- ABBRDOUBLE - Static variable in class de.unibi.techfak.scie.annotators.quantities.NumberAnnotator
-
- AbbreviationAnnotator - Class in de.unibi.techfak.scie.annotators.abbreviation
-
- AbbreviationAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.abbreviation.AbbreviationAnnotator
-
- ABBRINT - Static variable in class de.unibi.techfak.scie.annotators.quantities.NumberAnnotator
-
- AbstractAssociation - Class in de.unibi.techfak.scie.ontology.importer.small
-
- AbstractAssociation(int, AssociationType) - Constructor for class de.unibi.techfak.scie.ontology.importer.small.AbstractAssociation
-
- AbstractImporter - Class in de.unibi.techfak.scie.ontology.importer
-
- AbstractImporter(OntologyDatabase, String) - Constructor for class de.unibi.techfak.scie.ontology.importer.AbstractImporter
-
Instantiates the importer for the given database.
- AbstractLineSegment - Interface in de.unibi.techfak.scie.util
-
The AbstractLineSegment interface represents a simple line in one dimensional
space, given by a start position and an end position.
- add(X) - Method in class de.unibi.techfak.scie.util.CachedJCasUtil
-
Manually adds the given instance to the respective cache.
- add(Class<X>, X) - Method in class de.unibi.techfak.scie.util.CachedJCasUtil
-
Manually adds the given instance to the respective cache.
- addAll(Histogramm<H>) - Method in class de.unibi.techfak.scie.util.Histogramm
-
- addAssociationFrom(NodeHandle, AssociationType) - Method in class de.unibi.techfak.scie.ontology.Node
-
Adds a new association from the given node.
- addAssociationFrom(NodeHandle) - Method in class de.unibi.techfak.scie.ontology.Node
-
Adds a new association from the given node.
- addAssociationFrom(NodeDescriptor, AssociationType) - Method in class de.unibi.techfak.scie.ontology.Node
-
Adds a new association from the given node.
- addAssociationFrom(NodeDescriptor) - Method in class de.unibi.techfak.scie.ontology.Node
-
Adds a new association from the given node.
- addAssociationTo(NodeHandle, AssociationType) - Method in class de.unibi.techfak.scie.ontology.Node
-
Adds a new association to the given node.
- addAssociationTo(NodeHandle) - Method in class de.unibi.techfak.scie.ontology.Node
-
Adds a new association to the given node.
- addAssociationTo(NodeDescriptor, AssociationType) - Method in class de.unibi.techfak.scie.ontology.Node
-
Adds a new association to the given node.
- addAssociationTo(NodeDescriptor) - Method in class de.unibi.techfak.scie.ontology.Node
-
Adds a new association to the given node.
- addDataPoint(H) - Method in class de.unibi.techfak.scie.util.Histogramm
-
- AGEMODEL - Static variable in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator
-
- ALL - Static variable in enum de.unibi.techfak.scie.ontology.driver.AssociationType
-
Bit mask that represents all types.
- ALPHANUMERIC_CHARACTER - Static variable in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
-
Alphanumeric character.
- ALWAYS_TRUE - Static variable in class de.unibi.techfak.scie.configuration.ConfigurationEntry
-
- AnalysisAnnotator - Class in de.unibi.techfak.scie.analysis
-
- AnalysisAnnotator() - Constructor for class de.unibi.techfak.scie.analysis.AnalysisAnnotator
-
- AnnotationCandidate - Interface in de.unibi.techfak.scie.probability_model
-
This is an interface for candidates for annotations that are characterized by
their start and end position in the text.
- AnnotationCompositionUtil - Class in de.unibi.techfak.scie.probability_model
-
This class provides static methods that help to compose annotations to more
complex annotations in a probabilistic way.
- AnnotationCompositionUtil() - Constructor for class de.unibi.techfak.scie.probability_model.AnnotationCompositionUtil
-
- AnnotationCompositor<Y> - Interface in de.unibi.techfak.scie.probability_model
-
This is an interface for classes that are able to compose from a set of
candidates for each slot of a composition annotation the composition itself.
- AnnotationCounter - Class in de.unibi.techfak.scie.annotators
-
Used to count the number of unique annotations.
- AnnotationCounter() - Constructor for class de.unibi.techfak.scie.annotators.AnnotationCounter
-
- AnnotatorPipeline - Class in de.unibi.techfak.scie
-
This is a simple pipeline class modelling the iterative application of
different annotators.
- AnnotatorPipeline() - Constructor for class de.unibi.techfak.scie.AnnotatorPipeline
-
- AntiBodyAnnotator - Class in de.unibi.techfak.scie.annotators.treatment
-
- AntiBodyAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.treatment.AntiBodyAnnotator
-
- APPROXCHARSPERWORD - Static variable in class de.unibi.techfak.scie.probability_model.uima.UIMAWordSyntacticProbabilityModel
-
We approximate the number of chars per word with 7 (to be somewhat sure) to give a rough
approximation of what region this Model is considering effectively.
- Association - Class in de.unibi.techfak.scie.ontology.driver
-
The Association class represents a directed association between two nodes in
an ontology.
- Association(NodeHandle, NodeHandle, AssociationType) - Constructor for class de.unibi.techfak.scie.ontology.driver.Association
-
Constructor of the Association class.
- Association(NodeHandle, NodeHandle, int) - Constructor for class de.unibi.techfak.scie.ontology.driver.Association
-
Constructor of the Association class.
- Association(NodeHandle, NodeHandle) - Constructor for class de.unibi.techfak.scie.ontology.driver.Association
-
Constructor of the Association class.
- Association(OntologyHandle, int, int, AssociationType) - Constructor for class de.unibi.techfak.scie.ontology.driver.Association
-
Constructor of the Association class.
- Association(OntologyHandle, int, int) - Constructor for class de.unibi.techfak.scie.ontology.driver.Association
-
Constructor of the Association class.
- AssociationDirection - Enum in de.unibi.techfak.scie.ontology.driver
-
The AssociationDirection enum is used to specify the direction of an
association.
- AssociationList - Class in de.unibi.techfak.scie.ontology.importer.small
-
- AssociationList(int) - Constructor for class de.unibi.techfak.scie.ontology.importer.small.AssociationList
-
- AssociationType - Enum in de.unibi.techfak.scie.ontology.driver
-
The AssociationType enum is used to specify the type of an association.
- CachedJCasUtil - Class in de.unibi.techfak.scie.util
-
This is a custom wrapper implementation to reduce the necessary calls to UIMA JCasUtil, which
seems to be terribly slow.
- calculateComposita(AnnotationCandidate, SemanticProbabilityModel[], Collection[], AnnotationCompositor<Y>, double) - Static method in class de.unibi.techfak.scie.probability_model.AnnotationCompositionUtil
-
This calculates all composita that are possible to create given a certain
core annotation and a list of candidates for each slots of the
compositum.
- calculateComposita(AnnotationCandidate, SyntacticProbabilityModel, SemanticProbabilityModel[], Collection[], AnnotationCompositor<Y>) - Static method in class de.unibi.techfak.scie.probability_model.AnnotationCompositionUtil
-
This calculates all composita that are possible to create given a certain
core annotation and a list of candidates for each slots of the
compositum.
- calculateComposita(Annotation, UIMAAnnotationCompositionUtil.UIMASemanticProbabilityModel[], Class[], UIMACompositor<Y>, JCas, double) - Static method in class de.unibi.techfak.scie.probability_model.uima.UIMAAnnotationCompositionUtil
-
This calculates all composita that are possible to create given a certain core annotation and
a list of candidates for each slots of the compositum.
- calculateComposita(Annotation, SyntacticProbabilityModel, UIMAAnnotationCompositionUtil.UIMASemanticProbabilityModel[], Class[], UIMACompositor<Y>, JCas) - Static method in class de.unibi.techfak.scie.probability_model.uima.UIMAAnnotationCompositionUtil
-
This calculates all composita that are possible to create given a certain core annotation and
a list of candidates for each slots of the compositum.
- calculateMatches() - Method in class de.unibi.techfak.scie.ontology.dictionary_name_finder.DictionaryNameFinder
-
Calculates all matches for the given words.
