Uses of Class
org.incenp.obofoundry.sssom.model.Mapping

Packages that use Mapping

Package	Description
org.incenp.obofoundry.sssom
org.incenp.obofoundry.sssom.checks
org.incenp.obofoundry.sssom.extract
org.incenp.obofoundry.sssom.model
org.incenp.obofoundry.sssom.owl
org.incenp.obofoundry.sssom.rdf
org.incenp.obofoundry.sssom.slots
org.incenp.obofoundry.sssom.transform
org.incenp.obofoundry.sssom.uriexpr
org.incenp.obofoundry.sssom.util

Uses of Mapping in org.incenp.obofoundry.sssom

Methods in org.incenp.obofoundry.sssom that return Mapping

Modifier and Type	Method	Description
Mapping	YAMLConverter.convertMapping(Map<String,Object> rawMap)	Converts a generic dictionary (as may have been obtained from a YAML or JSON parser) into a Mapping object.
Mapping	YAMLConverter.convertMapping(Map<String,Object> rawMap, Version targetVersion)	Converts a generic dictionary (as may have been obtained from a YAML or JSON parser) into a Mapping object.

Methods in org.incenp.obofoundry.sssom with parameters of type Mapping

Modifier and Type	Method	Description
int	DefaultMappingComparator.compare(Mapping o1, Mapping o2)
String	Cardinalizer.getObject(Mapping mapping)	Gets a string representing the object of a mapping, that can be used for cardinality computation.
String	Cardinalizer.getSubject(Mapping mapping)	Gets a string representing the subject of a mapping, that can be used for cardinality computation.
String	MappingHasher.hash(Mapping mapping)	Hashes the given mapping.
String	Validator.validate(Mapping mapping)	Deprecated. Use Validator.validate(Mapping, boolean) instead, or Validator.validate(MappingSet) to validate an entire mapping set.
EnumSet<ValidationError>	Validator.validate(Mapping mapping, boolean earlyExit)	Validates an individual mapping.

Method parameters in org.incenp.obofoundry.sssom with type arguments of type Mapping

Modifier and Type	Method	Description
void	Cardinalizer.fillCardinality(List<Mapping> mappings)	Computes the cardinality of all mappings in the given set, according to the current scope, and fills the mapping_cardinality slot and the cardinality_scope slot accordingly.

Uses of Mapping in org.incenp.obofoundry.sssom.checks

Methods in org.incenp.obofoundry.sssom.checks with parameters of type Mapping

Modifier and Type	Method	Description
ValidationError	DuplicatedRecordIdValidator.validate(Mapping mapping)
ValidationError	IMappingValidator.validate(Mapping mapping)	Checks a mapping for a possible post-parsing error.
ValidationError	MissingJustificationValidator.validate(Mapping mapping)
ValidationError	MissingObjectValidator.validate(Mapping mapping)
ValidationError	MissingPredicateValidator.validate(Mapping mapping)
ValidationError	MissingRecordIdValidator.validate(Mapping mapping)
ValidationError	MissingReviewerValidator.validate(Mapping mapping)
ValidationError	MissingSubjectValidator.validate(Mapping mapping)
ValidationError	PredicateTypeValidator.validate(Mapping mapping)

Uses of Mapping in org.incenp.obofoundry.sssom.extract

Fields in org.incenp.obofoundry.sssom.extract with type parameters of type Mapping

Modifier and Type	Field	Description
protected SlotExtractor<Mapping>	MappingSlotExtractor.slotExtractor

Methods in org.incenp.obofoundry.sssom.extract with parameters of type Mapping

Modifier and Type	Method	Description
protected Object	HashExtractor.extract(Mapping mapping)
protected Object	MappingExtensionExtractor.extract(Mapping mapping)
protected Object	MappingSlotExtractor.extract(Mapping mapping)
protected abstract Object	MappingValueExtractor.extract(Mapping mapping)	Extracts the desired value from the given mapping.
Object	SExpressionExtractor.extract(Mapping mapping)

Constructor parameters in org.incenp.obofoundry.sssom.extract with type arguments of type Mapping

Constructor	Description
MappingSlotExtractor(int mappingNo, Slot<Mapping> slot, int itemNo)	Creates a new instance.

