Migrate from version 3.4 and 3.5 to 4.0

Java versions supported:

• Java 7 (minimum)
• Java 8 (compatible)

Other migration tricks and tips

These have been exchanged on the mailing list or kindly provided by other users. Find them here.

List of migration changes:

(This list comes from updating the test package for 3.5 to work with 4.0. It is likely to cover most of the compilation errors that typical client code might see)

• org.coode.owlapi.obo.parser.OBOOntologyFormat renamed to OBODocumentFormat.
• org.coode.owlapi.turtle.TurtleOntologyFormat renamed to TurtleDocumentFormat.
• org.semanticweb.owlapi.io.OWLFunctionalSyntaxOntologyFormat renamed to FunctionalSyntaxDocumentFormat.
• org.semanticweb.owlapi.io.OWLXMLOntologyFormat renamed to OWLXMLDocumentFormat.
• org.semanticweb.owlapi.io.RDFXMLOntologyFormat renamed to RDFXMLDocumentFormat.
• org.semanticweb.owlapi.model.OWLOntologyFormat renamed to OWLDocumentFormat.
• ontology.getOntologyID().getOntologyIRI() returns an Optional now; beware of using it in string concatenations without adding a get() call - the IRIs created will be different.
• cls.getAnnotationAssertionAxioms(ont); change to EntitySearcher.getAnnotationAssertionAxioms(cls, ont);
• cls.getAnnotations(ont); change to EntitySearcher.getAnnotations(cls, ont);
• ont.containsAxiom(axiom, false); change to EntitySearcher.containsAxiom(axiom, ont, false);
• ind.getDataPropertyValues(property, ont); change to EntitySearcher.getDataPropertyValues(ind, property, ont);
• ind.hasObjectPropertyValue(property, value, ont); change to EntitySearcher.hasObjectPropertyValue(ind, property, value, ont);
• ind.hasNegativeObjectPropertyValue(property, value, ont);change toEntitySearcher.hasNegativeObjectPropertyValue(ind, property, value, ont);`
• ind.hasObjectPropertyValue(property, value, ont); change to EntitySearcher.hasObjectPropertyValue(ind, property, value, ont);
• ind.getTypes(ont); change to EntitySearcher.getTypes(ind, ont);
• ind.hasDataPropertyValue(property, value, ont); change to EntitySearcher.hasDataPropertyValue(ind, property, value, ont);
• ind.getObjectPropertyValues(property, ont); change to EntitySearcher.getObjectPropertyValues(ind, property, ont);
• ind.getDataPropertyValues(property, ont); change to EntitySearcher.getDataPropertyValues(ind, property, ont);
• ind.getNegativeDataPropertyValues(property, ont); change to EntitySearcher.getNegativeDataPropertyValues(ind, property, ont);
• ind.hasNegativeDataPropertyValue(property, literal, ont); change to EntitySearcher.hasNegativeDataPropertyValue(ind, property, literal, ont);
• ind.getSameIndividuals(ont); change to EntitySearcher.getSameIndividuals(ind, ont);
• ind.getDifferentIndividuals(ont); change to EntitySearcher.getDifferentIndividuals(ind, ont);
• entity.isDefined(ont); change to EntitySearcher.isDefined(entity, ont);
• cls.getSuperClasses(ont); change to EntitySearcher.getSuperClasses(cls, ont);
• cls.getSubClasses(ont); change to EntitySearcher.getSubClasses(cls, ont);
• cls.getDisjointClasses(ont); change to EntitySearcher.getDisjointClasses(cls, ont);
• cls.getEquivalentClasses(ont); change to EntitySearcher.getEquivalentClasses(cls, ont);
• cls.getIndividuals(ont); change to EntitySearcher.getIndividuals(cls, ont);
• entity.getReferencingAxioms(ont, false); change to EntitySearcher.getReferencingAxioms(entity, ont);
• property.getDisjointProperties(ont); change to EntitySearcher.getDisjointProperties(property, ont);
• property.getSubProperties(ont); change to EntitySearcher.getSubProperties(property, ont);
• property.getEquivalentProperties(ont); change to EntitySearcher.getEquivalentProperties(property, ont);
• property.getSuperProperties(ont); change to EntitySearcher.getSuperProperties(property, ont);
• property.getDomains(ont); change to EntitySearcher.getDomains(property, ont);
• property.getRanges(ont); change to EntitySearcher.getRanges(property, ont);
• property.isFunctional(ont); change to EntitySearcher.isFunctional(property, ont);
• Map<OWLDataPropertyExpression, Set<OWLLiteral>> result = ind.getDataPropertyValues(ont); change to Multimap<OWLDataPropertyExpression, OWLLiteral> result = EntitySearcher.getDataPropertyValues(ind, ont);
• entity.getAnnotationAssertionAxioms(ont); change to EntitySearcher.getAnnotationAssertionAxioms( entity,ont);
• ont.containsAxiomIgnoreAnnotations(axiom, false); change to EntitySearcher.containsAxiomIgnoreAnnotations(axiom, ont, false);
• property.isAsymmetric(ont); change to EntitySearcher.isAsymmetric(property, ont);
• property.isInverseFunctional(ont); change to EntitySearcher.isInverseFunctional(property, ont);
• property.isSymmetric(ont); change to EntitySearcher.isSymmetric(property, ont);
• property.isReflexive(ont); change to EntitySearcher.isReflexive(property, ont);
• property.isIrreflexive(ont); change to EntitySearcher.isIrreflexive(property, ont);
• property.isTransitive(ont); change to EntitySearcher.isTransitive(property, ont);
• property.getInverses(ont); change to EntitySearcher.getInverses(property, ont);
• property.isFunctional(ont); change to EntitySearcher.isFunctional(property, ont);

