private void addEntailedKBSuccessors(OWLObjectSomeValuesFrom some) {
TRACKER.start(StaticValues.TIME_KB_SUCCESSORS, BlockOutputMode.COMPLETE, true);
// add all role-successors entailed by the TBox
addEntailedTBoxSuccessors(some, m_normalize); // for KB mode only normalize TBox contained roles
DomainNode<?> toNode = getDomainElement(some.getFiller());
OWLClass someClass = m_ontologyOperator.getFlatteningTransformer().getIntermediary(some);
long start = System.currentTimeMillis();
// StatStore.getInstance().enterValue("instance accessing", 1.0);
NodeSet<OWLNamedIndividual> instances =
m_ontologyOperator.getReasoner().getInstances(someClass, false);
sum += System.currentTimeMillis() - start;
// NodeSet<OWLNamedIndividual> instances =
// m_ontologyOperator.getReasoner().getInstances(getClassRepresentation(some), false);
// LOG.fine(" creating successors to " + some + " from instances: " + instances.toString());
Iterator<Node<OWLNamedIndividual>> it1 = instances.iterator();
while (it1.hasNext()) {
Iterator<OWLNamedIndividual> it2 = it1.next().iterator();
while (it2.hasNext()) {
DomainNode<?> from = m_domain.getDomainNode(it2.next());
if (from != null) {
// if(!isSuccessorRepresented(from, getDomainElement(some.getFiller()),
// (OWLObjectProperty)some.getProperty())){
from.addSuccessor((OWLObjectProperty) some.getProperty(), toNode);
// }
}
}
}
TRACKER.stop(StaticValues.TIME_KB_SUCCESSORS);
}
@Override
public void visit(OWLObjectSomeValuesFrom desc) {
desc.getProperty().accept(this);
OWLObjectPropertyExpression prop = (OWLObjectPropertyExpression) obj;
desc.getFiller().accept(this);
OWLClassExpression filler = (OWLClassExpression) obj;
obj = dataFactory.getOWLObjectSomeValuesFrom(prop, filler);
}
@Override
public void visit(OWLObjectSomeValuesFrom node) {
write(SOME);
writeSpace();
node.getProperty().accept(this);
writeSpace();
writeNested(node.getFiller());
}
/*
* (non-Javadoc)
*
* @see
* org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb
* .owlapi.model.OWLObjectSomeValuesFrom)
*/
@Override
public void visit(OWLObjectSomeValuesFrom axiom) {
sb.append(" ");
sb.append(RestrictionConcept.Restriction.VALUE_RESTRICTION.getId());
sb.append(" ");
axiom.getProperty().accept(this);
sb.append(". (");
axiom.getFiller().accept(this);
sb.append(")");
}
@Override
public void visit(OWLObjectSomeValuesFrom ce) {
if (isTop(ce.getFiller())) {
constructs.add(AL);
} else {
constructs.add(E);
}
ce.getProperty().accept(this);
ce.getFiller().accept(this);
}
private String getManchesterRendering(OWLObjectSomeValuesFrom desc) {
SimpleShortFormProvider fp = new SimpleShortFormProvider();
StringWriter wr = new StringWriter();
ManchesterOWLSyntaxObjectRenderer render = new ManchesterOWLSyntaxObjectRenderer(wr, fp);
desc.accept(render);
String str = wr.getBuffer().toString();
return str;
}
public static void main(String[] args) throws Exception {
String catalog = args[0];
String file = args[1];
final ParserWrapper pw = new ParserWrapper();
pw.addIRIMapper(new CatalogXmlIRIMapper(catalog));
final OWLOntology ontology = pw.parse(file);
final OWLGraphWrapper g = new OWLGraphWrapper(ontology);
OWLObjectProperty part_of = g.getOWLObjectPropertyByIdentifier("part_of");
OWLObjectProperty has_part = g.getOWLObjectPropertyByIdentifier("has_part");
OWLObjectProperty regulates = g.getOWLObjectPropertyByIdentifier("regulates");
OWLObjectProperty negatively_regulates =
g.getOWLObjectPropertyByIdentifier("negatively_regulates");
OWLObjectProperty positively_regulates =
g.getOWLObjectPropertyByIdentifier("positively_regulates");
final OWLClassFilter filter =
new OWLClassFilter() {
@Override
public boolean use(OWLClass cls) {
String id = g.getIdentifier(cls.getIRI());
return id.startsWith("GO:");
}
};
Set<OWLObjectProperty> props = Sets.newHashSet(part_of);
Map<OWLClass, Set<OWLObjectSomeValuesFrom>> expressions =
getExpressions(ontology, props, filter);
List<OWLClass> classes = new ArrayList<OWLClass>(expressions.keySet());
Collections.sort(classes);
OWLPrettyPrinter pp = new OWLPrettyPrinter(g);
int count = 0;
for (OWLClass cls : classes) {
Set<OWLObjectSomeValuesFrom> svfs = expressions.get(cls);
for (OWLObjectSomeValuesFrom svf : svfs) {
StringBuilder sb = new StringBuilder();
sb.append(pp.render(cls)).append("\t");
sb.append(pp.render(svf.getProperty())).append("\t");
