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## 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 `Classifier`s that are based on `Model`s
de.jstacs.classifier.scoringFunctionBased | Provides the classes for `Classifier`s that are based on `ScoringFunction`s.
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 `ScoringFunction`s that can be used in a `ScoreClassifier`.
de.jstacs.scoringFunctions.directedGraphicalModels | Provides `ScoringFunction`s that are equivalent to directed graphical models.
de.jstacs.scoringFunctions.homogeneous | Provides `ScoringFunction`s that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.scoringFunctions.mix | Provides `ScoringFunction`s that are mixtures of other `ScoringFunction`s.
de.jstacs.scoringFunctions.mix.motifSearch |

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` of the class to which the sequence is assigned with `0 < i < getNumberOfClasses()`.
`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 `Sequence`s.
`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 of the `Sequence.CompositeSequence`.

Methods in de.jstacs.data that return Sequence
`Sequence` | `Sequence.annotate(boolean add, SequenceAnnotation... annotation)` This method allows to append annotation to a `Sequence.CompositeSequence`.
`Sequence` | `Sequence.complement()` This method returns a new instance of `Sequence.CompositeSequence` containing the complementary current `Sequence.CompositeSequence`.
`Sequence` | `Sequence.complement(int start, int end)` This method returns a new instance of `Sequence.CompositeSequence` containing a part of the complementary current `Sequence.CompositeSequence`.
`static Sequence` | `Sequence.create(AlphabetContainer con, SequenceAnnotation[] annotation, String sequence, String delim)` Creates a `Sequence.CompositeSequence` from a `String` based on the given `AlphabetContainer` using the given delimiter `delim` and some `annotation` for the `Sequence.CompositeSequence`.
`static Sequence` | `Sequence.create(AlphabetContainer con, String sequence)` Creates a `Sequence.CompositeSequence` 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.CompositeSequence` from a `String` based on the given `AlphabetContainer` using the given delimiter `delim`.
`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 `Sequence`s containing all elements of this `Sample`.
`Sequence` | `Sequence.getCompositeSequence(AlphabetContainer abc, int[] starts, int[] lengths)` This method should be used if one wants to create a `Sample` of `Sequence.CompositeSequence`s.
`Sequence` | `Sequence.getCompositeSequence(int[] starts, int[] lengths)` This is a very efficient way to create a `Sequence.CompositeSequence` for sequences with a simple `AlphabetContainer`.
`Sequence` | `Sample.getElementAt(int i)` This method returns the element, i.e. the `Sequence`, 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 a very efficient way to create a subsequence/suffix for `Sequence.CompositeSequence`s with a simple `AlphabetContainer`.
`Sequence` | `Sequence.getSubSequence(int start, int length)` This is a very efficient way to create a subsequence of defined length for `Sequence.CompositeSequence`s with a simple `AlphabetContainer`.
`Sequence` | `Sample.ElementEnumerator.nextElement()`
`Sequence` | `DiscreteSequenceEnumerator.nextElement()`
`Sequence` | `Sequence.reverse()` This method returns a new instance of `Sequence.CompositeSequence` containing the reverse current `Sequence.CompositeSequence`.
`Sequence` | `Sequence.reverse(int start, int end)` This method returns a new instance of `Sequence.CompositeSequence` containing a part of the reverse current `Sequence.CompositeSequence`.
`Sequence` | `Sequence.reverseComplement()` This method returns a new instance of `Sequence.CompositeSequence` containing the reverse complementary current `Sequence.CompositeSequence`.
`Sequence` | `Sequence.reverseComplement(int start, int end)` This method returns a new instance of `Sequence.CompositeSequence` containing a reverse part of the complementary current `Sequence.CompositeSequence`.
`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)` Creates a new `Sample` from an array of `Sequence`s and a given annotation.
`Sequence.CompositeSequence(AlphabetContainer abc, Sequence seq, int[] starts, int[] lengths)` This constructor should be used if one wants to create a `Sample` of `Sequence.CompositeSequence`s.
`Sequence.CompositeSequence(Sequence seq, int[] starts, int[] lengths)` This is a very efficient way to create a `Sequence.CompositeSequence` for `Sequence`s 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 `Sequence.SubSequence`s of defined length.
`Sequence.SubSequence(Sequence seq, int start, int length)` This is a very efficient way to create a `Sequence.SubSequence` of defined length for `Sequence`s with a simple `AlphabetContainer`.

