Java 类org.semanticweb.owlapi.model.OWLAnonymousIndividual 实例源码

项目：sparql-dl-api 文件：QueryArgument.java

public String getValueAsString() {
    if (value instanceof IRI) {
        return value.toString();
    }
    else if (value instanceof OWLLiteral) {
        return ((OWLLiteral) value).getLiteral();
    }
    else if (value instanceof OWLAnonymousIndividual) {
        return ((OWLAnonymousIndividual) value).getID().toString();
    }
    else if (value instanceof Var) {
        return ((Var) value).getName();
    }
    else {
        return value.toString();
    }
}

项目：minerva 文件：LegoModelWalker.java

private String getStringValue(OWLAnnotationAssertionAxiom ax) {
    OWLAnnotationValue value = ax.getValue();
    String stringValue = value.accept(new OWLAnnotationValueVisitorEx<String>() {

        @Override
        public String visit(IRI iri) {
            return iri.toString();
        }

        @Override
        public String visit(OWLAnonymousIndividual individual) {
            return null;
        }

        @Override
        public String visit(OWLLiteral literal) {
            return literal.getLiteral();
        }
    });
    return stringValue;
}

项目：minerva 文件：JsonTools.java

private static JsonAnnotation create(final String key, OWLAnnotationValue value, final CurieHandler curieHandler) {
    return value.accept(new OWLAnnotationValueVisitorEx<JsonAnnotation>() {

        @Override
        public JsonAnnotation visit(IRI iri) {
            String iriString = curieHandler.getCuri(iri);
            return JsonAnnotation.create(key, iriString, VALUE_TYPE_IRI);
        }

        @Override
        public JsonAnnotation visit(OWLAnonymousIndividual individual) {
            return null; // do nothing
        }

        @Override
        public JsonAnnotation visit(OWLLiteral literal) {
            return JsonAnnotation.create(key, literal.getLiteral(), getType(literal));
        }
    });
}

项目：minerva 文件：CoreMolecularModelManager.java

private static void extractEvidenceIRIValues(OWLAnnotation annotation, final Set<IRI> iriSet) {
    if (annotation != null) {
        OWLAnnotationProperty property = annotation.getProperty();
        if (HAS_EVIDENCE_IRI.equals(property.getIRI()) || HAS_EVIDENCE_IRI_OLD.equals(property.getIRI())){
            annotation.getValue().accept(new OWLAnnotationValueVisitor() {

                @Override
                public void visit(OWLLiteral literal) {
                    // ignore
                }

                @Override
                public void visit(OWLAnonymousIndividual individual) {
                    // ignore
                }

                @Override
                public void visit(IRI iri) {
                    iriSet.add(iri);
                }
            });
        }
    }
}

项目：logmap-matcher 文件：ExtractStringFromAnnotationAssertionAxiom.java

/**
 * As in Mouse and NCI anatomy. Annotations al rdf:labels in anonymous individuals
 * It seems also GO ontology (to be checked)
 * @param entityAnnAx
 * @return
 */
private String asAnonymousIndividual(OWLAnnotationAssertionAxiom entityAnnAx, OWLOntology onto){
    try {
        geneid_value=((OWLAnonymousIndividual)entityAnnAx.getAnnotation().getValue()).asOWLAnonymousIndividual();//.getID()
        for (OWLAnnotationAssertionAxiom annGeneidAx : onto.getAnnotationAssertionAxioms(geneid_value)){

            if (annGeneidAx.getAnnotation().getProperty().getIRI().toString().equals(rdf_label_uri)){

                return ((OWLLiteral)annGeneidAx.getAnnotation().getValue()).getLiteral().toLowerCase();
            }
        }
        return "";
    }
    catch (Exception e){
        //In case of error. Accessing an object in an expected way
        return "";
    }
}

项目：HermiT-android 文件：EntailmentChecker.java

public void visit(OWLDataPropertyAssertionAxiom axiom) {
    if (!axiom.getSubject().isAnonymous()) {
        return; // not interesting for the anonymous individual forest
    }
    OWLAnonymousIndividual sub=axiom.getSubject().asOWLAnonymousIndividual();
    nodes.add(sub);
    OWLClassExpression c=factory.getOWLDataHasValue(axiom.getProperty(),axiom.getObject());
    if (nodelLabels.containsKey(sub)) {
        nodelLabels.get(sub).add(c);
    }
    else {
        Set<OWLClassExpression> labels=new HashSet<OWLClassExpression>();
        labels.add(c);
        nodelLabels.put(sub,labels);
    }
}

