Index (robot-core 1.9.0 API)

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

A

ABOX_CONTAINS_NOMINALS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
ABOX_CONTAINS_NOMINALS_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
ABOX_SIZE - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
ABOX_SIZE_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
AD_CLTIME_PER_ATOM - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
add(Object) - Method in class org.obolibrary.robot.Tuple
add(Cell) - Method in class org.obolibrary.robot.export.Row: Add a cell to the row.
add(OWLEntity) - Method in class org.obolibrary.robot.QuotedEntityChecker: Use annotation properties and the short form provider to add mappings for a single entity.
add(OWLEntity, String) - Method in class org.obolibrary.robot.QuotedEntityChecker: Add a specific mapping to the given entity.
add(OWLOntology, OWLEntity) - Method in class org.obolibrary.robot.QuotedEntityChecker: Use annotation properties and the short form provider to add mappings for a single entity.
addAll(Collection) - Method in class org.obolibrary.robot.Tuple
addAll(OWLOntology) - Method in class org.obolibrary.robot.QuotedEntityChecker: Use annotation properties and the short form provider to add mappings for all entities in the given ontology.
addAxiomAnnotation(OWLOntology, OWLAxiom, Set<OWLAnnotation>) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, an axiom, and a set of annotations, annotate the axiom with the annotations in the ontology.
addAxiomAnnotation(OWLOntology, OWLAxiom, IRI, OWLAnnotationValue) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, an axiom, a property IRI, and a value string, add an annotation to this ontology with that property and value.
addAxiomAnnotations(OWLOntology, IRI, OWLAnnotationValue) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, an annotation property IRI, and an annotation value, annotate all axioms in the ontology with that property and value.
addAxioms(OWLClass, OWLReasoner, OWLDataFactory, Set<OWLSubClassOfAxiom>) - Method in class org.obolibrary.robot.reason.InferredSubClassAxiomGeneratorIncludingIndirect
addAxioms(OWLNamedIndividual, OWLReasoner, OWLDataFactory, Set<OWLClassAssertionAxiom>) - Method in class org.obolibrary.robot.reason.InferredClassAssertionAxiomGeneratorDirectOnly
addAxioms(OWLObjectProperty, OWLReasoner, OWLDataFactory, Set<OWLObjectPropertyDomainAxiom>, Set<OWLObjectPropertyExpression>) - Method in class org.obolibrary.robot.reason.InferredObjectPropertyDomainAxiomGenerator
addAxioms(OWLObjectProperty, OWLReasoner, OWLDataFactory, Set<OWLObjectPropertyRangeAxiom>, Set<OWLObjectPropertyExpression>) - Method in class org.obolibrary.robot.reason.InferredObjectPropertyRangeAxiomGenerator
addAxioms(OWLObjectProperty, OWLReasoner, OWLDataFactory, Set<OWLSubObjectPropertyOfAxiom>, Set<OWLObjectPropertyExpression>) - Method in class org.obolibrary.robot.reason.InferredSubObjectPropertyAxiomGeneratorIncludingIndirect
addBaseNamespace(String) - Method in class org.obolibrary.robot.IOHelper: Add a base namespace to the IOHelper.
addBaseNamespaces(String) - Method in class org.obolibrary.robot.IOHelper: Add a set of base namespaces to the IOHelper from file.
addColumn(Column) - Method in class org.obolibrary.robot.export.Table: Add a Column to the Table.
addLabels(Map<IRI, String>, String) - Static method in class org.obolibrary.robot.DiffOperation: Deprecated.
This functionality is now provided by the owl-diff library and no longer used to format results in DiffOperation.
addLabels(IOHelper, Map<IRI, String>, String) - Static method in class org.obolibrary.robot.DiffOperation: Deprecated.
This functionality is now provided by the owl-diff library and no longer used to format results in DiffOperation.
addOntologyAnnotation(OWLOntology, IRI, OWLAnnotationValue) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, a property IRI, and a value string, add an annotation to this ontology with that property and value.
addOntologyAnnotation(OWLOntology, OWLAnnotation) - Static method in class org.obolibrary.robot.OntologyHelper: Annotate the ontology with the annotation.
addPrefix(String) - Method in class org.obolibrary.robot.IOHelper: Add a prefix mapping as a single string "foo: http://example.com#".
addPrefix(String, String) - Method in class org.obolibrary.robot.IOHelper: Add a prefix mapping to the current JSON-LD context, as a prefix string and target string.
addPrefixes(Context) - Method in class org.obolibrary.robot.IOHelper: Given a Context, add the prefix mappings to the current JSON-LD context.
addPrefixes(String) - Method in class org.obolibrary.robot.IOHelper: Given a path to a JSON-LD prefix file, add the prefix mappings in the file to the current JSON-LD context.
addPrefixesAndSave(OWLOntology, File, List<String>) - Method in class org.obolibrary.robot.IOHelper: Deprecated.
replaced by IOHelper.saveOntology(OWLOntology, OWLDocumentFormat, IRI, Map, boolean)
addProperty(OWLAnnotationProperty) - Method in class org.obolibrary.robot.QuotedEntityChecker: Add an annotation property for finding names.
addProvider(ShortFormProvider) - Method in class org.obolibrary.robot.QuotedEntityChecker: Add a short form providers for finding names.
addReportQuery(ReportQuery) - Method in class org.obolibrary.robot.checks.Report: Add a ReportQuery to this Report.
addRow(Row) - Method in class org.obolibrary.robot.export.Table: Add a Row to the Table.
addStatement(String, String) - Method in class org.obolibrary.robot.checks.Violation: Deprecated.
String properties are no longer recommended; create an OWLEntity for the property instead
addStatement(OWLEntity, String) - Method in class org.obolibrary.robot.checks.Violation: Add a literal statement to the Violation about the subject.
addStatement(OWLEntity, OWLEntity) - Method in class org.obolibrary.robot.checks.Violation: Add a statement with an OWLEntity value to the Violation about the subject.
addStatement(OWLEntity, OWLObject) - Method in class org.obolibrary.robot.checks.Violation: Deprecated.
OWLObjects are no longer supported; use OWLEntity or String literal instead
addToWorkbook(Workbook, List<Column>, String) - Method in class org.obolibrary.robot.export.Row: Add this Row to a Workbook.
addViolations(String, String, List<Violation>) - Method in class org.obolibrary.robot.checks.Report: Deprecated.
violations should be added to their appropriate ReportQuery object
addViolations(List<Violation>) - Method in class org.obolibrary.robot.checks.ReportQuery: Add multiple violations to this ReportQuery.
ALL - org.obolibrary.robot.reason.EquivalentClassReasoningMode: Allows all equivalent classes in the reason step.
ANCESTORS - org.obolibrary.robot.RelationType
ANNOTATION_PROP_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
ANNOTATION_PROP_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
ANNOTATION_PROPERTIES - org.obolibrary.robot.RelationType
ASSERTED_ONLY - org.obolibrary.robot.reason.EquivalentClassReasoningMode: Only allows directly asserted equivalent classes.
asWorkbook(String) - Method in class org.obolibrary.robot.export.Table: Render the Table as a Workbook.
AVG_ASSERT_N_SUBCLASS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
AVG_ASSERT_N_SUBCLASS_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
AVG_ASSERT_N_SUPERCLASS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
AVG_ASSERT_N_SUPERCLASS_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
AVG_INSTANCE_PER_CLASS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
AVG_INSTANCE_PER_CLASS_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
AVG_SIZE_COMPLEXRHS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
AVG_SIZE_COMPLEXRHS_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
AXIOM_COMPLEXRHS_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
AXIOM_COMPLEXRHS_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
AXIOM_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
AXIOM_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
AXIOM_TYPES - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
AXIOM_TYPES_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
AXIOMTYPE_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
AXIOMTYPE_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels

B

BOOL_PROFILE_OWL2 - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
BOOL_PROFILE_OWL2_DL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
BOOL_PROFILE_OWL2_EL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
BOOL_PROFILE_OWL2_QL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
BOOL_PROFILE_OWL2_RL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
BOOL_PROFILE_RDFS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels

C

CannotReadQuery - Exception in org.obolibrary.robot.exceptions: Created by edouglass on 8/9/17.
CannotReadQuery(String, Exception) - Constructor for exception org.obolibrary.robot.exceptions.CannotReadQuery
CatalogElementHandler - Class in org.obolibrary.robot: A SAX DefaultHandler for reading OWL Catalog files.
CatalogElementHandler(File, Map<IRI, IRI>) - Constructor for class org.obolibrary.robot.CatalogElementHandler: Initialize the element handler with required context.
CatalogXmlIRIMapper - Class in org.obolibrary.robot: OWLOntologyIRIMapper using the mappings from a catalog.xml file.
CatalogXmlIRIMapper(File) - Constructor for class org.obolibrary.robot.CatalogXmlIRIMapper: Given a catalog File, create a CatalogXmlIRIMapper that interprets any relative paths as relative to the catalog file location.
CatalogXmlIRIMapper(File, File) - Constructor for class org.obolibrary.robot.CatalogXmlIRIMapper: Given a catalog File and a parent folder, create a CatalogXmlIRIMapper that interprets any relative paths as relative to the parent folder.
CatalogXmlIRIMapper(String) - Constructor for class org.obolibrary.robot.CatalogXmlIRIMapper: Given a String path to a catalog file, create a CatalogXmlIRIMapper that interprets any relative paths as relative to the catalog file location.
CatalogXmlIRIMapper(URL) - Constructor for class org.obolibrary.robot.CatalogXmlIRIMapper: Given an URL, create a CatalogXmlIRIMapper that interprets any relative paths as relative to the catalog file location.
CatalogXmlIRIMapper(URL, File) - Constructor for class org.obolibrary.robot.CatalogXmlIRIMapper: Given an URL and a parent folder, create a CatalogXmlIRIMapper that interprets any relative paths as relative to the parent folder.
CatalogXmlIRIMapper(IRI) - Constructor for class org.obolibrary.robot.CatalogXmlIRIMapper: Given an IRI, create a CatalogXmlIRIMapper that interprets any relative paths as relative to the catalog file location.
Cell - Class in org.obolibrary.robot.export
Cell(Column, String) - Constructor for class org.obolibrary.robot.export.Cell: Init a Cell for a Column with single value in cell with no sort value.
Cell(Column, String, String) - Constructor for class org.obolibrary.robot.export.Cell: Init a Cell for a Column with single value in cell.
Cell(Column, List<String>) - Constructor for class org.obolibrary.robot.export.Cell: Init a new Cell for a Column with multiple display values and no sort values.
Cell(Column, List<String>, List<String>) - Constructor for class org.obolibrary.robot.export.Cell: Init a new Cell for a Column with mulitple values in a cell.
cellToA1(int, int) - Static method in class org.obolibrary.robot.IOHelper: Convert a row index and column index for a cell to A1 notation.
cellValue - Variable in exception org.obolibrary.robot.exceptions.RowParseException
checkImportModule(OWLOntology, OWLOntology) - Static method in class org.obolibrary.robot.checks.InvalidReferenceChecker: Checks an import module.
CHILDREN - org.obolibrary.robot.RelationType
CLASS_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
CLASS_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
CLASS_SGL_SUBCLASS_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
CLASS_SGL_SUBCLASS_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
CLASSES - org.obolibrary.robot.RelationType
CLASSEXPRESSION_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
CLASSEXPRESSION_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
CLASSIFICATION_CORRECT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
CLASSIFICATION_TS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
cleanTDB(String) - Static method in class org.obolibrary.robot.IOHelper: Given a directory containing TDB mappings, remove the files and directory.
clear() - Method in class org.obolibrary.robot.Tuple
COHERENT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
collapseOntology(OWLOntology, int, Set<IRI>, boolean) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, a threshold, and a set of precious IRIs (or empty set), minimize the input ontology's class hierarchy based on the threshold.
collapseOntology(OWLOntology, Set<IRI>) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology and a set of IRIs that must be retained, remove intermediate superclasses (classes that only have one child) and update the subclass relationships to preserve structure.
colNum - Variable in exception org.obolibrary.robot.exceptions.RowParseException
Column - Class in org.obolibrary.robot.export
Column(String) - Constructor for class org.obolibrary.robot.export.Column: Init a new column with a name.
Column(String, String) - Constructor for class org.obolibrary.robot.export.Column: Init a new column with a name and a display name.
Column(String, String, IRI, ShortFormProvider, String) - Constructor for class org.obolibrary.robot.export.Column: Init a new Column using an IRI.
Column(String, String, OWLAnnotationProperty, ShortFormProvider) - Constructor for class org.obolibrary.robot.export.Column: Init a new Column using an annotation property.
Column(String, String, OWLDataProperty, ShortFormProvider, String) - Constructor for class org.obolibrary.robot.export.Column: Init a new Column using a data property.
Column(String, String, OWLObjectProperty, ShortFormProvider, String) - Constructor for class org.obolibrary.robot.export.Column: Init a new column using an object property.
Column(String, Map<String, List<String>>, String, ShortFormProvider) - Constructor for class org.obolibrary.robot.export.Column: Init a new column using one or more rules for validate.
Column(String, ShortFormProvider) - Constructor for class org.obolibrary.robot.export.Column: Init a new column with a name and a provider.
ColumnException - Exception in org.obolibrary.robot.exceptions: Template column cannot be parsed.
ColumnException(String) - Constructor for exception org.obolibrary.robot.exceptions.ColumnException: Throw new ColumnException with message.
ColumnException(String, Exception) - Constructor for exception org.obolibrary.robot.exceptions.ColumnException: Throw new ColumnException with message and exception cause.
COMP_OVERHEAD - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
compare(OWLOntology, OWLOntology, Writer) - Static method in class org.obolibrary.robot.DiffOperation: Given two ontologies and a Writer, get their differences and write then to the writer.
compare(OWLOntology, OWLOntology, IOHelper, Writer, Map<String, String>) - Static method in class org.obolibrary.robot.DiffOperation: Given two ontologies, a Writer, and a set of diff options, get their differences and write then to the writer.
CONSISTENCYCHECK_TS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
CONSISTENT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
CONSTRUCTS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
CONSTRUCTS_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
contains(Object) - Method in class org.obolibrary.robot.Tuple
containsAll(Collection) - Method in class org.obolibrary.robot.Tuple
containsCycle(OWLOntology, Imports) - Static method in class org.obolibrary.robot.metrics.OntologyCycleDetector
convertModel(Model) - Static method in class org.obolibrary.robot.QueryOperation: Deprecated.
Use QueryOperation.convertModel(Model, IOHelper, String)
convertModel(Model, IOHelper, String) - Static method in class org.obolibrary.robot.QueryOperation: Given a Model, an IOHelper, and a path to an XML catalog, convert the model to an OWLOntology object.
convertModel(Model, IOHelper, String, boolean) - Static method in class org.obolibrary.robot.QueryOperation: Given a Model, an IOHelper, and a path to an XML catalog, convert the model to an OWLOntology object.
copy(OWLOntology, OWLOntology, OWLEntity, Set<OWLAnnotationProperty>) - Static method in class org.obolibrary.robot.OntologyHelper: Given input and output ontologies, a target entity, and a set of annotation properties, copy the target entity from the input ontology to the output ontology, along with the specified annotations.
copyAnnotations(OWLOntology, OWLOntology, OWLEntity, Set<OWLAnnotationProperty>) - Static method in class org.obolibrary.robot.OntologyHelper: Given an input ontology, an output ontology, an entity to copy annotations of, and the annotation properties to copy (or null for all), copy annotations of the entity from the input to the output ontology.
countResults(ResultSet) - Static method in class org.obolibrary.robot.QueryOperation: Count results.
create(OWLAxiom, OWLEntity, InvalidReferenceViolation.Category) - Static method in class org.obolibrary.robot.checks.InvalidReferenceViolation
createEmptyDataset() - Static method in class org.obolibrary.robot.QueryOperation
createExportTable(OWLOntology, IOHelper, List<String>, Map<String, String>) - Static method in class org.obolibrary.robot.ExportOperation: Given an ontology, an ioHelper, a list of columns, an output export file, and a map of options, export details about the entities in the ontology to the export file.
createIncoherentModule(OWLReasoner, IRI) - Static method in class org.obolibrary.robot.ReasonerHelper
createIRI(String) - Method in class org.obolibrary.robot.IOHelper: Given a term string, use the current prefixes to create an IRI.
createIRI(String, boolean) - Method in class org.obolibrary.robot.IOHelper: Deprecated.
replaced by IOHelper.createIRI(String)
createIRIs(Set<String>) - Method in class org.obolibrary.robot.IOHelper: Given a set of term identifier strings, return a set of IRIs.
createLiteral(String) - Static method in class org.obolibrary.robot.IOHelper: Create an OWLLiteral.
CREATEREASONER_TS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
createTaggedLiteral(String, String) - Static method in class org.obolibrary.robot.IOHelper: Create an OWLLiteral with a language tag.
createTypedLiteral(String, String) - Method in class org.obolibrary.robot.IOHelper: Create a typed OWLLiteral.
createTypedLiteral(String, IRI) - Method in class org.obolibrary.robot.IOHelper: Create a typed OWLLiteral.
CURIE_MAP - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
CURIEShortFormProvider - Class in org.obolibrary.robot.providers: ShortFormProvider to return CURIEs.
CURIEShortFormProvider(Map<String, String>) - Constructor for class org.obolibrary.robot.providers.CURIEShortFormProvider: Init a new CURIEShortFormProvider
CYCLE - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
CYCLE_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels

