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

A

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.

B

begin - Variable in class de.unibi.techfak.scie.util.LineSegment
Start position of the line.
boundariesEqual(AbstractLineSegment, AbstractLineSegment) - Static method in class de.unibi.techfak.scie.util.LineSegment
Returns true if the boundaries of the two line segments are equal.
boundariesEqual(AbstractLineSegment) - Method in class de.unibi.techfak.scie.util.LineSegment
Returns true if the boundaries of the two line segments are equal.

C

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.

D

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
 

E

editDistance(String, String) - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
Calculates the edit distance between word w1 and word w2.
end - Variable in class de.unibi.techfak.scie.util.LineSegment
End position of the line.
ensureSchema() - Method in class de.unibi.techfak.scie.db.DatabaseInstance
 
equals(Object) - Method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms.WordPosition
Two WordPosition instances equal if they point to the same string and have the same begin and end.
equals(Object) - Method in class de.unibi.techfak.scie.ontology.DictionaryMatch
Checks whether the two DictionaryMatch instances equal.
equals(Object) - Method in class de.unibi.techfak.scie.ontology.driver.Association
Checks whether the two given objects are equal.
equals(Object) - Method in class de.unibi.techfak.scie.ontology.driver.Handle
Two handles equal each other if their unique name is equal.
equals(Object) - Method in class de.unibi.techfak.scie.ontology.driver.NodeName
Checks whether both name and type equal.
ExactAgeAnnotator - Class in de.unibi.techfak.scie.annotators.animal
This annotates more specific description of a lab animals age based on a specific time like "27 years old" or "2 weeks of age".
ExactAgeAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.animal.ExactAgeAnnotator
 

F

finalizeStatements() - Method in class de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements
Closes the created prepared statements.
firstWhitespaceIndex(String) - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
Returns the position of the first whitespace in the given string or Integer.MAX_VALUE if there is no whitespace in the string.
flush(OntologyDatabase, OntologyHandle) - Method in class de.unibi.techfak.scie.ontology.importer.small.AssociationList
 
FolderImporter - Class in de.unibi.techfak.scie.ontology.importer
 
FolderImporter() - Constructor for class de.unibi.techfak.scie.ontology.importer.FolderImporter
 

G

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).

H

handle - Variable in class de.unibi.techfak.scie.annotators.abbreviation.RefInfo
 
Handle - Class in de.unibi.techfak.scie.ontology.driver
The Handle class is used to uniquely identify objects in the ontology database.
Handle() - Constructor for class de.unibi.techfak.scie.ontology.driver.Handle
 
handle - Variable in class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
The handle of the node the descriptor describes.
handleQuantity(Quantity, Unit, List<Token>, JCas) - Method in class de.unibi.techfak.scie.annotators.animal.WeightAnnotator
 
handleQuantity(Quantity, Unit, List<Token>, JCas) - Method in class de.unibi.techfak.scie.annotators.quantities.TimeAnnotator
 
handleQuantity(Quantity, Unit, List<Token>, JCas) - Method in class de.unibi.techfak.scie.annotators.quantities.UnitQuantityAnnotator
 
handleQuantity(Quantity, Unit, List<Token>, JCas) - Method in class de.unibi.techfak.scie.annotators.treatment.DoseAnnotator
 
handlesToNodeList(Collection<NodeHandle>) - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
Converts a list of NodeHandle instances to high-level "Node" instances.
hashCode() - Method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms.WordPosition
Returns the hash code which is constructed from the begin, the end position and the hash code of the string this name refers to.
hashCode() - Method in class de.unibi.techfak.scie.ontology.DictionaryMatch
Returns a hash code of the object that depends on the node handle, the node name and the begin and end.
hashCode() - Method in class de.unibi.techfak.scie.ontology.driver.Association
Calculates a hash code for the Association from the source node and target node.
hashCode() - Method in class de.unibi.techfak.scie.ontology.driver.Handle
Returns the hash code of the unique name.
hashCode() - Method in class de.unibi.techfak.scie.ontology.driver.NodeName
Computes an hash code from both name and type.
HeaderAnnotator - Class in de.unibi.techfak.scie.annotators.structure
This annotates headers/Überschriften of sections in the paper text.
HeaderAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.structure.HeaderAnnotator
 
HEIGHTMODEL - Static variable in class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator
 
Histogramm<H> - Class in de.unibi.techfak.scie.util
A convenience implementation for histogramms.
Histogramm() - Constructor for class de.unibi.techfak.scie.util.Histogramm
 

I

importOntology(File, boolean) - Method in class de.unibi.techfak.scie.ontology.importer.AbstractImporter
 
