Uses of Class
de.jstacs.data.Sequence

Packages that use Sequence

de.jstacs.algorithms	Provides classes for algorithms on graphs.
de.jstacs.classifier	This package provides the framework for any classifier.
de.jstacs.classifier.modelBased	Provides the classes for Classifiers that are based on Models
de.jstacs.classifier.scoringFunctionBased	Provides the classes for Classifiers that are based on ScoringFunctions.
de.jstacs.data	Provides classes for the representation of data.
de.jstacs.data.sequences	Provides classes for representing sequences.
de.jstacs.models	Provides the interface Model and its abstract implementation AbstractModel, which is the super class of all other models.
de.jstacs.models.discrete
de.jstacs.models.discrete.homogeneous
de.jstacs.models.discrete.inhomogeneous	This package contains various inhomogeneous models.
de.jstacs.models.mixture	This package is the super package for any mixture model.
de.jstacs.models.mixture.motif
de.jstacs.models.utils
de.jstacs.motifDiscovery	This package provides the framework including the interface for any de novo motif discoverer
de.jstacs.scoringFunctions	Provides ScoringFunctions that can be used in a ScoreClassifier.
de.jstacs.scoringFunctions.directedGraphicalModels	Provides ScoringFunctions that are equivalent to directed graphical models.
de.jstacs.scoringFunctions.homogeneous	Provides ScoringFunctions that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.scoringFunctions.mix	Provides ScoringFunctions that are mixtures of other ScoringFunctions.

Uses of Sequence in de.jstacs.algorithms

Methods in de.jstacs.algorithms with parameters of type Sequence

double	Alignment.SimpleCosts.getCostFor(Sequence s1, Sequence s2, int i, int j, Alignment.Costs.Direction from)
double	Alignment.Costs.getCostFor(Sequence s1, Sequence s2, int i, int j, Alignment.Costs.Direction from) Returns the costs for the alignment if s1(i) and s2(j) coming from from.

Constructors in de.jstacs.algorithms with parameters of type Sequence

Alignment(Sequence s1, Sequence s2, Alignment.Costs costs)
Creates a new Alignment.StringAlignment instance that aligns the sequences s1 and s2 using the costs defined in costs.

Uses of Sequence in de.jstacs.classifier

Methods in de.jstacs.classifier with parameters of type Sequence

protected void	AbstractScoreBasedClassifier.check(Sequence seq) This method checks if the given sequence can be used.
byte	AbstractScoreBasedClassifier.classify(Sequence seq)
abstract byte	AbstractClassifier.classify(Sequence seq) This method classifies a sequence and returns the index i, with 0 < i < getNumberOfClasses(), of the class to which the sequence is assigned.
protected byte	AbstractScoreBasedClassifier.classify(Sequence seq, boolean check) This method classifies a sequence.
double	AbstractScoreBasedClassifier.getPValue(Sequence candidate, Sample bg) Returns the p-value for a sequence candidate with respect to a given background sample.
double	AbstractScoreBasedClassifier.getScore(Sequence seq, int i) This method returns the score for a given sequence and a given class.
protected double	MappingClassifier.getScore(Sequence seq, int i, boolean check)
protected abstract double	AbstractScoreBasedClassifier.getScore(Sequence seq, int i, boolean check) This method returns the score for a given sequence and a given class.

Uses of Sequence in de.jstacs.classifier.modelBased

Methods in de.jstacs.classifier.modelBased with parameters of type Sequence

protected double

ModelBasedClassifier.getScore(Sequence seq, int i, boolean check)

Uses of Sequence in de.jstacs.classifier.scoringFunctionBased

Methods in de.jstacs.classifier.scoringFunctionBased with parameters of type Sequence

protected double

ScoreClassifier.getScore(Sequence seq, int i, boolean check)

Uses of Sequence in de.jstacs.data

Subclasses of Sequence in de.jstacs.data

protected static class	Sequence.CompositeSequence The class handles composite sequences.
protected static class	Sequence.SubSequence This class handles subsequences.

