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 Model
de.jstacs.classifier.scoringFunctionBased Provides the classes for Classifiers that are based on ScoringFunctions. 
de.jstacs.classifier.scoringFunctionBased.cll Provides the implementation of the log conditional likelihood as an OptimizableFunction and a classifier that uses log conditional likelihood or supervised posterior to learn the parameters of a set of 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.inhomogeneous This package contains various inhomogeneous models. 
de.jstacs.models.mixture This package is the super package for any mixture model. 
de.jstacs.models.utils   
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.classifier.scoringFunctionBased.cll
 

Methods in de.jstacs.classifier.scoringFunctionBased.cll with parameters of type Sequence
protected  double CLLClassifier.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 AlphabetContainer 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 AlphabetContainer with alphabets that use many different symbols.
 class SparseSequence
          This class is an implementation for sequence 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.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.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.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