InexactQuantityAnnotator - Class in de.unibi.techfak.scie.annotators.quantities
This annotates InexactQuantities, which means LanguageQuantifiers in the text.
InexactQuantityAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.quantities.InexactQuantityAnnotator
 
initialize(String) - Static method in class de.unibi.techfak.scie.db.DatabaseSingleton
 
initialize() - Static method in class de.unibi.techfak.scie.db.DatabaseSingleton
 
initializeSchema() - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
Creates all tables that do not exist yet.
InjuryAnnotator - Class in de.unibi.techfak.scie.annotators.injury
 
InjuryAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator
 
InjuryAnnotator.DurationModel - Class in de.unibi.techfak.scie.annotators.injury
The likelihood model for Durations.
InjuryAnnotator.DurationModel() - Constructor for class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator.DurationModel
 
InjuryAnnotator.InjuryCompositor - Class in de.unibi.techfak.scie.annotators.injury
 
InjuryAnnotator.InjuryCompositor() - Constructor for class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator.InjuryCompositor
 
InjuryAnnotator.InjuryDeviceModel - Class in de.unibi.techfak.scie.annotators.injury
The likelihood model for InjuryDevice.
InjuryAnnotator.InjuryDeviceModel() - Constructor for class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator.InjuryDeviceModel
 
InjuryAnnotator.InjuryHeightModel - Class in de.unibi.techfak.scie.annotators.injury
The likelihood model for InjuryHeight.
InjuryAnnotator.InjuryHeightModel() - Constructor for class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator.InjuryHeightModel
 
input - Variable in class de.unibi.techfak.scie.document_import.DocumentImporter
The input stream given in the constructor.
intersection(AbstractLineSegment, AbstractLineSegment) - Static method in class de.unibi.techfak.scie.util.LineSegment
Returns a new line which is the union of the two lines.
INTPATTERNS - Static variable in class de.unibi.techfak.scie.annotators.quantities.NumberAnnotator
 
InvalidAssociationException - Exception in de.unibi.techfak.scie.ontology.driver
The InvalidAssociationException is thrown whenever an association is created that is not valid.
InvalidAssociationException(String) - Constructor for exception de.unibi.techfak.scie.ontology.driver.InvalidAssociationException
Constructor of the InvalidAssociationException.
InvalidNameException - Exception in de.unibi.techfak.scie.ontology
The InvalidNameException is thrown whenever an ontology entry is created that does not adhere to certain naming conventions.
InvalidNameException(String) - Constructor for exception de.unibi.techfak.scie.ontology.InvalidNameException
Constructor of the InvalidNameException.
InvalidNodeException - Exception in de.unibi.techfak.scie.ontology
The InvalidNodeException is thrown whenever a node should be stored for which the ontology does not exist or a node should be updated that does not exist.
InvalidNodeException(String) - Constructor for exception de.unibi.techfak.scie.ontology.InvalidNodeException
Constructor of the InvalidNodeException.
isA(NodeHandle) - Method in class de.unibi.techfak.scie.ontology.Node
This checks whether there exists a list of nodes this, n_1, n_2, ..., n_k, p such that there exists an ISA-Association from each node in the list to the next one.
isAlphabetic(char) - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
 
isAlphanumeric(char) - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
 
isNumeric(char) - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
 
isPrimary() - Method in class de.unibi.techfak.scie.ontology.driver.NodeName
Returns whether this node is primary or not.
isRoot() - Method in class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
Returns whether the node is a root node or not.
isStopWord(String) - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
Returns true if the given word is a stop word.
isValid(String) - Method in class de.unibi.techfak.scie.configuration.ConfigurationEntry
 
isValid(String) - Method in interface de.unibi.techfak.scie.configuration.ConfigurationEntry.ValidityChecker
 
isValid(AbstractLineSegment) - Static method in class de.unibi.techfak.scie.util.LineSegment
Returns true if the given line is valid (its begin is smaller or equal to its end).
isValid() - Method in class de.unibi.techfak.scie.util.LineSegment
Returns true if this line is valid (its begin is smaller or equal to its end).

J

JDBCDatabaseDriver - Class in de.unibi.techfak.scie.ontology.driver.implementation
The JDBCDatabaseDriver builds the base class for ontology databases that are based on an relational SQL database.
JDBCDatabaseDriver(Connection, SQLStatements) - Constructor for class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
Constructor of the JDBCDatabaseDriver class.
JDBCDatabaseDriver.JDBCDatabaseDriverException - Exception in de.unibi.techfak.scie.ontology.driver.implementation
JDBCDatabaseDriverException is a thin wrapper around DatabaseDriverException that allows for a fast conversion from SQLException to DatabaseDriverException.
JDBCDatabaseDriver.JDBCDatabaseDriverException(String, Exception) - Constructor for exception de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver.JDBCDatabaseDriverException
Creates an instance of the JDBCDatabaseDriverException class.
JDBCDatabaseDriver.JDBCDatabaseDriverException(String) - Constructor for exception de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver.JDBCDatabaseDriverException
Creates an instance of the JDBCDatabaseDriverException class.
JDBCDatabaseDriver.JDBCDatabaseDriverException(SQLException) - Constructor for exception de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver.JDBCDatabaseDriverException
Creates an instance of the JDBCDatabaseDriverException class.
JDBCDatabaseDriver.JDBCOntologyHandle - Class in de.unibi.techfak.scie.ontology.driver.implementation
The JDBCOntologyHandle class is the OntologyHandle type used by the JDBC database.
JDBCDatabaseDriver.JDBCOntologyHandle(String, int) - Constructor for class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver.JDBCOntologyHandle
Constructor of the JDBCOntologyHandle class.
JDBCDatabaseInstance - Class in de.unibi.techfak.scie.db
 
