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L

L - Variable in class de.jstacs.algorithms.graphs.tensor.Tensor
 
length() - Method in class de.jstacs.data.Alphabet
Returns the length of the alphabet.
length() - Method in class de.jstacs.data.alphabets.ContinuousAlphabet
 
length() - Method in class de.jstacs.data.alphabets.DiscreteAlphabet
Returns the number of Symbols in the calling alphabet
length - Variable in class de.jstacs.models.AbstractModel
the length of the sequences the model can classify.
length - Variable in class de.jstacs.parameters.InstanceParameterSet
The length of sequences the model can work on or 0 for arbitrary length
length - Variable in class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
The length of the modeled sequences.
length() - Method in class de.jstacs.utils.DoubleList
Returns the number of inserted elements.
length() - Method in class de.jstacs.utils.IntList
Returns the number of inserted elements.
lengths - Variable in class de.jstacs.models.CompositeModel
The length for each component.
LEQ - Static variable in interface de.jstacs.parameters.validation.Constraint
The condition is less or equal
LimitedMedianStartDistance - Class in de.jstacs.algorithms.optimization
This class implements a StartDistanceForecaster that returns the median of a limited memory over the last values.
LimitedMedianStartDistance(int, double) - Constructor for class de.jstacs.algorithms.optimization.LimitedMedianStartDistance
This constructor creates an instance with slots memory slots that will initially be filled with value.
limitedMemoryBFGS(DifferentiableFunction, double[], byte, Optimizer.TerminationCondition, double, double, StartDistanceForecaster, SafeOutputStream, Time) - Static method in class de.jstacs.algorithms.optimization.Optimizer
The Broyden-Fletcher-Goldfarb-Shanno version of limited memory quasi Newton methods.
linearizeParameters() - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree
Extracts the Parameters from the leaves of this tree in left-to-right order (as specified by the order of the alphabet) and returns them as a LinkedList.
list - Variable in class de.jstacs.results.ListResult
The internal list of ResultSets that are part of this ListResult
ListResult - Class in de.jstacs.results
Class for a Result that contains a list or a matrix, respectively, of ResultSets.
ListResult(String, String, ResultSet, ResultSet...) - Constructor for class de.jstacs.results.ListResult
Creates a new ListResult from an array of ResultSets and a ResultSet of annotations, which may provide additional information on this ListResult
ListResult(StringBuffer) - Constructor for class de.jstacs.results.ListResult
Creates a new ListResult from the corresponding XML-representation.
loadParameters() - Method in class de.jstacs.classifier.assessment.ClassifierAssessmentAssessParameterSet
 
loadParameters() - Method in class de.jstacs.classifier.assessment.KFoldCVAssessParameterSet
 
loadParameters() - Method in class de.jstacs.classifier.assessment.RepeatedHoldOutAssessParameterSet
 
loadParameters() - Method in class de.jstacs.classifier.assessment.RepeatedSubSamplingAssessParameterSet
 
loadParameters() - Method in class de.jstacs.classifier.assessment.Sampled_RepeatedHoldOutAssessParameterSet
 
loadParameters() - Method in class de.jstacs.classifier.scoringFunctionBased.cll.CLLClassifierParameterSet
 
loadParameters() - Method in class de.jstacs.classifier.scoringFunctionBased.ScoreClassifierParameterSet
 
loadParameters() - Method in class de.jstacs.data.AlphabetContainerParameterSet
 
loadParameters() - Method in class de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
 
loadParameters() - Method in class de.jstacs.data.alphabets.ContinuousAlphabet.ContinuousAlphabetParameterSet
 
loadParameters() - Method in class de.jstacs.data.alphabets.DiscreteAlphabet.DiscreteAlphabetParameterSet
 
loadParameters() - Method in class de.jstacs.data.alphabets.DNAAlphabet.DNAAlphabetParameterSet
 
loadParameters() - Method in class de.jstacs.models.discrete.DGMParameterSet
 
loadParameters() - Method in class de.jstacs.models.discrete.inhomogeneous.parameters.BayesianNetworkModelParameterSet
 
loadParameters() - Method in class de.jstacs.models.discrete.inhomogeneous.parameters.FSDAGMParameterSet
 
loadParameters() - Method in class de.jstacs.parameters.ArrayParameterSet
 
loadParameters() - Method in class de.jstacs.parameters.ExpandableParameterSet
 
loadParameters() - Method in class de.jstacs.parameters.ParameterSet
Loads the parameters for this ParameterSet.
loadParameters() - Method in class de.jstacs.parameters.SimpleParameterSet
 