Fields in de.jstacs.data declared as Sequence

protected Sequence

Sequence.rc The pointer to the reverse complement

Methods in de.jstacs.data that return Sequence

Sequence	Sequence.annotate(boolean add, SequenceAnnotation... annotation) This method allows to append annotation to a sequence.
Sequence	Sequence.complement() This method returns a new instance of sequence containing the complementary current sequence.
Sequence	Sequence.complement(int start, int end) This method returns a new instance of sequence containing a part of the complementary current sequence.
static Sequence	Sequence.create(AlphabetContainer con, SequenceAnnotation[] annotation, String sequence, String delim) Creates a sequence from a string based on the given AlphabetContainer using the given delimiter.
static Sequence	Sequence.create(AlphabetContainer con, String sequence) Creates a sequence from a string based on the given AlphabetContainer using the standard delimiter for this AlphabetContainer.
static Sequence	Sequence.create(AlphabetContainer con, String sequence, String delim) Creates a sequence from a string based on the given AlphabetContainer using the given delimiter.
protected abstract Sequence	Sequence.flatCloneWithoutAnnotation() Works in analogy to Object.clone(), but does not clone the annotation.
protected Sequence	Sequence.CompositeSequence.flatCloneWithoutAnnotation()
protected Sequence	Sequence.SubSequence.flatCloneWithoutAnnotation()
Sequence[]	Sample.getAllElements() Returns an array of sequences containing all elements of this Sample.
Sequence	Sequence.getCompositeSequence(AlphabetContainer abc, int[] starts, int[] lengths) This constructor should be used if one wants to create a sample of composite sequences.
Sequence	Sequence.getCompositeSequence(int[] starts, int[] lengths) This is an very efficient way to create a composite sequence for sequences with a simple AlphabetContainer.
Sequence	Sample.getElementAt(int i) This method returns the element with index i.
Sequence	Sample.WeightedSampleFactory.getElementAt(int index) Returns the sequence with index index.
Sequence	Sequence.getSubSequence(AlphabetContainer abc, int start) This method should be used if one wants to create a sample of subsequences of defined length.
Sequence	Sequence.getSubSequence(AlphabetContainer abc, int start, int length) This method should be used if one wants to create a sample of subsequences of defined length.
Sequence	Sequence.getSubSequence(int start) This is an very efficient way to create a subsequence/suffix for sequences with a simple AlphabetContainer.
Sequence	Sequence.getSubSequence(int start, int length) This is an very efficient way to create a subsequence of defined length for sequences with a simple AlphabetContainer.
Sequence	Sample.ElementEnumerator.nextElement()
Sequence	DiscreteSequenceEnumerator.nextElement()
Sequence	Sequence.reverse() This method returns a new instance of sequence containing the reverse current sequence.
Sequence	Sequence.reverse(int start, int end) This method returns a new instance of sequence containing a part of the reverse current sequence.
Sequence	Sequence.reverseComplement() This method returns a new sequence instance containing the complementary current sequence.
Sequence	Sequence.reverseComplement(int start, int end) This method returns a new sequence instance containing a part of the complementary current sequence.
Sequence	Sequence.SubSequence.reverseComplement(int start, int end)

Methods in de.jstacs.data with parameters of type Sequence

int	Sequence.compareTo(Sequence s)

Constructors in de.jstacs.data with parameters of type Sequence

Sample(String annotation, Sequence... seqs)
This constructor is specially designed for the method Model.emitSample(int, int...).

Sequence.CompositeSequence(AlphabetContainer abc, Sequence seq, int[] starts, int[] lengths)
This constructor should be used if one wants to create a sample of composite sequences.

Sequence.CompositeSequence(Sequence seq, int[] starts, int[] lengths)
This is an very effient way to create a composite sequence for sequences with a simple AlphabetContainer.

Sequence.SubSequence(AlphabetContainer abc, Sequence seq, int start, int length)
This constructor should be used if one wants to create a sample of subsequences of defined length.

Sequence.SubSequence(Sequence seq, int start, int length)
This is an very efficient way to create a subsequence of defined length for sequences with a simple AlphabetContainer.

Uses of Sequence in de.jstacs.data.sequences

Subclasses of Sequence in de.jstacs.data.sequences

class	ArbitrarySequence The class for any continuous or hybrid sequence.
class	ByteSequence This class can be used for discrete AlphabetContainers with alphabets that use only few symbols.
class	DiscreteSequence The main class for any discrete sequence.
class	IntSequence This class can be used for discrete AlphabetContainer with alphabets that use a huge number of symbols.
class	PermutedSequence Class for a permuted sequence.
class	RecursiveSequence This is the main class for subsequences, composite sequences, ... .
class	ShortSequence This class can be used for discrete AlphabetContainers with alphabets that use many different symbols.
class	SparseSequence This class is an implementation for sequences on one alphabet with length 4.