D

DANGLING - org.obolibrary.robot.checks.InvalidReferenceViolation.Category
DATA_PROPERTIES - org.obolibrary.robot.RelationType
DATAPROPERTY_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
DATAPROPERTY_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
DATATYPE_AXIOMCOUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
DATATYPE_AXIOMCOUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
DATATYPE_BUILTIN_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
DATATYPE_BUILTIN_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
DATATYPE_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
DATATYPE_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
DATATYPE_NOTBUILTIN_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
DATATYPE_NOTBUILTIN_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
DATATYPES - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
DATATYPES_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
DATATYPES_NOT_BUILT_IN - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
DATATYPES_NOT_BUILT_IN_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
DELEGATE_REASONER_CT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
DEPRECATED - org.obolibrary.robot.checks.InvalidReferenceViolation.Category
DESCENDANTS - org.obolibrary.robot.RelationType
DiffOperation - Class in org.obolibrary.robot: Get the differences between two ontology files.
DiffOperation() - Constructor for class org.obolibrary.robot.DiffOperation
dispose() - Method in class org.obolibrary.robot.providers.CURIEShortFormProvider: Dispose of the ShortFormProvider
dispose() - Method in class org.obolibrary.robot.providers.EmptyShortFormProvider: Dispose of the provider.
dispose() - Method in class org.obolibrary.robot.providers.IRIValueShortFormProvider: Dispose of the short form provider.
DISPOSE_TS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels

E

EL_DELEGATE_REASONER_CT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
emptyIRIProvider - Static variable in class org.obolibrary.robot.ExportOperation
EmptyIRIShortFormProvider - Class in org.obolibrary.robot.providers: Implementation of IRIShortFormProvider that always returns an empty string.
EmptyIRIShortFormProvider() - Constructor for class org.obolibrary.robot.providers.EmptyIRIShortFormProvider
emptyProvider - Static variable in class org.obolibrary.robot.ExportOperation
EmptyShortFormProvider - Class in org.obolibrary.robot.providers: Implementation of ShortFormProvider that always returns an empty string.
EmptyShortFormProvider() - Constructor for class org.obolibrary.robot.providers.EmptyShortFormProvider
entity - Variable in class org.obolibrary.robot.checks.Violation
entityStatements - Variable in class org.obolibrary.robot.checks.Violation
equals(Object) - Method in class org.obolibrary.robot.Tuple
equals(OWLOntology, OWLOntology) - Static method in class org.obolibrary.robot.DiffOperation: Given two ontologies, compare their sets of axioms, annotations, imports, and ontology IDs, returning true if they are identical and false otherwise.
EquivalentAxiomReasoningTest - Interface in org.obolibrary.robot.reason: Created by edouglass on 5/9/17.
EquivalentClassReasoning - Class in org.obolibrary.robot.reason: Created by edouglass on 5/9/17.
EquivalentClassReasoning(OWLOntology, OWLReasoner, EquivalentClassReasoningMode) - Constructor for class org.obolibrary.robot.reason.EquivalentClassReasoning: Creates a new instance that will reason over the given ontology with the strategy specified by the EquivalentClassReasoningMode.
EquivalentClassReasoningMode - Enum in org.obolibrary.robot.reason: Created by edouglass on 5/5/17.
EQUIVALENTS - org.obolibrary.robot.RelationType
error - Variable in class org.obolibrary.robot.checks.Report: Deprecated.
ERROR_MESSAGE_REASONING - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
errorCountByRule - Variable in class org.obolibrary.robot.checks.Report: Map of rule name to number of violations for ERROR level.
escape(String) - Static method in class org.obolibrary.robot.QuotedEntityChecker: Escape single quotations marks inside a string.
execConstruct(Dataset, String) - Static method in class org.obolibrary.robot.QueryOperation: Execute a SPARQL CONSTRUCT query on a dataset and return a model.
execConstruct(DatasetGraph, String) - Static method in class org.obolibrary.robot.QueryOperation: Deprecated.
use QueryOperation.execConstruct(Dataset, String) instead.
execQuery(Dataset, String) - Static method in class org.obolibrary.robot.QueryOperation: Execute a SPARQL SELECT query on a dataset and return a result set.
execQuery(DatasetGraph, String) - Static method in class org.obolibrary.robot.QueryOperation: Deprecated.
use QueryOperation.execQuery(Dataset, String) instead.
execUpdate(Model, String) - Static method in class org.obolibrary.robot.QueryOperation: Given a Model and a SPARQL update (as string), update the model.
execVerify(Map<File, Tuple<ResultSetRewindable, OutputStream>>) - Static method in class org.obolibrary.robot.QueryOperation: Deprecated.
previously used as test method.
execVerify(Dataset, String, String) - Static method in class org.obolibrary.robot.QueryOperation: Given a dataset to query, a rule name, and the query string, execute the query over the dataset.
execVerify(DatasetGraph, String, String) - Static method in class org.obolibrary.robot.QueryOperation: Deprecated.
use QueryOperation.execVerify(Dataset, String, String) instead
expand(OWLOntology, ExpandOperation.ExpandConfig, Set<IRI>, Set<IRI>) - Static method in class org.obolibrary.robot.ExpandOperation: Expand macro relations using SPARQL CONSTRUCT
ExpandConfig() - Constructor for class org.obolibrary.robot.ExpandOperation.ExpandConfig
ExpandOperation - Class in org.obolibrary.robot: Expand ontology macro relations.
ExpandOperation() - Constructor for class org.obolibrary.robot.ExpandOperation
ExpandOperation.ExpandConfig - Class in org.obolibrary.robot
EXPERIMENT_DATE - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
EXPERIMENT_ID - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
EXPERIMENT_VERSION - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
explain(OWLAxiom, OWLOntology, OWLReasonerFactory, int) - Static method in class org.obolibrary.robot.ExplainOperation: Compute explanations for an entailed axiom.
explainInconsistent(OWLOntology, OWLReasonerFactory, int) - Static method in class org.obolibrary.robot.ExplainOperation: Compute explanations for inconsistent ontology
explainMostGeneralUnsatisfiableClasses(OWLOntology, OWLReasoner, OWLReasonerFactory, int) - Static method in class org.obolibrary.robot.ExplainOperation: Compute explanations for all most general unsatisfiable classes Note that this is a very naive implementation which assumes and acyclic class hierarchy.
ExplainOperation - Class in org.obolibrary.robot: Compute an explanation for an entailed axiom.
ExplainOperation() - Constructor for class org.obolibrary.robot.ExplainOperation
explainRootUnsatisfiableClasses(OWLOntology, OWLReasoner, OWLReasonerFactory, int) - Static method in class org.obolibrary.robot.ExplainOperation: Compute explanations for all root unsatisfiable classes See https://github.com/matthewhorridge/owlexplanation/blob/439c5ca67835f5e421adde725e4e8a3bcd760ac8/src/main/java/org/semanticweb/owl/explanation/impl/rootderived/StructuralRootDerivedReasoner.java#L122
explainUnsatisfiableClasses(OWLOntology, OWLReasoner, OWLReasonerFactory, int) - Static method in class org.obolibrary.robot.ExplainOperation: Compute explanations for all unsatisfiable classes
explainUnsatisfiableClasses(OWLOntology, OWLReasoner, OWLReasonerFactory, int, int) - Static method in class org.obolibrary.robot.ExplainOperation: Compute explanations for all unsatisfiable classes
EXPORT_EXCEPTION - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
ExportOperation - Class in org.obolibrary.robot
ExportOperation() - Constructor for class org.obolibrary.robot.ExportOperation
EXPRESSIVITY - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
EXPRESSIVITY_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
extendsAxiomTypes(Class<? extends OWLAxiom>, Set<Class<? extends OWLAxiom>>) - Static method in class org.obolibrary.robot.OntologyHelper: Given an OWLAxiom class and a set of OWLAxiom classes, determine if the axiom class provided extends at least one of the classes in the set.
extendsAxiomTypes(OWLAxiom, Set<Class<? extends OWLAxiom>>) - Static method in class org.obolibrary.robot.OntologyHelper: Given an OWLAxiom and a set of OWLAxiom class, determine if the axiom's class is an extension of at least one of the given set.
extract(OWLOntology, Set<IRI>, IRI, ModuleType) - Static method in class org.obolibrary.robot.ExtractOperation: Extract a set of terms from an ontology using the OWLAPI's SyntacticLocalityModuleExtractor (SLME) with default options.
extract(OWLOntology, Set<IRI>, IRI, ModuleType, Map<String, String>) - Static method in class org.obolibrary.robot.ExtractOperation
extract(OWLOntology, Set<IRI>, IRI, ModuleType, Map<String, String>, Map<IRI, IRI>) - Static method in class org.obolibrary.robot.ExtractOperation: Extract a set of terms from an ontology using the OWLAPI's SyntacticLocalityModuleExtractor (SLME).
ExtractOperation - Class in org.obolibrary.robot: Extract a set of OWLEntities from the input ontology to an output ontology.
ExtractOperation() - Constructor for class org.obolibrary.robot.ExtractOperation
extractTerms(String) - Method in class org.obolibrary.robot.IOHelper: Extract a set of term identifiers from an input string by removing comments, trimming lines, and removing empty lines.

F

fails(OWLAxiom) - Method in interface org.obolibrary.robot.reason.EquivalentAxiomReasoningTest: Returns true if the given axiom fails the type of Test this Reasoning Test is.
FILENAME - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
FILEPATH - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
FILESIZE - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
filter(OWLOntology, Set<OWLObjectProperty>) - Static method in class org.obolibrary.robot.FilterOperation: Remove axioms from the input ontology.
filterAxioms(Set<OWLAxiom>, Set<OWLObject>, List<String>, List<String>, boolean, boolean) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Filter a set of OWLAxioms based on the provided arguments.
filterAxiomsByAxiomType(Set<OWLAxiom>, Set<OWLObject>, Set<Class<? extends OWLAxiom>>, boolean, boolean) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given a set of OWLAxioms, a set of OWLObjects, a set of OWLAxiom Classes, a partial boolean, and a named-only boolean, return a set of OWLAxioms based on OWLAxiom type.
filterCompleteAxioms(Set<OWLAxiom>, Set<OWLObject>, Set<Class<? extends OWLAxiom>>, boolean) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given a st of axioms, a set of objects, and a set of axiom types, return a set of axioms where all the objects in those axioms are in the set of objects.
filterExistingTerms(OWLOntology, Set<IRI>, boolean) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology and a set of IRIs, filter the set of IRIs to only include those that exist in the ontology.
filterExistingTerms(OWLOntology, Set<IRI>, boolean, Imports) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology and a set of IRIs, filter the set of IRIs to only include those that exist in the ontology.
filterExternalAxioms(Set<OWLAxiom>, List<String>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given a list of base namespaces and a set of axioms, return only the axioms that DO NOT have a subject in the base namespaces.
filterInternalAxioms(Set<OWLAxiom>, List<String>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given a list of base namespaces and a set of axioms, return only the axioms that have a subject in the base namespaces.
FilterOperation - Class in org.obolibrary.robot: Filter the axioms of an ontology by given criteria.
FilterOperation() - Constructor for class org.obolibrary.robot.FilterOperation
filterPartialAxioms(Set<OWLAxiom>, Set<OWLObject>, Set<Class<? extends OWLAxiom>>, boolean) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given a set of axioms, a set of objects, and a set of axiom types, return a set of axioms where at least one object in those axioms is also in the set of objects.
filterTautologicalAxioms(Set<OWLAxiom>, boolean) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given a set of OWLAxioms and a structural boolean, filter for tautological axioms, i.e., those that would be true in any ontology.
FINISH_TS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
FIXED_VIOLATIONS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
from(String) - Static method in enum org.obolibrary.robot.reason.EquivalentClassReasoningMode: Canonical way to find make a Mode instance from a String (say from a command line argument).