JDBCDatabaseInstance(ConfigurationSet) - Constructor for class de.unibi.techfak.scie.db.JDBCDatabaseInstance
 
JDBCRemoteDatabaseInstance - Class in de.unibi.techfak.scie.db
 
JDBCRemoteDatabaseInstance(ConfigurationSet) - Constructor for class de.unibi.techfak.scie.db.JDBCRemoteDatabaseInstance
 
JudgementAnnotator - Class in de.unibi.techfak.scie.annotators.result
 
JudgementAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.result.JudgementAnnotator
 

K

KEYWORDS - Static variable in class de.unibi.techfak.scie.annotators.animal.ExactAgeAnnotator
 
KEYWORDWEIGHT - Static variable in class de.unibi.techfak.scie.annotators.structure.HeaderAnnotator
This determines how the occurence of a HeaderKeyword is weighted relative to the font size.

L

LabGroupAnnotator - Class in de.unibi.techfak.scie.annotators.animal
This Annotator accumulates the output of all other Taxonomy-Annotators to a Lab Group Annotation.
LabGroupAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator
 
LabGroupAnnotator.AgeModel - Class in de.unibi.techfak.scie.annotators.animal
The likelihood model for ages.
LabGroupAnnotator.AgeModel() - Constructor for class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator.AgeModel
 
LabGroupAnnotator.GenderModel - Class in de.unibi.techfak.scie.annotators.animal
The trivial likelihood Model for Gender.
LabGroupAnnotator.GenderModel() - Constructor for class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator.GenderModel
 
LabGroupAnnotator.LabGroupCompositor - Class in de.unibi.techfak.scie.annotators.animal
 
LabGroupAnnotator.LabGroupCompositor() - Constructor for class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator.LabGroupCompositor
 
LabGroupAnnotator.NumberModel - Class in de.unibi.techfak.scie.annotators.animal
The LikelihoodModel for numbers.
LabGroupAnnotator.NumberModel() - Constructor for class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator.NumberModel
 
LabGroupAnnotator.WeightModel - Class in de.unibi.techfak.scie.annotators.animal
The likelihood model for Weights.
LabGroupAnnotator.WeightModel() - Constructor for class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator.WeightModel
 
length(AbstractLineSegment) - Static method in class de.unibi.techfak.scie.util.LineSegment
Returns the length of the line segment.
length() - Method in class de.unibi.techfak.scie.util.LineSegment
Returns the length of the line segment.
LENGTHWEIGHT - Static variable in class de.unibi.techfak.scie.annotators.structure.HeaderAnnotator
This determines how the block length is weighted relative to the font size.
LineSegment - Class in de.unibi.techfak.scie.util
The LineSegment class implements the AbstractLineSegmentSegment interface and adds (static) utility functions that help to compare to lines.
LineSegment() - Constructor for class de.unibi.techfak.scie.util.LineSegment
Initializes the line segment as invalid, with begin being set to INF and end being set to -INF.
LineSegment(int, int) - Constructor for class de.unibi.techfak.scie.util.LineSegment
Initializes the line segment with the given begin and end.
loadConfigurationIfExists(String) - Static method in class de.unibi.techfak.scie.configuration.ConfigurationSingleton
 
loadXMLConfiguration(InputStream) - Method in class de.unibi.techfak.scie.configuration.Configuration
 

M

Main - Class in de.unibi.techfak.scie
This is the command line interface for the SCIE project.
Main() - Constructor for class de.unibi.techfak.scie.Main
 
main(String[]) - Static method in class de.unibi.techfak.scie.Main
 
main(String[]) - Static method in class de.unibi.techfak.scie.ontology.importer.FolderImporter
Imports all *.xml in a Folder as small ontology into db
main(String[]) - Static method in class de.unibi.techfak.scie.ontology.importer.XMLImporter
 
matchProbability(String, String) - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
Calculates the "match probability" between w1 and w2 as a value between 0.0f and 1.0f.
MAXAGE - Static variable in class de.unibi.techfak.scie.annotators.animal.ExactAgeAnnotator
The maximum age we accept in seconds. (200 years)
MAXOVERLAPPING - Static variable in class de.unibi.techfak.scie.annotators.result.ResultAnnotator
This determines how many aggregations in the same text we accept at max.
MemoryDatabaseDriver - Class in de.unibi.techfak.scie.ontology.driver.implementation
 
