private void checkOccurrence(Collection<OWLAnnotation> c) {
for (OWLAnnotation a : c) {
if (a.getValue() instanceof OWLAnonymousIndividual) {
checkAppearance((OWLAnonymousIndividual) a.getValue());
}
}
}
/**
* Renders the annotation property into a paragraph in the page.
*
* @param page The page to insert the paragraph into.
* @param annotation The annotation containing the property to be rendered.
* @param defaultForeground The default foreground color.
* @param defaultBackground The default background color.
* @param isSelected Specifies whether the associated cell is selected or not.
*/
private Paragraph renderAnnotationProperty(
Page page,
OWLAnnotation annotation,
Color defaultForeground,
Color defaultBackground,
boolean isSelected) {
OWLAnnotationProperty property = annotation.getProperty();
String rendering = editorKit.getOWLModelManager().getRendering(property);
Paragraph paragraph = page.addParagraph(rendering);
Color foreground = getAnnotationPropertyForeground(defaultForeground, isSelected);
paragraph.setForeground(foreground);
// if (isReferenceOntologyActive()) {
// paragraph.setBold(true);
// }
if (annotation.getValue() instanceof OWLLiteral) {
OWLLiteral literalValue = (OWLLiteral) annotation.getValue();
paragraph.append(" ", foreground);
appendTag(paragraph, literalValue, foreground, isSelected);
}
switch (annotationRenderingStyle) {
case COMFORTABLE:
paragraph.setMarginBottom(4);
break;
case COSY:
paragraph.setMarginBottom(2);
break;
case COMPACT:
paragraph.setMarginBottom(1);
break;
}
return paragraph;
}
/**
* Renders an annotation value into a {@link Page}.
*
* @param page The page that the value should be rendered into.
* @param annotation The annotation that contains the value to be rendered.
* @param defaultForeground The default foreground color.
* @param defaultBackground The default background color.
* @param isSelected Whether or not the cell containing the annotation is selected.
* @return A list of paragraphs that represent the rendering of the annotation value. These
* paragraphs will have been added to the Page specified by the page argument.
*/
private List<Paragraph> renderAnnotationValue(
final Page page,
OWLAnnotation annotation,
final Color defaultForeground,
final Color defaultBackground,
final boolean isSelected) {
OWLAnnotationValue annotationValue = annotation.getValue();
List<Paragraph> paragraphs =
annotationValue.accept(
new OWLAnnotationValueVisitorEx<List<Paragraph>>() {
public List<Paragraph> visit(IRI iri) {
return renderIRI(
page, iri, defaultForeground, defaultBackground, isSelected, hasFocus());
}
public List<Paragraph> visit(OWLAnonymousIndividual individual) {
return renderAnonymousIndividual(page, individual);
}
public List<Paragraph> visit(OWLLiteral literal) {
return renderLiteral(
page, literal, defaultForeground, defaultBackground, isSelected);
}
});
applyGlobalFormattingToAnnotationValueParagraphs(paragraphs);
return paragraphs;
}
public void visit(OWLAnnotation annotation) {
annotation.getProperty().accept(this);
annotation.getValue().accept(this);
for (OWLAnnotation anno : annotation.getAnnotations()) {
anno.accept(this);
}
}
@Override
public void visit(OWLAnnotation node) {
node.getProperty().accept(this);
OWLAnnotationProperty prop = (OWLAnnotationProperty) obj;
node.getValue().accept(this);
OWLAnnotationValue val = (OWLAnnotationValue) obj;
obj = dataFactory.getOWLAnnotation(prop, val);
}
@Override
public void handle(String currentId, String value, String qualifierBlock, String comment) {
if (currentId == null) {
return;
}
OWLAnnotation xrefAnnotation = getConsumer().parseXRef(value);
IRI subject = getIRIFromOBOId(currentId);
OWLAnnotationAssertionAxiom ax =
getDataFactory()
.getOWLAnnotationAssertionAxiom(
xrefAnnotation.getProperty(), subject, xrefAnnotation.getValue());
applyChange(new AddAxiom(getOntology(), ax));
if (getConsumer().isTypedef() && xrefAnnotation.getValue() instanceof IRI) {
IRI xrefIRI = (IRI) xrefAnnotation.getValue();
String typedefId = getConsumer().getCurrentId();
getConsumer().addSymbolicIdMapping(typedefId, xrefIRI);
}
}
private String getAnnotationValueByUri(OWLOntology o, OWLEntity owlEntity, String uri) {
for (OWLAnnotation annotation : owlEntity.getAnnotations(o)) {
if (annotation.getProperty().getIRI().toString().equals(uri)) {
OWLLiteral value = (OWLLiteral) annotation.getValue();
return value.getLiteral();
}
}
return null;
}
public static String getLabel(OWLOntology o, OWLEntity owlEntity) {
for (OWLAnnotation annotation : owlEntity.getAnnotations(o)) {
if (annotation.getProperty().isLabel()) {
OWLLiteral value = (OWLLiteral) annotation.getValue();
return value.getLiteral();
}
}
return owlEntity.getIRI().toString();
}
// this method retrieves all the geometric properties that have been
// pre-designated as "house setable" or "room setable",
// that is, if a geometric property is available for houses, it has been
// annotated as "houseSetable", for rooms, "roomSetable" and for both it
// has been designated with both annotations.