G

GCI_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
GCI_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
GCI_HIDDEN_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
GCI_HIDDEN_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
generateOutputOntology() - Method in class org.obolibrary.robot.Template: Generate an OWLOntology based on the rows of the template.
generateOutputOntology(String, boolean) - Method in class org.obolibrary.robot.Template: Generate an OWLOntology based on the rows of the template.
generateOutputOntology(String, boolean, String) - Method in class org.obolibrary.robot.Template: Generate an OWLOntology with given IRI based on the rows of the template.
getABoxAxioms(Set<OWLAxiom>) - Static method in class org.obolibrary.robot.metrics.MetricsUtils
getAllMetrics() - Method in class org.obolibrary.robot.metrics.OntologyMetrics
getAllMetrics(String) - Method in class org.obolibrary.robot.metrics.OntologyMetrics
getAncestors(OWLOntology, Set<IRI>, Set<IRI>, Set<OWLAnnotationProperty>) - Static method in class org.obolibrary.robot.MireotOperation: Given an ontology, a set of upper-level IRIs, a set of lower-level IRIs, and a set of annotation properties, return a new ontology with just the named ancestors of those terms, their subclass relations, and the selected annotations.
getAncestors(OWLOntology, Set<IRI>, Set<IRI>, Set<OWLAnnotationProperty>, boolean, Map<IRI, IRI>) - Static method in class org.obolibrary.robot.MireotOperation: Deprecated.
replaced by MireotOperation.getAncestors(OWLOntology, Set, Set, Set)
getAncestors(OWLOntology, Set<IRI>, Set<IRI>, Set<OWLAnnotationProperty>, Map<String, String>, Map<IRI, IRI>) - Static method in class org.obolibrary.robot.MireotOperation: Given an input ontology, a set of upper IRIs, a set of lower IRIs, a set of annotation properties (or null for all), and a map of extract options, get the ancestors of the lower IRIs up to the upper IRIs.
getAnnotateExpansionAxioms() - Method in class org.obolibrary.robot.ExpandOperation.ExpandConfig
getAnnotation(String, QuotedEntityChecker, IOHelper, String, String) - Static method in class org.obolibrary.robot.TemplateHelper: Deprecated.
getAnnotation(QuotedEntityChecker, String, String) - Static method in class org.obolibrary.robot.TemplateHelper: Deprecated.
getAnnotation(QuotedEntityChecker, IOHelper, String, String) - Static method in class org.obolibrary.robot.TemplateHelper: Deprecated.
getAnnotationAxioms(OWLEntity, Set<OWLAnnotation>, Map<OWLAnnotation, Map<OWLAnnotation, Set<OWLAnnotation>>>) - Static method in class org.obolibrary.robot.TemplateHelper: Deprecated.
TemplateOperation replaced with Template class
getAnnotationAxioms(OWLOntology, Set<OWLAnnotationProperty>, Set<IRI>) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of annotation assertion axioms for those subjects and those properties.
getAnnotationAxioms(OWLOntology, Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology and a set of objects, return the annotation axioms for all objects.
getAnnotationAxioms(OWLOntology, OWLAnnotationProperty) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, and an optional set of annotation properties, return a set of annotation assertion axioms for those properties, for all subjects.
getAnnotationAxioms(OWLOntology, OWLAnnotationProperty, IRI) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of annotation assertion axioms for those subjects and those properties.
getAnnotationProperties(QuotedEntityChecker, String, String) - Static method in class org.obolibrary.robot.TemplateHelper: Deprecated.
getAnnotationProperties(QuotedEntityChecker, String, String, int) - Static method in class org.obolibrary.robot.TemplateHelper: Given a QuotedEntityChecker, a string value, and a character to split the value string on (or null), return the value or values as a set of OWLAnnotationProperties.
getAnnotationProperty(QuotedEntityChecker, String) - Static method in class org.obolibrary.robot.TemplateHelper: Deprecated.
getAnnotationProperty(QuotedEntityChecker, String) - Static method in class org.obolibrary.robot.TemplateOperation: Deprecated.
getAnnotationProperty(QuotedEntityChecker, String, int) - Static method in class org.obolibrary.robot.TemplateHelper: Find an annotation property with the given name or create one.
getAnnotations(String, QuotedEntityChecker, String, String, int, int) - Static method in class org.obolibrary.robot.TemplateHelper: Create an OWLAnnotation based on the template string and cell value.
getAnnotations(OWLOntology, IOHelper, String) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an IOHelper and an annotation as CURIE=..., return the OWLAnnotation object(s).
getAnnotationString(OWLOntology, Set<OWLAnnotationProperty>, Set<IRI>) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, an optional set of annotation properties, and an optional set of subject, return the alphanumerically first annotation value string for those subjects and those properties.
getAnnotationString(OWLOntology, OWLAnnotationProperty, IRI) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, an optional set of annotation properties, and an optional set of subject, return the alphanumerically first annotation value string for those subjects and those properties.
getAnnotationStrings(OWLOntology, Set<OWLAnnotationProperty>, Set<IRI>) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of strings for those subjects and those properties.
getAnnotationStrings(OWLOntology, OWLAnnotationProperty, IRI) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of strings for those subjects and those properties.
getAnnotationValues(OWLOntology, Set<OWLAnnotationProperty>, Set<IRI>) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of annotation values for those subjects and those properties.
getAnnotationValues(OWLOntology, OWLAnnotationProperty, IRI) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, an optional set of annotation properties, and an optional set of subject, return a set of annotation values for those subjects and those properties.
getAnonymousAncestorAxioms(OWLOntology, OWLEntity) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, an entity, and an empty set, fill the set with axioms representing any anonymous superclasses in the line of ancestors.
getAnonymousDescendantAxioms(OWLOntology, OWLEntity) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology and an entity, return a set of axioms containing any anonymous entities referenced in the descendants of the entity.
getAnonymousEquivalentAxioms(OWLOntology, OWLEntity) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology and an entity, return a set of axioms containing any anonymous entities referenced in equivalent entities.
getAnonymousParentAxioms(OWLOntology, OWLEntity) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology and an entity, return a set of axioms only corresponding to anonymous parents.
getAxiom() - Method in class org.obolibrary.robot.checks.InvalidReferenceViolation
getAxioms(OWLOntology, Set<OWLObject>, Set<Class<? extends OWLAxiom>>, boolean, boolean) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Deprecated.
replaced by RelatedObjectsHelper.filterAxiomsByAxiomType(Set, Set, Set, boolean, boolean)
getAxiomStrings(OWLOntology) - Static method in class org.obolibrary.robot.DiffOperation: Deprecated.
This functionality is no longer used within DiffOperation.
getAxiomValues(String) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given a string axiom selector, return the OWLAxiom Class type(s) or null.
getBaseNamespaces() - Method in class org.obolibrary.robot.IOHelper: Get the base namespaces.
getCategory() - Method in class org.obolibrary.robot.checks.InvalidReferenceViolation
getCellColor() - Method in class org.obolibrary.robot.export.Cell: Get the cell background color for this cell in an XLSX workbook.
getCellContent(List<List<String>>, int, Integer) - Static method in class org.obolibrary.robot.TemplateHelper: Deprecated.
TemplateOperation replaced with Template class
getCellPattern() - Method in class org.obolibrary.robot.export.Cell: Get the cell background pattern for this cell in an XLSX workbook.
getChecker() - Method in class org.obolibrary.robot.Template: Return the QuotedEntityChecker.
getClassExpressions(String, QuotedEntityChecker, ManchesterOWLSyntaxClassExpressionParser, String, String, int, int) - Static method in class org.obolibrary.robot.TemplateHelper: Given a Quoted Entity checker, a Manchester Syntax parser, a template string, and a template value, insert the value into the template string and parse to a set of class expressions.
getClassExpressions(String, ManchesterOWLSyntaxClassExpressionParser, String, String, int, int) - Static method in class org.obolibrary.robot.TemplateHelper: Given a Manchester Syntax parser, a template string, and a template value, insert the value into the template string and parse to a set of class expressions.
getColumnName() - Method in class org.obolibrary.robot.export.Cell: Get the column name for a cell.
getColumns() - Method in class org.obolibrary.robot.export.Table: Get the Columns in a Table.
getComment() - Method in class org.obolibrary.robot.export.Cell: Get the comment for this Cell.
getCompleteAxioms(OWLOntology, Set<OWLObject>, Set<Class<? extends OWLAxiom>>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology, a set of objects, and a set of axiom types, return a set of axioms where all the objects in those axioms are in the set of objects.
getCompleteAxioms(OWLOntology, Set<OWLObject>, Set<Class<? extends OWLAxiom>>, boolean) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology, a set of objects, and a set of axiom types, return a set of axioms where all the objects in those axioms are in the set of objects.
getContext() - Method in class org.obolibrary.robot.IOHelper: Get a copy of the current context.
getContextString() - Method in class org.obolibrary.robot.IOHelper: Return the current prefixes as a JSON-LD string.
getCreateNewOntology() - Method in class org.obolibrary.robot.ExpandOperation.ExpandConfig
getData() - Method in class org.obolibrary.robot.metrics.MeasureResult
getDataPropertyExpressions(String, QuotedEntityChecker, String, String, int, int) - Static method in class org.obolibrary.robot.TemplateHelper: Given a QuotedEntityChecker, a template string, and a template value, return a set of data property expressions based on the value or values (if SPLIT is included in the template string).
getDatatype(String, QuotedEntityChecker, String, int, int) - Static method in class org.obolibrary.robot.TemplateHelper: Find a datatype with the given name or create one.
getDatatype(QuotedEntityChecker, String) - Static method in class org.obolibrary.robot.TemplateHelper: Find a datatype with the given name or create one.
getDatatype(QuotedEntityChecker, String) - Static method in class org.obolibrary.robot.TemplateOperation: Deprecated.
getDatatypes(String, QuotedEntityChecker, String, String, int, int) - Static method in class org.obolibrary.robot.TemplateHelper: Given a QuotedEntityChecker, a string value, and a character to split the value string on (or null), return the value or values as a set of OWLDatatypes.
getDefaultAnnotationProperties() - Static method in class org.obolibrary.robot.MireotOperation: Get a set of default annotation properties.
getDefaultContext() - Method in class org.obolibrary.robot.IOHelper: Get a copy of the default context.
getDefaultFormatName(String) - Static method in class org.obolibrary.robot.QueryOperation: Given a SPARQL query, return its default file format as a string.
getDefaultFormatName(Query) - Static method in class org.obolibrary.robot.QueryOperation: Given a SPARQL query, return its default file format as a string.
getDefaultOptions() - Static method in class org.obolibrary.robot.DiffOperation: Return default diff options.
getDefaultOptions() - Static method in class org.obolibrary.robot.ExportOperation: Return a map from option name to default option value, for all the available export options.
getDefaultOptions() - Static method in class org.obolibrary.robot.ExtractOperation: Return a map from option name to default option value.
getDefaultOptions() - Static method in class org.obolibrary.robot.MaterializeOperation: Return a map from option name to default option value, for all the available reasoner options.
getDefaultOptions() - Static method in class org.obolibrary.robot.MergeOperation: Return a map from option name to default option value, for all the available merge options.
getDefaultOptions() - Static method in class org.obolibrary.robot.ReasonOperation: Return a map from option name to default option value, for all the available reasoner options.
getDefaultOptions() - Static method in class org.obolibrary.robot.ReduceOperation: Return a map from option name to default option value, for all the available reasoner options.
getDefaultOptions() - Static method in class org.obolibrary.robot.RelaxOperation: Return a map from option name to default option value, for all the available reasoner options.
getDefaultOptions() - Static method in class org.obolibrary.robot.RepairOperation: Return a map from option name to default option value, for all the available repair options.
getDefaultOptions() - Static method in class org.obolibrary.robot.ReportOperation: Return a map from option name to default option value, for all the available report options.
getDefaultOptions() - Static method in class org.obolibrary.robot.TemplateOperation: Get the default template options.
getDescendants(OWLOntology, Set<IRI>, Set<OWLAnnotationProperty>) - Static method in class org.obolibrary.robot.MireotOperation: Given an ontology, a set of upper-level IRIs, and a set of annotation properties, return a new ontology with just those terms and their named descendants, their subclass relations, and the selected annotations.
getDescendants(OWLOntology, Set<IRI>, Set<OWLAnnotationProperty>, boolean, Map<IRI, IRI>) - Static method in class org.obolibrary.robot.MireotOperation: Deprecated.
replaced by MireotOperation.getDescendants(OWLOntology, Set, Set, Map, Map)
getDescendants(OWLOntology, Set<IRI>, Set<OWLAnnotationProperty>, Map<String, String>, Map<IRI, IRI>) - Static method in class org.obolibrary.robot.MireotOperation: Given an ontology, a set of upper-level IRIs, and a set of annotation properties, return a new ontology with just those terms and their named descendants, their subclass relations, and the selected annotations.
getDisplayName() - Method in class org.obolibrary.robot.export.Column: Get the display name of a column.
getDisplayRendererType() - Method in class org.obolibrary.robot.export.Table: Get the type of display renderer
getDisplayRule() - Method in class org.obolibrary.robot.export.Column: Get the display rule of a column for validation.
getDisplayValues() - Method in class org.obolibrary.robot.export.Cell: Get the value of a cell.
getDocumentIRI(IRI) - Method in class org.obolibrary.robot.CatalogXmlIRIMapper: Given an IRI, return the mapped IRI.
getEntities(OWLOntology) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, return a set of all the entities in its signature.
getEntities(OWLOntology, Set<IRI>) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology and a set of term IRIs, return a set of entities for those IRIs.
getEntity(QuotedEntityChecker, IRI, String, String) - Static method in class org.obolibrary.robot.TemplateHelper: Deprecated.
TemplateOperation replaced with Template class
getEntity(QuotedEntityChecker, IRI, String, String) - Static method in class org.obolibrary.robot.TemplateOperation: Deprecated.
getEntity(OWLOntology, IRI) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology and an IRI, get the OWLEntity object represented by the IRI.
getEntity(OWLOntology, IRI, boolean) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, an IRI, and a boolean specifying if a null return value is allowed, get the OWLEntity object represented by the IRI.
getEssentialMetrics() - Method in class org.obolibrary.robot.metrics.OntologyMetrics
getEssentialMetrics(String) - Method in class org.obolibrary.robot.metrics.OntologyMetrics
getExcludeProperties() - Method in class org.obolibrary.robot.ExpandOperation.ExpandConfig
getExpandProperties() - Method in class org.obolibrary.robot.ExpandOperation.ExpandConfig
getExplanation() - Method in enum org.obolibrary.robot.reason.EquivalentClassReasoningMode: Get the explanation.
getExtendedMetrics() - Method in class org.obolibrary.robot.metrics.OntologyMetrics
getExtendedMetrics(String) - Method in class org.obolibrary.robot.metrics.OntologyMetrics
getExtendedReasonerMetrics(String, OWLReasoner) - Method in class org.obolibrary.robot.metrics.OntologyMetrics
getExtendedReasonerMetrics(OWLReasoner) - Method in class org.obolibrary.robot.metrics.OntologyMetrics
getFontColor() - Method in class org.obolibrary.robot.export.Cell: Get the font color for this cell in an XLSX workbook.
getFormat() - Method in class org.obolibrary.robot.export.Table: Get the format of this table
getFormat(String) - Static method in class org.obolibrary.robot.IOHelper: Given the name of a file format, return an instance of it.
getFormatLang(String) - Static method in class org.obolibrary.robot.QueryOperation: Convert a format name string to a language code.
getHref() - Method in class org.obolibrary.robot.export.Cell: Get an href link for the cell or null.
getHTMLClass() - Method in class org.obolibrary.robot.export.Cell: Get the HTML class of a cell.
getIncludeAnonymous() - Method in class org.obolibrary.robot.export.Column
getIncludeNamed() - Method in class org.obolibrary.robot.export.Column
getIndividuals(QuotedEntityChecker, String, String) - Static method in class org.obolibrary.robot.TemplateHelper: Given a QuotedEntityChecker, a string value (maybe separated by a split character), and a split character (or null), return the value or values as a set of OWLIndividuals.