Uses of Sequence in de.jstacs.data.sequences

Subclasses of Sequence in de.jstacs.data.sequences
`class` | `ArbitrarySequence` This class is for any continuous or hybrid sequence.
`class` | `ByteSequence` This class is for sequences with the alphabet symbols encoded as `byte`s and can therefore be used for discrete `AlphabetContainer`s with alphabets that use only few symbols.
`class` | `DiscreteSequence` This is the main class for any discrete sequence.
`class` | `IntSequence` This class is for sequences with the alphabet symbols encoded as `int`s and can therefore be used for discrete `AlphabetContainer`s with alphabets that use a huge number of symbols.
`class` | `PermutedSequence` This class is for permuted sequences.
`class` | `RecursiveSequence` This is the main class for subsequences, composite sequences, ... .
`class` | `ShortSequence` This class is for sequences with the alphabet symbols encoded as `shorts`s and can therefore be used for discrete `AlphabetContainer`s 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)` Creates a new `PermutedSequence` by shuffling the symbols of a given `Sequence`.
`RecursiveSequence(AlphabetContainer alphabet, Sequence seq)` Creates a new `RecursiveSequence` on the `Sequence` `seq` with the `AlphabetContainer` `alphabet` using the annotation of the given `Sequence`.
`RecursiveSequence(AlphabetContainer alphabet, SequenceAnnotation[] annotation, Sequence seq)` Creates a new `RecursiveSequence` on the `Sequence` `seq` with the `AlphabetContainer` `alphabet` and the annotation `annotation`.

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 (a part 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 (a part 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 (a part 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 (a part 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` `seq` 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 fulfilled by the `Sequence` `seq` beginning at position `start`.
`abstract int` | `Constraint.satisfiesSpecificConstraint(Sequence seq, int start)` This method returns the index of the specific constraint that is fulfilled by the `Sequence` `seq` beginning at position `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 random `Sequence` from a trained homogeneous model.
`protected Sequence` | `HomogeneousMM.getRandomSequence(Random r, int length)`

Methods in de.jstacs.models.discrete.homogeneous with parameters of type Sequence
`void` | `HomogeneousModel.HomCondProb.addAll(Sequence seq, double weight, int start, int prevIndex)` Adds the given `weight` to the counts corresponding to the `Sequence` `seq` from `start` to the end of the `Sequence`.
`protected void` | `HomogeneousModel.check(Sequence sequence, int startpos, int endpos)` Checks some constraints, these are in general conditions on the `AlphabetContainer` of a (sub)`Sequence` between `startpos` und `endpos`.
`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 logarithm of the relative frequency (=probability) with the position in the distribution given by the index of the specific constraint that is fulfilled by the `Sequence` `s` beginning at `start`.
`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 logarithmic 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 logarithmic 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`.

Uses of Sequence in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery that return Sequence
`static Sequence` | `MutableMotifDiscovererToolbox.enumerate(Sample[] data, ScoringFunction[] funs, int classIndex, int motifIndex, double weight, OptimizableFunction opt, OutputStream out)` This method allows to enumerate all possible seeds for a motif in the `HiddenMotifsMixture` of a specific class.

Methods in de.jstacs.motifDiscovery with parameters of type Sequence
`MotifAnnotation[]` | `SignificantMotifOccurrencesFinder.findSignificantMotifOccurrences(int motif, Sequence seq, int start)` This method finds the significant motif occurrences in the 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` beginning at `startpos`.
`StrandedLocatedSequenceAnnotationWithLength.Strand` | `MotifDiscoverer.getStrandFor(int component, int motif, Sequence sequence, int startpos)` This method returns the strand for a given subsequence if it is considered 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 that have a higher score than `threshold`.

