Index (SSSOM-Java 1.8.2 API)

A B C D E F G H I J L M N O P R S T U V W X Y
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

accept(ISimpleSlotVisitor<T, V>, T, Object) - Method in class org.incenp.obofoundry.sssom.slots.Slot: Accepts a simple visitor.
accept(ISlotVisitor<T>, T, Object) - Method in class org.incenp.obofoundry.sssom.slots.CurieMapSlot
accept(ISlotVisitor<T>, T, Object) - Method in class org.incenp.obofoundry.sssom.slots.DateSlot
accept(ISlotVisitor<T>, T, Object) - Method in class org.incenp.obofoundry.sssom.slots.DoubleSlot
accept(ISlotVisitor<T>, T, Object) - Method in class org.incenp.obofoundry.sssom.slots.EntityReferenceSlot
accept(ISlotVisitor<T>, T, Object) - Method in class org.incenp.obofoundry.sssom.slots.EntityTypeSlot
accept(ISlotVisitor<T>, T, Object) - Method in class org.incenp.obofoundry.sssom.slots.ExtensionDefinitionSlot
accept(ISlotVisitor<T>, T, Object) - Method in class org.incenp.obofoundry.sssom.slots.ExtensionSlot
accept(ISlotVisitor<T>, T, Object) - Method in class org.incenp.obofoundry.sssom.slots.MappingCardinalitySlot
accept(ISlotVisitor<T>, T, Object) - Method in class org.incenp.obofoundry.sssom.slots.PredicateModifierSlot
accept(ISlotVisitor<T>, T, Object) - Method in class org.incenp.obofoundry.sssom.slots.Slot: Accepts a visitor.
accept(ISlotVisitor<T>, T, Object) - Method in class org.incenp.obofoundry.sssom.slots.StringSlot
accept(ISlotVisitor<T>, T, Object) - Method in class org.incenp.obofoundry.sssom.slots.URISlot
accept(ISlotVisitor<T>, T, Object) - Method in class org.incenp.obofoundry.sssom.slots.VersionSlot
add(String, String) - Method in class org.incenp.obofoundry.sssom.PrefixManager: Adds a new prefix.
add(Map<? extends String, ? extends String>) - Method in class org.incenp.obofoundry.sssom.PrefixManager: Adds new prefixes.
addAnnotationProperty(String) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker: Adds an annotation property to the entities known to this object.
addClass(String) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker: Adds a OWL class to the entities known to this object.
addDataproperty(String) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker: Adds a data property to the entities known to this object.
addDatatype(String) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker: Adds a datatype to the entities known to this object.
addDefinition(String, String, String) - Method in class org.incenp.obofoundry.sssom.ExtensionSlotManager: Defines a new extension slot.
addDelayedAssign(String, IMappingTransformer<String>) - Method in class org.incenp.obofoundry.sssom.transform.MappingEditor: Adds a change to be applied by transformer, when the new value to assign will only be known at the time the change is applied because it may depend on the mapping the change is applied to.
addedIn() - Element in annotation interface org.incenp.obofoundry.sssom.model.Versionable: The version of the specification in which the slot was first introduced.
addFilter(IMappingFilter, boolean) - Method in class org.incenp.obofoundry.sssom.transform.FilterSet: Adds a filter to the set.
addGeneratedListener(IMappingProcessorListener<T>) - Method in class org.incenp.obofoundry.sssom.transform.MappingProcessor: Adds a listener to react to "generated" events, when an object is generated by the application of a rule to a mapping.
addIndividual(String) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker: Adds an individual to the entities known to this object.
addObjectProperty(String) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker: Adds an object property to the entities known to this object.
addPrefix(String, String) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformReader: Adds a prefix to the reader's prefix map.
addPrefixMap(Map<String, String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformReader: Adds prefixes to the reader's prefix map.
addPrefixToPredicateMapping(String, String) - Method in class org.incenp.obofoundry.sssom.owl.XrefExtractor: Maps a prefix name to a predicate.
addReplacement(String, String, String) - Method in class org.incenp.obofoundry.sssom.transform.MappingEditor: Adds a replacement operation to be applied by this transformer.
addRule(IMappingFilter, IMappingTransformer<Mapping>, IMappingTransformer<OWLAxiom>) - Method in class org.incenp.obofoundry.sssom.owl.OWLGenerator: Adds a processing rule.
addRule(MappingProcessingRule<T>) - Method in class org.incenp.obofoundry.sssom.transform.MappingProcessor: Adds a rule to be applied to mappings.
addRules(List<MappingProcessingRule<T>>) - Method in class org.incenp.obofoundry.sssom.transform.MappingProcessor: Adds a list of rules to be applied.
addSimpleAssign(String, String) - Method in class org.incenp.obofoundry.sssom.transform.MappingEditor: Adds a change to be applied by this transformer.
addStopingRule(IMappingFilter) - Method in class org.incenp.obofoundry.sssom.transform.MappingProcessor: Adds a rule that stops any further processing for selected mappings.
addVariable(String, String) - Method in class org.incenp.obofoundry.sssom.transform.VariableManager: Defines a new variable to track.
addVariable(String, String, IMappingFilter) - Method in class org.incenp.obofoundry.sssom.transform.VariableManager: Defines a new variable to track for certain mappings.
ALL - Static variable in enum class org.incenp.obofoundry.sssom.owl.OWLHelper.UpdateMode
AlwaysReplace - Enum constant in enum class org.incenp.obofoundry.sssom.PropagationPolicy: Always propagate the value from the source object to the destination objects, regardless of whether a destination object already has a value for the slot being propagated.
annotate(MappingSet, OWLOntology) - Static method in class org.incenp.obofoundry.sssom.owl.OWLHelper: Annotates an ontology with annotations derived from the metadata of a mapping set.
annotate(MappingSet, OWLOntology, boolean, IMetadataTransformer<MappingSet, IRI>) - Static method in class org.incenp.obofoundry.sssom.owl.OWLHelper: Annotates an ontology with annotations derived from the metadata of a mapping set.
annotate(OWLAxiom) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor: Annotates an axiom with the annotations generated from the visited slots.
annotate(OWLOntology) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor: Annotates an ontology with the annotations generated from the visited slots.
AnnotatedAxiomGenerator - Class in org.incenp.obofoundry.sssom.owl: A class to generated annotated OWL axioms from a mapping.
AnnotatedAxiomGenerator(OWLOntology) - Constructor for class org.incenp.obofoundry.sssom.owl.AnnotatedAxiomGenerator: Creates a new instance that generate “direct” OWL axioms with standard annotations from the mapping metadata.
AnnotatedAxiomGenerator(OWLOntology, boolean) - Constructor for class org.incenp.obofoundry.sssom.owl.AnnotatedAxiomGenerator: Creates a new instance that generates “direct” OWL axioms with standard annotations from either the mapping metadata slots or all the mapping slots.
AnnotatedAxiomGenerator(OWLOntology, Collection<String>) - Constructor for class org.incenp.obofoundry.sssom.owl.AnnotatedAxiomGenerator: Creates a new instance that generates “direct” OWL axioms with standard annotations from the specified list of slots.
AnnotatedAxiomGenerator(OWLOntology, IMappingTransformer<OWLAxiom>, IMetadataTransformer<Mapping, IRI>) - Constructor for class org.incenp.obofoundry.sssom.owl.AnnotatedAxiomGenerator: Creates a new instance with the specified generator and metadata transformer.
AnnotatedAxiomGenerator(OWLOntology, IMappingTransformer<OWLAxiom>, IMetadataTransformer<Mapping, IRI>, boolean) - Constructor for class org.incenp.obofoundry.sssom.owl.AnnotatedAxiomGenerator: Creates a new instance with the specified generator and metadata transformer.
AnnotatedAxiomGenerator(OWLOntology, IMappingTransformer<OWLAxiom>, IMetadataTransformer<Mapping, IRI>, Collection<String>) - Constructor for class org.incenp.obofoundry.sssom.owl.AnnotatedAxiomGenerator: Creates a new instance with the specified generator and metadata transformer, and a customised list of slots to use to generate the annotations.
AnnotationAxiomGenerator - Class in org.incenp.obofoundry.sssom.owl: A class to generate OWL annotation assertion axioms from mappings.
AnnotationAxiomGenerator(OWLOntology, IRI, IMappingTransformer<String>) - Constructor for class org.incenp.obofoundry.sssom.owl.AnnotationAxiomGenerator: Creates a new instance.
AnnotationAxiomGenerator(OWLOntology, IRI, IMappingTransformer<String>, boolean) - Constructor for class org.incenp.obofoundry.sssom.owl.AnnotationAxiomGenerator: Creates a new instance to annotate the object of a mapping rather than the subject.
AnnotationVisitor<T> - Class in org.incenp.obofoundry.sssom.owl: A mapping slots visitor that converts mapping metadata to OWL annotations.
ANNOTS_KEYWORD - Static variable in class org.incenp.obofoundry.sssom.owl.SSSOMTHelper: The name of the parameter used to specify the annotations to generate on a mapping-derived axiom.
ANNOTS_URIS_KEYWORD - Static variable in class org.incenp.obofoundry.sssom.owl.SSSOMTHelper: The name of the parameter used to specify how SSSOM fields are translated to OWL annotation property IRIs.
app - Variable in class org.incenp.obofoundry.sssom.owl.SSSOMTAnnotateFunction
apply(Mapping) - Method in class org.incenp.obofoundry.sssom.transform.MappingProcessingRule: Checks whether the rule should be applied to the given mapping.
applyTemplate(UriExpression, String) - Method in class org.incenp.obofoundry.sssom.uriexpr.UriExpressionRegistry: Applies a template to a URI Expression.
asBoolean() - Method in class org.incenp.obofoundry.sssom.model.ExtensionValue
asDate() - Method in class org.incenp.obofoundry.sssom.model.ExtensionValue
asDatetime() - Method in class org.incenp.obofoundry.sssom.model.ExtensionValue
asDouble() - Method in class org.incenp.obofoundry.sssom.model.ExtensionValue
asInteger() - Method in class org.incenp.obofoundry.sssom.model.ExtensionValue
asString() - Method in class org.incenp.obofoundry.sssom.model.ExtensionValue
assumedVersion - Variable in class org.incenp.obofoundry.sssom.SSSOMReader
asURI() - Method in class org.incenp.obofoundry.sssom.model.ExtensionValue
authorId(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
authorLabel(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder

B

BOOLEAN - Enum constant in enum class org.incenp.obofoundry.sssom.model.ValueType
build() - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
build() - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry.MappingRegistryBuilder
build() - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
build() - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference.MappingSetReferenceBuilder
builder() - Static method in class org.incenp.obofoundry.sssom.model.Mapping
builder() - Static method in class org.incenp.obofoundry.sssom.model.MappingRegistry
builder() - Static method in class org.incenp.obofoundry.sssom.model.MappingSet
builder() - Static method in class org.incenp.obofoundry.sssom.model.MappingSetReference
BuiltinPrefix - Enum Class in org.incenp.obofoundry.sssom.model: URL prefixes considered builtin by the SSSOM specification.

C

call(Object, List<String>) - Method in interface org.incenp.obofoundry.sssom.transform.IFormatModifierFunction: Executes the function.
call(Object, List<String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTDefaultModifierFunction
call(Object, List<String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTFlattenFunction
call(Object, List<String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTFormatFunction
call(Object, List<String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTListItemFunction
call(Object, List<String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTShortFunction
call(Object, List<String>) - Method in class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionExpandFunction
call(Object, List<String>) - Method in class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionSlotValueFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTAnnotateFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTAnnotateObjectFunction: Deprecated.
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTAnnotateSubjectFunction: Deprecated.
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTCheckObjectExistenceFunction: Deprecated.
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTCheckSubjectExistenceFunction: Deprecated.
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTCreateAxiomFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTDeclareClassFunction: Deprecated.
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTDeclareFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTDeclareObjectPropertyFunction: Deprecated.
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTDirectFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTExistsFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTIsAFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTOwlSetvarFunction: Deprecated.
call(List<String>, Map<String, String>) - Method in interface org.incenp.obofoundry.sssom.transform.ISSSOMTFunction: Executes the function.
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTAssignFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTDuplicateFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTEditFunction: Deprecated.
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTHasExtensionFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTInferCardinalityFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTInvertFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTReplaceFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTSetvarCallbackFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTSetvarFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTStopFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionContainsFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionDeclareFormatFunction
call(List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionToExtFunction
call(List<Mapping>) - Method in class org.incenp.obofoundry.sssom.transform.MappingProcessingRule: Calls the custom callback associated with the rule, if any.
canEqual(Object) - Method in class org.incenp.obofoundry.sssom.model.Mapping
canEqual(Object) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
canEqual(Object) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
canEqual(Object) - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference
canonicalise(String) - Method in class org.incenp.obofoundry.sssom.util.ExtendedPrefixMap: Canonicalises an IRI.
canonicalise(List<String>, boolean) - Method in class org.incenp.obofoundry.sssom.util.ExtendedPrefixMap: Canonicalises a list of IRIs.
canonicalise(List<Mapping>) - Method in class org.incenp.obofoundry.sssom.util.ExtendedPrefixMap: Canonicalises a list of mappings.
canonicalise(MappingSet) - Method in class org.incenp.obofoundry.sssom.util.ExtendedPrefixMap: Canonicalises a mapping set.
cardinalityScope(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
cardinalityScope(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
Cardinalizer - Class in org.incenp.obofoundry.sssom: A helper object to compute cardinality values.
Cardinalizer() - Constructor for class org.incenp.obofoundry.sssom.Cardinalizer: Creates a new instance with an empty scope.
Cardinalizer(Collection<String>) - Constructor for class org.incenp.obofoundry.sssom.Cardinalizer: Creates a new instance with the specified slots as the scope.
check(MappingSet) - Method in class org.incenp.obofoundry.sssom.Validator: Checks whether the given mapping set is valid, and throws an exception if it is not.
classExists(String) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTOwlApplication: Deprecated.
Use SSSOMTOwlApplication.entityExists(String) instead.
COMMA - Enum constant in enum class org.incenp.obofoundry.sssom.TSVReader.SeparatorMode: Columns are expected to be separated by commas.
comment(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
comment(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
CommonPredicate - Enum Class in org.incenp.obofoundry.sssom.model: Represents some "well-known" mapping predicates for which we have built-in knowledge on how to invert them.
compare(Mapping, Mapping) - Method in class org.incenp.obofoundry.sssom.DefaultMappingComparator
COMPOSED_ENTITY_EXPRESSION - Enum constant in enum class org.incenp.obofoundry.sssom.model.EntityType
condensationPolicy - Variable in class org.incenp.obofoundry.sssom.SSSOMWriter
condense(MappingSet, boolean) - Method in class org.incenp.obofoundry.sssom.slots.SlotPropagator: Condenses a mapping set, i.e. move slot values from the level of individual mappings up to the mapping set level wherever possible.
condenseSet(MappingSet) - Method in class org.incenp.obofoundry.sssom.SSSOMWriter: Performs condensation of "propagatable slots" in a mapping set.
confidence(Double) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
Constants - Class in org.incenp.obofoundry.sssom.model: A class to hold constant values that may be used throughout the library and in client code.
Constants - Class in org.incenp.obofoundry.sssom.rdf: Constant values used throughout the RDF support package.
Constants() - Constructor for class org.incenp.obofoundry.sssom.model.Constants
Constants() - Constructor for class org.incenp.obofoundry.sssom.rdf.Constants
convertMapping(Map<String, Object>) - Method in class org.incenp.obofoundry.sssom.YAMLConverter: Converts a generic dictionary (as may have been obtained from a YAML or JSON parser) into a Mapping object.
convertMapping(Map<String, Object>, Version) - Method in class org.incenp.obofoundry.sssom.YAMLConverter: Converts a generic dictionary (as may have been obtained from a YAML or JSON parser) into a Mapping object.
convertMappingSet(Map<String, Object>) - Method in class org.incenp.obofoundry.sssom.YAMLConverter: Converts a generic dictionary (as may have been obtained from a YAML or JSON parser) into a MappingSet object.
createAnnotatedTransformer(IMappingTransformer<OWLAxiom>, String) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTOwlApplication: Deprecated.
Use SSSOMTHelper.maybeCreateAnnotatedTransformer(SSSOMTOwlApplication, IMappingTransformer, Map) instead.
creatorId(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
creatorId(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
creatorLabel(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
creatorLabel(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
CSV - Enum constant in enum class org.incenp.obofoundry.sssom.util.SerialisationFormat: SSSOM/CSV, variant used comma-separated columns.
curationRule(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
curationRule(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
curationRuleText(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
curationRuleText(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
curieMap(Map<String, String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
CurieMapSlot<T> - Class in org.incenp.obofoundry.sssom.slots: Represents a metadata slot that holds the prefix (or curie) map used by a mapping set.