getInferredAxiomGenerator(String) - Static method in class org.obolibrary.robot.ReasonerHelper: Given an axiom generator as a string, return the InferredAxiomGenerator object.
getInferredAxiomGenerator(String, boolean) - Static method in class org.obolibrary.robot.ReasonerHelper: Given an axiom generator as a string, return the InferredAxiomGenerator object.
getInferredAxiomGenerators(List<String>) - Static method in class org.obolibrary.robot.ReasonerHelper: Given a list of axiom generator strings, return a list of InferredAxiomGenerator objects.
getInferredAxiomGenerators(List<String>, boolean) - Static method in class org.obolibrary.robot.ReasonerHelper: Given a list of axiom generator strings, return a list of InferredAxiomGenerator objects.
getInvalidReferenceViolations(OWLOntology, boolean) - Static method in class org.obolibrary.robot.checks.InvalidReferenceChecker
getInvalidReferenceViolations(OWLOntology, Set<OWLAxiom>, boolean) - Static method in class org.obolibrary.robot.checks.InvalidReferenceChecker: Finds axioms that reference a deprecated or dangling entity.
getIOHelper() - Method in class org.obolibrary.robot.QuotedEntityChecker: Get the configured IOHelper.
getIRI() - Method in class org.obolibrary.robot.export.Column: Return the IRI used in a column, or null.
getIRI(String, boolean) - Method in class org.obolibrary.robot.QuotedEntityChecker: Get the IRI for the given name, or create a new IRI from the name.
getIRIAnnotation(QuotedEntityChecker, String, String) - Static method in class org.obolibrary.robot.TemplateHelper: Deprecated.
getIRIAnnotation(QuotedEntityChecker, String, String, int) - Static method in class org.obolibrary.robot.TemplateHelper: Return an IRI annotation for the given template string and string value.
getIRIAnnotation(QuotedEntityChecker, String, IRI) - Static method in class org.obolibrary.robot.TemplateHelper: Deprecated.
getIRIAnnotation(QuotedEntityChecker, String, IRI) - Static method in class org.obolibrary.robot.TemplateOperation: Deprecated.
getIRIAnnotation(QuotedEntityChecker, String, IRI, int) - Static method in class org.obolibrary.robot.TemplateHelper: Return an IRI annotation for the given template string and IRI value.
getIRIs() - Method in class org.obolibrary.robot.checks.Report: Return all the IRI strings in the current Violations.
getIRIs(String, List<List<String>>, IOHelper) - Static method in class org.obolibrary.robot.TemplateHelper: Get a list of the IRIs defined in a template table.
getIRIs(String, List<List<String>>, IOHelper) - Static method in class org.obolibrary.robot.TemplateOperation: Deprecated.
getIRIs(List<Violation>) - Method in class org.obolibrary.robot.checks.Report: Return all the IRI strings in the given list of Violations.
getIRIs(Map<String, List<List<String>>>, IOHelper) - Static method in class org.obolibrary.robot.TemplateHelper: Get a list of the IRIs defined in a set of template tables.
getIRIs(Map<String, List<List<String>>>, IOHelper) - Static method in class org.obolibrary.robot.TemplateOperation: Deprecated.
getIRIs(OWLOntology) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, return a set of IRIs for all the entities in its signature.
getIRIsInSignature(OWLAxiom) - Static method in class org.obolibrary.robot.OntologyHelper: Given an OWLAxiom, return all the IRIs in the signature.
getIsDefinedBy(OWLEntity, Map<IRI, IRI>) - Static method in class org.obolibrary.robot.ExtractOperation: Given an OWLEntity, return an OWLAnnotationAssertionAxiom indicating the source ontology with rdfs:isDefinedBy.
getLabel() - Method in class org.obolibrary.robot.reason.InferredClassAssertionAxiomGeneratorDirectOnly
getLabel() - Method in class org.obolibrary.robot.reason.InferredObjectPropertyDomainAxiomGenerator
getLabel() - Method in class org.obolibrary.robot.reason.InferredObjectPropertyRangeAxiomGenerator
getLabel() - Method in class org.obolibrary.robot.reason.InferredSubClassAxiomGeneratorIncludingIndirect
getLabel() - Method in class org.obolibrary.robot.reason.InferredSubObjectPropertyAxiomGeneratorIncludingIndirect
getLabel(IRI) - Method in class org.obolibrary.robot.QuotedEntityChecker: Get the label for the given IRI.
getLabelFunction(OWLOntology, boolean) - Static method in class org.obolibrary.robot.OntologyHelper: Generates a function that returns a label string for any named object in the ontology
getLabelIRIs(OWLOntology) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, return a map from rdfs:label to IRIs.
getLabels() - Static method in class org.obolibrary.robot.metrics.MetricsLabels
getLabels(OWLOntology) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, return a map from IRIs to rdfs:labels.
getLanguageAnnotation(QuotedEntityChecker, String, String) - Static method in class org.obolibrary.robot.TemplateHelper: Deprecated.
getLanguageAnnotation(QuotedEntityChecker, String, String) - Static method in class org.obolibrary.robot.TemplateOperation: Deprecated.
getLanguageAnnotations(QuotedEntityChecker, String, String, String) - Static method in class org.obolibrary.robot.TemplateHelper: Deprecated.
getLanguageAnnotations(QuotedEntityChecker, String, String, String, int) - Static method in class org.obolibrary.robot.TemplateHelper: Return a set of language tagged annotations for the given template and value(s).
getLevel() - Method in class org.obolibrary.robot.checks.ReportQuery: Return the violation level of this ReportQuery.
getListData() - Method in class org.obolibrary.robot.metrics.MeasureResult
getLiterals(String, QuotedEntityChecker, String, String, int, int) - Static method in class org.obolibrary.robot.TemplateHelper: Given a QuotedEntityChecker, a string value (maybe separated by a split character), and a split character (or null), return the value or values as a set of OWLLiterals.
getLogicalAxioms(OWLClass, String, Set<OWLClassExpression>, Map<OWLClassExpression, Set<OWLAnnotation>>) - Static method in class org.obolibrary.robot.TemplateHelper: Deprecated.
TemplateOperation replaced with Template class
getLogicalAxioms(OWLOntology, Imports, boolean, Set<AxiomType<?>>) - Static method in class org.obolibrary.robot.metrics.MetricsUtils
getMapData() - Method in class org.obolibrary.robot.metrics.MeasureResult
getMetrics(OWLOntology, String, CURIEShortFormProvider) - Static method in class org.obolibrary.robot.MeasureOperation: Compute metrics for a given ontology.
getMetrics(OWLOntology, OWLReasonerFactory, String, CURIEShortFormProvider) - Static method in class org.obolibrary.robot.MeasureOperation: Run the metrics command using the reasoner factory.
getName() - Method in class org.obolibrary.robot.export.Column: Get the name of a column.
getNamedObjects(OWLAxiom) - Static method in class org.obolibrary.robot.OntologyHelper: Get all named OWLObjects associated with an axiom.
getNamedObjects(OWLOntology) - Static method in class org.obolibrary.robot.OntologyHelper: Get all named OWLObjects from an input ontology.
getObjectPropertyExpressions(String, QuotedEntityChecker, String, String, int, int) - Static method in class org.obolibrary.robot.TemplateHelper: Given a QuotedEntityChecker, a template string, and a template value, return a set of object property expressions based on the value or values (if SPLIT is included in the template string).
getObjects(OWLAxiom) - Static method in class org.obolibrary.robot.OntologyHelper: Get all OWLObjects associated with an axiom.
getObjects(OWLOntology) - Static method in class org.obolibrary.robot.OntologyHelper: Get all OWLObjects from an input ontology.
getOntology() - Method in class org.obolibrary.robot.metrics.OntologyMetrics
getOption(Map<String, String>, String) - Static method in class org.obolibrary.robot.OptionsHelper: Given a map of options and a key name, return the value, or null if it is not specified.
getOption(Map<String, String>, String, String) - Static method in class org.obolibrary.robot.OptionsHelper: Given a map of options, a key name, and a default value, if the map contains the key, return its value, otherwise return the default value.
getOWLAnnotationProperty(String) - Method in class org.obolibrary.robot.QuotedEntityChecker: Find an annotation property with the given name, or create one.
getOWLAnnotationProperty(String, boolean) - Method in class org.obolibrary.robot.QuotedEntityChecker: Find an annotation property with the given name, or create one.
getOWLClass(String) - Method in class org.obolibrary.robot.QuotedEntityChecker: Find a class with the given name, or create one.
getOWLClass(String, boolean) - Method in class org.obolibrary.robot.QuotedEntityChecker: Find a class with the given name, or create one.
getOWLDataProperty(String) - Method in class org.obolibrary.robot.QuotedEntityChecker: Find a data property with the given name.
getOWLDatatype(String) - Method in class org.obolibrary.robot.QuotedEntityChecker: Find a datatype with the given name, or create one.
getOWLDatatype(String, boolean) - Method in class org.obolibrary.robot.QuotedEntityChecker: Find a datatype with the given name, or create one.
getOWLEntity(String) - Method in class org.obolibrary.robot.QuotedEntityChecker: Find any entity with the given name.
getOWLIndividual(String) - Method in class org.obolibrary.robot.QuotedEntityChecker: Find a named individual with the given name.
getOWLObjectProperty(String) - Method in class org.obolibrary.robot.QuotedEntityChecker: Find an object property with the given name.
getPartialAxioms(OWLOntology, Set<OWLObject>, Set<Class<? extends OWLAxiom>>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology, a set of objects, and a set of axiom types, return a set of axioms where at least one object in those axioms is also in the set of objects.
getPartialAxioms(OWLOntology, Set<OWLObject>, Set<Class<? extends OWLAxiom>>, boolean) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology, a set of objects, and a set of axiom types, return a set of axioms where at least one object in those axioms is also in the set of objects.
getPrefixes() - Method in class org.obolibrary.robot.IOHelper: Get a copy of the current prefix map.
getPrefixManager() - Method in class org.obolibrary.robot.IOHelper: Get a prefix manager with the current prefixes.
getProperty() - Method in class org.obolibrary.robot.export.Column: Return the OWLProperty used in a column, or null.
getQuery() - Method in class org.obolibrary.robot.checks.ReportQuery: Return the query contents of this ReportQuery.
getQueryTypeName(String) - Static method in class org.obolibrary.robot.QueryOperation: Given a SPARQL query, return its type as a string: ASK, CONSTRUCT, DESCRIBE, or SELECT.
getReferencedObject() - Method in class org.obolibrary.robot.checks.InvalidReferenceViolation
getRelationType(String) - Static method in enum org.obolibrary.robot.RelationType
getReport(OWLOntology, IOHelper, Map<String, String>) - Static method in class org.obolibrary.robot.ReportOperation: Given an ontology, an IOHelper, and a map of options, create a Report object and run the report queries specified in a profile (from options, or default).
getRuleName() - Method in class org.obolibrary.robot.checks.ReportQuery: Return the name of the rule for this ReportQuery.
getRules() - Method in class org.obolibrary.robot.export.Column: Return the rules used in column for validate, or null.
getRuleURL() - Method in class org.obolibrary.robot.checks.ReportQuery: Return the URL for rule documentation (or null) for this ReportQuery.
getShortForm(IRI) - Method in class org.obolibrary.robot.providers.CURIEShortFormProvider: Get the short form of an IRI as a CURIE.
getShortForm(IRI) - Method in class org.obolibrary.robot.providers.EmptyIRIShortFormProvider: Return an empty string as the short form of an IRI.
getShortForm(OWLEntity) - Method in class org.obolibrary.robot.providers.CURIEShortFormProvider: Get the short form of an OWLEntity as a CURIE.
getShortForm(OWLEntity) - Method in class org.obolibrary.robot.providers.EmptyShortFormProvider: Return an empty string as the short form of an entity.
getShortForm(OWLEntity) - Method in class org.obolibrary.robot.providers.IRIValueShortFormProvider: Return the IRI of the entity as the short form.
getShortForm(OWLEntity) - Method in class org.obolibrary.robot.providers.QuotedAnnotationValueShortFormProvider: Given an OWLEntity, return the short form based on annotation properties.
getShortFormProvider() - Method in class org.obolibrary.robot.export.Column: Return the short form provider for this column
getSimpleMetricValue(String) - Method in class org.obolibrary.robot.metrics.MeasureResult
getSimpleReasonerMetrics(String, OWLReasoner) - Method in class org.obolibrary.robot.metrics.OntologyMetrics
getSimpleReasonerMetrics(OWLReasoner) - Method in class org.obolibrary.robot.metrics.OntologyMetrics
getSortedPrefixMap() - Method in class org.obolibrary.robot.providers.CURIEShortFormProvider: Get a copy of the full current curie map.
getSortOrder() - Method in class org.obolibrary.robot.export.Column: Get the int sort order of the column.
getSortRendererType() - Method in class org.obolibrary.robot.export.Table: Get thee type of sort renderer
getSortValueString() - Method in class org.obolibrary.robot.export.Cell: Get the sort value of a cell.
getSortValueString(String) - Method in class org.obolibrary.robot.export.Row: Get the Cell sort value of a column.
getStringAnnotation(QuotedEntityChecker, String, String) - Static method in class org.obolibrary.robot.TemplateHelper: Deprecated.
getStringAnnotation(QuotedEntityChecker, String, String) - Static method in class org.obolibrary.robot.TemplateOperation: Deprecated.
getStringAnnotations(QuotedEntityChecker, String, String, String) - Static method in class org.obolibrary.robot.TemplateHelper: Deprecated.
getStringAnnotations(QuotedEntityChecker, String, String, String, int) - Static method in class org.obolibrary.robot.TemplateHelper: Return a set of string annotations for the given template string and value(s).
getSubject() - Method in class org.obolibrary.robot.export.Row: Return the subject of this row as an IRI.
getTautologies(Set<OWLAxiom>) - Static method in class org.obolibrary.robot.metrics.TautologyChecker
getTautologyChecker(boolean) - Static method in class org.obolibrary.robot.ReasonOperation: Create a tautology checker.
getTautologySyntactic(Set<OWLAxiom>) - Static method in class org.obolibrary.robot.metrics.TautologyChecker
getTBoxAxioms(Set<OWLAxiom>) - Static method in class org.obolibrary.robot.metrics.MetricsUtils
getTBoxAxiomTypes(boolean) - Static method in class org.obolibrary.robot.metrics.MetricsUtils
getTDBReport(String, Map<String, String>) - Static method in class org.obolibrary.robot.ReportOperation: Given an input path to an ontology and a map of options, create a Report object and run (on TDB dataset) the report queries specified in a profile (from options, or default).
getTDBReport(Dataset, Map<String, String>) - Static method in class org.obolibrary.robot.ReportOperation: Given a dataset and a map of options, create a Report object and run (on TDB dataset) the report queries specified in a profile (from options, or default).
getTDBReport(IOHelper, Dataset, Map<String, String>) - Static method in class org.obolibrary.robot.ReportOperation: Given a dataset and a map of options, create a Report object and run (on TDB dataset) the report queries specified in a profile (from options, or default).
getTotalViolations() - Method in class org.obolibrary.robot.checks.Report: Return the total violations from reporting.
getTotalViolations(String) - Method in class org.obolibrary.robot.checks.Report: Given a reporting level, return the number of violations.
getType(OWLAnnotationValue) - Static method in class org.obolibrary.robot.OntologyHelper: Given an annotation value, return its datatype, or null.
getTypedAnnotation(QuotedEntityChecker, String, String) - Static method in class org.obolibrary.robot.TemplateHelper: Deprecated.
getTypedAnnotation(QuotedEntityChecker, String, String) - Static method in class org.obolibrary.robot.TemplateOperation: Deprecated.
getTypedAnnotations(String, QuotedEntityChecker, String, String, String, int, int) - Static method in class org.obolibrary.robot.TemplateHelper: Return a set of typed annotations for the given template string and value(s).
getTypeIRI(OWLAnnotationValue) - Static method in class org.obolibrary.robot.OntologyHelper: Given an annotation value, return the IRI of its datatype, or null.
getValue(Set<OWLAnnotation>) - Static method in class org.obolibrary.robot.OntologyHelper: Given a set of OWLAnnotations, return the first string value as determined by natural string sorting.
getValue(OWLAnnotation) - Static method in class org.obolibrary.robot.OntologyHelper: Given an OWLAnnotation, return its value as a string.
getValue(OWLAnnotationAssertionAxiom) - Static method in class org.obolibrary.robot.OntologyHelper: Given an OWLAnnotationAssertionAxiom, return its value as a string.
getValue(OWLAnnotationValue) - Static method in class org.obolibrary.robot.OntologyHelper: Given an OWLAnnotationValue, return its value as a string.
getValueIRIs(QuotedEntityChecker, String, String) - Static method in class org.obolibrary.robot.TemplateHelper: Given a QuotedEntityChecker, a value, and a split character (or null), return the value (or values) as a set of IRIs.
getValues(Set<OWLAnnotation>) - Static method in class org.obolibrary.robot.OntologyHelper: Given a set of OWLAnnotations, return a set of their value strings.
getViolationCount(String) - Method in class org.obolibrary.robot.checks.Report: Given a rule name, return the violation count for that rule.
getViolations() - Method in class org.obolibrary.robot.checks.ReportQuery: Return the collection of violations for this ReportQuery.
getXMLEntityFlag() - Method in class org.obolibrary.robot.IOHelper: Get the useXMLEntities flag.
GRAPH_TRAVERSE_MODE - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
guessCatalogFile(File) - Method in class org.obolibrary.robot.IOHelper: Try to guess the location of the catalog.xml file.