Fields in de.jstacs.data.sequences declared as Sequence

protected Sequence

RecursiveSequence.content The internal sequence

Methods in de.jstacs.data.sequences that return Sequence

protected Sequence	SparseSequence.flatCloneWithoutAnnotation()
protected Sequence	ShortSequence.flatCloneWithoutAnnotation()
protected Sequence	PermutedSequence.flatCloneWithoutAnnotation()
protected Sequence	IntSequence.flatCloneWithoutAnnotation()
protected Sequence	ByteSequence.flatCloneWithoutAnnotation()
protected Sequence	ArbitrarySequence.flatCloneWithoutAnnotation()

Constructors in de.jstacs.data.sequences with parameters of type Sequence

PermutedSequence(Sequence seq)
This constructor creates an instance by shuffling the symbols.

RecursiveSequence(AlphabetContainer alphabet, Sequence seq)
This constructor creates a recursive sequence using the annotation of the given sequence.

RecursiveSequence(AlphabetContainer alphabet, SequenceAnnotation[] annotation, Sequence seq)
This constructor creates a recursive sequence.

Uses of Sequence in de.jstacs.models

Methods in de.jstacs.models with parameters of type Sequence

double	Model.getLogProbFor(Sequence sequence) Returns the logarithm of the probability of the given sequence given the model.
double	AbstractModel.getLogProbFor(Sequence sequence)
double	Model.getLogProbFor(Sequence sequence, int startpos) Returns the logarithm of the probability of the given sequence given the model.
double	AbstractModel.getLogProbFor(Sequence sequence, int startpos)
double	Model.getLogProbFor(Sequence sequence, int startpos, int endpos) Returns the logarithm of the probability of the given sequence given the model.
double	CompositeModel.getLogProbFor(Sequence sequence, int startpos, int endpos)
double	AbstractModel.getLogProbFor(Sequence sequence, int startpos, int endpos)
double	Model.getProbFor(Sequence sequence) Returns the probability of the given sequence given the model.
double	AbstractModel.getProbFor(Sequence sequence)
double	Model.getProbFor(Sequence sequence, int startpos) Returns the probability of the given sequence given the model.
double	AbstractModel.getProbFor(Sequence sequence, int startpos)
double	UniformModel.getProbFor(Sequence sequence, int startpos, int endpos)
double	Model.getProbFor(Sequence sequence, int startpos, int endpos) Returns the probability of the given sequence given the model.
double	CompositeModel.getProbFor(Sequence sequence, int startpos, int endpos)

Uses of Sequence in de.jstacs.models.discrete

Methods in de.jstacs.models.discrete with parameters of type Sequence

void	Constraint.add(Sequence seq, int start, double weight) This method determines the specific constraint that is fulfilled by the sequence and adds the weight to the specific counter.
protected void	DiscreteGraphicalModel.check(Sequence sequence, int startpos, int endpos) Checks some conditions on a sequence.
double	Constraint.getFreq(Sequence seq, int start) This method determines the specific constraint that is fullfilled by the sequence beginning at start.
abstract int	Constraint.satisfiesSpecificConstraint(Sequence seq, int start) This method returns the index of the specific constraint that is fullfilled by the sequence beginning at start.

Uses of Sequence in de.jstacs.models.discrete.homogeneous

Methods in de.jstacs.models.discrete.homogeneous that return Sequence

protected abstract Sequence	HomogeneousModel.getRandomSequence(Random r, int length) This method creates a sequence from a trained model.
protected Sequence	HomogeneousMM.getRandomSequence(Random r, int length)