项目：Hermit_1.3.8_android 文件：EntailmentChecker.java

public void visit(OWLDataPropertyAssertionAxiom axiom) {
    if (!axiom.getSubject().isAnonymous()) {
        return; // not interesting for the anonymous individual forest
    }
    OWLAnonymousIndividual sub=axiom.getSubject().asOWLAnonymousIndividual();
    nodes.add(sub);
    OWLClassExpression c=factory.getOWLDataHasValue(axiom.getProperty(),axiom.getObject());
    if (nodelLabels.containsKey(sub)) {
        nodelLabels.get(sub).add(c);
    }
    else {
        Set<OWLClassExpression> labels=new HashSet<OWLClassExpression>();
        labels.add(c);
        nodelLabels.put(sub,labels);
    }
}

项目：owltools 文件：ModelAnnotationSolrDocumentLoader.java

private OWLNamedIndividual findEvidenceIndividual(OWLAnnotationValue value) {
    return value.accept(new OWLAnnotationValueVisitorEx<OWLNamedIndividual>() {

        @Override
        public OWLNamedIndividual visit(final IRI iri) {
            OWLNamedIndividual i = null;
            for(OWLNamedIndividual current : model.getIndividualsInSignature()) {
                if (current.getIRI().equals(iri)) {
                    i = current;
                    break;
                }
            }
            return i;
        }

        @Override
        public OWLNamedIndividual visit(OWLAnonymousIndividual individual) {
            return null;
        }

        @Override
        public OWLNamedIndividual visit(OWLLiteral literal) {
            return null;
        }
    });
}

项目：snorocket 文件：DebugUtils.java

public static String getLabel(OWLEntity e, OWLOntology ont) {
      final Iterator<OWLAnnotation> iterator = EntitySearcher.getAnnotations(e, ont).iterator();
while (iterator.hasNext()) {
    final OWLAnnotation an = iterator.next();
          if (an.getProperty().isLabel()) {
              OWLAnnotationValue val = an.getValue();

              if (val instanceof IRI) {
                  return ((IRI) val).toString();
              } else if (val instanceof OWLLiteral) {
                  OWLLiteral lit = (OWLLiteral) val;
                  return lit.getLiteral();
              } else if (val instanceof OWLAnonymousIndividual) {
                  OWLAnonymousIndividual ind = (OWLAnonymousIndividual) val;
                  return ind.toStringID();
              } else {
                  throw new RuntimeException("Unexpected class "
                          + val.getClass());
              }
          }
      }
      return e.toStringID();
  }

项目：snorocket 文件：DebugUtils.java

public static String getLabel(OWLEntity e, OWLOntology ont) {
    return EntitySearcher.getAnnotations(e, ont)
        .filter(an -> an.getProperty().isLabel())
        .findFirst()
        .map(an -> {
            final OWLAnnotationValue val = an.getValue();

            if (val instanceof IRI) {
                return ((IRI) val).toString();
            } else if (val instanceof OWLLiteral) {
                OWLLiteral lit = (OWLLiteral) val;
                return lit.getLiteral();
            } else if (val instanceof OWLAnonymousIndividual) {
                OWLAnonymousIndividual ind = (OWLAnonymousIndividual) val;
                return ind.toStringID();
            } else {
                throw new RuntimeException("Unexpected class "
                        + val.getClass());
            }
        })
        .orElse(e.toStringID());
}

项目：OntoBench 文件：AnonymousIndividualFeature.java

@Override
public void addToOntology() {
  OWLClass clazz = featurePool.getReusableClass();
  OWLAnonymousIndividual individual = factory.getOWLAnonymousIndividual();

  addAxiomToOntology(factory.getOWLClassAssertionAxiom(clazz, individual));
}

项目：sparql-dl-api 文件：QueryArgumentTest.java

@Test
public void testIsBnode() 
{
    QueryArgument arg = new QueryArgument(mock(OWLAnonymousIndividual.class));
    assertTrue(arg.isBnode());
    QueryArgument arg2 = new QueryArgument(new Var("x"));
    assertFalse(arg2.isBnode());
}