- calculateMaxProbHypothesis(AnnotationCandidate, SemanticProbabilityModel<X>, Collection<X>, double) - Static method in class de.unibi.techfak.scie.probability_model.AnnotationCompositionUtil
-
This calculates the AnnotationCandidate with the maximum probability to
belong to some given core for a composit annotation and returns it with
the probability (without normalization!)
- calculateMaxProbHypothesis(AnnotationCandidate, SyntacticProbabilityModel, SemanticProbabilityModel<X>, Collection<X>) - Static method in class de.unibi.techfak.scie.probability_model.AnnotationCompositionUtil
-
This calculates the AnnotationCandidate with the maximum probability to
belong to some given core for a composit annotation and returns it with
the probability (without normalization!)
- calculateMaxProbHypothesis(Annotation, UIMAAnnotationCompositionUtil.UIMASemanticProbabilityModel<X>, Class<? extends X>, JCas, double) - Static method in class de.unibi.techfak.scie.probability_model.uima.UIMAAnnotationCompositionUtil
-
This calculates the AnnotationCandidate with the maximum probability to belong to some given
core for a composit annotation and returns it with the probability (without normalization!)
- calculateMaxProbHypothesis(Annotation, SyntacticProbabilityModel, UIMAAnnotationCompositionUtil.UIMASemanticProbabilityModel<X>, Class<? extends X>, JCas) - Static method in class de.unibi.techfak.scie.probability_model.uima.UIMAAnnotationCompositionUtil
-
This calculates the AnnotationCandidate with the maximum probability to belong to some given
core for a composit annotation and returns it with the probability (without normalization!)
- calculateNormalDistribution(double) - Method in class de.unibi.techfak.scie.probability_model.CharBasedSyntacticProbabilityModel
-
Calculates not the actual normal distribution N(input|0,sigma) /
N(0|0,sigma)
- calculateNormalDistribution(double) - Method in class de.unibi.techfak.scie.probability_model.uima.UIMAWordSyntacticProbabilityModel
-
Calculates not the actual normal distribution N(input|0,sigma) / N(0|0,sigma)
- calculateProbableHypotheses(AnnotationCandidate, SemanticProbabilityModel<X>, Collection<X>, double) - Static method in class de.unibi.techfak.scie.probability_model.AnnotationCompositionUtil
-
For any of the given candidates the probability is calculated, that this
candidate belongs to the given core annotation.
- calculateProbableHypotheses(AnnotationCandidate, SyntacticProbabilityModel, SemanticProbabilityModel<X>, Collection<X>) - Static method in class de.unibi.techfak.scie.probability_model.AnnotationCompositionUtil
-
For any of the given candidates the probability is calculated, that this
candidate belongs to the given core annotation.
- calculateProbableHypotheses(Annotation, UIMAAnnotationCompositionUtil.UIMASemanticProbabilityModel<X>, Class<? extends X>, JCas, double) - Static method in class de.unibi.techfak.scie.probability_model.uima.UIMAAnnotationCompositionUtil
-
For any of the given candidates the probability is calculated, that this candidate belongs to
the given core annotation.
- calculateProbableHypotheses(Annotation, SyntacticProbabilityModel, UIMAAnnotationCompositionUtil.UIMASemanticProbabilityModel<X>, Class<? extends X>, JCas, double) - Static method in class de.unibi.techfak.scie.probability_model.uima.UIMAAnnotationCompositionUtil
-
For any of the given candidates the probability is calculated, that this candidate belongs to
the given core annotation.
- calculateSemanticProbability(Age) - Method in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator.AgeModel
-
- calculateSemanticProbability(Gender) - Method in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator.GenderModel
-
- calculateSemanticProbability(Integer) - Method in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator.NumberModel
-
- calculateSemanticProbability(Weight) - Method in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator.WeightModel
-
- calculateSemanticProbability(Duration) - Method in class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator.DurationModel
-
- calculateSemanticProbability(InjuryDevice) - Method in class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator.InjuryDeviceModel
-
- calculateSemanticProbability(InjuryHeight) - Method in class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator.InjuryHeightModel
-
- calculateSemanticProbability(PValue) - Method in class de.unibi.techfak.scie.annotators.result.ResultAnnotator.PValueModel
-
- calculateSemanticProbability(Significance) - Method in class de.unibi.techfak.scie.annotators.result.ResultAnnotator.SignificanceModel
-
- calculateSemanticProbability(Trend) - Method in class de.unibi.techfak.scie.annotators.result.ResultAnnotator.TrendModel
-
- calculateSemanticProbability(Delivery) - Method in class de.unibi.techfak.scie.annotators.treatment.TreatmentAnnotator.DeliveryModel
-
- calculateSemanticProbability(Dose) - Method in class de.unibi.techfak.scie.annotators.treatment.TreatmentAnnotator.DoseModel
-
- calculateSemanticProbability(X) - Method in interface de.unibi.techfak.scie.probability_model.SemanticProbabilityModel
-
This should calculate the semantic probabilty of an AnnotationCandidate
belonging to another
If additional information is required to derive this value set those
parameters in some other way (e.g. the given AnnotationCandidate
implementation).
- calculateSemanticProbability(UIMAAnnotationCompositionUtil.UIMAAnnotationCandidate<X>) - Method in class de.unibi.techfak.scie.probability_model.uima.UIMAAnnotationCompositionUtil.UIMASemanticProbabilityModel
-
This should calculate the semantic probabilty of an AnnotationCandidate
belonging to another
If additional information is required to derive this value set those
parameters in some other way (e.g. the given AnnotationCandidate
implementation).
- calculateSemanticProbability(X) - Method in class de.unibi.techfak.scie.probability_model.uima.UIMAAnnotationCompositionUtil.UIMASemanticProbabilityModel
-
This should calculate the semantic probabilty of an AnnotationCandidate belonging to
another
If additional information is required to derive this value set those parameters in some
other way (e.g. the given AnnotationCandidate implementation).
- calculateSyntacticProbability(AnnotationCandidate, AnnotationCandidate) - Method in class de.unibi.techfak.scie.probability_model.CharBasedSyntacticProbabilityModel
-
Returns the probability that two given AnnotationCandidates belong
together from a syntactic perspective.
- calculateSyntacticProbability(AnnotationCandidate, AnnotationCandidate) - Method in interface de.unibi.techfak.scie.probability_model.SyntacticProbabilityModel
-
Returns the probability that two given AnnotationCandidates belong
together from a syntactic perspective.
- calculateSyntacticProbability(AnnotationCandidate, AnnotationCandidate) - Method in class de.unibi.techfak.scie.probability_model.uima.UIMAWordSyntacticProbabilityModel
-
Returns the probability that two given AnnotationCandidates belong
together from a syntactic perspective.
- calculateWordKeys(String, ComparisonMode) - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
-
Function that can be used to calculated dimensionalty reduced keys for
the given word.
- calculateWordKeys(String) - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
-
Function that can be used to calculated dimensionalty reduced keys for
the given word with "strict" as target comparison mode.
- CharBasedSyntacticProbabilityModel - Class in de.unibi.techfak.scie.probability_model
-
This calculates the syntactic probability based on the char distance.
- CharBasedSyntacticProbabilityModel(double) - Constructor for class de.unibi.techfak.scie.probability_model.CharBasedSyntacticProbabilityModel
-
- CHECKRANGE - Static variable in class de.unibi.techfak.scie.annotators.injury.VertebralPositionAnnotator
-
- CHECKRANGE - Static variable in class de.unibi.techfak.scie.annotators.result.PValueAnnotator
-
- CLASSES - Static variable in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator
-
- CLASSES - Static variable in class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator
-
- CLASSES - Static variable in class de.unibi.techfak.scie.annotators.result.ResultAnnotator
-
- CLASSES - Static variable in class de.unibi.techfak.scie.annotators.treatment.TreatmentAnnotator
-
- CLEAN_PARANTHESIS - Static variable in class de.unibi.techfak.scie.ontology.importer.AbstractImporter
-
- CLEAN_REDUCE - Static variable in class de.unibi.techfak.scie.ontology.importer.AbstractImporter
-
- cleanNodeNames(Collection<NodeName>) - Static method in class de.unibi.techfak.scie.ontology.importer.ncbi.NCBIImporter
-
- clear() - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
-
Clears the current ontology database.