Uses of Sequence in de.jstacs.scoringFunctions

Methods in de.jstacs.scoringFunctions with parameters of type Sequence
`int` | `IndependentProductScoringFunction.getIndexOfMaximalComponentFor(Sequence sequence)`
`double` | `ScoringFunction.getLogScore(Sequence seq)` Returns the logarithmic score for the `Sequence` `seq`.
`double` | `AbstractNormalizableScoringFunction.getLogScore(Sequence seq)` Returns the logarithmic score for a given `Sequence`.
`double` | `VariableLengthScoringFunction.getLogScore(Sequence seq, int start)`
`double` | `UniformScoringFunction.getLogScore(Sequence seq, int start)`
`double` | `ScoringFunction.getLogScore(Sequence seq, int start)` Returns the logarithmic score for the `Sequence` `seq` beginning at position `start` in the `Sequence`.
`double` | `NormalizedScoringFunction.getLogScore(Sequence seq, int start)`
`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 logarithmic score for a `Sequence` beginning at position `start` in the `Sequence` and fills lists with the indices and the partial derivations.
`double` | `NormalizedScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`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 logarithmic score for a `Sequence` `seq` and fills lists with the indices and the partial derivations.
`double` | `AbstractNormalizableScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, IntList indices, DoubleList partialDer)`
`double[]` | `IndependentProductScoringFunction.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile dist)`
`StrandedLocatedSequenceAnnotationWithLength.Strand` | `NormalizedScoringFunction.getStrand(Sequence seq, int startPos)` This method return the preferred `StrandedLocatedSequenceAnnotationWithLength.Strand` for a `Sequence` beginning at `startPos`.
`StrandedLocatedSequenceAnnotationWithLength.Strand` | `IndependentProductScoringFunction.getStrandFor(int component, int motif, Sequence sequence, int startpos)`

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)` Indicates if the `Sequence` `seq` fulfills all requirements defined in the `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`.
`double[]` | `BayesianNetworkScoringFunction.getPositionDependentKMerProb(Sequence kmer)`
`double` | `ParameterTree.getProbFor(Sequence sequence)`

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` | `StrandScoringFunction.fillComponentScores(Sequence seq, int start)`
`protected void` | `MixtureScoringFunction.fillComponentScores(Sequence seq, int start)`
`protected abstract void` | `AbstractMixtureScoringFunction.fillComponentScores(Sequence seq, int start)` Fills the internal array `AbstractMixtureScoringFunction.componentScore` with the logarithmic scores of the components given a `Sequence`.
`int` | `AbstractMixtureScoringFunction.getIndexOfMaximalComponentFor(Sequence seq, int start)` Returns the index of the component that has the greatest impact on the complete score for a `Sequence`.
`double` | `AbstractMixtureScoringFunction.getLogScore(Sequence seq, int start)`
`double` | `StrandScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `MixtureScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double[]` | `AbstractMixtureScoringFunction.getProbsForComponent(Sequence seq)` Returns the probabilities for each component given a `Sequence`.
`StrandedLocatedSequenceAnnotationWithLength.Strand` | `StrandScoringFunction.getStrand(Sequence seq, int startPos)` This method returns the preferred `StrandedLocatedSequenceAnnotationWithLength.Strand` for a given subsequence.

Uses of Sequence in de.jstacs.scoringFunctions.mix.motifSearch

Methods in de.jstacs.scoringFunctions.mix.motifSearch with parameters of type Sequence
`protected int` | `HiddenMotifsMixture.fillComponentScoreOf(int i, Sequence seq, int start)` This method fills an internal array with the partial scores.
`protected void` | `HiddenMotifsMixture.fillComponentScores(Sequence seq, int start)`
`int` | `HiddenMotifsMixture.getIndexOfMaximalComponentFor(Sequence sequence)`
`double` | `PositionScoringFunction.getLogScore(Sequence seq, int start)`
`double` | `HiddenMotifsMixture.getLogScore(Sequence seq, int start)`
`double` | `PositionScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double` | `HiddenMotifsMixture.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)`
`double[]` | `HiddenMotifsMixture.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile dist)`
`StrandedLocatedSequenceAnnotationWithLength.Strand` | `HiddenMotifsMixture.getStrandFor(int component, int motif, Sequence sequence, int startpos)`
`protected int[]` | `PositionScoringFunction.getValuesFromSequence(Sequence seq, int start)` This method extracts the values form a sequence.

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