项目：minerva 文件：GroupingTranslator.java

public static String getModelState(OWLOntology model, String defaultValue) {
    String modelState = defaultValue;
    Set<OWLAnnotation> modelAnnotations = model.getAnnotations();
    for (OWLAnnotation modelAnnotation : modelAnnotations) {
        IRI propIRI = modelAnnotation.getProperty().getIRI();
        if (AnnotationShorthand.modelstate.getAnnotationProperty().equals(propIRI)) {
            String value = modelAnnotation.getValue().accept(new OWLAnnotationValueVisitorEx<String>() {

                @Override
                public String visit(IRI iri) {
                    return null;
                }

                @Override
                public String visit(OWLAnonymousIndividual individual) {
                    return null;
                }

                @Override
                public String visit(OWLLiteral literal) {
                    return literal.getLiteral();
                }
            });
            if (value != null) {
                modelState = value;
            }
        }
    }
    return modelState;
}

项目：minerva 文件：ModelReaderHelper.java

static boolean isTagged(Set<OWLAnnotation> annotations, OWLAnnotationProperty p) {
    if (annotations != null && !annotations.isEmpty()) {
        for (OWLAnnotation annotation : annotations) {
            if (p.equals(annotation.getProperty())) {
                String value = annotation.getValue().accept(new OWLAnnotationValueVisitorEx<String>() {

                    @Override
                    public String visit(IRI iri) {
                        return null;
                    }

                    @Override
                    public String visit(OWLAnonymousIndividual individual) {
                        return null;
                    }

                    @Override
                    public String visit(OWLLiteral literal) {
                        return literal.getLiteral();
                    }
                });
                if (value != null && ModelWriterHelper.DERIVED_VALUE.equalsIgnoreCase(value)) {
                    return true;
                }
            }
    }
    }
    return false;
}

项目：HermiT-android 文件：EntailmentChecker.java

protected OWLClassExpression getClassExpressionFor(OWLDataFactory factory,OWLAnonymousIndividual node,OWLAnonymousIndividual predecessor) {
    Set<OWLAnonymousIndividual> successors=edges.get(node);
    if (successors==null||(successors.size()==1&&successors.iterator().next()==predecessor)) {
        // the tree consists of a single node
        if (!nodelLabels.containsKey(node)) {
            return factory.getOWLThing();
        }
        else if (nodelLabels.get(node).size()==1) {
            return nodelLabels.get(node).iterator().next();
        }
        else {
            return factory.getOWLObjectIntersectionOf(nodelLabels.get(node));
        }
    }
    Set<OWLClassExpression> concepts=new HashSet<OWLClassExpression>();
    for (OWLAnonymousIndividual successor : successors) {
        OWLObjectProperty op;
        Edge pair=new Edge(node,successor);
        if (edgeOPLabels.containsKey(pair)) {
            op=edgeOPLabels.get(pair);
        }
        else {
            pair=new Edge(successor,node);
            if (!edgeOPLabels.containsKey(pair)) {
                throw new RuntimeException("Internal error: some edge in the forest of anonymous individuals has no edge label although it should. ");
            }
            else {
                op=edgeOPLabels.get(pair);
            }
        }
        concepts.add(factory.getOWLObjectSomeValuesFrom(op,getClassExpressionFor(factory,successor,node)));
    }
    return concepts.size()==1 ? concepts.iterator().next() : factory.getOWLObjectIntersectionOf(concepts);
}

