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

Packages that use MappingSet

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.util

Uses of MappingSet in org.incenp.obofoundry.sssom

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

Modifier and Type	Method	Description
MappingSet	YAMLConverter.convertMappingSet(Map<String,Object> rawMap)	Converts a generic dictionary (as may have been obtained from a YAML or JSON parser) into a MappingSet object.
MappingSet	JSONReader.read()
abstract MappingSet	SSSOMReader.read()	Reads a mapping set from the source file.
MappingSet	TSVReader.read()	Reads a mapping set from the source file(s).
MappingSet	TSVReader.read(boolean metadataOnly)	Reads a mapping set from the source file(s), with the option of reading the metadata only.

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

Modifier and Type	Method	Description
void	Validator.check(MappingSet ms)	Checks whether the given mapping set is valid, and throws an exception if it is not.
protected Set<String>	SSSOMWriter.condenseSet(MappingSet mappingSet)	Performs condensation of "propagatable slots" in a mapping set.
protected void	JSONWriter.doWrite(MappingSet mappingSet)	Serialises a mapping set into the underlying file.
protected abstract void	SSSOMWriter.doWrite(MappingSet mappingSet)	Actually serialises a mapping set.
protected void	TSVWriter.doWrite(MappingSet mappingSet)
void	ExtensionSlotManager.fillFromExistingExtensions(MappingSet ms)	Gets definitions for all extensions used in the specified mapping set.
Version	Validator.getCompliantVersion(MappingSet set)	Deprecated. Use Version.getCompliantVersion(MappingSet) instead.
protected Set<String>	SSSOMWriter.getUsedPrefixes(MappingSet mappingSet)	Gets the prefix names that are actually used in the given set.
protected Set<String>	SSSOMWriter.getUsedPrefixes(MappingSet mappingSet, boolean includeBuiltin)	Gets the prefix names that are actually used in the given set, possibly including the builtin prefix names.
void	SetMerger.merge(MappingSet dst, MappingSet src)	Merges one set into another, according to the current configuration.
void	YAMLConverter.postMappings(MappingSet ms)	Finalise the conversion of a set.
protected void	SSSOMReader.validate(MappingSet mappingSet)	Validates a mapping set.
EnumSet<ValidationError>	Validator.validate(MappingSet ms)	Checks whether the given mapping set, including the mappings it contains, is valid.
EnumSet<ValidationError>	Validator.validate(MappingSet ms, boolean alwaysCheckMappings)	Checks whether the given mapping set is valid.
void	SetMerger.visit(CurieMapSlot<MappingSet> slot, MappingSet src, Map<String,String> values)
void	SetMerger.visit(ExtensionDefinitionSlot<MappingSet> slot, MappingSet object, List<ExtensionDefinition> values)
void	SetMerger.visit(ExtensionSlot<MappingSet> slot, MappingSet src, Map<String,ExtensionValue> values)
void	SetMerger.visit(Slot<MappingSet> slot, MappingSet src, Object value)
void	SetMerger.visit(StringSlot<MappingSet> slot, MappingSet src, List<String> values)
void	SSSOMWriter.write(MappingSet mappingSet)	Serialises a mapping set into the underlying file.

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

Modifier and Type	Method	Description
void	SetMerger.visit(CurieMapSlot<MappingSet> slot, MappingSet src, Map<String,String> values)
void	SetMerger.visit(ExtensionDefinitionSlot<MappingSet> slot, MappingSet object, List<ExtensionDefinition> values)
void	SetMerger.visit(ExtensionSlot<MappingSet> slot, MappingSet src, Map<String,ExtensionValue> values)
void	SetMerger.visit(Slot<MappingSet> slot, MappingSet src, Object value)
void	SetMerger.visit(StringSlot<MappingSet> slot, MappingSet src, List<String> values)

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

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

Modifier and Type	Method	Description
ValidationError	DuplicatedRecordIdValidator.validate(MappingSet ms)
ValidationError	IMappingSetValidator.validate(MappingSet ms)	Checks a mapping set for a possible post-parsing error.
ValidationError	MissingLicenseValidator.validate(MappingSet ms)
ValidationError	MissingRecordIdValidator.validate(MappingSet ms)
ValidationError	MissingSetIdValidator.validate(MappingSet ms)
ValidationError	RedefinedBuiltinPrefixValidator.validate(MappingSet ms)

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

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

Modifier and Type	Field	Description
protected SlotExtractor<MappingSet>	MappingSetSlotExtractor.slotExtractor

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

Modifier and Type	Method	Description
Object	IValueExtractor.extract(MappingSet ms)	Extracts the desired value from the given mapping set.
Object	MappingSetExtensionExtractor.extract(MappingSet ms)
Object	MappingSetSlotExtractor.extract(MappingSet ms)
Object	MappingValueExtractor.extract(MappingSet ms)

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

Modifier	Constructor	Description
	MappingSetSlotExtractor(Slot<MappingSet> slot, int itemNo)	Creates a new instance.