List of changes by package:

de.uulm.ecs.ai.owlapi.krssparser

Package change: from de.uulm.ecs.ai.owlapi.krssparser to de.uulm.ecs.ai.owlapi.krssparser

class visibility: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser is the main public class. All other clases are package protected.

de.uulm.ecs.ai.owlapi.krssrenderer

Package change: from de.uulm.ecs.ai.owlapi.krssrenderer to org.semanticweb.owlapi.krss2.renderer

method change: KRSS2ObjectRenderer: dropped manager

method visibility: KRSS2ObjectRenderer::write(): protected

method visibility: KRSS2OWLObjectRenderer::write(): protected

method change: KRSS2OWLSyntaxRenderer: dropped manager

method deleted: KRSS2OWLSyntaxRenderer::setOWLOntologyManager()

method change: KRSS2SyntaxRenderer: dropped manager

method deleted: KRSS2SyntaxRenderer::setOWLOntologyManager()

method change: KRSSObjectRenderer: dropped manager

method change: KRSSSyntaxRenderer: dropped manager

org.coode.owl.krssparser

Package change: from org.coode.owl.krssparser to org.semanticweb.owlapi.krss1.parser

class visibility: org.semanticweb.owlapi.krss1.parser.KRSSOWLParser main public class

org.coode.owlapi.functionalparser

Package change: from org.coode.owlapi.functionalparser to org.semanticweb.owlapi.functional.parser

class visibility: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.class main public class

org.coode.owlapi.functionalrenderer

Package change: from org.coode.owlapi.functionalrenderer to org.semanticweb.owlapi.functional.renderer

method change: OWLFunctionalSyntaxRenderer: dropped manager

method deleted: OWLFunctionalSyntaxRenderer::setOWLOntologyManager()

class refactored: OWLObjectRenderer to FunctionalSyntaxObjectRenderer

method visibility: varios write methods in FunctionalSyntaxObjectRenderer are now protected.

org.coode.owlapi.latex

Package change: from org.coode.owlapi.latex to org.semanticweb.owlapi.latex.renderer

method change: LatexRenderer : dropped manager

method deleted: LatexRenderer::setOWLOntologyManager()

org.coode.owlapi.manchesterowlsyntax

Package change: from org.coode.owlapi.manchesterowlsyntax to org.semanticweb.owlapi.mansyntax.parser

class visibility: org.semanticweb.owlapi.mansyntax.parser.ManchesterOWLSyntaxOntologyParser main public class

utils: org.semanticweb.owlapi.util.mansyntax.ManchesterOWLSyntaxParser Manchester parser interface

method removed: ManchesterOWLSyntaxParser::parseClassFrameEOF()

method removed: ManchesterOWLSyntaxParser::parseConstant(): use parseLiteral(null)

method arguments: ManchesterOWLSyntaxParser::parseClassExpressionList() : boolean removed

method removed: ManchesterOWLSyntaxParser::parseClassAxiom() : use parseAxiom()

org.coode.owlapi.obo.parser

Package change: from org.coode.owlapi.obo.parser to org.obolibrary.oboformat.parser

class visibility: org.obolibrary.oboformat.parser.OBOFormatParser main public class

org.coode.owlapi.obo.renderer

Package deleted: org.coode.owlapi.obo.renderer. Use the new obo package org.obolibrary.oboformat

org.coode.owlapi.oboformat

Package change: from org.coode.owlapi.oboformat to org.obolibrary.oboformat.parser

class visibility: org.obolibrary.oboformat.parser.OBOFormatParser main public class

org.coode.owlapi.owlxml.renderer

Package change: from org.coode.owlapi.owlxml.renderer to org.semanticweb.owlapi.owlxml.renderer

method modified: OWLXMLRenderer : manager dropped

method deleted: OWLXMLRenderer::setOntologyManager()

org.coode.owlapi.owlxmlparser

Package change: from org.coode.owlapi.owlxmlparser to org.semanticweb.owlapi.owlxml.parser

class visibility: OWLXMLParser main public class

org.coode.owlapi.rdf.model

Package change: from org.coode.owlapi.rdf.model to org.semanticweb.owlapi.io

org.coode.owlapi.rdf.rdfxml

Package change: from org.coode.owlapi.rdf.rdfxml to org.semanticweb.owlapi.rdf.rdfxml.renderer

method change: RDFXMLNamespaceManager : dropped manager

method change: RDFXMLNamespaceManager::getPrefixes() : return type is Iterable

method change: RDFXMLNamespaceManager::getNamespaces() : return type is Iterable

method deleted: RDFXMLNamespaceManager::getPrefixNamespaceMap()