D

DATE - Enum constant in enum class org.incenp.obofoundry.sssom.model.ValueType
DateSlot<T> - Class in org.incenp.obofoundry.sssom.slots: Represents a metadata slot that holds a date.
DATETIME - Enum constant in enum class org.incenp.obofoundry.sssom.model.ValueType
DEFAULT - Static variable in enum class org.incenp.obofoundry.sssom.MergeOption: Merge all mappings and all metadata from the source set into the destination set, except the scalar (single-valued) slots.
DEFAULT_TYPE_HINT - Static variable in class org.incenp.obofoundry.sssom.ExtensionSlotManager: The default type for extensions that are either undefined or that do not have an explicit type.
DefaultMappingComparator - Class in org.incenp.obofoundry.sssom: Comparator for mapping objects.
DefaultMappingComparator() - Constructor for class org.incenp.obofoundry.sssom.DefaultMappingComparator
DEFINED - Enum constant in enum class org.incenp.obofoundry.sssom.ExtraMetadataPolicy: Requires that non-standard metadata slots be defined.
DELETE_MISSING - Enum constant in enum class org.incenp.obofoundry.sssom.owl.OWLHelper.UpdateMode: Removes any mapping whose subject or object does not exist in the ontology.
DELETE_OBSOLETE - Enum constant in enum class org.incenp.obofoundry.sssom.owl.OWLHelper.UpdateMode: Removes any mapping whose subject or object is marked as obsolete.
DirectAxiomGenerator - Class in org.incenp.obofoundry.sssom.owl: A class to generate OWL axioms “directly”, that is without any external input outside of the mappings themselves.
DirectAxiomGenerator(OWLOntology) - Constructor for class org.incenp.obofoundry.sssom.owl.DirectAxiomGenerator: Creates a new instance.
DirectMetadataTransformer<T> - Class in org.incenp.obofoundry.sssom.owl: A class to transform mapping metadata slots into their corresponding IRIs according to the SSSOM specification.
DirectMetadataTransformer() - Constructor for class org.incenp.obofoundry.sssom.owl.DirectMetadataTransformer
Disabled - Enum constant in enum class org.incenp.obofoundry.sssom.PropagationPolicy: Never propagate values between mapping set level and individual mappings.
DISABLED - Enum constant in enum class org.incenp.obofoundry.sssom.ValidationLevel: Do not perform any validation at all.
documentation(String) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry.MappingRegistryBuilder
doesInferCardinality() - Method in class org.incenp.obofoundry.sssom.transform.MappingProcessingRule: Indicates whether this rule takes care of computing cardinality information.
DOUBLE - Enum constant in enum class org.incenp.obofoundry.sssom.model.ValueType
DoubleSlot<T> - Class in org.incenp.obofoundry.sssom.slots: Represents a metadata slot that holds a numerical value.
doWrite(MappingSet) - Method in class org.incenp.obofoundry.sssom.JSONWriter: Serialises a mapping set into the underlying file.
doWrite(MappingSet) - Method in class org.incenp.obofoundry.sssom.rdf.RDFWriter
doWrite(MappingSet) - Method in class org.incenp.obofoundry.sssom.SSSOMWriter: Actually serialises a mapping set.
doWrite(MappingSet) - Method in class org.incenp.obofoundry.sssom.TSVWriter
DUPLICATED_RECORD_ID - Enum constant in enum class org.incenp.obofoundry.sssom.ValidationError
DuplicatedRecordIdValidator - Class in org.incenp.obofoundry.sssom.checks: Check that no two records in a set have the same record ID.
DuplicatedRecordIdValidator() - Constructor for class org.incenp.obofoundry.sssom.checks.DuplicatedRecordIdValidator

E

EditableEntityChecker - Class in org.incenp.obofoundry.sssom.owl: A helper class used by SSSOMTOwlApplication and some of its functions.
enableCSV(boolean) - Method in class org.incenp.obofoundry.sssom.TSVWriter: Enables CSV mode.
entityExists(String) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTOwlApplication: Checks if a given entity exists in the helper ontology and if it is not obsolete.
EntityReference - Annotation Interface in org.incenp.obofoundry.sssom.model: An annotation to indicate that a SSSOM slot is an "entity reference".
EntityReferenceSlot<T> - Class in org.incenp.obofoundry.sssom.slots: Represents a metadata slot that is intended to hold an entity reference (which is internally represented by a String).
EntityType - Enum Class in org.incenp.obofoundry.sssom.model: Represents the type of an entity that is being mapped.
EntityTypeSlot<T> - Class in org.incenp.obofoundry.sssom.slots: Represents a metadata slot that holds an entity type enumeration value.
equals(Object) - Method in class org.incenp.obofoundry.sssom.model.Mapping
equals(Object) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
equals(Object) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
equals(Object) - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference
EquivalentAxiomGenerator - Class in org.incenp.obofoundry.sssom.owl: A class to generate OWL equivalence axioms from mappings.
EquivalentAxiomGenerator(OWLOntology, IMappingTransformer<OWLClassExpression>, boolean) - Constructor for class org.incenp.obofoundry.sssom.owl.EquivalentAxiomGenerator: Creates a new instance with a class expression that is derived from the mapping at application time.
EquivalentAxiomGenerator(OWLOntology, OWLClassExpression) - Constructor for class org.incenp.obofoundry.sssom.owl.EquivalentAxiomGenerator: Creates a new instance.
EquivalentAxiomGenerator(OWLOntology, OWLClassExpression, boolean) - Constructor for class org.incenp.obofoundry.sssom.owl.EquivalentAxiomGenerator: Creates a new instance, with the possibility of inverting the direction of the generated axioms.
errors - Variable in class org.incenp.obofoundry.sssom.transform.SSSOMTransformReader
excludeMappingSlots(Set<String>) - Method in class org.incenp.obofoundry.sssom.rdf.RDFConverter: When converting from SSSOM to RDF, do not convert the mapping slots in the provided list.
excludeRules(Set<String>) - Method in class org.incenp.obofoundry.sssom.transform.MappingProcessor: Sets the processor to exclude the rules that have at least one tag in the specified tag set.
excludeSlots(Collection<String>) - Method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Excludes the specified slots from being visited.
expandIdentifier(String) - Method in class org.incenp.obofoundry.sssom.PrefixManager: Expands a shortened identifier into its long, canonical form.
expandIdentifiers(List<String>) - Method in class org.incenp.obofoundry.sssom.PrefixManager: Expands all identifiers in the given list.
expandIdentifiers(List<String>, boolean) - Method in class org.incenp.obofoundry.sssom.PrefixManager: Expands all identifiers in the given list.
expandIdentifiers(T, PrefixManager) - Method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Expands identifiers in all slots holding entity references.
expandVariable(String, Mapping) - Method in class org.incenp.obofoundry.sssom.transform.VariableManager: Gets the value of a variable for a given mapping.
exportToOWL(MappingSet, OWLOntologyManager) - Static method in class org.incenp.obofoundry.sssom.owl.OWLHelper: Exports a mapping set as an ontology.
EXTENDED - Enum constant in enum class org.incenp.obofoundry.sssom.ValidationLevel: Perform more checks to ensure that both individual mappings and the set they belong to are correct.
ExtendedPrefixMap - Class in org.incenp.obofoundry.sssom.util: A basic implementation of the “Extended Prefix Map” concept promoted by the Bioregistry.
ExtendedPrefixMap(File) - Constructor for class org.incenp.obofoundry.sssom.util.ExtendedPrefixMap: Creates a new extended prefix map from the specified file.
ExtendedPrefixMap(InputStream) - Constructor for class org.incenp.obofoundry.sssom.util.ExtendedPrefixMap: Creates a new extended prefix map from the specified stream.
ExtendedPrefixMap(String) - Constructor for class org.incenp.obofoundry.sssom.util.ExtendedPrefixMap: Creates a new extended prefix map from the specified filename.
ExtensionDefinition - Class in org.incenp.obofoundry.sssom.model: Represents the definition of an extension slot.
ExtensionDefinition(String, String) - Constructor for class org.incenp.obofoundry.sssom.model.ExtensionDefinition: Creates a new instance with the default type.
ExtensionDefinition(String, String, String) - Constructor for class org.incenp.obofoundry.sssom.model.ExtensionDefinition: Creates a new instance with the specified type hint.
extensionDefinitions(List<ExtensionDefinition>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
ExtensionDefinitionSlot<T> - Class in org.incenp.obofoundry.sssom.slots: Represents a metadata slot that holds a list of extension definitions (describing the non-standard metadata slots in used within a mapping set).
extensionManager - Variable in class org.incenp.obofoundry.sssom.SSSOMWriter
extensions(Map<String, ExtensionValue>) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
extensions(Map<String, ExtensionValue>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
ExtensionSlot<T> - Class in org.incenp.obofoundry.sssom.slots: Represents a metadata slot that holds all extension values (non-standard metadata slots) for a SSSOM object.
ExtensionSlotManager - Class in org.incenp.obofoundry.sssom: A helper class to deal with non-standard metadata slots and their definitions.
ExtensionSlotManager(ExtraMetadataPolicy) - Constructor for class org.incenp.obofoundry.sssom.ExtensionSlotManager: Creates a new instance without a prefix manager.
ExtensionSlotManager(ExtraMetadataPolicy, PrefixManager) - Constructor for class org.incenp.obofoundry.sssom.ExtensionSlotManager: Creates a new instance.
ExtensionValue - Class in org.incenp.obofoundry.sssom.model: Represents the value of an extension slot.
ExtensionValue(boolean) - Constructor for class org.incenp.obofoundry.sssom.model.ExtensionValue: Creates a new boolean-typed value.
ExtensionValue(double) - Constructor for class org.incenp.obofoundry.sssom.model.ExtensionValue: Creates a new double-typed value.
ExtensionValue(int) - Constructor for class org.incenp.obofoundry.sssom.model.ExtensionValue: Creates a new integer-typed value.
ExtensionValue(Object) - Constructor for class org.incenp.obofoundry.sssom.model.ExtensionValue: Creates a new value with an unknown type.
ExtensionValue(String) - Constructor for class org.incenp.obofoundry.sssom.model.ExtensionValue: Creates a new string-typed value.
ExtensionValue(String, boolean) - Constructor for class org.incenp.obofoundry.sssom.model.ExtensionValue: Creates a new string-based value that may be an identifier.
ExtensionValue(URI) - Constructor for class org.incenp.obofoundry.sssom.model.ExtensionValue: Creates a new value representing a URI.
ExtensionValue(LocalDate) - Constructor for class org.incenp.obofoundry.sssom.model.ExtensionValue: Creates a new value representing a date.
ExtensionValue(ZonedDateTime) - Constructor for class org.incenp.obofoundry.sssom.model.ExtensionValue: Creates a new value representing a date and time.
extract(Mapping) - Method in class org.incenp.obofoundry.sssom.extract.HashExtractor
extract(Mapping) - Method in class org.incenp.obofoundry.sssom.extract.MappingExtensionExtractor
extract(Mapping) - Method in class org.incenp.obofoundry.sssom.extract.MappingSlotExtractor
extract(Mapping) - Method in class org.incenp.obofoundry.sssom.extract.MappingValueExtractor: Extracts the desired value from the given mapping.
extract(Mapping) - Method in class org.incenp.obofoundry.sssom.extract.SExpressionExtractor
extract(MappingSet) - Method in interface org.incenp.obofoundry.sssom.extract.IValueExtractor: Extracts the desired value from the given mapping set.
extract(MappingSet) - Method in class org.incenp.obofoundry.sssom.extract.MappingSetExtensionExtractor
extract(MappingSet) - Method in class org.incenp.obofoundry.sssom.extract.MappingSetSlotExtractor
extract(MappingSet) - Method in class org.incenp.obofoundry.sssom.extract.MappingValueExtractor
extract(OWLOntology) - Method in class org.incenp.obofoundry.sssom.owl.XrefExtractor: Extract mappings from cross-references in the specified ontology.
extract(OWLOntology, boolean, boolean) - Method in class org.incenp.obofoundry.sssom.owl.XrefExtractor: Extract mappings from cross-references in the specified ontology.
ExtractorSyntaxException - Exception Class in org.incenp.obofoundry.sssom.extract: An exception thrown when parsing an invalid “extractor expression”.
ExtractorSyntaxException() - Constructor for exception class org.incenp.obofoundry.sssom.extract.ExtractorSyntaxException: Creates a new instance with a generic error message.
ExtractorSyntaxException(String) - Constructor for exception class org.incenp.obofoundry.sssom.extract.ExtractorSyntaxException: Creates a new instance with the specified error message.
ExtractorSyntaxException(String, Object...) - Constructor for exception class org.incenp.obofoundry.sssom.extract.ExtractorSyntaxException: Creates a new instance with a constructed error message.
ExtraMetadataPolicy - Enum Class in org.incenp.obofoundry.sssom: Represents the behaviour to adopt regarding non-standard metadata slots.
extraPolicy - Variable in class org.incenp.obofoundry.sssom.SSSOMReader
extraPolicy - Variable in class org.incenp.obofoundry.sssom.SSSOMWriter

F

fillCardinality(List<Mapping>) - Method in class org.incenp.obofoundry.sssom.Cardinalizer: 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.
fillFromExistingExtensions(MappingSet) - Method in class org.incenp.obofoundry.sssom.ExtensionSlotManager: Gets definitions for all extensions used in the specified mapping set.
fillPrefixMap(Map<String, String>) - Method in class org.incenp.obofoundry.sssom.JSONReader
fillPrefixMap(Map<String, String>) - Method in class org.incenp.obofoundry.sssom.SSSOMReader: Declares all prefix names in the specified map.
fillPrefixMap(Map<String, String>) - Method in class org.incenp.obofoundry.sssom.TSVReader
fillPrefixToPredicateMap(OWLOntology) - Method in class org.incenp.obofoundry.sssom.owl.XrefExtractor: Gets the mappings between prefix names and predicates from annotations in the given ontology.
filter(Mapping) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTExistsFunction
filter(Mapping) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTIsAFunction
filter(Mapping) - Method in class org.incenp.obofoundry.sssom.transform.FilterSet
filter(Mapping) - Method in interface org.incenp.obofoundry.sssom.transform.IMappingFilter: Check if a mapping satisfies a given condition.
filter(Mapping) - Method in class org.incenp.obofoundry.sssom.transform.NamedFilter
filter(Mapping) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTDuplicateFunction
filter(Mapping) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTHasExtensionFunction
filter(Mapping) - Method in class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionContainsFunction
FilterSet - Class in org.incenp.obofoundry.sssom.transform: A set of filters.
FilterSet() - Constructor for class org.incenp.obofoundry.sssom.transform.FilterSet
format(Double) - Static method in class org.incenp.obofoundry.sssom.SSSOMUtils: Formats a double value.
format(Object) - Static method in class org.incenp.obofoundry.sssom.SSSOMUtils: Formats a value of an unknown type.
format(String, Mapping) - Method in class org.incenp.obofoundry.sssom.transform.MappingFormatter: Formats a string with values derived from a mapping.
format(LocalDate) - Static method in class org.incenp.obofoundry.sssom.SSSOMUtils: Formats a date value.
format(ZonedDateTime) - Static method in class org.incenp.obofoundry.sssom.SSSOMUtils: Formats a date and time value.
fromExtension(String) - Static method in enum class org.incenp.obofoundry.sssom.util.SerialisationFormat: Gets a serialisation format by its associated filename extension.
fromIRI(String) - Static method in enum class org.incenp.obofoundry.sssom.model.EntityType: Parses an IRI into the corresponding entity type enum value.
fromIRI(String) - Static method in enum class org.incenp.obofoundry.sssom.model.PredicateModifier: Parses an IRI into the corresponding predicate modifier value.
fromIRI(String) - Static method in enum class org.incenp.obofoundry.sssom.model.ValueType: Parses a type identifier into a ValueType object.
fromIRI(String) - Static method in enum class org.incenp.obofoundry.sssom.model.Version: Parses an IRI into the corresponding SSSOM version object.
fromName(String) - Static method in enum class org.incenp.obofoundry.sssom.util.SerialisationFormat: Gets a serialisation format by its name (long or short).
fromRDF(Model) - Method in class org.incenp.obofoundry.sssom.rdf.RDFConverter: Converts a RDF model to a MappingSet object.
fromString(String) - Static method in enum class org.incenp.obofoundry.sssom.model.BuiltinPrefix: Parses a prefix name into one of the built-in prefix.
fromString(String) - Static method in enum class org.incenp.obofoundry.sssom.model.CommonPredicate: Parses a string into a common predicate.
fromString(String) - Static method in enum class org.incenp.obofoundry.sssom.model.EntityType: Parses a string into a entity type enum value.
fromString(String) - Static method in enum class org.incenp.obofoundry.sssom.model.MappingCardinality: Parses a string into a mapping cardinality enum value.
fromString(String) - Static method in enum class org.incenp.obofoundry.sssom.model.PredicateModifier: Parses a string into a predicate modifier.
fromString(String) - Static method in enum class org.incenp.obofoundry.sssom.model.Version: Parses a string into the corresponding SSSOM version object.
FULL - Enum constant in enum class org.incenp.obofoundry.sssom.ValidationLevel: Perform an exhaustive validation.