项目：HermiT-android 文件：EntailmentChecker.java

protected Map<Set<OWLAnonymousIndividual>,OWLAnonymousIndividual> findSuitableRoots(Set<Set<OWLAnonymousIndividual>> components) {
    Map<Set<OWLAnonymousIndividual>,OWLAnonymousIndividual> componentsToRoots=new HashMap<Set<OWLAnonymousIndividual>,OWLAnonymousIndividual>();
    for (Set<OWLAnonymousIndividual> component : components) {
        // We have to find a node with at most one relation to the named individuals
        // if there is one with exactly one relation that is a bit nicer for the rolling-up
        // so we try to find that
        OWLAnonymousIndividual root=null;
        OWLAnonymousIndividual rootWithOneNamedRelation=null;
        for (OWLAnonymousIndividual ind : component) {
            if (specialOPEdges.containsKey(ind)) {
                if (specialOPEdges.get(ind).size()<2) {
                    rootWithOneNamedRelation=ind;
                }
            }
            else {
                root=ind;
            }
        }
        if (root==null&&rootWithOneNamedRelation==null) {
            throw new IllegalArgumentException("Invalid input ontology: One of the trees in the forst of anomnymous individuals has no root that satisfies the criteria on roots (cf. OWL 2 Structural Specification and Functional-Style Syntax, Sec. 11.2).");
        }
        else if (rootWithOneNamedRelation!=null) {
            componentsToRoots.put(component,rootWithOneNamedRelation);
        }
        else {
            componentsToRoots.put(component,root);
        }
    }
    return componentsToRoots;
}

项目：HermiT-android 文件：EntailmentChecker.java

protected Set<Set<OWLAnonymousIndividual>> getComponents() {
    Set<Set<OWLAnonymousIndividual>> components=new HashSet<Set<OWLAnonymousIndividual>>();
    if (nodes.isEmpty())
        return components;

    Set<OWLAnonymousIndividual> toProcess=nodes;
    Set<OWLAnonymousIndividual> currentComponent;
    List<Edge> workQueue=new ArrayList<Edge>();
    Edge nodePlusPredecessor;

    while (!toProcess.isEmpty()) {
        currentComponent=new HashSet<OWLAnonymousIndividual>();
        nodePlusPredecessor=new Edge(toProcess.iterator().next(),null);
        workQueue.add(nodePlusPredecessor);
        while (!workQueue.isEmpty()) {
            nodePlusPredecessor=workQueue.remove(0);
            currentComponent.add(nodePlusPredecessor.first);
            // see whether there are any successors that we have to check
            if (edges.containsKey(nodePlusPredecessor.first)) {
                // add successors to the workQueue
                for (OWLAnonymousIndividual ind : edges.get(nodePlusPredecessor.first)) {
                    if (nodePlusPredecessor.second==null||!(ind.getID().equals(nodePlusPredecessor.second.getID()))) {
                        // check for cycle
                        for (Edge pair : workQueue) {
                            if (pair.first==ind) {
                                throw new IllegalArgumentException("Invalid input ontology: The anonymous individuals cannot be arranged into a forest as required (cf. OWL 2 Structural Specification and Functional-Style Syntax, Sec. 11.2) because there is a cycle. ");
                            }
                        }
                        workQueue.add(new Edge(ind,nodePlusPredecessor.first));
                    }
                }
            }
        }
        components.add(currentComponent);
        toProcess.removeAll(currentComponent);
    }
    return components;
}

项目：Hermit_1.3.8_android 文件：EntailmentChecker.java

protected OWLClassExpression getClassExpressionFor(OWLDataFactory factory,OWLAnonymousIndividual node,OWLAnonymousIndividual predecessor) {
    Set<OWLAnonymousIndividual> successors=edges.get(node);
    if (successors==null||(successors.size()==1&&successors.iterator().next()==predecessor)) {
        // the tree consists of a single node
        if (!nodelLabels.containsKey(node)) {
            return factory.getOWLThing();
        }
        else if (nodelLabels.get(node).size()==1) {
            return nodelLabels.get(node).iterator().next();
        }
        else {
            return factory.getOWLObjectIntersectionOf(nodelLabels.get(node));
        }
    }
    Set<OWLClassExpression> concepts=new HashSet<OWLClassExpression>();
    for (OWLAnonymousIndividual successor : successors) {
        OWLObjectProperty op;
        Edge pair=new Edge(node,successor);
        if (edgeOPLabels.containsKey(pair)) {
            op=edgeOPLabels.get(pair);
        }
        else {
            pair=new Edge(successor,node);
            if (!edgeOPLabels.containsKey(pair)) {
                throw new RuntimeException("Internal error: some edge in the forest of anonymous individuals has no edge label although it should. ");
            }
            else {
                op=edgeOPLabels.get(pair);
            }
        }
        concepts.add(factory.getOWLObjectSomeValuesFrom(op,getClassExpressionFor(factory,successor,node)));
    }
    return concepts.size()==1 ? concepts.iterator().next() : factory.getOWLObjectIntersectionOf(concepts);
}