Methods in de.jstacs.models.discrete.homogeneous with parameters of type Sequence

protected void	HomogeneousModel.check(Sequence sequence, int startpos, int endpos) Checks some constraints
double	HomogeneousModel.getLogProbFor(Sequence sequence, int startpos, int endpos)
double	HomogeneousModel.getProbFor(Sequence sequence, int startpos, int endpos)
protected abstract double	HomogeneousModel.logProbFor(Sequence sequence, int startpos, int endpos) This method computes the logarithm of the probability of the given sequence in the given interval.
protected double	HomogeneousMM.logProbFor(Sequence sequence, int startpos, int endpos)
protected abstract double	HomogeneousModel.probFor(Sequence sequence, int startpos, int endpos) This method computes the probability of the given sequence in the given interval.
protected double	HomogeneousMM.probFor(Sequence sequence, int startpos, int endpos)
int	HomogeneousModel.HomCondProb.satisfiesSpecificConstraint(Sequence seq, int start)

Uses of Sequence in de.jstacs.models.discrete.inhomogeneous

Methods in de.jstacs.models.discrete.inhomogeneous with parameters of type Sequence

protected void	InhomogeneousDGM.check(Sequence sequence, int startpos, int endpos)
double	InhCondProb.getLnFreq(Sequence s, int start) Returns the logarithmic frequency.
double	DAGModel.getLogProbFor(Sequence sequence, int startpos, int endpos)
double	DAGModel.getProbFor(Sequence sequence, int startpos, int endpos)
int	InhConstraint.satisfiesSpecificConstraint(Sequence s, int start)

Uses of Sequence in de.jstacs.models.mixture

Methods in de.jstacs.models.mixture that return Sequence

protected Sequence[]	StrandModel.emitSampleUsingCurrentParameterSet(int n, int... lengths)
protected Sequence[]	MixtureModel.emitSampleUsingCurrentParameterSet(int n, int... lengths)
protected abstract Sequence[]	AbstractMixtureModel.emitSampleUsingCurrentParameterSet(int n, int... lengths) The method returns an array of sequences using the current parameter set.

Methods in de.jstacs.models.mixture with parameters of type Sequence

int	AbstractMixtureModel.getIndexOfMaximalComponentFor(Sequence s) Returns the index i of the component with P(i|s) maximal.
double	AbstractMixtureModel.getLogProbFor(int component, Sequence s) Returns the log probability for the sequence and the given component.
double	AbstractMixtureModel.getLogProbFor(Sequence sequence, int startpos, int endpos)
protected double	StrandModel.getLogProbUsingCurrentParameterSetFor(int component, Sequence s, int start, int end)
protected double	MixtureModel.getLogProbUsingCurrentParameterSetFor(int component, Sequence s, int start, int end)
protected abstract double	AbstractMixtureModel.getLogProbUsingCurrentParameterSetFor(int component, Sequence s, int start, int end) Returns the log probability for the sequence and the given component using the current parameter set.
double	AbstractMixtureModel.getProbFor(Sequence sequence, int startpos, int endpos)

Uses of Sequence in de.jstacs.models.mixture.motif

Methods in de.jstacs.models.mixture.motif that return Sequence

protected Sequence[]

HiddenMotifMixture.emitSampleUsingCurrentParameterSet(int n, int... lengths) Standard implementation throwing an OperationNotSupportedException.

Methods in de.jstacs.models.mixture.motif with parameters of type Sequence

protected double	SingleHiddenMotifMixture.getLogProbUsingCurrentParameterSetFor(int component, Sequence seq, int start, int end)
double[]	SingleHiddenMotifMixture.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile kind)
StrandedLocatedSequenceAnnotationWithLength.Strand	SingleHiddenMotifMixture.getStrandFor(int component, int motif, Sequence sequence, int startpos)

Uses of Sequence in de.jstacs.models.utils

Methods in de.jstacs.models.utils that return Sequence

static Sequence	ModelTester.getMostProbableSequence(Model m, int length) Returns one most probable sequence for the discrete model m.
Sequence	ModelTester.SeqIterator.getSequence()