LocatedSequenceAnnotation - Class in de.jstacs.data.sequences.annotation
Class for a SequenceAnnotation that has a position on the sequence, e.g for transcription start sites or intron-exon junctions.
LocatedSequenceAnnotation(int, String, String, Result...) - Constructor for class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation
Creates a new LocatedSequenceAnnotation of type type, with identifier identifier, and additional annotation (that does not fit the SequenceAnnotation definitions) result.
LocatedSequenceAnnotation(int, String, String, Collection<Result>) - Constructor for class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation
Creates a new LocatedSequenceAnnotation of type type, with identifier identifier, and additional annotation (that does not fit the SequenceAnnotation definitions) result.
LocatedSequenceAnnotation(int, String, String, SequenceAnnotation[], Result...) - Constructor for class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation
Creates a new LocatedSequenceAnnotation of type type, with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) result, and sub annotations.
LocatedSequenceAnnotation(String, String, LocatedSequenceAnnotation[], Result...) - Constructor for class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation
Creates a new LocatedSequenceAnnotation of type type, with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) result, and sub annotations.
LocatedSequenceAnnotation(StringBuffer) - Constructor for class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation
Re-creates a LocatedSequenceAnnotation from its XML-representation as returned by LocatedSequenceAnnotation.toXML().
LocatedSequenceAnnotationWithLength - Class in de.jstacs.data.sequences.annotation
Class for a SequenceAnnotation that has a position on the sequence and a length, e.g. for donor splice sites, exons, or genes.
LocatedSequenceAnnotationWithLength(int, int, String, String, Result...) - Constructor for class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotationWithLength
Creates a new LocatedSequenceAnnotationWithLength of type type, with identifier identifier, and additional annotation (that does not fit the SequenceAnnotation definitions) result.
LocatedSequenceAnnotationWithLength(int, int, String, String, Collection<Result>) - Constructor for class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotationWithLength
Creates a new LocatedSequenceAnnotationWithLength of type type, with identifier identifier, and additional annotation (that does not fit the SequenceAnnotation definitions) result.
LocatedSequenceAnnotationWithLength(int, int, String, String, SequenceAnnotation[], Result...) - Constructor for class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotationWithLength
Creates a new LocatedSequenceAnnotationWithLength of type type, with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) result, and sub-annotations.
LocatedSequenceAnnotationWithLength(String, String, LocatedSequenceAnnotation[], Result...) - Constructor for class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotationWithLength
Creates a new LocatedSequenceAnnotationWithLength of type type, with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) result, and sub-annotations.
LocatedSequenceAnnotationWithLength(StringBuffer) - Constructor for class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotationWithLength
Re-creates a LocatedSequenceAnnotationWithLength from its XML-representation as returned by LocatedSequenceAnnotationWithLength.toXML().
logGammaSum - Variable in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
This double contains sum of the logarithm of the gamma functions used in the prior.
logHiddenNorm - Variable in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
This double contains logarithm of the normalization constant of hidden parameters of the instance.
logHiddenPotential - Variable in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
This array contains the logarithm of the hidden potentials of the instance
LogPrior - Class in de.jstacs.classifier.scoringFunctionBased.logPrior
The abstract class for any log-prior used e.g. for maximum supervised posterior optimization.
LogPrior() - Constructor for class de.jstacs.classifier.scoringFunctionBased.logPrior.LogPrior
 
logSumNormalisation(double[]) - Static method in class de.jstacs.utils.Normalisation
log-sum-normalisation on d
logSumNormalisation(double[], int, int) - Static method in class de.jstacs.utils.Normalisation
log-sum-normalisation on d between startD and endD
logSumNormalisation(double[], int, int, double[]) - Static method in class de.jstacs.utils.Normalisation
log-sum-normalisation on d between startD and endD
logSumNormalisation(double[], int, int, double[], int) - Static method in class de.jstacs.utils.Normalisation
log-sum-normalisation on d between startD and endD, writing the result in dest starting at position startDest
logSumNormalisation(double[], int, int, double[], double[], int) - Static method in class de.jstacs.utils.Normalisation
log-sum-normalisation on d between startD and endD, writing the result in dest starting at position startDest
logSumNormalisation(double[], double) - Static method in class de.jstacs.utils.Normalisation
log-sum-normalisation on d using offset offset
logSumNormalisation(double[], int, int, double, double[], int) - Static method in class de.jstacs.utils.Normalisation
log-sum-normalisation on d between startD and endD, writing the result in dest starting at position startDest using offset offset
logSumNormalisation(double[], int, int, double, double[], double[], int) - Static method in class de.jstacs.utils.Normalisation
log-sum-normalisation on d, writing the result in dest starting at position start using offset offset
logWeights - Variable in class de.jstacs.models.mixture.AbstractMixtureModel
The log probabilities for each component.
LT - Static variable in interface de.jstacs.parameters.validation.Constraint
The condition is less than

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