MemoryDatabaseDriver() - Constructor for class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
 
MemoryDatabaseDriver.MemoryDatabaseOntologyHandle - Class in de.unibi.techfak.scie.ontology.driver.implementation
The JDBCOntologyHandle class is the OntologyHandle type used by the JDBC database.
MemoryDatabaseDriver.MemoryDatabaseOntologyHandle(String) - Constructor for class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver.MemoryDatabaseOntologyHandle
Constructor of the JDBCOntologyHandle class.
MeshImporter - Class in de.unibi.techfak.scie.ontology.importer.mesh
 
MeshImporter(OntologyDatabase) - Constructor for class de.unibi.techfak.scie.ontology.importer.mesh.MeshImporter
Instanciates the importer for the given database.
MeshImporter2 - Class in de.unibi.techfak.scie.ontology.importer.mesh
 
MeshImporter2(OntologyDatabase) - Constructor for class de.unibi.techfak.scie.ontology.importer.mesh.MeshImporter2
Instanciates the importer for the given database.
MIN_WORD_LENGTH - Static variable in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
Minimim word length.
MODEL - Static variable in class de.unibi.techfak.scie.annotators.animal.ExactAgeAnnotator
This decides whether a word is an age specifier as given by the Keywords pattern above.
MODELS - Static variable in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator
 
MODELS - Static variable in class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator
 
MODELS - Static variable in class de.unibi.techfak.scie.annotators.result.ResultAnnotator
 
MODELS - Static variable in class de.unibi.techfak.scie.annotators.treatment.TreatmentAnnotator
 
MySQLDatabaseInstance - Class in de.unibi.techfak.scie.db
 
MySQLDatabaseInstance(ConfigurationSet) - Constructor for class de.unibi.techfak.scie.db.MySQLDatabaseInstance
 
MySQLStatements - Class in de.unibi.techfak.scie.ontology.driver.implementation
Contains all deviations between the sql statements listed in the DefaultSQLStatements class and the statements needed for a PostgreSQL DB.
MySQLStatements(Connection) - Constructor for class de.unibi.techfak.scie.ontology.driver.implementation.MySQLStatements
 

N

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
 

O

OntologyAnnotator - Class in de.unibi.techfak.scie.annotators.ontology
The OntologyAnnotator is responsible for generating annotations that originate from the ontology database.
OntologyAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.ontology.OntologyAnnotator
 
OntologyAnnotator.ProbabilityComparator - Class in de.unibi.techfak.scie.annotators.ontology
 
OntologyAnnotator.ProbabilityComparator() - Constructor for class de.unibi.techfak.scie.annotators.ontology.OntologyAnnotator.ProbabilityComparator
 
OntologyDatabase - Class in de.unibi.techfak.scie.ontology
The OntologyDatabase class builds the main API of the ontology database.
OntologyDatabase(OntologyDatabaseDriver) - Constructor for class de.unibi.techfak.scie.ontology.OntologyDatabase
Constructor of the OntologyDatabase class.
OntologyDatabaseDriver - Class in de.unibi.techfak.scie.ontology.driver
The DatabaseDriver class describes an interface that must be implemented by the actual database backend.
OntologyDatabaseDriver() - Constructor for class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
 
OntologyDatabaseDriverException - Exception in de.unibi.techfak.scie.ontology.driver
The DatabaseDriverException is stored whenever an error occurs while using the ontology database backend.
OntologyDatabaseDriverException(String) - Constructor for exception de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriverException
Create the DatabaseDriver exception.
OntologyHandle - Class in de.unibi.techfak.scie.ontology.driver
The OntologyHandle class is used to uniquely identify ontologies in the ontology database.
OntologyHandle(String) - Constructor for class de.unibi.techfak.scie.ontology.driver.OntologyHandle
Creates a new instance of OntologyHandle and copies the given name.
ontologyName - Variable in class de.unibi.techfak.scie.ontology.importer.AbstractImporter
Name of the ncbi ontology.
overlaps(AbstractLineSegment, AbstractLineSegment) - Static method in class de.unibi.techfak.scie.util.LineSegment
Returns true if the boundaries of the two line segments overlap.
overlaps(AbstractLineSegment) - Method in class de.unibi.techfak.scie.util.LineSegment
Returns true if the boundaries of the two line segments overlap.