G

generate(Mapping) - Method in class org.incenp.obofoundry.sssom.transform.MappingProcessingRule: Generates the output object from the given mapping.
generated(MappingProcessingRule<T>, Mapping, T) - Method in interface org.incenp.obofoundry.sssom.transform.IMappingProcessorListener: This method is called whenever a rule is applied to a mapping and produces an object.
getAuthorId() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getAuthorId(boolean) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Gets the list of author_id values, optionally initializing the list if needed.
getAuthorLabel() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getAuthorLabel(boolean) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Gets the list of author_label values, optionally initializing the list if needed.
getCardinalityScope() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getCardinalityScope() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getCardinalityScope(boolean) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Gets the list of cardinality_scope values, optionally initializing the list if needed.
getCardinalityScope(boolean) - Method in class org.incenp.obofoundry.sssom.model.MappingSet: Gets the list of cardinality_scope values, optionally initializing the list if needed.
getComment() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getComment() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getCompliantVersion() - Method in class org.incenp.obofoundry.sssom.slots.Slot: Gets the earliest version of the SSSOM specification this slot is compatible with.
getCompliantVersion(MappingSet) - Method in class org.incenp.obofoundry.sssom.Validator: Gets the minimum version of the SSSOM specification that the given set is compliant with.
getComponent(String) - Method in class org.incenp.obofoundry.sssom.uriexpr.UriExpression: Gets the value of the given slot in this expression.
getComponentNames() - Method in class org.incenp.obofoundry.sssom.uriexpr.UriExpression: Gets the name of all slots present in this expression.
getConfidence() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getCreatorId() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getCreatorId() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getCreatorId(boolean) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Gets the list of creator_id values, optionally initializing the list if needed.
getCreatorId(boolean) - Method in class org.incenp.obofoundry.sssom.model.MappingSet: Gets the list of creator_id values, optionally initializing the list if needed.
getCreatorLabel() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getCreatorLabel() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getCreatorLabel(boolean) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Gets the list of creator_label values, optionally initializing the list if needed.
getCreatorLabel(boolean) - Method in class org.incenp.obofoundry.sssom.model.MappingSet: Gets the list of creator_label values, optionally initializing the list if needed.
getCurationRule() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getCurationRule() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getCurationRule(boolean) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Gets the list of curation_rule values, optionally initializing the list if needed.
getCurationRule(boolean) - Method in class org.incenp.obofoundry.sssom.model.MappingSet: Gets the list of curation_rule values, optionally initializing the list if needed.
getCurationRuleText() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getCurationRuleText() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getCurationRuleText(boolean) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Gets the list of curation_rule_text values, optionally initializing the list if needed.
getCurationRuleText(boolean) - Method in class org.incenp.obofoundry.sssom.model.MappingSet: Gets the list of curation_rule_text values, optionally initializing the list if needed.
getCurieMap() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getCurieMap(boolean) - Method in class org.incenp.obofoundry.sssom.model.MappingSet: Gets the prefix map, optionally initializing the map if needed.
getDefinitionForProperty(String) - Method in class org.incenp.obofoundry.sssom.ExtensionSlotManager: Looks up for an existing definition for the specified property.
getDefinitionForSlot(String) - Method in class org.incenp.obofoundry.sssom.ExtensionSlotManager: Looks up for an existing definition for the specified slot name.
getDefinitions(boolean, boolean) - Method in class org.incenp.obofoundry.sssom.ExtensionSlotManager: Gets the definitions known to this manager.
getDocumentation() - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
getEffectiveType() - Method in class org.incenp.obofoundry.sssom.model.ExtensionDefinition
getEntityChecker() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTOwlApplication: Gets the ontology checker used by this application.
getErrors() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformReader: Gets all syntax errors that were found when parsing, if any.
getExtension() - Method in enum class org.incenp.obofoundry.sssom.util.SerialisationFormat: Gets the typical filename extension associated with the format.
getExtensionDefinitions() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getExtensionDefinitions(boolean) - Method in class org.incenp.obofoundry.sssom.model.MappingSet: Gets the list of extension definitions, optionally initializing the underlying field to an empty list if needed.
getExtensions() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getExtensions() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getExtensions(boolean) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Gets the map of extension values, optionally initializing the map if needed.
getExtensions(boolean) - Method in class org.incenp.obofoundry.sssom.model.MappingSet: Gets the map of extension values, optionally initializing the map if needed.
getFormatter() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformApplication: Gets the mapping formatter used by this application.
getFullPrefixMap() - Method in class org.incenp.obofoundry.sssom.util.ExtendedPrefixMap: Gets the full prefix map, associating every known prefix names to the canonical URL prefix.
getHighestVersion(Collection<Version>) - Static method in enum class org.incenp.obofoundry.sssom.model.Version: Gets the most recent version of all the versions in the given collection.
getHomepage() - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
getImports() - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
getImports(boolean) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry: Gets the list of imports values, optionally initializing the list if needed.
getInverse() - Method in enum class org.incenp.obofoundry.sssom.model.CommonPredicate: Gets the inverse predicate for this predicate.
getInverse() - Method in enum class org.incenp.obofoundry.sssom.model.MappingCardinality: Gets the inverse of this cardinality (i.e., "1:n" -> "n:1").
getIRI() - Method in enum class org.incenp.obofoundry.sssom.model.EntityType: Gets the IRI associated to the enum value.
getIRI() - Method in enum class org.incenp.obofoundry.sssom.model.PredicateModifier: Gets the IRI associated with the enum value.
getIRI() - Method in enum class org.incenp.obofoundry.sssom.model.Version: Gets the IRI associated to the enum value.
getIssueTracker() - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
getIssueTracker() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getIssueTrackerItem() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getLabel(OWLOntology, IRI, String, boolean) - Static method in class org.incenp.obofoundry.sssom.owl.OWLHelper: Gets the label of an OWL entity, if any.
getLastUpdated() - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference
getLicense() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getLicense() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getLocalName() - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference
getMappingCardinality() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getMappingDate() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getMappingDate() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getMappingHelper() - Static method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Gets the default helper object to manipulate Mapping slots.
getMappingHelper(boolean) - Static method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Gets a helper object to manipulate Mapping slots.
getMappingJustification() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getMappingProvider() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getMappingProvider() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getMappingRegistryDescription() - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
getMappingRegistryId() - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
getMappingRegistryTitle() - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
getMappings() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getMappings(boolean) - Method in class org.incenp.obofoundry.sssom.model.MappingSet: Gets the list of mappings, optionally initializing the underlying field to an empty list if needed.
getMappingSetConfidence() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getMappingSetDescription() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getMappingSetGroup() - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference
getMappingSetHelper() - Static method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Gets the default helper object to manipulate MappingSet slots.
getMappingSetHelper(boolean) - Static method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Gets a helper object to manipulate MappingSet slots.
getMappingSetId() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getMappingSetId() - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference
getMappingSetReferences() - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
getMappingSetSource() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getMappingSetSource(boolean) - Method in class org.incenp.obofoundry.sssom.model.MappingSet: Gets the list of mapping_set_source values, optionally initializing the list if needed.
getMappingSetTitle() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getMappingSetVersion() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getMappingSlotList(String) - Static method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Helper method to construct a list of slot names from a string specification.
getMappingSource() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getMappingTool() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getMappingTool() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getMappingToolId() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getMappingToolId() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getMappingToolVersion() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getMappingToolVersion() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getMatchString() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getMatchString(boolean) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Gets the list of match_string values, optionally initializing the list if needed.
getMergeOptions() - Method in class org.incenp.obofoundry.sssom.SetMerger: Gets the options that define the behaviour of this object.
getMessage() - Method in enum class org.incenp.obofoundry.sssom.ValidationError: Gets the human-readable error message for this error.
getMessage(EnumSet<ValidationError>) - Static method in enum class org.incenp.obofoundry.sssom.ValidationError: Gets a human-readable error message for a set of validation errors.
getMirrorFrom() - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference
getName() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTAnnotateFunction
getName() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTAnnotateObjectFunction: Deprecated.
getName() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTAnnotateSubjectFunction: Deprecated.
getName() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTCheckObjectExistenceFunction: Deprecated.
getName() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTCheckSubjectExistenceFunction: Deprecated.
getName() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTCreateAxiomFunction
getName() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTDeclareClassFunction: Deprecated.
getName() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTDeclareFunction
getName() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTDeclareObjectPropertyFunction: Deprecated.
getName() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTDirectFunction
getName() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTExistsFunction
getName() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTIsAFunction
getName() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTOwlSetvarFunction: Deprecated.
getName() - Method in class org.incenp.obofoundry.sssom.slots.Slot: Gets the name of the slot as it appears in the SSSOM specification (e.g., mapping_justification, subject_id, etc.).
getName() - Method in interface org.incenp.obofoundry.sssom.transform.IFormatModifierFunction: Gets the name by which the function should be called in a placeholder.
getName() - Method in interface org.incenp.obofoundry.sssom.transform.ISSSOMTFunction: Gets the name of the function, by which it can be called in a SSSOM/T ruleset.
getName() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTAssignFunction
getName() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTDefaultModifierFunction
getName() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTDuplicateFunction
getName() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTEditFunction: Deprecated.
getName() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTFlattenFunction
getName() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTFormatFunction
getName() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTHasExtensionFunction
getName() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTInferCardinalityFunction
getName() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTInvertFunction
getName() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTListItemFunction
getName() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTReplaceFunction
getName() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTSetvarCallbackFunction
getName() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTSetvarFunction
getName() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTShortFunction
getName() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTStopFunction
getName() - Method in class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionContainsFunction
getName() - Method in class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionDeclareFormatFunction
getName() - Method in class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionExpandFunction
getName() - Method in class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionSlotValueFunction
getName() - Method in class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionToExtFunction
getName() - Method in enum class org.incenp.obofoundry.sssom.util.SerialisationFormat: Gets the user-facing name of the serialisation format.
getObject(Mapping) - Method in class org.incenp.obofoundry.sssom.Cardinalizer: Gets a string representing the object of a mapping, that can be used for cardinality computation.
getObject(Mapping) - Static method in enum class org.incenp.obofoundry.sssom.model.MappingCardinality: Deprecated.
Use Cardinalizer.getObject(Mapping) instead.
getObjectCategory() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getObjectId() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getObjectLabel() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getObjectMatchField() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getObjectMatchField() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getObjectMatchField(boolean) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Gets the list of object_match_field values, optionally initializing the list if needed.
getObjectMatchField(boolean) - Method in class org.incenp.obofoundry.sssom.model.MappingSet: Gets the list of object_match_field values, optionally initializing the list if needed.
getObjectPreprocessing() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getObjectPreprocessing() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getObjectPreprocessing(boolean) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Gets the list of object_preprocessing values, optionally initializing the list if needed.
getObjectPreprocessing(boolean) - Method in class org.incenp.obofoundry.sssom.model.MappingSet: Gets the list of object_preprocessing values, optionally initializing the list if needed.
getObjectSource() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getObjectSource() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getObjectSourceVersion() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getObjectSourceVersion() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getObjectType() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getObjectType() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getOntology() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTOwlApplication: Gets the helper ontology used by this application.
getOther() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getOther() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getOWLAnnotationProperty(String) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker
getOWLClass(String) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker
getOWLDataProperty(String) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker
getOWLDatatype(String) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker
getOWLIndividual(String) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker
getOWLObjectProperty(String) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker
getPredicateId() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getPredicateLabel() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getPredicateModifier() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getPredicateType() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getPredicateType() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getPrefix() - Method in enum class org.incenp.obofoundry.sssom.model.BuiltinPrefix
getPrefix(String) - Method in class org.incenp.obofoundry.sssom.PrefixManager: Gets the prefix associated with the given prefix name.
getPrefixManager() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformApplication: Gets the prefix manager used by this application.
getPrefixManager() - Method in class org.incenp.obofoundry.sssom.YAMLConverter: Gets the prefix manager used by this object to expand shortened entity references in values.
getPrefixMap() - Method in class org.incenp.obofoundry.sssom.PrefixManager: Gets the underlying map of prefix names to URL prefixes.
getPrefixMap() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformReader: Gets the effective prefix map used by this reader.
getPrefixName() - Method in enum class org.incenp.obofoundry.sssom.model.BuiltinPrefix
getPrefixName(String) - Method in class org.incenp.obofoundry.sssom.PrefixManager: Gets the name of the best (longest) prefix for a given identifier.
getProperty() - Method in class org.incenp.obofoundry.sssom.model.ExtensionDefinition
getPublicationDate() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getPublicationDate() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getReader(File) - Method in class org.incenp.obofoundry.sssom.util.ReaderFactory: Gets a SSSOM reader suitable for the format used in the provided file.
getReader(InputStream) - Method in class org.incenp.obofoundry.sssom.util.ReaderFactory: Gets a SSSOM reader suitable for the format used in the provided stream.
getReader(Reader) - Method in class org.incenp.obofoundry.sssom.util.ReaderFactory: Gets a SSSOM reader suitable for the format used in the provider Reader object.
getReader(Reader, String) - Method in class org.incenp.obofoundry.sssom.util.ReaderFactory: Gets a SSSOM reader suitable for the format used in the provided Reader object.
getReader(Reader, SerialisationFormat) - Method in class org.incenp.obofoundry.sssom.util.ReaderFactory: Gets a SSSOM reader for the specified reader object and format.
getReader(String) - Method in class org.incenp.obofoundry.sssom.util.ReaderFactory: Gets a SSSOM reader suitable for the format used in the file with the provided name.
getReader(String, boolean) - Method in class org.incenp.obofoundry.sssom.util.ReaderFactory: Gets a SSSOM reader suitable for the format used in the file with the provided name.
getReader(String, boolean, SerialisationFormat) - Method in class org.incenp.obofoundry.sssom.util.ReaderFactory: Gets a SSSOM reader for the provided file, with a possibly explicitly specified format.
getReader(String, String) - Method in class org.incenp.obofoundry.sssom.util.ReaderFactory: Gets a SSSOM reader suitable for the format used in the file with the provided name.
getReader(String, String, boolean) - Method in class org.incenp.obofoundry.sssom.util.ReaderFactory: Gets a SSSOM reader suitable for the format used in the file with the provided name.
getReader(String, String, boolean, SerialisationFormat) - Method in class org.incenp.obofoundry.sssom.util.ReaderFactory: Gets a SSSOM reader suitable for the specified file, with a possibly explicitly specified format.
getRecordId() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getRegistryConfidence() - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference
getReviewerId() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getReviewerId(boolean) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Gets the list of reviewer_id values, optionally initializing the list if needed.
getReviewerLabel() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getReviewerLabel(boolean) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Gets the list of reviewer_label values, optionally initializing the list if needed.
getRules() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformReader: Gets the SSSOM/T rules that have been parsed from the underlying source.
getSchema() - Method in class org.incenp.obofoundry.sssom.uriexpr.UriExpression: Gets the schema part of this expression.
getSeeAlso() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getSeeAlso() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getSeeAlso(boolean) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Gets the list of see_also values, optionally initializing the list if needed.
getSeeAlso(boolean) - Method in class org.incenp.obofoundry.sssom.model.MappingSet: Gets the list of see_also values, optionally initializing the list if needed.
getSemanticSimilarityMeasure() - Method in class org.incenp.obofoundry.sssom.model.Mapping: Deprecated.
Use #getSimilarityMeasure() instead.
getSemanticSimilarityScore() - Method in class org.incenp.obofoundry.sssom.model.Mapping: Deprecated.
Use #getSimilarityScore() instead.
getShortNames() - Static method in enum class org.incenp.obofoundry.sssom.util.SerialisationFormat: Gets a list of all available format short names.
getSignature() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTAnnotateFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTAnnotateObjectFunction: Deprecated.
getSignature() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTAnnotateSubjectFunction: Deprecated.
getSignature() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTCheckObjectExistenceFunction: Deprecated.
getSignature() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTCheckSubjectExistenceFunction: Deprecated.
getSignature() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTCreateAxiomFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTDeclareClassFunction: Deprecated.
getSignature() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTDeclareFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTDeclareObjectPropertyFunction: Deprecated.
getSignature() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTDirectFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTExistsFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTIsAFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTOwlSetvarFunction: Deprecated.
getSignature() - Method in interface org.incenp.obofoundry.sssom.transform.IFormatModifierFunction: Gets the expected signature of the function.
getSignature() - Method in interface org.incenp.obofoundry.sssom.transform.ISSSOMTFunction: Gets the expected signature of the function.
getSignature() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTAssignFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTDefaultModifierFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTDuplicateFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTEditFunction: Deprecated.
getSignature() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTFlattenFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTFormatFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTHasExtensionFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTInferCardinalityFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTInvertFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTListItemFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTReplaceFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTSetvarCallbackFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTSetvarFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTShortFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTStopFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionContainsFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionDeclareFormatFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionExpandFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionSlotValueFunction
getSignature() - Method in class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionToExtFunction
getSimilarityMeasure() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getSimilarityMeasure() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getSimilarityScore() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getSimplePrefixMap() - Method in class org.incenp.obofoundry.sssom.util.ExtendedPrefixMap: Gets a simple prefix map associating the canonical prefix name to the canonical URL prefix.
getSlotByName(String) - Method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Finds a slot by its name.
getSlotByURI(String) - Method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Finds a slot by its associated URI.
getSlotName() - Method in class org.incenp.obofoundry.sssom.model.ExtensionDefinition
getSlotNames() - Method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Gets the current list of slot names to be visited.
getSlots() - Method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Gets the current list of slots set to be visited.
getSlotsByName(Collection<String>) - Method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Finds slots by their names.
getSlotValue(T) - Method in class org.incenp.obofoundry.sssom.extract.SlotExtractor: Performs the actual extraction.
getSortName() - Method in enum class org.incenp.obofoundry.sssom.util.SerialisationFormat: Gets the short name of the serialisation format.
getSssomVersion() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getSubClassesOf(String) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTOwlApplication: Gets a list of all descendants of a given class.
getSubject(Mapping) - Method in class org.incenp.obofoundry.sssom.Cardinalizer: Gets a string representing the subject of a mapping, that can be used for cardinality computation.
getSubject(Mapping) - Static method in enum class org.incenp.obofoundry.sssom.model.MappingCardinality: Deprecated.
Use Cardinalizer.getSubject(Mapping) instead.
getSubjectCategory() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getSubjectId() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getSubjectLabel() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getSubjectMatchField() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getSubjectMatchField() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getSubjectMatchField(boolean) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Gets the list of subject_match_field values, optionally initializing the list if needed.
getSubjectMatchField(boolean) - Method in class org.incenp.obofoundry.sssom.model.MappingSet: Gets the list of subject_match_field values, optionally initializing the list if needed.
getSubjectPreprocessing() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getSubjectPreprocessing() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getSubjectPreprocessing(boolean) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Gets the list of subject_preprocessing values, optionally initializing the list if needed.
getSubjectPreprocessing(boolean) - Method in class org.incenp.obofoundry.sssom.model.MappingSet: Gets the list of subject_preprocessing values, optionally initializing the list if needed.
getSubjectSource() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getSubjectSource() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getSubjectSourceVersion() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getSubjectSourceVersion() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getSubjectType() - Method in class org.incenp.obofoundry.sssom.model.Mapping
getSubjectType() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
getSubPropertiesOf(String) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTOwlApplication: Gets a list of all descendants of a given property.
getTags() - Method in class org.incenp.obofoundry.sssom.transform.MappingProcessingRule: Gets the tags associated with the rule.
getTemplate(UriExpression, String) - Method in class org.incenp.obofoundry.sssom.uriexpr.UriExpressionRegistry: Gets a template in a given format for a URI Expression.
getTransformer(String) - Method in class org.incenp.obofoundry.sssom.transform.MappingFormatter: Gets a mapping transformer that can directly create a formatted string from a mapping by application of all the substitutions defined in this object.
getTransformer(String) - Method in class org.incenp.obofoundry.sssom.transform.VariableManager: Gets a mapping transformer that will return the value of the variable for the mapping it is applied to.
getTransformer(String, IFormatModifierFunction, List<String>) - Method in class org.incenp.obofoundry.sssom.transform.MappingFormatter: Gets a mapping transformer that can directly create a formatted string from a mapping by application of all the substitutions defined in this object.
getType() - Method in class org.incenp.obofoundry.sssom.extract.HashExtractor
getType() - Method in interface org.incenp.obofoundry.sssom.extract.IValueExtractor: Gets the type of the value that would be returned by IValueExtractor.extract(MappingSet).
getType() - Method in class org.incenp.obofoundry.sssom.extract.MappingExtensionExtractor
getType() - Method in class org.incenp.obofoundry.sssom.extract.MappingSetExtensionExtractor
getType() - Method in class org.incenp.obofoundry.sssom.extract.MappingSetSlotExtractor
getType() - Method in class org.incenp.obofoundry.sssom.extract.MappingSlotExtractor
getType() - Method in class org.incenp.obofoundry.sssom.extract.SExpressionExtractor
getType() - Method in class org.incenp.obofoundry.sssom.extract.SlotExtractor: Returns the type of the extracted value.
getType() - Method in class org.incenp.obofoundry.sssom.model.ExtensionValue
getType() - Method in class org.incenp.obofoundry.sssom.slots.Slot: Gets the underlying Java type for the slot.
getTypeHint() - Method in class org.incenp.obofoundry.sssom.model.ExtensionDefinition
getUnknownPrefixNames() - Method in class org.incenp.obofoundry.sssom.owl.XrefExtractor: Gets any prefix names encountered in cross-references that could not be resolved.
getUnresolvedPrefixNames() - Method in class org.incenp.obofoundry.sssom.PrefixManager: Gets the prefix names that this resolver could not expand.
getUnshortenedIRIs() - Method in class org.incenp.obofoundry.sssom.PrefixManager: Gets the IRIs that could not be shortened by PrefixManager.shortenIdentifier(String) for lack of a suitable prefix declaration.
getURI() - Method in class org.incenp.obofoundry.sssom.slots.Slot: Gets the URI of the slot.
getUriExpressionRegistry() - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTOwlApplication: Gets the registry of URI Expression templates, needed to expand a URI Expression into a OWL expression.
getUsedPrefixes() - Method in class org.incenp.obofoundry.sssom.ExtensionSlotManager: Gets all the prefix names used in extensions and extension definitions.
getUsedPrefixes(MappingSet) - Method in class org.incenp.obofoundry.sssom.SSSOMWriter: Gets the prefix names that are actually used in the given set.
getUsedPrefixes(MappingSet, boolean) - Method in class org.incenp.obofoundry.sssom.SSSOMWriter: Gets the prefix names that are actually used in the given set, possibly including the builtin prefix names.
getValue() - Method in class org.incenp.obofoundry.sssom.model.ExtensionValue
getValue(T) - Method in class org.incenp.obofoundry.sssom.slots.Slot: Gets the value of the slot for a given object.
getVariableManager() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformApplication: Gets the variable manager used by this application.
GUESS - Enum constant in enum class org.incenp.obofoundry.sssom.TSVReader.SeparatorMode: The reader should try to infer the separator used (with fallback to expecting tabs if the separator cannot be positively determined).