- clear() - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
-
- clear() - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Wipes the ontology database clean.
- close() - Method in class de.unibi.techfak.scie.db.DatabaseInstance
-
- close() - Method in class de.unibi.techfak.scie.db.JDBCDatabaseInstance
-
- close() - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
-
- close() - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Gives the driver the opportunity to shut down properly.
- close() - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
-
Shuts down the database.
- compare(OntologyReference, OntologyReference) - Method in class de.unibi.techfak.scie.annotators.ontology.OntologyAnnotator.ProbabilityComparator
-
- compareTo(DictionaryAlgorithms.WordPosition) - Method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms.WordPosition
- compareTo(DictionaryMatch) - Method in class de.unibi.techfak.scie.ontology.DictionaryMatch
-
Allows to sort the matches by their weight.
- compareTo(Handle) - Method in class de.unibi.techfak.scie.ontology.driver.Handle
-
Compares the unique name of the two handles.
- compareTo(ProbableHypothesis) - Method in class de.unibi.techfak.scie.probability_model.ProbableHypothesis
-
- ComparisonMode - Enum in de.unibi.techfak.scie.ontology.driver
-
ComparisonMode is used to determine the mode that is used for searching the
node names in the dictionary.
- compose(AnnotationCandidate, ArrayList<ProbableHypothesis>) - Method in interface de.unibi.techfak.scie.probability_model.AnnotationCompositor
-
- compose(AnnotationCandidate, ArrayList<ProbableHypothesis>) - Method in class de.unibi.techfak.scie.probability_model.uima.UIMACompositor
-
- COMPOSITOR - Static variable in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator
-
- COMPOSITOR - Static variable in class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator
-
- COMPOSITOR - Static variable in class de.unibi.techfak.scie.annotators.result.ResultAnnotator
-
- COMPOSITOR - Static variable in class de.unibi.techfak.scie.annotators.treatment.TreatmentAnnotator
-
- config - Variable in class de.unibi.techfak.scie.db.DatabaseInstance
-
- Configuration - Class in de.unibi.techfak.scie.configuration
-
- Configuration() - Constructor for class de.unibi.techfak.scie.configuration.Configuration
-
- ConfigurationEntry - Class in de.unibi.techfak.scie.configuration
-
- ConfigurationEntry(String, String, ConfigurationEntry.DefaultProvider, ConfigurationEntry.ValidityChecker) - Constructor for class de.unibi.techfak.scie.configuration.ConfigurationEntry
-
- ConfigurationEntry(String, String, String, ConfigurationEntry.ValidityChecker) - Constructor for class de.unibi.techfak.scie.configuration.ConfigurationEntry
-
- ConfigurationEntry(String, String, String) - Constructor for class de.unibi.techfak.scie.configuration.ConfigurationEntry
-
- ConfigurationEntry(String, String, ConfigurationEntry.DefaultProvider) - Constructor for class de.unibi.techfak.scie.configuration.ConfigurationEntry
-
- ConfigurationEntry.ConfiguationEntryType - Enum in de.unibi.techfak.scie.configuration
-
- ConfigurationEntry.DefaultProvider - Interface in de.unibi.techfak.scie.configuration
-
- ConfigurationEntry.ValidityChecker - Interface in de.unibi.techfak.scie.configuration
-
- configurationHash() - Method in class de.unibi.techfak.scie.configuration.Configuration
-
Calculates a hash that represents the current configuration.
- ConfigurationSet - Class in de.unibi.techfak.scie.configuration
-
- ConfigurationSet(String, Configuration) - Constructor for class de.unibi.techfak.scie.configuration.ConfigurationSet
-
- ConfigurationSingleton - Class in de.unibi.techfak.scie.configuration
-
- ConfigurationSingleton() - Constructor for class de.unibi.techfak.scie.configuration.ConfigurationSingleton
-
- containsAlphanumericChar(String) - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
-
Returns true if the given string contains at least one alphanumeric
character.
- convertToSIValue(Unit, double) - Static method in class de.unibi.techfak.scie.annotators.animal.WeightAnnotator
-
- convertToSIValue(Unit, double) - Static method in class de.unibi.techfak.scie.annotators.quantities.TimeAnnotator
-
- createOntologyReferenceAnnotation(JCas, DictionaryMatch) - Static method in class de.unibi.techfak.scie.annotators.ontology.OntologyAnnotator
-
Creates the OntologyReference instance depending on the ontlogy.
- DATABASE_CONFIG_FILE - Static variable in class de.unibi.techfak.scie.Main
-
- DatabaseInstance - Class in de.unibi.techfak.scie.db
-
- DatabaseInstance(ConfigurationSet) - Constructor for class de.unibi.techfak.scie.db.DatabaseInstance
-
- DatabaseSingleton - Class in de.unibi.techfak.scie.db
-
- DatabaseSingleton() - Constructor for class de.unibi.techfak.scie.db.DatabaseSingleton
-
- db - Variable in class de.unibi.techfak.scie.ontology.importer.AbstractImporter
-
Reference to the ontology database into which the data will be imported.
- de.unibi.techfak.scie - package de.unibi.techfak.scie
-
- de.unibi.techfak.scie.analysis - package de.unibi.techfak.scie.analysis
-
- de.unibi.techfak.scie.annotators - package de.unibi.techfak.scie.annotators
-
- de.unibi.techfak.scie.annotators.abbreviation - package de.unibi.techfak.scie.annotators.abbreviation
-
- de.unibi.techfak.scie.annotators.animal - package de.unibi.techfak.scie.annotators.animal
-
- de.unibi.techfak.scie.annotators.injury - package de.unibi.techfak.scie.annotators.injury
-
- de.unibi.techfak.scie.annotators.ontology - package de.unibi.techfak.scie.annotators.ontology
-
- de.unibi.techfak.scie.annotators.quantities - package de.unibi.techfak.scie.annotators.quantities
-
- de.unibi.techfak.scie.annotators.result - package de.unibi.techfak.scie.annotators.result
-
- de.unibi.techfak.scie.annotators.structure - package de.unibi.techfak.scie.annotators.structure
-
- de.unibi.techfak.scie.annotators.treatment - package de.unibi.techfak.scie.annotators.treatment
-
- de.unibi.techfak.scie.configuration - package de.unibi.techfak.scie.configuration
-
- de.unibi.techfak.scie.db - package de.unibi.techfak.scie.db
-
- de.unibi.techfak.scie.document_import - package de.unibi.techfak.scie.document_import
-
- de.unibi.techfak.scie.ontology - package de.unibi.techfak.scie.ontology
-
- de.unibi.techfak.scie.ontology.dictionary_name_finder - package de.unibi.techfak.scie.ontology.dictionary_name_finder
-
- de.unibi.techfak.scie.ontology.driver - package de.unibi.techfak.scie.ontology.driver
-
- de.unibi.techfak.scie.ontology.driver.implementation - package de.unibi.techfak.scie.ontology.driver.implementation
-
- de.unibi.techfak.scie.ontology.importer - package de.unibi.techfak.scie.ontology.importer
-
- de.unibi.techfak.scie.ontology.importer.drug_bank - package de.unibi.techfak.scie.ontology.importer.drug_bank
-
- de.unibi.techfak.scie.ontology.importer.mesh - package de.unibi.techfak.scie.ontology.importer.mesh
-
- de.unibi.techfak.scie.ontology.importer.ncbi - package de.unibi.techfak.scie.ontology.importer.ncbi
-
- de.unibi.techfak.scie.ontology.importer.small - package de.unibi.techfak.scie.ontology.importer.small
-
- de.unibi.techfak.scie.probability_model - package de.unibi.techfak.scie.probability_model
-
- de.unibi.techfak.scie.probability_model.uima - package de.unibi.techfak.scie.probability_model.uima
-
- de.unibi.techfak.scie.util - package de.unibi.techfak.scie.util
-
- deleteAssociation(Association) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Deletes the given association.
- deleteAssociationFrom(NodeHandle) - Method in class de.unibi.techfak.scie.ontology.Node
-
Deletes any present association frmo the given node (inbound, this node
is the target node).