P

paragraphMalus - Variable in class de.unibi.techfak.scie.probability_model.uima.UIMAWordSyntacticProbabilityModel
We punish if both Annotations are not in the same paragraph.
parseRomanInt(String, String, String, String) - Method in class de.unibi.techfak.scie.annotators.quantities.RomanNumberAnnotator
 
parseXML(OntologyHandle, XMLStreamReader) - Method in class de.unibi.techfak.scie.ontology.importer.AbstractImporter
Flushes all data from xml into db.
parseXML(OntologyHandle, XMLStreamReader) - Method in class de.unibi.techfak.scie.ontology.importer.drug_bank.DrugBankImporter
Flushes all data from Drugbank xml into db.
parseXML(OntologyHandle, XMLStreamReader) - Method in class de.unibi.techfak.scie.ontology.importer.mesh.MeshImporter
Flushes all data from desc xml(Mesh) into db.
parseXML(OntologyHandle, XMLStreamReader) - Method in class de.unibi.techfak.scie.ontology.importer.mesh.MeshImporter2
Flushes all data from desc xml(Mesh) into db.
parseXML(OntologyHandle, XMLStreamReader) - Method in class de.unibi.techfak.scie.ontology.importer.ncbi.NCBIImporter
 
parseXML(OntologyHandle, XMLStreamReader) - Method in class de.unibi.techfak.scie.ontology.importer.small.SmallImporter
 
PDFStructuredTextExtractorWrapper - Class in de.unibi.techfak.scie.document_import
This class is a wrapper for the SCIE PDFTextExtractor.
PDFStructuredTextExtractorWrapper(InputStream, JCas) - Constructor for class de.unibi.techfak.scie.document_import.PDFStructuredTextExtractorWrapper
 
PLAINDOUBLE - Static variable in class de.unibi.techfak.scie.annotators.quantities.NumberAnnotator
 
PLAININT - Static variable in class de.unibi.techfak.scie.annotators.quantities.NumberAnnotator
 
PostgreSQLDatabaseInstance - Class in de.unibi.techfak.scie.db
 
PostgreSQLDatabaseInstance(ConfigurationSet) - Constructor for class de.unibi.techfak.scie.db.PostgreSQLDatabaseInstance
 
PostgreSQLStatements - Class in de.unibi.techfak.scie.ontology.driver.implementation
Contains all deviations between the sql statements listed in the DefaultSQLStatements class and the statements needed for a PostgreSQL DB.
PostgreSQLStatements(Connection) - Constructor for class de.unibi.techfak.scie.ontology.driver.implementation.PostgreSQLStatements
 
preprocessRawDoubleString(String) - Method in class de.unibi.techfak.scie.annotators.quantities.NumberAnnotator
 
ProbableHypothesis<X extends AnnotationCandidate> - Class in de.unibi.techfak.scie.probability_model
This is a wrapper class to return a hypothesis with its probability to belong to an Annotation Composition.
ProbableHypothesis() - Constructor for class de.unibi.techfak.scie.probability_model.ProbableHypothesis
 
ProbableHypothesis(X, double) - Constructor for class de.unibi.techfak.scie.probability_model.ProbableHypothesis
 
process(JCas) - Method in class de.unibi.techfak.scie.analysis.AnalysisAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.AnnotatorPipeline
Runs all annotators stored in this pipeline on the given input JCas instance.
process(JCas) - Method in class de.unibi.techfak.scie.annotators.abbreviation.AbbreviationAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.animal.ExactAgeAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.injury.VertebralPositionAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.injury.VertebralPositionRangeAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.ontology.OntologyAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.quantities.DurationAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.quantities.InexactQuantityAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.quantities.NumberAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.quantities.RangeAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.quantities.RomanNumberAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.quantities.UnitQuantityAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.quantities.WordNumberAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.result.JudgementAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.result.PValueAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.result.ResultAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.structure.HeaderAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.structure.SectionAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.structure.StanfordTokenizer
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.structure.StructureAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.treatment.AntiBodyAnnotator
 
process(JCas) - Method in class de.unibi.techfak.scie.annotators.treatment.TreatmentAnnotator
 
processDocumentText() - Method in class de.unibi.techfak.scie.ontology.dictionary_name_finder.DictionaryNameFinder
Automatically processes all words that occur in the documentText given in the constructor.
processWord(String, int) - Method in class de.unibi.techfak.scie.ontology.dictionary_name_finder.DictionaryNameFinder
Searches for the given word in the dictionary (batched).
PROJECT_NAME - Static variable in class de.unibi.techfak.scie.Main
 
purgeWordsCache() - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
This clears the caches for the getWords method.
PVALUE - Static variable in class de.unibi.techfak.scie.annotators.result.ResultAnnotator
 
PValueAnnotator - Class in de.unibi.techfak.scie.annotators.result
This annotates P- or significance-values like P < 0.05.
PValueAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.result.PValueAnnotator
 

