protected void clausify(
        OWLAxioms.DisjunctiveRule rule, boolean restrictToNamed, OWLAxiom originalAxiom) {
      m_headAtoms.clear();
      m_bodyAtoms.clear();
      m_abstractVariables.clear();
      for (SWRLAtom atom : rule.m_body) m_bodyAtoms.add(atom.accept(this));
      for (SWRLAtom atom : rule.m_head) m_headAtoms.add(atom.accept(this));
      if (restrictToNamed) {
        for (Variable variable : m_abstractVariables)
          m_bodyAtoms.add(Atom.create(AtomicConcept.INTERNAL_NAMED, variable));
      }
      DLClause dlClause =
          DLClause.create(
              m_headAtoms.toArray(new Atom[m_headAtoms.size()]),
              m_bodyAtoms.toArray(new Atom[m_bodyAtoms.size()]));

      Collection<OWLAxiom> originalAxioms = m_dlClauses_map.get(dlClause);
      if (originalAxioms == null) {
        originalAxioms = new ArrayList<OWLAxiom>();
        m_dlClauses_map.put(dlClause, originalAxioms);
      }
      originalAxioms.add(originalAxiom);

      m_headAtoms.clear();
      m_bodyAtoms.clear();
      m_abstractVariables.clear();
    }
 public void visit(SWRLRule rule) {
   for (SWRLAtom atom : rule.getBody()) {
     atom.accept(this);
   }
   for (SWRLAtom atom : rule.getHead()) {
     atom.accept(this);
   }
   processAxiomAnnotations(rule);
 }
 @Override
 public void visit(SWRLRule node) {
   for (SWRLAtom atom : node.getBody()) {
     atom.accept(this);
   }
   for (SWRLAtom atom : node.getHead()) {
     atom.accept(this);
   }
 }
 @Override
 public void visit(SWRLRule rule) {
   write("SWRLRule");
   for (SWRLAtom a : rule.getHead()) {
     a.accept(this);
   }
   write("\\rightarrow");
   for (SWRLAtom a : rule.getBody()) {
     a.accept(this);
   }
 }
Exemple #5
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 @Override
 public SWRLRule visit(SWRLRule node) {
   Set<SWRLAtom> nodebody = new HashSet<SWRLAtom>();
   for (SWRLAtom atom : node.getBody()) {
     nodebody.add((SWRLAtom) atom.accept(this));
   }
   Set<SWRLAtom> nodehead = new HashSet<SWRLAtom>();
   for (SWRLAtom atom : node.getHead()) {
     nodehead.add((SWRLAtom) atom.accept(this));
   }
   return new SWRLRuleImpl(nodebody, nodehead, NO_ANNOTATIONS);
 }
 @Override
 public void visit(SWRLRule rule) {
   Set<SWRLAtom> antecedents = new HashSet<SWRLAtom>();
   Set<SWRLAtom> consequents = new HashSet<SWRLAtom>();
   for (SWRLAtom atom : rule.getBody()) {
     atom.accept(this);
     antecedents.add((SWRLAtom) obj);
   }
   for (SWRLAtom atom : rule.getHead()) {
     atom.accept(this);
     consequents.add((SWRLAtom) obj);
   }
   obj = dataFactory.getSWRLRule(antecedents, consequents);
 }
 public Set<OWLAxiom> write(OWLDataProperty property) {
   Set<OWLAxiom> axioms = new HashSet<OWLAxiom>();
   axioms.addAll(writeEntityStart(DATA_PROPERTY, property));
   if (!isFiltered(AxiomType.FUNCTIONAL_DATA_PROPERTY)) {
     for (OWLOntology ontology : getOntologies()) {
       SectionMap characteristics = new SectionMap();
       for (OWLAxiom ax : ontology.getFunctionalDataPropertyAxioms(property)) {
         if (isDisplayed(ax)) {
           characteristics.add(FUNCTIONAL.toString(), ax);
           axioms.add(ax);
         }
       }
       writeSection(CHARACTERISTICS, characteristics, ",", true, ontology);
     }
   }
   if (!isFiltered(AxiomType.DATA_PROPERTY_DOMAIN)) {
     for (OWLOntology ontology : getOntologies()) {
       SectionMap domains = new SectionMap();
       for (OWLDataPropertyDomainAxiom ax : ontology.getDataPropertyDomainAxioms(property)) {
         if (isDisplayed(ax)) {
           domains.add(ax.getDomain(), ax);
           axioms.add(ax);
         }
       }
       writeSection(DOMAIN, domains, ",", true, ontology);
     }
   }