H

hasErrors() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformReader: Indicates whether parsing errors occurred.
hash(Mapping) - Method in class org.incenp.obofoundry.sssom.MappingHasher: Hashes the given mapping using the SSSOM standard hash procedure.
hashCode() - Method in class org.incenp.obofoundry.sssom.model.Mapping
hashCode() - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
hashCode() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
hashCode() - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference
HashExtractor - Class in org.incenp.obofoundry.sssom.extract: Extracts the standard SSSOM hash for a mapping.
HashExtractor(int) - Constructor for class org.incenp.obofoundry.sssom.extract.HashExtractor: Creates a new instance.
hasRules() - Method in class org.incenp.obofoundry.sssom.transform.MappingProcessor: Indicates whether this processor has some rules to work with.
hasUnmappedObject() - Method in class org.incenp.obofoundry.sssom.model.Mapping: Indicates whether the subject of this mapping is not mapped to any entity on the object side.
hasUnmappedSubject() - Method in class org.incenp.obofoundry.sssom.model.Mapping: Indicates whether the object of this mapping is not mapped to any entity on the subject side.
hasVariable(String) - Method in class org.incenp.obofoundry.sssom.transform.VariableManager: Checks if a name is the name of a known variable.
homepage(String) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry.MappingRegistryBuilder

I

IDENTIFIER - Enum constant in enum class org.incenp.obofoundry.sssom.model.ValueType
IFormatModifierFunction - Interface in org.incenp.obofoundry.sssom.transform: Represents a SSSOM/T format modifier function.
IMappingFilter - Interface in org.incenp.obofoundry.sssom.transform: An interface to filter mappings according in a mapping set.
IMappingProcessorCallback - Interface in org.incenp.obofoundry.sssom.transform: Represents a custom processing step that can be called when applying rules to a mapping set.
IMappingProcessorListener<T> - Interface in org.incenp.obofoundry.sssom.transform: A listener invoked by the MappingProcessor engine when a rule is applied to a mapping and results in the production of an object.
IMappingSetValidator - Interface in org.incenp.obofoundry.sssom.checks: Represents a single check for a possible post-parsing error that can make a mapping set invalid.
IMappingTransformer<T> - Interface in org.incenp.obofoundry.sssom.transform: An interface to transform a mapping into another object.
IMappingValidator - Interface in org.incenp.obofoundry.sssom.checks: Represents a single check for a possible post-parsing error that can make an individual mapping invalid.
IMetadataTransformer<T,V> - Interface in org.incenp.obofoundry.sssom.transform: An interface to transform a metadata slot into another object.
imports(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry.MappingRegistryBuilder
includeObsoletes(boolean) - Method in class org.incenp.obofoundry.sssom.owl.XrefExtractor: Indicates whether cross-references on obsoleted terms should be extracted.
includeRules(Set<String>) - Method in class org.incenp.obofoundry.sssom.transform.MappingProcessor: Sets the processor to run only the rules that have at least one tag in the specified tag set.
inferCardinality(List<Mapping>) - Static method in enum class org.incenp.obofoundry.sssom.model.MappingCardinality: Deprecated.
Use Cardinalizer.fillCardinality(List) instead.
inferFormat(Reader) - Method in class org.incenp.obofoundry.sssom.util.ReaderFactory: Peeks inside a Reader object to try and guess the SSSOM serialisation format that is being used.
INTEGER - Enum constant in enum class org.incenp.obofoundry.sssom.model.ValueType
INVALID_PREDICATE_TYPE - Enum constant in enum class org.incenp.obofoundry.sssom.ValidationError
invert() - Method in class org.incenp.obofoundry.sssom.model.Mapping: Creates an inverted version of this mapping if possible.
invert(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Creates an inverted version of this mapping with an explicit predicate.
invert(Mapping) - Static method in enum class org.incenp.obofoundry.sssom.model.CommonPredicate: Deprecated.
Use Mapping.invert() instead.
isBoolean() - Method in class org.incenp.obofoundry.sssom.model.ExtensionValue
isCompatibleWith(Version) - Method in enum class org.incenp.obofoundry.sssom.model.Version: Checks whether this version is compatible with the indicated version.
isDate() - Method in class org.incenp.obofoundry.sssom.model.ExtensionValue
isDatetime() - Method in class org.incenp.obofoundry.sssom.model.ExtensionValue
isDouble() - Method in class org.incenp.obofoundry.sssom.model.ExtensionValue
isEmpty() - Method in class org.incenp.obofoundry.sssom.ExtensionSlotManager: Indicates whether this object contains any extension definition.
isEntityReference() - Method in class org.incenp.obofoundry.sssom.slots.Slot: Indicates whether the slot is intended to hold an entity reference.
isExact() - Method in enum class org.incenp.obofoundry.sssom.model.CommonPredicate: Indicates whether the predicate is “exact”.
isExtensionSlotNameValid(String) - Static method in class org.incenp.obofoundry.sssom.ExtensionSlotManager: Checks whether the specified name is usable as an extension slot name.
isIdentifier() - Method in class org.incenp.obofoundry.sssom.model.ExtensionValue
ISimpleSlotVisitor<T,V> - Interface in org.incenp.obofoundry.sssom.slots: A visitor interface to visit the different metadata slot of a SSSOM Java object.
isInteger() - Method in class org.incenp.obofoundry.sssom.model.ExtensionValue
isInvertible() - Method in enum class org.incenp.obofoundry.sssom.model.CommonPredicate: Indicates whether a predicate can be inverted.
isListOf(Object, Class<?>) - Static method in class org.incenp.obofoundry.sssom.YAMLConverter: Checks that an object is a list containing items of a given type.
isLiteral() - Method in class org.incenp.obofoundry.sssom.model.Mapping: Indicates whether this mapping represents a "literal" mapping.
ISlotVisitor<T> - Interface in org.incenp.obofoundry.sssom.slots: A visitor interface to visit the different types of metadata slots of a SSSOM object.
isMapOf(Object, Class<?>) - Static method in class org.incenp.obofoundry.sssom.YAMLConverter: Checks that an object is a dictionary with string keys and values of a given type.
isMultivalued() - Method in class org.incenp.obofoundry.sssom.slots.StringSlot: Indicates whether the slot holds a list of values rather than a single value.
isObsolete(OWLOntology, IRI) - Static method in class org.incenp.obofoundry.sssom.owl.OWLHelper: Checks whether an entity is marked as obsolete in the specified ontology.
isPropagatable() - Method in class org.incenp.obofoundry.sssom.slots.Slot: Indicates whether the slot is a "propagatable slot".
ISSSOMTFunction<T> - Interface in org.incenp.obofoundry.sssom.transform: Represents a function in a SSSOM/Transform application.
ISSSOMTransformApplication<T> - Interface in org.incenp.obofoundry.sssom.transform: Represents a specialised application of the SSSOM/Transform language.
isString() - Method in class org.incenp.obofoundry.sssom.model.ExtensionValue
issueTracker(String) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry.MappingRegistryBuilder
issueTracker(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
issueTrackerItem(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
isUnmapped() - Method in class org.incenp.obofoundry.sssom.model.Mapping: Indicates whether this mapping represents a "missing" mapping.
isURI() - Method in class org.incenp.obofoundry.sssom.slots.Slot: Indicates whether the slot is expected to contain a URI.
itemNo - Variable in class org.incenp.obofoundry.sssom.extract.SlotExtractor
IValueExtractor - Interface in org.incenp.obofoundry.sssom.extract: Extracts an arbitrary piece of content from a mapping set object.
IYAMLPreprocessor - Interface in org.incenp.obofoundry.sssom: An interface for applying arbitrary treatments to a YAML-derived dictionary.

J

JSON - Enum constant in enum class org.incenp.obofoundry.sssom.util.SerialisationFormat: SSSOM/JSON, the other format described in the SSSOM specification.
JsonLDConverter - Class in org.incenp.obofoundry.sssom.compatibility: A YAML preprocessor to convert SSSOM-Py’s JSON-LD output into a normalised form.
JsonLDConverter() - Constructor for class org.incenp.obofoundry.sssom.compatibility.JsonLDConverter
JSONReader - Class in org.incenp.obofoundry.sssom: A parser to read a SSSOM mapping set from a JSON serialisation format.
JSONReader(File) - Constructor for class org.incenp.obofoundry.sssom.JSONReader: Creates a new instance that will read data from the specified file.
JSONReader(InputStream) - Constructor for class org.incenp.obofoundry.sssom.JSONReader: Creates a new instance that will read data from the specified stream.
JSONReader(Reader) - Constructor for class org.incenp.obofoundry.sssom.JSONReader: Creates a new instance that will read data from the specified reader.
JSONReader(String) - Constructor for class org.incenp.obofoundry.sssom.JSONReader: Creates a new instance that will read data from a file with the specified name.
JSONWriter - Class in org.incenp.obofoundry.sssom: A writer to serialise a SSSOM mapping set into a JSON format.
JSONWriter(File) - Constructor for class org.incenp.obofoundry.sssom.JSONWriter: Creates a new instance that will write data to the specified file.
JSONWriter(OutputStream) - Constructor for class org.incenp.obofoundry.sssom.JSONWriter: Creates a new instance that will write data to the specified stream.
JSONWriter(String) - Constructor for class org.incenp.obofoundry.sssom.JSONWriter: Creates a new instance that will write data to a file with the specified filename.

L

lastUpdated(LocalDate) - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference.MappingSetReferenceBuilder
LATEST - Static variable in enum class org.incenp.obofoundry.sssom.model.Version: The latest version of the specification currently supported by this implementation.
license(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
license(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
LINKML - Enum constant in enum class org.incenp.obofoundry.sssom.model.BuiltinPrefix
LiteralProfileConverter - Class in org.incenp.obofoundry.sssom.compatibility: A YAML preprocessor to convert literal* slots.
LiteralProfileConverter() - Constructor for class org.incenp.obofoundry.sssom.compatibility.LiteralProfileConverter
localName(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference.MappingSetReferenceBuilder

M

MANY_TO_MANY - Enum constant in enum class org.incenp.obofoundry.sssom.model.MappingCardinality
MANY_TO_ONE - Enum constant in enum class org.incenp.obofoundry.sssom.model.MappingCardinality
Mapping - Class in org.incenp.obofoundry.sssom.model
Mapping() - Constructor for class org.incenp.obofoundry.sssom.model.Mapping
Mapping(String, String, String, String, String, String, PredicateModifier, String, String, String, String, List<String>, List<String>, List<String>, List<String>, List<String>, List<String>, String, EntityType, String, String, EntityType, String, String, EntityType, String, String, MappingCardinality, List<String>, String, String, String, LocalDate, LocalDate, Double, List<String>, List<String>, List<String>, List<String>, List<String>, List<String>, List<String>, Double, String, List<String>, String, String, String, Map<String, ExtensionValue>) - Constructor for class org.incenp.obofoundry.sssom.model.Mapping
Mapping.MappingBuilder - Class in org.incenp.obofoundry.sssom.model
mappingCardinality(MappingCardinality) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
MappingCardinality - Enum Class in org.incenp.obofoundry.sssom.model: Represents the cardinality of a mapping.
MappingCardinalitySlot<T> - Class in org.incenp.obofoundry.sssom.slots: Represents a metadata slot that holds a mapping cardinality value.
MappingCardinalitySlot(Field) - Constructor for class org.incenp.obofoundry.sssom.slots.MappingCardinalitySlot: Creates a new instance.
mappingDate(LocalDate) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
mappingDate(LocalDate) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
MappingEditor - Class in org.incenp.obofoundry.sssom.transform: A mapping transformer that applies arbitrary changes to a mapping.
MappingEditor() - Constructor for class org.incenp.obofoundry.sssom.transform.MappingEditor: Creates a new instance with the default SSSOM prefix manager.
MappingEditor(PrefixManager) - Constructor for class org.incenp.obofoundry.sssom.transform.MappingEditor: Creates a new instance with the specified prefix manager.
MappingExtensionExtractor - Class in org.incenp.obofoundry.sssom.extract: Extracts the value of an extension slot from a mapping object.
MappingExtensionExtractor(int, String) - Constructor for class org.incenp.obofoundry.sssom.extract.MappingExtensionExtractor: Creates a new instance.
MappingFormatter - Class in org.incenp.obofoundry.sssom.transform: Helper class to format mappings into strings.
MappingFormatter() - Constructor for class org.incenp.obofoundry.sssom.transform.MappingFormatter
mappingFromRDF(Model) - Method in class org.incenp.obofoundry.sssom.rdf.RDFConverter: Converts a RDF model to a Mapping object.
mappingFromRDF(Model, Version) - Method in class org.incenp.obofoundry.sssom.rdf.RDFConverter: Converts a RDF model to a Mapping object.
MappingHasher - Class in org.incenp.obofoundry.sssom: Creates deterministic hash values from mappings.
MappingHasher() - Constructor for class org.incenp.obofoundry.sssom.MappingHasher: Creates a new instance.
mappingJustification(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
mappingNo - Variable in class org.incenp.obofoundry.sssom.extract.MappingValueExtractor
MappingProcessingRule<T> - Class in org.incenp.obofoundry.sssom.transform: This class represents an arbitrary treatment applied to a mapping.
MappingProcessingRule(IMappingFilter, IMappingTransformer<Mapping>, IMappingTransformer<T>) - Constructor for class org.incenp.obofoundry.sssom.transform.MappingProcessingRule: Creates a new instance.
MappingProcessingRule(IMappingFilter, IMappingTransformer<Mapping>, IMappingTransformer<T>, IMappingProcessorCallback) - Constructor for class org.incenp.obofoundry.sssom.transform.MappingProcessingRule: Creates a new instance that includes a custom processing step.
MappingProcessor<T> - Class in org.incenp.obofoundry.sssom.transform: An engine for applying MappingProcessingRules to mappings.
MappingProcessor() - Constructor for class org.incenp.obofoundry.sssom.transform.MappingProcessor
mappingProvider(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
mappingProvider(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
MappingRegistry - Class in org.incenp.obofoundry.sssom.model
MappingRegistry() - Constructor for class org.incenp.obofoundry.sssom.model.MappingRegistry
MappingRegistry(String, String, String, List<String>, List<MappingSetReference>, String, String, String) - Constructor for class org.incenp.obofoundry.sssom.model.MappingRegistry
MappingRegistry.MappingRegistryBuilder - Class in org.incenp.obofoundry.sssom.model
mappingRegistryDescription(String) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry.MappingRegistryBuilder
mappingRegistryId(String) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry.MappingRegistryBuilder
mappingRegistryTitle(String) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry.MappingRegistryBuilder
mappings(List<Mapping>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
MappingSet - Class in org.incenp.obofoundry.sssom.model
MappingSet() - Constructor for class org.incenp.obofoundry.sssom.model.MappingSet
MappingSet(Version, Map<String, String>, List<Mapping>, String, String, List<String>, String, String, Double, List<String>, List<String>, String, EntityType, String, String, EntityType, String, String, EntityType, String, List<String>, String, String, String, LocalDate, LocalDate, List<String>, List<String>, List<String>, List<String>, String, List<String>, List<String>, List<String>, String, String, String, List<ExtensionDefinition>, Map<String, ExtensionValue>) - Constructor for class org.incenp.obofoundry.sssom.model.MappingSet
MappingSet.MappingSetBuilder - Class in org.incenp.obofoundry.sssom.model
mappingSetConfidence(Double) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
mappingSetDescription(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
MappingSetExtensionExtractor - Class in org.incenp.obofoundry.sssom.extract: Extracts the value of an extension slot from a mapping set object.
MappingSetExtensionExtractor(String) - Constructor for class org.incenp.obofoundry.sssom.extract.MappingSetExtensionExtractor: Creates a new instance.
mappingSetGroup(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference.MappingSetReferenceBuilder
mappingSetId(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
mappingSetId(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference.MappingSetReferenceBuilder
MappingSetReference - Class in org.incenp.obofoundry.sssom.model
MappingSetReference() - Constructor for class org.incenp.obofoundry.sssom.model.MappingSetReference
MappingSetReference(String, String, Double, String, LocalDate, String) - Constructor for class org.incenp.obofoundry.sssom.model.MappingSetReference
MappingSetReference.MappingSetReferenceBuilder - Class in org.incenp.obofoundry.sssom.model
mappingSetReferences(List<MappingSetReference>) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry.MappingRegistryBuilder
MappingSetSlotExtractor - Class in org.incenp.obofoundry.sssom.extract: Extracts the value of a slot from a mapping set object.
MappingSetSlotExtractor(Slot<MappingSet>, int) - Constructor for class org.incenp.obofoundry.sssom.extract.MappingSetSlotExtractor: Creates a new instance.
mappingSetSource(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
mappingSetTitle(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
mappingSetVersion(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
MappingSlotExtractor - Class in org.incenp.obofoundry.sssom.extract: Extracts the value of a slot from a mapping object.
MappingSlotExtractor(int, Slot<Mapping>, int) - Constructor for class org.incenp.obofoundry.sssom.extract.MappingSlotExtractor: Creates a new instance.
mappingSource(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
mappingTool(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
mappingTool(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
mappingToolId(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
mappingToolId(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
mappingToolVersion(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
mappingToolVersion(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
MappingValueExtractor - Class in org.incenp.obofoundry.sssom.extract: Base class for extractors that extract a value from a specific mapping record.
MappingValueExtractor(int) - Constructor for class org.incenp.obofoundry.sssom.extract.MappingValueExtractor: Creates a new instance.
matchString(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
MatchTermTypeConverter - Class in org.incenp.obofoundry.sssom.compatibility: A YAML preprocessor to convert a dictionary containing a match_term_type metadata slot into its standardised equivalents.
MatchTermTypeConverter() - Constructor for class org.incenp.obofoundry.sssom.compatibility.MatchTermTypeConverter
MatchTypeConverter - Class in org.incenp.obofoundry.sssom.compatibility: A YAML preprocessor to convert a dictionary containing a match_type metadata slot into its standardised equivalent.
MatchTypeConverter() - Constructor for class org.incenp.obofoundry.sssom.compatibility.MatchTypeConverter
maybeCreateAnnotatedTransformer(SSSOMTOwlApplication, IMappingTransformer<OWLAxiom>, Map<String, String>) - Static method in class org.incenp.obofoundry.sssom.owl.SSSOMTHelper: Given an axiom generator, maybe wraps it into another generator that would produce the same axiom but annotated with metadata from the mapping from which the axiom is derived.
maybeCreateAnnotatedTransformer(SSSOMTOwlApplication, IMappingTransformer<OWLAxiom>, Map<String, String>, List<String>, int) - Static method in class org.incenp.obofoundry.sssom.owl.SSSOMTHelper: Given an axiom generator, maybe wraps it into another generator that would produce the same axiom but annotated with metadata from the mapping from which the axiom is derived.
merge(MappingSet, MappingSet) - Method in class org.incenp.obofoundry.sssom.SetMerger: Merges one set into another, according to the current configuration.
MERGE_CURIE_MAP - Enum constant in enum class org.incenp.obofoundry.sssom.MergeOption: Merge the curie map from the source set into the destination set.
MERGE_EXTENSIONS - Enum constant in enum class org.incenp.obofoundry.sssom.MergeOption: Merge extension slots from the source set into the destination set.
MERGE_LISTS - Enum constant in enum class org.incenp.obofoundry.sssom.MergeOption: Merge the multi-valued slots of the source set into the corresponding slots of the destination set.
MERGE_MAPPINGS - Enum constant in enum class org.incenp.obofoundry.sssom.MergeOption: Add mappings of the source set to the mappings of the destination set.
MERGE_METADATA - Static variable in enum class org.incenp.obofoundry.sssom.MergeOption: Merge all metadata from the source set into the destination set.
MERGE_SCALARS - Enum constant in enum class org.incenp.obofoundry.sssom.MergeOption: Fill the scalar (single-valued) slots of the destination set with the values from the source set (overwriting any existing value).
MergeOption - Enum Class in org.incenp.obofoundry.sssom: Represents various possible behaviours when merging a mapping set into another.
MINIMAL - Enum constant in enum class org.incenp.obofoundry.sssom.ValidationLevel: Only perform the most basic checks, to ensure that individual mappings are valid.
mirrorFrom(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference.MappingSetReferenceBuilder
MISSING_JUSTIFICATION - Enum constant in enum class org.incenp.obofoundry.sssom.ValidationError
MISSING_LICENSE - Enum constant in enum class org.incenp.obofoundry.sssom.ValidationError
MISSING_OBJECT - Enum constant in enum class org.incenp.obofoundry.sssom.ValidationError
MISSING_PREDICATE - Enum constant in enum class org.incenp.obofoundry.sssom.ValidationError
MISSING_RECORD_ID - Enum constant in enum class org.incenp.obofoundry.sssom.ValidationError
MISSING_SET_ID - Enum constant in enum class org.incenp.obofoundry.sssom.ValidationError
MISSING_SUBJECT - Enum constant in enum class org.incenp.obofoundry.sssom.ValidationError
MissingJustificationValidator - Class in org.incenp.obofoundry.sssom.checks: Checks that a mapping has a mapping justification.
MissingJustificationValidator() - Constructor for class org.incenp.obofoundry.sssom.checks.MissingJustificationValidator
MissingLicenseValidator - Class in org.incenp.obofoundry.sssom.checks: Checks that a mapping set has a license.
MissingLicenseValidator() - Constructor for class org.incenp.obofoundry.sssom.checks.MissingLicenseValidator
MissingObjectValidator - Class in org.incenp.obofoundry.sssom.checks: Checks that a mapping has an object.
MissingObjectValidator() - Constructor for class org.incenp.obofoundry.sssom.checks.MissingObjectValidator
MissingPredicateValidator - Class in org.incenp.obofoundry.sssom.checks: Checks that a mapping has a predicate.
MissingPredicateValidator() - Constructor for class org.incenp.obofoundry.sssom.checks.MissingPredicateValidator
MissingRecordIdValidator - Class in org.incenp.obofoundry.sssom.checks: Checks that either all records in a set have a record ID, or none have one.
MissingRecordIdValidator() - Constructor for class org.incenp.obofoundry.sssom.checks.MissingRecordIdValidator
MissingSetIdValidator - Class in org.incenp.obofoundry.sssom.checks: Checks that a mapping set has a set identifier.
MissingSetIdValidator() - Constructor for class org.incenp.obofoundry.sssom.checks.MissingSetIdValidator
MissingSubjectValidator - Class in org.incenp.obofoundry.sssom.checks: Checks that a mapping has a subject.
MissingSubjectValidator() - Constructor for class org.incenp.obofoundry.sssom.checks.MissingSubjectValidator