Uses of Mapping in org.incenp.obofoundry.sssom.model

Methods in org.incenp.obofoundry.sssom.model that return Mapping

Modifier and Type	Method	Description
Mapping	Mapping.MappingBuilder.build()
static Mapping	CommonPredicate.invert(Mapping mapping)	Deprecated. Use invert() instead.
Mapping	Mapping.invert()	Creates an inverted version of this mapping if possible.
Mapping	Mapping.invert(String predicate)	Creates an inverted version of this mapping with an explicit predicate.

Methods in org.incenp.obofoundry.sssom.model that return types with arguments of type Mapping

Modifier and Type	Method	Description
List<Mapping>	MappingSet.getMappings()	Gets the value of the mappings slot.
List<Mapping>	MappingSet.getMappings(boolean set)	Gets the list of mappings values, optionally initializing the list if needed.

Methods in org.incenp.obofoundry.sssom.model with parameters of type Mapping

Modifier and Type	Method	Description
static String	MappingCardinality.getObject(Mapping mapping)	Deprecated. Use Cardinalizer.getObject(Mapping) instead.
static String	MappingCardinality.getSubject(Mapping mapping)	Deprecated. Use Cardinalizer.getSubject(Mapping) instead.
static Mapping	CommonPredicate.invert(Mapping mapping)	Deprecated. Use invert() instead.

Method parameters in org.incenp.obofoundry.sssom.model with type arguments of type Mapping

Modifier and Type	Method	Description
static void	MappingCardinality.inferCardinality(List<Mapping> mappings)	Deprecated. Use Cardinalizer.fillCardinality(List) instead.
MappingSet.MappingSetBuilder	MappingSet.MappingSetBuilder.mappings(List<Mapping> mappings)
void	MappingSet.setMappings(List<Mapping> value)	Sets the value of the mappings slot.

Constructor parameters in org.incenp.obofoundry.sssom.model with type arguments of type Mapping

Constructor

Description

MappingSet(Version sssomVersion, Map<String,String> curieMap, List<Mapping> mappings, String mappingSetId, String mappingSetVersion, List<String> mappingSetSource, String mappingSetTitle, String mappingSetDescription, Double mappingSetConfidence, List<String> creatorId, List<String> creatorLabel, String license, EntityType subjectType, String subjectSource, String subjectSourceVersion, EntityType objectType, String objectSource, String objectSourceVersion, EntityType predicateType, String mappingProvider, List<String> cardinalityScope, String mappingTool, String mappingToolId, String mappingToolVersion, LocalDate mappingDate, LocalDate publicationDate, List<String> subjectMatchField, List<String> objectMatchField, List<String> subjectPreprocessing, List<String> objectPreprocessing, String similarityMeasure, List<String> curationRule, List<String> curationRuleText, List<String> seeAlso, String issueTracker, String other, String comment, List<ExtensionDefinition> extensionDefinitions, Map<String,ExtensionValue> extensions)

Creates a new instance from the specified values.

Uses of Mapping in org.incenp.obofoundry.sssom.owl

Methods in org.incenp.obofoundry.sssom.owl with parameters of type Mapping

Modifier and Type	Method	Description
boolean	SSSOMTExistsFunction.filter(Mapping mapping)
boolean	SSSOMTIsAFunction.filter(Mapping mapping)
org.semanticweb.owlapi.model.OWLAxiom	AnnotatedAxiomGenerator.transform(Mapping mapping)
org.semanticweb.owlapi.model.OWLAxiom	AnnotationAxiomGenerator.transform(Mapping mapping)
org.semanticweb.owlapi.model.OWLAxiom	DirectAxiomGenerator.transform(Mapping mapping)
org.semanticweb.owlapi.model.OWLAxiom	EquivalentAxiomGenerator.transform(Mapping mapping)
org.semanticweb.owlapi.model.OWLAxiom	SSSOMTAnnotateFunction.transform(Mapping mapping)
org.semanticweb.owlapi.model.OWLAxiom	SSSOMTCreateAxiomFunction.transform(Mapping mapping)

Method parameters in org.incenp.obofoundry.sssom.owl with type arguments of type Mapping

Modifier and Type	Method	Description
void	OWLGenerator.addRule(IMappingFilter filter, IMappingTransformer<Mapping> preprocessor, IMappingTransformer<org.semanticweb.owlapi.model.OWLAxiom> generator)	Adds a processing rule.