   if (!isFiltered(AxiomType.DATA_PROPERTY_RANGE)) {
     for (OWLOntology ontology : getOntologies()) {
       SectionMap ranges = new SectionMap();
       for (OWLDataPropertyRangeAxiom ax : ontology.getDataPropertyRangeAxioms(property)) {
         if (isDisplayed(ax)) {
           ranges.add(ax.getRange(), ax);
           axioms.add(ax);
         }
       }
       writeSection(RANGE, ranges, ",", true, ontology);
     }
   }
   if (!isFiltered(AxiomType.SUB_DATA_PROPERTY)) {
     for (OWLOntology ontology : getOntologies()) {
       SectionMap supers = new SectionMap();
       for (OWLSubDataPropertyOfAxiom ax :
           ontology.getDataSubPropertyAxiomsForSubProperty(property)) {
         if (isDisplayed(ax)) {
           supers.add(ax.getSuperProperty(), ax);
           axioms.add(ax);
         }
       }
       writeSection(SUB_PROPERTY_OF, supers, ",", true, ontology);
     }
   }
   if (!isFiltered(AxiomType.EQUIVALENT_DATA_PROPERTIES)) {
     for (OWLOntology ontology : getOntologies()) {
       SectionMap props = new SectionMap();
       for (OWLEquivalentDataPropertiesAxiom ax :
           ontology.getEquivalentDataPropertiesAxioms(property)) {
         if (isDisplayed(ax) && ax.getProperties().size() == 2) {
           props.add(ax.getPropertiesMinus(property).iterator().next(), ax);
           axioms.add(ax);
         }
       }
       writeSection(EQUIVALENT_TO, props, ",", true, ontology);
     }
   }
   if (!isFiltered(AxiomType.DISJOINT_DATA_PROPERTIES)) {
     for (OWLOntology ontology : getOntologies()) {
       SectionMap props = new SectionMap();
       for (OWLDisjointDataPropertiesAxiom ax :
           ontology.getDisjointDataPropertiesAxioms(property)) {
         if (ax.getProperties().size() == 2 && isDisplayed(ax)) {
           props.add(ax.getPropertiesMinus(property).iterator().next(), ax);
           axioms.add(ax);
         }
       }
       props.remove(property);
       writeSection(DISJOINT_WITH, props, ",", true, ontology);
     }
   }
   if (!isFiltered(AxiomType.SWRL_RULE)) {
     for (OWLOntology ontology : getOntologies()) {
       Set<OWLAxiom> rules = new HashSet<OWLAxiom>();
       for (SWRLRule rule : ontology.getAxioms(AxiomType.SWRL_RULE)) {
         if (isDisplayed(rule)) {
           for (SWRLAtom atom : rule.getHead()) {
             if (atom.getPredicate().equals(property)) {
               writeSection(RULE, rules, "", true, ontology);
               break;
             }
           }
         }
       }
     }
   }
   writeEntitySectionEnd(DATA_PROPERTY.toString());
   return axioms;
 }
  public Set<OWLAxiom> write(OWLObjectPropertyExpression property) {
    Set<OWLAxiom> axioms = new HashSet<OWLAxiom>();
    axioms.addAll(writeEntityStart(OBJECT_PROPERTY, property));
    if (!isFiltered(AxiomType.SUB_OBJECT_PROPERTY)) {
      for (OWLOntology ontology : getOntologies()) {
        SectionMap properties = new SectionMap();
        for (OWLSubObjectPropertyOfAxiom ax :
            ontology.getObjectSubPropertyAxiomsForSubProperty(property)) {
          if (isDisplayed(ax)) {
            properties.add(ax.getSuperProperty(), ax);
            axioms.add(ax);
          }
        }
        writeSection(SUB_PROPERTY_OF, properties, ",", true, ontology);
      }
      if (renderExtensions) {
        for (OWLOntology ontology : getOntologies()) {
          SectionMap properties = new SectionMap();
          for (OWLSubObjectPropertyOfAxiom ax :
              ontology.getObjectSubPropertyAxiomsForSuperProperty(property)) {
            if (isDisplayed(ax)) {
              properties.add(ax.getSubProperty(), ax);
              axioms.add(ax);
            }
          }
          writeSection(SUPER_PROPERTY_OF, properties, ",", true, ontology);