N

NamedFilter - Class in org.incenp.obofoundry.sssom.transform: A filter that has a string representation.
NamedFilter(String, IMappingFilter) - Constructor for class org.incenp.obofoundry.sssom.transform.NamedFilter: Creates a new instance.
NamedMappingProcessorCallback - Class in org.incenp.obofoundry.sssom.transform: A processor callback that has a string representation.
NamedMappingProcessorCallback(String, IMappingProcessorCallback) - Constructor for class org.incenp.obofoundry.sssom.transform.NamedMappingProcessorCallback: Creates a new instance.
NamedMappingTransformer<T> - Class in org.incenp.obofoundry.sssom.transform: A mapping transformer that has a string representation.
NamedMappingTransformer(String, IMappingTransformer<T>) - Constructor for class org.incenp.obofoundry.sssom.transform.NamedMappingTransformer: Creates a new instance.
needsCardinality() - Method in class org.incenp.obofoundry.sssom.transform.MappingProcessingRule: Indicates whether this rule makes use of cardinality information.
NeverReplace - Enum constant in enum class org.incenp.obofoundry.sssom.PropagationPolicy: If any of the destination objects already has a value for the slot being propagated, do not propagate anything.
NONE - Enum constant in enum class org.incenp.obofoundry.sssom.ExtraMetadataPolicy: No non-standard metadata is ever allowed.
NONE_TO_NONE - Enum constant in enum class org.incenp.obofoundry.sssom.model.MappingCardinality
NONE_TO_ONE - Enum constant in enum class org.incenp.obofoundry.sssom.model.MappingCardinality
NOT - Enum constant in enum class org.incenp.obofoundry.sssom.model.PredicateModifier
NoTermFound - Static variable in class org.incenp.obofoundry.sssom.model.Constants: Special ID value to indicate that a given entity in a source domain is not mapped to any entity in a target domain.

O

objectCategory(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
objectId(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
objectLabel(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
objectMatchField(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
objectMatchField(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
objectPreprocessing(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
objectPreprocessing(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
objectSource(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
objectSource(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
objectSourceVersion(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
objectSourceVersion(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
objectType(EntityType) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
objectType(EntityType) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
onCallback(String, List<String>, Map<String, String>) - Method in interface org.incenp.obofoundry.sssom.transform.ISSSOMTransformApplication: Processes a callback action.
onCallback(String, List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformApplication
onDirectiveAction(String, List<String>, Map<String, String>) - Method in interface org.incenp.obofoundry.sssom.transform.ISSSOMTransformApplication: Processes a directive action.
onDirectiveAction(String, List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformApplication
ONE_TO_MANY - Enum constant in enum class org.incenp.obofoundry.sssom.model.MappingCardinality
ONE_TO_NONE - Enum constant in enum class org.incenp.obofoundry.sssom.model.MappingCardinality
ONE_TO_ONE - Enum constant in enum class org.incenp.obofoundry.sssom.model.MappingCardinality
onFilter(String, List<String>, Map<String, String>) - Method in interface org.incenp.obofoundry.sssom.transform.ISSSOMTransformApplication: Processes an application-specific filter.
onFilter(String, List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformApplication
onGeneratedProduct(MappingProcessingRule<T>, Mapping, T) - Method in class org.incenp.obofoundry.sssom.transform.MappingProcessor: Called when a rule generates an object from a mapping.
onGeneratingAction(String, List<String>, Map<String, String>) - Method in interface org.incenp.obofoundry.sssom.transform.ISSSOMTransformApplication: Processes a generating action.
onGeneratingAction(String, List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformApplication
onInit(PrefixManager) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTOwlApplication
onInit(PrefixManager) - Method in interface org.incenp.obofoundry.sssom.transform.ISSSOMTransformApplication: Initialises the application.
onInit(PrefixManager) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformApplication
ONLY_OBJECT - Enum constant in enum class org.incenp.obofoundry.sssom.owl.OWLHelper.UpdateMode: Only consider the object side of a mapping.
ONLY_SUBJECT - Enum constant in enum class org.incenp.obofoundry.sssom.owl.OWLHelper.UpdateMode: Only consider the subject side of a mapping.
onPreprocessingAction(String, List<String>, Map<String, String>) - Method in interface org.incenp.obofoundry.sssom.transform.ISSSOMTransformApplication: Processes a preprocessing action.
onPreprocessingAction(String, List<String>, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformApplication
org.incenp.obofoundry.sssom - package org.incenp.obofoundry.sssom
org.incenp.obofoundry.sssom.checks - package org.incenp.obofoundry.sssom.checks
org.incenp.obofoundry.sssom.compatibility - package org.incenp.obofoundry.sssom.compatibility
org.incenp.obofoundry.sssom.extract - package org.incenp.obofoundry.sssom.extract
org.incenp.obofoundry.sssom.model - package org.incenp.obofoundry.sssom.model
org.incenp.obofoundry.sssom.owl - package org.incenp.obofoundry.sssom.owl
org.incenp.obofoundry.sssom.rdf - package org.incenp.obofoundry.sssom.rdf
org.incenp.obofoundry.sssom.slots - package org.incenp.obofoundry.sssom.slots
org.incenp.obofoundry.sssom.transform - package org.incenp.obofoundry.sssom.transform
org.incenp.obofoundry.sssom.uriexpr - package org.incenp.obofoundry.sssom.uriexpr
org.incenp.obofoundry.sssom.util - package org.incenp.obofoundry.sssom.util
other(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
other(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
OTHER - Enum constant in enum class org.incenp.obofoundry.sssom.model.ValueType
OWL - Enum constant in enum class org.incenp.obofoundry.sssom.model.BuiltinPrefix
OWL_ANNOTATION_PROPERTY - Enum constant in enum class org.incenp.obofoundry.sssom.model.EntityType
OWL_AXIOM - Static variable in class org.incenp.obofoundry.sssom.rdf.Constants: The IRI used in RDF to represent a Mapping object.
OWL_CLASS - Enum constant in enum class org.incenp.obofoundry.sssom.model.EntityType
OWL_DATA_PROPERTY - Enum constant in enum class org.incenp.obofoundry.sssom.model.EntityType
OWL_EQUIVALENT_CLASS - Enum constant in enum class org.incenp.obofoundry.sssom.model.CommonPredicate
OWL_NAMED_INDIVIDUAL - Enum constant in enum class org.incenp.obofoundry.sssom.model.EntityType
OWL_OBJECT_PROPERTY - Enum constant in enum class org.incenp.obofoundry.sssom.model.EntityType
OWLGenerator - Class in org.incenp.obofoundry.sssom.owl: Generates OWL axioms from mappings.
OWLGenerator() - Constructor for class org.incenp.obofoundry.sssom.owl.OWLGenerator
OWLHelper - Class in org.incenp.obofoundry.sssom.owl: A class of helper methods to work with OWL ontologies.
OWLHelper() - Constructor for class org.incenp.obofoundry.sssom.owl.OWLHelper
OWLHelper.UpdateMode - Enum Class in org.incenp.obofoundry.sssom.owl: Modes of operation for the OWLHelper.updateMappingSet(MappingSet, OWLOntology, String, boolean, EnumSet) method.

P

parse(String) - Method in class org.incenp.obofoundry.sssom.extract.ValueExtractorFactory: Parses an “extractor expression” into a IValueExtractor.
parse(String, PrefixManager) - Static method in class org.incenp.obofoundry.sssom.uriexpr.UriExpression: Parses a string into a URI Expression object.
postMappings(MappingSet) - Method in class org.incenp.obofoundry.sssom.YAMLConverter: Finalise the conversion of a set.
predicateId(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
predicateLabel(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
predicateModifier(PredicateModifier) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
PredicateModifier - Enum Class in org.incenp.obofoundry.sssom.model: A value that modifies the meaning of a mapping predicate.
PredicateModifierSlot<T> - Class in org.incenp.obofoundry.sssom.slots: Represents a metadata slot that holds a predicate modifier enumeration value.
PredicateModifierSlot(Field) - Constructor for class org.incenp.obofoundry.sssom.slots.PredicateModifierSlot: Creates a new instance.
predicateType(EntityType) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
predicateType(EntityType) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
PredicateTypeValidator - Class in org.incenp.obofoundry.sssom.checks: Checks that a mapping has a predicate with a suitable type.
PredicateTypeValidator() - Constructor for class org.incenp.obofoundry.sssom.checks.PredicateTypeValidator
prefixManager - Variable in class org.incenp.obofoundry.sssom.SSSOMWriter
prefixManager - Variable in class org.incenp.obofoundry.sssom.transform.SSSOMTransformReader
PrefixManager - Class in org.incenp.obofoundry.sssom: Helper class to shorten/expand identifiers based on a prefix map.
PrefixManager() - Constructor for class org.incenp.obofoundry.sssom.PrefixManager: Creates a new instance.
preprocess(Mapping) - Method in class org.incenp.obofoundry.sssom.transform.MappingProcessingRule: Applies the preprocessing step to the given mapping.
process(List<Mapping>) - Method in class org.incenp.obofoundry.sssom.transform.MappingProcessor: Applies all the rules to the given mappings.
process(Map<String, Object>) - Method in class org.incenp.obofoundry.sssom.compatibility.JsonLDConverter
process(Map<String, Object>) - Method in class org.incenp.obofoundry.sssom.compatibility.LiteralProfileConverter
process(Map<String, Object>) - Method in class org.incenp.obofoundry.sssom.compatibility.MatchTermTypeConverter
process(Map<String, Object>) - Method in class org.incenp.obofoundry.sssom.compatibility.MatchTypeConverter
process(Map<String, Object>) - Method in class org.incenp.obofoundry.sssom.compatibility.SemanticSimilarityConverter
process(Map<String, Object>) - Method in interface org.incenp.obofoundry.sssom.IYAMLPreprocessor: Apply a treatment to the specified dictionary.
process(IMappingFilter, List<Mapping>) - Method in interface org.incenp.obofoundry.sssom.transform.IMappingProcessorCallback: Applies a custom process to a set of mappings.
process(IMappingFilter, List<Mapping>) - Method in class org.incenp.obofoundry.sssom.transform.NamedMappingProcessorCallback
process(IMappingFilter, List<Mapping>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTInferCardinalityFunction
Propagatable - Annotation Interface in org.incenp.obofoundry.sssom.model: An annotation to indicate that a SSSOM slot is "propagatable".
propagate(MappingSet) - Method in class org.incenp.obofoundry.sssom.slots.SlotPropagator: Propagates the values of slots from the mapping set level to the individual mappings.
propagate(MappingSet, boolean) - Method in class org.incenp.obofoundry.sssom.slots.SlotPropagator: Propagates the values of slots the mapping set level to the individual mappings.
propagationPolicy - Variable in class org.incenp.obofoundry.sssom.SSSOMReader
PropagationPolicy - Enum Class in org.incenp.obofoundry.sssom: The policy that defines how to propagate values between the mapping set level and the level of individual mappings.
property - Variable in class org.incenp.obofoundry.sssom.extract.MappingExtensionExtractor
property - Variable in class org.incenp.obofoundry.sssom.extract.MappingSetExtensionExtractor
publicationDate(LocalDate) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
publicationDate(LocalDate) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
putComponent(String, String) - Method in class org.incenp.obofoundry.sssom.uriexpr.UriExpression: Inserts a new component into this expression.

R

RDF - Enum constant in enum class org.incenp.obofoundry.sssom.model.BuiltinPrefix
RDF_PROPERTY - Enum constant in enum class org.incenp.obofoundry.sssom.model.EntityType
RDF_TURTLE - Enum constant in enum class org.incenp.obofoundry.sssom.util.SerialisationFormat: RDF/Turtle, a RDF representation of SSSOM objects in the Turtle syntax.
RDFConverter - Class in org.incenp.obofoundry.sssom.rdf: A helper class to convert SSSOM objects to and from a RDF model in the Rdf4J API.
RDFConverter() - Constructor for class org.incenp.obofoundry.sssom.rdf.RDFConverter: Creates a new instance with the default policy for converting non-standard metadata.
RDFConverter(ExtraMetadataPolicy) - Constructor for class org.incenp.obofoundry.sssom.rdf.RDFConverter: Creates a new instance with an explicit policy for converting non-standard metadata.
RDFConverter(ExtraMetadataPolicy, Version) - Constructor for class org.incenp.obofoundry.sssom.rdf.RDFConverter: Creates a new instance with an explicit policy for converting non-standard metadata and a default assumed version.
RDFReader - Class in org.incenp.obofoundry.sssom.rdf: A parser to read a SSSOM mapping set from the RDF Turtle serialisation format.
RDFReader(File) - Constructor for class org.incenp.obofoundry.sssom.rdf.RDFReader: Creates a new instance that will read data from the specified file.
RDFReader(InputStream) - Constructor for class org.incenp.obofoundry.sssom.rdf.RDFReader: Creates a new instance that will read data from the specified stream.
RDFReader(Reader) - Constructor for class org.incenp.obofoundry.sssom.rdf.RDFReader: Creates a new instance that will read data from the specified reader.
RDFReader(String) - Constructor for class org.incenp.obofoundry.sssom.rdf.RDFReader: Creates a new instance that will read data from a file with the specified name.
RDFS - Enum constant in enum class org.incenp.obofoundry.sssom.model.BuiltinPrefix
RDFS_CLASS - Enum constant in enum class org.incenp.obofoundry.sssom.model.EntityType
RDFS_DATATYPE - Enum constant in enum class org.incenp.obofoundry.sssom.model.EntityType
RDFS_LITERAL - Enum constant in enum class org.incenp.obofoundry.sssom.model.EntityType
RDFS_RESOURCE - Enum constant in enum class org.incenp.obofoundry.sssom.model.EntityType
RDFWriter - Class in org.incenp.obofoundry.sssom.rdf: A writer to serialise a SSSOM mapping set into the RDF Turtle format.
RDFWriter(File) - Constructor for class org.incenp.obofoundry.sssom.rdf.RDFWriter: Creates a new instance that will write data to the specified file.
RDFWriter(OutputStream) - Constructor for class org.incenp.obofoundry.sssom.rdf.RDFWriter: Creates a new instance that will write data to the specified stream.
RDFWriter(String) - Constructor for class org.incenp.obofoundry.sssom.rdf.RDFWriter: Creates a new instance that will write data to a file with the specified filename.
read() - Method in class org.incenp.obofoundry.sssom.JSONReader
read() - Method in class org.incenp.obofoundry.sssom.rdf.RDFReader
read() - Method in class org.incenp.obofoundry.sssom.SSSOMReader: Reads a mapping set from the source file.
read() - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformReader: Parses the SSSOM/T ruleset from the underlying source.
read() - Method in class org.incenp.obofoundry.sssom.TSVReader: Reads a mapping set from the source file(s).
read(boolean) - Method in class org.incenp.obofoundry.sssom.TSVReader: Reads a mapping set from the source file(s), with the option of reading the metadata only.
read(String) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformReader: Parses the SSSOM/T ruleset from the specified string.
ReaderFactory - Class in org.incenp.obofoundry.sssom.util: A class providing helper methods to obtain SSSOM reader objects.
ReaderFactory() - Constructor for class org.incenp.obofoundry.sssom.util.ReaderFactory: Creates a new instance.
ReaderFactory(boolean) - Constructor for class org.incenp.obofoundry.sssom.util.ReaderFactory: Creates a new instance that may optionally use a filename’s extension to infer the format of the file.
recordId(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
REDEFINED_BUILTIN_PREFIX - Enum constant in enum class org.incenp.obofoundry.sssom.ValidationError
RedefinedBuiltinPrefixValidator - Class in org.incenp.obofoundry.sssom.checks: Checks that the curie map embedded in a mapping set does not redefine any of the prefixes that are considered “builtin” by the SSSOM specification.
RedefinedBuiltinPrefixValidator() - Constructor for class org.incenp.obofoundry.sssom.checks.RedefinedBuiltinPrefixValidator
registerCallback(ISSSOMTFunction<IMappingProcessorCallback>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformApplication: Registers a new SSSOM/T callback function.
registerDirective(ISSSOMTFunction<Void>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformApplication: Registers a new SSSOM/T directive function.
registerFilter(ISSSOMTFunction<IMappingFilter>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformApplication: Registers a new SSSOM/T filter function.
registerGenerator(ISSSOMTFunction<IMappingTransformer<T>>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformApplication: Registers a new SSSOM/T generator function.
registerPreprocessor(ISSSOMTFunction<IMappingTransformer<Mapping>>) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformApplication: Registers a new SSSOM/T preprocessor function.
registerTemplate(String, String, String) - Method in class org.incenp.obofoundry.sssom.uriexpr.UriExpressionRegistry: Registers a new template.
registryConfidence(Double) - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference.MappingSetReferenceBuilder
renderURISlotsAsResources(boolean) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor: Specifies whether URI-typed slots (e.g., sssom:license) should be rendered as IRI-identified resources rather than as xsd:anyURI literals.
ReplaceIfUnset - Enum constant in enum class org.incenp.obofoundry.sssom.PropagationPolicy: Propagate the value from the source object to the destination objects, only for objects that do not already have a value for the slot being propagated.
reviewerId(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
reviewerLabel(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
rules - Variable in class org.incenp.obofoundry.sssom.transform.SSSOMTransformReader