Uses of Sequence in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery with parameters of type Sequence

int	MotifDiscoverer.getIndexOfMaximalComponentFor(Sequence sequence) Returns the index of the component with the maximal score for the sequence sequence.
double[]	MotifDiscoverer.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile kind) Returns the profile of the scores for component component and motif motif at all possible start-positions of the motif in the sequence sequence.
StrandedLocatedSequenceAnnotationWithLength.Strand	MotifDiscoverer.getStrandFor(int component, int motif, Sequence sequence, int startpos) This method returns the strand for a given subsequence if it is consider as site of the motif model in a specific component.
static ImageResult	MotifDiscovererToolBox.plot(MotifDiscoverer motifDisc, int component, int motif, Sequence sequence, int startpos, REnvironment r, int width, int height, MotifDiscoverer.KindOfProfile kind) This method creates a simple plot of the profile of scores for a sequence and a start position.
static ImageResult	MotifDiscovererToolBox.plotAndAnnotate(MotifDiscoverer motifDisc, int component, int motif, Sequence sequence, int startpos, REnvironment r, int width, int height, double yMin, double yMax, double threshold, MotifDiscoverer.KindOfProfile kind) This method creates a plot of the profile of scores for a sequence and a start position and annotates bindings sites in the plot.

Uses of Sequence in de.jstacs.scoringFunctions

Methods in de.jstacs.scoringFunctions with parameters of type Sequence

double	ScoringFunction.getLogScore(Sequence seq) Returns the log score for the sequence
double	AbstractNormalizableScoringFunction.getLogScore(Sequence seq) Returns the log score for the sequence
double	VariableLengthScoringFunction.getLogScore(Sequence seq, int start)
double	UniformScoringFunction.getLogScore(Sequence seq, int start)
double	ScoringFunction.getLogScore(Sequence seq, int start) Returns the log score for the sequence
double	MRFScoringFunction.getLogScore(Sequence seq, int start)
double	IndependentProductScoringFunction.getLogScore(Sequence seq, int start)
abstract double	VariableLengthScoringFunction.getLogScore(Sequence seq, int start, int length) This method computes the logarithm of the score for a given subsequence.
abstract double	VariableLengthScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList) This method computes the logarithm of the score and the partial derivations for a given subsequence.
double	VariableLengthScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList dList)
double	UniformScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList dList)
double	ScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer) Returns the log score for the sequence and fills the list with the indices and the partial derivations.
double	MRFScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double	IndependentProductScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double	ScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, IntList indices, DoubleList partialDer) Returns the log score for the sequence and fills the list with the indices and the partial derivations.
double	AbstractNormalizableScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, IntList indices, DoubleList partialDer)

Uses of Sequence in de.jstacs.scoringFunctions.directedGraphicalModels

Methods in de.jstacs.scoringFunctions.directedGraphicalModels with parameters of type Sequence

void	ParameterTree.addCount(Sequence seq, int start, double count) Adds count to the parameter as returned by ParameterTree.getParameterFor(Sequence, int).
double	Parameter.doesApplyFor(Sequence seq) Returns true if seq fulfills all requirements defined in the context (Parameter.context}).
double	BayesianNetworkScoringFunction.getLogScore(Sequence seq, int start)
double	BayesianNetworkScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
Parameter	ParameterTree.getParameterFor(Sequence seq, int start) Returns the Parameter that is responsible for the suffix of sequence seq starting at position start.

Uses of Sequence in de.jstacs.scoringFunctions.homogeneous

Methods in de.jstacs.scoringFunctions.homogeneous with parameters of type Sequence

double	UniformHomogeneousScoringFunction.getLogScore(Sequence seq, int start, int length)
double	HMMScoringFunction.getLogScore(Sequence seq, int start, int length)
double	HMM0ScoringFunction.getLogScore(Sequence seq, int start, int length)
double	UniformHomogeneousScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList)
double	HMMScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList)
double	HMM0ScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList)

Uses of Sequence in de.jstacs.scoringFunctions.mix

Methods in de.jstacs.scoringFunctions.mix with parameters of type Sequence

protected void	MixtureScoringFunction.fillComponentScores(Sequence seq, int start)
protected abstract void	AbstractMixtureScoringFunction.fillComponentScores(Sequence seq, int start) Fills the internal array componentScore with the log scores of the components.
int	AbstractMixtureScoringFunction.getIndexOfMaximalComponentFor(Sequence seq, int start) Returns the index of the component that has the greatest impact on the complete score
double	AbstractMixtureScoringFunction.getLogScore(Sequence seq, int start)
double	MixtureScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double[]	AbstractMixtureScoringFunction.getProbsForComponent(Sequence seq) Returns the probabilities for each component