public Map<String, OWLIndividual> returnSitesInOntology() {
// map that contains the correspondance between the names of the sites
// and their OWLIndividual representations.
Map<String, OWLIndividual> returnMap = new HashMap<>();
List<OWLIndividual> returnList = new ArrayList<>();
OWLAnnotationProperty hasNameAnnotationProperty =
OWLFactory.getOWLAnnotationProperty(":individualName", topIxPrefixManager);
OWLClassExpression tempSiteClassExpression =
OWLFactory.getOWLClass(":Site", topIxPrefixManager);
for (OWLClassAssertionAxiom tempClassAssAx :
topIxOnt.getClassAssertionAxioms(tempSiteClassExpression)) {
returnList.add(tempClassAssAx.getIndividual());
Set<OWLAnnotationAssertionAxiom> tempSiteAnnotationsSet =
topIxOnt.getAnnotationAssertionAxioms(
tempClassAssAx.getIndividual().asOWLNamedIndividual().getIRI());
for (OWLAnnotationAssertionAxiom tempAnnotationAssertionAxiom : tempSiteAnnotationsSet) {
if (tempAnnotationAssertionAxiom.getProperty().equals(hasNameAnnotationProperty)) {
String tempString = tempAnnotationAssertionAxiom.getValue().toString();
logger.info(tempString);
tempString =
tempString.substring(tempString.indexOf('"') + 1, tempString.indexOf('^') - 1);
logger.info(tempString);
logger.info(tempClassAssAx.getIndividual().toString());
returnMap.put(tempString, tempClassAssAx.getIndividual());
}
}
}
return returnMap;
}
public void visit(OWLClassAssertionAxiom axiom) {
addChildParent(axiom.getIndividual(), axiom.getClassExpression(), axiom);
axiom.getClassExpression().accept(this);
}