Q

query(Collection<String>) - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
Queries a set of words from the database an returns a map between these words and the corresponding dictionary entries.
query(String) - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
Queries a single word from the dictionary.
queryAllNodesExist(Collection<NodeHandle>) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
Checks whether all given nodes exist.
queryDictionary(Set<String>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
 
queryDictionary(Set<String>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
 
queryDictionary(Set<String>) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
Queries the dictionary for the given keys.
queryDictionary(String) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
Queries the dictionary for a given key.
queryNodeExists(NodeHandle) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
Checks whether the given node handle is valid.
queryNodesExist(Collection<NodeHandle>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
 
queryNodesExist(Collection<NodeHandle>) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.MemoryDatabaseDriver
 
queryNodesExist(Collection<NodeHandle>) - Method in class de.unibi.techfak.scie.ontology.driver.OntologyDatabaseDriver
Checks whether the given nodes exist.
queryOntologyExists(String) - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
Returns true if the given ontology exists.

R

RangeAnnotator - Class in de.unibi.techfak.scie.annotators.quantities
This annotates ranges of numbers such as 4 - 5 or 30 to 40.
RangeAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.quantities.RangeAnnotator
 
REDUCE_SPACES - Static variable in class de.unibi.techfak.scie.ontology.importer.AbstractImporter
 
reduceMatches(String, List<DictionaryMatch>) - Static method in class de.unibi.techfak.scie.ontology.DictionaryMatch
Removes all overlapping matches to the same node name that only differ in non-alphanumeric characters.
RefInfo - Class in de.unibi.techfak.scie.annotators.abbreviation
 
RefInfo(NodeName, NodeHandle) - Constructor for class de.unibi.techfak.scie.annotators.abbreviation.RefInfo
 
registerConfigurationSet(String, Collection<ConfigurationEntry>) - Method in class de.unibi.techfak.scie.configuration.Configuration
 
registerConfigurationSet(String, ConfigurationEntry[]) - Method in class de.unibi.techfak.scie.configuration.Configuration
 
remove(Class<X>, X) - Method in class de.unibi.techfak.scie.util.CachedJCasUtil
 
reset() - Static method in class de.unibi.techfak.scie.annotators.AnnotationCounter
Resets the id counter.
reset() - Method in class de.unibi.techfak.scie.configuration.Configuration
 
reset() - Static method in class de.unibi.techfak.scie.db.DatabaseSingleton
 
ResultAnnotator - Class in de.unibi.techfak.scie.annotators.result
 
ResultAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.result.ResultAnnotator
 
ResultAnnotator.PValueModel - Class in de.unibi.techfak.scie.annotators.result
The trivial likelihood Model for OutComePart.
ResultAnnotator.PValueModel() - Constructor for class de.unibi.techfak.scie.annotators.result.ResultAnnotator.PValueModel
 
ResultAnnotator.ResultCompositor - Class in de.unibi.techfak.scie.annotators.result
 
ResultAnnotator.ResultCompositor() - Constructor for class de.unibi.techfak.scie.annotators.result.ResultAnnotator.ResultCompositor
 
ResultAnnotator.SignificanceModel - Class in de.unibi.techfak.scie.annotators.result
The likelihood model for the Significance.
ResultAnnotator.SignificanceModel() - Constructor for class de.unibi.techfak.scie.annotators.result.ResultAnnotator.SignificanceModel
 
ResultAnnotator.TrendModel - Class in de.unibi.techfak.scie.annotators.result
The likelihood model for the Trend.
ResultAnnotator.TrendModel() - Constructor for class de.unibi.techfak.scie.annotators.result.ResultAnnotator.TrendModel
 
ROMANINT - Static variable in class de.unibi.techfak.scie.annotators.quantities.RomanNumberAnnotator
 
RomanNumberAnnotator - Class in de.unibi.techfak.scie.annotators.quantities
This annotates Roman Numbers like III or LXI.
RomanNumberAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.quantities.RomanNumberAnnotator
 
root - Variable in class de.unibi.techfak.scie.ontology.driver.NodeDescriptor
Specifies whether this node is a root node or not.

S

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.

T

tableExists(String) - Method in class de.unibi.techfak.scie.ontology.driver.implementation.JDBCDatabaseDriver
Checks whether an table with the given name exist.
target - Variable in class de.unibi.techfak.scie.document_import.DocumentImporter
The target CAS instance.
THRESHOLD - Static variable in class de.unibi.techfak.scie.annotators.animal.ExactAgeAnnotator
The threshold we require for the probability of an age specifier.
THRESHOLD - Static variable in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator
LabGroup annotations below this probability threshold are thrown away.
THRESHOLD - Static variable in class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator
Injury annotations below this probability threshold are thrown away.
THRESHOLD - Static variable in class de.unibi.techfak.scie.annotators.result.ResultAnnotator
OutCome annotations below this probability threshold are thrown away.
THRESHOLD - Static variable in class de.unibi.techfak.scie.annotators.structure.HeaderAnnotator
We regard everything as a header that has a higher confidence than THRESHOLD according to our logistic regression (see below).
THRESHOLD - Static variable in class de.unibi.techfak.scie.annotators.treatment.TreatmentAnnotator
Treatment annotations below this probability threshold are thrown away.
TimeAnnotator - Class in de.unibi.techfak.scie.annotators.quantities
This annotates times.
TimeAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.quantities.TimeAnnotator
 