S

seeAlso(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
seeAlso(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
SemanticSimilarityConverter - Class in org.incenp.obofoundry.sssom.compatibility: A YAML preprocessor to convert a dictionary containing a semantic_similarity_score or semantic_similarity_measure metadata slot into its standardised equivalent.
SemanticSimilarityConverter() - Constructor for class org.incenp.obofoundry.sssom.compatibility.SemanticSimilarityConverter
SEMAPV - Enum constant in enum class org.incenp.obofoundry.sssom.model.BuiltinPrefix
SEMAPV_CROSS_SPECIES_BROAD_MATCH - Enum constant in enum class org.incenp.obofoundry.sssom.model.CommonPredicate
SEMAPV_CROSS_SPECIES_EXACT_MATCH - Enum constant in enum class org.incenp.obofoundry.sssom.model.CommonPredicate
SEMAPV_CROSS_SPECIES_NARROW_MATCH - Enum constant in enum class org.incenp.obofoundry.sssom.model.CommonPredicate
SerialisationFormat - Enum Class in org.incenp.obofoundry.sssom.util: Represents a format able to serialise SSSOM data.
setAlphabeticalOrder() - Method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Configures this helper to visit slots in alphabetical order.
setAssumedVersion(Version) - Method in class org.incenp.obofoundry.sssom.SSSOMReader: Sets the version of the SSSOM specification that the reader should assume the set is compliant with, if the set does not have a sssom_version slot.
setAssumedVersion(Version) - Method in class org.incenp.obofoundry.sssom.YAMLConverter: Sets the version of the SSSOM specification that a set should be assumed to be compliant with, in the absence of an explicit sssom_version slot.
setAuthorId(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setAuthorLabel(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setCardinalityScope(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setCardinalityScope(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setCheckObjectExistence(OWLOntology) - Method in class org.incenp.obofoundry.sssom.owl.OWLGenerator: Enables checking for the existence of the mapping object.
setCheckSubjectExistence(OWLOntology) - Method in class org.incenp.obofoundry.sssom.owl.OWLGenerator: Enables checking for the existence of the mapping subject.
setComment(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setComment(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setCondensationEnabled(boolean) - Method in class org.incenp.obofoundry.sssom.SSSOMWriter: Enables or disables the condensation of "propagatable slots".
setConfidence(Double) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Sets the confidence field to a new value.
setCreatorId(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setCreatorId(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setCreatorLabel(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setCreatorLabel(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setCurationRule(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setCurationRule(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setCurationRuleText(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setCurationRuleText(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setCurieMap(Map<String, String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setCurieMap(Map<String, String>) - Method in class org.incenp.obofoundry.sssom.SSSOMWriter: Sets the Curie map to use to shorten identifiers.
setDocumentation(String) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
setExtensionDefinitions(List<ExtensionDefinition>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setExtensions(Map<String, ExtensionValue>) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setExtensions(Map<String, ExtensionValue>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setExtraMetadataPolicy(ExtraMetadataPolicy) - Method in class org.incenp.obofoundry.sssom.SSSOMReader: Sets the policy to deal with non-standard metadata in the input file.
setExtraMetadataPolicy(ExtraMetadataPolicy) - Method in class org.incenp.obofoundry.sssom.SSSOMWriter: Sets the policy to deal with non-standard metadata in the mapping set to write.
setExtraMetadataPolicy(ExtraMetadataPolicy) - Method in class org.incenp.obofoundry.sssom.YAMLConverter: Sets the policy to deal with non-standard metadata in the input file.
setHomepage(String) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
setImports(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
setIssueTracker(String) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
setIssueTracker(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setIssueTrackerItem(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setLastUpdated(LocalDate) - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference
setLicense(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setLicense(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setLocalName(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference
setMappingCardinality(MappingCardinality) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setMappingDate(LocalDate) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setMappingDate(LocalDate) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setMappingJustification(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setMappingProvider(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setMappingProvider(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setMappingRegistryDescription(String) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
setMappingRegistryId(String) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
setMappingRegistryTitle(String) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
setMappings(List<Mapping>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setMappingSetConfidence(Double) - Method in class org.incenp.obofoundry.sssom.model.MappingSet: Sets the mapping_set_confidence field to a new value.
setMappingSetDescription(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setMappingSetGroup(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference
setMappingSetId(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setMappingSetId(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference
setMappingSetReferences(List<MappingSetReference>) - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
setMappingSetSource(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setMappingSetTitle(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setMappingSetVersion(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setMappingSource(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setMappingTool(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setMappingTool(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setMappingToolId(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setMappingToolId(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setMappingToolVersion(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setMappingToolVersion(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setMatchString(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setMergeOptions(EnumSet<MergeOption>) - Method in class org.incenp.obofoundry.sssom.SetMerger: Sets the options to configure the behaviour of this object.
SetMerger - Class in org.incenp.obofoundry.sssom: Helper object to merge one mapping set into another.
SetMerger() - Constructor for class org.incenp.obofoundry.sssom.SetMerger
setMirrorFrom(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference
setModifier(IFormatModifierFunction) - Method in class org.incenp.obofoundry.sssom.transform.MappingFormatter: Registers a modifier function that can be used to alter the value of a substitution.
setObjectCategory(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setObjectId(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setObjectLabel(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setObjectMatchField(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setObjectMatchField(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setObjectPreprocessing(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setObjectPreprocessing(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setObjectSource(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setObjectSource(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setObjectSourceVersion(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setObjectSourceVersion(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setObjectType(EntityType) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setObjectType(EntityType) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setOther(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setOther(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setPredicateId(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setPredicateLabel(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setPredicateModifier(PredicateModifier) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setPredicateType(EntityType) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setPredicateType(EntityType) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setPrefixManager(PrefixManager) - Method in class org.incenp.obofoundry.sssom.transform.MappingFormatter: Sets the prefix manager to use when attempting to resolve a placeholder name into the name of an extension slot.
setPrefixManager(PrefixManager) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTransformReader: Sets the prefix manager to use.
setPrefixMap(Map<String, String>) - Method in class org.incenp.obofoundry.sssom.owl.XrefExtractor: Sets the prefix map to be used when processing cross-reference annotations.
setPropagationEnabled(boolean) - Method in class org.incenp.obofoundry.sssom.SSSOMReader: Enables or disables the propagation of "propagatable slots".
setPublicationDate(LocalDate) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setPublicationDate(LocalDate) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setRecordId(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setRegistryConfidence(Double) - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference: Sets the registry_confidence field to a new value.
setReviewerId(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setReviewerLabel(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setSeeAlso(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setSeeAlso(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setSemanticSimilarityMeasure(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Deprecated.
Use #setSimilarityMeasure(String) instead.
setSemanticSimilarityScore(Double) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Deprecated.
Use #setSimilarityScore(Double) instead.
setSeparatorMode(TSVReader.SeparatorMode) - Method in class org.incenp.obofoundry.sssom.TSVReader: Sets the behaviour of the reader regarding the column separator character.
setShortenIRIs(boolean) - Method in class org.incenp.obofoundry.sssom.JSONWriter: Enables or disables shortening of identifiers.
setSimilarityMeasure(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setSimilarityMeasure(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setSimilarityScore(Double) - Method in class org.incenp.obofoundry.sssom.model.Mapping: Sets the similarity_score field to a new value.
setSlotName(String) - Method in class org.incenp.obofoundry.sssom.model.ExtensionDefinition: Sets the slot name.
setSlots(Collection<String>) - Method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Explicitly sets the list of slots to visit.
setSlots(List<String>, boolean) - Method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Explicitly sets the list of slots to visit.
setSortingEnabled(boolean) - Method in class org.incenp.obofoundry.sssom.SSSOMWriter: Enables or disables sorting the mappings when writing them.
setSssomVersion(Version) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setStandardSubstitutions() - Method in class org.incenp.obofoundry.sssom.transform.MappingFormatter: Defines “standard” substitutions using the name of mapping fields as defined in the SSSOM specification.
setStrategy(PropagationPolicy) - Method in class org.incenp.obofoundry.sssom.slots.SlotPropagator: Sets the propagation policy to use.
setSubjectCategory(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setSubjectId(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setSubjectLabel(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setSubjectMatchField(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setSubjectMatchField(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setSubjectPreprocessing(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setSubjectPreprocessing(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setSubjectSource(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setSubjectSource(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setSubjectSourceVersion(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setSubjectSourceVersion(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setSubjectType(EntityType) - Method in class org.incenp.obofoundry.sssom.model.Mapping
setSubjectType(EntityType) - Method in class org.incenp.obofoundry.sssom.model.MappingSet
setSubstitution(String, IMappingTransformer<Object>) - Method in class org.incenp.obofoundry.sssom.transform.MappingFormatter: Defines a placeholder text to be substituted by a value derived from a mapping.
setTypeHint(String) - Method in class org.incenp.obofoundry.sssom.model.ExtensionDefinition: Sets the type hint.
setValidation(ValidationLevel) - Method in class org.incenp.obofoundry.sssom.SSSOMReader: Controls whether a mapping set should be validated after it has been parsed, and how.
setValidationEnabled(boolean) - Method in class org.incenp.obofoundry.sssom.SSSOMReader: Enables or disables post-parsing validation of mappings.
setValue(T, Object) - Method in class org.incenp.obofoundry.sssom.slots.Slot: Sets the value of the slot for a given object.
setValue(T, String) - Method in class org.incenp.obofoundry.sssom.slots.DateSlot: Parses a string value into a date and assigns it to the slot for the given object.
setValue(T, String) - Method in class org.incenp.obofoundry.sssom.slots.DoubleSlot: Parses a string value into a numerical value and assigns it to the slot for the given object.
setValue(T, String) - Method in class org.incenp.obofoundry.sssom.slots.EntityTypeSlot: Parses a string into an entity type value and assigns it to the slot for the given object.
setValue(T, String) - Method in class org.incenp.obofoundry.sssom.slots.MappingCardinalitySlot: Parses a string into a mapping cardinality value.
setValue(T, String) - Method in class org.incenp.obofoundry.sssom.slots.PredicateModifierSlot: Parses a string into a predicate modifier enumeration value.
setValue(T, String) - Method in class org.incenp.obofoundry.sssom.slots.Slot: Tries setting the value of the slot for a given object, using a string as input.
setValue(T, String) - Method in class org.incenp.obofoundry.sssom.slots.StringSlot
setValue(T, String) - Method in class org.incenp.obofoundry.sssom.slots.VersionSlot: Parses a string value into a SSSOM version and assigns it to the slot for the given object.
setWriteCurieMapInContext(boolean) - Method in class org.incenp.obofoundry.sssom.JSONWriter: Enables writing the curie map in a JSON-LD-like "@context" object.
SExpressionExtractor - Class in org.incenp.obofoundry.sssom.extract: Extracts the canonical S-expression that represents a mapping.
SExpressionExtractor(int) - Constructor for class org.incenp.obofoundry.sssom.extract.SExpressionExtractor: Creates a new instance.
shortenIdentifier(String) - Method in class org.incenp.obofoundry.sssom.PrefixManager: Shortens an identifier according to the prefix map.
shortenIdentifiers(List<String>) - Method in class org.incenp.obofoundry.sssom.PrefixManager: Shortens all identifiers in the given list.
shortenIdentifiers(List<String>, boolean) - Method in class org.incenp.obofoundry.sssom.PrefixManager: Shortens all identifiers in the given list.
similarityMeasure(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
similarityMeasure(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
similarityScore(Double) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
SKOS - Enum constant in enum class org.incenp.obofoundry.sssom.model.BuiltinPrefix
SKOS_BROAD_MATCH - Enum constant in enum class org.incenp.obofoundry.sssom.model.CommonPredicate
SKOS_CONCEPT - Enum constant in enum class org.incenp.obofoundry.sssom.model.EntityType
SKOS_EXACT_MATCH - Enum constant in enum class org.incenp.obofoundry.sssom.model.CommonPredicate
SKOS_NARROW_MATCH - Enum constant in enum class org.incenp.obofoundry.sssom.model.CommonPredicate
slot - Variable in class org.incenp.obofoundry.sssom.extract.SlotExtractor
Slot<T> - Class in org.incenp.obofoundry.sssom.slots: Represents a metadata slot on a SSSOM object.
slotExtractor - Variable in class org.incenp.obofoundry.sssom.extract.MappingSetSlotExtractor
slotExtractor - Variable in class org.incenp.obofoundry.sssom.extract.MappingSlotExtractor
SlotExtractor<T> - Class in org.incenp.obofoundry.sssom.extract: Common logic used by both the MappingSetSlotExtractor and the MappingSlotExtractor classes.
SlotExtractor(Slot<T>) - Constructor for class org.incenp.obofoundry.sssom.extract.SlotExtractor: Creates a new instance.
SlotExtractor(Slot<T>, int) - Constructor for class org.incenp.obofoundry.sssom.extract.SlotExtractor: Creates a new instance.
SlotHelper<T> - Class in org.incenp.obofoundry.sssom.slots: A class to facilitate the manipulation of SSSOM slots.
SlotPropagator - Class in org.incenp.obofoundry.sssom.slots: A helper class to implement the propagation of slots from the mapping set level to the level of individual mappings and the other way round.
SlotPropagator() - Constructor for class org.incenp.obofoundry.sssom.slots.SlotPropagator: Creates a new instance using the default propagation policy (always replace).
SlotPropagator(PropagationPolicy) - Constructor for class org.incenp.obofoundry.sssom.slots.SlotPropagator: Creates a new instance with the specified propagation policy.
SlotURI - Annotation Interface in org.incenp.obofoundry.sssom.model: An annotation to indicate the URI associated with a SSSOM slot.
SlotVisitorBase<T> - Class in org.incenp.obofoundry.sssom.slots: A default implementation of the ISlotVisitor interface that does nothing for every slot type.
SlotVisitorBase() - Constructor for class org.incenp.obofoundry.sssom.slots.SlotVisitorBase
SSSOM - Enum constant in enum class org.incenp.obofoundry.sssom.model.BuiltinPrefix
SSSOM_1_0 - Enum constant in enum class org.incenp.obofoundry.sssom.model.Version: SSSOM specification version 1.0.
SSSOM_1_1 - Enum constant in enum class org.incenp.obofoundry.sssom.model.Version: SSSOM specification version 1.1.
SSSOM_EXT_DEFINITIONS - Static variable in class org.incenp.obofoundry.sssom.rdf.Constants: The IRI of the property that links a “Extension Definition” to the MappingSet it belongs to.
SSSOM_EXT_PROPERTY - Static variable in class org.incenp.obofoundry.sssom.rdf.Constants: The IRI of the property that gives the property associated with an extension slot.
SSSOM_EXT_SLOTNAME - Static variable in class org.incenp.obofoundry.sssom.rdf.Constants: The IRI of the property that gives the name of an extension slot.
SSSOM_EXT_TYPEHINT - Static variable in class org.incenp.obofoundry.sssom.rdf.Constants: The IRI of the property that gives the optional type hint for an extension slot.
SSSOM_MAPPING_SET - Static variable in class org.incenp.obofoundry.sssom.rdf.Constants: The IRI used in RDF to represent a MappingSet object.
SSSOM_MAPPINGS - Static variable in class org.incenp.obofoundry.sssom.rdf.Constants: The IRI of the property that links a Mapping to the MappingSet it belongs to.
SSSOM_VERSION - Static variable in class org.incenp.obofoundry.sssom.rdf.Constants: The IRI of the property that links a SSSOM Version value to a mapping set.
SSSOMFormatException - Exception Class in org.incenp.obofoundry.sssom: This exception is thrown when processing data that do not conform to the SSSOM format specification.
SSSOMFormatException(String) - Constructor for exception class org.incenp.obofoundry.sssom.SSSOMFormatException: Creates a new instance with the specified error message.
SSSOMFormatException(String, Throwable) - Constructor for exception class org.incenp.obofoundry.sssom.SSSOMFormatException: Creates a new instance with the specifier error message and cause.
SSSOMReader - Class in org.incenp.obofoundry.sssom: Base class to read a mapping set from any of the supported serialisation formats.
SSSOMReader() - Constructor for class org.incenp.obofoundry.sssom.SSSOMReader
SSSOMTAnnotateFunction - Class in org.incenp.obofoundry.sssom.owl: Represents the SSSOM/T-OWL generator function "annotate".
SSSOMTAnnotateFunction(SSSOMTOwlApplication) - Constructor for class org.incenp.obofoundry.sssom.owl.SSSOMTAnnotateFunction: Creates a new instance.
SSSOMTAnnotateFunction(SSSOMTOwlApplication, String, String, String, String) - Constructor for class org.incenp.obofoundry.sssom.owl.SSSOMTAnnotateFunction
SSSOMTAnnotateObjectFunction - Class in org.incenp.obofoundry.sssom.owl: Deprecated.
Maintained for backwards compatibility only; use annotate(%{object_id}, ...); instead.
SSSOMTAnnotateObjectFunction(SSSOMTOwlApplication) - Constructor for class org.incenp.obofoundry.sssom.owl.SSSOMTAnnotateObjectFunction: Deprecated.