        }
      }
    }
    if (!isFiltered(AxiomType.EQUIVALENT_OBJECT_PROPERTIES)) {
      for (OWLOntology ontology : getOntologies()) {
        SectionMap properties = new SectionMap();
        for (OWLEquivalentObjectPropertiesAxiom ax :
            ontology.getEquivalentObjectPropertiesAxioms(property)) {
          if (isDisplayed(ax) && ax.getProperties().size() == 2) {
            Set<OWLObjectPropertyExpression> props = ax.getPropertiesMinus(property);
            properties.add(props.iterator().next(), ax);
            axioms.add(ax);
          }
        }
        writeSection(EQUIVALENT_TO, properties, ",", true, ontology);
      }
    }
    if (!isFiltered(AxiomType.DISJOINT_OBJECT_PROPERTIES)) {
      for (OWLOntology ontology : getOntologies()) {
        SectionMap properties = new SectionMap();
        for (OWLDisjointObjectPropertiesAxiom ax :
            ontology.getDisjointObjectPropertiesAxioms(property)) {
          if (ax.getProperties().size() == 2 && isDisplayed(ax)) {
            Set<OWLObjectPropertyExpression> props = ax.getPropertiesMinus(property);
            properties.add(props.iterator().next(), ax);
            axioms.add(ax);
          }
        }
        writeSection(DISJOINT_WITH, properties, ",", true, ontology);
      }
    }
    if (!isFiltered(AxiomType.SUB_PROPERTY_CHAIN_OF)) {
      for (OWLOntology ontology : getOntologies()) {
        for (OWLSubPropertyChainOfAxiom ax : ontology.getAxioms(AxiomType.SUB_PROPERTY_CHAIN_OF)) {
          if (ax.getSuperProperty().equals(property)) {
            if (isDisplayed(ax)) {
              SectionMap map = new SectionMap();
              map.add(ax.getPropertyChain(), ax);
              writeSection(SUB_PROPERTY_CHAIN, map, " o ", false, ontology);
              axioms.add(ax);
            }
          }
        }
      }
    }

    for (OWLOntology ontology : getOntologies()) {
      SectionMap characteristics = new SectionMap();
      if (!isFiltered(AxiomType.FUNCTIONAL_OBJECT_PROPERTY)) {
        for (OWLFunctionalObjectPropertyAxiom ax :
            ontology.getFunctionalObjectPropertyAxioms(property)) {
          if (isDisplayed(ax)) {
            characteristics.add(FUNCTIONAL.toString(), ax);
            axioms.add(ax);
          }
        }
      }

      if (!isFiltered(AxiomType.INVERSE_FUNCTIONAL_OBJECT_PROPERTY)) {
        for (OWLAxiom ax : ontology.getInverseFunctionalObjectPropertyAxioms(property)) {
          if (isDisplayed(ax)) {
            characteristics.add(INVERSE_FUNCTIONAL.toString(), ax);
            axioms.add(ax);
          }
        }
      }
      if (!isFiltered(AxiomType.SYMMETRIC_OBJECT_PROPERTY)) {
        for (OWLAxiom ax : ontology.getSymmetricObjectPropertyAxioms(property)) {
          if (isDisplayed(ax)) {
            characteristics.add(SYMMETRIC.toString(), ax);
            axioms.add(ax);
          }
        }
      }
      if (!isFiltered(AxiomType.TRANSITIVE_OBJECT_PROPERTY)) {
        for (OWLAxiom ax : ontology.getTransitiveObjectPropertyAxioms(property)) {
          if (isDisplayed(ax)) {
            characteristics.add(TRANSITIVE.toString(), ax);
            axioms.add(ax);
          }
        }
      }
      if (!isFiltered(AxiomType.REFLEXIVE_OBJECT_PROPERTY)) {
        for (OWLAxiom ax : ontology.getReflexiveObjectPropertyAxioms(property)) {
          if (isDisplayed(ax)) {
            characteristics.add(REFLEXIVE.toString(), ax);
            axioms.add(ax);
          }
        }
      }
      if (!isFiltered(AxiomType.IRREFLEXIVE_OBJECT_PROPERTY)) {
        for (OWLAxiom ax : ontology.getIrreflexiveObjectPropertyAxioms(property)) {
          if (isDisplayed(ax)) {