toString() - Method in class de.unibi.techfak.scie.ontology.driver.Handle
Returns the unique name.
toString() - Method in class de.unibi.techfak.scie.ontology.driver.NodeName
Returns the name in a string representation of the form "name [type]" if the type is non-null or returns just the name.
TreatmentAnnotator - Class in de.unibi.techfak.scie.annotators.treatment
 
TreatmentAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.treatment.TreatmentAnnotator
 
TreatmentAnnotator.DeliveryModel - Class in de.unibi.techfak.scie.annotators.treatment
The trivial likelihood Model for Delivery.
TreatmentAnnotator.DeliveryModel() - Constructor for class de.unibi.techfak.scie.annotators.treatment.TreatmentAnnotator.DeliveryModel
 
TreatmentAnnotator.DoseModel - Class in de.unibi.techfak.scie.annotators.treatment
The likelihood model for the Dose.
TreatmentAnnotator.DoseModel() - Constructor for class de.unibi.techfak.scie.annotators.treatment.TreatmentAnnotator.DoseModel
 
TreatmentAnnotator.TreatmentCompositor - Class in de.unibi.techfak.scie.annotators.treatment
 
TreatmentAnnotator.TreatmentCompositor() - Constructor for class de.unibi.techfak.scie.annotators.treatment.TreatmentAnnotator.TreatmentCompositor
 
TREND - Static variable in class de.unibi.techfak.scie.annotators.result.ResultAnnotator
 
TYPESYSTEM - Static variable in class de.unibi.techfak.scie.Main
 

U

UIMAAnnotationCompositionUtil - Class in de.unibi.techfak.scie.probability_model.uima
This class provides some convenience functions to use the AnnotationCompositionUtil with UIMA annotations.
UIMAAnnotationCompositionUtil() - Constructor for class de.unibi.techfak.scie.probability_model.uima.UIMAAnnotationCompositionUtil
 
UIMAAnnotationCompositionUtil.UIMAAnnotationCandidate<X extends org.apache.uima.jcas.tcas.Annotation> - Class in de.unibi.techfak.scie.probability_model.uima
 
UIMAAnnotationCompositionUtil.UIMAAnnotationCandidate(X) - Constructor for class de.unibi.techfak.scie.probability_model.uima.UIMAAnnotationCompositionUtil.UIMAAnnotationCandidate
 
UIMAAnnotationCompositionUtil.UIMASemanticProbabilityModel<X extends org.apache.uima.jcas.tcas.Annotation> - Class in de.unibi.techfak.scie.probability_model.uima
 
UIMAAnnotationCompositionUtil.UIMASemanticProbabilityModel() - Constructor for class de.unibi.techfak.scie.probability_model.uima.UIMAAnnotationCompositionUtil.UIMASemanticProbabilityModel
 
UIMACompose(Annotation, ArrayList<ProbableHypothesis>, int, int, JCas) - Method in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator.LabGroupCompositor
 
UIMACompose(Annotation, ArrayList<ProbableHypothesis>, int, int, JCas) - Method in class de.unibi.techfak.scie.annotators.injury.InjuryAnnotator.InjuryCompositor
 
UIMACompose(Annotation, ArrayList<ProbableHypothesis>, int, int, JCas) - Method in class de.unibi.techfak.scie.annotators.result.ResultAnnotator.ResultCompositor
 
UIMACompose(Annotation, ArrayList<ProbableHypothesis>, int, int, JCas) - Method in class de.unibi.techfak.scie.annotators.treatment.TreatmentAnnotator.TreatmentCompositor
 
UIMACompose(Annotation, ArrayList<ProbableHypothesis>, int, int, JCas) - Method in class de.unibi.techfak.scie.probability_model.uima.UIMACompositor
 
UIMACompositor<Y extends org.apache.uima.jcas.tcas.Annotation> - Class in de.unibi.techfak.scie.probability_model.uima
This is an interface for classes that are able to compose from one candidate for each attribute of a composition annotation the composition.
UIMACompositor() - Constructor for class de.unibi.techfak.scie.probability_model.uima.UIMACompositor
 
UIMAWordSyntacticProbabilityModel - Class in de.unibi.techfak.scie.probability_model.uima
This calculates the syntactic probability based on the distance in words and some other syntactic considerations like sentence boundaries.
UIMAWordSyntacticProbabilityModel(JCas) - Constructor for class de.unibi.techfak.scie.probability_model.uima.UIMAWordSyntacticProbabilityModel
 