Creates a new instance.
SSSOMTAnnotateSubjectFunction - Class in org.incenp.obofoundry.sssom.owl: Deprecated.
Maintained for backwards compatibility only; use annotate(%{subject_id}, ...); instead.
SSSOMTAnnotateSubjectFunction(SSSOMTOwlApplication) - Constructor for class org.incenp.obofoundry.sssom.owl.SSSOMTAnnotateSubjectFunction: Deprecated.

Creates a new instance.
SSSOMTAssignFunction - Class in org.incenp.obofoundry.sssom.transform: Represents the SSSOM/T standard preprocessor function "assign".
SSSOMTAssignFunction(SSSOMTransformApplication<T>) - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTAssignFunction: Creates a new instance.
SSSOMTCheckObjectExistenceFunction - Class in org.incenp.obofoundry.sssom.owl: Deprecated.
Maintained for backwards compatibility only. Use !exists(%{object_id}) -> stop(); instead.
SSSOMTCheckObjectExistenceFunction(SSSOMTOwlApplication) - Constructor for class org.incenp.obofoundry.sssom.owl.SSSOMTCheckObjectExistenceFunction: Deprecated.

Creates a new instance.
SSSOMTCheckSubjectExistenceFunction - Class in org.incenp.obofoundry.sssom.owl: Deprecated.
Maintained for backwards compatibility only. Use !exists(%{subject_id}) -> stop(); instead.
SSSOMTCheckSubjectExistenceFunction(SSSOMTOwlApplication) - Constructor for class org.incenp.obofoundry.sssom.owl.SSSOMTCheckSubjectExistenceFunction: Deprecated.

Creates a new instance.
SSSOMTCreateAxiomFunction - Class in org.incenp.obofoundry.sssom.owl: Represents the SSSOM/T-OWL generator function "create_axiom".
SSSOMTCreateAxiomFunction(SSSOMTOwlApplication) - Constructor for class org.incenp.obofoundry.sssom.owl.SSSOMTCreateAxiomFunction: Creates a new instance.
SSSOMTDeclareClassFunction - Class in org.incenp.obofoundry.sssom.owl: Deprecated.
Maintained for backwards compatibility only; use declare(CLASS[,...]) instead.
SSSOMTDeclareClassFunction(SSSOMTOwlApplication) - Constructor for class org.incenp.obofoundry.sssom.owl.SSSOMTDeclareClassFunction: Deprecated.

Creates a new instance.
SSSOMTDeclareFunction - Class in org.incenp.obofoundry.sssom.owl: Represents the SSSOM/T-OWL "declare" function.
SSSOMTDeclareFunction(SSSOMTOwlApplication) - Constructor for class org.incenp.obofoundry.sssom.owl.SSSOMTDeclareFunction: Creates a new instance.
SSSOMTDeclareObjectPropertyFunction - Class in org.incenp.obofoundry.sssom.owl: Deprecated.
Maintained for backwards compatibility only; use declare(PROPERY[,...], /type="object_property") instead.
SSSOMTDeclareObjectPropertyFunction(SSSOMTOwlApplication) - Constructor for class org.incenp.obofoundry.sssom.owl.SSSOMTDeclareObjectPropertyFunction: Deprecated.
SSSOMTDefaultModifierFunction - Class in org.incenp.obofoundry.sssom.transform: Represents the SSSOM/T substitution modifier function "default".
SSSOMTDefaultModifierFunction() - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTDefaultModifierFunction
SSSOMTDirectFunction - Class in org.incenp.obofoundry.sssom.owl: Represents the SSSOM/T-OWL generator function "direct".
SSSOMTDirectFunction(SSSOMTOwlApplication) - Constructor for class org.incenp.obofoundry.sssom.owl.SSSOMTDirectFunction
SSSOMTDuplicateFunction - Class in org.incenp.obofoundry.sssom.transform: Represents the SSSOM/T filter function "is_duplicate".
SSSOMTDuplicateFunction(SSSOMTransformApplication<T>) - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTDuplicateFunction: Creates a new instance.
SSSOMTEditFunction - Class in org.incenp.obofoundry.sssom.transform: Deprecated.
Maintained for backwards compatibility only. The "assign" function (SSSOMTAssignFunction) should be preferred.
SSSOMTEditFunction(SSSOMTransformApplication<T>) - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTEditFunction: Deprecated.

Creates a new instance.
SSSOMTExistsFunction - Class in org.incenp.obofoundry.sssom.owl: Represents the SSSOM/T-OWL filter function "exists".
SSSOMTExistsFunction(SSSOMTOwlApplication) - Constructor for class org.incenp.obofoundry.sssom.owl.SSSOMTExistsFunction: Creates a new instance.
SSSOMTFlattenFunction - Class in org.incenp.obofoundry.sssom.transform: Represents the SSSOM/T modifier function "flatten".
SSSOMTFlattenFunction() - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTFlattenFunction
SSSOMTFormatFunction - Class in org.incenp.obofoundry.sssom.transform: Represents the SSSOM/T modifier function "format".
SSSOMTFormatFunction() - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTFormatFunction
SSSOMTHasExtensionFunction - Class in org.incenp.obofoundry.sssom.transform: Represents the SSSOM/T filter function "has_extension".
SSSOMTHasExtensionFunction() - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTHasExtensionFunction
SSSOMTHelper - Class in org.incenp.obofoundry.sssom.owl: A helper class intended to host some methods used throughout the SSSOM/T-OWL code.
SSSOMTHelper() - Constructor for class org.incenp.obofoundry.sssom.owl.SSSOMTHelper
SSSOMTInferCardinalityFunction - Class in org.incenp.obofoundry.sssom.transform: Represents the SSSOM/T standard callback function “infer_cardinality”.
SSSOMTInferCardinalityFunction() - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTInferCardinalityFunction
SSSOMTInvertFunction - Class in org.incenp.obofoundry.sssom.transform: Represents the SSSOM/T standard preprocessor function "invert".
SSSOMTInvertFunction(SSSOMTransformApplication<T>) - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTInvertFunction
SSSOMTIsAFunction - Class in org.incenp.obofoundry.sssom.owl: Represents the SSSOM/T-OWL filter function "is_a".
SSSOMTIsAFunction(SSSOMTOwlApplication) - Constructor for class org.incenp.obofoundry.sssom.owl.SSSOMTIsAFunction: Creates a new instance.
SSSOMTListItemFunction - Class in org.incenp.obofoundry.sssom.transform: Represents the SSSOM/T modifier function "list_item".
SSSOMTListItemFunction() - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTListItemFunction
SSSOMTOwlApplication - Class in org.incenp.obofoundry.sssom.owl: A specialised application of the SSSOM/Transform language to read mapping processing rules that produce OWL axioms.
SSSOMTOwlApplication(OWLOntology, OWLReasonerFactory) - Constructor for class org.incenp.obofoundry.sssom.owl.SSSOMTOwlApplication: Creates a new instance.
SSSOMTOwlSetvarFunction - Class in org.incenp.obofoundry.sssom.owl: Deprecated.
Maintained for backwards compatibility only.
SSSOMTOwlSetvarFunction(SSSOMTOwlApplication) - Constructor for class org.incenp.obofoundry.sssom.owl.SSSOMTOwlSetvarFunction: Deprecated.

Creates a new instance.
SSSOMTransformApplication<T> - Class in org.incenp.obofoundry.sssom.transform: Represents a SSSOM/Transform application, that is, a specialisation of the SSSOM/Transform language (also called a “SSSOM/Transform dialect”) with its own functions and that produces its own type of mapping-derived objects.
SSSOMTransformApplication() - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTransformApplication
SSSOMTransformError - Exception Class in org.incenp.obofoundry.sssom.transform: A syntax error encountered when parsing a SSSOM/T ruleset.
SSSOMTransformError(int, int, String) - Constructor for exception class org.incenp.obofoundry.sssom.transform.SSSOMTransformError: Creates a new instance with an error message from the ANTLR parser.
SSSOMTransformError(String) - Constructor for exception class org.incenp.obofoundry.sssom.transform.SSSOMTransformError: Creates a new instance for an application-specific error.
SSSOMTransformError(String, Object...) - Constructor for exception class org.incenp.obofoundry.sssom.transform.SSSOMTransformError: Creates a new instance for an application-specific errors.
SSSOMTransformReader<T> - Class in org.incenp.obofoundry.sssom.transform: A parser to read mapping processing rules in the SSSOM Transform language.
SSSOMTransformReader(ISSSOMTransformApplication<T>) - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTransformReader: Creates a new instance without an input source.
SSSOMTransformReader(ISSSOMTransformApplication<T>, File) - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTransformReader: Creates a new instance to read from a file.
SSSOMTransformReader(ISSSOMTransformApplication<T>, InputStream) - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTransformReader: Creates a new instance to read from a stream.
SSSOMTransformReader(ISSSOMTransformApplication<T>, Reader) - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTransformReader: Creates a new instance to read from a reader object.
SSSOMTransformReader(ISSSOMTransformApplication<T>, String) - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTransformReader: Creates a new instance to read from a file.
SSSOMTReplaceFunction - Class in org.incenp.obofoundry.sssom.transform: Represents the SSSOM/T standard preprocessor function "replace".
SSSOMTReplaceFunction(SSSOMTransformApplication<T>) - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTReplaceFunction: Creates a new instance.
SSSOMTSetvarCallbackFunction - Class in org.incenp.obofoundry.sssom.transform: Represents the SSSOM/T standard callback function "set_var".
SSSOMTSetvarCallbackFunction(SSSOMTransformApplication<T>) - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTSetvarCallbackFunction: Creates a new instance.
SSSOMTSetvarFunction - Class in org.incenp.obofoundry.sssom.transform: Represents the SSSOM/T standard directive function "set_var".
SSSOMTSetvarFunction(SSSOMTransformApplication<T>) - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTSetvarFunction: Creates a new instance.
SSSOMTShortFunction - Class in org.incenp.obofoundry.sssom.transform: Represents the SSSOM/T substitution modifier function "short".
SSSOMTShortFunction(PrefixManager) - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTShortFunction: Creates a new instance.
SSSOMTStopFunction - Class in org.incenp.obofoundry.sssom.transform: Represents the SSSOM/T standard preprocessor function "stop".
SSSOMTStopFunction() - Constructor for class org.incenp.obofoundry.sssom.transform.SSSOMTStopFunction
SSSOMTUriExpressionContainsFunction<T> - Class in org.incenp.obofoundry.sssom.uriexpr: Represents the SSSOM/T filter function "uriexpr_contains".
SSSOMTUriExpressionContainsFunction(SSSOMTransformApplication<T>) - Constructor for class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionContainsFunction: Creates a new instance.
SSSOMTUriExpressionDeclareFormatFunction - Class in org.incenp.obofoundry.sssom.uriexpr: Represents the SSSOM/T-OWL directive function "uriexpr_declare_format".
SSSOMTUriExpressionDeclareFormatFunction(SSSOMTOwlApplication) - Constructor for class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionDeclareFormatFunction: Creates a new instance.
SSSOMTUriExpressionExpandFunction - Class in org.incenp.obofoundry.sssom.uriexpr: Represents the SSSOM/T-OWL substitution modifier function "uriexpr_expand".
SSSOMTUriExpressionExpandFunction(SSSOMTOwlApplication) - Constructor for class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionExpandFunction
SSSOMTUriExpressionSlotValueFunction - Class in org.incenp.obofoundry.sssom.uriexpr: Represents the SSSOM/T substitution modifier function "uriexpr_slot_value".
SSSOMTUriExpressionSlotValueFunction(PrefixManager) - Constructor for class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionSlotValueFunction: Creates a new instance.
SSSOMTUriExpressionToExtFunction<T> - Class in org.incenp.obofoundry.sssom.uriexpr: Represents the SSSOM/T preprocessor function "uriexpr_toext".
SSSOMTUriExpressionToExtFunction(SSSOMTransformApplication<T>) - Constructor for class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionToExtFunction: Creates a new instance.
SSSOMUtils - Class in org.incenp.obofoundry.sssom: Helper methods for SSSOM.
SSSOMUtils() - Constructor for class org.incenp.obofoundry.sssom.SSSOMUtils
sssomVersion(Version) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
SSSOMWriter - Class in org.incenp.obofoundry.sssom: Base class to serialise a mapping set.
SSSOMWriter() - Constructor for class org.incenp.obofoundry.sssom.SSSOMWriter
StandardMapMetadataTransformer<T> - Class in org.incenp.obofoundry.sssom.owl: A class to transform mapping metadata slots into into their mapped IRIs according to the SSSOM specification.
StandardMapMetadataTransformer() - Constructor for class org.incenp.obofoundry.sssom.owl.StandardMapMetadataTransformer
STRING - Enum constant in enum class org.incenp.obofoundry.sssom.model.ValueType
StringSlot<T> - Class in org.incenp.obofoundry.sssom.slots: Represents a metadata slot that is backed by a String-typed field.
subjectCategory(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
subjectId(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
subjectLabel(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
subjectMatchField(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
subjectMatchField(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
subjectPreprocessing(List<String>) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
subjectPreprocessing(List<String>) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
subjectSource(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
subjectSource(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
subjectSourceVersion(String) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
subjectSourceVersion(String) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
subjectType(EntityType) - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
subjectType(EntityType) - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder

T

TAB - Enum constant in enum class org.incenp.obofoundry.sssom.TSVReader.SeparatorMode: Columns are expected to be separated by tabs.
toBuilder() - Method in class org.incenp.obofoundry.sssom.model.Mapping
toBuilder() - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
toBuilder() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
toBuilder() - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference
toRDF(MappingSet) - Method in class org.incenp.obofoundry.sssom.rdf.RDFConverter: Converts a MappingSet to a Rdf4J model.
toRDF(MappingSet, boolean) - Method in class org.incenp.obofoundry.sssom.rdf.RDFConverter: Converts a MappingSet to a Rdf4J model, optionally including namespace declarations for the prefixes found in the set’s prefix map.
toRDF(MappingSet, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.rdf.RDFConverter: Converts a MappingSet to a Rdf4J model, including namespace declarations for all prefixes in the specified prefix map.
toRDF(MappingSet, PrefixManager) - Method in class org.incenp.obofoundry.sssom.rdf.RDFConverter: Converts a MappingSet to a Rdf4J model, optional including namespace declarations for all prefixes held in the specified PrefixManager.
toSExpr() - Method in class org.incenp.obofoundry.sssom.model.Mapping: Creates a canonical S-expression representing this mapping.
toString() - Method in enum class org.incenp.obofoundry.sssom.model.CommonPredicate
toString() - Method in enum class org.incenp.obofoundry.sssom.model.EntityType
toString() - Method in class org.incenp.obofoundry.sssom.model.ExtensionValue
toString() - Method in class org.incenp.obofoundry.sssom.model.Mapping.MappingBuilder
toString() - Method in class org.incenp.obofoundry.sssom.model.Mapping
toString() - Method in enum class org.incenp.obofoundry.sssom.model.MappingCardinality
toString() - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry.MappingRegistryBuilder
toString() - Method in class org.incenp.obofoundry.sssom.model.MappingRegistry
toString() - Method in class org.incenp.obofoundry.sssom.model.MappingSet.MappingSetBuilder
toString() - Method in class org.incenp.obofoundry.sssom.model.MappingSet
toString() - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference.MappingSetReferenceBuilder
toString() - Method in class org.incenp.obofoundry.sssom.model.MappingSetReference
toString() - Method in enum class org.incenp.obofoundry.sssom.model.PredicateModifier
toString() - Method in enum class org.incenp.obofoundry.sssom.model.ValueType
toString() - Method in enum class org.incenp.obofoundry.sssom.model.Version
toString() - Method in class org.incenp.obofoundry.sssom.transform.FilterSet
toString() - Method in class org.incenp.obofoundry.sssom.transform.MappingProcessingRule
toString() - Method in class org.incenp.obofoundry.sssom.transform.NamedFilter
toString() - Method in class org.incenp.obofoundry.sssom.transform.NamedMappingProcessorCallback
toString() - Method in class org.incenp.obofoundry.sssom.transform.NamedMappingTransformer
toURI(PrefixManager) - Method in class org.incenp.obofoundry.sssom.uriexpr.UriExpression: Turns this object back to a string representation.
toZBase32(byte[]) - Static method in class org.incenp.obofoundry.sssom.MappingHasher: Encodes a buffer into its Z-Base32 string representation.
transform(Mapping) - Method in class org.incenp.obofoundry.sssom.owl.AnnotatedAxiomGenerator
transform(Mapping) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationAxiomGenerator
transform(Mapping) - Method in class org.incenp.obofoundry.sssom.owl.DirectAxiomGenerator
transform(Mapping) - Method in class org.incenp.obofoundry.sssom.owl.EquivalentAxiomGenerator
transform(Mapping) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTAnnotateFunction
transform(Mapping) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTCheckObjectExistenceFunction: Deprecated.
transform(Mapping) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTCheckSubjectExistenceFunction: Deprecated.
transform(Mapping) - Method in class org.incenp.obofoundry.sssom.owl.SSSOMTCreateAxiomFunction
transform(Mapping) - Method in interface org.incenp.obofoundry.sssom.transform.IMappingTransformer: Transform a mapping into something else.
transform(Mapping) - Method in class org.incenp.obofoundry.sssom.transform.MappingEditor
transform(Mapping) - Method in class org.incenp.obofoundry.sssom.transform.NamedMappingTransformer
transform(Mapping) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTInvertFunction
transform(Mapping) - Method in class org.incenp.obofoundry.sssom.transform.SSSOMTStopFunction
transform(Mapping) - Method in class org.incenp.obofoundry.sssom.uriexpr.SSSOMTUriExpressionToExtFunction
transform(Slot<T>) - Method in class org.incenp.obofoundry.sssom.owl.DirectMetadataTransformer
transform(Slot<T>) - Method in class org.incenp.obofoundry.sssom.owl.StandardMapMetadataTransformer
transform(Slot<T>) - Method in interface org.incenp.obofoundry.sssom.transform.IMetadataTransformer: Transforms a metadata slot into something else.
TSV - Enum constant in enum class org.incenp.obofoundry.sssom.util.SerialisationFormat: SSSOM/TSV, the main format specifically designed to serialise SSSOM mappings.
TSVReader - Class in org.incenp.obofoundry.sssom: A parser to read a SSSOM mapping set from the TSV serialisation format.
TSVReader(File) - Constructor for class org.incenp.obofoundry.sssom.TSVReader: Creates a new instance that will read data from a single file.
TSVReader(File, File) - Constructor for class org.incenp.obofoundry.sssom.TSVReader: Creates a new instance that will read data from the specified files.
TSVReader(InputStream) - Constructor for class org.incenp.obofoundry.sssom.TSVReader: Creates a new instance that will read data from a single stream.
TSVReader(InputStream, InputStream) - Constructor for class org.incenp.obofoundry.sssom.TSVReader: Creates a new instance that will read data from the specified streams.
TSVReader(Reader) - Constructor for class org.incenp.obofoundry.sssom.TSVReader: Creates a new instance that will read data from the specified reader.
TSVReader(Reader, Reader) - Constructor for class org.incenp.obofoundry.sssom.TSVReader: Creates a new instance that will read data from the specified reader.
TSVReader(Reader, Reader, String) - Constructor for class org.incenp.obofoundry.sssom.TSVReader: Creates a new instance that will read data from the specified reader.
TSVReader(String) - Constructor for class org.incenp.obofoundry.sssom.TSVReader: Creates a new instance that will read data from a single file.
TSVReader(String, String) - Constructor for class org.incenp.obofoundry.sssom.TSVReader: Creates a new instance that will read data from the specified files.
TSVReader.SeparatorMode - Enum Class in org.incenp.obofoundry.sssom: Defines what separator character the reader should expect when parsing the TSV section.
TSVWriter - Class in org.incenp.obofoundry.sssom: A writer to serialise a SSSOM mapping set into the TSV format.
TSVWriter(File) - Constructor for class org.incenp.obofoundry.sssom.TSVWriter: Creates a new instance that will write data to the specified file in embedded mode (metadata block and TSV section in the same file).
TSVWriter(File, File) - Constructor for class org.incenp.obofoundry.sssom.TSVWriter: Creates a new instance that will write data to the specified files.
TSVWriter(OutputStream) - Constructor for class org.incenp.obofoundry.sssom.TSVWriter: Creates a new instance that will write data to the specified stream in embedded mode.
TSVWriter(OutputStream, OutputStream) - Constructor for class org.incenp.obofoundry.sssom.TSVWriter: Creates a new instance that will write data to the specified streams.
TSVWriter(String) - Constructor for class org.incenp.obofoundry.sssom.TSVWriter: Creates a new instance that will write data to a file with the specified filename, in embedded mode.
TSVWriter(String, String) - Constructor for class org.incenp.obofoundry.sssom.TSVWriter: Creates a new instance that will write data to files with the specified filenames.