项目：Hermit_1.3.8_android 文件：EntailmentChecker.java

protected Map<Set<OWLAnonymousIndividual>,OWLAnonymousIndividual> findSuitableRoots(Set<Set<OWLAnonymousIndividual>> components) {
    Map<Set<OWLAnonymousIndividual>,OWLAnonymousIndividual> componentsToRoots=new HashMap<Set<OWLAnonymousIndividual>,OWLAnonymousIndividual>();
    for (Set<OWLAnonymousIndividual> component : components) {
        // We have to find a node with at most one relation to the named individuals
        // if there is one with exactly one relation that is a bit nicer for the rolling-up
        // so we try to find that
        OWLAnonymousIndividual root=null;
        OWLAnonymousIndividual rootWithOneNamedRelation=null;
        for (OWLAnonymousIndividual ind : component) {
            if (specialOPEdges.containsKey(ind)) {
                if (specialOPEdges.get(ind).size()<2) {
                    rootWithOneNamedRelation=ind;
                }
            }
            else {
                root=ind;
            }
        }
        if (root==null&&rootWithOneNamedRelation==null) {
            throw new IllegalArgumentException("Invalid input ontology: One of the trees in the forst of anomnymous individuals has no root that satisfies the criteria on roots (cf. OWL 2 Structural Specification and Functional-Style Syntax, Sec. 11.2).");
        }
        else if (rootWithOneNamedRelation!=null) {
            componentsToRoots.put(component,rootWithOneNamedRelation);
        }
        else {
            componentsToRoots.put(component,root);
        }
    }
    return componentsToRoots;
}

项目：Hermit_1.3.8_android 文件：EntailmentChecker.java

protected Set<Set<OWLAnonymousIndividual>> getComponents() {
    Set<Set<OWLAnonymousIndividual>> components=new HashSet<Set<OWLAnonymousIndividual>>();
    if (nodes.isEmpty())
        return components;

    Set<OWLAnonymousIndividual> toProcess=nodes;
    Set<OWLAnonymousIndividual> currentComponent;
    List<Edge> workQueue=new ArrayList<Edge>();
    Edge nodePlusPredecessor;

    while (!toProcess.isEmpty()) {
        currentComponent=new HashSet<OWLAnonymousIndividual>();
        nodePlusPredecessor=new Edge(toProcess.iterator().next(),null);
        workQueue.add(nodePlusPredecessor);
        while (!workQueue.isEmpty()) {
            nodePlusPredecessor=workQueue.remove(0);
            currentComponent.add(nodePlusPredecessor.first);
            // see whether there are any successors that we have to check
            if (edges.containsKey(nodePlusPredecessor.first)) {
                // add successors to the workQueue
                for (OWLAnonymousIndividual ind : edges.get(nodePlusPredecessor.first)) {
                    if (nodePlusPredecessor.second==null||!(ind.getID().equals(nodePlusPredecessor.second.getID()))) {
                        // check for cycle
                        for (Edge pair : workQueue) {
                            if (pair.first==ind) {
                                throw new IllegalArgumentException("Invalid input ontology: The anonymous individuals cannot be arranged into a forest as required (cf. OWL 2 Structural Specification and Functional-Style Syntax, Sec. 11.2) because there is a cycle. ");
                            }
                        }
                        workQueue.add(new Edge(ind,nodePlusPredecessor.first));
                    }
                }
            }
        }
        components.add(currentComponent);
        toProcess.removeAll(currentComponent);
    }
    return components;
}

项目：owltools 文件：Mooncat.java

public static Set<OWLObject> findTaggedEntities(OWLAnnotationProperty p, Set<OWLAnnotationValue> values, final OWLGraphWrapper graph) {
    if (p == null || values == null || values.isEmpty()) {
        return Collections.emptySet();
    }
    final Set<OWLObject> entities = new HashSet<OWLObject>();
    Set<OWLOntology> allOntologies = graph.getAllOntologies();
    for (OWLOntology ontology : allOntologies) {
        Set<OWLAnnotationAssertionAxiom> axioms = ontology.getAxioms(AxiomType.ANNOTATION_ASSERTION);
        for (OWLAnnotationAssertionAxiom axiom : axioms) {
            if (p.equals(axiom.getProperty()) && values.contains(axiom.getValue())) {
                axiom.getSubject().accept(new OWLAnnotationSubjectVisitor(){