method change: RDFXMLRenderer : dropped manager

method deleted: RDFXMLRenderer::getOntology()

method deleted: RDFXMLRenderer::getGraph()

org.coode.owlapi.rdf.renderer

Package change: from org.coode.owlapi.rdf.renderer to org.semanticweb.owlapi.rdf

method deleted : RDFRendererBase::getOntology()

method deleted : RDFRendererBase::getGraph()

org.coode.owlapi.rdfxml.parser

Package change: from org.coode.owlapi.rdfxml.parser to org.semanticweb.owlapi.rdf.rdfxml.parser

class visibility: RDFXMLParser main public class

Package change: from org.semanticweb.owlapi.io.RDFOntologyFormat to org.semanticweb.owlapi.formats.RDFOntologyFormat

org.coode.owlapi.turtle

Package change: org.coode.owlapi.turtle to org.semanticweb.owlapi.rdf.turtle.renderer

Package change: All OWLOntologyFormats to org.semanticweb.owlapi.formats

method arguments: TurtleRenderer : dropped manager

method removed: TurtleRenderer::getOntology()

method removed: TurtleRenderer::getGraph()

class refactored: RDFResourceNode to RDFResource

org.coode.string

Package change: org.coode.string to org.semanticweb.owlapi.util

org.coode.xml

Package change: from org.coode.xml to org.semanticweb.owlapi.rdf.rdfxml.renderer

method change: OWLOntologyXMLNamespaceManager : dropped manager, added format

method deleted: XMLWriterFactory::getInstance() : all methods are static

method refactored: XMLWriterImpl::getXMLBaseAsURI() : getXMLBase()

org.obolibrary.macro

method change: AbstractMacroExpansionVisitor : dropped logger

method change: ManchesterSyntaxTool : dropped boolean

org.semanticweb.owlapi.change

org.semanticweb.owlapi.io

Package change: from org.semanticweb.owlapi.vocab.PrefixOWLOntologyFormat to org.semanticweb.owlapi.formats.PrefixOWLOntologyFormat

method change: XMLUtils : private. All methods are static.

class removed: IOProperties : all settings are on OWLOntologyLoaderConfiguration

method change: OWLOntologyDocumentSourceBase::getNextDocumentIRI() : added string argument

class removed: DefaultOntologyFormat

method change: UnparsableOntologyException::isIncludeStackTraceInMessage() :setting moved to OWLOntologyLoaderConfiguration

method change: OWLOntologyDocumentSource constructors : added nullable format and MIME type arguments

class removed: OWLParserFactoryRegistry : Parsers are managed through Guice modules and class path loading

class removed: OWLParserIOException

class removed: OWLParserSAXException

class removed: OWLParserSAXException

class refactored: RDFResource : abstract

method change: RDFParserMetaData : ArrayListMultimap<IRI, Class<?>> added

method change: RDFLiteral::getLiteral() : getLexicalValue()

method removed: OWLRenderer::setOWLOntologyManager()

method changed: OWLParserFactory::createParser() : dropped manager

org.semanticweb.owlapi.metrics

method changed: AbstractOWLMetric : manager dropped, OWLOntology added

method changed: AverageAssertedNamedSuperclassCount : manager dropped, OWLOntology added

method changed: AxiomCount : manager dropped, OWLOntology added

method changed: AxiomCountMetric : manager dropped, OWLOntology added

method visibility: AxiomTypeCountMetricFactory : private. Use Factory method.

method changed: AxiomTypeCountMetricFactory::createMetrics() : manager dropped, OWLOntology added

method changed: AxiomTypeMetric : manager dropped, OWLOntology added

method changed: DLExpressivity : manager dropped, OWLOntology added

method changed: DoubleValuedMetric : manager dropped, OWLOntology added

method changed: GCICount : manager dropped, OWLOntology added

method changed: HiddenGCICount : manager dropped, OWLOntology added

method changed: IntegerValuedMetric : manager dropped, OWLOntology added

method changed: ImportClosureSize : manager dropped, OWLOntology added

method changed: LogicalAxiomCount : manager dropped, OWLOntology added

method changed: MaximumNumberOfNamedSuperclasses : manager dropped, OWLOntology added

method changed: NumberOfClassesWithMultipleInheritance : manager dropped, OWLOntology added

method changed: ObjectCountMetric : manager dropped, OWLOntology added

method changed: ReferencedClassCount : manager dropped, OWLOntology added

method changed: ReferencedDataPropertyCount : manager dropped, OWLOntology added

method changed: UnsatisfiableClassCountMetric : manager dropped

method changed: ReferencedIndividualCount : manager dropped, OWLOntology added

method changed: ReferencedObjectPropertyCount : manager dropped, OWLOntology added

org.semanticweb.owlapi.model

method change: OWLOntologyRenameException : from OWLOntologyChange to OWLOntologyChangeData

class deleted: OWLOntologyManagerProperties

method change: OWLOntologyLoaderConfiguration::getIgnoredImports() : isIgnoredImport()

method change: OWLOntologyLoaderConfiguration::setSilentMissingImportsHandling() : setMissingImportsHandlingStrategy()

method change: OWLOntologyLoaderConfiguration::isSilentMissingImportsHandling() : gettMissingImportsHandlingStrategy()