- deleteAssociationFrom(NodeDescriptor) - Method in class de.unibi.techfak.scie.ontology.Node
-
Deletes any present association frmo the given node (inbound, this node
is the target node).
- deleteAssociations(Collection<Association>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
-
- deleteAssociations(Collection<Association>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
-
- deleteAssociations(Collection<Association>) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Deletes the given associations.
- deleteAssociationTo(NodeHandle) - Method in class de.unibi.techfak.scie.ontology.Node
-
Deletes any present association to the given node (outbound, this node is
the source node).
- deleteAssociationTo(NodeDescriptor) - Method in class de.unibi.techfak.scie.ontology.Node
-
Deletes any present association to the given node (outbound, this node is
the source node).
- deleteDictionaryEntries(Collection<NodeHandle>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
-
- deleteDictionaryEntries(Collection<NodeHandle>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
-
- deleteDictionaryEntries(Collection<NodeHandle>) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Deletes the dictionary entries for the given nodes from the db.
- deleteDictionaryEntry(NodeHandle) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Deletes the dictionary entries for a single node.
- deleteNode(NodeHandle) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Deletes a single node from the database.
- deleteNode(NodeHandle) - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
-
Deletes the node the given handle refers to from the database and deletes
all corresponding dictionary entries.
- deleteNode(NodeDescriptor) - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
-
Deletes the node the given descriptor refers to from the database and
removes all corresponding dictionary entries.
- deleteNodeDescriptors(Collection<NodeDescriptor>) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Deletes the given nodes from the database.
- deleteNodes(Collection<NodeHandle>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
-
- deleteNodes(Collection<NodeHandle>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
-
- deleteNodes(Collection<NodeHandle>) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Deletes the given nodes from the database.
- deleteOntology(OntologyHandle) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
-
- deleteOntology(OntologyHandle) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
-
- deleteOntology(OntologyHandle) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Deletes the ontology with the given ontology handle.
- deleteOntology(OntologyHandle) - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
-
Deletes the ontology with the given handle.
- DELIVERYMODEL - Static variable in class de.unibi.techfak.scie.annotators.treatment.TreatmentAnnotator
-
- descriptorsToNodeList(Collection<NodeDescriptor>) - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
-
Converts a list of NodeDesciptor instances to high-level "Node"
instances.
- DEVICEMODEL - Static variable in class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator
-
- DictionaryAlgorithms - Class in de.unibi.techfak.scie.ontology
-
Collection of static algorithms used throughout the ontology dictionary.
- DictionaryAlgorithms() - Constructor for class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
-
- DictionaryAlgorithms.WordPosition - Class in de.unibi.techfak.scie.ontology
-
The WordPosition class is used to classify a word position within a
NodeName instance.
- DictionaryAlgorithms.WordPosition(String, int, int) - Constructor for class de.unibi.techfak.scie.ontology.DictionaryAlgorithms.WordPosition
-
Constructor of the WordPosition class.
- DictionaryAlgorithms.WordPosition(int, int) - Constructor for class de.unibi.techfak.scie.ontology.DictionaryAlgorithms.WordPosition
-
Constructor of the WordPosition class.
- DictionaryMatch - Class in de.unibi.techfak.scie.ontology
-
The DictionaryMatch represents a match between a single word in a NodeName
instance together with its match probability.
- DictionaryMatch(NodeHandle, NodeName, int, int, double, LineSegment) - Constructor for class de.unibi.techfak.scie.ontology.DictionaryMatch
-
Creates a new instance of DictionaryMatch.
- DictionaryMatch(NodeHandle, NodeName, int, int, double) - Constructor for class de.unibi.techfak.scie.ontology.DictionaryMatch
-
Creates a new instance of DictionaryMatch.
- DictionaryMatch(NodeHandle, NodeName) - Constructor for class de.unibi.techfak.scie.ontology.DictionaryMatch
-
- DictionaryMatch(int, int) - Constructor for class de.unibi.techfak.scie.ontology.DictionaryMatch
-
- DictionaryNameFinder - Class in de.unibi.techfak.scie.ontology.dictionary_name_finder
-
DictionaryNameFinder is used to finde complete NodeName instances in a text.
- DictionaryNameFinder(OntologyDatabase, String, double, SyntacticProbabilityModel) - Constructor for class de.unibi.techfak.scie.ontology.dictionary_name_finder.DictionaryNameFinder
-
Creates a new instance of the DictionaryNameFinder class and connects it
to the given database and the given probability model.
- DocumentImporter - Class in de.unibi.techfak.scie.document_import
-
The DocumentImporter class describes a very simple interface that has to be
implemented by every component that is capable of parsing document content
and transforming it into a UIMA CAS (Common Analysis Structure) using the
annotations defined in this package.
- DocumentImporter(InputStream, JCas) - Constructor for class de.unibi.techfak.scie.document_import.DocumentImporter
-
Creates the instance of DocumentImporter.
- doImport() - Method in class de.unibi.techfak.scie.document_import.DocumentImporter
-
Imports the document provided by the input stream and writes the
contents to the given CAS instance.
- doImport() - Method in class de.unibi.techfak.scie.document_import.PDFStructuredTextExtractorWrapper
-
- DoseAnnotator - Class in de.unibi.techfak.scie.annotators.treatment
-
This annotates Doses
- DoseAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.treatment.DoseAnnotator
-
- DOSEMODEL - Static variable in class de.unibi.techfak.scie.annotators.treatment.TreatmentAnnotator
-
- DOTINT - Static variable in class de.unibi.techfak.scie.annotators.quantities.NumberAnnotator
-
- DOUBLEE - Static variable in class de.unibi.techfak.scie.annotators.quantities.NumberAnnotator
-
- DOUBLEEXP - Static variable in class de.unibi.techfak.scie.annotators.quantities.NumberAnnotator
-
- DOUBLEPATTERNS - Static variable in class de.unibi.techfak.scie.annotators.quantities.NumberAnnotator
-
- DrugBankImporter - Class in de.unibi.techfak.scie.ontology.importer.drug_bank
-
- DrugBankImporter(OntologyDatabase) - Constructor for class de.unibi.techfak.scie.ontology.importer.drug_bank.DrugBankImporter
-
Instanciates the importer for the given database.
- DurationAnnotator - Class in de.unibi.techfak.scie.annotators.quantities
-
- DurationAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.quantities.DurationAnnotator
-
- DURATIONMODEL - Static variable in class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator
-
- GENDERMODEL - Static variable in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator
-
- getAnnotation() - Method in class de.unibi.techfak.scie.probability_model.uima.UIMAAnnotationCompositionUtil.UIMAAnnotationCandidate
-
- getAnnotators() - Method in class de.unibi.techfak.scie.AnnotatorPipeline
-
- getAssociatedNodes(int, AssociationDirection) - Method in class de.unibi.techfak.scie.ontology.Node
-
Return a collection of nodes that are associated to this node.
- getAssociatedNodes() - Method in class de.unibi.techfak.scie.ontology.Node
-
Returns a list of associated nodes with all types and regardless of the
association direction.
- getAssociatedNodes(int) - Method in class de.unibi.techfak.scie.ontology.Node
-
Return a collection of nodes that are associated to this node, for both
association directions.
- getAssociatedNodes(AssociationDirection) - Method in class de.unibi.techfak.scie.ontology.Node
-
Return a collection of nodes that are associated to this node, regardless
of the association type.
- getAssociations(Collection<NodeHandle>, int, AssociationDirection) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
-
- getAssociations(Collection<NodeHandle>, int, AssociationDirection) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
-
- getAssociations(Collection<NodeHandle>, int, AssociationDirection) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Returns the associations for a given set of nodes.
- getAssociations(NodeHandle, int, AssociationDirection) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Returns the associations for a single node.
- getAverage() - Method in class de.unibi.techfak.scie.util.Histogramm
-
This only works if the given class type is a number.
- getBackingMap() - Method in class de.unibi.techfak.scie.util.Histogramm
-
- getBegin() - Method in class de.unibi.techfak.scie.probability_model.uima.UIMAAnnotationCompositionUtil.UIMAAnnotationCandidate
-
- getBegin() - Method in interface de.unibi.techfak.scie.util.AbstractLineSegment
-
Returns the start index of the word in the text.