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

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

Modifier and Type	Method	Description
MappingSet	MappingSet.MappingSetBuilder.build()

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

Modifier and Type	Method	Description
void	Version.enforceCompliance(MappingSet ms)	Ensures the provided mapping set is compatible with this version.
static Version	Version.getCompliantVersion(MappingSet ms)	Gets the minimum version of the SSSOM specification that the given set is compliant with.
boolean	Version.isCompliant(MappingSet ms)	Checks that the given mapping set is compatible with this version.

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

Methods in org.incenp.obofoundry.sssom.owl that return MappingSet

Modifier and Type	Method	Description
MappingSet	XrefExtractor.extract(org.semanticweb.owlapi.model.OWLOntology ontology)	Extract mappings from cross-references in the specified ontology.
MappingSet	XrefExtractor.extract(org.semanticweb.owlapi.model.OWLOntology ontology, boolean permissive, boolean includeGeneric)	Extract mappings from cross-references in the specified ontology.

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

Modifier and Type	Method	Description
static void	OWLHelper.annotate(MappingSet ms, org.semanticweb.owlapi.model.OWLOntology ontology)	Annotates an ontology with annotations derived from the metadata of a mapping set.
static void	OWLHelper.annotate(MappingSet ms, org.semanticweb.owlapi.model.OWLOntology ontology, boolean setOntologyIRI, IMetadataTransformer<MappingSet,org.semanticweb.owlapi.model.IRI> mapper)	Annotates an ontology with annotations derived from the metadata of a mapping set.
static org.semanticweb.owlapi.model.OWLOntology	OWLHelper.exportToOWL(MappingSet ms, org.semanticweb.owlapi.model.OWLOntologyManager mgr)	Exports a mapping set as an ontology.
static void	OWLHelper.updateMappingSet(MappingSet ms, org.semanticweb.owlapi.model.OWLOntology ontology, String language, boolean strict)	Updates the subject label, object label, subject source, and object source in the mapping set using informations from the specified ontology.
static void	OWLHelper.updateMappingSet(MappingSet ms, org.semanticweb.owlapi.model.OWLOntology ontology, String language, boolean langStrict, EnumSet<OWLHelper.UpdateMode> mode)	Generic helper method to update a mapping set from a specified ontology.

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

Modifier and Type	Method	Description
static void	OWLHelper.annotate(MappingSet ms, org.semanticweb.owlapi.model.OWLOntology ontology, boolean setOntologyIRI, IMetadataTransformer<MappingSet,org.semanticweb.owlapi.model.IRI> mapper)	Annotates an ontology with annotations derived from the metadata of a mapping set.

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

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

Modifier and Type	Method	Description
MappingSet	RDFConverter.fromRDF(org.eclipse.rdf4j.model.Model model)	Converts a RDF model to a MappingSet object.
MappingSet	RDFReader.read()

Methods in org.incenp.obofoundry.sssom.rdf with parameters of type MappingSet

Modifier and Type	Method	Description
protected void	RDFWriter.doWrite(MappingSet mappingSet)
org.eclipse.rdf4j.model.Model	RDFConverter.toRDF(MappingSet ms)	Converts a MappingSet to a Rdf4J model.
org.eclipse.rdf4j.model.Model	RDFConverter.toRDF(MappingSet ms, boolean includeNamespaces)	Converts a MappingSet to a Rdf4J model, optionally including namespace declarations for the prefixes found in the set’s prefix map.
org.eclipse.rdf4j.model.Model	RDFConverter.toRDF(MappingSet ms, Map<String,String> prefixMap)	Converts a MappingSet to a Rdf4J model, including namespace declarations for all prefixes in the specified prefix map.
org.eclipse.rdf4j.model.Model	RDFConverter.toRDF(MappingSet ms, PrefixManager prefixManager)	Converts a MappingSet to a Rdf4J model, optional including namespace declarations for all prefixes held in the specified PrefixManager.

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

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

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

Methods in org.incenp.obofoundry.sssom.slots with parameters of type MappingSet

Modifier and Type	Method	Description
Set<String>	SlotPropagator.condense(MappingSet mappingSet, boolean preserve)	Condenses a mapping set, i.e. move slot values from the level of individual mappings up to the mapping set level wherever possible.
Set<String>	SlotPropagator.propagate(MappingSet mappingSet)	Propagates the values of slots from the mapping set level to the individual mappings.
Set<String>	SlotPropagator.propagate(MappingSet mappingSet, boolean preserve)	Propagates the values of slots the mapping set level to the individual mappings.

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

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

Modifier and Type	Method	Description
void	ExtendedPrefixMap.canonicalise(MappingSet set)	Canonicalises a mapping set.
static void	ExtensionSlotHelper.fromOther(MappingSet ms, boolean remove)	Decodes the values of other slots into proper extension slots.
static void	ExtensionSlotHelper.toOther(MappingSet ms, boolean remove)	Encodes extension slots into other values.