method refactored: OWLOntologyManager::add/remove/getOntologyFactories() : managed through a PriorityCollection and get/setOntologyFactories()

method refactored: OWLOntologyManager::add/remove/getOntologyStorers() : managed through a PriorityCollection and get/setOntologyStorers()

method refactored: OWLOntologyManager::add/remove/getIRIMappers() : managed through a PriorityCollection and get/setIRIMappers()

method refactored: IRI::getFragment() : use IRI::getRemainder(), IRI::getShortForm(), IRI::prefixedBy()

method arguments: OWLDataFactory::getSWRLRule() : dropped deprecated id

method deleted: IRI::getStart() : use getNamespace()

method refactored: OWLCardinalityRestriction::getProperty() : pushed down to data and object restrictions

method refactored: OWLCardinalityRestriction::getValue() : use getFiller()

method refactored: OWLOntology::applyChange() : return type is no longer a list but an AppliedChange value.

org.semanticweb.owlapi.profiles

Package change: from org.semanticweb.owlapi.profiles to org.semanticweb.owlapi.profiles.violations

interface removed: OWL2DLProfileViolation

interface removed: OWL2ELProfileViolationVisitor

interface removed: OWL2ProfileViolationVisitor

interface removed: OWL2QLProfileViolationVisitor

interface removed: OWL2RLProfileViolationVisitor

method changed: OWLProfileViolation::getDocumetIRI() to getOntologyID()

method removed: OWLProfileViolation::getImportsClosure()

generics: OWLProfileViolation is now generic

method changed: DatatypeIRIAlsoUsedAsClassIRI::getIRI() : getExpression()

method changed: UseOfNonSimplePropertyInObjectHasSelf::getOWLObjectHasSelf() : getExpression()

method changed: UseOfNonSubClassExpression::getOWLClassExpression() : getExpression()

method changed: UseOfNonSuperClassExpression::getOWLClassExpression() : getExpression()

method changed: UseOfObjectOneOfWithMultipleIndividuals::getOWLObjectOneOf() : getExpression()

method changed: UseOfObjectOneOfWithMultipleIndividuals::getIRI() : getExpression()

method changed: UseOfObjectPropertyInverse::getOWLPropertyExpression() : getExpression()

method changed: UseOfPropertyInChainCausesCycle::getOWLObjectProperty() : getExpression()

method changed: UseOfReservedVocabularyForAnnotationPropertyIRI::getOWLAnnotationProperty() : getExpression()

method changed: UseOfReservedVocabularyForClassIRI::getOWLClass() : getExpression()

method changed: UseOfReservedVocabularyForDataPropertyIRI::getOWLDataProperty() : getExpression()

method changed: UseOfReservedVocabularyForIndividualIRI::getOWLNamedIndividual() : getExpression()

method changed: UseOfReservedVocabularyForObjectPropertyIRI::getOWLObjectProperty() : getExpression()

method changed: UseOfUndeclaredObjectProperty::getOWLObjectProperty() : getExpression()

method changed: UseOfNonSimplePropertyInDisjointPropertiesAxiom::getOWLObjectProperty() : getExpression()

method changed: UseOfPropertyInChainCausesCycle::getOWLObjectProperty() : getExpression()

method changed: UseOfUndeclaredDatatype::getDatatype() : getExpression()

method changed: UseOfUnknownDatatype::getDatatype() : getExpression()

method changed: UseOfUndeclaredAnnotationProperty::getOWLAnnotation() : getExpression()

method changed: UseOfUndeclaredAnnotationProperty::getOWLAnnotationProperty() : getExpression()

method changed: UseOfUndeclaredClass::getOWLClass() : getExpression()

method changed: UseOfNonAtomicClassExpression::getOWLClassExpression() : getExpression()

method changed: UseOfNonEquivalentClassExpression::getOWLClassExpression() : getExpression()

method changed: UseOfIllegalClassExpression::getOWLClassExpression() : getExpression()

method changed: UseOfDefinedDatatypeInDatatypeRestriction::getOWLDatatypeRestriction() : getExpression()

method changed: UseOfNonSimplePropertyInCardinalityRestriction::getOWLCardinalityRestriction() : getExpression()

method changed: UseOfUndeclaredDataProperty::getOWLDataProperty() : getExpression()

method changed: UseOfIllegalDataRange::getOWLDataRange() : getExpression()

method changed: UseOfIllegalFacetRestriction::getFacet() : getExpression()

method deleted: UseOfIllegalFacetRestriction::getFacet()

method changed: LexicalNotInLexicalSpace::getLiteral() : getExpression()

method changed: UseOfAnonymousIndividual::getOWLAnonymousIndividual() : getExpression()

method changed: UseOfDataOneOfWithMultipleLiterals::getOWLDataRange() : getExpression()

method deleted: UseOfDataOneOfWithMultipleLiterals::getDataOneOf()

method changed: LastPropertyInChainNotInImposedRange::getOWLSubPropertyChainOfAxiom() : getAxiom()

class changed: OWLProfileViolation is abstract

org.semanticweb.owlapi.rdf.syntax

Package change: from org.semanticweb.owlapi.rdf.syntax to org.semanticweb.owlapi.rdf.rdfxml.parser

org.semanticweb.owlapi.rdf.util

Package change: from org.semanticweb.owlapi.rdf.util to org.semanticweb.owlapi.rdf.rdfxml.parser

org.semanticweb.owlapi.reasoner.impl

method change: NodeFactory : private. All methods are static.