- getBegin() - Method in class de.unibi.techfak.scie.util.LineSegment
-
Returns the begin position of the line.
- getCandidate() - Method in class de.unibi.techfak.scie.probability_model.ProbableHypothesis
-
Get the value of candidate
- getComparisonMode() - Method in class de.unibi.techfak.scie.ontology.driver.NodeName
-
Returns the comparison mode of the name.
- getConfiguration() - Method in class de.unibi.techfak.scie.configuration.ConfigurationSet
-
- getConfiguration() - Static method in class de.unibi.techfak.scie.configuration.ConfigurationSingleton
-
- getConfigurationEntries(int) - Static method in class de.unibi.techfak.scie.db.JDBCRemoteDatabaseInstance
-
- getConfigurationEntries() - Static method in class de.unibi.techfak.scie.db.MySQLDatabaseInstance
-
- getConfigurationEntries() - Static method in class de.unibi.techfak.scie.db.PostgreSQLDatabaseInstance
-
- getConnection() - Method in class de.unibi.techfak.scie.db.JDBCDatabaseInstance
-
- getDefault() - Method in class de.unibi.techfak.scie.configuration.ConfigurationEntry
-
- getDefaultValue() - Method in interface de.unibi.techfak.scie.configuration.ConfigurationEntry.DefaultProvider
-
- getDescription() - Method in class de.unibi.techfak.scie.configuration.ConfigurationEntry
-
- getDistanceInCoveringClass(Class<X>, JCas, AnnotationCandidate, AnnotationCandidate) - Method in class de.unibi.techfak.scie.probability_model.uima.UIMAWordSyntacticProbabilityModel
-
This calculates the distance of two annotations counted in the instance of the given Class.
- getEmptyOntology(String) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Returns an empty instance of the ontology with the given name.
- getEmptyOntology(String) - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
-
Returns an ontology handle for an ontology with the given name, if such
an ontology does not exist yet, it is created and the new ontology handle
is returned.
- getEnd() - Method in class de.unibi.techfak.scie.probability_model.uima.UIMAAnnotationCompositionUtil.UIMAAnnotationCandidate
-
- getEnd() - Method in interface de.unibi.techfak.scie.util.AbstractLineSegment
-
Returns the end index of the word in the text.
- getEnd() - Method in class de.unibi.techfak.scie.util.LineSegment
-
Returns the end position of the line.
- getHandle() - Method in class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Returns the handle of the node this instance describes.
- getHost() - Method in class de.unibi.techfak.scie.db.NetworkDatabaseConfiguration
-
- getId() - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver.JDBCOntologyHandle
-
Returns the database id.
- getId() - Method in class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Returns the id of the described node.
- getId() - Method in class de.unibi.techfak.scie.ontology.driver.NodeHandle
-
Returns the unique id of the ontology node.
- getInstance() - Static method in class de.unibi.techfak.scie.db.DatabaseSingleton
-
- getInstance(JCas) - Static method in class de.unibi.techfak.scie.util.CachedJCasUtil
-
Returns the JCasUtil instance for the given JCas instance.
- getJcas() - Method in class de.unibi.techfak.scie.probability_model.uima.UIMACompositor
-
- getJcas() - Method in class de.unibi.techfak.scie.util.CachedJCasUtil
-
- getKey() - Method in class de.unibi.techfak.scie.configuration.ConfigurationEntry
-
- getMaxElement() - Method in class de.unibi.techfak.scie.util.Histogramm
-
Returns the element that was counted the most.
- getMaximumCharBasedRange() - Method in class de.unibi.techfak.scie.probability_model.CharBasedSyntacticProbabilityModel
-
Returns a heuristic approximation which region of the text should be
considered at all from a syntactic perspective.
- getMaximumCharBasedRange() - Method in interface de.unibi.techfak.scie.probability_model.SyntacticProbabilityModel
-
Returns a heuristic approximation which region of the text should be
considered at all from a syntactic perspective.
- getMaximumCharBasedRange() - Method in class de.unibi.techfak.scie.probability_model.uima.UIMAWordSyntacticProbabilityModel
-
Returns a heuristic approximation which region of the text should be
considered at all from a syntactic perspective.
- getMode(int) - Static method in enum de.unibi.techfak.scie.ontology.driver.ComparisonMode
-
Converts an comparison type value to the corresponding ComparisonMode
instance.
- getMode(String) - Static method in enum de.unibi.techfak.scie.ontology.driver.ComparisonMode
-
- getModificationDate() - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver.MemoryDatabaseOntologyHandle
-
- getName() - Method in class de.unibi.techfak.scie.db.NetworkDatabaseConfiguration
-
- getName() - Method in class de.unibi.techfak.scie.ontology.DictionaryMatch
-
Returns the name of the NodeName this match refers to.
- getName() - Method in class de.unibi.techfak.scie.ontology.driver.NodeName
-
Returns the actual name of the node.
- getName() - Method in class de.unibi.techfak.scie.ontology.driver.OntologyHandle
-
Returns the name of the ontology.
- getNameDescr() - Method in class de.unibi.techfak.scie.ontology.DictionaryMatch
-
Returns the reference to the NodeName this match refers to.
- getNames() - Method in class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Returns the names of the described node.
- getNode() - Method in class de.unibi.techfak.scie.ontology.DictionaryMatch
-
Returns the reference to the related node.
- getNode(NodeHandle) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Returns the node descriptor for a single node.
- getNode(NodeHandle) - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
-
Returns a "Node" instance for the given node handle.
- getNode(NodeDescriptor) - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
-
Returns a "Node" instance for the given node handle.
- getNodes(Collection<NodeHandle>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
-
- getNodes(Collection<NodeHandle>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
-
- getNodes(Collection<NodeHandle>) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Returns the node descriptors for the given node handles.
- getNormalizedName() - Method in enum de.unibi.techfak.scie.annotators.quantities.Unit
-
- getNumber(H) - Method in class de.unibi.techfak.scie.util.Histogramm
-
- getOntologies() - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
-
- getOntologies() - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
-
- getOntologies() - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Returns a list containing all ontologies in the database and an empty
list if no ontologies are present.
- getOntologies() - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
-
Returns a list containing handles to all currently available ontologies.
- getOntology(String, boolean) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
-
- getOntology(String, boolean) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
-
- getOntology() - Method in class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Returns the ontology the described node belongs to.
- getOntology() - Method in class de.unibi.techfak.scie.ontology.driver.NodeHandle
-
Returns the ontology handle.
- getOntology(String, boolean) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Returns a the handle for the ontology with the given name or creates the
ontology if it does not exist.
- getOntology(String) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Returns the handle for the ontology with the given name or creates the
ontology if it does not exist.
- getOntology(String, boolean) - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
-
Returns an ontology handle for an ontology with the given name, if such
an ontology does not exist yet and the "create" flag is set to true, it
is created and the new ontology handle is returned.
- getOntology(String) - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
-
Returns an ontology handle for an ontology with the given name, if such
an ontology does not exist yet, it is created and the new ontology handle
is returned.
- getOntologyDatabase() - Method in class de.unibi.techfak.scie.db.DatabaseInstance
-
- getOntologyDatabase() - Method in class de.unibi.techfak.scie.db.JDBCDatabaseInstance
-
- getOntologyDatabaseDriver() - Method in class de.unibi.techfak.scie.db.DatabaseInstance
-
- getOntologyDatabaseDriver() - Method in class de.unibi.techfak.scie.db.JDBCDatabaseInstance
-
- getOntologyModificationDate(OntologyHandle) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
-
- getOntologyModificationDate(OntologyHandle) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
-
- getOntologyModificationDate(OntologyHandle) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Returns the last update date for the given ontology handle.
- getOntologyModificationDate(OntologyHandle) - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
-
Returns the modification date of the given ontology.
- getParagraphMalus() - Method in class de.unibi.techfak.scie.probability_model.uima.UIMAWordSyntacticProbabilityModel
-
- getParentException() - Method in exception de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver.JDBCDatabaseDriverException
-
Returns the parent exception.
- getPartialMatch() - Method in class de.unibi.techfak.scie.ontology.DictionaryMatch
-
Returns the partial match position (if any).