Constructor parameters in org.incenp.obofoundry.sssom.owl with type arguments of type Mapping

Constructor	Description
AnnotatedAxiomGenerator(org.semanticweb.owlapi.model.OWLOntology ontology, IMappingTransformer<org.semanticweb.owlapi.model.OWLAxiom> innerGenerator, IMetadataTransformer<Mapping,org.semanticweb.owlapi.model.IRI> slotTranslator)	Creates a new instance with the specified generator and metadata transformer.
AnnotatedAxiomGenerator(org.semanticweb.owlapi.model.OWLOntology ontology, IMappingTransformer<org.semanticweb.owlapi.model.OWLAxiom> innerGenerator, IMetadataTransformer<Mapping,org.semanticweb.owlapi.model.IRI> slotTranslator, boolean onlyMetadata)	Creates a new instance with the specified generator and metadata transformer.
AnnotatedAxiomGenerator(org.semanticweb.owlapi.model.OWLOntology ontology, IMappingTransformer<org.semanticweb.owlapi.model.OWLAxiom> innerGenerator, IMetadataTransformer<Mapping,org.semanticweb.owlapi.model.IRI> slotTranslator, Collection<String> slots)	Creates a new instance with the specified generator and metadata transformer, and a customised list of slots to use to generate the annotations.

Uses of Mapping in org.incenp.obofoundry.sssom.rdf

Methods in org.incenp.obofoundry.sssom.rdf that return Mapping

Modifier and Type	Method	Description
Mapping	RDFConverter.mappingFromRDF(org.eclipse.rdf4j.model.Model model)	Converts a RDF model to a Mapping object.
Mapping	RDFConverter.mappingFromRDF(org.eclipse.rdf4j.model.Model model, Version targetVersion)	Converts a RDF model to a Mapping object.

Uses of Mapping in org.incenp.obofoundry.sssom.slots

Methods in org.incenp.obofoundry.sssom.slots that return types with arguments of type Mapping

Modifier and Type	Method	Description
static SlotHelper<Mapping>	SlotHelper.getMappingHelper()	Gets the default helper object to manipulate Mapping slots.
static SlotHelper<Mapping>	SlotHelper.getMappingHelper(boolean newHelper)	Gets a helper object to manipulate Mapping slots.

Uses of Mapping in org.incenp.obofoundry.sssom.transform

Methods in org.incenp.obofoundry.sssom.transform that return Mapping

Modifier and Type	Method	Description
Mapping	MappingProcessingRule.preprocess(Mapping mapping)	Applies the preprocessing step to the given mapping.
Mapping	MappingEditor.transform(Mapping mapping)
Mapping	SSSOMTInvertFunction.transform(Mapping mapping)
Mapping	SSSOMTStopFunction.transform(Mapping mapping)

Methods in org.incenp.obofoundry.sssom.transform that return types with arguments of type Mapping

Modifier and Type	Method	Description
IMappingTransformer<Mapping>	SSSOMTAssignFunction.call(List<String> arguments, Map<String,String> keyedArguments)
IMappingTransformer<Mapping>	SSSOMTInvertFunction.call(List<String> arguments, Map<String,String> keyedArguments)
IMappingTransformer<Mapping>	SSSOMTReplaceFunction.call(List<String> arguments, Map<String,String> keyedArguments)
IMappingTransformer<Mapping>	SSSOMTStopFunction.call(List<String> arguments, Map<String,String> keyedArguments)
IMappingTransformer<Mapping>	ISSSOMTransformApplication.onPreprocessingAction(String name, List<String> arguments, Map<String,String> keyedArguments)	Processes a preprocessing action.
IMappingTransformer<Mapping>	SSSOMTransformApplication.onPreprocessingAction(String name, List<String> arguments, Map<String,String> keyedArguments)