                    @Override
                    public void visit(IRI iri) {
                        OWLObject owlObject = graph.getOWLObject(iri);
                        if (owlObject != null) {
                            entities.add(owlObject);
                        }
                    }

                    @Override
                    public void visit(OWLAnonymousIndividual individual) {
                        // do nothing
                    }
                });
            }
        }
    }
    return entities;
}

项目：SciGraph 文件：OwlApiUtils.java

public static String getIri(OWLIndividual individual) {
  if (individual.isAnonymous()) {
    return ((OWLAnonymousIndividual)individual).getID().getID();
  } else {
    return individual.asOWLNamedIndividual().getIRI().toString();
  }
}

项目：owlapi-gwt 文件：OWLQuantifiedDataRestrictionImpl.java

@Override
public void addAnonymousIndividualsToSet(Set<OWLAnonymousIndividual> anons) {
    addAnonymousIndividualsToSetForValue(anons, getFiller());
    addAnonymousIndividualsToSetForValue(anons, property);
    if (property instanceof HasIncrementalSignatureGenerationSupport) {
        HasIncrementalSignatureGenerationSupport property1 = (HasIncrementalSignatureGenerationSupport) property;
        property1.addAnonymousIndividualsToSet(anons);
    }
}

项目：owlapi-gwt 文件：OWLDataPropertyAssertionAxiomImpl.java

@Override
public void addAnonymousIndividualsToSet(Set<OWLAnonymousIndividual> anons) {
    if (getSubject().isAnonymous()) {
        anons.add(getSubject().asOWLAnonymousIndividual());
    }
    addAnonymousIndividualsToSetForValue(anons, getProperty());
    addAnonymousIndividualsToSetForValue(anons, getObject());
}

项目：owlapi-gwt 文件：OWLIndividualRelationshipAxiomImpl.java

@Override
public void addAnonymousIndividualsToSet(Set<OWLAnonymousIndividual> anons) {
    if (getSubject().isAnonymous()) {
        anons.add(getSubject().asOWLAnonymousIndividual());
    }
    addAnonymousIndividualsToSetForValue(anons, getProperty());
    addAnonymousIndividualsToSetForValue(anons, getObject());
}

项目：owlapi-gwt 文件：OWLEntityCollectionContainerCollector.java

@Override
public void visit(OWLAnonymousIndividual individual) {
    // Anon individuals aren't entities
    // But store them in a set anyway for utility
    if (anonymousIndividuals != null) {
        verifyNotNull(anonymousIndividuals).add(individual);
    }
}

项目：owlapi-gwt 文件：OWLObjectOneOfImpl.java

@Override
public void addAnonymousIndividualsToSet(Set<OWLAnonymousIndividual> anons) {
    for (OWLIndividual individual : values) {
        if (individual.isAnonymous()) {
            anons.add(individual.asOWLAnonymousIndividual());
        }
    }
}

项目：owlapi-gwt 文件：OWLNaryIndividualAxiomImpl.java

@Override
public void addAnonymousIndividualsToSet(Set<OWLAnonymousIndividual> anons) {
    for (OWLIndividual individual : individuals) {
        if (individual.isAnonymous()) {
            anons.add(individual.asOWLAnonymousIndividual());
        }
    }
}

项目：binaryowl 文件：AnonymousIndividualLookupTable.java

public int getIndex(OWLAnonymousIndividual ind) {
    Integer i = indexMap.get(ind);
    if(i == null) {
        i = indexMap.size();
        indexMap.put(ind, i);
    }
    return i;
}

项目：sparql-dl-api 文件：QueryArgument.java

public QueryArgument(OWLAnonymousIndividual value) {
    this.type = QueryArgumentType.BNODE;
    this.value = value;
}

项目：sparql-dl-api 文件：QueryArgument.java

public OWLAnonymousIndividual getValueAsBNode() {
    return (OWLAnonymousIndividual) value;
}