- getPassword() - Method in class de.unibi.techfak.scie.db.NetworkDatabaseConfiguration
-
- getPatterns() - Method in enum de.unibi.techfak.scie.annotators.quantities.Unit
-
- getPort() - Method in class de.unibi.techfak.scie.db.NetworkDatabaseConfiguration
-
- getPrimaryName() - Method in class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Returns the name part of the primary node name.
- getPrimaryNameDescr() - Method in class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Returns the NodeName instance of the primary node name.
- getProbability() - Method in class de.unibi.techfak.scie.ontology.DictionaryMatch
-
Returns the match probability as a value between 0.0f and 1.0f
- getProbability() - Method in class de.unibi.techfak.scie.probability_model.ProbableHypothesis
-
Returns the probability that this candidate belongs to an Annotation
compositon.
- getProperties() - Method in class de.unibi.techfak.scie.db.JDBCDatabaseInstance
-
- getProperties() - Method in class de.unibi.techfak.scie.db.JDBCRemoteDatabaseInstance
-
- getRelativeMatchProbability(int) - Method in class de.unibi.techfak.scie.ontology.DictionaryMatch
-
Returns the relative match probability (relative to the length of the
complete word).
- getRootNodes(OntologyHandle) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
-
- getRootNodes(OntologyHandle) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
-
- getRootNodes(OntologyHandle) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Returns a list containing all root nodes in the given ontology.
- getRootNodes(OntologyHandle) - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
-
Returns all the nodes that were marked as "root node" in the given
ontology.
- getSchemaSQLForTable(String) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MySQLStatements
-
- getSchemaSQLForTable(String) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.PostgreSQLStatements
-
- getSchemaSQLForTable(String) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns a number of SQL statments that create the schema for the given
table.
- getSchemaVersion() - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
-
- getSchemaVersion() - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Gives the driver the opportunity to return a database version number.
- getSentenceMalus() - Method in class de.unibi.techfak.scie.probability_model.uima.UIMAWordSyntacticProbabilityModel
-
- getSet(String) - Method in class de.unibi.techfak.scie.configuration.Configuration
-
- getSigma() - Method in class de.unibi.techfak.scie.probability_model.uima.UIMAWordSyntacticProbabilityModel
-
- getSource() - Method in class de.unibi.techfak.scie.ontology.driver.Association
-
Returns a reference to the source node.
- getSQLDropTableIfExists(String) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the an SQL string that can be used to drop a table with the given
name.
- getStatement(SQLStatements.SID) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns a prepared statement for the given SID.
- getStatementDeleteAssociation(int, int, int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "deleteAssociation".
- getStatementDeleteAssociationsForOntology(int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "deleteAssociationsForOntology".
- getStatementDeleteDictionaryEntriesForOntology(int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "deleteDictionaryEntriesForOntology".
- getStatementDeleteDictionaryEntry(int, int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "deleteDictionaryEntry".
- getStatementDeleteNodeAssociations(int, int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "deleteNodeAssociations".
- getStatementDeleteNodeID(int, int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "deleteNodeID".
- getStatementDeleteNodeNames(int, int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "deleteNodeNames".
- getStatementDeleteNodeNamesForOntology(int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "deleteNodeNamesForOntology".
- getStatementDeleteNodesForOntology(int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "deleteNodesForOntology".
- getStatementDeleteOntology(int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "deleteNodesForOntology".
- getStatementDeleteTableIfExists(String) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "deleteTableIfExists".
- getStatementGetInboundAssociations(int, int, int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "getInboundAssociations".
- getStatementGetIsRootNode(int, int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "getIsRootNode".
- getStatementGetNodeExists(int, int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "getNodeExists".
- getStatementGetNodeNames(int, int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "getNodeNames".
- getStatementGetOntologies() - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "getOntologies".
- getStatementGetOntologyByID(int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "getOntologyByID".
- getStatementGetOntologyByName(String) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statment "getOntologyByName".
- getStatementGetOntologyDate(int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "getOntologyDate".
- getStatementGetOutboundAssociations(int, int, int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "getOutboundAssociations".
- getStatementGetRootNodes(int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "getRootNodes".
- getStatementGetUndirectedAssociations(int, int, int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "getUndirectedAssociations".
- getStatementInsertAssociation(int, int, int, int) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "insertAssociation".
- getStatementInsertDictionaryEntry(int, int, String) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "insertDictionaryEntry".
- getStatementInsertNodeID(int, int, boolean) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "insertNodeID".
- getStatementInsertNodeName(int, int, String, String, int, boolean) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "insertNodeName".
- getStatementInsertOntology(String) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "insertOntology".
- getStatementQueryDictionary(String) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "queryDictionary".
- getStatements(Connection) - Method in class de.unibi.techfak.scie.db.JDBCDatabaseInstance
-
- getStatements(Connection) - Method in class de.unibi.techfak.scie.db.MySQLDatabaseInstance
-
- getStatements(Connection) - Method in class de.unibi.techfak.scie.db.PostgreSQLDatabaseInstance
-
- getStatementSetOntologyDate(int, Timestamp) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the statement "getOntologyDate".
- getStatementSQL(SQLStatements.SID) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns the SQL for the corresponding statement id.
- getSyntacticModel() - Method in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator.LabGroupCompositor
-
- getSyntacticModel() - Method in class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator.InjuryCompositor
-
- getSyntacticModel() - Method in class de.unibi.techfak.scie.annotators.result.ResultAnnotator.ResultCompositor
-
- getSyntacticModel() - Method in class de.unibi.techfak.scie.annotators.treatment.TreatmentAnnotator.TreatmentCompositor
-
- getTables() - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Returns an array containg the names of each table entry.
- getTarget() - Method in class de.unibi.techfak.scie.ontology.driver.Association
-
Returns a reference to the target node.
- getTarget() - Method in class de.unibi.techfak.scie.ontology.importer.small.AbstractAssociation
-
- getType() - Method in class de.unibi.techfak.scie.ontology.driver.Association
-
Returns the type of the association.
- getType(int) - Static method in enum de.unibi.techfak.scie.ontology.driver.AssociationType
-
Converts an association type value to the corresponding AssociationType
instance.
- getType(String) - Static method in enum de.unibi.techfak.scie.ontology.driver.AssociationType
-
- getType() - Method in class de.unibi.techfak.scie.ontology.driver.NodeName
-
Returns the type of the name (e.g. whether this is a colloquial name, a
brand name, ...).
- getType() - Method in class de.unibi.techfak.scie.ontology.importer.small.AbstractAssociation
-
- getUniqueId() - Static method in class de.unibi.techfak.scie.annotators.AnnotationCounter
-
Returns a unique id.
- getUniqueName() - Method in class de.unibi.techfak.scie.ontology.driver.Handle
-
Function which returns a unique name of the handle.
- getUniqueName() - Method in class de.unibi.techfak.scie.ontology.driver.NodeHandle
-
Returns a unique name of the scheme "ontology:id", or just "id" if the
ontology is null (which does not happen in a real world application).
- getUniqueName() - Method in class de.unibi.techfak.scie.ontology.driver.OntologyHandle
-
Returns the name of the ontology, which uniquely represents the ontology.
- getURL() - Method in class de.unibi.techfak.scie.db.JDBCDatabaseInstance
-
- getURL() - Method in class de.unibi.techfak.scie.db.JDBCRemoteDatabaseInstance
-
- getURLPrefix() - Method in class de.unibi.techfak.scie.db.JDBCRemoteDatabaseInstance
-
- getURLPrefix() - Method in class de.unibi.techfak.scie.db.MySQLDatabaseInstance
-
- getURLPrefix() - Method in class de.unibi.techfak.scie.db.PostgreSQLDatabaseInstance
-
- getUseAuthentication() - Method in class de.unibi.techfak.scie.db.NetworkDatabaseConfiguration
-
- getUser() - Method in class de.unibi.techfak.scie.db.NetworkDatabaseConfiguration
-
- getValue(String, String) - Method in class de.unibi.techfak.scie.configuration.Configuration
-
- getValue(String) - Method in class de.unibi.techfak.scie.configuration.ConfigurationSet
-
- getValue() - Method in enum de.unibi.techfak.scie.ontology.driver.AssociationType
-
Returns the associated value.