org.semanticweb.owlapi.util

class removed: MultiMap : use Guava Multimap

class removed: OWLDataUtil

class refactored: OWLOntologyChangeVisitorAdapterEx to OWLOntologyChangeVisitorExAdapter

method deleted: OWLOntologyChangeVisitorExAdapter(no args)

class deleted: OWLAxiomTypeProcessor : just use the type already on the axiom

method deleted: EscapeUtils : all methods are static

method changed: ImportsStructureEntitySorter : dropped manager

method changed: ImportsStructureObjectSorter : dropped manager

method changed: DefaultPrefixManager : changed to nullable parameers

method changed: InferredAxiomGenerator::createAxioms() : manager changed to OWLDataFactory

method changed: OWLEntityRemover : dropped manager

class refactored: OWLOntologyURIChanger : OWLOntologyIRIChanger

class refactored: NamespaceUtil : methods to split namespace and local name removed, use IRI methods

method changed: ImportsStructureObjectSorter : dropped manager

method changed: DefaultPRefixManager::addPrefixes() : copyPrefixesFrom()

method changed: AnnotationValueShortFormProvider : OWLAnnotationValueVisitorEx removed

method visibility: CachingBidirectionalShortFormProvider::remove() : protected

method visibility: CachingBidirectionalShortFormProvider::rebuild() : protected

method deleted: CachingBidirectionalShortFormProvider::update()

org.semanticweb.owlapi.vocab

Package change: org.semanticweb.owlapi.vocab.PrefixOWLOntologyFormat to org.semanticweb.owlapi.formats.PrefixOWLOntologyFormat

method deleted: DublinCoreVocabulary::getURI()

method deleted: OWL2Datatype::getURI()

method deleted: OWLRDFVocabulary::getURI()

method deleted: OWLXMLVocabulary::getURI()

method deleted: SWRLVocabulary::getURI()

method deleted: SKOSVocabulary::getURI()

method changed: PrefixOWLOntologyFormat::clearPrefixes() : clear()

method changed: OWL2Datatype::getShortName() : getShortForm()

method changed: OWLRDFVocabulary::getShortName() : getShortForm()

method changed: OWLXMLVocabulary::getShortName() : getShortForm()

method changed: SWRLVocabulary::getShortName() : getShortForm()

method changed: SKOSVocabulary::getShortName() : getShortForm()

method changed: OWLFacet::getShortName() : getShortForm()

method changed: DublinCoreVocabulary::getQName() : getPrefixedName()

method changed: SWRLBuiltInsVocabulary::getShortName() : getShortForm()

method changed: SWRLBuiltInsVocabulary::getArity() : getMinArity(), getMaxArity()

method changed: SWRLBuiltInsVocabulary::getShortName() : getShortForm()

org.semanticweb.owlapi

Package change: from org.semanticweb.owlapi to org.semanticweb.owlapi.change

method changed: AmalgamateSubClassAxioms : arguments swapped

method changed: MakePrimitiveSubClassesMutuallyDisjoint : set of OWLOntology removed

method changed: ShortForm2AnnotationGenerator : add OWLDataFactory

uk.ac.manchester.cs.bhig.util

Package change: from uk.ac.manchester.cs.bhig.util to uk.ac.manchester.cs.owl.explanation.ordering

method removed: MutableTree::replace(MutableTree) : unused

method removed: MutableTree::getSize() : unused

method removed: MutableTree::setParent(MutableTree) : unused

method removed: MutableTree::addChild(MutableTree, Object) : unused

method removed: MutableTree::getEdge(Tree) : unused

method removed: Tree::getEdge(Tree) : unused

method removed: MutableTree::clearChildren() : unused

method removed: MutableTree::getMaxDepth() : unused

uk.ac.manchester.cs.owl.explanation.ordering

class removed: DefaultExplanationOrderer : use ExplanationOrdererImpl

uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer

Package change: from uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer to org.semanticweb.owlapi.mansyntax.renderer

method visibility: AbstractRenderer : protected

method visibility: AbstractRenderer::flush() : protected

method visibility: AbstractRenderer::setUseTabbing() : protected

method visibility: AbstractRenderer::setUseWrapping() : protected

method visibility: AbstractRenderer::isUseWrapping() : protected

method visibility: AbstractRenderer::isUseTabbing() : protected

method visibility: AbstractRenderer : protected

class visibility: SectionMap : private

method arguments: ManchesterOWLSyntaxFrameRenderer : dropped manager, dropped variants

method arguments: ManchesterOWLSyntaxOntologyStorer::storeOntology() : dropped manager from all variants

method arguments: ManchesterOWLSyntaxPrefixNameShortFormProvider : dropped manager

method removed: ManchesterOWLSyntaxPrefixNameShortFormProvider::getPrefixManager() : use methods to access prefixes directly