项目：minerva 文件：AbstractLegoTranslator.java

static void fillAspects(OWLOntology model, OWLReasoner reasoner, CurieHandler curieHandler, Set<OWLClass> bpSet, Set<OWLClass> mfSet, Set<OWLClass> ccSet, 
        OWLClass bp, OWLClass mf, OWLClass cc) {
    final IRI namespaceIRI = Obo2Owl.trTagToIRI(OboFormatTag.TAG_NAMESPACE.getTag());
    final OWLDataFactory df = model.getOWLOntologyManager().getOWLDataFactory();
    final OWLAnnotationProperty namespaceProperty = df.getOWLAnnotationProperty(namespaceIRI);
    final Set<OWLOntology> ontologies = model.getImportsClosure();
    for(OWLClass cls : model.getClassesInSignature(Imports.INCLUDED)) {
        if (cls.isBuiltIn()) {
            continue;
        }
        String id = curieHandler.getCuri(cls);
        if (id.startsWith("GO:") == false) {
            continue;
        }

        // if a reasoner object is passed, use inference to populate
        // the 3 subset
        if (reasoner != null) {
            if (reasoner.getSuperClasses(cls, false).containsEntity(mf) ||
                    reasoner.getEquivalentClasses(cls).contains(mf)) {
                mfSet.add(cls);
            }
            if (reasoner.getSuperClasses(cls, false).containsEntity(bp) ||
                    reasoner.getEquivalentClasses(cls).contains(bp)) {
                bpSet.add(cls);
            }
            if (reasoner.getSuperClasses(cls, false).containsEntity(cc) ||
                    reasoner.getEquivalentClasses(cls).contains(cc)) {
                ccSet.add(cls);
            }
        }


        for (OWLAnnotation annotation : OwlHelper.getAnnotations(cls, ontologies)) {
            if (annotation.getProperty().equals(namespaceProperty)) {
                String value = annotation.getValue().accept(new OWLAnnotationValueVisitorEx<String>() {

                    @Override
                    public String visit(IRI iri) {
                        return null;
                    }

                    @Override
                    public String visit(OWLAnonymousIndividual individual) {
                        return null;
                    }

                    @Override
                    public String visit(OWLLiteral literal) {
                        return literal.getLiteral();
                    }
                });
                if (value != null) {
                    if ("molecular_function".equals(value)) {
                        mfSet.add(cls);
                    }
                    else if ("biological_process".equals(value)) {
                        bpSet.add(cls);
                    }
                    else if ("cellular_component".equals(value)) {
                        ccSet.add(cls);
                    }
                }
            }
        }
    }
}

项目：logmap-matcher 文件：OWLAlignmentReader.java

public void visit(OWLAnonymousIndividual individual){
    //Do nothing
}

项目：HermiT-android 文件：Reasoner.java

protected static Individual H(OWLAnonymousIndividual anonymousIndividual) {
    return Individual.createAnonymous(anonymousIndividual.getID()
            .toString());
}

项目：HermiT-android 文件：Reasoner.java

protected static Individual H(OWLIndividual individual) {
    if (individual.isAnonymous())
        return H((OWLAnonymousIndividual) individual);
    else
        return H((OWLNamedIndividual) individual);
}

项目：HermiT-android 文件：EntailmentChecker.java

public Edge(OWLAnonymousIndividual first,OWLAnonymousIndividual second) {
    this.first=first;
    this.second=second;
}

项目：elk-reasoner 文件：AbstractElkObjectConverter.java

@Override
public OWLAnonymousIndividual visit(ElkAnonymousIndividual expression) {
    return owlFactory_.getOWLAnonymousIndividual(expression.getNodeId());
}

项目：elk-reasoner 文件：OwlConverter.java

@SuppressWarnings("static-method")
public ElkAnonymousIndividual convert(
        OWLAnonymousIndividual owlAnonymousIndividual) {
    return new ElkAnonymousIndividualWrap<OWLAnonymousIndividual>(
            owlAnonymousIndividual);
}

项目：elk-reasoner 文件：OwlIndividualConverterVisitor.java

@Override
public ElkAnonymousIndividual visit(
        OWLAnonymousIndividual owlAnonymousIndividual) {
    return CONVERTER.convert(owlAnonymousIndividual);
}

项目：elk-reasoner 文件：OwlAnnotationSubjectValueVisitor.java

@Override
public ElkAnonymousIndividual visit(OWLAnonymousIndividual anon) {
    return CONVERTER.convert(anon);
}