- getValue() - Method in enum de.unibi.techfak.scie.ontology.driver.ComparisonMode
-
Returns the value with which the ComparisonMode is stored in the db.
- getWord() - Method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms.WordPosition
-
Returns the word this WordPosition refers to.
- getWords(String, boolean) - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
-
Returns a list of words from the given string.
- getWords(String) - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
-
Returns a list of words from the given string (both strict and non-strict
matches).
- name - Variable in class de.unibi.techfak.scie.annotators.abbreviation.RefInfo
-
- names - Variable in class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
The list of names attached to the node.
- NCBIImporter - Class in de.unibi.techfak.scie.ontology.importer.ncbi
-
The NCBIImporter class imports the nodes and names from the NCBI database
into the ontology database.
- NCBIImporter(OntologyDatabase) - Constructor for class de.unibi.techfak.scie.ontology.importer.ncbi.NCBIImporter
-
Instanciates the importer for the given database.
- NetworkDatabaseConfiguration - Class in de.unibi.techfak.scie.db
-
- NetworkDatabaseConfiguration() - Constructor for class de.unibi.techfak.scie.db.NetworkDatabaseConfiguration
-
- Node - Class in de.unibi.techfak.scie.ontology
-
The Node class extends NodeDescriptor and adds convenience functions that
allow to list all associated nodes or to simply add new associated nodes.
- Node(OntologyDatabase, NodeHandle, Collection<NodeName>, boolean) - Constructor for class de.unibi.techfak.scie.ontology.Node
-
Constructor of the Node class.
- Node(OntologyDatabase, NodeHandle, NodeName, boolean) - Constructor for class de.unibi.techfak.scie.ontology.Node
-
Constructor of the Node class.
- Node(OntologyDatabase, NodeHandle, Collection<NodeName>) - Constructor for class de.unibi.techfak.scie.ontology.Node
-
Constructor of the Node class.
- Node(OntologyDatabase, NodeHandle, NodeName) - Constructor for class de.unibi.techfak.scie.ontology.Node
-
Constructor of the Node class.
- Node(OntologyDatabase, NodeHandle, String, boolean) - Constructor for class de.unibi.techfak.scie.ontology.Node
-
Constructor of the Node class.
- Node(OntologyDatabase, NodeHandle, String) - Constructor for class de.unibi.techfak.scie.ontology.Node
-
Constructor of the Node class.
- Node(OntologyDatabase, OntologyHandle, int, Collection<NodeName>, boolean) - Constructor for class de.unibi.techfak.scie.ontology.Node
-
Constructor of the Node class.
- Node(OntologyDatabase, OntologyHandle, int, Collection<NodeName>) - Constructor for class de.unibi.techfak.scie.ontology.Node
-
Constructor of the Node class.
- Node(OntologyDatabase, OntologyHandle, int, NodeName, boolean) - Constructor for class de.unibi.techfak.scie.ontology.Node
-
Constructor of the Node class.
- Node(OntologyDatabase, OntologyHandle, int, NodeName) - Constructor for class de.unibi.techfak.scie.ontology.Node
-
Constructor of the Node class.
- Node(OntologyDatabase, OntologyHandle, int, String, boolean) - Constructor for class de.unibi.techfak.scie.ontology.Node
-
Constructor of the Node class.
- Node(OntologyDatabase, OntologyHandle, int, String) - Constructor for class de.unibi.techfak.scie.ontology.Node
-
Constructor of the Node class.
- Node(OntologyDatabase, NodeDescriptor) - Constructor for class de.unibi.techfak.scie.ontology.Node
-
Constructor of the Node class.
- NodeDescriptor - Class in de.unibi.techfak.scie.ontology.driver
-
The NodeDescriptor represents the properties of a single node in the ontology
database.
- NodeDescriptor(NodeHandle, Collection<NodeName>, boolean) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Constructor of the NodeDescriptor class.
- NodeDescriptor(NodeHandle, NodeName, boolean) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Constructor of the NodeDescriptor class.
- NodeDescriptor(NodeHandle, Collection<NodeName>) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Constructor of the NodeDescriptor class.
- NodeDescriptor(NodeHandle, NodeName) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Constructor of the NodeDescriptor class.
- NodeDescriptor(NodeHandle, String, boolean) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Constructor of the NodeDescriptor class.
- NodeDescriptor(NodeHandle, String) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Constructor of the NodeDescriptor class.
- NodeDescriptor(OntologyHandle, int, Collection<NodeName>, boolean) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Constructor of the NodeDescriptor class.
- NodeDescriptor(OntologyHandle, int, Collection<NodeName>) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Constructor of the NodeDescriptor class.
- NodeDescriptor(OntologyHandle, int, NodeName, boolean) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Constructor of the NodeDescriptor class.
- NodeDescriptor(OntologyHandle, int, NodeName) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Constructor of the NodeDescriptor class.
- NodeDescriptor(OntologyHandle, int, String, boolean) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Constructor of the NodeDescriptor class.
- NodeDescriptor(OntologyHandle, int, String) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
-
Constructor of the NodeDescriptor class.
- NodeHandle - Class in de.unibi.techfak.scie.ontology.driver
-
The NodeHandle class is used to uniquely identify nodes in the ontology
database.
- NodeHandle(OntologyHandle, int) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeHandle
-
Constructor of the NodeHandle class.
- nodeHandlesFromDescriptors(Collection<NodeDescriptor>) - Static method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Converts a list of node descriptors to a list of node handles.
- NodeName - Class in de.unibi.techfak.scie.ontology.driver
-
The NodeName class represents a single "name" that is attached to a ontology
node.
- NodeName(String, String, ComparisonMode, boolean) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeName
-
Creates a new NodeName instance.
- NodeName(String, String, ComparisonMode) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeName
-
Creates a new NodeName instance.
- NodeName(String, String, boolean) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeName
-
Creates a new NodeName instance.
- NodeName(String, ComparisonMode, boolean) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeName
-
Creates a new NodeName instance.
- NodeName(String, boolean) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeName
-
Creates a new NodeName instance.
- NodeName(String, String) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeName
-
Creates a new NodeName instance.
- NodeName(String, ComparisonMode) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeName
-
Creates a new NodeName instance.
- NodeName(String) - Constructor for class de.unibi.techfak.scie.ontology.driver.NodeName
-
Creates a new NodeName instance.
- normalize(AbstractLineSegment) - Static method in class de.unibi.techfak.scie.util.LineSegment
-
Normalizes the line segment by swapping begin and end if they are in the
wrong order.
- normalize() - Method in class de.unibi.techfak.scie.util.LineSegment
-
Swaps begin and end if the line is not valid.
- normalizedBounds(AbstractLineSegment) - Static method in class de.unibi.techfak.scie.util.LineSegment
-
Returns the boundaries of the normalized line as a two-element array --
normalization means that begin and end are swapped if end is larger than
begin.
- normalizeWord(String, ComparisonMode) - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
-
Normalizes the node name according to the given comparison mode.
- NumberAnnotator - Class in de.unibi.techfak.scie.annotators.quantities
-
This annotates Integers and Floating point numbers in the text and creates
Integer and Double annotations out of it.
- NumberAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.quantities.NumberAnnotator
-
- NUMBERMODEL - Static variable in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator
-
- s - Variable in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms.WordPosition
-
The string this word position refers to.
- SCHEMA_CONFIG_COMMENT - Static variable in class de.unibi.techfak.scie.db.DatabaseInstance
-
- SCHEMA_DEFAULT_VERSION - Static variable in class de.unibi.techfak.scie.db.DatabaseInstance
-
- SCHEMA_KEY_ONTOLOGY - Static variable in class de.unibi.techfak.scie.db.DatabaseInstance
-
- SectionAnnotator - Class in de.unibi.techfak.scie.annotators.structure
-
This annotates sections in the text.
- SectionAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.structure.SectionAnnotator
-
- select(Class<X>) - Method in class de.unibi.techfak.scie.util.CachedJCasUtil
-
Returns all annotations of the given class.
- selectCovered(Class<X>, int, int) - Method in class de.unibi.techfak.scie.util.CachedJCasUtil
-
Returns all annotations of the given class that are contained in the text region specified by
the given begin and end (inclusive).