method arguments: ManchesterOWLSyntaxRenderer : dropped manager

method removed: ManchesterOWLSyntaxRenderer::setOWLOntologyManager(OWLOntologyManager) : use OWLOntology manager

method arguments: ManchesterOWLSyntaxFrameRenderer::writeSection() : SectionMap to Collection

method removed: ManchesterOWLSyntaxFrameRenderer::getOntologies() : SectionMap to Collection

uk.ac.manchester.cs.owl.owlapi.turtle.parser

Package change: from uk.ac.manchester.cs.owl.owlapi.turtle to org.semanticweb.owlapi.rdf.turtle.parser

class visibility: ConsoleTripleHandler : package

class visibility: JavaCharStream : package

Package change: uk.ac.manchester.cs.BOMSafeJavaCharStream to org.semanticweb.owlapi.BOMSafeJavaCharStream

method arguments: TripleHandler::handleBaseDirective() : from String to IRI

method arguments: OWLRDFConsumerAdapter : dropped manager, dropped anonymous node checker

method visibility: OWLRDFConsumerAdapter::getConfiguration() : protected

class visibility: ParseException : package

class visibility: TurtleParserTokenManager : package

class visibility: TurtleParserConstants : package

class visibility: TurtleParserException : package

class visibility: TurtleParser : package

class visibility: Token : package

class visibility: TokenMgrError : package

method visibility: OWLRDFConsumerAdapter::getConfiguration() : protected

method visibility: OWLRDFConsumerAdapter::addTriple() : protected

method visibility: OWLRDFConsumerAdapter::addFirst() : protected

method visibility: OWLRDFConsumerAdapter::translateAnnotations() : protected

method visibility: OWLRDFConsumerAdapter::addOntology() : protected

method visibility: OWLRDFConsumerAdapter::getResourceObject() : protected

method visibility: OWLRDFConsumerAdapter::getLiteralObject() : protected

method visibility: OWLRDFConsumerAdapter::isDataRange() : protected

method visibility: OWLRDFConsumerAdapter::translateDataRange() : protected

method visibility: OWLRDFConsumerAdapter::translateToDataRangeSet() : protected

method visibility: OWLRDFConsumerAdapter::translateToConstantSet() : protected

method removed: OWLRDFConsumerAdapter::addModelAttribte()

method removed: OWLRDFConsumerAdapter::handle()

method visibility: OWLRDFConsumerAdapter::importsClosureChanged() : protected

method visibility: OWLRDFConsumerAdapter::setIRIProvider() : protected

method visibility: OWLRDFConsumerAdapter::setPendingAnnotations() : protected

method visibility: OWLRDFConsumerAdapter::isTriplePresent() : protected

method visibility: OWLRDFConsumerAdapter::translateIndividual() : protected

method visibility: OWLRDFConsumerAdapter::getSynonym() : protected

method visibility: OWLRDFConsumerAdapter::translateDataPropertyExpression() : protected

method visibility: OWLRDFConsumerAdapter::translateObjectPropertyExpression() : protected

method visibility: OWLRDFConsumerAdapter::getPredicatesBySubject() : protected

method visibility: OWLRDFConsumerAdapter::getResourceObjects() : protected

method visibility: OWLRDFConsumerAdapter::getLiteralObjects() : protected

method visibility: OWLRDFConsumerAdapter::hasPredicate() : protected

method visibility: OWLRDFConsumerAdapter::addRest() : protected

method visibility: OWLRDFConsumerAdapter::getFirstResource() : protected

method visibility: OWLRDFConsumerAdapter::getFirstLiteral() : protected

method visibility: OWLRDFConsumerAdapter::getRest() : protected

method visibility: OWLRDFConsumerAdapter::isAxiom() : protected

method visibility: OWLRDFConsumerAdapter::getOntologies() : protected

method visibility: OWLRDFConsumerAdapter::addAxiom() : protected

method visibility: OWLRDFConsumerAdapter::getOntologies() : protected

method removed: OWLRDFConsumerAdapter::translateToFacetRestrictionSet()

method removed: OWLRDFConsumerAdapter::getClassExpressionIfTranslated()

method removed: OWLRDFConsumerAdapter::translateToObjectPropertyList()

method removed: OWLRDFConsumerAdapter::translateToDataPropertyList()

method removed: OWLRDFConsumerAdapter::translateToClassExpressionSet()

method removed: OWLRDFConsumerAdapter::translateToIndividualSet()

method arguments: OWLRDFConsumerAdapter::startModel() : from String to IRI

method arguments: OWLRDFConsumerAdapter::logicalURI() : from String to IRI

method arguments: TurtleOntologyParser::parse() : added OWLOntologyLoaderConfiguration

method removed: TurtleOntologyParser::setOWLOntologyManager()

method removed: TurtleOntologyParser::getOWLOntologyManager()

class removed: TurtleOntologyParserFactory

uk.ac.manchester.cs.owl.owlapi

Class refactored: from uk.ac.manchester.cs.owl.owlapi.Internals.Pointer to uk.ac.manchester.cs.owl.owlapi.MapPointer