H

hashCode() - Method in class org.obolibrary.robot.Tuple
hasResult(ResultSet) - Static method in class org.obolibrary.robot.QueryOperation: If a result set has results, return true, otherwise false.
hasResult(Model) - Static method in class org.obolibrary.robot.QueryOperation: If a model has statements, return true, otherwise false.

I

importMetrics(MeasureResult) - Method in class org.obolibrary.robot.metrics.MeasureResult
IncoherentRBoxException - Exception in org.obolibrary.robot.exceptions: Ontology contains unsatisfiable properties.
IncoherentRBoxException(Set<OWLObjectProperty>) - Constructor for exception org.obolibrary.robot.exceptions.IncoherentRBoxException
IncoherentTBoxException - Exception in org.obolibrary.robot.exceptions: Ontology contains unsatisfiable classes.
IncoherentTBoxException(Set<OWLClass>) - Constructor for exception org.obolibrary.robot.exceptions.IncoherentTBoxException
InconsistentOntologyException - Exception in org.obolibrary.robot.exceptions: Ontology contains logical inconsistencies.
InconsistentOntologyException() - Constructor for exception org.obolibrary.robot.exceptions.InconsistentOntologyException
INCREMENTAL_REASONER_NR_CLASSIFY_CALLS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
INDIVIDUAL_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
INDIVIDUAL_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
INDIVIDUALS - org.obolibrary.robot.RelationType
INF_CLASSHIERARCHY_DEPTH - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
INFERRED_ONLY_ENTAILMENT_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
INFERRED_SUBSUMPTIONS_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
INFERRED_TAXONOMY_AXIOM_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
InferredClassAssertionAxiomGeneratorDirectOnly - Class in org.obolibrary.robot.reason: An InferredAxiomGenerator which returns only direct class assettion axioms.
InferredClassAssertionAxiomGeneratorDirectOnly() - Constructor for class org.obolibrary.robot.reason.InferredClassAssertionAxiomGeneratorDirectOnly
InferredObjectPropertyDomainAxiomGenerator - Class in org.obolibrary.robot.reason: An InferredAxiomGenerator which returns both direct and indirect inferred object property domain axioms.
InferredObjectPropertyDomainAxiomGenerator() - Constructor for class org.obolibrary.robot.reason.InferredObjectPropertyDomainAxiomGenerator
InferredObjectPropertyRangeAxiomGenerator - Class in org.obolibrary.robot.reason: An InferredAxiomGenerator which returns both direct and indirect inferred object property range axioms.
InferredObjectPropertyRangeAxiomGenerator() - Constructor for class org.obolibrary.robot.reason.InferredObjectPropertyRangeAxiomGenerator
InferredSubClassAxiomGeneratorIncludingIndirect - Class in org.obolibrary.robot.reason: An InferredAxiomGenerator which returns both direct and indirect inferred subclass axioms.
InferredSubClassAxiomGeneratorIncludingIndirect() - Constructor for class org.obolibrary.robot.reason.InferredSubClassAxiomGeneratorIncludingIndirect
InferredSubObjectPropertyAxiomGeneratorIncludingIndirect - Class in org.obolibrary.robot.reason: An InferredAxiomGenerator which returns both direct and indirect inferred subobjectproperty axioms.
InferredSubObjectPropertyAxiomGeneratorIncludingIndirect() - Constructor for class org.obolibrary.robot.reason.InferredSubObjectPropertyAxiomGeneratorIncludingIndirect
info - Variable in class org.obolibrary.robot.checks.Report: Deprecated.
infoCountByRule - Variable in class org.obolibrary.robot.checks.Report: Map of rule name to number of violations for INFO level.
InvalidReferenceChecker - Class in org.obolibrary.robot.checks: Checks to determine if axioms contain invalid references: to dangling classes or deprecated classes.
InvalidReferenceChecker() - Constructor for class org.obolibrary.robot.checks.InvalidReferenceChecker
InvalidReferenceException - Exception in org.obolibrary.robot.exceptions: Ontology contains unsatisfiable classes.
InvalidReferenceException(Set<InvalidReferenceViolation>) - Constructor for exception org.obolibrary.robot.exceptions.InvalidReferenceException
InvalidReferenceViolation - Class in org.obolibrary.robot.checks: Represents a reference violation
InvalidReferenceViolation.Category - Enum in org.obolibrary.robot.checks: A reference may be invalid for different reasons
IOHelper - Class in org.obolibrary.robot: Provides convenience methods for working with ontology and term files.
IOHelper() - Constructor for class org.obolibrary.robot.IOHelper: Create a new IOHelper with the default prefixes.
IOHelper(boolean) - Constructor for class org.obolibrary.robot.IOHelper: Create a new IOHelper with or without the default prefixes.
IOHelper(File) - Constructor for class org.obolibrary.robot.IOHelper: Create a new IOHelper with prefixes from a file.
IOHelper(String) - Constructor for class org.obolibrary.robot.IOHelper: Create a new IOHelper with prefixes from a file path.
IOHelper(Map<String, Object>) - Constructor for class org.obolibrary.robot.IOHelper: Create a new IOHelper with the specified prefixes.
IRIValueShortFormProvider - Class in org.obolibrary.robot.providers: A short form provider that returns full IRIs.
IRIValueShortFormProvider() - Constructor for class org.obolibrary.robot.providers.IRIValueShortFormProvider: Create a new IRIValueShortFormProvider
isDangling(OWLOntology, OWLEntity) - Static method in class org.obolibrary.robot.checks.InvalidReferenceChecker: Checks if entity is dangling.
isDeprecated(OWLOntology, OWLEntity) - Static method in class org.obolibrary.robot.checks.InvalidReferenceChecker: Checks if entity is deprecated.
isEmpty() - Method in class org.obolibrary.robot.metrics.MeasureResult
isEmpty() - Method in class org.obolibrary.robot.Tuple
isRelationType(String) - Static method in enum org.obolibrary.robot.RelationType
isReverseSort() - Method in class org.obolibrary.robot.export.Column: Get reverse sort for column.
isTautological(OWLAxiom, OWLReasoner, boolean) - Static method in class org.obolibrary.robot.ReasonOperation: Given an OWLAxiom, a tautology checker reasoner, and a boolean, determine if the axiom is a tautology.
isTautology(OWLAxiom) - Static method in class org.obolibrary.robot.metrics.TautologyChecker
isValidCURIE(CharSequence) - Static method in class org.obolibrary.robot.IOHelper: Determine if a string is a CURIE.
iterator() - Method in class org.obolibrary.robot.Tuple

J

JAVA_EXCEPTION - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
JAVA_EXCEPTION_CAUSE - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
JAVA_EXCEPTION_MESSAGE - Static variable in class org.obolibrary.robot.metrics.MetricsLabels

L

left() - Method in class org.obolibrary.robot.Tuple
literalStatements - Variable in class org.obolibrary.robot.checks.Violation
loadOntology(File) - Method in class org.obolibrary.robot.IOHelper: Load an ontology from a File, using a catalog file if available.
loadOntology(File, boolean) - Method in class org.obolibrary.robot.IOHelper: Load an ontology from a File, with option to use a catalog file.
loadOntology(File, File) - Method in class org.obolibrary.robot.IOHelper: Load an ontology from a File, with optional catalog File.
loadOntology(InputStream) - Method in class org.obolibrary.robot.IOHelper: Load an ontology from an InputStream, without a catalog file.
loadOntology(InputStream, String) - Method in class org.obolibrary.robot.IOHelper: Load an ontology from an InputStream with a catalog file.
loadOntology(String) - Method in class org.obolibrary.robot.IOHelper: Load an ontology from a String path, using a catalog file if available.
loadOntology(String, boolean) - Method in class org.obolibrary.robot.IOHelper: Load an ontology from a String path, with option to use catalog file.
loadOntology(String, String) - Method in class org.obolibrary.robot.IOHelper: Load an ontology from a String path, with optional catalog file.
loadOntology(IRI) - Method in class org.obolibrary.robot.IOHelper: Given an ontology IRI, load the ontology from the IRI.
loadOntology(IRI, String) - Method in class org.obolibrary.robot.IOHelper: Given an IRI and a path to a catalog file, load the ontology from the IRI with the catalog.
loadOntology(OWLOntology) - Static method in class org.obolibrary.robot.QueryOperation: Deprecated.
use QueryOperation.loadOntologyAsDataset(OWLOntology) instead.
loadOntology(OWLOntologyManager, OWLOntologyDocumentSource) - Method in class org.obolibrary.robot.IOHelper: Given an ontology manager and a document source, load the ontology from the source using the manager.
loadOntologyAsDataset(OWLOntology) - Static method in class org.obolibrary.robot.QueryOperation: Given an ontology, return a dataset containing that ontology as the only graph.
loadOntologyAsDataset(OWLOntology, boolean) - Static method in class org.obolibrary.robot.QueryOperation: Given an ontology and a boolean indicating if imports should be included as graphs, return a dataset either with just the ontology, or the ontology and its imports as separate graphs.
loadOntologyAsModel(OWLOntology) - Static method in class org.obolibrary.robot.QueryOperation: Given an OWLOntology, return the Model representation of the axioms.
loadToTDBDataset(String, String) - Static method in class org.obolibrary.robot.IOHelper: Given a path to an RDF/XML or TTL file and a RDF language, load the file as the default model of a TDB dataset backed by a directory to improve processing time.
loadTriplesAsDataset(String, String) - Static method in class org.obolibrary.robot.QueryOperation: Deprecated.
moved to IOHelper.loadToTDBDataset(String, String)
LOGICAL_AXIOM_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
LOGICAL_AXIOM_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
LOGICAL_AXIOM_COUNT_REASONER - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
logReport(Logger) - Method in class org.obolibrary.robot.reason.EquivalentClassReasoning: Uses the provided logger to print out the results of the reasoning operation.

M

main(String[]) - Method in class org.obolibrary.robot.PythonOperation: Run a Gateway Server.
makePrefixManager(Map<String, String>) - Static method in class org.obolibrary.robot.IOHelper: Make an OWLAPI DefaultPrefixManager from a map of prefixes.
ManchesterOWLSyntaxObjectHTMLRenderer - Class in org.obolibrary.robot: A version of ManchesterOWLSyntaxObjectRenderer adapted to output named objects as hyperlinks
ManchesterOWLSyntaxObjectHTMLRenderer(Writer, ShortFormProvider) - Constructor for class org.obolibrary.robot.ManchesterOWLSyntaxObjectHTMLRenderer: Initialize the renderer with the given Writer and ShortFormProvider
manchesterParseError - Static variable in class org.obolibrary.robot.TemplateHelper: Error message when a given class expression is not able to be parsed.
materialize(OWLOntology, OWLReasonerFactory, Set<OWLObjectProperty>, Map<String, String>) - Static method in class org.obolibrary.robot.MaterializeOperation: Replace EquivalentClass axioms with weaker SubClassOf axioms.
materialize(OWLOntology, OWLReasonerFactory, Set<OWLObjectProperty>, Map<String, String>, boolean) - Static method in class org.obolibrary.robot.MaterializeOperation: Replace EquivalentClass axioms with weaker SubClassOf axioms.
MaterializeOperation - Class in org.obolibrary.robot: Materialize SubClassOf axioms using Expression Materializing Reasoner.
MaterializeOperation() - Constructor for class org.obolibrary.robot.MaterializeOperation
MAX_AXIOMLENGTH - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
MAX_AXIOMLENGTH_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
MAX_NUM_NAMED_SUPERCLASS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
MAX_NUM_NAMED_SUPERCLASS_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
maybeWriteResult(ResultSet, String, OutputStream) - Static method in class org.obolibrary.robot.QueryOperation: If a result set has results, write to the output stream and return true.
maybeWriteResult(Model, String, OutputStream) - Static method in class org.obolibrary.robot.QueryOperation: If a model has statements, write to the output stream and return true.
maybeWriteResult(MeasureResult, String, File) - Static method in class org.obolibrary.robot.MeasureOperation: If a result set has results, write to the output stream and return true.
measure(OWLOntology, OWLReasonerFactory, String, String, File, Map<String, String>) - Static method in class org.obolibrary.robot.MeasureOperation: Running the measure command
MeasureOperation - Class in org.obolibrary.robot: Compute metrics for the ontology.
MeasureOperation() - Constructor for class org.obolibrary.robot.MeasureOperation
MeasureResult - Class in org.obolibrary.robot.metrics
MeasureResult() - Constructor for class org.obolibrary.robot.metrics.MeasureResult
merge(List<OWLOntology>) - Static method in class org.obolibrary.robot.MergeOperation: Merge one or more ontologies with the default merge options (do not include annotations, do not collapse import closure).
merge(List<OWLOntology>, boolean, boolean) - Static method in class org.obolibrary.robot.MergeOperation: Given one or more ontologies, add all their axioms first ontology, and return the first ontology.
merge(List<OWLOntology>, Map<String, String>) - Static method in class org.obolibrary.robot.MergeOperation: Given one or more ontologies, add all their axioms (including their imports closures) into the first ontology, and return the first ontology.
merge(OWLOntology) - Static method in class org.obolibrary.robot.MergeOperation: Given a single ontology with zero or more imports, add all the imported axioms into the ontology itself, return the modified ontology.
mergeAxiomAnnotations(OWLOntology) - Static method in class org.obolibrary.robot.RepairOperation: Given an ontology, merge the annotations of duplicate axioms to create one axiom with all annotations.
mergeInto(List<OWLOntology>, OWLOntology) - Static method in class org.obolibrary.robot.MergeOperation: Given a list of ontologies and a target ontology, add all the axioms from the listed ontologies and their import closure into the target ontology.
mergeInto(List<OWLOntology>, OWLOntology, boolean) - Static method in class org.obolibrary.robot.MergeOperation: Given one or more ontologies and a target ontology, add all the axioms from the listed ontologies to the target ontology.
mergeInto(List<OWLOntology>, OWLOntology, boolean, boolean) - Static method in class org.obolibrary.robot.MergeOperation: Given a list of ontologies and a target ontology, add all the axioms from the listed ontologies and their import closure into the target ontology.
mergeInto(OWLOntology, OWLOntology) - Static method in class org.obolibrary.robot.MergeOperation: Given a source ontology and a target ontology, add all the axioms from the source ontology and its import closure into the target ontology.
mergeInto(OWLOntology, OWLOntology, boolean) - Static method in class org.obolibrary.robot.MergeOperation: Given a source ontology and a target ontology, add all the axioms from the source ontology and its import closure into the target ontology.
mergeInto(OWLOntology, OWLOntology, boolean, boolean) - Static method in class org.obolibrary.robot.MergeOperation: Given a source ontology and a target ontology, add all the axioms from the source ontology into the target ontology.
MergeOperation - Class in org.obolibrary.robot: Merge multiple ontologies into a single ontology.
MergeOperation() - Constructor for class org.obolibrary.robot.MergeOperation
MetricsLabels - Class in org.obolibrary.robot.metrics
MetricsLabels() - Constructor for class org.obolibrary.robot.metrics.MetricsLabels
MetricsUtils - Class in org.obolibrary.robot.metrics
MetricsUtils() - Constructor for class org.obolibrary.robot.metrics.MetricsUtils
MireotOperation - Class in org.obolibrary.robot: Implements several variations on MIREOT, as first described in "MIREOT: The minimum information to reference an external ontology term" (link).
MireotOperation() - Constructor for class org.obolibrary.robot.MireotOperation
mirror(OWLOntology, File, File) - Static method in class org.obolibrary.robot.MirrorOperation: Mirrors ontologies on local filesystem.
MirrorOperation - Class in org.obolibrary.robot: Mirrors ontologies on filesystem.
MirrorOperation() - Constructor for class org.obolibrary.robot.MirrorOperation
MOST_FRQUENTLY_USED_CONCEPT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
MOST_FRQUENTLY_USED_CONCEPT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
MULTI_INHERITANCE_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
MULTI_INHERITANCE_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels

