int length) Creates a new DataSet.WeightedDataSetFactory on the given array of DataSets and an array of weights with a given length and DataSet.WeightedDataSetFactory.SortOperation sort.
DataSet.WeightedDataSetFactory(DataSet.WeightedDataSetFactory.SortOperation sort, DataSet data, double[] weights) Creates a new DataSet.WeightedDataSetFactory on the given DataSet and an array of weights with DataSet.WeightedDataSetFactory.SortOperation sort.
DataSet.WeightedDataSetFactory(DataSet.WeightedDataSetFactory.SortOperation sort, DataSet data, double[] weights, int length) Creates a new DataSet.WeightedDataSetFactory on the given DataSet and an array of weights with a given length and DataSet.WeightedDataSetFactory.SortOperation sort.
DataSet(AlphabetContainer abc, AbstractStringExtractor se) Creates a new DataSet from a StringExtractor using the given AlphabetContainer.
DataSet(AlphabetContainer abc, AbstractStringExtractor se, int subsequenceLength) Creates a new DataSet from a StringExtractor using the given AlphabetContainer and all overlapping windows of length subsequenceLength.
DataSet(AlphabetContainer abc, AbstractStringExtractor se, String delim) Creates a new DataSet from a StringExtractor using the given AlphabetContainer and a delimiter delim.
DataSet(AlphabetContainer abc, AbstractStringExtractor se, String delim, int subsequenceLength) Creates a new DataSet from a StringExtractor using the given AlphabetContainer, the given delimiter delim and all overlapping windows of length subsequenceLength.
DataSet(AlphabetContainer abc, AbstractStringExtractor se, String delim, int subsequenceLength, double percentage) Creates a new DataSet from a StringExtractor using the given AlphabetContainer, the given delimiter delim and all overlapping windows of length subsequenceLength.
DataSet(DataSet s, int subsequenceLength) Creates a new DataSet from a given DataSet and a given length subsequenceLength. This constructor enables you to use subsequences of the elements of a DataSet.
DNADataSet(String fName) Creates a new data set of DNA sequence from a FASTA file with file name fName.
DNADataSet(String fName, char ignore) Creates a new data set of DNA sequence from a file with file name fName.
DNADataSet(String fName, char ignore, SequenceAnnotationParser parser) Creates a new data set of DNA sequence from a file with file name fName using the given parser.

Uses of WrongLengthException in de.jstacs.data.sequences

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

Modifier and Type	Method and Description
protected abstract MultiDimensionalSequence<T>	MultiDimensionalSequence.getInstance(SequenceAnnotation[] seqAn, Sequence... seqs)
protected MultiDimensionalDiscreteSequence	MultiDimensionalDiscreteSequence.getInstance(SequenceAnnotation[] seqAn, Sequence... seqs)
protected MultiDimensionalArbitrarySequence	MultiDimensionalArbitrarySequence.getInstance(SequenceAnnotation[] seqAn, Sequence... seqs)

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

Constructor and Description
MultiDimensionalArbitrarySequence(SequenceAnnotation[] seqAn, ArbitrarySequence... sequence) This constructor creates an MultiDimensionalDiscreteSequence from a set of individual Sequences.
MultiDimensionalDiscreteSequence(SequenceAnnotation[] seqAn, SimpleDiscreteSequence... sequence) This constructor creates an MultiDimensionalDiscreteSequence from a set of individual Sequences.
MultiDimensionalSequence(SequenceAnnotation[] seqAn, Sequence... sequence) This constructor creates an MultiDimensionalSequence from a set of individual Sequences.

Uses of WrongLengthException in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery that throw WrongLengthException

Modifier and Type	Method and Description
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.sequenceScores.differentiable

Methods in de.jstacs.sequenceScores.differentiable that throw WrongLengthException

Modifier and Type	Method and Description
double	AbstractDifferentiableSequenceScore.getLogScoreAndPartialDerivation(Sequence seq, int startpos, int endpos, IntList indices, DoubleList partialDer)
double	AbstractDifferentiableSequenceScore.getLogScoreFor(Sequence seq, int startpos, int endpos)

Uses of WrongLengthException in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif that throw WrongLengthException

Modifier and Type	Method and Description
double[]	ExtendedZOOPSDiffSM.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile dist)

Uses of WrongLengthException in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models that throw WrongLengthException

Modifier and Type	Method and Description
protected void	HigherOrderHMM.fillFwdMatrix(int startPos, int endPos, Sequence seq)

Uses of WrongLengthException in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states that throw WrongLengthException

Modifier and Type	Method and Description
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	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.
double	SimpleState.getLogScoreFor(int startPos, int endPos, Sequence seq)