UIMAWordSyntacticProbabilityModel(double, JCas) - Constructor for class de.unibi.techfak.scie.probability_model.uima.UIMAWordSyntacticProbabilityModel
 
union(AbstractLineSegment, AbstractLineSegment) - Static method in class de.unibi.techfak.scie.util.LineSegment
Returns a new line which is the union of the two lines.
Unit - Enum in de.unibi.techfak.scie.annotators.quantities
This is an enum describing all Units that are recognized by an UnitQuantityAnnotator.
UnitQuantityAnnotator - Class in de.unibi.techfak.scie.annotators.quantities
This annotates quantities that have a unit following after them.
UnitQuantityAnnotator(Unit[], int) - Constructor for class de.unibi.techfak.scie.annotators.quantities.UnitQuantityAnnotator
UnitQuantityAnnotator that compares the <followingTokens> following Tokens after each Quantity.
UnitQuantityAnnotator(Unit[]) - Constructor for class de.unibi.techfak.scie.annotators.quantities.UnitQuantityAnnotator
UnitQuantityAnnotator that compares the first Token after each Quantity.
update(Class<X>) - Method in class de.unibi.techfak.scie.util.CachedJCasUtil
Updates the cache for the given class and inserts all new instances of the given class.
updateOntologyModificationDate(OntologyHandle) - Method in class de.unibi.techfak.scie.ontology.OntologyDatabase
Updates the modification date of the given ontology to now.

V

ValidityException - Exception in de.unibi.techfak.scie.configuration
 
ValidityException(String) - Constructor for exception de.unibi.techfak.scie.configuration.ValidityException
 
ValidityException(String, String, String) - Constructor for exception de.unibi.techfak.scie.configuration.ValidityException
 
valueOf(String) - Static method in enum de.unibi.techfak.scie.annotators.quantities.Unit
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unibi.techfak.scie.configuration.ConfigurationEntry.ConfiguationEntryType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unibi.techfak.scie.ontology.driver.AssociationDirection
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unibi.techfak.scie.ontology.driver.AssociationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unibi.techfak.scie.ontology.driver.ComparisonMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements.SID
Returns the enum constant of this type with the specified name.
values() - Static method in enum de.unibi.techfak.scie.annotators.quantities.Unit
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unibi.techfak.scie.configuration.ConfigurationEntry.ConfiguationEntryType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unibi.techfak.scie.ontology.driver.AssociationDirection
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unibi.techfak.scie.ontology.driver.AssociationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unibi.techfak.scie.ontology.driver.ComparisonMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unibi.techfak.scie.ontology.driver.implementation.SQLStatements.SID
Returns an array containing the constants of this enum type, in the order they are declared.
VertebralPositionAnnotator - Class in de.unibi.techfak.scie.annotators.injury
This annotates a Vertebtral position in T-notation (e.g.
VertebralPositionAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.injury.VertebralPositionAnnotator
 
VertebralPositionRangeAnnotator - Class in de.unibi.techfak.scie.annotators.injury
This annotates ranges of numbers such as 4 - 5 or 30 to 40.
VertebralPositionRangeAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.injury.VertebralPositionRangeAnnotator
 

W

WeightAnnotator - Class in de.unibi.techfak.scie.annotators.animal
This annotates weights.
WeightAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.animal.WeightAnnotator
 
WEIGHTMODEL - Static variable in class de.unibi.techfak.scie.annotators.animal.LabGroupAnnotator
 
WORD - Static variable in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
Pattern used to extract words from a string.
WORD_STRICT - Static variable in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
Pattern used to extract words from a string.
WordNumberAnnotator - Class in de.unibi.techfak.scie.annotators.quantities
This transforms WordNumberAnnotations as done by the OntologyAnnotator into Integer annotations.
WordNumberAnnotator() - Constructor for class de.unibi.techfak.scie.annotators.quantities.WordNumberAnnotator
 
wordStem(String) - Static method in class de.unibi.techfak.scie.ontology.DictionaryAlgorithms
Extracts the word stem of a certain word.
wrap(Collection<? extends X>) - Static method in class de.unibi.techfak.scie.probability_model.uima.UIMAAnnotationCompositionUtil
 

X

XMLImporter - Class in de.unibi.techfak.scie.ontology.importer
 
XMLImporter() - Constructor for class de.unibi.techfak.scie.ontology.importer.XMLImporter
 
A B C D E F G H I J K L M N O P Q R S T U V W X 

Copyright (C) 2013, 2014 Raphael Dickfelder, Jan Göpfert, Benjamin Paassen, Andreas Stöckel, licensed under the AGPL v. 3: http://openresearch.cit-ec.de/projects/scie