Methods in org.incenp.obofoundry.sssom.transform with parameters of type Mapping

Modifier and Type	Method	Description
boolean	MappingProcessingRule.apply(Mapping mapping)	Checks whether the rule should be applied to the given mapping.
String	VariableManager.expandVariable(String name, Mapping mapping)	Gets the value of a variable for a given mapping.
boolean	FilterSet.filter(Mapping mapping)
boolean	IMappingFilter.filter(Mapping mapping)	Check if a mapping satisfies a given condition.
boolean	NamedFilter.filter(Mapping mapping)
boolean	SSSOMTConfidenceFilterFunction.filter(Mapping mapping)
boolean	SSSOMTDuplicateFunction.filter(Mapping mapping)
boolean	SSSOMTHasExtensionFunction.filter(Mapping mapping)
String	MappingFormatter.format(String format, Mapping mapping)	Formats a string with values derived from a mapping.
T	MappingProcessingRule.generate(Mapping mapping)	Generates the output object from the given mapping.
void	IMappingProcessorListener.generated(MappingProcessingRule<T> rule, Mapping mapping, T product)	This method is called whenever a rule is applied to a mapping and produces an object.
protected void	MappingProcessor.onGeneratedProduct(MappingProcessingRule<T> rule, Mapping mapping, T product)	Called when a rule generates an object from a mapping.
Mapping	MappingProcessingRule.preprocess(Mapping mapping)	Applies the preprocessing step to the given mapping.
T	IMappingTransformer.transform(Mapping mapping)	Transform a mapping into something else.
Mapping	MappingEditor.transform(Mapping mapping)
T	NamedMappingTransformer.transform(Mapping mapping)
Mapping	SSSOMTInvertFunction.transform(Mapping mapping)
Mapping	SSSOMTStopFunction.transform(Mapping mapping)
Void	MappingEditor.visit(Slot<Mapping> slot, Mapping object, Object value)

Method parameters in org.incenp.obofoundry.sssom.transform with type arguments of type Mapping

Modifier and Type	Method	Description
boolean	MappingProcessingRule.call(List<Mapping> mappings)	Calls the custom callback associated with the rule, if any.
void	IMappingProcessorCallback.process(IMappingFilter filter, List<Mapping> mappings)	Applies a custom process to a set of mappings.
List<T>	MappingProcessor.process(List<Mapping> mappings)	Applies all the rules to the given mappings.
void	NamedMappingProcessorCallback.process(IMappingFilter filter, List<Mapping> mappings)
void	SSSOMTInferCardinalityFunction.process(IMappingFilter filter, List<Mapping> mappings)
void	SSSOMTransformApplication.registerPreprocessor(ISSSOMTFunction<IMappingTransformer<Mapping>> function)	Registers a new SSSOM/T preprocessor function.
Void	MappingEditor.visit(Slot<Mapping> slot, Mapping object, Object value)

Constructor parameters in org.incenp.obofoundry.sssom.transform with type arguments of type Mapping

Constructor	Description
MappingProcessingRule(IMappingFilter filter, IMappingTransformer<Mapping> preprocessor, IMappingTransformer<T> generator)	Creates a new instance.
MappingProcessingRule(IMappingFilter filter, IMappingTransformer<Mapping> preprocessor, IMappingTransformer<T> generator, IMappingProcessorCallback callback)	Creates a new instance that includes a custom processing step.

Uses of Mapping in org.incenp.obofoundry.sssom.uriexpr

Methods in org.incenp.obofoundry.sssom.uriexpr that return Mapping

Modifier and Type	Method	Description
Mapping	SSSOMTUriExpressionToExtFunction.transform(Mapping mapping)

Methods in org.incenp.obofoundry.sssom.uriexpr that return types with arguments of type Mapping

Modifier and Type	Method	Description
IMappingTransformer<Mapping>	SSSOMTUriExpressionToExtFunction.call(List<String> arguments, Map<String,String> keyedArguments)

Methods in org.incenp.obofoundry.sssom.uriexpr with parameters of type Mapping

Modifier and Type	Method	Description
boolean	SSSOMTUriExpressionContainsFunction.filter(Mapping mapping)
Mapping	SSSOMTUriExpressionToExtFunction.transform(Mapping mapping)

Uses of Mapping in org.incenp.obofoundry.sssom.util

Methods in org.incenp.obofoundry.sssom.util with parameters of type Mapping

Modifier and Type	Method	Description
double	ConfidenceHelper.aggregate(Mapping mapping)	Computes the aggregated confidence value for a mapping.

Method parameters in org.incenp.obofoundry.sssom.util with type arguments of type Mapping

Modifier and Type	Method	Description
void	ExtendedPrefixMap.canonicalise(List<Mapping> mappings)	Canonicalises a list of mappings.