N

NONE - org.obolibrary.robot.reason.EquivalentClassReasoningMode: Does not allow any detected equivalent classes.
NS_USE_AXIOMS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
NS_USE_AXIOMS_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
NS_USE_SIGNATURE - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
NS_USE_SIGNATURE_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels

O

OBJECT_HTML_RENDERER - org.obolibrary.robot.export.RendererType
OBJECT_PROPERTIES - org.obolibrary.robot.RelationType
OBJECT_RENDERER - org.obolibrary.robot.export.RendererType
OBJPROPERTY_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
OBJPROPERTY_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
ONTOLOGY_ANNOTATIONS_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
ONTOLOGY_ID - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
ONTOLOGY_VERSION_ID - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
OntologyCycleDetector - Class in org.obolibrary.robot.metrics
OntologyCycleDetector() - Constructor for class org.obolibrary.robot.metrics.OntologyCycleDetector
OntologyHelper - Class in org.obolibrary.robot: Provides convenience methods for working with OWL ontologies.
OntologyHelper() - Constructor for class org.obolibrary.robot.OntologyHelper
OntologyLogicException - Exception in org.obolibrary.robot.exceptions: Ontology contains unsatisfiable classes, properties or inconsistencies.
OntologyLogicException() - Constructor for exception org.obolibrary.robot.exceptions.OntologyLogicException: Default constructor
OntologyLogicException(String) - Constructor for exception org.obolibrary.robot.exceptions.OntologyLogicException: Throw a new OntologyLogicException with string message.
OntologyLogicException(Set<? extends OWLEntity>) - Constructor for exception org.obolibrary.robot.exceptions.OntologyLogicException: Throw a new OntologyLogicException with a set of unsatisfiable classes or properties.
OntologyMetrics - Class in org.obolibrary.robot.metrics
OntologyMetrics(OWLOntology) - Constructor for class org.obolibrary.robot.metrics.OntologyMetrics
OntologyMetrics(OWLOntology, CURIEShortFormProvider) - Constructor for class org.obolibrary.robot.metrics.OntologyMetrics
OntologyStructureException - Exception in org.obolibrary.robot.exceptions: Ontology contains contains structure that constitutes an exception
OntologyStructureException() - Constructor for exception org.obolibrary.robot.exceptions.OntologyStructureException
openTDBDataset(String) - Static method in class org.obolibrary.robot.IOHelper: Given a path to a TDB directory, load the TDB as a Dataset.
OptionsHelper - Class in org.obolibrary.robot: Provides convenience methods for getting options.
OptionsHelper() - Constructor for class org.obolibrary.robot.OptionsHelper
org.obolibrary.robot - package org.obolibrary.robot
org.obolibrary.robot.checks - package org.obolibrary.robot.checks
org.obolibrary.robot.exceptions - package org.obolibrary.robot.exceptions
org.obolibrary.robot.export - package org.obolibrary.robot.export
org.obolibrary.robot.metrics - package org.obolibrary.robot.metrics
org.obolibrary.robot.providers - package org.obolibrary.robot.providers
org.obolibrary.robot.reason - package org.obolibrary.robot.reason
OWL_DELEGATE_REASONER_CT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
OWLAPI_VERSION - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
OWLAPILOAD_TS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels

P

PARENTS - org.obolibrary.robot.RelationType
parseContext(String) - Static method in class org.obolibrary.robot.IOHelper: Load a map of prefixes from the "@context" of a JSON-LD string.
parseTerms(String) - Method in class org.obolibrary.robot.IOHelper: Parse a set of IRIs from a space-separated string, ignoring '#' comments.
POSTPROCESSING_TS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
PREPROCESSING_TS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
PREREASONINGOPTIMISATION_TS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
processReport(Report, String, Map<String, String>) - Static method in class org.obolibrary.robot.ReportOperation: Given a Report, an output path, and a map of report options, process the Report results and save the report to the output path.
processSplit(String, String, List<String>) - Static method in class org.obolibrary.robot.TemplateHelper: Deprecated.
TemplateOperation replaced with Template class
PROPERTIES - org.obolibrary.robot.RelationType
put(String, Object) - Method in class org.obolibrary.robot.metrics.MeasureResult: add an individual data item
putMap(String, Map<String, ?>) - Method in class org.obolibrary.robot.metrics.MeasureResult
putSet(String, Set<?>) - Method in class org.obolibrary.robot.metrics.MeasureResult
PythonOperation - Class in org.obolibrary.robot: Starts a gateway server for Py4J to execute ROBOT operations via Python.
PythonOperation() - Constructor for class org.obolibrary.robot.PythonOperation

Q

QueryOperation - Class in org.obolibrary.robot: Query an ontology using SPARQL.
QueryOperation() - Constructor for class org.obolibrary.robot.QueryOperation
QuotedAnnotationValueShortFormProvider - Class in org.obolibrary.robot.providers: A custom AnnotationValueShortFormProvider that surrounds multi-word values with single quotes when returning the short form when quoting is true.
QuotedAnnotationValueShortFormProvider(OWLOntologySetProvider, ShortFormProvider, IRIShortFormProvider, List<OWLAnnotationProperty>, Map<OWLAnnotationProperty, List<String>>) - Constructor for class org.obolibrary.robot.providers.QuotedAnnotationValueShortFormProvider: Constructs a quoted annotation value short form provider.
QuotedEntityChecker - Class in org.obolibrary.robot: A custom OWLEntityChecker that also resolves names inside single and double quotation marks.
QuotedEntityChecker() - Constructor for class org.obolibrary.robot.QuotedEntityChecker