            characteristics.add(IRREFLEXIVE.toString(), ax);
            axioms.add(ax);
          }
        }
      }
      if (!isFiltered(AxiomType.ASYMMETRIC_OBJECT_PROPERTY)) {
        for (OWLAxiom ax : ontology.getAsymmetricObjectPropertyAxioms(property)) {
          if (isDisplayed(ax)) {
            characteristics.add(ASYMMETRIC.toString(), ax);
            axioms.add(ax);
          }
        }
      }
      writeSection(CHARACTERISTICS, characteristics, ",", true, ontology);
    }

    if (!isFiltered(AxiomType.OBJECT_PROPERTY_DOMAIN)) {
      for (OWLOntology ontology : getOntologies()) {
        SectionMap expressions = new SectionMap();
        for (OWLObjectPropertyDomainAxiom ax : ontology.getObjectPropertyDomainAxioms(property)) {
          if (isDisplayed(ax)) {
            expressions.add(ax.getDomain(), ax);
            axioms.add(ax);
          }
        }
        writeSection(DOMAIN, expressions, ",", true, ontology);
      }
    }
    if (!isFiltered(AxiomType.OBJECT_PROPERTY_RANGE)) {
      for (OWLOntology ontology : getOntologies()) {
        SectionMap expressions = new SectionMap();
        for (OWLObjectPropertyRangeAxiom ax : ontology.getObjectPropertyRangeAxioms(property)) {
          if (isDisplayed(ax)) {
            expressions.add(ax.getRange(), ax);
            axioms.add(ax);
          }
        }
        writeSection(RANGE, expressions, ",", true, ontology);
      }
    }
    if (!isFiltered(AxiomType.INVERSE_OBJECT_PROPERTIES)) {
      for (OWLOntology ontology : getOntologies()) {
        Set<OWLObjectPropertyExpression> properties = new TreeSet<OWLObjectPropertyExpression>();
        for (OWLInverseObjectPropertiesAxiom ax :
            ontology.getInverseObjectPropertyAxioms(property)) {
          if (isDisplayed(ax)) {
            if (ax.getFirstProperty().equals(property)) {
              properties.add(ax.getSecondProperty());
            } else {
              properties.add(ax.getFirstProperty());
            }
            axioms.add(ax);
          }
        }
        writeSection(INVERSE_OF, properties, ",", true, ontology);
      }
    }

    if (!isFiltered(AxiomType.SWRL_RULE)) {
      for (OWLOntology ontology : getOntologies()) {
        Set<OWLAxiom> rules = new HashSet<OWLAxiom>();
        for (SWRLRule rule : ontology.getAxioms(AxiomType.SWRL_RULE)) {
          if (isDisplayed(rule)) {
            for (SWRLAtom atom : rule.getHead()) {
              if (atom.getPredicate().equals(property)) {
                rules.add(rule);
                // XXX attempted patching
                writeSection(RULE, rules, ",", true, ontology);
                break;
              }
            }
          }
        }
      }
    }
    writeEntitySectionEnd(OBJECT_PROPERTY.toString());
    return axioms;
  }
  public Set<OWLAxiom> write(OWLClass cls) {
    Set<OWLAxiom> axioms = new HashSet<OWLAxiom>();
    axioms.addAll(writeEntityStart(CLASS, cls));

    if (!isFiltered(AxiomType.EQUIVALENT_CLASSES)) {
      for (OWLOntology ontology : getOntologies()) {
        SectionMap equivalentClasses = new SectionMap();
        for (OWLEquivalentClassesAxiom ax : ontology.getEquivalentClassesAxioms(cls)) {
          if (ax.getClassExpressions().size() == 2) {
            if (isDisplayed(ax)) {
              for (OWLClassExpression equivCls : ax.getClassExpressionsMinus(cls)) {
                equivalentClasses.add(equivCls, ax);
              }
              axioms.add(ax);
            }
          }
        }
        equivalentClasses.remove(cls);
        writeSection(EQUIVALENT_TO, equivalentClasses, ",", true, ontology);
      }
    }

    if (!isFiltered(AxiomType.SUBCLASS_OF)) {
      for (OWLOntology ontology : getOntologies()) {