- selectCovering(Class<X>, int, int) - Method in class de.unibi.techfak.scie.util.CachedJCasUtil
-
Returns all annotations of the given class that contain at least the text region specified by
the given begin and end (inclusive).
- selectOverlapping(Class<X>, int, int) - Method in class de.unibi.techfak.scie.util.CachedJCasUtil
-
Returns all annotations of the given class that are overlapping with the text region specified by
the given begin and end (inclusive).
- SemanticProbabilityModel<X extends AnnotationCandidate> - Interface in de.unibi.techfak.scie.probability_model
-
This is a common interface for classes that implement the functionality to
model the semantic probability
P(w' semanticly belongs to w|w' syntactically belongs to w)
- sentenceMalus - Variable in class de.unibi.techfak.scie.probability_model.uima.UIMAWordSyntacticProbabilityModel
-
We punish if both Annotations are not in the same sentence.
- setBegin(int) - Method in class de.unibi.techfak.scie.util.LineSegment
-
Sets the start position of the line.
- setCandidate(X) - Method in class de.unibi.techfak.scie.probability_model.ProbableHypothesis
-
Set the value of candidate
- setCurrentAge(Age) - Method in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator.NumberModel
-
- setCurrentWeight(Weight) - Method in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator.NumberModel
-
- setEnd(int) - Method in class de.unibi.techfak.scie.util.LineSegment
-
Sets the end position of the line.
- setHost(String) - Method in class de.unibi.techfak.scie.db.NetworkDatabaseConfiguration
-
- setJcas(JCas) - Method in class de.unibi.techfak.scie.probability_model.uima.UIMACompositor
-
- setModificationDate(Date) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver.MemoryDatabaseOntologyHandle
-
- setName(String) - Method in class de.unibi.techfak.scie.db.NetworkDatabaseConfiguration
-
- setOntologyModificationDate(OntologyHandle, Date) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
-
- setOntologyModificationDate(OntologyHandle, Date) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
-
- setOntologyModificationDate(OntologyHandle, Date) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Returns the last update date for the given ontology handle.
- setParagraphMalus(int) - Method in class de.unibi.techfak.scie.probability_model.uima.UIMAWordSyntacticProbabilityModel
-
- setPassword(String) - Method in class de.unibi.techfak.scie.db.NetworkDatabaseConfiguration
-
- setPort(int) - Method in class de.unibi.techfak.scie.db.NetworkDatabaseConfiguration
-
- setProbability(double) - Method in class de.unibi.techfak.scie.ontology.DictionaryMatch
-
Sets the probability to the given value.
- setProbability(double) - Method in class de.unibi.techfak.scie.probability_model.ProbableHypothesis
-
- setSentenceMalus(int) - Method in class de.unibi.techfak.scie.probability_model.uima.UIMAWordSyntacticProbabilityModel
-
- setSigma(double) - Method in class de.unibi.techfak.scie.probability_model.uima.UIMAWordSyntacticProbabilityModel
-
- setSyntacticModel(SyntacticProbabilityModel) - Method in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator.LabGroupCompositor
-
- setSyntacticModel(SyntacticProbabilityModel) - Method in class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator.InjuryCompositor
-
- setSyntacticModel(SyntacticProbabilityModel) - Method in class de.unibi.techfak.scie.annotators.result.ResultAnnotator.ResultCompositor
-
- setSyntacticModel(SyntacticProbabilityModel) - Method in class de.unibi.techfak.scie.annotators.treatment.TreatmentAnnotator.TreatmentCompositor
-
- setUseAuthentication(boolean) - Method in class de.unibi.techfak.scie.db.NetworkDatabaseConfiguration
-
- setUser(String) - Method in class de.unibi.techfak.scie.db.NetworkDatabaseConfiguration
-
- setValue(String, String, String) - Method in class de.unibi.techfak.scie.configuration.Configuration
-
- setValue(String, String) - Method in class de.unibi.techfak.scie.configuration.ConfigurationSet
-
- SHARPNESS - Static variable in class de.unibi.techfak.scie.annotators.structure.HeaderAnnotator
-
A constant factor for the scalar product inside the logistic regression.
- SIGMA - Static variable in class de.unibi.techfak.scie.annotators.animal.ExactAgeAnnotator
-
We expect an age specifier roughly in 10 characters distance.
- SIGMA - Static variable in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator
-
This specifies about how far we search for annotations that belong to a lab group.
- SIGMA - Static variable in class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator
-
This specifies about how far we search for annotations that belong to a Injury.
- SIGMA - Static variable in class de.unibi.techfak.scie.annotators.result.ResultAnnotator
-
This specifies about how far we search for annotations that belong to a OutCome.
- SIGMA - Static variable in class de.unibi.techfak.scie.annotators.treatment.TreatmentAnnotator
-
This specifies about how far we search for annotations that belong to a
Treatment.
- SIGNIFICANCE - Static variable in class de.unibi.techfak.scie.annotators.result.ResultAnnotator
-
- SmallImporter - Class in de.unibi.techfak.scie.ontology.importer.small
-
- SmallImporter(OntologyDatabase, String) - Constructor for class de.unibi.techfak.scie.ontology.importer.small.SmallImporter
-
- SQLStatements - Class in de.unibi.techfak.scie.ontology.driver.implementation
-
The SQLStatements class bundles the possible SQL statments that can be made
on the OntologyDatabase.
- SQLStatements(Connection) - Constructor for class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
-
Initializes the JDBCSQLStatments class.
- SQLStatements.SID - Enum in de.unibi.techfak.scie.ontology.driver.implementation
-
Enum that contains IDS for all possible statements (statement
identifiers, SID)
- StanfordTokenizer - Class in de.unibi.techfak.scie.annotators.structure
-
This uses the Stanford POS Tagger to tokenize sentences and words and give the words a POS
feature.
- StanfordTokenizer() - Constructor for class de.unibi.techfak.scie.annotators.structure.StanfordTokenizer
-
- STOPWORD - Static variable in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
-
Pattern containing all stop-words.
- storeAssociation(Association) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Stores the given associations.
- storeAssociations(Collection<Association>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
-
- storeAssociations(Collection<Association>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
-
- storeAssociations(Collection<Association>) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Stores the given associations.
- storeDictionaryEntries(Map<NodeHandle, Set<String>>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
-
- storeDictionaryEntries(Map<NodeHandle, Set<String>>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
-
- storeDictionaryEntries(Map<NodeHandle, Set<String>>) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Stores the given node to key associations in the dictionary.
- storeDictionaryEntry(NodeHandle, Set<String>) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Stores the given node to key association in the dictionary.
- storeNode(NodeDescriptor) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Stores a single node in the database.
- storeNode(NodeDescriptor) - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
-
Stores the given NodeDescriptor in the database.
- storeNodes(Collection<NodeDescriptor>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
-
- storeNodes(Collection<NodeDescriptor>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
-
- storeNodes(Collection<NodeDescriptor>) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
-
Stores the given nodes in the database.
- storeXMLConfiguration(OutputStream) - Method in class de.unibi.techfak.scie.configuration.Configuration
-
- stripNonAlphabetic(String) - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
-
Convert the incomming string to lowercase, remove any special character.
- stripNonAlphanumeric(String) - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
-
Convert the incomming string to lowercase, remove any non alphanumeric
character.
- stripWhitespace(String) - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
-
Strip all whitespace from the given string.
- StructureAnnotator - Class in de.unibi.techfak.scie.annotators.structure
-
This annotates the page structure in Documents that have been imported by the
PDFStructuredTextExctractor.
- StructureAnnotator(Document) - Constructor for class de.unibi.techfak.scie.annotators.structure.StructureAnnotator
-
- SUFFIXES - Static variable in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
-
Pattern containing all suffixes which should be removed.
- SWITCHLENGTH - Static variable in class de.unibi.techfak.scie.annotators.structure.HeaderAnnotator
-
We think that a "normal" header should have less characters than this
number.
- SyntacticProbabilityModel - Interface in de.unibi.techfak.scie.probability_model
-
This is an interface for classes that are able to calculate the probability
that two given AnnotationCandidates belong together from a syntactic
perspective.