A B C D E F G H I K L M N O P Q R S T U V W X

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