R

RBOX_SIZE - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
RBOX_SIZE_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
readCSV(InputStream) - Static method in class org.obolibrary.robot.IOHelper: Read comma-separated values from a stream to a list of lists of strings.
readCSV(InputStream) - Static method in class org.obolibrary.robot.TemplateHelper: Read comma-separated values from a stream to a list of lists of strings.
readCSV(Reader) - Static method in class org.obolibrary.robot.IOHelper: Read comma-separated values from a reader to a list of lists of strings.
readCSV(Reader) - Static method in class org.obolibrary.robot.TemplateHelper: Read comma-separated values from a reader to a list of lists of strings.
readCSV(String) - Static method in class org.obolibrary.robot.IOHelper: Read comma-separated values from a path to a list of lists of strings.
readCSV(String) - Static method in class org.obolibrary.robot.TemplateHelper: Read comma-separated values from a path to a list of lists of strings.
readTable(String) - Static method in class org.obolibrary.robot.IOHelper: Read a table from a path to a list of lists of strings.
readTable(String) - Static method in class org.obolibrary.robot.TemplateHelper: Read a table from a path to a list of lists of strings.
readTSV(InputStream) - Static method in class org.obolibrary.robot.IOHelper: Read tab-separated values from a stream to a list of lists of strings.
readTSV(InputStream) - Static method in class org.obolibrary.robot.TemplateHelper: Read tab-separated values from a stream to a list of lists of strings.
readTSV(Reader) - Static method in class org.obolibrary.robot.IOHelper: Read tab-separated values from a reader to a list of lists of strings.
readTSV(Reader) - Static method in class org.obolibrary.robot.TemplateHelper: Read tab-separated values from a reader to a list of lists of strings.
readTSV(String) - Static method in class org.obolibrary.robot.IOHelper: Read tab-separated values from a path to a list of lists of strings.
readTSV(String) - Static method in class org.obolibrary.robot.TemplateHelper: Read tab-separated values from a path to a list of lists of strings.
reason() - Method in class org.obolibrary.robot.reason.EquivalentClassReasoning: Uses the reasoner to find all equivalent classes in the ontology, and then adds the axioms that are not allowed the the list of failed axioms.
reason(OWLOntology, OWLReasonerFactory) - Static method in class org.obolibrary.robot.ReasonOperation: Given an ontology and a reasoner factory, return the ontology with inferred axioms added after reasoning.
reason(OWLOntology, OWLReasonerFactory, Map<String, String>) - Static method in class org.obolibrary.robot.ReasonOperation: Given an ontology, a reasoner factory, and a map of options, return the ontology with inferred axioms added after reasoning.
REASONER_DISPOSE_TIME - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REASONER_ID - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REASONER_JAR - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REASONER_TIMEOUT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
ReasonerHelper - Class in org.obolibrary.robot: Provides convenience methods for working with OWL reasoning.
ReasonerHelper() - Constructor for class org.obolibrary.robot.ReasonerHelper
REASONERNAME - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REASONERNAME_CLASS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REASONERVERSION - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REASONING_CONSISTENCY_TIME - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REASONING_DECOMPOSITION_TIME - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REASONING_MODULARREASONING_TIME - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REASONING_POSTROCESSING_TIME - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REASONING_PREPROCESSING_TIME - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REASONING_PREREASONINGOPTIMISATION_TIME - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REASONING_TRAVERSALPHASE_TIME - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
ReasonOperation - Class in org.obolibrary.robot: Reason over an ontology and add axioms.
ReasonOperation() - Constructor for class org.obolibrary.robot.ReasonOperation
reduce(OWLOntology, OWLReasonerFactory) - Static method in class org.obolibrary.robot.ReduceOperation: Remove redundant SubClassOf axioms.
reduce(OWLOntology, OWLReasonerFactory, Map<String, String>) - Static method in class org.obolibrary.robot.ReduceOperation: Remove redundant SubClassOf axioms.
ReduceOperation - Class in org.obolibrary.robot: Reason over an ontology and remove redundant SubClassOf axioms
ReduceOperation() - Constructor for class org.obolibrary.robot.ReduceOperation
REF_CLASS_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REF_CLASS_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REF_DATAPROP_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REF_DATAPROP_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REF_INDIV_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REF_INDIV_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REF_OBJPROP_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
REF_OBJPROP_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
RelatedObjectsHelper - Class in org.obolibrary.robot: Convenience methods to get related entities for a set of IRIs.
RelatedObjectsHelper() - Constructor for class org.obolibrary.robot.RelatedObjectsHelper
RelationType - Enum in org.obolibrary.robot: Enum containing all possible relation types.
relax(OWLOntology, Map<String, String>) - Static method in class org.obolibrary.robot.RelaxOperation: Replace EquivalentClass axioms with weaker SubClassOf axioms.
RelaxOperation - Class in org.obolibrary.robot: Add additional SubClassOf axioms that are relaxed forms of equivalence axioms.
RelaxOperation() - Constructor for class org.obolibrary.robot.RelaxOperation
remove(Object) - Method in class org.obolibrary.robot.Tuple
removeAll(Collection) - Method in class org.obolibrary.robot.Tuple
removeImports(OWLOntology) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, remove the import declarations.
removeOntologyAnnotations(OWLOntology) - Static method in class org.obolibrary.robot.OntologyHelper: Remove all annotations on this ontology.
removeRedundantSubClassAxioms(OWLReasoner) - Static method in class org.obolibrary.robot.ReasonOperation: Remove subClassAxioms where there is a more direct axiom, and the subClassAxiom does not have any annotations.
removeRedundantSubClassAxioms(OWLReasoner, Map<String, String>) - Static method in class org.obolibrary.robot.ReasonOperation: Remove subClassAxioms where there is a more direct axiom, and the subClassAxiom does not have any annotations.
renameFull(OWLOntology, IOHelper, Map<String, String>) - Static method in class org.obolibrary.robot.RenameOperation: Given an ontology, an IOHelper, and a map of old IRIs to new IRIs, rename each old IRI with the new IRI.
renameFull(OWLOntology, IOHelper, Map<String, String>, boolean) - Static method in class org.obolibrary.robot.RenameOperation: Given an ontology, an IOHelper, and a map of old IRIs to new IRIs, rename each old IRI with the new IRI.
renameFull(OWLOntology, IOHelper, Map<String, String>, Map<IRI, String>, boolean) - Static method in class org.obolibrary.robot.RenameOperation: Given an ontology, an IOHelper, and a map of old IRIs to new IRIs, rename each old IRI with the new IRI.
RenameOperation - Class in org.obolibrary.robot: Rename entity IRIs in an ontology.
RenameOperation() - Constructor for class org.obolibrary.robot.RenameOperation
renamePrefixes(OWLOntology, IOHelper, Map<String, String>) - Static method in class org.obolibrary.robot.RenameOperation: Given an ontology, an IOHelper, and a map of old IRI bases to new IRI bases, rename each IRI with the 'old base' as a prefix, replacing it with the 'new base'.
renderAxiomImpactSummary(Map<OWLAxiom, Integer>, OWLOntology, OWLOntologyManager) - Static method in class org.obolibrary.robot.ExplainOperation
RendererType - Enum in org.obolibrary.robot.export
renderExplanationAsMarkdown(Explanation<OWLAxiom>, OWLOntologyManager) - Static method in class org.obolibrary.robot.ExplainOperation: Render an Explanation object as Markdown text, linking text labels to term IRIs and indenting axioms.
renderManchester(OWLObject, ShortFormProvider) - Static method in class org.obolibrary.robot.OntologyHelper: Render a Manchester string for an OWLObject.
renderManchester(OWLObject, ShortFormProvider, RendererType) - Static method in class org.obolibrary.robot.OntologyHelper: Render a Manchester string for an OWLObject.
repair(OWLOntology, IOHelper) - Static method in class org.obolibrary.robot.RepairOperation: Repairs ontology
repair(OWLOntology, IOHelper, boolean) - Static method in class org.obolibrary.robot.RepairOperation: Repairs ontology
repair(OWLOntology, IOHelper, boolean, Set<OWLAnnotationProperty>) - Static method in class org.obolibrary.robot.RepairOperation: Repairs ontology
repair(OWLOntology, IOHelper, Map<String, String>) - Static method in class org.obolibrary.robot.RepairOperation: Repairs ontology
repair(OWLOntology, IOHelper, Map<String, String>, boolean) - Static method in class org.obolibrary.robot.RepairOperation: Repairs ontology
repair(OWLOntology, IOHelper, Map<String, String>, boolean, Set<OWLAnnotationProperty>) - Static method in class org.obolibrary.robot.RepairOperation: Repairs ontology
repairInvalidReferences(IOHelper, OWLOntology, Set<InvalidReferenceViolation>) - Static method in class org.obolibrary.robot.RepairOperation: Repairs invalid references
repairInvalidReferences(IOHelper, OWLOntology, Set<InvalidReferenceViolation>, Set<OWLAnnotationProperty>) - Static method in class org.obolibrary.robot.RepairOperation: Repairs invalid references
RepairOperation - Class in org.obolibrary.robot: Repair an ontology
RepairOperation() - Constructor for class org.obolibrary.robot.RepairOperation
report(OWLOntology, String, String, String, String) - Static method in class org.obolibrary.robot.ReportOperation: Given an ontology, a profile path (or null), an output path (or null), and a report format (or null) report on the ontology using the rules within the profile and write results to the output path.
report(OWLOntology, IOHelper) - Static method in class org.obolibrary.robot.ReportOperation: Report on the ontology using the rules within the profile and print results.
report(OWLOntology, IOHelper, String, String, String, String) - Static method in class org.obolibrary.robot.ReportOperation: Given an ontology, an IOHelper, a profile path (or null), an output path (or null), a report format (or null), and a level to fail on, report on the ontology using the rules within the profile and write results to the output path.
report(OWLOntology, IOHelper, String, String, String, String, boolean) - Static method in class org.obolibrary.robot.ReportOperation: Given an ontology, an IOHelper, a profile path (or null), an output path (or null), a report format (or null), a level to fail on, and a boolean indicating to use labels, report on the ontology using the rules within the profile and write results to the output path.
report(OWLOntology, IOHelper, String, Map<String, String>) - Static method in class org.obolibrary.robot.ReportOperation: Given an ontology, an IOHelper, an output path (or null), and a map of options (or null), report on the ontology using the rules within the profile specified by the options and write results to the output path.
report(OWLOntology, IOHelper, Map<String, String>) - Static method in class org.obolibrary.robot.ReportOperation: Report on the ontology using the rules within the profile and print results.
Report - Class in org.obolibrary.robot.checks
Report() - Constructor for class org.obolibrary.robot.checks.Report: Create a new report object without an ontology or predefined IOHelper.
Report(Map<IRI, String>) - Constructor for class org.obolibrary.robot.checks.Report: Create a new report object with a QuotedEntityChecker loaded with entries from the label map.
Report(OWLOntology) - Constructor for class org.obolibrary.robot.checks.Report: Deprecated.
Report will not do anything with the ontology when not using labels. Use either Report() or Report(OWLOntology, boolean) or Report(OWLOntology, IOHelper, boolean).
Report(OWLOntology, boolean) - Constructor for class org.obolibrary.robot.checks.Report: Create a new report object with an ontology (maybe) using labels for output.
Report(OWLOntology, IOHelper) - Constructor for class org.obolibrary.robot.checks.Report: Deprecated.
Report will not do anything with the ontology when not using labels. Use either Report(OWLOntology, boolean) or Report(OWLOntology, IOHelper, boolean).
Report(OWLOntology, IOHelper, boolean) - Constructor for class org.obolibrary.robot.checks.Report: Create a new report object with an ontology to (maybe) get labels from and a defined IOHelper.
ReportOperation - Class in org.obolibrary.robot: Report issues with an ontology using a series of QC SPARQL queries.
ReportOperation() - Constructor for class org.obolibrary.robot.ReportOperation
ReportQuery - Class in org.obolibrary.robot.checks
ReportQuery(String, String, String) - Constructor for class org.obolibrary.robot.checks.ReportQuery: Create a new ReportQuery object.
ReportQuery(String, String, String, String) - Constructor for class org.obolibrary.robot.checks.ReportQuery: Create a new ReportQuery object.
retainAll(Collection) - Method in class org.obolibrary.robot.Tuple
right() - Method in class org.obolibrary.robot.Tuple
Row - Class in org.obolibrary.robot.export
Row() - Constructor for class org.obolibrary.robot.export.Row: Init a new Row.
Row(String) - Constructor for class org.obolibrary.robot.export.Row: Init a new Row for a Report with a violation level.
Row(IRI) - Constructor for class org.obolibrary.robot.export.Row: Init a new Row with a subject.
rowNum - Variable in exception org.obolibrary.robot.exceptions.RowParseException
RowParseException - Exception in org.obolibrary.robot.exceptions: Template row cannot be parsed.
RowParseException(String) - Constructor for exception org.obolibrary.robot.exceptions.RowParseException: Throw new RowParseException with message.
RowParseException(String, int, int, String) - Constructor for exception org.obolibrary.robot.exceptions.RowParseException: Throw a new RowParseException with message and location.
RowParseException(String, Exception) - Constructor for exception org.obolibrary.robot.exceptions.RowParseException: Throw new RowParseException with message amd cause.
RULE_CT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
RULE_CT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
ruleID - Variable in exception org.obolibrary.robot.exceptions.RowParseException
ruleName - Variable in exception org.obolibrary.robot.exceptions.RowParseException
run(Integer) - Static method in class org.obolibrary.robot.PythonOperation: Run a Gateway Server.
runConstruct(Dataset, String, File, Lang) - Static method in class org.obolibrary.robot.QueryOperation: Run a CONSTRUCT query and write the result to a file.
RUNID - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
runQuery(Dataset, String, File, Lang) - Static method in class org.obolibrary.robot.QueryOperation: Run a SELECT query on a dataset and write the result to a file.
runQuery(DatasetGraph, String, File, Lang) - Static method in class org.obolibrary.robot.QueryOperation: Deprecated.
use QueryOperation.runQuery(Dataset, String, File, Lang) instead.
runSparqlQuery(Dataset, String, String, OutputStream) - Static method in class org.obolibrary.robot.QueryOperation: Given a dataset, a query string, a format name, and an output stream, run the SPARQL query over the named graphs and write the output to the stream.
runSparqlQuery(QueryExecution, String, OutputStream) - Static method in class org.obolibrary.robot.QueryOperation: Given a query execution, a format name, and an output stream, run the query and write to output.
runSparqlQuery(DatasetGraph, String, String, OutputStream) - Static method in class org.obolibrary.robot.QueryOperation: Deprecated.
use QueryOperation.runSparqlQuery(Dataset, String, String, OutputStream) instead.
runUpdate(Model, String, File, Lang) - Static method in class org.obolibrary.robot.QueryOperation: Given a Model, a SPARQL update string, an output stream, and the output format, update the model and write it to the output.
runVerify(Dataset, String, String, Path, Lang) - Static method in class org.obolibrary.robot.QueryOperation: Run a SELECT query over the union of named graphs in a dataset and write the result to a file.
runVerify(DatasetGraph, String, String, Path, Lang) - Static method in class org.obolibrary.robot.QueryOperation: Deprecated.
use QueryOperation.runVerify(Dataset, String, String, Path, Lang) instead.

S

saveContext(File) - Method in class org.obolibrary.robot.IOHelper: Write the current context as a JSON-LD file.
saveContext(String) - Method in class org.obolibrary.robot.IOHelper: Write the current context as a JSON-LD file.
saveOntology(OWLOntology, File) - Method in class org.obolibrary.robot.IOHelper: Save an ontology to a File.
saveOntology(OWLOntology, String) - Method in class org.obolibrary.robot.IOHelper: Save an ontology to a String path.
saveOntology(OWLOntology, IRI) - Method in class org.obolibrary.robot.IOHelper: Save an ontology to an IRI, using the file extension to determine the format.
saveOntology(OWLOntology, OWLDocumentFormat, File) - Method in class org.obolibrary.robot.IOHelper: Save an ontology in the given format to a file.
saveOntology(OWLOntology, OWLDocumentFormat, File, boolean) - Method in class org.obolibrary.robot.IOHelper: Save an ontology in the given format to a file, with the option to ignore OBO document checks.
saveOntology(OWLOntology, OWLDocumentFormat, String, boolean) - Method in class org.obolibrary.robot.IOHelper: Save an ontology in the given format to a path, with the option to ignore OBO document checks.
saveOntology(OWLOntology, OWLDocumentFormat, IRI) - Method in class org.obolibrary.robot.IOHelper: Save an ontology in the given format to an IRI.
saveOntology(OWLOntology, OWLDocumentFormat, IRI, boolean) - Method in class org.obolibrary.robot.IOHelper: Save an ontology in the given format to an IRI, with the option to ignore OBO document checks.
saveOntology(OWLOntology, OWLDocumentFormat, IRI, Map<String, String>, boolean) - Method in class org.obolibrary.robot.IOHelper: Save an ontology in the given format to an IRI, with option to add prefixes and option to ignore OBO document checks.
saveTable(Table, String, Map<String, String>) - Static method in class org.obolibrary.robot.ExportOperation: Save the Table object as: csv, tsv, html, json, or xlsx.
select(OWLOntology, IOHelper, Set<OWLObject>, String) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology, a set of objects, and a selector, return the related objects related to the set of OWL objects based on the selector.
select(OWLOntology, IOHelper, Set<OWLObject>, List<String>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology, a set of objects, and a list of selector strings, return the objects related to the set of OWLObjects based on the set of selectors.
selectAncestors(OWLOntology, Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology and a set of objects, return all ancestors (recursively) of those objects.
selectAnnotationProperties(Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given a set of objects, return a set of annotation properties from the starting set.
selectAnonymous(Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given a set of objects, return a set of anonymous objects from the starting set.
selectChildren(OWLOntology, Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology and a set of objects, return the children of the starting set.
selectClasses(Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given a set of objects, return a set of OWLClasses from the starting set.
selectComplement(OWLOntology, Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology and a set of objects, return all objects contained in the ontology that are NOT in the starting set.
selectCURIE(IOHelper, Set<OWLObject>, String) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an IOHelper, a set of objects, and a selector string for CURIE pattern, return a set of objects matching that CURIE pattern.
selectDataProperties(Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given a set of objects, return a set of OWLDataProperties from the starting set.
selectDescendants(OWLOntology, Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology and a set of objects, return all descendants (recursively) of those objects.
selectDomains(OWLOntology, Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology and a set of objects, return all domains of any properties in the set.
selectEquivalents(OWLOntology, Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology and a set of objects, return all equivalent objects of the starting set.
selectGroups(OWLOntology, IOHelper, Set<OWLObject>, List<List<String>>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology, a set of objects, and a list of select groups (as lists), return the objects related to the set of OWLObjects based on each set of selectors.
selectIndividuals(Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given a set of objects, return a set of OWLIndividuals from the starting set.
selectInstances(OWLOntology, Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology and a set of objects, select all the instances of the classes in the set of objects.
selectIRI(Set<OWLObject>, String) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given a set of objects, and a selector string (IRI pattern in angle brackets), select all the objects that have an IRI matching that pattern.
selectNamed(Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given a set of objects, return a set of named objects from the starting set.
selectObjectProperties(Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given a set of objects, return a set of OWLObjectProperties from the starting set.
selectParents(OWLOntology, Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology and a set of objects, return the parent objects of all objects in the set.
selectPattern(OWLOntology, IOHelper, Set<OWLObject>, String) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology, a set of objects, and a pattern to match annotations to, return a set of objects that are annotated with the matching annotation.
selectProperties(Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given a set of objects, return a set of all OWLProperties from the starting set.
selectRanges(OWLOntology, Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology and a set of objects, return all ranges of any properties in the set.
selectTypes(OWLOntology, Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology and a set of objects, return a set of all the types of the individuals in that set.
SELF - org.obolibrary.robot.RelationType
setAnnotateExpansionAxioms(boolean) - Method in class org.obolibrary.robot.ExpandOperation.ExpandConfig
setCellColor(IndexedColors) - Method in class org.obolibrary.robot.export.Cell: Set the cell background color for this cell in an XLSX workbook.
setCellPattern(FillPatternType) - Method in class org.obolibrary.robot.export.Cell: Set the cell background pattern for this cell in an XLSX workbook.
setComment(String) - Method in class org.obolibrary.robot.export.Cell: Add a comment to this Cell.
setContext() - Method in class org.obolibrary.robot.IOHelper: Set an empty context.
setContext(Context) - Method in class org.obolibrary.robot.IOHelper: Set the current JSON-LD context to the given context.
setContext(String) - Method in class org.obolibrary.robot.IOHelper: Set the current JSON-LD context to the given context.
setContext(Map<String, Object>) - Method in class org.obolibrary.robot.IOHelper: Set the current JSON-LD context to the given map.
setCreateNewOntology(boolean) - Method in class org.obolibrary.robot.ExpandOperation.ExpandConfig
setExcludeProperties(Set<IRI>) - Method in class org.obolibrary.robot.ExpandOperation.ExpandConfig
setExpandProperties(Set<IRI>) - Method in class org.obolibrary.robot.ExpandOperation.ExpandConfig
setFontColor(IndexedColors) - Method in class org.obolibrary.robot.export.Cell: Set the font color for this cell in an XLSX workbook.
setHref(String) - Method in class org.obolibrary.robot.export.Cell: Add a link to this Cell.
setHTMLClass(String) - Method in class org.obolibrary.robot.export.Cell: Add an HTML class to this Cell.
setIOHelper(IOHelper) - Method in class org.obolibrary.robot.QuotedEntityChecker: Add an IOHelper for resolving names to IRIs.
setOntologyIRI(OWLOntology, String, String) - Static method in class org.obolibrary.robot.OntologyHelper: Set the ontology IRI and version IRI using strings.
setOntologyIRI(OWLOntology, IRI, IRI) - Static method in class org.obolibrary.robot.OntologyHelper: Set the ontology IRI and version IRI.
setPrefixes(Map<String, Object>) - Method in class org.obolibrary.robot.IOHelper: Set the current prefix map.
setSort(int) - Method in class org.obolibrary.robot.export.Column: Set the sort order for this column.
setSort(int, boolean) - Method in class org.obolibrary.robot.export.Column: Set the sort order for this column and if it should be sorted in reverse.
setSortColumns() - Method in class org.obolibrary.robot.export.Table: Once all Columns have been added to a Table, set the columns to sort on.
setStrict(Boolean) - Method in class org.obolibrary.robot.IOHelper: Set "strict" value.
setXMLEntityFlag(Boolean) - Method in class org.obolibrary.robot.IOHelper: Set whether or not XML entities will be swapped into URIs in saveOntology XML output formats.
SIGNATURE_NO_URIS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
SIGNATURE_SIZE - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
SIGNATURE_SIZE_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
size() - Method in class org.obolibrary.robot.Tuple
sortRows() - Method in class org.obolibrary.robot.export.Table: Once all Rows have been added to a Table, sort Rows based on the sort Columns.
spanGaps(OWLOntology, List<String>, Set<OWLObject>, boolean, boolean, boolean) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology and a set of objects, construct a set of subClassOf axioms that span the gaps between classes to maintain a hierarchy.
spanGaps(OWLOntology, Set<OWLObject>) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology and a set of objects, construct a set of subClassOf axioms that span the gaps between classes to maintain a hierarchy.
spanGaps(OWLOntology, Set<OWLObject>, boolean) - Static method in class org.obolibrary.robot.RelatedObjectsHelper: Given an ontology and a set of objects, construct a set of subClassOf axioms that span the gaps between classes to maintain a hierarchy.
startElement(String, String, String, Attributes) - Method in class org.obolibrary.robot.CatalogElementHandler: Handle startElement events by looking for 'uri' elements, and their 'name' and 'uri' attributes, and updating 'mappings'.
STARTPROCESS_TS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
statements - Variable in class org.obolibrary.robot.checks.Violation
STRIPPED_AXIOMTYPES - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
subject - Variable in class org.obolibrary.robot.checks.Violation
SUBSUMPTIONS_ATOMIC_AVOIDED - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
SUBSUMPTIONS_ATOMIC_AVOIDED_REASONER - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
SUBSUMPTIONS_ATOMIC_POSSIBLE - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
SUBSUMPTIONS_ATOMIC_REASONER - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
SUBSUMPTIONS_ATOMIC_REDUNDANT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
SYNTAX - Static variable in class org.obolibrary.robot.metrics.MetricsLabels