U

UNDEFINED - Enum constant in enum class org.incenp.obofoundry.sssom.ExtraMetadataPolicy: Accepts all non-standard metadata without requiring a definition.
UNDEFINED_EXTENSION_NAMESPACE - Static variable in class org.incenp.obofoundry.sssom.ExtensionSlotManager: The default namespace for auto-generated properties for undefined extensions.
UNKNOWN - Enum constant in enum class org.incenp.obofoundry.sssom.model.Version: Represents an unrecognised version of the specification (possibly, a version more recent than the latest supported by this implementation).
UPDATE_LABEL - Enum constant in enum class org.incenp.obofoundry.sssom.owl.OWLHelper.UpdateMode: Updates the object and subject labels from the labels of the corresponding entities in the ontology.
UPDATE_SOURCE - Enum constant in enum class org.incenp.obofoundry.sssom.owl.OWLHelper.UpdateMode: If the subject (respectively the object) exists in the ontology, sets the subject_source (respectively the object_source) field to the ontology IRI.
updateMappingSet(MappingSet, OWLOntology, String, boolean) - Static method in class org.incenp.obofoundry.sssom.owl.OWLHelper: Updates the subject label, object label, subject source, and object source in the mapping set using informations from the specified ontology.
updateMappingSet(MappingSet, OWLOntology, String, boolean, EnumSet<OWLHelper.UpdateMode>) - Static method in class org.incenp.obofoundry.sssom.owl.OWLHelper: Generic helper method to update a mapping set from a specified ontology.
URI - Enum constant in enum class org.incenp.obofoundry.sssom.model.ValueType
URI - Annotation Interface in org.incenp.obofoundry.sssom.model: An annotation to indicate that a SSSOM slot is a URI.
UriExpression - Class in org.incenp.obofoundry.sssom.uriexpr: Represents a “URI Expression ID”, a way to encode composed entities in a URI.
UriExpression(String) - Constructor for class org.incenp.obofoundry.sssom.uriexpr.UriExpression: Creates a new blank expression in the given schema.
UriExpressionRegistry - Class in org.incenp.obofoundry.sssom.uriexpr: A basic registry of URI Expression schemas.
UriExpressionRegistry() - Constructor for class org.incenp.obofoundry.sssom.uriexpr.UriExpressionRegistry
URISlot<T> - Class in org.incenp.obofoundry.sssom.slots: Represents a metadata slot that is intended to hold a URI (which is internally represented by a string).

V

validate(Mapping) - Method in class org.incenp.obofoundry.sssom.checks.DuplicatedRecordIdValidator
validate(Mapping) - Method in interface org.incenp.obofoundry.sssom.checks.IMappingValidator: Checks a mapping for a possible post-parsing error.
validate(Mapping) - Method in class org.incenp.obofoundry.sssom.checks.MissingJustificationValidator
validate(Mapping) - Method in class org.incenp.obofoundry.sssom.checks.MissingObjectValidator
validate(Mapping) - Method in class org.incenp.obofoundry.sssom.checks.MissingPredicateValidator
validate(Mapping) - Method in class org.incenp.obofoundry.sssom.checks.MissingRecordIdValidator
validate(Mapping) - Method in class org.incenp.obofoundry.sssom.checks.MissingSubjectValidator
validate(Mapping) - Method in class org.incenp.obofoundry.sssom.checks.PredicateTypeValidator
validate(Mapping) - Method in class org.incenp.obofoundry.sssom.Validator: Deprecated.
Use Validator.validate(MappingSet) to validate an entire mapping set instead.
validate(MappingSet) - Method in class org.incenp.obofoundry.sssom.checks.DuplicatedRecordIdValidator
validate(MappingSet) - Method in interface org.incenp.obofoundry.sssom.checks.IMappingSetValidator: Checks a mapping set for a possible post-parsing error.
validate(MappingSet) - Method in class org.incenp.obofoundry.sssom.checks.MissingLicenseValidator
validate(MappingSet) - Method in class org.incenp.obofoundry.sssom.checks.MissingRecordIdValidator
validate(MappingSet) - Method in class org.incenp.obofoundry.sssom.checks.MissingSetIdValidator
validate(MappingSet) - Method in class org.incenp.obofoundry.sssom.checks.RedefinedBuiltinPrefixValidator
validate(MappingSet) - Method in class org.incenp.obofoundry.sssom.SSSOMReader: Validates a mapping set.
validate(MappingSet) - Method in class org.incenp.obofoundry.sssom.Validator: Checks whether the given mapping set, including the mappings it contains, is valid.
validate(MappingSet, boolean) - Method in class org.incenp.obofoundry.sssom.Validator: Checks whether the given mapping set is valid.
ValidationError - Enum Class in org.incenp.obofoundry.sssom: Represents all the post-parsing errors that can make a mapping set invalid.
ValidationLevel - Enum Class in org.incenp.obofoundry.sssom: Represents different levels of strictness when validating a mapping set.
Validator - Class in org.incenp.obofoundry.sssom: Helper class to validate MappingSet and Mapping objects.
Validator() - Constructor for class org.incenp.obofoundry.sssom.Validator: Creates a new instance.
Validator(ValidationLevel) - Constructor for class org.incenp.obofoundry.sssom.Validator: Creates a new instance with the specified validation level.
value() - Element in annotation interface org.incenp.obofoundry.sssom.model.SlotURI
ValueExtractorFactory - Class in org.incenp.obofoundry.sssom.extract: Builds IValueExtractor instances from a string representation.
ValueExtractorFactory() - Constructor for class org.incenp.obofoundry.sssom.extract.ValueExtractorFactory
valueOf(String) - Static method in enum class org.incenp.obofoundry.sssom.ExtraMetadataPolicy: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.incenp.obofoundry.sssom.MergeOption: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.incenp.obofoundry.sssom.model.BuiltinPrefix: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.incenp.obofoundry.sssom.model.CommonPredicate: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.incenp.obofoundry.sssom.model.EntityType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.incenp.obofoundry.sssom.model.MappingCardinality: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.incenp.obofoundry.sssom.model.PredicateModifier: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.incenp.obofoundry.sssom.model.ValueType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.incenp.obofoundry.sssom.model.Version: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.incenp.obofoundry.sssom.owl.OWLHelper.UpdateMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.incenp.obofoundry.sssom.PropagationPolicy: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.incenp.obofoundry.sssom.TSVReader.SeparatorMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.incenp.obofoundry.sssom.util.SerialisationFormat: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.incenp.obofoundry.sssom.ValidationError: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.incenp.obofoundry.sssom.ValidationLevel: Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.incenp.obofoundry.sssom.ExtraMetadataPolicy: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.incenp.obofoundry.sssom.MergeOption: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.incenp.obofoundry.sssom.model.BuiltinPrefix: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.incenp.obofoundry.sssom.model.CommonPredicate: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.incenp.obofoundry.sssom.model.EntityType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.incenp.obofoundry.sssom.model.MappingCardinality: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.incenp.obofoundry.sssom.model.PredicateModifier: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.incenp.obofoundry.sssom.model.ValueType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.incenp.obofoundry.sssom.model.Version: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.incenp.obofoundry.sssom.owl.OWLHelper.UpdateMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.incenp.obofoundry.sssom.PropagationPolicy: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.incenp.obofoundry.sssom.TSVReader.SeparatorMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.incenp.obofoundry.sssom.util.SerialisationFormat: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.incenp.obofoundry.sssom.ValidationError: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.incenp.obofoundry.sssom.ValidationLevel: Returns an array containing the constants of this enum class, in the order they are declared.
ValueType - Enum Class in org.incenp.obofoundry.sssom.model: Represents the type of an extension value.
VariableManager - Class in org.incenp.obofoundry.sssom.transform: A helper class to track variables that can have a different value depending on the mapping that is currently being processed.
VariableManager() - Constructor for class org.incenp.obofoundry.sssom.transform.VariableManager
Version - Enum Class in org.incenp.obofoundry.sssom.model: Represents a version of the SSSOM specification.
Versionable - Annotation Interface in org.incenp.obofoundry.sssom.model: An annotation to provide information about the version of the SSSOM specification a slot is compliant with.
VersionSlot<T> - Class in org.incenp.obofoundry.sssom.slots: Represents a metadata slot that holds a SSSOM version.
visit(CurieMapSlot<MappingSet>, MappingSet, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.SetMerger
visit(CurieMapSlot<T>, T, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor
visit(CurieMapSlot<T>, T, Map<String, String>) - Method in interface org.incenp.obofoundry.sssom.slots.ISlotVisitor: Visits a slot that holds a curie map.
visit(CurieMapSlot<T>, T, Map<String, String>) - Method in class org.incenp.obofoundry.sssom.slots.SlotVisitorBase
visit(DateSlot<T>, T, LocalDate) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor
visit(DateSlot<T>, T, LocalDate) - Method in interface org.incenp.obofoundry.sssom.slots.ISlotVisitor: Visits a date-typed slot.
visit(DateSlot<T>, T, LocalDate) - Method in class org.incenp.obofoundry.sssom.slots.SlotVisitorBase
visit(DoubleSlot<T>, T, Double) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor
visit(DoubleSlot<T>, T, Double) - Method in interface org.incenp.obofoundry.sssom.slots.ISlotVisitor: Visits a double-typed slot.
visit(DoubleSlot<T>, T, Double) - Method in class org.incenp.obofoundry.sssom.slots.SlotVisitorBase
visit(EntityReferenceSlot<T>, T, String) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor
visit(EntityReferenceSlot<T>, T, String) - Method in interface org.incenp.obofoundry.sssom.slots.ISlotVisitor: Visits a slot that holds an entity reference.
visit(EntityReferenceSlot<T>, T, String) - Method in class org.incenp.obofoundry.sssom.slots.SlotVisitorBase
visit(EntityReferenceSlot<T>, T, List<String>) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor
visit(EntityReferenceSlot<T>, T, List<String>) - Method in interface org.incenp.obofoundry.sssom.slots.ISlotVisitor: Visits a multi-valued slot that holds entity references.
visit(EntityReferenceSlot<T>, T, List<String>) - Method in class org.incenp.obofoundry.sssom.slots.SlotVisitorBase
visit(EntityTypeSlot<T>, T, EntityType) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor
visit(EntityTypeSlot<T>, T, EntityType) - Method in interface org.incenp.obofoundry.sssom.slots.ISlotVisitor: Visits a slot that holds an entity type enumeration value.
visit(EntityTypeSlot<T>, T, EntityType) - Method in class org.incenp.obofoundry.sssom.slots.SlotVisitorBase
visit(ExtensionDefinitionSlot<MappingSet>, MappingSet, List<ExtensionDefinition>) - Method in class org.incenp.obofoundry.sssom.SetMerger
visit(ExtensionDefinitionSlot<T>, T, List<ExtensionDefinition>) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor
visit(ExtensionDefinitionSlot<T>, T, List<ExtensionDefinition>) - Method in interface org.incenp.obofoundry.sssom.slots.ISlotVisitor: Visits a slot that holds a list of extension definitions for non-standard metadata.
visit(ExtensionDefinitionSlot<T>, T, List<ExtensionDefinition>) - Method in class org.incenp.obofoundry.sssom.slots.SlotVisitorBase
visit(ExtensionSlot<MappingSet>, MappingSet, Map<String, ExtensionValue>) - Method in class org.incenp.obofoundry.sssom.SetMerger
visit(ExtensionSlot<T>, T, Map<String, ExtensionValue>) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor
visit(ExtensionSlot<T>, T, Map<String, ExtensionValue>) - Method in interface org.incenp.obofoundry.sssom.slots.ISlotVisitor: Visits a slot that holds extension values (non-standard metadata).
visit(ExtensionSlot<T>, T, Map<String, ExtensionValue>) - Method in class org.incenp.obofoundry.sssom.slots.SlotVisitorBase
visit(MappingCardinalitySlot<T>, T, MappingCardinality) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor
visit(MappingCardinalitySlot<T>, T, MappingCardinality) - Method in interface org.incenp.obofoundry.sssom.slots.ISlotVisitor: Visits a slot that holds a mapping cardinality enumeration value.
visit(MappingCardinalitySlot<T>, T, MappingCardinality) - Method in class org.incenp.obofoundry.sssom.slots.SlotVisitorBase
visit(PredicateModifierSlot<T>, T, PredicateModifier) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor
visit(PredicateModifierSlot<T>, T, PredicateModifier) - Method in interface org.incenp.obofoundry.sssom.slots.ISlotVisitor: Visits a slot that holds a predicate modifier enumeration value.
visit(PredicateModifierSlot<T>, T, PredicateModifier) - Method in class org.incenp.obofoundry.sssom.slots.SlotVisitorBase
visit(Slot<Mapping>, Mapping, Object) - Method in class org.incenp.obofoundry.sssom.transform.MappingEditor
visit(Slot<MappingSet>, MappingSet, Object) - Method in class org.incenp.obofoundry.sssom.SetMerger
visit(Slot<T>, T, Object) - Method in class org.incenp.obofoundry.sssom.extract.SlotExtractor
visit(Slot<T>, T, Object) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor
visit(Slot<T>, T, Object) - Method in interface org.incenp.obofoundry.sssom.slots.ISimpleSlotVisitor: Visits a SSSOM slot.
visit(Slot<T>, T, Object) - Method in interface org.incenp.obofoundry.sssom.slots.ISlotVisitor: Visits a generic slot.
visit(Slot<T>, T, Object) - Method in class org.incenp.obofoundry.sssom.slots.SlotVisitorBase
visit(StringSlot<MappingSet>, MappingSet, List<String>) - Method in class org.incenp.obofoundry.sssom.SetMerger
visit(StringSlot<T>, T, String) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor
visit(StringSlot<T>, T, String) - Method in interface org.incenp.obofoundry.sssom.slots.ISlotVisitor: Visits a string-typed slot.
visit(StringSlot<T>, T, String) - Method in class org.incenp.obofoundry.sssom.slots.SlotVisitorBase
visit(StringSlot<T>, T, List<String>) - Method in class org.incenp.obofoundry.sssom.extract.SlotExtractor
visit(StringSlot<T>, T, List<String>) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor
visit(StringSlot<T>, T, List<String>) - Method in interface org.incenp.obofoundry.sssom.slots.ISlotVisitor: Visits a multi-valued string-typed slot.
visit(StringSlot<T>, T, List<String>) - Method in class org.incenp.obofoundry.sssom.slots.SlotVisitorBase
visit(URISlot<T>, T, String) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor
visit(URISlot<T>, T, String) - Method in interface org.incenp.obofoundry.sssom.slots.ISlotVisitor: Visits a URI-typed slot.
visit(URISlot<T>, T, String) - Method in class org.incenp.obofoundry.sssom.slots.SlotVisitorBase
visit(URISlot<T>, T, List<String>) - Method in class org.incenp.obofoundry.sssom.owl.AnnotationVisitor
visit(URISlot<T>, T, List<String>) - Method in interface org.incenp.obofoundry.sssom.slots.ISlotVisitor: Visits a multi-valued URI-typed slot.
visit(URISlot<T>, T, List<String>) - Method in class org.incenp.obofoundry.sssom.slots.SlotVisitorBase
visit(VersionSlot<T>, T, Version) - Method in interface org.incenp.obofoundry.sssom.slots.ISlotVisitor: Visits a slot that holds a SSSOM version value.
visit(VersionSlot<T>, T, Version) - Method in class org.incenp.obofoundry.sssom.slots.SlotVisitorBase
visit(OWLAnnotationProperty) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker
visit(OWLClass) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker
visit(OWLDataProperty) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker
visit(OWLDatatype) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker
visit(OWLNamedIndividual) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker
visit(OWLObjectProperty) - Method in class org.incenp.obofoundry.sssom.owl.EditableEntityChecker
visitSlots(T, ISimpleSlotVisitor<T, V>) - Method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Visits the slots of a given object, with a visitor that does not distinguish between slot types.
visitSlots(T, ISimpleSlotVisitor<T, V>, boolean) - Method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Visits the slots of a given object, with a visitor that does not distinguish between slot types.
visitSlots(T, ISlotVisitor<T>) - Method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Visits the slots of a given object.
visitSlots(T, ISlotVisitor<T>, boolean) - Method in class org.incenp.obofoundry.sssom.slots.SlotHelper: Visits the slots of a given object.

W

write(MappingSet) - Method in class org.incenp.obofoundry.sssom.SSSOMWriter: Serialises a mapping set into the underlying file.

X

XrefExtractor - Class in org.incenp.obofoundry.sssom.owl: Extract mappings from cross-references (oboInOwl:hasDbXref annotations) in a ontology.
XrefExtractor() - Constructor for class org.incenp.obofoundry.sssom.owl.XrefExtractor
XSD - Enum constant in enum class org.incenp.obofoundry.sssom.model.BuiltinPrefix

Y

YAMLConverter - Class in org.incenp.obofoundry.sssom: A helper class to convert generic YAML dictionaries into SSSOM objects.
YAMLConverter() - Constructor for class org.incenp.obofoundry.sssom.YAMLConverter: Creates a new YAML converter.

A B C D E F G H I J L M N O P R S T U V W X Y
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form