Generic types: OWLPropertyExpression no longer generic

Generic types: OWLAxiomSearchFilter no longer generic

class refactored: AbstractInternalsImpl

class refactored: ImplUtils

class removed: OWLOntologyManagerProperties

method removed: OWLOntologyManager::getProperties()

class visibility: InitVisitorFactory : package

method arguments: EmptyInMemOWLOntologyFactory : added OWLOntologyBuilder

method arguments: ParsableOWLOntologyFactory : added OWLOntologyBuilder

method arguments: OWLOntologyFactory::loadOntology() : added OWLOntologyManager, OWLOntologyLoaderConfiguration

method deleted: OWLOntologyFactory::setOWLOntologyManager()

method deleted: OWLOntologyFactory::getOWLOntologyManager()

method arguments: OWLOntologyFactory::createOWLOntology() : added OWLOntologyManager

method arguments: OWLOntologyManager::makeLoadImportRequest() : added OWLOntologyLoaderConfiguration

method deleted: OWL2DatatypeImpl::getDatatype()

method deleted: OWL2DatatypeImpl::getOWLEntity()

generics: OWLNaryAxiom is generic

method changed: OWLOntology::containsReference() : imports flag added

method deleted: OWLDataFactory::getOWLTypedLiteral() : use getOWLLiteral()

method deleted: OWLAnnotation::isComment()

method deleted: OWLAnnotation::isLabel()

method refactored: OWLClass::getSubClassAxioms() : use method on OWLOntology

method refactored: OWLClass::getEquivalentClassesAxioms() : use method on OWLOntology

method refactored: OWLClass::getDisjointClassesAxioms() : use method on OWLOntology

method refactored: OWLClass::getDisjointUnionAxioms() : use method on OWLOntology

method changed: OWLSameIndividualAxiom::asPairwiseSameIndividualAxioms() : asPairwiseAxioms()

method changed: OWLOntology::containsReference() : imports flag added

method changed: OWLOntology::containsObjectPropertyInSignature() : imports flag added

method changed: OWLOntology::containsDataPropertyInSignature() : imports flag added

method changed: OWLOntology::containsClassInSignature() : imports flag added

method changed: OWLOntology::containsEntityInSignature() : imports flag added

method changed: OWLOntology::containsIndividualInSignature() : imports flag added

method changed: OWLOntology::containsAnnotationPropertyInSignature() : imports flag added

method changed: OWLOntology::isDeclared() : imports flag added

method changed: OWLOntology::getObjectPropertiesInSignature() : imports flag added

method changed: OWLOntology::getDataPropertiesInSignature() : imports flag added

method changed: OWLOntology::getClassesInSignature() : imports flag added

method changed: OWLOntology::getEntitiesInSignature() : imports flag added

method changed: OWLOntology::getReferencedAnonymousIndividuals() : imports flag added

method deleted: OWLOntology::getReferencedObjects() : imports flag added

method deleted: OWLOntology::getReferencedAnnotationProperties() : imports flag added

method changed: OWLOntology::getSignature() : imports flag added

method changed: OWLOntology::getIndividualsInSignature() : imports flag added

method changed: OWLOntology::getAnnotationPropertiesInSignature() : imports flag added

method changed: OWLOntology::getTBoxAxioms() : imports flag added

method changed: OWLOntology::getABoxAxioms() : imports flag added

method changed: OWLOntology::getRBoxAxioms() : imports flag added

method refactored: OWLProperty::getSubProperties() : Searcher.sub(ontology.getObjectSubPropertyAxiomsForSuperProperty(superProperty))

method refactored: OWLProperty::getSuperProperties() : Searcher.sup(ontology.getObjectSubPropertyAxiomsForSubProperty(subProperty))

method refactored: OWLClass::getSubClasses() : Searcher.sub(ontology.getSubClassAxiomsForSuperClass(superClass))

method refactored: OWLClass::getSuperClasses() : Searcher.sup(ontology.getSubClassAxiomsForSubClass(subClass))

method refactored: OWLProperty::getDisjointProperties() : Searcher.different(ontology.getDisjointObjectPropertiesAxioms(property))

method refactored: OWLProperty::getDisjointProperties() : Searcher.different(ontology.getDisjointDataPropertiesAxioms(property))

method refactored: OWLClass::getDisjointClassesAxioms() : Searcher.different(ontology.getDisjointClassesAxioms(class))

method refactored: OWLIndividual::getDifferentIndividuals() : Searcher.different(ontology.getDifferentIndividualAxioms(individual))

method refactored: OWLProperty::getEquivalentProperties() : Searcher.different(ontology.getEquivalentObjectPropertiesAxioms(property))

method refactored: OWLProperty::getEquivalentProperties() : Searcher.different(ontology.getEquivalentDataPropertiesAxioms(property))

method refactored: OWLClass::getEquivalentClassesAxioms() : Searcher.different(ontology.getEquivalentClassesAxioms(class))

method refactored: OWLIndividual::getSameIndividuals() : Searcher.different(ontology.getSameIndividualAxioms(individual))

method refactored: OWLObject::getAnnotations() : Searcher.annotations(ontology.getAnnotationAssertionAxioms(annotationSubject))

method refactored: OWLObject::getReferencingAxioms() : OWLOntology::getReferencingAxioms()

method refactored: OWLProperty::getDomains() : Searcher.domain(ontology.getObjectPropertyDomainAxioms(property))