sb.append(pp.render(svf.getFiller()));
System.out.println(sb);
count += 1;
}
}
System.out.println("Count: " + count);
}
public Boolean visit(OWLObjectSomeValuesFrom ce) {
return !ce.isAnonymous();
}
@Override
public void visit(OWLObjectSomeValuesFrom desc) {
handleObject(desc);
desc.getProperty().accept(this);
desc.getFiller().accept(this);
}
private void addEntailedTBoxSuccessors(OWLObjectSomeValuesFrom some, boolean doNormalizing) {
// StatStore.getInstance().enterValue("lookup " + some.getFiller(), 1.0);
// StatStore.getInstance().enterValue("restrictions handled", 1.0);
TRACKER.start(StaticValues.TIME_TBOX_SUCCESSORS, BlockOutputMode.COMPLETE, true);
// TRACKER.start("fetch domain element and intermediary", BlockOutputMode.COMPLETE, true);
DomainNode<?> toNode = getDomainElement(some.getFiller());
// the super class, intermediary stands for (some r B)
OWLClass superClass = m_ontologyOperator.getFlatteningTransformer().getIntermediary(some);
// TRACKER.stop("fetch domain element and intermediary");
// add successors from all
// TRACKER.start("query elk", BlockOutputMode.COMPLETE, true);
// StatStore.getInstance().enterValue("subclass accessing", 1.0);
NodeSet<OWLClass> classes = m_ontologyOperator.getReasoner().getSubClasses(superClass, false);
// fill current class relations from Id
// StatStore.getInstance().enterValue("subclass accessing", 1.0);
currentIdSubClasses = m_ontologyOperator.getReasoner().getSubClasses(some.getFiller(), false);
// StatStore.getInstance().enterValue("superclass accessing", 1.0);
currentIdSuperClasses =
m_ontologyOperator.getReasoner().getSuperClasses(some.getFiller(), false);
// StatStore.getInstance().enterValue("equivalent classes accessing", 1.0);
currentIdEqClasses = m_ontologyOperator.getReasoner().getEquivalentClasses(some.getFiller());
// TRACKER.stop("query elk");
// LOG.fine(" creating successors to " + some + ": " + classes.toString());
Iterator<Node<OWLClass>> nodeIt = classes.iterator();
while (nodeIt.hasNext()) {
Iterator<OWLClass> it = nodeIt.next().iterator();
while (it.hasNext()) {
DomainNode<?> node = m_domain.getDomainNode(it.next());
// if it.next() yields no domain node, there exists an ABox identity for it
// and this case is covered by addEntailedKBSuccessors
if (node != null) {
if (doNormalizing) {
// if(!isSuccessorRepresented(node, (OWLObjectProperty)some.getProperty(),
// some.getFiller())){
TRACKER.start("normalizing and adding", BlockOutputMode.COMPLETE, true);
if (!isSuccessorRepresented(node, toNode, (OWLObjectProperty) some.getProperty())) {
removeIncludedSuccessors(
(OWLObjectProperty) some.getProperty(), node, some.getFiller());
node.addSuccessor((OWLObjectProperty) some.getProperty(), toNode);
}
TRACKER.stop("normalizing and adding");
} else {
node.addSuccessor((OWLObjectProperty) some.getProperty(), toNode);
}
}
}
}
// add all equivalent class successors
// TRACKER.start("query elk", BlockOutputMode.COMPLETE, true);
Iterator<OWLClass> cIt =
m_ontologyOperator.getReasoner().getEquivalentClasses(superClass).iterator();
// TRACKER.stop("query elk");
while (cIt.hasNext()) {
DomainNode<?> node = m_domain.getDomainNode(cIt.next());
if (node != null) {
if (doNormalizing) {
// if(!isSuccessorRepresented(node, (OWLObjectProperty)some.getProperty(),
// some.getFiller())){
TRACKER.start("normalizing and adding", BlockOutputMode.COMPLETE, true);
if (!isSuccessorRepresented(node, toNode, (OWLObjectProperty) some.getProperty())) {
removeIncludedSuccessors(
(OWLObjectProperty) some.getProperty(), node, some.getFiller());
node.addSuccessor((OWLObjectProperty) some.getProperty(), toNode);
}
TRACKER.stop("normalizing and adding");
} else {
node.addSuccessor((OWLObjectProperty) some.getProperty(), toNode);
}
}
}
TRACKER.stop(StaticValues.TIME_TBOX_SUCCESSORS);
}
public Integer visit(OWLObjectSomeValuesFrom ce) {
return 1 + ce.getFiller().accept(this);
}
@Override
public void visit(OWLObjectSomeValuesFrom arg0) {
containsEquality(arg0.getFiller());
}
public void visit(OWLObjectSomeValuesFrom desc) {
desc.getProperty().accept(this);
desc.getFiller().accept(this);
}
public void visit(OWLObjectSomeValuesFrom desc) {
edgeName = desc.getProperty().toString();
}
public void visit(OWLObjectSomeValuesFrom desc) {
addChildParent(desc, desc.getFiller(), desc);
}