public void retrieveGeometricPropertiesMaps() {
OWLDataProperty geometricProperty =
OWLFactory.getOWLDataProperty(":GeometricProperty", topIxPrefixManager);
OWLAnnotationProperty propertyID =
OWLFactory.getOWLAnnotationProperty(":propertyID", topIxPrefixManager);
logger.info(propertyID);
OWLAnnotationProperty houseSetable =
OWLFactory.getOWLAnnotationProperty(":houseSetable", topIxPrefixManager);
OWLAnnotationProperty roomSetable =
OWLFactory.getOWLAnnotationProperty(":roomSetable", topIxPrefixManager);
Set<OWLSubDataPropertyOfAxiom> tempGeometricDataPropertiesSet =
topIxOnt.getDataSubPropertyAxiomsForSuperProperty(geometricProperty);
for (OWLSubDataPropertyOfAxiom tempGeomPropAxiom : tempGeometricDataPropertiesSet) {
OWLDataProperty tempDataProperty = tempGeomPropAxiom.getSubProperty().asOWLDataProperty();
// the following two local vars will become an entry for geometricPropertiesMap
String tempString = tempDataProperty.getAnnotations(topIxOnt, propertyID).toString();
tempString = tempString.substring(tempString.indexOf('"') + 1, tempString.indexOf("^") - 1);
IRI tempIRI = tempGeomPropAxiom.getSubProperty().asOWLDataProperty().getIRI();
geometricPropertiesMap.put(tempString, tempIRI);
// the following code decides whether the above entry should also be contained
// in the houseSetableGeometricPropertiesMap
Set<OWLAnnotation> tempDataPropAnnotationSet = tempDataProperty.getAnnotations(topIxOnt);
for (OWLAnnotation tempDataPropAnnotation : tempDataPropAnnotationSet) {
if (tempDataPropAnnotation.getProperty() == houseSetable
&& tempDataPropAnnotation.getValue().toString().equals("\"true\"^^xsd:boolean")) {
houseSetableGeometricPropertiesMap.put(tempString, tempIRI);
}
if (tempDataPropAnnotation.getProperty() == roomSetable
&& tempDataPropAnnotation.getValue().toString().equals("\"true\"^^xsd:boolean")) {
roomSetableGeometricPropertiesMap.put(tempString, tempIRI);
}
}
}
}
private OntologyManager() {
_manager = OWLManager.createOWLOntologyManager();
try {
_ontology = _manager.loadOntology(IRI.create(getClass().getResource(ONTOLOGY_RESOURCE_PATH)));
for (OWLAnnotation anon : _ontology.getAnnotations()) {
if (anon.getProperty().getIRI().toString().equals(DomainOntology.taxonomyDefinedBy)) {
_taxonomyType = anon.getValue().toString().replace("\"", "");
break;
}
}
_reasoner = new StructuralReasonerFactory().createReasoner(_ontology);
} catch (OWLOntologyCreationException ex) {
Log.e(TAG, "Error while loading the domain ontology");
_taxonomyType = null;
}
}
protected ArrayList<PossibleValueType> getAnnotationValuesByUri(
OWLOntology o, OWLEntity owlEntity, String uri) {
ArrayList<PossibleValueType> possibleValueTypes = new ArrayList<PossibleValueType>();
for (OWLAnnotation annotation : owlEntity.getAnnotations(o)) {
if (annotation.getProperty().getIRI().toString().equals(uri)) {
OWLLiteral value = (OWLLiteral) annotation.getValue();
String[] possibleValues = value.getLiteral().split(",");
for (String possibleValue : possibleValues) {
String[] parsedValue = possibleValue.split(":");
checkArgument(
parsedValue.length == 2, "Possible values must be in the format mapping:value");
possibleValueTypes.add(new PossibleValueType(parsedValue[0], parsedValue[1]));
}
}
}
return possibleValueTypes;
}
@Override
public void visit(OWLAnnotation annotation) {
write("Annotation");
annotation.getProperty().getIRI().accept(this);
annotation.getValue().accept(this);
}