method refactored: OWLProperty::getDomains() : Searcher.domain(ontology.getObjectPropertyRangeAxioms(property))

method refactored: OWLProperty::getRanges() : Searcher.range(ontology.getDataPropertyDomainAxioms(property))

method refactored: OWLProperty::getRanges() : Searcher.range(ontology.getDataPropertyRangeAxioms(property))

method refactored: OWLObject::getTypes() : Searcher.types(ontology.getClassAssertionAxioms(individual))

method refactored: OWLObject::getIndividuals() : Searcher.instances(ontology.getClassAssertionAxioms(class))

method deleted: OWLObject::getOWLEntity()

method refactored: OWLIndividual::getObjectPropertyValues() : Searcher.values(ontology.getObjectPropertyAssertionAxioms(individual), property)

method refactored: OWLIndividual::getNegativeObjectPropertyValues() : Searcher.negValues(ontology.getNegativeObjectPropertyAssertionAxioms(individual), property)

method refactored: OWLIndividual::getDataPropertyValues() : Searcher.values(ontology.getDataPropertyAssertionAxioms(individual), property)

method refactored: OWLIndividual::getNegativeDataPropertyValues() : Searcher.negValues(ontology.getNegativeDataPropertyAssertionAxioms(individual), property)

method refactored: OWLIndividual::hasObjectPropertyValues() : Searcher.values(ontology.getObjectPropertyAssertionAxioms(individual), property).isEmpty()

method refactored: OWLIndividual::hasNegativeObjectPropertyValues() : Searcher.negValues(ontology.getNegativeObjectPropertyAssertionAxioms(individual), property).isEmpty()

method refactored: OWLIndividual::hasDataPropertyValues() : Searcher.values(ontology.getDataPropertyAssertionAxioms(individual), property).isEmpty()

method refactored: OWLIndividual::hasNegativeDataPropertyValues() : Searcher.negValues(ontology.getNegativeDataPropertyAssertionAxioms(individual), property).isEmpty()

method refactored: OWLProperty::isTransitive() : Searcher.isTransitive()

method refactored: OWLProperty::isSymmetric() : Searcher.isSymmetric()

method refactored: OWLProperty::isReflexive() : Searcher.isReflexive()

method refactored: OWLProperty::isIrreflexive() : Searcher.isIrreflexive()

method refactored: OWLProperty::isAsymmetric() : Searcher.isAsymmetric()

method refactored: OWLProperty::isInverseFunctional() : Searcher.isInverseFunctional()

method refactored: OWLProperty::isFunctional() : Searcher.isFunctional()

method refactored: OWLProperty::getInverses() : Searcher.inverses(ontology.getInverseObjectPropertyAxioms(property))

method refactored: OWLClass::isDefined() : Searcher.isDefined()

method refactored: OWLObject::getAnnotationAssertionAxioms() : OWLOntology::getAnnotationAssertionAxioms()

method deleted: OWLOntologyManager::setSilentMissingImportsHandling() : the setting is in OWLOntologyLoaderConfiguration

method deleted: OWLOntologyManager::isSilentMissingImportsHandling() : the setting is in OWLOntologyLoaderConfiguration

method deleted: OWLOntologyManager::getEntities() : use getSignature()

method changed: OWLOntology::getAxioms() : imports flag added

method changed: OWLOntology::getAxiomsCount() : imports flag added

method changed: OWLOntology::containsAxiomIgnoreAnnotations() : use containsAxiom() with imports flag and Search flag

method changed: OWLOntology::getAxiomIgnoreAnnotations() : use getAxiom() with imports flag and Search flag

method deleted: OWLSubClassOfAxiom::contains()

method deleted: OWLSubClassOfAxiom::getClassExpressionsMinus()

method deleted: OWLSubClassOfAxiom::getClassExpressions()

method deleted: OWLOntologyManager::createOntology(IRI, IRI) : pass an OWLOntologyID

uk.ac.manchester.cs.owlapi.dlsyntax.parser

Package change: from uk.ac.manchester.cs.owlapi.dlsyntax.parser to org.semanticweb.owlapi.dlsyntax.parser

new class: DLSyntaxOWLParser : public parser for use in actual parsing

class visibility: JavaCharStream : package

class visibility: ParseException : package

class visibility: DLSyntaxParserTokenManager : package

class visibility: DLSyntaxParser : package

class visibility: DLSyntaxParserConstants : package

class visibility: Token : package

class visibility: Token : TokenMgrError

uk.ac.manchester.cs.owlapi.dlsyntax

Package change: from uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxHTMLOntologyFormat to org.semanticweb.owlapi.formats.DLSyntaxHTMLOntologyFormat

Package change: from uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxOntologyFormat to org.semanticweb.owlapi.formats.DLSyntaxOntologyFormat

Package change: from uk.ac.manchester.cs.owlapi.dlsyntax to org.semanticweb.owlapi.dlsyntax.renderer

method arguments: DLSyntaxHTMLOntologyStorer::storeOntology() : dropped manager

uk.ac.manchester.cs.owlapi.modularity

Enum change: ModuleType.BOT_OF_TOP removed: use STAR

Enum change: ModuleType.TOP_OF_BOT removed: use STAR