T

Table - Class in org.obolibrary.robot.export
Table() - Constructor for class org.obolibrary.robot.export.Table: Init a new Table.
Table(String) - Constructor for class org.obolibrary.robot.export.Table: Init a new Table with a format.
TautologyChecker - Class in org.obolibrary.robot.metrics
TautologyChecker() - Constructor for class org.obolibrary.robot.metrics.TautologyChecker
TAUTOLOGYCOUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
TAUTOLOGYCOUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
TBOX_CONTAINS_NOMINALS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
TBOX_CONTAINS_NOMINALS_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
TBOX_SIZE - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
TBOX_SIZE_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
TBOXRBOX_SIZE - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
TBOXRBOX_SIZE_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
tdbReport(String, String, Map<String, String>) - Static method in class org.obolibrary.robot.ReportOperation: Given an input path, an output path (or null), and a map of options, report on the ontology using the rules within the profile specified by the options and write results to the output path.
template(Map<String, List<List<String>>>) - Static method in class org.obolibrary.robot.TemplateOperation: Deprecated.
template(Map<String, List<List<String>>>, OWLOntology) - Static method in class org.obolibrary.robot.TemplateOperation: Deprecated.
template(Map<String, List<List<String>>>, OWLOntology, IOHelper) - Static method in class org.obolibrary.robot.TemplateOperation: Deprecated.
template(Map<String, List<List<String>>>, OWLOntology, QuotedEntityChecker) - Static method in class org.obolibrary.robot.TemplateOperation: Deprecated.
template(Map<String, List<List<String>>>, OWLOntology, QuotedEntityChecker, IOHelper) - Static method in class org.obolibrary.robot.TemplateOperation: Deprecated.
template(OWLOntology, IOHelper, String, List<List<String>>) - Static method in class org.obolibrary.robot.TemplateOperation: Given an OWLOntology, an IOHelper, a table name, and the table contents, use the table as the template to generate an output OWLOntology.
template(OWLOntology, IOHelper, String, List<List<String>>, Map<String, String>) - Static method in class org.obolibrary.robot.TemplateOperation: Given an OWLOntology, an IOHelper, a table name, the table contents, and a map of template options, use the table as the template to generate an output OWLOntology.
template(OWLOntology, IOHelper, Map<String, List<List<String>>>, Map<String, String>) - Static method in class org.obolibrary.robot.TemplateOperation: Given an OWLOntology, an IOHelper, a map of table names to table contents, and a map of template options, use the tables as templates to generate a merged output ontology.
Template - Class in org.obolibrary.robot
Template(String, List<List<String>>) - Constructor for class org.obolibrary.robot.Template: Given a template name and a list of rows, create a template object with a new IOHelper and QuotedEntityChecker.
Template(String, List<List<String>>, IOHelper) - Constructor for class org.obolibrary.robot.Template: Given a template name, a list of rows, and an IOHelper, create a template object with a new QuotedEntityChecker.
Template(String, List<List<String>>, OWLOntology) - Constructor for class org.obolibrary.robot.Template: Given a template name, a list of rows, and an input ontology, create a template object with a new IOHelper and QuotedEntityChecker populated by the input ontology.
Template(String, List<List<String>>, OWLOntology, IOHelper) - Constructor for class org.obolibrary.robot.Template: Given a template name, a list of rows, an input ontology, and an IOHelper, create a template object with a new QuotedEntityChecker with the IOHelper populated by the input ontology.
Template(String, List<List<String>>, OWLOntology, IOHelper, QuotedEntityChecker) - Constructor for class org.obolibrary.robot.Template: Given a template name, a list of rows, an IOHelper, and a QuotedEntityChecker, create a template object.
TemplateHelper - Class in org.obolibrary.robot: Convenience methods for working with templates.
TemplateHelper() - Constructor for class org.obolibrary.robot.TemplateHelper
TemplateOperation - Class in org.obolibrary.robot: Generate OWL from tables.
TemplateOperation() - Constructor for class org.obolibrary.robot.TemplateOperation
toArray() - Method in class org.obolibrary.robot.Tuple
toArray(Object[]) - Method in class org.obolibrary.robot.Tuple
toArray(List<Column>, String) - Method in class org.obolibrary.robot.export.Row: Render the Row as an array.
toCSV() - Method in class org.obolibrary.robot.checks.Report: Deprecated.
toggleQuoting() - Method in class org.obolibrary.robot.providers.QuotedAnnotationValueShortFormProvider: Turn quoting on or off.
toHTML(String) - Method in class org.obolibrary.robot.export.Table: Render the Table as an HTML string.
toHTML(String, boolean) - Method in class org.obolibrary.robot.export.Table: Render the Table as an HTML string.
toHTML(String, boolean, boolean) - Method in class org.obolibrary.robot.export.Table: Render the Table as an HTML string.
toHTML(List<Column>, String) - Method in class org.obolibrary.robot.export.Row: Render the Row as a row in an HTML table.
toHTMLList() - Method in class org.obolibrary.robot.export.Table
toHTMLList(List<Column>) - Method in class org.obolibrary.robot.export.Row: Convert a row into an item in an HTML list.
toJSON() - Method in class org.obolibrary.robot.checks.Report: Return the report in JSON format.
toJSON() - Method in class org.obolibrary.robot.export.Table: Render the Table as a JSON string.
toJSON(List<Column>) - Method in class org.obolibrary.robot.export.Row: Render the Row as a JsonObject
toList(String) - Method in class org.obolibrary.robot.export.Table: Render the Table as List of Arrays for writing to CSV/TSV.
toString() - Method in class org.obolibrary.robot.checks.InvalidReferenceViolation
toString() - Method in enum org.obolibrary.robot.RelationType: Return the name of the RelationType.
toTable(String) - Method in class org.obolibrary.robot.checks.Report: Convert the report details to a Table object to save.
toTSV() - Method in class org.obolibrary.robot.checks.Report: Deprecated.
toYAML() - Method in class org.obolibrary.robot.checks.Report: Return the report in YAML format.
toYAML() - Method in class org.obolibrary.robot.export.Table: Render the Table as a YAML string.
TRAVERSAL_TS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
trimOntology(OWLOntology) - Static method in class org.obolibrary.robot.OntologyHelper: Given an ontology, remove any dangling entities.
tryParse(String, QuotedEntityChecker, ManchesterOWLSyntaxClassExpressionParser, String, int, int) - Static method in class org.obolibrary.robot.TemplateHelper: Given a Quoted Entity Checker to resolve labels, a Manchester class expression parser, and a content string, try to parse the content string.
tryParse(String, ManchesterOWLSyntaxClassExpressionParser, String, int, int) - Static method in class org.obolibrary.robot.TemplateHelper: Given a Manchester class expression parser and a content string, try to parse the content string.
Tuple<A,B> - Class in org.obolibrary.robot: Created by edouglass on 8/14/17.
TYPES - org.obolibrary.robot.RelationType

U

UNDECLARED_ENTITY_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
UNDECLARED_ENTITY_COUNT_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
unmerge(List<OWLOntology>) - Static method in class org.obolibrary.robot.UnmergeOperation: Given one or more ontologies, remove all the axioms from the listed ontologies and their import closure from the first ontology, and return the first ontology
unmergeFrom(List<OWLOntology>, OWLOntology) - Static method in class org.obolibrary.robot.UnmergeOperation: Given a list of ontologies and a target ontology, remove all the axioms from the listed ontologies and their import closure from the target ontology.
unmergeFrom(List<OWLOntology>, OWLOntology, boolean) - Static method in class org.obolibrary.robot.UnmergeOperation: Given a list of ontologies and a target ontology, remove all the axioms from the listed ontologies and their import closure from the target ontology.
unmergeFrom(OWLOntology, OWLOntology) - Static method in class org.obolibrary.robot.UnmergeOperation: Given a source ontology and a target ontology, remove all the axioms from the listed ontologies and their import closure from the target ontology.
unmergeFrom(OWLOntology, OWLOntology, boolean) - Static method in class org.obolibrary.robot.UnmergeOperation: Given a source ontology and a target ontology, remove all the axioms from the listed ontologies and their import closure from the target ontology.
UnmergeOperation - Class in org.obolibrary.robot: Remove axioms from an ontology.
UnmergeOperation() - Constructor for class org.obolibrary.robot.UnmergeOperation
UNSATISFIABLECLASSES - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
UNSATISFIABLECLASSES_COUNT - Static variable in class org.obolibrary.robot.metrics.MetricsLabels

V

VALID_IMPORTS - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
VALID_IMPORTS_INCL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
validate(OWLReasoner) - Static method in class org.obolibrary.robot.ReasonerHelper: Validates ontology.
validate(OWLReasoner, String) - Static method in class org.obolibrary.robot.ReasonerHelper: Validates ontology.
validate(OWLReasoner, String, IOHelper) - Static method in class org.obolibrary.robot.ReasonerHelper: Validates ontology, writes unsatisfiable module.
validates(String) - Method in enum org.obolibrary.robot.reason.EquivalentClassReasoningMode: Checks if the given string counts as this mode.
validateTemplateString(String) - Static method in class org.obolibrary.robot.TemplateHelper: Return true if the template string is valid, false otherwise.
validateTemplateString(String) - Static method in class org.obolibrary.robot.TemplateOperation: Deprecated.
valueOf(String) - Static method in enum org.obolibrary.robot.checks.InvalidReferenceViolation.Category: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.obolibrary.robot.export.RendererType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.obolibrary.robot.reason.EquivalentClassReasoningMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.obolibrary.robot.RelationType: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.obolibrary.robot.checks.InvalidReferenceViolation.Category: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.obolibrary.robot.export.RendererType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.obolibrary.robot.reason.EquivalentClassReasoningMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.obolibrary.robot.RelationType: Returns an array containing the constants of this enum type, in the order they are declared.
Violation - Class in org.obolibrary.robot.checks
Violation(String) - Constructor for class org.obolibrary.robot.checks.Violation: Create a new Violation object about a String.
Violation(OWLEntity) - Constructor for class org.obolibrary.robot.checks.Violation: Create a new Violation object about an OWL entity.
VIOLATION_PROFILE_OWL2_DL - Static variable in class org.obolibrary.robot.metrics.MetricsLabels
visit(OWLAnnotationProperty) - Method in class org.obolibrary.robot.ManchesterOWLSyntaxObjectHTMLRenderer: Given an OWLAnnotationProperty, write a hyperlink describing it to the writer.
visit(OWLClass) - Method in class org.obolibrary.robot.ManchesterOWLSyntaxObjectHTMLRenderer: Given an OWLClass, write a hyperlink describing it to the writer.
visit(OWLClassExpression) - Method in class org.obolibrary.robot.ManchesterOWLSyntaxObjectHTMLRenderer: Given an OWLClassExpression, determine the particular type of OWLClassExpression that it is, and then call the appropriate visit() function for it.
visit(OWLDataProperty) - Method in class org.obolibrary.robot.ManchesterOWLSyntaxObjectHTMLRenderer: Given an OWLDataProperty, write a hyperlink describing it to the writer.
visit(OWLDatatype) - Method in class org.obolibrary.robot.ManchesterOWLSyntaxObjectHTMLRenderer: Given an OWLDataType, write a hyperlink describing it to the writer.
visit(OWLNamedIndividual) - Method in class org.obolibrary.robot.ManchesterOWLSyntaxObjectHTMLRenderer: Given an OWLNamedIndividual, write a hyperlink describing it to the writer.
visit(OWLObjectProperty) - Method in class org.obolibrary.robot.ManchesterOWLSyntaxObjectHTMLRenderer: Given an OWLObjectProperty, write a hyperlink describing it to the writer.

W

warn - Variable in class org.obolibrary.robot.checks.Report: Deprecated.
warnCountByRule - Variable in class org.obolibrary.robot.checks.Report: Map of rule name to number of violations for WARN level.
wrap(String) - Static method in class org.obolibrary.robot.QuotedEntityChecker: Given a string that may be a name or a class expression, if it starts with quotation mark or parenthesis then return it, if it contains no spaces then return it, otherwise return it wrapped in single quotes.
write(String, String) - Method in class org.obolibrary.robot.export.Table: Given a path and a split character, write the table to a path.
write(String, String, boolean) - Method in class org.obolibrary.robot.export.Table: Given a path, a split character, and boolean if standalone, write the table to a path.
writeCatalog(File, Map<IRI, String>) - Static method in class org.obolibrary.robot.MirrorOperation: Writes a catalog-v001.xml file.
writeResult(boolean, OutputStream) - Static method in class org.obolibrary.robot.QueryOperation: Write a boolean result to an output stream.
writeResult(ResultSet, String, OutputStream) - Static method in class org.obolibrary.robot.QueryOperation: Write a result set to an output stream.
writeResult(ResultSet, Lang, OutputStream) - Static method in class org.obolibrary.robot.QueryOperation: Write a result set to an output stream.
writeResult(Model, String, OutputStream) - Static method in class org.obolibrary.robot.QueryOperation: Write a model to an output stream.
writeResult(Model, Lang, OutputStream) - Static method in class org.obolibrary.robot.QueryOperation: Write a model to an output stream.
writeResult(MeasureResult, String, File) - Static method in class org.obolibrary.robot.MeasureOperation: Write a model to an output stream.
writeTable(List<String[]>, File, char) - Static method in class org.obolibrary.robot.IOHelper: Write a table from a list of arrays.
writeTable(List<String[]>, Writer, char) - Static method in class org.obolibrary.robot.IOHelper: Write a table from a list of arrays.
writeTable(List<String[]>, String) - Static method in class org.obolibrary.robot.IOHelper: Write a table from a list of arrays.
written() - Method in enum org.obolibrary.robot.reason.EquivalentClassReasoningMode: Change mode to command line format.

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