        SectionMap superclasses = new SectionMap();
        for (OWLSubClassOfAxiom ax : ontology.getSubClassAxiomsForSubClass(cls)) {
          if (isDisplayed(ax)) {
            superclasses.add(ax.getSuperClass(), ax);
            axioms.add(ax);
          }
        }
        writeSection(SUBCLASS_OF, superclasses, ",", true, ontology);
      }
      if (renderExtensions) {
        for (OWLOntology ont : getOntologies()) {
          SectionMap subClasses = new SectionMap();
          for (OWLSubClassOfAxiom ax : ont.getSubClassAxiomsForSuperClass(cls)) {
            if (isDisplayed(ax)) {
              subClasses.add(ax.getSubClass(), ax);
              axioms.add(ax);
            }
          }
          writeSection(SUPERCLASS_OF, subClasses, ",", true, ont);
        }
      }
    }
    if (!isFiltered(AxiomType.DISJOINT_CLASSES)) {
      for (OWLOntology ontology : getOntologies()) {
        Set<OWLAxiom> pairwiseDisjointClassesAxioms = new HashSet<OWLAxiom>();
        SectionMap disjointClasses = new SectionMap();
        for (OWLDisjointClassesAxiom ax : ontology.getDisjointClassesAxioms(cls)) {
          if (isDisplayed(ax)) {
            if (ax.getClassExpressions().size() == 2) {
              pairwiseDisjointClassesAxioms.add(ax);
              OWLClassExpression disjointWith = ax.getClassExpressionsMinus(cls).iterator().next();
              disjointClasses.add(disjointWith, ax);
            }
            axioms.add(ax);
          }
        }
        writeSection(DISJOINT_WITH, disjointClasses, ", ", false, ontology);
        if (renderExtensions) {
          // Handling of nary in frame style
          for (OWLDisjointClassesAxiom ax : ontology.getDisjointClassesAxioms(cls)) {
            if (isDisplayed(ax)) {
              if (ax.getClassExpressions().size() > 2) {
                Set<OWLClassExpression> allDisjointClasses =
                    new TreeSet<OWLClassExpression>(ax.getClassExpressions());
                allDisjointClasses.remove(cls);
                axioms.add(ax);
                writeSection(DISJOINT_CLASSES, allDisjointClasses, ", ", false, ontology);
              }
            }
          }
        }
      }
    }
    if (!isFiltered(AxiomType.HAS_KEY)) {
      for (OWLOntology ontology : getOntologies()) {
        for (OWLHasKeyAxiom ax : ontology.getHasKeyAxioms(cls)) {
          if (isDisplayed(ax)) {
            SectionMap map = new SectionMap();
            map.add(ax.getPropertyExpressions(), ax);
            writeSection(HAS_KEY, map, ", ", true, ontology);
          }
        }
      }
    }
    if (!isFiltered(AxiomType.CLASS_ASSERTION)) {
      for (OWLOntology ontology : getOntologies()) {
        SectionMap individuals = new SectionMap();
        for (OWLClassAssertionAxiom ax : ontology.getClassAssertionAxioms(cls)) {
          if (isDisplayed(ax)) {
            if (renderExtensions || ax.getIndividual().isAnonymous()) {
              individuals.add(ax.getIndividual(), ax);
              axioms.add(ax);
            }
          }
        }
        writeSection(INDIVIDUALS, individuals, ",", true, ontology);
      }
    }
    if (!isFiltered(AxiomType.SWRL_RULE)) {
      for (OWLOntology ontology : getOntologies()) {
        Set<OWLAxiom> rules = new HashSet<OWLAxiom>();
        for (SWRLRule rule : ontology.getAxioms(AxiomType.SWRL_RULE)) {
          if (isDisplayed(rule)) {
            for (SWRLAtom atom : rule.getHead()) {
              if (atom.getPredicate().equals(cls)) {
                writeSection(RULE, rules, ", ", true, ontology);
                break;
              }
            }
          }
        }
      }
    }
    writeEntitySectionEnd(CLASS.toString());
    return axioms;
  }